Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167959.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_219, 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: 48896
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.37
Found at i:4105 original size:9 final size:8
Alignment explanation
Indices: 4089--4140 Score: 54
Period size: 8 Copynumber: 6.4 Consensus size: 8
4079 TGACTTTTTT
4089 TTTTCTTC
1 TTTTCTTC
4097 TTCTTCTTC
1 TT-TTCTTC
4106 TTTTTCTT-
1 -TTTTCTTC
4114 TTTTCTAT-
1 TTTTCT-TC
*
4122 TTTCCTTC
1 TTTTCTTC
4130 TTTTCTTC
1 TTTTCTTC
4138 TTT
1 TTT
4141 CATATTTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
7 7 0.18
8 18 0.47
9 11 0.29
10 2 0.05
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.75
Consensus pattern (8 bp):
TTTTCTTC
Found at i:4129 original size:24 final size:24
Alignment explanation
Indices: 4102--4147 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
4092 TCTTCTTCTT
*
4102 CTTCTTTTTCTTTTTTC-TATTTTC
1 CTTC-TTTTCTTCTTTCATATTTTC
4126 CTTCTTTTCTTCTTTCATATTT
1 CTTCTTTTCTTCTTTCATATTT
4148 AATAATATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.72
Consensus pattern (24 bp):
CTTCTTTTCTTCTTTCATATTTTC
Found at i:4133 original size:16 final size:14
Alignment explanation
Indices: 4094--4141 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 14
4084 TTTTTTTTTC
4094 TTCTTCTTCTTCTTT
1 TTCTTCTT-TTCTTT
4109 TTCTT-TTTTCTATT
1 TTCTTCTTTTCT-TT
4123 TTCCTTCTTTTCTTCT
1 TT-CTTCTTTTCTT-T
4139 TTC
1 TTC
4142 ATATTTAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
13 4 0.14
14 6 0.21
15 10 0.34
16 9 0.31
ACGTcount: A:0.02, C:0.25, G:0.00, T:0.73
Consensus pattern (14 bp):
TTCTTCTTTTCTTT
Found at i:5058 original size:9 final size:9
Alignment explanation
Indices: 5044--5068 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
5034 TATGTATTAA
5044 TTAATATAT
1 TTAATATAT
5053 TTAATATAT
1 TTAATATAT
5062 TTAATAT
1 TTAATAT
5069 TATATTCAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TTAATATAT
Found at i:14686 original size:2 final size:2
Alignment explanation
Indices: 14681--14715 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
14671 AGGTGTCCAC
14681 AT AT AT 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 AT AT AT A
14716 AACTGCCAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17099 original size:13 final size:13
Alignment explanation
Indices: 17083--17121 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
17073 AAATAATTTA
17083 AAAAATTAAAATC
1 AAAAATTAAAATC
*
17096 AAAAATTAAAATG
1 AAAAATTAAAATC
17109 AATAAATTAAAAT
1 AA-AAATTAAAAT
17122 ATCTTGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.26
Consensus pattern (13 bp):
AAAAATTAAAATC
Found at i:17637 original size:28 final size:29
Alignment explanation
Indices: 17606--17676 Score: 69
Period size: 28 Copynumber: 2.5 Consensus size: 29
17596 TTAATACTAT
17606 ATATATATTATTTATAAATTAATT-ATTA
1 ATATATATTATTTATAAATTAATTCATTA
*
17634 ATATA-A-TACTTAACTAAATTAATTCATTA
1 ATATATATTA-TTTA-TAAATTAATTCATTA
* *
17663 A-ATATCTTAATTAT
1 ATATATATTATTTAT
17677 GATTTTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
26 2 0.06
27 4 0.12
28 19 0.56
29 7 0.21
30 2 0.06
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (29 bp):
ATATATATTATTTATAAATTAATTCATTA
Found at i:21202 original size:238 final size:235
Alignment explanation
Indices: 20923--21723 Score: 611
Period size: 238 Copynumber: 3.4 Consensus size: 235
20913 ATACTTGCAA
* * * *
20923 AAAAAAATAATTAATTAAAATTTTATATTAT-TATCATAATTATTTACATTATAATAGTATACTT
1 AAAATAATAATTAATTAAAATTTTATATT-TCAAT-ATAATTATTTACATTACAATAATATACTT
* * * * *
20987 -TTACGGTTGCTCTTACTTTTGATTATGTTTAGAATTGTTATAACTTTTTTTTAACATGTTACA-
64 ATTATGGTTGTTCTTACTTTTCATTATGTTTAAAATTATTATAACTTTTTTTTAACATGTTA-AG
* * **
21050 ATACTTC-TAATCCATTTTACTCAAAATGATACTAATTTTACT-TTACTTCTTC-CTTGTTTATG
128 ACACTTCATAA-CCATTTTACGCAAAATGATACTAATTTTA-TGTTACTTC-TCACTTGTTTAAA
**
21112 TTATTAATTTTATTTTTTAAATTT-TAGCTATTTTTCCAATA-TATTTAG-
190 TTACCAA-TTTATTTTTT-AATTTATAGCTA-TTTTCC-ATACTATTT-GT
* * *
21160 AGGAATAATAATTAATTAAAATTTTACATTGTCAATATAATTATTTACTTTACAATAATAT-CTT
1 A-AAATAATAATTAATTAAAATTTTATATT-TCAATATAATTATTTACATTACAATAATATACTT
* * * * * * * * **
21224 CTAATGGTTGTTTTTACTTTCCATTATATTAACAAATTATCATAACTCTTTTTTAATGTGTTAAG
64 ATTATGGTTGTTCTTACTTTTCATTATGTTTA-AAATTATTATAACTTTTTTTTAACATGTTAAG
* * * * **
21289 ACACTTCATAACTATTTTACGCCAAATTATACTACTTTTATGTTTGTTCTCACTTGTTTAAATTA
128 ACACTTCATAACCATTTTACGCAAAATGATACTAATTTTATGTTACTTCTCACTTGTTTAAATTA
* *
21354 CCAATTTATTTTTTAATTTATAGTTATTTTCCGTAGCTATTTGT
193 CCAATTTATTTTTTAATTTATAGCTATTTTCCATA-CTATTTGT
* *
21398 AAAATAATAATTAATTAAAATTTTATATTACTAATATAATTATTTACATTACAATATTATA-TTA
1 AAAATAATAATTAATTAAAATTTTATATTTC-AATATAATTATTTACATTACAATAATATACTTA
** * * ** *
21462 TTATAATTATTCTTACTTTTCATTATGTTTAAAATTATTGTAAC-TTTTTTTAATGTATTACA-A
65 TTATGGTTGTTCTTACTTTTCATTATGTTTAAAATTATTATAACTTTTTTTTAACATGTTA-AGA
* * * ** * * ** * *
21525 CAATTTATAACTATTTTATACTAAATTATACTAATTTTACATT-TTTCTCACTTGTTTACATTAC
129 CACTTCATAACCATTTTACGCAAAATGATACTAATTTTATGTTACTTCTCACTTGTTTAAATTAC
* *
21589 CAATATGT-TTTTTTAATTT-TCAG-TAATTTTTCGTA-TATGTT-T
194 CAAT-T-TATTTTTTAATTTAT-AGCT-ATTTTCCATACTAT-TTGT
* * * * * **
21631 AAAAAAATAAATAATTAAAATTTTATGTTAACAACT-TAATTATTTACGTTACAATAAT-TTTTT
1 AAAATAATAATTAATTAAAATTTTATATT-TCAA-TATAATTATTTACATTACAATAATATACTT
* * * *
21694 TTTATGATTGTTCTTACCTTTAATTA-GTTT
64 ATTATGGTTGTTCTTACTTTTCATTATGTTT
21724 TAGAATTGTA
Statistics
Matches: 465, Mismatches: 76, Indels: 51
0.79 0.13 0.09
Matches are distributed among these distances:
232 5 0.01
233 75 0.16
234 30 0.06
235 73 0.16
236 16 0.03
237 93 0.20
238 96 0.21
239 74 0.16
240 3 0.01
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.50
Consensus pattern (235 bp):
AAAATAATAATTAATTAAAATTTTATATTTCAATATAATTATTTACATTACAATAATATACTTAT
TATGGTTGTTCTTACTTTTCATTATGTTTAAAATTATTATAACTTTTTTTTAACATGTTAAGACA
CTTCATAACCATTTTACGCAAAATGATACTAATTTTATGTTACTTCTCACTTGTTTAAATTACCA
ATTTATTTTTTAATTTATAGCTATTTTCCATACTATTTGT
Found at i:21437 original size:237 final size:233
Alignment explanation
Indices: 20923--21688 Score: 601
Period size: 237 Copynumber: 3.2 Consensus size: 233
20913 ATACTTGCAA
* * * *
20923 AAAAAAATAATTAATTAAAATTTTATATTA-TTATCATAATTATTTACATTATAATAGTATACTT
1 AAAATAATAATTAATTAAAATTTTATATTACTAAT-ATAATTATTTACATTACAATAATATA-TT
* *** ** ** * * * * * ** *
20987 -TTACGGTTGCTCTTACTTTTGATTATGTTTAGAATTGTTATAACTTTTTTTTAACATGTTACAA
64 ATAATAATTATTCTTACTTTCCATTATATTAAAAATTATCATAAC-TTTTTTTAATGTATTACAA
* * * * * * **
21051 TACTTC-TAATCCATTTTACTCAAAATGATACTAATTTTAC-TTTACTTCTTC-CTTGTTTATGT
128 CAATTCATAA-CTATTTTACACCAAATTATACTAATTTTACATTT--TTC-TCACTTGTTTAAAT
** * * * *
21113 TATTAAT-TTTATTTTTTAAATTTT-AGCTATTTTTCC-AATATATTT
189 TACCAATATGT-TTTTTT-AATTTTCAG-TAATTTTCCGTATATGTTT
* * * *
21158 AGAGGAATAATAATTAATTAAAATTTTACATT-GTCAATATAATTATTTACTTTACAATAATATC
1 A-A--AATAATAATTAATTAAAATTTTATATTACT-AATATAATTATTTACATTACAATAATATA
* ** * * *
21222 TTCTAATGGTTGTTTTTACTTTCCATTATATTAACAAATTATCATAACTCTTTTTTAATGTGTTA
62 TTATAATAATTATTCTTACTTTCCATTATATTAA-AAATTATCATAACT-TTTTTTAATGTATTA
* * * **
21287 -AGACACTTCATAACTATTTTACGCCAAATTATACTACTTTTATGTTTGTTCTCACTTGTTTAAA
125 CA-ACAATTCATAACTATTTTACACCAAATTATACTAATTTTACATTT-TTCTCACTTGTTTAAA
*
21351 TTACCAAT-T-TATTTTTTAATTTAT-AGTTATTTTCCGTAGCTAT-TTGT
188 TTACCAATATGT-TTTTTTAATTT-TCAGTAATTTTCCGTA--TATGTT-T
*
21398 AAAATAATAATTAATTAAAATTTTATATTACTAATATAATTATTTACATTACAATATTATATTAT
1 AAAATAATAATTAATTAAAATTTTATATTACTAATATAATTATTTACATTACAATAATATATTAT
* * * * **
21463 TATAATTATTCTTACTTTTCATTATGTTTAAAATTATTGTAACTTTTTTTAATGTATTACAACAA
66 AATAATTATTCTTACTTTCCATTATATTAAAAATTATCATAACTTTTTTTAATGTATTACAACAA
* * * *
21528 TTTATAACTATTTTATACTAAATTATACTAATTTTACATTTTTCTCACTTGTTTACATTACCAAT
131 TTCATAACTATTTTACACCAAATTATACTAATTTTACATTTTTCTCACTTGTTTAAATTACCAAT
*
21593 ATGTTTTTTTAATTTTCAGTAATTTTTCGTATATGTTT
196 ATGTTTTTTTAATTTTCAGTAATTTTCCGTATATGTTT
* * * *
21631 AAAAAAATAAATAATTAAAATTTTATGTTAAC-AACT-TAATTATTTACGTTACAATAAT
1 AAAATAATAATTAATTAAAATTTTATATT-ACTAA-TATAATTATTTACATTACAATAAT
21689 TTTTTTTTAT
Statistics
Matches: 438, Mismatches: 68, Indels: 52
0.78 0.12 0.09
Matches are distributed among these distances:
233 52 0.12
234 29 0.07
235 76 0.17
236 15 0.03
237 91 0.21
238 88 0.20
239 76 0.17
240 11 0.03
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.49
Consensus pattern (233 bp):
AAAATAATAATTAATTAAAATTTTATATTACTAATATAATTATTTACATTACAATAATATATTAT
AATAATTATTCTTACTTTCCATTATATTAAAAATTATCATAACTTTTTTTAATGTATTACAACAA
TTCATAACTATTTTACACCAAATTATACTAATTTTACATTTTTCTCACTTGTTTAAATTACCAAT
ATGTTTTTTTAATTTTCAGTAATTTTCCGTATATGTTT
Found at i:21443 original size:21 final size:22
Alignment explanation
Indices: 21419--21463 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
21409 TAATTAAAAT
*
21419 TTTATATTACTAATA-TA-ATTA
1 TTTACATTAC-AATATTATATTA
21440 TTTACATTACAATATTATATTA
1 TTTACATTACAATATTATATTA
21462 TT
1 TT
21464 ATAATTATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 11 0.52
22 6 0.29
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTACATTACAATATTATATTA
Found at i:21458 original size:34 final size:31
Alignment explanation
Indices: 21411--21472 Score: 79
Period size: 34 Copynumber: 1.9 Consensus size: 31
21401 ATAATAATTA
*
21411 ATTAAAATTTTATATTACTAATATAATTATTTAC
1 ATTAAAATATTATATTA-T--TATAATTATTTAC
*
21445 ATTACAATATTATATTATTATAATTATT
1 ATTAAAATATTATATTATTATAATTATT
21473 CTTACTTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 10 0.38
33 1 0.04
34 15 0.58
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (31 bp):
ATTAAAATATTATATTATTATAATTATTTAC
Found at i:24298 original size:58 final size:59
Alignment explanation
Indices: 24197--24316 Score: 170
Period size: 58 Copynumber: 2.1 Consensus size: 59
24187 CAATTTTCAG
* * * *
24197 GTAACCTCCATGAGACTATCCAACAAAGTTAATGCTTGTATAACTAAATTAAAG-TTAA
1 GTAACCTCCATGACACTATCCAACAAAGTTAATGCCTGCATAACCAAATTAAAGTTTAA
* * *
24255 GTAACCTTCATGACACTATTCAACAAAGTTAGTGCCTGCATAACCAAATTAAAGTTTAA
1 GTAACCTCCATGACACTATCCAACAAAGTTAATGCCTGCATAACCAAATTAAAGTTTAA
24314 GTA
1 GTA
24317 TTATATAATA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
58 47 0.87
59 7 0.13
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.29
Consensus pattern (59 bp):
GTAACCTCCATGACACTATCCAACAAAGTTAATGCCTGCATAACCAAATTAAAGTTTAA
Found at i:24876 original size:18 final size:20
Alignment explanation
Indices: 24853--24892 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
24843 CATGAAAATA
*
24853 TTAAAAA-AAA-AATCCCAG
1 TTAAAAAGAAAGAAACCCAG
24871 TTAAAAAGAAAGAAACCCAG
1 TTAAAAAGAAAGAAACCCAG
24891 TT
1 TT
24893 TATTGGAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 3 0.16
20 9 0.47
ACGTcount: A:0.57, C:0.15, G:0.10, T:0.17
Consensus pattern (20 bp):
TTAAAAAGAAAGAAACCCAG
Found at i:25756 original size:17 final size:16
Alignment explanation
Indices: 25736--25771 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
25726 TCATAAATTT
25736 AAAAAAT-AAAAGTAAA
1 AAAAAATGAAAA-TAAA
25752 AAAAAATGAAAATAAA
1 AAAAAATGAAAATAAA
25768 AAAA
1 AAAA
25772 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.83, C:0.00, G:0.06, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAATAAA
Found at i:26817 original size:23 final size:24
Alignment explanation
Indices: 26791--26835 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
26781 TTTTTGTATT
*
26791 TTTATTATTATTCT-TTTATTTTA
1 TTTATTATTATCCTATTTATTTTA
*
26814 TTTATTTTTATCCTATTTATTT
1 TTTATTATTATCCTATTTATTT
26836 CAATTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTATTATTATCCTATTTATTTTA
Found at i:32135 original size:46 final size:47
Alignment explanation
Indices: 31949--32135 Score: 152
Period size: 46 Copynumber: 4.1 Consensus size: 47
31939 TTTTAAAAAT
* * * *
31949 GAATCTTTGAAATTTTAGATGTGAAA-CCAAAAAATTTTTCAAATGA
1 GAATCTTTAAAACTTTGGATGTGAAATCCTAAAAATTTTTCAAATGA
* * * * ** *
31995 GAATCTTTAAAATTTTGGTTCTAAAATATTAAAAA-TTTTCGAAT-A
1 GAATCTTTAAAACTTTGGATGTGAAATCCTAAAAATTTTTCAAATGA
* * * ** *
32040 TGAATATTTGAAACTTTCGATGT-AAATCCT-AAAATTTTTTGAATAA
1 -GAATCTTTAAAACTTTGGATGTGAAATCCTAAAAATTTTTCAAATGA
* *
32086 GAATCTTTAAAACTTTGGATGTGAAATCCTGAAATTTTTTC-AATGA
1 GAATCTTTAAAACTTTGGATGTGAAATCCTAAAAATTTTTCAAATGA
32132 GAAT
1 GAAT
32136 ATTTGAATTT
Statistics
Matches: 111, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
44 4 0.04
45 33 0.30
46 61 0.55
47 13 0.12
ACGTcount: A:0.40, C:0.09, G:0.12, T:0.39
Consensus pattern (47 bp):
GAATCTTTAAAACTTTGGATGTGAAATCCTAAAAATTTTTCAAATGA
Found at i:32148 original size:45 final size:44
Alignment explanation
Indices: 32030--32148 Score: 130
Period size: 46 Copynumber: 2.6 Consensus size: 44
32020 ATATTAAAAA
* *
32030 TTTTCGAATATGAATATTTGAAACTTTCGATGTAAATCCTAAAATT
1 TTTTC-AATAAGAATATTTG-AACTTTGGATGTAAATCCTAAAATT
* * * *
32076 TTTTGAATAAGAATCTTTAAAACTTTGGATGTGAAATCCTGAAATT
1 TTTTCAATAAGAATATTT-GAACTTTGGATGT-AAATCCTAAAATT
* *
32122 TTTTCAATGAGAATATTTGAATTTTGG
1 TTTTCAATAAGAATATTTGAACTTTGG
32149 CTATGAGACT
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
45 29 0.48
46 31 0.52
ACGTcount: A:0.35, C:0.08, G:0.14, T:0.42
Consensus pattern (44 bp):
TTTTCAATAAGAATATTTGAACTTTGGATGTAAATCCTAAAATT
Found at i:32680 original size:35 final size:35
Alignment explanation
Indices: 32634--32722 Score: 108
Period size: 35 Copynumber: 2.5 Consensus size: 35
32624 AACTTTTACA
* * *
32634 AATCTGAAACCTATGTGAAACTTGAAATCTTTGT-G
1 AATCTAAAACCTTTGTGAAAATTGAAATCTTT-TAG
**
32669 AATCTAAAACCTTTACGAAAATTGAAATCTTTTAG
1 AATCTAAAACCTTTGTGAAAATTGAAATCTTTTAG
*
32704 AATCTAAAACTTTTGTGAA
1 AATCTAAAACCTTTGTGAA
32723 TATGAAACCT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
34 1 0.02
35 44 0.98
ACGTcount: A:0.39, C:0.13, G:0.12, T:0.35
Consensus pattern (35 bp):
AATCTAAAACCTTTGTGAAAATTGAAATCTTTTAG
Found at i:33180 original size:9 final size:9
Alignment explanation
Indices: 33150--33182 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
33140 GGATTTAAAT
33150 TCTTACAAA
1 TCTTACAAA
33159 TCTTA-AAA
1 TCTTACAAA
*
33167 CCTTACAAA
1 TCTTACAAA
33176 TCTTACA
1 TCTTACA
33183 TTTTTGTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
8 7 0.33
9 14 0.67
ACGTcount: A:0.42, C:0.24, G:0.00, T:0.33
Consensus pattern (9 bp):
TCTTACAAA
Found at i:34110 original size:13 final size:13
Alignment explanation
Indices: 34094--34135 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
34084 ATTTTTCAAG
34094 AAAAGAAAGAAAT
1 AAAAGAAAGAAAT
*
34107 AAAAGAAATAAAAT
1 AAAAGAAA-GAAAT
34121 AAAA-AAGAGAAAT
1 AAAAGAA-AGAAAT
34134 AA
1 AA
34136 TGATTCAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 16 0.64
14 9 0.36
ACGTcount: A:0.79, C:0.00, G:0.12, T:0.10
Consensus pattern (13 bp):
AAAAGAAAGAAAT
Found at i:34339 original size:60 final size:58
Alignment explanation
Indices: 34198--34441 Score: 214
Period size: 60 Copynumber: 4.2 Consensus size: 58
34188 TGCTTTTGTA
* * * **
34198 CAAGAAAAATTTATACTTTCAACTTTTTCTTAAAGCA----TTTGAAGATTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTGAA-ATTTTTATTTT
* *
34253 -AAGAAAAATTGATACTTTCAATTTTTCCTTAAAATATTTTTCTTGATAATTTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTT-TTGA-AATTTTTATTTT
* * * * *
34312 TAAGAAAAATTGGTA-TTTCTAACTTTTCGTCAAAATATTTTTTTTTTGAAA-TTTTAATTT
1 CAAGAAAAATTGATACTTTC-AACTTTTCCT-AAAA-A-TATTTTTTTGAAATTTTTATTTT
* * *
34372 CAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATATATTTTTTTAAAATTTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCT-AAAAATAT-TTTTTTGAAATTTTTATTTT
*
34432 CAAGGAAAAT
1 CAAGAAAAAT
34442 ATTTTTTTAA
Statistics
Matches: 156, Mismatches: 19, Indels: 23
0.79 0.10 0.12
Matches are distributed among these distances:
54 31 0.20
58 3 0.02
59 29 0.19
60 73 0.47
61 9 0.06
62 5 0.03
63 6 0.04
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.48
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTGAAATTTTTATTTT
Found at i:34471 original size:30 final size:31
Alignment explanation
Indices: 34403--34471 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 31
34393 ACTTTTTCTC
* *
34403 AAAAATATATTTTTTTAAAATTTTATTTTCA
1 AAAAAAATATTTTTTTAAAATTTGATTTTCA
**
34434 AGGAAAATATTTTTTT-AAATTTGATTTTCA
1 AAAAAAATATTTTTTTAAAATTTGATTTTCA
34464 AAAAAAAT
1 AAAAAAAT
34472 TGATACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 19 0.59
31 13 0.41
ACGTcount: A:0.45, C:0.03, G:0.04, T:0.48
Consensus pattern (31 bp):
AAAAAAATATTTTTTTAAAATTTGATTTTCA
Found at i:34613 original size:3 final size:3
Alignment explanation
Indices: 34605--34632 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
34595 ACTAAACAGA
34605 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
34633 TAAATAAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:37538 original size:11 final size:11
Alignment explanation
Indices: 37509--37567 Score: 55
Period size: 11 Copynumber: 5.0 Consensus size: 11
37499 ACTTTTCCAC
37509 CTTTTTCTTTCT
1 CTTTTT-TTTCT
37521 CTTTTTTTTTTCT
1 C--TTTTTTTTCT
*
37534 CTTTTTTTTTT
1 CTTTTTTTTCT
*
37545 CTTTTTTTTTT
1 CTTTTTTTTCT
*
37556 CCTTTATTTTCT
1 -CTTTTTTTTCT
37568 TCTTCATCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
11 20 0.49
12 10 0.24
13 6 0.15
14 5 0.12
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
CTTTTTTTTCT
Found at i:37565 original size:13 final size:13
Alignment explanation
Indices: 37510--37555 Score: 76
Period size: 13 Copynumber: 3.6 Consensus size: 13
37500 CTTTTCCACC
*
37510 TTTTTCTTTCTCT
1 TTTTTTTTTCTCT
37523 TTTTTTTTTCTCT
1 TTTTTTTTTCTCT
37536 TTTTTTTTTCT-T
1 TTTTTTTTTCTCT
37548 TTTTTTTT
1 TTTTTTTT
37556 CCTTTATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
12 9 0.28
13 23 0.72
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (13 bp):
TTTTTTTTTCTCT
Found at i:37565 original size:24 final size:24
Alignment explanation
Indices: 37511--37571 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
37501 TTTTCCACCT
37511 TTTTCTTTC-TCTTTTTTTTTTCTC
1 TTTT-TTTCTTCTTTTTTTTTTCTC
*
37535 TTTTTTTTTTCTTTTTTTTTTC-C
1 TTTTTTTCTTCTTTTTTTTTTCTC
37558 TTTATTTTCTTCTT
1 TTT-TTTTCTTCTT
37572 CATCTCTCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 7 0.21
24 26 0.79
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (24 bp):
TTTTTTTCTTCTTTTTTTTTTCTC
Found at i:38745 original size:19 final size:20
Alignment explanation
Indices: 38721--38760 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
38711 CAAAATTATG
38721 ATTGAAATT-AGACTTTAAA
1 ATTGAAATTAAGACTTTAAA
* *
38740 ATTGAATTTAAGCCTTTAAA
1 ATTGAAATTAAGACTTTAAA
38760 A
1 A
38761 AAATGAACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (20 bp):
ATTGAAATTAAGACTTTAAA
Found at i:39953 original size:42 final size:40
Alignment explanation
Indices: 39906--39983 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
39896 ACTTAATTAT
* *
39906 TTATATTAAAGTAATTTTTC-TAACTTGTTTTTTTACATTGAA
1 TTATATTAAAG--A-TTTTCATAACTGGTTTTTTAACATTGAA
*
39948 TTATATTTAAGATTTTCATAACTGGTTTTTTAACAT
1 TTATATTAAAGATTTTCATAACTGGTTTTTTAACAT
39984 GTTACATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
39 5 0.16
40 17 0.53
42 10 0.31
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (40 bp):
TTATATTAAAGATTTTCATAACTGGTTTTTTAACATTGAA
Found at i:40158 original size:22 final size:21
Alignment explanation
Indices: 40122--40176 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
40112 AGAATTTTTA
40122 TATTAATAATTTTTTAATTTC
1 TATTAATAATTTTTTAATTTC
* *
40143 TATTGAATTATTTTTTCATTT-
1 TATT-AATAATTTTTTAATTTC
*
40164 TA-TAATACTTTTT
1 TATTAATAATTTTT
40177 AGCTATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 8 0.28
20 1 0.03
21 6 0.21
22 14 0.48
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TATTAATAATTTTTTAATTTC
Found at i:44194 original size:2 final size:2
Alignment explanation
Indices: 44187--44212 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44177 AAGATCCAAA
44187 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
44213 GTTGTACAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48596 original size:17 final size:14
Alignment explanation
Indices: 48569--48621 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
48559 ATATTTTTTA
*
48569 ATAAAAAAATATTGT
1 ATAATAAAATATT-T
48584 GATAGATAAAATATTT
1 -ATA-ATAAAATATTT
48600 ATAATAAAATATTT
1 ATAATAAAATATTT
48614 -TAA-AAAAT
1 ATAATAAAAT
48622 TTAACTATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 5 0.14
13 3 0.09
14 11 0.31
15 3 0.09
16 4 0.11
17 9 0.26
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (14 bp):
ATAATAAAATATTT
Done.