Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D06
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 68668488
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1920000 characters in sequence are not A, C, G, or T
File 181 of 230
Found at i:54351290 original size:770 final size:766
Alignment explanation
Indices: 54349355--54351512 Score: 2914
Period size: 769 Copynumber: 2.8 Consensus size: 766
54349345 ATTATTTGTT
* * * *
54349355 ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTATTTCGACAACCGTCAAACCACCTTCTAT
1 ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCT
* * * * * * **
54349420 TTAGCTACACATTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTGTTTCTCTCTTTTCCACTTT
66 TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTTTCTTTTCTTCTTT
** * ** *
54349485 CTTTCCTTCTTTTTCACCTTGCCAACACTGACTCATTCTTTTACTATTGTGCCCATTGCAAAATC
131 CTTTCCTTCTTTTTTGCCTTGCCAACACTGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATC
* * * *
54349550 TTTCTTTTGTTGCATAAGAACACTGCTGTGGCTTGTTACGATTCTATTGTTCGCTTGTTTCTTTC
196 TTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTGTTTCTTTC
*
54349615 TTCTCCTT-ATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTG
261 TT-TTCTTCATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTG
* * * *
54349679 GGG-TTTGTTGTTTTAAGC-GAAAAAGT-TCGTAGATTAATGATTTTACGATCGATACAGTATTG
325 GGGTTTTGTTGTTTTAAGCAGAAAAA-TCT-GTAGATTAATGATTTTATGATAGATATAGTGTTG
* * * ** * * *
54349741 TGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGAACGCCCTCTGAAAAATTAAGTTT
388 TGGCTGGTTGTTGTGGATAGGAGAAGAGTG-GAGGTGATAG-ACAACTTCTGACAAATTAAGGTT
* * * *
54349806 TTGGAGTAGTTGCTGGAAGTTTGTGGTAATTGCTTGTTTATGAATATAGGGACTGTTTCTTTGAG
451 TTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAG
* * * *
54349871 AAAAGAGTGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATCGTTGATTTTGGTGTT
516 AAAAGAGTGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTT-AGTTTGATGCT
* * *
54349936 ATTTGTAGGATTTTAAGTGTACGACTGCTTGGTGGATTAATCTCGCAGTCAGGTGTGTGAAAACA
580 GTTTGTAGGATTTTAAGTGTACGACTGCGTAGTGGATTAATCTCGCAGTCAGGTGTGTGAAAACA
* * * * * * *
54350001 ATCCTAAAACTCGGTAGAAACTCGTTAAATATTGAAACAGGGGTTGTTTTTCAAAATTTCCTAGT
645 ATCCTAAAACTCGATAGAAACTCGTTAAATAGTGAAACAGGGCTTGTTTTTCAAAACTGCCCAAT
* * * *
54350066 GCCACACAGCCGTGTGTCAGGCCGTGTGGTAGATTATGTGCGCCACACGGCCGTTTA
710 GCCACACAGCCGTGTGTCAGGCCGTATGGTAAATTATGTGCGCCACACGGCCATGTA
* *
54350123 GTTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCTTCAAACCAACTTCTC
1 ATTTTA-TTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTC
* * * *
54350188 TTTGGTTGCATG-TTCTTTCCCTTCTTTCAATTTTCTTTTAAATTTTTTTCGTTCTTTTCTTCTT
65 TTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTTTCTTTTCTTCTT
* * * *
54350252 TCTTTCCTTATTTTTTGCCTTGCCAACACCGACTCCTTCTGTTGTTATTCTGCCAATTGCAAAAT
130 TCTTTCCTTCTTTTTTGCCTTGCCAACACTGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAAT
*
54350317 CTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCAATTGTTCGCTTGTTTCTTT
195 CTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTGTTTCTTT
* * *
54350382 CTTTTCTTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGAGGAAGATTAGTTCTTTATAAGGTTG
260 CTTTTCTTCATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTG
* * *
54350447 GGGTATTGTTGTTTTAAGCAAAAAAATCTGTAGATTAATGATTTTATGATTGATATAGTGTTGTG
325 GGGTTTTGTTGTTTTAAGCAGAAAAATCTGTAGATTAATGATTTTATGATAGATATAGTGTTGTG
* * * *
54350512 GCTGGTTGTTATGGATAGGAGAAGAGTGTGAGGTGATAGACAATCTTTTGGCAAATTAAGGTTTC
390 GCTGGTTGTTGTGGATAGGAGAAGAGTG-GAGGTGATAGACAA-CTTCTGACAAATTAAGGTTTT
*
54350577 GGTGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAA
453 GGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAA
* * * *
54350642 AATAGTGAGTTTAAATGGTAATGTTCGTGTTAAATTGAAGTTTTAATAGTTAGTTGTGATGCTGT
518 AAGAGTGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTTAGTT-TGATGCTGT
* * * * * *
54350707 TTGTAGGATTTTACGTGTACGACTACGTCGTGGATTAATGTCGCTA-TTAGGTGTGTGAAAACGA
582 TTGTAGGATTTTAAGTGTACGACTGCGTAGTGGATTAATCTCGC-AGTCAGGTGTGTGAAAACAA
* * *
54350771 TCCTAAAACTTGATAGAAACTCGTTATATCGTGAAACAAGGGCTT-TTTTTCAAAACTGCCCAAT
646 TCCTAAAACTCGATAGAAACTCGTTAAATAGTGAAAC-AGGGCTTGTTTTTCAAAACTGCCCAAT
* * * * * *
54350835 GCCACACGGTCGTGTGTCAGGCTGTATGGTAAATTGTGTGTGTCACACGGCCATGTA
710 GCCACACAGCCGTGTGTCAGGCCGTATGGTAAATTATGTGCGCCACACGGCCATGTA
* * * * * *
54350892 ATTTTACTTTTAAAATTAAATCCCTATTATTTTTCTCTTTCGGTATCCGTCAAAGCAACTTCTCT
1 ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCT
54350957 TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTGTTTTTCTTTCTTTTCTTCTT
66 TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATT-TTTTTCTTTCTTTTCTTCTT
*
54351022 TCTTTCCTTCTTTTTTGCCTTGCCAACGCTGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAAT
130 TCTTTCCTTCTTTTTTGCCTTGCCAACACTGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAAT
* * * *
54351087 ATTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTTTTATGATTCTGTTGTTCGCTTGCTTCTTT
195 CTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTGTTTCTTT
* * *
54351152 CTTTTCTTCATCGTGGCTTGGTTGTGTTGGCAAGTTTTGTGGAAGATTAGTTCTTTATAAGGTTG
260 CTTTTCTTCATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTG
* *
54351217 GGGTTTTGTTGTTTTAAGCAGAAAAATCTGTAGATTAGTGATTTTATGATAGATATAGTGTTGTT
325 GGGTTTTGTTGTTTTAAGCAGAAAAATCTGTAGATTAATGATTTTATGATAGATATAGTGTTGTG
* * * * **
54351282 GATGGTTGTTGTGGATAGGAGAAGAGTGCATGGTGGTAGACAACTCTCCGACAAATTGTGGTTTT
390 GCTGGTTGTTGTGGATAGGAGAAGAGTGGA-GGTGATAGACAACT-TCTGACAAATTAAGGTTTT
* * * * *
54351347 GGAGTAGTTGTTGCAAGTTTGTGGTAACTACTTGTTTATGGATATAGGAACGATTTATTTGAGAA
453 GGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAA
* ** * *
54351412 AAGAGCGAATTTATGTGGTAATGTTTGTGTTAAATCGAAGTTGTAATCA--TAGGTTT-ATGCCG
518 AAGAGTGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAAT-AGTTA-GTTTGATGCTG
*
54351474 TTTGTAGGATTTTAAATGTACGACTGCGTAGTGGATTAA
581 TTTGTAGGATTTTAAGTGTACGACTGCGTAGTGGATTAA
54351513 AGTTGCTGTC
Statistics
Matches: 1217, Mismatches: 158, Indels: 30
0.87 0.11 0.02
Matches are distributed among these distances:
767 4 0.00
768 331 0.27
769 458 0.38
770 423 0.35
771 1 0.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.42
Consensus pattern (766 bp):
ATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCT
TTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTTTCTTTTCTTCTTT
CTTTCCTTCTTTTTTGCCTTGCCAACACTGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATC
TTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTGTTTCTTTC
TTTTCTTCATGGTGGCTTGGTTGTGTTGGTAAGTTATGTGGAAGATTAGTTCTTTATAAGGTTGG
GGTTTTGTTGTTTTAAGCAGAAAAATCTGTAGATTAATGATTTTATGATAGATATAGTGTTGTGG
CTGGTTGTTGTGGATAGGAGAAGAGTGGAGGTGATAGACAACTTCTGACAAATTAAGGTTTTGGA
GTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTATTTCTTTGAGAAAAG
AGTGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTGTAATAGTTAGTTTGATGCTGTTTGT
AGGATTTTAAGTGTACGACTGCGTAGTGGATTAATCTCGCAGTCAGGTGTGTGAAAACAATCCTA
AAACTCGATAGAAACTCGTTAAATAGTGAAACAGGGCTTGTTTTTCAAAACTGCCCAATGCCACA
CAGCCGTGTGTCAGGCCGTATGGTAAATTATGTGCGCCACACGGCCATGTA
Found at i:54353661 original size:768 final size:765
Alignment explanation
Indices: 54351519--54356527 Score: 5760
Period size: 756 Copynumber: 6.6 Consensus size: 765
54351509 TTAAAGTTGC
* * * *
54351519 TGTCAGGCCGTGTGGTAGATTTTTGTGT--CACATGACCATGTAATTTTCTTTTTTTAAATCAAA
1 TGTCAGGCCGTGTGGTAGA-TTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAA
* * * * *
54351582 TCTCTATTATTTTT-TCTTTCGGAAACCATCAAACCAACTTCTCTTTCGTTGCAC-TTGTCTTTT
65 TCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTT-TCTTTC
* * * * *
54351645 CTTTCTGTCATTTTTGTTTTACATTTTTTAGTCTTTCCTTTTTTCTTTCTTTCCATCT-TTTTCA
129 CCTTCTTTCA-ATTTGTTTTACATTTTTT-TTC-TT-CTTTCTTCTTTCTTTCC-T-TGTTTTCA
* * * *
54351709 CCTTTCCAATGTTCG-CT-C--CTTTTGTTATTGTGCCAATTACGAAATCTTTCTTTTGTTGTGT
188 CCTTGCCAACG-TCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGT
* * * *
54351770 AAAAACACTGTTGAGGCATGTTATGATTCTGTTGTTCGCTTGTTTGTTTATTTTCCTCGTGGTGG
252 AAGAACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGG
* *
54351835 CTTGGTTGTGTTTGTAAGTTGTGTGGAAGATTATGTT-TATATAAGGTTGGGGTTTTGTTGTTTT
317 CTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTA-GTTCTTTATAAGGTTGGGGTTTTGTTGTTTT
* * * **
54351899 TAGTAGAAAAATTCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTCATTGTTGTGGA
381 AAGCAAAAAAATT-GTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGA
* * * * * *
54351964 TATGAGAAGAGCACATGGTGATAGACAACACTTCGACAAATTAAGGTTTTGGAGTAGTTGTTGCA
445 TAGGAGAAGAGCGCATGGTGATAGACAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCA
* * * **
54352029 AGTTTGTGTTAACGACTTGTTTATGAATATAGGGACTGTTTATTTGAGAAAAGAATGAATTTAAG
510 AGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAG
* * * * *
54352094 TGGTAATGTTCGTGTTTAATCGAAGTTGTAACCGTTGGTTTTGGTGTCGATTGTAGGATTTTAAG
575 TGGTAATGTTCATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAG
* * * ** *
54352159 TGTACGATTGTGTGGTGGATTAATGTCGCTATCAAGTGTGTGAAAATGATCTTAAAACTCGATAG
640 TGTACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAG
** * * * * *
54352224 AAACTTATTAAATGGTGAAACAGGGGCTATTTTTCGAAACTGCCCAGTTCCACACGGCTGTG
705 AAACTCGTTAAATCGTGAAACA-GGGCTATTTTTCGAAACTACCCAGTGCCACACAGCAGTG
* * ** * *
54352286 TGTCAGGCCGTTTGGTAGGTTGTGTGTGTCACACGACCGTGCAATTTTATTTTTTAAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * *
54352351 CCCTATTATTTTTCTCTTTCTGTAACCTTCAAACCAACTTCTCTTTGGTTGCACG-TTCTTTCCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
*
54352415 TTCTTTCAATTATGTTTTACA--TTTTTTCTT-TATT-TTC-TTCTTATAC--G---T---CTTG
131 TTCTTTCAATT-TGTTTTACATTTTTTTTCTTCT-TTCTTCTTTCTT-TCCTTGTTTTCACCTTG
* * **
54352467 CCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCGAAATATTTCTTTTGTTACGTAAGAAC
193 CCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGAAC
* * * * *
54352532 ACTGTTGGGGCTTATTATGATTTTATTGTTTGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGT
258 ACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGT
*
54352597 TGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGTTTTTGTTGTTTTAAGCAAA
323 TGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
* *
54352662 AAAATCCGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGA
388 AAAAT-TGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGA
* * ** * *
54352727 AGAGCGCGTGGTGATAGACAAC-CTTTCGTCAAATTAAGGTTTTGGTGTAGTCGCTGCAAGTTTG
452 AGAGCGCATGGTGATAGACAACTC-TCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTG
* * * *
54352791 TAGTAACAACTTGTTTATGAATATAGGGATTGTTTCTTTGAGAAAAGAGCGAATGTAAGTGGTAA
516 TGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAA
*
54352856 TGTTCATGTTAAATCGAATTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACG
581 TGTTCATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACG
* * * * * *
54352921 ACTGCATGGTGGATTAATCTCGCTATCAGGTGTGTTAAAACGATCTTAAAACTCGGTAGAAACTC
646 ACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTC
* *
54352986 GTTAAATCGTGAAACATGGGCTATTTTTCG-AACTTACCTAGTGCCACACAGTAGTG
711 GTTAAATCGTGAAACA-GGGCTATTTTTCGAAAC-TACCCAGTGCCACACAGCAGTG
* * * * *
54353042 TGTTAGGCCGTGTGGTAGATTGTGTGCACCACATGATCGTGTGATTTTATTTTTTAATATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * *
54353107 TCCTATTATTTTTCTATTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCAC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* **
54353172 TTCTTTCAAGTTTGTTTTATATTTTTTTTCTTCTTTCATTCTTTCTTTCCTTGTTTTCACCCAGC
131 TTCTTTCAA-TTTGTTTTACATTTTTTTTCTTCTTTC-TTCTTTCTTTCCTTGTTTTCACCTTGC
* * * * *
54353237 CAACGTCGACTCCTTCTTTTGTTATTGTTCAAATAGAAAAATCTTTCTTTTTTTGTGTAAGAACA
194 CAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGAACA
* * *
54353302 TTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCATGGTGCCTTGGTT
259 CTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTT
* * * *
54353367 GTGTTGTTAAGTTGT-TGGAAGTTTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGTAGAA
324 GTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAA
* **
54353431 AAATATGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGTTGGTTGTTGTGGATTTGAGAA
389 AAAT-TGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAA
* * * *
54353496 GAGCGCGTGGTGATAGAAAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGTTGCAATTTTGTG
453 GAGCGCATGGTGATAGACAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTG
* * * * * * ** * *
54353561 ATAACTACAAT-TTTATGAATAAAAGGACTCTTTCTCTGAGAAAAGAGAAAATTTAAATGGAAAT
518 GTAACTAC-TTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAAT
* * * *
54353625 GTTCATGTTAAACCAAAGTTGTAATCGTTTG-TTT--TG--G--TG-AGGATTTTAAATGTACGA
582 GTTCATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACGA
* * * *
54353682 CTGCATGGTGGATTAATGTCACTATTAGGTGTGTGAAAAGAATCCTAAAACTCGATAGAAACTCG
647 CTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTCG
* * * * * * * *
54353747 TTAAATC-TGAAATAGGGGTATTTTTTGAAACTGCCCAGTGCCATACGGCCGAG
712 TTAAATCGTGAAACAGGGCTATTTTTCGAAACTACCCAGTGCCACACAGCAGTG
* * * ** * * ** * *
54353800 TGTCAAGCCGTTTGGTAGATTGTATGTGTCACACGGCTATGTAACTTTATTTTTTTAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
54353865 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTAGG-TGCACGTTTCTTTCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTT-GGTTGCACGTTTCTTTCC
* * * *
54353929 GTTCTTTCAATATTGTTTTACA-TTTTTTTCTTTTTTTCTTCTTTCTTTCCTTCTTTTTCGCCTT
130 CTTCTTTCAAT-TTGTTTTACATTTTTTTTC-TTCTTTCTTCTTTCTTTCCTT-GTTTTCACCTT
* * *
54353993 GCCAATG-CTGACT-C--CTTTTGTTATTGTGCCAATTGTAAAATCTTTCTCTTGTTGCT-TAAG
192 GCCAACGTC-GACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTG-TGTAAG
* * *
54354053 AACACTATTGAGGCTTGTTATGATTCTGTTGTTCACTTGTTTCTTTCTTTTCCTGGTGGTGGCCT
255 AACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGG-CT
* * * *
54354118 T-GTTGCT-TTGGCAAGTTATGTGGAAGATTAGTTCTTTATAATGTTGGAGTTTTGTTGTTTTAA
319 TGGTTG-TGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAA
* *
54354181 GCAAAAAAATCTGTAGATTAATGATTTTATGATAGATATAGTGTTGTGGTTGGTTGTTGTGGATA
383 GCAAAAAAAT-TGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATA
* * * * * * * *
54354246 GGAGAAGTGCACGTGGTGGTAGACAACCCTCCGAA-AAATTAAAGTTTTGGAGTAGTTGCAGTAA
447 GGAGAAGAGCGCATGGTGATAGACAACTCTCC-AACAAATTAAGGTTTTGGAGTAGTTGCTGCAA
* * *
54354310 GTTTGTGGTAACTACTTGTTTATGAACATAGGGACTGTTTCTTTGAGAAAAGAGCGACTGTAAGT
511 GTTTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGT
* * *
54354375 CGTAATGTTCGTGTTAAATTGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGT
576 GGTAATGTTCATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGT
* * *
54354440 GTACAAATGCGTGGTGGATTAATGTCACTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGA
641 GTACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGA
* * * * * *
54354505 AATTCGTTACATCGTGAAACATGTGCTATTTTACTAAACTACCAAGTGCCACA-AGGCCA-TG
706 AACTCGTTAAATCGTGAAACA-GGGCTATTTTTCGAAACTACCCAGTGCCACACA-G-CAGTG
** * * * *
54354566 TGTCAGGCTATGTGGTAGATTGTGTGGGACACACA--ACCGTGAAATTTTAATTTCTAAAATCAA
1 TGTCAGGCCGTGTGGTAGATTGTGT-GTAC-CACATGACCGTGTAATTTTATTTTTTAAAATCAA
* *
54354629 ATCCCTATTATTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTCGGTTGCACGTTTCTTTC
64 ATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTC
* * *
54354694 CCTTCTTTCAAATTTGTTTTACA--TTTTTCCTTCTTTTCCTCTTT-TTTCCCCTTCTTTTTCAC
129 CCTTCTTTC-AATTTGTTTTACATTTTTTTTCTTC-TTTCTTCTTTCTTT--CCTT-GTTTTCAC
* *
54354756 CTTGCCAACGTCGGCTCCTTCTTTTGTTATTGAT-CCAATTG-AGAAATCTTTCTTTTGTTGCGT
189 CTTGCCAACGTCGACTCCTTCTTTTGTTATTG-TGCCAATTGCA-AAATCTTTCTTTTGTTGTGT
* * * *
54354819 AAGAACACTATTGAGGCTTGTTATGATTTTGTTGTTTGCTTGTTTCTTTCTTTTCCTCAT-GTGG
252 AAGAACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGG
* *
54354883 CTTGGTTGTGTTGGTAAGTTGTGTGCAATATTAGTTCTTTATAAGGTTGGGGTTTTGTT-TTTTA
317 CTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTA
* * * * * *
54354947 AGTAGAAAAATCCGTAGATTAATGATTTTATGATAGATATAGCT-TAGTGGCTGATTGTTGTGGA
382 AGCAAAAAAAT-TGTAGATTAATGATTTTATGATTGATATAG-TGTTGTGGCTGGTTGTTGTGGA
* * * * * *
54355011 TATGAGAAGAGTGCATAGTGATAGACAACTCTCTAACAAATTAACGTTTTGGAGTAGTTGTTGCA
445 TAGGAGAAGAGCGCATGGTGATAGACAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCA
* * *
54355076 AGTTTGTGGTAACTACTTGTTTATGAATATAGGGATTGCTTCTCTGAGAAAAGAGCGAATTTAAG
510 AGTTTGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAG
** * * * * * * **
54355141 TGGTAACATTCGTGTTAAATCGAAGGTCTAATCGTTGGTTTTGGGGCTGTTTTTTATTATTTTAA
575 TGGTAATGTTCATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCG-TTTGTAGGATTTTAA
* * *
54355206 GTGTATGACTGCGTGGTGGATTGATGTTGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATA
639 GTGTACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATA
* * * * * *
54355271 AAAACTCGTTAAATCATGAAACAGAGGCTATTTTTTGAAACTACCCAGTGGCACACGGCCGTG
704 GAAACTCGTTAAATCGTGAAACAG-GGCTATTTTTCGAAACTACCCAGTGCCACACAGCAGTG
* * ** * * * *
54355334 TGTCAGGCCGTATGGTAGATTGTATGTGTCACAGGGCTGTGTGATTTTATTTTTTAAAATCAAAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
* * * *
54355399 CCCTATTATTTTTCTCTTTCGACAACCGTTAAACCAACTTCTCTTTGGTTGAACGTTTCTTTCAC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
* * * *
54355464 TTCCTTT-ATTTTTGTTTTACA-TATTTTTCTTTCTTTTCTTCTTTATTTCCTTCTTTTTCACCT
131 TT-CTTTCA-ATTTGTTTTACATTTTTTTTC-TTC-TTTCTTCTTTCTTTCCTT-GTTTTCACCT
* *
54355527 TGCCAACGTCGACTCCTTCTTTTGTTGTTGTGCCAATTGCAAAATCTTTCTTTTGTTTTGTAAGA
191 TGCCAACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGA
* * * *
54355592 TCACTGTTGAGGCTTTTTATGATTCTGTTGTTCGCTTATTTCTTTCTTTTCCTCGTGGTGGCCTG
256 ACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTG
* * *
54355657 GTTGTGTTGGTAAGTTGTATGGAAGATTAGTTTTTTTATAAGGTTGGGGTTTTGTTGTTTTAAGG
321 GTTGTGTTGGTAAGTTGTGTGGAAGATTAG-TTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGC
*
54355722 AAAAAAATTGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTCTGGATAGGA
385 AAAAAAATTGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGA
* * * *
54355787 GAAGAACGCATGGTGATAGACAA-TCCTTCGAGAAATTAAGGTTTTGGAGTAGTTGCTGCAAG-T
450 GAAGAGCGCATGGTGATAGACAACT-CTCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTT
* * * * *
54355850 TGTGGTAACTACTTATTTGTGAATATAAGGTCTTTTTCTTTGAGAAAAGAGCGAATTTAAGTGGT
514 TGTGGTAACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGT
* * * *
54355915 AATATTCATGTTTAAATTGAAGTTGTAATCGTTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGT
579 AATGTTCATG-TTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGT
* * * * ** *
54355980 ATGACTTCGTGGTGGATTAATCTCGCTATCATGTGTAAGAAAACAATCCTAAAACTCGAGAGAAA
643 ACGACTGCGTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAA
* * * * * **
54356045 CTCGTTAAGTCGTGAAACAGGGGT-TGGTTTTCAAAACTGCCCTA-TGCGACACAGCAGCA
708 CTCGTTAAATCGTGAAACAGGGCTAT--TTTTCGAAACTACCC-AGTGCCACACAGCAGTG
* * * * * * * * *
54356104 TGTCTGACCGTGTGGTAGATTTTGTGTGCCACTTGGCTGTTTAATTTTATTTTTTAAAATCATAT
1 TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
* *
54356169 CCCTATTATTTTTATCATTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
66 CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
*
54356234 TTCTTTCAAATTTGTTTT--A---TTTTT-TTC--T-TTCTTTCTTT-C-T-TTTTCGCCTTG-C
131 TTCTTTC-AATTTGTTTTACATTTTTTTTCTTCTTTCTTCTTTCTTTCCTTGTTTTCACCTTGCC
* * * *
54356286 AACGCCAACACCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACAC
195 AACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGAACAC
*
54356351 TGTTGAGGCTTG-T-T-A------TGTT-GC----TTCTTTCTGTTCCTCGTGGTGGCTTGGTTG
260 TGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTG
* * *
54356402 TGGTGGTAAGGTT-TGTTGG-AGATTAGTTCTTTATAAGGTTGGGGTTTTTTTATTTTAAGCAAA
325 TGTTGGTAA-GTTGTG-TGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAA
* * * * *
54356465 ATAATTCGTAGATTAACGATTTTAGGATTGATATAGTGTAGTGGCTAGTTGTTGTGGATAGGA
388 AAAATT-GTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGA
54356528 AAAGCAAGTT
Statistics
Matches: 3632, Mismatches: 507, Indels: 232
0.83 0.12 0.05
Matches are distributed among these distances:
740 38 0.01
741 95 0.03
742 6 0.00
745 2 0.00
746 4 0.00
752 4 0.00
753 11 0.00
754 2 0.00
755 185 0.05
756 838 0.23
757 55 0.02
758 177 0.05
759 25 0.01
760 91 0.03
761 14 0.00
762 11 0.00
763 6 0.00
764 92 0.03
765 27 0.01
766 190 0.05
767 247 0.07
768 593 0.16
769 397 0.11
770 351 0.10
771 157 0.04
772 14 0.00
ACGTcount: A:0.23, C:0.14, G:0.21, T:0.42
Consensus pattern (765 bp):
TGTCAGGCCGTGTGGTAGATTGTGTGTACCACATGACCGTGTAATTTTATTTTTTAAAATCAAAT
CCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCC
TTCTTTCAATTTGTTTTACATTTTTTTTCTTCTTTCTTCTTTCTTTCCTTGTTTTCACCTTGCCA
ACGTCGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGTGTAAGAACACT
GTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGT
GTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAAA
ATTGTAGATTAATGATTTTATGATTGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAG
CGCATGGTGATAGACAACTCTCCAACAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTA
ACTACTTGTTTATGAATATAGGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTC
ATGTTAAATCGAAGTTGTAATCGTTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACGACTGC
GTGGTGGATTAATGTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTCGTTAA
ATCGTGAAACAGGGCTATTTTTCGAAACTACCCAGTGCCACACAGCAGTG
Found at i:54356939 original size:12 final size:12
Alignment explanation
Indices: 54356920--54356953 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
54356910 TTGTTTTAAA
54356920 TTTT-TTCTTTC
1 TTTTCTTCTTTC
54356931 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
54356943 TTTCCTTCTTT
1 TTTTCTTCTTT
54356954 TTCACCTAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 4 0.19
12 17 0.81
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:54358081 original size:748 final size:749
Alignment explanation
Indices: 54356779--54360439 Score: 3603
Period size: 808 Copynumber: 4.8 Consensus size: 749
54356769 GTGTTAGGCG
* *
54356779 GTGTGGTACATTGTGTGCG-TCA-CACGACCGTGTAATTTTATTTTTGTAAATCAAAT-CCTATT
1 GTGTGGTAGATTGTGGGCGCT-AGCACGACCGTGTAATTTTATTTTT-TAAATCAAATCCCTATT
** * *
54356841 ATTTTTCTCTTTCAGCAATAGTCAAACCAACCTCTCTTTGGTTGCACATTTCTTTCCTTTCTTTC
64 ATTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTC
54356906 AATTTTGTTTTA-AATTTTTTCTTTCTTTTCTTCTTTCTTTCCTTCTTTTTCACCTAGCCAACCT
129 AATTTTGTTTTACAA--TTTT-TTTC----CTTCTTT-TTTCC--C--TTT--CCTA--C-ACC-
* * * *
54356970 GACTCCTTCTTTTGTTAATGTGCCAATTGCAAAATCTTTATTTTTTTGCTTAAGAACACTGTTGA
176 GACT-C--CTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGA
* *
54357035 GGCTTGTTATGATTCTGCTGTTCGCTTGTTTCTTTCTTTTCCTCGGGGTGGCTTGGTTGTGTTGG
238 GGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGG
* *
54357100 TAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTGTAAGCAATAAAATCCG
303 TAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAAAATCCG
* * * * * * * *
54357165 TAGATTAATGATTTTATGATATATATAGTGTTGTTGTTGGTTATTTTGGATATGAGAAGAGTGCG
368 TAGATTAATGATTTTATGATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCG
* * * * *
54357230 TGGTGATAGACAACCCTCCAAAAAATTTAGGTTTTTGAGTAGTTGCTGCAAGTTTGTGGTAACTA
433 TGGTGATAGACAACTCTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTA
* * * * * * * *
54357295 ATTGTTTATGAATGTAAGGACTATTTATTTGGGAAAAGATCGAATGTAAGTGGTAATGTTTGTGT
498 CTTGTTTATGAATAT-AGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGT
* *
54357360 TAAATCAGAGTTGTAATCGTTGG-TTTGTATGTCATTTATAAGATTTTAAGTGTACGATTACGTG
562 TAAATCAGAGTTGTAATCGTTGGTTTTG-GTGTCATTTGTAAGATTTTAAGTGTACGATTACGTG
* *
54357424 GTGGATTAATCTCGCTATCAGGTGTGTAAAAACAATCCAAAAACTCGGTAGAAACTCGTTAAATC
626 GTGGATTAATCTCGCTATCAGGTGTGTGAAAACAATCCTAAAACTCGGTAGAAACTCGTTAAATC
* * * * * * *
54357489 ATGAAACATGAGCTGTTTTTCAAAAACTGCCTAGCCCCGCACAACCCTGTGTCAGGCT-
691 ATGAAACAGGGGATGTTTTTCGAAAACTGCCCAGCGCCACACAACCCTGTGTCAGGCTA
*
54357547 GTGTGGTAGAATGTGGGCGCT-GCACGACCGTGTAATTTTATTTTTTAAATCAAATCCCTATTAT
1 GTGTGGTAGATTGTGGGCGCTAGCACGACCGTGTAATTTTATTTTTTAAATCAAATCCCTATTAT
** * * *
54357611 TTTTCTCTTTTTGCAACTGTTAAACCAACTTCTCTTTGGTTGCA-AGTTTCTTTCCCTTCTTTCG
66 TTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTTGGTTGCACA-TTTCTTTCCCTTCTTTCA
54357675 ATTTTGTTTTACAATTTTTTTCCTTC-TTTTTCACCTTTCCTACACCGACTCCTTTTGTTATTGT
130 ATTTTGTTTTACAATTTTTTTCCTTCTTTTTTC-CCTTTCCTACACCGACTCCTTTTGTTATTGT
* * *
54357739 TCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGGGGCTTGTTATAATTCTGTTGT
194 GCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTGTTGT
* * * *
54357804 TCGCTTATTTCTTTCTTTTCCTTGTGGTGGCCTGGTTGTGTTGGTAAGTTGT-TGGAAGGTTAGT
259 TCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGT
* * *
54357868 TCTTGATAAGGTTGGGGTTTTGTTGTTTTAA-CAAAAAAAAAATCCGTAGATTAATAATTTTGTG
324 TCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGC---AAAAAAATCCGTAGATTAATGATTTTATG
* *
54357932 ATAGAGATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGAGTGGTGATAGACAACTCTC
386 ATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAACTCTC
* * * *
54357997 CGACAAATTAAGGCTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTAATGAATATAGG
451 CGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGG
* * * * * * *
54358062 ATTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGGTCATGTTAATTCAAAGTTGTATTCA
516 ACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCAGAGTTGTAATCG
* * *
54358127 TTGGTTTTGGTG-CTATTTGTAGGATTTTACA-TGTACGACTACGCGGTGGATTAATCTCGCTAT
581 TTGGTTTTGGTGTC-ATTTGTAAGATTTTA-AGTGTACGATTACGTGGTGGATTAATCTCGCTAT
* *
54358190 CAGGTGTGTGAAAACAATCCTAAAACTCGGTAGAAACTCGTTGAATCATGAAATAGGGGATGTTT
644 CAGGTGTGTGAAAACAATCCTAAAACTCGGTAGAAACTCGTTAAATCATGAAACAGGGGATGTTT
** *
54358255 TTCGAAAA-TGCCCA-CTGCCACACGGCCGTGTGTCAGGCCATATTCTA
709 TTCGAAAACTGCCCAGC-GCCACACAACCCTGTGTCAGG-------CTA
* * * ***
54358302 GATTGTTAGTGTCACACGGCCGTGTGTCAGGCCGTATTCTAG-ATTGTTAGTGTCACACGTCCGT
1 G--TG-T-G-GT---A--G--AT-TGT--GGGCG----CTAGCA-CGACCGTGT-A-A--T---T
* *
54358366 GTAATTTTATTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAACCAACTTC
39 -T--TAT---TTTTTAAATCAAATCCCTATTATTTTTCTCTTTCAGCAACCGTCAAACCAACTTC
* * *
54358431 TCTTTGGTTGCACGTTTC-TTCCCTTCTTTCAATTTTCTTTTACATTTTTTCCTTCTTTTCTTAT
98 TCTTTGGTTGCACATTTCTTTCCCTTCTTTCAATTTTGTTTTACAATTTTT--TTC----C----
* * * * * *
54358495 TTCTTTCCTTCTTTCTCACATTTCCAACGCCGACTCCTTCATTTTTTATTGTGCAAATTACAGAA
153 TTC--T--TT-TTTC-C-C-TTTCCTACACCGACTCC-T--TTTGTTATTGTGCCAATTGCAAAA
* *
54358560 TCTTTCTTTTGTTGCGTAAGAACATTGTTGAGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTT
207 TCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTGTTGTTCGCTTGTTTCTT
*
54358625 TCTTTTCCTCATGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTT
272 TCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTT
* * *
54358690 GGGGTTTTGTTGTTTTAAGCAGAAAAATTCGTAGGTTAATGATTTTATGATAGATATAGTGTTGT
337 GGGGTTTTGTTGTTTTAAGCAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAGTGTTGT
* * * *
54358755 GG-TTGATTGTTGTGGATATGAGAAGAGTGCGTGGTGATAGACAACTCTCCGAGAAATTAAGGTT
402 GGCTAG-TTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAACTCTCCGAAAAATTAAGGTT
* * * *
54358819 TTGGAGTAGTTGTTGGATGTTTGTGGTAAGTACTTGTTTATGAATATAGGGACTGTTTTTTTGAG
466 TTGGAGTAGTTGTTGCAAGTTTGTGGTAACTACTTGTTTATGAATATA-GGACTGTTTCTTTGAG
* ** * *
54358884 AAAAGAGCGAATTTATGTGGTAACATTCGTGTTAAAT-AGAAGTTGTAATCGTTTGTTTTGGTGC
530 AAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCAG-AGTTGTAATCGTTGGTTTTGGTGT
* * * * * *
54358948 CGTTTGTAAGATTTTAAGTGTACGATTGCGTGGTGGATTAATGTCACTATCAGGTGTTTGAAAAT
594 CATTTGTAAGATTTTAAGTGTACGATTACGTGGTGGATTAATCTCGCTATCAGGTGTGTGAAAAC
* * *
54359013 GATCCTAAAACTCGATAGAAACTCGTTAAATCGTGAAACATGGGG-TGTTTTTCG-AAACTGCCC
659 AATCCTAAAACTCGGTAGAAACTCGTTAAATCATGAAACA-GGGGATGTTTTTCGAAAACTGCCC
* ** *
54359076 AGTGCCACATGACCCTGTGTCAGG-TC
723 AGCGCCACACAACCCTGTGTCAGGCTA
* * * **
54359102 GTATGGTAGATTGTGTGAG-TCA-CACGGTCGTGTAATTTTATTTTTTTGAAATCAAATCCCTAT
1 GTGTGGTAGATTGTGGGCGCT-AGCACGACCGTGTAATTTTA-TTTTTT-AAATCAAATCCCTAT
* *
54359165 TATTTTTTCTCTTTCGGCAACCATCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTT
63 TA-TTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTT
* * * **
54359230 TCAA------TTT-C----TTCTT--TTC-TTTTTCGCCTTGCC-AAAGTTGACTCCTTCTTTTG
127 TCAATTTTGTTTTACAATTTTTTTCCTTCTTTTTTC-CCTTTCCTACA-CCGACT-C--CTTTTG
* * * ** **
54359280 TTATTGTGCCAATTGCAAAATCTATCTTCTGTTGAGTAAGAACACTAATGAATCTTGTTATGATT
187 TTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATT
* * * *
54359345 CTGTTGTTCGCTAGTTTCTTTCTTTTCCTCGTAGTGGCTTGGATGTGTTGGTAAGCTGTGTGGAA
252 CTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAA
* *
54359410 GATTAGTTCTTTATAAGGTT-GGG--TT-TT-TTTTAAGCAAAAAAATCCGTAGATTAATGGTAT
317 GATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAAAATCCGTAGATTAATGATTT
* * * *
54359470 TATGATAGATATCGTGTTGTGGCTGGTGGTTGTGGATAGGAGAAGAGCGTGTGGTGATAGACAA-
382 TATGATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAAC
* **
54359534 TCCTTCGAAAAATTAAGGTTTTGGAGTAACTGTTGCAAGTTTGTGGTAACTACTTGTTTATGAAT
447 T-CTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTACTTGTTTATGAAT
* ** *
54359599 ATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATACTCGTGTTAAATCAAAGTTG
511 AT-AGGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCAGAGTTG
* * * *
54359664 TATTCGTTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTAAGAATT-CATGGTGGATTAATCTC
575 TAATCGTTGGTTTTGGTGTCATTTGTAAGATTTTAAGTGTACG-ATTACGTGGTGGATTAATCTC
* * *
54359728 GCTATTA--TGTGTG--AGCAATCCTAAAACTCGAG-AGAAACTCGTTAAATCTTGAAACAGGGG
639 GCTATCAGGTGTGTGAAAACAATCCTAAAACTCG-GTAGAAACTCGTTAAATCATGAAACAGGGG
* * ** * * * *
54359788 TTGGTTTTT-GAAAAC-ACCTTGTGCGTCACAGCAA--C-ATGTCTGGC-C
703 AT-GTTTTTCGAAAACTGCC--CAGCGCCACA-CAACCCTGTGTCAGGCTA
* * * ** * * *
54359833 GTGTGGTAGATTTTGTGCGCCA-CTTGGCCGTTTAATTTTATTTTTTAAAATCATATCCCTATTA
1 GTGTGGTAGATTGTGGGCGCTAGCACGACCGTGTAATTTTATTTTTT-AAATCAAATCCCTATTA
** *
54359897 TTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTTTTTCA
65 TTTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCA
* *** * *
54359962 ATTTAGTTTTATTTTTTTCTTTATTTTCTTCTTTGTTTCCTTCTTTTTCGGCTTGCCAACGTCGA
130 ATTTTGTTTTA---CAAT-TTT-TTTCCTTCTTT-TTTCC--C--TTTC--C-T-AC-AC--CG-
* *
54360027 CACCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTATTGCGTAAGAACACTGTTGAGG
177 -A-CTCCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGG
* * * * * * *
54360092 CTTGTTATGATTTTGTTGTTCGTTTGTTACCTTCTGTTCCTCGTGGAGGCTTGGTTGTGGTGGTA
240 CTTGTTATGATTCTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTA
* * *
54360157 AGTT-TCGTGGAAGATTAGTTCTTTATAAGGTTGGGATTTTGTTGTTTTAAGTAAAAATATCCGT
305 AGTTGT-GTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAAAATCCGT
* * *
54360221 AGATTAATGCTTTT-TGGATTGATATAGTGTAGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCG
369 AGATTAATGATTTTAT-GATAGATATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCG
* * *
54360285 TGGTGATAGAGAA-TCCTCCGGAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACT
433 TGGTGATAGACAACT-CTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACT
* * * *
54360349 ACTTGTTTATGAATATATGGACTGTTTCATTGAGAAAAGAGCAAATTTCAGTGGTAATGTTTGTG
497 ACTTGTTTATGAATATA-GGACTGTTTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTG
* *
54360414 CTAAATC-GAAGTTGTACTCGTTGGTT
561 TTAAATCAG-AGTTGTAATCGTTGGTT
54360440 GATGGTTGTC
Statistics
Matches: 2424, Mismatches: 314, Indels: 314
0.79 0.10 0.10
Matches are distributed among these distances:
729 61 0.03
730 26 0.01
731 79 0.03
732 11 0.00
733 11 0.00
734 2 0.00
735 254 0.10
736 9 0.00
737 2 0.00
739 4 0.00
740 144 0.06
741 2 0.00
742 6 0.00
743 3 0.00
744 2 0.00
745 2 0.00
746 2 0.00
747 65 0.03
748 293 0.12
749 143 0.06
750 2 0.00
751 4 0.00
752 6 0.00
753 1 0.00
754 3 0.00
755 5 0.00
757 5 0.00
758 5 0.00
759 138 0.06
760 10 0.00
761 4 0.00
762 8 0.00
763 5 0.00
764 211 0.09
765 4 0.00
766 4 0.00
767 15 0.01
768 120 0.05
769 20 0.01
770 54 0.02
771 15 0.01
772 1 0.00
773 1 0.00
774 3 0.00
775 6 0.00
776 2 0.00
777 1 0.00
778 1 0.00
779 2 0.00
780 7 0.00
781 2 0.00
782 1 0.00
783 1 0.00
785 4 0.00
787 32 0.01
788 68 0.03
789 3 0.00
790 1 0.00
792 1 0.00
793 1 0.00
795 2 0.00
796 1 0.00
797 4 0.00
798 1 0.00
800 2 0.00
802 2 0.00
803 5 0.00
804 1 0.00
805 15 0.01
806 3 0.00
807 142 0.06
808 301 0.12
809 46 0.02
810 1 0.00
ACGTcount: A:0.23, C:0.15, G:0.21, T:0.41
Consensus pattern (749 bp):
GTGTGGTAGATTGTGGGCGCTAGCACGACCGTGTAATTTTATTTTTTAAATCAAATCCCTATTAT
TTTTCTCTTTCAGCAACCGTCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCAA
TTTTGTTTTACAATTTTTTTCCTTCTTTTTTCCCTTTCCTACACCGACTCCTTTTGTTATTGTGC
CAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTGTTGTTC
GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTC
TTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAAAAAAATCCGTAGATTAATGATTTTATGATAGA
TATAGTGTTGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGCGTGGTGATAGACAACTCTCCGAAA
AATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGACTGT
TTCTTTGAGAAAAGAGCGAATTTAAGTGGTAATGTTCGTGTTAAATCAGAGTTGTAATCGTTGGT
TTTGGTGTCATTTGTAAGATTTTAAGTGTACGATTACGTGGTGGATTAATCTCGCTATCAGGTGT
GTGAAAACAATCCTAAAACTCGGTAGAAACTCGTTAAATCATGAAACAGGGGATGTTTTTCGAAA
ACTGCCCAGCGCCACACAACCCTGTGTCAGGCTA
Found at i:54358330 original size:41 final size:41
Alignment explanation
Indices: 54358273--54358367 Score: 172
Period size: 41 Copynumber: 2.3 Consensus size: 41
54358263 TGCCCACTGC
54358273 CACACGGCCGTGTGTCAGGCCATATTCTAGATTGTTAGTGT
1 CACACGGCCGTGTGTCAGGCCATATTCTAGATTGTTAGTGT
*
54358314 CACACGGCCGTGTGTCAGGCCGTATTCTAGATTGTTAGTGT
1 CACACGGCCGTGTGTCAGGCCATATTCTAGATTGTTAGTGT
*
54358355 CACACGTCCGTGT
1 CACACGGCCGTGT
54358368 AATTTTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (41 bp):
CACACGGCCGTGTGTCAGGCCATATTCTAGATTGTTAGTGT
Found at i:54359982 original size:735 final size:739
Alignment explanation
Indices: 54358525--54360439 Score: 2281
Period size: 735 Copynumber: 2.6 Consensus size: 739
54358515 TTTCCAACGC
* * * *
54358525 CGACTCCTTCATTTT-TTATTGTGCAAATTACAGAATCTTTCTTTTGTTGCGTAAGAACATTGTT
1 CGACTCCTTC-TTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTT
*
54358589 GAGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTTTCTTTTCCTCATGGTGGCTTGGTTGTGTT
65 GAGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTT
* *
54358654 GGTAAGTTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGGTTTTGTTGTTTTAAGCAGAAAAATT
130 GGTAAG-TGTGTGGAAGATTAGTTCTTTATAAGGTT-GGG-TTTGTTGTTTTAAGCAAAAAAATC
* * * * *
54358719 CGTAGGTTAATGATTTTATGATAGATATAGTGTTGTGGTTGATTGTTGTGGATATGAGAAGAGTG
192 CGTAGATTAATGA-TTTATGATAGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGCG
* * *
54358784 CGTGGTGATAGACAA-CTCTCCGAGAAATTAAGGTTTTGGAGTAGTTGTTGGATGTTTGTGGTAA
256 CGTGGTGATAGACAATC-CTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAA
* * * * * *
54358848 GTACTTGTTTATGAATATAGGGACTGTTTTTTTGAGAAAAGAGCGAATTTATGTGGTAACATTCG
320 CTACTTGTTTATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCG
* * *
54358913 TGTTAAAT-AGAAGTTGTAATCGTTTGTTTTGGTGCCGTTTGTAAGATTTTAAGTGTACGATTGC
385 TGTTAAATCA-AAGTTGTAATCGTTGGTTTTGGTGCCATTTGTAAGATTTTAAGTGTAAGATTGC
* * * *
54358977 GTGGTGGATTAATGTCACTATCAGGTGTTTGAAAATGATCCTAAAACTCGATAGAAACTCGTTAA
449 ATGGTGGATTAATCTCACTATCA-GTGTGTGAAAA-GATCCTAAAACTCGAGAGAAACTCGTTAA
* * * *
54359042 ATCGTGAAACATGGGGTGTTTTTCGAAACTGCCCAGTGCCACATGACCCTGTGTCAGGTCGTATG
512 ATCGTGAAACATGGGGTGTTTTTCGAAACTACCCAGTGCCACATGACACTATGTCAGGCCGTATG
* * *
54359107 GTAGATTGTGTGAGTCACACGGTCGTGTAATTTTATTTTTTTGAAATCAAATCCCTATTATTTTT
577 GTAGATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTTTTAAAATCAAATCCCTATTATTTTT
* **
54359172 TCTCTTTCGGCAACCATCAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCAATTT
642 TCTCTTTCAGCAACCATCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTCTTTCAATTT
*
54359237 CTTCTTTTC-TTT-TTC-G-C-CTTGCCAAAGT
707 ATTCTTTTCTTTTCTTCTGTCGCTTGCCAAAGT
* * * * **
54359265 TGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTATCTTCTGTTGAGTAAGAACACTAATG
1 CGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTG
** * * * *
54359330 AATCTTGTTATGATTCTGTTGTTCGCTAGTTTCTTTCTTTTCCTCGTAGTGGCTTGGATGTGTTG
66 AGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTG
54359395 GTAAGCTGTGTGGAAGATTAGTTCTTTATAAGGTTGGG-TT-TT-TTTTAAGCAAAAAAATCCGT
131 GTAAG-TGTGTGGAAGATTAGTTCTTTATAAGGTTGGGTTTGTTGTTTTAAGCAAAAAAATCCGT
* * * *
54359457 AGATTAATGGTATTATGATAGATATCGTGTTGTGGCTGGTGGTTGTGGATAGGAGAAGAGCGTGT
195 AGATTAATGAT-TTATGATAGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGCGCGT
* **
54359522 GGTGATAGACAATCCTTCGAAAAATTAAGGTTTTGGAGTAACTGTTGCAAGTTTGTGGTAACTAC
259 GGTGATAGACAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTAC
*
54359587 TTGTTTATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATACTCGTGTT
324 TTGTTTATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTT
* * *
54359652 AAATCAAAGTTGTATTCGTTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTAAGAATT-CATGG
389 AAATCAAAGTTGTAATCGTTGGTTTTGGTGCCATTTGTAAGATTTTAAGTGTAAG-ATTGCATGG
* * ** *
54359716 TGGATTAATCTCGCTATTA-TGTGTGAGCA-ATCCTAAAACTCGAGAGAAACTCGTTAAATCTTG
453 TGGATTAATCTCACTATCAGTGTGTGAAAAGATCCTAAAACTCGAGAGAAACTCGTTAAATCGTG
** * *
54359779 AAACA-GGGGTTGGTTTTT-GAAAAC-ACCTTGTGCGTCACA-G-CAAC-ATGTCTGGCCGTGTG
518 AAACATGGGG-T-GTTTTTCG-AAACTACCCAGTGC--CACATGAC-ACTATGTCAGGCCGTATG
* * ** * *
54359838 GTAGATTTTGTGCGCCACTTGGCCGTTTAATTTTA-TTTTTTAAAATCATATCCCTATTA-TTTT
577 GTAGATTGTGTGAGCCACACGGCCGTGTAATTTTATTTTTTTAAAATCAAATCCCTATTATTTTT
* *
54359901 TCTCTTTCAGCAACCGTCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTTTTTCAATTT
642 TCTCTTTCAGCAACCATCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTCTTTC-A---
* *
54359966 AGTTTTATTTTTTTCTTTATTTTCTTCTTTGTTTCCTTCTTTTTCGGCTTGCCAACGT
703 A--TTTA-----TTC------TT-TTC--T-TTT-CTTC--TGTC-GCTTGCCAAAGT
* *
54360024 CGACACCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTATTGCGTAAGAACACTGTTG
1 CGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTG
* * * * * *
54360089 AGGCTTGTTATGATTTTGTTGTTCGTTTGTTACCTTCTGTTCCTCGTGGAGGCTTGGTTGTGGTG
66 AGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTG
* * *
54360154 GTAAGTTTCGTGGAAGATTAGTTCTTTATAAGGTTGGGATTTTGTTGTTTTAAGTAAAAATATCC
131 GTAAGTGT-GTGGAAGATTAGTTCTTTATAAGGTTGGG--TTTGTTGTTTTAAGCAAAAAAATCC
* * * * *
54360219 GTAGATTAATGCTTTTTGGATTGATATAGTGTAGTGGCTAGTTGTTGTGGATAGGAGAAGAGCGC
193 GTAGATTAATGATTTAT-GATAGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGCGC
* * *
54360284 GTGGTGATAGAGAATCCTCCGGAAAATTAAGGTTTTGGAGTAGTTATTGCAAGTTTGTGGTAACT
257 GTGGTGATAGACAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACT
* * * * *
54360349 ACTTGTTTATGAATATATGGACTGTTTCATTGAGAAAAGAGCAAATTTCAGTGGTAATGTTTGTG
322 ACTTGTTTATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTG
* * *
54360414 CTAAATCGAAGTTGTACTCGTTGGTT
387 TTAAATCAAAGTTGTAATCGTTGGTT
54360440 GATGGTTGTC
Statistics
Matches: 999, Mismatches: 128, Indels: 72
0.83 0.11 0.06
Matches are distributed among these distances:
729 59 0.06
730 27 0.03
731 85 0.09
732 12 0.01
733 12 0.01
734 1 0.00
735 257 0.26
736 7 0.01
737 2 0.00
739 7 0.01
740 145 0.15
746 2 0.00
747 3 0.00
751 3 0.00
753 3 0.00
757 1 0.00
758 2 0.00
759 154 0.15
762 2 0.00
763 5 0.01
764 210 0.21
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.41
Consensus pattern (739 bp):
CGACTCCTTCTTTTGTTATTGTGCCAATTGCAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTG
AGGCTTGTTATGATTTTGTTGTTCGCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTG
GTAAGTGTGTGGAAGATTAGTTCTTTATAAGGTTGGGTTTGTTGTTTTAAGCAAAAAAATCCGTA
GATTAATGATTTATGATAGATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGCGCGTGG
TGATAGACAATCCTCCGAAAAATTAAGGTTTTGGAGTAGTTGTTGCAAGTTTGTGGTAACTACTT
GTTTATGAATATAAGGACTGTTTCTTTGAGAAAAGAGCAAATTTAAGTGGTAATATTCGTGTTAA
ATCAAAGTTGTAATCGTTGGTTTTGGTGCCATTTGTAAGATTTTAAGTGTAAGATTGCATGGTGG
ATTAATCTCACTATCAGTGTGTGAAAAGATCCTAAAACTCGAGAGAAACTCGTTAAATCGTGAAA
CATGGGGTGTTTTTCGAAACTACCCAGTGCCACATGACACTATGTCAGGCCGTATGGTAGATTGT
GTGAGCCACACGGCCGTGTAATTTTATTTTTTTAAAATCAAATCCCTATTATTTTTTCTCTTTCA
GCAACCATCAAACCAACTTCTCTTCAGTTGCACATTTCTTTCCCTTCTTTCAATTTATTCTTTTC
TTTTCTTCTGTCGCTTGCCAAAGT
Found at i:54359984 original size:12 final size:12
Alignment explanation
Indices: 54359969--54360007 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
54359959 TCAATTTAGT
*
54359969 TTTATTTTTTTC
1 TTTATTTTCTTC
54359981 TTTATTTTCTTC
1 TTTATTTTCTTC
* *
54359993 TTTGTTTCCTTC
1 TTTATTTTCTTC
54360005 TTT
1 TTT
54360008 TTCGGCTTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.77
Consensus pattern (12 bp):
TTTATTTTCTTC
Found at i:54368925 original size:12 final size:12
Alignment explanation
Indices: 54368910--54368943 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
54368900 TTGTTTTACA
*
54368910 TTTTTTTCTTTC
1 TTTTCTTCTTTC
54368922 TTTTCTTCTTTC
1 TTTTCTTCTTTC
*
54368934 TTTCCTTCTT
1 TTTTCTTCTT
54368944 ATACACCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTTCTTCTTTC
Found at i:54369316 original size:772 final size:761
Alignment explanation
Indices: 54367080--54369519 Score: 3483
Period size: 759 Copynumber: 3.2 Consensus size: 761
54367070 TTTTAGCATT
* * * * *
54367080 TAATCATTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTATAACTTCGTGGTGGATTAATCTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
* * * *
54367145 CTATCAGGTGTGTGAAAATAATCTTAAAACTTGATAGAAACTTGTTAAATCGTGAAATAGGGGCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAACAGGGGCT
* *
54367210 ATTTTTCGAAACTGCCTC-GTGCCACACGGCCCTGGGTCAGGCCGTGTGGTAGATTGTGTGCGTC
131 ATTTTTCGAAACTGCC-CAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTC
* * ** *
54367274 ACACGACCGTGTACTTTTATTTTTTTAAATCAAATCCTTATTATTTTTCTCTTTCGATAACTGTC
195 ACACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTC
* * * * *
54367339 AAACAAACTTCTCTTTGCTGGCACGTTTCTTTCCTTTCTTTCAATTTTGTTTTAAATTTTTTTCT
260 AAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCT
*
54367404 TTCTTTCCTTCTTTT-T-CACCTTGCCAACGCCGA-ATC--CTTTTGTTATTGTGCCAATTGTAA
325 TTCTTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTAA
* **
54367464 AATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTAATTC
390 AATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTCGCTTGTTTC
*
54367529 TTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTTTTTTATAAA
455 TTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAG-TTATTTATAAA
* ** * * *
54367594 GTTTGGGTTTTGTTGTTTT-A-AGTAGAAAAATCCATAGATTAATGATTTTATGATAGATATACT
519 GTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAGT
* * * *
54367657 GTTCTAGCTAGTTGTTGTGGATATGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTAA
584 GTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTAA
* * * * *
54367722 GGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTAATAGTTGATGAATATAGGGACTATTTATT
649 GGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATA-GGACTGTTTCTT
* * * *
54367787 TGGGAAAAGTGAGAATGTAAGTGGTAATGTTCGTGTTTAATC-AGAGTTG
713 TGAGAAAAGAGAGAATTTAAGTGGTAATGTTCGTGTTAAATCGA-AGTTG
* *
54367836 TAATCGTTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACGACTACGTGGTGGATTAATCTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
** * * *
54367901 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTG-TAGAAACTCATTAAATTGTGAAACATGGTC
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTC-GATAGAAACTTGTTAAATCGTGAAACAGGGGC
* * * * * * *
54367965 TTTTTTTCAAAACTGCCTAGTGCCACACGGTCGAGTGTCAGGCCGTGTTGTAGATTGTGTGCGCC
130 TATTTTTCGAAACTGCCCAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTC
* * * * *
54368030 ACACGACCGTCTAATTTTATTTTTTAAAATCAAATACCTATTATTTTTCTCTTTCAGCAACCGTT
195 ACACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTC
*
54368095 AAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCT
260 AAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCT
* * *
54368160 TTCTTTCCTTC-TTTA-A-ACCTTGCCAACACCGACTCCTTCTTTTGTTATTGTGCCAATTGCAA
325 TTCTTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTAA
* * *
54368222 AATCTTTCTTTTGTTGTGTAAGAACACTGTTGAGGCTTGC-TATGATTCTGTTGTTCACTTGTTT
390 AATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTT-CTTATGATTCTATTGTTCGCTTGTTT
* *
54368286 CTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGT-TGGAAGATTAGTTCTTTATAAG
454 CTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTATTTATAAA
* *
54368350 GTTGGAGTTTTGTTGTTTTAAGCAAAAAAAAAATACGTAGATTAATGATTTTATGATAGATATAG
519 GTTGGGGTTTTGTTGTTTTAA-CAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAG
* *
54368415 TGTTGTGCCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAA-CTCTCCGACAATTT
583 TGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCT-TCCGACAAATT
54368479 AAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAAGGACTGTTTC
647 AAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATAT-AGGACTGTTTC
* * *
54368544 TTTGAGAAAAGAGCGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTT
711 TTTGAGAAAAGAGAGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* ** * * * *
54368595 TAATCGTTAGTTTTGGTGTTGTTTGTAGGATTTTACGTGTACAACGACGTGGTGGATTAATGTTG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
* *
54368660 CTATCAGGTGTGTGAAAACGATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAATAGGGGCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAACAGGGGCT
* * * *
54368725 ATTTTTTGAAACTGCCCAGTGCCACACGGCCGTGTGTCAGGCCGTATGGTAGATTGTGTGTGTGA
131 ATTTTTCGAAACTGCCCAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTCA
* *
54368790 CACGTCCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCATCA
196 CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCA
*
54368855 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTCCAATTTTGTTTTACATTTTTTTCTT
261 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTT
*
54368920 TCTTTTCTTCTTTCTTTCCTTCTTATACACCTTGCCAACGCTGACTTCTTCTTTTGTTATTGTGC
326 TC---T-TTC---C-TT-CTT-TTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGC
* *
54368985 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATTATTCAATTGTTC
381 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTC
** * *
54369050 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTTATTGTGTTGGTAAGTTGTGTGAAAGATAAGTTA
446 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTA
* *
54369115 TTAATAAAGTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATT
511 TTTATAAAGTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATA
* * * *
54369180 TATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGTGCGTGGTGGTAGACAACCTTCCGA
576 GATATAGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGA
*
54369245 CAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGTGAT
641 CAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAG-GAC
54369310 TGTTTCTTTGAGAAAAGAGTA-AATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
705 TGTTTCTTTGAGAAAAGAG-AGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* ** *
54369367 TAATCATTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATGTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
** * * * *
54369432 CTATCAGGTGTGTGAAAATGATTCTAAAACCCTATAGAAACTAGTTAAATCGTGAAACAGGGGCT
66 CTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAACAGGGGCT
*
54369497 ATTTTTCGAAACTACCCAGTGCC
131 ATTTTTCGAAACTGCCCAGTGCC
54369520 GTACAGCGGT
Statistics
Matches: 1492, Mismatches: 159, Indels: 50
0.88 0.09 0.03
Matches are distributed among these distances:
755 18 0.01
756 318 0.21
757 13 0.01
758 125 0.08
759 482 0.32
760 2 0.00
762 1 0.00
763 3 0.00
766 1 0.00
767 2 0.00
768 1 0.00
769 1 0.00
770 3 0.00
771 4 0.00
772 479 0.32
773 39 0.03
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (761 bp):
TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
CTATCAGGTGTGTGAAAACAATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAACAGGGGCT
ATTTTTCGAAACTGCCCAGTGCCACACGGCCGTGTGTCAGGCCGTGTGGTAGATTGTGTGCGTCA
CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCA
AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTT
TCTTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTAAA
ATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTCGCTTGTTTCT
TTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTATTTATAAAGT
TGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAGTGT
TGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTAAGG
TTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGACTGTTTCTTTGA
GAAAAGAGAGAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
Found at i:54369541 original size:772 final size:758
Alignment explanation
Indices: 54367080--54369544 Score: 3393
Period size: 772 Copynumber: 3.2 Consensus size: 758
54367070 TTTTAGCATT
* * * * *
54367080 TAATCATTGGTTTTGGTGTCATTTGTAGGATTTTAAGTGTATAACTTCGTGGTGGATTAATCTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
** * * * *
54367145 CTATCAGGTGTGTGAAAATAATCTTAAAA-CTTGATAGAAACTTGTTAAATCGTGAAATAGGGGC
66 CTATCAGGTGTGTGAAAACGATCCTAAAACCCT-ATAGAAACTAGTTAAATCGTGAAACAGGGGC
**
54367209 TATTTTTCGAAACTGCCTC-GTGCCACACGGCCCTGGGTCAGGCCGTGTGGTAGATTGTGTGCGT
130 TATTTTTCGAAACTGCC-CAGTGCCACACGG-TAT-GGTCAGGCCGTGTGGTAGATTGTGTGCGT
* * ** *
54367273 CACACGACCGTGTACTTTTATTTTTTTAAATCAAATCCTTATTATTTTTCTCTTTCGATAACTGT
192 CACACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGT
* * * * *
54367338 CAAACAAACTTCTCTTTGCTGGCACGTTTCTTTCCTTTCTTTCAATTTTGTTTTAAATTTTTTTC
257 CAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTC
*
54367403 TTTCTTTCCTTCTTTT-T-CACCTTGCCAACGCCGA-ATC--CTTTTGTTATTGTGCCAATTGTA
322 TTTCTTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTA
* **
54367463 AAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTGTTATGATTCTATTGTTCGCTTAATT
387 AAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTCGCTTGTTT
*
54367528 CTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTTTTTTATAA
452 CTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAG-TTATTTATAA
* ** * * *
54367593 AGTTTGGGTTTTGTTGTTTT-A-AGTAGAAAAATCCATAGATTAATGATTTTATGATAGATATAC
516 AGTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAG
* * * *
54367656 TGTTCTAGCTAGTTGTTGTGGATATGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTA
581 TGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTA
* * * * *
54367721 AGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTAATAGTTGATGAATATAGGGACTATTTAT
646 AGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATA-GGACTGTTTCT
* * * *
54367786 TTGGGAAAAGTGAGAATGTAAGTGGTAATGTTCGTGTTTAATC-AGAGTTG
710 TTGAGAAAAGAGA-AATTTAAGTGGTAATGTTCGTGTTAAATCGA-AGTTG
* *
54367836 TAATCGTTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACGACTACGTGGTGGATTAATCTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
* * * * * *
54367901 CTATCAGGTGTGTGAAAACAATCCTAAAACTCTGTAGAAACTCA-TTAAATTGTGAAACATGGTC
66 CTATCAGGTGTGTGAAAACGATCCTAAAACCCTATAGAAACT-AGTTAAATCGTGAAACAGGGGC
* * * * *
54367965 TTTTTTTCAAAACTGCCTAGTGCCACACGGTCGA-GTGTCAGGCCGTGTTGTAGATTGTGTGCGC
130 TATTTTTCGAAACTGCCCAGTGCCACACGGT--ATG-GTCAGGCCGTGTGGTAGATTGTGTGCGT
* * * *
54368029 CACACGACCGTCTAATTTTATTTTTTAAAATCAAATACCTATTATTTTTCTCTTTCAGCAACCGT
192 CACACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGT
* *
54368094 TAAACCAACTTCTCTTTGGTTGCACATTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTC
257 CAAACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTC
* * *
54368159 TTTCTTTCCTTC-TTTA-A-ACCTTGCCAACACCGACTCCTTCTTTTGTTATTGTGCCAATTGCA
322 TTTCTTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTA
* * *
54368221 AAATCTTTCTTTTGTTGTGTAAGAACACTGTTGAGGCTTGC-TATGATTCTGTTGTTCACTTGTT
387 AAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTT-CTTATGATTCTATTGTTCGCTTGTT
*
54368285 TCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGT-TGGAAGATTAGTTCTTTATAA
451 TCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTATTTATAA
* * *
54368349 GGTTGGAGTTTTGTTGTTTTAAGCAAAAAAAAAATACGTAGATTAATGATTTTATGATAGATATA
516 AGTTGGGGTTTTGTTGTTTTAA-CAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATA
* *
54368414 GTGTTGTGCCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAA-CTCTCCGACAATT
580 GTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCT-TCCGACAAAT
54368478 TAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAAGGACTGTTT
644 TAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATAT-AGGACTGTTT
* * *
54368543 CTTTGAGAAAAGAGCGAATTTAAATGGTAATGTTCGTGTTAAATCGAAGTTT
708 CTTTGAGAAAAGAG-AAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* ** * * * *
54368595 TAATCGTTAGTTTTGGTGTTGTTTGTAGGATTTTACGTGTACAACGACGTGGTGGATTAATGTTG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
* * * *
54368660 CTATCAGGTGTGTGAAAACGATCCTAAAACTCGATAGAAACTTGTTAAATCGTGAAATAGGGGCT
66 CTATCAGGTGTGTGAAAACGATCCTAAAACCCTATAGAAACTAGTTAAATCGTGAAACAGGGGCT
* ** * * *
54368725 ATTTTTTGAAACTGCCCAGTGCCACACGGCCGTGTGTCAGGCCGTATGGTAGATTGTGTGTGTGA
131 ATTTTTCGAAACTGCCCAGTGCCACACGG-TATG-GTCAGGCCGTGTGGTAGATTGTGTGCGTCA
* *
54368790 CACGTCCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCATCA
194 CACGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCA
*
54368855 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTCCAATTTTGTTTTACATTTTTTTCTT
259 AACCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTT
*
54368920 TCTTTTCTTCTTTCTTTCCTTCTTATACACCTTGCCAACGCTGACTTCTTCTTTTGTTATTGTGC
324 TC---T-TTC---C-TT-CTT-TTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGC
* *
54368985 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATTATTCAATTGTTC
379 CAATTGTAAAATCTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTC
** * *
54369050 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTTATTGTGTTGGTAAGTTGTGTGAAAGATAAGTTA
444 GCTTGTTTCTTTCTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTA
* *
54369115 TTAATAAAGTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATT
509 TTTATAAAGTTGGGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATA
* * * *
54369180 TATATAGTGTTGTGGCTGGTTGTTGTGGATAGGAGAAGAGTGCGTGGTGGTAGACAACCTTCCGA
574 GATATAGTGTTGTGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGA
*
54369245 CAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGTGAT
639 CAAATTAAGGTTTTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAG-GAC
54369310 TGTTTCTTTGAGAAAAGAGTAAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
703 TGTTTCTTTGAGAAAAGAG-AAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
* ** *
54369367 TAATCATTGGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTATGACTACGTGGTGGATTAATGTCG
1 TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
* *
54369432 CTATCAGGTGTGTGAAAATGATTCTAAAACCCTATAGAAACTAGTTAAATCGTGAAACAGGGGCT
66 CTATCAGGTGTGTGAAAACGATCCTAAAACCCTATAGAAACTAGTTAAATCGTGAAACAGGGGCT
*
54369497 ATTTTTCGAAACTACCCAGTGCCGTACAGCGGTATGGT-AGGCCGTGTG
131 ATTTTTCGAAACTGCCCAGTGCC--ACA-CGGTATGGTCAGGCCGTGTG
54369545 CCAGACCGTG
Statistics
Matches: 1504, Mismatches: 163, Indels: 68
0.87 0.09 0.04
Matches are distributed among these distances:
755 19 0.01
756 314 0.21
757 13 0.01
758 124 0.08
759 479 0.32
760 2 0.00
762 1 0.00
763 3 0.00
766 1 0.00
767 2 0.00
768 1 0.00
769 1 0.00
770 3 0.00
771 4 0.00
772 488 0.32
773 41 0.03
774 5 0.00
775 3 0.00
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.40
Consensus pattern (758 bp):
TAATCATTAGTTTTGGTGCCGTTTGTAGGATTTTAAGTGTACAACTACGTGGTGGATTAATCTCG
CTATCAGGTGTGTGAAAACGATCCTAAAACCCTATAGAAACTAGTTAAATCGTGAAACAGGGGCT
ATTTTTCGAAACTGCCCAGTGCCACACGGTATGGTCAGGCCGTGTGGTAGATTGTGTGCGTCACA
CGACCGTGTAATTTTATTTTTTTAAATCAAATCCCTATTATTTTTCTCTTTCGGCAACCGTCAAA
CCAACTTCTCTTTGGTTGCACGTTTCTTTCCCTTCTTTCAATTTTGTTTTACATTTTTTTCTTTC
TTTCCTTCTTTTATACACCTTGCCAACGCCGACTTCTTCTTTTGTTATTGTGCCAATTGTAAAAT
CTTTCTTTTGTTGCGTAAGAACACTGTTGAGGCTTCTTATGATTCTATTGTTCGCTTGTTTCTTT
CTTTTCCTCGTGGTGGCTTGGTTGTGTTGGTAAGTTGTGTGGAAGATTAGTTATTTATAAAGTTG
GGGTTTTGTTGTTTTAACAAAAAAAAAATCCGTAGATTAATGATTTTATGATAGATATAGTGTTG
TGGCTGGTTGTTGTGGATAAGAGAAGAGCGCGTGGTGATAGACAACCTTCCGACAAATTAAGGTT
TTGGAGTAGTTGCTGCAAGTTTGTGGTAACTACTTGTTTATGAATATAGGACTGTTTCTTTGAGA
AAAGAGAAATTTAAGTGGTAATGTTCGTGTTAAATCGAAGTTG
Found at i:54378168 original size:43 final size:41
Alignment explanation
Indices: 54378110--54378264 Score: 163
Period size: 43 Copynumber: 3.7 Consensus size: 41
54378100 TGTATTTTCA
54378110 TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTATACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCAA-TTGTG-ATACG
* * * **
54378153 TGTAAGACCATGTCTGGGACATTGGCATCGTATT-TGATTTG
1 TGTAAGACCACGTCTGGGACGTTGGCATC-AATTGTGATACG
* *
54378194 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAAT-TGTGA-TACG
54378237 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
54378265 TGTACGAGCC
Statistics
Matches: 93, Mismatches: 11, Indels: 16
0.77 0.09 0.13
Matches are distributed among these distances:
40 2 0.02
41 29 0.31
42 6 0.06
43 54 0.58
44 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (41 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAATTGTGATACG
Found at i:54378252 original size:84 final size:84
Alignment explanation
Indices: 54378110--54378264 Score: 210
Period size: 84 Copynumber: 1.8 Consensus size: 84
54378100 TGTATTTTCA
* *
54378110 TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTATACGTGTAAGACCATGTCTGGGACAT
1 TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTATACATGTAAGACCACGTCTGGGACAT
54378175 TGGCATCGTATTTGATTTG
66 TGGCATCGTATTTGATTTG
*
54378194 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGA-TATGTG-ATTACATGTAAGACCACGTCTGGG
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCAACT-TGTGTA-TACATGTAAGACCACGTCTGGG
*
54378255 ACGTTGGCAT
62 ACATTGGCAT
54378265 TGTACGAGCC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
83 3 0.05
84 59 0.94
85 1 0.02
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTATACATGTAAGACCACGTCTGGGACAT
TGGCATCGTATTTGATTTG
Found at i:54378454 original size:16 final size:17
Alignment explanation
Indices: 54378425--54378456 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
54378415 TGAATTGATG
54378425 ATATGAAGTTATGTGAA
1 ATATGAAGTTATGTGAA
54378442 ATATGAA-TTATGTGA
1 ATATGAAGTTATGTGA
54378457 TTGCATATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.41, C:0.00, G:0.22, T:0.38
Consensus pattern (17 bp):
ATATGAAGTTATGTGAA
Found at i:54385019 original size:21 final size:21
Alignment explanation
Indices: 54384995--54385045 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
54384985 CACTGAGGAA
** *
54384995 AAGAAGTTTGTTGCCATTGAG
1 AAGAAGTTTGTCACCAATGAG
* *
54385016 AAGAAGTCTGTCACTAATGAG
1 AAGAAGTTTGTCACCAATGAG
54385037 AAGAAGTTT
1 AAGAAGTTT
54385046 ATTTCCGCTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (21 bp):
AAGAAGTTTGTCACCAATGAG
Found at i:54386561 original size:16 final size:17
Alignment explanation
Indices: 54386542--54386575 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54386532 AAGATTTTAA
*
54386542 TGTTTAAA-GATTAAAT
1 TGTTTAAATGATAAAAT
54386558 TGTTTAAATGATAAAAT
1 TGTTTAAATGATAAAAT
54386575 T
1 T
54386576 TCAAGGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (17 bp):
TGTTTAAATGATAAAAT
Found at i:54386794 original size:38 final size:38
Alignment explanation
Indices: 54386743--54386816 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
54386733 TGATAAAAAG
*
54386743 GGATTTAGTTAATTGAATGGAATTATTATTTTAGATGT
1 GGATTTAGTTAATTGAATGGAATTATTATTTCAGATGT
54386781 GGATTTAGTTAATTGAATGGAATTATTATTTCAGAT
1 GGATTTAGTTAATTGAATGGAATTATTATTTCAGAT
54386817 CAAGAATGTG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.32, C:0.01, G:0.20, T:0.46
Consensus pattern (38 bp):
GGATTTAGTTAATTGAATGGAATTATTATTTCAGATGT
Found at i:54397887 original size:17 final size:17
Alignment explanation
Indices: 54397865--54397897 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
54397855 CTATTATTTT
54397865 AATTTAATCTAATATTA
1 AATTTAATCTAATATTA
54397882 AATTTAATCTAATATT
1 AATTTAATCTAATATT
54397898 TAATCATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (17 bp):
AATTTAATCTAATATTA
Found at i:54409042 original size:6 final size:6
Alignment explanation
Indices: 54409031--54409060 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
54409021 TTTAGTTGTC
54409031 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT
1 TGAAAT TGAAAT TGAAAT TGAAAT TGAAAT
54409061 CGAAGTGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
TGAAAT
Found at i:54409580 original size:23 final size:23
Alignment explanation
Indices: 54409551--54409597 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
54409541 ATCTCTAACC
54409551 AAATATTGAAACCTCTAACATAT
1 AAATATTGAAACCTCTAACATAT
*
54409574 AAATATTGAAATCTCTAACATAT
1 AAATATTGAAACCTCTAACATAT
54409597 A
1 A
54409598 CCCAAATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.04, T:0.32
Consensus pattern (23 bp):
AAATATTGAAACCTCTAACATAT
Found at i:54409679 original size:32 final size:32
Alignment explanation
Indices: 54409636--54409705 Score: 104
Period size: 32 Copynumber: 2.2 Consensus size: 32
54409626 GTAAACAAAT
* *
54409636 ACCAAAGTCTCTAATGGATACCAAAATTTGTA
1 ACCAAAATCTCTAACGGATACCAAAATTTGTA
* *
54409668 ACCAAAATCTCTTACGGGTACCAAAATTTGTA
1 ACCAAAATCTCTAACGGATACCAAAATTTGTA
54409700 ACCAAA
1 ACCAAA
54409706 TATCAAAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.26
Consensus pattern (32 bp):
ACCAAAATCTCTAACGGATACCAAAATTTGTA
Found at i:54409731 original size:19 final size:19
Alignment explanation
Indices: 54409686--54409799 Score: 75
Period size: 19 Copynumber: 5.9 Consensus size: 19
54409676 CTCTTACGGG
* *
54409686 TACCAAAATTTGTAACCAAA
1 TACCAAAATCTCTAA-CAAA
* * *
54409706 TATCAAAATCTTTAATAAA
1 TACCAAAATCTCTAACAAA
54409725 TACCAAAATCTCTAACAAA
1 TACCAAAATCTCTAACAAA
*** *
54409744 TATTGAAATTTCTAACAAA
1 TACCAAAATCTCTAACAAA
* * * * *
54409763 CACCAAATTTTCTAACCGAC
1 TACCAAAATCTCTAA-CAAA
*
54409783 TGCCAAAATCTCTAACA
1 TACCAAAATCTCTAACA
54409800 GGGACCAAAA
Statistics
Matches: 70, Mismatches: 23, Indels: 3
0.73 0.24 0.03
Matches are distributed among these distances:
19 45 0.64
20 25 0.36
ACGTcount: A:0.46, C:0.22, G:0.04, T:0.28
Consensus pattern (19 bp):
TACCAAAATCTCTAACAAA
Found at i:54416048 original size:89 final size:89
Alignment explanation
Indices: 54415885--54416129 Score: 325
Period size: 89 Copynumber: 2.7 Consensus size: 89
54415875 ATTCAAATTT
* * ** * *
54415885 TTTGTATTATTTTTGTATATGTAAATCAAATTTAGTCAGTATTATTTGTTGTTCGAATTTTATAT
1 TTTGTATT-TTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATAT
* * *
54415950 TTTCGTGTATTGATTTTTTAGAATG
65 TTTCGTGTATTAATATTCTAGAATG
54415975 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
54416040 TTCGTGTATTAATATTCTAGAATG
66 TTCGTGTATTAATATTCTAGAATG
* * *
54416064 TTTGTATTTTCTTGTATCTATAAATTTAATTT-GT-TGCGTATTA-TTATTTTTTCGAATTATAT
1 TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCT--GTATTATTTA-TTGTTCGAATTTTAT
54416126 ATTT
63 ATTT
54416130 GTTCTATTAA
Statistics
Matches: 140, Mismatches: 12, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
87 1 0.01
88 5 0.04
89 126 0.90
90 8 0.06
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.57
Consensus pattern (89 bp):
TTTGTATTTTCTTGTATCTGTAAATTTAATTTAGTCTGTATTATTTATTGTTCGAATTTTATATT
TTCGTGTATTAATATTCTAGAATG
Found at i:54416138 original size:16 final size:17
Alignment explanation
Indices: 54416092--54416145 Score: 58
Period size: 16 Copynumber: 3.2 Consensus size: 17
54416082 TATAAATTTA
54416092 ATTTGTTGCGTATTAT-T
1 ATTTGTT-CGTATTATAT
* *
54416109 ATTTTTTCGAATTATAT
1 ATTTGTTCGTATTATAT
*
54416126 ATTTGTTC-TATTAAAT
1 ATTTGTTCGTATTATAT
54416142 ATTT
1 ATTT
54416146 TGAAGTCATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 17 0.55
17 14 0.45
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (17 bp):
ATTTGTTCGTATTATAT
Found at i:54416190 original size:22 final size:20
Alignment explanation
Indices: 54416165--54416214 Score: 50
Period size: 19 Copynumber: 2.5 Consensus size: 20
54416155 TTATCCAAAC
*
54416165 AAATAATTATTTTAGAAAAATT
1 AAATAATTATATT-GAAAAA-T
54416187 AAAT--TTATATTGAAAAAT
1 AAATAATTATATTGAAAAAT
54416205 AGAATAATTA
1 A-AATAATTA
54416215 CAAACTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
18 2 0.08
19 9 0.38
20 6 0.25
21 3 0.12
22 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (20 bp):
AAATAATTATATTGAAAAAT
Found at i:54419421 original size:79 final size:78
Alignment explanation
Indices: 54419287--54419445 Score: 212
Period size: 79 Copynumber: 2.0 Consensus size: 78
54419277 TCACATGCAC
* ***
54419287 GGTTATAAATCAGAATCAATAACAATCAGTCTAACATATTCAGATATCGTGTATTCCTCATCAAC
1 GGTTATAAATCAGAATCAATAACAATCAATCTAACATATTCAGATATCACATATTCCTCATCAAC
54419352 AAAGTAACGCAGAA
66 AAAGTAACGCA-AA
* * *
54419366 GGTTATAAATCAGAATCAGTAACAATCAATCTAACATAATT-AGATGTCACATATTCTTCATCAA
1 GGTTATAAATCAGAATCAATAACAATCAATCTAACAT-ATTCAGATATCACATATTCCTCATCAA
* *
54419430 TAGAGTAACGCAAA
65 CAAAGTAACGCAAA
54419444 GG
1 GG
54419446 CGTATCAACA
Statistics
Matches: 70, Mismatches: 9, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
78 4 0.06
79 63 0.90
80 3 0.04
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (78 bp):
GGTTATAAATCAGAATCAATAACAATCAATCTAACATATTCAGATATCACATATTCCTCATCAAC
AAAGTAACGCAAA
Found at i:54421611 original size:12 final size:12
Alignment explanation
Indices: 54421580--54421617 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
54421570 TTTTTATTTT
54421580 ATTTGAATTTC-
1 ATTTGAATTTCA
*
54421591 ATTTCAATTTCA
1 ATTTGAATTTCA
54421603 ATTTGAATTTCA
1 ATTTGAATTTCA
54421615 ATT
1 ATT
54421618 CAATGCAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.32, C:0.11, G:0.05, T:0.53
Consensus pattern (12 bp):
ATTTGAATTTCA
Found at i:54421621 original size:5 final size:6
Alignment explanation
Indices: 54421580--54421634 Score: 53
Period size: 6 Copynumber: 9.5 Consensus size: 6
54421570 TTTTTATTTT
* * *
54421580 ATTTGA ATTTC- ATTTCA ATTTCA ATTTGA ATTTCA A-TTCA A-TGCA
1 ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA ATTTCA
54421625 ACTTTCA ATT
1 A-TTTCA ATT
54421635 AAATTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
5 14 0.34
6 23 0.56
7 4 0.10
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (6 bp):
ATTTCA
Found at i:54421634 original size:23 final size:23
Alignment explanation
Indices: 54421580--54421634 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
54421570 TTTTTATTTT
* * *
54421580 ATTTGAATTTCATTTCAATTTCA
1 ATTTCAATTTCAATTCAATTGCA
*
54421603 ATTTGAATTTCAATTCAA-TGCA
1 ATTTCAATTTCAATTCAATTGCA
54421625 ACTTTCAATT
1 A-TTTCAATT
54421635 AAATTTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (23 bp):
ATTTCAATTTCAATTCAATTGCA
Found at i:54423744 original size:22 final size:23
Alignment explanation
Indices: 54423690--54423750 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
54423680 CCGGCCCATT
*
54423690 TTTTAATTAAAATTAAAATTATAC
1 TTTT-ATTAAAATTAAAACTATAC
54423714 TTTTATTAAAATTAAAACTA-A-
1 TTTTATTAAAATTAAAACTATAC
54423735 TTGTTATTAAAATTAA
1 TT-TTATTAAAATTAA
54423751 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
21 2 0.06
22 14 0.40
23 15 0.43
24 4 0.11
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (23 bp):
TTTTATTAAAATTAAAACTATAC
Found at i:54423745 original size:16 final size:16
Alignment explanation
Indices: 54423724--54423780 Score: 96
Period size: 16 Copynumber: 3.6 Consensus size: 16
54423714 TTTTATTAAA
*
54423724 ATTAAAACTAATTGTT
1 ATTAAAATTAATTGTT
54423740 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
54423756 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
54423772 ATTAAAATT
1 ATTAAAATT
54423781 GTATCTAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:54423931 original size:93 final size:93
Alignment explanation
Indices: 54423825--54424008 Score: 341
Period size: 93 Copynumber: 2.0 Consensus size: 93
54423815 TTTGTAAAAT
54423825 CTAACATTTTGTTAGTAAAATTATTAATTATTAATTGTATTAATTGTTACTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTATTAATTGTATTAATTGTTACTAAAATTATCAAATT
54423890 ATATCAAATTATTAATTATTAATTGTTA
66 ATATCAAATTATTAATTATTAATTGTTA
* *
54423918 CTAACATTTTGTTAGTAAAATTATTAATTGTTAATTGTATTAATTGTTAGTAAAATTATCAAATT
1 CTAACATTTTGTTAGTAAAATTATTAATTATTAATTGTATTAATTGTTACTAAAATTATCAAATT
*
54423983 ATATCAAATTATTAATTGTTAATTGT
66 ATATCAAATTATTAATTATTAATTGT
54424009 ATTAATTGTT
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 88 1.00
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (93 bp):
CTAACATTTTGTTAGTAAAATTATTAATTATTAATTGTATTAATTGTTACTAAAATTATCAAATT
ATATCAAATTATTAATTATTAATTGTTA
Found at i:54424082 original size:22 final size:22
Alignment explanation
Indices: 54424057--54424103 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
54424047 AAACTTAAAA
* *
54424057 TAAAACTAAAACTAGTATAT-TT
1 TAAAAATAAAAATA-TATATATT
54424079 TAAAAATAAAAATATATATATT
1 TAAAAATAAAAATATATATATT
54424101 TAA
1 TAA
54424104 TATATTTTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (22 bp):
TAAAAATAAAAATATATATATT
Found at i:54424283 original size:5 final size:5
Alignment explanation
Indices: 54424249--54424275 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
54424239 AGCGGGCCAT
54424249 CGGGC CGGGC CGGGC CGGGC CGGGC CG
1 CGGGC CGGGC CGGGC CGGGC CGGGC CG
54424276 CCCGGCCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.00, C:0.41, G:0.59, T:0.00
Consensus pattern (5 bp):
CGGGC
Found at i:54425682 original size:52 final size:51
Alignment explanation
Indices: 54425567--54425707 Score: 178
Period size: 52 Copynumber: 2.8 Consensus size: 51
54425557 AAAAAGGTGT
* ** * **
54425567 TGTCGGCCATCTATGGGCCAAAACCAAAGAAAAAGA-AAT-TTAAGTGTTGG
1 TGTCGGCCATCTATTGGCCAAAACCCCA-AAAAATATTTTATTAAGTGTTGG
*
54425617 TGTCGGCCCTCTATTGGCCAAAACCCCCAAAAAATATTTTATTAAGTGTTGG
1 TGTCGGCCATCTATTGGCCAAAA-CCCCAAAAAATATTTTATTAAGTGTTGG
*
54425669 TGTCGGCCATCTATTGGCCAAAACCCTAAAAAATATTTT
1 TGTCGGCCATCTATTGGCCAAAACCCCAAAAAATATTTT
54425708 TTTTTCTCGT
Statistics
Matches: 79, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
50 27 0.34
51 19 0.24
52 33 0.42
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.28
Consensus pattern (51 bp):
TGTCGGCCATCTATTGGCCAAAACCCCAAAAAATATTTTATTAAGTGTTGG
Found at i:54427213 original size:4 final size:4
Alignment explanation
Indices: 54427204--54427251 Score: 60
Period size: 4 Copynumber: 12.0 Consensus size: 4
54427194 ATTTCATTTG
* * * *
54427204 ATGT ATGT ATGT GTGT CTGT ATGT ATGT ATGT GTGT ATGT GTGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
54427252 GGAGTATATA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.17, C:0.02, G:0.31, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:54427252 original size:16 final size:16
Alignment explanation
Indices: 54427205--54427252 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
54427195 TTTCATTTGA
* *
54427205 TGTATGTATGTGTGTC
1 TGTATGTATGTATGTG
54427221 TGTATGTATGTATGTG
1 TGTATGTATGTATGTG
*
54427237 TGTATGTGTGTATGTG
1 TGTATGTATGTATGTG
54427253 GAGTATATAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.15, C:0.02, G:0.33, T:0.50
Consensus pattern (16 bp):
TGTATGTATGTATGTG
Found at i:54430874 original size:20 final size:19
Alignment explanation
Indices: 54430842--54430888 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
54430832 CTCTATGAAG
* *
54430842 AAATATGAAAATTTTCTAT
1 AAATAGGAAAAATTTCTAT
54430861 AAATAGGAAAAATTTCTAT
1 AAATAGGAAAAATTTCTAT
54430880 AAATAGGAA
1 AAATAGGAA
54430889 TGAGATTTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.11, T:0.32
Consensus pattern (19 bp):
AAATAGGAAAAATTTCTAT
Found at i:54432321 original size:80 final size:77
Alignment explanation
Indices: 54432198--54432393 Score: 257
Period size: 80 Copynumber: 2.5 Consensus size: 77
54432188 TTTAAATTGC
* * * * * *
54432198 AAAAAACTCCTAAAATTAATAATTGAAATAGCGAAAAAGTCATTACATAAATACAAAGTTGACAA
1 AAAAAACTCATAAAATTAATAAATAAAATGGCAAAAAAATCATTACATAAATACAAAGTTGACAA
54432263 TTTAAATTGTAAA
66 TTTAAATTG-AAA
*
54432276 AAATTAAACTCATAAAATTAATAAATAAAATGGCAAAAAAATCATTACATAAATACAAAGTTGAT
1 AAA--AAACTCATAAAATTAATAAATAAAATGGCAAAAAAATCATTACATAAATACAAAGTTGAC
* *
54432341 TATTTAAATTGGAA
64 AATTTAAATTGAAA
* * *
54432355 AAAAAACCCATAAAATTAATAACTAAAATGGAAAAAAAA
1 AAAAAACTCATAAAATTAATAAATAAAATGGCAAAAAAA
54432394 GTTATTGTAT
Statistics
Matches: 104, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
77 33 0.32
78 3 0.03
79 5 0.05
80 63 0.61
ACGTcount: A:0.58, C:0.09, G:0.08, T:0.26
Consensus pattern (77 bp):
AAAAAACTCATAAAATTAATAAATAAAATGGCAAAAAAATCATTACATAAATACAAAGTTGACAA
TTTAAATTGAAA
Found at i:54432696 original size:33 final size:33
Alignment explanation
Indices: 54432646--54432715 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
54432636 AGGGGGAGTA
* * *
54432646 GATACGGGTCGAGAGGAGTGGAGTACGGCGGTG
1 GATACGGGCCGAGAGGAGCGGAGTACGGAGGTG
*
54432679 GATACGGGCC-AGAAGGAGCGGAGTACTGAGGTG
1 GATACGGGCCGAG-AGGAGCGGAGTACGGAGGTG
54432712 GATA
1 GATA
54432716 TGAGCCGGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 2 0.06
33 30 0.94
ACGTcount: A:0.26, C:0.13, G:0.47, T:0.14
Consensus pattern (33 bp):
GATACGGGCCGAGAGGAGCGGAGTACGGAGGTG
Found at i:54439499 original size:103 final size:100
Alignment explanation
Indices: 54439381--54439823 Score: 481
Period size: 103 Copynumber: 4.3 Consensus size: 100
54439371 CATTATATAA
54439381 AAATTACATTA--AAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAATCA
1 AAATTACATTACTAAAAAATCACAAAACAC-AAACTAAACACTAACAA-TT-TATAACCTAATCA
54439444 TAAATTACTAACAAAATAACTATAAAATTATTATTTTTT
63 TAAATTACTAACAAAATAACTATAAAATTATT-TTTTTT
*
54439483 AAA-TACATTACTAAAAAATCACAAAACACATAACTAAACACTAATAATTTATATAACCTAATCA
1 AAATTACATTACTAAAAAATCACAAAACACA-AACTAAACACTAACAA-TT-TATAACCTAATCA
*
54439547 TAAATTACTAACAAAATAACTATAAAATTATTTTTTTAAA
63 TAAATTACTAACAAAATAACTATAAAATTATTTTTTT--T
* * * * *
54439587 AAATTACATTACTAAAAAATCACAAAACCCTAAATTAAATACTAATAATTTGTAACCTAATCCCA
1 AAATTACATTACTAAAAAATCACAAAACAC-AAACTAAACACTAACAATTTATAACCTAAT--CA
* ****
54439652 TAAATTACTAACAAAGTAAATAACTATAACATT-TTTTAAAAG
63 TAAATTACTAAC--A--AAATAACTATAAAATTATTTT-TTTT
* *
54439694 AAATTACATTACTAAAAAAT-A-AAAA-AGC--ACAAAATACTAACAATTTATAACCTAATCATA
1 AAATTACATTACTAAAAAATCACAAAACA-CAAACTAAACACTAACAATTTATAACCTAATCATA
* **
54439754 AACTACTAACAAAATAACTATAATTTTATTTTTTTTT
65 AATTACTAACAAAATAACTATAAAATTA-TTTTTTTT
*
54439791 AAATTTACATTACTAAAAACTCACAAAACACAA
1 AAA-TTACATTACTAAAAAATCACAAAACACAA
54439824 CAATTTATAA
Statistics
Matches: 294, Mismatches: 24, Indels: 46
0.81 0.07 0.13
Matches are distributed among these distances:
96 14 0.05
97 3 0.01
98 21 0.07
99 1 0.00
100 18 0.06
101 8 0.03
102 33 0.11
103 91 0.31
104 5 0.02
105 58 0.20
106 2 0.01
107 21 0.07
108 4 0.01
109 15 0.05
ACGTcount: A:0.53, C:0.15, G:0.01, T:0.31
Consensus pattern (100 bp):
AAATTACATTACTAAAAAATCACAAAACACAAACTAAACACTAACAATTTATAACCTAATCATAA
ATTACTAACAAAATAACTATAAAATTATTTTTTTT
Found at i:54439568 original size:50 final size:50
Alignment explanation
Indices: 54439411--54439568 Score: 149
Period size: 50 Copynumber: 3.1 Consensus size: 50
54439401 CAAAACACTA
*
54439411 AACTAAACACTAACAATTTATATAACCTAATCATAAATTACTAACAAAAT
1 AACTAAACACTAATAATTTATATAACCTAATCATAAATTACTAACAAAAT
* * * * * * * * * * *
54439461 AACTATAAAATTATTATTTTTTAAATACATTACTAAAAAATCAC-AA-AACACAT
1 AACTA-AACACTAATAATTTATATA-AC-CTAATCATAAATTACTAACAA-A-AT
54439514 AACTAAACACTAATAATTTATATAACCTAATCATAAATTACTAACAAAAT
1 AACTAAACACTAATAATTTATATAACCTAATCATAAATTACTAACAAAAT
54439564 AACTA
1 AACTA
54439569 TAAAATTATT
Statistics
Matches: 78, Mismatches: 23, Indels: 14
0.68 0.20 0.12
Matches are distributed among these distances:
50 22 0.28
51 19 0.24
52 20 0.26
53 17 0.22
ACGTcount: A:0.54, C:0.16, G:0.00, T:0.30
Consensus pattern (50 bp):
AACTAAACACTAATAATTTATATAACCTAATCATAAATTACTAACAAAAT
Found at i:54439785 original size:205 final size:206
Alignment explanation
Indices: 54439379--54439821 Score: 523
Period size: 205 Copynumber: 2.2 Consensus size: 206
54439369 TACATTATAT
54439379 AAAAATTACATTA--AAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAAT
1 AAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAAT
****
54439442 CATAAATTACTAACAAAATAACTATAAAATTATTATTTTTTAAATACATTACTAAAAAATCACAA
66 CATAAATTACTAACAAAATAACTATAAAATTATTATTAAAGAAATACATTACTAAAAAATCACAA
* * *
54439507 AACACATAACTAAACACTAATAATTTATATAACCTAATCATAAATTACTAACAAAATAACTATAA
131 AACAC--AACAAAACACTAACAATTTATATAACCTAATCATAAACTACTAACAAAATAACTATAA
54439572 AATTATTTTTTTA
194 AATTATTTTTTTA
* * * * *
54439585 AAAAATTACATTACTAAAAAATCACAAAACCCTAAATTAAATACTAATAA-TT-TGTAACCTAAT
1 AAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAAT
*
54439648 CCCATAAATTACTAACAAAGTAAATAACTATAACATT-TT-TTAAAAGAAATTACATTACTAAAA
66 --CATAAATTACTAAC--A--AAATAACTATAAAATTATTATT-AAAGAAA-TACATTACTAAAA
*
54439711 AAT-A-AAAA-AGC-ACAAAATACTAACAA-TT-TATAACCTAATCATAAACTACTAACAAAATA
123 AATCACAAAACA-CAACAAAACACTAACAATTTATATAACCTAATCATAAACTACTAACAAAATA
** *
54439770 ACTATAATTTTATTTTTTTT
187 ACTATAAAATTATTTTTTTA
* * *
54439790 TAAATTTACATTACTAAAAACTCACAAAACAC
1 AAAAATTACATTACTAAAAAATCACAAAACAC
54439822 AACAATTTAT
Statistics
Matches: 205, Mismatches: 21, Indels: 23
0.82 0.08 0.09
Matches are distributed among these distances:
205 75 0.37
206 25 0.12
207 14 0.07
208 45 0.22
209 1 0.00
210 8 0.04
211 6 0.03
212 31 0.15
ACGTcount: A:0.53, C:0.15, G:0.01, T:0.31
Consensus pattern (206 bp):
AAAAATTACATTACTAAAAAATCACAAAACACTAAACTAAACACTAACAATTTATATAACCTAAT
CATAAATTACTAACAAAATAACTATAAAATTATTATTAAAGAAATACATTACTAAAAAATCACAA
AACACAACAAAACACTAACAATTTATATAACCTAATCATAAACTACTAACAAAATAACTATAAAA
TTATTTTTTTA
Found at i:54439973 original size:60 final size:59
Alignment explanation
Indices: 54439899--54440021 Score: 210
Period size: 60 Copynumber: 2.1 Consensus size: 59
54439889 AATACTAAAC
54439899 TAAACACAACAATTTATAACATAATCCTAAATTACTAATAAATTAATTTTAAAATAATTA
1 TAAACACAACAATTTATAACATAATCCTAAATTACTAA-AAATTAATTTTAAAATAATTA
* * *
54439959 TAAACACAATAATTTATAACATAATCCTAAATTACTAACAATTAATTTTAAAGTAATTA
1 TAAACACAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
54440018 TAAA
1 TAAA
54440022 AAAAATTACA
Statistics
Matches: 60, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
59 23 0.38
60 37 0.62
ACGTcount: A:0.53, C:0.11, G:0.01, T:0.35
Consensus pattern (59 bp):
TAAACACAACAATTTATAACATAATCCTAAATTACTAAAAATTAATTTTAAAATAATTA
Found at i:54440131 original size:13 final size:13
Alignment explanation
Indices: 54440113--54440137 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54440103 AAAATTTCAC
54440113 AACATCTTAATTG
1 AACATCTTAATTG
54440126 AACATCTTAATT
1 AACATCTTAATT
54440138 AAAGTCTTTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (13 bp):
AACATCTTAATTG
Found at i:54440153 original size:3 final size:3
Alignment explanation
Indices: 54440145--54440186 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
54440135 ATTAAAGTCT
54440145 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT- TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
54440187 CCTTTCTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:54440418 original size:27 final size:27
Alignment explanation
Indices: 54440388--54440443 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
54440378 GGCAGTGGCA
*
54440388 CCTACTTGGCAGGCACGACCAGTGCCG
1 CCTACTTGACAGGCACGACCAGTGCCG
* **
54440415 CCTATTTGACAGGCACGACTGGTGCCG
1 CCTACTTGACAGGCACGACCAGTGCCG
54440442 CC
1 CC
54440444 AGTCCAGGTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.18, C:0.36, G:0.29, T:0.18
Consensus pattern (27 bp):
CCTACTTGACAGGCACGACCAGTGCCG
Found at i:54442234 original size:41 final size:40
Alignment explanation
Indices: 54442153--54442339 Score: 263
Period size: 41 Copynumber: 4.6 Consensus size: 40
54442143 AATAAATATA
* *
54442153 TTTATTTTTTTTAATTTTAAAATATTTTTTACATAC-TTT
1 TTTATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
54442192 TTTATTTTTTTTAAATTTTAAAATATTTTT-AAATACTTTT
1 TTTATTTTTTTT-AATTTTAAAATATTTTTAAAATACTTTT
54442232 TTTAATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
1 TTT-ATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
54442273 TTTAATTTTTTTTTAATTTT-AAATATTTTTAAAATACTTTT
1 TTT-A-TTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
**
54442314 TTTAATTTTTTAAAATTTTTAAAATA
1 TTT-ATTTTTTTTAA-TTTTAAAATA
54442340 AAAATGGGCC
Statistics
Matches: 138, Mismatches: 3, Indels: 11
0.91 0.02 0.07
Matches are distributed among these distances:
39 17 0.12
40 48 0.35
41 54 0.39
42 19 0.14
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (40 bp):
TTTATTTTTTTTAATTTTAAAATATTTTTAAAATACTTTT
Found at i:54442297 original size:30 final size:31
Alignment explanation
Indices: 54442258--54442339 Score: 89
Period size: 31 Copynumber: 2.7 Consensus size: 31
54442248 TTTAAAATAT
** *
54442258 TTTTAAAATACTTTTTTTAAT-TTTTTTTTAA
1 TTTTAAAATA-TTTTTAAAATACTTTTTTTAA
54442289 TTTT-AAATATTTTTAAAATACTTTTTTTAA
1 TTTTAAAATATTTTTAAAATACTTTTTTTAA
*
54442319 TTTTTTAAA-ATTTTTAAAATA
1 -TTTTAAAATATTTTTAAAATA
54442340 AAAATGGGCC
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
29 8 0.18
30 14 0.31
31 20 0.44
32 3 0.07
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (31 bp):
TTTTAAAATATTTTTAAAATACTTTTTTTAA
Found at i:54442332 original size:31 final size:30
Alignment explanation
Indices: 54442280--54442339 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 30
54442270 TTTTTTAATT
54442280 TTTTTTTAATTTTAAATATTTTTAAAATAC
1 TTTTTTTAATTTTAAATATTTTTAAAATAC
54442310 TTTTTTTAATTTTTTAAA-ATTTTTAAAATA
1 TTTTTTTAA--TTTTAAATATTTTTAAAATA
54442340 AAAATGGGCC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 9 0.32
31 12 0.43
32 7 0.25
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (30 bp):
TTTTTTTAATTTTAAATATTTTTAAAATAC
Found at i:54450410 original size:11 final size:11
Alignment explanation
Indices: 54450394--54450445 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
54450384 TCAATTATTT
54450394 TCTCAAATTCC
1 TCTCAAATTCC
* *
54450405 TCTCAATTTGC
1 TCTCAAATTCC
*
54450416 TCTCAATTTCC
1 TCTCAAATTCC
*
54450427 T-TCCAAATTTC
1 TCT-CAAATTCC
54450438 TCTCAAAT
1 TCTCAAAT
54450446 CCATATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
10 1 0.03
11 32 0.94
12 1 0.03
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (11 bp):
TCTCAAATTCC
Found at i:54450426 original size:22 final size:22
Alignment explanation
Indices: 54450390--54450445 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
54450380 TCTCTCAATT
54450390 ATTT-TCTCAAATTCC-TCTC-A
1 ATTTCTCTCAAATTCCTTC-CAA
*
54450410 ATTTGCTCTCAATTTCCTTCCAA
1 ATTT-CTCTCAAATTCCTTCCAA
54450433 ATTTCTCTCAAAT
1 ATTTCTCTCAAAT
54450446 CCATATTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.13
22 19 0.63
23 7 0.23
ACGTcount: A:0.25, C:0.29, G:0.02, T:0.45
Consensus pattern (22 bp):
ATTTCTCTCAAATTCCTTCCAA
Found at i:54450465 original size:51 final size:51
Alignment explanation
Indices: 54450407--54450504 Score: 153
Period size: 51 Copynumber: 1.9 Consensus size: 51
54450397 CAAATTCCTC
54450407 TCAATTTGCTCTCAATTTCCT-TCCAAATTTCTCTCAAATCCATATTTAATA
1 TCAATTTGCTCTCAATTTCCTCT-CAAATTTCTCTCAAATCCATATTTAATA
* * *
54450458 TCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
54450505 TTAATTTTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.02, T:0.46
Consensus pattern (51 bp):
TCAATTTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAATA
Found at i:54451446 original size:20 final size:21
Alignment explanation
Indices: 54451412--54451455 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
54451402 ATAACGAGGT
54451412 AAATTTTATATTAGA-TTTTA
1 AAATTTTATATTAGATTTTTA
54451432 AAATTATTATA-TAGATTTTTA
1 AAATT-TTATATTAGATTTTTA
54451453 AAA
1 AAA
54451456 ATAATAGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
AAATTTTATATTAGATTTTTA
Found at i:54452199 original size:29 final size:31
Alignment explanation
Indices: 54452134--54452200 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 31
54452124 GACGACGACT
*
54452134 CAGGCCCATCAATGAGGCCCAGACAATCACC
1 CAGGCCCATCAATCAGGCCCAGACAATCACC
* **
54452165 CA-GCCCATC-ATCAGGGCCATTCAATCA-C
1 CAGGCCCATCAATCAGGCCCAGACAATCACC
54452193 CAGGCCCA
1 CAGGCCCA
54452201 GCGAGAGCAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 3 0.10
29 19 0.61
30 7 0.23
31 2 0.06
ACGTcount: A:0.30, C:0.40, G:0.18, T:0.12
Consensus pattern (31 bp):
CAGGCCCATCAATCAGGCCCAGACAATCACC
Found at i:54452320 original size:18 final size:18
Alignment explanation
Indices: 54452284--54452326 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
54452274 TGCCAGGTGC
*
54452284 GTATCCTAGCTCTTTTAT
1 GTATCCTAACTCTTTTAT
54452302 GTATCCTAAC-CTTTATAT
1 GTATCCTAACTCTTT-TAT
*
54452320 GTTTCCT
1 GTATCCT
54452327 TTTTCGAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 4 0.18
18 18 0.82
ACGTcount: A:0.19, C:0.23, G:0.09, T:0.49
Consensus pattern (18 bp):
GTATCCTAACTCTTTTAT
Found at i:54452905 original size:21 final size:21
Alignment explanation
Indices: 54452875--54454127 Score: 1627
Period size: 21 Copynumber: 58.9 Consensus size: 21
54452865 CAAAAACCCT
54452875 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54452896 AACACTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* * *
54452917 AATCCTAGCCCTTAACATAAA
1 AACCCTAACCCTTAACTTAAA
54452938 AACCCTTAAACCCTTAACTTAAA
1 AACCC-T-AACCCTTAACTTAAA
*
54452961 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54452982 AACCTTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453003 AACTCTAACCCTTAATTTAAA
1 AACCCTAACCCTTAACTTAAA
**
54453024 AACCCTAAAGCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453045 AACTCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453066 AACCGTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
** *
54453088 AATTCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453109 AACCCTAACCCTTAACTAAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453130 AATCTTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
54453152 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
* * * *
54453173 AGCCTTAACCTTTAATTTAAAA
1 AACCCTAACCCTTAACTT-AAA
54453195 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
54453217 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453238 AACCCTAACCCTTAACATAAA
1 AACCCTAACCCTTAACTTAAA
54453259 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
54453281 ACCCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453302 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
54453323 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
54453345 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453366 AACCCTAACCCATAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453387 AACCCTAACCCTTCACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453408 AACTCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453429 AACCCTAATCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453450 AACACTAACACTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
54453470 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
54453492 AACTCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453513 AGCCCTAA-CCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453533 AACCCTAAACCCTTAACATAAAA
1 AACCCT-AACCCTTAAC-TTAAA
*
54453556 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453577 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
*
54453599 AACTCTAACCCTTAA-TCTAAA
1 AACCCTAACCCTTAACT-TAAA
*
54453620 AACCCTAACCCTTAACATAAAA
1 AACCCTAACCCTTAAC-TTAAA
54453642 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453663 AACCGTAACCCTTAACCT-AA
1 AACCCTAACCCTTAACTTAAA
54453683 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453704 AACACTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453725 AACCCTAAGCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453746 AACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453767 AACCGTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
*
54453788 AACCCTAATCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453809 AACACTAACCATTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
* *
54453830 AACCCTAACCTTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453851 AACCCTAACCCCTTAACTTAAA
1 AACCCTAA-CCCTTAACTTAAA
** *
54453873 AACTTTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453894 AACCCTAAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
54453916 AACCCAAAACCCTTAACTAAAA
1 AACCC-TAACCCTTAACTTAAA
*
54453938 AACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAA
54453959 AACCCTAACCCTTAA-TATAAA
1 AACCCTAACCCTTAACT-TAAA
*
54453980 AAGCCCTAAACCATTAACTTAAA
1 AA-CCCT-AACCCTTAACTTAAA
54454003 AACCCTAACCCTTAACTT-AA
1 AACCCTAACCCTTAACTTAAA
*
54454023 AACCCTTAACCCTTAACCTAAA
1 AACCC-TAACCCTTAACTTAAA
* * *
54454045 AACTCGAACCCTTAACTTTAA
1 AACCCTAACCCTTAACTTAAA
* *
54454066 AACCTTAAATCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAA
* *
54454088 AACACTAGCCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAA
*
54454109 AACCCTAACCCTAAACTTA
1 AACCCTAACCCTTAACTTA
54454128 GCCCTAATAT
Statistics
Matches: 1067, Mismatches: 137, Indels: 56
0.85 0.11 0.04
Matches are distributed among these distances:
20 50 0.05
21 723 0.68
22 241 0.23
23 52 0.05
24 1 0.00
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.23
Consensus pattern (21 bp):
AACCCTAACCCTTAACTTAAA
Found at i:54454126 original size:64 final size:63
Alignment explanation
Indices: 54452875--54454127 Score: 1627
Period size: 64 Copynumber: 19.6 Consensus size: 63
54452865 CAAAAACCCT
* * * *
54452875 AACCCTAACCCTTAACTTAAAAACACTAACCCTTAACTTAAAAATCCTAGCCCTTAACATAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
54452938 AACCCTTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCTTAACCCTTAACTTAAA
1 AACCC-T-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * ** * *
54453003 AACTCTAACCCTTAATTTAAAAACCCTAAAGCTTAACTTAAAAACTCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* ** * *
54453066 AACCGTAAACCCTTAACTTAAAAATTCTAACCCTTAACCTAAAAACCCTAACCCTTAACTAAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * * * * *
54453130 AATCTTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAGCCTTAACCTTTAATTTAAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTT-AAA
* *
54453195 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACCTAAAAACCCTAACCCTTAACATAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
54453259 AACCCTAAACCCTTAACTTAAAACCCCTAACCCTTAACCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* *
54453323 AACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCATAACCTAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
54453387 AACCCTAACCCTTCACTTAAAAACTCTAACCCTTAACTTAAAAACCCTAATCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * *
54453450 AACACTAACACTTAACTT-AAAACCCTAAACCCTTAACTTAAAAACTCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * *
54453513 AGCCCTAA-CCTTAACCTAAAAACCCTAAACCCTTAACATAAAAAACCCTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAAC-TTAAAAACCCTAACCCTTAACTTAAA
* *
54453577 AACCCTAAACCCTTAACTTAAAAACTCTAACCCTTAA-TCTAAAAACCCTAACCCTTAACATAAA
1 AACCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACT-TAAAAACCCTAACCCTTAAC-TTAA
54453641 A
63 A
* *
54453642 AACCCTAACCCTTAACTTAAAAACCGTAACCCTTAACCT-AAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
54453704 AACACTAACCCTTAACTTAAAAACCCTAAGCCTTAACCTAAAAACCCTAACCCTTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * * * *
54453767 AACCGTAACCCTTAACCTAAAAACCCTAATCCTTAACTTAAAAACACTAACCATTAACTTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * ** *
54453830 AACCCTAACCTTTAACCTAAAAACCCTAACCCCTTAACTTAAAAACTTTAACCCTTAACCTAAA
1 AACCCTAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
* * *
54453894 AACCCTAAACCCTTAACTTAAAAACCCAAAACCCTTAACTAAAAAACCCTAACCCTTAACCTAAA
1 AACCCT-AACCCTTAACTTAAAAACCC-TAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
*
54453959 AACCCTAACCCTTAA-TATAAAAAGCCCTAAACCATTAACTTAAAAACCCTAACCCTTAACTT-A
1 AACCCTAACCCTTAACT-TAAAAA-CCCT-AACCCTTAACTTAAAAACCCTAACCCTTAACTTAA
54454022 A
63 A
* * * * * *
54454023 AACCCTTAACCCTTAACCTAAAAACTCGAACCCTTAACTTTAAAACCTTAAATCCTTAACTTAAA
1 AACCC-TAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
* * *
54454088 AACACTAGCCCTTAACTTAAAAACCCTAACCCTAAACTTA
1 AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTA
54454128 GCCCTAATAT
Statistics
Matches: 1051, Mismatches: 116, Indels: 45
0.87 0.10 0.04
Matches are distributed among these distances:
62 54 0.05
63 328 0.31
64 409 0.39
65 242 0.23
66 18 0.02
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.23
Consensus pattern (63 bp):
AACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAA
Found at i:54458666 original size:22 final size:21
Alignment explanation
Indices: 54458629--54458681 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
54458619 TTAATTTTCA
*
54458629 AAATTA-ATGAACTTTTATTAT
1 AAATTAGATGAATTTTTATT-T
54458650 AAATTAGATGAATTTTTATTT
1 AAATTAGATGAATTTTTATTT
54458671 -AATTAG-TGAAT
1 AAATTAGATGAAT
54458682 ATATATTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.17
20 6 0.20
21 7 0.23
22 12 0.40
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (21 bp):
AAATTAGATGAATTTTTATTT
Found at i:54458688 original size:19 final size:20
Alignment explanation
Indices: 54458651--54458689 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
54458641 TTTTATTATA
* *
54458651 AATTAGATGAATTTTTATTT
1 AATTAGATGAATATATATTT
54458671 AATTAG-TGAATATATATTT
1 AATTAGATGAATATATATTT
54458690 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.51
Consensus pattern (20 bp):
AATTAGATGAATATATATTT
Found at i:54458705 original size:21 final size:23
Alignment explanation
Indices: 54458679--54458724 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
54458669 TTAATTAGTG
*
54458679 AATATA-TATTTTA-AAATTAAA
1 AATATATTATTTAATAAATTAAA
54458700 AATATATTATTTAATAAATTAAA
1 AATATATTATTTAATAAATTAAA
54458723 AA
1 AA
54458725 ATACATAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 6 0.27
23 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
AATATATTATTTAATAAATTAAA
Found at i:54466293 original size:43 final size:43
Alignment explanation
Indices: 54466232--54466597 Score: 446
Period size: 43 Copynumber: 8.5 Consensus size: 43
54466222 ACTTTCACCA
*
54466232 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * * *
54466275 CATGACCTTTAGCGGCGCTTATCCGACAAATGCCGCTAAGGTC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* *
54466318 CATGACCTTTAGCGGTGCTTATCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * * *
54466361 CCTGACCTTTAGTGGTGCTTATCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * * *
54466404 AATGACCTTTAGCGGTGCTTTTCCAACAAATGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * *
54466447 CATAACCTTTAGCGACGCTTATCCGACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* * *
54466490 AATAACCTTTAGCGGCGC-TTTCCAAACAAACGCCGCTAAAGAC
1 CATGACCTTTAGCGGCGCTTTTCC-GACAAACGCCGCTAAAGAC
* * * * * * *
54466533 CCTGATCTTTAGCAGCACTTTTCCCACAAACGCCGCAAAAGAT
1 CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
* *
54466576 CATGACCTTTAGTGGCGTTTTT
1 CATGACCTTTAGCGGCGCTTTT
54466598 TAAAAAACAC
Statistics
Matches: 278, Mismatches: 43, Indels: 4
0.86 0.13 0.01
Matches are distributed among these distances:
42 4 0.01
43 269 0.97
44 5 0.02
ACGTcount: A:0.28, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTCCGACAAACGCCGCTAAAGAC
Found at i:54467065 original size:66 final size:66
Alignment explanation
Indices: 54466976--54467123 Score: 208
Period size: 66 Copynumber: 2.2 Consensus size: 66
54466966 TTGCTGCCGT
* * * *
54466976 ATCTGCTTTAAGCTGCAGCTGGAGTTCTTCATA-CTTTCATTAAACCTCAGCTTCTCTCGCTGTT
1 ATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTT-ATTAAACCTCAGCTTCTCTCGATGCT
54467040 GC
65 GC
* *
54467042 ATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTTTTGAACCTCAGCTTCTCTCGATGCTG
1 ATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTATTAAACCTCAGCTTCTCTCGATGCTG
54467107 C
66 C
* *
54467108 CTCCGCTTTAAGTTGT
1 ATCTGCTTTAAGTTGT
54467124 GTAATTTGCT
Statistics
Matches: 73, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
66 69 0.95
67 4 0.05
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.41
Consensus pattern (66 bp):
ATCTGCTTTAAGTTGTAGCTGGAGTTCTTCATATCTTTATTAAACCTCAGCTTCTCTCGATGCTG
C
Found at i:54470619 original size:9 final size:9
Alignment explanation
Indices: 54470605--54470654 Score: 54
Period size: 9 Copynumber: 6.0 Consensus size: 9
54470595 AGTATAAATG
54470605 AGTTATGTA
1 AGTTATGTA
54470614 AGTTATGT-
1 AGTTATGTA
54470622 A-TTATGTA
1 AGTTATGTA
*
54470630 AGTTGTGT-
1 AGTTATGTA
54470638 A-TTATGTA
1 AGTTATGTA
*
54470646 AATTATGTA
1 AGTTATGTA
54470655 TTATGCAAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
7 11 0.31
8 4 0.11
9 20 0.57
ACGTcount: A:0.32, C:0.00, G:0.20, T:0.48
Consensus pattern (9 bp):
AGTTATGTA
Found at i:54470628 original size:16 final size:16
Alignment explanation
Indices: 54470607--54470665 Score: 91
Period size: 16 Copynumber: 3.7 Consensus size: 16
54470597 TATAAATGAG
54470607 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
*
54470623 TTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTA
*
54470639 TTATGTAAATTATGTA
1 TTATGTAAGTTATGTA
*
54470655 TTATGCAAGTT
1 TTATGTAAGTT
54470666 TTGGAAAAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 38 1.00
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.49
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:54470986 original size:69 final size:69
Alignment explanation
Indices: 54470906--54471053 Score: 233
Period size: 69 Copynumber: 2.1 Consensus size: 69
54470896 AAATATAAGG
* * * * *
54470906 GTTAATATTTAGAAAATAACATTTACAATTATTTTTCAAATTGTAAAATTTATTGTTCCAAATAT
1 GTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTCAAAATAT
54470971 AGAT
66 AGAT
* *
54470975 GTTAATCTTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATAT
1 GTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTCAAAATAT
54471040 AGAT
66 AGAT
54471044 GTTAATATTT
1 GTTAATATTT
54471054 TCTCATAATT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 71 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (69 bp):
GTTAATATTTAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTCAAAATAT
AGAT
Found at i:54471666 original size:26 final size:26
Alignment explanation
Indices: 54471637--54471693 Score: 96
Period size: 26 Copynumber: 2.2 Consensus size: 26
54471627 ATATATTTAT
*
54471637 ATTATTTTATAAGCTATAGAGTAAAA
1 ATTATTTGATAAGCTATAGAGTAAAA
*
54471663 ATTATTTGATAAGCTATAGAGTAAGA
1 ATTATTTGATAAGCTATAGAGTAAAA
54471689 ATTAT
1 ATTAT
54471694 CATGCAACGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.44, C:0.04, G:0.14, T:0.39
Consensus pattern (26 bp):
ATTATTTGATAAGCTATAGAGTAAAA
Found at i:54474017 original size:7 final size:7
Alignment explanation
Indices: 54473983--54474016 Score: 59
Period size: 7 Copynumber: 4.9 Consensus size: 7
54473973 ACCCTTGACA
54473983 CCCTAAC
1 CCCTAAC
54473990 CCCTAAC
1 CCCTAAC
54473997 CCCTAAC
1 CCCTAAC
*
54474004 CCCTAAT
1 CCCTAAC
54474011 CCCTAA
1 CCCTAA
54474017 TTCATACCCC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.29, C:0.53, G:0.00, T:0.18
Consensus pattern (7 bp):
CCCTAAC
Found at i:54475123 original size:41 final size:40
Alignment explanation
Indices: 54474953--54475193 Score: 137
Period size: 41 Copynumber: 5.8 Consensus size: 40
54474943 GCACTTCAAC
* * * * * *
54474953 AAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAA
1 AAAAACGCCGCTAAAAACCTTAGCATTAGCGGCGGTTAT--T
* * *
54474995 AAAAACGCCACTAAAAATCTTAGCTTTAGCGGCGCG-TATTT
1 AAAAACGCCGCTAAAAACCTTAGCATTAGCGGCG-GTTA-TT
* * * *
54475036 AAAAACGCCGCTAAAAGACC-AAACATTAGCGGCGTTTCA-A
1 AAAAACGCCGCTAAAA-ACCTTAGCATTAGCGGCGGTT-ATT
*
54475076 AGAAAACGCCGCTAAATACCTTAGCATTAGCGGCGGTTGATT
1 A-AAAACGCCGCTAAAAACCTTAGCATTAGCGGCGGTT-ATT
* * * * * * **
54475118 AAAAACACCACGAAAACCCTCGACCATTAGCGGCGAATACTT
1 AAAAACGCCGCTAAAAACCT-TAGCATTAGCGGCGGTTA-TT
** **
54475160 AAAAACGCCGCTAAAAGTCACAGCATTAGCGGCG
1 AAAAACGCCGCTAAAAACCTTAGCATTAGCGGCG
54475194 CTAATACAAA
Statistics
Matches: 150, Mismatches: 39, Indels: 21
0.71 0.19 0.10
Matches are distributed among these distances:
40 4 0.03
41 83 0.55
42 62 0.41
43 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (40 bp):
AAAAACGCCGCTAAAAACCTTAGCATTAGCGGCGGTTATT
Found at i:54475123 original size:82 final size:83
Alignment explanation
Indices: 54474953--54475110 Score: 230
Period size: 82 Copynumber: 1.9 Consensus size: 83
54474943 GCACTTCAAC
* * *
54474953 AAAAACGCCGCTAAAACCCCTAACATTAGCGGCGCTTCTCAAAAAAACGCCACTAAAAATCTTAG
1 AAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTCTCAAAAAAACGCCACTAAAAACCTTAG
*
54475018 CTTTAGCGGCGCGTATTT
66 CATTAGCGGCGCGTATTT
* * *
54475036 AAAAACGCCGCTAAAAGACCAAACATTAGCGGCG-TT-TCAAAGAAAACGCCGCTAAATACCTTA
1 AAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTCTCAAA-AAAACGCCACTAAAAACCTTA
54475099 GCATTAGCGGCG
65 GCATTAGCGGCG
54475111 GTTGATTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 5 0.07
82 31 0.46
83 31 0.46
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.19
Consensus pattern (83 bp):
AAAAACGCCGCTAAAACACCAAACATTAGCGGCGCTTCTCAAAAAAACGCCACTAAAAACCTTAG
CATTAGCGGCGCGTATTT
Found at i:54477087 original size:3 final size:3
Alignment explanation
Indices: 54477081--54477136 Score: 103
Period size: 3 Copynumber: 18.7 Consensus size: 3
54477071 AAATAAACAA
*
54477081 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
54477129 AAT AAT AA
1 AAT AAT AA
54477137 ATAAATTATT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:54483981 original size:15 final size:15
Alignment explanation
Indices: 54483946--54483990 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
54483936 AATTCAAAAA
54483946 AAAAAGATGAAAAAT-
1 AAAAA-ATGAAAAATG
54483961 AAAAAATGAAAAATG
1 AAAAAATGAAAAATG
54483976 AAAAAA-GTAAAAATG
1 AAAAAATG-AAAAATG
54483991 GAGAGGCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 10 0.36
15 18 0.64
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:54483987 original size:14 final size:14
Alignment explanation
Indices: 54483941--54483981 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
54483931 GGACCAATTC
54483941 AAAAA-AAAAAGATG
1 AAAAATAAAAA-ATG
54483955 AAAAATAAAAAATG
1 AAAAATAAAAAATG
54483969 AAAAATGAAAAAA
1 AAAAAT-AAAAAA
54483982 GTAAAAATGG
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 14 0.56
15 11 0.44
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (14 bp):
AAAAATAAAAAATG
Found at i:54485546 original size:131 final size:129
Alignment explanation
Indices: 54485240--54485728 Score: 736
Period size: 131 Copynumber: 3.8 Consensus size: 129
54485230 GTGAAATCAT
* **
54485240 AAGTCCTATGTCCTTGACCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTTTCCTTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGTTTCC-TAAGCAG
54485305 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCCAGGAGTAGGGAAACAGATTT----AC
65 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCCAGGAGTAGGGAAACAGATTTAAGCAC
*
54485366 AAGTCCTATGTCTCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGTCTTCCTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGT-TTCCTAAGCAG
** * * * *
54485431 TAGCGGAGCAGATTAAAAATGGCGAATCTTATCTTC-CTTAGGAGTAGGGAAACATATTTAAGCC
65 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTC-CAGGAGTAGGGAAACAGATTTAAG-C
54485495 AC
128 AC
54485497 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGTCTTCCTAAGCAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGT-TTCCTAAGCAG
* *
54485562 TAGCGGAGTAGATCGAAGACGGTGAATCTTATCTTCTCCAGGAGTAGGGAAACAGATTTAAGTCA
65 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCCAGGAGTAGGGAAACAGATTTAAG-CA
54485627 C
129 C
* *
54485628 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGATTGGAAATTGTAGATCTTGTTTCCCTAAGTAG
1 AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGTTT-CCTAAGCAG
* *
54485693 TAGCGGAGCAGACCGAAGACGGCAAATCTTATCTTC
65 TAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTC
54485729 AAGTATAAGG
Statistics
Matches: 328, Mismatches: 26, Indels: 13
0.89 0.07 0.04
Matches are distributed among these distances:
125 1 0.00
126 107 0.33
127 4 0.01
130 2 0.01
131 213 0.65
132 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.27
Consensus pattern (129 bp):
AAGTCCTATGTCCCTGACCAGCAGTGGAATAGGTTGGAAATTGTAGATCTTGTTTCCTAAGCAGT
AGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCTCCAGGAGTAGGGAAACAGATTTAAGCAC
Found at i:54485908 original size:44 final size:44
Alignment explanation
Indices: 54485840--54486074 Score: 197
Period size: 44 Copynumber: 5.1 Consensus size: 44
54485830 TAGATCGCAT
*
54485840 CAGATTGAAGCTAGAAATCTTATCTCCCTGAGATTACAGAGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGAGGAG
* *
54485884 CAGATTGAAGCTAGTAATCGTATCTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGAGGAG
* ** * * **
54485928 CGGATT-AAAATAAATGATCTTATCTCTTTGA-AGTTACAGTAGAGTAGATCG
1 CAGATTGAAGCT-AGTAATCTTATCTCCCTGAGA-TTAC---AGAG--GA--G
* * *
54485979 CATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 ---CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGAGGAG
* *
54486026 CAGATTGAAGCTAGTAATCCTA-CTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGAGGAG
*
54486069 CGGATT
1 CAGATT
54486075 AAAACAAAGG
Statistics
Matches: 150, Mismatches: 27, Indels: 29
0.73 0.13 0.14
Matches are distributed among these distances:
43 29 0.19
44 83 0.55
47 4 0.03
49 4 0.03
51 4 0.03
54 23 0.15
55 3 0.02
ACGTcount: A:0.32, C:0.18, G:0.23, T:0.27
Consensus pattern (44 bp):
CAGATTGAAGCTAGTAATCTTATCTCCCTGAGATTACAGAGGAG
Found at i:54485999 original size:142 final size:142
Alignment explanation
Indices: 54485743--54486125 Score: 633
Period size: 142 Copynumber: 2.7 Consensus size: 142
54485733 ATAAGGAAGT
* ** * * *
54485743 AGATTTAAGCTAGTAATATTATCTCCCTGAAATTATAGTGGAGCGGATTAAAATAAAAGGTCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
*
54485808 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCTAGAAATCTTATCTCCCTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
54485873 TTACAGAGGAGC
131 TTACAGAGGAGC
* *
54485885 AGATTGAAGCTAGTAATCGTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAATGATCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
*
54485950 TCTCTTTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
*
54486015 TTACAGCGGAGC
131 TTACAGAGGAGC
* *
54486027 AGATTGAAGCTAGTAATCCTA-CTCCCTGAGATTACAGTGGAGCGGATTAAAACAAAGGATCTTA
1 AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
*
54486091 TCTCTCTGAAGTTACAGTAGAGTAGATCACATCAG
66 TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAG
54486126 GTCTTATCTC
Statistics
Matches: 226, Mismatches: 15, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
141 74 0.33
142 152 0.67
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (142 bp):
AGATTGAAGCTAGTAATCCTATCTCCCTGAGATTACAGTGGAGCGGATTAAAATAAAAGATCTTA
TCTCTCTGAAGTTACAGTAGAGTAGATCGCATCAGATTGAAGCCAGAAATCTTATCTCCCTGAGA
TTACAGAGGAGC
Found at i:54486058 original size:43 final size:44
Alignment explanation
Indices: 54485982--54486074 Score: 134
Period size: 43 Copynumber: 2.1 Consensus size: 44
54485972 TAGATCGCAT
*
54485982 CAGATTGAAGCCAGAAATCTTATCTCCCTGAGATTACAGCGGAG
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAG
* * *
54486026 CAGATTGAAGCTAGTAATCCTA-CTCCCTGAGATTACAGTGGAG
1 CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAG
*
54486069 CGGATT
1 CAGATT
54486075 AAAACAAAGG
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
43 25 0.57
44 19 0.43
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.25
Consensus pattern (44 bp):
CAGATTGAAGCCAGAAATCCTATCTCCCTGAGATTACAGCGGAG
Found at i:54486260 original size:50 final size:49
Alignment explanation
Indices: 54486201--54486510 Score: 235
Period size: 50 Copynumber: 6.2 Consensus size: 49
54486191 GTAGTGGAAC
*** * * *
54486201 AGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGACATTACAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTACCTCCC-GACATTGCAGTTAAAA
* * * ** *
54486251 AGATTAAAGCTACAACAGCGAATCTTACCTCCCAAGCGA-TGCAGTGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTACCTCCCGA-C-ATTGCAGTTAAAA
*** * *
54486301 AGATTAAAGCCACATTGGTGAATCTTGCTTCCCCGACATTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTACCT-CCCGACATTGCAGTTAAAA
* * * * * * ** *
54486351 AGATTAAAGCTACAGCAGTGAATCCTACCTCTCGGCAATGCAGTGGAAC
1 AGATTAAAGCCACAACAGTGAATCTTACCTCCCGACATTGCAGTTAAAA
* ** *
54486400 AGATTAAAGCCACAACGGTGAATCTGGCCTCCCTGACATTGCGGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTACCTCCC-GACATTGCAGTTAAAA
* * * * *
54486450 AGATTAAAGCTACAACAGCGAATCTTACATTCCCAGTCAGTGCAGTTAAAA
1 AGATTAAAGCCACAACAGTGAATCTTAC-CTCCC-GACATTGCAGTTAAAA
54486501 AGATTAAAGC
1 AGATTAAAGC
54486511 TAGGATGGCG
Statistics
Matches: 195, Mismatches: 59, Indels: 11
0.74 0.22 0.04
Matches are distributed among these distances:
49 41 0.21
50 122 0.63
51 32 0.16
ACGTcount: A:0.35, C:0.23, G:0.19, T:0.24
Consensus pattern (49 bp):
AGATTAAAGCCACAACAGTGAATCTTACCTCCCGACATTGCAGTTAAAA
Found at i:54486346 original size:100 final size:100
Alignment explanation
Indices: 54486172--54486477 Score: 470
Period size: 100 Copynumber: 3.1 Consensus size: 100
54486162 AAAATTACAG
* *
54486172 ATCTTATCTCCCAAGCGATGTAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGA
1 ATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGA
*
54486237 CATTACAGTTAAAAAGATTAAAGCTACAACAGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
*
54486272 ATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCCGA
1 ATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGA
* *
54486337 CATTGCAGTTAAAAAGATTAAAGCTACAGCAGTGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
* * * * ** * *
54486372 ATCCTACCTCTC-GGCAATGCAGTGGAACAGATTAAAGCCACAACGGTGAATCTGGCCTCCCTGA
1 ATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGA
*
54486436 CATTGCGGTTAAAAAGATTAAAGCTACAACAGCGA
66 CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
54486471 ATCTTAC
1 ATCTTAC
54486478 ATTCCCAGTC
Statistics
Matches: 187, Mismatches: 19, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
99 83 0.44
100 104 0.56
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (100 bp):
ATCTTACCTCCCAAGCGATGCAGTGGAACAGATTAAAGCCACATTGGTGAATCTTGCTTCCCTGA
CATTGCAGTTAAAAAGATTAAAGCTACAACAGCGA
Found at i:54489948 original size:43 final size:46
Alignment explanation
Indices: 54489887--54489989 Score: 140
Period size: 43 Copynumber: 2.3 Consensus size: 46
54489877 TACAAACTGC
*
54489887 TTCCCTTTTCTTTCGCAAACGACGCCATTTTA-TT-TCTCCCCC-A
1 TTCCCTTTTCTTTCGCAAACGACACCATTTTATTTCTCTCCCCCGA
* ** *
54489930 TTCCCTTTTCTTTTGCAAACGGTACCGTTTTATTTCTCTCCCCCGA
1 TTCCCTTTTCTTTCGCAAACGACACCATTTTATTTCTCTCCCCCGA
54489976 TTCCCTTTTCTTTC
1 TTCCCTTTTCTTTC
54489990 CCGATACCCT
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
43 27 0.53
44 2 0.04
45 8 0.16
46 14 0.27
ACGTcount: A:0.13, C:0.35, G:0.08, T:0.45
Consensus pattern (46 bp):
TTCCCTTTTCTTTCGCAAACGACACCATTTTATTTCTCTCCCCCGA
Found at i:54489994 original size:18 final size:18
Alignment explanation
Indices: 54489971--54490007 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
54489961 ATTTCTCTCC
*
54489971 CCCGATTCCCTTTTCTTT
1 CCCGATACCCTTTTCTTT
54489989 CCCGATACCCTTTTCTTT
1 CCCGATACCCTTTTCTTT
54490007 C
1 C
54490008 TCAGCCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.08, C:0.41, G:0.05, T:0.46
Consensus pattern (18 bp):
CCCGATACCCTTTTCTTT
Found at i:54494313 original size:13 final size:13
Alignment explanation
Indices: 54494295--54494319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
54494285 AATTAAAGGG
54494295 TTAAAATTTAAAC
1 TTAAAATTTAAAC
54494308 TTAAAATTTAAA
1 TTAAAATTTAAA
54494320 GATGATAATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAAAATTTAAAC
Found at i:54494366 original size:35 final size:35
Alignment explanation
Indices: 54494321--54494387 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
54494311 AAATTTAAAG
54494321 ATGATAATCATAACTTACATAAACATTTAAAGTTT
1 ATGATAATCATAACTTACATAAACATTTAAAGTTT
* *
54494356 ATGATTATCATAACTTACATAATCATTTAAAG
1 ATGATAATCATAACTTACATAAACATTTAAAG
54494388 AATAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.37
Consensus pattern (35 bp):
ATGATAATCATAACTTACATAAACATTTAAAGTTT
Found at i:54494493 original size:36 final size:36
Alignment explanation
Indices: 54494408--54494493 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
54494398 AACTTTGGAC
* *
54494408 CATAATTTACAGAACTTACATAAATATATATCACAT
1 CATAACTTACATAACTTACATAAATATATATCACAT
* * *
54494444 CATAACTTGCATAACTTATATAAATATATATCATAT
1 CATAACTTACATAACTTACATAAATATATATCACAT
54494480 CATAACTTACATAA
1 CATAACTTACATAA
54494494 AACTTTGAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 44 1.00
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (36 bp):
CATAACTTACATAACTTACATAAATATATATCACAT
Found at i:54496198 original size:49 final size:49
Alignment explanation
Indices: 54496120--54496219 Score: 157
Period size: 49 Copynumber: 2.0 Consensus size: 49
54496110 ACATGTTCGA
*
54496120 AGTGGTTACATAATAGGAAGTTTTCTTATATGGGGCATTGTCGGTGGTT
1 AGTGGTTACATAATAGGAAGTTTTCTTATATGGGGCATCGTCGGTGGTT
* *
54496169 AGTGGTTATATAATGGGAAGTTCTT-TTATATGGGGCATCGTCGGTGGTT
1 AGTGGTTACATAATAGGAAGTT-TTCTTATATGGGGCATCGTCGGTGGTT
54496218 AG
1 AG
54496220 ATGAAAATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
49 45 0.96
50 2 0.04
ACGTcount: A:0.22, C:0.08, G:0.32, T:0.38
Consensus pattern (49 bp):
AGTGGTTACATAATAGGAAGTTTTCTTATATGGGGCATCGTCGGTGGTT
Found at i:54505360 original size:14 final size:14
Alignment explanation
Indices: 54505322--54505364 Score: 54
Period size: 13 Copynumber: 3.1 Consensus size: 14
54505312 TAAAATGTAC
54505322 AATATAATTAAA-T
1 AATATAATTAAATT
54505335 AATATAAATTAAATT
1 AATAT-AATTAAATT
*
54505350 AA-ATAATTTAATT
1 AATATAATTAAATT
54505363 AA
1 AA
54505365 CTGTTTATCT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
13 15 0.56
14 9 0.33
15 3 0.11
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATAATTAAATT
Found at i:54508175 original size:16 final size:16
Alignment explanation
Indices: 54508156--54508188 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
54508146 ATTAAATCTT
*
54508156 ATTATTTTAAAATAAA
1 ATTATTTAAAAATAAA
54508172 ATTATTTAAAAATAAA
1 ATTATTTAAAAATAAA
54508188 A
1 A
54508189 AATATCATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
ATTATTTAAAAATAAA
Found at i:54511529 original size:20 final size:21
Alignment explanation
Indices: 54511490--54511529 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54511480 AACAAAAGGT
*
54511490 AATTTGAACATTTTATGACTA
1 AATTTGAACATTTTACGACTA
*
54511511 AATTTTAACA-TTTACGACT
1 AATTTGAACATTTTACGACT
54511530 TATTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.38, C:0.12, G:0.07, T:0.42
Consensus pattern (21 bp):
AATTTGAACATTTTACGACTA
Found at i:54514293 original size:34 final size:34
Alignment explanation
Indices: 54514219--54514321 Score: 95
Period size: 34 Copynumber: 3.0 Consensus size: 34
54514209 ATAAAACATT
* * * *
54514219 AGTTCATA-TGATATAATAGTTCATACCAAATAGC
1 AGTTCATACT-ATATAACAGTTCATAACACATAAC
54514253 AGTTCATACTATATAACAGTTCATAACACATAAC
1 AGTTCATACTATATAACAGTTCATAACACATAAC
* * *
54514287 ATTTCATAGC-ACATAACAGATT-ATATCACATAAC
1 AGTTCATA-CTATATAACAG-TTCATAACACATAAC
54514321 A
1 A
54514322 ATGCATACCA
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
34 55 0.93
35 4 0.07
ACGTcount: A:0.44, C:0.18, G:0.08, T:0.30
Consensus pattern (34 bp):
AGTTCATACTATATAACAGTTCATAACACATAAC
Found at i:54514316 original size:17 final size:17
Alignment explanation
Indices: 54514231--54514321 Score: 78
Period size: 17 Copynumber: 5.4 Consensus size: 17
54514221 TTCATATGAT
* * *
54514231 ATAATAGTTCATACCAA
1 ATAACAGTTCATAACAC
* *
54514248 ATAGCAGTTCAT-ACTAT
1 ATAACAGTTCATAAC-AC
54514265 ATAACAGTTCATAACAC
1 ATAACAGTTCATAACAC
* *
54514282 ATAACATTTCATAGCAC
1 ATAACAGTTCATAACAC
*
54514299 ATAACAGATT-ATATCAC
1 ATAACAG-TTCATAACAC
54514316 ATAACA
1 ATAACA
54514322 ATGCATACCA
Statistics
Matches: 61, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
16 1 0.02
17 56 0.92
18 4 0.07
ACGTcount: A:0.45, C:0.20, G:0.07, T:0.29
Consensus pattern (17 bp):
ATAACAGTTCATAACAC
Found at i:54514333 original size:17 final size:16
Alignment explanation
Indices: 54514273--54514334 Score: 52
Period size: 17 Copynumber: 3.7 Consensus size: 16
54514263 ATATAACAGT
*
54514273 TCATAACACATAACATT
1 TCATAACACATAACA-A
*
54514290 TCATAGCACATAACAGA
1 TCATAACACATAACA-A
* *
54514307 TTATATCACATAACAA
1 TCATAACACATAACAA
*
54514323 TGCATACCACAT
1 T-CATAACACAT
54514335 CATAACTCAT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
16 2 0.05
17 35 0.95
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (16 bp):
TCATAACACATAACAA
Found at i:54514334 original size:34 final size:34
Alignment explanation
Indices: 54514265--54514334 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
54514255 TTCATACTAT
* * *
54514265 ATAACAGTTCATAACACATAACATTTCATAGCAC
1 ATAACAGTTCATAACACATAACAATGCATACCAC
*
54514299 ATAACAGATT-ATATCACATAACAATGCATACCAC
1 ATAACAG-TTCATAACACATAACAATGCATACCAC
54514333 AT
1 AT
54514335 CATAACTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 29 0.94
35 2 0.06
ACGTcount: A:0.46, C:0.23, G:0.06, T:0.26
Consensus pattern (34 bp):
ATAACAGTTCATAACACATAACAATGCATACCAC
Found at i:54515360 original size:35 final size:33
Alignment explanation
Indices: 54515295--54515360 Score: 80
Period size: 35 Copynumber: 1.9 Consensus size: 33
54515285 CAAGCATTAC
* *
54515295 AAAACCCATATACATATTTATTATATATATAAT
1 AAAACCCATATAAATATTTATTATACATATAAT
54515328 AAAACCCACGTATAAATATTGTA-TATACATATA
1 AAAACCCA--TATAAATATT-TATTATACATATA
54515361 CCTTTTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
33 8 0.29
35 18 0.64
36 2 0.07
ACGTcount: A:0.48, C:0.14, G:0.03, T:0.35
Consensus pattern (33 bp):
AAAACCCATATAAATATTTATTATACATATAAT
Found at i:54518115 original size:5 final size:5
Alignment explanation
Indices: 54518105--54518138 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
54518095 CAAAAATTAG
*
54518105 AAAGA AAAGA AAAGA AAAGA AAA-C AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA AAAGA
54518139 GAAGGAAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
4 3 0.12
5 23 0.88
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:54518132 original size:14 final size:15
Alignment explanation
Indices: 54518105--54518138 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
54518095 CAAAAATTAG
54518105 AAAGAAAAGAAAAGA
1 AAAGAAAAGAAAAGA
*
54518120 AAAGAAAA-CAAAGA
1 AAAGAAAAGAAAAGA
54518134 AAAGA
1 AAAGA
54518139 GAAGGAAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.56
15 8 0.44
ACGTcount: A:0.79, C:0.03, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAGA
Found at i:54519849 original size:197 final size:196
Alignment explanation
Indices: 54519514--54519908 Score: 745
Period size: 197 Copynumber: 2.0 Consensus size: 196
54519504 CGGATTATGG
*
54519514 AAATACCACTAGTTATACTCAGCGCACAGTTTTGTTTTTCTGTGCGCAGGTTAGGTACATTTCAG
1 AAATACCACTAGTTACACTCAGCGCACAGTTTTGTTTTTCTGTGCGCAGGTTAGGTACATTTCAG
54519579 CTTACAATCAACTCAGCATCCAACCTCAATCCTGAACTCAAGTGTGGTGATATTTCATTTTGTAA
66 CTTACAATCAACTCAGCATCCAACCTCAATCCTGAACTCAAGTGTGGTGATATTTCATTTTGTAA
*
54519644 TTGCATGTACCTAGGAAGTCCTTGGTTGATAATTTTTTTTTGTTAATGTGGTGCTATTTTAGGTT
131 TTGCATGTAACTAGGAAGTCCTTGGTTGATAA-TTTTTTTTGTTAATGTGGTGCTATTTTAGGTT
54519709 TC
195 TC
54519711 AAATACCACTAGTTACACTCAGCGCACAGTTTTGTTTTTCTGTGCGCAGGTTAGGTACATTTCAG
1 AAATACCACTAGTTACACTCAGCGCACAGTTTTGTTTTTCTGTGCGCAGGTTAGGTACATTTCAG
*
54519776 CTTACAATCAATTCAGCATCCAACCTCAATCCTGAACTCAAGTGTGGTGATATTTCATTTTGTAA
66 CTTACAATCAACTCAGCATCCAACCTCAATCCTGAACTCAAGTGTGGTGATATTTCATTTTGTAA
*
54519841 TTGCATGTAATTAGGAAGTCCTTGGTTGATAATTTTTTTTGTTAATGTGGTGCTATTTTAGGTTT
131 TTGCATGTAACTAGGAAGTCCTTGGTTGATAATTTTTTTTGTTAATGTGGTGCTATTTTAGGTTT
54519906 C
196 C
54519907 AA
1 AA
54519909 GTACTATGAT
Statistics
Matches: 194, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
196 36 0.19
197 158 0.81
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (196 bp):
AAATACCACTAGTTACACTCAGCGCACAGTTTTGTTTTTCTGTGCGCAGGTTAGGTACATTTCAG
CTTACAATCAACTCAGCATCCAACCTCAATCCTGAACTCAAGTGTGGTGATATTTCATTTTGTAA
TTGCATGTAACTAGGAAGTCCTTGGTTGATAATTTTTTTTGTTAATGTGGTGCTATTTTAGGTTT
C
Found at i:54520464 original size:42 final size:42
Alignment explanation
Indices: 54520418--54520513 Score: 111
Period size: 42 Copynumber: 2.3 Consensus size: 42
54520408 GCGACATGGC
* * *
54520418 CGTGTGACCCAAGTCAGCGAGTTACACGAGCTAGGACACGGT
1 CGTGTGTCCCAAGTCAACGAGTTACACGAGCTAGGACACGAT
* * * * * *
54520460 CGTGTGTCTCAAGTCAATGAGTTACATGGGTTGGGACACGAT
1 CGTGTGTCCCAAGTCAACGAGTTACACGAGCTAGGACACGAT
54520502 CGTGTGTCCCAA
1 CGTGTGTCCCAA
54520514 CTTCGAAAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.24, C:0.23, G:0.30, T:0.23
Consensus pattern (42 bp):
CGTGTGTCCCAAGTCAACGAGTTACACGAGCTAGGACACGAT
Found at i:54531087 original size:68 final size:69
Alignment explanation
Indices: 54530946--54531090 Score: 179
Period size: 68 Copynumber: 2.1 Consensus size: 69
54530936 TTAATCACTT
* * * *
54530946 TAATATTAAATTAATATAATACTTATCAAGATAAATATTAAATTGAATTTAATGTTAAGATAATC
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATGTTAAAATAATA
**
54531011 AATT
66 AAAA
* *
54531015 TAATATTAAATTAATAAAATAC-TATTAAGATAAGTATTAAATTAAATTTAA-GATTAAAACT-A
1 TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATG-TTAAAA-TAA
54531077 TAAAAA
64 TAAAAA
54531083 TAATATTA
1 TAATATTA
54531091 CTTTTGGAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
67 1 0.02
68 43 0.65
69 22 0.33
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (69 bp):
TAATATTAAATTAATAAAATACTTATCAAGATAAATATTAAATTAAATTTAATGTTAAAATAATA
AAAA
Found at i:54540402 original size:9 final size:9
Alignment explanation
Indices: 54540385--54540421 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
54540375 TGAGTTTTCA
54540385 AATTCGAAT
1 AATTCGAAT
*
54540394 AACTCGAAT
1 AATTCGAAT
54540403 AATTCGAAT
1 AATTCGAAT
54540412 AATTCGAAT
1 AATTCGAAT
54540421 A
1 A
54540422 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:54540498 original size:21 final size:21
Alignment explanation
Indices: 54540457--54540499 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
54540447 ACCCCAAACT
* *
54540457 CTCAAATCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
54540478 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
54540499 C
1 C
54540500 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.35, G:0.00, T:0.44
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:54540669 original size:30 final size:31
Alignment explanation
Indices: 54540635--54540694 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
54540625 AAACCTTTTA
*
54540635 TTTTCTCCC-AAAATTTTTACTCCC-TCCCAC
1 TTTTC-CCCTAAAACTTTTACTCCCTTCCCAC
*
54540665 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCCTAAAACTTTTACTCCCTTCCCA
54540695 TCCCACCTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 3 0.12
30 18 0.69
31 5 0.19
ACGTcount: A:0.20, C:0.38, G:0.00, T:0.42
Consensus pattern (31 bp):
TTTTCCCCTAAAACTTTTACTCCCTTCCCAC
Found at i:54540963 original size:9 final size:9
Alignment explanation
Indices: 54540949--54540977 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54540939 AATTTCACAT
54540949 TTTATATTA
1 TTTATATTA
54540958 TTTATATTA
1 TTTATATTA
54540967 TTTATATTA
1 TTTATATTA
54540976 TT
1 TT
54540978 GAATTGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (9 bp):
TTTATATTA
Found at i:54547790 original size:10 final size:11
Alignment explanation
Indices: 54547775--54547823 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
54547765 AACTAAATCC
54547775 TTTCTCTC-AA
1 TTTCTCTCAAA
*
54547785 TTTCTCTCTAA
1 TTTCTCTCAAA
54547796 TATTCTCTCAAA
1 T-TTCTCTCAAA
*
54547808 TTCCTCTCAAA
1 TTTCTCTCAAA
54547819 TTTCT
1 TTTCT
54547824 ATTTAAAAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
10 8 0.24
11 16 0.47
12 10 0.29
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (11 bp):
TTTCTCTCAAA
Found at i:54547801 original size:22 final size:22
Alignment explanation
Indices: 54547775--54547823 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 22
54547765 AACTAAATCC
* *
54547775 TTTCTCTC-AATTTCTCTCTAA
1 TTTCTCTCAAATTCCTCTCAAA
54547796 TATTCTCTCAAATTCCTCTCAAA
1 T-TTCTCTCAAATTCCTCTCAAA
54547819 TTTCT
1 TTTCT
54547824 ATTTAAAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 11 0.46
23 12 0.50
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTCTCTCAAATTCCTCTCAAA
Found at i:54550158 original size:49 final size:49
Alignment explanation
Indices: 54550104--54550420 Score: 553
Period size: 49 Copynumber: 6.5 Consensus size: 49
54550094 GTTTATATTA
*
54550104 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* *
54550153 ATGTAATAAAATACAAAATAGTTAATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
*
54550202 ATGAAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
*
54550251 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
54550300 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* *
54550349 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTC
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
* *
54550398 ATTTAATCAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
54550421 AATATTCTTA
Statistics
Matches: 255, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 255 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.44
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATAATTTGATATTATTTG
Found at i:54553887 original size:125 final size:124
Alignment explanation
Indices: 54553626--54554037 Score: 644
Period size: 125 Copynumber: 3.3 Consensus size: 124
54553616 CCCAAACATG
* * *
54553626 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* *
54553691 TTGAAGCATTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
66 TTAAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
* *
54553750 CTACTATAGCAAAAGCGTGTCCACGTGGGAGCGATTTCAGAAATTCTTCTAATAAAGCATCCTGC
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
*
54553815 TTCAAGCGTTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
66 TTAAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
* * * *
54553875 CTATTATAGCAAAAGCGCGTCCACATGTGAGCGATTTCAGAAATTCTTTTGATAAAGCATCCTGC
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
* * * **
54553940 TTAAAGCATTTTTTATATTATTTTCTCAGAAATGTCAACTCAAAATTATTTTTTCAGGAC
66 TTAAAGC-TTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
*
54554000 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
1 CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
54554038 CTTAATAAAT
Statistics
Matches: 263, Mismatches: 24, Indels: 1
0.91 0.08 0.00
Matches are distributed among these distances:
124 66 0.25
125 197 0.75
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (124 bp):
CTACTATAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAGAAATTCTTCTGATAAAGCATCCTGC
TTAAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACTTGAAATTATTTTTTCAGGAC
Found at i:54561283 original size:34 final size:31
Alignment explanation
Indices: 54561215--54561273 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
54561205 TAGCTCAATA
54561215 ATTTAAATAAAAACTTTCGAATAATTTAATC
1 ATTTAAATAAAAACTTTCGAATAATTTAATC
* *
54561246 ATTTAAATAAAAATTTTCGAATAGTTTA
1 ATTTAAATAAAAACTTTCGAATAATTTA
54561274 TTAATCATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTTAAATAAAAACTTTCGAATAATTTAATC
Found at i:54564512 original size:32 final size:32
Alignment explanation
Indices: 54564476--54564538 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
54564466 TAATCAAAAC
*
54564476 TTTTAGTTAATTT-TTTTTTCCTTCAATCAAGT
1 TTTTA-TTAATTTATTTTTTACTTCAATCAAGT
* *
54564508 TTTTATTTATTTATTTTTTACTTTAATCAAG
1 TTTTATTAATTTATTTTTTACTTCAATCAAG
54564539 CATGAGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.62
Consensus pattern (32 bp):
TTTTATTAATTTATTTTTTACTTCAATCAAGT
Found at i:54565150 original size:32 final size:29
Alignment explanation
Indices: 54565113--54565172 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
54565103 AGTTAAAACA
*
54565113 ATAAAATAGAGTTTTAAGTTCCTTAAAAGTTG
1 ATAAAATA-A-TTTTAAG-CCCTTAAAAGTTG
*
54565145 ATAAAATAATTTTGAGCCCTTAAAAGTT
1 ATAAAATAATTTTAAGCCCTTAAAAGTT
54565173 AAATTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 11 0.42
30 6 0.23
31 1 0.04
32 8 0.31
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.37
Consensus pattern (29 bp):
ATAAAATAATTTTAAGCCCTTAAAAGTTG
Found at i:54566881 original size:12 final size:12
Alignment explanation
Indices: 54566864--54566906 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
54566854 TAAACAGATG
54566864 TTAATTTTTTTA
1 TTAATTTTTTTA
*
54566876 TTAA--TTTTTG
1 TTAATTTTTTTA
54566886 TTAATTTTTTTA
1 TTAATTTTTTTA
54566898 TTAATTTTT
1 TTAATTTTT
54566907 GAGTGATTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
TTAATTTTTTTA
Found at i:54566890 original size:22 final size:22
Alignment explanation
Indices: 54566862--54566907 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
54566852 AGTAAACAGA
54566862 TGTTAATTTTTTTATTAATTTT
1 TGTTAATTTTTTTATTAATTTT
54566884 TGTTAATTTTTTTATTAATTTT
1 TGTTAATTTTTTTATTAATTTT
54566906 TG
1 TG
54566908 AGTGATTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.22, C:0.00, G:0.07, T:0.72
Consensus pattern (22 bp):
TGTTAATTTTTTTATTAATTTT
Found at i:54572875 original size:13 final size:13
Alignment explanation
Indices: 54572857--54572885 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
54572847 GCCTAATGAT
54572857 TTGCTAGTATATA
1 TTGCTAGTATATA
54572870 TTGCTAGTATATA
1 TTGCTAGTATATA
54572883 TTG
1 TTG
54572886 TTTACTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (13 bp):
TTGCTAGTATATA
Found at i:54588855 original size:27 final size:27
Alignment explanation
Indices: 54588825--54589002 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
54588815 ATATTGAGTC
* * * *
54588825 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
54588852 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54588879 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
54588907 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
54588934 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
54588961 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
54588988 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
54589003 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:54588964 original size:82 final size:81
Alignment explanation
Indices: 54588846--54589001 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
54588836 TGCTATATAA
* *
54588846 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
54588911 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
54588928 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
54588992 CACTTAGTGC
65 CACTTAGTGC
54589002 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:54596758 original size:38 final size:38
Alignment explanation
Indices: 54596716--54596837 Score: 158
Period size: 38 Copynumber: 3.2 Consensus size: 38
54596706 ATAGAAACGT
*
54596716 GGTGATATTTGGGCTCTATGCCTAGCAGGCTTTGTGCC
1 GGTGATATTCGGGCTCTATGCCTAGCAGGCTTTGTGCC
**
54596754 GGTGATATTCGGGCTCCGTGCCTAGCAGGCTTTGTGCC
1 GGTGATATTCGGGCTCTATGCCTAGCAGGCTTTGTGCC
* * * *
54596792 GGTGATATTCGAGCT-TCATGCCTAGCAGACTTCGTGTC
1 GGTGATATTCGGGCTCT-ATGCCTAGCAGGCTTTGTGCC
54596830 GGTG-TATT
1 GGTGATATT
54596838 ATATTAAGCT
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
37 4 0.05
38 70 0.95
ACGTcount: A:0.14, C:0.22, G:0.31, T:0.33
Consensus pattern (38 bp):
GGTGATATTCGGGCTCTATGCCTAGCAGGCTTTGTGCC
Found at i:54596859 original size:41 final size:41
Alignment explanation
Indices: 54596814--54596919 Score: 104
Period size: 41 Copynumber: 2.6 Consensus size: 41
54596804 GCTTCATGCC
* * *
54596814 TAGCAGACTTCGTGTCGGTGTATTATATTAAGCTTTGTGCT
1 TAGCAGACTTCGTGCCAGTGTATTATATCAAGCTTTGTGCT
* * * * *
54596855 TAGCAGGCTTCGTGCCAGTGTGTTATATCACGCTTTGAGCC
1 TAGCAGACTTCGTGCCAGTGTATTATATCAAGCTTTGTGCT
* * * *
54596896 TAGTAGTCTTTGTGCCAATGTATT
1 TAGCAGACTTCGTGCCAGTGTATT
54596920 GTAATAGGTA
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.39
Consensus pattern (41 bp):
TAGCAGACTTCGTGCCAGTGTATTATATCAAGCTTTGTGCT
Found at i:54598422 original size:18 final size:19
Alignment explanation
Indices: 54598399--54598437 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
54598389 ATTAATTTTG
54598399 ATCAAGTAAATT-AAATTA
1 ATCAAGTAAATTAAAATTA
*
54598417 ATCAAGTCAATTAAAATTA
1 ATCAAGTAAATTAAAATTA
54598436 AT
1 AT
54598438 ATGATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.54, C:0.08, G:0.05, T:0.33
Consensus pattern (19 bp):
ATCAAGTAAATTAAAATTA
Found at i:54598913 original size:37 final size:36
Alignment explanation
Indices: 54598850--54598960 Score: 102
Period size: 37 Copynumber: 3.0 Consensus size: 36
54598840 ATTCCAAACA
* *
54598850 TAATATTATTTTAATAGTGTAATATTAAATTTAAT-T
1 TAATATTATCTTAATAGTATAATATT-AATTTAATAT
**
54598886 TAATATTTATCTTAATAGTATCTTATTAATTTAATAT
1 TAATA-TTATCTTAATAGTATAATATTAATTTAATAT
* *
54598923 TAAAGTGATTATCTTAATATTA-AAT-TTAATCTAATAT
1 T-AA-T-ATTATCTTAATAGTATAATATTAATTTAATAT
54598960 T
1 T
54598961 TATCAAATCA
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
36 13 0.21
37 31 0.50
38 3 0.05
39 14 0.23
40 1 0.02
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.51
Consensus pattern (36 bp):
TAATATTATCTTAATAGTATAATATTAATTTAATAT
Found at i:54604186 original size:9 final size:9
Alignment explanation
Indices: 54604172--54604197 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
54604162 TTAAGCTCCC
54604172 GATGGATAT
1 GATGGATAT
54604181 GATGGATAT
1 GATGGATAT
54604190 GATGGATA
1 GATGGATA
54604198 AGTGTCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (9 bp):
GATGGATAT
Found at i:54608558 original size:21 final size:20
Alignment explanation
Indices: 54608534--54608574 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
54608524 ATGCAATATT
* *
54608534 TTCATTATTTTTAATTTTTTA
1 TTCATT-TTTTAAAATTTTTA
54608555 TTCATTTTTTAAAATTTTTA
1 TTCATTTTTTAAAATTTTTA
54608575 GGTTGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.68
Consensus pattern (20 bp):
TTCATTTTTTAAAATTTTTA
Found at i:54624825 original size:97 final size:98
Alignment explanation
Indices: 54624638--54624833 Score: 331
Period size: 97 Copynumber: 2.0 Consensus size: 98
54624628 GTGCAATAAA
* *
54624638 ACTTTAAAAGAATATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
54624703 CCTCTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
* *
54624736 ACTTTAAAAGAACATCCACTTATCCATGATTTAAGAAATCAC-CCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
54624800 CCTTTAAAATCCCAAACTCGGAATATTTCATTT
66 CCTCTAAAATCCCAAACTCGGAATATTTCATTT
54624833 A
1 A
54624834 TTATTTTTAA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 52 0.57
98 40 0.43
ACGTcount: A:0.37, C:0.24, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTCTAAAATCCCAAACTCGGAATATTTCATTT
Done.