Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016591.1 Corchorus olitorius cultivar O-4 contig16624, 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: 4143
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:1621 original size:333 final size:331
Alignment explanation
Indices: 88--2817 Score: 3957
Period size: 331 Copynumber: 8.3 Consensus size: 331
78 AAAACAGTGA
* *
88 TAAAATTTTGAAAAAATTGACCTGAATG-TTTTTCCTCATTTTATGGCCTAATACTTAT-AAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
151 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTTAATATT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCA-TTTTTTAATATT
* * *
216 TTTTAGAATTAATTTCTATTTAATTAGAAACAAGATTCAGATACTCCTAAAATCAAATACTTGAA
130 TTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAA
*
281 TCCAATGTGGATGGGATTTGGCTGGATGAATAAAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
195 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
*
346 ATGCGAAACTGAGTCGGGGTCCCGGAACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
260 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
411 TTTCGGC
325 TTTCGGC
* *
418 T-AAATTTTGAAAGAATTGACCCGAATGTTTTTTCCTCATTTTCTGGCCAAATACTTATAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
*
482 TATAT-ATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATTTCATTTTTTAATATTT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATATTT
* *
546 TTTAAAATTAATTTCTATTTAAATCGAAACAAGTTTCAGATACTCGTAAAATCAAATACTTGAAT
131 TTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAAT
* **
611 CCAATGTGGATGAGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCACGGCGACAAAAAACA
196 CCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACA
* *
676 TGCGAAACTGAGTCGGGGTCCCTGAACGCGATTTTAGCCAAAAAACCGTGA----T-G---ACGA
261 TGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTAGTACACGA
733 TTTCGGC
325 TTTCGGC
* * **
740 TAAAATTTTGAGAAAATTGACCCGAATGTTTTTTCCTCATTTAATGGCTTAATACTTATAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
* * *
805 TATATAATTCAATGCGAAAAAGATTAAAGTGCTTTCCACGCTTCTAATATCATTTTTTCATATTT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATA-TT
870 TTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAA
130 TTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAA
*
935 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGTGACAAAAAAC
195 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
*
1000 ATGCGAAACTGAGTCGGGGTCCCGGAACACGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
260 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
*
1065 TTTCGAC
325 TTTCGGC
* *
1072 TAAAATTTTGAAAAAATTGACCCGAAT-TGTTTTTCCGT-GTTTTATGGCCTAATACTTATAAAA
1 TAAAATTTTGAAAAAATTGACCCGAATGT-TTTTTCC-TCATTTTATGGCCAAATACTTATAAAA
1135 ATTATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATAG
64 ATTATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATA-
* * * *
1200 TTTTATAGAATTAGTTTCTATTTAACTCGAAACAAGATTCAGATACTCGTAAAATCAAATACCTG
128 TTTTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTG
*
1265 AATCCAATGTGGATGCGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAA
193 AATCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGAC-AAAA
* * * *
1330 AACATGCGAAACTGAGTCGGTGTCCCGAAACTAC-TTTTTAGCTAAAAAACCGTGATGGTTAGTA
257 AACATGCGAAACTGAGTCGGGGTCCCGGAAC-GCGTTTTTAGC-CAAAAACCGTGATGGTTAGTA
1394 CACGATTTCGGC
320 CACGATTTCGGC
*
1406 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTCTGGCCAAATACTTATAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
*
1471 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTAAATATTT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATATTT
* * *
1536 TTTAGAATTAATTTCTACTTAAATCGAAACAAGATTCAGATACTCTTAAAATCACATACTTGAAT
131 TTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAAT
1601 CCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAAC
196 CCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGAC-AAAAAAC
* * *
1666 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTAATGGTGATTACACGA
260 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
1731 TTTCGGC
325 TTTCGGC
* * * * * ** * *
1738 TAAAACTTTGCAAAAACTGATCTGAAAATGTTTTCCTCAATTTT-TGGCGACAATA-TTCATAAA
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTC-ATTTTATGGCCA-AATACTT-AT-AA
* * * * * * ** * *
1801 AAAATATAAAATTCAACGCCAAAACGATGGAAG-GATTTTTTACG-TATTTAATATCGTTTTTCT
62 AAATTATATAATTCAATGCCAAAAAGATTGAAGTG-CTTTCCACGCT-TCTAATATCATTTTT-T
* * * *
1864 --TTTTTTTTCA-AATTTATTTCTCA-TTAAATCGAAACAAGATTCAGATGCTCGTTAAAA-AAA
124 AATATTTTTT-AGAATTAATTTCT-ATTTAAATCGAAACAAGATTCAGATACTCG-TAAAATCAA
* * ** ** * * * **
1924 ATCCTTAAATCCAATGTGGCA-GCTATTTGATTAGATGAATATAGATATTCCAAGAAGTCTTAGC
186 ATACTTGAATCCAATGTGG-ATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGC
* * * *
1988 GCCAAAAATCATGCAAAACTGAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
250 GACAAAAAACATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
*
2053 TAGTACACGATTTCTGC
315 TAGTACACGATTTCGGC
* *
2070 TAAAATTTTGAAAAAATTGACCCGAAAGTTTTTTCCTCAATTTATGGCCAAATACTTATAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
* * * * ** *
2135 TATATAATTGAATGCCAAAAAGGTTGAAG-GATTTCCACTCTTCTAATATCATTTTAAAAATACT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTT-TTAATATT
* *
2199 TTTGAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAACTACTTGAA
130 TTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAA
* * *
2264 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGAAATCTCAAGGAGTCTAGGCGACAAAAAAC
195 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
* * * *
2329 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGTCAAAAATCGTGTTGATTAGTACACGA
260 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
*
2394 TTTCGGT
325 TTTCGGC
* * * * *
2401 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTTCTTAATTTCTGGCCAAATACTTTTAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
* * *
2466 TAT-TAATTCAATGCCAAAAAGGTTGAAGGGCTTTCCACGCTTCTAATAGCATTTTTTAAATATT
66 TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTT-AATATT
* * * * *
2530 TTTTTGAATTAATTTCTACTTAAATCGAAACAAGATTCAGGTACTCTTAAAATCACATACTTGAA
130 TTTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAA
* * *
2595 TTCAATGTGGATGGGATTTGACTTGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
195 TCCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAAC
*
2660 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTGTTTAGCCAAAAACCGTGATGGTTAGTACACGA
260 ATGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
2725 TTTCGGC
325 TTTCGGC
* *
2732 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCAATTTCTGGCCAAATACTTATAAAAAT
1 TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
2797 TATATAATTCAATGCCAAAAA
66 TATATAATTCAATGCCAAAAA
2818 CCGTGATGGT
Statistics
Matches: 2147, Mismatches: 207, Indels: 90
0.88 0.08 0.04
Matches are distributed among these distances:
322 12 0.01
323 62 0.03
324 63 0.03
325 164 0.08
326 1 0.00
328 1 0.00
329 212 0.10
330 147 0.07
331 524 0.24
332 439 0.20
333 312 0.15
334 209 0.10
335 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (331 bp):
TAAAATTTTGAAAAAATTGACCCGAATGTTTTTTCCTCATTTTATGGCCAAATACTTATAAAAAT
TATATAATTCAATGCCAAAAAGATTGAAGTGCTTTCCACGCTTCTAATATCATTTTTTAATATTT
TTTAGAATTAATTTCTATTTAAATCGAAACAAGATTCAGATACTCGTAAAATCAAATACTTGAAT
CCAATGTGGATGGGATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACA
TGCGAAACTGAGTCGGGGTCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
TTCGGC
Found at i:2899 original size:113 final size:113
Alignment explanation
Indices: 2697--2913 Score: 305
Period size: 113 Copynumber: 1.9 Consensus size: 113
2687 CGCGTGTTTA
* * **
2697 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAATTGACCCGAATGTT
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAATGAA
* *
2762 TTTTCCTCAATTTCTGGCCAAATACT-TATAAAAATTATATAATTCAAT
66 ATTTCCTCAATTTCTGGCCAAATACTCT-TAAAAAATATATAATTCAAT
* * *
2810 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGCAAAAACTGATCTGAA-GAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAATGAA
2874 ATTTCCTCAAATTT-TGGCCACAATACTCTTAAAAAATATA
66 ATTTCCTC-AATTTCTGGCCA-AATACTCTTAAAAAATATA
2914 AAATATAACG
Statistics
Matches: 92, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
112 14 0.15
113 77 0.84
114 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (113 bp):
GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAATGAA
ATTTCCTCAATTTCTGGCCAAATACTCTTAAAAAATATATAATTCAAT
Found at i:3589 original size:773 final size:773
Alignment explanation
Indices: 2035--3589 Score: 2051
Period size: 773 Copynumber: 2.0 Consensus size: 773
2025 CGCGTTTTTA
* * * **
2035 GCCAAAAACCGTGATGGTTAGTACACGATTTCTGCTAAAATTTTGAAAAAATTGACCCGAAAGTT
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAAAGAA
* * * * * *
2100 TTTTCCTCAATTTATGGCCAAATACTTATAAAAATTATATAATTGAATGCCAAAAAGGTTGAAGG
66 ATTTCCTCAATTTATGGCCAAATACTTATAAAAAATATAAAATTGAACGCCAAAAAGATGGAAGG
* * *
2165 ATTTCCACTCTTCTAATATCATTTTAAAAATACTTTTGAGAATTAATTTCTATTTAAATCGAAAC
131 ATTTCCACTATTCTAATATCATTTT-AAAATACTTTTCAGAATTAATTTCTATTTAAATAGAAAC
* * * * *
2230 AAGATTCAGATACTCGTAAAATCAACTACTTGAATCCAATGTGGATGGGATTTGGCTGGATGAAT
195 AAGATTCAGATACTCGTAAAATAAAATACTTGAATCCAATGTGGATGCGATTTGACTAGATGAAT
* * * * *
2295 ATAGAAATCTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGTCGGGGTCCCGGAACGCG
260 ATAGAAATCTCAAGAAGTCTAGGCGACAAAAAACATGCAAAACTAAGCCGGGGCCCCGGAACGCG
* *
2360 TTTTTAGTCAAAAATCGTGTTGATTAGTACACGATTTCGGTTAAAATTTTGAAAAAATTGACCCG
325 TTTTTAGTCAAAAATCG-GTTGATCAGTACACGATTTCGGATAAAATTTTGAAAAAATTGACCCG
* * * **
2425 AATGTTTTTTTCTTAATTTCTGGCCAAATACTTTTAAAAATTATTAATTCAATGCCAAAAAGGTT
389 AAAGTTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATTAATTCAATGCCAAAAAGGTT
* *
2490 GAAGGGCTTTCCACGCTTCTAATAGCATTTTTTAAATATTTTTTTGAATTAATTTCTACTTAAAT
454 GAAGGGCTTTCCACGCTTCTAATAGCATTTTTTAAATATTTTTTTGAATTAATATATACTTAAAT
* * * * *
2555 CGAAACAAGATTCAGGTACTCTTAAAATCACATACTTGAATTCAATGTGGATGGGATTTGACTTG
519 CGAAACAAGATTCAGATACTCGTAAAATCACACACTTGAATCCAATGTGGATGGGATTTGACTGG
* * *
2620 ATGAATATAGATATTTCAAGGAGTCTGGGCGACAAAAAACATGCGAAACTGAGTCGGGGTCCCGG
584 ATGAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGTCAGGGTCCCAG
* * *
2685 AACGCGTGTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAAAAAATT
649 AACGCGTGTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGAAAAAACT
** * * * *
2750 GACCCGAATGTTTTTTCCTCAATTTCTGGCCAAATACTTATAAAAATTATATAATTCAAT
714 GACCCGAAAATTTTTTCCTCAATTTATGGCCAAATACTCATAAAAATTATAAAATTCAAC
* * *
2810 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGCAAAAACTGATCTG-AAGAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAAAGAA
*
2874 ATTTCCTCAAATTT-TGGCCACAATACTCT-TAAAAAATATAAAATAT-AACGCCAAAACGATGG
66 ATTTCCTC-AATTTATGGCCA-AATACT-TATAAAAAATATAAAAT-TGAACGCCAAAAAGATGG
* * *** ** *
2936 AAGGATTTTTCACGTATT-TAATATCGTTTT-TGTTTTTTCTTCA-AATTTATTTCTCA-TTAAA
127 AAGGA-TTTCCAC-TATTCTAATATCATTTTAAAATACTT-TTCAGAATTAATTTCT-ATTTAAA
** * * * *
2997 TAGAAACAAGATTCAGATGTTCGTTAAAA-AAAATCCTTGAATCCAATGTGGCTGCTATTTGATT
188 TAGAAACAAGATTCAGATACTCG-TAAAATAAAATACTTGAATCCAATGTGGATGCGATTTGACT
** * * * *
3061 AGATGAATATAGATGT-TCCAATAAGTTTTA-GCGCCAAAAATCATGCAAAACTAAGCCGGGGCC
252 AGATGAATATAGAAATCT-CAAGAAG-TCTAGGCGACAAAAAACATGCAAAACTAAGCCGGGGCC
* *
3124 CCGGAACGCGTTTTTAGTCCAACATC-G-TGATCAGTACACGATTTCGGATAAAATTTTGAAAAA
315 CCGGAACGCGTTTTTAGTCAAAAATCGGTTGATCAGTACACGATTTCGGATAAAATTTTGAAAAA
*
3187 ATTGACCCGAAAGTTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATATAATTCTATGC
380 ATTGACCCGAAAGTTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTAT-TAATTCAATGC
* * *
3252 CAAAAAAGTTTGAAGGGCTTTCTACGCTTCTAATATCATTTTTTAAATATTTTTTTGAATTAATA
444 C-AAAAAGGTTGAAGGGCTTTCCACGCTTCTAATAGCATTTTTTAAATATTTTTTTGAATTAATA
* * *
3317 TATATTTAAATCGAAATAAGATTCAGATACTCGTACAATCACACACTTGAATCCAATGTGGATGG
508 TATACTTAAATCGAAACAAGATTCAGATACTCGTAAAATCACACACTTGAATCCAATGTGGATGG
*
3382 GATTTGGCTGGATGAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGT
573 GATTTGACTGGATGAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGT
* *
3447 CAGGGTCCCAGAACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGACTAAAACT
638 CAGGGTCCCAGAACGCGTGTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACT
* * *
3512 TTGCAAAAACTGATCTGAAAAATTTTTT-CTCAATTTATGGCCACAATACTCATAAAAA-TATAA
703 TTGAAAAAACTGACCCG-AAAATTTTTTCCTCAATTTATGGCCA-AATACTCATAAAAATTATAA
3575 AATTCAAC
766 AATTCAAC
3583 GCCAAAA
1 GCCAAAA
3590 CGATGGAAGG
Statistics
Matches: 676, Mismatches: 89, Indels: 32
0.85 0.11 0.04
Matches are distributed among these distances:
771 82 0.12
772 12 0.02
773 283 0.42
774 171 0.25
775 106 0.16
776 19 0.03
777 3 0.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (773 bp):
GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAACTGACCCGAAAGAA
ATTTCCTCAATTTATGGCCAAATACTTATAAAAAATATAAAATTGAACGCCAAAAAGATGGAAGG
ATTTCCACTATTCTAATATCATTTTAAAATACTTTTCAGAATTAATTTCTATTTAAATAGAAACA
AGATTCAGATACTCGTAAAATAAAATACTTGAATCCAATGTGGATGCGATTTGACTAGATGAATA
TAGAAATCTCAAGAAGTCTAGGCGACAAAAAACATGCAAAACTAAGCCGGGGCCCCGGAACGCGT
TTTTAGTCAAAAATCGGTTGATCAGTACACGATTTCGGATAAAATTTTGAAAAAATTGACCCGAA
AGTTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATTAATTCAATGCCAAAAAGGTTGA
AGGGCTTTCCACGCTTCTAATAGCATTTTTTAAATATTTTTTTGAATTAATATATACTTAAATCG
AAACAAGATTCAGATACTCGTAAAATCACACACTTGAATCCAATGTGGATGGGATTTGACTGGAT
GAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGTCAGGGTCCCAGAA
CGCGTGTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGAAAAAACTGA
CCCGAAAATTTTTTCCTCAATTTATGGCCAAATACTCATAAAAATTATAAAATTCAAC
Found at i:4088 original size:646 final size:656
Alignment explanation
Indices: 2810--4143 Score: 1961
Period size: 646 Copynumber: 2.0 Consensus size: 656
2800 ATAATTCAAT
*
2810 GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGCAAAAACTGATCTGAAGAAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAAACTGATCTGAAGAAA
*
2875 TTTCCTCAAATTTTGGCCACAATACTCTTAAAAAATATAAAATATAACGCCAAAACGATGGAAGG
66 TTTCCTCAAATTTTGGCCACAATACTCATAAAAAATATAAAATATAACGCCAAAACGATGGAAGG
*
2940 ATTTTTCACGTATTTAATATCGTTTTTGTTTTTTCTTCAAATTTATTTCTCATTAAATAGAAACA
131 ATTTTTCACGTATTTAATATCATTTTTGTTTTTTCTTCAAATTTATTTCTCATTAAATAGAAACA
* * *
3005 AGATTCAGATGTTCGTTAAAAAAAATCCTTGAATCCAATGTGGCTGCTATTTGATTAGATGAATA
196 AGATTCAGATGCTCGATAAAAAAAATCCTTAAATCCAATGTGGCTGCTATTTGATTAGATGAATA
* * * *
3070 TAGATGTTCCAATAAGTTTTAGCGCCAAAAATCATGCAAAACTAAGCCGGGGCCCCGGAACGCGT
261 TAGATATTCCAAGAAGTTTTAGCGACAAAAATCATGCAAAACTAAGCCGGGGCCCCGGAACGCAT
*
3135 TTTTAGTCCAACATCGTGATCAGTACACGATTTCGGATAAAATTTTGAAAAAATTGACCCGAAAG
326 TTTTAGTCCAACA---TGA-CAGTACACGATTTCGGATAAAATTTTCAAAAAATTGACCCGAAAG
* *
3200 TTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATATAATTCTATGCCAAAAAAGTTTGA
387 TTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATATAATTCAATGCCAAAAAAGGTTGA
* * *
3265 AGGGCTTTCTACGCTTCTAATATCATTTTTTAAATATTTTTTTGAATTAATATATATTTAAATCG
452 AGGGATTTCCACGCTTCTAATATCATTTTTTAAACATTTTTTTGAATTAATATATATTTAAATCG
* * * ** *
3330 AAATAAGATTCAGATACTCGTACAATCACACACTTGAATCCAATGTGGATGGGATTTGGCTGGAT
517 AAACAAGATTCAGATACTCGTAAAATCAAACACTTGAATCCAATAAGGATGGGATTCGGCTGGAT
*
3395 GAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATGCGAAACTGAGTCAGGGTCCCAGAA
582 GAATATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATACGAAACTGAGTCAGGGTCCCAGAA
*
3460 CGCGTTTTTA
647 CGCGTTTTGA
*
3470 GCCAAAAATCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAAACTGATCTGAA-AAA
1 GCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAAACTGATCTGAAGAAA
*
3534 TTTTTTCTC-AATTTATGGCCACAATACTCAT-AAAAATATAAAAT-TCAACGCCAAAACGATGG
66 --TTTCCTCAAATTT-TGGCCACAATACTCATAAAAAATATAAAATAT-AACGCCAAAACGATGG
* *
3596 AAGGATTTTTCACGTATTTAATATCATTCTTCTGTTTTTTTTTTCAGATTTATTTCTCATTAAAT
127 AAGGATTTTTCACGTATTTAATATCATT-TT-TG-TTTTTTCTTCAAATTTATTTCTCATTAAAT
* * *
3661 CGAACCAAGATTTAGATGCTCGAT-AAAAAAATCCTTAAATCCAATGTGGCTGCTATTTGATTAG
189 AGAAACAAGATTCAGATGCTCGATAAAAAAAATCCTTAAATCCAATGTGGCTGCTATTTGATTAG
* * *
3725 ATGAATATAGATATTTCAAGAA-TTCTTAGCGACAAAAATCATGCAAAACTGAGTCGGGGCCCCG
254 ATGAATATAGATATTCCAAGAAGTT-TTAGCGACAAAAATCATGCAAAACTAAGCCGGGGCCCCG
3789 GAACGCATTTTTAG-CC-A-A-GA-A-TACACGATTTC-GACTAAAATTTTCAAAAAATTGACCC
318 GAACGCATTTTTAGTCCAACATGACAGTACACGATTTCGGA-TAAAATTTTCAAAAAATTGACCC
* * * *
3847 GAAAGTTTTTTCCTTAATTT-TGGTCAAATACTTAT-AAAATTAT-TAATTCAATGCC-AAAAAG
382 GAAAGTTTTTTACTCAATTTCTGGCCAAATACTCATAAAAATTATATAATTCAATGCCAAAAAAG
* * * *
3908 GTTGAA-GGATTTCCACGTTTCTAATATCATTTTTT-AACATTTTTTTGAATTAATTTCTTTTTA
447 GTTGAAGGGATTTCCACGCTTCTAATATCATTTTTTAAACATTTTTTTGAATTAATATATATTTA
* *
3971 AATCGAAACAAGATTTAGATACTCGTAAAATCAAATACTTGAATCCAATAAGGATGGGATTCGGC
512 AATCGAAACAAGATTCAGATACTCGTAAAATCAAACACTTGAATCCAATAAGGATGGGATTCGGC
*
4036 TGGATGAATATAGATATTTCAAGGAGTCTAGGCGAGC-AAAAACATACGAAACTGAGTCGGGGTC
577 TGGATGAATATAGATATTTCAAGGAGTCTAGGCGA-CAAAAAACATACGAAACTGAGTCAGGGTC
*
4100 CCGGAACGCGTTTTGA
641 CCAGAACGCGTTTTGA
*
4116 GCGAAAAACCGTGATGGTGTTAGTACAC
1 GCCAAAAACCGTGAT-G-GTTAGTACAC
Statistics
Matches: 614, Mismatches: 48, Indels: 36
0.88 0.07 0.05
Matches are distributed among these distances:
646 168 0.27
647 28 0.05
648 21 0.03
649 11 0.02
650 8 0.01
651 15 0.02
652 51 0.08
653 1 0.00
655 2 0.00
659 5 0.01
660 121 0.20
661 27 0.04
662 109 0.18
663 47 0.08
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.32
Consensus pattern (656 bp):
GCCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAACTTTGCAAAAACTGATCTGAAGAAA
TTTCCTCAAATTTTGGCCACAATACTCATAAAAAATATAAAATATAACGCCAAAACGATGGAAGG
ATTTTTCACGTATTTAATATCATTTTTGTTTTTTCTTCAAATTTATTTCTCATTAAATAGAAACA
AGATTCAGATGCTCGATAAAAAAAATCCTTAAATCCAATGTGGCTGCTATTTGATTAGATGAATA
TAGATATTCCAAGAAGTTTTAGCGACAAAAATCATGCAAAACTAAGCCGGGGCCCCGGAACGCAT
TTTTAGTCCAACATGACAGTACACGATTTCGGATAAAATTTTCAAAAAATTGACCCGAAAGTTTT
TTACTCAATTTCTGGCCAAATACTCATAAAAATTATATAATTCAATGCCAAAAAAGGTTGAAGGG
ATTTCCACGCTTCTAATATCATTTTTTAAACATTTTTTTGAATTAATATATATTTAAATCGAAAC
AAGATTCAGATACTCGTAAAATCAAACACTTGAATCCAATAAGGATGGGATTCGGCTGGATGAAT
ATAGATATTTCAAGGAGTCTAGGCGACAAAAAACATACGAAACTGAGTCAGGGTCCCAGAACGCG
TTTTGA
Done.