Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168207.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_442, 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: 26740
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Found at i:45 original size:17 final size:17
Alignment explanation
Indices: 23--112 Score: 126
Period size: 17 Copynumber: 5.0 Consensus size: 17
13 ATATACTCGC
23 TTAGATATACTTAGTAT
1 TTAGATATACTTAGTAT
40 TTAGATATACTTAGTAT
1 TTAGATATACTTAGTAT
57 TTAGATATACTTAGTATAATAT
1 TTAGATATACTTAG-----TAT
79 TTAGATATACTTAGTAT
1 TTAGATATACTTAGTAT
*
96 TTCGATATACTTAGTAT
1 TTAGATATACTTAGTAT
113 AATATTTAGA
Statistics
Matches: 67, Mismatches: 1, Indels: 10
0.86 0.01 0.13
Matches are distributed among these distances:
17 50 0.75
22 17 0.25
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (17 bp):
TTAGATATACTTAGTAT
Found at i:79 original size:22 final size:22
Alignment explanation
Indices: 54--139 Score: 128
Period size: 22 Copynumber: 4.1 Consensus size: 22
44 ATATACTTAG
54 TATTTAGATATACTTAGTATAA
1 TATTTAGATATACTTAGTATAA
76 TATTTAGATATACTTAG-----
1 TATTTAGATATACTTAGTATAA
*
93 TATTTCGATATACTTAGTATAA
1 TATTTAGATATACTTAGTATAA
115 TATTTAGATATACTTAGTATAA
1 TATTTAGATATACTTAGTATAA
137 TAT
1 TAT
140 ACGAATTATA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
17 16 0.28
22 41 0.72
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (22 bp):
TATTTAGATATACTTAGTATAA
Found at i:91 original size:39 final size:39
Alignment explanation
Indices: 37--134 Score: 187
Period size: 39 Copynumber: 2.5 Consensus size: 39
27 ATATACTTAG
37 TATTTAGATATACTTAGTATTTAGATATACTTAGTATAA
1 TATTTAGATATACTTAGTATTTAGATATACTTAGTATAA
*
76 TATTTAGATATACTTAGTATTTCGATATACTTAGTATAA
1 TATTTAGATATACTTAGTATTTAGATATACTTAGTATAA
115 TATTTAGATATACTTAGTAT
1 TATTTAGATATACTTAGTAT
135 AATATACGAA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (39 bp):
TATTTAGATATACTTAGTATTTAGATATACTTAGTATAA
Found at i:4731 original size:17 final size:17
Alignment explanation
Indices: 4709--4742 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
4699 TTAGATTTAC
4709 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
4726 TTATAATAGATAATAGA
1 TTATAATAGATAATAGA
4743 ATAAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (17 bp):
TTATAATAGATAATAGA
Found at i:4786 original size:21 final size:20
Alignment explanation
Indices: 4729--4859 Score: 90
Period size: 20 Copynumber: 6.2 Consensus size: 20
4719 TAATAGATTA
*
4729 TAAT-AGATAATAGAATAAG
1 TAATAAGATAATATAATAAG
**
4748 TAATAA-AGTAATCGAATAAG
1 TAATAAGA-TAATATAATAAG
4768 TAATAAGGATAATATAATAAG
1 TAATAA-GATAATATAATAAG
*
4789 T-ATAAAATAAGTATAAATAAG
1 TAATAAGATAA-TAT-AATAAG
4810 TATAAAATAAGTATAAGTATAAATAAG
1 --T--AATAAG-ATAA-TAT-AATAAG
*
4837 T-ATAATATAATATAATAAG
1 TAATAAGATAATATAATAAG
4856 TAAT
1 TAAT
4860 GGACAACCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
19 16 0.17
20 30 0.32
21 21 0.23
22 5 0.05
23 1 0.01
25 1 0.01
26 4 0.04
27 15 0.16
ACGTcount: A:0.58, C:0.01, G:0.11, T:0.30
Consensus pattern (20 bp):
TAATAAGATAATATAATAAG
Found at i:4793 original size:27 final size:25
Alignment explanation
Indices: 4769--4846 Score: 92
Period size: 21 Copynumber: 3.2 Consensus size: 25
4759 TCGAATAAGT
4769 AATAAGGATAATATAATAAGTATAA
1 AATAAGGATAATATAATAAGTATAA
4794 AATAA-G-T-ATA-AATAAGTATAA
1 AATAAGGATAATATAATAAGTATAA
*
4815 AATAAGTATAAGTATAAATAAGTATAA
1 AATAAGGATAA-TAT-AATAAGTATAA
*
4842 TATAA
1 AATAA
4847 TATAATAAGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
21 16 0.36
22 3 0.07
23 2 0.04
24 2 0.04
25 7 0.16
27 15 0.33
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.29
Consensus pattern (25 bp):
AATAAGGATAATATAATAAGTATAA
Found at i:4797 original size:11 final size:11
Alignment explanation
Indices: 4783--4825 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
4773 AGGATAATAT
4783 AATAAGTATAA
1 AATAAGTATAA
4794 AATAAGTAT-A
1 AATAAGTATAA
4804 AATAAGTATAA
1 AATAAGTATAA
4815 AATAAGTATAA
1 AATAAGTATAA
4826 GTATAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 10 0.32
11 21 0.68
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (11 bp):
AATAAGTATAA
Found at i:4798 original size:32 final size:31
Alignment explanation
Indices: 4762--4857 Score: 97
Period size: 32 Copynumber: 2.9 Consensus size: 31
4752 AAAGTAATCG
*
4762 AATAAGTAATAAGGATAATATAATAAGTATAA
1 AATAAGTAATAAGTATAATATAATAAGTAT-A
*
4794 AATAAGTATAAATAAGTATAAAATAAGTATAAGTATA
1 AATAAG--T-AATAAGTATAATAT-A--ATAAGTATA
4831 AATAAGT-ATAA-TATAATATAATAAGTA
1 AATAAGTAATAAGTATAATATAATAAGTA
4858 ATGGACAACC
Statistics
Matches: 55, Mismatches: 3, Indels: 15
0.75 0.04 0.21
Matches are distributed among these distances:
29 7 0.13
31 1 0.02
32 13 0.24
33 4 0.07
34 1 0.02
35 13 0.24
36 1 0.02
37 7 0.13
38 8 0.15
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.30
Consensus pattern (31 bp):
AATAAGTAATAAGTATAATATAATAAGTATA
Found at i:5047 original size:13 final size:13
Alignment explanation
Indices: 5031--5100 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
5021 AAAAAAAAAG
5031 AAATATTAAAATT
1 AAATATTAAAATT
5044 AAATATTAAAATATT
1 AAATATT-AAA-ATT
5059 AAA-ATTAAATATT
1 AAATATTAAA-ATT
5072 AAA-A--AAAATT
1 AAATATTAAAATT
5082 AAATATTAAAATT
1 AAATATTAAAATT
5095 AAATAT
1 AAATAT
5101 ATATTGTGAT
Statistics
Matches: 52, Mismatches: 0, Indels: 10
0.84 0.00 0.16
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
13 30 0.58
14 6 0.12
15 6 0.12
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
AAATATTAAAATT
Found at i:5055 original size:21 final size:21
Alignment explanation
Indices: 5031--5093 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
5021 AAAAAAAAAG
5031 AAATATTAAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
5052 AAATATTAAAATTAAATATT-
1 AAATATTAAAATTAAATATTA
5072 AAA-A--AAAATTAAATATTA
1 AAATATTAAAATTAAATATTA
5090 AAAT
1 AAAT
5094 TAAATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
17 13 0.32
18 3 0.08
19 1 0.03
20 3 0.08
21 20 0.50
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAATATTAAAATTAAATATTA
Found at i:8549 original size:22 final size:22
Alignment explanation
Indices: 8518--8568 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
8508 GTTGTTTTTA
*
8518 GAATTATAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
8540 GAATTCTAATTATATAAGAAAT
1 GAATTCTAATTATATAAGAAAT
8562 -AATTCTA
1 GAATTCTA
8569 TTTAGTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
21 7 0.25
22 21 0.75
ACGTcount: A:0.51, C:0.04, G:0.08, T:0.37
Consensus pattern (22 bp):
GAATTCTAATTATATAAGAAAT
Found at i:9544 original size:15 final size:17
Alignment explanation
Indices: 9523--9564 Score: 61
Period size: 15 Copynumber: 2.6 Consensus size: 17
9513 CAATATTCTT
9523 TTATTTTTTTTTA-TTC
1 TTATTTTTTTTTAGTTC
*
9539 -TATTTTTATTTAGTTC
1 TTATTTTTTTTTAGTTC
9555 TTATTTTTTT
1 TTATTTTTTT
9565 AATAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 11 0.50
16 3 0.14
17 8 0.36
ACGTcount: A:0.14, C:0.05, G:0.02, T:0.79
Consensus pattern (17 bp):
TTATTTTTTTTTAGTTC
Found at i:9636 original size:25 final size:25
Alignment explanation
Indices: 9603--9654 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
9593 ATTATTTATT
*
9603 TTTTTAGTTTACCGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
9628 TTTTTAGTTTACAGTCTTCGAATGA
1 TTTTTAGTTTACAGTCTTCGAATGA
9653 TT
1 TT
9655 AGGAGTTGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTTTAGTTTACAGTCTTCGAATGA
Found at i:9661 original size:25 final size:25
Alignment explanation
Indices: 9608--9661 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 25
9598 TTATTTTTTT
* ***
9608 AGTTTACCGTCTTCGAATGATTTTT
1 AGTTTACAGTCTTCGAATGATTAGG
9633 AGTTTACAGTCTTCGAATGATTAGG
1 AGTTTACAGTCTTCGAATGATTAGG
9658 AGTT
1 AGTT
9662 GGATTTTCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.13, G:0.20, T:0.43
Consensus pattern (25 bp):
AGTTTACAGTCTTCGAATGATTAGG
Found at i:9761 original size:15 final size:15
Alignment explanation
Indices: 9741--9790 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
9731 CATAATGATT
9741 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
9756 ATTTTAATATTGTTGTTA
1 ATTTTAATA---TTGTTA
9774 ATTTTAATATTGTTA
1 ATTTTAATATTGTTA
9789 AT
1 AT
9791 ATTGTATTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 17 0.53
18 15 0.47
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (15 bp):
ATTTTAATATTGTTA
Found at i:9773 original size:18 final size:18
Alignment explanation
Indices: 9750--9787 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
9740 TATTTTAATA
9750 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
9768 TTGTTAATTTTAATATTG
1 TTGTTAATTTTAATATTG
9786 TT
1 TT
9788 AATATTGTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (18 bp):
TTGTTAATTTTAATATTG
Found at i:9809 original size:17 final size:17
Alignment explanation
Indices: 9789--9822 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
9779 AATATTGTTA
*
9789 ATATTGTATTATTTATT
1 ATATTGTATGATTTATT
9806 ATATTGTATGATTTATT
1 ATATTGTATGATTTATT
9823 CATTACTATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (17 bp):
ATATTGTATGATTTATT
Found at i:9846 original size:19 final size:19
Alignment explanation
Indices: 9824--9873 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
9814 TGATTTATTC
*
9824 ATTACTATATTTTTTAGTT
1 ATTACTATATTTTGTAGTT
*
9843 ATTACTATATTTTGTATTT
1 ATTACTATATTTTGTAGTT
9862 ATTACTATATTT
1 ATTACTATATTT
9874 CATTATTTAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.28, C:0.06, G:0.04, T:0.62
Consensus pattern (19 bp):
ATTACTATATTTTGTAGTT
Found at i:9891 original size:19 final size:19
Alignment explanation
Indices: 9857--9911 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
9847 CTATATTTTG
*
9857 TATTTATTACTATATTTCAT
1 TATTTATTTCT-TATTTCAT
*
9877 TATTTATTTCTTATTTTAT
1 TATTTATTTCTTATTTCAT
* *
9896 TAATTATTTATTATTT
1 TATTTATTTCTTATTT
9912 TCGTGTCGGT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 21 0.68
20 10 0.32
ACGTcount: A:0.27, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTATTTCTTATTTCAT
Found at i:9892 original size:38 final size:38
Alignment explanation
Indices: 9819--9893 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
9809 TTGTATGATT
*
9819 TATTCATTACTATATTTTTTAGTTATTACTATATTTTG
1 TATTCATTACTATATTTATTAGTTATTACTATATTTTG
* * *
9857 TATTTATTACTATATTTCATTATTTATTTCT-TATTTT
1 TATTCATTACTATATTT-ATTAGTTATTACTATATTTT
9894 ATTAATTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
38 22 0.69
39 10 0.31
ACGTcount: A:0.25, C:0.08, G:0.03, T:0.64
Consensus pattern (38 bp):
TATTCATTACTATATTTATTAGTTATTACTATATTTTG
Found at i:9950 original size:17 final size:18
Alignment explanation
Indices: 9924--10112 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
9914 GTGTCGGTTC
*
9924 TATATATATTTA-TAAAT
1 TATATTTATTTATTAAAT
9941 TATATTTATTTATT--AT
1 TATATTTATTTATTAAAT
* * *
9957 T-TATGTA-TTATCACAGT
1 TATATTTATTTATTA-AAT
**
9974 TATAGATATTTATTTAAAT
1 TATATTTATTTA-TTAAAT
*
9993 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* **
10010 TATATTAAAATATTAAAT
1 TATATTTATTTATTAAAT
10028 TATATTTATATT-TTATATAT
1 TATATTTAT-TTATTA-A-AT
** *
10048 TAAATATATTAAAATATGAAAT
1 T--ATAT-TT-ATTTATTAAAT
*
10070 TATATTTATATATTAAA-
1 TATATTTATTTATTAAAT
* ** *
10087 TATATTAAAATATGAAAT
1 TATATTTATTTATTAAAT
10105 TATATTTA
1 TATATTTA
10113 AATAAATATC
Statistics
Matches: 130, Mismatches: 25, Indels: 33
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.03
15 5 0.04
16 3 0.02
17 42 0.32
18 35 0.27
19 18 0.14
20 9 0.07
22 7 0.05
23 4 0.03
24 3 0.02
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (18 bp):
TATATTTATTTATTAAAT
Found at i:10006 original size:8 final size:8
Alignment explanation
Indices: 9993--10099 Score: 72
Period size: 8 Copynumber: 12.6 Consensus size: 8
9983 TTATTTAAAT
*
9993 TATATTTA
1 TATATTAA
10001 TATATTAAA
1 TATATT-AA
10010 TATATTAA
1 TATATTAA
*
10018 AATATTAAA
1 TATATT-AA
*
10027 TTATATTTA
1 -TATATTAA
*
10036 TAT-TTTA
1 TATATTAA
10043 TATATTAAA
1 TATATT-AA
10052 TATATTAA
1 TATATTAA
* *
10060 AATATGAAA
1 TATAT-TAA
*
10069 TTATATTTA
1 -TATATTAA
10078 TATATTAAA
1 TATATT-AA
10087 TATATTAA
1 TATATTAA
*
10095 AATAT
1 TATAT
10100 GAAATTATAT
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
7 7 0.09
8 36 0.46
9 27 0.34
10 9 0.11
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.50
Consensus pattern (8 bp):
TATATTAA
Found at i:10023 original size:77 final size:76
Alignment explanation
Indices: 9954--10112 Score: 205
Period size: 77 Copynumber: 2.1 Consensus size: 76
9944 ATTTATTTAT
* * * *
9954 TATTTATGTATTATCACAGTTATAGATATT-TAT-TTAAATTATATTTATATATTAAATATATTA
1 TATTTATATATTAT-ACA-TTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTA
10017 AAATATTAAATTA
64 AAATATTAAATTA
* * *
10030 TATTTATATTTTATATATTAAATATATTAAAATATGAAATTATATTTATATATTAAATATATTAA
1 TATTTATATATTATACATTAAAGATATT-AAATATGAAATTATATTTATATATTAAATATATTAA
*
10095 AATATGAAATTA
65 AATATTAAATTA
10107 TATTTA
1 TATTTA
10113 AATAAATATC
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
74 9 0.12
75 2 0.03
76 14 0.19
77 47 0.65
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.50
Consensus pattern (76 bp):
TATTTATATATTATACATTAAAGATATTAAATATGAAATTATATTTATATATTAAATATATTAAA
ATATTAAATTA
Found at i:10026 original size:35 final size:35
Alignment explanation
Indices: 9989--10112 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
9979 ATATTTATTT
*
9989 AAATTATATTTATATATTAAATATATTAAAATATTAA
1 AAATTATATTTATATATTAAATATATTAAAATA-T-G
10026 ATTATATTTATATTTTATATATTAAATATATTAAAATATG
1 A--A-A-TTATA-TTTATATATTAAATATATTAAAATATG
10066 AAATTATATTTATATATTAAATATATTAAAATATG
1 AAATTATATTTATATATTAAATATATTAAAATATG
10101 AAATTATATTTA
1 AAATTATATTTA
10113 AATAAATATC
Statistics
Matches: 81, Mismatches: 1, Indels: 12
0.86 0.01 0.13
Matches are distributed among these distances:
35 39 0.48
36 5 0.06
37 2 0.02
38 1 0.01
39 1 0.01
40 2 0.02
41 6 0.07
42 25 0.31
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (35 bp):
AAATTATATTTATATATTAAATATATTAAAATATG
Found at i:10131 original size:4 final size:4
Alignment explanation
Indices: 10124--10251 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
10114 ATAAATATCT
*
10124 ATAA AT-A ATATA AT-A ATAAA ATAA ACT-A ATAAA ATAA ACAA ATAA
1 ATAA ATAA ATA-A ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA
* *
10169 AT-A ATAA ATAA ATAA TTAAA ATAA ACT-A ATAAA ATAA ACAA ATAA AT-A
1 ATAA ATAA ATAA ATAA AT-AA ATAA A-TAA AT-AA ATAA ATAA ATAA ATAA
*
10217 AGAA ATAA AT-A ATAA ATAA AT-A ATACA AT-A ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A ATAA ATAA A
10252 AAAAACAAAG
Statistics
Matches: 99, Mismatches: 8, Indels: 34
0.70 0.06 0.24
Matches are distributed among these distances:
3 22 0.22
4 57 0.58
5 20 0.20
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:10146 original size:13 final size:13
Alignment explanation
Indices: 10137--10214 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
10127 AATAATATAA
10137 TAATAAAATAAAC
1 TAATAAAATAAAC
10150 TAATAAAATAAAC
1 TAATAAAATAAAC
10163 -----AAATAAA-
1 TAATAAAATAAAC
10170 TAAT-AAATAAA-
1 TAATAAAATAAAC
10181 TAATTAAAATAAAC
1 TAA-TAAAATAAAC
10195 TAATAAAATAAAC
1 TAATAAAATAAAC
*
10208 AAATAAA
1 TAATAAA
10215 TAAGAAATAA
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 7 0.12
11 10 0.18
12 1 0.02
13 36 0.63
14 3 0.05
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (13 bp):
TAATAAAATAAAC
Found at i:10251 original size:45 final size:44
Alignment explanation
Indices: 10130--10247 Score: 186
Period size: 45 Copynumber: 2.7 Consensus size: 44
10120 ATCTATAAAT
*
10130 AATATAATAATAAAATAAACTAATAAAATAAACAAATAAATAATA
1 AATA-AATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
10175 AATAAATAATTAAAATAAACTAATAAAATAAACAAATAAATAAGA
1 AATAAATAA-TAAAATAAACTAATAAAATAAACAAATAAATAAGA
*
10220 AATAAATAAT-AAATAAA-TAATACAATAA
1 AATAAATAATAAAATAAACTAATAAAATAA
10248 TAAAAAAAAC
Statistics
Matches: 70, Mismatches: 2, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
42 10 0.14
43 7 0.10
44 6 0.09
45 47 0.67
ACGTcount: A:0.71, C:0.04, G:0.01, T:0.24
Consensus pattern (44 bp):
AATAAATAATAAAATAAACTAATAAAATAAACAAATAAATAAGA
Found at i:12370 original size:30 final size:30
Alignment explanation
Indices: 12336--12675 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
12326 AAATGGTGTT
12336 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12366 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12396 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12426 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12456 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12486 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12516 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12546 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12576 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12606 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12636 CCATTGTCGTCAAATGGTGGTCTTCCATTG
1 CCATTGTCGTCAAATGGTGGTCTTCCATTG
12666 CCATTGTCGT
1 CCATTGTCGT
12676 TAACTAGTCT
Statistics
Matches: 310, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 310 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (30 bp):
CCATTGTCGTCAAATGGTGGTCTTCCATTG
Found at i:12716 original size:18 final size:18
Alignment explanation
Indices: 12689--12923 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
12679 CTAGTCTCCA
*
12689 TTTTTTATTCACTATAGG
1 TTTTTCATTCACTATAGG
12707 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
12725 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
12743 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
12761 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12779 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12797 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12815 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12833 TTTGTT-ATTCACTATAGG
1 TTT-TTCATTCACTATAGG
12851 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12869 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12887 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12905 TTTTTCATTCACTATAGG
1 TTTTTCATTCACTATAGG
12923 T
1 T
12924 CTCGATTCTG
Statistics
Matches: 213, Mismatches: 0, Indels: 8
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.02
18 205 0.96
19 4 0.02
ACGTcount: A:0.22, C:0.14, G:0.13, T:0.51
Consensus pattern (18 bp):
TTTTTCATTCACTATAGG
Found at i:13264 original size:18 final size:18
Alignment explanation
Indices: 13241--13278 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13231 TTTTTTGCGC
13241 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
13259 ATTGCATACGGCTTTACA
1 ATTGCATACGGCTTTACA
13277 AT
1 AT
13279 GGAATTCTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (18 bp):
ATTGCATACGGCTTTACA
Found at i:15212 original size:78 final size:78
Alignment explanation
Indices: 15083--15251 Score: 320
Period size: 78 Copynumber: 2.2 Consensus size: 78
15073 AGTAAAAAGA
* *
15083 ATGTAAAATTATATTTCGCTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
15148 TTATCTTAATAAT
66 TTATCTTAATAAT
15161 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
1 ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
15226 TTATCTTAATAAT
66 TTATCTTAATAAT
15239 ATGTAATATTATA
1 ATGTAATATTATA
15252 ATATGTAATA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
78 89 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (78 bp):
ATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAATGGTC
TTATCTTAATAAT
Found at i:15254 original size:15 final size:15
Alignment explanation
Indices: 15234--15266 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
15224 TCTTATCTTA
15234 ATAATATGTAATATT
1 ATAATATGTAATATT
15249 ATAATATGTAATATT
1 ATAATATGTAATATT
15264 ATA
1 ATA
15267 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:15347 original size:15 final size:15
Alignment explanation
Indices: 15327--15359 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
15317 TCTTATCTTA
15327 ATAATATGTAATATT
1 ATAATATGTAATATT
15342 ATAATATGTAATATT
1 ATAATATGTAATATT
15357 ATA
1 ATA
15360 TTTCACTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
ATAATATGTAATATT
Found at i:15448 original size:93 final size:93
Alignment explanation
Indices: 15156--15432 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
15146 TCTTATCTTA
15156 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
15221 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
15249 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
15314 TGGTCTTATCTTAATAATATGTAATATT
66 TGGTCTTATCTTAATAATATGTAATATT
15342 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
1 ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
15407 TGGTCTTATCTTAATAATATGTAATA
66 TGGTCTTATCTTAATAATATGTAATA
15433 ATGGTCTTAA
Statistics
Matches: 184, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
93 184 1.00
ACGTcount: A:0.37, C:0.08, G:0.14, T:0.42
Consensus pattern (93 bp):
ATAATATGTAATATTATATTTCACTTTGATTGTGGAAGCGTAATACGTAATGTAATACGTAATAA
TGGTCTTATCTTAATAATATGTAATATT
Found at i:17837 original size:21 final size:20
Alignment explanation
Indices: 17812--17879 Score: 86
Period size: 21 Copynumber: 3.4 Consensus size: 20
17802 TTCCATTATT
*
17812 ATATAATTATATAAATAATAT
1 ATATAATTATATAAAT-ATAA
17833 ATATAA--ATATAAATATAA
1 ATATAATTATATAAATATAA
*
17851 ATATAAATAATATAAATATAA
1 ATAT-AATTATATAAATATAA
17872 ATATAATT
1 ATATAATT
17880 TCAAGATCAC
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 7 0.17
19 10 0.24
20 3 0.07
21 22 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
ATATAATTATATAAATATAA
Found at i:17844 original size:6 final size:6
Alignment explanation
Indices: 17820--17877 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
17810 TTATATAATT
*
17820 ATATAA ATAATAT ATATAA ATATAA ATATAA ATAT-A A-AT-A ATATAA
1 ATATAA AT-ATAA ATATAA ATATAA ATATAA ATATAA ATATAA ATATAA
17866 ATATAA ATATAA
1 ATATAA ATATAA
17878 TTTCAAGATC
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
4 4 0.09
5 4 0.09
6 34 0.72
7 5 0.11
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (6 bp):
ATATAA
Found at i:17856 original size:27 final size:26
Alignment explanation
Indices: 17812--17877 Score: 89
Period size: 27 Copynumber: 2.5 Consensus size: 26
17802 TTCCATTATT
*
17812 ATATAATTATATAAAT-AATATATATAA
1 ATATAAATATA-AAATAAATA-ATATAA
17839 ATATAAATATAAATATAAATAATATAA
1 ATATAAATATAAA-ATAAATAATATAA
17866 ATATAAATATAA
1 ATATAAATATAA
17878 TTTCAAGATC
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (26 bp):
ATATAAATATAAAATAAATAATATAA
Found at i:19841 original size:23 final size:23
Alignment explanation
Indices: 19815--19860 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
19805 TATATTGTAA
19815 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
19838 CCAATCATTTATCTTATTACTTG
1 CCAATCATTTATCTTATTACTTG
19861 GGGGAGGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.22, G:0.04, T:0.48
Consensus pattern (23 bp):
CCAATCATTTATCTTATTACTTG
Found at i:25364 original size:21 final size:21
Alignment explanation
Indices: 25340--25383 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
25330 GATTCTTTGC
25340 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
25361 TTTGAGATTTTATCTGATCTA
1 TTTGAGATTTTATCTGATCTA
25382 TT
1 TT
25384 ATAAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.09, G:0.14, T:0.55
Consensus pattern (21 bp):
TTTGAGATTTTATCTGATCTA
Found at i:25391 original size:21 final size:21
Alignment explanation
Indices: 25340--25391 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
25330 GATTCTTTGC
*
25340 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
*
25361 TTTGAGATTTTATCTGATCTA
1 TTTGAAATTTTATCTGATCTA
25382 TTAT-AAATTT
1 TT-TGAAATTT
25392 GTATATCTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.54
Consensus pattern (21 bp):
TTTGAAATTTTATCTGATCTA
Found at i:25586 original size:20 final size:20
Alignment explanation
Indices: 25561--25639 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
25551 AACAATCAAA
25561 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
***
25581 TAAAATGAAAATAAAA-AAA
1 TAAAATGAAAATAAAATTTT
*
25600 AAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
25620 TAAAATGAAAATAAAATTTT
1 TAAAATGAAAATAAAATTTT
25640 CGCGGGCGAA
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
19 15 0.30
20 35 0.70
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
TAAAATGAAAATAAAATTTT
Found at i:25914 original size:24 final size:25
Alignment explanation
Indices: 25871--25934 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
25861 TGGAGCCTTA
**
25871 ATTTAATATTTAATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
25896 ATTTAATAAA-AATAAAAATTTAAT
1 ATTTAATAAATAATAAAAATTTAAT
25920 ATTTAATAAATAATA
1 ATTTAATAAATAATA
25935 TTTAATAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 24 0.67
25 12 0.33
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
ATTTAATAAATAATAAAAATTTAAT
Found at i:25929 original size:18 final size:18
Alignment explanation
Indices: 25870--25908 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
25860 ATGGAGCCTT
25870 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
25888 AATTTAATATTTAATAAA
1 AATTTAATATTTAATAAA
25906 AAT
1 AAT
25909 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTTAATATTTAATAAA
Found at i:25935 original size:14 final size:14
Alignment explanation
Indices: 25916--25943 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25906 AATAAAAATT
25916 TAATATTTAATAAA
1 TAATATTTAATAAA
25930 TAATATTTAATAAA
1 TAATATTTAATAAA
25944 AAAATTTGTT
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:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
TAATATTTAATAAA
Found at i:25948 original size:18 final size:18
Alignment explanation
Indices: 25874--25948 Score: 73
Period size: 18 Copynumber: 4.1 Consensus size: 18
25864 AGCCTTAATT
**
25874 TAATATTTAATAAAAATT
1 TAATATTTAATAAAAAAA
25892 TAATATTTAATAAAAATAA
1 TAATATTTAATAAAAA-AA
*
25911 -AA-ATTTAATATTTAATAAA
1 TAATATTTAATA---AAAAAA
25930 TAATATTTAATAAAAAAA
1 TAATATTTAATAAAAAAA
25948 T
1 T
25949 TTGTTAATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 12
0.75 0.06 0.19
Matches are distributed among these distances:
17 8 0.17
18 24 0.51
19 2 0.04
20 5 0.11
21 8 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATATTTAATAAAAAAA
Done.