Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002557.1 Hibiscus syriacus cultivar Beakdansim tig00005188_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: 93052
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:6688 original size:65 final size:65
Alignment explanation
Indices: 6555--6714 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
6545 TGCACTAAGA
* *
6555 GTGCATCGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
* * *
6619 GTGCATCGATGCATCAAATACATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGATACATAG-
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CAGAGTGCATCGATACATAGC
*
6681 TAT
64 T-G
*
6684 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
6715 CAATTTATTC
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 29 0.35
65 52 0.62
66 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCAGAGTGCATCGATACATAGCTG
Found at i:11354 original size:3 final size:3
Alignment explanation
Indices: 11348--11433 Score: 111
Period size: 3 Copynumber: 28.0 Consensus size: 3
11338 TTACCCATTT
*
11348 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* *
11393 TAA TTA TTA TTA TTA TTA TTA TATA TTA TTTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA TTA TTA
11434 CAAAACCCAA
Statistics
Matches: 73, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
2 2 0.03
3 63 0.86
4 8 0.11
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:13044 original size:116 final size:120
Alignment explanation
Indices: 12827--13056 Score: 285
Period size: 116 Copynumber: 1.9 Consensus size: 120
12817 ATATAAATAT
* *
12827 ATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATTTTAATATTTATTTTTCAATAT
1 ATATATAATAAATAATAATTTATATTTTTTTTAAATAAATTATATTAATATTTA--TTTCAATAT
* * *
12892 CGAAGAAAAGGGCAGTCTTAATACAACTAGATGTCCTATTCTGGTATTTTAAAATTAA
64 CGAAGAAAAGAGCAGTCTTAATAC-ACTAGAAGTCCTATTCTGATATTTTAAAATTAA
*
12950 ATATCATAA-AAATAATAATTTA-A-TTTTTTTAAAT-TATTATATTAATATTTA-TT-AATATC
1 ATAT-ATAATAAATAATAATTTATATTTTTTTTAAATAAATTATATTAATATTTATTTCAATATC
* *
13009 GAAGAAAAGAGCTGTCTTAAGGTAC-CTAGAAGTCCTTTTCTGATATTT
65 GAAGAAAAGAGCAGTCTTAA--TACACTAGAAGTCCTATTCTGATATTT
13057 CTAATTAAAT
Statistics
Matches: 96, Mismatches: 8, Indels: 13
0.82 0.07 0.11
Matches are distributed among these distances:
116 44 0.46
117 2 0.02
118 3 0.03
120 15 0.16
121 10 0.10
122 1 0.01
123 17 0.18
124 4 0.04
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (120 bp):
ATATATAATAAATAATAATTTATATTTTTTTTAAATAAATTATATTAATATTTATTTCAATATCG
AAGAAAAGAGCAGTCTTAATACACTAGAAGTCCTATTCTGATATTTTAAAATTAA
Found at i:24244 original size:15 final size:15
Alignment explanation
Indices: 24221--24259 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
24211 GCTTGAAGAG
24221 AAAAAGAAA-AGAAA
1 AAAAAGAAAGAGAAA
24235 AAAAAGGAAAGAGAAA
1 AAAAA-GAAAGAGAAA
*
24251 AAAGAGAAA
1 AAAAAGAAA
24260 AAAGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 8 0.36
16 9 0.41
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAGAGAAA
Found at i:24270 original size:24 final size:23
Alignment explanation
Indices: 24227--24278 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
24217 AGAGAAAAAG
*
24227 AAAAGAAAAAAAAGGAAAGAGAA
1 AAAAGAAAAAAAAGAAAAGAGAA
*
24250 AAAAGAGAAAAAAGAAGAAGAGAA
1 AAAAGAAAAAAAAGAA-AAGAGAA
24274 AAAAG
1 AAAAG
24279 GGGGTCAAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (23 bp):
AAAAGAAAAAAAAGAAAAGAGAA
Found at i:25551 original size:92 final size:92
Alignment explanation
Indices: 25394--25824 Score: 801
Period size: 92 Copynumber: 4.7 Consensus size: 92
25384 AGAAGACCCA
25394 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
25459 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
25486 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
25551 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
25578 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
25643 TATTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
*
25670 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGATATGAACCACAGAACCAGT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
*
25735 TACTGAATTTGGAAGAGGAATGTGCTC
66 TATTGAATTTGGAAGAGGAATGTGCTC
* * *
25762 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGGTTTGATATAAAACC-CAGAACCA
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAT-GAACCACAGAACCA
25825 ATCATTGGAA
Statistics
Matches: 334, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 330 0.99
93 4 0.01
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.35
Consensus pattern (92 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTATGAACCACAGAACCAGT
TATTGAATTTGGAAGAGGAATGTGCTC
Found at i:26879 original size:113 final size:113
Alignment explanation
Indices: 26533--27210 Score: 792
Period size: 113 Copynumber: 6.0 Consensus size: 113
26523 GCAAAGATTC
* * * * * *
26533 AAATCCATCAATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCATTTG
1 AAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATC---TG
26598 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TT
63 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * *
26648 AAATTCATTATTTGATGGATCAACATTACCA-AAAAGAGTTCATAATAAGAAGAACTCATCTAAA
1 AAATTCATCATTTGATGGATCAACATTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAA
* * *
26712 GAA-AAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGCTT
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
26760 GAATTCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
1 AAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* *
26825 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * *
26873 GAATTCATCATTTGATGGATTAAAATTTCTAG-GTAGAGTTCATAATGAGAAGAACTCATCATTT
1 AAATTCATCATTTGATGGATCAACATTTCCAGAG-AAAGTTCATAATGAGAAGAACTCATC---T
* *
26937 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
62 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * * **** *
26989 AAATCCATCATTTGATGGGTCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGAAG
1 AAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
* * * *
27054 AAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTCTG-TT
66 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
* * * *
27101 CAAATTCATTATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACTTATTTGAA
1 -AAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAA
* * ** *
27166 G-AGGAAGAAGAAGTTCAAAATAAGAAGAGCTTATTCAACCTTTTG
65 GAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG
27211 AATGACTCTA
Statistics
Matches: 480, Mismatches: 73, Indels: 23
0.83 0.13 0.04
Matches are distributed among these distances:
111 39 0.08
112 101 0.21
113 191 0.40
114 2 0.00
115 50 0.10
116 97 0.20
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (113 bp):
AAATTCATCATTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAG
AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
Found at i:27014 original size:229 final size:228
Alignment explanation
Indices: 26531--27210 Score: 910
Period size: 229 Copynumber: 3.0 Consensus size: 228
26521 TAGCAAAGAT
* *
26531 TCAAATCCATCAATTGATGGATCAGCATTACCAGATAGAGTTCATAATGAGAAGAACTCATCATT
1 TCAAATCCATCAATTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATC---
*
26596 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTG-TTAAATTCATTATT
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATTATT
* ** * *
26660 TGATGGATCAACATTACCAAAAAGAGTTCATAATAAGAAGAACTCATC---TAAAGAA-AAAGAA
128 TGATGGATCAACATTTCC-AGGAGAGTTCATAATAAGAAGAACTCATCATTTGAAGAAGGAAGAA
*
26721 GAAATTCATAATGAGAAGAATTTGTTCAACTTTTTGC
192 GAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
** * * * *
26758 TTGAATTCATCACTTGATGGATCAGCTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAATTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
* *
26823 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTGAATTCATCATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATTATTTGA
* * * *
26888 TGGATTAAAATTTCTAGGTAGAGTTCATAATGAGAAGAACTCATCATTTGAAGAAGGAAGAAGAA
131 TGGATCAACATTTCCAGG-AGAGTTCATAATAAGAAGAACTCATCATTTGAAGAAGGAAGAAGAA
26953 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
195 ATTCATAATGAGAAGAATTTGTTCAACCTTTTGC
* * * * *
26987 TCAAATCCATCATTTGATGGGTCAGCTTTTCCAGTTCGAGTTCATAATGAGAAGAATTCATCTGA
1 TCAAATCCATCAATTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
* * * *
27052 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAAACTTCTGTTCAAATTCATTATTTGA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATTATTTGA
*
27117 TGGATCAACATTTCCAGAGAAAGTTCATAATAAGAAGAACT--T-ATTTGAAG-AGGAAGAAGAA
131 TGGATCAACATTTCCAG-GAGAGTTCATAATAAGAAGAACTCATCATTTGAAGAAGGAAGAAGAA
* * * ** *
27178 GTTCAAAATAAGAAGAGCTTATTCAACCTTTTG
195 ATTCATAATGAGAAGAATTTGTTCAACCTTTTG
27211 AATGACTCTA
Statistics
Matches: 398, Mismatches: 48, Indels: 16
0.86 0.10 0.03
Matches are distributed among these distances:
224 50 0.13
225 89 0.22
226 8 0.02
227 55 0.14
228 6 0.02
229 189 0.47
230 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.30
Consensus pattern (228 bp):
TCAAATCCATCAATTGATGGATCAGCTTTTCCAGATAGAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTTAACCTTTTGTTTAAATTCATTATTTGA
TGGATCAACATTTCCAGGAGAGTTCATAATAAGAAGAACTCATCATTTGAAGAAGGAAGAAGAAA
TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
Found at i:27079 original size:24 final size:23
Alignment explanation
Indices: 27036--27080 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
27026 GTTCATAATG
*
27036 AGAAGAATTCATCTGAAGAAGGA
1 AGAAGAATTCATATGAAGAAGGA
27059 AGAAGAAGTTCATAATG-AGAAG
1 AGAAGAA-TTCAT-ATGAAGAAG
27081 AACTTGTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.07, G:0.27, T:0.18
Consensus pattern (23 bp):
AGAAGAATTCATATGAAGAAGGA
Found at i:27442 original size:3 final size:3
Alignment explanation
Indices: 27436--27506 Score: 72
Period size: 3 Copynumber: 23.0 Consensus size: 3
27426 TTACCCATTT
* *
27436 TTA TTA TTA TTG TTA -TA TTTA TAA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
27481 TTA ATA TATA TTA TTAA TTA ATA TTA
1 TTA TTA T-TA TTA TT-A TTA TTA TTA
27507 CAAAACCCAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 2 0.04
3 46 0.82
4 8 0.14
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:29128 original size:116 final size:121
Alignment explanation
Indices: 28905--29139 Score: 279
Period size: 116 Copynumber: 2.0 Consensus size: 121
28895 ATATAAATAT
* *
28905 ATATATAATAAATAATAATTTATATTTTTTTTACATAAATTATTTTAATATTTATTTTTCAATAT
1 ATATATAAAAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTA--TTTCAATAT
* * * *
28970 CGAAGAAAAGGGCAGTCTTAATACAACTAGATGTCCTATTCTGGTATTT-TAAAATTAA
64 CGAAGAAAAGAGCAGTCTTAATAC-ACTAGAAGTCATATTCTGATATTTCTAAAATTAA
*
29028 ATATCATAAAAAATAATAATTTA-A-TTTTTTTA-AT-TATTATATTAATATTTA-TT-AATATC
1 ATAT-ATAAAAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTATTTCAATATC
* *
29087 GAAGAAAAGAGCTGTCTTAAGGTAC-CTAGAAGTCATTTTCTGATATTTCTAAA
65 GAAGAAAAGAGCAGTCTTAA--TACACTAGAAGTCATATTCTGATATTTCTAAA
29140 TAAATTAATA
Statistics
Matches: 99, Mismatches: 9, Indels: 14
0.81 0.07 0.11
Matches are distributed among these distances:
116 43 0.43
117 6 0.06
118 3 0.03
120 15 0.15
121 2 0.02
122 8 0.08
123 5 0.05
124 17 0.17
ACGTcount: A:0.40, C:0.08, G:0.09, T:0.43
Consensus pattern (121 bp):
ATATATAAAAAATAATAATTTATATTTTTTTTACATAAATTATATTAATATTTATTTCAATATCG
AAGAAAAGAGCAGTCTTAATACACTAGAAGTCATATTCTGATATTTCTAAAATTAA
Found at i:40823 original size:20 final size:21
Alignment explanation
Indices: 40786--40827 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40776 GTCATGCAAC
40786 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
40807 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
40827 T
1 T
40828 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:40884 original size:23 final size:23
Alignment explanation
Indices: 40831--40885 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
40821 AATGCATTGT
* * *
40831 AAGTTGGCAATAATAATGGTTCA
1 AAGTTGACACTAATAATGGTTAA
*
40854 TAGTTGACACTAATAATGGTTGAA
1 AAGTTGACACTAATAATGGTT-AA
40878 AAG-TGACA
1 AAGTTGACA
40886 TGGCAAAATT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
23 23 0.88
24 3 0.12
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.29
Consensus pattern (23 bp):
AAGTTGACACTAATAATGGTTAA
Found at i:44174 original size:23 final size:23
Alignment explanation
Indices: 44144--44194 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
44134 TGAAAAGGTA
44144 GAAGAAGGGACGGTAGATATGCG
1 GAAGAAGGGACGGTAGATATGCG
44167 GAAGAAGGGACGGTAGATATGCG
1 GAAGAAGGGACGGTAGATATGCG
44190 GAAGA
1 GAAGA
44195 TCCATACCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.37, C:0.08, G:0.43, T:0.12
Consensus pattern (23 bp):
GAAGAAGGGACGGTAGATATGCG
Found at i:44422 original size:20 final size:21
Alignment explanation
Indices: 44385--44426 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
44375 GTCATGCAAC
44385 TAATAATAGTTGCATAATGCA
1 TAATAATAGTTGCATAATGCA
*
44406 TAATAATGGTT-CATAATGCA
1 TAATAATAGTTGCATAATGCA
44426 T
1 T
44427 TGTAAGTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (21 bp):
TAATAATAGTTGCATAATGCA
Found at i:48712 original size:38 final size:39
Alignment explanation
Indices: 48656--48788 Score: 115
Period size: 42 Copynumber: 3.3 Consensus size: 39
48646 TTTACTTCAA
* ** *
48656 TAGTGATAAAAATTATTATCGTCGCAAATC-ACCAAGAC
1 TAGTGACAAAAACAATTATCGTCACAAATCAACCAAGAC
* *
48694 TAGTGACAAAAACAATTATCGTCACAAGTCATCAACTAAGAT
1 TAGTGACAAAAACAATTATCGTCACAA---ATCAACCAAGAC
* * *
48736 TAATGACAAAAACAATTATCATCACAAATAATCAACTAAGAC
1 TAGTGACAAAAACAATTATCGTCAC--A-AATCAACCAAGAC
*
48778 TAGTAACAAAA
1 TAGTGACAAAA
48789 TGTTTTCATC
Statistics
Matches: 77, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
38 23 0.30
41 3 0.04
42 49 0.64
44 1 0.01
45 1 0.01
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.23
Consensus pattern (39 bp):
TAGTGACAAAAACAATTATCGTCACAAATCAACCAAGAC
Found at i:48787 original size:42 final size:42
Alignment explanation
Indices: 48689--48788 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
48679 GCAAATCACC
* * *
48689 AAGACTAGTGACAAAAACAATTATCGTCACAAGTCATCAACT
1 AAGACTAGTGACAAAAACAATTATCATCACAAATAATCAACT
* *
48731 AAGATTAATGACAAAAACAATTATCATCACAAATAATCAACT
1 AAGACTAGTGACAAAAACAATTATCATCACAAATAATCAACT
*
48773 AAGACTAGTAACAAAA
1 AAGACTAGTGACAAAA
48789 TGTTTTCATC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.52, C:0.18, G:0.09, T:0.21
Consensus pattern (42 bp):
AAGACTAGTGACAAAAACAATTATCATCACAAATAATCAACT
Found at i:49392 original size:39 final size:39
Alignment explanation
Indices: 49312--49393 Score: 107
Period size: 39 Copynumber: 2.1 Consensus size: 39
49302 TAACAAGTTG
*
49312 AAAATATTTATATATTTTATTTAAAAAAATTAAATTCAT
1 AAAATATTTATATATTTTATTTAAAAAAATTAAAATCAT
49351 AAAAT-TTATATATATTTT-TTTAAAAAAAATTGAAAAT-AT
1 AAAATATT-TATATATTTTATTT-AAAAAAATT-AAAATCAT
49390 AAAA
1 AAAA
49394 AAGGTTTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
38 5 0.13
39 30 0.77
40 4 0.10
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
AAAATATTTATATATTTTATTTAAAAAAATTAAAATCAT
Found at i:57190 original size:21 final size:21
Alignment explanation
Indices: 57164--57203 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
57154 ACTAGGGTTG
57164 ATTTTTAC-TATTGAATTTTAA
1 ATTTTT-CTTATTGAATTTTAA
*
57185 ATTTTTCTTATTTAATTTT
1 ATTTTTCTTATTGAATTTT
57204 TTACTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
ATTTTTCTTATTGAATTTTAA
Found at i:58296 original size:2 final size:2
Alignment explanation
Indices: 58291--58317 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
58281 TGTGTGTGTG
58291 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
58318 TAAAATAGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:66602 original size:89 final size:89
Alignment explanation
Indices: 66448--66628 Score: 326
Period size: 89 Copynumber: 2.0 Consensus size: 89
66438 CCTTATTTGG
* *
66448 CTAAGCTTTGGCTCGGTTGTTGGTTCTGGCATATTTGACATAACAGGTCAAGAAGCTCATGATCA
1 CTAAGCTTTGGCTCAGTTGTTGGTTCTGGCATATTTGACATAACAGGTCAAGAAGCTCATAATCA
66513 TGCAGGTCCAGCTATTGTATTGTC
66 TGCAGGTCCAGCTATTGTATTGTC
*
66537 CTAAGCTTTGGCTCAGTTGTTGGTTCTGGCATATTTGTCATAACAGGTCAAGAAGCTCATAATCA
1 CTAAGCTTTGGCTCAGTTGTTGGTTCTGGCATATTTGACATAACAGGTCAAGAAGCTCATAATCA
*
66602 TGCAGGTCCAGCTATTGTCTTGTC
66 TGCAGGTCCAGCTATTGTATTGTC
66626 CTA
1 CTA
66629 TGCTGTCTCT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
89 88 1.00
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (89 bp):
CTAAGCTTTGGCTCAGTTGTTGGTTCTGGCATATTTGACATAACAGGTCAAGAAGCTCATAATCA
TGCAGGTCCAGCTATTGTATTGTC
Found at i:75387 original size:34 final size:34
Alignment explanation
Indices: 75343--75409 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 34
75333 AATAGGAATT
*
75343 ACAACTTCTCTC-GATCTAACAAGGAGAAAACAATA
1 ACAACTTCTCTCTGA--TAAAAAGGAGAAAACAATA
75378 ACAA-TTCTCTCTTGATAAAAAGGAGAAAACAA
1 ACAACTTCTCTC-TGATAAAAAGGAGAAAACAA
75410 CTCTCAAGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
34 23 0.79
35 4 0.14
36 2 0.07
ACGTcount: A:0.48, C:0.19, G:0.12, T:0.21
Consensus pattern (34 bp):
ACAACTTCTCTCTGATAAAAAGGAGAAAACAATA
Found at i:82315 original size:15 final size:15
Alignment explanation
Indices: 82295--82324 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
82285 ATCTTTCTTT
82295 ATTATGCTTTCATCA
1 ATTATGCTTTCATCA
*
82310 ATTATGCTTTTATCA
1 ATTATGCTTTCATCA
82325 GCTTTCACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (15 bp):
ATTATGCTTTCATCA
Found at i:85054 original size:12 final size:12
Alignment explanation
Indices: 85037--85061 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
85027 CCGACGGTTC
85037 TATTTTAACTAT
1 TATTTTAACTAT
85049 TATTTTAACTAT
1 TATTTTAACTAT
85061 T
1 T
85062 TTTAACTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAACTAT
Found at i:86700 original size:2 final size:2
Alignment explanation
Indices: 86693--86721 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
86683 AGCAATATTA
86693 AT AT 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 AT AT A
86722 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87279 original size:30 final size:30
Alignment explanation
Indices: 87213--87279 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 30
87203 ACAGAGCCGA
* * *
87213 CGGTTCAAACCGATTTTGCCGGTTCCCAGC
1 CGGTTCAAACCGATTCTACCGGTTCCCAAC
** * *
87243 TAGTTCACACCGATTCTACTGGTTCCCAAC
1 CGGTTCAAACCGATTCTACCGGTTCCCAAC
87273 CGGTTCA
1 CGGTTCA
87280 TTGCAGAATT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.19, C:0.33, G:0.19, T:0.28
Consensus pattern (30 bp):
CGGTTCAAACCGATTCTACCGGTTCCCAAC
Found at i:90389 original size:59 final size:59
Alignment explanation
Indices: 90321--90439 Score: 143
Period size: 59 Copynumber: 2.0 Consensus size: 59
90311 ACAAACGGTC
* * *
90321 CCTCGATTATAG-GATATTTTTTTATTGAGTCAT-GCGACTATTAAAATAAATAAAATGAT
1 CCTCAATTATAGTG-TATTTCTTTATTGAGTC-TCGCGACTATTAAAAGAAATAAAATGAT
* * **
90380 CCTCAATTATAGTGTATTTCTTTGTTGAGTCTCTCGACTATTAAAAGCTATAAAATGAT
1 CCTCAATTATAGTGTATTTCTTTATTGAGTCTCGCGACTATTAAAAGAAATAAAATGAT
90439 C
1 C
90440 ATCTGACTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
58 1 0.02
59 49 0.96
60 1 0.02
ACGTcount: A:0.34, C:0.13, G:0.13, T:0.39
Consensus pattern (59 bp):
CCTCAATTATAGTGTATTTCTTTATTGAGTCTCGCGACTATTAAAAGAAATAAAATGAT
Done.