Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005602.1 Hibiscus syriacus cultivar Beakdansim tig00013030_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: 70845
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:857 original size:3 final size:3
Alignment explanation
Indices: 839--882 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
829 TTATTGTTGA
*
839 TAT T-T TAT TTT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
883 TGAATTGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
2 4 0.11
3 33 0.89
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:870 original size:17 final size:16
Alignment explanation
Indices: 839--883 Score: 67
Period size: 17 Copynumber: 2.9 Consensus size: 16
829 TTATTGTTGA
839 TATT-TTATT-TTTAT
1 TATTATTATTATTTAT
853 TATTATTATTATTATAT
1 TATTATTATTATT-TAT
870 TATTATTATTATTT
1 TATTATTATTATTT
884 GAATTGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
14 4 0.14
15 5 0.18
16 3 0.11
17 16 0.57
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TATTATTATTATTTAT
Found at i:4201 original size:16 final size:16
Alignment explanation
Indices: 4180--4210 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4170 CTAATTTTTT
4180 TTTTTGAGTTCAAGTC
1 TTTTTGAGTTCAAGTC
4196 TTTTTGAGTTCAAGT
1 TTTTTGAGTTCAAGT
4211 TTCAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.10, G:0.19, T:0.52
Consensus pattern (16 bp):
TTTTTGAGTTCAAGTC
Found at i:5400 original size:10 final size:9
Alignment explanation
Indices: 5365--5443 Score: 61
Period size: 10 Copynumber: 8.3 Consensus size: 9
5355 GCTGCTGGAA
*
5365 ACCGGTTTA
1 ACCGGTTTG
*
5374 ACCGGTTTTCA
1 ACCGG-TTT-G
5385 ACCGGTTCTG
1 ACCGGTT-TG
5395 ACCGG-TTG
1 ACCGGTTTG
*
5403 ACCGGTTTCA
1 ACCGGTTT-G
*
5413 ACCGGTTCG
1 ACCGGTTTG
5422 AACCGGTTTG
1 -ACCGGTTTG
*
5432 ACCGGTCTG
1 ACCGGTTTG
5441 ACC
1 ACC
5444 CGACCGACCG
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
8 7 0.12
9 19 0.33
10 25 0.43
11 7 0.12
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:5408 original size:18 final size:17
Alignment explanation
Indices: 5385--5443 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 17
5375 CCGGTTTTCA
5385 ACCGGTTCTGACCGGTTG
1 ACCGGTT-TGACCGGTTG
*
5403 ACCGGTTTCAACCGGTTCG
1 ACCGGTTT-GACCGGTT-G
5422 AACCGGTTTGACCGGTCTG
1 -ACCGGTTTGACCGGT-TG
5441 ACC
1 ACC
5444 CGACCGACCG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 1 0.03
18 17 0.49
19 8 0.23
20 9 0.26
ACGTcount: A:0.15, C:0.31, G:0.29, T:0.25
Consensus pattern (17 bp):
ACCGGTTTGACCGGTTG
Found at i:5409 original size:29 final size:30
Alignment explanation
Indices: 5364--5437 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 30
5354 GGCTGCTGGA
*
5364 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGGTTTTCAACCGGTTC-G
5395 -ACCGG-TTGACCGG-TTTCAACCGGTTCG
1 AACCGGTTTGACCGGTTTTCAACCGGTTCG
5422 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
5438 CTGACCCGAC
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
27 1 0.03
28 18 0.46
29 15 0.38
30 5 0.13
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTTCAACCGGTTCG
Found at i:5426 original size:38 final size:37
Alignment explanation
Indices: 5365--5443 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 37
5355 GCTGCTGGAA
5365 ACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGT-TG
1 ACCGGTTTAACCGG-TTTCAACCGGTT-TGACCGGTCTG
5403 ACCGGTTTCAACCGG-TTCGAACCGGTTTGACCGGTCTG
1 ACCGGTTT-AACCGGTTTC-AACCGGTTTGACCGGTCTG
5441 ACC
1 ACC
5444 CGACCGACCG
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
37 11 0.29
38 21 0.55
39 6 0.16
ACGTcount: A:0.16, C:0.29, G:0.27, T:0.28
Consensus pattern (37 bp):
ACCGGTTTAACCGGTTTCAACCGGTTTGACCGGTCTG
Found at i:5464 original size:12 final size:12
Alignment explanation
Indices: 5447--5486 Score: 66
Period size: 12 Copynumber: 3.5 Consensus size: 12
5437 TCTGACCCGA
5447 CCGACCGTTGAC
1 CCGACCGTTGAC
5459 CCGACC--TGAC
1 CCGACCGTTGAC
5469 CCGACCGTTGAC
1 CCGACCGTTGAC
5481 CCGACC
1 CCGACC
5487 CGACCGTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 10 0.38
12 16 0.62
ACGTcount: A:0.17, C:0.47, G:0.23, T:0.12
Consensus pattern (12 bp):
CCGACCGTTGAC
Found at i:5475 original size:22 final size:22
Alignment explanation
Indices: 5440--5491 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
5430 TGACCGGTCT
5440 GACCCGA-CCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
5461 GACCTGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
5483 GACCCGACC
1 GACCCGACC
5492 GTGATCGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.19, C:0.48, G:0.23, T:0.10
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:5481 original size:17 final size:17
Alignment explanation
Indices: 5439--5493 Score: 58
Period size: 17 Copynumber: 3.0 Consensus size: 17
5429 TTGACCGGTC
5439 TGACCCGA-CCGACCGT
1 TGACCCGACCCGACCGT
5455 TGACCCGACCTGACCCGACCGT
1 TGA--C--CC-GACCCGACCGT
5477 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
5494 GATCGTTGAC
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
16 3 0.09
17 11 0.33
18 3 0.09
20 3 0.09
21 2 0.06
22 11 0.33
ACGTcount: A:0.18, C:0.45, G:0.24, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:12685 original size:9 final size:9
Alignment explanation
Indices: 12663--12731 Score: 75
Period size: 9 Copynumber: 7.3 Consensus size: 9
12653 GCTGCTGGAA
12663 ACCGGTTCTG
1 ACCGGTT-TG
12673 ACCGGTTTG
1 ACCGGTTTG
*
12682 ACCGGTTTCA
1 ACCGGTTT-G
*
12692 ACCGGTTCG
1 ACCGGTTTG
12701 AACCGGTTTG
1 -ACCGGTTTG
*
12711 ACAGGTTTG
1 ACCGGTTTG
*
12720 ACCGGTCTG
1 ACCGGTTTG
12729 ACC
1 ACC
12732 TGACCCGACC
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
9 28 0.56
10 22 0.44
ACGTcount: A:0.16, C:0.28, G:0.29, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:12705 original size:29 final size:29
Alignment explanation
Indices: 12662--12731 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
12652 GGCTGCTGGA
*
12662 AACCGGTTCTGACCGGTTTGACCGGTTTC
1 AACCGGTTCTGACCGGTTTGACAGGTTTC
12691 AACCGGTTC-GAACCGGTTTGACAGGTTT-
1 AACCGGTTCTG-ACCGGTTTGACAGGTTTC
*
12719 GACCGG-TCTGACC
1 AACCGGTTCTGACC
12732 TGACCCGACC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
27 5 0.14
28 7 0.19
29 25 0.68
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (29 bp):
AACCGGTTCTGACCGGTTTGACAGGTTTC
Found at i:12753 original size:17 final size:17
Alignment explanation
Indices: 12727--12763 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
12717 TTGACCGGTC
*
12727 TGACCTGACCCGACCGT
1 TGACCCGACCCGACCGT
12744 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
12761 TGA
1 TGA
12764 TCGTTGACCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.19, C:0.41, G:0.24, T:0.16
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:14954 original size:21 final size:21
Alignment explanation
Indices: 14930--14999 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
14920 ATTTTTATAA
14930 TATTAAAATATATTATTTAAT
1 TATTAAAATATATTATTTAAT
* * * *
14951 TATTTAATTATAATAAATT-AT
1 TATTAAAATAT-ATTATTTAAT
*
14972 TA-TAAAATAAATTATTTTAAT
1 TATTAAAATATATTA-TTTAAT
*
14993 AATTAAA
1 TATTAAA
15000 TAATAATAAT
Statistics
Matches: 35, Mismatches: 10, Indels: 7
0.67 0.19 0.13
Matches are distributed among these distances:
19 3 0.09
20 7 0.20
21 16 0.46
22 9 0.26
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATTAAAATATATTATTTAAT
Found at i:14986 original size:41 final size:41
Alignment explanation
Indices: 14933--15012 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
14923 TTTATAATAT
* * * *
14933 TAAAATATATTA-TTTAATTATTTAATTATAATAAATTATTA
1 TAAAATAAATTATTTTAATAATTAAATAATAAT-AATTATTA
14974 TAAAATAAATTATTTTAATAATTAAATAATAATAATTAT
1 TAAAATAAATTATTTTAATAATTAAATAATAATAATTAT
15013 AAATATATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 17 0.50
42 17 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (41 bp):
TAAAATAAATTATTTTAATAATTAAATAATAATAATTATTA
Found at i:15048 original size:13 final size:15
Alignment explanation
Indices: 14930--15049 Score: 61
Period size: 13 Copynumber: 8.9 Consensus size: 15
14920 ATTTTTATAA
14930 TATTAAA-ATA-TAT
1 TATTAAATATATTAT
*
14943 TATTTAAT-TATT-T
1 TATTAAATATATTAT
* *
14956 AATTATAATAAATTAT
1 TATTA-AATATATTAT
* *
14972 TATAAAATAAATTAT
1 TATTAAATATATTAT
14987 T-TT-AATA-ATTA-
1 TATTAAATATATTAT
* *
14998 -AAT-AATA-ATAAT
1 TATTAAATATATTAT
15010 TA-TAAATATATTAT
1 TATTAAATATATTAT
*
15024 TATAAAATATATTAT
1 TATTAAATATATTAT
15039 T-TTAAA-ATATT
1 TATTAAATATATT
15050 GATATATTTG
Statistics
Matches: 84, Mismatches: 12, Indels: 22
0.71 0.10 0.19
Matches are distributed among these distances:
11 8 0.10
12 5 0.06
13 26 0.31
14 15 0.18
15 26 0.31
16 4 0.05
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TATTAAATATATTAT
Found at i:15048 original size:15 final size:15
Alignment explanation
Indices: 14933--15048 Score: 69
Period size: 15 Copynumber: 8.5 Consensus size: 15
14923 TTTATAATAT
14933 TAAAATATATTATT-
1 TAAAATATATTATTA
*
14947 T-AATTAT-TTAATTA
1 TAAAATATATT-ATTA
*
14961 T--AATAAATTATTA
1 TAAAATATATTATTA
*
14974 TAAAATAAATTATT-
1 TAAAATATATTATTA
*
14988 T-TAATA-ATTA--A
1 TAAAATATATTATTA
* *
14999 -ATAATA-ATAATTA
1 TAAAATATATTATTA
15012 T-AAATATATTATTA
1 TAAAATATATTATTA
*
15026 TAAAATATATTATTT
1 TAAAATATATTATTA
15041 TAAAATAT
1 TAAAATAT
15049 TGATATATTT
Statistics
Matches: 82, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
11 8 0.10
12 6 0.07
13 25 0.30
14 12 0.15
15 31 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
TAAAATATATTATTA
Found at i:24699 original size:21 final size:18
Alignment explanation
Indices: 24660--24708 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
24650 TTAGATATGA
*
24660 TAATAATTAATTTGTATT
1 TAATTATTAATTTGTATT
24678 TAAATTTATTAATTTGGTATT
1 T-AA-TTATTAATTT-GTATT
24699 TAATTATTAA
1 TAATTATTAA
24709 ATAATGAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
18 1 0.04
19 9 0.33
20 11 0.41
21 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
TAATTATTAATTTGTATT
Found at i:24703 original size:20 final size:19
Alignment explanation
Indices: 24665--24708 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
24655 TATGATAATA
24665 ATTAATTTGTATTTAAATTT
1 ATTAATTTGTATTTAAA-TT
24685 ATTAATTTGGTATTT-AATT
1 ATTAATTT-GTATTTAAATT
24704 ATTAA
1 ATTAA
24709 ATAATGAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.30
20 10 0.43
21 6 0.26
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (19 bp):
ATTAATTTGTATTTAAATT
Found at i:24761 original size:3 final size:3
Alignment explanation
Indices: 24753--24786 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
24743 TAATTTTTTC
24753 TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
24787 AATAAATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:26644 original size:20 final size:21
Alignment explanation
Indices: 26621--26672 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
26611 AGAAATTAAA
26621 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
26641 AATTCTTTTCTTTAAAATTTTT
1 AATTCATTTATTT-AAATTTTT
26663 -ATT-ATTTATT
1 AATTCATTTATT
26673 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:33624 original size:83 final size:83
Alignment explanation
Indices: 33485--33701 Score: 355
Period size: 83 Copynumber: 2.6 Consensus size: 83
33475 AACATTAACT
33485 AGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTAAAC
1 AGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAAAC
33549 AGAACCAATCATTGAATTC
66 AGAA-CAATCATTGAATTC
* **
33568 AGAAGATAAATTTGCCAATATCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGAC
1 AGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAAAC
* *
33633 AGAACAATCATTGAGTTT
66 AGAACAATCATTGAATTC
* *
33651 AGAAGATGAATTTGCCAATAGCATCTTATGGAAGTGTTCTTTGAGTTATCT
1 AGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCT
33702 AGTTTGGTAT
Statistics
Matches: 125, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
83 117 0.94
84 8 0.06
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (83 bp):
AGAAGATAAATTTGCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTAAAC
AGAACAATCATTGAATTC
Found at i:36265 original size:22 final size:22
Alignment explanation
Indices: 36236--36290 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
36226 ATCTACACTC
36236 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
36258 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
36280 TTCAAAGATGA
1 TTCAAAGATGA
36291 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:37050 original size:76 final size:76
Alignment explanation
Indices: 36968--37730 Score: 1438
Period size: 76 Copynumber: 10.0 Consensus size: 76
36958 CTATTTCCCA
*
36968 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37033 ATCCTTCGGGT
66 ATCCTTCGGGT
37044 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37109 ATCCTTCGGGT
66 ATCCTTCGGGT
* *
37120 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCATTCGGGAGCTTTTTGATGTTTGCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37185 ATCCTTCGGGT
66 ATCCTTCGGGT
37196 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37261 ATCCTTCGGGT
66 ATCCTTCGGGT
37272 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37337 ATCCTTCGGGT
66 ATCCTTCGGGT
37348 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37413 ATCCTTCGGGT
66 ATCCTTCGGGT
37424 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
37489 AGCCTTCGGGT
66 ATCCTTCGGGT
*
37500 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37565 ATCCTTCGGGT
66 ATCCTTCGGGT
37576 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
37641 ATCCTTCGGGT
66 ATCCTTCGGGT
* *
37652 CATCTGTAAGCCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
37717 A-CCCTCAGGGT
66 ATCCTTC-GGGT
37728 CAT
1 CAT
37731 TCATAAGACC
Statistics
Matches: 674, Mismatches: 12, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
75 4 0.01
76 670 0.99
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (76 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
ATCCTTCGGGT
Found at i:37888 original size:3 final size:3
Alignment explanation
Indices: 37882--37915 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
37872 AATTTTTTTC
37882 TTA TTA TTA TTA TTA TTA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
37916 AATAAATATA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:41681 original size:15 final size:15
Alignment explanation
Indices: 41661--41691 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
41651 AATTCGGTGG
41661 GAGAAAGGAAAACCA
1 GAGAAAGGAAAACCA
41676 GAGAAAGGAAAACCA
1 GAGAAAGGAAAACCA
41691 G
1 G
41692 TATGCCAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.58, C:0.13, G:0.29, T:0.00
Consensus pattern (15 bp):
GAGAAAGGAAAACCA
Found at i:43206 original size:45 final size:45
Alignment explanation
Indices: 43157--43255 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 45
43147 AAGATCTGGG
* *
43157 TCACATAGCATTAGCATCTCA-AGAGTACCTTAAG-TAAGGTTCGGA
1 TCACATAGCATCAGCACCTCACAGA-TACCTTAAGCT-AGGTTCGGA
* * * * *
43202 TCACAAAGTATCAGCACCTCACTGATATCTTAAGCTAGGTTCGGG
1 TCACATAGCATCAGCACCTCACAGATACCTTAAGCTAGGTTCGGA
43247 TCACATAGC
1 TCACATAGC
43256 GTAGGAACCA
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
45 40 0.93
46 3 0.07
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.26
Consensus pattern (45 bp):
TCACATAGCATCAGCACCTCACAGATACCTTAAGCTAGGTTCGGA
Found at i:46170 original size:19 final size:19
Alignment explanation
Indices: 46146--46185 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
46136 AATAATATAA
*
46146 ATAAAGTTTATAATATTTG
1 ATAAAGTTTATAAAATTTG
*
46165 ATAAAGTTTGTAAAATTTG
1 ATAAAGTTTATAAAATTTG
46184 AT
1 AT
46186 TTTTGAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (19 bp):
ATAAAGTTTATAAAATTTG
Found at i:47935 original size:19 final size:19
Alignment explanation
Indices: 47911--47962 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
47901 TTTAAGCGAG
47911 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
47930 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
47949 TGCATCGATGCACT
1 TGCATCGATGCACT
47963 AATGGCATTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.21, C:0.31, G:0.17, T:0.31
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:47942 original size:83 final size:84
Alignment explanation
Indices: 47847--48022 Score: 200
Period size: 83 Copynumber: 2.1 Consensus size: 84
47837 CCTTGACGGG
* * **
47847 TGCATCGATGCACT-GTCTATGCATCGGTGCA-TAAATCCCATTCGATGTTTGTA-TTTTAA-GC
1 TGCATCGATGCACTCCT-TATGCATCGATGCACT-AATCCCATTCGATGTTTCCATTTTTAATG-
47908 GAGTGCATCGATGCAC-TCCTTA
63 GAGTGCATCGATGCACTTCC-TA
** *
47930 TGCATCGATGCACTCCTTATGCATCGATGCACTAATGGCATTCGATGTTTCCATTTTTAATGGGG
1 TGCATCGATGCACTCCTTATGCATCGATGCACTAATCCCATTCGATGTTTCCATTTTTAATGGAG
* *
47995 TGCATTGATGCACTTCCTG
66 TGCATCGATGCACTTCCTA
48014 TGCATCGAT
1 TGCATCGAT
48023 ACACACTGAA
Statistics
Matches: 79, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
83 43 0.54
84 32 0.41
85 4 0.05
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.35
Consensus pattern (84 bp):
TGCATCGATGCACTCCTTATGCATCGATGCACTAATCCCATTCGATGTTTCCATTTTTAATGGAG
TGCATCGATGCACTTCCTA
Found at i:50623 original size:32 final size:32
Alignment explanation
Indices: 50576--50640 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 32
50566 CCATCCCAGG
* * *
50576 GTGTGAATGCAAAAAATAGTAACTATTTGAAA
1 GTGTAAATGAAAAAAATAATAACTATTTGAAA
50608 GTGTAAATGAAAAAAATAATAACTATTTGAAA
1 GTGTAAATGAAAAAAATAATAACTATTTGAAA
50640 G
1 G
50641 AGTGAATGCA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.51, C:0.05, G:0.17, T:0.28
Consensus pattern (32 bp):
GTGTAAATGAAAAAAATAATAACTATTTGAAA
Found at i:55864 original size:158 final size:158
Alignment explanation
Indices: 55474--55865 Score: 479
Period size: 158 Copynumber: 2.5 Consensus size: 158
55464 GAAAAATAAC
* * * * * * *
55474 AATTGAACTTACATAGGTATTCTAGTGTGGTATATGAGCATATGTTTCAAATTTGGTGAAAAAAA
1 AATTGAACATACATAAGTAATCTACTAT-GTTTATGAGCATATGATTCAAATTTGGT-AAAAAAA
* * *
55539 -AGACTTAAAATAAATCACAAATTAAAGGAATAAGGAGATTATGAAAAATTGAAGGTTTAAATTG
64 TATACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAAAAATTGAAGGTCTAAATTG
*
55603 AAAAATAAAAAATTTGTTATTAAAAAGAGG
129 AAAAATAAAAAATTTGTTATCAAAAAGAGG
* *
55633 AATT-AA-AGTACATAAGTAATCTACTATGATTTAAGAGCATATGACTCAAATTTGGTAAAAAAA
1 AATTGAACA-TACATAAGTAATCTACTATG-TTTATGAGCATATGATTCAAATTTGGTAAAAAAA
** * * * *
55696 TATAAATAAAATAAATGACGAATTAAATAAATAAGTAGATTATGAAAAATTGAA-GTACTAAATT
64 TATACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAAAAATTGAAGGT-CTAAATT
*
55760 GAAAAATAAAAAATTTGTTATCAAAAAGAGT
128 GAAAAATAAAAAATTTGTTATCAAAAAGAGG
* * * *
55791 AATTGAACATACATATGTAATCTACTATAGTTTATGAGCATGTGGTTCAAATTTGGT-TAAAAAT
1 AATTGAACATACATAAGTAATCTACTAT-GTTTATGAGCATATGATTCAAATTTGGTAAAAAAAT
55855 ATACTTAAAAT
65 ATACTTAAAAT
55866 GAAGGAGGAA
Statistics
Matches: 198, Mismatches: 28, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
157 10 0.05
158 139 0.70
159 47 0.24
160 2 0.01
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (158 bp):
AATTGAACATACATAAGTAATCTACTATGTTTATGAGCATATGATTCAAATTTGGTAAAAAAATA
TACTTAAAATAAATCACAAATTAAAGAAATAAGGAGATTATGAAAAATTGAAGGTCTAAATTGAA
AAATAAAAAATTTGTTATCAAAAAGAGG
Found at i:57858 original size:3 final size:3
Alignment explanation
Indices: 57850--57905 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
57840 ACATTACACG
57850 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
57898 TTA TTA TT
1 TTA TTA TT
57906 TATAAACATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:62778 original size:36 final size:38
Alignment explanation
Indices: 62731--62811 Score: 114
Period size: 36 Copynumber: 2.2 Consensus size: 38
62721 TTAAACTTTC
*
62731 AAATGTTTAAATAAAA-AA-TAA-TAATAAAATAATACA
1 AAATTTTTAAATAAAATAATTAATTAATAAAATAATA-A
*
62767 AAATTTTTAAATAAAATAATTAATTACTAAAATAATAA
1 AAATTTTTAAATAAAATAATTAATTAATAAAATAATAA
62805 AAATTTT
1 AAATTTT
62812 GATAAATGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
36 15 0.38
37 2 0.05
38 11 0.28
39 12 0.30
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (38 bp):
AAATTTTTAAATAAAATAATTAATTAATAAAATAATAA
Found at i:62834 original size:36 final size:36
Alignment explanation
Indices: 62731--62834 Score: 97
Period size: 36 Copynumber: 2.8 Consensus size: 36
62721 TTAAACTTTC
* * * *
62731 AAATGTTTAAATAAAAAATAATAATAAAATAATACA
1 AAATTTTTAAATAAAATATTATTATAAAATAATACA
62767 AAATTTTTAAATAAAATAATTAATTACTAAAATAATA-A
1 AAATTTTTAAATAAAAT-ATT-ATTA-TAAAATAATACA
62805 AAATTTTGATAAATGAAAAT-TT-TTATAAAA
1 AAATTTT--TAAAT-AAAATATTATTATAAAA
62835 ATACTTATAC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
36 20 0.34
37 5 0.09
38 11 0.19
39 12 0.21
40 5 0.09
41 5 0.09
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (36 bp):
AAATTTTTAAATAAAATATTATTATAAAATAATACA
Found at i:63643 original size:12 final size:12
Alignment explanation
Indices: 63626--63657 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
63616 TATACCACCA
63626 TCACCATCTCCG
1 TCACCATCTCCG
63638 TCACCATCTCCG
1 TCACCATCTCCG
63650 TCACCATC
1 TCACCATC
63658 GTATCTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.19, C:0.50, G:0.06, T:0.25
Consensus pattern (12 bp):
TCACCATCTCCG
Found at i:69116 original size:2 final size:2
Alignment explanation
Indices: 69109--69147 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
69099 AGCTTTTACA
69109 AT AT AT AT AT AT AT A- 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
69148 GCACACCAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:69691 original size:23 final size:23
Alignment explanation
Indices: 69661--69708 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
69651 CCTTTTGAAT
69661 CTCTGTGAGCTTAGAGTAGGTAG
1 CTCTGTGAGCTTAGAGTAGGTAG
69684 CTCTGTGAGCTTAGAGTAGGTAG
1 CTCTGTGAGCTTAGAGTAGGTAG
69707 CT
1 CT
69709 TTATTAAACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (23 bp):
CTCTGTGAGCTTAGAGTAGGTAG
Done.