Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017658.1 Corchorus olitorius cultivar O-4 contig17691, 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: 93918
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:3806 original size:20 final size:21
Alignment explanation
Indices: 3781--3820 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
3771 CGACTTGAGA
*
3781 AAAATTCGAGTTCG-GCTCGG
1 AAAATTCGAGCTCGAGCTCGG
3801 AAAATTCGAGCTCGAGCTCG
1 AAAATTCGAGCTCGAGCTCG
3821 AGCTCGAGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.23
Consensus pattern (21 bp):
AAAATTCGAGCTCGAGCTCGG
Found at i:3817 original size:6 final size:6
Alignment explanation
Indices: 3806--3830 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3796 CTCGGAAAAT
3806 TCGAGC TCGAGC TCGAGC TCGAGC T
1 TCGAGC TCGAGC TCGAGC TCGAGC T
3831 ACTCGAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.32, T:0.20
Consensus pattern (6 bp):
TCGAGC
Found at i:4148 original size:32 final size:32
Alignment explanation
Indices: 4112--4186 Score: 125
Period size: 32 Copynumber: 2.4 Consensus size: 32
4102 CATCTTTCAA
4112 ATCTTTCAAAGAATTAGCAAGCAAAACAAAAT
1 ATCTTTCAAAGAATTAGCAAGCAAAACAAAAT
*
4144 ATCTTTCGAAGAATTAGCAAGCAAAACAAAAT
1 ATCTTTCAAAGAATTAGCAAGCAAAACAAAAT
*
4176 AGC-TTCAAAGA
1 ATCTTTCAAAGA
4187 GGCAAACTAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
31 7 0.17
32 33 0.82
ACGTcount: A:0.51, C:0.16, G:0.12, T:0.21
Consensus pattern (32 bp):
ATCTTTCAAAGAATTAGCAAGCAAAACAAAAT
Found at i:5717 original size:41 final size:40
Alignment explanation
Indices: 5660--5743 Score: 123
Period size: 41 Copynumber: 2.1 Consensus size: 40
5650 ACGTTATCTA
* * *
5660 ACGTTTTTATTCCGTTTCTCTCTTCGTTCTCTCTTCCATCG
1 ACGTTTTTATTCCGTTTCTCACTTCCTTCCCTC-TCCATCG
*
5701 ACGTTTTTATTTCGTTTCTCACTTCCTTCCCTCTCCATCG
1 ACGTTTTTATTCCGTTTCTCACTTCCTTCCCTCTCCATCG
5741 ACG
1 ACG
5744 ACAATAGTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 10 0.26
41 29 0.74
ACGTcount: A:0.10, C:0.33, G:0.10, T:0.48
Consensus pattern (40 bp):
ACGTTTTTATTCCGTTTCTCACTTCCTTCCCTCTCCATCG
Found at i:7763 original size:2 final size:2
Alignment explanation
Indices: 7756--7781 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
7746 CCCTTGTTAC
7756 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
7782 TATGAGCCTT
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:7960 original size:43 final size:43
Alignment explanation
Indices: 7815--8141 Score: 284
Period size: 43 Copynumber: 7.7 Consensus size: 43
7805 AGAAGTGTCT
** *
7815 CTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAGGTGCCC
1 CTGTGTTATAAATGTGTTTGAGGACTTTT-AGATAGAATTGCTC
*
7859 CTGTGTTATAAATGTGTTTGGGGAC-TTTAGTATAG-A-TGC-C
1 CTGTGTTATAAATGTGTTTGAGGACTTTTAG-ATAGAATTGCTC
*
7899 TCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAATTGCTC
1 -CTGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAATTGCTC
* * *
7943 CTGTGTTATAAATGTGTTT-AGGGACTTTGATATAG-A-TGCTT
1 CTGTGTTATAAATGTGTTTGA-GGACTTTTAGATAGAATTGCTC
* * *
7984 CTGTGTTATAAATGTGTTTGAGGAC-TTTGGAATA-AAGATGCCC
1 CTGTGTTATAAATGTGTTTGAGGACTTTTAG-ATAGAA-TTGCTC
* * *
8027 CTGTGTTATAATTGTGTTTGGGGACTTTT-GATA-TATGTGCCTC
1 CTGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAAT-TG-CTC
* * * *
8070 C-GTGTTATAATTGTGTTTAAGGAC-TTTAGAAAGAGAATTGCAC
1 CTGTGTTATAAATGTGTTTGAGGACTTTTAG--ATAGAATTGCTC
* * *
8113 CGGTGTTATAATTGTGTTTGGGGACTTTT
1 CTGTGTTATAAATGTGTTTGAGGACTTTT
8142 GGTTATTGGG
Statistics
Matches: 237, Mismatches: 25, Indels: 41
0.78 0.08 0.14
Matches are distributed among these distances:
40 3 0.01
41 64 0.27
42 39 0.16
43 73 0.31
44 53 0.22
45 5 0.02
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (43 bp):
CTGTGTTATAAATGTGTTTGAGGACTTTTAGATAGAATTGCTC
Found at i:8095 original size:85 final size:85
Alignment explanation
Indices: 7813--8142 Score: 402
Period size: 84 Copynumber: 3.9 Consensus size: 85
7803 AGAGAAGTGT
* * *
7813 CTCTGTGTTATAAATGTGTTTGAGGACTTTTGAGATAGAGGTGCCCCTGTGTTATAAATGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGA-AAAGATGCCCCTGTGTTATAAATGTGTTT
*
7878 GGGGACTTTAG-TATAGATGC
65 GGGGACTTTTGATATAGATGC
* * *
7898 CTCTGTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAA-TTGCTCCTGTGTTATAAATGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGAC-TTTAGAGAAAAGATGCCCCTGTGTTATAAATGTGTTT
*
7962 AGGGAC-TTTGATATAGATGC
65 GGGGACTTTTGATATAGATGC
* * *
7982 TTCTGTGTTATAAATGTGTTTGAGGACTTTGGA-ATAAAGATGCCCCTGTGTTATAATTGTGTTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGA-AAAGATGCCCCTGTGTTATAAATGTGTTT
8046 GGGGACTTTTGATATATG-TGC
65 GGGGACTTTTGATATA-GATGC
* * * * * * *
8067 CTCCGTGTTATAATTGTGTTTAAGGACTTTAGA-AAGAGAATTGCACCGGTGTTATAATTGTGTT
1 CTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAAAAG-A-TGCCCCTGTGTTATAAATGTGTT
8131 TGGGGACTTTTG
64 TGGGGACTTTTG
8143 GTTATTGGGT
Statistics
Matches: 215, Mismatches: 22, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
82 1 0.00
83 10 0.05
84 93 0.43
85 70 0.33
86 41 0.19
ACGTcount: A:0.23, C:0.10, G:0.26, T:0.40
Consensus pattern (85 bp):
CTCTGTGTTATAAATGTGTTTGAGGACTTTAGAGAAAAGATGCCCCTGTGTTATAAATGTGTTTG
GGGACTTTTGATATAGATGC
Found at i:12992 original size:13 final size:13
Alignment explanation
Indices: 12957--13040 Score: 73
Period size: 13 Copynumber: 6.6 Consensus size: 13
12947 GAACTGAAAA
12957 CAGAAACTGATTT
1 CAGAAACTGATTT
* *
12970 CATAATCTGATTT
1 CAGAAACTGATTT
**
12983 CAGAAACTGAAAT
1 CAGAAACTGATTT
12996 CAG--ACTGATTT
1 CAGAAACTGATTT
* **
13007 TAGAATTTGATTT
1 CAGAAACTGATTT
* *
13020 CAGATATTGATTT
1 CAGAAACTGATTT
13033 CAGAAACT
1 CAGAAACT
13041 ACAAACAACA
Statistics
Matches: 53, Mismatches: 16, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
11 8 0.15
13 45 0.85
ACGTcount: A:0.37, C:0.13, G:0.14, T:0.36
Consensus pattern (13 bp):
CAGAAACTGATTT
Found at i:13006 original size:37 final size:38
Alignment explanation
Indices: 12948--13023 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 38
12938 ATGGAAATAG
*
12948 AACTGAAAACAGAAACTGATTTCATAATCTGATTTCAGA
1 AACTGAAAACAG-AACTGATTTCAGAATCTGATTTCAGA
* * *
12987 AACTGAAATCAG-ACTGATTTTAGAATTTGATTTCAGA
1 AACTGAAAACAGAACTGATTTCAGAATCTGATTTCAGA
13024 TATTGATTTC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 22 0.67
39 11 0.33
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (38 bp):
AACTGAAAACAGAACTGATTTCAGAATCTGATTTCAGA
Found at i:29030 original size:83 final size:82
Alignment explanation
Indices: 28890--29127 Score: 309
Period size: 83 Copynumber: 2.8 Consensus size: 82
28880 AAGTGCCCCT
* * *
28890 GTGTTATAAATGTGTTTGAGGACTTTTAGAGAGAA-TTGCCCCTATGTTATAAATGTGTTTGGGG
1 GTGTTATAAATGTGTTTGAGGAC-TTTAGA-A-AAGATGCCCCTGTGTTATAATTGTGTTTGGGG
*
28954 ACTTTGATATAGATGCCT-G
63 ACTTTAATATAGATGCCTCG
*
28973 GTGTTATAAATGTGTTTGAGGACTTTGGAATATAGATGCCCCTGTGTTATAATTGTGTTTGGGGA
1 GTGTTATAAATGTGTTTGAGGACTTTAGAA-A-AGATGCCCCTGTGTTATAATTGTGTTTGGGGA
* *
29038 CTTTTAATATAGGTGCCTCT
64 C-TTTAATATAGATGCCTCG
*
29058 GTGTTATAATTGTGTTTGAGGACTTTAGAAAGAGAATTGCCCCTGTGTTATAATTGTGTTTGGGG
1 GTGTTATAAATGTGTTTGAGGACTTTAGAAA-AG-A-TGCCCCTGTGTTATAATTGTGTTTGGGG
29123 ACTTT
63 ACTTT
29128 TGGTTATTGG
Statistics
Matches: 138, Mismatches: 11, Indels: 10
0.87 0.07 0.06
Matches are distributed among these distances:
81 2 0.01
82 6 0.04
83 51 0.37
84 17 0.12
85 32 0.23
86 30 0.22
ACGTcount: A:0.24, C:0.10, G:0.26, T:0.40
Consensus pattern (82 bp):
GTGTTATAAATGTGTTTGAGGACTTTAGAAAAGATGCCCCTGTGTTATAATTGTGTTTGGGGACT
TTAATATAGATGCCTCG
Found at i:29047 original size:42 final size:42
Alignment explanation
Indices: 28883--29128 Score: 259
Period size: 43 Copynumber: 5.8 Consensus size: 42
28873 TAAAGAGAAG
* *
28883 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTT-AGAGAGAA
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAATATAG-A
* * *
28925 TTGCCCCTATGTTATAAATGTGTTTGGGGAC-TTTGATATAGA
1 -TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAATATAGA
*
28967 TG--CCTGGTGTTATAAATGTGTTTGAGGACTTTGGAATATAGA
1 TGCCCCT-GTGTTATAAATGTGTTTGAGGACTTT-TAATATAGA
* * *
29009 TGCCCCTGTGTTATAATTGTGTTTGGGGACTTTTAATATAGG
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAATATAGA
* * * *
29051 TGCCTCTGTGTTATAATTGTGTTTGAGGAC-TTTAGAAAGAGAA
1 TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTA-ATATAG-A
* *
29094 TTGCCCCTGTGTTATAATTGTGTTTGGGGACTTTT
1 -TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTT
29129 GGTTATTGGG
Statistics
Matches: 174, Mismatches: 19, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
39 3 0.02
40 21 0.12
41 8 0.05
42 52 0.30
43 56 0.32
44 31 0.18
45 3 0.02
ACGTcount: A:0.23, C:0.11, G:0.26, T:0.40
Consensus pattern (42 bp):
TGCCCCTGTGTTATAAATGTGTTTGAGGACTTTTAATATAGA
Found at i:31333 original size:15 final size:15
Alignment explanation
Indices: 31315--31348 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
31305 ACTAACTCAA
* *
31315 CAAACTTAACTGATT
1 CAAACTAAACTGACT
31330 CAAACTAAACTGACT
1 CAAACTAAACTGACT
31345 CAAA
1 CAAA
31349 TATCTAAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (15 bp):
CAAACTAAACTGACT
Found at i:32459 original size:65 final size:65
Alignment explanation
Indices: 32386--32516 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
32376 TCCACGTCTC
32386 TTCCTCACTCTTCTCCTTCCCTATTCAAAACACAGAGCTATCTAAATTATGTAAATATATAGATA
1 TTCCTCACTCTTCTCCTTCCCTATTCAAAACACAGAGCTATCTAAATTATGTAAATATATAGATA
* * *
32451 TTCCTCACTCTTCTCCTTCCCTATTCAAAACGCAGAGCTATCTACATTATGTAAATATATGGATA
1 TTCCTCACTCTTCTCCTTCCCTATTCAAAACACAGAGCTATCTAAATTATGTAAATATATAGATA
32516 T
1 T
32517 AACCTCTACA
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.31, C:0.25, G:0.08, T:0.36
Consensus pattern (65 bp):
TTCCTCACTCTTCTCCTTCCCTATTCAAAACACAGAGCTATCTAAATTATGTAAATATATAGATA
Found at i:32732 original size:61 final size:61
Alignment explanation
Indices: 32629--32744 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
32619 TTATACAAAA
* *
32629 TTTGTTATTAGGCAACATGTAATAATTAGAAACCTCCAGATTATTCAACAAACACTTTTAC
1 TTTGTTATTAGGCAACATGTAATAATTAAAAACCTACAGATTATTCAACAAACACTTTTAC
* * **
32690 TTTGTTATTAGGCAATATGTAATAATTAAAAATCTATTGATTATTCAACAAACAC
1 TTTGTTATTAGGCAACATGTAATAATTAAAAACCTACAGATTATTCAACAAACAC
32745 GCTATTACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.40, C:0.15, G:0.09, T:0.36
Consensus pattern (61 bp):
TTTGTTATTAGGCAACATGTAATAATTAAAAACCTACAGATTATTCAACAAACACTTTTAC
Found at i:39063 original size:28 final size:28
Alignment explanation
Indices: 39032--39088 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
39022 AAAATCATGA
* *
39032 AAGCTTTTATAGAAAGAAAGAGAAATTT
1 AAGCTTTTAGAAAAAGAAAGAGAAATTT
39060 AAGCTTTTAGAAAAAGAAAGAGAAATTT
1 AAGCTTTTAGAAAAAGAAAGAGAAATTT
39088 A
1 A
39089 TTACTGTGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.04, G:0.18, T:0.26
Consensus pattern (28 bp):
AAGCTTTTAGAAAAAGAAAGAGAAATTT
Found at i:40163 original size:2 final size:2
Alignment explanation
Indices: 40156--40221 Score: 54
Period size: 2 Copynumber: 36.0 Consensus size: 2
40146 AACCGATGAA
40156 AT AT AT AT AT AT AT AT AT -T A- AT AT -T AT AT AT A- AT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
40193 TT AT AT AT AT -T AT AG AT TT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40222 TTTATATTAT
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
1 6 0.12
2 44 0.88
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (2 bp):
AT
Found at i:40184 original size:23 final size:23
Alignment explanation
Indices: 40157--40260 Score: 73
Period size: 23 Copynumber: 4.7 Consensus size: 23
40147 ACCGATGAAA
40157 TATATATATATATATATTAATAT
1 TATATATATATATATATTAATAT
40180 TATATATA-AT-TAT-TT-ATA-
1 TATATATATATATATATTAATAT
* * *
40198 TATATTATAGATTTATATTTATAT
1 TATA-TATATATATATATTAATAT
*
40222 T-T-TATAT-TAT-TTTTAATTAGT
1 TATATATATATATATATTAA-TA-T
40243 TATATATATATAATATAT
1 TATATATATAT-ATATAT
40261 CAGAAATAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 23
0.69 0.05 0.25
Matches are distributed among these distances:
18 4 0.06
19 11 0.17
20 8 0.13
21 12 0.19
22 5 0.08
23 17 0.27
24 2 0.03
25 2 0.03
26 2 0.03
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TATATATATATATATATTAATAT
Found at i:41165 original size:17 final size:17
Alignment explanation
Indices: 41145--41181 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
41135 GCTCTGGATT
41145 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
41162 TTATTTGTATAAGCATG
1 TTATTTGTATAAGCATG
41179 TTA
1 TTA
41182 ATAGTTTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.16, T:0.49
Consensus pattern (17 bp):
TTATTTGTATAAGCATG
Found at i:41551 original size:24 final size:23
Alignment explanation
Indices: 41524--41601 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
41514 TTAGACTTGT
41524 TTGTTCTCTGCTGCCACACTTTTC
1 TTGTT-TCTGCTGCCACACTTTTC
* * * *
41548 TTGTTTCTGAAT--TAGACTTGT-
1 TTGTTTCTG-CTGCCACACTTTTC
41569 TTGTTCTCTGCTGCCACACTTTTC
1 TTGTT-TCTGCTGCCACACTTTTC
41593 TTGTTTCTG
1 TTGTTTCTG
41602 AATTAAGATC
Statistics
Matches: 41, Mismatches: 8, Indels: 11
0.68 0.13 0.18
Matches are distributed among these distances:
21 6 0.15
22 10 0.24
23 14 0.34
24 11 0.27
ACGTcount: A:0.10, C:0.24, G:0.15, T:0.50
Consensus pattern (23 bp):
TTGTTTCTGCTGCCACACTTTTC
Found at i:41575 original size:45 final size:45
Alignment explanation
Indices: 41511--41606 Score: 192
Period size: 45 Copynumber: 2.1 Consensus size: 45
41501 AGGGCTATAG
41511 GAATTAGACTTGTTTGTTCTCTGCTGCCACACTTTTCTTGTTTCT
1 GAATTAGACTTGTTTGTTCTCTGCTGCCACACTTTTCTTGTTTCT
41556 GAATTAGACTTGTTTGTTCTCTGCTGCCACACTTTTCTTGTTTCT
1 GAATTAGACTTGTTTGTTCTCTGCTGCCACACTTTTCTTGTTTCT
41601 GAATTA
1 GAATTA
41607 AGATCATTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 51 1.00
ACGTcount: A:0.16, C:0.21, G:0.16, T:0.48
Consensus pattern (45 bp):
GAATTAGACTTGTTTGTTCTCTGCTGCCACACTTTTCTTGTTTCT
Found at i:42557 original size:27 final size:27
Alignment explanation
Indices: 42527--42581 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
42517 AGAAAAGCTG
42527 TTGCAACTATGATTATAGTTGATGAGC
1 TTGCAACTATGATTATAGTTGATGAGC
42554 TTGCAACTATGATTATAGTTGATGAGC
1 TTGCAACTATGATTATAGTTGATGAGC
42581 T
1 T
42582 GCCTTTTAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (27 bp):
TTGCAACTATGATTATAGTTGATGAGC
Found at i:45058 original size:30 final size:29
Alignment explanation
Indices: 45015--45076 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 29
45005 GCAACTAGCT
*
45015 ATTGAAGTTTAAGTTTTCTGACTTCAGTG
1 ATTGAAGTTTAAGTATTCTGACTTCAGTG
*
45044 ATTGAAGTTTTAAGTATTCTGATTTCAGTG
1 ATTGAAG-TTTAAGTATTCTGACTTCAGTG
45074 ATT
1 ATT
45077 TGTATGTATG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.26, C:0.08, G:0.19, T:0.47
Consensus pattern (29 bp):
ATTGAAGTTTAAGTATTCTGACTTCAGTG
Found at i:46818 original size:260 final size:260
Alignment explanation
Indices: 46357--46883 Score: 858
Period size: 260 Copynumber: 2.0 Consensus size: 260
46347 CGACTACAAC
* *
46357 ATTATTGCCACCCCAGGAAGCAACTGTGACACTTTGAGCCACAAAGTGTTTAGTGCCCATCTTAA
1 ATTATTGCCACCCCAGGAAGCAACTGTGAAACTTTAAGCCACAAAGTGTTTAGTGCCCATCTTAA
* * * * *
46422 AAGCAATGGGAGATTGGATGAACAAGCAGTTGCTTATTCCAGATAGTCATTATGCCATGAGGGTT
66 AAGCAATGGGAGATTGGATGAACAAACAGTTGCTTATTCCAGACACTCATTATGCCAAGAGGGTC
46487 TGAAGCTTCCTCGGATCTCACTTTTTCTACTCTTTGTTCTATCCCAGGTTTGTATACATCATTCT
131 TGAAGCTTCCTCGGATCTCACTTTTTCTACTCTTTGTTCTATCCCAGGTTTGTATACATCATTCT
* *
46552 AACGTTATATCTTCTCCGTTTTTTGCCTCCGAAGTTATGATTAATCTTAGTTTCTGCTTCATTTG
196 AACGTTATATCTTCTCCGTTTTTGGCCTCCGAAGTTATGATTAATCTTAGTTTCTCCTTCATTTG
* *
46617 ATTATTGCCACCCCAGGAAGCAACTGTGAAACTTTAAGCTACAAAGTGTTTAGTGGCCATCTTAA
1 ATTATTGCCACCCCAGGAAGCAACTGTGAAACTTTAAGCCACAAAGTGTTTAGTGCCCATCTTAA
* *
46682 AAGCAATGGGAGATTGGATGAACAAACAGTTGCTTATTCCAGGCACTTATTATG-CAAGCAGGGT
66 AAGCAATGGGAGATTGGATGAACAAACAGTTGCTTATTCCAGACACTCATTATGCCAAG-AGGGT
* * *
46746 CTGAAGCTTCCTCGGATTTCACTTTTTCTACTCTTTGTTCTATCCCAGGTTTGTATATATCATTT
130 CTGAAGCTTCCTCGGATCTCACTTTTTCTACTCTTTGTTCTATCCCAGGTTTGTATACATCATTC
* * * *
46811 TAACGTTATATCTTCTCTGTTTTTGGCCTCTGAAGTTATGATTAATGTTAGTTTCTCCTTCTTTT
195 TAACGTTATATCTTCTCCGTTTTTGGCCTCCGAAGTTATGATTAATCTTAGTTTCTCCTTCATTT
46876 G
260 G
46877 ATTATTG
1 ATTATTG
46884 GGTAATTGGT
Statistics
Matches: 246, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
259 3 0.01
260 243 0.99
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (260 bp):
ATTATTGCCACCCCAGGAAGCAACTGTGAAACTTTAAGCCACAAAGTGTTTAGTGCCCATCTTAA
AAGCAATGGGAGATTGGATGAACAAACAGTTGCTTATTCCAGACACTCATTATGCCAAGAGGGTC
TGAAGCTTCCTCGGATCTCACTTTTTCTACTCTTTGTTCTATCCCAGGTTTGTATACATCATTCT
AACGTTATATCTTCTCCGTTTTTGGCCTCCGAAGTTATGATTAATCTTAGTTTCTCCTTCATTTG
Found at i:48184 original size:7 final size:7
Alignment explanation
Indices: 48172--48198 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
48162 TGATCTTGCC
48172 TGTTGAT
1 TGTTGAT
48179 TGTTGAT
1 TGTTGAT
48186 TGTTGAT
1 TGTTGAT
48193 TGTTGA
1 TGTTGA
48199 AGCTATTCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.30, T:0.56
Consensus pattern (7 bp):
TGTTGAT
Found at i:48825 original size:45 final size:45
Alignment explanation
Indices: 48760--48867 Score: 164
Period size: 45 Copynumber: 2.4 Consensus size: 45
48750 TCTAATTTTA
* *
48760 GGTGGG-ATGTCATTCTCATCACTTTCCCATCCAAGTGAGAAAGT
1 GGTGGGAATGACATTCCCATCACTTTCCCATCCAAGTGAGAAAGT
* *
48804 GGTGGGAATGGCATTCCCATCACTTTCCCATCCAAGTGGGAAAGT
1 GGTGGGAATGACATTCCCATCACTTTCCCATCCAAGTGAGAAAGT
*
48849 GGTGGAAATGACATTCCCA
1 GGTGGGAATGACATTCCCA
48868 CCTACAAGGG
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
44 6 0.10
45 52 0.90
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (45 bp):
GGTGGGAATGACATTCCCATCACTTTCCCATCCAAGTGAGAAAGT
Found at i:48955 original size:30 final size:29
Alignment explanation
Indices: 48921--48981 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
48911 ATTTTTATCT
48921 TGACTTTCCTCTTATACCCTCAAATTTTAA
1 TGACTTTCCTCTTATA-CCTCAAATTTTAA
* * *
48951 TGACTTTTCTTTTATACCTGAAATTTTAA
1 TGACTTTCCTCTTATACCTCAAATTTTAA
48980 TG
1 TG
48982 GCTTATTAAC
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 14 0.50
30 14 0.50
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.48
Consensus pattern (29 bp):
TGACTTTCCTCTTATACCTCAAATTTTAA
Found at i:54054 original size:14 final size:14
Alignment explanation
Indices: 54011--54060 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
54001 TACTCCCTTC
54011 GTCCTTTTTTATCT
1 GTCCTTTTTTATCT
**
54025 GTCGC-TTTTGCT-T
1 GTC-CTTTTTTATCT
54038 GTCCTTTTTTATCT
1 GTCCTTTTTTATCT
*
54052 GTCATTTTT
1 GTCCTTTTT
54061 GGAAATAATT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
12 1 0.04
13 9 0.32
14 17 0.61
15 1 0.04
ACGTcount: A:0.06, C:0.20, G:0.12, T:0.62
Consensus pattern (14 bp):
GTCCTTTTTTATCT
Found at i:61158 original size:27 final size:27
Alignment explanation
Indices: 61076--61169 Score: 107
Period size: 27 Copynumber: 3.4 Consensus size: 27
61066 ATTTTCTTAA
* * *
61076 TTGGTCATTTGCACACTCAGGGGTATT
1 TTGGTCATTTACGCACTCAGGGGCATT
* * *
61103 TCGGTCATTTGCGCATTCAGGGGCATT
1 TTGGTCATTTACGCACTCAGGGGCATT
*
61130 TTGGTCATTTATGCACTCAGGGGCATT
1 TTGGTCATTTACGCACTCAGGGGCATT
*
61157 TTAGTCACTTTAC
1 TTGGTCA-TTTAC
61170 ACGATCTAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
27 52 0.93
28 4 0.07
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.37
Consensus pattern (27 bp):
TTGGTCATTTACGCACTCAGGGGCATT
Found at i:62214 original size:14 final size:14
Alignment explanation
Indices: 62195--62226 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
62185 AATGCCAACG
62195 ATACCATCCAGTAA
1 ATACCATCCAGTAA
62209 ATACCATCCAGTAA
1 ATACCATCCAGTAA
62223 ATAC
1 ATAC
62227 AGCAAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.06, T:0.22
Consensus pattern (14 bp):
ATACCATCCAGTAA
Found at i:69242 original size:8 final size:8
Alignment explanation
Indices: 69229--69257 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
69219 TCAAGTATTC
69229 CCCCCCCT
1 CCCCCCCT
69237 CCCCCCCT
1 CCCCCCCT
69245 CCCCCCCT
1 CCCCCCCT
69253 CCCCC
1 CCCCC
69258 ATACTTAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.90, G:0.00, T:0.10
Consensus pattern (8 bp):
CCCCCCCT
Found at i:70768 original size:22 final size:25
Alignment explanation
Indices: 70740--70799 Score: 72
Period size: 27 Copynumber: 2.4 Consensus size: 25
70730 TGGCAAGGGA
70740 CATGGCACGG-ATGG-GG-GCGCGG
1 CATGGCACGGCATGGCGGTGCGCGG
*
70762 CATGGCACGGGCCTGGCTGGTGCGCGG
1 CATGGCAC-GGCATGGC-GGTGCGCGG
70789 CATGGCACGGC
1 CATGGCACGGC
70800 CTGTGCGCGC
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 8 0.25
23 2 0.06
24 3 0.09
26 5 0.16
27 14 0.44
ACGTcount: A:0.12, C:0.28, G:0.48, T:0.12
Consensus pattern (25 bp):
CATGGCACGGCATGGCGGTGCGCGG
Found at i:89219 original size:28 final size:28
Alignment explanation
Indices: 89187--89260 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 28
89177 AGGGTCATCT
* * *
89187 AGGGGCATTTTGGTCATTTTTATA-TTCG
1 AGGGGCATTTTGGTCATTTTGA-ACGTCC
*
89215 AGGGGCATTTTAGTCA-TTTGAACGTCC
1 AGGGGCATTTTGGTCATTTTGAACGTCC
89242 AGGGGCATTTTGGTCATTT
1 AGGGGCATTTTGGTCATTT
89261 GCACACTCAA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.54
28 17 0.44
ACGTcount: A:0.19, C:0.14, G:0.27, T:0.41
Consensus pattern (28 bp):
AGGGGCATTTTGGTCATTTTGAACGTCC
Found at i:89257 original size:27 final size:27
Alignment explanation
Indices: 89187--89288 Score: 98
Period size: 28 Copynumber: 3.7 Consensus size: 27
89177 AGGGTCATCT
* * * *
89187 AGGGGCATTTTGGTCATTTTTATATTCG
1 AGGGGCATTTTGGTCA-TTTGACACTCA
* *
89215 AGGGGCATTTTAGTCATTTGA-ACGTCC
1 AGGGGCATTTTGGTCATTTGACAC-TCA
89242 AGGGGCATTTTGGTCATTTGCACACTCA
1 AGGGGCATTTTGGTCATTTG-ACACTCA
* *
89270 AGGGGCGTTGTGGTCATTT
1 AGGGGCATTTTGGTCATTT
89289 TAAGTTCACA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 25 0.40
28 35 0.56
29 2 0.03
ACGTcount: A:0.19, C:0.16, G:0.28, T:0.37
Consensus pattern (27 bp):
AGGGGCATTTTGGTCATTTGACACTCA
Done.