Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008621.1 Corchorus capsularis cultivar CVL-1 contig08642, 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: 90731
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1090 original size:13 final size:13
Alignment explanation
Indices: 1072--1096 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1062 TAATCAAGAA
1072 AATTAAAGAAAAC
1 AATTAAAGAAAAC
1085 AATTAAAGAAAA
1 AATTAAAGAAAA
1097 AGCAGTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
AATTAAAGAAAAC
Found at i:2404 original size:19 final size:18
Alignment explanation
Indices: 2371--2408 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2361 TTGAAATAAT
2371 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
2389 TCTTCAAATTATCTTCAAA
1 TCTTC-AATGATCTTCAAA
2408 T
1 T
2409 AAGTCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:9445 original size:11 final size:11
Alignment explanation
Indices: 9429--9454 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9419 AATCTGATAG
9429 AAAAAGAAAAT
1 AAAAAGAAAAT
9440 AAAAAGAAAAT
1 AAAAAGAAAAT
9451 AAAA
1 AAAA
9455 CACAATCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.85, C:0.00, G:0.08, T:0.08
Consensus pattern (11 bp):
AAAAAGAAAAT
Found at i:9610 original size:5 final size:5
Alignment explanation
Indices: 9596--9625 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
9586 TTATTTTTCT
*
9596 TAAAA CAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA
9626 AGAATTTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.80, C:0.03, G:0.00, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:9719 original size:13 final size:13
Alignment explanation
Indices: 9701--9725 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
9691 AGATCAAGAA
9701 AATTAAAGAAAAC
1 AATTAAAGAAAAC
9714 AATTAAAGAAAA
1 AATTAAAGAAAA
9726 AGCAGTGAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.04, G:0.08, T:0.16
Consensus pattern (13 bp):
AATTAAAGAAAAC
Found at i:11036 original size:19 final size:18
Alignment explanation
Indices: 11003--11040 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
10993 TTGAAATAAT
11003 TCTTCAATGATCTTCAAA
1 TCTTCAATGATCTTCAAA
*
11021 TCTTCAAATTATCTTCAAA
1 TCTTC-AATGATCTTCAAA
11040 T
1 T
11041 AAGTCTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.34, C:0.21, G:0.03, T:0.42
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAA
Found at i:19598 original size:51 final size:52
Alignment explanation
Indices: 19509--19635 Score: 188
Period size: 51 Copynumber: 2.5 Consensus size: 52
19499 AAAAATTGCC
19509 ACAAAA-AATAATTATTTTATTTTTCTCAAAAAAAAAAAAAGCTGCCACAAACT
1 ACAAAATAATAATTATTTTATTTTTCTC-AAAAAAAAAAAA-CTGCCACAAACT
19562 A-AAAATAATAATTATTTTATTTTTCTC-AAAAAAAAAAACTGCCACAAACT
1 ACAAAATAATAATTATTTTATTTTTCTCAAAAAAAAAAAACTGCCACAAACT
***
19612 ACCTTATAATAATTATTTTATTTT
1 ACAAAATAATAATTATTTTATTTT
19636 CATATATACT
Statistics
Matches: 69, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
50 13 0.19
51 30 0.43
52 4 0.06
53 22 0.32
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.35
Consensus pattern (52 bp):
ACAAAATAATAATTATTTTATTTTTCTCAAAAAAAAAAAACTGCCACAAACT
Found at i:20021 original size:13 final size:13
Alignment explanation
Indices: 19998--20030 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19988 ATTTGTTTTG
19998 TTTTG-TTTTGTA
1 TTTTGTTTTTGTA
*
20010 TTTTGTTTTTGTT
1 TTTTGTTTTTGTA
20023 TTTTGTTT
1 TTTTGTTT
20031 GTCTGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.03, C:0.00, G:0.15, T:0.82
Consensus pattern (13 bp):
TTTTGTTTTTGTA
Found at i:22214 original size:13 final size:13
Alignment explanation
Indices: 22196--22220 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22186 TTTTTTGTGT
22196 GTGAGAGAGAATA
1 GTGAGAGAGAATA
22209 GTGAGAGAGAAT
1 GTGAGAGAGAAT
22221 CTGTCAGATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.40, T:0.16
Consensus pattern (13 bp):
GTGAGAGAGAATA
Found at i:24411 original size:32 final size:32
Alignment explanation
Indices: 24375--24446 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
24365 TCTTTATCCT
24375 TTCTTTCCCTCTATTCATTTTAAACATTTCAA
1 TTCTTTCCCTCTATTCATTTTAAACATTTCAA
24407 TTCTTTCCCTCTATTCATTTTAAACATTTCAA
1 TTCTTTCCCTCTATTCATTTTAAACATTTCAA
*
24439 AT-TTTCCC
1 TTCTTTCCC
24447 CCTCTTCTCT
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 6 0.15
32 33 0.85
ACGTcount: A:0.24, C:0.26, G:0.00, T:0.50
Consensus pattern (32 bp):
TTCTTTCCCTCTATTCATTTTAAACATTTCAA
Found at i:28077 original size:8 final size:8
Alignment explanation
Indices: 28064--28089 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
28054 ATACCACCCC
28064 ACCCAACA
1 ACCCAACA
28072 ACCCAACA
1 ACCCAACA
28080 ACCCAACA
1 ACCCAACA
28088 AC
1 AC
28090 AGTTCATGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (8 bp):
ACCCAACA
Found at i:35382 original size:52 final size:52
Alignment explanation
Indices: 35318--35421 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
35308 CTTTTTTTAT
35318 CTCCAAACGCAATGCCAAACCAGCCCTTATAGTGTTTCAAAAGTATTACTAC
1 CTCCAAACGCAATGCCAAACCAGCCCTTATAGTGTTTCAAAAGTATTACTAC
*
35370 CTCCAAATGCAATGCCAAACCAGCCCTTATAGTGTTTCAAAAGTATTACTAC
1 CTCCAAACGCAATGCCAAACCAGCCCTTATAGTGTTTCAAAAGTATTACTAC
35422 GTAAGCAGTG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.35, C:0.28, G:0.12, T:0.26
Consensus pattern (52 bp):
CTCCAAACGCAATGCCAAACCAGCCCTTATAGTGTTTCAAAAGTATTACTAC
Found at i:35664 original size:45 final size:45
Alignment explanation
Indices: 35600--35689 Score: 180
Period size: 45 Copynumber: 2.0 Consensus size: 45
35590 CTAAGGTTCT
35600 CATGTTCATGAAACAGGTAGCACAACTAATTCCCCTATTGTTTTG
1 CATGTTCATGAAACAGGTAGCACAACTAATTCCCCTATTGTTTTG
35645 CATGTTCATGAAACAGGTAGCACAACTAATTCCCCTATTGTTTTG
1 CATGTTCATGAAACAGGTAGCACAACTAATTCCCCTATTGTTTTG
35690 TATCTCTCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (45 bp):
CATGTTCATGAAACAGGTAGCACAACTAATTCCCCTATTGTTTTG
Found at i:37080 original size:1 final size:1
Alignment explanation
Indices: 37074--37098 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
37064 CTTATGTACC
37074 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
37099 GACAACCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:41039 original size:20 final size:20
Alignment explanation
Indices: 41014--41055 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
41004 ATAAAATTAT
41014 ATACCACATATCTAATAAGC
1 ATACCACATATCTAATAAGC
41034 ATACCACATATCTAATAAGC
1 ATACCACATATCTAATAAGC
41054 AT
1 AT
41056 GGCAGAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.45, C:0.24, G:0.05, T:0.26
Consensus pattern (20 bp):
ATACCACATATCTAATAAGC
Found at i:43288 original size:2 final size:2
Alignment explanation
Indices: 43283--43308 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
43273 TATCAGTGTG
43283 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
43309 AGATAAGATT
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:46585 original size:39 final size:39
Alignment explanation
Indices: 46542--46616 Score: 150
Period size: 39 Copynumber: 1.9 Consensus size: 39
46532 AGCAATACAA
46542 TGATTACAATCTATATAAAGCAAACTGAACAAACAATAT
1 TGATTACAATCTATATAAAGCAAACTGAACAAACAATAT
46581 TGATTACAATCTATATAAAGCAAACTGAACAAACAA
1 TGATTACAATCTATATAAAGCAAACTGAACAAACAA
46617 AACTGAACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (39 bp):
TGATTACAATCTATATAAAGCAAACTGAACAAACAATAT
Found at i:46697 original size:13 final size:13
Alignment explanation
Indices: 46679--46704 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
46669 ACCTGTTCAT
46679 CAAAGAATATATA
1 CAAAGAATATATA
46692 CAAAGAATATATA
1 CAAAGAATATATA
46705 AGTATAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
CAAAGAATATATA
Found at i:48142 original size:32 final size:32
Alignment explanation
Indices: 48101--48165 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
48091 CAAGTAAAAC
48101 AAACTTAAACGAAATTGATCAGAGAATCAGCG
1 AAACTTAAACGAAATTGATCAGAGAATCAGCG
*
48133 AAACTTAAACGAAATTTATCAGAGAATCAGCG
1 AAACTTAAACGAAATTGATCAGAGAATCAGCG
48165 A
1 A
48166 GAATCAGGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.48, C:0.15, G:0.17, T:0.20
Consensus pattern (32 bp):
AAACTTAAACGAAATTGATCAGAGAATCAGCG
Found at i:48399 original size:20 final size:20
Alignment explanation
Indices: 48376--48417 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
48366 AACGCGCTTT
48376 TTTTTAAAAAAACGCGGTAA
1 TTTTTAAAAAAACGCGGTAA
***
48396 TTTTTTTTAAAACGCGGTAA
1 TTTTTAAAAAAACGCGGTAA
48416 TT
1 TT
48418 GAAAAAGGGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (20 bp):
TTTTTAAAAAAACGCGGTAA
Found at i:49102 original size:26 final size:26
Alignment explanation
Indices: 49073--49128 Score: 85
Period size: 26 Copynumber: 2.2 Consensus size: 26
49063 TACTTAGTTT
* * *
49073 ATTATTTTATGTTTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGCATTTA
49099 ATTAGTTTATGATTAATTAGCATTTA
1 ATTAGTTTATGATTAATTAGCATTTA
49125 ATTA
1 ATTA
49129 ATCATGAATT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.02, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGCATTTA
Found at i:49139 original size:26 final size:26
Alignment explanation
Indices: 49085--49143 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
49075 TATTTTATGT
* * *
49085 TTAATTAGTATTTAATTAGTTTATGA
1 TTAATTAGCATTTAATTAGATCATGA
49111 TTAATTAGCATTTAATTA-ATCATGAA
1 TTAATTAGCATTTAATTAGATCATG-A
49137 TTAATTA
1 TTAATTA
49144 ATCATAAACT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 4 0.14
26 25 0.86
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.49
Consensus pattern (26 bp):
TTAATTAGCATTTAATTAGATCATGA
Found at i:49140 original size:15 final size:15
Alignment explanation
Indices: 49122--49159 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
49112 TAATTAGCAT
*
49122 TTAATTAATCATGAA
1 TTAATTAATCATAAA
49137 TTAATTAATCATAAA
1 TTAATTAATCATAAA
*
49152 CTAATTAA
1 TTAATTAA
49160 ATACTAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (15 bp):
TTAATTAATCATAAA
Found at i:49182 original size:15 final size:15
Alignment explanation
Indices: 49123--49186 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 15
49113 AATTAGCATT
* * *
49123 TAATTAATCATGAAT
1 TAATTAAACATAAAC
*
49138 TAATTAATCATAAAC
1 TAATTAAACATAAAC
49153 TAATT-AA-AT--AC
1 TAATTAAACATAAAC
49164 TAATTAAACATAAAC
1 TAATTAAACATAAAC
49179 TAA-TAAAC
1 TAATTAAAC
49187 TAAGTAATTT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
11 7 0.17
12 2 0.05
13 4 0.10
14 6 0.14
15 23 0.55
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.33
Consensus pattern (15 bp):
TAATTAAACATAAAC
Found at i:49978 original size:159 final size:159
Alignment explanation
Indices: 49689--50004 Score: 596
Period size: 159 Copynumber: 2.0 Consensus size: 159
49679 CATCTAAATA
*
49689 AGAATTTAACCCAAACTAGAAATTATACCTTAAATAAACTACCTACCTACTAAAGAAGCAAACAA
1 AGAATTCAACCCAAACTAGAAATTATACCTTAAATAAACTACCTACCTACTAAAGAAGCAAACAA
49754 ATTACAAAGAAACTCACATCCGTGAGAGTTGAACCTAAGACCTCATGGTCTAGGTAAGCTGAAAC
66 ATTACAAAGAAACTCACATCCGTGAGAGTTGAACCTAAGACCTCATGGTCTAGGTAAGCTGAAAC
49819 TAAGAGTCCAATACTCTATCATCAGGCAT
131 TAAGAGTCCAATACTCTATCATCAGGCAT
*
49848 AGAATTCAACCCAAACTAGAAATTATACCTTAAATAAACTACCTACCTACTAAATAAGCAAACAA
1 AGAATTCAACCCAAACTAGAAATTATACCTTAAATAAACTACCTACCTACTAAAGAAGCAAACAA
* *
49913 ATTACAAAGAAACTCACATCTGTGAGAGTTGAACCTAAGACCTCATGGTCTAGGTAGGCTGAAAC
66 ATTACAAAGAAACTCACATCCGTGAGAGTTGAACCTAAGACCTCATGGTCTAGGTAAGCTGAAAC
49978 TAAGAGTCCAATACTCTATCATCAGGC
131 TAAGAGTCCAATACTCTATCATCAGGC
50005 CAAATGCCTG
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
159 153 1.00
ACGTcount: A:0.42, C:0.22, G:0.13, T:0.23
Consensus pattern (159 bp):
AGAATTCAACCCAAACTAGAAATTATACCTTAAATAAACTACCTACCTACTAAAGAAGCAAACAA
ATTACAAAGAAACTCACATCCGTGAGAGTTGAACCTAAGACCTCATGGTCTAGGTAAGCTGAAAC
TAAGAGTCCAATACTCTATCATCAGGCAT
Found at i:51780 original size:52 final size:52
Alignment explanation
Indices: 51702--51809 Score: 198
Period size: 52 Copynumber: 2.1 Consensus size: 52
51692 AAGAGTCTTA
* *
51702 TCGGCCTTCATATATGCTGCAAGAAACTGGCATGGACTACCCTTAGAAGTGT
1 TCGGCCTTCATATATACTGCAAGAAACTGGCATGGACTACCCTCAGAAGTGT
51754 TCGGCCTTCATATATACTGCAAGAAACTGGCATGGACTACCCTCAGAAGTGT
1 TCGGCCTTCATATATACTGCAAGAAACTGGCATGGACTACCCTCAGAAGTGT
51806 TCGG
1 TCGG
51810 GCGCTATAAG
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (52 bp):
TCGGCCTTCATATATACTGCAAGAAACTGGCATGGACTACCCTCAGAAGTGT
Found at i:59229 original size:42 final size:42
Alignment explanation
Indices: 59140--59230 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
59130 AAAGGATCGA
* ***
59140 ATGGCCGGTTGTGGCCGGATGGCCTGTGCCATGGCTTGTGCG
1 ATGGCCGGTTGTGGCCGAATGGCCTGTGCCATGGCCCATGCG
* *
59182 ATGGCCGGTTGTGGCCGAATGG-CTCGTGCGATGTCCCATGCG
1 ATGGCCGGTTGTGGCCGAATGGCCT-GTGCCATGGCCCATGCG
*
59224 TTGGCCG
1 ATGGCCG
59231 CTCATGGCCG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 2 0.05
42 39 0.95
ACGTcount: A:0.09, C:0.25, G:0.41, T:0.25
Consensus pattern (42 bp):
ATGGCCGGTTGTGGCCGAATGGCCTGTGCCATGGCCCATGCG
Found at i:64653 original size:42 final size:41
Alignment explanation
Indices: 64589--64683 Score: 129
Period size: 42 Copynumber: 2.3 Consensus size: 41
64579 AAAGGATCAA
64589 ATGGCCGGTTGTGGCCGAATGGC-CTGTGCCATGGCCCATGC
1 ATGGCCGGTTGTGGCCGAATGGCTC-GTGCCATGGCCCATGC
* * *
64630 GATGGCCGGTTGTGGCCGGATGGCTCGTGCGATGTCCCATGC
1 -ATGGCCGGTTGTGGCCGAATGGCTCGTGCCATGGCCCATGC
64672 ATTGGCCGGTTG
1 A-TGGCCGGTTG
64684 CTCCATGCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
41 1 0.02
42 46 0.96
43 1 0.02
ACGTcount: A:0.11, C:0.26, G:0.39, T:0.24
Consensus pattern (41 bp):
ATGGCCGGTTGTGGCCGAATGGCTCGTGCCATGGCCCATGC
Found at i:66476 original size:2 final size:2
Alignment explanation
Indices: 66462--66496 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
66452 ATAAAGGGGC
*
66462 TA TA TA AA T- 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 TA TA
66497 ACTATTACTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:66684 original size:47 final size:48
Alignment explanation
Indices: 66631--66725 Score: 174
Period size: 47 Copynumber: 2.0 Consensus size: 48
66621 TTAGCGCAAG
*
66631 TAATTTTACACAGAAGGTGACATTTAATTTTGTTGTCATA-GGGTCAA
1 TAATTTTACACAGAAGGTGACATTTAATTTTGCTGTCATAGGGGTCAA
66678 TAATTTTACACAGAAGGTGACATTTAATTTTGCTGTCATAGGGGTCAA
1 TAATTTTACACAGAAGGTGACATTTAATTTTGCTGTCATAGGGGTCAA
66726 CTGTAGAGCC
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
47 39 0.85
48 7 0.15
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (48 bp):
TAATTTTACACAGAAGGTGACATTTAATTTTGCTGTCATAGGGGTCAA
Found at i:82197 original size:15 final size:15
Alignment explanation
Indices: 82173--82240 Score: 100
Period size: 15 Copynumber: 4.5 Consensus size: 15
82163 CACAACATGA
*
82173 TTGTTCGCACCATTG
1 TTGTTTGCACCATTG
82188 TTGTTTGCACCATTG
1 TTGTTTGCACCATTG
* **
82203 TGGTTTGCATAATTG
1 TTGTTTGCACCATTG
82218 TTGTTTGCACCATTG
1 TTGTTTGCACCATTG
82233 TTGTTTGC
1 TTGTTTGC
82241 GCTATTCACC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.13, C:0.18, G:0.22, T:0.47
Consensus pattern (15 bp):
TTGTTTGCACCATTG
Found at i:84423 original size:9 final size:9
Alignment explanation
Indices: 84409--84447 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
84399 ATTTTCAACA
84409 TAATTTAAT
1 TAATTTAAT
**
84418 TAATTTCTT
1 TAATTTAAT
84427 TAATTTAAT
1 TAATTTAAT
*
84436 TAATTAAAT
1 TAATTTAAT
84445 TAA
1 TAA
84448 AAGAAATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (9 bp):
TAATTTAAT
Found at i:87239 original size:1 final size:1
Alignment explanation
Indices: 87233--87263 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
87223 TAAGTGACAG
87233 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
87264 ATGAATTATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Done.