Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003704.1 Hibiscus syriacus cultivar Beakdansim tig00007919_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: 79699
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:555 original size:17 final size:17
Alignment explanation
Indices: 533--566 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
523 CGTTAACAAA
533 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
550 AATTAAATCATAGCTTG
1 AATTAAATCATAGCTTG
567 TAAGCAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (17 bp):
AATTAAATCATAGCTTG
Found at i:1451 original size:2 final size:2
Alignment explanation
Indices: 1444--1480 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1434 TAATAGATAA
1444 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1481 AACTCACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:7423 original size:2 final size:2
Alignment explanation
Indices: 7416--7444 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
7406 TCATGTGGTC
7416 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
7445 CCTTGTTTCG
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:14068 original size:2 final size:2
Alignment explanation
Indices: 14055--14084 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
14045 TCCAACGATG
*
14055 AT AT AC 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
14085 GAGTTATTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:15373 original size:10 final size:10
Alignment explanation
Indices: 15358--15411 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
15348 CATTTAAATG
15358 ATAAACGAAC
1 ATAAACGAAC
*
15368 ATAAACGAATATA
1 ATAAACG-A-A-C
*
15381 ATAAACGAAT
1 ATAAACGAAC
15391 ATAAACGAAC
1 ATAAACGAAC
15401 ATAAACGAAC
1 ATAAACGAAC
15411 A
1 A
15412 ACACAAAAAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
10 27 0.71
11 2 0.05
12 2 0.05
13 7 0.18
ACGTcount: A:0.61, C:0.15, G:0.09, T:0.15
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:15385 original size:23 final size:23
Alignment explanation
Indices: 15358--15404 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
15348 CATTTAAATG
*
15358 ATAAACGAACATAAACGAATATA
1 ATAAACGAACATAAACGAACATA
*
15381 ATAAACGAATATAAACGAACATA
1 ATAAACGAACATAAACGAACATA
15404 A
1 A
15405 ACGAACAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.13, G:0.09, T:0.17
Consensus pattern (23 bp):
ATAAACGAACATAAACGAACATA
Found at i:15386 original size:13 final size:13
Alignment explanation
Indices: 15368--15394 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
15358 ATAAACGAAC
15368 ATAAACGAATATA
1 ATAAACGAATATA
15381 ATAAACGAATATA
1 ATAAACGAATATA
15394 A
1 A
15395 ACGAACATAA
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:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (13 bp):
ATAAACGAATATA
Found at i:18156 original size:2 final size:2
Alignment explanation
Indices: 18144--18173 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
18134 ATCAAAACTC
18144 AT AT A- 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
18174 ATTCATTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24754 original size:37 final size:36
Alignment explanation
Indices: 24679--24754 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
24669 TTTTATATTT
*
24679 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
24715 TTTAATTTTTTAAAGAAAA-TATATAAATATTTTACAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTAT-CAA
24752 TTT
1 TTT
24755 GTAATATTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
36 26 0.74
37 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:24977 original size:20 final size:20
Alignment explanation
Indices: 24904--24970 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
24894 TATTCCCTGG
* *
24904 TAATCTTTTATTTCAACTGA
1 TAATCTTTTATTCCCACTGA
24924 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
24944 TAATCTTTTATTCCCACTGA
1 TAATCTTTTATTCCCACTGA
24964 TAATCTT
1 TAATCTT
24971 ACATTCCGTA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.04, T:0.48
Consensus pattern (20 bp):
TAATCTTTTATTCCCACTGA
Found at i:25532 original size:48 final size:48
Alignment explanation
Indices: 25469--25574 Score: 178
Period size: 48 Copynumber: 2.2 Consensus size: 48
25459 TAAATTTAAA
* *
25469 TATT-AATTTTATTTTTAATTAGATTAACGTGATCATAAGTTAATATC
1 TATTAAATTTTATTTTTAATTAGATTAACGTGATCATAAGATAACATC
25516 TATTAAATTTTATTTTTAATTAGATTAACGTGATCATAAGATAACATC
1 TATTAAATTTTATTTTTAATTAGATTAACGTGATCATAAGATAACATC
*
25564 TGTTAAATTTT
1 TATTAAATTTT
25575 TTAAGAGTGA
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
47 4 0.07
48 51 0.93
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.48
Consensus pattern (48 bp):
TATTAAATTTTATTTTTAATTAGATTAACGTGATCATAAGATAACATC
Found at i:29114 original size:2 final size:2
Alignment explanation
Indices: 29107--29134 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
29097 TCAAAAGAAG
29107 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
29135 CACGTGTGTG
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):
TA
Found at i:40227 original size:21 final size:21
Alignment explanation
Indices: 40201--40245 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40191 GATTTCTGGG
* *
40201 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
40222 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
40243 CAA
1 CAA
40246 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:41610 original size:32 final size:31
Alignment explanation
Indices: 41568--41667 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
41558 AGAGTCGAGG
41568 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* *
41599 TTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 -GTTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
41631 GTATATCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
41662 GTTTAC
1 GTTTAC
41668 TGAGGATCTT
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
31 28 0.51
32 27 0.49
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:41705 original size:30 final size:30
Alignment explanation
Indices: 41656--41749 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
41646 AAGGAACATA
*
41656 TGGACAGTTTACTGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
41687 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
41717 TGGATAGTTACCG-GGGTCTGTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
41746 TGGA
1 TGGA
41750 TAGGTCATTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.31
30 34 0.58
31 7 0.12
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:45251 original size:30 final size:30
Alignment explanation
Indices: 45215--45347 Score: 169
Period size: 30 Copynumber: 4.2 Consensus size: 30
45205 TAATAAGGTT
45215 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
45245 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
45275 AATTATTTTAAAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A
*
45309 TTGATTTATTTTAAAATAATTTATT-TTAAATA
1 ---ATTTATTTTAAAATAATTTATTATAAAATA
45341 ATTTATT
1 ATTTATT
45348 AGTATGGATT
Statistics
Matches: 91, Mismatches: 5, Indels: 15
0.82 0.05 0.14
Matches are distributed among these distances:
29 7 0.08
30 52 0.57
31 3 0.03
32 3 0.03
34 3 0.03
35 2 0.02
36 1 0.01
37 20 0.22
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.50
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:45318 original size:22 final size:22
Alignment explanation
Indices: 45292--45392 Score: 94
Period size: 22 Copynumber: 4.5 Consensus size: 22
45282 TTAAAATAAA
*
45292 TTATTATAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
** * *
45314 TTATTTTAAAATAATTTATTTTAA
1 TTATTTTAAAAT-ATGGA-TTGAT
* * * *
45338 ATAATTTATTAGTATGGATTGAT
1 TTATTTTA-AAATATGGATTGAT
45361 TTATTTTAAAATATGGATTGAT
1 TTATTTTAAAATATGGATTGAT
45383 TTATTTTAAA
1 TTATTTTAAA
45393 TAATTTATTA
Statistics
Matches: 59, Mismatches: 17, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
22 33 0.56
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (22 bp):
TTATTTTAAAATATGGATTGAT
Found at i:45341 original size:14 final size:15
Alignment explanation
Indices: 45215--45347 Score: 151
Period size: 15 Copynumber: 8.5 Consensus size: 15
45205 TAATAAGGTT
45215 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
45230 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
45245 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
45260 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
45275 AATTATTTTAAAATA
1 ATTTATTTTAAAATA
* *
45290 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
45309 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
45327 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
45341 ATTTATT
1 ATTTATT
45348 AGTATGGATT
Statistics
Matches: 103, Mismatches: 8, Indels: 15
0.82 0.06 0.12
Matches are distributed among these distances:
14 12 0.12
15 71 0.69
16 4 0.04
17 2 0.02
18 1 0.01
19 1 0.01
20 2 0.02
21 4 0.04
22 6 0.06
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.50
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:45365 original size:32 final size:32
Alignment explanation
Indices: 45327--45421 Score: 120
Period size: 32 Copynumber: 3.3 Consensus size: 32
45317 TTTTAAAATA
45327 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
45359 ATTTA-TTT---TAA---A--A-TATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
45381 ATTTATTTTAAATAATTTATTAGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTG
45413 ATTTATTTT
1 ATTTATTTT
45422 TAAAATATGG
Statistics
Matches: 53, Mismatches: 0, Indels: 20
0.73 0.00 0.27
Matches are distributed among these distances:
22 14 0.26
23 4 0.08
25 1 0.02
26 3 0.06
28 3 0.06
29 1 0.02
31 4 0.08
32 23 0.43
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.55
Consensus pattern (32 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTG
Found at i:45383 original size:69 final size:67
Alignment explanation
Indices: 45245--45402 Score: 203
Period size: 69 Copynumber: 2.3 Consensus size: 67
45235 TTATAAAATA
45245 ATTTATTTTAAAATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
45310 TG
66 TG
* * ** * * * *
45312 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAAATTATT--T-TAAAATAAATTATTATAAAATATG
45376 GATTG
63 GATTG
45381 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
45403 GTATGGATTG
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
66 12 0.15
67 22 0.28
68 13 0.16
69 32 0.41
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAAATTATTTTAAAATAAATTATTATAAAATATGGAT
TG
Found at i:45494 original size:32 final size:32
Alignment explanation
Indices: 45452--45569 Score: 200
Period size: 32 Copynumber: 3.7 Consensus size: 32
45442 TATTGTAGTT
*
45452 GTATGTATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
45484 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
45516 GTATGGATTGGTTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
45548 GTATGGATTTATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
45570 ATATGGATTG
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 81 1.00
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.55
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:45722 original size:18 final size:18
Alignment explanation
Indices: 45699--45746 Score: 51
Period size: 22 Copynumber: 2.4 Consensus size: 18
45689 ATTTTAAATA
*
45699 ATTTATTAGTATGGATTG
1 ATTTATTAATATGGATTG
45717 ATTTATTTTAAAATATGGATTG
1 ATTTA--TT--AATATGGATTG
45739 ATTTATTA
1 ATTTATTA
45747 TTGTAGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 6 0.24
20 4 0.16
22 15 0.60
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (18 bp):
ATTTATTAATATGGATTG
Found at i:45744 original size:80 final size:80
Alignment explanation
Indices: 45516--45808 Score: 525
Period size: 80 Copynumber: 3.7 Consensus size: 80
45506 TAATTTATTA
* * *
45516 GTATGGATTGGTTTATTTTAAATAATTTATTTGTATGGATTTATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
45581 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
* *
45596 GTATAGATTGATTTA-TTTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
45660 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
45675 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
45740 TTTATTATTGTAGTT
66 TTTATTATTGTAGTT
*
45755 GTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAA
45809 TAATTTATTA
Statistics
Matches: 204, Mismatches: 8, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
79 75 0.37
80 129 0.63
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (80 bp):
GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
TTTATTATTGTAGTT
Found at i:45779 original size:303 final size:308
Alignment explanation
Indices: 45372--45973 Score: 1124
Period size: 303 Copynumber: 2.0 Consensus size: 308
45362 TATTTTAAAA
45372 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTGA
* *
45437 TTTATTATTGTAGTTGTATGTATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
66 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
*
45502 TAAATAATTTATTAGTATGGATTGGTTTATTTTAAATAATTTATTTGTATGGA-T-TT-ATTTAT
131 TAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTATTGATTTAT
45564 TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATT-TAAATAATTTATTAG
196 TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTGTAAATAATTTATTAG
45628 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
261 TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
45676 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-TTTTAAAATATGGATTGA
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTGA
45740 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
66 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
45805 TAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTA
131 TAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATT-ATTGATTTA
*
45870 TTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTGTAAATAATTTATTA
195 TTTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTGTAAATAATTTATTA
45935 GTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
260 GTATGAATTGATTTATTTTAAAATATGGATTGATTTATT
45974 TTAAATAATT
Statistics
Matches: 289, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
303 133 0.46
304 47 0.16
306 2 0.01
307 54 0.19
308 53 0.18
ACGTcount: A:0.32, C:0.00, G:0.15, T:0.53
Consensus pattern (308 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTTAAAATATGGATTGA
TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
TAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTATTGATTTAT
TTTAAAATATGGATTGATTTATTATTGTAGTTGTATAGATTGATTTATTGTAAATAATTTATTAG
TATGAATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTG
Found at i:45801 original size:32 final size:32
Alignment explanation
Indices: 45755--45956 Score: 232
Period size: 32 Copynumber: 6.7 Consensus size: 32
45745 TATTGTAGTT
45755 GTATGGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
45787 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
45819 GTATGGATTGATTTATTTTAAATAATTTATTT
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
45851 GTATGGATTGATTGA-TTT--AT--TTTA-AA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
* *
45877 ATATGGATTGATTTA--TT--AT--TGTAGTT-
1 GTATGGATTGATTTATTTTAAATAATTTA-TTA
*
45903 GTATGGATTGATTTATTGTAAATAATTTATTA
1 GTATGGATTGATTTATTTTAAATAATTTATTA
*
45935 GTATGAATTGATTTATTTTAAA
1 GTATGGATTGATTTATTTTAAA
45957 ATATGGATTG
Statistics
Matches: 146, Mismatches: 15, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
25 7 0.05
26 27 0.18
27 4 0.03
28 1 0.01
29 2 0.01
30 2 0.01
31 5 0.03
32 98 0.67
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.52
Consensus pattern (32 bp):
GTATGGATTGATTTATTTTAAATAATTTATTA
Found at i:45802 original size:18 final size:18
Alignment explanation
Indices: 45779--45835 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
45769 ATTTTAAATA
45779 ATTTATTAGTATAGATTG
1 ATTTATTAGTATAGATTG
* *
45797 ATTTATT--T-TA-AATA
1 ATTTATTAGTATAGATTG
*
45811 ATTTATTAGTATGGATTG
1 ATTTATTAGTATAGATTG
45829 ATTTATT
1 ATTTATT
45836 TTAAATAATT
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
14 9 0.30
15 2 0.07
16 2 0.07
17 1 0.03
18 16 0.53
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.54
Consensus pattern (18 bp):
ATTTATTAGTATAGATTG
Found at i:45926 original size:84 final size:80
Alignment explanation
Indices: 45819--45973 Score: 256
Period size: 84 Copynumber: 1.9 Consensus size: 80
45809 TAATTTATTA
* *
45819 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGA
1 GTATGGATTGATTTATTGTAAATAATTTATTAGTAT-GA---ATTGATTTATTTTAAAATATGGA
45884 TTGATTTATTATTGTAGTT
62 TTGATTTATTATTGTAGTT
45903 GTATGGATTGATTTATTGTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTGTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
45968 TTTATT
66 TTTATT
45974 TTAAATAATT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
80 33 0.48
83 2 0.03
84 34 0.49
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (80 bp):
GTATGGATTGATTTATTGTAAATAATTTATTAGTATGAATTGATTTATTTTAAAATATGGATTGA
TTTATTATTGTAGTT
Found at i:45945 original size:148 final size:144
Alignment explanation
Indices: 45675--45956 Score: 494
Period size: 148 Copynumber: 1.9 Consensus size: 144
45665 TATTGTAGTT
45675 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
*
45740 TTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTT
66 TTTATTATTGTAGTTGTATGGATTGATTTATTGTAAATAATTTATTAGTATAGATTGATTTATTT
45805 TAAATAATTTATTA
131 TAAATAATTTATTA
*
45819 GTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTGATTTATTTTAAAATATGGA
1 GTATGGATTGATTTATTTTAAATAATTTATTAGTAT-G---GATTGATTTATTTTAAAATATGGA
45884 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTGTAAATAATTTATTAGTAT-GAATTGATT
62 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTGTAAATAATTTATTAGTATAG-ATTGATT
45948 TATTTTAAA
126 TATTTTAAA
45957 ATATGGATTG
Statistics
Matches: 131, Mismatches: 2, Indels: 6
0.94 0.01 0.04
Matches are distributed among these distances:
144 35 0.27
145 1 0.01
147 1 0.01
148 94 0.72
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (144 bp):
GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGA
TTTATTATTGTAGTTGTATGGATTGATTTATTGTAAATAATTTATTAGTATAGATTGATTTATTT
TAAATAATTTATTA
Found at i:45950 original size:18 final size:17
Alignment explanation
Indices: 45901--45951 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
45891 ATTATTGTAG
*
45901 TTGTATGGATTGATTTA
1 TTGTATGAATTGATTTA
*
45918 TTGTA--AA-TAATTTA
1 TTGTATGAATTGATTTA
45932 TTAGTATGAATTGATTTA
1 TT-GTATGAATTGATTTA
45950 TT
1 TT
45952 TTAAAATATG
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
17 7 0.26
18 8 0.30
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (17 bp):
TTGTATGAATTGATTTA
Found at i:45952 original size:22 final size:22
Alignment explanation
Indices: 45936--45978 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
45926 AATTTATTAG
45936 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
*
45958 TATGGATTGATTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
45979 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:46647 original size:6 final size:6
Alignment explanation
Indices: 46636--46663 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
46626 ATGCTTCATC
46636 GGAGCT GGAGCT GGAGCT GGAGCT GGAG
1 GGAGCT GGAGCT GGAGCT GGAGCT GGAG
46664 ATCTATGAGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.14, G:0.54, T:0.14
Consensus pattern (6 bp):
GGAGCT
Found at i:50967 original size:76 final size:78
Alignment explanation
Indices: 50850--50997 Score: 237
Period size: 76 Copynumber: 1.9 Consensus size: 78
50840 AACATATCAC
* * *
50850 AAGGAAAACCATTTGCAGTAAACTGAATGGCTTGTGATAATTAAAAACTTAAAAGC-AAAAACCC
1 AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
50914 AAAAACATGTCCT
66 AAAAACATGTCCT
* *
50927 AAGGAAAA-CATTTGCAGTAAACAGAACGTCTTGTGGTAATTAAAAAATTAAAAGCAAAAAACCC
1 AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
50991 AAAAACA
66 AAAAACA
50998 GACTGTAATA
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
76 42 0.65
77 23 0.35
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (78 bp):
AAGGAAAACCATTTGCAGTAAACAGAACGGCTTGTGATAATTAAAAAATTAAAAGCAAAAAACCC
AAAAACATGTCCT
Found at i:51400 original size:67 final size:68
Alignment explanation
Indices: 51294--51428 Score: 175
Period size: 68 Copynumber: 2.0 Consensus size: 68
51284 TTAAACACAT
* *
51294 AGTAATAAAGAATGAAAAAAAAATAAGCTCAAATATAGT-AATAAACATCTATTGAGCCGGTTTT
1 AGTAATAAAGAAT-AAAAAAAAATAAGCTCAAATATAGTAAATAAACATCTATGGAGCCAGTTTT
51358 CATC
65 CATC
*** * *
51362 AGTAATAAAGAAT-AAAAAGTGTAAGCTCAAAATATAGTAAATATACCTCTATGGAGCCAGTTTT
1 AGTAATAAAGAATAAAAAAAAATAAGCTC-AAATATAGTAAATAAACATCTATGGAGCCAGTTTT
51426 CAT
65 CAT
51429 TTTCTTATTA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 12 0.21
67 9 0.16
68 37 0.64
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (68 bp):
AGTAATAAAGAATAAAAAAAAATAAGCTCAAATATAGTAAATAAACATCTATGGAGCCAGTTTTC
ATC
Found at i:60954 original size:76 final size:73
Alignment explanation
Indices: 60868--61118 Score: 272
Period size: 76 Copynumber: 3.3 Consensus size: 73
60858 CATATACGTC
***
60868 TATATATTATATAGTTTGCAAATGGTTTTTGAAAATATATATAATATATAGTTTTGAAAACATGT
1 TATATATTATATAGTTTG-AAA-ACATTTTGAAAATATATATAATATATAGTTTTGAAAACAT-T
60933 TTGAAAACATT
63 TTGAAAACATT
60944 TATATATTATATAGTTTTTTTGAAAACATTTTGAAAATACGTATATAATATATAGTTTTGAAAAC
1 TATATATTATATAG----TTTGAAAACATTTTGAAAATA--TATATAATATATAGTTTTGAAAAC
*
61009 ATTTTGAAAACGTT
60 ATTTTGAAAACATT
* * * * *
61023 TAAATATTATATAGTTTTTAAAACATTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTT
1 TATATATTATATAG-TTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACA--TT
*
61088 TTGTAAA-A-T
63 TTGAAAACATT
* *
61097 TATATAATATATAGTTTTAAAA
1 TATATATTATATAGTTTGAAAA
61119 ACTTTTTTTT
Statistics
Matches: 154, Mismatches: 13, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
73 8 0.05
74 36 0.23
76 42 0.27
78 11 0.07
79 27 0.18
80 30 0.19
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (73 bp):
TATATATTATATAGTTTGAAAACATTTTGAAAATATATATAATATATAGTTTTGAAAACATTTTG
AAAACATT
Found at i:61126 original size:38 final size:36
Alignment explanation
Indices: 60893--61199 Score: 232
Period size: 38 Copynumber: 8.1 Consensus size: 36
60883 TTGCAAATGG
60893 TTTTTGAAAA-TATATATAATATATAGTTTTGAAAAC
1 TTTTTGAAAACT-TATATAATATATAGTTTTGAAAAC
* *
60929 ATGTTTGAAAACATTTATATATTATATAGTTTTTTTGAAAAC
1 -TTTTTGAAAAC--TTATATAATATATAG---TTTTGAAAAC
* *
60971 ATTTTGAAAATACGTATATAATATATAGTTTTGAAAAC
1 TTTTTG-AAA-ACTTATATAATATATAGTTTTGAAAAC
* * * *
61009 ATTTTGAAAACGTTTAAATATTATATAGTTTTTAAAAC
1 TTTTTGAAAAC--TTATATAATATATAGTTTTGAAAAC
* * * *
61047 ATTTTGAAAACATATATAGTATATAGTTTTAAAAAC
1 TTTTTGAAAACTTATATAATATATAGTTTTGAAAAC
*
61083 ATTTTTTGTAAAA-TTATATAATATATAGTTTTAAAAAC
1 --TTTTTG-AAAACTTATATAATATATAGTTTTGAAAAC
*
61121 TTTTTTTTTTTGAAAACTTATAT-A-ATAT--TTTTAAAAAC
1 ------TTTTTGAAAACTTATATAATATATAGTTTTGAAAAC
* *
61159 ATTTTTGGAAAC-TATGTAATATATAGTTTTGAAAAC
1 -TTTTTGAAAACTTATATAATATATAGTTTTGAAAAC
61195 TTTTT
1 TTTTT
61200 TAAAGTATAT
Statistics
Matches: 226, Mismatches: 22, Indels: 46
0.77 0.07 0.16
Matches are distributed among these distances:
32 4 0.02
33 11 0.05
34 4 0.02
35 5 0.02
36 32 0.14
37 12 0.05
38 86 0.38
39 17 0.08
40 5 0.02
41 22 0.10
42 26 0.12
43 2 0.01
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTTGAAAACTTATATAATATATAGTTTTGAAAAC
Found at i:61179 original size:74 final size:80
Alignment explanation
Indices: 61048--61200 Score: 219
Period size: 74 Copynumber: 2.0 Consensus size: 80
61038 TTTTAAAACA
*
61048 TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTAAAATTATATAATATATAGTT
1 TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTAAAACTATATAATATATAGTT
61113 TTAAAAACTTTTTTT
66 TTAAAAACTTTTTTT
* * *
61128 TTTTGAAAAC-T-TATA-TA-ATATTTTTAAAAACA-TTTTTG-GAAACTATGTAATATATAGTT
1 TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTAAAACTATATAATATATAGTT
*
61187 TTGAAAACTTTTTT
66 TTAAAAACTTTTTT
61201 AAAGTATATA
Statistics
Matches: 68, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
74 31 0.46
75 6 0.09
76 14 0.21
77 2 0.03
78 4 0.06
79 1 0.01
80 10 0.15
ACGTcount: A:0.40, C:0.05, G:0.07, T:0.48
Consensus pattern (80 bp):
TTTTGAAAACATATATAGTATATAGTTTTAAAAACATTTTTTGTAAAACTATATAATATATAGTT
TTAAAAACTTTTTTT
Found at i:61274 original size:5 final size:5
Alignment explanation
Indices: 61266--61300 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
61256 TTATATCATA
61266 TTATT TTATT TTATT TTATT TTATT TCT-TT TTATT
1 TTATT TTATT TTATT TTATT TTATT T-TATT TTATT
61301 AATTTCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.04
5 26 0.93
6 1 0.04
ACGTcount: A:0.17, C:0.03, G:0.00, T:0.80
Consensus pattern (5 bp):
TTATT
Found at i:62707 original size:22 final size:20
Alignment explanation
Indices: 62665--62726 Score: 61
Period size: 23 Copynumber: 2.8 Consensus size: 20
62655 TTAATTTAAT
62665 TTTTTTTATTTTACTTTACTACA
1 TTTTTTTATTTT--TTTACTA-A
62688 TTTTTTTATTTTTTTAACTAA
1 TTTTTTTATTTTTTT-ACTAA
62709 TCTTTTATTATTGTTTTT
1 T-TTTT-TTATT-TTTTT
62727 TATTATTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.14
22 8 0.23
23 17 0.49
24 5 0.14
ACGTcount: A:0.19, C:0.08, G:0.02, T:0.71
Consensus pattern (20 bp):
TTTTTTTATTTTTTTACTAA
Found at i:76520 original size:42 final size:43
Alignment explanation
Indices: 76450--76646 Score: 151
Period size: 41 Copynumber: 4.7 Consensus size: 43
76440 AAAAATGATT
* * * *
76450 AAATTAGGGGCCTAAACTATAAAAGTAAAAGT-ATAATTGAAA
1 AAATTAGGGACCTCAATTATAAAGGTAAAAGTGATAATTGAAA
* * *
76492 AAATTAGAGACCTTAATTATAGAGGTAAAAGTGATAA---AAA
1 AAATTAGGGACCTCAATTATAAAGGTAAAAGTGATAATTGAAA
* * * * *
76532 AAAATAGGGGCATCAATTTTAAAGGTAAAAAGTGAT-GTTGAAAA
1 AAATTAGGGACCTCAATTATAAAGGT-AAAAGTGATAATTG-AAA
* * *
76576 AAATTAGGGACCTAAATTAT-GA-GTAAAA--AATAGGATTGAAA
1 AAATTAGGGACCTCAATTATAAAGGTAAAAGTGATA--ATTGAAA
*
76617 AAATTAGGGACCTCAATTATAAAGGGAAAA
1 AAATTAGGGACCTCAATTATAAAGGTAAAA
76647 AAGCGAGAAT
Statistics
Matches: 119, Mismatches: 25, Indels: 21
0.72 0.15 0.13
Matches are distributed among these distances:
39 2 0.02
40 22 0.18
41 35 0.29
42 32 0.27
43 10 0.08
44 18 0.15
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (43 bp):
AAATTAGGGACCTCAATTATAAAGGTAAAAGTGATAATTGAAA
Found at i:76970 original size:22 final size:22
Alignment explanation
Indices: 76940--76981 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
76930 ATAGCAAAAA
*
76940 AAAATAAAATAAT-ATTTTAATG
1 AAAAGAAAA-AATAATTTTAATG
76962 AAAAGAAAAAATAATTTTAA
1 AAAAGAAAAAATAATTTTAA
76982 AATATCATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.31
Consensus pattern (22 bp):
AAAAGAAAAAATAATTTTAATG
Done.