Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167858.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_128, 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: 72428
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:20258 original size:1 final size:1
Alignment explanation
Indices: 20254--20278 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
20244 TAAAAAAATG
20254 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
20279 CCAAATGGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:22319 original size:201 final size:201
Alignment explanation
Indices: 21974--22375 Score: 603
Period size: 201 Copynumber: 2.0 Consensus size: 201
21964 TGATTCCTGT
* * * * *
21974 CTTATTTGCGATTTAACGGACTTTGGCCTATTCGAAACAGAAGCTGCATTGTACTCATGGGGTTT
1 CTTATTTGCCATTTAACGGACTTCGGCCTATTAGAAACAAAAGCTGCATTGTACTCAGGGGGTTT
* * *
22039 CGCAGTTTGTGCAGTTTCTAAACCACCCTCATTCACACTACTCTTGGTTACCAACTTGGCTTTAG
66 CACAGTTTGGGCAGTTTCTAAACCACCCTCATTCACACTACTCTTGGTTACCAACTTGGCTTGAG
* * * *
22104 AAGGTTCTTGTGCAGCAGCTTCTTGTTTCTGAGCAATGCGAGTGTTAGGTGCTTCAAGTCTGG-T
131 AAGGTTCCTGTGCAGCAGCTTCTTGTTTCTGAGCAATGCAAGTATCAGGTGCTTCAAGTCTGGCT
22168 TCGTGAC
196 T-GTGAC
*
22175 CTTATTTGCCATTTAACGGACTTCGGCCTATTAGAAACAAAAGCTGCATTGT-CTTCGGGGGGTT
1 CTTATTTGCCATTTAACGGACTTCGGCCTATTAGAAACAAAAGCTGCATTGTAC-TCAGGGGGTT
*
22239 TCACAGTTTGGGCAGTTTTTAAACCACCCTCATTCACACT-CGTCTTGGTTACCAACTTGGCTTG
65 TCACAGTTTGGGCAGTTTCTAAACCACCCTCATTCACACTAC-TCTTGGTTACCAACTTGGCTTG
* * *
22303 AGAAGGTTCCTGTGCAGCAGCTTCTTTTTTCTGAGTAATGCAAGTATCAGTTGCTTCAAGTCTGG
129 AGAAGGTTCCTGTGCAGCAGCTTCTTGTTTCTGAGCAATGCAAGTATCAGGTGCTTCAAGTCTGG
22368 CTTGTGAC
194 CTTGTGAC
22376 ATAACCAACT
Statistics
Matches: 181, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
200 2 0.01
201 177 0.98
202 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.22, T:0.35
Consensus pattern (201 bp):
CTTATTTGCCATTTAACGGACTTCGGCCTATTAGAAACAAAAGCTGCATTGTACTCAGGGGGTTT
CACAGTTTGGGCAGTTTCTAAACCACCCTCATTCACACTACTCTTGGTTACCAACTTGGCTTGAG
AAGGTTCCTGTGCAGCAGCTTCTTGTTTCTGAGCAATGCAAGTATCAGGTGCTTCAAGTCTGGCT
TGTGAC
Found at i:23266 original size:21 final size:21
Alignment explanation
Indices: 23219--23266 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
23209 ACTCCTTTTG
*
23219 CTTCC-TCTTTTATCCTTCTC
1 CTTCCTTCTTCTATCCTTCTC
** *
23239 CAACCTTCTTCTATCTTTCTC
1 CTTCCTTCTTCTATCCTTCTC
23260 CTTCCTT
1 CTTCCTT
23267 TCTGATCTGC
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
20 3 0.14
21 18 0.86
ACGTcount: A:0.08, C:0.40, G:0.00, T:0.52
Consensus pattern (21 bp):
CTTCCTTCTTCTATCCTTCTC
Found at i:24239 original size:15 final size:15
Alignment explanation
Indices: 24219--24247 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
24209 TCAAAGAAGA
24219 TGATTTTCCCATCTT
1 TGATTTTCCCATCTT
24234 TGATTTTCCCATCT
1 TGATTTTCCCATCT
24248 GCAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.52
Consensus pattern (15 bp):
TGATTTTCCCATCTT
Found at i:26659 original size:10 final size:10
Alignment explanation
Indices: 26644--26669 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
26634 ATAAAAATAA
26644 AATTTTATTT
1 AATTTTATTT
26654 AATTTTATTT
1 AATTTTATTT
26664 AATTTT
1 AATTTT
26670 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (10 bp):
AATTTTATTT
Found at i:27488 original size:16 final size:16
Alignment explanation
Indices: 27469--27501 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
27459 TGAATAAATA
*
27469 TGTGTATGTGCATGTG
1 TGTGCATGTGCATGTG
27485 TGTGCATGTGCATGTG
1 TGTGCATGTGCATGTG
27501 T
1 T
27502 CAGACGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.36, T:0.42
Consensus pattern (16 bp):
TGTGCATGTGCATGTG
Found at i:29931 original size:27 final size:24
Alignment explanation
Indices: 29901--29949 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 24
29891 TTACGCATTT
29901 CTTAAAATATTTATATTTTATTTATAG
1 CTTAAAATA--TAT-TTTTATTTATAG
*
29928 CTTAACATATATTTTTATTTAT
1 CTTAAAATATATTTTTATTTAT
29950 GGTATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 3 0.14
27 8 0.38
ACGTcount: A:0.35, C:0.06, G:0.02, T:0.57
Consensus pattern (24 bp):
CTTAAAATATATTTTTATTTATAG
Found at i:37871 original size:16 final size:16
Alignment explanation
Indices: 37846--37880 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
37836 ATCAATCAAC
37846 AAAATATTTAAACATAA
1 AAAATATTTAAA-ATAA
37863 AAAAT-TTTAAAATAA
1 AAAATATTTAAAATAA
37878 AAA
1 AAA
37881 CTCAAATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 6 0.33
17 5 0.28
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATATTTAAAATAA
Found at i:38029 original size:10 final size:11
Alignment explanation
Indices: 38009--38078 Score: 54
Period size: 12 Copynumber: 6.2 Consensus size: 11
37999 AAAATTATTT
38009 TTAATAATTAA
1 TTAATAATTAA
38020 TTAA-AATTAA
1 TTAATAATTAA
*
38030 TTTAATAAGTAA
1 -TTAATAATTAA
*
38042 TTGATTAATTGAA
1 TT-AATAATT-AA
* *
38055 TTAA-ATTTAT
1 TTAATAATTAA
38065 TTAATAAATTAA
1 TTAAT-AATTAA
38077 TT
1 TT
38079 CCATTAAAAT
Statistics
Matches: 45, Mismatches: 8, Indels: 11
0.70 0.12 0.17
Matches are distributed among these distances:
10 11 0.24
11 13 0.29
12 17 0.38
13 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (11 bp):
TTAATAATTAA
Found at i:38036 original size:22 final size:23
Alignment explanation
Indices: 37999--38043 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
37989 AAATTTTTAA
* *
37999 AAAATTATTTTTAATAATTAATT
1 AAAATTATATTTAATAAGTAATT
38022 AAAATTA-ATTTAATAAGTAATT
1 AAAATTATATTTAATAAGTAATT
38044 GATTAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
AAAATTATATTTAATAAGTAATT
Found at i:38638 original size:22 final size:22
Alignment explanation
Indices: 38611--38654 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
38601 TTTATTGGAT
38611 TTTTATATCTAATAAA-TTAAAA
1 TTTTATATCTAA-AAATTTAAAA
*
38633 TTTTATATTTAAAAATTTAAAA
1 TTTTATATCTAAAAATTTAAAA
38655 AAATTAATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TTTTATATCTAAAAATTTAAAA
Found at i:38793 original size:16 final size:16
Alignment explanation
Indices: 38757--38790 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
38747 AAATTTTTTT
38757 AAATAATTTCATTTAA
1 AAATAATTTCATTTAA
*
38773 AAATAATTT-TTTTAA
1 AAATAATTTCATTTAA
38788 AAA
1 AAA
38791 ATATAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATAATTTCATTTAA
Found at i:39362 original size:15 final size:17
Alignment explanation
Indices: 39331--39363 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
39321 ATTTTTTTAA
39331 TCAAATTGAATTTTGAT
1 TCAAATTGAATTTTGAT
39348 TCAAATT-AA-TTTGAT
1 TCAAATTGAATTTTGAT
39363 T
1 T
39364 TATTGATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.09, T:0.48
Consensus pattern (17 bp):
TCAAATTGAATTTTGAT
Found at i:40403 original size:22 final size:23
Alignment explanation
Indices: 40361--40403 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
40351 CTTTTTTTAA
*
40361 TTTTAATTTTTTTTTTGTTTCTT
1 TTTTAATTTTTTTTATGTTTCTT
*
40384 TTTTTATTTTTTTTAT-TTTC
1 TTTTAATTTTTTTTATGTTTC
40404 ATGAATTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (23 bp):
TTTTAATTTTTTTTATGTTTCTT
Found at i:40622 original size:21 final size:20
Alignment explanation
Indices: 40592--40631 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
40582 GTAAAATTTT
40592 ATTTAATTATAT-ATTAATTA
1 ATTTAATTAT-TCATTAATTA
40612 ATTTAATTTATTCATTAATT
1 ATTTAA-TTATTCATTAATT
40632 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAATTATTCATTAATTA
Found at i:41613 original size:26 final size:23
Alignment explanation
Indices: 41612--41690 Score: 50
Period size: 27 Copynumber: 3.1 Consensus size: 23
41602 AGTAAATATA
41612 TTTTATTAAATAATATAAATTATT
1 TTTTATTAAATAATATAAATTA-T
* * *
41636 ATTTTAAATTAAACAAAATTAATATAT
1 -TTTT--ATTAAATAATATAAAT-TAT
*
41663 TTTTATTTAAAATATATATTAATTAT
1 TTTTA-TT-AAATA-ATATAAATTAT
41689 TT
1 TT
41691 GTAAAAAATT
Statistics
Matches: 43, Mismatches: 5, Indels: 11
0.73 0.08 0.19
Matches are distributed among these distances:
24 1 0.02
25 6 0.14
26 13 0.30
27 21 0.49
28 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTTATTAAATAATATAAATTAT
Found at i:41638 original size:25 final size:25
Alignment explanation
Indices: 41587--41644 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
41577 GTATTTGTAT
*
41587 TTTTATTATATATATAGTAAATATA
1 TTTTATTAAATATATAGTAAATATA
41612 TTTTATTAAATA-ATA-TAAAT-TA
1 TTTTATTAAATATATAGTAAATATA
41634 TTATT-TTAAAT
1 TT-TTATTAAAT
41645 TAAACAAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 10 0.32
23 7 0.23
24 3 0.10
25 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (25 bp):
TTTTATTAAATATATAGTAAATATA
Found at i:41710 original size:50 final size:50
Alignment explanation
Indices: 41604--41712 Score: 116
Period size: 50 Copynumber: 2.2 Consensus size: 50
41594 ATATATATAG
41604 TAAATATA-TTTTATTAAATAATATAAATTATTATTTTAAATTAAACAAAA
1 TAAATATATTTTTATTAAATAATATAAATTATTATTTTAAA-TAAACAAAA
* * * ** *
41654 TTAATATATTTTTATTTAA-AATATATATTAATTATTTGTAAA-AAATTACA
1 TAAATATATTTTTATTAAATAATATAAATT-ATTATTT-TAAATAAACAAAA
41704 TAAATATAT
1 TAAATATAT
41713 AAGATAAAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
50 29 0.59
51 16 0.33
52 4 0.08
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (50 bp):
TAAATATATTTTTATTAAATAATATAAATTATTATTTTAAATAAACAAAA
Found at i:41890 original size:37 final size:42
Alignment explanation
Indices: 41802--41892 Score: 111
Period size: 43 Copynumber: 2.3 Consensus size: 42
41792 AAATATTTAC
* *
41802 AAAAATAAAAATAAATTTAAATTTAAAATATTCCATTAAATAT
1 AAAAATAAAAATAAATATAAATTTAAAATATT-CATAAAATAT
*
41845 AAATATAAAAATAAATAT-AATTTAAAAT-TT-A-AAAATA-
1 AAAAATAAAAATAAATATAAATTTAAAATATTCATAAAATAT
41882 AAAAATAAAAA
1 AAAAATAAAAA
41893 ATAACTTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
37 10 0.23
38 5 0.11
39 1 0.02
41 2 0.05
42 10 0.23
43 16 0.36
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (42 bp):
AAAAATAAAAATAAATATAAATTTAAAATATTCATAAAATAT
Found at i:45876 original size:11 final size:11
Alignment explanation
Indices: 45860--45889 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
45850 ATCCCATAAA
45860 AGATTTGTTTG
1 AGATTTGTTTG
45871 AGATTTGTTTG
1 AGATTTGTTTG
45882 AGATTTGT
1 AGATTTGT
45890 CAGATATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:45994 original size:52 final size:52
Alignment explanation
Indices: 45915--46070 Score: 179
Period size: 52 Copynumber: 3.0 Consensus size: 52
45905 GGACAAGAAA
* * *
45915 ACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGCAAGTTTG
* * ** *
45967 ACTTGCAAGAGAAGAATTCTAAAAGAAAAAAAATTCTTAATAGACAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGCAAGTTTG
* * * * *
46019 ACTTACAGGAAAAGAATTCTAAGAG-GAGAGAGATTCTTAATGGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAG-GATTCTTAATAGGCAAGTTTG
46071 TATGGTTATA
Statistics
Matches: 85, Mismatches: 18, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
51 2 0.02
52 83 0.98
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.25
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGCAAGTTTG
Found at i:46245 original size:15 final size:16
Alignment explanation
Indices: 46225--46256 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
46215 AGAAGAGATT
46225 GAGA-GGTCCACATAG
1 GAGAGGGTCCACATAG
46240 GAGAGGGTCCACATAG
1 GAGAGGGTCCACATAG
46256 G
1 G
46257 TATGATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.31, C:0.19, G:0.38, T:0.12
Consensus pattern (16 bp):
GAGAGGGTCCACATAG
Found at i:46677 original size:25 final size:25
Alignment explanation
Indices: 46649--46713 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
46639 TCAAATGTTT
* **
46649 GAGATGTGGGAAGAGTTGATGGTTC
1 GAGATATGGGAAGAGTTGACAGTTC
* *
46674 GAGACATGGGAAAAGTTGACAGTTC
1 GAGATATGGGAAGAGTTGACAGTTC
46699 GAGATATGGGAAGAG
1 GAGATATGGGAAGAG
46714 CTTGGTTTGA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.32, C:0.06, G:0.40, T:0.22
Consensus pattern (25 bp):
GAGATATGGGAAGAGTTGACAGTTC
Found at i:46728 original size:23 final size:22
Alignment explanation
Indices: 46649--46735 Score: 66
Period size: 25 Copynumber: 3.6 Consensus size: 22
46639 TCAAATGTTT
*
46649 GAGATGTGGGAAGAGTTGATGGTTC
1 GAGATATGGGAAGAG-T--TGGTTC
* *
46674 GAGACATGGGAAAAGTTGACAGTTC
1 GAGATATGGGAAGAGTTG---GTTC
*
46699 GAGATATGGGAAGAGCTTGGTTT
1 GAGATATGGGAAGAG-TTGGTTC
*
46722 GAGATATGAGAAGA
1 GAGATATGGGAAGA
46736 AGTAAGCTTA
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
22 2 0.04
23 16 0.31
24 1 0.02
25 29 0.57
26 3 0.06
ACGTcount: A:0.32, C:0.06, G:0.38, T:0.24
Consensus pattern (22 bp):
GAGATATGGGAAGAGTTGGTTC
Found at i:46963 original size:11 final size:11
Alignment explanation
Indices: 46947--46976 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
46937 ATCCCATAAA
46947 AGATTTGTTTG
1 AGATTTGTTTG
46958 AGATTTGTTTG
1 AGATTTGTTTG
46969 AGATTTGT
1 AGATTTGT
46977 CAGATATTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (11 bp):
AGATTTGTTTG
Found at i:47082 original size:52 final size:52
Alignment explanation
Indices: 47003--47158 Score: 190
Period size: 52 Copynumber: 3.0 Consensus size: 52
46993 GGACAAGAAA
* * *
47003 ACTTGCAAAAGAAGAATTCCAAGAGAAAGAGGATTCTTAATAGGTAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGCAAGTTTG
* *
47055 ACTTGCAAGAGAAGAATTCTAAAAGAAA-AGAGATTCTTAATAGACAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGAG-GATTCTTAATAGGCAAGTTTG
* * * * *
47107 ACTTACAGGAAAAGAATTCTAAGAG-GAGAGGGATTCTTAATGGGCAAGTTTG
1 ACTTGCAAGAGAAGAATTCTAAGAGAAAGA-GGATTCTTAATAGGCAAGTTTG
47159 TATGGTTATA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
51 3 0.03
52 85 0.96
53 1 0.01
ACGTcount: A:0.42, C:0.10, G:0.24, T:0.25
Consensus pattern (52 bp):
ACTTGCAAGAGAAGAATTCTAAGAGAAAGAGGATTCTTAATAGGCAAGTTTG
Found at i:47335 original size:16 final size:16
Alignment explanation
Indices: 47314--47346 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
47304 AGAAGAGACT
47314 GAGAGGGTCCACATAG
1 GAGAGGGTCCACATAG
47330 GAGAGGGTCCACATAG
1 GAGAGGGTCCACATAG
47346 G
1 G
47347 TATGATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.39, T:0.12
Consensus pattern (16 bp):
GAGAGGGTCCACATAG
Found at i:53172 original size:41 final size:41
Alignment explanation
Indices: 53115--53195 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
53105 TCTTCAGGAG
*
53115 AAATGGAATCTATTTCCATA-GAGTTTTCTTAATTAAACATA
1 AAATGGAATCTATTTCCA-ACCAGTTTTCTTAATTAAACATA
*
53156 AAATGGAATCTATTTCCAACCAGTTTTGTTAATTAAACAT
1 AAATGGAATCTATTTCCAACCAGTTTTCTTAATTAAACAT
53196 GACTGACAGC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.38
Consensus pattern (41 bp):
AAATGGAATCTATTTCCAACCAGTTTTCTTAATTAAACATA
Found at i:53645 original size:16 final size:16
Alignment explanation
Indices: 53624--53675 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 16
53614 ATTAATTAAT
53624 TATTTATATATATATA
1 TATTTATATATATATA
53640 TATTTATATA-ATGATA
1 TATTTATATATAT-ATA
* *
53656 T-TTT-TAAATATTTA
1 TATTTATATATATATA
53670 TATTTA
1 TATTTA
53676 AAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 6 0.20
15 10 0.33
16 14 0.47
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (16 bp):
TATTTATATATATATA
Found at i:53672 original size:30 final size:30
Alignment explanation
Indices: 53624--53689 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
53614 ATTAATTAAT
* * * * *
53624 TATTTATATATATATATATTTATATAATGA
1 TATTTTTAAATATATATATTTAAAAAATAA
*
53654 TATTTTTAAATATTTATATTTAAAAAATAA
1 TATTTTTAAATATATATATTTAAAAAATAA
53684 TATTTT
1 TATTTT
53690 ATTAATTTCG
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (30 bp):
TATTTTTAAATATATATATTTAAAAAATAA
Found at i:55014 original size:20 final size:19
Alignment explanation
Indices: 54969--55011 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
54959 ATATTGTCTA
*
54969 TATTTAATAAATTAATTTT
1 TATTTAATAAATAAATTTT
54988 TATTTAATAATATAAA-TTT
1 TATTTAATAA-ATAAATTTT
55007 TATTT
1 TATTT
55012 TAAATTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTTAATAAATAAATTTT
Found at i:55214 original size:2 final size:2
Alignment explanation
Indices: 55207--55233 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55197 TACCCATTAA
55207 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 A
55234 AAGATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56054 original size:16 final size:16
Alignment explanation
Indices: 56045--56078 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56035 ATTTAATTTT
56045 AAATCAATTTAGATTC
1 AAATCAATTTAGATTC
* *
56061 AAATCAATATGGATTC
1 AAATCAATTTAGATTC
56077 AA
1 AA
56079 TCGAGTTTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (16 bp):
AAATCAATTTAGATTC
Found at i:63875 original size:34 final size:34
Alignment explanation
Indices: 63809--63888 Score: 92
Period size: 34 Copynumber: 2.4 Consensus size: 34
63799 TTATTATTAA
*
63809 TTTTTTATTTTATCTCACTAGGCTAGTGTTTTTT
1 TTTTTTAATTTATCTCACTAGGCTAGTGTTTTTT
* *
63843 TTTTTTAATTTATTTCATTAGGCT-G-GCTTTTTT
1 TTTTTTAATTTATCTCACTAGGCTAGTG-TTTTTT
*
63876 TTAATTTAATTTA
1 TT-TTTTAATTTA
63889 AAATTTTGAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
32 1 0.03
33 9 0.22
34 30 0.75
ACGTcount: A:0.19, C:0.09, G:0.10, T:0.62
Consensus pattern (34 bp):
TTTTTTAATTTATCTCACTAGGCTAGTGTTTTTT
Found at i:64480 original size:16 final size:17
Alignment explanation
Indices: 64461--64492 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
64451 AGTTATTATT
64461 TAACATATTA-ATTTAA
1 TAACATATTATATTTAA
64477 TAACATATTATATTTA
1 TAACATATTATATTTA
64493 TATATAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (17 bp):
TAACATATTATATTTAA
Found at i:64500 original size:28 final size:27
Alignment explanation
Indices: 64465--64518 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
64455 ATTATTTAAC
64465 ATATTAATTTAATAACAT-A-TTATATTT
1 ATATTAA-TTAA-AACATAATTTATATTT
64492 ATATATAATTAAAACATAATTTATATT
1 ATAT-TAATTAAAACATAATTTATATT
64519 AAAAAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 5 0.21
27 9 0.38
28 10 0.42
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTAATTAAAACATAATTTATATTT
Found at i:64764 original size:23 final size:23
Alignment explanation
Indices: 64712--64764 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
64702 CCATGTGGCT
* *
64712 TCCTATTTGGTTCATTTTCATTT
1 TCCTTTTTGGTTCATTTTCATTA
* *
64735 TCATTTTTGGTTCTTTTTC-TTGA
1 TCCTTTTTGGTTCATTTTCATT-A
64758 TCCTTTT
1 TCCTTTT
64765 ATTTTTAGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
22 2 0.08
23 22 0.92
ACGTcount: A:0.09, C:0.17, G:0.09, T:0.64
Consensus pattern (23 bp):
TCCTTTTTGGTTCATTTTCATTA
Found at i:65154 original size:21 final size:22
Alignment explanation
Indices: 65106--65149 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
65096 TGAGAAAGCA
65106 AAAGTCTTTCACTCATTTTTCT
1 AAAGTCTTTCACTCATTTTTCT
65128 AAAGTC-TTCTACTCATTTTTCT
1 AAAGTCTTTC-ACTCATTTTTCT
65150 TAGTCATGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 3 0.14
22 18 0.86
ACGTcount: A:0.23, C:0.23, G:0.05, T:0.50
Consensus pattern (22 bp):
AAAGTCTTTCACTCATTTTTCT
Found at i:67199 original size:20 final size:20
Alignment explanation
Indices: 67174--67214 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
67164 AATTTGAACC
67174 TGACTCCCACTAACTACTAT
1 TGACTCCCACTAACTACTAT
67194 TGACTCCCACTAACTACTAT
1 TGACTCCCACTAACTACTAT
67214 T
1 T
67215 TTTTTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.34, G:0.05, T:0.32
Consensus pattern (20 bp):
TGACTCCCACTAACTACTAT
Found at i:71253 original size:13 final size:14
Alignment explanation
Indices: 71237--71268 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
71227 TTAACATTAA
71237 ATATTATATTTT-T
1 ATATTATATTTTAT
71250 ATATT-TATTTTAT
1 ATATTATATTTTAT
71263 ATATTA
1 ATATTA
71269 AAAATATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
ATATTATATTTTAT
Found at i:71942 original size:20 final size:20
Alignment explanation
Indices: 71906--71962 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
71896 TTAATTTTTA
* *
71906 ATTGTA-AAAGAAAAAATTGG
1 ATTGTATAAA-AATAAATGGG
71926 ATTGTATAAAAATAAATGGG
1 ATTGTATAAAAATAAATGGG
*
71946 AATG-ATAAAATATAAAT
1 ATTGTATAAAA-ATAAAT
71963 AATCAATTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 6 0.19
20 23 0.72
21 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.28
Consensus pattern (20 bp):
ATTGTATAAAAATAAATGGG
Done.