Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167888.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_155, 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: 64109
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
Found at i:2935 original size:145 final size:144
Alignment explanation
Indices: 2638--2917 Score: 350
Period size: 145 Copynumber: 1.9 Consensus size: 144
2628 TTAAAGCACC
**
2638 AAAAATCATGAAATATTATAAAATTGAGATCTAAAAAGTTACATGAAAATTCAAGCTCGAAAAGG
1 AAAAATCATGAAATATTATAAAATCAAGATCTAAAAAGTTACATGAAAATTCAAGCTCGAAAAGG
* * * * * ***
2703 TTAAATTATGAAAATACCCTTATAGGAGTAATTTGGTAATTTCACATTTTTTAGGGTATTGCTGT
66 TCAAATTAAGAAAATACCCTTATAGGAGTAATTTGGTAATTTCACATTTCTCAGGGTAAT-CAAA
*
2768 GATTTCAAATATATT
130 AATTTCAAATATATT
* *
2783 AAAAATCATGAAATATTATGAAATCAAGATCTGAAAAA-TTTCATGAAAATTCAAGCTCGAAAAG
1 AAAAATCATGAAATATTATAAAATCAAGATCT-AAAAAGTTACATGAAAATTCAAGCTCGAAAAG
* * *
2847 GTCAAATTAAGAAAATACCCTTATAGG-GATATTTTGTTAATTTCACACTTCTCTCAGTGTAAT-
65 GTCAAATTAAGAAAATACCCTTATAGGAG-TAATTTGGTAATTTCACA-TT-TCTCAGGGTAATC
2910 AAAAATTT
127 AAAAATTT
2918 TTAGTGTTTT
Statistics
Matches: 115, Mismatches: 16, Indels: 8
0.83 0.12 0.06
Matches are distributed among these distances:
144 1 0.01
145 99 0.86
146 7 0.06
147 8 0.07
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (144 bp):
AAAAATCATGAAATATTATAAAATCAAGATCTAAAAAGTTACATGAAAATTCAAGCTCGAAAAGG
TCAAATTAAGAAAATACCCTTATAGGAGTAATTTGGTAATTTCACATTTCTCAGGGTAATCAAAA
ATTTCAAATATATT
Found at i:3834 original size:96 final size:95
Alignment explanation
Indices: 3502--3826 Score: 454
Period size: 96 Copynumber: 3.4 Consensus size: 95
3492 TCTGCTAATA
* * ** * * *
3502 AGAGGCATTGAAACTTTGAAAATTTAAAATAGTTTGCCTGGAGATCTTAGAGATTATGCTCGAAG
1 AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGCCCAGAGGTCTTAGAAATTATGCCCGAA-
* *
3567 GTCTTAAAAATCTTTGAATGCTCCCCGTATA
65 GTCTTAAAAATCTTTGAATGCTCCCCATATT
* * *
3598 AGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCCCAGAGGTCTTAGAAATTATGCCTGGAG
1 AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGCCCAGAGGTCTTAGAAATTATGCC-CGAA
*
3663 GTCATAAAAATCTTTGAATGCTCCCCATATT
65 GTCTTAAAAATCTTTGAATGCTCCCCATATT
*
3694 AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGCCCAGAGGT-TTTGAAAATTATGCCCAGA
1 AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGCCCAGAGGTCTTAG-AAATTATGCCC-GA
* *
3758 AGTCTTAATAATCTTTGAAGGCTCCCCATATT
64 AGTCTTAAAAATCTTTGAATGCTCCCCATATT
*
3790 AGAGGCATTGAAGCTTTAAAAATTTAAAATATTTTGC
1 AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGC
3827 TTGGAGGTCT
Statistics
Matches: 205, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
95 3 0.01
96 200 0.98
97 2 0.01
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (95 bp):
AGAGGCATTGAAACTTTAAAAATTTAAAATATTTTGCCCAGAGGTCTTAGAAATTATGCCCGAAG
TCTTAAAAATCTTTGAATGCTCCCCATATT
Found at i:4614 original size:44 final size:42
Alignment explanation
Indices: 4549--4824 Score: 222
Period size: 44 Copynumber: 6.5 Consensus size: 42
4539 CTTTTTTTTT
*
4549 ATGCAAATGCAAATTTCTTTTTTCTTGTGACACAGATGCAAGTG
1 ATGCAAATGCAAATATCTTTTTT-TTGTGACA-AGATGCAAGTG
* * ** * *
4593 ACGCAAATACAAATATCTTTTTTCTTGTGATGTAGGTGCTAGTG
1 ATGCAAATGCAAATATCTTTTTT-TTGTGA-CAAGATGCAAGTG
* * * *
4637 ATACAAATGCAAATGTC-TTTTTATGATG--TAGATGCAAGTG
1 ATGCAAATGCAAATATCTTTTTTTTG-TGACAAGATGCAAGTG
* * * *
4677 ATGCAAATGCGAATATCTTTTTTATGTTACAA-ATGTAAGTG
1 ATGCAAATGCAAATATCTTTTTTTTGTGACAAGATGCAAGTG
* * *
4718 ATGTAAATGCAAATATCTTTTTTTTAATG-CAA-ATGCAAGTA
1 ATGCAAATGCAAATATCTTTTTTTT-GTGACAAGATGCAAGTG
* * *
4759 ATGCAAATGCAAATATCTTTTTTCTTGTAATACAGATGCAAATG
1 ATGCAAATGCAAATATCTTTTTT-TTGTGACA-AGATGCAAGTG
***
4803 ATGCAAACATAAATATCTTTTT
1 ATGCAAATGCAAATATCTTTTT
4825 CATGATGCAA
Statistics
Matches: 186, Mismatches: 36, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
40 25 0.13
41 71 0.38
42 7 0.04
43 8 0.04
44 75 0.40
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (42 bp):
ATGCAAATGCAAATATCTTTTTTTTGTGACAAGATGCAAGTG
Found at i:4677 original size:40 final size:41
Alignment explanation
Indices: 4549--5016 Score: 270
Period size: 41 Copynumber: 11.2 Consensus size: 41
4539 CTTTTTTTTT
* *
4549 ATGCAAATGCAAATTTCTTTTTTCTTG-TGACACAGATGCAAGTG
1 ATGCAAATGCAAATATCTTTTTT-ATGATG-CA-A-ATGCAAGTG
* * * * ** *
4593 ACGCAAATACAAATATCTTTTTTCTTGTGATGTAGGTGCTAGTG
1 ATGCAAATGCAAATATC--TTTT-TTATGATGCAAATGCAAGTG
* * * *
4637 ATACAAATGCAAATGTC-TTTTTATGATGTAGATGCAAGTG
1 ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
* * * *
4677 ATGCAAATGCGAATATCTTTTTTATGTTACAAATGTAAGTG
1 ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
* * * *
4718 ATGTAAATGCAAATATCTTTTTTTTAATGCAAATGCAAGTA
1 ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
* * * *
4759 ATGCAAATGCAAATATCTTTTTTCTTGTAATACAGATGCAAATG
1 ATGCAAATGCAAATATCTTTTTT-ATG--ATGCAAATGCAAGTG
*** * * **
4803 ATGCAAACATAAATATCTTTTTCATGATGCAAATGTAAGCA
1 ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
* * * *
4844 ATGTAAATGTC---T-T-TTTTCTTGTGATGCAGATGCAAGCG
1 ATGCAAATG-CAAATATCTTTT-TTATGATGCAAATGCAAGTG
** * * *
4882 ATATAAATGCAAAT-GCTTTTTTTATGATGCAAAAGCAAGCG
1 ATGCAAATGCAAATATC-TTTTTTATGATGCAAATGCAAGTG
* * *
4923 ATGCAAATGCAAATGTCCTTTTTCT-TGTAATGCAAGTGCTAGTG
1 ATGCAAATGCAAATAT-CTTTTT-TATG--ATGCAAATGCAAGTG
* * * * **
4967 ATGTAAATGCAAATGTCTTTCTTATGATGCAAATGTAAGCA
1 ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
5008 ATGCAAATG
1 ATGCAAATG
5017 TAAGCAATGC
Statistics
Matches: 326, Mismatches: 77, Indels: 45
0.73 0.17 0.10
Matches are distributed among these distances:
37 5 0.02
38 24 0.07
39 1 0.00
40 32 0.10
41 138 0.42
42 14 0.04
43 11 0.03
44 90 0.28
46 7 0.02
47 4 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.36
Consensus pattern (41 bp):
ATGCAAATGCAAATATCTTTTTTATGATGCAAATGCAAGTG
Found at i:4762 original size:15 final size:15
Alignment explanation
Indices: 4742--4770 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
4732 ATCTTTTTTT
4742 TAATGCAAATGCAAG
1 TAATGCAAATGCAAG
4757 TAATGCAAATGCAA
1 TAATGCAAATGCAA
4771 ATATCTTTTT
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:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (15 bp):
TAATGCAAATGCAAG
Found at i:4852 original size:85 final size:84
Alignment explanation
Indices: 4595--5016 Score: 353
Period size: 85 Copynumber: 5.1 Consensus size: 84
4585 TGCAAGTGAC
* * * * * ** *
4595 GCAAATACAAATATCTTTTTTCTTGTGATGTAGGTGCTAGTGATACAAATGCAAATGTC-TTTTT
1 GCAAATGCAAAT-TCTTTTTTCTTGTAATGCAGATGCAAGTGATGTAAATGCAAATATCTTTTTT
* * **
4659 ATGATGTAGATGCAAGTGAT
65 ATGATGCAAATGCAAGCAAT
* * * * *
4679 GCAAATGCGAATATCTTTTTT-ATGT--TACAAATGTAAGTGATGTAAATGCAAATATCTTTTTT
1 GCAAATGCAAAT-TCTTTTTTCTTGTAATGCAGATGCAAGTGATGTAAATGCAAATATCTTTTTT
* * *
4741 TTAATGCAAATGCAAGTAAT
65 ATGATGCAAATGCAAGCAAT
* * * *** *
4761 GCAAATGCAAATATCTTTTTTCTTGTAATACAGATGCAAATGATGCAAACATAAATATCTTTTTC
1 GCAAATGCAAAT-TCTTTTTTCTTGTAATGCAGATGCAAGTGATGTAAATGCAAATATCTTTTTT
*
4826 ATGATGCAAATGTAAGCAAT
65 ATGATGCAAATGCAAGCAAT
* * * * *
4846 GTAAATG-----TCTTTTTTCTTGTGATGCAGATGCAAGCGATATAAATGCAAAT-GCTTTTTTT
1 GCAAATGCAAATTCTTTTTTCTTGTAATGCAGATGCAAGTGATGTAAATGCAAATATC-TTTTTT
* *
4905 ATGATGCAAAAGCAAGCGAT
65 ATGATGCAAATGCAAGCAAT
* * * *
4925 GCAAATGCAAATGTCCTTTTTCTTGTAATGCA-AGTGCTAGTGATGTAAATGCAAATGTCTTTCT
1 GCAAATGCAAAT-TCTTTTTTCTTGTAATGCAGA-TGCAAGTGATGTAAATGCAAATATCTTTTT
*
4989 TATGATGCAAATGTAAGCAAT
64 TATGATGCAAATGCAAGCAAT
5010 GCAAATG
1 GCAAATG
5017 TAAGCAATGC
Statistics
Matches: 268, Mismatches: 57, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
78 1 0.00
79 62 0.23
81 22 0.08
82 40 0.15
83 6 0.02
84 20 0.07
85 116 0.43
86 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (84 bp):
GCAAATGCAAATTCTTTTTTCTTGTAATGCAGATGCAAGTGATGTAAATGCAAATATCTTTTTTA
TGATGCAAATGCAAGCAAT
Found at i:4896 original size:44 final size:43
Alignment explanation
Indices: 4843--4986 Score: 159
Period size: 44 Copynumber: 3.3 Consensus size: 43
4833 AAATGTAAGC
* *
4843 AATGTAAATGTCTTTTTTCTTGTGATGCAGATGCAAGCGATATA
1 AATGCAAATGTCTTTTTTCTTGTGATGCA-ATGCAAGCGATGTA
* * *
4887 AATGCAAATG-C-TTTTT-TTATGATGCAAAAGCAAGCGATGCA
1 AATGCAAATGTCTTTTTTCTTGTGATGC-AATGCAAGCGATGTA
* * * *
4928 AATGCAAATGTCCTTTTTCTTGTAATGCAAGTGCTAGTGATGTA
1 AATGCAAATGTCTTTTTTCTTGTGATGCAA-TGCAAGCGATGTA
4972 AATGCAAATGTCTTT
1 AATGCAAATGTCTTT
4987 CTTATGATGC
Statistics
Matches: 83, Mismatches: 12, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
41 29 0.35
42 7 0.08
43 8 0.10
44 39 0.47
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.36
Consensus pattern (43 bp):
AATGCAAATGTCTTTTTTCTTGTGATGCAATGCAAGCGATGTA
Found at i:4930 original size:164 final size:164
Alignment explanation
Indices: 4721--5017 Score: 402
Period size: 164 Copynumber: 1.8 Consensus size: 164
4711 GTAAGTGATG
* * * *
4721 TAAATGCAAATATCTTTTTTTTAATGCAAATGCAAGTAATGCAAATGCAAATATCTTTTTTCTTG
1 TAAATGCAAATAGCTTTTTTTTAATGCAAAAGCAAGCAATGCAAATGCAAATATCCTTTTTCTTG
* *
4786 TAATAC-AGATGCAAATGATGCAAACATAAATATCTTT-TTCATGATGCAAATGTAAGCAATGTA
66 TAATACAAG-TGCAAATGATGCAAACACAAATATCTTTCTT-ATGATGCAAATGTAAGCAATGCA
4849 AATGTCTTTTTTCTTGTGATGCAGATGCAAGCGATA
129 AATGTCTTTTTTCTTGTGATGCAGATGCAAGCGATA
* * *
4885 TAAATGCAAAT-GCTTTTTTTATGATGCAAAAGCAAGCGATGCAAATGCAAATGTCCTTTTTCTT
1 TAAATGCAAATAGCTTTTTTT-TAATGCAAAAGCAAGCAATGCAAATGCAAATATCCTTTTTCTT
* * * * ** *
4949 GTAATGCAAGTGCTAGTGATGTAAATGCAAATGTCTTTCTTATGATGCAAATGTAAGCAATGCAA
65 GTAATACAAGTGCAAATGATGCAAACACAAATATCTTTCTTATGATGCAAATGTAAGCAATGCAA
5014 ATGT
130 ATGT
5018 AAGCAATGCA
Statistics
Matches: 114, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
163 8 0.07
164 102 0.89
165 4 0.04
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.35
Consensus pattern (164 bp):
TAAATGCAAATAGCTTTTTTTTAATGCAAAAGCAAGCAATGCAAATGCAAATATCCTTTTTCTTG
TAATACAAGTGCAAATGATGCAAACACAAATATCTTTCTTATGATGCAAATGTAAGCAATGCAAA
TGTCTTTTTTCTTGTGATGCAGATGCAAGCGATA
Found at i:5013 original size:15 final size:15
Alignment explanation
Indices: 4993--5061 Score: 138
Period size: 15 Copynumber: 4.6 Consensus size: 15
4983 CTTTCTTATG
4993 ATGCAAATGTAAGCA
1 ATGCAAATGTAAGCA
5008 ATGCAAATGTAAGCA
1 ATGCAAATGTAAGCA
5023 ATGCAAATGTAAGCA
1 ATGCAAATGTAAGCA
5038 ATGCAAATGTAAGCA
1 ATGCAAATGTAAGCA
5053 ATGCAAATG
1 ATGCAAATG
5062 CAAATGTATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 54 1.00
ACGTcount: A:0.46, C:0.13, G:0.20, T:0.20
Consensus pattern (15 bp):
ATGCAAATGTAAGCA
Found at i:5031 original size:21 final size:20
Alignment explanation
Indices: 5020--5069 Score: 56
Period size: 15 Copynumber: 2.7 Consensus size: 20
5010 GCAAATGTAA
5020 GCAATGCAAATGTAAGC-A-
1 GCAATGCAAATGTAAGCAAT
5038 ---ATGCAAATGTAAGCAAT
1 GCAATGCAAATGTAAGCAAT
5055 GCAAATGCAAATGTA
1 GC-AATGCAAATGTA
5070 TTTTTTCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
15 14 0.54
16 1 0.04
21 11 0.42
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (20 bp):
GCAATGCAAATGTAAGCAAT
Found at i:6167 original size:21 final size:22
Alignment explanation
Indices: 6143--6187 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
6133 TTTCTTTTCC
6143 TTCTTTT-ATTCTTTCTTTC-TT
1 TTCTTTTCATT-TTTCTTTCATT
*
6164 TTCTTTTCATTTTTTTTTCATT
1 TTCTTTTCATTTTTCTTTCATT
6186 TT
1 TT
6188 GTTTATGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.78
Consensus pattern (22 bp):
TTCTTTTCATTTTTCTTTCATT
Found at i:17926 original size:17 final size:19
Alignment explanation
Indices: 17904--17941 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
17894 AAAATAACAT
17904 AAAATT-TGATTTT-TTTA
1 AAAATTATGATTTTATTTA
17921 AAAATTATGATTTTATTTA
1 AAAATTATGATTTTATTTA
17940 AA
1 AA
17942 TTTGAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.32
18 7 0.37
19 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (19 bp):
AAAATTATGATTTTATTTA
Found at i:17942 original size:17 final size:16
Alignment explanation
Indices: 17903--17946 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 16
17893 AAAAATAACA
17903 TAAAATTTGATTTTTT
1 TAAAATTTGATTTTTT
17919 TAAAAATTATGATTTTATT
1 T-AAAATT-TGATTTT-TT
17938 T-AAATTTGA
1 TAAAATTTGA
17947 AATTTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 4 0.16
17 11 0.44
18 7 0.28
19 3 0.12
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.55
Consensus pattern (16 bp):
TAAAATTTGATTTTTT
Found at i:22194 original size:24 final size:24
Alignment explanation
Indices: 22167--22214 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
22157 AATTTTCAAT
*
22167 TTTAATTTGATTTGACTTGATTTA
1 TTTAATTTAATTTGACTTGATTTA
* * *
22191 TTTATTTTAATTTTACTTGTTTTA
1 TTTAATTTAATTTGACTTGATTTA
22215 AAAAAAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (24 bp):
TTTAATTTAATTTGACTTGATTTA
Found at i:23957 original size:132 final size:131
Alignment explanation
Indices: 23719--23957 Score: 320
Period size: 132 Copynumber: 1.8 Consensus size: 131
23709 TGGCCAATCA
* * * * *
23719 TACATTATTTCATTTGTTGGAAAAATTTTTGCCTTTTCAATCTTGTACATAGATTTGGATATGAA
1 TACATTATTTCATTTGTTAGAAAAATCTTTGCCTTTCCAATCTTGTACATAGATTTGAACATGAA
* * *
23784 TTTTTTTTTCGTCTTTGTATTACATACTTGTATTTGCATATAAATCCATGTAAACATCTTTGTAT
66 TTTTTTTTTCATCTATGTATTACATACATGTATTTGCATATAAATCCATGTAAACATCTTTGTAT
23849 G
131 G
* *
23850 TACATTATTTCATTTGTTTAGAAAAATCTTTGCCTTTCCAATTTTGTACATAGTTTTGAACATGA
1 TACATTATTTCATTTG-TTAGAAAAATCTTTGCCTTTCCAATCTTGTACATAGATTTGAACATGA
* * *
23915 ATTTTTGTTGTT-AT-TATGTATTGCATTCATGTATTTGTATATA
65 ATTTTT-TT-TTCATCTATGTATTACATACATGTATTTGCATATA
23958 CATTTTTTTA
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
131 16 0.17
132 71 0.77
133 3 0.03
134 2 0.02
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.50
Consensus pattern (131 bp):
TACATTATTTCATTTGTTAGAAAAATCTTTGCCTTTCCAATCTTGTACATAGATTTGAACATGAA
TTTTTTTTTCATCTATGTATTACATACATGTATTTGCATATAAATCCATGTAAACATCTTTGTAT
G
Found at i:24748 original size:15 final size:15
Alignment explanation
Indices: 24724--24761 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
24714 TTTGAGTTGC
24724 AAAAAA-AAAAAAGA
1 AAAAAAGAAAAAAGA
* *
24738 AGAAAAGAAAAATGA
1 AAAAAAGAAAAAAGA
24753 AAAAAAGAA
1 AAAAAAGAA
24762 TTGATTGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAAAGAAAAAAGA
Found at i:26047 original size:12 final size:12
Alignment explanation
Indices: 26030--26070 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
26020 TTACTTAAGC
26030 TAAATGAAGAAT
1 TAAATGAAGAAT
*
26042 TAAATGAAGAAC
1 TAAATGAAGAAT
* *
26054 TAAATGTAGATT
1 TAAATGAAGAAT
26066 TAAAT
1 TAAAT
26071 TACAAAAACA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.54, C:0.02, G:0.15, T:0.29
Consensus pattern (12 bp):
TAAATGAAGAAT
Found at i:33052 original size:20 final size:19
Alignment explanation
Indices: 33029--33074 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
33019 TGAAAAAATC
*
33029 AAACAAAAGAAGAATAAGAA
1 AAACAAAACAAGAATAAG-A
* *
33049 AAACTAAACAAGATTAAGA
1 AAACAAAACAAGAATAAGA
33068 AAACAAA
1 AAACAAA
33075 GAAAATAGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.72, C:0.09, G:0.11, T:0.09
Consensus pattern (19 bp):
AAACAAAACAAGAATAAGA
Found at i:35872 original size:2 final size:2
Alignment explanation
Indices: 35865--35891 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
35855 GAACAAACAA
35865 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
35892 TATATATATA
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:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36714 original size:45 final size:45
Alignment explanation
Indices: 36664--36753 Score: 105
Period size: 45 Copynumber: 2.0 Consensus size: 45
36654 TAAATATTTT
36664 GATA-TTTGAATAAATTCAAAATTAT-TTA-ATTTGTAATTAAAAGAA
1 GATATTTTGAATAAA---AAAATTATCTTACATTTGTAATTAAAAGAA
** *
36709 GATATTTTGTTTAGAAAAATTATCTTACATTTGTAATTAAAAGAA
1 GATATTTTGAATAAAAAAATTATCTTACATTTGTAATTAAAAGAA
36754 ATTATAGTCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
43 8 0.21
44 3 0.08
45 21 0.54
46 7 0.18
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (45 bp):
GATATTTTGAATAAAAAAATTATCTTACATTTGTAATTAAAAGAA
Found at i:38372 original size:31 final size:32
Alignment explanation
Indices: 38302--38377 Score: 91
Period size: 32 Copynumber: 2.4 Consensus size: 32
38292 GATTTCATTT
* * * *
38302 GATTTTATTTGGTAAAATATGAATGAATGTTT
1 GATTTCATTTGATAAAATATGAATGAATCTTG
* *
38334 GATTTCATTTGATAAAATATTAATGCA-CTTG
1 GATTTCATTTGATAAAATATGAATGAATCTTG
38365 GATTTCATTTGAT
1 GATTTCATTTGAT
38378 TTCATTTGTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 15 0.39
32 23 0.61
ACGTcount: A:0.33, C:0.05, G:0.16, T:0.46
Consensus pattern (32 bp):
GATTTCATTTGATAAAATATGAATGAATCTTG
Found at i:40767 original size:2 final size:2
Alignment explanation
Indices: 40760--40787 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
40750 TGACGCCGAA
40760 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
40788 TTCGATCTCT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42581 original size:16 final size:15
Alignment explanation
Indices: 42560--42589 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42550 ATCCGAGTCT
42560 TTGGTTTTGTGGGTGG
1 TTGGTTTTG-GGGTGG
42576 TTGGTTTTGGGGTG
1 TTGGTTTTGGGGTG
42590 TTTTAACAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (15 bp):
TTGGTTTTGGGGTGG
Found at i:45132 original size:26 final size:26
Alignment explanation
Indices: 45077--45141 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
45067 GCATGACTAT
*
45077 GTTTAATTTAATTTTATATTGACTTT
1 GTTTAATTTAATTTTATATTGACTTG
* * *
45103 GTTTAATTT-ATTTGTTTATTTAGTTG
1 GTTTAATTTAATTT-TATATTGACTTG
45129 GTTT-A-TTAATTTT
1 GTTTAATTTAATTTT
45142 TTTTCTACAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 3 0.09
25 9 0.27
26 21 0.64
ACGTcount: A:0.23, C:0.02, G:0.11, T:0.65
Consensus pattern (26 bp):
GTTTAATTTAATTTTATATTGACTTG
Found at i:50606 original size:13 final size:13
Alignment explanation
Indices: 50575--50625 Score: 61
Period size: 13 Copynumber: 3.9 Consensus size: 13
50565 TAATGATACC
50575 TTTTAATTTATTAA
1 TTTTAATTT-TTAA
*
50589 TTTTAATTTTTGA
1 TTTTAATTTTTAA
50602 TTTTAA-TTTTAA
1 TTTTAATTTTTAA
50614 -TTTAATTATTTA
1 TTTTAATT-TTTA
50626 TAATAAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
11 5 0.15
12 6 0.18
13 13 0.39
14 9 0.27
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (13 bp):
TTTTAATTTTTAA
Found at i:50625 original size:19 final size:19
Alignment explanation
Indices: 50576--50625 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
50566 AATGATACCT
50576 TTTAATT-TATTAATTTTAA
1 TTTAATTAT-TTAATTTTAA
50595 TTT--TTGATTTTAATTTTAA
1 TTTAATT-A-TTTAATTTTAA
50614 TTTAATTATTTA
1 TTTAATTATTTA
50626 TAATAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 10
0.72 0.00 0.28
Matches are distributed among these distances:
17 2 0.08
19 20 0.77
20 2 0.08
21 2 0.08
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTAATTATTTAATTTTAA
Found at i:52772 original size:19 final size:19
Alignment explanation
Indices: 52750--52811 Score: 53
Period size: 18 Copynumber: 3.4 Consensus size: 19
52740 TATATTATAA
52750 TAAAAATTATATTAAAAAT
1 TAAAAATTATATTAAAAAT
* *
52769 T--AAATTAT-TTAATATT
1 TAAAAATTATATTAAAAAT
52785 TATAAAA-T-TATTAAATAAT
1 TA-AAAATTATATTAAA-AAT
52804 TAAAAATT
1 TAAAAATT
52812 TTAAATTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
16 7 0.21
17 8 0.24
18 9 0.27
19 9 0.27
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TAAAAATTATATTAAAAAT
Found at i:57000 original size:31 final size:31
Alignment explanation
Indices: 56965--57080 Score: 121
Period size: 31 Copynumber: 3.8 Consensus size: 31
56955 ATTTTCTCTT
* *
56965 CTCAATCCCTCTCTATTCTCTTTTTAGTCTC
1 CTCAATCCCTCTCTGTTCTCTTCTTAGTCTC
* * * *
56996 CTCAATTCTTTTCTGTTCTCTTCTTAGTCTT
1 CTCAATCCCTCTCTGTTCTCTTCTTAGTCTC
* *
57027 TTCAAT-TCTCTCTGTTCTCTTCTTAGTCTC
1 CTCAATCCCTCTCTGTTCTCTTCTTAGTCTC
* *
57057 TTCAAT--CTTTCTGTTCTCTTCTTA
1 CTCAATCCCTCTCTGTTCTCTTCTTA
57081 ATCTTTAAAC
Statistics
Matches: 73, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
29 17 0.23
30 26 0.36
31 30 0.41
ACGTcount: A:0.11, C:0.29, G:0.05, T:0.54
Consensus pattern (31 bp):
CTCAATCCCTCTCTGTTCTCTTCTTAGTCTC
Found at i:57077 original size:59 final size:61
Alignment explanation
Indices: 56973--57086 Score: 178
Period size: 61 Copynumber: 1.9 Consensus size: 61
56963 TTCTCAATCC
* *
56973 CTCTCTATTCTCTTTTTAGTCTCCTCAATTCTTTTCTGTTCTCTTCTTAGTCTTTTCAATT
1 CTCTCTATTCTCTTCTTAGTCTCCTCAATTCTTTTCTGTTCTCTTCTTAATCTTTTCAATT
* *
57034 CTCTCTGTTCTCTTCTTAGTCTCTTCAA-TC-TTTCTGTTCTCTTCTTAATCTTT
1 CTCTCTATTCTCTTCTTAGTCTCCTCAATTCTTTTCTGTTCTCTTCTTAATCTTT
57087 AAACCCTAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 22 0.45
60 2 0.04
61 25 0.51
ACGTcount: A:0.11, C:0.27, G:0.05, T:0.57
Consensus pattern (61 bp):
CTCTCTATTCTCTTCTTAGTCTCCTCAATTCTTTTCTGTTCTCTTCTTAATCTTTTCAATT
Done.