Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009631.1 Corchorus capsularis cultivar CVL-1 contig09652, 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: 60917
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.34
Found at i:601 original size:67 final size:67
Alignment explanation
Indices: 514--648 Score: 234
Period size: 67 Copynumber: 2.0 Consensus size: 67
504 GGATTGTCAA
* * *
514 ATCTCTAATTTCATCTATAACTATCAATATACCAAATACATAAACAAATAAATTACAAAGAAAAC
1 ATCTATAATTTCATCAATAACTACCAATATACCAAATACATAAACAAATAAATTACAAAGAAAAC
579 TC
66 TC
*
581 ATCTATAATTTCATCAATAACTACCAATATACGAAATACATAAACAAATAAATTACAAAGAAAAC
1 ATCTATAATTTCATCAATAACTACCAATATACCAAATACATAAACAAATAAATTACAAAGAAAAC
646 TC
66 TC
648 A
1 A
649 CATTCCGTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 64 1.00
ACGTcount: A:0.53, C:0.19, G:0.02, T:0.27
Consensus pattern (67 bp):
ATCTATAATTTCATCAATAACTACCAATATACCAAATACATAAACAAATAAATTACAAAGAAAAC
TC
Found at i:1132 original size:17 final size:16
Alignment explanation
Indices: 1112--1158 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 16
1102 TTTACTTCTA
1112 ATAATTATTTTTAGATT
1 ATAATTATTTTTA-ATT
*
1129 ATAA-TATATTTAATT
1 ATAATTATTTTTAATT
1144 ATATATTATTATTTA
1 ATA-ATTATT-TTTA
1159 TAGTAATGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
15 6 0.24
16 8 0.32
17 7 0.28
18 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
ATAATTATTTTTAATT
Found at i:2199 original size:331 final size:326
Alignment explanation
Indices: 1504--2641 Score: 1168
Period size: 331 Copynumber: 3.4 Consensus size: 326
1494 TAATTTACAA
* * * * *
1504 CATCTAACCAAATTTCAGCAACATTGGATTTAAAAATTTATTTTTACGAGCATGTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTT
* * * * *
1569 TCGATTTAATTAGAAACTAATTTAGAAAAA-AA-AAATATGATATTAAAAGCATAAAAAGCCCTC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAATAATATTAAAAGCGTAAAAAGCCCTC
*
1632 CAATCTTTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTTTAGCCAAAAATTAAGGGAAAAA
131 CAATC-TTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATT--GGGAAAAA
* * * * *
1696 TCTTTCGTGTCAATTTTTGA-AAAATTTTAACCGAAATTGTGTACTAACAAACAATCACGGTTTT
193 TTTTTCGT-TCAATTTTT-ACAAAATTTTAGCCGAAATCGTG---TAA-TAACAATCAC-GATTT
* * * * *
1760 TGGCTAAAAACGCGTTCCGAGCACCCGGCTCAATTTTGCATGATTTTTGGCT-CCGAGACTACTT
251 TGGATAAAAACGTGTT-CGGGC-CCCGGCTCAATTTTGCATGATTTTT-GCTGCCGACACTCCTT
1824 GAAATATCTATATT
313 GAAATATCTATATT
* * *
1838 CATCTAATCAAATCTCAGTCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTT
* ** ** * * *
1903 TCAATTTAATTAGAAATTAATTTGGAAAAAATAAGAAAAAGGATATCAGAAA-CGTCAAAAGTCC
66 TCGATTTAATTAGAAATTAATTCAG-AAAAATAAGAAAAATAATATTA-AAAGCGTAAAAAGCCC
* * *
1967 TTCAATTTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGCGGAAATA
129 TCCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG-GGAAAAA
2032 TTTTTCTGTTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACAATCACAGATTTTGGAT
193 TTTTTC-GTTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACAATCAC-GATTTTGGAT
** * * * * *
2097 AGAAAA-GTGTTCTGGGCCCCGGCTCAATTTTGCATGATTTTTTTTGCCAATATTCCGTGAGATA
256 A-AAAACGTGTTC-GGGCCCCGGCTCAATTTTGCATGATTTTTGCTGCCGACACTCCTTGAAATA
*
2161 TCCATATT
319 TCTATATT
* * * * *
2169 CATCTACTCAAATCTCAGCCACATTGGATTTAATAATTTGTTTTTACAAGTATCTGAATCTTGTT
1 CATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTT
* * *
2234 TCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAATAATATTAAAAGCGTGAAAA-CTCAT
66 TCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAATAATATTAAAAGCGTAAAAAGC-CCT
** * * * * * *
2298 CCAATCTTTTT-AAAGTTAAATTATATATATATTATTAGTATTTTATCCAAAAATTGAAGAAAAA
130 CCAATCTTTTTGGCA-TTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTG-GGAAAAA
* * * * * * * * *
2362 ATTATCAGGTCACTTTTTACAAAATTTTAGCCAAAATCGTGTACTAACCATCACTATTTT-TATC
193 TTTTTC-GTTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACAATCACGATTTTGGA--
* * *
2426 TAAAAACACGT-TTCGTGGCCCCGACTCAGTTTTACATGATTTTTGGC-GCCGACACTCCTTGAA
255 T-AAAA-ACGTGTTCG-GGCCCCGGCTCAATTTTGCATGATTTTT-GCTGCCGACACTCCTTGAA
2489 ATATCTATATT
316 ATATCTATATT
* * * ** * * *
2500 CATCTAATAAAATTTTAGCCACATTACATTTAAGGATTTATTTTTACGAGCATCTAAATCTTATT
1 CATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTT
*
2565 TCGATTTAATTAGAAATTAATTCAGAAAAA-ACATGAAAAACAATATTAAAAGCGTAAAAAGCCC
66 TCGATTTAATTAGAAATTAATTCAGAAAAATA-A-GAAAAATAATATTAAAAGCGTAAAAAGCCC
*
2629 TTCAATCTTTTTG
129 TCCAATCTTTTTG
2642 AGGAAATATC
Statistics
Matches: 673, Mismatches: 106, Indels: 51
0.81 0.13 0.06
Matches are distributed among these distances:
328 1 0.00
329 9 0.01
330 130 0.19
331 259 0.38
332 63 0.09
333 8 0.01
334 79 0.12
335 7 0.01
336 61 0.09
337 53 0.08
338 3 0.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.37
Consensus pattern (326 bp):
CATCTAATCAAATCTCAGCCACATTGGATTTAAGAATTTATTTTTACGAGCATCTGAATCTTGTT
TCGATTTAATTAGAAATTAATTCAGAAAAATAAGAAAAATAATATTAAAAGCGTAAAAAGCCCTC
CAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGGGAAAAATTT
TTCGTTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAATAACAATCACGATTTTGGATAAAAA
CGTGTTCGGGCCCCGGCTCAATTTTGCATGATTTTTGCTGCCGACACTCCTTGAAATATCTATAT
T
Found at i:3047 original size:11 final size:12
Alignment explanation
Indices: 3026--3050 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3016 AACATCACGG
3026 TTTCTTTTTTTT
1 TTTCTTTTTTTT
3038 TTTCTTTTTTTT
1 TTTCTTTTTTTT
3050 T
1 T
3051 GCTAAAAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (12 bp):
TTTCTTTTTTTT
Found at i:4514 original size:671 final size:655
Alignment explanation
Indices: 2822--6323 Score: 2922
Period size: 671 Copynumber: 5.3 Consensus size: 655
2812 AATCCAGCCA
** * * * ** *
2822 TTGTTTTTAAAAGTATCTAAATCATGTTTCCTTTTAATTAGAAATTAATTC-AGAA-AA-A--AA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAATAATATGAA
* * * *
2882 AAACGATATT-TGAAGTGTGAAAAGACCTTCAATCTTTTTGGCGTTGAATTTATATTATTTTTAT
66 AAACGATATTAAGAA-TGTAAAAAGTCCTTCAATCTTTTTGGCGTTGAA-TTATA-TAATTTTAT
* * * *
2946 GAGTATTGTGACTAAAAATTGA-GAAAAACTATTTCGGGTCAA-TTTTGCAAAATATTAGCTGAA
128 GAGTATTGTGGCT-AAAATTGAGGAAAAA-TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAA
* * *
3009 ATCGTGTA-ACATCACGGTTTCTTTTTTTTTTTCTTTTTTTTTGCTAAAAACTGTGTTCTGGGGC
191 ATCGTGTATA-A-C-C---ATC----------ACTTTTTTTTTGCTAAAAAC-GCGTTCTGGGGC
* * * *
3073 CTTGAGTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATCTAATCA
239 CCTG-CTCAGTTTTGCATAATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCA
* * * ** *
3138 AATCTCAGCCACATTGGATTTAAGGATTTGCTTTTATGAGCATCAAAATCTTGTTTCAATTTAAT
303 AATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAAT
* * * ** *
3203 TAGAAATTAATTCGGAAAAAGTAGGAAAAATGATATTAGTAGCGTAAAAA--CCTTTCAATATTT
368 TAGAAATTAATTCAGAAAAA-TATGAAAAACGATATTAAAAGCGTAAAAAGTCC-TTCAATCTTT
* * * * * * *
3266 TTGGCGTTGACTTATATATTTTTTATGATTATTTTAGCCAAGAATTGAG-GAAATATCCTTCCGG
431 TTGGAGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGAAAAATAT--TTCGGG
* * * * *
3330 ACAA-TTTTGAAAAAATTTTAGCCGAAATCGTGTAATAATGATCACGG-TTTTAGCT-AAAACGC
494 TCAATTTTTG-CAAAATTTTAGCCGAAATCGTGT-ATTATGATCATGGTTTTTGGCTAAAAACGC
* ** * * * *
3392 GTTCCAGGTCCCGGGTCAGTTTTGCATGATTTTTGACGCTAAGACTCCTTGAGATATAC-ACATT
557 GTTCC-GGGCCC-ATTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATAT-CTATATT
* *
3456 CATCTAATCAAATGTCAGCCACATTGCATTTAAGGAT
619 CATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
3493 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAT-ATATGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA-AAAATAATATGA
* * * * *** * * *
3557 AAAATGATATTAAAAATGTGAAAAGTAC-TCATAT-TTTTTGATATTAAATTATAT-ATTTCACG
65 AAAACGATATTAAGAATGTAAAAAGTCCTTCA-ATCTTTTTGGCGTTGAATTATATAATTTTATG
* * * * ** *
3619 AGTATTTTAGCGAAAAATTGAGG-AAAATTTTTTTGGTCATTTTTTGCAAAATTTTAGCCGAAAT
129 AGTATTGTGGC-TAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAAT
* * ** * *
3683 CATG--TACCCATCAC-GGTTTTTTGCTAAAAACGCATT-TCGTGGCCCTGTCTCAGTTTTGCAT
193 CGTGTATAACCATCACTTTTTTTTTGCTAAAAACGCGTTCT-GGGGCCCTG-CTCAGTTTTGCAT
* * * * * * *
3744 AATTTTTAGCGTTGAGACTCCTTGAAATATCTATATTCATCTAATCAAATATTAGCCACATTGCA
256 AATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCACATTGGA
* *
3809 TTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTCAATTAGAAATTAATTCAGAAA
321 TTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAA
* *
3874 AATATGAAAAACGATATTAAAAGCGTAAAAAGTCCTACAATCTTTTTGGAGTAGAATTATATATA
386 AATATGAAAAACGATATTAAAAGCGTAAAAAGTCCTTCAATCTTTTTGGAGTTGAATTATATATA
* ** *
3939 TTTTATGAGTATTTTAGACAAAAATTGAGTAAAAATATTTATGGTCAATTTTTGCAAAATATTAG
451 TTTTATGAGTATTTTAGCCAAAAATTGAG-AAAAATATTTCGGGTCAATTTTTGCAAAATTTTAG
* *
4004 CCGAAATCGTGTATGTTAGTTGAAGTTATGGTTTTTGGTTAAAAACGCGTTCCGGAGCCCTACTT
515 CCGAAATCGTGTA--TTA--TG-A-TCATGGTTTTTGGCTAAAAACGCGTTCCGG-GCCC-A-TT
* * * * *
4069 CAGTGTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTCA
571 CAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCA
4134 GCCACATTGGATTTAAGGAT
636 GCCACATTGGATTTAAGGAT
*** * * * *
4154 TT-TTAAAACAAGTATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGAAAAATAATAGGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC-AAAAATAATATGA
* * * * *
4218 AAAACGATATTGGAAGCATG-AAAAAGCCCTTCAATCTATTTGGCGTTGAATTTTATAATTTGTG
65 AAAACGATATT--AAGAATGTAAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATAATTT-TA
* * *
4282 TGAGTATTGTGGCTAAAATTTGAGGAAATAA-CTTTCGAGTTAATTTTTGCAAAATTCTAGCCGA
127 TGAGTATTGTGGCTAAAA-TTGAGGAAA-AATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGA
* * * *
4346 AACCGTGTAATAATCATCACATTTTTTTTTGCTAAGAACGCGTTCTGGGGCCCTGCCTAAGTTTT
190 AATCGTGT-ATAACCATCAC-TTTTTTTTTGCTAAAAACGCGTTCTGGGGCCCTG-CTCAGTTTT
* * * * * ** * *
4411 GCATGATTTTTTGCGCCAAGACTCTTTGAGATATCCATATTCATCTAATCAAATCTCAGCTACGT
252 GCATAATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCACAT
* * *
4476 TGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTGGAAATTAATTTA
317 TGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCA
* * * ** *
4541 GAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTCCTCCAAT-TTTCTTGTCGTTTAATTAT
382 GAAAAATATGAAAAACGATATTAAAAGCGTAAAAAGTCCTTCAATCTTT-TTGGAGTTGAATTAT
* * * *
4605 ATATATTTTATGAGTATTTTAGCCAAAAATTAACGGAAAAATTTTTAGGGTCATTTTTTGCAAAA
446 ATATATTTTATGAGTATTTTAGCCAAAAATTGA--GAAAAATATTTCGGGTCAATTTTTGCAAAA
** * * * ***
4670 TTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTTGC---AAA---TTTTTAGG--C-TT-A
509 TTTTAGCCGAAATCGTGTATT-ATGATCATGGTTTTTGGCTAAAAACGCGTTCCGGGCCCATTCA
* * * * *
4725 GTTTTGAATGATTTTTAGCACCAAGACTCCTTGAAATATCTTTATTCATCTAATAAAATCTCAGC
573 GTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGC
*
4790 CACATTGAATTTAAGGAT
638 CACATTGGATTTAAGGAT
*
4808 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC--AGATAATATGAA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAATAATATGAA
* * * * *
4871 AAACAATATTAA-AAGTGTAAACAGTCCTCCAATCTTTTTGGTGTTTAATTATATATATATATAT
66 AAACGATATTAAGAA-TGTAAAAAGTCCTTCAATCTTTTTGGCG-TTGA--AT-TATATA-AT-T
* * * *
4935 ATATATTCTGTGAGGATTGTGGCAAAAAGTTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAAT
124 -T-TA-----TGAGTATTGTGGCTAAAA-TTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAAT
* * * *
5000 TTTAGCTGAAATCGTG--T-ACCATCAACGGTTTTTTTTGGCTAAAAACGCGTTCCGGGGCCCCA
181 TTTAGCCGAAATCGTGTATAACCATC-AC--TTTTTTTTTGCTAAAAACGCGTTCTGGGG-CCCT
* * *
5062 GGTCAGTTTTGCATAATTTTTGTG-G-TAAAACTCCTTGAAATATTTATATTCATCTAACCAAAT
242 GCTCAGTTTTGCATAATTTTTG-GCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCAAAT
* * * * * *
5125 CTTAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTACTAAG
306 CTCAGCCACATTGGATTTAAGAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
* * * * *
5190 AAATTATTTGA-AAACAATATAGGAAAAACGATATTAGAAA-CGTGAGAAGTCCTTCAATTTTTT
371 AAATTAATTCAGAAA-AATAT--GAAAAACGATATTA-AAAGCGTAAAAAGTCCTTCAATCTTTT
* * * * * * *
5253 TGGTGTTGAATTATATTTTTTTTATGAGTATTGTGGCTAAAAATTGAGAAAACTATTTCGGGTCA
432 TGGAGTTGAATTATATATATTTTATGAGTATTTTAGCCAAAAATTGAGAAAAATATTTCGGGTCA
* * * ** ** * *
5318 ATTTTTGCAAAATTTTAGCTGAAATCGTGTACCATCATGGTTTTTTTTTTTTTGCTAAAAACGTG
497 ATTTTTGCAAAATTTTAGCCGAAATCGTGT---ATTAT-GATCATGGTTTTTGGCTAAAAACGCG
* * * * * * * *
5383 TTCTGGGGCCTTGAGTCAGTTTTG-ATGATTTTTTGTGCCAAGACTTCTAAAGATATATCTATAT
558 TTC-CGGGCC--CATTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCT--TGAAATATCTATAT
* *
5447 TCATCTAACCAAATCTCAGCCACATTGTATTTAAGGAT
618 TCATCTAATCAAATCTCAGCCACATTGGATTTAAGGAT
* ** * * * * *
5485 TTGTTTTTACAAGTTTCTAAATCTTGTTTCGATTTAATAAAAAATTAATTTGGAAATAA-AATAG
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TT-CAAA-AATAATAT
* * *
5549 GAAAAACGATATT-AGAAGCGTGAAAAATGGT--TTCAATTTTTTTGGCGTTGAATTATATATTT
63 GAAAAACGATATTAAGAA-TGT-AAAAA--GTCCTTCAATCTTTTTGGCGTTGAATTATATA-AT
* * * * * *
5611 TTTATTATTATTTTCGCTAGAAATCGAGGAAAAATCTTTCGGGTCAATTTTTGCAATA-TTTAGC
123 TTTATGAGTATTGTGGCTA-AAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGC
** ** * ** * *
5675 CGAAATCGTGTACTAACCATCAC-GGTTTTCGGCTAAAAACGCATTCCCGGTCCCGGCTCAGTTT
187 CGAAATCGTGTA-TAACCATCACTTTTTTTTTGCTAAAAACGCGTTCTGGGGCCCTGCTCAGTTT
* * * * * * *
5739 TTCATTATTTTTGGTGCTAAGACTTCTTGAAATATTTATATTCATCTAACCAAATCTCAACCATA
251 TGCATAATTTTTGGCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCACA
* ** * * *
5804 TTAGATTTAA-AGATTTGTACTTACGAGTATCTGAATCTTGTTTTGATTTAATTATAAATTAATT
316 TTGGATTTAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT
* * * * * * * *
5868 CATTAAAAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTCTT-GATGTCGA
380 C---AGAAAAATATGAAAAACGATATTAAAAGCGTAAAAAGTCCTTCAATCTTTTTGGA-GTTGA
* *
5932 ATTATATAT-TTTTATGAGTATCTTT-GTCAAAAATTGAGAAAATATCTTTCGGGTCAA-TTTTG
441 ATTATATATATTTTATGAGTAT-TTTAGCCAAAAATTGAGAAAA-ATATTTCGGGTCAATTTTTG
* ** * * **
5994 CAAAATTTTAGCCGAAATCGTGTACTAACCATCACT-GTTTTTGACTAAAAACGTGTTATAGGGT
504 CAAAATTTTAGCCGAAATCGTGTA-TTATGATCA-TGGTTTTTGGCTAAAAACGCGTT-CCGGG-
* * * * *
6058 CACGATTCTA-TTTTGCATAATTTTTGGCGCCGAGACTCCCTGAAATATCTTTATTCATCTAATC
565 C-CCATTC-AGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATC
6122 AAATCTCAGCCACATTGGATTTAAGGAT
628 AAATCTCAGCCACATTGGATTTAAGGAT
* * *
6150 TTGTTTTTATGTGCATCTGAATCTTGTTTCGATTTAAATAGAAATTAATTC-AAAATAAATATGA
1 TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAAT-AATATGA
* * * * * *
6214 AACACGATATTAAAAATGTGAAAAGACCTTCAATCCTTTTGGCGTTGAATTATATATATTTTATA
65 AAAACGATATTAAGAATGTAAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATA-ATTTTATG
* * * *
6279 AGTATTTTTGCCAAAAATTGAAGAAAAATCTTTCGGGTC-ATTTTT
129 AGTA-TTGTGGCTAAAATTGAGGAAAAATCTTTCGGGTCAATTTTT
6324 ACCATCATGG
Statistics
Matches: 2286, Mismatches: 413, Indels: 274
0.77 0.14 0.09
Matches are distributed among these distances:
649 1 0.00
650 4 0.00
651 20 0.01
652 49 0.02
653 216 0.09
654 101 0.04
655 56 0.02
656 4 0.00
657 2 0.00
658 7 0.00
659 16 0.01
660 211 0.09
661 147 0.06
662 149 0.07
663 121 0.05
664 16 0.01
665 104 0.05
666 68 0.03
667 36 0.02
668 27 0.01
669 198 0.09
670 105 0.05
671 288 0.13
672 102 0.04
673 16 0.01
674 6 0.00
675 36 0.02
676 31 0.01
677 91 0.04
678 10 0.00
679 2 0.00
680 1 0.00
681 25 0.01
682 18 0.01
684 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (655 bp):
TTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAAAAATAATATGAA
AAACGATATTAAGAATGTAAAAAGTCCTTCAATCTTTTTGGCGTTGAATTATATAATTTTATGAG
TATTGTGGCTAAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
GTATAACCATCACTTTTTTTTTGCTAAAAACGCGTTCTGGGGCCCTGCTCAGTTTTGCATAATTT
TTGGCGCTAAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTCAGCCACATTGGATTTAA
GAATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAT
GAAAAACGATATTAAAAGCGTAAAAAGTCCTTCAATCTTTTTGGAGTTGAATTATATATATTTTA
TGAGTATTTTAGCCAAAAATTGAGAAAAATATTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAA
TCGTGTATTATGATCATGGTTTTTGGCTAAAAACGCGTTCCGGGCCCATTCAGTTTTGCATGATT
TTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTGGATTTA
AGGAT
Found at i:4605 original size:996 final size:980
Alignment explanation
Indices: 3079--6323 Score: 3271
Period size: 996 Copynumber: 3.3 Consensus size: 980
3069 GGGCCTTGAG
* * *
3079 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATTTATATTCATCTAATCAAATCTC
1 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
* * ** * *
3144 AGCCACATTGGATTTAAGGATTTGCTTTTATGAGCATCAAAATCTTGTTTCAATTTAATTAGAAA
66 AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAA
* * * * * * * *
3209 TTAATTCGGAAAAAGTAGGAAAAATGATATTAGTAGCGT-AAAAA-CCTTTCAATATTTTTGGCG
131 TTAATTCGAAAAAAATAGGAAAAACGATATTAGAAACATGAAAAAGCCCTTCAATCTTTTTGGCG
* * * * * * * * *
3272 TTGACTTATATATTTTTTATGATTATTTTAGCCAAGAATTGAGGAAATATCCTTCCGGACAA-TT
196 TTGAATTATATAATTTTTATGAGTATTGTGGCTAA-AATTGAGGAAATA-ACTTTCGGTCAATTT
* * ** * **
3336 TTGAAAAAATTTTAGCCGAAATCGTGTAATAATGATCAC--GGTTTTAGCTAAAACGCGTTCCAG
259 TTG-CAAAATTTTAGCCGAAATCGTGTAATAATCATCACTTTTTTTTTGCTAAAACGCGTTCTGG
* * * * * *
3399 GTCCC-GGGTCAGTTTTGCATGA-TTTTTGACGCTAAGACTCCTTGAGATATACACATTCATCTA
323 GGCCCTGAGTCAGTTTTGCATGATTTTTTG-CGCCAAGACTCTTTGAGATATCCATATTCATCTA
* *
3462 ATCAAATGTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
387 ATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATT
* * *
3527 TAATTAGAAATTAATTCAGAAAATATATGAAAAATGATATTAAAAATGTGAAAAGTACTCATATT
452 TAATTAGAAATTAATTTAGAAAA-ATATGAAAAACGATATTAAAAGTGTGAAAAGTACTCA-ATT
* * * * **
3592 TTTTGAT-ATTAAATTATATATTTCACGAGTATTTTAGCGAAAAATTGAGG-AAAATTTTTTTGG
515 TTTTG-TCGTTAAATTATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTAGGG
*
3655 TCATTTTTTGCAAAATTTTAGCCGAAATCATGTACCCATCACGGTTTTTTGCTAAAAACGCATTT
579 TCATTTTTTGCAAAATTTTAGCCGAAATCGTGTACCCATCACGGTTTTTTGCTAAAAACGCATTT
* *
3720 CGTGGCCCTGTCTCAGTTTTGCATAATTTTTAGCGTTGAGACTCCTTGAAATATCTATATTCATC
644 CGTGGCCC-GTCTCAGTTTTGCATAATTTTTAGCGCTAAGACTCCTTGAAATATCTATATTCATC
* *
3785 TAATCAAATATTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
708 TAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGA
* *
3850 TTCAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGTAAAAAGTCCTACAAT
772 TTTAATTAGAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCGTAAAAAGTCCTACAAT
3915 CTTTTTGGAGTAGAATTATATATATTTTATGAGTATTTTAGACAAAAATTGAGTAAAAATATTTA
837 CTTTTTGGAGTAGAATTATATATATTTTATGAGTATTTTAGACAAAAATTGAG-AAAAATATTT-
* * * *
3980 TGGTCAATTTTTGCAAAATATTAGCCGAAATCGTGTATGTTAGTTGAAGTTATGGTTTTTGGTTA
900 TGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTA--CTA--TCAAGTTAT-GTTTTTGGCTA
*
4045 AAAACGCGTTCCGGAGCCCTACT
960 AAAACGCGTTCCGG-GCCCCA-T
* * * * *
4068 TCAGTGTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTTATCTAACCAAATTTC
1 TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
*** * *
4133 AGCCACATTGGATTTAAGGATTT-TTAAAACAAGTATCTGAATCATGTTTCGATTTAATTAGAAA
66 AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAA
* * *
4197 TTAATTCGAAAAATAATAGGAAAAACGATATTGGAAGCATGAAAAAGCCCTTCAATCTATTTGGC
131 TTAATTCGAAAAA-AATAGGAAAAACGATATTAGAAACATGAAAAAGCCCTTCAATCTTTTTGGC
* * * *
4262 GTTGAATTTTATAATTTGTGTGAGTATTGTGGCTAAAATTTGAGGAAATAACTTTCGAGTTAATT
195 GTTGAATTATATAATTTTTATGAGTATTGTGGCTAAAA-TTGAGGAAATAACTTTCG-GTCAATT
* *
4327 TTTGCAAAATTCTAGCCGAAACCGTGTAATAATCATCACATTTTTTTTTGCTAAGAACGCGTTCT
258 TTTGCAAAATTTTAGCCGAAATCGTGTAATAATCATCAC-TTTTTTTTTGCTAA-AACGCGTTCT
** *
4392 GGGGCCCTGCCTAAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTGAGATATCCATATTCATCT
321 GGGGCCCTGAGTCAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTGAGATATCCATATTCATCT
* * * *
4457 AATCAAATCTCAGCTACGTTGGATTTAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGAT
386 AATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGAT
* *
4522 TTAATTGGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTCCTCCAATT
451 TTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTACT-CAATT
* *
4587 TTCTTGTCGTTTAATTATATATATTTTATGAGTATTTTAGCCAAAAATTAACGGAAAAATTTTTA
515 TT-TTGTCG-TTAAAT-TATATATTTTATGAGTATTTTAGCCAAAAATTGA-GGAAAAATTTTTA
*
4652 GGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTTGC----AA-
576 GGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTG---TACCCATCACGGTTTTTTGCTAAAAAC
* * * * * *
4712 --ATTT-TTAGG--C-T-T-AGTTTTGAATGATTTTTAGCACCAAGACTCCTTGAAATATCTTTA
638 GCATTTCGT-GGCCCGTCTCAGTTTTGCATAATTTTTAGCGCTAAGACTCCTTGAAATATCTATA
*
4769 TTCATCTAATAAAATCTCAGCCACATTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
702 TTCATCTAATCAAATCTCAGCCACATTG-ATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTG
* * *
4834 TTTCGATTTAATTAGAAATTAATTCAG-ATAATATGAAAAACAATATTAAAAGTGTAAACAGTCC
766 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCGTAAAAAGTCC
* * **
4898 TCCAATCTTTTTGGTGTTTAATTATATATATATATATAT-A-TATTCTGTGAGGATTGTGGCAAA
831 TACAATCTTTTTGGAGTAGAATTATATATAT-T-T-TATGAGTATT-T-T-A-GA------CAAA
* *
4961 AAGTTGAGGAAAAATATTTTGGGTCAATTTTTGCAAAATTTTAGCTGAAATCGTGTACCATCAAC
883 AA-TTGA-GAAAAATATTTT-GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCAA-
*
5026 GGTT-T-TTTTTGGCTAAAAACGCGTTCCGGGGCCCCAGG
944 -GTTATGTTTTTGGCTAAAAACGCGTTCC-GGGCCCCA-T
* * *
5064 TCAGTTTTGCATAATTTTTGTG-G-TAAAACTCCTTGAAATATTTATATTCATCTAACCAAATCT
1 TCAGTTTTGCATAATTTTTG-GCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
* * * * * *
5127 TAGCCACATTGAATTTAAGAATTTGTTTTTACGAGCATTTGAATCATGTTTCGATTTACTAAGAA
65 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAA
* * * * *
5192 ATT-ATTTGAAAACAATATAGGAAAAACGATATTAGAAACGTG-AGAAGTCCTTCAATTTTTTTG
130 ATTAATTCGAAAA-AA-ATAGGAAAAACGATATTAGAAACATGAAAAAGCCCTTCAATCTTTTTG
* ** *
5255 GTGTTGAATTATATTTTTTTTATGAGTATTGTGGCTAAAAATTGAGAAAACT-A-TTTCGGGTCA
193 GCGTTGAATTATATAATTTTTATGAGTATTGTGGCT-AAAATTGAGGAAA-TAACTTTC-GGTCA
* * ** *** *
5318 ATTTTTGCAAAATTTTAGCTGAAATCGTGTACCATCATGGTTTTTTTTTTTTTGCTAAAAACGTG
255 ATTTTTGCAAAATTTTAGCCGAAATCGTGTA--ATAATCATCACTTTTTTTTTGCT-AAAACGCG
* * ** * *
5383 TTCTGGGGCCTTGAGTCAGTTTTG-ATGATTTTTTGTGCCAAGACTTCTAAAGATATATCTATAT
317 TTCTGGGGCCCTGAGTCAGTTTTGCATGATTTTTTGCGCCAAGAC-TCT-TTGAGATATCCATAT
* * * **
5447 TCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACAAGTTTCTAAATCTTGT
380 TCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGT
* * * * * *
5512 TTCGATTTAATAAAAAATTAATTTGGAAATAAAATAGGAAAAACGATATTAGAAGCGTGAAAAAT
445 TTCGATTTAATTAGAAATTAATTT--AGA-AAAATATGAAAAACGATATTAAAAGTGTG-AAAA-
* * * * * * * * *
5577 GGT-TTCAATTTTTTTGGCGTTGAATTATATATTTTTTATTATTATTTTCGCTAGAAATCGAGGA
505 -GTACTCAA-TTTTTTGTCGTTAAATTATATA--TTTTATGAGTATTTTAGCCAAAAATTGAGGA
* * * * *
5641 AAAATCTTTCGGGTCAATTTTTGCAATA-TTTAGCCGAAATCGTGTACTAACCATCACGGTTTTC
566 AAAATTTTTAGGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAC---CCATCACGGTTTTT
* * * * * * * * *
5705 GGCTAAAAACGCATTCCCG-GTCCCGGCTCAGTTTTTCATTATTTTTGGTGCTAAGACTTCTTGA
628 TGCTAAAAACGCATT-TCGTGGCCCGTCTCAGTTTTGCATAATTTTTAGCGCTAAGACTCCTTGA
* * * * * ** *
5769 AATATTTATATTCATCTAACCAAATCTCAACCATATTAGATTTAAAGATTTGTACTTACGAGTAT
692 AATATCTATATTCATCTAATCAAATCTCAGCCACATT-GATTTAAGGATTTGTTTTTACGAGCAT
* * * * *
5834 CTGAATCTTGTTTTGATTTAATTATAAATTAATTCATTAAAAAAATAGGAAAAACAATATTAGAA
756 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTC---AGAAAAATATGAAAAACAATATTAAAA
* * * * * *
5899 GCGTTAAAAGCCCTTCAATCTTCTT-GATGTCGAATTATATAT-TTTTATGAGTATCTTT-GTCA
818 GCGTAAAAAGTCCTACAATCTTTTTGGA-GTAGAATTATATATATTTTATGAGTAT-TTTAGACA
* *
5961 AAAATTGAG-AAAATATCTTTCGGGTCAA-TTTTGCAAAATTTTAGCCGAAATCGTGTACTAACC
881 AAAATTGAGAAAAATAT-TTT--GGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACTATCA
* * * ** * *
6024 A-TCACTGTTTTTGACTAAAAACGTGTTATAGGGTCACGAT
943 AGTTA-TGTTTTTGGCTAAAAACGCGTT-CCGGG-CCCCAT
* * * *
6064 TCTA-TTTTGCATAATTTTTGGCGCCGAGACTCCCTGAAATATCTTTATTCATCTAATCAAATCT
1 TC-AGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCT
* * * *
6128 CAGCCACATTGGATTTAAGGATTTGTTTTTATGTGCATCTGAATCTTGTTTCGATTTAAATAGAA
65 CAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAA
* * * * *
6193 ATTAATTC-AAAATAAATATGAAACACGATATTA-AAA-ATGTGAAAAGACCTTCAATCCTTTTG
130 ATTAATTCGAAAA-AAATAGGAAAAACGATATTAGAAACATG-AAAAAGCCCTTCAATCTTTTTG
* * * * *
6255 GCGTTGAATTATAT-ATATTTTATAAGTATTTTTGCCAAAAATTGAAGAAA-AATCTTTCGGGTC
193 GCGTTGAATTATATAAT-TTTTATGAGTA-TTGTGGCTAAAATTGAGGAAATAA-CTTTC-GGTC
6318 -ATTTTT
254 AATTTTT
6324 ACCATCATGG
Statistics
Matches: 1871, Mismatches: 278, Indels: 203
0.80 0.12 0.09
Matches are distributed among these distances:
988 42 0.02
989 163 0.09
990 142 0.08
991 91 0.05
992 10 0.01
993 1 0.00
994 66 0.04
995 216 0.12
996 340 0.18
997 18 0.01
998 72 0.04
999 79 0.04
1000 231 0.12
1001 179 0.10
1002 14 0.01
1003 19 0.01
1005 4 0.00
1007 1 0.00
1008 1 0.00
1009 1 0.00
1010 116 0.06
1011 4 0.00
1012 5 0.00
1013 4 0.00
1014 52 0.03
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.38
Consensus pattern (980 bp):
TCAGTTTTGCATAATTTTTGGCGCCAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTC
AGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAA
TTAATTCGAAAAAAATAGGAAAAACGATATTAGAAACATGAAAAAGCCCTTCAATCTTTTTGGCG
TTGAATTATATAATTTTTATGAGTATTGTGGCTAAAATTGAGGAAATAACTTTCGGTCAATTTTT
GCAAAATTTTAGCCGAAATCGTGTAATAATCATCACTTTTTTTTTGCTAAAACGCGTTCTGGGGC
CCTGAGTCAGTTTTGCATGATTTTTTGCGCCAAGACTCTTTGAGATATCCATATTCATCTAATCA
AATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAAT
TAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGTGTGAAAAGTACTCAATTTTTTGT
CGTTAAATTATATATTTTATGAGTATTTTAGCCAAAAATTGAGGAAAAATTTTTAGGGTCATTTT
TTGCAAAATTTTAGCCGAAATCGTGTACCCATCACGGTTTTTTGCTAAAAACGCATTTCGTGGCC
CGTCTCAGTTTTGCATAATTTTTAGCGCTAAGACTCCTTGAAATATCTATATTCATCTAATCAAA
TCTCAGCCACATTGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAG
AAATTAATTCAGAAAAATATGAAAAACAATATTAAAAGCGTAAAAAGTCCTACAATCTTTTTGGA
GTAGAATTATATATATTTTATGAGTATTTTAGACAAAAATTGAGAAAAATATTTTGGTCAATTTT
TGCAAAATTTTAGCCGAAATCGTGTACTATCAAGTTATGTTTTTGGCTAAAAACGCGTTCCGGGC
CCCAT
Found at i:8430 original size:24 final size:24
Alignment explanation
Indices: 8399--8519 Score: 73
Period size: 24 Copynumber: 4.8 Consensus size: 24
8389 CCACCCGGTC
8399 TGCCCAAGCCTGAATTGCCTCCAT
1 TGCCCAAGCCTGAATTGCCTCCAT
** * *
8423 TGCCCAAGGTTGAACTGCCACCA-
1 TGCCCAAGCCTGAATTGCCTCCAT
* *
8446 GGCCTGCCAATGCCTGAATTGCCTCCAG
1 TG-C--CCAA-GCCTGAATTGCCTCCAT
** * * *
8474 TGCCCAAGGTTGAACTGCCACCCGGT
1 TGCCCAAGCCTGAATTGCC-TCC-AT
8500 CTGCCCAAGCCTGAATTGCC
1 -TGCCCAAGCCTGAATTGCC
8520 ACCCCTACCA
Statistics
Matches: 70, Mismatches: 19, Indels: 13
0.69 0.19 0.13
Matches are distributed among these distances:
23 1 0.01
24 29 0.41
25 6 0.09
26 4 0.06
27 29 0.41
28 1 0.01
ACGTcount: A:0.21, C:0.36, G:0.22, T:0.21
Consensus pattern (24 bp):
TGCCCAAGCCTGAATTGCCTCCAT
Found at i:8463 original size:51 final size:51
Alignment explanation
Indices: 8387--8519 Score: 223
Period size: 51 Copynumber: 2.6 Consensus size: 51
8377 TTGCCCGAAT
*
8387 TGCCACCCGGTCTGCCCAAGCCTGAATTGCCTCCATTGCCCAAGGTTGAAC
1 TGCCACCCGGTCTGCCCAAGCCTGAATTGCCTCCAGTGCCCAAGGTTGAAC
* *
8438 TGCCACCAGGCCTG-CCAATGCCTGAATTGCCTCCAGTGCCCAAGGTTGAAC
1 TGCCACCCGGTCTGCCCAA-GCCTGAATTGCCTCCAGTGCCCAAGGTTGAAC
8489 TGCCACCCGGTCTGCCCAAGCCTGAATTGCC
1 TGCCACCCGGTCTGCCCAAGCCTGAATTGCC
8520 ACCCCTACCA
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
50 4 0.05
51 67 0.89
52 4 0.05
ACGTcount: A:0.20, C:0.38, G:0.23, T:0.20
Consensus pattern (51 bp):
TGCCACCCGGTCTGCCCAAGCCTGAATTGCCTCCAGTGCCCAAGGTTGAAC
Found at i:8523 original size:27 final size:27
Alignment explanation
Indices: 8383--8523 Score: 116
Period size: 27 Copynumber: 5.4 Consensus size: 27
8373 AGCATTGCCC
8383 GAATTGCCACCCGGTCTGCCCAAGCCT
1 GAATTGCCACCCGGTCTGCCCAAGCCT
* * **
8410 GAATTGCC-TCC-AT-TGCCCAAGGTT
1 GAATTGCCACCCGGTCTGCCCAAGCCT
* * *
8434 GAACTGCCACCAGGCCTG-CCAATGCCT
1 GAATTGCCACCCGGTCTGCCCAA-GCCT
* * **
8461 GAATTGCC-TCCAG--TGCCCAAGGTT
1 GAATTGCCACCCGGTCTGCCCAAGCCT
*
8485 GAACTGCCACCCGGTCTGCCCAAGCCT
1 GAATTGCCACCCGGTCTGCCCAAGCCT
8512 GAATTGCCACCC
1 GAATTGCCACCC
8524 CTACCAAAAG
Statistics
Matches: 83, Mismatches: 23, Indels: 16
0.68 0.19 0.13
Matches are distributed among these distances:
24 27 0.33
25 9 0.11
26 8 0.10
27 39 0.47
ACGTcount: A:0.21, C:0.38, G:0.22, T:0.20
Consensus pattern (27 bp):
GAATTGCCACCCGGTCTGCCCAAGCCT
Found at i:10752 original size:169 final size:166
Alignment explanation
Indices: 10364--10758 Score: 526
Period size: 165 Copynumber: 2.4 Consensus size: 166
10354 TGAGTCATTT
*
10364 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGATAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
* * * * * * * ** *
10429 TTAAGTAATCTGCCAAGTAGGTAAAGACGAATAAGATTAGTTTTCTAACTCATCATCAATCCTTG
66 TTAAGTAATCTACAAAATAGGAAAAGACGAAAAAGATAAGTTCTCTAACTCAAAAGCAATCCTTG
* * * *
10494 ATGGGGATCTTTTATTAATTTCACTACTCTATTCAA
131 ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
* * * *
10530 -TCCATTGAGAAATGACCAAAAAGATTACTTATTTAATCCCCTCAATAATCAAAAGTTAGGACAT
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
*
10594 TTAAGTAATCTACAAAATAGGAAAAGACGAAAAA-AGTAAGTTCTCTAGCTCCAAAAGCAAGT-C
66 TTAAGTAATCTACAAAATAGGAAAAGACGAAAAAGA-TAAGTTCTCTAACT-CAAAAGCAA-TCC
10657 TTGATAGGGATCTTTTAGTAATTCCACTATTCTCTATTAAA
128 TTGATAGGGATCTTTTAGTAATTCCACTA--CTCTATTAAA
**
10698 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATGACCTCAAGAATCAAAAGTTAGG
1 GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGG
10759 GTATTTAAAT
Statistics
Matches: 197, Mismatches: 26, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
164 1 0.01
165 99 0.50
166 33 0.17
167 1 0.01
168 9 0.05
169 54 0.27
ACGTcount: A:0.39, C:0.15, G:0.14, T:0.31
Consensus pattern (166 bp):
GTCAATTGAGAAATGACCAAAAAGTTTAGTTATTTAATCCCCTCAAGAATCAAAAGTTAGGACAT
TTAAGTAATCTACAAAATAGGAAAAGACGAAAAAGATAAGTTCTCTAACTCAAAAGCAATCCTTG
ATAGGGATCTTTTAGTAATTCCACTACTCTATTAAA
Found at i:12376 original size:7 final size:7
Alignment explanation
Indices: 12366--12394 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
12356 TTATTAATAT
12366 TGTTCTA
1 TGTTCTA
12373 TGTTCTA
1 TGTTCTA
12380 TGTTCTA
1 TGTTCTA
12387 TGTTCTA
1 TGTTCTA
12394 T
1 T
12395 TTCATTTTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.14, T:0.59
Consensus pattern (7 bp):
TGTTCTA
Found at i:17625 original size:27 final size:27
Alignment explanation
Indices: 17594--17674 Score: 153
Period size: 27 Copynumber: 3.0 Consensus size: 27
17584 TCACCACGTA
*
17594 TATTGTTTGCAAAAATGGGATTTTTTT
1 TATTGTTTGTAAAAATGGGATTTTTTT
17621 TATTGTTTGTAAAAATGGGATTTTTTT
1 TATTGTTTGTAAAAATGGGATTTTTTT
17648 TATTGTTTGTAAAAATGGGATTTTTTT
1 TATTGTTTGTAAAAATGGGATTTTTTT
17675 GGTAAAAAAA
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 53 1.00
ACGTcount: A:0.26, C:0.01, G:0.19, T:0.54
Consensus pattern (27 bp):
TATTGTTTGTAAAAATGGGATTTTTTT
Found at i:19908 original size:20 final size:20
Alignment explanation
Indices: 19870--19908 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
19860 TGATAATGGT
*
19870 AAAAGCCCAACATCGATATA
1 AAAAGCCCAACATCCATATA
19890 AAAAGCCCATACA-CCATAT
1 AAAAGCCCA-ACATCCATAT
19909 TCGTTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.49, C:0.28, G:0.08, T:0.15
Consensus pattern (20 bp):
AAAAGCCCAACATCCATATA
Found at i:36870 original size:19 final size:20
Alignment explanation
Indices: 36835--36872 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
36825 TTAATCACCT
36835 GATTAGATTGCTAATGAGTA
1 GATTAGATTGCTAATGAGTA
*
36855 GATTAGA-TGTTAATGAGT
1 GATTAGATTGCTAATGAGT
36873 GAATGGCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.37
Consensus pattern (20 bp):
GATTAGATTGCTAATGAGTA
Found at i:40929 original size:3 final size:3
Alignment explanation
Indices: 40921--40962 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
40911 TGCTTTACTC
*
40921 TGA TGA TGA TGA TGA TGA TGA TGA TGA TTA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
40963 AGTGATGAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.31, T:0.36
Consensus pattern (3 bp):
TGA
Found at i:45042 original size:17 final size:18
Alignment explanation
Indices: 45020--45060 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
45010 ATGGCATTCT
45020 GTTTTTATTTTTGTTT-A
1 GTTTTTATTTTTGTTTCA
* *
45037 GTTTTTTTTTTTTTTTCA
1 GTTTTTATTTTTGTTTCA
45055 GTTTTT
1 GTTTTT
45061 TCTTGGACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.07, C:0.02, G:0.10, T:0.80
Consensus pattern (18 bp):
GTTTTTATTTTTGTTTCA
Found at i:45048 original size:18 final size:18
Alignment explanation
Indices: 45021--45061 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45011 TGGCATTCTG
45021 TTTTTATTTTTGTTT-AGT
1 TTTTTATTTTT-TTTCAGT
*
45039 TTTTTTTTTTTTTTCAGT
1 TTTTTATTTTTTTTCAGT
45057 TTTTT
1 TTTTT
45062 CTTGGACCCT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.07, C:0.02, G:0.07, T:0.83
Consensus pattern (18 bp):
TTTTTATTTTTTTTCAGT
Found at i:48813 original size:77 final size:76
Alignment explanation
Indices: 48667--48821 Score: 301
Period size: 77 Copynumber: 2.0 Consensus size: 76
48657 GAGTTTTTAT
48667 TAATTTGAAATCGAATCACGTCAAATCTGATTTTTTTTTTGCTACTCATGAACTTTTATTGAAAT
1 TAATTTGAAATCGAATCACGTCAAATCTGATTTTTTTTTTGCTACTCATGAACTTTTATTGAAAT
48732 GGAATACACAA
66 GGAATACACAA
48743 TAATTTGAAATCGAATCACGTCAAATCTGATTTTTTTTTTTGCTACTCATGAACTTTTATTGAAA
1 TAATTTGAAATCGAATCACGTCAAATCTGA-TTTTTTTTTTGCTACTCATGAACTTTTATTGAAA
48808 TGGAATACACAA
65 TGGAATACACAA
48820 TA
1 TA
48822 GCAAGTAGTT
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
76 30 0.38
77 48 0.62
ACGTcount: A:0.34, C:0.14, G:0.12, T:0.40
Consensus pattern (76 bp):
TAATTTGAAATCGAATCACGTCAAATCTGATTTTTTTTTTGCTACTCATGAACTTTTATTGAAAT
GGAATACACAA
Found at i:58857 original size:187 final size:187
Alignment explanation
Indices: 58542--58920 Score: 713
Period size: 187 Copynumber: 2.0 Consensus size: 187
58532 GTAATCACAA
58542 TCAAAGAAAAAGTGATCTCTAGATTCAGGGCATAATCCACAAAGCACACAATCGACATTATCAAT
1 TCAAAGAAAAAGTGATCTCTAGATTCAGGGCATAATCCACAAAGCACACAATCGACATTATCAAT
* *
58607 CAGGATGTTCTAGTGAAGCAGTCTATCTTTAGTGGGTAACCTATTAAGAATGGCCATCCAAGTCA
66 CAGGATGTTCCAGTGAAGCAGTCTATCTTTAGTGGGTAACCTATCAAGAATGGCCATCCAAGTCA
58672 CAATAGAGTGCTTTGACAAATTGCAAGAATACCAAAACAGTCTATGCCAACTCACCT
131 CAATAGAGTGCTTTGACAAATTGCAAGAATACCAAAACAGTCTATGCCAACTCACCT
* *
58729 TCAAAGAAAAGGTGATCTTTAGATTCAGGGCATAATCCACAAAGCACACAATCGACATTATCAAT
1 TCAAAGAAAAAGTGATCTCTAGATTCAGGGCATAATCCACAAAGCACACAATCGACATTATCAAT
*
58794 TAGGATGTTCCAGTGAAGCAGTCTATCTTTAGTGGGTAACCTATCAAGAATGGCCATCCAAGTCA
66 CAGGATGTTCCAGTGAAGCAGTCTATCTTTAGTGGGTAACCTATCAAGAATGGCCATCCAAGTCA
58859 CAATAGAGTGCTTTGACAAATTGCAAGAATACCAAAACAGTCTATGCCAACTCACCT
131 CAATAGAGTGCTTTGACAAATTGCAAGAATACCAAAACAGTCTATGCCAACTCACCT
58916 TCAAA
1 TCAAA
58921 TTCTTATGTC
Statistics
Matches: 187, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
187 187 1.00
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (187 bp):
TCAAAGAAAAAGTGATCTCTAGATTCAGGGCATAATCCACAAAGCACACAATCGACATTATCAAT
CAGGATGTTCCAGTGAAGCAGTCTATCTTTAGTGGGTAACCTATCAAGAATGGCCATCCAAGTCA
CAATAGAGTGCTTTGACAAATTGCAAGAATACCAAAACAGTCTATGCCAACTCACCT
Done.