Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006854.1 Hibiscus syriacus cultivar Beakdansim tig00017440_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: 65219
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:2160 original size:31 final size:31
Alignment explanation
Indices: 2124--2183 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
2114 TCAATAGGTG
* * *
2124 ATGGAACTTATTTTGGATCAATATGTTGTAT
1 ATGGAACTTATGTTGGATAAATATCTTGTAT
*
2155 ATGGAACTTATGTTGTATAAATATCTTGT
1 ATGGAACTTATGTTGGATAAATATCTTGT
2184 TTGAATGAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.07, G:0.18, T:0.45
Consensus pattern (31 bp):
ATGGAACTTATGTTGGATAAATATCTTGTAT
Found at i:10761 original size:21 final size:20
Alignment explanation
Indices: 10721--10762 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10711 CCAACTTACA
*
10721 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
10741 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
10762 A
1 A
10763 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:10974 original size:21 final size:20
Alignment explanation
Indices: 10934--10975 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
10924 CCAACTTACA
*
10934 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
10954 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
10975 A
1 A
10976 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:11035 original size:213 final size:213
Alignment explanation
Indices: 10668--11093 Score: 825
Period size: 213 Copynumber: 2.0 Consensus size: 213
10658 TGCCATGTCA
10668 CTTTTCAACCATTATTAGTGCCAACTATGAACCATTATTGTTGCCAACTTACAATGCATTATGAA
1 CTTTTCAACCATTATTAGTGCCAACTATGAACCATTATTGTTGCCAACTTACAATGCATTATGAA
10733 CCATTATTATGCATTATACAACTATTATTAGTTGTATGACAACTAATAATTTTGCATGACAACTA
66 CCATTATTATGCATTATACAACTATTATTAGTTGTATGACAACTAATAATTTTGCATGACAACTA
*
10798 ATAATCTCCCACTTGAAGATTTGATTAGAATAATCATATCTTCACACCATTCTTTCTACCTTGTA
131 ATAATCTCCCACTTGAAGATTTGATTAGAATAATCATATCTTCACACCATTATTTCTACCTTGTA
10863 CCTTCATGTTGCTTACGT
196 CCTTCATGTTGCTTACGT
* *
10881 CTTTTCAACCATTATTAGTGTCAACTATGAATCATTATTGTTGCCAACTTACAATGCATTATGAA
1 CTTTTCAACCATTATTAGTGCCAACTATGAACCATTATTGTTGCCAACTTACAATGCATTATGAA
10946 CCATTATTATGCATTATACAACTATTATTAGTTGTATGACAACTAATAATTTTGCATGACAACTA
66 CCATTATTATGCATTATACAACTATTATTAGTTGTATGACAACTAATAATTTTGCATGACAACTA
11011 ATAATCTCCCACTTGAAGATTTGATTAGAATAATCATATCTTCACACCATTATTTCTACCTTGTA
131 ATAATCTCCCACTTGAAGATTTGATTAGAATAATCATATCTTCACACCATTATTTCTACCTTGTA
11076 CCTTCATGTTGCTTACGT
196 CCTTCATGTTGCTTACGT
11094 TTCTGATAGG
Statistics
Matches: 210, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
213 210 1.00
ACGTcount: A:0.32, C:0.20, G:0.10, T:0.38
Consensus pattern (213 bp):
CTTTTCAACCATTATTAGTGCCAACTATGAACCATTATTGTTGCCAACTTACAATGCATTATGAA
CCATTATTATGCATTATACAACTATTATTAGTTGTATGACAACTAATAATTTTGCATGACAACTA
ATAATCTCCCACTTGAAGATTTGATTAGAATAATCATATCTTCACACCATTATTTCTACCTTGTA
CCTTCATGTTGCTTACGT
Found at i:14431 original size:15 final size:15
Alignment explanation
Indices: 14411--14444 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
14401 ACTGGTGGTC
14411 AAAGGATATGCTCAA
1 AAAGGATATGCTCAA
14426 AAAGGATATGCTCAA
1 AAAGGATATGCTCAA
14441 AAAG
1 AAAG
14445 AAGGTATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.21, T:0.18
Consensus pattern (15 bp):
AAAGGATATGCTCAA
Found at i:20785 original size:21 final size:20
Alignment explanation
Indices: 20745--20786 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
20735 CTAACTTACA
*
20745 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
20765 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
20786 A
1 A
20787 ATTATATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:25494 original size:2 final size:2
Alignment explanation
Indices: 25487--25515 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
25477 GAGTTTTGAT
25487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25516 TGTTCTAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:26193 original size:60 final size:60
Alignment explanation
Indices: 26129--26259 Score: 131
Period size: 60 Copynumber: 2.2 Consensus size: 60
26119 GTTCAGTGAT
* * *
26129 CATTTTGTAACTTTTAATAGTTGGGGGACTTAACAAAGTAACATCC-TATAGTCAAAGGAC
1 CATTTTGTAACTTTTAATAGTTGAGGGACTTAACAAAGCAA-AGCCATATAGTCAAAGGAC
* ** * * * *
26189 CA-TTTATATTTTTTTAATTGTTGAGGGACTTGATAAAGCAAAGCCATATAGTCAGAGGAC
1 CATTTTGTA-ACTTTTAATAGTTGAGGGACTTAACAAAGCAAAGCCATATAGTCAAAGGAC
26249 CATTTGTGTAA
1 CATTT-TGTAA
26260 TTTACCCTAA
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
59 8 0.15
60 42 0.76
61 2 0.04
62 3 0.05
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTTGAGGGACTTAACAAAGCAAAGCCATATAGTCAAAGGAC
Found at i:27257 original size:21 final size:21
Alignment explanation
Indices: 27233--27274 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
27223 CAGCAGCTTG
27233 GAGTTGAAGAAAGAGGATCCA
1 GAGTTGAAGAAAGAGGATCCA
27254 GAGTTGAAGAAAGAGGATCCA
1 GAGTTGAAGAAAGAGGATCCA
27275 CTGAATGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.33, T:0.14
Consensus pattern (21 bp):
GAGTTGAAGAAAGAGGATCCA
Found at i:27658 original size:66 final size:65
Alignment explanation
Indices: 27552--27685 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 65
27542 TAGAGGAATT
* * * *
27552 TTGGAAAGAAGATGAGAGAGAGCAAACGAGCTGAAGAAAGGTGGGGATTACACACACTCACTTTT
1 TTGGAAAGAAGATCAGAGAGAACAAACGAGCTGAAGAAAGGTGGGGATCACACAC-CTCACTTTC
27617 C
65 C
*
27618 TTGGAAAGAAGATCAGAGAGAACAAACGAGTTGAAGAAAGGTGGGGATCACACACCTCACTTTCC
1 TTGGAAAGAAGATCAGAGAGAACAAACGAGCTGAAGAAAGGTGGGGATCACACACCTCACTTTCC
27683 TTG
1 TTG
27686 ATCTCTCTCG
Statistics
Matches: 63, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 12 0.19
66 51 0.81
ACGTcount: A:0.37, C:0.16, G:0.28, T:0.19
Consensus pattern (65 bp):
TTGGAAAGAAGATCAGAGAGAACAAACGAGCTGAAGAAAGGTGGGGATCACACACCTCACTTTCC
Found at i:29682 original size:17 final size:17
Alignment explanation
Indices: 29662--29697 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
29652 AAGTCAACGA
*
29662 TCAATGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
29679 TCAACGGTCGGGTCGGG
1 TCAACGGTCGGGTCGGG
29696 TC
1 TC
29698 GGGTCAGTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.22, G:0.44, T:0.22
Consensus pattern (17 bp):
TCAACGGTCGGGTCGGG
Found at i:29695 original size:22 final size:24
Alignment explanation
Indices: 29667--29721 Score: 78
Period size: 22 Copynumber: 2.4 Consensus size: 24
29657 AACGATCAAT
29667 GGTCGGGTCGGGTCA-ACG-GTCG
1 GGTCGGGTCGGGTCAGACGAGTCG
*
29689 GGTCGGGTCGGGTCAGTCGAGTCG
1 GGTCGGGTCGGGTCAGACGAGTCG
*
29713 AGTCGGGTC
1 GGTCGGGTC
29722 AGACCTGTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 15 0.52
23 2 0.07
24 12 0.41
ACGTcount: A:0.09, C:0.22, G:0.49, T:0.20
Consensus pattern (24 bp):
GGTCGGGTCGGGTCAGACGAGTCG
Found at i:29712 original size:19 final size:19
Alignment explanation
Indices: 29668--29723 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 19
29658 ACGATCAATG
*
29668 GTCGGGTCGGGTCAACGGTCGG
1 GTCGGGTCGGGTC-A--GTCGA
29690 GTCGGGTCGGGTCAGTCGA
1 GTCGGGTCGGGTCAGTCGA
*
29709 GTCGAGTCGGGTCAG
1 GTCGGGTCGGGTCAG
29724 ACCTGTTCAG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
19 18 0.56
21 1 0.03
22 13 0.41
ACGTcount: A:0.11, C:0.21, G:0.48, T:0.20
Consensus pattern (19 bp):
GTCGGGTCGGGTCAGTCGA
Found at i:32775 original size:2 final size:2
Alignment explanation
Indices: 32768--32806 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32758 ATTAAAGCTC
32768 AT AT AT AT 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 AT AT AT AT A
32807 AGACCAGATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34937 original size:60 final size:60
Alignment explanation
Indices: 34841--35001 Score: 184
Period size: 60 Copynumber: 2.7 Consensus size: 60
34831 AAAGTATGAC
* * * * *
34841 ATCATTTTAAATTAGTCCCTAAACTTCTAAATATTTCAATTCAATTCCTAAACTATGA-TT
1 ATCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTC-ATCCCTAAACTATGACTT
* *
34901 ATCATTCTAAATTAGTCCATAAAGTTTTGAACATTTCAATTTCATCCCTAAACTATGACTT
1 ATCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAA-TTCATCCCTAAACTATGACTT
* * *
34962 -T-ATTCTAAATTGGTCCCTAAACTTTTTGAGCATTCCAATT
1 ATCATTCTAAATTAGTCCCTAAAC-TTTTGAACATTTCAATT
35002 TTAGCACAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
59 20 0.23
60 61 0.71
61 5 0.06
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.41
Consensus pattern (60 bp):
ATCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCAATTCATCCCTAAACTATGACTT
Found at i:35287 original size:59 final size:59
Alignment explanation
Indices: 35133--35306 Score: 215
Period size: 60 Copynumber: 2.9 Consensus size: 59
35123 TATTTAGATG
* * * * ** *
35133 AATTTGAGGATGAAATTGGAAGACTCAAAAGTTTGGGGACCAATTTAGAAAGAGAGTCAT
1 AATTT-AGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* *
35193 ACTTTATGGATGAAATT-AGAATATTTAAAAGTTTAAGGACTAATTTAGAATGAGAGTCAT
1 AATTTA-GGATGAAATTGA-AATATTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* *
35253 AATTTAGGATGAAATTGAAATATTTAAAATTTTAAGGACCAATTTAAAATGAGA
1 AATTTAGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGAGA
35307 ATTATAGTTT
Statistics
Matches: 98, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
59 44 0.45
60 54 0.55
ACGTcount: A:0.43, C:0.06, G:0.20, T:0.31
Consensus pattern (59 bp):
AATTTAGGATGAAATTGAAATATTTAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
Found at i:47250 original size:16 final size:15
Alignment explanation
Indices: 47213--47252 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
47203 AAAATTATAT
*
47213 AAAAAGTAAAACTTA
1 AAAAAATAAAACTTA
*
47228 ACAAAATAAAACTTA
1 AAAAAATAAAACTTA
47243 AAACAAATAA
1 AAA-AAATAA
47253 TATAGATTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.70, C:0.10, G:0.03, T:0.17
Consensus pattern (15 bp):
AAAAAATAAAACTTA
Found at i:55576 original size:32 final size:32
Alignment explanation
Indices: 55540--55698 Score: 165
Period size: 32 Copynumber: 5.0 Consensus size: 32
55530 AATATATTGA
* * *
55540 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* *
55572 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* * * * * * * *
55604 GGCTTTAGAGTCTACTTAAGGAAATGCCCTGG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
* * *
55636 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
*
55668 GGCCTAAGAGCTTACCTAAGGAAGTACCTTA
1 GGCCTAAGAGCCTACCTAAGGAAGTACCTTA
55699 AGGCTTCAGA
Statistics
Matches: 98, Mismatches: 29, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
32 98 1.00
ACGTcount: A:0.28, C:0.24, G:0.27, T:0.21
Consensus pattern (32 bp):
GGCCTAAGAGCCTACCTAAGGAAGTACCTTAG
Found at i:55688 original size:96 final size:96
Alignment explanation
Indices: 55540--55741 Score: 368
Period size: 96 Copynumber: 2.1 Consensus size: 96
55530 AATATATTGA
55540 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
1 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
* *
55605 GCTTTAGAGTCTACTTAAGGAAATGCCCTGG
66 GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
55636 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
1 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
*
55701 GCTTCAGAGTCTACTCAAGGAAATGCCTTGG
66 GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
*
55732 GGCCTCAGAG
1 GGCCTGAGAG
55742 TTTGCCCAAG
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 102 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (96 bp):
GGCCTGAGAGCCTACCCAAGGGAGTACCTTAGGGCCTAAGAGCTTACCTAAGGAAGTACCTTAAG
GCTTCAGAGTCTACTCAAGGAAATGCCCTGG
Found at i:55752 original size:32 final size:32
Alignment explanation
Indices: 55540--55741 Score: 143
Period size: 32 Copynumber: 6.3 Consensus size: 32
55530 AATATATTGA
* * *
55540 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
55572 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * ** * * *
55604 GGCTTTAGAGTCTACTTAAGGAAATGCCCTGG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * *
55636 GGCCTGAGAGCCTACCCAAGGGAGTACCTTAG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
55668 GGCCTAAGAGCTTACCTAAGGAAGTACCTTAA
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
* * * * *
55700 GGCTTCAGAGTCTACTCAAGGAAATGCCTTGG
1 GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
55732 GGCCTCAGAG
1 GGCCTCAGAG
55742 TTTGCCCAAG
Statistics
Matches: 129, Mismatches: 41, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
32 129 1.00
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (32 bp):
GGCCTCAGAGCCTACCCAAGGAAATACCTTAG
Found at i:56867 original size:28 final size:28
Alignment explanation
Indices: 56836--56902 Score: 109
Period size: 27 Copynumber: 2.4 Consensus size: 28
56826 ATAGGGATTG
56836 GGGGTATTTTAGGTCATTTTACACTTCA
1 GGGGTATTTTAGGTCATTTTACACTTCA
*
56864 GGGGTATTTT-GGTCATTTTACAGTTCA
1 GGGGTATTTTAGGTCATTTTACACTTCA
*
56891 AGGGTATTTTAG
1 GGGGTATTTTAG
56903 TCTTTTCTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 25 0.69
28 11 0.31
ACGTcount: A:0.21, C:0.10, G:0.25, T:0.43
Consensus pattern (28 bp):
GGGGTATTTTAGGTCATTTTACACTTCA
Found at i:60203 original size:16 final size:16
Alignment explanation
Indices: 60164--60206 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
60154 GTGTATAATT
* *
60164 ATAATAATTT-AAGTG
1 ATAATAATTTAAAATA
60179 ATAATTAATTTAAAATA
1 ATAA-TAATTTAAAATA
60196 ATAATAATTTA
1 ATAATAATTTA
60207 TTCTTGATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 4 0.17
16 13 0.54
17 7 0.29
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (16 bp):
ATAATAATTTAAAATA
Found at i:60634 original size:11 final size:11
Alignment explanation
Indices: 60615--60652 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
60605 AAGAAAAGAA
*
60615 AATTCTTTTTG
1 AATTGTTTTTG
60626 AATTGTTTTTG
1 AATTGTTTTTG
*
60637 AGTTG-TTTTG
1 AATTGTTTTTG
60647 AATTGT
1 AATTGT
60653 GTTTAACCTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.18, C:0.03, G:0.18, T:0.61
Consensus pattern (11 bp):
AATTGTTTTTG
Found at i:61115 original size:43 final size:43
Alignment explanation
Indices: 61061--61399 Score: 407
Period size: 43 Copynumber: 7.9 Consensus size: 43
61051 ACACCGTAAT
61061 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
61104 AGGTCGAGATCTATAGTGGCGTTTTTGGAACAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* *
61147 AGGTCAACATCTATAGCGGCGTTTTTGTAACAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * * *
61190 AGGTCAACATATATAGCGGCATTTTTGTAACACACG-CGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * *
61232 AGGTC-AGATCTATAGCGGCATTTTTGGAATAAACGCCGTAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
* * * *
61274 AGGTCGATATATATAGCGGCGTTTTTGGAATAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
** * * *
61317 A-GTTGATATCTATAGCGGCGTTTTCGGGAAAAAACGCCGCAAA
1 AGGTCAAGATCTATAGCGGCGTTTT-TGGAACAAACGCCGCAAA
* * * *
61360 ATGAC-AGATCTATAGAGGCGTTTTTGGATTCAAACGCCGC
1 AGGTCAAGATCTATAGCGGCGTTTTTGGA-ACAAACGCCGC
61400 TAATTACCTT
Statistics
Matches: 261, Mismatches: 30, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
41 25 0.10
42 45 0.17
43 190 0.73
44 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.24
Consensus pattern (43 bp):
AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAACGCCGCAAA
Found at i:64776 original size:40 final size:39
Alignment explanation
Indices: 64707--64837 Score: 133
Period size: 40 Copynumber: 3.3 Consensus size: 39
64697 ACTTAAACTT
*
64707 TAGCGGCGTTTTTAAACACAAACGCCACTAAAGTACGAGTCTA
1 TAGCGGCG--TTTAAA-ATAAACGCCACTAAAGTA-GAGTCTA
*
64750 TAGCGGCGTTTAAAATAAACGCCACTAAA--ATAGTCTA
1 TAGCGGCGTTTAAAATAAACGCCACTAAAGTAGAGTCTA
** * *
64787 TAGCGGCGTTT-GTATAAAACGCCATTAGAGTATGAGTCTA
1 TAGCGGCGTTTAAAAT-AAACGCCACTAAAGTA-GAGTCTA
64827 TAGCGGCGTTT
1 TAGCGGCGTTT
64838 GTATAAAAAT
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
36 2 0.03
37 28 0.36
38 1 0.01
39 1 0.01
40 31 0.40
41 6 0.08
43 8 0.10
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (39 bp):
TAGCGGCGTTTAAAATAAACGCCACTAAAGTAGAGTCTA
Found at i:64838 original size:40 final size:39
Alignment explanation
Indices: 64726--64930 Score: 149
Period size: 40 Copynumber: 5.3 Consensus size: 39
64716 TTTTAAACAC
* * *
64726 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTT-AAAA
1 AAACGCCACT-AAGTATGAGTCTATAGCGGCGTTTGTATA
*
64765 TAAACGCCACTAA-AAT-AGTCTATAGCGGCGTTTGTATA
1 -AAACGCCACTAAGTATGAGTCTATAGCGGCGTTTGTATA
*
64803 AAACGCCATTAGAGTATGAGTCTATAGCGGCGTTTGTATAA
1 AAACGCCACTA-AGTATGAGTCTATAGCGGCGTTTGTAT-A
* * * *
64844 AAATGCCACTAA--AT-ACTCTAT-GCAGCGTTTTTGA-A
1 AAACGCCACTAAGTATGAGTCTATAGCGGCGTTTGT-ATA
* * * * *
64879 AAATGCCACTATAG-ATGAATCTATTGTGGCGTTTTTATA
1 AAACGCCACTA-AGTATGAGTCTATAGCGGCGTTTGTATA
*
64918 TAAACGCCGCTAA
1 -AAACGCCACTAA
64931 AGTACTACTC
Statistics
Matches: 137, Mismatches: 16, Indels: 25
0.77 0.09 0.14
Matches are distributed among these distances:
35 12 0.09
36 10 0.07
37 36 0.26
38 13 0.09
39 15 0.11
40 41 0.30
41 10 0.07
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (39 bp):
AAACGCCACTAAGTATGAGTCTATAGCGGCGTTTGTATA
Found at i:64858 original size:77 final size:76
Alignment explanation
Indices: 64726--64970 Score: 192
Period size: 77 Copynumber: 3.1 Consensus size: 76
64716 TTTTAAACAC
*
64726 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTAAAATAAACGCCACTAAAATAGTCTATAGC
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTAAAATAAACGCCACTAAAATACTCTAT-GC
*
64791 GGCGTTTGTATA
65 AGCGTTTGTATA
* * * * *
64803 AAACGCCATTAGAGTATGAGTCTATAGCGGCGTTTGTATAA-AAATGCCACT-AAATACTCTATG
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TT-TAAAATAAACGCCACTAAAATACTCTATG
*
64866 CAGCGTTTTTGA-A
64 CAGCGTTTGT-ATA
* * * * * * * * * * *
64879 AAATGCCACTATAG-ATGAATCTATTGTGGCGTTTTTATATAAACGCCGCTAAAGTACTACTCTG
1 AAACGCCACTAAAGTACGAGTCTATAGCGGCG-TTTAAAATAAACGCCACTAAAATACT-CTATG
*
64943 TCACGACGTTTGTTAAA
64 -CA-G-CGTTTG-TATA
64960 AAACGCCACTA
1 AAACGCCACTA
64971 CTGATGAACC
Statistics
Matches: 134, Mismatches: 23, Indels: 18
0.77 0.13 0.10
Matches are distributed among these distances:
74 2 0.01
75 25 0.19
76 27 0.20
77 44 0.33
78 13 0.10
79 5 0.04
80 6 0.04
81 12 0.09
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (76 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTAAAATAAACGCCACTAAAATACTCTATGCA
GCGTTTGTATA
Done.