Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168458.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_669, 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: 20042
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.31
Found at i:5113 original size:23 final size:23
Alignment explanation
Indices: 5087--5132 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
5077 GTTCCTCCCC
5087 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
5110 CAAGTAATAAGATAAATGATTGG
1 CAAGTAATAAGATAAATGATTGG
5133 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:7088 original size:6 final size:6
Alignment explanation
Indices: 7077--7134 Score: 77
Period size: 6 Copynumber: 10.0 Consensus size: 6
7067 GATCTTGAAA
7077 TTATAT TTATAT TTATA- -T-TAT TTATAT TTATAT TTATAT TTATAT
1 TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT TTATAT
*
7122 ATATTAT TTATAT
1 TTA-TAT TTATAT
7135 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:7103 original size:21 final size:21
Alignment explanation
Indices: 7077--7143 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
7067 GATCTTGAAA
7077 TTATATTTATATTTATATTAT
1 TTATATTTATATTTATATTAT
7098 TTATATTTATATTTATATT-T
1 TTATATTTATATTTATATTAT
* * *
7118 ATATATAT-TATTTATATAAT
1 TTATATTTATATTTATATTAT
7138 TATATA
1 T-TATA
7144 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:7135 original size:27 final size:27
Alignment explanation
Indices: 7077--7134 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
7067 GATCTTGAAA
7077 TTATATTTATATTTATATTATTTATAT
1 TTATATTTATATTTATATTATTTATAT
*
7104 TTATATTTATATTTATA-TATAT-TAT
1 TTATATTTATATTTATATTATTTATAT
7129 TTATAT
1 TTATAT
7135 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:7140 original size:27 final size:29
Alignment explanation
Indices: 7075--7142 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 29
7065 GTGATCTTGA
7075 AATTATATTTATATTTATATTATTTATATTT
1 AATTATATTTATA-TTATATTATTTATA-TT
7106 ATATTTATATTTATA-TATATTATTTATA-T
1 A-A-TTATATTTATATTATATTATTTATATT
7135 AATTATAT
1 AATTATAT
7143 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:9616 original size:15 final size:15
Alignment explanation
Indices: 9596--9628 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9586 CAAAGTGAAA
9596 TATAATATTACATAT
1 TATAATATTACATAT
9611 TATAATATTACATAT
1 TATAATATTACATAT
9626 TAT
1 TAT
9629 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:9695 original size:78 final size:78
Alignment explanation
Indices: 9611--9872 Score: 301
Period size: 78 Copynumber: 3.2 Consensus size: 78
9601 TATTACATAT
9611 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
9676 AATCAAAGTGAAA
66 AATCAAAGTGAAA
* * ** * *
9689 TATAATATTACATATTA-TAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTA
1 TATAATATTACATATTATTAAGA-TA-AGACCATT---AT--TA-C-GTATTAC--A-----TTA
9753 CGTATTACGCTTCCACAATCAAAGTGAAA
50 CGTATTACGCTTCCACAATCAAAGTGAAA
9782 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
1 TATAATATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCAC
*
9847 AATCAAAGCGAAA
66 AATCAAAGTGAAA
*
9860 TATAATTTTACAT
1 TATAATATTACAT
9873 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:9709 original size:15 final size:15
Alignment explanation
Indices: 9689--9721 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
9679 CAAAGTGAAA
9689 TATAATATTACATAT
1 TATAATATTACATAT
9704 TATAATATTACATAT
1 TATAATATTACATAT
9719 TAT
1 TAT
9722 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:9830 original size:93 final size:93
Alignment explanation
Indices: 9523--9799 Score: 554
Period size: 93 Copynumber: 3.0 Consensus size: 93
9513 TTAAGACCAT
9523 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
9588 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
9616 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
9681 AAGTGAAATATAATATTACATATTATAA
66 AAGTGAAATATAATATTACATATTATAA
9709 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
1 TATTACATATTATTAAGATAAGACCATTATTACGTATTACATTACGTATTACGCTTCCACAATCA
9774 AAGTGAAATATAATATTACATATTAT
66 AAGTGAAATATAATATTACATATTAT
9800 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:11698 original size:18 final size:18
Alignment explanation
Indices: 11675--11712 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
11665 AGAGAATTCC
11675 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
11693 ATTGTAAAGCCGTATGCA
1 ATTGTAAAGCCGTATGCA
11711 AT
1 AT
11713 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:12053 original size:18 final size:18
Alignment explanation
Indices: 12030--12263 Score: 397
Period size: 18 Copynumber: 13.1 Consensus size: 18
12020 CAGAATCGAG
12030 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12048 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12066 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12084 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12102 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
12120 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12138 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12156 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12174 ACCTATAGTGAATGAAAA
1 ACCTATAGTGAATGAAAA
12192 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
12210 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
12228 ACCTATAGTGAAT-AACAA
1 ACCTATAGTGAATGAA-AA
12246 ACCTATAGTGAAT-AAAA
1 ACCTATAGTGAATGAAAA
12263 A
1 A
12264 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:12312 original size:30 final size:30
Alignment explanation
Indices: 12278--12617 Score: 680
Period size: 30 Copynumber: 11.3 Consensus size: 30
12268 AGACTAGTTA
12278 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12308 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12338 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12368 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12398 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12428 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12458 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12488 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12518 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12548 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12578 ACGACAATGGCAATGGAAGACCACCATTTG
1 ACGACAATGGCAATGGAAGACCACCATTTG
12608 ACGACAATGG
1 ACGACAATGG
12618 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:14753 original size:45 final size:44
Alignment explanation
Indices: 14707--14830 Score: 186
Period size: 45 Copynumber: 2.9 Consensus size: 44
14697 GTTTTTTTTA
* *
14707 TTATTGTATTA-TTTA-TTTATTATTTATTTCTTATTTATTTGT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTATTTGT
14749 TTATTTTATTAGTTTATTTTAATTATTTATTTATTATTTATTTGT
1 TTATTTTATTAGTTTATTTT-ATTATTTATTTATTATTTATTTGT
14794 TTATTTTATTAGTTTATTTTATTA-TTA--TATTATTTAT
1 TTATTTTATTAGTTTATTTTATTATTTATTTATTATTTAT
14831 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:14824 original size:13 final size:13
Alignment explanation
Indices: 14740--14817 Score: 82
Period size: 13 Copynumber: 6.5 Consensus size: 13
14730 TTATTTCTTA
*
14740 TTTATTTGTTTAT
1 TTTATTAGTTTAT
14753 TTTATTAGTTTAT
1 TTTATTAGTTTAT
14766 TTTAATTA-TTTA-
1 TTT-ATTAGTTTAT
14778 TTTATTA-TTTA-
1 TTTATTAGTTTAT
14789 --T-TT-GTTTAT
1 TTTATTAGTTTAT
14798 TTTATTAGTTTAT
1 TTTATTAGTTTAT
14811 TTTATTA
1 TTTATTA
14818 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:14843 original size:4 final size:4
Alignment explanation
Indices: 14703--14830 Score: 85
Period size: 4 Copynumber: 32.2 Consensus size: 4
14693 CTTTGTTTTT
* *
14703 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
* *
14748 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
14797 TTT- TATTA GTTTA TTT- TATTA -TTA TATTA TTTA T
1 TTTA T-TTA -TTTA TTTA T-TTA TTTA T-TTA TTTA T
14831 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:14881 original size:35 final size:35
Alignment explanation
Indices: 14842--14965 Score: 176
Period size: 35 Copynumber: 3.3 Consensus size: 35
14832 GATATTTATT
14842 TAAATATAATTTCATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
14877 TAAATATAATTTCATATTTTAATATATTTAATATATAAAATA
1 TAAATATAATTTCATATTTTAATATA-TT--TA-AT---ATA
*
14919 TAAATATAATTTAATATTTTAATATATTTAATATA
1 TAAATATAATTTCATATTTTAATATATTTAATATA
14954 TAAATATAATTT
1 TAAATATAATTT
14966 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:14936 original size:42 final size:42
Alignment explanation
Indices: 14855--14962 Score: 166
Period size: 42 Copynumber: 2.6 Consensus size: 42
14845 ATATAATTTC
* *
14855 ATAT-TTTAATATATTTAATATATAAATATAATTTCATATTTTA
1 ATATATTTAATATA--TAAAATATAAATATAATTTAATATTTTA
14898 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
1 ATATATTTAATATATAAAATATAAATATAATTTAATATTTTA
14940 ATATATTTAATATAT-AAATATAA
1 ATATATTTAATATATAAAATATAA
14963 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:15012 original size:77 final size:77
Alignment explanation
Indices: 14855--15012 Score: 187
Period size: 77 Copynumber: 2.1 Consensus size: 77
14845 ATATAATTTC
* * * *
14855 ATATTTTAATATATTTAATATATAAATATAATTTCATATTTTAATATATTTAATATATAAAATAT
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAATATATAAAACAT
* *
14920 AAATATAATTTA
66 AAATATAAATAA
* * *
14932 ATATTTTAATATATTTAATATATAAATATAATTT-A-A-ATAAATATCTATAACTGTGATAATAC
1 ATATTTTAATATATTTAATATATAAATATAATTTCATATATAAATATATATAA-TAT-ATAAAAC
14994 ATAAATAATAAATAA
64 ATAAAT-ATAAATAA
15009 ATAT
1 ATAT
15013 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:15021 original size:17 final size:18
Alignment explanation
Indices: 14842--15030 Score: 79
Period size: 17 Copynumber: 10.4 Consensus size: 18
14832 GATATTTATT
* **
14842 TAAATATAATTTCATATT
1 TAAATATAATTTAATAAA
* *
14860 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
*
14877 TAAATATAATTTCATATTTTAA
1 TAAATATAATTT-A-A--TAAA
* *
14899 TATATTTAATATATAA-AATA
1 TAAATATAAT-T-TAATAA-A
**
14919 TAAATATAATTTAATATT
1 TAAATATAATTTAATAAA
* *
14937 TTAATAT-ATTTAATATA
1 TAAATATAATTTAATAAA
14954 TAAATATAATTTAAATAAA
1 TAAATATAATTT-AATAAA
** * *
14973 TATCTATAACTGTGAT-AA
1 TAAATATAA-TTTAATAAA
*
14991 TACATA-AA--TAATAAA
1 TAAATATAATTTAATAAA
15006 TAAATATAATTT-ATAAA
1 TAAATATAATTTAATAAA
*
15023 TATATATA
1 TAAATATA
15031 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:15066 original size:19 final size:19
Alignment explanation
Indices: 15042--15123 Score: 69
Period size: 19 Copynumber: 4.3 Consensus size: 19
15032 AACCGACACG
* *
15042 AAAATAATAAATAATTAAT
1 AAAATAAGAAATAAATAAT
15061 AAAATAAGAAATAAATAAT
1 AAAATAAGAAATAAATAAT
* * *
15080 GAAATATAGTAATAAAT-AC
1 AAAATA-AGAAATAAATAAT
* *
15099 AAAATATAGTAATAACTAA-
1 AAAATA-AGAAATAAATAAT
15118 AAAATA
1 AAAATA
15124 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:15124 original size:19 final size:19
Alignment explanation
Indices: 15051--15137 Score: 95
Period size: 19 Copynumber: 4.5 Consensus size: 19
15041 GAAAATAATA
* *
15051 AATAATTAATAAAATA-AGA
1 AATAAATAA-AAAATATAGT
*
15070 AATAAATAATGAAATATAGT
1 AATAAATAA-AAAATATAGT
*
15090 AATAAATACAAAATATAGT
1 AATAAATAAAAAATATAGT
*
15109 AATAACTAAAAAATATAGT
1 AATAAATAAAAAATATAGT
*
15128 AATGAATAAA
1 AATAAATAAA
15138 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:15154 original size:17 final size:17
Alignment explanation
Indices: 15132--15165 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
15122 TATAGTAATG
*
15132 AATAAATCATACAATAT
1 AATAAATAATACAATAT
15149 AATAAATAATACAATAT
1 AATAAATAATACAATAT
15166 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:15184 original size:15 final size:15
Alignment explanation
Indices: 15164--15213 Score: 73
Period size: 15 Copynumber: 3.1 Consensus size: 15
15154 ATAATACAAT
15164 ATTAACAATATTAAA
1 ATTAACAATATTAAA
15179 ATTAACAACAATATTAAA
1 ATT---AACAATATTAAA
15197 ATTAACAATATTAAA
1 ATTAACAATATTAAA
15212 AT
1 AT
15214 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:15190 original size:18 final size:18
Alignment explanation
Indices: 15167--15204 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
15157 ATACAATATT
15167 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
15185 AACAATATTAAAATTAAC
1 AACAATATTAAAATTAAC
15203 AA
1 AA
15205 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:15327 original size:25 final size:25
Alignment explanation
Indices: 15299--15350 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
15289 TCCAACTCCT
*
15299 AATCATTCGAAGACTGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
15324 AATCATTCGAAGACGGTAAACTAAA
1 AATCATTCGAAGACGGTAAACTAAA
15349 AA
1 AA
15351 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:15418 original size:17 final size:16
Alignment explanation
Indices: 15389--15437 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
15379 AAAAATTATT
15389 AAAAAAATAAGAACTAA
1 AAAAAAATAAGAA-TAA
15406 ATAAAAAAT-AGAATAA
1 A-AAAAAATAAGAATAA
*
15422 AAAAAATAAAAGAATA
1 AAAAAA-ATAAGAATA
15438 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:16420 original size:22 final size:22
Alignment explanation
Indices: 16385--16435 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
16375 AAAAACTAAA
16385 TAGAATT-ATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
16406 TAGAATTCATTTCTTATATAAT
1 TAGAATTCATTTCTTATATAAT
*
16428 TATAATTC
1 TAGAATTC
16436 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:17410 original size:1 final size:1
Alignment explanation
Indices: 17404--17428 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
17394 CACCGAACTG
17404 AAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAA
17429 TTGAACAGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:19907 original size:21 final size:21
Alignment explanation
Indices: 19863--19925 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
19853 TATATATTTA
19863 ATTTTAATATTTAA-TTT--T
1 ATTTTAATATTTAATTTTAAT
19881 -TTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
19901 ATTTTAATATTTAATTTTAAT
1 ATTTTAATATTTAATTTTAAT
19922 ATTT
1 ATTT
19926 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:19931 original size:13 final size:13
Alignment explanation
Indices: 19856--19925 Score: 85
Period size: 13 Copynumber: 5.5 Consensus size: 13
19846 ATCACAATAT
19856 ATATTTAATTTTA
1 ATATTTAATTTTA
19869 ATATTTAATTTT-
1 ATATTTAATTTTA
19881 -T-TTTAATATTTA
1 ATATTTAAT-TTTA
19893 AT-TTTAATATTTTA
1 ATATTT-A-ATTTTA
19907 ATATTTAATTTTA
1 ATATTTAATTTTA
19920 ATATTT
1 ATATTT
19926 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
Done.