Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168352.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_573, 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: 22678
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:517 original size:14 final size:15
Alignment explanation
Indices: 491--519 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
481 TAACAAATTT
491 TTTATTAAAATATTA
1 TTTATTAAAATATTA
506 TTTATT-AAATATTA
1 TTTATTAAAATATTA
520 AATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATTAAAATATTA
Found at i:536 original size:23 final size:24
Alignment explanation
Indices: 501--563 Score: 92
Period size: 23 Copynumber: 2.6 Consensus size: 24
491 TTTATTAAAA
501 TATTATTTATTAAATATTAAATTT
1 TATTATTTATTAAATATTAAATTT
525 TATT-TTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAA-TTT
**
549 TATTAAATATTAAAT
1 TATTATTTATTAAAT
564 TAAGGCTCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 16 0.46
24 11 0.31
25 8 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TATTATTTATTAAATATTAAATTT
Found at i:549 original size:18 final size:18
Alignment explanation
Indices: 526--564 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
516 ATTAAATTTT
526 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
544 ATTTTTATTAAATATTAA
1 ATTTTTATTAAATATTAA
562 ATT
1 ATT
565 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:820 original size:20 final size:20
Alignment explanation
Indices: 795--872 Score: 115
Period size: 20 Copynumber: 4.0 Consensus size: 20
785 TTCGCCCGCG
795 AAAATTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
815 AAAATTTTATTTTCATTTT-
1 AAAATTTTATTTTCATTTTA
***
834 -TTTTTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
853 AAAATTTTATTTTCATTTTA
1 AAAATTTTATTTTCATTTTA
873 TTTGATTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.30
20 35 0.70
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.65
Consensus pattern (20 bp):
AAAATTTTATTTTCATTTTA
Found at i:850 original size:38 final size:38
Alignment explanation
Indices: 799--871 Score: 146
Period size: 38 Copynumber: 1.9 Consensus size: 38
789 CCCGCGAAAA
799 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
837 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
872 ATTTGATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (38 bp):
TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
Found at i:889 original size:38 final size:37
Alignment explanation
Indices: 798--889 Score: 105
Period size: 38 Copynumber: 2.4 Consensus size: 37
788 GCCCGCGAAA
* *
798 ATTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCA-TTTTT
* * *
836 TTTTTATTTTCATTTTAAAAATTTTATTTTCA-TTTT
1 ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
872 ATTTGATTGTTAAATTTT
1 ATTTGATT-TT-AATTTT
890 TGTCGATCCG
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
36 10 0.21
37 2 0.04
38 36 0.75
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (37 bp):
ATTTGATTTTAATTTTAAAAATTTTATTTTCATTTTT
Found at i:1075 original size:21 final size:21
Alignment explanation
Indices: 1051--1094 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
1041 ACAAATTTAT
1051 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
1072 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
1093 AA
1 AA
1095 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:6603 original size:23 final size:23
Alignment explanation
Indices: 6577--6622 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6567 GTTCCTCCCC
6577 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6600 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6623 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:8577 original size:6 final size:6
Alignment explanation
Indices: 8566--8623 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
8556 GATCTTGAAA
8566 TTATAT TTATAT TTATA- -T-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
8611 ATATTAT TTATAT
1 TTA-TAT TTATAT
8624 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:8592 original size:21 final size:21
Alignment explanation
Indices: 8566--8632 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
8556 GATCTTGAAA
8566 TTATATTTATATTTATATTAT
1 TTATATTTATATTTATATTAT
8587 TTATATTTATATTTATATT-T
1 TTATATTTATATTTATATTAT
* * *
8607 ATATATAT-TATTTATATAAT
1 TTATATTTATATTTATATTAT
8627 TATATA
1 T-TATA
8633 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:8624 original size:27 final size:27
Alignment explanation
Indices: 8566--8623 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
8556 GATCTTGAAA
8566 TTATATTTATATTTATATTATTTATAT
1 TTATATTTATATTTATATTATTTATAT
*
8593 TTATATTTATATTTATA-TATAT-TAT
1 TTATATTTATATTTATATTATTTATAT
8618 TTATAT
1 TTATAT
8624 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:8629 original size:27 final size:29
Alignment explanation
Indices: 8564--8631 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
8554 GTGATCTTGA
8564 AATTATATTTATATTTATATTATTTATATTT
1 AATTATATTTATA-TTATATTATTTATA-TT
8595 ATATTTATATTTATA-TATATTATTTATA-T
1 A-A-TTATATTTATATTATATTATTTATATT
8624 AATTATAT
1 AATTATAT
8632 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:11105 original size:15 final size:15
Alignment explanation
Indices: 11085--11117 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11075 CAAAGTGAAA
11085 TATAATATTACATAT
1 TATAATATTACATAT
11100 TATAATATTACATAT
1 TATAATATTACATAT
11115 TAT
1 TAT
11118 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:11184 original size:78 final size:78
Alignment explanation
Indices: 11100--11361 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 78
11090 TATTACATAT
11100 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
11165 AATCAAAGTGAAA
66 AATCAAAGTGAAA
* * ** * *
11178 TATAATATTACATATTA-TAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTA
1 TATAATATTACATATTATTAAGA-TA-AGACCATT---AT--TA-C-GTATTAC--A-----TTA
11242 CGTATTACGCTTCCACAATCAAAGTGAAA
50 CGTATTACGCTTCCACAATCAAAGTGAAA
11271 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
*
11336 AATCAAAGCGAAA
66 AATCAAAGTGAAA
*
11349 TATAATTTTACAT
1 TATAATATTACAT
11362 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:11198 original size:15 final size:15
Alignment explanation
Indices: 11178--11210 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
11168 CAAAGTGAAA
11178 TATAATATTACATAT
1 TATAATATTACATAT
11193 TATAATATTACATAT
1 TATAATATTACATAT
11208 TAT
1 TAT
11211 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:11319 original size:93 final size:93
Alignment explanation
Indices: 11012--11288 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
11002 TTAAGACCAT
11012 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11077 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
11105 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11170 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
11198 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11263 AAGTGAAATATAATATTACATATTAT
66 AAGTGAAATATAATATTACATATTAT
11289 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:13192 original size:18 final size:18
Alignment explanation
Indices: 13169--13206 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
13159 AGAGAATTCC
13169 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
13187 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
13205 AT
1 AT
13207 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:13547 original size:18 final size:18
Alignment explanation
Indices: 13524--13757 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
13514 CAGAATCGAG
13524 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13542 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13560 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13578 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13596 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13614 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13632 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13650 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13668 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13686 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13704 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13722 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13740 ACCTATAGTGAAT-AAAA
1 ACCTATAGTGAATGAAAA
13757 A
1 A
13758 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:13806 original size:30 final size:30
Alignment explanation
Indices: 13772--14110 Score: 671
Period size: 30 Copynumber: 11.3 Consensus size: 30
13762 AGACTAGTTA
13772 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13802 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13832 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13862 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13892 ACGACAATGGCAATGGAAGACCACCA-TTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13921 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13951 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13981 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14011 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14041 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14071 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
14101 ACGACAATGG
1 ACGACAATGG
14111 AACACCATTT
Statistics
Matches: 308, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
29 29 0.09
30 279 0.91
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.16
Consensus pattern (30 bp):
ACGACAATGGCAATGGAAGACCACCATTTG
Found at i:16245 original size:45 final size:44
Alignment explanation
Indices: 16199--16322 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 44
16189 GTTTTTTTTA
* *
16199 TTATTGTATTA-TTTA-TTTATTATTTATTTCTTATTTATTTGT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTATTTGT
16241 TTATTTTATTAGTTTATTTTAATTATTTATTTATTATTTATTTGT
1 TTATTTTATTAGTTTATTTT-ATTATTTATTTATTATTTATTTGT
16286 TTATTTTATTAGTTTATTTTATTA-TTA--TATTATTTAT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTAT
16323 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:16316 original size:13 final size:13
Alignment explanation
Indices: 16232--16309 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
16222 TTATTTCTTA
*
16232 TTTATTTGTTTAT
1 TTTATTAGTTTAT
16245 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16258 TTTAATTA-TTTA-
1 TTT-ATTAGTTTAT
16270 TTTATTA-TTTA-
1 TTTATTAGTTTAT
16281 --T-TT-GTTTAT
1 TTTATTAGTTTAT
16290 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16303 TTTATTA
1 TTTATTA
16310 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:16335 original size:4 final size:4
Alignment explanation
Indices: 16195--16322 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
16185 CTTTGTTTTT
* *
16195 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
* *
16240 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
16289 TTT- TATTA GTTTA TTT- TATTA -TTA TATTA TTTA T
1 TTTA T-TTA -TTTA TTTA T-TTA TTTA T-TTA TTTA T
16323 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:16373 original size:35 final size:35
Alignment explanation
Indices: 16334--16457 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
16324 GATATTTATT
16334 TAAATATAATTTCATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16369 TAAATATAATTTCATATTTTAATATATTTAATATATAAAATA
1 TAAATATAATTTCATATTTTAATATA-TT--TA-AT---ATA
*
16411 TAAATATAATTTAATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16446 TAAATATAATTT
1 TAAATATAATTT
16458 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:16428 original size:42 final size:42
Alignment explanation
Indices: 16347--16454 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
16337 ATATAATTTC
* *
16347 ATAT-TTTAATATATTTAATATATAAATATAATTTCATATTTTA
1 ATATATTTAATATA--TAAAATATAAATATAATTTAATATTTTA
16390 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
1 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
16432 ATATATTTAATATAT-AAATATAA
1 ATATATTTAATATATAAAATATAA
16455 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:16504 original size:77 final size:77
Alignment explanation
Indices: 16347--16504 Score: 187
Period size: 77 Copynumber: 2.1 Consensus size: 77
16337 ATATAATTTC
* * * *
16347 ATATTTTAATATATTTAATATATAAATATAATTTCATATTTTAATATATTTAATATATAAAATAT
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAATATATAAAACAT
* *
16412 AAATATAATTTA
66 AAATATAAATAA
* * *
16424 ATATTTTAATATATTTAATATATAAATATAATTT-A-A-ATAAATATCTATAACTGTGATAATAC
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAA-TAT-ATAAAAC
16486 ATAAATAATAAATAA
64 ATAAAT-ATAAATAA
16501 ATAT
1 ATAT
16505 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:16513 original size:17 final size:18
Alignment explanation
Indices: 16334--16522 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
16324 GATATTTATT
* **
16334 TAAATATAATTTCATATT
1 TAAATATAATTTAATAAA
* *
16352 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
*
16369 TAAATATAATTTCATATTTTAA
1 TAAATATAATTT-A-A--TAAA
* *
16391 TATATTTAATATATAA-AATA
1 TAAATATAAT-T-TAATAA-A
**
16411 TAAATATAATTTAATATT
1 TAAATATAATTTAATAAA
* *
16429 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
16446 TAAATATAATTTAAATAAA
1 TAAATATAATTT-AATAAA
** * *
16465 TATCTATAACTGTGAT-AA
1 TAAATATAA-TTTAATAAA
*
16483 TACATA-AA--TAATAAA
1 TAAATATAATTTAATAAA
16498 TAAATATAATTT-ATAAA
1 TAAATATAATTTAATAAA
*
16515 TATATATA
1 TAAATATA
16523 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:16558 original size:19 final size:19
Alignment explanation
Indices: 16534--16589 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
16524 AACCGACACG
* *
16534 AAAATAATAAATAATTAAT
1 AAAATAAGAAATAAATAAT
16553 AAAATAAGAAATAAATAAT
1 AAAATAAGAAATAAATAAT
* *
16572 GAAATATAGTAATAAATA
1 AAAATA-AGAAATAAATA
16590 CAAAATATAG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 22 0.69
20 10 0.31
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (19 bp):
AAAATAAGAAATAAATAAT
Found at i:16595 original size:19 final size:18
Alignment explanation
Indices: 16553--16628 Score: 91
Period size: 19 Copynumber: 4.1 Consensus size: 18
16543 AATAATTAAT
*
16553 AAAATA-AGAAATAAATA
1 AAAATATAGTAATAAATA
16570 ATGAAATATAGTAATAAATA
1 A--AAATATAGTAATAAATA
*
16590 CAAAATATAGTAATAACTA
1 -AAAATATAGTAATAAATA
*
16609 AAAATATAGTAATGAATA
1 AAAATATAGTAATAAATA
16627 AA
1 AA
16629 TCATACAATA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
17 1 0.02
18 18 0.35
19 21 0.41
20 10 0.20
21 1 0.02
ACGTcount: A:0.64, C:0.03, G:0.08, T:0.25
Consensus pattern (18 bp):
AAAATATAGTAATAAATA
Found at i:16614 original size:18 final size:19
Alignment explanation
Indices: 16573--16626 Score: 83
Period size: 18 Copynumber: 2.9 Consensus size: 19
16563 ATAAATAATG
16573 AAATATAGTAATAAATACA
1 AAATATAGTAATAAATACA
*
16592 AAATATAGTAATAACTA-A
1 AAATATAGTAATAAATACA
*
16610 AAATATAGTAATGAATA
1 AAATATAGTAATAAATA
16627 AATCATACAA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
18 16 0.50
19 16 0.50
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (19 bp):
AAATATAGTAATAAATACA
Found at i:16645 original size:17 final size:17
Alignment explanation
Indices: 16623--16656 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16613 TATAGTAATG
*
16623 AATAAATCATACAATAT
1 AATAAATAATACAATAT
16640 AATAAATAATACAATAT
1 AATAAATAATACAATAT
16657 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:16675 original size:15 final size:15
Alignment explanation
Indices: 16655--16704 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
16645 ATAATACAAT
16655 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16670 ATTAACAACAATATTAAA
1 ATT---AACAATATTAAA
16688 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16703 AT
1 AT
16705 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:16681 original size:18 final size:18
Alignment explanation
Indices: 16658--16695 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16648 ATACAATATT
16658 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16676 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16694 AA
1 AA
16696 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:16819 original size:25 final size:25
Alignment explanation
Indices: 16791--16842 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16781 TCCAACTCCT
*
16791 AATCATTCGAAGACTGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16816 AATCATTCGAAGACGGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16841 AA
1 AA
16843 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:16910 original size:17 final size:16
Alignment explanation
Indices: 16881--16929 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
16871 AAAAATTATT
16881 AAAAAAATAAGAACTAA
1 AAAAAAATAAGAA-TAA
16898 ATAAAAAAT-AGAATAA
1 A-AAAAAATAAGAATAA
*
16914 AAAAAATAAAAGAATA
1 AAAAAA-ATAAGAATA
16930 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:17912 original size:22 final size:22
Alignment explanation
Indices: 17877--17927 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
17867 AAAAACTAAA
17877 TAGAATT-ATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
17898 TAGAATTCATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
*
17920 TATAATTC
1 TAGAATTC
17928 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:21368 original size:7 final size:7
Alignment explanation
Indices: 21347--21414 Score: 72
Period size: 7 Copynumber: 9.9 Consensus size: 7
21337 ATCACAATAT
21347 ATATTTA
1 ATATTTA
21354 AT-TTTA
1 ATATTTA
21360 ATATTTA
1 ATATTTA
*
21367 ATTTTTTTA
1 A--TATTTA
21376 ATATTTA
1 ATATTTA
21383 AT-TTTA
1 ATATTTA
21389 ATATTTTA
1 ATA-TTTA
21397 ATATTT-
1 ATATTTA
21403 A-ATTTA
1 ATATTTA
21409 ATATTT
1 ATATTT
21415 CTTTTTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
5 4 0.08
6 14 0.27
7 21 0.40
8 7 0.13
9 6 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (7 bp):
ATATTTA
Found at i:21376 original size:16 final size:16
Alignment explanation
Indices: 21355--21387 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21345 ATATATTTAA
21355 TTTTAATATTTAATTT
1 TTTTAATATTTAATTT
21371 TTTTAATATTTAATTT
1 TTTTAATATTTAATTT
21387 T
1 T
21388 AATATTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTTTAATATTTAATTT
Found at i:21389 original size:29 final size:32
Alignment explanation
Indices: 21347--21414 Score: 106
Period size: 29 Copynumber: 2.2 Consensus size: 32
21337 ATCACAATAT
21347 ATATTTAATTTTAATA-TTTAAT-TTT-TTTA
1 ATATTTAATTTTAATATTTTAATATTTATTTA
21376 ATATTTAATTTTAATATTTTAATATTTAATTTA
1 ATATTTAATTTTAATATTTTAATATTT-ATTTA
21409 ATATTT
1 ATATTT
21415 CTTTTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 16 0.46
30 6 0.17
31 3 0.09
33 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (32 bp):
ATATTTAATTTTAATATTTTAATATTTATTTA
Found at i:21402 original size:16 final size:15
Alignment explanation
Indices: 21354--21414 Score: 60
Period size: 16 Copynumber: 4.3 Consensus size: 15
21344 TATATATTTA
21354 ATTTTAATATTTAATT
1 ATTTTAATATTTAA-T
*
21370 TTTTTAATATTT-A-
1 ATTTTAATATTTAAT
21383 ATTTTAATATTTTAAT
1 ATTTTAATA-TTTAAT
21399 A-TTT-A-ATTTAAT
1 ATTTTAATATTTAAT
21411 ATTT
1 ATTT
21415 CTTTTTTTTT
Statistics
Matches: 39, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 7 0.18
13 11 0.28
14 4 0.10
15 5 0.13
16 12 0.31
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (15 bp):
ATTTTAATATTTAAT
Found at i:21407 original size:13 final size:13
Alignment explanation
Indices: 21347--21405 Score: 73
Period size: 13 Copynumber: 4.2 Consensus size: 13
21337 ATCACAATAT
21347 ATATTTAATTTTA
1 ATATTTAATTTTA
21360 ATATTTAATTTTTTTA
1 ATATTTAA---TTTTA
21376 ATATTTAATTTTA
1 ATATTTAATTTTA
21389 ATATTTTAATATTTA
1 ATA-TTTAAT-TTTA
21404 AT
1 AT
21406 TTAATATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
13 16 0.39
14 6 0.15
15 6 0.15
16 13 0.32
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
ATATTTAATTTTA
Found at i:21607 original size:10 final size:10
Alignment explanation
Indices: 21592--21669 Score: 63
Period size: 10 Copynumber: 7.6 Consensus size: 10
21582 GTCCATTACT
21592 TATTATATTA
1 TATTATATTA
21602 TATTATACTTA
1 TATTATA-TTA
21613 T-TTATACTTA
1 TATTATA-TTA
*
21623 TACTTATTTTA
1 TA-TTATATTA
21634 TACTTAT-TTA
1 TA-TTATATTA
*
21644 TACTTATTTTA
1 TA-TTATATTA
*
21655 TACT-TATTA
1 TATTATATTA
21664 TATTAT
1 TATTAT
21670 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:21634 original size:27 final size:26
Alignment explanation
Indices: 21594--21661 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
21584 CCATTACTTA
21594 TTATATTATATTATACTTATTTATAC
1 TTATATTATATTATACTTATTTATAC
*
21620 TTATACTTATTTTATACTTATTTATAC
1 TTATA-TTATATTATACTTATTTATAC
*
21647 TTATTTTATACTTAT
1 TTATATTATA-TTAT
21662 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:21636 original size:11 final size:11
Alignment explanation
Indices: 21620--21662 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
21610 TTATTTATAC
21620 TTATACTTATT
1 TTATACTTATT
21631 TTATACTTA-T
1 TTATACTTATT
21641 TTATACTTATT
1 TTATACTTATT
21652 TTATACTTATT
1 TTATACTTATT
21663 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:21675 original size:20 final size:21
Alignment explanation
Indices: 21660--21717 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
21650 TTTTATACTT
*
21660 ATTATATTATCCTTATTACTT
1 ATTATATTATCTTTATTACTT
**
21681 ATTCGATTA-CTTTATTACTT
1 ATTATATTATCTTTATTACTT
*
21701 ATTCTATTATCTATTAT
1 ATTATATTATCT-TTAT
21718 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:21679 original size:21 final size:21
Alignment explanation
Indices: 21590--21711 Score: 73
Period size: 21 Copynumber: 6.0 Consensus size: 21
21580 TTGTCCATTA
*
21590 CTTATTA--TATTATATTATA
1 CTTATTACTTATTATATTATC
21609 CTTATT--TATACTTATACTTAT-
1 CTTATTACT-TA-TTATA-TTATC
*
21630 TTTA-TACTTATTTATACTTAT-
1 CTTATTACTTA-TTATA-TTATC
*
21651 TTTA-TACTTATTATATTATC
1 CTTATTACTTATTATATTATC
**
21671 CTTATTACTTATTCGATTA-C
1 CTTATTACTTATTATATTATC
* *
21691 TTTATTACTTATTCTATTATC
1 CTTATTACTTATTATATTATC
21712 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:21682 original size:27 final size:24
Alignment explanation
Indices: 21592--21676 Score: 95
Period size: 21 Copynumber: 3.5 Consensus size: 24
21582 GTCCATTACT
* *
21592 TATTATATTATATTATACTTATTTA
1 TATTATCTTATTTTATACTTA-TTA
21617 TACTTATACTTATTTTATACTTATT-
1 TA-TTAT-CTTATTTTATACTTATTA
21642 TA-TA-CTTATTTTATACTTATTA
1 TATTATCTTATTTTATACTTATTA
21664 TATTATCCTTATT
1 TATTAT-CTTATT
21677 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:21725 original size:17 final size:17
Alignment explanation
Indices: 21703--21736 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21693 TATTACTTAT
21703 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21720 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21737 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.