Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020384.1 Corchorus olitorius cultivar O-4 contig20417, 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: 20453
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5085 original size:21 final size:22
Alignment explanation
Indices: 5061--5106 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 22
5051 ATAGTAATTG
5061 ATAGA-CTTTTTTTTTGTCAGA
1 ATAGATCTTTTTTTTTGTCAGA
5082 ATAGACTTCTTTTTTTTTGTCAGA
1 ATAGA--TCTTTTTTTTTGTCAGA
5106 A
1 A
5107 AAGCTGTTGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 5 0.23
24 17 0.77
ACGTcount: A:0.24, C:0.11, G:0.13, T:0.52
Consensus pattern (22 bp):
ATAGATCTTTTTTTTTGTCAGA
Found at i:6141 original size:26 final size:26
Alignment explanation
Indices: 6112--6170 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
6102 AGTGAAATGT
* *
6112 ACCAATTGAACAACCCCCAGTAGCTA
1 ACCAAATGAACAACCCCCAATAGCTA
* *
6138 ACCAAAATGGACAACTCCCAATAGCTA
1 ACC-AAATGAACAACCCCCAATAGCTA
6165 ACCAAA
1 ACCAAA
6171 ATGCAACTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.44, C:0.32, G:0.10, T:0.14
Consensus pattern (26 bp):
ACCAAATGAACAACCCCCAATAGCTA
Found at i:6152 original size:27 final size:27
Alignment explanation
Indices: 6121--6173 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
6111 TACCAATTGA
*
6121 ACAACCCCCAGTAGCTAACCAAAATGG
1 ACAACCCCCAATAGCTAACCAAAATGG
*
6148 ACAACTCCCAATAGCTAACCAAAATG
1 ACAACCCCCAATAGCTAACCAAAATG
6174 CAACTAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.32, G:0.11, T:0.13
Consensus pattern (27 bp):
ACAACCCCCAATAGCTAACCAAAATGG
Found at i:8947 original size:106 final size:107
Alignment explanation
Indices: 8755--8950 Score: 295
Period size: 106 Copynumber: 1.8 Consensus size: 107
8745 CATCAGCAAT
8755 TTTCTTTTATTTTGTGACGATCAATAATTTTTGATGGCGCTATTGTGTAATATTCCATGACGAAA
1 TTTCTTTTATTTTGTGACGATCAAT-ATTTTTGATGGCGCTATTGTGTAATATTCCATGACGAAA
*
8820 TCTACGTTACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA
65 TCTACGTCACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA
* ** * * *
8863 TTTCTTTTATTTTGTGATGATCAAT-TTTTTTTTGGCGTTATTGTGTAGTATTTCATGACGAAAT
1 TTTCTTTTATTTTGTGACGATCAATATTTTTGATGGCGCTATTGTGTAATATTCCATGACGAAAT
* *
8927 CTACGTCACCTATTATTGTGACGT
66 CTACGTCACCAATTAGTGTGACGT
8951 CGTTGTGGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
106 55 0.70
108 24 0.30
ACGTcount: A:0.22, C:0.15, G:0.17, T:0.45
Consensus pattern (107 bp):
TTTCTTTTATTTTGTGACGATCAATATTTTTGATGGCGCTATTGTGTAATATTCCATGACGAAAT
CTACGTCACCAATTAGTGTGACGTTCTCATTTTCCGTCACGA
Found at i:17329 original size:333 final size:331
Alignment explanation
Indices: 16725--17478 Score: 959
Period size: 333 Copynumber: 2.3 Consensus size: 331
16715 GTAGCCCTGT
* * * *
16725 AACGCGTTTGTACCCAAAAACCGTGATGGTTATTACATGATTTCGGCTAAAACTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGGTTA-TACACGATTTCGGCT-AAATTTTGCAAAAATT
* *
16790 GACCCGAAAGATATTTT-CTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCGACATC
64 GACCCGAAAGAT-TTTTCCTCAATTTTTAGCGAAAATACTCATAAAAAATATATAATTCGACATC
* * * * *
16854 AAAAAGATTGAAGGGCTTTTCACACTTCTAATATTGTTTTTCCTATTTTTTCCGAATTAATTTCT
128 AAAAAAATTGAAAGCCTTTTCACACTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCT
* ** *
16919 AATTAAATCGAAACAAGATTTAGATGCTCATGAAAACAAATCCTTAAATCTAATGTAGCTGAGAT
193 AAGTAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATCCTTAAATCTAATGTAGCTGAGAT
*
16984 TTGGTTAGATGAATATAG-ATATGTCAAGGAGTCTTCACACCAAAAATCATGCAAAACTGAGC-A
258 TTGGTTAGATGAATATAGAATATGTCAAGGAGACTTCACACCAAAAATCATGCAAAACTGAGCTA
*
17047 GGGCCCCGG
323 GGGCCCCGA
* *
17056 AACGCGTTTTTAGCCGAAAACCGTGATGGTTAATACACAATTTCGGCTAAATTTTGCAAAAATTG
1 AACGCGTTTTTAGCCAAAAACCGTGATGGTT-ATACACGATTTCGGCTAAATTTTGCAAAAATTG
* * * *
17121 ACCCGAAAGATTTTTCCTCGATTTTTAGCGATAATACTCATAAAAGATATATAATTC-AGCGTCA
65 ACCCGAAAGATTTTTCCTCAATTTTTAGCGAAAATACTCATAAAAAATATATAATTCGA-CATCA
**
17185 AAAAAATTGAAAGCCTTTTTCATGCTTCTAATATCGTTTTTCCTATTTTATTTCCAAATTAATTT
129 AAAAAATTGAAAGCC-TTTTCACACTTCTAATATCGTTTTTCCTA-TTT-TTTCCAAATTAATTT
* * *
17250 CTGAGTAAATCGAAACAAGATTTAGAAACTCGTAAAAACAAATCCTTAAATAC-AATGTGGCTGA
191 CTAAGTAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATCCTTAAAT-CTAATGTAGCTGA
* * ** * *
17314 GATTTGGTTAGATGAATATAGATATATTTTAAGGAGACTTGGCGCCAAAAATCATGCAAAATTGA
255 GATTTGGTTAGATGAATATAGA-ATATGTCAAGGAGACTTCACACCAAAAATCATGCAAAACTGA
*
17379 TCTAGGGCCCCGA
319 GCTAGGGCCCCGA
** * *
17392 AACGCGTTTTTAGCCAAAGAACAATGATGG---TACACGATTTCGACCAAAATTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAA-AACCGTGATGGTTATACACGATTTCG-GCTAAATTTTGCAAAAATT
* * *
17454 GACCCAAAATATTTTT-CTTAATTTT
64 GACCCGAAAGATTTTTCCTCAATTTT
17479 AAGCCATAAA
Statistics
Matches: 366, Mismatches: 45, Indels: 22
0.85 0.10 0.05
Matches are distributed among these distances:
329 5 0.01
330 79 0.22
331 67 0.18
332 4 0.01
333 108 0.30
334 32 0.09
335 36 0.10
336 26 0.07
337 9 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
AACGCGTTTTTAGCCAAAAACCGTGATGGTTATACACGATTTCGGCTAAATTTTGCAAAAATTGA
CCCGAAAGATTTTTCCTCAATTTTTAGCGAAAATACTCATAAAAAATATATAATTCGACATCAAA
AAAATTGAAAGCCTTTTCACACTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTTCTAAG
TAAATCGAAACAAGATTTAGAAACTCATAAAAACAAATCCTTAAATCTAATGTAGCTGAGATTTG
GTTAGATGAATATAGAATATGTCAAGGAGACTTCACACCAAAAATCATGCAAAACTGAGCTAGGG
CCCCGA
Found at i:18741 original size:13 final size:13
Alignment explanation
Indices: 18723--18750 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
18713 GATTTTAGCT
18723 AAAATTTTGCAAA
1 AAAATTTTGCAAA
18736 AAAATTTTGCAAA
1 AAAATTTTGCAAA
18749 AA
1 AA
18751 TTGACCCGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (13 bp):
AAAATTTTGCAAA
Found at i:18825 original size:329 final size:318
Alignment explanation
Indices: 18091--19568 Score: 1070
Period size: 331 Copynumber: 4.5 Consensus size: 318
18081 GGCTAAAACT
* * * * ** * * *
18091 TTGCAAAAACTGACCGGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATTAAAAATATATA
1 TTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTATCCATAATACTCATAAAAAATATATA
* * * * * * * * * *
18156 ATTCAACGCCAAAAATATTGAAGGGTTTTTTACGATTCTAATATAGTTTTTCCTA-CTTTTCCGA
66 ATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGA
* * * * * *
18220 ATTAATTTCTAATTTAATCCAAACAAGATTTAGATGCTTGTAAATCCTTAAATCCAATGTGGTTG
131 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT-AA-----AAA--CAA-CTGGCTA
* * * ** *
18285 AGATTTGATTAGATGAATATAGATATTTCAAGGA-TTCTAGGCGATAAAAATCATGTAAAACT-G
187 AGATTTTATTAGATGAATATAGATATTTCAAGGAGTGC-CGGCGCCAAAAATCATGCAAAA-TGG
* * * ** * * * *
18348 A-CCTGGGGCTCCGGAACGCGTTTTTAGCCAAAAAAAGTGATGTTACACGA-TTTCGGT-TAA-T
250 AGCC-GGGACCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTACACGATTTTAGCTAAAATT
*
18409 AT--A
314 TTGCA
* * * *
18412 TTGCAAAAATTGACTC-AAAATATTTTTTTCTCAATTTTTAGCCATAATACTCATAAAAAATACA
1 TTGCAAAAATTGACCCGAAAA-A-TTTTTCCTCAATTTTTATCCATAATACTCATAAAAAATATA
* ** *
18476 TTATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCCTATTTTTTTC
64 TAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTTC
* * * * * **
18541 CGAATTAATTCCTAATTAAAACGAAACATGATTGAGATGCTTGTAAAAACAA-TGGCTCGGATTT
128 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAACTGGCTAAGATTT
* * *
18605 TGTTAGATGAATATAGATATTTCAAGGAGT-CTCGG-GACCGAAAATCATTCAAAACTGGA-CCG
193 TATTAGATGAATATAGATATTTCAAGGAGTGC-CGGCG-CCAAAAATCATGCAAAA-TGGAGCCG
*
18667 GG-CCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGAATATTACACGATTTTAGCTAAAATTTT
255 GGACCCCGAAACGCGTTTTTAGCCAAAAATCGTGATG----GTACACGATTTTAGCTAAAATTTT
18731 GCAAAAAAA
316 GC------A
* * * *
18740 TTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTGATCCATAATACTCATAAAAAGTATA
1 --TTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTATCCATAATACTCATAAAAAATATA
** * *
18805 TAATTCAATGCCAGAAAGATTGAAGGGCTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTCT
64 TAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCT
* * * * *
18870 GAATTAATTTCAAATCAAATCGAAACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATGCAA
129 GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT-------AA-----AAA--CAA
18935 CGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGCCGGCGCCAAAAATCATGCA
180 C-TGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGCCGGCGCCAAAAATCATGCA
* * *
19000 AAATTGAGCCGGGACCCCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTACACGATTTTTGCTA
244 AAATGGAGCCGGGACCCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTACACGATTTTAGCTA
19065 AAATTTTGCA
309 AAATTTTGCA
* **
19075 ----AAAAA-TGACCCGAAAAATTTTTCCTCAAATTTTTTTGGATAAAATACTCATAAAAAATAT
1 TTGCAAAAATTGACCCGAAAAATTTTTCCTC-AATTTTTATCCAT--AATACTCATAAAAAATAT
* * * *
19135 ATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTTCATATTTTTTC
63 ATAATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTC
* *
19200 TAAATTAATTTCTAACTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCA
128 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGT---AA-AAA--C---AA--C-
* * * * * *
19265 ATGTGGCTGAGATTTGATTAGATGAATATGGATATCTAAAGGAGT-CTTGGCGCCAAAAATCATG
181 ---TGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGC-CGGCGCCAAAAATCATG
* * * * * * *
19329 TAAAACGGAGCTGGGGCCCC-AGAACGC-TTTCTTATCCGAAAATTGTGATGGTTATTACACGAT
242 CAAAATGGAGCCGGGACCCCGA-AACGCGTTT-TTAGCCAAAAATCGTGATGG----TACACGAT
** *
19392 TTCGGTTAAAATTTTG--
301 TTTAGCTAAAATTTTGCA
* * ** * *
19408 -T--AAAAATTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATA
1 TTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTATCCATAATACTCATAAAAAATATATA
* * * * * * **
19470 ATTCAACGCCAAAAAGATTGAAGGGCTTTTGAC-ATTTCTAATATCATTTTCCCTATTTTTTCCA
66 ATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCATATTTTTTCTG
*
19534 AATTAATTTCTAATTAAATCGAAACATGATTCAGA
130 AATTAATTTCTAATTAAATCGAAACAAGATTCAGA
19569 GTAAAAATAA
Statistics
Matches: 951, Mismatches: 140, Indels: 121
0.78 0.12 0.10
Matches are distributed among these distances:
313 31 0.03
314 56 0.06
315 5 0.01
316 3 0.00
317 8 0.01
318 8 0.01
319 2 0.00
320 5 0.01
321 14 0.01
322 83 0.09
323 7 0.01
324 43 0.05
326 2 0.00
327 4 0.00
328 63 0.07
329 98 0.10
330 21 0.02
331 207 0.22
332 105 0.11
334 13 0.01
335 43 0.05
340 3 0.00
341 24 0.03
342 3 0.00
343 3 0.00
344 62 0.07
345 35 0.04
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (318 bp):
TTGCAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTATCCATAATACTCATAAAAAATATATA
ATTCAACACCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGA
ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAACTGGCTAAGATTTTAT
TAGATGAATATAGATATTTCAAGGAGTGCCGGCGCCAAAAATCATGCAAAATGGAGCCGGGACCC
CGAAACGCGTTTTTAGCCAAAAATCGTGATGGTACACGATTTTAGCTAAAATTTTGCA
Found at i:19529 original size:663 final size:639
Alignment explanation
Indices: 18037--19564 Score: 1641
Period size: 663 Copynumber: 2.3 Consensus size: 639
18027 GGGGTCTTGG
* * * * * *
18037 AACGCGTTTTCAACCAAAAACTGTGATGATTATTACACGATTTCGGCTAAAACTTTGCAAAAACT
1 AACGCGTTTTTAGCCAAAAATTGTGATGATTATTACACGATTTCGGTTAAAATTTTGCAAAAATT
* *
18102 GACCGGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATTAAAAATATATAATTCAACGCCA
66 GACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
* * * *
18167 AAAATATTGAAGGGTTTTTTACGA-TTCTAATAT-AGTTTTTCCTA-CTTTTCCGAATTAATTTC
131 AAAAGATTGAAGGGCTTTTCAC-ATTTCTAATATCA-TTTTTCCTATTTTTTCCGAATTAATTTC
* * * * * *
18229 TAATTTAATCCAAACAAGATTTAGATGCTTGTAAATCCTTAAATCCAATGTGGTTGAGATTTGAT
194 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAATCCTTAAATCCAACGTGGCTAAGATTTGAT
* * * * *
18294 TAGATGAATATAGATATTTCAAGGATTCTAGGCGATAAAAATCATGTAAAACTGACCTGGGGCTC
259 TAGATGAATATAGATATTTCAAGGATGCTAGGCGACAAAAATCATGCAAAACTGACCTGGGACCC
* * * * *
18359 CGGAACGCGTTTTTAGCCAAAAAAAGTGATGTTACACGATTTCGGTTAATATATTGCAAAAATTG
324 CGAAACGCGTTTTTAGCCAAAAAAAGTGATGGTACACGATTTCGGCTAAAATATTGCAAAAAATG
* * *
18424 ACTCAAAATATTTTTTTCTCAATTTTTAGCCATAATACTCATAAAAAATACATTATTCAACACCA
389 ACCCAAAATATTTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATACATAATTCAACACCA
* * * *
18489 AAAAGATTGAAGGGCTTTTCACGCTTCAAATATCGTTTTTCCTATTTTTTTCCGAATTAATTCCT
454 AAAAGATTGAAGGACTTTTCACGCTTCAAATATCATTTTTCATATTTTTTTCCAAATTAATTCCT
* * *
18554 AATTAAAACGAAACATGATTGAGATGCTTGTAAAAACAATGGCTCGGATTTTGTTAGATGAATAT
519 AACTAAAACGAAACAAGATTCAGATGCTTGTAAAAACAATGGCTCGGATTTTGTTAGATGAATAT
* * *
18619 AGATATTTCAAGGAGTCTCGGGACCGAAAATCATTCAAAACTGGACCGGGCCCCGA
584 AGATATCTAAAGGAGTCTCGGGACCAAAAATCATTCAAAACTGGACCGGGCCCCGA
* * **
18675 AACGCGTTTTTAGCCAAAAATCGTGATGAATATTACACGATTTTAGCTAAAATTTTGCAAAAAAA
1 AACGCGTTTTTAGCCAAAAATTGTGATGATTATTACACGA-TTT--C-----GGTT-----AAAA
* * * *
18740 TTTTGCAAAAATTGACCCGAAAGATATTTCCTCAA-TTTTGATCCATAATACTCATAAAAAGTAT
53 TTTTGCAAAAATTGACCCGAAAGATATTTCCTCAATTTTTG-GCTAAAATACTCATAAAAAATAT
* * * * * *
18804 ATAATTCAATGCCAGAAAGATTGAAGGGCTTTTCACGTTTTTAATATCGTTTTTCATATTTTTTC
117 ATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCACATTTCTAATATCATTTTTCCTATTTTTTC
* * * * *
18869 TGAATTAATTTCAAATCAAATCGAAACAAGATTTAGATTCTCGTAAAAACAAATCCTTAAATGCA
182 CGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT------AAATCCTTAAATCCA
* * *
18934 ACGTGGCTAAGATTTTATTAGATGAATATAGATATTTCAAGGAGTGC-CGGCGCCAAAAATCATG
241 ACGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGA-TGCTAGGCGACAAAAATCATG
* * ** **
18998 CAAAATTGAGCC-GGGACCCCGAAATGCGTTTTTAGCCAAAAATCGTGATGGTACACGATTTTTG
305 CAAAACTGA-CCTGGGACCCCGAAACGCGTTTTTAGCCAAAAAAAGTGATGGTACACGATTTCGG
* * *
19062 CTAAAATTTTGCAAAAAATGACCCGAAAA-A-TTTTTCCTCAAATTTTTTTG-GATAAAATACTC
369 CTAAAATATTGCAAAAAATGACCC-AAAATATTTTTTCCTC-AA-TTTTTAGCCAT--AATACTC
* * * **
19124 ATAAAAAATATATAATTTAACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCATTTTT
429 ATAAAAAATACATAATTCAACACCAAAAAGATTGAAGGACTTTTCACGCTTCAAATATCATTTTT
* * *
19189 CATA-TTTTTTCTAAATTAATTTCTAACTAAATCGAAACAAGATTCAGATGCTTGTAAAAACAAA
494 CATATTTTTTTCCAAATTAATTCCTAACTAAAACGAAACAAGATTCAGATGCTTGT-------AA
* *
19253 TTCTTAAATCCAATGTGGCT-GAGA-TTTGATTAGATGAATATGGATATCTAAAGGAGTCTTGGC
552 -----AAA--CAA--TGGCTCG-GATTTTG-TTAGATGAATATAGATATCTAAAGGAGTCTCGG-
*
19316 G-CCAAAAATCATGT-AAAAC-GGAGCTGGGGCCCC-A
605 GACCAAAAATCAT-TCAAAACTGGA-C-CGGGCCCCGA
* * * *
19350 GAACGC-TTTCTTATCCGAAAATTGTGATGGTTATTACACGATTTCGGTTAAAATTTTGTAAAAA
1 -AACGCGTTT-TTAGCCAAAAATTGTGATGATTATTACACGATTTCGGTTAAAATTTTGCAAAAA
19414 TTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGC
64 TTGACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * *
19479 CAAAAAGATTGAAGGGCTTTTGACATTTCTAATATCATTTTCCCTATTTTTTCCAAATTAATTTC
129 CAAAAAGATTGAAGGGCTTTTCACATTTCTAATATCATTTTTCCTATTTTTTCCGAATTAATTTC
*
19544 TAATTAAATCGAAACATGATT
194 TAATTAAATCGAAACAAGATT
19565 CAGAGTAAAA
Statistics
Matches: 727, Mismatches: 108, Indels: 85
0.79 0.12 0.09
Matches are distributed among these distances:
638 35 0.05
639 3 0.00
641 1 0.00
646 1 0.00
650 5 0.01
651 101 0.14
652 42 0.06
657 8 0.01
658 141 0.19
659 58 0.08
660 67 0.09
663 142 0.20
664 5 0.01
666 2 0.00
668 2 0.00
671 3 0.00
673 4 0.01
674 8 0.01
675 59 0.08
676 40 0.06
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (639 bp):
AACGCGTTTTTAGCCAAAAATTGTGATGATTATTACACGATTTCGGTTAAAATTTTGCAAAAATT
GACCCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCCA
AAAAGATTGAAGGGCTTTTCACATTTCTAATATCATTTTTCCTATTTTTTCCGAATTAATTTCTA
ATTAAATCGAAACAAGATTTAGATGCTCGTAAATCCTTAAATCCAACGTGGCTAAGATTTGATTA
GATGAATATAGATATTTCAAGGATGCTAGGCGACAAAAATCATGCAAAACTGACCTGGGACCCCG
AAACGCGTTTTTAGCCAAAAAAAGTGATGGTACACGATTTCGGCTAAAATATTGCAAAAAATGAC
CCAAAATATTTTTTCCTCAATTTTTAGCCATAATACTCATAAAAAATACATAATTCAACACCAAA
AAGATTGAAGGACTTTTCACGCTTCAAATATCATTTTTCATATTTTTTTCCAAATTAATTCCTAA
CTAAAACGAAACAAGATTCAGATGCTTGTAAAAACAATGGCTCGGATTTTGTTAGATGAATATAG
ATATCTAAAGGAGTCTCGGGACCAAAAATCATTCAAAACTGGACCGGGCCCCGA
Found at i:19981 original size:15 final size:16
Alignment explanation
Indices: 19957--19986 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
19947 ATAAATAATA
19957 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
19972 ATATTATAATCTAAA
1 ATATTATAATCTAAA
19987 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Done.