Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168395.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_611, 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: 21588
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.36
Found at i:705 original size:2 final size:2
Alignment explanation
Indices: 698--750 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
688 AATAAAATAT
698 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
740 GA GA GA GA GA G
1 GA GA GA GA GA G
751 TTGGGTATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:1539 original size:35 final size:34
Alignment explanation
Indices: 1498--1586 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 34
1488 TGAAATAAAA
1498 TTTCAAATAATTTTAAAAATTTTT-TAAAATTGAT
1 TTTCAAA-AATTTTAAAAATTTTTCTAAAATTGAT
* * *
1532 TTCTCAAAACTTTT-AAAATTTTTCTTAAATTTAT
1 TT-TCAAAAATTTTAAAAATTTTTCTAAAATTGAT
1566 TTTCAAAAATTTTTAAAAATT
1 TTTCAAAAA-TTTTAAAAATT
1587 CATTTTTTGA
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
33 15 0.32
34 21 0.45
35 11 0.23
ACGTcount: A:0.42, C:0.07, G:0.01, T:0.51
Consensus pattern (34 bp):
TTTCAAAAATTTTAAAAATTTTTCTAAAATTGAT
Found at i:2091 original size:33 final size:34
Alignment explanation
Indices: 2045--2130 Score: 113
Period size: 35 Copynumber: 2.5 Consensus size: 34
2035 TTTAATTATT
*
2045 TTTAATAAATTTTTGAAAAA-GAAATTTCAAAAA-
1 TTTAA-AAATTTTTTAAAAATGAAATTTCAAAAAC
* *
2078 TTTAAAAATTTTTTAAAAATTAATTTTCAAAAACC
1 TTTAAAAATTTTTTAAAAATGAAATTTCAAAAA-C
2113 TTTAAAAATTTTTTAAAA
1 TTTAAAAATTTTTTAAAA
2131 TCTATTTTCA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
32 13 0.28
33 16 0.34
35 18 0.38
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (34 bp):
TTTAAAAATTTTTTAAAAATGAAATTTCAAAAAC
Found at i:2094 original size:11 final size:11
Alignment explanation
Indices: 2078--2211 Score: 69
Period size: 11 Copynumber: 11.7 Consensus size: 11
2068 ATTTCAAAAA
2078 TTTAAAAATTT
1 TTTAAAAATTT
2089 TTTAAAAATTAAT
1 TTTAAAAATT--T
**
2102 TTTCAAAAA-CC
1 TTT-AAAAATTT
2113 TTTAAAAATTT
1 TTTAAAAATTT
2124 TTT-AAAATCTAT
1 TTTAAAAAT-T-T
* * *
2136 TTTCATAAGTT
1 TTTAAAAATTT
*
2147 TTTAAAAGTTT
1 TTTAAAAATTT
* *
2158 TTGAAAATTTTTT
1 TTTAAAA--ATTT
*
2171 TTTGAAAA--T
1 TTTAAAAATTT
*
2180 TTTAAAGATTT
1 TTTAAAAATTT
2191 TTTAAAAATTCAT
1 TTTAAAAATT--T
2204 TTTAAAAA
1 TTTAAAAA
2212 ATTATGAATT
Statistics
Matches: 92, Mismatches: 18, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
9 7 0.08
10 10 0.11
11 41 0.45
12 5 0.05
13 24 0.26
14 5 0.05
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (11 bp):
TTTAAAAATTT
Found at i:2131 original size:34 final size:33
Alignment explanation
Indices: 2044--2214 Score: 130
Period size: 34 Copynumber: 5.1 Consensus size: 33
2034 ATTTAATTAT
* ** *
2044 TTTTAATAAATTTTTGAAAAAGAAATTTCAAAAA
1 TTTTAA-AAATTTTTTAAAATTAATTTTCAAAAA
2078 -TTTAAAAATTTTTTAAAAATTAATTTTCAAAAA
1 TTTTAAAAATTTTTT-AAAATTAATTTTCAAAAA
* **
2111 CCTTTAAAAATTTTTTAAAATCT-ATTTTCATAAGT
1 -TTTTAAAAATTTTTTAAAAT-TAATTTTCA-AAAA
* * ** **
2146 TTTTAAAAGTTTTTGAAAATTTTTTTTTGAAAA
1 TTTTAAAAATTTTTTAAAATTAATTTTCAAAAA
* * *
2179 TTTTAAAGATTTTTTAAAAATTCATTTTAAAAAA
1 TTTTAAAAATTTTTT-AAAATTAATTTTCAAAAA
2213 TT
1 TT
2215 ATGAATTGCA
Statistics
Matches: 109, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
32 8 0.07
33 35 0.32
34 49 0.45
35 17 0.16
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (33 bp):
TTTTAAAAATTTTTTAAAATTAATTTTCAAAAA
Found at i:2182 original size:13 final size:14
Alignment explanation
Indices: 2155--2182 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2145 TTTTTAAAAG
2155 TTTTTGAAAATTTT
1 TTTTTGAAAATTTT
2169 TTTTTGAAAATTTT
1 TTTTTGAAAATTTT
2183 AAAGATTTTT
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:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTTGAAAATTTT
Found at i:8120 original size:29 final size:30
Alignment explanation
Indices: 8085--8168 Score: 91
Period size: 31 Copynumber: 2.7 Consensus size: 30
8075 GATCATATCT
* *
8085 TAATTAAGTATAAATATAACATTT-TTATTA
1 TAATTAAATATAAATATAA-ATTTATTAATA
8115 -AATTAATATATTAAATAATAAATTTATTAATA
1 TAATTAA-ATA-TAAAT-ATAAATTTATTAATA
8147 TAATATAAATATAAATATAAAT
1 TAAT-TAAATATAAATATAAAT
8169 ATAAAATATC
Statistics
Matches: 46, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
29 6 0.13
30 2 0.04
31 15 0.33
32 14 0.30
33 6 0.13
34 3 0.07
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (30 bp):
TAATTAAATATAAATATAAATTTATTAATA
Found at i:8143 original size:24 final size:25
Alignment explanation
Indices: 8116--8162 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
8106 TTTTTATTAA
8116 ATTAATAT-AT-TAAATAATAAATTT
1 ATTAATATAATATAAAT-ATAAATTT
8140 ATTAATATAATATAAATATAAAT
1 ATTAATATAATATAAATATAAAT
8163 ATAAATATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 8 0.38
25 8 0.38
26 5 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
ATTAATATAATATAAATATAAATTT
Found at i:8159 original size:6 final size:6
Alignment explanation
Indices: 8143--8173 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
8133 TAAATTTATT
8143 AATAT- AATATA AATATA AATATA AATATA AA
1 AATATA AATATA AATATA AATATA AATATA AA
8174 ATATCAAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AATATA
Found at i:8386 original size:26 final size:27
Alignment explanation
Indices: 8357--8412 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
8347 TTTATTAACT
8357 AAATCAAAAAAGGAA-AAAGA-GAAAAA
1 AAATCAAAAAAGGAATAAA-ATGAAAAA
* *
8383 AAATGAAAAAAGTAATAAAATGAAAAA
1 AAATCAAAAAAGGAATAAAATGAAAAA
8410 AAA
1 AAA
8413 AATAGCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (27 bp):
AAATCAAAAAAGGAATAAAATGAAAAA
Found at i:8402 original size:18 final size:17
Alignment explanation
Indices: 8362--8414 Score: 63
Period size: 17 Copynumber: 3.1 Consensus size: 17
8352 TAACTAAATC
*
8362 AAAAAAGGAAAAAGAGAA
1 AAAAAATGAAAAA-AGAA
*
8380 AAAAAATGAAAAAAGTA
1 AAAAAATGAAAAAAGAA
*
8397 ATAAAATGAAAAAA-AA
1 AAAAAATGAAAAAAGAA
8413 AA
1 AA
8415 TAGCATACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 2 0.07
17 16 0.53
18 12 0.40
ACGTcount: A:0.79, C:0.00, G:0.13, T:0.08
Consensus pattern (17 bp):
AAAAAATGAAAAAAGAA
Found at i:8611 original size:24 final size:24
Alignment explanation
Indices: 8577--8626 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
8567 AAAAATTATT
* ** *
8577 AAAAAATATTTACTAAATATAAAA
1 AAAAAACATTTAAAAAAAATAAAA
8601 AAAAAACATTTAAAAAAAATAAAA
1 AAAAAACATTTAAAAAAAATAAAA
8625 AA
1 AA
8627 TCAACAGTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.74, C:0.04, G:0.00, T:0.22
Consensus pattern (24 bp):
AAAAAACATTTAAAAAAAATAAAA
Found at i:8632 original size:24 final size:25
Alignment explanation
Indices: 8595--8642 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
8585 TTTACTAAAT
8595 ATAAAAAAAAAACA-TTTAAAAAAA
1 ATAAAAAAAAAACAGTTTAAAAAAA
** *
8619 ATAAAAAATCAACAGTTTTAAAAA
1 ATAAAAAAAAAACAGTTTAAAAAA
8643 GCATTTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (25 bp):
ATAAAAAAAAAACAGTTTAAAAAAA
Found at i:8946 original size:18 final size:18
Alignment explanation
Indices: 8909--8951 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
8899 TAGAAAAATC
**
8909 AAAAAATTAAAAAAGTAA
1 AAAAAATTAAAAAAAAAA
8927 AAAAAATTAAAAAAAAAA
1 AAAAAATTAAAAAAAAAA
8945 AAGAAAA
1 AA-AAAA
8952 GGAAAAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.12
Consensus pattern (18 bp):
AAAAAATTAAAAAAAAAA
Found at i:10708 original size:10 final size:10
Alignment explanation
Indices: 10685--10716 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
10675 TGGGTCCCAC
10685 TTTTAAAA-A
1 TTTTAAAATA
10694 TTTTAAAATA
1 TTTTAAAATA
10704 TTTTAAAATA
1 TTTTAAAATA
10714 TTT
1 TTT
10717 GTCACATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 8 0.36
10 14 0.64
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:15383 original size:17 final size:17
Alignment explanation
Indices: 15363--15396 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
15353 AATTTTCCTC
* *
15363 AAAAAATTTTTTTTTAA
1 AAAAAATGTATTTTTAA
15380 AAAAAATGTATTTTTAA
1 AAAAAATGTATTTTTAA
15397 GGAAAATTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AAAAAATGTATTTTTAA
Found at i:15552 original size:178 final size:179
Alignment explanation
Indices: 15218--15554 Score: 563
Period size: 178 Copynumber: 1.9 Consensus size: 179
15208 TTTTGTCTAG
** *
15218 GGAAAATTGATACTTTCAACTTTTTTCCAAAAATACTTTTTAGAAAACTTTTAATTTCGAGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTAGAAAACTTTTAATTTCAAGAAAA
*
15283 ATTGATACTTTCAACTTTTCCTCAAAAATCTTTTTTAAAAATTTATTTTTAAGGAAAATTGATAC
66 ATTGATACTTTCAACTTTCCCTCAAAAATCTTTTTTAAAAATTTATTTTTAAGGAAAATTGATAC
15348 TTTCAAATTTTCCTCAAAAAATTTTTTTTTAAAAAAAATGTATTTTTAA
131 TTTCAAATTTTCCTCAAAAAATTTTTTTTTAAAAAAAATGTATTTTTAA
* **
15397 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGAAAACTTTTAATTTCAAGGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTAGAAAACTTTTAATTTCAAGAAAA
15461 ATTGATACTTTCAACTTTCCCTCAAAAATC-TTTTTAAAAATTTATTTTTAAGGAAAATTGATAC
66 ATTGATACTTTCAACTTTCCCTCAAAAATCTTTTTTAAAAATTTATTTTTAAGGAAAATTGATAC
*
15525 TTTCAACTTTTTCC-CAAAAATATTTTTTTT
131 TTTCAA-ATTTTCCTCAAAAA-ATTTTTTTT
15555 ATTTTATTTA
Statistics
Matches: 148, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
177 46 0.31
178 69 0.47
179 33 0.22
ACGTcount: A:0.37, C:0.13, G:0.07, T:0.43
Consensus pattern (179 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATACTTTTTAGAAAACTTTTAATTTCAAGAAAA
ATTGATACTTTCAACTTTCCCTCAAAAATCTTTTTTAAAAATTTATTTTTAAGGAAAATTGATAC
TTTCAAATTTTCCTCAAAAAATTTTTTTTTAAAAAAAATGTATTTTTAA
Found at i:15576 original size:5 final size:5
Alignment explanation
Indices: 15568--15666 Score: 76
Period size: 5 Copynumber: 18.6 Consensus size: 5
15558 TTATTTAAAG
*
15568 AAAAT AAAAT --AAT AAAAC AAAAT AAAAGT GAAAAAT AAAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA-T --AAAAT -AAAAT AAAAT
* * *
15615 AAAAGT AAAACA AAAAT AAAAAT AAAAT AAAGAT AAAAT AATAT TAAAT
1 AAAA-T AAAA-T AAAAT -AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT
15664 AAA
1 AAA
15667 CCTAATCTAA
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
3 3 0.04
5 43 0.56
6 26 0.34
7 1 0.01
8 4 0.05
ACGTcount: A:0.76, C:0.02, G:0.04, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:15604 original size:23 final size:22
Alignment explanation
Indices: 15578--15652 Score: 82
Period size: 23 Copynumber: 3.3 Consensus size: 22
15568 AAAATAAAAT
*
15578 AATAAAACAAAATAAAAGTGAAA
1 AATAAAAAAAAATAAAAGT-AAA
15601 AATAAAAATAAAATAAAAGTAAA
1 AATAAAAA-AAAATAAAAGTAAA
15624 ACA-AAAATAAAAATAAAA-TAAA
1 A-ATAAAA-AAAAATAAAAGTAAA
*
15646 GATAAAA
1 AATAAAA
15653 TAATATTAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
21 1 0.02
22 8 0.17
23 24 0.52
24 13 0.28
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (22 bp):
AATAAAAAAAAATAAAAGTAAA
Found at i:15609 original size:6 final size:6
Alignment explanation
Indices: 15568--15652 Score: 72
Period size: 6 Copynumber: 14.5 Consensus size: 6
15558 TTATTTAAAG
*
15568 AAAAT- AAAATA ATAAA-A CAAAATA AAAGTGA AAAATA AAAAT- AAAATA
1 AAAATA AAAATA A-AAATA -AAAATA AAAAT-A AAAATA AAAATA AAAATA
* * *
15616 AAAGT- AAAACA AAAATA AAAAT- AAAATA AAGATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAA
15653 TAATATTAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
5 18 0.28
6 36 0.56
7 10 0.16
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:15615 original size:11 final size:11
Alignment explanation
Indices: 15568--15655 Score: 74
Period size: 11 Copynumber: 7.6 Consensus size: 11
15558 TTATTTAAAG
15568 AAAATAAAATAAT
1 AAAAT-AAA-AAT
*
15581 AAAA-CAAAAT
1 AAAATAAAAAT
15591 AAAAGTGAAAAAT
1 AAAA-T-AAAAAT
15604 AAAA-ATAAAAT
1 AAAATA-AAAAT
15615 AAAAGTAAAACA-
1 AAAA-TAAAA-AT
15627 AAAATAAAAAT
1 AAAATAAAAAT
*
15638 AAAATAAAGAT
1 AAAATAAAAAT
15649 AAAATAA
1 AAAATAA
15656 TATTAAATAA
Statistics
Matches: 64, Mismatches: 3, Indels: 18
0.75 0.04 0.21
Matches are distributed among these distances:
10 9 0.14
11 33 0.52
12 7 0.11
13 15 0.23
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:15618 original size:17 final size:17
Alignment explanation
Indices: 15568--15652 Score: 86
Period size: 17 Copynumber: 4.8 Consensus size: 17
15558 TTATTTAAAG
15568 AAAATAAAATAATAAA-A
1 AAAATAAAATAA-AAATA
15585 CAAAATAAAAGTGAAAAATA
1 -AAAATAAAA-T-AAAAATA
*
15605 AAAATAAAATAAAAGTA
1 AAAATAAAATAAAAATA
15622 AAACA-AAAATAAAAAT-
1 AAA-ATAAAATAAAAATA
15638 AAAATAAAGATAAAA
1 AAAATAAA-ATAAAA
15653 TAATATTAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 13
0.80 0.03 0.18
Matches are distributed among these distances:
15 1 0.02
16 6 0.10
17 25 0.42
18 11 0.19
19 13 0.22
20 3 0.05
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.15
Consensus pattern (17 bp):
AAAATAAAATAAAAATA
Found at i:16548 original size:22 final size:21
Alignment explanation
Indices: 16494--16576 Score: 77
Period size: 21 Copynumber: 4.0 Consensus size: 21
16484 AAAAAAAATC
16494 AGATAAA-AAAAATAA-TAAT-
1 AGATAAATAAAAA-AATTAATA
*
16513 AGATAATTAGAAAAAATTAATA
1 AGATAAATA-AAAAAATTAATA
* *
16535 AGATAAATCAAAAATATT-ACA
1 AGATAAAT-AAAAAAATTAATA
16556 AGATAAATAAAAAAA-TAATA
1 AGATAAATAAAAAAATTAATA
16576 A
1 A
16577 TAACAGATAA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
19 7 0.13
20 12 0.23
21 18 0.35
22 14 0.27
23 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.23
Consensus pattern (21 bp):
AGATAAATAAAAAAATTAATA
Found at i:16606 original size:20 final size:17
Alignment explanation
Indices: 16568--16615 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 17
16558 ATAAATAAAA
16568 AAATAATAATAACAGAT
1 AAATAATAATAACAGAT
16585 AAATGAATATATAACTAGAT
1 AAAT-AATA-ATAAC-AGAT
*
16605 AAATAAAAATA
1 AAATAATAATA
16616 CATATAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 4 0.15
18 7 0.26
19 8 0.30
20 8 0.30
ACGTcount: A:0.65, C:0.04, G:0.06, T:0.25
Consensus pattern (17 bp):
AAATAATAATAACAGAT
Found at i:16615 original size:22 final size:22
Alignment explanation
Indices: 16494--16615 Score: 75
Period size: 22 Copynumber: 5.7 Consensus size: 22
16484 AAAAAAAATC
16494 AGATAAA-AAAAATA-ATAA-T
1 AGATAAATAAAAATATATAACT
* *
16513 AGATAATTAGAAAAAAT-TAA-T
1 AGATAAATA-AAAATATATAACT
*
16534 AAGATAAATCAAAAATAT-T-ACA
1 -AGATAAAT-AAAAATATATAACT
16556 AGATAAATAAAAAAATAATAATAAC-
1 AGATAAAT--AAAAAT-AT-ATAACT
*
16581 AGATAAAT--GAATATATAACT
1 AGATAAATAAAAATATATAACT
16601 AGATAAATAAAAATA
1 AGATAAATAAAAATA
16616 CATATAAAAT
Statistics
Matches: 81, Mismatches: 8, Indels: 25
0.71 0.07 0.22
Matches are distributed among these distances:
19 11 0.14
20 11 0.14
21 21 0.26
22 24 0.30
23 3 0.04
25 9 0.11
26 2 0.02
ACGTcount: A:0.66, C:0.03, G:0.07, T:0.24
Consensus pattern (22 bp):
AGATAAATAAAAATATATAACT
Found at i:17062 original size:42 final size:41
Alignment explanation
Indices: 16951--17227 Score: 279
Period size: 41 Copynumber: 6.7 Consensus size: 41
16941 GCAAATGTTT
* * * *
16951 AACGACTTTGAGAAACATAAATGGCTCCTCTAATCAGAGACTC
1 AACGACTTTGA-AAA-ATAAATTGCTCCTCTAAACAGAGGCAC
* * * * **
16994 AACTACTTTAAAAAATAAATGGCTCCTCTAATCAGAGGCTT
1 AACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAC
*
17035 AACAACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCAC
1 AACGACTTTG-AAAAATAAATTGCTCCTCTAAACAGAGGCAC
* * *
17077 CACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCAC
1 AACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAC
* * *
17118 CACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAAGCATC
1 AACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCA-C
*
17161 -ACGACTTTTG-AAAGTAAATTGCTCCTCTAAACAGAGGCAC
1 AACGAC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAC
* * * * *
17201 CATGACTTTGGAAAGTAAATTACTCCT
1 AACGACTTTGAAAAATAAATTGCTCCT
17228 TGACAATCAT
Statistics
Matches: 210, Mismatches: 19, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
40 5 0.02
41 115 0.55
42 80 0.38
43 10 0.05
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.25
Consensus pattern (41 bp):
AACGACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCAC
Found at i:17199 original size:83 final size:82
Alignment explanation
Indices: 16952--17227 Score: 304
Period size: 83 Copynumber: 3.3 Consensus size: 82
16942 CAAATGTTTA
* * * * ** * *
16952 ACGACTTTGAGAAACATAAATGGCTCCTCTAATCAG-AG-ACTCAACTACTTTAAAAAATAAATG
1 ACGACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAAGCAC-C-ACGACTTTGGAAAGTAAATT
* ***
17015 GCTCCTCTAATCAGAGGCTTA
62 GCTCCTCTAAACAGAGGCACC
* * *
17036 ACAACTTTGAAAAAATAAATTGCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCT
1 ACGACTTTG-AAAAGTAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTGCT
17101 CCTCTAAACAGAGGCACC
65 CCTCTAAACAGAGGCACC
* *
17119 ACGACTTTTGAAAAGTAAATTGCTCCTCTAAACAGAAGCATCACGACTTTTGAAAGTAAATTGCT
1 ACGAC-TTTGAAAAGTAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTGCT
17184 CCTCTAAACAGAGGCACC
65 CCTCTAAACAGAGGCACC
* * *
17202 ATGACTTTGGAAAGTAAATTACTCCT
1 ACGACTTTGAAAAGTAAATTGCTCCT
17228 TGACAATCAT
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
82 19 0.11
83 128 0.77
84 17 0.10
85 3 0.02
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.25
Consensus pattern (82 bp):
ACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAAGCACCACGACTTTGGAAAGTAAATTGCTC
CTCTAAACAGAGGCACC
Found at i:18245 original size:8 final size:8
Alignment explanation
Indices: 18234--18290 Score: 96
Period size: 8 Copynumber: 7.0 Consensus size: 8
18224 CCTTTTTCAT
18234 TTTTTTTA
1 TTTTTTTA
18242 TTTTTTTA
1 TTTTTTTA
18250 TTTTTTTA
1 TTTTTTTA
18258 TTTTTTTA
1 TTTTTTTA
18266 TTTTTTTCA
1 TTTTTTT-A
*
18275 TTTTTTCA
1 TTTTTTTA
18283 TTTTTTTA
1 TTTTTTTA
18291 AGCATAGTAT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
8 39 0.85
9 7 0.15
ACGTcount: A:0.12, C:0.04, G:0.00, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:18246 original size:17 final size:17
Alignment explanation
Indices: 18226--18289 Score: 94
Period size: 17 Copynumber: 3.8 Consensus size: 17
18216 TAAGTTTTCC
18226 TTTTTCATTTTTTTTAT
1 TTTTTCATTTTTTTTAT
*
18243 TTTTTTA-TTTTTTTAT
1 TTTTTCATTTTTTTTAT
* *
18259 TTTTTTATTTTTTTCAT
1 TTTTTCATTTTTTTTAT
18276 TTTTTCATTTTTTT
1 TTTTTCATTTTTTT
18290 AAGCATAGTA
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
16 16 0.37
17 27 0.63
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTCATTTTTTTTAT
Found at i:18290 original size:25 final size:24
Alignment explanation
Indices: 18226--18290 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 24
18216 TAAGTTTTCC
18226 TTTTTCATTTTTTTTATTTTTTTAT
1 TTTTTCA-TTTTTTTATTTTTTTAT
*
18251 TTTTTTATTTTTTTATTTTTTTCAT
1 TTTTTCATTTTTTTATTTTTTT-AT
18276 TTTTTCATTTTTTTA
1 TTTTTCATTTTTTTA
18291 AGCATAGTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
24 15 0.41
25 22 0.59
ACGTcount: A:0.12, C:0.05, G:0.00, T:0.83
Consensus pattern (24 bp):
TTTTTCATTTTTTTATTTTTTTAT
Done.