Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001982.1 Hibiscus syriacus cultivar Beakdansim tig00004040_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: 146253
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4954 original size:22 final size:22
Alignment explanation
Indices: 4886--4968 Score: 62
Period size: 22 Copynumber: 3.7 Consensus size: 22
4876 TTGGTGCAGA
* * *
4886 GGGAATCGA-TCCCCCCCCCTG
1 GGGAACCGATTCCCCCCCACAG
**
4907 AGGGAACCGATTCCCCCTTTGA-AG
1 -GGGAACCGATTCCCCC--CCACAG
4931 GGGAACCGATTCCCCCCCACAG
1 GGGAACCGATTCCCCCCCACAG
* *
4953 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
4969 ATGGGGTTCT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
21 1 0.02
22 24 0.50
23 22 0.46
24 1 0.02
ACGTcount: A:0.22, C:0.40, G:0.24, T:0.14
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCCACAG
Found at i:10621 original size:12 final size:12
Alignment explanation
Indices: 10606--10633 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10596 ATCTTTAACT
10606 CATATTTTAATA
1 CATATTTTAATA
10618 CATATTTTAATA
1 CATATTTTAATA
10630 CATA
1 CATA
10634 AGGTAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.46
Consensus pattern (12 bp):
CATATTTTAATA
Found at i:10691 original size:25 final size:27
Alignment explanation
Indices: 10664--10744 Score: 81
Period size: 29 Copynumber: 2.8 Consensus size: 27
10654 TCTTTTAGTT
*
10664 TTTTAATTTATTAAATATATTTATTTTTA
1 TTTTAACTTATTAAATATATTTA--TTTA
10693 TTTTAACTTATTAAATATATTTTATTCTTA
1 TTTTAACTTATTAAATATA-TTTA-T-TTA
* **
10723 TTTTAAATTAAAAAATATATTT
1 TTTTAACTTATTAAATATATTT
10745 TATTCTTCAC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 23 0.50
30 23 0.50
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTAACTTATTAAATATATTTATTTA
Found at i:10724 original size:30 final size:30
Alignment explanation
Indices: 10664--10751 Score: 124
Period size: 30 Copynumber: 3.0 Consensus size: 30
10654 TCTTTTAGTT
* *
10664 TTTTAATTTATTAAATATA-TTTATTTTTA
1 TTTTAAATTATTAAATATATTTTATTCTTA
*
10693 TTTTAACTTATTAAATATATTTTATTCTTA
1 TTTTAAATTATTAAATATATTTTATTCTTA
**
10723 TTTTAAATTAAAAAATATATTTTATTCTT
1 TTTTAAATTATTAAATATATTTTATTCTT
10752 CACTTAAAAG
Statistics
Matches: 53, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
29 18 0.34
30 35 0.66
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (30 bp):
TTTTAAATTATTAAATATATTTTATTCTTA
Found at i:10851 original size:14 final size:13
Alignment explanation
Indices: 10811--10848 Score: 51
Period size: 12 Copynumber: 2.8 Consensus size: 13
10801 TAAAATATTT
10811 AAATATATTTTAA
1 AAATATATTTTAA
10824 ATTAATATA-TTTAA
1 A--AATATATTTTAA
10838 AAATATATTTT
1 AAATATATTTT
10849 TAAGTGATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
12 6 0.27
13 4 0.18
14 6 0.27
15 6 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AAATATATTTTAA
Found at i:10965 original size:31 final size:31
Alignment explanation
Indices: 10886--10958 Score: 103
Period size: 30 Copynumber: 2.4 Consensus size: 31
10876 TTTTTACATT
* * *
10886 AAAATAAAAAAATATTTAATAAGTTAAGACA
1 AAAATAAAAATATATTTAATAAGATAAAACA
*
10917 AAAGT-AAAATATATTTAATAAGATAAAACA
1 AAAATAAAAATATATTTAATAAGATAAAACA
10947 AAAATAAAAATA
1 AAAATAAAAATA
10959 CTTTTAAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
30 26 0.72
31 10 0.28
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAATAAAAATATATTTAATAAGATAAAACA
Found at i:13117 original size:26 final size:25
Alignment explanation
Indices: 13067--13114 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
13057 TTTGTCTATA
13067 TAATATTAAAAAGATGTTATTTTAT
1 TAATATTAAAAAGATGTTATTTTAT
* * *
13092 TAATATTGAAAAGGTTTTATTTT
1 TAATATTAAAAAGATGTTATTTT
13115 TATATATAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (25 bp):
TAATATTAAAAAGATGTTATTTTAT
Found at i:13134 original size:2 final size:2
Alignment explanation
Indices: 13129--13158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
13119 TATAATGTTA
13129 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
13159 GAGTAAATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14564 original size:18 final size:18
Alignment explanation
Indices: 14541--14591 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
14531 TAAAAAAATT
*
14541 AAATTATTTTATATTTTA
1 AAATTATTTTATATCTTA
14559 AAATTATTTTATATCTTA
1 AAATTATTTTATATCTTA
*
14577 AAATCATTTATATAT
1 AAATTATTT-TATAT
14592 ATTTTTTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 25 0.83
19 5 0.17
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.55
Consensus pattern (18 bp):
AAATTATTTTATATCTTA
Found at i:16190 original size:28 final size:27
Alignment explanation
Indices: 16158--16215 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 27
16148 TAGCACAAAT
*
16158 GATGGAGCGAGTTTTGATTTAAAAAAAG
1 GATGGAGCGAGTTTTGA-TAAAAAAAAG
*
16186 GATGGAGTGAGTTTTGATAAAAAAAAG
1 GATGGAGCGAGTTTTGATAAAAAAAAG
16213 GAT
1 GAT
16216 CGGAACTAGC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 12 0.43
28 16 0.57
ACGTcount: A:0.41, C:0.02, G:0.29, T:0.28
Consensus pattern (27 bp):
GATGGAGCGAGTTTTGATAAAAAAAAG
Found at i:36534 original size:6 final size:6
Alignment explanation
Indices: 36523--36552 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
36513 TTATTAACAC
36523 GCGCCA GCGCCA GCGCCA GCGCCA GCGCCA
1 GCGCCA GCGCCA GCGCCA GCGCCA GCGCCA
36553 ACGAATATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.50, G:0.33, T:0.00
Consensus pattern (6 bp):
GCGCCA
Found at i:44163 original size:26 final size:27
Alignment explanation
Indices: 44134--44195 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 27
44124 TTTTTCCTTT
44134 TAATACTCTAGAGTAATTACAAAATA-
1 TAATACTCTAGAGTAATTACAAAATAG
44160 TAATACTCTAGAGTAATTACAAAATAG
1 TAATACTCTAGAGTAATTACAAAATAG
44187 T-ATACTCTA
1 TAATACTCTA
44196 TTAAAAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 34 0.97
27 1 0.03
ACGTcount: A:0.47, C:0.13, G:0.08, T:0.32
Consensus pattern (27 bp):
TAATACTCTAGAGTAATTACAAAATAG
Found at i:45609 original size:21 final size:20
Alignment explanation
Indices: 45585--45645 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
45575 CTCAAAGAAA
45585 CATTTACCAAACTTTGAAAAC
1 CATTTACCAAA-TTTGAAAAC
*
45606 CATTT-TCAAA---G-AAA-
1 CATTTACCAAATTTGAAAAC
45620 CATTTACCAAATTTTGAAAAC
1 CATTTACCAAA-TTTGAAAAC
45641 CATTT
1 CATTT
45646 TCAAAGTTGG
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
14 5 0.16
15 7 0.23
16 1 0.03
19 1 0.03
20 7 0.23
21 10 0.32
ACGTcount: A:0.43, C:0.20, G:0.05, T:0.33
Consensus pattern (20 bp):
CATTTACCAAATTTGAAAAC
Found at i:45615 original size:35 final size:35
Alignment explanation
Indices: 45537--45651 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
45527 ACCCATTCCT
* * *
45537 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
45571 ATTTCTCAAAGAAACATTTACCAAACTTTGAAAACC
1 ATTT-TCAAAGAAACATTTACCAAACTTTGAAAACC
*
45607 ATTTTCAAAGAAACATTTACCAAATTTTGAAAACC
1 ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
45642 ATTTTCAAAG
1 ATTTTCAAAG
45652 TTGGTTGCCA
Statistics
Matches: 75, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
34 4 0.05
35 42 0.56
36 29 0.39
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (35 bp):
ATTTTCAAAGAAACATTTACCAAACTTTGAAAACC
Found at i:50226 original size:35 final size:34
Alignment explanation
Indices: 50171--50239 Score: 120
Period size: 35 Copynumber: 2.0 Consensus size: 34
50161 AACATCTACC
50171 AAACTTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACTTTACCAAACTTTGAAAACCATTTTCAAAG
*
50205 AAACATTTATCAAACTTTGAAAACCATTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAACCATTTTCAAAG
50240 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 4 0.12
35 29 0.88
ACGTcount: A:0.45, C:0.19, G:0.06, T:0.30
Consensus pattern (34 bp):
AAACTTTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:50762 original size:28 final size:31
Alignment explanation
Indices: 50677--50880 Score: 132
Period size: 32 Copynumber: 6.5 Consensus size: 31
50667 CAAAATATAT
* *
50677 TAAGGGCTCATTTGGTTATCAATTAAAGTGTG
1 TAAGGGCTCATTTGGATAT-AATTAAAGTGTA
50709 TAAGGGCTCATTTGGATATCAATTAAAGTGTA
1 TAAGGGCTCATTTGGATAT-AATTAAAGTGTA
* *
50741 TAAGGGCTTATTTGGTTATTAATTAAAGTGTA
1 TAAGGGCTCATTTGGATA-TAATTAAAGTGTA
* * ** * *
50773 CAAGAGCGT-ATTTGTTTATCAATTAAAATCTA
1 TAAGGGC-TCATTTGGATAT-AATTAAAGTGTA
* * * *
50805 TAAGGTCTTATTTTGGA-CTAA-TAAAGCGTA
1 TAAGGGCTCA-TTTGGATATAATTAAAGTGTA
* * *
50835 TAAGGGATTATTTTGGA-CTAA-TAAAG-GCTA
1 TAAGGGCTCA-TTTGGATATAATTAAAGTG-TA
*
50865 TAAGGGCTTATTTGGA
1 TAAGGGCTCATTTGGA
50881 CTAAAAAAAG
Statistics
Matches: 145, Mismatches: 21, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
29 7 0.05
30 41 0.28
31 4 0.03
32 87 0.60
33 6 0.04
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (31 bp):
TAAGGGCTCATTTGGATATAATTAAAGTGTA
Found at i:50817 original size:32 final size:32
Alignment explanation
Indices: 50677--50817 Score: 174
Period size: 32 Copynumber: 4.4 Consensus size: 32
50667 CAAAATATAT
* *
50677 TAAGGGCTCATTTGGTTATCAATTAAAGTGTG
1 TAAGGGCTTATTTGGTTATCAATTAAAGTGTA
* *
50709 TAAGGGCTCATTTGGATATCAATTAAAGTGTA
1 TAAGGGCTTATTTGGTTATCAATTAAAGTGTA
*
50741 TAAGGGCTTATTTGGTTATTAATTAAAGTGTA
1 TAAGGGCTTATTTGGTTATCAATTAAAGTGTA
* * * * * *
50773 CAAGAGCGTATTTGTTTATCAATTAAAATCTA
1 TAAGGGCTTATTTGGTTATCAATTAAAGTGTA
*
50805 TAAGGTCTTATTT
1 TAAGGGCTTATTT
50818 TGGACTAATA
Statistics
Matches: 93, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 93 1.00
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.40
Consensus pattern (32 bp):
TAAGGGCTTATTTGGTTATCAATTAAAGTGTA
Found at i:50837 original size:30 final size:30
Alignment explanation
Indices: 50802--50884 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
50792 CAATTAAAAT
*
50802 CTATAAGGTCTTATTTTGGACTAATAAA-G
1 CTATAAGGGCTTATTTTGGACTAATAAAGG
*
50831 CGTATAAGGGATTATTTTGGACTAATAAAGG
1 C-TATAAGGGCTTATTTTGGACTAATAAAGG
50862 CTATAAGGGCTTA-TTTGGACTAA
1 CTATAAGGGCTTATTTTGGACTAA
50885 AAAAAGTGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
29 11 0.22
30 36 0.73
31 2 0.04
ACGTcount: A:0.34, C:0.10, G:0.22, T:0.35
Consensus pattern (30 bp):
CTATAAGGGCTTATTTTGGACTAATAAAGG
Found at i:56732 original size:16 final size:16
Alignment explanation
Indices: 56703--56733 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
56693 TCTCTGTCTC
56703 TCTGTTCTTCTTTTTT
1 TCTGTTCTTCTTTTTT
56719 TCTG-TCTTCTTTTTT
1 TCTGTTCTTCTTTTTT
56734 CTCTTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.74
Consensus pattern (16 bp):
TCTGTTCTTCTTTTTT
Found at i:56740 original size:22 final size:24
Alignment explanation
Indices: 56695--56742 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 24
56685 GGATCTGTTC
*
56695 TCTGTCTCTCTGTTCTTCTTTTTT
1 TCTGTCTCTCTGTTCTTCTCTTTT
*
56719 TCTGTCT-TCT-TTTTTCTCTTTT
1 TCTGTCTCTCTGTTCTTCTCTTTT
56741 TC
1 TC
56743 AGGTTCGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 12 0.55
23 3 0.14
24 7 0.32
ACGTcount: A:0.00, C:0.25, G:0.06, T:0.69
Consensus pattern (24 bp):
TCTGTCTCTCTGTTCTTCTCTTTT
Found at i:57172 original size:11 final size:10
Alignment explanation
Indices: 57142--57182 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
57132 GGGCTTTGTA
57142 ATTTAATATT
1 ATTTAATATT
57152 ATTTATATATGT
1 ATTTA-ATAT-T
57164 ATTTAATATAT
1 ATTTAATAT-T
57175 ATTTAATA
1 ATTTAATA
57183 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:57186 original size:3 final size:3
Alignment explanation
Indices: 57178--57257 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
57168 AATATATATT
* *
57178 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
57226 TAA TAA TAA TAA TAA TAA TAA TAA TTA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
57258 TGGGTAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 71 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:57820 original size:114 final size:114
Alignment explanation
Indices: 57573--58235 Score: 1125
Period size: 114 Copynumber: 5.8 Consensus size: 114
57563 GATAGAATTA
* * *
57573 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTAT
* * * * * * * ***
57638 GAACTCTAC-CTGGCAATGTTGATACATCAA-ATGATGAATTCAAACAAAAGG
63 GAACT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
57689 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
57754 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
*
57803 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
*
57868 CTTTCTCTGGAAAAGATAATCCATCAA-ATGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
57916 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
57981 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
58030 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
58095 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
66 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
58144 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
58209 CTTTCTCTGGAAAAGATAATCCATCAA
66 CTTTCTCTGGAAAAGATAATCCATCAA
58236 ATGATAGATT
Statistics
Matches: 527, Mismatches: 17, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
112 2 0.00
113 147 0.28
114 333 0.63
116 45 0.09
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:57916 original size:227 final size:227
Alignment explanation
Indices: 57573--58235 Score: 1139
Period size: 227 Copynumber: 2.9 Consensus size: 227
57563 GATAGAATTA
* * *
57573 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTATCATTAT
* * * * * * *** *
57638 GAACTCTAC-CTGGCAATGTTGATACATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCT
63 GAACT-TTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCT
57702 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
127 TCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAA
57767 AGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
192 AGATAATCCATCAATTTGATGAATTCAGGTAAAAGG
57803 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAA
57868 CTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTC
66 CTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTC
57933 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
131 ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
57998 AATCCATCAATTTGATGAATTCAGGTAAAAGG
196 AATCCATCAATTTGATGAATTCAGGTAAAAGG
*
58030 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAA
*
58095 CTTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCT
66 CTTTCTCTGGAAAAGATAATCCATCAA-ATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCT
58160 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA
130 CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA
58225 TAATCCATCAA
195 TAATCCATCAA
58236 ATGATAGATT
Statistics
Matches: 416, Mismatches: 15, Indels: 6
0.95 0.03 0.01
Matches are distributed among these distances:
226 2 0.00
227 258 0.62
228 112 0.27
230 44 0.11
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (227 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTATCATTATGAA
CTTTCTCTGGAAAAGATAATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTC
ATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGAT
AATCCATCAATTTGATGAATTCAGGTAAAAGG
Found at i:58059 original size:341 final size:341
Alignment explanation
Indices: 57573--58240 Score: 1151
Period size: 341 Copynumber: 2.0 Consensus size: 341
57563 GATAGAATTA
* * *
57573 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTTTCATTAT
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-A-GAGTTCTTCTCATTAT
* * * * *
57638 GAACTCTACCTGGCAATGTTGATACATCAAATGATGAATTCAAACAAAAGGTTGAACAAGTTCTT
64 GAACTCTACCTGGAAAAGATAATACATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTT
57703 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
129 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
57768 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
194 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
57833 TCTTCCTTCTTCAGATGAGTTCTTATCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATG
259 TCTTCCTTCTTCAGATGAGTTCTTATCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATG
57898 ATGAATTCAGGTAAAAGG
324 ATGAATTCAGGTAAAAGG
57916 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT-GAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
* * * ***
57980 ACT-TTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTT
66 ACTCTAC-CTGGAAAAGATAATACATCAA-ATGATGAATTCAAACAAAAGGTTGAACAAATTCTT
58044 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
129 CTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAA
58109 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
194 GATAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCT
*
58174 TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATG
259 TCTTCCTTCTTCAGATGAGTTCTTATCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATG
58239 AT
324 AT
58241 AGATTTGAAT
Statistics
Matches: 308, Mismatches: 15, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
339 2 0.01
340 36 0.12
341 226 0.73
343 44 0.14
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.38
Consensus pattern (341 bp):
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATAGAGTTCTTCTCATTATGA
ACTCTACCTGGAAAAGATAATACATCAAATGATGAATTCAAACAAAAGGTTGAACAAATTCTTCT
CATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGA
TAATCCATCAATTTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTC
TTCCTTCTTCAGATGAGTTCTTATCATTATGAACTTTCTCTGGAAAAGATAATCCATCAAATGAT
GAATTCAGGTAAAAGG
Found at i:59136 original size:83 final size:83
Alignment explanation
Indices: 59033--59463 Score: 817
Period size: 83 Copynumber: 5.2 Consensus size: 83
59023 CTTATTTCTA
*
59033 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
59098 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
59116 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
59181 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
59199 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
59264 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
59282 CTATGAGCACATTCATCTTCCAAATTCAATGATTAGTTTTGCCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
59347 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
59365 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAATTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
59430 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
59448 CTATGAGCACATTCAT
1 CTATGAGCACATTCAT
59464 TTGTTCCATT
Statistics
Matches: 343, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 343 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTTTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:71257 original size:15 final size:13
Alignment explanation
Indices: 71225--71262 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
71215 TCTGACAGAA
71225 AAAT-AAATAATG
1 AAATAAAATAATG
71237 AAATAAAATAATTG
1 AAATAAAATAA-TG
71251 CAAATAAAATAA
1 -AAATAAAATAA
71263 AATGAAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.17
13 6 0.26
14 2 0.09
15 11 0.48
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (13 bp):
AAATAAAATAATG
Found at i:71288 original size:29 final size:28
Alignment explanation
Indices: 71256--71343 Score: 74
Period size: 29 Copynumber: 3.1 Consensus size: 28
71246 AATTGCAAAT
71256 AAAATAAAATGAAACATATAAATATTATG
1 AAAATAAAATGAAA-ATATAAATATTATG
* * *
71285 AAAATAATAA-GTAAATATAAAAATTTTG
1 AAAATAA-AATGAAAATATAAATATTATG
*
71313 AAAAGATAAAATTAAAA-ATTAAATA-TATG
1 -AAA-ATAAAATGAAAATA-TAAATATTATG
71342 AA
1 AA
71344 TTTTTAATTT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
28 14 0.30
29 19 0.40
30 14 0.30
ACGTcount: A:0.64, C:0.01, G:0.07, T:0.28
Consensus pattern (28 bp):
AAAATAAAATGAAAATATAAATATTATG
Found at i:72999 original size:24 final size:23
Alignment explanation
Indices: 72972--73020 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
72962 GGATCTGTTC
72972 TCTGTCTCTCTGTTCTTCT-TTTTT
1 TCTGTCT-TCT-TTCTTCTCTTTTT
*
72996 TCTGTCTTCTTTTTTCTCTTTTT
1 TCTGTCTTCTTTCTTCTCTTTTT
73019 TC
1 TC
73021 AGGTTCGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 6 0.26
23 10 0.43
24 7 0.30
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.69
Consensus pattern (23 bp):
TCTGTCTTCTTTCTTCTCTTTTT
Found at i:73009 original size:16 final size:16
Alignment explanation
Indices: 72980--73010 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
72970 TCTCTGTCTC
72980 TCTGTTCTTCTTTTTT
1 TCTGTTCTTCTTTTTT
72996 TCTG-TCTTCTTTTTT
1 TCTGTTCTTCTTTTTT
73011 CTCTTTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.00, C:0.19, G:0.06, T:0.74
Consensus pattern (16 bp):
TCTGTTCTTCTTTTTT
Found at i:73444 original size:11 final size:10
Alignment explanation
Indices: 73414--73454 Score: 55
Period size: 11 Copynumber: 3.8 Consensus size: 10
73404 GGGCTTTGTA
73414 ATTTAATATT
1 ATTTAATATT
73424 ATTTATATATGT
1 ATTTA-ATAT-T
73436 ATTTAATATAT
1 ATTTAATAT-T
73447 ATTTAATA
1 ATTTAATA
73455 ATAATAATAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 5 0.18
11 17 0.61
12 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:73458 original size:3 final size:3
Alignment explanation
Indices: 73450--73513 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
73440 AATATATATT
* *
73450 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
73498 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
73514 TATTATTATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:74463 original size:14 final size:14
Alignment explanation
Indices: 74444--74479 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
74434 AATTCAATCC
74444 TCCGTAAACACTGT
1 TCCGTAAACACTGT
74458 TCCGTAAACACTGT
1 TCCGTAAACACTGT
74472 TCCGTAAA
1 TCCGTAAA
74480 GGTCAAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.31, C:0.28, G:0.14, T:0.28
Consensus pattern (14 bp):
TCCGTAAACACTGT
Found at i:87927 original size:44 final size:47
Alignment explanation
Indices: 87871--87958 Score: 155
Period size: 44 Copynumber: 1.9 Consensus size: 47
87861 TCGAATAAAT
87871 GCATGCGAATTAGATATCATGCGGTTAGG-TTTATTTTT-TGAACAA
1 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
87916 GCATGC-AATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
1 GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAA
87959 TAACAAAGCA
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
44 22 0.54
45 15 0.37
46 4 0.10
ACGTcount: A:0.28, C:0.10, G:0.23, T:0.39
Consensus pattern (47 bp):
GCATGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAACAA
Found at i:97636 original size:16 final size:17
Alignment explanation
Indices: 97617--97655 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
97607 AATAAAAGAA
97617 AAAAATGA-GAAAAAAC
1 AAAAATGAGGAAAAAAC
97633 AAAAATGATGGAAAAAAC
1 AAAAATGA-GGAAAAAAC
97651 AAAAA
1 AAAAA
97656 GAAAGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.05, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAATGAGGAAAAAAC
Found at i:97636 original size:18 final size:18
Alignment explanation
Indices: 97610--97655 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
97600 AAGAAGAAAT
*
97610 AAAAGAAAAA-AATGAGAA
1 AAAACAAAAATAATG-GAA
*
97628 AAAACAAAAATGATGGAA
1 AAAACAAAAATAATGGAA
97646 AAAACAAAAA
1 AAAACAAAAA
97656 GAAAGAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.76, C:0.04, G:0.13, T:0.07
Consensus pattern (18 bp):
AAAACAAAAATAATGGAA
Found at i:97663 original size:17 final size:18
Alignment explanation
Indices: 97624--97665 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
97614 GAAAAAAATG
*
97624 AGAAAAAACAAAAATGAT
1 AGAAAAAACAAAAATGAA
*
97642 GGAAAAAACAAAAA-GAA
1 AGAAAAAACAAAAATGAA
97659 AGAAAAA
1 AGAAAAA
97666 GAAGAAAATG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.76, C:0.05, G:0.14, T:0.05
Consensus pattern (18 bp):
AGAAAAAACAAAAATGAA
Found at i:97680 original size:26 final size:26
Alignment explanation
Indices: 97651--97709 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
97641 TGGAAAAAAC
*
97651 AAAAAGAAAGAAAAAGAAG-AAAATGG
1 AAAAAGAAAGAAAAA-AAGAAAAATGA
* * *
97677 AAAAGGGAAGAAAAAATGAAAAATGA
1 AAAAAGAAAGAAAAAAAGAAAAATGA
97703 AAAAAGA
1 AAAAAGA
97710 GAAAAATGAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 2 0.08
26 24 0.92
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.05
Consensus pattern (26 bp):
AAAAAGAAAGAAAAAAAGAAAAATGA
Found at i:97699 original size:8 final size:8
Alignment explanation
Indices: 97686--97723 Score: 53
Period size: 8 Copynumber: 4.9 Consensus size: 8
97676 GAAAAGGGAA
97686 GAAAAAAT
1 GAAAAAAT
97694 G-AAAAAT
1 GAAAAAAT
97701 GAAAAAA-
1 GAAAAAAT
97708 GAGAAAAAT
1 GA-AAAAAT
97717 GAAAAAA
1 GAAAAAA
97724 GAGAAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 9 0.33
8 16 0.59
9 2 0.07
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:97713 original size:16 final size:16
Alignment explanation
Indices: 97694--97729 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
97684 AAGAAAAAAT
97694 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAGA
97710 GAAAAATGAAAAAAGA
1 GAAAAATGAAAAAAGA
97726 GAAA
1 GAAA
97730 TAAAAGGAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.19, T:0.06
Consensus pattern (16 bp):
GAAAAATGAAAAAAGA
Found at i:98791 original size:16 final size:17
Alignment explanation
Indices: 98756--98788 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
98746 GTTTCTCAAT
98756 GATAGTTGAAGATTGAA
1 GATAGTTGAAGATTGAA
98773 GATA-TTGAAGCATTGA
1 GATAGTTGAAG-ATTGA
98789 GATGAAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.30
Consensus pattern (17 bp):
GATAGTTGAAGATTGAA
Found at i:99018 original size:51 final size:51
Alignment explanation
Indices: 98946--99356 Score: 498
Period size: 51 Copynumber: 7.9 Consensus size: 51
98936 AATTCGTTTA
*
98946 TTGAAGATTGAGTCCTATACTCTCTGAATGAATGGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
98997 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
*
99048 TTGAAGATTGAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
99099 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
* * * * * * * *
99150 TTGAAGATCGAGTTCTATACTCCCTGAACGGATAGGGAGCGAACACGTTTG
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
* * ** **
99201 TTAAAGATTGAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTA
1 TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
* * * * ** **
99252 TTTAAGATTTTTCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTA
1 TTGAAGA---TT-GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCG
* * *
99308 TTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACA
1 TTGAAGATTG----AGTCCTATACTCTCTGAATGAATAGGGAGCGGACA
99357 CATTTTATGA
Statistics
Matches: 319, Mismatches: 32, Indels: 13
0.88 0.09 0.04
Matches are distributed among these distances:
51 240 0.75
52 1 0.00
53 2 0.01
54 2 0.01
55 34 0.11
56 40 0.13
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (51 bp):
TTGAAGATTGAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAGTTCG
Found at i:99334 original size:56 final size:56
Alignment explanation
Indices: 99006--99406 Score: 233
Period size: 51 Copynumber: 7.6 Consensus size: 56
98996 GTTGAAGATT
* * * ** **
99006 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * ** **
99057 GAGTCTTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA---TT-
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * ** **
99108 GAGTCCTATACTCTCTGAATGAATAGGGAGCGGACAAG-TTCGTTGAAGA----TC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * *
99159 GAGT-TCTATACTCCCTGAACGG-ATAGGGAGCGAACACG-TTTGTTAAAGA---TT-
1 GAGTCT-TATACTCTCTGAA-GGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * *
99210 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTG-TTTATTTAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
99265 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
* * * * * *
99321 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGCTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
*
99376 GAGTCTTATACT-TCCTGAAGGAATAGGGAGC
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGC
99407 AGGCTCGTCA
Statistics
Matches: 304, Mismatches: 32, Indels: 24
0.84 0.09 0.07
Matches are distributed among these distances:
50 2 0.01
51 175 0.58
52 2 0.01
54 3 0.01
55 70 0.23
56 51 0.17
57 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (56 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
Found at i:99407 original size:55 final size:54
Alignment explanation
Indices: 99210--99408 Score: 215
Period size: 55 Copynumber: 3.6 Consensus size: 54
99200 GTTAAAGATT
* * * * * *
99210 GAGTCCTATACTCTCTGAAAGAATAGGGAGCGGACCTGTTTATTTAAGATTTTTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCT-TTTATTGAAGATTGTTC
*
99265 GAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTTATTGAAGATTGTTC
1 GAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGA-CC-TTTTATTGAAGATTGTTC
* * *
99321 AAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACATTTTA-TGAAGATTGCTC
1 GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGAC-C-TTTTATTGAAGATTGTTC
*
99376 GAGTCTTATACT-TCCTGAAGGAATAGGGAGCAG
1 GAGTCTTATACTCT-CTGAAGGAATAGAGAGCAG
99409 GCTCGTCATT
Statistics
Matches: 125, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
54 1 0.01
55 70 0.56
56 52 0.42
57 2 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (54 bp):
GAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACCTTTTATTGAAGATTGTTC
Found at i:99436 original size:55 final size:54
Alignment explanation
Indices: 99250--99436 Score: 157
Period size: 55 Copynumber: 3.4 Consensus size: 54
99240 CGGACCTGTT
* * * * *
99250 TATTT-AAGATTTTTCGAGT-TCTATACTCTCTGAAGGAATAGAGAGCGGACCCGT
1 TATTTGAAGATTGTTCAAGTCT-TATACTCTCTGAAGGAATAGAGAGCAGACAC-A
* *
99304 TTTATTGAAGATTGTTCAAGTCTTATACTCTCTGAATGAATAGAGAGCAGACACA
1 TAT-TTGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACA
* * * * * * *
99359 TTTTATGAAGATTGCTCGAGTCTTATACT-TCCTGAAGGAATAGGGAGCAGGCTCG
1 TATT-TGAAGATTGTTCAAGTCTTATACTCT-CTGAAGGAATAGAGAGCAGACACA
99414 TCATTTGAAGA-TGTTTCAAGTCT
1 T-ATTTGAAGATTG-TTCAAGTCT
99437 CATTTATCCT
Statistics
Matches: 109, Mismatches: 17, Indels: 13
0.78 0.12 0.09
Matches are distributed among these distances:
54 6 0.06
55 60 0.55
56 42 0.39
57 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.34
Consensus pattern (54 bp):
TATTTGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGAGAGCAGACACA
Found at i:115462 original size:2 final size:2
Alignment explanation
Indices: 115455--115492 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
115445 TTTCTTTTTA
115455 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115493 ACTTTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:115591 original size:19 final size:19
Alignment explanation
Indices: 115549--115591 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
115539 AAAATGTGTC
*
115549 ACTT-AACGGTCCGTCACG
1 ACTTAAACGGTCCATCACG
*
115567 ATTTAAACGGTCCATCACG
1 ACTTAAACGGTCCATCACG
*
115586 GCTTAA
1 ACTTAA
115592 CCCGTTTTGA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.26
Consensus pattern (19 bp):
ACTTAAACGGTCCATCACG
Found at i:130670 original size:3 final size:3
Alignment explanation
Indices: 130657--130720 Score: 71
Period size: 3 Copynumber: 22.0 Consensus size: 3
130647 GTTTTTTCCG
** *
130657 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
130702 TTA TTA TTA TTTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA
130721 CAATTTTTGC
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
2 5 0.10
3 43 0.84
4 3 0.06
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:130698 original size:32 final size:32
Alignment explanation
Indices: 130655--130718 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
130645 GGGTTTTTTC
*
130655 CGTTATTTTATTATTATTATTATTA-TTATTAT
1 CGTTATCTTATTATT-TTATTATTATTTATTAT
130687 CGTTATCTTATTATTTTATTATTATTTATTAT
1 CGTTATCTTATTATTTTATTATTATTTATTAT
130719 TACAATTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
31 9 0.30
32 21 0.70
ACGTcount: A:0.27, C:0.05, G:0.03, T:0.66
Consensus pattern (32 bp):
CGTTATCTTATTATTTTATTATTATTTATTAT
Found at i:130868 original size:25 final size:25
Alignment explanation
Indices: 130839--130962 Score: 207
Period size: 25 Copynumber: 5.0 Consensus size: 25
130829 GAACCAACCC
130839 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
130864 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
130889 ATCAGATTAGGGTTTTAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
130914 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
130939 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
130963 TCCCCTAACT
Statistics
Matches: 95, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
24 9 0.09
25 86 0.91
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Found at i:145591 original size:43 final size:41
Alignment explanation
Indices: 145541--145737 Score: 121
Period size: 46 Copynumber: 4.5 Consensus size: 41
145531 CCAGATCTCT
* *
145541 TCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCC
1 TCATCACGTAAGAGCCGTGT-AACC-TAGATAACCAGTCGTCC
* * ** *
145584 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGATC-TCT
1 TCATCACGTAAGAGCCGTG-TA--ACC--TAGATAACCAG-TCGTCC
145630 TCATCACGTAAGAGCCGTGTAACCT-GATAACCAGTCGTCC
1 TCATCACGTAAGAGCCGTGTAACCTAGATAACCAGTCGTCC
* * * *
145670 TCATTACGTAGGAACCGAGTTATCATCCCTAAAGATAACCAGATC-TCC
1 TCATCACGTAAGAGCCGTG-TA--A--CCT--AGATAACCAG-TCGTCC
*
145718 TCATCACGTAGGAGCCGTGT
1 TCATCACGTAAGAGCCGTGT
145738 CACCCTTAGA
Statistics
Matches: 120, Mismatches: 19, Indels: 26
0.73 0.12 0.16
Matches are distributed among these distances:
39 2 0.02
40 24 0.20
41 3 0.03
43 22 0.18
44 1 0.01
45 8 0.07
46 28 0.23
47 2 0.02
48 28 0.23
49 2 0.02
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (41 bp):
TCATCACGTAAGAGCCGTGTAACCTAGATAACCAGTCGTCC
Found at i:145685 original size:86 final size:90
Alignment explanation
Indices: 145530--145739 Score: 293
Period size: 88 Copynumber: 2.4 Consensus size: 90
145520 CATCCCCCGG
*
145530 ACCAGATCTCTTCATCACGTATGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAG
1 ACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAG
* ** *
145595 GAACCGTGTTATCA-CCTTTAGATG
66 GAACCGAGTTATCACCCTAAAGATA
* * *
145619 GCCAGATCTCTTCATCACGTAAGAGCCGTGT-AACC-T-GATAACCAGTCGTCCTCATTACGTAG
1 ACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAG
145681 GAACCGAGTTATCATCCCTAAAGATA
66 GAACCGAGTTATCA-CCCTAAAGATA
* *
145707 ACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 ACCAGATCTCTTCATCACGTAAGAGCCGTGTCA
145740 CCCTTAGACG
Statistics
Matches: 107, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
86 37 0.35
87 1 0.01
88 39 0.36
89 30 0.28
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.25
Consensus pattern (90 bp):
ACCAGATCTCTTCATCACGTAAGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAG
GAACCGAGTTATCACCCTAAAGATA
Found at i:145956 original size:3 final size:3
Alignment explanation
Indices: 145943--146001 Score: 59
Period size: 3 Copynumber: 19.7 Consensus size: 3
145933 GTTTTTTCCG
** *
145943 TTA TT- TTA TTA TTA TTA TTA TTA TTA TCG TTA -TC TTA TTA TTTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
145987 TTA TTA TTTA TTA TT
1 TTA TTA -TTA TTA TT
146002 TACAATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 3 0.07
3 37 0.80
4 6 0.13
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:145997 original size:17 final size:17
Alignment explanation
Indices: 145951--146003 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
145941 CGTTATTTTA
145951 TTATTATTA-TTATTA-
1 TTATTATTATTTATTAT
**
145966 TTATCGTTATCTTATTAT
1 TTATTATTAT-TTATTAT
145984 TTATTATTATTTATTAT
1 TTATTATTATTTATTAT
146001 TTA
1 TTA
146004 CAATTTTTGC
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.23
17 16 0.52
18 8 0.26
ACGTcount: A:0.28, C:0.04, G:0.02, T:0.66
Consensus pattern (17 bp):
TTATTATTATTTATTAT
Found at i:146148 original size:25 final size:25
Alignment explanation
Indices: 146119--146242 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
146109 GAACCAACCC
146119 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
146144 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
146169 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
146194 ATCAGATTAGGGTTTCAAACCCTAA
1 ATCAGATTAGGGTTTCAAACCCTAA
*
146219 AACA-ATTTAGGGTTTC-AACCCTAA
1 ATCAGA-TTAGGGTTTCAAACCCTAA
146243 TCCCCTAACT
Statistics
Matches: 97, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
24 9 0.09
25 88 0.91
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.28
Consensus pattern (25 bp):
ATCAGATTAGGGTTTCAAACCCTAA
Done.