Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168059.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_309, 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: 36282
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:65 original size:19 final size:18
Alignment explanation
Indices: 13--92 Score: 63
Period size: 19 Copynumber: 4.3 Consensus size: 18
3 ACAGTTCAAT
* *
13 TTTAGGTTTTGGGTTTGG
1 TTTAGGATTAGGGTTTGG
** *
31 TTTAGTTTTAGAGTTTGG
1 TTTAGGATTAGGGTTTGG
49 TTTAAGGATTAGGGTTTGG
1 TTT-AGGATTAGGGTTTGG
* *
68 TTT-GAGATTTAAGGTTTGT
1 TTTAG-GA-TTAGGGTTTGG
87 TTTAGG
1 TTTAGG
93 GTTTGAAGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
17 1 0.02
18 20 0.40
19 28 0.56
20 1 0.02
ACGTcount: A:0.16, C:0.00, G:0.33, T:0.51
Consensus pattern (18 bp):
TTTAGGATTAGGGTTTGG
Found at i:141 original size:19 final size:19
Alignment explanation
Indices: 24--147 Score: 78
Period size: 19 Copynumber: 6.5 Consensus size: 19
14 TTAGGTTTTG
*
24 GGTTTGGTTTA--GTTTTA
1 GGTTTGGTTTAGGGTTTAA
* * *
41 GAGTTTGGTTTAAGGATTAG
1 G-GTTTGGTTTAGGGTTTAA
*
61 GGTTTGGTTT-GAGATTTAA
1 GGTTTGGTTTAG-GGTTTAA
*
80 GGTTTGTTTTAGGGTTTGAA
1 GGTTTGGTTTAGGGTTT-AA
* * **
100 GGTTTATGTTT--GCTATTGG
1 GGTTT-GGTTTAGGGT-TTAA
119 GGTTTGGTTTAGGGTTTAA
1 GGTTTGGTTTAGGGTTTAA
138 GGTTTGGTTT
1 GGTTTGGTTT
148 TGGTTTGGGG
Statistics
Matches: 79, Mismatches: 18, Indels: 18
0.69 0.16 0.16
Matches are distributed among these distances:
17 1 0.01
18 14 0.18
19 45 0.57
20 16 0.20
21 3 0.04
ACGTcount: A:0.15, C:0.01, G:0.34, T:0.50
Consensus pattern (19 bp):
GGTTTGGTTTAGGGTTTAA
Found at i:149 original size:25 final size:26
Alignment explanation
Indices: 121--173 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
111 GCTATTGGGG
*
121 TTTGGTTTAGGGTTTAA-GGTTTGGT
1 TTTGGTTTAGGGTTCAAGGGTTTGGT
*
146 TTTGGTTTGGGGTTCAAGGGTTTGGT
1 TTTGGTTTAGGGTTCAAGGGTTTGGT
172 TT
1 TT
174 AAGGTCTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.09, C:0.02, G:0.38, T:0.51
Consensus pattern (26 bp):
TTTGGTTTAGGGTTCAAGGGTTTGGT
Found at i:227 original size:13 final size:13
Alignment explanation
Indices: 211--235 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
201 GAGAGTTAGG
211 TTATGGTTTAAGC
1 TTATGGTTTAAGC
224 TTATGGTTTAAG
1 TTATGGTTTAAG
236 GGTTTTGTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
TTATGGTTTAAGC
Found at i:253 original size:20 final size:20
Alignment explanation
Indices: 228--265 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
218 TTAAGCTTAT
*
228 GGTTTAAGGGTTTTGTTTGG
1 GGTTTAAGGGTTTAGTTTGG
248 GGTTTAAGGGTTTAGTTT
1 GGTTTAAGGGTTTAGTTT
266 TGGTTTGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.13, C:0.00, G:0.37, T:0.50
Consensus pattern (20 bp):
GGTTTAAGGGTTTAGTTTGG
Found at i:1915 original size:64 final size:64
Alignment explanation
Indices: 1805--1929 Score: 155
Period size: 64 Copynumber: 1.9 Consensus size: 64
1795 CCTCCAAGTG
* *
1805 TAATCTCAAAGACTTTCAAGCACGATCTATAAGACTTTCAGACATAATTTTTTAAGACCTTAAAA
1 TAATCTCAAAGA-TTTCAAGCACGATCTATAAGACTTTCAGACATAATCTTTTAAAACCTTAAAA
* * * *
1870 TAATCTCAAAG-TTCTCGAGCATGATCTATAAGATCTTT-GGGCATAATCTTTTAAAACCTT
1 TAATCTCAAAGATT-TCAAGCACGATCTATAAGA-CTTTCAGACATAATCTTTTAAAACCTT
1930 CAAGTACCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
63 2 0.04
64 35 0.67
65 15 0.29
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.34
Consensus pattern (64 bp):
TAATCTCAAAGATTTCAAGCACGATCTATAAGACTTTCAGACATAATCTTTTAAAACCTTAAAA
Found at i:2434 original size:13 final size:13
Alignment explanation
Indices: 2416--2440 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2406 TTTTCACAAA
2416 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
2429 AAAAAAAAAAAA
1 AAAAAAAAAAAA
2441 TTTAAATGTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:3920 original size:92 final size:94
Alignment explanation
Indices: 3804--4030 Score: 259
Period size: 93 Copynumber: 2.4 Consensus size: 94
3794 GTTTTTAATT
* * *
3804 TTATCAAATTATTAAAAAATTTAAATTTCAAGTTAAATCTT-TAAAATTATT-GAAAAACTTAAT
1 TTATCAAACTATTGAAAGATTTAAATTTCAAGTTAAATCTTATAAAATTATTAG-AAAACTTAAT
*
3867 GAATTTTTA-TAAAAATAAAAATTTCAATC
65 AAATTTTTATTAAAAATAAAAATTTCAATC
* * * ** * *
3896 TTATCAAACTATTGAAAGATTTAAATCTCAAGTTAAGTCTTATCAAATTATTAGAGGATTTAGTA
1 TTATCAAACTATTGAAAGATTTAAATTTCAAGTTAAATCTTATAAAATTATTAGAAAACTTAATA
*
3961 AATTTTTATTAAAAATAAAATTTTCAATC
66 AATTTTTATTAAAAATAAAAATTTCAATC
* *
3990 TTA-CTAAACTATTG-GAGATTTAAATATT-AAATTAAATCTTA
1 TTATC-AAACTATTGAAAGATTTAAAT-TTCAAGTTAAATCTTA
4031 CCAAGCTATT
Statistics
Matches: 114, Mismatches: 16, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
92 36 0.32
93 45 0.39
94 33 0.29
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (94 bp):
TTATCAAACTATTGAAAGATTTAAATTTCAAGTTAAATCTTATAAAATTATTAGAAAACTTAATA
AATTTTTATTAAAAATAAAAATTTCAATC
Found at i:4050 original size:93 final size:93
Alignment explanation
Indices: 3804--4059 Score: 250
Period size: 93 Copynumber: 2.8 Consensus size: 93
3794 GTTTTTAATT
* * * * * * * *
3804 TTATCAAATTATTAAAAAATTTAAATTTCAAGTTAAATCTTTA--AAATTATTGAAAAACTTAAT
1 TTATCAAACTATTGAAAGATTTAAATATCAAATTAAATC-TTACCAAACTATTAAAAAATTTAAT
*
3867 GAATTTTTATAAAAATAAAAATTTCAATC
65 AAATTTTTATAAAAATAAAAATTTCAATC
* * * * * * ** *
3896 TTATCAAACTATTGAAAGATTTAAATCTCAAGTTAAGTCTTATCAAATTATTAGAGGATTTAGTA
1 TTATCAAACTATTGAAAGATTTAAATATCAAATTAAATCTTACCAAACTATTAAAAAATTTAATA
*
3961 AATTTTTATTAAAAATAAAATTTTCAATC
66 AATTTTTA-TAAAAATAAAAATTTCAATC
* * *
3990 TTA-CTAAACTATTG-GAGATTTAAATATTAAATTAAATCTTACCAAGCTATTAAAAAATTTAAT
1 TTATC-AAACTATTGAAAGATTTAAATATCAAATTAAATCTTACCAAACTATTAAAAAATTTAAT
*
4053 AACTTTT
65 AAATTTT
4060 CTAAAATTTT
Statistics
Matches: 134, Mismatches: 26, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
91 3 0.02
92 34 0.25
93 66 0.49
94 31 0.23
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (93 bp):
TTATCAAACTATTGAAAGATTTAAATATCAAATTAAATCTTACCAAACTATTAAAAAATTTAATA
AATTTTTATAAAAATAAAAATTTCAATC
Found at i:4679 original size:23 final size:23
Alignment explanation
Indices: 4652--4696 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
4642 AAATTTAATT
*
4652 ATGTTTTCTTTTATTTACTTTTC
1 ATGTTTTCTATTATTTACTTTTC
*
4675 ATGTTTTCTATTGTTTACTTTT
1 ATGTTTTCTATTATTTACTTTT
4697 TAAACAGAAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (23 bp):
ATGTTTTCTATTATTTACTTTTC
Found at i:12480 original size:52 final size:52
Alignment explanation
Indices: 12409--12555 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 52
12399 TATAATCATA
* *
12409 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTATAAAT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
* * * * *
12461 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
* * *
12513 CAAACTTACCTATTAAGAAT-CCTCTTTCTCTTGGAATTCTTCT
1 CAAACTTGCCTATTAAGAATCCCTC-TCCTCTTAGAATTCTTCT
12556 TTTGCTAGTC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 3 0.04
52 79 0.96
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
Found at i:12629 original size:11 final size:11
Alignment explanation
Indices: 12586--12630 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
12576 TCAAGCAATA
*
12586 TCAAACAAATA
1 TCAAACAAATC
*
12597 TCAAAAAAATC
1 TCAAACAAATC
*
12608 TCTAACAAATC
1 TCAAACAAATC
12619 TCAAACAAATC
1 TCAAACAAATC
12630 T
1 T
12631 TTTATGAGAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (11 bp):
TCAAACAAATC
Found at i:12879 original size:23 final size:22
Alignment explanation
Indices: 12849--12916 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
12839 TAAGCTTACT
*
12849 TCTTCCCATGTCTCAAACCAAGC
1 TCTTCCCATGTCTCGAACCAA-C
* *
12872 TCTTCCCATATCTCGAACTGTCGAC
1 TCTTCCCATGTCTCGAAC---CAAC
12897 TCTTCCCATGTCTCGAACCA
1 TCTTCCCATGTCTCGAACCA
12917 TTGACTCTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 16 0.43
25 18 0.49
26 2 0.05
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.29
Consensus pattern (22 bp):
TCTTCCCATGTCTCGAACCAAC
Found at i:12903 original size:25 final size:24
Alignment explanation
Indices: 12871--12951 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
12861 TCAAACCAAG
12871 CTCTTCCCATATCTCGAACTGTCGA
1 CTCTTCCCATATCTCGAACT-TCGA
*
12896 CTCTTCCCATGTCTCGAACCATT-GA
1 CTCTTCCCATATCTCGAA-C-TTCGA
* * *
12921 CTCTTCCCACATCTTGAATCTTCAA
1 CTCTTCCCATATCTCGAA-CTTCGA
12946 CTCTTC
1 CTCTTC
12952 TCATGTTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.04
25 42 0.89
26 2 0.04
27 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.09, T:0.35
Consensus pattern (24 bp):
CTCTTCCCATATCTCGAACTTCGA
Found at i:12950 original size:50 final size:48
Alignment explanation
Indices: 12849--12965 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 48
12839 TAAGCTTACT
* * *
12849 TCTTCCCATGTCTCAAACCAAGCTCTTCCCATATCTCGAACTGTCGAC
1 TCTTCCCATGTCTCGAACCAAGCTCTTCCCACATCTCGAACTGTCAAC
* *
12897 TCTTCCCATGTCTCGAACCATTGACTCTTCCCACATCTTGAATCT-TCAAC
1 TCTTCCCATGTCTCGAACCA-AG-CTCTTCCCACATCTCGAA-CTGTCAAC
* *
12947 TCTTCTCATGTTTCGAACC
1 TCTTCCCATGTCTCGAACC
12966 TTCAGCTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 19 0.32
49 1 0.02
50 37 0.63
51 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.09, T:0.33
Consensus pattern (48 bp):
TCTTCCCATGTCTCGAACCAAGCTCTTCCCACATCTCGAACTGTCAAC
Found at i:13611 original size:51 final size:51
Alignment explanation
Indices: 13505--13661 Score: 188
Period size: 51 Copynumber: 3.0 Consensus size: 51
13495 TATAATCATA
* * ** *
13505 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTATAAAT
1 CAAACTTGCCTATTAAGAATCCCT-TCCTCTTAGAATTCTTCTCTTGCAAGT
*
13557 CAAACTTGCCTATTAAGAATCCCTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * * *
13608 CAAACTTACCTATTAAGGAATCCTCTTTCTCTTGGAATTCTTCTTTTGCTAGT
1 CAAACTTGCCTATTAA-GAATCC-CTTCCTCTTAGAATTCTTCTCTTGCAAGT
13661 C
1 C
13662 TTCTTATCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
51 37 0.41
52 29 0.32
53 25 0.27
ACGTcount: A:0.25, C:0.27, G:0.09, T:0.39
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:13725 original size:11 final size:11
Alignment explanation
Indices: 13682--13726 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
13672 TCAAGCAATA
*
13682 TCAAACAAATA
1 TCAAACAAATC
13693 TCAAACAAATC
1 TCAAACAAATC
*
13704 TCTAACAAATC
1 TCAAACAAATC
13715 TCAAACAAATC
1 TCAAACAAATC
13726 T
1 T
13727 TTTATGAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (11 bp):
TCAAACAAATC
Found at i:14724 original size:53 final size:51
Alignment explanation
Indices: 14599--14745 Score: 197
Period size: 51 Copynumber: 2.8 Consensus size: 51
14589 TATAATCATA
* * *
14599 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTATAAT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTACAAT
* *
14650 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTCTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTC-CTACAA-T
* *
14703 CAAACTTACCTATTAAGAATCCTCTTT-CTCTTGGAATTCTTCT
1 CAAACTTGCCTATTAAGAATCC-CTTTCCTCTTAGAATTCTTCT
14746 TTTGCTAGTC
Statistics
Matches: 85, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
51 41 0.48
52 4 0.05
53 36 0.42
54 4 0.05
ACGTcount: A:0.26, C:0.28, G:0.07, T:0.39
Consensus pattern (51 bp):
CAAACTTGCCTATTAAGAATCCCTTTCCTCTTAGAATTCTTCTCCTACAAT
Found at i:14806 original size:11 final size:11
Alignment explanation
Indices: 14777--14820 Score: 63
Period size: 11 Copynumber: 4.1 Consensus size: 11
14767 TCAAGCAATA
*
14777 TCAAAC-AATA
1 TCAAACAAATC
14787 TCAAACAAATC
1 TCAAACAAATC
*
14798 TCTAACAAATC
1 TCAAACAAATC
14809 TCAAACAAATC
1 TCAAACAAATC
14820 T
1 T
14821 TTTATGAGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
10 6 0.20
11 24 0.80
ACGTcount: A:0.52, C:0.25, G:0.00, T:0.23
Consensus pattern (11 bp):
TCAAACAAATC
Found at i:15069 original size:23 final size:22
Alignment explanation
Indices: 15039--15106 Score: 73
Period size: 25 Copynumber: 2.9 Consensus size: 22
15029 TAAGCTTACT
*
15039 TCTTCCCATGTCTCAAACCAAGC
1 TCTTCCCATGTCTCGAACCAA-C
* *
15062 TCTTCCCATATCTCGAACTGTCGAC
1 TCTTCCCATGTCTCGAAC---CAAC
15087 TCTTCCCATGTCTCGAACCA
1 TCTTCCCATGTCTCGAACCA
15107 TTGACTCTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 1 0.03
23 16 0.43
25 18 0.49
26 2 0.05
ACGTcount: A:0.22, C:0.38, G:0.10, T:0.29
Consensus pattern (22 bp):
TCTTCCCATGTCTCGAACCAAC
Found at i:15093 original size:25 final size:24
Alignment explanation
Indices: 15061--15141 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 24
15051 TCAAACCAAG
15061 CTCTTCCCATATCTCGAACTGTCGA
1 CTCTTCCCATATCTCGAACT-TCGA
*
15086 CTCTTCCCATGTCTCGAACCATT-GA
1 CTCTTCCCATATCTCGAA-C-TTCGA
* * *
15111 CTCTTCCCACATCTTGAATCTTCAA
1 CTCTTCCCATATCTCGAA-CTTCGA
15136 CTCTTC
1 CTCTTC
15142 TCATGTTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
24 2 0.04
25 42 0.89
26 2 0.04
27 1 0.02
ACGTcount: A:0.20, C:0.37, G:0.09, T:0.35
Consensus pattern (24 bp):
CTCTTCCCATATCTCGAACTTCGA
Found at i:15140 original size:50 final size:48
Alignment explanation
Indices: 15039--15155 Score: 137
Period size: 50 Copynumber: 2.4 Consensus size: 48
15029 TAAGCTTACT
* * *
15039 TCTTCCCATGTCTCAAACCAAGCTCTTCCCATATCTCGAACTGTCGAC
1 TCTTCCCATGTCTCGAACCAAGCTCTTCCCACATCTCGAACTGTCAAC
* *
15087 TCTTCCCATGTCTCGAACCATTGACTCTTCCCACATCTTGAATCT-TCAAC
1 TCTTCCCATGTCTCGAACCA-AG-CTCTTCCCACATCTCGAA-CTGTCAAC
* *
15137 TCTTCTCATGTTTCGAACC
1 TCTTCCCATGTCTCGAACC
15156 TTCAGCTCTG
Statistics
Matches: 59, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
48 19 0.32
49 1 0.02
50 37 0.63
51 2 0.03
ACGTcount: A:0.21, C:0.36, G:0.09, T:0.33
Consensus pattern (48 bp):
TCTTCCCATGTCTCGAACCAAGCTCTTCCCACATCTCGAACTGTCAAC
Found at i:15766 original size:52 final size:52
Alignment explanation
Indices: 15695--15841 Score: 188
Period size: 52 Copynumber: 2.8 Consensus size: 52
15685 TATAATCATA
* *
15695 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTATAAAT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
* * * * *
15747 CAAACTTGCCTATTAAGAATCCCTTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
* * *
15799 CAAACTTACCTATTAAGAAT-CCTCTTTCTCTTGGAATTCTTCT
1 CAAACTTGCCTATTAAGAATCCCTC-TCCTCTTAGAATTCTTCT
15842 TTTGCTAGTC
Statistics
Matches: 82, Mismatches: 12, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
51 3 0.04
52 79 0.96
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.39
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTACAAAT
Found at i:15915 original size:11 final size:11
Alignment explanation
Indices: 15872--15916 Score: 72
Period size: 11 Copynumber: 4.1 Consensus size: 11
15862 TCAAGCAATA
*
15872 TCAAACAAATA
1 TCAAACAAATC
15883 TCAAACAAATC
1 TCAAACAAATC
*
15894 TCTAACAAATC
1 TCAAACAAATC
15905 TCAAACAAATC
1 TCAAACAAATC
15916 T
1 T
15917 TTTATGAGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (11 bp):
TCAAACAAATC
Found at i:17939 original size:3 final size:3
Alignment explanation
Indices: 17931--17957 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17921 ATTTATTTAT
17931 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
17958 GATTTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17995 original size:19 final size:19
Alignment explanation
Indices: 17973--18020 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
17963 GTTTAATATT
17973 CTTTTATTTTTTATCTTTA
1 CTTTTATTTTTTATCTTTA
*
17992 C-TTTATTTTTTTATTTTTA
1 CTTTTA-TTTTTTATCTTTA
18011 -TTTTATTTTT
1 CTTTTATTTTT
18021 CTTTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 9 0.35
19 17 0.65
ACGTcount: A:0.15, C:0.06, G:0.00, T:0.79
Consensus pattern (19 bp):
CTTTTATTTTTTATCTTTA
Found at i:18033 original size:6 final size:6
Alignment explanation
Indices: 17974--18035 Score: 51
Period size: 6 Copynumber: 10.5 Consensus size: 6
17964 TTTAATATTC
*
17974 TTTTATT TTTTAT CTTTACT TTATT-T TTTTAT TTTTA- TTTTA- TTTT-T
1 TTTTA-T TTTTAT TTTTA-T TT-TTAT TTTTAT TTTTAT TTTTAT TTTTAT
*
18021 CTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTT
18036 CACTTTCATT
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
5 14 0.30
6 23 0.50
7 7 0.15
8 2 0.04
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTAT
Found at i:18041 original size:46 final size:47
Alignment explanation
Indices: 17975--18064 Score: 123
Period size: 46 Copynumber: 1.9 Consensus size: 47
17965 TTAATATTCT
* *
17975 TTTATTTTTTATCTTTACTTT-ATTTTTTTATTTTTATTTTATTTTTC
1 TTTATTTTTTATCTTTACTTTCATTTTGTT-TTATTATTTTATTTTTC
18022 TTTA-TTTTTAT-TTTCACTTTCATTTTGTTTTATTATTTTATTT
1 TTTATTTTTTATCTTT-ACTTTCATTTTGTTTTATTATTTTATTT
18065 CCTTTAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
45 3 0.08
46 25 0.64
47 11 0.28
ACGTcount: A:0.16, C:0.07, G:0.01, T:0.77
Consensus pattern (47 bp):
TTTATTTTTTATCTTTACTTTCATTTTGTTTTATTATTTTATTTTTC
Found at i:18042 original size:21 final size:22
Alignment explanation
Indices: 18001--18055 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
17991 ACTTTATTTT
*
18001 TTTATTTTTATTTTATTTTTC-
1 TTTATTTTTATTTTATCTTTCA
18022 TTTATTTTTATTTTCA-CTTTCA
1 TTTATTTTTATTTT-ATCTTTCA
18044 TTT-TGTTTTATT
1 TTTAT-TTTTATT
18056 ATTTTATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (22 bp):
TTTATTTTTATTTTATCTTTCA
Found at i:18047 original size:17 final size:15
Alignment explanation
Indices: 17981--18064 Score: 68
Period size: 16 Copynumber: 5.5 Consensus size: 15
17971 TTCTTTTATT
17981 TTTTATCTTTACTTTA
1 TTTTAT-TTTACTTTA
*
17997 -TTT-TTTTATTTTTA
1 TTTTATTTTA-CTTTA
*
18011 TTTTATTTTTCTTTA
1 TTTTATTTTACTTTA
18026 TTTTTATTTTCACTTTCA
1 -TTTTATTTT-ACTTT-A
*
18044 TTTTGTTTTA--TTA
1 TTTTATTTTACTTTA
18057 TTTTATTT
1 TTTTATTT
18065 CCTTTAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
13 12 0.21
14 7 0.12
15 10 0.18
16 14 0.25
17 12 0.21
18 1 0.02
ACGTcount: A:0.15, C:0.07, G:0.01, T:0.76
Consensus pattern (15 bp):
TTTTATTTTACTTTA
Found at i:18146 original size:58 final size:58
Alignment explanation
Indices: 18083--18239 Score: 244
Period size: 58 Copynumber: 2.7 Consensus size: 58
18073 TAAAATCCAA
* *
18083 AAAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAGTTTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAA-ATTTC
* *
18142 -AAAAAATATTTTTGGGAAAAAGTTAAAAGTATCAATTTTTCTCGAAATTAAAATTTC
1 AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
*
18199 AAAAAAATATATTTTTGGAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAATAT-TTTTGGGAAAAAGTTGAAAGTATCAATTTT
18240 TTCTTGTACA
Statistics
Matches: 90, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
57 4 0.04
58 58 0.64
59 28 0.31
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (58 bp):
AAAAAAATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTCGAAATTAAAATTTC
Found at i:19121 original size:143 final size:142
Alignment explanation
Indices: 18714--19130 Score: 365
Period size: 143 Copynumber: 2.9 Consensus size: 142
18704 GAAGTTATGA
* * *
18714 CAAGGTGCATTCTTGGTTTTTAATGCATTAAAATTCATGAAATAATATCAAAATATGATTAGGAG
1 CAAGGTGCAATCATGGTTTTTAATGCATTAAAATTCATGAAATAATATCAAAACATGATTAGGAG
** * * * * ** *
18779 CTTTTCATGAAAAATCGACCTTGGGATGGTAAAATTATGGAAATAACCCTTAAAAGGCATTTTGG
66 CTTTTCATGAAAAATTAACCTTGAGAAGGTAAAATTATAG-AAT-ACTCTT-AAAGGTTTTTTGA
*
18844 TGATTTCAACCCTTT
128 TAATTTCAACCCTTT
** * * ** * * *
18859 CAACATGCGATCAAT-GTTTTTAATGTACCAAAAATCATGAAATAATATGAAAACATGATTCGGA
1 CAAGGTGCAATC-ATGGTTTTTAATGCATTAAAATTCATGAAATAATATCAAAACATGATTAGGA
* * * * * * * *
18923 GCTTTTCA--CAAAATCTAACCTCGTGAAAGTCAAATTATAAAAAAACTTCTAAAAGGTTTTTTG
65 GCTTTTCATGAAAAAT-TAACCTTGAGAAGGTAAAATTAT-AGAATAC-TCTTAAAGGTTTTTTG
*
18986 ATAATTTCAAGCCTTT
127 ATAATTTCAACCCTTT
* * * * * * *
19002 CAAGGTGCAATCATGGTTTTTAATACATTAAAATTTACGAAATAAGATTAAAACATGATTTGAAG
1 CAAGGTGCAATCATGGTTTTTAATGCATTAAAATTCATGAAATAATATCAAAACATGATTAGGAG
19067 CCTTTT-ATGAAAAATTAACCTTGAGAAGGTAAAATTACTAGAATACTCTTAAAGGGTATTTTTG
66 -CTTTTCATGAAAAATTAACCTTGAGAAGGTAAAATTA-TAGAATACTCTTAAA-GGT-TTTTTG
19131 TGATTTTACA
Statistics
Matches: 209, Mismatches: 52, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
142 2 0.01
143 85 0.41
144 51 0.24
145 70 0.33
146 1 0.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.34
Consensus pattern (142 bp):
CAAGGTGCAATCATGGTTTTTAATGCATTAAAATTCATGAAATAATATCAAAACATGATTAGGAG
CTTTTCATGAAAAATTAACCTTGAGAAGGTAAAATTATAGAATACTCTTAAAGGTTTTTTGATAA
TTTCAACCCTTT
Found at i:19411 original size:22 final size:22
Alignment explanation
Indices: 19386--19427 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
19376 CATAGTCTTA
* * *
19386 AAGATCTCCAGGCATGATCTAT
1 AAGACCTCAAGGCATAATCTAT
19408 AAGACCTCAAGGCATAATCT
1 AAGACCTCAAGGCATAATCT
19428 TTTAAGTCTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (22 bp):
AAGACCTCAAGGCATAATCTAT
Found at i:21180 original size:7 final size:7
Alignment explanation
Indices: 21157--21198 Score: 66
Period size: 7 Copynumber: 6.0 Consensus size: 7
21147 TTTTGCTCAC
*
21157 ATAAAAG
1 ATAAAAA
*
21164 ATATAAA
1 ATAAAAA
21171 ATAAAAA
1 ATAAAAA
21178 ATAAAAA
1 ATAAAAA
21185 ATAAAAA
1 ATAAAAA
21192 ATAAAAA
1 ATAAAAA
21199 GAGAGAGGGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (7 bp):
ATAAAAA
Found at i:21847 original size:94 final size:95
Alignment explanation
Indices: 21674--21847 Score: 208
Period size: 94 Copynumber: 1.8 Consensus size: 95
21664 ACTTAATGAA
* * **
21674 TTTTATAATAAAATAAAAATTTCAATCTTATCAAACTATTGAAAGATTTAAATCTCAAGTTACGT
1 TTTTATAATAAAATAAAAATTTCAATCTTATCAAACTATTGAAAGATTTAAATATCAAATTAAAT
* *
21739 CTTATCAAATTATTAGAGGATTTAGTAAAT
66 CTTACCAAACTATTAGAGGATTTAGTAAAT
* * * * * *
21769 TTTTATTA-AAAATAAAATTTTTAATCTTA-CTAAACTATTGGAGGATTTAAATATTAAATTAAA
1 TTTTATAATAAAATAAAAATTTCAATCTTATC-AAACTATTGAAAGATTTAAATATCAAATTAAA
*
21832 TCTTACCAAGCTATTA
65 TCTTACCAAACTATTA
21848 AAAAATTTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
93 1 0.02
94 57 0.88
95 7 0.11
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (95 bp):
TTTTATAATAAAATAAAAATTTCAATCTTATCAAACTATTGAAAGATTTAAATATCAAATTAAAT
CTTACCAAACTATTAGAGGATTTAGTAAAT
Found at i:22502 original size:23 final size:23
Alignment explanation
Indices: 22475--22519 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
22465 AAATTTAATT
*
22475 ATGTTTTCTTTTATTTACTTTTC
1 ATGTTTTCTATTATTTACTTTTC
*
22498 ATGTTTTCTATTGTTTACTTTT
1 ATGTTTTCTATTATTTACTTTT
22520 TAAACAGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.69
Consensus pattern (23 bp):
ATGTTTTCTATTATTTACTTTTC
Found at i:23612 original size:9 final size:9
Alignment explanation
Indices: 23598--23626 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
23588 GAATAAAATA
23598 TTATTTTAT
1 TTATTTTAT
23607 TTATTTT-T
1 TTATTTTAT
23615 TTATTTTAT
1 TTATTTTAT
23624 TTA
1 TTA
23627 AATTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (9 bp):
TTATTTTAT
Done.