Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167950.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_210, 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: 50706
ACGTcount: A:0.45, C:0.06, G:0.06, T:0.43
File 2 of 2
Found at i:38802 original size:17 final size:17
Alignment explanation
Indices: 38766--38811 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
38756 AAATATTATA
38766 TAATTATATTAATAATT
1 TAATTATATTAATAATT
38783 TAATTATA-TAATAATAT
1 TAATTATATTAATAAT-T
*
38800 TAATTTTATTAA
1 TAATTATATTAA
38812 ACAATTGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 7 0.27
17 16 0.62
18 3 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
TAATTATATTAATAATT
Found at i:39018 original size:22 final size:22
Alignment explanation
Indices: 38993--39056 Score: 56
Period size: 25 Copynumber: 2.8 Consensus size: 22
38983 AAACAAATTT
38993 TTAAAATTAATTTTTAAAATAA
1 TTAAAATTAATTTTTAAAATAA
* * *
39015 TTAAGATAAATTAATATTATAATAA
1 TTAAAATTAATT--T-TTAAAATAA
* *
39040 TTATAATTAATATTTAA
1 TTAAAATTAATTTTTAA
39057 CCTATTAAAG
Statistics
Matches: 31, Mismatches: 8, Indels: 6
0.69 0.18 0.13
Matches are distributed among these distances:
22 13 0.42
23 1 0.03
24 1 0.03
25 16 0.52
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
TTAAAATTAATTTTTAAAATAA
Found at i:39507 original size:15 final size:15
Alignment explanation
Indices: 39464--39507 Score: 54
Period size: 15 Copynumber: 3.0 Consensus size: 15
39454 CAATAATTGT
39464 AATTA-TAATTATTA
1 AATTATTAATTATTA
* * *
39478 TATTATCAATAATTA
1 AATTATTAATTATTA
39493 AATTATTAATTATTA
1 AATTATTAATTATTA
39508 CAAATTGTCA
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
14 4 0.17
15 19 0.83
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTATTAATTATTA
Found at i:39912 original size:20 final size:22
Alignment explanation
Indices: 39889--39929 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
39879 TGATTAATAT
39889 ATTAATTAT-A-AAATATTATA
1 ATTAATTATCATAAATATTATA
39909 ATTAATTATCATAAATATTAT
1 ATTAATTATCATAAATATTAT
39930 TAATATTAAA
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:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAATTATCATAAATATTATA
Found at i:40364 original size:20 final size:19
Alignment explanation
Indices: 40341--40404 Score: 53
Period size: 17 Copynumber: 3.4 Consensus size: 19
40331 TTAATATTAA
40341 ATTAATTAAATTATTTATAT
1 ATTAATTAAATTATTTAT-T
* *
40361 ATTAAATCAATATTAATTATT
1 ATT-AATTAA-ATTATTTATT
*
40382 -TTAA-TAAATTATTGATT
1 ATTAATTAAATTATTTATT
40399 A-TAATT
1 ATTAATT
40405 TATAAATTTA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
17 11 0.31
18 3 0.09
19 2 0.06
20 5 0.14
21 6 0.17
22 8 0.23
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTAATTAAATTATTTATT
Found at i:40421 original size:17 final size:18
Alignment explanation
Indices: 40391--40436 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
40381 TTTAATAAAT
*
40391 TATTGATTATAATTTATAA
1 TATTTATTATAATTT-TAA
40410 -ATTTATTA-AATTTTAA
1 TATTTATTATAATTTTAA
40426 TATTTATTATA
1 TATTTATTATA
40437 TTATTATTAA
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:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
TATTTATTATAATTTTAA
Found at i:40907 original size:36 final size:36
Alignment explanation
Indices: 40838--40941 Score: 113
Period size: 36 Copynumber: 2.8 Consensus size: 36
40828 TAATTAAATA
* *
40838 TATAATACTTAATAAATAATATAAT-TATATATTAATTT
1 TATAATAATTTAT-AAT-ATATAATATAT-TATTAATTT
*
40876 TATAATATTTTATAATATATAATATATTATTAATTT
1 TATAATAATTTATAATATATAATATATTATTAATTT
* *
40912 TATAATAAATTATAAAATTATAATA-ATTAT
1 TATAATAATTTATAATA-TATAATATATTAT
40942 ATATAAATTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
36 35 0.59
37 13 0.22
38 11 0.19
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (36 bp):
TATAATAATTTATAATATATAATATATTATTAATTT
Found at i:40909 original size:18 final size:18
Alignment explanation
Indices: 40834--40985 Score: 70
Period size: 18 Copynumber: 8.4 Consensus size: 18
40824 TTTATAATTA
* *
40834 AATATATAATACT-TAATA
1 AATATATAATA-TATTATT
40852 AATAATATAAT-TATATATT
1 AAT-ATATAATATAT-TATT
* *
40871 AATTTTATAATATTTTA-T
1 AA-TATATAATATATTATT
40889 AATATATAATATATTATT
1 AATATATAATATATTATT
* *
40907 AATTTTATAATAAATTA-T
1 AA-TATATAATATATTATT
*
40925 AAAATTATAATA-ATTA-T
1 AATA-TATAATATATTATT
* *
40942 ATATAAATTAATATA-TATA
1 A-ATATA-TAATATATTATT
*
40961 AATTATTTAATATA-TATT
1 AA-TATATAATATATTATT
40979 AAT-TATA
1 AATATATA
40986 GTGTAAAACA
Statistics
Matches: 104, Mismatches: 17, Indels: 28
0.70 0.11 0.19
Matches are distributed among these distances:
16 3 0.03
17 21 0.20
18 42 0.40
19 35 0.34
20 3 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (18 bp):
AATATATAATATATTATT
Found at i:40935 original size:26 final size:26
Alignment explanation
Indices: 40882--40951 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 26
40872 ATTTTATAAT
* * *
40882 ATTTTATAATATATAATATATTATTA
1 ATTTTATAATAAATTATAAATTATTA
40908 ATTTTATAATAAATTATAAAATTA-TA
1 ATTTTATAATAAATTAT-AAATTATTA
*
40934 ATAATTATATATAAATTA
1 AT-TTTATA-ATAAATTA
40952 ATATATATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
26 19 0.51
27 10 0.27
28 8 0.22
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
ATTTTATAATAAATTATAAATTATTA
Found at i:40948 original size:21 final size:18
Alignment explanation
Indices: 40875--40942 Score: 59
Period size: 17 Copynumber: 3.8 Consensus size: 18
40865 TATATTAATT
** *
40875 TTATAATATTTTATAATA
1 TTATAATAAATTATAAAA
* **
40893 -TATAATATATTATTAATT
1 TTATAATAAATTA-TAAAA
40911 TTATAATAAATTATAAAA
1 TTATAATAAATTATAAAA
40929 TTATAAT-AATTATA
1 TTATAATAAATTATA
40943 TATAAATTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
17 18 0.42
18 14 0.33
19 11 0.26
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATAATAAATTATAAAA
Found at i:40974 original size:14 final size:14
Alignment explanation
Indices: 40939--40965 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40929 TTATAATAAT
40939 TATATATAAATTAA
1 TATATATAAATTAA
40953 TATATATAAATTA
1 TATATATAAATTA
40966 TTTAATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TATATATAAATTAA
Found at i:41152 original size:21 final size:23
Alignment explanation
Indices: 41128--41169 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
41118 AAATTTTTTG
41128 TTATTAA-AAATT-AAAAAATTC
1 TTATTAATAAATTCAAAAAATTC
*
41149 TTATTAATATATTCAAAAAAT
1 TTATTAATAAATTCAAAAAAT
41170 AATATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 4 0.22
23 7 0.39
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (23 bp):
TTATTAATAAATTCAAAAAATTC
Found at i:41489 original size:16 final size:17
Alignment explanation
Indices: 41468--41501 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
41458 AAAATAATAA
41468 ATAATATAGT-ATAATT
1 ATAATATAGTAATAATT
*
41484 ATAATATATTAATAATT
1 ATAATATAGTAATAATT
41501 A
1 A
41502 ATTAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
ATAATATAGTAATAATT
Found at i:41797 original size:28 final size:28
Alignment explanation
Indices: 41766--41820 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
41756 TAAGAAAAAG
* *
41766 TTATAATAGTATATAAATTA-TAATAATA
1 TTATAATAATATA-AAATAATTAATAATA
41794 TTATAATAATATAAAATAATTAATAAT
1 TTATAATAATATAAAATAATTAATAAT
41821 TATTTAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (28 bp):
TTATAATAATATAAAATAATTAATAATA
Found at i:41798 original size:11 final size:11
Alignment explanation
Indices: 41768--41805 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41758 AGAAAAAGTT
*
41768 ATAATAGTAT-
1 ATAATATTATA
41778 ATAA-ATTATA
1 ATAATATTATA
41788 ATAATATTATA
1 ATAATATTATA
41799 ATAATAT
1 ATAATAT
41806 AAAATAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
9 4 0.16
10 8 0.32
11 13 0.52
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (11 bp):
ATAATATTATA
Found at i:42061 original size:25 final size:24
Alignment explanation
Indices: 42027--42094 Score: 59
Period size: 25 Copynumber: 2.8 Consensus size: 24
42017 TACTAATATC
*
42027 TTATAATAATATAAATTAAATATAA
1 TTATTATAATATAAATTAAAT-TAA
*
42052 TTATTATAAT-TAATTTTATAATTAA
1 TTATTATAATATAA-ATTA-AATTAA
* *
42077 TTAATATTATA-AAATTAA
1 TTATTATAATATAAATTAA
42095 TGATAAATTA
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATTATAATATAAATTAAATTAA
Found at i:42072 original size:12 final size:13
Alignment explanation
Indices: 42049--42079 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
42039 AAATTAAATA
42049 TAATTATTATAAT
1 TAATTATTATAAT
42062 TAATT-TTATAAT
1 TAATTATTATAAT
42074 TAATTA
1 TAATTA
42080 ATATTATAAA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
TAATTATTATAAT
Found at i:42079 original size:16 final size:16
Alignment explanation
Indices: 42058--42088 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42048 ATAATTATTA
*
42058 TAATTAATTTTATAAT
1 TAATTAATATTATAAT
42074 TAATTAATATTATAA
1 TAATTAATATTATAA
42089 AATTAATGAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
TAATTAATATTATAAT
Found at i:42253 original size:14 final size:14
Alignment explanation
Indices: 42231--42264 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
42221 ATATTAGATA
42231 ATTAA-TAATATTT
1 ATTAATTAATATTT
42244 ATTAATTAATATTT
1 ATTAATTAATATTT
42258 ATTAATT
1 ATTAATT
42265 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
ATTAATTAATATTT
Found at i:42780 original size:24 final size:24
Alignment explanation
Indices: 42752--42811 Score: 61
Period size: 24 Copynumber: 2.5 Consensus size: 24
42742 TAATAAATTA
*
42752 TATATTAAAATAATAATTATT-AT
1 TATATTAAAATAATAATAATTAAT
*
42775 CTATA-TAACAATAATTATAATTAAT
1 -TATATTAA-AATAATAATAATTAAT
42800 TATATTATAAAT
1 TATATTA-AAAT
42812 TATTTATTCA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
23 3 0.10
24 19 0.63
25 7 0.23
26 1 0.03
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (24 bp):
TATATTAAAATAATAATAATTAAT
Found at i:43017 original size:24 final size:24
Alignment explanation
Indices: 42963--43041 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
42953 TTATATTATT
* *
42963 ATTAAAATTATTAA-TATTTAAATA
1 ATTAAAATTATTAATTA-ATAATTA
* *
42987 ATCAAAATTATTAATTAATAATTT
1 ATTAAAATTATTAATTAATAATTA
* *
43011 ATTAAAAGTATTAGTTTAATATATTA
1 ATTAAAATTATTA-ATTAATA-ATTA
43037 ATTAA
1 ATTAA
43042 TCTTCTGTTT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 28 0.64
25 8 0.18
26 8 0.18
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (24 bp):
ATTAAAATTATTAATTAATAATTA
Found at i:43629 original size:12 final size:12
Alignment explanation
Indices: 43612--43650 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
43602 TTTTTCTTAG
*
43612 TTATATTGATAA
1 TTATATTAATAA
43624 TTATATTAATAA
1 TTATATTAATAA
*
43636 TTAATATAAATAA
1 TT-ATATTAATAA
43649 TT
1 TT
43651 GCTTACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (12 bp):
TTATATTAATAA
Found at i:43712 original size:14 final size:15
Alignment explanation
Indices: 43695--43729 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
43685 ATAAATAATT
43695 TAATATTATT-TAAA
1 TAATATTATTCTAAA
*
43709 TAATAATATTCTAAA
1 TAATATTATTCTAAA
43724 TAATAT
1 TAATAT
43730 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:44250 original size:13 final size:13
Alignment explanation
Indices: 44232--44265 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
44222 TAGTTTATAA
44232 ATTATTAAAAATT
1 ATTATTAAAAATT
*
44245 ATTATTAACAATT
1 ATTATTAAAAATT
44258 ATTTATTA
1 A-TTATTA
44266 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:44475 original size:11 final size:11
Alignment explanation
Indices: 44426--44467 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
44416 TAATAATGAT
*
44426 TATATTAAATT
1 TATATTAAATA
*
44437 TATATT-AGTA
1 TATATTAAATA
44447 TA-ATTAAATA
1 TATATTAAATA
44457 TATATTAAATA
1 TATATTAAATA
44468 ATTATTAATG
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
9 3 0.12
10 9 0.35
11 14 0.54
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (11 bp):
TATATTAAATA
Found at i:44645 original size:30 final size:30
Alignment explanation
Indices: 44600--44671 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
44590 ATTTAAAATG
*
44600 ATAATTTAAAATAATTAATAA-ATTATTATCA
1 ATAATTT-TAATAATT-ATAATATTATTATCA
* *
44631 ATAATTTTAATAATTATAATATTTTTATTA
1 ATAATTTTAATAATTATAATATTATTATCA
44661 A-AATTATTAAT
1 ATAATT-TTAAT
44672 CTTATATAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 8 0.22
30 21 0.58
31 7 0.19
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (30 bp):
ATAATTTTAATAATTATAATATTATTATCA
Found at i:45053 original size:47 final size:47
Alignment explanation
Indices: 45002--45145 Score: 108
Period size: 47 Copynumber: 3.1 Consensus size: 47
44992 AACAAATATT
45002 TTTATAATTATTATTAAATATATATTAATTTTAAATATTAAATCTAA
1 TTTATAATTATTATTAAATATATATTAATTTTAAATATTAAATCTAA
* * *
45049 TTTAT--TTATATAATTAAA-ATA-ATTGTTATAATTAAATAAT-AATCTAA
1 TTTATAATTAT-T-ATTAAATATATA-T-TAAT-TTTAAATATTAAATCTAA
* * *
45096 -TTA-AATTATAATATAAATAT-T-TAAATTTTAAATATTAAAACTAA
1 TTTATAATTATTAT-TAAATATATATTAATTTTAAATATTAAATCTAA
*
45140 TATATA
1 TTTATA
45146 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:45098 original size:16 final size:16
Alignment explanation
Indices: 45077--45107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45067 ATAATTGTTA
45077 TAATTAAATAATAATC
1 TAATTAAATAATAATC
*
45093 TAATTAAATTATAAT
1 TAATTAAATAATAAT
45108 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:45257 original size:13 final size:13
Alignment explanation
Indices: 45241--45265 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45231 AATACAAATA
45241 AATCTAATTATTT
1 AATCTAATTATTT
45254 AATCTAATTATT
1 AATCTAATTATT
45266 AATAAAGTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (13 bp):
AATCTAATTATTT
Found at i:45726 original size:18 final size:18
Alignment explanation
Indices: 45683--45726 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
45673 AGGTTGAGGA
*
45683 AAATTATATTATTATAAT
1 AAATTATATAATTATAAT
* * *
45701 ATAGTATATAATTATTAT
1 AAATTATATAATTATAAT
45719 AAATTATA
1 AAATTATA
45727 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:45757 original size:19 final size:18
Alignment explanation
Indices: 45732--45782 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
45722 TTATAATTAA
*
45732 TAAATAATTTATTAATAT
1 TAAATAATTTATTAACAT
*
45750 TAATATAA-GTATTAACAT
1 TAA-ATAATTTATTAACAT
45768 TAAATAATTATATTA
1 TAAATAATT-TATTA
45783 TAATTAAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 14 0.52
19 9 0.33
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATAATTTATTAACAT
Found at i:45850 original size:19 final size:20
Alignment explanation
Indices: 45822--45860 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
45812 CAATATCTGC
45822 TTCAAGTTA-TTATATATTTA
1 TTCAAGTTATTTATA-ATTTA
45842 TTCAA-TTATTTATAATTTA
1 TTCAAGTTATTTATAATTTA
45861 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:45884 original size:21 final size:23
Alignment explanation
Indices: 45853--45898 Score: 78
Period size: 21 Copynumber: 2.1 Consensus size: 23
45843 TCAATTATTT
45853 ATAATTTAATATTTGAA-ATTAA
1 ATAATTTAATATTTGAATATTAA
45875 ATAA-TTAATATTTGAATATTAA
1 ATAATTTAATATTTGAATATTAA
45897 AT
1 AT
45899 TGATATTATC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 12 0.52
22 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (23 bp):
ATAATTTAATATTTGAATATTAA
Found at i:46754 original size:181 final size:180
Alignment explanation
Indices: 46381--46727 Score: 446
Period size: 180 Copynumber: 1.9 Consensus size: 180
46371 CAATAAACAA
46381 ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
1 ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
** * * *
46446 CAAATAAGCTTGTACGAACAAAACAATTGTTTTATGTTAAAAGAAAAGGTTATAACGATTTGAAA
66 CAAATAAAATAGTACGAACAAAACAATTGTTTGATGATAAAAGAAAAGGTTATAACGATTTGAAA
* * ** * *
46511 TAGATAATCATTCATAGTGTCTTAACTATTTGAACTAGTTCAACAATTAG
131 TAAATAATCATTCATAATGTCAAAACTATTTGAAATAGTTCAACAACTAG
* ** * *
46561 ATTTATTTTTTAATTTTCTTGGTTATTAAGTTTT-GAAATATTATTAAATTAGTATTATTTTATT
1 ATTTATTTTTTAAATTTCTTACTTATTAA-TTTTCAAAATATTATTAAATTAGTATTATTTTAAT
* * * * *
46625 CTAAATAAAATAGTATGAACAGAACCAATTGTTTGATGATAAAATAAAAGGTTATATCGATTTGA
65 CCAAATAAAATAGTACGAACA-AAACAATTGTTTGATGATAAAAGAAAAGGTTATAACGATTTGA
* *
46690 AATAAATAATTATTGA-AATAGTCAAAACTATTTGAAAT
129 AATAAATAATCATTCATAAT-GTCAAAACTATTTGAAAT
46728 GGTTTGGTAA
Statistics
Matches: 142, Mismatches: 22, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
180 72 0.51
181 70 0.49
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.42
Consensus pattern (180 bp):
ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
CAAATAAAATAGTACGAACAAAACAATTGTTTGATGATAAAAGAAAAGGTTATAACGATTTGAAA
TAAATAATCATTCATAATGTCAAAACTATTTGAAATAGTTCAACAACTAG
Found at i:46783 original size:181 final size:180
Alignment explanation
Indices: 46381--46892 Score: 480
Period size: 181 Copynumber: 2.8 Consensus size: 180
46371 CAATAAACAA
*
46381 ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAATC
1 ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATTC
* ** * * * *
46446 CAAATAAGCTTGTACGAACAAAACAATTGTTTTATGTTAAAAGAAAAGGTTATAACGATTTGAAA
66 TAAATAAAATAGTATGAACAAAACAATTGTTTTATGATAAAACAAAAGGTTATAACGATTTGAAA
* * * ** * *
46511 TAGATAATCATTCATAGT-GTCTTAACTATTTGAACTAGTTCAACAATTAG
131 TAAATAATTATTCA-AATAGTCAAAACTATTTGAAATAGTTCAACAACTAG
* ** *
46561 ATTTATTTTTTAATTTTCTTGGTTATTAAGTTTT-GAAATATTATTAAATTAGTATTATTTTATT
1 ATTTATTTTTTAAATTTCTTACTTATTAA-TTTTCAAAATATTATTAAATTAGTATTATTTTATT
* * * *
46625 CTAAATAAAATAGTATGAACAGAACCAATTGTTTGATGATAAAATAAAAGGTTATATCGATTTGA
65 CTAAATAAAATAGTATGAACA-AAACAATTGTTTTATGATAAAACAAAAGGTTATAACGATTTGA
* * ****
46690 AATAAATAATTATTGAAATAGTCAAAACTATTTGAAATGGTTTGGTAAGCT-G
129 AATAAATAATTATTCAAATAGTCAAAACTATTTGAAATAGTTCAACAA-CTAG
** * * * ** *
46742 ATTT-TCTTTTTAAATCTT-TTACAGATTTATTTTCTAAATATTAATAAAACAATATTATTTTAT
1 ATTTAT-TTTTTAAAT-TTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTAT
* * * * * * *
46805 T-TCAAACAAACTTA-TATTAACAAAAATAATTGTTTTATGACAGAACAAAAGGTAATAACGATT
64 TCT-AAATAAA-ATAGTATGAAC-AAAACAATTGTTTTATGATAAAACAAAAGGTTATAACGATT
* *
46868 TAAAATAAATAATTGTTCAAATAGT
126 TGAAATAAATAATTATTCAAATAGT
46893 TACAATTATT
Statistics
Matches: 269, Mismatches: 53, Indels: 19
0.79 0.16 0.06
Matches are distributed among these distances:
180 78 0.29
181 185 0.69
182 6 0.02
ACGTcount: A:0.41, C:0.08, G:0.10, T:0.42
Consensus pattern (180 bp):
ATTTATTTTTTAAATTTCTTACTTATTAATTTTCAAAATATTATTAAATTAGTATTATTTTATTC
TAAATAAAATAGTATGAACAAAACAATTGTTTTATGATAAAACAAAAGGTTATAACGATTTGAAA
TAAATAATTATTCAAATAGTCAAAACTATTTGAAATAGTTCAACAACTAG
Found at i:47411 original size:12 final size:12
Alignment explanation
Indices: 47381--47454 Score: 55
Period size: 12 Copynumber: 6.3 Consensus size: 12
47371 TTAATGTTGT
47381 ATTAA-ATAA-A
1 ATTAATATAATA
47391 ATTAATATAATA
1 ATTAATATAATA
*
47403 ATTATTATAATA
1 ATTAATATAATA
* *
47415 AATAATATTAT-
1 ATTAATATAATA
**
47426 ATTGTTATAATA
1 ATTAATATAATA
* *
47438 AATAATAATTATA
1 ATTAAT-ATAATA
47451 ATTA
1 ATTA
47455 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:47415 original size:15 final size:15
Alignment explanation
Indices: 47393--47426 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 15
47383 TAAATAAAAT
47393 TAATATAATAATTATTA
1 TAATA-AATAA-TATTA
47410 TAATAAATAATATTA
1 TAATAAATAATATTA
47425 TA
1 TA
47427 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:47471 original size:17 final size:17
Alignment explanation
Indices: 47449--47491 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
47439 ATAATAATTA
*
47449 TAATTATTTTCATAAAT
1 TAATTATTTTAATAAAT
* *
47466 TAATTAATTTAATTAAT
1 TAATTATTTTAATAAAT
47483 TAATATATT
1 TAAT-TATT
47492 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:48339 original size:30 final size:30
Alignment explanation
Indices: 48281--48340 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
48271 TATATAGTTC
* * *
48281 TAAATATATAATTTACTTATATATTATTAA
1 TAAATATATAACTTAATTATATAATATTAA
48311 TAAATTATATAACTTAATT-TATAATATTAA
1 TAAA-TATATAACTTAATTATATAATATTAA
48341 GTAATAATAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TAAATATATAACTTAATTATATAATATTAA
Found at i:48358 original size:10 final size:10
Alignment explanation
Indices: 48345--48369 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48335 TATTAAGTAA
48345 TAATAGTTAT
1 TAATAGTTAT
48355 TAATAGTTAT
1 TAATAGTTAT
48365 TAATA
1 TAATA
48370 TTAATATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (10 bp):
TAATAGTTAT
Found at i:48468 original size:23 final size:23
Alignment explanation
Indices: 48437--48573 Score: 65
Period size: 23 Copynumber: 5.8 Consensus size: 23
48427 ATATTAATAA
*
48437 ATAATTTATTATATTTAATTTAT
1 ATAAATTATTATATTTAATTTAT
48460 ATAAATTATTATAATTTTATAATCTTATT
1 ATAAATTATTAT-A--TT-TAAT-TTA-T
*
48489 ATAAATTAATTATA--AAATTAATAT
1 ATAAATT-ATTATATTTAATT--TAT
* * *
48513 AAAAATAATTATAATT-ATTTAT
1 ATAAATTATTATATTTAATTTAT
48535 -TAAA-TATTAAATATTTAA-TTAT
1 ATAAATTATT--ATATTTAATTTAT
*
48557 A-AAATTATT-TGTTTAAT
1 ATAAATTATTATATTTAAT
48574 AATTTAATTA
Statistics
Matches: 88, Mismatches: 9, Indels: 36
0.66 0.07 0.27
Matches are distributed among these distances:
20 9 0.10
21 3 0.03
22 15 0.17
23 23 0.26
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:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (23 bp):
ATAAATTATTATATTTAATTTAT
Found at i:48476 original size:19 final size:19
Alignment explanation
Indices: 48448--48492 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
48438 TAATTTATTA
48448 TATT-TAATTTATATAA-AT
1 TATTATAATTT-TATAATAT
*
48466 TATTATAATTTTATAATCT
1 TATTATAATTTTATAATAT
48485 TATTATAA
1 TATTATAA
48493 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:48501 original size:22 final size:22
Alignment explanation
Indices: 48437--48544 Score: 66
Period size: 23 Copynumber: 4.9 Consensus size: 22
48427 ATATTAATAA
*
48437 ATAAT-TTATTAT-ATTTAATTT
1 ATAATATTATTATAAATTAA-TT
*
48458 ATATAAATTATTAT-AATT--TT
1 ATA-ATATTATTATAAATTAATT
*
48478 ATAATCTTATTATAAATTAATT
1 ATAATATTATTATAAATTAATT
* * *
48500 ATAAAATTAATATAAAAATAATT
1 ATAATATTATTAT-AAATTAATT
48523 ATAATTATTTATTA-AATATTAA
1 ATAA-TA-TTATTATAA-ATTAA
48545 ATATTTAATT
Statistics
Matches: 67, Mismatches: 11, Indels: 15
0.72 0.12 0.16
Matches are distributed among these distances:
19 8 0.12
20 9 0.13
21 3 0.04
22 13 0.19
23 24 0.36
24 5 0.07
25 5 0.07
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATATTATTATAAATTAATT
Found at i:48504 original size:11 final size:11
Alignment explanation
Indices: 48459--48559 Score: 51
Period size: 11 Copynumber: 9.5 Consensus size: 11
48449 ATTTAATTTA
48459 TATAAATT-AT
1 TATAAATTAAT
48469 TAT-AATT--T
1 TATAAATTAAT
*
48477 TAT-AATCTTAT
1 TATAAAT-TAAT
48488 TATAAATTAAT
1 TATAAATTAAT
48499 TATAAAATTAA-
1 TAT-AAATTAAT
*
48510 TATAAAAATAAT
1 TAT-AAATTAAT
*
48522 TAT-AATTATT
1 TATAAATTAAT
48532 TATTAAA-T-AT
1 TA-TAAATTAAT
48542 TA-AATATTTAAT
1 TATAA-A-TTAAT
48554 TATAAA
1 TATAAA
48560 ATTATTTGTT
Statistics
Matches: 73, Mismatches: 5, Indels: 24
0.72 0.05 0.24
Matches are distributed among these distances:
8 9 0.12
9 6 0.08
10 13 0.18
11 23 0.32
12 20 0.27
13 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:48508 original size:12 final size:12
Alignment explanation
Indices: 48486--48563 Score: 62
Period size: 12 Copynumber: 7.0 Consensus size: 12
48476 TTATAATCTT
48486 ATTAT-AAATTA
1 ATTATAAAATTA
48497 ATTATAAAATTA
1 ATTATAAAATTA
*
48509 A-TATAAAAATA
1 ATTATAAAATTA
48520 ATTAT--AATTA
1 ATTATAAAATTA
* *
48530 TTTATTAAA-T-
1 ATTATAAAATTA
*
48540 ATTA-AATATTTA
1 ATTATAA-AATTA
48552 ATTATAAAATTA
1 ATTATAAAATTA
48564 TTTGTTTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 15
0.70 0.09 0.20
Matches are distributed among these distances:
9 1 0.02
10 12 0.23
11 17 0.33
12 20 0.38
13 2 0.04
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATTATAAAATTA
Found at i:49062 original size:30 final size:29
Alignment explanation
Indices: 49002--49058 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 29
48992 TTAACATTTG
*
49002 AAAAATTAAAAATAACTGTTAATTGTATT
1 AAAAATTAAAAATAACTGTTAATAGTATT
49031 AAAAATTAATAAAT-A-TGTTAATAG-ATT
1 AAAAATTAA-AAATAACTGTTAATAGTATT
49058 A
1 A
49059 TTAATTTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
27 4 0.15
28 8 0.31
29 10 0.38
30 4 0.15
ACGTcount: A:0.54, C:0.02, G:0.07, T:0.37
Consensus pattern (29 bp):
AAAAATTAAAAATAACTGTTAATAGTATT
Found at i:49535 original size:17 final size:17
Alignment explanation
Indices: 49513--49545 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
49503 TTATCAAATA
49513 ATTTATATAA-ATTATTT
1 ATTTAT-TAATATTATTT
49530 ATTTATTAATATTATT
1 ATTTATTAATATTATT
49546 AATTAATTAT
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATTTATTAATATTATTT
Found at i:49726 original size:18 final size:17
Alignment explanation
Indices: 49695--49736 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
49685 CTATTTTAAT
49695 TTAATATAATT-AAATAA
1 TTAATATAATTAAAAT-A
*
49712 TTAATATAGTATAAAATA
1 TTAATATAAT-TAAAATA
49730 TTAATAT
1 TTAATAT
49737 GTTATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 9 0.41
18 9 0.41
19 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (17 bp):
TTAATATAATTAAAATA
Found at i:49927 original size:9 final size:9
Alignment explanation
Indices: 49913--50008 Score: 62
Period size: 9 Copynumber: 10.9 Consensus size: 9
49903 TAATAAGAGC
49913 ATATAATTA
1 ATATAATTA
49922 ATATAATT-
1 ATATAATTA
49930 AT-T-A-TA
1 ATATAATTA
*
49936 TTATAATTA
1 ATATAATTA
*
49945 ATATAATAA
1 ATATAATTA
*
49954 ATCTAATT-
1 ATATAATTA
49962 A-ATAATTA
1 ATATAATTA
49970 ATAATTAA-TA
1 AT-A-TAATTA
49980 ATATTAATTA
1 ATA-TAATTA
49990 TATTATAATTA
1 -A-TATAATTA
*
50001 ATTTAATT
1 ATATAATT
50009 TAATTTAATA
Statistics
Matches: 69, Mismatches: 7, Indels: 22
0.70 0.07 0.22
Matches are distributed among these distances:
5 1 0.01
6 2 0.03
7 7 0.10
8 5 0.07
9 34 0.49
10 8 0.12
11 10 0.14
12 2 0.03
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (9 bp):
ATATAATTA
Done.