Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009181.1 Hibiscus syriacus cultivar Beakdansim tig00112749_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: 95860
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:8361 original size:9 final size:9
Alignment explanation
Indices: 8330--8354 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
8320 TTTCTTCGTA
8330 ATTTTTTAT
1 ATTTTTTAT
8339 ATTTTTTAT
1 ATTTTTTAT
8348 ATTTTTT
1 ATTTTTT
8355 TCATTTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (9 bp):
ATTTTTTAT
Found at i:20394 original size:26 final size:27
Alignment explanation
Indices: 20350--20401 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
20340 TTTATTTGAT
* *
20350 TAAATTGATATAATTTAATTAAATATC
1 TAAATCGATATAAATTAATTAAATATC
*
20377 TAAATCGA-ATAAATTAATTATATAT
1 TAAATCGATATAAATTAATTAAATAT
20402 AATTAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 15 0.68
27 7 0.32
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.42
Consensus pattern (27 bp):
TAAATCGATATAAATTAATTAAATATC
Found at i:21422 original size:2 final size:2
Alignment explanation
Indices: 21415--21457 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
21405 TAAACTGCTA
*
21415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT 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 AT
21457 A
1 A
21458 GCCTGGAACA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27697 original size:2 final size:2
Alignment explanation
Indices: 27690--27725 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
27680 TTTACACATA
27690 AT 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
27726 TATCTTTTCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27914 original size:21 final size:23
Alignment explanation
Indices: 27890--27938 Score: 66
Period size: 21 Copynumber: 2.2 Consensus size: 23
27880 ATTGTACAAT
* *
27890 AAAATATCATAAAAT-TAAT-TA
1 AAAATATAAAAAAATATAATATA
27911 AAAATATAAAAAAATATAATATA
1 AAAATATAAAAAAATATAATATA
27934 AAAAT
1 AAAAT
27939 CTTTTTTATG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 13 0.54
22 4 0.17
23 7 0.29
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
AAAATATAAAAAAATATAATATA
Found at i:29062 original size:88 final size:88
Alignment explanation
Indices: 28909--29075 Score: 289
Period size: 88 Copynumber: 1.9 Consensus size: 88
28899 AAAAATCATA
** *
28909 AGTACCTCCAATATCAGTGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGTTGAT
1 AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
28974 GGTCCCATCTGCATAGAAAGTCC
66 GGTCCCATCTGCATAGAAAGTCC
* *
28997 AGTACCTCCAATATCCCAGGATTTTGCATCACTGTACTAAGTACACGAGAGACCGACTTGCTGAT
1 AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
29062 GGTCCCATCTGCAT
66 GGTCCCATCTGCAT
29076 TAACCCAAGG
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
88 74 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (88 bp):
AGTACCTCCAATATCACAGGATTTTGCATCACTGTACTAAGAACACGAGAGACCGACTTGCTGAT
GGTCCCATCTGCATAGAAAGTCC
Found at i:31558 original size:16 final size:16
Alignment explanation
Indices: 31537--31570 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
31527 TTACTATTCA
*
31537 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
31553 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
31569 CG
1 CG
31571 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:47660 original size:15 final size:15
Alignment explanation
Indices: 47624--47671 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
47614 TATAAAATTT
**
47624 TAAAAAATATAAATT
1 TAAAAAATATAAAAA
* *
47639 TATAAAATTTTAAAAA
1 TA-AAAAATATAAAAA
47655 TAAAAAATATAAAAA
1 TAAAAAATATAAAAA
47670 TA
1 TA
47672 TCTAAAAACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAAATATAAAAA
Found at i:47662 original size:25 final size:25
Alignment explanation
Indices: 47610--47668 Score: 86
Period size: 25 Copynumber: 2.4 Consensus size: 25
47600 TAATGGTATC
*
47610 AATTTATAAAATTTTAAAAAATATA
1 AATTTATAAAATTTTAAAAAATAAA
47635 AATTTATAAAATTTT-AAAAATAAA
1 AATTTATAAAATTTTAAAAAATAAA
*
47659 AA-ATATAAAA
1 AATTTATAAAA
47669 ATATCTAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 7 0.22
24 10 0.31
25 15 0.47
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (25 bp):
AATTTATAAAATTTTAAAAAATAAA
Found at i:47670 original size:8 final size:8
Alignment explanation
Indices: 47626--47672 Score: 51
Period size: 8 Copynumber: 6.0 Consensus size: 8
47616 TAAAATTTTA
47626 AAAAATAT
1 AAAAATAT
**
47634 AAATTTAT
1 AAAAATAT
* *
47642 AAAATTTT
1 AAAAATAT
47650 AAAAATA-
1 AAAAATAT
47657 AAAAATAT
1 AAAAATAT
47665 AAAAATAT
1 AAAAATAT
47673 CTAAAAACAC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
7 7 0.22
8 25 0.78
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (8 bp):
AAAAATAT
Found at i:48258 original size:2 final size:2
Alignment explanation
Indices: 48251--48276 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
48241 TAAAAATTGT
48251 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
48277 AACAAATGTT
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:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:52920 original size:2 final size:2
Alignment explanation
Indices: 52913--52950 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
52903 TACCATAATA
52913 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
52951 ATTATAGAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:53305 original size:29 final size:29
Alignment explanation
Indices: 53263--53320 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
53253 CAAAGCATGC
53263 ATCCCACCCACCAGCTGTCCATCGCCACT
1 ATCCCACCCACCAGCTGTCCATCGCCACT
53292 ATCCCACCCACCAGCTGTCCATCGCCACT
1 ATCCCACCCACCAGCTGTCCATCGCCACT
53321 GTCGCCCCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.21, C:0.52, G:0.10, T:0.17
Consensus pattern (29 bp):
ATCCCACCCACCAGCTGTCCATCGCCACT
Found at i:54694 original size:14 final size:11
Alignment explanation
Indices: 54665--54695 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
54655 TACCCATCAT
54665 GGGTGGTGGGC
1 GGGTGGTGGGC
54676 GGGTGGTGGGC
1 GGGTGGTGGGC
54687 GGGTGGTGG
1 GGGTGGTGG
54696 ATTGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.00, C:0.06, G:0.74, T:0.19
Consensus pattern (11 bp):
GGGTGGTGGGC
Found at i:55268 original size:60 final size:60
Alignment explanation
Indices: 55156--55344 Score: 220
Period size: 60 Copynumber: 3.2 Consensus size: 60
55146 TATTTGGATG
* * * *
55156 AATTTGAGAATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAAAATGAGAGTCAT
1 AATTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * * * *
55216 ATTTTGAGGATAAAATTGGAATCTTCAAAAGTTTAAGGACTAGTATAGAATGA-AGTCAT
1 AATTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
* * * * *
55275 AGTCTG-GGAATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAATCAG
1 AATTTGAGG-ATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
55335 AATTTGAGGA
1 AATTTGAGGA
55345 CATATGACAC
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
58 2 0.02
59 48 0.46
60 52 0.50
61 2 0.02
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.29
Consensus pattern (60 bp):
AATTTGAGGATGAAATTGGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGAGTCAT
Found at i:55302 original size:59 final size:61
Alignment explanation
Indices: 55163--55329 Score: 196
Period size: 59 Copynumber: 2.8 Consensus size: 61
55153 ATGAATTTGA
* * * * *
55163 GAATGAAATTGGAAGATTCAAAAGTTTAGGGACCAATTTAAAATGAGAGTCATATTTTGAG
1 GAATGAAATTGGAATATTCAAAAGTTTAAGGACCAATATAAAATGAGAGTCATAGTCTGAG
* * * * *
55224 G-ATAAAATTGGAATCTTCAAAAGTTTAAGGACTAGTATAGAATGA-AGTCATAGTCTG-G
1 GAATGAAATTGGAATATTCAAAAGTTTAAGGACCAATATAAAATGAGAGTCATAGTCTGAG
* * *
55282 GAATGAAATTAGAATATTCAAAAGTTTAAGGACCAATTTAGAATGAGA
1 GAATGAAATTGGAATATTCAAAAGTTTAAGGACCAATATAAAATGAGA
55330 ATCAGAATTT
Statistics
Matches: 88, Mismatches: 16, Indels: 5
0.81 0.15 0.05
Matches are distributed among these distances:
58 2 0.02
59 48 0.55
60 37 0.42
61 1 0.01
ACGTcount: A:0.43, C:0.07, G:0.22, T:0.29
Consensus pattern (61 bp):
GAATGAAATTGGAATATTCAAAAGTTTAAGGACCAATATAAAATGAGAGTCATAGTCTGAG
Found at i:56962 original size:10 final size:9
Alignment explanation
Indices: 56927--57025 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
56917 GCTGCTGGAA
*
56927 ACCGGTTTA
1 ACCGGTTTG
*
56936 ACCGGTTTTCA
1 ACCGG-TTT-G
56947 ACCGGTTCTG
1 ACCGGTT-TG
56957 ACCGGTTTG
1 ACCGGTTTG
*
56966 ACCGGTTTCA
1 ACCGGTTT-G
*
56976 ACCGGTTCG
1 ACCGGTTTG
56985 AACCGGTTTG
1 -ACCGGTTTG
*
56995 ACCGGTCTG
1 ACCGGTTTG
* *
57004 AATCGATTTG
1 -ACCGGTTTG
*
57014 ACCGGTCTG
1 ACCGGTTTG
57023 ACC
1 ACC
57026 CGACCCGACC
Statistics
Matches: 72, Mismatches: 12, Indels: 12
0.75 0.12 0.12
Matches are distributed among these distances:
9 32 0.44
10 33 0.46
11 7 0.10
ACGTcount: A:0.17, C:0.27, G:0.26, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:56971 original size:19 final size:19
Alignment explanation
Indices: 56928--57025 Score: 69
Period size: 19 Copynumber: 5.1 Consensus size: 19
56918 CTGCTGGAAA
* * *
56928 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
56948 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
56967 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
56987 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
* *
57006 TCGATTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
57024 CC
1 CC
57026 CGACCCGACC
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
18 5 0.08
19 38 0.58
20 15 0.23
21 8 0.12
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:56989 original size:29 final size:30
Alignment explanation
Indices: 56926--57000 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
56916 GGCTGCTGGA
*
56926 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
56957 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
56985 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
57001 CTGAATCGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:57032 original size:5 final size:5
Alignment explanation
Indices: 57022--57101 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
57012 TGACCGGTCT
* **
57022 GACCC GACCC GACCGTT GACCC GACCC GACCC GACTGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GAC--CC GACCC GACCC
*
57071 GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACC--C GACCC GACCC GACCC GACC
57102 GTTGACCGTT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 50 0.82
7 11 0.18
ACGTcount: A:0.19, C:0.50, G:0.23, T:0.09
Consensus pattern (5 bp):
GACCC
Found at i:57048 original size:22 final size:22
Alignment explanation
Indices: 57022--57108 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
57012 TGACCGGTCT
57022 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
57044 GACCCGACCCGACTGTTGACCC
1 GACCCGACCCGACCGTTGACCC
57066 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
57088 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
57109 GTTGACCTTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.18, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:64310 original size:10 final size:9
Alignment explanation
Indices: 64275--64373 Score: 81
Period size: 10 Copynumber: 10.3 Consensus size: 9
64265 GCTGCTGGAA
*
64275 ACCGGTTTA
1 ACCGGTTTG
*
64284 ACCGGTTTTCA
1 ACCGG-TTT-G
64295 ACCGGTTCTG
1 ACCGGTT-TG
64305 ACCGGTTTG
1 ACCGGTTTG
*
64314 ACCGGTTTCA
1 ACCGGTTT-G
*
64324 ACCGGTTCG
1 ACCGGTTTG
64333 AACCGGTTTG
1 -ACCGGTTTG
*
64343 ACCGGTCTG
1 ACCGGTTTG
*
64352 AATCGGTTTG
1 -ACCGGTTTG
*
64362 ACCGGTCTG
1 ACCGGTTTG
64371 ACC
1 ACC
64374 CGACCCGACC
Statistics
Matches: 74, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
9 33 0.45
10 34 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:64319 original size:19 final size:19
Alignment explanation
Indices: 64276--64373 Score: 78
Period size: 19 Copynumber: 5.1 Consensus size: 19
64266 CTGCTGGAAA
* * *
64276 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
64296 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
64315 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
64335 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
*
64354 TCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
64372 CC
1 CC
64374 CGACCCGACC
Statistics
Matches: 67, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
18 5 0.07
19 39 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.28, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:64337 original size:29 final size:30
Alignment explanation
Indices: 64274--64373 Score: 118
Period size: 29 Copynumber: 3.4 Consensus size: 30
64264 GGCTGCTGGA
*
64274 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
64305 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
* * *
64333 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
*
64362 -ACCGGTCTGACC
1 AACCGGTTTGACC
64374 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
28 12 0.19
29 37 0.60
30 13 0.21
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:64380 original size:5 final size:5
Alignment explanation
Indices: 64370--64427 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
64360 TGACCGGTCT
* *
64370 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
64419 GACCC GACC
1 GACCC GACC
64428 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:64396 original size:22 final size:22
Alignment explanation
Indices: 64370--64434 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
64360 TGACCGGTCT
64370 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
64392 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
64414 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
64435 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:64436 original size:7 final size:7
Alignment explanation
Indices: 64424--64453 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
64414 GACCCGACCC
64424 GACCGTT
1 GACCGTT
64431 GACCGTT
1 GACCGTT
64438 GACCGTT
1 GACCGTT
64445 GACCGTT
1 GACCGTT
64452 GA
1 GA
64454 TCATTGACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.27
Consensus pattern (7 bp):
GACCGTT
Found at i:66375 original size:2 final size:2
Alignment explanation
Indices: 66325--66367 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
66315 CCCTTTTTTA
66325 AT AT AT AT 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 AT
66367 A
1 A
66368 AGATATATTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67675 original size:22 final size:22
Alignment explanation
Indices: 67631--67671 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
67621 TTATCGTATT
*
67631 TATATAAATAATAATATTATAA
1 TATATAAATAATAATATCATAA
*
67653 TATATAAA-ATTAATATCAT
1 TATATAAATAATAATATCAT
67672 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.41
Consensus pattern (22 bp):
TATATAAATAATAATATCATAA
Found at i:87549 original size:18 final size:17
Alignment explanation
Indices: 87521--87559 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
87511 GATTCAGACC
87521 ATTGATACATGACCGGA
1 ATTGATACATGACCGGA
87538 ATTGACTACATGACCGGA
1 ATTGA-TACATGACCGGA
87556 ATTG
1 ATTG
87560 GCTCTCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (17 bp):
ATTGATACATGACCGGA
Found at i:87905 original size:150 final size:149
Alignment explanation
Indices: 87553--87955 Score: 470
Period size: 150 Copynumber: 2.7 Consensus size: 149
87543 CTACATGACC
* * * *** * *
87553 GGAATTGGCTCTCATTATTCTGGTAAACCAATGTTTGAAAAAGATGTCATAGCTGATGGAGAAGG
1 GGAATTGGTTC-CATTATCCTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATAGAGAAGG
* * * * ** * * ** ** * *
87618 CTCTAGATACAAAACCAAAGTAGAGCATGGTAAGGTAG-TTCAGATTTCTTGATGCCACTGGAGA
65 CTCTAGATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTTAGGTTTGATGGCGCCAGTGAAGA
87682 TGGGAACGCAATCCCCGAGT
130 TGGGAACGCAATCCCCGAGT
* * *
87702 GGAATTGGTTCCATTATCCTGGTAAAGTAATACGTGAAAAAGATGTCATAGCTGATAGAGAAGGC
1 GGAATTGGTTCCATTATCCTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATAGAGAAGGC
* *
87767 TCTAGGTAT-C-GAAGCATTGTAGAGCAGGGTGGGGTAGTTTTAGGTTTGATGGCGCCAGTGAAG
66 TCTA-G-ATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTTAGGTTTGATGGCGCCAGTGAAG
* *
87830 ATGGGAATGCAATCCTCGAGT
129 ATGGGAACGCAATCCCCGAGT
* *
87851 GGAATTGGTTCCCATTATCGTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATGGAGAAGG
1 GGAATTGGTT-CCATTATCCTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATAGAGAAGG
87916 CTCTAGATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTT
65 CTCTAGATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTT
87956 CAGATGTGTT
Statistics
Matches: 216, Mismatches: 32, Indels: 11
0.83 0.12 0.04
Matches are distributed among these distances:
148 73 0.34
149 60 0.28
150 83 0.38
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (149 bp):
GGAATTGGTTCCATTATCCTGGTAAAGCAATAAGTGAAAAAAATGTCATAGCTGATAGAGAAGGC
TCTAGATGCAGAACCAATGTAGAGCAGGGTGGGGTAGTTTTAGGTTTGATGGCGCCAGTGAAGAT
GGGAACGCAATCCCCGAGT
Found at i:88936 original size:30 final size:30
Alignment explanation
Indices: 88900--88956 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
88890 CTCTAAAATT
88900 TAATCTAATGGCCTAGTTTAATAAAAAAAA
1 TAATCTAATGGCCTAGTTTAATAAAAAAAA
88930 TAATCTAATGGCCTAGTTTAATAAAAA
1 TAATCTAATGGCCTAGTTTAATAAAAA
88957 TATGGGGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.32
Consensus pattern (30 bp):
TAATCTAATGGCCTAGTTTAATAAAAAAAA
Found at i:93687 original size:24 final size:25
Alignment explanation
Indices: 93655--93706 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
93645 TAGAGCGTAC
93655 GAGGGAATGT-CTTAAAGCTACAGG
1 GAGGGAATGTCCTTAAAGCTACAGG
93679 GAGGGAATGTCCTTAAAGCTACAGG
1 GAGGGAATGTCCTTAAAGCTACAGG
93704 GAG
1 GAG
93707 TCGCACTTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 10 0.37
25 17 0.63
ACGTcount: A:0.33, C:0.13, G:0.35, T:0.19
Consensus pattern (25 bp):
GAGGGAATGTCCTTAAAGCTACAGG
Found at i:95490 original size:22 final size:22
Alignment explanation
Indices: 95456--95505 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
95446 TGACTTATTT
*
95456 AATTTT-TAAAAAAAAAATTAA
1 AATTTTATAAAAAAAAAACTAA
95477 AATTTTATAAAAAAAAAACTAA
1 AATTTTATAAAAAAAAAACTAA
95499 AATTTTA
1 AATTTTA
95506 AGCAAATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 6 0.22
22 21 0.78
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AATTTTATAAAAAAAAAACTAA
Done.