Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 128 of 198
Found at i:40864201 original size:44 final size:44
Alignment explanation
Indices: 40864151--40864244 Score: 134
Period size: 44 Copynumber: 2.1 Consensus size: 44
40864141 AATTCTTGCG
* **
40864151 TCCTTCTTGCCCAATTTCTTGAATTCCCAAATCTGTAAATCGCC
1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
* **
40864195 TCCTTCTTGCCGAATTTCTTGAAATCTGAAATCCCTAAATCGCC
1 TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
40864239 TCCTTC
1 TCCTTC
40864245 CTCCTTCCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.22, C:0.32, G:0.10, T:0.36
Consensus pattern (44 bp):
TCCTTCTTGCCCAATTTCTTGAAATCCCAAATCCCTAAATCGCC
Found at i:40865966 original size:35 final size:35
Alignment explanation
Indices: 40865879--40865959 Score: 144
Period size: 35 Copynumber: 2.3 Consensus size: 35
40865869 TAAAGTTATA
* *
40865879 TTTTAAATATTTTATTTTATTTTAATCACGAATTT
1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
40865914 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
1 TTTTAAATATTTTATTTTATTTGAATCACGAATAT
40865949 TTTTAAATATT
1 TTTTAAATATT
40865960 AAATTTTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (35 bp):
TTTTAAATATTTTATTTTATTTGAATCACGAATAT
Found at i:40866009 original size:18 final size:17
Alignment explanation
Indices: 40865978--40866033 Score: 78
Period size: 16 Copynumber: 3.3 Consensus size: 17
40865968 TTAAAGTTCA
40865978 AATTTCATAACTTACGT
1 AATTTCATAACTTACGT
* *
40865995 AATTTACATATCTTACAT
1 AATTT-CATAACTTACGT
40866013 AA-TTCATAACTTACGT
1 AATTTCATAACTTACGT
40866029 AATTT
1 AATTT
40866034 AAATTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 12 0.36
17 9 0.27
18 12 0.36
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (17 bp):
AATTTCATAACTTACGT
Found at i:40866053 original size:29 final size:33
Alignment explanation
Indices: 40865983--40866055 Score: 100
Period size: 34 Copynumber: 2.3 Consensus size: 33
40865973 GTTCAAATTT
*
40865983 CATAACTTACGTAATTTACATATCTTACATAATT
1 CATAACTTACGTAATTTACATATCTTA-ATAATA
40866017 CATAACTTACGTAATTTA-A-AT-TT-ATAATA
1 CATAACTTACGTAATTTACATATCTTAATAATA
40866046 CATAACTTAC
1 CATAACTTAC
40866056 ATAACTTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
29 15 0.39
31 2 0.05
32 2 0.05
33 1 0.03
34 18 0.47
ACGTcount: A:0.41, C:0.16, G:0.03, T:0.40
Consensus pattern (33 bp):
CATAACTTACGTAATTTACATATCTTAATAATA
Found at i:40866105 original size:19 final size:19
Alignment explanation
Indices: 40866083--40866120 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
40866073 ATATATAGTT
40866083 TTTATATATATATTTAAAA
1 TTTATATATATATTTAAAA
*
40866102 TTTATATATATTTTTAAAA
1 TTTATATATATATTTAAAA
40866121 ATTGATACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTATATATATATTTAAAA
Found at i:40866175 original size:23 final size:22
Alignment explanation
Indices: 40866125--40866325 Score: 65
Period size: 24 Copynumber: 9.3 Consensus size: 22
40866115 TTAAAAATTG
40866125 ATACATTACATAACTTACATAAC
1 ATACA-TACATAACTTACATAAC
*
40866148 CTACATACATAAGCTTACAT---
1 ATACATACATAA-CTTACATAAC
*
40866168 ATA-ATACATAACTTATATAAC
1 ATACATACATAACTTACATAAC
* * * *
40866189 TTAAATTTAGCA-ATCATATCATAAC
1 ATACA--TA-CATAACTTA-CATAAC
* *
40866214 TTACATACATAA-TTA-GT-A-
1 ATACATACATAACTTACATAAC
* *
40866232 AT-CATATCACAATTTACATAACC
1 ATACATA-CATAACTTACATAA-C
*
40866255 A-ACATA-ATGACTTACATAATAAC
1 ATACATACATAACTTAC---ATAAC
* *
40866278 CTACATA-ATAACTTACATAATA
1 ATACATACATAACTTACATAA-C
40866300 ATACATA-ATAA--TACATAAC
1 ATACATACATAACTTACATAAC
40866319 ATACATA
1 ATACATA
40866326 AATTAAATAA
Statistics
Matches: 134, Mismatches: 22, Indels: 48
0.66 0.11 0.24
Matches are distributed among these distances:
17 4 0.03
18 11 0.08
19 19 0.14
20 11 0.08
21 13 0.10
22 22 0.16
23 20 0.15
24 23 0.17
25 11 0.08
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.31
Consensus pattern (22 bp):
ATACATACATAACTTACATAAC
Found at i:40866212 original size:34 final size:31
Alignment explanation
Indices: 40866142--40866251 Score: 89
Period size: 31 Copynumber: 3.4 Consensus size: 31
40866132 ACATAACTTA
* *
40866142 CATAACCTACATACATAAGCTTA-CATATAATA-
1 CATAACTTACATACATAA--TTAGCA-ATCATAT
* *
40866174 CATAACTTATATAACTTAAATTTAGCAATCATAT
1 CATAACTTACAT-ACAT-AA-TTAGCAATCATAT
*
40866208 CATAACTTACATACATAATTAGTAATCATAT
1 CATAACTTACATACATAATTAGCAATCATAT
* *
40866239 CACAATTTACATA
1 CATAACTTACATA
40866252 ACCAACATAA
Statistics
Matches: 64, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
31 23 0.36
32 12 0.19
33 14 0.22
34 15 0.23
ACGTcount: A:0.45, C:0.18, G:0.03, T:0.34
Consensus pattern (31 bp):
CATAACTTACATACATAATTAGCAATCATAT
Found at i:40866273 original size:12 final size:12
Alignment explanation
Indices: 40866256--40866310 Score: 78
Period size: 12 Copynumber: 4.8 Consensus size: 12
40866246 TACATAACCA
*
40866256 ACATAATGACTT
1 ACATAATAACTT
*
40866268 ACATAATAACCT
1 ACATAATAACTT
40866280 ACATAATAACTT
1 ACATAATAACTT
40866292 ACATAATAA--T
1 ACATAATAACTT
40866302 ACATAATAA
1 ACATAATAA
40866311 TACATAACAT
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
10 10 0.25
12 30 0.75
ACGTcount: A:0.53, C:0.16, G:0.02, T:0.29
Consensus pattern (12 bp):
ACATAATAACTT
Found at i:40866283 original size:24 final size:24
Alignment explanation
Indices: 40866249--40866317 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 24
40866239 CACAATTTAC
* *
40866249 ATAACCAACATAATGACTTACATA
1 ATAACCTACATAATAACTTACATA
40866273 ATAACCTACATAATAACTTACATA
1 ATAACCTACATAATAACTTACATA
40866297 ATAA--TACATAATAA--TACATA
1 ATAACCTACATAATAACTTACATA
40866317 A
1 A
40866318 CATACATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.16
22 10 0.23
24 26 0.60
ACGTcount: A:0.54, C:0.17, G:0.01, T:0.28
Consensus pattern (24 bp):
ATAACCTACATAATAACTTACATA
Found at i:40866306 original size:10 final size:10
Alignment explanation
Indices: 40866267--40866326 Score: 68
Period size: 12 Copynumber: 5.7 Consensus size: 10
40866257 CATAATGACT
40866267 TACATAATAA
1 TACATAATAA
40866277 CCTACATAATAA
1 --TACATAATAA
40866289 CTTACATAATAA
1 --TACATAATAA
40866301 TACATAATAA
1 TACATAATAA
*
40866311 TACATAA-CA
1 TACATAATAA
40866320 TACATAA
1 TACATAA
40866327 ATTAAATAAG
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
9 8 0.17
10 17 0.37
12 21 0.46
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.28
Consensus pattern (10 bp):
TACATAATAA
Found at i:40866310 original size:34 final size:34
Alignment explanation
Indices: 40866267--40866411 Score: 91
Period size: 34 Copynumber: 4.2 Consensus size: 34
40866257 CATAATGACT
40866267 TACATAATAACCTACATAATAACTTACATAATAA
1 TACATAATAACCTACATAATAACTTACATAATAA
* * *
40866301 TACATAATAA--TACATAACATACATAAATTAAATAA
1 TACATAATAACCTACATAATA-ACTTACA-T-AATAA
** * * * *
40866336 GTTACATAATACACAAAAACAAAAACTTACATAA-AT
1 --TACATAATA-ACCTACATAATAACTTACATAATAA
* **
40866372 TACATAATATCCTACATCCCT-ACTTACATAATAA
1 TACATAATAACCTACAT-AATAACTTACATAATAA
40866406 TACATA
1 TACATA
40866412 CCGTACATAA
Statistics
Matches: 82, Mismatches: 19, Indels: 20
0.68 0.16 0.17
Matches are distributed among these distances:
32 8 0.10
33 18 0.22
34 27 0.33
35 5 0.06
36 1 0.01
37 11 0.13
38 2 0.02
39 5 0.06
40 5 0.06
ACGTcount: A:0.53, C:0.18, G:0.01, T:0.28
Consensus pattern (34 bp):
TACATAATAACCTACATAATAACTTACATAATAA
Found at i:40866376 original size:9 final size:9
Alignment explanation
Indices: 40866285--40866378 Score: 52
Period size: 9 Copynumber: 10.4 Consensus size: 9
40866275 AACCTACATA
*
40866285 ATAACTTAC
1 ATAAATTAC
*
40866294 ATAATAATAC
1 ATAA-ATTAC
*
40866304 ATAATAATAC
1 ATAA-ATTAC
40866314 ATAACA-TAC
1 ATAA-ATTAC
*
40866323 ATAAATTAA
1 ATAAATTAC
*
40866332 ATAAGTTAC
1 ATAAATTAC
40866341 AT-AA-TAC
1 ATAAATTAC
* *
40866348 ACAAA-AAC
1 ATAAATTAC
*
40866356 AAAAACTTAC
1 ATAAA-TTAC
40866366 ATAAATTAC
1 ATAAATTAC
40866375 ATAA
1 ATAA
40866379 TATCCTACAT
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
7 4 0.06
8 10 0.15
9 30 0.44
10 24 0.35
ACGTcount: A:0.59, C:0.14, G:0.01, T:0.27
Consensus pattern (9 bp):
ATAAATTAC
Found at i:40866411 original size:95 final size:95
Alignment explanation
Indices: 40866301--40866707 Score: 595
Period size: 95 Copynumber: 4.5 Consensus size: 95
40866291 TACATAATAA
* *
40866301 TACATAATAATACATAACATACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
*
40866366 ATAAATTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
*
40866396 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATGCACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
40866461 ATAACTTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
*
40866491 TACATAATAATACATACCGTACATAAATTAAATAAGTAACATAATACACAAAAAC----A---A-
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
40866548 A-AACTTACATAATATCCTACATCCCTACT
66 ATAACTTACATAATATCCTACATCCCTACT
*
40866577 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
40866642 ATAACTTACAT-A-A---T--A-----ACT
66 ATAACTTACATAATATCCTACATCCCTACT
* *
40866660 TACATAATAATGCATACCCTACATAAATTAAATAAGTTACATAATACA
1 TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACA
40866708 TTGAAGAGTT
Statistics
Matches: 292, Mismatches: 11, Indels: 30
0.88 0.03 0.09
Matches are distributed among these distances:
83 48 0.16
86 81 0.28
87 1 0.00
88 2 0.01
90 2 0.01
91 1 0.00
93 2 0.01
94 2 0.01
95 153 0.52
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (95 bp):
TACATAATAATACATACCGTACATAAATTAAATAAGTTACATAATACACAAAAACAAAAACTTAC
ATAACTTACATAATATCCTACATCCCTACT
Found at i:40866419 original size:52 final size:52
Alignment explanation
Indices: 40866363--40866525 Score: 164
Period size: 52 Copynumber: 3.3 Consensus size: 52
40866353 AACAAAAACT
*
40866363 TACATAAATTACATAATATCCTACATCCCTACTTACATAATAATACATACCG
1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG
* ** * * * * *
40866415 TACATAAATTAAATAA-GT--TACAT-AATGC--ACA-AA-AACA-AAAACT
1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG
* *
40866458 TACATAACTTACATAATATCCTACATCCCTACTTACATAATAATACATACCG
1 TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG
40866510 TACATAAATTAAATAA
1 TACATAAATTAAATAA
40866526 GTAACATAAT
Statistics
Matches: 81, Mismatches: 21, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
43 17 0.21
44 4 0.05
45 2 0.02
46 8 0.10
47 2 0.02
48 2 0.02
49 8 0.10
50 2 0.02
51 4 0.05
52 32 0.40
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (52 bp):
TACATAAATTAAATAATATCCTACATCCCTACTTACATAATAATACATACCG
Found at i:40866506 original size:181 final size:178
Alignment explanation
Indices: 40866285--40866707 Score: 572
Period size: 181 Copynumber: 2.4 Consensus size: 178
40866275 AACCTACATA
40866285 ATAACTTACATAATAA--TACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC
1 ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC
40866348 ACA-AA-A-ACAAAAACTTACATAAA-TTACATAATATCCTACATCCCTACTTACATAATAATAC
66 ACATAATACACAAAAAC--A-A-AAACTTACATAATATCCTACATCCCTACTTACATAATAATAC
**
40866409 ATACCGTACATAAATTAAATAAGTTACATAATGCACAAAAACAAAAACTTAC
127 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
* ** * * *** * * *
40866461 ATAACTTACATAATATCCTACATCCCTACTTACATAATAATACATACCGTACATAAATTAAATAA
1 ATAACTTACATAATAACCTACAT-AATA-ATACATAA-CATACATAAATTAAATAAGTTACATAA
40866526 GTA-ACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATAC
63 -TACACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATAC
40866590 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
127 ATACCGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
* * * *
40866642 ATAACTTACATAATAACTTACATAATAATGCATACCCTACATAAATTAAATAAGTTACATAATAC
1 ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC
40866707 A
66 A
40866708 TTGAAGAGTT
Statistics
Matches: 208, Mismatches: 28, Indels: 20
0.81 0.11 0.08
Matches are distributed among these distances:
176 15 0.07
177 2 0.01
178 25 0.12
179 7 0.03
180 12 0.06
181 133 0.64
182 5 0.02
183 1 0.00
184 8 0.04
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (178 bp):
ATAACTTACATAATAACCTACATAATAATACATAACATACATAAATTAAATAAGTTACATAATAC
ACATAATACACAAAAACAAAAACTTACATAATATCCTACATCCCTACTTACATAATAATACATAC
CGTACATAAATTAAATAAGTTACATAATAAACAAAAACAAAAACTTAC
Found at i:40866618 original size:37 final size:37
Alignment explanation
Indices: 40866576--40866705 Score: 109
Period size: 37 Copynumber: 3.3 Consensus size: 37
40866566 ACATCCCTAC
*
40866576 TTACATAATAATACATACCGTACATAAATTAAATAAG
1 TTACATAATAATACATACCCTACATAAATTAAATAAG
* * * *
40866613 TTACATAATAA-ACAAAAACAAAAACTTACATAACTTACATAATAAC
1 TTACATAATAATAC--ATAC-----CCTACATAAATT--A-AATAAG
*
40866659 TTACATAATAATGCATACCCTACATAAATTAAATAAG
1 TTACATAATAATACATACCCTACATAAATTAAATAAG
40866696 TTACATAATA
1 TTACATAATA
40866706 CATTGAAGAG
Statistics
Matches: 73, Mismatches: 9, Indels: 22
0.70 0.09 0.21
Matches are distributed among these distances:
36 2 0.03
37 26 0.36
38 4 0.05
40 10 0.14
43 10 0.14
45 4 0.05
46 16 0.22
47 1 0.01
ACGTcount: A:0.53, C:0.15, G:0.03, T:0.28
Consensus pattern (37 bp):
TTACATAATAATACATACCCTACATAAATTAAATAAG
Found at i:40866659 original size:12 final size:12
Alignment explanation
Indices: 40866642--40866669 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
40866632 AAAAACTTAC
40866642 ATAACTTACATA
1 ATAACTTACATA
40866654 ATAACTTACATA
1 ATAACTTACATA
40866666 ATAA
1 ATAA
40866670 TGCATACCCT
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:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (12 bp):
ATAACTTACATA
Found at i:40870610 original size:21 final size:21
Alignment explanation
Indices: 40870584--40870652 Score: 93
Period size: 21 Copynumber: 3.3 Consensus size: 21
40870574 CAACAACTTA
** *
40870584 AAGCAGAGGCGGCAGCGAGGG
1 AAGCAGAGGCCACAGCGAGAG
* *
40870605 AAGCAGATGCTACAGCGAGAG
1 AAGCAGAGGCCACAGCGAGAG
40870626 AAGCAGAGGCCACAGCGAGAG
1 AAGCAGAGGCCACAGCGAGAG
40870647 AAGCAG
1 AAGCAG
40870653 CGATAGAAGC
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.36, C:0.20, G:0.41, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCCACAGCGAGAG
Found at i:40871192 original size:43 final size:42
Alignment explanation
Indices: 40871091--40871231 Score: 144
Period size: 42 Copynumber: 3.3 Consensus size: 42
40871081 TTTGTGAAAT
* * * *
40871091 AAGCGCCGCTAAATAACACTACTATTAGCGGCGTTTTTGAAC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTCAAC
* *
40871133 AAGCGCCGCTATAGAACATTACTTTTAGCGGCGTTTTCTC-CC
1 AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTT-TCAAC
* *
40871175 AAAGCGCCGCTAAAGAACATGA-TCTTTAGCGGCGTTTTTTC-AT
1 -AAGCGCCGCTAAAGAACATTACT-TTTAGCGGCG-TTTTTCAAC
*
40871218 AAGCGCCGCAAAAG
1 AAGCGCCGCTAAAG
40871232 TTAGCGACGT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
42 48 0.57
43 32 0.38
44 4 0.05
ACGTcount: A:0.28, C:0.25, G:0.21, T:0.26
Consensus pattern (42 bp):
AAGCGCCGCTAAAGAACATTACTTTTAGCGGCGTTTTTCAAC
Found at i:40871378 original size:16 final size:16
Alignment explanation
Indices: 40871343--40871385 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
40871333 TGGTGTAGTG
* **
40871343 TCTATTCTATTACAGT
1 TCTATTCCATTACAAC
40871359 TCTATTCCATTACAAC
1 TCTATTCCATTACAAC
40871375 TCTATTCCATT
1 TCTATTCCATT
40871386 CCTCCAACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.26, G:0.02, T:0.47
Consensus pattern (16 bp):
TCTATTCCATTACAAC
Found at i:40875870 original size:13 final size:13
Alignment explanation
Indices: 40875852--40875882 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
40875842 GGCTCAACCC
40875852 ATATATATTAAAT
1 ATATATATTAAAT
*
40875865 ATATATATTTAAT
1 ATATATATTAAAT
40875878 ATATA
1 ATATA
40875883 ATTCGGGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATTAAAT
Found at i:40877058 original size:19 final size:19
Alignment explanation
Indices: 40876999--40877059 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
40876989 ATTTTCGAGG
* *
40876999 ATATACAATCTTA-AATAT
1 ATATGCAATCTTAGAAGAT
*
40877017 GATATGCATTCTTAGATATGAT
1 -ATATGCAATCTTAGA-A-GAT
40877039 ATATGCAATCTTAGAAGAT
1 ATATGCAATCTTAGAAGAT
40877058 AT
1 AT
40877060 GATTTTGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
19 16 0.46
20 2 0.06
21 15 0.43
22 2 0.06
ACGTcount: A:0.41, C:0.10, G:0.11, T:0.38
Consensus pattern (19 bp):
ATATGCAATCTTAGAAGAT
Found at i:40878119 original size:25 final size:23
Alignment explanation
Indices: 40878052--40878131 Score: 74
Period size: 21 Copynumber: 3.3 Consensus size: 23
40878042 AATCATTATT
*
40878052 TTTTATGTATATATGT-AA-TTA
1 TTTTATATATATATGTAAATTTA
40878073 TTTTATATATATATGTACAAATTTA
1 TTTTATATATATATGT--AAATTTA
* *
40878098 TTATATATATGTATATGTAAATATA
1 TT-T-TATATATATATGTAAATTTA
40878123 TTGTTATAT
1 TT-TTATAT
40878132 TTTTTAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
21 15 0.31
24 7 0.14
25 14 0.29
26 1 0.02
27 12 0.24
ACGTcount: A:0.38, C:0.01, G:0.07, T:0.54
Consensus pattern (23 bp):
TTTTATATATATATGTAAATTTA
Found at i:40879660 original size:29 final size:30
Alignment explanation
Indices: 40879601--40879658 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40879591 TCCGAGCCTT
*
40879601 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
40879631 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
40879659 AGAGTCAAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:40879888 original size:13 final size:13
Alignment explanation
Indices: 40879870--40879901 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
40879860 TTTCCAGCAA
40879870 TTATGAATTTATT
1 TTATGAATTTATT
40879883 TTATGAATTTATT
1 TTATGAATTTATT
*
40879896 TGATGA
1 TTATGA
40879902 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:40880107 original size:50 final size:50
Alignment explanation
Indices: 40879996--40880244 Score: 318
Period size: 50 Copynumber: 4.8 Consensus size: 50
40879986 ATTTGGGTAA
*
40879996 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-CC----GA-CATG
* *
40880052 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * *
40880102 AGAGGTCCCATGTAAGACCATGTTTGGGTCATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
* * * *
40880152 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
** *
40880202 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
40880245 TGTTATTATC
Statistics
Matches: 173, Mismatches: 19, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
50 95 0.55
51 36 0.21
55 2 0.01
56 40 0.23
ACGTcount: A:0.27, C:0.22, G:0.29, T:0.22
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGACATG
Found at i:40889293 original size:2 final size:2
Alignment explanation
Indices: 40889286--40889325 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
40889276 CCCAAGCTGA
40889286 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40889326 GTCAGTTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40898123 original size:5 final size:6
Alignment explanation
Indices: 40898106--40898130 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
40898096 GCTATTGGCC
40898106 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
40898131 GATTCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:40900607 original size:14 final size:13
Alignment explanation
Indices: 40900588--40900621 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
40900578 TATATAATTT
40900588 TATATTAATATTAA
1 TATATTAATA-TAA
40900602 TATATTAATATAA
1 TATATTAATATAA
40900615 -ATATTAA
1 TATATTAA
40900622 AATATTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 7 0.35
13 3 0.15
14 10 0.50
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
TATATTAATATAA
Found at i:40900617 original size:20 final size:20
Alignment explanation
Indices: 40900589--40900628 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
40900579 ATATAATTTT
* *
40900589 ATATTAATATTAATATATTA
1 ATATAAATATTAAAATATTA
40900609 ATATAAATATTAAAATATTA
1 ATATAAATATTAAAATATTA
40900629 TTAAAATGTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATATAAATATTAAAATATTA
Found at i:40900649 original size:38 final size:44
Alignment explanation
Indices: 40900606--40900710 Score: 116
Period size: 45 Copynumber: 2.5 Consensus size: 44
40900596 TATTAATATA
*
40900606 TTAATA-TAAATATTAAAATAT-TAT-TA-A-AA-TGTATACTT
1 TTAATATTAAATATTAAAATATATATCTATATAATTGTATAATT
*
40900644 TTAATATTAATATAATAAAATATAATATCTATATAATTGTATAATT
1 TTAATATTAA-ATATTAAAATAT-ATATCTATATAATTGTATAATT
40900690 TT-ATATTAAATATATAAAATA
1 TTAATATTAAATAT-TAAAATA
40900711 ATAAAATATT
Statistics
Matches: 55, Mismatches: 3, Indels: 11
0.80 0.04 0.16
Matches are distributed among these distances:
38 6 0.11
39 3 0.05
40 11 0.20
42 3 0.05
43 2 0.04
44 4 0.07
45 16 0.29
46 10 0.18
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (44 bp):
TTAATATTAAATATTAAAATATATATCTATATAATTGTATAATT
Found at i:40900774 original size:20 final size:20
Alignment explanation
Indices: 40900749--40900790 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
40900739 AATAATAAAA
40900749 TATATATTTT-TATTAACATT
1 TATATATTTTATATTAA-ATT
40900769 TATATATTTTATATTAAATT
1 TATATATTTTATATTAAATT
40900789 TA
1 TA
40900791 AATAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 15 0.71
21 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATATTTTATATTAAATT
Found at i:40912303 original size:18 final size:17
Alignment explanation
Indices: 40912280--40912313 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
40912270 ACCCGACCCA
40912280 TTTTTAAATTAAAATTAT
1 TTTTTAAA-TAAAATTAT
40912298 TTTTTAAATAAAATTA
1 TTTTTAAATAAAATTA
40912314 AAACTAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTAAATAAAATTAT
Found at i:40912347 original size:16 final size:16
Alignment explanation
Indices: 40912312--40912350 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
40912302 TAAATAAAAT
* * *
40912312 TAAAACTAATTGTTAT
1 TAAAATTAATTGGTAG
40912328 TAAAATTAATTGGTAG
1 TAAAATTAATTGGTAG
40912344 TAAAATT
1 TAAAATT
40912351 TTGAAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.46, C:0.03, G:0.10, T:0.41
Consensus pattern (16 bp):
TAAAATTAATTGGTAG
Found at i:40912436 original size:9 final size:9
Alignment explanation
Indices: 40912424--40912466 Score: 72
Period size: 9 Copynumber: 5.0 Consensus size: 9
40912414 TTTATCAAAT
40912424 TATTAATTG
1 TATTAATTG
40912433 TATTAATTG
1 TATTAATTG
40912442 --TTAATTG
1 TATTAATTG
40912449 TATTAATTG
1 TATTAATTG
40912458 TATTAATTG
1 TATTAATTG
40912467 CTAATTTGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.22
9 25 0.78
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.56
Consensus pattern (9 bp):
TATTAATTG
Found at i:40912440 original size:16 final size:16
Alignment explanation
Indices: 40912421--40912466 Score: 65
Period size: 16 Copynumber: 2.8 Consensus size: 16
40912411 AAATTTATCA
40912421 AATTATTAATTGTATT
1 AATTATTAATTGTATT
*
40912437 AATTGTTAATTGTATT
1 AATTATTAATTGTATT
40912453 AATTGTATTAATTG
1 AA-T-TATTAATTG
40912467 CTAATTTGCT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 17 0.65
17 1 0.04
18 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.11, T:0.54
Consensus pattern (16 bp):
AATTATTAATTGTATT
Found at i:40912452 original size:25 final size:25
Alignment explanation
Indices: 40912424--40912472 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40912414 TTTATCAAAT
*
40912424 TATTAATTGTATTAATTGTTAATTG
1 TATTAATTGTATTAATTGCTAATTG
40912449 TATTAATTGTATTAATTGCTAATT
1 TATTAATTGTATTAATTGCTAATT
40912473 TGCTATAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (25 bp):
TATTAATTGTATTAATTGCTAATTG
Found at i:40912472 original size:16 final size:16
Alignment explanation
Indices: 40912421--40912458 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
40912411 AAATTTATCA
*
40912421 AATTATTAATTGTATT
1 AATTGTTAATTGTATT
40912437 AATTGTTAATTGTATT
1 AATTGTTAATTGTATT
40912453 AATTGT
1 AATTGT
40912459 ATTAATTGCT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (16 bp):
AATTGTTAATTGTATT
Found at i:40916061 original size:14 final size:14
Alignment explanation
Indices: 40916044--40916071 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40916034 CTCACATTTC
40916044 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
40916058 TTTTCTTTTCTCCA
1 TTTTCTTTTCTCCA
40916072 GATTTCTGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTTCTTTTCTCCA
Found at i:40916062 original size:19 final size:18
Alignment explanation
Indices: 40916024--40916068 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
40916014 TACGATACGC
40916024 TTCTTTTC-TTCTCACAT
1 TTCTTTTCTTTCTCACAT
40916041 TTCTTTTCTTTTCTC-CATT
1 TTCTTTTC-TTTCTCACA-T
40916060 TTCTTTTCT
1 TTCTTTTCT
40916069 CCAGATTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.32
18 3 0.12
19 14 0.56
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.67
Consensus pattern (18 bp):
TTCTTTTCTTTCTCACAT
Found at i:40916141 original size:6 final size:6
Alignment explanation
Indices: 40916132--40916173 Score: 59
Period size: 6 Copynumber: 7.2 Consensus size: 6
40916122 GTAAAATCGA
* *
40916132 TTTTGA TTTTG- TTTTGC TTTTGC TTTTGC TTTTGC TTGTGC T
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC T
40916174 CAAATTTGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.02, C:0.12, G:0.19, T:0.67
Consensus pattern (6 bp):
TTTTGC
Found at i:40919011 original size:15 final size:15
Alignment explanation
Indices: 40918987--40919027 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
40918977 AAGCTCTGTG
40918987 ATAT-TTTAATTATA
1 ATATATTTAATTATA
*
40919001 ATATATTTAATAATA
1 ATATATTTAATTATA
40919016 AT-TATGTTAATT
1 ATATAT-TTAATT
40919028 TATATTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
14 7 0.30
15 16 0.70
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATATTTAATTATA
Found at i:40919131 original size:15 final size:15
Alignment explanation
Indices: 40919096--40919147 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
40919086 TTAAGAATTT
*
40919096 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40919110 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40919124 TATTTAATAATAAT-
1 TATTTAATTATAATA
40919138 TATGTTAATT
1 TAT-TTAATT
40919148 TATATTTTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 8 0.25
14 8 0.25
15 16 0.50
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40919200 original size:120 final size:120
Alignment explanation
Indices: 40918987--40919381 Score: 745
Period size: 120 Copynumber: 3.3 Consensus size: 120
40918977 AAGCTCTGTG
40918987 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
*
40919052 TGATTTGAGTAATTTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
40919107 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
* *
40919172 TGATTTGAGTAAATTCATGTAAGAATATTGGTTATTAAGAATTTTATTAAATTAT
66 TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
40919227 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
1 ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
*
40919292 TGATTTGAGTAATATTCATATAAGAATATTAATTATTAAGAATTTTATTAAATTAT
66 TGATTTGAGTAA-ATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
40919348 ATATTTTAATTATAATATATTTAATAATAATTAT
1 ATATTTTAATTATAATATATTTAATAATAATTAT
40919382 ATTTAAATAT
Statistics
Matches: 268, Mismatches: 6, Indels: 1
0.97 0.02 0.00
Matches are distributed among these distances:
120 194 0.72
121 74 0.28
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.51
Consensus pattern (120 bp):
ATATTTTAATTATAATATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATATATTA
TGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAATTAT
Found at i:40919251 original size:15 final size:15
Alignment explanation
Indices: 40919216--40919387 Score: 60
Period size: 15 Copynumber: 11.5 Consensus size: 15
40919206 TTAAGAATTT
*
40919216 TATTAAATTAT-ATA
1 TATTTAATTATAATA
40919230 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
40919244 TATTTAATAATAAT-
1 TATTTAATTATAATA
40919258 TATGTTAATT-T-ATA
1 TAT-TTAATTATAATA
* *
40919272 T-TTTATAGTATCATA
1 TATTTA-ATTATAATA
* *
40919287 TATTATGATT-TGAGTA
1 TATT-TAATTAT-AATA
* *
40919303 -ATATTCA-TATAAGA
1 TAT-TTAATTATAATA
*
40919317 -ATATTAATTATTAAGA
1 TAT-TTAATTA-TAATA
* *
40919333 -ATTTTATTAAATTATA
1 TATTTAATT--ATAATA
40919349 TATTTTAATTATAATA
1 TA-TTTAATTATAATA
*
40919365 TATTTAATAATAATTA
1 TATTTAATTATAA-TA
40919381 TATTTAA
1 TATTTAA
40919388 ATATGATTAA
Statistics
Matches: 121, Mismatches: 18, Indels: 36
0.69 0.10 0.21
Matches are distributed among these distances:
12 3 0.02
13 13 0.11
14 20 0.17
15 43 0.36
16 33 0.27
17 3 0.02
18 6 0.05
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:40919396 original size:16 final size:16
Alignment explanation
Indices: 40919347--40919387 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
40919337 TATTAAATTA
*
40919347 TATATTTTAATTATAA-
1 TATA-TTTAATAATAAT
40919363 TATATTTAATAATAAT
1 TATATTTAATAATAAT
40919379 TATATTTAA
1 TATATTTAA
40919388 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.43
16 13 0.57
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TATATTTAATAATAAT
Found at i:40919558 original size:39 final size:40
Alignment explanation
Indices: 40919515--40919619 Score: 113
Period size: 44 Copynumber: 2.5 Consensus size: 40
40919505 TTCAATTATG
40919515 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
* *** *
40919554 CTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
40919599 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
40919620 ACACCTCTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
39 15 0.28
40 5 0.09
44 17 0.31
45 17 0.31
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.34
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:40919613 original size:45 final size:44
Alignment explanation
Indices: 40919513--40919622 Score: 131
Period size: 45 Copynumber: 2.6 Consensus size: 44
40919503 TTTTCAATTA
40919513 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* * ***
40919552 TACTATTACGCCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
40919597 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
40919623 CCTCTAATCC
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
39 16 0.28
40 1 0.02
44 16 0.28
45 25 0.43
ACGTcount: A:0.32, C:0.29, G:0.05, T:0.34
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:40919622 original size:16 final size:16
Alignment explanation
Indices: 40919601--40919638 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
40919591 TTGATTTGCT
*
40919601 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
40919617 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
40919633 AATACA
1 ATTACA
40919639 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:40919777 original size:21 final size:21
Alignment explanation
Indices: 40919751--40919794 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
40919741 GAATCTGTTC
40919751 TATATAATAATATAATAATATAT
1 TATATAAT-AT-TAATAATATAT
* *
40919774 TATATATTATTTATAATATAT
1 TATATAATATTAATAATATAT
40919795 ACAACAATCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATATAATATTAATAATATAT
Found at i:40920238 original size:23 final size:23
Alignment explanation
Indices: 40920207--40920285 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 23
40920197 ATCAGTCTTT
40920207 TAAATTAATAACTTTAATTTGCTA
1 TAAA-TAATAACTTTAATTTGCTA
**
40920231 TAAATAATATA-TAGAATTT--TA
1 TAAATAATA-ACTTTAATTTGCTA
*
40920252 -AATTAATAACTCTTTAATTTGCTA
1 TAAATAATAA--CTTTAATTTGCTA
40920276 TAAATAATAA
1 TAAATAATAA
40920286 AAATTGTACT
Statistics
Matches: 42, Mismatches: 6, Indels: 13
0.69 0.10 0.21
Matches are distributed among these distances:
19 1 0.02
20 7 0.17
21 2 0.05
22 6 0.14
23 11 0.26
24 7 0.17
25 8 0.19
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (23 bp):
TAAATAATAACTTTAATTTGCTA
Found at i:40921288 original size:2 final size:2
Alignment explanation
Indices: 40921281--40921312 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
40921271 ATGGAAGGGA
40921281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
40921313 TTCAACAACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40922787 original size:31 final size:33
Alignment explanation
Indices: 40922752--40922821 Score: 90
Period size: 31 Copynumber: 2.1 Consensus size: 33
40922742 TTTTCTAAAT
*
40922752 GGGCCTAAATTTTTGCCC-AA-TCCCATATTTC
1 GGGCCTAAATTTTTACCCGAACTCCCATATTTC
*
40922783 GGGCCTATATTTTTACCCGAACCCTCCCATATTTC
1 GGGCCTAAATTTTTACCCGAA--CTCCCATATTTC
40922818 GGGC
1 GGGC
40922822 GGGCCGTCGG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 16 0.48
32 2 0.06
35 15 0.45
ACGTcount: A:0.20, C:0.31, G:0.16, T:0.33
Consensus pattern (33 bp):
GGGCCTAAATTTTTACCCGAACTCCCATATTTC
Found at i:40927556 original size:24 final size:25
Alignment explanation
Indices: 40927492--40927562 Score: 81
Period size: 25 Copynumber: 2.9 Consensus size: 25
40927482 GAAGCTTGCA
* * * *
40927492 AGAGCCATATAATGGGAAGCTCGTG
1 AGAGCCAAATAACGGGATGCTCATG
*
40927517 AGAGCCAAATATCGGGATGCTCATG
1 AGAGCCAAATAACGGGATGCTCATG
*
40927542 AGAG-CTAATAACGGGATGCTC
1 AGAGCCAAATAACGGGATGCTC
40927563 TTTCGAGCTG
Statistics
Matches: 39, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
24 15 0.38
25 24 0.62
ACGTcount: A:0.32, C:0.18, G:0.30, T:0.20
Consensus pattern (25 bp):
AGAGCCAAATAACGGGATGCTCATG
Found at i:40931435 original size:44 final size:45
Alignment explanation
Indices: 40931362--40931448 Score: 158
Period size: 44 Copynumber: 2.0 Consensus size: 45
40931352 CTATTTTTAG
40931362 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT
1 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT
*
40931407 TTTC-CACTTAAACTCTGATTAGTGTAGGTTATTTTAATATTA
1 TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTA
40931449 TTTGACCTAC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
44 37 0.90
45 4 0.10
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.48
Consensus pattern (45 bp):
TTTCTCACTTAAACTCTGATTAGTATAGGTTATTTTAATATTAAT
Found at i:40933506 original size:11 final size:11
Alignment explanation
Indices: 40933490--40933523 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
40933480 AAAATTGATG
40933490 AATAATGACAA
1 AATAATGACAA
40933501 AATAATGA-AA
1 AATAATGACAA
40933511 ATATAATGACAA
1 A-ATAATGACAA
40933523 A
1 A
40933524 CTTTGTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 15 0.71
12 3 0.14
ACGTcount: A:0.65, C:0.06, G:0.09, T:0.21
Consensus pattern (11 bp):
AATAATGACAA
Found at i:40938261 original size:4 final size:4
Alignment explanation
Indices: 40938252--40938277 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
40938242 AGAAACGCAC
40938252 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
40938278 CCAAAAATGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:40939060 original size:45 final size:44
Alignment explanation
Indices: 40939026--40939365 Score: 116
Period size: 44 Copynumber: 7.8 Consensus size: 44
40939016 TTCGCTGTTG
* * *
40939026 TCAATCTGC-CCTACTGCAACTTCAGGGGGATAAGACTTGCTTTC
1 TCAATCTGCTCC-ACTACAACCTCAGGGAGATAAGACTTGCTTTC
* * * *
40939070 TCAGTCTGCTCCACTACAACCTCAGGGAGATAAGACCTG--ATG
1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC
* * ** * * *
40939112 T-GATCTACTCTGC-GCAACTTCAGAGAGATAAGATCTAT--TATT-
1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGA-CT-TGCT-TTC
** * * ** *
40939154 TCAATCCACTCCACTGCAACTTCAGGGAGATAAGA-TTTATTAC
1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC
* * * * * *
40939197 TTTAATCCGCTCCACTACAACTTCAGGGAGATAGGA-TT-ATTGGC
1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTT-TC
* * * *
40939241 TTCAATTTGCTCCACTGCAACCTCAAGGAGATAAGATTATCGGC--T-
1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACT-T--GCTTTC
* * *
40939286 TCAATCTACTCCACTGCAACCTCAGGGAGATAAGATTTGC-TTC
1 TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC
** * ** *
40939329 TTCGGTCTGCTCCGCTGGAACCTCAGGGAAATAAGAC
1 -TCAATCTGCTCCACTACAACCTCAGGGAGATAAGAC
40939366 CTGATGCGAT
Statistics
Matches: 229, Mismatches: 47, Indels: 40
0.72 0.15 0.13
Matches are distributed among these distances:
40 17 0.07
41 11 0.05
42 7 0.03
43 14 0.06
44 176 0.77
45 3 0.01
46 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
TCAATCTGCTCCACTACAACCTCAGGGAGATAAGACTTGCTTTC
Found at i:40939177 original size:44 final size:43
Alignment explanation
Indices: 40939125--40939451 Score: 228
Period size: 44 Copynumber: 7.5 Consensus size: 43
40939115 TCTACTCTGC
* *
40939125 GCAACTTCAGAGAGATAAGATCTATTATTTCAATCCACTCCACT
1 GCAACTTCAGGGAGATAAGAT-TATTACTTCAATCCACTCCACT
* *
40939169 GCAACTTCAGGGAGATAAGATTTATTACTTTAATCCGCTCCACT
1 GCAACTTCAGGGAGATAAGA-TTATTACTTCAATCCACTCCACT
* * * ***
40939213 ACAACTTCAGGGAGATAGGATTATTGGCTTCAATTTGCTCCACT
1 GCAACTTCAGGGAGATAAGATTATT-ACTTCAATCCACTCCACT
* * ** *
40939257 GCAACCTCAAGGAGATAAGATTATCGGCTTCAATCTACTCCACT
1 GCAACTTCAGGGAGATAAGATTAT-TACTTCAATCCACTCCACT
* * ** ** *
40939301 GCAACCTCAGGGAGATAAGATT-TGCTTCTTCGGTCTGCTCCGCT
1 GCAACTTCAGGGAGATAAGATTAT--TACTTCAATCCACTCCACT
* * * ** * * * * *
40939345 GGAACCTCAGGGAAATAAGA-CCTGA-TGCGATCTACTCTACT
1 GCAACTTCAGGGAGATAAGATTATTACTTCAATCCACTCCACT
* * * *
40939386 ACAACTTCAGAGAGATAAGATCTATTACTTTAATCCGCTCCACT
1 GCAACTTCAGGGAGATAAGAT-TATTACTTCAATCCACTCCACT
* *
40939430 ACAACTTCAGGGAGATAGGATT
1 GCAACTTCAGGGAGATAAGATT
40939452 TGTGGCTTAA
Statistics
Matches: 225, Mismatches: 50, Indels: 17
0.77 0.17 0.06
Matches are distributed among these distances:
41 26 0.12
43 9 0.04
44 189 0.84
45 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
GCAACTTCAGGGAGATAAGATTATTACTTCAATCCACTCCACT
Found at i:40940205 original size:25 final size:25
Alignment explanation
Indices: 40940177--40940225 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
40940167 ATTTTTCGGC
*
40940177 TTTT-CTTCTCCCAGTTAAACTCTAT
1 TTTTACTT-TCCCACTTAAACTCTAT
*
40940202 TTTTAGTTTCCCACTTAAACTCTA
1 TTTTACTTTCCCACTTAAACTCTA
40940226 AAAAGTGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 19 0.90
26 2 0.10
ACGTcount: A:0.22, C:0.27, G:0.04, T:0.47
Consensus pattern (25 bp):
TTTTACTTTCCCACTTAAACTCTAT
Found at i:40940267 original size:44 final size:44
Alignment explanation
Indices: 40940204--40940294 Score: 155
Period size: 44 Copynumber: 2.1 Consensus size: 44
40940194 AACTCTATTT
40940204 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA
* **
40940248 TTAGTTTCCCACTTAAACTCTGATTAGTGTAGGTTATTTTAATA
1 TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA
40940292 TTA
1 TTA
40940295 TTTTACCTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.31, C:0.13, G:0.12, T:0.44
Consensus pattern (44 bp):
TTAGTTTCCCACTTAAACTCTAAAAAGTGTAGGTTATTTTAATA
Found at i:40942606 original size:19 final size:17
Alignment explanation
Indices: 40942573--40942605 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
40942563 ATATATTTTA
40942573 TTTTTAATCAAATATAC
1 TTTTTAATCAAATATAC
40942590 TTTTTAATCAAATATA
1 TTTTTAATCAAATATA
40942606 TATATTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (17 bp):
TTTTTAATCAAATATAC
Found at i:40943148 original size:31 final size:29
Alignment explanation
Indices: 40943112--40943197 Score: 79
Period size: 28 Copynumber: 2.9 Consensus size: 29
40943102 CATCCAACTA
40943112 TCATTTTTTAATTTGGTCACGTAATTATTG
1 TCATTTTTTAATTTGGTCAC-TAATTATTG
* **
40943142 TTCATTTTCTT-TTTTGGTCACCCA-T-TTG
1 -TCATTTT-TTAATTTGGTCACTAATTATTG
40943170 TCAATTTTTTAATTTGGTCACCTAATTA
1 TC-ATTTTTTAATTTGGTCA-CTAATTA
40943198 ATTGAGATTG
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
27 4 0.09
28 16 0.37
29 3 0.07
30 2 0.05
31 16 0.37
32 2 0.05
ACGTcount: A:0.21, C:0.15, G:0.10, T:0.53
Consensus pattern (29 bp):
TCATTTTTTAATTTGGTCACTAATTATTG
Found at i:40945072 original size:14 final size:14
Alignment explanation
Indices: 40945053--40945079 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40945043 TCTCAAACCT
40945053 AATGATATATGTAG
1 AATGATATATGTAG
40945067 AATGATATATGTA
1 AATGATATATGTA
40945080 TCGATTTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.37
Consensus pattern (14 bp):
AATGATATATGTAG
Found at i:40946462 original size:14 final size:14
Alignment explanation
Indices: 40946443--40946470 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
40946433 TTTATATGTA
40946443 ATAAAAACACGTAT
1 ATAAAAACACGTAT
40946457 ATAAAAACACGTAT
1 ATAAAAACACGTAT
40946471 GTATATATGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATAAAAACACGTAT
Found at i:40946767 original size:3 final size:3
Alignment explanation
Indices: 40946759--40946861 Score: 188
Period size: 3 Copynumber: 33.7 Consensus size: 3
40946749 GATTAAATGC
40946759 AAT AAT AAT AAT AAT AAT AAT AAT GCAAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT --AAT AAT AAT AAT AAT AAT AAT
40946806 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
40946854 AAT AAT AA
1 AAT AAT AA
40946862 ACTAAATAAA
Statistics
Matches: 98, Mismatches: 0, Indels: 4
0.96 0.00 0.04
Matches are distributed among these distances:
3 95 0.97
5 3 0.03
ACGTcount: A:0.66, C:0.01, G:0.01, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:40952896 original size:9 final size:9
Alignment explanation
Indices: 40952882--40952925 Score: 74
Period size: 9 Copynumber: 5.1 Consensus size: 9
40952872 TTTTGTTATA
40952882 ACAATTAAT
1 ACAATTAAT
40952891 ACAATTAAT
1 ACAATTAAT
40952900 ACAATT-A-
1 ACAATTAAT
40952907 ACAATTAAT
1 ACAATTAAT
40952916 ACAATTAAT
1 ACAATTAAT
40952925 A
1 A
40952926 ATTTGATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
7 6 0.18
8 2 0.06
9 25 0.76
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:40952912 original size:16 final size:16
Alignment explanation
Indices: 40952891--40952928 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
40952881 AACAATTAAT
40952891 ACAATTAATACAATTA
1 ACAATTAATACAATTA
40952907 ACAATTAATACAATTA
1 ACAATTAATACAATTA
*
40952923 ATAATT
1 ACAATT
40952929 TGATAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (16 bp):
ACAATTAATACAATTA
Found at i:40957401 original size:32 final size:31
Alignment explanation
Indices: 40957337--40957401 Score: 78
Period size: 32 Copynumber: 2.1 Consensus size: 31
40957327 TTATATAAAT
* *
40957337 AAAAATTATAAAAGAATTATTTAAAATATAA
1 AAAAATAATAAAAGAATTATGTAAAATATAA
*
40957368 AAAAATAATTAAAAGAA-TATGTAAGAATGTAA
1 AAAAATAA-TAAAAGAATTATGTAA-AATATAA
40957400 AA
1 AA
40957402 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.65, C:0.00, G:0.08, T:0.28
Consensus pattern (31 bp):
AAAAATAATAAAAGAATTATGTAAAATATAA
Found at i:40958827 original size:20 final size:20
Alignment explanation
Indices: 40958786--40958838 Score: 54
Period size: 20 Copynumber: 2.6 Consensus size: 20
40958776 TATTTTTACT
* **
40958786 ATTTTT-ATATTTTTTTCTA
1 ATTTTTAATATTTTATTAAA
40958805 ATTTTTAATATTTTATTAAA
1 ATTTTTAATATTTTATTAAA
*
40958825 ATTTAATAATATTT
1 ATTT-TTAATATTT
40958839 ATAGCTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 6 0.21
20 14 0.50
21 8 0.29
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (20 bp):
ATTTTTAATATTTTATTAAA
Found at i:40959037 original size:89 final size:89
Alignment explanation
Indices: 40958886--40959060 Score: 237
Period size: 89 Copynumber: 2.0 Consensus size: 89
40958876 TAATAAAAGC
* * * *
40958886 AGGGGCTTAATTGCTTTTCTTGAAAAAGTTTGAGAGTCTTTTTGATGTATTTTGAAAGTTCAAGT
1 AGGGGCTTAATTACTTTTCTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGT
*
40958951 AC-CTAATTGAGTGAAAAAAAAAAT
66 ACTC-AAATGAGTGAAAAAAAAAAT
* * *
40958975 AGGGGCTTAATTACTTTTTTTG-AAAAGATTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAG
1 AGGGGCTTAATTACTTTTCTTGAAAAAG-TTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAG
*
40959039 TACTCAAATGAGTGTAAAAAAA
65 TACTCAAATGAGTGAAAAAAAA
40959061 CAAGCAGAAA
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
88 5 0.07
89 69 0.92
90 1 0.01
ACGTcount: A:0.35, C:0.07, G:0.19, T:0.38
Consensus pattern (89 bp):
AGGGGCTTAATTACTTTTCTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGT
ACTCAAATGAGTGAAAAAAAAAAT
Found at i:40959083 original size:89 final size:87
Alignment explanation
Indices: 40958891--40959084 Score: 194
Period size: 89 Copynumber: 2.2 Consensus size: 87
40958881 AAAGCAGGGG
* * * *
40958891 CTTAATTGCTTTTCTTGAAAAAGTTTGAGAGTCTTTTTGATGTATTTTGAAAGTTCAAGTACCTA
1 CTTAATT-ATTTT-TTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCTA
* * ***
40958956 ATTGAGTGAAAAAAAAAATAGGGG
64 AATGAGTGAAAAAAAAAACAGAAA
* *
40958980 CTTAATTACTTTTTTTG-AAAAGATTTGAGGGTTTTTTTAATGCATTTTAAAAGTTCAAGTA-CT
1 CTTAATTA--TTTTTTGAAAAAG-TTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCT
*
40959043 CAAATGAGTGTAAAAAAACAAGCAGAAA
63 -AAATGAGTG-AAAAAAA-AAACAGAAA
40959071 CTTAATTATTTTTT
1 CTTAATTATTTTTT
40959085 TGGGAGAGTT
Statistics
Matches: 87, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
88 7 0.08
89 57 0.66
90 11 0.13
91 12 0.14
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (87 bp):
CTTAATTATTTTTTGAAAAAGTTTGAGAGTCTTTTTAATGCATTTTAAAAGTTCAAGTACCTAAA
TGAGTGAAAAAAAAAACAGAAA
Found at i:40959451 original size:21 final size:19
Alignment explanation
Indices: 40959427--40959476 Score: 50
Period size: 21 Copynumber: 2.6 Consensus size: 19
40959417 TACCTATTAT
40959427 TTACTTATTTATTCTTTATAA
1 TTAC-TATTTATTCTTT-TAA
*
40959448 TTACGTAATT-TTCTTTTAA
1 TTAC-TATTTATTCTTTTAA
40959467 TTA-TATTTAT
1 TTACTATTTAT
40959477 CTAGTTCCAC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
17 4 0.16
18 1 0.04
19 6 0.24
20 6 0.24
21 8 0.32
ACGTcount: A:0.28, C:0.08, G:0.02, T:0.62
Consensus pattern (19 bp):
TTACTATTTATTCTTTTAA
Found at i:40962291 original size:15 final size:15
Alignment explanation
Indices: 40962273--40962310 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
40962263 CATCCACCAA
*
40962273 TCATTCATTCA-TTTT
1 TCATTC-TTCACTTAT
40962288 TCATTCTTCACTTAT
1 TCATTCTTCACTTAT
40962303 TCATTCTT
1 TCATTCTT
40962311 ATTCTTTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.18, C:0.24, G:0.00, T:0.58
Consensus pattern (15 bp):
TCATTCTTCACTTAT
Found at i:40964787 original size:131 final size:129
Alignment explanation
Indices: 40964536--40965259 Score: 490
Period size: 131 Copynumber: 5.7 Consensus size: 129
40964526 ATTCAGGATC
* * * * * *
40964536 GTAAATC-AATAAACTTAGGCTGTGATCATAAATCAATGAGACTTAATAATATCAATTGCGATAT
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
* * * * * *
40964600 TAAATTAACTAGTTGTTTAGAGTAGTGGCA-AG-AAATCAATTAACTTAGAGGAGATTGCTCATG
66 TAAATCAGCTAGATGTTTGGAGTAG-CG-ATAGTAAATCAACTAACTTAGA-GAGATTG-TCATG
40964663 ATA
127 ATA
*
40964666 GTAAATCAAATGAACTTAGGTTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
* * *
40964731 TAAATCAGCTAGCTGTTTGGAGTAGCGATAGTAAATCAACTAACTCAGAGATGATTGTTCGTGAT
66 TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAGA-GATTG-TCATGAT
40964796 A
129 A
* ** * * *
40964797 GTAAATCAAATGAACTTAGGTTGTGATATTAAATCAGCGAGCCTTAATAATATCAACT-CTGACA
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGC-GATA
* * * *
40964861 TTAAATCAGCTAGATGTTTGGAATAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATT-TCATG
65 TTAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAG---AGAGATTGTCATG
40964925 ATA
127 ATA
* * * *
40964928 GTAATTCAAATGAATTTAGGCTGTGATCGTAAATCAGC-AACCCTTAATAATATCAACT---ATG
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCC-TAATAATATCAACTGCGAT-
* * * * * * * * *
40964989 A-T--ATC-G---GA-G-TAGCGA-TAG-TA-AAT-CAGCTAACTTA--GAGA-AAATTTTTCAT
64 ATTAAATCAGCTAGATGTTTG-GAGTAGCGATAGTAAATC-AACTAACTTAGAGAGA-TTGTCAT
40965038 GATA
126 GATA
* * * * * * * * * *
40965042 GTAAATCAAATGAACTTAGGTTGTGACCATAAATTAGCAAGTCTTAATAATATCAGCTGTGATAT
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
* * * * * * * *
40965107 TAAATTAGCGAGTTGTTTGGAGTAACGATAATAAATTAGCTAACTTAGAGAAAATTGTTCATGAT
66 TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAG-AGATTG-TCATGAT
*
40965172 G
129 A
* * * ** * ** *
40965173 GTAAATCAAATAAACTTAGGTTGTGATCATAAATCAGTGAGCCTTAATAATATCAGTTGCGATCT
1 GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
* * *
40965238 TAAATCAACGAGCTGTTTGGAG
66 TAAATCAGCTAGATGTTTGGAG
40965260 CAATGATAGA
Statistics
Matches: 479, Mismatches: 79, Indels: 71
0.76 0.13 0.11
Matches are distributed among these distances:
112 3 0.01
113 3 0.01
114 53 0.11
115 2 0.00
116 3 0.01
117 5 0.01
118 6 0.01
119 3 0.01
120 6 0.01
121 3 0.01
122 2 0.00
123 1 0.00
124 3 0.01
125 5 0.01
126 4 0.01
127 7 0.01
128 3 0.01
129 5 0.01
130 18 0.04
131 339 0.71
133 3 0.01
134 2 0.00
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (129 bp):
GTAAATCAAATGAACTTAGGCTGTGATCGTAAATCAACGAGCCCTAATAATATCAACTGCGATAT
TAAATCAGCTAGATGTTTGGAGTAGCGATAGTAAATCAACTAACTTAGAGAGATTGTCATGATA
Found at i:40965088 original size:114 final size:114
Alignment explanation
Indices: 40964884--40965106 Score: 329
Period size: 114 Copynumber: 2.0 Consensus size: 114
40964874 ATGTTTGGAA
* *
40964884 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAATTCAAATGAATTTAGGC
1 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC
* *
40964949 TGTGATCGTAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG
66 TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG
* ** *
40964998 TAGCGATAGTAAATCAGCTAACTTAGAGAAAATTTTTCATGATAGTAAATCAAATGAACTTAGGT
1 TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC
* ** * *
40965063 TGTGACCATAAATTAGCAAGTCTTAATAATATCAGCTGTGATAT
66 TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATAT
40965107 TAAATTAGCG
Statistics
Matches: 96, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
114 96 1.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.30
Consensus pattern (114 bp):
TAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATGAACTTAGGC
TGTGACCATAAATCAGCAACCCTTAATAATATCAACTATGATATCGGAG
Found at i:40965200 original size:245 final size:245
Alignment explanation
Indices: 40964749--40965227 Score: 647
Period size: 245 Copynumber: 2.0 Consensus size: 245
40964739 CTAGCTGTTT
** *
40964749 GGAGTAGCGATAGTAAATCAACTAACTCAGAGATGATTGTTCGTGATAGTAAATCAAATGAACTT
1 GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT
* * *
40964814 AGGTTGTGATATTAAATCAGCGAGCCTTAATAATATCAACTCTGACATTAAATCAGCTAGATGTT
66 AGGTTGTGACATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGTT
* * * * *
40964879 TGGAATAGCGATAGTAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAATTCAAATGAATT
131 TGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATAAACT
*
40964944 TAGGCTGTGATCGTAAATCAGCAACCCTTAATAATATCAACTATGATATC
196 TAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCAACTATGATATC
* * *
40964994 GGAGTAGCGATAGTAAATCAGCTAACTTAGAGAAAATTTTTCATGATAGTAAATCAAATGAACTT
1 GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT
* * * * * * *
40965059 AGGTTGTGACCA-TAAATTAGCAAGTCTTAATAATATCAGCTGTGATATTAAATTAGCGAGTTGT
66 AGGTTGTGA-CATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGT
* * * * *
40965123 TTGGAGTAACGATAATAAATTAGCTAACTTAG-AGAAAATTGTTCATGATGGTAAATCAAATAAA
130 TTGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAAT-TTCATGATAGTAAATCAAATAAA
* ** *
40965187 CTTAGGTTGTGATCATAAATCAGTGAGCCTTAATAATATCA
194 CTTAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCA
40965228 GTTGCGATCT
Statistics
Matches: 201, Mismatches: 31, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
244 6 0.03
245 194 0.97
246 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.31
Consensus pattern (245 bp):
GGAGTAGCGATAGTAAATCAACTAACTCAGAGAAAATTGTTCATGATAGTAAATCAAATGAACTT
AGGTTGTGACATTAAATCAGCAAGCCTTAATAATATCAACTCTGACATTAAATCAGCGAGATGTT
TGGAATAACGATAATAAATCAGCTAACTTAGAAAAAAAATTTCATGATAGTAAATCAAATAAACT
TAGGCTGTGATCATAAATCAGCAACCCTTAATAATATCAACTATGATATC
Found at i:40970491 original size:26 final size:26
Alignment explanation
Indices: 40970462--40970532 Score: 106
Period size: 26 Copynumber: 2.7 Consensus size: 26
40970452 TTTTATAATG
**
40970462 TTGCTCACACGAGCTGTGAAATGGTT
1 TTGCTCACACGAGCTGTGAAATGGGC
*
40970488 TTGCTCACATGAGCTGTGAAATGGGC
1 TTGCTCACACGAGCTGTGAAATGGGC
*
40970514 CTGCTCACACGAGCTGTGA
1 TTGCTCACACGAGCTGTGA
40970533 GTCAGAATGT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.23, C:0.23, G:0.28, T:0.27
Consensus pattern (26 bp):
TTGCTCACACGAGCTGTGAAATGGGC
Found at i:40981259 original size:35 final size:35
Alignment explanation
Indices: 40981212--40981287 Score: 118
Period size: 35 Copynumber: 2.2 Consensus size: 35
40981202 AAAACATCTA
40981212 ATTTT-TCATTAGAACAATATTTTGATTTTTTAGT
1 ATTTTATCATTAGAACAATATTTTGATTTTTTAGT
* * *
40981246 ATTTTATCTTTAGAATAATTTTTTGATTTTTTAGT
1 ATTTTATCATTAGAACAATATTTTGATTTTTTAGT
40981281 ATTTTAT
1 ATTTTAT
40981288 TTTTTTATCT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
34 5 0.13
35 33 0.87
ACGTcount: A:0.28, C:0.04, G:0.08, T:0.61
Consensus pattern (35 bp):
ATTTTATCATTAGAACAATATTTTGATTTTTTAGT
Found at i:40991642 original size:3 final size:3
Alignment explanation
Indices: 40991636--40991689 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
40991626 AAGAAGAAGA
*
40991636 AGG AGG AGG AGA AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG
40991684 AGG AGG
1 AGG AGG
40991690 TGCCGGAAAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
AGG
Found at i:40991922 original size:39 final size:39
Alignment explanation
Indices: 40991874--40992026 Score: 123
Period size: 39 Copynumber: 3.8 Consensus size: 39
40991864 GTTTAGTTAT
*
40991874 TAATAATTATTGTTACTTAGTATTATTGTTAGTAAAAAAC
1 TAAT-ATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC
* * *
40991914 TAATATTATTATTATGGTTAGTTATTA-AGATTAGTAAAAACC
1 TAATATTATTGTTA--GTTAG-TATTATTG-TTAGTAAAAAAC
* * ****
40991956 TACTTATTATT-TTAGTTAGTATGATTGTTAGT-TTTTAC
1 TA-ATATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC
*
40991994 ATTATATTATTGTTAGTTAGTATTATTGTTAGT
1 -TAATATTATTGTTAGTTAGTATTATTGTTAGT
40992027 TAGTATTATT
Statistics
Matches: 90, Mismatches: 15, Indels: 17
0.74 0.12 0.14
Matches are distributed among these distances:
38 8 0.09
39 39 0.43
40 10 0.11
41 5 0.06
42 21 0.23
43 7 0.08
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.50
Consensus pattern (39 bp):
TAATATTATTGTTAGTTAGTATTATTGTTAGTAAAAAAC
Found at i:40992019 original size:16 final size:16
Alignment explanation
Indices: 40991998--40992036 Score: 78
Period size: 16 Copynumber: 2.4 Consensus size: 16
40991988 TTTTACATTA
40991998 TATTATTGTTAGTTAG
1 TATTATTGTTAGTTAG
40992014 TATTATTGTTAGTTAG
1 TATTATTGTTAGTTAG
40992030 TATTATT
1 TATTATT
40992037 TTGAGTATAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (16 bp):
TATTATTGTTAGTTAG
Found at i:40997531 original size:154 final size:153
Alignment explanation
Indices: 40997245--40998009 Score: 1007
Period size: 154 Copynumber: 5.0 Consensus size: 153
40997235 CTTCAAAAAA
* * *
40997245 AAATTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTT
1 AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTA
*
40997310 AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAGATTTA
66 AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
*
40997375 TTATTTTAGTGTGTTTTTTAAAT
131 TTAATTTAGTGTGTTTTTTAAAT
* *
40997398 AAATTA-AAAAAAACCCCTTATTTC-TCCCTTTGCTCGTATTTTTTTCCCGAATTTTATTACTTT
1 AAATTAGAAAAAAA-CCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
* * * *
40997461 CAATAAAAATATATTATTTTCGT-ATTTTATCATTTTACTTTATTTTAGTAAATTATGTTTGAAA
65 -AA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* * * * *
40997525 TGTATTAATTAATTTTATTTTTT---T
127 TTTATTAATTTAGTGTGTTTTTTAAAT
* * *
40997549 AAATTTAGTAAAAAACTCTTATTTCGGACCTTTGTTCGTA-TTTTTTCCCGAATTTTATTACTTT
1 AAA-TTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
* *
40997613 GAAAAAATATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
65 AAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTT
40997678 ATTAATTTAGTGTGTTTTTTAAAT
130 ATTAATTTAGTGTGTTTTTTAAAT
* ** *
40997702 ATATTTA-AAAAAAACCCTTATTTCGGCCCTTTACTCGTA-TTTTTTCTCGAATTTTATTACTTT
1 A-AATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTT
* *
40997765 CAATAAAAATATATTATTTTCGT-ATTTTATAATTTTACATTATTTTAGTACATTATGTTTGAAA
65 -AA-AAAAATATACTATTTTC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
* * * *
40997829 TGTATTAA-TTATTTCTGTTTTTTTAA-
127 TTTATTAATTTA-GTGTGTTTTTTAAAT
* * * * *
40997855 AATTTAGTAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACTTT
1 AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTC-CCGAATTTTATTACTTT
40997920 AAAAAAATAT-CATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
65 AAAAAAATATAC-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
40997984 TATTAATTTAGTGTGTTTTTTAAAT
129 TATTAATTTAGTGTGTTTTTTAAAT
40998009 A
1 A
40998010 TACAATTCTT
Statistics
Matches: 529, Mismatches: 60, Indels: 45
0.83 0.09 0.07
Matches are distributed among these distances:
149 1 0.00
150 71 0.13
151 5 0.01
152 134 0.25
153 144 0.27
154 157 0.30
155 17 0.03
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.52
Consensus pattern (153 bp):
AAATTAGAAAAAAACCCTTATTTCGGCCCTTTGTTCGTATTTTTTTCCCGAATTTTATTACTTTA
AAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATTTA
TTAATTTAGTGTGTTTTTTAAAT
Found at i:40997802 original size:304 final size:307
Alignment explanation
Indices: 40997243--40998011 Score: 1284
Period size: 304 Copynumber: 2.5 Consensus size: 307
40997233 AACTTCAAAA
*
40997243 AAAAATTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT
1 AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT
* *
40997308 TTAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAGATT
66 TAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
* * *
40997373 TATTATTTTAGTGTGTTTTTTAAATA-AATTAAAAAAAACCCCTTATTTCTCCCTTTGCTCGTAT
131 TATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTCGCCCTTTACTCGTAT
* *
40997437 TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATCATTTTACTTT
196 TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACATT
40997502 ATTTTAGTAAATTATGTTTGAAATGTATTAATTAATTT-TATTTTTTT
261 ATTTTAGTAAATTATGTTTGAAATGTATTAATT-ATTTCTATTTTTTT
*
40997549 -AAATTTAGTAAAAAACTCTTATTTCGGACC-TTTGTTCGTA-TTTTTTCCCGAATTTTATTACT
1 AAAATTTAGTAAAAAACCCTTATTTCGG-CCATTTGTTCGTATTTTTTTCCCGAATTTTATTACT
* *
40997611 TTGAAAAAATATACTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
65 TTAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAAT
*
40997676 TTATTAATTTAGTGTGTTTTTTAAATATATTTAAAAAAAA-CCCTTATTTCGGCCCTTTACTCGT
130 TTATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTC-GCCCTTTACTCGT
*
40997740 A-TTTTTTCTCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACA
194 ATTTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACA
* *
40997804 TTATTTTAGTACATTATGTTTGAAATGTATTAATTATTTCTGTTTTTTT
259 TTATTTTAGTAAATTATGTTTGAAATGTATTAATTATTTCTATTTTTTT
* *
40997853 AAAATTTAGTAAAAAACCCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTACT
1 AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTC-CCGAATTTTATTACT
40997918 TTAAAAAAATAT-CATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
65 TTAAAAAAATATAC-TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAA
40997982 TTTATTAATTTAGTGTGTTTTTTAAATATA
129 TTTATTAATTTAGTGTGTTTTTTAAATATA
40998012 CAATTCTTTT
Statistics
Matches: 435, Mismatches: 19, Indels: 17
0.92 0.04 0.04
Matches are distributed among these distances:
303 4 0.01
304 224 0.51
305 93 0.21
306 10 0.02
307 104 0.24
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (307 bp):
AAAATTTAGTAAAAAACCCTTATTTCGGCCATTTGTTCGTATTTTTTTCCCGAATTTTATTACTT
TAAAAAAATATACTATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATT
TATTAATTTAGTGTGTTTTTTAAATATAATTAAAAAAAACCCCTTATTTCGCCCTTTACTCGTAT
TTTTTTCCCGAATTTTATTACTTTCAATAAAAATATATTATTTTCGTATTTTATAATTTTACATT
ATTTTAGTAAATTATGTTTGAAATGTATTAATTATTTCTATTTTTTT
Found at i:40998400 original size:4 final size:4
Alignment explanation
Indices: 40998378--40998504 Score: 82
Period size: 4 Copynumber: 29.2 Consensus size: 4
40998368 TTCCCTCTTC
*
40998378 TTCT TCTCT TT-T TTTT TTCT TTCT TCTCAT TTCCTT TTCT TTCT TTC-
1 TTCT T-TCT TTCT TTCT TTCT TTCT T-TC-T TT-C-T TTCT TTCT TTCT
40998425 TT-T TTCT TTCT TCTCCT TTCATT TTCT TTCT TTCT TTCT TCTCCT TTCCTT
1 TTCT TTCT TTCT T-T-CT TTC--T TTCT TTCT TTCT TTCT T-T-CT TT-C-T
*
40998476 TTCT TTCT TT-T TCTTT TTCT TTCT TTCT T
1 TTCT TTCT TTCT T-TCT TTCT TTCT TTCT T
40998505 CTCCTTTCCC
Statistics
Matches: 104, Mismatches: 3, Indels: 32
0.75 0.02 0.23
Matches are distributed among these distances:
3 9 0.09
4 59 0.57
5 17 0.16
6 19 0.18
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (4 bp):
TTCT
Found at i:40998420 original size:24 final size:20
Alignment explanation
Indices: 40998378--40998507 Score: 99
Period size: 20 Copynumber: 6.4 Consensus size: 20
40998368 TTCCCTCTTC
40998378 TTCTTCTCTTTTTTTTTTCT
1 TTCTTCTCTTTTTTTTTTCT
* **
40998398 TTCTTCTCATTTCCTTTTCT
1 TTCTTCTCTTTTTTTTTTCT
40998418 TTCTT-TCTTTTTCTTTCTTC-
1 TTCTTCTCTTTTT-TTT-TTCT
*
40998438 TCCTT-TCATTTTCTTTCTTTCT
1 TTCTTCTC-TTTT-TTT-TTTCT
* **
40998460 TTCTTCTCCTTTCCTTTTCT
1 TTCTTCTCTTTTTTTTTTCT
40998480 TTCTT-T-TTCTTTTTCTTTCT
1 TTCTTCTCTT-TTTTT-TTTCT
40998500 TTCTTCTC
1 TTCTTCTC
40998508 CTTTCCCTCT
Statistics
Matches: 85, Mismatches: 14, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
18 1 0.01
19 9 0.11
20 50 0.59
21 14 0.16
22 9 0.11
23 2 0.02
ACGTcount: A:0.02, C:0.27, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTCTCTTTTTTTTTTCT
Found at i:40998426 original size:44 final size:42
Alignment explanation
Indices: 40998343--40998507 Score: 121
Period size: 44 Copynumber: 4.0 Consensus size: 42
40998333 CCTTTACTTC
* **
40998343 TTTTTTTTTCTTTCTGTTTCCTTCCTTCCCTCTTC-TTCTTCTCT
1 TTTTTTTTTCTTTC--TTTCTTTCCTTTTCT-TTCTTTCTTCTCT
40998387 TTTTTTTTTCTTTCTTCTCATTTCCTTTTCTTTCTTTC-T-T-T
1 TTTTTTTTTCTTTCTT-TC-TTTCCTTTTCTTTCTTTCTTCTCT
* * * * *
40998428 TTCTTTCTTC-TCCTTTCATTTTC-TTTCTTTCTTTCTTCTCC
1 TTTTTTTTTCTTTCTTTC-TTTCCTTTTCTTTCTTTCTTCTCT
** *
40998469 TTTCCTTTTCTTTC-TT-TTTCTTTTTCTTTCTTTCTTCTC
1 TTTTTTTTTCTTTCTTTCTTTCCTTTTCTTTCTTTCTTCTC
40998508 CTTTCCCTCT
Statistics
Matches: 98, Mismatches: 15, Indels: 20
0.74 0.11 0.15
Matches are distributed among these distances:
38 12 0.12
39 11 0.11
40 22 0.22
41 17 0.17
42 5 0.05
43 6 0.06
44 25 0.26
ACGTcount: A:0.01, C:0.28, G:0.01, T:0.70
Consensus pattern (42 bp):
TTTTTTTTTCTTTCTTTCTTTCCTTTTCTTTCTTTCTTCTCT
Found at i:40998429 original size:34 final size:33
Alignment explanation
Indices: 40998400--40998511 Score: 128
Period size: 34 Copynumber: 3.4 Consensus size: 33
40998390 TTTTTTCTTT
40998400 CTTCTCATTTCCTTTTCTTTCTTTCTTTTTCTTT
1 CTTCTC-TTTCCTTTTCTTTCTTTCTTTTTCTTT
*
40998434 CTTCTCCTTTCATTTTCTTTCTTTC--TTTC-TT
1 CTTCT-CTTTCCTTTTCTTTCTTTCTTTTTCTTT
40998465 C-TC-CTTTCCTTTTCTTTCTTTTTCTTTTTCTTT
1 CTTCTCTTTCCTTTTCTTTC--TTTCTTTTTCTTT
40998498 CTT-TCTTCTCCTTT
1 CTTCTCTT-TCCTTT
40998512 CCCTCTCATT
Statistics
Matches: 67, Mismatches: 2, Indels: 17
0.78 0.02 0.20
Matches are distributed among these distances:
28 14 0.21
30 6 0.09
31 3 0.04
32 8 0.12
33 3 0.04
34 26 0.39
35 7 0.10
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.70
Consensus pattern (33 bp):
CTTCTCTTTCCTTTTCTTTCTTTCTTTTTCTTT
Found at i:40998511 original size:10 final size:10
Alignment explanation
Indices: 40998373--40998512 Score: 84
Period size: 10 Copynumber: 14.2 Consensus size: 10
40998363 CTTCCTTCCC
40998373 TCTTCTTC-T
1 TCTTCTTCTT
40998382 TC-TCTT-TT
1 TCTTCTTCTT
*
40998390 T-TTTTTCTT
1 TCTTCTTCTT
40998399 TCTTC-TCATT
1 TCTTCTTC-TT
40998409 TCCTTTTCTTTCTT
1 T-C--TTC-TTCTT
*
40998423 TCTTTTTCTT
1 TCTTCTTCTT
*
40998433 TCTTCTCCTT
1 TCTTCTTCTT
40998443 TCATT-TTCTT
1 TC-TTCTTCTT
40998453 TC-T-TTCTT
1 TCTTCTTCTT
*
40998461 TCTTCTCCTT
1 TCTTCTTCTT
40998471 TCCTT-TTCTT
1 T-CTTCTTCTT
*
40998481 TCTTTTTCTT
1 TCTTCTTCTT
40998491 T-TTCTTTCTT
1 TCTTC-TTCTT
*
40998501 TCTTCTCCTT
1 TCTTCTTCTT
40998511 TC
1 TC
40998513 CCTCTCATTT
Statistics
Matches: 104, Mismatches: 10, Indels: 33
0.71 0.07 0.22
Matches are distributed among these distances:
8 17 0.16
9 13 0.12
10 54 0.52
11 11 0.11
13 4 0.04
14 3 0.03
15 2 0.02
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (10 bp):
TCTTCTTCTT
Found at i:40998525 original size:62 final size:62
Alignment explanation
Indices: 40998395--40998530 Score: 163
Period size: 62 Copynumber: 2.2 Consensus size: 62
40998385 CTTTTTTTTT
* * * *
40998395 TCTTTCTTCTCATTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTTCTTTCTT
1 TCTTTCTTCTCCTTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTCCTCTCTA
*
40998457 TCTTTCTTCTCCTTTCCTTTTCTTTCTTTTTCTTTTTCTTTCTT-T-CTTCTCCTTTCC-CTCTC
1 TCTTTCTTCTCCTTTCCTTTTCTTTC--TTTCTTTTTCTTTCTTCTCCTT-TCATTTCCTCTCT-
40998519 A
62 A
40998520 T-TTTCTTCTCC
1 TCTTTCTTCTCC
40998531 ACCCACCAGC
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
62 41 0.63
63 8 0.12
64 16 0.25
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (62 bp):
TCTTTCTTCTCCTTTCCTTTTCTTTCTTTCTTTTTCTTTCTTCTCCTTTCATTTCCTCTCTA
Found at i:40999710 original size:10 final size:10
Alignment explanation
Indices: 40999695--40999724 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
40999685 ATTTAAATTC
40999695 TAAAGATAAA
1 TAAAGATAAA
40999705 TAAAGATAAA
1 TAAAGATAAA
*
40999715 TAAAGGTAAA
1 TAAAGATAAA
40999725 AGCTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.13, T:0.20
Consensus pattern (10 bp):
TAAAGATAAA
Found at i:41001480 original size:8 final size:8
Alignment explanation
Indices: 41001467--41001516 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
41001457 GTGCAAGAAA
41001467 ATAAAAAT
1 ATAAAAAT
41001475 ATAAAAAT
1 ATAAAAAT
41001483 ATAAAAAAT
1 AT-AAAAAT
*
41001492 ATATAAAT
1 ATAAAAAT
*
41001500 A-AAATAAA
1 ATAAA-AAT
41001508 ATAAAAAT
1 ATAAAAAT
41001516 A
1 A
41001517 AAATTGGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 2 0.06
8 22 0.63
9 11 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
ATAAAAAT
Found at i:41001491 original size:17 final size:16
Alignment explanation
Indices: 41001469--41001519 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 16
41001459 GCAAGAAAAT
41001469 AAAAATATAAAAATATA
1 AAAAATATAAAAATA-A
*
41001486 AAAAATATATAAATAA
1 AAAAATATAAAAATAA
41001502 AATAAA-ATAAAAATAA
1 AA-AAATATAAAAATAA
41001518 AA
1 AA
41001520 TTGGGTTGCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
16 14 0.45
17 17 0.55
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAAAATATAAAAATAA
Found at i:41001520 original size:11 final size:11
Alignment explanation
Indices: 41001464--41001520 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
41001454 AAAGTGCAAG
41001464 AAAATAAAAAT
1 AAAATAAAAAT
41001475 ---ATAAAAAT
1 AAAATAAAAAT
*
41001483 ATAAA-AAATAT
1 A-AAATAAAAAT
41001494 ATAAAT-AAAAT
1 A-AAATAAAAAT
41001505 AAAATAAAAAT
1 AAAATAAAAAT
41001516 AAAAT
1 AAAAT
41001521 TGGGTTGCCT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
8 8 0.21
10 4 0.11
11 25 0.66
12 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:41002644 original size:13 final size:13
Alignment explanation
Indices: 41002626--41002652 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41002616 TTTTCAAAAA
41002626 TTATGCATTTATT
1 TTATGCATTTATT
41002639 TTATGCATTTATT
1 TTATGCATTTATT
41002652 T
1 T
41002653 AATGTTGACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.07, G:0.07, T:0.63
Consensus pattern (13 bp):
TTATGCATTTATT
Found at i:41002894 original size:50 final size:52
Alignment explanation
Indices: 41002758--41002894 Score: 156
Period size: 50 Copynumber: 2.7 Consensus size: 52
41002748 GTAAAGAGGT
* * * * * *
41002758 CCCATTTAAGACCATGTCTAGGATATGGCGTTGGCACCGAGATGAGAGATCT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA
* *
41002810 CCC--GTAAGACCATGTCTGGGACATGGCATCGGCATCGATATGAGA-A-CA
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA
* *
41002858 CCCATGTAAGACCATGTTTGGGACATGGCTTTGGCAT
1 CCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
41002895 GTTATTATCA
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
48 4 0.06
49 1 0.01
50 64 0.89
52 3 0.04
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (52 bp):
CCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAGATCA
Found at i:41015484 original size:12 final size:12
Alignment explanation
Indices: 41015467--41015491 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41015457 TTTATTATTA
41015467 TTATTTCTTTAT
1 TTATTTCTTTAT
41015479 TTATTTCTTTAT
1 TTATTTCTTTAT
41015491 T
1 T
41015492 AATATTATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTTCTTTAT
Found at i:41017084 original size:6 final size:6
Alignment explanation
Indices: 41017070--41017108 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
41017060 TTTTGTTTTG
* *
41017070 TTTTGT TTTTAT TTTTAT TTTTAT TTTTAT TGTTAT TTT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTT
41017109 CTTCTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.13, C:0.00, G:0.05, T:0.82
Consensus pattern (6 bp):
TTTTAT
Found at i:41017096 original size:18 final size:18
Alignment explanation
Indices: 41017070--41017164 Score: 61
Period size: 18 Copynumber: 5.1 Consensus size: 18
41017060 TTTTGTTTTG
* *
41017070 TTTTGTTTTTATTTTTAT
1 TTTTATTTTTATTGTTAT
41017088 TTTTATTTTTATTGTTAT
1 TTTTATTTTTATTGTTAT
*
41017106 TTTCT-TCTATTTA-TGTCAT
1 TTT-TAT-T-TTTATTGTTAT
* *
41017125 TTTTATCTTTTGAACT-ATAT
1 TTTTAT-TTTT--ATTGTTAT
*
41017145 TTTTATTTTTATGGTTAT
1 TTTTATTTTTATTGTTAT
41017163 TT
1 TT
41017165 CTAATCGAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 16
0.72 0.09 0.19
Matches are distributed among these distances:
17 1 0.02
18 29 0.48
19 17 0.28
20 13 0.21
21 1 0.02
ACGTcount: A:0.17, C:0.05, G:0.06, T:0.72
Consensus pattern (18 bp):
TTTTATTTTTATTGTTAT
Found at i:41018916 original size:17 final size:17
Alignment explanation
Indices: 41018894--41018932 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
41018884 TATTACATAA
41018894 AAGTCTGCAAGAAAGAT
1 AAGTCTGCAAGAAAGAT
*
41018911 AAGTCTGCATGAAAGAT
1 AAGTCTGCAAGAAAGAT
41018928 AAGTC
1 AAGTC
41018933 CGTTGACTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.44, C:0.13, G:0.23, T:0.21
Consensus pattern (17 bp):
AAGTCTGCAAGAAAGAT
Found at i:41036310 original size:21 final size:21
Alignment explanation
Indices: 41036286--41036337 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
41036276 AGAGGGATTG
*
41036286 AAATTGTATAAATTGAAATCA
1 AAATTGTAAAAATTGAAATCA
41036307 AAATTGTAAAAATTGAAATCA
1 AAATTGTAAAAATTGAAATCA
41036328 AAATTGTAAA
1 AAATTGTAAA
41036338 GAGAAACAGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.56, C:0.04, G:0.10, T:0.31
Consensus pattern (21 bp):
AAATTGTAAAAATTGAAATCA
Found at i:41040039 original size:22 final size:24
Alignment explanation
Indices: 41039987--41040040 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 24
41039977 TTTTTTATGA
41039987 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATTAAATAT-CT
* *
41040012 TGAAATTATTG-TATTATATAT-T
1 TTAAATTATTGTTATTAAATATCT
41040034 TTAAATT
1 TTAAATT
41040041 GAATTTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
22 7 0.27
24 9 0.35
25 10 0.38
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATTGTTATTAAATATCT
Found at i:41043034 original size:22 final size:22
Alignment explanation
Indices: 41042992--41043034 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
41042982 AAAAGATATA
* *
41042992 AAATTAATTAAATAATGAAAAC
1 AAATTAAATAAATAATCAAAAC
41043014 AAATTAAATAAA-ACATCAAAA
1 AAATTAAATAAATA-ATCAAAA
41043035 GAGAACACTA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.67, C:0.07, G:0.02, T:0.23
Consensus pattern (22 bp):
AAATTAAATAAATAATCAAAAC
Found at i:41044639 original size:20 final size:18
Alignment explanation
Indices: 41044602--41044641 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
41044592 TTAAGGTTAA
*
41044602 AATAGTAAAAAGTAAAAT
1 AATAGTAAAAAATAAAAT
41044620 AATATGTAATAAAATAAAAT
1 AATA-GTAA-AAAATAAAAT
41044640 AA
1 AA
41044642 AACATGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
20 11 0.58
ACGTcount: A:0.68, C:0.00, G:0.07, T:0.25
Consensus pattern (18 bp):
AATAGTAAAAAATAAAAT
Found at i:41045593 original size:42 final size:42
Alignment explanation
Indices: 41045493--41045649 Score: 176
Period size: 43 Copynumber: 3.7 Consensus size: 42
41045483 TGTGATATCA
*
41045493 TGTAAGACCACGTCTAGGACTTTGGCATCG-ATTTGAGATTTACG
1 TGTAAGACCACGTCTAGGACATTGGCATCGTATTT--GA-TTACG
* * *
41045537 TGTAAGACCATGTCTAGGACATTGGCGTCGTATATGATTACG
1 TGTAAGACCACGTCTAGGACATTGGCATCGTATTTGATTACG
* *
41045579 TGTAAGACC-CTGTCT-GAGACAGTGGCATCGTTATTTGATTACA
1 TGTAAGACCAC-GTCTAG-GACATTGGCATCG-TATTTGATTACG
*
41045622 TGTAAGACCACGTCTAGGACGTTGGCAT
1 TGTAAGACCACGTCTAGGACATTGGCAT
41045650 TGTACGAGCT
Statistics
Matches: 96, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
41 1 0.01
42 29 0.30
43 34 0.35
44 29 0.30
45 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (42 bp):
TGTAAGACCACGTCTAGGACATTGGCATCGTATTTGATTACG
Found at i:41052486 original size:52 final size:52
Alignment explanation
Indices: 41052423--41052526 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 52
41052413 CAACAAAGTC
*
41052423 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGTCCATCCGGACCACTGAT
1 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT
*
41052475 ATTCTATTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT
1 ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT
41052527 CCTAACCAAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.25
Consensus pattern (52 bp):
ATTCTACTCTTAAAACGCAAAACTAACTTAAAGGCCCATCCGGACCACTGAT
Found at i:41052692 original size:16 final size:16
Alignment explanation
Indices: 41052654--41052695 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
41052644 ATCAATTGTT
*
41052654 TAAATAATTTTATAAA
1 TAAATATTTTTATAAA
*
41052670 TATATATTTTTAATAAA
1 TAAATATTTTT-ATAAA
41052687 -AAATATTTT
1 TAAATATTTT
41052696 CATTCACCGG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATATTTTTATAAA
Found at i:41060710 original size:3 final size:3
Alignment explanation
Indices: 41060702--41060745 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
41060692 TTTTTTAAAG
41060702 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
41060746 GATATTTTAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:41062046 original size:16 final size:16
Alignment explanation
Indices: 41062025--41062063 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
41062015 AATAATGGAA
41062025 ATATATAAAAACATGT
1 ATATATAAAAACATGT
* **
41062041 ATATATGAAAGTATGT
1 ATATATAAAAACATGT
41062057 ATATATA
1 ATATATA
41062064 TAAATTAAAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.51, C:0.03, G:0.10, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:41062111 original size:31 final size:31
Alignment explanation
Indices: 41062076--41062142 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
41062066 AATTAAAGAG
*
41062076 TATATAAAAAGTATAGAAT-TACATATATATA
1 TATATAAAAAGTA-AGAATATACATATAAATA
* * **
41062107 TATATGAAAATTAAGAATATGTATATAAATA
1 TATATAAAAAGTAAGAATATACATATAAATA
41062138 TATAT
1 TATAT
41062143 GTATATATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 5 0.17
31 25 0.83
ACGTcount: A:0.54, C:0.01, G:0.07, T:0.37
Consensus pattern (31 bp):
TATATAAAAAGTAAGAATATACATATAAATA
Found at i:41063478 original size:15 final size:15
Alignment explanation
Indices: 41063445--41063493 Score: 59
Period size: 15 Copynumber: 3.4 Consensus size: 15
41063435 CTTTTGAATA
41063445 TTGGGCTATAGGT--T
1 TTGGGCT-TAGGTGAT
41063459 TTGGGCTTAGGTGAT
1 TTGGGCTTAGGTGAT
*
41063474 TTGGGTTTAGGTGA-
1 TTGGGCTTAGGTGAT
41063488 TTGGGC
1 TTGGGC
41063494 CTTGGGTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 5 0.16
14 12 0.39
15 14 0.45
ACGTcount: A:0.12, C:0.06, G:0.41, T:0.41
Consensus pattern (15 bp):
TTGGGCTTAGGTGAT
Found at i:41063569 original size:19 final size:20
Alignment explanation
Indices: 41063547--41063605 Score: 86
Period size: 20 Copynumber: 3.0 Consensus size: 20
41063537 CAAAATTTAA
*
41063547 AATTTTTATAAA-TATTTTG
1 AATTTTTAAAAATTATTTTG
*
41063566 AA-TTTTAAAAATTATTTTC
1 AATTTTTAAAAATTATTTTG
41063585 AATTTTTAAAAATTATTTTG
1 AATTTTTAAAAATTATTTTG
41063605 A
1 A
41063606 TTATTTTGTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.23
19 10 0.29
20 17 0.49
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (20 bp):
AATTTTTAAAAATTATTTTG
Found at i:41063850 original size:5 final size:5
Alignment explanation
Indices: 41063840--41063865 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
41063830 TTTAATTTTT
41063840 TCGAA TCGAA TCGAA TCGAA TCGAA T
1 TCGAA TCGAA TCGAA TCGAA TCGAA T
41063866 TTTATTCGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (5 bp):
TCGAA
Found at i:41073724 original size:37 final size:37
Alignment explanation
Indices: 41073621--41073829 Score: 343
Period size: 37 Copynumber: 5.7 Consensus size: 37
41073611 TACGTATGAT
* *
41073621 CACTTATCAC-TTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41073656 CACCTATCACTTTGTTTC-TGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
41073692 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41073729 CACTTATCACTTTATTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41073766 CACTTATCACTTTGTTTCTTGATAAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
41073803 CACTTATCACTTTGTCTCTTGATCAGA
1 CACTTATCACTTTGTTTCTTGATCAGA
41073830 AGTACTCAAA
Statistics
Matches: 163, Mismatches: 8, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
35 9 0.06
36 38 0.23
37 116 0.71
ACGTcount: A:0.25, C:0.21, G:0.15, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:41081844 original size:19 final size:19
Alignment explanation
Indices: 41081820--41081868 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
41081810 CACTTCGTGT
*
41081820 GCCAATATGCGCTTTGTGC
1 GCCAATATGCGCTTTGAGC
**
41081839 GCCAATGATGATCTTTGAGC
1 GCCAAT-ATGCGCTTTGAGC
*
41081859 ACCAATATGC
1 GCCAATATGC
41081869 ACTATATGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.24, C:0.24, G:0.22, T:0.29
Consensus pattern (19 bp):
GCCAATATGCGCTTTGAGC
Found at i:41083220 original size:17 final size:19
Alignment explanation
Indices: 41083198--41083233 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
41083188 AAAATTTATG
41083198 AAAAATT-TT-AAAATATA
1 AAAAATTATTAAAAATATA
41083215 AAAAATTATTAAAAATATA
1 AAAAATTATTAAAAATATA
41083234 GAAAGTGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
18 2 0.12
19 8 0.47
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTATTAAAAATATA
Found at i:41083261 original size:17 final size:18
Alignment explanation
Indices: 41083225--41083262 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
41083215 AAAAATTATT
* *
41083225 AAAAATATAGAAAGTGGA
1 AAAAATATAGAAAATAGA
41083243 AAAAATATA-AAAATAGA
1 AAAAATATAGAAAATAGA
41083260 AAA
1 AAA
41083263 TTTTAAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (18 bp):
AAAAATATAGAAAATAGA
Found at i:41083648 original size:10 final size:10
Alignment explanation
Indices: 41083630--41083691 Score: 53
Period size: 10 Copynumber: 6.4 Consensus size: 10
41083620 TAAGTTTCTA
*
41083630 ATAACATTTT
1 ATAATATTTT
41083640 ATAATATTTT
1 ATAATATTTT
41083650 -TAA-ATTTTT
1 ATAATA-TTTT
41083659 ATTAAT-TTTT
1 A-TAATATTTT
41083669 -TAATAATTTT
1 ATAAT-ATTTT
41083679 A-AATATTTT
1 ATAATATTTT
41083688 ATAA
1 ATAA
41083692 AATCATAATT
Statistics
Matches: 43, Mismatches: 1, Indels: 16
0.72 0.02 0.27
Matches are distributed among these distances:
8 5 0.12
9 13 0.30
10 22 0.51
11 3 0.07
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (10 bp):
ATAATATTTT
Found at i:41083678 original size:28 final size:29
Alignment explanation
Indices: 41083635--41083689 Score: 85
Period size: 28 Copynumber: 1.9 Consensus size: 29
41083625 TTCTAATAAC
*
41083635 ATTTTATAATATTTTTAAAT-TTTTATTA
1 ATTTTATAATAATTTTAAATATTTTATTA
*
41083663 ATTTTTTAATAATTTTAAATATTTTAT
1 ATTTTATAATAATTTTAAATATTTTAT
41083690 AAAATCATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 18 0.75
29 6 0.25
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (29 bp):
ATTTTATAATAATTTTAAATATTTTATTA
Found at i:41083731 original size:15 final size:16
Alignment explanation
Indices: 41083711--41083768 Score: 61
Period size: 15 Copynumber: 3.8 Consensus size: 16
41083701 TATTACAATT
41083711 TTTATATATTTT-TAA
1 TTTATATATTTTATAA
41083726 TTTATAT-TTTTATAA
1 TTTATATATTTTATAA
*
41083741 TATATAT-TTTATATAA
1 TTTATATATTT-TATAA
*
41083757 TTT-TTTATTTTA
1 TTTATATATTTTA
41083769 ATAAAGTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.11
15 23 0.62
16 10 0.27
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTATATATTTTATAA
Done.