Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011769.1 Corchorus olitorius cultivar O-4 contig11802, 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: 3441
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Found at i:478 original size:154 final size:154
Alignment explanation
Indices: 8--3064 Score: 4371
Period size: 154 Copynumber: 19.9 Consensus size: 154
1 CAAATAA
* *
8 CTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAAGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * *
73 AAAAGCCTTGAGGTTTACCAAATCGAAGACGATTCAAAATGTACACTAATAGGCCCCGATAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCC
*
138 CAAAATAACAAGTGATCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* * *
163 CTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGTCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* ** *
228 AAAAGCATTCGAGGATTGCCAAAATCGAAGACGATTCAAAACGTCACTAATGGGTCCCGATAGGC
66 AAAAGCATT-GAGGTTTGCC-AAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
293 CCAAAATAACAAGTGTTCCAAATGAG
129 CCAAAATAACAAGTGTTCCAAATGAG
319 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
384 AAAAGCATTGAGAG-TTGCGAAATCGGAGACGATTCAAAACGGAACTAATGGGCCCCGATAGACC
66 AAAAGCATTGAG-GTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
448 CAAAATAACAAGTGTTACAAATTAG
130 CAAAATAACAAGTGTTCCAAATGAG
*
473 CTAAAAACTTCACAGTGGACTAATCTCACCATAATGATTATAGTTAGGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* *
538 AAAAGCATTGAGGTTTGCCAATTCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGACCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* *
603 AAAATAACAAGTGTTACAAATTAG
131 AAAATAACAAGTGTTCCAAATGAG
627 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * ** *
692 AAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* * *
757 AAAATAACAATTGTTCTAAAAGAG
131 AAAATAACAAGTGTTCCAAATGAG
* * *
781 CGAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
** * *
846 AAAAGCATTTTGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTTATGGGCCTCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
911 AAAATAACAAGTGTTCCAAATGAG
131 AAAATAACAAGTGTTCCAAATGAG
* *
935 TTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* *
1000 GAAAGCATTGAGGTTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
*
1065 AAAATAACAAGTGTTCCAAATTAG
131 AAAATAACAAGTGTTCCAAATGAG
* * *
1089 TTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAA
* * *
1153 GAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAACAGAACTAAGGGGCCCCGATAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
1218 CAAAATAACAAGTGTTCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* * *
1243 TTAAAAACCTCACAGTGGACT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
** * * * * *
1307 AAAAGTTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGTACTAATGAGCCCCGAAAGACCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* *
1372 AAAATAACAACTGTTCCAAATCAG
131 AAAATAACAAGTGTTCCAAATGAG
* * * * * * *
1396 CTAAAAATTTCACAGTGGACAAATCTTAGCAAAATGATTATAGTTAGGCCATATATAATGGATAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * ** *
1461 AAAAGCTTTTAGGTTTGCCAAATCGAA-ATATATTCAAAACGGAACTAATGGGCCCCGAAAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
*
1525 CAAAATAACAAGTGTTCCAAATCAG
130 CAAAATAACAAGTGTTCCAAATGAG
* * * *
1550 CTAAAAATTTCACAGTGGACTAATCTTAGCAAAATGATTATAGTTAGGCCATAAATAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * *
1615 AAAAGCTTTTAGTTTTGCCAAATCGAA-ATCTATTCAAAACGGAACTAATGGG-CCCGAAAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
1678 CAAAATAACAAGTGTTCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* *
1703 CTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGATA
1 CTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * * * *
1767 GAAAAGCTTTGAGATTTGCCAAATCGAAGCCGATTCAAAACGGTACTAATGAGCCCCGAAAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
1832 TAAAATAACAAGTGTTCCAAATCAG
130 CAAAATAACAAGTGTTCCAAATGAG
* * *
1857 CTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATCATAGTTAGGCCATAAACAATGGAATG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* ** *
1922 AAAA-CTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
1986 AAAATAACAAGTGTTCCAAATGAG
131 AAAATAACAAGTGTTCCAAATGAG
* * * *
2010 CTAAGAACTGCACAGTGGACTAATCTCATCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAA
* * ** *
2074 GAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAACGTCACTAATGGGCCCAGATAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
2139 CAAAATAACAAGTGTTCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* ** *
2164 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTGTAGTTAGTTCATAAATAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
2229 AAAAGCTTTAAGGTTTGCCACATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
*
2294 AAAATAACAAGTGTACCAAATGAG
131 AAAATAACAAGTGTTCCAAATGAG
* * * *
2318 CTAAGAACATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAA
* * * * ** *
2382 -AAAAACTTTGAGGTTAGCCAAATTGAAGGTGATTCAAAACGGAACTAATAGG-CCCGATAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
2445 CAAAATAACAACTGTTCCGAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* *
2470 TTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGTAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * ** *
2535 AAAAGCCTAGAGGTTTGCCAAATCGAAGACGATTCAAAATGTCAGTAATGGGCCCCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* *
2600 AAAAT-AGAAGTGATCCAAATGAG
131 AAAATAACAAGTGTTCCAAATGAG
* *
2623 CTAAAAACTTCACAATGGACTAATCTCACC-AAATTATTATAGTTAGGGCCATAAACAATGGAAA
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTA-GGCCATAAACAATGGAAA
* * * * * *
2687 AAAAAGCATCGAGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
2752 TAAAATAACAAGGGTTCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* * * *
2777 CTAAAAACTTCATAGTGGATTAATCTCACCAAAATGATTATAGTTAGGCCATCAACAATGTAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
2842 AAAAGCATTGAGGTTTCCCAAATCGAAGACGGTTCAAAAC-GACACTAATGGGCCCCGATAGGAC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCC
*
2906 CAAAATAACAAGTATTCCAAATGAG
130 CAAAATAACAAGTGTTCCAAATGAG
* *
2931 CAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAACG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * ** *
2996 AAAAGCATTGAGGGTTGTCAAATTGAAGAGGATTCAAAAACGTCACAAATGGGCCCCGATAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAACGGAACTAATGGGCCCCGATAGGCC
3061 CAAA
130 CAAA
3065 GGGTTGCCAA
Statistics
Matches: 2617, Mismatches: 260, Indels: 50
0.89 0.09 0.02
Matches are distributed among these distances:
151 1 0.00
152 105 0.04
153 611 0.23
154 1635 0.62
155 120 0.05
156 123 0.05
157 22 0.01
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
AAAATAACAAGTGTTCCAAATGAG
Found at i:1526 original size:461 final size:462
Alignment explanation
Indices: 8--3064 Score: 4429
Period size: 461 Copynumber: 6.6 Consensus size: 462
1 CAAATAA
* *
8 CTAAAAACTTCATAGTGGACTAATCTCACCAAAATGATTATAGTTAAGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * * * *
73 AAAAGCCTTGAGGTTTACCAAATCGAAGACGATTCAAAATGTACACTAATAGGCCCCGATAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCC
* * *
138 CAAAATAACAAGTGATCCAAATGAGCTAAGAACTTCACAGTGGACTAATCTCACCAAATTGATTA
130 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* *
203 TAGTTAGTCCATAAACAATGGAAAGAAAAGCATTCGAGGATTGCCAAAATCGAAGACGATTCAAA
195 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GAGGTTTGCC-AAATCGAAGACGATTCAAA
*
268 ACGTCACTAATGGGTCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
258 ACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACA
*
333 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGAG
323 GTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAG-G
* * * *
398 -TTGCGAAATCGGAGACGATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAACAAGTG
387 TTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
* *
462 TTACAAATTAG
452 TTCCAAATGAG
*
473 CTAAAAACTTCACAGTGGACTAATCTCACCATAATGATTATAGTTAGGCCATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* *
538 AAAAGCATTGAGGTTTGCCAATTCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGACCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* *
603 AAAATAACAAGTGTTACAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
131 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
668 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTTAGGGTTGCCAAATCGAAGACGATTCAAAACG
196 AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
* * * * * *
733 TCACTAATGGACCCCGATAGGCCCAAAATAACAATTGTTCTAAAAGAGCGAAAAACTTCATAGTG
261 TCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
* *
798 GACTAATCTCACCAAAATGATTATAGTTAGGGCATAAACAATGGAAAGAAAAGCATTT-TGGTTT
326 GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-TTTGAGGTTT
* * *
862 GCCAAATCGAAGACGATTCAAAACGGAACTTATGGGCCTCGATAGGCCCAAAATAACAAGTGTTC
390 GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTC
927 CAAATGAG
455 CAAATGAG
* *
935 TTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCTATAAACAATGGAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* *
1000 GAAAGCATTGAGGTTTGCCAAATCGATGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* * *
1065 AAAATAACAAGTGTTCCAAATTAGTTAAAAACTTCACAGTGTACTAATCTCACCAAAATGATTAT
131 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* *
1130 AGTTAGGCCATAAACAACT-TAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGATGATTCAAAAC
196 AGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * * *
1194 AG-AACTAAGGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACCTCACAG
260 -GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* *
1258 TGGACT-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGATAGAAAAGTTTTGAGGTT
324 TGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTT
* * * * *
1322 TGCCAAATCGAAGTCGATTCAAAACGGTACTAATGAGCCCCGAAAGACCCAAAATAACAACTGTT
389 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTT
*
1387 CCAAATCAG
454 CCAAATGAG
* * * * * * *
1396 CTAAAAATTTCACAGTGGACAAATCTTAGCAAAATGATTATAGTTAGGCCATATATAATGGATAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * ** *
1461 AAAAGCTTTTAGGTTTGCCAAATCGAA-ATATATTCAAAACGGAACTAATGGGCCCCGAAAGGCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * * *
1525 CAAAATAACAAGTGTTCCAAATCAGCTAAAAATTTCACAGTGGACTAATCTTAGCAAAATGATTA
130 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * * * *
1590 TAGTTAGGCCATAAATAATGGAAAGAAAAGCTTTTAGTTTTGCCAAATCGAA-ATCTATTCAAAA
195 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGA-CGATTCAAAA
** *
1654 CGGAACTAATGGG-CCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
259 CGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAG
* * *
1718 TGGAC-ATATCTCACCAAAATTATTATAGTTAGGCCATAAACAATGGATAGAAAAGCTTTGAGAT
324 TGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGT
* * * *
1782 TTGCCAAATCGAAGCCGATTCAAAACGGTACTAATGAGCCCCGAAAGGCCTAAAATAACAAGTGT
388 TTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGT
*
1847 TCCAAATCAG
453 TCCAAATGAG
* * *
1857 CTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATCATAGTTAGGCCATAAACAATGGAATG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* ** *
1922 AAAA-CTTTGAGGTTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCGGATAGGCCC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
* * *
1986 AAAATAACAAGTGTTCCAAATGAGCTAAGAACTGCACAGTGGACTAATCTCATCAAAATGATTAT
131 AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
* * *
2051 AGTTAGGCCATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAAACGATTCAAAAC
196 AGTTAGGCCATAAACAA-TGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
*
2115 GTCACTAATGGGCCCAGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
260 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
* ** * *
2180 GGACTAATCTCACCAAAATGATTGTAGTTAGTTCATAAATAATGGAAAGAAAAGCTTTAAGGTTT
325 GGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTT
* * *
2245 GCCACATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTAC
390 GCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTC
2310 CAAATGAG
455 CAAATGAG
* * * *
2318 CTAAGAACATCATAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAACT-TAAA
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAA
* * * * ** *
2382 -AAAAACTTTGAGGTTAGCCAAATTGAAGGTGATTCAAAACGGAACTAATAGG-CCCGATAGGCC
65 GAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * *
2445 CAAAATAACAACTGTTCCGAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
130 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * * *
2510 TAGTTAGGCCATAAACAATGGTAAGAAAAGCCTAGAGGTTTGCCAAATCGAAGACGATTCAAAAT
195 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAAC
* * * *
2575 GTCAGTAATGGGCCCCGATAGGCCCAAAAT-AGAAGTGATCCAAATGAGCTAAAAACTTCACAAT
260 GTCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGT
* * * * *
2639 GGACTAATCTCACC-AAATTATTATAGTTAGGGCCATAAACAATGGAAAAAAAAGCATCGAGGGT
325 GGACTAATCTCACCAAAATGATTATAGTTA-GGCCATAAACAATGGAAAGAAAAGCTTTGAGGTT
* * * *
2703 TGCCAGATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAAGGCCTAAAATAACAAGGGTT
389 TGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTT
2768 CCAAATGAG
454 CCAAATGAG
* * * *
2777 CTAAAAACTTCATAGTGGATTAATCTCACCAAAATGATTATAGTTAGGCCATCAACAATGTAAAG
1 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
* * *
2842 AAAAGCATTGAGGTTTCCCAAATCGAAGACGGTTCAAAAC-GACACTAATGGGCCCCGATAGGAC
66 AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGA-ACTAATGGGCCCCGATAGGCC
* *
2906 CAAAATAACAAGTATTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
130 CAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * * * *
2971 TAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGGGTTGTCAAATTGAAGAGGATTCAAAAA
195 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTC-AAAA
*
3036 CGTCACAAATGGGCCCCGATAGGCCCAAA
259 CGTCACTAATGGGCCCCGATAGGCCCAAA
3065 GGGTTGCCAA
Statistics
Matches: 2329, Mismatches: 238, Indels: 53
0.89 0.09 0.02
Matches are distributed among these distances:
458 14 0.01
459 200 0.09
460 433 0.19
461 923 0.40
462 535 0.23
463 12 0.01
464 112 0.05
465 100 0.04
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (462 bp):
CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
AAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCC
AAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
AGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACG
TCACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTG
GACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTTGAGGTTTG
CCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCC
AAATGAG
Found at i:3120 original size:57 final size:58
Alignment explanation
Indices: 3006--3121 Score: 180
Period size: 57 Copynumber: 2.0 Consensus size: 58
2996 AAAAGCATTG
* * *
3006 AGGGTTGTCAAATTGAAGAGGATTCAAAAACGTCACAAATGGGCCCCGATAGGCCCAA
1 AGGGTTGCCAAATTGAAGACGATTCAAAAACGTCACAAATGGGCCCCGATACGCCCAA
* *
3064 AGGGTTGCCAAATTGAAGACGATTC-AAAACGTCACTAATGGGCCCCTATACGCCCAA
1 AGGGTTGCCAAATTGAAGACGATTCAAAAACGTCACAAATGGGCCCCGATACGCCCAA
3121 A
1 A
3122 ATAACAAGTG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
57 30 0.57
58 23 0.43
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.18
Consensus pattern (58 bp):
AGGGTTGCCAAATTGAAGACGATTCAAAAACGTCACAAATGGGCCCCGATACGCCCAA
Found at i:3233 original size:211 final size:212
Alignment explanation
Indices: 2859--3272 Score: 625
Period size: 211 Copynumber: 2.0 Consensus size: 212
2849 TTGAGGTTTC
* *
2859 CCAAATCGAAGACGGTTCAAAACGACACTAATGGGCCCCGATAGGACCAAAATAACAAGTATTCC
1 CCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATACGACCAAAATAACAAGTATTCC
*
2924 AAATGAGCAAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
66 AAATGAGCAAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * * * *
2989 TGGAACGAAAAGCATTGAGGGTTGTCAAATTGAAGAGGATTCAAAAACGTCACAAATGGG-CCCC
131 TGGAAAGAAAAGCATTGAGAGTTGCCAAATTGAAGACGATTC-AAAACATCACAAATGGGACCCC
*
3053 GATAGGCCCAAAGGGTTG
195 GATAAGCCCAAAGGGTTG
* * * * *
3071 CCAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCTATACGCCCAAAATAACAAGTGTTCC
1 CCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATACGACCAAAATAACAAGTATTCC
* * *
3136 AAATGAGC-AAAACCTTCACAGAGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAAGAA
66 AAATGAGCAAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
3200 TGGAAAGAAAAGCATTGAGATTTGCCGAATTGAAGACGATTCAAAACATCACTAATGGGACCCCG
131 TGGAAAGAAAAGCATTGAGAGTTGCCAAATTGAAGACGATTCAAAACATCACAAATGGGACCCCG
3265 ATAAGCCC
196 ATAAGCCC
3273 GAAAATAACA
Statistics
Matches: 181, Mismatches: 20, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
210 15 0.08
211 100 0.55
212 66 0.36
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (212 bp):
CCAAATCGAAGACGATTCAAAACGACACTAATGGGCCCCGATACGACCAAAATAACAAGTATTCC
AAATGAGCAAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGAGTTGCCAAATTGAAGACGATTCAAAACATCACAAATGGGACCCCG
ATAAGCCCAAAGGGTTG
Found at i:3318 original size:155 final size:152
Alignment explanation
Indices: 3067--3441 Score: 529
Period size: 155 Copynumber: 2.4 Consensus size: 152
3057 GGCCCAAAGG
* *
3067 GTTGCCAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCTATACGCCCAAAATAACAAGTG
1 GTTGCC-AATTGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTG
* *
3132 TTCCAAATGAGCAAAACCTTCACAGAGGACTAATCTCACCAAATTGATTATAGTTAGGCCATAAA
65 TTCCAAATGAGCAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
3197 GAATGGAAAGAAAAGC-ATTGAGA
130 CAATGGAAAG-AAAGCAATTGAGA
* *
3220 TTTGCCGAATTGAAGACGATTCAAAACATCACTAATGGGACCCCGATAAGCCCGAAAATAACAAG
1 GTTGCC-AATTGAAGACGATTCAAAACGTCACTAATGGG-CCCCGATAAGCCC-AAAATAACAAG
* *
3285 TGTTCCAAATGAGCTAAAAAC-TCTCAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
63 TGTTCCAAATGAGC-AAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCAT
* *
3349 AAACAATGTAAAGAAAGCAATTGAGG
127 AAACAATGGAAAGAAAGCAATTGAGA
** *
3375 GTTGCTACAATCAAAGTACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAAAATAACAAG
1 GTTGC--CAATTGAAG-ACGATTCAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAG
3440 TG
63 TG
Statistics
Matches: 198, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
153 36 0.18
154 16 0.08
155 99 0.50
156 23 0.12
157 24 0.12
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (152 bp):
GTTGCCAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAAGCCCAAAATAACAAGTGT
TCCAAATGAGCAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGAAAGAAAGCAATTGAGA
Found at i:3374 original size:366 final size:367
Alignment explanation
Indices: 2698--3431 Score: 1068
Period size: 366 Copynumber: 2.0 Consensus size: 367
2688 AAAAGCATCG
* * *
2698 AGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAAGGCCTAAAATAACAA
1 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAACGCCCAAAATAACAA
* * *
2763 GGGTTCCAAATGAGCTAAAAACTTCATAGTGGATTAATCTCACCAAAATGATTATAGTTAGGCCA
66 GGGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * *
2828 TCAACAATGTAAAGAAAAGCATTGAGGTTTCCCAAATCGAAGACGGTTCAAAACGACACTAATGG
131 TAAACAATGGAAAGAAAAGCATTGAGATTTCCCAAATCGAAGACGATTCAAAACGACACTAATGG
*
2893 GCCCCGATAGGACCAAAATAACAAGTATTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTC
196 GCCCCGATAAGACCAAAATAACAAGTATTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTC
* **
2958 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAACGAAAAGCATTGAGGGTTG-T-CAAATTG
261 ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCTAC-AATCA
*
3021 AAG-AGGATTCAAAAACGTCACAAATGGGCCCCGATAGGCCCAA
325 AAGTACGATTC-AAAACGTCACAAATGGGCCCCGATAGGCCCAA
* ** * *
3064 AGGGTTGCCAAATTGAAGACGATTCAAAACGTCACTAATGGGCCCCTATACGCCCAAAATAACAA
1 AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAACGCCCAAAATAACAA
* * *
3129 GTGTTCCAAATGAGC-AAAACCTTCACAGAGGACTAATCTCACCAAATTGATTATAGTTAGGCCA
66 GGGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
* * * *
3193 TAAAGAATGGAAAGAAAAGCATTGAGATTTGCCGAATTGAAGACGATTCAAAAC-ATCACTAATG
131 TAAACAATGGAAAGAAAAGCATTGAGATTTCCCAAATCGAAGACGATTCAAAACGA-CACTAATG
* * * *
3257 GGACCCCGATAAGCCCGAAAATAACAAGTGTTCCAAATGAGCTAAAAAC-TCTCAGTGGACTAAT
195 GG-CCCCGATAAGACC-AAAATAACAAGTATTCCAAATGAGCAAAAAACTTCACAGTGGACTAAT
*
3321 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGTAAAG-AAAGCAATTGAGGGTTGCTACAA
258 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC-ATTGAGGGTTGCTACAA
*
3385 TCAAAGTACGATTCAAAACGTCACTAATGGGCCCCGATAGGCCCAA
322 TCAAAGTACGATTCAAAACGTCACAAATGGGCCCCGATAGGCCCAA
3431 A
1 A
3432 ATAACAAGTG
Statistics
Matches: 328, Mismatches: 33, Indels: 13
0.88 0.09 0.03
Matches are distributed among these distances:
364 1 0.00
365 105 0.32
366 146 0.45
367 69 0.21
368 7 0.02
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.20
Consensus pattern (367 bp):
AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCAAAACGCCCAAAATAACAA
GGGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
TAAACAATGGAAAGAAAAGCATTGAGATTTCCCAAATCGAAGACGATTCAAAACGACACTAATGG
GCCCCGATAAGACCAAAATAACAAGTATTCCAAATGAGCAAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCTACAATCAA
AGTACGATTCAAAACGTCACAAATGGGCCCCGATAGGCCCAA
Done.