Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013698.1 Corchorus capsularis cultivar CVL-1 contig13719, 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: 157847
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1189 original size:30 final size:31
Alignment explanation
Indices: 1125--1189 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
1115 AACTTTATGT
* *
1125 TTTCCGATTGTACCCTTATTTTTAAAACATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
* *
1156 TTTCCAATTGTATCCTT-TTTTAAAAATATA
1 TTTCCAATTGTACCCTTATTTTAAAAACATA
1186 TTTC
1 TTTC
1190 TAAATTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCCTTATTTTAAAAACATA
Found at i:1196 original size:31 final size:31
Alignment explanation
Indices: 1131--1196 Score: 80
Period size: 30 Copynumber: 2.1 Consensus size: 31
1121 ATGTTTTCCG
* *
1131 ATTGTACCCTTATTTTTAAAACATATTTCCA
1 ATTGTACCCTTATTTTAAAAACATATTTCAA
* *
1162 ATTGTATCCTT-TTTTAAAAATATATTTCTAA
1 ATTGTACCCTTATTTTAAAAACATATTTC-AA
1193 ATTG
1 ATTG
1197 CCATTACTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 15 0.50
31 15 0.50
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (31 bp):
ATTGTACCCTTATTTTAAAAACATATTTCAA
Found at i:1489 original size:22 final size:22
Alignment explanation
Indices: 1461--1644 Score: 83
Period size: 22 Copynumber: 8.3 Consensus size: 22
1451 TGTCTCTATG
1461 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * * *
1483 TGGTTATTATAATTCCATGAGGA
1 TGGTTATCAAAATTTCAT-AAGA
* * *
1506 -GGTTATTAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
1527 TGGTTACCAAAATTTCAT-AG-
1 TGGTTATCAAAATTTCATAAGA
*
1547 TGCGGTTACCAAAATTTCAT-AG-
1 T--GGTTATCAAAATTTCATAAGA
* *
1569 TGTAGTTACCAAAATTTCATAGGA
1 TG--GTTATCAAAATTTCATAAGA
* * * *
1593 TCAGGTTATTAAAATTTCTTAGGT
1 T--GGTTATCAAAATTTCATAAGA
** * *
1617 TGGTTATTGAAATTTCATAGGG
1 TGGTTATCAAAATTTCATAAGA
1639 TGGTTA
1 TGGTTA
1645 ATTATCACAA
Statistics
Matches: 133, Mismatches: 18, Indels: 22
0.77 0.10 0.13
Matches are distributed among these distances:
20 3 0.02
22 107 0.80
23 4 0.03
24 18 0.14
26 1 0.01
ACGTcount: A:0.33, C:0.10, G:0.19, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:1554 original size:44 final size:45
Alignment explanation
Indices: 1505--1608 Score: 140
Period size: 44 Copynumber: 2.3 Consensus size: 45
1495 TTCCATGAGG
*
1505 AGGTTATTAAAATTCCATAGTGTGGTTACCAAAATTTCATAGTG-C
1 AGGTTATTAAAATTCCATAGTGTAGTTACCAAAATTTCATAG-GAC
** *
1550 -GGTTACCAAAATTTCATAGTGTAGTTACCAAAATTTCATAGGATC
1 AGGTTATTAAAATTCCATAGTGTAGTTACCAAAATTTCATAGGA-C
1595 AGGTTATTAAAATT
1 AGGTTATTAAAATT
1609 TCTTAGGTTG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 1 0.02
44 37 0.74
45 1 0.02
46 11 0.22
ACGTcount: A:0.36, C:0.12, G:0.16, T:0.36
Consensus pattern (45 bp):
AGGTTATTAAAATTCCATAGTGTAGTTACCAAAATTTCATAGGAC
Found at i:48323 original size:31 final size:33
Alignment explanation
Indices: 48265--48333 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 33
48255 AATTTCCCCT
* * *
48265 ATATTTTTTTAAAAAAAAAGTATAATC-GG-AA
1 ATATATTTCTAAAAAAAAAGTACAATCGGGAAA
**
48296 ATATATTTCTAAAAAAATGGTACAATCGGGAAA
1 ATATATTTCTAAAAAAAAAGTACAATCGGGAAA
48329 ATATA
1 ATATA
48334 AAGTTTCCCC
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 22 0.71
32 2 0.06
33 7 0.23
ACGTcount: A:0.51, C:0.06, G:0.12, T:0.32
Consensus pattern (33 bp):
ATATATTTCTAAAAAAAAAGTACAATCGGGAAA
Found at i:48933 original size:73 final size:73
Alignment explanation
Indices: 48814--48959 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
48804 ACATGAAAGA
48814 GAATTAGAGAAGAAACTAAAAGGAAGAGTTAAAGAGTTCAGTTCGTCAAAAATATCTTGTATATC
1 GAATTAGAGAAGAAACTAAAAGGAAGAGTTAAAGAGTTCAGTTCGTCAAAAATATCTTGTATATC
48879 TCGTTCCG
66 TCGTTCCG
48887 GAATTAGAGAAGAAACTAAAAGGAAGAGTTAAAGAGTTCAGTTCGTCAAAAATATCTTGTATATC
1 GAATTAGAGAAGAAACTAAAAGGAAGAGTTAAAGAGTTCAGTTCGTCAAAAATATCTTGTATATC
48952 TCGTTCCG
66 TCGTTCCG
48960 TTTTCATTTT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.27
Consensus pattern (73 bp):
GAATTAGAGAAGAAACTAAAAGGAAGAGTTAAAGAGTTCAGTTCGTCAAAAATATCTTGTATATC
TCGTTCCG
Found at i:52444 original size:40 final size:40
Alignment explanation
Indices: 52389--52464 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
52379 AAATAGGAGC
*
52389 TAAACCGTGATTTAATTTCTTACCTTAATTATTAGGGTGT
1 TAAACCGTGATTTAATTTATTACCTTAATTATTAGGGTGT
*
52429 TAAACC-TGGATTTAATTTATTTCCTTAATTATTAGG
1 TAAACCGT-GATTTAATTTATTACCTTAATTATTAGG
52465 AGGGTCAAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 1 0.03
40 32 0.97
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.46
Consensus pattern (40 bp):
TAAACCGTGATTTAATTTATTACCTTAATTATTAGGGTGT
Found at i:73817 original size:31 final size:31
Alignment explanation
Indices: 73742--73817 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 31
73732 TTTTTTGCAT
* *
73742 GTGGCATGCCACGTGTCACTTTTTGGTACAT
1 GTGGCATGCCACGTATCACTTTTTGGTACAC
* ** * * *
73773 ATAACGTGACACGTATCACTTTTTTGTACAC
1 GTGGCATGCCACGTATCACTTTTTGGTACAC
73804 GTGGCATGCCACGT
1 GTGGCATGCCACGT
73818 CGGACACCGT
Statistics
Matches: 32, Mismatches: 13, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (31 bp):
GTGGCATGCCACGTATCACTTTTTGGTACAC
Found at i:75337 original size:2 final size:2
Alignment explanation
Indices: 75330--75395 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
75320 ATAAGATGTA
75330 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
75372 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
75396 CAAGAGACTG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:81711 original size:59 final size:59
Alignment explanation
Indices: 81639--81872 Score: 360
Period size: 59 Copynumber: 3.9 Consensus size: 59
81629 TTCATGATGG
* * * * *
81639 AATCAATGCAGGTCTACCGCAGGATCATGATTGAAGCTTCATTATAGTGGGATCCAAATC
1 AATCAA-GCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAAATC
81699 AATCAAGCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAAATC
1 AATCAAGCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAAATC
* * *
81758 AATCAAGTAGGTCTATCGCATGATTATGATTGAAGCATGATTACAGCGGGATCCAAATC
1 AATCAAGCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAAATC
* * *
81817 AATCAAGTAGGTCTATCGCATGATTATGATTGAAGCATGATTACAGCGGGATCCAA
1 AATCAAGCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAA
81873 GATTGAAGCA
Statistics
Matches: 166, Mismatches: 8, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
59 160 0.96
60 6 0.04
ACGTcount: A:0.33, C:0.19, G:0.22, T:0.26
Consensus pattern (59 bp):
AATCAAGCAGGTCTACCGCATGATCATGATTGAAGCATGATTACAGCGGGATCCAAATC
Found at i:86022 original size:31 final size:31
Alignment explanation
Indices: 85984--86045 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
85974 TATGTTAGAC
*
85984 AAATAAGGATATAAT-AGACGTTTCAAAAGTT
1 AAATAAGGATACAATAAG-CGTTTCAAAAGTT
86015 AAATAAGGATACAATAAGCGTTTCAAAAGTT
1 AAATAAGGATACAATAAGCGTTTCAAAAGTT
86046 TTACAAAACT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 27 0.93
32 2 0.07
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.27
Consensus pattern (31 bp):
AAATAAGGATACAATAAGCGTTTCAAAAGTT
Found at i:96159 original size:6 final size:6
Alignment explanation
Indices: 96148--96177 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
96138 CACGACTGAT
96148 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC
1 CCAGCC CCAGCC CCAGCC CCAGCC CCAGCC
96178 TCAACCCCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.67, G:0.17, T:0.00
Consensus pattern (6 bp):
CCAGCC
Found at i:96185 original size:18 final size:18
Alignment explanation
Indices: 96148--96186 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
96138 CACGACTGAT
*
96148 CCAGCCCCAGCCCCAGCC
1 CCAGCCCCAGCCCCAACC
*
96166 CCAGCCCCAGCCTCAACC
1 CCAGCCCCAGCCCCAACC
96184 CCA
1 CCA
96187 AACCCAAACC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.21, C:0.64, G:0.13, T:0.03
Consensus pattern (18 bp):
CCAGCCCCAGCCCCAACC
Found at i:104715 original size:70 final size:70
Alignment explanation
Indices: 104633--104865 Score: 306
Period size: 70 Copynumber: 3.2 Consensus size: 70
104623 TTGTTTAGGT
* *
104633 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATT
104697 ATTTTA
65 ATTTTA
104703 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTGTAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATAT-CTT-T-A-TA
*
104768 TTATATTTTACCA
62 AT-TATTTT---A
* * *
104781 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
*
104846 TTATA
66 TTTTA
*
104851 TTTTACAATTTTACT
1 TTTTACTATTTTACT
104866 ATTTTTGTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 18
0.84 0.05 0.10
Matches are distributed among these distances:
70 64 0.44
71 5 0.03
72 1 0.01
73 6 0.04
74 5 0.03
75 7 0.05
76 1 0.01
77 2 0.01
78 54 0.37
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCTTTATAATTA
TTTTA
Found at i:104715 original size:78 final size:76
Alignment explanation
Indices: 104633--104870 Score: 328
Period size: 78 Copynumber: 3.1 Consensus size: 76
104623 TTGTTTAGGT
* *
104633 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-T-A-TA
1 TTTTATA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
*
104694 AT-TATTTT--A
65 TTATATTTTACA
*
104703 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTGTAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
104768 TTATATTTTACCA
65 TTATATTTTA-CA
*
104781 TTTTACTATTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTA-TATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
104846 TTATATTTTACAA
65 TTATATTTTAC-A
104859 TTTTACTATTTT
1 TTTTA-TATTTT
104871 TGTTAAAAAA
Statistics
Matches: 153, Mismatches: 5, Indels: 12
0.90 0.03 0.07
Matches are distributed among these distances:
70 49 0.32
71 5 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.57
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.50
Consensus pattern (76 bp):
TTTTATATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTAT
TATATTTTACA
Found at i:105125 original size:70 final size:69
Alignment explanation
Indices: 105043--105257 Score: 222
Period size: 70 Copynumber: 3.2 Consensus size: 69
105033 TTGTTTAGGT
*
105043 TTTTA-TAGTTTTACTCAACTAAAAACTTTATTTTTATTTAATTAAATATAATATCTTTATAATT
1 TTTTACTAGTTTTACTCAACTAAAAACTCTATTTTTA-TTAATTAAATATAATATC-TTATAATT
*
105107 ATTTTA
64 ATTATA
* *
105113 TTTTACTA-TTTTACTCAATTAAAAACTCTATTTTTA-T-ATT--ATA-ACTA--TTAT-ATT-T
1 TTTTACTAGTTTTACTCAACTAAAAACTCTATTTTTATTAATTAAATATAATATCTTATAATTAT
*
105168 TACCA
66 TA-TA
* * *
105173 TTTTACTA-TTTTACTCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACT
1 TTTTACTAGTTTTACTCAACTAAAAACTCTATTTTTAT-TAATTAAATATAATAT-CTTATAATT
105237 ATTATA
64 ATTATA
105243 TTTTAC-AGTTTTACT
1 TTTTACTAGTTTTACT
105258 ATTTTAATTA
Statistics
Matches: 120, Mismatches: 11, Indels: 28
0.75 0.07 0.18
Matches are distributed among these distances:
59 2 0.02
60 38 0.32
61 4 0.03
62 1 0.01
63 3 0.03
64 3 0.03
65 5 0.04
66 3 0.03
67 3 0.03
68 1 0.01
69 5 0.04
70 47 0.39
71 5 0.04
ACGTcount: A:0.36, C:0.12, G:0.01, T:0.51
Consensus pattern (69 bp):
TTTTACTAGTTTTACTCAACTAAAAACTCTATTTTTATTAATTAAATATAATATCTTATAATTAT
TATA
Found at i:105302 original size:410 final size:401
Alignment explanation
Indices: 104536--105338 Score: 1381
Period size: 410 Copynumber: 2.0 Consensus size: 401
104526 AATCTTAATC
104536 TATACTATATTAAAAAGTACGTTAAGCTGTAAAACTTTTGAACCGCCTATTATACCCTTATTTGT
1 TATACTATATTAAAAAGTACGTTAAGCTGTAAAACTTTTGAACCGCCTATTATACCCTTATTTGT
104601 TAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTT
66 TAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTT
104666 TTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTC
131 TTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTC
104731 TATTTTTATATAATTAAATCTAATATCCTTGTAACTATTATATTTTACCATTTTACTATTTTACT
196 TA-TTTTATATAATT-AA-CT-ATA----T-TAACTATTATATTTTACCATTTTACTATTTTACT
104796 CAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATT
252 CAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATT
**
104861 TTACTATTTTTGTTAAAAAAACTTGATATATTAGTTTTTTAAAATATATTTCTTGAATGACATTG
317 TTACTATTTTAATTAAAAAAACTTGATATATTAGTTTTTTAAAATATATTTCTTGAATGACATTG
104926 TTTAAACTTTTACAATTTTT
382 TTTAAACTTTTACAATTTTT
* * *
104946 TATACTATATTAAAAAGTACGTTCAGCTGTAAAACTTTTGAATCGCCTATTATATCCTTATTTGT
1 TATACTATATTAAAAAGTACGTTAAGCTGTAAAACTTTTGAACCGCCTATTATACCCTTATTTGT
*
105011 TAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGTTTTACTCAACTAAAAACTTTATTT
66 TAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTT
*
105076 TTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAATTAAAAACTC
131 TTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTC
105141 TA-TTT-T-T-A-T-A-T-TA-TAACTATTATATTTTACCATTTTACTATTTTACTCAACTAAAA
196 TATTTTATATAATTAACTATATTAACTATTATATTTTACCATTTTACTATTTTACTCAACTAAAA
*
105197 ACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAGTTTTACTATTT
261 ACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTACTATTT
*
105262 TAATTAAAAAAACTTGATATATTAGTTTTTTTAAATATATTTCTTGAATGACATTGTTTAAACTT
326 TAATTAAAAAAACTTGATATATTAGTTTTTTAAAATATATTTCTTGAATGACATTGTTTAAACTT
105327 TTACAATTTTT
391 TTACAATTTTT
105338 T
1 T
105339 TTAAAAATAA
Statistics
Matches: 384, Mismatches: 9, Indels: 18
0.93 0.02 0.04
Matches are distributed among these distances:
392 181 0.47
398 2 0.01
400 1 0.00
402 1 0.00
404 1 0.00
405 1 0.00
406 1 0.00
407 1 0.00
408 3 0.01
410 192 0.50
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (401 bp):
TATACTATATTAAAAAGTACGTTAAGCTGTAAAACTTTTGAACCGCCTATTATACCCTTATTTGT
TAAATATATTTCTAAATTGCCATTGTTTAGGTTTTTATAGTTTTACTCAACTAAAAACTCTATTT
TTATTTAATTAAATATAATATCTTTATAATTATTTTATTTTACTATTTTACTCAACTAAAAACTC
TATTTTATATAATTAACTATATTAACTATTATATTTTACCATTTTACTATTTTACTCAACTAAAA
ACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTATTATATTTTACAATTTTACTATTT
TAATTAAAAAAACTTGATATATTAGTTTTTTAAAATATATTTCTTGAATGACATTGTTTAAACTT
TTACAATTTTT
Found at i:106523 original size:16 final size:16
Alignment explanation
Indices: 106502--106532 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
106492 TTGAAAAATA
106502 TTACTAAATATTTATT
1 TTACTAAATATTTATT
*
106518 TTACTAAATCTTTAT
1 TTACTAAATATTTAT
106533 AATATGTAGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (16 bp):
TTACTAAATATTTATT
Found at i:107400 original size:201 final size:192
Alignment explanation
Indices: 106865--107650 Score: 874
Period size: 190 Copynumber: 4.0 Consensus size: 192
106855 AAGCTTTATA
* * * * *
106865 ATAAGGATTATTATACAATATAATGTCAATGTAAA-TTT-GACTCCATAAGCGGGTTAAGAAATT
1 ATAA-GATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTT--GAAGTT
* *
106928 GACACATACTCTATTTCATAATTAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACGT
63 GACACATACCCCATTTC---A-TAATTAAATATTTAATATTAATACATATTCCCTAAGGGGA---
* * * ** * * * * *
106993 CACATGTCAACTCATAAATCCTACACGTGCAGCCTGCTAAAATCCATTGACGTGTATAGTATAAT
121 CACATGTCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAAGTGTATTGTATAAT
107058 TTTTCTT
186 TTTTCTT
*
107065 AT-AGAATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTT-AAGTTAA
1 ATAAG-ATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTGAAGTTGA
* * *
107128 CACATACGCCATTTCATAATTAAATATTTGATATTAATACATATTCCCTAAGGGTACACATGTCA
65 CACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCA
* * *
107193 ACCCTTAAAGTTAAACCCCGCACGTGCAGTATGCTAAACTCCACTGATAGTATATTGTATAAATT
130 ACCC------TTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGA-AGTGTATTGTATAATTT
107258 TTCTT
188 TTCTT
* * *
107263 ATAAGATTATTATACAATACACTATCAGTGTGAATTTTGGACTTCATAAACGGGTTAAGAAGTTG
1 ATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTT--GAAGTTG
* *
107328 ACACATACCCCATTTCACAATTAAATATTTAATATTAATACATATTCCCTAAGGGTACACATGTC
64 ACACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTC
** * * *
107393 AACCCTTAAACCAAGCACTTGCAATTTGCTAAACTCCACTGAAGGTGTATTGTATAATTTTTCTT
129 AACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAA-GTGTATTGTATAATTTTTCTT
* * *
107458 ATAGGATTATTATACAATACACTGTTAGTGTAAATTTTGGACTCCAT-AA-GCG--G--G-TGAC
1 ATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTGAAGTTGAC
** * *
107516 ACATACCATATTTCAAAATTAATCTTATATTTAATACTAATACATATTCCCTAAGGGGACACATG
66 ACATACCCCATTTCATAATTAA----ATATTTAATATTAATACATATTCCCTAAGGGGACACATG
* *
107581 TCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGACGATGTATTATATAATTTTTC
127 TCAACCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAAG-TGTATTGTATAATTTTTC
107646 TT
191 TT
107648 ATA
1 ATA
107651 GTGAACTTAT
Statistics
Matches: 511, Mismatches: 55, Indels: 50
0.83 0.09 0.08
Matches are distributed among these distances:
186 23 0.05
187 1 0.00
189 2 0.00
190 98 0.19
191 12 0.02
193 2 0.00
194 41 0.08
195 94 0.18
197 29 0.06
198 87 0.17
199 29 0.06
200 5 0.01
201 88 0.17
ACGTcount: A:0.35, C:0.18, G:0.13, T:0.34
Consensus pattern (192 bp):
ATAAGATTATTATACAATACACTGTCAGTGTAAATTTTGGACTCCATAAACGGGTTGAAGTTGAC
ACATACCCCATTTCATAATTAAATATTTAATATTAATACATATTCCCTAAGGGGACACATGTCAA
CCCTTAAACCCCGCACGTGCAGTCTGCTAAACTCCACTGAAGTGTATTGTATAATTTTTCTT
Found at i:115037 original size:3 final size:3
Alignment explanation
Indices: 115031--115084 Score: 99
Period size: 3 Copynumber: 17.7 Consensus size: 3
115021 GAGATTTTGT
115031 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
115077 ATA ATA AT
1 ATA ATA AT
115085 GAAATCATTA
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 47 0.94
4 3 0.06
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:136092 original size:2 final size:2
Alignment explanation
Indices: 136085--136120 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
136075 ACCTCTATTT
136085 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
136121 GATCAAGTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:148467 original size:87 final size:87
Alignment explanation
Indices: 148321--148486 Score: 314
Period size: 87 Copynumber: 1.9 Consensus size: 87
148311 TACTTCCTTG
* *
148321 ATGCCAAAATATCAGCCACATCCAATTTAAAGACGTAATGAACAAAATTATGGATTCCTCAATAA
1 ATGCCAAAAGATCAGCCACATCCAATTTAAAGACGTAATGAACAAAATTACGGATTCCTCAATAA
148386 TCGTCTAAGGTTCAGTAACTTA
66 TCGTCTAAGGTTCAGTAACTTA
148408 ATGCCAAAAGATCAGCCACATCCAATTTAAAGACGTAATGAACAAAATTACGGATTCCTCAATAA
1 ATGCCAAAAGATCAGCCACATCCAATTTAAAGACGTAATGAACAAAATTACGGATTCCTCAATAA
148473 TCGTCTAAGGTTCA
66 TCGTCTAAGGTTCA
148487 TTGGTTCACT
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.26
Consensus pattern (87 bp):
ATGCCAAAAGATCAGCCACATCCAATTTAAAGACGTAATGAACAAAATTACGGATTCCTCAATAA
TCGTCTAAGGTTCAGTAACTTA
Found at i:150204 original size:93 final size:93
Alignment explanation
Indices: 150042--150222 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 93
150032 TCTCAATTAG
* * *
150042 TCAATTAGTGTCCAATATGACTCGATTCTAAATTAGTCGAGACTTAATATAAAATATGACTACGA
1 TCAATTAGTGTCCAATATGACTCGATCCTAAATTAGTAGAGACTTAATACAAAATATGACTACGA
*
150107 GATATTGATAAGAGAATAGATACAGTTT
66 GATATTAATAAGAGAATAGATACAGTTT
* * * *
150135 TCAATTAGTGTCCAATATGACTTGATCCTAAATTAGTAGAGACTTGATACAAAATATGATTACGG
1 TCAATTAGTGTCCAATATGACTCGATCCTAAATTAGTAGAGACTTAATACAAAATATGACTACGA
150200 GATATTAATAAGAGAATAGATAC
66 GATATTAATAAGAGAATAGATAC
150223 TTACAGAGAT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 80 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (93 bp):
TCAATTAGTGTCCAATATGACTCGATCCTAAATTAGTAGAGACTTAATACAAAATATGACTACGA
GATATTAATAAGAGAATAGATACAGTTT
Found at i:157329 original size:2 final size:2
Alignment explanation
Indices: 157322--157362 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
157312 AAGTAGATGC
157322 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
157363 ACAGCATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Done.