Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168472.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_71, 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: 128422
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
File 2 of 2
Found at i:101868 original size:59 final size:58
Alignment explanation
Indices: 101744--101909 Score: 158
Period size: 59 Copynumber: 2.8 Consensus size: 58
101734 AAAAGGTTTG
* *
101744 AAAAAAAA-AATTTTAGGAAAAAGTTGGAAGTATCAAATTTTCCTTGAAATTAAAATTTAAA
1 AAAAAAAACAATTTAAGG-AAAAGTTGGAAGTA-CTAATTTTCCTT-AAA-TAAAATTTAAA
* **
101805 AAAAAAAAGCAATTTGAGGAAAAGTTGGAAGTACTAATTTTCCTTAAA-AAGTTTGTAAAA
1 AAAAAAAA-CAATTTAAGGAAAAGTTGGAAGTACTAATTTTCCTTAAATAAAATT-T-AAA
** * *
101865 AAAAAAAACGTTTTAAGAAAAAGTTGAAAGTA-TCAATTTTCCTTA
1 AAAAAAAACAATTTAAGGAAAAGTTGGAAGTACT-AATTTTCCTTA
101910 TACAAAAGTA
Statistics
Matches: 91, Mismatches: 9, Indels: 12
0.81 0.08 0.11
Matches are distributed among these distances:
58 5 0.05
59 31 0.34
60 14 0.15
61 19 0.21
62 14 0.15
63 8 0.09
ACGTcount: A:0.50, C:0.07, G:0.13, T:0.30
Consensus pattern (58 bp):
AAAAAAAACAATTTAAGGAAAAGTTGGAAGTACTAATTTTCCTTAAATAAAATTTAAA
Found at i:102555 original size:28 final size:28
Alignment explanation
Indices: 102522--102575 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
102512 TTTTCAAAAA
*
102522 ATAACTTATTATATGATTACATTGAAGC
1 ATAACTTATTATATGATTACAATGAAGC
102550 ATAACTTATTATATGATTACAATGAA
1 ATAACTTATTATATGATTACAATGAA
102576 ATATGAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.39
Consensus pattern (28 bp):
ATAACTTATTATATGATTACAATGAAGC
Found at i:102755 original size:41 final size:41
Alignment explanation
Indices: 102692--102770 Score: 131
Period size: 41 Copynumber: 1.9 Consensus size: 41
102682 GATATTAAAT
* **
102692 TTGTGCATCTAATCTAGTTGCATATATAACATCACAAAGAA
1 TTGTGCATCTAATCCACATGCATATATAACATCACAAAGAA
102733 TTGTGCATCTAATCCACATGCATATATAACATCACAAA
1 TTGTGCATCTAATCCACATGCATATATAACATCACAAA
102771 AAAAAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.30
Consensus pattern (41 bp):
TTGTGCATCTAATCCACATGCATATATAACATCACAAAGAA
Found at i:104550 original size:22 final size:21
Alignment explanation
Indices: 104524--104564 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
104514 GAGCTTTCCA
*
104524 TTAAGGTTAATATATATATTTT
1 TTAAGGTTAACATAT-TATTTT
104546 TTAAGGTTAACATATTATT
1 TTAAGGTTAACATATTATT
104565 AATTGATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAAGGTTAACATATTATTTT
Found at i:108010 original size:7 final size:7
Alignment explanation
Indices: 107937--107991 Score: 92
Period size: 7 Copynumber: 7.9 Consensus size: 7
107927 TTATTTTTTT
107937 ATTTTCA
1 ATTTTCA
107944 ATTTTCA
1 ATTTTCA
107951 ATTTTCA
1 ATTTTCA
107958 ATTTTCA
1 ATTTTCA
*
107965 AGTTTCA
1 ATTTTCA
*
107972 AGTTTCA
1 ATTTTCA
107979 ATTTTCA
1 ATTTTCA
107986 ATTTTC
1 ATTTTC
107992 GCTTTTGATT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 46 1.00
ACGTcount: A:0.27, C:0.15, G:0.04, T:0.55
Consensus pattern (7 bp):
ATTTTCA
Found at i:108017 original size:20 final size:19
Alignment explanation
Indices: 107979--108045 Score: 64
Period size: 20 Copynumber: 3.5 Consensus size: 19
107969 TCAAGTTTCA
* *
107979 ATTTTCAATTTTCGCTTTT
1 ATTTTCTATTTTAGCTTTT
*
107998 GATTTTCTATTTTAGTTTTT
1 -ATTTTCTATTTTAGCTTTT
* *
108018 ATTTTTTATTTT-GATTTT
1 ATTTTCTATTTTAGCTTTT
*
108036 ATTTTTTATT
1 ATTTTCTATT
108046 ATTTCTGTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
18 15 0.36
19 11 0.26
20 16 0.38
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.72
Consensus pattern (19 bp):
ATTTTCTATTTTAGCTTTT
Found at i:108043 original size:32 final size:33
Alignment explanation
Indices: 107994--108074 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 33
107984 CAATTTTCGC
* * *
107994 TTTTGATTTTCTATTTTAGTT-TTTATTTTTTA-
1 TTTTGATTTTATTTTTTA-TTATTTATGTTTTAT
*
108026 TTTTGATTTTATTTTTTATTATTTCTGTTTTAT
1 TTTTGATTTTATTTTTTATTATTTATGTTTTAT
108059 TTATTGATTTTATTTT
1 TT-TTGATTTTATTTT
108075 ATTGAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
31 2 0.05
32 25 0.60
33 2 0.05
34 13 0.31
ACGTcount: A:0.16, C:0.02, G:0.06, T:0.75
Consensus pattern (33 bp):
TTTTGATTTTATTTTTTATTATTTATGTTTTAT
Found at i:108049 original size:21 final size:20
Alignment explanation
Indices: 108019--108060 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
108009 TTAGTTTTTA
108019 TTTTTTATTT-TGATTTTATT
1 TTTTTTATTTCTG-TTTTATT
108039 TTTTATTATTTCTGTTTTATT
1 TTTT-TTATTTCTGTTTTATT
108060 T
1 T
108061 ATTGATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.14, C:0.02, G:0.05, T:0.79
Consensus pattern (20 bp):
TTTTTTATTTCTGTTTTATT
Found at i:108061 original size:18 final size:18
Alignment explanation
Indices: 108014--108077 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 18
108004 CTATTTTAGT
*
108014 TTTTATTTT-TTATTTTGA
1 TTTTATTTTATT-TATTGA
108032 TTTTA-TTT-TTTATT-A
1 TTTTATTTTATTTATTGA
*
108047 TTTCTGTTTTATTTATTGA
1 TTT-TATTTTATTTATTGA
108066 TTTTATTTTATT
1 TTTTATTTTATT
108078 GAAAAAAAAG
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
15 4 0.10
16 4 0.10
17 8 0.21
18 19 0.49
19 4 0.10
ACGTcount: A:0.17, C:0.02, G:0.05, T:0.77
Consensus pattern (18 bp):
TTTTATTTTATTTATTGA
Found at i:108075 original size:14 final size:14
Alignment explanation
Indices: 108014--108079 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 14
108004 CTATTTTAGT
108014 TTTTATTTT-TT-A
1 TTTTATTTTATTGA
108026 TTTTGATTTTATT--
1 TTTT-ATTTTATTGA
108039 TTTTATTATT-TCTG-
1 TTTTATT-TTAT-TGA
108053 TTTTA-TTTATTGA
1 TTTTATTTTATTGA
108066 TTTTATTTTATTGA
1 TTTTATTTTATTGA
108080 AAAAAAAGGA
Statistics
Matches: 46, Mismatches: 0, Indels: 14
0.77 0.00 0.23
Matches are distributed among these distances:
12 12 0.26
13 19 0.41
14 15 0.33
ACGTcount: A:0.18, C:0.02, G:0.06, T:0.74
Consensus pattern (14 bp):
TTTTATTTTATTGA
Found at i:120144 original size:24 final size:24
Alignment explanation
Indices: 120117--120183 Score: 111
Period size: 24 Copynumber: 2.9 Consensus size: 24
120107 TTGGATTTTG
120117 ATTTTGGTTATTATTTCAATTCAA
1 ATTTTGGTTATTATTTCAATTCAA
*
120141 ATTTTGGTTATTATTTTAATTCAA
1 ATTTTGGTTATTATTTCAATTCAA
120165 ATTTTGGTTA-TA-TTCAATT
1 ATTTTGGTTATTATTTCAATT
120184 GTTTTAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
22 6 0.15
23 2 0.05
24 33 0.80
ACGTcount: A:0.28, C:0.06, G:0.09, T:0.57
Consensus pattern (24 bp):
ATTTTGGTTATTATTTCAATTCAA
Found at i:120977 original size:119 final size:118
Alignment explanation
Indices: 120751--120995 Score: 343
Period size: 119 Copynumber: 2.1 Consensus size: 118
120741 AATATTTTTT
* *
120751 ACTTTTT-TTAAATGGAGAAGTTATCAACACCAAAATATCAAAAAATTCATTTTGAATGATGGTA
1 ACTTTTTATTAAATGGAGAAGTGATCAACACCAAAATATCAAAAAAGTCATTTTGAATGATGGTA
*
120815 ATAAGAATGAAGTAACAATTAAAAATATACAATATTTTCATTTAGTAAAAGAA
66 ATAAGAACGAAGTAACAATTAAAAATATACAATATTTTCATTTAGTAAAAGAA
**
120868 ACTTTTTATTCAAATGGAGAAGTGATTGACACCAAAATATCAAAAAAGTCATTTTGAATGATGGT
1 ACTTTTTATT-AAATGGAGAAGTGATCAACACCAAAATATCAAAAAAGTCATTTTGAATGATGGT
* * * * * *
120933 AGTAAGAACGAAGTAACATTTAAAAATGTATC-ATCTTTTTATTTAGTAGAAGAA
65 AATAAGAACGAAGTAACAATTAAAAATATA-CAATATTTTCATTTAGTAAAAGAA
120987 A-TTCTTTAT
1 ACTT-TTTAT
120996 GGAAAATGCA
Statistics
Matches: 113, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
117 7 0.06
118 4 0.04
119 101 0.89
120 1 0.01
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.34
Consensus pattern (118 bp):
ACTTTTTATTAAATGGAGAAGTGATCAACACCAAAATATCAAAAAAGTCATTTTGAATGATGGTA
ATAAGAACGAAGTAACAATTAAAAATATACAATATTTTCATTTAGTAAAAGAA
Found at i:123346 original size:16 final size:16
Alignment explanation
Indices: 123325--123410 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 16
123315 TAGGTAAGTA
123325 TATTTTCTTTTT-TCTT
1 TATTTT-TTTTTATCTT
*
123341 TATTTTATTTTTATTTT
1 TATTTT-TTTTTATCTT
123358 TATTTTTTTTGTAT-TT
1 TATTTTTTTT-TATCTT
123374 TACATTTTATTTTTAT-TT
1 T--ATTTT-TTTTTATCTT
*
123392 TATTTTATTATTAT-TT
1 TATTTT-TTTTTATCTT
123408 TAT
1 TAT
123411 ATATATATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
16 35 0.56
17 12 0.19
18 11 0.18
19 4 0.06
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (16 bp):
TATTTTTTTTTATCTT
Found at i:123352 original size:6 final size:6
Alignment explanation
Indices: 123339--123435 Score: 80
Period size: 6 Copynumber: 16.8 Consensus size: 6
123329 TTCTTTTTTC
* *
123339 TTTA-T TTTATT TTTATT TTTATT TTT-TT TGTA-T TTTACAT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT
* * * *
123385 TTTA-T TTTA-T TTTATT ATTATT TTATATA TATATT TTT-CT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TT-TATT TTTATT TTTATT TTTATT
123431 TTTAT
1 TTTAT
123436 CTTAGGTATT
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
5 26 0.35
6 39 0.53
7 9 0.12
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:123353 original size:11 final size:11
Alignment explanation
Indices: 123339--123435 Score: 99
Period size: 11 Copynumber: 8.5 Consensus size: 11
123329 TTCTTTTTTC
123339 TTTATTTTATT
1 TTTATTTTATT
123350 TTTATTTTTATT
1 TTTA-TTTTATT
123362 TTT-TTTGTATT
1 TTTATTT-TATT
*
123373 TTACATTTTATT
1 TT-TATTTTATT
123385 TTTATTTTA-T
1 TTTATTTTATT
123395 TTTATTATTATT
1 TTTATT-TTATT
*
123407 TTATATATATATT
1 TT-TAT-TTTATT
*
123420 TTTCTTTTATT
1 TTTATTTTATT
123431 TTTAT
1 TTTAT
123436 CTTAGGTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.14
11 28 0.39
12 21 0.29
13 12 0.17
14 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:123372 original size:23 final size:22
Alignment explanation
Indices: 123325--123435 Score: 102
Period size: 23 Copynumber: 4.9 Consensus size: 22
123315 TAGGTAAGTA
* *
123325 TATTTTCTTTTT-TCTTTATTT
1 TATTTTATTTTTATTTTTATTT
123346 TATTTTTATTTTTATTTTT-TTT
1 TA-TTTTATTTTTATTTTTATTT
*
123368 GTATTTTACATTTTATTTTTATTT
1 -TATTTTA-TTTTTATTTTTATTT
* *
123392 TATTTTATTATTATTTTATATATA
1 TATTTTATTTTTATTTT-TAT-TT
123416 TATTTT-TCTTTTATTTTTAT
1 TATTTTAT-TTTTATTTTTAT
123436 CTTAGGTATT
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.03
22 25 0.33
23 30 0.40
24 18 0.24
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (22 bp):
TATTTTATTTTTATTTTTATTT
Found at i:123382 original size:35 final size:33
Alignment explanation
Indices: 123342--123433 Score: 112
Period size: 35 Copynumber: 2.7 Consensus size: 33
123332 TTTTTTCTTT
*
123342 ATTTTATTTTTATTTTTATTTTTTTTGTATTTTAC
1 ATTTTATTTTTA-TTTTATTTTTTAT-TATTTTAC
*
123377 ATTTTATTTTTATTTTATTTTATTATTATTTTAT
1 ATTTTATTTTTATTTTATTTT-TTATTATTTTAC
* *
123411 ATATATATTTTTCTTTTATTTTT
1 AT-TTTATTTTTATTTTATTTTT
123434 ATCTTAGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 19 0.37
35 32 0.63
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (33 bp):
ATTTTATTTTTATTTTATTTTTTATTATTTTAC
Found at i:123427 original size:5 final size:5
Alignment explanation
Indices: 123325--123410 Score: 73
Period size: 5 Copynumber: 15.6 Consensus size: 5
123315 TAGGTAAGTA
* * *
123325 TATTT TCTTT TTTCTT TATTT TATTTT TATTTT TATTT TTTTT GTATTT
1 TATTT TATTT TAT-TT TATTT TA-TTT TA-TTT TATTT TATTT -TATTT
123374 TACATTT TATTTT TATTT TATTT TATTAT TATTT TAT
1 T--ATTT TA-TTT TATTT TATTT TATT-T TATTT TAT
123411 ATATATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
5 35 0.51
6 29 0.42
7 5 0.07
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:123594 original size:22 final size:20
Alignment explanation
Indices: 123569--123651 Score: 78
Period size: 22 Copynumber: 3.9 Consensus size: 20
123559 ATATGTTATA
123569 ATTTATCTGTTATTTAATTTTT
1 ATTTATCTGTTATTT--TTTTT
*
123591 ATTTATCTATTATTTTTTTT
1 ATTTATCTGTTATTTTTTTT
*
123611 ATTTATCTGATTTATTTTCATTTG
1 ATTTATCTG--TTATTTT--TTTT
*
123635 ATTTAT-TTTTATTTTTT
1 ATTTATCTGTTATTTTTT
123652 ATTTTTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 7 0.13
22 21 0.40
23 1 0.02
24 9 0.17
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTATCTGTTATTTTTTTT
Found at i:123638 original size:15 final size:15
Alignment explanation
Indices: 123618--123656 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
123608 TTTATTTATC
123618 TGATTTATTTTCATT
1 TGATTTATTTTCATT
*
123633 TGATTTATTTTTATT
1 TGATTTATTTTCATT
123648 T--TTTATTTT
1 TGATTTATTTT
123657 TTTTAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
15 15 0.65
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (15 bp):
TGATTTATTTTCATT
Found at i:123925 original size:23 final size:24
Alignment explanation
Indices: 123892--123943 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
123882 GAATCGAAAA
* *
123892 AAAAAAATTT-TGGAGATTTTTGG
1 AAAAATATTTCTGGAAATTTTTGG
*
123915 CAAAAATTTTTCTGGAAATTTTTGG
1 -AAAAATATTTCTGGAAATTTTTGG
123940 AAAA
1 AAAA
123944 TTTCCAGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 12 0.50
25 12 0.50
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (24 bp):
AAAAATATTTCTGGAAATTTTTGG
Found at i:124604 original size:16 final size:16
Alignment explanation
Indices: 124583--124668 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 16
124573 TAGGTAAGTA
124583 TATTTTCTTTTT-TCTT
1 TATTTT-TTTTTATCTT
*
124599 TATTTTATTTTTATTTT
1 TATTTT-TTTTTATCTT
124616 TATTTTTTTTGTAT-TT
1 TATTTTTTTT-TATCTT
124632 TACATTTTATTTTTAT-TT
1 T--ATTTT-TTTTTATCTT
*
124650 TATTTTATTATTAT-TT
1 TATTTT-TTTTTATCTT
124666 TAT
1 TAT
124669 ATATATATTT
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
16 35 0.56
17 12 0.19
18 11 0.18
19 4 0.06
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (16 bp):
TATTTTTTTTTATCTT
Found at i:124610 original size:6 final size:6
Alignment explanation
Indices: 124597--124693 Score: 80
Period size: 6 Copynumber: 16.8 Consensus size: 6
124587 TTCTTTTTTC
* *
124597 TTTA-T TTTATT TTTATT TTTATT TTT-TT TGTA-T TTTACAT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTA-TT TTTATT
* * * *
124643 TTTA-T TTTA-T TTTATT ATTATT TTATATA TATATT TTT-CT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TT-TATT TTTATT TTTATT TTTATT
124689 TTTAT
1 TTTAT
124694 CTTAGGTATT
Statistics
Matches: 74, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
5 26 0.35
6 39 0.53
7 9 0.12
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:124611 original size:11 final size:11
Alignment explanation
Indices: 124597--124693 Score: 99
Period size: 11 Copynumber: 8.5 Consensus size: 11
124587 TTCTTTTTTC
124597 TTTATTTTATT
1 TTTATTTTATT
124608 TTTATTTTTATT
1 TTTA-TTTTATT
124620 TTT-TTTGTATT
1 TTTATTT-TATT
*
124631 TTACATTTTATT
1 TT-TATTTTATT
124643 TTTATTTTA-T
1 TTTATTTTATT
124653 TTTATTATTATT
1 TTTATT-TTATT
*
124665 TTATATATATATT
1 TT-TAT-TTTATT
*
124678 TTTCTTTTATT
1 TTTATTTTATT
124689 TTTAT
1 TTTAT
124694 CTTAGGTATT
Statistics
Matches: 72, Mismatches: 6, Indels: 16
0.77 0.06 0.17
Matches are distributed among these distances:
10 10 0.14
11 28 0.39
12 21 0.29
13 12 0.17
14 1 0.01
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (11 bp):
TTTATTTTATT
Found at i:124630 original size:23 final size:22
Alignment explanation
Indices: 124583--124693 Score: 102
Period size: 23 Copynumber: 4.9 Consensus size: 22
124573 TAGGTAAGTA
* *
124583 TATTTTCTTTTT-TCTTTATTT
1 TATTTTATTTTTATTTTTATTT
124604 TATTTTTATTTTTATTTTT-TTT
1 TA-TTTTATTTTTATTTTTATTT
*
124626 GTATTTTACATTTTATTTTTATTT
1 -TATTTTA-TTTTTATTTTTATTT
* *
124650 TATTTTATTATTATTTTATATATA
1 TATTTTATTTTTATTTT-TAT-TT
124674 TATTTT-TCTTTTATTTTTAT
1 TATTTTAT-TTTTATTTTTAT
124694 CTTAGGTATT
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
21 2 0.03
22 25 0.33
23 30 0.40
24 18 0.24
ACGTcount: A:0.19, C:0.04, G:0.01, T:0.77
Consensus pattern (22 bp):
TATTTTATTTTTATTTTTATTT
Found at i:124640 original size:35 final size:33
Alignment explanation
Indices: 124600--124691 Score: 112
Period size: 35 Copynumber: 2.7 Consensus size: 33
124590 TTTTTTCTTT
*
124600 ATTTTATTTTTATTTTTATTTTTTTTGTATTTTAC
1 ATTTTATTTTTA-TTTTATTTTTTAT-TATTTTAC
*
124635 ATTTTATTTTTATTTTATTTTATTATTATTTTAT
1 ATTTTATTTTTATTTTATTTT-TTATTATTTTAC
* *
124669 ATATATATTTTTCTTTTATTTTT
1 AT-TTTATTTTTATTTTATTTTT
124692 ATCTTAGGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
34 19 0.37
35 32 0.63
ACGTcount: A:0.21, C:0.02, G:0.01, T:0.76
Consensus pattern (33 bp):
ATTTTATTTTTATTTTATTTTTTATTATTTTAC
Found at i:124685 original size:5 final size:5
Alignment explanation
Indices: 124583--124668 Score: 73
Period size: 5 Copynumber: 15.6 Consensus size: 5
124573 TAGGTAAGTA
* * *
124583 TATTT TCTTT TTTCTT TATTT TATTTT TATTTT TATTT TTTTT GTATTT
1 TATTT TATTT TAT-TT TATTT TA-TTT TA-TTT TATTT TATTT -TATTT
124632 TACATTT TATTTT TATTT TATTT TATTAT TATTT TAT
1 T--ATTT TA-TTT TATTT TATTT TATT-T TATTT TAT
124669 ATATATATTT
Statistics
Matches: 69, Mismatches: 5, Indels: 14
0.78 0.06 0.16
Matches are distributed among these distances:
5 35 0.51
6 29 0.42
7 5 0.07
ACGTcount: A:0.17, C:0.03, G:0.01, T:0.78
Consensus pattern (5 bp):
TATTT
Found at i:124852 original size:22 final size:20
Alignment explanation
Indices: 124827--124909 Score: 78
Period size: 22 Copynumber: 3.9 Consensus size: 20
124817 ATATGTTATA
124827 ATTTATCTGTTATTTAATTTTT
1 ATTTATCTGTTATTT--TTTTT
*
124849 ATTTATCTATTATTTTTTTT
1 ATTTATCTGTTATTTTTTTT
*
124869 ATTTATCTGATTTATTTTCATTTG
1 ATTTATCTG--TTATTTT--TTTT
*
124893 ATTTAT-TTTTATTTTTT
1 ATTTATCTGTTATTTTTT
124910 ATTTTTTTTA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
19 2 0.04
20 13 0.25
21 7 0.13
22 21 0.40
23 1 0.02
24 9 0.17
ACGTcount: A:0.20, C:0.05, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTATCTGTTATTTTTTTT
Found at i:124896 original size:15 final size:15
Alignment explanation
Indices: 124876--124914 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
124866 TTTATTTATC
124876 TGATTTATTTTCATT
1 TGATTTATTTTCATT
*
124891 TGATTTATTTTTATT
1 TGATTTATTTTCATT
124906 T--TTTATTTT
1 TGATTTATTTT
124915 TTTTAATTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 8 0.35
15 15 0.65
ACGTcount: A:0.18, C:0.03, G:0.05, T:0.74
Consensus pattern (15 bp):
TGATTTATTTTCATT
Found at i:125180 original size:23 final size:24
Alignment explanation
Indices: 125149--125200 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
125139 AGGAATCGAA
* *
125149 AAAAAATTTT-TGGAGATTTTTGG
1 AAAAATTTTTCTGGAAATTTTTGG
125172 CAAAAATTTTTCTGGAAATTTTTGG
1 -AAAAATTTTTCTGGAAATTTTTGG
125197 AAAA
1 AAAA
125201 TTTCTAGATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 13 0.52
25 12 0.48
ACGTcount: A:0.38, C:0.04, G:0.17, T:0.40
Consensus pattern (24 bp):
AAAAATTTTTCTGGAAATTTTTGG
Found at i:125772 original size:5 final size:5
Alignment explanation
Indices: 125755--125849 Score: 83
Period size: 5 Copynumber: 18.8 Consensus size: 5
125745 TTTAATGTTC
*
125755 TTTTA TCTTTA TTTTA TTTTA TTTTTA TTTTA CTTTT- CTTTA TTTTA
1 TTTTA T-TTTA TTTTA TTTTA -TTTTA TTTTA -TTTTA TTTTA TTTTA
*
125802 TTTT- TATTT- TTTTA TTTTCA CTTTTA TTTTG TTTTA --TTA TTTTA
1 TTTTA T-TTTA TTTTA TTTT-A -TTTTA TTTTA TTTTA TTTTA TTTTA
125846 TTTT
1 TTTT
125850 CTTTAAATAA
Statistics
Matches: 76, Mismatches: 4, Indels: 20
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.04
4 7 0.09
5 46 0.61
6 16 0.21
7 4 0.05
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:125790 original size:26 final size:25
Alignment explanation
Indices: 125762--125849 Score: 103
Period size: 26 Copynumber: 3.5 Consensus size: 25
125752 TTCTTTTATC
125762 TTTATTTTATTTTATTTTTATTTTA
1 TTTATTTTATTTTATTTTTATTTTA
125787 CTTT-TCTTTATTTTATTTTTATTTT-
1 -TTTAT-TTTATTTTATTTTTATTTTA
*
125812 TTTATTTTCACTTTTA-TTTTGTTTTA
1 TTTATTTT-A-TTTTATTTTTATTTTA
125838 -TTATTTTATTTT
1 TTTATTTTATTTT
125850 CTTTAAATAA
Statistics
Matches: 56, Mismatches: 1, Indels: 13
0.80 0.01 0.19
Matches are distributed among these distances:
23 4 0.07
24 7 0.12
25 18 0.32
26 27 0.48
ACGTcount: A:0.16, C:0.05, G:0.01, T:0.78
Consensus pattern (25 bp):
TTTATTTTATTTTATTTTTATTTTA
Found at i:125828 original size:31 final size:29
Alignment explanation
Indices: 125761--125854 Score: 95
Period size: 31 Copynumber: 3.2 Consensus size: 29
125751 GTTCTTTTAT
*
125761 CTTTATTTTATTTTATTTTTATTTTACTTTT-
1 CTTTATTTTATTTT-TATTT-TTTTA-TTTTC
125792 CTTTATTTTATTTTTATTTTTTTATTTTC
1 CTTTATTTTATTTTTATTTTTTTATTTTC
* *
125821 ACTTTTATTTT-GTTTTATTATTTTATTTT-
1 -C-TTTATTTTATTTTTATTTTTTTATTTTC
125850 CTTTA
1 CTTTA
125855 AATAAAATCT
Statistics
Matches: 57, Mismatches: 3, Indels: 10
0.81 0.04 0.14
Matches are distributed among these distances:
27 4 0.07
28 5 0.09
29 5 0.09
30 21 0.37
31 22 0.39
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (29 bp):
CTTTATTTTATTTTTATTTTTTTATTTTC
Found at i:125839 original size:30 final size:31
Alignment explanation
Indices: 125766--125850 Score: 94
Period size: 30 Copynumber: 2.9 Consensus size: 31
125756 TTTATCTTTA
125766 TTTTATTTTA--TTT-TTATTTTACTTTT--C
1 TTTTATTTTAGTTTTATTATTTTA-TTTTCAC
* *
125793 -TTTATTTTATTTTTATTTTTTTATTTTCAC
1 TTTTATTTTAGTTTTATTATTTTATTTTCAC
125823 TTTTATTTT-GTTTTATTATTTTATTTTC
1 TTTTATTTTAGTTTTATTATTTTATTTTC
125851 TTTAAATAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
26 9 0.18
28 7 0.14
29 7 0.14
30 18 0.37
31 8 0.16
ACGTcount: A:0.15, C:0.06, G:0.01, T:0.78
Consensus pattern (31 bp):
TTTTATTTTAGTTTTATTATTTTATTTTCAC
Found at i:126018 original size:57 final size:58
Alignment explanation
Indices: 125867--126083 Score: 321
Period size: 59 Copynumber: 3.7 Consensus size: 58
125857 TAAAATCTAA
* * *
125867 AAAAAAACATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCAAAAATCAAAGTTTCT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAAT-AAAGTTT-T
* *
125927 AAAAAAATATTTTTG-GGAAAAGTTGAAAGAATCAATTTTCCTTAAAAATAAA-TTTT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTT
* * *
125983 CAAAAAAGGTTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTT
1 AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTT
126041 AAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
1 -AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
126084 CTGCACAAAA
Statistics
Matches: 145, Mismatches: 9, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
56 13 0.09
57 39 0.27
58 7 0.05
59 72 0.50
60 14 0.10
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.34
Consensus pattern (58 bp):
AAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAGTTTT
Found at i:127283 original size:30 final size:30
Alignment explanation
Indices: 127249--127310 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
127239 GTCAAAAAAG
* * *
127249 ATTCAACTGAAGGTGGGAGATTGCTTGCTA
1 ATTCAACTAAAGATGGGAGATTGCTTACTA
127279 ATTCAACTAAAGATGGGAGATTGCTTACTA
1 ATTCAACTAAAGATGGGAGATTGCTTACTA
127309 AT
1 AT
127311 CGGGTATGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.32, C:0.13, G:0.24, T:0.31
Consensus pattern (30 bp):
ATTCAACTAAAGATGGGAGATTGCTTACTA
Done.