Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010704.1 Corchorus capsularis cultivar CVL-1 contig10725, 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: 122516
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:702 original size:11 final size:11
Alignment explanation
Indices: 687--725 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
677 ACAACACAAT
687 AAAAACAAAAC
1 AAAAACAAAAC
* *
698 GAAAACGAAAC
1 AAAAACAAAAC
709 AAAAACAAAAAC
1 AAAAAC-AAAAC
721 AAAAA
1 AAAAA
726 ACAGAAAAAC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 14 0.61
12 9 0.39
ACGTcount: A:0.79, C:0.15, G:0.05, T:0.00
Consensus pattern (11 bp):
AAAAACAAAAC
Found at i:8059 original size:37 final size:37
Alignment explanation
Indices: 8017--8090 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
8007 AACAATCTCC
8017 CCCGATTTACATGTTATCCAAGACTTAACCCATGGAG
1 CCCGATTTACATGTTATCCAAGACTTAACCCATGGAG
8054 CCCGATTTACATGTTATCCAAGACTTAACCCATGGAG
1 CCCGATTTACATGTTATCCAAGACTTAACCCATGGAG
8091 TGGTACAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.30, C:0.27, G:0.16, T:0.27
Consensus pattern (37 bp):
CCCGATTTACATGTTATCCAAGACTTAACCCATGGAG
Found at i:8848 original size:32 final size:32
Alignment explanation
Indices: 8807--8870 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
8797 TGCCTTAAAT
8807 TCAAGGTTTGTGTCCAAAGGAAGAAAAAAAAA
1 TCAAGGTTTGTGTCCAAAGGAAGAAAAAAAAA
*
8839 TCAAGGTTTGTGTCCAAAGGAAGGAAAAAAAA
1 TCAAGGTTTGTGTCCAAAGGAAGAAAAAAAAA
8871 GAAGAGGGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.09, G:0.23, T:0.19
Consensus pattern (32 bp):
TCAAGGTTTGTGTCCAAAGGAAGAAAAAAAAA
Found at i:10329 original size:33 final size:33
Alignment explanation
Indices: 10282--10411 Score: 206
Period size: 33 Copynumber: 3.9 Consensus size: 33
10272 CTATTCTTGA
*
10282 ATATTAGTGGCACCTGAAGTTGTCACATCAAGC
1 ATATCAGTGGCACCTGAAGTTGTCACATCAAGC
*
10315 ATATCAGTGGCACCTGAATTTGTCACATCAAGC
1 ATATCAGTGGCACCTGAAGTTGTCACATCAAGC
*
10348 ATATCAGTGGCACTTGAAGTTGTCACATCAAGC
1 ATATCAGTGGCACCTGAAGTTGTCACATCAAGC
* * *
10381 ATATTAATGGCACCTGAAATTGTCACATCAA
1 ATATCAGTGGCACCTGAAGTTGTCACATCAA
10412 AAATATAGTA
Statistics
Matches: 89, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (33 bp):
ATATCAGTGGCACCTGAAGTTGTCACATCAAGC
Found at i:10458 original size:29 final size:29
Alignment explanation
Indices: 10416--10476 Score: 104
Period size: 29 Copynumber: 2.1 Consensus size: 29
10406 CATCAAAAAT
*
10416 ATAGTATCGCTTTGACACCCGAAGTTGTC
1 ATAGTATCACTTTGACACCCGAAGTTGTC
*
10445 ATAGTATCATTTTGACACCCGAAGTTGTC
1 ATAGTATCACTTTGACACCCGAAGTTGTC
10474 ATA
1 ATA
10477 TTAAGGATGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (29 bp):
ATAGTATCACTTTGACACCCGAAGTTGTC
Found at i:15941 original size:64 final size:64
Alignment explanation
Indices: 15852--15988 Score: 213
Period size: 64 Copynumber: 2.1 Consensus size: 64
15842 TCAGTCAACC
*
15852 AAAAAAAAAAGCCTCGCTAAGTTGAAAATCCTGCAAATG-ACAGCTTAAGCAAAAGTTAGAGCAA
1 AAAAAAAAAAGCCTCGCTAAGTTGAAAATCCTGCAAA-GAACAGCTTAAGCAAAACTTAGAGCAA
* * * *
15916 AAAAAAAAAAGGCTCGCTAAGTTGAAAATCCTGCAAAGAACGGCTTAGGCAAAACTTAGAGCAC
1 AAAAAAAAAAGCCTCGCTAAGTTGAAAATCCTGCAAAGAACAGCTTAAGCAAAACTTAGAGCAA
15980 AAAAAAAAA
1 AAAAAAAAA
15989 TGAACTACGT
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
63 1 0.01
64 66 0.99
ACGTcount: A:0.50, C:0.17, G:0.18, T:0.15
Consensus pattern (64 bp):
AAAAAAAAAAGCCTCGCTAAGTTGAAAATCCTGCAAAGAACAGCTTAAGCAAAACTTAGAGCAA
Found at i:18440 original size:38 final size:38
Alignment explanation
Indices: 18350--18460 Score: 174
Period size: 38 Copynumber: 3.0 Consensus size: 38
18340 ATATCGGATA
* *
18350 GTGCAAATTTGATTGAAGGCTCCAGAAGAGCCAGTATT
1 GTGCAAATTTGATTGAAAGCTCCAGAAGAGCTAGTATT
*
18388 -T--AAATTTGATTGAAAGCTCCGGAAGAGCTAGTATT
1 GTGCAAATTTGATTGAAAGCTCCAGAAGAGCTAGTATT
18423 GTGCAAATTTGATTGAAAGCTCCAGAAGAGCTAGTATT
1 GTGCAAATTTGATTGAAAGCTCCAGAAGAGCTAGTATT
18461 AAGGCTCTGG
Statistics
Matches: 66, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
35 31 0.47
36 1 0.02
37 1 0.02
38 33 0.50
ACGTcount: A:0.33, C:0.14, G:0.24, T:0.29
Consensus pattern (38 bp):
GTGCAAATTTGATTGAAAGCTCCAGAAGAGCTAGTATT
Found at i:18833 original size:83 final size:82
Alignment explanation
Indices: 18724--18878 Score: 265
Period size: 83 Copynumber: 1.9 Consensus size: 82
18714 GATTGAAACA
* *
18724 TATGTTTTTGTAAACAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCAGTTAGGC
1 TATGCTTTTGTAAACAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCAGTTAGAC
18789 CATCCCGATAATACACT
66 CATCCCGATAATACACT
* *
18806 TATGCTTTTGTAAACCAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCGGTTTGA
1 TATGCTTTTGTAAA-CAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCAGTTAGA
18871 CCATCCCG
65 CCATCCCG
18879 GTTCAATTAT
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
82 13 0.19
83 55 0.81
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.41
Consensus pattern (82 bp):
TATGCTTTTGTAAACAGAAGTTTATTGATTGCATTATGTTTATTGTTTGGCATGACCAGTTAGAC
CATCCCGATAATACACT
Found at i:22853 original size:2 final size:2
Alignment explanation
Indices: 22794--22834 Score: 66
Period size: 2 Copynumber: 20.5 Consensus size: 2
22784 GTTTGGTGCC
22794 TA TA TA T- TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22835 TTTGTACCGA
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.95
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30908 original size:15 final size:14
Alignment explanation
Indices: 30883--30918 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
30873 TCATAGACTA
*
30883 TTAATGAGTTAAAT
1 TTAAAGAGTTAAAT
30897 TTATAAGAGTTAAAT
1 TTA-AAGAGTTAAAT
30912 TTAAAGA
1 TTAAAGA
30919 AATGAAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (14 bp):
TTAAAGAGTTAAAT
Found at i:44354 original size:73 final size:70
Alignment explanation
Indices: 44277--44429 Score: 173
Period size: 73 Copynumber: 2.1 Consensus size: 70
44267 TAATATATCA
* * * *
44277 AGTTTTTTAATTAAAATAGTAAAATGGTAAAATA-TAAGTAATAAGGATATTAGATTTAATTATA
1 AGTTTTTTAAGTAAAATAGTAAAA---TAAAATAGTAACT-ATAAAGATATTAGATTTAATTAAA
44341 TAAAAATAG
62 TAAAAATAG
* * *
44350 AGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAAT
1 AG-TTTT--TTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAAT
44415 AAAAATAG
63 AAAAATAG
44423 AGTTTTT
1 AGTTTTT
44430 AGTTAAATAA
Statistics
Matches: 69, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
70 1 0.01
72 4 0.06
73 41 0.59
74 7 0.10
76 16 0.23
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.39
Consensus pattern (70 bp):
AGTTTTTTAAGTAAAATAGTAAAATAAAATAGTAACTATAAAGATATTAGATTTAATTAAATAAA
AATAG
Found at i:44375 original size:68 final size:70
Alignment explanation
Indices: 44294--44455 Score: 195
Period size: 73 Copynumber: 2.3 Consensus size: 70
44284 TAATTAAAAT
* * *
44294 AGTAAAATGGTAAAATATAAG-TA-ATAAGGATATTAGATTTAATTATATAAAAATAGAGTTTTT
1 AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
*
44357 AGTTG
66 AGTTA
* *
44362 AGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTATATTTAATTAAATAAAAATAGAGTT
1 AGTAAAATAGTAAAAT-ATA-AGTTAC-ATAAAGATATTAGATTTAATTAAATAAAAATAGAGTT
44427 TTTAGTTA
63 TTTAGTTA
*
44435 AATAAAACTA-TAAAAATATAA
1 AGTAAAA-TAGT-AAAATATAA
44456 AAATAGAGTT
Statistics
Matches: 79, Mismatches: 8, Indels: 10
0.81 0.08 0.10
Matches are distributed among these distances:
68 15 0.19
69 2 0.03
70 2 0.03
71 2 0.03
72 1 0.01
73 50 0.63
74 7 0.09
ACGTcount: A:0.52, C:0.01, G:0.11, T:0.35
Consensus pattern (70 bp):
AGTAAAATAGTAAAATATAAGTTACATAAAGATATTAGATTTAATTAAATAAAAATAGAGTTTTT
AGTTA
Found at i:44480 original size:39 final size:39
Alignment explanation
Indices: 44413--44488 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
44403 ATTTAATTAA
44413 ATAAAAATAGAGTTTTTAGTTAAATAAAACTA-TAAAAAT
1 ATAAAAATAGAGTTTTTAGTTAAATAAAA-TAGTAAAAAT
* *
44452 ATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAA
1 ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAA
44489 TAAAATAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.54, C:0.01, G:0.12, T:0.33
Consensus pattern (39 bp):
ATAAAAATAGAGTTTTTAGTTAAATAAAATAGTAAAAAT
Found at i:44548 original size:109 final size:111
Alignment explanation
Indices: 44338--44559 Score: 412
Period size: 109 Copynumber: 2.0 Consensus size: 111
44328 AGATTTAATT
44338 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTACTATAAAGATATTAT
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTA-TATAAAGATATTAT
44403 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
65 ATTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
*
44450 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAG-T-TATAAATATATTATA
1 ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
44513 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
66 TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
44559 A
1 A
44560 CTTAAACAAT
Statistics
Matches: 109, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
109 61 0.56
111 1 0.01
112 47 0.43
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.36
Consensus pattern (111 bp):
ATATAAAAATAGAGTTTTTAGTTGAGTAAAATAGTAAAATAAAATAGTTATATAAAGATATTATA
TTTAATTAAATAAAAATAGAGTTTTTAGTTAAATAAAACTATAAAA
Found at i:44664 original size:2 final size:2
Alignment explanation
Indices: 44646--44679 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
44636 GTACTTTTTA
*
44646 AT AT AGT AT AG AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT A
44680 ATAACTAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:47603 original size:2 final size:2
Alignment explanation
Indices: 47596--47652 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
47586 GGAGTCAAAA
47596 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
47638 AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC A
47653 TATATATAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:51748 original size:2 final size:2
Alignment explanation
Indices: 51741--51771 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51731 ATAATTTGCC
51741 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51772 TCAATCTGAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:63378 original size:23 final size:23
Alignment explanation
Indices: 63351--63398 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
63341 GCAAGGCATA
63351 TTCCATGCATTTAGTTGTAATAT
1 TTCCATGCATTTAGTTGTAATAT
63374 TTCCATGCATTTAGTTGTAATAT
1 TTCCATGCATTTAGTTGTAATAT
63397 TT
1 TT
63399 AGGCAAATTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (23 bp):
TTCCATGCATTTAGTTGTAATAT
Found at i:63553 original size:22 final size:22
Alignment explanation
Indices: 63509--63555 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
63499 CGTCTGTACA
**
63509 TGCCATGTCACCAGGGCTCTCC
1 TGCCATGTCACCAAAGCTCTCC
* *
63531 TGCCATGTCACCAAAGTTTTCC
1 TGCCATGTCACCAAAGCTCTCC
63553 TGC
1 TGC
63556 AAAAGGTTGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.36, G:0.19, T:0.28
Consensus pattern (22 bp):
TGCCATGTCACCAAAGCTCTCC
Found at i:63973 original size:10 final size:10
Alignment explanation
Indices: 63958--63982 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
63948 TCTTAGCAAA
63958 AAAAAAATAG
1 AAAAAAATAG
63968 AAAAAAATAG
1 AAAAAAATAG
63978 AAAAA
1 AAAAA
63983 GAGGAAAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:65419 original size:49 final size:49
Alignment explanation
Indices: 65312--65540 Score: 325
Period size: 49 Copynumber: 4.6 Consensus size: 49
65302 AAATTTTAAT
65312 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTT-ATTTTACTTGCTA
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGCTA
65360 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGCTA
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGCTA
* *
65409 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGTTTTTACCTGCTA
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGCTA
* * ** ** *
65458 TCTCCCAAAATGCCCTTCCCGGACGGAAGACAGTTTTTTTTTACTGTTTTT
1 TTTCCCAAAATGCCCTTCCCGGACGGAAGGCA-TTTGATTTTACT-TGCTA
* *
65509 TTTCCTAAAACGCCCCTTCCCGGACGGAAGGC
1 TTTCCCAAAATG-CCCTTCCCGGACGGAAGGC
65541 GTTGCTTCTT
Statistics
Matches: 164, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
48 35 0.21
49 90 0.55
50 10 0.06
51 11 0.07
52 18 0.11
ACGTcount: A:0.21, C:0.28, G:0.18, T:0.32
Consensus pattern (49 bp):
TTTCCCAAAATGCCCTTCCCGGACGGAAGGCATTTGATTTTACTTGCTA
Found at i:92366 original size:3 final size:3
Alignment explanation
Indices: 92358--92390 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
92348 TAATTTTTTA
92358 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
92391 TGCTGCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:94944 original size:2 final size:2
Alignment explanation
Indices: 94937--94981 Score: 63
Period size: 2 Copynumber: 22.5 Consensus size: 2
94927 CTAGATTTAC
* * *
94937 AT AT AT AT AT AT AT AT AT AT AT AT GT AT GT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
94979 AT A
1 AT A
94982 ATCAGCATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
AT
Found at i:95346 original size:22 final size:22
Alignment explanation
Indices: 95318--95363 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
95308 CTTTATTTCC
95318 CATCCCAGCATTGCATACATCT
1 CATCCCAGCATTGCATACATCT
95340 CATCCCAGCATTGCATACATCT
1 CATCCCAGCATTGCATACATCT
95362 CA
1 CA
95364 ATTGTCTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.28, C:0.37, G:0.09, T:0.26
Consensus pattern (22 bp):
CATCCCAGCATTGCATACATCT
Found at i:100168 original size:6 final size:6
Alignment explanation
Indices: 100157--100188 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
100147 GATGATTGTG
*
100157 TCTGGC TCTGGC TCTGCC TCTGGC TCTGGC TC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TC
100189 GGGGTTGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.38, G:0.28, T:0.34
Consensus pattern (6 bp):
TCTGGC
Found at i:104610 original size:3 final size:3
Alignment explanation
Indices: 104602--104630 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
104592 AATCCTAAAT
104602 CCG CCG CCG CCG CCG CCG CCG CCG CCG CC
1 CCG CCG CCG CCG CCG CCG CCG CCG CCG CC
104631 ACCACTGTCG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.69, G:0.31, T:0.00
Consensus pattern (3 bp):
CCG
Found at i:107166 original size:63 final size:63
Alignment explanation
Indices: 107090--107212 Score: 237
Period size: 63 Copynumber: 2.0 Consensus size: 63
107080 TTACGAGCAG
*
107090 ACAATGCATTTGGACTAGTCATCGGTATAAGTATCAAAGCAGCCATTGCAATGAAGAGAACTA
1 ACAATGCATTTGGACTAGTCATCGGTATAAGCATCAAAGCAGCCATTGCAATGAAGAGAACTA
107153 ACAATGCATTTGGACTAGTCATCGGTATAAGCATCAAAGCAGCCATTGCAATGAAGAGAA
1 ACAATGCATTTGGACTAGTCATCGGTATAAGCATCAAAGCAGCCATTGCAATGAAGAGAA
107213 AACTATCAAG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.38, C:0.18, G:0.21, T:0.23
Consensus pattern (63 bp):
ACAATGCATTTGGACTAGTCATCGGTATAAGCATCAAAGCAGCCATTGCAATGAAGAGAACTA
Found at i:111943 original size:6 final size:6
Alignment explanation
Indices: 111932--111961 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
111922 CAATTATCAA
111932 ATTCAT ATTCAT ATTCAT ATTCAT ATTCAT
1 ATTCAT ATTCAT ATTCAT ATTCAT ATTCAT
111962 GGAGCTAAAA
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:0.33, C:0.17, G:0.00, T:0.50
Consensus pattern (6 bp):
ATTCAT
Found at i:117358 original size:3 final size:3
Alignment explanation
Indices: 117350--117404 Score: 83
Period size: 3 Copynumber: 17.7 Consensus size: 3
117340 AAAAAAGAAA
*
117350 AAT AAT AAT AAT ACT AAT AAT ATAT AAT AAAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT A-AT AAT -AAT AAT AAT AAT AAT AAT
117397 AAT AAT AA
1 AAT AAT AA
117405 AAGTAAATCG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:117535 original size:36 final size:37
Alignment explanation
Indices: 117488--117557 Score: 124
Period size: 36 Copynumber: 1.9 Consensus size: 37
117478 CCGAAAGACA
*
117488 AAATCGATTTAGGTCTAAAGCTAAAAAGA-AGGGGGG
1 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGGGGG
117524 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGG
1 AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGG
117558 AAAAAGAGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 28 0.88
37 4 0.12
ACGTcount: A:0.43, C:0.09, G:0.30, T:0.19
Consensus pattern (37 bp):
AAATCGATTTAGGGCTAAAGCTAAAAAGAGAGGGGGG
Found at i:118831 original size:21 final size:21
Alignment explanation
Indices: 118805--118845 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
118795 AGTGGGGTAG
*
118805 AGGCTGCTGAAGATGCAAATA
1 AGGCTGCTGAAAATGCAAATA
*
118826 AGGCTGCTGAAAATGTAAAT
1 AGGCTGCTGAAAATGCAAAT
118846 GGTGTTTCTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.12, G:0.27, T:0.22
Consensus pattern (21 bp):
AGGCTGCTGAAAATGCAAATA
Found at i:120028 original size:144 final size:144
Alignment explanation
Indices: 119768--120056 Score: 578
Period size: 144 Copynumber: 2.0 Consensus size: 144
119758 TGCTGGCAAC
119768 TACAATGAAGAATTTGCTTTGATGTGGGATTATGCCAATGAATTGCTAGACAAGAATGTTGGAAG
1 TACAATGAAGAATTTGCTTTGATGTGGGATTATGCCAATGAATTGCTAGACAAGAATGTTGGAAG
119833 CACTGTTAAGTTGGAAGTTCAAAGAGTGACATAGGACTCCCCTCCACATTTTAGGAGGTTTTATT
66 CACTGTTAAGTTGGAAGTTCAAAGAGTGACATAGGACTCCCCTCCACATTTTAGGAGGTTTTATT
119898 GTTGTTTTGCTGCT
131 GTTGTTTTGCTGCT
119912 TACAATGAAGAATTTGCTTTGATGTGGGATTATGCCAATGAATTGCTAGACAAGAATGTTGGAAG
1 TACAATGAAGAATTTGCTTTGATGTGGGATTATGCCAATGAATTGCTAGACAAGAATGTTGGAAG
119977 CACTGTTAAGTTGGAAGTTCAAAGAGTGACATAGGACTCCCCTCCACATTTTAGGAGGTTTTATT
66 CACTGTTAAGTTGGAAGTTCAAAGAGTGACATAGGACTCCCCTCCACATTTTAGGAGGTTTTATT
120042 GTTGTTTTGCTGCT
131 GTTGTTTTGCTGCT
120056 T
1 T
120057 TGAAAATGGG
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.34
Consensus pattern (144 bp):
TACAATGAAGAATTTGCTTTGATGTGGGATTATGCCAATGAATTGCTAGACAAGAATGTTGGAAG
CACTGTTAAGTTGGAAGTTCAAAGAGTGACATAGGACTCCCCTCCACATTTTAGGAGGTTTTATT
GTTGTTTTGCTGCT
Done.