Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168321.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_545, 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: 23492
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:2668 original size:61 final size:59
Alignment explanation
Indices: 2365--2835 Score: 634
Period size: 61 Copynumber: 7.9 Consensus size: 59
2355 TTGTGCAGGA
* * *
2365 AAAATTGATACTTTCAACTTTTCCCTAAAGATA-TTTTTTTGAAATTTTAATTTTGAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTATTTTTAAGG
* * *
2423 AAAATTGATACTTTCAACTTTT-CCTCAAAATTTTATTTTTTTGAAAATTTA---TTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAATAT-TTTTTTTGAAATTTTATTTTTAAGG
*
2480 AAAATTGATACTTTCAACTTTT-CCTCAAAAATCTTTTTTTTTGAAATTTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCT-AAAAAT-ATTTTTTTTGAAATTTTATTTTTAAGG
* ***
2540 AAAATTGATACTTTCAACTTTTCCCCAAAACCCTTTTTTTTGAAA-TTTATTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTATTTTTAAGG
*
2598 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTG-AAATTTT-ATTTTTAAGG
*
2659 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGAAATTTTGATTTTCAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTTGAAATTTT-ATTTTTAAGG
* *
2720 AAAATTGATACTTTCAACTTTTCCCCAAAAAT-CTTTTTTTGAAATTTTATTTTTTTAAGG
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTA--TTTTTAAGG
* *
2780 AAAATTGATACTTTCAACTTTTCCCTAAAAACATTTTTTTGGAAATTTTGATTTTT
1 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTT-ATTTTT
2836 TATTTAAAGA
Statistics
Matches: 374, Mismatches: 23, Indels: 30
0.88 0.05 0.07
Matches are distributed among these distances:
57 54 0.14
58 80 0.21
59 30 0.08
60 93 0.25
61 107 0.29
62 10 0.03
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.47
Consensus pattern (59 bp):
AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTTATTTTTAAGG
Found at i:2888 original size:18 final size:18
Alignment explanation
Indices: 2867--2926 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
2857 TAAAAAAGTG
2867 AAAATAAATAAAGATAAA
1 AAAATAAATAAAGATAAA
*
2885 AAAATAAAGGAAAG-TAAA
1 AAAATAAA-TAAAGATAAA
**
2903 ACCA-AAATAAAGATAAA
1 AAAATAAATAAAGATAAA
2920 AAGAATA
1 AA-AATA
2927 TTAAATAAAC
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
16 4 0.12
17 8 0.25
18 15 0.47
19 5 0.16
ACGTcount: A:0.73, C:0.03, G:0.10, T:0.13
Consensus pattern (18 bp):
AAAATAAATAAAGATAAA
Found at i:2891 original size:35 final size:36
Alignment explanation
Indices: 2840--2931 Score: 93
Period size: 35 Copynumber: 2.6 Consensus size: 36
2830 ATTTTTTATT
* *
2840 TAAAGA-AAATAGAATAATAAAAAAGTGAAAA-TAAA
1 TAAAGATAAAAAGAATAATAAAAAAGT-AAAACAAAA
**
2875 TAAAGATAAAAA-AATAA-AGGAAAGTAAAACCAAAA
1 TAAAGATAAAAAGAATAATAAAAAAGTAAAA-CAAAA
*
2910 TAAAGATAAAAAGAATATTAAA
1 TAAAGATAAAAAGAATAATAAA
2932 TAAACCTAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
33 4 0.09
34 6 0.13
35 26 0.58
36 8 0.18
37 1 0.02
ACGTcount: A:0.71, C:0.02, G:0.11, T:0.16
Consensus pattern (36 bp):
TAAAGATAAAAAGAATAATAAAAAAGTAAAACAAAA
Found at i:3407 original size:20 final size:20
Alignment explanation
Indices: 3384--3425 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
3374 TCACCGATTT
3384 CTGGGAACCTCCACCGAAAA
1 CTGGGAACCTCCACCGAAAA
* **
3404 CTGGGCAGGTCCACCGAAAA
1 CTGGGAACCTCCACCGAAAA
3424 CT
1 CT
3426 TCAAGGTTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.33, G:0.24, T:0.12
Consensus pattern (20 bp):
CTGGGAACCTCCACCGAAAA
Found at i:3522 original size:24 final size:23
Alignment explanation
Indices: 3493--3538 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
3483 CGGAATCTGG
*
3493 AATTTCCAAAAATTCCCAGAAAAA
1 AATTTCAAAAAATTCCCA-AAAAA
3517 AATTTCAAAAAATTCCCAAAAA
1 AATTTCAAAAAATTCCCAAAAA
3539 TTTTTTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (23 bp):
AATTTCAAAAAATTCCCAAAAAA
Found at i:3861 original size:21 final size:22
Alignment explanation
Indices: 3837--3882 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3827 AAAACTAGAT
3837 AATTA-GAAAAGATAAATAAAA
1 AATTATGAAAAGATAAATAAAA
* * *
3858 AATTATTATAGGATAAATAAAA
1 AATTATGAAAAGATAAATAAAA
3880 AAT
1 AAT
3883 AATATCAGAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 5 0.24
22 16 0.76
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (22 bp):
AATTATGAAAAGATAAATAAAA
Found at i:3893 original size:21 final size:21
Alignment explanation
Indices: 3846--3898 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
3836 TAATTAGAAA
*
3846 AGATAAATAAAAAATTATTAT
1 AGATAAATAAAAAATTAATAT
3867 AGGATAAATAAAAAA-TAATAT
1 A-GATAAATAAAAAATTAATAT
*
3888 CAGATATATAA
1 -AGATAAATAA
3899 TTAGATAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (21 bp):
AGATAAATAAAAAATTAATAT
Found at i:3931 original size:9 final size:9
Alignment explanation
Indices: 3903--4021 Score: 51
Period size: 9 Copynumber: 14.1 Consensus size: 9
3893 ATATAATTAG
3903 ATAAATAAA
1 ATAAATAAA
*
3912 ATACA-AAA
1 ATAAATAAA
3920 ATAAATAAA
1 ATAAATAAA
*
3929 ATAAA-AAG
1 ATAAATAAA
3937 AT-AA-AAA
1 ATAAATAAA
3944 AT-AATAAA
1 ATAAATAAA
* *
3952 A-ATATATAT
1 ATAAATA-AA
* *
3961 ATTACTAATA
1 ATAAATAA-A
*
3971 ATACAT-AA
1 ATAAATAAA
3979 AT-AATAAA
1 ATAAATAAA
* **
3987 ATACATAGG
1 ATAAATAAA
*
3996 ATATATAAA
1 ATAAATAAA
4005 AT--ATAAA
1 ATAAATAAA
4012 ATAAATAAA
1 ATAAATAAA
4021 A
1 A
4022 ATGACCAAGA
Statistics
Matches: 80, Mismatches: 20, Indels: 20
0.67 0.17 0.17
Matches are distributed among these distances:
7 17 0.21
8 25 0.31
9 33 0.41
10 5 0.06
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (9 bp):
ATAAATAAA
Found at i:3991 original size:16 final size:16
Alignment explanation
Indices: 3906--4021 Score: 59
Period size: 16 Copynumber: 7.4 Consensus size: 16
3896 TAATTAGATA
*
3906 AATAAAATACAAAAAT
1 AATAAAATACATAAAT
*
3922 AAATAAAATA-AAAAGAT
1 -AATAAAATACATAA-AT
3939 AA-AAAATA-ATAAA-
1 AATAAAATACATAAAT
* * * *
3952 AAT-ATATATATTACT
1 AATAAAATACATAAAT
3967 AAT--AATACATAAAT
1 AATAAAATACATAAAT
*
3981 AATAAAATACATAGGAT
1 AATAAAATACATA-AAT
*
3998 ATATAAAATATA-AAAT
1 A-ATAAAATACATAAAT
4014 AAATAAAA
1 -AATAAAA
4022 ATGACCAAGA
Statistics
Matches: 79, Mismatches: 11, Indels: 19
0.72 0.10 0.17
Matches are distributed among these distances:
13 6 0.08
14 14 0.18
15 12 0.15
16 22 0.28
17 16 0.20
18 9 0.11
ACGTcount: A:0.69, C:0.03, G:0.03, T:0.25
Consensus pattern (16 bp):
AATAAAATACATAAAT
Found at i:4190 original size:1 final size:1
Alignment explanation
Indices: 4184--4234 Score: 93
Period size: 1 Copynumber: 51.0 Consensus size: 1
4174 TCAACATTTC
*
4184 TTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4235 ACCAAAGCTC
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.00, C:0.00, G:0.02, T:0.98
Consensus pattern (1 bp):
T
Found at i:4417 original size:39 final size:40
Alignment explanation
Indices: 4241--4640 Score: 450
Period size: 39 Copynumber: 10.0 Consensus size: 40
4231 TTTTACCAAA
* *
4241 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCAC-ACGACTTTG-GAAA-GTAAATT
* * * *
4284 GCTCCTCCAAACAGA-GTACCACGACTTTGAAAAATAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATT
*
4324 GCTCTTCTAAACAGAGGCCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGG-CA-CACGACTTTGG-AAAGTAAATT
4367 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAGT-AATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATT
*
4406 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCA-CACGACTTTGGAAAGTAAATT
* *
4447 GCTCCTCTAAATAGAGGCA-ACGAAC-TTGGAAAATAAATT
1 GCTCCTCTAAACAGAGGCACACG-ACTTTGGAAAGTAAATT
*
4486 GCTCCTCTAAATAGAGGCA-ACGAAACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACACG--ACTTTGGAAAGTAAATT
*
4527 GCTCCTCTAACCAGAGGCA-ACGAAC-TTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACACG-ACTTTGGAAAGTAAATT
4566 GCT-CTCTAAACAGAGGCA-ACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACACGACTTTGG-AAAGTAAATT
*
4605 GCTCCTC--AA-AGAGGCA-ACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAACAGAGGCACACG-ACTTTGGAAAGTAAAT
4641 ACTCCTACAA
Statistics
Matches: 325, Mismatches: 19, Indels: 32
0.86 0.05 0.09
Matches are distributed among these distances:
37 21 0.06
38 29 0.09
39 101 0.31
40 39 0.12
41 59 0.18
42 36 0.11
43 40 0.12
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (40 bp):
GCTCCTCTAAACAGAGGCACACGACTTTGGAAAGTAAATT
Found at i:4457 original size:80 final size:80
Alignment explanation
Indices: 4241--4640 Score: 464
Period size: 80 Copynumber: 5.0 Consensus size: 80
4231 TTTTACCAAA
* * * * * *
4241 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTGCTCCTCCAAACAGAGTACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAG-GCAAC
*
4306 G-ACTTTGAAAAATAAATT
63 GAAC-TTGGAAAATAAATT
*
4324 GCTCTTCTAAACAGAGGCCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 GCTCCTCTAAACAGAGG-CACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCA--A
*
4389 CG-ACTTTGG-AAGT-AATT
62 CGAAC-TTGGAAAATAAATT
* *
4406 GCTCCTCTAAACAGAGGCACCATGACTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCAACGAA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
4471 CTTGGAAAATAAATT
66 CTTGGAAAATAAATT
* *
4486 GCTCCTCTAAATAGAGGCA--ACGAAACTTTGGAAAGTAAATTGCTCCTCTAACCAGAGGCAACG
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACG
*
4549 AACTTGGAAAGTAAATT
64 AACTTGGAAAATAAATT
4566 GCT-CTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATTGCTCCTC--AA-AGAGGCAACGA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCAACGA
*
4625 ACTTTGAAAAGTAAAT
65 ACTTGGAAAA-TAAAT
4641 ACTCCTACAA
Statistics
Matches: 284, Mismatches: 22, Indels: 29
0.85 0.07 0.09
Matches are distributed among these distances:
75 19 0.07
76 6 0.02
77 7 0.02
78 26 0.09
79 22 0.08
80 106 0.37
81 13 0.05
82 21 0.07
83 41 0.14
84 23 0.08
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (80 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGAA
CTTGGAAAATAAATT
Found at i:4514 original size:119 final size:120
Alignment explanation
Indices: 4241--4640 Score: 484
Period size: 119 Copynumber: 3.3 Consensus size: 120
4231 TTTTACCAAA
* * *
4241 GCTCCTCTAAACAGAGGCTCAACG-ACTTTGAGAAACATAAATTGCTCCTCCAAACAGA-GTACC
1 GCTCCTCTAAA-AGAGG--CAACGAACTTTG-GAAA-GTAAATTGCTCCTCTAAACAGAGGCACC
* * *
4304 ACGACTTTGAAAAATAAATTGCTCTTCTAAACAGAGGCCACCACGACTTTGGAAAAGTAAATT
61 ACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGG-CA--ACGACTTTGGAAAAGTAAATT
*
4367 GCTCCTCTAAACAGAGGCACCACG-ACTTTGG-AAGT-AATTGCTCCTCTAAACAGAGGCACCAT
1 GCTCCTCTAAA-AGAGGCA--ACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
*
4429 GACTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCAACGAAC-TTGGAAAA-TAAATT
63 GACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACG-ACTTTGGAAAAGTAAATT
*
4486 GCTCCTCTAAATAGAGGCAACGAAACTTTGGAAAGTAAATTGCTCCTCTAACCAGAGGCA--ACG
1 GCTCCTCTAAA-AGAGGCAACG-AACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
4549 AAC-TTGGAAAGTAAATTGCT-CTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
64 -ACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
*
4605 GCTCCTC--AAAGAGGCAACGAACTTTGAAAAGTAAAT
1 GCTCCTCTAAAAGAGGCAACGAACTTTGGAAAGTAAAT
4641 ACTCCTACAA
Statistics
Matches: 250, Mismatches: 13, Indels: 33
0.84 0.04 0.11
Matches are distributed among these distances:
115 16 0.06
116 10 0.04
117 7 0.03
118 25 0.10
119 63 0.25
120 17 0.07
121 24 0.10
122 20 0.08
123 37 0.15
124 4 0.02
125 1 0.00
126 26 0.10
ACGTcount: A:0.37, C:0.21, G:0.18, T:0.23
Consensus pattern (120 bp):
GCTCCTCTAAAAGAGGCAACGAACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGAC
TTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAACGACTTTGGAAAAGTAAATT
Found at i:5859 original size:27 final size:27
Alignment explanation
Indices: 5821--5882 Score: 124
Period size: 27 Copynumber: 2.3 Consensus size: 27
5811 AATGAATCTC
5821 CTTTTTTTTTTTTTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTTTTTTTTTTTTTT
5848 CTTTTTTTTTTTTTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTTTTTTTTTTTTTT
5875 CTTTTTTT
1 CTTTTTTT
5883 CACTTTTCTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.00, C:0.05, G:0.00, T:0.95
Consensus pattern (27 bp):
CTTTTTTTTTTTTTTTTTTTTTTTTTT
Found at i:5889 original size:27 final size:27
Alignment explanation
Indices: 5832--5889 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
5822 TTTTTTTTTT
***
5832 TTTTTTTTTTTTTTTTCTTTTTTTTTT
1 TTTTTTTTTTTTTTTTCTTTTTTTCAC
5859 TTTTTTTTTTTTTTTTCTTTTTTTCAC
1 TTTTTTTTTTTTTTTTCTTTTTTTCAC
5886 TTTT
1 TTTT
5890 CTCATTTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.02, C:0.07, G:0.00, T:0.91
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTCTTTTTTTCAC
Found at i:5898 original size:1 final size:1
Alignment explanation
Indices: 5822--5882 Score: 104
Period size: 1 Copynumber: 61.0 Consensus size: 1
5812 ATGAATCTCC
* *
5822 TTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
5883 CACTTTTCTC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 56 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:9947 original size:58 final size:59
Alignment explanation
Indices: 9707--10160 Score: 684
Period size: 58 Copynumber: 7.8 Consensus size: 59
9697 TTTTTTTGTG
*
9707 AGGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTT-GAAATTTATTTC--A
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTTA
* *
9762 AGGAAAATTGATACTTTCAACTTTT-CCTCAAAAATTTTTTTTTGAAAATTTA--T-TTA
1 AGGAAAATTGATACTTTCAACTTTTCCCT-AAAAATATTTTTTTGGAAATTTATTTCTTA
*
9818 AGGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTGAAATTTTATTT-TTAAA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAA-TTTATTTCTT--A
9878 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTGGAAATTTATTTCTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTTA
*
9936 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTC-TA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTTA
*
9994 AGGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTTGAAATTTATTTC-TA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTTA
10051 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAAATTTATTTCTTTTA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAAATTTATTTC--TTA
10113 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTTGGAA
1 AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTTGGAA
10161 TTTTTTATTT
Statistics
Matches: 370, Mismatches: 9, Indels: 33
0.90 0.02 0.08
Matches are distributed among these distances:
54 2 0.01
55 48 0.13
56 36 0.10
57 66 0.18
58 77 0.21
59 44 0.12
60 41 0.11
61 8 0.02
62 48 0.13
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (59 bp):
AGGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTTA
Found at i:10200 original size:10 final size:10
Alignment explanation
Indices: 10185--10217 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
10175 TAAAGAAAAT
10185 AAAATAATAA
1 AAAATAATAA
10195 AAAATAAT-A
1 AAAATAATAA
10204 AAAATAAATAA
1 AAAAT-AATAA
10215 AAA
1 AAA
10218 GAATATTACA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.29
10 11 0.52
11 4 0.19
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (10 bp):
AAAATAATAA
Found at i:10222 original size:19 final size:19
Alignment explanation
Indices: 10185--10222 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
10175 TAAAGAAAAT
*
10185 AAAATAATAAAAAATAATA
1 AAAATAATAAAAAAGAATA
10204 AAAATAA-ATAAAAAGAATA
1 AAAATAATA-AAAAAGAATA
10223 TTACATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (19 bp):
AAAATAATAAAAAAGAATA
Found at i:10262 original size:1 final size:1
Alignment explanation
Indices: 10247--10299 Score: 79
Period size: 1 Copynumber: 53.0 Consensus size: 1
10237 TCTAATAAAT
* * *
10247 AAAAAATAAACAAAAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10300 CCTGGAGCGG
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.94, C:0.02, G:0.00, T:0.04
Consensus pattern (1 bp):
A
Found at i:10269 original size:17 final size:16
Alignment explanation
Indices: 10247--10299 Score: 90
Period size: 15 Copynumber: 3.3 Consensus size: 16
10237 TCTAATAAAT
10247 AAAAAATAAACAAAAAA
1 AAAAAATAAA-AAAAAA
10264 AAAAAATAAAAAAAAA
1 AAAAAATAAAAAAAAA
10280 AAAAAA-AAAAAAAAA
1 AAAAAATAAAAAAAAA
10295 AAAAA
1 AAAAA
10300 CCTGGAGCGG
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
15 14 0.39
16 12 0.33
17 10 0.28
ACGTcount: A:0.94, C:0.02, G:0.00, T:0.04
Consensus pattern (16 bp):
AAAAAATAAAAAAAAA
Found at i:10273 original size:28 final size:28
Alignment explanation
Indices: 10240--10297 Score: 89
Period size: 28 Copynumber: 2.1 Consensus size: 28
10230 AACCTAATCT
* * *
10240 AATAAATAAAAAATAAACAAAAAAAAAA
1 AATAAAAAAAAAAAAAAAAAAAAAAAAA
10268 AATAAAAAAAAAAAAAAAAAAAAAAAAA
1 AATAAAAAAAAAAAAAAAAAAAAAAAAA
10296 AA
1 AA
10298 AACCTGGAGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.91, C:0.02, G:0.00, T:0.07
Consensus pattern (28 bp):
AATAAAAAAAAAAAAAAAAAAAAAAAAA
Found at i:10324 original size:5 final size:5
Alignment explanation
Indices: 10307--10337 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
10297 AAACCTGGAG
*
10307 CGGCT CGGAT CGGCT CGGCT CGGCT CGGCT C
1 CGGCT CGGCT CGGCT CGGCT CGGCT CGGCT C
10338 AAGGAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.03, C:0.39, G:0.39, T:0.19
Consensus pattern (5 bp):
CGGCT
Found at i:10637 original size:19 final size:19
Alignment explanation
Indices: 10608--10652 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
10598 AACACCCGGT
*
10608 GCCGGATTCTGGAAATTTC
1 GCCGGAATCTGGAAATTTC
*
10627 GTCGGAATCTGGAAATTTC
1 GCCGGAATCTGGAAATTTC
10646 GCCGGAA
1 GCCGGAA
10653 GTTGGCCGGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (19 bp):
GCCGGAATCTGGAAATTTC
Found at i:10747 original size:29 final size:30
Alignment explanation
Indices: 10705--10771 Score: 100
Period size: 30 Copynumber: 2.3 Consensus size: 30
10695 ACTGGGCTGG
* * *
10705 TGCCGGAAACTTC-AAGTTGGCCGGAATTT
1 TGCCGGAAAATTCAAACTTCGCCGGAATTT
10734 TGCCGGAAAATTCAAACTTCGCCGGAATTT
1 TGCCGGAAAATTCAAACTTCGCCGGAATTT
10764 TGCCGGAA
1 TGCCGGAA
10772 TCTGGAAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
29 12 0.35
30 22 0.65
ACGTcount: A:0.27, C:0.22, G:0.25, T:0.25
Consensus pattern (30 bp):
TGCCGGAAAATTCAAACTTCGCCGGAATTT
Found at i:10824 original size:24 final size:24
Alignment explanation
Indices: 10780--10831 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
10770 AATCTGGAAA
*
10780 TTTCCCAGAAATTTCCAAAAAATT
1 TTTCCCAAAAATTTCCAAAAAATT
*
10804 TTTCGCCAAAAATTT-CTAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAATT
10828 TTTC
1 TTTC
10832 TCACTCCCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.64
25 9 0.36
ACGTcount: A:0.38, C:0.19, G:0.04, T:0.38
Consensus pattern (24 bp):
TTTCCCAAAAATTTCCAAAAAATT
Found at i:11174 original size:28 final size:26
Alignment explanation
Indices: 11121--11192 Score: 69
Period size: 28 Copynumber: 2.7 Consensus size: 26
11111 AGAAAATCAA
*
11121 AATTAAAAAATAAAA-ATAATATCAGAT
1 AATTAAAAAA-AAAATA-AATAACAGAT
11148 AATTCAAAAAAAAAATAAATTAACAGAT
1 AATT-AAAAAAAAAATAAA-TAACAGAT
11176 -A-TAAAAAAAATAATAAA
1 AATTAAAAAAAA-AATAAA
11193 AATAAAATAA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
25 8 0.20
26 7 0.17
27 11 0.28
28 14 0.35
ACGTcount: A:0.71, C:0.04, G:0.03, T:0.22
Consensus pattern (26 bp):
AATTAAAAAAAAAATAAATAACAGAT
Found at i:11218 original size:28 final size:28
Alignment explanation
Indices: 11126--11218 Score: 64
Period size: 30 Copynumber: 3.2 Consensus size: 28
11116 ATCAAAATTA
* * **
11126 AAAAATAAAAATAATATCAGAT-AATTC
1 AAAAATAAAAATAAAATAAGATAAAAAC
* *
11153 AAAAA-AAAAATAAATTAACAGATATAAAAA
1 AAAAATAAAAATAAAAT-A-AGATA-AAAAC
**
11183 AAATAATAAAAATAAAATAAGATAAACCC
1 AAA-AATAAAAATAAAATAAGATAAAAAC
11212 AAAAATA
1 AAAAATA
11219 TATTACAAAA
Statistics
Matches: 50, Mismatches: 10, Indels: 11
0.70 0.14 0.15
Matches are distributed among these distances:
26 9 0.18
27 5 0.10
28 8 0.16
29 5 0.10
30 10 0.20
31 3 0.06
32 10 0.20
ACGTcount: A:0.71, C:0.06, G:0.03, T:0.19
Consensus pattern (28 bp):
AAAAATAAAAATAAAATAAGATAAAAAC
Found at i:11295 original size:31 final size:28
Alignment explanation
Indices: 11234--11339 Score: 83
Period size: 28 Copynumber: 3.6 Consensus size: 28
11224 CAAAAAAAAA
* *
11234 AAATAATAATAATAATATATAACTATAT
1 AAATAATAATAATAAAATATAACTAAAT
*
11262 AAATAATAATACATATAAATCTAATCTAAAT
1 AAATAATAATA-ATA-AAATATAA-CTAAAT
11293 AAAAATAAATAAATAAATAAAATAT-AC-ATAAT
1 --AAAT-AAT-AAT-AATAAAATATAACTA-AAT
11325 -AATAATAATAATAAA
1 AAATAATAATAATAAA
11340 TACATAAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
26 6 0.09
27 3 0.05
28 14 0.22
29 6 0.09
30 6 0.09
31 6 0.09
32 4 0.06
33 5 0.08
34 8 0.12
35 6 0.09
36 1 0.02
ACGTcount: A:0.65, C:0.05, G:0.00, T:0.30
Consensus pattern (28 bp):
AAATAATAATAATAAAATATAACTAAAT
Found at i:11323 original size:23 final size:23
Alignment explanation
Indices: 11297--11347 Score: 54
Period size: 23 Copynumber: 2.2 Consensus size: 23
11287 CTAAATAAAA
11297 ATAAATAAATAAATAA-AAT-ATAC
1 ATAAAT-AAT-AATAATAATAATAC
11320 AT-AATAATAATAATAATAAATAC
1 ATAAATAATAATAATAAT-AATAC
11343 ATAAA
1 ATAAA
11348 ATACAAAAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
20 5 0.21
21 6 0.25
22 3 0.12
23 8 0.33
24 2 0.08
ACGTcount: A:0.69, C:0.04, G:0.00, T:0.27
Consensus pattern (23 bp):
ATAAATAATAATAATAATAATAC
Found at i:14950 original size:10 final size:10
Alignment explanation
Indices: 14935--14961 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
14925 AAAAAAATAT
14935 TTTTAATAAG
1 TTTTAATAAG
14945 TTTTAATAAG
1 TTTTAATAAG
14955 TTTTAAT
1 TTTTAAT
14962 TAAATTAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (10 bp):
TTTTAATAAG
Found at i:16270 original size:38 final size:38
Alignment explanation
Indices: 16219--16292 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
16209 AGAAATTTAA
*
16219 ACTTGACATCTTATCCGAAGGTGAAGCGTGGGCTTTTT
1 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTTTT
16257 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTT
1 ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTT
16293 GTTCAAAGAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (38 bp):
ACTTGACATCTTATCCGAAGGTGAAGCATGGGCTTTTT
Found at i:18561 original size:43 final size:43
Alignment explanation
Indices: 18500--18587 Score: 149
Period size: 43 Copynumber: 2.0 Consensus size: 43
18490 TTAAATTATA
18500 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
1 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
* * *
18543 TTAGTAACTAAACTAAATTTGTACTTATTACGTGGCTTGCAAG
1 TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
18586 TT
1 TT
18588 GAGAAAGCTA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (43 bp):
TTAGTAACTAAACTAAATTTATACTTATTACATGGCTTACAAG
Found at i:19496 original size:10 final size:10
Alignment explanation
Indices: 19481--19513 Score: 50
Period size: 9 Copynumber: 3.3 Consensus size: 10
19471 TTGCAAATAA
19481 AAAAGAAAAT
1 AAAAGAAAAT
19491 AAAAG-AAAT
1 AAAAGAAAAT
19500 AAAAGAATAAT
1 AAAAGAA-AAT
19511 AAA
1 AAA
19514 GGCAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 9 0.43
10 6 0.29
11 6 0.29
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (10 bp):
AAAAGAAAAT
Found at i:20237 original size:2 final size:2
Alignment explanation
Indices: 20230--20259 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
20220 TGATAATCTA
20230 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20260 ACAACATACA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21641 original size:14 final size:13
Alignment explanation
Indices: 21621--21659 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
21611 TTTAGTGAAC
21621 AATATTATTTATA
1 AATATTATTTATA
*
21634 ATATATTATATATA
1 A-ATATTATTTATA
21648 AATTATTATTTA
1 AA-TATTATTTA
21660 ATTATAACTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.09
14 20 0.91
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTATTTATA
Found at i:21800 original size:2 final size:2
Alignment explanation
Indices: 21793--21824 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
21783 ATAGATTGTA
*
21793 AT AT AT AT AT AT AT AT AT AT AT AT AT AG AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21825 GATTTGGTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Done.