Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012609.1 Corchorus capsularis cultivar CVL-1 contig12630, 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: 93369
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:1901 original size:16 final size:16
Alignment explanation
Indices: 1876--2002 Score: 132
Period size: 16 Copynumber: 7.8 Consensus size: 16
1866 TGGTGACCTC
1876 ACCAGGTGAGTATTGT
1 ACCAGGTGAGTATTGT
** *
1892 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTAT-TGT
*
1908 ACCAGGTGAGTATTGC
1 ACCAGGTGAGTATTGT
1924 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTA-TTGT
* *
1941 ACTAGGTGAGTGTTTGT
1 ACCAGGTGAGT-ATTGT
1958 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTA-TTGT
1975 ACCAGGTGAGTATT-T
1 ACCAGGTGAGTATTGT
*
1990 GCACAGGTGAGTA
1 AC-CAGGTGAGTA
2003 GGGTAGGAAC
Statistics
Matches: 94, Mismatches: 11, Indels: 12
0.80 0.09 0.10
Matches are distributed among these distances:
15 3 0.03
16 47 0.50
17 44 0.47
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.31
Consensus pattern (16 bp):
ACCAGGTGAGTATTGT
Found at i:1949 original size:17 final size:17
Alignment explanation
Indices: 1876--2002 Score: 154
Period size: 17 Copynumber: 7.7 Consensus size: 17
1866 TGGTGACCTC
1876 ACCAGGTGAGTA-TTGT
1 ACCAGGTGAGTATTTGT
** * *
1892 ACTGGGTGAGTATCT-C
1 ACCAGGTGAGTATTTGT
*
1908 ACCAGGTGAGTA-TTGC
1 ACCAGGTGAGTATTTGT
1924 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
* *
1941 ACTAGGTGAGTGTTTGT
1 ACCAGGTGAGTATTTGT
1958 ACCAGGTGAGTATTTGT
1 ACCAGGTGAGTATTTGT
*
1975 ACCAGGTGAGTATTTGC
1 ACCAGGTGAGTATTTGT
1992 A-CAGGTGAGTA
1 ACCAGGTGAGTA
2003 GGGTAGGAAC
Statistics
Matches: 95, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
15 1 0.01
16 43 0.45
17 51 0.54
ACGTcount: A:0.24, C:0.13, G:0.31, T:0.31
Consensus pattern (17 bp):
ACCAGGTGAGTATTTGT
Found at i:8285 original size:47 final size:47
Alignment explanation
Indices: 8252--8351 Score: 148
Period size: 47 Copynumber: 2.1 Consensus size: 47
8242 CTAAAATAGC
* *
8252 CTTTTTAATTCTAAAGGTTAGTCTTCAATTAAAAGGGTAAACATGTA
1 CTTTTTAATTCTAAAGGTTAGTCTTCAATTAAAAAGCTAAACATGTA
* * *
8299 TTTTTTAATTCTAAAGGTTAGTCTTCAATTAAAAGGGTAAACATGTA
1 CTTTTTAATTCTAAAGGTTAGTCTTCAATTAAAAAGCTAAACATGTA
8346 -TTTTTA
1 CTTTTTA
8352 TTAACAAAAA
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
46 6 0.12
47 46 0.88
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (47 bp):
CTTTTTAATTCTAAAGGTTAGTCTTCAATTAAAAAGCTAAACATGTA
Found at i:12007 original size:23 final size:23
Alignment explanation
Indices: 11981--12028 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
11971 ATAAGATTAC
*
11981 TGTAGGTAGTAATATAACCATTT
1 TGTAGATAGTAATATAACCATTT
**
12004 TGTAGATAGTTCTATAACCATTT
1 TGTAGATAGTAATATAACCATTT
12027 TG
1 TG
12029 ATAGTATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (23 bp):
TGTAGATAGTAATATAACCATTT
Found at i:12731 original size:28 final size:29
Alignment explanation
Indices: 12689--12753 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 29
12679 TAAATGAAAA
* *
12689 TTTTTTTGCTAGAAAAG-AGGAAAACTTTT
1 TTTTTTTGATAG-AAAGCAGCAAAACTTTT
*
12718 TTTTTTTGAT-GAAAGCTTGCAAAACTTTT
1 TTTTTTTGATAGAAAGC-AGCAAAACTTTT
12747 TTTTTTT
1 TTTTTTT
12754 TTCGCTACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 1 0.03
29 26 0.84
ACGTcount: A:0.28, C:0.08, G:0.14, T:0.51
Consensus pattern (29 bp):
TTTTTTTGATAGAAAGCAGCAAAACTTTT
Found at i:21126 original size:11 final size:11
Alignment explanation
Indices: 21112--21149 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
21102 ATTCATAACA
21112 AATTTATAATT
1 AATTTATAATT
21123 AATTTATAATT
1 AATTTATAATT
21134 -ATTTGATAATT
1 AATTT-ATAATT
*
21145 TATTT
1 AATTT
21150 TATATAGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:23477 original size:30 final size:29
Alignment explanation
Indices: 23443--23507 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
23433 CGAAAAGGGT
* **
23443 TTATTTAGCCTCTTTTAAGAGTTCAGGGGC
1 TTATTTAGCCGCAATTAA-AGTTCAGGGGC
* *
23473 TTATTTGGCCGCAATTAAAGTTCATGGGC
1 TTATTTAGCCGCAATTAAAGTTCAGGGGC
23502 TTATTT
1 TTATTT
23508 GCCCGTTTTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.42
Consensus pattern (29 bp):
TTATTTAGCCGCAATTAAAGTTCAGGGGC
Found at i:23694 original size:22 final size:21
Alignment explanation
Indices: 23650--23693 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
23640 TTTATCTGGA
23650 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
23671 TTGCTAAATACCGCCCCCCTT
1 TTGCTAAATACCGCCCCCCTT
23692 TT
1 TT
23694 TACACTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.41, G:0.09, T:0.32
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCCCTT
Found at i:23824 original size:24 final size:25
Alignment explanation
Indices: 23764--23815 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
23754 TTCAAACCCT
*
23764 AAACTTCATTTCTAACAACTTCTTC
1 AAACTTCATTTCTAACAACATCTTC
23789 AAACTTCATTTCTAACAA-ATCTTC
1 AAACTTCATTTCTAACAACATCTTC
23813 AAA
1 AAA
23816 TTGATTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 8 0.31
25 18 0.69
ACGTcount: A:0.38, C:0.25, G:0.00, T:0.37
Consensus pattern (25 bp):
AAACTTCATTTCTAACAACATCTTC
Found at i:23861 original size:26 final size:26
Alignment explanation
Indices: 23832--23899 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
23822 TTCCTTCATT
23832 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
23858 TTAATCATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
23884 TTAAACATAAATTAAT
1 TTAATCATAAACTAAT
23900 AAACTAAGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.53, C:0.10, G:0.01, T:0.35
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:23862 original size:15 final size:15
Alignment explanation
Indices: 23832--23875 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
23822 TTCCTTCATT
23832 TTAATCATAAACTAA
1 TTAATCATAAACTAA
23847 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
23858 TTAATCATAAACTAA
1 TTAATCATAAACTAA
23873 TTA
1 TTA
23876 GATACTAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 9 0.36
13 4 0.16
15 12 0.48
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:24241 original size:21 final size:21
Alignment explanation
Indices: 24215--24259 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
24205 AAAAATTATA
* * *
24215 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGAGGGCGCTGTTCAGC
24236 AAAAGGAGGGCGCTGTTCAGC
1 AAAAGGAGGGCGCTGTTCAGC
24257 AAA
1 AAA
24260 CCCCTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.13, G:0.40, T:0.16
Consensus pattern (21 bp):
AAAAGGAGGGCGCTGTTCAGC
Found at i:24305 original size:13 final size:12
Alignment explanation
Indices: 24274--24316 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
24264 TTATTTATAT
*
24274 TTTTCAAACACA
1 TTTTCAAAAACA
*
24286 ATTTCAAAAACA
1 TTTTCAAAAACA
24298 CTTTTCAAAAAACA
1 -TTTTC-AAAAACA
24312 TTTTC
1 TTTTC
24317 CAAACCGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 10 0.38
13 9 0.35
14 7 0.27
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (12 bp):
TTTTCAAAAACA
Found at i:24634 original size:15 final size:15
Alignment explanation
Indices: 24614--24643 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
24604 TTAGTAAATA
24614 TAAATGGGAAAAGCT
1 TAAATGGGAAAAGCT
*
24629 TAAATGGGGAAAGCT
1 TAAATGGGAAAAGCT
24644 ATAAGTAGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.30, T:0.20
Consensus pattern (15 bp):
TAAATGGGAAAAGCT
Found at i:26451 original size:14 final size:13
Alignment explanation
Indices: 26424--26468 Score: 63
Period size: 13 Copynumber: 3.4 Consensus size: 13
26414 AAAAACTAAC
26424 AAAATTTAGTAAA
1 AAAATTTAGTAAA
*
26437 AAAATTCTGGTAAA
1 AAAATT-TAGTAAA
*
26451 AACATTTAGTAAA
1 AAAATTTAGTAAA
26464 AAAAT
1 AAAAT
26469 ATTTGAAATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
13 16 0.59
14 11 0.41
ACGTcount: A:0.58, C:0.04, G:0.09, T:0.29
Consensus pattern (13 bp):
AAAATTTAGTAAA
Found at i:31950 original size:3 final size:3
Alignment explanation
Indices: 31942--31976 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
31932 CCGCGCCGGT
31942 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31977 TCCAATAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:32822 original size:21 final size:20
Alignment explanation
Indices: 32784--32822 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
32774 AAAAAACAAA
**
32784 TACCGCCCCCTTTTACTAGC
1 TACCGCCCCCTTAAACTAGC
32804 TACCGCCCCCCTTAAACTA
1 TACCG-CCCCCTTAAACTA
32823 TTTTGCCCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.21, C:0.46, G:0.08, T:0.26
Consensus pattern (20 bp):
TACCGCCCCCTTAAACTAGC
Found at i:33158 original size:32 final size:31
Alignment explanation
Indices: 33122--33212 Score: 103
Period size: 32 Copynumber: 2.7 Consensus size: 31
33112 TAAAAACGTT
33122 AAAGAAAAAAA-AAAGAAGAACAAGAAAAAGAA
1 AAAGAAAAAAAGAAAGAAGAACAAG-AAAA-AA
33154 AAAGAAAAAAAACGTTAAAGAAGAACAAGAAAAAA
1 AAAG-AAAAAAA-G--AAAGAAGAACAAGAAAAAA
*
33189 AAAGAAAGAAAAGAAAGATGAACA
1 AAAGAAA-AAAAGAAAGAAGAACA
33213 GAGAGGCGGG
Statistics
Matches: 52, Mismatches: 1, Indels: 12
0.80 0.02 0.18
Matches are distributed among these distances:
32 14 0.27
33 7 0.13
34 4 0.08
35 10 0.19
36 4 0.08
37 13 0.25
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.03
Consensus pattern (31 bp):
AAAGAAAAAAAGAAAGAAGAACAAGAAAAAA
Found at i:35302 original size:2 final size:2
Alignment explanation
Indices: 35295--35323 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
35285 AATTAAGGTG
35295 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 T
35324 GTAGATTTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37738 original size:30 final size:31
Alignment explanation
Indices: 37686--37747 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
37676 AACTTTATGT
* * *
37686 TTTCCGATTGTACCATTATTTTTAAAACATA
1 TTTCCAATTATACCATTATTTTTAAAAAATA
*
37717 TTTCCAATTATACCCTT-TTTTTAAAAAATA
1 TTTCCAATTATACCATTATTTTTAAAAAATA
37747 T
1 T
37748 ATTTCTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 13 0.48
31 14 0.52
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTCCAATTATACCATTATTTTTAAAAAATA
Found at i:42988 original size:30 final size:30
Alignment explanation
Indices: 42952--43011 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
42942 ATCTCCACCT
42952 TGACTTAAGTTTACCAAATCACCATAATAA
1 TGACTTAAGTTTACCAAATCACCATAATAA
42982 TGACTTAAGTTTACCAAATCACCATAATAA
1 TGACTTAAGTTTACCAAATCACCATAATAA
43012 GCCAAGCTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (30 bp):
TGACTTAAGTTTACCAAATCACCATAATAA
Found at i:48823 original size:22 final size:24
Alignment explanation
Indices: 48792--48842 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
48782 TTGATTTTTT
**
48792 TTTTTGGGCTCTGT-ACGGTTCTG
1 TTTTTGGGCTCTGTCAAAGTTCTG
48815 TTTTT-GGCTCTGTCAAAGTTCTG
1 TTTTTGGGCTCTGTCAAAGTTCTG
48838 TTTTT
1 TTTTT
48843 AAGCCTCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.08, C:0.16, G:0.24, T:0.53
Consensus pattern (24 bp):
TTTTTGGGCTCTGTCAAAGTTCTG
Found at i:50783 original size:27 final size:27
Alignment explanation
Indices: 50729--50783 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
50719 TTCTTTGTAT
*
50729 GAATTGTATGAAAGTGCATTTTAGTTA
1 GAATTGTATGAAAGTGCATTTGAGTTA
*
50756 GAATTGTATGCAAGTGCAATTTGA-TTA
1 GAATTGTATGAAAGTGC-ATTTGAGTTA
50783 G
1 G
50784 TAGTACAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 20 0.80
28 5 0.20
ACGTcount: A:0.33, C:0.05, G:0.24, T:0.38
Consensus pattern (27 bp):
GAATTGTATGAAAGTGCATTTGAGTTA
Found at i:53030 original size:39 final size:39
Alignment explanation
Indices: 52997--53073 Score: 102
Period size: 39 Copynumber: 2.0 Consensus size: 39
52987 AAGGAGGGCG
*
52997 AAGAGGAG-AAGAAGAAGAAGGAAGAGGAGAAGGAGGAGA
1 AAGAGGAGAAAG-AGAAGAAAGAAGAGGAGAAGGAGGAGA
* **
53036 AAGAGGAGAAAGAGAAGAAAGAGGAGGAGGCGGAGGAG
1 AAGAGGAGAAAGAGAAGAAAGAAGAGGAGAAGGAGGAG
53074 GTGAAGAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 30 0.91
40 3 0.09
ACGTcount: A:0.51, C:0.01, G:0.48, T:0.00
Consensus pattern (39 bp):
AAGAGGAGAAAGAGAAGAAAGAAGAGGAGAAGGAGGAGA
Found at i:53039 original size:18 final size:18
Alignment explanation
Indices: 52997--53061 Score: 76
Period size: 18 Copynumber: 3.4 Consensus size: 18
52987 AAGGAGGGCG
*
52997 AAGAGGAGAAGAAGAAGAAGG
1 AAGAGGAG-A-AAG-AGAAGA
* *
53018 AAGAGGAGAAGGAGGAGA
1 AAGAGGAGAAAGAGAAGA
53036 AAGAGGAGAAAGAGAAGA
1 AAGAGGAGAAAGAGAAGA
53054 AAGAGGAG
1 AAGAGGAG
53062 GAGGCGGAGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
18 28 0.72
19 2 0.05
20 1 0.03
21 8 0.21
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (18 bp):
AAGAGGAGAAAGAGAAGA
Found at i:59644 original size:29 final size:30
Alignment explanation
Indices: 59606--59676 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
59596 CTTGTTGTTT
* *
59606 AGGGAACAAAACGTCCAAAGT-TA-AAGTTC
1 AGGGAGCAAAACATCCAAA-TCTACAAGTTC
*
59635 AGGGGGCAAAACATCCAAATCGTACAAGTTC
1 AGGGAGCAAAACATCCAAATC-TACAAGTTC
59666 AGGGAGCAAAA
1 AGGGAGCAAAA
59677 AGGACACTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
28 1 0.03
29 16 0.46
30 2 0.06
31 16 0.46
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (30 bp):
AGGGAGCAAAACATCCAAATCTACAAGTTC
Found at i:60061 original size:20 final size:20
Alignment explanation
Indices: 60012--60061 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
60002 TTATATCTTA
60012 TAAAACATATAAGAAATA-T
1 TAAAACATATAAGAAATATT
* *
60031 TAAAATAATATAA-ATATATT
1 TAAAA-CATATAAGAAATATT
60051 TAAAGACATAT
1 TAAA-ACATAT
60062 TATAGTTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 9 0.36
20 15 0.60
21 1 0.04
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.32
Consensus pattern (20 bp):
TAAAACATATAAGAAATATT
Found at i:60154 original size:31 final size:31
Alignment explanation
Indices: 60119--60183 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
60109 AACTTTATGT
* *
60119 TTTCCGATTGTACCCTTATT-TTTAAAACATA
1 TTTCCAATTGTACCATT-TTCTTTAAAACATA
*
60150 TTTCCAATTGTACCATTTTCTTTAAAATATA
1 TTTCCAATTGTACCATTTTCTTTAAAACATA
60181 TTT
1 TTT
60184 TTAAATTGCC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 2 0.07
31 28 0.93
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTCCAATTGTACCATTTTCTTTAAAACATA
Found at i:60532 original size:20 final size:20
Alignment explanation
Indices: 60495--60533 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
60485 TACTATTATT
60495 TTTTGAATTTAATATTTTAC
1 TTTTGAATTTAATATTTTAC
*
60515 TTTT-AATTTCAATTTTTTA
1 TTTTGAATTT-AATATTTTA
60534 AATGTCAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (20 bp):
TTTTGAATTTAATATTTTAC
Found at i:60720 original size:22 final size:22
Alignment explanation
Indices: 60692--60770 Score: 74
Period size: 22 Copynumber: 3.7 Consensus size: 22
60682 TATCTCTACG
60692 TGGTTATCAAAATTTCATAAGA
1 TGGTTATCAAAATTTCATAAGA
* * *
60714 TGGTTATTATAATTTCA-AGGA
1 TGGTTATCAAAATTTCATAAGA
* *
60735 -GGTTATCAAAATTCCAT-AGTG
1 TGGTTATCAAAATTTCATAAG-A
*
60756 TGGTTACCAAAATTT
1 TGGTTATCAAAATTT
60771 TTTTATAGGA
Statistics
Matches: 44, Mismatches: 10, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
20 14 0.32
21 3 0.07
22 27 0.61
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
TGGTTATCAAAATTTCATAAGA
Found at i:61072 original size:22 final size:22
Alignment explanation
Indices: 61020--61252 Score: 113
Period size: 22 Copynumber: 10.5 Consensus size: 22
61010 TAAGAAGTAC
*
61020 CAAAATTTGATAGAAG-G-TTAT
1 CAAAATTTCATA-AAGTGATTAT
*
61041 C-AAATCTCATAAAGTGATTAT
1 CAAAATTTCATAAAGTGATTAT
* *
61062 CGAAATTTCATAGAGATCGGATTAT
1 CAAAATTTCATAAAG-T--GATTAT
**
61087 CAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCATAAAG-TGATTAT
*
61109 CAAAATTTC--AAAGCGAGGTTAT
1 CAAAATTTCATAAAGTGA--TTAT
* *
61131 CAAAATTACATAATGTGATTAT
1 CAAAATTTCATAAAGTGATTAT
* * * * * *
61153 CAGAATTTCATAGAGGGGTCAA
1 CAAAATTTCATAAAGTGATTAT
* ** *
61175 CAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCATAAAGTGATTAT
** *
61197 CAAAATTTCATAAAAAGGTTAT
1 CAAAATTTCATAAAGTGATTAT
* *
61219 CAAATTTTCA-AAATATGATTA-
1 CAAAATTTCATAAA-GTGATTAT
61240 CAAAAATTTCATA
1 C-AAAATTTCATA
61253 GTGGTATTTT
Statistics
Matches: 165, Mismatches: 33, Indels: 26
0.74 0.15 0.12
Matches are distributed among these distances:
19 4 0.02
20 11 0.07
21 10 0.06
22 112 0.68
23 3 0.02
24 5 0.03
25 20 0.12
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (22 bp):
CAAAATTTCATAAAGTGATTAT
Found at i:61153 original size:44 final size:43
Alignment explanation
Indices: 61020--61250 Score: 139
Period size: 44 Copynumber: 5.2 Consensus size: 43
61010 TAAGAAGTAC
* * *
61020 CAAAATTTGATAGA-AGGTTATC-AAATCTCATAAAGTGATTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAAT-TCATAATGTGATTAT
* * *
61062 CGAAATTTCATAGAGATCGGATTATCAAAATTTCATAGTGTTG-TTAT
1 CAAAATTTCAAAGAGA--GG-TTATCAAAA-TTCATAATG-TGATTAT
*
61109 CAAAATTTCAAAGCGAGGTTATCAAAATTACATAATGTGATTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAATT-CATAATGTGATTAT
* * * * * * *** *
61153 CAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAAAGGTTAT
1 CAAAATTTCAAAGAGAGGTTATCAAAA-TTCATAATGTGATTAT
* * * *
61197 CAAAATTTCATAA-AAAGGTTATCAAATTTTCAAAATATGATTA-
1 CAAAATTTCA-AAGAGAGGTTATCAAA-ATTCATAATGTGATTAT
61240 CAAAAATTTCA
1 C-AAAATTTCA
61251 TAGTGGTATT
Statistics
Matches: 145, Mismatches: 31, Indels: 24
0.73 0.16 0.12
Matches are distributed among these distances:
42 12 0.08
43 6 0.04
44 86 0.59
45 7 0.05
46 5 0.03
47 26 0.18
48 3 0.02
ACGTcount: A:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (43 bp):
CAAAATTTCAAAGAGAGGTTATCAAAATTCATAATGTGATTAT
Found at i:61179 original size:66 final size:66
Alignment explanation
Indices: 61081--61209 Score: 152
Period size: 66 Copynumber: 2.0 Consensus size: 66
61071 ATAGAGATCG
* ** * * **
61081 GATTATCAAAATTTCATAGTGTTGTTATCAAAATTTCA-AAGCGAGGTTATCAAAATTACATAAT
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAA-AAAGGTTATCAAAATTACATAAT
61145 GT
65 GT
* * *
61147 GATTATCAGAATTTCATAGAGGGGTCAACAAAATTTTATAAAAAGGTTATCAAAATTTCATAA
1 GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAAAGGTTATCAAAATTACATAA
61210 AAAGGTTATC
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
66 50 0.96
67 2 0.04
ACGTcount: A:0.42, C:0.10, G:0.14, T:0.34
Consensus pattern (66 bp):
GATTATCAAAATTTCATAGAGGGGTCAACAAAATTTCATAAAAAGGTTATCAAAATTACATAATG
T
Found at i:61359 original size:20 final size:20
Alignment explanation
Indices: 61334--61384 Score: 86
Period size: 19 Copynumber: 2.6 Consensus size: 20
61324 TTATGGAGTA
61334 ATCAAAATTTCAAGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
*
61354 ATCAAAA-TTCAGGGAGGAT
1 ATCAAAATTTCAAGGAGGAT
61373 ATCAAAATTTCA
1 ATCAAAATTTCA
61385 TATGAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.62
20 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCAAAATTTCAAGGAGGAT
Found at i:61488 original size:22 final size:21
Alignment explanation
Indices: 61328--61666 Score: 182
Period size: 22 Copynumber: 15.9 Consensus size: 21
61318 CTTTTATTAT
*
61328 GGAGTAATCAAAATTTCA-A-
1 GGAGTTATCAAAATTTCATAG
*
61347 GGAGGATATCAAAA-TTC--AG
1 GGA-GTTATCAAAATTTCATAG
* *
61366 GGAGGATATCAAAATTTCATAT
1 GGA-GTTATCAAAATTTCATAG
* * *
61388 GAAGGTTATGAACATTTCATAG
1 GGA-GTTATCAAAATTTCATAG
** * *
61410 TTTAGTTTTCAAAATTTCACAAG
1 -GGAGTTATCAAAATTTCA-TAG
61433 AGG-GTTATCAAAATTTCATA-
1 -GGAGTTATCAAAATTTCATAG
* *
61453 GTATGTAGATCAAAATTTCATAG
1 GGA-GT-TATCAAAATTTCATAG
* *
61476 GGAGATTAACAAAATTTCATAA
1 GGAG-TTATCAAAATTTCATAG
* **
61498 TGACGTTATCAAAAAATCATAG
1 GGA-GTTATCAAAATTTCATAG
61520 GGAGGTTATCAAAA-TT--T--
1 GGA-GTTATCAAAATTTCATAG
* *
61537 GTAGTTATCAAGATTTCATAAG
1 GGAGTTATCAAAATTTCAT-AG
** *
61559 AAAGTTATCAAAATTTTATAG
1 GGAGTTATCAAAATTTCATAG
61580 GGAGGTTTATCAAAATTTCATAG
1 GGA-G-TTATCAAAATTTCATAG
*
61603 GAAGATTTATCAAAATTTCATAG
1 G--GAGTTATCAAAATTTCATAG
* *
61626 CGAGGTTATCACAATTTCATAG
1 GGA-GTTATCAAAATTTCATAG
61648 TGTGA-TTATCAAAATTTCA
1 -G-GAGTTATCAAAATTTCA
61667 AACTTTGATT
Statistics
Matches: 246, Mismatches: 48, Indels: 49
0.72 0.14 0.14
Matches are distributed among these distances:
16 9 0.04
17 4 0.02
18 1 0.00
19 23 0.09
20 11 0.04
21 9 0.04
22 144 0.59
23 41 0.17
24 2 0.01
25 2 0.01
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (21 bp):
GGAGTTATCAAAATTTCATAG
Found at i:61675 original size:22 final size:22
Alignment explanation
Indices: 61609--61677 Score: 59
Period size: 22 Copynumber: 3.1 Consensus size: 22
61599 ATAGGAAGAT
* * *
61609 TTATCAAAATTTCATAGC-GAGG
1 TTATCAAAATTTCA-AACTGTGA
* * *
61631 TTATCACAATTTCATAGTGTGA
1 TTATCAAAATTTCAAACTGTGA
*
61653 TTATCAAAATTTCAAACTTTGA
1 TTATCAAAATTTCAAACTGTGA
61675 TTA
1 TTA
61678 CTAACAATTC
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.36, C:0.13, G:0.12, T:0.39
Consensus pattern (22 bp):
TTATCAAAATTTCAAACTGTGA
Found at i:61755 original size:22 final size:22
Alignment explanation
Indices: 61730--61863 Score: 83
Period size: 22 Copynumber: 5.9 Consensus size: 22
61720 TATTAATATA
* *
61730 TCATATGGAGGTTATCAACATC
1 TCATATGGAGGTTATCAAAATT
*
61752 TCATAGTGTTA-GTTATCAAAATT
1 TCATA-TG-GAGGTTATCAAAATT
*
61775 TCAT-TGGGAAGTTATCAAAATT
1 TCATAT-GGAGGTTATCAAAATT
*
61797 TCATATTGAGGTATACTTCAAAATT
1 TCATATGGAGGT-TA--TCAAAATT
* * * * *
61822 CCTTAGGGAGGTTAACCAAATT
1 TCATATGGAGGTTATCAAAATT
* * *
61844 TCATAAGAAGGTTAACAAAA
1 TCATATGGAGGTTATCAAAA
61864 ATTTATTTGA
Statistics
Matches: 87, Mismatches: 17, Indels: 16
0.73 0.14 0.13
Matches are distributed among these distances:
21 2 0.02
22 47 0.54
23 19 0.22
24 3 0.03
25 16 0.18
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.34
Consensus pattern (22 bp):
TCATATGGAGGTTATCAAAATT
Found at i:62978 original size:22 final size:22
Alignment explanation
Indices: 62953--62996 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
62943 AAAATGTTGC
*
62953 AGTGATTATTTTAAAAAGTATA
1 AGTGATTATTCTAAAAAGTATA
*
62975 AGTGATTGTTCTAAAAAGTATA
1 AGTGATTATTCTAAAAAGTATA
62997 TTATTATCCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.16, T:0.39
Consensus pattern (22 bp):
AGTGATTATTCTAAAAAGTATA
Found at i:67695 original size:23 final size:22
Alignment explanation
Indices: 67646--67691 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
67636 AGCTATCCAG
67646 TTGAATCGGTGTTTAATTTTTTC
1 TTGAATCGGTGTTT-ATTTTTTC
67669 TTGAATCGGTGTTT-TTTTTTC
1 TTGAATCGGTGTTTATTTTTTC
67690 TT
1 TT
67692 TTGAGGTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.13, C:0.09, G:0.17, T:0.61
Consensus pattern (22 bp):
TTGAATCGGTGTTTATTTTTTC
Found at i:69987 original size:20 final size:19
Alignment explanation
Indices: 69964--70003 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
69954 TTAATAAGAT
*
69964 AAATGTATAATATATATAAA
1 AAATGTAAAATATAT-TAAA
*
69984 AAATTTAAAATATATTAAA
1 AAATGTAAAATATATTAAA
70003 A
1 A
70004 TATTAAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (19 bp):
AAATGTAAAATATATTAAA
Found at i:71270 original size:14 final size:14
Alignment explanation
Indices: 71247--71281 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
71237 TTTTTCTACT
*
71247 TTTA-ATTTATTTA
1 TTTATATTTATATA
71260 TTTATATTTATATA
1 TTTATATTTATATA
71274 TTTATATT
1 TTTATATT
71282 ATTAATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTATATTTATATA
Found at i:73018 original size:73 final size:74
Alignment explanation
Indices: 72939--73089 Score: 270
Period size: 74 Copynumber: 2.1 Consensus size: 74
72929 ATTAAGGAAT
*
72939 GTGTAATTACGAAAAAGGGTAGAAGGAAAAGGAAT-GGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
73003 ATCC-GAAAA
66 A-CCTGAAAA
73012 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
1 GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
73077 ACCTGAAAA
66 ACCTGAAAA
73086 GTGT
1 GTGT
73090 GAAAAGACCA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
73 36 0.48
74 39 0.52
ACGTcount: A:0.40, C:0.09, G:0.30, T:0.21
Consensus pattern (74 bp):
GTGTAATTACAAAAAAGGGTAGAAGGAAAAGGAATAGGGGAAACTCATAGAGGGGCTTTTTAGTC
ACCTGAAAA
Found at i:78869 original size:51 final size:51
Alignment explanation
Indices: 78788--78891 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
78778 TTAATCCTCA
78788 ATTTGGCCTTTTAGTAATTTCCATTATAGTTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTTAGTAATTTCCATTATAGTTAAAAATAATATATAGTATAT
*
78839 ATTTGGCCTTTTAGTAATTTCCATTGTAGTTAAAAATAATATATAGTATAT
1 ATTTGGCCTTTTAGTAATTTCCATTATAGTTAAAAATAATATATAGTATAT
78890 AT
1 AT
78892 GAGCATTGAA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.45
Consensus pattern (51 bp):
ATTTGGCCTTTTAGTAATTTCCATTATAGTTAAAAATAATATATAGTATAT
Found at i:80928 original size:21 final size:21
Alignment explanation
Indices: 80895--80937 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
80885 TCTGATGCCC
*
80895 TTCCAAATTGCCACAAAAAAG
1 TTCCAAATGGCCACAAAAAAG
* *
80916 TTCCAGATGGCCACAACAAAG
1 TTCCAAATGGCCACAAAAAAG
80937 T
1 T
80938 CCCTTATTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.14, T:0.19
Consensus pattern (21 bp):
TTCCAAATGGCCACAAAAAAG
Found at i:83758 original size:10 final size:10
Alignment explanation
Indices: 83745--83770 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
83735 CATTTCTAAC
83745 AACTTCTTCA
1 AACTTCTTCA
83755 AACTTCTTCA
1 AACTTCTTCA
83765 AACTTC
1 AACTTC
83771 ATTTCTAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
AACTTCTTCA
Found at i:89068 original size:3 final size:3
Alignment explanation
Indices: 89058--89103 Score: 76
Period size: 3 Copynumber: 15.7 Consensus size: 3
89048 TTTTTTTAAA
*
89058 ATT A-T ATT ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
89104 CTATAAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:90376 original size:109 final size:109
Alignment explanation
Indices: 90180--90475 Score: 441
Period size: 109 Copynumber: 2.7 Consensus size: 109
90170 ACTATTATAG
* *
90180 TTTTATTCTACTAGAAACTCTATTTTTATTCAATTAAATTAAATCTAATATCTTTATAATTACTT
1 TTTTATTCTACTAAAAACTCTA---TT-TTC-ATTTAATTAAATCTAATATCTTTATAATTACTT
90245 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
61 TATTTTTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
90294 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
* *
90359 TTACCAAAATATTTGGATATATTAAAATTTTTTCTAATATACAA
66 TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
* * **
90403 TTTTATTCTACTAAAAACTCTATTATCATTTAATTAAAT-TCAATATTTTATATAATTTTTTTTA
1 TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCT-AATATCTT-TATAA-TTACTTTA
90467 TTTTTACCA
63 TTTTTACCA
90476 TTTTAATTTA
Statistics
Matches: 171, Mismatches: 8, Indels: 9
0.91 0.04 0.05
Matches are distributed among these distances:
108 1 0.01
109 124 0.73
110 8 0.05
111 17 0.10
114 21 0.12
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (109 bp):
TTTTATTCTACTAAAAACTCTATTTTCATTTAATTAAATCTAATATCTTTATAATTACTTTATTT
TTACCAAAAAATTTGGATATACTAAAATTTTTTCTAATATACAA
Done.