Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009194.1 Corchorus capsularis cultivar CVL-1 contig09215, 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: 12637
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.29
Found at i:623 original size:200 final size:200
Alignment explanation
Indices: 280--653 Score: 705
Period size: 200 Copynumber: 1.9 Consensus size: 200
270 CGTAATGGTT
280 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
1 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
* *
345 TAAATAATATATAATTCAATGTCAAAAAGATTGGAGGGTTTTTCACGCTTCTAATATCGTTTTTC
66 TAAATAATATATAATTCAATGTCAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTTC
410 CATTGTTTTCAAATTAATTTCTAATTAAATCCAAACAAGATTCATAAATAATATATAATTCACGC
131 CATTGTTTTCAAATTAATTTCTAATTAAATCCAAACAAGATTCATAAATAATATATAATTCACGC
475 TTCTA
196 TTCTA
480 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
1 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
545 TAAATAATATATAATTCAAT-TGCAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTT
66 TAAATAATATATAATTCAATGT-CAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTT
*
609 CCATTGTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCA
130 CCATTGTTTTCAAATTAATTTCTAATTAAATCCAAACAAGATTCA
654 GATGCCCATA
Statistics
Matches: 170, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
199 1 0.01
200 169 0.99
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (200 bp):
AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
TAAATAATATATAATTCAATGTCAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTTC
CATTGTTTTCAAATTAATTTCTAATTAAATCCAAACAAGATTCATAAATAATATATAATTCACGC
TTCTA
Found at i:1065 original size:321 final size:321
Alignment explanation
Indices: 480--2971 Score: 2192
Period size: 316 Copynumber: 7.9 Consensus size: 321
470 CACGCTTCTA
* * * *
480 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTC-
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* * * *
544 ATAAATAATATATAATTCAATTG-CAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTT
66 TTAAA-AATATATAATTCAA-CGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTT
* *
608 TCCATTGTTTT-CAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCATAAATACAAA
129 TCCATT-TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAA
* * * **
672 TCGTTAAATCCAATTTGACTGGGATTTGGTTCGAAGAATTTAGAAATTCCAAGGAGTCTTTACGC
193 TCGTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGAAGGAGTCTTTACGC
* *
737 CAAAAATCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTGTTTAACCAAAAACCGTGATGTTT
258 CAAAAATCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
* * * *
801 AGTACACGATTTCAGCTAAAAACTGACCTGGAAATTTTTTTCCCAACTTTTTACCACAATACTCT
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* *
866 TTAAAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGATTCTAATAACGTTTTTC
66 TTAAAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTTTC
* * *
931 CATCTTTTTCCAAA-TAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCTTAAAAACAAATT
131 CAT-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATC
* * ** * ** * * **
995 ATTAAATCAAATTTGACTGGGATTCAACTCGATTAATATAGTTATTTGAAGGAGTCCTTACGTTA
195 GTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGAAGGAGTCTTTACGCCA
* * * * *
1060 AAAATCACGCAAAACTGAGCCGGGGCTCC-GGAATGCGTTTTTAGCCAAAAACCGTGA-----
260 AAAATCATGCAAAACTGAGTCGAGGC-CCTGAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
* * * * * *
1117 CGTACACAATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTC-
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* * * * *
1181 ATAAATAATATATAATTTAATGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
66 TTAAA-AATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTTT
* * * * *
1246 CCATTGTTTT-TAAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCCATAAATAGAAAT
130 CCATT-TTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
* * *
1310 CGTTAAATCCAATTTGACTGGGATTTGGTTCGAAGAATATAAAAATTTCG-AGGAGTCTTTACGC
194 CGTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTT-GAAGGAGTCTTTACGC
* * * *
1374 CGAAAATCATGCAAAACTGAGTCGAGG-TCTAGAAACACATTTTTAGCCAAAAACCGTGATG---
258 CAAAAATCATGCAAAACTGAGTCGAGGCCCT-GAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
* * * * *
1435 -GTAAACGATTTCGGCTAAAAACTGACCTGAAAATTTTTTTCCTAA-TTTTTACTACACTACTCT
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* *
1498 TTAAAAATATATAATTCAACGACAAAAAGATTGAAAGGG-TTTTCATGACTCTAATATCGTTTTT
66 TTAAAAATATATAATTCAACGACAAAAAGATTG-AAGGGTTTTTCACGATTCTAATATCGTTTTT
* * * *
1562 CCATCTTTTTCCAAA-TAATTTCTAATTAAATCTACACAAGATTCAGATACTCGTAAAAACAAAT
130 CCAT-TTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
* * * **
1626 CGTTAAATCGAATTCGACTGGGATTTGAGTC-AATGAATATATTTATTTGAAGGAGTCTTTACGC
194 CGTTAAATCCAATTTGACTGGGATTTGATTCGAA-GAATATAGATATTTGAAGGAGTCTTTACGC
* * * * * * * *
1690 CAAAAATTATGCAAAACTAAGCCGGGGCCCAGGAAA-GCGTTTTTAGCCAAAAACTGTAATGGTT
258 CAAAAATCATGCAAAACTGAGTCGAGGCCC-TGAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
* * * * * * *
1754 AGTACACGATTTCAGTTAAAAACTTACCTGAAAACTTTTTTCTCAATTTTTTGCCACAAAACTCA
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* * * *
1819 TAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGTTTTTTCACGTTTCTAATATCGTTTTT
66 TTAAAAATATATAATTCAACGACAAAAAGATTGAAGGG-TTTTTCACGATTCTAATATCGTTTTT
*
1884 CCATTTTTTTTCAAATTAATTTCTAATTAAATCGAAAC---A---AGAT--T--T---AA-AAAT
130 CCA-TTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
** * * * **
1935 CGTTAAATCCAATTTGGGTGAGATTTGGTTCGAAGAATATAGATATTTCAAGGAGTCTTTACGTA
194 CGTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGAAGGAGTCTTTACGCC
* * * * * * *
2000 AAAAATCATGTAAAACAGAATCGAGACCGTAAAACGCGTTTTTAGCCAAAAACAGTGATGTTT
259 AAAAATCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
* * * *
2063 AGTACACGATTTCAGCTAAAAATTGACCTGAAAATTTTTTTTCCCAATTTTTGACCACAATACTC
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAA-CTTTTTTCCCAATTTTTTACCACAATACTC
* * ** * *
2128 TTTAAAAAGATATAATTCAACCACAAAAAGATTGAAGGGTTTTTCGTGATTTTAATTTCGTTTTT
65 TTTAAAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTTT
*
2193 CCATTTTTTCCCAAA-TAATTTC----T-AAT----A-AA-A--C-GATGCTCGTAAAAA-AAAT
130 CCATTTTTT-CCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAAT
** * * *
2242 CGTTAAATTAAATTTGACTGGGATTTGACTCGATGAATATAGTTATTTGAAGGAGTCTTTACGCC
194 CGTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGAAGGAGTCTTTACGCC
* * *
2307 AAAAATCATGCAAAACTAAGTCGGGGCCCTGGAATAC-C-TTTTTAGCCAAAAACCATGATAGTT
259 AAAAATCATGCAAAACTGAGTCGAGGCCCT-GAA-ACGCGTTTTTAGCCAAAAACCGTGAT-GTT
*
2370 G
321 T
* * ** * * *
2371 A-TACACGATTTCGGCAAAAATTTTGCAAAAATTGA-TTAGAAAGGTTTTTCTACC-ATATTTTG
1 AGTACACGATTTCGGC--------T--AAAAACTGACCT-GAAAACTTTTT-TCCCAATTTTTTA
* **** * * * *
2433 CCACAATATTAAGAAAAAACA-ATAATT-AATTG-CTAAAAATATTGAAAGGG-TTTTCACGCTT
54 CCACAATACTCTTTAAAAATATATAATTCAA-CGAC-AAAAAGATTG-AAGGGTTTTTCACGATT
* * * ** * * *
2494 CGAAAATCTTTTTTCCATTTTTTTTCTGAATTTATTTATATTTAAATCGAAACAAGATTCAGATG
116 CTAATATCGTTTTTCCA--TTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATG
* * * * ** * * * *
2559 CTCCTAAAACCAAATCCTTAAATCTAATGCGGCTGAGATTTGATTAGAAGAATATAGATATTTCA
179 CTCATAAAAACAAATCGTTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGA
** * * * * ** *
2624 AGGAGTCTTTATACTAAAAACCATGCAGAATTGAGAT-GAGGCCCCAAAATGCGTTTTTAGCCAA
244 AGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-TCGAGGCCCTGAAACGCGTTTTTAGCCAA
*
2688 AAATCGTGA-----
308 AAACCGTGATGTTT
* ** * * * *
2697 CGTACACGATTTCGATTAAAACCTGACCTGACAACTTTTTTCTCAATTTTTTGCCACAATACTC-
1 AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
* * * * * * * * * *
2761 ATAAACATTATATGATTCAATGTCAAAATGATTGAAGTG-TTTTCATGCTTCTAATATCGTTTTC
66 TTAAA-AATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTTT
* * * * * * *
2825 CCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAATAAGATTTAGATGCTCGTAAAAGCAAA
130 CC--ATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAA
* * ** * * * * *
2890 TCGATAAATCCAATGTGGTTGGGAATTGACTC-AATGAATATAGATATTTCAAGGAGTTTTTATG
193 TCGTTAAATCCAATTTGACTGGGATTTGATTCGAA-GAATATAGATATTTGAAGGAGTCTTTACG
*
2954 CCAAAAATCATGGAAAAC
257 CCAAAAATCATGCAAAAC
2972 AAAGTCACTT
Statistics
Matches: 1745, Mismatches: 333, Indels: 190
0.77 0.15 0.08
Matches are distributed among these distances:
299 1 0.00
300 4 0.00
302 1 0.00
303 3 0.00
304 2 0.00
307 114 0.07
308 23 0.01
309 160 0.09
310 62 0.04
313 1 0.00
314 4 0.00
315 48 0.03
316 498 0.29
317 261 0.15
318 16 0.01
319 4 0.00
320 45 0.03
321 301 0.17
322 48 0.03
323 21 0.01
326 1 0.00
327 14 0.01
328 1 0.00
330 2 0.00
331 15 0.01
332 94 0.05
333 1 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
AGTACACGATTTCGGCTAAAAACTGACCTGAAAACTTTTTTCCCAATTTTTTACCACAATACTCT
TTAAAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCACGATTCTAATATCGTTTTTC
CATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAAACAAATCG
TTAAATCCAATTTGACTGGGATTTGATTCGAAGAATATAGATATTTGAAGGAGTCTTTACGCCAA
AAATCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTTTTTAGCCAAAAACCGTGATGTTT
Found at i:1774 original size:637 final size:634
Alignment explanation
Indices: 480--2971 Score: 2752
Period size: 637 Copynumber: 3.9 Consensus size: 634
470 CACGCTTCTA
*
480 AGTACACGATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
1 AGTACACGATTTCAGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
* *
545 TAAATAATATATAATTCAATTG-CAAAAAGATTGAAAGGTTTTTCACGCTTCTAATATCGTTTTT
66 TAAAAAATATATAATTCAATTGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
* *
609 CCATTGTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCCCATAAATACAAATC
131 CCATTGTTTTTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCC-TAAA-ACAAATC
* * *
674 GTTAAATCCAATTTGACTGGGATTTGGTTCGAAGAATTTAGAAATTCCAAGGAGTCTTTACGCCA
194 GTTAAATCCAATTTGACTGAGATTTGGTTCGAAGAATATAGAAATTTCAAGGAGTCTTTACGCCA
* * *
739 AAAATCATGCAAAACTGAGTCGAGGCCCTGAAACGCGTGTTTAACCAAAAACCGTGATGTTTAGT
259 AAAATCATGCAAAACTGAGTCGAGGCCCTAAAACGCGTTTTTAGCCAAAAACCGTGATG--T-GT
*
804 ACACGATTTCAGCTAAAAACTGACCTGGAAATTTTTTTCCCAACTTTTTACCACAATACTCTTTA
321 ACACGATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCCCAACTTTTTACCACAATACTCTTTA
* *
869 AAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGATTCTAATAACGTTTTTCCAT
386 AAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGACTCTAATATCGTTTTTCCAT
* * **
934 CTTTTTCCAAATAATTTCTAATTAAATAGAAACAAGATTCAGATGCTCTTAAAAACAAATTATTA
451 CTTTTTCCAAATAATTTCTAATTAAAT-CAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTA
** * * * **
999 AATCAAATTTGACTGGGATTCAACTCGATTAATATAGTTATTTGAAGGAGTCCTTACGTTAAAAA
515 AATCAAATTTGACTGGGATTTGACTCAATGAATATAGTTATTTGAAGGAGTCTTTACGCCAAAAA
* * *
1064 TCACGCAAAACTGAGCCGGGGCTCCGGAATGCGTTTTTAGCCAAAAACCG--TG--
580 TCATGCAAAACTAAGCCGGGGC-CCGGAAAGCGTTTTTAGCCAAAAACCGTATGTT
* *
1116 ACGTACACAATTTCGGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTC
1 A-GTACACGATTTCAGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTC
* *
1181 ATAAATAATATATAATTTAA-TGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT
65 ATAAAAAATATATAATTCAATTGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTT
*
1245 TCCATTGTTTTTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCCATAAATAGAAAT
130 TCCATTGTTTTTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCC-TAAA-ACAAAT
* * *
1310 CGTTAAATCCAATTTGACTGGGATTTGGTTCGAAGAATATAAAAATTTCGAGGAGTCTTTACGCC
193 CGTTAAATCCAATTTGACTGAGATTTGGTTCGAAGAATATAGAAATTTCAAGGAGTCTTTACGCC
* * * *
1375 GAAAATCATGCAAAACTGAGTCGAGG-TCTAGAAACACATTTTTAGCCAAAAACCGTGATG-GTA
258 AAAAATCATGCAAAACTGAGTCGAGGCCCTA-AAACGCGTTTTTAGCCAAAAACCGTGATGTGTA
* * * * *
1438 AACGATTTCGGCTAAAAACTGACCTGAAAATTTTTTTCCTAA-TTTTTACTACACTACTCTTTAA
322 CACGATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCCCAACTTTTTACCACAATACTCTTTAA
1502 AAATATATAATTCAACGACAAAAAGATTGAAAGGG-TTTTCATGACTCTAATATCGTTTTTCCAT
387 AAATATATAATTCAACGACAAAAAGATTG-AAGGGTTTTTCATGACTCTAATATCGTTTTTCCAT
* *
1566 CTTTTTCCAAATAATTTCTAATTAAATCTACACAAGATTCAGATACTCGTAAAAACAAATCGTTA
451 CTTTTTCCAAATAATTTCTAATTAAATC-AAACAAGATTCAGATGCTCGTAAAAACAAATCGTTA
* * * *
1631 AATCGAATTCGACTGGGATTTGAGTCAATGAATATATTTATTTGAAGGAGTCTTTACGCCAAAAA
515 AATCAAATTTGACTGGGATTTGACTCAATGAATATAGTTATTTGAAGGAGTCTTTACGCCAAAAA
* *
1696 TTATGCAAAACTAAGCCGGGGCCCAGGAAAGCGTTTTTAGCCAAAAACTGTAATGGTT
580 TCATGCAAAACTAAGCCGGGGCCC-GGAAAGCGTTTTTAGCCAAAAACCGT-AT-GTT
* * *
1754 AGTACACGATTTCAGTTAAAAACTTACCTGAAAACTTTTTTCTCAATTTTTTGCCACAAAACTCA
1 AGTACACGATTTCAGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
*
1819 TAAAAAATATATAATTCAA-TGCCAAAAAGATTGAAGGGTTTTTTCACGTTTCTAATATCGTTTT
66 TAAAAAATATATAATTCAATTGCCAAAAAGATTGAAGGG-TTTTTCACGCTTCTAATATCGTTTT
* *
1883 TCCATTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGA-T----T----T--AA-AAATC
130 TCCATTGTTTTT-AAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCCTAAAACAAATC
** * **
1936 GTTAAATCCAATTTGGGTGAGATTTGGTTCGAAGAATATAGATATTTCAAGGAGTCTTTACGTAA
194 GTTAAATCCAATTTGACTGAGATTTGGTTCGAAGAATATAGAAATTTCAAGGAGTCTTTACGCCA
* * * * * *
2001 AAAATCATGTAAAACAGAATCGAGACCGTAAAACGCGTTTTTAGCCAAAAACAGTGATGTTTAGT
259 AAAATCATGCAAAACTGAGTCGAGGCCCTAAAACGCGTTTTTAGCCAAAAACCGTGATG--T-GT
*
2066 ACACGATTTCAGCTAAAAATTGACCTGAAAATTTTTTTTCCCAA-TTTTTGACCACAATACTCTT
321 ACACGATTTCAGCTAAAAACTGACCTGAAAA-TTTTTTTCCCAACTTTTT-ACCACAATACTCTT
* * * * * *
2130 TAAAAAGATATAATTCAACCACAAAAAGATTGAAGGGTTTTTCGTGATTTTAATTTCGTTTTTCC
384 TAAAAATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGACTCTAATATCGTTTTTCC
2195 AT-TTTTTCCCAAATAATTTC----T-AAT---A-AA-A--C-GATGCTCGTAAAAA-AAATCGT
449 ATCTTTTT-CCAAATAATTTCTAATTAAATCAAACAAGATTCAGATGCTCGTAAAAACAAATCGT
* *
2245 TAAATTAAATTTGACTGGGATTTGACTCGATGAATATAGTTATTTGAAGGAGTCTTTACGCCAAA
513 TAAATCAAATTTGACTGGGATTTGACTCAATGAATATAGTTATTTGAAGGAGTCTTTACGCCAAA
* * *
2310 AATCATGCAAAACTAAGTCGGGGCCCTGGAATA-CCTTTTTAGCCAAAAACCATGATAGTT
578 AATCATGCAAAACTAAGCCGGGGCCC-GGAA-AGCGTTTTTAGCCAAAAACCGT-AT-GTT
* * * ** * *
2370 -GATACACGATTTCGGCAAAAATTTTGCAAAAATTGA-TTAGAAAGGTTT-TTCTACCATATTTT
1 AG-TACACGATTT---C----A-GTT--AAAAACTGACCT-GAAAACTTTATTCT-CAATTTTTT
* * * * * *
2432 GCCACAATATTAAGAAAAAACA-ATAATT-AATTGCTAAAAATATTGAAAGGG-TTTTCACGCTT
53 GCCACAATACTCATAAAAAATATATAATTCAATTGCCAAAAAGATTG-AAGGGTTTTTCACGCTT
* * * * * * *
2494 CGAAAATCTTTTTTCCATTTTTTTTCTGAATTTATTT-ATATTTAAATCGAAACAAGATTCAGAT
117 CTAATATCGTTTTTCCA-TTGTTTT-TAAATTAATTTCA-AATTAAATCGAAACAAGATTCAGAT
* * ** * * * *
2558 GCTCCTAAAACCAAATCCTTAAATCTAATGCGGCTGAGATTTGATTAGAAGAATATAGATATTTC
179 GC-CCTAAAA-CAAATCGTTAAATCCAATTTGACTGAGATTTGGTTCGAAGAATATAGAAATTTC
** * * * * * *
2623 AAGGAGTCTTTATACTAAAAACCATGCAGAATTGAGAT-GAGGCCCCAAAATGCGTTTTTAGCCA
242 AAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAG-TCGAGGCCCTAAAACGCGTTTTTAGCCA
* * * * * * * *
2687 AAAATCGTGA--CGTACACGATTTC-GATTAAAACCTGACCTGACAACTTTTTTCTCAATTTTTT
306 AAAACCGTGATGTGTACACGATTTCAG-CTAAAAACTGACCTGAAAATTTTTTTCCCAACTTTTT
* * * * * * * *
2749 GCCACAATACTC-ATAAACATTATATGATTCAATGTCAAAATGATTGAAGTG-TTTTCATG-CTT
370 ACCACAATACTCTTTAAA-AATATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGAC-T
* * * * * *
2811 CTAATATCGTTTTCCCTTTTTTTTTCCGAATTAATTTCTAATTAAATCAAAATAAGATTTAGATG
433 CTAATATCGTTTTTCC-ATCTTTTTCC-AAATAATTTCTAATTAAATC-AAACAAGATTCAGATG
* * * * ** * * *
2876 CTCGTAAAAGCAAATCGATAAATCCAATGTGGTTGGGAATTGACTCAATGAATATAGATATTTCA
495 CTCGTAAAAACAAATCGTTAAATCAAATTTGACTGGGATTTGACTCAATGAATATAGTTATTTGA
* * *
2941 AGGAGTTTTTATGCCAAAAATCATGGAAAAC
560 AGGAGTCTTTACGCCAAAAATCATGCAAAAC
2972 AAAGTCACTT
Statistics
Matches: 1590, Mismatches: 187, Indels: 145
0.83 0.10 0.08
Matches are distributed among these distances:
615 1 0.00
616 126 0.08
617 14 0.01
618 1 0.00
619 1 0.00
620 1 0.00
621 2 0.00
622 1 0.00
623 1 0.00
624 28 0.02
625 163 0.10
626 51 0.03
627 2 0.00
629 31 0.02
630 27 0.02
631 81 0.05
632 255 0.16
633 96 0.06
634 47 0.03
635 2 0.00
636 6 0.00
637 391 0.25
638 38 0.02
639 134 0.08
640 1 0.00
643 1 0.00
644 2 0.00
645 1 0.00
648 13 0.01
649 72 0.05
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (634 bp):
AGTACACGATTTCAGTTAAAAACTGACCTGAAAACTTTATTCTCAATTTTTTGCCACAATACTCA
TAAAAAATATATAATTCAATTGCCAAAAAGATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT
CCATTGTTTTTAAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCCCTAAAACAAATCGT
TAAATCCAATTTGACTGAGATTTGGTTCGAAGAATATAGAAATTTCAAGGAGTCTTTACGCCAAA
AATCATGCAAAACTGAGTCGAGGCCCTAAAACGCGTTTTTAGCCAAAAACCGTGATGTGTACACG
ATTTCAGCTAAAAACTGACCTGAAAATTTTTTTCCCAACTTTTTACCACAATACTCTTTAAAAAT
ATATAATTCAACGACAAAAAGATTGAAGGGTTTTTCATGACTCTAATATCGTTTTTCCATCTTTT
TCCAAATAATTTCTAATTAAATCAAACAAGATTCAGATGCTCGTAAAAACAAATCGTTAAATCAA
ATTTGACTGGGATTTGACTCAATGAATATAGTTATTTGAAGGAGTCTTTACGCCAAAAATCATGC
AAAACTAAGCCGGGGCCCGGAAAGCGTTTTTAGCCAAAAACCGTATGTT
Found at i:3527 original size:26 final size:25
Alignment explanation
Indices: 3491--4872 Score: 1401
Period size: 26 Copynumber: 53.8 Consensus size: 25
3481 TACATGACTA
*
3491 CTACTGAATATGCAACTATATGGTTC
1 CTACTGAATATGCAACTATATGG-CC
3517 CTACTGAATATGCAATGCAACTATATGAGCC
1 CTACTG-A-AT---ATGCAACTATATG-GCC
* *
3548 CTACAGAATATGCAACTATATAAGCC
1 CTACTGAATATGCAACTATAT-GGCC
*
3574 TTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
*
3600 CTACTGAATATACAATGCAACTATATGAGCT
1 CTACTG-A-AT---ATGCAACTATATG-GCC
*
3631 CTACAGAATATGCAACTATATGGCCC
1 CTACTGAATATGCAACTATATGG-CC
*
3657 CTACTGAATATGCAACAATATGAG-C
1 CTACTGAATATGCAACTATATG-GCC
*
3682 CTAATGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
* * *
3708 CTACTGAATGTGCAACTATGT-CCC
1 CTACTGAATATGCAACTATATGGCC
*
3732 CTACTGAATATGCAATTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
*
3758 CTACTGAATATGCAATTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
* * *
3784 CTACTGAATATGGAACTATAAAGCCC
1 CTACTGAATATGCAACTAT-ATGGCC
*
3810 CTACTTAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
*
3836 CTAATGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
* *
3862 CTACTGAATATGCAACTATGT-CCC
1 CTACTGAATATGCAACTATATGGCC
* *
3886 CTACTGAAAATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
* *
3912 CTACTGAAAATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
* * *
3938 CTACTGAAAATGCAACAATATGACCC
1 CTACTGAATATGCAACTATATG-GCC
3964 CTACTGAATATGCAACTATATGGCC
1 CTACTGAATATGCAACTATATGGCC
* * * * * *
3989 CTTATTAAATAAGCAATTGTAAGGCCC
1 C-TACTGAATATGCAACTATATGG-CC
*
4016 CTACTGAATATGCAACTCTATGGCCC
1 CTACTGAATATGCAACTATATGG-CC
4042 CTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
4068 CTACTGAATATGCAACTATATGAGCCC
1 CTACTGAATATGCAACTATATG-G-CC
* * * *
4095 CTACAGAAAATGCGACTATATGTCAC
1 CTACTGAATATGCAACTATATGGC-C
* * *
4121 TTACAGAATATGCAACTATATGAACC
1 CTACTGAATATGCAACTATATG-GCC
4147 CTACTGAATATGCAACTATATGGCC
1 CTACTGAATATGCAACTATATGGCC
4172 CATACTGAATATGCAACTATATGGCC
1 C-TACTGAATATGCAACTATATGGCC
*
4198 CTACTGAATATGCAACTATATTAGCC
1 CTACTGAATATGCAACTATA-TGGCC
*
4224 ACTACT---TATGCAACTATATTAGCC
1 -CTACTGAATATGCAACTATA-TGGCC
4248 CTACTGAATATGCAACTATATGGCC
1 CTACTGAATATGCAACTATATGGCC
*
4273 CTTACTGAATATGCAACCATATGAGCC
1 C-TACTGAATATGCAACTATATG-GCC
4300 CTTACTGAATATGCAACTATATGGCC
1 C-TACTGAATATGCAACTATATGGCC
4326 CTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
4352 CTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
*
4378 CTACTGAATATGCAACTATATGTCC
1 CTACTGAATATGCAACTATATGGCC
4403 CTTACTGAATATGCAACTATATGAGCC
1 C-TACTGAATATGCAACTATATG-GCC
4430 CTACTGAATATGCAACTATAT-GCGC
1 CTACTGAATATGCAACTATATGGC-C
* * * *
4455 C-A-T-CA-A--CTA-TAT-GGGTC
1 CTACTGAATATGCAACTATATGGCC
*
4472 CTACTGAATATGCAACTATACGGGCC
1 CTACTGAATATGCAACTATA-TGGCC
*
4498 CTACTGAATATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
*
4524 CTACTGAATATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
4550 CTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
* **
4576 CTACTGAATATGCAAATATATCTCCC
1 CTACTGAATATGCAACTATAT-GGCC
*
4602 CTACTGAATATGCAAATATATGAGCC
1 CTACTGAATATGCAACTATATG-GCC
* * *
4628 TTATTGAATATGCAACTATATGAGTC
1 CTACTGAATATGCAACTATATG-GCC
* * *
4654 CTACTGAATATGGGC-CCTA-CT-G-A
1 CTACTGAATAT--GCAACTATATGGCC
* * * *
4677 ATA-TGCA-A--CTA-TAT-GGGCC
1 CTACTGAATATGCAACTATATGGCC
4696 CTACTGAATATGCAACTATATGGGCC
1 CTACTGAATATGCAACTATAT-GGCC
*
4722 CTACTGAATATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
*
4748 CTACTGAATATGCAACTATATGAGCG
1 CTACTGAATATGCAACTATATG-GCC
*
4774 CTACTAAATATGCAACTATATGGGCC
1 CTACTGAATATGCAACTATAT-GGCC
*
4800 CTACTGAATATGCAATTATATTGGCC
1 CTACTGAATATGCAACTATA-TGGCC
*
4826 CTACTGAATATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATG-GCC
4852 CTACTGAATATGCAACTATAT
1 CTACTGAATATGCAACTATAT
4873 TGCCTTATTG
Statistics
Matches: 1170, Mismatches: 116, Indels: 140
0.82 0.08 0.10
Matches are distributed among these distances:
17 5 0.00
18 6 0.01
19 5 0.00
20 4 0.00
21 4 0.00
22 4 0.00
23 12 0.01
24 69 0.06
25 87 0.07
26 852 0.73
27 69 0.06
28 6 0.01
29 4 0.00
30 2 0.00
31 40 0.03
32 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (25 bp):
CTACTGAATATGCAACTATATGGCC
Found at i:3535 original size:31 final size:31
Alignment explanation
Indices: 3500--3645 Score: 134
Period size: 31 Copynumber: 5.0 Consensus size: 31
3490 ACTACTGAAT
* *
3500 ATGCAACTATATG-GTTCCTACTGAATATGCA
1 ATGCAACTATATGAG-CCCTACAGAATATGCA
3531 ATGCAACTATATGAGCCCTACAG-A-AT---
1 ATGCAACTATATGAGCCCTACAGAATATGCA
* * *
3557 ATGCAACTATATAAGCCTTACTG-A-AT---
1 ATGCAACTATATGAGCCCTACAGAATATGCA
* *
3583 ATGCAACTATATGAGCCCTACTGAATATACA
1 ATGCAACTATATGAGCCCTACAGAATATGCA
*
3614 ATGCAACTATATGAGCTCTACAGAATATGCA
1 ATGCAACTATATGAGCCCTACAGAATATGCA
3645 A
1 A
3646 CTATATGGCC
Statistics
Matches: 99, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
26 44 0.44
27 1 0.01
28 2 0.02
29 2 0.02
30 1 0.01
31 48 0.48
32 1 0.01
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (31 bp):
ATGCAACTATATGAGCCCTACAGAATATGCA
Found at i:3609 original size:52 final size:52
Alignment explanation
Indices: 3491--4872 Score: 1604
Period size: 52 Copynumber: 26.9 Consensus size: 52
3481 TACATGACTA
*
3491 CTACTGAATATGCAACTATATG-GTTCCTACTGAATATGCAATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAG-CCCTACTG-A-AT---ATGCAACTATATGAGCC
* * *
3548 CTACAGAATATGCAACTATATAAGCCTTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* *
3600 CTACTGAATATACAATGCAACTATATGAGCTCTACAGAATATGCAACTATATG-GCCC
1 CTACTG-A-AT---ATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAG-CC
* *
3657 CTACTGAATATGCAACAATATGAG-CCTAATGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* ** *
3708 CTACTGAATGTGCAAC--TATGTCCCCTACTGAATATGCAATTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* * *
3758 CTACTGAATATGCAATTATATGAGCCCTACTGAATATGGAACTATA-AAGCCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAG-CC
* *
3810 CTACTTAATATGCAACTATATGAGCCCTAATGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
** * **
3862 CTACTGAATATGCAAC--TATGTCCCCTACTGAAAATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* ** * * *
3912 CTACTGAAAATGCAACTATATGTCCCCTACTGAAAATGCAACAATATGACCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* * * * * *
3964 CTACTGAATATGCAACTATATG-GCCCTTATTAAATAAGCAATTGTAAG-GCCC
1 CTACTGAATATGCAACTATATGAGCCC-TACTGAATATGCAACTATATGAG-CC
*
4016 CTACTGAATATGCAACTCTATG-GCCCCTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAG-CCCTACTGAATATGCAACTATATGAGCC
* * * *
4068 CTACTGAATATGCAACTATATGAGCCCCTACAGAAAATGCGACTATATG-TCAC
1 CTACTGAATATGCAACTATATGAG-CCCTACTGAATATGCAACTATATGAGC-C
* * *
4121 TTACAGAATATGCAACTATATGAACCCTACTGAATATGCAACTATATG-GCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
*
4172 CATACTGAATATGCAACTATATG-GCCCTACTGAATATGCAACTATATTAGCC
1 C-TACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
*
4224 ACTACT---TATGCAACTATATTAGCCCTACTGAATATGCAACTATATG-GCC
1 -CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
*
4273 CTTACTGAATATGCAACCATATGAGCCCTTACTGAATATGCAACTATATG-GCC
1 C-TACTGAATATGCAACTATATGAGCCC-TACTGAATATGCAACTATATGAGCC
4326 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
*
4378 CTACTGAATATGCAACTATATG-TCCCTTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCC-TACTGAATATGCAACTATATGAGCC
* * *
4430 CTACTGAATATGCAACTATAT--GCGC--C-----AT-CAACTATATGGGTC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* * **
4472 CTACTGAATATGCAACTATACGGGCCCTACTGAATATGCAACTATATGTCCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
**
4524 CTACTGAATATGCAACTATATGTCCCCTACTGAATATGCAACTATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* *** *
4576 CTACTGAATATGCAAATATATCTCCCCTACTGAATATGCAAATATATGAGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* * *
4628 TTATTGAATATGCAACTATATGAGTCCTACTGAATATG---------G-GCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* *
4670 CTACTGAATATGCAACTATATGGGCCCTACTGAATATGCAACTATATGGGCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
** *
4722 CTACTGAATATGCAACTATATGTCCCCTACTGAATATGCAACTATATGAGCG
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
* * *
4774 CTACTAAATATGCAACTATATGGGCCCTACTGAATATGCAATTATATTG-GCC
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATA-TGAGCC
**
4826 CTACTGAATATGCAACTATATGTCCCCTACTGAATATGCAACTATAT
1 CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATAT
4873 TGCCTTATTG
Statistics
Matches: 1151, Mismatches: 121, Indels: 112
0.83 0.09 0.08
Matches are distributed among these distances:
42 69 0.06
43 3 0.00
44 3 0.00
46 1 0.00
48 2 0.00
49 24 0.02
50 106 0.09
51 96 0.08
52 688 0.60
53 80 0.07
54 2 0.00
55 4 0.00
56 3 0.00
57 69 0.06
58 1 0.00
ACGTcount: A:0.34, C:0.23, G:0.15, T:0.28
Consensus pattern (52 bp):
CTACTGAATATGCAACTATATGAGCCCTACTGAATATGCAACTATATGAGCC
Found at i:4672 original size:16 final size:16
Alignment explanation
Indices: 4653--4733 Score: 60
Period size: 16 Copynumber: 5.8 Consensus size: 16
4643 CTATATGAGT
4653 CCTACTGAATATGGGC
1 CCTACTGAATATGGGC
4669 CCTACTGAATAT--G-
1 CCTACTGAATATGGGC
*
4682 -CAACT--ATATGGGC
1 CCTACTGAATATGGGC
4695 CCTACTGAATAT--G-
1 CCTACTGAATATGGGC
*
4708 -CAACT--ATATGGGC
1 CCTACTGAATATGGGC
4721 CCTACTGAATATG
1 CCTACTGAATATG
4734 CAACTATATG
Statistics
Matches: 49, Mismatches: 4, Indels: 24
0.64 0.05 0.31
Matches are distributed among these distances:
10 8 0.16
12 10 0.20
14 10 0.20
16 21 0.43
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (16 bp):
CCTACTGAATATGGGC
Found at i:5093 original size:35 final size:35
Alignment explanation
Indices: 4932--5095 Score: 150
Period size: 35 Copynumber: 4.5 Consensus size: 35
4922 GCCACAAAAG
* * * *
4932 AATGAACCATATGATGCATGATGTATGACCCAAATGAG
1 AATGAACTATATGATGCA-G-TG-ATGACCCTACTGAA
* *
4970 AATGAACTTATATGATAATGGAGCGATGACCCTACTGAA
1 AATGAAC-TATATG---ATGCAGTGATGACCCTACTGAA
* * * * *
5009 ACTTAACTATATGACGGAGTGATGACCCTATTGAA
1 AATGAACTATATGATGCAGTGATGACCCTACTGAA
5044 AATGAACTATATGATGCAGTGATGGA-CCTACTGAA
1 AATGAACTATATGATGCAGTGAT-GACCCTACTGAA
5079 AATGAACTATATGATGC
1 AATGAACTATATGATGC
5096 GGTTATATAG
Statistics
Matches: 105, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
35 63 0.60
36 2 0.02
38 13 0.12
39 21 0.20
40 1 0.01
41 1 0.01
42 4 0.04
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (35 bp):
AATGAACTATATGATGCAGTGATGACCCTACTGAA
Done.