Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007420.1 Hibiscus syriacus cultivar Beakdansim tig00020082_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: 56011
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Found at i:3806 original size:20 final size:20
Alignment explanation
Indices: 3771--3823 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3761 CCTTAGGGTT
* *
3771 GTATATTGGCTATTGTCTATT
1 GTATA-TGGTTATTGTCTATG
*
3792 GTTTATGGTTATTGTCTATG
1 GTATATGGTTATTGTCTATG
3812 GTATATGGTTAT
1 GTATATGGTTAT
3824 GGAATAATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 24 0.86
21 4 0.14
ACGTcount: A:0.19, C:0.06, G:0.23, T:0.53
Consensus pattern (20 bp):
GTATATGGTTATTGTCTATG
Found at i:6443 original size:24 final size:24
Alignment explanation
Indices: 6414--6474 Score: 70
Period size: 24 Copynumber: 2.5 Consensus size: 24
6404 ATTAATATTG
6414 GTATATAAATTATATAACTATAAA
1 GTATATAAATTATATAACTATAAA
* * *
6438 GTATATAAAATAGTATAAGTATATA
1 GTATATAAATTA-TATAACTATAAA
*
6463 -TATATATATTAT
1 GTATATAAATTAT
6475 GCATGTATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
23 1 0.03
24 20 0.65
25 10 0.32
ACGTcount: A:0.51, C:0.02, G:0.07, T:0.41
Consensus pattern (24 bp):
GTATATAAATTATATAACTATAAA
Found at i:6454 original size:36 final size:34
Alignment explanation
Indices: 6388--6454 Score: 82
Period size: 36 Copynumber: 1.9 Consensus size: 34
6378 ATATACTTAT
* *
6388 ATTATATATATAAAGTATTAATATTGGTATATAA
1 ATTATATATATAAAGTATTAATAATAGTATATAA
6422 ATTATATAACTATAAAGTATATAA-AATAGTATA
1 ATTATAT-A-TATAAAGTAT-TAATAATAGTATA
6455 AGTATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 7 0.25
35 1 0.04
36 17 0.61
37 3 0.11
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.40
Consensus pattern (34 bp):
ATTATATATATAAAGTATTAATAATAGTATATAA
Found at i:7376 original size:13 final size:14
Alignment explanation
Indices: 7358--7386 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7348 GTGTGACGAA
7358 AACCTAT-GGGGAT
1 AACCTATGGGGGAT
7371 AACCTATGGGGGAT
1 AACCTATGGGGGAT
7385 AA
1 AA
7387 AAGAGCTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.34, C:0.14, G:0.31, T:0.21
Consensus pattern (14 bp):
AACCTATGGGGGAT
Found at i:7508 original size:13 final size:13
Alignment explanation
Indices: 7490--7516 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7480 ATAACATCAC
7490 TTTTCTTTCATTT
1 TTTTCTTTCATTT
7503 TTTTCTTTCATTT
1 TTTTCTTTCATTT
7516 T
1 T
7517 ATGAATTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (13 bp):
TTTTCTTTCATTT
Found at i:11935 original size:8 final size:8
Alignment explanation
Indices: 11922--11947 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
11912 TCGGCATGAA
11922 ATTTTTAG
1 ATTTTTAG
11930 ATTTTTAG
1 ATTTTTAG
11938 ATTTTTAG
1 ATTTTTAG
11946 AT
1 AT
11948 CGAGACCTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
ATTTTTAG
Found at i:13561 original size:16 final size:15
Alignment explanation
Indices: 13540--13570 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
13530 ATTAAAAGAT
13540 ACATATATTTTTAAAA
1 ACATAT-TTTTTAAAA
13556 ACATATTTTTTAAAA
1 ACATATTTTTTAAAA
13571 TTCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.45
Consensus pattern (15 bp):
ACATATTTTTTAAAA
Found at i:15276 original size:13 final size:13
Alignment explanation
Indices: 15254--15283 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
15244 GTACGAATTT
*
15254 TCATGGTACTTTC
1 TCATGATACTTTC
15267 TCATGATACTTTC
1 TCATGATACTTTC
15280 TCAT
1 TCAT
15284 TAAGAGTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.20, C:0.23, G:0.10, T:0.47
Consensus pattern (13 bp):
TCATGATACTTTC
Found at i:22264 original size:32 final size:32
Alignment explanation
Indices: 22181--22304 Score: 78
Period size: 31 Copynumber: 4.0 Consensus size: 32
22171 CTAATGTGAC
* * *
22181 TCTTAGGTAGGCTCT-GCGGCCCTGAGAT-CA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
** * * *
22211 TTCTCGGGTAGGCCCT-GCGGCCCTAAGATGTGT
1 -TCTTAGGTAGGCTCTCACGGCCCTAAGATGT-A
* * *
22244 TCTTAGGTAGGC-CTCACGGCCCCAAAATCTA
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
* *
22275 TCTTGGGTAGGCTCTCA-GGGCCTAAGATGT
1 TCTTAGGTAGGCTCTCACGGCCCTAAGATGT
22305 TCCCTTAGGT
Statistics
Matches: 71, Mismatches: 18, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
31 46 0.65
32 25 0.35
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (32 bp):
TCTTAGGTAGGCTCTCACGGCCCTAAGATGTA
Found at i:28648 original size:23 final size:22
Alignment explanation
Indices: 28621--28670 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 22
28611 TGTATATTAT
*
28621 ATATATATACAATATAGTATAA
1 ATATATAAACAATATAGTATAA
28643 AGTATATAAACAATATAGTATAA
1 A-TATATAAACAATATAGTATAA
28666 ATATA
1 ATATA
28671 AGTATATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.56, C:0.04, G:0.06, T:0.34
Consensus pattern (22 bp):
ATATATAAACAATATAGTATAA
Found at i:28702 original size:16 final size:16
Alignment explanation
Indices: 28675--28718 Score: 70
Period size: 16 Copynumber: 2.7 Consensus size: 16
28665 AATATAAGTA
28675 TATAAAATTATATAAAC
1 TATAAAA-TATATAAAC
28692 TATAAAATATATAAAC
1 TATAAAATATATAAAC
*
28708 TATATAATATA
1 TATAAAATATA
28719 AGTATATAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (16 bp):
TATAAAATATATAAAC
Found at i:29283 original size:50 final size:49
Alignment explanation
Indices: 29209--29318 Score: 157
Period size: 50 Copynumber: 2.2 Consensus size: 49
29199 AAATATTTTT
**
29209 ACGAATAGTATTGTACTGTATGAATAGTACCGATAATGTGTGAACAACA
1 ACGAATAGTACCGTACTGTATGAATAGTACCGATAATGTGTGAACAACA
* **
29258 ACGAATAGTACCGATACTGTATGAATAGTATCGATAATGTGTGAACAGTA
1 ACGAATAGTACCG-TACTGTATGAATAGTACCGATAATGTGTGAACAACA
*
29308 ACGAACAGTAC
1 ACGAATAGTAC
29319 TGATGCTCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
49 11 0.20
50 43 0.80
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.26
Consensus pattern (49 bp):
ACGAATAGTACCGTACTGTATGAATAGTACCGATAATGTGTGAACAACA
Found at i:29285 original size:20 final size:20
Alignment explanation
Indices: 29260--29307 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
29250 GAACAACAAC
*
29260 GAATAGTACCGATACTGTAT
1 GAATAGTACCGATAATGTAT
* *
29280 GAATAGTATCGATAATGTGT
1 GAATAGTACCGATAATGTAT
*
29300 GAACAGTA
1 GAATAGTA
29308 ACGAACAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.29
Consensus pattern (20 bp):
GAATAGTACCGATAATGTAT
Found at i:31373 original size:113 final size:113
Alignment explanation
Indices: 31234--31460 Score: 454
Period size: 113 Copynumber: 2.0 Consensus size: 113
31224 GAAGCTATGA
31234 TGAACATTTTAAAATTTTAATGATTTTTCATAATTTTTAGTTCATCATAATGAATTTTGGTCAAA
1 TGAACATTTTAAAATTTTAATGATTTTTCATAATTTTTAGTTCATCATAATGAATTTTGGTCAAA
31299 ATTGATTTTAAATGCAAATGATATCTCTCTAACAATTGATATCGACTT
66 ATTGATTTTAAATGCAAATGATATCTCTCTAACAATTGATATCGACTT
31347 TGAACATTTTAAAATTTTAATGATTTTTCATAATTTTTAGTTCATCATAATGAATTTTGGTCAAA
1 TGAACATTTTAAAATTTTAATGATTTTTCATAATTTTTAGTTCATCATAATGAATTTTGGTCAAA
31412 ATTGATTTTAAATGCAAATGATATCTCTCTAACAATTGATATCGACTT
66 ATTGATTTTAAATGCAAATGATATCTCTCTAACAATTGATATCGACTT
31460 T
1 T
31461 TCAAATACTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.35, C:0.11, G:0.10, T:0.44
Consensus pattern (113 bp):
TGAACATTTTAAAATTTTAATGATTTTTCATAATTTTTAGTTCATCATAATGAATTTTGGTCAAA
ATTGATTTTAAATGCAAATGATATCTCTCTAACAATTGATATCGACTT
Found at i:34705 original size:17 final size:18
Alignment explanation
Indices: 34668--34711 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
34658 GTGGTGATTC
34668 TTTCATAAAATGAATTTTA
1 TTTCAT-AAATGAATTTTA
*
34687 TTTCATAAATGGA-TTTA
1 TTTCATAAATGAATTTTA
*
34704 TTTAATAA
1 TTTCATAA
34712 CCAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 11 0.48
18 6 0.26
19 6 0.26
ACGTcount: A:0.41, C:0.05, G:0.07, T:0.48
Consensus pattern (18 bp):
TTTCATAAATGAATTTTA
Found at i:35101 original size:12 final size:12
Alignment explanation
Indices: 35084--35108 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35074 GGTTTCAAAC
35084 ATGATTAATTAA
1 ATGATTAATTAA
35096 ATGATTAATTAA
1 ATGATTAATTAA
35108 A
1 A
35109 GGATGATGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGATTAATTAA
Found at i:36798 original size:20 final size:20
Alignment explanation
Indices: 36758--36800 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
36748 TATATTGGGC
* *
36758 TATTGTCTATTGTTTACGGT
1 TATTGTCTATGGTATACGGT
*
36778 TATTGTCTATGGTATATGGT
1 TATTGTCTATGGTATACGGT
36798 TAT
1 TAT
36801 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.19, C:0.07, G:0.21, T:0.53
Consensus pattern (20 bp):
TATTGTCTATGGTATACGGT
Found at i:39570 original size:2 final size:2
Alignment explanation
Indices: 39283--39553 Score: 132
Period size: 2 Copynumber: 139.5 Consensus size: 2
39273 TGGAAATAAT
* *
39283 TA TA -A TA TA TA TA TA TA TA TA -A TA TA TA -A TA TGA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA
*
39323 TA TA TA TA TA TA TA TA TA TA TG TA TA T- TA TA CT- TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* *
39363 TA TA TA TA TA AA GTA T- TA -A TA T- TG T- TA TA TA -A T- TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
39400 TA AA CTA TA AA GTA TA TA -A AA TA TA TA GTA TA -A GTA TA TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA TA
* * * * *
39442 GTA TA T- TA TG CA TG TA TA TA CT- TA -A GTG TA TG TGA -A TA TA
1 -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA T-A TA TA TA
* * *
39482 TA TG T- TA TA CA TG TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
39523 TA TA TA TA TA T- TA TA TG TG TA TA TCA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA T
39554 GTTATACATG
Statistics
Matches: 209, Mismatches: 28, Indels: 64
0.69 0.09 0.21
Matches are distributed among these distances:
1 20 0.10
2 176 0.84
3 13 0.06
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.45
Consensus pattern (2 bp):
TA
Found at i:39575 original size:10 final size:10
Alignment explanation
Indices: 39287--39620 Score: 103
Period size: 10 Copynumber: 33.5 Consensus size: 10
39277 AATAATTATA
*
39287 ATATATATAT
1 ATATATATGT
*
39297 ATATATA-AT
1 ATATATATGT
39306 ATATAATATG-
1 ATAT-ATATGT
* * *
39316 ACACATATAT
1 ATATATATGT
*
39326 ATATATATAT
1 ATATATATGT
39336 ATATATATGT
1 ATATATATGT
39346 ATATTATACT-T
1 ATA-TATA-TGT
*
39357 ATAT-TATAT
1 ATATATATGT
*
39366 ATATATAAAGT
1 ATATAT-ATGT
39377 AT-TAATATTGT
1 ATAT-ATA-TGT
39388 -TATATAAT-T
1 ATATAT-ATGT
**
39397 ATATA-AACT
1 ATATATATGT
39406 ATA-A-A-GT
1 ATATATATGT
* *
39413 ATATAAAATAT
1 ATAT-ATATGT
*
39424 ATAGTATAAGT
1 ATA-TATATGT
39435 ATATATA-GT
1 ATATATATGT
39444 ATATTATGCATGT
1 ATA-TAT--ATGT
*
39457 ATATA-CT-T
1 ATATATATGT
*
39465 A-AGTGTATGT
1 ATA-TATATGT
39475 GAATATATATGT
1 --ATATATATGT
*
39487 -TATACATGT
1 ATATATATGT
*
39496 ATATATATAT
1 ATATATATGT
*
39506 ATATATATAT
1 ATATATATGT
*
39516 ATATATATAT
1 ATATATATGT
39526 ATATATAT-T
1 ATATATATGT
* * *
39535 ATATGTGTAT
1 ATATATATGT
39545 ATCATATATGT
1 AT-ATATATGT
*
39556 -TATACATGT
1 ATATATATGT
*
39565 ATATATGTGT
1 ATATATATGT
* **
39575 ATGTATATAAA
1 ATATATAT-GT
39586 AGTATATATGT
1 A-TATATATGT
* *
39597 -GATGTATGT
1 ATATATATGT
*
39606 ACATATATGT
1 ATATATATGT
39616 ATATA
1 ATATA
39621 CAAAAGTATA
Statistics
Matches: 245, Mismatches: 43, Indels: 72
0.68 0.12 0.20
Matches are distributed among these distances:
7 5 0.02
8 7 0.03
9 59 0.24
10 116 0.47
11 34 0.14
12 18 0.07
13 6 0.02
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (10 bp):
ATATATATGT
Found at i:39593 original size:41 final size:39
Alignment explanation
Indices: 39548--39630 Score: 94
Period size: 41 Copynumber: 2.1 Consensus size: 39
39538 TGTGTATATC
* * * *
39548 ATATATGTTATACATGTATATATGTGTATGTATATAAAAGT
1 ATATATGTGATACATGTACATATATGTA--TATACAAAAGT
**
39589 ATATATGTGATGTATGTACATATATGTATATACAAAAGT
1 ATATATGTGATACATGTACATATATGTATATACAAAAGT
39628 ATA
1 ATA
39631 GACATAAGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
39 13 0.36
41 23 0.64
ACGTcount: A:0.41, C:0.04, G:0.14, T:0.41
Consensus pattern (39 bp):
ATATATGTGATACATGTACATATATGTATATACAAAAGT
Found at i:42173 original size:12 final size:12
Alignment explanation
Indices: 42156--42184 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
42146 ACCTGAAAAG
42156 GTGAGTAATAGA
1 GTGAGTAATAGA
42168 GTGAGTAATAGA
1 GTGAGTAATAGA
42180 GTGAG
1 GTGAG
42185 CTTTGGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.38, T:0.24
Consensus pattern (12 bp):
GTGAGTAATAGA
Found at i:42694 original size:24 final size:25
Alignment explanation
Indices: 42648--42707 Score: 86
Period size: 24 Copynumber: 2.4 Consensus size: 25
42638 CAGAAATAAA
*
42648 AACATAATTCAGGGTAAGATATCAG
1 AACATAATTCAGGATAAGATATCAG
* *
42673 AACAAAATTCA-GATAAGGTATCAG
1 AACATAATTCAGGATAAGATATCAG
42697 AACATAATTCA
1 AACATAATTCA
42708 AATCGGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.48, C:0.13, G:0.15, T:0.23
Consensus pattern (25 bp):
AACATAATTCAGGATAAGATATCAG
Found at i:46576 original size:16 final size:16
Alignment explanation
Indices: 46555--46586 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46545 GTGAAAAGAT
46555 ACATATATTTTTAAAA
1 ACATATATTTTTAAAA
*
46571 ACATATTTTTTTAAAA
1 ACATATATTTTTAAAA
46587 TTCAAAAAGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (16 bp):
ACATATATTTTTAAAA
Found at i:46827 original size:24 final size:24
Alignment explanation
Indices: 46764--46834 Score: 72
Period size: 24 Copynumber: 3.0 Consensus size: 24
46754 AAATGGAGAT
* *
46764 ATCAGAAATCA-AAAAATAATTCAG
1 ATCAGATATCAGAACAA-AATTCAG
* * *
46788 GTCAGATATCATAACAGAATTCAG
1 ATCAGATATCAGAACAAAATTCAG
*
46812 ATCAGGTATCAGAACAAAATTCA
1 ATCAGATATCAGAACAAAATTCA
46835 AATCGAAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
24 35 0.92
25 3 0.08
ACGTcount: A:0.49, C:0.15, G:0.13, T:0.23
Consensus pattern (24 bp):
ATCAGATATCAGAACAAAATTCAG
Found at i:53516 original size:9 final size:9
Alignment explanation
Indices: 53504--53561 Score: 57
Period size: 9 Copynumber: 6.6 Consensus size: 9
53494 TATAATATAG
53504 TATAAAGTA
1 TATAAAGTA
*
53513 TATAAA-CA
1 TATAAAGTA
53521 -ATAAAGTA
1 TATAAAGTA
*
53529 TAAATAAGTA
1 TATA-AAGTA
*
53539 TATAAATTA
1 TATAAAGTA
*
53548 TATAAACTA
1 TATAAAGTA
53557 TATAA
1 TATAA
53562 TATAAGTATA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
7 5 0.12
8 2 0.05
9 25 0.62
10 8 0.20
ACGTcount: A:0.59, C:0.03, G:0.05, T:0.33
Consensus pattern (9 bp):
TATAAAGTA
Found at i:53581 original size:23 final size:22
Alignment explanation
Indices: 53477--53584 Score: 70
Period size: 23 Copynumber: 5.0 Consensus size: 22
53467 TGTTATAATG
*
53477 TATATTATATATA-TATATATAA
1 TATAGTATATA-AGTATATATAA
*
53499 TATAGTATA-AAGTATATAAACAA
1 TATAGTATATAAGTATAT--ATAA
*
53522 TAAAGTATAAATAAGTATATA-AA
1 TATAGTAT--ATAAGTATATATAA
*
53545 T-TA-TATA-AA--CTATATAA
1 TATAGTATATAAGTATATATAA
53562 TATAAGTATATAAGTATATATAA
1 TAT-AGTATATAAGTATATATAA
53585 GTGTATATGT
Statistics
Matches: 67, Mismatches: 6, Indels: 25
0.68 0.06 0.26
Matches are distributed among these distances:
16 4 0.06
17 3 0.04
18 3 0.04
19 2 0.03
20 5 0.07
21 11 0.16
22 9 0.13
23 20 0.30
24 1 0.01
25 1 0.01
26 8 0.12
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
TATAGTATATAAGTATATATAA
Found at i:54110 original size:50 final size:48
Alignment explanation
Indices: 54051--54146 Score: 138
Period size: 50 Copynumber: 2.0 Consensus size: 48
54041 ATGTATATAC
*
54051 TGTATGAATAGTAACGATAATGTGTCAACAACAACGAATAGTACTGATAT
1 TGTATGAATAGTAACGATAATGTG--AACAACAACGAACAGTACTGATAT
* **
54101 TGTATGAATAGTATCGATAATGTGAACAGTAACGAACAGTACTGAT
1 TGTATGAATAGTAACGATAATGTGAACAACAACGAACAGTACTGAT
54147 GCTCAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
48 19 0.45
50 23 0.55
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.28
Consensus pattern (48 bp):
TGTATGAATAGTAACGATAATGTGAACAACAACGAACAGTACTGATAT
Found at i:54201 original size:19 final size:20
Alignment explanation
Indices: 54173--54212 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
54163 ATGCAAAATG
*
54173 AGTATTGATACT-CTACAGT
1 AGTATCGATACTACTACAGT
54192 AGTATCGATACTACTACAGT
1 AGTATCGATACTACTACAGT
54212 A
1 A
54213 AAATCAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (20 bp):
AGTATCGATACTACTACAGT
Found at i:54600 original size:34 final size:34
Alignment explanation
Indices: 54557--54623 Score: 89
Period size: 34 Copynumber: 2.0 Consensus size: 34
54547 TGTAAAAGGA
* *
54557 AAGGTTCTAGCCGAGCCCTTGAAAAGCTAGGGAT
1 AAGGTTCTAGCCGAGCCCGTGAAAAACTAGGGAT
***
54591 AAGGTTCTAGTTTAGCCCGTGAAAAACTAGGGA
1 AAGGTTCTAGCCGAGCCCGTGAAAAACTAGGGA
54624 GTTGTAAAGG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.31, C:0.18, G:0.28, T:0.22
Consensus pattern (34 bp):
AAGGTTCTAGCCGAGCCCGTGAAAAACTAGGGAT
Done.