Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006259.1 Corchorus capsularis cultivar CVL-1 contig06278, 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: 39833
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Found at i:130 original size:21 final size:21
Alignment explanation
Indices: 104--143 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
94 ATTGGATATG
104 TTGATTTTGTGTTTGTTTATT
1 TTGATTTTGTGTTTGTTTATT
125 TTGATTTTGTGTTTGTTTA
1 TTGATTTTGTGTTTGTTTA
144 ATTGCTGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.10, C:0.00, G:0.20, T:0.70
Consensus pattern (21 bp):
TTGATTTTGTGTTTGTTTATT
Found at i:1146 original size:2 final size:2
Alignment explanation
Indices: 1139--1191 Score: 65
Period size: 2 Copynumber: 27.0 Consensus size: 2
1129 AAAGAAAAAC
* *
1139 AT AT AT AT -T A- AT AT AT AT AT CT AT AT AT AT AT AT AT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1179 AT AGT AT AT AT AT
1 AT A-T AT AT AT AT
1192 TTTATGTAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
1 2 0.05
2 40 0.91
3 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6325 original size:39 final size:39
Alignment explanation
Indices: 6282--6359 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
6272 TTACCTTGTT
*
6282 ACACCATTTTATCCCATTTGAATCATGTTCTATGAATTC
1 ACACCATTTTATCCCATTTGAATCATGTTCTATAAATTC
*
6321 ACACCATTTTATCCCATTTGGATCATGTTCTATAAATTC
1 ACACCATTTTATCCCATTTGAATCATGTTCTATAAATTC
6360 TCACAATTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (39 bp):
ACACCATTTTATCCCATTTGAATCATGTTCTATAAATTC
Found at i:7037 original size:106 final size:107
Alignment explanation
Indices: 6548--7080 Score: 906
Period size: 107 Copynumber: 5.0 Consensus size: 107
6538 TGGAGCTAAA
* * *
6548 AAAAATGCAAGGAGTGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
1 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
*
6613 GCACTTTAAACTTGGGTCGCACCTCAAGAAGATATTGTTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTTT
* *
6655 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTTAGAGAGTATTTCCTGAGTATT
1 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
* *
6720 GCACTTTAAACTTGGGTCACATCTCAAGAAAATATTGTTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTTT
* *
6762 AAAATTGTAAGAAACGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
1 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
* * *
6827 ACATTTTAAACTTGGGTCGCATCTCAAGAAAATATTGTTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTTT
*
6869 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTACATCTCAGAGAGTATTTCCTGAGTGTT
1 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
* *
6934 GCACTTTAAACTTGGGTCACACCTTAAGAAAATATTGTTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTTT
6976 -AAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
1 AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
*
7040 GCACTTTAAACTTGGGTCGCACCTGAAGAAAATATTGTTTT
66 GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTT
7081 CTATCAACGT
Statistics
Matches: 400, Mismatches: 26, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
106 102 0.25
107 298 0.75
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (107 bp):
AAAATTGCAAGAAGCGTTGCACCTTAGAGTTTTAGTTGCATCTCAGAGAGTATTTCCTGAGTGTT
GCACTTTAAACTTGGGTCGCACCTCAAGAAAATATTGTTTTT
Found at i:14406 original size:21 final size:21
Alignment explanation
Indices: 14382--14430 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
14372 CAGCTGGGGG
* * *
14382 CCCATGTGGTATGCTTGGCGC
1 CCCATGTGGTATGCCTCGCGA
*
14403 CCCATGTGGTTTGCCTCGCGA
1 CCCATGTGGTATGCCTCGCGA
14424 CCCATGT
1 CCCATGT
14431 CCTTCAGTGC
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:0.10, C:0.33, G:0.29, T:0.29
Consensus pattern (21 bp):
CCCATGTGGTATGCCTCGCGA
Found at i:20243 original size:21 final size:21
Alignment explanation
Indices: 20210--20258 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
20200 AAGAATTGTA
**
20210 GCTT-CTTGGAAATGGCTCTT
1 GCTTCCTTGGAAATCCCTCTT
*
20230 GCTTCCTTTGAAATCCCTCTT
1 GCTTCCTTGGAAATCCCTCTT
20251 GCATTCCT
1 GC-TTCCT
20259 AAAGCATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.14, C:0.29, G:0.16, T:0.41
Consensus pattern (21 bp):
GCTTCCTTGGAAATCCCTCTT
Found at i:23610 original size:15 final size:16
Alignment explanation
Indices: 23590--23619 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
23580 AAAAAAATTT
23590 TCTTTTT-TTTTTCTC
1 TCTTTTTCTTTTTCTC
23605 TCTTTTTCTTTTTCT
1 TCTTTTTCTTTTTCT
23620 TCCCTTCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (16 bp):
TCTTTTTCTTTTTCTC
Found at i:24770 original size:36 final size:36
Alignment explanation
Indices: 24638--24756 Score: 158
Period size: 36 Copynumber: 3.4 Consensus size: 36
24628 CTCTTTTTAG
*
24638 ATTAAGTTCTTTATTGACTTCACTTAATTACCTTGA
1 ATTAAGTTCTTTATTGACTTCACTTAATTACCCTGA
24674 ATTAAGTTCTTTATT--C-T-ACTTAATTACCCTGA
1 ATTAAGTTCTTTATTGACTTCACTTAATTACCCTGA
* * *
24706 ATTAAG-CCTTTTATTGACTTCGCTTAATTACCCTAA
1 ATTAAGTTC-TTTATTGACTTCACTTAATTACCCTGA
24742 ATTAAGTTCTTTATT
1 ATTAAGTTCTTTATT
24757 CTACTTAATT
Statistics
Matches: 72, Mismatches: 5, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
31 1 0.01
32 26 0.36
33 1 0.01
34 2 0.03
35 1 0.01
36 40 0.56
37 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.47
Consensus pattern (36 bp):
ATTAAGTTCTTTATTGACTTCACTTAATTACCCTGA
Found at i:24822 original size:33 final size:32
Alignment explanation
Indices: 24774--24896 Score: 117
Period size: 33 Copynumber: 3.7 Consensus size: 32
24764 ATTAATTTCC
* *
24774 TTTCCTGAAATTAAGCCAATCTTTTTACTTAA
1 TTTCCTGAAATTAAGCCAGTCTTTTTACCTAA
24806 TTTCCTCGAAATTAAGCCAGTCTATCTTTACCTAA
1 TTTCCT-GAAATTAAGCCAGTCT-T-TTTACCTAA
*
24841 -TT--TGAAATTAAGCCAGTCTTTTTTTTACCTAG
1 TTTCCTGAAATTAAGCCAGTC---TTTTTACCTAA
* *
24873 TTTCCTTGAAACTAAGTCAGTCTT
1 TTTCC-TGAAATTAAGCCAGTCTT
24897 CTTTCAGTCT
Statistics
Matches: 76, Mismatches: 5, Indels: 19
0.76 0.05 0.19
Matches are distributed among these distances:
31 15 0.20
32 15 0.20
33 20 0.26
34 4 0.05
35 8 0.11
36 14 0.18
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.42
Consensus pattern (32 bp):
TTTCCTGAAATTAAGCCAGTCTTTTTACCTAA
Found at i:24851 original size:31 final size:31
Alignment explanation
Indices: 24778--24863 Score: 104
Period size: 31 Copynumber: 2.7 Consensus size: 31
24768 ATTTCCTTTC
* *
24778 CTGAAATTAAGCCAATCTTTTTACTTAATTT
1 CTGAAATTAAGCCAGTCTTTTTACCTAATTT
24809 CCTCGAAATTAAGCCAGTCTATCTTTACCTAA-TT
1 -CT-GAAATTAAGCCAGTCT-T-TTTACCTAATTT
24843 -TGAAATTAAGCCAGTCTTTTT
1 CTGAAATTAAGCCAGTCTTTTT
24864 TTTACCTAGT
Statistics
Matches: 49, Mismatches: 2, Indels: 9
0.82 0.03 0.15
Matches are distributed among these distances:
29 3 0.06
30 1 0.02
31 16 0.33
32 3 0.06
33 15 0.31
34 3 0.06
35 8 0.16
ACGTcount: A:0.30, C:0.20, G:0.09, T:0.41
Consensus pattern (31 bp):
CTGAAATTAAGCCAGTCTTTTTACCTAATTT
Found at i:24905 original size:11 final size:11
Alignment explanation
Indices: 24889--24957 Score: 84
Period size: 11 Copynumber: 6.1 Consensus size: 11
24879 TGAAACTAAG
24889 TCAGTCTTCTT
1 TCAGTCTTCTT
*
24900 TCAGTCTTTTTTT
1 TCAGTC--TTCTT
24913 TCAGTCTTCTT
1 TCAGTCTTCTT
* *
24924 TCAGTATTTTT
1 TCAGTCTTCTT
*
24935 TCAGTCTTTTT
1 TCAGTCTTCTT
24946 TCAGTCTTCTT
1 TCAGTCTTCTT
24957 T
1 T
24958 TGCCTAATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
11 40 0.80
13 10 0.20
ACGTcount: A:0.10, C:0.20, G:0.09, T:0.61
Consensus pattern (11 bp):
TCAGTCTTCTT
Found at i:24916 original size:24 final size:24
Alignment explanation
Indices: 24889--24958 Score: 99
Period size: 22 Copynumber: 3.0 Consensus size: 24
24879 TGAAACTAAG
24889 TCAGTCTTCTTTCAGTCTTTTTTT
1 TCAGTCTTCTTTCAGTCTTTTTTT
*
24913 TCAGTCTTCTTTCAG--TATTTTT
1 TCAGTCTTCTTTCAGTCTTTTTTT
* *
24935 TCAGTCTTTTTTCAGTCTTCTTTT
1 TCAGTCTTCTTTCAGTCTTTTTTT
24959 GCCTAATTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 20 0.50
24 20 0.50
ACGTcount: A:0.10, C:0.20, G:0.09, T:0.61
Consensus pattern (24 bp):
TCAGTCTTCTTTCAGTCTTTTTTT
Found at i:25156 original size:107 final size:107
Alignment explanation
Indices: 25030--25317 Score: 540
Period size: 107 Copynumber: 2.7 Consensus size: 107
25020 CTTTGCTGAC
* *
25030 TTTACTTAATTCTTGTGAAATTAAGTTTTTGCTAATTTTAGTTAATTCTTGTGAAATTAAGTCTT
1 TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTT
25095 TGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA
66 TGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA
*
25137 TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTT
1 TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTT
*
25202 TGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA
66 TGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA
25244 TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTT
1 TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTT
25309 TGCTAATTT
66 TGCTAATTT
25318 CTTTCCTTGA
Statistics
Matches: 175, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
107 175 1.00
ACGTcount: A:0.28, C:0.10, G:0.11, T:0.50
Consensus pattern (107 bp):
TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTT
TGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA
Found at i:25158 original size:20 final size:20
Alignment explanation
Indices: 25102--25158 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
25092 CTTTGCTAAT
25102 TTTACTTAATTCTTGTG-AA
1 TTTACTTAATTCTTGTGAAA
*
25121 ---A-TTAAGTCTT-TGATAA
1 TTTACTTAATTCTTGTGA-AA
25137 TTTACTTAATTCTTGTGAAA
1 TTTACTTAATTCTTGTGAAA
25157 TT
1 TT
25159 AAGTCTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 3 0.10
19 1 0.03
20 12 0.41
21 3 0.10
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTACTTAATTCTTGTGAAA
Found at i:25177 original size:71 final size:72
Alignment explanation
Indices: 25013--25314 Score: 518
Period size: 71 Copynumber: 4.2 Consensus size: 72
25003 TCATCTTTGG
* * * *
25013 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAAATTAAGTTTTTGCTAATTTTAGTTAATTC
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
25078 TTGTGAA
66 TTGTGAA
* *
25085 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAAATTAAGTCTTTGATAA-TTTACTTAATTC
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
25149 TTGTGAA
66 TTGTGAA
*
25156 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAACTTTACTTAATTC
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
25221 TTGTGAA
66 TTGTGAA
*
25228 ATTAAGTCTTTGATAA-TTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
1 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
25292 TTGTGAA
66 TTGTGAA
25299 ATTAAGTCTTTGCTAA
1 ATTAAGTCTTTGCTAA
25315 TTTCTTTCCT
Statistics
Matches: 218, Mismatches: 11, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
71 137 0.63
72 81 0.37
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.49
Consensus pattern (72 bp):
ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAAATTAAGTCTTTGCTAATTTTACTTAATTC
TTGTGAA
Found at i:25186 original size:21 final size:21
Alignment explanation
Indices: 25157--25222 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
25147 TCTTGTGAAA
25157 TTAAGTCTTTGCTAACTTTAC
1 TTAAGTCTTTGCTAACTTTAC
*
25178 TTAATTC-TTG-TGAA----A-
1 TTAAGTCTTTGCT-AACTTTAC
25193 TTAAGTCTTTGCTAACTTTAC
1 TTAAGTCTTTGCTAACTTTAC
*
25214 TTAATTCTT
1 TTAAGTCTT
25223 GTGAAATTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 16
0.64 0.06 0.30
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 1 0.03
19 1 0.03
20 6 0.18
21 14 0.41
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (21 bp):
TTAAGTCTTTGCTAACTTTAC
Found at i:25265 original size:20 final size:20
Alignment explanation
Indices: 25209--25265 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
25199 CTTTGCTAAC
25209 TTTACTTAATTCTTGTG-AA
1 TTTACTTAATTCTTGTGAAA
*
25228 ---A-TTAAGTCTT-TGATAA
1 TTTACTTAATTCTTGTGA-AA
25244 TTTACTTAATTCTTGTGAAA
1 TTTACTTAATTCTTGTGAAA
25264 TT
1 TT
25266 AAGTCTTTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 13
0.66 0.05 0.30
Matches are distributed among these distances:
14 2 0.07
15 8 0.28
16 3 0.10
19 1 0.03
20 12 0.41
21 3 0.10
ACGTcount: A:0.30, C:0.09, G:0.11, T:0.51
Consensus pattern (20 bp):
TTTACTTAATTCTTGTGAAA
Found at i:25315 original size:36 final size:36
Alignment explanation
Indices: 25013--25317 Score: 515
Period size: 36 Copynumber: 8.5 Consensus size: 36
25003 TCATCTTTGG
* * *
25013 ATTAAATCTTTGCTGACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
* *
25049 ATTAAGTTTTTGCTAATTTTAGTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
25085 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
*
25121 ATTAAGTCTTTGATAA-TTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
*
25156 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
*
25192 ATTAAGTCTTTGCTAACTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
*
25228 ATTAAGTCTTTGATAA-TTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
25263 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
1 ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
25299 ATTAAGTCTTTGCTAATTT
1 ATTAAGTCTTTGCTAATTT
25318 CTTTCCTTGA
Statistics
Matches: 256, Mismatches: 11, Indels: 4
0.94 0.04 0.01
Matches are distributed among these distances:
35 68 0.27
36 188 0.73
ACGTcount: A:0.29, C:0.11, G:0.11, T:0.49
Consensus pattern (36 bp):
ATTAAGTCTTTGCTAATTTTACTTAATTCTTGTGAA
Found at i:25398 original size:38 final size:37
Alignment explanation
Indices: 25348--25579 Score: 191
Period size: 34 Copynumber: 6.4 Consensus size: 37
25338 GTGCTTATCC
* * *
25348 TTACCTAATTTCCTTTCCTAAAACTGAGCCAGTCTTTT
1 TTACCTAATTTCCTTT-CTGAAATTAAGCCAGTCTTTT
* *
25386 TTACTTAATTTCC--T-TGAAATTAAGCCAATCTTCTCT
1 TTACCTAATTTCCTTTCTGAAATTAAGCCAGTCTT-T-T
*
25422 TTACCTAATTTCCTTTCTTGAAATTAAGCCAGTATTTT
1 TTACCTAATTTCCTTTC-TGAAATTAAGCCAGTCTTTT
* *
25460 TTACTTAATTTCC--T-TGAAATTAAACCAGTCTTTTCT
1 TTACCTAATTTCCTTTCTGAAATTAAGCCAGTC-TTT-T
* *
25496 TTACCTAGTTTCC--T-TGAAACTAAGCCAGTCTTTT
1 TTACCTAATTTCCTTTCTGAAATTAAGCCAGTCTTTT
* *
25530 TTACTTAATTTCC--T-TGAAATTAAGCCAGACTTTTCT
1 TTACCTAATTTCCTTTCTGAAATTAAGCCAGTC-TTT-T
*
25566 TTACCTAGTTTCCT
1 TTACCTAATTTCCT
25580 GAATTGAGAC
Statistics
Matches: 162, Mismatches: 21, Indels: 23
0.79 0.10 0.11
Matches are distributed among these distances:
34 55 0.34
35 10 0.06
36 54 0.33
38 26 0.16
39 1 0.01
40 16 0.10
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.45
Consensus pattern (37 bp):
TTACCTAATTTCCTTTCTGAAATTAAGCCAGTCTTTT
Found at i:25453 original size:74 final size:74
Alignment explanation
Indices: 25319--25579 Score: 336
Period size: 74 Copynumber: 3.6 Consensus size: 74
25309 TGCTAATTTC
* * * * * *
25319 TTTCCTTGAAATTAAGTCC-GTGCTTATCCTTACCTAATTTCCTTTCCTAAAACTGAGCCAGTCT
1 TTTCCTTGAAATTAAG-CCAAT-CTTTTCTTTACCTAATTTCCTTTCTTGAAACTAAGCCAGTCT
25383 TTTTTACTTAA
64 TTTTTACTTAA
* * *
25394 TTTCCTTGAAATTAAGCCAATCTTCTCTTTACCTAATTTCCTTTCTTGAAATTAAGCCAGTATTT
1 TTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTAATTTCCTTTCTTGAAACTAAGCCAGTCTTT
25459 TTTACTTAA
66 TTTACTTAA
* * *
25468 TTTCCTTGAAATTAAACCAGTCTTTTCTTTACCTAGTTT-C---CTTGAAACTAAGCCAGTCTTT
1 TTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTAATTTCCTTTCTTGAAACTAAGCCAGTCTTT
25529 TTTACTTAA
66 TTTACTTAA
*
25538 TTTCCTTGAAATTAAGCCAGA-CTTTTCTTTACCTAGTTTCCT
1 TTTCCTTGAAATTAAGCCA-ATCTTTTCTTTACCTAATTTCCT
25580 GAATTGAGAC
Statistics
Matches: 166, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
70 64 0.39
71 1 0.01
73 1 0.01
74 83 0.50
75 17 0.10
ACGTcount: A:0.25, C:0.22, G:0.08, T:0.44
Consensus pattern (74 bp):
TTTCCTTGAAATTAAGCCAATCTTTTCTTTACCTAATTTCCTTTCTTGAAACTAAGCCAGTCTTT
TTTACTTAA
Found at i:25481 original size:34 final size:34
Alignment explanation
Indices: 25374--25563 Score: 236
Period size: 34 Copynumber: 5.4 Consensus size: 34
25364 CCTAAAACTG
25374 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
* *
25408 AGCCAATCTTCTCTTTACCTAATTTCCTTTCTTGAAATTA
1 AGCCAGTCTT-T-TTTACTTAATTT-C---CTTGAAATTA
*
25448 AGCCAGTATTTTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
* * * *
25482 AACCAGTCTTTTCTTTACCTAGTTTCCTTGAAACTA
1 AGCCAGTC-TTT-TTTACTTAATTTCCTTGAAATTA
25518 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
1 AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
*
25552 AGCCAGACTTTT
1 AGCCAGTCTTTT
25564 CTTTACCTAG
Statistics
Matches: 133, Mismatches: 15, Indels: 16
0.81 0.09 0.10
Matches are distributed among these distances:
34 56 0.42
35 7 0.05
36 38 0.29
37 2 0.02
38 11 0.08
39 1 0.01
40 18 0.14
ACGTcount: A:0.26, C:0.21, G:0.08, T:0.45
Consensus pattern (34 bp):
AGCCAGTCTTTTTTACTTAATTTCCTTGAAATTA
Found at i:36203 original size:20 final size:21
Alignment explanation
Indices: 36164--36203 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
36154 GCTTGGTCCC
* *
36164 TTTGCTTCCAAATTTCAATTT
1 TTTGCTACCAAATCTCAATTT
36185 TTTGCTACCAAA-CTCAATT
1 TTTGCTACCAAATCTCAATT
36204 CCAACTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.23, G:0.05, T:0.45
Consensus pattern (21 bp):
TTTGCTACCAAATCTCAATTT
Found at i:38370 original size:21 final size:22
Alignment explanation
Indices: 38346--38386 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
38336 TAGCTTCTTG
*
38346 GAAATGACTCTTGT-TTCCTTT
1 GAAATCACTCTTGTATTCCTTT
*
38367 GAAATCCCTCTTGTATTCCT
1 GAAATCACTCTTGTATTCCT
38387 AAAGCATTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.20, C:0.24, G:0.12, T:0.44
Consensus pattern (22 bp):
GAAATCACTCTTGTATTCCTTT
Done.