Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015500.1 Corchorus capsularis cultivar CVL-1 contig15521, 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: 17870
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Found at i:977 original size:16 final size:16
Alignment explanation
Indices: 958--1062 Score: 115
Period size: 16 Copynumber: 6.6 Consensus size: 16
948 TATTGTACTG
958 GGTGAGTATCTCACCA
1 GGTGAGTATCTCACCA
*
974 GGTGAGAATCTCACCA
1 GGTGAGTATCTCACCA
*
990 GGTGAGTAT-TTACCA
1 GGTGAGTATCTCACCA
* *
1005 GGTGAGAATCTCACTA
1 GGTGAGTATCTCACCA
* *
1021 GGTGAGTATTTTGTACCA
1 GGTGAGTA-TCT-CACCA
*
1039 GGTGAGTAT-TTACCA
1 GGTGAGTATCTCACCA
1054 GGTGAGTAT
1 GGTGAGTAT
1063 TTGTATATGG
Statistics
Matches: 76, Mismatches: 10, Indels: 7
0.82 0.11 0.08
Matches are distributed among these distances:
15 27 0.36
16 35 0.46
17 3 0.04
18 11 0.14
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (16 bp):
GGTGAGTATCTCACCA
Found at i:1008 original size:31 final size:31
Alignment explanation
Indices: 958--1064 Score: 135
Period size: 31 Copynumber: 3.4 Consensus size: 31
948 TATTGTACTG
*
958 GGTGAGTATCTCACCAGGTGAGAATCTCACCA
1 GGTGAGTAT-TTACCAGGTGAGAATCTCACCA
*
990 GGTGAGTATTTACCAGGTGAGAATCTCACTA
1 GGTGAGTATTTACCAGGTGAGAATCTCACCA
* *
1021 GGTGAGTATTTTGTACCAGGTGAGTAT-TTACCA
1 GGTGAGTA--TT-TACCAGGTGAGAATCTCACCA
1054 GGTGAGTATTT
1 GGTGAGTATTT
1065 GTATATGGGT
Statistics
Matches: 67, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
30 1 0.01
31 30 0.45
32 9 0.13
33 14 0.21
34 13 0.19
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (31 bp):
GGTGAGTATTTACCAGGTGAGAATCTCACCA
Found at i:1043 original size:18 final size:17
Alignment explanation
Indices: 986--1064 Score: 78
Period size: 15 Copynumber: 4.9 Consensus size: 17
976 TGAGAATCTC
986 ACCAGGTGAGTA--TTT
1 ACCAGGTGAGTATTTTT
* * *
1001 ACCAGGTGAG-AATCTC
1 ACCAGGTGAGTATTTTT
*
1017 ACTAGGTGAGTATTTTGT
1 ACCAGGTGAGTATTTT-T
1035 ACCAGGTGAGTA--TTT
1 ACCAGGTGAGTATTTTT
1050 ACCAGGTGAGTATTT
1 ACCAGGTGAGTATTT
1065 GTATATGGGT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.02
15 23 0.45
16 12 0.24
17 4 0.08
18 11 0.22
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (17 bp):
ACCAGGTGAGTATTTTT
Found at i:1054 original size:49 final size:47
Alignment explanation
Indices: 935--1059 Score: 151
Period size: 49 Copynumber: 2.6 Consensus size: 47
925 TGAGCATGGC
* ** *
935 CTCACCAGGTGTGTATTGTACTGGGTGAGTATCTCACCAGGTGAGAAT
1 CTCACCAGGTGAGTATT-TACCAGGTGAGAATCTCACCAGGTGAGAAT
* *
983 CTCACCAGGTGAGTATTTACCAGGTGAGAATCTCACTAGGTGAGTATT
1 CTCACCAGGTGAGTATTTACCAGGTGAGAATCTCACCAGGTGAG-AAT
* *
1031 TTGTACCAGGTGAGTATTTACCAGGTGAG
1 CT-CACCAGGTGAGTATTTACCAGGTGAG
1060 TATTTGTATA
Statistics
Matches: 67, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
47 23 0.34
48 19 0.28
49 25 0.37
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.30
Consensus pattern (47 bp):
CTCACCAGGTGAGTATTTACCAGGTGAGAATCTCACCAGGTGAGAAT
Found at i:1508 original size:1 final size:1
Alignment explanation
Indices: 1459--1492 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
1449 TGTTCACCAG
1459 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1493 ACGGTTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:1960 original size:25 final size:26
Alignment explanation
Indices: 1932--1984 Score: 74
Period size: 25 Copynumber: 2.1 Consensus size: 26
1922 TTTTTAACTC
1932 ATTATTTA-TTATTTAAAATATAT-TT
1 ATTATTTATTTA-TTAAAATATATATT
*
1957 ATTATTTATTTATTAATATATATATT
1 ATTATTTATTTATTAAAATATATATT
1983 AT
1 AT
1985 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
25 18 0.72
26 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (26 bp):
ATTATTTATTTATTAAAATATATATT
Found at i:2597 original size:24 final size:24
Alignment explanation
Indices: 2570--2638 Score: 104
Period size: 24 Copynumber: 2.9 Consensus size: 24
2560 ATTAAATATT
2570 GCGGCGTCTGGACGCCCCTATTTG
1 GCGGCGTCTGGACGCCCCTATTTG
*
2594 GCGGCGTCCT-GACGCCCCTATTTT
1 GCGGCGT-CTGGACGCCCCTATTTG
*
2618 GCGGCGTCTGGACGCCGCTAT
1 GCGGCGTCTGGACGCCCCTAT
2639 ATGCAATTAG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.05
24 37 0.90
25 2 0.05
ACGTcount: A:0.09, C:0.35, G:0.32, T:0.25
Consensus pattern (24 bp):
GCGGCGTCTGGACGCCCCTATTTG
Found at i:2665 original size:13 final size:13
Alignment explanation
Indices: 2647--2674 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2637 ATATGCAATT
2647 AGTTAAATATAGC
1 AGTTAAATATAGC
2660 AGTTAAATATAGC
1 AGTTAAATATAGC
2673 AG
1 AG
2675 CGTTTTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.07, G:0.18, T:0.29
Consensus pattern (13 bp):
AGTTAAATATAGC
Found at i:2710 original size:32 final size:32
Alignment explanation
Indices: 2674--2735 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
2664 AAATATAGCA
2674 GCGTTTTGTTCGTTAGACGCCGCTATATAAGG
1 GCGTTTTGTTCGTTAGACGCCGCTATATAAGG
*
2706 GCGTTTTGTTCTTTAGACGCCGCTATATAA
1 GCGTTTTGTTCGTTAGACGCCGCTATATAA
2736 AGGTATACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.37
Consensus pattern (32 bp):
GCGTTTTGTTCGTTAGACGCCGCTATATAAGG
Found at i:4253 original size:17 final size:17
Alignment explanation
Indices: 4231--4265 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
4221 TGCATAATGT
4231 TAATGTACCAACAAGAA
1 TAATGTACCAACAAGAA
**
4248 TAATGTGTCAACAAGAA
1 TAATGTACCAACAAGAA
4265 T
1 T
4266 GCACTTTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.23
Consensus pattern (17 bp):
TAATGTACCAACAAGAA
Found at i:5083 original size:27 final size:27
Alignment explanation
Indices: 5045--5162 Score: 182
Period size: 27 Copynumber: 4.3 Consensus size: 27
5035 CGACCCGAGG
*
5045 CGAAGTGGGAGGATCCACTGCTGGGGT
1 CGAAGTGGGAGGATCCACTTCTGGGGT
* **
5072 CGAAGTGGGAGGATCCACTACTTAGGT
1 CGAAGTGGGAGGATCCACTTCTGGGGT
*
5099 CGAAGTGAGGAGGATCGACTTCTGGGGT
1 CGAAGTG-GGAGGATCCACTTCTGGGGT
5127 CGAAGTGGGAGGATCCACTTCTGGGGT
1 CGAAGTGGGAGGATCCACTTCTGGGGT
5154 CGAAGTGGG
1 CGAAGTGGG
5163 GAGAGCCGGA
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
27 59 0.72
28 23 0.28
ACGTcount: A:0.21, C:0.17, G:0.42, T:0.20
Consensus pattern (27 bp):
CGAAGTGGGAGGATCCACTTCTGGGGT
Found at i:5128 original size:55 final size:54
Alignment explanation
Indices: 5041--5162 Score: 183
Period size: 55 Copynumber: 2.3 Consensus size: 54
5031 GAACCGACCC
5041 GAGG-CGAAGTGGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACT
1 GAGGTCGAAGTGGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACT
* * * *
5094 TAGGTCGAAGTGAGGAGGATCGACTTCTGGGGTCGAAGTGGGAGGATCCACTTCT
1 GAGGTCGAAGTG-GGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACT
*
5149 GGGGTCGAAGTGGG
1 GAGGTCGAAGTGGG
5163 GAGAGCCGGA
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.05
54 9 0.15
55 49 0.80
ACGTcount: A:0.21, C:0.16, G:0.43, T:0.20
Consensus pattern (54 bp):
GAGGTCGAAGTGGGAGGATCCACTGCTGGGGTCGAAGTGGGAGGATCCACTACT
Found at i:6410 original size:21 final size:21
Alignment explanation
Indices: 6384--6449 Score: 66
Period size: 21 Copynumber: 3.3 Consensus size: 21
6374 AACCTACAGA
6384 GAACAAAACACACAAGCATGG
1 GAACAAAACACACAAGCATGG
** ** *
6405 GAACAAAGTA-A-GTG-ATGC
1 GAACAAAACACACAAGCATGG
6423 GAACAAAACACACAAGCATGG
1 GAACAAAACACACAAGCATGG
6444 GAACAA
1 GAACAA
6450 GAAAAACATA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
18 11 0.34
19 2 0.06
20 2 0.06
21 17 0.53
ACGTcount: A:0.52, C:0.20, G:0.21, T:0.08
Consensus pattern (21 bp):
GAACAAAACACACAAGCATGG
Found at i:6688 original size:11 final size:11
Alignment explanation
Indices: 6674--6722 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
6664 GAGGAGAAAG
6674 GAAGGAAAGGA
1 GAAGGAAAGGA
6685 GAAGGAAAGGA
1 GAAGGAAAGGA
6696 G-A--AAA-GA
1 GAAGGAAAGGA
*
6703 AAAGGAAAGGA
1 GAAGGAAAGGA
6714 GAATGGAAA
1 GAA-GGAAA
6723 AATTAGACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
7 2 0.06
8 4 0.13
10 4 0.13
11 16 0.52
12 5 0.16
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (11 bp):
GAAGGAAAGGA
Found at i:6703 original size:76 final size:75
Alignment explanation
Indices: 6547--6705 Score: 196
Period size: 76 Copynumber: 2.1 Consensus size: 75
6537 ATTGAAACCG
*
6547 AAGAAAATGAATTTAGGGTTTTAGAAATTTGGGAATGAAAGGAGAAGGAAAGGAGAAAAGGAAAG
1 AAGAAAATGAATTTAGGGTTTTAGAAATTTGGGAATGAAACGAGAAGGAAAGGAGAAAAGGAAAG
* *
6612 AAAATGAACCG
66 AAAAGGAA-CA
** * *
6623 AAGAAAATGAATTTAGGGTTTTAGAAATTTGGGAATGATTCGAGGA-GAAAGGAAGGAAAGGAGA
1 AAGAAAATGAATTTAGGGTTTTAGAAATTTGGGAATGAAACGAGAAGGAAAGG-AGAAAAGGA-A
*
6687 AGGAAAGGAGA-A
64 AGAAAAGGA-ACA
6699 AAGAAAA
1 AAGAAAA
6706 GGAAAGGAGA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
75 6 0.08
76 57 0.79
77 8 0.11
78 1 0.01
ACGTcount: A:0.50, C:0.02, G:0.31, T:0.17
Consensus pattern (75 bp):
AAGAAAATGAATTTAGGGTTTTAGAAATTTGGGAATGAAACGAGAAGGAAAGGAGAAAAGGAAAG
AAAAGGAACA
Found at i:6722 original size:18 final size:17
Alignment explanation
Indices: 6665--6723 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 17
6655 GAATGATTCG
6665 AGGAGAAAGG-AAGGA-A
1 AGGA-AAAGGAAAGGAGA
*
6681 AGGAGAAGGAAAGGAGAA
1 AGGAAAAGGAAAGGAG-A
*
6699 AAGAAAAGGAAAGGAGA
1 AGGAAAAGGAAAGGAGA
6716 ATGGAAAA
1 A-GGAAAA
6724 ATTAGACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
15 4 0.11
16 9 0.26
17 2 0.06
18 20 0.57
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (17 bp):
AGGAAAAGGAAAGGAGA
Found at i:8379 original size:25 final size:25
Alignment explanation
Indices: 8347--8404 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
8337 AATCCATATA
8347 TAAGTAACTTATATACAACCCATTG
1 TAAGTAACTTATATACAACCCATTG
8372 TAAGTAACTTATATACAACCCATTG
1 TAAGTAACTTATATACAACCCATTG
8397 TAAGTAAC
1 TAAGTAAC
8405 ATAACAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.31
Consensus pattern (25 bp):
TAAGTAACTTATATACAACCCATTG
Found at i:10471 original size:43 final size:43
Alignment explanation
Indices: 10408--10495 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
10398 TTCTAGGTTA
*
10408 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACAAAATT
1 ACCAATTTACTTAATCACACCGAATTAAGTTGCTTACAAAATT
* *
10451 ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATCACACCGAATTAAGTTGCTTACAAAATT
10494 AC
1 AC
10496 TTAATTTAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (43 bp):
ACCAATTTACTTAATCACACCGAATTAAGTTGCTTACAAAATT
Found at i:10518 original size:56 final size:56
Alignment explanation
Indices: 10451--10557 Score: 196
Period size: 56 Copynumber: 1.9 Consensus size: 56
10441 TTACAAAATT
10451 ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
1 ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
* *
10507 ACCAATTTACTTAATTACATCGAATTAAGTTGTTTACCAAATTACTTAATT
1 ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATTACTTAATT
10558 ACACCGAATC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (56 bp):
ACCAATTTACTTAATCACACCGAATTAAGTTGTTTACCAAATTACTTAATTTAATC
Found at i:10546 original size:35 final size:35
Alignment explanation
Indices: 10507--10592 Score: 145
Period size: 35 Copynumber: 2.5 Consensus size: 35
10497 TAATTTAATC
* * *
10507 ACCAATTTACTTAATTACATCGAATTAAGTTGTTT
1 ACCAAATTACTTAATTACACCGAATCAAGTTGTTT
10542 ACCAAATTACTTAATTACACCGAATCAAGTTGTTT
1 ACCAAATTACTTAATTACACCGAATCAAGTTGTTT
10577 ACCAAATTACTTAATT
1 ACCAAATTACTTAATT
10593 TAATCACCAA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 48 1.00
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.38
Consensus pattern (35 bp):
ACCAAATTACTTAATTACACCGAATCAAGTTGTTT
Found at i:10604 original size:91 final size:92
Alignment explanation
Indices: 10408--10788 Score: 493
Period size: 97 Copynumber: 3.9 Consensus size: 92
10398 TTCTAGGTTA
*
10408 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACAAAATTACCAATTTACTTAATCACACCG
1 ACCAATTTACTTAATTACA-CGAATTAAGTTGC-T-----ATTACCAATTTACTTAATTACACCG
10473 AATTAAGTTGTTTACCAAATTACTTAATTTAATC
59 AATTAAGTTGTTTACCAAATTACTTAATTTAATC
* *
10507 ACCAATTTACTTAATTACATCGAATTAAGTTG-T-TTACCAAATTACTTAATTACACCGAATCAA
1 ACCAATTTACTTAATTACA-CGAATTAAGTTGCTATTACCAATTTACTTAATTACACCGAATTAA
10570 GTTGTTTACCAAATTACTTAATTTAATC
65 GTTGTTTACCAAATTACTTAATTTAATC
10598 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATTACCAATTTACTTAATTACACCG
1 ACCAATTTACTTAATTACA-CGAATTAAGTTGC-T-----ATTACCAATTTACTTAATTACACCG
10663 AATTAAGTTGTTTACCAAATTACTTAA-TT-A-C
59 AATTAAGTTGTTTACCAAATTACTTAATTTAATC
10694 ACCGAATTTACTTAATTACACTGAATTAAGTTGCTTACCAAATTACCAATTTACTTAATTACACC
1 ACC-AATTTACTTAATTACAC-GAATTAAGTTGC-T-----ATTACCAATTTACTTAATTACACC
10759 GAATTAAGTTGTTTACCAAATTACTTAATT
58 GAATTAAGTTGTTTACCAAATTACTTAATT
10789 ACACCGAATT
Statistics
Matches: 264, Mismatches: 7, Indels: 23
0.90 0.02 0.08
Matches are distributed among these distances:
91 86 0.33
93 1 0.00
96 5 0.02
97 89 0.34
98 3 0.01
99 80 0.30
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.37
Consensus pattern (92 bp):
ACCAATTTACTTAATTACACGAATTAAGTTGCTATTACCAATTTACTTAATTACACCGAATTAAG
TTGTTTACCAAATTACTTAATTTAATC
Found at i:10646 original size:43 final size:43
Alignment explanation
Indices: 10598--10782 Score: 244
Period size: 43 Copynumber: 4.0 Consensus size: 43
10588 TAATTTAATC
10598 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATT
*
10641 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATTACTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACC-----A---AATT
*
10692 ACACCGAATTTACTTAATTACACTGAATTAAGTTGCTTACCAAATT
1 --ACC-AATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATT
*
10738 ACCAATTTACTTAATTACACCGAATTAAGTTGTTTACCAAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATT
10781 AC
1 AC
10783 TTAATTACAC
Statistics
Matches: 126, Mismatches: 5, Indels: 22
0.82 0.03 0.14
Matches are distributed among these distances:
43 77 0.61
44 3 0.02
46 4 0.03
48 1 0.01
49 1 0.01
51 4 0.03
53 3 0.02
54 33 0.26
ACGTcount: A:0.37, C:0.19, G:0.07, T:0.36
Consensus pattern (43 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGCTTACCAAATT
Found at i:10706 original size:19 final size:19
Alignment explanation
Indices: 10644--10720 Score: 79
Period size: 19 Copynumber: 4.2 Consensus size: 19
10634 CCAAATTACC
10644 AATTTACTTAATTACACCG
1 AATTTACTTAATTACACCG
* * * *
10663 AATTAAGTT-GTT-TACC-
1 AATTTACTTAATTACACCG
*
10679 AAATTACTTAATTACACCG
1 AATTTACTTAATTACACCG
*
10698 AATTTACTTAATTACACTG
1 AATTTACTTAATTACACCG
10717 AATT
1 AATT
10721 AAGTTGCTTA
Statistics
Matches: 44, Mismatches: 11, Indels: 6
0.72 0.18 0.10
Matches are distributed among these distances:
16 6 0.14
17 5 0.11
18 5 0.11
19 28 0.64
ACGTcount: A:0.38, C:0.17, G:0.06, T:0.39
Consensus pattern (19 bp):
AATTTACTTAATTACACCG
Found at i:10774 original size:19 final size:19
Alignment explanation
Indices: 10751--10809 Score: 61
Period size: 17 Copynumber: 3.3 Consensus size: 19
10741 AATTTACTTA
10751 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
* * * *
10770 -TT-TACCAAATT-ACTTA
1 ATTACACCGAATTAAGTTG
10786 ATTACACCGAATTAAGTTG
1 ATTACACCGAATTAAGTTG
10805 ATTAC
1 ATTAC
10810 CCACTGATTT
Statistics
Matches: 29, Mismatches: 8, Indels: 6
0.67 0.19 0.14
Matches are distributed among these distances:
16 3 0.10
17 9 0.31
18 9 0.31
19 8 0.28
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.36
Consensus pattern (19 bp):
ATTACACCGAATTAAGTTG
Found at i:10775 original size:35 final size:35
Alignment explanation
Indices: 10735--10810 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
10725 TGCTTACCAA
*
10735 ATTACCAATTTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
*
10770 TTTACCAAATTACTTAATTACACCGAATTAAGTTG
1 ATTACCAAATTACTTAATTACACCGAATTAAGTTG
10805 ATTACC
1 ATTACC
10811 CACTGATTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.08, T:0.37
Consensus pattern (35 bp):
ATTACCAAATTACTTAATTACACCGAATTAAGTTG
Found at i:11028 original size:102 final size:106
Alignment explanation
Indices: 10912--11134 Score: 337
Period size: 102 Copynumber: 2.1 Consensus size: 106
10902 ATTACCTTGC
*
10912 CTTAATTACTGATTTACGGATTACTATTACATTGACTCTGATTAATCTC-TTTTATTTAATTACT
1 CTTAATTACTGATTTACGGATTACTATTACATTGACTCTGATTAATCTCTTTTTACTTAATTACT
10976 G-A-T-TTACTATTACATTGACTCTGATTAATCTCTTTTTA
66 GTACTATTACTATTACATTGACTCTGATTAATCTCTTTTTA
* * *
11014 CTTAATTACTGATTTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACT
1 CTTAATTACTGATTTACGGATTACTATTACATTGACTCTGATTAATCTCTTTTTACTTAATTACT
*
11079 GATTTACTGATTACTATTACATTGTCTCTGATTAATCTCTTTTTA
66 G---TACT-ATTACTATTACATTGACTCTGATTAATCTCTTTTTA
11124 CTTAATTACTG
1 CTTAATTACTG
11135 TTGCCCCTTT
Statistics
Matches: 108, Mismatches: 5, Indels: 8
0.89 0.04 0.07
Matches are distributed among these distances:
102 46 0.43
103 15 0.14
107 1 0.01
108 1 0.01
110 45 0.42
ACGTcount: A:0.26, C:0.17, G:0.08, T:0.50
Consensus pattern (106 bp):
CTTAATTACTGATTTACGGATTACTATTACATTGACTCTGATTAATCTCTTTTTACTTAATTACT
GTACTATTACTATTACATTGACTCTGATTAATCTCTTTTTA
Found at i:11054 original size:55 final size:55
Alignment explanation
Indices: 10971--11134 Score: 301
Period size: 55 Copynumber: 3.0 Consensus size: 55
10961 TTTTATTTAA
*
10971 TTACTGATTTACTATTACATTGACTCTGATTAATCTCTTTTTACTTAATTACTGAT
1 TTACTGA-TTACTATTACATTGTCTCTGATTAATCTCTTTTTACTTAATTACTGAT
*
11027 TTACTGATTACTATTACCTTGTCTCTGATTAATCTCTTTTTACTTAATTACTGAT
1 TTACTGATTACTATTACATTGTCTCTGATTAATCTCTTTTTACTTAATTACTGAT
11082 TTACTGATTACTATTACATTGTCTCTGATTAATCTCTTTTTACTTAATTACTG
1 TTACTGATTACTATTACATTGTCTCTGATTAATCTCTTTTTACTTAATTACTG
11135 TTGCCCCTTT
Statistics
Matches: 105, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
55 98 0.93
56 7 0.07
ACGTcount: A:0.25, C:0.17, G:0.07, T:0.51
Consensus pattern (55 bp):
TTACTGATTACTATTACATTGTCTCTGATTAATCTCTTTTTACTTAATTACTGAT
Found at i:11055 original size:29 final size:29
Alignment explanation
Indices: 11022--11111 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 29
11012 TACTTAATTA
11022 CTGATTTACTGATTACTATTACCTTGTCT
1 CTGATTTACTGATTACTATTACCTTGTCT
* * *
11051 CTGATTAATCT-CTT--T-TTA-CTTAAT-T
1 CTGATTTA-CTGATTACTATTACCTT-GTCT
*
11076 ACTGATTTACTGATTACTATTACATTGTCT
1 -CTGATTTACTGATTACTATTACCTTGTCT
11106 CTGATT
1 CTGATT
11112 AATCTCTTTT
Statistics
Matches: 45, Mismatches: 7, Indels: 18
0.64 0.10 0.26
Matches are distributed among these distances:
25 6 0.13
26 13 0.29
27 1 0.02
28 1 0.02
29 19 0.42
30 5 0.11
ACGTcount: A:0.23, C:0.18, G:0.09, T:0.50
Consensus pattern (29 bp):
CTGATTTACTGATTACTATTACCTTGTCT
Found at i:12023 original size:51 final size:52
Alignment explanation
Indices: 11956--12178 Score: 294
Period size: 51 Copynumber: 4.3 Consensus size: 52
11946 ACTTTTTTTA
* * **
11956 AAAAATTCAATCTTTTGTTC-AAAGGTTACATTTTTTATTTACTAATTACTT
1 AAAAATTCAATCTTTTATTCAAAAGGTTACATTCTTTATAAACTAATTACTT
* ** * *
12007 AAAAATTTAATCTTTTGCTC-AAAGGTGACATT-TTTATTATTTACTAATTACTT
1 AAAAATTCAATCTTTTATTCAAAAGGTTACATTCTTTA-TA--AACTAATTACTT
12060 AAAAATTCAATCTTTTATTCAAAAGGTTACA-TCTTTATAAACTAATTACTT
1 AAAAATTCAATCTTTTATTCAAAAGGTTACATTCTTTATAAACTAATTACTT
*
12111 AAAAATTCAATCTTTTATTCAAAAGGTTA-AATCTTTATAAACTAATTACTT
1 AAAAATTCAATCTTTTATTCAAAAGGTTACATTCTTTATAAACTAATTACTT
12162 AAAAATTCAATCTTTTA
1 AAAAATTCAATCTTTTA
12179 GCATAAAGAT
Statistics
Matches: 157, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
50 5 0.03
51 107 0.68
53 32 0.20
54 13 0.08
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (52 bp):
AAAAATTCAATCTTTTATTCAAAAGGTTACATTCTTTATAAACTAATTACTT
Found at i:12097 original size:104 final size:102
Alignment explanation
Indices: 11956--12178 Score: 297
Period size: 104 Copynumber: 2.2 Consensus size: 102
11946 ACTTTTTTTA
* * ** *
11956 AAAAATTCAATCTTTTGTTCAAAGGTTACATTTTTTATTTACTAATTACTTAAAAATTTAATCTT
1 AAAAATTCAATCTTTTATTCAAAGGTTACATTCTTTATAAACTAATTACTTAAAAATTCAATCTT
* * * *
12021 TTGCTC-AAAGGTGACATTTTTATTATTTACTAATTACTT
66 TTACTCAAAAGGTGAAATCTTTA-TA--AACTAATTACTT
12060 AAAAATTCAATCTTTTATTCAAAAGGTTACA-TCTTTATAAACTAATTACTTAAAAATTCAATCT
1 AAAAATTCAATCTTTTATTC-AAAGGTTACATTCTTTATAAACTAATTACTTAAAAATTCAATCT
* *
12124 TTTATTCAAAAGGTTAAATCTTTATAAACTAATTACTT
65 TTTACTCAAAAGGTGAAATCTTTATAAACTAATTACTT
12162 AAAAATTCAATCTTTTA
1 AAAAATTCAATCTTTTA
12179 GCATAAAGAT
Statistics
Matches: 106, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
102 28 0.26
104 55 0.52
105 23 0.22
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (102 bp):
AAAAATTCAATCTTTTATTCAAAGGTTACATTCTTTATAAACTAATTACTTAAAAATTCAATCTT
TTACTCAAAAGGTGAAATCTTTATAAACTAATTACTT
Found at i:14169 original size:33 final size:34
Alignment explanation
Indices: 14132--14205 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 34
14122 CCGAGTCATT
*
14132 TGGCCGGTTG-TAGCCGGCCATGTCCATGTCGCA
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
* * *
14165 TGGCCGG-TGATGGTCGGACATGTCCATGTCGCG
1 TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
14198 TGGCCGGT
1 TGGCCGGT
14206 CTTGTGGCCG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 2 0.06
33 33 0.94
ACGTcount: A:0.11, C:0.27, G:0.38, T:0.24
Consensus pattern (34 bp):
TGGCCGGTTGATAGCCGGACATGTCCATGTCGCA
Done.