Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005543.1 Corchorus capsularis cultivar CVL-1 contig05561, 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: 4113
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:315 original size:184 final size:184
Alignment explanation
Indices: 5--339 Score: 449
Period size: 184 Copynumber: 1.8 Consensus size: 184
1 GAAT
* ** *
5 TTTTTTTTCGGAGTCATTCTTAGCCGAAACCGTGTAATAACCATCACTATTATTGGTTTAAAAAT
1 TTTTTTTTCGGAGTCATTCTTAGCCGAAACAGTGTAATAACCATCACTATTATTGGGCTAAAAAC
* ** * **
70 GCGTTTCGGAGCCCAATCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGGAATATCTCTA
66 GCATTTCGGAGCCCAAGATCAGTTTAGCATGATTTTTGGCAGAAAGCCTCCTTCAAATATCTCTA
*
135 TTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTTTTTTTCAGAAAA
131 TTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTTTTTTTCAGAAAA
* * *
189 TTTTTTTT-GG-GTCCATTTTTAGCCGAAAACAGTGTATTAACCATCACTGTTATTGGGCTAAAA
1 TTTTTTTTCGGAGT-CATTCTTAGCCG-AAACAGTGTAATAACCATCACTATTATTGGGCTAAAA
* * ** * *
252 ACGCATTTTGGGGCCCCGGATCAGTTTAGCATGATTTTTGGCAGAAATCCTCTTTCAAATATCTC
64 ACGCATTTCGGAGCCCAAGATCAGTTTAGCATGATTTTTGGCAGAAAGCCTCCTTCAAATATCTC
*
317 TATTCATTGAACCAAATCTCAGC
129 TATTCATCGAACCAAATCTCAGC
340 TAGATTGGGT
Statistics
Matches: 128, Mismatches: 21, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
182 2 0.02
183 13 0.10
184 113 0.88
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (184 bp):
TTTTTTTTCGGAGTCATTCTTAGCCGAAACAGTGTAATAACCATCACTATTATTGGGCTAAAAAC
GCATTTCGGAGCCCAAGATCAGTTTAGCATGATTTTTGGCAGAAAGCCTCCTTCAAATATCTCTA
TTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTTTTTTTCAGAAAA
Found at i:1197 original size:321 final size:323
Alignment explanation
Indices: 179--4113 Score: 4436
Period size: 322 Copynumber: 12.1 Consensus size: 323
169 AGGATTTTTT
* * *
179 TTTCAGAAAATTTTTTTT-GG-GTCCATTTTTAGCCGAAAACAGTGTATTAACCATCACTGTTAT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCG-AAACAGTGTACTAACCATCACTGTTAT
* * * * * * * *
242 TGGGCTAAAAACGCATTTTGGGGCCCCGGATCAGTTTAGCATGATTTTTGGCAGAAATCCTCTTT
65 TTGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
* * * * * * * * ** * *
307 CAAATATCTCTATTCATTGAACCAAATCTCAGCTAGATTGGGTTTTGGGATTTGTTTTTATGTGC
130 GAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGC
** * * * *
372 ATAGGAATTATGTTTTGATTTAATTAGAAATAAATTCAGAAAAAAATGAAAAAACGATATTGGAA
195 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAG--AAAAATGGAAAAACAATATTGGAA
* * *
437 GCGTGCAAAACCCTTCAAATTTTTTTTGTATTGAATTATATATTTTTTTCCGAGTATTGTGGCAA
258 GCGTGAAAAACCCTTC-AATTTTTTTGGTATTGAATTATATA-TTTTTTCCGAGTATTGTGGAAA
*
502 CAA
321 AAA
***** *
505 TTTCAGAAAAAAAATTTTCGGA-TCCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * * * * *
569 GGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTCGCATGATTTTTGGTAGAAATCCTCCTTG
66 TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
* * * * * *
634 AAATATCTCTATTCATCGAACCAAAGCTCAGCTACATTGGATTTAAGGATTTGTTTTTATGAGCA
131 AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
** * * * * *
699 TAGGAATTGTGTTTTGATTTAATTAGAAATAAATTCGGGAAAAATGAAAAAACGATATTGGAAGC
196 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTC-AGAAAAATGGAAAAACAATATTGGAAGC
764 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
260 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* * * * *
828 TTCCAGAAATTATTTTTTCCG-TTCCATTCTTAGCCGAAACAGTGTACTAACCAT-ACCGTTATT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * *
891 TGGCTAAAAACGCGTTCCGGTGCCACGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
66 TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
* * * *
956 GAATATCTCTATTTATCGAACCAAATCTCAGCCACAATAGATTTAAGGTTTTGTTTTTACGAGCA
131 AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* * *
1021 TCTGAATTTTATTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAAACG
196 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCG
* *
1086 TGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATCTTTTCCGAGTATTGTGGAAAAAA
261 TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* * *
1149 TTTCAGAAATTTTTTTTTCGGAGT-CATTCTTAGCCAAAACAATGTACTAACCATCACTG-TAAT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * *
1212 TGGCCTAAAAACGTGTTTCGGAGCACCGGCACAGTTTTGCAT-AGTTTTTGGCAGAAAGCCTCCT
66 TGG-CTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGA-TTTTTGGCAGAAAGCCTCCT
* *
1276 TGAAATATCTCTATTCATCGTACCAAATCTCAACCACAATGGATTTAAGGATTTGTTTTTACGAG
129 TGAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAG
* * *
1341 CATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAATAATATTGGAAG
194 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAG
*
1406 CGAGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTCTTTCCGAGTATTGT-GACA
259 CGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATA--TTT-TTTCCGAGTATTGTGGA-A
1470 AAAA
320 AAAA
* * * * *
1474 TTTTAGAAA-ATCTTTTTC-GAGTCCATTCTTAGCCGAAACAGTGTAC---CCATTACCGTTATT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * * * * * * *
1534 GGGCTAAAAACGTGTTTCGGGGTCCTGGCTCAGTTTTGCTTGATATTTGGCAAAAAGCCTCCTTG
66 TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
* * *
1599 GAATATCTCTATTCATCGTACCAAATATCAGTCACAATAGATTTAAGGATTTGTTTTTACGAGCA
131 AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* * *
1664 TCTGAATTTTGTTTCGATTTAATGAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAAACG
196 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCG
* *
1729 TGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATCTTTTCCGAGTATTGTGGAAAAAA
261 TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* * *
1792 TTTCAG-AATTTTTTTTTCGGAGT-CATTCTTAGCCGAAACCGTGTAATAACCATCACTATTA-T
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
*
1854 TGGTCTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCT-C--
66 TGG-CTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
* * *
1916 GAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTCATGATTTGTTTTTACAAGC
130 GAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGC
* * *
1981 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCTGAAAATTGAAAAAACAATATTGGAAGC
195 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGC
* * *
2046 GAGAAAAACCCTTTAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGT-G-ACAAA
260 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* **** * *
2108 TTTTAGAAA-AAAATTTTCGG-GTCCATTCTTAGCCGAAACAGTGTACTAACCATTACCGTTATT
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * *
2171 GGGTTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
66 TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
*
2236 GAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
131 AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* * * * *
2301 TCTGACTTTTGTTTCGATTCAATTAGAAATAAATACAGAAAAATAGAAAAATAATATTGGAAGCG
196 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCG
*
2366 TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGATAAAA
261 TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
***** * * *
2429 TTTCAGAAAAAAAATTTTCGTA-TCCATTTTTAGCCGAAACCGTGTACTAACCATCACTGTTA-T
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* * * * *
2492 TGGTCTAAAAACGCGTTTCGGAGCCGCGGCTTAGTTTTGCATAATTTTTAGCCA-AAAGTCTCCT
66 TGG-CTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTT-GGCAGAAAGCCTCCT
* *
2556 TGAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGTG
129 TGAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAG
* * *
2621 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACGATATAGGAAG
194 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAG
* * *
2686 CGTGAAAAACCCTTCAATTTTTTTGGTATAGAATTATATATTTTATCCGAGTATTGTGGCAAAAA
259 CGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* * * * * * *
2751 TTTCAAGAAA-ATTCTTTTCGG-GTCCATTCTTAGCCGAAAGAATATACTAAACATCACTATTAT
1 TTTC-AGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTAT
* * * *
2814 TGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGAGTTTTGGCAGAAAGCCTCCTT
65 TTGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
* * * * * * * *
2879 GAAATATCTCCATTCATCGAACCAAATCTCACCCACATTGGATTTAAGGATCTGTTTTTACGCGT
130 GAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGC
* * * * * *
2944 ATCTGAATTATGTTTCGATTTAATTAAAAATAAATTCGGAAAAACGAAAAAACGATATTGGAAGC
195 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGC
* * *
3009 GTGAAAAACCCTTCAATATTTTTGGTATTGAATTATAGATTTTTTCCGAGTATTGTGGCAAAAA
260 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
**** * *** * * *
3073 TTTCAGGAAATCTTTTCCGAATATTGT-GGAAAAAATTC----CAGAAATTTTTTTTTACGGAGC
1 TTTCA-GAAAT-TTTT-----T-TT-TCGGAGTCCATTCTTAGCCGAAA---CAGTGTAC-TAAC
** *** * * **** *
3133 CATTC-CTGGCCGAAACCGTG-TACAAATCATCACAGTTATTGGTCTAAAAACGCGCTTCGAG-G
53 CA-TCACT-G--TTATTTG-GCTA-AAA--A-CGC-GTT-TCGG---AGCCCCG-GC-TC-AGTT
*** * * **** * * * ***
3195 CCCCAGCTCAGTTTT-GCATG-ATTTTTGGC-AGAAA-ACCTCCTTGGAATATC-TC-TA-TTTA
101 TTGCA--TGATTTTTGGCA-GAAAGCCT-CCTTGAAATATCT-C-T---AT-TCATCGTACCAAA
** *
3253 TCGT-A-CCA-AATCTCAG-TCACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTG
156 TC-TCAGCCACAA--T-AGAT-TTAA-GGA-TT-------TGTTTTTACGAGCATCTGAATTTTG
*
3314 TTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCCT
207 TTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCGTGAAAAACCCT
* *
3379 TCAATTTTTTTGGTATTGAATTATATATTTTTTCGGAATATTGTGGAAAAAA
272 TCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
* * * * *
3431 TTCCAGAAATTTTTTTTTCGGAGT-CATTCTTAGCCGAAACCGTGTAATAACCATCACTATTATA
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* ** * *
3495 TGTCTAAAAACGCGTTTCGGAGCCCCATCTCAGTCTTGCATGATTTTTGGAAGAAAGCCTCCTTG
66 TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
* *
3560 GAATATCTCTATTCATCGTACTAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
131 AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* *
3625 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAAACG
196 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCG
* *
3690 TGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATATTTTCCGAGTATTGTGGAAAAAA
261 TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
*
3753 TTTCAGAAATTTTTTTTTCGGAGT-CATTCTTAGCCGAAACAATGTACTAACCATCACTGTTA-T
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
* *
3816 TGGCTTAAAAACGCGTTTCGGAGCACCGGCACAGTTTTGCAT-AGTTTTTGGCAGAAAGCCTCCT
66 TGGC-TAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGA-TTTTTGGCAGAAAGCCTCCT
* *
3880 TGAAATATCTCTATTCATCGTACCAAATCTCAACCACAATGGATTTAAGGATTTGTTTTTACGAG
129 TGAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAG
* * * *
3945 TATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAATGGAAAAATAATATTGGAAG
194 CATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAG
* * * *
4009 CGAGAAAAACCCTTCAACTTTTTTTTTGTATTTAATTATATATTTTTTCCGAGTATTGTGGCAAA
259 CGTGAAAAACCCTTCAA--TTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAA
4074 AA
322 AA
* ***
4076 TTTTAGAAA--AAATTTTCGG-GTCCATTCTTAGCCGAAAC
1 TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAAC
Statistics
Matches: 3088, Mismatches: 403, Indels: 241
0.83 0.11 0.06
Matches are distributed among these distances:
315 2 0.00
316 103 0.03
317 9 0.00
318 222 0.07
319 180 0.06
320 7 0.00
321 493 0.16
322 1265 0.41
323 135 0.04
324 58 0.02
325 66 0.02
326 190 0.06
327 21 0.01
329 5 0.00
330 14 0.00
331 17 0.01
332 9 0.00
333 12 0.00
334 16 0.01
335 11 0.00
336 1 0.00
337 3 0.00
338 2 0.00
339 3 0.00
340 6 0.00
341 3 0.00
342 2 0.00
343 3 0.00
344 1 0.00
345 10 0.00
346 17 0.01
347 12 0.00
348 8 0.00
349 16 0.01
350 14 0.00
351 4 0.00
353 5 0.00
356 4 0.00
357 5 0.00
358 134 0.04
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (323 bp):
TTTCAGAAATTTTTTTTTCGGAGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACTGTTATT
TGGCTAAAAACGCGTTTCGGAGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
AAATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAGCG
TGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAAA
Found at i:2963 original size:644 final size:643
Alignment explanation
Indices: 179--4113 Score: 5098
Period size: 644 Copynumber: 6.1 Consensus size: 643
169 AGGATTTTTT
* * * * *
179 TTTC-AGAAAATTTTTTTTGGGTCCATTTTTAGCCGAAAACAGTGTATTAACCATCACTGTTATT
1 TTTCTAGAAAATTATTTTCGGGTCCATTCTTAGCCG-AAACAGTGTACTAACCATCACCGTTATT
* * * * *
243 GGGCTAAAAACGCATTTTGGGGCCCCGGA-TCAGTTTAGCATGATTTTTGGCAGAAATCCTCTTT
65 GGGCTAAAAACGCGTTTCGGGGCCCC-GACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
** * * * * * * ** * *
307 CAAATATCTCTATTCATTGAACCAAATCTCAGCTAGATTGGGTTTTGGGATTTGTTTTTATGTGC
129 GGAATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGC
** * * * *
372 ATAGGAATTATGTTTTGATTTAATTAGAAATAAATTCAGAAAAAAATGAAAAAACGATATTGGAA
194 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAG--AAAAATGGAAAAACAATATTGGAA
* * * * *
437 GCGTGCAAAACCCTTCAAATTTTTTTTGTATTGAATTATATATTTTTTTCCGAGTATTGTGGCAA
257 ACGTGAAAAACCCTTC-AATTTTTTTGGTATTGAATCATATA-TTTTTTCCGAGTATTGTGGAAA
* **
502 CAATTTCAGAAAAAAAATTTTCGGA-TCCATTCTTAGCCGAAACAATGTACTAACCATCACTGTT
320 AAATTTCAGAAAAAATTTTTTCGGAGT-CATTCTTAGCCGAAACAATGTACTAACCATCACTGTT
* * * * * * * *
566 ATTGGGCTAAAAACGCGTTTCGGGGCCCCGGCTAAGTTTCGCATGATTTTTGGTAGAAATCCTCC
384 ATTGGTCTAAAAACGCGTTTCGGAGCACCGGCTCAGTTTTGCATAATTTTTGGCAGAAAGCCTCC
* * * * *
631 TTGAAATATCTCTATTCATCGAACCAAAGCTCAGCTACATTGGATTTAAGGATTTGTTTTTATGA
449 TTGAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGA
** * * * *
696 GCATAGGAATTGTGTTTTGATTTAATTAGAAATAAATTCGGGAAAAATGAAAAAACGATATTGGA
514 GCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTC-GGAAAAATGGAAAAACAATATTGGA
*
761 AGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAA
578 AGCGAGAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAA
826 A
643 A
* * * *
827 ATTCCAG-AAATTATTTTTTCCGTTCCATTCTTAGCCGAAACAGTGTACTAACCAT-ACCGTTAT
1 TTTCTAGAAAATTA--TTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTAT
* * * * *
890 TTGGCTAAAAACGCGTTCCGGTGCCACGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
64 TGGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTT
* *
955 GGAATATCTCTATTTATCGAACCAAATCTCAGCCACAATAGATTTAAGGTTTTGTTTTTACGAGC
129 GGAATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGC
* *
1020 ATCTGAATTTTATTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAAAC
194 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAAC
*
1085 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATCTTTTCCGAGTATTGTGGAAAAAAT
259 GTGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGGAAAAAAT
*** * *
1150 TTCAGAAATTTTTTTTTCGGAGTCATTCTTAGCCAAAACAATGTACTAACCATCACTGTAATTGG
324 TTCAGAAAAAATTTTTTCGGAGTCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATTGG
* * * *
1215 CCTAAAAACGTGTTTCGGAGCACCGGCACAGTTTTGCATAGTTTTTGGCAGAAAGCCTCCTTGAA
389 TCTAAAAACGCGTTTCGGAGCACCGGCTCAGTTTTGCATAATTTTTGGCAGAAAGCCTCCTTGAA
*
1280 ATATCTCTATTCATCGTACCAAATCTCAACCACAATGGATTTAAGGATTTGTTTTTACGAGCATC
454 ATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATC
* *
1345 TAAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAATAATATTGGAAGCGAG
519 TGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACAATATTGGAAGCGAG
*
1410 AAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTCTTTCCGAGTATTGTGACAAAAA
584 AAAAACCCTTCAATTTTTTTGGTATTGAATTATATA--TTT-TTTCCGAGTATTGTG-GAAAAA
* *
1474 TTT-TAGAAAATCT-TTTTCGAGTCCATTCTTAGCCGAAACAGTGTAC---CCATTACCGTTATT
1 TTTCTAGAAAAT-TATTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTATT
* * * * * * *
1534 GGGCTAAAAACGTGTTTCGGGGTCCTGGCTCAGTTTTGCTTGATATTTGGCAAAAAGCCTCCTTG
65 GGGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTG
* * *
1599 GAATATCTCTATTCATCGTACCAAATATCAGTCACAATAGATTTAAGGATTTGTTTTTACGAGCA
130 GAATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCA
* *
1664 TCTGAATTTTGTTTCGATTTAATGAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAAACG
195 TCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAACG
*
1729 TGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATCTTTTCCGAGTATTGTGGAAAAAATT
260 TGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGGAAAAAATT
*** ** * *
1794 TCAG-AATTTTTTTTTCGGAGTCATTCTTAGCCGAAACCGTGTAATAACCATCACTATTATTGGT
325 TCAGAAAAAATTTTTTCGGAGTCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATTGGT
* * *
1858 CTAAAAACGCGTTTCGGAACCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCT-C--GAAA
390 CTAAAAACGCGTTTCGGAGCACCGGCTCAGTTTTGCATAATTTTTGGCAGAAAGCCTCCTTGAAA
* * * *
1920 TATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTCATGATTTGTTTTTACAAGCATCT
455 TATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCT
* * *
1985 GAATTTTGTTTCGATTTAATTAGAAATAAATTCTGAAAATTGAAAAAACAATATTGGAAGCGAGA
520 GAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACAATATTGGAAGCGAGA
* *
2050 AAAACCCTTTAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGT-GACAAA
585 AAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAA
** *
2108 TTT-TAGAAAAAAATTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATTACCGTTATTG
1 TTTCTAGAAAATTATTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTATTG
* *
2172 GGTTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGG
66 GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGG
*
2237 AATATCTCTATTCATCGTACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCAT
131 AATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * *
2302 CTGACTTTTGTTTCGATTCAATTAGAAATAAATACAGAAAAATAGAAAAATAATATTGGAAGCGT
196 CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAACGT
* *
2367 GAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGATAAAATTT
261 GAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGGAAAAAATTT
** * * **
2432 CAGAAAAAAAATTTTCGTA-TCCATTTTTAGCCGAAACCGTGTACTAACCATCACTGTTATTGGT
326 CAGAAAAAATTTTTTCGGAGT-CATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATTGGT
* * *
2496 CTAAAAACGCGTTTCGGAGC-CGCGGCTTAGTTTTGCATAATTTTTAGCCA-AAAGTCTCCTTGA
390 CTAAAAACGCGTTTCGGAGCAC-CGGCTCAGTTTTGCATAATTTTT-GGCAGAAAGCCTCCTTGA
*
2559 AATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGTGCAT
453 AATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCAT
* * *
2624 CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACGATATAGGAAGCGT
518 CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACAATATTGGAAGCGA
* *
2689 GAAAAACCCTTCAATTTTTTTGGTATAGAATTATATATTTTATCCGAGTATTGTGGCAAAAA
583 GAAAAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGG-AAAAA
* * * * * * **
2751 TTTCAAGAAAATTCTTTTCGGGTCCATTCTTAGCCGAAAGAATATACTAAACATCACTATTATTG
1 TTTCTAGAAAATTATTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTATTG
* *
2816 GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGAGTTTTGGCAGAAAGCCTCCTTGA
66 GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGG
* * * * * * *
2881 AATATCTCCATTCATCGAACCAAATCTCACCCACATTGGATTTAAGGATCTGTTTTTACGCGTAT
131 AATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCAT
* * * * * * *
2946 CTGAATTATGTTTCGATTTAATTAAAAATAAATTCGGAAAAACGAAAAAACGATATTGGAAGCGT
196 CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAACGT
* * *
3011 GAAAAACCCTTCAATATTTTTGGTATTGAATTATAGATTTTTTCCGAGTATTGTGGCAAAAATTT
261 GAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGG----AA---
* * *
3076 CAGGAAATCTTTTCCGAATATTGTGGAAAAAATTCCAGAAATTTTTTTTTACGGAGCCATTCCTG
319 -A--AAA---TTT-C----A-----G----AA----A-AAA---TTTTTT-CGGAGTCATTCTTA
** * * * * * *
3141 GCCGAAACCGTGTACAAATCATCACAGTTATTGGTCTAAAAACGCGCTTC-GAGGCCCCAGCTCA
355 GCCGAAACAATGTACTAACCATCACTGTTATTGGTCTAAAAACGCGTTTCGGA-GCACCGGCTCA
* * * * *
3205 GTTTTGCATGATTTTTGGCAGAAAACCTCCTTGGAATATCTCTATTTATCGTACCAAATCTCAGT
419 GTTTTGCATAATTTTTGGCAGAAAGCCTCCTTGAAATATCTCTATTCATCGTACCAAATCTCAGC
*
3270 CACAATAGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAA
484 CACAATGGATTTAAGGATTTGTTTTTACGAGCATCTGAATTTTGTTTCGATTTAATTAGAAATAA
* * *
3335 ATTCAGAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTGGTATTGAAT
549 ATTCGGAAAAATGGAAAAACAATATTGGAAGCGAGAAAAACCCTTCAATTTTTTTGGTATTGAAT
* *
3400 TATATATTTTTTCGGAATATTGTGGAAAAA
614 TATATATTTTTTCCGAGTATTGTGGAAAAA
* * * * * * **
3430 ATTCCAGAAATTTTTTTTTCGGAGT-CATTCTTAGCCGAAACCGTGTAATAACCATCACTATTAT
1 TTTCTAGAAA-ATTATTTTCGG-GTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTAT
* * * *
3494 AT-GTCTAAAAACGCGTTTCGGAGCCCC-ATCTCAGTCTTGCATGATTTTTGGAAGAAAGCCTCC
64 -TGGGCTAAAAACGCGTTTCGGGGCCCCGA-CTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCC
* *
3557 TTGGAATATCTCTATTCATCGTACTAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGA
127 TTGGAATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGA
*
3622 GCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTTGAA
192 GCATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAA
*
3687 ACGTGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATATTTTCCGAGTATTGTGGAAAAA
257 ACGTGAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGGAAAAA
***
3752 ATTTCAGAAATTTTTTTTTCGGAGTCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATT
322 ATTTCAGAAAAAATTTTTTCGGAGTCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATT
* *
3817 GG-CTTAAAAACGCGTTTCGGAGCACCGGCACAGTTTTGCATAGTTTTTGGCAGAAAGCCTCCTT
387 GGTC-TAAAAACGCGTTTCGGAGCACCGGCTCAGTTTTGCATAATTTTTGGCAGAAAGCCTCCTT
* *
3881 GAAATATCTCTATTCATCGTACCAAATCTCAACCACAATGGATTTAAGGATTTGTTTTTACGAGT
451 GAAATATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGC
* *
3946 ATCTAAATTTTGTTTCGATTTAATTAGAAATAAATTCGG-AAAATGGAAAAATAATATTGGAAGC
516 ATCTGAATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACAATATTGGAAGC
* *
4010 GAGAAAAACCCTTCAACTTTTTTTTTGTATTTAATTATATATTTTTTCCGAGTATTGTGGCAAAA
581 GAGAAAAACCCTTCAA--TTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGG-AAAA
4075 A
643 A
*
4076 TTT-TAGAAAA-AATTTTCGGGTCCATTCTTAGCCGAAAC
1 TTTCTAGAAAATTATTTTCGGGTCCATTCTTAGCCGAAAC
Statistics
Matches: 2890, Mismatches: 321, Indels: 157
0.86 0.10 0.05
Matches are distributed among these distances:
634 46 0.02
636 14 0.00
637 263 0.09
638 95 0.03
639 162 0.06
641 173 0.06
642 111 0.04
643 388 0.13
644 683 0.24
645 108 0.04
646 59 0.02
647 12 0.00
648 155 0.05
649 20 0.01
650 18 0.01
652 1 0.00
653 2 0.00
654 3 0.00
657 4 0.00
658 1 0.00
662 2 0.00
666 1 0.00
667 4 0.00
670 3 0.00
671 2 0.00
672 1 0.00
675 1 0.00
676 5 0.00
679 23 0.01
680 526 0.18
681 4 0.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (643 bp):
TTTCTAGAAAATTATTTTCGGGTCCATTCTTAGCCGAAACAGTGTACTAACCATCACCGTTATTG
GGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGCCTCCTTGG
AATATCTCTATTCATCGAACCAAATCTCAGCCACAATAGATTTAAGGATTTGTTTTTACGAGCAT
CTGAATTTTGTTTCGATTTAATTAGAAATAAATTCAGAAAAATGGAAAAACAATATTGGAAACGT
GAAAAACCCTTCAATTTTTTTGGTATTGAATCATATATTTTTTCCGAGTATTGTGGAAAAAATTT
CAGAAAAAATTTTTTCGGAGTCATTCTTAGCCGAAACAATGTACTAACCATCACTGTTATTGGTC
TAAAAACGCGTTTCGGAGCACCGGCTCAGTTTTGCATAATTTTTGGCAGAAAGCCTCCTTGAAAT
ATCTCTATTCATCGTACCAAATCTCAGCCACAATGGATTTAAGGATTTGTTTTTACGAGCATCTG
AATTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAATGGAAAAACAATATTGGAAGCGAGAA
AAACCCTTCAATTTTTTTGGTATTGAATTATATATTTTTTCCGAGTATTGTGGAAAAA
Found at i:3117 original size:34 final size:35
Alignment explanation
Indices: 3050--3122 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
3040 ATTATAGATT
* * *
3050 TTTTCCGAGTATTGTGGCAAAAATTTCAGGAAATC
1 TTTTCCGAATATTGTGGAAAAAATTCCAGGAAATC
*
3085 TTTTCCGAATATTGTGGAAAAAATTCCA-GAAATT
1 TTTTCCGAATATTGTGGAAAAAATTCCAGGAAATC
3119 TTTT
1 TTTT
3123 TTTACGGAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
34 9 0.26
35 25 0.74
ACGTcount: A:0.33, C:0.12, G:0.16, T:0.38
Consensus pattern (35 bp):
TTTTCCGAATATTGTGGAAAAAATTCCAGGAAATC
Done.