Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013492.1 Corchorus capsularis cultivar CVL-1 contig13513, 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: 87721
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:150 original size:32 final size:32
Alignment explanation
Indices: 106--192 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
96 AAAAACTAGC
*
106 CGAA-CCG-CCCACCGGGGCGGCCTGCCGAGG
1 CGAAGCCGCCCCACCGGGGCGGCCTGCCCAGG
* * *
136 CGAAGCCGCCCCACCGGGACGACCTGCCCTGG
1 CGAAGCCGCCCCACCGGGGCGGCCTGCCCAGG
* **
168 CTAAGCCGCCCCAGTGGGGCGGCCT
1 CGAAGCCGCCCCACCGGGGCGGCCT
193 TTTCATGGGG
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
30 4 0.09
31 3 0.07
32 39 0.85
ACGTcount: A:0.14, C:0.44, G:0.36, T:0.07
Consensus pattern (32 bp):
CGAAGCCGCCCCACCGGGGCGGCCTGCCCAGG
Found at i:2543 original size:28 final size:28
Alignment explanation
Indices: 2503--2559 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
2493 AATGTTGCAC
2503 TTATTTTGAATGGGAGGGAATATAAAGA
1 TTATTTTGAATGGGAGGGAATATAAAGA
2531 TTATTTTGAATGGGAGGGAATATAAAGA
1 TTATTTTGAATGGGAGGGAATATAAAGA
2559 T
1 T
2560 GGACGAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.39, C:0.00, G:0.28, T:0.33
Consensus pattern (28 bp):
TTATTTTGAATGGGAGGGAATATAAAGA
Found at i:3920 original size:31 final size:31
Alignment explanation
Indices: 3878--3938 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
3868 GAACTAACTC
*
3878 AAACATCCAAGATCTAAAGATCTTGAGACTT
1 AAACATCCAAGATCTAAAGATCTGGAGACTT
*
3909 AAACATTCAAGATCTAAAGATCTGGAGACT
1 AAACATCCAAGATCTAAAGATCTGGAGACT
3939 GATAACCCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.15, T:0.25
Consensus pattern (31 bp):
AAACATCCAAGATCTAAAGATCTGGAGACTT
Found at i:6130 original size:14 final size:15
Alignment explanation
Indices: 6111--6145 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
6101 TGTAATAACT
*
6111 AATCTCCCCAT-TCC
1 AATCTCCCCATCACC
6125 AATCTCCCCATCACC
1 AATCTCCCCATCACC
6140 AATCTC
1 AATCTC
6146 ACAACTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.58
15 8 0.42
ACGTcount: A:0.26, C:0.49, G:0.00, T:0.26
Consensus pattern (15 bp):
AATCTCCCCATCACC
Found at i:8008 original size:30 final size:30
Alignment explanation
Indices: 7972--8030 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
7962 AAATTATCAA
* *
7972 TTTTTTTATG-AATAAAAAGTTTAAGATCT
1 TTTTTTTTTGCAAGAAAAAGTTTAAGATCT
**
8001 TTTTTTTTTGCCGGAAAAAGTTTAAGATCT
1 TTTTTTTTTGCAAGAAAAAGTTTAAGATCT
8031 AGATAACCTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.32, C:0.07, G:0.14, T:0.47
Consensus pattern (30 bp):
TTTTTTTTTGCAAGAAAAAGTTTAAGATCT
Found at i:8815 original size:20 final size:21
Alignment explanation
Indices: 8780--8821 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
8770 GATGGGTAAA
*
8780 GTTAACGGTGTTAAGTAATTT
1 GTTAACGGTATTAAGTAATTT
8801 GTTAACGG-ATTAAGTAATTT
1 GTTAACGGTATTAAGTAATTT
8821 G
1 G
8822 CTTACAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.31, C:0.05, G:0.24, T:0.40
Consensus pattern (21 bp):
GTTAACGGTATTAAGTAATTT
Found at i:9631 original size:16 final size:16
Alignment explanation
Indices: 9605--9645 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 16
9595 ATTCATTTAT
9605 TATAGTATTAT-TATTA
1 TATA-TATTATATATTA
9621 TAATATATTATATATTA
1 T-ATATATTATATATTA
9638 TATATATT
1 TATATATT
9646 TTTAATATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (16 bp):
TATATATTATATATTA
Found at i:10212 original size:4 final size:4
Alignment explanation
Indices: 10205--10229 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
10195 TATATATATA
10205 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
10230 TTCTTCCTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:15475 original size:15 final size:14
Alignment explanation
Indices: 15453--15496 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
15443 ATAAAAATTA
15453 AATAATTTTATTTT
1 AATAATTTTATTTT
15467 AATATATTTTATTTT
1 AATA-ATTTTATTTT
* *
15482 ATTGAAATTTATTTT
1 AAT-AATTTTATTTT
15497 TGAAAAATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 21 0.81
16 1 0.04
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (14 bp):
AATAATTTTATTTT
Found at i:15494 original size:20 final size:20
Alignment explanation
Indices: 15457--15496 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
15447 AAATTAAATA
**
15457 ATTTTATTTTAATATATTTT
1 ATTTTATTGAAATATATTTT
*
15477 ATTTTATTGAAATTTATTTT
1 ATTTTATTGAAATATATTTT
15497 TGAAAAATAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.68
Consensus pattern (20 bp):
ATTTTATTGAAATATATTTT
Found at i:16814 original size:20 final size:20
Alignment explanation
Indices: 16789--16828 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
16779 TTATTTTTCA
**
16789 AAAATAAATTTCAATAAAAT
1 AAAATAAATTAAAATAAAAT
*
16809 AAAATATATTAAAATAAAAT
1 AAAATAAATTAAAATAAAAT
16829 TATTTAATTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATAAATTAAAATAAAAT
Found at i:16821 original size:15 final size:14
Alignment explanation
Indices: 16789--16832 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
16779 TTATTTTTCA
* *
16789 AAAATAAATTTCAAT
1 AAAATAAAATT-ATT
16804 AAAATAAAATATATT
1 AAAATAAAAT-TATT
16819 AAAATAAAATTATT
1 AAAATAAAATTATT
16833 TAATTTTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
14 4 0.15
15 21 0.81
16 1 0.04
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (14 bp):
AAAATAAAATTATT
Found at i:16835 original size:15 final size:15
Alignment explanation
Indices: 16803--16832 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16793 TAAATTTCAA
16803 TAAAATAAAATATAT
1 TAAAATAAAATATAT
16818 TAAAATAAAAT-TAT
1 TAAAATAAAATATAT
16832 T
1 T
16833 TAATTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATAAAATATAT
Found at i:22955 original size:437 final size:436
Alignment explanation
Indices: 22197--23001 Score: 1025
Period size: 438 Copynumber: 1.8 Consensus size: 436
22187 ACGCGTTACC
*
22197 TTTTATTTTTGTATTTTTTTCTATTTGTCCGATTAAACTGATTCAAGTGTCTATTAGAAAATAAT
1 TTTTATTTTTGTATTTTTTTCTATTTGTCCAATTAAACTGATTCAAGTGTCTATTAGAAAATAAT
* * * * ** *
22262 TTCATGATCTACAATTTTCATTAAGAACTCAAAACTCAATTTTAATGTTTTGATTATAAAAAAAC
66 TTAATAATCTACAACTTTCATTAAGAACTCAAAACTAAATTTTAATGTTTCAATTACAAAAAAAC
* * * *
22327 GCTTCCAAAATTTTGTGGTTTTGATTACCGGTTAATTTAATATCGTATAATTTTTTGTCCACATA
131 GCTTCCAAAATTTTGTCGTTTTGATTACCGGTTAATTTAATACCATATAATTTTTCGTCCACATA
* * * * * * *
22392 TCCGATTGAAGTTATTGAAGTGTCGGTTAAAAGGTTATTGCATGATTTACGACTTTCATGAAGGA
196 TCCAATTAAAGTTATTCAAGTCTCGGTTAAAAGGTTACTGCATAATTTACGACTTTCATGAAGAA
* * * *
22457 CCCGCAAGCTAAATTTGATCTACGAGTTTCGTGAAGGGTTCAAAAGGGAATTTTTATGTTTCAAA
261 CCCGAAAGCTAAATCTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAA
*
22522 ATCTCCATTAACAAACATTTTCTTATTTGGATTA-TTCATCAAATGACTCTCTTACTTTTCTTCT
326 ATCT-CATTAACAAACATTTTCTTATTTGAATTAGTT-ATCAAATGACTCTCTTACTTTTCTTCT
22586 TTATACTACTTAGTCCTTTATAAATTCTATCTTAATCTAACGTTTAAG
389 TTATACTACTTAGTCCTTTATAAATTCTATCTTAATCTAACGTTTAAG
** * * *
22634 TTTTATTTCTT-TATTCTTTGTTCTATTTGTCCAATTAAGTTGATTTATGTGTCTATTA-AAAGG
1 TTTTATTT-TTGTATT-TTT-TTCTATTTGTCCAATTAAACTGATTCAAGTGTCTATTAGAAA-A
* * *
22697 TAATTTAATAATTTACAACTTTCATTAAGGACTCAAAAGC-AAATTTTTATGTTTCAATT-CAAA
62 TAATTTAATAATCTACAACTTTCATTAAGAACTCAAAA-CTAAATTTTAATGTTTCAATTACAAA
* * * *** *
22760 AAAATGCTTCCTAAA-TTTGTTCGTTTTTATTGTTGGTCT-ATTTTATACCATATAA-TTTTCGA
126 AAAACGCTTCCAAAATTTTG-TCGTTTTGATTACCGGT-TAATTTAATACCATATAATTTTTCG-
* * * *
22822 TCCATATGTCCAATTAAAGTTATTCAAGTCTCGGTTAAAGGGTTACTGTATAATTTACGACTTTC
188 TCCACATATCCAATTAAAGTTATTCAAGTCTCGGTTAAAAGGTTACTGCATAATTTACGACTTTC
* *
22887 ATGAAGAACCCGAAAG-TTAATCTGATCTACGAGTTTTATGAAGGGTTCAAAAGGAAATTTTTAT
253 ATGAAGAACCCGAAAGCTAAATCTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTAT
* * *
22951 GTTTCAAGATCTCATTAACAGATATTTTCTTATTTGAATTAGTTATCAAAT
318 GTTTCAAAATCTCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAAT
23002 CACCCACATA
Statistics
Matches: 311, Mismatches: 48, Indels: 19
0.82 0.13 0.05
Matches are distributed among these distances:
436 33 0.11
437 77 0.25
438 118 0.38
439 82 0.26
440 1 0.00
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.43
Consensus pattern (436 bp):
TTTTATTTTTGTATTTTTTTCTATTTGTCCAATTAAACTGATTCAAGTGTCTATTAGAAAATAAT
TTAATAATCTACAACTTTCATTAAGAACTCAAAACTAAATTTTAATGTTTCAATTACAAAAAAAC
GCTTCCAAAATTTTGTCGTTTTGATTACCGGTTAATTTAATACCATATAATTTTTCGTCCACATA
TCCAATTAAAGTTATTCAAGTCTCGGTTAAAAGGTTACTGCATAATTTACGACTTTCATGAAGAA
CCCGAAAGCTAAATCTGATCTACGAGTTTCATGAAGGGTTCAAAAGGAAATTTTTATGTTTCAAA
ATCTCATTAACAAACATTTTCTTATTTGAATTAGTTATCAAATGACTCTCTTACTTTTCTTCTTT
ATACTACTTAGTCCTTTATAAATTCTATCTTAATCTAACGTTTAAG
Found at i:25771 original size:45 final size:45
Alignment explanation
Indices: 25716--25805 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
25706 AACAAAAGCT
* * *
25716 CATTCCCATAATATTGGTTATTTCTTGTTGATCTCCATGATAGCA
1 CATTCCCATAACATTGGTTACTTCTCGTTGATCTCCATGATAGCA
* * *
25761 CATTCTCATAACATTGGTTCCTTCTCGTTGATCTTCATGATAGCA
1 CATTCCCATAACATTGGTTACTTCTCGTTGATCTCCATGATAGCA
25806 ATTAAACACA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (45 bp):
CATTCCCATAACATTGGTTACTTCTCGTTGATCTCCATGATAGCA
Found at i:47420 original size:27 final size:27
Alignment explanation
Indices: 47365--47420 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
47355 GAAATAGTAC
* *
47365 ACATATCATGCAAATTTTTTTGATCAAT
1 ACATATCATGCAAATTTTGTTCA-CAAT
47393 ACATATCATGCAAATTTTAGTTCA-AAT
1 ACATATCATGCAAATTTT-GTTCACAAT
47420 A
1 A
47421 GTTTGATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 4 0.16
28 18 0.72
29 3 0.12
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.39
Consensus pattern (27 bp):
ACATATCATGCAAATTTTGTTCACAAT
Found at i:48981 original size:34 final size:34
Alignment explanation
Indices: 48911--49384 Score: 350
Period size: 34 Copynumber: 13.5 Consensus size: 34
48901 TGATTAATAT
* * *
48911 TTTATTCTTTACCATTTTTTCTTTACTGATTCCTC
1 TTTACTCTTTACCA-TTTTTCTTTACTAATTACTC
* *
48946 TTTAGTCTTTACCATTCTTCTTTACTAATTACTCTTTACTC
1 TTTACTCTTTACCATTTTTCTTTACT-A--A----TTACTC
48987 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
** * *
49021 TCCATTCTTTACCATTTTTCTTTACTGATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* *
49055 TTTACTGTTTACCATTTTTC--T--T-A--ACTG
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* *
49082 GTTACTCTTTACCATTTTCCTTTACTAATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* * * *
49116 TTCATTCTTTACCATTTTTTTTTACTGATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* ** ** ** *
49150 TTTTTTTACTCTTTACCCTTTACCATTTTTTCTTTACTA
1 ----TTTACTCTTTACCATTTTTC-TTTACTAATTACTC
* *
49189 ATTACTCTTTACCGTTTTTCTTTACTAATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* * *
49223 TTCATTCTTTACCATTTTTCTTTACTGATTACTCTTTACTT
1 TTTACTCTTTACCATTTTTCTTTACT-A--A----TTACTC
49264 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* * * * *
49298 TTCATTCTTTACCATTTTTATTTACTGATTATTC
1 TTTACTCTTTACCATTTTTCTTTACTAATTACTC
* * *
49332 TTTACTTTTTACCACTTTTCTTTTACTGATTACTC
1 TTTACTCTTTACCATTTTTC-TTTACTAATTACTC
* *
49367 TTTACTTTTTACTATTTT
1 TTTACTCTTTACCATTTT
49385 ACTGTTTAAT
Statistics
Matches: 346, Mismatches: 66, Indels: 54
0.74 0.14 0.12
Matches are distributed among these distances:
27 20 0.06
29 2 0.01
30 1 0.00
31 1 0.00
32 2 0.01
34 174 0.50
35 59 0.17
37 2 0.01
38 16 0.05
39 9 0.03
40 2 0.01
41 58 0.17
ACGTcount: A:0.18, C:0.22, G:0.02, T:0.57
Consensus pattern (34 bp):
TTTACTCTTTACCATTTTTCTTTACTAATTACTC
Found at i:48983 original size:14 final size:14
Alignment explanation
Indices: 48964--49021 Score: 64
Period size: 14 Copynumber: 4.2 Consensus size: 14
48954 TTACCATTCT
48964 TCTTTACTAATTAC
1 TCTTTACTAATTAC
**
48978 TCTTTACTCTTTAC
1 TCTTTACTAATTAC
* **
48992 TCTTTAC-CATTTT
1 TCTTTACTAATTAC
49005 TCTTTACTAATTAC
1 TCTTTACTAATTAC
49019 TCT
1 TCT
49022 CCATTCTTTA
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 10 0.29
14 25 0.71
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (14 bp):
TCTTTACTAATTAC
Found at i:48988 original size:41 final size:41
Alignment explanation
Indices: 48943--49066 Score: 154
Period size: 41 Copynumber: 3.2 Consensus size: 41
48933 TTACTGATTC
* *
48943 CTCTTTAGTCTTTACCATTCTTCTTTACTAATTACTCTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTA
48984 CTCTTTACTCTTTACCATTTTTCTTTACTAATTACTC--T-
1 CTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTA
* *
49022 C-C---ATTCTTTACCATTTTTCTTTACTGATTACTCTTTA
1 CTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTA
*
49059 CTGTTTAC
1 CTCTTTAC
49067 CATTTTTCTT
Statistics
Matches: 70, Mismatches: 6, Indels: 14
0.78 0.07 0.16
Matches are distributed among these distances:
34 29 0.41
36 1 0.01
37 2 0.03
38 1 0.01
39 1 0.01
41 36 0.51
ACGTcount: A:0.19, C:0.25, G:0.02, T:0.54
Consensus pattern (41 bp):
CTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTTTA
Found at i:49008 original size:27 final size:27
Alignment explanation
Indices: 48978--49261 Score: 96
Period size: 27 Copynumber: 9.8 Consensus size: 27
48968 TACTAATTAC
48978 TCTTTACTCTTTACTCTTTACCATTTT
1 TCTTTACTCTTTACTCTTTACCATTTT
* *
49005 TCTTTACTAATTACTCTCCATTCTTTACCATTTT
1 TCTTTAC----T-CT-T-TACTCTTTACCATTTT
*
49039 TCTTTACTGATTACTCTTTACTGTTTACCATTTT
1 TC--T--T--T-ACTCTTTACTCTTTACCATTTT
* **
49073 TCTTAACTGGTTACTCTTTACCATTTT
1 TCTTTACTCTTTACTCTTTACCATTTT
* **
49100 CCTTTACTAATTACTC-TT--CATTCTT
1 TCTTTACTCTTTACTCTTTACCATT-TT
* * **
49125 TACCATTT-TTTTTTACTGATTA-C-TCTTT
1 T--C-TTTACTCTTTACTCTTTACCAT-TTT
*
49153 T-TTTACTCTTTACCCTTTACCATTTTT
1 TCTTTACTCTTTACTCTTTACCA-TTTT
** *
49180 TCTTTACTAATTACTCTTTACCGTTTT
1 TCTTTACTCTTTACTCTTTACCATTTT
*
49207 TCTTTACTAATTACTCTTCATTCTTTACCATTTT
1 TCTTTAC----T-CT-TT-ACTCTTTACCATTTT
**
49241 TCTTTACTGATTACTCTTTAC
1 TCTTTACTCTTTACTCTTTAC
49262 TTTTTACTCT
Statistics
Matches: 190, Mismatches: 34, Indels: 66
0.66 0.12 0.23
Matches are distributed among these distances:
24 7 0.04
25 11 0.06
26 3 0.02
27 68 0.36
28 29 0.15
29 2 0.01
30 2 0.01
31 2 0.01
32 3 0.02
33 3 0.02
34 51 0.27
35 1 0.01
36 3 0.02
37 1 0.01
38 1 0.01
40 1 0.01
41 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.02, T:0.56
Consensus pattern (27 bp):
TCTTTACTCTTTACTCTTTACCATTTT
Found at i:49030 original size:75 final size:76
Alignment explanation
Indices: 48911--49343 Score: 289
Period size: 75 Copynumber: 6.1 Consensus size: 76
48901 TGATTAATAT
* * * **
48911 TTTATTCTTTACCATTTTTTCTTTACTGATTCCTCTTTAGTCTTTACCATTCTTCTTTACTAATT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTTCTTTACTAATT
48976 ACTCTTTACTC
66 ACTCTTTACTC
*
48987 TTTACTCTTTACCA-TTTTTCTTTACTAATTACTCTCCATTCTTTACCA---TT-TTT-CT--TT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTTCTTTACTAATT
**
49044 ACTGATTACTC
66 ACTCTTTACTC
* * **
49055 TTTACTGTTTACCA-TTTTTCTTAACTGGTTA--CT-----CTTTACCATT-TTCCTTTACTAAT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTT-CTTTACTAAT
49111 TACTC--T--TC
65 TACTCTTTACTC
* * * * * * * *
49119 ---ATTCTTTACCATTTTTT-TTTACTGATTACTCT---TTTTTTACTCTTTAC-CCTTTACCAT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTAC-CATT-CTTCTTTACTAA
** *
49176 TTTTTCTTTACTA
64 TTACTCTTTACTC
* * * * * *
49189 ATTACTCTTTACC-GTTTTTCTTTACTAATTACTCTTCATTCTTTACCATTTTTCTTTACTGATT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTTCTTTACTAATT
*
49253 ACTCTTTACTT
66 ACTCTTTACTC
* * * * *
49264 TTTACTCTTTACCA-TTTTTCTTTACTAATTACTCTTCATTCTTTACCATTTTTATTTACTGATT
1 TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTTCTTTACTAATT
* *
49328 ATTCTTTACTT
66 ACTCTTTACTC
49339 TTTAC
1 TTTAC
49344 CACTTTTCTT
Statistics
Matches: 288, Mismatches: 41, Indels: 57
0.75 0.11 0.15
Matches are distributed among these distances:
61 26 0.09
62 5 0.02
63 4 0.01
64 2 0.01
65 8 0.03
66 19 0.07
68 44 0.15
70 3 0.01
71 3 0.01
72 7 0.02
73 23 0.08
75 124 0.43
76 20 0.07
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.57
Consensus pattern (76 bp):
TTTACTCTTTACCATTTTTTCTTTACTAATTACTCTCCAGTCTTTACCATTCTTCTTTACTAATT
ACTCTTTACTC
Found at i:49091 original size:61 final size:61
Alignment explanation
Indices: 49026--49152 Score: 182
Period size: 61 Copynumber: 2.1 Consensus size: 61
49016 TACTCTCCAT
* * * * *
49026 TCTTTACCATTTTTCTTTACTGATTACTCTTTACTGTTTACCATTTTTCTTAACTGGTTAC
1 TCTTTACCATTTTCCTTTACTAATTACTCTTCACTCTTTACCATTTTTCTTAACTGATTAC
* * *
49087 TCTTTACCATTTTCCTTTACTAATTACTCTTCATTCTTTACCATTTTTTTTTACTGATTAC
1 TCTTTACCATTTTCCTTTACTAATTACTCTTCACTCTTTACCATTTTTCTTAACTGATTAC
49148 TCTTT
1 TCTTT
49153 TTTTACTCTT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.18, C:0.22, G:0.04, T:0.56
Consensus pattern (61 bp):
TCTTTACCATTTTCCTTTACTAATTACTCTTCACTCTTTACCATTTTTCTTAACTGATTAC
Found at i:49159 original size:45 final size:46
Alignment explanation
Indices: 49110--49198 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 46
49100 CCTTTACTAA
** *
49110 TTACTCTTCATTCTTTACCATTTTTT-TTTACTGATTACTCTTTTT
1 TTACTCTTCACCCTTTACCATTTTTTCTTTACTAATTACTCTTTTT
*
49155 TTACTCTTTACCCTTTACCATTTTTTCTTTACTAATTACTCTTT
1 TTACTCTTCACCCTTTACCATTTTTTCTTTACTAATTACTCTTT
49199 ACCGTTTTTC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
45 23 0.59
46 16 0.41
ACGTcount: A:0.17, C:0.22, G:0.01, T:0.60
Consensus pattern (46 bp):
TTACTCTTCACCCTTTACCATTTTTTCTTTACTAATTACTCTTTTT
Found at i:49165 original size:18 final size:18
Alignment explanation
Indices: 49132--49170 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
49122 CTTTACCATT
* *
49132 TTTTTTTACTGATTACTC
1 TTTTTTTACTCATTACCC
*
49150 TTTTTTTACTCTTTACCC
1 TTTTTTTACTCATTACCC
49168 TTT
1 TTT
49171 ACCATTTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.21, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTTTTTACTCATTACCC
Found at i:49212 original size:107 final size:102
Alignment explanation
Indices: 48914--49379 Score: 453
Period size: 107 Copynumber: 4.4 Consensus size: 102
48904 TTAATATTTT
* * * **
48914 ATTCTTTACCATTTTTTCTTTACTGATTCCTCTTTAGTCTTTACCATTCTTCTTTACTAATTACT
1 ATTCTTTACCA-TTTTTCTTTACTGATTACTCTTTACTCTTT---A--C-TCTTTAC-CATTTTT
** * *
48979 CTTTACTCTTTACTCTTTACCATTTTTCTTTACTAATTACTCTCC
58 CTTTACTAATTACTCTTTACCATTTTCCTTTACTAATTACTCTTC
* * *
49024 ATTCTTTACCATTTTTCTTTACTG---A----TTACTCTTTACTGTTTACCATTTTTCTTAACTG
1 ATTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACTCTTTACCATTTTTCTTTACTA
*
49082 GTTACTCTTTACCATTTTCCTTTACTAATTACTCTTC
66 ATTACTCTTTACCATTTTCCTTTACTAATTACTCTTC
* *
49119 ATTCTTTACCATTTTTTTTTACTGATTACTCTTTTTTTACTCTTTACCCTTTACCATTTTTTCTT
1 ATTCTTTACCATTTTTCTTTACTGATTACTC----TTTACTCTTTACTCTTTACCA-TTTTTCTT
* *
49184 TACTAATTACTCTTTACCGTTTTTCTTTACTAATTACTCTTC
61 TACTAATTACTCTTTACCATTTTCCTTTACTAATTACTCTTC
*
49226 ATTCTTTACCATTTTTCTTTACTGATTACTCTTTACTTTTTACTCTTTACCATTTTTCTTTACTA
1 ATTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACTCTTTACCATTTTTCTTTACTA
** * * *
49291 ATTACTCTTCATTCTTTACCATTTTTATTTACTGATTATTCTTT
66 ATTA-----C--TCTTTACCATTTTCCTTTACTAATTACTCTTC
* *
49335 ACTT-TTTACCACTTTTCTTTTACTGATTACTCTTTACTTTTTACT
1 A-TTCTTTACCATTTTTC-TTTACTGATTACTCTTTACTCTTTACT
49380 ATTTTACTGT
Statistics
Matches: 307, Mismatches: 28, Indels: 42
0.81 0.07 0.11
Matches are distributed among these distances:
95 67 0.22
96 6 0.02
97 1 0.00
98 1 0.00
99 1 0.00
102 25 0.08
103 19 0.06
106 18 0.06
107 76 0.25
109 53 0.17
110 40 0.13
ACGTcount: A:0.18, C:0.23, G:0.02, T:0.56
Consensus pattern (102 bp):
ATTCTTTACCATTTTTCTTTACTGATTACTCTTTACTCTTTACTCTTTACCATTTTTCTTTACTA
ATTACTCTTTACCATTTTCCTTTACTAATTACTCTTC
Found at i:49260 original size:14 final size:14
Alignment explanation
Indices: 49241--49299 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
49231 TTACCATTTT
*
49241 TCTTTACTGATTAC
1 TCTTTACTAATTAC
**
49255 TCTTTACTTTTTAC
1 TCTTTACTAATTAC
* **
49269 TCTTTAC-CATTTT
1 TCTTTACTAATTAC
49282 TCTTTACTAATTAC
1 TCTTTACTAATTAC
49296 TCTT
1 TCTT
49300 CATTCTTTAC
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
13 9 0.26
14 26 0.74
ACGTcount: A:0.19, C:0.22, G:0.02, T:0.58
Consensus pattern (14 bp):
TCTTTACTAATTAC
Found at i:49368 original size:15 final size:15
Alignment explanation
Indices: 49352--49409 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 15
49342 ACCACTTTTC
*
49352 TTTTACTGATTACT-
1 TTTTACTGTTTACTA
* *
49366 CTTTACTTTTTACTA
1 TTTTACTGTTTACTA
*
49381 TTTTACTGTTTAATA
1 TTTTACTGTTTACTA
*
49396 TTTTACTTTTTACT
1 TTTTACTGTTTACT
49410 GATTGCCATT
Statistics
Matches: 35, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
14 11 0.31
15 24 0.69
ACGTcount: A:0.21, C:0.14, G:0.03, T:0.62
Consensus pattern (15 bp):
TTTTACTGTTTACTA
Found at i:49387 original size:50 final size:50
Alignment explanation
Indices: 49332--49443 Score: 129
Period size: 50 Copynumber: 2.2 Consensus size: 50
49322 CTGATTATTC
* * *
49332 TTTACTTTTTACCACTTTT-C-TTTTACTGATTACTCTTTACTTTTTACTAT
1 TTTACTCTTTACCA-TTTTACTTTTTACTGATTAC-CATTACTTTTTACCAT
* ** *
49382 TTTACTGTTTAATATTTTACTTTTTACTGATTGCCATTACTTTTTACCAT
1 TTTACTCTTTACCATTTTACTTTTTACTGATTACCATTACTTTTTACCAT
49432 TTTACTCTTTAC
1 TTTACTCTTTAC
49444 TGATTGCCTT
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
49 4 0.08
50 36 0.69
51 12 0.23
ACGTcount: A:0.20, C:0.19, G:0.04, T:0.58
Consensus pattern (50 bp):
TTTACTCTTTACCATTTTACTTTTTACTGATTACCATTACTTTTTACCAT
Found at i:49428 original size:7 final size:7
Alignment explanation
Indices: 49361--49409 Score: 53
Period size: 7 Copynumber: 6.7 Consensus size: 7
49351 CTTTTACTGA
*
49361 TTACTCT
1 TTACTTT
49368 TTACTTT
1 TTACTTT
49375 TTACTATT
1 TTACT-TT
*
49383 TTACTGT
1 TTACTTT
*
49390 TTAATATT
1 TTACT-TT
49398 TTACTTT
1 TTACTTT
49405 TTACT
1 TTACT
49410 GATTGCCATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
7 23 0.66
8 12 0.34
ACGTcount: A:0.20, C:0.14, G:0.02, T:0.63
Consensus pattern (7 bp):
TTACTTT
Found at i:49579 original size:53 final size:53
Alignment explanation
Indices: 49522--49625 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
49512 ATTATTATTG
* * * *
49522 CTCTTTTCTTACTCTTTTTACTGGACATTGTTTCCTACTCTTTTTAGTGATGA
1 CTCTTTTCTTACTCTTTTTACTGAACACTATTTCCTACTCTTTTTACTGATGA
* *
49575 CTCTTTTCTTACTCTTTTTACTGAATACTATTTCTTACTCTTTTTACTGAT
1 CTCTTTTCTTACTCTTTTTACTGAACACTATTTCCTACTCTTTTTACTGAT
49626 TACTGATTAC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.16, C:0.21, G:0.08, T:0.55
Consensus pattern (53 bp):
CTCTTTTCTTACTCTTTTTACTGAACACTATTTCCTACTCTTTTTACTGATGA
Found at i:49582 original size:27 final size:26
Alignment explanation
Indices: 49525--49625 Score: 118
Period size: 26 Copynumber: 3.8 Consensus size: 26
49515 ATTATTGCTC
49525 TTTTCTTACTCTTTTTACTG--GACAT
1 TTTTCTTACTCTTTTTACTGATGAC-T
* *
49550 TGTTTCCTACTCTTTTTAGTGATGACT
1 T-TTTCTTACTCTTTTTACTGATGACT
49577 CTTTTCTTACTCTTTTTACTGAAT-ACT
1 -TTTTCTTACTCTTTTTACTG-ATGACT
*
49604 ATTTCTTACTCTTTTTACTGAT
1 TTTTCTTACTCTTTTTACTGAT
49626 TACTGATTAC
Statistics
Matches: 66, Mismatches: 5, Indels: 10
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.05
26 36 0.55
27 21 0.32
28 6 0.09
ACGTcount: A:0.17, C:0.20, G:0.08, T:0.55
Consensus pattern (26 bp):
TTTTCTTACTCTTTTTACTGATGACT
Found at i:53820 original size:23 final size:23
Alignment explanation
Indices: 53790--53837 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
53780 GAAGATAAAG
*
53790 AAGAAAAAATAAAAATAAAAATA
1 AAGAAAAAATAAAAAGAAAAATA
* *
53813 AAGAAAAATTTAAAAGAAAAATA
1 AAGAAAAAATAAAAAGAAAAATA
53836 AA
1 AA
53838 TCAGAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (23 bp):
AAGAAAAAATAAAAAGAAAAATA
Found at i:56269 original size:37 final size:37
Alignment explanation
Indices: 56149--56285 Score: 130
Period size: 37 Copynumber: 3.7 Consensus size: 37
56139 GCAGTGACTT
* * * * *
56149 GTAAGGGGAGCGCTGTGGTAAAGAGGGTGTTGTCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCA
* * * * * *
56186 GCAAGGATAACTCTGCGGTGAAGATGGGAGCCGCCGCA
1 GTAAGGAGAGCTCTGCGGTAAAGA-GGGTGCTGCCGCA
* *
56224 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTACCGCG
1 GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCA
* *
56261 GTAAGGAGAGTTCTGCGATAAAGAG
1 GTAAGGAGAGCTCTGCGGTAAAGAG
56286 TGTTATCGCA
Statistics
Matches: 78, Mismatches: 21, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
37 49 0.63
38 29 0.37
ACGTcount: A:0.26, C:0.16, G:0.40, T:0.18
Consensus pattern (37 bp):
GTAAGGAGAGCTCTGCGGTAAAGAGGGTGCTGCCGCA
Found at i:58246 original size:29 final size:30
Alignment explanation
Indices: 58209--58273 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 30
58199 CTCTAATGTA
*
58209 TGTGTGAAAT-TCA-TGGGCCTCTTTCAGTG
1 TGTGTGAAATAT-ATTGGGCCCCTTTCAGTG
*
58238 TGTGTGAAATATATTGGGCCCCTTTTAGTG
1 TGTGTGAAATATATTGGGCCCCTTTCAGTG
58268 TGTGTG
1 TGTGTG
58274 GATCAAATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 11 0.34
30 21 0.66
ACGTcount: A:0.17, C:0.14, G:0.29, T:0.40
Consensus pattern (30 bp):
TGTGTGAAATATATTGGGCCCCTTTCAGTG
Found at i:59265 original size:26 final size:26
Alignment explanation
Indices: 59235--59303 Score: 111
Period size: 26 Copynumber: 2.7 Consensus size: 26
59225 CTTAAGTCTA
59235 AGTTTATGAAATCTACACAGACTTGC
1 AGTTTATGAAATCTACACAGACTTGC
* * *
59261 GGTTTATGAAATCTACACATACTTGT
1 AGTTTATGAAATCTACACAGACTTGC
59287 AGTTTATGAAATCTACA
1 AGTTTATGAAATCTACA
59304 TAGAAATTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (26 bp):
AGTTTATGAAATCTACACAGACTTGC
Found at i:61096 original size:15 final size:15
Alignment explanation
Indices: 61078--61119 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
61068 TATTTGCATC
*
61078 ATATATATAATATTT
1 ATATATATAATATTA
*
61093 ATATATAAAATATTA
1 ATATATATAATATTA
*
61108 ATA-ATCTAATAT
1 ATATATATAATAT
61120 ATATTAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATATATAATATTA
Found at i:63094 original size:14 final size:15
Alignment explanation
Indices: 63070--63106 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
63060 GTTTTAGGCT
63070 TGTTT-AATTAA-CA
1 TGTTTAAATTAATCA
63083 TGTTTAAATTAATCA
1 TGTTTAAATTAATCA
63098 TGTTTAAAT
1 TGTTTAAAT
63107 GTTTAAATCG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 5 0.23
14 6 0.27
15 11 0.50
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.49
Consensus pattern (15 bp):
TGTTTAAATTAATCA
Found at i:66152 original size:36 final size:36
Alignment explanation
Indices: 66067--66152 Score: 91
Period size: 36 Copynumber: 2.4 Consensus size: 36
66057 TAGCCTGTGT
* * *
66067 CAGAGAAGCATCATGTGGTAAAACATCAGTTTGTGG
1 CAGAGAAGCAACATGTGGCAAAACATCAGTTTGCGG
* * * * *
66103 AAGAGAAGTAACATGTGGCATATCATCGGTTTGCGG
1 CAGAGAAGCAACATGTGGCAAAACATCAGTTTGCGG
*
66139 CAGAAAAGCAACAT
1 CAGAGAAGCAACAT
66153 ATCATAGAGC
Statistics
Matches: 39, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.27, T:0.22
Consensus pattern (36 bp):
CAGAGAAGCAACATGTGGCAAAACATCAGTTTGCGG
Found at i:72426 original size:15 final size:15
Alignment explanation
Indices: 72408--72457 Score: 72
Period size: 15 Copynumber: 3.6 Consensus size: 15
72398 CTAATTAAAT
72408 ACTAATTAATCATAA
1 ACTAATTAATCATAA
72423 ACTAATTAAT--T--
1 ACTAATTAATCATAA
72434 ACTAATTAATCATAA
1 ACTAATTAATCATAA
72449 ACTAATTAA
1 ACTAATTAA
72458 ATTAAACCTA
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
11 10 0.32
13 2 0.06
15 19 0.61
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (15 bp):
ACTAATTAATCATAA
Found at i:72428 original size:26 final size:26
Alignment explanation
Indices: 72398--72459 Score: 115
Period size: 26 Copynumber: 2.4 Consensus size: 26
72388 TTACTTAATT
72398 CTAATTAAATACTAATTAATCATAAA
1 CTAATTAAATACTAATTAATCATAAA
*
72424 CTAATTAATTACTAATTAATCATAAA
1 CTAATTAAATACTAATTAATCATAAA
72450 CTAATTAAAT
1 CTAATTAAAT
72460 TAAACCTACT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.37
Consensus pattern (26 bp):
CTAATTAAATACTAATTAATCATAAA
Found at i:72443 original size:11 final size:11
Alignment explanation
Indices: 72370--72443 Score: 53
Period size: 11 Copynumber: 6.5 Consensus size: 11
72360 ATGATTAATT
72370 TTAATTGACTAA
1 TTAATT-ACTAA
* * *
72382 TTAA-AATTAC
1 TTAATTACTAA
72392 TTAATT-CTAA
1 TTAATTACTAA
*
72402 TTAAATACTAA
1 TTAATTACTAA
72413 TTAATCATAAACTAA
1 TTAAT--T--ACTAA
72428 TTAATTACTAA
1 TTAATTACTAA
72439 TTAAT
1 TTAAT
72444 CATAAACTAA
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
10 14 0.29
11 18 0.38
12 4 0.08
13 2 0.04
15 10 0.21
ACGTcount: A:0.47, C:0.09, G:0.01, T:0.42
Consensus pattern (11 bp):
TTAATTACTAA
Found at i:77556 original size:31 final size:32
Alignment explanation
Indices: 77520--77587 Score: 104
Period size: 31 Copynumber: 2.2 Consensus size: 32
77510 ATAGAATAAA
77520 ATTTTCCATTTTACTCATACA-AA-TCCTTAT
1 ATTTTCCATTTTACTCATACATAAGTCCTTAT
*
77550 ACTTTTCCATTTTACTCATATATAAGTCCTTAT
1 A-TTTTCCATTTTACTCATACATAAGTCCTTAT
77583 ATTTT
1 ATTTT
77588 ACTCATGATG
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 1 0.03
31 19 0.56
32 6 0.18
33 8 0.24
ACGTcount: A:0.28, C:0.21, G:0.01, T:0.50
Consensus pattern (32 bp):
ATTTTCCATTTTACTCATACATAAGTCCTTAT
Found at i:79144 original size:24 final size:24
Alignment explanation
Indices: 79117--79173 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
79107 GAATGAAAAT
*
79117 AAAACCGAAGACACAAACCAAGGC
1 AAAACCGAAGACACAAACCAAGAC
*
79141 AAAACCAAAGACACAAACCAAGAC
1 AAAACCGAAGACACAAACCAAGAC
*
79165 AAAAACGAA
1 AAAACCGAA
79174 TATCCAGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.26, G:0.12, T:0.00
Consensus pattern (24 bp):
AAAACCGAAGACACAAACCAAGAC
Found at i:79165 original size:12 final size:13
Alignment explanation
Indices: 79118--79170 Score: 58
Period size: 12 Copynumber: 4.3 Consensus size: 13
79108 AATGAAAATA
*
79118 AAACCGAAGACAC
1 AAACCAAAGACAC
*
79131 AAACC-AAGGCA-
1 AAACCAAAGACAC
79142 AAACCAAAGACAC
1 AAACCAAAGACAC
*
79155 AAACC-AAGACAA
1 AAACCAAAGACAC
79167 AAAC
1 AAAC
79171 GAATATCCAG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
11 5 0.14
12 20 0.57
13 10 0.29
ACGTcount: A:0.60, C:0.28, G:0.11, T:0.00
Consensus pattern (13 bp):
AAACCAAAGACAC
Found at i:80480 original size:25 final size:26
Alignment explanation
Indices: 80446--80498 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
80436 CTTCACTTTC
80446 GTTATTGTTGT-CAAACGACCAGAAA
1 GTTATTGTTGTCCAAACGACCAGAAA
*
80471 GTTATTGTTGTCCAAATGACCAGAAA
1 GTTATTGTTGTCCAAACGACCAGAAA
80497 GT
1 GT
80499 CACCAAGCCT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.30
Consensus pattern (26 bp):
GTTATTGTTGTCCAAACGACCAGAAA
Found at i:82401 original size:24 final size:24
Alignment explanation
Indices: 82346--82403 Score: 98
Period size: 24 Copynumber: 2.4 Consensus size: 24
82336 AAAGACACGA
*
82346 ACCAAGACAAAAACGAAGACCCAG
1 ACCAAGGCAAAAACGAAGACCCAG
82370 ACCAAGGCAAAAACGAAGACCCAG
1 ACCAAGGCAAAAACGAAGACCCAG
*
82394 ACCTAGGCAA
1 ACCAAGGCAA
82404 TTCTGGTCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.50, C:0.29, G:0.19, T:0.02
Consensus pattern (24 bp):
ACCAAGGCAAAAACGAAGACCCAG
Found at i:83857 original size:3 final size:3
Alignment explanation
Indices: 83849--83888 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
83839 CATGCTGGGT
83849 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
83889 GTCATGGGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:85380 original size:14 final size:14
Alignment explanation
Indices: 85361--85397 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
85351 TCGATTAGAT
* *
85361 CCATCACCTCGTAC
1 CCATCAACTCGCAC
85375 CCATCAACTCGCAC
1 CCATCAACTCGCAC
85389 CCATCAACT
1 CCATCAACT
85398 AATCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.27, C:0.49, G:0.05, T:0.19
Consensus pattern (14 bp):
CCATCAACTCGCAC
Done.