Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168466.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_676, 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: 10311
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.44
Found at i:150 original size:9 final size:9
Alignment explanation
Indices: 107--156 Score: 57
Period size: 9 Copynumber: 5.7 Consensus size: 9
97 TTTATAATCT
107 TATTATAAA
1 TATTATAAA
*
116 TATTA-AGA
1 TATTATAAA
* *
124 GATTATAAT
1 TATTATAAA
*
133 TATTTTAAA
1 TATTATAAA
142 TATTATAAA
1 TATTATAAA
151 TATTAT
1 TATTAT
157 TATTTAATTA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
8 6 0.19
9 26 0.81
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (9 bp):
TATTATAAA
Found at i:258 original size:17 final size:15
Alignment explanation
Indices: 227--256 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
217 ATTTATTTAG
227 TTTATATTTTAATAA
1 TTTATATTTTAATAA
242 TTTATA-TTTAATAA
1 TTTATATTTTAATAA
256 T
1 T
257 AACTAATGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTATATTTTAATAA
Found at i:380 original size:13 final size:12
Alignment explanation
Indices: 363--434 Score: 67
Period size: 13 Copynumber: 5.9 Consensus size: 12
353 GATAATTATT
*
363 ATTTTTTTTTAA
1 ATTTTTTTTTTA
375 TATTTTTTTTTTA
1 -ATTTTTTTTTTA
* *
388 AATTTTATTTT-
1 ATTTTTTTTTTA
*
399 -TTTTTTATTTA
1 ATTTTTTTTTTA
410 ATTTTTTATTTTA
1 ATTTTTT-TTTTA
423 ATTTTTTATTTT
1 ATTTTTT-TTTT
435 TTAAAATAAT
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
10 7 0.14
12 15 0.31
13 27 0.55
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (12 bp):
ATTTTTTTTTTA
Found at i:411 original size:36 final size:35
Alignment explanation
Indices: 364--436 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
354 ATAATTATTA
*
364 TTTTTTTTTAATATTTTTTTTTTAA-ATTTTATTTT
1 TTTTTTTTTAAT-TTTTTATTTTAATATTTTATTTT
*
399 TTTTTTATTTAATTTTTTATTTTAATTTTTTATTTT
1 TTTTTT-TTTAATTTTTTATTTTAATATTTTATTTT
435 TT
1 TT
437 AAAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
35 17 0.50
36 17 0.50
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (35 bp):
TTTTTTTTTAATTTTTTATTTTAATATTTTATTTT
Found at i:494 original size:23 final size:23
Alignment explanation
Indices: 466--553 Score: 63
Period size: 23 Copynumber: 3.7 Consensus size: 23
456 AATTATTAAA
466 TAATTTTTAATATTTTAATTTAT
1 TAATTTTTAATATTTTAATTTAT
* *
489 TAATTTTATTTATATTTT-ATTAAT
1 TAA-TTT-TTAATATTTTAATTTAT
* * *
513 ATAATATTTAATA-ATTAATATTGT
1 -TAATTTTTAATATTTTAAT-TTAT
*
537 TAATTATTAATTATTTT
1 TAATTTTTAA-TATTTT
554 TAATATAATA
Statistics
Matches: 48, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
22 2 0.04
23 18 0.38
24 14 0.29
25 14 0.29
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (23 bp):
TAATTTTTAATATTTTAATTTAT
Found at i:521 original size:16 final size:15
Alignment explanation
Indices: 500--566 Score: 52
Period size: 15 Copynumber: 4.4 Consensus size: 15
490 AATTTTATTT
500 ATATTTTATTAATATA
1 ATATTTTATTAAT-TA
*
516 ATA-TTTAATAATTA
1 ATATTTTATTAATTA
530 ATATTGTTAATT-ATTA
1 ATATT-TT-ATTAATTA
546 AT-TATTT-TTAATATA
1 ATAT-TTTATTAAT-TA
561 ATATTT
1 ATATTT
567 ATAAGTAACT
Statistics
Matches: 42, Mismatches: 2, Indels: 15
0.71 0.03 0.25
Matches are distributed among these distances:
13 2 0.05
14 7 0.17
15 18 0.43
16 13 0.31
17 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (15 bp):
ATATTTTATTAATTA
Found at i:540 original size:48 final size:45
Alignment explanation
Indices: 474--567 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 45
464 AATAATTTTT
*
474 AATATTTTAATTTATTAATTTTATTTATATT-TTATTAATATAATATTT
1 AATATATTAATTTATTAA--TTA-TTA-ATTATTATTAATATAATATTT
* *
522 AATA-ATTAATATTGTTAATTATTAATTATTTTTAATATAATATTT
1 AATATATTAAT-TTATTAATTATTAATTATTATTAATATAATATTT
567 A
1 A
568 TAAGTAACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
44 3 0.07
45 20 0.49
46 3 0.07
47 5 0.12
48 10 0.24
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (45 bp):
AATATATTAATTTATTAATTATTAATTATTATTAATATAATATTT
Found at i:546 original size:7 final size:7
Alignment explanation
Indices: 441--551 Score: 54
Period size: 7 Copynumber: 16.1 Consensus size: 7
431 TTTTTTAAAA
*
441 TAATAAT
1 TAATTAT
448 TAATTAT
1 TAATTAT
455 TAATTAT
1 TAATTAT
462 TAA--A-
1 TAATTAT
*
466 TAATTTT
1 TAATTAT
*
473 TAATATTT
1 TAAT-TAT
481 TAATTTAT
1 TAA-TTAT
489 TAATT-T
1 TAATTAT
*
495 TATTTA-
1 TAATTAT
*
501 TATTTTAT
1 TA-ATTAT
*
509 TAATATAA
1 TAAT-TAT
* *
517 TATTTAA
1 TAATTAT
*
524 TAATTAA
1 TAATTAT
*
531 T-ATTGT
1 TAATTAT
537 TAATTAT
1 TAATTAT
544 TAATTAT
1 TAATTAT
551 T
1 T
552 TTTAATATAA
Statistics
Matches: 83, Mismatches: 11, Indels: 20
0.73 0.10 0.18
Matches are distributed among these distances:
4 3 0.04
5 1 0.01
6 11 0.13
7 49 0.59
8 18 0.22
9 1 0.01
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (7 bp):
TAATTAT
Found at i:557 original size:73 final size:73
Alignment explanation
Indices: 406--553 Score: 169
Period size: 73 Copynumber: 2.0 Consensus size: 73
396 TTTTTTTTTA
* * *
406 TTTAATTTTTTATTTTAATTTTTTATTTTTTAAAATAATAATTAATTATTAATTATTAAATAATT
1 TTTAATTTTTAATTTTAATTTTATATTTTTTAAAATAATAATTAATAATTAATTATTAAATAATT
*
471 TTTAATAT
66 ATTAATAT
* * **
479 TTTAATTTATTAATTTT-A-TTTATATTTTATTAATATAATATTTAATAATTAA-TATT-GTTAA
1 TTTAATTT-TTAATTTTAATTTTATATTTT-TTAAAATAATAATTAATAATTAATTATTAAATAA
540 TTATTAATTAT
64 TTATTAA-TAT
551 TTT
1 TTT
554 TAATATAATA
Statistics
Matches: 64, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
71 9 0.14
72 19 0.30
73 29 0.45
74 7 0.11
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (73 bp):
TTTAATTTTTAATTTTAATTTTATATTTTTTAAAATAATAATTAATAATTAATTATTAAATAATT
ATTAATAT
Found at i:824 original size:26 final size:24
Alignment explanation
Indices: 794--848 Score: 58
Period size: 26 Copynumber: 2.2 Consensus size: 24
784 ATATTATTGT
794 AATTAACTTA-TAATAAATTAATATA
1 AATT-ACTTACTAAT-AATTAATATA
*
819 CAATTATTTACTTAATAATTAATATA
1 -AATTACTTAC-TAATAATTAATATA
845 AATT
1 AATT
849 TATATTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
25 8 0.31
26 14 0.54
27 4 0.15
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (24 bp):
AATTACTTACTAATAATTAATATA
Found at i:1476 original size:18 final size:20
Alignment explanation
Indices: 1451--1501 Score: 65
Period size: 19 Copynumber: 2.7 Consensus size: 20
1441 TATTAGTAAT
1451 TTATTATTATAAATTAATA-
1 TTATTATTATAAATTAATAG
1470 TTA-TATTTATAAA-TAATAG
1 TTATTA-TTATAAATTAATAG
1489 TTATTATT-TAAAT
1 TTATTATTATAAAT
1502 ATTTATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
18 11 0.39
19 15 0.54
20 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTATTATTATAAATTAATAG
Found at i:1502 original size:18 final size:18
Alignment explanation
Indices: 1447--1502 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 18
1437 AATTTATTAG
1447 TAAT-TTATTATTATAAA
1 TAATATTATTATTATAAA
1464 TTAATATTA-TATTTATAAA
1 -TAATATTATTA-TTATAAA
1483 TAATAGTTATTATT-TAAA
1 TAATA-TTATTATTATAAA
1501 TA
1 TA
1503 TTTATTTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
18 17 0.50
19 15 0.44
20 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (18 bp):
TAATATTATTATTATAAA
Found at i:2985 original size:12 final size:13
Alignment explanation
Indices: 2970--2999 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
2960 TTAAATAACA
2970 ATATAAATTA-TT
1 ATATAAATTATTT
2982 ATATAAATTATTT
1 ATATAAATTATTT
2995 ATATA
1 ATATA
3000 TAAAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATAAATTATTT
Found at i:3073 original size:15 final size:15
Alignment explanation
Indices: 3055--3087 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
3045 AATATATAAA
*
3055 ATAAATTTATTTTAT
1 ATAAAATTATTTTAT
3070 ATAAAATTATTTTAT
1 ATAAAATTATTTTAT
3085 ATA
1 ATA
3088 TTATAACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAAATTATTTTAT
Found at i:3621 original size:21 final size:21
Alignment explanation
Indices: 3579--3622 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3569 AATAAATCAG
*
3579 TTTATCAAATTTTAATATTAT
1 TTTATCAAATTTTAATACTAT
*
3600 TTTAT-AAATTATTTATACTAT
1 TTTATCAAATT-TTAATACTAT
3621 TT
1 TT
3623 ATTATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (21 bp):
TTTATCAAATTTTAATACTAT
Found at i:3908 original size:16 final size:16
Alignment explanation
Indices: 3889--3927 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3879 AATTAATAAT
3889 ATAATTAATTTATATA
1 ATAATTAATTTATATA
*
3905 ATAATCAATTTATATA
1 ATAATTAATTTATATA
*
3921 ATTATTA
1 ATAATTA
3928 TGCAATAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (16 bp):
ATAATTAATTTATATA
Found at i:4098 original size:12 final size:12
Alignment explanation
Indices: 4081--4105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4071 TAAAATTATT
4081 AATATAATAATA
1 AATATAATAATA
4093 AATATAATAATA
1 AATATAATAATA
4105 A
1 A
4106 TTTAATTAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
AATATAATAATA
Found at i:4208 original size:29 final size:30
Alignment explanation
Indices: 4174--4235 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
4164 ATATACAACT
4174 TATAATCTATTCAATAAATATTAT-ATTAA
1 TATAATCTATTCAATAAATATTATAATTAA
* * * *
4203 TATAATTTATTTAATTATTATTATAATTAA
1 TATAATCTATTCAATAAATATTATAATTAA
4233 TAT
1 TAT
4236 TATTAATTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 20 0.71
30 8 0.29
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (30 bp):
TATAATCTATTCAATAAATATTATAATTAA
Found at i:4565 original size:27 final size:26
Alignment explanation
Indices: 4494--4565 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
4484 ATTAATAAAA
* *
4494 TATTAATTAAT-ATTTAATTGAGTTT
1 TATTAAATAATAATTTAATTGAGTAT
**
4519 TATTAAATTAATAAAATAATTGAGTAAAT
1 TATTAAA-TAATAATTTAATTGAGT--AT
4548 TATTAAA-AATAATTTAAT
1 TATTAAATAATAATTTAAT
4566 AATATTTATA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
25 6 0.16
26 4 0.11
27 19 0.51
29 8 0.22
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (26 bp):
TATTAAATAATAATTTAATTGAGTAT
Found at i:4578 original size:20 final size:17
Alignment explanation
Indices: 4556--4600 Score: 65
Period size: 17 Copynumber: 2.7 Consensus size: 17
4546 ATTATTAAAA
*
4556 ATAATTTAATAATATTT
1 ATAATATAATAATATTT
*
4573 ATAATATATTAATATTT
1 ATAATATAATAATATTT
4590 ATAAT-TAATAA
1 ATAATATAATAA
4601 ATAAATTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
16 5 0.20
17 20 0.80
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATATAATAATATTT
Found at i:4739 original size:15 final size:14
Alignment explanation
Indices: 4706--4747 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
4696 AATATTTTAA
*
4706 TATAAT-TATTATAT
1 TATAATATATT-TTT
4720 TATAATATTATTTTT
1 TATAATA-TATTTTT
4735 TATAATATATTTT
1 TATAATATATTTT
4748 AATAGTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 12 0.48
15 9 0.36
16 4 0.16
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TATAATATATTTTT
Found at i:4827 original size:50 final size:47
Alignment explanation
Indices: 4773--4866 Score: 118
Period size: 47 Copynumber: 1.9 Consensus size: 47
4763 TATTATTAAC
4773 AATTATTAATATT-ATAATTATAAATTTATAAGTAAATAATATTAATAAAT
1 AATTA-TAATATTAATAATTATAAA-TTATAA--AAATAATATTAATAAAT
** *
4823 AATTATAATATTAATTGTTATAAATTATTAAAATAATATTAATA
1 AATTATAATATTAATAATTATAAATTATAAAAATAATATTAATA
4867 TTAATATAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
47 14 0.35
49 12 0.30
50 14 0.35
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (47 bp):
AATTATAATATTAATAATTATAAATTATAAAAATAATATTAATAAAT
Found at i:4832 original size:19 final size:19
Alignment explanation
Indices: 4776--4837 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
4766 TATTAACAAT
*
4776 TATTAATATTATAATTATAA
1 TATTAATA-AATAATTATAA
* *
4796 -ATTTATAAGTAA--ATAA
1 TATTAATAAATAATTATAA
4812 TATTAATAAATAATTATAA
1 TATTAATAAATAATTATAA
4831 TATTAAT
1 TATTAAT
4838 TGTTATAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
16 4 0.12
17 10 0.29
18 3 0.09
19 17 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (19 bp):
TATTAATAAATAATTATAA
Found at i:4867 original size:6 final size:6
Alignment explanation
Indices: 4856--4900 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
4846 ATTATTAAAA
4856 TAATAT TAATAT TAATA- TAAT-T TAAGTAT TAATAT TAATTAT TAA
1 TAATAT TAATAT TAATAT TAATAT TAA-TAT TAATAT TAA-TAT TAA
4901 ATAACTTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
5 7 0.20
6 18 0.51
7 10 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (6 bp):
TAATAT
Found at i:4888 original size:17 final size:16
Alignment explanation
Indices: 4809--4895 Score: 61
Period size: 17 Copynumber: 5.0 Consensus size: 16
4799 TATAAGTAAA
4809 TAATATTAATAAATAATT
1 TAATATTAAT--ATAATT
*
4827 ATAATATTAAT-T-GTT
1 -TAATATTAATATAATT
*
4842 ATAAATTATTAAAATAATAT
1 -T-AA-TATTAATATAAT-T
4862 TAATATTAATATAATT
1 TAATATTAATATAATT
4878 TAAGTATTAATATTAATT
1 TAA-TATTAATA-TAATT
4896 ATTAAATAAC
Statistics
Matches: 57, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
15 4 0.07
16 7 0.12
17 25 0.44
18 8 0.14
19 12 0.21
20 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TAATATTAATATAATT
Found at i:4896 original size:47 final size:47
Alignment explanation
Indices: 4806--4901 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 47
4796 ATTTATAAGT
* *
4806 AAATAATATTAATAAATAATTATAATATTAATTGTTATAAATTATTA
1 AAATAATATTAATAAATAATTATAATATTAAGTATTATAAATTATTA
*
4853 AAATAATATTAAT-ATTAA-TATAAT-TTAAGTATTAATATTAATTATTA
1 AAATAATATTAATAAATAATTATAATATTAAGTATT-ATA--AATTATTA
4900 AA
1 AA
4902 TAACTTGATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
44 7 0.16
45 9 0.21
46 4 0.09
47 23 0.53
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (47 bp):
AAATAATATTAATAAATAATTATAATATTAAGTATTATAAATTATTA
Found at i:4950 original size:22 final size:21
Alignment explanation
Indices: 4923--4983 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
4913 TAAATTAATT
*
4923 AATAATTTTATAATTATTTCTA
1 AATAATTTTATAATT-TTTATA
**
4945 AATAATTAAATAAATTTTTATA
1 AATAATTTTAT-AATTTTTATA
*
4967 TATAATTATTATAATTT
1 AATAATT-TTATAATTT
4984 AAATATTTAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
22 25 0.81
23 6 0.19
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATAATTTTATAATTTTTATA
Found at i:6469 original size:22 final size:21
Alignment explanation
Indices: 6438--6486 Score: 62
Period size: 22 Copynumber: 2.3 Consensus size: 21
6428 ACAAAACTAT
6438 TTAATATATAATAATTATAATA
1 TTAATATATAATAATTA-AATA
* * *
6460 TTAATTTATAATTATTAACTA
1 TTAATATATAATAATTAAATA
6481 TTAATA
1 TTAATA
6487 ATGATAAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 8 0.35
22 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAATATATAATAATTAAATA
Found at i:6529 original size:18 final size:17
Alignment explanation
Indices: 6502--6536 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
6492 AAACATTTCA
6502 ATAATTATTATAATAAT
1 ATAATTATTATAATAAT
*
6519 ATAATTTATTATACTAAT
1 ATAA-TTATTATAATAAT
6537 TAAGTAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (17 bp):
ATAATTATTATAATAAT
Found at i:7178 original size:14 final size:14
Alignment explanation
Indices: 7159--7188 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
7149 CTTACTTTAA
*
7159 ATTATAGTAAATTT
1 ATTATACTAAATTT
7173 ATTATACTAAATTT
1 ATTATACTAAATTT
7187 AT
1 AT
7189 AATCTCTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.50
Consensus pattern (14 bp):
ATTATACTAAATTT
Found at i:7743 original size:13 final size:13
Alignment explanation
Indices: 7725--7749 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
7715 ATACTTTATT
7725 AATAATTAGATTA
1 AATAATTAGATTA
7738 AATAATTAGATT
1 AATAATTAGATT
7750 TATTGTATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (13 bp):
AATAATTAGATTA
Found at i:9020 original size:31 final size:31
Alignment explanation
Indices: 8985--9049 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
8975 ATCTTTTTAC
*
8985 TTATTAATT-TTGGAATATTAATTAATTAGAA
1 TTATTAATTATTAGAAT-TTAATTAATTAGAA
* *
9016 TTATTAATTATTATAATTTAATTAATTATAA
1 TTATTAATTATTAGAATTTAATTAATTAGAA
9047 TTA
1 TTA
9050 AAAATGAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 25 0.83
32 5 0.17
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (31 bp):
TTATTAATTATTAGAATTTAATTAATTAGAA
Found at i:9050 original size:14 final size:13
Alignment explanation
Indices: 9003--9050 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
8993 TTTGGAATAT
**
9003 TAATTAATTAGAA
1 TAATTAATTATTA
*
9016 TTATTAATTATTA
1 TAATTAATTATTA
9029 TAATTTAATTAATTA
1 TAA-TTAATT-ATTA
9044 TAATTAA
1 TAATTAA
9051 AAATGAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 12 0.41
14 10 0.34
15 7 0.24
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (13 bp):
TAATTAATTATTA
Found at i:9446 original size:22 final size:22
Alignment explanation
Indices: 9420--9463 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
9410 TGTATATTTA
* *
9420 TATTTGTATCTCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
9442 TATTTATATCCCTAGAATTAAG
1 TATTTATATCCCTAGAATTAAG
9464 GTCAAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.11, G:0.11, T:0.43
Consensus pattern (22 bp):
TATTTATATCCCTAGAATTAAG
Found at i:9791 original size:24 final size:23
Alignment explanation
Indices: 9744--9790 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
9734 CTCTCATACC
9744 ATGTGGAAAAACTAAGAAATAAA
1 ATGTGGAAAAACTAAGAAATAAA
*
9767 ATGTGTGAAAAACTAA-AAGTAAA
1 ATGTG-GAAAAACTAAGAAATAAA
9790 A
1 A
9791 ACTAAATGTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.60, C:0.04, G:0.17, T:0.19
Consensus pattern (23 bp):
ATGTGGAAAAACTAAGAAATAAA
Found at i:10050 original size:24 final size:24
Alignment explanation
Indices: 10023--10070 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
10013 ATCTCATACC
10023 ATGT-GGAAAAACTAAGAAATAAAA
1 ATGTAGGAAAAACTAA-AAATAAAA
* *
10047 ATGTATGAAAAACTAAAAGTAAAA
1 ATGTAGGAAAAACTAAAAATAAAA
10071 CTAAATGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 11 0.52
25 10 0.48
ACGTcount: A:0.62, C:0.04, G:0.15, T:0.19
Consensus pattern (24 bp):
ATGTAGGAAAAACTAAAAATAAAA
Found at i:10084 original size:279 final size:279
Alignment explanation
Indices: 9567--10310 Score: 1316
Period size: 279 Copynumber: 2.7 Consensus size: 279
9557 ACCTAAGGTA
* * *
9567 CTTGTATACTAAACTTATTAAATTATTAATATTAAAATAAAAATTAAATAATTTTTAGATATAAT
1 CTTGTATAATAAAGTTATTAAATTATTAATATTAAAATAAAAATTAAATAATTTTTTGATATAAT
* * ** *
9632 ATTAGTTATTTAAACTTTTAATAGGCCCC-ATCATGTGTAGGTGAAGAGGAAAGAAGCCTT-CAC
66 ATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCAT
** * *
9695 ATGACAAATTAGGAAAGGGCAACAGAAAGAAAGTCCTAGCTCTCATACCATGTGGAAAAACTAAG
131 ATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAAAACTAAG
* *
9760 AAATAAAATGTGTGAAAAACTAAAAGTAAAAACTAAATGTATATTGAAAAATTGCTCATAAAGAA
196 AAATAAAATGTATGAAAAACTAAAAGTAAAAACTAAATGTATATTGAAAAACTGCTCATAAAGAA
9825 TTATACAAGCAATTATGTG
261 TTATACAAGCAATTATGTG
9844 CTTGTATAATAAAGTTATTAAATTATTAATATTAAAATAAAAATTAAATAATTTTTTGATATAAT
1 CTTGTATAATAAAGTTATTAAATTATTAATATTAAAATAAAAATTAAATAATTTTTTGATATAAT
9909 ATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCAT
66 ATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCAT
9974 ATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAAAACTAAG
131 ATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAAAACTAAG
10039 AAATAAAAATGTATGAAAAACTAAAAGT-AAAACTAAATGTATATTGAAAAACTGCTCATAAAGA
196 AAAT-AAAATGTATGAAAAACTAAAAGTAAAAACTAAATGTATATTGAAAAACTGCTCATAAAGA
10103 ATTATACAAGCAATTATGTG
260 ATTATACAAGCAATTATGTG
10123 CTTGTATAATAAAGTTATTAAATTATT-ATATTAAAATAAAAAATTAAATAATTTTTTGATATAA
1 CTTGTATAATAAAGTTATTAAATTATTAATATTAAAAT-AAAAATTAAATAATTTTTTGATATAA
10187 TATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCA
65 TATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCA
10252 TATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAA
130 TATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAA
10311 C
Statistics
Matches: 449, Mismatches: 14, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
277 90 0.20
278 38 0.08
279 299 0.67
280 22 0.05
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.30
Consensus pattern (279 bp):
CTTGTATAATAAAGTTATTAAATTATTAATATTAAAATAAAAATTAAATAATTTTTTGATATAAT
ATTAGTTATTTAAACTTTTAACAGGCCCCTATTACATGTAGGTGAAGAGGAAAGAAGCCTTCCAT
ATGACAAATTAGGAAAGGGCAATGGAAAGAAAGTCCTGGATCTCATACCATGTGGAAAAACTAAG
AAATAAAATGTATGAAAAACTAAAAGTAAAAACTAAATGTATATTGAAAAACTGCTCATAAAGAA
TTATACAAGCAATTATGTG
Done.