Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003965.1 Hibiscus syriacus cultivar Beakdansim tig00008592_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: 107155
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:159 original size:50 final size:50
Alignment explanation
Indices: 84--180 Score: 176
Period size: 50 Copynumber: 1.9 Consensus size: 50
74 CAGGGGAGAG
*
84 AGTTACAAGGAATTTCAGCCTGTTCAAACCGATATTTCTTTACAGCCATT
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCATT
*
134 AGTTACAAGGAATTTCAACTTGTTCAAACCGATATTTCTTTACAGCC
1 AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCC
181 TATCCTTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.31, C:0.22, G:0.13, T:0.34
Consensus pattern (50 bp):
AGTTACAAGGAATTTCAACCTGTTCAAACCGATATTTCTTTACAGCCATT
Found at i:2391 original size:14 final size:14
Alignment explanation
Indices: 2372--2399 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2362 ATAAGACTTA
2372 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
2386 TCTGTTTTCTACAG
1 TCTGTTTTCTACAG
2400 AAAATGTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
TCTGTTTTCTACAG
Found at i:5473 original size:18 final size:18
Alignment explanation
Indices: 5439--5473 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5429 TTAAATACAA
* *
5439 CGAATTCGGTGCTCCCAC
1 CGAATTCGGCGCCCCCAC
5457 CGAATTCGGCGCCCCCA
1 CGAATTCGGCGCCCCCA
5474 ATTCTTGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (18 bp):
CGAATTCGGCGCCCCCAC
Found at i:10480 original size:20 final size:19
Alignment explanation
Indices: 10441--10492 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
10431 TTTCCCAAAA
* *
10441 AGTTTCGACACTTTTCAAG
1 AGTTTCGAAACTTATCAAG
10460 AGTTTCGAAACTATATCAAG
1 AGTTTCGAAACT-TATCAAG
*
10480 AGTTTCAAAACTT
1 AGTTTCGAAACTT
10493 TCCCTAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (19 bp):
AGTTTCGAAACTTATCAAG
Found at i:18127 original size:29 final size:29
Alignment explanation
Indices: 18095--18152 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
18085 TTCATGCTGC
* * *
18095 AATTAATGTATAATTTATAATAGTTTATA
1 AATTAATATATAACTTATAATAATTTATA
*
18124 AATTATTATATAACTTATAATAATTTATA
1 AATTAATATATAACTTATAATAATTTATA
18153 TGATTTATTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (29 bp):
AATTAATATATAACTTATAATAATTTATA
Found at i:25267 original size:5 final size:5
Alignment explanation
Indices: 25252--25281 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
25242 TTTTAGCTTG
25252 TGAGTT TGAGT TGAGT TGAGT TGAGT TGAG
1 TGAG-T TGAGT TGAGT TGAGT TGAGT TGAG
25282 CTTACTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 20 0.83
6 4 0.17
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
TGAGT
Found at i:25749 original size:31 final size:31
Alignment explanation
Indices: 25706--25796 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 31
25696 AGTTATGTCG
*
25706 GGGATCATATTGCAAACGGACTAAATGTTGA
1 GGGACCATATTGCAAACGGACTAAATGTTGA
* *
25737 GGGACCATATTGCAAACAGACTAAATGTTGG
1 GGGACCATATTGCAAACGGACTAAATGTTGA
*
25768 GGGACCATATTGCAAACGAACTAAATGTT
1 GGGACCATATTGCAAACGGACTAAATGTT
25797 TGGGGATTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 55 1.00
ACGTcount: A:0.36, C:0.15, G:0.24, T:0.24
Consensus pattern (31 bp):
GGGACCATATTGCAAACGGACTAAATGTTGA
Found at i:32572 original size:33 final size:33
Alignment explanation
Indices: 32530--32624 Score: 190
Period size: 33 Copynumber: 2.9 Consensus size: 33
32520 AGTTGACAAG
32530 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
32563 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
32596 TTGGAAATTTCATCTTGGTTGGTGGCCAA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAA
32625 ACTTTGAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.21, C:0.15, G:0.25, T:0.39
Consensus pattern (33 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAACTTA
Found at i:34197 original size:31 final size:31
Alignment explanation
Indices: 34158--34225 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
34148 TAATATAATC
34158 CCCT-AACATTTAGTCCATTTGCAATATGGT
1 CCCTCAACATTTAGTCCATTTGCAATATGGT
* *
34188 CCCTCAACATTTAGTCCGTTTGTAATATGGT
1 CCCTCAACATTTAGTCCATTTGCAATATGGT
34219 CCC-CAAC
1 CCCTCAAC
34226 GTTACTTTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
30 8 0.23
31 27 0.77
ACGTcount: A:0.25, C:0.28, G:0.13, T:0.34
Consensus pattern (31 bp):
CCCTCAACATTTAGTCCATTTGCAATATGGT
Found at i:49762 original size:19 final size:20
Alignment explanation
Indices: 49738--49777 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
49728 TTATGACTTA
49738 TTTTTG-AAAATTTGAATTT
1 TTTTTGTAAAATTTGAATTT
**
49757 TTTTTGTTTAATTTGAATTT
1 TTTTTGTAAAATTTGAATTT
49777 T
1 T
49778 AGAGACATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (20 bp):
TTTTTGTAAAATTTGAATTT
Found at i:49853 original size:16 final size:18
Alignment explanation
Indices: 49834--49873 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
49824 AATGTCTCTT
49834 AAAAA-CAATTTTAAG-C
1 AAAAATCAATTTTAAGAC
*
49850 AAAAATCATTTTTAAGAC
1 AAAAATCAATTTTAAGAC
49868 AAAAAT
1 AAAAAT
49874 TAATCCGCGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 5 0.24
17 9 0.43
18 7 0.33
ACGTcount: A:0.57, C:0.10, G:0.05, T:0.28
Consensus pattern (18 bp):
AAAAATCAATTTTAAGAC
Found at i:50717 original size:2 final size:2
Alignment explanation
Indices: 50710--50741 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50700 CAATGCACAA
50710 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
50742 GTATGTATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52403 original size:13 final size:13
Alignment explanation
Indices: 52379--52433 Score: 65
Period size: 13 Copynumber: 4.2 Consensus size: 13
52369 AATTACTACC
*
52379 ATTAATACTAACA
1 ATTAATATTAACA
*
52392 ATTAACATTAACA
1 ATTAATATTAACA
* *
52405 ATTGATATTAGCA
1 ATTAATATTAACA
*
52418 ATTAATATTAATA
1 ATTAATATTAACA
52431 ATT
1 ATT
52434 CGTAATTACA
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (13 bp):
ATTAATATTAACA
Found at i:55287 original size:22 final size:20
Alignment explanation
Indices: 55256--55295 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
55246 TCTCATGTTA
55256 ATAAAAAAAATTTATCTTTTAC
1 ATAAAAAAAA--TATCTTTTAC
*
55278 ATAAATAAAATATCTTTT
1 ATAAAAAAAATATCTTTT
55296 GTTTTATTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (20 bp):
ATAAAAAAAATATCTTTTAC
Found at i:57599 original size:2 final size:2
Alignment explanation
Indices: 57592--57622 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
57582 ATGTATAAAC
57592 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
57623 CATAAAGTGT
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:58696 original size:24 final size:24
Alignment explanation
Indices: 58668--58749 Score: 94
Period size: 24 Copynumber: 3.4 Consensus size: 24
58658 TAGAGAAGTC
* *
58668 CAAGCAAAAGCCGAAGCCGATACT
1 CAAGCACAAGCCGAAGCCGAAACT
* *
58692 GAAGCACAAGCCCAAGACC-AAACT
1 CAAGCACAAGCCGAAG-CCGAAACT
* *
58716 CAAGCTCAAGCCGAAGCCGAAACC
1 CAAGCACAAGCCGAAGCCGAAACT
58740 CAAGCACAAG
1 CAAGCACAAG
58750 ACCAAGTTCA
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
23 2 0.04
24 43 0.91
25 2 0.04
ACGTcount: A:0.43, C:0.33, G:0.20, T:0.05
Consensus pattern (24 bp):
CAAGCACAAGCCGAAGCCGAAACT
Found at i:58773 original size:48 final size:48
Alignment explanation
Indices: 58675--58779 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 48
58665 GTCCAAGCAA
* ** * * *
58675 AAGCCGAAGCCGATACTGAAGCACAAGCCCAAGACCAAACTCAAGCTC
1 AAGCCGAAGCCGAAACCCAAGCACAAGACCAAGACCAAACCCAAGATC
** *
58723 AAGCCGAAGCCGAAACCCAAGCACAAGACCAAGTTCAAGCCCAAGATC
1 AAGCCGAAGCCGAAACCCAAGCACAAGACCAAGACCAAACCCAAGATC
*
58771 AAGCTGAAG
1 AAGCCGAAG
58780 GCCATGTCCA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.41, C:0.31, G:0.20, T:0.08
Consensus pattern (48 bp):
AAGCCGAAGCCGAAACCCAAGCACAAGACCAAGACCAAACCCAAGATC
Found at i:60432 original size:2 final size:2
Alignment explanation
Indices: 60425--60459 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60415 GCCTATCCAA
60425 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 A
60460 AATGTTAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:63642 original size:22 final size:22
Alignment explanation
Indices: 63609--63655 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
63599 CGAGACATTG
63609 ATAAAGAGGACCAAATGTGTGA
1 ATAAAGAGGACCAAATGTGTGA
63631 ATAACAGA-GACCAAATGTGTGA
1 ATAA-AGAGGACCAAATGTGTGA
63653 ATA
1 ATA
63656 TATCAAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 21 0.88
23 3 0.12
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (22 bp):
ATAAAGAGGACCAAATGTGTGA
Found at i:64728 original size:31 final size:31
Alignment explanation
Indices: 64693--64752 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
64683 CAAAATACAA
64693 AAGATATGACCACTTACATTTTTATTTAAAC
1 AAGATATGACCACTTACATTTTTATTTAAAC
* ** * *
64724 AAGATTTGGTCATTTTCATTTTTATTTAA
1 AAGATATGACCACTTACATTTTTATTTAA
64753 TTAAGATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (31 bp):
AAGATATGACCACTTACATTTTTATTTAAAC
Found at i:65232 original size:39 final size:39
Alignment explanation
Indices: 65189--65264 Score: 100
Period size: 39 Copynumber: 1.9 Consensus size: 39
65179 TATAAAATCC
*
65189 TAATTTATTAAATT-TTGACACCGTAACGTTCTAAATTCT
1 TAATTTATTAAATTATT-ACACAGTAACGTTCTAAATTCT
* * *
65228 TAATTTTTTAAATTATTTCACATTAACGTTCTAAATT
1 TAATTTATTAAATTATTACACAGTAACGTTCTAAATT
65265 ATTTTTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
39 30 0.94
40 2 0.06
ACGTcount: A:0.34, C:0.13, G:0.05, T:0.47
Consensus pattern (39 bp):
TAATTTATTAAATTATTACACAGTAACGTTCTAAATTCT
Found at i:65537 original size:24 final size:23
Alignment explanation
Indices: 65509--65575 Score: 68
Period size: 25 Copynumber: 2.9 Consensus size: 23
65499 ATATCATATA
65509 ATTTTATATATATTAACTTAAAAT
1 ATTTT-TATATATTAACTTAAAAT
65533 A-TTTT-TATATTAACTTATTAAAT
1 ATTTTTATATATTAACTTA--AAAT
*
65556 ATATTTTA-CTATTAACTTAA
1 AT-TTTTATATATTAACTTAA
65576 TTTATAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 12 0.32
22 1 0.03
23 9 0.24
24 1 0.03
25 14 0.38
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (23 bp):
ATTTTTATATATTAACTTAAAAT
Found at i:65541 original size:21 final size:22
Alignment explanation
Indices: 65517--65575 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
65507 TAATTTTATA
65517 TATATTAACTTAAAATAT-TTT
1 TATATTAACTTAAAATATATTT
65538 TATATTAACTTATTAAATATATTT
1 TATATTAACTTA--AAATATATTT
65562 TACTATTAACTTAA
1 TA-TATTAACTTAA
65576 TTTATAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (22 bp):
TATATTAACTTAAAATATATTT
Found at i:65559 original size:25 final size:24
Alignment explanation
Indices: 65526--65590 Score: 78
Period size: 25 Copynumber: 2.5 Consensus size: 24
65516 ATATATTAAC
65526 TTAAAATATTTTTA-TATTAACTTA
1 TTAAAATA-TTTTACTATTAACTTA
65550 TTAAATATATTTTACTATTAACTTAA
1 TTAAA-ATATTTTACTATTAACTT-A
65576 TTTATAAATATTTTA
1 -TTA-AAATATTTTA
65591 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
24 10 0.28
25 12 0.33
26 1 0.03
27 11 0.31
28 2 0.06
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (24 bp):
TTAAAATATTTTACTATTAACTTA
Found at i:71331 original size:6 final size:6
Alignment explanation
Indices: 71320--71392 Score: 128
Period size: 6 Copynumber: 12.2 Consensus size: 6
71310 GACACGTATT
*
71320 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
71368 ACCTCG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
71393 GCCGAGCCGA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:71400 original size:5 final size:5
Alignment explanation
Indices: 71390--71443 Score: 81
Period size: 5 Copynumber: 10.8 Consensus size: 5
71380 ACCACGACCA
* * *
71390 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGTGC CGTGC CGAGC CGAGA
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC
71440 CGAG
1 CGAG
71444 ACGGACGGAC
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.19, C:0.37, G:0.41, T:0.04
Consensus pattern (5 bp):
CGAGC
Found at i:77319 original size:6 final size:6
Alignment explanation
Indices: 77308--77386 Score: 140
Period size: 6 Copynumber: 13.2 Consensus size: 6
77298 GACACGTATT
*
77308 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCTCG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
*
77356 ACCTCG ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG ACCACG A
77387 GCCGAGCCGA
Statistics
Matches: 71, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.32, C:0.49, G:0.16, T:0.03
Consensus pattern (6 bp):
ACCACG
Found at i:77394 original size:5 final size:5
Alignment explanation
Indices: 77384--77427 Score: 61
Period size: 5 Copynumber: 8.8 Consensus size: 5
77374 ACCACGACCA
* * *
77384 CGAGC CGAGC CGAGC CGTGC CGTGC CGTGC CGAGC CGAGC CGAG
1 CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAGC CGAG
77428 ACGGACGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 37 1.00
ACGTcount: A:0.14, C:0.39, G:0.41, T:0.07
Consensus pattern (5 bp):
CGAGC
Found at i:77700 original size:3 final size:3
Alignment explanation
Indices: 77692--77751 Score: 56
Period size: 3 Copynumber: 20.0 Consensus size: 3
77682 TATGTGTGTG
77692 AGA AGA AGA AGGA A-A A-A TAGA AGA AGA AGA AGA AGA AGA AGGA A-A
1 AGA AGA AGA A-GA AGA AGA -AGA AGA AGA AGA AGA AGA AGA A-GA AGA
77737 A-A TAGA AGA AGA AGA
1 AGA -AGA AGA AGA AGA
77752 GGTGAACGGA
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
2 6 0.12
3 37 0.73
4 8 0.16
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (3 bp):
AGA
Found at i:77715 original size:15 final size:15
Alignment explanation
Indices: 77695--77747 Score: 74
Period size: 15 Copynumber: 3.5 Consensus size: 15
77685 GTGTGTGAGA
77695 AGAAGAAGGAAAAAT
1 AGAAGAAGGAAAAAT
77710 AGAAGAA-GAAGAAGA-
1 AGAAGAAGGAA-AA-AT
77725 AGAAGAAGGAAAAAT
1 AGAAGAAGGAAAAAT
77740 AGAAGAAG
1 AGAAGAAG
77748 AAGAGGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.12
15 26 0.76
16 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.30, T:0.04
Consensus pattern (15 bp):
AGAAGAAGGAAAAAT
Found at i:77715 original size:18 final size:18
Alignment explanation
Indices: 77692--77750 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 18
77682 TATGTGTGTG
77692 AGAAGAAGAAGGAAAAAT
1 AGAAGAAGAAGGAAAAAT
77710 AGAAGAAGAA-G----A-
1 AGAAGAAGAAGGAAAAAT
77722 AGAAGAAGAAGGAAAAAT
1 AGAAGAAGAAGGAAAAAT
77740 AGAAGAAGAAG
1 AGAAGAAGAAG
77751 AGGTGAACGG
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
12 10 0.29
13 2 0.06
17 2 0.06
18 21 0.60
ACGTcount: A:0.66, C:0.00, G:0.31, T:0.03
Consensus pattern (18 bp):
AGAAGAAGAAGGAAAAAT
Found at i:77728 original size:30 final size:30
Alignment explanation
Indices: 77692--77751 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
77682 TATGTGTGTG
77692 AGAAGAAGAAGGAAAAATAGAAGAAGAAGA
1 AGAAGAAGAAGGAAAAATAGAAGAAGAAGA
77722 AGAAGAAGAAGGAAAAATAGAAGAAGAAGA
1 AGAAGAAGAAGGAAAAATAGAAGAAGAAGA
77752 GGTGAACGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (30 bp):
AGAAGAAGAAGGAAAAATAGAAGAAGAAGA
Found at i:78920 original size:39 final size:38
Alignment explanation
Indices: 78876--78954 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 38
78866 TATCACATAA
78876 ATAA-TTAAA-CAAATATAATATTTTTTTATAATTATTTTT
1 ATAATTTAAATCAAATATAA-A-TTTTTTA-AATTATTTTT
* * *
78915 ATAATTTAAATTAAATTTAAATTTTTTAATTTATTTTT
1 ATAATTTAAATCAAATATAAATTTTTTAAATTATTTTT
78953 AT
1 AT
78955 CGTAAATCTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
38 11 0.31
39 11 0.31
40 6 0.17
41 7 0.20
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (38 bp):
ATAATTTAAATCAAATATAAATTTTTTAAATTATTTTT
Found at i:79874 original size:34 final size:30
Alignment explanation
Indices: 79836--79904 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 30
79826 TTGATATAAC
79836 AATTTAAGGCAAAATGGTTTTTGGACTTGAATTG
1 AATTTAA--CAAAAT-GTTTTTGGACTT-AATTG
79870 AATTT-ACAAAATGTTTTTGGACTTAATTG
1 AATTTAACAAAATGTTTTTGGACTTAATTG
79899 AATTTA
1 AATTTA
79905 TTCAAAGTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
29 10 0.29
30 12 0.35
31 6 0.18
33 1 0.03
34 5 0.15
ACGTcount: A:0.35, C:0.06, G:0.17, T:0.42
Consensus pattern (30 bp):
AATTTAACAAAATGTTTTTGGACTTAATTG
Found at i:79915 original size:29 final size:30
Alignment explanation
Indices: 79845--79904 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
79835 CAATTTAAGG
79845 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
79876 CAAAATGTTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
79905 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:80107 original size:20 final size:20
Alignment explanation
Indices: 80082--80195 Score: 138
Period size: 20 Copynumber: 5.7 Consensus size: 20
80072 AATGCAATTA
*
80082 GTGCATCGATGCATCATTCT
1 GTGCATCGATGCATCCTTCT
80102 GTGCATCGATGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
* * *
80122 ATGCATCAACGCATCCTTCT
1 GTGCATCGATGCATCCTTCT
***
80142 GTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATC-CTTCT
*
80163 GTGCATCGATGCATCCTGCT
1 GTGCATCGATGCATCCTTCT
*
80183 GTGCATCCATGCA
1 GTGCATCGATGCA
80196 CGAAGGCTGC
Statistics
Matches: 80, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
20 63 0.79
21 17 0.21
ACGTcount: A:0.20, C:0.29, G:0.21, T:0.30
Consensus pattern (20 bp):
GTGCATCGATGCATCCTTCT
Found at i:80166 original size:21 final size:21
Alignment explanation
Indices: 80140--80204 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
80130 ACGCATCCTT
80140 CTGTGCATCGATGCATCAAGG
1 CTGTGCATCGATGCATCAAGG
**
80161 CTGTGCATCGATGCATC-CTG
1 CTGTGCATCGATGCATCAAGG
*
80181 CTGTGCATCCATGCA-CGAAGG
1 CTGTGCATCGATGCATC-AAGG
80202 CTG
1 CTG
80205 CAACGGCTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.03
20 15 0.41
21 21 0.57
ACGTcount: A:0.20, C:0.28, G:0.28, T:0.25
Consensus pattern (21 bp):
CTGTGCATCGATGCATCAAGG
Found at i:80185 original size:41 final size:41
Alignment explanation
Indices: 80082--80204 Score: 142
Period size: 41 Copynumber: 3.0 Consensus size: 41
80072 AATGCAATTA
* ***
80082 GTGCATCGATGCATCATTCTGTGCATCGATGCATC-CTTCT
1 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
* * *
80122 ATGCATCAACGCATCCTTCTGTGCATCGATGCATCAAGGCT
1 GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
* *
80163 GTGCATCGATGCATCCTGCTGTGCATCCATGCA-CGAAGGCT
1 GTGCATCGATGCATCCTTCTGTGCATCGATGCATC-AAGGCT
80204 G
1 G
80205 CAACGGCTAG
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
40 32 0.46
41 37 0.54
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.28
Consensus pattern (41 bp):
GTGCATCGATGCATCCTTCTGTGCATCGATGCATCAAGGCT
Found at i:80602 original size:34 final size:32
Alignment explanation
Indices: 80563--80632 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
80553 TTTTGTAAAG
* *
80563 GGGAAAGGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
* *
80597 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
80629 GGGA
1 GGGA
80633 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:81030 original size:32 final size:31
Alignment explanation
Indices: 80990--81068 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
80980 GGTCCAATTG
*
80990 TTTT-TAATATTTGTTACTAAAAGTTTAATAT
1 TTTTCTAATATTTATTACTAAAAGTTT-ATAT
* ** *
81021 TTTTCTAATATTTATTATTATGAGTTTATTT
1 TTTTCTAATATTTATTACTAAAAGTTTATAT
81052 TTTTCTAATATTTATTA
1 TTTTCTAATATTTATTA
81069 TTAGGGTTTA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 24 0.57
32 18 0.43
ACGTcount: A:0.30, C:0.04, G:0.05, T:0.61
Consensus pattern (31 bp):
TTTTCTAATATTTATTACTAAAAGTTTATAT
Found at i:81089 original size:34 final size:32
Alignment explanation
Indices: 81011--81098 Score: 108
Period size: 31 Copynumber: 2.7 Consensus size: 32
81001 TGTTACTAAA
*
81011 AGTTTAATATTTTTCTAATATTTATTATTATG
1 AGTTTATTATTTTTCTAATATTTATTATTATG
81043 AGTTTATT-TTTTTCTAATATTTATTATTA-G
1 AGTTTATTATTTTTCTAATATTTATTATTATG
* *
81073 GGTTTACTCTTATTTTTTTAATATTT
1 AGTTTA---TTATTTTTCTAATATTT
81099 GTATAAATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
30 6 0.12
31 21 0.43
32 7 0.14
33 2 0.04
34 13 0.27
ACGTcount: A:0.26, C:0.05, G:0.07, T:0.62
Consensus pattern (32 bp):
AGTTTATTATTTTTCTAATATTTATTATTATG
Found at i:81205 original size:29 final size:29
Alignment explanation
Indices: 81141--81198 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
81131 CTAACATTTG
*
81141 TTATTAAGGGCCTAAATTTTTAATACTTA
1 TTATTAAGGGCCTAAATTTTTAATACATA
81170 TTATTAAGGGCCT-AATTTTTCAATACATA
1 TTATTAAGGGCCTAAATTTTT-AATACATA
81199 CTTTTAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 7 0.26
29 20 0.74
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (29 bp):
TTATTAAGGGCCTAAATTTTTAATACATA
Found at i:86258 original size:17 final size:17
Alignment explanation
Indices: 86211--86267 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 17
86201 AGTATGTTGT
86211 TTCATTCAATAAAGCTAG
1 TTCATTCAATAAA-CTAG
*
86229 TTCA-CCAACTAAACTAG
1 TTCATTCAA-TAAACTAG
*
86246 TTCATTCATTAAAACTAG
1 TTCATTCAAT-AAACTAG
86264 TTCA
1 TTCA
86268 ATTAGTCACA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.36
18 21 0.64
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.33
Consensus pattern (17 bp):
TTCATTCAATAAACTAG
Found at i:86838 original size:17 final size:17
Alignment explanation
Indices: 86816--86849 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
86806 TTGGACACCT
*
86816 AAGTGTCTACATACATC
1 AAGTGTCCACATACATC
*
86833 AAGTGTCCACATTCATC
1 AAGTGTCCACATACATC
86850 CTCCATTCTT
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:0.32, C:0.26, G:0.12, T:0.29
Consensus pattern (17 bp):
AAGTGTCCACATACATC
Found at i:87315 original size:20 final size:20
Alignment explanation
Indices: 87290--87332 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
87280 GAATGAAAAT
87290 TTGGCTTGAAATGCTCAAAC
1 TTGGCTTGAAATGCTCAAAC
87310 TTGGCTTGAAATGCTCAAAC
1 TTGGCTTGAAATGCTCAAAC
87330 TTG
1 TTG
87333 AGGTTTGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.33
Consensus pattern (20 bp):
TTGGCTTGAAATGCTCAAAC
Found at i:90274 original size:44 final size:44
Alignment explanation
Indices: 90200--90398 Score: 263
Period size: 44 Copynumber: 4.5 Consensus size: 44
90190 GATTTAATAC
* * * * * *
90200 CCTTCATATTGTATCGATGAACATTAAAGGAATGCAACGGTTCA
1 CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACA
* *
90244 CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATTGGTTCA
1 CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACA
* *
90288 CCTTCATAGTGTATCGATGTATATTCAAGGAATGCATTGGTACA
1 CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACA
* * *
90332 CTTTCATAGTGTATCGATGCATATTCAAAGAATGCATCAGTACA
1 CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACA
* *
90376 CTTTCATAGTGTATCAATGCATA
1 CCTTCATAGTGTATCGATGCATA
90399 GTGCAAAAAA
Statistics
Matches: 141, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 141 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (44 bp):
CCTTCATAGTGTATCGATGCATATTCAAGGAATGCATCGGTACA
Found at i:90391 original size:21 final size:21
Alignment explanation
Indices: 90327--90391 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
90317 GAATGCATTG
90327 GTACACTTTCATAGTGTATC-
1 GTACACTTTCATAGTGTATCA
* * *
90347 GATGCA-TATTCAAAGAATGCATCA
1 G-TACACT-TTCATAG--TGTATCA
90371 GTACACTTTCATAGTGTATCA
1 GTACACTTTCATAGTGTATCA
90392 ATGCATAGTG
Statistics
Matches: 33, Mismatches: 6, Indels: 11
0.66 0.12 0.22
Matches are distributed among these distances:
20 2 0.06
21 15 0.45
23 14 0.42
24 2 0.06
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Consensus pattern (21 bp):
GTACACTTTCATAGTGTATCA
Found at i:94452 original size:117 final size:117
Alignment explanation
Indices: 94232--94452 Score: 295
Period size: 117 Copynumber: 1.9 Consensus size: 117
94222 CTTTCAAATC
* *
94232 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATTCTTCTTCAAGATTT
1 GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAACTCTTCTTCAACATTT
* *
94297 CATTTTGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGCTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTCCTTTCTAAAAGAAGTTTGCTTAATTT
* * *
94349 GAAAATTTCTTTTTCAA-AGTTTTCAAATTTTATTTTTGAAAGCTCT-AACTCATTTTTCAACAT
1 GAAAATTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAACTC-TTCTTCAACAT
* * **
94412 TTCATTTTGATTTTCCAAGTCTGTTTTACCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCATTTT-CCTTTCTAAAAGAA
94453 TATCATTTTT
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
116 5 0.06
117 80 0.89
118 5 0.06
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.48
Consensus pattern (117 bp):
GAAAATTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAACTCTTCTTCAACATTT
CATTTTGATTTTCAAAATCCATTTTCCTTTCTAAAAGAAGTTTGCTTAATTT
Done.