Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006078.1 Hibiscus syriacus cultivar Beakdansim tig00014397_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: 65052
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1788 original size:15 final size:15
Alignment explanation
Indices: 1770--1815 Score: 83
Period size: 15 Copynumber: 3.0 Consensus size: 15
1760 TCAAACAATG
1770 TAGTGCAGAAAAAAA
1 TAGTGCAGAAAAAAA
1785 TAGTGCAGAAAAAAAA
1 TAGTGCAG-AAAAAAA
1801 TAGTGCAGAAAAAAA
1 TAGTGCAGAAAAAAA
1816 ACAGATTTGG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 15 0.50
16 15 0.50
ACGTcount: A:0.61, C:0.07, G:0.20, T:0.13
Consensus pattern (15 bp):
TAGTGCAGAAAAAAA
Found at i:1799 original size:16 final size:16
Alignment explanation
Indices: 1770--1816 Score: 87
Period size: 16 Copynumber: 3.0 Consensus size: 16
1760 TCAAACAATG
1770 TAGTGCAG-AAAAAAA
1 TAGTGCAGAAAAAAAA
1785 TAGTGCAGAAAAAAAA
1 TAGTGCAGAAAAAAAA
1801 TAGTGCAGAAAAAAAA
1 TAGTGCAGAAAAAAAA
1817 CAGATTTGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 8 0.26
16 23 0.74
ACGTcount: A:0.62, C:0.06, G:0.19, T:0.13
Consensus pattern (16 bp):
TAGTGCAGAAAAAAAA
Found at i:4210 original size:18 final size:18
Alignment explanation
Indices: 4182--4229 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
4172 AATCTTTTTA
4182 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
*
4201 ATTTTTTATTTAATTCTT
1 ATTTTTTATTTAATTATT
4219 ATTTTTTATTT
1 ATTTTTTATTT
4230 TAACCACAAC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
18 24 0.86
19 4 0.14
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:4588 original size:24 final size:21
Alignment explanation
Indices: 4538--4593 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 21
4528 TCCCTTTGAA
*
4538 GTGCATCGATACATTCTACAT
1 GTGCATCGATGCATTCTACAT
4559 -T-CATCGATGCATTCTTTAACAT
1 GTGCATCGATGCATTC--T-ACAT
4581 GTGCATCGATGCA
1 GTGCATCGATGCA
4594 CTACCCATGC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
19 12 0.41
20 1 0.03
21 1 0.03
22 4 0.14
23 1 0.03
24 10 0.34
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (21 bp):
GTGCATCGATGCATTCTACAT
Found at i:7853 original size:19 final size:20
Alignment explanation
Indices: 7801--7856 Score: 62
Period size: 19 Copynumber: 2.8 Consensus size: 20
7791 CTATTATGTT
*
7801 CATATCATATATCTTATAACA
1 CATA-CATATATCATATAACA
*
7822 TATACA-ATAATCAT-TAACA
1 CATACATAT-ATCATATAACA
7841 CATACATATATCATAT
1 CATACATATATCATAT
7857 TATATAATTC
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
19 17 0.59
20 9 0.31
21 3 0.10
ACGTcount: A:0.46, C:0.18, G:0.00, T:0.36
Consensus pattern (20 bp):
CATACATATATCATATAACA
Found at i:7890 original size:2 final size:2
Alignment explanation
Indices: 7883--7910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
7873 CAAAACATAC
7883 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
7911 CGCATACATT
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:8729 original size:24 final size:20
Alignment explanation
Indices: 8673--8730 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
8663 TTCCCCTTGA
*
8673 AGTGCATCAATACATTCTAC
1 AGTGCATCAATGCATTCTAC
*
8693 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCAATGCATTC--T-AC
8716 ATGTGCATCAATGCA
1 A-GTGCATCAATGCA
8731 CTACCAATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (20 bp):
AGTGCATCAATGCATTCTAC
Found at i:8852 original size:21 final size:21
Alignment explanation
Indices: 8826--8881 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
8816 TCTTTAAAGA
8826 GTGCATCGATACACATTGAAT
1 GTGCATCGATACACATTGAAT
8847 GTGCATCGATACACATTGAAT
1 GTGCATCGATACACATTGAAT
8868 GTGCATCGATACAC
1 GTGCATCGATACAC
8882 CTTGCCCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (21 bp):
GTGCATCGATACACATTGAAT
Found at i:11793 original size:13 final size:13
Alignment explanation
Indices: 11770--11803 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
11760 AGTTTATATA
11770 TGTTCAGTGATGAC
1 TGTT-AGTGATGAC
11784 TGTTAGTGATGAC
1 TGTTAGTGATGAC
11797 TGTTAGT
1 TGTTAGT
11804 TTTTGCTTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.21, C:0.09, G:0.29, T:0.41
Consensus pattern (13 bp):
TGTTAGTGATGAC
Found at i:15389 original size:3 final size:3
Alignment explanation
Indices: 15332--15374 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
15322 TTTTCATTTG
*
15332 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
15375 CTAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:16965 original size:35 final size:35
Alignment explanation
Indices: 16896--17009 Score: 192
Period size: 35 Copynumber: 3.2 Consensus size: 35
16886 ACTATTATTA
*
16896 TTATTTAGTCATGTATATATATGTATATAAATAATAT
1 TTATTTAGTCATGTA-A-ATATATATATAAATAATAT
16933 TTATTTAGTCATGTAAATATATATATAAATAATAT
1 TTATTTAGTCATGTAAATATATATATAAATAATAT
*
16968 TTATTTTGTCATGTAAATATATATATAAATAATAT
1 TTATTTAGTCATGTAAATATATATATAAATAATAT
17003 TTATTTA
1 TTATTTA
17010 TTTTCCTATT
Statistics
Matches: 74, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
35 58 0.78
36 1 0.01
37 15 0.20
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (35 bp):
TTATTTAGTCATGTAAATATATATATAAATAATAT
Found at i:18605 original size:267 final size:267
Alignment explanation
Indices: 18124--18614 Score: 964
Period size: 267 Copynumber: 1.8 Consensus size: 267
18114 GAGTTTGTGA
18124 AATAGGATATTCATCAAAATCAGACATTTAATACTGGTCAACATCACTTGTTTTAAATAGGGTTC
1 AATAGGATATTCATCAAAATCAGACATTTAATACTGGTCAACATCACTTGTTTTAAATAGGGTTC
*
18189 TTGACTGTTCTGTAATAATCTTGTCTACTTTGGTTACACCTTTCCTCGGTACATTTGAATGATCA
66 TTGACTGTTCTGTAATAATCTTGTCTACTTTGGGTACACCTTTCCTCGGTACATTTGAATGATCA
18254 ATTTTGTATCGAATTACGACAAGCTATCTTCATCTTAATCATTGTTTTCTCCCCAAAATTTTCCA
131 ATTTTGTATCGAATTACGACAAGCTATCTTCATCTTAATCATTGTTTTCTCCCCAAAATTTTCCA
18319 CCTGCATTGCTATTACCGGTATAACTCTGGCTTGTTTCGAATTACGACAAGCTATCTTCATCACT
196 CCTGCATTGCTATTACCGGTATAACTCTGGCTTGTTTCGAATTACGACAAGCTATCTTCATCACT
18384 TGTTTTT
261 TGTTTTT
*
18391 AATAGTATATTCATCAAAATCAGACATTTAATACTGGTCAACATCACTTGTTTTAAATAGGGTTC
1 AATAGGATATTCATCAAAATCAGACATTTAATACTGGTCAACATCACTTGTTTTAAATAGGGTTC
18456 TTGACTGTTCTGTAATAATCTTGTCTACTTTGGGTACACCTTTCCTCGGTACATTTGAATGATCA
66 TTGACTGTTCTGTAATAATCTTGTCTACTTTGGGTACACCTTTCCTCGGTACATTTGAATGATCA
18521 ATTTTGTATCGAATTACGACAAGCTATCTTCATCTTAATCATTGTTTTCTCCCCAAAATTTTCCA
131 ATTTTGTATCGAATTACGACAAGCTATCTTCATCTTAATCATTGTTTTCTCCCCAAAATTTTCCA
18586 CCTGCATTGCTATTACCGGTATAACTCTG
196 CCTGCATTGCTATTACCGGTATAACTCTG
18615 TGGCTTGCTC
Statistics
Matches: 222, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
267 222 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (267 bp):
AATAGGATATTCATCAAAATCAGACATTTAATACTGGTCAACATCACTTGTTTTAAATAGGGTTC
TTGACTGTTCTGTAATAATCTTGTCTACTTTGGGTACACCTTTCCTCGGTACATTTGAATGATCA
ATTTTGTATCGAATTACGACAAGCTATCTTCATCTTAATCATTGTTTTCTCCCCAAAATTTTCCA
CCTGCATTGCTATTACCGGTATAACTCTGGCTTGTTTCGAATTACGACAAGCTATCTTCATCACT
TGTTTTT
Found at i:20472 original size:2 final size:2
Alignment explanation
Indices: 20465--20493 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
20455 TTATAAATAA
20465 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 A
20494 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20499 original size:3 final size:3
Alignment explanation
Indices: 20491--20515 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
20481 ATATATATAT
20491 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
20516 AAAGATCCTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:26259 original size:14 final size:14
Alignment explanation
Indices: 26240--26266 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26230 CAAAACATGG
26240 GAGAGAGAAAAGTA
1 GAGAGAGAAAAGTA
26254 GAGAGAGAAAAGT
1 GAGAGAGAAAAGT
26267 TAGAAAGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.37, T:0.07
Consensus pattern (14 bp):
GAGAGAGAAAAGTA
Found at i:26466 original size:17 final size:19
Alignment explanation
Indices: 26444--26478 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
26434 GCTTTTGTTC
26444 AGTTTG-AGAGGG-AATCT
1 AGTTTGAAGAGGGCAATCT
26461 AGTTTGAAGAGGGCAATC
1 AGTTTGAAGAGGGCAATC
26479 GAGATGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 6 0.38
19 4 0.25
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (19 bp):
AGTTTGAAGAGGGCAATCT
Found at i:36576 original size:20 final size:20
Alignment explanation
Indices: 36528--36589 Score: 62
Period size: 18 Copynumber: 3.2 Consensus size: 20
36518 AACTTAAATC
*
36528 AAAATAATTAAAATAA-ATAT
1 AAAATAATT-TAATAATATAT
36548 AAAAT--TTTAATAATATAT
1 AAAATAATTTAATAATATAT
36566 AAAATAATTT-AT-ATGATAT
1 AAAATAATTTAATAAT-ATAT
36585 AAAAT
1 AAAAT
36590 TAAATATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
17 5 0.14
18 13 0.35
19 11 0.30
20 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
AAAATAATTTAATAATATAT
Found at i:36659 original size:63 final size:63
Alignment explanation
Indices: 36584--36738 Score: 228
Period size: 63 Copynumber: 2.5 Consensus size: 63
36574 TTATATGATA
* * *
36584 TAAAATTAAATATGTATAATATAATATT-AAAAAATAATATTTAATTTATTTGAAAAATTAATAT
1 TAAAATT-AATATCTATAATATAATATTAAAAAAACAATATTTAATTT-TTTAAAAAATTAATAT
36648 TAAAATTAATATCTATAATATAATATTAAAAAAACAATATTTAATTTTTTAAAAAATTAATAT
1 TAAAATTAATATCTATAATATAATATTAAAAAAACAATATTTAATTTTTTAAAAAATTAATAT
*
36711 TAAAATTAAAATC-A-AATATAATA-TAAAA
1 TAAAATTAATATCTATAATATAATATTAAAA
36739 TTAAATATAA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
60 5 0.06
61 9 0.10
62 1 0.01
63 46 0.53
64 25 0.29
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (63 bp):
TAAAATTAATATCTATAATATAATATTAAAAAAACAATATTTAATTTTTTAAAAAATTAATAT
Found at i:36673 original size:14 final size:12
Alignment explanation
Indices: 36584--36678 Score: 59
Period size: 13 Copynumber: 7.4 Consensus size: 12
36574 TTATATGATA
36584 TAAAATTAAATAT
1 TAAAATT-AATAT
*
36597 GTATAATATAATAT
1 -TAAAAT-TAATAT
*
36611 TAAAAAATAATAT
1 T-AAAATTAATAT
* *
36624 T-TAATTTAT-T
1 TAAAATTAATAT
36634 TGAAAAATTAATAT
1 T--AAAATTAATAT
36648 TAAAATTAATAT
1 TAAAATTAATAT
*
36660 CTATAATATAATAT
1 -TAAAAT-TAATAT
36674 TAAAA
1 TAAAA
36679 AAACAATATT
Statistics
Matches: 63, Mismatches: 10, Indels: 17
0.70 0.11 0.19
Matches are distributed among these distances:
10 2 0.03
11 5 0.08
12 11 0.17
13 23 0.37
14 21 0.33
15 1 0.02
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.41
Consensus pattern (12 bp):
TAAAATTAATAT
Found at i:36715 original size:12 final size:11
Alignment explanation
Indices: 36700--36750 Score: 57
Period size: 12 Copynumber: 4.4 Consensus size: 11
36690 AATTTTTTAA
36700 AAAATTAATATT
1 AAAATTAATA-T
*
36712 AAAATTAAAAT
1 AAAATTAATAT
*
36723 CAAATATAATAT
1 AAAAT-TAATAT
36735 AAAATTAAATAT
1 AAAATT-AATAT
36747 AAAA
1 AAAA
36751 CCTCTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 6 0.18
12 27 0.82
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
AAAATTAATAT
Found at i:37644 original size:20 final size:20
Alignment explanation
Indices: 37619--37656 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
37609 ATTTGATTTG
*
37619 CGAAATTCGTGTTGCGAAAA
1 CGAAATTCGCGTTGCGAAAA
37639 CGAAATTCGCGTTGCGAA
1 CGAAATTCGCGTTGCGAA
37657 TAGTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.24
Consensus pattern (20 bp):
CGAAATTCGCGTTGCGAAAA
Found at i:37735 original size:20 final size:20
Alignment explanation
Indices: 37710--37761 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
37700 CCATATTCGA
37710 GTTGCGAATTTGGAAACT-GT
1 GTTGCGAATTTGG-AACTCGT
* * *
37730 GTTGCGAAATAGGAATTCGT
1 GTTGCGAATTTGGAACTCGT
37750 GTTGCGAATTTG
1 GTTGCGAATTTG
37762 TTGGTTATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
19 3 0.12
20 23 0.88
ACGTcount: A:0.25, C:0.10, G:0.31, T:0.35
Consensus pattern (20 bp):
GTTGCGAATTTGGAACTCGT
Found at i:40147 original size:3 final size:3
Alignment explanation
Indices: 40141--40230 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
40131 TTTATTATTA
40141 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
40189 -TG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG T
40231 CGCCGTTGTC
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:41432 original size:16 final size:18
Alignment explanation
Indices: 41400--41433 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
41390 TATTAATGTA
41400 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
41418 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
41434 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:42103 original size:130 final size:130
Alignment explanation
Indices: 41899--42146 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
41889 AATTTTCTTC
* * *
41899 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCAACAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** *
41964 CCTGGTTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* *
42029 TAATTAGGTGGTGACATGTGTCAACAATGACACATGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGTGTCAACAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
42094 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
42147 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGTGTCAACAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:42593 original size:35 final size:35
Alignment explanation
Indices: 42543--42618 Score: 134
Period size: 35 Copynumber: 2.2 Consensus size: 35
42533 AATTGAATTT
* *
42543 AATTGAATTATTTTGGAATTTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
42578 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
42613 AATTGA
1 AATTGA
42619 GGATTGTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.37, C:0.01, G:0.22, T:0.39
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTTAGAATGA
Found at i:43152 original size:31 final size:30
Alignment explanation
Indices: 43112--43170 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 30
43102 GTTACAAAAC
* *
43112 AATATTATAAAATGATAATTAATTTTATCG
1 AATATTATAAAATAATAATTAAATTTATCG
43142 AATAGTTATAAAATAATAATTAAATTTAT
1 AATA-TTATAAAATAATAATTAAATTTAT
43171 TTAATTTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (30 bp):
AATATTATAAAATAATAATTAAATTTATCG
Found at i:59942 original size:2 final size:2
Alignment explanation
Indices: 59935--59964 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59925 ATTCAACATA
59935 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
59965 TGATAATTTT
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):
AT
Done.