Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168374.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_593, 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: 21989
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Found at i:598 original size:14 final size:14
Alignment explanation
Indices: 579--606 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
569 AACAAATTTT
579 TTTATTAAATATTA
1 TTTATTAAATATTA
593 TTTATTAAATATTA
1 TTTATTAAATATTA
607 AATTTTTATT
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:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTATTAAATATTA
Found at i:624 original size:17 final size:18
Alignment explanation
Indices: 614--652 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
604 TTAAATTTTT
614 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
632 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
650 ATT
1 ATT
653 AAGGCTCCAT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTATTAAATATTAA
Found at i:624 original size:24 final size:25
Alignment explanation
Indices: 588--651 Score: 103
Period size: 24 Copynumber: 2.6 Consensus size: 25
578 TTTTATTAAA
588 TATTATTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAATTTT
613 TATT-TTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAATTTT
**
637 TATTAAATATTAAAT
1 TATTATTTATTAAAT
652 TAAGGCTCCA
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:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (25 bp):
TATTATTTATTAAATATTAAATTTT
Found at i:927 original size:12 final size:12
Alignment explanation
Indices: 907--962 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
897 ATTTTAAAAA
907 TTTTATTTTCAT
1 TTTTATTTTCAT
* *
919 TTTTTTTTTTAT
1 TTTTATTTTCAT
* * *
931 TTTCATTTTAAAA
1 TTTTATTTT-CAT
944 TTTTATTTTCA-
1 TTTTATTTTCAT
955 TTTTATTT
1 TTTTATTT
963 GATTGTTAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 8 0.23
12 18 0.51
13 9 0.26
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTATTTTCAT
Found at i:930 original size:18 final size:19
Alignment explanation
Indices: 883--959 Score: 111
Period size: 20 Copynumber: 4.1 Consensus size: 19
873 TTCGCCCGCG
883 AAAATTTTATTTTCATTTT
1 AAAATTTTATTTTCATTTT
902 AAAAATTTTATTTTCATTTT
1 -AAAATTTTATTTTCATTTT
***
922 -TTTTTTTATTTTCATTTT
1 AAAATTTTATTTTCATTTT
940 AAAATTTTATTTTCATTTT
1 AAAATTTTATTTTCATTTT
959 A
1 A
960 TTTGATTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
18 15 0.30
19 16 0.32
20 19 0.38
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (19 bp):
AAAATTTTATTTTCATTTT
Found at i:953 original size:37 final size:38
Alignment explanation
Indices: 887--958 Score: 137
Period size: 37 Copynumber: 1.9 Consensus size: 38
877 CCCGCGAAAA
887 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
925 TTTTATTTTCATTTT-AAAATTTTATTTTCATTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
959 ATTTGATTGT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 19 0.56
38 15 0.44
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (38 bp):
TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
Found at i:976 original size:37 final size:37
Alignment explanation
Indices: 886--976 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 37
876 GCCCGCGAAA
* *
886 ATTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCA-TTTTT
* * *
924 TTTTTATTTTCATTTT-AAAATTTTATTTTCA-TTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
959 ATTTGATTGTTAAATTTT
1 ATTTGATT-TT-AATTTT
977 GTCGATCCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
35 10 0.21
36 2 0.04
37 20 0.43
38 15 0.32
ACGTcount: A:0.25, C:0.04, G:0.02, T:0.68
Consensus pattern (37 bp):
ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
Found at i:1161 original size:21 final size:21
Alignment explanation
Indices: 1137--1180 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1127 ACAAATTTAT
1137 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
1158 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
1179 AA
1 AA
1181 GCAAAGAATC
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:0.55, C:0.14, G:0.09, T:0.23
Consensus pattern (21 bp):
AATAGATCAGATAAAATCTCA
Found at i:6692 original size:23 final size:23
Alignment explanation
Indices: 6666--6711 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6656 GTTCCTCCCC
6666 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6689 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6712 TTACAATATA
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:0.48, C:0.04, G:0.22, T:0.26
Consensus pattern (23 bp):
CAAGTAATAAGATAAATGATTGG
Found at i:8667 original size:6 final size:6
Alignment explanation
Indices: 8656--8713 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
8646 GATCTTGAAA
8656 TTATAT TTATAT TTATA- -T-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
8701 ATATTAT TTATAT
1 TTA-TAT TTATAT
8714 AATTATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
3 2 0.04
4 1 0.02
5 1 0.02
6 37 0.80
7 5 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTATAT
Found at i:8682 original size:21 final size:21
Alignment explanation
Indices: 8656--8722 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
8646 GATCTTGAAA
8656 TTATATTTATATTTATATTAT
1 TTATATTTATATTTATATTAT
8677 TTATATTTATATTTATATT-T
1 TTATATTTATATTTATATTAT
* * *
8697 ATATATAT-TATTTATATAAT
1 TTATATTTATATTTATATTAT
8717 TATATA
1 T-TATA
8723 ATAATGGAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.22
20 8 0.20
21 23 0.57
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
TTATATTTATATTTATATTAT
Found at i:8714 original size:27 final size:27
Alignment explanation
Indices: 8656--8713 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
8646 GATCTTGAAA
8656 TTATATTTATATTTATATTATTTATAT
1 TTATATTTATATTTATATTATTTATAT
*
8683 TTATATTTATATTTATA-TATAT-TAT
1 TTATATTTATATTTATATTATTTATAT
8708 TTATAT
1 TTATAT
8714 AATTATATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 9 0.30
26 4 0.13
27 17 0.57
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (27 bp):
TTATATTTATATTTATATTATTTATAT
Found at i:8719 original size:27 final size:29
Alignment explanation
Indices: 8654--8721 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
8644 GTGATCTTGA
8654 AATTATATTTATATTTATATTATTTATATTT
1 AATTATATTTATA-TTATATTATTTATA-TT
8685 ATATTTATATTTATA-TATATTATTTATA-T
1 A-A-TTATATTTATATTATATTATTTATATT
8714 AATTATAT
1 AATTATAT
8722 AATAATGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.17
28 1 0.03
29 2 0.06
31 14 0.40
32 1 0.03
33 11 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (29 bp):
AATTATATTTATATTATATTATTTATATT
Found at i:11195 original size:15 final size:15
Alignment explanation
Indices: 11175--11207 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11165 CAAAGTGAAA
11175 TATAATATTACATAT
1 TATAATATTACATAT
11190 TATAATATTACATAT
1 TATAATATTACATAT
11205 TAT
1 TAT
11208 TAAGATAAGA
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATTACATAT
Found at i:11274 original size:78 final size:78
Alignment explanation
Indices: 11190--11451 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 78
11180 TATTACATAT
11190 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
11255 AATCAAAGTGAAA
66 AATCAAAGTGAAA
* * ** * *
11268 TATAATATTACATATTA-TAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTA
1 TATAATATTACATATTATTAAGA-TA-AGACCATT---AT--TA-C-GTATTAC--A-----TTA
11332 CGTATTACGCTTCCACAATCAAAGTGAAA
50 CGTATTACGCTTCCACAATCAAAGTGAAA
11361 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
*
11426 AATCAAAGCGAAA
66 AATCAAAGTGAAA
*
11439 TATAATTTTACAT
1 TATAATATTACAT
11452 TCTTTTTACT
Statistics
Matches: 153, Mismatches: 14, Indels: 34
0.76 0.07 0.17
Matches are distributed among these distances:
77 4 0.03
78 62 0.41
79 5 0.03
82 2 0.01
83 1 0.01
84 1 0.01
85 7 0.05
86 7 0.05
87 1 0.01
88 1 0.01
89 2 0.01
92 5 0.03
93 51 0.33
94 4 0.03
ACGTcount: A:0.41, C:0.15, G:0.08, T:0.36
Consensus pattern (78 bp):
TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
AATCAAAGTGAAA
Found at i:11288 original size:15 final size:15
Alignment explanation
Indices: 11268--11300 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11258 CAAAGTGAAA
11268 TATAATATTACATAT
1 TATAATATTACATAT
11283 TATAATATTACATAT
1 TATAATATTACATAT
11298 TAT
1 TAT
11301 TAAGATAAGA
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:0.45, C:0.06, G:0.00, T:0.48
Consensus pattern (15 bp):
TATAATATTACATAT
Found at i:11409 original size:93 final size:93
Alignment explanation
Indices: 11102--11378 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
11092 TTAAGACCAT
11102 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11167 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
11195 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11260 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
11288 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11353 AAGTGAAATATAATATTACATATTAT
66 AAGTGAAATATAATATTACATATTAT
11379 TAAGATAAGA
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:0.42, C:0.14, G:0.08, T:0.37
Consensus pattern (93 bp):
TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
AAGTGAAATATAATATTACATATTATAA
Found at i:13282 original size:18 final size:18
Alignment explanation
Indices: 13259--13296 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13249 AGAGAATTCC
13259 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
13277 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
13295 AT
1 AT
13297 GCGCAAAAAA
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:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (18 bp):
ATTGTAAAGCCGTATGCA
Found at i:13637 original size:18 final size:18
Alignment explanation
Indices: 13614--13847 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
13604 CAGAATCGAG
13614 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13632 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13650 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13668 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13686 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13704 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13722 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13740 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13758 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13776 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13794 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13812 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13830 ACCTATAGTGAAT-AAAA
1 ACCTATAGTGAATGAAAA
13847 A
1 A
13848 ATGGAGACTA
Statistics
Matches: 213, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
17 7 0.03
18 204 0.96
19 2 0.01
ACGTcount: A:0.50, C:0.13, G:0.15, T:0.22
Consensus pattern (18 bp):
ACCTATAGTGAATGAAAA
Found at i:13896 original size:30 final size:30
Alignment explanation
Indices: 13862--14201 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
13852 AGACTAGTTA
13862 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13892 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13922 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13952 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13982 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14012 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14042 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14072 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14102 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14132 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14162 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14192 ACGACAATGG
1 ACGACAATGG
14202 AACACCATTT
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:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (30 bp):
ACGACAATGGCAATGGAAGACCACCATTTG
Found at i:16337 original size:45 final size:44
Alignment explanation
Indices: 16291--16414 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 44
16281 GTTTTTTTTA
* *
16291 TTATTGTATTA-TTTA-TTTATTATTTATTTCTTATTTATTTGT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTATTTGT
16333 TTATTTTATTAGTTTATTTTAATTATTTATTTATTATTTATTTGT
1 TTATTTTATTAGTTTATTTT-ATTATTTATTTATTATTTATTTGT
16378 TTATTTTATTAGTTTATTTTATTA-TTA--TATTATTTAT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTAT
16415 AGATATTTAT
Statistics
Matches: 77, Mismatches: 2, Indels: 7
0.90 0.02 0.08
Matches are distributed among these distances:
41 10 0.13
42 10 0.13
43 7 0.09
44 7 0.09
45 43 0.56
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (44 bp):
TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTATTTGT
Found at i:16408 original size:13 final size:13
Alignment explanation
Indices: 16324--16401 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
16314 TTATTTCTTA
*
16324 TTTATTTGTTTAT
1 TTTATTAGTTTAT
16337 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16350 TTTAATTA-TTTA-
1 TTT-ATTAGTTTAT
16362 TTTATTA-TTTA-
1 TTTATTAGTTTAT
16373 --T-TT-GTTTAT
1 TTTATTAGTTTAT
16382 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16395 TTTATTA
1 TTTATTA
16402 TTATATTATT
Statistics
Matches: 57, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
8 6 0.11
9 1 0.02
11 9 0.16
12 5 0.09
13 32 0.56
14 4 0.07
ACGTcount: A:0.23, C:0.00, G:0.05, T:0.72
Consensus pattern (13 bp):
TTTATTAGTTTAT
Found at i:16427 original size:4 final size:4
Alignment explanation
Indices: 16287--16414 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
16277 CTTTGTTTTT
* *
16287 TTTA -TTA TTGTA -TTA TTTA TTTA -TTA TTTA TTT- CTTA TTTA TTTG
1 TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
16332 TTTA TTT- TATTA GTTTA TTTTA ATTA TTTA TTTA -TTA TTTA TTTG TTTA
1 TTTA TTTA T-TTA -TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
16381 TTT- TATTA GTTTA TTT- TATTA -TTA TATTA TTTA T
1 TTTA T-TTA -TTTA TTTA T-TTA TTTA T-TTA TTTA T
16415 AGATATTTAT
Statistics
Matches: 99, Mismatches: 9, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
3 19 0.19
4 62 0.63
5 16 0.16
6 2 0.02
ACGTcount: A:0.24, C:0.01, G:0.04, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:16465 original size:35 final size:35
Alignment explanation
Indices: 16426--16549 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
16416 GATATTTATT
16426 TAAATATAATTTCATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16461 TAAATATAATTTCATATTTTAATATATTTAATATATAAAATA
1 TAAATATAATTTCATATTTTAATATA-TT--TA-AT---ATA
*
16503 TAAATATAATTTAATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16538 TAAATATAATTT
1 TAAATATAATTT
16550 AAATAAATAT
Statistics
Matches: 81, Mismatches: 1, Indels: 14
0.84 0.01 0.15
Matches are distributed among these distances:
35 41 0.51
36 2 0.02
38 4 0.05
39 4 0.05
41 2 0.02
42 28 0.35
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (35 bp):
TAAATATAATTTCATATTTTAATATATTTAATATA
Found at i:16520 original size:42 final size:42
Alignment explanation
Indices: 16439--16546 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
16429 ATATAATTTC
* *
16439 ATAT-TTTAATATATTTAATATATAAATATAATTTCATATTTTA
1 ATATATTTAATATA--TAAAATATAAATATAATTTAATATTTTA
16482 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
1 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
16524 ATATATTTAATATAT-AAATATAA
1 ATATATTTAATATATAAAATATAA
16547 TTTAAATAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
41 8 0.13
42 41 0.66
43 4 0.06
44 9 0.15
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
Found at i:16596 original size:77 final size:77
Alignment explanation
Indices: 16439--16596 Score: 187
Period size: 77 Copynumber: 2.1 Consensus size: 77
16429 ATATAATTTC
* * * *
16439 ATATTTTAATATATTTAATATATAAATATAATTTCATATTTTAATATATTTAATATATAAAATAT
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAATATATAAAACAT
* *
16504 AAATATAATTTA
66 AAATATAAATAA
* * *
16516 ATATTTTAATATATTTAATATATAAATATAATTT-A-A-ATAAATATCTATAACTGTGATAATAC
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAA-TAT-ATAAAAC
16578 ATAAATAATAAATAA
64 ATAAAT-ATAAATAA
16593 ATAT
1 ATAT
16597 AATTTATAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
74 10 0.14
75 3 0.04
76 12 0.17
77 44 0.64
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (77 bp):
ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAATATATAAAACAT
AAATATAAATAA
Found at i:16605 original size:17 final size:18
Alignment explanation
Indices: 16426--16614 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
16416 GATATTTATT
* **
16426 TAAATATAATTTCATATT
1 TAAATATAATTTAATAAA
* *
16444 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
*
16461 TAAATATAATTTCATATTTTAA
1 TAAATATAATTT-A-A--TAAA
* *
16483 TATATTTAATATATAA-AATA
1 TAAATATAAT-T-TAATAA-A
**
16503 TAAATATAATTTAATATT
1 TAAATATAATTTAATAAA
* *
16521 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
16538 TAAATATAATTTAAATAAA
1 TAAATATAATTT-AATAAA
** * *
16557 TATCTATAACTGTGAT-AA
1 TAAATATAA-TTTAATAAA
*
16575 TACATA-AA--TAATAAA
1 TAAATATAATTTAATAAA
16590 TAAATATAATTT-ATAAA
1 TAAATATAATTTAATAAA
*
16607 TATATATA
1 TAAATATA
16615 GAACCGACAC
Statistics
Matches: 129, Mismatches: 26, Indels: 33
0.69 0.14 0.18
Matches are distributed among these distances:
14 3 0.02
15 7 0.05
16 2 0.02
17 43 0.33
18 30 0.23
19 18 0.14
20 12 0.09
22 11 0.09
23 2 0.02
24 1 0.01
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (18 bp):
TAAATATAATTTAATAAA
Found at i:16650 original size:19 final size:19
Alignment explanation
Indices: 16626--16707 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
16616 AACCGACACG
* *
16626 AAAATAATAAATAATTAAT
1 AAAATAAGAAATAAATAAT
16645 AAAATAAGAAATAAATAAT
1 AAAATAAGAAATAAATAAT
* * *
16664 GAAATATAGTAATAAAT-AC
1 AAAATA-AGAAATAAATAAT
* *
16683 AAAATATAGTAATAACTAA-
1 AAAATA-AGAAATAAATAAT
16702 AAAATA
1 AAAATA
16708 TAGTAATGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
19 44 0.81
20 10 0.19
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (19 bp):
AAAATAAGAAATAAATAAT
Found at i:16708 original size:19 final size:19
Alignment explanation
Indices: 16635--16721 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
16625 GAAAATAATA
* *
16635 AATAATTAATAAAATA-AGA
1 AATAAATAA-AAAATATAGT
*
16654 AATAAATAATGAAATATAGT
1 AATAAATAA-AAAATATAGT
*
16674 AATAAATACAAAATATAGT
1 AATAAATAAAAAATATAGT
*
16693 AATAACTAAAAAATATAGT
1 AATAAATAAAAAATATAGT
*
16712 AATGAATAAA
1 AATAAATAAA
16722 TCATACAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
19 48 0.83
20 10 0.17
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.26
Consensus pattern (19 bp):
AATAAATAAAAAATATAGT
Found at i:16738 original size:17 final size:17
Alignment explanation
Indices: 16716--16749 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16706 TATAGTAATG
*
16716 AATAAATCATACAATAT
1 AATAAATAATACAATAT
16733 AATAAATAATACAATAT
1 AATAAATAATACAATAT
16750 TAACAATATT
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:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (17 bp):
AATAAATAATACAATAT
Found at i:16768 original size:15 final size:15
Alignment explanation
Indices: 16748--16797 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
16738 ATAATACAAT
16748 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16763 ATTAACAACAATATTAAA
1 ATT---AACAATATTAAA
16781 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16796 AT
1 AT
16798 AATCATTATG
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:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (15 bp):
ATTAACAATATTAAA
Found at i:16774 original size:18 final size:18
Alignment explanation
Indices: 16751--16788 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16741 ATACAATATT
16751 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16769 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16787 AA
1 AA
16789 TATTAAAATA
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:0.63, C:0.11, G:0.00, T:0.26
Consensus pattern (18 bp):
AACAATATTAAAATTAAC
Found at i:16911 original size:25 final size:25
Alignment explanation
Indices: 16883--16934 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16873 TCCAACTCCT
*
16883 AATCATTCGAAGACTGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16908 AATCATTCGAAGACGGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16933 AA
1 AA
16935 AATAAATAAT
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:0.50, C:0.15, G:0.13, T:0.21
Consensus pattern (25 bp):
AATCATTCGAAGACGGTAAACTAAA
Found at i:17002 original size:17 final size:16
Alignment explanation
Indices: 16973--17021 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
16963 AAAAATTATT
16973 AAAAAAATAAGAACTAA
1 AAAAAAATAAGAA-TAA
16990 ATAAAAAAT-AGAATAA
1 A-AAAAAATAAGAATAA
*
17006 AAAAAATAAAAGAATA
1 AAAAAA-ATAAGAATA
17022 TTGATACAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
15 5 0.18
16 5 0.18
17 11 0.39
18 7 0.25
ACGTcount: A:0.78, C:0.02, G:0.06, T:0.14
Consensus pattern (16 bp):
AAAAAAATAAGAATAA
Found at i:18004 original size:22 final size:22
Alignment explanation
Indices: 17969--18019 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
17959 AAAAACTAAA
17969 TAGAATT-ATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
17990 TAGAATTCATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
*
18012 TATAATTC
1 TAGAATTC
18020 TAAAAACAAC
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:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (22 bp):
TAGAATTCATTTCTTATATAAT
Found at i:21477 original size:21 final size:21
Alignment explanation
Indices: 21433--21495 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
21423 TATATATTTA
21433 ATTTTAATATTTAA-TTT--T
1 ATTTTAATATTTAATTTTAAT
21451 -TTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
21471 ATTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
21492 ATTT
1 ATTT
21496 CTTTTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.32
18 3 0.07
20 1 0.02
21 24 0.59
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
ATTTTAATATTTAATTTTAAT
Found at i:21501 original size:13 final size:13
Alignment explanation
Indices: 21426--21495 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
21416 ATCACAATAT
21426 ATATTTAATTTTA
1 ATATTTAATTTTA
21439 ATATTTAATTTT-
1 ATATTTAATTTTA
21451 -T-TTTAATATTTA
1 ATATTTAAT-TTTA
21463 AT-TTTAATATTTTA
1 ATATTT-A-ATTTTA
21477 ATATTTAATTTTA
1 ATATTTAATTTTA
21490 ATATTT
1 ATATTT
21496 CTTTTTTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 12
0.81 0.00 0.19
Matches are distributed among these distances:
10 6 0.12
11 4 0.08
13 28 0.55
14 8 0.16
15 5 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
ATATTTAATTTTA
Found at i:21689 original size:10 final size:10
Alignment explanation
Indices: 21674--21751 Score: 63
Period size: 10 Copynumber: 7.6 Consensus size: 10
21664 GTCCATTACT
21674 TATTATATTA
1 TATTATATTA
21684 TATTATACTTA
1 TATTATA-TTA
21695 T-TTATACTTA
1 TATTATA-TTA
*
21705 TACTTATTTTA
1 TA-TTATATTA
21716 TACTTAT-TTA
1 TA-TTATATTA
*
21726 TACTTATTTTA
1 TA-TTATATTA
*
21737 TACT-TATTA
1 TATTATATTA
21746 TATTAT
1 TATTAT
21752 CCTTATTACT
Statistics
Matches: 59, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
9 7 0.12
10 29 0.49
11 19 0.32
12 4 0.07
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (10 bp):
TATTATATTA
Found at i:21716 original size:27 final size:26
Alignment explanation
Indices: 21676--21743 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
21666 CCATTACTTA
21676 TTATATTATATTATACTTATTTATAC
1 TTATATTATATTATACTTATTTATAC
*
21702 TTATACTTATTTTATACTTATTTATAC
1 TTATA-TTATATTATACTTATTTATAC
*
21729 TTATTTTATACTTAT
1 TTATATTATA-TTAT
21744 TATATTATCC
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.24
27 28 0.76
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (26 bp):
TTATATTATATTATACTTATTTATAC
Found at i:21718 original size:11 final size:11
Alignment explanation
Indices: 21702--21744 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
21692 TTATTTATAC
21702 TTATACTTATT
1 TTATACTTATT
21713 TTATACTTA-T
1 TTATACTTATT
21723 TTATACTTATT
1 TTATACTTATT
21734 TTATACTTATT
1 TTATACTTATT
21745 ATATTATCCT
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:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (11 bp):
TTATACTTATT
Found at i:21757 original size:20 final size:21
Alignment explanation
Indices: 21742--21799 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
21732 TTTTATACTT
*
21742 ATTATATTATCCTTATTACTT
1 ATTATATTATCTTTATTACTT
**
21763 ATTCGATTA-CTTTATTACTT
1 ATTATATTATCTTTATTACTT
*
21783 ATTCTATTATCTATTAT
1 ATTATATTATCT-TTAT
21800 AATCTATTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 18 0.58
21 9 0.29
22 4 0.13
ACGTcount: A:0.28, C:0.14, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTATATTATCTTTATTACTT
Found at i:21761 original size:21 final size:21
Alignment explanation
Indices: 21672--21793 Score: 73
Period size: 21 Copynumber: 6.0 Consensus size: 21
21662 TTGTCCATTA
*
21672 CTTATTA--TATTATATTATA
1 CTTATTACTTATTATATTATC
21691 CTTATT--TATACTTATACTTAT-
1 CTTATTACT-TA-TTATA-TTATC
*
21712 TTTA-TACTTATTTATACTTAT-
1 CTTATTACTTA-TTATA-TTATC
*
21733 TTTA-TACTTATTATATTATC
1 CTTATTACTTATTATATTATC
**
21753 CTTATTACTTATTCGATTA-C
1 CTTATTACTTATTATATTATC
* *
21773 TTTATTACTTATTCTATTATC
1 CTTATTACTTATTATATTATC
21794 TATTATAATC
Statistics
Matches: 87, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
19 10 0.11
20 29 0.33
21 43 0.49
22 5 0.06
ACGTcount: A:0.29, C:0.12, G:0.01, T:0.58
Consensus pattern (21 bp):
CTTATTACTTATTATATTATC
Found at i:21764 original size:27 final size:24
Alignment explanation
Indices: 21674--21758 Score: 95
Period size: 21 Copynumber: 3.5 Consensus size: 24
21664 GTCCATTACT
* *
21674 TATTATATTATATTATACTTATTTA
1 TATTATCTTATTTTATACTTA-TTA
21699 TACTTATACTTATTTTATACTTATT-
1 TA-TTAT-CTTATTTTATACTTATTA
21724 TA-TA-CTTATTTTATACTTATTA
1 TATTATCTTATTTTATACTTATTA
21746 TATTATCCTTATT
1 TATTAT-CTTATT
21759 ACTTATTCGA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
21 17 0.33
22 2 0.04
23 4 0.08
25 10 0.19
26 6 0.12
27 13 0.25
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATCTTATTTTATACTTATTA
Found at i:21807 original size:17 final size:17
Alignment explanation
Indices: 21785--21818 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21775 TATTACTTAT
21785 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21802 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21819 GTAAATCTAA
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:0.35, C:0.12, G:0.00, T:0.53
Consensus pattern (17 bp):
TCTATTATCTATTATAA
Done.