Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007647.1 Corchorus capsularis cultivar CVL-1 contig07668, whole genome shotgun sequence
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: 8658
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Found at i:487 original size:2 final size:2
Alignment explanation
Indices: 480--504 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
470 AATACTCATA
480 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
505 ATTCAACGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4513 original size:655 final size:650
Alignment explanation
Indices: 2336--8649 Score: 3639
Period size: 655 Copynumber: 9.6 Consensus size: 650
2326 GAACGCGTTT
* * * * * * * *
2336 GTACACGATTTCAGATAAAATTTTGTAAAAACTGACTCGAAAA-GTTTTTCCTTAATTTTTTTCC
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGAC-CCAAAATTTTTTTCCTCAATTTTTTGCC
* * * * *
2400 ACAATACTCAGAAACAAATATATAATTTAACGCCAAAAAAACTGAAGGGTTTTTCACGCTTCTAA
65 ACAATACT-AGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCTAA
* *
2465 TATCGTTTTTCCATTATTTTCCCAAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCG
129 TATCGTTTTTCCATT-TTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
*
2530 TAAAGCCAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGAATATAGATATTTC-AGGA
193 TAAA--CAAATCCTTAAATCCAATGT-GCAAAGATTTGGTTAGATGAATATAGATATTTCAAGG-
* * *
2594 AGTCTTTATGTCAAAAACCATGCAAAACTGAGTCGAGGCCCCGAAACGCGTTTTTAGCCAAAAAC
254 AGTCTTTATGCCAAAAACTATGGAAAACTGAGTCGAGG-CCCGAAACGCGTTTTTAGCCAAAAAC
* * * *
2659 TGTGATGGATAGTACACGATTTCGGC----------TAAAAACTGACCTGTAAAACTTTTTCTCA
318 --CG-T---TACTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCG-AAAA-TTTTCCTCA
* * * * **
2714 ATTTTTTGCCACAATACTC--ATAAAAAATATATAATTCAATGCCAAAAATATTGAAGAGTTTTT
375 ATTCTTTGCCACAATACTCTGA-AAAAAATATTTAATTCAACGCCAAAAAAATTGAAG-G-GGTT
* * * *
2777 TTCACGTTTCTAATATCGTTTTGT-CATTTTTTTTCGGAATTAATTTCTATTTAAATCGAGACAA
437 TTCACGCTTCTAATATCGTTTT-TCCA--TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAA
* * * * *
2841 GATTCAGATGCTCGTAAAAACAAATCGTTAAATCCAATGTGGCTGGGATTTGGTTCGATGAATAT
499 GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATAT
* * * * * * *
2906 AGATAATTCAAGGAGTCTTTAC-ACCAAAAAATCATGTAAAAATGAGCCAGGG-TCCCGGAATGC
564 AGA-ATTTCAAGGAGTCTTT-CTGCC-AAAAATCATGCAAAACTAAGCC-GGGCT-CCGAAACGC
* * *
2969 GTTTTTTGCCAAAAACAGTG--CG-TA
624 GTTTTTAGCCAAAAACCGTGATGGTTA
* * * * ** * * * *
2993 -AAC-GGATTTCGGCTAAAATTTTTCAAAAACTGGCCCAAAAAATTTCTCCTTAATTCTATGCCT
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCC-
* *
3056 AC---AC-AG-AAAAAATATATAATTCAATGCCAAAAAAATTGAA--A--G-----G-GT-T--T
65 ACAATACTAGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCTAAT
* * **
3103 -TC--TTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATATTCGTA
130 ATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * *
3165 AAGCCAAATCCATAAATCCAATGTGGCTAAGATTT-GATAGATGAATATAAATATTTCAAGGAGT
195 AA--CAAATCCTTAAATCCAATGT-GCAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * *
3229 CTTTATGCTAAAAACGATGCG-AAACTGAGTCGACGCCCCGAAACGCTTTTTTTAGCCAAAAACC
257 CTTTATGCCAAAAACTATG-GAAAACTGAGTCGA-GGCCCGAAACGC-GTTTTTAGCCAAAAACC
* * * * *
3293 GTGA-T---TG--TT-AG-TAGACAGTTTCGGATAAAAACTGACCCGAAAAGGCTTTT--TACAA
319 GTTACTACACGATTTCGGCTA-A-AATTT-TG-TAAAAACTGACCCGAAAA---TTTTCCT-CAA
* * * * * * *
3348 TTTTTTG-CA-ATATA-T-TCAGAAAAAT-TTATAATTGAACTCCAAAAAGATTGATA-GGCTTT
376 TTCTTTGCCACA-ATACTCTGAAAAAAATATT-TAATTCAACGCCAAAAAAATTGA-AGGGGTTT
* * *
3407 TCACGCTTATAATATCGTTTTTGCA-TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATT
438 TCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
* * * * ** * * * * *
3471 CAGCTGCGCGTAAAAACAGATACTTATTTCCAATGTTGCTGAGATATGGTTCGATGAATATAGAT
503 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATATAGA-
* * * * * * *
3536 ATTACAAGGAATCTTTGTGCCAAAAATCATGTAAAATTAAAGCTGGAGCTCCGGAACGCGTTTTT
567 ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACT-AAGCCGG-GCTCCGAAACGCGTTTTT
* *
3601 AGCAAAAAAAACCGTGATTGTTA
630 AGC--CAAAAACCGTGATGGTTA
* * * * ** *
3624 GTACACGATTTCGGCTAAAATTTTGGAAAAAGTGTCCCGAAAA--GGTTTCCTCAATTCTTTGCC
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCC-AAAATTTTTTTCCTCAATTTTTTGCC
* * *
3687 ACAATACTCAGAAAAAAACATATAATTCAACGCC-AAAAAATTGAAGGGTTGTCCACGCTTCTAA
65 ACAATACT-AGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCTAA
* * *
3751 TATCGTTTTTCCATTTTTTTCCGAATTTATTT-TTATAAAATCGAAACAAGATTCAGATGCTCGG
129 TATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-G
* * * * *
3815 ATAAACAAATCCATAAATCCAATCTGCAAGAGATTTAGTTAGATGAATAGATATATTTCAAGGAG
193 -TAAACAAATCCTTAAATCCAATGTGCAA-AGATTTGGTTAGATGAATATAGATATTTCAAGGAG
* * *
3880 TCTTTATGCCAAAAACTATGGAAAACTAAGTCGAGGCCACGAAACACGTTTTTAGCAAAAAACCG
256 TCTTTATGCCAAAAACTATGGAAAACTGAGTCGAGGCC-CGAAACGCGTTTTTAGCCAAAAACCG
3945 TTACTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATGTTTCCTCAATTCTTTG
320 TTACTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCG-AAAAT-TTTCCTCAATTCTTTG
* * * *
4010 CCACAATAGTCTGAAAAAAATATTTAATTGAACGCCAAAAAAATTGTAGGGGTTTTCACGTTTCT
383 CCACAATACTCTGAAAAAAATATTTAATTCAACGCCAAAAAAATTGAAGGGGTTTTCACGCTTCT
* * *
4075 AATATCGTTTTTCTATTTTTTCCGAATTAATTTCTAAATAAATCGAAACAAGGTTCAGATGCTCG
448 AATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * * * *
4140 TAAAAACAAATCCTTAGATCCATTGTGGCTGAGATTAATTTAGATAAATATAG-ATTT-ATGGAA
513 TAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATATAGAATTTCAAGGAG
* * * * * * *
4203 TCTTTCTACCAGACATCATGCAAAACTAAGCCGGGCTCTGAAACGCATTTTTAGCTAAAAACCCT
578 TCTTTCTGCCAAAAATCATGCAAAACTAAGCCGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGT
*
4268 GATGGTTG
643 GATGGTTA
*
4276 GTACAAGATTTTGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCCA
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCCA
* * *
4341 CAATACTAAAATAAAAGACATATAATTCAACGCAAAAAAAATTTGAAGGATTGTTCACGCTTCTA
66 CAATACTAGAA-AAAA-ATATATAATTCAACGCCAAAAAAA-TTGAAGGATTGTTCACGCTTCTA
* * * *
4406 ATATCGTTTTTCTATTTTTTCCCGAATTTATTTCAAATTAAATCGAAATAAGATTCAGATTCTCG
128 ATATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
* * * *
4471 TAAAAAAATCCATAAATCCAATGTGTCAAAGTTTTGGTTAGATGAATATAGATATTTCAAGGAGG
193 TAAACAAATCCTTAAATCCAATGTG-CAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * * * ** *
4536 CTTTATGCCAAAAACCATGCAAAACTTAGTCCAAGCCCTGAAACAAGTTTTTAGCAAAAAACCGT
257 CTTTATGCCAAAAACTATGGAAAACTGAGTCGAGGCCC-GAAACGCGTTTTTAGCCAAAAACCGT
* ** * * *
4601 AACGTACACGATTTCGGCTAAAATTTTACAAAAACTGACCTGGAATATTTTACCTCTATTCTTTG
321 TAC-TACACGATTTCGGCTAAAATTTTGTAAAAACTGACC-CGAAAATTTT-CCTCAATTCTTTG
* * * *
4666 TCC-CAATACTCTG-AAAAAATATTTAATTCAATGCCGAAAAAATTGAAGGGTTTTTTCACGCTA
383 -CCACAATACTCTGAAAAAAATATTTAATTCAACGCCAAAAAAATTGAAGGG-GTTTTCACGCTT
** * * * * * *
4729 CTAATATCGTTTTTTCCATTTTCCCCGAATTTATTTCAAATTAAATCGAAGCAATATTCAAATGA
446 CTAATATCG-TTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGC
* * * * * * *
4794 TTGTAAAAACAAATCCTTATATCCAATATGGCTGAGTTTTGGTTCA-ATTAATATAGATATTTAA
510 TCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTT-AGATAAATATAGA-ATTTCA
* * * ** * *
4858 AGTAGTCTTTGC-GCCAAAAATCATGCAAAATTGAGTAGGGGTTCCGAAATGCGTTTTTAGCCAA
573 AGGAGTCTTT-CTGCCAAAAATCATGCAAAACTAAG-CCGGGCTCCGAAACGCGTTTTTAGCCAA
* *
4922 AATCTGTGATGGTTA
636 AAACCGTGATGGTTA
* * * * * *
4937 GTACACA-ATTTCGGCTTAAATTTTGCAAAAATTGACTCGAATTTTTTATTCCTCAATTCTTTGC
1 GTACA-AGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTT-TTCCTCAATTTTTTGC
* * * * * *
5001 CACAATACTGTGAAAAAAA-ATTTAATTCAATGCCAGAAAAAACTCAAGGGATT-TTCATGCTTC
64 CACAATACT-AGAAAAAAATATATAATTCAACGCCA-AAAAAATTGAA-GGATTGTTCACGCTTC
* *
5064 TAATATCG-TTTTCCATTTTTTCCCAAATTTATTTCTAATTAAATCGAAACAAGATACAGATGCT
126 TAATATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCT
** *
5128 CGTAAAAACAAATCCTTAAATCCGTTGTGACTAAA-ATTTGCTTAGATGAATATAGATATTTCAA
191 CGT--AAACAAATCCTTAAATCCAATGTG-C-AAAGATTTGGTTAGATGAATATAGATATTTCAA
* * ** * * * *
5192 GGAGTCTTTCTGCCAAAAA-TCATGCAAAACAAAGGCGGGGCCCCGAACCGCGTTTTTAGCCCAA
252 GGAGTCTTTATGCCAAAAACT-ATGGAAAACTGAGTCGAGG-CCCGAAACGCGTTTTTAGCCAAA
* * * * * *
5256 AA-C--TA-TGATA-G--TT-AGC-ACACAATTTTCAGCTAAAATCTAACACGAAAATTTTTTCT
315 AACCGTTACT-ACACGATTTCGGCTA-A-AATTTT--G-TAAAAACTGACCCGAAAA-TTTTCCT
* * * * * ** *
5312 CAAATT-TTTGCCACATTACTCAT-AATATATATATATAAATCAGTGCCAAAATAATTGAAGGGG
373 C-AATTCTTTGCCACAATACTC-TGAA-AAAAATATTTAATTCAACGCCAAAAAAATTGAAGGGG
* *
5375 TTTTCACGCTTAC-AAAATC-TATTTTCC-GTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
435 TTTTCACGCTT-CTAATATCGT-TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * ** * * ** *
5437 AGATTTAGATGTTCGTAAAGCCAAATCCGTAAATCCAACGTGGCCAAGATTTAGTTGGATAAATA
498 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATA
* * * * * * *
5502 TAGATATTTCAAGGAGTCTTTATGCTAAAAA-CCTAGCAAAACTGAGTCGAGAC-CCAGAAACGT
563 TAGA-ATTTCAAGGAGTCTTTCTGCCAAAAATCAT-GCAAAACTAAGCCG-GGCTCC-GAAACGC
** **
5565 GTTTTTAGTAAAAAACCGTGATTATTA
624 GTTTTTAGCCAAAAACCGTGATGGTTA
* ** * *
5592 GTACACGATTTCGGCTAAAA------ACTAACT---CGAAAATTTTTTT-CTCAATTTTTTTG-A
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAA-TTTTTTGCC
* * * * * * * *
5646 AAAACATTCAG-GAGAAATATATAATTCAACGCCAAAAAGATTGACAAGCTT-TTCACGCTTAC-
65 ACAATACT-AGAAAAAAATATATAATTCAACGCCAAAAAAATTGA-AGGATTGTTCACGCTT-CT
* * * * *
5708 AATGTCGTTTTCCCATTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTC
127 AATATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * ** * * * *
5773 GTCAAGCCAAATCCTTCAATCCAATGTGTCTTAGATTTGATTCGATGAATAAAGAAATTTCAAGG
192 GT-AA-ACAAATCCTTAAATCCAATGTG-CAAAGATTTGGTTAGATGAATATAGATATTTCAAGG
** * * *
5838 AGTCTTTGCGCCAAAAA-TCATGGTAAATTGAG-CTGTGGCTCC-AGAACGCGTTTTTAGCCAAA
254 AGTCTTTATGCCAAAAACT-ATGGAAAACTGAGTC-GAGGC-CCGA-AACGCGTTTTTAGCCAAA
* * * ** **
5900 ACCCATGAAGCTTAAGTCACGATTTCGGCTAAAATTTTGCCAAAACTGA-CC--TTA-TTTCCTC
315 AACCGT-TA-C-T-A--CACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAATTTTCCTC
** * *
5961 AATTCTTTGCCACAATACTCTGAAAAAAAATATATTTAATTCAACGCTGATAAAATTGAAAGGGT
374 AATTCTTTGCCACAATACTCTG--AAAAAA-ATATTTAATTCAACGCCAAAAAAATTG-AAGGGG
* *
6026 TTTTCACGC-TCTCAATATCGTTTTTCCATATTTTTCCGAATTTATTTCTAATTGAATCGAAACA
435 TTTTCACGCTTCT-AATATCGTTTTTCCAT-TTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * * *
6090 AGATTTAGATGCTCGTAAAAA-AAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATTAAAT
498 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGA-TAAAT
* * * ** *
6154 -TAGATATTTCAAAGAGTCTTTCTGCCAACATTCATGCAAAACTAAGTGGGGGCCCCGAAACGCG
562 ATAGA-ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAG-CCGGGCTCCGAAACGCG
* * *
6218 TTTTTTTG-CAAAAACTGTGATAGTTA
625 -TTTTTAGCCAAAAACCGTGATGGTTA
* * * * *
6244 GTACACGATTTCGGCTAAAA-ATTG----ACCTG----AAAATTTTTTTTCTCAATTTTTTGCCG
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCCA
* * * * * *
6300 CAATACTCA-TAAAATATATATAATTCAACGCCAAAAAGATGGAAGGTTTTTTCACGCTT-TAAA
66 CAATACT-AGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCT-AA
* * * * * * * * * **
6363 TATCATTTTTCTATTTTTTTCCAAATTAACTTCTAATTAAAACGAAACAAGAGTCAAATAATCGT
129 TATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
** * * * *
6428 AAAAACAAATCCTTAAATGGAATGTCGCAGAGATTTGATCT-GATGAATATAAATATTTCAAGTA
194 --AAACAAATCCTTAAATCCAATGT-GCAAAGATTTGGT-TAGATGAATATAGATATTTCAAGGA
** * * *
6492 GTCTTTGCGCCAAAAAAAC-ATGGCAAA-TGGAGTCGGGGCTCC-AGAACGTGTTTTTA-CCAAA
255 GTCTTTATGCC--AAAAACTATGGAAAACT-GAGTCGAGGC-CCGA-AACGCGTTTTTAGCC-AA
* * * * * *
6553 AAACCATGATGGTTAGGT-CACGATTTGGGCTAAAATTTTGCAAAAATTGACTC---TA-TTTCC
314 AAACC------GTTA-CTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAATTTTCC
** * * **
6613 TTGATTCTTTGCCACTATACTCTGAAAAAAATATTTAATTCAACGCCAATAAAATTGAAAAGGTT
372 TCAATTCTTTGCCACAATACTCTGAAAAAAATATTTAATTCAACGCCAAAAAAATTGAAGGGGTT
* * * * * *
6678 TGTCATGCTGCTAATATCGTTTTTCCATATATTCCGAATTTATTTCTAATTAAATCGAAACAAAA
437 T-TCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGA
* * * * * * *
6743 TTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAG
501 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATATAG
*
6808 ATATTTCAAGGAGTCTTTCTGCAAAAAATCATGCAAAACTAA-CTCGGG-TCCACGAAACGCGTT
566 A-ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGC-CGGGCT-C-CGAAACGCG--
* *
6871 TTTTTTGCCAAAAA-C-TG-T-GATA
625 TTTTTAGCCAAAAACCGTGATGGTTA
* * * *
6893 GTACACGATTTTGGCT-AAA---T------ACTGACCTGAAAATTTTTTT-CTCAAGTTTTTGCC
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACC-CAAAATTTTTTTCCTCAATTTTTTGCC
*
6947 ACAATACTCATAAAATTTTGCAAAAACTGACCTTATTTCCTTAATTTTTTGCCACAATACTCTGA
65 ACAATA--C-TAGAA------AAAAA-T-A---TA------TAA----TT----C-A-A--C-G-
* * *
7012 AAAAAAATATTTAATTCAATGCTAATAAAATTGAAATGG-TTTTTCACACTT-TCAATATC-TTT
96 ----------------C----C-AAAAAAATTG-AA-GGATTGTTCACGCTTCT-AATATCGTTT
*
7074 TTCCCTGATTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC
137 TTCCAT--TTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT--AAAC
* * * * ** * * *
7138 AAATGCTTCAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAATATTTCAAGGAGTCTTTC
198 AAATCCTTAAATCCAATGTG-CAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTA
* * * * * * * *
7203 TACCAACAA-TCATGCAAAACTAAGTCG-GGATCCGAAACGTGTTCTTTTGCCAAAAACTGTGAT
262 TGCCAAAAACT-ATGGAAAACTGAGTCGAGG-CCCGAAACGCGTT-TTTAGCCAAAAACCGT--T
* ** * *
7266 ACTTGGTACACGATTTCGGC---------G-AAAAATTGACCTAAAATTATTTTTCTCAATTTTT
322 AC----TACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAA--ATTTTCCTCAATTCTT
* ** * * * * * *
7321 TGCCACAATACTC--ATAAAATATATACAATTCACCGACAAAAAGA-TGGAGAAGTTTTTCACGC
381 TGCCACAATACTCTGA-AAAAAATATTTAATTCAACGCCAAAAAAATTGAAG-GGGTTTTCACGC
* * * * *
7383 TTCTAATATCGTTTTTCTATTTTTTTCGGAATTAATTTCTAATTAAGTCGAAACAAAATTCAAAT
444 TTCTAATATCGTTTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGAT
* ** * * *
7448 GATCGTAAAAACAAATCCTTAAATGGAATGTGGCAGAGATTT-GATTCA-ATGAATAAAGATATT
508 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAG-TT-AGATAAATATAGA-ATT
* * * * * * * *
7511 TCAAGGAGTCTTTGC-GCCAAAAATCATGGAAAATTGAGCCGAGGTTTCGGAACACGCTTTTAGC
570 TCAAGGAGTCTTT-CTGCCAAAAATCATGCAAAACTAAGCCG-GGCTCCGAAACGCGTTTTTAGC
*
7575 C-AAAACCATGATGGTTA
633 CAAAAACCGTGATGGTTA
* * * *
7592 GCT-CACGATTTCGGCTCAAATTTTGCAAAAACTGA-CC-----TTATTTCCTCAATTCTTTGCC
1 G-TACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCC
* * * * * *
7650 ACAATACT-GTGAAAAAATATTTAATTCAATCGCTAATAAAATTGAAAGGGTTTTTCACGCTATC
65 ACAATACTAG-AAAAAAATATATAATTCAA-CGCCAAAAAAATTG-AAGGATTGTTCACGCT-TC
* * * *
7714 -AATATCTTTTTTCCATATTTTT-CCAAATTTAATTCTAATTAAATCGAAACAAGATTCAGATGG
126 TAATATCGTTTTTCCAT-TTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGC
* * * ** * *
7777 TCGTAAAAACAAATCCTTAAATTCATTGAGACTGAGATTTGGTTAGATGAATTTAGATATTTGAA
190 TCGT--AAACAAATCCTTAAATCCAATGTG-CAAAGATTTGGTTAGATGAATATAGATATTTCAA
* ** * * * * *
7842 GGAGTCTTTTTGCCAACCATTATGCAAAACTAAGTCGGAGCCCCGAAACGCGTTTTTTTGCCAGA
252 GGAGTCTTTATGCCAAAAACTATGGAAAACTGAGTC-GAGGCCCGAAACGCG-TTTTTAGCCA-A
** * * * * *
7907 AATTGTGATAGTTAGTACACGATTTCAGCTAAAA-ATTG----ACCTGA----AAAAATTT-CTC
314 AA-----ACCGTTACTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAATTTTCCTC
** * * * * * *
7962 TTTTTTTTGCCAAAATACTC--ATAAAATATATATAATTCAACGCCAAAAAGA-TGAAAGGGTTT
374 AATTCTTTGCCACAATACTCTGA-AAAAAATATTTAATTCAACGCCAAAAAAATTG-AAGGGGTT
* * * * * * *
8024 TTCACGCTTTTAATATTGATTTTCCA-TTTTTCCGAATTTATTTCTGATTAAGTCGAAACAATAT
437 TTCACGCTTCTAATATCGTTTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * * * * * * * *
8088 TCAAATGCTCGTAATAACAAATCCTTGAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAA
502 TCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATATAGA
* * *
8153 TATTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGGGGC-CCGAAACACGTTTTT
567 -ATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAG-CCGGGCTCCGAAACGCG-TTTT
** * **
8217 TTCCCAAAAACTGTGATACTTA
629 TAGCCAAAAACCGTGATGGTTA
* * *
8239 GTACACGATTTCGGCTAAAA-ATTG----ACCTG-----AAATTATTTTT-CTCAATTTTTTGCC
1 GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATT-TTTTTCCTCAATTTTTTGCC
* * * * * * * *
8293 ACAACACTCATG--AAATATATATAATTCAACGACAAAAAGATGGAGGGGTTTTTCACGCTTCTA
65 ACAATACT-A-GAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCTA
* * * * * * * *
8356 ATATCGTTTTTCTATTTTTTTCTGAATTAATTTCTAATTAAGTCGAAACAAAATTCAAATGATCG
128 ATATCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
** * * * * *
8421 TAAAAACAAATCCTTAAATGGAATGTGGCAGAGATTTGATTCGATGAATAAAAATATTTCAAGGA
193 T--AAACAAATCCTTAAATCCAATGT-GCAAAGATTTGGTTAGATGAATATAGATATTTCAAGGA
* ** * * * *
8486 TTCTTTGCGCCAAAAA-TCATGGAAAATTGAG-CTGGGGCTCCGGAACACGTTTTTAGCC-AAAA
255 GTCTTTATGCCAAAAACT-ATGGAAAACTGAGTC-GAGGC-CCGAAACGCGTTTTTAGCCAAAAA
* **
8548 CCATAATGGTTAGCT-CACGATTTCGGCTAAAATTTTGCAAAAACTGA-CC--TTA-TTTCCTCA
317 CC------GTTA-CTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAATTTTCCTCA
*
8608 ATTTTTTGCCACAATACTCTGAAAAAAATATTTAATTCAACG
375 ATTCTTTGCCACAATACTCTGAAAAAAATATTTAATTCAACG
8650 TTAATAAAA
Statistics
Matches: 4508, Mismatches: 761, Indels: 787
0.74 0.13 0.13
Matches are distributed among these distances:
620 1 0.00
621 2 0.00
623 1 0.00
625 18 0.00
626 126 0.03
627 2 0.00
628 10 0.00
629 24 0.01
630 4 0.00
631 32 0.01
632 90 0.02
633 150 0.03
634 20 0.00
636 15 0.00
637 21 0.00
638 3 0.00
639 21 0.00
640 26 0.01
641 147 0.03
642 14 0.00
643 70 0.02
644 188 0.04
645 41 0.01
646 159 0.04
647 39 0.01
648 120 0.03
649 207 0.05
650 166 0.04
651 251 0.06
652 285 0.06
653 285 0.06
654 158 0.04
655 396 0.09
656 211 0.05
657 170 0.04
658 92 0.02
659 149 0.03
660 61 0.01
661 179 0.04
662 37 0.01
663 2 0.00
668 3 0.00
671 1 0.00
672 4 0.00
673 1 0.00
674 1 0.00
675 1 0.00
676 1 0.00
677 1 0.00
678 1 0.00
679 2 0.00
680 1 0.00
681 1 0.00
683 3 0.00
689 1 0.00
692 1 0.00
693 11 0.00
694 6 0.00
695 4 0.00
696 8 0.00
697 31 0.01
698 158 0.04
699 45 0.01
700 7 0.00
701 1 0.00
702 23 0.01
703 67 0.01
704 118 0.03
705 7 0.00
708 1 0.00
709 5 0.00
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.33
Consensus pattern (650 bp):
GTACAAGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTGCCA
CAATACTAGAAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGATTGTTCACGCTTCTAATA
TCGTTTTTCCATTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
ACAAATCCTTAAATCCAATGTGCAAAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
ATGCCAAAAACTATGGAAAACTGAGTCGAGGCCCGAAACGCGTTTTTAGCCAAAAACCGTTACTA
CACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAATTTTCCTCAATTCTTTGCCACAATA
CTCTGAAAAAAATATTTAATTCAACGCCAAAAAAATTGAAGGGGTTTTCACGCTTCTAATATCGT
TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
AATCCTTAAATCCAATGTGGCTGAGATTTAGTTAGATAAATATAGAATTTCAAGGAGTCTTTCTG
CCAAAAATCATGCAAAACTAAGCCGGGCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTA
Found at i:5504 original size:322 final size:319
Alignment explanation
Indices: 3105--6962 Score: 2158
Period size: 322 Copynumber: 11.8 Consensus size: 319
3095 AAGGGTTTTC
* ** *
3105 TTTTCCATTTTTTCCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGATATTCGTAAAGCC
1 TTTTCCATTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
* * * * *
3170 AAATCCATAAATCCAATGTGGCTAAGATTTGA-TAGATGAATATAAATATTTCAAGGAGTCTTTA
65 AAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTC
* * * * ** * * *
3234 TGCTAAAAA-CGATGCGAAACTGAGTCGACGCCCCGAAACGCTTTTTTTAGCCAAAAACCGTGAT
130 TGCCAAAAATC-ATGCAAAACTAAGGCGGGGCCCAGAAACGC-GTTTTTAG-CAAAAACCATGAT
* * * * * ** * *
3298 TGTTAGTAGAC-AGTTTCGGATAAAAACTGACCCGAAAAGGCTTTTT-ACAATTTTTTG-CA-AT
192 AGTTAGTACACGA-TTTCGGCTAAAATCT-AACCGAAAA-TTTTTTTCTCAAATTTTTGCCACA-
* * * * * * *
3359 ATATTCAGAAAA-ATTTATAATTGAACTCCAAAAAGATTGATA-GGCTTTTCACGCTTATAATAT
253 ATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGA-AGGGTTTTTCACGCTTACAATAT
3422 CGT
317 CGT
* * * * *
3425 TTTTGCA-TTTTTCCGAATTAATTTCTAATTAAATCGAAATAAGATTCAGCTGCGCGTAAAAACA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGACA
* * ** * * * * * * * *
3489 GATACTTATTTCCAATGTTG-CTGAGATATGGTTCGATGAATATAGATATTACAAGGAATCTTTG
66 AATCCTTAAATCCAATG-TGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTC
* * * * * *
3553 TGCCAAAAATCATGTAAAATTAAAGCTGGAGCTCC-GGAACGCGTTTTTAGCAAAAAAAACCGTG
130 TGCCAAAAATCATGCAAAACTAAGGC-GGGGC-CCAGAAACGCGTTTTTAGC---AAAAACCATG
* * ** *
3617 ATTGTTAGTACACGATTTCGGCTAAAATTTTGGAAAAAGTGTCCCGAAAA-GGTTTCCTC-AATT
190 ATAGTTAGTACACGATTTCGGCTAAAA-TCT-----AA-----CCGAAAATTTTTTTCTCAAATT
* * * * *
3680 CTTTGCCACAATACTCAGAAAAAAACATATAATTCAACGCCAAAAA-ATTGAAGGGTTGTCCACG
244 -TTTGCCACAATACTCA-TAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACG
3744 CTT-CTAATATCGT
307 CTTAC-AATATCGT
* * * *
3757 TTTTCCATTTTTTTCCGAATTTATTT-TTATAAAATCGAAACAAGATTCAGATGCTCGGATAA-A
1 TTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA-AAGA
* * * * * *
3820 CAAATCCATAAATCCAATCTG-CAAGAGATTT-AGTTAGATGAATAGATATATTTCAAGGAGTCT
64 CAAATCCTTAAATCCAATGTGACTA-AGATTTGA-TTAGATAAATATAGATATTTCAAGGAGTCT
* * * * *
3883 TTATGCCAAAAA-CTATGGAAAACTAAGTCGAGG-CCACGAAACACGTTTTTAGCAAAAAACC--
127 TTCTGCCAAAAATC-ATGCAAAACTAAGGCGGGGCCCA-GAAACGCGTTTTTAGC-AAAAACCAT
* * * * *
3944 ----GTTACTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCGAAAAATGTTTCCTC-AAT
189 GATAGTTAGTACACGATTTCGGCTAAAA-----T-----CT-AACCGAAAATTTTTTTCTCAAAT
* * * * * * *
4004 TCTTTGCCACAATAGTC-TGAAAAAAATATTTAATTGAACGCCAAAAAAATTGTAGGGGTTTTCA
243 T-TTTGCCACAATACTCAT--AAAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCA
*
4068 CG-TTTCTAATATCGT
305 CGCTTAC-AATATCGT
* * * *
4083 TTTTCTATTTTTTCCGAATTAATTTCTAAATAAATCGAAACAAGGTTCAGATGCTCGTAAAAACA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGACA
* * * * * * *
4148 AATCCTTAGATCCATTGTGGCTGAGA-TTAATTTAGATAAATATAG--ATTT-ATGGAATCTTTC
66 AATCCTTAAATCCAATGTGACTAAGATTTGA-TTAGATAAATATAGATATTTCAAGGAGTCTTTC
* * * * * * * * *
4209 TACCAGACATCATGCAAAACTAA-GCCGGGCTCTGAAACGCATTTTTAGCTAAAAACCCTGATGG
130 TGCCAAAAATCATGCAAAACTAAGGCGGGGCCCAGAAACGCGTTTTTAGC-AAAAACCATGATAG
* * * * * *
4273 TTGGTACAAGATTTTGGCTAAAATTTTGCAAAAACTGACCCAAAATTTTTTTCCTCAATTTTTTG
194 TTAGTACACGATTTCGGCTAAAA---T-------CTAACCGAAAATTTTTTT-CTCAAATTTTTG
* * * * * * *
4338 CCACAATACTAAAATAAAAGACATATAATTCAACGCAAAAAAAATTTGAAGGATTGTTCACGCTT
248 CCACAATACT--CATAAAATATATATAATTCAACGCCAAAAAGA-TTGAAGGGTTTTTCACGCTT
4403 -CTAATATCGT
310 AC-AATATCGT
* * * * *
4413 TTTTCTATTTTTTCCCGAATTTATTTCAAATTAAATCGAAATAAGATTCAGATTCTCGTAAA-A-
1 TTTTCCATTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
* * * * * * * *
4476 AAATCCATAAATCCAATGTGTCAAAGTTTTGGTTAGATGAATATAGATATTTCAAGGAGGCTTTA
65 AAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTC
* * * *** * **
4541 TGCCAAAAACCATGCAAAACTTAGTCCAAGCCCTGAAACAAGTTTTTAGCAAAAAACC--G-TA-
130 TGCCAAAAATCATGCAAAACTAAGGCGGGGCCCAGAAACGCGTTTTTAGC-AAAAACCATGATAG
* * * *
4602 --ACGTACACGATTTCGGCTAAAATTTTA-CAAAAACTGACCTGGAATATTTTACCTC-TATTCT
194 TTA-GTACACGATTTCGGCTAAAATCTAACCGAAAA-T----T----T-TTTT--CTCAAATT-T
* * *
4663 TTGTCC-CAATACTC-TGAAAAAATATTTAATTCAATGCCGAAAAA-ATTGAAGGGTTTTTTCAC
245 TTG-CCACAATACTCAT-AAAATATATATAATTCAACGCC-AAAAAGATTGAAGGG-TTTTTCAC
4725 GC-TACTAATATCGTT
306 GCTTAC-AATATCG-T
** * * * * * * * *
4740 TTTTCCATTTTCCCCGAATTTATTTCAAATTAAATCGAAGCAATATTCAAATGATTGTAAAAACA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGACA
* * * * * * * * *
4805 AATCCTTATATCCAATATGGCTGAGTTTTGGTTCA-ATTAATATAGATATTTAAAGTAGTCTTTG
66 AATCCTTAAATCCAATGTGACTAAGATTTGATT-AGATAAATATAGATATTTCAAGGAGTCTTT-
* * ** * * * **
4869 C-GCCAAAAATCATGCAAAATTGAGTAGGGGTTCC-GAAATGCGTTTTTAGCCAAAATCTGTGAT
129 CTGCCAAAAATCATGCAAAACTAAGGCGGGG-CCCAGAAACGCGTTTTTAG-CAAAAACCATGAT
* * * * *
4932 GGTTAGTACACAATTTCGGCTTAAATTTTGCAAAAATTGACTCG-AATTTTTTATTCCTC-AATT
192 AGTTAGTACACGATTTCGGC-TAAA--AT-C------TAAC-CGAAAATTTTT-TT-CTCAAATT
* * * * * * * * * *
4995 CTTTGCCACAATACT-GTGAAAAAAAATTTAATTCAATGCCAGAAAAAACTCAAGGGATTTTCAT
244 -TTTGCCACAATACTCAT-AAAATATATATAATTCAACGCCA-AAAAGATTGAAGGGTTTTTCAC
5059 GCTT-CTAATATCG-
306 GCTTAC-AATATCGT
* * * *
5072 TTTTCCATTTTTTCCCAAATTTATTTCTAATTAAATCGAAACAAGATACAGATGCTCGTAAAAAC
1 TTTTCCATTTTTT-CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
** * * *
5137 AAATCCTTAAATCCGTTGTGACTAAAATTTGCTTAGATGAATATAGATATTTCAAGGAGTCTTTC
65 AAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTC
* * * * *
5202 TGCCAAAAATCATGCAAAACAAAGGCGGGGCCCCGAACCGCGTTTTTAGCCCAAAACTATGATAG
130 TGCCAAAAATCATGCAAAACTAAGGCGGGGCCCAGAAACGCGTTTTTAG-CAAAAACCATGATAG
* * * *
5267 TTAGCACACAATTTTCAGCTAAAATCTAACACGAAAA-TTTTTTCTCAAATTTTTGCCACATTAC
194 TTAGTACACGA-TTTCGGCTAAAATCTAAC-CGAAAATTTTTTTCTCAAATTTTTGCCACAATAC
* ** * *
5331 TCATAATATATATATATAAATCAGTGCCAAAATA-ATTGAAGGGGTTTTCACGCTTACAAAATC-
257 TCATAA-A-ATATATATAATTCAACGCCAAAA-AGATTGAAGGGTTTTTCACGCTTACAATATCG
5394 T
319 T
* * * *
5395 ATTTTCC-GTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGTTCGTAAAGCC
1 -TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
* * * * *
5459 AAATCCGTAAATCCAACGTGGCCAAGATTT-AGTTGGATAAATATAGATATTTCAAGGAGTCTTT
65 AAATCCTTAAATCCAATGTGACTAAGATTTGA-TTAGATAAATATAGATATTTCAAGGAGTCTTT
* * * * * * * * * *
5523 ATGCTAAAAA-CCTAGCAAAACTGAGTCGAGACCCAGAAACGTGTTTTTAGTAAAAAACCGTGAT
129 CTGCCAAAAATCAT-GCAAAACTAAGGCGGGGCCCAGAAACGCGTTTTTAG-CAAAAACCATGA-
* * * *
5587 TA-TTAGTACACGATTTCGGCTAAAAACTAACTCGAAAATTTTTTTCTCAATTTTTTTG-AAAAA
191 TAGTTAGTACACGATTTCGGCTAAAATCTAAC-CGAAAATTTTTTTCTCAA-ATTTTTGCCACAA
* * * * * * *
5650 CATTCAGGAGAA-ATATATAATTCAACGCCAAAAAGATTGACA-AGCTTTTCACGCTTACAATGT
254 TACTCA-TAAAATATATATAATTCAACGCCAAAAAGATTGA-AGGGTTTTTCACGCTTACAATAT
5713 CGT
317 CGT
* * * *
5716 TTTCCCATTTTTTTCCGAATTAATTTTTAATTAAATCGAAACAAGATTCAGATGCTCGTCAAGCC
1 TTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
* * * * * * *
5781 AAATCCTTCAATCCAATGTGTCTTAGATTTGATTCGATGAATAAAGAAATTTCAAGGAGTCTTTG
65 AAATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTT-
** * * * *
5846 C-GCCAAAAATCATGGTAAATTGA-GCTGTGGCTCCAG-AACGCGTTTTTAGCCAAAACCCATGA
129 CTGCCAAAAATCATGCAAAACTAAGGC-GGGGC-CCAGAAACGCGTTTTTAG-CAAAAACCATGA
* ** *
5908 -AGCTTAAGT-CACGATTTCGGCTAAAATTTTGCC-AAAACTGACCTTATTTCCTC-AATTCTTT
191 TAG-TT-AGTACACGATTTCGGCTAAAATCTAACCGAAAA-T----TT-TTTTCTCAAATT-TTT
* * * *
5969 GCCACAATACTCTGAAAAAAAATATATTTAATTCAACGCTGATAAA-ATTGAAAGGGTTTTTCAC
247 GCCACAATACTC----ATAAAATATATATAATTCAACGC-CAAAAAGATTG-AAGGGTTTTTCAC
6033 GCTCT-CAATATCGT
306 GCT-TACAATATCGT
* * * *
6047 TTTTCCATATTTTTCCGAATTTATTTCTAATTGAATCGAAACAAGATTTAGATGCTCGTAAA-AA
1 TTTTCCAT-TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
* * * * *
6111 AAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATTAAAT-TAGATATTTCAAAGAGTCTTT
65 AAATCCTTAAATCCAATGTGACTAAGATTTGATTAGA-TAAATATAGATATTTCAAGGAGTCTTT
* * * * **
6175 CTGCCAACATTCATGCAAAACTAAGTG-GGGGCCCCGAAACGCGTTTTTTTGCAAAAACTGTGAT
129 CTGCCAAAAATCATGCAAAACTAAG-GCGGGGCCCAGAAACGCG-TTTTTAGCAAAAACCATGAT
* * *
6239 AGTTAGTACACGATTTCGGCTAAAAAT-TGACCTGAAAATTTTTTTTCTCAATTTTTTGCCGCAA
192 AGTTAGTACACGATTTCGGCT-AAAATCTAACC-GAAAA-TTTTTTTCTCAAATTTTTGCCACAA
* *
6303 TACTCATAAAATATATATAATTCAACGCCAAAAAGATGGAAGGTTTTTTCACGCTTTA-AATATC
254 TACTCATAAAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGC-TTACAATATC
*
6367 AT
318 GT
* * * * * * ** *
6369 TTTTCTATTTTTTTCCAAATTAACTTCTAATTAAAACGAAACAAGAGTCAAATAATCGTAAAAAC
1 TTTTCCA-TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGAC
** * * *
6434 AAATCCTTAAATGGAATGTCG-C-AGAGATTTGATCT-GATGAATATAAATATTTCAAGTAGTCT
65 AAATCCTTAAATCCAATGT-GACTA-AGATTTGAT-TAGATAAATATAGATATTTCAAGGAGTCT
* * * * *
6496 TTGC-GCCAAAAAAACATGGC-AAA-TGGAGTCGGGGCTCCAG-AACGTGTTTTTACCAAAAAAC
127 TT-CTGCC-AAAAATCAT-GCAAAACT-AAGGCGGGGC-CCAGAAACGCGTTTTTAGC-AAAAAC
* * *** * **
6557 CATGATGGTTAGGT-CACGATTTGGGCTAAAAT-TTTGCAAAAATTGACTCTATTTC-CTTGATT
186 CATGATAGTTA-GTACACGATTTCGGCTAAAATCTAACCGAAAATT---T-T-TTTCTC-AAATT
* * * * *
6619 CTTTGCCACTATACTC-TGAAAAAAATATTTAATTCAACGCCAATAAA-ATTGAAAAGGTTTGTC
244 -TTTGCCACAATACTCAT--AAAATATATATAATTCAACGCCAA-AAAGATTG-AAGGGTTTTTC
* *
6682 ATGC-TGCTAATATCGT
304 ACGCTTAC-AATATCGT
* * * * * *
6698 TTTTCCATATATTCCGAATTTATTTCTAATTAAATCGAAACAAAATTCAGATGCTCGTAAAAAGA
1 TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGACA
* * * * * *
6763 AATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAGATATTTCAAGGAGTCTTTCT
66 AATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTCT
* ** * *
6828 GCAAAAAATCATGCAAAACTAACTC-GGGTCCACGAAACGCGTTTTTTTTGCCAAAAA-C-TG-T
131 GCCAAAAATCATGCAAAACTAAGGCGGGGCCCA-GAAACGCG--TTTTTAG-CAAAAACCATGAT
* * * *
6889 -GATAGTACACGATTTTGGCT-AAATACTGACCTGAAAATTTTTTTCTCAAGTTTTTGCCACAAT
192 AGTTAGTACACGATTTCGGCTAAAAT-CTAACC-GAAAATTTTTTTCTCAAATTTTTGCCACAAT
6952 ACTCATAAAAT
255 ACTCATAAAAT
6963 TTTGCAAAAA
Statistics
Matches: 2760, Mismatches: 543, Indels: 470
0.73 0.14 0.12
Matches are distributed among these distances:
317 5 0.00
318 70 0.03
319 59 0.02
320 71 0.03
321 81 0.03
322 466 0.17
323 174 0.06
324 127 0.05
325 120 0.04
326 201 0.07
327 98 0.04
328 297 0.11
329 120 0.04
330 181 0.07
331 163 0.06
332 103 0.04
333 311 0.11
334 94 0.03
335 11 0.00
336 1 0.00
339 1 0.00
343 3 0.00
344 2 0.00
345 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (319 bp):
TTTTCCATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGACA
AATCCTTAAATCCAATGTGACTAAGATTTGATTAGATAAATATAGATATTTCAAGGAGTCTTTCT
GCCAAAAATCATGCAAAACTAAGGCGGGGCCCAGAAACGCGTTTTTAGCAAAAACCATGATAGTT
AGTACACGATTTCGGCTAAAATCTAACCGAAAATTTTTTTCTCAAATTTTTGCCACAATACTCAT
AAAATATATATAATTCAACGCCAAAAAGATTGAAGGGTTTTTCACGCTTACAATATCGT
Found at i:8479 original size:322 final size:322
Alignment explanation
Indices: 6989--8547 Score: 1602
Period size: 322 Copynumber: 4.8 Consensus size: 322
6979 TTATTTCCTT
* * * * *
6989 AATTTTTTGCCACAATACTCTGAAAAAAAATATTTAATTCAATG-CTAATAAA-ATTGAAATGGT
1 AATTTTTTGCCACAATACTC--ATAAAATATATATAATTCAACGAC-AA-AAAGA-TGAAAGGGT
* * * * *
7052 TTTTCACACTT-TCAATATC-TTTTTCCCTGATTTTTCCGAATTTATTTCTAATTAAATCGAAAC
61 TTTTCACGCTTCT-AATATCGTTTTTCCAT-TTTTTTCCGAATTAATTTCTAATTAAGTCGAAAC
* * * * *
7115 AAGATTCAGATGCTCGTAAAAACAAATGCTTCAATCCATTGAGACTGAGATTTGGTTAGATGAAT
124 AAAATTCAAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAAT
* ** **
7180 TTAAATATTTCAAGGAGTCTTTCTACCAACAATCATGCAAAACTAAGTCGGGATCCGAAACGTGT
189 TTAAATATTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGGGGCCCGAAACACGT
* * * *
7245 TCTTTTGCCAAAAACTGTGATACTTGGTACACGATTTCGGCGAAAAATTGACCTAAAATTATTTT
254 TTTTTTGCCAAAAACTGTGATACTTAGTACACGATTTCGGCTAAAAATTGACCTGAAATTATTTT
7310 TCTC
319 TCTC
* *
7314 AATTTTTTGCCACAATACTCATAAAATATATACAATTCACCGACAAAAAGATGGAGAA--GTTTT
1 AATTTTTTGCCACAATACTCATAAAATATATATAATTCAACGACAAAAAGAT-GA-AAGGGTTTT
* *
7377 TCACGCTTCTAATATCGTTTTTCTATTTTTTTCGGAATTAATTTCTAATTAAGTCGAAACAAAAT
64 TCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAGTCGAAACAAAAT
** * * * * * *
7442 TCAAATGATCGTAAAAACAAATCCTTAAATGGAATGTGGCAGAGATTTGATTCA-ATGAA-TAAA
129 TCAAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTT-AGATGAATTTAA
* * * * * *** * *
7505 GATATTTCAAGGAGTCTTTGC-GCCAAAAATCATGGAAAATTGAGCCGAGGTTTCGGAACACG-C
193 -ATATTTCAAGGAGTCTTT-CTGCCAACAATCATGCAAAACTAAGTCG-GGGCCCGAAACACGTT
* ** ** ** * **
7568 TTTTAGCC-AAAACCATGATGGTTAGCT-CACGATTTCGGCTCAAATTTTGCAAAAACTGACCTT
255 TTTTTGCCAAAAACTGTGATACTTAG-TACACGATTTCGGCT-AAAAATTG----ACCTGAAATT
*
7631 A-TTTCCTC
314 ATTTTTCTC
* * * *
7639 AATTCTTTGCCACAATACT-GTGAAAAAATATTTAATTCAATCG-CTAATAAA-ATTGAAAGGGT
1 AATTTTTTGCCACAATACTCAT-AAAATATATATAATTCAA-CGAC-AA-AAAGA-TGAAAGGGT
* * * *
7701 TTTTCACGCTATC-AATATCTTTTTTCCATATTTTTCCAAATTTAA-TTCTAATTAAATCGAAAC
61 TTTTCACGCT-TCTAATATCGTTTTTCCATTTTTTTCCGAA-TTAATTTCTAATTAAGTCGAAAC
* * * *
7764 AAGATTCAGATGGTCGTAAAAACAAATCCTTAAATTCATTGAGACTGAGATTTGGTTAGATGAAT
124 AAAATTCAAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAAT
* * * * * * *
7829 TTAGATATTTGAAGGAGTCTTTTTGCCAACCATTATGCAAAACTAAGTCGGAGCCCCGAAACGCG
189 TTAAATATTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGG-GGCCCGAAACACG
* * * * **
7894 TTTTTTTGCCAGAAATTGTGATAGTTAGTACACGATTTCAGCTAAAAATTGACCTGAAA--AAAT
253 TTTTTTTGCCAAAAACTGTGATACTTAGTACACGATTTCGGCTAAAAATTGACCTGAAATTATTT
7957 TTCTC
318 TTCTC
** * *
7962 TTTTTTTTGCCAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATGAAAGGGTTTTTC
1 AATTTTTTGCCACAATACTCATAAAATATATATAATTCAACGACAAAAAGATGAAAGGGTTTTTC
* * * * * *
8027 ACGCTTTTAATATTGATTTTCCA--TTTTTCCGAATTTATTTCTGATTAAGTCGAAACAATATTC
66 ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAGTCGAAACAAAATTC
* * *
8090 AAATGCTCGTAATAACAAATCCTTGAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAATA
131 AAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAATA
*
8155 TTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGGGGCCCGAAACACGTTTTTTTC
196 TTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGGGGCCCGAAACACGTTTTTTTG
8220 CCAAAAACTGTGATACTTAGTACACGATTTCGGCTAAAAATTGACCTGAAATTATTTTTCTC
261 CCAAAAACTGTGATACTTAGTACACGATTTCGGCTAAAAATTGACCTGAAATTATTTTTCTC
* * * *
8282 AATTTTTTGCCACAACACTCATGAAATATATATAATTCAACGACAAAAAGATGGAGGGGTTTTTC
1 AATTTTTTGCCACAATACTCATAAAATATATATAATTCAACGACAAAAAGATGAAAGGGTTTTTC
* *
8347 ACGCTTCTAATATCGTTTTTCTATTTTTTTCTGAATTAATTTCTAATTAAGTCGAAACAAAATTC
66 ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAGTCGAAACAAAATTC
** * * * * * * **
8412 AAATGATCGTAAAAACAAATCCTTAAATGGAATGTGGCAGAGATTTGATTCGATGAATAAAAATA
131 AAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAATA
* * * * * *
8477 TTTCAAGGATTCTTTGC-GCCAAAAATCATGGAAAATTGAG-CTGGGGCTCCGGAACACG-TTTT
196 TTTCAAGGAGTCTTT-CTGCCAACAATCATGCAAAACTAAGTC-GGGGC-CCGAAACACGTTTTT
*
8539 TAGCCAAAA
258 TTGCCAAAA
8548 CCATAATGGT
Statistics
Matches: 1011, Mismatches: 178, Indels: 93
0.79 0.14 0.07
Matches are distributed among these distances:
318 68 0.07
319 130 0.13
320 84 0.08
321 62 0.06
322 296 0.29
323 87 0.09
324 10 0.01
325 61 0.06
326 16 0.02
327 151 0.15
328 22 0.02
329 24 0.02
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (322 bp):
AATTTTTTGCCACAATACTCATAAAATATATATAATTCAACGACAAAAAGATGAAAGGGTTTTTC
ACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAGTCGAAACAAAATTC
AAATGATCGTAAAAACAAATCCTTAAATCCATTGAGACTGAGATTTGGTTAGATGAATTTAAATA
TTTCAAGGAGTCTTTCTGCCAACAATCATGCAAAACTAAGTCGGGGCCCGAAACACGTTTTTTTG
CCAAAAACTGTGATACTTAGTACACGATTTCGGCTAAAAATTGACCTGAAATTATTTTTCTC
Done.