Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004750.1 Hibiscus syriacus cultivar Beakdansim tig00010721_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: 88094
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:7312 original size:14 final size:15
Alignment explanation
Indices: 7293--7328 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
7283 TATAATTTTC
7293 TTTT-AAATTTTTAT
1 TTTTAAAATTTTTAT
7307 TTTTAAAATTTTTA-
1 TTTTAAAATTTTTAT
7321 TTTTAAAA
1 TTTTAAAA
7329 AATTATTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
TTTTAAAATTTTTAT
Found at i:7317 original size:15 final size:14
Alignment explanation
Indices: 7288--7328 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
7278 AATTGTATAA
*
7288 TTTTCTTTT-AAAT
1 TTTTATTTTAAAAT
7301 TTTTATTTTTAAAAT
1 TTTTA-TTTTAAAAT
7316 TTTTATTTTAAAA
1 TTTTATTTTAAAA
7329 AATTATTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 4 0.16
14 12 0.48
15 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATTTTAAAAT
Found at i:7329 original size:15 final size:15
Alignment explanation
Indices: 7297--7329 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
7287 ATTTTCTTTT
*
7297 AAATTTTTATTTTTA
1 AAATTTTTATTTTAA
7312 AAATTTTTATTTTAA
1 AAATTTTTATTTTAA
7327 AAA
1 AAA
7330 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (15 bp):
AAATTTTTATTTTAA
Found at i:10441 original size:171 final size:170
Alignment explanation
Indices: 10069--10558 Score: 554
Period size: 177 Copynumber: 2.8 Consensus size: 170
10059 ACACAAGATG
* * * * *
10069 AGACTTAA-CCAACCACATTGTAAAACTAAACATCTAATTTCATAGATTTTGCATGCAAAAACCA
1 AGACTCAACCCAA-CACATTATAAAACTAAACATCT-ATTTCAAAGTTTTTGCATGCAAAAACTA
* * *
10133 AACCTTATTCATAAGTAATTTTAACACGAAA-ATCGCACTTACAAGCATATGATGTCTTGCATAG
64 AACCTTATTCATAAGTAATTTTAACAC-AAAGACCGCACTTTCAAGCATATGATG-C---C-T-T
* * * * *
10197 CCATAGTTGTAACTTGCAATAATATATGTACGTTATACAGCTCAAGACT
122 CCTTAGTTGTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* *
10246 AGACTCAACCCACCACATTATAAAACTAAACATCGTATTTCAAAGTTTTTGCATGCAAAAACTAC
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGTTTTTGCATGCAAAAACTAA
* * * * *
10311 ACTTTATTCCTATGAAATTTCAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
65 ACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
* *
10376 GTAACTTGCCACAATATATGTACATTACGCAGCCCAAGACT
130 GTAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
* * * * * *
10417 AGACTCAACCCAACTCATTATAAAACTAGACATCTTATCTCAAA-TATTTGCAAGCAAAATCTAA
1 AGACTCAACCCAACACATTATAAAACTAAACATC-TATTTCAAAGTTTTTGCATGCAAAAACTAA
** * * * *
10481 ACCTTATTCATAAGTAATTTTAATGCAAAGACCACACTTTCAAGCATGTGATGCATTGCTTAGTT
65 ACCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTT
10546 GTAACTTGCAACA
130 GTAACTTGCAACA
10559 GTGACACAGC
Statistics
Matches: 267, Mismatches: 43, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
170 82 0.31
171 81 0.30
172 1 0.00
173 1 0.00
176 4 0.01
177 94 0.35
178 4 0.01
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (170 bp):
AGACTCAACCCAACACATTATAAAACTAAACATCTATTTCAAAGTTTTTGCATGCAAAAACTAAA
CCTTATTCATAAGTAATTTTAACACAAAGACCGCACTTTCAAGCATATGATGCCTTCCTTAGTTG
TAACTTGCAACAATATATGTACATTACACAGCCCAAGACT
Found at i:17421 original size:2 final size:2
Alignment explanation
Indices: 17416--17446 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17406 ATATTTTTTT
17416 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17447 TAGTGGTTGG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17746 original size:35 final size:34
Alignment explanation
Indices: 17706--17818 Score: 154
Period size: 35 Copynumber: 3.2 Consensus size: 34
17696 AAAACAATCC
* *
17706 TCAATTTCATTATAAACCACAAATTCCAAAGTAAT
1 TCAATTTCATTCTAAACC-CAAATTCCAAAATAAT
17741 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCC-AAATTCCAAAATAAT
* * *
17776 TCAATTACATTCTAAAACCCAAATTCTAAAATACT
1 TCAATTTCATTCT-AAACCCAAATTCCAAAATAAT
17811 TCAATTTC
1 TCAATTTC
17819 TGTCTTTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
34 1 0.01
35 63 0.90
36 6 0.09
ACGTcount: A:0.43, C:0.22, G:0.01, T:0.34
Consensus pattern (34 bp):
TCAATTTCATTCTAAACCCAAATTCCAAAATAAT
Found at i:18916 original size:35 final size:34
Alignment explanation
Indices: 18868--18979 Score: 161
Period size: 35 Copynumber: 3.2 Consensus size: 34
18858 ATTCCTCCTT
* *
18868 AAATTGAAATATTTTAGAATTTGGGTTTTAGAATG
1 AAATTGAATTATTTTGGAATTTGGG-TTTAGAATG
*
18903 CAATTGAATTATTTTGGAATTTAGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
*
18938 AAATTGAATTACTTTGGAATTTGGGGTTTAGAATG
1 AAATTGAATTATTTTGGAATTT-GGGTTTAGAATG
18973 AAATTGA
1 AAATTGA
18980 GGAATGTTTT
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
35 67 0.96
36 3 0.04
ACGTcount: A:0.35, C:0.02, G:0.22, T:0.41
Consensus pattern (34 bp):
AAATTGAATTATTTTGGAATTTGGGTTTAGAATG
Found at i:20082 original size:26 final size:24
Alignment explanation
Indices: 20040--20089 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
20030 GTCTTGGATA
* *
20040 TATATATACAAATATTATTTTATT
1 TATATATACAAAAATTATTATATT
20064 TATATATACAATCAAATTATTATATT
1 TATATATACAA--AAATTATTATATT
20090 ATTCAGGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 11 0.50
26 11 0.50
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (24 bp):
TATATATACAAAAATTATTATATT
Found at i:21563 original size:42 final size:42
Alignment explanation
Indices: 21504--21587 Score: 168
Period size: 42 Copynumber: 2.0 Consensus size: 42
21494 AAAATTATCA
21504 GACACACTGAGCTTGCATGGTTTATGTAAATGGAGAGTAAAG
1 GACACACTGAGCTTGCATGGTTTATGTAAATGGAGAGTAAAG
21546 GACACACTGAGCTTGCATGGTTTATGTAAATGGAGAGTAAAG
1 GACACACTGAGCTTGCATGGTTTATGTAAATGGAGAGTAAAG
21588 ATGGGTCATC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 42 1.00
ACGTcount: A:0.33, C:0.12, G:0.29, T:0.26
Consensus pattern (42 bp):
GACACACTGAGCTTGCATGGTTTATGTAAATGGAGAGTAAAG
Found at i:29748 original size:60 final size:60
Alignment explanation
Indices: 29599--29756 Score: 160
Period size: 60 Copynumber: 2.6 Consensus size: 60
29589 ATTGGTTCTT
* * * *
29599 AAACTTTTAAATATTACAATTCCATCCCTAAACTAT-TACTATCATTCTAAATTTATCCTC
1 AAACTTTTTAATATTTCAATTTCATCCC-AAACTATATACTATCATTCTAAATTGATCCTC
* * * *
29659 AAACTTTTTAATATTTTATTTTCATTCCCAAACTATATCCT-TCATTCTAAATTGGTCC-C
1 AAACTTTTTAATATTTCAATTTCA-TCCCAAACTATATACTATCATTCTAAATTGATCCTC
* * *
29718 TAAACTTTTTCAGTGTTTCAATTTCATCCCAAATTATAT
1 -AAACTTTTT-AATATTTCAATTTCATCCCAAACTATAT
29757 GTATATACTA
Statistics
Matches: 81, Mismatches: 13, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
59 1 0.01
60 62 0.77
61 18 0.22
ACGTcount: A:0.32, C:0.22, G:0.03, T:0.44
Consensus pattern (60 bp):
AAACTTTTTAATATTTCAATTTCATCCCAAACTATATACTATCATTCTAAATTGATCCTC
Found at i:30009 original size:60 final size:60
Alignment explanation
Indices: 29934--30060 Score: 150
Period size: 61 Copynumber: 2.1 Consensus size: 60
29924 ACTGAGGGTC
* * * *
29934 TAGTTTGAAGATGAAATTGGAATGA-TCAAAAGTTTAAGGACTAACTTAAAATGAGTATCA
1 TAGTTTGAAGATGAAATTGGAAT-ATTAAAAAGTTTAAGGACCAACTTAAAATGAGAATAA
* * *
29994 TAGTTTG-AGTATGAAATTGGAATATTTAAAAATTTTAGGGACCAATTTAAAATGAGAATAA
1 TAGTTTGAAG-ATGAAATTGGAATA-TTAAAAAGTTTAAGGACCAACTTAAAATGAGAATAA
30055 TAGTTT
1 TAGTTT
30061 AGGGACATAT
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
59 3 0.05
60 20 0.35
61 34 0.60
ACGTcount: A:0.43, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
TAGTTTGAAGATGAAATTGGAATATTAAAAAGTTTAAGGACCAACTTAAAATGAGAATAA
Found at i:34791 original size:31 final size:31
Alignment explanation
Indices: 34747--34817 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
34737 CATTTTGTAG
* *
34747 TTTGTACATGTGGTATGTGTCACAT-CATCAC
1 TTTGAACACGTGGTATGTGTCACATCCAT-AC
* *
34778 TTTGAACACGTGGTATGTGTCACGTCCGTAC
1 TTTGAACACGTGGTATGTGTCACATCCATAC
34809 TTTGAACAC
1 TTTGAACAC
34818 ATATAACTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.94
32 2 0.06
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (31 bp):
TTTGAACACGTGGTATGTGTCACATCCATAC
Found at i:40936 original size:6 final size:6
Alignment explanation
Indices: 40925--40949 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40915 CTCAACCATT
40925 CAAACC CAAACC CAAACC CAAACC C
1 CAAACC CAAACC CAAACC CAAACC C
40950 CCACGATCCG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (6 bp):
CAAACC
Found at i:42314 original size:91 final size:91
Alignment explanation
Indices: 42159--42329 Score: 229
Period size: 91 Copynumber: 1.9 Consensus size: 91
42149 AATTTGTAGC
* * *
42159 GGATTTTAACTTAAAATGTTACCATGTCTAATATAAAAAGTGATACAATTGGCAATAGTTTTAGT
1 GGATTTTAACTTAAAATGTTACCATGTCTAACATAAAAAGTGATACAATTAGCAATAATTTTAGT
42224 TACAATCGAGAATGTTACATTGTGGT
66 TACAATCGAGAATGTTACATTGTGGT
* * * * * *
42250 GGATTTTAACCTTAAAATGTT-GCATGTTTACCCTAAAAAGTTATA-AACTTAGTAATAATTTTA
1 GGATTTTAA-CTTAAAATGTTACCATGTCTAACATAAAAAGTGATACAA-TTAGCAATAATTTTA
42313 GTTACAATCGAGAATGT
64 GTTACAATCGAGAATGT
42330 CTTGAGGGTA
Statistics
Matches: 69, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
90 2 0.03
91 56 0.81
92 11 0.16
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.37
Consensus pattern (91 bp):
GGATTTTAACTTAAAATGTTACCATGTCTAACATAAAAAGTGATACAATTAGCAATAATTTTAGT
TACAATCGAGAATGTTACATTGTGGT
Found at i:42489 original size:21 final size:21
Alignment explanation
Indices: 42463--42505 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42453 CTTAGTAAAA
42463 TTTCCGATTATTGTCTTTTTT
1 TTTCCGATTATTGTCTTTTTT
*
42484 TTTCCGATTTTTGTCTTTTTT
1 TTTCCGATTATTGTCTTTTTT
42505 T
1 T
42506 CCGTCGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.07, C:0.14, G:0.09, T:0.70
Consensus pattern (21 bp):
TTTCCGATTATTGTCTTTTTT
Found at i:46452 original size:51 final size:51
Alignment explanation
Indices: 46332--46438 Score: 187
Period size: 51 Copynumber: 2.1 Consensus size: 51
46322 CATTTTAATT
* *
46332 TGCAATAACATATCATTTTTGGATTTTGATAGGCAATTTTTCTACAAAGGG
1 TGCAATAACATACCATTTTTGGATTTTGATAGGCAATTTTTCCACAAAGGG
*
46383 TGCAATAACATACCATTTTTGGATTTTGATATGCAATTTTTCCACAAAGGG
1 TGCAATAACATACCATTTTTGGATTTTGATAGGCAATTTTTCCACAAAGGG
46434 TGCAA
1 TGCAA
46439 ATAGCTCTTA
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (51 bp):
TGCAATAACATACCATTTTTGGATTTTGATAGGCAATTTTTCCACAAAGGG
Found at i:48630 original size:2 final size:2
Alignment explanation
Indices: 48623--48653 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
48613 ATTATCTTGA
48623 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48654 TATTCTACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54696 original size:20 final size:20
Alignment explanation
Indices: 54660--54697 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
54650 ATCCTATTTC
**
54660 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
54680 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
54698 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:58013 original size:18 final size:17
Alignment explanation
Indices: 57984--58060 Score: 57
Period size: 18 Copynumber: 4.4 Consensus size: 17
57974 ATAATATAAG
57984 TTTATATATAAACTATA
1 TTTATATATAAACTATA
*
58001 TTTATATTATAAATTATA
1 TTTATA-TATAAACTATA
**
58019 TAATTAT-TATAAGTTATA
1 T--TTATATATAAACTATA
* * * *
58037 TATATATATATATTATG
1 TTTATATATAAACTATA
58054 TTTATAT
1 TTTATAT
58061 GAATTATATA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
16 3 0.06
17 20 0.41
18 22 0.45
20 4 0.08
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTATATATAAACTATA
Found at i:58020 original size:20 final size:20
Alignment explanation
Indices: 57986--58045 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
57976 AATATAAGTT
*
57986 TATA-TATAAACTATAT-T-
1 TATATTATAAATTATATATA
58003 TATATTATAAATTATATA-A
1 TATATTATAAATTATATATA
*
58022 T-TATTATAAGTTATATATA
1 TATATTATAAATTATATATA
58041 TATAT
1 TATAT
58046 ATATTATGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
17 4 0.11
18 26 0.72
19 3 0.08
20 3 0.08
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATTATAAATTATATATA
Found at i:58129 original size:34 final size:33
Alignment explanation
Indices: 58091--58192 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 33
58081 ATATGTATAA
*
58091 ATATTAAAAATATATAATTTATAAACTATAATTT
1 ATATTAAAAATATATAATTTATAAACTATAA-CT
*
58125 ATATTAATATAGTGTATATATATATGTATAAACTATAACT
1 ATATTAA-A-A----ATATATA-ATTTATAAACTATAACT
*
58165 ATA-T-AAACTATAT-ATTTATAAACTATAA
1 ATATTAAAAATATATAATTTATAAACTATAA
58193 AAAAATTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 18
0.72 0.05 0.23
Matches are distributed among these distances:
30 14 0.25
32 5 0.09
34 7 0.12
35 1 0.02
36 2 0.04
37 1 0.02
38 1 0.02
39 1 0.02
40 11 0.19
41 14 0.25
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (33 bp):
ATATTAAAAATATATAATTTATAAACTATAACT
Found at i:58161 original size:15 final size:15
Alignment explanation
Indices: 58143--58191 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
58133 ATAGTGTATA
*
58143 TATATATGTATAAAC
1 TATATATATATAAAC
58158 TATA-ACTATATAAAC
1 TATATA-TATATAAAC
*
58173 TATATATTTATAAAC
1 TATATATATATAAAC
58188 TATA
1 TATA
58192 AAAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
14 1 0.03
15 28 0.93
16 1 0.03
ACGTcount: A:0.49, C:0.08, G:0.02, T:0.41
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:58690 original size:2 final size:2
Alignment explanation
Indices: 58683--58739 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
58673 TATGTTTAAT
* * * *
58683 TA TA TA TA TA AA TT TA TG TA TA TA CT- TT 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
58725 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
58740 TATTCAAGTG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
1 1 0.02
2 44 0.96
3 1 0.02
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (2 bp):
TA
Found at i:59042 original size:2 final size:2
Alignment explanation
Indices: 59035--59091 Score: 96
Period size: 2 Copynumber: 28.0 Consensus size: 2
59025 TACTTTTAGT
59035 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
*
59077 TA AA CTA TA TA TA TA
1 TA TA -TA TA TA TA TA
59092 AAATATAGCT
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 51 0.98
3 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:59355 original size:20 final size:20
Alignment explanation
Indices: 59316--59363 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
59306 TATAGTACAT
* *
59316 GTATGTATAAACAATGTATA
1 GTATATATAAACAATATATA
*
59336 GTATATATAAACTATATATA
1 GTATATATAAACAATATATA
59356 -TATATATA
1 GTATATATA
59364 CACATACACC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 8 0.32
20 17 0.68
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (20 bp):
GTATATATAAACAATATATA
Found at i:59402 original size:2 final size:2
Alignment explanation
Indices: 59332--59393 Score: 52
Period size: 2 Copynumber: 30.0 Consensus size: 2
59322 ATAAACAATG
* * * * **
59332 TA TA GTA TA TA TA AA CTA TA TA TA TA TA TA TA CA CA TA CA CC TA
1 TA TA -TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59376 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
59394 AACTATATAA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 47 0.94
3 3 0.06
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (2 bp):
TA
Found at i:59499 original size:14 final size:14
Alignment explanation
Indices: 59482--59536 Score: 67
Period size: 14 Copynumber: 3.9 Consensus size: 14
59472 TATATAAATC
*
59482 CTAAATCATAAACT
1 CTAAACCATAAACT
*
59496 CTAAACCCTAAACT
1 CTAAACCATAAACT
*
59510 TTAAACCATAAA-T
1 CTAAACCATAAACT
59523 ACTAAACCATAAAC
1 -CTAAACCATAAAC
59537 CATAAACCCT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
13 1 0.03
14 33 0.97
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.24
Consensus pattern (14 bp):
CTAAACCATAAACT
Found at i:59521 original size:21 final size:21
Alignment explanation
Indices: 59475--59548 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
59465 TATAGTTTAT
* *
59475 ATAAATCCTAAATCATAAACTC
1 ATAAACCCTAAACCATAAAC-C
**
59497 -TAAACCCTAAACTTTAAACC
1 ATAAACCCTAAACCATAAACC
**
59517 ATAAATACTAAACCATAAACC
1 ATAAACCCTAAACCATAAACC
59538 ATAAACCCTAA
1 ATAAACCCTAA
59549 TATAAATAGA
Statistics
Matches: 41, Mismatches: 10, Indels: 3
0.76 0.19 0.06
Matches are distributed among these distances:
20 1 0.02
21 40 0.98
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (21 bp):
ATAAACCCTAAACCATAAACC
Found at i:60795 original size:14 final size:14
Alignment explanation
Indices: 60776--60868 Score: 80
Period size: 14 Copynumber: 6.6 Consensus size: 14
60766 TAAAATATAG
* *
60776 AAACCCTAAGTCTT
1 AAACCCTAAATCAT
60790 AAACCCTAAATCAT
1 AAACCCTAAATCAT
*
60804 AAACCCTAAATCCT
1 AAACCCTAAATCAT
** *
60818 AAACTTTAAACCAT
1 AAACCCTAAATCAT
* *
60832 AATCCATAAA-CACT
1 AAACCCTAAATCA-T
* *
60846 AAACCATAAACCAT
1 AAACCCTAAATCAT
60860 AAACCCTAA
1 AAACCCTAA
60869 TGTAAATGGA
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
13 2 0.03
14 61 0.94
15 2 0.03
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (14 bp):
AAACCCTAAATCAT
Found at i:60855 original size:7 final size:7
Alignment explanation
Indices: 60789--60864 Score: 66
Period size: 7 Copynumber: 10.9 Consensus size: 7
60779 CCCTAAGTCT
*
60789 TAAACCC
1 TAAACCA
*
60796 TAAATCA
1 TAAACCA
*
60803 TAAACCC
1 TAAACCA
60810 TAAATCC-
1 TAAA-CCA
**
60817 TAAACTT
1 TAAACCA
60824 TAAACCA
1 TAAACCA
*
60831 TAATCCA
1 TAAACCA
60838 TAAA-CA
1 TAAACCA
60844 CTAAACCA
1 -TAAACCA
60852 TAAACCA
1 TAAACCA
60859 TAAACC
1 TAAACC
60865 CTAATGTAAA
Statistics
Matches: 56, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
6 3 0.05
7 49 0.88
8 4 0.07
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (7 bp):
TAAACCA
Found at i:60868 original size:21 final size:21
Alignment explanation
Indices: 60789--60868 Score: 74
Period size: 21 Copynumber: 3.8 Consensus size: 21
60779 CCCTAAGTCT
* *
60789 TAAACCCTAAATCA-TAAACCC
1 TAAACCATAAA-CACTAAACCA
**
60810 TAAATCC-TAAACTTTAAACCA
1 TAAA-CCATAAACACTAAACCA
*
60831 TAATCCATAAACACTAAACCA
1 TAAACCATAAACACTAAACCA
*
60852 TAAACCATAAACCCTAA
1 TAAACCATAAACACTAA
60869 TGTAAATGGA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 3 0.06
21 44 0.90
22 2 0.04
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (21 bp):
TAAACCATAAACACTAAACCA
Found at i:61323 original size:16 final size:16
Alignment explanation
Indices: 61304--61342 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
61294 CAGATCATTT
61304 ACAGGTCAGGTTAAAA
1 ACAGGTCAGGTTAAAA
* *
61320 ACAGGTCATGTTGAAA
1 ACAGGTCAGGTTAAAA
61336 ACAGGTC
1 ACAGGTC
61343 GGGTAATACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.15, G:0.26, T:0.21
Consensus pattern (16 bp):
ACAGGTCAGGTTAAAA
Found at i:67846 original size:25 final size:24
Alignment explanation
Indices: 67818--67888 Score: 90
Period size: 24 Copynumber: 2.9 Consensus size: 24
67808 CTCAAAAAAA
* *
67818 AAAATTAGAAGTTCGATTGAAGCCT
1 AAAATTAG-AGCTCAATTGAAGCCT
*
67843 AAAATTTGAGCTCAATTGAAGCCT
1 AAAATTAGAGCTCAATTGAAGCCT
67867 AAAAGTT-GAGCTCAATTGAAGC
1 AAAA-TTAGAGCTCAATTGAAGC
67889 GAAAGAATAG
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
24 33 0.79
25 9 0.21
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (24 bp):
AAAATTAGAGCTCAATTGAAGCCT
Found at i:67862 original size:24 final size:24
Alignment explanation
Indices: 67833--67888 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
67823 TAGAAGTTCG
*
67833 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAAGTTGAGCTCA
67857 ATTGAAGCCTAAAAGTTGAGCTCA
1 ATTGAAGCCTAAAAGTTGAGCTCA
67881 ATTGAAGC
1 ATTGAAGC
67889 GAAAGAATAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.38, C:0.16, G:0.20, T:0.27
Consensus pattern (24 bp):
ATTGAAGCCTAAAAGTTGAGCTCA
Found at i:68483 original size:30 final size:30
Alignment explanation
Indices: 68449--68510 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
68439 GTTCAATGTC
68449 CGGTCCAATTTTAAAAACATTACTTTTGCA
1 CGGTCCAATTTTAAAAACATTACTTTTGCA
* *
68479 CGGTCCGATTTTGAAAACATTACTTTTGCA
1 CGGTCCAATTTTAAAAACATTACTTTTGCA
68509 CG
1 CG
68511 TTCATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (30 bp):
CGGTCCAATTTTAAAAACATTACTTTTGCA
Found at i:73501 original size:60 final size:59
Alignment explanation
Indices: 73348--73502 Score: 161
Period size: 60 Copynumber: 2.6 Consensus size: 59
73338 GTATTCAAGG
* * * * *
73348 TATGACCTTAATTTTAAAATGGTCTCTAAACTTTTAAATATTACAATTTTATCCTTAAAC
1 TATGACCTTCA-TTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTATCCCTAAAC
* * * * *
73408 TATGA-TTATCAATTTAAATTAGTTCTCAGACTTTTAAATATTACAATTTTATTCCCT-AAC
1 TATGACCT-TC-ATTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTA-TCCCTAAAC
73468 TATGACCTTCATTCTAAATTGGTCCCCAAACTTTT
1 TATGACCTTCATT-TAAATTGGTCCCCAAACTTTT
73503 TGAACATTCT
Statistics
Matches: 75, Mismatches: 15, Indels: 10
0.75 0.15 0.10
Matches are distributed among these distances:
59 4 0.05
60 65 0.87
61 6 0.08
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (59 bp):
TATGACCTTCATTTAAATTGGTCCCCAAACTTTTAAATATTACAATTTTATCCCTAAAC
Found at i:73751 original size:28 final size:27
Alignment explanation
Indices: 73660--73751 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 27
73650 TTGGGTATGG
**
73660 AATTTGAATATTCGAAAGACTGGGGACT
1 AATTTGAATATTC-AAAGTTTGGGGACT
* *
73688 AATTTAAAAATAAATTCATAGTTTGGGGA-T
1 AATTT--GAAT--ATTCAAAGTTTGGGGACT
73718 GCAATTTGAATATTCAAAAGTTTGGGGACT
1 --AATTTGAATATTC-AAAGTTTGGGGACT
73748 AATT
1 AATT
73752 AAAAACAATA
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
28 13 0.26
29 11 0.22
30 8 0.16
31 9 0.18
32 9 0.18
ACGTcount: A:0.38, C:0.08, G:0.21, T:0.34
Consensus pattern (27 bp):
AATTTGAATATTCAAAGTTTGGGGACT
Found at i:73805 original size:29 final size:28
Alignment explanation
Indices: 73768--73859 Score: 76
Period size: 29 Copynumber: 3.2 Consensus size: 28
73758 AATACCATAG
*
73768 TTTATGGATGAAATTAGAATGTTAAAAAA
1 TTTAAGGATGAAATTAGAATGTT-AAAAA
* * * * * *
73797 TTTAAGGATTAATTTAGAATGAGTCATAT
1 TTTAAGGATGAAATTAGAATG-TTAAAAA
* *
73826 TTTAAGGATGAAATTAGAATATTCAAAAG
1 TTTAAGGATGAAATTAGAATGTT-AAAAA
73855 TTTAA
1 TTTAA
73860 TGACCAATTT
Statistics
Matches: 47, Mismatches: 14, Indels: 4
0.72 0.22 0.06
Matches are distributed among these distances:
28 1 0.02
29 45 0.96
30 1 0.02
ACGTcount: A:0.45, C:0.02, G:0.16, T:0.37
Consensus pattern (28 bp):
TTTAAGGATGAAATTAGAATGTTAAAAA
Found at i:73838 original size:58 final size:58
Alignment explanation
Indices: 73763--73877 Score: 149
Period size: 58 Copynumber: 2.0 Consensus size: 58
73753 AAAACAATAC
* * ** *
73763 CATAGTTTATGGATGAAATTAGAATGTTAAAAAATTTAAGGATTAATTTAGAATGAGT
1 CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAGT
* * * *
73821 CATATTTTAAGGATGAAATTAGAATATTCAAAAGTTTAATGACCAATTTAAAATGAG
1 CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAG
73878 GGTTATAGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.44, C:0.04, G:0.17, T:0.35
Consensus pattern (58 bp):
CATAGTTTAAGGATGAAATTAGAATATTAAAAAATTTAAGGACCAATTTAAAATGAGT
Found at i:76637 original size:32 final size:32
Alignment explanation
Indices: 76601--76666 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
76591 TACCTTATAG
*
76601 AGTGCAGCTTAGGTTAAATTTGAAACATTGAA
1 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
76633 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
1 AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
76665 AG
1 AG
76667 GTTAGAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (32 bp):
AGTGCAGCTTAGGTTAAATCTGAAACATTGAA
Found at i:78883 original size:13 final size:13
Alignment explanation
Indices: 78865--78891 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
78855 TAACTATTCA
78865 AATTCAGAAAATG
1 AATTCAGAAAATG
78878 AATTCAGAAAATG
1 AATTCAGAAAATG
78891 A
1 A
78892 GTTTTAGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (13 bp):
AATTCAGAAAATG
Found at i:79138 original size:19 final size:19
Alignment explanation
Indices: 79114--79152 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
79104 AACTTTATTT
* *
79114 AAAAAATATTTATATTTTA
1 AAAAAATAATTAGATTTTA
79133 AAAAAATAATTAGATTTTA
1 AAAAAATAATTAGATTTTA
79152 A
1 A
79153 TTTTAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAATAATTAGATTTTA
Found at i:83030 original size:78 final size:78
Alignment explanation
Indices: 82901--83061 Score: 277
Period size: 78 Copynumber: 2.1 Consensus size: 78
82891 TTTATCGAGG
82901 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
1 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
82966 ATATATTACTATT
66 ATATATTACTATT
* * * *
82979 AAAAAATGAAATTAGAAGAAGAAAAAATCACCCTGTGAACAACTGTAGGATAGCAGACTTGTCAA
1 AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
*
83044 GTATATTACTATT
66 ATATATTACTATT
83057 AAAAA
1 AAAAA
83062 GCTTAGACTT
Statistics
Matches: 78, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.50, C:0.14, G:0.13, T:0.24
Consensus pattern (78 bp):
AAAAAATCAAATTAGAAGAAAAAAAAATCACCCTGTGAACAACTCTAGGATAACAGACTTGTCAA
ATATATTACTATT
Found at i:86080 original size:59 final size:60
Alignment explanation
Indices: 85927--86080 Score: 159
Period size: 60 Copynumber: 2.6 Consensus size: 60
85917 TATAATATCA
** * * * ***
85927 AAAAGTTTGGGGAATAATTTAGAATGAA-AGTCATAGTTTAGGGATGAAATTGAAATGTTT
1 AAAAGTTTAAGGACTAATTTAAAATGAAGA-TCATAGTTTAGGGATAAAATTGAAAACATT
* *
85987 AAAAGTTTAAGGACTAATTTAAAATGATGGTCATAGTTTAGGGATAAAATT-AAAACATT
1 AAAAGTTTAAGGACTAATTTAAAATGAAGATCATAGTTTAGGGATAAAATTGAAAACATT
* * * *
86046 CAAAGTTTAATGATTAATTTAAAATTAAGATCATA
1 AAAAGTTTAAGGACTAATTTAAAATGAAGATCATA
86081 ATTTGAAGTT
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
59 34 0.44
60 43 0.56
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (60 bp):
AAAAGTTTAAGGACTAATTTAAAATGAAGATCATAGTTTAGGGATAAAATTGAAAACATT
Done.