Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168094.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_340, 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: 33156
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:731 original size:56 final size:57
Alignment explanation
Indices: 644--949 Score: 275
Period size: 56 Copynumber: 5.4 Consensus size: 57
634 TTTTGTGCAG
* * * * *
644 GGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAATTTTA-TCTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAACATTTTTTAGAAAATTTATTTTCAA
*
700 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCATTTTTTTA-AAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAA-CA-TTTTTTAGAAAATTTATTTTCAA
* * * * ** * *
759 GGAACATTGAT--TTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCTC-AAAACATTTTTTAGAAAATTTATTTTCAA
* * ** * * *
815 GGAAAATTGATACTTTTAGCTTTTCCTCAAAA-ACCTTCTAAAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAACATTTTTTAGAAAATTTATTTTCAA
* *** *
871 GAAAAATTGATACTTTCAACTTTTCCTCAAAACATTTGAAAAAAAAATTT-TTTT-AA
1 GGAAAATTGATACTTTCAACTTTTCCTCAAAACATTT-TTTAGAAAATTTATTTTCAA
*
927 GGGAAATTGATACTTTCAACTTT
1 GGAAAATTGATACTTTCAACTTT
950 CCCTAAACTG
Statistics
Matches: 202, Mismatches: 39, Indels: 18
0.78 0.15 0.07
Matches are distributed among these distances:
55 6 0.03
56 114 0.56
57 33 0.16
58 29 0.14
59 20 0.10
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.41
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCTCAAAACATTTTTTAGAAAATTTATTTTCAA
Found at i:3041 original size:1 final size:1
Alignment explanation
Indices: 3035--3092 Score: 53
Period size: 1 Copynumber: 58.0 Consensus size: 1
3025 TAGAGGCAAC
* * * * * * *
3035 TTTTTTTTGTTTTTTATTTTTTTTGTTTTTTTGTTTTATTGTTTTTTTTTGTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3093 ATCAAAGCTC
Statistics
Matches: 43, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 43 1.00
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.88
Consensus pattern (1 bp):
T
Found at i:3049 original size:8 final size:8
Alignment explanation
Indices: 3036--3092 Score: 71
Period size: 8 Copynumber: 6.9 Consensus size: 8
3026 AGAGGCAACT
3036 TTTTTTTG
1 TTTTTTTG
3044 TTTTTTAT-
1 TTTTTT-TG
3052 TTTTTTTG
1 TTTTTTTG
3060 TTTTTTTG
1 TTTTTTTG
*
3068 TTTTATTGTT
1 TTTT-TT-TG
3078 TTTTTTTG
1 TTTTTTTG
3086 TTTTTTT
1 TTTTTTT
3093 ATCAAAGCTC
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
7 1 0.02
8 32 0.74
9 5 0.12
10 5 0.12
ACGTcount: A:0.04, C:0.00, G:0.09, T:0.88
Consensus pattern (8 bp):
TTTTTTTG
Found at i:3198 original size:42 final size:42
Alignment explanation
Indices: 3099--3272 Score: 298
Period size: 42 Copynumber: 4.2 Consensus size: 42
3089 TTTTATCAAA
* *
3099 GCTCCTCTAAACAGAGGCTCAACGACTTTG-GAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
*
3140 GCTCCTCTAAATAGAGGCACCACGACTTTGA-AAAGTAAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGT-AAATT
3182 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
3224 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
3266 GCTCCTC
1 GCTCCTC
3273 GACTTTGAGA
Statistics
Matches: 126, Mismatches: 4, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
41 32 0.25
42 89 0.71
43 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (42 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATT
Found at i:3275 original size:26 final size:26
Alignment explanation
Indices: 3246--3298 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
3236 AGAGGCACCA
3246 CGACTTTGAGAAAGTAAATTGCTCCT
1 CGACTTTGAGAAAGTAAATTGCTCCT
3272 CGACTTTGAGAAAGTAAATTGCTCCT
1 CGACTTTGAGAAAGTAAATTGCTCCT
3298 C
1 C
3299 TAAACAGAGG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
CGACTTTGAGAAAGTAAATTGCTCCT
Found at i:3313 original size:68 final size:68
Alignment explanation
Indices: 3204--3340 Score: 265
Period size: 68 Copynumber: 2.0 Consensus size: 68
3194 AGAGGCACCA
*
3204 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCT
1 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
3269 CCT
66 CCT
3272 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
1 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
3337 CCT
66 CCT
3340 C
1 C
3341 TAAACAGAGG
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (68 bp):
CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
CCT
Found at i:3355 original size:110 final size:109
Alignment explanation
Indices: 3162--3377 Score: 398
Period size: 110 Copynumber: 2.0 Consensus size: 109
3152 AGAGGCACCA
*
3162 CGACTTTGAAAAGTAAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCT
1 CGACTTTGAAAAGTAAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
3227 CCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCT
66 CCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATTGCTCCT
3272 CGACTTTGAGAAAGT-AAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGC
1 CGACTTTGA-AAAGTAAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGC
3336 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCT
65 TCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCT
3378 TCTCTAAACA
Statistics
Matches: 104, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
109 14 0.13
110 85 0.82
111 5 0.05
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.24
Consensus pattern (109 bp):
CGACTTTGAAAAGTAAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGTAAATTGCT
CCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCT
Found at i:3383 original size:41 final size:42
Alignment explanation
Indices: 3272--3421 Score: 266
Period size: 42 Copynumber: 3.6 Consensus size: 42
3262 AATTGCTCCT
3272 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
*
3314 CGACTTTGAAAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
1 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
*
3356 CGACTTTG-GAAAGTAAATTGCTTCTCTAAACAGAGGCACCA
1 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
3397 CGACTTTTGAGAAAGTAAATTGCTC
1 CGAC-TTTGAGAAAGTAAATTGCTC
3422 TTTGACAATC
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
41 35 0.34
42 53 0.52
43 14 0.14
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (42 bp):
CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCA
Found at i:3406 original size:152 final size:151
Alignment explanation
Indices: 3121--3421 Score: 543
Period size: 152 Copynumber: 2.0 Consensus size: 151
3111 AGAGGCTCAA
*
3121 CGACTTTGGAAAGTAAATTGCTCCTCTAAATAGAGGCACCACGACTTTGAAAAGTAAAATTGCTC
1 CGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAAATTGCTC
3186 CTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACT
66 CTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACT
3251 TTGAGAAAGTAAATTGCTCCT
131 TTGAGAAAGTAAATTGCTCCT
3272 CGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAAGT-AAATTGC
1 CGACTTTG-GAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAAATTGC
*
3336 TCCTCTAAACAGAGGCACCACGACTTTG-GAAAGTAAATTGCTTCTCTAAACAGAGGCACCACGA
64 TCCTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGA
3400 CTTTTGAGAAAGTAAATTGCTC
129 C-TTTGAGAAAGTAAATTGCTC
3422 TTTGACAATC
Statistics
Matches: 145, Mismatches: 2, Indels: 5
0.95 0.01 0.03
Matches are distributed among these distances:
151 44 0.30
152 95 0.66
153 6 0.04
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (151 bp):
CGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAAATTGCTC
CTCTAAACAGAGGCACCACGACTTTGAGAAAGTAAATTGCTCCTCTAAACAGAGGCACCACGACT
TTGAGAAAGTAAATTGCTCCT
Found at i:4670 original size:21 final size:21
Alignment explanation
Indices: 4646--4686 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
4636 TCTTTTTTAT
4646 TTTCTCATTTTTTTCTTTTTC
1 TTTCTCATTTTTTTCTTTTTC
** *
4667 TTTCTTTTTTTTTTTTTTTT
1 TTTCTCATTTTTTTCTTTTT
4687 TTTTTTTTAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.85
Consensus pattern (21 bp):
TTTCTCATTTTTTTCTTTTTC
Found at i:4673 original size:33 final size:35
Alignment explanation
Indices: 4636--4723 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 35
4626 AATTTGAATC
4636 TCTTTTTTATTTTCTCATTTTTTTCTTTT-TC-T-T
1 TCTTTTTT-TTTTCTCATTTTTTTCTTTTATCATCT
* *
4669 TCTTTTTTTTTT-T-TTTTTTTTTTTTTATCATCT
1 TCTTTTTTTTTTCTCATTTTTTTCTTTTATCATCT
*
4702 TCTTTTCTTTTTACTCATTTTT
1 TCTTTT-TTTTTTCTCATTTTT
4724 CATCCATTGT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
30 11 0.24
31 3 0.07
32 5 0.11
33 15 0.33
34 5 0.11
35 1 0.02
36 5 0.11
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.80
Consensus pattern (35 bp):
TCTTTTTTTTTTCTCATTTTTTTCTTTTATCATCT
Found at i:4713 original size:1 final size:1
Alignment explanation
Indices: 4653--4694 Score: 57
Period size: 1 Copynumber: 42.0 Consensus size: 1
4643 TATTTTCTCA
* * *
4653 TTTTTTTCTTTTTCTTTCTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
4695 ATCATCTTCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:8976 original size:9 final size:10
Alignment explanation
Indices: 8962--8987 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
8952 ATTTAACATT
8962 AAAAAAATAA
1 AAAAAAATAA
8972 AAAAAAATAA
1 AAAAAAATAA
8982 AAAAAA
1 AAAAAA
8988 GAAGAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:9196 original size:118 final size:117
Alignment explanation
Indices: 9016--9265 Score: 364
Period size: 118 Copynumber: 2.2 Consensus size: 117
9006 TTTTATGCAG
**
9016 GGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAATTTTAATCTCGAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAACCTTAATCTCGAGGAAAATT
9081 GATACTTTCAACTTTTCCTCAAAAACCTTTTTTTAAAAAAATTTATTTTTAA
66 GATACTTTCAACTTTTCCTCAAAAACCTTTTTTTAAAAAAATTTATTTTTAA
* * *
9133 GGAACATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTAATTTCGAGGAAAAT
1 GGAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTAGAAACCTTAATCTCGAGGAAAAT
* * * *
9198 TGATACTTTCAGCTTTTCCTCAAAAACC---TTCT-AAAAATTTTTTTTTTAA
65 TGATACTTTCAACTTTTCCTCAAAAACCTTTTTTTAAAAAAATTTATTTTTAA
* *
9247 GGGAAATTAATACTTTCAA
1 GGAAAATTGATACTTTCAA
9266 ATTGTTTGTT
Statistics
Matches: 120, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
114 31 0.26
115 3 0.03
117 27 0.22
118 59 0.49
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTAGAAACCTTAATCTCGAGGAAAATT
GATACTTTCAACTTTTCCTCAAAAACCTTTTTTTAAAAAAATTTATTTTTAA
Found at i:9203 original size:58 final size:58
Alignment explanation
Indices: 9016--9223 Score: 258
Period size: 58 Copynumber: 3.6 Consensus size: 58
9006 TTTTATGCAG
* *
9016 GGAAAATTGATACTTTCAACTTTTCCCC-AAAATATTTTTTAGAAATTTTAATCTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAAAATTTAATTTCGA
* * * **
9073 GGAAAATTGATACTTTCAACTTTTCCTCAAAAACCT-TTTTTTAAAAAAATTTATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA--TATTTTTT-AGAAAATTTAATTTCGA
* * **
9133 GGAACATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAACCTTAATTTCGA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAAAATTTAATTTCGA
* *
9191 GGAAAATTGATACTTTCAGCTTTTCCTCAAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAA
9224 CCTTCTAAAA
Statistics
Matches: 127, Mismatches: 19, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
57 27 0.21
58 45 0.35
59 12 0.09
60 43 0.34
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.39
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTAGAAAATTTAATTTCGA
Found at i:11590 original size:54 final size:55
Alignment explanation
Indices: 11489--11597 Score: 148
Period size: 55 Copynumber: 2.0 Consensus size: 55
11479 CACATCAATA
* * * * *
11489 GTAATAATTATCTTTATTAAATTAATGTCCACATTGCAAAATATAAAAATTTAAG
1 GTAAAAATTATCTTTATTAAATCAATATACACATTACAAAATATAAAAATTTAAG
* *
11544 GTAAAAATTATTTTTGTTAAATCAATATACA-ATTACAAAATATAAAAATTTAAG
1 GTAAAAATTATCTTTATTAAATCAATATACACATTACAAAATATAAAAATTTAAG
11598 TTGAGTTGTT
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
54 22 0.47
55 25 0.53
ACGTcount: A:0.49, C:0.07, G:0.06, T:0.38
Consensus pattern (55 bp):
GTAAAAATTATCTTTATTAAATCAATATACACATTACAAAATATAAAAATTTAAG
Found at i:16427 original size:15 final size:17
Alignment explanation
Indices: 16414--16447 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
16404 CTTTTTCTTC
16414 TTTTTTTCTTTCTTACA
1 TTTTTTTCTTTCTTACA
*
16431 TTTTTTTTCTTTATTAC
1 -TTTTTTTCTTTCTTAC
16448 GGTGGGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.12, C:0.15, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTTTTTCTTTCTTACA
Found at i:16768 original size:21 final size:21
Alignment explanation
Indices: 16705--16770 Score: 59
Period size: 17 Copynumber: 3.3 Consensus size: 21
16695 ATAATTACGG
*
16705 TTTTTTACTATTAGATTACGAT
1 TTTTTTA-TATTAGACTACGAT
* **
16727 TTTTTTA-A--A-AGTAATAT
1 TTTTTTATATTAGACTACGAT
16744 TTTTTTATATTAGACTACGAT
1 TTTTTTATATTAGACTACGAT
16765 TTTTTT
1 TTTTTT
16771 TTTCTAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
17 12 0.35
18 2 0.06
20 2 0.06
21 11 0.32
22 7 0.21
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.58
Consensus pattern (21 bp):
TTTTTTATATTAGACTACGAT
Found at i:16912 original size:19 final size:19
Alignment explanation
Indices: 16890--16926 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
16880 ACTTGTAATC
*
16890 TTTTTAATATTAAACTATA
1 TTTTTAATACTAAACTATA
*
16909 TTTTTCATACTAAACTAT
1 TTTTTAATACTAAACTAT
16927 TATATATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (19 bp):
TTTTTAATACTAAACTATA
Found at i:17238 original size:32 final size:31
Alignment explanation
Indices: 17202--17270 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
17192 ATCAAATTAT
17202 TTAAAAAATAAGAATAA-AATTA-ATTAAATGAA
1 TTAAAAAATAA-AA-AATAATTATATTAAAT-AA
* *
17234 TTAAATAATAAAAAATAATTATTTTAAATAA
1 TTAAAAAATAAAAAATAATTATATTAAATAA
17265 TTAAAA
1 TTAAAA
17271 TTTTTTTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
30 2 0.06
31 14 0.44
32 16 0.50
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (31 bp):
TTAAAAAATAAAAAATAATTATATTAAATAA
Found at i:17292 original size:29 final size:30
Alignment explanation
Indices: 17249--17314 Score: 118
Period size: 29 Copynumber: 2.3 Consensus size: 30
17239 TAATAAAAAA
17249 TAAT-TATTTTAAATAATTAAAATTTTTTT
1 TAATATATTTTAAATAATTAAAATTTTTTT
17278 TAATATATTTT-AATAATTAAAATTTTTTT
1 TAATATATTTTAAATAATTAAAATTTTTTT
17307 TAATATAT
1 TAATATAT
17315 ATACAAAAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 30 0.83
30 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TAATATATTTTAAATAATTAAAATTTTTTT
Found at i:22640 original size:21 final size:18
Alignment explanation
Indices: 22602--22637 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22592 TATATGATAG
22602 ATTTTTAAAAATTTATTA
1 ATTTTTAAAAATTTATTA
* *
22620 ATTTTTATAAATATATTA
1 ATTTTTAAAAATTTATTA
22638 TTATAAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAAAATTTATTA
Found at i:23735 original size:21 final size:19
Alignment explanation
Indices: 23711--23749 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
23701 TAAAATCAAT
23711 AATTTGATTATAAATTTTTAG
1 AATTT-ATT-TAAATTTTTAG
*
23732 AATTTATTTATATTTTTA
1 AATTTATTTAAATTTTTA
23750 AAATCGATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
AATTTATTTAAATTTTTAG
Found at i:25785 original size:14 final size:15
Alignment explanation
Indices: 25747--25787 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
25737 ATGAATAAAA
25747 ATTTATATAATTATAT
1 ATTTATA-AATTATAT
*
25763 ATTTA-AAATTGT-T
1 ATTTATAAATTATAT
25776 ATTTATAAATTA
1 ATTTATAAATTA
25788 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
13 6 0.27
14 10 0.45
15 1 0.05
16 5 0.23
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATAAATTATAT
Found at i:28965 original size:144 final size:144
Alignment explanation
Indices: 28756--29501 Score: 1077
Period size: 144 Copynumber: 5.2 Consensus size: 144
28746 ACTATCTACG
* * * ***
28756 TGGTTCTATCCCTGCTTCCGTAGGAAACTTGACCTA-CTTATCTGTTCTCCACCTCTATCAAAAT
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACC-AGTTTATCCACTCTCCACCTCTATCAAAAT
* * * *
28820 ATGTTTTGTGGATCGATACCTCAAGAAATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAT
65 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
*
28885 TCATAATAATTTCTC
130 TCAAAATAATTTCTC
* * * *
28900 TGGTTCAATTCCTGCTTCCATAAGAAACTTGACCAGTTTATCCACTCTCCACCT-TCACCATAAT
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTTTATCCACTCTCCACCTCT-ATCAAAAT
*
28964 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTTAG
65 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
*
29029 TCATAATAATTTCTC
130 TCAAAATAATTTCTC
* * * *
29044 TGGTTCAGTCCCTGCTTCCATAAGAAACTTGACCAGTTTATCCAGTCTCCACCT-TCATCATAAT
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTTTATCCACTCTCCACCTCT-ATCAAAAT
* *
29108 ATGTTTTCTGGGTCGTTACCTCAAGAGATAAGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
65 ATGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAG
*
29173 CCAAAATAATTTCTC
130 TCAAAATAATTTCTC
** *** * *
29188 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAACTTATCTTTTCTCTACCTCTACCAAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTTTATCCACTCTCCACCTCTATCAAAATA
* *
29253 TGTTTTCTGGATCGATACCTCAAGAGATAGGCATGCTTAAATCTCTCACTGA-TATTGAGTTGAG
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACT-TTGAGTTGAG
*
29317 TCAAAATAATTTCTT
130 TCAAAATAATTTCTC
* ** *
29332 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTCTATCCACTCTTTACCTCGATCAAAATA
1 TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTTTATCCACTCTCCACCTCTATCAAAATA
*
29397 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGGGTTGAGT
66 TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
29462 CAAAATAATTTCTC
131 CAAAATAATTTCTC
29476 TGGTTCAATCCCTGCTTCCATAGGAA
1 TGGTTCAATCCCTGCTTCCATAGGAA
29502 GCATGTCGAA
Statistics
Matches: 544, Mismatches: 53, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
143 3 0.01
144 539 0.99
145 2 0.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.35
Consensus pattern (144 bp):
TGGTTCAATCCCTGCTTCCATAGGAAACTTGACCAGTTTATCCACTCTCCACCTCTATCAAAATA
TGTTTTCTGGGTCGATACCTCAAGAGATAGGGATGCTTAAATCTCTCACTGACTTTGAGTTGAGT
CAAAATAATTTCTC
Found at i:31939 original size:11 final size:11
Alignment explanation
Indices: 31923--32061 Score: 63
Period size: 11 Copynumber: 12.3 Consensus size: 11
31913 TTTAAAGAAT
31923 AATAAATAAAA
1 AATAAATAAAA
31934 AATAAATAAAA
1 AATAAATAAAA
* *
31945 AACAAA-GAAA
1 AATAAATAAAA
* ***
31955 AGTAACGCAAA
1 AATAAATAAAA
31966 AATAAA-AATAA
1 AATAAATAA-AA
*
31977 GATAAAGATAAAA
1 AAT-AA-ATAAAA
*
31990 AAT-ATTAAATA
1 AATAAATAAA-A
* *
32001 AATATAATCTAAT
1 AATA-AAT-AAAA
32014 AA-AAATAATAA
1 AATAAATAA-AA
32025 AAT-AATAAACA
1 AATAAATAAA-A
*
32036 AATAAACAAATA
1 AATAAATAAA-A
32048 AATAAATAAAA
1 AATAAATAAAA
32059 AAT
1 AAT
32062 TCCAAAAAAA
Statistics
Matches: 95, Mismatches: 20, Indels: 26
0.67 0.14 0.18
Matches are distributed among these distances:
10 13 0.14
11 51 0.54
12 18 0.19
13 9 0.09
14 4 0.04
ACGTcount: A:0.73, C:0.04, G:0.04, T:0.19
Consensus pattern (11 bp):
AATAAATAAAA
Found at i:32039 original size:16 final size:16
Alignment explanation
Indices: 32010--32058 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
32000 AAATATAATC
32010 TAATAAAAATAATAAAA
1 TAATAAAAA-AATAAAA
*
32027 TAATAAACAAATAAACA
1 TAATAAAAAAATAAA-A
*
32044 -AATAAATAAATAAAA
1 TAATAAAAAAATAAAA
32059 AATTCCAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 1 0.03
16 19 0.66
17 9 0.31
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (16 bp):
TAATAAAAAAATAAAA
Found at i:32220 original size:22 final size:23
Alignment explanation
Indices: 32177--32220 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
32167 GGGGCAGGGC
32177 ACGCGCGGGTCAGGATCGGGTCG
1 ACGCGCGGGTCAGGATCGGGTCG
* *
32200 ACGCTCGGGTC-GGGTCGGGTC
1 ACGCGCGGGTCAGGATCGGGTC
32221 ACGGTAAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.09, C:0.27, G:0.48, T:0.16
Consensus pattern (23 bp):
ACGCGCGGGTCAGGATCGGGTCG
Found at i:32601 original size:25 final size:24
Alignment explanation
Indices: 32570--32629 Score: 75
Period size: 25 Copynumber: 2.4 Consensus size: 24
32560 CAGAATCTGG
*
32570 AAATTTTTCTCAGAAATTTCCAGAA
1 AAATTTTTCTCAAAAATTTCCA-AA
* *
32595 AAATTTTTCACCAAAAATTTCTAAA
1 AAATTTTTC-TCAAAAATTTCCAAA
32620 AAATTTTTCT
1 AAATTTTTCT
32630 TACTCCCAGA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 20 0.67
26 10 0.33
ACGTcount: A:0.42, C:0.15, G:0.03, T:0.40
Consensus pattern (24 bp):
AAATTTTTCTCAAAAATTTCCAAA
Found at i:33108 original size:4 final size:4
Alignment explanation
Indices: 33071--33121 Score: 50
Period size: 4 Copynumber: 12.2 Consensus size: 4
33061 ATATAACTAT
* *
33071 ATAA ATAA ATACA TATAA TATTA ATAG A-AA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATA-A -ATAA -ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
33121 A
1 A
33122 GATATACATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 2 0.05
4 29 0.73
5 6 0.15
6 3 0.08
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:33150 original size:46 final size:47
Alignment explanation
Indices: 33037--33150 Score: 115
Period size: 46 Copynumber: 2.4 Consensus size: 47
33027 AGAAAAAATA
* * * * * *
33037 ATAATAATAAAAATAATAATATATATATAACTATATAAATAAATACAT
1 ATAATAAT-AATATAATAATAAATAAATAAATAAATAAAGAAATACAT
* * *
33085 ATAATATTAATAGAA-AATAAATAAATAAATAAATAAAGATATACAT
1 ATAATAATAATATAATAATAAATAAATAAATAAATAAAGAAATACAT
*
33131 ATATTAAT-ATATAATAATAA
1 ATAATAATAATATAATAATAA
33151 TTAATA
Statistics
Matches: 53, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
45 5 0.09
46 36 0.68
47 5 0.09
48 7 0.13
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (47 bp):
ATAATAATAATATAATAATAAATAAATAAATAAATAAAGAAATACAT
Done.