Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001261.1 Hibiscus syriacus cultivar Beakdansim tig00002479_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: 85243
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:7593 original size:2 final size:2
Alignment explanation
Indices: 7586--7612 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7576 ATTGGATCAC
7586 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
7613 ATGAAGTTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8788 original size:2 final size:2
Alignment explanation
Indices: 8777--8815 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
8767 TTAAGTAATA
8777 AT AT -T AT 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 AT AT AT AT
8816 TATTGGTGAA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9024 original size:21 final size:21
Alignment explanation
Indices: 9000--9046 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8990 ATTCTGACTA
9000 TCGCATTGTGATTTCCCAAAT
1 TCGCATTGTGATTTCCCAAAT
* * *
9021 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGTGATTTCCCAAAT
9042 TCGCA
1 TCGCA
9047 ATGCGAATAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGTGATTTCCCAAAT
Found at i:9081 original size:20 final size:20
Alignment explanation
Indices: 9042--9087 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
9032 TTTTCCTAAT
*
9042 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
9062 TCGCAATGCGAAT-CTATAAA
1 TCGCAATGCGAATAC-ATAAA
*
9082 TTGCAA
1 TCGCAA
9088 CGAGATTCTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 22 0.96
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:12450 original size:20 final size:20
Alignment explanation
Indices: 12425--12493 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
12415 CAACGCGGAA
12425 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
12445 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
12465 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
12485 ATCGCAACG
1 ATCGCAACG
12494 AGAGAATCGC
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
20 43 0.93
21 3 0.07
ACGTcount: A:0.36, C:0.26, G:0.22, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:12515 original size:33 final size:33
Alignment explanation
Indices: 12406--12545 Score: 129
Period size: 33 Copynumber: 4.0 Consensus size: 33
12396 GACATTCATT
*
12406 TGACTATCGCAACGCG-GAAATCGCAACGCGAATA
1 TGACTATCGCAACGAGAG-AATCGCAACGCGAA-A
*
12440 TGACTATCGCAACACGGAAATGACTATCGCAACGCGGAAA
1 TGACTATCGC-A-AC-GAGA-GA--ATCGCAACGC-GAAA
*
12480 TGACTATCGCAACGAGAGAATCGCAATGCGAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAA
** * *
12513 TGAAAATCGCAACGAGTGAATCGCAATGCGAAA
1 TGACTATCGCAACGAGAGAATCGCAACGCGAAA
12546 ATAAAAATCG
Statistics
Matches: 91, Mismatches: 7, Indels: 17
0.79 0.06 0.15
Matches are distributed among these distances:
33 34 0.37
34 19 0.21
35 1 0.01
36 4 0.04
37 4 0.04
38 3 0.03
39 2 0.02
40 21 0.23
41 3 0.03
ACGTcount: A:0.39, C:0.23, G:0.24, T:0.15
Consensus pattern (33 bp):
TGACTATCGCAACGAGAGAATCGCAACGCGAAA
Found at i:12558 original size:34 final size:33
Alignment explanation
Indices: 12485--12560 Score: 125
Period size: 33 Copynumber: 2.3 Consensus size: 33
12475 GGAAATGACT
*
12485 ATCGCAACGAGAGAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
*
12518 ATCGCAACGAGTGAATCGCAATGCGAAAATAAAA
1 ATCGCAACGAGAGAATCGCAATGCG-AAATAAAA
12552 ATCGCAACG
1 ATCGCAACG
12561 CGATAGTCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 24 0.60
34 16 0.40
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAGAATCGCAATGCGAAATAAAA
Found at i:12705 original size:14 final size:14
Alignment explanation
Indices: 12686--12722 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
12676 CATCAATTAA
12686 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
12700 ACAAATCATCTTTT
1 ACAAATCAACATTT
12714 ACAAATCAA
1 ACAAATCAA
12723 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:14183 original size:42 final size:42
Alignment explanation
Indices: 14076--14185 Score: 107
Period size: 42 Copynumber: 2.6 Consensus size: 42
14066 TCTAGAATGT
* * *
14076 TGGGAG-GGACCTCTTCAACGATGACAATGGCCTCTTGAACGG
1 TGGGAGAGG-CCTCTTGAACGATGACAAGGGCCTCTTGAACGA
* * ** * *
14118 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGA
1 TGGGAGAGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGA
14160 TAGGG-GAGGCCTCTTGAACGATGACA
1 T-GGGAGAGGCCTCTTGAACGATGACA
14186 GGTGAGTCGG
Statistics
Matches: 53, Mismatches: 13, Indels: 4
0.76 0.19 0.06
Matches are distributed among these distances:
42 48 0.91
43 5 0.09
ACGTcount: A:0.24, C:0.19, G:0.36, T:0.21
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAAGGGCCTCTTGAACGA
Found at i:14691 original size:20 final size:20
Alignment explanation
Indices: 14668--14754 Score: 122
Period size: 20 Copynumber: 4.3 Consensus size: 20
14658 GAAGCTTAAA
14668 ATCGCAACT-TGAAAATGACT
1 ATCGCAA-TGTGAAAATGACT
14688 ATCGCAATGTGAAAATGACT
1 ATCGCAATGTGAAAATGACT
*
14708 ATCGCAATGCGAAAATGACT
1 ATCGCAATGTGAAAATGACT
* **
14728 ATCGCAATGCGAATTTGACT
1 ATCGCAATGTGAAAATGACT
14748 ATCGCAA
1 ATCGCAA
14755 CGAGAGAATC
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (20 bp):
ATCGCAATGTGAAAATGACT
Found at i:14913 original size:20 final size:20
Alignment explanation
Indices: 14888--14937 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
14878 AATTCTTTCG
14888 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
**
14908 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCAAATTCGCA
14928 TTGCGATAGT
1 TTGCGATAGT
14938 AAACTATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:16667 original size:23 final size:23
Alignment explanation
Indices: 16641--16685 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
16631 CACCACAGCT
*
16641 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
16664 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
16686 ATATAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:16923 original size:149 final size:149
Alignment explanation
Indices: 16653--16967 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
16643 TATAATTGCA
16653 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATAATA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATAATA
*
16717 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
16782 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
* *
16802 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATAATAT
16867 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
16932 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
*
16951 CCGAATGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
16968 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAACAATGTCCATAAGGACCACATAATAT
TCCTTAAGAATCATATACATATACTAAGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:17743 original size:21 final size:21
Alignment explanation
Indices: 17719--17763 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
17709 TTTTGTTCGT
* *
17719 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
17740 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
17761 TTG
1 TTG
17764 CCCAGAAATC
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:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:19336 original size:20 final size:20
Alignment explanation
Indices: 19313--19376 Score: 94
Period size: 20 Copynumber: 3.2 Consensus size: 20
19303 CTGAAACTTT
19313 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
19333 AAATCGCAACACGAAAATGA
1 AAATCGCAACACGAAAATGA
** *
19353 CTATCGCAACGCG-AAATGA
1 AAATCGCAACACGAAAATGA
19372 AAATC
1 AAATC
19377 ACATTGCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
19 9 0.23
20 30 0.77
ACGTcount: A:0.50, C:0.22, G:0.16, T:0.12
Consensus pattern (20 bp):
AAATCGCAACACGAAAATGA
Found at i:19419 original size:20 final size:20
Alignment explanation
Indices: 19394--19440 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
19384 GATTCTCTCG
19394 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCAAATTCGCA
** *
19414 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCAAATTCGCA
19434 TTGCGAT
1 TTGCGAT
19441 TCACTCGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (20 bp):
TTGCGATAGTCAAATTCGCA
Found at i:20052 original size:20 final size:20
Alignment explanation
Indices: 20029--20100 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
20019 ATAGTCAGAA
20029 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
**
20049 TCGCATTGCGATTT-TTTAAAT
1 TCGCATTGCGATTTACGT--AT
*
20070 TCGCGTTGCGATTTACGTAT
1 TCGCATTGCGATTTACGTAT
20090 TCGCATTGCGA
1 TCGCATTGCGA
20101 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.02
20 26 0.60
21 15 0.35
22 1 0.02
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACGTAT
Found at i:20121 original size:21 final size:21
Alignment explanation
Indices: 20097--20142 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
20087 TATTCGCATT
20097 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* *
20118 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
20139 GCGA
1 GCGA
20143 TAGTAAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.17, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:21535 original size:17 final size:16
Alignment explanation
Indices: 21494--21532 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
21484 ATTGAAAAAT
21494 AAAAAAATAAATTAAG
1 AAAAAAATAAATTAAG
*
21510 AAAAAAATATATTAAG
1 AAAAAAATAAATTAAG
21526 AAAAAAA
1 AAAAAAA
21533 ATAAGTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.18
Consensus pattern (16 bp):
AAAAAAATAAATTAAG
Found at i:24400 original size:14 final size:15
Alignment explanation
Indices: 24383--24411 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
24373 TAAAACTATA
24383 TAAAAATA-CAAAAT
1 TAAAAATACCAAAAT
24397 TAAAAATACCAAAAT
1 TAAAAATACCAAAAT
24412 AGATATTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.10, G:0.00, T:0.21
Consensus pattern (15 bp):
TAAAAATACCAAAAT
Found at i:26423 original size:37 final size:37
Alignment explanation
Indices: 26381--26458 Score: 147
Period size: 37 Copynumber: 2.1 Consensus size: 37
26371 ACTCTGATGA
26381 AGTTTAGCTGATAACGGATTTGTGATTTTGATTGTTT
1 AGTTTAGCTGATAACGGATTTGTGATTTTGATTGTTT
*
26418 AGTTTAGCTGATGACGGATTTGTGATTTTGATTGTTT
1 AGTTTAGCTGATAACGGATTTGTGATTTTGATTGTTT
26455 AGTT
1 AGTT
26459 GGTGCACTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.21, C:0.05, G:0.26, T:0.49
Consensus pattern (37 bp):
AGTTTAGCTGATAACGGATTTGTGATTTTGATTGTTT
Found at i:28916 original size:19 final size:20
Alignment explanation
Indices: 28892--28931 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
28882 AATTATTCTC
28892 ATTTTATAAATTTTTT-TAA
1 ATTTTATAAATTTTTTGTAA
*
28911 ATTTTATATATTTTTTGTAA
1 ATTTTATAAATTTTTTGTAA
28931 A
1 A
28932 ACACACACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (20 bp):
ATTTTATAAATTTTTTGTAA
Found at i:31496 original size:80 final size:80
Alignment explanation
Indices: 31363--31522 Score: 320
Period size: 80 Copynumber: 2.0 Consensus size: 80
31353 GCCACTTGTG
31363 ATCGGATCTTTGTGATTGCTCATGAACTCCTGCATTAACCAAAGAATCAGCAATCTCAACAAGTT
1 ATCGGATCTTTGTGATTGCTCATGAACTCCTGCATTAACCAAAGAATCAGCAATCTCAACAAGTT
31428 AATAACATCCATTTA
66 AATAACATCCATTTA
31443 ATCGGATCTTTGTGATTGCTCATGAACTCCTGCATTAACCAAAGAATCAGCAATCTCAACAAGTT
1 ATCGGATCTTTGTGATTGCTCATGAACTCCTGCATTAACCAAAGAATCAGCAATCTCAACAAGTT
31508 AATAACATCCATTTA
66 AATAACATCCATTTA
31523 CGTAACTCGA
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
80 80 1.00
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.30
Consensus pattern (80 bp):
ATCGGATCTTTGTGATTGCTCATGAACTCCTGCATTAACCAAAGAATCAGCAATCTCAACAAGTT
AATAACATCCATTTA
Found at i:32356 original size:2 final size:2
Alignment explanation
Indices: 32349--32433 Score: 170
Period size: 2 Copynumber: 42.5 Consensus size: 2
32339 GATTTATGTT
32349 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
32391 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
32433 T
1 T
32434 GAATACTTCA
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:40446 original size:5 final size:5
Alignment explanation
Indices: 40436--40499 Score: 54
Period size: 5 Copynumber: 14.2 Consensus size: 5
40426 GAAGAAAGAA
*
40436 GAAGG GAAGGG GAA-- GAAGG GAAGG GAAGG GAA-- GAAGG GAATG G-A-G
1 GAAGG GAA-GG GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG GAAGG
40481 GAAGG GAA-- GAAGG GAAGG G
1 GAAGG GAAGG GAAGG GAAGG G
40500 GTAGAATGGT
Statistics
Matches: 49, Mismatches: 1, Indels: 18
0.72 0.01 0.26
Matches are distributed among these distances:
3 11 0.22
4 2 0.04
5 31 0.63
6 5 0.10
ACGTcount: A:0.42, C:0.00, G:0.56, T:0.02
Consensus pattern (5 bp):
GAAGG
Found at i:40456 original size:8 final size:8
Alignment explanation
Indices: 40433--40497 Score: 59
Period size: 8 Copynumber: 8.5 Consensus size: 8
40423 AGTGAAGAAA
40433 GAAGAAGG
1 GAAGAAGG
40441 GAAG--GG
1 GAAGAAGG
40447 GAAGAAGG
1 GAAGAAGG
40455 GAAGGGAAGG
1 GAA--GAAGG
40465 GAAGAA-G
1 GAAGAAGG
*
40472 G--GAATG
1 GAAGAAGG
*
40478 GAGGAAGG
1 GAAGAAGG
40486 GAAGAAGG
1 GAAGAAGG
40494 GAAG
1 GAAG
40498 GGGTAGAATG
Statistics
Matches: 48, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 3 0.06
6 8 0.17
7 2 0.04
8 27 0.56
10 8 0.17
ACGTcount: A:0.45, C:0.00, G:0.54, T:0.02
Consensus pattern (8 bp):
GAAGAAGG
Found at i:40463 original size:13 final size:13
Alignment explanation
Indices: 40433--40499 Score: 68
Period size: 13 Copynumber: 5.1 Consensus size: 13
40423 AGTGAAGAAA
40433 GAAGAAGGGAAGGG
1 GAAGAAGGGAA-GG
40447 GAAGAAGGGAAGG
1 GAAGAAGGGAAGG
40460 GAAG--GGAAGAAGG
1 GAAGAAGG--GAAGG
*
40473 GAATGGA-GGAAGG
1 GAA-GAAGGGAAGG
40486 GAAGAAGGGAAGG
1 GAAGAAGGGAAGG
40499 G
1 G
40500 GTAGAATGGT
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
11 2 0.04
12 2 0.04
13 29 0.63
14 12 0.26
15 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.55, T:0.01
Consensus pattern (13 bp):
GAAGAAGGGAAGG
Found at i:41853 original size:18 final size:18
Alignment explanation
Indices: 41832--41874 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
41822 AATGGTTCTT
41832 CGGGACATAGTGGTCCTA
1 CGGGACATAGTGGTCCTA
*
41850 CGGGACATAGTGGTCCTT
1 CGGGACATAGTGGTCCTA
41868 CGGGACA
1 CGGGACA
41875 AATATTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.35, T:0.21
Consensus pattern (18 bp):
CGGGACATAGTGGTCCTA
Found at i:42703 original size:22 final size:22
Alignment explanation
Indices: 42650--42787 Score: 109
Period size: 22 Copynumber: 6.8 Consensus size: 22
42640 AGTGAATATT
42650 TGTCCCGAAGGACCA-T---TA
1 TGTCCCGAAGGACCACTAGATA
* *
42668 CGTCCCTAAGGACCACTAGATA
1 TGTCCCGAAGGACCACTAGATA
*
42690 TGTCTCGAAGGACCAC----TA
1 TGTCCCGAAGGACCACTAGATA
* * *
42708 CGTCCCGAAAGACCACTGGATA
1 TGTCCCGAAGGACCACTAGATA
*
42730 TGTCCCGAAAGACCACTAGATA
1 TGTCCCGAAGGACCACTAGATA
* *
42752 TGTCCTGAAGG---ACTGGATA
1 TGTCCCGAAGGACCACTAGATA
*
42771 TGTCCCGAAAGACCACT
1 TGTCCCGAAGGACCACT
42788 GTAACCCTCA
Statistics
Matches: 94, Mismatches: 15, Indels: 18
0.74 0.12 0.14
Matches are distributed among these distances:
18 28 0.30
19 17 0.18
22 49 0.52
ACGTcount: A:0.30, C:0.28, G:0.22, T:0.20
Consensus pattern (22 bp):
TGTCCCGAAGGACCACTAGATA
Found at i:42710 original size:40 final size:40
Alignment explanation
Indices: 42650--42747 Score: 142
Period size: 40 Copynumber: 2.5 Consensus size: 40
42640 AGTGAATATT
* * *
42650 TGTCCCGAAGGACCATTACGTCCCTAAGGACCACTAGATA
1 TGTCCCGAAGGACCACTACGTCCCGAAAGACCACTAGATA
* *
42690 TGTCTCGAAGGACCACTACGTCCCGAAAGACCACTGGATA
1 TGTCCCGAAGGACCACTACGTCCCGAAAGACCACTAGATA
*
42730 TGTCCCGAAAGACCACTA
1 TGTCCCGAAGGACCACTA
42748 GATATGTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.31, C:0.31, G:0.20, T:0.18
Consensus pattern (40 bp):
TGTCCCGAAGGACCACTACGTCCCGAAAGACCACTAGATA
Found at i:42747 original size:62 final size:62
Alignment explanation
Indices: 42669--42788 Score: 163
Period size: 62 Copynumber: 1.9 Consensus size: 62
42659 GGACCATTAC
* *
42669 GTCCCTAAGGACCACTAGATATGT-CTCGAAGGAC-CACTACGTCCCGAAAGACCACTGGATAT
1 GTCCCGAAAGACCACTAGATATGTCCT-GAAGGACGCA-TACGTCCCGAAAGACCACTGGATAT
* *
42731 GTCCCGAAAGACCACTAGATATGTCCTGAAGGACTGGATATGTCCCGAAAGACCACTG
1 GTCCCGAAAGACCACTAGATATGTCCTGAAGGAC-GCATACGTCCCGAAAGACCACTG
42789 TAACCCTCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
62 29 0.57
63 21 0.41
64 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.19
Consensus pattern (62 bp):
GTCCCGAAAGACCACTAGATATGTCCTGAAGGACGCATACGTCCCGAAAGACCACTGGATAT
Found at i:43312 original size:20 final size:20
Alignment explanation
Indices: 43284--43335 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
43274 AATGAAGGTA
43284 TGCATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
*
43304 TGTATCGATGCACTCTACAG
1 TGCATCGATGCACTCTACAG
43324 TGCATCGATGCA
1 TGCATCGATGCA
43336 TCCCTTAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (20 bp):
TGCATCGATGCACTCTACAG
Found at i:43458 original size:63 final size:63
Alignment explanation
Indices: 43340--43502 Score: 157
Period size: 63 Copynumber: 2.6 Consensus size: 63
43330 GATGCATCCC
* * * * *
43340 TTAACGGGTGCATCGATGCACTA-TCTGTGCATCGGTACACAAATCTCATTTGATGTTTGAATA
1 TTAAGGGGTGCATCAATGCACTACT-TGTGCATCGATACACAAATCACATTCGATGTTTGAATA
* ** * ** *
43403 TTAAGGGGTGCATCTATGCACTACTTGTGCATCGATACACTGATGACATTCGATGTTTTTATT
1 TTAAGGGGTGCATCAATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTGAATA
* * * *
43466 TTAAAGGAGTGCATCAATACACTTCATGTGCATCGAT
1 TT-AAGGGGTGCATCAATGCACTACTTGTGCATCGAT
43503 GCACCTTCAA
Statistics
Matches: 82, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
63 52 0.63
64 30 0.37
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
TTAAGGGGTGCATCAATGCACTACTTGTGCATCGATACACAAATCACATTCGATGTTTGAATA
Found at i:51748 original size:18 final size:18
Alignment explanation
Indices: 51718--51829 Score: 89
Period size: 18 Copynumber: 5.8 Consensus size: 18
51708 GTGAATATTT
*
51718 GTCCCGAATGACCATTAC
1 GTCCCGAAGGACCATTAC
* *
51736 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCA-T---TAC
*
51758 GTCCCGAAGAACCATTGGAC
1 GTCCCGAAGGACCATT--AC
*
51778 ATGTCCCGAAGGACCACTAC
1 --GTCCCGAAGGACCATTAC
*
51798 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCATTAC
*
51816 GTCCCGAAGAACCA
1 GTCCCGAAGGACCA
51830 CTGAATATGT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
18 44 0.57
19 1 0.01
20 3 0.04
21 1 0.01
22 28 0.36
ACGTcount: A:0.29, C:0.33, G:0.21, T:0.16
Consensus pattern (18 bp):
GTCCCGAAGGACCATTAC
Found at i:51771 original size:22 final size:21
Alignment explanation
Indices: 51736--51851 Score: 91
Period size: 22 Copynumber: 5.7 Consensus size: 21
51726 TGACCATTAC
*
51736 GTCCCTAAGGACCACTGGATAT
1 GTCCCGAAGGACCACT-GATAT
* * *
51758 GTCCCGAAGAACCATTGGACAT
1 GTCCCGAAGGACCACT-GATAT
*
51780 GTCCCGAAGGACCAC---TAC
1 GTCCCGAAGGACCACTGATAT
*
51798 GTCCCGAAGGACCAC---TAC
1 GTCCCGAAGGACCACTGATAT
*
51816 GTCCCGAAGAACCACTGAATAT
1 GTCCCGAAGGACCACTG-ATAT
*
51838 GTCCCGAATGACCA
1 GTCCCGAAGGACCA
51852 TTGTAACCCT
Statistics
Matches: 78, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
18 33 0.42
22 45 0.58
ACGTcount: A:0.30, C:0.32, G:0.22, T:0.16
Consensus pattern (21 bp):
GTCCCGAAGGACCACTGATAT
Found at i:51772 original size:40 final size:39
Alignment explanation
Indices: 51717--51853 Score: 138
Period size: 40 Copynumber: 3.4 Consensus size: 39
51707 AGTGAATATT
*
51717 TGTCCCGAATGACCATTACGTCCCTAAGGACCACTGGATA
1 TGTCCCGAATGACCATTACGTCCCGAAGGACCACT-GATA
51757 TGTCCCGAA-GAACCATTGGACATGTCCCGAAGGACCAC---TA
1 TGTCCCGAATG-ACCATT--AC--GTCCCGAAGGACCACTGATA
* * * *
51797 CGTCCCGAAGGACCACTACGTCCCGAAGAACCACTGAATA
1 TGTCCCGAATGACCATTACGTCCCGAAGGACCACTG-ATA
51837 TGTCCCGAATGACCATT
1 TGTCCCGAATGACCATT
51854 GTAACCCTCG
Statistics
Matches: 80, Mismatches: 7, Indels: 20
0.75 0.07 0.19
Matches are distributed among these distances:
36 14 0.17
38 2 0.03
39 1 0.01
40 46 0.57
41 1 0.01
42 2 0.03
44 14 0.17
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.19
Consensus pattern (39 bp):
TGTCCCGAATGACCATTACGTCCCGAAGGACCACTGATA
Found at i:51830 original size:18 final size:18
Alignment explanation
Indices: 51780--51831 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
51770 CATTGGACAT
51780 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
51798 GTCCCGAAGGACCACTAC
1 GTCCCGAAGGACCACTAC
*
51816 GTCCCGAAGAACCACT
1 GTCCCGAAGGACCACT
51832 GAATATGTCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.29, C:0.38, G:0.21, T:0.12
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAC
Found at i:52470 original size:63 final size:63
Alignment explanation
Indices: 52395--52515 Score: 161
Period size: 63 Copynumber: 1.9 Consensus size: 63
52385 GATGCATCCC
*
52395 TTAACGGGTGCATCGATGCACTACCTGTGCATCGGTACACAAATCTCATTCGATGTTTGAATA
1 TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCTCATTCGATGTTTGAATA
* * * * * ** *
52458 TTAAGGGGTGCATCGATGTACTACTTGTGTATCGATTCACTGATGTCATTCGATGTTT
1 TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCTCATTCGATGTTT
52516 TTATTTTAAA
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
63 49 1.00
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (63 bp):
TTAACGGGTGCATCGATGCACTACCTGTGCATCGATACACAAATCTCATTCGATGTTTGAATA
Found at i:55918 original size:31 final size:30
Alignment explanation
Indices: 55875--55932 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
55865 AATCAAAAAA
*
55875 TTAAGAAGTTTAATCGAAATTTTCAAAAGTT
1 TTAAGAAATTTAA-CGAAATTTTCAAAAGTT
* *
55906 TTAAGAAATTTAACGATATTTTTAAAA
1 TTAAGAAATTTAACGAAATTTTCAAAA
55933 AATATGAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 12 0.50
31 12 0.50
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (30 bp):
TTAAGAAATTTAACGAAATTTTCAAAAGTT
Found at i:60178 original size:16 final size:18
Alignment explanation
Indices: 60147--60185 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
60137 TCTAATTATA
60147 TATTTTTTGAATTATTGT
1 TATTTTTTGAATTATTGT
60165 TATTTTTT-AA-TATTGT
1 TATTTTTTGAATTATTGT
60181 T-TTTT
1 TATTTT
60186 AGCATTTCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 4 0.19
16 7 0.33
17 2 0.10
18 8 0.38
ACGTcount: A:0.21, C:0.00, G:0.08, T:0.72
Consensus pattern (18 bp):
TATTTTTTGAATTATTGT
Found at i:72141 original size:33 final size:33
Alignment explanation
Indices: 72104--72168 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
72094 TCTTAACTTC
72104 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
1 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
72137 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACA
1 TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACA
72169 CCGGCTGTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.57
Consensus pattern (33 bp):
TGTTTTCTTCTCGTTTGCTTTTTGTTGAAACAT
Found at i:79881 original size:24 final size:22
Alignment explanation
Indices: 79841--79903 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 22
79831 AAGCGACGGT
*
79841 GGGGGTGGGCGGAGGAGCGGGCGGA
1 GGGGGT-GG-GGAGGAGAGGG-GGA
*
79866 GGGGGTGGGGATGGAGATGGGGA
1 GGGGGTGGGGA-GGAGAGGGGGA
79889 GGGGGATGGGGAGGA
1 GGGGG-TGGGGAGGA
79904 ACATTTTTTC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
23 14 0.41
24 14 0.41
25 6 0.18
ACGTcount: A:0.16, C:0.05, G:0.71, T:0.08
Consensus pattern (22 bp):
GGGGGTGGGGAGGAGAGGGGGA
Found at i:83391 original size:23 final size:23
Alignment explanation
Indices: 83364--83411 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
83354 ATATATATAT
83364 ATATATATATATATTTAAATTAA
1 ATATATATATATATTTAAATTAA
* *
83387 ATATATATTTTTATTTAAATTAA
1 ATATATATATATATTTAAATTAA
83410 AT
1 AT
83412 TTATTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATATATATATATTTAAATTAA
Found at i:83394 original size:2 final size:2
Alignment explanation
Indices: 83353--83377 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83343 TCGGGCCGGG
83353 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 T
83378 TTAAATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:84058 original size:16 final size:16
Alignment explanation
Indices: 84026--84060 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
84016 TAACGCCTTT
* *
84026 AATCATTAAACAGAGG
1 AATCATTAAAAAAAGG
84042 AATCATTAAAAAAAGG
1 AATCATTAAAAAAAGG
84058 AAT
1 AAT
84061 AATTTCGGGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.57, C:0.09, G:0.14, T:0.20
Consensus pattern (16 bp):
AATCATTAAAAAAAGG
Done.