Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015075.1 Corchorus capsularis cultivar CVL-1 contig15096, 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: 33924
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:3009 original size:399 final size:398
Alignment explanation
Indices: 2299--3072 Score: 1250
Period size: 399 Copynumber: 1.9 Consensus size: 398
2289 GGTCTGTCTG
*
2299 GGTTCAAGGCCCACCGAGCGACCCAATATACATGTGGACACCAATCCGAACCCAAAAGTCTAGAC
1 GGTTCAAGGCCCACCGAGCGACCCAATATACATGTGGACACCAATCCGAACCCAAAAGCCTAGAC
* * *
2364 TGATGGTTTCTTGGGTCCTTCATGTATATATGCCACTCAAACAACCCATCTTTTTATGATGTGGG
66 TGATGGTTTCTTGGGTCCTTCATGTATATAAGCCACTCAAACAACCCATCTCTTCATGATGTGGG
2429 ATGTTTCCCTCACATGTGAATCCCTAACAATCTCCCCCGATTCACTTGTGAGTCCTCATCTCTCC
131 ATGTTTCCCTCACATGTGAATCCCTAACAATCTCCCCCGATTCACTTGTGAGTCCTCATCTCTCC
* * *
2494 CCCGTGCGGCCCAACCCGTCAAGTCTTTAGCCAGTTACCGGCCATCCAAGACTTAACCCTGGAGT
196 CCCGTGCGCCCCAACCCGTCAAGTCTTAAGCCAATTACCGGCCATCCAAGACTTAACCCTGGAGT
2559 GGTGCAAGCTACGAACACTCCACAATCGCACGCCCCTGGCCCTGCAGCCAACCAGGTTTACCGTG
261 GGTGCAAGCTACGAACACTCCACAATCGCACGCCCCTGGCCCTGCAGCCAACCAGGTTTACCGTG
* * * *
2624 TTCCTGGGCCACACTGATCGAGTCAAACCGGGCTCTGATACCACTTGTTGGGAGAGGAACCGGAC
326 CTCATGGGCCACACAGATCGAGTCAAACCGAGCTCTGATACCACTTGTTGGGAGAGGAACCGGAC
2689 CGTGTCAA
391 CGTGTCAA
**
2697 GGTTCAAGGCCCATTGAGCGACCCAATATACATGTCGGACACCAA-CCTGAACCCAAAAGCCTAG
1 GGTTCAAGGCCCACCGAGCGACCCAATATACATGT-GGACACCAATCC-GAACCCAAAAGCCTAG
* * * *
2761 ACTGATGATTTTTCTTGGGTCTTTCATGTATATAAGCTACTCCAACAACCCATCTCTTCATGATG
64 ACTGATG--GTTTCTTGGGTCCTTCATGTATATAAGCCACTCAAACAACCCATCTCTTCATGATG
* *
2826 TGGGATG-TTCCCTCATATGTGAATCCTTAACAATCTCCCCCGA-TCACTTGTGAGTCCTCATCT
127 TGGGATGTTTCCCTCACATGTGAATCCCTAACAATCTCCCCCGATTCACTTGTGAGTCCTCATCT
* *
2889 CTCCCTCGTGCGCCCCAACCTGTCAAGTCTTAAGCCAATTACCGGCCATCCAAGACTTAACCCAT
192 CTCCCCCGTGCGCCCCAACCCGTCAAGTCTTAAGCCAATTACCGGCCATCCAAGACTTAACCC-T
* * *
2954 GGAGTGGTGCAAGCTACGAACATTCCACAATCGCACGCCCCTGG-CGTGTAGCCAACCAGGTTTA
256 GGAGTGGTGCAAGCTACGAACACTCCACAATCGCACGCCCCTGGCCCTGCAGCCAACCAGGTTTA
*
3018 CCGTGCTCATGGGCCACACAGATCGAGTCTAACCGAGCTCTGATACCACTTGTTG
321 CCGTGCTCATGGGCCACACAGATCGAGTCAAACCGAGCTCTGATACCACTTGTTG
3073 AACCTGGTGT
Statistics
Matches: 346, Mismatches: 25, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
398 35 0.10
399 177 0.51
400 78 0.23
401 56 0.16
ACGTcount: A:0.24, C:0.31, G:0.20, T:0.24
Consensus pattern (398 bp):
GGTTCAAGGCCCACCGAGCGACCCAATATACATGTGGACACCAATCCGAACCCAAAAGCCTAGAC
TGATGGTTTCTTGGGTCCTTCATGTATATAAGCCACTCAAACAACCCATCTCTTCATGATGTGGG
ATGTTTCCCTCACATGTGAATCCCTAACAATCTCCCCCGATTCACTTGTGAGTCCTCATCTCTCC
CCCGTGCGCCCCAACCCGTCAAGTCTTAAGCCAATTACCGGCCATCCAAGACTTAACCCTGGAGT
GGTGCAAGCTACGAACACTCCACAATCGCACGCCCCTGGCCCTGCAGCCAACCAGGTTTACCGTG
CTCATGGGCCACACAGATCGAGTCAAACCGAGCTCTGATACCACTTGTTGGGAGAGGAACCGGAC
CGTGTCAA
Found at i:7200 original size:21 final size:21
Alignment explanation
Indices: 7161--7209 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
7151 TCAATGCTTT
**
7161 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
7183 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
7204 A-GAAGC
1 AGGAAGC
7210 TACAATTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:13521 original size:21 final size:22
Alignment explanation
Indices: 13497--13856 Score: 102
Period size: 22 Copynumber: 16.5 Consensus size: 22
13487 ATCACTATTT
13497 TACTGATTA-TTCTTTACTTTG
1 TACTGATTACTTCTTTACTTTG
13518 TACTGATTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
*
13541 T--TGATTACCTTC-TTACTTTT
1 TACTGATTA-CTTCTTTACTTTG
* * * *
13561 TACTGATTCCAT-TTTGCTCTTT
1 TACTGATTACTTCTTTACT-TTG
* *
13583 TACTGATTACTATTTTCTTCTCCTTTTT
1 TACTGATTAC----TTCTT-TAC-TTTG
* *
13611 TGCTGATTAC-TCTTTTACTTTT
1 TACTGATTACTTC-TTTACTTTG
* * * *
13633 TACTGATTGCCT-TTTGCTTTT
1 TACTGATTACTTCTTTACTTTG
13654 TACTGATTACCTT-TTTACTTCT-
1 TACTGATTA-CTTCTTTACTT-TG
* *
13676 TGCTGATTAGCCT-TTTACTCTTG
1 TACTGATTA-CTTCTTTACT-TTG
* *
13699 -ACTGATCACCTT-TTTACTCT-
1 TACTGATTA-CTTCTTTACTTTG
* *
13719 TACTGATTTCCT-TTTACTTCT-
1 TACTGATTACTTCTTTACTT-TG
* * *
13740 TACTTATTACTTTTTTACTCT-
1 TACTGATTACTTCTTTACTTTG
* *
13761 TACTGATTAC-TATTTACTTTT
1 TACTGATTACTTCTTTACTTTG
*
13782 TACTGACTACTAT-TTTACTCTTG
1 TACTGATTACT-TCTTTACT-TTG
* *
13805 T--TGGTTACATTC-TTACTTTT
1 TACTGATTAC-TTCTTTACTTTG
13825 TACTGATTACTAT-TTTACTCTT-
1 TACTGATTACT-TCTTTACT-TTG
*
13847 TACTAATTAC
1 TACTGATTAC
13857 CATTCTACCC
Statistics
Matches: 262, Mismatches: 41, Indels: 71
0.70 0.11 0.19
Matches are distributed among these distances:
20 22 0.08
21 91 0.35
22 111 0.42
23 18 0.07
24 2 0.01
26 1 0.00
27 2 0.01
28 14 0.05
29 1 0.00
ACGTcount: A:0.18, C:0.20, G:0.07, T:0.55
Consensus pattern (22 bp):
TACTGATTACTTCTTTACTTTG
Found at i:13568 original size:43 final size:42
Alignment explanation
Indices: 13509--13846 Score: 245
Period size: 42 Copynumber: 7.7 Consensus size: 42
13499 CTGATTATTC
*
13509 TTTACTTTGTACTGATTACTATTTTACTCTTGTTGATTACCT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * *
13551 TCTTACTTTTTACTGATT-CCATTTTGCTCTTTTACTGATTACTATTTTCT
1 T-TTACTTTTTACTGATTACTATTTTACTCTTGT--TGATTAC------CT
* * * * * *
13601 TCTCCTTTTTTGCTGATTACTCTTTTACT-TTTTACTGATTGCCT
1 TTTAC-TTTTTACTGATTACTATTTTACTCTTGT--TGATTACCT
* *
13645 TTTGCTTTTTACTGATTACCT-TTTTACTTCTTGCTGATTAGCCT
1 TTTACTTTTTACTGATTA-CTATTTTAC-TCTTGTTGATTA-CCT
* * * ** *
13689 TTTACTCTTGACTGATCACCT-TTTTACTCTTACTGATTTCCT
1 TTTACTTTTTACTGATTA-CTATTTTACTCTTGTTGATTACCT
* * * **
13731 TTTACTTCTTACTTATTACTTTTTTACTCTTACTGATTA-CT
1 TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
* * *
13772 ATTTACTTTTTACTGACTACTATTTTACTCTTGTTGGTTACAT
1 -TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
13815 TCTTACTTTTTACTGATTACTATTTTACTCTT
1 T-TTACTTTTTACTGATTACTATTTTACTCTT
13847 TACTAATTAC
Statistics
Matches: 239, Mismatches: 38, Indels: 37
0.76 0.12 0.12
Matches are distributed among these distances:
41 4 0.02
42 79 0.33
43 78 0.33
44 41 0.17
45 2 0.01
49 2 0.01
50 26 0.11
51 7 0.03
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.56
Consensus pattern (42 bp):
TTTACTTTTTACTGATTACTATTTTACTCTTGTTGATTACCT
Found at i:13593 original size:36 final size:34
Alignment explanation
Indices: 13553--13672 Score: 102
Period size: 36 Copynumber: 3.4 Consensus size: 34
13543 GATTACCTTC
13553 TTACTTTTTACTGATTCCATTTTGCTCTTTTACTGA
1 TTACTTTTTACTGATTCC-TTTTGCT-TTTTACTGA
** **
13589 TTACTATTTT-CT--TCTCCTTTTTTGCTGATTACTCTT
1 TTACT-TTTTACTGAT-TCC--TTTTGCTTTTTACT-GA
13625 TTACTTTTTACTGATTGCCTTTTGCTTTTTACTGA
1 TTACTTTTTACTGATT-CCTTTTGCTTTTTACTGA
13660 TTACCTTTTTACT
1 TTA-CTTTTTACT
13673 TCTTGCTGAT
Statistics
Matches: 66, Mismatches: 9, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
34 1 0.02
35 15 0.23
36 42 0.64
37 5 0.08
38 3 0.05
ACGTcount: A:0.14, C:0.20, G:0.07, T:0.58
Consensus pattern (34 bp):
TTACTTTTTACTGATTCCTTTTGCTTTTTACTGA
Found at i:13784 original size:14 final size:13
Alignment explanation
Indices: 13708--13785 Score: 57
Period size: 14 Copynumber: 5.7 Consensus size: 13
13698 GACTGATCAC
*
13708 CTTTTTACTCTTA
1 CTTTTTACTTTTA
* *
13721 CTGATTTCCTTTTA
1 CT-TTTTACTTTTA
*
13735 CTTCTTACTTATTA
1 CTTTTTACTT-TTA
*
13749 CTTTTTTACTCTTA
1 C-TTTTTACTTTTA
**
13763 CTGATTACTATTTA
1 CTTTTTACT-TTTA
13777 CTTTTTACT
1 CTTTTTACT
13786 GACTACTATT
Statistics
Matches: 48, Mismatches: 13, Indels: 7
0.71 0.19 0.10
Matches are distributed among these distances:
13 13 0.27
14 28 0.58
15 7 0.15
ACGTcount: A:0.18, C:0.21, G:0.03, T:0.59
Consensus pattern (13 bp):
CTTTTTACTTTTA
Found at i:13869 original size:22 final size:22
Alignment explanation
Indices: 13823--13869 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
13813 ATTCTTACTT
* * * *
13823 TTTACTGATTACTATTTTACTC
1 TTTACTAATTACCATTCTACCC
13845 TTTACTAATTACCATTCTACCC
1 TTTACTAATTACCATTCTACCC
13867 TTT
1 TTT
13870 CAGATACCTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.23, G:0.02, T:0.51
Consensus pattern (22 bp):
TTTACTAATTACCATTCTACCC
Found at i:14143 original size:55 final size:54
Alignment explanation
Indices: 14082--14312 Score: 249
Period size: 55 Copynumber: 4.3 Consensus size: 54
14072 CGTTTTAACT
*
14082 CTTAATTA-TCGATTTACTGATTACTATTACCATGACTCTGATTAATCTCTTTTTA
1 CTTAATTACT-GATTTACTGATTACTATTACTAT-ACTCTGATTAATCTCTTTTTA
* *
14137 CTTAATTACTGATTTACTGATTACTACTACTTTTACTCTGATTAATC-CTTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTAC-TATACTCTGATTAATCTC-TTTTTA
* * * * * *
14192 CTTTAATTACTAACTTACTGA-T--TATTATTA-ACTTTGACTCATCTCTTTTTA
1 C-TTAATTACTGATTTACTGATTACTATTACTATACTCTGATTAATCTCTTTTTA
* * *
14243 CTCAATTACTGATTTACTGTTTACTATTACTTTAACTCTGATTAATCTCTTTTTA
1 CTTAATTACTGATTTACTGATTACTATTACTAT-ACTCTGATTAATCTCTTTTTA
*
14298 CTTATTTACTGATTT
1 CTTAATTACTGATTT
14313 TCTTTTTACA
Statistics
Matches: 144, Mismatches: 22, Indels: 20
0.77 0.12 0.11
Matches are distributed among these distances:
50 15 0.10
51 18 0.12
52 2 0.01
53 10 0.07
54 1 0.01
55 79 0.55
56 19 0.13
ACGTcount: A:0.26, C:0.18, G:0.06, T:0.51
Consensus pattern (54 bp):
CTTAATTACTGATTTACTGATTACTATTACTATACTCTGATTAATCTCTTTTTA
Found at i:14261 original size:50 final size:50
Alignment explanation
Indices: 14186--14280 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 50
14176 GATTAATCCT
* * *
14186 TTTTTACTTTAATTACTAACTTACTGATTATTATTAACTTTGACTCATCTC
1 TTTTTACTTCAATTACTAACTTACTGATTACTATT-ACTTTAACTCATCTC
* * *
14237 TTTTTAC-TCAATTACTGATTTACTGTTTACTATTACTTTAACTC
1 TTTTTACTTCAATTACTAACTTACTGATTACTATTACTTTAACTC
14281 TGATTAATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
49 9 0.24
50 22 0.58
51 7 0.18
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (50 bp):
TTTTTACTTCAATTACTAACTTACTGATTACTATTACTTTAACTCATCTC
Found at i:15074 original size:50 final size:48
Alignment explanation
Indices: 15003--15255 Score: 174
Period size: 50 Copynumber: 5.1 Consensus size: 48
14993 AACTAATCGA
** * * *
15003 TTTATTTACTAATGGCCTAAAAGTTCACACTTCTATTTCAAAAATGACAT
1 TTTATTTACTAATTACTTAAAAATTCA-ACTT-TATTTCAAAGATGACAT
* * *
15053 TTTATTTACTAATTACTTAAAAATTCAATCTTT-TATTCAAAGGTTAAAT
1 TTTATTTACTAATTACTTAAAAATTCAA-CTTTAT-TTCAAAGATGACAT
*
15102 CTTTATTTACTAATTACTCTAAAAATTCAA-TTTTTTACTCAAAGATGACATT
1 -TTTATTTACTAATTACT-TAAAAATTCAACTTTATT--TCAAAGATGACA-T
* * * * * *
15154 TTTATTTACCATTTACTTAAAAA-ACAATCTTT-TATTCAAAGGTTAAAT
1 TTTATTTACTAATTACTTAAAAATTCAA-CTTTAT-TTCAAAGATGACAT
* **
15202 CTTTATTTACTAATTACTCTAAAAGTTCAATCTTT-TACCCAAAGATGACAT
1 -TTTATTTACTAATTACT-TAAAAATTCAA-CTTTAT-TTCAAAGATGACAT
15253 TTT
1 TTT
15256 TTACTTAAGT
Statistics
Matches: 163, Mismatches: 26, Indels: 28
0.75 0.12 0.13
Matches are distributed among these distances:
48 2 0.01
49 43 0.26
50 59 0.36
51 58 0.36
52 1 0.01
ACGTcount: A:0.37, C:0.15, G:0.05, T:0.43
Consensus pattern (48 bp):
TTTATTTACTAATTACTTAAAAATTCAACTTTATTTCAAAGATGACAT
Found at i:15138 original size:51 final size:50
Alignment explanation
Indices: 15053--15238 Score: 257
Period size: 51 Copynumber: 3.7 Consensus size: 50
15043 AAAATGACAT
15053 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * * * * *
15103 TTTATTTACTAATTACTCTAAAAATTCAATTTTTTACTCAAAGATGACATT
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTATTCAAAGGTTAAATC
* * *
15154 TTTATTTACCATTTACTTAAAAA-ACAATCTTTTATTCAAAGGTTAAATC
1 TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
*
15203 TTTATTTACTAATTACTCTAAAAGTTCAATCTTTTA
1 TTTATTTACTAATTACT-TAAAAATTCAATCTTTTA
15239 CCCAAAGATG
Statistics
Matches: 114, Mismatches: 19, Indels: 5
0.83 0.14 0.04
Matches are distributed among these distances:
49 34 0.30
50 28 0.25
51 52 0.46
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (50 bp):
TTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATC
Found at i:15144 original size:100 final size:100
Alignment explanation
Indices: 15040--15289 Score: 355
Period size: 100 Copynumber: 2.5 Consensus size: 100
15030 CACTTCTATT
*
15040 TCAAAAATGACATTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
1 TCAAAGATGACATTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
*
15105 TATTTACTAATTACTCTAAAAATTCAATTTTTTAC
66 TATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * *
15140 TCAAAGATGACATTTTTATTTACCATTTACTTAAAAA-ACAATCTTTTATTCAAAGGTTAAATCT
1 TCAAAGATGACA-TTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCT
*
15204 TTATTTACTAATTACTCTAAAAGTTCAATCTTTTAC
65 TTATTTACTAATTACTCTAAAAATTCAATCTTTTAC
* * *
15240 CCAAAGATGACA-TTT-TTTACTTAAGTTA-TTAAAAGCTTCAACCTTTTATT
1 TCAAAGATGACATTTTATTTAC-TAA-TTACTTAAAA-ATTCAATCTTTTATT
15290 TACAAGCTAC
Statistics
Matches: 133, Mismatches: 12, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
97 5 0.04
98 10 0.08
99 3 0.02
100 93 0.70
101 22 0.17
ACGTcount: A:0.37, C:0.14, G:0.05, T:0.44
Consensus pattern (100 bp):
TCAAAGATGACATTTTATTTACTAATTACTTAAAAATTCAATCTTTTATTCAAAGGTTAAATCTT
TATTTACTAATTACTCTAAAAATTCAATCTTTTAC
Found at i:20737 original size:13 final size:13
Alignment explanation
Indices: 20719--20763 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
20709 ATTTTATTAC
20719 TGTTTTAATAAAT
1 TGTTTTAATAAAT
20732 TGTTTTAA-AAAT
1 TGTTTTAATAAAT
* *
20744 GGTTTTTGATAAAT
1 TG-TTTTAATAAAT
20758 TGTTTT
1 TGTTTT
20764 GGGTGCATGA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
12 5 0.19
13 17 0.63
14 5 0.19
ACGTcount: A:0.31, C:0.00, G:0.13, T:0.56
Consensus pattern (13 bp):
TGTTTTAATAAAT
Found at i:22480 original size:19 final size:19
Alignment explanation
Indices: 22436--22483 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
22426 CAGATAAACC
* * *
22436 CAAACAACCTGGAAATAGA
1 CAAACATCCAGGAAACAGA
22455 CAAACATCCAGGAAACAGA
1 CAAACATCCAGGAAACAGA
22474 CAAACATCCA
1 CAAACATCCA
22484 ATACATACAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.52, C:0.27, G:0.12, T:0.08
Consensus pattern (19 bp):
CAAACATCCAGGAAACAGA
Found at i:23160 original size:15 final size:15
Alignment explanation
Indices: 23131--23172 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
23121 CTCTCGCCTG
23131 CCCCTCT-TCCTCTTC
1 CCCCTCTCT-CTCTTC
**
23146 CCTTTCTCTCTCTTC
1 CCCCTCTCTCTCTTC
23161 CCCCTCTCTCTC
1 CCCCTCTCTCTC
23173 GACTCGACAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.43
Consensus pattern (15 bp):
CCCCTCTCTCTCTTC
Found at i:26545 original size:28 final size:29
Alignment explanation
Indices: 26514--26583 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 29
26504 ACCTAGAGGC
*
26514 ATTTTGGTCATTTTTTACATCCA-GGGGT
1 ATTTTGGTCATTTTGTACATCCAGGGGGT
* * *
26542 ATTTGGGTCA-TTTGTGCATCTAGGGGGT
1 ATTTTGGTCATTTTGTACATCCAGGGGGT
*
26570 ATTTTAGTCATTTT
1 ATTTTGGTCATTTT
26584 ACTAGTTCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
27 9 0.26
28 22 0.65
29 3 0.09
ACGTcount: A:0.17, C:0.11, G:0.24, T:0.47
Consensus pattern (29 bp):
ATTTTGGTCATTTTGTACATCCAGGGGGT
Found at i:28504 original size:16 final size:17
Alignment explanation
Indices: 28483--28515 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28473 GAAAAGAAGG
*
28483 CTCTTCCTTCT-CTCAT
1 CTCTTCCCTCTCCTCAT
28499 CTCTTCCCTCTCCTCAT
1 CTCTTCCCTCTCCTCAT
28516 AAAAATCTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.06, C:0.48, G:0.00, T:0.45
Consensus pattern (17 bp):
CTCTTCCCTCTCCTCAT
Found at i:32376 original size:40 final size:42
Alignment explanation
Indices: 32320--32404 Score: 138
Period size: 40 Copynumber: 2.1 Consensus size: 42
32310 AAAAGAAGGT
* *
32320 TTTTTTAAGCAACTCCAAAAGAAGATTTTTGGAAAATAAATG
1 TTTTTTAAGCAACTCCAAAAGAAGACTTTTGGAAAATAAAAG
32362 TTTTTT-A-CAACTCCAAAAGAAGACTTTTGGAAAATAAAAG
1 TTTTTTAAGCAACTCCAAAAGAAGACTTTTGGAAAATAAAAG
32402 TTT
1 TTT
32405 GGAAATCCAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
40 34 0.83
41 1 0.02
42 6 0.15
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (42 bp):
TTTTTTAAGCAACTCCAAAAGAAGACTTTTGGAAAATAAAAG
Found at i:32423 original size:37 final size:40
Alignment explanation
Indices: 32329--32431 Score: 140
Period size: 40 Copynumber: 2.6 Consensus size: 40
32319 TTTTTTTAAG
* * **
32329 CAACTCCAAAAGAAGATTTTTGGAAAATAAATGTTTTTTA
1 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
32369 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAG-TTTGGA
1 CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
*
32408 -AA-TCCAAGAGAAGACTTTTGGAAA
1 CAACTCCAAAAGAAGACTTTTGGAAA
32432 TTAATAAAAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
37 21 0.36
38 2 0.03
39 4 0.07
40 31 0.53
ACGTcount: A:0.45, C:0.12, G:0.17, T:0.27
Consensus pattern (40 bp):
CAACTCCAAAAGAAGACTTTTGGAAAATAAAAGTTTTGGA
Found at i:33850 original size:19 final size:19
Alignment explanation
Indices: 33832--33867 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33822 GGAAATTAAT
33832 TAAT-ATAATAATATATAA
1 TAATAATAATAATATATAA
*
33850 TAATAATAATATTATATA
1 TAATAATAATAATATATA
33868 TATACATGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
TAATAATAATAATATATAA
Found at i:33857 original size:16 final size:15
Alignment explanation
Indices: 33832--33871 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
33822 GGAAATTAAT
33832 TAATATAATAATATA
1 TAATATAATAATATA
33847 TAATAATAATAATATTA
1 TAAT-ATAATAATA-TA
33864 TATATATA
1 TA-ATATA
33872 CATGGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 7 0.32
18 2 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATAATAATATA
Done.