Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168103.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_349, 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: 32276
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.39
Found at i:145 original size:18 final size:18
Alignment explanation
Indices: 104--148 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
94 TATAGTGTTT
*
104 ATTAATTATAAATTAATTG
1 ATTAATTA-AAATTAATTA
*
123 A-TAATTAAATTTAATTA
1 ATTAATTAAAATTAATTA
140 ATTAATTAA
1 ATTAATTAA
149 TTATAACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 9 0.39
18 13 0.57
19 1 0.04
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
ATTAATTAAAATTAATTA
Found at i:396 original size:19 final size:19
Alignment explanation
Indices: 372--441 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 19
362 ATTTATAATT
372 ATTTATTAATTATGAATAA
1 ATTTATTAATTATGAATAA
****
391 ATTTATTAGATTGCCTATAA
1 ATTTATTA-ATTATGAATAA
411 ATTTATATAATTATGTAATATA
1 ATTTAT-TAATTATG-AATA-A
433 ATTATATTA
1 ATT-TATTA
442 CATAACAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
19 8 0.21
20 16 0.42
21 5 0.13
22 6 0.16
23 3 0.08
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.49
Consensus pattern (19 bp):
ATTTATTAATTATGAATAA
Found at i:488 original size:18 final size:18
Alignment explanation
Indices: 449--490 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
439 TTACATAACA
* *
449 AATAGTTTATTTTTTATT
1 AATAATTTATTTTTAATT
467 -ATAATTTATTTTTAATT
1 AATAATTTATTTTTAATT
484 AATAATT
1 AATAATT
491 AATATTTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 15 0.71
18 6 0.29
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
AATAATTTATTTTTAATT
Found at i:1286 original size:16 final size:17
Alignment explanation
Indices: 1257--1314 Score: 55
Period size: 16 Copynumber: 3.4 Consensus size: 17
1247 AAAAATTTTT
1257 AAAACAACGAAAAAATA
1 AAAACAACGAAAAAATA
* *
1274 AAAACAA-GTAAAAATG
1 AAAACAACGAAAAAATA
* * *
1290 AAAGCATATGAAAAAAAA
1 AAAACA-ACGAAAAAATA
1308 AAAACAA
1 AAAACAA
1315 AAAGAAGGAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
16 12 0.38
17 9 0.28
18 11 0.34
ACGTcount: A:0.74, C:0.09, G:0.09, T:0.09
Consensus pattern (17 bp):
AAAACAACGAAAAAATA
Found at i:1681 original size:45 final size:43
Alignment explanation
Indices: 1625--1722 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 43
1615 CAAATAGAGG
1625 AAAAAGATATAAAA-TATGAAAGATGAAAAATAAAATAAAAGTTAAT
1 AAAAAGATATAAAATTAT-AAAGA--AAAAATAAAA-AAAAGTTAAT
* *
1671 AAAAA-ATATAAAATTATAAAGAAGAAATAAAAAAAAGTGTGAAC
1 AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGT-T-AAT
1715 AAAAAGAT
1 AAAAAGAT
1723 TTAAGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
42 6 0.13
43 10 0.22
44 7 0.15
45 15 0.33
46 8 0.17
ACGTcount: A:0.68, C:0.01, G:0.11, T:0.19
Consensus pattern (43 bp):
AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGTTAAT
Found at i:1700 original size:19 final size:19
Alignment explanation
Indices: 1651--1702 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
1641 TGAAAGATGA
1651 AAAATAAAATAAAAGTTAAT
1 AAAA-AAAATAAAAGTTAAT
*
1671 AAAAAATATAAAA-TT-AT
1 AAAAAAAATAAAAGTTAAT
1688 AAAGAAGAAATAAAA
1 AAA-AA-AAATAAAA
1703 AAAAGTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 15 0.54
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAAAAATAAAAGTTAAT
Found at i:2153 original size:18 final size:18
Alignment explanation
Indices: 2092--2160 Score: 70
Period size: 18 Copynumber: 3.8 Consensus size: 18
2082 AGAGCAAAAG
*
2092 AAAAAAGATAAATAAAGCAC
1 AAAAAA-ATAAA-AAAGGAC
*
2112 AAAAAAA-AGAAAAAGG-T
1 AAAAAAATA-AAAAAGGAC
*
2129 AAGAAAATAAAAAAGGAC
1 AAAAAAATAAAAAAGGAC
2147 AAAAAAATAAAAAA
1 AAAAAAATAAAAAA
2161 TGAAATGGAA
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
17 13 0.32
18 19 0.46
19 3 0.07
20 6 0.15
ACGTcount: A:0.77, C:0.04, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAAAAATAAAAAAGGAC
Found at i:2471 original size:28 final size:29
Alignment explanation
Indices: 2423--2477 Score: 69
Period size: 28 Copynumber: 1.9 Consensus size: 29
2413 TAAAACAACG
* *
2423 AAAAAATAAAAACAAGTAAAAATGAAAGC
1 AAAAAATAAAAACAAGCAAAAAGGAAAGC
2452 AAAAAA-AAAAA-AAGGCAAAAAGGAAA
1 AAAAAATAAAAACAA-GCAAAAAGGAAA
2478 ATTATGAAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 2 0.09
28 15 0.65
29 6 0.26
ACGTcount: A:0.76, C:0.05, G:0.13, T:0.05
Consensus pattern (29 bp):
AAAAAATAAAAACAAGCAAAAAGGAAAGC
Found at i:2878 original size:42 final size:43
Alignment explanation
Indices: 2814--2960 Score: 129
Period size: 42 Copynumber: 3.4 Consensus size: 43
2804 CAAATAGAGG
*
2814 AAAAAGATATAAAATATGAAAGATGAAAAAAAAAAAAGTTAAT
1 AAAAAGATATAAAATATGAAAGAAGAAAAAAAAAAAAGTTAAT
* *
2857 AAAAA-ATATAAAATTAT-AAAGAAGAAATAAAAAAAAGTGTGAAC
1 AAAAAGATATAAAA-TATGAAAGAAGAAAAAAAAAAAAGT-T-AAT
* * * * * **
2901 AAAAAGATTTAAGAAAAAGCAAGAA-AAAAAATAAAAAGAAAAT
1 AAAAAGATATAA-AATATGAAAGAAGAAAAAAAAAAAAGTTAAT
*
2944 ACAAAATATATAAAATA
1 A-AAAAGATATAAAATA
2961 AAATTTGAGA
Statistics
Matches: 82, Mismatches: 15, Indels: 14
0.74 0.14 0.13
Matches are distributed among these distances:
42 27 0.33
43 15 0.18
44 16 0.20
45 17 0.21
46 7 0.09
ACGTcount: A:0.71, C:0.02, G:0.10, T:0.17
Consensus pattern (43 bp):
AAAAAGATATAAAATATGAAAGAAGAAAAAAAAAAAAGTTAAT
Found at i:3007 original size:20 final size:18
Alignment explanation
Indices: 2914--3000 Score: 57
Period size: 18 Copynumber: 4.3 Consensus size: 18
2904 AAGATTTAAG
2914 AAAAAGCAAGAAAAAAAAT
1 AAAAAG-AAGAAAAAAAAT
*
2933 AAAAAGAAAATACAAAATATAT
1 AAAAAGAAGA-A-AAAA-A-AT
*
2955 AAAATAAAATTTGAGAAAAAAAT
1 AAAA-AGAA---GA-AAAAAAAT
*
2978 GAAAAGAAGAAAAAAAAT
1 AAAAAGAAGAAAAAAAAT
2996 AAAAA
1 AAAAA
3001 ATGAAGAGGC
Statistics
Matches: 53, Mismatches: 7, Indels: 17
0.69 0.09 0.22
Matches are distributed among these distances:
18 15 0.28
19 9 0.17
20 4 0.08
21 1 0.02
22 9 0.17
23 8 0.15
24 1 0.02
25 4 0.08
26 2 0.04
ACGTcount: A:0.76, C:0.02, G:0.09, T:0.13
Consensus pattern (18 bp):
AAAAAGAAGAAAAAAAAT
Found at i:4068 original size:45 final size:43
Alignment explanation
Indices: 4012--4109 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 43
4002 CAAATAGAGG
4012 AAAAAGATATAAAA-TATGAAAGATGAAAAATAAAATAAAAGTTAAT
1 AAAAAGATATAAAATTAT-AAAGA--AAAAATAAAA-AAAAGTTAAT
* *
4058 AAAAA-ATATAAAATTATAAAGAAGAAATAAAAAAAAGTGTGAAC
1 AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGT-T-AAT
4102 AAAAAGAT
1 AAAAAGAT
4110 TTAAGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
42 6 0.13
43 10 0.22
44 7 0.15
45 15 0.33
46 8 0.17
ACGTcount: A:0.68, C:0.01, G:0.11, T:0.19
Consensus pattern (43 bp):
AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGTTAAT
Found at i:4087 original size:19 final size:19
Alignment explanation
Indices: 4038--4089 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
4028 TGAAAGATGA
4038 AAAATAAAATAAAAGTTAAT
1 AAAA-AAAATAAAAGTTAAT
*
4058 AAAAAATATAAAA-TT-AT
1 AAAAAAAATAAAAGTTAAT
4075 AAAGAAGAAATAAAA
1 AAA-AA-AAATAAAA
4090 AAAAGTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 15 0.54
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAAAAATAAAAGTTAAT
Found at i:4201 original size:15 final size:15
Alignment explanation
Indices: 4169--4226 Score: 57
Period size: 15 Copynumber: 3.8 Consensus size: 15
4159 AATAAAATTT
4169 GAGAAAAAAAATGAAAA
1 GAGAAAAAAAAT--AAA
4186 GAGAAAAAAAATAAA
1 GAGAAAAAAAATAAA
*
4201 GA-AAACAAAAAGAAA
1 GAGAAA-AAAAATAAA
*
4216 -AAAAAAAAAAT
1 GAGAAAAAAAAT
4227 TTATAGAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
14 9 0.24
15 16 0.43
17 12 0.32
ACGTcount: A:0.81, C:0.02, G:0.12, T:0.05
Consensus pattern (15 bp):
GAGAAAAAAAATAAA
Found at i:4205 original size:11 final size:10
Alignment explanation
Indices: 4170--4225 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
4160 ATAAAATTTG
4170 AGAAAAAAAA
1 AGAAAAAAAA
* *
4180 TGAAAAGAGAA
1 AGAAAA-AAAA
*
4191 A-AAAAATAA
1 AGAAAAAAAA
4200 AGAAAACAAAA
1 AGAAAA-AAAA
4211 AGAAAAAAAA
1 AGAAAAAAAA
4221 A-AAAA
1 AGAAAA
4226 TTTATAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 8 0.21
10 18 0.47
11 12 0.32
ACGTcount: A:0.84, C:0.02, G:0.11, T:0.04
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:4235 original size:31 final size:31
Alignment explanation
Indices: 4157--4236 Score: 78
Period size: 31 Copynumber: 2.6 Consensus size: 31
4147 CAAAATATAT
* * *
4157 AAAATAAAATTT-GAGAAAAAAAATGAAAAG
1 AAAAAAAAATTTAAAGAAAAAAAAAGAAAAG
4187 AGAAAAAAAA--TAAAGAAAACAAAAAGAAAA-
1 A-AAAAAAAATTTAAAGAAAA-AAAAAGAAAAG
*
4217 AAAAAAAAATTTATAGAAAA
1 AAAAAAAAATTTAAAGAAAA
4237 TTTTAAAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
29 9 0.22
30 8 0.20
31 24 0.59
ACGTcount: A:0.76, C:0.01, G:0.10, T:0.12
Consensus pattern (31 bp):
AAAAAAAAATTTAAAGAAAAAAAAAGAAAAG
Found at i:4447 original size:21 final size:21
Alignment explanation
Indices: 4422--4461 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
4412 ATGAAACTAT
4422 AAATAAAGA-AAGAAAAAAAAA
1 AAATAAA-ATAAGAAAAAAAAA
4443 AAATAAAATAAGAAAAAAA
1 AAATAAAATAAGAAAAAAA
4462 TTAGAGCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.85, C:0.00, G:0.07, T:0.07
Consensus pattern (21 bp):
AAATAAAATAAGAAAAAAAAA
Found at i:4828 original size:17 final size:16
Alignment explanation
Indices: 4808--4868 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
4798 AAAAATTTTT
4808 AAAACAACGAAAAAATA
1 AAAACAA-GAAAAAATA
* *
4825 AAAACAAGTAAAAATG
1 AAAACAAGAAAAAATA
* *
4841 AAAGCATATGAAAAAAAA
1 AAAACA-A-GAAAAAATA
*
4859 AAAAAAAGAA
1 AAAACAAGAA
4869 GGAAAATTAT
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
16 15 0.44
17 9 0.26
18 10 0.29
ACGTcount: A:0.75, C:0.07, G:0.10, T:0.08
Consensus pattern (16 bp):
AAAACAAGAAAAAATA
Found at i:5261 original size:45 final size:43
Alignment explanation
Indices: 5205--5302 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 43
5195 CAAATAGAGG
5205 AAAAAGATATAAAA-TATGAAAGATGAAAAATAAAATAAAAGTTAAT
1 AAAAAGATATAAAATTAT-AAAGA--AAAAATAAAA-AAAAGTTAAT
* *
5251 AAAAA-ATATAAAATTATAAAGAAGAAATAAAAAAAAGTGTGAAC
1 AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGT-T-AAT
5295 AAAAAGAT
1 AAAAAGAT
5303 TTAAGAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 9
0.81 0.04 0.16
Matches are distributed among these distances:
42 6 0.13
43 10 0.22
44 7 0.15
45 15 0.33
46 8 0.17
ACGTcount: A:0.68, C:0.01, G:0.11, T:0.19
Consensus pattern (43 bp):
AAAAAGATATAAAATTATAAAGAAAAAATAAAAAAAAGTTAAT
Found at i:5280 original size:19 final size:19
Alignment explanation
Indices: 5231--5282 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
5221 TGAAAGATGA
5231 AAAATAAAATAAAAGTTAAT
1 AAAA-AAAATAAAAGTTAAT
*
5251 AAAAAATATAAAA-TT-AT
1 AAAAAAAATAAAAGTTAAT
5268 AAAGAAGAAATAAAA
1 AAA-AA-AAATAAAA
5283 AAAAGTGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 15 0.54
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAAAAATAAAAGTTAAT
Found at i:5381 original size:19 final size:19
Alignment explanation
Indices: 5346--5398 Score: 58
Period size: 18 Copynumber: 2.8 Consensus size: 19
5336 CAAAATATAT
*
5346 AAAATAAAATTTG-AGAAAA
1 AAAATAAAA-ATGAAGAAAA
5365 AAAATGAAAAA-GAAG-AAA
1 AAAAT-AAAAATGAAGAAAA
5383 AAAATAAAAATGAAGA
1 AAAATAAAAATGAAGA
5399 GGCAAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
17 5 0.17
18 13 0.45
19 7 0.24
20 4 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (19 bp):
AAAATAAAAATGAAGAAAA
Found at i:5647 original size:13 final size:12
Alignment explanation
Indices: 5629--5724 Score: 50
Period size: 13 Copynumber: 7.2 Consensus size: 12
5619 ATGAAACTAT
5629 AAATAAAGAAAGA
1 AAATAAA-AAAGA
*
5642 AAATAAAAAATAA
1 AAATAAAAAA-GA
5655 AAATAAAATAAGA
1 AAATAAAA-AAGA
*
5668 AAA-AAATTAGAGCA
1 AAATAAA--AAAG-A
*
5682 AAAGAAAAAAGA
1 AAATAAAAAAGA
*
5694 TAAATAAAGCACAAAA
1 -AAATAAA--A-AAGA
*
5710 AAAGAAAAAAGA
1 AAATAAAAAAGA
5722 AAA
1 AAA
5725 AATTGAATAA
Statistics
Matches: 65, Mismatches: 8, Indels: 21
0.69 0.09 0.22
Matches are distributed among these distances:
12 13 0.20
13 32 0.49
14 7 0.11
15 10 0.15
16 3 0.05
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.09
Consensus pattern (12 bp):
AAATAAAAAAGA
Found at i:6142 original size:12 final size:12
Alignment explanation
Indices: 6127--6154 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
6117 ACAAAATAGC
6127 AAAAAAAAATAA
1 AAAAAAAAATAA
6139 AAAAAAAAATAA
1 AAAAAAAAATAA
6151 AAAA
1 AAAA
6155 TTTGAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.00, T:0.07
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:6481 original size:19 final size:19
Alignment explanation
Indices: 6432--6483 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
6422 TGAAAGATGA
6432 AAAATAAAATAAAAGTTAAT
1 AAAA-AAAATAAAAGTTAAT
*
6452 AAAAAATATAAAA-TT-AT
1 AAAAAAAATAAAAGTTAAT
6469 AAAGAAGAAATAAAA
1 AAA-AA-AAATAAAA
6484 AAAGTGTGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 5 0.18
18 4 0.14
19 15 0.54
20 4 0.14
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (19 bp):
AAAAAAAATAAAAGTTAAT
Found at i:6600 original size:15 final size:13
Alignment explanation
Indices: 6560--6627 Score: 60
Period size: 12 Copynumber: 5.6 Consensus size: 13
6550 AAATTTGAGA
6560 AAAAAAATGAAAG
1 AAAAAAATGAAAG
*
6573 -AAGAAA--AAA-
1 AAAAAAATGAAAG
6582 AAAAAAATGAAGAG
1 AAAAAAATGAA-AG
6596 CAAAAAAATGAAAG
1 -AAAAAAATGAAAG
6610 -AAAAAA--AAAG
1 AAAAAAATGAAAG
6620 AAAAAAAT
1 AAAAAAAT
6628 TTATAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 17
0.70 0.03 0.27
Matches are distributed among these distances:
10 12 0.27
11 6 0.13
12 13 0.29
13 1 0.02
14 2 0.04
15 11 0.24
ACGTcount: A:0.79, C:0.01, G:0.13, T:0.06
Consensus pattern (13 bp):
AAAAAAATGAAAG
Found at i:6872 original size:20 final size:21
Alignment explanation
Indices: 6839--6882 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
6829 TTGCTCTAAT
* *
6839 TTTTTTCTTATTTTATTTTTA
1 TTTTTTATTATTTTATCTTTA
*
6860 TTTTTTATT-TTTTCTCTTTA
1 TTTTTTATTATTTTATCTTTA
6880 TTT
1 TTT
6883 ATAGTTTCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.11, C:0.07, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTATTATTTTATCTTTA
Found at i:7150 original size:29 final size:28
Alignment explanation
Indices: 7114--7168 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
7104 TTGGATTAGA
* *
7114 ATAATATAGTATTAAATTAGTAATTTTG
1 ATAATATAGTATCAAATAAGTAATTTTG
* *
7142 ATAATTATATTATCAAATAATTAATTT
1 ATAA-TATAGTATCAAATAAGTAATTT
7169 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 4 0.18
29 18 0.82
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.47
Consensus pattern (28 bp):
ATAATATAGTATCAAATAAGTAATTTTG
Found at i:7314 original size:19 final size:19
Alignment explanation
Indices: 7287--7327 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
7277 ATAATTGTTG
* *
7287 TTTATAATAGTAAATATTA
1 TTTAAAATAGTAAATAATA
*
7306 TTTAAAATAGTTAATAATA
1 TTTAAAATAGTAAATAATA
7325 TTT
1 TTT
7328 TGAAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
TTTAAAATAGTAAATAATA
Found at i:7440 original size:19 final size:19
Alignment explanation
Indices: 7416--7455 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
7406 ATAAATGAAG
*
7416 ATTAAA-TAATATTAATTAA
1 ATTAAATTAATAGT-ATTAA
7435 ATTAAATTAATAGTATTAA
1 ATTAAATTAATAGTATTAA
7454 AT
1 AT
7456 ATTATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (19 bp):
ATTAAATTAATAGTATTAA
Found at i:10178 original size:73 final size:73
Alignment explanation
Indices: 10051--10197 Score: 210
Period size: 73 Copynumber: 2.0 Consensus size: 73
10041 TTTTGGGAAC
* * *
10051 ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAGAACCAATTGTTTTATGAC
1 ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAAAAACAATTGCTTTATGAC
10116 AAAACAAA
66 AAAACAAA
*
10124 ATTAATAAA-TTAGTATTATTTTATTTCG-AATAAGCTTGTATG-ATAAAAAACAATTGCTTTAT
1 ATTAATAAATTTA-TATTATTTTATTT-GAAATAAGCTTGAATGAAT-AAAAACAATTGCTTTAT
10186 GACAAAACAAA
63 GACAAAACAAA
10197 A
1 A
10198 GGTTATTTAT
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
72 5 0.07
73 61 0.91
74 1 0.01
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (73 bp):
ATTAATAAATTTATATTATTTTATTTGAAATAAGCTTGAATGAATAAAAACAATTGCTTTATGAC
AAAACAAA
Found at i:10329 original size:28 final size:28
Alignment explanation
Indices: 10274--10329 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
10264 ATAAACTATT
* *
10274 TTTAAATTTATATATTAATAATAGTTTA
1 TTTAAATTTAAATATTAATAATAATTTA
*
10302 TTTAATATTTAAATATT-ATATTAATTTA
1 TTTAA-ATTTAAATATTAATAATAATTTA
10330 AATATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 14 0.58
29 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TTTAAATTTAAATATTAATAATAATTTA
Found at i:10740 original size:27 final size:27
Alignment explanation
Indices: 10708--10759 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
10698 GTAATTTTAA
10708 TAATTATT-TATAAATTAATTAAATATT
1 TAATTATTAT-TAAATTAATTAAATATT
* *
10735 TAATTATTATTTAATTAATTTAATA
1 TAATTATTATTAAATTAATTAAATA
10760 ATTGTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 21 0.95
28 1 0.05
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
TAATTATTATTAAATTAATTAAATATT
Found at i:10741 original size:23 final size:23
Alignment explanation
Indices: 10706--10752 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
10696 TCGTAATTTT
*
10706 AATAATTATTTATAAATTAATTA
1 AATAATTAATTATAAATTAATTA
* * *
10729 AATATTTAATTATTATTTAATTA
1 AATAATTAATTATAAATTAATTA
10752 A
1 A
10753 TTTAATAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (23 bp):
AATAATTAATTATAAATTAATTA
Found at i:10930 original size:23 final size:22
Alignment explanation
Indices: 10895--10984 Score: 75
Period size: 23 Copynumber: 4.3 Consensus size: 22
10885 GCTAATATAA
*
10895 ATTAATT-TAAATATATAAATT
1 ATTAATTATTAATATATAAATT
* *
10916 ATTAATTATTAAATATTTAATTT
1 ATTAATTATT-AATATATAAATT
* *
10939 ATTAATGATT-ATAT-TAATTT
1 ATTAATTATTAATATATAAATT
*
10959 ATTAA-TATTAATA-AT-AATA
1 ATTAATTATTAATATATAAATT
10978 ATTAATT
1 ATTAATT
10985 TAACTAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 11
0.76 0.09 0.15
Matches are distributed among these distances:
19 10 0.18
20 16 0.28
21 11 0.19
22 1 0.02
23 19 0.33
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (22 bp):
ATTAATTATTAATATATAAATT
Found at i:10942 original size:16 final size:16
Alignment explanation
Indices: 10917--10967 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
10907 ATATAAATTA
10917 TTAA-TTATTAAATAT
1 TTAATTTATTAAATAT
10932 TTAATTTATTAATGATTAT
1 TTAATTTATTAA--A-TAT
10951 ATTAATTTATT-AATAT
1 -TTAATTTATTAAATAT
10967 T
1 T
10968 AATAATAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 5 0.16
16 10 0.32
17 1 0.03
18 1 0.03
19 4 0.13
20 10 0.32
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (16 bp):
TTAATTTATTAAATAT
Found at i:10957 original size:20 final size:19
Alignment explanation
Indices: 10866--10968 Score: 76
Period size: 19 Copynumber: 5.5 Consensus size: 19
10856 ACTATATTAT
*
10866 TTAATTTTATATTAATTTA
1 TTAATATTATATTAATTTA
* *
10885 GCTAATA-TAAATTAATTTA
1 -TTAATATTATATTAATTTA
10904 --AATA-TATA--AA-TTA
1 TTAATATTATATTAATTTA
10917 TTAATTATTAAATATTTAATTTA
1 TTAA-TATT--ATA-TTAATTTA
10940 TTAATGATTATATTAATTTA
1 TTAAT-ATTATATTAATTTA
10960 TTAATATTA
1 TTAATATTA
10969 ATAATAATAA
Statistics
Matches: 68, Mismatches: 4, Indels: 23
0.72 0.04 0.24
Matches are distributed among these distances:
13 3 0.04
14 2 0.03
15 2 0.03
16 9 0.13
17 1 0.01
19 18 0.26
20 17 0.25
21 3 0.04
22 3 0.04
23 10 0.15
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATATTATATTAATTTA
Found at i:11044 original size:10 final size:10
Alignment explanation
Indices: 11029--11078 Score: 61
Period size: 9 Copynumber: 5.3 Consensus size: 10
11019 ATAAATGAAG
11029 ATTAAATATT
1 ATTAAATATT
11039 ATTAAATATT
1 ATTAAATATT
*
11049 ATT-ATTATT
1 ATTAAATATT
*
11058 A-TATATATT
1 ATTAAATATT
11067 ATTAAA-ATT
1 ATTAAATATT
11076 ATT
1 ATT
11079 GTATTATTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
8 1 0.03
9 17 0.50
10 16 0.47
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (10 bp):
ATTAAATATT
Found at i:11051 original size:3 final size:3
Alignment explanation
Indices: 11035--11102 Score: 50
Period size: 3 Copynumber: 22.0 Consensus size: 3
11025 GAAGATTAAA
* * * *
11035 TAT TAT TAAA TAT TAT TAT TAT TA- TAT ATAT TAT TAA AAT TAT T-G
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT
11080 TAT TAT TGAT ATAT TAT TAT TAT
1 TAT TAT T-AT -TAT TAT TAT TAT
11103 CGATAATTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
2 3 0.06
3 38 0.75
4 9 0.18
5 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:11071 original size:28 final size:30
Alignment explanation
Indices: 11034--11101 Score: 97
Period size: 28 Copynumber: 2.3 Consensus size: 30
11024 TGAAGATTAA
11034 ATATTATTAAATATTA-T-TATTATT-ATAT
1 ATATTATTAAA-ATTATTGTATTATTGATAT
11062 ATATTATTAAAATTATTGTATTATTGATAT
1 ATATTATTAAAATTATTGTATTATTGATAT
11092 ATTATTATTA
1 A-TATTATTA
11102 TCGATAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
27 4 0.11
28 12 0.33
29 7 0.19
30 5 0.14
31 8 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (30 bp):
ATATTATTAAAATTATTGTATTATTGATAT
Found at i:11076 original size:21 final size:21
Alignment explanation
Indices: 11029--11086 Score: 56
Period size: 21 Copynumber: 3.0 Consensus size: 21
11019 ATAAATGAAG
11029 ATTAAATATTATTA-A-ATATT
1 ATTAAA-ATTATTATATATATT
11049 ATT---ATTATTATATATATT
1 ATTAAAATTATTATATATATT
*
11067 ATTAAAATTATTGTAT-TATT
1 ATTAAAATTATTATATATATT
11087 GATATATTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
16 7 0.22
17 1 0.03
18 8 0.25
20 7 0.22
21 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTAAAATTATTATATATATT
Found at i:11173 original size:17 final size:16
Alignment explanation
Indices: 11142--11180 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
11132 TATAGTATAT
11142 TAATGAATTATTATTAA
1 TAAT-AATTATTATTAA
*
11159 TAATAATTATATATTAC
1 TAATAATTAT-TATTAA
11176 TAATA
1 TAATA
11181 TAATAAGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (16 bp):
TAATAATTATTATTAA
Found at i:11484 original size:18 final size:16
Alignment explanation
Indices: 11456--11524 Score: 56
Period size: 18 Copynumber: 4.2 Consensus size: 16
11446 AATATTTGTT
11456 AATTTATATTAATTATA
1 AATTTATATTAA-TATA
11473 AATTTAATATT-A-AT-
1 AATTT-ATATTAATATA
11487 AATTT-TATTAATTATA
1 AATTTATATTAA-TATA
11503 ATATATTAATATTAATATA
1 A-AT-TT-ATATTAATATA
11522 AAT
1 AAT
11525 ATATTATAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 17
0.72 0.00 0.28
Matches are distributed among these distances:
12 4 0.09
13 1 0.02
14 5 0.12
15 4 0.09
16 1 0.02
17 8 0.19
18 9 0.21
19 5 0.12
20 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AATTTATATTAATATA
Found at i:11494 original size:32 final size:32
Alignment explanation
Indices: 11455--11519 Score: 107
Period size: 30 Copynumber: 2.1 Consensus size: 32
11445 AAATATTTGT
11455 TAATTTATATTAATTATAA-AT-TTAATATTAA
1 TAATTT-TATTAATTATAATATATTAATATTAA
11486 TAATTTTATTAATTATAATATATTAATATTAA
1 TAATTTTATTAATTATAATATATTAATATTAA
11518 TA
1 TA
11520 TAAATATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
30 12 0.38
31 8 0.25
32 12 0.38
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
TAATTTTATTAATTATAATATATTAATATTAA
Found at i:11508 original size:26 final size:30
Alignment explanation
Indices: 11455--11519 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 30
11445 AAATATTTGT
11455 TAATTTATATTAATTATAAATTTAATATTAA
1 TAATTTATATTAATTATAAA-TTAATATTAA
11486 TAATTT-TATTAATTATAATATATTAATATTAA
1 TAATTTATATTAATTAT-A-A-ATTAATATTAA
11518 TA
1 TA
11520 TAAATATATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
30 10 0.32
31 7 0.23
32 13 0.42
33 1 0.03
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
TAATTTATATTAATTATAAATTAATATTAA
Found at i:11518 original size:14 final size:14
Alignment explanation
Indices: 11460--11536 Score: 52
Period size: 14 Copynumber: 5.2 Consensus size: 14
11450 TTTGTTAATT
11460 TATATTAATTATAA
1 TATATTAATTATAA
11474 -AT-TTAATATTAATAA
1 TATATT-A-ATT-ATAA
*
11489 TTTTATTAATTATAA
1 -TATATTAATTATAA
11504 TATATTAA-TATTAA
1 TATATTAATTA-TAA
*
11518 TATAAATATATTATAA
1 TAT-ATTA-ATTATAA
11534 TAT
1 TAT
11537 TTCTATAATG
Statistics
Matches: 50, Mismatches: 3, Indels: 18
0.70 0.04 0.25
Matches are distributed among these distances:
12 2 0.04
13 5 0.10
14 16 0.32
15 11 0.22
16 10 0.20
17 4 0.08
18 2 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATTAATTATAA
Found at i:11544 original size:22 final size:20
Alignment explanation
Indices: 11492--11530 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
11482 TTAATAATTT
11492 TATTAAT-TATAATATATTAA
1 TATTAATATA-AATATATTAA
11512 TATTAATATAAATATATTA
1 TATTAATATAAATATATTA
11531 TAATATTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 16 0.89
21 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTAATATAAATATATTAA
Found at i:12147 original size:14 final size:15
Alignment explanation
Indices: 12128--12156 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12118 TTACTTAAAT
12128 CAATTATT-TATTAA
1 CAATTATTATATTAA
12142 CAATTATTATATTAA
1 CAATTATTATATTAA
12157 AAATAAGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.45, C:0.07, G:0.00, T:0.48
Consensus pattern (15 bp):
CAATTATTATATTAA
Found at i:13009 original size:21 final size:21
Alignment explanation
Indices: 12968--13011 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
12958 TATTAATAAA
12968 ATAAATAATATAATTATATAT
1 ATAAATAATATAATTATATAT
12989 ATAAATAA-ATAATTATAATAT
1 ATAAATAATATAATTAT-ATAT
13010 AT
1 AT
13012 TTAGATAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAATAATATAATTATATAT
Found at i:13019 original size:23 final size:25
Alignment explanation
Indices: 12966--13036 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 25
12956 ATTATTAATA
12966 AAATAAATAATATAATTATATATAT
1 AAATAAATAATATAATTATATATAT
* *
12991 AAATAAATAATTATAATATATTTAGAT
1 AAATAAATAA-TATAAT-TATATATAT
*
13018 AAAT-AACAATAT-ATTATAT
1 AAATAAATAATATAATTATAT
13037 TTAAGTATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
23 4 0.10
24 2 0.05
25 13 0.32
26 10 0.25
27 11 0.28
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (25 bp):
AAATAAATAATATAATTATATATAT
Found at i:13046 original size:27 final size:28
Alignment explanation
Indices: 12966--13046 Score: 75
Period size: 25 Copynumber: 3.1 Consensus size: 28
12956 ATTATTAATA
* *
12966 AAATAAATAA-TATAAT-TATATA-TAT
1 AAATAAACAATTATAATATATTTAGTAT
*
12991 AAATAAATAATTATAATATATTTAG-AT
1 AAATAAACAATTATAATATATTTAGTAT
*
13018 AAAT-AACAA-TATATTATATTTAAGTAT
1 AAATAAACAATTATAATATATTT-AGTAT
13045 AA
1 AA
13047 TAGTTTATCT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
25 21 0.44
26 12 0.25
27 15 0.31
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (28 bp):
AAATAAACAATTATAATATATTTAGTAT
Found at i:13152 original size:21 final size:23
Alignment explanation
Indices: 13123--13170 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
13113 AATTAATTAC
* *
13123 ATTACTAATTAATTTAA-CAAAT
1 ATTACTAATAAAATTAATCAAAT
*
13145 ATTA-TAATAAAATTAATCAATT
1 ATTACTAATAAAATTAATCAAAT
13167 ATTA
1 ATTA
13171 ATTAACTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (23 bp):
ATTACTAATAAAATTAATCAAAT
Found at i:13376 original size:21 final size:20
Alignment explanation
Indices: 13341--13379 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
13331 TTTAATGTTA
13341 TAATTAAATATATATTATAT
1 TAATTAAATATATATTATAT
*
13361 TAATTAAGTAATATATTAT
1 TAATTAAAT-ATATATTAT
13380 TACTATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TAATTAAATATATATTATAT
Found at i:13416 original size:25 final size:25
Alignment explanation
Indices: 13363--13432 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
13353 TATTATATTA
* **
13363 ATTAAGTAATATATTATTACTATTTTT
1 ATTAA-TAATAT-TTAATACTATAATT
13390 ATTAATAATATTTAATACTATAATT
1 ATTAATAATATTTAATACTATAATT
13415 ATATAA-AATATTTGAATA
1 AT-TAATAATATTT-AATA
13433 GATTCATATA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
25 20 0.53
26 13 0.34
27 5 0.13
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (25 bp):
ATTAATAATATTTAATACTATAATT
Found at i:13491 original size:20 final size:20
Alignment explanation
Indices: 13454--13492 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
13444 AATAAATTTA
*
13454 TAATTTATTATTTGTAATTG
1 TAATTTATTATATGTAATTG
13474 TAATTTATGTATAT-TAATT
1 TAATTTAT-TATATGTAATT
13493 AATTAATAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TAATTTATTATATGTAATTG
Found at i:14989 original size:52 final size:54
Alignment explanation
Indices: 14924--15050 Score: 195
Period size: 52 Copynumber: 2.4 Consensus size: 54
14914 AAATATATCT
*
14924 AATTATTCTACCATTTGGGCCAAATTAGAAATATTTTCTC-TTTT-GAATTTCTA
1 AATT-TTCCACCATTTGGGCCAAATTAGAAATATTTTCTCTTTTTGGAATTTCTA
* * *
14977 AATTTTCCACCATTTAGGTCAATTTAGAAATATTTTCTCTTTTTGGAATTTCTA
1 AATTTTCCACCATTTGGGCCAAATTAGAAATATTTTCTCTTTTTGGAATTTCTA
15031 AATTTTCCACCATTTGGGCC
1 AATTTTCCACCATTTGGGCC
15051 TATTCAAAAA
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
52 31 0.47
53 8 0.12
54 27 0.41
ACGTcount: A:0.28, C:0.17, G:0.10, T:0.45
Consensus pattern (54 bp):
AATTTTCCACCATTTGGGCCAAATTAGAAATATTTTCTCTTTTTGGAATTTCTA
Found at i:17001 original size:15 final size:16
Alignment explanation
Indices: 16974--17017 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
16964 ATGTTTAGTT
* *
16974 ATAATTAATAATATTA
1 ATAATTTATAATAATA
*
16990 TTAATTTA-AATAATA
1 ATAATTTATAATAATA
17005 ATAATTTATAATA
1 ATAATTTATAATA
17018 CATGTAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
15 13 0.57
16 10 0.43
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAATTTATAATAATA
Found at i:17049 original size:9 final size:10
Alignment explanation
Indices: 17035--17067 Score: 52
Period size: 9 Copynumber: 3.5 Consensus size: 10
17025 TAACCTAAAG
17035 TTATAATTA-
1 TTATAATTAT
17044 TTATAATTAT
1 TTATAATTAT
17054 TTATAA-TAT
1 TTATAATTAT
17063 TTATA
1 TTATA
17068 TATAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 17 0.74
10 6 0.26
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TTATAATTAT
Found at i:17233 original size:23 final size:22
Alignment explanation
Indices: 17194--17260 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 22
17184 TTATATGATT
*
17194 AATATATTAAAGCATATAATATA
1 AATATATTAAA-TATATAATATA
17217 AATATAATTAAATATATAA-AT-
1 AATAT-ATTAAATATATAATATA
* *
17238 AATAGATAAAATACTATAATATA
1 AATATATTAAATA-TATAATATA
17261 GTATTTATTG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
20 7 0.19
21 9 0.24
22 4 0.11
23 11 0.30
24 6 0.16
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (22 bp):
AATATATTAAATATATAATATA
Found at i:17489 original size:19 final size:17
Alignment explanation
Indices: 17462--17502 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
17452 TAATTAATAC
17462 AATTAATTTAACTACTAAT
1 AATTAATTTAA-TA-TAAT
*
17481 AATTTATTTAATATAAT
1 AATTAATTTAATATAAT
17498 AATTA
1 AATTA
17503 TAATATACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATTTAATATAAT
Found at i:17636 original size:18 final size:18
Alignment explanation
Indices: 17615--17659 Score: 63
Period size: 20 Copynumber: 2.4 Consensus size: 18
17605 TTAATTAATA
17615 ATATATAAAATTTTAAGT
1 ATATATAAAATTTTAAGT
*
17633 ATATTAATAAAGTTTTAAGT
1 ATA-T-ATAAAATTTTAAGT
17653 ATATATA
1 ATATATA
17660 CATAACCTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 6 0.25
19 2 0.08
20 16 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (18 bp):
ATATATAAAATTTTAAGT
Found at i:17664 original size:22 final size:20
Alignment explanation
Indices: 17619--17656 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17609 TTAATAATAT
17619 ATAAAATTTTAAGTATATTA
1 ATAAAATTTTAAGTATATTA
*
17639 ATAAAGTTTTAAGTATAT
1 ATAAAATTTTAAGTATAT
17657 ATACATAACC
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:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
ATAAAATTTTAAGTATATTA
Found at i:17816 original size:24 final size:23
Alignment explanation
Indices: 17767--17829 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 23
17757 TATAATTATG
*
17767 TATATTAATAAATATTTAAATAA
1 TATATTAATAAATAGTTAAATAA
*
17790 TATACTTAAT-AATAGTTAATATTA
1 TATA-TTAATAAATAGTTAA-ATAA
17814 TATATATAATTAAATA
1 TATAT-TAA-TAAATA
17830 AACATAATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
23 13 0.39
24 15 0.45
25 1 0.03
26 4 0.12
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (23 bp):
TATATTAATAAATAGTTAAATAA
Found at i:18240 original size:19 final size:20
Alignment explanation
Indices: 18218--18260 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
18208 AATTAATACC
18218 ATTTATTCAAAT-TTAATAA-
1 ATTTA-TCAAATATTAATAAT
*
18237 ATTTATCATATATTAATAAT
1 ATTTATCAAATATTAATAAT
18257 ATTT
1 ATTT
18261 TAATTTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 5 0.24
19 12 0.57
20 4 0.19
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTATCAAATATTAATAAT
Found at i:18702 original size:19 final size:18
Alignment explanation
Indices: 18670--18708 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
18660 ACGTTATTTT
18670 ATTAAAAATAAATTATTA
1 ATTAAAAATAAATTATTA
*
18688 ATTAAAATATTAATTATTA
1 ATTAAAA-ATAAATTATTA
18707 AT
1 AT
18709 ATTTCAAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
ATTAAAAATAAATTATTA
Found at i:19046 original size:11 final size:11
Alignment explanation
Indices: 19026--19152 Score: 64
Period size: 11 Copynumber: 11.5 Consensus size: 11
19016 ACAAAATTAC
*
19026 TAATATTATAA
1 TAATAATATAA
*
19037 AAATAATATAA
1 TAATAATATAA
* *
19048 TAATTATATTA
1 TAATAATATAA
19059 TAATAATAT--
1 TAATAATATAA
* *
19068 TAATTAT-TAG
1 TAATAATATAA
*
19078 TAATATTATAAA
1 TAATAATAT-AA
*
19090 TATTAATATAA
1 TAATAATATAA
19101 TAAATTAA-ATAA
1 T-AA-TAATATAA
* *
19113 TGACAATATTAA
1 TAATAATA-TAA
* * *
19125 TTAGTAGTTTAA
1 -TAATAATATAA
19137 TAATAATATAA
1 TAATAATATAA
19148 TAATA
1 TAATA
19153 CTAATTACAA
Statistics
Matches: 84, Mismatches: 23, Indels: 18
0.67 0.18 0.14
Matches are distributed among these distances:
8 1 0.01
9 6 0.07
10 7 0.08
11 44 0.52
12 20 0.24
13 6 0.07
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (11 bp):
TAATAATATAA
Found at i:19056 original size:25 final size:25
Alignment explanation
Indices: 19026--19103 Score: 77
Period size: 27 Copynumber: 3.0 Consensus size: 25
19016 ACAAAATTAC
19026 TAATATTATAAAAATAATATAATAA
1 TAATATTATAAAAATAATATAATAA
* * *
19051 TTATATTATAATAATATTAAT-TATTAG
1 TAATATTATAA-AA-A-TAATATAATAA
*
19078 TAATATTATAAATATTAATATAATAA
1 TAATATTATAAA-AATAATATAATAA
19104 ATTAAATAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
25 14 0.34
26 7 0.17
27 16 0.39
28 4 0.10
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (25 bp):
TAATATTATAAAAATAATATAATAA
Found at i:19093 original size:18 final size:18
Alignment explanation
Indices: 19053--19094 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
19043 TATAATAATT
19053 ATATTATAATAATATTAA
1 ATATTATAATAATATTAA
* *
19071 TTATTAGTAATATTA-TAA
1 ATATTA-TAATAATATTAA
19089 ATATTA
1 ATATTA
19095 ATATAATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (18 bp):
ATATTATAATAATATTAA
Found at i:19396 original size:20 final size:21
Alignment explanation
Indices: 19371--19411 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
19361 AAATTTTTAA
19371 TTTAATAATT-ATATAA-ATTT
1 TTTAAT-ATTAATATAACATTT
19391 TTTAATATTAATATAACATTT
1 TTTAATATTAATATAACATTT
19412 AACTATTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.16
20 12 0.63
21 4 0.21
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTAATATTAATATAACATTT
Found at i:20850 original size:182 final size:179
Alignment explanation
Indices: 20662--21017 Score: 442
Period size: 180 Copynumber: 2.0 Consensus size: 179
20652 AATCTGCTTA
* ** ** * *
20662 CCAAACCATTTCAAATAGTTTTGACTATTTCAATAATTATTTATTTCAAATCATTATAACCTTTT
1 CCAAACCAGTTCAAATAGTTAAGACTAGATCAATAATTATCTATTTCAAATCATTATAA-CATTT
* * * **
20727 TATTTTATCATCAAACAATTGGTTTTGTTCATACTATTTTATTTAGAATAAAATAATACTAATTT
65 TATTTTAACATAAAACAATT-GTTTTGTTCATACAAGCTTATTTAGAATAAAATAATACTAATTT
* *
20792 AATAATATTTTGAAACTTAATAACTAAGAAAATTAAAAAATAAATTTAATTG
129 AATAATATTTTAAAAATTAATAACTAAG-AAATTAAAAAATAAATTTAATTG
* * * * *
20844 CCAAACCAGTTCAAATAGTTAAGACTCGATGAATGATTATCTATTTCAAATCGTTATGACATTTT
1 CCAAACCAGTTCAAATAGTTAAGACTAGATCAATAATTATCTATTTCAAATCATTATAACATTTT
* * * * *
20909 CTTTTAACGTAAAACAATTGTTTTGTTCGTACAAGCTTATTTGGATTAAAATAATACTAATTTAA
66 ATTTTAACATAAAACAATTGTTTTGTTCATACAAGCTTATTTAGAATAAAATAATACTAATTTAA
* * *
20974 TAATATTTTAAAAATTAATAAGTAAGAGATTTAAAAATAAATTT
131 TAATATTTTAAAAATTAATAACTAAGAAATTAAAAAATAAATTT
21018 GTTTACTGAA
Statistics
Matches: 147, Mismatches: 27, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
179 16 0.11
180 63 0.43
181 20 0.14
182 48 0.33
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (179 bp):
CCAAACCAGTTCAAATAGTTAAGACTAGATCAATAATTATCTATTTCAAATCATTATAACATTTT
ATTTTAACATAAAACAATTGTTTTGTTCATACAAGCTTATTTAGAATAAAATAATACTAATTTAA
TAATATTTTAAAAATTAATAACTAAGAAATTAAAAAATAAATTTAATTG
Found at i:21184 original size:25 final size:24
Alignment explanation
Indices: 21151--21216 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 24
21141 TTTAAATTGT
21151 ATTATTAATAATATAATATAATAA
1 ATTATTAATAATATAATATAATAA
*
21175 ATCTATTAATACT-TAATAT--TAA
1 AT-TATTAATAATATAATATAATAA
* *
21197 ATTATTTAT-TTATAATATAA
1 ATTATTAATAATATAATATAA
21217 ATAGTCATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 1 0.03
21 12 0.34
22 5 0.14
24 8 0.23
25 9 0.26
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (24 bp):
ATTATTAATAATATAATATAATAA
Found at i:21645 original size:120 final size:121
Alignment explanation
Indices: 21483--21701 Score: 280
Period size: 120 Copynumber: 1.8 Consensus size: 121
21473 AATATGAACA
* * * *
21483 AAAATAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAATAATTGTTCCAATAA
1 AAAATAATTATTTTATAACAAAACAAAAGGTCATAATAATTTGAAATAAATAATTGTTCAAATAA
*
21548 TCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACGAATAG
66 CCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACGAATAG
* * * *
21604 AAAA-AATTATTTTATAACAATACAAAAGGTTATAGA-AATTTGAACTAGATAATTGTTCAAATA
1 AAAATAATTATTTTATAACAAAACAAAAGGTCATA-ATAATTTGAAATAAATAATTGTTCAAATA
* * ** * *
21667 GCCATAATTATTTGAACTTGTTCGGTAAACAAATT
65 ACCATAACTATTCAAAATTATTCGGTAAACAAATT
21702 CATTTTTTAA
Statistics
Matches: 82, Mismatches: 15, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
120 77 0.94
121 5 0.06
ACGTcount: A:0.46, C:0.10, G:0.11, T:0.33
Consensus pattern (121 bp):
AAAATAATTATTTTATAACAAAACAAAAGGTCATAATAATTTGAAATAAATAATTGTTCAAATAA
CCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACGAATAG
Found at i:21710 original size:300 final size:300
Alignment explanation
Indices: 21341--21881 Score: 753
Period size: 300 Copynumber: 1.8 Consensus size: 300
21331 GGTCATAATG
* ** * * * *
21341 ATTTGAAATAGATAATTATTCAGATAGTTATTACTATTTGAACTTATTTGATAAACATATTTATT
1 ATTTGAAATAGATAATTATTCAAATAGCCATAACTATTTGAACTTATTCGATAAACAAATTCATT
* *
21406 TTTTAAATCTTTTACTTATTAATTGTTGAAATATTAATAAATTA-ATATTAT-TTAATATGAATA
66 TTTTAAATCTCTCACTTATTAATTGTTGAAATATTAATAAATTAGA-ATTATGTTAATATGAATA
* * *
21469 AGCTAATATGAACAAAAATAATTGTTTTATGACAAAACAAAAGGTCATAATGATTTGAAATAAAT
130 AGCTAATACGAACAAAAACAATTGTTTTATAACAAAAC-AAAGGTCATAATGATTTGAAATAAAT
* * *
21534 AATTGTTCCAATAATCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACG
194 AATTGCTCAAATAACCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACG
21599 AATAGAAAAAATTATTTTATAACAATACAAAAGGTTATAGAA
259 AATAGAAAAAATTATTTTATAACAATACAAAAGGTTATAGAA
* * * * *
21641 ATTTGAACTAGATAATTGTTCAAATAGCCATAATTATTTGAACTTGTTCGGTAAACAAATTCATT
1 ATTTGAAATAGATAATTATTCAAATAGCCATAACTATTTGAACTTATTCGATAAACAAATTCATT
* * *
21706 TTTTAAATCTCTCACTTATTAATTTTTGGAATATTAATAAATTAGAATTATGTTAATCTGAATAA
66 TTTTAAATCTCTCACTTATTAATTGTTGAAATATTAATAAATTAGAATTATGTTAATATGAATAA
** * *
21771 GCTTGTACGAACAAAAACAATTGTTTTGTAAGAAAACAAAGGTCATAATGATTTGAAATAAATAA
131 GCTAATACGAACAAAAACAATTGTTTTATAACAAAACAAAGGTCATAATGATTTGAAATAAATAA
* * ** * *
21836 TTGCTCAAATAGCCATAATTATTTGAACTTGTTCGGTAAACAAATT
196 TTGCTCAAATAACCATAACTATTCAAAATTATTCGGTAAACAAATT
21882 CATTTTTTAA
Statistics
Matches: 206, Mismatches: 33, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
300 163 0.79
301 43 0.21
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (300 bp):
ATTTGAAATAGATAATTATTCAAATAGCCATAACTATTTGAACTTATTCGATAAACAAATTCATT
TTTTAAATCTCTCACTTATTAATTGTTGAAATATTAATAAATTAGAATTATGTTAATATGAATAA
GCTAATACGAACAAAAACAATTGTTTTATAACAAAACAAAGGTCATAATGATTTGAAATAAATAA
TTGCTCAAATAACCATAACTATTCAAAATTATTCGGTAAACAAATTTGAAATAAGCTTGTACGAA
TAGAAAAAATTATTTTATAACAATACAAAAGGTTATAGAA
Found at i:21943 original size:180 final size:180
Alignment explanation
Indices: 21585--22337 Score: 844
Period size: 180 Copynumber: 4.2 Consensus size: 180
21575 ACAAATTTGA
* * * * * *
21585 AATAAGCTTGTACGAATAGAAAA-AATTATTTTATAACAATACAAAAGGTTATAGA-AATTTGAA
1 AATAAGCTTGTACGAACA-AAAACAATTGTTTTATAAGAAAAC-AAAGGTCATA-ATGATTTGAA
* * *
21648 CTAGATAATTGTTCAAATAGCCATAATTATTTGAACTTGTTCGGTAAACAAATTCATTTTTTAAA
63 ATAAATAATTGTTCAAATAGCCATAATTATTTGAACTTGTTCGGCAAACAAATTCATTTTTTAAA
*
21713 TCTCTCACTTATTAATTTTTGGAATATTAATAAATTAGAATTATGTTAATCTG
128 TCTCTCACTTATTAATTTTTGAAATATTAATAAATTAGAATTATGTTAATCTG
*
21766 AATAAGCTTGTACGAACAAAAACAATTGTTTTGTAAGAAAACAAAGGTCATAATGATTTGAAATA
1 AATAAGCTTGTACGAACAAAAACAATTGTTTTATAAGAAAACAAAGGTCATAATGATTTGAAATA
* *
21831 AATAATTGCTCAAATAGCCATAATTATTTGAACTTGTTCGGTAAACAAATTCATTTTTTAAATCT
66 AATAATTGTTCAAATAGCCATAATTATTTGAACTTGTTCGGCAAACAAATTCATTTTTTAAATCT
*
21896 CTCACTTATTAATTTTTGGAATATTAATAAATTAGAATTATGTTAATCTG
131 CTCACTTATTAATTTTTGAAATATTAATAAATTAGAATTATGTTAATCTG
*
21946 AATAAGCTTGTATGAACAAAAACAATTGTTTTATAAGAAAACAAAGGTCATAATGATTTGAAATA
1 AATAAGCTTGTACGAACAAAAACAATTGTTTTATAAGAAAACAAAGGTCATAATGATTTGAAATA
* * * * * * * * * *
22011 GATAATTGTTCAAATAGTCATAATTGTTTGCACTAGTTAAGCCAAA-AGATACATTTTCTAAATC
66 AATAATTGTTCAAATAGCCATAATTATTTGAACTTGTT-CGGCAAACAAATTCATTTTTTAAATC
* * * *
22075 -CATTACTTATTAATTTTTAAAATATTAATAAATTAGCATTACT-TT-ATTTCG
130 TC-TCACTTATTAATTTTTGAAATATTAATAAATTAGAATTA-TGTTAATCT-G
* * * * * * *
22126 AATAAGATTATATGAAC-AAAACAATTGTTTTATGATAAAAGAAATGATCATAATGATTTGAAAT
1 AATAAGCTTGTACGAACAAAAACAATTGTTTTATAAGAAAACAAA-GGTCATAATGATTTGAAAT
* * ** * * * *
22190 AAATATTTGGTCAAATAGTTATAACTAATTGAACTGGTAT-GGCAAACAAATTTA-TTTTTAAAT
65 AAATAATTGTTCAAATAGCCATAATTATTTGAACTTGT-TCGGCAAACAAATTCATTTTTTAAAT
* * * * **
22253 CTCTTACGTATTAA-TTTTGAAATATTAATAAATTA-ATATTATTTTATTCCA
129 CTCTCACTTATTAATTTTTGAAATATTAATAAATTAGA-ATTATGTTAATCTG
* * * * *
22304 AACAAACTTATATGAACAAAAACATTTGTTTTAT
1 AATAAGCTTGTACGAACAAAAACAATTGTTTTAT
22338 GACAAAATTG
Statistics
Matches: 498, Mismatches: 60, Indels: 30
0.85 0.10 0.05
Matches are distributed among these distances:
177 1 0.00
178 40 0.08
179 69 0.14
180 350 0.70
181 38 0.08
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.38
Consensus pattern (180 bp):
AATAAGCTTGTACGAACAAAAACAATTGTTTTATAAGAAAACAAAGGTCATAATGATTTGAAATA
AATAATTGTTCAAATAGCCATAATTATTTGAACTTGTTCGGCAAACAAATTCATTTTTTAAATCT
CTCACTTATTAATTTTTGAAATATTAATAAATTAGAATTATGTTAATCTG
Found at i:22027 original size:16 final size:17
Alignment explanation
Indices: 22006--22038 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
21996 TAATGATTTG
22006 AAATAG-ATAATTGTTC
1 AAATAGCATAATTGTTC
22022 AAATAGTCATAATTGTT
1 AAATAG-CATAATTGTT
22039 TGCACTAGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.42, C:0.06, G:0.12, T:0.39
Consensus pattern (17 bp):
AAATAGCATAATTGTTC
Found at i:22731 original size:23 final size:23
Alignment explanation
Indices: 22682--22732 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
22672 ATGATAAGTT
* **
22682 ATTATCTATTTATTTAATTATGT
1 ATTATCTATTTAATTAATTATAA
22705 ATTATCTATTATAATTAA-TATAA
1 ATTATCTATT-TAATTAATTATAA
22728 ATTAT
1 ATTAT
22733 TAATAATTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.39, C:0.04, G:0.02, T:0.55
Consensus pattern (23 bp):
ATTATCTATTTAATTAATTATAA
Found at i:23059 original size:18 final size:19
Alignment explanation
Indices: 23028--23078 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
23018 TACTAATCTG
*
23028 TATATAATAGAATT-ATTA
1 TATATAATACAATTAATTA
*
23046 TATATAATTCAATTAATTA
1 TATATAATACAATTAATTA
23065 TGA-ATAATAACAAT
1 T-ATATAAT-ACAAT
23079 AATACTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 12 0.44
19 10 0.37
20 5 0.19
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (19 bp):
TATATAATACAATTAATTA
Found at i:23173 original size:29 final size:30
Alignment explanation
Indices: 23139--23199 Score: 88
Period size: 29 Copynumber: 2.0 Consensus size: 30
23129 TACAATATTA
*
23139 ATTAAATAAATACTTA-ATTTATTTAATAT
1 ATTAAATAAATACTTATAATTATTTAATAT
*
23168 ATTAAATAAATTCTTATTAATTATTTAATAT
1 ATTAAATAAATACTTA-TAATTATTTAATAT
23199 A
1 A
23200 ATAGAATATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 15 0.54
31 13 0.46
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (30 bp):
ATTAAATAAATACTTATAATTATTTAATAT
Found at i:23229 original size:13 final size:14
Alignment explanation
Indices: 23132--23231 Score: 50
Period size: 16 Copynumber: 7.1 Consensus size: 14
23122 TTTTAATTAC
*
23132 AATATTAATTAAATA
1 AATATTAATT-AATT
*
23147 AATACTTAATTTATTT
1 AATA-TTAA-TTAATT
*
23163 AATA-T-ATTAAAT
1 AATATTAATTAATT
*
23175 AA-ATT-CTT-ATT
1 AATATTAATTAATT
*
23186 AATTATTTAATATAATAG
1 AA-TA-TTAAT-TAAT-T
23204 AATATTAATTAATT
1 AATATTAATTAATT
23218 AATATT-ATTAATT
1 AATATTAATTAATT
23231 A
1 A
23232 TCTAAATATT
Statistics
Matches: 66, Mismatches: 9, Indels: 22
0.68 0.09 0.23
Matches are distributed among these distances:
11 5 0.08
12 9 0.14
13 10 0.15
14 9 0.14
15 9 0.14
16 16 0.24
17 6 0.09
18 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (14 bp):
AATATTAATTAATT
Found at i:23300 original size:12 final size:13
Alignment explanation
Indices: 23279--23370 Score: 51
Period size: 14 Copynumber: 6.9 Consensus size: 13
23269 TTCAATTGTT
*
23279 TAATAAAATTA-A
1 TAATATAATTATA
23291 TAATATAATTATA
1 TAATATAATTATA
*
23304 TAATATTTATTATA
1 TAATA-TAATTATA
* * *
23318 TTATAATAAATATT
1 TAAT-ATAATTATA
* * *
23332 TAATTTAAATATT
1 TAATATAATTATA
**
23345 TAATATATAAAATA
1 TAATATA-ATTATA
*
23359 TTATATAATTAT
1 TAATATAATTAT
23371 CCTAATAATA
Statistics
Matches: 62, Mismatches: 14, Indels: 7
0.75 0.17 0.08
Matches are distributed among these distances:
12 10 0.16
13 23 0.37
14 28 0.45
15 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAATATAATTATA
Found at i:23397 original size:21 final size:21
Alignment explanation
Indices: 23355--23413 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
23345 TAATATATAA
23355 AATATTATATAATTATCCTAAT
1 AATATTA-ATAATTATCCTAAT
* **
23377 AATATTAATCATTATGTTAAT
1 AATATTAATAATTATCCTAAT
23398 AATATTAAGTAATTAT
1 AATATTAA-TAATTAT
23414 TAATATTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 19 0.59
22 13 0.41
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (21 bp):
AATATTAATAATTATCCTAAT
Found at i:23419 original size:17 final size:16
Alignment explanation
Indices: 23396--23441 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 16
23386 CATTATGTTA
23396 ATAATATTAAGTAATT
1 ATAATATTAAGTAATT
*
23412 ATTAATATTAATTAAATT
1 A-TAATATTAAGT-AATT
23430 ATAA-ATTAAGTA
1 ATAATATTAAGTA
23442 CTTTAAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 1 0.04
16 7 0.27
17 13 0.50
18 5 0.19
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (16 bp):
ATAATATTAAGTAATT
Found at i:23553 original size:20 final size:19
Alignment explanation
Indices: 23502--23565 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
23492 TAATATTAGT
*
23502 TATT-TAATAATTATCAAT
1 TATTATAATAATTATCAAA
23520 TA-TATGAATAAATTATCCAAA
1 TATTAT-AAT-AATTAT-CAAA
*
23541 TATTATAATAATTATAATAA
1 TATTATAATAATTATCA-AA
23561 TATTA
1 TATTA
23566 GTTATAAAAC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.03
18 3 0.08
19 4 0.11
20 19 0.50
21 8 0.21
22 3 0.08
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (19 bp):
TATTATAATAATTATCAAA
Found at i:23712 original size:16 final size:18
Alignment explanation
Indices: 23676--23714 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
23666 TATTATAATA
*
23676 AATATTATAATTACTATT
1 AATATTATAATTACAATT
23694 AATATT-TAATT-CAATT
1 AATATTATAATTACAATT
23710 AATAT
1 AATAT
23715 ATTATAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 5 0.25
18 6 0.30
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (18 bp):
AATATTATAATTACAATT
Found at i:23924 original size:30 final size:31
Alignment explanation
Indices: 23861--23934 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
23851 CTTAATTATT
*
23861 ATTAATATT-TATT-TTTAATATTAAATATAA
1 ATTAAT-TTATATTATTTAATAATAAATATAA
23891 ATTAATTTATATTATTTAATAATATAA-AT-A
1 ATTAATTTATATTATTTAATAATA-AATATAA
23921 ATT-ATTATATATTA
1 ATTAATT-TATATTA
23935 ATCTATTTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 5 0.13
30 21 0.54
31 11 0.28
32 2 0.05
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
ATTAATTTATATTATTTAATAATAAATATAA
Found at i:23946 original size:19 final size:19
Alignment explanation
Indices: 23922--23975 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 19
23912 ATATAAATAA
23922 TTATTATATATTAATCTAT
1 TTATTATATATTAATCTAT
*
23941 TTATTATATAATAAT-TAT
1 TTATTATATATTAATCTAT
23959 TATATT-TAT-TT-ATCTAT
1 T-TATTATATATTAATCTAT
23976 CAATATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
16 2 0.06
17 4 0.13
18 7 0.23
19 18 0.58
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATATATTAATCTAT
Found at i:23992 original size:26 final size:28
Alignment explanation
Indices: 23952--24025 Score: 71
Period size: 27 Copynumber: 2.6 Consensus size: 28
23942 TATTATATAA
* *
23952 TAATTATTATATTTATTTAT-CTATCAA-
1 TAATAATTAT-TTTATTTATACTATAAAT
* *
23979 TATTAATTATTTTAATTAATACTATAAAT
1 TAATAATTATTTT-ATTTATACTATAAAT
*
24008 TAATAATTATTTAATTTA
1 TAATAATTATTTTATTTA
24026 ATGTTAAACT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
26 3 0.08
27 13 0.35
28 10 0.27
29 11 0.30
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (28 bp):
TAATAATTATTTTATTTATACTATAAAT
Found at i:24163 original size:46 final size:45
Alignment explanation
Indices: 24095--24191 Score: 110
Period size: 46 Copynumber: 2.1 Consensus size: 45
24085 TATTAAGAAT
* *
24095 AATT-AATTATTATATCAATTATT-TTAATAATTAATATAATAATTA
1 AATTAAATTATTATATCAATTATTATT-ATAATT-ATAAAATAATAA
*
24140 AATTAAATTATTATAT-ATTTTATTACTTATAATTATAAAATAATAA
1 AATTAAATTATTATATCA-ATTATTA-TTATAATTATAAAATAATAA
24186 AATTAA
1 AATTAA
24192 TATATCAATT
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
45 5 0.11
46 32 0.71
47 6 0.13
48 2 0.04
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (45 bp):
AATTAAATTATTATATCAATTATTATTATAATTATAAAATAATAA
Found at i:24211 original size:41 final size:41
Alignment explanation
Indices: 24046--24212 Score: 105
Period size: 46 Copynumber: 4.0 Consensus size: 41
24036 AACCTATTAT
* * * *
24046 TTATAATATAATAAATTTATATTTATATATT-TATATTATTA
1 TTATAAAATAATAAAATTA-ATATATATATTATATATTATAA
* * *
24087 TTA-AGAATAAT-TAATTATTATATCA-ATTAT-T-TTAATAA
1 TTATAAAATAATAAAATTAATATAT-ATATTATATATT-ATAA
* * *
24125 TTAATATAATAATTAAATTAAATTATTATATATTTTATTACTTATAA
1 TT-ATAAAATAATAAAATT-AA-TA-TATATATTATA-TA-TTATAA
24172 TTATAAAATAATAAAATTAATATATCA-ATTATATATTATAA
1 TTATAAAATAATAAAATTAATATAT-ATATTATATATTATAA
24213 GATTATAATA
Statistics
Matches: 97, Mismatches: 14, Indels: 30
0.69 0.10 0.21
Matches are distributed among these distances:
37 2 0.02
38 13 0.13
39 7 0.07
40 13 0.13
41 13 0.13
42 3 0.03
43 11 0.11
44 10 0.10
45 2 0.02
46 15 0.15
47 6 0.06
48 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.49
Consensus pattern (41 bp):
TTATAAAATAATAAAATTAATATATATATTATATATTATAA
Found at i:24260 original size:36 final size:36
Alignment explanation
Indices: 24220--24288 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
24210 TAAGATTATA
* *
24220 ATATTTATTTA-AATAATAAATAATTATAA-ATAAGGT
1 ATATTAATTTATAA-AAT-AATAACTATAATATAAGGT
24256 ATATTAATTTATAAAATAATAACTATAATATAA
1 ATATTAATTTATAAAATAATAACTATAATATAA
24289 TTATAAGTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 10 0.34
36 17 0.59
37 2 0.07
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (36 bp):
ATATTAATTTATAAAATAATAACTATAATATAAGGT
Found at i:25216 original size:34 final size:34
Alignment explanation
Indices: 25178--25264 Score: 90
Period size: 34 Copynumber: 2.6 Consensus size: 34
25168 AATGTTTATC
* *
25178 ATTATAATATATTTAATTTATTT-AATTATATA-AT
1 ATTATAATATA-TTAA-ATATTTAAATTAAATATAT
* *
25212 ATTATTATATATTAAATATTTAAATTAAATATTT
1 ATTATAATATATTAAATATTTAAATTAAATATAT
*
25246 ATTATAATATAAT-AATATT
1 ATTATAATATATTAAATATT
25265 ATATTATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
32 5 0.11
33 18 0.40
34 22 0.49
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
ATTATAATATATTAAATATTTAAATTAAATATAT
Found at i:25506 original size:13 final size:13
Alignment explanation
Indices: 25490--25537 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
25480 ATAATAAACA
25490 AATTTATTAAATT
1 AATTTATTAAATT
*
25503 AATTTA-TAAAAT
1 AATTTATTAAATT
*
25515 AATTGATATAAATT
1 AATTTAT-TAAATT
25529 AATATTATT
1 AAT-TTATT
25538 GACAATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
12 10 0.36
13 6 0.21
14 9 0.32
15 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (13 bp):
AATTTATTAAATT
Found at i:25595 original size:24 final size:24
Alignment explanation
Indices: 25568--25613 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
25558 CCTATTAAAG
*
25568 TATTTTT-ATTATTAGTATAATAAC
1 TATTTTTAATTAATAGT-TAATAAC
25592 TATTTTTAATTAATAGTTAATA
1 TATTTTTAATTAATAGTTAATA
25614 TTATATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TATTTTTAATTAATAGTTAATAAC
Found at i:25948 original size:17 final size:19
Alignment explanation
Indices: 25913--25948 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
25903 TTATTAAGTA
25913 AAATATTATTAATTCATAT
1 AAATATTATTAATTCATAT
25932 AAAT-TTATTAA-TCATAT
1 AAATATTATTAATTCATAT
25949 TATTGGAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
18 7 0.41
19 4 0.24
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (19 bp):
AAATATTATTAATTCATAT
Found at i:26507 original size:39 final size:37
Alignment explanation
Indices: 26459--26538 Score: 97
Period size: 39 Copynumber: 2.1 Consensus size: 37
26449 TCCATAGGTC
* ** *
26459 ATTACTAAATATATGTATAATATATATAATTTAATAAAT
1 ATTAATAAATATATAAATAATATA-ATAATATAAT-AAT
*
26498 ATTAATAAATATATAAATACTATAATAATATAATAAT
1 ATTAATAAATATATAAATAATATAATAATATAATAAT
26535 ATTA
1 ATTA
26539 TATATTATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
37 7 0.19
38 9 0.25
39 20 0.56
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.41
Consensus pattern (37 bp):
ATTAATAAATATATAAATAATATAATAATATAATAAT
Found at i:26524 original size:8 final size:8
Alignment explanation
Indices: 26475--26549 Score: 59
Period size: 8 Copynumber: 9.6 Consensus size: 8
26465 AAATATATGT
26475 ATAATATA
1 ATAATATA
*
26483 TATAATTTA
1 -ATAATATA
26492 ATAA-ATA
1 ATAATATA
*
26499 TTAATA-A
1 ATAATATA
26506 AT-ATATAA
1 ATAATAT-A
*
26514 ATACTATA
1 ATAATATA
26522 ATAATATA
1 ATAATATA
*
26530 ATAATATT
1 ATAATATA
*
26538 AT-ATATT
1 ATAATATA
26545 ATAAT
1 ATAAT
26550 TAGATTATTA
Statistics
Matches: 54, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
6 3 0.06
7 14 0.26
8 27 0.50
9 10 0.19
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (8 bp):
ATAATATA
Found at i:26548 original size:35 final size:36
Alignment explanation
Indices: 26466--26548 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 36
26456 GTCATTACTA
* *
26466 AATATATGTAT-AATATATATAATTTAATAAATATT
1 AATATATATATAAATATATATAATATAATAAATATT
*
26501 AATAAATATATAAATACTATAATAATATAAT-AATATT
1 AATATATATATAAATA-TAT-ATAATATAATAAATATT
26538 -ATATAT-TATAA
1 AATATATATATAA
26549 TTAGATTATT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
35 14 0.34
36 9 0.22
37 9 0.22
38 9 0.22
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.42
Consensus pattern (36 bp):
AATATATATATAAATATATATAATATAATAAATATT
Found at i:26549 original size:18 final size:18
Alignment explanation
Indices: 26467--26569 Score: 56
Period size: 18 Copynumber: 5.6 Consensus size: 18
26457 TCATTACTAA
26467 ATATATGTATAAT-ATA-T
1 ATATAT-TATAATAATATT
26484 ATA-ATT-TAATAAATATT
1 ATATATTATAAT-AATATT
* *
26501 A-ATA-AATATATAAATACT
1 ATATATTATA-AT-AATATT
*
26519 ATAATAATATAATAATATT
1 AT-ATATTATAATAATATT
26538 ATATATTATAATTAGATTATT
1 ATATATTATAA-TA-A-TATT
*
26559 ATTTATTATAA
1 ATATATTATAA
26570 CAATTATTTT
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
14 4 0.06
15 1 0.01
16 6 0.09
17 8 0.12
18 17 0.25
19 9 0.13
20 6 0.09
21 17 0.25
ACGTcount: A:0.51, C:0.01, G:0.02, T:0.46
Consensus pattern (18 bp):
ATATATTATAATAATATT
Found at i:27909 original size:16 final size:15
Alignment explanation
Indices: 27853--27915 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 15
27843 ATAAATAAGT
*
27853 TTATCTAATAT-TTAA
1 TTATATAATATATT-A
*
27868 TTATATAATTATAATA
1 TTATATAA-TATATTA
27884 TTACTATAATATATTA
1 TTA-TATAATATATTA
*
27900 TTATACTAATAAATTA
1 TTATA-TAATATATTA
27916 GGTAATTATT
Statistics
Matches: 40, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
15 9 0.22
16 25 0.62
17 6 0.15
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
TTATATAATATATTA
Found at i:28666 original size:17 final size:18
Alignment explanation
Indices: 28640--28698 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 18
28630 GAGTAAATTT
*
28640 ATTTAATTATCTAT-TAA
1 ATTTATTTATCTATATAA
*
28657 ATTTATTTATCTTTATAA
1 ATTTATTTATCTATATAA
*
28675 ATTATATTATAACTAGTATAA
1 ATT-TATT-TATCTA-TATAA
28696 ATT
1 ATT
28699 AATAGTTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
17 12 0.35
18 6 0.18
19 4 0.12
20 4 0.12
21 8 0.24
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.53
Consensus pattern (18 bp):
ATTTATTTATCTATATAA
Found at i:28980 original size:22 final size:21
Alignment explanation
Indices: 28938--28980 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
28928 ATTATAATAA
*
28938 TTAAATTAAATAAGTATAATT
1 TTAAATTAAATAAGTAAAATT
* *
28959 TTAATATTAAATTATTAAAATT
1 TTAA-ATTAAATAAGTAAAATT
28981 ATTTATCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (21 bp):
TTAAATTAAATAAGTAAAATT
Found at i:29001 original size:19 final size:19
Alignment explanation
Indices: 28973--29019 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
28963 TATTAAATTA
*
28973 TTAA-AATTATTTATCTAT
1 TTAATAATTATTAATCTAT
* *
28991 TTATTAATTATTAATTTAT
1 TTAATAATTATTAATCTAT
29010 TTAATAATTA
1 TTAATAATTA
29020 ATAACTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
18 3 0.12
19 21 0.88
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TTAATAATTATTAATCTAT
Found at i:29849 original size:21 final size:21
Alignment explanation
Indices: 29825--29892 Score: 56
Period size: 19 Copynumber: 3.4 Consensus size: 21
29815 TTCAATTGTT
29825 TAATAAAATTAATATATTATA
1 TAATAAAATTAATATATTATA
* *
29846 TAAT--ATTTATTATA-T-TA
1 TAATAAAATTAATATATTATA
*
29863 TAATAAATATTTA-ATATTATA
1 TAATAAA-ATTAATATATTATA
*
29884 TAATTAAAT
1 TAATAAAAT
29893 AAATTAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 11
0.68 0.11 0.21
Matches are distributed among these distances:
17 6 0.17
18 1 0.03
19 12 0.33
20 5 0.14
21 12 0.33
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TAATAAAATTAATATATTATA
Found at i:29861 original size:19 final size:18
Alignment explanation
Indices: 29836--29887 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 18
29826 AATAAAATTA
29836 ATATATTATATAATATTT
1 ATATATTATATAATATTT
29854 ATTATATTATAATAAATATTT
1 A-TATATTAT-AT-AATATTT
29875 A-ATATTATATAAT
1 ATATATTATATAAT
29888 TAAATAAATT
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 3 0.10
18 3 0.10
19 15 0.48
20 2 0.06
21 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
ATATATTATATAATATTT
Found at i:29964 original size:14 final size:14
Alignment explanation
Indices: 29928--29965 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
29918 CATTTACTTA
29928 TTAATTATTATAAT
1 TTAATTATTATAAT
*
29942 TTAACTATTAT-AT
1 TTAATTATTATAAT
29955 TTAATTTATTA
1 TTAA-TTATTA
29966 ACATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 6 0.29
14 15 0.71
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATTATTATAAT
Found at i:30428 original size:17 final size:17
Alignment explanation
Indices: 30408--30444 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
30398 ATTATAAGGA
30408 TTTAATT-TTAATATTAT
1 TTTAATTATTAAT-TTAT
30425 TTTAATTATTAATTTAT
1 TTTAATTATTAATTTAT
30442 TTT
1 TTT
30445 TAATATGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (17 bp):
TTTAATTATTAATTTAT
Found at i:31589 original size:29 final size:27
Alignment explanation
Indices: 31548--31603 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 27
31538 AATATTTGTT
**
31548 TATAAATCTAATAAGTAATTTATAATTAC
1 TATAAATAAAATAA-TAA-TTATAATTAC
*
31577 TATAAATAAAATAATAATTATATTTAC
1 TATAAATAAAATAATAATTATAATTAC
31604 AAATAATTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 9 0.38
28 3 0.12
29 12 0.50
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (27 bp):
TATAAATAAAATAATAATTATAATTAC
Found at i:31687 original size:14 final size:14
Alignment explanation
Indices: 31668--31735 Score: 61
Period size: 14 Copynumber: 5.0 Consensus size: 14
31658 AAATATAGTT
31668 TATAATATATATAA
1 TATAATATATATAA
* * *
31682 TTTAATAAATATTA
1 TATAATATATATAA
31696 TATAATATATA-AA
1 TATAATATATATAA
*
31709 CTATAATATA-ATAT
1 -TATAATATATATAA
*
31723 TATATTAT-TATAA
1 TATAATATATATAA
31736 ATTAGATTAT
Statistics
Matches: 42, Mismatches: 9, Indels: 7
0.72 0.16 0.12
Matches are distributed among these distances:
13 12 0.29
14 30 0.71
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (14 bp):
TATAATATATATAA
Found at i:31698 original size:5 final size:5
Alignment explanation
Indices: 31668--31727 Score: 56
Period size: 5 Copynumber: 12.6 Consensus size: 5
31658 AAATATAGTT
* *
31668 TATAA TAT-A TATAA TTTAA TA-AA TATTA TATAA TAT-A TA-AA CTATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA -TATAA
*
31715 TATAA TATTA TAT
1 TATAA TATAA TAT
31728 TATTATAAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
4 12 0.27
5 31 0.69
6 2 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (5 bp):
TATAA
Found at i:31699 original size:19 final size:18
Alignment explanation
Indices: 31671--31722 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
31661 TATAGTTTAT
*
31671 AATA-TATATAATTTAATA
1 AATATTATATAATAT-ATA
31689 AATATTATATAATATATA
1 AATATTATATAATATATA
*
31707 AACTATAATATAATAT
1 AA-TATTATATAATAT
31723 TATATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 9 0.30
19 21 0.70
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATTATATAATATATA
Found at i:31715 original size:28 final size:28
Alignment explanation
Indices: 31668--31737 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
31658 AAATATAGTT
*
31668 TATAATATATATAATTTAATA-AATATTA
1 TATAATATATA-AATATAATATAATATTA
31696 TATAATATATAAACTATAATATAATATTA
1 TATAATATATAAA-TATAATATAATATTA
*
31725 TATTAT-TATAAAT
1 TATAATATATAAAT
31738 TAGATTATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
27 3 0.08
28 23 0.61
29 12 0.32
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATATATAAATATAATATAATATTA
Found at i:31809 original size:23 final size:24
Alignment explanation
Indices: 31783--31836 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 24
31773 TTAATTATAT
31783 AAATAAAT-TAGATT-TAATATTTA
1 AAATAAATATAGATTATAATA-TTA
* *
31806 AAATTAATATATATTATAATATTA
1 AAATAAATATAGATTATAATATTA
31830 AATATAA
1 AA-ATAA
31837 CTAGTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
23 7 0.28
24 10 0.40
25 8 0.32
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
AAATAAATATAGATTATAATATTA
Found at i:31861 original size:25 final size:24
Alignment explanation
Indices: 31824--31884 Score: 59
Period size: 25 Copynumber: 2.5 Consensus size: 24
31814 ATATATTATA
31824 ATATTAAATATAACTAGTAAAAAT
1 ATATTAAATATAACTAGTAAAAAT
* * *
31848 ATATTTAATAATAATTATTAAAATAT
1 ATATTAAAT-ATAACTAGTAAAA-AT
* *
31874 TTGTTAAATAT
1 ATATTAAATAT
31885 TTTGAAAATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
24 8 0.28
25 13 0.45
26 8 0.28
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
ATATTAAATATAACTAGTAAAAAT
Done.