Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011936.1 Corchorus olitorius cultivar O-4 contig11969, 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: 31308
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30
Found at i:369 original size:154 final size:154
Alignment explanation
Indices: 9--2969 Score: 4175
Period size: 154 Copynumber: 19.3 Consensus size: 154
1 CCAAATAT
* * * *
9 GCTAAGAACATCACAATGGAGTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
74 TAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACCTAATGGGCCCCGATAGTC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA-CTAATGGGCCCCGATAGGC
* *
139 CCAAAATAACAAGTGTTTCGAA-TGA
130 CCAAAATAAAAAGTG-TTCAAATTGA
* * * * *
164 GCTAAGAACATCACAGTGGACTCATCTCACCAAAATGATTATAGTTCGGCCATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
229 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATAGGCCCCGTTAGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
*
294 CAAAATAAAAAGTGTTCTAATTGA
131 CAAAATAAAAAGTGTTCAAATTGA
* * *
318 GCTAAAAAGTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* ** * *
383 GAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAGTGGGCCCCGATAGGAC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * *
448 TAAAATAAAAAGTGTTCCAATTTA
131 CAAAATAAAAAGTGTTCAAATTGA
* * *
472 GCT-AAAAGTTCACAATGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
536 GAAAAGCATAT-AGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGC
66 GAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
*
600 ACAAAATAAAAAGTGTTCCAAATT-A
130 CCAAAATAAAAAGTGTT-CAAATTGA
625 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
690 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAACGGAACTAATGGGCCCCGAT-GGAC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGG-C
* *
753 CCAAAATAAAAAGTGTTCCAAATAGC
130 CCAAAATAAAAAGTGTT-CAAATTGA
*
779 GCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * *
844 GAAAAGCATTGAGGGTT-ACAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGTCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
908 CAAAATAACAAGTGTTTCGAA-TGA
131 CAAAATAAAAAGTG-TTCAAATTGA
* * * * * *
932 GCTAAGAACATCACCGTGGAGTCATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * *
997 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCGCGATAGGGC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
1062 CAAAATAAAAAGTGTTCTAAA-TGA
131 CAAAATAAAAAGTGTTC-AAATTGA
* * *
1086 GCTAAAAACTTCACAGTGGACTGATCTCACGAAAATGATTATAGTTAAGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1151 GAAAAGCATAT-AGGGTTCCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
66 GAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
*
1215 ACAAAATAAAAAGTGTTCCAAATT-A
130 CCAAAATAAAAAGTGTT-CAAATTGA
* *
1240 GCTAAAAACTTCACCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAT
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * * ***
1305 G-AAAGCATTGGGGGTTGTCGAATCGAA-AGCAATTCAAAACGGAACTAATGGG---C-ATAAAA
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGC
*
1364 CCAAAATAACAAGTGTTCCAAA-TGA
130 CCAAAATAAAAAGTGTT-CAAATTGA
* *
1389 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAACAATTGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * **
1454 GAAAAGCATTGACGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCCGATAGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * *
1519 TAAAATAAAAAGTGTTCCAATTTA
131 CAAAATAAAAAGTGTTCAAATTGA
* *
1543 GCTAAAAACTTCACAATGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1608 GAAAAGCATAT-AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGC
66 GAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGC
*
1672 ACAAAATAAAAAGTGTTCCAAATT-A
130 CCAAAATAAAAAGTGTT-CAAATTGA
1697 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * **
1762 G-AAAGCACTGAGGGTTGCCGAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGATC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
1826 CAAAATAAAAAGTGTTCCAAA-TGA
131 CAAAATAAAAAGTGTT-CAAATTGA
* *
1850 GCTAAAAACTTCAAAGTGGACTAATGTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * **
1915 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTTAAAACGGAACTAATGGGCCTCGATAGATC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
1980 CAAAATAAAAAGTGTTCCAAA-TGA
131 CAAAATAAAAAGTGTT-CAAATTGA
* *
2004 GCTAAAAACTTTAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
** * *
2069 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGACCCCGATTGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
*
2134 CAAACTAAAAAGTGTTGCAAA-TGA
131 CAAAATAAAAAGTGTT-CAAATTGA
* * * * * *
2158 GCTAAAAACTTCACA-AGGACTAATCTCACCAAAATGATTACAATTACGCTATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * *
2222 GAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCA
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
*
2287 AAAAATAAAAAGTGTTCCAAATT-A
131 CAAAATAAAAAGTGTT-CAAATTGA
**
2311 GCTAAAAACTTCACAGTTCACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
2376 GAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* *
2441 CAAAATAACAAGTGTTTCGAA-TGA
131 CAAAATAAAAAGTG-TTCAAATTGA
* * *
2465 GCTAAGAACATCACAGTGGACTCATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
2530 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
* * *
2595 CAGAATAACAAGTGTTTCGAA-TGA
131 CAAAATAAAAAGTG-TTCAAATTGA
* * ** * *
2619 GCTAAGAACATCTTAGTGGACTCATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * * * *
2684 GAAAAGCATTGAGGGTTGCTAAATCCAAGACGATTCAAAACAGAACTAGTAGGCCCCGTTAGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
2749 CAAAATAAAAAGTGTTCTAAA-TGA
131 CAAAATAAAAAGTGTTC-AAATTGA
* * * * *
2773 GCTAAAAACGTCACAATGGACTGATATTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * ** *
2838 GAAAAGC-TTCGAGGATTGCCAAATGGAAGACGATTCAAAAACGTCACTAACGGGCCCCGATAGG
66 GAAAAGCATT-GAGGGTTGCCAAATCGAAGACGATTC-AAAACGGAACTAATGGGCCCCGATAGG
* * *
2902 ACTAAAACAAAAAGTGTTCCAAATT-A
129 CCCAAAATAAAAAGTGTT-CAAATTGA
* *
2928 GCTAAAAACTTCACAATGGACTAATTTCACCAAAATGATTAT
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTAT
2970 GATTCAAAAC
Statistics
Matches: 2526, Mismatches: 241, Indels: 78
0.89 0.08 0.03
Matches are distributed among these distances:
148 1 0.00
149 86 0.03
150 42 0.02
151 1 0.00
152 6 0.00
153 605 0.24
154 1588 0.63
155 195 0.08
156 2 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCC
CAAAATAAAAAGTGTTCAAATTGA
Found at i:607 original size:307 final size:308
Alignment explanation
Indices: 9--2969 Score: 4255
Period size: 307 Copynumber: 9.6 Consensus size: 308
1 CCAAATAT
* * * *
9 GCTAAGAACATCACAATGGAGTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* **
74 TAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACCTAATGGGCCCCGATAGTC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA-CTAATGGGCCCCGATAGGA
* * * * * *
139 CCAAAATAACAAGTGTTTCGAATGAGCTAAGAACATCACAGTGGACTCATCTCACCAAAATGATT
130 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* *
204 ATAGTTCGGCCATAAATAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
195 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * *
269 CGGAACTAATAGGCCCCGTTAGGCCCAAAATAAAAAGTGTTCTAATTGA
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCAAATTGA
* * *
318 GCTAAAAAGTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* ** *
383 GAAAAGCATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAGTGGGCCCCGATAGGAC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGAC
* * * * * *
448 TAAAATAAAAAGTGTTCCAATTTAGCT-AAAAGTTCACAATGGACTAATTTCACCAAAATGATTA
131 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
*
512 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTGCCAGATCGAAGACGATTCAAAA
196 TAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAA
* *
576 CGGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATT-A
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTT-CAAATTGA
625 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
690 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTC-AAACGGAACTAATGGGCCCCGAT-GGAC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGA-
* *
753 CCAAAATAAAAAGTGTTCCAAATAGCGCTAAAAACTTCAAAGTGGACTAATCTCACCAAAATGAT
130 CCAAAATAAAAAGTGTTCCAAAT-GAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
*
818 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTT-ACAAATCGAAGACGATTCAAA
194 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* * * *
882 ACGAAACTAATGGGCCCCGATAGTCCCAAAATAACAAGTGTTTCGAA-TGA
259 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTG-TTCAAATTGA
* * * * * *
932 GCTAAGAACATCACCGTGGAGTCATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * *
997 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCGCGATAGGGC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGAC
* * *
1062 CAAAATAAAAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACGAAAATGATTA
131 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* *
1127 TAGTTAAGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTCCCAAATCGAAGACGATTCAAAA
196 TAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAA
*
1191 CGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAATT-A
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTT-CAAATTGA
* *
1240 GCTAAAAACTTCACCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAT
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * * * **
1305 G-AAAGCATTGGGGGTTGTCGAATCGAA-AGCAATTCAAAACGGAACTAATGGG---C-ATAAAA
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGA
* *
1364 CCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATT
130 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
* * *
1429 ATAGTTAGGCCATAAACAATTGAAAGAAAAGCATTGACGATTGCCAAATCGAAGACGATTCAAAA
195 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
** * * *
1494 CGTCACTAATGGGCCCCGATAGGCCTAAAATAAAAAGTGTTCCAATTTA
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCAAATTGA
* *
1543 GCTAAAAACTTCACAATGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
*
1608 GAAAAGCATAT-AGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGG-
66 GAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGA
*
1671 CACAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
130 C-CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
* *
1736 TATAGTTAGGCCATAAACAATGGAAAG-AAAGCACTGAGGGTTGCCGAATCGAAGACGATTCAAA
194 TATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAA
* **
1800 ACGGAACTAATGGTCCCCGATAGATCCAAAATAAAAAGTGTTCCAAA-TGA
259 ACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTT-CAAATTGA
* *
1850 GCTAAAAACTTCAAAGTGGACTAATGTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
1915 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTTAAAACGGAACTAATGGGCCTCGATA-GAT
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGA-
* *
1979 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTTAAAGTGGACTAATCTCACCAAAATGATT
130 CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
2044 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
195 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
** * * *
2109 CGTCACTAATGGACCCCGATTGGCCCAAACTAAAAAGTGTTGCAAA-TGA
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTT-CAAATTGA
* * * * * *
2158 GCTAAAAACTTCACA-AGGACTAATCTCACCAAAATGATTACAATTACGCTATAAATAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
2222 GAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGG-C
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGAC
* * **
2286 AAAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTTCACTAATCTCACCAAAATGATT
131 -CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATT
*
2351 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAA
195 ATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAA
* * *
2416 CGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCGAA-TGA
260 CGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTG-TTCAAATTGA
* * *
2465 GCTAAGAACATCACAGTGGACTCATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* *
2530 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCC
66 GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGAC
* * * * * * ** *
2595 CAGAATAACAAGTGTTTCGAATGAGCTAAGAACATCTTAGTGGACTCATCTCACCAAAATGATTA
131 CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
* * *
2660 TAGTTAGGCCATAAATAATGGAAAGAAAAGCATTGAGGGTTGCTAAATCCAAGACGATTCAAAAC
196 TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
* * * *
2725 AGAACTAGTAGGCCCCGTTAGGCCCAAAATAAAAAGTGTTCTAAA-TGA
261 GGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTC-AAATTGA
* * * * *
2773 GCTAAAAACGTCACAATGGACTGATATTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
1 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
* * ** *
2838 GAAAAGC-TTCGAGGATTGCCAAATGGAAGACGATTCAAAAACGTCACTAACGGGCCCCGATAGG
66 GAAAAGCATT-GAGGGTTGCCAAATCGAAGACGATTC-AAAACGGAACTAATGGGCCCCGATAGG
* * * * *
2902 ACTAAAACAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAATGGACTAATTTCACCAAAATGAT
129 ACCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGAT
2967 TAT
194 TAT
2970 GATTCAAAAC
Statistics
Matches: 2372, Mismatches: 242, Indels: 76
0.88 0.09 0.03
Matches are distributed among these distances:
302 6 0.00
303 221 0.09
304 43 0.02
305 5 0.00
306 46 0.02
307 1061 0.45
308 811 0.34
309 179 0.08
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (308 bp):
GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA
GAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGAC
CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTA
TAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAAC
GGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCAAATTGA
Found at i:964 original size:461 final size:462
Alignment explanation
Indices: 1--2969 Score: 4263
Period size: 461 Copynumber: 6.4 Consensus size: 462
* * * *
1 CCAAAT-ATGCTAAGAACATCACAATGGAGTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
1 CCAAATGA-GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAA
*
65 CAATGGAAATAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACCTAATGGGCC
65 CAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAA-CTAATGGGCC
* * * * * * *
130 CCGATAGTCCCAAAATAACAAGTGTTTCGAATGAGCTAAGAACATCACAGTGGACTCATCTCACC
129 CCGATAG-GCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
* *
195 AAAATGATTATAGTTCGGCCATAAATAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
193 AAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
* * * *
260 GATTCAAAACGGAACTAATAGGCCCCGTTAGGCCCAAAATAAAAAGTGTT-CTAATTGAGCTAAA
258 GATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAA
* * *
324 AAGTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
323 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* ** * * *
389 CATTGAGGATTGCCAAATCGAAGACGATTCAAAACGTCACTAGTGGGCCCCGATAGGACTAAAAT
388 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
454 AAAAAGTGTT
453 AAAAAGTGTT
* * * * *
464 CCAATTTAGCT-AAAAGTTCACAATGGACTAATTTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
528 AATGGAAAGAAAAGCATAT-AGGGTTGCCAGATCGAAGACGATTCAAAACGGAACTAATGAGCCC
66 AATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
*
592 CGATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCA
130 CGATAGGC-CAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCA
657 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
194 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACG
*
722 ATTC-AAACGGAACTAATGGGCCCCGAT-GGACCCAAAATAAAAAGTGTTCCAAATAGCGCTAAA
259 ATTCAAAACGGAACTAATGGGCCCCGATAGG-CCCAAAATAAAAAGTGTTCCAAATAGAGCTAAA
*
785 AACTTCAAAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
323 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
* * *
850 CATTGAGGGTT-ACAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGATAGTCCCAAAAT
388 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
*
914 AACAAGTGTT
453 AAAAAGTGTT
* * * * * * * *
924 TCGAATGAGCTAAGAACATCACCGTGGAGTCATCTCACCAAAATGATTATAGTTAGGCCATAAAT
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
989 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCGC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
1054 GATAGGGCCAAAATAAAAAGTGTTCTAAATGAGCTAAAAACTTCACAGTGGACTGATCTCACGAA
131 GATA-GGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
1119 AATGATTATAGTTAAGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTCCCAAATCGAAGACG
195 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACG
* *
1183 ATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAAT-TAGCTAAAA
259 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAAA
* *
1247 ACTTCACCGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAATG-AAAGC
324 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * * ***
1311 ATTGGGGGTTGTCGAATCGAA-AGCAATTCAAAACGGAACTAATGGG---C-ATAAAACCAAAAT
389 ATTGAGGGTTGCCAAATCGAAGA-CGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAAT
*
1371 AACAAGTGTT
453 AAAAAGTGTT
*
1381 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATTATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * * **
1446 AATTGAAAGAAAAGCATTGACGATTGCCAAATCGAAGACGATTCAAAACGTCACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * * *
1511 GATAGGCCTAAAATAAAAAGTGTTCCAATTTAGCTAAAAACTTCACAATGGACTAATTTCACCAA
131 GATAGGCC-AAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
1576 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATAT-AGGGTTGCCAAATCGAAGACG
195 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACG
* * *
1640 ATTCAAAACGGAACTAATGAGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAAT-TAGCTAAAA
259 ATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAAA
1704 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGC
324 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
* * * **
1768 ACTGAGGGTTGCCGAATCGAAGACGATTCAAAACGGAACTAATGGTCCCCGATAGATCCAAAATA
389 ATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATA
1833 AAAAGTGTT
454 AAAAGTGTT
* *
1842 CCAAATGAGCTAAAAACTTCAAAGTGGACTAATGTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
1907 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTTAAAACGGAACTAATGGGCCTC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * *
1972 GATAGATCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTTAAAGTGGACTAATCTCACCAA
131 GATAG-GCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
2037 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
195 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
** * * * *
2102 TTCAAAACGTCACTAATGGACCCCGATTGGCCCAAACTAAAAAGTGTTGCAAAT-GAGCTAAAAA
260 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAAAA
* * * * * *
2166 CTTCACA-AGGACTAATCTCACCAAAATGATTACAATTACGCTATAAATAATGGAAAGAAAAGCA
325 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * **
2230 TTGAGGGTTGTCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAGATAGGCAAAAAATAA
390 TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
2295 AAAGTGTT
455 AAAGTGTT
* **
2303 CCAAATTAGCTAAAAACTTCACAGTTCACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* *
2368 AATGGAAAGAAAAGCATTGAGGGTTGTCAAATCGAAGACGATTCAAAACGAAACTAATGGGCCCC
66 AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
* * * * * *
2433 GATAGGCCCAAAATAACAAGTGTTTCGAATGAGCTAAGAACATCACAGTGGACTCATCTCACCAA
131 GATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
2498 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
195 AATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGA
* * * * * *
2563 TTCAAAACGGAACTAATGGGCCCCGATTGGCCCAGAATAACAAGTGTTTCGAAT-GAGCTAAGAA
260 TTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAAAA
* ** * *
2627 CATCTTAGTGGACTCATCTCACCAAAATGATTATAGTTAGGCCATAAATAATGGAAAGAAAAGCA
325 CTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCA
* * * * * *
2692 TTGAGGGTTGCTAAATCCAAGACGATTCAAAACAGAACTAGTAGGCCCCGTTAGGCCCAAAATAA
390 TTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAA
2757 AAAGTGTT
455 AAAGTGTT
* * * * * *
2765 CTAAATGAGCTAAAAACGTCACAATGGACTGATATTACCAAAATGATTATAGTTAGGCCATAAAC
1 CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
* * ** *
2830 AATGGAAAGAAAAGC-TTCGAGGATTGCCAAATGGAAGACGATTCAAAAACGTCACTAACGGGCC
66 AATGGAAAGAAAAGCATT-GAGGGTTGCCAAATCGAAGACGATTC-AAAACGGAACTAATGGGCC
* * * * *
2894 CCGATAGGACTAAAACAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAATGGACTAATTTCACC
129 CCGATAGG-CCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACC
2959 AAAATGATTAT
193 AAAATGATTAT
2970 GATTCAAAAC
Statistics
Matches: 2258, Mismatches: 222, Indels: 52
0.89 0.09 0.02
Matches are distributed among these distances:
456 4 0.00
457 413 0.18
458 2 0.00
459 2 0.00
460 164 0.07
461 1224 0.54
462 357 0.16
463 91 0.04
464 1 0.00
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (462 bp):
CCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAAC
AATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCC
GATAGGCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
TCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATAGAGCTAAAAAC
TTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT
TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCCCAAAATAAA
AAGTGTT
Found at i:2993 original size:100 final size:101
Alignment explanation
Indices: 2869--3069 Score: 291
Period size: 100 Copynumber: 2.0 Consensus size: 101
2859 AATGGAAGAC
** * *
2869 GATTCAAAAACGTCACTAACGGGCCCCGATAGGA-CTAAAACAAAAAGTGTTCCAAATTAGCTAA
1 GATTCAAAAACGGAACTAACGGGCCCCGATA-GACCCAAAACAAAAAGTGTTCCAAATGAGCTAA
* *
2933 AAACTTCACAA-TGGACTAATTTCACCAAAATGATTAT
65 AAACTTCA-AAGTGGACTAATCTCACCAAAATAATTAT
* *
2970 GATTC-AAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAA
1 GATTCAAAAACGGAACTAACGGGCCCCGATAGACCCAAAACAAAAAGTGTTCCAAATGAGCTAAA
3034 AACTTCAAAGTGGACTAATCTCACCAAAATAATTAT
66 AACTTCAAAGTGGACTAATCTCACCAAAATAATTAT
3070 TGTTAGACCA
Statistics
Matches: 90, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
99 4 0.04
100 81 0.90
101 5 0.06
ACGTcount: A:0.43, C:0.20, G:0.14, T:0.22
Consensus pattern (101 bp):
GATTCAAAAACGGAACTAACGGGCCCCGATAGACCCAAAACAAAAAGTGTTCCAAATGAGCTAAA
AACTTCAAAGTGGACTAATCTCACCAAAATAATTAT
Found at i:3474 original size:153 final size:154
Alignment explanation
Indices: 2970--3593 Score: 982
Period size: 154 Copynumber: 4.1 Consensus size: 154
2960 AAATGATTAT
*
2970 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAACTAAAA
* * * *
3035 ACTTCAAAGTGGACTAATCTCACCAAAATAATTATTGTTAGACCATAAACAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
3100 ATTGAGGGTTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
* * * * *
3124 GATTCAAAACGGAACTAATGAGCCCCGATAGGCCAAAAATAAAAAGTGTTCAAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAACTAAAA
* * * *
3189 ACTTCGCAGTGGAATGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
3254 ATTGAGGGTTGCCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
* * *
3278 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAAT-ATACTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGA-ACTAAA
*
3342 AACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAG
65 AACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAG
*
3406 CATTGGGGGTTGCCAAATCGAAGAC
130 CATTGAGGGTTGCCAAATCGAAGAC
* * *
3431 GATTCAAAACGGAACTAATGGGCCCCGATAAACCCAATATAAAAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAACTAAAA
* * *
3496 ACTTCACAGAGGACTAATCTCACTAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGC
66 ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
*
3561 ATTGAGGGTTGGCAAATCGAAGAC
131 ATTGAGGGTTGCCAAATCGAAGAC
*
3585 GATTTAAAA
1 GATTCAAAA
3594 TGAGCTAAAA
Statistics
Matches: 430, Mismatches: 37, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
153 141 0.33
154 289 0.67
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (154 bp):
GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAACTAAAA
ACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGC
ATTGAGGGTTGCCAAATCGAAGAC
Found at i:3526 original size:307 final size:308
Alignment explanation
Indices: 2970--3593 Score: 1000
Period size: 307 Copynumber: 2.0 Consensus size: 308
2960 AAATGATTAT
* *
2970 GATTCAAAACGGAACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAA
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACACAAAATAAAAAGTGTTCCAAATGAACTAAAA
* *
3035 ACTTCAAAGTGGACTAATCTCACCAAAATAATTATTGTTAGACCATAAACAATGGAAAGAAAAGC
66 ACATCAAAGTGGACTAATCTCACCAAAATAATTATAGTTAGACCATAAACAATGGAAAGAAAAGC
**
3100 ATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCAAAAATA
131 ATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAAACCAAAAATA
* * * * *
3165 AAAAGTGTTCAAAATGAGCTAAAAACTTCGCAGTGGAATGATCTTACCAAAATGATTATAGTTAG
196 AAAAGTGTTCAAAATGAGCTAAAAACTTCACAGAGGAATAATCTCACCAAAATGATTACAGTTAG
3230 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
261 GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
* *
3278 GATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTGTTCCAAAT-ATACTAAG
1 GATTCAAAACGGAACTAATGGGCCCCGATAGACACAAAATAAAAAGTGTTCCAAATGA-ACTAAA
* * *
3342 AACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAG
65 AACATCAAAGTGGACTAATCTCACCAAAATAATTATAGTTAGACCATAAACAATGGAAAGAAAAG
* * * *
3406 CATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAAACCCAATAT
130 CATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAAACCAAAAAT
* * *
3471 AAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACTAAAATGATTACAGTTA
195 AAAAAGTGTTCAAAATGAGCTAAAAACTTCACAGAGGAATAATCTCACCAAAATGATTACAGTTA
*
3536 GGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGGCAAATCGAAGAC
260 GGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
*
3585 GATTTAAAA
1 GATTCAAAA
3594 TGAGCTAAAA
Statistics
Matches: 290, Mismatches: 25, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
307 177 0.61
308 113 0.39
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (308 bp):
GATTCAAAACGGAACTAATGGGCCCCGATAGACACAAAATAAAAAGTGTTCCAAATGAACTAAAA
ACATCAAAGTGGACTAATCTCACCAAAATAATTATAGTTAGACCATAAACAATGGAAAGAAAAGC
ATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCGATAAACCAAAAATA
AAAAGTGTTCAAAATGAGCTAAAAACTTCACAGAGGAATAATCTCACCAAAATGATTACAGTTAG
GCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAC
Found at i:3665 original size:415 final size:415
Alignment explanation
Indices: 3172--4008 Score: 1349
Period size: 415 Copynumber: 2.0 Consensus size: 415
3162 ATAAAAAGTG
* * * * *
3172 TTCAAAATGAGCTAAAAACTTCGCAGTGGAATGATCTTACCAAAATGATTATAGTTAGGCCATAA
1 TTCAAAATGAGCTAAAAACTTCACAGTGGAATAATCTAACCAAAATGATTACAATTAGGCCATAA
*
3237 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCC
66 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCC
*
3302 CCGATAGGCACAAAATAAAAAGTGTTCCAAAT-ATACTAAGAACATCACAGTGGACTAATC-TCA
131 CCGATAGGCACAAAATAAAAAGTGTT-CAAATGAT-CTAAAAACATCACAGTGGACTAATCGT-A
* *
3365 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGGGGGTTGCCAAATCGAAG
193 CCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAG
* * *
3429 ACGATTCAAAACGGAACTAATGGGCCCCGATAAACCCAATATAAAAAGTGTTCCAAATGAGCTAA
258 ACGATTCAAAACGGAACTAATGAGCCCCGATAAACCCAAAATAAAAAGTGTTCCAAATAAGCTAA
* *
3494 AAACTTCACAGAGGACTAATCTCACTAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAA
323 AAACTTCACAGAGGACTAATCTCACTAAAATGAATACAGTTAGGCCATAAACAATAGAAAGAAAA
*
3559 GCAT-TGAGGGTTGGCAAATCGAAGACGA
388 GCATATG-GGGTTGCCAAATCGAAGACGA
* *
3587 TTTAAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGGCCATAA
1 TTCAAAATGAGCTAAAAACTTCACAGTGGAATAATCTAACCAAAATGATTACAATTAGGCCATAA
*
3652 ACAATGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCC
66 ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCC
* * * *
3717 CCGATAGGCCCAAAATAAAAAGTGTTCTAATGATCTAAAAACTTCACAGTGGACTGATCGTACCA
131 CCGATAGGCACAAAATAAAAAGTGTTCAAATGATCTAAAAACATCACAGTGGACTAATCGTACCA
3782 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACG
196 AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACG
***
3847 ATTCAAAACGGAACTAATGAGCCCCGATAGTTCCAAAATAAAAAGTGTTCCAAATAAGCTAAAAA
261 ATTCAAAACGGAACTAATGAGCCCCGATAAACCCAAAATAAAAAGTGTTCCAAATAAGCTAAAAA
* * * *
3912 CTTCACAGTGGACTGATCTTACTAAAATGAATATAGTTAGGCCATAAACAATAGAAAGAAAAGCA
326 CTTCACAGAGGACTAATCTCACTAAAATGAATACAGTTAGGCCATAAACAATAGAAAGAAAAGCA
3977 TATGGGGTTGCCAAATCGAAGACGA
391 TATGGGGTTGCCAAATCGAAGACGA
4002 TTCAAAA
1 TTCAAAA
4009 CGGAACTAAT
Statistics
Matches: 388, Mismatches: 30, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
414 64 0.16
415 322 0.83
416 2 0.01
ACGTcount: A:0.43, C:0.17, G:0.19, T:0.21
Consensus pattern (415 bp):
TTCAAAATGAGCTAAAAACTTCACAGTGGAATAATCTAACCAAAATGATTACAATTAGGCCATAA
ACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCC
CCGATAGGCACAAAATAAAAAGTGTTCAAATGATCTAAAAACATCACAGTGGACTAATCGTACCA
AAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACG
ATTCAAAACGGAACTAATGAGCCCCGATAAACCCAAAATAAAAAGTGTTCCAAATAAGCTAAAAA
CTTCACAGAGGACTAATCTCACTAAAATGAATACAGTTAGGCCATAAACAATAGAAAGAAAAGCA
TATGGGGTTGCCAAATCGAAGACGA
Found at i:3672 original size:108 final size:108
Alignment explanation
Indices: 3483--3701 Score: 366
Period size: 108 Copynumber: 2.0 Consensus size: 108
3473 AAAGTGTTCC
* * *
3483 AAATGAGCTAAAAACTTCACAGAGGACTAATCTCACTAAAATGATTACAGTTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGAGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
* * *
3548 TGGAAAGAAAAGCATTGAGGGTTGGCAAATCGAAGACGATTTA
66 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCA
*
3591 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGAGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
*
3656 TGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCA
66 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCA
3699 AAA
1 AAA
3702 CGGAACTAAT
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
108 103 1.00
ACGTcount: A:0.45, C:0.15, G:0.19, T:0.21
Consensus pattern (108 bp):
AAATGAGCTAAAAACTTCACAGAGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCA
Found at i:3871 original size:153 final size:154
Alignment explanation
Indices: 3591--4237 Score: 1005
Period size: 153 Copynumber: 4.2 Consensus size: 154
3581 AGACGATTTA
* *
3591 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAA
* *
3656 TGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
3721 TAGGCCCAAAATAAAAAGTGTT-C
131 TAGGCCCAAAATAAAAAGTGTTCC
* * *
3744 TAATGATCTAAAAACTTCACAGTGGACTGATCGT-ACCAAAATGATTATAGTTAGGCCATAAACA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATC-TAACCAAAATGATTATAGTTAGGCCATAAACA
* *
3808 ATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGAGCCCCG
65 ATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
**
3873 ATAGTTCCAAAATAAAAAGTGTTCC
130 ATAGGCCCAAAATAAAAAGTGTTCC
* * * * *
3898 AAATAAGCTAAAAACTTCACAGTGGACTGATCTTACTAAAATGAATATAGTTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAA
*
3963 TAGAAAGAAAAGCATATG-GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
66 TGGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
*
4027 ATAGGCACAAAATAAAAAGTGTTCC
130 ATAGGCCCAAAATAAAAAGTGTTCC
* * *
4052 AAATTAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAACGATTATAGTTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAA
* * *
4117 TGGAAAG-AAAGCATTGGGGGTTGCCGAATCGAAGACGATTCAAAACGAAACTAATGGGCCCCGA
66 TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
* *
4181 TAGACCCAAAATAAAATGTGTTCC
131 TAGGCCCAAAATAAAAAGTGTTCC
*
4205 AAATGAGCTAAAAACTTCAAAGTGGACTAATCT
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCT
4238 TGATACGAAT
Statistics
Matches: 453, Mismatches: 36, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
152 2 0.00
153 244 0.54
154 205 0.45
155 2 0.00
ACGTcount: A:0.43, C:0.18, G:0.19, T:0.21
Consensus pattern (154 bp):
AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTATAGTTAGGCCATAAACAA
TGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGA
TAGGCCCAAAATAAAAAGTGTTCC
Found at i:3953 original size:722 final size:720
Alignment explanation
Indices: 2152--4237 Score: 2899
Period size: 722 Copynumber: 2.9 Consensus size: 720
2142 AAAGTGTTGC
* * *
2152 AAATGAGCTAAAAACTTCACA-AGGACTAATCTCACCAAAATGATTACAATTACGCTATAAATAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTA-GCCATAAA-AA
* *
2216 TGGAAAGAAAAGCATTGAGGGTTGT-CAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCAG
64 TGGAAAGAAAAGCATTGAGGGTT-TCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCG
** * **
2280 ATAGGCAAAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTTCACTAATCTCACCAAA
128 ATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
*
2345 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGTCAAATCGAAGACGAT
193 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
* * * * * * *
2410 TCAAAACGAAACTAATGGGCCCCGATAGGCCCAAAATAACAAGTGTTTCGAATGAGCTAAGAACA
258 TCAAAACGGAACTAATGAGCCCCGATA-GCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
* *
2475 TCACAGTGGACTCATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
322 TCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATT
* * * *
2540 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATTGGCCCAGAATAACA
387 GAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAA
* * * ** *
2605 AGTGTTTCGAATGA-GCTAAGAACATCTTAGTGGACTCATCTCACCAAAATGATTATAGTTAGGC
452 AGTGTTCCAAAT-ATACTAAGAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * * * *
2669 CATAAATAATGGAAAGAAAAGCATTGAGGGTTGCTAAATCCAAGACGATTCAAAACAGAACTAGT
516 CATAAACAATGGAAAG-AAAGCATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * * * * *
2734 AGGCCCCGTTAGGCCCAAAATAAAAAGTGTTCTAAATGAGCTAAAAACGTCACA-ATGGACTGAT
580 GGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGA-GGACTAAT
* * * *
2798 ATTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCTTCGAGGATTGCCAAATG
644 CTCACCAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCTTCGAGGATTGCCAAATC
2863 GAAGACGATTCA
709 GAAGACGATTCA
** ** * * * *
2875 AAA--A-CGTCACTAACGGGCCCCGATAGGACTAA---AACAAAAAGTG-TTCCAAATTAG-C-T
1 AAATGAGC-T-AAAAAC-TTCACAG-T-GGACTAATCTAACCAAAA-TGATTAC-AATTAGCCAT
** * * * * * ** *
2931 AAAAACT--TCA-CAATGGACT-A--ATTTCACCAAAAT-GATTATGATTCAAAACGGAACTAAT
59 AAAAA-TGGAAAGAAAAGCATTGAGGGTTT--CC-AAATCGAAGAAGATTCAAAACGGAACTAAT
* *
2989 GGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATC
120 GGGCCCCGATAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * *
3054 TCACCAAAATAATTATTGTTAGACCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
185 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCG
* *
3119 AAGACGATTCAAAACGGAACTAATGAGCCCCGATAGGCCAAAAATAAAAAGTGTTCAAAATGAGC
250 AAGACGATTCAAAACGGAACTAATGAGCCCCGATA-GCCCAAAATAAAAAGTGTTCCAAATGAGC
* *
3184 TAAAAACTTCGCAGTGGAATGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
314 TAAAAACTTCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
3249 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACA
379 AAAGCATTGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACA
3314 AAATAAAAAGTGTTCCAAATATACTAAGAACATCACAGTGGACTAATCTCACCAAAATGATTATA
444 AAATAAAAAGTGTTCCAAATATACTAAGAACATCACAGTGGACTAATCTCACCAAAATGATTATA
3379 GTTAGGCCATAAACAATGGAAAGAAAGCATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGA
509 GTTAGGCCATAAACAATGGAAAGAAAGCATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGA
* *
3444 ACTAATGGGCCCCGATAAACCCAATATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGA
574 ACTAATGGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGA
* * *
3509 CTAATCTCACTAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCATT-GAGGGTTGG
639 CTAATCTCACCAAAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGC-TTCGAGGATTGC
*
3573 CAAATCGAAGACGATTTA
703 CAAATCGAAGACGATTCA
3591 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTA-GCCATAAA-AA
3656 TGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
64 TGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
* * *
3721 TAGGCCCAAAATAAAAAGTGTT-CTAATGATCTAAAAACTTCACAGTGGACTGATCGT-ACCAAA
129 TAGGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC-TCACCAAA
*
3784 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGAT
193 ATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGAT
* *
3849 TCAAAACGGAACTAATGAGCCCCGATAGTTCCAAAATAAAAAGTGTTCCAAATAAGCTAAAAACT
258 TCAAAACGGAACTAATGAGCCCCGATAG-CCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACT
* * *
3914 TCACAGTGGACTGATCTTACTAAAATGAATATAGTTAGGCCATAAACAATAGAAAGAAAAGCATA
322 TCACAGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCAT-
3979 TG-GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAA
386 TGAGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAA
* * *
4043 AAGTGTTCCAAAT-TAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAACGATTATAGTTAGG
451 AAGTGTTCCAAATATA-CTAAGAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* *
4107 CCATAAACAATGGAAAGAAAGCATTGGGGGTTGCCGAATCGAAGACGATTCAAAACGAAACTAAT
515 CCATAAACAATGGAAAGAAAGCATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAAT
* * *
4172 GGGCCCCGATAGACCCAAAATAAAATGTGTTCCAAATGAGCTAAAAACTTCAAAGTGGACTAATC
580 GGGCCCCGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATC
4237 T
645 T
4238 TGATACGAAT
Statistics
Matches: 1201, Mismatches: 124, Indels: 77
0.86 0.09 0.05
Matches are distributed among these distances:
714 8 0.01
715 3 0.00
716 177 0.15
717 417 0.35
718 12 0.01
719 7 0.01
720 5 0.00
721 11 0.01
722 471 0.39
723 73 0.06
724 7 0.01
725 3 0.00
726 7 0.01
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (720 bp):
AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGCCATAAAAATG
GAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGATA
GGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATG
ATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGACGATTCA
AAACGGAACTAATGAGCCCCGATAGCCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCAC
AGTGGACTGATCTTACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAAAGCATTGAGG
GTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCGATAGGCACAAAATAAAAAGTG
TTCCAAATATACTAAGAACATCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAA
ACAATGGAAAGAAAGCATTGGGGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCC
CGATAGACCCAAAATAAAAAGTGTTCCAAATGAGCTAAAAACTTCACAGAGGACTAATCTCACCA
AAATGATTACAGTTAGGCCATAAACAATGGAAAGAAAAGCTTCGAGGATTGCCAAATCGAAGACG
ATTCA
Found at i:4150 original size:307 final size:307
Alignment explanation
Indices: 3591--4238 Score: 1023
Period size: 307 Copynumber: 2.1 Consensus size: 307
3581 AGACGATTTA
* *
3591 AAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAATGATTACAATTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGAATACAATTAGGCCATAAACAA
* *
3656 TGGAAAGAAAAGCATTGAGGGTTTCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
66 TAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
* * * * *
3721 TAGGCCCAAAATAAAAAGTGTTCTAATGATCTAAAAACTTCACAGTGGACTGATCGTACCAAAAT
131 TAGGCACAAAATAAAAAGTGTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCGTACCAAAAC
3786 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTC
196 GATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTC
* **
3851 AAAACGGAACTAATGAGCCCCGATAGTTCCAAAATAAAAAGTGTTCC
261 AAAACGAAACTAATGAGCCCCGATAGACCCAAAATAAAAAGTGTTCC
* * * * *
3898 AAATAAGCTAAAAACTTCACAGTGGACTGATCTTACTAAAATGAATATAGTTAGGCCATAAACAA
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGAATACAATTAGGCCATAAACAA
*
3963 TAGAAAGAAAAGCATATG-GGGTTGCCAAATCGAAGACGATTCAAAACGGAACTAATGGGCCCCG
66 TAGAAAGAAAAGCAT-TGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCG
*
4027 ATAGGCACAAAATAAAAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGACTAATC-TCACCAA
130 ATAGGCACAAAATAAAAAGTGTT-CAAATGAGCTAAAAACTTCACAGTGGACTAATCGT-ACCAA
* * *
4091 AACGATTATAGTTAGGCCATAAACAATGGAAAG-AAAGCATTGGGGGTTGCCGAATCGAAGACGA
193 AACGATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGA
* *
4155 TTCAAAACGAAACTAATGGGCCCCGATAGACCCAAAATAAAATGTGTTCC
258 TTCAAAACGAAACTAATGAGCCCCGATAGACCCAAAATAAAAAGTGTTCC
*
4205 AAATGAGCTAAAAACTTCAAAGTGGACTAATCTT
1 AAATGAGCTAAAAACTTCACAGTGGACTAATCTT
4239 GATACGAATC
Statistics
Matches: 311, Mismatches: 27, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
307 243 0.78
308 68 0.22
ACGTcount: A:0.42, C:0.18, G:0.19, T:0.21
Consensus pattern (307 bp):
AAATGAGCTAAAAACTTCACAGTGGACTAATCTTACCAAAATGAATACAATTAGGCCATAAACAA
TAGAAAGAAAAGCATTGAGGGTTGCCAAATCGAAGAAGATTCAAAACGGAACTAATGGGCCCCGA
TAGGCACAAAATAAAAAGTGTTCAAATGAGCTAAAAACTTCACAGTGGACTAATCGTACCAAAAC
GATTATAGTTAGGCCATAAACAATGGAAAGAAAAACATTGAGGGTTGCCAAATCGAAGACGATTC
AAAACGAAACTAATGAGCCCCGATAGACCCAAAATAAAAAGTGTTCC
Found at i:6128 original size:26 final size:23
Alignment explanation
Indices: 6098--6144 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
6088 CTTGAAAATT
6098 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAAC-TTGAT-GAT-AGATGGA
6124 TGAAAAACTTGATGATAGATG
1 TGAAAAACTTGATGATAGATG
6145 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (23 bp):
TGAAAAACTTGATGATAGATGGA
Found at i:8741 original size:13 final size:14
Alignment explanation
Indices: 8714--8742 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
8704 ATGTGGTGTT
8714 TTTAATAATAATAA
1 TTTAATAATAATAA
8728 TTTAATAA-AATAA
1 TTTAATAATAATAA
8741 TT
1 TT
8743 ATTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATAATAATAA
Found at i:8765 original size:19 final size:20
Alignment explanation
Indices: 8714--8765 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
8704 ATGTGGTGTT
*
8714 TTTAATAA-TAATAATTTAA
1 TTTAATAATTAATTATTTAA
**
8733 TAAAATAATT-ATTATTT-A
1 TTTAATAATTAATTATTTAA
8751 TTTAATAATTAATTA
1 TTTAATAATTAATTA
8766 ATTTCAGCCC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 9 0.35
19 16 0.62
20 1 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTTAATAATTAATTATTTAA
Found at i:12367 original size:16 final size:16
Alignment explanation
Indices: 12335--12438 Score: 133
Period size: 16 Copynumber: 6.6 Consensus size: 16
12325 GGGTTCGGAT
12335 GGGTTCGGGTA-TTTC
1 GGGTTCGGGTATTTTC
*
12350 GGGTTCGGGTTTTTTC
1 GGGTTCGGGTATTTTC
12366 -GGTTACGGGTATTTTC
1 GGGTT-CGGGTATTTTC
*
12382 AGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
* *
12398 GGGTTCAGGT-TATGTC
1 GGGTTCGGGTAT-TTTC
12414 GGGTTCGGGTATTTTC
1 GGGTTCGGGTATTTTC
12430 GGGTTCGGG
1 GGGTTCGGG
12439 CTCGAGTTTG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
15 15 0.19
16 57 0.74
17 5 0.06
ACGTcount: A:0.08, C:0.12, G:0.38, T:0.41
Consensus pattern (16 bp):
GGGTTCGGGTATTTTC
Found at i:13368 original size:2 final size:2
Alignment explanation
Indices: 13363--13429 Score: 70
Period size: 2 Copynumber: 35.5 Consensus size: 2
13353 TACTTTAAGT
* * *
13363 TA TA TA AA T- TA TT TA TA TA TA TA -A TA TA TA TA TA TA TA TT
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
13403 TA TA TA TA TA TA TC TA -A T- TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13430 TTAGTAGTTT
Statistics
Matches: 53, Mismatches: 8, Indels: 8
0.77 0.12 0.12
Matches are distributed among these distances:
1 4 0.08
2 49 0.92
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:15105 original size:19 final size:19
Alignment explanation
Indices: 15081--15119 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
15071 TCACAAACAT
15081 AAAGTTACACTAAAATCAC
1 AAAGTTACACTAAAATCAC
*
15100 AAAGTTAGACTAAAATCAC
1 AAAGTTACACTAAAATCAC
15119 A
1 A
15120 TGCATTGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.54, C:0.18, G:0.08, T:0.21
Consensus pattern (19 bp):
AAAGTTACACTAAAATCAC
Found at i:16519 original size:11 final size:11
Alignment explanation
Indices: 16476--16513 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
16466 TTTCTATATA
*
16476 AAATAAATTAT
1 AAATTAATTAT
16487 CAAA-TAATTAT
1 -AAATTAATTAT
16498 AAATTAATTAT
1 AAATTAATTAT
16509 AAATT
1 AAATT
16514 TGTTATCAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:16731 original size:17 final size:17
Alignment explanation
Indices: 16709--16754 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
16699 AATTTCTTTC
16709 CTTCTTCATATTTTCTT
1 CTTCTTCATATTTTCTT
16726 CTTCTTCATATTTTCTT
1 CTTCTTCATATTTTCTT
*
16743 CTTCTCCATATT
1 CTTCTTCATATT
16755 CTATTGTCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.61
Consensus pattern (17 bp):
CTTCTTCATATTTTCTT
Found at i:16906 original size:28 final size:31
Alignment explanation
Indices: 16848--16909 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
16838 TTCAATATTT
* * *
16848 ATTTTTTTTGTATTATTAGTATGTAACATTA
1 ATTTTTTGTGTATTATTAATATATAACATTA
16879 ATTTTTTGTGTATTA-TAATA-ATAA-ATTA
1 ATTTTTTGTGTATTATTAATATATAACATTA
16907 ATT
1 ATT
16910 ATAGATTGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.25
29 3 0.11
30 4 0.14
31 14 0.50
ACGTcount: A:0.34, C:0.02, G:0.08, T:0.56
Consensus pattern (31 bp):
ATTTTTTGTGTATTATTAATATATAACATTA
Found at i:27285 original size:13 final size:13
Alignment explanation
Indices: 27267--27292 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
27257 TTCAGCCTCA
27267 AGTCAGTGTGGAG
1 AGTCAGTGTGGAG
27280 AGTCAGTGTGGAG
1 AGTCAGTGTGGAG
27293 GAGGTTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.46, T:0.23
Consensus pattern (13 bp):
AGTCAGTGTGGAG
Found at i:28920 original size:14 final size:14
Alignment explanation
Indices: 28898--28934 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
28888 ATCACATACC
28898 TTCTCTTCTTATTT
1 TTCTCTTCTTATTT
*
28912 TTCTATTCTTATTT
1 TTCTCTTCTTATTT
28926 TTCTCTTCT
1 TTCTCTTCT
28935 AGTTCTAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.08, C:0.22, G:0.00, T:0.70
Consensus pattern (14 bp):
TTCTCTTCTTATTT
Done.