Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014972.1 Corchorus olitorius cultivar O-4 contig15005, 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: 141220
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:3259 original size:27 final size:27
Alignment explanation
Indices: 3229--3347 Score: 175
Period size: 27 Copynumber: 4.4 Consensus size: 27
3219 TGTTTCTTAA
* *
3229 TTGGTCATTTGTACACTTAGGGGCATT
1 TTGGTCATTTATACACTCAGGGGCATT
*
3256 TTGGTCATTTATGCACTCAGGGGCATT
1 TTGGTCATTTATACACTCAGGGGCATT
* *
3283 TTGGTCATTTGTACACTCAGGGGGCAGT
1 TTGGTCATTTATACACTCA-GGGGCATT
*
3311 TTGGTCATTTATGCACTCAGGGGCATT
1 TTGGTCATTTATACACTCAGGGGCATT
3338 TTGGTCATTT
1 TTGGTCATTT
3348 TGCATGCTCT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 58 0.71
28 24 0.29
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.39
Consensus pattern (27 bp):
TTGGTCATTTATACACTCAGGGGCATT
Found at i:3325 original size:55 final size:54
Alignment explanation
Indices: 3229--3347 Score: 211
Period size: 55 Copynumber: 2.2 Consensus size: 54
3219 TGTTTCTTAA
* *
3229 TTGGTCATTTGTACACTTAGGGGCATTTTGGTCATTTATGCACTCAGGGGCATT
1 TTGGTCATTTGTACACTCAGGGGCAGTTTGGTCATTTATGCACTCAGGGGCATT
3283 TTGGTCATTTGTACACTCAGGGGGCAGTTTGGTCATTTATGCACTCAGGGGCATT
1 TTGGTCATTTGTACACTCA-GGGGCAGTTTGGTCATTTATGCACTCAGGGGCATT
3338 TTGGTCATTT
1 TTGGTCATTT
3348 TGCATGCTCT
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
54 18 0.29
55 44 0.71
ACGTcount: A:0.18, C:0.17, G:0.27, T:0.39
Consensus pattern (54 bp):
TTGGTCATTTGTACACTCAGGGGCAGTTTGGTCATTTATGCACTCAGGGGCATT
Found at i:16168 original size:32 final size:32
Alignment explanation
Indices: 16122--16202 Score: 126
Period size: 32 Copynumber: 2.5 Consensus size: 32
16112 TACGGTGGCA
* *
16122 TTTTCTTCAAAAGACGCCCCTATCTAGCGTTG
1 TTTTCTTCAAAAGACGCCCCTATCTACCGGTG
*
16154 TTTTCTTCACAAGACGCCCCTATCTACCGGTG
1 TTTTCTTCAAAAGACGCCCCTATCTACCGGTG
*
16186 TTTTCTTTAAAAGACGC
1 TTTTCTTCAAAAGACGC
16203 TGTCATATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 44 1.00
ACGTcount: A:0.22, C:0.28, G:0.15, T:0.35
Consensus pattern (32 bp):
TTTTCTTCAAAAGACGCCCCTATCTACCGGTG
Found at i:18968 original size:42 final size:44
Alignment explanation
Indices: 18921--19008 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 44
18911 TTACCTAAAC
* *
18921 TCTACT-C-CATCTCTAGGTAATTCATCAAAACAAAGCTAATAT
1 TCTACTCCGCATCTCTAGATAATTCATCAAAACAAAACTAATAT
*
18963 TCTACTCCTGCATCTCTAGATAATTCATCAAAATAAAACTAATAT
1 TCTACTCC-GCATCTCTAGATAATTCATCAAAACAAAACTAATAT
19008 T
1 T
19009 AATTGTTGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
42 6 0.15
43 1 0.03
45 33 0.82
ACGTcount: A:0.39, C:0.23, G:0.06, T:0.33
Consensus pattern (44 bp):
TCTACTCCGCATCTCTAGATAATTCATCAAAACAAAACTAATAT
Found at i:47374 original size:13 final size:13
Alignment explanation
Indices: 47356--47383 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
47346 AATTTGCTTC
47356 AAATAAAATATTA
1 AAATAAAATATTA
47369 AAATAAAATATTA
1 AAATAAAATATTA
47382 AA
1 AA
47384 TTGCTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAAATATTA
Found at i:47652 original size:28 final size:28
Alignment explanation
Indices: 47594--47647 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
47584 ATTAATAAGT
* *
47594 AAACTTTGCCTTCCCTTCTGGCCAAGAA
1 AAACTTTGCCTTCCCTTCAGGCAAAGAA
47622 AAACTTTGCCTTCCC-TCAGG-AAAGAA
1 AAACTTTGCCTTCCCTTCAGGCAAAGAA
47648 GAAAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 5 0.21
27 4 0.17
28 15 0.62
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (28 bp):
AAACTTTGCCTTCCCTTCAGGCAAAGAA
Found at i:48373 original size:7 final size:7
Alignment explanation
Indices: 48361--48386 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
48351 GAAATGGCGT
48361 CTGCAGA
1 CTGCAGA
48368 CTGCAGA
1 CTGCAGA
48375 CTGCAGA
1 CTGCAGA
48382 CTGCA
1 CTGCA
48387 ACAACCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.15
Consensus pattern (7 bp):
CTGCAGA
Found at i:63870 original size:16 final size:16
Alignment explanation
Indices: 63849--63880 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
63839 AGTATTAGAA
63849 ATTTAACAATTGACAT
1 ATTTAACAATTGACAT
63865 ATTTAACAATTGACAT
1 ATTTAACAATTGACAT
63881 TTGTCAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (16 bp):
ATTTAACAATTGACAT
Found at i:66778 original size:28 final size:28
Alignment explanation
Indices: 66725--66781 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
66715 AGTTAACACC
*** *
66725 AAAAGGAAATACTATATTGCTCAAAAAA
1 AAAAGGAAATACTATATAAATAAAAAAA
66753 AAAAGGAAATACTATATAAATAAAAAAA
1 AAAAGGAAATACTATATAAATAAAAAAA
66781 A
1 A
66782 TAAAAAATCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.65, C:0.07, G:0.09, T:0.19
Consensus pattern (28 bp):
AAAAGGAAATACTATATAAATAAAAAAA
Found at i:79619 original size:84 final size:84
Alignment explanation
Indices: 79499--79668 Score: 331
Period size: 84 Copynumber: 2.0 Consensus size: 84
79489 ACAATGTATC
*
79499 ATCACTACATGTTAGTTTTAACACTGATCATGAGCTTGGGACCAAAGCTCAGTTGCTTCCCTTAG
1 ATCACTAAATGTTAGTTTTAACACTGATCATGAGCTTGGGACCAAAGCTCAGTTGCTTCCCTTAG
79564 GTAGAAAACGTATGCCAAT
66 GTAGAAAACGTATGCCAAT
79583 ATCACTAAATGTTAGTTTTAACACTGATCATGAGCTTGGGACCAAAGCTCAGTTGCTTCCCTTAG
1 ATCACTAAATGTTAGTTTTAACACTGATCATGAGCTTGGGACCAAAGCTCAGTTGCTTCCCTTAG
79648 GTAGAAAACGTATGCCAAT
66 GTAGAAAACGTATGCCAAT
79667 AT
1 AT
79669 AATAAGAAAC
Statistics
Matches: 85, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.30
Consensus pattern (84 bp):
ATCACTAAATGTTAGTTTTAACACTGATCATGAGCTTGGGACCAAAGCTCAGTTGCTTCCCTTAG
GTAGAAAACGTATGCCAAT
Found at i:80444 original size:2 final size:2
Alignment explanation
Indices: 80437--80469 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
80427 CAAGCCTATA
*
80437 AG AG AG AG AG CG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
80470 AGAAGAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.03, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:80475 original size:3 final size:3
Alignment explanation
Indices: 80467--80497 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
80457 AGAGAGAGAG
80467 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A
80498 TTAGGGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:81158 original size:2 final size:2
Alignment explanation
Indices: 81153--81178 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81143 CCCAGGAAGT
81153 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
81179 TCTTGCCTGT
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:86720 original size:108 final size:108
Alignment explanation
Indices: 86524--86830 Score: 422
Period size: 108 Copynumber: 2.8 Consensus size: 108
86514 TTTAACTCTT
* ** * * * *
86524 TTATTAATATCCAATAGTTATATTTTGTTTTGAA-TCTCGAATAATCTAGAGTCAGAGTCATATT
1 TTATCAATATCCTGTAGTCATATTTTGTATT-AAGTCTCGACTAATTTAGAGTCA-AGTCATATT
* *
86588 GGACACTAATTGAGAACTAGAAGATCTCCGTAAGTA-TCTATTTTC
64 GGACACTAATTGAGAACTAAAAGATCTCCGTAAGTACTC-ATTCTC
*
86633 TTATCAATATCCTGTAGTCATATTTTGTATTAAGTCTCGACTAATTTAGAATCAAGTCATATTGG
1 TTATCAATATCCTGTAGTCATATTTTGTATTAAGTCTCGACTAATTTAGAGTCAAGTCATATTGG
*
86698 ACACTAATTGAGAACTAAAAGATCTCTGTAAGTACTCATTCTC
66 ACACTAATTGAGAACTAAAAGATCTCCGTAAGTACTCATTCTC
** **
86741 TTATCAATAT-CTCGTAGTCATATTTTGTATTAAGTCTCGACTAATTTAGAGTTGAGTTGTATTG
1 TTATCAATATCCT-GTAGTCATATTTTGTATTAAGTCTCGACTAATTTAGAGTCAAGTCATATTG
86805 GACACTAATTGAGAACTAAAAGATCT
65 GACACTAATTGAGAACTAAAAGATCT
86831 TGAGTATCTA
Statistics
Matches: 179, Mismatches: 16, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
107 2 0.01
108 132 0.74
109 45 0.25
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (108 bp):
TTATCAATATCCTGTAGTCATATTTTGTATTAAGTCTCGACTAATTTAGAGTCAAGTCATATTGG
ACACTAATTGAGAACTAAAAGATCTCCGTAAGTACTCATTCTC
Found at i:88733 original size:87 final size:87
Alignment explanation
Indices: 88587--88752 Score: 314
Period size: 87 Copynumber: 1.9 Consensus size: 87
88577 AGTGAACCAA
*
88587 TGAACCTTAGACGATTATTGAGGAATCCTTAATTTTGTTCATTACGTCTTTAAATTGGATGTGGC
1 TGAACCTTAGACGATTATTGAGGAATCCATAATTTTGTTCATTACGTCTTTAAATTGGATGTGGC
*
88652 TGATTTTTTGGCATTAAGTTAC
66 TGATATTTTGGCATTAAGTTAC
88674 TGAACCTTAGACGATTATTGAGGAATCCATAATTTTGTTCATTACGTCTTTAAATTGGATGTGGC
1 TGAACCTTAGACGATTATTGAGGAATCCATAATTTTGTTCATTACGTCTTTAAATTGGATGTGGC
88739 TGATATTTTGGCAT
66 TGATATTTTGGCAT
88753 CAAGGAAGCA
Statistics
Matches: 77, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.26, C:0.13, G:0.20, T:0.42
Consensus pattern (87 bp):
TGAACCTTAGACGATTATTGAGGAATCCATAATTTTGTTCATTACGTCTTTAAATTGGATGTGGC
TGATATTTTGGCATTAAGTTAC
Found at i:88968 original size:53 final size:53
Alignment explanation
Indices: 88888--88996 Score: 218
Period size: 53 Copynumber: 2.1 Consensus size: 53
88878 TGGTATTGAC
88888 TGTAGAATGTAGTGACTAGTGAGTAAGCTGGAATTATTGCAGCTCATTTTCTT
1 TGTAGAATGTAGTGACTAGTGAGTAAGCTGGAATTATTGCAGCTCATTTTCTT
88941 TGTAGAATGTAGTGACTAGTGAGTAAGCTGGAATTATTGCAGCTCATTTTCTT
1 TGTAGAATGTAGTGACTAGTGAGTAAGCTGGAATTATTGCAGCTCATTTTCTT
88994 TGT
1 TGT
88997 TATATTTCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 56 1.00
ACGTcount: A:0.26, C:0.11, G:0.25, T:0.39
Consensus pattern (53 bp):
TGTAGAATGTAGTGACTAGTGAGTAAGCTGGAATTATTGCAGCTCATTTTCTT
Found at i:93342 original size:1 final size:1
Alignment explanation
Indices: 93336--93368 Score: 66
Period size: 1 Copynumber: 33.0 Consensus size: 1
93326 AAATTTCTTG
93336 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
93369 CTTTACTCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:99691 original size:21 final size:21
Alignment explanation
Indices: 99667--99710 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
99657 CCTTGCCTTT
99667 TATAGCTGATTCCATGGTAGA
1 TATAGCTGATTCCATGGTAGA
99688 TATAGCTGATTCCATGGTAGA
1 TATAGCTGATTCCATGGTAGA
99709 TA
1 TA
99711 CCGGGTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.14, G:0.23, T:0.34
Consensus pattern (21 bp):
TATAGCTGATTCCATGGTAGA
Found at i:101898 original size:12 final size:13
Alignment explanation
Indices: 101873--101897 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
101863 AATAAACAAT
101873 TTCTTATAAAAAA
1 TTCTTATAAAAAA
101886 TTCTTATAAAAA
1 TTCTTATAAAAA
101898 TGGTAAAACA
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:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (13 bp):
TTCTTATAAAAAA
Found at i:104408 original size:130 final size:131
Alignment explanation
Indices: 104209--104471 Score: 395
Period size: 130 Copynumber: 2.0 Consensus size: 131
104199 GTTATTTAAG
** * * * *
104209 AAATATATTTTAAAATTTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAATTGATAAAAATA
1 AAATATATTAAAAAAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAATTGATAAAAATA
104274 AAATAGGTATAAGGATATTA-GATTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTAT
66 AAATAGGTATAAGGATATTATG-TTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTAT
104338 AA
130 AA
* *
104340 AAATATATTAAAAAAATTCTAATATATATAA-ATTTTTAATTAAAATAGTAAATTGGTAAAAATT
1 AAATATATTAAAAAAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAATTGATAAAAATA
* * * *
104404 AAATAGTTATGAGGATATTATGTTTAATTAAATAAAGATAGAGTTTTTAGTTGAGTAAAACTATA
66 AAATAGGTATAAGGATATTATGTTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
104469 A
131 A
104470 AA
1 AA
104472 GTCTAATGAC
Statistics
Matches: 119, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
130 91 0.76
131 28 0.24
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (131 bp):
AAATATATTAAAAAAATTCTAATATATATAAGATTTTTAATTAAAATAGTAAATTGATAAAAATA
AAATAGGTATAAGGATATTATGTTTAATTAAATAAAAAAAGAGTTTTTAGTTGAGTAAAACTATA
A
Found at i:115582 original size:23 final size:23
Alignment explanation
Indices: 115556--115600 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
115546 ATTACTCGAA
*
115556 CCCGACCCGAGACCGAGCCCGAT
1 CCCGACCCGAGACCGAACCCGAT
* * *
115579 CCCGGCTCGAGCCCGAACCCGA
1 CCCGACCCGAGACCGAACCCGA
115601 AATAATTTGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.20, C:0.49, G:0.27, T:0.04
Consensus pattern (23 bp):
CCCGACCCGAGACCGAACCCGAT
Found at i:116578 original size:16 final size:16
Alignment explanation
Indices: 116557--116678 Score: 115
Period size: 16 Copynumber: 7.7 Consensus size: 16
116547 CTATCCGAGA
116557 CCGAACCCGAAAATAC
1 CCGAACCCGAAAATAC
*
116573 CCGAACCCG-ACATAAC
1 CCGAACCCGAAAAT-AC
* * *
116589 CCGAGCCCGAAAAAAG
1 CCGAACCCGAAAATAC
**
116605 CCGAACCCG-ACTTAAC
1 CCGAACCCGAAAAT-AC
* *
116621 CCGAGCTCGAAAATAC
1 CCGAACCCGAAAATAC
*
116637 CCGAACCCGAAAAAAC
1 CCGAACCCGAAAATAC
*
116653 CCGAACCCG-AAGTAC
1 CCGAACCCGAAAATAC
116668 CCGAACCCGAA
1 CCGAACCCGAA
116679 CCCGCCCAAT
Statistics
Matches: 82, Mismatches: 19, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
15 17 0.21
16 61 0.74
17 4 0.05
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.06
Consensus pattern (16 bp):
CCGAACCCGAAAATAC
Found at i:116609 original size:32 final size:32
Alignment explanation
Indices: 116557--116677 Score: 154
Period size: 32 Copynumber: 3.8 Consensus size: 32
116547 CTATCCGAGA
116557 CCGAACCCGAAAATACCCGAACCCGACATAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* * * *
116589 CCGAGCCCGAAAAAAGCCGAACCCGACTTAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
* * * *
116621 CCGAGCTCGAAAATACCCGAACCCGAAAAAAC
1 CCGAACCCGAAAATACCCGAACCCGACATAAC
*
116653 CCGAACCCG-AAGTACCCGAACCCGA
1 CCGAACCCGAAAATACCCGAACCCGA
116678 ACCCGCCCAA
Statistics
Matches: 76, Mismatches: 13, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
31 15 0.20
32 61 0.80
ACGTcount: A:0.39, C:0.39, G:0.17, T:0.06
Consensus pattern (32 bp):
CCGAACCCGAAAATACCCGAACCCGACATAAC
Found at i:116623 original size:48 final size:47
Alignment explanation
Indices: 116557--116678 Score: 138
Period size: 48 Copynumber: 2.6 Consensus size: 47
116547 CTATCCGAGA
* * * *
116557 CCGAACCCGAAAATACCCGAACCCG-ACATAACCCGAGCCCGAAAAAAG
1 CCGAACCCG-AAGTACCCGAACCCGAAAAT-ACCCGAACCCGAAAAAAC
** * *
116605 CCGAACCCGACTTAACCCGAGCTCGAAAATACCCGAACCCGAAAAAAC
1 CCGAACCCGAAGT-ACCCGAACCCGAAAATACCCGAACCCGAAAAAAC
116653 CCGAACCCGAAGTACCCGAACCCGAA
1 CCGAACCCGAAGTACCCGAACCCGAA
116679 CCCGCCCAAT
Statistics
Matches: 61, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
47 13 0.21
48 45 0.74
49 3 0.05
ACGTcount: A:0.39, C:0.39, G:0.16, T:0.06
Consensus pattern (47 bp):
CCGAACCCGAAGTACCCGAACCCGAAAATACCCGAACCCGAAAAAAC
Found at i:117354 original size:22 final size:25
Alignment explanation
Indices: 117306--117354 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
117296 ATTTGTTTTG
117306 TATACTTTATTTAGTAAAAAAGTATTC
1 TATACTTTATTTAG-AAAAAAG-ATTC
117333 TATA-TTTATTTA-AAAAAA-ATTC
1 TATACTTTATTTAGAAAAAAGATTC
117355 AATGTGCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
22 4 0.18
24 6 0.27
26 8 0.36
27 4 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (25 bp):
TATACTTTATTTAGAAAAAAGATTC
Found at i:119121 original size:137 final size:137
Alignment explanation
Indices: 118871--119145 Score: 523
Period size: 137 Copynumber: 2.0 Consensus size: 137
118861 ACCCGAACCC
118871 GAAACCCGTCCAACCCGCCCGATTGACTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGT
1 GAAACCCGTCCAACCCGCCCGATTGACTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGT
* *
118936 TACTCTTCTTTTTATTTTTAAAAACTTTATAAGTTTTTTTAATTAAATTAGTAAAATGGTAAAAA
66 TACTCTTCTTTTTACTTTTAAAAACTTTATAAGTTTTTTTAATAAAATTAGTAAAATGGTAAAAA
119001 TAAAATA
131 TAAAATA
*
119008 GAAACCCGTCCAACCCGCCCGATTGACTCATCTAGCTTTATAAGTCAAATGAAATAATTGCATGT
1 GAAACCCGTCCAACCCGCCCGATTGACTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGT
119073 TACTCTTCTTTTTACTTTTAAAAACTTTATAAGTTTTTTTAATAAAATTAGTAAAATGGTAAAAA
66 TACTCTTCTTTTTACTTTTAAAAACTTTATAAGTTTTTTTAATAAAATTAGTAAAATGGTAAAAA
119138 TAAAATA
131 TAAAATA
119145 G
1 G
119146 GTATAAAAAT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
137 135 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (137 bp):
GAAACCCGTCCAACCCGCCCGATTGACTCATCTAACTTTATAAGTCAAATGAAATAATTGCATGT
TACTCTTCTTTTTACTTTTAAAAACTTTATAAGTTTTTTTAATAAAATTAGTAAAATGGTAAAAA
TAAAATA
Found at i:120449 original size:23 final size:23
Alignment explanation
Indices: 120420--120477 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 23
120410 GGAAGGTTAC
120420 AAAATTTCATAGGAATG-TTTATT
1 AAAATTTCATAGGAA-GATTTATT
120443 AAAATTTCATAGGAAGATTTATT
1 AAAATTTCATAGGAAGATTTATT
120466 AAAATTTCATAG
1 AAAATTTCATAG
120478 TTAGGTTATC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.43, C:0.05, G:0.12, T:0.40
Consensus pattern (23 bp):
AAAATTTCATAGGAAGATTTATT
Found at i:132568 original size:17 final size:17
Alignment explanation
Indices: 132546--132579 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
132536 GTGTTTAATT
132546 GCTCTAATTGCTCTTGC
1 GCTCTAATTGCTCTTGC
132563 GCTCTAATTGCTCTTGC
1 GCTCTAATTGCTCTTGC
132580 AAATCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (17 bp):
GCTCTAATTGCTCTTGC
Found at i:132716 original size:17 final size:17
Alignment explanation
Indices: 132694--132727 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
132684 GTGTTTAATT
132694 GCTCTAATTGCTCTTGC
1 GCTCTAATTGCTCTTGC
132711 GCTCTAATTGCTCTTGC
1 GCTCTAATTGCTCTTGC
132728 AAATCAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (17 bp):
GCTCTAATTGCTCTTGC
Found at i:132802 original size:148 final size:148
Alignment explanation
Indices: 132534--132829 Score: 583
Period size: 148 Copynumber: 2.0 Consensus size: 148
132524 TTTTGTTAGT
132534 TTGTGTTTAATTGCTCTAATTGCTCTTGCGCTCTAATTGCTCTTGCAAATCAACAAGGTTCACCG
1 TTGTGTTTAATTGCTCTAATTGCTCTTGCGCTCTAATTGCTCTTGCAAATCAACAAGGTTCACCG
132599 TATACAAAGGAATCAATTTTGTTAGTTTGTGTTTAATTGCTCTAATTGCTCTTGCAAAATCAACA
66 TATACAAAGGAATCAATTTTGTTAGTTTGTGTTTAATTGCTCTAATTGCTCTTGCAAAATCAACA
132664 AGAAGGAAGGAATCAATC
131 AGAAGGAAGGAATCAATC
132682 TTGTGTTTAATTGCTCTAATTGCTCTTGCGCTCTAATTGCTCTTGCAAATCAACAAGGTTCACCG
1 TTGTGTTTAATTGCTCTAATTGCTCTTGCGCTCTAATTGCTCTTGCAAATCAACAAGGTTCACCG
*
132747 TATACAAAGGAGTCAATTTTGTTAGTTTGTGTTTAATTGCTCTAATTGCTCTTGCAAAATCAACA
66 TATACAAAGGAATCAATTTTGTTAGTTTGTGTTTAATTGCTCTAATTGCTCTTGCAAAATCAACA
132812 AGAAGGAAGGAATCAATC
131 AGAAGGAAGGAATCAATC
132830 GAGAGTTAGT
Statistics
Matches: 147, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
148 147 1.00
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.36
Consensus pattern (148 bp):
TTGTGTTTAATTGCTCTAATTGCTCTTGCGCTCTAATTGCTCTTGCAAATCAACAAGGTTCACCG
TATACAAAGGAATCAATTTTGTTAGTTTGTGTTTAATTGCTCTAATTGCTCTTGCAAAATCAACA
AGAAGGAAGGAATCAATC
Found at i:133016 original size:71 final size:71
Alignment explanation
Indices: 132898--133035 Score: 240
Period size: 71 Copynumber: 1.9 Consensus size: 71
132888 AAAAGGTAGA
*
132898 TAAGACACTACATTTCTTTGTAAAAGGGTAGATGACTCTATGTTGGCTCTAACGAGTTCCTAGTA
1 TAAGACACTACATTTCTTTGTAAAAGGGTAGATGACTCTATGCTGGCTCTAACGAGTTCCTAGTA
132963 TAAAGC
66 TAAAGC
* * *
132969 TAAGACACTACATTTCTTTGTAAAAGGGTATATGTCTTTATGCTGGCTCTAACGAGTTCCTAGTA
1 TAAGACACTACATTTCTTTGTAAAAGGGTAGATGACTCTATGCTGGCTCTAACGAGTTCCTAGTA
133034 TA
66 TA
133036 GAGTTCCAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
71 63 1.00
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (71 bp):
TAAGACACTACATTTCTTTGTAAAAGGGTAGATGACTCTATGCTGGCTCTAACGAGTTCCTAGTA
TAAAGC
Found at i:140178 original size:12 final size:12
Alignment explanation
Indices: 140161--140189 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
140151 GGTAATGTAA
140161 TTGCAGATGCTC
1 TTGCAGATGCTC
140173 TTGCAGATGCTC
1 TTGCAGATGCTC
140185 TTGCA
1 TTGCA
140190 AAAGCAGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.24, G:0.24, T:0.34
Consensus pattern (12 bp):
TTGCAGATGCTC
Found at i:140846 original size:108 final size:107
Alignment explanation
Indices: 140677--140893 Score: 389
Period size: 108 Copynumber: 2.0 Consensus size: 107
140667 TTGACCTGAA
140677 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTA
1 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTA
* *
140742 TCAAATTAAACTTTTAATTAAGGTTCAATATGCAATTTCATTT
66 TCAAATTAAACTTTTAATT-AGATTCAATATGCAATTTAATTT
*
140785 ATATCTAAAATAACCTTTTTAATTTTAGAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTA
1 ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTA
*
140850 TCAAATTAAACTTTTAATTAGATTCAATATGTAATTTAATTT
66 TCAAATTAAACTTTTAATTAGATTCAATATGCAATTTAATTT
140892 AT
1 AT
140894 CAATTAAATT
Statistics
Matches: 105, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 22 0.21
108 83 0.79
ACGTcount: A:0.39, C:0.08, G:0.08, T:0.44
Consensus pattern (107 bp):
ATATCTAAAATAACCTTTTTAATTTTAAAAGTTTAGTATTCATTTAAAGGGTAAACATGTATTTA
TCAAATTAAACTTTTAATTAGATTCAATATGCAATTTAATTT
Found at i:140975 original size:21 final size:21
Alignment explanation
Indices: 140951--141014 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 21
140941 GTAATATATA
*
140951 TAATAACTAAAATACTTACAT
1 TAATAACTGAAATACTTACAT
* *
140972 TAATTAAATGTAATA-TT--A-
1 TAA-TAACTGAAATACTTACAT
140990 TAATAACTGAAATACTTACAT
1 TAATAACTGAAATACTTACAT
141011 TAAT
1 TAAT
141015 TAAATTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
17 9 0.27
18 5 0.15
19 1 0.03
20 1 0.03
21 9 0.27
22 8 0.24
ACGTcount: A:0.50, C:0.09, G:0.03, T:0.38
Consensus pattern (21 bp):
TAATAACTGAAATACTTACAT
Found at i:140996 original size:39 final size:40
Alignment explanation
Indices: 140939--141019 Score: 146
Period size: 39 Copynumber: 2.0 Consensus size: 40
140929 TTTAATTCCT
140939 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
*
140979 ATGTAATAT-TATAATAACTGAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
141018 AT
1 AT
141020 TCTTAGGTAT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 31 0.77
40 9 0.22
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Done.