Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168022.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_276, 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: 40149
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
File 2 of 2
Found at i:28387 original size:13 final size:13
Alignment explanation
Indices: 28334--28389 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
28324 TAATTTTATA
* *
28334 ATTTTATTTAATA
1 ATTTTAATTAATT
*
28347 ATATTATATTAAATT
1 ATTTTA-ATT-AATT
*
28362 ATTATAATTAATT
1 ATTTTAATTAATT
28375 ATTTTAATTAATT
1 ATTTTAATTAATT
28388 AT
1 AT
28390 ATAAATAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
13 23 0.66
14 5 0.14
15 7 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTAATTAATT
Found at i:28486 original size:29 final size:29
Alignment explanation
Indices: 28454--28510 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
28444 TTAATTTTCT
*
28454 AATAAATAATT-TATAATATAATAATAAAA
1 AATAAAAAATTAT-TAATATAATAATAAAA
**
28483 AATAAAAAATTATTAATATTTTAATAAA
1 AATAAAAAATTATTAATATAATAATAAA
28511 TTAGGTAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (29 bp):
AATAAAAAATTATTAATATAATAATAAAA
Found at i:28617 original size:16 final size:16
Alignment explanation
Indices: 28596--28634 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
28586 TTAAATTAAC
28596 ATTATAA-TAATATAA
1 ATTATAATTAATATAA
*
28611 TATTATAATTAATATTA
1 -ATTATAATTAATATAA
28628 ATTATAA
1 ATTATAA
28635 GTATTAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTATAATTAATATAA
Found at i:29085 original size:20 final size:20
Alignment explanation
Indices: 29062--29115 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
29052 ATAATTAAGT
*
29062 TATAATTATATTTTAAATTA
1 TATAATTATATTTTAAACTA
*
29082 TATAA-TATAATTTAAACTA
1 TATAATTATATTTTAAACTA
29101 -ATAATTATTATTTTA
1 TATAATTA-TATTTTA
29116 CTTAATTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 4 0.14
19 14 0.48
20 11 0.38
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (20 bp):
TATAATTATATTTTAAACTA
Found at i:29423 original size:14 final size:14
Alignment explanation
Indices: 29400--29430 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
29390 CATAATTATT
*
29400 ATATATAATAATTA
1 ATATAAAATAATTA
29414 ATATAAAATAATTA
1 ATATAAAATAATTA
29428 ATA
1 ATA
29431 ATATCCAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
ATATAAAATAATTA
Found at i:29599 original size:22 final size:21
Alignment explanation
Indices: 29565--29618 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 21
29555 ATTAAATATT
*
29565 TAATTACTAATCACTTATTATA
1 TAATTA-TAATCAATTATTATA
29587 GTAATTATAATCAATTATTATA
1 -TAATTATAATCAATTATTATA
29609 TAATTATAAT
1 TAATTATAAT
29619 TATATAAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 10 0.33
22 14 0.47
23 6 0.20
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (21 bp):
TAATTATAATCAATTATTATA
Found at i:29750 original size:16 final size:16
Alignment explanation
Indices: 29704--29752 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
29694 CTAAATATAG
*
29704 TTAATTTATAATATTA
1 TTAATTAATAATATTA
*
29720 TTTA-TAATATATATTA
1 TTAATTAATA-ATATTA
*
29736 TTAATTAATACTATTA
1 TTAATTAATAATATTA
29752 T
1 T
29753 ATTTCACTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
15 4 0.15
16 18 0.67
17 5 0.19
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
TTAATTAATAATATTA
Found at i:29804 original size:16 final size:16
Alignment explanation
Indices: 29782--29820 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
29772 TATTGTTTAA
*
29782 TTTAATAATTATAT-T
1 TTTAATAAGTATATAT
29797 TATTAATAAGTATATAT
1 T-TTAATAAGTATATAT
29814 TTTAATA
1 TTTAATA
29821 TAATTACTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 18 0.86
17 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTAATAAGTATATAT
Found at i:29858 original size:17 final size:17
Alignment explanation
Indices: 29818--29879 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 17
29808 ATATATTTTA
*
29818 ATATAATTACTAAATA-
1 ATATATTTACTAAATAT
29834 ACTATATTTACTAAATAT
1 A-TATATTTACTAAATAT
*
29852 ATCTATTT--T--ATAT
1 ATATATTTACTAAATAT
*
29865 ATTTATTTACTAAAT
1 ATATATTTACTAAAT
29880 TTAACAATTA
Statistics
Matches: 37, Mismatches: 3, Indels: 11
0.73 0.06 0.22
Matches are distributed among these distances:
13 11 0.30
15 2 0.05
16 1 0.03
17 22 0.59
18 1 0.03
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATTTACTAAATAT
Found at i:30011 original size:22 final size:22
Alignment explanation
Indices: 29975--30016 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
29965 TTTATTAAAA
**
29975 TATAAATATTTATAAACTATAT
1 TATAAATATAGATAAACTATAT
*
29997 TATAAATATAGATAATCTAT
1 TATAAATATAGATAAACTAT
30017 CACTTGTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
TATAAATATAGATAAACTATAT
Found at i:30181 original size:29 final size:30
Alignment explanation
Indices: 30140--30198 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 30
30130 TATTTATATT
*
30140 AATTATTAAATT-AGTATCTATTAT-TAATA
1 AATTATTAAATTAAAT-TCTATTATATAATA
* *
30169 AATTTTTATATTAAATTCTATTATATAATA
1 AATTATTAAATTAAATTCTATTATATAATA
30199 TTAATTAAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (30 bp):
AATTATTAAATTAAATTCTATTATATAATA
Found at i:30298 original size:20 final size:20
Alignment explanation
Indices: 30268--30324 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
30258 TTGTTATTAT
30268 TAATAAAATTATATATTAAA-A
1 TAAT-AAATTAT-TATTAAATA
*
30289 TAATAAATTATTTATTAAATT
1 TAATAAATTA-TTATTAAATA
30310 TAATAAATTATTATT
1 TAATAAATTATTATT
30325 TATTGTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
20 18 0.55
21 15 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATAAATTATTATTAAATA
Found at i:30334 original size:21 final size:21
Alignment explanation
Indices: 30267--30321 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
30257 ATTGTTATTA
*
30267 TTAATAAAATTATATATTAAA-
1 TTAAT-AAATTATTTATTAAAT
*
30288 ATAATAAATTATTTATTAAAT
1 TTAATAAATTATTTATTAAAT
30309 TTAATAAATTATT
1 TTAATAAATTATT
30322 ATTTATTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TTAATAAATTATTTATTAAAT
Found at i:30466 original size:25 final size:23
Alignment explanation
Indices: 30436--30492 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 23
30426 ATAGTCAAAA
30436 TTGTTTATATTATT-ATTAAAATT
1 TTGTTTA-ATTATTAATTAAAATT
*
30459 ATTAGTTTAATATATTAATTAATATT
1 -TT-GTTTAAT-TATTAATTAAAATT
30485 TTGTTTAA
1 TTGTTTAA
30493 ATTAATCTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 10 0.34
25 11 0.38
26 8 0.28
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (23 bp):
TTGTTTAATTATTAATTAAAATT
Found at i:30972 original size:41 final size:39
Alignment explanation
Indices: 30925--31001 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 39
30915 CTTTTTTTAT
*
30925 TATATTTATAACTATA-ATTAATATAATATATTACTTATATG
1 TATATTTATAACTATATATAAAT-TAAT-TATTA-TTATATG
*
30966 TATATTTATAAGTATATATAAATTAATTATTATTAT
1 TATATTTATAACTATATATAAATTAATTATTATTAT
31002 TAATAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
39 4 0.12
40 5 0.15
41 19 0.58
42 5 0.15
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (39 bp):
TATATTTATAACTATATATAAATTAATTATTATTATATG
Found at i:31060 original size:36 final size:36
Alignment explanation
Indices: 30994--31077 Score: 93
Period size: 36 Copynumber: 2.4 Consensus size: 36
30984 TAAATTAATT
* *
30994 ATTATTATTAATAAATAATATAATAAATATTATA-TA
1 ATTATTATTATTAAATAATACAATAAATATTA-ACTA
*
31030 ATTATTATTATTAAATAATAACAAT-TATATTAACTA
1 ATTATTATTATTAAATAAT-ACAATAAATATTAACTA
*
31066 A-TATTACTATTA
1 ATTATTATTATTA
31078 TTATAGAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
35 11 0.26
36 27 0.64
37 4 0.10
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (36 bp):
ATTATTATTATTAAATAATACAATAAATATTAACTA
Found at i:31470 original size:19 final size:18
Alignment explanation
Indices: 31430--31473 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
31420 AAATTCTTAT
* *
31430 AATATTATTACTAAATCC
1 AATATTATTAATAAATCA
*
31448 AATATTATCTAATAAATTA
1 AATATTAT-TAATAAATCA
31467 AATATTA
1 AATATTA
31474 ATTTAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.50, C:0.09, G:0.00, T:0.41
Consensus pattern (18 bp):
AATATTATTAATAAATCA
Found at i:31504 original size:24 final size:22
Alignment explanation
Indices: 31483--31570 Score: 68
Period size: 24 Copynumber: 3.7 Consensus size: 22
31473 AATTTAATTA
*
31483 ATATATTAATAATATTTATAAT
1 ATATATTAATATTATTTATAAT
* *
31505 ATATAATTAGATATTATTAATTATT
1 ATAT-ATTA-ATATTATTTA-TAAT
*
31530 TTATATTAATTATTATATATAATAAT
1 ATATATTAA-TATTAT-T-T-ATAAT
*
31556 ATATATAAATATTAT
1 ATATATTAATATTAT
31571 ACAATTATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
22 4 0.08
23 5 0.10
24 18 0.35
25 13 0.25
26 10 0.20
27 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATATATTAATATTATTTATAAT
Found at i:31521 original size:20 final size:20
Alignment explanation
Indices: 31481--31569 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
31471 TTAATTTAAT
31481 TAATATATTAATAATATTTA
1 TAATATATTAATAATATTTA
31501 TAATATA-TAATTAGATA-TTA
1 TAATATATTAA-TA-ATATTTA
* * *
31521 TTAAT-TATTTTATATTAATTA
1 -TAATATA-TTAATAATATTTA
* *
31542 TTATATA-TAATAATATATA
1 TAATATATTAATAATATTTA
31561 TAA-ATATTA
1 TAATATATTA
31570 TACAATTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
18 3 0.06
19 15 0.28
20 19 0.36
21 14 0.26
22 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (20 bp):
TAATATATTAATAATATTTA
Found at i:31536 original size:14 final size:14
Alignment explanation
Indices: 31463--31571 Score: 64
Period size: 14 Copynumber: 7.4 Consensus size: 14
31453 TATCTAATAA
*
31463 ATTAAATATTAATTT
1 ATTATATATTAA-TT
31478 AATTAATATATTAATAAT
1 -ATT-ATATATTAAT--T
31496 ATTTATAATATATAATT
1 A-TTAT-ATAT-TAATT
*
31513 A-GATATTATTAATT
1 ATTATA-TATTAATT
*
31527 ATTTTATATTAATT
1 ATTATATATTAATT
31541 ATTATATA-TAA-T
1 ATTATATATTAATT
* *
31553 AATATATA-TAAAT
1 ATTATATATTAATT
31566 ATTATA
1 ATTATA
31572 CAATTATATA
Statistics
Matches: 77, Mismatches: 7, Indels: 21
0.73 0.07 0.20
Matches are distributed among these distances:
12 11 0.14
13 9 0.12
14 22 0.29
15 7 0.09
16 4 0.05
17 13 0.17
18 7 0.09
19 4 0.05
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (14 bp):
ATTATATATTAATT
Found at i:31604 original size:10 final size:10
Alignment explanation
Indices: 31483--31607 Score: 51
Period size: 10 Copynumber: 12.1 Consensus size: 10
31473 AATTTAATTA
*
31483 ATATATTAAT
1 ATATATTATT
*
31493 A-ATATTTATA
1 ATATA-TTATT
*
31503 ATATATAATT
1 ATATATTATT
*
31513 AGATATTATT
1 ATATATTATT
31523 A-ATTATT-TT
1 ATA-TATTATT
31532 ATATTAATTATT
1 ATA-T-ATTATT
*
31544 ATATATAATAAT
1 ATATAT--TATT
* *
31556 ATATATAAAT
1 ATATATTATT
**
31566 ATTATACAATT
1 A-TATATTATT
*
31577 ATATAATACTT
1 ATATATTA-TT
*
31588 -CATATTATT
1 ATATATTATT
31597 ATATATTATT
1 ATATATTATT
31607 A
1 A
31608 AAAATAAATA
Statistics
Matches: 89, Mismatches: 15, Indels: 22
0.71 0.12 0.17
Matches are distributed among these distances:
9 9 0.10
10 49 0.55
11 17 0.19
12 14 0.16
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (10 bp):
ATATATTATT
Found at i:32348 original size:15 final size:14
Alignment explanation
Indices: 32320--32365 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
32310 TTATCTATAT
*
32320 TTAATTCTTAAATA
1 TTAATTATTAAATA
*
32334 TTAATTAATTTAATA
1 TTAATT-ATTAAATA
*
32349 TGAATTATTAAATA
1 TTAATTATTAAATA
32363 TTA
1 TTA
32366 TCATATTGTA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.58
15 11 0.42
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (14 bp):
TTAATTATTAAATA
Found at i:32676 original size:3 final size:3
Alignment explanation
Indices: 32662--32700 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
32652 ATTATATATA
*
32662 AAT AAT ATAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AA
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
32701 AGGATGGAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:33524 original size:12 final size:12
Alignment explanation
Indices: 33504--33537 Score: 52
Period size: 12 Copynumber: 2.8 Consensus size: 12
33494 ATTAATCTAT
33504 ATATATTATTATA
1 ATAT-TTATTATA
33517 ATATTTATTATA
1 ATATTTATTATA
33529 ATA-TTATTA
1 ATATTTATTA
33538 ATTATTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 6 0.29
12 11 0.52
13 4 0.19
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
ATATTTATTATA
Found at i:33525 original size:15 final size:15
Alignment explanation
Indices: 33502--33544 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
33492 AAATTAATCT
*
33502 ATATATATTATTATA
1 ATATTTATTATTATA
*
33517 ATATTTATTATAATA
1 ATATTTATTATTATA
* *
33532 TTATTAATTATTA
1 ATATTTATTATTA
33545 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTATTATTATA
Found at i:33705 original size:11 final size:11
Alignment explanation
Indices: 33689--33734 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
33679 TCATTGAAAA
33689 TAATTAAATAT
1 TAATTAAATAT
33700 TAATTAAATAT
1 TAATTAAATAT
33711 TAAAATTAAA-A-
1 T--AATTAAATAT
*
33722 TAAATAAATAT
1 TAATTAAATAT
33733 TA
1 TA
33735 TATAATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
9 6 0.20
10 1 0.03
11 15 0.50
12 1 0.03
13 7 0.23
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAATTAAATAT
Found at i:33725 original size:18 final size:18
Alignment explanation
Indices: 33686--33727 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
33676 GATTCATTGA
*
33686 AAATAATTAAATATTAATT
1 AAAT-ATTAAATATTAAAT
33705 AAATATTAAA-ATTAAAAT
1 AAATATTAAATATT-AAAT
33723 AAATA
1 AAATA
33728 AATATTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 14 0.67
19 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAATATTAAATATTAAAT
Found at i:33760 original size:12 final size:12
Alignment explanation
Indices: 33737--33775 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
33727 AAATATTATA
33737 TAAT-TAATAAT
1 TAATCTAATAAT
* *
33748 TAATTTTATAAT
1 TAATCTAATAAT
33760 TAATCTAATAAT
1 TAATCTAATAAT
33772 TAAT
1 TAAT
33776 AACTTTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
TAATCTAATAAT
Found at i:34214 original size:9 final size:9
Alignment explanation
Indices: 34197--34314 Score: 50
Period size: 9 Copynumber: 13.3 Consensus size: 9
34187 TAATGTTAAA
34197 TATTAATAT
1 TATTAATAT
*
34206 TATTCATAT
1 TATTAATAT
34215 TA-TAATAT
1 TATTAATAT
* *
34223 T-TATAGTTAA
1 TAT-TA-ATAT
*
34233 TAATAATAT
1 TATTAATAT
*
34242 TATTAATTAA
1 TATTAA-TAT
*
34252 TATTTAT-T
1 TATTAATAT
*
34260 TATTATTAT
1 TATTAATAT
*
34269 TAATAA-AT
1 TATTAATAT
* * *
34277 AATAAATAA
1 TATTAATAT
34286 TATTAA-AT
1 TATTAATAT
34294 TAATT-ATAT
1 T-ATTAATAT
*
34303 AATTAATAT
1 TATTAATAT
34312 TAT
1 TAT
34315 ATGTTTAATA
Statistics
Matches: 75, Mismatches: 24, Indels: 20
0.63 0.20 0.17
Matches are distributed among these distances:
8 22 0.29
9 41 0.55
10 12 0.16
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (9 bp):
TATTAATAT
Found at i:34216 original size:15 final size:15
Alignment explanation
Indices: 34196--34255 Score: 52
Period size: 16 Copynumber: 3.9 Consensus size: 15
34186 TTAATGTTAA
*
34196 ATATTAATATTATTC
1 ATATTAATAATATTC
*
34211 ATATT-ATAATATTT
1 ATATTAATAATATTC
*
34225 ATAGTTAATAATAAT-
1 ATA-TTAATAATATTC
34240 ATTATTAATTAATATT
1 A-TATTAA-TAATATT
34256 TATTTATTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 10 0.27
15 12 0.32
16 15 0.41
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
ATATTAATAATATTC
Found at i:34313 original size:14 final size:14
Alignment explanation
Indices: 34195--34316 Score: 53
Period size: 14 Copynumber: 8.7 Consensus size: 14
34185 ATTAATGTTA
*
34195 AATATTAATATTATT
1 AATATT-ATATAATT
*
34210 CATATTATA-ATATT
1 AATATTATATA-ATT
*
34224 TATAGTTA-ATAA-T
1 AATA-TTATATAATT
34237 AATATTAT-TAATT
1 AATATTATATAATT
34250 AATATT-TAT--TT
1 AATATTATATAATT
* *
34261 ATTATTAT-TAATA
1 AATATTATATAATT
* *
34274 AATAATAAATAATATT
1 AATATTATAT-A-ATT
34290 AAATTAATTATATAATT
1 -AA-T-ATTATATAATT
34307 AATATTATAT
1 AATATTATAT
34317 GTTTAATAAT
Statistics
Matches: 80, Mismatches: 12, Indels: 31
0.65 0.10 0.25
Matches are distributed among these distances:
11 8 0.10
12 8 0.10
13 18 0.22
14 19 0.24
15 11 0.14
16 4 0.05
17 5 0.06
18 2 0.03
19 5 0.06
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (14 bp):
AATATTATATAATT
Found at i:34358 original size:16 final size:18
Alignment explanation
Indices: 34329--34361 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
34319 TTAATAATTA
34329 AATATAACTATTATTAAC
1 AATATAACTATTATTAAC
34347 AATATAA-T-TTATTAA
1 AATATAACTATTATTAA
34362 TATAAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 1 0.07
18 7 0.47
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATAACTATTATTAAC
Found at i:34531 original size:17 final size:19
Alignment explanation
Indices: 34497--34557 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 19
34487 TATTAATTGC
* *
34497 ATATAATATTAAATAATTT
1 ATATAATATTAAACAATTA
34516 ATAT-ATATT-AACAATTA
1 ATATAATATTAAACAATTA
34533 ATATGAAATATTAATA-AATTA
1 ATAT--AATATTAA-ACAATTA
34554 ATAT
1 ATAT
34558 TTGTTAATGA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
17 10 0.29
18 5 0.14
19 4 0.11
20 5 0.14
21 10 0.29
22 1 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (19 bp):
ATATAATATTAAACAATTA
Found at i:35358 original size:30 final size:29
Alignment explanation
Indices: 35321--35399 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 29
35311 AAAAATAATT
*
35321 AATTATTAATTATTTAAATGAAT-ATTTTA
1 AATTATTAATTATTTAAAT-AATAATATTA
*
35350 ATATTATT-A-TATTTTAATAATAATATTA
1 A-ATTATTAATTATTTAAATAATAATATTA
35378 AATTATTAA-TA-TT-AATAATAAT
1 AATTATTAATTATTTAAATAATAAT
35400 GGCTGAATAG
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
26 9 0.20
27 11 0.24
28 17 0.38
29 2 0.04
30 6 0.13
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (29 bp):
AATTATTAATTATTTAAATAATAATATTA
Found at i:35363 original size:16 final size:16
Alignment explanation
Indices: 35342--35391 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 16
35332 ATTTAAATGA
35342 ATATTTTAATATTATT
1 ATATTTTAATATTATT
35358 ATATTTTAATAATAATATT
1 ATATTTTAAT-AT--TATT
*
35377 AAATTATTAATATTA
1 ATATT-TTAATATTA
35392 ATAATAATGG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 10 0.34
17 4 0.14
19 10 0.34
20 5 0.17
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
ATATTTTAATATTATT
Found at i:35386 original size:8 final size:9
Alignment explanation
Indices: 35341--35397 Score: 55
Period size: 9 Copynumber: 6.4 Consensus size: 9
35331 TATTTAAATG
35341 AATATT-TT
1 AATATTATT
35349 AATATTATT
1 AATATTATT
* *
35358 ATATTTTAAT
1 A-ATATTATT
*
35368 AATAATATT
1 AATATTATT
35377 AA-ATTATT
1 AATATTATT
*
35385 AATATTAAT
1 AATATTATT
35394 AATA
1 AATA
35398 ATGGCTGAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
8 13 0.33
9 19 0.49
10 7 0.18
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (9 bp):
AATATTATT
Found at i:35893 original size:11 final size:14
Alignment explanation
Indices: 35860--35890 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
35850 AATTTATTTG
35860 TAATATTAATAATT
1 TAATATTAATAATT
35874 TAATATTAAT-ATT
1 TAATATTAATAATT
35887 TAAT
1 TAAT
35891 TAAACTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (14 bp):
TAATATTAATAATT
Found at i:36144 original size:12 final size:12
Alignment explanation
Indices: 36092--36163 Score: 51
Period size: 12 Copynumber: 6.0 Consensus size: 12
36082 AATAAATTAT
36092 ATTTA-TTAATA
1 ATTTATTTAATA
*
36103 ATTTATTTAAATT
1 ATTTATTT-AATA
***
36116 ATTTAAAAAATA
1 ATTTATTTAATA
*
36128 A-TTATTTTATA
1 ATTTATTTAATA
36139 ATTTATATTAATAA
1 ATTTAT-TTAAT-A
36153 ATTTA-TTAATA
1 ATTTATTTAATA
36164 TATATATAGT
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
11 13 0.28
12 15 0.33
13 12 0.26
14 6 0.13
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTTATTTAATA
Found at i:36191 original size:15 final size:15
Alignment explanation
Indices: 36153--36197 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
36143 ATATTAATAA
*
36153 ATTTATTAA-TATAT
1 ATTTATTAATTAAAT
*
36167 ATATAGTTAATTAAAT
1 ATTTA-TTAATTAAAT
36183 ATTTATTAATTAAAT
1 ATTTATTAATTAAAT
36198 GAGAATTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTAATTAAAT
Found at i:36453 original size:18 final size:16
Alignment explanation
Indices: 36431--36472 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 16
36421 AAATTGTTAA
36431 ATAATTATTTATAATAT
1 ATAATTATTTATAA-AT
36448 ATTAA-TAGTTTATAAAT
1 A-TAATTA-TTTATAAAT
36465 ATAATTAT
1 ATAATTAT
36473 AAATATTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 7
0.76 0.00 0.24
Matches are distributed among these distances:
16 4 0.18
17 8 0.36
18 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (16 bp):
ATAATTATTTATAAAT
Found at i:36507 original size:31 final size:29
Alignment explanation
Indices: 36405--36513 Score: 91
Period size: 32 Copynumber: 3.7 Consensus size: 29
36395 AAAATAATAT
* * *
36405 TAATTATATT-AATAT-TAAATTGTTAAA
1 TAATTATATTAAATATATTAATAGTTATA
36432 TAATTAT-TTATAATATATTAATAGTT-TA
1 TAATTATATTA-AATATATTAATAGTTATA
* *
36460 TAAATATAATTATAAATATTATTAATAGTTATT
1 TAATTAT-A-T-TAAATA-TATTAATAGTTATA
36493 TAATTATAATTAAATATATTA
1 TAATTAT-ATTAAATATATTA
36514 TTATATACTA
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
26 2 0.03
27 7 0.10
28 12 0.18
29 7 0.10
30 5 0.07
31 11 0.16
32 14 0.21
33 9 0.13
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.50
Consensus pattern (29 bp):
TAATTATATTAAATATATTAATAGTTATA
Found at i:36512 original size:33 final size:32
Alignment explanation
Indices: 36439--36516 Score: 99
Period size: 33 Copynumber: 2.5 Consensus size: 32
36429 AAATAATTAT
36439 TTAT-AATA-TATTAATAGTTTATAAATATAA
1 TTATAAATATTATTAATAGTTTATAAATATAA
* *
36469 TTATAAATATTATTAATAGTTATTTAATTATAA
1 TTATAAATATTATTAATAGTT-TATAAATATAA
36502 TTA-AATATATTATTA
1 TTATAA-ATATTATTA
36517 TATACTATAA
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
30 4 0.10
31 4 0.10
32 13 0.31
33 21 0.50
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (32 bp):
TTATAAATATTATTAATAGTTTATAAATATAA
Found at i:36994 original size:19 final size:18
Alignment explanation
Indices: 36948--36997 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
36938 AATTTTATAA
36948 AAATTATAATTATTTTAAT
1 AAATTATAA-TATTTTAAT
* *
36967 AAATAATAATATTATTTAT
1 AAATTATAATATT-TTAAT
*
36986 ATATTATAATAT
1 AAATTATAATAT
36998 ATAATATTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATTATAATATTTTAAT
Found at i:37001 original size:26 final size:25
Alignment explanation
Indices: 36956--37025 Score: 94
Period size: 26 Copynumber: 2.9 Consensus size: 25
36946 AAAAATTATA
36956 ATTATTTTA-A-TA-AATA-ATAAT
1 ATTATTTTATATTATAATATATAAT
36977 ATTATTTATATATTATAATATATAAT
1 ATTATTT-TATATTATAATATATAAT
37003 ATTATTTTATATTATAATCATAT
1 ATTATTTTATATTATAAT-ATAT
37026 TAGTATTGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.16
22 2 0.05
23 1 0.02
24 2 0.05
25 15 0.35
26 16 0.37
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (25 bp):
ATTATTTTATATTATAATATATAAT
Found at i:37291 original size:49 final size:49
Alignment explanation
Indices: 37238--37332 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
37228 ATATTATAGT
*
37238 TAATACATTATATTATAATGTTATA-ACAATTATAT-ATTAAATTTTAATC
1 TAATA-ATTATA-TATAATATTATATACAATTATATAATTAAATTTTAATC
* * * *
37287 TAATAATTTTATATTATATTATATACAATTTTATAATTAATTTTTA
1 TAATAATTATATATAATATTATATACAATTATATAATTAAATTTTA
37333 TAATTAATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
47 10 0.26
48 14 0.36
49 15 0.38
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.52
Consensus pattern (49 bp):
TAATAATTATATATAATATTATATACAATTATATAATTAAATTTTAATC
Found at i:37333 original size:13 final size:13
Alignment explanation
Indices: 37315--37341 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
37305 TTATATACAA
37315 TTTTATAATTAAT
1 TTTTATAATTAAT
37328 TTTTATAATTAAT
1 TTTTATAATTAAT
37341 T
1 T
37342 AATTATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTTATAATTAAT
Found at i:37369 original size:23 final size:21
Alignment explanation
Indices: 37291--37390 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 21
37281 TTAATCTAAT
*
37291 AATT-TTATATTATATTATATA
1 AATTATTATATTAT-TTAAATA
**
37312 CAATT-TTATAATTAATTTTTAT-
1 -AATTATTAT-ATT-ATTTAAATA
37334 AATTAATTA-ATTATTTAAATAGA
1 AATT-ATTATATTATTTAAAT--A
37357 AATTATTATATTA-TTAAATA
1 AATTATTATATTATTTAAATA
*
37377 AATTATTATGTTAT
1 AATTATTATATTAT
37391 AATAAACAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 19
0.74 0.05 0.22
Matches are distributed among these distances:
20 19 0.29
21 7 0.11
22 18 0.28
23 19 0.29
24 2 0.03
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.53
Consensus pattern (21 bp):
AATTATTATATTATTTAAATA
Found at i:38900 original size:13 final size:12
Alignment explanation
Indices: 38883--38925 Score: 54
Period size: 13 Copynumber: 3.6 Consensus size: 12
38873 AAATATTTAG
38883 AATATAT-A-TT
1 AATATATAATTT
38893 AATTATATAATTT
1 AA-TATATAATTT
38906 AATATATAATTGT
1 AATATATAATT-T
38919 AATATAT
1 AATATAT
38926 TATAGATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
10 2 0.07
11 5 0.17
12 10 0.34
13 12 0.41
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
AATATATAATTT
Found at i:39051 original size:24 final size:24
Alignment explanation
Indices: 39008--39056 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
38998 ACTTATTTAT
*
39008 TATAATTATAACATTTATAAATAA
1 TATAATTATAACATTAATAAATAA
* * *
39032 TATAATTATTATATTAATAATTAA
1 TATAATTATAACATTAATAAATAA
39056 T
1 T
39057 TTTAAATATT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (24 bp):
TATAATTATAACATTAATAAATAA
Found at i:39078 original size:34 final size:34
Alignment explanation
Indices: 39020--39134 Score: 94
Period size: 34 Copynumber: 3.3 Consensus size: 34
39010 TAATTATAAC
*
39020 ATTTATAAATAATATAATTA-TTATATTAATAATTA
1 ATTTATAAATATTA-AATTATTTATATT-ATAATTA
**
39055 ATTT-TAAATATTAAATTATTTATAAGATTAATTA
1 ATTTATAAATATTAAATTATTTATATTA-TAATTA
* *
39089 AATTA-ATATATTAAATATATTATAATATT-TAATATA
1 ATTTATAAATATTAAAT-TATT-T-ATATTATAAT-TA
39125 ATTTATAAAT
1 ATTTATAAAT
39135 TAACTAAATT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
33 6 0.10
34 32 0.51
35 12 0.19
36 7 0.11
37 6 0.10
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (34 bp):
ATTTATAAATATTAAATTATTTATATTATAATTA
Found at i:39157 original size:26 final size:25
Alignment explanation
Indices: 39075--39177 Score: 68
Period size: 26 Copynumber: 3.9 Consensus size: 25
39065 TTAAATTATT
39075 TATAAGATTAATTAAATTAATATATTAA
1 TATAA-ATTAA-TAAATTAATATA-TAA
* *
39103 -ATATATT-ATAATATTTAATATA-ATT
1 TATAAATTAATAA-A-TTAATATATA-A
39128 TATAAATTAACTAAATTAATATATAA
1 TATAAATTAA-TAAATTAATATATAA
* *
39154 TATAATATTTATAATATTTATATA
1 TATAA-ATTAATAA-ATTAATATA
39178 ATTTAATAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 19
0.71 0.07 0.22
Matches are distributed among these distances:
24 4 0.07
25 2 0.03
26 33 0.55
27 18 0.30
28 3 0.05
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (25 bp):
TATAAATTAATAAATTAATATATAA
Found at i:39168 original size:9 final size:9
Alignment explanation
Indices: 39092--39194 Score: 58
Period size: 9 Copynumber: 11.3 Consensus size: 9
39082 TTAATTAAAT
39092 TAATATATTA
1 TAATAT-TTA
39102 -AATATATTA
1 TAATAT-TTA
39111 TAATATTTA
1 TAATATTTA
39120 -ATATAATTTA
1 TA-AT-ATTTA
*
39130 TAA-ATTAA
1 TAATATTTA
*
39138 CTAA-ATTAA
1 -TAATATTTA
*
39147 T-ATATAATA
1 TAATAT-TTA
39156 TAATATTTA
1 TAATATTTA
39165 TAATATTTA
1 TAATATTTA
39174 T-ATAATTTAA
1 TAAT-ATTT-A
39184 TAATA-TTA
1 TAATATTTA
39192 TAA
1 TAA
39195 ATTATTAATA
Statistics
Matches: 78, Mismatches: 4, Indels: 24
0.74 0.04 0.23
Matches are distributed among these distances:
7 1 0.01
8 14 0.18
9 42 0.54
10 18 0.23
11 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (9 bp):
TAATATTTA
Found at i:39243 original size:27 final size:27
Alignment explanation
Indices: 39146--39253 Score: 90
Period size: 25 Copynumber: 4.2 Consensus size: 27
39136 AACTAAATTA
39146 ATATATAATATAA-T-AT-TTATAATAT
1 ATATATAATATAATTAATATTATAA-AT
* *
39171 TTATATAATTTAA-TAATATTATAAAT
1 ATATATAATATAATTAATATTATAAAT
39197 -TAT-TAATATAATTATTATATTATAAAT
1 ATATATAATATAATTA--ATATTATAAAT
*
39224 ATATATACATA-AGTTAATA-TAT-AAT
1 ATATATA-ATATAATTAATATTATAAAT
39249 ATATA
1 ATATA
39254 CTATTTAATA
Statistics
Matches: 71, Mismatches: 4, Indels: 16
0.78 0.04 0.18
Matches are distributed among these distances:
24 7 0.10
25 25 0.35
26 7 0.10
27 20 0.28
28 3 0.04
29 6 0.08
30 3 0.04
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.47
Consensus pattern (27 bp):
ATATATAATATAATTAATATTATAAAT
Found at i:39798 original size:22 final size:22
Alignment explanation
Indices: 39765--39807 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
39755 CTTTTAGTTA
*
39765 TATTCAAATAATACTATAATAT
1 TATTCAAATAATACAATAATAT
39787 TATT-AAATTAATACAATAATA
1 TATTCAAA-TAATACAATAATA
39808 ATTGTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (22 bp):
TATTCAAATAATACAATAATAT
Done.