Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001391.1 Hibiscus syriacus cultivar Beakdansim tig00002715_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: 143905
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.32
Found at i:8551 original size:27 final size:26
Alignment explanation
Indices: 8490--8548 Score: 91
Period size: 26 Copynumber: 2.2 Consensus size: 26
8480 GGACAAATTT
*
8490 AATACTTGGTTCAAAATGTTTTCTATA
1 AATA-TTGGTTCAAAACGTTTTCTATA
*
8517 AATATTGGTTCAAAACGTTTTTTATA
1 AATATTGGTTCAAAACGTTTTCTATA
8543 AATATT
1 AATATT
8549 TGGGTTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (26 bp):
AATATTGGTTCAAAACGTTTTCTATA
Found at i:9472 original size:28 final size:28
Alignment explanation
Indices: 9441--9495 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
9431 ATGATGATTT
9441 AATA-AAATAATAATAATTTAATT-ATAAC
1 AATAGAAA-AATAATAA-TTAATTGATAAC
*
9469 AATAGAAAATTAATAATTAATTGATAA
1 AATAGAAAAATAATAATTAATTGATAA
9496 ATAATAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
27 6 0.25
28 15 0.62
29 3 0.12
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.35
Consensus pattern (28 bp):
AATAGAAAAATAATAATTAATTGATAAC
Found at i:11835 original size:97 final size:97
Alignment explanation
Indices: 11669--11864 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 97
11659 AGATTCTAAG
*
11669 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
1 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAAACATTTAAAGTTGATACTT
11734 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
11766 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAAACATTTAAAGTTGATACTT
1 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAAACATTTAAAGTTGATACTT
11831 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
11863 AA
1 AA
11865 GAGTTCAGGA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (97 bp):
AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAAACATTTAAAGTTGATACTT
TAGAATTCCACTATTATTCATGTGCATCAGGA
Found at i:20747 original size:49 final size:49
Alignment explanation
Indices: 20694--20844 Score: 109
Period size: 49 Copynumber: 3.1 Consensus size: 49
20684 AACCGATCTA
20694 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
1 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
* * * * * * ** * *
20743 ATCAGGA-A---ACAG--GGTCCTATTGGAGAGAATCGATTATTAACCGATCT-A
1 ATCA-GACATTTAAAGTTGATACT-TT--AGA-ATTCCACTATTATTC-ATGTGC
20791 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
1 ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
20840 ATCAG
1 ATCAG
20845 GAAAGCGTTC
Statistics
Matches: 69, Mismatches: 20, Indels: 26
0.60 0.17 0.23
Matches are distributed among these distances:
44 4 0.06
45 2 0.03
46 3 0.04
47 5 0.07
48 18 0.26
49 23 0.33
50 5 0.07
51 3 0.04
52 2 0.03
53 4 0.06
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Consensus pattern (49 bp):
ATCAGACATTTAAAGTTGATACTTTAGAATTCCACTATTATTCATGTGC
Found at i:20819 original size:97 final size:97
Alignment explanation
Indices: 20653--20848 Score: 383
Period size: 97 Copynumber: 2.0 Consensus size: 97
20643 GGATTCTAAG
20653 AACAGGGTCATATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
1 AACAGGGTCATATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
20718 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
*
20750 AACAGGGTCCTATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
1 AACAGGGTCATATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
20815 TAGAATTCCACTATTATTCATGTGCATCAGGA
66 TAGAATTCCACTATTATTCATGTGCATCAGGA
20847 AA
1 AA
20849 GCGTTCAGGA
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
97 98 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (97 bp):
AACAGGGTCATATTGGAGAGAATCGATTATTAACCGATCTAATCAGACATTTAAAGTTGATACTT
TAGAATTCCACTATTATTCATGTGCATCAGGA
Found at i:29658 original size:31 final size:31
Alignment explanation
Indices: 29620--29690 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
29610 CTTTTAAAAC
*
29620 TTGCAATATAATCCCCCAACATTTAGTCCGT
1 TTGCAATATAATCACCCAACATTTAGTCCGT
** *
29651 TTGCAATATGGTCACTCAACATTTAGTCCGT
1 TTGCAATATAATCACCCAACATTTAGTCCGT
29682 TTGCAATAT
1 TTGCAATAT
29691 GGTTCCTGAC
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.28, C:0.24, G:0.13, T:0.35
Consensus pattern (31 bp):
TTGCAATATAATCACCCAACATTTAGTCCGT
Found at i:32348 original size:29 final size:29
Alignment explanation
Indices: 32316--32377 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
32306 CTTTCATTTA
32316 AGTCACACAACTTTTAAAACTTGCAATAC
1 AGTCACACAACTTTTAAAACTTGCAATAC
* * *
32345 AGTCCCTCAACTTTTAAAACTTGCAATAT
1 AGTCACACAACTTTTAAAACTTGCAATAC
32374 AGTC
1 AGTC
32378 CCCCAACATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.37, C:0.24, G:0.08, T:0.31
Consensus pattern (29 bp):
AGTCACACAACTTTTAAAACTTGCAATAC
Found at i:32378 original size:29 final size:29
Alignment explanation
Indices: 32323--32389 Score: 107
Period size: 29 Copynumber: 2.3 Consensus size: 29
32313 TTAAGTCACA
*
32323 CAACTTTTAAAACTTGCAATACAGTCCCT
1 CAACTTTTAAAACTTGCAATACAGTCCCC
*
32352 CAACTTTTAAAACTTGCAATATAGTCCCC
1 CAACTTTTAAAACTTGCAATACAGTCCCC
*
32381 CAACATTTA
1 CAACTTTTA
32390 GTTTGTTTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.36, C:0.27, G:0.06, T:0.31
Consensus pattern (29 bp):
CAACTTTTAAAACTTGCAATACAGTCCCC
Found at i:32469 original size:31 final size:31
Alignment explanation
Indices: 32426--32502 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
32416 AGTTACGTCG
* *
32426 GGGACCATATTGCAAACGGACTAAATGTTGA
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
32457 GGGATCATATTGCAAACAGACTAAATGTTGG
1 GGGATCATATTGCAAACAGACTAAATGTTGA
*
32488 GGGATTATATTGCAA
1 GGGATCATATTGCAA
32503 GTTTTAAAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.13, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGATCATATTGCAAACAGACTAAATGTTGA
Found at i:40158 original size:21 final size:22
Alignment explanation
Indices: 40123--40167 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
40113 AGTAATAACT
*
40123 CAGTAACAGTCAG-AATATTAA
1 CAGTAACAGTCAGAAATAGTAA
40144 CAGTAACA-TCTAGAAATAGTAA
1 CAGTAACAGTC-AGAAATAGTAA
40166 CA
1 CA
40168 ATTAGGATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 2 0.10
21 10 0.48
22 9 0.43
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.22
Consensus pattern (22 bp):
CAGTAACAGTCAGAAATAGTAA
Found at i:48638 original size:22 final size:21
Alignment explanation
Indices: 48596--48635 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48586 GAGTTTATTT
*
48596 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
48617 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
48636 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:51155 original size:2 final size:2
Alignment explanation
Indices: 51148--51178 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
51138 GAATTAAATA
51148 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
51179 CTCGAATAAA
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:52162 original size:17 final size:18
Alignment explanation
Indices: 52135--52173 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
52125 TTTAGGCCTG
52135 GCCTGGGCCTGTTTAAAA
1 GCCTGGGCCTGTTTAAAA
52153 GCCT-GGCCTGTTTAAAA
1 GCCTGGGCCTGTTTAAAA
52170 GCCT
1 GCCT
52174 ATTTAAAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.28
Consensus pattern (18 bp):
GCCTGGGCCTGTTTAAAA
Found at i:52173 original size:12 final size:12
Alignment explanation
Indices: 52158--52191 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
52148 TAAAAGCCTG
52158 GCCTGTTTAAAA
1 GCCTGTTTAAAA
*
52170 GCCTATTTAAAA
1 GCCTGTTTAAAA
52182 GCCTGTTTAA
1 GCCTGTTTAA
52192 CAATAAACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (12 bp):
GCCTGTTTAAAA
Found at i:53517 original size:3 final size:3
Alignment explanation
Indices: 53509--53551 Score: 63
Period size: 3 Copynumber: 14.7 Consensus size: 3
53499 ACAATTATAT
53509 TAA TAA TAA TAA TAA TAA T-A TAA TTAA -AA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA TA
53552 TTTTGGACGA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 4 0.11
3 30 0.81
4 3 0.08
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:59131 original size:67 final size:67
Alignment explanation
Indices: 59050--59175 Score: 198
Period size: 67 Copynumber: 1.9 Consensus size: 67
59040 CTCAAATGAG
* * * * *
59050 AAATTCCATAATGTCATGGGGGTACCGATTCCACCCCAGAGGGGTACCGATACTCCCCTTGACAA
1 AAATTACAGAATGTCATAGGGGTACCGATTCCACCCCAGAGGGGTACAGATACCCCCCTTGACAA
59115 AA
66 AA
*
59117 AAATTACAGAATGTCATAGGGGTACCGATTCCCCCCCAGAGGGGTACAGATACCCCCCT
1 AAATTACAGAATGTCATAGGGGTACCGATTCCACCCCAGAGGGGTACAGATACCCCCCT
59176 AAAGGAAGAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 53 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.20
Consensus pattern (67 bp):
AAATTACAGAATGTCATAGGGGTACCGATTCCACCCCAGAGGGGTACAGATACCCCCCTTGACAA
AA
Found at i:64495 original size:64 final size:64
Alignment explanation
Indices: 64415--64535 Score: 197
Period size: 64 Copynumber: 1.9 Consensus size: 64
64405 CTCAAACGAG
* * * * *
64415 AAATTCCATAATGTCATGGGGGTACCGATTCCCCCCATAGGGGTACTGATACCCCCTTGACAAA
1 AAATTACAGAATGTCATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCTTGACAAA
64479 AAATTACAGAATGTCATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCT
1 AAATTACAGAATGTCATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCT
64536 AAAAGAAGAA
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.28, C:0.29, G:0.21, T:0.21
Consensus pattern (64 bp):
AAATTACAGAATGTCATAGGGGTACCGATTCCCCCCAGAGGGGTACCGATACCCCCTTGACAAA
Found at i:66105 original size:23 final size:23
Alignment explanation
Indices: 66079--66146 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
66069 AATCTTATAT
* *
66079 GGCACTTCGGTGTATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
66102 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
66125 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
66147 AGTTATGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:71604 original size:12 final size:13
Alignment explanation
Indices: 71584--71646 Score: 51
Period size: 12 Copynumber: 5.0 Consensus size: 13
71574 CCAAACACTT
*
71584 TTATACAAAT-AA
1 TTATTCAAATCAA
71596 TTATTCAAATCAA
1 TTATTCAAATCAA
*
71609 -TATCTCAAATCGA
1 TTAT-TCAAATCAA
* *
71622 CTAATCAAATC-A
1 TTATTCAAATCAA
*
71634 TTAATCAAATCAA
1 TTATTCAAATCAA
71647 CTACTAAAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
12 23 0.53
13 18 0.42
14 2 0.05
ACGTcount: A:0.49, C:0.17, G:0.02, T:0.32
Consensus pattern (13 bp):
TTATTCAAATCAA
Found at i:75514 original size:2 final size:2
Alignment explanation
Indices: 75507--75534 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
75497 ACTGATTTTA
75507 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
75535 TCTTAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90645 original size:30 final size:29
Alignment explanation
Indices: 90579--90645 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 29
90569 ATCATAACCT
** *
90579 GCGGTTCACATCGGTTTTACTTGTTTTCA
1 GCGGTTCACATCGGTTTTACCGGTTCTCA
90608 GCTGGTTCACATCGGTTTTACCGGTTCTCA
1 GC-GGTTCACATCGGTTTTACCGGTTCTCA
90638 GACGGTTC
1 G-CGGTTC
90646 TACTAGTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 30 0.91
31 1 0.03
ACGTcount: A:0.13, C:0.24, G:0.24, T:0.39
Consensus pattern (29 bp):
GCGGTTCACATCGGTTTTACCGGTTCTCA
Found at i:91548 original size:13 final size:15
Alignment explanation
Indices: 91530--91562 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
91520 AATTTATTTA
91530 AATTTCA-GTTTGT-
1 AATTTCATGTTTGTC
91543 AATTTCATGTTTGTC
1 AATTTCATGTTTGTC
91558 AATTT
1 AATTT
91563 AATCCTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.24, C:0.09, G:0.12, T:0.55
Consensus pattern (15 bp):
AATTTCATGTTTGTC
Found at i:92024 original size:2 final size:2
Alignment explanation
Indices: 92017--92046 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
92007 TAACATATGT
92017 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
92047 CGAACTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:92207 original size:2 final size:2
Alignment explanation
Indices: 92200--92229 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
92190 ATCACTTCAT
92200 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
92230 ATTAGACTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93477 original size:16 final size:16
Alignment explanation
Indices: 93449--93501 Score: 63
Period size: 16 Copynumber: 3.2 Consensus size: 16
93439 TAATAATTTT
93449 AAAA-ATTTATTTAAA
1 AAAATATTTATTTAAA
*
93464 AAAATATTTTTTTAAA
1 AAAATATTTATTTAAA
*
93480 AAAATAAATATATTTAAA
1 AAAAT--ATTTATTTAAA
93498 AAAA
1 AAAA
93502 AACCTTTTCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
15 4 0.12
16 15 0.47
18 13 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATATTTATTTAAA
Found at i:93495 original size:34 final size:35
Alignment explanation
Indices: 93451--93519 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
93441 ATAATTTTAA
* * *
93451 AAATTTATTTAAAAAAATA-TTTTTTTAAAAAAAT
1 AAATATATTTAAAAAAAAACTTTTCTTAAAAAAAT
93485 AAATATATTTAAAAAAAAACCTTTTCTTAAAAAAA
1 AAATATATTTAAAAAAAAA-CTTTTCTTAAAAAAA
93520 ATCCTCCCAC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
34 17 0.57
36 13 0.43
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (35 bp):
AAATATATTTAAAAAAAAACTTTTCTTAAAAAAAT
Found at i:95975 original size:18 final size:18
Alignment explanation
Indices: 95952--95987 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
95942 TCTTTGTAAC
95952 AAAATAAAATCGGTAAGT
1 AAAATAAAATCGGTAAGT
*
95970 AAAATAACATCGGTAAGT
1 AAAATAAAATCGGTAAGT
95988 GATTCCTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.08, G:0.17, T:0.22
Consensus pattern (18 bp):
AAAATAAAATCGGTAAGT
Found at i:96951 original size:20 final size:20
Alignment explanation
Indices: 96928--96998 Score: 142
Period size: 20 Copynumber: 3.5 Consensus size: 20
96918 CCTTAGTCTT
96928 GGTATCGATACTGATATGGA
1 GGTATCGATACTGATATGGA
96948 GGTATCGATACTGATATGGA
1 GGTATCGATACTGATATGGA
96968 GGTATCGATACTGATATGGA
1 GGTATCGATACTGATATGGA
96988 GGTATCGATAC
1 GGTATCGATAC
96999 CAAAAGTAAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.30, C:0.11, G:0.30, T:0.30
Consensus pattern (20 bp):
GGTATCGATACTGATATGGA
Found at i:96954 original size:40 final size:40
Alignment explanation
Indices: 96910--96999 Score: 121
Period size: 40 Copynumber: 2.2 Consensus size: 40
96900 CTATGAACAA
**
96910 TATCGATACCT-TAGTCTTGGTATCGATACTGATATGGAGG
1 TATCGATACCTATA-TCGAGGTATCGATACTGATATGGAGG
*
96950 TATCGATA-CTGATATGGAGGTATCGATACTGATATGGAGG
1 TATCGATACCT-ATATCGAGGTATCGATACTGATATGGAGG
96990 TATCGATACC
1 TATCGATACC
97000 AAAAGTAAGG
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
39 2 0.05
40 39 0.89
41 3 0.07
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (40 bp):
TATCGATACCTATATCGAGGTATCGATACTGATATGGAGG
Found at i:97011 original size:40 final size:40
Alignment explanation
Indices: 96928--97017 Score: 128
Period size: 40 Copynumber: 2.2 Consensus size: 40
96918 CCTTAGTCTT
** * *
96928 GGTATCGATACTGATATGGAGGTATCGATACTGATATGGA
1 GGTATCGATACTGATATGGAGGTATCGATACCAAAATGAA
96968 GGTATCGATACTGATATGGAGGTATCGATACCAAAA-GTAA
1 GGTATCGATACTGATATGGAGGTATCGATACCAAAATG-AA
97008 GGTATCGATA
1 GGTATCGATA
97018 TTGTAATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.02
40 44 0.98
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (40 bp):
GGTATCGATACTGATATGGAGGTATCGATACCAAAATGAA
Found at i:97732 original size:15 final size:15
Alignment explanation
Indices: 97675--97733 Score: 55
Period size: 15 Copynumber: 3.9 Consensus size: 15
97665 TAATATGAGT
* *
97675 ATATGTTATAGGTGA
1 ATATGATATATGTGA
* *
97690 ATATGTTATACGTGAA
1 ATATGATATATGTG-A
* *
97706 AAATGATCTATGTGA
1 ATATGATATATGTGA
97721 ATATGATATATGT
1 ATATGATATATGT
97734 CAATGTGTTC
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
15 25 0.69
16 11 0.31
ACGTcount: A:0.37, C:0.03, G:0.20, T:0.39
Consensus pattern (15 bp):
ATATGATATATGTGA
Found at i:97924 original size:23 final size:23
Alignment explanation
Indices: 97898--98021 Score: 99
Period size: 23 Copynumber: 5.3 Consensus size: 23
97888 AGTTGAAGGT
* *
97898 TCTACGCGGTCATTTGGGACAAA
1 TCTACGCGGTCCTTCGGGACAAA
* * * *
97921 TCTACGTGGACCTTTGAGACAAA
1 TCTACGCGGTCCTTCGGGACAAA
* *
97944 TCTATGTGGT-CTTCGGGACAAA
1 TCTACGCGGTCCTTCGGGACAAA
*
97966 TTCTACACGGTCCTTCGGGACAAA
1 -TCTACGCGGTCCTTCGGGACAAA
* **
97990 TCTACGTGGAACTTCGGTG-CAAA
1 TCTACGCGGTCCTTCGG-GACAAA
98013 TTCTACGCG
1 -TCTACGCG
98022 ACACTTCGAT
Statistics
Matches: 81, Mismatches: 16, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
22 10 0.12
23 51 0.63
24 20 0.25
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (23 bp):
TCTACGCGGTCCTTCGGGACAAA
Found at i:98029 original size:47 final size:46
Alignment explanation
Indices: 97913--98018 Score: 117
Period size: 46 Copynumber: 2.3 Consensus size: 46
97903 GCGGTCATTT
** * * * *
97913 GGGACAAA-TCTACGTGGACCTTTGAGACAAATCTATGTGGTCTTC
1 GGGACAAATTCTACACGGACCTTCGGGACAAATCTACGTGGACTTC
*
97958 GGGACAAATTCTACACGGTCCTTCGGGACAAATCTACGTGGAACTTC
1 GGGACAAATTCTACACGGACCTTCGGGACAAATCTACGTGG-ACTTC
98005 GGTG-CAAATTCTAC
1 GG-GACAAATTCTAC
98019 GCGACACTTC
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
45 8 0.16
46 26 0.51
47 16 0.31
48 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.24, T:0.26
Consensus pattern (46 bp):
GGGACAAATTCTACACGGACCTTCGGGACAAATCTACGTGGACTTC
Found at i:102455 original size:90 final size:90
Alignment explanation
Indices: 102355--102532 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
102345 TTCATCATTT
*
102355 AAAAATAATATATAATTTAAACTCGTTTAAGAATAATTATTTTACAATTATTTTTAAATGATAAA
1 AAAAATAATATATAATTTAAACTCGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAA
*
102420 TGAATAATAAACATTGTAAGAAAGA
66 TGAATAACAAACATTGTAAGAAAGA
* * * *
102445 AAAAATAATATATAATTTAAATTTGTTTAACAGTAATTATTTTATAATTATTTTTAAATGATAAA
1 AAAAATAATATATAATTTAAACTCGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAA
* *
102510 TGAATAGCAAACCTTGTAAGAAA
66 TGAATAACAAACATTGTAAGAAA
102533 TACTTTTTTA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.38
Consensus pattern (90 bp):
AAAAATAATATATAATTTAAACTCGTTTAACAATAATTATTTTACAATTATTTTTAAATGATAAA
TGAATAACAAACATTGTAAGAAAGA
Found at i:103196 original size:30 final size:30
Alignment explanation
Indices: 103160--103217 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
103150 AAAACAAATT
103160 TGAAAATGGTCATTTCGATACTAACCCTTC
1 TGAAAATGGTCATTTCGATACTAACCCTTC
103190 TGAAAATGGTCATTTCGATACTAACCCT
1 TGAAAATGGTCATTTCGATACTAACCCT
103218 ATATTTGGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (30 bp):
TGAAAATGGTCATTTCGATACTAACCCTTC
Found at i:106762 original size:2 final size:2
Alignment explanation
Indices: 106757--106782 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
106747 GTGTGTGTGT
106757 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
106783 CGTTGCCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:109001 original size:32 final size:32
Alignment explanation
Indices: 108913--109014 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
108903 GAGCTAACCT
* * *
108913 AAGGGAATGCCTTGGGTCCTTAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
* * * *
108945 GA-TGAATATCTTGGGGACTCAGAGCCTACCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
* * *
108976 AAGGGAGTACCTTGGGGCCTGAGAGCCTATCC
1 AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
109008 AAGGGAA
1 AAGGGAA
109015 CATCTCGAAA
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 24 0.44
32 30 0.56
ACGTcount: A:0.25, C:0.25, G:0.30, T:0.20
Consensus pattern (32 bp):
AAGGGAATACCTTGGGGCCTCAGAGCCTACCC
Found at i:109875 original size:22 final size:22
Alignment explanation
Indices: 109847--109907 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
109837 GGCATGTGAA
* *
109847 ATTTGTCCAGAATGACCTATGT
1 ATTTGTCCCGAAGGACCTATGT
*
109869 ATTTGTCCCGAAGGACCTTTGT
1 ATTTGTCCCGAAGGACCTATGT
*
109891 ATATGTCCCGAAGGACC
1 ATTTGTCCCGAAGGACC
109908 GCGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCGAAGGACCTATGT
Found at i:114598 original size:22 final size:22
Alignment explanation
Indices: 114549--114606 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
114539 ATGTGAAATT
* * *
114549 TGTCCAGAATGACATATGTATT
1 TGTCCCGAATGACCTATGTATA
*
114571 TGTCCCGAATGACCTCTGTATA
1 TGTCCCGAATGACCTATGTATA
*
114593 TGTCCCGAAAGACC
1 TGTCCCGAATGACC
114607 GCGTAGACCC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (22 bp):
TGTCCCGAATGACCTATGTATA
Found at i:118642 original size:2 final size:2
Alignment explanation
Indices: 118635--118659 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
118625 GAAACGACAC
118635 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
118660 TATTTTGTTG
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:120872 original size:15 final size:15
Alignment explanation
Indices: 120839--120872 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
120829 AATAAATATT
*
120839 TATTTTAGAATTTAA
1 TATTTTAGAAATTAA
120854 -ATTTTAGAAATTAA
1 TATTTTAGAAATTAA
120868 TATTT
1 TATTT
120873 ATTTGATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
TATTTTAGAAATTAA
Found at i:122005 original size:18 final size:17
Alignment explanation
Indices: 121982--122052 Score: 63
Period size: 18 Copynumber: 4.1 Consensus size: 17
121972 TTATTATTCT
121982 ATATCTGACAATTGTAAA
1 ATATCTGACAATTGT-AA
*
122000 ATATCTGATC-TTTGTAA
1 ATATCTGA-CAATTGTAA
* * *
122017 TTATCTGATAACTGTAA
1 ATATCTGACAATTGTAA
*
122034 ATCATCTGATAATTGTAA
1 AT-ATCTGACAATTGTAA
122052 A
1 A
122053 CATTTAGAAT
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
17 15 0.35
18 27 0.63
19 1 0.02
ACGTcount: A:0.38, C:0.11, G:0.11, T:0.39
Consensus pattern (17 bp):
ATATCTGACAATTGTAA
Found at i:122050 original size:35 final size:35
Alignment explanation
Indices: 121983--122051 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
121973 TATTATTCTA
* **
121983 TATCTGACAATTGTAAAATATCTGATCTTTGTAAT
1 TATCTGACAACTGTAAAATATCTGATAATTGTAAT
*
122018 TATCTGATAACTGT-AAATCATCTGATAATTGTAA
1 TATCTGACAACTGTAAAAT-ATCTGATAATTGTAA
122052 ACATTTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
34 4 0.14
35 25 0.86
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.41
Consensus pattern (35 bp):
TATCTGACAACTGTAAAATATCTGATAATTGTAAT
Found at i:124990 original size:30 final size:30
Alignment explanation
Indices: 124954--125042 Score: 85
Period size: 30 Copynumber: 3.0 Consensus size: 30
124944 TAAAATATAT
*
124954 AACTTTTAAAAATTATAATTTTGATCC-CTA
1 AACTTTTAAAAATTATAATTTT-AGCCACTA
*
124984 AACTTTTAAATATT-TATATTTTAGCCACTA
1 AACTTTTAAAAATTATA-ATTTTAGCCACTA
* * * *
125014 AACTTTCAAAACTTACAA-TTTAGTCACTA
1 AACTTTTAAAAATTATAATTTTAGCCACTA
125043 GACAAAATTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
29 15 0.31
30 33 0.67
31 1 0.02
ACGTcount: A:0.39, C:0.16, G:0.03, T:0.42
Consensus pattern (30 bp):
AACTTTTAAAAATTATAATTTTAGCCACTA
Found at i:127207 original size:5 final size:5
Alignment explanation
Indices: 127197--127221 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
127187 GGTTGTTTTG
127197 AAAGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA AAAGA
127222 TGAGAGAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:134200 original size:26 final size:26
Alignment explanation
Indices: 134171--134222 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
134161 CACAACATAC
134171 AGCATAAATATCTACAAGGACTTCAA
1 AGCATAAATATCTACAAGGACTTCAA
134197 AGCATAAATATCTACAAGGACTTCAA
1 AGCATAAATATCTACAAGGACTTCAA
134223 GAATTGGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (26 bp):
AGCATAAATATCTACAAGGACTTCAA
Found at i:141903 original size:19 final size:20
Alignment explanation
Indices: 141873--141910 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
141863 ATGTGATTTG
*
141873 TTGAGAAGAAAAACAGTTGA
1 TTGAGAAGAAAAAAAGTTGA
141893 TTGAG-AGAAAAAAAGTTG
1 TTGAGAAGAAAAAAAGTTG
141911 TTTTGTGTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.50, C:0.03, G:0.26, T:0.21
Consensus pattern (20 bp):
TTGAGAAGAAAAAAAGTTGA
Done.