Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168029.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_282, 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: 39010
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1156 original size:17 final size:18
Alignment explanation
Indices: 1134--1169 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1124 AATTTTCTTG
1134 TTCTAG-TTCTTTAAGTT
1 TTCTAGCTTCTTTAAGTT
1151 TTCTAGCTTCTTTAAGTT
1 TTCTAGCTTCTTTAAGTT
1169 T
1 T
1170 CTTTTACAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.17, C:0.14, G:0.11, T:0.58
Consensus pattern (18 bp):
TTCTAGCTTCTTTAAGTT
Found at i:9912 original size:25 final size:24
Alignment explanation
Indices: 9884--9931 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9874 AATGATATTG
*
9884 TATTGGAATTGTTGTAATTTTTTTA
1 TATTGGAA-TGTTATAATTTTTTTA
* *
9909 TATTGTAATGTTATTATTTTTTT
1 TATTGGAATGTTATAATTTTTTT
9932 GGTATTAGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.23, C:0.00, G:0.12, T:0.65
Consensus pattern (24 bp):
TATTGGAATGTTATAATTTTTTTA
Found at i:12391 original size:19 final size:19
Alignment explanation
Indices: 12329--12392 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
12319 CAGTTTCCGG
*
12329 TTGAATTTTCCGGCCAATC-
1 TTGAAGTTTCCGGCCAA-CA
12348 TTGAAGTTTCCGGCC-A-A
1 TTGAAGTTTCCGGCCAACA
12365 ---AA--TTCCGGCCAACA
1 TTGAAGTTTCCGGCCAACA
12379 TTGAAGTTTCCGGC
1 TTGAAGTTTCCGGC
12393 GACCTGCCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
12 8 0.22
13 1 0.03
14 3 0.08
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (19 bp):
TTGAAGTTTCCGGCCAACA
Found at i:12430 original size:20 final size:20
Alignment explanation
Indices: 12407--12449 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
12397 TGCCCAGTTT
12407 CCGGCGAAGAATCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
12427 CCGGCGAAGAATCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
12447 CCG
1 CCG
12450 TCAAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.26, T:0.05
Consensus pattern (20 bp):
CCGGCGAAGAATCCCAGAAA
Found at i:12511 original size:20 final size:20
Alignment explanation
Indices: 12468--12512 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
12458 CCGGCCAACT
*
12468 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
12488 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
12508 TCCGG
1 TCCGG
12513 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:12890 original size:20 final size:19
Alignment explanation
Indices: 12840--12895 Score: 89
Period size: 19 Copynumber: 3.0 Consensus size: 19
12830 GCGCTCCAGG
12840 TTTTTTTTT--TTTTTTTT
1 TTTTTTTTTGATTTTTTTT
12857 TTTTTTTTTGATTTTTTTT
1 TTTTTTTTTGATTTTTTTT
12876 TTTTTTTTTGAATTTTTTTT
1 TTTTTTTTTG-ATTTTTTTT
12896 ATTTGACTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
17 9 0.25
19 18 0.50
20 9 0.25
ACGTcount: A:0.05, C:0.00, G:0.04, T:0.91
Consensus pattern (19 bp):
TTTTTTTTTGATTTTTTTT
Found at i:12891 original size:26 final size:26
Alignment explanation
Indices: 12842--12891 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
12832 GCTCCAGGTT
***
12842 TTTTTTTTTTTTTTTTTTTTTTTTGA
1 TTTTTTTTTTTTTTTTTGAATTTTGA
12868 TTTTTTTTTTTTTTTTTGAATTTT
1 TTTTTTTTTTTTTTTTTGAATTTT
12892 TTTTATTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.04, T:0.90
Consensus pattern (26 bp):
TTTTTTTTTTTTTTTTTGAATTTTGA
Found at i:12891 original size:27 final size:27
Alignment explanation
Indices: 12841--12892 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
12831 CGCTCCAGGT
***
12841 TTTTTTTTTTTTTTTTTTTTTTTTTGA
1 TTTTTTTTTTTTTTTTTGAATTTTTGA
12868 TTTTTTTTTTTTTTTTTGAATTTTT
1 TTTTTTTTTTTTTTTTTGAATTTTT
12893 TTTATTTGAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.06, C:0.00, G:0.04, T:0.90
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTGAATTTTTGA
Found at i:12891 original size:28 final size:28
Alignment explanation
Indices: 12840--12893 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
12830 GCGCTCCAGG
***
12840 TTTTTTTTTTTTTTTTTTTTTTTTTTGA
1 TTTTTTTTTTTTTTTTTGAATTTTTTGA
12868 TTTTTTTTTTTTTTTTTGAATTTTTT
1 TTTTTTTTTTTTTTTTTGAATTTTTT
12894 TTATTTGACT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.06, C:0.00, G:0.04, T:0.91
Consensus pattern (28 bp):
TTTTTTTTTTTTTTTTTGAATTTTTTGA
Found at i:12892 original size:34 final size:31
Alignment explanation
Indices: 12840--12901 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 31
12830 GCGCTCCAGG
12840 TTTTTTTTTTTTTTTTTTTTTTT-TTTGATT
1 TTTTTTTTTTTTTTTTTTTTTTTATTTGATT
12870 TTTTTTTTTTTTTTTGAATTTTTTTTATTTGA
1 TTTTTTTTTTTTTTT---TTTTTTTTATTTGA
12902 CTTTGATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
30 15 0.54
33 8 0.29
34 5 0.18
ACGTcount: A:0.08, C:0.00, G:0.05, T:0.87
Consensus pattern (31 bp):
TTTTTTTTTTTTTTTTTTTTTTTATTTGATT
Found at i:12895 original size:1 final size:1
Alignment explanation
Indices: 12840--12884 Score: 72
Period size: 1 Copynumber: 45.0 Consensus size: 1
12830 GCGCTCCAGG
**
12840 TTTTTTTTTTTTTTTTTTTTTTTTTTGATTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
12885 GAATTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 41 1.00
ACGTcount: A:0.02, C:0.00, G:0.02, T:0.96
Consensus pattern (1 bp):
T
Found at i:13177 original size:161 final size:157
Alignment explanation
Indices: 12916--13385 Score: 697
Period size: 153 Copynumber: 3.0 Consensus size: 157
12906 GATTTTGACT
* * *
12916 TGATTTTTTTTTTCTTTTTCTTTAATCAAT-CG-CGACGAGAG-CTCTACAAGT-AAACAGTAGT
1 TGATTTTGTTTTT-TTTTTCTTTAATAAATCCGACGACG-GAGCCTCTGCAAGTGAAACAGTAGT
12977 TTTTC-TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
64 TTTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAAT
* *
13041 TGAGAATAATTTCCGATAATTAATTACTTTGC
129 TGAGAATAATTTCC-A-AA-TAATTACTTGGA
*
13073 TGATTTTGATTTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
1 TGATTTTG-TTTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTT
* *
13138 TTTCTTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATT
65 TTTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATT
*
13203 GAGAATAATTTCC-AATAATTAATTGGA
130 GAGAATAATTTCCAAATAATTACTTGGA
*
13230 TGATTTTG---TTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTT
1 TGATTTTGTTTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
13292 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
66 TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
*
13357 AGAATCATTTCCAACAACTAATTACTTGG
131 AGAATAATTTCC-A-AA-TAATTACTTGG
13386 TAAAATTTTA
Statistics
Matches: 289, Mismatches: 14, Indels: 20
0.89 0.04 0.06
Matches are distributed among these distances:
153 126 0.44
156 2 0.01
157 49 0.17
158 12 0.04
159 14 0.05
160 15 0.05
161 71 0.25
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.39
Consensus pattern (157 bp):
TGATTTTGTTTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTT
TTCTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTG
AGAATAATTTCCAAATAATTACTTGGA
Found at i:16663 original size:1 final size:1
Alignment explanation
Indices: 16657--16690 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
16647 GTAAATTTTG
*
16657 AAAAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
16691 CACCACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:17102 original size:7 final size:7
Alignment explanation
Indices: 17080--17139 Score: 63
Period size: 7 Copynumber: 8.7 Consensus size: 7
17070 ATGATGAAAA
17080 AAAAATG
1 AAAAATG
17087 AAAAA--
1 AAAAATG
17092 AAAAATG
1 AAAAATG
17099 AAAAATG
1 AAAAATG
*
17106 AAAAA-A
1 AAAAATG
*
17112 AAAGAAGG
1 AAA-AATG
17120 AAAAATG
1 AAAAATG
17127 AGAAAATG
1 A-AAAATG
17135 AAAAA
1 AAAAA
17140 AAGAGATCCA
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
5 5 0.11
6 3 0.07
7 27 0.60
8 10 0.22
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (7 bp):
AAAAATG
Found at i:17109 original size:29 final size:29
Alignment explanation
Indices: 17073--17141 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 29
17063 AAAAAAGATG
17073 ATGAAAAAAAAATGAAAAAAAAAATGA-AAA
1 ATGAAAAAAAAA-G-AAAAAAAAATGAGAAA
**
17103 ATGAAAAAAAAAGAAGGAAAAATGAGAAA
1 ATGAAAAAAAAAGAAAAAAAAATGAGAAA
17132 ATGAAAAAAA
1 ATGAAAAAAA
17142 GAGATCCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 10 0.28
29 14 0.39
30 12 0.33
ACGTcount: A:0.77, C:0.00, G:0.14, T:0.09
Consensus pattern (29 bp):
ATGAAAAAAAAAGAAAAAAAAATGAGAAA
Found at i:17114 original size:12 final size:12
Alignment explanation
Indices: 17058--17103 Score: 65
Period size: 12 Copynumber: 3.7 Consensus size: 12
17048 TCAACAATGG
*
17058 ATGAAAAAAAAG
1 ATGAAAAAAAAA
17070 ATGATGAAAAAAAA
1 ATGA--AAAAAAAA
17084 ATGAAAAAAAAA
1 ATGAAAAAAAAA
17096 ATGAAAAA
1 ATGAAAAA
17104 TGAAAAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 20 0.65
14 11 0.35
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (12 bp):
ATGAAAAAAAAA
Found at i:17123 original size:12 final size:12
Alignment explanation
Indices: 17062--17143 Score: 55
Period size: 11 Copynumber: 6.8 Consensus size: 12
17052 CAATGGATGA
17062 AAAAAAAGATGATG
1 AAAAAAAGA--ATG
17076 AAAAAAA-AATG
1 AAAAAAAGAATG
*
17087 AAAAAAAAAATG
1 AAAAAAAGAATG
*
17099 -AAAAATGAA--
1 AAAAAAAGAATG
*
17108 AAAAAAAGAAGG
1 AAAAAAAGAATG
*
17120 AAAAATGAGAAAATG
1 AAAAA--A-AGAATG
17135 AAAAAAAGA
1 AAAAAAAGA
17144 GATCCAAATT
Statistics
Matches: 55, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
10 8 0.15
11 17 0.31
12 11 0.20
13 2 0.04
14 8 0.15
15 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAAAAAAGAATG
Found at i:17132 original size:19 final size:19
Alignment explanation
Indices: 17080--17132 Score: 70
Period size: 21 Copynumber: 2.6 Consensus size: 19
17070 ATGATGAAAA
*
17080 AAAAATGAAAAAAAAAATG
1 AAAAATGAAAAAAAAAAGG
17099 AAAAATGAAAAAAAAAGAAGG
1 AAAAATG-AAAAAAAA-AAGG
17120 AAAAATGAGAAAA
1 AAAAATGA-AAAA
17133 TGAAAAAAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 7 0.23
20 9 0.30
21 14 0.47
ACGTcount: A:0.77, C:0.00, G:0.15, T:0.08
Consensus pattern (19 bp):
AAAAATGAAAAAAAAAAGG
Found at i:17189 original size:1 final size:1
Alignment explanation
Indices: 17183--17212 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
17173 TTTGGTACCC
*
17183 AAAAAAAAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
17213 GATTCAGGTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:18384 original size:40 final size:40
Alignment explanation
Indices: 18340--19010 Score: 1042
Period size: 40 Copynumber: 16.6 Consensus size: 40
18330 GTCTAGGAGT
18340 ATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
18380 ATTTACTTTTCCAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
18420 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
18462 ATTTACTTTTCAAAGTTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-TCGTGTGCCTCTGTTTAGAGGAGCA
*
18502 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
18543 ATTTAC-TTTCAAAGTTCCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAG-T-CGTGTGCCTCTGTTTAGAGGAGCA
18583 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTC-AAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
18625 ATTTATTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
18666 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
18706 ATTTACTTTTCAAAGTC--GTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
18744 ATTTACTTTTCAAAGTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
18783 ATTTACTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
18825 ATTTATTTTTCCAAAGTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTT-CAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
18865 ATTTACTTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCA
*
18906 ATTTATTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
18946 ATTTAC-TTTCAAAGTCGT-TGCCTCTGTTTAGAGGAGCA
1 ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
*
18984 ATTTACTTTCCAAAGTCGTGGTGCCTC
1 ATTTACTTTTCAAAGTCGT-GTGCCTC
19011 AAAAAAAACA
Statistics
Matches: 596, Mismatches: 12, Indels: 45
0.91 0.02 0.07
Matches are distributed among these distances:
38 64 0.11
39 66 0.11
40 226 0.38
41 131 0.22
42 109 0.18
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (40 bp):
ATTTACTTTTCAAAGTCGTGTGCCTCTGTTTAGAGGAGCA
Found at i:18564 original size:81 final size:80
Alignment explanation
Indices: 18340--19010 Score: 1040
Period size: 81 Copynumber: 8.3 Consensus size: 80
18330 GTCTAGGAGT
* *
18340 ATTTACTTTTCAAAGTTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAGTTCGTTGC
1 ATTTACTTTCCAAAG-TCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTGC
18403 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
*
18420 ATTTATTTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTTCGTTGC
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-TCGTTGC
18485 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
18502 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTTCCGTTGC
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAG-T-CGTTGC
18566 CTCTGTTTAGAGGAGCA
64 CTCTGTTTAGAGGAGCA
* *
18583 ATTTACTTTTCAAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTATTTTTCAAAGTCGTGGTG
1 ATTTAC-TTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TG
18648 CCTCTGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCA
*
18666 ATTTA-TTTTCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCG-TGCCT
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
18729 CTGTTTAGAGGAGCA
66 CTGTTTAGAGGAGCA
*
18744 ATTTACTTTTCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCCAAAGTCGTGGTG
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTT-CAAAGTCGT--TG
18807 CCTCTGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCA
*
18825 ATTTATTTTTCCAAAGTCGT--TGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTGGTG
1 ATTTA-CTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGT--TG
18888 CCTCTGTTTAGAGGAGCA
63 CCTCTGTTTAGAGGAGCA
* *
18906 ATTTATTTTTCAAAGTCGT-GTGCCTCTGTTTAGAGGAGCAATTTAC-TTTCAAAGTCGTTGCCT
1 ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
18969 CTGTTTAGAGGAGCA
66 CTGTTTAGAGGAGCA
18984 ATTTACTTTCCAAAGTCGTGGTGCCTC
1 ATTTACTTTCCAAAGTCGTGGTGCCTC
19011 AAAAAAAACA
Statistics
Matches: 561, Mismatches: 14, Indels: 33
0.92 0.02 0.05
Matches are distributed among these distances:
77 30 0.05
78 70 0.12
79 20 0.04
80 44 0.08
81 218 0.39
82 146 0.26
83 33 0.06
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (80 bp):
ATTTACTTTCCAAAGTCGTGGTGCCTCTGTTTAGAGGAGCAATTTACTTTTCAAAGTCGTTGCCT
CTGTTTAGAGGAGCA
Found at i:19025 original size:8 final size:8
Alignment explanation
Indices: 19012--19094 Score: 71
Period size: 8 Copynumber: 9.9 Consensus size: 8
19002 TGGTGCCTCA
19012 AAAAAAAC
1 AAAAAAAC
19020 AAAAAAAC
1 AAAAAAAC
19028 AAAAAAA-
1 AAAAAAAC
19035 AAACAAAA-
1 AAA-AAAAC
19043 ATAAAAAAC
1 A-AAAAAAC
*
19052 AAAAAATC
1 AAAAAAAC
*
19060 AAACAAAATAA
1 -AA-AAAA-AC
*
19071 AAAAAAAT
1 AAAAAAAC
19079 AAAAAAATC
1 AAAAAAA-C
19088 AAAAAAA
1 AAAAAAA
19095 ATCAAAAAAT
Statistics
Matches: 63, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
7 3 0.05
8 38 0.60
9 16 0.25
10 6 0.10
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (8 bp):
AAAAAAAC
Found at i:19026 original size:10 final size:10
Alignment explanation
Indices: 19011--19103 Score: 77
Period size: 10 Copynumber: 9.5 Consensus size: 10
19001 GTGGTGCCTC
19011 AAAAAAAACA
1 AAAAAAAACA
*
19021 AAAAAACA-A
1 AAAAAAAACA
19030 AAAAAAAACA
1 AAAAAAAACA
19040 AAAATAAAA-A
1 AAAA-AAAACA
*
19050 ACAAAAAATC-
1 A-AAAAAAACA
* *
19060 AAACAAAATA
1 AAAAAAAACA
*
19070 AAAAAAAA-T
1 AAAAAAAACA
*
19079 AAAAAAATCA
1 AAAAAAAACA
*
19089 AAAAAAATCA
1 AAAAAAAACA
19099 AAAAA
1 AAAAA
19104 TGTTGAGTTG
Statistics
Matches: 67, Mismatches: 10, Indels: 12
0.75 0.11 0.13
Matches are distributed among these distances:
9 20 0.30
10 40 0.60
11 7 0.10
ACGTcount: A:0.85, C:0.09, G:0.00, T:0.06
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:19035 original size:19 final size:19
Alignment explanation
Indices: 19011--19095 Score: 93
Period size: 19 Copynumber: 4.3 Consensus size: 19
19001 GTGGTGCCTC
19011 AAAAAAAACAAAAAAACAA
1 AAAAAAAACAAAAAAACAA
19030 AAAAAAAACAAAAATAA-AA
1 AAAAAAAACAAAAA-AACAA
*
19049 AACAAAAAATCAAACAAAATAA
1 AA-AAAAAA-CAAA-AAAACAA
*
19071 AAAAAAATA-AAAAAATCAA
1 AAAAAAA-ACAAAAAAACAA
19090 AAAAAA
1 AAAAAA
19096 TCAAAAAATG
Statistics
Matches: 58, Mismatches: 2, Indels: 12
0.81 0.03 0.17
Matches are distributed among these distances:
19 29 0.50
20 11 0.19
21 11 0.19
22 7 0.12
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (19 bp):
AAAAAAAACAAAAAAACAA
Found at i:19048 original size:24 final size:24
Alignment explanation
Indices: 19021--19092 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 24
19011 AAAAAAAACA
19021 AAAAAACAAAAAAAAAACAAAAAT
1 AAAAAACAAAAAAAAAACAAAAAT
*
19045 AAAAAACAAAAAATCAAAC-AAAAT
1 AAAAAACAAAAAA-AAAACAAAAAT
19069 AAAAAA-AAATAAAAAAATCAAAAA
1 AAAAAACAAA-AAAAAAA-CAAAAA
19093 AAATCAAAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.14
24 28 0.67
25 8 0.19
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.07
Consensus pattern (24 bp):
AAAAAACAAAAAAAAAACAAAAAT
Found at i:19073 original size:36 final size:36
Alignment explanation
Indices: 19011--19093 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 36
19001 GTGGTGCCTC
* * *
19011 AAAAAAAACAAAAAAAC-AA-AAAAAAAACAAAAAT
1 AAAAAAATCAAAAAATCAAACAAAAAAAAAAAAAAT
*
19045 -AAAAAA-CAAAAAATCAAACAAAATAAAAAAAAAT
1 AAAAAAATCAAAAAATCAAACAAAAAAAAAAAAAAT
19079 AAAAAAATCAAAAAA
1 AAAAAAATCAAAAAA
19094 AATCAAAAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
32 8 0.19
33 8 0.19
34 13 0.31
35 6 0.14
36 7 0.17
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (36 bp):
AAAAAAATCAAAAAATCAAACAAAAAAAAAAAAAAT
Found at i:19101 original size:19 final size:19
Alignment explanation
Indices: 19009--19103 Score: 97
Period size: 18 Copynumber: 4.9 Consensus size: 19
18999 TCGTGGTGCC
19009 TCAAAAAAAA-CAAAAAAA
1 TCAAAAAAAATCAAAAAAA
*
19027 -CAAAAAAAAAACAAAAATAA
1 TC-AAAAAAAATCAAAAA-AA
**
19047 AAAACAAAAAATCAAACAAAA
1 TCAA-AAAAAATCAAA-AAAA
*
19068 TAAAAAAAAAT-AAAAAAA
1 TCAAAAAAAATCAAAAAAA
19086 TCAAAAAAAATCAAAAAA
1 TCAAAAAAAATCAAAAAA
19104 TGTTGAGTTG
Statistics
Matches: 66, Mismatches: 4, Indels: 13
0.80 0.05 0.16
Matches are distributed among these distances:
17 1 0.02
18 22 0.33
19 15 0.23
20 11 0.17
21 15 0.23
22 2 0.03
ACGTcount: A:0.83, C:0.09, G:0.00, T:0.07
Consensus pattern (19 bp):
TCAAAAAAAATCAAAAAAA
Found at i:19103 original size:1 final size:1
Alignment explanation
Indices: 19011--19095 Score: 62
Period size: 1 Copynumber: 85.0 Consensus size: 1
19001 GTGGTGCCTC
* * * * * ** * *
19011 AAAAAAAACAAAAAAACAAAAAAAAAACAAAAATAAAAAACAAAAAATCAAACAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* **
19076 AATAAAAAAATCAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAA
19096 TCAAAAAATG
Statistics
Matches: 62, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.86, C:0.08, G:0.00, T:0.06
Consensus pattern (1 bp):
A
Found at i:19309 original size:3 final size:3
Alignment explanation
Indices: 19288--19393 Score: 55
Period size: 3 Copynumber: 34.3 Consensus size: 3
19278 TCTTCTTTTG
19288 TAT T-T TAT GTAT T-T TAT TAT TAT TAT TAT TAT GTAT ATAT TATT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TA-T TAT
* *
19335 T-T T-T TAT TA- GAT TA- GAT T-T ATAT GTAT ATAGT TAT ATATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT -TA-T TAT -TA-T TAT
19378 TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT T
19394 TTTTTTTGTA
Statistics
Matches: 83, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
2 11 0.13
3 46 0.55
4 24 0.29
5 2 0.02
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:19945 original size:19 final size:19
Alignment explanation
Indices: 19883--19946 Score: 54
Period size: 19 Copynumber: 3.7 Consensus size: 19
19873 CAGTTTCCGG
*
19883 TTGAATTTTCCGGCCAATC-
1 TTGAAGTTTCCGGCCAA-CA
19902 TTGAAGTTTCCGGCC-A-A
1 TTGAAGTTTCCGGCCAACA
19919 ---AA--TTCCGGCCAACA
1 TTGAAGTTTCCGGCCAACA
19933 TTGAAGTTTCCGGC
1 TTGAAGTTTCCGGC
19947 GACCTGCCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 16
0.68 0.02 0.30
Matches are distributed among these distances:
12 8 0.22
13 1 0.03
14 3 0.08
17 2 0.06
18 1 0.03
19 21 0.58
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (19 bp):
TTGAAGTTTCCGGCCAACA
Found at i:19984 original size:20 final size:20
Alignment explanation
Indices: 19961--20003 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
19951 TGCCCAGTTT
19961 CCGGCGAAGAATCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
19981 CCGGCGAAGAATCCCAGAAA
1 CCGGCGAAGAATCCCAGAAA
20001 CCG
1 CCG
20004 TCAAATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.33, G:0.26, T:0.05
Consensus pattern (20 bp):
CCGGCGAAGAATCCCAGAAA
Found at i:20065 original size:20 final size:20
Alignment explanation
Indices: 20022--20066 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
20012 CCGGCCAACT
*
20022 TCCGGCGAAAAAACCCAGAT
1 TCCGGCGAAAAAACCCAGAA
***
20042 TCCGGCGAAAATTTCCAGAA
1 TCCGGCGAAAAAACCCAGAA
20062 TCCGG
1 TCCGG
20067 TGAATCTTCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (20 bp):
TCCGGCGAAAAAACCCAGAA
Found at i:20724 original size:160 final size:156
Alignment explanation
Indices: 20452--20921 Score: 730
Period size: 153 Copynumber: 3.0 Consensus size: 156
20442 TGATCTTGAT
* * * *
20452 TTTTTTTTTCTTTTTCTTTAATCAATCCGACGACGGAGCCTCTACAAGTAAAAACAGTAGTTTTT
1 TTTTGTTTT-TTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGT-GAAACAGTAGTTTTT
20517 CTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAG
64 CTTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAG
* *
20582 AATAATTTCCGATAATTAATTACTTTGCTGA
129 AATAATTTCC-A-AA-TAATTACTTGGATGA
*
20613 TTTTGATTTTTTTTTCTTTAATTAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTC
1 TTTTG-TTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTC
* *
20678 TTGCATACTCTTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTTAATTGAGA
65 TTGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGA
*
20743 ATAATTTCC-AATAATTAATTGGATGA
130 ATAATTTCCAAATAATTACTTGGATGA
*
20769 TTTTG--TTTTTTTCTTTAATAAATCCGACGACGGAGCCCCTGCAAGTGAAACAGTAGTTTTTCT
1 TTTTGTTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCT
20832 TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
66 TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
*
20897 TCATTTCCAACAACTAATTACTTGG
131 TAATTTCC-A-AA-TAATTACTTGG
20922 TAAAATTTTA
Statistics
Matches: 289, Mismatches: 15, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
153 126 0.44
156 19 0.07
157 12 0.04
160 87 0.30
161 41 0.14
162 4 0.01
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.39
Consensus pattern (156 bp):
TTTTGTTTTTTTTTCTTTAATAAATCCGACGACGGAGCCTCTGCAAGTGAAACAGTAGTTTTTCT
TGCATACTCCTGAGGTGAGGGAATTTTCTCAATTTTCTGCTAAAAGTATTAGAGTCAATTGAGAA
TAATTTCCAAATAATTACTTGGATGA
Found at i:30336 original size:70 final size:70
Alignment explanation
Indices: 30210--30346 Score: 168
Period size: 71 Copynumber: 2.0 Consensus size: 70
30200 CCCCCATTTC
* * * *
30210 TGGATTTTAAACGAGGATAGCATTTTGTATGAAAAACAAATCGATCCCTTTAAGGGAGGGATCGA
1 TGGATTTTAAACGAGGATAGCATTATGTATGAAAAACAAATCAATCCATTTAAGGGAAGGATCGA
30275 TCCTT
66 TCCTT
* ** * * *
30280 TGGATTTTTAAACGGGGATTTCATTATGTATGAAGAACAGATCAAT-CATTTAAGGGAAGGATTG
1 TGGA-TTTTAAACGAGGATAGCATTATGTATGAAAAACAAATCAATCCATTTAAGGGAAGGATCG
30344 ATC
65 ATC
30347 GGGTAAGTAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
70 22 0.39
71 34 0.61
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (70 bp):
TGGATTTTAAACGAGGATAGCATTATGTATGAAAAACAAATCAATCCATTTAAGGGAAGGATCGA
TCCTT
Found at i:37907 original size:36 final size:35
Alignment explanation
Indices: 37860--37944 Score: 145
Period size: 34 Copynumber: 2.4 Consensus size: 35
37850 GGGAGAGACA
37860 ATGGTATGAAAAATTTCTATTTGATTGATGATCTTG
1 ATGGTATGAAAAATTT-TATTTGATTGATGATCTTG
37896 ATGGTATG-AAAATTTTATTTGATTGATGATCTTG
1 ATGGTATGAAAAATTTTATTTGATTGATGATCTTG
*
37930 ATGGCATGAAAAATT
1 ATGGTATGAAAAATT
37945 CCCACTTGAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
34 26 0.55
35 13 0.28
36 8 0.17
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (35 bp):
ATGGTATGAAAAATTTTATTTGATTGATGATCTTG
Done.