Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011772.1 Corchorus capsularis cultivar CVL-1 contig11793, 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: 56371
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:3772 original size:29 final size:30
Alignment explanation
Indices: 3705--3772 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 30
3695 CCGTTACACA
* *
3705 TTTATGTTTTATGCAATTTACTCCTTAAAAT
1 TTTAT-TTTTATACAATTTACTCCCTAAAAT
* *
3736 TTTA-TTTTATACAATTTAGTCCCT-CAAT
1 TTTATTTTTATACAATTTACTCCCTAAAAT
3764 TTTATTTTT
1 TTTATTTTT
3773 TTTAACTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
28 7 0.22
29 21 0.66
31 4 0.12
ACGTcount: A:0.26, C:0.13, G:0.04, T:0.56
Consensus pattern (30 bp):
TTTATTTTTATACAATTTACTCCCTAAAAT
Found at i:3799 original size:15 final size:16
Alignment explanation
Indices: 3779--3811 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3769 TTTTTTTAAC
*
3779 TTTTAACT-ATTATTA
1 TTTTAACTCATTAATA
3794 TTTTAACTCATTAATA
1 TTTTAACTCATTAATA
3810 TT
1 TT
3812 CTATGAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAACTCATTAATA
Found at i:5242 original size:42 final size:42
Alignment explanation
Indices: 5171--5252 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
5161 TAGATATTAA
** *
5171 TTTTGAATATTAAATACATAATTGTTTATCATGTGAGGTAGG
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
*
5213 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTA
5253 TGTGTCAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.41
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGAGGTAGG
Found at i:8257 original size:43 final size:43
Alignment explanation
Indices: 8196--8282 Score: 174
Period size: 43 Copynumber: 2.0 Consensus size: 43
8186 CCCAATATTT
8196 GTGGAGCTATTTTTCCTGTATGGCGTTTTCCTAATCAGAATAA
1 GTGGAGCTATTTTTCCTGTATGGCGTTTTCCTAATCAGAATAA
8239 GTGGAGCTATTTTTCCTGTATGGCGTTTTCCTAATCAGAATAA
1 GTGGAGCTATTTTTCCTGTATGGCGTTTTCCTAATCAGAATAA
8282 G
1 G
8283 AACTAATGTT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 44 1.00
ACGTcount: A:0.23, C:0.16, G:0.22, T:0.39
Consensus pattern (43 bp):
GTGGAGCTATTTTTCCTGTATGGCGTTTTCCTAATCAGAATAA
Found at i:8393 original size:41 final size:41
Alignment explanation
Indices: 8330--8411 Score: 146
Period size: 41 Copynumber: 2.0 Consensus size: 41
8320 TTTGTGTGCC
8330 GTATGGTTTGCTCCCAAAATTGGCTTGCTCCCAAAATTAAT
1 GTATGGTTTGCTCCCAAAATTGGCTTGCTCCCAAAATTAAT
* *
8371 GTATGGTTTGCTCCTAAGATTGGCTTGCTCCCAAAATTAAT
1 GTATGGTTTGCTCCCAAAATTGGCTTGCTCCCAAAATTAAT
8412 AAGAATATCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.35
Consensus pattern (41 bp):
GTATGGTTTGCTCCCAAAATTGGCTTGCTCCCAAAATTAAT
Found at i:11300 original size:13 final size:13
Alignment explanation
Indices: 11282--11307 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11272 ATTTTGGGTC
11282 AATTTTTCATATA
1 AATTTTTCATATA
11295 AATTTTTCATATA
1 AATTTTTCATATA
11308 GCAAAACTCT
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:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
AATTTTTCATATA
Found at i:11877 original size:26 final size:26
Alignment explanation
Indices: 11834--11884 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
11824 GAAAGTGATA
* *
11834 TAATTTTCCTAAGTTGATTTATTATC
1 TAATTTTCCAAAGCTGATTTATTATC
11860 TAATTTTCCAAAGCTGATTTATTAT
1 TAATTTTCCAAAGCTGATTTATTAT
11885 ATACAAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (26 bp):
TAATTTTCCAAAGCTGATTTATTATC
Found at i:14902 original size:83 final size:83
Alignment explanation
Indices: 14748--14902 Score: 197
Period size: 83 Copynumber: 1.9 Consensus size: 83
14738 TCGTCACGTT
* * * * * *
14748 AAATTGGCCCATTTTATTTGGATTTTGGACTTTTTTTTTCTTTTTGTTGAGATTTTGGATTTTAA
1 AAATTAGCCCATTTTATTTGGAATTTGGACTTTTTTTTTCTTTTGGTTGAGATATTGAACTTTAA
14813 TACAAGCATATACGTCAC
66 TACAAGCATATACGTCAC
*
14831 AAATTAGCCCATTTTATTTGGAATTTGG-TTCTTTTTTTTCTTTTGGTTGA-AGTATTGAACTTT
1 AAATTAGCCCATTTTATTTGGAATTTGGACT-TTTTTTTTCTTTTGGTTGAGA-TATTGAACTTT
* *
14894 CATTCAAGC
64 AATACAAGC
14903 TTATGCTTTG
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
82 2 0.03
83 59 0.97
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.50
Consensus pattern (83 bp):
AAATTAGCCCATTTTATTTGGAATTTGGACTTTTTTTTTCTTTTGGTTGAGATATTGAACTTTAA
TACAAGCATATACGTCAC
Found at i:20159 original size:22 final size:22
Alignment explanation
Indices: 20125--20518 Score: 149
Period size: 22 Copynumber: 17.6 Consensus size: 22
20115 CTAATCCCTG
* *
20125 TGAAACTTTGATACCCACACTA
1 TGAAATTTTGATAACCACACTA
*
20147 TGAAATTTCGATAACCATC-CTA
1 TGAAATTTTGATAACCA-CACTA
* *
20169 TGAAATTTTGATTACCACA-AA
1 TGAAATTTTGATAACCACACTA
20190 TGAAATTTTGATAACCACACTA
1 TGAAATTTTGATAACCACACTA
* ** *
20212 TAAAATAGTGATAACCTCTAC-A
1 TGAAATTTTGATAACCAC-ACTA
* **
20234 TGAAATTAATTTTGCTGAA-TTCACTA
1 TG--A--AATTTTGAT-AACCACACTA
* *
20260 TAAAATTTTGATAACCACAATAA
1 TGAAATTTTGATAACCACACT-A
** ****
20283 TTGTGAAAGGTTGATTTGGTACACTA
1 ---TGAAATTTTGA-TAACCACACTA
* * *
20309 TGAAATTTGGATAACCATATTA
1 TGAAATTTTGATAACCACACTA
* *
20331 TGAAATTTTGATAACCTCCCTA
1 TGAAATTTTGATAACCACACTA
* * ** *
20353 -GGAATGTTGATAACTTCCCTA
1 TGAAATTTTGATAACCACACTA
* * *
20374 T-AGAATTTTGTTAATCTCACTA
1 TGA-AATTTTGATAACCACACTA
*
20396 TGAAATTTTGATAAGCACAACT-
1 TGAAATTTTGATAACCAC-ACTA
* * * ***
20418 TCAAATTTTAATTACC-TTTTA
1 TGAAATTTTGATAACCACACTA
* *
20439 TGAAATTTTTG-TAACGACATTA
1 TGAAA-TTTTGATAACCACACTA
* ** * *
20461 TGAAATTTGGATAATTATATTA
1 TGAAATTTTGATAACCACACTA
**
20483 TGAAATTTTGATAGTCACACTA
1 TGAAATTTTGATAACCACACTA
20505 TGAAATTTTGATAA
1 TGAAATTTTGATAA
20519 TCTGTAAAGT
Statistics
Matches: 269, Mismatches: 79, Indels: 48
0.68 0.20 0.12
Matches are distributed among these distances:
20 1 0.00
21 51 0.19
22 171 0.64
23 16 0.06
24 2 0.01
25 2 0.01
26 19 0.07
27 7 0.03
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.37
Consensus pattern (22 bp):
TGAAATTTTGATAACCACACTA
Found at i:21138 original size:30 final size:31
Alignment explanation
Indices: 21104--21168 Score: 114
Period size: 31 Copynumber: 2.1 Consensus size: 31
21094 TGGCAATTTA
*
21104 GAAATATGTTTTTAAAA-AAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
21134 GAAATATGTTTTAAAAATAAGGGTACAATTG
1 GAAATATGTTTTAAAAATAAGGGTACAATTG
21165 GAAA
1 GAAA
21169 ACATAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 16 0.48
31 17 0.52
ACGTcount: A:0.46, C:0.03, G:0.20, T:0.31
Consensus pattern (31 bp):
GAAATATGTTTTAAAAATAAGGGTACAATTG
Found at i:35213 original size:15 final size:15
Alignment explanation
Indices: 35193--35223 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
35183 CATTGTTTAT
35193 GCTGTAGACTCTCCC
1 GCTGTAGACTCTCCC
35208 GCTGTAGACTCTCCC
1 GCTGTAGACTCTCCC
35223 G
1 G
35224 GTCTCCCCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.13, C:0.39, G:0.23, T:0.26
Consensus pattern (15 bp):
GCTGTAGACTCTCCC
Found at i:50646 original size:104 final size:105
Alignment explanation
Indices: 50493--50728 Score: 323
Period size: 105 Copynumber: 2.3 Consensus size: 105
50483 TTGAAACATG
* * * * * * *
50493 AAACTTAAGTATTCATCAATTAATACTGGCTTCGGGTTCGCTGTTAACACTGCCAC-TTTTTCAA
1 AAACTGAAGTTTTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACTTTTTTAAA
50557 AG-TGAAGACTTGGAGTTTTAGTCGATTAATACTAAAACTA
66 AGAT-AAGACTTGGAGTTTTAGTCGATTAATACTAAAACTA
* * *
50597 AAACTGGAGTTTTTATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGTCACTTTTTTAAA
1 AAACTGAAGTTTTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACTTTTTTAAA
** *
50662 AGATAAGACTTGGAGTTTTAGTCGATTAATACTGGAATTA
66 AGATAAGACTTGGAGTTTTAGTCGATTAATACTAAAACTA
*
50702 AAACTGAAGTTTTCATCGACTAATACT
1 AAACTGAAGTTTTCATCGATTAATACT
50729 TTTCTGACAG
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
104 47 0.41
105 66 0.58
106 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (105 bp):
AAACTGAAGTTTTCATCGATTAATACTGCCTCCGGGTTCGCTGTCAACACTGCCACTTTTTTAAA
AGATAAGACTTGGAGTTTTAGTCGATTAATACTAAAACTA
Found at i:51545 original size:17 final size:16
Alignment explanation
Indices: 51523--51581 Score: 68
Period size: 17 Copynumber: 3.7 Consensus size: 16
51513 GAAAGAGAAT
51523 AAGGAAGAGGAAAAGGA
1 AAGGAAGA-GAAAAGGA
51540 AAGGAAGAGAAGAAGGA
1 AAGGAAGAGAA-AAGGA
* *
51557 ATGG--GAGAAGAGGA
1 AAGGAAGAGAAAAGGA
51571 AAGGAAGAGAA
1 AAGGAAGAGAA
51582 GAAGATGAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 8 0.22
17 16 0.44
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (16 bp):
AAGGAAGAGAAAAGGA
Found at i:51548 original size:29 final size:31
Alignment explanation
Indices: 51515--51585 Score: 103
Period size: 31 Copynumber: 2.4 Consensus size: 31
51505 GTGAGAGAGA
*
51515 AAGAGAATAAGGAA-GAGGA-AA-AGGAAAGG
1 AAGAGAAGAAGGAATG-GGAGAAGAGGAAAGG
51544 AAGAGAAGAAGGAATGGGAGAAGAGGAAAGG
1 AAGAGAAGAAGGAATGGGAGAAGAGGAAAGG
51575 AAGAGAAGAAG
1 AAGAGAAGAAG
51586 ATGAGTCAGT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
29 16 0.42
30 3 0.08
31 19 0.50
ACGTcount: A:0.56, C:0.00, G:0.41, T:0.03
Consensus pattern (31 bp):
AAGAGAAGAAGGAATGGGAGAAGAGGAAAGG
Found at i:52603 original size:23 final size:23
Alignment explanation
Indices: 52573--52666 Score: 89
Period size: 23 Copynumber: 3.8 Consensus size: 23
52563 TTTTTTTTTT
52573 GAGATCAATTAATGTTTGTGAAG
1 GAGATCAATTAATGTTTGTGAAG
****
52596 GAGATCAATTAATGTTTGAATTTTTTTTTT
1 GAGATCAATTAATGTTTG-------TGAAG
52626 GAGATCAATTAATGTTTGTGAAG
1 GAGATCAATTAATGTTTGTGAAG
52649 GAGATCAATTAATGTTTG
1 GAGATCAATTAATGTTTG
52667 ATTAAAGGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 14
0.72 0.10 0.18
Matches are distributed among these distances:
23 37 0.66
30 19 0.34
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (23 bp):
GAGATCAATTAATGTTTGTGAAG
Found at i:52624 original size:53 final size:53
Alignment explanation
Indices: 52550--52667 Score: 229
Period size: 53 Copynumber: 2.2 Consensus size: 53
52540 CATCTCTCCT
52550 AATTAATGTTTG-ATTTTTTTTTTGAGATCAATTAATGTTTGTGAAGGAGATC
1 AATTAATGTTTGAATTTTTTTTTTGAGATCAATTAATGTTTGTGAAGGAGATC
52602 AATTAATGTTTGAATTTTTTTTTTGAGATCAATTAATGTTTGTGAAGGAGATC
1 AATTAATGTTTGAATTTTTTTTTTGAGATCAATTAATGTTTGTGAAGGAGATC
52655 AATTAATGTTTGA
1 AATTAATGTTTGA
52668 TTAAAGGATA
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 12 0.18
53 53 0.82
ACGTcount: A:0.31, C:0.03, G:0.19, T:0.47
Consensus pattern (53 bp):
AATTAATGTTTGAATTTTTTTTTTGAGATCAATTAATGTTTGTGAAGGAGATC
Found at i:52681 original size:23 final size:23
Alignment explanation
Indices: 52626--52682 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
52616 TTTTTTTTTT
* *
52626 GAGATCAATTAATGTTTGTGAAG
1 GAGATAAATTAATGTTTGTGAAA
* *
52649 GAGATCAATTAATGTTTGATTAAA
1 GAGATAAATTAATGTTTG-TGAAA
52673 G-GATAAATTA
1 GAGATAAATTA
52683 CAAATATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.40, C:0.04, G:0.21, T:0.35
Consensus pattern (23 bp):
GAGATAAATTAATGTTTGTGAAA
Found at i:53634 original size:108 final size:107
Alignment explanation
Indices: 53468--53682 Score: 421
Period size: 108 Copynumber: 2.0 Consensus size: 107
53458 CTTCCTATTT
53468 CAACGAAAGGGTACAAATTATAATTGTTTCAACGATACTATGGAATTTCAAGAACCTTTTTATAA
1 CAACGAAAGGGTACAAATTATAATTGTTTCAACGATACTATGGAATTTCAAGAACCTTTTTATAA
53533 TTTTTTTTAACCTTCTTTTGAAATTTGGTTAACCTCCCTAAGG
66 -TTTTTTTAACCTTCTTTTGAAATTTGGTTAACCTCCCTAAGG
53576 CAACGAAAGGGTACAAATTATAATTGTTTCAACGATACTATGGAATTTCAAGAACCTTTTTATAA
1 CAACGAAAGGGTACAAATTATAATTGTTTCAACGATACTATGGAATTTCAAGAACCTTTTTATAA
53641 TTTTTTTAACCTTCTTTTGAAATTTGGTTAACCTCCCTAAGG
66 TTTTTTTAACCTTCTTTTGAAATTTGGTTAACCTCCCTAAGG
53683 AATTTTGAAG
Statistics
Matches: 107, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
107 42 0.39
108 65 0.61
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.39
Consensus pattern (107 bp):
CAACGAAAGGGTACAAATTATAATTGTTTCAACGATACTATGGAATTTCAAGAACCTTTTTATAA
TTTTTTTAACCTTCTTTTGAAATTTGGTTAACCTCCCTAAGG
Found at i:53792 original size:22 final size:21
Alignment explanation
Indices: 53731--53792 Score: 52
Period size: 22 Copynumber: 2.8 Consensus size: 21
53721 CAATGAAATT
* *
53731 TTGATAACCAACACTATGAGATG
1 TTGATAACC-AC-TTATGAGATA
* *
53754 TTGATAACCTCTATATGATATA
1 TTGATAACCACT-TATGAGATA
53776 TTGATAACCACGTTATG
1 TTGATAACCAC-TTATG
53793 GAAATTTAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (21 bp):
TTGATAACCACTTATGAGATA
Found at i:53885 original size:44 final size:43
Alignment explanation
Indices: 53835--54144 Score: 196
Period size: 44 Copynumber: 7.3 Consensus size: 43
53825 AATTACACTC
* *
53835 TGAAATTTTGATAATCATACTATGAAATTGTGATAACCTCGCTA
1 TGAAATTTTGATAATCATCCTATGAAATTTTGATAACCTC-CTA
* *
53879 TGAAATTTTGATAAATCTTCCTATAAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGAT-AATCATCCTATGAAATTTTGAT-AACC-TCCTA
* * * * *
53925 TAAAAATTTGATAA-CTTTCTTATGAAATCTTGATAA----CTA
1 TGAAATTTTGATAATC-ATCCTATGAAATTTTGATAACCTCCTA
* * ** * *
53964 -CAAATTTTGATAA-CCTCCCTATGATTTTTTGATAATCTCATTA
1 TGAAATTTTGATAATCAT-CCTATGAAATTTTGATAACCTC-CTA
* * *
54007 TGAAATTTTGTTAATC-TCCCTATGAAATTTTGATAACCCTCTTG
1 TGAAATTTTGATAATCAT-CCTATGAAATTTTGATAA-CCTCCTA
* ** *
54051 TGAAATTTTGA-AAACTAAACTATGAAATTTTGATAACCTTCATA
1 TGAAATTTTGATAATC-ATCCTATGAAATTTTGATAACC-TCCTA
* * * *
54095 TGAAATTTTGAT-ATCCTCC-CTG-AATCTTGATATCCTCCT-
1 TGAAATTTTGATAATCATCCTATGAAATTTTGATAACCTCCTA
54134 TGAAATTTTGA
1 TGAAATTTTGA
54145 ATACTTCATA
Statistics
Matches: 212, Mismatches: 37, Indels: 39
0.74 0.13 0.14
Matches are distributed among these distances:
37 1 0.00
38 26 0.12
39 14 0.07
40 3 0.01
41 11 0.05
42 2 0.01
43 8 0.04
44 89 0.42
45 39 0.18
46 17 0.08
47 2 0.01
ACGTcount: A:0.34, C:0.15, G:0.10, T:0.41
Consensus pattern (43 bp):
TGAAATTTTGATAATCATCCTATGAAATTTTGATAACCTCCTA
Found at i:53907 original size:23 final size:23
Alignment explanation
Indices: 53835--54107 Score: 143
Period size: 22 Copynumber: 12.6 Consensus size: 23
53825 AATTACACTC
* *
53835 TGAAATTTTGAT-AATCATACTA
1 TGAAATTTTGATAAATCTTCCTA
* *
53857 TGAAATTGTGAT-AA-CCTCGCTA
1 TGAAATTTTGATAAATCTTC-CTA
53879 TGAAATTTTGATAAATCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* *
53902 TAAAATTTTGATAAACCTTCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * * *
53925 TAAAAATTTGATAACT-TTCTTA
1 TGAAATTTTGATAAATCTTCCTA
*
53947 TGAAATCTTGAT-AA-----CTA
1 TGAAATTTTGATAAATCTTCCTA
* * *
53964 -CAAATTTTGATA-ACCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
** *
53985 TGATTTTTTGAT-AATC-TCATTA
1 TGAAATTTTGATAAATCTTC-CTA
* *
54007 TGAAATTTTG-TTAATCTCCCTA
1 TGAAATTTTGATAAATCTTCCTA
* * * *
54029 TGAAATTTTGAT-AACCCTCTTG
1 TGAAATTTTGATAAATCTTCCTA
**
54051 TGAAATTTTGA-AAA-CTAAACTA
1 TGAAATTTTGATAAATCT-TCCTA
* *
54073 TGAAATTTTGAT-AACCTTCATA
1 TGAAATTTTGATAAATCTTCCTA
54095 TGAAATTTTGATA
1 TGAAATTTTGATA
54108 TCCTCCCTGA
Statistics
Matches: 190, Mismatches: 41, Indels: 39
0.70 0.15 0.14
Matches are distributed among these distances:
16 10 0.05
17 2 0.01
21 9 0.05
22 123 0.65
23 43 0.23
24 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.41
Consensus pattern (23 bp):
TGAAATTTTGATAAATCTTCCTA
Found at i:53959 original size:45 final size:45
Alignment explanation
Indices: 53841--53960 Score: 113
Period size: 45 Copynumber: 2.7 Consensus size: 45
53831 ACTCTGAAAT
* * * *
53841 TTTGAT-AATCATACTATGAAATTGTGAT-AACCTCGCTATGAAAT
1 TTTGATAAATCTTCCTATGAAATT-TGATAAACCTCGCTATAAAAA
*
53885 TTTGATAAATCTTCCTATAAAATTTTGATAAACCTTC-CTATAAAAA
1 TTTGATAAATCTTCCTATGAAA-TTTGATAAACC-TCGCTATAAAAA
* *
53931 TTTGATAACT-TTCTTATGAAATCTTGATAA
1 TTTGATAAATCTTCCTATGAAAT-TTGATAA
53961 CTACAAATTT
Statistics
Matches: 63, Mismatches: 8, Indels: 9
0.79 0.10 0.11
Matches are distributed among these distances:
44 7 0.11
45 32 0.51
46 22 0.35
47 2 0.03
ACGTcount: A:0.38, C:0.13, G:0.09, T:0.40
Consensus pattern (45 bp):
TTTGATAAATCTTCCTATGAAATTTGATAAACCTCGCTATAAAAA
Found at i:54282 original size:22 final size:22
Alignment explanation
Indices: 54251--54497 Score: 132
Period size: 22 Copynumber: 11.3 Consensus size: 22
54241 AATCACATTT
*
54251 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
54273 CGAAATTTTGATAATCTCTTTA
1 TGAAATTTTGATAACCTCTTTA
* * * * *
54295 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTTTA
* * * *
54317 TGAAATTCTGATAATCACATTA
1 TGAAATTTTGATAACCTCTTTA
*
54339 TGTAATTTTGATAACCTCGCTTTA
1 TGAAATTTTGATAACCT--CTTTA
** **
54363 --AAATTTTGATAACAACACTA
1 TGAAATTTTGATAACCTCTTTA
* *
54383 TGGAATTTTGATAATCT-TTCTA
1 TGAAATTTTGATAACCTCTT-TA
*
54405 T-AAATTTTGATAACCCGATCTCTA
1 TGAAATTTTGATAA-CC--TCTTTA
* * *
54429 TGAAATTTCGATAATCACTTTA
1 TGAAATTTTGATAACCTCTTTA
* *
54451 TGAGA-TTTGATAACCT-TCTA
1 TGAAATTTTGATAACCTCTTTA
* * *
54471 TCAAATTTTGGT-A-CTCCTTA
1 TGAAATTTTGATAACCTCTTTA
54491 TGAAATT
1 TGAAATT
54498 GAGAGTTTTA
Statistics
Matches: 161, Mismatches: 52, Indels: 26
0.67 0.22 0.11
Matches are distributed among these distances:
19 2 0.01
20 18 0.11
21 24 0.15
22 96 0.60
24 9 0.06
25 12 0.07
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.41
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTTTA
Found at i:54288 original size:44 final size:43
Alignment explanation
Indices: 54230--54417 Score: 118
Period size: 44 Copynumber: 4.3 Consensus size: 43
54220 ATACCATTGT
54230 GAAATTTTTG-TAATCACATTTTGAAAATTTGATAACCTCTTTA
1 GAAA-TTTTGATAATCACATTTTGAAAATTTGATAACCTCTTTA
* * * * *
54273 CGAAATTTTGATAATCTC-TTTAT-AAAATTTTGTTGACCCCTCTA
1 -GAAATTTTGATAATCACATTT-TGAAAA-TTTGATAACCTCTTTA
* * * *
54317 TGAAATTCTGATAATCACATTATGTAATTTTGATAACCTCGCTTTA
1 -GAAATTTTGATAATCACATTTTGAAAATTTGATAACCT--CTTTA
* * * * *
54363 -AAATTTTGATAA-CAACACTATGGAATTTTGATAATCT-TTCTA
1 GAAATTTTGATAATC-ACATTTTGAAAATTTGATAACCTCTT-TA
*
54405 TAAATTTTGATAA
1 GAAATTTTGATAA
54418 CCCGATCTCT
Statistics
Matches: 115, Mismatches: 19, Indels: 21
0.74 0.12 0.14
Matches are distributed among these distances:
41 2 0.02
42 2 0.02
43 25 0.22
44 78 0.68
45 4 0.03
46 4 0.03
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.43
Consensus pattern (43 bp):
GAAATTTTGATAATCACATTTTGAAAATTTGATAACCTCTTTA
Found at i:54532 original size:22 final size:21
Alignment explanation
Indices: 54503--54557 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
54493 AAATTGAGAG
54503 TTTT-ATAACCTTCATATGAAA
1 TTTTGATAACCTTC-TATGAAA
** *
54524 TTTTGATAACCACACTATAAAA
1 TTTTGATAACC-TTCTATGAAA
54546 TTTTGATAACCT
1 TTTTGATAACCT
54558 CCCCATGAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
21 4 0.14
22 23 0.82
23 1 0.04
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (21 bp):
TTTTGATAACCTTCTATGAAA
Found at i:54568 original size:22 final size:22
Alignment explanation
Indices: 54518--54568 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
54508 TAACCTTCAT
*
54518 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCACACC
* * *
54540 ATAAAATTTTGATAACCTCCCC
1 ATGAAATTTTGATAACCACACC
54562 ATGAAAT
1 ATGAAAT
54569 ATTTAATGAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.31
Consensus pattern (22 bp):
ATGAAATTTTGATAACCACACC
Found at i:54590 original size:34 final size:34
Alignment explanation
Indices: 54543--54607 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
54533 CCACACTATA
* *
54543 AAATTTTGATAACCTCCCCATGAAATATTTAATG
1 AAATTTTGATAACCACACCATGAAATATTTAATG
* *
54577 AAATTTTGTTAACCACACCATGAAATTTTTA
1 AAATTTTGATAACCACACCATGAAATATTTA
54608 TAACCTCGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (34 bp):
AAATTTTGATAACCACACCATGAAATATTTAATG
Found at i:54693 original size:22 final size:22
Alignment explanation
Indices: 54668--54830 Score: 121
Period size: 22 Copynumber: 7.3 Consensus size: 22
54658 TTGTGATAAT
*
54668 TAACCACCCTATGAAATTTTAA
1 TAACCACCCTATGAAATTTTGA
* * * * *
54690 TAACCAACCTAAGATATTCTAA
1 TAACCACCCTATGAAATTTTGA
* *
54712 TAACCTGATCCTATGAAATTTTGG
1 TAACC--ACCCTATGAAATTTTGA
* *
54736 TAACCACACTATGAAATTTTGG
1 TAACCACCCTATGAAATTTTGA
* * *
54758 TAACTACACTATGGAATTTTGA
1 TAACCACCCTATGAAATTTTGA
* * * *
54780 TAAGC-TCCTCATGAAATTATAA
1 TAACCACCCT-ATGAAATTTTGA
* *
54802 TAACCATCTTATGAAATTTTGA
1 TAACCACCCTATGAAATTTTGA
54824 TAACCAC
1 TAACCAC
54831 ATAGAGACAA
Statistics
Matches: 110, Mismatches: 27, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
21 2 0.02
22 89 0.81
23 3 0.03
24 16 0.15
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.33
Consensus pattern (22 bp):
TAACCACCCTATGAAATTTTGA
Found at i:55024 original size:19 final size:20
Alignment explanation
Indices: 54993--55030 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54983 TATTGACATT
54993 TAAAAATTGAAATT-AAAAG
1 TAAAAATTGAAATTCAAAAG
55012 TAAAATATT-AAATTCAAAA
1 TAAAA-ATTGAAATTCAAAA
55031 AATAATAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAAATTGAAATTCAAAAG
Found at i:55378 original size:31 final size:31
Alignment explanation
Indices: 55343--55408 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
55333 TGGCAATTTA
* *
55343 GAAATATGTTTTAAAGAA-AAGGGTACAATTG
1 GAAATATATTTTAAA-AATAAGGGTACAATCG
55374 GAAATATATTTTAAAAATAAGGGTACAATCG
1 GAAATATATTTTAAAAATAAGGGTACAATCG
55405 GAAA
1 GAAA
55409 ACATAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 2 0.06
31 30 0.94
ACGTcount: A:0.48, C:0.05, G:0.20, T:0.27
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAGGGTACAATCG
Found at i:56346 original size:2 final size:2
Alignment explanation
Indices: 56330--56371 Score: 68
Period size: 2 Copynumber: 21.0 Consensus size: 2
56320 TAANAAAATT
56330 TA TA TGA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 35 0.92
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Done.