Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005328.1 Hibiscus syriacus cultivar Beakdansim tig00012065_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: 115943
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:3865 original size:4 final size:4
Alignment explanation
Indices: 3856--3882 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3846 GGATATACAT
3856 ATAC ATAC ATAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATA
3883 TGTGTATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:14108 original size:20 final size:22
Alignment explanation
Indices: 14070--14109 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
14060 TTTTTATAGA
14070 AAAACAATCCCCAAACGGCTCC
1 AAAACAATCCCCAAACGGCTCC
14092 AAAAC-ATCCCC-AACGGCT
1 AAAACAATCCCCAAACGGCT
14110 ATATACGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.40, C:0.40, G:0.10, T:0.10
Consensus pattern (22 bp):
AAAACAATCCCCAAACGGCTCC
Found at i:14393 original size:33 final size:34
Alignment explanation
Indices: 14321--14393 Score: 85
Period size: 34 Copynumber: 2.1 Consensus size: 34
14311 CCTTTTATAA
* *
14321 AGGGAAAATATTCTAGCTTAGCCCGTGTAAAAGCT
1 AGGG-AAATATTCTAGCTTAGCCCGAGTAAAAACT
* * *
14356 AGGGAAATGTTCTAGTTTATCCCGAG-AAAAACT
1 AGGGAAATATTCTAGCTTAGCCCGAGTAAAAACT
14389 AGGGA
1 AGGGA
14394 GTTGTAAAGG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
33 11 0.33
34 18 0.55
35 4 0.12
ACGTcount: A:0.36, C:0.15, G:0.25, T:0.25
Consensus pattern (34 bp):
AGGGAAATATTCTAGCTTAGCCCGAGTAAAAACT
Found at i:17282 original size:23 final size:22
Alignment explanation
Indices: 17237--17295 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
17227 ATAAATTGCA
17237 CCGAAGTG-CCACAT-ATTTGTC
1 CCGAA-TGACCACATAATTTGTC
17258 CCGAATGACCACATAATTTTGTC
1 CCGAATGACCACATAA-TTTGTC
*
17281 CCGAAGGACCACATA
1 CCGAATGACCACATA
17296 GAACCCTCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.06
21 11 0.32
22 1 0.03
23 20 0.59
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.24
Consensus pattern (22 bp):
CCGAATGACCACATAATTTGTC
Found at i:18270 original size:22 final size:22
Alignment explanation
Indices: 18242--18286 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
18232 AATCATGCTC
18242 TTAATCAATTCTAAACTTTCTA
1 TTAATCAATTCTAAACTTTCTA
18264 TTAATCAATTCTAAACTTTCTA
1 TTAATCAATTCTAAACTTTCTA
18286 T
1 T
18287 CTCCTTTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.47
Consensus pattern (22 bp):
TTAATCAATTCTAAACTTTCTA
Found at i:19174 original size:21 final size:21
Alignment explanation
Indices: 19150--19189 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
19140 TTTTCAAAGG
19150 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
19171 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
19190 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:19239 original size:19 final size:19
Alignment explanation
Indices: 19215--19253 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
19205 TCGAATGCAT
19215 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
19234 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
19253 T
1 T
19254 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:19278 original size:64 final size:65
Alignment explanation
Indices: 19150--19314 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 65
19140 TTTTCAAAGG
*
19150 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
19213 ATTC
62 ATTC
* * *
19217 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * ** *
19281 GATGCATCGATGCACAATTCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
19315 CAGGCTATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 53 0.61
65 15 0.17
66 3 0.03
67 14 0.16
68 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:19332 original size:64 final size:63
Alignment explanation
Indices: 19150--19359 Score: 181
Period size: 64 Copynumber: 3.2 Consensus size: 63
19140 TTTTCAAAGG
* ** ** *
19150 CATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCATCGATGCA-CAAT-CCATGCATCGATGCA-CGCTG-ATTTATTAAAACATCGAATGCAT
*
19215 TC
62 TT
* ** *
19217 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGCATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * * * *
19281 GATGCATCGATGCACAATTCATGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATTCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCATT
19344 T
63 T
*
19345 CATGCATCGGTGCAC
1 CATGCATCGATGCAC
19360 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.02
64 80 0.67
65 16 0.13
66 6 0.05
67 16 0.13
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:24197 original size:24 final size:22
Alignment explanation
Indices: 24148--24189 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
24138 CCAGAATGTC
24148 AAGG-GGGAACCGATACCCCCA
1 AAGGAGGGAACCGATACCCCCA
* *
24169 CAGGAGGGAACCGATTCCCCC
1 AAGGAGGGAACCGATACCCCC
24190 CTAAAGGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.29, C:0.36, G:0.29, T:0.07
Consensus pattern (22 bp):
AAGGAGGGAACCGATACCCCCA
Found at i:25220 original size:103 final size:103
Alignment explanation
Indices: 24892--25212 Score: 624
Period size: 103 Copynumber: 3.1 Consensus size: 103
24882 GTCGAGGGTC
24892 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
24957 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
24995 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
25060 TTGATCCCTAGTATATGTATTTAATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
25098 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
25163 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
25201 TATGTGGTCCTT
1 TATGTGGTCCTT
25213 ATGGACATTA
Statistics
Matches: 214, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 214 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:25295 original size:23 final size:23
Alignment explanation
Indices: 25219--25296 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
25209 CCTTATGGAC
*
25219 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
25243 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
25266 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
25289 ATTATATG
1 ATTATATG
25297 AGCTGTGGTG
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
23 42 0.93
24 3 0.07
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.32
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:30086 original size:23 final size:22
Alignment explanation
Indices: 30044--30086 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30034 TGTCAAGGGG
*
30044 GAACCGATACCCCCACAGGAGA
1 GAACCGATACCCCCAAAGGAGA
*
30066 GAACCGATTCCCCCTAAAGGA
1 GAACCGATACCCCC-AAAGGA
30087 AAATTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.35, C:0.35, G:0.21, T:0.09
Consensus pattern (22 bp):
GAACCGATACCCCCAAAGGAGA
Found at i:31109 original size:103 final size:103
Alignment explanation
Indices: 30781--31101 Score: 615
Period size: 103 Copynumber: 3.1 Consensus size: 103
30771 GTCGAGGGTC
* *
30781 TATGTGGTTCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
30846 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
30884 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
30949 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
30987 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
31052 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
31090 TATGTGGTCCTT
1 TATGTGGTCCTT
31102 ATGGACATTA
Statistics
Matches: 214, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 214 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:31162 original size:47 final size:47
Alignment explanation
Indices: 31108--31227 Score: 197
Period size: 47 Copynumber: 2.6 Consensus size: 47
31098 CCTTATGGAC
*
31108 ATTATTATATGGCACTACGGTGCAATTCTACGTGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
*
31155 ATTATTATATGGCACTACGGTACAATTCTACGCGGCACTCCGGTGCA
1 ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
* *
31202 ATTA-TATGTGGCACTTCGGTGCAATT
1 ATTATTATATGGCACTACGGTGCAATT
31228 ATATGAGCTG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
46 19 0.28
47 49 0.72
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (47 bp):
ATTATTATATGGCACTACGGTGCAATTCTACGCGGCACTCCGGTGCA
Found at i:31228 original size:23 final size:23
Alignment explanation
Indices: 31108--31232 Score: 133
Period size: 23 Copynumber: 5.3 Consensus size: 23
31098 CCTTATGGAC
*
31108 ATTATTATATGGCACTACGGTGCA
1 ATTA-TATGTGGCACTACGGTGCA
* * *
31132 ATTCTACGTGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
* *
31155 ATTATTATATGGCACTACGGTACA
1 ATTA-TATGTGGCACTACGGTGCA
* * * *
31179 ATTCTACGCGGCACTCCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
*
31202 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGTGGCACTACGGTGCA
31225 ATTATATG
1 ATTATATG
31233 AGCTGTGGTG
Statistics
Matches: 81, Mismatches: 19, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
23 60 0.74
24 21 0.26
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (23 bp):
ATTATATGTGGCACTACGGTGCA
Found at i:33575 original size:24 final size:22
Alignment explanation
Indices: 33547--33626 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
33537 CACTTAACAA
33547 TGCATCGATGCATCACTTTGAATG
1 TGCATCGATGCATC-C-TTGAATG
*
33571 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
*
33591 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
33615 TGCATCGATGCA
1 TGCATCGATGCA
33627 CAAGATCAAG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 4 0.08
21 12 0.25
22 2 0.04
23 12 0.25
24 18 0.38
ACGTcount: A:0.24, C:0.25, G:0.24, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:36271 original size:19 final size:19
Alignment explanation
Indices: 36247--36285 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
36237 TCGAATTCAT
36247 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
36266 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
36285 T
1 T
36286 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:36318 original size:64 final size:65
Alignment explanation
Indices: 36204--36411 Score: 212
Period size: 64 Copynumber: 3.2 Consensus size: 65
36194 CATCAATACT
* * * * * *
36204 ATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATTCATTCCATGCACCGATGCACTCTC
1 ATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTC
36268 C
65 C
* **
36269 ATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAATCC
1 ATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCC
* * *
36333 ATGCATCGATGCAC-CAGGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTCT
1 ATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCT
*
36395 -T
64 CC
*
36396 AGTGCACCGATGCACT
1 A-TGCATCGATGCACT
36412 AGGAGTCCAA
Statistics
Matches: 120, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
63 2 0.02
64 99 0.82
65 13 0.11
66 6 0.05
ACGTcount: A:0.31, C:0.25, G:0.16, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTTCATGCATCGATGCACTCTCC
Found at i:36391 original size:17 final size:19
Alignment explanation
Indices: 36363--36411 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
36353 ATTTTTCAAA
36363 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
36381 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
36400 CACCGATGCACT
1 CATCGATGCACT
36412 AGGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:38276 original size:19 final size:19
Alignment explanation
Indices: 38252--38289 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
38242 ACACTATTCA
38252 ATACCTCCAGCTGCTGTTC
1 ATACCTCCAGCTGCTGTTC
38271 ATACCTCCAGCTGCTGTTC
1 ATACCTCCAGCTGCTGTTC
38290 CTACATCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.16, C:0.37, G:0.16, T:0.32
Consensus pattern (19 bp):
ATACCTCCAGCTGCTGTTC
Found at i:39726 original size:15 final size:14
Alignment explanation
Indices: 39699--39810 Score: 80
Period size: 15 Copynumber: 7.6 Consensus size: 14
39689 TCTACTACTG
*
39699 GTGGCTTTGGTGGT
1 GTGGCTTCGGTGGT
*
39713 TTGGCTTCTGGTGGT
1 GTGGCTTC-GGTGGT
* * *
39728 GGGGGATTCAGTGGT
1 -GTGGCTTCGGTGGT
*
39743 CTGGCTTCAGGTGGT
1 GTGGCTTC-GGTGGT
*
39758 GGTGGATTCGGTGGT
1 -GTGGCTTCGGTGGT
*
39773 TTGGCTTCAGGTGGT
1 GTGGCTTC-GGTGGT
*
39788 GGTGGATTCGGTGGT
1 -GTGGCTTCGGTGGT
*
39803 CTGGCTTC
1 GTGGCTTC
39811 AGCTTGTGGT
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
14 23 0.31
15 34 0.46
16 17 0.23
ACGTcount: A:0.05, C:0.12, G:0.46, T:0.37
Consensus pattern (14 bp):
GTGGCTTCGGTGGT
Found at i:39772 original size:60 final size:60
Alignment explanation
Indices: 39697--39812 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 60
39687 CCTCTACTAC
* * *
39697 TGGTGGCTTTGGTGGTTTGGCTTCTGGTGGTGGGGGATTCAGTGGTCTGGCTTCAGGTGG
1 TGGTGGATTCGGTGGTTTGGCTTCAGGTGGTGGGGGATTCAGTGGTCTGGCTTCAGGTGG
* *
39757 TGGTGGATTCGGTGGTTTGGCTTCAGGTGGTGGTGGATTCGGTGGTCTGGCTTCAG
1 TGGTGGATTCGGTGGTTTGGCTTCAGGTGGTGGGGGATTCAGTGGTCTGGCTTCAG
39813 CTTGTGGTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 51 1.00
ACGTcount: A:0.06, C:0.12, G:0.46, T:0.36
Consensus pattern (60 bp):
TGGTGGATTCGGTGGTTTGGCTTCAGGTGGTGGGGGATTCAGTGGTCTGGCTTCAGGTGG
Found at i:39820 original size:30 final size:30
Alignment explanation
Indices: 39697--39812 Score: 169
Period size: 30 Copynumber: 3.9 Consensus size: 30
39687 CCTCTACTAC
* * * *
39697 TGGTGGCTTTGGTGGTTTGGCTTCTGGTGG
1 TGGTGGATTCGGTGGTCTGGCTTCAGGTGG
* *
39727 TGGGGGATTCAGTGGTCTGGCTTCAGGTGG
1 TGGTGGATTCGGTGGTCTGGCTTCAGGTGG
*
39757 TGGTGGATTCGGTGGTTTGGCTTCAGGTGG
1 TGGTGGATTCGGTGGTCTGGCTTCAGGTGG
39787 TGGTGGATTCGGTGGTCTGGCTTCAG
1 TGGTGGATTCGGTGGTCTGGCTTCAG
39813 CTTGTGGTTC
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 76 1.00
ACGTcount: A:0.06, C:0.12, G:0.46, T:0.36
Consensus pattern (30 bp):
TGGTGGATTCGGTGGTCTGGCTTCAGGTGG
Found at i:75821 original size:27 final size:27
Alignment explanation
Indices: 75794--75892 Score: 112
Period size: 26 Copynumber: 3.7 Consensus size: 27
75784 ATTTTAATTT
75794 AAAAAATCTTAAAATTTTTAATCTTTTA
1 AAAAAATCTTAAAATTTTTAAT-TTTTA
* * *
75822 AATGAAAT-TTAAAATCTTTAATTTTTC
1 AA-AAAATCTTAAAATTTTTAATTTTTA
* * *
75849 AAACAACCTT-AAATTTTTATTTTTTA
1 AAAAAATCTTAAAATTTTTAATTTTTA
75875 AAAAAATCTTAAAATTTT
1 AAAAAATCTTAAAATTTT
75893 GAAGAAAAAA
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
26 23 0.40
27 15 0.26
28 15 0.26
29 4 0.07
ACGTcount: A:0.44, C:0.08, G:0.01, T:0.46
Consensus pattern (27 bp):
AAAAAATCTTAAAATTTTTAATTTTTA
Found at i:76369 original size:128 final size:128
Alignment explanation
Indices: 76141--76381 Score: 419
Period size: 128 Copynumber: 1.9 Consensus size: 128
76131 TTTTTATAAA
* * *
76141 TTACTGATTGAAAGATTTAGGAATTTCATGCGACGATAAAGGGACAATCGAGTAATGAAAATATG
1 TTACTAATTGAAAGATTTAGAAATTTCATGCGACGATAAAGGGACAATCGAGTAATAAAAATATG
76206 TTGATGAAATAAGTGAATGGCTGGGTGGTTGTTGATTCGATGCGATGTGAGGGATTTAATATT
66 TTGATGAAATAAGTGAATGGCTGGGTGGTTGTTGATTCGATGCGATGTGAGGGATTTAATATT
* *
76269 TTACTAATTGAAAGATTTAGAAATTTCGTGTGACGATAAAGGGACAATCGAGTAATAAAAATATG
1 TTACTAATTGAAAGATTTAGAAATTTCATGCGACGATAAAGGGACAATCGAGTAATAAAAATATG
* *
76334 TTGATGAAATAAGTGATTGGGTGGGTGGTTGTTGATTCGATGCGATGT
66 TTGATGAAATAAGTGAATGGCTGGGTGGTTGTTGATTCGATGCGATGT
76382 TGATGAAATA
Statistics
Matches: 106, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
128 106 1.00
ACGTcount: A:0.33, C:0.07, G:0.28, T:0.32
Consensus pattern (128 bp):
TTACTAATTGAAAGATTTAGAAATTTCATGCGACGATAAAGGGACAATCGAGTAATAAAAATATG
TTGATGAAATAAGTGAATGGCTGGGTGGTTGTTGATTCGATGCGATGTGAGGGATTTAATATT
Found at i:76623 original size:31 final size:31
Alignment explanation
Indices: 76578--76674 Score: 106
Period size: 32 Copynumber: 3.1 Consensus size: 31
76568 CAAAAAATAT
* *
76578 AAAACGGTCAATAAATTTTATCAAAATGTTAC
1 AAAATGGTC-ATAAATTTTATCGAAATGTTAC
* *
76610 AAAATGGTCATAAAATTTTATCGAACTGTTAT
1 AAAATGGTCAT-AAATTTTATCGAAATGTTAC
* *
76642 AAAATGATCATTAAA-TTTATCGAATTGTTAC
1 AAAATGGTCA-TAAATTTTATCGAAATGTTAC
76673 AA
1 AA
76675 GTATTATAAT
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
31 18 0.32
32 37 0.66
33 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.35
Consensus pattern (31 bp):
AAAATGGTCATAAATTTTATCGAAATGTTAC
Found at i:76626 original size:32 final size:32
Alignment explanation
Indices: 76590--76674 Score: 109
Period size: 32 Copynumber: 2.7 Consensus size: 32
76580 AACGGTCAAT
* *
76590 AAATTTTATCAAAATGTTACAAAATGGTCATA
1 AAATTTTATCGAAATGTTACAAAATGATCATA
* * *
76622 AAATTTTATCGAACTGTTATAAAATGATCATT
1 AAATTTTATCGAAATGTTACAAAATGATCATA
*
76654 AAA-TTTATCGAATTGTTACAA
1 AAATTTTATCGAAATGTTACAA
76675 GTATTATAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 16 0.35
32 30 0.65
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (32 bp):
AAATTTTATCGAAATGTTACAAAATGATCATA
Found at i:80558 original size:32 final size:32
Alignment explanation
Indices: 80522--80583 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
80512 AGTGATGATA
80522 TATGTGAT-ATGTCATCACTTATACACATGTAC
1 TATGTG-TCATGTCATCACTTATACACATGTAC
*
80554 TATGTGTCATGTCATCACTTATATACATGT
1 TATGTGTCATGTCATCACTTATACACATGT
80584 GTAATGTACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 1 0.04
32 27 0.96
ACGTcount: A:0.29, C:0.18, G:0.13, T:0.40
Consensus pattern (32 bp):
TATGTGTCATGTCATCACTTATACACATGTAC
Found at i:80611 original size:34 final size:35
Alignment explanation
Indices: 80573--80641 Score: 88
Period size: 34 Copynumber: 2.0 Consensus size: 35
80563 TGTCATCACT
*
80573 TATATACATGT-GTAATGTACTACATTATCA-TTTA
1 TATATACATGTGGT-ATGTACCACATTATCACTTTA
* *
80607 TATATATATGTGGTATGTACCACGTTATCACTTTA
1 TATATACATGTGGTATGTACCACATTATCACTTTA
80642 AACATGTGAC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.43
Consensus pattern (35 bp):
TATATACATGTGGTATGTACCACATTATCACTTTA
Found at i:81794 original size:61 final size:61
Alignment explanation
Indices: 81712--81834 Score: 176
Period size: 61 Copynumber: 2.0 Consensus size: 61
81702 CAGGTGAAGT
* * *
81712 TGAGCAGCTAACCACCTACACTTAAGTTCAAAATTCAA-GAAATTTTCAGTTCTCAGATAAG
1 TGAGCAGCTAACCACCAACACTTAAGTTCAAAA-TCAAGGAAATTTCCAATTCTCAGATAAG
* * *
81773 TGAGCAGCTAGCCAGCAACACTTAAGTTCAATATCAAGGAAATTTCCAATTCTCAGATAAG
1 TGAGCAGCTAACCACCAACACTTAAGTTCAAAATCAAGGAAATTTCCAATTCTCAGATAAG
81834 T
1 T
81835 TTATTTGTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
60 4 0.07
61 51 0.93
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.27
Consensus pattern (61 bp):
TGAGCAGCTAACCACCAACACTTAAGTTCAAAATCAAGGAAATTTCCAATTCTCAGATAAG
Found at i:84195 original size:12 final size:12
Alignment explanation
Indices: 84178--84203 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
84168 TAAATTATTT
84178 TTAAAAATTATA
1 TTAAAAATTATA
84190 TTAAAAATTATA
1 TTAAAAATTATA
84202 TT
1 TT
84204 TCGATCACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
TTAAAAATTATA
Found at i:84301 original size:46 final size:45
Alignment explanation
Indices: 84249--84335 Score: 106
Period size: 43 Copynumber: 1.9 Consensus size: 45
84239 CTATATTGAT
84249 ATATTATTATAAAGTAATATCATATTATTATTTAA-AA-AATTAGAAA
1 ATATTA-TATAAA-TAATATCAT-TTATTATTTAATAATAATTAGAAA
* * *
84295 ATATTATATTAATAATTTCATTTATTTTTTAATAATAATTA
1 ATATTATATAAATAATATCATTTATTATTTAATAATAATTA
84336 ATCAAAATAG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
43 10 0.28
44 10 0.28
45 10 0.28
46 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.48
Consensus pattern (45 bp):
ATATTATATAAATAATATCATTTATTATTTAATAATAATTAGAAA
Found at i:84755 original size:2 final size:2
Alignment explanation
Indices: 84748--84785 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
84738 ATCATTGATA
84748 AT AT AT AT AT 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 AT AT
84786 TTGAACTCAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:84978 original size:22 final size:22
Alignment explanation
Indices: 84936--84979 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
84926 AATTAATTTT
*
84936 TATTACCAAAAGAAACAATATC
1 TATTACCAAAACAAACAATATC
*
84958 TATTA-CAAAACAATCACATATC
1 TATTACCAAAACAAACA-ATATC
84980 ACTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.52, C:0.20, G:0.02, T:0.25
Consensus pattern (22 bp):
TATTACCAAAACAAACAATATC
Found at i:95958 original size:2 final size:2
Alignment explanation
Indices: 95941--96007 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
95931 GTGAGGCATA
* *
95941 AT AT AA AT AA AT AT 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 AT AT AT AT
95983 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
96008 ACAATGAATT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:99000 original size:20 final size:22
Alignment explanation
Indices: 98966--99022 Score: 75
Period size: 24 Copynumber: 2.6 Consensus size: 22
98956 TTCCCATTGA
98966 AGTGCATCG-TGCATTC-TT-C
1 AGTGCATCGATGCATTCTTTAC
98985 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTCTTT-AC
99008 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
99023 CTACCATGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 9 0.27
20 7 0.21
21 2 0.06
23 2 0.06
24 13 0.39
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.33
Consensus pattern (22 bp):
AGTGCATCGATGCATTCTTTAC
Found at i:99097 original size:19 final size:19
Alignment explanation
Indices: 99073--99125 Score: 106
Period size: 19 Copynumber: 2.8 Consensus size: 19
99063 TTTTAAGGGG
99073 ATGCATCGATGCACTCCTC
1 ATGCATCGATGCACTCCTC
99092 ATGCATCGATGCACTCCTC
1 ATGCATCGATGCACTCCTC
99111 ATGCATCGATGCACT
1 ATGCATCGATGCACT
99126 AACTGTACTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.23, C:0.34, G:0.17, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACTCCTC
Found at i:106801 original size:127 final size:127
Alignment explanation
Indices: 106281--106784 Score: 857
Period size: 127 Copynumber: 4.0 Consensus size: 127
106271 TAAATTAGGG
* * * * *
106281 TTTATAAATTTCACAAATTAATATGTGATCTAATTATAATTAAAATATGATTATAAAACCTAATT
1 TTTATAAATTTCCCATATT-A-ATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATA
* *
106346 TTATATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTAACAT
64 TTGTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
*
106410 TTTATAAATTTCTCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
1 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
106475 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
66 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
* *
106537 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAATTAATATC
1 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
* *
106602 GTATAAATATTGTATTTTAATTAAATTATATTTATATTTTTAATTAATTTATAATTTGACAT
66 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
106664 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAA-TAATATT
1 TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
* *
106728 GTATAAATATTATATTTTAATTAAATTATATTTAAATTTTTAACTAATTTATAATTT
66 GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTT
106785 TACGTACTTT
Statistics
Matches: 359, Mismatches: 16, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
126 60 0.17
127 281 0.78
128 1 0.00
129 17 0.05
ACGTcount: A:0.43, C:0.05, G:0.04, T:0.48
Consensus pattern (127 bp):
TTTATAAATTTCCCATATTAATGTGATCTAATTATAATTAAAATAAGATTATAAAAACTAATATT
GTATAAATATTGTATTTTAATTAAATTATATTTAGATTTTTAACTAATTTATAATTTGACAT
Done.