Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005064.1 Hibiscus syriacus cultivar Beakdansim tig00011368_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: 46179
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Found at i:7905 original size:24 final size:24
Alignment explanation
Indices: 7878--7962 Score: 143
Period size: 24 Copynumber: 3.5 Consensus size: 24
7868 AACCATTTGT
7878 AACATCTGAGAAGGCACTTGATGG
1 AACATCTGAGAAGGCACTTGATGG
*
7902 AACATCTGAGAAGGCACATGATGG
1 AACATCTGAGAAGGCACTTGATGG
*
7926 AACATATGAGAAGGCACTTGATGG
1 AACATCTGAGAAGGCACTTGATGG
*
7950 AATATCTGAGAAG
1 AACATCTGAGAAG
7963 CTGTTATGTA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 56 1.00
ACGTcount: A:0.38, C:0.14, G:0.28, T:0.20
Consensus pattern (24 bp):
AACATCTGAGAAGGCACTTGATGG
Found at i:9743 original size:24 final size:24
Alignment explanation
Indices: 9715--9761 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
9705 CACATGAATA
*
9715 TTTTATCTAAATTTTGTTCTGATT
1 TTTTATCTAAATTTTGTTATGATT
**
9739 TTTTATCTGGATTTTGTTATGAT
1 TTTTATCTAAATTTTGTTATGAT
9762 ATCTCCATTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.62
Consensus pattern (24 bp):
TTTTATCTAAATTTTGTTATGATT
Found at i:13123 original size:21 final size:21
Alignment explanation
Indices: 13099--13143 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13089 GATTTCTGGG
* *
13099 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
13120 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
13141 CAA
1 CAA
13144 ACGACAGAAT
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:14007 original size:31 final size:31
Alignment explanation
Indices: 13969--14122 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
13959 GGGTCGAGGG
13969 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
14000 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
14031 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGT
* * *
14062 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGT
*
14093 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
14123 GTCCTTCGGG
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGT
Found at i:17107 original size:21 final size:21
Alignment explanation
Indices: 17083--17127 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17073 GATTTCTGGG
* *
17083 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
17104 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
17125 CAA
1 CAA
17128 ACGACAGAAT
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:18029 original size:31 final size:31
Alignment explanation
Indices: 17991--18082 Score: 132
Period size: 31 Copynumber: 3.0 Consensus size: 31
17981 GGGTCGAGGG
*
17991 TTACCTATGTTCTTCGGAACATATGGACTGT
1 TTACCTATGTTCTTCGGAACATATGGACTGA
* *
18022 TTACCTATGTCCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGAACATATGGACTGA
*
18053 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGAA-CATATGGACTG
18083 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 53 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGAACATATGGACTGA
Found at i:19592 original size:20 final size:21
Alignment explanation
Indices: 19551--19593 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
19541 GTAAAATAAG
19551 CTGTGTTATTGATATAAAACT
1 CTGTGTTATTGATATAAAACT
19572 CTGTGTTATTGATAT-AAACT
1 CTGTGTTATTGATATAAAACT
19592 CT
1 CT
19594 TATATGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (21 bp):
CTGTGTTATTGATATAAAACT
Found at i:19734 original size:44 final size:44
Alignment explanation
Indices: 19709--19833 Score: 205
Period size: 44 Copynumber: 2.8 Consensus size: 44
19699 AGATATGAGA
*
19709 ATAAGATATAAGCTATGTGACATGATCTACGTGATTACATAAAC
1 ATAAGATATAAGCTATGTGACATGATCTACGTGATTACATGAAC
* *
19753 ACAAGACATAAGCTATGTGACATGATCTACGTGATTACATGAAC
1 ATAAGATATAAGCTATGTGACATGATCTACGTGATTACATGAAC
* *
19797 ATAAGATATAAGCTATGTGATATAATCTACGTGATTA
1 ATAAGATATAAGCTATGTGACATGATCTACGTGATTA
19834 TTGGTCTATG
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 74 1.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.30
Consensus pattern (44 bp):
ATAAGATATAAGCTATGTGACATGATCTACGTGATTACATGAAC
Found at i:19820 original size:14 final size:14
Alignment explanation
Indices: 19801--19852 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
19791 ATGAACATAA
19801 GATATAAGCTATGT
1 GATATAAGCTATGT
* *
19815 GATATAATCTACGT
1 GATATAAGCTATGT
**
19829 GATTATTGGTCTATGT
1 GA-TATAAG-CTATGT
19845 GATATAAG
1 GATATAAG
19853 ATATAATAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 3
0.72 0.21 0.08
Matches are distributed among these distances:
14 14 0.50
15 7 0.25
16 7 0.25
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (14 bp):
GATATAAGCTATGT
Found at i:19970 original size:23 final size:22
Alignment explanation
Indices: 19944--20029 Score: 93
Period size: 23 Copynumber: 3.9 Consensus size: 22
19934 GGTTCTAAGC
19944 GGTCCTTCGGGACAATTCTACGT
1 GGTCCTTCGGGAC-ATTCTACGT
* * *
19967 GGTCATTCGAGACATTTCTACGC
1 GGTCCTTCGGGACA-TTCTACGT
* *
19990 GGTCCTTCGGGACA-TATATGT
1 GGTCCTTCGGGACATTCTACGT
*
20011 GGTCTTTCGGGACATTCTA
1 GGTCCTTCGGGACATTCTA
20030 TATGGCACTT
Statistics
Matches: 51, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
21 17 0.33
22 4 0.08
23 30 0.59
ACGTcount: A:0.19, C:0.23, G:0.26, T:0.33
Consensus pattern (22 bp):
GGTCCTTCGGGACATTCTACGT
Found at i:20052 original size:24 final size:24
Alignment explanation
Indices: 20025--20074 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
20015 TTTCGGGACA
* *
20025 TTCTATATGGCACTTTGGTGTATT
1 TTCTATACGGCACTTCGGTGTATT
* *
20049 TTCTATGCGGCTCTTCGGTGTATT
1 TTCTATACGGCACTTCGGTGTATT
20073 TT
1 TT
20075 ATACGATCTG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.50
Consensus pattern (24 bp):
TTCTATACGGCACTTCGGTGTATT
Found at i:21687 original size:22 final size:22
Alignment explanation
Indices: 21627--21687 Score: 54
Period size: 24 Copynumber: 2.7 Consensus size: 22
21617 AATATAGTTT
* *
21627 ATAATT-TTTTAATAATAATAT
1 ATAATTCTTTTAAAAATAATAA
*
21648 A-AATTCATATTTATAAAATATTAA
1 ATAATTC-T-TTTA-AAAATAATAA
21672 ATAATTCTTTTAAAAA
1 ATAATTCTTTTAAAAA
21688 ACAGGGCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 5 0.16
23 8 0.25
24 9 0.28
25 5 0.16
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (22 bp):
ATAATTCTTTTAAAAATAATAA
Found at i:25706 original size:44 final size:44
Alignment explanation
Indices: 25643--25731 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
25633 GAGAAACTAC
25643 AGCAATCGAAAGAAGTAAGGCTAAAGACTAAAATAATAAATTAA
1 AGCAATCGAAAGAAGTAAGGCTAAAGACTAAAATAATAAATTAA
*
25687 AGCAATGGAAAGAAGTAAGGCTAAAGACTAAAATAATAAATTAA
1 AGCAATCGAAAGAAGTAAGGCTAAAGACTAAAATAATAAATTAA
25731 A
1 A
25732 ATATTACAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.57, C:0.08, G:0.17, T:0.18
Consensus pattern (44 bp):
AGCAATCGAAAGAAGTAAGGCTAAAGACTAAAATAATAAATTAA
Found at i:31208 original size:20 final size:20
Alignment explanation
Indices: 31165--31235 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
31155 GATCTCAAAT
* *
31165 TCGCAACGCGAA-CTGCAATT
1 TCGCAACGCGAATCTGTAA-A
31185 TCGCAACGCGAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
** *
31205 TCGCAACTTGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
31225 TCTCAACGCGA
1 TCGCAACGCGA
31236 TAGTCAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 37 0.88
21 5 0.12
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.24
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:31323 original size:19 final size:20
Alignment explanation
Indices: 31279--31370 Score: 82
Period size: 19 Copynumber: 4.7 Consensus size: 20
31269 AACACAAAAG
**
31279 TCAAATTCGCAACGCGGAATT
1 TCAAATTCGCAAC-TAGAATT
* *
31300 CCAAATTCGTAACT-GAATT
1 TCAAATTCGCAACTAGAATT
*
31319 TCAAATTCGCAACTAGATTT
1 TCAAATTCGCAACTAGAATT
*
31339 TCGAATTCGCAAC-ACGAATT
1 TCAAATTCGCAACTA-GAATT
*
31359 T-AATTTCGCAAC
1 TCAAATTCGCAAC
31371 AAGTTTTAGT
Statistics
Matches: 59, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
19 27 0.46
20 21 0.36
21 11 0.19
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (20 bp):
TCAAATTCGCAACTAGAATT
Found at i:31371 original size:19 final size:18
Alignment explanation
Indices: 31344--31390 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
31334 GATTTTCGAA
31344 TTCGCAACACGAATTTAAT
1 TTCGCAACACG-ATTTAAT
* * *
31363 TTCGCAACAAGTTTTAGT
1 TTCGCAACACGATTTAAT
31381 TTCGCAACAC
1 TTCGCAACAC
31391 AAATGTTTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 14 0.58
19 10 0.42
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (18 bp):
TTCGCAACACGATTTAAT
Found at i:32141 original size:12 final size:12
Alignment explanation
Indices: 32120--32153 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
32110 ATCACATTTC
*
32120 CAATACCAAACA
1 CAATATCAAACA
32132 CAATATCAAACA
1 CAATATCAAACA
*
32144 CAATCTCAAA
1 CAATATCAAA
32154 ACCCACAACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.56, C:0.29, G:0.00, T:0.15
Consensus pattern (12 bp):
CAATATCAAACA
Found at i:33423 original size:20 final size:20
Alignment explanation
Indices: 33398--33448 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
33388 AATGAGATAC
33398 TGCCAATAGCTAACAATGGA
1 TGCCAATAGCTAACAATGGA
33418 TGCCAATAGCTAACAATGGA
1 TGCCAATAGCTAACAATGGA
33438 TGCCAATAGCT
1 TGCCAATAGCT
33449 GTGTATAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGCCAATAGCTAACAATGGA
Found at i:33693 original size:18 final size:18
Alignment explanation
Indices: 33672--33708 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
33662 GTAATTGGAG
33672 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
33690 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
33708 T
1 T
33709 ATCTCCACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:34053 original size:39 final size:39
Alignment explanation
Indices: 34010--34098 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
34000 TCTGATGCTC
34010 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
* * *
34049 ATCAACATCCAAATCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
34088 ATCAAAATCTA
1 ATCAAAATCTA
34099 CAACTTGAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.46, C:0.20, G:0.15, T:0.19
Consensus pattern (39 bp):
ATCAAAATCTAAAGCTCATATGGTGCCAAGCAAAAGGAA
Found at i:36691 original size:20 final size:20
Alignment explanation
Indices: 36666--36706 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
36656 GCGTAAAAAC
*
36666 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
36686 ATTTGACTATCGCGTTGCGA
1 ATTTGACTATCGCGTTGCGA
36706 A
1 A
36707 ATTGGAAACT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (20 bp):
ATTTGACTATCGCGTTGCGA
Found at i:36742 original size:20 final size:19
Alignment explanation
Indices: 36674--36746 Score: 67
Period size: 20 Copynumber: 3.7 Consensus size: 19
36664 ACATTTGACT
*
36674 TTCGCGTTGCG-AATTTGA
1 TTCGCGTTGCGAAATTGGA
36692 CTATCGCGTTGCGAAATTGGA
1 -T-TCGCGTTGCGAAATTGGA
** *
36713 AACTGGGTTGCGAAATTGGA
1 TTC-GCGTTGCGAAATTGGA
36733 GTTCGCGTTGCGAA
1 -TTCGCGTTGCGAA
36747 TTTGTTGGTC
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
19 2 0.05
20 34 0.79
21 7 0.16
ACGTcount: A:0.22, C:0.16, G:0.32, T:0.30
Consensus pattern (19 bp):
TTCGCGTTGCGAAATTGGA
Found at i:37438 original size:17 final size:17
Alignment explanation
Indices: 37416--37454 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
37406 TGAATCAATT
37416 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
37433 TAATTAGATATTATTTA
1 TAATTAGATATTATTTA
37450 -AATTA
1 TAATTA
37455 ATTGTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (17 bp):
TAATTAGATATTATTTA
Found at i:38879 original size:15 final size:15
Alignment explanation
Indices: 38859--38889 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
38849 CAACGGATAA
38859 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
38874 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
38889 A
1 A
38890 TTTAGAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:39832 original size:53 final size:53
Alignment explanation
Indices: 39775--39875 Score: 161
Period size: 53 Copynumber: 1.9 Consensus size: 53
39765 AGTCGAATTG
*
39775 AACTTTTATAATAATTACATATA-TATAACTT-TTATAATAATTACATATATTAT
1 AACTTTTATAATAATTACATATATTATAACTTAATATAAT-ATTA-ATATATTAT
39828 AACTTTTATAATAATTACATATATTATAACTTAATATAATATTAATAT
1 AACTTTTATAATAATTACATATATTATAACTTAATATAATATTAATAT
39876 TATAATATTT
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
53 27 0.60
54 12 0.27
55 6 0.13
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (53 bp):
AACTTTTATAATAATTACATATATTATAACTTAATATAATATTAATATATTAT
Found at i:39836 original size:27 final size:27
Alignment explanation
Indices: 39775--39875 Score: 163
Period size: 27 Copynumber: 3.8 Consensus size: 27
39765 AGTCGAATTG
39775 AACTTTTATAATAATTACATATA-TAT
1 AACTTTTATAATAATTACATATATTAT
39801 AACTTTTATAATAATTACATATATTAT
1 AACTTTTATAATAATTACATATATTAT
39828 AACTTTTATAATAATTACATATATTAT
1 AACTTTTATAATAATTACATATATTAT
*
39855 AACTTAATATAAT-ATTA-ATAT
1 AACTT-TTATAATAATTACATAT
39876 TATAATATTT
Statistics
Matches: 72, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
26 27 0.38
27 39 0.54
28 6 0.08
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (27 bp):
AACTTTTATAATAATTACATATATTAT
Found at i:40260 original size:79 final size:80
Alignment explanation
Indices: 40102--40267 Score: 210
Period size: 80 Copynumber: 2.1 Consensus size: 80
40092 ACAATTGTTA
* * * * * *
40102 CATTAAAAGAGTTGTTCTTCTATATAGATAATGAGATGAAAACAATAAACATAACACATAATCAT
1 CATTAAAAGAGTTCTTCATCCACATACATAAGGAGATGAAAACAATAAACATAACACATAATCAT
*
40167 AAACTTCATGCATTG
66 AAACTTCATACATTG
* * **
40182 CATTAAAAGAGTTCTTCATCCACATACCTAAGGAGATGAAAACAA-CAACATTTCACATAATCAT
1 CATTAAAAGAGTTCTTCATCCACATACATAAGGAGATGAAAACAATAAACATAACACATAATCAT
40246 AAACTTCCA-ACATTG
66 AAACTT-CATACATTG
40261 CATTAAA
1 CATTAAA
40268 TGATTTATCC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
79 34 0.46
80 40 0.54
ACGTcount: A:0.45, C:0.18, G:0.10, T:0.28
Consensus pattern (80 bp):
CATTAAAAGAGTTCTTCATCCACATACATAAGGAGATGAAAACAATAAACATAACACATAATCAT
AAACTTCATACATTG
Found at i:40288 original size:79 final size:80
Alignment explanation
Indices: 40102--40329 Score: 221
Period size: 79 Copynumber: 2.9 Consensus size: 80
40092 ACAATTGTTA
* * * ** *
40102 CATTAAAAGAGTTGTTCTTCTATATAGATAATGAGATGAAAACAATAAACATAACACATAATCAT
1 CATTAAAAGAGTTATCCATCTATATACCTAAGGAGATGAAAACAATAAACATAACACATAATCAT
*
40167 AAACTTCATGCATTG
66 AAACTTCATACATTG
* * * * * **
40182 CATTAAAAGAGTTCTTCATCCACATACCTAAGGAGATGAAAACAA-CAACATTTCACATAATCAT
1 CATTAAAAGAGTTATCCATCTATATACCTAAGGAGATGAAAACAATAAACATAACACATAATCAT
40246 AAACTTCCA-ACATTG
66 AAACTT-CATACATTG
* * * * * *
40261 CATTAAATGATTTATCCATCTATATACCTAAGAAGATTG-AAATAATAAACATTAA-ATATAAGC
1 CATTAAAAGAGTTATCCATCTATATACCTAAGGAGA-TGAAAACAATAAACA-TAACACATAATC
40324 ATAAAC
64 ATAAAC
40330 ATACGACTCT
Statistics
Matches: 120, Mismatches: 24, Indels: 8
0.79 0.16 0.05
Matches are distributed among these distances:
79 61 0.51
80 58 0.48
81 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (80 bp):
CATTAAAAGAGTTATCCATCTATATACCTAAGGAGATGAAAACAATAAACATAACACATAATCAT
AAACTTCATACATTG
Found at i:42171 original size:36 final size:36
Alignment explanation
Indices: 42131--42214 Score: 141
Period size: 36 Copynumber: 2.3 Consensus size: 36
42121 TGATTGATAA
42131 ATGTTATATGATTCATATGAATAAATGAAAGTACAC
1 ATGTTATATGATTCATATGAATAAATGAAAGTACAC
* * *
42167 ATGTTATATGATTCATATGAATAGATGAAAGTATAT
1 ATGTTATATGATTCATATGAATAAATGAAAGTACAC
42203 ATGTTATATGAT
1 ATGTTATATGAT
42215 ACGAGATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (36 bp):
ATGTTATATGATTCATATGAATAAATGAAAGTACAC
Found at i:44081 original size:31 final size:31
Alignment explanation
Indices: 44046--44170 Score: 135
Period size: 31 Copynumber: 4.0 Consensus size: 31
44036 GATCCTTGGC
* *
44046 AACTGTCCATAGGTTCCAAAGAACCTAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
**
44077 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTTCCAAAGAACATAGGTA
* *
44108 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGT-TCCAAAGAACATAGGTA
* * **
44139 ATTCTGTCCATATGCTCCGTAGAACATAGGTA
1 A-ACTGTCCATATGTTCCAAAGAACATAGGTA
44171 TACCCTCGAC
Statistics
Matches: 77, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
31 53 0.69
32 24 0.31
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (31 bp):
AACTGTCCATATGTTCCAAAGAACATAGGTA
Found at i:44162 original size:63 final size:62
Alignment explanation
Indices: 44047--44173 Score: 175
Period size: 63 Copynumber: 2.0 Consensus size: 62
44037 ATCCTTGGCA
* * *
44047 ACTGTCCATAGGTTCCAAAGAACCTAGGTAAACTGTCCATATGTTCCTTAGAACATAGGTAT
1 ACTGTCCATAGGTTCCAAAGAACATAGGTAAACTGTCCATATGCTCCGTAGAACATAGGTAT
* * *
44109 ACTGTCCATATGTCTCGAAAG-ACATAGGTAATTCTGTCCATATGCTCCGTAGAACATAGGTAT
1 ACTGTCCATAGGT-TCCAAAGAACATAGGTAA-ACTGTCCATATGCTCCGTAGAACATAGGTAT
44172 AC
1 AC
44174 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
62 21 0.37
63 36 0.63
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (62 bp):
ACTGTCCATAGGTTCCAAAGAACATAGGTAAACTGTCCATATGCTCCGTAGAACATAGGTAT
Found at i:45417 original size:64 final size:63
Alignment explanation
Indices: 45265--45420 Score: 151
Period size: 63 Copynumber: 2.5 Consensus size: 63
45255 CAATAAGGGT
* **
45265 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATACATTCGATGTTGTATATTATTGGG
1 ATGCATCGATGCACTACCTG-TGCATCGATGCATAAAATACATTCGATGTTGTATATTATTAAG
* * * * *
45328 ATGCATCGATGCA-TGCCTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCTATT-TTAAA
1 ATGCATCGATGCACTACC-TGTGCATCGATGCA-TAAAATACATTCGATGTTGTATATTATT--A
45389 AG
62 AG
45391 AGTGCATCGATGCACTACCTGTGCATCGAT
1 A-TGCATCGATGCACTACCTGTGCATCGAT
45421 ACACCTTCAA
Statistics
Matches: 76, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
61 2 0.03
62 6 0.08
63 41 0.54
64 24 0.32
65 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (63 bp):
ATGCATCGATGCACTACCTGTGCATCGATGCATAAAATACATTCGATGTTGTATATTATTAAG
Done.