Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002623.1 Hibiscus syriacus cultivar Beakdansim tig00005339_pilon, 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: 105194
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:5376 original size:74 final size:74
Alignment explanation
Indices: 5255--5395 Score: 239
Period size: 74 Copynumber: 1.9 Consensus size: 74
5245 GACAAGATGG
* * *
5255 GATATATTCAGCAATGTTAAGAGTTTTAGTAGCTGTTTCTGGGTGAATGTCCAGCTTGTATAACT
1 GATATATTCAGCAATGTTAAGAGCTTTAGTAACTGTTTCTGGGTGAATGACCAGCTTGTATAACT
5320 TTTGGAGCA
66 TTTGGAGCA
5329 GATATATTCAGCCAA-GTTAAGAGCTTTAGTAACTGTTTCTGGGTGAATGACCAGCTTGTATAAC
1 GATATATTCAG-CAATGTTAAGAGCTTTAGTAACTGTTTCTGGGTGAATGACCAGCTTGTATAAC
5393 TTT
65 TTT
5396 GCAACAGATT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
74 60 0.95
75 3 0.05
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (74 bp):
GATATATTCAGCAATGTTAAGAGCTTTAGTAACTGTTTCTGGGTGAATGACCAGCTTGTATAACT
TTTGGAGCA
Found at i:10440 original size:4 final size:4
Alignment explanation
Indices: 10431--10493 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
10421 GGGGCATTGG
10431 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA
10479 GAAA GAAA GAAA GAA
1 GAAA GAAA GAAA GAA
10494 GATGAGAGCC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:16636 original size:21 final size:21
Alignment explanation
Indices: 16611--16651 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16601 TCTGGGCAAA
* *
16611 GGGAATCGGTACCCATTCAAG
1 GGGAACCGATACCCATTCAAG
*
16632 GGGAACCGATACCCCTTCAA
1 GGGAACCGATACCCATTCAA
16652 ACGAACAACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.17
Consensus pattern (21 bp):
GGGAACCGATACCCATTCAAG
Found at i:18309 original size:29 final size:30
Alignment explanation
Indices: 18183--18306 Score: 205
Period size: 30 Copynumber: 4.1 Consensus size: 30
18173 TCGAGACATA
18183 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
18214 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
18244 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
18274 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
18303 TGGA
1 TGGA
18307 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
29 18 0.20
30 65 0.72
31 7 0.08
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:23651 original size:3 final size:3
Alignment explanation
Indices: 23643--23668 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
23633 TACAGCACTG
23643 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
23669 CCTGAGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:25547 original size:146 final size:146
Alignment explanation
Indices: 25175--25680 Score: 969
Period size: 146 Copynumber: 3.5 Consensus size: 146
25165 TCATCATCAG
*
25175 CTTTTTGGTTATTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
1 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
*
25240 CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGT-AAAGTTAAGTCTT
66 CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGTAAAAATTAAGTCTT
25304 TATTATGATTATTTAA
131 TATTATGATTATTTAA
25320 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
1 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
25385 CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGTAAAAATTAAGTCTT
66 CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGTAAAAATTAAGTCTT
25450 TATTATGATTATTTAA
131 TATTATGATTATTTAA
25466 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
1 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
*
25531 CAATCATTAAATCATGAACGATATAATAATATTATGATTTATTTTTTACGTAAAAATTAAGTCTT
66 CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGTAAAAATTAAGTCTT
25596 TATTATGATTATTTAA
131 TATTATGATTATTTAA
*
25612 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTTGATTTTGTCCCT
1 CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
25677 CAAT
66 CAAT
25681 AATAGAGGTA
Statistics
Matches: 356, Mismatches: 4, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
145 115 0.32
146 241 0.68
ACGTcount: A:0.29, C:0.12, G:0.09, T:0.49
Consensus pattern (146 bp):
CTTTTTGGTTACTATACTTTGCCAATTTGATTATTTAACTTTTATACTGTTTCGATTTTGTCCCT
CAATCATTAAATCATGAACGATATAATAATATTATGATTTACTTTTTACGTAAAAATTAAGTCTT
TATTATGATTATTTAA
Found at i:27548 original size:83 final size:83
Alignment explanation
Indices: 27409--27572 Score: 240
Period size: 83 Copynumber: 2.0 Consensus size: 83
27399 GAAATTTCGA
* * * * *
27409 GAGAGTTTTTCTCCAACTAAATCTCTTTTAATAACTAAATTTAAACAGATAATAATATCTTTTAA
1 GAGAGATTTACTCCAACCAAATATCTTTTAATAACTAAATTTAAACAGATAATAATATATTTTAA
*
27474 ATTTAAAATATTAAACCT
66 AATTAAAATATTAAACCT
* *
27492 GAGAGATTTACTCCAACCAGATATCTTTTAATATA-TAAATTTAAATAGATAATAATATATTTTA
1 GAGAGATTTACTCCAACCAAATATCTTTTAATA-ACTAAATTTAAACAGATAATAATATATTTTA
27556 AAATTAAAATATTAAAC
65 AAATTAAAATATTAAAC
27573 AAATATATAC
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
83 71 0.99
84 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.05, T:0.38
Consensus pattern (83 bp):
GAGAGATTTACTCCAACCAAATATCTTTTAATAACTAAATTTAAACAGATAATAATATATTTTAA
AATTAAAATATTAAACCT
Found at i:31793 original size:64 final size:64
Alignment explanation
Indices: 31720--31882 Score: 152
Period size: 64 Copynumber: 2.5 Consensus size: 64
31710 ATTGTTTGAA
* *** * *
31720 GGTGTATCGATGCACAGGTAGTGCATCGATGCA-CTCTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC-CCAGTAAT-AAACAAACATCGAATACAAT
31783 T
64 T
* * * * *
31784 GGTGCATCGATGCATAAGGCA-TGCATCGATGTATCCCAGTAATAAACAAACATCGAATATATTT
1 GGTGCATCGATGCA-CAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATACAATT
** *
31848 TATGCACCGATGCACAGGTAGTGCATCGATGCATC
1 GGTGCATCGATGCACAGGTAGTGCATCGATGCATC
31883 GATAGGGAAT
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
63 6 0.08
64 67 0.86
65 5 0.06
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (64 bp):
GGTGCATCGATGCACAGGTAGTGCATCGATGCATCCCAGTAATAAACAAACATCGAATACAATT
Found at i:32856 original size:103 final size:103
Alignment explanation
Indices: 32667--32884 Score: 346
Period size: 103 Copynumber: 2.1 Consensus size: 103
32657 GTCGAGGGTC
* *
32667 TATGTGGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
* * *
32732 TTGATCCTTGGCATATATATATGATTCTTAAGGATTGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
* *
32770 TATGTGGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGATACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
* *
32835 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
*
32873 TATCTGGTCCTT
1 TATGTGGTCCTT
32885 ATGGACATTA
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTAAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATATATATGATTCTTAAGGAATGA
Found at i:32967 original size:23 final size:23
Alignment explanation
Indices: 32891--32968 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
32881 CCTTATGGAC
* *
32891 ATTATTATATGGCACTACGGTGTA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
32915 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
32938 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
32961 ATTATATG
1 ATTATATG
32969 AGATGTGGTG
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
23 41 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.33
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:44741 original size:20 final size:20
Alignment explanation
Indices: 44718--44812 Score: 172
Period size: 20 Copynumber: 4.8 Consensus size: 20
44708 ATCTCTTTGA
*
44718 GACCTTAAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
44738 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
44758 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
44778 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
*
44798 GACCTTGAAACATTC
1 GACCTTGAAATATTC
44813 CCTCTCTTTA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 73 1.00
ACGTcount: A:0.27, C:0.21, G:0.09, T:0.42
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:45510 original size:11 final size:10
Alignment explanation
Indices: 45461--45511 Score: 50
Period size: 10 Copynumber: 5.1 Consensus size: 10
45451 AGATCCAATT
45461 AAAACAAAGA
1 AAAACAAAGA
* *
45471 AAAAGAGAGA
1 AAAACAAAGA
*
45481 AAAA-AAACA
1 AAAACAAAGA
*
45490 ACAACAAAGA
1 AAAACAAAGA
45500 AAAAGCAAAGA
1 AAAA-CAAAGA
45511 A
1 A
45512 CAAAAAGAGG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
9 6 0.19
10 19 0.59
11 7 0.22
ACGTcount: A:0.76, C:0.10, G:0.14, T:0.00
Consensus pattern (10 bp):
AAAACAAAGA
Found at i:46417 original size:24 final size:23
Alignment explanation
Indices: 46364--46420 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
46354 TGAAAGGGGT
46364 AATATTTTCAAAATCTTTGATTA
1 AATATTTTCAAAATCTTTGATTA
* *
46387 AACATTTTTAAAACTCTTTTGA-TA
1 AATATTTTCAAAA-TC-TTTGATTA
*
46411 GATATTTTCA
1 AATATTTTCA
46421 TACTTTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
23 11 0.41
24 11 0.41
25 5 0.19
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (23 bp):
AATATTTTCAAAATCTTTGATTA
Found at i:47432 original size:36 final size:36
Alignment explanation
Indices: 47391--47528 Score: 165
Period size: 36 Copynumber: 3.8 Consensus size: 36
47381 TTTTCATATT
**
47391 AAACAAA-GTTGATCTCACTTGAGATCGTTTTCTC-AA
1 AAACAAATGTTG-TCTCACTTGAGA-CAATTTCTCTAA
*
47427 AAACAAATGTTGTCTCGCTTGAGACAATTTCTCTAA
1 AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
* * * *
47463 AAACAATTTTTGTGT-AGTTTGAGACAATTTCTCTAA
1 AAACAAATGTTGTCTCA-CTTGAGACAATTTCTCTAA
47499 AAACAAATGTTGTCTCACTTGAGACAATTT
1 AAACAAATGTTGTCTCACTTGAGACAATTT
47529 TCCAAATTAT
Statistics
Matches: 86, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
35 7 0.08
36 74 0.86
37 5 0.06
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.36
Consensus pattern (36 bp):
AAACAAATGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:47593 original size:32 final size:32
Alignment explanation
Indices: 47552--47625 Score: 98
Period size: 31 Copynumber: 2.3 Consensus size: 32
47542 TTTGTTTCAC
47552 TTGAAACAAACATCATCTTTGAG-TCATTTATT
1 TTGAAACAAA-ATCATCTTTGAGTTCATTTATT
* * *
47584 TTGAAAC-AAATGATCTTTGAGTTTATTTCTT
1 TTGAAACAAAATCATCTTTGAGTTCATTTATT
47615 TTGAAACAAAA
1 TTGAAACAAAA
47626 CTTTGTCTCT
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 11 0.30
31 16 0.43
32 10 0.27
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (32 bp):
TTGAAACAAAATCATCTTTGAGTTCATTTATT
Found at i:48158 original size:65 final size:64
Alignment explanation
Indices: 48077--48199 Score: 183
Period size: 65 Copynumber: 1.9 Consensus size: 64
48067 GATGTAATCC
* *
48077 ATCTTTGAGTTTGTTTCTTTTGAAACAAAATTTTATATCTTAATGACAATTTCTTTTGAGAAAAA
1 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTATATCTCAA-GACAATTTCTTTTGAGAAAAA
* * * *
48142 ATCTTTGAGTTTGTTTCCTTTGAAACAAACTTTTGTCTCTCGAGACAATTTCTTTTGA
1 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTATATCTCAAGACAATTTCTTTTGA
48200 AAATACCCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
64 15 0.29
65 37 0.71
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (64 bp):
ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTATATCTCAAGACAATTTCTTTTGAGAAAAA
Found at i:49144 original size:43 final size:43
Alignment explanation
Indices: 49097--49285 Score: 125
Period size: 43 Copynumber: 4.3 Consensus size: 43
49087 AGATCTCTTT
* *
49097 ATCACGTAGGAGTCGTGTCACCCCTAGATAACCAGAAGTCCTC
1 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGAACTCCTC
* * * ** *
49140 ATCACGTGGGAACCGTGTTATCTCCCTTCCTAAAGATGGCCAGAACTCTTC
1 ATCACGTAGGAGCCGTG---TC-ACC--CCT--AGATAACCAGAACTCCTC
* * ** *
49191 ATCACGTATGAGTCGTGTCATCCCCCCG---ACCAGATCTCCTC
1 ATCACGTAGGAGCCGTGTCA-CCCCTAGATAACCAGAACTCCTC
* *
49232 ATCGCGTAGGAGCCGTGTCACCCCTAGATAACCA-ACCGTCCTC
1 ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGAAC-TCCTC
49275 ATCACGTAGGA
1 ATCACGTAGGA
49286 ATCGAGTTAT
Statistics
Matches: 108, Mismatches: 25, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
40 5 0.05
41 27 0.25
42 2 0.02
43 33 0.31
44 1 0.01
46 4 0.04
47 2 0.02
48 4 0.04
49 3 0.03
51 27 0.25
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.23
Consensus pattern (43 bp):
ATCACGTAGGAGCCGTGTCACCCCTAGATAACCAGAACTCCTC
Found at i:49249 original size:41 final size:40
Alignment explanation
Indices: 49179--49255 Score: 100
Period size: 41 Copynumber: 1.9 Consensus size: 40
49169 CTAAAGATGG
* * *
49179 CCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCCGA
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCA-CCCCCCGA
* *
49220 CCAGATCTCCTCATCGCGTAGGAGCCGTGTCACCCC
1 CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCC
49256 TAGATAACCA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
40 4 0.13
41 27 0.87
ACGTcount: A:0.19, C:0.39, G:0.19, T:0.22
Consensus pattern (40 bp):
CCAGAACTCCTCATCACGTAGGAGCCGTGTCACCCCCCGA
Found at i:49275 original size:135 final size:134
Alignment explanation
Indices: 49034--49417 Score: 497
Period size: 135 Copynumber: 2.9 Consensus size: 134
49024 AATCATTATC
* * * * *
49034 CCTAAAGATGGCTAGAACTCTTCATCACGTATAAGTCGTGTCATCTCCTGACCAGATCTCTTTAT
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCTCCCGACCAGATCTCCTCAT
* * * *
49099 CACGTAGGAGTCGTGTCACCCCTAGATAACCAGAAGTCCTCATCACGTGGGAACCGTGTTATCTC
66 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGAAGTCCTCATCACGTAGGAACCGAGTTATCAC
49164 CCTT
131 CCTT
*
49168 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCCCCCCGACCAGATCTCCTCA
1 CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCAT-CTCCCGACCAGATCTCCTCA
* * *
49233 TCGCGTAGGAGCCGTGTCACCCCTAGATAACCA-ACCGTCCTCATCACGTAGGAATCGAGTTATC
65 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGA-AGTCCTCATCACGTAGGAACCGAGTTATC
49297 ACCCTT
129 ACCCTT
*
49303 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCTCTCGACCAGAGT-TCCT
1 CCTAAAGATGGCC-AGAACTCTTCATCACGTATGAGTC-GTGTCATCTCCCGACCAGA-TCTCCT
* * * * * * *
49366 CATCACGTAGGAACCATGTTACCCTTAGATGACCCA-AACTCTTCATCACGTA
63 CATCACGTAGGAGCCGTGTCACCCCTAGAT-AACCAGAAGTCCTCATCACGTA
49418 TGAGCAGTGT
Statistics
Matches: 220, Mismatches: 24, Indels: 11
0.86 0.09 0.04
Matches are distributed among these distances:
134 43 0.20
135 142 0.65
136 35 0.16
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.26
Consensus pattern (134 bp):
CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGTCGTGTCATCTCCCGACCAGATCTCCTCAT
CACGTAGGAGCCGTGTCACCCCTAGATAACCAGAAGTCCTCATCACGTAGGAACCGAGTTATCAC
CCTT
Found at i:49614 original size:9 final size:9
Alignment explanation
Indices: 49600--49629 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
49590 TTTTGTTTTG
*
49600 TTATTATTA
1 TTATTATCA
49609 TTATTATCA
1 TTATTATCA
49618 TTATTATCA
1 TTATTATCA
49627 TTA
1 TTA
49630 GGTTTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (9 bp):
TTATTATCA
Found at i:50445 original size:12 final size:11
Alignment explanation
Indices: 50423--50465 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
50413 GATCTCTGGA
*
50423 TCTCATCTCTC
1 TCTCTTCTCTC
50434 TCTCTGTCTCTC
1 TCTCT-TCTCTC
*
50446 TCT-TACTCTC
1 TCTCTTCTCTC
50456 TCTCTTCTCT
1 TCTCTTCTCT
50466 AGGTGAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 8 0.30
11 10 0.37
12 9 0.33
ACGTcount: A:0.05, C:0.42, G:0.02, T:0.51
Consensus pattern (11 bp):
TCTCTTCTCTC
Found at i:56901 original size:21 final size:20
Alignment explanation
Indices: 56873--56934 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
56863 GTTATTTTAA
56873 AATTTAAATATT-CAAAAAAT
1 AATTTAAA-ATTACAAAAAAT
*
56893 AATTATAAAATTACTAAAAAT
1 AATT-TAAAATTACAAAAAAT
**
56914 AAAATAAAATTACTAAAAAAT
1 AATTTAAAATTAC-AAAAAAT
56935 TGAATATACA
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
20 16 0.46
21 19 0.54
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.31
Consensus pattern (20 bp):
AATTTAAAATTACAAAAAAT
Found at i:56911 original size:20 final size:21
Alignment explanation
Indices: 56887--56932 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
56877 TAAATATTCA
56887 AAAAATAATTATAAAATTACT
1 AAAAATAATTATAAAATTACT
*
56908 AAAAATAA-AATAAAATTACT
1 AAAAATAATTATAAAATTACT
56928 AAAAA
1 AAAAA
56933 ATTGAATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
AAAAATAATTATAAAATTACT
Found at i:57474 original size:2 final size:2
Alignment explanation
Indices: 57463--57495 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
57453 ATTTTATAAC
57463 AT AT -T 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 AT AT AT
57496 TATTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:57567 original size:24 final size:24
Alignment explanation
Indices: 57540--57587 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
57530 TATATTCAAT
*
57540 TTTTAGTA-ATTTATTTTTTTAATA
1 TTTT-GTATATTTATTTTTTGAATA
*
57564 TTTTTTATATTTATTTTTTGAATA
1 TTTTGTATATTTATTTTTTGAATA
57588 ATTGAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 19 0.90
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTTGTATATTTATTTTTTGAATA
Found at i:57767 original size:21 final size:21
Alignment explanation
Indices: 57743--57785 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
57733 TATCATAGAT
*
57743 TGTTATGTCAATATTATAAAC
1 TGTTATGTCAACATTATAAAC
*
57764 TGTTATGTTAACATTATAAAC
1 TGTTATGTCAACATTATAAAC
57785 T
1 T
57786 ATCACGCCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.44
Consensus pattern (21 bp):
TGTTATGTCAACATTATAAAC
Found at i:61463 original size:21 final size:21
Alignment explanation
Indices: 61439--61478 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
61429 CCCAAACAAA
*
61439 ATAAA-TTAATATATCAATTTT
1 ATAAACTTAAAATAT-AATTTT
61460 ATAAACTTAAAATATAATT
1 ATAAACTTAAAATATAATT
61479 AAACGAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (21 bp):
ATAAACTTAAAATATAATTTT
Found at i:65315 original size:108 final size:108
Alignment explanation
Indices: 65084--65283 Score: 301
Period size: 108 Copynumber: 1.8 Consensus size: 108
65074 TAAAAACACG
* * ** * * *
65084 CTAAACTTAGAGGGACCAAATAGTGAATAACCCAAAAATTACAAAGCATTCAAATAAAAGGGAAA
1 CTAAAGTTAGAGGGACTAAACGGTGAATAACCCAAAAATTACAAAGCATGCAAAGAAAAAGGAAA
*
65149 ATAATAGTTTAAACCCTACAGGTGACCATAATGCAAAAATGCA
66 ATAATAGTTTAAACCCTACAGATGACCATAATGCAAAAATGCA
*
65192 CTAAAGTTAGAGGGACTAAACGGTGAATAACCCAAAAATTATAAAGCATGCAAAGAAAAAGGAAA
1 CTAAAGTTAGAGGGACTAAACGGTGAATAACCCAAAAATTACAAAGCATGCAAAGAAAAAGGAAA
*
65257 ATAATAGTTTTAAACCCTATAGATGAC
66 ATAATAG-TTTAAACCCTACAGATGAC
65284 TATTTTGTAA
Statistics
Matches: 81, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
108 64 0.79
109 17 0.21
ACGTcount: A:0.49, C:0.15, G:0.16, T:0.20
Consensus pattern (108 bp):
CTAAAGTTAGAGGGACTAAACGGTGAATAACCCAAAAATTACAAAGCATGCAAAGAAAAAGGAAA
ATAATAGTTTAAACCCTACAGATGACCATAATGCAAAAATGCA
Found at i:66289 original size:12 final size:12
Alignment explanation
Indices: 66245--66294 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
66235 GTTTTGGATA
*
66245 TTTAGGTTGGGC
1 TTTAGGTTGGGT
*
66257 TTT-GGTTGGGG
1 TTTAGGTTGGGT
*
66268 CTT--GTTGGGT
1 TTTAGGTTGGGT
66278 TTTAGGTTGGGT
1 TTTAGGTTGGGT
66290 TTTAG
1 TTTAG
66295 TTTTAGTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 8 0.25
11 9 0.28
12 15 0.47
ACGTcount: A:0.06, C:0.04, G:0.42, T:0.48
Consensus pattern (12 bp):
TTTAGGTTGGGT
Found at i:66314 original size:17 final size:18
Alignment explanation
Indices: 66275--66314 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
66265 GGGCTTGTTG
*
66275 GGTTTTAGGTTGGGTTTT
1 GGTTTTAGGTTGGGCTTT
*
66293 AGTTTTA-GTTGGGCTTT
1 GGTTTTAGGTTGGGCTTT
66310 GGTTT
1 GGTTT
66315 AATAATAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.07, C:0.03, G:0.35, T:0.55
Consensus pattern (18 bp):
GGTTTTAGGTTGGGCTTT
Found at i:67590 original size:21 final size:23
Alignment explanation
Indices: 67547--67590 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
67537 ATTTAGCCCT
*
67547 CAATATTTTATTTTAAATTAAAA
1 CAATATTTTATTTTAAATGAAAA
*
67570 CAATA-TTT-TTTTAGATGAAAA
1 CAATATTTTATTTTAAATGAAAA
67591 TCACTAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.45, C:0.05, G:0.05, T:0.45
Consensus pattern (23 bp):
CAATATTTTATTTTAAATGAAAA
Found at i:68664 original size:18 final size:18
Alignment explanation
Indices: 68637--68671 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
68627 CGGAATGTAA
68637 GATTACCAGCGAGAATAG
1 GATTACCAGCGAGAATAG
* *
68655 GATTATCAGCGGGAATA
1 GATTACCAGCGAGAATA
68672 AAATTACTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (18 bp):
GATTACCAGCGAGAATAG
Found at i:72461 original size:10 final size:10
Alignment explanation
Indices: 72446--72471 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
72436 ACCTTCGATT
72446 TTTTTTTTTA
1 TTTTTTTTTA
72456 TTTTTTTTTA
1 TTTTTTTTTA
72466 TTTTTT
1 TTTTTT
72472 AATAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTA
Found at i:72524 original size:23 final size:22
Alignment explanation
Indices: 72490--72555 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
72480 TAATTTTGTT
72490 TGTGTTAGACGTTTATCTCTATA
1 TGTGTT-GACGTTTATCTCTATA
* * *
72513 TGTGTTGCACGTTTATCTTTGTT
1 TGTGTTG-ACGTTTATCTCTATA
72536 TGTGTTGTACGTTTATCTCT
1 TGTGTTG-ACGTTTATCTCT
72556 GTCTTTGTGA
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.53
Consensus pattern (22 bp):
TGTGTTGACGTTTATCTCTATA
Found at i:78677 original size:28 final size:27
Alignment explanation
Indices: 78623--78678 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
78613 TTGACTAGAT
* * * *
78623 TAAAAATATTTAACTATTTATTTTATA
1 TAAAAATATTCAACCATTTAATATATA
78650 TAAAAATTATTCAACCATTTAATATATA
1 TAAAAA-TATTCAACCATTTAATATATA
78678 T
1 T
78679 TAATAAAGGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (27 bp):
TAAAAATATTCAACCATTTAATATATA
Found at i:90405 original size:20 final size:20
Alignment explanation
Indices: 90382--90468 Score: 79
Period size: 20 Copynumber: 4.3 Consensus size: 20
90372 GTTTCTAATT
90382 TCGCAACGCGAATATGTAAA
1 TCGCAACGCGAATATGTAAA
* *
90402 TCGCAACGCGAATTTTTAAA
1 TCGCAACGCGAATATGTAAA
* * *
90422 TCGTAACAC-AA-AAGTCAAA
1 TCGCAACGCGAATATGT-AAA
* *
90441 TTCGCAACGCGAATTTATAAA
1 -TCGCAACGCGAATATGTAAA
90462 TCGCAAC
1 TCGCAAC
90469 ACAAAAGTCA
Statistics
Matches: 51, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
18 1 0.02
19 5 0.10
20 39 0.76
21 5 0.10
22 1 0.02
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (20 bp):
TCGCAACGCGAATATGTAAA
Found at i:90446 original size:40 final size:40
Alignment explanation
Indices: 90402--90532 Score: 165
Period size: 40 Copynumber: 3.3 Consensus size: 40
90392 AATATGTAAA
* *
90402 TCGCAACGCGAATTTTTAAATCGTAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTATAAATCGCAACACAAAAGTCAAAT
90442 TCGCAACGCGAATTTATAAATCGCAACACAAAAGTCAAAT
1 TCGCAACGCGAATTTATAAATCGCAACACAAAAGTCAAAT
* *** * * *
90482 TCGCAATGCGATAGCCA-AATTCGCAACACGATAGTCAAAT
1 TCGCAACGCGA-ATTTATAAATCGCAACACAAAAGTCAAAT
90522 TCGCAACGCGA
1 TCGCAACGCGA
90533 TAGTCAAATT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 78 0.98
41 2 0.03
ACGTcount: A:0.40, C:0.24, G:0.15, T:0.21
Consensus pattern (40 bp):
TCGCAACGCGAATTTATAAATCGCAACACAAAAGTCAAAT
Found at i:90485 original size:20 final size:20
Alignment explanation
Indices: 90426--90554 Score: 116
Period size: 20 Copynumber: 6.5 Consensus size: 20
90416 TTTAAATCGT
*
90426 AACACAAAAGTCAAATTCGC
1 AACACGAAAGTCAAATTCGC
* * * *
90446 AACGCG-AATTTATAAATCGC
1 AACACGAAAGTCA-AATTCGC
*
90466 AACACAAAAGTCAAATTCGC
1 AACACGAAAGTCAAATTCGC
** * *
90486 AATGCGATAGCCAAATTCGC
1 AACACGAAAGTCAAATTCGC
*
90506 AACACGATAGTCAAATTCGC
1 AACACGAAAGTCAAATTCGC
* * *
90526 AACGCGATAGTCAAATTCGT
1 AACACGAAAGTCAAATTCGC
90546 AACACGAAA
1 AACACGAAA
90555 CACAATATTA
Statistics
Matches: 85, Mismatches: 22, Indels: 4
0.77 0.20 0.04
Matches are distributed among these distances:
19 4 0.05
20 77 0.91
21 4 0.05
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
AACACGAAAGTCAAATTCGC
Found at i:90533 original size:40 final size:40
Alignment explanation
Indices: 90426--90554 Score: 161
Period size: 40 Copynumber: 3.2 Consensus size: 40
90416 TTTAAATCGT
* * * *
90426 AACACAAAAGTCAAATTCGCAACGCGA-ATTTATAAATCGC
1 AACACGAAAGTCAAATTCGCAACGCGATAGTCA-AATTCGC
* * *
90466 AACACAAAAGTCAAATTCGCAATGCGATAGCCAAATTCGC
1 AACACGAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
* *
90506 AACACGATAGTCAAATTCGCAACGCGATAGTCAAATTCGT
1 AACACGAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
90546 AACACGAAA
1 AACACGAAA
90555 CACAATATTA
Statistics
Matches: 77, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
40 75 0.97
41 2 0.03
ACGTcount: A:0.43, C:0.23, G:0.15, T:0.19
Consensus pattern (40 bp):
AACACGAAAGTCAAATTCGCAACGCGATAGTCAAATTCGC
Found at i:91087 original size:19 final size:19
Alignment explanation
Indices: 91063--91117 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
91053 AAATCGCAAC
91063 GCGATTTTAGTTTCACGTT
1 GCGATTTTAGTTTCACGTT
* * *
91082 GCGATTTTCATTTTCGCTTT
1 GCGATTTT-AGTTTCACGTT
*
91102 GCGAATTTAAGTTTCA
1 GCG-ATTTTAGTTTCA
91118 GAAACTACTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 8 0.29
20 16 0.57
21 4 0.14
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (19 bp):
GCGATTTTAGTTTCACGTT
Found at i:92845 original size:21 final size:21
Alignment explanation
Indices: 92814--92863 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
92804 GTTAAGGGAG
*
92814 TTACGTGATGAGGTCGGTGCT
1 TTACGTTATGAGGTCGGTGCT
*
92835 TTGCGTTATGAGGTCGGTGCT
1 TTACGTTATGAGGTCGGTGCT
92856 TTACGTTA
1 TTACGTTA
92864 AGATAATGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.14, G:0.34, T:0.38
Consensus pattern (21 bp):
TTACGTTATGAGGTCGGTGCT
Found at i:93288 original size:39 final size:39
Alignment explanation
Indices: 93234--93311 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
93224 CACCCCACTA
93234 GTGCCAAGACTCCGTAAAAAGAAGCCCGATGCACCTATC
1 GTGCCAAGACTCCGTAAAAAGAAGCCCGATGCACCTATC
* *
93273 GTGCCAATACTCCGTAAGAAGAAGCCCGATGCACCTATC
1 GTGCCAAGACTCCGTAAAAAGAAGCCCGATGCACCTATC
93312 ATCATTCAAG
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:0.32, C:0.31, G:0.21, T:0.17
Consensus pattern (39 bp):
GTGCCAAGACTCCGTAAAAAGAAGCCCGATGCACCTATC
Found at i:93356 original size:21 final size:21
Alignment explanation
Indices: 93310--93408 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
93300 GATGCACCTA
* **
93310 TCATCATTCAAGAGGCGTCTC
1 TCATCGTTCAAGAGGCCCCTC
93331 -CTATCGTTCAAGAGGCCCCTC
1 TC-ATCGTTCAAGAGGCCCCTC
* * * *
93352 TTATC-ATCGAAAAAGCCCCT-
1 TCATCGTTC-AAGAGGCCCCTC
* *
93372 TCCACCGTTCAAGAGGCCCCTG
1 T-CATCGTTCAAGAGGCCCCTC
93394 TCATCGTTCAAGAGG
1 TCATCGTTCAAGAGG
93409 TCCCGTCCGC
Statistics
Matches: 59, Mismatches: 13, Indels: 12
0.70 0.15 0.14
Matches are distributed among these distances:
20 4 0.07
21 52 0.88
22 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:93422 original size:21 final size:21
Alignment explanation
Indices: 93366--93428 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
93356 CATCGAAAAA
93366 GCCCCT-TCCACCGTTCAAGAG
1 GCCCCTGT-CACCGTTCAAGAG
*
93387 GCCCCTGTCATCGTTCAAGAG
1 GCCCCTGTCACCGTTCAAGAG
* *
93408 GTCCC-GTCCGCCGTTCAAGAG
1 GCCCCTGT-CACCGTTCAAGAG
93429 CCCGATTCAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
20 2 0.06
21 33 0.92
22 1 0.03
ACGTcount: A:0.17, C:0.38, G:0.24, T:0.21
Consensus pattern (21 bp):
GCCCCTGTCACCGTTCAAGAG
Found at i:94922 original size:66 final size:65
Alignment explanation
Indices: 94756--94929 Score: 212
Period size: 66 Copynumber: 2.6 Consensus size: 65
94746 TGTGGTACAC
*
94756 TTTTTTTGCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTATTTAACTGATGAGGAAATAA
1 TTTTTTTGCTTGTTTAATT-AATTTGT--A---AAAGTTGATTTGTTTAACTGATGAGGAAATAA
94820 GAATTA
60 GAATTA
* * * *
94826 -TTTTTT--TTGTTTAATTGATTTGTAAAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATT
1 TTTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTTTAA-CTGATGAGGAAATAAGAATT
94888 A
65 A
94889 TTTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTT
1 TTTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTT
94930 GTTTTAAATT
Statistics
Matches: 93, Mismatches: 6, Indels: 14
0.82 0.05 0.12
Matches are distributed among these distances:
62 16 0.17
63 18 0.19
64 6 0.06
65 1 0.01
66 35 0.38
67 11 0.12
69 6 0.06
ACGTcount: A:0.29, C:0.02, G:0.16, T:0.53
Consensus pattern (65 bp):
TTTTTTTGCTTGTTTAATTAATTTGTAAAAGTTGATTTGTTTAACTGATGAGGAAATAAGAATTA
Found at i:95052 original size:20 final size:20
Alignment explanation
Indices: 95004--95052 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
94994 CGCGAAATAA
*
95004 GCGTTACGATAGTCAAATTC
1 GCGTTACGAAAGTCAAATTC
****
95024 GTAACACGAAAGTCAAATTC
1 GCGTTACGAAAGTCAAATTC
95044 GCGTTACGA
1 GCGTTACGA
95053 TTTTCGGTTT
Statistics
Matches: 20, Mismatches: 9, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.24
Consensus pattern (20 bp):
GCGTTACGAAAGTCAAATTC
Found at i:95127 original size:17 final size:17
Alignment explanation
Indices: 95105--95150 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
95095 TAATCGCAAC
95105 ATACAACATCAAGTTAT
1 ATACAACATCAAGTTAT
*
95122 ATACAACATAAAGTTAT
1 ATACAACATCAAGTTAT
95139 ATACAACATCAA
1 ATACAACATCAA
95151 ACACATTCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.17, G:0.04, T:0.26
Consensus pattern (17 bp):
ATACAACATCAAGTTAT
Found at i:95420 original size:18 final size:18
Alignment explanation
Indices: 95397--95432 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
95387 AAGCCGGTTG
95397 TGATTGGGATTTTGATTT
1 TGATTGGGATTTTGATTT
*
95415 TGATTGTGATTTTGATTT
1 TGATTGGGATTTTGATTT
95433 CCTTTTGCTT
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:0.00, G:0.25, T:0.58
Consensus pattern (18 bp):
TGATTGGGATTTTGATTT
Found at i:97876 original size:12 final size:12
Alignment explanation
Indices: 97844--97877 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
97834 GGTTGTGGGT
97844 TTTGATATTGTG
1 TTTGATATTGTG
*
97856 TTTAATATTGTG
1 TTTGATATTGTG
*
97868 TTTGGTATTG
1 TTTGATATTG
97878 GAAATGTGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.24, T:0.59
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:98648 original size:21 final size:19
Alignment explanation
Indices: 98565--98655 Score: 85
Period size: 19 Copynumber: 4.7 Consensus size: 19
98555 AAATATTTGT
* * *
98565 GTTGCGAAATT-AAAACCT
1 GTTGCGAATTTGAAATCCA
* *
98583 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTG-AAATCCA
*
98603 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATCCA
*
98622 GTTGCGAATTTGAAATGCCGC
1 GTTGCGAATTTGAAAT-CC-A
98643 GTTGCGAATTTGA
1 GTTGCGAATTTGA
98656 CTTATGTGTT
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
18 9 0.15
19 21 0.36
20 16 0.27
21 13 0.22
ACGTcount: A:0.31, C:0.14, G:0.23, T:0.32
Consensus pattern (19 bp):
GTTGCGAATTTGAAATCCA
Found at i:98688 original size:20 final size:20
Alignment explanation
Indices: 98663--98702 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
98653 TGACTTATGT
98663 GTTACGATTTACAAATTCGC
1 GTTACGATTTACAAATTCGC
*
98683 GTTACGATTTACAGATTCGC
1 GTTACGATTTACAAATTCGC
98703 ATTGCGAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (20 bp):
GTTACGATTTACAAATTCGC
Found at i:98769 original size:19 final size:19
Alignment explanation
Indices: 98724--98772 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
98714 AGAAACTGAG
* * *
98724 TTGCGAAATTAGAGTTCGCA
1 TTGCG-AATTTGAGATCGAA
*
98744 TTACGAATTTGAGATCGAA
1 TTGCGAATTTGAGATCGAA
98763 TTGCGAATTT
1 TTGCGAATTT
98773 TTTAATGTAA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
19 20 0.83
20 4 0.17
ACGTcount: A:0.31, C:0.12, G:0.22, T:0.35
Consensus pattern (19 bp):
TTGCGAATTTGAGATCGAA
Found at i:98799 original size:14 final size:15
Alignment explanation
Indices: 98774--98807 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
98764 TGCGAATTTT
98774 TTAATGTAAAAGAAC
1 TTAATGTAAAAGAAC
98789 TTAAT-TAAAAGAAC
1 TTAATGTAAAAGAAC
98803 TTAAT
1 TTAAT
98808 AATTTAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 14 0.74
15 5 0.26
ACGTcount: A:0.53, C:0.06, G:0.09, T:0.32
Consensus pattern (15 bp):
TTAATGTAAAAGAAC
Found at i:102674 original size:3 final size:3
Alignment explanation
Indices: 102666--102715 Score: 93
Period size: 3 Copynumber: 17.0 Consensus size: 3
102656 TCACATGTAA
102666 AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
102713 AAT
1 AAT
102716 CCGAAAGATA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Done.