Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168003.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_259, 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: 41719
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:624 original size:7 final size:7
Alignment explanation
Indices: 612--643 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
602 AAACATGCCT
612 TTTCACC
1 TTTCACC
619 TTTCACC
1 TTTCACC
*
626 TTTCACA
1 TTTCACC
633 TTTCACC
1 TTTCACC
640 TTTC
1 TTTC
644 CTTTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.16, C:0.38, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTCACC
Found at i:1041 original size:14 final size:14
Alignment explanation
Indices: 1022--1049 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1012 ATAATCAACT
1022 CTTTTTTTTTTTTG
1 CTTTTTTTTTTTTG
1036 CTTTTTTTTTTTTG
1 CTTTTTTTTTTTTG
1050 GAACTCATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.86
Consensus pattern (14 bp):
CTTTTTTTTTTTTG
Found at i:4353 original size:4 final size:4
Alignment explanation
Indices: 4346--4381 Score: 56
Period size: 4 Copynumber: 9.2 Consensus size: 4
4336 ATGAAAAGAG
*
4346 ACAA ACAA ACAA ACAA A-AA AAAA ACAA ACAA ACAA A
1 ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA ACAA A
4382 TAAATAAATA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
3 3 0.10
4 27 0.90
ACGTcount: A:0.81, C:0.19, G:0.00, T:0.00
Consensus pattern (4 bp):
ACAA
Found at i:7781 original size:16 final size:16
Alignment explanation
Indices: 7739--7782 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
7729 TTTTCATATA
*
7739 TATTTTTATTTTTATT
1 TATTTTTATATTTATT
*
7755 CA-TTTTA-ATTTATT
1 TATTTTTATATTTATT
7769 TATTTTTATATTTA
1 TATTTTTATATTTA
7783 ATGGCCAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
14 7 0.30
15 10 0.43
16 6 0.26
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTTTTATATTTATT
Found at i:10434 original size:63 final size:63
Alignment explanation
Indices: 10356--10479 Score: 203
Period size: 63 Copynumber: 2.0 Consensus size: 63
10346 TTCTAATATG
* **
10356 ATTTTATACATTTTTCCATTTTCATGAAGATTGGGATCAAAGAAATCCCTAAAATCATTCATT
1 ATTTTATACATTTTTCCATTTTCATGAAAATTACGATCAAAGAAATCCCTAAAATCATTCATT
* *
10419 ATTTTATGCATTTTTCCATTTTCATGAAAATTACGATCAAAGAAATCCTTAAAATCATTCA
1 ATTTTATACATTTTTCCATTTTCATGAAAATTACGATCAAAGAAATCCCTAAAATCATTCA
10480 ATCGTTAGAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 56 1.00
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.40
Consensus pattern (63 bp):
ATTTTATACATTTTTCCATTTTCATGAAAATTACGATCAAAGAAATCCCTAAAATCATTCATT
Found at i:11637 original size:21 final size:21
Alignment explanation
Indices: 11612--11651 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
11602 TGCAAGAATA
* *
11612 GAATTTAACCTAAACAATAGC
1 GAATTAAACCAAAACAATAGC
*
11633 GAATTAAATCAAAACAATA
1 GAATTAAACCAAAACAATA
11652 AATAAAGTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.55, C:0.15, G:0.07, T:0.23
Consensus pattern (21 bp):
GAATTAAACCAAAACAATAGC
Found at i:12106 original size:18 final size:18
Alignment explanation
Indices: 12083--12120 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
12073 AAATCGCATG
*
12083 AATTGAATTGAAAACTTA
1 AATTGAATTGAAAACCTA
12101 AATTGAATTGAAAACCTA
1 AATTGAATTGAAAACCTA
12119 AA
1 AA
12121 AAACTAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.53, C:0.08, G:0.11, T:0.29
Consensus pattern (18 bp):
AATTGAATTGAAAACCTA
Found at i:14697 original size:2 final size:2
Alignment explanation
Indices: 14690--14715 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
14680 AATGAAAGGA
14690 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
14716 GTATGTATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19869 original size:8 final size:8
Alignment explanation
Indices: 19856--19880 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
19846 TTACATTAAA
19856 ATTTTATC
1 ATTTTATC
19864 ATTTTATC
1 ATTTTATC
19872 ATTTTATC
1 ATTTTATC
19880 A
1 A
19881 CCTCATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.28, C:0.12, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTTATC
Found at i:21715 original size:20 final size:22
Alignment explanation
Indices: 21669--21718 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
21659 AATTAATAGT
21669 TAGTTA-TTTTTGGTTACATAC
1 TAGTTAGTTTTTGGTTACATAC
21690 TAGTTAGTTTTT-GTTAC-TAC
1 TAGTTAGTTTTTGGTTACATAC
*
21710 TTGTTAGTT
1 TAGTTAGTT
21719 ACTTTTTGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 11 0.41
21 11 0.41
22 5 0.19
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (22 bp):
TAGTTAGTTTTTGGTTACATAC
Found at i:29209 original size:13 final size:13
Alignment explanation
Indices: 29193--29225 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
29183 TTCGAACATG
29193 TATTTATTTTGTA
1 TATTTATTTTGTA
29206 TATTTATTTTGTA
1 TATTTATTTTGTA
*
29219 TTTTTAT
1 TATTTAT
29226 ATAATTAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (13 bp):
TATTTATTTTGTA
Found at i:29569 original size:14 final size:14
Alignment explanation
Indices: 29550--29582 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
29540 TTATTGATAG
29550 AATTTTCCATCGAT
1 AATTTTCCATCGAT
*
29564 AATTTTCCGTCGAT
1 AATTTTCCATCGAT
29578 AATTT
1 AATTT
29583 ACTAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (14 bp):
AATTTTCCATCGAT
Found at i:38437 original size:16 final size:16
Alignment explanation
Indices: 38416--38484 Score: 59
Period size: 16 Copynumber: 4.1 Consensus size: 16
38406 GTGATGTTAC
38416 AAATAATATATTAATA
1 AAATAATATATTAATA
*
38432 AAATAATATTTTGATTATA
1 AAATAATATATT-A--ATA
* *
38451 TAAATATTTTATTAAT-
1 -AAATAATATATTAATA
*
38467 AAATAATATATTGATA
1 AAATAATATATTAATA
38483 AA
1 AA
38485 TATGATTATA
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
15 12 0.29
16 13 0.32
17 3 0.07
19 4 0.10
20 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
AAATAATATATTAATA
Found at i:38470 original size:15 final size:15
Alignment explanation
Indices: 38436--38487 Score: 59
Period size: 15 Copynumber: 3.3 Consensus size: 15
38426 TTAATAAAAT
38436 AATATTTTGATTATATA
1 AATATTTT-ATTA-ATA
38453 AATATTTTATTAATA
1 AATATTTTATTAATA
* * *
38468 AATAATATATTGATA
1 AATATTTTATTAATA
38483 AATAT
1 AATAT
38488 GATTATATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 19 0.61
16 4 0.13
17 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (15 bp):
AATATTTTATTAATA
Found at i:38515 original size:21 final size:21
Alignment explanation
Indices: 38489--38722 Score: 64
Period size: 21 Copynumber: 11.4 Consensus size: 21
38479 GATAAATATG
38489 ATTATATTTATTATATATAAT
1 ATTATATTTATTATATATAAT
** ** *
38510 ATTATATAAAAAATAAATAAT
1 ATTATATTTATTATATATAAT
* * *
38531 ATCATA-TTAATAAATA-ATAT
1 ATTATATTTATTATATATA-AT
* **
38551 ATTATA-TTAATA-ATGCAAT
1 ATTATATTTATTATATATAAT
38570 ATTATTTATTTATTA-ATATAAT
1 ATTA--TATTTATTATATATAAT
* * * *
38592 A-T-TGTTTATAATATTTATT
1 ATTATATTTATTATATATAAT
** *
38611 AAAATA-TTATTATAT-TCAT
1 ATTATATTTATTATATATAAT
* *
38630 ATAATATTTATTAT-TTTAAT
1 ATTATATTTATTATATATAAT
*
38650 A-TATTATTATATTA-AGATAAT
1 ATTA-TATT-TATTATATATAAT
* *
38671 A-TATTATTTATAATATATTATTT
1 ATTA-TATTTATTATATA-TA-AT
* *
38694 ATAATATTTATTA-ATATATT
1 ATTATATTTATTATATATAAT
38714 ATTAATATT
1 ATT-ATATT
38723 AATATCATAA
Statistics
Matches: 159, Mismatches: 36, Indels: 36
0.69 0.16 0.16
Matches are distributed among these distances:
18 7 0.04
19 24 0.15
20 50 0.31
21 51 0.32
22 16 0.10
23 10 0.06
24 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (21 bp):
ATTATATTTATTATATATAAT
Found at i:38586 original size:22 final size:22
Alignment explanation
Indices: 38535--38760 Score: 84
Period size: 24 Copynumber: 9.7 Consensus size: 22
38525 AATAATATCA
*
38535 TATTAATAAATAATATATTATAT
1 TATTAATAAATATTAT-TTATAT
* *
38558 TAATAATGCAATATTATTTAT-T
1 TATTAAT-AAATATTATTTATAT
* *
38580 TATTAATATAATATTGTTTATAA
1 TATTAATA-AATATTATTTATAT
*
38603 TATTTATTAAAATATTA-TTATAT
1 TA-TTAAT-AAATATTATTTATAT
**
38626 TCATATAATATTTATTATTTTAATATAT
1 T-AT-TAATAAATATTA--TT--TATAT
* * *
38654 TATTATATTAAGA-TA-ATATAT
1 TATTA-ATAAATATTATTTATAT
* *
38675 TATTTATAATATATTATTTATAA
1 TATTAATAA-ATATTATTTATAT
* *
38698 TATTTATTAATATATTATTAATAT
1 TA-TTAATAA-ATATTATTTATAT
* * *
38722 TAATATCATAAATTATTAATAATA-
1 T-AT-TAATAAA-TATTATTTATAT
*
38746 TATTAATATATATTA
1 TATTAATAAATATTA
38761 CTAGCCAAGG
Statistics
Matches: 151, Mismatches: 32, Indels: 42
0.67 0.14 0.19
Matches are distributed among these distances:
20 3 0.02
21 16 0.11
22 25 0.17
23 33 0.22
24 42 0.28
25 16 0.11
26 5 0.03
27 5 0.03
28 6 0.04
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (22 bp):
TATTAATAAATATTATTTATAT
Found at i:38594 original size:41 final size:40
Alignment explanation
Indices: 38480--38594 Score: 106
Period size: 41 Copynumber: 2.8 Consensus size: 40
38470 TAATATATTG
*
38480 ATAAATATGATTATATTTATTATATATAATATTATATAAAAA
1 ATAAATATTATT-TATTTATTA-ATATAATATTATATAAAAA
* * * * * *
38522 ATAAATAATATCATATTAATAAATA-ATATATTATATTAATA
1 ATAAATATTAT-TTATTTATTAATATA-ATATTATATAAAAA
*
38563 ATGCAATATTATTTATTTATTAATATAATATT
1 AT-AAATATTATTTATTTATTAATATAATATT
38595 GTTTATAATA
Statistics
Matches: 57, Mismatches: 12, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
40 1 0.02
41 32 0.56
42 24 0.42
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (40 bp):
ATAAATATTATTTATTTATTAATATAATATTATATAAAAA
Found at i:38610 original size:31 final size:32
Alignment explanation
Indices: 38572--38723 Score: 104
Period size: 31 Copynumber: 4.8 Consensus size: 32
38562 AATGCAATAT
*
38572 TATTTATT-TATTAATATAATATTGTTTATAA
1 TATTTATTATATTAATATAATATTATTTATAA
* * * *
38603 TATTTATTAAAATATTATTATATTCA--TATAA
1 TATTTATTATATTAATATAATATT-ATTTATAA
* *
38634 TATTTATTATTTTAATATATTATTATATTA-AGA
1 TATTTATTATATTAATATAATATTAT-TTATA-A
*
38667 TAATATATTAT-TT-ATA-ATATATTATTTATAA
1 T-ATTTATTATATTAATATA-ATATTATTTATAA
*
38698 TATTTATTA-ATATATTATTAATATTA
1 TATTTATTATAT-TAATA-TAATATTA
38724 ATATCATAAA
Statistics
Matches: 92, Mismatches: 15, Indels: 26
0.69 0.11 0.20
Matches are distributed among these distances:
30 9 0.10
31 38 0.41
32 24 0.26
33 12 0.13
34 9 0.10
ACGTcount: A:0.42, C:0.01, G:0.01, T:0.56
Consensus pattern (32 bp):
TATTTATTATATTAATATAATATTATTTATAA
Found at i:38611 original size:38 final size:39
Alignment explanation
Indices: 38569--38716 Score: 119
Period size: 43 Copynumber: 3.7 Consensus size: 39
38559 AATAATGCAA
38569 TATTAT-TTATT-TATTAATATAATATTGTTTATAATATT
1 TATTATATTATTATATTAATATAATATT-TTTATAATATT
* *
38607 TATTAAAATATTATTATATTCATATAATA--TTTATTAT-TT
1 TATT---ATATTATTATATTAATATAATATTTTTATAATATT
* *
38646 TAATATATTATTATATTAAGATAATATATTATTTATAATATAT
1 TATTATATTATTATATTAATAT-A-ATATT-TTTATAATAT-T
* *
38689 TATTTATAATATT-TATTAATATATTATT
1 TA-TTATATTATTATATTAATATAATATT
38717 AATATTAATA
Statistics
Matches: 87, Mismatches: 10, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
36 16 0.18
37 1 0.01
38 7 0.08
39 5 0.06
40 7 0.08
41 13 0.15
42 7 0.08
43 23 0.26
44 8 0.09
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (39 bp):
TATTATATTATTATATTAATATAATATTTTTATAATATT
Found at i:38685 original size:14 final size:14
Alignment explanation
Indices: 38666--38750 Score: 75
Period size: 14 Copynumber: 5.8 Consensus size: 14
38656 TTATATTAAG
38666 ATAATATATTATTT
1 ATAATATATTATTT
38680 ATAATATATTATTT
1 ATAATATATTATTT
*
38694 ATAATAT-TTATTA
1 ATAATATATTATTT
38707 AT-ATATTATTAATATT
1 ATAATA-TATT-AT-TT
* *
38723 AATATCATAAATTATTA
1 -ATA--ATATATTATTT
38740 ATAATATATTA
1 ATAATATATTA
38751 ATATATATTA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
12 3 0.05
13 8 0.14
14 30 0.52
15 2 0.03
16 4 0.07
17 3 0.05
18 2 0.03
19 3 0.05
20 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAATATATTATTT
Found at i:38696 original size:9 final size:9
Alignment explanation
Indices: 38596--38722 Score: 58
Period size: 9 Copynumber: 14.2 Consensus size: 9
38586 TATAATATTG
38596 TTTATAATA
1 TTTATAATA
*
38605 TTTATTAAAA
1 TTTA-TAATA
*
38615 TATTATTATA
1 T-TTATAATA
38625 TTCATATAATA
1 TT--TATAATA
38636 TTTAT--TA
1 TTTATAATA
38643 TTT-TAATA
1 TTTATAATA
*
38651 TATTATTATA
1 T-TTATAATA
38661 -TTA-AGATA
1 TTTATA-ATA
* *
38669 -ATATATTA
1 TTTATAATA
38677 TTTATAATA
1 TTTATAATA
38686 --TAT--TA
1 TTTATAATA
38691 TTTATAATA
1 TTTATAATA
38700 TTTATTAATA
1 TTTA-TAATA
38710 TATTATTAATA
1 T-TTA-TAATA
38721 TT
1 TT
38723 AATATCATAA
Statistics
Matches: 91, Mismatches: 10, Indels: 33
0.68 0.07 0.25
Matches are distributed among these distances:
5 2 0.02
6 1 0.01
7 11 0.12
8 13 0.14
9 23 0.25
10 20 0.22
11 21 0.23
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.56
Consensus pattern (9 bp):
TTTATAATA
Found at i:38696 original size:36 final size:35
Alignment explanation
Indices: 38598--38692 Score: 120
Period size: 36 Copynumber: 2.7 Consensus size: 35
38588 TAATATTGTT
* * * *
38598 TATAATATTTATTAAAATATTATTATATTCATATAA
1 TATATTATTTA-TAATATATTATTATATTAAGATAA
38634 TATTTATTATTT-TAATATATTATTATATTAAGATAA
1 TA--TATTATTTATAATATATTATTATATTAAGATAA
38670 TATATTATTTATAATATATTATT
1 TATATTATTTATAATATATTATT
38693 TATAATATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
34 8 0.15
35 12 0.23
36 25 0.48
38 7 0.13
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TATATTATTTATAATATATTATTATATTAAGATAA
Found at i:39342 original size:15 final size:15
Alignment explanation
Indices: 39324--39472 Score: 97
Period size: 15 Copynumber: 9.5 Consensus size: 15
39314 TAATATTCAG
39324 TAATATATTATTTAT
1 TAATATATTATTTAT
39339 TAATATAATATTATTTATT
1 T-A-AT-ATATTATTTA-T
39358 TATTAGTATATTATTTAT
1 TA--A-TATATTATTTAT
* *
39376 TAA-A-ATTATATAAA
1 TAATATATTAT-TTAT
39390 TAATATATTATTTAT
1 TAATATATTATTTAT
* *
39405 AAATATAATATTTAT
1 TAATATATTATTTAT
*
39420 TAATATATTATTAAT
1 TAATATATTATTTAT
* * *
39435 ATATTACATTATGTTAA
1 -TAATATATTAT-TTAT
* *
39452 TAATATATAATATAT
1 TAATATATTATTTAT
39467 T-ATATA
1 TAATATA
39473 ATAAATAATA
Statistics
Matches: 105, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
13 5 0.05
14 11 0.10
15 32 0.30
16 24 0.23
17 4 0.04
18 14 0.13
19 14 0.13
20 1 0.01
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (15 bp):
TAATATATTATTTAT
Found at i:39371 original size:11 final size:10
Alignment explanation
Indices: 39329--39440 Score: 56
Period size: 11 Copynumber: 11.2 Consensus size: 10
39319 TTCAGTAATA
*
39329 TATTATTTAT
1 TATTATATAT
*
39339 TAATATAATAT
1 TATTAT-ATAT
39350 TATT-TAT-T
1 TATTATATAT
39358 TATTAGTATAT
1 TATTA-TATAT
*
39369 TATT-TATTAA
1 TATTATA-TAT
*
39379 AATTATATA-
1 TATTATATAT
* *
39388 AATAATATAT
1 TATTATATAT
*
39398 TATT-TATAAA
1 TATTATAT-AT
*
39408 TATAATAT-T
1 TATTATATAT
39417 TATTAATATAT
1 TATT-ATATAT
39428 TATTAATATAT
1 TATT-ATATAT
39439 TA
1 TA
39441 CATTATGTTA
Statistics
Matches: 79, Mismatches: 12, Indels: 21
0.71 0.11 0.19
Matches are distributed among these distances:
8 5 0.06
9 18 0.23
10 26 0.33
11 30 0.38
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (10 bp):
TATTATATAT
Found at i:39399 original size:37 final size:37
Alignment explanation
Indices: 39327--39399 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
39317 TATTCAGTAA
* * * * *
39327 TATATTATTTATTAATATAATATTATTTATTTATTAG
1 TATATTATTTATTAAAATAATATAAATAATATATTAG
*
39364 TATATTATTTATTAAAATTATATAAATAATATATTA
1 TATATTATTTATTAAAATAATATAAATAATATATTA
39400 TTTATAAATA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (37 bp):
TATATTATTTATTAAAATAATATAAATAATATATTAG
Found at i:39401 original size:44 final size:44
Alignment explanation
Indices: 39335--39468 Score: 135
Period size: 46 Copynumber: 2.9 Consensus size: 44
39325 AATATATTAT
*
39335 TTATTAATATAATATTATTTATTTATTAGTATATTATTTATTAAAA
1 TTATTAATATAATA-TA-TTATTTATTAATATATTATTTATTAAAA
* *
39381 TTATATAA-ATAATATATTATTTATAAATATAATATTTATTAATATA
1 TTAT-TAATATAATATATTATTTATTAATATATTATTTATTAA-A-A
* * * * *
39427 TTATTAATATATTACATTATGTTAATAATATATAATATATTA
1 TTATTAATATAATATATTAT-TTATTAATATATTATTTATTA
39469 TATAATAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
44 23 0.32
45 6 0.08
46 25 0.34
47 19 0.26
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (44 bp):
TTATTAATATAATATATTATTTATTAATATATTATTTATTAAAA
Found at i:39439 original size:19 final size:19
Alignment explanation
Indices: 39417--39487 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
39407 ATATAATATT
39417 TATTAATATATTATTAATA
1 TATTAATATATTATTAATA
* *
39436 TATTACATTATGTTAATAATA
1 TATTA-A-TATATTATTAATA
39457 TA-TAATATATTATATAATA
1 TATTAATATATTAT-TAATA
*
39476 -AATAATATATTA
1 TATTAATATATTA
39488 ATAAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 7 0.16
19 21 0.48
20 3 0.07
21 13 0.30
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (19 bp):
TATTAATATATTATTAATA
Found at i:39468 original size:47 final size:45
Alignment explanation
Indices: 39396--39487 Score: 107
Period size: 47 Copynumber: 2.0 Consensus size: 45
39386 TAAATAATAT
* *
39396 ATTATTTATAAATATAATATTTATTA-ATATATTATTAATATATTAC
1 ATTATTTATAAATATAATA-TTATTATATA-ATAAATAATATATTAC
39442 ATTATGTTAATAATATATAATA-TATTATATAATAAATAATATATTA
1 ATTAT-TT-ATAA-ATATAATATTATTATATAATAAATAATATATTA
39488 ATAAAAAATA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
46 5 0.12
47 20 0.50
48 7 0.17
49 8 0.20
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (45 bp):
ATTATTTATAAATATAATATTATTATATAATAAATAATATATTAC
Found at i:39499 original size:37 final size:39
Alignment explanation
Indices: 39420--39500 Score: 96
Period size: 37 Copynumber: 2.1 Consensus size: 39
39410 TAATATTTAT
* * * *
39420 TAATATATTATTAATATATTACATTATGTTAATAATATA
1 TAATATATTATTAATATAATACATTATATTAATAAAAAA
39459 TAATATATTATATAATA-AATA-A-TATATTAATAAAAAA
1 TAATATATTAT-TAATATAATACATTATATTAATAAAAAA
39496 TAATA
1 TAATA
39501 GCTTAAAAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
37 17 0.46
38 1 0.03
39 14 0.38
40 5 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (39 bp):
TAATATATTATTAATATAATACATTATATTAATAAAAAA
Found at i:39506 original size:18 final size:18
Alignment explanation
Indices: 39448--39506 Score: 55
Period size: 18 Copynumber: 3.2 Consensus size: 18
39438 TTACATTATG
* * *
39448 TTAATAATATATAATATA
1 TTAATAAAAAATAATAGA
* *
39466 TTATATAATAAATAATATA
1 TTA-ATAAAAAATAATAGA
*
39485 TTAATAAAAAATAATAGC
1 TTAATAAAAAATAATAGA
39503 TTAA
1 TTAA
39507 AAGTTTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
18 19 0.53
19 17 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (18 bp):
TTAATAAAAAATAATAGA
Found at i:39848 original size:19 final size:19
Alignment explanation
Indices: 39826--39895 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
39816 TCAAAGCAAA
39826 ATTTCCAAGTCAATGTAGG
1 ATTTCCAAGTCAATGTAGG
* *
39845 ATTTCCTAA-TCAAGGTTGG
1 ATTTCC-AAGTCAATGTAGG
*
39864 ATTTCCAAATCAATGTAGG
1 ATTTCCAAGTCAATGTAGG
*
39883 AATTCCAAGTCAA
1 ATTTCCAAGTCAA
39896 AATAGAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
18 2 0.05
19 39 0.91
20 2 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.31
Consensus pattern (19 bp):
ATTTCCAAGTCAATGTAGG
Found at i:41432 original size:3 final size:3
Alignment explanation
Indices: 41419--41466 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
41409 AAACATACAC
*
41419 ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41466 A
1 A
41467 AACATACTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Done.