Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015549.1 Corchorus capsularis cultivar CVL-1 contig15570, 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: 89544
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Found at i:1190 original size:13 final size:13
Alignment explanation
Indices: 1172--1197 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1162 AACCGGAAAG
1172 TGCTTAATGAACA
1 TGCTTAATGAACA
1185 TGCTTAATGAACA
1 TGCTTAATGAACA
1198 CAGGCTACTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGCTTAATGAACA
Found at i:4218 original size:17 final size:19
Alignment explanation
Indices: 4182--4218 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
4172 ACCAATTAAA
*
4182 TTAACAATCCAAAAATAAC
1 TTAACAATCCAAAAACAAC
4201 TTAA-AATCC-AAAACAAC
1 TTAACAATCCAAAAACAAC
4218 T
1 T
4219 ACTTATGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 8 0.47
18 5 0.29
19 4 0.24
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (19 bp):
TTAACAATCCAAAAACAAC
Found at i:10490 original size:21 final size:21
Alignment explanation
Indices: 10464--10512 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
10454 GCGCTGGGTG
* *
10464 CCCATGTGGCATGCTTGGCAC
1 CCCATGTGGCATGCCTCGCAC
**
10485 CCCATGTGGTTTGCCTCGCAC
1 CCCATGTGGCATGCCTCGCAC
10506 CCCATGT
1 CCCATGT
10513 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (21 bp):
CCCATGTGGCATGCCTCGCAC
Found at i:12642 original size:13 final size:13
Alignment explanation
Indices: 12597--12643 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
12587 ATCATTTTTA
12597 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
12610 CT-TTTTACTAATT
1 CTCTTTT-CTTACT
12623 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
12637 CTCTTTT
1 CTCTTTT
12644 ATTGATTATC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:12728 original size:21 final size:21
Alignment explanation
Indices: 12704--13014 Score: 109
Period size: 21 Copynumber: 14.9 Consensus size: 21
12694 ACTCTTTGAA
*
12704 TTACTGATCACCTTTTACTCT
1 TTACTGATTACCTTTTACTCT
*
12725 TTACTGATTACTATTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
* * *
12746 TTACTAATTACCACTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
* *
12767 TTATTGATTACTGTTTTACTC-
1 TTACTGATTAC-CTTTTACTCT
**
12788 TTACTGATTACCTTTTACTGA
1 TTACTGATTACCTTTTACTCT
**
12809 TTACT-ATTTTA-CTCTTTACTGA
1 TTACTGA--TTACCT-TTTACTCT
* *
12831 TTAC------CATTTTACTTT
1 TTACTGATTACCTTTTACTCT
*
12846 TTACTGATTACTATTTTTAC-C-
1 TTACTGATTAC--CTTTTACTCT
* * *
12867 TTACTGATTAACTTCTTGCTTT
1 TTACTGATTACCTT-TTACTCT
12889 TTACTGATTA-CTACTTTACTCT
1 TTACTGATTACCT--TTTACTCT
* *
12911 TTACTGATTATCATTTTGCTC-
1 TTACTGATTA-CCTTTTACTCT
* * *
12932 TCATTGATTACCATTTTGCTC-
1 TTACTGATTACC-TTTTACTCT
*
12953 TTACTGATTACTATTTTAC-CTT
1 TTACTGATTAC-CTTTTACTC-T
* * *
12975 TTACTGATTATC-ATTACTTTT
1 TTACTGATTACCTTTTAC-TCT
*
12996 TTATTGATTACCTTTTACT
1 TTACTGATTACCTTTTACT
13015 ATTTCATTCT
Statistics
Matches: 219, Mismatches: 41, Indels: 60
0.68 0.13 0.19
Matches are distributed among these distances:
15 10 0.05
16 1 0.00
19 2 0.01
20 17 0.08
21 113 0.52
22 68 0.31
23 7 0.03
24 1 0.00
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.52
Consensus pattern (21 bp):
TTACTGATTACCTTTTACTCT
Found at i:12826 original size:22 final size:22
Alignment explanation
Indices: 12801--12984 Score: 184
Period size: 22 Copynumber: 8.5 Consensus size: 22
12791 CTGATTACCT
12801 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACTATTTTACTC
* *
12823 TTTACTGATTACCATTTTACTT
1 TTTACTGATTACTATTTTACTC
12845 TTTACTGATTACTATTTTTAC-C
1 TTTACTGATTACTA-TTTTACTC
* * *
12867 -TTACTGATTAACT-TCTTGCTT
1 TTTACTGATT-ACTATTTTACTC
*
12888 TTTACTGATTACTACTTTACTC
1 TTTACTGATTACTATTTTACTC
*
12910 TTTACTGATTA-TCATTTTGCTC
1 TTTACTGATTACT-ATTTTACTC
* * * *
12932 -TCATTGATTACCATTTTGCTC
1 TTTACTGATTACTATTTTACTC
12953 -TTACTGATTACTATTTTAC-C
1 TTTACTGATTACTATTTTACTC
12973 TTTTACTGATTA
1 -TTTACTGATTA
12985 TCATTACTTT
Statistics
Matches: 133, Mismatches: 20, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
20 5 0.04
21 45 0.34
22 77 0.58
23 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.53
Consensus pattern (22 bp):
TTTACTGATTACTATTTTACTC
Found at i:12983 original size:43 final size:44
Alignment explanation
Indices: 12795--12984 Score: 203
Period size: 43 Copynumber: 4.4 Consensus size: 44
12785 CTCTTACTGA
*
12795 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACCATT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACTATT
* *
12839 TTACTTTTTACTGATTACTATTTTTAC-C-TTACTGATTAACT-TC
1 TTACCTTTTACTGATTACTA-TTTTACTCTTTACTGATT-ACTATT
* * *
12882 TTGCTTTTTACTGATTACTACTTTACTCTTTACTGATTA-TCATT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACT-ATT
* * * * * *
12926 TT-GCTCTCATTGATTACCATTTTGCTC-TTACTGATTACTATT
1 TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACTATT
12968 TTACCTTTTACTGATTA
1 TTACCTTTTACTGATTA
12985 TCATTACTTT
Statistics
Matches: 120, Mismatches: 18, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
42 21 0.17
43 59 0.49
44 34 0.28
45 6 0.05
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.53
Consensus pattern (44 bp):
TTACCTTTTACTGATTACTATTTTACTCTTTACTGATTACTATT
Found at i:13014 original size:50 final size:50
Alignment explanation
Indices: 12960--13106 Score: 129
Period size: 51 Copynumber: 2.8 Consensus size: 50
12950 CTCTTACTGA
* * *
12960 TTACTATTTTAC-CTTTTACTGATTATC-ATTACTTTTTTATTGATTACCTT
1 TTACTATTTCACTC-TTTACTGATTATCTATTAC-TTTTTACTGATTACCCT
* *
13010 TTACTATTTCATTCTTTACTGATTATCTTTTTACTTTTTACTGATTACCCT
1 TTACTATTTCACTCTTTACTGATTATC-TATTACTTTTTACTGATTACCCT
*
13061 TTACTCTTTACCATTCTTCCTTTACTGATTACTCT-TTACTTTTTAC
1 TTACTATTT--CA--C-T-CTTTACTGATTA-TCTATTACTTTTTAC
13107 AATTCTTCTT
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
50 23 0.29
51 24 0.30
52 4 0.05
53 2 0.03
56 12 0.15
57 13 0.16
58 2 0.03
ACGTcount: A:0.20, C:0.20, G:0.03, T:0.56
Consensus pattern (50 bp):
TTACTATTTCACTCTTTACTGATTATCTATTACTTTTTACTGATTACCCT
Found at i:13032 original size:29 final size:33
Alignment explanation
Indices: 12968--13040 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 33
12958 GATTACTATT
*
12968 TTACCTTTTACTGATTATCATTACTTTTTTATTGA
1 TTACCTTTTACTGATTATCATTAC--TTTTACTGA
13003 TTACCTTTTACT-ATT-TCATT-C-TTTACTGA
1 TTACCTTTTACTGATTATCATTACTTTTACTGA
*
13032 TTATCTTTT
1 TTACCTTTT
13041 TACTTTTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
29 15 0.42
32 1 0.03
33 5 0.14
34 3 0.08
35 12 0.33
ACGTcount: A:0.21, C:0.16, G:0.04, T:0.59
Consensus pattern (33 bp):
TTACCTTTTACTGATTATCATTACTTTTACTGA
Found at i:13087 original size:35 final size:35
Alignment explanation
Indices: 13045--13205 Score: 225
Period size: 35 Copynumber: 4.6 Consensus size: 35
13035 TCTTTTTACT
* *
13045 TTTTACTGATTACCCTTTACTCTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTACCATTCTTC
* *
13080 CTTTACTGATTACTCTTTACTTTTTACAATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTACCATTCTTC
13115 TTTTACTGATTACTCTTTACTTTTTACCATTCTTC
1 TTTTACTGATTACTCTTTACTTTTTACCATTCTTC
**
13150 TTTTACTGATTACTCTTTACTTTTTGTCATT-TTAC
1 TTTTACTGATTACTCTTTACTTTTTACCATTCTT-C
* *
13185 TCTTTACTAATTACTCCTTAC
1 T-TTTACTGATTACTCTTTAC
13206 AAATTATTCT
Statistics
Matches: 114, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
34 2 0.02
35 95 0.83
36 17 0.15
ACGTcount: A:0.19, C:0.24, G:0.03, T:0.55
Consensus pattern (35 bp):
TTTTACTGATTACTCTTTACTTTTTACCATTCTTC
Found at i:13200 original size:14 final size:14
Alignment explanation
Indices: 13181--13220 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
13171 TTTTGTCATT
13181 TTACTCTTTACTAA
1 TTACTCTTTACTAA
* *
13195 TTACTCCTTACAAA
1 TTACTCTTTACTAA
*
13209 TTATTCTTTACT
1 TTACTCTTTACT
13221 CTTTACGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.28, C:0.23, G:0.00, T:0.50
Consensus pattern (14 bp):
TTACTCTTTACTAA
Found at i:13755 original size:41 final size:41
Alignment explanation
Indices: 13653--13752 Score: 105
Period size: 41 Copynumber: 2.4 Consensus size: 41
13643 TAATCCATTG
* *
13653 ACTCTTATTTACTGATTTACTGATTACTATTTTTTACCTTG
1 ACTCTGATTTACTGATTTACTGATTACTATTTTTTACCTTA
* * *
13694 ACTCTTAATCA-TCGATTTACTGATTACTATCTTTTTA-CTTA
1 ACTCTGATTTACT-GATTTACTGATTACTAT-TTTTTACCTTA
*
13735 ATTGCTGATTTACTGATT
1 ACT-CTGATTTACTGATT
13753 ACTACTTTTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
40 1 0.02
41 31 0.65
42 15 0.31
43 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.08, T:0.51
Consensus pattern (41 bp):
ACTCTGATTTACTGATTTACTGATTACTATTTTTTACCTTA
Found at i:17089 original size:26 final size:24
Alignment explanation
Indices: 17058--17108 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 24
17048 TCAACTATGA
17058 AAATGACCAAAATGCCCCCTAATGCG
1 AAATGACCAAAATG-CCCCT-ATGCG
17084 AAATGACCAAAATGCCCCTATGCG
1 AAATGACCAAAATGCCCCTATGCG
17108 A
1 A
17109 CCCTAATAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
24 6 0.24
25 5 0.20
26 14 0.56
ACGTcount: A:0.39, C:0.29, G:0.16, T:0.16
Consensus pattern (24 bp):
AAATGACCAAAATGCCCCTATGCG
Found at i:24191 original size:21 final size:21
Alignment explanation
Indices: 24165--24213 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
24155 GCGCTGGGTG
* *
24165 CCCATGTGGCATGCTTGGCAC
1 CCCATGTGGCATGCCTCGCAC
**
24186 CCCATGTGGTTTGCCTCGCAC
1 CCCATGTGGCATGCCTCGCAC
24207 CCCATGT
1 CCCATGT
24214 ACTCCAGTGC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.12, C:0.37, G:0.24, T:0.27
Consensus pattern (21 bp):
CCCATGTGGCATGCCTCGCAC
Found at i:26173 original size:12 final size:11
Alignment explanation
Indices: 26156--26222 Score: 73
Period size: 12 Copynumber: 5.8 Consensus size: 11
26146 GTTCAGTTAC
*
26156 AAAAAATAACAA
1 AAAAAAAAAC-A
26168 AAAAAAAAACA
1 AAAAAAAAACA
26179 AAACAAAAAACA
1 AAA-AAAAAACA
26191 AAAACAAAAAC-
1 AAAA-AAAAACA
*
26202 AAAACAAAACA
1 AAAAAAAAACA
26213 AAACAAAAAA
1 AAA-AAAAAA
26223 ACATATGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 5 0.10
11 12 0.25
12 31 0.65
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.01
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:26181 original size:6 final size:6
Alignment explanation
Indices: 26163--26221 Score: 72
Period size: 6 Copynumber: 10.3 Consensus size: 6
26153 TACAAAAAAT
*
26163 AACAAA AAAAAA AAC-AA AACAAAA AACAAA AACAAA AAC-AA AAC-AA
1 AACAAA AACAAA AACAAA AAC-AAA AACAAA AACAAA AACAAA AACAAA
26209 AAC-AA AACAAA AA
1 AACAAA AACAAA AA
26222 AACATATGTT
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
5 20 0.42
6 23 0.48
7 5 0.10
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (6 bp):
AACAAA
Found at i:26199 original size:24 final size:24
Alignment explanation
Indices: 26158--26221 Score: 89
Period size: 24 Copynumber: 2.8 Consensus size: 24
26148 TCAGTTACAA
*
26158 AAAATAACAAAAAAAAAAACAAAAC
1 AAAA-AACAAAAACAAAAACAAAAC
26183 AAAAAACAAAAACAAAAACAAAAC
1 AAAAAACAAAAACAAAAACAAAAC
26207 --AAAAC-AAAACAAAAA
1 AAAAAACAAAAACAAAAA
26222 AACATATGTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
21 10 0.26
22 5 0.13
24 19 0.50
25 4 0.11
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.02
Consensus pattern (24 bp):
AAAAAACAAAAACAAAAACAAAAC
Found at i:26200 original size:29 final size:29
Alignment explanation
Indices: 26157--26225 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
26147 TTCAGTTACA
26157 AAAAATAACAAAAAAAAAAACAAAACAAAA-
1 AAAAA-AAC-AAAAAAAAAACAAAACAAAAC
*
26187 AACAAAAACAAAAACAAAACAAAACAAAAC
1 AA-AAAAACAAAAAAAAAACAAAACAAAAC
26217 AAAAAAACA
1 AAAAAAACA
26226 TATGTTTACA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 26 0.72
30 7 0.19
31 3 0.08
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.01
Consensus pattern (29 bp):
AAAAAAACAAAAAAAAAACAAAACAAAAC
Found at i:26281 original size:39 final size:40
Alignment explanation
Indices: 26233--26309 Score: 138
Period size: 39 Copynumber: 1.9 Consensus size: 40
26223 ACATATGTTT
26233 ACATATACAACAACAATGGCCTATGTCG-CCATATATACA
1 ACATATACAACAACAATGGCCTATGTCGTCCATATATACA
*
26272 ACATTTACAACAACAATGGCCTATGTCGTCCATATATA
1 ACATATACAACAACAATGGCCTATGTCGTCCATATATA
26310 TTAAATGGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (40 bp):
ACATATACAACAACAATGGCCTATGTCGTCCATATATACA
Found at i:26354 original size:35 final size:35
Alignment explanation
Indices: 26315--26393 Score: 131
Period size: 35 Copynumber: 2.3 Consensus size: 35
26305 ATATATTAAA
* *
26315 TGGCCTATTTCGCCACATATCATGTACTATTACCT
1 TGGCCTATGTCGCCACATATCATGAACTATTACCT
*
26350 TGGCCTATGTCGTCACATATCATGAACTATTACCT
1 TGGCCTATGTCGCCACATATCATGAACTATTACCT
26385 TGGCCTATG
1 TGGCCTATG
26394 ACGTCATTCC
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 41 1.00
ACGTcount: A:0.23, C:0.27, G:0.15, T:0.35
Consensus pattern (35 bp):
TGGCCTATGTCGCCACATATCATGAACTATTACCT
Found at i:26476 original size:27 final size:29
Alignment explanation
Indices: 26415--26481 Score: 93
Period size: 27 Copynumber: 2.4 Consensus size: 29
26405 TGTATACAAA
26415 AATGGCCTATGATGCCACACATATATAAC
1 AATGGCCTATGATGCCACACATATATAAC
* *
26444 ATTGGCCTATGATG-C-CACATATATAAT
1 AATGGCCTATGATGCCACACATATATAAC
*
26471 AATGGCTTATG
1 AATGGCCTATG
26482 TCACCAAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 20 0.59
28 1 0.03
29 13 0.38
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.30
Consensus pattern (29 bp):
AATGGCCTATGATGCCACACATATATAAC
Found at i:26675 original size:88 final size:87
Alignment explanation
Indices: 26557--26783 Score: 260
Period size: 88 Copynumber: 2.5 Consensus size: 87
26547 AAAAATATTT
* *
26557 TCATTGCCGCTAATCAAAGCGAGCTAAATATCTAAATGTTCCCTCCAAGTAGCAGAA-TCTTTTC
1 TCATTGCAGCTAA-CAAAGCGAGCTCAATATCTAAATG-TCCCTCCAAGTAGCAGAATTCTTTTC
26621 TCCTTGTAGAGGTCGAAAGCACTC
64 TCCTTGTAGAGGTCGAAAGCACTC
* * * *
26645 TCATTGCTGCTAACAAACGCAAGCTCAATATCTAAATGCTCCCTCCAAGTAGTAGAATTTTTTTT
1 TCATTGCAGCTAACAAA-GCGAGCTCAATATCTAAATG-TCCCTCCAAGTAGCAGAA---TTCTT
* *
26710 TTCTCCTTGTAGAGGTTGAAAGCACTT
61 TTCTCCTTGTAGAGGTCGAAAGCACTC
* **
26737 TCCTTGCAGCTGTCAAAGCGAGCTC-ATCATCTAAATGTCTCCTCCAA
1 TCATTGCAGCTAACAAAGCGAGCTCAAT-ATCTAAATGTC-CCTCCAA
26784 AATGAACTTC
Statistics
Matches: 119, Mismatches: 13, Indels: 11
0.83 0.09 0.08
Matches are distributed among these distances:
87 4 0.03
88 47 0.39
90 4 0.03
91 23 0.19
92 41 0.34
ACGTcount: A:0.28, C:0.25, G:0.16, T:0.31
Consensus pattern (87 bp):
TCATTGCAGCTAACAAAGCGAGCTCAATATCTAAATGTCCCTCCAAGTAGCAGAATTCTTTTCTC
CTTGTAGAGGTCGAAAGCACTC
Found at i:28214 original size:31 final size:31
Alignment explanation
Indices: 28151--28226 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
28141 AAAAGCCTGC
* *
28151 TACAGGTAATACCC-ACGTGGTTATACATGT
1 TACAGGTAATACCCTACGTGGTTACACACGT
*
28181 TACAGGTAATACCCTACTTGGTTACACACGT
1 TACAGGTAATACCCTACGTGGTTACACACGT
* *
28212 TACAAGTAACACCCT
1 TACAGGTAATACCCT
28227 GTAACTGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 14 0.35
31 26 0.65
ACGTcount: A:0.32, C:0.25, G:0.16, T:0.28
Consensus pattern (31 bp):
TACAGGTAATACCCTACGTGGTTACACACGT
Found at i:28253 original size:16 final size:16
Alignment explanation
Indices: 28232--28287 Score: 69
Period size: 16 Copynumber: 3.5 Consensus size: 16
28222 ACCCTGTAAC
28232 TGGTAATACATGTTGA
1 TGGTAATACATGTTGA
*
28248 TGGTAATACTTG-TGA
1 TGGTAATACATGTTGA
* *
28263 CTAGTAATACATGTTGT
1 -TGGTAATACATGTTGA
28280 TGGTAATA
1 TGGTAATA
28288 TCCTGTGAAC
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
15 3 0.09
16 28 0.85
17 2 0.06
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.39
Consensus pattern (16 bp):
TGGTAATACATGTTGA
Found at i:28727 original size:11 final size:11
Alignment explanation
Indices: 28711--28753 Score: 68
Period size: 11 Copynumber: 3.9 Consensus size: 11
28701 TATACTATAT
28711 CTAATTAATAG
1 CTAATTAATAG
*
28722 CTAATTAATAT
1 CTAATTAATAG
28733 CTAATTAATAG
1 CTAATTAATAG
*
28744 TTAATTAATA
1 CTAATTAATA
28754 ATGAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.47, C:0.07, G:0.05, T:0.42
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:28735 original size:22 final size:22
Alignment explanation
Indices: 28707--28753 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
28697 CCATTATACT
28707 ATATCTAATTAATAGCTAATTA
1 ATATCTAATTAATAGCTAATTA
*
28729 ATATCTAATTAATAGTTAATTA
1 ATATCTAATTAATAGCTAATTA
28751 ATA
1 ATA
28754 ATGAATAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (22 bp):
ATATCTAATTAATAGCTAATTA
Found at i:30052 original size:41 final size:41
Alignment explanation
Indices: 29975--30071 Score: 124
Period size: 41 Copynumber: 2.3 Consensus size: 41
29965 TATATATTTA
*
29975 AGAGATAACTATGGTCATTATATAATTAACCATATTATCCAT
1 AGAGATAATTATGG-CATTATATAATTAACCATATTATCCAT
* **
30017 AGAGATAATTATGG-ATTATATTTATTAACCATATTATCTTT
1 AGAGATAATTATGGCATTATA-TAATTAACCATATTATCCAT
*
30058 AAAGATAATTATGG
1 AGAGATAATTATGG
30072 TAATTATCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
40 6 0.12
41 30 0.61
42 13 0.27
ACGTcount: A:0.40, C:0.09, G:0.11, T:0.39
Consensus pattern (41 bp):
AGAGATAATTATGGCATTATATAATTAACCATATTATCCAT
Found at i:31445 original size:2 final size:2
Alignment explanation
Indices: 31432--31471 Score: 71
Period size: 2 Copynumber: 19.5 Consensus size: 2
31422 TGCTTCTTTT
31432 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31472 TCTCATCATG
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 35 0.95
3 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:34312 original size:25 final size:25
Alignment explanation
Indices: 34283--34340 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
34273 TACCTTCTCC
34283 TTTTACTAATTACCT-TTCTTACTCA
1 TTTTACTAATTA-CTATTCTTACTCA
* * *
34308 TTTTACTTATTACTATTTTTACTCT
1 TTTTACTAATTACTATTCTTACTCA
34333 TTTTACTA
1 TTTTACTA
34341 TTGAATGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
24 2 0.07
25 26 0.93
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (25 bp):
TTTTACTAATTACTATTCTTACTCA
Found at i:34389 original size:28 final size:28
Alignment explanation
Indices: 34358--34411 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
34348 CCATTTTTAC
* * *
34358 CTTTTTTTACTTATTATCCTTTTCTTCT
1 CTTTTTTTACTGATTACCCTCTTCTTCT
34386 CTTTTTTTACTGATTACCCTCTTCTT
1 CTTTTTTTACTGATTACCCTCTTCTT
34412 ACTTTTTCAC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.11, C:0.24, G:0.02, T:0.63
Consensus pattern (28 bp):
CTTTTTTTACTGATTACCCTCTTCTTCT
Found at i:34418 original size:28 final size:28
Alignment explanation
Indices: 34354--34418 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 28
34344 AATGCCATTT
* * * *
34354 TTACCTTTTTTTACTTATTATCCTTTTC
1 TTACTTTTTTTTACTGATTACCCTCTTC
34382 TT-CTCTTTTTTTACTGATTACCCTCTTC
1 TTACT-TTTTTTTACTGATTACCCTCTTC
34410 TTACTTTTT
1 TTACTTTTT
34419 CACTGAATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 1 0.03
28 28 0.90
29 2 0.06
ACGTcount: A:0.12, C:0.23, G:0.02, T:0.63
Consensus pattern (28 bp):
TTACTTTTTTTTACTGATTACCCTCTTC
Found at i:34478 original size:23 final size:23
Alignment explanation
Indices: 34452--34533 Score: 98
Period size: 23 Copynumber: 3.7 Consensus size: 23
34442 CTTTTTTTTC
* * *
34452 TTTTCCTTTCTTACTGATCACCA
1 TTTTACTTTCTTACTGATTACTA
* *
34475 TTTTACTTTTTTACTTATTACTA
1 TTTTACTTTCTTACTGATTACTA
34498 TTTTAC--TCTTACTGATTACTA
1 TTTTACTTTCTTACTGATTACTA
34519 TTTTACTTT-TTACTG
1 TTTTACTTTCTTACTG
34534 TCGATTACTA
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
21 19 0.38
22 6 0.12
23 25 0.50
ACGTcount: A:0.20, C:0.20, G:0.04, T:0.57
Consensus pattern (23 bp):
TTTTACTTTCTTACTGATTACTA
Found at i:34508 original size:44 final size:42
Alignment explanation
Indices: 34460--34811 Score: 200
Period size: 40 Copynumber: 8.5 Consensus size: 42
34450 TCTTTTCCTT
34460 TCTTACTGATCACCATTTTACTTTTTTACTTATTACTATTTTAC
1 TCTTACTGATCACC-TTTTAC-TTTTTACTTATTACTATTTTAC
* *
34504 TCTTACTGATTACTATTTTACTTTTTACTGTCGATTACTA--TTAC
1 TCTTACTGATCAC-CTTTTACTTTTTACT-T--ATTACTATTTTAC
* * * *
34548 TCTTACTGATCATCCTCTTAC-TCTTACTGATTA-TCTTTTAC
1 TCTTACTGATCA-CCTTTTACTTTTTACTTATTACTATTTTAC
* * *
34589 TCTTACTGATCATCTTTTAC-TCTTACTGT-TTA-TCTTTTAC
1 TCTTACTGATCACCTTTTACTTTTTACT-TATTACTATTTTAC
* * * *
34629 T-TTTCTTGATCACCTTTTAC-TTTTCCTGATTA-TCTTTTAC
1 TCTTAC-TGATCACCTTTTACTTTTTACTTATTACTATTTTAC
* * * * * *
34669 T-TCTACTAATCATCTTTTGC-TTTTACTGATT-GTCTTTTAC
1 TCT-TACTGATCACCTTTTACTTTTTACTTATTACTATTTTAC
* * * * *
34709 TTTTTACTGATCATCTTTTAC-TTTTCCTGATTA-TCTTTTA-
1 -TCTTACTGATCACCTTTTACTTTTTACTTATTACTATTTTAC
* * *
34749 TCCTTACTAATCACCTTTTAC-TTTTACTGATTA-TCTTTTAC
1 T-CTTACTGATCACCTTTTACTTTTTACTTATTACTATTTTAC
* *
34790 TTTTTACTGATCATCTTTTACT
1 -TCTTACTGATCACCTTTTACT
34812 CTCGTTGATT
Statistics
Matches: 258, Mismatches: 31, Indels: 40
0.78 0.09 0.12
Matches are distributed among these distances:
39 5 0.02
40 123 0.48
41 67 0.26
42 2 0.01
43 14 0.05
44 39 0.15
45 1 0.00
46 7 0.03
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (42 bp):
TCTTACTGATCACCTTTTACTTTTTACTTATTACTATTTTAC
Found at i:34590 original size:20 final size:20
Alignment explanation
Indices: 34498--34886 Score: 309
Period size: 20 Copynumber: 18.9 Consensus size: 20
34488 CTTATTACTA
*
34498 TTTTACTCTTACTGATTACTA
1 TTTTACTCTTACTGATTA-TC
*
34519 TTTTACTTTTTACTGTCGATTA-C
1 TTTTAC-TCTTAC--T-GATTATC
* *
34542 TATTACTCTTACTGATCATCC
1 TTTTACTCTTACTGATTAT-C
*
34563 TCTTACTCTTACTGATTATC
1 TTTTACTCTTACTGATTATC
*
34583 TTTTACTCTTACTGATCATC
1 TTTTACTCTTACTGATTATC
*
34603 TTTTACTCTTACTGTTTATC
1 TTTTACTCTTACTGATTATC
* * *
34623 TTTTACT-TTTCTTGATCACC
1 TTTTACTCTTAC-TGATTATC
* *
34643 TTTTACTTTTCCTGATTATC
1 TTTTACTCTTACTGATTATC
* *
34663 TTTTACT-TCTACTAATCATC
1 TTTTACTCT-TACTGATTATC
* * *
34683 TTTTGCTTTTACTGATTGTC
1 TTTTACTCTTACTGATTATC
* *
34703 TTTTACTTTTTACTGATCATC
1 TTTTAC-TCTTACTGATTATC
* *
34724 TTTTACTTTTCCTGATTATC
1 TTTTACTCTTACTGATTATC
* * *
34744 TTTTA-TCCTTACTAATCACC
1 TTTTACT-CTTACTGATTATC
*
34764 TTTTACTTTTACTGATTATC
1 TTTTACTCTTACTGATTATC
* *
34784 TTTTACTTTTTACTGATCATC
1 TTTTAC-TCTTACTGATTATC
***
34805 TTTTACTCTCGTTGATTATC
1 TTTTACTCTTACTGATTATC
* * *
34825 TTTTACTTTTTATTGATCATC
1 TTTTAC-TCTTACTGATTATC
*
34846 TTTTACTCTTGCTGATTATC
1 TTTTACTCTTACTGATTATC
*
34866 TTTTACTTCTTTACTGTTTAT
1 TTTTAC-TC-TTACTGATTAT
34887 TAATTACCAA
Statistics
Matches: 296, Mismatches: 55, Indels: 33
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.03
20 173 0.58
21 84 0.28
22 19 0.06
23 5 0.02
24 1 0.00
25 5 0.02
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTACTCTTACTGATTATC
Found at i:34609 original size:40 final size:40
Alignment explanation
Indices: 34460--34881 Score: 393
Period size: 41 Copynumber: 10.2 Consensus size: 40
34450 TCTTTTCCTT
* * *
34460 TCTTACTGATCACCATTTTACTTTTTTACTTATTACTATTTTAC
1 TCTTACTGATCATC-TTTTAC--TTTTACTGATTA-TCTTTTAC
* * *
34504 TCTTACTGATTACTATTTTACTTTTTACTGTCGATTA-CTATTAC
1 TCTTACTGATCA-TCTTTTAC-TTTTAC--T-GATTATCTTTTAC
* *
34548 TCTTACTGATCATCCTCTTACTCTTACTGATTATCTTTTAC
1 TCTTACTGATCAT-CTTTTACTTTTACTGATTATCTTTTAC
* *
34589 TCTTACTGATCATCTTTTACTCTTACTGTTTATCTTTTAC
1 TCTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
* * *
34629 T-TTTCTTGATCACCTTTTACTTTTCCTGATTATCTTTTAC
1 TCTTAC-TGATCATCTTTTACTTTTACTGATTATCTTTTAC
* * *
34669 T-TCTACTAATCATCTTTTGCTTTTACTGATTGTCTTTTAC
1 TCT-TACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
* *
34709 TTTTTACTGATCATCTTTTACTTTTCCTGATTATCTTTTA-
1 -TCTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
* *
34749 TCCTTACTAATCACCTTTTACTTTTACTGATTATCTTTTAC
1 T-CTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
* * ***
34790 TTTTTACTGATCATCTTTTACTCTCGTTGATTATCTTTTAC
1 -TCTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
* * * *
34831 TTTTTATTGATCATCTTTTACTCTTGCTGATTATCTTTTAC
1 -TCTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
34872 TTCTTTACTG
1 -TC-TTACTG
34882 TTTATTAATT
Statistics
Matches: 320, Mismatches: 44, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
39 4 0.01
40 126 0.39
41 127 0.40
42 7 0.02
43 13 0.04
44 38 0.12
45 1 0.00
46 4 0.01
ACGTcount: A:0.19, C:0.21, G:0.05, T:0.55
Consensus pattern (40 bp):
TCTTACTGATCATCTTTTACTTTTACTGATTATCTTTTAC
Found at i:40062 original size:178 final size:178
Alignment explanation
Indices: 39835--40193 Score: 675
Period size: 178 Copynumber: 2.0 Consensus size: 178
39825 TTGTCCATCT
39835 CATCGTAATACTTGCAAGTTAATGAAGCAAACAGAAAAAGATGGTATAGTTTAGTTGCTATAACA
1 CATCGTAATACTTGCAAGTTAATGAAGCAAACAGAAAAAGATGGTATAGTTTAGTTGCTATAACA
* *
39900 AAAGCAAGCATTGC-CTTCTTTTCTTGGATCACTACAAGCACTCCTTTTCCCTTCAAACCACCTA
66 AAAGCAAGCATTGCTC-CCTTTTCTTGGATCACTACAAGCACTCATTTTCCCTTCAAACCACCTA
*
39964 ATTTATAATTAACTATAAACTGAGAAATAGTTCCACCAGCATAAACCAC
130 ATTTATAATTAACTATAAACTGAGAAATAGTCCCACCAGCATAAACCAC
40013 CATCGTAATACTTGCAAGTTAATGAAGCAAACAGAAAAAGATGGTATAGTTTAGTTGCTATAACA
1 CATCGTAATACTTGCAAGTTAATGAAGCAAACAGAAAAAGATGGTATAGTTTAGTTGCTATAACA
40078 AAAGCAAGCATTGCTCCCTTTTCTTGGATCACTACAAGCACTCATTTTCCCTTCAAACCACCTAA
66 AAAGCAAGCATTGCTCCCTTTTCTTGGATCACTACAAGCACTCATTTTCCCTTCAAACCACCTAA
40143 TTTATAATTAACTATAAACTGAGAAATAGTCCCACCAGCATAAACCAC
131 TTTATAATTAACTATAAACTGAGAAATAGTCCCACCAGCATAAACCAC
40191 CAT
1 CAT
40194 GTCACGGTTG
Statistics
Matches: 177, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
178 176 0.99
179 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.28
Consensus pattern (178 bp):
CATCGTAATACTTGCAAGTTAATGAAGCAAACAGAAAAAGATGGTATAGTTTAGTTGCTATAACA
AAAGCAAGCATTGCTCCCTTTTCTTGGATCACTACAAGCACTCATTTTCCCTTCAAACCACCTAA
TTTATAATTAACTATAAACTGAGAAATAGTCCCACCAGCATAAACCAC
Found at i:41556 original size:14 final size:14
Alignment explanation
Indices: 41526--41554 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
41516 ACTTCTATTT
41526 AATGCATGGATGCA
1 AATGCATGGATGCA
41540 AATG-ATGGATGCA
1 AATGCATGGATGCA
41553 AA
1 AA
41555 ATCCAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.21
Consensus pattern (14 bp):
AATGCATGGATGCA
Found at i:45278 original size:39 final size:39
Alignment explanation
Indices: 45224--45301 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
45214 GGGTCCTACT
45224 TATGGCATGCCTAAGAGGGTGATTTAATCAATGAATTAA
1 TATGGCATGCCTAAGAGGGTGATTTAATCAATGAATTAA
45263 TATGGCATGCCTAAGAGGGTGATTTAATCAATGAATTAA
1 TATGGCATGCCTAAGAGGGTGATTTAATCAATGAATTAA
45302 ATTGAGTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (39 bp):
TATGGCATGCCTAAGAGGGTGATTTAATCAATGAATTAA
Found at i:51762 original size:18 final size:18
Alignment explanation
Indices: 51741--51776 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
51731 TGTTATTACC
51741 ATTCTTTTTTCACTTCCA
1 ATTCTTTTTTCACTTCCA
51759 ATTCTTTTTTCACTTCCA
1 ATTCTTTTTTCACTTCCA
51777 TTTGATTCTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTCTTTTTTCACTTCCA
Found at i:63258 original size:2 final size:2
Alignment explanation
Indices: 63247--63294 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
63237 TACATGAGAA
* * *
63247 AT AT -T AT AT AT AT AT AT AT AT AT AT AG AT AT AG AT AT AT CT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63288 AT AT AT A
1 AT AT AT A
63295 CAATGTGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:71648 original size:100 final size:100
Alignment explanation
Indices: 71475--71680 Score: 389
Period size: 100 Copynumber: 2.1 Consensus size: 100
71465 GTAAATTTCA
71475 TTAAAATTGGATTATTTCCAGAGGAAAATGTTGATAAACCAAACCATTGAAAGTACTCTCCATGG
1 TTAAAATTGGATTATTTCCAGAGGAAAATGTTGATAAACCAAACCATTGAAAGTACTCTCCATGG
71540 AATTTAATTGTTACTTTCCCTAGAGTTACTTTCCC
66 AATTTAATTGTTACTTTCCCTAGAGTTACTTTCCC
71575 TTAAAATTGGATTATTTTCCA-AGGAAAATGTTGATAAACCAAACCATTGAAAGTACTCTCCATG
1 TTAAAATTGGATTA-TTTCCAGAGGAAAATGTTGATAAACCAAACCATTGAAAGTACTCTCCATG
71639 GAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCC
65 GAATTTAATTGTTACTTTCCCTAGAGTTACTTTCCC
71675 -TAAAAT
1 TTAAAAT
71681 CACTCTCCAA
Statistics
Matches: 105, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
99 6 0.06
100 93 0.89
101 6 0.06
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.35
Consensus pattern (100 bp):
TTAAAATTGGATTATTTCCAGAGGAAAATGTTGATAAACCAAACCATTGAAAGTACTCTCCATGG
AATTTAATTGTTACTTTCCCTAGAGTTACTTTCCC
Found at i:72960 original size:16 final size:16
Alignment explanation
Indices: 72939--72998 Score: 111
Period size: 16 Copynumber: 3.8 Consensus size: 16
72929 CCAACCCGGG
72939 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
*
72955 CCCGAACCCGAAAAAA
1 CCCGAACCCGAAAATA
72971 CCCGAACCCGAAAATA
1 CCCGAACCCGAAAATA
72987 CCCGAACCCGAA
1 CCCGAACCCGAA
72999 CCCGCCTGAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 42 1.00
ACGTcount: A:0.43, C:0.40, G:0.13, T:0.03
Consensus pattern (16 bp):
CCCGAACCCGAAAATA
Found at i:73010 original size:32 final size:32
Alignment explanation
Indices: 72921--73012 Score: 114
Period size: 32 Copynumber: 2.8 Consensus size: 32
72911 TCGAAAGTGA
72921 ACCCGAACCC-AACCCGGGCCCGAACCCGAAAAT
1 ACCCGAACCCGAACCC--GCCCGAACCCGAAAAT
****
72954 ACCCGAACCCGAAAAAACCCGAACCCGAAAAT
1 ACCCGAACCCGAACCCGCCCGAACCCGAAAAT
*
72986 ACCCGAACCCGAACCCGCCTGAACCCG
1 ACCCGAACCCGAACCCGCCCGAACCCG
73013 CCCAATTGCC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
32 37 0.76
33 10 0.20
34 2 0.04
ACGTcount: A:0.36, C:0.45, G:0.16, T:0.03
Consensus pattern (32 bp):
ACCCGAACCCGAACCCGCCCGAACCCGAAAAT
Found at i:73933 original size:2 final size:2
Alignment explanation
Indices: 73926--73960 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
73916 TGATTGATTA
73926 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
73961 AAAGCGAGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:74702 original size:11 final size:11
Alignment explanation
Indices: 74659--74696 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
74649 TTCCTATATA
*
74659 AAATAAATTAT
1 AAATTAATTAT
74670 CAAA-TAATTAT
1 -AAATTAATTAT
74681 AAATTAATTAT
1 AAATTAATTAT
74692 AAATT
1 AAATT
74697 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:76949 original size:17 final size:17
Alignment explanation
Indices: 76927--76968 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
76917 GAATTTCGAA
76927 TTTTGAATTGCCGAAAC
1 TTTTGAATTGCCGAAAC
*
76944 TTTTGAATTTCCGAAAC
1 TTTTGAATTGCCGAAAC
76961 TTTTGAAT
1 TTTTGAAT
76969 CCGGATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (17 bp):
TTTTGAATTGCCGAAAC
Found at i:82066 original size:68 final size:67
Alignment explanation
Indices: 81797--82076 Score: 488
Period size: 67 Copynumber: 4.1 Consensus size: 67
81787 GTCTTTCGTT
*
81797 TTTACGATACAAGAATCGTTTAATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTTG
1 TTTACGATACAAGGATCGTTTAATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTTG
81862 AG
66 AG
* *
81864 TTTACGATACAAGGATCGTTTAGTTTTTTTTGATAAAACGGTCTCAGGGGAGACGTTCGTCTTAT
1 TTTACGATACAAGGATCGTTTA---ATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTAT
81929 TTGAG
63 TTGAG
*
81934 TTTACGATATAAGGATCGTTTAATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTTG
1 TTTACGATACAAGGATCGTTTAATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTTG
81999 AG
66 AG
82001 TTTACGATACAAGGATCGTTTAATTTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTT
1 TTTACGATACAAGGATCGTTTAA-TTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTT
82066 GAG
65 GAG
82069 TTTACGAT
1 TTTACGAT
82077 TTTAATCTCT
Statistics
Matches: 202, Mismatches: 7, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
67 86 0.43
68 52 0.26
70 64 0.32
ACGTcount: A:0.28, C:0.13, G:0.22, T:0.38
Consensus pattern (67 bp):
TTTACGATACAAGGATCGTTTAATTTTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTATTTG
AG
Found at i:82067 original size:36 final size:36
Alignment explanation
Indices: 81959--82067 Score: 95
Period size: 36 Copynumber: 3.1 Consensus size: 36
81949 TCGTTTAATT
81959 TTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTA
1 TTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTA
** * * * * *
81995 TTTGAGT-TTACGAT-ACAA-GGA-TCGTT--TAATTT
1 TTTGA-TAAAACGGTCTCAAGGGAGACGTTCGT-CTTA
82027 TTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTA
1 TTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTA
82063 TTTGA
1 TTTGA
82068 GTTTACGATT
Statistics
Matches: 51, Mismatches: 14, Indels: 16
0.63 0.17 0.20
Matches are distributed among these distances:
31 2 0.04
32 11 0.22
33 7 0.14
34 6 0.12
35 7 0.14
36 16 0.31
37 2 0.04
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.36
Consensus pattern (36 bp):
TTTGATAAAACGGTCTCAAGGGAGACGTTCGTCTTA
Done.