Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168364.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_584, 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: 22302
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:289 original size:14 final size:15
Alignment explanation
Indices: 264--292 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
254 TAACAAATTT
264 TTTATTACAATATTA
1 TTTATTACAATATTA
279 TTTATTA-AATATTA
1 TTTATTACAATATTA
293 AATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATTACAATATTA
Found at i:307 original size:23 final size:24
Alignment explanation
Indices: 274--326 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
264 TTTATTACAA
274 TATTATTTATTAAATATTAAATTT
1 TATTATTTATTAAATATTAAATTT
298 TATT-TTTATTAAATATTAAATTTT
1 TATTATTTATTAAATATTAAA-TTT
322 TATTA
1 TATTA
327 AATATTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (24 bp):
TATTATTTATTAAATATTAAATTT
Found at i:322 original size:18 final size:19
Alignment explanation
Indices: 288--338 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 19
278 ATTTATTAAA
288 TATTAAAT-TTT--ATTTT
1 TATTAAATATTTAAATTTT
304 TATTAAATA-TTAAATTTT
1 TATTAAATATTTAAATTTT
322 TATTAAATATTTAAATT
1 TATTAAATATTTAAATT
339 AAGGCTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 10 0.32
18 14 0.45
19 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTAAATATTTAAATTTT
Found at i:625 original size:37 final size:38
Alignment explanation
Indices: 575--646 Score: 137
Period size: 37 Copynumber: 1.9 Consensus size: 38
565 CCCGCGAAAA
575 TTTTATTTTCATTTTAAAAA-TTTATTTTCATTTTTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
612 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
1 TTTTATTTTCATTTTAAAAATTTTATTTTCATTTT
647 ATTGATTGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 20 0.59
38 14 0.41
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.69
Consensus pattern (38 bp):
TTTTATTTTCATTTTAAAAATTTTATTTTCATTTTTTT
Found at i:663 original size:37 final size:37
Alignment explanation
Indices: 585--663 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 37
575 TTTTATTTTC
* ** * **
585 ATTTTAAAAATTTATTTTCATTTTTTTTTTTATTTTC
1 ATTTTAAAAATTTATTTTCATTTTATTGATTAGTTAA
622 ATTTTAAAAATTTTATTTTCATTTTATTGATT-GTTAA
1 ATTTTAAAAA-TTTATTTTCATTTTATTGATTAGTTAA
659 ATTTT
1 ATTTT
664 TGTCGATCCG
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
37 17 0.49
38 18 0.51
ACGTcount: A:0.28, C:0.04, G:0.03, T:0.66
Consensus pattern (37 bp):
ATTTTAAAAATTTATTTTCATTTTATTGATTAGTTAA
Found at i:849 original size:21 final size:21
Alignment explanation
Indices: 825--868 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
815 ACAAATTTAT
825 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
846 AATAGATCAGATAAAATCTCA
1 AATAGATCAGATAAAATCTCA
867 AA
1 AA
869 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:6380 original size:23 final size:23
Alignment explanation
Indices: 6354--6399 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
6344 GTTCCTCCCC
6354 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6377 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
6400 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:8353 original size:6 final size:6
Alignment explanation
Indices: 8342--8399 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
8332 GATCTTGAAA
8342 TTATAT TTATAT TTATA- -T-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
8387 ATATTAT TTATAT
1 TTA-TAT TTATAT
8400 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:8368 original size:21 final size:21
Alignment explanation
Indices: 8342--8408 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
8332 GATCTTGAAA
8342 TTATATTTATATTTATATTAT
1 TTATATTTATATTTATATTAT
8363 TTATATTTATATTTATATT-T
1 TTATATTTATATTTATATTAT
* * *
8383 ATATATAT-TATTTATATAAT
1 TTATATTTATATTTATATTAT
8403 TATATA
1 T-TATA
8409 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:8400 original size:27 final size:27
Alignment explanation
Indices: 8342--8399 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
8332 GATCTTGAAA
8342 TTATATTTATATTTATATTATTTATAT
1 TTATATTTATATTTATATTATTTATAT
*
8369 TTATATTTATATTTATA-TATAT-TAT
1 TTATATTTATATTTATATTATTTATAT
8394 TTATAT
1 TTATAT
8400 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:8405 original size:27 final size:29
Alignment explanation
Indices: 8340--8407 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
8330 GTGATCTTGA
8340 AATTATATTTATATTTATATTATTTATATTT
1 AATTATATTTATA-TTATATTATTTATA-TT
8371 ATATTTATATTTATA-TATATTATTTATA-T
1 A-A-TTATATTTATATTATATTATTTATATT
8400 AATTATAT
1 AATTATAT
8408 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:10881 original size:15 final size:15
Alignment explanation
Indices: 10861--10893 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10851 CAAAGTGAAA
10861 TATAATATTACATAT
1 TATAATATTACATAT
10876 TATAATATTACATAT
1 TATAATATTACATAT
10891 TAT
1 TAT
10894 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:10960 original size:78 final size:78
Alignment explanation
Indices: 10876--11137 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 78
10866 TATTACATAT
10876 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
10941 AATCAAAGTGAAA
66 AATCAAAGTGAAA
* * ** * *
10954 TATAATATTACATATTA-TAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTA
1 TATAATATTACATATTATTAAGA-TA-AGACCATT---AT--TA-C-GTATTAC--A-----TTA
11018 CGTATTACGCTTCCACAATCAAAGTGAAA
50 CGTATTACGCTTCCACAATCAAAGTGAAA
11047 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
*
11112 AATCAAAGCGAAA
66 AATCAAAGTGAAA
*
11125 TATAATTTTACAT
1 TATAATATTACAT
11138 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:10974 original size:15 final size:15
Alignment explanation
Indices: 10954--10986 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
10944 CAAAGTGAAA
10954 TATAATATTACATAT
1 TATAATATTACATAT
10969 TATAATATTACATAT
1 TATAATATTACATAT
10984 TAT
1 TAT
10987 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:11095 original size:93 final size:93
Alignment explanation
Indices: 10788--11064 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
10778 TTAAGACCAT
10788 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
10853 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
10881 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
10946 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
10974 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
11039 AAGTGAAATATAATATTACATATTAT
66 AAGTGAAATATAATATTACATATTAT
11065 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:12967 original size:18 final size:18
Alignment explanation
Indices: 12944--12981 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
12934 AGAGAATTCC
12944 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
12962 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
12980 AT
1 AT
12982 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:13322 original size:18 final size:18
Alignment explanation
Indices: 13299--13532 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
13289 CAGAATCGAG
13299 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13317 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13335 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13353 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13371 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13389 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13407 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13425 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13443 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
13461 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13479 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13497 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
13515 ACCTATAGTGAAT-AAAA
1 ACCTATAGTGAATGAAAA
13532 A
1 A
13533 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:13581 original size:30 final size:30
Alignment explanation
Indices: 13547--13886 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
13537 AGACTAGTTA
13547 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13577 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13607 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13637 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13667 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13697 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13727 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13757 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13787 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13817 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13847 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
13877 ACGACAATGG
1 ACGACAATGG
13887 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:16022 original size:45 final size:44
Alignment explanation
Indices: 15976--16099 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 44
15966 GTTTTTTTTA
* *
15976 TTATTGTATTA-TTTA-TTTATTATTTATTTCTTATTTATTTGT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTATTTGT
16018 TTATTTTATTAGTTTATTTTAATTATTTATTTATTATTTATTTGT
1 TTATTTTATTAGTTTATTTT-ATTATTTATTTATTATTTATTTGT
16063 TTATTTTATTAGTTTATTTTATTA-TTA--TATTATTTAT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTAT
16100 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:16093 original size:13 final size:13
Alignment explanation
Indices: 16009--16086 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
15999 TTATTTCTTA
*
16009 TTTATTTGTTTAT
1 TTTATTAGTTTAT
16022 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16035 TTTAATTA-TTTA-
1 TTT-ATTAGTTTAT
16047 TTTATTA-TTTA-
1 TTTATTAGTTTAT
16058 --T-TT-GTTTAT
1 TTTATTAGTTTAT
16067 TTTATTAGTTTAT
1 TTTATTAGTTTAT
16080 TTTATTA
1 TTTATTA
16087 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:16112 original size:4 final size:4
Alignment explanation
Indices: 15972--16099 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
15962 CTTTGTTTTT
* *
15972 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
* *
16017 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
16066 TTT- TATTA GTTTA TTT- TATTA -TTA TATTA TTTA T
1 TTTA T-TTA -TTTA TTTA T-TTA TTTA T-TTA TTTA T
16100 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:16150 original size:35 final size:35
Alignment explanation
Indices: 16111--16234 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
16101 GATATTTATT
16111 TAAATATAATTTCATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16146 TAAATATAATTTCATATTTTAATATATTTAATATATAAAATA
1 TAAATATAATTTCATATTTTAATATA-TT--TA-AT---ATA
*
16188 TAAATATAATTTAATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
16223 TAAATATAATTT
1 TAAATATAATTT
16235 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:16205 original size:42 final size:42
Alignment explanation
Indices: 16124--16231 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
16114 ATATAATTTC
* *
16124 ATAT-TTTAATATATTTAATATATAAATATAATTTCATATTTTA
1 ATATATTTAATATA--TAAAATATAAATATAATTTAATATTTTA
16167 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
1 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
16209 ATATATTTAATATAT-AAATATAA
1 ATATATTTAATATATAAAATATAA
16232 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:16281 original size:77 final size:77
Alignment explanation
Indices: 16124--16281 Score: 187
Period size: 77 Copynumber: 2.1 Consensus size: 77
16114 ATATAATTTC
* * * *
16124 ATATTTTAATATATTTAATATATAAATATAATTTCATATTTTAATATATTTAATATATAAAATAT
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAATATATAAAACAT
* *
16189 AAATATAATTTA
66 AAATATAAATAA
* * *
16201 ATATTTTAATATATTTAATATATAAATATAATTT-A-A-ATAAATATCTATAACTGTGATAATAC
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAA-TAT-ATAAAAC
16263 ATAAATAATAAATAA
64 ATAAAT-ATAAATAA
16278 ATAT
1 ATAT
16282 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:16290 original size:17 final size:18
Alignment explanation
Indices: 16111--16299 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
16101 GATATTTATT
* **
16111 TAAATATAATTTCATATT
1 TAAATATAATTTAATAAA
* *
16129 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
*
16146 TAAATATAATTTCATATTTTAA
1 TAAATATAATTT-A-A--TAAA
* *
16168 TATATTTAATATATAA-AATA
1 TAAATATAAT-T-TAATAA-A
**
16188 TAAATATAATTTAATATT
1 TAAATATAATTTAATAAA
* *
16206 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
16223 TAAATATAATTTAAATAAA
1 TAAATATAATTT-AATAAA
** * *
16242 TATCTATAACTGTGAT-AA
1 TAAATATAA-TTTAATAAA
*
16260 TACATA-AA--TAATAAA
1 TAAATATAATTTAATAAA
16275 TAAATATAATTT-ATAAA
1 TAAATATAATTTAATAAA
*
16292 TATATATA
1 TAAATATA
16300 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:16335 original size:19 final size:19
Alignment explanation
Indices: 16311--16392 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
16301 AACCGACACG
* *
16311 AAAATAATAAATAATTAAT
1 AAAATAAGAAATAAATAAT
16330 AAAATAAGAAATAAATAAT
1 AAAATAAGAAATAAATAAT
* * *
16349 GAAATATAGTAATAAAT-AC
1 AAAATA-AGAAATAAATAAT
* *
16368 AAAATATAGTAATAACTAA-
1 AAAATA-AGAAATAAATAAT
16387 AAAATA
1 AAAATA
16393 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:16393 original size:19 final size:19
Alignment explanation
Indices: 16320--16406 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
16310 GAAAATAATA
* *
16320 AATAATTAATAAAATA-AGA
1 AATAAATAA-AAAATATAGT
*
16339 AATAAATAATGAAATATAGT
1 AATAAATAA-AAAATATAGT
*
16359 AATAAATACAAAATATAGT
1 AATAAATAAAAAATATAGT
*
16378 AATAACTAAAAAATATAGT
1 AATAAATAAAAAATATAGT
*
16397 AATGAATAAA
1 AATAAATAAA
16407 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:16423 original size:17 final size:17
Alignment explanation
Indices: 16401--16434 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16391 TATAGTAATG
*
16401 AATAAATCATACAATAT
1 AATAAATAATACAATAT
16418 AATAAATAATACAATAT
1 AATAAATAATACAATAT
16435 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:16453 original size:15 final size:15
Alignment explanation
Indices: 16433--16482 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
16423 ATAATACAAT
16433 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16448 ATTAACAACAATATTAAA
1 ATT---AACAATATTAAA
16466 ATTAACAATATTAAA
1 ATTAACAATATTAAA
16481 AT
1 AT
16483 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:16459 original size:18 final size:18
Alignment explanation
Indices: 16436--16473 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16426 ATACAATATT
16436 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16454 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
16472 AA
1 AA
16474 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:16596 original size:25 final size:25
Alignment explanation
Indices: 16568--16619 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
16558 TCCAACTCCT
*
16568 AATCATTCGAAGACTGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16593 AATCATTCGAAGACGGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
16618 AA
1 AA
16620 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:16687 original size:17 final size:16
Alignment explanation
Indices: 16658--16706 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
16648 AAAAATTATT
16658 AAAAAAATAAGAACTAA
1 AAAAAAATAAGAA-TAA
16675 ATAAAAAAT-AGAATAA
1 A-AAAAAATAAGAATAA
*
16691 AAAAAATAAAAGAATA
1 AAAAAA-ATAAGAATA
16707 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:17689 original size:22 final size:22
Alignment explanation
Indices: 17654--17704 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
17644 AAAAACTAAA
17654 TAGAATT-ATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
17675 TAGAATTCATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
*
17697 TATAATTC
1 TAGAATTC
17705 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:21176 original size:21 final size:21
Alignment explanation
Indices: 21132--21194 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
21122 TATATATTTA
21132 ATTTTAATATTTAA-TTT--T
1 ATTTTAATATTTAATTTTAAT
21150 -TTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
21170 ATTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
21191 ATTT
1 ATTT
21195 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:21200 original size:13 final size:13
Alignment explanation
Indices: 21125--21194 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
21115 ATCACAATAT
21125 ATATTTAATTTTA
1 ATATTTAATTTTA
21138 ATATTTAATTTT-
1 ATATTTAATTTTA
21150 -T-TTTAATATTTA
1 ATATTTAAT-TTTA
21162 AT-TTTAATATTTTA
1 ATATTT-A-ATTTTA
21176 ATATTTAATTTTA
1 ATATTTAATTTTA
21189 ATATTT
1 ATATTT
21195 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:21388 original size:10 final size:10
Alignment explanation
Indices: 21373--21450 Score: 63
Period size: 10 Copynumber: 7.6 Consensus size: 10
21363 GTCCATTACT
21373 TATTATATTA
1 TATTATATTA
21383 TATTATACTTA
1 TATTATA-TTA
21394 T-TTATACTTA
1 TATTATA-TTA
*
21404 TACTTATTTTA
1 TA-TTATATTA
21415 TACTTAT-TTA
1 TA-TTATATTA
*
21425 TACTTATTTTA
1 TA-TTATATTA
*
21436 TACT-TATTA
1 TATTATATTA
21445 TATTAT
1 TATTAT
21451 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:21415 original size:27 final size:26
Alignment explanation
Indices: 21375--21442 Score: 100
Period size: 27 Copynumber: 2.5 Consensus size: 26
21365 CCATTACTTA
21375 TTATATTATATTATACTTATTTATAC
1 TTATATTATATTATACTTATTTATAC
*
21401 TTATACTTATTTTATACTTATTTATAC
1 TTATA-TTATATTATACTTATTTATAC
*
21428 TTATTTTATACTTAT
1 TTATATTATA-TTAT
21443 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:21417 original size:11 final size:11
Alignment explanation
Indices: 21401--21443 Score: 79
Period size: 11 Copynumber: 4.0 Consensus size: 11
21391 TTATTTATAC
21401 TTATACTTATT
1 TTATACTTATT
21412 TTATACTTA-T
1 TTATACTTATT
21422 TTATACTTATT
1 TTATACTTATT
21433 TTATACTTATT
1 TTATACTTATT
21444 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:21456 original size:20 final size:21
Alignment explanation
Indices: 21441--21498 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
21431 TTTTATACTT
*
21441 ATTATATTATCCTTATTACTT
1 ATTATATTATCTTTATTACTT
**
21462 ATTCGATTA-CTTTATTACTT
1 ATTATATTATCTTTATTACTT
*
21482 ATTCTATTATCTATTAT
1 ATTATATTATCT-TTAT
21499 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:21460 original size:21 final size:21
Alignment explanation
Indices: 21371--21492 Score: 73
Period size: 21 Copynumber: 6.0 Consensus size: 21
21361 TTGTCCATTA
*
21371 CTTATTA--TATTATATTATA
1 CTTATTACTTATTATATTATC
21390 CTTATT--TATACTTATACTTAT-
1 CTTATTACT-TA-TTATA-TTATC
*
21411 TTTA-TACTTATTTATACTTAT-
1 CTTATTACTTA-TTATA-TTATC
*
21432 TTTA-TACTTATTATATTATC
1 CTTATTACTTATTATATTATC
**
21452 CTTATTACTTATTCGATTA-C
1 CTTATTACTTATTATATTATC
* *
21472 TTTATTACTTATTCTATTATC
1 CTTATTACTTATTATATTATC
21493 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:21463 original size:27 final size:24
Alignment explanation
Indices: 21373--21457 Score: 95
Period size: 21 Copynumber: 3.5 Consensus size: 24
21363 GTCCATTACT
* *
21373 TATTATATTATATTATACTTATTTA
1 TATTATCTTATTTTATACTTA-TTA
21398 TACTTATACTTATTTTATACTTATT-
1 TA-TTAT-CTTATTTTATACTTATTA
21423 TA-TA-CTTATTTTATACTTATTA
1 TATTATCTTATTTTATACTTATTA
21445 TATTATCCTTATT
1 TATTAT-CTTATT
21458 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:21506 original size:17 final size:17
Alignment explanation
Indices: 21484--21517 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
21474 TATTACTTAT
21484 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21501 TCTATTATCTATTATAA
1 TCTATTATCTATTATAA
21518 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.