Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004643.1 Hibiscus syriacus cultivar Beakdansim tig00010405_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: 120006
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:6626 original size:10 final size:10
Alignment explanation
Indices: 6611--6637 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
6601 AATCATGTAT
6611 TTATTTTATA
1 TTATTTTATA
6621 TTATTTTATA
1 TTATTTTATA
6631 TTATTTT
1 TTATTTT
6638 CAAATATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (10 bp):
TTATTTTATA
Found at i:9217 original size:31 final size:31
Alignment explanation
Indices: 9179--9241 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
9169 AAACTGATGA
**
9179 TTTTTTTTACTATTTAAATGCTTTAAACACT
1 TTTTTTTTACTATGAAAATGCTTTAAACACT
** *
9210 TTTTTTTTTGTGTGAAAATGCTTTAAACACT
1 TTTTTTTTACTATGAAAATGCTTTAAACACT
9241 T
1 T
9242 AATTTTGTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.54
Consensus pattern (31 bp):
TTTTTTTTACTATGAAAATGCTTTAAACACT
Found at i:9404 original size:18 final size:18
Alignment explanation
Indices: 9381--9416 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9371 CAAAGAGTTT
* *
9381 AATTATTATATATTTATA
1 AATTATAATAAATTTATA
9399 AATTATAATAAATTTATA
1 AATTATAATAAATTTATA
9417 TTATTAGTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AATTATAATAAATTTATA
Found at i:14184 original size:18 final size:18
Alignment explanation
Indices: 14161--14198 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
14151 AGGCCAAGTA
14161 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
14179 ACATGATCAGAGGAATTT
1 ACATGATCAGAGGAATTT
14197 AC
1 AC
14199 GTGCATCGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (18 bp):
ACATGATCAGAGGAATTT
Found at i:15368 original size:21 final size:21
Alignment explanation
Indices: 15306--15368 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
15296 ATGTAAGATT
* *
15306 TGTCCCGAAGGATCTCATGTA
1 TGTCCCGAAGGACCTCATATA
* *
15327 TATCCCAAAGGACCT-AGTATA
1 TGTCCCGAAGGACCTCA-TATA
*
15348 TGTCCTGAAGGACCTCATATA
1 TGTCCCGAAGGACCTCATATA
15369 ATAACTCGAC
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 31 0.94
22 1 0.03
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (21 bp):
TGTCCCGAAGGACCTCATATA
Found at i:21869 original size:21 final size:21
Alignment explanation
Indices: 21843--21899 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 21
21833 GATTTGTCCC
*
21843 GAAGGACCTCATGTATGCCCT
1 GAAGGACCTCATATATGCCCT
* *
21864 GAAGGACCTCGTATATGTCCT
1 GAAGGACCTCATATATGCCCT
*
21885 GAAGAACCTCATATA
1 GAAGGACCTCATATA
21900 ATCCCTCGAC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (21 bp):
GAAGGACCTCATATATGCCCT
Found at i:23646 original size:20 final size:21
Alignment explanation
Indices: 23617--23655 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
23607 ATCGATACCA
*
23617 ACCTCTGAGTATCGATATTGG
1 ACCTCTGAGTATCAATATTGG
23638 ACCTC-GAGTATCAATATT
1 ACCTCTGAGTATCAATATT
23656 TCCCTTGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (21 bp):
ACCTCTGAGTATCAATATTGG
Found at i:24967 original size:2 final size:2
Alignment explanation
Indices: 24962--25005 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
24952 TATATTTTTC
*
24962 AT AT AT A- AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
25003 AT A
1 AT A
25006 ATGCAGAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:27885 original size:44 final size:44
Alignment explanation
Indices: 27836--27922 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
27826 ACACTTATCT
27836 ATCTATTTTCCACAAATCCATCCTCACCATCATCTTCTTTACCG
1 ATCTATTTTCCACAAATCCATCCTCACCATCATCTTCTTTACCG
27880 ATCTATTTTCCACAAATCCATCCTCACCATCATCTTCTTTACC
1 ATCTATTTTCCACAAATCCATCCTCACCATCATCTTCTTTACC
27923 ATTCACCTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.25, C:0.37, G:0.01, T:0.37
Consensus pattern (44 bp):
ATCTATTTTCCACAAATCCATCCTCACCATCATCTTCTTTACCG
Found at i:32145 original size:3 final size:3
Alignment explanation
Indices: 32022--32129 Score: 145
Period size: 3 Copynumber: 36.7 Consensus size: 3
32012 ATGATTTTTC
32022 TAT TATT TAT TA- TAT TAT TAT TAT T-T TAT TAT TAT TAT TATT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
32067 TAT TAT TAT TAT TAA TAT TAT TAT T-T ATAT TAT T-T TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
32110 TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
32130 ATAATAAAAT
Statistics
Matches: 95, Mismatches: 2, Indels: 16
0.84 0.02 0.14
Matches are distributed among these distances:
2 9 0.09
3 79 0.83
4 7 0.07
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:32594 original size:15 final size:15
Alignment explanation
Indices: 32574--32602 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32564 CAAGGACGGG
32574 GAACCAAACAACAAC
1 GAACCAAACAACAAC
32589 GAACCAAACAACAA
1 GAACCAAACAACAA
32603 AAAAACCACG
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:0.62, C:0.31, G:0.07, T:0.00
Consensus pattern (15 bp):
GAACCAAACAACAAC
Found at i:44868 original size:15 final size:14
Alignment explanation
Indices: 44850--44890 Score: 57
Period size: 13 Copynumber: 2.9 Consensus size: 14
44840 AAAAAAAAGA
44850 AAAAAAATGAAATG
1 AAAAAAATGAAATG
44864 -AAAAAATGAAAAATG
1 AAAAAAATG--AAATG
44879 AAAAAAATGAAA
1 AAAAAAATGAAA
44891 AATGATGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 8 0.33
14 3 0.12
15 5 0.21
16 8 0.33
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (14 bp):
AAAAAAATGAAATG
Found at i:44891 original size:15 final size:15
Alignment explanation
Indices: 44850--44891 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
44840 AAAAAAAAGA
44850 AAAAAAATG-AAATG
1 AAAAAAATGAAAATG
44864 -AAAAAATGAAAAATG
1 AAAAAAATG-AAAATG
44879 AAAAAAATGAAAA
1 AAAAAAATGAAAA
44892 ATGATGAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.32
15 9 0.36
16 8 0.32
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (15 bp):
AAAAAAATGAAAATG
Found at i:44902 original size:16 final size:16
Alignment explanation
Indices: 44850--44895 Score: 71
Period size: 16 Copynumber: 3.1 Consensus size: 16
44840 AAAAAAAAGA
44850 AAAAAAATG--AAATG
1 AAAAAAATGAAAAATG
44864 -AAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
44879 AAAAAAATGAAAAATG
1 AAAAAAATGAAAAATG
44895 A
1 A
44896 TGAAAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.28
15 5 0.17
16 16 0.55
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:46733 original size:122 final size:121
Alignment explanation
Indices: 46595--46937 Score: 462
Period size: 122 Copynumber: 2.8 Consensus size: 121
46585 CTTTTTCCAG
* * *
46595 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTTG
1 AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
* *
46660 TTCAACCTTTTGTTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATTTCC
66 TTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
*
46716 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAAAAGTTCATAATGAGAAGAACTT
1 AGAAG-GTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTT
* * * * *
46781 GTTCAACC-TTTGCATGACTCTATCGCAGAAGGAGATAGATCAGCATTAACATGTCT
65 GTTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
* *
46837 AGAAGGAATTCATAATGAGAAGAACTCATCT---GACGAAGAAGAAGTTCAAAATGAGAAGAACT
1 AGAAGG--TTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACT
* * *
46899 TGTTCAAACTTTTTGCTAGATTAC-ATCACAGAAGGAGAT
64 TGTTC-AACCTTTTGCTTGACT-CTATCACAGAAGGAGAT
46938 GAATTGACAT
Statistics
Matches: 197, Mismatches: 19, Indels: 12
0.86 0.08 0.05
Matches are distributed among these distances:
119 33 0.17
120 4 0.02
121 72 0.37
122 88 0.45
ACGTcount: A:0.40, C:0.14, G:0.21, T:0.25
Consensus pattern (121 bp):
AGAAGGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCTTGACTCTATCACAGAAGGAGATAGATCAACATCAACATGTCC
Found at i:47242 original size:3 final size:3
Alignment explanation
Indices: 47125--47229 Score: 139
Period size: 3 Copynumber: 35.7 Consensus size: 3
47115 ATGGTTTTTC
47125 TAT TATT TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT
1 TAT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
47169 TATT TAT TAT TAT TAT TAA TAT TAT TAT T-T ATAT TAT T-T TA- TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT
47213 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
47230 ATAAAATATT
Statistics
Matches: 92, Mismatches: 2, Indels: 16
0.84 0.02 0.15
Matches are distributed among these distances:
2 9 0.10
3 76 0.83
4 7 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:53092 original size:50 final size:50
Alignment explanation
Indices: 53052--53155 Score: 131
Period size: 50 Copynumber: 2.1 Consensus size: 50
53042 TGCACAGTGC
* * *
53052 TATACGTTGATTTGGCGCCACGTAGATATAGCGCGTCCCCTGTCCCGCGA
1 TATACGGTGATCTGGCGCCACGTAGATATAGCGCGTCCCCTGTCCAGCGA
* * *
53102 TATACGGTGATCTGGCGCCACGTGGATATAACGC-TCCCCTGATCC-GCGC
1 TATACGGTGATCTGGCGCCACGTAGATATAGCGCGTCCCCTG-TCCAGCGA
53151 TATAC
1 TATAC
53156 CTGGATATCT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
49 15 0.31
50 33 0.69
ACGTcount: A:0.19, C:0.31, G:0.25, T:0.25
Consensus pattern (50 bp):
TATACGGTGATCTGGCGCCACGTAGATATAGCGCGTCCCCTGTCCAGCGA
Found at i:53288 original size:10 final size:10
Alignment explanation
Indices: 53273--53314 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
53263 TTTTATCACA
53273 TCAAATTCTC
1 TCAAATTCTC
53283 TCAAATTCTC
1 TCAAATTCTC
53293 T-AAATTCCTC
1 TCAAATT-CTC
*
53303 TCAAATACTC
1 TCAAATTCTC
53313 TC
1 TC
53315 TTTTTAAGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.17
10 20 0.69
11 4 0.14
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (10 bp):
TCAAATTCTC
Found at i:53630 original size:15 final size:15
Alignment explanation
Indices: 53606--53655 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
53596 ACATGCTCAG
*
53606 GATGACGACGACGAC
1 GATGATGACGACGAC
*
53621 GATGATGACGATGAC
1 GATGATGACGACGAC
*
53636 GATGGTGACGACGAC
1 GATGATGACGACGAC
53651 GATGA
1 GATGA
53656 AGATGATGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 30 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (15 bp):
GATGATGACGACGAC
Found at i:53673 original size:21 final size:21
Alignment explanation
Indices: 53628--53673 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
53618 GACGATGATG
* * *
53628 ACGATGACGATGGTGACGACG
1 ACGATGAAGATGATGACGACA
*
53649 ACGATGAAGATGATGATGACA
1 ACGATGAAGATGATGACGACA
53670 ACGA
1 ACGA
53674 GGAGTCAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.33, T:0.15
Consensus pattern (21 bp):
ACGATGAAGATGATGACGACA
Found at i:56104 original size:51 final size:50
Alignment explanation
Indices: 56049--56169 Score: 120
Period size: 50 Copynumber: 2.4 Consensus size: 50
56039 TATAGCGCGG
* * *
56049 GTATAGCGCGGATCAGGGGGGAACGCTATACCCACGTGGCACCAGATCACC
1 GTATAACGCGG-TCAGGGGGGAACACTATACCCACGTGGCACCAAATCACC
* * * *
56100 GTATATCGCGGGGT-A-GGGGGAGCACTATACCCACGTGGCGCCAAATCAGC
1 GTATAACGC--GGTCAGGGGGGAACACTATACCCACGTGGCACCAAATCACC
*
56150 ATATAACGCGGTGCAGGGGG
1 GTATAACGCGGT-CAGGGGG
56170 CGCGCTTTCC
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
48 3 0.05
50 38 0.67
51 13 0.23
52 1 0.02
53 2 0.04
ACGTcount: A:0.25, C:0.26, G:0.35, T:0.15
Consensus pattern (50 bp):
GTATAACGCGGTCAGGGGGGAACACTATACCCACGTGGCACCAAATCACC
Found at i:56160 original size:50 final size:50
Alignment explanation
Indices: 56065--56169 Score: 129
Period size: 50 Copynumber: 2.1 Consensus size: 50
56055 CGCGGATCAG
* * * * *
56065 GGGGGAACGCTATACCCACGTGGCACCAGATCACCGTATATCGCGGGGTA
1 GGGGGAACACTATACCCACGTGGCACCAAATCACCATATAACGCGGGGCA
* * * *
56115 GGGGGAGCACTATACCCACGTGGCGCCAAATCAGCATATAACGCGGTGCA
1 GGGGGAACACTATACCCACGTGGCACCAAATCACCATATAACGCGGGGCA
56165 GGGGG
1 GGGGG
56170 CGCGCTTTCC
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.25, C:0.27, G:0.34, T:0.14
Consensus pattern (50 bp):
GGGGGAACACTATACCCACGTGGCACCAAATCACCATATAACGCGGGGCA
Found at i:57241 original size:22 final size:21
Alignment explanation
Indices: 57216--57256 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
57206 TATAAAAAAT
57216 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
57238 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
57257 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:57946 original size:19 final size:19
Alignment explanation
Indices: 57922--57958 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
57912 TCATCATTAT
57922 ATTACTAAATTTACTTTAA
1 ATTACTAAATTTACTTTAA
57941 ATTACTAAATTTACTTTA
1 ATTACTAAATTTACTTTA
57959 TATATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (19 bp):
ATTACTAAATTTACTTTAA
Found at i:67038 original size:42 final size:41
Alignment explanation
Indices: 66991--67074 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 41
66981 ATTCATTTCT
*
66991 ATGCTTGCTGAAATTTATGAAAACTAATCAAAAAGTAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAA-TAGTAGC
* *
67033 ATGCTTGCTGAAATTCATGAAAATTAATGAAAAATAGTAGC
1 ATGCTTGCTGAAATTCATGAAAACTAATCAAAAATAGTAGC
67074 A
1 A
67075 CCCTACAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
41 8 0.21
42 31 0.79
ACGTcount: A:0.44, C:0.11, G:0.17, T:0.29
Consensus pattern (41 bp):
ATGCTTGCTGAAATTCATGAAAACTAATCAAAAATAGTAGC
Found at i:69073 original size:25 final size:26
Alignment explanation
Indices: 69017--69075 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
69007 GAATAGCCTC
*
69017 AACAAA-AAATAAATAAATAACAGAA
1 AACAAATAAACAAATAAATAACAGAA
*
69042 AACAAATAAACAAATAAA-AATAG-A
1 AACAAATAAACAAATAAATAACAGAA
69066 AACTAAATAA
1 AAC-AAATAA
69076 TAAAAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
24 4 0.13
25 16 0.53
26 10 0.33
ACGTcount: A:0.75, C:0.08, G:0.03, T:0.14
Consensus pattern (26 bp):
AACAAATAAACAAATAAATAACAGAA
Found at i:69079 original size:20 final size:18
Alignment explanation
Indices: 69020--69090 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
69010 TAGCCTCAAC
* *
69020 AAAAAATAAATAAATAAC
1 AAAAAAGAAATAAATAAT
* * *
69038 AGAAAACAAATAAACAAAT
1 AAAAAAGAAATAAA-TAAT
69057 AAAAATAGAAACTAAATAAT
1 AAAAA-AGAAA-TAAATAAT
69077 AAAAAAGAAATAAA
1 AAAAAAGAAATAAA
69091 AAAGAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
18 16 0.37
19 11 0.26
20 12 0.28
21 4 0.09
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAAAAGAAATAAATAAT
Found at i:69088 original size:11 final size:10
Alignment explanation
Indices: 69074--69144 Score: 72
Period size: 10 Copynumber: 6.7 Consensus size: 10
69064 GAAACTAAAT
69074 AATAAAAAAGA
1 AATAAAAAA-A
69085 AATAAAAAAGAA
1 AAT-AAAAA-AA
69097 AATAAAAAAA
1 AATAAAAAAA
*
69107 CAT-AAAAAA
1 AATAAAAAAA
69116 AATAAAAAAA
1 AATAAAAAAA
*
69126 CATAAATAAAA
1 AATAAA-AAAA
69137 ACATAAAA
1 A-ATAAAA
69145 CAATATAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 10
0.78 0.06 0.15
Matches are distributed among these distances:
9 8 0.16
10 15 0.29
11 13 0.25
12 14 0.27
13 1 0.02
ACGTcount: A:0.82, C:0.04, G:0.03, T:0.11
Consensus pattern (10 bp):
AATAAAAAAA
Found at i:69099 original size:12 final size:11
Alignment explanation
Indices: 69074--69124 Score: 63
Period size: 11 Copynumber: 4.8 Consensus size: 11
69064 GAAACTAAAT
69074 AATAAAAAAGA
1 AATAAAAAAGA
69085 AATAAAAAAGAA
1 AATAAAAAAG-A
69097 AATAAAAAA-A
1 AATAAAAAAGA
*
69107 CAT-AAAAA-A
1 AATAAAAAAGA
69116 AATAAAAAA
1 AATAAAAAA
69125 ACATAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
9 8 0.22
10 8 0.22
11 10 0.28
12 10 0.28
ACGTcount: A:0.84, C:0.02, G:0.04, T:0.10
Consensus pattern (11 bp):
AATAAAAAAGA
Found at i:69138 original size:12 final size:10
Alignment explanation
Indices: 69075--69144 Score: 70
Period size: 12 Copynumber: 6.6 Consensus size: 10
69065 AAACTAAATA
*
69075 ATAAAAAAGAA
1 ATAAAAAA-AC
*
69086 ATAAAAAAGAAA
1 AT-AAAAA-AAC
69098 ATAAAAAAAC
1 ATAAAAAAAC
69108 ATAAAAAAA-
1 ATAAAAAAAC
69117 ATAAAAAAAC
1 ATAAAAAAAC
69127 ATAAATAAAAAC
1 AT-AA-AAAAAC
69139 ATAAAA
1 ATAAAA
69145 CAATATAAGA
Statistics
Matches: 53, Mismatches: 1, Indels: 11
0.82 0.02 0.17
Matches are distributed among these distances:
9 9 0.17
10 15 0.28
11 11 0.21
12 17 0.32
13 1 0.02
ACGTcount: A:0.81, C:0.04, G:0.03, T:0.11
Consensus pattern (10 bp):
ATAAAAAAAC
Found at i:69146 original size:19 final size:19
Alignment explanation
Indices: 69090--69137 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 19
69080 AAAGAAATAA
69090 AAAAGAAAATAAAAAAACAT
1 AAAA-AAAATAAAAAAACAT
69110 AAAAAAAATAAAAAAACAT
1 AAAAAAAATAAAAAAACAT
69129 AAATAAAAA
1 AAA-AAAAA
69138 CATAAAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.10
Consensus pattern (19 bp):
AAAAAAAATAAAAAAACAT
Found at i:69152 original size:22 final size:22
Alignment explanation
Indices: 69023--69144 Score: 80
Period size: 22 Copynumber: 5.7 Consensus size: 22
69013 CCTCAACAAA
*
69023 AAATAAATAAATAACAGAAAAC--
1 AAATAAAAAAATAA-A-AAAACAT
* * *
69045 AAATAAACAAATAAAAATAGA-
1 AAATAAAAAAATAAAAAAACAT
* * *
69066 AACT-AAATAATAAAAAAGAAAT
1 AAATAAAAAAATAAAAAA-ACAT
69088 AAA-AAAGAAAATAAAAAAACAT
1 AAATAAA-AAAATAAAAAAACAT
69110 --A-AAAAAAATAAAAAAACAT
1 AAATAAAAAAATAAAAAAACAT
*
69129 AAATAAAAACATAAAA
1 AAATAAAAAAATAAAA
69145 CAATATAAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
19 15 0.19
20 17 0.21
21 7 0.09
22 31 0.39
23 10 0.12
ACGTcount: A:0.78, C:0.06, G:0.03, T:0.13
Consensus pattern (22 bp):
AAATAAAAAAATAAAAAAACAT
Found at i:69226 original size:32 final size:32
Alignment explanation
Indices: 69173--69248 Score: 127
Period size: 32 Copynumber: 2.4 Consensus size: 32
69163 ATTCAATGTT
*
69173 CTTCACATTAAC-TTAAGAATCAGCTAATATC
1 CTTCACATTAACATTAAGAATCAACTAATATC
69204 CTTCACATTAACATTAAGAATCAACTAATATC
1 CTTCACATTAACATTAAGAATCAACTAATATC
*
69236 CTTCACATCAACA
1 CTTCACATTAACA
69249 AATAAAAACA
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
31 12 0.29
32 30 0.71
ACGTcount: A:0.41, C:0.25, G:0.04, T:0.30
Consensus pattern (32 bp):
CTTCACATTAACATTAAGAATCAACTAATATC
Found at i:69304 original size:31 final size:31
Alignment explanation
Indices: 69268--69330 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
69258 ATAAAACAAT
*
69268 ATAAGAATCAACTAATATCCTTCACATTAAC
1 ATAAGAATCAACTAATATACTTCACATTAAC
** *
69299 ATAAGAATCATTTAATATATTTCACATTAAC
1 ATAAGAATCAACTAATATACTTCACATTAAC
69330 A
1 A
69331 AATAAAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.33
Consensus pattern (31 bp):
ATAAGAATCAACTAATATACTTCACATTAAC
Found at i:69335 original size:82 final size:83
Alignment explanation
Indices: 69186--69402 Score: 276
Period size: 82 Copynumber: 2.6 Consensus size: 83
69176 CACATTAACT
* *
69186 TAAGAATCAGCTAATATCCTTCACATTAACATTAAGAATCAACTAATATCCTTCACATCAACAAA
1 TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
*
69251 TAAAAACATAAAACAATA
66 TAAAAACAGAAAACAATA
** * *
69269 TAAGAATCAACTAATATCCTTCACATTAACA-TAAGAATCATTTAATATATTTCACATTAACAAA
1 TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
*
69333 TAAAAATAGAAAACAATA
66 TAAAAACAGAAAACAATA
* * *
69351 TAAGAATCATCTAATTCAAAGTCGTTCACATGAACA-TAAGAATCAACTAATA
1 TAAGAATCAACTAA-T---A-TCCTTCACATTAACATTAAGAATCAACTAATA
69403 AAAAACAAAG
Statistics
Matches: 116, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
82 57 0.49
83 31 0.27
86 1 0.01
87 27 0.23
ACGTcount: A:0.50, C:0.18, G:0.05, T:0.27
Consensus pattern (83 bp):
TAAGAATCAACTAATATCCTTCACATTAACATTAAGAATCAACTAATATACTTCACATCAACAAA
TAAAAACAGAAAACAATA
Found at i:69817 original size:2 final size:2
Alignment explanation
Indices: 69812--69842 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
69802 TTTTTAGATC
69812 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
69843 AAACAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:73538 original size:17 final size:17
Alignment explanation
Indices: 73516--73549 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
73506 TGAAAAACAT
*
73516 TAAAATATGACTTTTTG
1 TAAAATATAACTTTTTG
*
73533 TAAAATTTAACTTTTTG
1 TAAAATATAACTTTTTG
73550 GTCAAAGTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (17 bp):
TAAAATATAACTTTTTG
Found at i:73620 original size:14 final size:14
Alignment explanation
Indices: 73601--73677 Score: 79
Period size: 14 Copynumber: 5.6 Consensus size: 14
73591 CTCTGTTCGA
73601 GTTGACTCAACGGG
1 GTTGACTCAACGGG
**
73615 GTTGACTC-A-GTAA
1 GTTGACTCAACG-GG
73628 GTTGACTCAACGGG
1 GTTGACTCAACGGG
***
73642 GTTGACTCAA-TAA
1 GTTGACTCAACGGG
73655 GTTGACTCAACGGG
1 GTTGACTCAACGGG
73669 GTTGACTCA
1 GTTGACTCA
73678 TCTTAACTGG
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
12 1 0.02
13 19 0.39
14 28 0.57
15 1 0.02
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (14 bp):
GTTGACTCAACGGG
Found at i:73634 original size:27 final size:27
Alignment explanation
Indices: 73600--73677 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
73590 ACTCTGTTCG
*
73600 AGTTGACTCAACGGGGTTGACTCAGTA
1 AGTTGACTCAACGGGGTTGACTCAATA
73627 AGTTGACTCAACGGGGTTGACTCAATA
1 AGTTGACTCAACGGGGTTGACTCAATA
73654 AGTTGACTCAACGGGGTTGACTCA
1 AGTTGACTCAACGGGGTTGACTCA
73678 TCTTAACTGG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.26
Consensus pattern (27 bp):
AGTTGACTCAACGGGGTTGACTCAATA
Found at i:73664 original size:13 final size:13
Alignment explanation
Indices: 73615--73664 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
73605 ACTCAACGGG
*
73615 GTTGACTCAGTAA
1 GTTGACTCAATAA
***
73628 GTTGACTCAACGGG
1 GTTGACTCAA-TAA
73642 GTTGACTCAATAA
1 GTTGACTCAATAA
73655 GTTGACTCAA
1 GTTGACTCAA
73665 CGGGGTTGAC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (13 bp):
GTTGACTCAATAA
Found at i:77824 original size:19 final size:19
Alignment explanation
Indices: 77804--77870 Score: 107
Period size: 19 Copynumber: 3.5 Consensus size: 19
77794 GTAATTAGTG
* *
77804 CATCGATGCATAAGGAGTG
1 CATCGATGCATGAGGAGTA
77823 CATCGATGCATGAGGAGTA
1 CATCGATGCATGAGGAGTA
*
77842 CATCAATGCATGAGGAGTA
1 CATCGATGCATGAGGAGTA
77861 CATCGATGCA
1 CATCGATGCA
77871 CCTACTTAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (19 bp):
CATCGATGCATGAGGAGTA
Found at i:78664 original size:18 final size:18
Alignment explanation
Indices: 78636--78695 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
78626 GGACATATAC
* *
78636 AGTGATCCTTCGGGATAT
1 AGTGGTCCTTCGGGAAAT
* *
78654 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGA-AAT
*
78673 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGAAAT
78692 AGTG
1 AGTG
78696 TCCCTTTGGG
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
18 16 0.48
19 4 0.12
20 13 0.39
ACGTcount: A:0.22, C:0.18, G:0.30, T:0.30
Consensus pattern (18 bp):
AGTGGTCCTTCGGGAAAT
Found at i:84191 original size:19 final size:19
Alignment explanation
Indices: 84167--84218 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
84157 GAATGCAATT
84167 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
84186 AGTGCATCGATGCATGAGG
1 AGTGCATCGATGCATGAGG
84205 AGTGCATCGATGCA
1 AGTGCATCGATGCA
84219 CCTACTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.17, G:0.35, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATGAGG
Found at i:86378 original size:17 final size:17
Alignment explanation
Indices: 86356--86389 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
86346 CATCGAAAAA
86356 CATAAAATTTGACTTTT
1 CATAAAATTTGACTTTT
86373 CATAAAATTTGACTTTT
1 CATAAAATTTGACTTTT
86390 TGGTCAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (17 bp):
CATAAAATTTGACTTTT
Found at i:86410 original size:16 final size:15
Alignment explanation
Indices: 86389--86434 Score: 74
Period size: 16 Copynumber: 2.9 Consensus size: 15
86379 ATTTGACTTT
86389 TTGGTCAAAGTCAAC
1 TTGGTCAAAGTCAAC
86404 GTTGGTCAAAGTCAAC
1 -TTGGTCAAAGTCAAC
86420 TCTGGTCAAAGTCAA
1 T-TGGTCAAAGTCAA
86435 TAAGTTGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (15 bp):
TTGGTCAAAGTCAAC
Found at i:87655 original size:15 final size:15
Alignment explanation
Indices: 87620--87669 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 15
87610 AAATGATAAA
*
87620 AAAATACAAAAACAT
1 AAAATATAAAAACAT
87635 --AATATAAAAACAT
1 AAAATATAAAAACAT
87648 AAAATATAAAAAAACAT
1 AAAATAT--AAAAACAT
87665 AAAAT
1 AAAAT
87670 TTTAACACAT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
13 12 0.40
15 5 0.17
17 13 0.43
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATATAAAAACAT
Found at i:88841 original size:19 final size:19
Alignment explanation
Indices: 88819--88867 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
88809 ACTTTCTACT
88819 TATATAT-TATACTTATAAG
1 TATATATGTATACTTAT-AG
*
88838 TATA-ATGTATACTTATAT
1 TATATATGTATACTTATAG
88856 TATATATGTATA
1 TATATATGTATA
88868 TATATATAAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
18 7 0.26
19 20 0.74
ACGTcount: A:0.41, C:0.04, G:0.06, T:0.49
Consensus pattern (19 bp):
TATATATGTATACTTATAG
Found at i:88869 original size:2 final size:2
Alignment explanation
Indices: 88851--89010 Score: 156
Period size: 2 Copynumber: 82.0 Consensus size: 2
88841 AATGTATACT
* *
88851 TA TA T- TA TA TA TG TA TA TA TA TA TA -A CT- TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * *
88891 TA TA CT- TA TA -A TG TA T- TG TT TA TA CTA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA
88932 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
88974 TA TA TA TT TA -A AA TA TA TA CT- TA TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
89011 CTTATAATGT
Statistics
Matches: 133, Mismatches: 13, Indels: 24
0.78 0.08 0.14
Matches are distributed among these distances:
1 8 0.06
2 121 0.91
3 4 0.03
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:88998 original size:8 final size:8
Alignment explanation
Indices: 88987--89050 Score: 50
Period size: 8 Copynumber: 8.5 Consensus size: 8
88977 ATATTTAAAA
88987 TATATACT
1 TATATACT
*
88995 TATATATAT
1 TATATA-CT
89004 GTATATACT
1 -TATATACT
89013 TATA-A--
1 TATATACT
*
89018 TGTATACT
1 TATATACT
89026 TATATACT
1 TATATACT
89034 TA-A-A-T
1 TATATACT
89039 TATATACT
1 TATATACT
89047 TATA
1 TATA
89051 AGTATAGTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 16
0.69 0.06 0.25
Matches are distributed among these distances:
5 6 0.14
6 3 0.07
7 3 0.07
8 24 0.55
9 2 0.05
10 6 0.14
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.48
Consensus pattern (8 bp):
TATATACT
Found at i:89029 original size:21 final size:21
Alignment explanation
Indices: 88997--89050 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
88987 TATATACTTA
88997 TATATA-TGTATATACTTATAA-
1 TATATACT-TATATACTTA-AAT
*
89018 TGTATACTTATATACTTAAAT
1 TATATACTTATATACTTAAAT
89039 TATATACTTATA
1 TATATACTTATA
89051 AGTATAGTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (21 bp):
TATATACTTATATACTTAAAT
Found at i:89161 original size:32 final size:31
Alignment explanation
Indices: 89119--89180 Score: 97
Period size: 32 Copynumber: 2.0 Consensus size: 31
89109 TATGTAAACT
89119 ATATAGTATATATAGTTTATTATATAGTTTAC
1 ATATAGTATATATAGTTTA-TATATAGTTTAC
* *
89151 ATATATTATATATGGTTTATATATAGTTTA
1 ATATAGTATATATAGTTTATATATAGTTTA
89181 TATTAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 11 0.39
32 17 0.61
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.52
Consensus pattern (31 bp):
ATATAGTATATATAGTTTATATATAGTTTAC
Found at i:89170 original size:11 final size:11
Alignment explanation
Indices: 89125--89183 Score: 77
Period size: 11 Copynumber: 5.5 Consensus size: 11
89115 AACTATATAG
89125 TATATATAGTT
1 TATATATAGTT
89136 TATTATATAGTT
1 TA-TATATAGTT
*
89148 TACATATA--T
1 TATATATAGTT
*
89157 TATATATGGTT
1 TATATATAGTT
89168 TATATATAGTT
1 TATATATAGTT
89179 TATAT
1 TATAT
89184 TAATAAAATA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.17
11 23 0.56
12 11 0.27
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (11 bp):
TATATATAGTT
Found at i:89182 original size:20 final size:19
Alignment explanation
Indices: 89138--89183 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
89128 ATATAGTTTA
89138 TTATATAGTTTACATATAT
1 TTATATAGTTTACATATAT
* *
89157 TATATATGGTTTATATATAGT
1 T-TATATAGTTTACATATA-T
89178 TTATAT
1 TTATAT
89184 TAATAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
19 1 0.04
20 20 0.87
21 2 0.09
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (19 bp):
TTATATAGTTTACATATAT
Found at i:89982 original size:21 final size:22
Alignment explanation
Indices: 89947--89988 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
89937 AATCCAAAAA
*
89947 TGCTTAGTGTTTTTAGCATTTT
1 TGCTTAATGTTTTTAGCATTTT
*
89969 TGCTTAAT-TTTTTAGGATTT
1 TGCTTAATGTTTTTAGCATTT
89989 GATAATGGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.60
Consensus pattern (22 bp):
TGCTTAATGTTTTTAGCATTTT
Found at i:91678 original size:45 final size:46
Alignment explanation
Indices: 91629--91716 Score: 133
Period size: 45 Copynumber: 1.9 Consensus size: 46
91619 GAACATCGAA
* * * *
91629 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATACACTTAG
91674 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATACACT
1 TGCATTTGATGCATCGATGCACAAGACCATGAATCGATACACT
91717 CGGGCTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
45 21 0.55
46 17 0.45
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGAATCGATACACTTAG
Found at i:97209 original size:20 final size:21
Alignment explanation
Indices: 97184--97244 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
97174 TTGTGCTTCA
97184 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-AG
* *
97204 TGCATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAAAG
*
97226 TGCATCGATACACCATGAA
1 TGCATCGATACACCTTGAA
97245 GGTGAACCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
20 11 0.32
21 8 0.24
22 13 0.38
23 2 0.06
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAAAG
Found at i:97231 original size:22 final size:21
Alignment explanation
Indices: 97203--97274 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 21
97193 ACACCTAACA
97203 GTGCATCGATGCATCCTTGAAT
1 GTGCATCGATGCA-CCTTGAAT
* * *
97225 GTGCATCGATACACCATGAAG
1 GTGCATCGATGCACCTTGAAT
* * *
97246 GTGAACCAATGCACGCCTTGAAT
1 GTGCATCGATGCA--CCTTGAAT
97269 GTGCAT
1 GTGCAT
97275 TCTATTCACA
Statistics
Matches: 37, Mismatches: 11, Indels: 3
0.73 0.22 0.06
Matches are distributed among these distances:
21 15 0.41
22 12 0.32
23 10 0.27
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (21 bp):
GTGCATCGATGCACCTTGAAT
Found at i:100073 original size:45 final size:46
Alignment explanation
Indices: 100024--100111 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
100014 GAACATCGAA
* *
100024 TGCATTTTATGCATCGATGCAC-ATACCATGCATCAATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTTAG
*
100069 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACT
100112 CAGGCTATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.28
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCAATGCACTTAG
Found at i:100181 original size:19 final size:19
Alignment explanation
Indices: 100143--100181 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
100133 ATGCATTTTA
* *
100143 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTCATAG
*
100162 TGCACCGATGCACTGATAG
1 TGCACCGATGCACTCATAG
100181 T
1 T
100182 CCAACGGTCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (19 bp):
TGCACCGATGCACTCATAG
Found at i:101709 original size:13 final size:13
Alignment explanation
Indices: 101657--101717 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 13
101647 ATAAACGAAC
101657 ATAAACGAACACAA
1 ATAAACGAACAC-A
*
101671 ATGAACG-A-AC-
1 ATAAACGAACACA
* *
101681 ATAAACGAATATA
1 ATAAACGAACACA
*
101694 ATAAATGAACACA
1 ATAAACGAACACA
101707 ATAAACGAACA
1 ATAAACGAACA
101718 TAAACGAACA
Statistics
Matches: 37, Mismatches: 7, Indels: 7
0.73 0.14 0.14
Matches are distributed among these distances:
10 6 0.16
11 1 0.03
12 3 0.08
13 21 0.57
14 6 0.16
ACGTcount: A:0.61, C:0.16, G:0.10, T:0.13
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:102015 original size:14 final size:14
Alignment explanation
Indices: 101996--102110 Score: 100
Period size: 14 Copynumber: 9.4 Consensus size: 14
101986 CTGTTCAAAA
101996 ATAAATGAACGAAC
1 ATAAATGAACGAAC
102010 ATAAAT----GAAC
1 ATAAATGAACGAAC
*
102020 ATAAATGAACGGAC
1 ATAAATGAACGAAC
102034 ATAAAT----GAAC
1 ATAAATGAACGAAC
102044 ATAAATGAACGAAC
1 ATAAATGAACGAAC
102058 ATAAAT----GAAC
1 ATAAATGAACGAAC
*
102068 ATAAATGAACGGAC
1 ATAAATGAACGAAC
102082 ATAAAT----GAAC
1 ATAAATGAACGAAC
102092 ATAAATGAACGAAC
1 ATAAATGAACGAAC
102106 ATAAA
1 ATAAA
102111 CAAACATATA
Statistics
Matches: 81, Mismatches: 4, Indels: 32
0.69 0.03 0.27
Matches are distributed among these distances:
10 38 0.47
14 43 0.53
ACGTcount: A:0.57, C:0.12, G:0.14, T:0.17
Consensus pattern (14 bp):
ATAAATGAACGAAC
Found at i:102021 original size:10 final size:10
Alignment explanation
Indices: 102006--102101 Score: 84
Period size: 10 Copynumber: 8.4 Consensus size: 10
101996 ATAAATGAAC
102006 GAACATAAAT
1 GAACATAAAT
102016 GAACATAAAT
1 GAACATAAAT
102026 GAACGGACATAAAT
1 G-A---ACATAAAT
102040 GAACATAAAT
1 GAACATAAAT
102050 GAACGAACATAAAT
1 ----GAACATAAAT
102064 GAACATAAAT
1 GAACATAAAT
102074 GAACGGACATAAAT
1 G-A---ACATAAAT
102088 GAACATAAAT
1 GAACATAAAT
102098 GAAC
1 GAAC
102102 GAACATAAAC
Statistics
Matches: 74, Mismatches: 0, Indels: 24
0.76 0.00 0.24
Matches are distributed among these distances:
10 42 0.57
11 2 0.03
13 2 0.03
14 28 0.38
ACGTcount: A:0.56, C:0.12, G:0.15, T:0.17
Consensus pattern (10 bp):
GAACATAAAT
Found at i:102028 original size:24 final size:24
Alignment explanation
Indices: 101996--102128 Score: 212
Period size: 24 Copynumber: 5.5 Consensus size: 24
101986 CTGTTCAAAA
101996 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
*
102020 ATAAATGAACGGACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
102044 ATAAATGAACGAACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
*
102068 ATAAATGAACGGACATAAATGAAC
1 ATAAATGAACGAACATAAATGAAC
**
102092 ATAAATGAACGAACATAAACAAAC
1 ATAAATGAACGAACATAAATGAAC
102116 ATATAATCGAACG
1 ATA-AAT-GAACG
102129 TTCATGAACG
Statistics
Matches: 101, Mismatches: 6, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
24 93 0.92
25 3 0.03
26 5 0.05
ACGTcount: A:0.56, C:0.14, G:0.14, T:0.17
Consensus pattern (24 bp):
ATAAATGAACGAACATAAATGAAC
Found at i:103634 original size:29 final size:30
Alignment explanation
Indices: 103577--103640 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
103567 ACAAGCCTTA
* * ** *
103577 GAAAATTTGGGGATCATTTTGTAAGTTTT-
1 GAAAAGTTGGGGATCAATTCATAAATTTTG
103606 GAAAAGTTGGGGATCAATTCATAAATTTTG
1 GAAAAGTTGGGGATCAATTCATAAATTTTG
103636 GAAAA
1 GAAAA
103641 TTGATGAGTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.36, C:0.05, G:0.23, T:0.36
Consensus pattern (30 bp):
GAAAAGTTGGGGATCAATTCATAAATTTTG
Found at i:110842 original size:39 final size:39
Alignment explanation
Indices: 110764--110842 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
110754 ACCGCTTTCA
* *
110764 GCAGGCTCATCTGCTTTGTGCACAGGATAAGACCTTACT
1 GCAGGCTCATCTGCTTTATGCACAGGATAAGACCCTACT
* * *
110803 GCAGGCTCCTCTGCTTTATGCA-ATGGGTAAGCCCCTACT
1 GCAGGCTCATCTGCTTTATGCACA-GGATAAGACCCTACT
110842 G
1 G
110843 GGTGTACAAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.20, C:0.28, G:0.24, T:0.28
Consensus pattern (39 bp):
GCAGGCTCATCTGCTTTATGCACAGGATAAGACCCTACT
Found at i:111392 original size:2 final size:2
Alignment explanation
Indices: 111385--111885 Score: 138
Period size: 2 Copynumber: 256.0 Consensus size: 2
111375 TTATACATAG
* *
111385 TA TA TA TA -A TT TA TA -A T- TA TA TA TA -A TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
111423 AA T- TA TA CA T- TT TA TA TA TA GT- TCA TA TA TA -A TT TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA -TA T-A TA TA TA TA TA TA TA TA
* * * *
111462 T- TA TA CA TA GTA TA TA TA GCA TA TA TA AA TA TA AA CTA TA TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA
* * * *
111504 GTT TA TA TA TA AA T- TA TA TA TA -A AA CTA TA TA GTT TA T- TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* *
111544 -A TA TA AA CTA TA TA TA TA TA TA T- TA TA TA AA T- TA TA TA TGA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A
* * * *
111585 -A CTA TA TA TA -A AA TG TA TA GTT TA TA TT TA TA TA T- TA TA TA
1 TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
111626 TA -A T- TA TA AA T- TA TA TA TA TGA -A CTA TA TA -A AA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA TA TA
* * * *
111665 GTT TA CA TA TA AA TA TA TA TGA -A CTA TA TA TA GA -A CTA TA TA
1 -TA TA TA TA TA TA TA TA TA T-A TA -TA TA TA TA TA TA -TA TA TA
* * * *
111707 -A TT TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
111748 TA TA TA TA T- TA TG TA TA -A T- TA TA AA T- TA TA TA TA CTA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
* * * *
111787 TA TA AA T- TA CA TA GTT TA TA TA TA AA T- TA TA TGA -A CTA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA T-A TA -TA TA
* * * * *
111827 TA TA GTT TA TA TA TA GTA TA TA AA TA TA AA T- TG TA TA GTT TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
111869 TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA
111886 ATTGTTTCAA
Statistics
Matches: 360, Mismatches: 78, Indels: 122
0.64 0.14 0.22
Matches are distributed among these distances:
1 36 0.10
2 296 0.82
3 28 0.08
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
TA
Found at i:111513 original size:37 final size:34
Alignment explanation
Indices: 111402--111881 Score: 123
Period size: 37 Copynumber: 13.4 Consensus size: 34
111392 AATTTATAAT
* *
111402 TATATATAATATATAAATATAAATTATACATTT-
1 TATATATAATATATAAATATAAACTATATATTTA
* * * * *
111435 TATATATAGTTCATATATAATTTATAATTATACATAGTA
1 TATATATA-AT-ATATA-AATATA-AACTATATAT-TTA
**
111474 TATATAGCATATATAAATATAAACTATATAGTTTA
1 TATATATAATATATAAATATAAACTATATA-TTTA
*
111509 TATATA-AAT-TATATATA-AAACTATATAGTTTA
1 TATATATAATATATAAATATAAACTATATA-TTTA
* * * *
111541 T-TAATATAAACTATATATATATATATTATATAAATTA
1 TAT-ATAT-AA-TATATAAATATAAACTATAT-ATTTA
* * * *
111578 TATATGA-ACTATATATAAAATGTATAGTTTATATTTA
1 TATAT-ATA--ATATAT-AAATATAAACTATATATTTA
* * *
111615 TATAT-T-ATATATAATTATAAATTATATATATGA
1 TATATATAATATATAAATATAAACTATATAT-TTA
* * * * * * *
111648 -ACTATATAAAATGTATAGTTTACA-TATAAATATA
1 TA-TATATAATATATA-AATATAAACTATATATTTA
*
111682 TATGA-ACT-ATATATAGAACTATATAA-TTTATATTTA
1 TAT-ATA-TAATATATA-AA-TATA-AACTATATATTTA
*
111718 TATATATATATATATATATATATATACAC-ATATATATA
1 TATATATA-ATATATA-A-ATATA-A-ACTATATATTTA
* *
111756 TTATGTATAAT-TATAAATTATATATACTATGTATAAATTA
1 -TATATATAATATATAAA-TATA-A-ACTA--TAT-ATTTA
* *
111796 CATAGT-TTATATATAAATTATATGAACTATATATAGTT-
1 TATA-TATAATATATAAA-TATA--AACTATATAT--TTA
* * *
111834 TATATATAGTATATAAATATAAATTGTATAGTTTA
1 TATATATAATATATAAATATAAACTATATA-TTTA
111869 TATATAT-ATATAT
1 TATATATAATATAT
111882 TATAATTGTT
Statistics
Matches: 336, Mismatches: 61, Indels: 99
0.68 0.12 0.20
Matches are distributed among these distances:
31 1 0.00
32 32 0.10
33 26 0.08
34 22 0.07
35 55 0.16
36 47 0.14
37 67 0.20
38 43 0.13
39 23 0.07
40 19 0.06
41 1 0.00
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (34 bp):
TATATATAATATATAAATATAAACTATATATTTA
Found at i:111523 original size:13 final size:13
Alignment explanation
Indices: 111507--111655 Score: 58
Period size: 13 Copynumber: 12.3 Consensus size: 13
111497 CTATATAGTT
111507 TATATATAAATTA
1 TATATATAAATTA
*
111520 TATATA-AAACTA
1 TATATATAAATTA
*
111532 TATA-GT---TTA
1 TATATATAAATTA
*
111541 T-TAATATAAACTA
1 TAT-ATATAAATTA
*
111554 TATATATATA-TA
1 TATATATAAATTA
111566 T-TATATAAA-T-
1 TATATATAAATTA
* *
111576 TATATATGAACTA
1 TATATATAAATTA
111589 TATATA-AAATGTA
1 TATATATAAAT-TA
* *
111602 TAGTTTAT-ATTTA
1 TA-TATATAAATTA
*
111615 TATAT-TATA-TA
1 TATATATAAATTA
111626 TA-ATTATAAATTA
1 TATA-TATAAATTA
* *
111639 TATATATGAACTA
1 TATATATAAATTA
111652 TATA
1 TATA
111656 AAATGTATAG
Statistics
Matches: 100, Mismatches: 18, Indels: 36
0.65 0.12 0.23
Matches are distributed among these distances:
8 1 0.01
9 4 0.04
10 3 0.03
11 21 0.21
12 20 0.20
13 44 0.44
14 7 0.07
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (13 bp):
TATATATAAATTA
Found at i:111640 original size:61 final size:61
Alignment explanation
Indices: 111552--111684 Score: 182
Period size: 61 Copynumber: 2.2 Consensus size: 61
111542 TAATATAAAC
*
111552 TATATATATATATATTATATAAA-T-TATATATGAACTATATATAAAATGTATAGTTTATATT
1 TATATATATATATAATATATAAATTATATATATGAAC--TATATAAAATGTATAGTTTATATT
* *
111613 TATATATTATATATAAT-TATAAATTATATATATGAACTATATAAAATGTATAGTTTACATA
1 TATATA-TATATATAATATATAAATTATATATATGAACTATATAAAATGTATAGTTTATATT
*
111674 TAAATATATAT
1 TATATATATAT
111685 GAACTATATA
Statistics
Matches: 65, Mismatches: 4, Indels: 7
0.86 0.05 0.09
Matches are distributed among these distances:
60 5 0.08
61 39 0.60
62 10 0.15
63 11 0.17
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (61 bp):
TATATATATATATAATATATAAATTATATATATGAACTATATAAAATGTATAGTTTATATT
Found at i:111837 original size:11 final size:11
Alignment explanation
Indices: 111823--111881 Score: 50
Period size: 11 Copynumber: 5.5 Consensus size: 11
111813 TTATATGAAC
*
111823 TATATATAGTT
1 TATATATAGTA
111834 TATATATAGTA
1 TATATATAGTA
*
111845 TATAAATA-TA
1 TATATATAGTA
* * *
111855 AATTGTATAGTT
1 TA-TATATAGTA
111867 TATATATA-TA
1 TATATATAGTA
111877 TATAT
1 TATAT
111882 TATAATTGTT
Statistics
Matches: 37, Mismatches: 9, Indels: 5
0.73 0.18 0.10
Matches are distributed among these distances:
10 9 0.24
11 26 0.70
12 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (11 bp):
TATATATAGTA
Found at i:111871 original size:135 final size:136
Alignment explanation
Indices: 111613--111880 Score: 328
Period size: 137 Copynumber: 2.0 Consensus size: 136
111603 AGTTTATATT
**
111613 TATATATTATATATAATTATAAATTATATATATGAACTATATAAAATGTATAGTTTACATATAAA
1 TATATATTATATATAATTATAAATTATATATAT-AACTATATAAAATACATAGTTTACATATAAA
* ** *
111678 TATATATGAACTATATATAGAACTATATAATTTATATTTATATATATATATATATATATATATAT
65 TATATATGAACTATATATAGAACTATATAATATATAAATATAAATATATATATATATATATATAT
111743 ACACATA
130 ACACATA
* * * *
111750 TATATATTATGTATAATTATAAATTATATATACT-A-TGTATAAATTACATAGTTTATATATAAA
1 TATATATTATATATAATTATAAATTATATATA-TAACTATATAAAATACATAGTTTACATATAAA
* * * *
111813 T-TATATGAACTATATATAGTTTA-TATATAGTATATAAATATAAATTGTATAGTTTATATATAT
65 TATATATGAACTATATATAG--AACTATATAATATATAAATATAAA-TATATA-TATATATATAT
111876 ATATA
126 ATATA
111881 TTATAATTGT
Statistics
Matches: 112, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
134 18 0.16
135 40 0.36
136 7 0.06
137 46 0.41
138 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (136 bp):
TATATATTATATATAATTATAAATTATATATATAACTATATAAAATACATAGTTTACATATAAAT
ATATATGAACTATATATAGAACTATATAATATATAAATATAAATATATATATATATATATATATA
CACATA
Done.