Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016186.1 Corchorus capsularis cultivar CVL-1 contig16207, 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: 36249
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Found at i:1096 original size:18 final size:19
Alignment explanation
Indices: 1073--1108 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1063 ATATAATAAT
*
1073 TATTAGTGTTA-TTATTAA
1 TATTAGTATTATTTATTAA
1091 TATTAGTATTATTTATTA
1 TATTAGTATTATTTATTA
1109 TTAGTAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATTAGTATTATTTATTAA
Found at i:5403 original size:40 final size:40
Alignment explanation
Indices: 5348--5427 Score: 151
Period size: 40 Copynumber: 2.0 Consensus size: 40
5338 TTGATCCGAC
5348 ATGATTTTGGATGTTGATTTGCTTGAAAAATTGAGATTTT
1 ATGATTTTGGATGTTGATTTGCTTGAAAAATTGAGATTTT
*
5388 ATGATTTTGGATGTTGATTTGCTTGAAAATTTGAGATTTT
1 ATGATTTTGGATGTTGATTTGCTTGAAAAATTGAGATTTT
5428 TAGGTTGAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.49
Consensus pattern (40 bp):
ATGATTTTGGATGTTGATTTGCTTGAAAAATTGAGATTTT
Found at i:5997 original size:26 final size:26
Alignment explanation
Indices: 5967--6022 Score: 80
Period size: 26 Copynumber: 2.2 Consensus size: 26
5957 ATTTTAATGT
5967 TTAAATT-TTATTTT-TTATTAAAAAAA
1 TTAAATTATTATTTTATT-TT-AAAAAA
5993 TTAAATTATTATTTTATTTTAAAAAA
1 TTAAATTATTATTTTATTTTAAAAAA
6019 TTAA
1 TTAA
6023 CAAGAGCGGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 17 0.61
27 9 0.32
28 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (26 bp):
TTAAATTATTATTTTATTTTAAAAAA
Found at i:8936 original size:2 final size:2
Alignment explanation
Indices: 8931--8969 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
8921 TTTATTTAAC
*
8931 AT AT AT AT AT AT AT AC AT A- 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 AT AT AT AT AT AT
8970 TTCGGGACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:11368 original size:15 final size:15
Alignment explanation
Indices: 11318--11360 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
11308 TTTGACCATT
* *
11318 AATTATAAAAAA-AA
1 AATTTTAAAAAATTA
11332 AATTTT-AAAAATTA
1 AATTTTAAAAAATTA
11346 AATTTTAAAAAATTA
1 AATTTTAAAAAATTA
11361 TGTTTTAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 5 0.20
14 12 0.48
15 8 0.32
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (15 bp):
AATTTTAAAAAATTA
Found at i:15838 original size:31 final size:31
Alignment explanation
Indices: 15781--15843 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
15771 AAATAAATTC
* * * *
15781 TATATTAATTAAATATAGTTATTGTT-ATGA
1 TATATTAATAAAATACAATTAATGTTAATGA
15811 TATATTAATGAAAATACAATTAATGTTAATGA
1 TATATTAAT-AAAATACAATTAATGTTAATGA
15843 T
1 T
15844 TGTTATGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 13 0.48
32 5 0.19
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (31 bp):
TATATTAATAAAATACAATTAATGTTAATGA
Found at i:16013 original size:19 final size:19
Alignment explanation
Indices: 15989--16035 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 19
15979 CACTATTTTT
15989 TTTTGACC-TCCTTATGAAA
1 TTTTGACCTTCC-TATGAAA
16008 TTTTGATAACCTTCCTATGAAA
1 TTTTG---ACCTTCCTATGAAA
16030 TTTTGA
1 TTTTGA
16036 TAACGATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
19 6 0.25
22 15 0.62
23 3 0.12
ACGTcount: A:0.28, C:0.17, G:0.11, T:0.45
Consensus pattern (19 bp):
TTTTGACCTTCCTATGAAA
Found at i:16047 original size:22 final size:22
Alignment explanation
Indices: 16001--16054 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
15991 TTGACCTCCT
* *
16001 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACCATAC
*
16023 TATGAAATTTTGATAACGATAC
1 TATGAAATTTTGATAACCATAC
*
16045 TATGGAATTT
1 TATGAAATTT
16055 CGAGAACTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.11, G:0.13, T:0.41
Consensus pattern (22 bp):
TATGAAATTTTGATAACCATAC
Found at i:16347 original size:15 final size:16
Alignment explanation
Indices: 16309--16351 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
16299 TCCCGAACCC
*
16309 ACCCGAACCCGAAATT
1 ACCCGAACCCGAAAAT
*
16325 ACCCGAACCTGAAAAT
1 ACCCGAACCCGAAAAT
16341 A-CCGAACCCGA
1 ACCCGAACCCGA
16352 TCCCGACCCG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.40, C:0.37, G:0.14, T:0.09
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:16539 original size:2 final size:2
Alignment explanation
Indices: 16532--16557 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16522 GCTAATCTAC
16532 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
16558 ACTTAAAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17316 original size:16 final size:16
Alignment explanation
Indices: 17295--17398 Score: 133
Period size: 16 Copynumber: 6.6 Consensus size: 16
17285 ATCCGAGCCT
17295 GAACCCGAAAATACCC
1 GAACCCGAAAATACCC
*
17311 GAACCCG-ACATAACCC
1 GAACCCGAAAAT-ACCC
*
17327 GAACCCGAAAATACTC
1 GAACCCGAAAATACCC
*
17343 GAATCCGAAAA-ACCC
1 GAACCCGAAAATACCC
*
17358 GAGCCCGAAAATACCC
1 GAACCCGAAAATACCC
17374 GAACCCGAAAA-AGCCC
1 GAACCCGAAAATA-CCC
17390 GAACCCGAA
1 GAACCCGAA
17399 CCCACCCGAG
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
15 16 0.21
16 57 0.75
17 3 0.04
ACGTcount: A:0.42, C:0.37, G:0.15, T:0.06
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:17331 original size:32 final size:31
Alignment explanation
Indices: 17295--17398 Score: 154
Period size: 32 Copynumber: 3.3 Consensus size: 31
17285 ATCCGAGCCT
*
17295 GAACCCGAAAATACCCGAACCCGACATAACCC
1 GAACCCGAAAATACCCGAACCCGA-AAAACCC
* *
17327 GAACCCGAAAATACTCGAATCCGAAAAACCC
1 GAACCCGAAAATACCCGAACCCGAAAAACCC
*
17358 GAGCCCGAAAATACCCGAACCCGAAAAAGCCC
1 GAACCCGAAAATACCCGAACCCGAAAAA-CCC
17390 GAACCCGAA
1 GAACCCGAA
17399 CCCACCCGAG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
31 31 0.48
32 33 0.52
ACGTcount: A:0.42, C:0.37, G:0.15, T:0.06
Consensus pattern (31 bp):
GAACCCGAAAATACCCGAACCCGAAAAACCC
Found at i:17511 original size:22 final size:22
Alignment explanation
Indices: 17486--17679 Score: 112
Period size: 22 Copynumber: 8.9 Consensus size: 22
17476 AAATTGTTAG
*
17486 TAATCACACTCTGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
17508 TAATCACACTATAAAATTGTGA
1 TAATCACACTATGAAATTTTGA
*
17530 T-AT-TC-CTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* * * *
17549 TAAACCTCCCTATAAAATTTTGA
1 T-AATCACACTATGAAATTTTGA
* * **
17572 TAACCTTC-CTATGATTTTTTGA
1 TAATC-ACACTATGAAATTTTGA
* * * *
17594 TAACCTCATTATGAAATTTTGT
1 TAATCACACTATGAAATTTTGA
* *
17616 TAATCTCCCTATGAAATTTTGA
1 TAATCACACTATGAAATTTTGA
* *
17638 T-CTACATACTATGAAATTTTGA
1 TAAT-CACACTATGAAATTTTGA
**
17660 TAACTGTCA-TATGAAATTTT
1 TAA-TCACACTATGAAATTTT
17680 TATATCCTCC
Statistics
Matches: 136, Mismatches: 27, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
19 13 0.10
20 1 0.01
21 6 0.04
22 98 0.72
23 17 0.12
24 1 0.01
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (22 bp):
TAATCACACTATGAAATTTTGA
Found at i:17566 original size:23 final size:22
Alignment explanation
Indices: 17534--17702 Score: 148
Period size: 22 Copynumber: 7.7 Consensus size: 22
17524 TTGTGATATT
17534 CCTATGAAATTTTGATAAACCTC
1 CCTATGAAATTTTGAT-AACCTC
* *
17557 CCTATAAAATTTTGATAACCTT
1 CCTATGAAATTTTGATAACCTC
**
17579 CCTATGATTTTTTGATAACCTC
1 CCTATGAAATTTTGATAACCTC
** * *
17601 ATTATGAAATTTTGTTAATCTC
1 CCTATGAAATTTTGATAACCTC
* *
17623 CCTATGAAATTTTGATCTACAT-
1 CCTATGAAATTTTGAT-AACCTC
* *
17645 ACTATGAAATTTTGATAA-CTGT
1 CCTATGAAATTTTGATAACCT-C
* * *
17667 CATATGAAATTTTTATATCCTC
1 CCTATGAAATTTTGATAACCTC
17689 CC--TGAAATTTTGAT
1 CCTATGAAATTTTGAT
17703 TACTTCATGA
Statistics
Matches: 114, Mismatches: 28, Indels: 11
0.75 0.18 0.07
Matches are distributed among these distances:
20 12 0.11
21 1 0.01
22 82 0.72
23 19 0.17
ACGTcount: A:0.32, C:0.17, G:0.09, T:0.43
Consensus pattern (22 bp):
CCTATGAAATTTTGATAACCTC
Found at i:17614 original size:44 final size:45
Alignment explanation
Indices: 17497--17679 Score: 164
Period size: 44 Copynumber: 4.2 Consensus size: 45
17487 AATCACACTC
* * * *
17497 TGAAATTTTGAT-AATCACACTATAAAATTGTGAT-A--TTCCTA
1 TGAAATTTTGATAAACCTCACTATGAAATTTTGATAACCTTCCTA
* *
17538 TGAAATTTTGATAAACCTCCCTATAAAATTTTGATAACCTTCCTA
1 TGAAATTTTGATAAACCTCACTATGAAATTTTGATAACCTTCCTA
** * * * *
17583 TGATTTTTTGAT-AACCTCATTATGAAATTTTGTTAATCTCCCTA
1 TGAAATTTTGATAAACCTCACTATGAAATTTTGATAACCTTCCTA
** * *
17627 TGAAATTTTGATCTACAT-ACTATGAAATTTTGATAA-CTGTCATA
1 TGAAATTTTGATAAACCTCACTATGAAATTTTGATAACCT-TCCTA
17671 TGAAATTTT
1 TGAAATTTT
17680 TATATCCTCC
Statistics
Matches: 116, Mismatches: 20, Indels: 9
0.80 0.14 0.06
Matches are distributed among these distances:
41 12 0.10
42 18 0.16
43 3 0.03
44 64 0.55
45 19 0.16
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.42
Consensus pattern (45 bp):
TGAAATTTTGATAAACCTCACTATGAAATTTTGATAACCTTCCTA
Found at i:17650 original size:66 final size:66
Alignment explanation
Indices: 17497--17702 Score: 178
Period size: 66 Copynumber: 3.2 Consensus size: 66
17487 AATCACACTC
* * * * * * *
17497 TGAAATTTTGATAATCACACTATAAAATTGTGAT-A-T-TCCTATGAAATTTTGATAAACCTCCC
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACTCTCATATGAAATTTTG-TTAATCTCCC
17559 TA
65 TA
* * * **
17561 TAAAATTTTGATAACCTTCCTATGATTTTTTGATAAC-CTCATTATGAAATTTTGTTAATCTCCC
1 TGAAATTTTGATAACCATACTATGAAATTTTGATAACTCTCA-TATGAAATTTTGTTAATCTCCC
17625 TA
65 TA
* *
17627 TGAAATTTTGATCTA-CATACTATGAAATTTTGATAACTGTCATATGAAA-TTT-TTATATCCTC
1 TGAAATTTTGAT-AACCATACTATGAAATTTTGATAACTCTCATATGAAATTTTGTTA-AT-CTC
17689 CC--
63 CCTA
17691 TGAAATTTTGAT
1 TGAAATTTTGAT
17703 TACTTCATGA
Statistics
Matches: 115, Mismatches: 19, Indels: 16
0.77 0.13 0.11
Matches are distributed among these distances:
64 40 0.35
65 6 0.05
66 53 0.46
67 16 0.14
ACGTcount: A:0.33, C:0.15, G:0.09, T:0.42
Consensus pattern (66 bp):
TGAAATTTTGATAACCATACTATGAAATTTTGATAACTCTCATATGAAATTTTGTTAATCTCCCT
A
Found at i:17834 original size:22 final size:22
Alignment explanation
Indices: 17809--17929 Score: 109
Period size: 22 Copynumber: 5.5 Consensus size: 22
17799 AATCACATTT
* *
17809 TGAAAATTTGATAACCTCTTTA
1 TGAAATTTTGATAACCTCTCTA
*
17831 TGAAATTTTAATAACCTCTCTA
1 TGAAATTTTGATAACCTCTCTA
* * * *
17853 TAAAATTTTGTTGACCCCTCTA
1 TGAAATTTTGATAACCTCTCTA
* *
17875 TGAAATTTTGATAATCACAT-TA
1 TGAAATTTTGATAACCTC-TCTA
* ** *
17897 TGTAATTTTGATAACCTCGATT
1 TGAAATTTTGATAACCTCTCTA
17919 TGAAATTTTGA
1 TGAAATTTTGA
17930 ATAAAGTGAA
Statistics
Matches: 78, Mismatches: 19, Indels: 4
0.77 0.19 0.04
Matches are distributed among these distances:
22 77 0.99
23 1 0.01
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (22 bp):
TGAAATTTTGATAACCTCTCTA
Found at i:17835 original size:44 final size:44
Alignment explanation
Indices: 17785--17929 Score: 134
Period size: 44 Copynumber: 3.3 Consensus size: 44
17775 GAAATACCAC
* *
17785 TATGAAATTTTGCTAATCACATTTTGAAAATTTGATAACCTCTT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
* * * * * * *
17829 TATGAAATTTTAATAACCTC-TCTAT-AAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAATCACAT-TATGAAAA-TTTGATAACCTCTT
* * *
17873 TATGAAATTTTGATAATCACATTATGTAATTTTGATAACCTCGAT
1 TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTC-TT
17918 T-TGAAATTTTGA
1 TATGAAATTTTGA
17930 ATAAAGTGAA
Statistics
Matches: 77, Mismatches: 19, Indels: 10
0.73 0.18 0.09
Matches are distributed among these distances:
43 5 0.06
44 68 0.88
45 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (44 bp):
TATGAAATTTTGATAATCACATTATGAAAATTTGATAACCTCTT
Found at i:20169 original size:23 final size:21
Alignment explanation
Indices: 20143--20191 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
20133 CTGGATATGA
20143 GTTTTGTGCTACTTTATGTGTGG
1 GTTTTGTGCTACTTTAT-TG-GG
* *
20166 GTTTTGTGTTCCTTTATTGGG
1 GTTTTGTGCTACTTTATTGGG
20187 GTTTT
1 GTTTT
20192 TTAGGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 7 0.29
22 2 0.08
23 15 0.62
ACGTcount: A:0.06, C:0.08, G:0.29, T:0.57
Consensus pattern (21 bp):
GTTTTGTGCTACTTTATTGGG
Found at i:20393 original size:3 final size:3
Alignment explanation
Indices: 20385--20417 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
20375 TTTGTAGCAA
20385 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20418 GGTTCAACCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:23066 original size:35 final size:35
Alignment explanation
Indices: 23016--23087 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
23006 GACCACAACC
23016 AAGTCTAAACCATACTATTACAACTCAATTGTTTA
1 AAGTCTAAACCATACTATTACAACTCAATTGTTTA
* *
23051 AAGTCTGAACTATACTATTACAACTCAATTGTTTA
1 AAGTCTAAACCATACTATTACAACTCAATTGTTTA
23086 AA
1 AA
23088 CGAAAAAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (35 bp):
AAGTCTAAACCATACTATTACAACTCAATTGTTTA
Found at i:24534 original size:78 final size:78
Alignment explanation
Indices: 24391--24545 Score: 211
Period size: 78 Copynumber: 2.0 Consensus size: 78
24381 TGATAATATC
* * ** ****
24391 AAAAATACAAAAATTTAAAAATTTTAAACTTCTCCCTTATCTTGCCGAAATTCCAAATTTTTTGG
1 AAAAATACAAAAAATTAAAAATTTTAAACTTCTCCATTATCTTGCCGAAATTAAAAAAAAATTGG
24456 ATAAAAAAATTTA
66 ATAAAAAAATTTA
* *
24469 AAAAATACAAAAAATTAAAGATTTTAAACTTCTCCATTATCTTGCCTAAATTAAAAAAAAATTGG
1 AAAAATACAAAAAATTAAAAATTTTAAACTTCTCCATTATCTTGCCGAAATTAAAAAAAAATTGG
*
24534 ATACAAAAATTT
66 ATAAAAAAATTT
24546 CAAATATAAA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.48, C:0.13, G:0.05, T:0.34
Consensus pattern (78 bp):
AAAAATACAAAAAATTAAAAATTTTAAACTTCTCCATTATCTTGCCGAAATTAAAAAAAAATTGG
ATAAAAAAATTTA
Found at i:26884 original size:18 final size:18
Alignment explanation
Indices: 26854--26950 Score: 115
Period size: 18 Copynumber: 5.4 Consensus size: 18
26844 CCAACCTGTT
*
26854 AACACAGTTCCAGCACCA
1 AACACAGTCCCAGCACCA
* *
26872 AATACAGTCCCAGCACCG
1 AACACAGTCCCAGCACCA
26890 AACACAGTCCCAGCACC-
1 AACACAGTCCCAGCACCA
* * *
26907 GACAATAGTCCCAGCACCG
1 AAC-ACAGTCCCAGCACCA
*
26926 AACACAATCCCAGCACCA
1 AACACAGTCCCAGCACCA
26944 AACACAG
1 AACACAG
26951 ATTTTGTTCC
Statistics
Matches: 66, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
17 2 0.03
18 62 0.94
19 2 0.03
ACGTcount: A:0.38, C:0.40, G:0.13, T:0.08
Consensus pattern (18 bp):
AACACAGTCCCAGCACCA
Found at i:26894 original size:36 final size:36
Alignment explanation
Indices: 26854--26950 Score: 135
Period size: 36 Copynumber: 2.7 Consensus size: 36
26844 CCAACCTGTT
*
26854 AACACAGTTCCAGCACCAAATACAGTCCCAGCACCG
1 AACACAGTCCCAGCACCAAATACAGTCCCAGCACCG
26890 AACACAGTCCCAGCACCGACAAT--AGTCCCAGCACCG
1 AACACAGTCCCAGCACC-A-AATACAGTCCCAGCACCG
* *
26926 AACACAATCCCAGCACCAAACACAG
1 AACACAGTCCCAGCACCAAATACAG
26951 ATTTTGTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
34 2 0.04
35 1 0.02
36 47 0.87
37 1 0.02
38 3 0.06
ACGTcount: A:0.38, C:0.40, G:0.13, T:0.08
Consensus pattern (36 bp):
AACACAGTCCCAGCACCAAATACAGTCCCAGCACCG
Found at i:32401 original size:23 final size:24
Alignment explanation
Indices: 32375--32423 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
32365 AATATTTTTT
32375 GTGTAGG-ATTAAAAACCATGGCA
1 GTGTAGGAATTAAAAACCATGGCA
*
32398 GTGTAGGAATATTAACAACCATGGCA
1 GTGTAGG-A-ATTAAAAACCATGGCA
32424 TTGTTGATGG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
26 15 0.68
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (24 bp):
GTGTAGGAATTAAAAACCATGGCA
Found at i:34919 original size:198 final size:199
Alignment explanation
Indices: 34514--35068 Score: 808
Period size: 198 Copynumber: 2.8 Consensus size: 199
34504 ATGAGTTTAT
* * *
34514 TATAAGAAAAATTATAAAATACATCGTCAGTGAAGTTTAGCA-ACTGCACGTTTGGGGTTTAAGG
1 TATAAGAAAAATTATAAAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTTCGGGGTTTAAGG
*
34578 GTTGACATGTGTCCCCTTAGGGAATAAGTATTAATATTAAATATATTTAATTAATTATGAAATGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATT-AA-ATATTTAATTAATTATGAAATGG
* * **
34643 GGTGTGTGTCAACTTCTTTACCCGCTTATGGAGTTTAAAATTTACACTAACAGTGTATTGTATAA
129 GGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAA
34708 TAATCC
194 TAATCC
* * * * *
34714 CATAAGAAAAATTATATAATACACCATCATTGGAGTTTAGCAGACTGCACGTTCAGGGTTTAAGG
1 TATAAGAAAAATTATAAAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTTCGGGGTTTAAGG
* * *
34779 GTTGTCATGTGTCCCCTTAGGGAATATGTCTTAATATTAAATATTTAATTAATTATAAAATGGGG
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
* *
34844 TATGTGT-AACTTCTTAACCCACTTATGGAGTCCAAAATTTACACTGACAGTGTATTGTATAATA
131 TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATA
34908 ATCC
196 ATCC
* * * ** *
34912 TATAAGAAAAATTATACAATATACCGTTAGTGGAGTTTAGCAGACTGCACGGGCGGGGTTTATGG
1 TATAAGAAAAATTATAAAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTTCGGGGTTTAAGG
* ** * **
34977 GTTGACATGTGTCCGCTTAAAGAATATGTATTAATATTAAATATTTAATTAATTATGAAATAGAC
66 GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
35042 TATGTGTCAACTTCTTAACCCGCTTAT
131 TATGTGTCAACTTCTTAACCCGCTTAT
35069 AAATATTCAT
Statistics
Matches: 315, Mismatches: 38, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
198 174 0.55
199 48 0.15
200 38 0.12
201 55 0.17
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (199 bp):
TATAAGAAAAATTATAAAATACACCGTCAGTGGAGTTTAGCAGACTGCACGTTCGGGGTTTAAGG
GTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTAATTATGAAATGGGG
TATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAAATTTACACTAACAGTGTATTGTATAATA
ATCC
Done.