Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168454.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_665, 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: 20211
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Found at i:567 original size:19 final size:19
Alignment explanation
Indices: 545--582 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
535 TTATATTAAT
545 TAATT-ATTATAATGTATTA
1 TAATTGATTA-AATGTATTA
*
564 TAATTGATTAATTGTATTA
1 TAATTGATTAAATGTATTA
583 GTTTAATAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (19 bp):
TAATTGATTAAATGTATTA
Found at i:2323 original size:180 final size:181
Alignment explanation
Indices: 1802--2322 Score: 482
Period size: 181 Copynumber: 2.9 Consensus size: 181
1792 GATTAAGTTT
* * * * * * ** * *
1802 AAATAGTTATGACTATTTGAATAAATTATTTATTTAAAATTATTATGAGTATTTGTTTT-TGACA
1 AAATAATTATGACTATTTCAA-CAATTATCTATTTAAAATCAATATGA-CCTTTGTTTTGTCATA
* * * * *
1866 AAACAAATTGTTTCAGTTCATAAAAGCTTATCTAAAATAAAATTATAACTAATTTCTTAATATTT
64 AAAC-AATTGTTTCAGTTCATACAAGCTT-TCAAAAATAAAATAAT-ACTAATTTATTAATATTC
* * * ** * * * * ****
1931 TAAAAATTAATAAGCAAGATGTTTGAAAAATTAATT-TGTTTA-CTGAACAAATTC-
126 CAAAAACTAATAAGTAAGAAATTTAAAAAAATGATTCTCTTTATC-GAATTGGTTCA
* * *
1985 AAATAGTTATGACTATTTGAACAATTATCTATTTAAAATCATTATGACCTTTGTTTTGTCATAAA
1 AAATAATTATGACTATTTCAACAATTATCTATTTAAAATCAATATGACCTTTGTTTTGTCATAAA
* *
2050 ATAATTGTTTCAGTTCATACAAGCTTATTCAAAAATAAAATAATAGTAATTTATTAATATTCCAA
66 ACAATTGTTTCAGTTCATACAAGC-T-TTCAAAAATAAAATAATACTAATTTATTAATATTCCAA
* **
2115 AAATTAATAAGTAAGTGATTTAAAAAAATGATTCTCTTTATCGAATTGGTTCA
129 AAACTAATAAGTAAGAAATTTAAAAAAATGATTCTCTTTATCGAATTGGTTCA
* * *
2168 AAATAATTATGGCTATTTCAACAATTATCTATTTGAAATCAATATTACCTTT-TGTTTGATCATA
1 AAATAATTATGACTATTTCAACAATTATCTATTTAAAATCAATATGACCTTTGT-TTTG-TCATA
* ** * *
2232 TAACAATTGTTT-TTTATCATACAAGC-TTC-AAAATAAAATAATACTAATTTATTAATCTTTCA
64 AAACAATTGTTTCAGT-TCATACAAGCTTTCAAAAATAAAATAATACTAATTTATTAATATTCCA
2294 AAAAGCTAATAAGTAAGAAATTTAAAAAA
128 AAAA-CTAATAAGTAAGAAATTTAAAAAA
2323 TAAATTTATT
Statistics
Matches: 285, Mismatches: 43, Indels: 22
0.81 0.12 0.06
Matches are distributed among these distances:
180 34 0.12
181 96 0.34
182 56 0.20
183 74 0.26
184 25 0.09
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.40
Consensus pattern (181 bp):
AAATAATTATGACTATTTCAACAATTATCTATTTAAAATCAATATGACCTTTGTTTTGTCATAAA
ACAATTGTTTCAGTTCATACAAGCTTTCAAAAATAAAATAATACTAATTTATTAATATTCCAAAA
ACTAATAAGTAAGAAATTTAAAAAAATGATTCTCTTTATCGAATTGGTTCA
Found at i:3065 original size:24 final size:25
Alignment explanation
Indices: 3038--3089 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 25
3028 ATATAGTATA
*
3038 AATTTA-AATAATTAATATTATAAT
1 AATTTATAATAATTAATAATATAAT
* *
3062 AA-TTATAATTATTACTAATATAAT
1 AATTTATAATAATTAATAATATAAT
3086 AATT
1 AATT
3090 ATGTTTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
23 3 0.13
24 19 0.83
25 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
AATTTATAATAATTAATAATATAAT
Found at i:3097 original size:24 final size:22
Alignment explanation
Indices: 3052--3129 Score: 86
Period size: 24 Copynumber: 3.4 Consensus size: 22
3042 TAAATAATTA
*
3052 ATATTATAATAATTATAATTATT
1 ATATTATAATAATTAT-TTTATT
*
3075 ACTAATATAATAATTATGTTTATT
1 A-TATTATAATAATTAT-TTTATT
*
3099 AGT-TTAAAATAATTATTTTATT
1 A-TATTATAATAATTATTTTATT
3121 ATATTATAA
1 ATATTATAA
3130 ATTATAATAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
21 1 0.02
22 12 0.26
23 12 0.26
24 21 0.46
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (22 bp):
ATATTATAATAATTATTTTATT
Found at i:3272 original size:16 final size:16
Alignment explanation
Indices: 3251--3285 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3241 CAATAAATTA
* *
3251 TTATATTAGTTATAAT
1 TTATATTAATAATAAT
3267 TTATATTAATAATAAT
1 TTATATTAATAATAAT
3283 TTA
1 TTA
3286 AACAATAGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTATATTAATAATAAT
Found at i:4367 original size:33 final size:36
Alignment explanation
Indices: 4305--4373 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 36
4295 TAAATTAGTA
4305 TTATATAATAATATATAATAATATTAATTTTACTATC
1 TTATATAATAATATATAATAATA-TAATTTTACTATC
*
4342 TTATA-AATATTAT-TAATAATA-AATTTTACTAT
1 TTATATAATAATATATAATAATATAATTTTACTAT
4374 TAATACTAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 11 0.35
35 8 0.26
36 7 0.23
37 5 0.16
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (36 bp):
TTATATAATAATATATAATAATATAATTTTACTATC
Found at i:4529 original size:13 final size:13
Alignment explanation
Indices: 4510--4550 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
4500 GTTTTGAAAA
4510 ATAATTAATTAATT
1 ATAATTAA-TAATT
4524 -TAATTAATAATT
1 ATAATTAATAATT
4536 ATAATATAATAATT
1 ATAAT-TAATAATT
4550 A
1 A
4551 ATAACAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.20
13 11 0.44
14 9 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
ATAATTAATAATT
Found at i:4732 original size:11 final size:11
Alignment explanation
Indices: 4709--4751 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
4699 AACAATTTTA
4709 AATATTATTATT
1 AATATT-TTATT
4721 AATATTTTATT
1 AATATTTTATT
*
4732 AATTGTTTATATT
1 AA-TATTT-TATT
4745 AATATTT
1 AATATTT
4752 AAATAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 7 0.26
12 14 0.52
13 6 0.22
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
AATATTTTATT
Found at i:4733 original size:24 final size:24
Alignment explanation
Indices: 4706--4751 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4696 AGTAACAATT
4706 TTAAATA-TTATTATTAATATTTTA
1 TTAAATATTTA-TATTAATATTTTA
* *
4730 TTAATTGTTTATATTAATATTT
1 TTAAATATTTATATTAATATTT
4752 AAATAATTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
TTAAATATTTATATTAATATTTTA
Found at i:4985 original size:42 final size:46
Alignment explanation
Indices: 4898--4985 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 46
4888 AATTAGTTTA
*
4898 ATTTATATTAAATTAATTCATAAATATAATAAATATTTAAAATTTT
1 ATTTATATTAAATTAATTCATAAATATAATAAATAATTAAAATTTT
* *
4944 ATTTAT-TT-AATTAATT-A-AAATATAA-ATATCAATTAATATTTT
1 ATTTATATTAAATTAATTCATAAATATAATAAAT-AATTAAAATTTT
4986 TAAATAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
41 3 0.08
42 18 0.47
43 1 0.03
44 8 0.21
45 2 0.05
46 6 0.16
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (46 bp):
ATTTATATTAAATTAATTCATAAATATAATAAATAATTAAAATTTT
Found at i:5094 original size:15 final size:15
Alignment explanation
Indices: 5074--5107 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
5064 TTATTTATAT
5074 AATTAAAATTATTTA
1 AATTAAAATTATTTA
5089 AATTAAAATTATTTA
1 AATTAAAATTATTTA
5104 AATT
1 AATT
5108 TTGTTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTAAAATTATTTA
Found at i:5194 original size:15 final size:14
Alignment explanation
Indices: 5174--5208 Score: 54
Period size: 13 Copynumber: 2.5 Consensus size: 14
5164 ATAGTTAATA
5174 ATTTAATAATTATAT
1 ATTTAA-AATTATAT
5189 ATTT-AAATTATAT
1 ATTTAAAATTATAT
5202 ATTTAAA
1 ATTTAAA
5209 TCATAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.63
14 3 0.16
15 4 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATTTAAAATTATAT
Found at i:5199 original size:13 final size:13
Alignment explanation
Indices: 5181--5209 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
5171 ATAATTTAAT
5181 AATTATATATTTA
1 AATTATATATTTA
5194 AATTATATATTTA
1 AATTATATATTTA
5207 AAT
1 AAT
5210 CATAAGAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATTATATATTTA
Found at i:5457 original size:17 final size:17
Alignment explanation
Indices: 5435--5479 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
5425 CCATTTATGA
5435 AATATTAGA-TAATTAAT
1 AATATTA-ATTAATTAAT
5452 AATATTAATTAATTAAT
1 AATATTAATTAATTAAT
*
5469 ATTTATTAATT
1 A-ATATTAATT
5480 TTATTAATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AATATTAATTAATTAAT
Found at i:7936 original size:19 final size:19
Alignment explanation
Indices: 7912--7948 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
7902 AAATTTATTT
7912 TTAAAT-TTAATTTAAATAA
1 TTAAATATTAA-TTAAATAA
7931 TTAAATATTAATTAAATA
1 TTAAATATTAATTAAATA
7949 TATGACTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATATTAATTAAATAA
Found at i:8498 original size:16 final size:17
Alignment explanation
Indices: 8466--8498 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
8456 AACAAGTACA
8466 AATAATTATAACTATTTG
1 AATAATTAT-ACTATTTG
8484 AATAATTAT-CTATTT
1 AATAATTATACTATTT
8499 CTAATCGCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.03, T:0.48
Consensus pattern (17 bp):
AATAATTATACTATTTG
Found at i:9455 original size:13 final size:13
Alignment explanation
Indices: 9437--9482 Score: 53
Period size: 13 Copynumber: 3.8 Consensus size: 13
9427 ATAGTTATTA
*
9437 ATATTAATATACT
1 ATATTAATATAAT
*
9450 ATATTATTATAAT
1 ATATTAATATAAT
9463 A-ATT--TATAAT
1 ATATTAATATAAT
9473 ATATTAATAT
1 ATATTAATAT
9483 TTAAATTATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
10 7 0.25
11 3 0.11
12 3 0.11
13 15 0.54
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (13 bp):
ATATTAATATAAT
Found at i:9687 original size:22 final size:21
Alignment explanation
Indices: 9659--9726 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
9649 ATTTTATATG
9659 TATTATATAAATATTAAGTAAT
1 TATTATATAAATATTAA-TAAT
* *
9681 TATTATATAATTTATTTATAAT
1 TATTATATAA-ATATTAATAAT
* * *
9703 T-TAATATAAATATAAATATT
1 TATTATATAAATATTAATAAT
9723 TATT
1 TATT
9727 TGAACAATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 5
0.73 0.16 0.10
Matches are distributed among these distances:
20 8 0.22
21 8 0.22
22 15 0.42
23 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.51
Consensus pattern (21 bp):
TATTATATAAATATTAATAAT
Found at i:10579 original size:13 final size:13
Alignment explanation
Indices: 10561--10602 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
10551 ATCTATTAAT
10561 TAATTAAAATCAA
1 TAATTAAAATCAA
*
10574 TAATTAAAAT-ATT
1 TAATTAAAATCA-A
10587 TAAATTAAAATCAA
1 T-AATTAAAATCAA
10601 TA
1 TA
10603 TTCAGATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
12 1 0.04
13 12 0.50
14 10 0.42
15 1 0.04
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (13 bp):
TAATTAAAATCAA
Found at i:10622 original size:27 final size:28
Alignment explanation
Indices: 10555--10622 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
10545 TTAAATATCT
10555 ATTAATTAATTAAAATCAATAATTAAAATA
1 ATTAA-TAA-TAAAATCAATAATTAAAATA
* * * *
10585 TTTAA-ATTAAAATCAAT-ATTCAGATA
1 ATTAATAATAAAATCAATAATTAAAATA
10611 ATTAATAATAAA
1 ATTAATAATAAA
10623 TTATAAGTAT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
26 11 0.35
27 15 0.48
28 1 0.03
30 4 0.13
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.37
Consensus pattern (28 bp):
ATTAATAATAAAATCAATAATTAAAATA
Found at i:10964 original size:14 final size:13
Alignment explanation
Indices: 10942--11057 Score: 53
Period size: 14 Copynumber: 8.7 Consensus size: 13
10932 CAGTCTTTTT
10942 ATTAATATTAATA
1 ATTAATATTAATA
*
10955 ATTCAATATTATTA
1 ATT-AATATTAATA
*
10969 TTTAA-ATATAATA
1 ATTAATAT-TAATA
10982 A-TAATATTAA-A
1 ATTAATATTAATA
*
10993 A-TATTATTTAAATA
1 ATTAATA-TT-AATA
* *
11007 ATTAATTTTTAATT
1 ATTAA-TATTAATA
**
11021 ATTTTTAATTAATAAA
1 ATTAAT-ATTAAT--A
*
11037 ATAAATATTAATA
1 ATTAATATTAATA
11050 A-TAATATT
1 ATTAATATT
11058 TCATTATTAT
Statistics
Matches: 76, Mismatches: 16, Indels: 23
0.66 0.14 0.20
Matches are distributed among these distances:
11 6 0.08
12 16 0.21
13 16 0.21
14 24 0.32
15 10 0.13
16 4 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTAATATTAATA
Found at i:10986 original size:30 final size:30
Alignment explanation
Indices: 10950--11006 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
10940 TTATTAATAT
*
10950 TAATAAT-TCAATATTATTATTTAAATATAA
1 TAATAATATCAA-AATATTATTTAAATATAA
*
10980 TAATAATATTAAAATATTATTTAAATA
1 TAATAATATCAAAATATTATTTAAATA
11007 ATTAATTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 21 0.88
31 3 0.12
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.46
Consensus pattern (30 bp):
TAATAATATCAAAATATTATTTAAATATAA
Found at i:11006 original size:25 final size:24
Alignment explanation
Indices: 10978--11035 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
10968 ATTTAAATAT
10978 AATAATAATATTAAAATATTATTTA
1 AATAATAATATTAAAATATT-TTTA
* * *
11003 AATAATTAATTTTTAATTATTTTTA
1 AATAA-TAATATTAAAATATTTTTA
*
11028 ATTAATAA
1 AATAATAA
11036 AATAAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
24 3 0.11
25 13 0.46
26 12 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
AATAATAATATTAAAATATTTTTA
Found at i:11044 original size:56 final size:60
Alignment explanation
Indices: 10962--11087 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 60
10952 ATAATTCAAT
*
10962 ATTATTATTTAAATATAATAATAATATTAA-AATATTATTT-A-AATAATTAATTT-TTA
1 ATTATTATTTAAATATAATAATAATATTAATAATAATATTTCATAATAATTAATTTGTTA
* * *
11018 ATTATT-TTTAATTAATAA-AATAAATATTAATAATAATATTTCATTATTATTAATTTGTTA
1 ATTATTATTTAAAT-ATAATAAT-AATATTAATAATAATATTTCATAATAATTAATTTGTTA
*
11078 ATTAATATTT
1 ATTATTATTT
11088 GTCATGAATA
Statistics
Matches: 58, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
55 9 0.16
56 18 0.31
57 9 0.16
58 1 0.02
59 10 0.17
60 8 0.14
61 3 0.05
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.52
Consensus pattern (60 bp):
ATTATTATTTAAATATAATAATAATATTAATAATAATATTTCATAATAATTAATTTGTTA
Found at i:11571 original size:19 final size:19
Alignment explanation
Indices: 11523--11572 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
11513 AAAGTAAATG
*
11523 CTAATTAATTAATTTAATTA
1 CTAA-TAATTAAATTAATTA
*
11543 ATGAAT-ATTAAATTAATTA
1 CT-AATAATTAAATTAATTA
11562 CTAATAATTAA
1 CTAATAATTAA
11573 TTTATTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.12
19 18 0.72
20 2 0.08
21 2 0.08
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
CTAATAATTAAATTAATTA
Found at i:12001 original size:31 final size:31
Alignment explanation
Indices: 11939--12004 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
11929 TATTTAAATA
*
11939 ATTAATATTTATTATCTATTATAAATTTATT
1 ATTAATATTTATTATCTATTATAAATATATT
* *
11970 ATTAATTTTTATTA-CTA-TAT-AATATAAT
1 ATTAATATTTATTATCTATTATAAATATATT
11998 ATTAATA
1 ATTAATA
12005 ATAGATTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 12 0.39
29 3 0.10
30 3 0.10
31 13 0.42
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (31 bp):
ATTAATATTTATTATCTATTATAAATATATT
Found at i:12591 original size:19 final size:18
Alignment explanation
Indices: 12533--12601 Score: 63
Period size: 19 Copynumber: 3.9 Consensus size: 18
12523 AACAAAAGGT
*
12533 TATAATAATTTGAAATA-
1 TATAATTATTTGAAATAG
* *
12550 TATAATTGTTT-AAGTAG
1 TATAATTATTTGAAATAG
*
12567 TAATAATTATTTGAACTAG
1 T-ATAATTATTTGAAATAG
12586 TCATAATTATTT-AAAT
1 T-ATAATTATTTGAAAT
12602 TGGTTTGGTA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
16 4 0.10
17 10 0.24
18 12 0.29
19 16 0.38
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (18 bp):
TATAATTATTTGAAATAG
Found at i:12892 original size:26 final size:28
Alignment explanation
Indices: 12832--12893 Score: 85
Period size: 26 Copynumber: 2.3 Consensus size: 28
12822 TAATAAAGTA
*
12832 ATATTATTTTAATAGTACAATAATTATT
1 ATATTATTCTAATAGTACAATAATTATT
12860 -TATTTATTCTAA-A-TACAATAATTATT
1 ATA-TTATTCTAATAGTACAATAATTATT
12886 ATATTATT
1 ATATTATT
12894 TATAATTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
26 18 0.58
27 5 0.16
28 8 0.26
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (28 bp):
ATATTATTCTAATAGTACAATAATTATT
Found at i:13061 original size:24 final size:24
Alignment explanation
Indices: 13014--13080 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
13004 ATCATACTAT
**
13014 TATTATTAATATTAATAATTATAA
1 TATTATTAATATTAATAAAAATAA
* *
13038 TATTATTTATCTTAATAAAAATAA
1 TATTATTAATATTAATAAAAATAA
* *
13062 TTTTA-TATGTATTAATAAA
1 TATTATTA-ATATTAATAAA
13081 TATTAAGTAA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
23 1 0.03
24 33 0.97
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
TATTATTAATATTAATAAAAATAA
Found at i:14386 original size:35 final size:35
Alignment explanation
Indices: 14321--14388 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
14311 AATATAAAAC
*
14321 AATAAATATTTAATATTATTTTACAAATAATATAT
1 AATAAATATTTAATATTATTTGACAAATAATATAT
*
14356 AATATATATTT-ATA-TATTTGACTAATATAATAT
1 AATAAATATTTAATATTATTTGAC-AA-ATAATAT
14389 TATTTACTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 7 0.24
34 5 0.17
35 17 0.59
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (35 bp):
AATAAATATTTAATATTATTTGACAAATAATATAT
Found at i:14414 original size:28 final size:28
Alignment explanation
Indices: 14352--14412 Score: 83
Period size: 26 Copynumber: 2.3 Consensus size: 28
14342 TACAAATAAT
14352 ATATAATATATATTTATATATTTGACTA
1 ATATAATATATATTTATATATTTGACTA
* *
14380 ATATAATAT-TATTTA-CTATTTGATTA
1 ATATAATATATATTTATATATTTGACTA
14406 AT-TAATA
1 ATATAATA
14413 ATTGTTGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 5 0.16
26 11 0.35
27 6 0.19
28 9 0.29
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (28 bp):
ATATAATATATATTTATATATTTGACTA
Found at i:14508 original size:18 final size:18
Alignment explanation
Indices: 14485--14536 Score: 56
Period size: 17 Copynumber: 3.0 Consensus size: 18
14475 TTAATTTGTC
14485 ATTAATTTTATAATATTA
1 ATTAATTTTATAATATTA
*
14503 ATTAATTATA-AATATT-
1 ATTAATTTTATAATATTA
*
14519 A-TAATACTTATAATATTA
1 ATTAAT-TTTATAATATTA
14537 TAAATTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
15 4 0.14
16 3 0.11
17 12 0.43
18 9 0.32
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAATTTTATAATATTA
Found at i:14518 original size:17 final size:17
Alignment explanation
Indices: 14485--14578 Score: 55
Period size: 18 Copynumber: 5.1 Consensus size: 17
14475 TTAATTTGTC
*
14485 ATTAATTTTATAATATTA
1 ATTAATTATA-AATATTA
14503 ATTAATTATAAATATTA
1 ATTAATTATAAATATTA
* * *
14520 TAATACTTATAATATTATAA
1 -ATTAATTATAA-A-TATTA
14540 ATTAATATGAATAAATTATTAA
1 ATTAAT-T--ATAAA-TATT-A
*
14562 ATTATTTATAAAT-TTA
1 ATTAATTATAAATATTA
14578 A
1 A
14579 AGTAATAGAT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.03
17 9 0.15
18 19 0.31
19 10 0.16
20 5 0.08
21 6 0.10
22 10 0.16
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (17 bp):
ATTAATTATAAATATTA
Found at i:14521 original size:9 final size:8
Alignment explanation
Indices: 14487--14543 Score: 55
Period size: 8 Copynumber: 7.0 Consensus size: 8
14477 AATTTGTCAT
*
14487 TAATTTTA
1 TAATATTA
14495 TAATATTA
1 TAATATTA
*
14503 -ATTAATTA
1 TAAT-ATTA
14511 TAAATATTA
1 T-AATATTA
14520 TAATACTTA
1 TAATA-TTA
14529 TAATATTA
1 TAATATTA
14537 TAA-ATTA
1 TAATATTA
14544 ATATGAATAA
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
7 6 0.14
8 21 0.50
9 13 0.31
10 2 0.05
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (8 bp):
TAATATTA
Found at i:15517 original size:18 final size:18
Alignment explanation
Indices: 15494--15551 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
15484 TTAAATATTA
*
15494 ATTATTAATGATAACTAT
1 ATTATTAATCATAACTAT
*
15512 ATTATT-ATCTTAA-T-T
1 ATTATTAATCATAACTAT
*
15527 ATTATTAATTATAAC-ATT
1 ATTATTAATCATAACTA-T
15545 ATTATTA
1 ATTATTA
15552 TTATCTTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
15 7 0.22
16 6 0.19
17 5 0.16
18 14 0.44
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (18 bp):
ATTATTAATCATAACTAT
Found at i:15541 original size:33 final size:35
Alignment explanation
Indices: 15494--15561 Score: 104
Period size: 36 Copynumber: 2.0 Consensus size: 35
15484 TTAAATATTA
15494 ATTATTAATGATAAC-TA-TATTATTATCTTAATT
1 ATTATTAATGATAACATATTATTATTATCTTAATT
*
15527 ATTATTAATTATAACATTATTATTATTATCTTAAT
1 ATTATTAATGATAACA-TATTATTATTATCTTAAT
15562 AATAACAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
33 14 0.45
35 2 0.06
36 15 0.48
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (35 bp):
ATTATTAATGATAACATATTATTATTATCTTAATT
Found at i:17461 original size:27 final size:27
Alignment explanation
Indices: 17431--17485 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
17421 TTTGTTTAAA
17431 TTAATAA-ATAA-ATTATTATTGAAAATT
1 TTAATAATATAATATT-TTATT-AAAATT
17458 TTAATAATTATAATATTTTATTAAAATT
1 TTAATAA-TATAATATTTTATTAAAATT
17486 ATTATTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
27 7 0.28
28 6 0.24
29 9 0.36
30 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (27 bp):
TTAATAATATAATATTTTATTAAAATT
Found at i:18003 original size:16 final size:15
Alignment explanation
Indices: 17963--18015 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 15
17953 AAATAATTGT
*
17963 TATAATTAATAATAA
1 TATAATTAATTATAA
*
17978 TCTAATTTAATTATATA
1 TATAA-TTAATTATA-A
*
17995 TATAATTAATTAAAA
1 TATAATTAATTATAA
18010 TATAAT
1 TATAAT
18016 ACAATATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.34
16 16 0.50
17 5 0.16
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
TATAATTAATTATAA
Found at i:18007 original size:20 final size:20
Alignment explanation
Indices: 17965--18005 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
17955 ATAATTGTTA
17965 TAATTAATAATAATCTAATT
1 TAATTAATAATAATCTAATT
17985 TAATTATATATATAAT-TAATT
1 TAATTA-ATA-ATAATCTAATT
18006 AAAATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATTAATAATAATCTAATT
Found at i:18313 original size:14 final size:14
Alignment explanation
Indices: 18290--18326 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
18280 TTGTCCAAAA
18290 TAAA-AATAATTAT
1 TAAATAATAATTAT
*
18303 TTAATAATAATTAT
1 TAAATAATAATTAT
18317 TAAAT-ATAAT
1 TAAATAATAAT
18327 AAACAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAATAATAATTAT
Found at i:18520 original size:18 final size:18
Alignment explanation
Indices: 18472--18521 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
18462 TATTAAAGAT
18472 ATTATTTATATATAATTTA
1 ATTATTTATAT-TAATTTA
**
18491 A-TAAATATTATTAATTTA
1 ATTATTTA-TATTAATTTA
18509 ATTATTTATATTA
1 ATTATTTATATTA
18522 TATATAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTATTTATATTAATTTA
Found at i:18541 original size:35 final size:37
Alignment explanation
Indices: 18472--18547 Score: 95
Period size: 37 Copynumber: 2.1 Consensus size: 37
18462 TATTAAAGAT
*
18472 ATTATTTATATATAATTTAATAAATATTATTAATTTA
1 ATTATTTATATATAATATAATAAATATTATTAATTTA
* *
18509 ATTATTTATAT-TATATATAATATA-ATTA-TAATTTG
1 ATTATTTATATATA-ATATAATAAATATTATTAATTTA
18544 ATTA
1 ATTA
18548 ATAATAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
35 10 0.29
36 6 0.17
37 19 0.54
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (37 bp):
ATTATTTATATATAATATAATAAATATTATTAATTTA
Found at i:18716 original size:18 final size:18
Alignment explanation
Indices: 18680--18718 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18670 AATTAGAATT
**
18680 AATATATTGTTATTGAAA
1 AATATATTGTTATAAAAA
*
18698 AATATATTTTTATAAAAA
1 AATATATTGTTATAAAAA
18716 AAT
1 AAT
18719 TATCTAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (18 bp):
AATATATTGTTATAAAAA
Found at i:19148 original size:14 final size:15
Alignment explanation
Indices: 19107--19172 Score: 54
Period size: 14 Copynumber: 4.7 Consensus size: 15
19097 ATGTAATAAT
19107 TTAATAA-ATTATTA
1 TTAATAATATTATTA
19121 -TAATTAA-A-TATTA
1 TTAA-TAATATTATTA
19134 TTAATAATATT-TTA
1 TTAATAATATTATTA
* *
19148 TGAATCATATTAATTA
1 TTAATAATATT-ATTA
19164 TT-ATAATAT
1 TTAATAATAT
19173 GTAATTATAA
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 11 0.26
14 20 0.48
15 7 0.17
16 4 0.10
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (15 bp):
TTAATAATATTATTA
Found at i:19207 original size:15 final size:17
Alignment explanation
Indices: 19114--19223 Score: 65
Period size: 16 Copynumber: 6.8 Consensus size: 17
19104 AATTTAATAA
* *
19114 ATTATTATA-ATTAAAT
1 ATTATTATATAATAATT
19130 ATTATTA-ATAAT-ATT
1 ATTATTATATAATAATT
* *
19145 -TTATGAATCATATTAATT
1 ATTAT-TAT-ATAATAATT
* *
19163 ATTATAATAT-GTAATT
1 ATTATTATATAATAATT
* *
19179 ATAATTGTAT-ATAA-T
1 ATTATTATATAATAATT
19194 A-TATTATATAATAATT
1 ATTATTATATAATAATT
19210 ATTTATTATATAAT
1 A-TTATTATATAAT
19224 TTAATTGGAC
Statistics
Matches: 73, Mismatches: 11, Indels: 18
0.72 0.11 0.18
Matches are distributed among these distances:
14 10 0.14
15 10 0.14
16 26 0.36
17 6 0.08
18 17 0.23
19 4 0.05
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTATTATATAATAATT
Found at i:19224 original size:15 final size:15
Alignment explanation
Indices: 19154--19224 Score: 58
Period size: 15 Copynumber: 4.7 Consensus size: 15
19144 TTTATGAATC
*
19154 ATAT-TAATTATTATA
1 ATATATAATTA-TATT
*
19169 ATATGTAATTATAATT
1 ATATATAATTAT-ATT
*
19185 GTATATAA-TATATT
1 ATATATAATTATATT
19199 ATATAATAATTAT-TT
1 ATAT-ATAATTATATT
19214 ATTATATAATT
1 A-TATATAATT
19225 TAATTGGACA
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.13
15 21 0.45
16 20 0.43
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATATAATTATATT
Done.