Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006700.1 Corchorus capsularis cultivar CVL-1 contig06721, 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: 25628
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:3744 original size:68 final size:68
Alignment explanation
Indices: 3665--4323 Score: 614
Period size: 67 Copynumber: 10.0 Consensus size: 68
3655 TTTTTTTTTG
* *
3665 TTTT-TTT-TCCAAAAATACCCTTTCAGTCGAAGGGTCATTTTCGTCTTTTCGTATTTAAGTTTA
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
*
3728 GCA
66 GTA
* * *
3731 TTTTGTTTCTCCAAAAATACCCTTTCGATCGAAGGGTCATTTTCGTCTTTTCGCCTTTATGTTTA
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
3796 GTA
66 GTA
* * * * *
3799 TCTTGTTTTTCCAAAAATACCCTTTCGGTCGAGGGGTCATTCTCGTCTTTTCGCATTCAAGTTTA
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
*
3864 GCA
66 GTA
* ** * * *
3867 TTCTCATTC-CCAAAAATACCCTTTCGGTCAAAGGGTCA-TTTCTGTCTTTTTGCATCTAAGTTT
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTC-GTCTTTTCGCATTTAAGTTT
3930 AGTA
65 AGTA
* * * * *
3934 TCTTGTTTTTTCCAAAAATACCCTTTCAGTGGAAGGGTCATTTTCGTCTTTTCGCATTTTAGTTT
1 TTTTG-TTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTT
*
3999 AGCA
65 AGTA
* *
4003 TTTTGTTTCTCCAAAAATA-CC-TT---T------GTCATTTTCGTCTTTT-GCATTCAAGTTCA
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
4056 GTA
66 GTA
* ** * *
4059 TTCTCATTC-CCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCCTTT-GCATTTAAGTTTA
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
4122 GTA
66 GTA
* * * * *
4125 TTTTCTTT-TCCCAAGAGTACCCTTTCGGTCAAAGGGTCATTGTT-GTCTTTT-GCATTCAAGTT
1 TTTTGTTTCT-CCAAAAATACCCTTTCGGTCGAAGGGTCATT-TTCGTCTTTTCGCATTTAAGTT
4187 TAGTA
64 TAGTA
** * * * * * *
4192 TCTTCATTTC-CAAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTTTTGCATCTGAGTCT
1 T-TTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTT
4256 AG--
65 AGTA
* * * * * *
4258 TTTTGTAT-TCCAAAAATGCCTTTTCGGT-GAAAGGGTCAGTTTCTTCATTTTTCGCATCTAAGT
1 TTTTGTTTCTCCAAAAATACCCTTTCGGTCG-AAGGGTCATTTTCGTC--TTTTCGCATTTAAGT
4321 TTA
63 TTA
4324 CTTGCAAATT
Statistics
Matches: 483, Mismatches: 82, Indels: 55
0.78 0.13 0.09
Matches are distributed among these distances:
55 9 0.02
56 20 0.04
57 18 0.04
60 1 0.00
63 1 0.00
64 1 0.00
65 33 0.07
66 47 0.10
67 151 0.31
68 148 0.31
69 50 0.10
70 4 0.01
ACGTcount: A:0.21, C:0.20, G:0.15, T:0.43
Consensus pattern (68 bp):
TTTTGTTTCTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTA
GTA
Found at i:3851 original size:136 final size:134
Alignment explanation
Indices: 3666--4300 Score: 673
Period size: 136 Copynumber: 4.8 Consensus size: 134
3656 TTTTTTTTGT
* *
3666 TTTTTTTCCAAAAATACCCTTTCAGTCGAAGGGTCATTTTCGTCTTTTCGTATTTAAGTTTAGCA
1 TTTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAGCA
* * * * * *
3731 TTTTGTTTCTCCAAAAATACCCTTTCGATCGAAGGGTCATTTTCGTCTTTTCGCCTTTATGTTTA
66 TTTTCTTTCTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTT-GCATTCAAGTTTA
3796 GTATC
130 GTATC
* * *
3801 TTGTTTTTCCAAAAATACCCTTTCGGTCGAGGGGTCATTCTCGTCTTTTCGCATTCAAGTTTAGC
1 TT-TTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAGC
* *
3866 ATTCTCATTC-CCAAAAATACCCTTTCGGTCAAAGGGTCA-TTTCTGTCTTTTTGCA-TCTAAGT
65 ATTTTCTTTCTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTC-GTC-TTTTGCATTC-AAGT
3928 TTAGTATC
127 TTAGTATC
* * *
3936 TTGTTTTTTCCAAAAATACCCTTTCAGTGGAAGGGTCATTTTCGTCTTTTCGCATTTTAGTTTAG
1 -T-TTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAG
* *
4001 CATTTTGTTTCTCCAAAAATA-CC-TT---T------GTCATTTTCGTCTTTTGCATTCAAGTTC
64 CATTTTCTTTCTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTGCATTCAAGTTT
4055 AGTAT-
129 AGTATC
** * * * *
4060 TCTCATTCCCAAAAATACCCTTTCGGTGGAAGGGTCATTTTCGTCCTTT-GCATTTAAGTTTAGT
1 T-TTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAGC
* *
4124 ATTTTCTTT-TCCCAAGAGTACCCTTTCGGTCAAAGGGTCATTGTT-GTCTTTTGCATTCAAGTT
65 ATTTTCTTTCT-CCAAAAATACCCTTTCGGTCAAAGGGTCATT-TTCGTCTTTTGCATTCAAGTT
4187 TAGTATC
128 TAGTATC
** * * * * *
4194 TTCATTTCCAAAAAATACCCTTCCGGTCGAAGGGTCATTTTCGTCTTTTTGCATCTGAGTCTAG-
1 TTTTTTTCC-AAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAGC
* * * * * *
4258 -TTTTGTAT-TCCAAAAATGCCTTTTCGGTGAAAGGGTCAGTTTC
65 ATTTTCTTTCTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTC
4301 TTCATTTTTC
Statistics
Matches: 424, Mismatches: 50, Indels: 55
0.80 0.09 0.10
Matches are distributed among these distances:
121 1 0.00
122 28 0.07
123 45 0.11
124 2 0.00
125 17 0.04
126 9 0.02
127 5 0.01
131 2 0.00
132 26 0.06
133 43 0.10
134 44 0.10
135 58 0.14
136 134 0.32
137 10 0.02
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (134 bp):
TTTTTTTCCAAAAATACCCTTTCGGTCGAAGGGTCATTTTCGTCTTTTCGCATTTAAGTTTAGCA
TTTTCTTTCTCCAAAAATACCCTTTCGGTCAAAGGGTCATTTTCGTCTTTTGCATTCAAGTTTAG
TATC
Found at i:7789 original size:15 final size:16
Alignment explanation
Indices: 7769--7798 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
7759 TCATACATAC
7769 CCAAATAC-CAAATAT
1 CCAAATACTCAAATAT
7784 CCAAATACTCAAATA
1 CCAAATACTCAAATA
7799 CCCATCAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (16 bp):
CCAAATACTCAAATAT
Found at i:12414 original size:21 final size:21
Alignment explanation
Indices: 12388--12436 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
12378 GCACTGGAGG
* * *
12388 ACATGGGTCGCGAGGCAAACC
1 ACATGGGGCGCCAAGCAAACC
*
12409 ACATGGGGCGCCAAGCATACC
1 ACATGGGGCGCCAAGCAAACC
12430 ACATGGG
1 ACATGGG
12437 CCCCCAATTG
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:0.29, C:0.29, G:0.33, T:0.10
Consensus pattern (21 bp):
ACATGGGGCGCCAAGCAAACC
Found at i:13214 original size:83 final size:83
Alignment explanation
Indices: 13072--13235 Score: 319
Period size: 83 Copynumber: 2.0 Consensus size: 83
13062 TGGATTGCTT
13072 GCAATCCATGAGTAGCTAAACCTTAATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATTATC
1 GCAATCCATGAGTAGCTAAACCTTAATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATTATC
13137 GGTGAGACTTTTGTTCAA
66 GGTGAGACTTTTGTTCAA
*
13155 GCAATCCATGAGTAGCTAAACCTTAATACTTCTTTTCCTTAGGTACTTTTGATCGATGAATTATC
1 GCAATCCATGAGTAGCTAAACCTTAATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATTATC
13220 GGTGAGACTTTTGTTC
66 GGTGAGACTTTTGTTC
13236 TTAATAATTT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (83 bp):
GCAATCCATGAGTAGCTAAACCTTAATACTTCTTTTCCTTAGGTACTTTTGATCAATGAATTATC
GGTGAGACTTTTGTTCAA
Found at i:14765 original size:30 final size:28
Alignment explanation
Indices: 14658--14881 Score: 117
Period size: 30 Copynumber: 7.6 Consensus size: 28
14648 ATCCAATAAT
*
14658 TAAAGTCCTCAAACACA-AGGGCAT-T-TA
1 TAAAGTCC-CAAACACAGA-GGCATCTATC
14685 T-AAGTCCCTAAACACAGAGGCATCTATATC
1 TAAAGTCCC-AAACACAGAGGCATC--TATC
* * *
14715 AAAAGTCCTCAACTAAACACAGAGGCAACTCTC
1 TAAAGT-C-C--C-AAACACAGAGGCATCTATC
14748 TACAAGTCCTCAAACACA-AGGGCA--T-TC
1 TA-AAGTCC-CAAACACAGA-GGCATCTATC
* *
14775 -ATAAGTCCCTAAACACAGAGACATCTCTC
1 TA-AAGTCCC-AAACACAGAGGCATCTATC
*
14804 TCAAAGTCCTCAAGCACA-AGGGCATCTATAC
1 T-AAAGTCC-CAAACACAGA-GGCATCTAT-C
14835 TAAAGTCCCTAAACACAGAGGCATCTATAC
1 TAAAGTCCC-AAACACAGAGGCATCTAT-C
14865 TAAAGTCCCCAAACACA
1 TAAAGT-CCCAAACACA
14882 TATAACACTG
Statistics
Matches: 159, Mismatches: 12, Indels: 49
0.72 0.05 0.22
Matches are distributed among these distances:
25 2 0.01
26 35 0.22
27 5 0.03
28 2 0.01
29 6 0.04
30 68 0.43
31 13 0.08
32 2 0.01
33 6 0.04
34 4 0.03
35 16 0.10
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (28 bp):
TAAAGTCCCAAACACAGAGGCATCTATC
Found at i:14789 original size:56 final size:60
Alignment explanation
Indices: 14727--14881 Score: 196
Period size: 56 Copynumber: 2.6 Consensus size: 60
14717 AAGTCCTCAA
*
14727 CTAAACACAGAGGCAACTCTCTACAAGTCCTCAAACACAAGGGCAT-T-CA-T-AAGTCC
1 CTAAACACAGAGGCATCTCTCTACAAGTCCTCAAACACAAGGGCATCTACACTAAAGTCC
* * *
14783 CTAAACACAGAGACATCTCTCT-CAAAGTCCTCAAGCACAAGGGCATCTATACTAAAGTCC
1 CTAAACACAGAGGCATCTCTCTAC-AAGTCCTCAAACACAAGGGCATCTACACTAAAGTCC
* *
14843 CTAAACACAGAGGCATCTATACTA-AAGTCCCCAAACACA
1 CTAAACACAGAGGCATCTCT-CTACAAGTCCTCAAACACA
14882 TATAACACTG
Statistics
Matches: 84, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
55 1 0.01
56 41 0.49
57 1 0.01
58 1 0.01
59 1 0.01
60 37 0.44
61 2 0.02
ACGTcount: A:0.39, C:0.30, G:0.13, T:0.18
Consensus pattern (60 bp):
CTAAACACAGAGGCATCTCTCTACAAGTCCTCAAACACAAGGGCATCTACACTAAAGTCC
Found at i:16517 original size:2 final size:2
Alignment explanation
Indices: 16505--16537 Score: 57
Period size: 2 Copynumber: 16.0 Consensus size: 2
16495 TAGACTTATC
16505 TA TA CTA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
16538 AAGTACGAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 28 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17663 original size:23 final size:23
Alignment explanation
Indices: 17631--17675 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
17621 GTTCGGGTTA
17631 TTCGGCTCTCGGATCATACGGGT
1 TTCGGCTCTCGGATCATACGGGT
* * *
17654 TTCGGGTCTCGGGTCATTCGGG
1 TTCGGCTCTCGGATCATACGGG
17676 CTCCCGGTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.09, C:0.24, G:0.36, T:0.31
Consensus pattern (23 bp):
TTCGGCTCTCGGATCATACGGGT
Found at i:17675 original size:16 final size:15
Alignment explanation
Indices: 17592--17661 Score: 52
Period size: 16 Copynumber: 4.5 Consensus size: 15
17582 GGTAGTTTTC
17592 TCGGGTCATTCGGGT
1 TCGGGTCATTCGGGT
*
17607 TATGGGTCA-TCTGGGT
1 T-CGGGTCATTC-GGGT
* *
17623 TCGGGTTATTCGGCT
1 TCGGGTCATTCGGGT
* *
17638 CTCGGATCATACGGGTT
1 -TCGGGTCATTCGGG-T
17655 TCGGGTC
1 TCGGGTC
17662 TCGGGTCATT
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
15 11 0.27
16 29 0.71
17 1 0.02
ACGTcount: A:0.10, C:0.20, G:0.36, T:0.34
Consensus pattern (15 bp):
TCGGGTCATTCGGGT
Found at i:17980 original size:42 final size:42
Alignment explanation
Indices: 17932--18013 Score: 164
Period size: 42 Copynumber: 2.0 Consensus size: 42
17922 TTGATATTAA
17932 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAAT
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAAT
17974 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
1 TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTA
18014 TGTGTCAACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.38, C:0.05, G:0.17, T:0.40
Consensus pattern (42 bp):
TTTTGAATATTAAATACATAATTAATTATCAGGTGGGGTAAT
Found at i:18570 original size:32 final size:32
Alignment explanation
Indices: 18532--18622 Score: 112
Period size: 32 Copynumber: 2.8 Consensus size: 32
18522 CGGGTTAACT
** *
18532 TCTCGGGTTTTTCGAGTTTCGGGTCATATGAA
1 TCTCGGGTCATTCGGGTTTCGGGTCATATGAA
* * *
18564 TCTCGGGTCATTCGGGTTTCGGGTTATCTGGA
1 TCTCGGGTCATTCGGGTTTCGGGTCATATGAA
18596 T-TACGGGTCATTCGGGTTTCGGGTCAT
1 TCT-CGGGTCATTCGGGTTTCGGGTCAT
18623 CTGGGTTGCG
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 1 0.02
32 50 0.98
ACGTcount: A:0.12, C:0.18, G:0.32, T:0.38
Consensus pattern (32 bp):
TCTCGGGTCATTCGGGTTTCGGGTCATATGAA
Found at i:18585 original size:16 final size:16
Alignment explanation
Indices: 18547--18637 Score: 78
Period size: 16 Copynumber: 5.7 Consensus size: 16
18537 GGTTTTTCGA
* *
18547 GTTTCGGGTCATATGA
1 GTTTCGGGTCATCTGG
* *
18563 ATCTCGGGTCAT-TCGG
1 GTTTCGGGTCATCT-GG
*
18579 GTTTCGGGTTATCTGG
1 GTTTCGGGTCATCTGG
* *
18595 ATTACGGGTCAT-TCGG
1 GTTTCGGGTCATCT-GG
18611 GTTTCGGGTCATCTGG
1 GTTTCGGGTCATCTGG
*
18627 GTTGCGGGTCA
1 GTTTCGGGTCA
18638 CGGGTTTGTA
Statistics
Matches: 59, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
15 2 0.03
16 55 0.93
17 2 0.03
ACGTcount: A:0.12, C:0.18, G:0.35, T:0.35
Consensus pattern (16 bp):
GTTTCGGGTCATCTGG
Found at i:18625 original size:32 final size:31
Alignment explanation
Indices: 18542--18644 Score: 120
Period size: 32 Copynumber: 3.3 Consensus size: 31
18532 TCTCGGGTTT
* * *
18542 TTCGAGTTTCGGGTCATATGAATCTCGGGTCA
1 TTCGGGTTTCGGGTCATCTGGAT-TCGGGTCA
*
18574 TTCGGGTTTCGGGTTATCTGGATTACGGGTCA
1 TTCGGGTTTCGGGTCATCTGGATT-CGGGTCA
*
18606 TTCGGGTTTCGGGTCATCTGGGTTGCGGGTCA
1 TTCGGGTTTCGGGTCATCTGGATT-CGGGTCA
18638 --CGGGTTT
1 TTCGGGTTT
18645 GTAGGGTCTC
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
30 7 0.11
31 1 0.02
32 55 0.87
ACGTcount: A:0.12, C:0.17, G:0.35, T:0.36
Consensus pattern (31 bp):
TTCGGGTTTCGGGTCATCTGGATTCGGGTCA
Found at i:18726 original size:26 final size:27
Alignment explanation
Indices: 18697--18747 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
18687 TGGTCAAAAC
*
18697 GGGTTGGGCGGGTT-TCGGGTTCGGAT
1 GGGTTGGGCGGGTTCTCGGATTCGGAT
*
18723 GGGTTGGGCGGTTTCTCGGATTCGG
1 GGGTTGGGCGGGTTCTCGGATTCGG
18748 GGTCAGGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 13 0.59
27 9 0.41
ACGTcount: A:0.04, C:0.14, G:0.51, T:0.31
Consensus pattern (27 bp):
GGGTTGGGCGGGTTCTCGGATTCGGAT
Found at i:19578 original size:52 final size:52
Alignment explanation
Indices: 19522--19625 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 52
19512 AGTGTAAGAA
*
19522 CATGAAAAATATGAATCCAATGAAGGCGTTATTTTGAGTGCCCCAAGATAGT
1 CATGAAAAATATGAATCCAATGAAGACGTTATTTTGAGTGCCCCAAGATAGT
* * *
19574 CATGAGAAATATGAATCCAATGAAGACGTTATTTTGAGTGTCCCAAGGTAGT
1 CATGAAAAATATGAATCCAATGAAGACGTTATTTTGAGTGCCCCAAGATAGT
19626 TTATTTTAGA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (52 bp):
CATGAAAAATATGAATCCAATGAAGACGTTATTTTGAGTGCCCCAAGATAGT
Found at i:20135 original size:26 final size:25
Alignment explanation
Indices: 20106--20162 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 25
20096 TCTTTCTTTC
20106 TATTTCCAATATTATCCTTTATCTCT
1 TATTT-CAATATTATCCTTTATCTCT
**
20132 TATTGTTTATATTATCCTTTATCTCT
1 TATT-TCAATATTATCCTTTATCTCT
20158 TATTT
1 TATTT
20163 TTATTACTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 1 0.04
26 26 0.93
27 1 0.04
ACGTcount: A:0.21, C:0.18, G:0.02, T:0.60
Consensus pattern (25 bp):
TATTTCAATATTATCCTTTATCTCT
Found at i:22302 original size:38 final size:37
Alignment explanation
Indices: 22254--22334 Score: 103
Period size: 38 Copynumber: 2.2 Consensus size: 37
22244 AATTCAAAAA
* *
22254 TTAAT-ACTATTATTCAACGTAATTTA-TAATAATATT
1 TTAATAACTATT-TTAAACATAATTTAGTAATAATATT
*
22290 TTAGATAACTATTTTAAATATAATTTAGTAATAATATT
1 TTA-ATAACTATTTTAAACATAATTTAGTAATAATATT
22328 TTAATAA
1 TTAATAA
22335 TCAATAAATT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
36 3 0.08
37 17 0.44
38 19 0.49
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (37 bp):
TTAATAACTATTTTAAACATAATTTAGTAATAATATT
Found at i:22303 original size:25 final size:24
Alignment explanation
Indices: 22275--22335 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
22265 ATTCAACGTA
*
22275 ATTTATAATAATATTTTAG-ATAACT
1 ATTT-TAATAATAATTTAGAATAA-T
22300 ATTTTAA-ATATAATTTAGTAATAAT
1 ATTTTAATA-ATAATTTAG-AATAAT
22325 ATTTTAATAAT
1 ATTTTAATAAT
22336 CAATAAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
23 1 0.03
24 11 0.35
25 14 0.45
26 5 0.16
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (24 bp):
ATTTTAATAATAATTTAGAATAAT
Found at i:25460 original size:25 final size:24
Alignment explanation
Indices: 25418--25484 Score: 84
Period size: 25 Copynumber: 2.8 Consensus size: 24
25408 TCTCAACCTT
*
25418 CAAATCCT-AAACTTCATTTCTAA
1 CAAATCTTCAAACTTCATTTCTAA
* *
25441 CAACTTCTTCAAACTTCATTTTTAA
1 CAA-ATCTTCAAACTTCATTTCTAA
25466 CAAATCTTCAAA-TTCATTT
1 CAAATCTTCAAACTTCATTT
25485 TCCTTCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.26
24 11 0.29
25 17 0.45
ACGTcount: A:0.36, C:0.24, G:0.00, T:0.40
Consensus pattern (24 bp):
CAAATCTTCAAACTTCATTTCTAA
Found at i:25523 original size:26 final size:26
Alignment explanation
Indices: 25494--25561 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
25484 TTCCTTCATT
25494 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
25520 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
25546 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
25562 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:25585 original size:52 final size:51
Alignment explanation
Indices: 25494--25597 Score: 122
Period size: 52 Copynumber: 2.0 Consensus size: 51
25484 TTCCTTCATT
* *
25494 TTAATCATAAACTAATTAAATACTAATTAATAATAAACTAATTAGATACTAA
1 TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTA-AAACTAA
* * *
25546 TTAAACATAAACTAA-TAAACTAAGTAATT-TTAATTAACTAATTAAAACTAA
1 TTAAACATAAACTAATTAAA-T-ACTAATTAATAATAAACTAATTAAAACTAA
25597 T
1 T
25598 CATAAACTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
51 11 0.24
52 28 0.62
53 6 0.13
ACGTcount: A:0.54, C:0.10, G:0.02, T:0.35
Consensus pattern (51 bp):
TTAAACATAAACTAATTAAATACTAATTAATAATAAACTAATTAAAACTAA
Done.