Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013042.1 Corchorus capsularis cultivar CVL-1 contig13063, 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: 57004
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:847 original size:4 final size:4
Alignment explanation
Indices: 838--862 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
828 CATTGCTTTC
838 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
863 CAATCTTTCT
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:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:3223 original size:44 final size:44
Alignment explanation
Indices: 3157--3247 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
3147 GTTGAATTGG
* * *
3157 ATGGTAAATATATATTTTCCCCCTAATGGACTGTTTTCATTTTT
1 ATGGTAAATATATATGTCCCCCCTAACGGACTGTTTTCATTTTT
3201 ATGGTAAATATATATGTCCCCCCTAACGGACTGTTTTCATTTTT
1 ATGGTAAATATATATGTCCCCCCTAACGGACTGTTTTCATTTTT
3245 ATG
1 ATG
3248 TCCAGCTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (44 bp):
ATGGTAAATATATATGTCCCCCCTAACGGACTGTTTTCATTTTT
Found at i:5429 original size:74 final size:74
Alignment explanation
Indices: 5339--5485 Score: 258
Period size: 74 Copynumber: 2.0 Consensus size: 74
5329 TCTTTTCACA
* *
5339 CTTTTCAGGTGACTAAAAAGCCCCTCTATGAGTTTCCCATATTCCTTTTCCTTCTACCCTTTTTC
1 CTTTTCAGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTTTTC
5404 GTAATTACG
66 GTAATTACG
* *
5413 CTTTTCAGATGGCTAAAAAGCCCCTCTATGAGTTTCCCCCATTCCTTTTCCTTCTACCCTTTTTC
1 CTTTTCAGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTTTTC
5478 GTAATTAC
66 GTAATTAC
5486 ACATTTCCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
74 69 1.00
ACGTcount: A:0.20, C:0.30, G:0.10, T:0.40
Consensus pattern (74 bp):
CTTTTCAGATGACTAAAAAGCCCCTCTATGAGTTTCCCACATTCCTTTTCCTTCTACCCTTTTTC
GTAATTACG
Found at i:5530 original size:20 final size:21
Alignment explanation
Indices: 5499--5537 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
5489 TTTCCCTTCC
5499 TTAATGGTTTTTAATTAATGT
1 TTAATGGTTTTTAATTAATGT
5520 TTAAT-GTTTTTAATTAAT
1 TTAATGGTTTTTAATTAAT
5538 TGCTTCTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.10, T:0.59
Consensus pattern (21 bp):
TTAATGGTTTTTAATTAATGT
Found at i:13500 original size:35 final size:33
Alignment explanation
Indices: 13449--13953 Score: 497
Period size: 35 Copynumber: 14.8 Consensus size: 33
13439 TTCTTACTAA
* *
13449 ACTTTATTACCCTGAATTAAGTTACTTATTGAACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTG-ACT
* * *
13484 ACTTAATTACCCTGAATTAAGTTACTCATTAACT
1 ACTTAATTACCCTGAATTAAGTTA-TTACTGACT
*
13518 CACTTAATTACCCCGAATTAGAGTTGATTACTGACT
1 -ACTTAATTACCCTGAATTA-AGTT-ATTACTGACT
*
13554 CACTTAATTACCCTGAATTAAGTCGATTACTGACTT
1 -ACTTAATTACCCTGAATTAAGT-TATTACTGAC-T
13590 ACTTAATTACCCTGAATTAAGTTATTCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGAC-T
** * *
13625 ACTTAATTGTCCTGAATTGAGTTGACTAACTGACT
1 ACTTAATTACCCTGAATTAAGTT-A-TTACTGACT
*
13660 CACTTAATTACCCTGAATTAAGTTGATTACTAAACT
1 -ACTTAATTACCCTGAATTAAGTT-ATTACT-GACT
* * * *
13696 GCTTAATTACCCTGAATTAAATTAATAACTGAATT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTG-ACT
*
13731 ACTTAATTACCCTGAATTAAGTTAATTATTGACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACT
*
13765 AACTTAATTACCCTGAATTAAGTTA--CCT-ACT
1 -ACTTAATTACCCTGAATTAAGTTATTACTGACT
*
13796 GCTTAATTACCCTGAATTAAGTTA--A-T---T
1 ACTTAATTACCCTGAATTAAGTTATTACTGACT
13823 ACTTAATTACCCTGAATTAAGTTAATTACTGACT
1 ACTTAATTACCCTGAATTAAGTT-ATTACTGACT
*
13857 CACTTAATTACCCTGAATTAAGTTTATTACTGATTT
1 -ACTTAATTACCCTGAATTAAG-TTATTACTGA-CT
*
13893 ACTTAATTACCCTGAATTGAGTTATTCACTGACTT
1 ACTTAATTACCCTGAATTAAGTTATT-ACTGAC-T
* * *
13928 ACTTAATTGCCCTAAATTAAATTATT
1 ACTTAATTACCCTGAATTAAGTTATT
13954 TATTACTGAT
Statistics
Matches: 404, Mismatches: 42, Indels: 48
0.82 0.09 0.10
Matches are distributed among these distances:
27 23 0.06
28 1 0.00
29 1 0.00
30 24 0.06
31 4 0.01
32 1 0.00
34 15 0.04
35 268 0.66
36 65 0.16
37 2 0.00
ACGTcount: A:0.33, C:0.18, G:0.10, T:0.39
Consensus pattern (33 bp):
ACTTAATTACCCTGAATTAAGTTATTACTGACT
Found at i:13642 original size:106 final size:103
Alignment explanation
Indices: 13449--13947 Score: 563
Period size: 106 Copynumber: 4.9 Consensus size: 103
13439 TTCTTACTAA
* * * * *
13449 ACTTTATTACCCTGAATTAAGTTACTTATTGAACTACTTAATTACCCTGAATTAAGTTACTCATT
1 ACTTAATTACCCTGAATTAAGTGA-TTACTG-ACTACTTAATTACCCTGAATTAAGTTATTCACT
* * * *
13514 AACTCACTTAATTACCCCGAATTAGAGTTGATTACTGACTC
64 GACTTACTTAATTACCCTGAATTA-AGTTAATTACTGACTC
13555 ACTTAATTACCCTGAATTAAGTCGATTACTGACTTACTTAATTACCCTGAATTAAGTTATTCACT
1 ACTTAATTACCCTGAATTAAGT-GATTACTGAC-TACTTAATTACCCTGAATTAAGTTATTCACT
** * * *
13620 GACTTACTTAATTGTCCTGAATTGAGTTGACTAACTGACTC
64 GACTTACTTAATTACCCTGAATTAAGTT-AATTACTGACTC
* * * * *
13661 ACTTAATTACCCTGAATTAAGTTGATTACTAAACTGCTTAATTACCCTGAATTAAATTAATAACT
1 ACTTAATTACCCTGAATTAAG-TGATTACT-GACTACTTAATTACCCTGAATTAAGTTATTCACT
* * *
13726 GAATTACTTAATTACCCTGAATTAAGTTAATTATTGACTA
64 GACTTACTTAATTACCCTGAATTAAGTTAATTACTGACTC
*
13766 ACTTAATTACCCTGAATTAA--G-TTACCT-ACTGCTTAATTACCCTGAATTAAG---TT-A---
1 ACTTAATTACCCTGAATTAAGTGATTA-CTGACTACTTAATTACCCTGAATTAAGTTATTCACTG
13820 A-TTACTTAATTACCCTGAATTAAGTTAATTACTGACTC
65 ACTTACTTAATTACCCTGAATTAAGTTAATTACTGACTC
* * *
13858 ACTTAATTACCCTGAATTAAGTTTATTACTGATTTACTTAATTACCCTGAATTGAGTTATTCACT
1 ACTTAATTACCCTGAATTAAG-TGATTACTGA-CTACTTAATTACCCTGAATTAAGTTATTCACT
* *
13923 GACTTACTTAATTGCCCTAAATTAA
64 GACTTACTTAATTACCCTGAATTAA
13948 ATTATTTATT
Statistics
Matches: 336, Mismatches: 37, Indels: 41
0.81 0.09 0.10
Matches are distributed among these distances:
92 55 0.16
93 1 0.00
95 2 0.01
96 5 0.01
97 21 0.06
100 25 0.07
101 4 0.01
102 3 0.01
104 1 0.00
105 54 0.16
106 161 0.48
107 4 0.01
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (103 bp):
ACTTAATTACCCTGAATTAAGTGATTACTGACTACTTAATTACCCTGAATTAAGTTATTCACTGA
CTTACTTAATTACCCTGAATTAAGTTAATTACTGACTC
Found at i:13835 original size:27 final size:27
Alignment explanation
Indices: 13766--13852 Score: 129
Period size: 27 Copynumber: 3.1 Consensus size: 27
13756 TTATTGACTA
*
13766 ACTTAATTACCCTGAATTAAGTTACCTACT
1 ACTTAATTACCCTGAATTAAGTTA---ATT
*
13796 GCTTAATTACCCTGAATTAAGTTAATT
1 ACTTAATTACCCTGAATTAAGTTAATT
13823 ACTTAATTACCCTGAATTAAGTTAATT
1 ACTTAATTACCCTGAATTAAGTTAATT
13850 ACT
1 ACT
13853 GACTCACTTA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
27 31 0.57
30 23 0.43
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.39
Consensus pattern (27 bp):
ACTTAATTACCCTGAATTAAGTTAATT
Found at i:13888 original size:92 final size:93
Alignment explanation
Indices: 13727--13916 Score: 285
Period size: 92 Copynumber: 2.0 Consensus size: 93
13717 TTAATAACTG
*
13727 AATTACTTAATTACCCTGAATTAAGTTAATTATTGACTAACTTAATTACCCTGAATTAAGTTACC
1 AATTACTTAATTACCCTGAATTAAGTTAATTACTGACTAACTTAATTACCCTGAATTAAGTTACC
13792 TACTG-CTTAATTACCCTGAATTAAGTT
66 TACTGTCTTAATTACCCTGAATTAAGTT
*
13819 AATTACTTAATTACCCTGAATTAAGTTAATTACTGACTCACTTAATTACCCTGAATTAAGTTTA-
1 AATTACTTAATTACCCTGAATTAAGTTAATTACTGACTAACTTAATTACCCTGAATTAAG-TTAC
* *
13883 TTACTGATTTACTTAATTACCCTGAATTGAGTT
65 CTACTG---T-CTTAATTACCCTGAATTAAGTT
13916 A
1 A
13917 TTCACTGACT
Statistics
Matches: 88, Mismatches: 4, Indels: 7
0.89 0.04 0.07
Matches are distributed among these distances:
92 63 0.72
93 3 0.03
97 22 0.25
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (93 bp):
AATTACTTAATTACCCTGAATTAAGTTAATTACTGACTAACTTAATTACCCTGAATTAAGTTACC
TACTGTCTTAATTACCCTGAATTAAGTT
Found at i:14598 original size:20 final size:20
Alignment explanation
Indices: 14570--14612 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
14560 CCGTTTTTGC
* *
14570 TCTTCTTTTCTTCTTCTTTT
1 TCTTATTTTCTTCTTCTTCT
*
14590 TCTTATTTTCTTTTTCTTCT
1 TCTTATTTTCTTCTTCTTCT
14610 TCT
1 TCT
14613 CCCTCTTTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.74
Consensus pattern (20 bp):
TCTTATTTTCTTCTTCTTCT
Found at i:15499 original size:15 final size:18
Alignment explanation
Indices: 15462--15497 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
15452 AAAAACTGTC
15462 CTCCTCTATTTATTTTCTG
1 CTCCTCTATTTA-TTTCTG
15481 CTCCTCTATTTATTTCT
1 CTCCTCTATTTATTTCT
15498 CCCTTACTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.11, C:0.28, G:0.03, T:0.58
Consensus pattern (18 bp):
CTCCTCTATTTATTTCTG
Found at i:20086 original size:18 final size:18
Alignment explanation
Indices: 20060--20095 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
20050 GTATCATCCC
*
20060 TCTGGTGTATCAGGTGTA
1 TCTGCTGTATCAGGTGTA
20078 TCTGCTGTATCAGGTGTA
1 TCTGCTGTATCAGGTGTA
20096 GTCCTCTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.14, G:0.31, T:0.39
Consensus pattern (18 bp):
TCTGCTGTATCAGGTGTA
Found at i:20600 original size:156 final size:154
Alignment explanation
Indices: 20422--20954 Score: 558
Period size: 156 Copynumber: 3.4 Consensus size: 154
20412 TTCATACCCT
* *
20422 AAACTGTCCTTTAATGAAAAACTAGCATAAGTTTTTCAC-CTTAAGTCTGTTTGAGCTGAAACTT
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCACTC-TAAGTCTGTTTGAGATGAAACTT
* * * *
20486 TACCAAGGGACTTATATTCTCTCCATAAGACTATGGAAAAAATTCTAAGTAAAACCGAGCTCCCC
65 TACCAAGAGACTTACATTATCTCCATAA-ACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCC
** *
20551 TTGATAGTGAACTGGGTTTCTCTTCTT
129 TTGATAGTGAACT-GGTTTCTCACCTC
* *** * ** *
20578 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCATTCTAAGTC-CAATGAAGCTGATTCTC
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCACTCTAAGTCTGTTTG-AGATGAAACTT
* *
20642 CACC-AGTAGACTTACATTAT-TCCCATAAAGCTATGGGAAAAAA-CCTAAGTAAAACCGAACTC
65 TACCAAG-AGACTTACATTATCT-CCATAAA-CTAT-GGAAAAAATTCTAAGTAAAACCGAACTC
**
20704 CCCTTGATAGTGAACTGACTTCTCACCTC
126 CCCTTGATAGTGAACTGGTTTCTCACCTC
* * * *
20733 AAACTGTCCTTAATTGAAAAACTTGCATAAGTTTTTCATTCTAAGTCTGTTTGAGATGAAATTTT
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCACTCTAAGTCTGTTTGAGATGAAACTTT
* * * *
20798 GGCCAAGAGACTTAGATTATCTCCACAAACTTATGGAAAAAAAATTCTAAGTAAAAACGAACT-C
66 -ACCAAGAGACTTACATTATCTCCATAAAC-TATGG--AAAAAATTCTAAGTAAAACCGAACTCC
* * * *
20862 CCTATCATGGTGAAGTGGTTTCTCACCCC
127 CCT-TGATAGTGAACTGGTTTCTCACCTC
* * * *
20891 AAACTATCCTTAATTGAAAAACTTGCATAAATTTTTCA-TCTTAAGTCTGTTTGAGATGAAACTT
1 AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCACTC-TAAGTCTGTTTGAGATGAAACTT
20955 AGCTAAGATG
Statistics
Matches: 317, Mismatches: 44, Indels: 30
0.81 0.11 0.08
Matches are distributed among these distances:
155 68 0.21
156 132 0.42
157 24 0.08
158 93 0.29
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (154 bp):
AAACTGTCCTTAAATGAAAAACTAGCATAAGTTTTTCACTCTAAGTCTGTTTGAGATGAAACTTT
ACCAAGAGACTTACATTATCTCCATAAACTATGGAAAAAATTCTAAGTAAAACCGAACTCCCCTT
GATAGTGAACTGGTTTCTCACCTC
Found at i:22031 original size:2 final size:2
Alignment explanation
Indices: 22024--22051 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
22014 TTAATAGATA
22024 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22052 TACTGTTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22640 original size:31 final size:31
Alignment explanation
Indices: 22605--22677 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 31
22595 TTTGGCTCTA
* *
22605 GGGACTGATTTGAG-CTGATTTTGCAACATTT
1 GGGACTAATTTGAGTC-AATTTTGCAACATTT
*
22636 GGGACTAATTTGAGTCAATTTTGCAACGTTT
1 GGGACTAATTTGAGTCAATTTTGCAACATTT
22667 GGGACTTAATT
1 GGGAC-TAATT
22678 AACCAAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 31 0.84
32 6 0.16
ACGTcount: A:0.25, C:0.12, G:0.25, T:0.38
Consensus pattern (31 bp):
GGGACTAATTTGAGTCAATTTTGCAACATTT
Found at i:24324 original size:60 final size:60
Alignment explanation
Indices: 24259--24374 Score: 223
Period size: 60 Copynumber: 1.9 Consensus size: 60
24249 TATATGATTA
*
24259 TAATGAAATTCGGGTATATAATTGTAATGAAATTTGGCTAAAAATTTGGGTATTTAATTG
1 TAATGAAATTCGGGTATATAACTGTAATGAAATTTGGCTAAAAATTTGGGTATTTAATTG
24319 TAATGAAATTCGGGTATATAACTGTAATGAAATTTGGCTAAAAATTTGGGTATTTA
1 TAATGAAATTCGGGTATATAACTGTAATGAAATTTGGCTAAAAATTTGGGTATTTA
24375 CTAATAAGAA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.37, C:0.04, G:0.20, T:0.39
Consensus pattern (60 bp):
TAATGAAATTCGGGTATATAACTGTAATGAAATTTGGCTAAAAATTTGGGTATTTAATTG
Found at i:24327 original size:24 final size:24
Alignment explanation
Indices: 24300--24355 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
24290 ATTTGGCTAA
* *
24300 AAATTTGGGTATTTAATTGTAATG
1 AAATTTGGGTATATAACTGTAATG
*
24324 AAATTCGGGTATATAACTGTAATG
1 AAATTTGGGTATATAACTGTAATG
24348 AAATTTGG
1 AAATTTGG
24356 CTAAAAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.21, T:0.39
Consensus pattern (24 bp):
AAATTTGGGTATATAACTGTAATG
Found at i:24588 original size:3 final size:3
Alignment explanation
Indices: 24580--24618 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
24570 CCTCTTGCAA
24580 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
24619 CCAAGGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:27553 original size:141 final size:141
Alignment explanation
Indices: 27295--27567 Score: 440
Period size: 141 Copynumber: 1.9 Consensus size: 141
27285 TCTCCATAAG
*
27295 ACTATGGAAAAAATTCTAAGTAAAAACGAGCTCCTCTTGATGTTGAACTTGGTTTCACACCCCAA
1 ACTATGGAAAAAATTCTAAGTAAAAACGAGCTCCTCTTGATGGTGAACTTGGTTTCACACCCCAA
* *
27360 ACTGTCCTTAAATGAAAACCATGCATAAGTTATTCATTCTACGTCCAATTGAGATGAAACTTGGC
66 ACTGTCCTTAAATGAAAAACATGCATAAGTTATTCATTCTAAGTCCAATTGAGATGAAACTTGGC
27425 CACGAGACAAA
131 CACGAGACAAA
* *
27436 ACTATGGAAAAAATTCTAAGTAAAAATGAGCT-CTCCTTGATGGTGAACTTGGTTTCTCACCCCA
1 ACTATGGAAAAAATTCTAAGTAAAAACGAGCTCCT-CTTGATGGTGAACTTGGTTTCACACCCCA
* * ***
27500 AACTGTCCTTAACTGAAAAACATGCATAAGTTTTTCATTCTAAGTCTGTTTGAGATGAAACTTGG
65 AACTGTCCTTAAATGAAAAACATGCATAAGTTATTCATTCTAAGTCCAATTGAGATGAAACTTGG
27565 CCA
130 CCA
27568 AGATGGTCCT
Statistics
Matches: 121, Mismatches: 10, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
140 2 0.02
141 119 0.98
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (141 bp):
ACTATGGAAAAAATTCTAAGTAAAAACGAGCTCCTCTTGATGGTGAACTTGGTTTCACACCCCAA
ACTGTCCTTAAATGAAAAACATGCATAAGTTATTCATTCTAAGTCCAATTGAGATGAAACTTGGC
CACGAGACAAA
Found at i:53175 original size:12 final size:12
Alignment explanation
Indices: 53146--53189 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
53136 TAAATGTGTT
*
53146 AAATTAAATAAA
1 AAATTAAAAAAA
**
53158 TTATTAAAAAAA
1 AAATTAAAAAAA
*
53170 AAATTATAAAAA
1 AAATTAAAAAAA
53182 AAATTAAA
1 AAATTAAA
53190 TCCAATAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATTAAAAAAA
Found at i:53181 original size:14 final size:15
Alignment explanation
Indices: 53155--53184 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
53145 TAAATTAAAT
53155 AAATTATTAAAAAAA
1 AAATTATTAAAAAAA
53170 AAATTA-TAAAAAAA
1 AAATTATTAAAAAAA
53184 A
1 A
53185 TTAAATCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AAATTATTAAAAAAA
Found at i:53562 original size:11 final size:11
Alignment explanation
Indices: 53546--53580 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
53536 TTGACAGCGC
53546 AACAAAAACAA
1 AACAAAAACAA
*
53557 AACAAAAACGA
1 AACAAAAACAA
53568 AACAAAAACAA
1 AACAAAAACAA
53579 AA
1 AA
53581 AATAGGAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.80, C:0.17, G:0.03, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:56787 original size:18 final size:18
Alignment explanation
Indices: 56764--56799 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
56754 ATAAATTATT
56764 AAAGTGAAAAAATAAAAA
1 AAAGTGAAAAAATAAAAA
*
56782 AAAGTGCAAAAATAAAAA
1 AAAGTGAAAAAATAAAAA
56800 CCATCACCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.03, G:0.11, T:0.11
Consensus pattern (18 bp):
AAAGTGAAAAAATAAAAA
Done.