Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023890.1 Corchorus olitorius cultivar O-4 contig23923, 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: 14294
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.28
Found at i:3643 original size:154 final size:154
Alignment explanation
Indices: 440--3638 Score: 4324
Period size: 154 Copynumber: 20.7 Consensus size: 154
430 ATTATAGTTA
* * * *
440 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCAAAGTTGATTCAAAACGGATCTAATGGGCCCCAAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
505 AGGCCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
* *
569 TGATTATAGTTAGACCATTAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* * * *
594 GGAAA-AAATAGCTCTGAGGTTTGTCAAATCGAAATCGATTCAAAACGAAACTAATGGGCCCCGA
1 GGAAAGAAA-AGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGA
*
658 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCAGCAAAA
65 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
*
723 TGATTATATTTAGGCCATAAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* * * * * * **
748 TGAAA-AAAAGCATTGGGGTTTGGCAAATTGAAGACGATTCAAAACATAACTAATGGGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
*
812 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAG
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
877 GATTATATTTAGGCCATAAACAAT
131 GATTATAGTTAGGCCATAAACAAT
* * * * * * * *
901 TGAAA-AAAGAGCATTGGGGTTTGGCAAATTGAAGACGATTCAAAACAGAACTGATGGGCCCCGA
1 GGAAAGAAA-AGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGA
* *
965 AAGGCCCAAAATAACAAGTG-TCCTAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCTAA
65 AAGGCCCAAAATAACAAGTGTTCC-AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
*
1029 ATGATTATAATTAGGCCATAAACAAT
129 ATGATTATAGTTAGGCCATAAACAAT
* * * * * *
1055 GGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTATTGTGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
** *
1120 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACTCTTCACAGTGGACTAATCTCACCAAAAG
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
1185 GATTATAGTTAGGCCATTAACAAT
131 GATTATAGTTAGGCCATAAACAAT
* * * * **
1209 GGAAAGAAAAGCATTGTGCTTTGCCAAATCGAAGAT-GATTCAAACCGTCACTAATGGGCCCCGA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAG-TCGATTCAAAACGGAACTAATGGGCCCCGA
* ** *
1273 AAAGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACGCTTCACAGTGGAGTAATCTCACCAAAA
65 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* *
1338 GGATTATAGTTAGGCCATTAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* * ** *
1363 GGAAAGAAAAGCATTT-TGGTTTGCGAAATCGAAGAT-GATTCAAAACGTCACTATTGGGCCCC-
1 GGAAAGAAAAGC-TTTGAGGTTTGCCAAATCGAAG-TCGATTCAAAACGGAACTAATGGGCCCCG
*
1425 AATAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA
64 AA-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
*
1490 ATTGATTATAGTTAGGCCATAAACAACT
128 AATGATTATAGTTAGGCCATAAACAA-T
* * * * * *
1518 -TAAAGAAAAGCTTTGAGGTTTGCCAAATCAAAGTTGATTCAAAACGGATCTAATGGGCGCCAAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
1582 AGGCCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
* *
1646 TGATTATAGTTAGACCATTAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* * * * *
1671 GGAAA-AAATAGCTCTGAGGTTTGCCAAATCGAAATTGATTCAAAACGAAACTAATGGGCCCCAA
1 GGAAAGAAA-AGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGA
*
1735 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACATCACAGTGGACTAATCTCACCAAAA
65 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* *
1800 TGATTATATTTAGGCCACAAACAATT
130 TGATTATAGTTAGGCCATAAACAA-T
* * * * * * **
1826 GAAAAAAAAAGCATTGGGGTTTAG-CAAATTGAAGACGATTCAAAACATAACTAATGGGCCCCGA
1 GGAAAGAAAAGCTTTGAGGTTT-GCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGA
1890 AAGGCCCAAAATAACAAGTG-TCCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
65 AAGGCCCAAAATAACAAGTGTTCC-AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAA
1954 ATGATTATAGTTAGGCCATAAACAAACAGT
129 ATGATTATAGTTAGGCCATAAAC--A-A-T
* * * * * * * * *
1984 TGAAAAAAAAGCATTGGGGTTTGGCAAATTGAAGACGATTCAAAACAGAACTAATGGGCGCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
2049 AGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCTAAAT
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
2114 GATTATAGTTAGGCCATAAACAAT
131 GATTATAGTTAGGCCATAAACAAT
* * * *
2138 GGAAAAAAAAGCATTGAGGTTTGCCAAATCAAAG-AGTATTCAAAACGGAACTAATGGGCCCCGA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCG-ATTCAAAACGGAACTAATGGGCCCCGA
* *
2202 AAGGCCCAAAATAACAAGTGTTCCAAATGAGTTAAAATCTTCACAGTGGACTAATCTCACCAAAA
65 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAA
* * * *
2267 GGATTATATTTAGGCCATTAACAGT
130 TGATTATAGTTAGGCCATAAACAAT
* **
2292 GGAAAGAAAAGCATTT-TGGTTTGCCAAATCGAAGAT-GATTCAAAACGTCACTAATGGGCCCC-
1 GGAAAGAAAAGC-TTTGAGGTTTGCCAAATCGAAG-TCGATTCAAAACGGAACTAATGGGCCCCG
* *
2354 AATAGGTCCAAAATAACAAGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAA
64 AA-AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAA
* *
2419 AATGATTATAGTTAGGCTATAAACATT
128 AATGATTATAGTTAGGCCATAAACAAT
* *
2446 GGAAAGAAAAGCTTTGAGATTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* * * *
2511 AGGCCCAAAATAACAAGTGTTCCAAATGAGATAAGAACCTCATAGTGGAC-ATATCTCACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
* * *
2575 TGATTATTGTCAGGCCATAATCAACT
130 TGATTATAGTTAGGCCATAAACAA-T
* * * * *
2601 -TAAAGGAAAGCTTTGAGGTTTACCAAATCGAAGACGATTCAAAACGGAACTAATGGACCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
2665 AAGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
* *
2730 GATTATAGTTAGTCCAAAAACAAT
131 GATTATAGTTAGGCCATAAACAAT
* * * * *
2754 GTAAAGAAAAGTTTTGAGGTTTGCAAAATCGAAGTCGATTCAAAACGGATCTAATGGGCCCAGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
2819 AGGCCAAAAATAACAAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
2883 TGATTATAGTTAGGCCATAAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
**
2908 GGATGGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
2973 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
*
3038 GATTATAGTTAGTCCATAAACAAT
131 GATTATAGTTAGGCCATAAACAAT
* * * * * * **
3062 GGAAAGAAATA-TTTTGAGGTTTGCCAAATCGATGTCGAATCAAAACAGATCTACTAAGCCCCGA
1 GGAAAGAAA-AGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGA
* ** *
3126 AAGGCCCAAAATAACAAGTATTCCAAATGAGCTAAAAGTTTCACAGTGGAC-ATATCTCTCCAAA
65 AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAA
3190 ATGATTATAGTTAGGCCATAAACAAT
129 ATGATTATAGTTAGGCCATAAACAAT
* * * **
3216 GGAAAGAAAAGCTTTTAGGTTTGCCAAATCGAAATCTATTCAAAACGGAACTAATGGGATCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* ** * *
3281 AGGCGCAAAATAACAAGTGTTTTAAATGAGCTAAAAGCTTCACAGTGGAC-ATATCACACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
3345 TGATTATAGTTAGGCCATAAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* *
3370 GGATAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCGAAACGGAACTAATGGGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* * * *
3435 AGGCCCAAAATTACAAGTGTTCCAGATGAGTTAAAAACTTCACAGTGGAC-ATATCGCACCAAAA
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAA
3499 TGATTATAGTTAGGCCATAAACAAT
130 TGATTATAGTTAGGCCATAAACAAT
* * * * * *
3524 TGATAGAAAAGCTTTCAGGTTTGCCAAATCGTAGTCGATTCAAAACGGTACTAGTGGGCCCCGAA
1 GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
* *
3589 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAATTTCACAATGGAC
66 AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
3639 ATATCTGATC
Statistics
Matches: 2733, Mismatches: 269, Indels: 86
0.89 0.09 0.03
Matches are distributed among these distances:
153 171 0.06
154 2260 0.83
155 151 0.06
156 5 0.00
157 2 0.00
158 142 0.05
159 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (154 bp):
GGAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAA
AGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAAT
GATTATAGTTAGGCCATAAACAAT
Found at i:3644 original size:462 final size:462
Alignment explanation
Indices: 5--3638 Score: 4784
Period size: 462 Copynumber: 7.9 Consensus size: 462
1 ATTG
* * *
5 AGGTTTGCCGAATCGAAGA-CGATTCAAAACAGAATTAATGGGCCTCGAAAGGCCCAAAATAACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGGCC-CGAAAGGCCCAAAATAACA
* *
69 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTAACCAAAGTGATTATAGTTAGGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * * * * * * **
134 TTAAACAATTGAAAAAAAAAAGGCATTGGGGTTTGGCAAATTGAAGACGATTCAAAACAAAACTA
130 ATAAACAA-TG-GAAAAAAAA-GCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTA
* *
199 ATGGGCCTCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGACTAA
192 ATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAA
* *
264 TCTCACCTAAATGATTATAGTTAGGCCATAAACATTGG-AAAAAAAGCATTGAGGTTTGCCAAAT
257 TCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAAT
*
328 CGAAG-AGTATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
322 CGAAGTCG-ATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATG
392 AGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAG-T------T-----A-GGA
386 AGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGA
*
443 AAGAAAAGCTTTG
450 AAGAAAAGCTTTT
* * * * *
456 AGGTTTGCCAAATCAAAG-TTGATTCAAAACGGATCTAATGGGCCCCAAAAGGCCCAAAATTACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAACA
* *
520 ATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGAC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGC
* * * * * *
584 CATTAACAATGGAAAAAATAGCTCTGAGGTTTGTCAAATCGAAATCGATTCAAAACGAAACTAAT
129 CATAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAT
649 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
194 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * * * *
714 TCAGCAAAATGATTATATTTAGGCCATAAACAATTG-AAAAAAAGCATTGGGGTTTGGCAAATTG
259 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCG
* **
778 AAGACGATTCAAAACATAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGC
324 AAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGC
* * *
843 TAAAAACTTCACAGTGGACTAATCTCACCAAAAGGATTATATTTAGGCCATAAACAATTGAAA-A
389 TAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGA
* *
907 AAGAGCATTG
454 AA-AGCTTTT
* * * * *
917 GGGTTTGGCAAATTGAAGA-CGATTCAAAACAGAACTGATGGGCCCCGAAAGGCCCAAAATAACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAACA
* * *
981 AGTG-TCCTAAATGAGCTAAAAACTTCACAGTGGAGTAATCTCACCTAAATGATTATAATTAGGC
65 AGTGTTCC-AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGC
* * * *
1045 CATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAAGACGATTCAAAACAGAACTATT
129 CATAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAT
* **
1110 GTGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAACTCTTCACAGTGGACTAATC
194 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATC
* * * * *
1175 TCACCAAAAGGATTATAGTTAGGCCATTAACAATGGAAAGAAAAGCATTGTGCTTTGCCAAATCG
259 TCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCG
* ** *
1240 AAGAT-GATTCAAACCGTCACTAATGGGCCCCGAAAAGCCCAAAATAACAAGTGTTCCAAATGAG
324 AAG-TCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
** * * *
1304 CTAAACGCTTCACAGTGGAGTAATCTCACCAAAAGGATTATAGTTAGGCCATTAACAATGGAAAG
388 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
1369 AAAAGCATTTT
453 AAAAGC-TTTT
* ** * *
1380 -GGTTTGCGAAATCGAAGAT-GATTCAAAACGTCACTATTGGGCCCCAATAGGCCCAAAATAACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGGCCCGAA-AGGCCCAAAATAACA
* *
1443 AGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAATTGATTATAGTTAGGCC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * * * *
1508 ATAAACAACT-TAAAGAAAAGCTTTGAGGTTTGCCAAATCAAAGTTGATTCAAAACGGATCTAAT
130 ATAAACAA-TGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAT
* * * *
1572 GGGCGCCAAAAGGCCCAAAATTACAATTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC-ATAT
194 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-AT
* * *
1636 CTCACCAAAATGATTATAGTTAGACCATTAACAATGGAAAAAATAGC-TCTGAGGTTTGCCAAAT
258 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCAT-TGAGGTTTGCCAAAT
* * * *
1700 CGAAATTGATTCAAAACGAAACTAATGGGCCCCAAAAGGCCCAAAATAACAAGTGTTCCAAATGA
322 CGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
* * * *
1765 GCTAAAAACATCACAGTGGACTAATCTCACCAAAATGATTATATTTAGGCCACAAACAATTGAAA
387 GCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAA
* * *
1830 AAAAAAGCATTG
451 AGAAAAGCTTTT
* * **
1842 GGGTTTAG-CAAATTGAAGA-CGATTCAAAACATAACTAATGGGCCCCGAAAGGCCCAAAATAAC
1 AGGTTT-GCCAAATCGAAGATCGATTCAAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAAC
1905 AAGTG-TCCTAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
64 AAGTGTTCC-AAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGG
* * * * * * *
1969 CCATAAACAAACAGTTGAAAAAAAAGCATTGGGGTTTGGCAAATTGAAGACGATTCAAAACAGAA
128 CCATAAAC--A-A-TGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAA
* *
2034 CTAATGGGCGCCGAAAGGCCCAAAATAACAAGTGTCCCAAATGAGCTAAAAACTTCACAGTGGAC
189 CTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGAC
*
2099 TAATCTCACCTAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCA
254 TAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCA
* *
2164 AATCAAAG-AGTATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAA
319 AATCGAAGTCG-ATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAA
* * * * * *
2228 ATGAGTTAAAATCTTCACAGTGGACTAATCTCACCAAAAGGATTATATTTAGGCCATTAACAGTG
383 ATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATG
2293 GAAAGAAAAGCATTTT
448 GAAAGAAAAGC-TTTT
** * *
2309 -GGTTTGCCAAATCGAAGAT-GATTCAAAACGTCACTAATGGGCCCCAATAGGTCCAAAATAACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGGCCCGAA-AGGCCCAAAATAACA
* *
2372 AGTGTTCCAAATGAGTTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCT
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCC
* * * *
2437 ATAAACATTGGAAAGAAAAGCTTTGAGATTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATG
130 ATAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATG
* * * *
2502 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGATAAGAACCTCATAGTGGAC-ATATC
195 GGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATC
* * * * ** * *
2566 TCACCAAAATGATTATTGTCAGGCCATAATCAACT-TAAAGGAAAGCTTTGAGGTTTACCAAATC
259 TCACCAAAATGATTATAGTTAGGCCATAAACAA-TGGAAAAAAAAGCATTGAGGTTTGCCAAATC
* * * *
2630 GAAGACGATTCAAAACGGAACTAATGGACCCCGAAAAGCCCAAAATAAGAAGTGTTCCAAATGAG
323 GAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
* * *
2695 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGTCCAAAAACAATGTAAAG
388 CTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAG
2760 AAAAG-TTTT
453 AAAAGCTTTT
* * *
2769 GAGGTTTGCAAAATCGAAG-TCGATTCAAAACGGATCTAATGGGCCCAGAAAGGCCAAAAATAAC
1 -AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGGCCC-GAAAGGCCCAAAATAAC
*
2833 AAGTGTTCCAAATTAGCTAAAAACTTCACAGTGGAC-ATATCTCACCAAAATGATTATAGTTAGG
64 AAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGG
***
2897 CCATAAACAATGGATGGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAA
128 CCATAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAA
2962 TGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
193 TGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAAT
* * **
3027 CTCACCAAAATGATTATAGTTAGTCCATAAACAATGGAAAGAAATA-TTTTGAGGTTTGCCAAAT
258 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAA-AAAAAGCATTGAGGTTTGCCAAAT
* * * * * ** *
3091 CGATGTCGAATCAAAACAGATCTACTAAGCCCCGAAAGGCCCAAAATAACAAGTATTCCAAATGA
322 CGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGA
** *
3156 GCTAAAAGTTTCACAGTGGAC-ATATCTCTCCAAAATGATTATAGTTAGGCCATAAACAATGGAA
387 GCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAA
3220 AGAAAAGCTTTT
451 AGAAAAGCTTTT
* * *
3232 AGGTTTGCCAAATCGAA-ATCTATTCAAAACGGAACTAATGGGATCCGAAAGGCGCAAAATAACA
1 AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGG-CCCGAAAGGCCCAAAATAACA
** * *
3296 AGTGTTTTAAATGAGCTAAAAGCTTCACAGTGGAC-ATATCACACCAAAATGATTATAGTTAGGC
65 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-ATCTCACCAAAATGATTATAGTTAGGC
* * *
3360 CATAAACAATGGATAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCGAAACGGAACTAAT
129 CATAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAAT
* * *
3425 GGGCCCCGAAAGGCCCAAAATTACAAGTGTTCCAGATGAGTTAAAAACTTCACAGTGGAC-ATAT
194 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTA-AT
* * * * * *
3489 CGCACCAAAATGATTATAGTTAGGCCATAAACAATTGATAGAAAAGCTTTCAGGTTTGCCAAATC
258 CTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATC
* * *
3554 GTAGTCGATTCAAAACGGTACTAGTGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
323 GAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
* *
3619 CTAAAAATTTCACAATGGAC
388 CTAAAAACTTCACAGTGGAC
3639 ATATCTGATC
Statistics
Matches: 2795, Mismatches: 320, Indels: 125
0.86 0.10 0.04
Matches are distributed among these distances:
448 254 0.09
449 10 0.00
450 3 0.00
451 117 0.04
452 2 0.00
455 1 0.00
460 11 0.00
461 281 0.10
462 1552 0.56
463 146 0.05
464 7 0.00
465 7 0.00
466 128 0.05
467 274 0.10
468 2 0.00
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (462 bp):
AGGTTTGCCAAATCGAAGATCGATTCAAAACGGAACTAATGGGCCCGAAAGGCCCAAAATAACAA
GTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCA
TAAACAATGGAAAAAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGG
GCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACTAATCTC
ACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAAAAAAGCATTGAGGTTTGCCAAATCGAA
GTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTA
AAAACTTCACAGTGGACTAATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAAGAAA
AGCTTTT
Found at i:7418 original size:18 final size:18
Alignment explanation
Indices: 7395--7429 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
7385 TCTTCATCAA
7395 CTTCCA-ATGATGGTTGTC
1 CTTCCACATG-TGGTTGTC
7413 CTTCCACATGTGGTTGT
1 CTTCCACATGTGGTTGT
7430 TCAAGTCCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.40
Consensus pattern (18 bp):
CTTCCACATGTGGTTGTC
Found at i:9521 original size:12 final size:12
Alignment explanation
Indices: 9504--9538 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
9494 CTAAAACTAA
9504 TAAAAAGAAAAT
1 TAAAAAGAAAAT
9516 TAAAAAGAAAAT
1 TAAAAAGAAAAT
9528 TAAAAAGAAAA
1 TAAAAAGAAAA
9539 GGATAGATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (12 bp):
TAAAAAGAAAAT
Found at i:14060 original size:21 final size:21
Alignment explanation
Indices: 14036--14080 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
14026 GGCGCCCACA
* *
14036 TGGTTGCCTTGAGCACCCATG
1 TGGTTGCCTTGAGAACCCAGG
*
14057 TGGTTTCCTTGAGAACCCAGG
1 TGGTTGCCTTGAGAACCCAGG
14078 TGG
1 TGG
14081 GCAGTGTCAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.31, T:0.29
Consensus pattern (21 bp):
TGGTTGCCTTGAGAACCCAGG
Done.