Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002514.1 Hibiscus syriacus cultivar Beakdansim tig00005115_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: 206048
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:1742 original size:24 final size:24
Alignment explanation
Indices: 1698--1744 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
1688 ATAAAGAACC
*
1698 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
1722 AAAATAAAGTTTAAACA-ACCATT
1 AAAATAAA-CTTAAACATACCATT
1745 CAACCAACCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.57, C:0.13, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:6198 original size:82 final size:83
Alignment explanation
Indices: 6037--6238 Score: 212
Period size: 82 Copynumber: 2.4 Consensus size: 83
6027 AGTCGATTAT
* * * *
6037 ATTGAAAGTTTTGCCCTTTAATGAGGAAAC-GATGTTAGAATTTACACCTTTAAGGTTGAAGTTC
1 ATTGAAAATTTTACCCTTTAATGAGG-AACTGATGTTAGAATTTACACATTTAAGGTTGAAGTTA
* *
6101 AACTAAAAGAGTTAATTAA
65 AACTAAAAGAATTAATCAA
* * * * * *
6120 ATTG-GAATTTTACCTTTTAATGAGGAACTGGTGTTAGAATTTATATATTTAAGGTTTAA-TTGA
1 ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTAGAATTTACACATTTAAGGTTGAAGTT-A
* * *
6183 AACTGAAATAATTAATCAT
65 AACTAAAAGAATTAATCAA
* *
6202 ATTGAAAATTTTACCCTTTACTGAGGAACTGAAGTTA
1 ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTA
6239 CAGTTTGGAG
Statistics
Matches: 96, Mismatches: 20, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
81 5 0.05
82 60 0.62
83 31 0.32
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (83 bp):
ATTGAAAATTTTACCCTTTAATGAGGAACTGATGTTAGAATTTACACATTTAAGGTTGAAGTTAA
ACTAAAAGAATTAATCAA
Found at i:6528 original size:83 final size:82
Alignment explanation
Indices: 6445--6597 Score: 184
Period size: 82 Copynumber: 1.9 Consensus size: 82
6435 ATAATTTTAC
* * *
6445 CCCTT-AATCAGTAACTGAAGTTAGAATTTAGAGCTAGT-AGGTTGAAGTGAAACTTAAAGAATC
1 CCCTTCAATCAGTAACTGAAGTCACAATTTAGAG-T-GTAAGGTTGAAGTGAAACATAAAGAATC
6508 AATTAAATCGGAAATGTTA
64 AATTAAATCGGAAATGTTA
* * * * * * *
6527 CCTTTCAATGAGTAACTGAAGTCACAATTTGGAGTTTAAGGTTGAATTGAAACATCAAGATTCAA
1 CCCTTCAATCAGTAACTGAAGTCACAATTTAGAGTGTAAGGTTGAAGTGAAACATAAAGAATCAA
6592 TTAAAT
66 TTAAAT
6598 TGAATAATTT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
81 1 0.02
82 34 0.58
83 24 0.41
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (82 bp):
CCCTTCAATCAGTAACTGAAGTCACAATTTAGAGTGTAAGGTTGAAGTGAAACATAAAGAATCAA
TTAAATCGGAAATGTTA
Found at i:32632 original size:16 final size:16
Alignment explanation
Indices: 32611--32646 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
32601 CCCACCGGTT
32611 GGATTAAGGGAAACTC
1 GGATTAAGGGAAACTC
*
32627 GGATTAAGGGAAACTT
1 GGATTAAGGGAAACTC
32643 GGAT
1 GGAT
32647 GGGGCTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.36, C:0.08, G:0.33, T:0.22
Consensus pattern (16 bp):
GGATTAAGGGAAACTC
Found at i:39068 original size:23 final size:20
Alignment explanation
Indices: 39017--39076 Score: 77
Period size: 23 Copynumber: 2.9 Consensus size: 20
39007 TTTTGGTGCA
*
39017 GAGGGAATCGA-TCCCCCTT
1 GAGGGAACCGATTCCCCCTT
39036 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCC-TT
39057 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
39077 CACAGGGGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 10 0.28
20 6 0.17
21 3 0.08
22 1 0.03
23 16 0.44
ACGTcount: A:0.22, C:0.33, G:0.27, T:0.18
Consensus pattern (20 bp):
GAGGGAACCGATTCCCCCTT
Found at i:39085 original size:21 final size:21
Alignment explanation
Indices: 39059--39098 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
39049 CCCCCTTTGA
*
39059 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
39080 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
39099 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:41040 original size:9 final size:8
Alignment explanation
Indices: 41018--41068 Score: 52
Period size: 9 Copynumber: 6.2 Consensus size: 8
41008 TGTTTCAACA
41018 TTTTGGAT
1 TTTTGGAT
41026 ATTTTGGAT
1 -TTTTGGAT
41035 TGTTT-GAT
1 T-TTTGGAT
41043 TTTGTGGAT
1 TTT-TGGAT
*
41052 TGTTGGA-
1 TTTTGGAT
41059 TTTTGGAT
1 TTTTGGAT
41067 TT
1 TT
41069 ATGAATGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
7 8 0.22
8 12 0.33
9 16 0.44
ACGTcount: A:0.14, C:0.00, G:0.27, T:0.59
Consensus pattern (8 bp):
TTTTGGAT
Found at i:41052 original size:17 final size:17
Alignment explanation
Indices: 41020--41063 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
41010 TTTCAACATT
41020 TTGGATATTT-TGGATTG
1 TTGGAT-TTTGTGGATTG
*
41037 TTTGATTTTGTGGATTG
1 TTGGATTTTGTGGATTG
41054 TTGGATTTTG
1 TTGGATTTTG
41064 GATTTATGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (17 bp):
TTGGATTTTGTGGATTG
Found at i:44058 original size:2 final size:2
Alignment explanation
Indices: 44053--44088 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
44043 ATATTTTTTA
44053 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
44089 GCGGGATGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45339 original size:2 final size:2
Alignment explanation
Indices: 45332--45357 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45322 AGTATCTGAA
45332 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
45358 TGAATTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48128 original size:31 final size:31
Alignment explanation
Indices: 48097--48207 Score: 134
Period size: 31 Copynumber: 3.6 Consensus size: 31
48087 GTGAGCCTTG
* * * * *
48097 GGTAGGCTCTGAGGCCCTGAGAACCTTCTTG
1 GGTAGGCTCTCAGGCCCCGATAACTTTCTTA
* *
48128 GGTGGGC-CCCAAGGCCCCGATAACTTTCTTA
1 GGTAGGCTCTC-AGGCCCCGATAACTTTCTTA
*
48159 GGTAGGCTCTCAGACCCCGATAACTTTCTTA
1 GGTAGGCTCTCAGGCCCCGATAACTTTCTTA
48190 GGTAGGCTCTCAGGCCCC
1 GGTAGGCTCTCAGGCCCC
48208 AAGATGCTCC
Statistics
Matches: 67, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 1 0.01
31 64 0.96
32 2 0.03
ACGTcount: A:0.18, C:0.31, G:0.27, T:0.24
Consensus pattern (31 bp):
GGTAGGCTCTCAGGCCCCGATAACTTTCTTA
Found at i:57055 original size:23 final size:22
Alignment explanation
Indices: 57029--57076 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
57019 TATTATTTTT
57029 AAAAAATATTTTTAAAAGTAAAA
1 AAAAAATA-TTTTAAAAGTAAAA
* *
57052 AAAAAATATTTTAAAATTATAA
1 AAAAAATATTTTAAAAGTAAAA
57074 AAA
1 AAA
57077 TATAGTTAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (22 bp):
AAAAAATATTTTAAAAGTAAAA
Found at i:59675 original size:18 final size:18
Alignment explanation
Indices: 59652--59692 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
59642 ACCGGTCACA
59652 ACCCGACCCAACCCGTTG
1 ACCCGACCCAACCCGTTG
*
59670 ACCCGACCCGACCCGTTG
1 ACCCGACCCAACCCGTTG
59688 ACCCG
1 ACCCG
59693 TTGACCACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.51, G:0.20, T:0.10
Consensus pattern (18 bp):
ACCCGACCCAACCCGTTG
Found at i:69500 original size:21 final size:22
Alignment explanation
Indices: 69453--69500 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
69443 TTTGGTTAAT
69453 TATT-AATATTTTTAAAAAACCA
1 TATTAAATATTTTTAAAAAA-CA
*
69475 T-TTAAATTTTTTTAAAAAA-A
1 TATTAAATATTTTTAAAAAACA
69495 TATTAA
1 TATTAA
69501 TTGAGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 2 0.09
21 6 0.26
22 15 0.65
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (22 bp):
TATTAAATATTTTTAAAAAACA
Found at i:73856 original size:25 final size:22
Alignment explanation
Indices: 73804--73857 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 22
73794 AACATGTCAC
* *
73804 ATTTATATTTTTTTAAAAATCT
1 ATTTTTATTTTTTTAAAAAACT
73826 ATTTTTTATTCTTTTTAAAAAACATT
1 A-TTTTTATT-TTTTTAAAAAAC--T
73852 ATTTTT
1 ATTTTT
73858 GAAAAACTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 1 0.04
23 7 0.27
24 11 0.42
25 5 0.19
26 2 0.08
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (22 bp):
ATTTTTATTTTTTTAAAAAACT
Found at i:75034 original size:22 final size:20
Alignment explanation
Indices: 74997--75047 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
74987 TTCAGAATAT
*
74997 AAAAAATTTCTCAAAAACAAC
1 AAAAAATGTCTC-AAAACAAC
* *
75018 AAATAAATGTCTTAAAAGAAC
1 AAA-AAATGTCTCAAAACAAC
75039 AAAAAATGT
1 AAAAAATGT
75048 ACTGAACAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 6 0.23
21 13 0.50
22 7 0.27
ACGTcount: A:0.61, C:0.12, G:0.06, T:0.22
Consensus pattern (20 bp):
AAAAAATGTCTCAAAACAAC
Found at i:77022 original size:22 final size:22
Alignment explanation
Indices: 76971--77022 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
76961 CGGTAAGTCA
*
76971 TTTTACGGGAGACAGGAAGGAG
1 TTTTACGTGAGACAGGAAGGAG
76993 TTTTACGTGAGACAGGAAGGAG
1 TTTTACGTGAGACAGGAAGGAG
77015 TTTTACGT
1 TTTTACGT
77023 TGACCGTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.27
Consensus pattern (22 bp):
TTTTACGTGAGACAGGAAGGAG
Found at i:78138 original size:118 final size:120
Alignment explanation
Indices: 77942--78156 Score: 346
Period size: 118 Copynumber: 1.8 Consensus size: 120
77932 TAATTAATTT
* *
77942 TTTAACTGTTAATCGAACTGATTTTTTATAAAAAAAATATCAATCGAATTGAACAAAGTTTGATT
1 TTTAACTGTTAACCGAACTGATTTTTTATAAAAAAAATATCAATCAAATTGAACAAAGTTTGATT
* * *
78007 AATTCAACAGGTAAAATTAATTTTTTATATATTTTTTGAATTAATTAATTTTTTC
66 AATTCAACAGGTAAAACTAAATTTATATATATTTTTTGAATTAATTAATTTTTTC
78062 TTTAACTGTTAACCGAACTGATTTTTT-T-AAAAAAATATCAATCAAATTGAACAAA-TTTCGAT
1 TTTAACTGTTAACCGAACTGATTTTTTATAAAAAAAATATCAATCAAATTGAACAAAGTTT-GAT
*
78124 TAATTCAACCGGTAAAACTAAATTTATATATAT
65 TAATTCAACAGGTAAAACTAAATTTATATATAT
78157 ATATATATAT
Statistics
Matches: 88, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
117 3 0.03
118 58 0.66
119 1 0.01
120 26 0.30
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (120 bp):
TTTAACTGTTAACCGAACTGATTTTTTATAAAAAAAATATCAATCAAATTGAACAAAGTTTGATT
AATTCAACAGGTAAAACTAAATTTATATATATTTTTTGAATTAATTAATTTTTTC
Found at i:78340 original size:16 final size:14
Alignment explanation
Indices: 78290--78332 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
78280 TTAAAATATG
78290 TATTTAATATAT-A
1 TATTTAATATATAA
*
78303 TATAT-ATATATAA
1 TATTTAATATATAA
*
78316 TATTTAATATTTAA
1 TATTTAATATATAA
78330 TAT
1 TAT
78333 CTTCAATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
12 6 0.24
13 9 0.36
14 10 0.40
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATTTAATATATAA
Found at i:88234 original size:5 final size:6
Alignment explanation
Indices: 88217--88241 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
88207 AATTATCATA
88217 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
88242 TTATTGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:88244 original size:14 final size:14
Alignment explanation
Indices: 88217--88257 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
88207 AATTATCATA
88217 TATTTTTA--TTTT
1 TATTTTTATTTTTT
88229 TATTTTTATTTTTT
1 TATTTTTATTTTTT
**
88243 TATTGATATTTTTT
1 TATTTTTATTTTTT
88257 T
1 T
88258 CTTAGAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 8 0.32
14 17 0.68
ACGTcount: A:0.17, C:0.00, G:0.02, T:0.80
Consensus pattern (14 bp):
TATTTTTATTTTTT
Found at i:90822 original size:21 final size:21
Alignment explanation
Indices: 90798--90838 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
90788 GGTAAAAAAT
*
90798 TACCTAAAACATTATTATTTC
1 TACCTAAAACATTAATATTTC
90819 TACCTAAAACATTAATATTT
1 TACCTAAAACATTAATATTT
90839 TTTAACAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.41
Consensus pattern (21 bp):
TACCTAAAACATTAATATTTC
Found at i:91402 original size:23 final size:23
Alignment explanation
Indices: 91370--91420 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
91360 ATGTTCATTT
* *
91370 ATTTATTGTTCGCGAATATGTTC
1 ATTTAATGTTCGCAAATATGTTC
* *
91393 GTTTAATGTTCGCAAATGTGTTC
1 ATTTAATGTTCGCAAATATGTTC
91416 ATTTA
1 ATTTA
91421 TATTCCCATA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.47
Consensus pattern (23 bp):
ATTTAATGTTCGCAAATATGTTC
Found at i:94219 original size:33 final size:33
Alignment explanation
Indices: 94171--94259 Score: 124
Period size: 33 Copynumber: 2.7 Consensus size: 33
94161 AGTTGAAAGG
* * * *
94171 GAGGAAGGCGAGTTCTTCCCAGATGGGGACGTC
1 GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
*
94204 GAGGAAGGTGGGTTCTTACCAAATGGGAACGTC
1 GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
*
94237 GAGGAAGGTGAGTTCTTTCCAAA
1 GAGGAAGGTGAGTTCTTACCAAA
94260 GGGGGATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 49 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (33 bp):
GAGGAAGGTGAGTTCTTACCAAATGGGAACGTC
Found at i:96163 original size:3 final size:3
Alignment explanation
Indices: 96144--96190 Score: 76
Period size: 3 Copynumber: 15.0 Consensus size: 3
96134 ATATTATAAA
96144 TAT TAAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
96191 CTTTAATATT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:99463 original size:21 final size:21
Alignment explanation
Indices: 99441--99534 Score: 111
Period size: 21 Copynumber: 4.5 Consensus size: 21
99431 CCAAGGATGA
99441 GAAGACCATTCATAAAGACGA-
1 GAAGACCATTCATAAAGAC-AT
*
99462 GAAGATCATTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
99483 GAAGACTC-TTCATAAAGACAT
1 GAAGAC-CATTCATAAAGACAT
* *
99504 GAATACCCTTCATAAAGACAT
1 GAAGACCATTCATAAAGACAT
* *
99525 GGAGATCATT
1 GAAGACCATT
99535 TCGCATTGGA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
20 2 0.03
21 60 0.95
22 1 0.02
ACGTcount: A:0.44, C:0.18, G:0.16, T:0.22
Consensus pattern (21 bp):
GAAGACCATTCATAAAGACAT
Found at i:101318 original size:20 final size:21
Alignment explanation
Indices: 101285--101352 Score: 129
Period size: 21 Copynumber: 3.3 Consensus size: 21
101275 TTTGAAAATG
101285 TTTTTGTTGTTTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
101306 TTTTTGTTGTTTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
101327 TTTTTGTTG-TTTTTCTCAAC
1 TTTTTGTTGTTTTTTCTCAAC
101347 TTTTTG
1 TTTTTG
101353 AAAGGATTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.09, C:0.13, G:0.10, T:0.68
Consensus pattern (21 bp):
TTTTTGTTGTTTTTTCTCAAC
Found at i:102072 original size:19 final size:19
Alignment explanation
Indices: 102048--102119 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 19
102038 TGTAGAAAGA
102048 GAAAAAGAAA-AGAAAAAAT
1 GAAAAA-AAAGAGAAAAAAT
102067 GAAAAAAAAGAGAAAAAAAT
1 GAAAAAAAAGAG-AAAAAAT
*
102087 GGAAATAAAAA-A-ATGAAAAT
1 -GAAA-AAAAAGAGA-AAAAAT
102107 -AAAAAAAAGAGAA
1 GAAAAAAAAGAGAA
102120 GGAAAGAAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
17 5 0.11
18 7 0.16
19 10 0.23
20 12 0.27
21 5 0.11
22 5 0.11
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (19 bp):
GAAAAAAAAGAGAAAAAAT
Found at i:102074 original size:9 final size:10
Alignment explanation
Indices: 102043--102085 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
102033 AGAAATGTAG
102043 AAAGAGAAAA
1 AAAGAGAAAA
*
102053 AGAAAAGAAAA
1 A-AAGAGAAAA
*
102064 AATGA-AAAA
1 AAAGAGAAAA
102073 AAAGAGAAAA
1 AAAGAGAAAA
102083 AAA
1 AAA
102086 TGGAAATAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
9 8 0.30
10 10 0.37
11 9 0.33
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.02
Consensus pattern (10 bp):
AAAGAGAAAA
Found at i:103590 original size:124 final size:125
Alignment explanation
Indices: 103370--103612 Score: 348
Period size: 124 Copynumber: 2.0 Consensus size: 125
103360 TGTGATATGT
* * *
103370 TGGGGCATGACTGAACCCACATCATGTTGAGATGGCAAGATTCAAACCAAGGAGGCATGAAGAAT
1 TGGGGAATGACTGAACCCACATCATATTGAGATGGCAAGATTCAAACCAAGAAGGCATGAAGAAT
* * * *
103435 GAGCCTTACAATTTGAGGTGATGAGGCATTTTGAAGGCTCGTACCAGT-TAAGACACTGA
66 AAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGACACTGA
*
103494 TGGGGAATGACTGAACCCACATCATATTGAGA-GGACAAGATTTAAACCAAGAAGGCAAT-AAGA
1 TGGGGAATGACTGAACCCACATCATATTGAGATGG-CAAGATTCAAACCAAGAAGGC-ATGAAGA
* * *
103557 GTAAGCCTTACAATCTGAGATGTTGGGGCATTTTGAAGGCCCGTACCAGTATAAGA
64 ATAAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGA
103613 TGATGTTGCG
Statistics
Matches: 105, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
123 2 0.02
124 96 0.91
125 7 0.07
ACGTcount: A:0.34, C:0.17, G:0.26, T:0.22
Consensus pattern (125 bp):
TGGGGAATGACTGAACCCACATCATATTGAGATGGCAAGATTCAAACCAAGAAGGCATGAAGAAT
AAGCCTTACAATCTGAGATGATGAGGCATTTTGAAGGCCCGTACCAGTATAAGACACTGA
Found at i:105401 original size:54 final size:54
Alignment explanation
Indices: 105320--106269 Score: 1501
Period size: 54 Copynumber: 17.6 Consensus size: 54
105310 GTAGTGAAGC
*
105320 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
105374 GAAGAAGATATCCGAGTTTCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * * * *
105428 GAAGAATATGTTCGAGTTCCATACTCACTAAAGAAAGAAGGAGCGAACCTGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
105482 GAAGAAGTTGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
105536 GAAGAAGATGTCCAAGTTCCATACTCCCTAAAGAAAGAGGGAGAGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
105590 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * * *
105644 GAAAAAGATGTTCGATTTCCATACTCCCTAGAGAAAGAGGGAGCGAACACGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
105698 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCG--T
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
105750 -AAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
105803 GAAGAAAATGTCCGAGTTCTATACTCCCTAGAGAAAGTGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
105857 GAAGAAAATGTTCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
** ** * **
105911 GAAGAAGATGTCTAAGTTTTATACTCCCTAGAGAAAGAGGGAGTGAACATGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
105965 GAAGAAGATGTTCGAGTTCTATATTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* * *
106019 GAAGAAGATGTCCAAGTTACATACTCCCTAGAGAAAGAGGGAGCGAACTCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
106073 GAAGAAGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAATCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
106127 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
* *
106181 GAAGAAAATGTTCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
*
106235 GAAGAAGATGTTCGAGTTCCATACTCCCTAGAGAA
1 GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAA
106270 TAGGGAACAT
Statistics
Matches: 823, Mismatches: 70, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
51 49 0.06
52 1 0.00
53 1 0.00
54 772 0.94
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.21
Consensus pattern (54 bp):
GAAGAAGATGTCCGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGTTT
Found at i:106729 original size:55 final size:55
Alignment explanation
Indices: 106218--106713 Score: 479
Period size: 55 Copynumber: 9.2 Consensus size: 55
106208 CTAGAGAAAG
* ** * *
106218 AGGGAGCGAACCCGTTTGAAGAAGA-TGTTCGAGT-TCCATACTCCCT--AGAGAAT
1 AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAG-GAAT
* * * * * *
106271 AGGGAAC-ATACACGATTT-TTGGAGTTTGTTCGAGTCTCATACTATCTGAAAGAAT
1 AGGGAGCGA-ACACG-TTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
*
106326 AGGGAGC-AGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
1 AGGGAGCGA-ACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* *
106381 AGGGAGCGGACACGATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
1 AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * *
106436 AGGGAG-TAGACACGTTTGTTGAAGATTGTTCAAGTCCTATACTCTCTGAAGGAAT
1 AGGGAGCGA-ACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * * * * * *
106491 AGGGAGCAAACACGTTTATTAAAGGTTGTTCAAGTCATATACTCTCTGAAGAAAT
1 AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * *
106546 AGGGAGCGGACACGTTTGTTGAAGA---TT-AAGTCCTATACTCTCTGAAGGAAT
1 AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* *
106597 AGGGAGCGGACACGTTTGTTGAAGA---TT-GAGTCATATACTCTCTGAAGGAAT
1 AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
* * * * * *
106648 AGGGAACGAAC-CTGTTT-TATTAAGATTGTTTGAGTTTTATACTCCCTGAAGCAAT
1 AGGGAGCGAACAC-GTTTGT-TGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
106703 AGGGAGCGAAC
1 AGGGAGCGAAC
106714 CCGATGGTCG
Statistics
Matches: 381, Mismatches: 46, Indels: 30
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.01
51 89 0.23
52 3 0.01
53 13 0.03
54 24 0.06
55 248 0.65
56 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (55 bp):
AGGGAGCGAACACGTTTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGGAAT
Found at i:106898 original size:3 final size:3
Alignment explanation
Indices: 106879--106928 Score: 82
Period size: 3 Copynumber: 16.0 Consensus size: 3
106869 ATATTATAAA
106879 TAT TAAT TAT ATAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
106926 TAT
1 TAT
106929 CTTTAATATT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
3 39 0.87
4 6 0.13
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:107703 original size:21 final size:21
Alignment explanation
Indices: 107677--107721 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
107667 GATTTCTGTG
* *
107677 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
107698 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
107719 CAA
1 CAA
107722 ACGAACAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:108329 original size:18 final size:18
Alignment explanation
Indices: 108306--108340 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
108296 CTAGGAGATT
108306 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
108324 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
108341 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:109421 original size:149 final size:149
Alignment explanation
Indices: 109238--109541 Score: 547
Period size: 149 Copynumber: 2.0 Consensus size: 149
109228 GAGTCGAGGG
109238 TCTACGCGGTTCTTTGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTCGAAAGACACAT
1 TCTACGCGGTTCTTTGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTCGAAAGACACAT
*
109303 ACTTGATCCTTAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
66 ACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
109368 TATGGCACTACGGTGCAAT
131 TATGGCACTACGGTGCAAT
* *
109387 TCTACTCGGTTCTTT-AGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACA
1 TCTACGCGGTTCTTTGA-GACATATGTATATTCTTTGGAACATGTGTGAAGTCTCGAAAGACACA
* *
109451 TACTTGATCCATAGTATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGATATCATT
65 TACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATT
109516 ATATGGCACTACGGTGCAAT
130 ATATGGCACTACGGTGCAAT
109536 TCTACG
1 TCTACG
109542 GGGCACTTCG
Statistics
Matches: 148, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 147 0.99
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
TCTACGCGGTTCTTTGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTCGAAAGACACAT
ACTTGATCCATAGCATATGTATATGATTCTTAAGGAATTCTATGTGGTCCTTATGGACATCATTA
TATGGCACTACGGTGCAAT
Found at i:109564 original size:23 final size:23
Alignment explanation
Indices: 109520--109564 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
109510 ATCATTATAT
*
109520 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
109543 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
109565 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:111081 original size:23 final size:23
Alignment explanation
Indices: 111055--111099 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
111045 CACCACAGCT
*
111055 CGTATAAATGCACAGAAGTGCCC
1 CGTAGAAATGCACAGAAGTGCCC
* * *
111078 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAAATGCACAGAAGTGCC
111100 ATATAATGAT
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:0.29, C:0.27, G:0.24, T:0.20
Consensus pattern (23 bp):
CGTAGAAATGCACAGAAGTGCCC
Found at i:111272 original size:149 final size:149
Alignment explanation
Indices: 111078--111381 Score: 599
Period size: 149 Copynumber: 2.0 Consensus size: 149
111068 AGAAGTGCCC
*
111078 CGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
111143 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
111208 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
111227 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
111292 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
66 CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
111357 CATATGTCCCGAAGAACCG
131 CATATGTCCCGAAGAACCG
111376 CGTAGA
1 CGTAGA
111382 CCCTCGACTC
Statistics
Matches: 154, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 154 1.00
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATAGAATTCTTTAAGAAT
CATATACATATGCTAGGGATCAAGTATGTGTCTTTCCAGACTTCACACATGTTCCAAAGAATATA
CATATGTCCCGAAGAACCG
Found at i:111841 original size:2 final size:2
Alignment explanation
Indices: 111834--111871 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
111824 TCTCTTAGAC
111834 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
111872 TCACATGTTC
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:112850 original size:21 final size:21
Alignment explanation
Indices: 112820--112864 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
112810 ATTTTGTCGT
* *
112820 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
112841 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
112862 TTG
1 TTG
112865 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:130741 original size:15 final size:15
Alignment explanation
Indices: 130721--130749 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
130711 TATATATATA
130721 TAAACTTACTAGATT
1 TAAACTTACTAGATT
130736 TAAACTTACTAGAT
1 TAAACTTACTAGAT
130750 AGAATTCACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAACTTACTAGATT
Found at i:131452 original size:112 final size:112
Alignment explanation
Indices: 131287--131751 Score: 696
Period size: 112 Copynumber: 4.1 Consensus size: 112
131277 TTGTCGGTTT
* * * *
131287 GTGTCGATACTTTATAAAAATATATTGATCTATAACAATATAACAAGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
131352 GGTCTATAAATGACAAAACAAGTAAAGCGCTATCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
* * *
131399 GTGTCAATACTTTATAAAAATGCATCTATCCCATAACAATATAACAGGTAAAAAAAATGACAAAA
1 GTGTCGATACTTTATAAAAATGTATCGAT-CCATAACAATATAACAGGT-AAAAAAATGACAAAA
* *
131464 CCGGTCTATAAATGACAAAACAAGTAAAGCGTTACCGAATATATTGAAA
64 CCGGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
* *
131513 GTGTCGATACTTTATAGAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAATC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
131578 GGTCTATAAATGACAAAATAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
* *
131625 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAATAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * * *
131690 GATCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
*
131737 GTGTCAATACTTTAT
1 GTGTCGATACTTTAT
131752 TATAAGTATC
Statistics
Matches: 322, Mismatches: 29, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
112 200 0.62
113 36 0.11
114 86 0.27
ACGTcount: A:0.46, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
Found at i:131931 original size:182 final size:182
Alignment explanation
Indices: 131624--132072 Score: 684
Period size: 182 Copynumber: 2.5 Consensus size: 182
131614 ATATGTTGAT
* * *
131624 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATAAAATAGGTAAAAAAATGACAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
* ** *
131689 CGATCTATAAATGAAAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCAATACTTTATTA
66 TGATCTCGAAATGAAAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTATTA
* *
131754 TAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* *
131806 AGTGTCGATACTTTATAAAAATATATCGATCCATAACAATATAACAGGTAAAAATATGATAAAAC
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
* * * * ** *
131871 TGGTCTCGAAATGACAAAACCGGTAAAGAGGTATTGGATATGTTGATAGTGTCGATACTTTATTA
66 TGATCTCGAAATGAAAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTATTA
*
131936 TAAGTATCGACACTTTTGGAATTTAAAAGAAAATAAGTTATAGCGCCAATAA
131 TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
* *
131988 AGTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAACATGTAAAAATATGACAAAA-
1 AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
*
132052 TCGATCTCGAAATGATAAAAC
66 T-GATCTCGAAATGAAAAAAC
132073 TAGTAGTAAA
Statistics
Matches: 241, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 1 0.00
182 240 1.00
ACGTcount: A:0.44, C:0.12, G:0.16, T:0.28
Consensus pattern (182 bp):
AGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGACAAAAC
TGATCTCGAAATGAAAAAACAGGTAAAGAGCTACCGGATATGTTGATAGTGTCAATACTTTATTA
TAAGTATCGACACTTTTGGAATTTAAAAGAAAAGAAGTTATAGCGCCAATAA
Found at i:135348 original size:2 final size:2
Alignment explanation
Indices: 135341--135376 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
135331 AATAATTAGA
135341 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
135377 AATTTGGGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:136094 original size:17 final size:15
Alignment explanation
Indices: 136072--136106 Score: 52
Period size: 17 Copynumber: 2.2 Consensus size: 15
136062 ATATTTTGTT
136072 TTTAATTTATTTAAGTA
1 TTTAATTT-TTTAA-TA
136089 TTTAATTTTTTAATA
1 TTTAATTTTTTAATA
136104 TTT
1 TTT
136107 TTTTAATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 5 0.28
17 8 0.44
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (15 bp):
TTTAATTTTTTAATA
Found at i:136097 original size:24 final size:23
Alignment explanation
Indices: 136048--136106 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
136038 TTAAGGTATA
**
136048 TTTTATTATATTTAATATTTTGT
1 TTTTATTATATTTAATATTTAAT
136071 TTTTAATT-TATTTAAGTATTTAAT
1 TTTT-ATTATATTTAA-TATTTAAT
*
136095 TTTT-TAATATTT
1 TTTTATTATATTT
136107 TTTTAATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 13 0.43
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (23 bp):
TTTTATTATATTTAATATTTAAT
Found at i:138453 original size:34 final size:33
Alignment explanation
Indices: 138386--138473 Score: 106
Period size: 33 Copynumber: 2.6 Consensus size: 33
138376 TAATACTTAC
**
138386 TTTATTTCATTAATTTTGTTGGATTTATTTTAA
1 TTTATTTTGTTAATTTTGTTGGATTTATTTTAA
*
138419 TTTATTTTGTTAAATTTGTTGGACTTT-TTGTTAA
1 TTTATTTTGTTAATTTTGTTGGA-TTTATT-TTAA
*
138453 TATATTTTGGTTAATTTTGTT
1 TTTATTTT-GTTAATTTTGTT
138474 TATTACCATT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 22 0.47
34 14 0.30
35 11 0.23
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (33 bp):
TTTATTTTGTTAATTTTGTTGGATTTATTTTAA
Found at i:143954 original size:14 final size:14
Alignment explanation
Indices: 143937--143967 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
143927 AACAAACGTA
143937 AACGAACACAAACG
1 AACGAACACAAACG
*
143951 AACGAACATAAACG
1 AACGAACACAAACG
143965 AAC
1 AAC
143968 ATAATAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.58, C:0.26, G:0.13, T:0.03
Consensus pattern (14 bp):
AACGAACACAAACG
Found at i:143964 original size:10 final size:12
Alignment explanation
Indices: 143951--143995 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
143941 AACACAAACG
143951 AACGAACAT-A-
1 AACGAACATAAT
143961 AACGAACATAAT
1 AACGAACATAAT
*
143973 AATGAACATAAT
1 AACGAACATAAT
*
143985 AATGAACATAA
1 AACGAACATAA
143996 ACGAACAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 9 0.28
11 1 0.03
12 22 0.69
ACGTcount: A:0.60, C:0.13, G:0.09, T:0.18
Consensus pattern (12 bp):
AACGAACATAAT
Found at i:143981 original size:12 final size:12
Alignment explanation
Indices: 143964--143995 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
143954 GAACATAAAC
143964 GAACATAATAAT
1 GAACATAATAAT
143976 GAACATAATAAT
1 GAACATAATAAT
143988 GAACATAA
1 GAACATAA
143996 ACGAACAACA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.09, G:0.09, T:0.22
Consensus pattern (12 bp):
GAACATAATAAT
Found at i:145458 original size:87 final size:87
Alignment explanation
Indices: 145303--145476 Score: 258
Period size: 87 Copynumber: 2.0 Consensus size: 87
145293 TCTATCTGGT
* ** * *
145303 GATTCCTGTTTCTTTTGTATTTCTTAACAGTATTTTATGGTTACTGAATTTTCATTCTTATACAG
1 GATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACAG
*
145368 TGCTTTATCATTTACATTCCTA
66 TGCTTTATCATTCACATTCCTA
* * *
145390 GATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGCATTTTCATTCTTGCACGG
1 GATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACAG
*
145455 TGCTTTCTCATTCACATTCCTA
66 TGCTTTATCATTCACATTCCTA
145477 TAATATTATA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
87 77 1.00
ACGTcount: A:0.20, C:0.20, G:0.11, T:0.49
Consensus pattern (87 bp):
GATTCCCGTTTCTTTCATATTTCTCAACAGTATTTTATGGTTACTGAATTTTCATTCTTACACAG
TGCTTTATCATTCACATTCCTA
Found at i:152269 original size:2 final size:2
Alignment explanation
Indices: 152262--152286 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
152252 AAGAACTATG
152262 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 T
152287 TACTGGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:154214 original size:22 final size:23
Alignment explanation
Indices: 154164--154215 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
154154 AAGACTTATA
* *
154164 ATAAAAAATTGATATTATTCATT
1 ATAAAAACTTAATATTATTCATT
154187 AT-AAAACTTAATATTATT-ATT
1 ATAAAAACTTAATATTATTCATT
*
154208 TTAAAAAC
1 ATAAAAAC
154216 ATTATAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 4 0.16
22 19 0.76
23 2 0.08
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (23 bp):
ATAAAAACTTAATATTATTCATT
Found at i:158909 original size:2 final size:2
Alignment explanation
Indices: 158902--158936 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
158892 CTTAGTCTTT
158902 TA TA TA TA 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 TA TA TA TA T
158937 TTGTTTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:159248 original size:14 final size:15
Alignment explanation
Indices: 159222--159250 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
159212 TTTAGATAAA
159222 TATTTTATTAATATT
1 TATTTTATTAATATT
159237 TATTTT-TTAATATT
1 TATTTTATTAATATT
159251 AAGAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:159855 original size:19 final size:18
Alignment explanation
Indices: 159831--159883 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
159821 TTCTTTCAAA
159831 TTTTTTATTACTTATTATT
1 TTTTTTATTA-TTATTATT
159850 TTTTTTATATATTATTATT
1 TTTTTTAT-TATTATTATT
*
159869 TTATTTATTTATTAT
1 TTTTTTA-TTATTAT
159884 ATTCAAGAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 28 0.90
20 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTTTTATTATTATTATT
Found at i:164560 original size:15 final size:14
Alignment explanation
Indices: 164540--164583 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
164530 TCCAGCAAAG
164540 AAAGAAGAAGAAGAA
1 AAAGAAGAAGAA-AA
164555 AAAGAAGAAGAAAA
1 AAAGAAGAAGAAAA
164569 AAA-AAGAA-AAAA
1 AAAGAAGAAGAAAA
164581 AAA
1 AAA
164584 AAAGGAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.24
13 5 0.17
14 5 0.17
15 12 0.41
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
AAAGAAGAAGAAAA
Found at i:164578 original size:6 final size:6
Alignment explanation
Indices: 164536--164584 Score: 50
Period size: 6 Copynumber: 8.5 Consensus size: 6
164526 CTCATCCAGC
* *
164536 AAAGAA AGAAGAA GAAGAA AAAGAA GAAG-A AAA-AA AAAGAA AAA-AA
1 AAAGAA A-AAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
164582 AAA
1 AAA
164585 AAGGAAAATC
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
5 12 0.33
6 19 0.53
7 5 0.14
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:164582 original size:14 final size:15
Alignment explanation
Indices: 164540--164592 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 15
164530 TCCAGCAAAG
*
164540 AAAGAAGAAG-AAGAA
1 AAAGAA-AAGAAAAAA
164555 AAAGAAGAAGAAAAAA
1 AAAGAA-AAGAAAAAA
164571 AAAGAAAA-AAAAAA
1 AAAGAAAAGAAAAAA
*
164585 AAGGAAAA
1 AAAGAAAA
164593 TCGAATAAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 13 0.37
15 12 0.34
16 10 0.29
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAA
Found at i:164583 original size:13 final size:13
Alignment explanation
Indices: 164553--164592 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
164543 GAAGAAGAAG
* *
164553 AAAAAGAAGAAGA
1 AAAAAAAAGAAAA
164566 AAAAAAAAGAAAA
1 AAAAAAAAGAAAA
164579 AAAAAAAAGGAAAA
1 AAAAAAAA-GAAAA
164593 TCGAATAAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAA
Found at i:166921 original size:83 final size:83
Alignment explanation
Indices: 166820--167084 Score: 460
Period size: 83 Copynumber: 3.2 Consensus size: 83
166810 AATGGAACAA
166820 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
166885 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
166903 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
*
166968 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* * * *
166986 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTAATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAAAAC
167050 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
167069 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
167085 TAGAAATAAA
Statistics
Matches: 174, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
82 4 0.02
83 170 0.98
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.37
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
AATCATTGAATTTGGAAG
Found at i:169566 original size:22 final size:22
Alignment explanation
Indices: 169538--169658 Score: 179
Period size: 22 Copynumber: 5.5 Consensus size: 22
169528 ATCTACATTC
169538 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
169560 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* * *
169582 TTCAAAGATGATATATTTTCTC
1 TTCAAAGATGATAGATTCTCTT
*
169604 TTCAAAGATGATAAATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
* *
169626 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
169648 TTCAAAGATGA
1 TTCAAAGATGA
169659 AAGCTTTATT
Statistics
Matches: 87, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 87 1.00
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:170616 original size:113 final size:113
Alignment explanation
Indices: 170418--171054 Score: 955
Period size: 113 Copynumber: 5.6 Consensus size: 113
170408 TCATCTGTAG
* *
170418 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * *
170483 AACCTTTTGCTTGAATTCATCATTCGATGAATCAGCATTTCCAGA-AGA
66 AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGA-A
* * *
170531 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTATTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
170596 AACCTTTTGCTCGAATTCATCATTCAATGGATCAACTTTTCCAGAGAA
66 AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
*
170644 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* * * * *
170709 AA-CTTTTCGCTTGAATTCATTATTCGATGGATCAACATTGCCAG-GTCA
66 AACCTTTT-GCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAG-AA
* *
170757 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
170822 AACCTTTTGC-CTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTC-GAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAA
* *
170870 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAAAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
170935 AACCTTTTGC-CTGAATTCATCACTT-GATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCTC-GAATTCATCA-TTCGATGGATCAACTTTTCCAGAGAA
*
170983 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTTC
1 AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
171048 AACCTTT
66 AACCTTT
171055 GTTTGATGCT
Statistics
Matches: 489, Mismatches: 28, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
112 6 0.01
113 474 0.97
114 9 0.02
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATATGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGCTCGAATTCATCATTCGATGGATCAACTTTTCCAGAGAA
Found at i:173133 original size:2 final size:2
Alignment explanation
Indices: 173126--173154 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
173116 CTTAGTCTTT
173126 TA 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 TA T
173155 TTGTTTAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:173468 original size:14 final size:15
Alignment explanation
Indices: 173442--173470 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
173432 TTTAGATAAA
173442 TATTTTATTAATATT
1 TATTTTATTAATATT
173457 TATTTT-TTAATATT
1 TATTTTATTAATATT
173471 AAGAAAAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TATTTTATTAATATT
Found at i:175823 original size:2 final size:2
Alignment explanation
Indices: 175816--175852 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
175806 TGAAAAGGTT
175816 TA TA TA TA TA 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 TA TA TA TA TA T
175853 TCTCTGGACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:180047 original size:16 final size:17
Alignment explanation
Indices: 180007--180050 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
179997 CCCTACTTGA
180007 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** *
180024 TTGTATATTT-TTAAAT
1 TTAAATATTTAATAAAT
180040 TTAAATATTTA
1 TTAAATATTTA
180051 TTTTTACATG
Statistics
Matches: 21, Mismatches: 5, Indels: 2
0.75 0.18 0.07
Matches are distributed among these distances:
16 13 0.62
17 8 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:183808 original size:106 final size:106
Alignment explanation
Indices: 183621--184362 Score: 1096
Period size: 106 Copynumber: 7.0 Consensus size: 106
183611 AAGATTGTTC
* *
183621 TGAGTCCAATATCC-TC-CTTCGTGAAGTTGAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGA
1 TGAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGA
* *
183684 CAACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
64 CAACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
*
183727 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * ** * *
183792 ACCAATGGTCCATTCGTTTTGAAGTTGAACTTGCATCGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
183833 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
183898 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
183939 GGAGTCCAACATCCTTCGCTATGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
184004 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * *
184045 GGAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
184110 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* ** * *
184151 CGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
** * * * * *
184216 GTCAGCCGCCCCTTCG-CTGTGAAGTTGAGCTTGTGCTGTCT
66 ACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* *
184257 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
184322 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
184363 GGAGAGAAAC
Statistics
Matches: 578, Mismatches: 53, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
105 1 0.00
106 572 0.99
107 4 0.01
108 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:184418 original size:36 final size:36
Alignment explanation
Indices: 184371--184502 Score: 144
Period size: 36 Copynumber: 3.7 Consensus size: 36
184361 CTGGAGAGAA
184371 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
1 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
* *
184407 ACTGTCTCAAGGGAGACGAAATTTGTTTCAAAGGAAA
1 ACTGTCTCAAGGGAGACAAAATTTGTTTC-AAGGAAG
* * * * *
184444 ACTATCTCAA--GCGATAAAATCTTGTTTTAAATG-AG
1 ACTGTCTCAAGGGAGACAAAAT-TTG-TTTCAAGGAAG
*
184479 ACTGTCTCAAGCGAGACAAAATTT
1 ACTGTCTCAAGGGAGACAAAATTT
184503 ATATTGGAAA
Statistics
Matches: 79, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
35 17 0.22
36 36 0.46
37 26 0.33
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.27
Consensus pattern (36 bp):
ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
Found at i:185287 original size:22 final size:22
Alignment explanation
Indices: 185256--185332 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
185246 TTGTGTTTGG
185256 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* * *
185278 TCAAATGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
*
185300 TCAAAGGTTTGGCATTTTATGC
1 TCAAAGGTTTGGCATTTGATGC
185322 TCAAAGGTTTG
1 TCAAAGGTTTG
185333 ATGGGGTAGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 48 1.00
ACGTcount: A:0.23, C:0.10, G:0.25, T:0.42
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:185960 original size:19 final size:18
Alignment explanation
Indices: 185936--185979 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
185926 TTGTCCCTTT
185936 TCTTTTTGATTTTGTTCTC
1 TCTTTTTGATTTTGTT-TC
**
185955 TCTTTTTTCTTTTGTTTC
1 TCTTTTTGATTTTGTTTC
185973 TCTTTTT
1 TCTTTTT
185980 TCTTTATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.02, C:0.16, G:0.07, T:0.75
Consensus pattern (18 bp):
TCTTTTTGATTTTGTTTC
Found at i:185974 original size:18 final size:19
Alignment explanation
Indices: 185945--185984 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
185935 TTCTTTTTGA
185945 TTTTGTTCTCTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
185964 TTTTGTT-TCTCTTTTTTC
1 TTTTGTTCTCTCTTTTTTC
185982 TTT
1 TTT
185985 ATTTTTGATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.00, C:0.17, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTGTTCTCTCTTTTTTC
Found at i:189293 original size:2 final size:2
Alignment explanation
Indices: 189280--189310 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
189270 AAAATAAGAA
*
189280 AT AT AT AA 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 AT A
189311 ATAACACTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:189774 original size:36 final size:37
Alignment explanation
Indices: 189728--189822 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 37
189718 GGATCCTATC
* * *
189728 TTTAAGAGTTTAAATCATAGTAGAACTCTATCATA-T
1 TTTAGGAGTTTAAATCCTAGTAAAACTCTATCATATT
* ** * *
189764 TTTAGGAGTTTGAATCCTAACAAAATTCTATCTTATT
1 TTTAGGAGTTTAAATCCTAGTAAAACTCTATCATATT
189801 TTTAGGAGTTTAAATCCTAGTA
1 TTTAGGAGTTTAAATCCTAGTA
189823 TGACGAAAAG
Statistics
Matches: 47, Mismatches: 11, Indels: 1
0.80 0.19 0.02
Matches are distributed among these distances:
36 27 0.57
37 20 0.43
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTAAATCCTAGTAAAACTCTATCATATT
Found at i:190423 original size:43 final size:43
Alignment explanation
Indices: 190360--190447 Score: 131
Period size: 43 Copynumber: 2.0 Consensus size: 43
190350 GGTACAACAC
* *
190360 TTGAACCGGTTCTAACGCGTGTTCGAGCTATTTTAACAAATCT
1 TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
** *
190403 TTGAACCGGTTCTATTGCGTGTTCAACCTATTTTAATAAATCT
1 TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
190446 TT
1 TT
190448 TATAAGGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (43 bp):
TTGAACCGGTTCTAACGCGTGTTCAACCTATTTTAACAAATCT
Found at i:190650 original size:16 final size:18
Alignment explanation
Indices: 190629--190664 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
190619 AAATATACCA
190629 AAATTTT-AA-TCAAAAT
1 AAATTTTAAATTCAAAAT
190645 AAATTTTAAATTCAAAAT
1 AAATTTTAAATTCAAAAT
190663 AA
1 AA
190665 TTCGTATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 2 0.11
18 9 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATTTTAAATTCAAAAT
Found at i:194626 original size:23 final size:23
Alignment explanation
Indices: 194596--194652 Score: 114
Period size: 23 Copynumber: 2.5 Consensus size: 23
194586 GACCCTAAAT
194596 AATAAAAAATATTATTTTTATTC
1 AATAAAAAATATTATTTTTATTC
194619 AATAAAAAATATTATTTTTATTC
1 AATAAAAAATATTATTTTTATTC
194642 AATAAAAAATA
1 AATAAAAAATA
194653 ATGATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (23 bp):
AATAAAAAATATTATTTTTATTC
Done.