Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168431.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_644, 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: 20823
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Found at i:514 original size:22 final size:20
Alignment explanation
Indices: 489--531 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
479 TAATATAACA
489 TTATAGAAATATTATAATATAT
1 TTATAGAAATA-T-TAATATAT
**
511 TTATATTAATATTAATATAT
1 TTATAGAAATATTAATATAT
531 T
1 T
532 ATAATTAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTATAGAAATATTAATATAT
Found at i:528 original size:20 final size:20
Alignment explanation
Indices: 503--541 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
493 AGAAATATTA
503 TAATATATT-TATATTAATAT
1 TAATATATTATA-ATTAATAT
523 TAATATATTATAATTAATA
1 TAATATATTATAATTAATA
542 AAATTATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (20 bp):
TAATATATTATAATTAATAT
Found at i:529 original size:14 final size:14
Alignment explanation
Indices: 497--573 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 14
487 CATTATAGAA
*
497 ATATTATAATATATTT
1 ATATTATAAT-TA-AT
513 ATATTA-ATATTAAT
1 ATATTATA-ATTAAT
527 ATATTATAATTAAT
1 ATATTATAATTAAT
*
541 AAAATTATTAATATTAA-
1 -ATATTA-T-A-ATTAAT
558 AT-TTATAATTAAT
1 ATATTATAATTAAT
571 ATA
1 ATA
574 AATTAACAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
12 5 0.10
13 3 0.06
14 14 0.28
15 12 0.24
16 10 0.20
17 1 0.02
18 5 0.10
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATATTATAATTAAT
Found at i:555 original size:32 final size:31
Alignment explanation
Indices: 514--578 Score: 105
Period size: 30 Copynumber: 2.1 Consensus size: 31
504 AATATATTTA
514 TATTAATATTAATATATTATAATTAATA-AAAT
1 TATTAATATTAA-AT-TTATAATTAATATAAAT
546 TATTAATATTAAATTTATAATTAATATAAAT
1 TATTAATATTAAATTTATAATTAATATAAAT
577 TA
1 TA
579 ACAAATATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 12 0.38
31 8 0.25
32 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (31 bp):
TATTAATATTAAATTTATAATTAATATAAAT
Found at i:568 original size:18 final size:16
Alignment explanation
Indices: 509--577 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 16
499 ATTATAATAT
509 ATTTATATTAATATTAA
1 ATTTATATTAATA-TAA
526 TATATTATAATTAATA-AA
1 -AT-TTAT-ATTAATATAA
544 A--T-TATTAATATTAA
1 ATTTATATTAATA-TAA
558 ATTTATAATTAATATAA
1 ATTTAT-ATTAATATAA
575 ATT
1 ATT
578 AACAAATATT
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
12 7 0.16
13 1 0.02
14 4 0.09
16 1 0.02
17 8 0.19
18 11 0.26
19 4 0.09
20 7 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
ATTTATATTAATATAA
Found at i:586 original size:32 final size:32
Alignment explanation
Indices: 518--587 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
508 TATTTATATT
**
518 AATATTAATATATTATAATTAATAAAATTATT
1 AATATTAATATATTATAATTAATAAAATTACA
550 AATATTAA-AT-TTATAATTAATATAAATTAACA
1 AATATTAATATATTATAATTAATA-AAATT-ACA
582 AATATT
1 AATATT
588 TTTATTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
30 12 0.35
31 7 0.21
32 15 0.44
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (32 bp):
AATATTAATATATTATAATTAATAAAATTACA
Found at i:876 original size:17 final size:16
Alignment explanation
Indices: 856--894 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
846 AATCTTATTA
856 TATTAGTAATATATAAT
1 TATTAGTAATA-ATAAT
*
873 TATTATTAATAATAAT
1 TATTAGTAATAATAAT
889 TCATTA
1 T-ATTA
895 ATATACTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (16 bp):
TATTAGTAATAATAAT
Found at i:975 original size:16 final size:16
Alignment explanation
Indices: 963--996 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
953 ACAATAATTT
963 TAATAATATATAATAA
1 TAATAATATATAATAA
*
979 TAATAATATTTAATAA
1 TAATAATATATAATAA
995 TA
1 TA
997 TTTAATCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATATATAATAA
Found at i:2288 original size:73 final size:73
Alignment explanation
Indices: 2161--2307 Score: 210
Period size: 73 Copynumber: 2.0 Consensus size: 73
2151 TTTTTGGAAC
* * *
2161 ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAGAACCAATTGTTTTATGAC
1 ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAAAAACAATTGCTTTATGAC
2226 AAAACAAA
66 AAAACAAA
*
2234 ATTAATAAA-TTAGTATTATTTTATTTCG-AATAAGCTTGTATG-ATAAAAAACAATTGCTTTAT
1 ATTAATAAATTTA-TATTATTTTATTT-GAAATAAGCTTGAATGAAT-AAAAACAATTGCTTTAT
2296 GACAAAACAAA
63 GACAAAACAAA
2307 A
1 A
2308 GGTTATTTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
72 5 0.07
73 61 0.91
74 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (73 bp):
ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAAAAACAATTGCTTTATGAC
AAAACAAA
Found at i:2442 original size:28 final size:28
Alignment explanation
Indices: 2387--2443 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
2377 ATAAACTATT
* *
2387 TTTAAATTTATATATTAATAATAGTTTA
1 TTTAAATTTAAATATTAATAATAATTTA
*
2415 TTTAATATTTAAATATT-ATATTAATTTA
1 TTTAA-ATTTAAATATTAATAATAATTTA
2443 T
1 T
2444 AAATATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 15 0.60
29 10 0.40
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTTAAATTTAAATATTAATAATAATTTA
Found at i:2446 original size:19 final size:18
Alignment explanation
Indices: 2412--2451 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2402 TAATAATAGT
2412 TTATTTAATATTTAAATA
1 TTATTTAATATTTAAATA
2430 TTATATTAAT-TTATAAATA
1 TTAT-TTAATATT-TAAATA
2449 TTA
1 TTA
2452 ATAACTAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
TTATTTAATATTTAAATA
Found at i:2855 original size:27 final size:27
Alignment explanation
Indices: 2823--2874 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2813 GTAATTTTAA
2823 TAATTATT-TATAAATTAATTAAATATT
1 TAATTATTAT-TAAATTAATTAAATATT
* *
2850 TAATTATTATTTAATTAATTTAATA
1 TAATTATTATTAAATTAATTAAATA
2875 ATTGTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATTATTATTAAATTAATTAAATATT
Found at i:2856 original size:23 final size:23
Alignment explanation
Indices: 2821--2867 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
2811 TCGTAATTTT
*
2821 AATAATTATTTATAAATTAATTA
1 AATAATTAATTATAAATTAATTA
* * *
2844 AATATTTAATTATTATTTAATTA
1 AATAATTAATTATAAATTAATTA
2867 A
1 A
2868 TTTAATAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAATTAATTATAAATTAATTA
Found at i:3046 original size:23 final size:23
Alignment explanation
Indices: 3017--3107 Score: 91
Period size: 23 Copynumber: 4.0 Consensus size: 23
3007 ATAAATTAAT
*
3017 TTAAATATATAAATTATTAATTA
1 TTAAATATATAATTTATTAATTA
* *
3040 TTAAATATTTAATTTATTAATGA
1 TTAAATATATAATTTATTAATTA
3063 TT--ATAT-TAATTTATTAA-TA
1 TTAAATATATAATTTATTAATTA
*
3082 TTAATAAATATATATTTATTGAATTA
1 TTAA-ATATATA-ATTTATT-AATTA
3108 ATTGATATAA
Statistics
Matches: 56, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
19 3 0.05
20 11 0.20
21 4 0.07
22 3 0.05
23 24 0.43
24 7 0.12
25 2 0.04
26 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAAATATATAATTTATTAATTA
Found at i:3058 original size:16 final size:16
Alignment explanation
Indices: 3033--3083 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
3023 ATATAAATTA
3033 TTAA-TTATTAAATAT
1 TTAATTTATTAAATAT
3048 TTAATTTATTAATGATTAT
1 TTAATTTATTAA--A-TAT
3067 ATTAATTTATT-AATAT
1 -TTAATTTATTAAATAT
3083 T
1 T
3084 AATAAATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.16
16 10 0.32
17 1 0.03
18 1 0.03
19 4 0.13
20 10 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTAATTTATTAAATAT
Found at i:3073 original size:20 final size:19
Alignment explanation
Indices: 2983--3084 Score: 76
Period size: 19 Copynumber: 5.5 Consensus size: 19
2973 ACTGTATTAT
2983 TTAAT-TTATATTAATTTA
1 TTAATATTATATTAATTTA
* *
3001 GCTAATA-TAAATTAATTTA
1 -TTAATATTATATTAATTTA
3020 --AATA-TATA--AA-TTA
1 TTAATATTATATTAATTTA
3033 TTAATTATTAAATATTTAATTTA
1 TTAA-TATT--ATA-TTAATTTA
3056 TTAATGATTATATTAATTTA
1 TTAAT-ATTATATTAATTTA
3076 TTAATATTA
1 TTAATATTA
3085 ATAAATATAT
Statistics
Matches: 68, Mismatches: 3, Indels: 24
0.72 0.03 0.25
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 2 0.03
16 9 0.13
17 1 0.01
19 22 0.32
20 13 0.19
21 3 0.04
22 3 0.04
23 10 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATATTATATTAATTTA
Found at i:4613 original size:19 final size:19
Alignment explanation
Indices: 4577--4616 Score: 64
Period size: 19 Copynumber: 2.1 Consensus size: 19
4567 TTATAATAAT
4577 ATTTAATAATATTAATTTA
1 ATTTAATAATATTAATTTA
4596 ATTTAATTAATATT-ATTTA
1 ATTTAA-TAATATTAATTTA
4615 AT
1 AT
4617 CTTCATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTAATAATATTAATTTA
Found at i:4727 original size:19 final size:19
Alignment explanation
Indices: 4705--4745 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
4695 ATAATTTTCA
* *
4705 AAATATTATTAACTATTTT
1 AAATAATATTAACTATTAT
*
4724 AAATAATATTTACTATTAT
1 AAATAATATTAACTATTAT
4743 AAA
1 AAA
4746 CAACAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (19 bp):
AAATAATATTAACTATTAT
Found at i:5029 original size:17 final size:18
Alignment explanation
Indices: 4987--5029 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
4977 TAATAGTTGA
4987 TATTAATAAATATCAAAT
1 TATTAATAAATATCAAAT
5005 TATT-ATAAATATC-AAT
1 TATTAATAAATATCAAAT
5021 TATTAATAA
1 TATTAATAA
5030 TAGGAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.29
17 13 0.54
18 4 0.17
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (18 bp):
TATTAATAAATATCAAAT
Found at i:5619 original size:19 final size:16
Alignment explanation
Indices: 5586--5624 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
5576 AATATTAATC
5586 ATTATAATTAAATATT
1 ATTATAATTAAATATT
*
5602 ATTATTAATTAATTA-T
1 ATTA-TAATTAAATATT
5618 ATTATAA
1 ATTATAA
5625 ATAGTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATAATTAAATATT
Found at i:7325 original size:13 final size:13
Alignment explanation
Indices: 7299--7345 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
7289 TAATATATAT
7299 TATATTAATAATTAA
1 TATATT-AT-ATTAA
7314 TATATTATATTAA
1 TATATTATATTAA
*
7327 TTTATTATA-TAA
1 TATATTATATTAA
*
7339 TAAATTA
1 TATATTA
7346 AAAAATATCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
12 8 0.28
13 13 0.45
14 2 0.07
15 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TATATTATATTAA
Found at i:7336 original size:20 final size:20
Alignment explanation
Indices: 7287--7337 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
7277 TTTTTGCTAT
*
7287 TTTAATATATATTATATTAA
1 TTTATTATATATTATATTAA
*
7307 -TAATTAATATATTATATTAA
1 TTTATT-ATATATTATATTAA
7327 TTTATTATATA
1 TTTATTATATA
7338 ATAAATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
21 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTATTATATATTATATTAA
Found at i:7926 original size:11 final size:11
Alignment explanation
Indices: 7910--7941 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
7900 GTTTTGAAAA
7910 TAATTATAAAT
1 TAATTATAAAT
7921 TAATTATAAAT
1 TAATTATAAAT
7932 T-ATTATAAAT
1 TAATTATAAAT
7942 AATAATAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:7949 original size:10 final size:10
Alignment explanation
Indices: 7907--7949 Score: 59
Period size: 10 Copynumber: 4.2 Consensus size: 10
7897 TAGGTTTTGA
7907 AAATAATTAT
1 AAATAATTAT
7917 AAATTAATTAT
1 AAA-TAATTAT
*
7928 AAATTATTAT
1 AAATAATTAT
*
7938 AAATAATAAT
1 AAATAATTAT
7948 AA
1 AA
7950 GCTTTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (10 bp):
AAATAATTAT
Found at i:8148 original size:17 final size:19
Alignment explanation
Indices: 8126--8161 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
8116 AATTCCAATA
8126 ATATG-ATTAATAA-ATTT
1 ATATGAATTAATAATATTT
8143 ATATGAATTAATAATATTT
1 ATATGAATTAATAATATTT
8162 TACGTAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 8 0.47
19 4 0.24
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (19 bp):
ATATGAATTAATAATATTT
Found at i:8290 original size:16 final size:15
Alignment explanation
Indices: 8265--8302 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 15
8255 TTTTAAATCC
8265 TTATATATATAATTA
1 TTATATATATAATTA
8280 TTATA-ATAT-ATTA
1 TTATATATATAATTA
*
8293 TTATAAATAT
1 TTATATATAT
8303 TGTATAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 9 0.41
14 8 0.36
15 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TTATATATATAATTA
Found at i:8297 original size:28 final size:28
Alignment explanation
Indices: 8265--8368 Score: 74
Period size: 28 Copynumber: 3.7 Consensus size: 28
8255 TTTTAAATCC
8265 TTATATATATAATTATTATAATATATTA
1 TTATATATATAATTATTATAATATATTA
* * *
8293 TTATAAATATTGTATAATT-TAATAT-TTA
1 TTATATATA-T-AATTATTATAATATATTA
8321 TTATATA-ATAA-TATTACTAA-ATTATTTA
1 TTATATATATAATTATTA-TAATA-TA-TTA
* *
8349 TAATATAAATAATTAATTAT
1 TTATATATATAATT-ATTAT
8369 GTACTTGGGA
Statistics
Matches: 59, Mismatches: 7, Indels: 18
0.70 0.08 0.21
Matches are distributed among these distances:
24 3 0.05
25 2 0.03
26 5 0.08
27 1 0.02
28 26 0.44
29 11 0.19
30 7 0.12
31 4 0.07
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (28 bp):
TTATATATATAATTATTATAATATATTA
Found at i:9319 original size:10 final size:9
Alignment explanation
Indices: 9302--9378 Score: 66
Period size: 9 Copynumber: 8.0 Consensus size: 9
9292 AAATTGATAT
9302 AATT-ATTA
1 AATTAATTA
9310 AATTAAATTA
1 AATT-AATTA
9320 AATTAATTA
1 AATTAATTA
9329 TAATATAATTA
1 -AAT-TAATTA
9340 ATATTAATTA
1 A-ATTAATTA
9350 ATTATTAATTA
1 A--ATTAATTA
* *
9361 GATTTATTA
1 AATTAATTA
*
9370 TATTAATTA
1 AATTAATTA
9379 TAATATAATA
Statistics
Matches: 59, Mismatches: 4, Indels: 11
0.80 0.05 0.15
Matches are distributed among these distances:
8 4 0.07
9 19 0.32
10 19 0.32
11 17 0.29
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (9 bp):
AATTAATTA
Found at i:9391 original size:32 final size:29
Alignment explanation
Indices: 9334--9404 Score: 79
Period size: 32 Copynumber: 2.3 Consensus size: 29
9324 AATTATAATA
*
9334 TAATTAATATTAATTAATTATTAATTAGAT
1 TAATT-ATATTAATTAATTAATAATTAGAT
* *
9364 TTATTATATTAATTATAATATAATAATTATAT
1 TAATTATATTAA-T-TAAT-TAATAATTAGAT
9396 TAATTATAT
1 TAATTATAT
9405 GCTCTTATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
29 7 0.21
30 5 0.15
31 4 0.12
32 18 0.53
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (29 bp):
TAATTATATTAATTAATTAATAATTAGAT
Found at i:9397 original size:5 final size:5
Alignment explanation
Indices: 9305--9404 Score: 52
Period size: 5 Copynumber: 20.6 Consensus size: 5
9295 TTGATATAAT
* * * *
9305 TATTA AATTA AATTA AATTA -ATTA TAATA TAATTAA TATTA -ATTA -ATTA
1 TATTA TATTA TATTA TATTA TATTA TATTA T-ATT-A TATTA TATTA TATTA
* * *
9354 TTAATTA GATT- TATTA TATTA -ATTA TAATA TAATA -ATTA TATTA -ATTA
1 -T-ATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA TATTA
9402 TAT
1 TAT
9405 GCTCTTATTA
Statistics
Matches: 78, Mismatches: 7, Indels: 20
0.74 0.07 0.19
Matches are distributed among these distances:
4 26 0.33
5 41 0.53
6 5 0.06
7 6 0.08
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (5 bp):
TATTA
Found at i:9404 original size:9 final size:9
Alignment explanation
Indices: 9315--9404 Score: 71
Period size: 9 Copynumber: 9.9 Consensus size: 9
9305 TATTAAATTA
*
9315 AATTAAATT
1 AATTATATT
9324 AATTATAATAT
1 AATTAT-AT-T
9335 AATTAATATT
1 AATT-ATATT
9345 AATTAATTATT
1 AATT-A-TATT
*
9356 AATTAGATT
1 AATTATATT
*
9365 TATTATATT
1 AATTATATT
9374 AA-T-TA-T
1 AATTATATT
*
9380 AA-TATAAT
1 AATTATATT
9388 AATTATATT
1 AATTATATT
9397 AATTATAT
1 AATTATAT
9405 GCTCTTATTA
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
6 4 0.06
7 4 0.06
8 4 0.06
9 29 0.43
10 10 0.15
11 15 0.22
12 2 0.03
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (9 bp):
AATTATATT
Found at i:9612 original size:18 final size:17
Alignment explanation
Indices: 9565--9622 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
9555 ATATAATTTT
*
9565 TATTAATATTAATAAC-A
1 TATTAATATT-TTAACTA
9582 TATTAATATTTTATACTA
1 TATTAATATTTTA-ACTA
*
9600 TATTAAT-TATTTAATTA
1 TATTAATAT-TTTAACTA
9617 TATTAA
1 TATTAA
9623 ATTAAAATAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
16 2 0.06
17 22 0.61
18 12 0.33
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATTAATATTTTAACTA
Found at i:9792 original size:17 final size:17
Alignment explanation
Indices: 9772--9804 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
9762 ATAATTAATT
9772 AATAATATTA-ATAAATA
1 AATAAT-TTATATAAATA
9789 AATAATTTATATAAAT
1 AATAATTTATATAAAT
9805 TATTTGATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AATAATTTATATAAATA
Found at i:10800 original size:28 final size:25
Alignment explanation
Indices: 10750--10816 Score: 66
Period size: 27 Copynumber: 2.6 Consensus size: 25
10740 AAATTATCAT
10750 AATAA-TATTAATTAAATTATTAAACA
1 AATAATTA-TAATTAAATTATT-AACA
*
10776 AATAATTTTATAATTAAA-TATTTAATA
1 AATAA--TTATAATTAAATTA-TTAACA
10803 AATAATTATAATTA
1 AATAATTATAATTA
10817 TTTTTATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
25 9 0.25
26 5 0.14
27 10 0.28
28 10 0.28
29 2 0.06
ACGTcount: A:0.55, C:0.01, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAATTATAATTAAATTATTAACA
Found at i:10802 original size:23 final size:23
Alignment explanation
Indices: 10776--10840 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 23
10766 TTATTAAACA
10776 AATAATTTTATAATTAAATATTT
1 AATAATTTTATAATTAAATATTT
* *
10799 AATAAATAATTATAATT--ATTTTT
1 AAT-AAT-TTTATAATTAAATATTT
10822 ATATTAATTTTATAATTAA
1 A-A-TAATTTTATAATTAA
10841 TTTATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
23 17 0.52
24 7 0.21
25 9 0.27
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATTTTATAATTAAATATTT
Found at i:10831 original size:12 final size:13
Alignment explanation
Indices: 10781--10843 Score: 53
Period size: 12 Copynumber: 5.2 Consensus size: 13
10771 AAACAAATAA
*
10781 TTTTATAATTAAA
1 TTTTATAATTAAT
* *
10794 TATT-TAATAAAT
1 TTTTATAATTAAT
**
10806 AATTATAATT-AT
1 TTTTATAATTAAT
10818 TTTTAT-ATTAA-
1 TTTTATAATTAAT
10829 TTTTATAATTAAT
1 TTTTATAATTAAT
10842 TT
1 TT
10844 ATAATAAGAT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
11 9 0.23
12 21 0.54
13 9 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TTTTATAATTAAT
Found at i:10832 original size:11 final size:12
Alignment explanation
Indices: 10778--10848 Score: 69
Period size: 11 Copynumber: 6.0 Consensus size: 12
10768 ATTAAACAAA
10778 TAATTTTATAAT
1 TAATTTTATAAT
*
10790 TAAATATTTAATAAA
1 T-AAT-TTT-ATAAT
10805 TAA--TTATAAT
1 TAATTTTATAAT
*
10815 TATTTTTAT-AT
1 TAATTTTATAAT
10826 TAATTTTATAAT
1 TAATTTTATAAT
10838 TAA-TTTATAAT
1 TAATTTTATAAT
10849 AAGATTATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
10 6 0.12
11 20 0.41
12 10 0.20
13 3 0.06
14 5 0.10
15 5 0.10
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TAATTTTATAAT
Found at i:10856 original size:22 final size:22
Alignment explanation
Indices: 10807--10869 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 22
10797 TTAATAAATA
* * *
10807 ATTATAATTATTTTTATATTAAT
1 ATTATAATTA-ATTTATAATAAG
*
10830 TTTATAATTAATTTATAATAAG
1 ATTATAATTAATTTATAATAAG
10852 ATTATAA--AA-TTATAATAA
1 ATTATAATTAATTTATAATAA
10870 TTTATATAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 9 0.26
20 2 0.06
22 15 0.43
23 9 0.26
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATTATAATTAATTTATAATAAG
Found at i:10864 original size:19 final size:19
Alignment explanation
Indices: 10842--10886 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10832 TATAATTAAT
10842 TTATAATAAGATTATA-AAA
1 TTATAATAA-ATTATATAAA
*
10861 TTATAATAATTTATATAAA
1 TTATAATAAATTATATAAA
10880 TTA-AATA
1 TTATAATA
10887 TAATAAATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
TTATAATAAATTATATAAA
Found at i:11028 original size:30 final size:30
Alignment explanation
Indices: 10994--11053 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
10984 CTATTATTAC
* * *
10994 TTAATATTATA-AATTAAGTTATATAATTTA
1 TTAATAATATATAAGTAAATTATAT-ATTTA
11024 TTAATAATATATAAGTAAATTATATATTTA
1 TTAATAATATATAAGTAAATTATATATTTA
11054 GAACTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (30 bp):
TTAATAATATATAAGTAAATTATATATTTA
Found at i:12420 original size:19 final size:18
Alignment explanation
Indices: 12389--12426 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
12379 CTGTTTAAAT
12389 TAATCTATTTATTATGTAA
1 TAATCTATTTATTAT-TAA
12408 TAAT-TATTATATTATTAA
1 TAATCTATT-TATTATTAA
12426 T
1 T
12427 TTTATAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (18 bp):
TAATCTATTTATTATTAA
Found at i:13043 original size:14 final size:15
Alignment explanation
Indices: 13026--13060 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
13016 ATAAATAATT
13026 TAATATTATT-TAAA
1 TAATATTATTCTAAA
*
13040 TAATAATATTCTAAA
1 TAATATTATTCTAAA
13055 TAATAT
1 TAATAT
13061 AAATAAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
TAATATTATTCTAAA
Found at i:13168 original size:18 final size:19
Alignment explanation
Indices: 13141--13190 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 19
13131 GAACAAGTTC
*
13141 AAATAGTTATGACTATTT-
1 AAATAATTATGACTATTTA
*
13159 CAATAATTAT--CTATTTA
1 AAATAATTATGACTATTTA
*
13176 AAATCATTATGACTA
1 AAATAATTATGACTA
13191 GTTATTTTGT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
16 6 0.24
17 8 0.32
18 8 0.32
19 3 0.12
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (19 bp):
AAATAATTATGACTATTTA
Found at i:13582 original size:13 final size:13
Alignment explanation
Indices: 13564--13597 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
13554 TAGTTCATAA
13564 ATTATTAAAAATT
1 ATTATTAAAAATT
*
13577 ATTATTAACAATT
1 ATTATTAAAAATT
13590 ATTTATTA
1 A-TTATTA
13598 GTATTATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (13 bp):
ATTATTAAAAATT
Found at i:13799 original size:11 final size:11
Alignment explanation
Indices: 13783--13809 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
13773 TATTAGTATA
13783 ATTAAATAATT
1 ATTAAATAATT
13794 ATTAAATAATT
1 ATTAAATAATT
13805 ATTAA
1 ATTAA
13810 TGCTAATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
ATTAAATAATT
Found at i:13980 original size:30 final size:30
Alignment explanation
Indices: 13934--14006 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
13924 ATTTAAAATG
13934 ATAATTTTAAAATAATTAATAA-ATTATTATCA
1 ATAATTTT--AATAATT-ATAATATTATTATCA
* *
13966 ATAATTTTAATAATTATAATATTTTTATTA
1 ATAATTTTAATAATTATAATATTATTATCA
13996 A-AATTATTAAT
1 ATAATT-TTAAT
14007 CTTATATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
29 8 0.22
30 21 0.57
32 8 0.22
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAATTTTAATAATTATAATATTATTATCA
Found at i:14373 original size:47 final size:47
Alignment explanation
Indices: 14322--14465 Score: 108
Period size: 47 Copynumber: 3.1 Consensus size: 47
14312 AACAAATATT
14322 TTTATAATTATTATTAAATATATATTAATTTTAAATATTAAATCTAA
1 TTTATAATTATTATTAAATATATATTAATTTTAAATATTAAATCTAA
* * *
14369 TTTAT--TTATATAATTAAA-ATA-ATTGTTATAATTAAATAAT-AATCTAA
1 TTTATAATTAT-T-ATTAAATATATA-T-TAAT-TTTAAATATTAAATCTAA
* * *
14416 -TTA-AATTATAATATAAATAT-T-TAAATTTTAAATATTAAAACTAA
1 TTTATAATTATTAT-TAAATATATATTAATTTTAAATATTAAATCTAA
*
14460 TATATA
1 TTTATA
14466 TTGTTTTAAT
Statistics
Matches: 74, Mismatches: 10, Indels: 27
0.67 0.09 0.24
Matches are distributed among these distances:
43 8 0.11
44 8 0.11
45 10 0.14
46 13 0.18
47 27 0.36
48 8 0.11
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (47 bp):
TTTATAATTATTATTAAATATATATTAATTTTAAATATTAAATCTAA
Found at i:14418 original size:16 final size:16
Alignment explanation
Indices: 14397--14427 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
14387 ATAATTGTTA
14397 TAATTAAATAATAATC
1 TAATTAAATAATAATC
*
14413 TAATTAAATTATAAT
1 TAATTAAATAATAAT
14428 ATAAATATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATTAAATAATAATC
Found at i:15031 original size:18 final size:18
Alignment explanation
Indices: 14988--15031 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
14978 AGGTTGAGGA
*
14988 AAATTATATTATTATAAT
1 AAATTATATAATTATAAT
* * *
15006 ATAGTATATAATTATTAT
1 AAATTATATAATTATAAT
15024 AAATTATA
1 AAATTATA
15032 ATTAATAAAT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
AAATTATATAATTATAAT
Found at i:15155 original size:19 final size:20
Alignment explanation
Indices: 15127--15165 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
15117 CAATATCTGC
15127 TTCAAGTTA-TTATATATTTA
1 TTCAAGTTATTTATA-ATTTA
15147 TTCAA-TTATTTATAATTTA
1 TTCAAGTTATTTATAATTTA
15166 ATATTTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.36, C:0.05, G:0.03, T:0.56
Consensus pattern (20 bp):
TTCAAGTTATTTATAATTTA
Found at i:16070 original size:181 final size:180
Alignment explanation
Indices: 15668--16163 Score: 464
Period size: 181 Copynumber: 2.8 Consensus size: 180
15658 CAATAAACAA
* *
15668 ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
1 ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAATATTATTTTATTC
** * * *
15733 CAAACAAGCTTGTACGAACAAAACAATTGTTTTATGTTAAAAGAAAAGGTCATAACGATTTGAAA
66 CAAACAAAATAGTACGAACAAAACAATTGTTTGATGATAAAAGAAAAGGTCATAACGATTTGAAA
* * ** * *
15798 TAGATAATCATTCATAGAGTCTTAACTATTTGAACTGGTTCAACAATTAG
131 TAAATAATCATTCAAAGAGTCAAAACTATTTGAAATGGTTCAACAACTAG
* * ** *
15848 ATTTATTTTTTAATTTTCTTGGTTATTAAGTTTT-GAAATATTATTAAATTAATATTATTTTATT
1 ATTTATTTTTTAAATCTCTTACTTATTAA-TTTTCAAAATATTATTAAATTAATATTATTTTATT
* * * * * * *
15912 CTAAATAAAATAGTATGAACAGAACCAATTGTTTGATGATAAAATAAAAGGTTATATCGATTTGA
65 CCAAACAAAATAGTACGAACA-AAACAATTGTTTGATGATAAAAGAAAAGGTCATAACGATTTGA
* * * ****
15977 AATAAATAATTATTGAAATAGTCAAAACTATTTGAAATGGTTTGGTAAGCT-G
129 AATAAATAATCATTCAAAGAGTCAAAACTATTTGAAATGGTTCAACAA-CTAG
** * * * **
16029 ATTT-TCTTTTTAAATCTCTTACAGATTTATTTTCTAAATATTAATAAAACAATATTATTTTATT
1 ATTTAT-TTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAATATTATTTTATT
* * ** * * * * *
16093 TCAAACAAACTTA-TATTAACAAAAACAATTGTTTTATGA-CAAA-CAAAGGTAATAACGATTTA
65 CCAAACAAA-ATAGTACGAAC-AAAACAATTGTTTGATGATAAAAGAAAAGGTCATAACGATTTG
16155 AAATAAATA
128 AAATAAATA
16164 TTGTTCAAAT
Statistics
Matches: 254, Mismatches: 55, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
179 24 0.09
180 75 0.30
181 151 0.59
182 4 0.02
ACGTcount: A:0.41, C:0.09, G:0.09, T:0.41
Consensus pattern (180 bp):
ATTTATTTTTTAAATCTCTTACTTATTAATTTTCAAAATATTATTAAATTAATATTATTTTATTC
CAAACAAAATAGTACGAACAAAACAATTGTTTGATGATAAAAGAAAAGGTCATAACGATTTGAAA
TAAATAATCATTCAAAGAGTCAAAACTATTTGAAATGGTTCAACAACTAG
Found at i:16695 original size:12 final size:12
Alignment explanation
Indices: 16665--16738 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
16655 TTAATGTTGT
16665 ATTAA-ATAA-A
1 ATTAATATAATA
16675 ATTAATATAATA
1 ATTAATATAATA
*
16687 ATTATTATAATA
1 ATTAATATAATA
* *
16699 AATAATATTAT-
1 ATTAATATAATA
**
16710 ATTGTTATAATA
1 ATTAATATAATA
* *
16722 AATAATAATTATA
1 ATTAAT-ATAATA
16735 ATTA
1 ATTA
16739 TTTTCATAAA
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
10 5 0.11
11 11 0.23
12 23 0.49
13 8 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (12 bp):
ATTAATATAATA
Found at i:16699 original size:15 final size:15
Alignment explanation
Indices: 16677--16710 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
16667 TAAATAAAAT
16677 TAATATAATAATTATTA
1 TAATA-AATAA-TATTA
16694 TAATAAATAATATTA
1 TAATAAATAATATTA
16709 TA
1 TA
16711 TTGTTATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 5 0.29
17 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
TAATAAATAATATTA
Found at i:16755 original size:17 final size:17
Alignment explanation
Indices: 16733--16775 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
16723 ATAATAATTA
*
16733 TAATTATTTTCATAAAT
1 TAATTATTTTAATAAAT
* *
16750 TAATTAATTTAATTAAT
1 TAATTATTTTAATAAAT
16767 TAATATATT
1 TAAT-TATT
16776 ACAAATATTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATTTTAATAAAT
Found at i:17176 original size:16 final size:16
Alignment explanation
Indices: 17155--17185 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17145 ATCATTAATT
*
17155 TTATAATATTAATTAA
1 TTATAAAATTAATTAA
17171 TTATAAAATTAATTA
1 TTATAAAATTAATTA
17186 TAATAATTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTATAAAATTAATTAA
Found at i:17182 original size:12 final size:13
Alignment explanation
Indices: 17164--17194 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
17154 TTTATAATAT
17164 TAATTAATTATAA
1 TAATTAATTATAA
17177 -AATTAATTATAA
1 TAATTAATTATAA
17189 TAATTA
1 TAATTA
17195 TATTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TAATTAATTATAA
Found at i:17210 original size:25 final size:24
Alignment explanation
Indices: 17149--17216 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
17139 TAATTTATCA
* *
17149 TTAATTT-TATAATATTAATTAAT
1 TTAATTTATATTATAATAATTAAT
*
17172 TATAAAATTA-ATTATAATAATTATAT
1 T-T-AATTTATATTATAATAATTA-AT
*
17198 TTAATTTATATTATTATAA
1 TTAATTTATATTATAATAA
17217 GATATTAGTA
Statistics
Matches: 35, Mismatches: 5, Indels: 8
0.73 0.10 0.17
Matches are distributed among these distances:
23 1 0.03
24 6 0.17
25 25 0.71
26 3 0.09
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (24 bp):
TTAATTTATATTATAATAATTAAT
Found at i:17453 original size:11 final size:11
Alignment explanation
Indices: 17439--17476 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
17429 AATTATTTGT
17439 ATATTATTATA
1 ATATTATTATA
17450 ATATTATTATA
1 ATATTATTATA
17461 AT-TTA-TATA
1 ATATTATTATA
*
17470 CTATTAT
1 ATATTAT
17477 AACTTTTTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
9 5 0.21
10 6 0.25
11 13 0.54
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
ATATTATTATA
Found at i:17474 original size:28 final size:29
Alignment explanation
Indices: 17423--17478 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 29
17413 AATTTAAATA
* * *
17423 ATTATTAATTATTTGTATATTATTATAAT
1 ATTATTAATAATTTATATACTATTATAAT
17452 ATTATT-ATAATTTATATACTATTATAA
1 ATTATTAATAATTTATATACTATTATAA
17479 CTTTTTCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (29 bp):
ATTATTAATAATTTATATACTATTATAAT
Found at i:17771 original size:16 final size:17
Alignment explanation
Indices: 17740--17773 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
17730 ATAAATTAAT
17740 TAATTATTAATATATTA
1 TAATTATTAATATATTA
*
17757 TAATTA-TACTATATTA
1 TAATTATTAATATATTA
17773 T
1 T
17774 TTATTATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TAATTATTAATATATTA
Found at i:18115 original size:21 final size:23
Alignment explanation
Indices: 18077--18118 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
18067 ATTTAATATT
18077 ATTTTTTGAATATATTAATAAGA
1 ATTTTTTGAATATATTAATAAGA
*
18100 ATTTTTT-AAT-TTTTAATAA
1 ATTTTTTGAATATATTAATAA
18119 CAAAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 3 0.17
23 7 0.39
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
ATTTTTTGAATATATTAATAAGA
Found at i:18314 original size:23 final size:23
Alignment explanation
Indices: 18283--18419 Score: 65
Period size: 23 Copynumber: 5.8 Consensus size: 23
18273 ATATTAATAA
*
18283 ATAATTTATTATATTTAATTTAT
1 ATAAATTATTATATTTAATTTAT
18306 ATAAATTATTATAATTTTATAATCTTATT
1 ATAAATTATTAT-A--TT-TAAT-TTA-T
*
18335 ATAAATTAATTATA--AAATTAATAT
1 ATAAATT-ATTATATTTAATT--TAT
* * *
18359 AAAAATAATTATAATT-ATTTAT
1 ATAAATTATTATATTTAATTTAT
18381 -TAAGTATTA-TATATTTAA-TTAT
1 ATAA--ATTATTATATTTAATTTAT
*
18403 A-AAATTATT-TGTTTAAT
1 ATAAATTATTATATTTAAT
18420 AATAAGCTAT
Statistics
Matches: 88, Mismatches: 9, Indels: 36
0.66 0.07 0.27
Matches are distributed among these distances:
20 10 0.11
21 3 0.03
22 15 0.17
23 22 0.25
24 13 0.15
25 2 0.02
26 2 0.02
27 4 0.05
28 3 0.03
29 9 0.10
30 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (23 bp):
ATAAATTATTATATTTAATTTAT
Found at i:18322 original size:19 final size:19
Alignment explanation
Indices: 18294--18338 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
18284 TAATTTATTA
18294 TATT-TAATTTATATAA-AT
1 TATTATAATTT-TATAATAT
*
18312 TATTATAATTTTATAATCT
1 TATTATAATTTTATAATAT
18331 TATTATAA
1 TATTATAA
18339 ATTAATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATAATTTTATAATAT
Found at i:18347 original size:22 final size:22
Alignment explanation
Indices: 18283--18382 Score: 66
Period size: 23 Copynumber: 4.5 Consensus size: 22
18273 ATATTAATAA
*
18283 ATAAT-TTATTAT-ATTTAATTT
1 ATAATATTATTATAAATTAA-TT
*
18304 ATATAAATTATTAT-AATT--TT
1 ATA-ATATTATTATAAATTAATT
*
18324 ATAATCTTATTATAAATTAATT
1 ATAATATTATTATAAATTAATT
* * *
18346 ATAAAATTAATATAAAAATAATT
1 ATAATATTATTAT-AAATTAATT
18369 ATAATTATTTATTA
1 ATAA-TA-TTATTA
18383 AGTATTATAT
Statistics
Matches: 61, Mismatches: 10, Indels: 12
0.73 0.12 0.14
Matches are distributed among these distances:
19 8 0.13
20 9 0.15
21 3 0.05
22 13 0.21
23 22 0.36
24 1 0.02
25 5 0.08
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
ATAATATTATTATAAATTAATT
Found at i:18350 original size:11 final size:11
Alignment explanation
Indices: 18305--18405 Score: 56
Period size: 11 Copynumber: 9.5 Consensus size: 11
18295 ATTTAATTTA
18305 TATAAATT-AT
1 TATAAATTAAT
18315 TAT-AATT--T
1 TATAAATTAAT
*
18323 TAT-AATCTTAT
1 TATAAAT-TAAT
18334 TATAAATTAAT
1 TATAAATTAAT
18345 TATAAAATTAA-
1 TAT-AAATTAAT
*
18356 TATAAAAATAAT
1 TAT-AAATTAAT
*
18368 TAT-AATTATT
1 TATAAATTAAT
* *
18378 TATTAAGT-AT
1 TATAAATTAAT
*
18388 TATATATTTAAT
1 TATA-AATTAAT
18400 TATAAA
1 TATAAA
18406 ATTATTTGTT
Statistics
Matches: 72, Mismatches: 10, Indels: 17
0.73 0.10 0.17
Matches are distributed among these distances:
8 7 0.10
9 5 0.07
10 15 0.21
11 26 0.36
12 19 0.26
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.49
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:18354 original size:12 final size:12
Alignment explanation
Indices: 18332--18409 Score: 60
Period size: 11 Copynumber: 7.0 Consensus size: 12
18322 TTATAATCTT
18332 ATTAT-AAATTA
1 ATTATAAAATTA
18343 ATTATAAAATTA
1 ATTATAAAATTA
*
18355 A-TATAAAAATA
1 ATTATAAAATTA
18366 ATTAT--AATTA
1 ATTATAAAATTA
* * *
18376 TTTAT-TAAGT-
1 ATTATAAAATTA
* *
18386 ATTATATATTTA
1 ATTATAAAATTA
18398 ATTATAAAATTA
1 ATTATAAAATTA
18410 TTTGTTTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 9
0.75 0.13 0.13
Matches are distributed among these distances:
10 12 0.23
11 21 0.40
12 20 0.38
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (12 bp):
ATTATAAAATTA
Found at i:18409 original size:20 final size:20
Alignment explanation
Indices: 18386--18424 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
18376 TTTATTAAGT
*
18386 ATTATATATTTAATTATAAA
1 ATTATATATTTAATAATAAA
* *
18406 ATTATTTGTTTAATAATAA
1 ATTATATATTTAATAATAA
18425 GCTATTATTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (20 bp):
ATTATATATTTAATAATAAA
Found at i:18815 original size:17 final size:19
Alignment explanation
Indices: 18793--18838 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
18783 TTAATAATAA
18793 TATAATAAATATTA-AAAT
1 TATAATAAATATTATAAAT
18811 T-TAATAAAT-TTATAAAT
1 TATAATAAATATTATAAAT
*
18828 TATAATCAATA
1 TATAATAAATA
18839 ATTTATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 3 0.12
17 13 0.54
18 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (19 bp):
TATAATAAATATTATAAAT
Found at i:18905 original size:26 final size:25
Alignment explanation
Indices: 18848--18914 Score: 73
Period size: 26 Copynumber: 2.6 Consensus size: 25
18838 AATTTATTAA
* *
18848 AAATAATTAATATTGATTTAATATAT
1 AAATAATTTA-ATTAATTTAATATAT
18874 AAATAATTTAATTAATTTAATAT-T
1 AAATAATTTAATTAATTTAATATAT
*
18898 AATTATAATTTTATTAA
1 AA--ATAATTTAATTAA
18915 CCTAATTAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
24 3 0.08
25 12 0.33
26 21 0.58
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (25 bp):
AAATAATTTAATTAATTTAATATAT
Found at i:19182 original size:18 final size:17
Alignment explanation
Indices: 19155--19192 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
19145 ATTAGTTATT
19155 AATTATTATATCAATTTTA
1 AATTATTATAT-AA-TTTA
19174 AATTA-TATATAATTTA
1 AATTATTATATAATTTA
19190 AAT
1 AAT
19193 GAAATAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.37
17 2 0.11
18 5 0.26
19 5 0.26
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
AATTATTATATAATTTA
Found at i:19189 original size:16 final size:16
Alignment explanation
Indices: 19155--19204 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 16
19145 ATTAGTTATT
19155 AATTATTATATCAATTTTA
1 AATTA-TATAT-AA-TTTA
19174 AATTATATATAATTTA
1 AATTATATATAATTTA
*
19190 AATGA-A-ATAATTTA
1 AATTATATATAATTTA
19204 A
1 A
19205 TAAAATTCAA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
14 9 0.30
15 1 0.03
16 8 0.27
17 2 0.07
18 5 0.17
19 5 0.17
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (16 bp):
AATTATATATAATTTA
Found at i:19339 original size:20 final size:22
Alignment explanation
Indices: 19302--19342 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
19292 TTTAATATTA
19302 ATAATATTTATGATAATTAATT
1 ATAATATTTATGATAATTAATT
19324 ATAATATTT-T-ATAATTAAT
1 ATAATATTTATGATAATTAAT
19343 AAATTAATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAATATTTATGATAATTAATT
Found at i:20267 original size:23 final size:24
Alignment explanation
Indices: 20237--20283 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
20227 AAATTAATTT
*
20237 TACAAATTTGTTTATTA-TAAATA
1 TACAAATTTATTTATTATTAAATA
20260 TACAAATTTATTTATTATTAAATA
1 TACAAATTTATTTATTATTAAATA
20284 CATTATAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 16 0.73
24 6 0.27
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
TACAAATTTATTTATTATTAAATA
Found at i:20447 original size:13 final size:13
Alignment explanation
Indices: 20431--20533 Score: 62
Period size: 13 Copynumber: 8.3 Consensus size: 13
20421 TTAATAAAAT
20431 TAATATTATTATA
1 TAATATTATTATA
*
20444 TAAT-TAAATTAT-
1 TAATAT-TATTATA
*
20456 TAATATAATTATA
1 TAATATTATTATA
20469 TAATA-T-TTAT-
1 TAATATTATTATA
*
20479 T-ATATTATAATA
1 TAATATTATTATA
20491 -AATATTTAATT-TA
1 TAATA-TT-ATTATA
*
20504 -AATATTTAATATA
1 TAATA-TTATTATA
*
20517 TAATAATATTATA
1 TAATATTATTATA
20530 TAAT
1 TAAT
20534 TAAATAAATT
Statistics
Matches: 72, Mismatches: 7, Indels: 22
0.71 0.07 0.22
Matches are distributed among these distances:
9 3 0.04
10 2 0.03
11 7 0.10
12 16 0.22
13 38 0.53
14 6 0.08
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TAATATTATTATA
Found at i:20450 original size:17 final size:17
Alignment explanation
Indices: 20421--20466 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
20411 ATTCAATTGT
*
20421 TTAATAAAATTAATATTA
1 TTAATATAATTAA-ATTA
20439 TT-ATATAATTAAATTA
1 TTAATATAATTAAATTA
20455 TTAATATAATTA
1 TTAATATAATTA
20467 TATAATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 6 0.23
17 18 0.69
18 2 0.08
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAATATAATTAAATTA
Found at i:20495 original size:34 final size:35
Alignment explanation
Indices: 20456--20562 Score: 114
Period size: 34 Copynumber: 3.1 Consensus size: 35
20446 ATTAAATTAT
*
20456 TAATATAATTATATAATATTTATTATATTATAATA
1 TAATATAATTATATAATATTTAATATATTATAATA
*
20491 -AATATTTAATT-TA-AATATTTAATATATAATAATA
1 TAATA--TAATTATATAATATTTAATATATTATAATA
* * *
20525 TTATATAATTAAATAA-ATTAAATATATTATAATGA
1 TAATATAATTATATAATATTTAATATATTATAAT-A
20560 TAA
1 TAA
20563 ACATTTACTT
Statistics
Matches: 59, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
33 5 0.08
34 39 0.66
35 10 0.17
36 5 0.08
ACGTcount: A:0.52, C:0.00, G:0.01, T:0.47
Consensus pattern (35 bp):
TAATATAATTATATAATATTTAATATATTATAATA
Found at i:20544 original size:17 final size:17
Alignment explanation
Indices: 20438--20544 Score: 57
Period size: 17 Copynumber: 6.2 Consensus size: 17
20428 AATTAATATT
*
20438 ATTATATAATTAAAT-T
1 ATTATATAATTAAATAA
*
20454 ATTAATATAATTATATAA
1 ATT-ATATAATTAAATAA
20472 TATT-TATTATATTATAATAA
1 -ATTATA-TA-ATTA-AATAA
*
20492 A-TATTTAATT---TAA
1 ATTATATAATTAAATAA
*
20505 A-TATTTAATATATAATAA
1 ATTATATAAT-TA-AATAA
20523 TATTATATAATTAAATAA
1 -ATTATATAATTAAATAA
20541 ATTA
1 ATTA
20545 AATATATTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 27
0.69 0.05 0.26
Matches are distributed among these distances:
13 12 0.17
14 1 0.01
16 3 0.04
17 20 0.28
18 13 0.18
19 12 0.17
20 11 0.15
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
ATTATATAATTAAATAA
Done.