Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008350.1 Corchorus capsularis cultivar CVL-1 contig08371, 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: 36751
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:8807 original size:2 final size:2
Alignment explanation
Indices: 8800--8825 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8790 AAATTATCCA
8800 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
8826 GTTGTCACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11103 original size:22 final size:23
Alignment explanation
Indices: 11078--11126 Score: 59
Period size: 22 Copynumber: 2.2 Consensus size: 23
11068 GAATTTCGGG
*
11078 AACCTTTC-TAT-AAATTTTTTTT
1 AACCTTTCTTATGAAA-TTTTGTT
11100 AACC-TTCTTATGAAATTTTGTT
1 AACCTTTCTTATGAAATTTTGTT
11122 AACCT
1 AACCT
11127 CCCAAAGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
21 3 0.13
22 17 0.74
23 3 0.13
ACGTcount: A:0.29, C:0.16, G:0.04, T:0.51
Consensus pattern (23 bp):
AACCTTTCTTATGAAATTTTGTT
Found at i:13061 original size:22 final size:22
Alignment explanation
Indices: 13036--13080 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
13026 ATTGTTAGTG
* *
13036 ATCACACTCTGAAATTTTGATA
1 ATCACACTATGAAATTGTGATA
13058 ATCACACTATGAAATTGTGATA
1 ATCACACTATGAAATTGTGATA
13080 A
1 A
13081 CCTCGCTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.11, T:0.33
Consensus pattern (22 bp):
ATCACACTATGAAATTGTGATA
Found at i:13136 original size:22 final size:22
Alignment explanation
Indices: 13111--13233 Score: 81
Period size: 22 Copynumber: 5.6 Consensus size: 22
13101 CCCTATGATG
* *
13111 TTTTAATAACCTCATTATGAAA
1 TTTTGATAACCTCACTATGAAA
* * *
13133 TTTTGTTAATCTCCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
13155 TTTTGATCTACAT-ACTATGAAA
1 TTTTGAT-AACCTCACTATGAAA
* *
13177 TTTTGATAACCCTC-TTATAAAA
1 TTTTGATAA-CCTCACTATGAAA
* * *
13199 TTTTGA-AAACTAAAGTATGAAA
1 TTTTGATAACCT-CACTATGAAA
*
13221 TTTTGATATCCTC
1 TTTTGATAACCTC
13234 CCTGAAATTT
Statistics
Matches: 74, Mismatches: 21, Indels: 12
0.69 0.20 0.11
Matches are distributed among these distances:
20 2 0.03
21 3 0.04
22 64 0.86
23 5 0.07
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:13949 original size:22 final size:21
Alignment explanation
Indices: 13911--13986 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 21
13901 GAAATACCAC
13911 TATGAAATTTTTG-TAATCACATT
1 TATGAAA--TTTGATAATCAC-TT
*
13934 T-TGAAAATTTGATAATCTCTT
1 TATG-AAATTTGATAATCACTT
*
13955 TATGAAATTTCGATAATCTCTT
1 TATGAAATTT-GATAATCACTT
*
13977 TATAAAATTT
1 TATGAAATTT
13987 TGTTGACCCC
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
21 13 0.28
22 30 0.64
23 4 0.09
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.47
Consensus pattern (21 bp):
TATGAAATTTGATAATCACTT
Found at i:13962 original size:21 final size:22
Alignment explanation
Indices: 13937--13986 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
13927 TCACATTTTG
13937 AAAATTT-GATAATCTCTTTAT
1 AAAATTTCGATAATCTCTTTAT
*
13958 GAAATTTCGATAATCTCTTTAT
1 AAAATTTCGATAATCTCTTTAT
13980 AAAATTT
1 AAAATTT
13987 TGTTGACCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
21 6 0.23
22 20 0.77
ACGTcount: A:0.38, C:0.10, G:0.06, T:0.46
Consensus pattern (22 bp):
AAAATTTCGATAATCTCTTTAT
Found at i:14215 original size:22 final size:23
Alignment explanation
Indices: 14186--14240 Score: 80
Period size: 22 Copynumber: 2.5 Consensus size: 23
14176 AAATTGAGAC
*
14186 TTTT-ATAACCTTCA-TATAAAA
1 TTTTGATAACCTACACTATAAAA
14207 TTTTGATAACC-ACACTATAAAA
1 TTTTGATAACCTACACTATAAAA
14229 TTTTGATAACCT
1 TTTTGATAACCT
14241 CCCCATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
21 6 0.20
22 24 0.80
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (23 bp):
TTTTGATAACCTACACTATAAAA
Found at i:14385 original size:22 final size:22
Alignment explanation
Indices: 14360--14547 Score: 108
Period size: 22 Copynumber: 8.3 Consensus size: 22
14350 TTGTGACAAT
*
14360 TAACCACCCTATGAAATTTCAA
1 TAACCACCCTATGAAATTTTAA
*
14382 TAACCAACCTAATTAGAAATTTTAA
1 TAACCACCCT-A-T-GAAATTTTAA
* * *
14407 TAACTTGATCCTATGAAATTTTGA
1 TAAC--CACCCTATGAAATTTTAA
* *
14431 TAACCACACTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTAA
*** * **
14453 TAACTTTCTTATGAAATTTTGG
1 TAACCACCCTATGAAATTTTAA
** * * *
14475 TGGCCACACTATGGAATTTTGA
1 TAACCACCCTATGAAATTTTAA
* *
14497 TAACC-TCCTCATGAAATTATAA
1 TAACCACCCT-ATGAAATTTTAA
* * *
14519 TAACCATCTTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTAA
14541 TAACCAC
1 TAACCAC
14548 ATAGAGACAA
Statistics
Matches: 125, Mismatches: 34, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.02
22 86 0.69
23 4 0.03
24 14 0.11
25 14 0.11
26 1 0.01
27 4 0.03
ACGTcount: A:0.37, C:0.18, G:0.10, T:0.35
Consensus pattern (22 bp):
TAACCACCCTATGAAATTTTAA
Found at i:14421 original size:49 final size:44
Alignment explanation
Indices: 14367--14544 Score: 121
Period size: 44 Copynumber: 3.9 Consensus size: 44
14357 AATTAACCAC
14367 CCTATGAAATTTCAATAACCA-ACCTAATTAGAAATTTTAATAACTTGAT
1 CCTATGAAATTTCAATAACCACA-CT-A-T-GAAATTTTAATAACTT--T
** *
14416 CCTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTT
1 CCTATGAAATTTCAATAACCACACTATGAAATTTTAATAACTTT
* *** ** * * *
14460 CTTATGAAATTTTGGTGGCCACACTATGGAATTTTGATAAC-CT
1 CCTATGAAATTTCAATAACCACACTATGAAATTTTAATAACTTT
* *
14503 CCTCATGAAATTAT-AATAACCATC-TTATGAAATTTTGATAAC
1 CCT-ATGAAATT-TCAATAACCA-CACTATGAAATTTTAATAAC
14545 CACATAGAGA
Statistics
Matches: 109, Mismatches: 16, Indels: 13
0.79 0.12 0.09
Matches are distributed among these distances:
43 3 0.03
44 65 0.60
45 2 0.02
46 15 0.14
47 1 0.01
48 1 0.01
49 21 0.19
50 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.10, T:0.37
Consensus pattern (44 bp):
CCTATGAAATTTCAATAACCACACTATGAAATTTTAATAACTTT
Found at i:14482 original size:44 final size:44
Alignment explanation
Indices: 14397--14544 Score: 154
Period size: 44 Copynumber: 3.3 Consensus size: 44
14387 AACCTAATTA
* *
14397 GAAATTTTAATAACTTGATCCTATGAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACTT--TCTTATGAAATTTTGATAACCACACTAT
* **
14443 GAAATTTTGATAACTTTCTTATGAAATTTTGGTGGCCACACTAT
1 GAAATTTTGATAACTTTCTTATGAAATTTTGATAACCACACTAT
* * * * * * *
14487 GGAATTTTGATAACCTCCTCATGAAATTATAATAACCATC-TTAT
1 GAAATTTTGATAACTTTCTTATGAAATTTTGATAACCA-CACTAT
14531 GAAATTTTGATAAC
1 GAAATTTTGATAAC
14545 CACATAGAGA
Statistics
Matches: 85, Mismatches: 16, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
44 69 0.81
45 1 0.01
46 15 0.18
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (44 bp):
GAAATTTTGATAACTTTCTTATGAAATTTTGATAACCACACTAT
Found at i:14548 original size:66 final size:66
Alignment explanation
Indices: 14417--14548 Score: 167
Period size: 66 Copynumber: 2.0 Consensus size: 66
14407 TAACTTGATC
* * ** * **
14417 CTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTTCTTATGAAATTTTGGTGGCCAC
1 CTATGAAATTTTGATAACCACACTATGAAATTATAATAACCATCTTATGAAATTTTGATAACCAC
14482 A
66 A
* *
14483 CTATGGAATTTTGATAACCTC-CTCATGAAATTATAATAACCATCTTATGAAATTTTGATAACCA
1 CTATGAAATTTTGATAACCACACT-ATGAAATTATAATAACCATCTTATGAAATTTTGATAACCA
14547 CA
65 CA
14549 TAGAGACAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 2 0.04
66 54 0.96
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (66 bp):
CTATGAAATTTTGATAACCACACTATGAAATTATAATAACCATCTTATGAAATTTTGATAACCAC
A
Found at i:14743 original size:19 final size:20
Alignment explanation
Indices: 14712--14749 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
14702 TATTGACATT
14712 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
14731 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
14750 ATAATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:15871 original size:45 final size:45
Alignment explanation
Indices: 15820--15909 Score: 153
Period size: 45 Copynumber: 2.0 Consensus size: 45
15810 TAATAGAGTA
15820 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
** *
15865 GTGGAATTACTAAAAGATCCCTACCCCGGATTAATGATGAGCTGG
1 GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
15910 AGAAGTAATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.24
Consensus pattern (45 bp):
GTGGAATTACTAAAAGATCCCTACCCCAAATTAATGATAAGCTGG
Found at i:16844 original size:38 final size:38
Alignment explanation
Indices: 16771--16849 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
16761 GACAAAGACA
* *
16771 AAAAGGAAAATTAAATACAACGATTGGGAATAAAA-GC
1 AAAAGGAAAATTAAATACAACGATTGGAAAAAAAAGGC
**
16808 AAAAGGCAAAATTAAATAGGAC-ATTGGAAACAAAAAGGC
1 AAAAGG-AAAATTAAATACAACGATTGGAAA-AAAAAGGC
16847 AAA
1 AAA
16850 TTGACTTTCT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
37 13 0.37
38 17 0.49
39 5 0.14
ACGTcount: A:0.58, C:0.09, G:0.19, T:0.14
Consensus pattern (38 bp):
AAAAGGAAAATTAAATACAACGATTGGAAAAAAAAGGC
Found at i:17007 original size:30 final size:32
Alignment explanation
Indices: 16962--17027 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 32
16952 TGACAATTTA
* *
16962 GAAATATGTTTTTAAA-AAAAGGGTATAATTG
1 GAAATATGTTTTTAAACAAAAGGGTACAATCG
*
16993 GAAATATG-TTTTAAACATAAGGGTACAATCG
1 GAAATATGTTTTTAAACAAAAGGGTACAATCG
17024 GAAA
1 GAAA
17028 ATATAAAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
30 7 0.23
31 24 0.77
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (32 bp):
GAAATATGTTTTTAAACAAAAGGGTACAATCG
Found at i:17969 original size:15 final size:15
Alignment explanation
Indices: 17936--17984 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
17926 TTTTTCAGTG
17936 AAATAAA-A-AAT-A
1 AAATAAATATAATAA
17948 AAA-AAATATAATAA
1 AAATAAATATAATAA
*
17962 ATATAAATATAATAA
1 AAATAAATATAATAA
17977 AAATAAAT
1 AAATAAAT
17985 TGTTTCTTCT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
11 3 0.10
12 4 0.13
13 3 0.10
14 3 0.10
15 18 0.58
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAATATAATAA
Found at i:19886 original size:16 final size:17
Alignment explanation
Indices: 19860--19891 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
19850 GTCATATTTT
19860 TTTTATTAAAAAAAATA
1 TTTTATTAAAAAAAATA
19877 TTTT-TTAAAAAAAAT
1 TTTTATTAAAAAAAAT
19892 TTAGTGAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TTTTATTAAAAAAAATA
Found at i:20059 original size:18 final size:17
Alignment explanation
Indices: 20023--20055 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
20013 AAAAATTCAT
20023 TTTTCTTCTTTTCTTTTC
1 TTTTCTT-TTTTCTTTTC
20041 TTTTC-TTTTTCTTTT
1 TTTTCTTTTTTCTTTT
20056 TTCTGTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.60
17 1 0.07
18 5 0.33
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTTCTTTTC
Found at i:22311 original size:13 final size:12
Alignment explanation
Indices: 22289--22347 Score: 59
Period size: 12 Copynumber: 4.8 Consensus size: 12
22279 TTATGCACCA
22289 AAAACA-TTTAT
1 AAAACATTTTAT
22300 CAAAACATTTTAT
1 -AAAACATTTTAT
*
22313 AAAGCATTTATAT
1 AAAACATTT-TAT
*
22326 AAAAACA-TTAAT
1 -AAAACATTTTAT
22338 AAAACATTTT
1 AAAACATTTT
22348 CTCAACAGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
11 6 0.15
12 18 0.46
13 10 0.26
14 5 0.13
ACGTcount: A:0.53, C:0.10, G:0.02, T:0.36
Consensus pattern (12 bp):
AAAACATTTTAT
Found at i:22530 original size:13 final size:13
Alignment explanation
Indices: 22512--22541 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
22502 GTATCATAAT
*
22512 CAAAGTCATAAAC
1 CAAAGTAATAAAC
22525 CAAAGTAATAAAC
1 CAAAGTAATAAAC
22538 CAAA
1 CAAA
22542 ATACCTTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.60, C:0.20, G:0.07, T:0.13
Consensus pattern (13 bp):
CAAAGTAATAAAC
Found at i:23519 original size:3 final size:3
Alignment explanation
Indices: 23496--23539 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
23486 TTTAATTTCC
*
23496 TTA TT- TTA TTTA TTT TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23540 TTCCTTTCTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.05
3 32 0.86
4 3 0.08
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:23925 original size:17 final size:18
Alignment explanation
Indices: 23903--23936 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
23893 TAACAACCCC
*
23903 AAACCATCAT-AAACATA
1 AAACCAACATCAAACATA
23920 AAACCAACATCAAACAT
1 AAACCAACATCAAACAT
23937 CCATAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.59, C:0.26, G:0.00, T:0.15
Consensus pattern (18 bp):
AAACCAACATCAAACATA
Found at i:34214 original size:18 final size:18
Alignment explanation
Indices: 34191--34264 Score: 78
Period size: 19 Copynumber: 4.0 Consensus size: 18
34181 TTGAGCCGAT
34191 TTAAAAATATTAAAAAAA
1 TTAAAAATATTAAAAAAA
*
34209 TTAAAAAT-TAAAAAAAA
1 TTAAAAATATTAAAAAAA
* *
34226 GTAAAAAAATATTTAAAAAA
1 -T-TAAAAATATTAAAAAAA
*
34246 TTAAAAAATAATAAAAAAA
1 TT-AAAAATATTAAAAAAA
34265 ATATTTTAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
17 8 0.18
18 9 0.20
19 21 0.47
20 7 0.16
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.24
Consensus pattern (18 bp):
TTAAAAATATTAAAAAAA
Found at i:34222 original size:17 final size:18
Alignment explanation
Indices: 34191--34266 Score: 73
Period size: 20 Copynumber: 4.1 Consensus size: 18
34181 TTGAGCCGAT
*
34191 TTAAAAATATTAAAAAAA
1 TTAAAAATATAAAAAAAA
34209 TTAAAAAT-TAAAAAAAA
1 TTAAAAATATAAAAAAAA
* **
34226 GTAAAAAAATATTTAAAAAA
1 -T-TAAAAATATAAAAAAAA
34246 TTAAAAAATAATAAAAAAAA
1 TT-AAAAAT-ATAAAAAAAA
34266 T
1 T
34267 ATTTTAAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
17 8 0.17
18 9 0.20
19 13 0.28
20 16 0.35
ACGTcount: A:0.74, C:0.00, G:0.01, T:0.25
Consensus pattern (18 bp):
TTAAAAATATAAAAAAAA
Found at i:34247 original size:30 final size:31
Alignment explanation
Indices: 34211--34276 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
34201 TAAAAAAATT
34211 AAAAATTAAAAAA-AAGT-AAAAAAATATTTA
1 AAAAATTAAAAAATAA-TAAAAAAAATATTTA
*
34241 AAAAATTAAAAAATAATAAAAAAAATATTTT
1 AAAAATTAAAAAATAATAAAAAAAATATTTA
34272 AAAAA
1 AAAAA
34277 GCCACGTAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 14 0.42
31 19 0.58
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (31 bp):
AAAAATTAAAAAATAATAAAAAAAATATTTA
Found at i:34267 original size:9 final size:9
Alignment explanation
Indices: 34202--34267 Score: 53
Period size: 10 Copynumber: 7.0 Consensus size: 9
34192 TAAAAATATT
34202 AAAAAAAT-
1 AAAAAAATA
* *
34210 TAAAAATTA
1 AAAAAAATA
34219 AAAAAAAGTA
1 AAAAAAA-TA
*
34229 AAAAAATATTT
1 AAAAAA-A-TA
*
34240 AAAAAATTA
1 AAAAAAATA
34249 AAAAATAATA
1 AAAAA-AATA
34259 AAAAAAATA
1 AAAAAAATA
34268 TTTTAAAAAG
Statistics
Matches: 45, Mismatches: 9, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
8 6 0.13
9 15 0.33
10 16 0.36
11 8 0.18
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (9 bp):
AAAAAAATA
Found at i:35268 original size:60 final size:60
Alignment explanation
Indices: 35184--35343 Score: 194
Period size: 60 Copynumber: 2.7 Consensus size: 60
35174 GCTAATTGCT
* * * * * * *
35184 CAAATAAGAGCCTAACGTTTGTCAAAATATTTAAATAAGGATTTGATCTTTTAATTTGGC
1 CAAATAAGGGTCTAACGTTTGTCAAAATACTCAAATAAGGACTCGATCTTTGAATTTGGC
* * * *
35244 CAAATAAGGGTCTAATGTTTGTCAAAATGCTCAAATAAGGGCTCGGTCTTTGAATTTGGC
1 CAAATAAGGGTCTAACGTTTGTCAAAATACTCAAATAAGGACTCGATCTTTGAATTTGGC
* * *
35304 CAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGG
1 CAAATAAGGGTCTAACGTTTGTCAAAATACTCAAATAAGG
35344 GCCTATCTCA
Statistics
Matches: 86, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 86 1.00
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (60 bp):
CAAATAAGGGTCTAACGTTTGTCAAAATACTCAAATAAGGACTCGATCTTTGAATTTGGC
Found at i:35282 original size:31 final size:31
Alignment explanation
Indices: 35244--35344 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 31
35234 TTAATTTGGC
*
35244 CAAATAAGGGTCTAATGTTTGTCAAAATGCT
1 CAAATAAGGGTCTAACGTTTGTCAAAATGCT
* **
35275 CAAATAAGGG-CT--CGGTCTT-TGAATTTGGC-
1 CAAATAAGGGTCTAAC-GT-TTGTCAAAAT-GCT
* *
35304 CAAATAAGGGTCTAACATTTGCCAAAATGCT
1 CAAATAAGGGTCTAACGTTTGTCAAAATGCT
35335 CAAATAAGGG
1 CAAATAAGGG
35345 CCTATCTCAT
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
29 16 0.30
30 12 0.23
31 24 0.45
32 1 0.02
ACGTcount: A:0.35, C:0.16, G:0.22, T:0.28
Consensus pattern (31 bp):
CAAATAAGGGTCTAACGTTTGTCAAAATGCT
Found at i:35344 original size:60 final size:60
Alignment explanation
Indices: 35230--35345 Score: 196
Period size: 60 Copynumber: 1.9 Consensus size: 60
35220 AAGGATTTGA
* ** *
35230 TCTTTTAATTTGGCCAAATAAGGGTCTAATGTTTGTCAAAATGCTCAAATAAGGGCTCGG
1 TCTTTGAATTTGGCCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCTCGG
35290 TCTTTGAATTTGGCCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGC
1 TCTTTGAATTTGGCCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGC
35346 CTATCTCATA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (60 bp):
TCTTTGAATTTGGCCAAATAAGGGTCTAACATTTGCCAAAATGCTCAAATAAGGGCTCGG
Found at i:35418 original size:31 final size:30
Alignment explanation
Indices: 35378--35573 Score: 150
Period size: 31 Copynumber: 6.5 Consensus size: 30
35368 TGAAACCAGT
35378 CCCTTATTTGAGCATTTTAGATAACGTTAGG
1 CCCTTATTTGAGCATTTTA-ATAACGTTAGG
* *
35409 CTCTTATTTGAGCATTTTCAATAACATTAGG
1 CCCTTATTTGAGCATTTT-AATAACGTTAGG
** **
35440 CCCTTATTTG-GCCAAATTAA-AA-GATCGGG
1 CCCTTATTTGAG-CATTTTAATAACG-TTAGG
*
35469 CCCTTATTTGAGCATTTTCGATAACGTTAGG
1 CCCTTATTTGAGCATTTT-AATAACGTTAGG
* * ** * *
35500 CTCTTATTTGACCAAATTAA-AA-GATCAGA
1 CCCTTATTTGAGCATTTTAATAACG-TTAGG
** *
35529 CCCTTATTTGAGCATTTTAGCAAGCATTAGG
1 CCCTTATTTGAGCATTTTAATAA-CGTTAGG
35560 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
35574 ATTATCCGTT
Statistics
Matches: 126, Mismatches: 28, Indels: 22
0.72 0.16 0.12
Matches are distributed among these distances:
28 1 0.01
29 39 0.31
30 8 0.06
31 76 0.60
32 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (30 bp):
CCCTTATTTGAGCATTTTAATAACGTTAGG
Found at i:35480 original size:60 final size:60
Alignment explanation
Indices: 35411--35570 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
35401 ACGTTAGGCT
* * *
35411 CTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGGCCAAATTAAAAGATCGGGCC
1 CTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGACC
* * *
35471 CTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGACCAAATTAAAAGATCAGACC
1 CTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGACC
**
35531 CTTATTTGAGCATTTT-AGCAAGCATTAGGCCCTTATTTGA
1 CTTATTTGAGCATTTTCAATAA-CATTAGGCCCTTATTTGA
35571 GCAATTATCC
Statistics
Matches: 88, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 2 0.02
60 86 0.98
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.36
Consensus pattern (60 bp):
CTTATTTGAGCATTTTCAATAACATTAGGCCCTTATTTGACCAAATTAAAAGATCAGACC
Found at i:35539 original size:29 final size:29
Alignment explanation
Indices: 35437--35539 Score: 91
Period size: 29 Copynumber: 3.5 Consensus size: 29
35427 CAATAACATT
*
35437 AGGCCCTTATTTGGCCAAATTAAAAGATC
1 AGGCCCTTATTTGACCAAATTAAAAGATC
* * ** * *
35466 GGGCCCTTATTTGAGCATTTTCGATAACG-TT
1 AGGCCCTTATTTGACCAAATT--A-AAAGATC
*
35497 AGGCTCTTATTTGACCAAATTAAAAGATC
1 AGGCCCTTATTTGACCAAATTAAAAGATC
*
35526 AGACCCTTATTTGA
1 AGGCCCTTATTTGA
35540 GCATTTTAGC
Statistics
Matches: 54, Mismatches: 16, Indels: 8
0.69 0.21 0.10
Matches are distributed among these distances:
28 3 0.06
29 30 0.56
31 18 0.33
32 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.33
Consensus pattern (29 bp):
AGGCCCTTATTTGACCAAATTAAAAGATC
Found at i:35562 original size:91 final size:91
Alignment explanation
Indices: 35378--35573 Score: 236
Period size: 91 Copynumber: 2.2 Consensus size: 91
35368 TGAAACCAGT
* ** * *
35378 CCCTTATTTGAGCATTTTAGATAACGTTAGGCTCTTATTTGAGCATTTTCAATAACATTAGGCCC
1 CCCTTATTTGAGCATTTTAGATAACGTTAGGCTCTTATTTGACCAAATTCAATAACATCAGACCC
*
35443 TTATTTGGCCAAATTAAAAGATCGGG
66 TTATTTGGCCAAATTAAAAGATCAGG
* *
35469 CCCTTATTTGAGCATTTTCGATAACGTTAGGCTCTTATTTGACCAAATT-AA-AAGATCAGACCC
1 CCCTTATTTGAGCATTTTAGATAACGTTAGGCTCTTATTTGACCAAATTCAATAACATCAGACCC
** * *
35532 TTATTTGAG-CATTTTAGCAAGCATTAGG
66 TTATTTG-GCCAAATTA-AAAG-ATCAGG
35560 CCCTTATTTGAGCA
1 CCCTTATTTGAGCA
35574 ATTATCCGTT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
89 21 0.23
90 6 0.07
91 63 0.70
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.36
Consensus pattern (91 bp):
CCCTTATTTGAGCATTTTAGATAACGTTAGGCTCTTATTTGACCAAATTCAATAACATCAGACCC
TTATTTGGCCAAATTAAAAGATCAGG
Done.