Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010904.1 Corchorus capsularis cultivar CVL-1 contig10925, 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: 32490
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:615 original size:323 final size:322
Alignment explanation
Indices: 62--2607 Score: 3298
Period size: 323 Copynumber: 7.9 Consensus size: 322
52 ATATATATAT
* * * * * * *
62 ATATATATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGTCGTGGCCGCGG-AAC
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGAAAC
** * * * ** *
126 GCGTTTTTAG-CTAAAAACAAATGATAGTTTTGTACACGATTTTTGACT-AAAACTGACCCGAAA
65 GCGTTTTTAGCCT-AAAAC-CGTGAT-GGTTAGTACACGA-TTTCGGTTAAAAACTGACCAGAAA
* * *
189 -ATTTTTTTCTCAA-TTTTTGCCACTATACTTAGAAAAAA-ATATAATTCAGCGCAAAATAAAAA
126 TA-TTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC--AA-AAAAA
* * *
251 ATTGTAGGGGTTTTCAGGATTTTAATATCGCTTTT-CA-TTTTTTTCAGAA-TTATTTCTAATTA
187 ATTGTAGGGGTTTTCACGCTTCTAATATCG-TTTTCCATTTTTTTTCAGAATTTATTTCTAATTA
* * *
313 TATCGAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGAT
251 TATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
378 TTAATGA
316 TTAATGA
* ** * *
385 ATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCAAACAAATCTGAGCCGGGGCCCGGAAACG
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAACG
*
450 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAAAAATATTT
66 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATA-TT
* *
515 TTTTCTCAAATTTTTTGCCATAATACTCAGGAAAAAATATATAATTCAACACAAAAAAAATTGTA
130 TTTTCTC-AATTTTTTGCCACAATACTCA-GAAAAAATATATAATTCAACGCAAAAAAAATTGTA
* *
580 TGGGTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTTTTTCCTAGAATTTATTTCTAATTATA
193 GGGGTTTTCACGCTTCTAATATCGTTTTCCA---TTTTTTTT-C-AGAATTTATTTCTAATTATA
*
645 TCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG-TT
253 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTT
709 AGATGA
318 A-ATGA
* * * * *
715 ATATAGATATTTCAAGGAGACATTCTGCGAAAAACCATGCAAAACTGGGCCGTGGCCCCGG-AAC
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGAAAC
* * * * * * * *
779 GCATTTTTAGCCAAAAACCATGATAGTTTTGTACACGATTTCGGCT-AAAACTGACCCGAAAAAT
65 GCGTTTTTAGCCTAAAACCGTGAT-GGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATAT
* * * * *
843 ATTTTCTCAATTTTTCGCCACAATACTTAGAAAAAAATATATAATTCAGCGCAAAAAAAATTTTA
129 TTTTTCTCAATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACGCAAAAAAAATTGTA
* * *
908 GGGGTTTTTCA-G-TATTTAAATATCGTTTTTC-TTTTTTTTCATAATTTATTTCTAATTATATC
193 GGGG-TTTTCACGCT-TCT-AATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATC
* *
970 GAAA-AAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAA
255 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAA
1034 TGA
320 TGA
* * * * *
1037 ATATAGATATTTCAAGGAGACATTCTGCCAAAAA-CAATGCAAAACTGGGCTGTGTCCCCGG-AA
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC-ATGCAAAACTGAGCCG-GGCCCCGGAAA
** * * * * * * * *
1100 CGCGTTTTTAAACAAAAACCGTTATAGTTTGTACACGGTTTCGGCT-AAAACAGACCCGAAATA-
64 CGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATAT
* * * ** *
1163 TTTTTCTCAATTTTTTGCCACAATACTTATAAAAAAAATGTATAATTCAGTGCAAAAAAATTTTG
129 TTTTTCTCAATTTTTTGCCACAATAC-T-CAGAAAAAATATATAATTCAACGCAAAAAAA-ATTG
*
1228 TAGGGGTTTTCA-GCATT-TAAATATCGTTTTTCATTTTTTTTCAGAATTTATTTCTAATTATAT
191 TAGGGGTTTTCACGC-TTCT-AATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATAT
* * * * * * *
1291 CGAAACAAGATTTAGATTCTCGTAAAAATAAATCCTTATATCCACTGTCGCTGAGATTTGGTTCA
254 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTA
1356 ATGA
319 ATGA
* *
1360 ATATACATATTT-AAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAACG
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAACG
* *
1424 CGTTTTTAGCCTAAAATCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTA
66 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTT
* *
1489 TTTCTCAATTTTTTACCACAATACTCAGAAAAAATATATAATTCGACGCAAAAAAAATTGTAGGG
131 TTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAAATTGTAGGG
** ** *
1554 GTTTTCAAACTTCTAATATCGTTTTCCATTCATTTTCAGAATTTATTTCTAATTAATATCGAAAT
196 GTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATT-ATATCGAAAC
1619 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAATGA
260 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAATGA
* * *
1682 ACATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGACCCGGAAACG
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAACG
* *
1747 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGCTTAAAAACTGACCAGAAATATTA
66 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTT
* *
1812 TTTCTCAATTTTTTGCCACAATACACAGAAAAAATATATAATTCAACGCAAAAAAAAATTGTAAG
131 TTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGC-AAAAAAAATTGTAGG
* *
1877 GGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAAAATTTATTTCTAATTATATCGAAAT
195 GGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAAAC
* *
1942 AAGATTTAGATGCTCGTAAAAACAAATCCTTCAATCCAATGTGGCTGAGATTTGG-TTAGATGA
260 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTA-ATGA
* * * **
2005 ATATAGATATTTCAAGGAGTCATTCTGCCAAAAACCATGCAAAACTGGGTTGTGGCCCCGG-AAC
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGAAAC
* * ** * * *
2069 GCGTTTTTAGCCAAAAACCGTGATAGTTTTTACACGATTTCGGCT-AAAACAGACCCGAAATA-T
65 GCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATT
*
2132 TTTTCTCAATTTTTTGCCACAATACAT-AGAAAAAAATATATAATTCAGCGCAAAAAAAATT-TA
130 TTTTCTCAATTTTTTGCCACAATAC-TCAG-AAAAAATATATAATTCAACGCAAAAAAAATTGTA
* * * * *
2195 GTGGTTTTCAGGATTCTAATATCATTTTTCA-TTTTTTTCAGAATTTATTTCTAATTATATCGAA
193 GGGGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAA
* * *
2259 ACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTCAATGA
258 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAATGA
*
2324 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAACG
1 ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAACG
2389 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTT
66 CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTT
* *
2454 TTTCTCAATTTTTTGCCACAATACTCAGAAAAATATATATAATTCGACGCAAAAAAAAATTGTAT
131 TTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACGC-AAAAAAAATTGTAG
*
2519 GGGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGCATTTATTTCTAATTATATCGAAA
194 GGGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAAA
* *
2584 AAAGATTTAGATGCTCGTAAAAAC
259 CAAGATTCAGATGCTCGTAAAAAC
2608 GGCTTAATAG
Statistics
Matches: 1962, Mismatches: 207, Indels: 107
0.86 0.09 0.05
Matches are distributed among these distances:
318 7 0.00
319 178 0.09
320 79 0.04
321 246 0.13
322 428 0.22
323 548 0.28
324 169 0.09
325 15 0.01
326 12 0.01
327 9 0.00
328 56 0.03
329 32 0.02
330 158 0.08
331 25 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (322 bp):
ATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAAACG
CGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTT
TTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCAAAAAAAATTGTAGGG
GTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAAACA
AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAATGA
Found at i:1662 original size:645 final size:644
Alignment explanation
Indices: 62--2607 Score: 3639
Period size: 645 Copynumber: 3.9 Consensus size: 644
52 ATATATATAT
* * *
62 ATATATATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGTCGTGGCCGCGGAACG
1 ATATAGATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGCCGTGGCCCCGGAACG
* * * * *
127 CGTTTTTAGCTAAAAACAAATGATAGTTTTGTACACGATTTTTGACTAAAACTGACCCGAAAATT
66 CGTTTTTAGCCAAAAAC-CATGATAGGTTTGTACACGA-TTTCGGCTAAAACTGACCCGAAAA-T
* *
192 TTTTTCTCAA-TTTTTGCCACTATACTTAG-AAAAAA-ATATAATTCAGCGCAAAATAAAAAATT
128 TATTTCTCAATTTTTTGCCACAATACTTAGAAAAAAATATATAATTCAGCGC--AA-AAAAAATT
* *
254 GTAGGGGTTTTCAGGATTTTAATATCGCTTTTCATTTTTTTCAGAA-TTATTTCTAATTATATCG
190 GTAGGGGTTTTCAGGATTCTAATATCGTTTTTCATTTTTTTCAGAATTTATTTCTAATTATATCG
* * *
318 AAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGATTTAAT
255 AAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAAT
** *
383 GAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCAAACAAATCTGAGCCGGGGCCCGGAAA
320 GAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAA
* *
448 CGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAAAAATAT
385 CGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAGAAATA-
* ** *
513 TTTTTTCTCAAATTTTTTGCCATAATACTCAGGAAAAAATATATAATTCAACAC-AAAAAAAATT
449 TTTTTTCTC-AATTTTTTGCCACAATACTCAAAAAAAAATATATAATTCAACGCAAAAAAAAATT
*
577 GTATGGGTTTTCACGCTTCTGATATCGTTTTCCATTTTTTTTTTTCCTAGAATTTATTTCTAATT
513 GTATGGGTTTTCACGCTTCTAATATCGTTTTCCA---TTTTTTTT-C-AGAATTTATTTCTAATT
*
642 ATATCGAAAAAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG
573 ATATCGAAAAAAGATTTAGATGCTCGTAAAAACAAATCCTT-AATCCAATGTGGCTGAGATTTGG
707 TTAGATGA
637 TTAGATGA
*
715 ATATAGATATTTCAAGGAGACATTCTGCGAAAAACCATGCAAAACTGGGCCGTGGCCCCGGAACG
1 ATATAGATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGCCGTGGCCCCGGAACG
* * *
780 CATTTTTAGCCAAAAACCATGATAGTTTTGTACACGATTTCGGCTAAAACTGACCCGAAAAATAT
66 CGTTTTTAGCCAAAAACCATGATAGGTTTGTACACGATTTCGGCTAAAACTGACCCGAAAATTA-
* *
845 TTTCTCAATTTTTCGCCACAATACTTAGAAAAAAATATATAATTCAGCGCAAAAAAAATTTTAGG
130 TTTCTCAATTTTTTGCCACAATACTTAGAAAAAAATATATAATTCAGCGCAAAAAAAATTGTAGG
* * *
910 GGTTTTTCAGTATT-TAAATATCGTTTTTCTTTTTTTTCATAATTTATTTCTAATTATATCGAAA
195 GG-TTTTCAGGATTCT-AATATCGTTTTTCATTTTTTTCAGAATTTATTTCTAATTATATCGAAA
974 -AAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAA
258 CAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAA
* * * * * **
1038 TATAGATATTTCAAGGAGACATTCTGCCAAAAA-CAATGCAAAACTGGGCTGTGTCCCCGG-AAC
323 TATAGATATTTCAAGGAGTCTTTCTACCAAAAATC-ATGCAAAACTGAGCCG-GGGCCCGGAAAC
** * * * * * * *
1101 GCGTTTTTAAACAAAAACCGTTATAGTTTGTACACGGTTTCGGCT-AAAACAGACCCGAAATA-T
386 GCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAGAAATATT
* * ** **
1164 TTTTCTCAATTTTTTGCCACAATACTTATAAAAAAAATGTATAATTCAGTGCAAAAAAATTTTGT
451 TTTTCTCAATTTTTTGCCACAATACTCA-AAAAAAAATATATAATTCAACGCAAAAAAAAATTGT
* *
1229 AGGGGTTTTCA-GCATT-TAAATATCGTTTTTCATTTTTTTTCAGAATTTATTTCTAATTATATC
515 ATGGGTTTTCACGC-TTCT-AATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATC
* * * * *
1292 GAAACAAGATTTAGATTCTCGTAAAAATAAATCCTTATATCCACTGTCGCTGAGATTTGGTTCA-
578 GAAAAAAGATTTAGATGCTCGTAAAAACAAATCCTTA-ATCCAATGTGGCTGAGATTTGGTT-AG
1356 ATGA
641 ATGA
* * * * * *
1360 ATATACATATTT-AAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCG-GGGCCCGGAAAC
1 ATATAGATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGCCGTGGCCCCGG-AAC
* * * * * *
1423 GCGTTTTTAGCCTAAAATCGTGAT-GGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATAT
65 GCGTTTTTAGCCAAAAACCATGATAGGTTTGTACACGATTTCGGCT-AAAACTGACCCGAAA-AT
* *
1487 TATTTCTCAATTTTTTACCACAATACTCAG-AAAAAATATATAATTC-GACGCAAAAAAAATTGT
128 TATTTCTCAATTTTTTGCCACAATACTTAGAAAAAAATATATAATTCAG-CGCAAAAAAAATTGT
* * *
1550 AGGGGTTTTCA-AACTTCTAATATCGTTTTCCATTCATTTTCAGAATTTATTTCTAATTAATATC
192 AGGGGTTTTCAGGA-TTCTAATATCGTTTTTCATT-TTTTTCAGAATTTATTTCTAATT-ATATC
* * *
1614 GAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTTAA
254 GAAACAAGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAA
* *
1679 TGAACATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGACCCGGAA
319 TGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAA
1744 ACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTC-GCTTAAAAACTGACCAGAAAT
384 ACGCGTTTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGC-TAAAAACTGACCAGAAAT
* * *
1808 ATTATTTCTCAATTTTTTGCCACAATACAC-AGAAAAAATATATAATTCAACGCAAAAAAAAATT
448 ATTTTTTCTCAATTTTTTGCCACAATACTCAAAAAAAAATATATAATTCAACGCAAAAAAAAATT
* *
1872 GTAAGGGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAAAATTTATTTCTAATTATATC
513 GTATGGGTTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATC
*
1937 GAAATAAGATTTAGATGCTCGTAAAAACAAATCCTTCAATCCAATGTGGCTGAGATTTGGTTAGA
578 GAAAAAAGATTTAGATGCTCGTAAAAACAAATCCTT-AATCCAATGTGGCTGAGATTTGGTTAGA
2002 TGA
642 TGA
* **
2005 ATATAGATATTTCAAGGAGTCATTCTGCCAAAAACCATGCAAAACTGGGTTGTGGCCCCGGAACG
1 ATATAGATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGCCGTGGCCCCGGAACG
* * *
2070 CGTTTTTAGCCAAAAACCGTGATA-GTTTTTACACGATTTCGGCTAAAACAGACCCGAAATATT-
66 CGTTTTTAGCCAAAAACCATGATAGGTTTGTACACGATTTCGGCTAAAACTGACCCGAAA-ATTA
* *
2133 TTTCTCAATTTTTTGCCACAATACATAGAAAAAAATATATAATTCAGCGCAAAAAAAATT-TAGT
130 TTTCTCAATTTTTTGCCACAATACTTAGAAAAAAATATATAATTCAGCGCAAAAAAAATTGTAGG
*
2197 GGTTTTCAGGATTCTAATATCATTTTTCATTTTTTTCAGAATTTATTTCTAATTATATCGAAACA
195 GGTTTTCAGGATTCTAATATCGTTTTTCATTTTTTTCAGAATTTATTTCTAATTATATCGAAACA
*
2262 AGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCACTGTGGCTGAGATTTGGTTCAATGAATA
260 AGATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATA
*
2327 TAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAACGCGT
325 TAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAACGCGT
*
2392 TTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGTTAAAAACTGACCAGAAATATTTTTT
390 TTTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAGAAATATTTTTT
* * *
2457 CTCAATTTTTTGCCACAATACTCAGAAAAATATATATAATTCGACGCAAAAAAAAATTGTATGGG
455 CTCAATTTTTTGCCACAATACTCAAAAAAAAATATATAATTCAACGCAAAAAAAAATTGTATGGG
*
2522 TTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGCATTTATTTCTAATTATATCGAAAAAA
520 TTTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAAAAAA
2587 GATTTAGATGCTCGTAAAAAC
585 GATTTAGATGCTCGTAAAAAC
2608 GGCTTAATAG
Statistics
Matches: 1690, Mismatches: 162, Indels: 92
0.87 0.08 0.05
Matches are distributed among these distances:
641 1 0.00
642 240 0.14
643 224 0.13
644 169 0.10
645 439 0.26
646 99 0.06
647 40 0.02
648 19 0.01
649 28 0.02
650 35 0.02
651 60 0.04
652 213 0.13
653 109 0.06
654 14 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (644 bp):
ATATAGATATTTCAAGGAGACATTCTGCCAAAAACCATGCAAAACTGGGCCGTGGCCCCGGAACG
CGTTTTTAGCCAAAAACCATGATAGGTTTGTACACGATTTCGGCTAAAACTGACCCGAAAATTAT
TTCTCAATTTTTTGCCACAATACTTAGAAAAAAATATATAATTCAGCGCAAAAAAAATTGTAGGG
GTTTTCAGGATTCTAATATCGTTTTTCATTTTTTTCAGAATTTATTTCTAATTATATCGAAACAA
GATTCAGATTCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTCAATGAATAT
AGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGGCCCGGAAACGCGTT
TTTAGCCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCAGAAATATTTTTTC
TCAATTTTTTGCCACAATACTCAAAAAAAAATATATAATTCAACGCAAAAAAAAATTGTATGGGT
TTTCACGCTTCTAATATCGTTTTCCATTTTTTTTCAGAATTTATTTCTAATTATATCGAAAAAAG
ATTTAGATGCTCGTAAAAACAAATCCTTAATCCAATGTGGCTGAGATTTGGTTAGATGA
Found at i:2715 original size:30 final size:29
Alignment explanation
Indices: 2648--2719 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
2638 ACACCGAACC
***
2648 GTCAAATAAGCCCCTGAACTATTATTTCA
1 GTCAAATAAGCCCCTGAACTATTAAAACA
* * *
2677 GCCAAATAAGCCCCTGAACTCTTAAAAAGA
1 GTCAAATAAGCCCCTGAACTATT-AAAACA
2707 GTCAAATAAGCCC
1 GTCAAATAAGCCC
2720 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 21 0.60
30 14 0.40
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (29 bp):
GTCAAATAAGCCCCTGAACTATTAAAACA
Found at i:3740 original size:86 final size:83
Alignment explanation
Indices: 3605--3790 Score: 309
Period size: 86 Copynumber: 2.2 Consensus size: 83
3595 GAGATTTGGT
* *
3605 ACACGACACTCACGAAGGTACACGAGGACAGCGGCTCTCAGCAGTGAGGCACTCAAAACGGCCAC
1 ACACGACACACACGAAGGTACACGAGGACAACGGCTCTCAGCAGTGAGGCACTCAAAACGGCCAC
3670 CGACTGCGAGGCTCGCGG
66 CGACTGCGAGGCTCGCGG
*
3688 ACACGACACACACGAAGGTACACGAGAAGGACAACGGCTCTCAGCAGTGAGGCTCTCAAAACGGC
1 ACACGACACACACGAAGGTACAC--G-AGGACAACGGCTCTCAGCAGTGAGGCACTCAAAACGGC
3753 CACCGACTGCGAGGCTCGCGG
63 CACCGACTGCGAGGCTCGCGG
*
3774 ACATGACACACACGAAG
1 ACACGACACACACGAAG
3791 ACACAGAGGT
Statistics
Matches: 96, Mismatches: 4, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
83 22 0.23
85 1 0.01
86 73 0.76
ACGTcount: A:0.31, C:0.32, G:0.28, T:0.09
Consensus pattern (83 bp):
ACACGACACACACGAAGGTACACGAGGACAACGGCTCTCAGCAGTGAGGCACTCAAAACGGCCAC
CGACTGCGAGGCTCGCGG
Found at i:3940 original size:24 final size:24
Alignment explanation
Indices: 3908--3985 Score: 122
Period size: 24 Copynumber: 3.2 Consensus size: 24
3898 AGCGAGAGAG
3908 GACACACACAAAGGTAAACAAGAA
1 GACACACACAAAGGTAAACAAGAA
*
3932 GACACACACGAAGGTAAACAAGAA
1 GACACACACAAAGGTAAACAAGAA
*
3956 GACACACA-AGAAGGTAAACGAGAA
1 GACACACACA-AAGGTAAACAAGAA
3980 GACACA
1 GACACA
3986 ATGGTGCTCC
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.55, C:0.21, G:0.21, T:0.04
Consensus pattern (24 bp):
GACACACACAAAGGTAAACAAGAA
Found at i:3956 original size:12 final size:12
Alignment explanation
Indices: 3918--3980 Score: 54
Period size: 12 Copynumber: 5.2 Consensus size: 12
3908 GACACACACA
3918 AAGGTAAACAAG
1 AAGGTAAACAAG
** * *
3930 AAGACACACACG
1 AAGGTAAACAAG
3942 AAGGTAAACAAG
1 AAGGTAAACAAG
** *
3954 AAGACACACAAG
1 AAGGTAAACAAG
*
3966 AAGGTAAACGAG
1 AAGGTAAACAAG
3978 AAG
1 AAG
3981 ACACAATGGT
Statistics
Matches: 36, Mismatches: 15, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.56, C:0.16, G:0.24, T:0.05
Consensus pattern (12 bp):
AAGGTAAACAAG
Found at i:10372 original size:2 final size:2
Alignment explanation
Indices: 10365--10406 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
10355 CAAAGCATGC
10365 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
10406 A
1 A
10407 AAAAAGAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15450 original size:2 final size:2
Alignment explanation
Indices: 15443--15477 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
15433 GTGTCAGCTG
*
15443 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15478 GAGATAAGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:15934 original size:1 final size:1
Alignment explanation
Indices: 15928--15952 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
15918 TTTTAGTGAG
15928 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
15953 GAGGAAACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:17733 original size:17 final size:16
Alignment explanation
Indices: 17693--17735 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
17683 CATGTAATCT
*
17693 TTGATCACCGGTGATC
1 TTGATCACTGGTGATC
17709 TTGTATCACTGGTGATC
1 TTG-ATCACTGGTGATC
17726 TTAGATCACT
1 TT-GATCACT
17736 AGTCATCTGG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 20 0.83
18 1 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (16 bp):
TTGATCACTGGTGATC
Done.