Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D11
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: 68311261
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 408745 characters in sequence are not A, C, G, or T
File 133 of 226
Found at i:41361172 original size:27 final size:27
Alignment explanation
Indices: 41361071--41361182 Score: 109
Period size: 27 Copynumber: 4.1 Consensus size: 27
41361061 CAAGTTTGGG
* * **
41361071 CATGCACTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
* * **
41361098 CATGCTTTCCATGCATTCCATGCAAAA
1 CATGCATTCCATGCATACCATGCAACC
*
41361125 CATGCATTCCATGCATTCCATGCAACC
1 CATGCATTCCATGCATACCATGCAACC
* *
41361152 CATGCATTTCATGCGA-ACCATGCATCC
1 CATGCATTCCATGC-ATACCATGCAACC
41361179 CATG
1 CATG
41361183 GAATTTGCTA
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
27 75 0.99
28 1 0.01
ACGTcount: A:0.29, C:0.33, G:0.12, T:0.26
Consensus pattern (27 bp):
CATGCATTCCATGCATACCATGCAACC
Found at i:41361182 original size:9 final size:9
Alignment explanation
Indices: 41361071--41361165 Score: 91
Period size: 9 Copynumber: 10.6 Consensus size: 9
41361061 CAAGTTTGGG
*
41361071 CATGCACTC
1 CATGCATTC
41361080 CATGCATTC
1 CATGCATTC
***
41361089 CATGCAAAA
1 CATGCATTC
*
41361098 CATGCTTTC
1 CATGCATTC
41361107 CATGCATTC
1 CATGCATTC
***
41361116 CATGCAAAA
1 CATGCATTC
41361125 CATGCATTC
1 CATGCATTC
41361134 CATGCATTC
1 CATGCATTC
**
41361143 CATGCAACC
1 CATGCATTC
*
41361152 CATGCATTT
1 CATGCATTC
41361161 CATGC
1 CATGC
41361166 GAACCATGCA
Statistics
Matches: 66, Mismatches: 20, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
9 66 1.00
ACGTcount: A:0.28, C:0.33, G:0.12, T:0.27
Consensus pattern (9 bp):
CATGCATTC
Found at i:41361347 original size:41 final size:41
Alignment explanation
Indices: 41361300--41361383 Score: 141
Period size: 41 Copynumber: 2.0 Consensus size: 41
41361290 GTTTAGACAT
*
41361300 TTTAAATGTGTGTCTTAAATACTGCACTTTAATTATAAGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
* *
41361341 TTTAAATATGTGTCTTAAATATTGCACTTTAATTATATGTC
1 TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
41361382 TT
1 TT
41361384 AGTTCTTACA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.48
Consensus pattern (41 bp):
TTTAAATATGTGTCTTAAATACTGCACTTTAATTATAAGTC
Found at i:41363047 original size:37 final size:37
Alignment explanation
Indices: 41363006--41363080 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
41362996 CCCCAAAAAG
41363006 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
41363043 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
1 AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
41363080 A
1 A
41363081 CCAAGCTCTC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.23, C:0.16, G:0.32, T:0.29
Consensus pattern (37 bp):
AATGATGCTTGGGGTGGTGGTGTGCCCAATCTAACAT
Found at i:41364534 original size:27 final size:27
Alignment explanation
Indices: 41364494--41364588 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
41364484 CGAGTTTAGG
* *
41364494 CATGCACTCTATGCATTCTATGAAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* ** *
41364521 CCTGCATTCCATGCGCTCTATGTAAAA
1 CATGCATTCCATGCATTCTATGAAAAA
* * * **
41364548 CATGCATTTCATGCATTCCATGCAACC
1 CATGCATTCCATGCATTCTATGAAAAA
*
41364575 CATGCATTTCATGC
1 CATGCATTCCATGC
41364589 GAATGCATCC
Statistics
Matches: 54, Mismatches: 14, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 54 1.00
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (27 bp):
CATGCATTCCATGCATTCTATGAAAAA
Found at i:41367386 original size:20 final size:20
Alignment explanation
Indices: 41367361--41367437 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 20
41367351 CATGCGGTTT
* *
41367361 AGCTCACTTGAGCTCAAGTC
1 AGCTCATTTAAGCTCAAGTC
* *
41367381 AGCTCATTTGAGCTCAAGTA
1 AGCTCATTTAAGCTCAAGTC
*
41367401 AGCTCATTCAAGCTCAAGTC
1 AGCTCATTTAAGCTCAAGTC
*
41367421 GGCTCATTTAAGCTCAA
1 AGCTCATTTAAGCTCAA
41367438 TTCAAAGTAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.29, C:0.26, G:0.18, T:0.27
Consensus pattern (20 bp):
AGCTCATTTAAGCTCAAGTC
Found at i:41367455 original size:40 final size:40
Alignment explanation
Indices: 41367361--41367468 Score: 114
Period size: 40 Copynumber: 2.7 Consensus size: 40
41367351 CATGCGGTTT
*
41367361 AGCTCACTT-GAGCTCAAGTCAGCTCATTTGAGCTCAAGTA
1 AGCTCA-TTCGAGCTCAAGTCAGCTCATTTAAGCTCAAGTA
* * *
41367401 AGCTCATTCAAGCTCAAGTCGGCTCATTTAAGCTCAATTCAA
1 AGCTCATTCGAGCTCAAGTCAGCTCATTTAAGCTCAAGT--A
* *
41367443 AG-T-ATTCGAGCTCAATTTAGCTCATT
1 AGCTCATTCGAGCTCAAGTCAGCTCATT
41367469 GAGCTCGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
39 2 0.04
40 51 0.89
41 1 0.02
42 3 0.05
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.31
Consensus pattern (40 bp):
AGCTCATTCGAGCTCAAGTCAGCTCATTTAAGCTCAAGTA
Found at i:41369489 original size:39 final size:38
Alignment explanation
Indices: 41369404--41369567 Score: 183
Period size: 39 Copynumber: 4.3 Consensus size: 38
41369394 GCTCCTCGTT
* * * *
41369404 CAAATGCCTTCGGGACATAGCCCGGTTAGTAA-CT--CA
1 CAAATGCCTTCGGGACTTAACCCGG-AATTAATCTCGCA
* *
41369440 C-AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATT-AATCTCGCA
* *
41369478 CGAATGCCTTCGGGACTTAACCCGGAATTGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATT-AATCTCGCA
*
41369517 CAAAGGCCTTCGGGACTTAACCCGGAATTAATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGAATTAATCTCGCA
*
41369555 CAAATACCTTCGG
1 CAAATGCCTTCGG
41369568 ATCTTAGTCC
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
34 1 0.01
35 23 0.21
36 3 0.03
38 22 0.20
39 60 0.55
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (38 bp):
CAAATGCCTTCGGGACTTAACCCGGAATTAATCTCGCA
Found at i:41369540 original size:78 final size:78
Alignment explanation
Indices: 41369438--41369620 Score: 212
Period size: 78 Copynumber: 2.3 Consensus size: 78
41369428 GTTAGTAACT
* * * *
41369438 CACAATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACGAATGCCTTCGGGA-CTTAACCCG
1 CACAAAGCCTTCGGGACTTAACCCGGAATT-AAACTCGCACAAATACCTTC-GGATCTTAACCCG
* *
41369502 GA-ATTGT-A-TCTCG
64 GATATAGTCACT-TAG
* **
41369515 CACAAAGGCCTTCGGGACTTAACCCGGAATTAATCTCGCACAAATACCTTCGGATCTTAGTCCGG
1 CACAAA-GCCTTCGGGACTTAACCCGGAATTAAACTCGCACAAATACCTTCGGATCTTAACCCGG
41369580 ATATAGTCACTTAG
65 ATATAGTCACTTAG
*
41369594 CACAAAGCCTTCGGGACTTAGCCCGGA
1 CACAAAGCCTTCGGGACTTAACCCGGA
41369621 CAGCATTCAA
Statistics
Matches: 91, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
76 3 0.03
77 31 0.34
78 47 0.52
79 9 0.10
80 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (78 bp):
CACAAAGCCTTCGGGACTTAACCCGGAATTAAACTCGCACAAATACCTTCGGATCTTAACCCGGA
TATAGTCACTTAG
Found at i:41369580 original size:38 final size:39
Alignment explanation
Indices: 41369441--41369567 Score: 184
Period size: 39 Copynumber: 3.3 Consensus size: 39
41369431 AGTAACTCAC
* * * *
41369441 AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGAATTGAATCTCGCACA
*
41369480 AATGCCTTCGGGACTTAACCCGGAATTGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTGAATCTCGCACA
*
41369519 AAGGCCTTCGGGACTTAACCCGGAATT-AATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGAATTGAATCTCGCACA
*
41369557 AATACCTTCGG
1 AATGCCTTCGG
41369568 ATCTTAGTCC
Statistics
Matches: 79, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
38 19 0.24
39 60 0.76
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGAATTGAATCTCGCACA
Found at i:41377028 original size:40 final size:39
Alignment explanation
Indices: 41376976--41377159 Score: 165
Period size: 40 Copynumber: 4.6 Consensus size: 39
41376966 TAACTCATTC
*
41376976 AATGCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGA-TTTAAAACTCGCACA
*** *
41377016 AATGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGG-ATTTAAAACTCGCACA
* *
41377056 AAGGCCTTCGGGACTTAACCCGGAATTAATAACTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAA-AACTCGCACA
* ** * ** *
41377096 AATACCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACA
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-AAAC-TCGCACA
*
41377137 AA-GCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
41377160 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 22, Indels: 12
0.77 0.15 0.08
Matches are distributed among these distances:
39 5 0.04
40 99 0.85
41 12 0.10
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAAAACTCGCACA
Found at i:41377038 original size:79 final size:80
Alignment explanation
Indices: 41376939--41377159 Score: 193
Period size: 80 Copynumber: 2.8 Consensus size: 80
41376929 CTCGTTCAAG
* * ** * *
41376939 TGCCTTCGGGACATAGCCCGGTCA-TAGTAACTCATTC-AATGCCTTCGGGACTTAACCCGGATT
1 TGCCTTCGGGACATAACCCGG-AATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGA-A
*
41377002 TTAA-AACTCGCACGAA
64 TTAATAACTCGCACAAA
* * * *
41377018 TGCCTTCGGGACTTAACCCGGAATTGGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAATT
1 TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
41377083 AATAACTCGCACAAA
66 AATAACTCGCACAAA
* * ** * * *
41377098 TACCTTC-GGATCTTAGTCCGG-ATATAGTCACTTAGCACAAA-GCCTTCGGGACTTAGCCCGGA
1 TGCCTTCGGGA-CATAACCCGGAAT-TAGTAACTCA-CACAAAGGCCTTCGGGACTTAACCCGGA
41377160 CAGCATTCAA
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
78 1 0.01
79 36 0.31
80 73 0.63
81 6 0.05
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (80 bp):
TGCCTTCGGGACATAACCCGGAATTAGTAACTCACACAAAGGCCTTCGGGACTTAACCCGGAATT
AATAACTCGCACAAA
Found at i:41377119 original size:80 final size:80
Alignment explanation
Indices: 41376979--41377159 Score: 210
Period size: 80 Copynumber: 2.3 Consensus size: 80
41376969 CTCATTCAAT
* * *
41376979 GCCTTCGGGACTTAACCCGGATTTTAAAACTCGCACGAATGCCTTCGGGACTTAACCCGGA-ATT
1 GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATA-T
* *
41377043 GGT-A-TCTCGCACAAA
65 AGTCACT-TAGCACAAA
**
41377058 GGCCTTCGGGACTTAACCCGGA-ATTAATAACTCGCACAAATACCTTC-GGATCTTAGTCCGGAT
1 -GCCTTCGGGACTTAACCCGGATATTAA-AACTCGCACAAATACCTTCGGGA-CTTAACCCGGAT
41377121 ATAGTCACTTAGCACAAA
63 ATAGTCACTTAGCACAAA
*
41377139 GCCTTCGGGACTTAGCCCGGA
1 GCCTTCGGGACTTAACCCGGA
41377160 CAGCATTCAA
Statistics
Matches: 88, Mismatches: 8, Indels: 10
0.83 0.08 0.09
Matches are distributed among these distances:
79 7 0.08
80 70 0.80
81 10 0.11
82 1 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGACTTAACCCGGATATTAAAACTCGCACAAATACCTTCGGGACTTAACCCGGATATA
GTCACTTAGCACAAA
Found at i:41380654 original size:21 final size:20
Alignment explanation
Indices: 41380625--41380663 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
41380615 AAGCAATCGA
*
41380625 AAAAGAAAAAGAGAGTGAAG
1 AAAAGAAAAAGAAAGTGAAG
41380645 AAAAGCAAAAAGAAAGTGA
1 AAAAG-AAAAAGAAAGTGA
41380664 GGGTGAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.67, C:0.03, G:0.26, T:0.05
Consensus pattern (20 bp):
AAAAGAAAAAGAAAGTGAAG
Found at i:41380669 original size:27 final size:27
Alignment explanation
Indices: 41380624--41380675 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
41380614 CAAGCAATCG
*
41380624 AAAAAGAAAAAGAGAGTGAAGAAAAGC
1 AAAAAGAAAAAGAGAGTGAAAAAAAGC
** *
41380651 AAAAAGAAAGTGAGGGTGAAAAAAA
1 AAAAAGAAAAAGAGAGTGAAAAAAA
41380676 ATTTGAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAGTGAAAAAAAGC
Found at i:41380689 original size:18 final size:18
Alignment explanation
Indices: 41380668--41380702 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
41380658 AAGTGAGGGT
41380668 GAAAA-AAAATTTGAAAAC
1 GAAAAGAAAA-TTGAAAAC
41380686 GAAAAGAAAATTGAAAA
1 GAAAAGAAAATTGAAAA
41380703 TGAGATTGAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.69, C:0.03, G:0.14, T:0.14
Consensus pattern (18 bp):
GAAAAGAAAATTGAAAAC
Found at i:41382493 original size:10 final size:9
Alignment explanation
Indices: 41382478--41382591 Score: 59
Period size: 10 Copynumber: 11.6 Consensus size: 9
41382468 CATGTGGTTT
41382478 AGCTCACTTG
1 AGCTCA-TTG
41382488 AGCTCAAGTT-
1 AGCTC-A-TTG
41382498 AGCTCATTCG
1 AGCTCATT-G
* *
41382508 AGCTCAAGTC
1 AGCTC-ATTG
41382518 AGCTCATTCG
1 AGCTCATT-G
* *
41382528 AGCTCAAGTC
1 AGCTC-ATTG
41382538 AGCTCATTTG
1 AGCTCA-TTG
* *
41382548 AGCTCAAATC
1 AGCTC-ATTG
41382558 AGCTCATTCG
1 AGCTCATT-G
*
41382568 AGCTCAATTT
1 AGCTC-ATTG
41382578 AGCTCATTG
1 AGCTCATTG
41382587 AGCTC
1 AGCTC
41382592 GTTGTTAGCT
Statistics
Matches: 79, Mismatches: 15, Indels: 21
0.69 0.13 0.18
Matches are distributed among these distances:
8 2 0.03
9 14 0.18
10 52 0.66
11 11 0.14
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (9 bp):
AGCTCATTG
Found at i:41382501 original size:20 final size:20
Alignment explanation
Indices: 41382478--41382591 Score: 160
Period size: 20 Copynumber: 5.8 Consensus size: 20
41382468 CATGTGGTTT
*
41382478 AGCTCACTT-GAGCTCAAGTT
1 AGCTCA-TTCGAGCTCAAGTC
41382498 AGCTCATTCGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTC
41382518 AGCTCATTCGAGCTCAAGTC
1 AGCTCATTCGAGCTCAAGTC
* *
41382538 AGCTCATTTGAGCTCAAATC
1 AGCTCATTCGAGCTCAAGTC
* *
41382558 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAAGTC
41382578 AGCTCATT-GAGCTC
1 AGCTCATTCGAGCTC
41382592 GTTGTTAGCT
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
19 8 0.09
20 79 0.91
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAAGTC
Found at i:41394005 original size:40 final size:40
Alignment explanation
Indices: 41393948--41394177 Score: 327
Period size: 40 Copynumber: 5.8 Consensus size: 40
41393938 ATTTGAATAC
* * * *
41393948 ATCCGGGCTAAGTCCCGAAGGCATTTATGCTAG-TGATTTT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGA-TAT
41393988 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
41394028 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
41394068 ATTCGGGCTAAGACCCGAAGGCATTTGTGCGAGATGATAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
41394108 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
* * *
41394148 ACCCGGGTTAAGACCCGAAGGCAATTGTGC
1 ATCCGGGCTAAGACCCGAAGGCATTTGTGC
41394178 TTGTGGTTAT
Statistics
Matches: 174, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
40 171 0.98
41 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
Found at i:41404219 original size:105 final size:105
Alignment explanation
Indices: 41404079--41404270 Score: 294
Period size: 105 Copynumber: 1.8 Consensus size: 105
41404069 TGAATATAAA
* * * * * *
41404079 GGGGGTTGCTAAGTGCTGATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCTGACTCATTGGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTAGTGG
* *
41404144 TTGCTGAGTGCTGATTCCACCGTATCTTTGAATGTAAAAG
66 TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
*
41404184 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTGCTGATTCCCCGAATCACTAGTGG
1 GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTAGTGG
*
41404249 TTGCTAAGTTCTGAATCCACCG
66 TTGCTAAGTGCTGAATCCACCG
41404271 ATAACGGACA
Statistics
Matches: 77, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
105 77 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.30
Consensus pattern (105 bp):
GGGGGTTACTAAGTGCTAATTCCCCCAAGGGGTTGCTAAGTACTGATTCCCCGAATCACTAGTGG
TTGCTAAGTGCTGAATCCACCGTATCTTTGAATGTAAAAG
Found at i:41409066 original size:79 final size:81
Alignment explanation
Indices: 41408964--41409148 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41408954 GCTCCTCGTT
* *
41408964 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41409027 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
41409044 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
41409108 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
41409124 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41409149 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:41409148 original size:40 final size:40
Alignment explanation
Indices: 41408964--41409148 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
41408954 GCTCCTCGTT
* *
41408964 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41409004 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41409044 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
41409083 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
41409124 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41409149 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41417045 original size:79 final size:81
Alignment explanation
Indices: 41416943--41417127 Score: 236
Period size: 79 Copynumber: 2.3 Consensus size: 81
41416933 GCTCCTCGTT
* *
41416943 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCC
1 CAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAACCC
* *
41417006 GGATTTAGTAAC-TCGCA
64 GGATATAGTAACTTAGCA
* **
41417023 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
* *
41417087 ATATGGTCACTTAGCA
66 ATATAGTAACTTAGCA
41417103 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41417128 CATCATTCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 3 0.03
79 55 0.60
80 34 0.37
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (81 bp):
CAAATGCCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGG
ATATAGTAACTTAGCA
Found at i:41417127 original size:40 final size:40
Alignment explanation
Indices: 41416943--41417127 Score: 234
Period size: 40 Copynumber: 4.7 Consensus size: 40
41416933 GCTCCTCGTT
* *
41416943 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
41416983 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
41417023 CAAATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
41417062 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
41417103 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
41417128 CATCATTCAA
Statistics
Matches: 126, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
38 2 0.02
39 32 0.25
40 80 0.63
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:41421108 original size:11 final size:11
Alignment explanation
Indices: 41421087--41421122 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
41421077 TAAAACCTGC
41421087 TAAAA-CAAAT
1 TAAAAGCAAAT
41421097 TAAAAGCAAAT
1 TAAAAGCAAAT
*
41421108 TTAAAGCAAAT
1 TAAAAGCAAAT
41421119 TAAA
1 TAAA
41421123 CACACAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 5 0.22
11 18 0.78
ACGTcount: A:0.64, C:0.08, G:0.06, T:0.22
Consensus pattern (11 bp):
TAAAAGCAAAT
Found at i:41423662 original size:28 final size:28
Alignment explanation
Indices: 41423620--41423682 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
41423610 CTATTCACTA
*
41423620 ACAGT-ACAATGTGGGCCTTATCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
*
41423647 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAATGTGGGCCTTAGCCCAAT
41423675 ACAGTAAC
1 ACAGTAAC
41423683 CAATACAGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
27 5 0.15
28 28 0.85
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (28 bp):
ACAGTAACAATGTGGGCCTTAGCCCAAT
Found at i:41424055 original size:27 final size:27
Alignment explanation
Indices: 41424035--41424435 Score: 376
Period size: 27 Copynumber: 14.9 Consensus size: 27
41424025 GGGTATAACA
* *
41424035 GTCATTTTACCTTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* ** * *
41424062 GTCATTCTACCCTACAGAGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
41424089 GCCATTTTACCCTACGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* **
41424116 GTCATTTTACCCTATGGTGGTATTTTA
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41424143 GTCATTTTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * ** *
41424170 GTCATTTTATCTTATAAGGGTATTCCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41424197 ATCATTTTACCCTGTGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
41424224 ATTATTTTACCCTATGGGGGGA-TTCTG
1 GTCATTTTACCCTATGGGGGTATTTC-G
* * * *
41424251 GTCATTTTACACTATGAGGGTATTGCT
1 GTCATTTTACCCTATGGGGGTATTTCG
41424278 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
41424305 ATTATTTTACCATATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
41424332 GTCATTTTACCTTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * * *
41424359 GTTAATTTATCCTATGGGGATATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
41424386 GTAATTTTACCCTAT--GGATATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
41424411 TTCATTTTACCCTATGGGGGTATTT
1 GTCATTTTACCCTATGGGGGTATTT
41424436 GGGCTCTCGA
Statistics
Matches: 297, Mismatches: 73, Indels: 8
0.79 0.19 0.02
Matches are distributed among these distances:
25 22 0.07
26 3 0.01
27 270 0.91
28 2 0.01
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.43
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:41432273 original size:33 final size:34
Alignment explanation
Indices: 41432222--41432296 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
41432212 AGAGTTAAAC
*
41432222 AAATTAATTACTAACACTTATTTAAGTTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41432256 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41432289 AATTTAAT
1 AAATTAAT
41432297 AAACCAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.39
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:41433444 original size:27 final size:27
Alignment explanation
Indices: 41433412--41433464 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
41433402 CTTGTCTGTT
41433412 TCTTTTTCACTCTCAATCTCTTTTTTC
1 TCTTTTTCACTCTCAATCTCTTTTTTC
* **
41433439 TCTTTTTCATTCTCTTTCTCTTTTTT
1 TCTTTTTCACTCTCAATCTCTTTTTT
41433465 GATTTCTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.08, C:0.26, G:0.00, T:0.66
Consensus pattern (27 bp):
TCTTTTTCACTCTCAATCTCTTTTTTC
Found at i:41434312 original size:11 final size:11
Alignment explanation
Indices: 41434296--41434321 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
41434286 TTAGAAAGTG
41434296 TAAAGGATGAA
1 TAAAGGATGAA
41434307 TAAAGGATGAA
1 TAAAGGATGAA
41434318 TAAA
1 TAAA
41434322 AGCAAAACAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.23, T:0.19
Consensus pattern (11 bp):
TAAAGGATGAA
Found at i:41439041 original size:24 final size:24
Alignment explanation
Indices: 41439009--41439057 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
41438999 AATTATTGAG
41439009 TTAGTTAAATTAGTTAAATACAGC
1 TTAGTTAAATTAGTTAAATACAGC
41439033 TTAGTTAAATTAGTTAAATACAGC
1 TTAGTTAAATTAGTTAAATACAGC
41439057 T
1 T
41439058 CAATTAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.41, C:0.08, G:0.12, T:0.39
Consensus pattern (24 bp):
TTAGTTAAATTAGTTAAATACAGC
Found at i:41439064 original size:24 final size:24
Alignment explanation
Indices: 41439013--41439064 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
41439003 ATTGAGTTAG
* *
41439013 TTAAATTAGTTAAATACAGCTTAG
1 TTAAATTAGTTAAATACAGCTCAA
41439037 TTAAATTAGTTAAATACAGCTCAA
1 TTAAATTAGTTAAATACAGCTCAA
41439061 TTAA
1 TTAA
41439065 TCATCATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (24 bp):
TTAAATTAGTTAAATACAGCTCAA
Found at i:41440588 original size:20 final size:20
Alignment explanation
Indices: 41440555--41440599 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
41440545 TAAATTCACA
41440555 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
41440575 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
41440595 TAATT
1 TAATT
41440600 CGGTTAGGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.53, C:0.11, G:0.04, T:0.31
Consensus pattern (20 bp):
TAATTAAAACAAGACCTAAT
Found at i:41442529 original size:27 final size:26
Alignment explanation
Indices: 41442495--41442551 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
41442485 TTTCACATCC
* *
41442495 TTTT-TCAATCTCAATTTCTTTTTTCT
1 TTTTCTCAATCTCAATCTC-ATTTTCT
*
41442521 TTTTCTCAATCTCACTCTCATTTTCT
1 TTTTCTCAATCTCAATCTCATTTTCT
41442547 TTTTC
1 TTTTC
41442552 AATTTCTTGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 15 0.56
27 12 0.44
ACGTcount: A:0.14, C:0.25, G:0.00, T:0.61
Consensus pattern (26 bp):
TTTTCTCAATCTCAATCTCATTTTCT
Found at i:41452401 original size:20 final size:20
Alignment explanation
Indices: 41452378--41452421 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
41452368 CGCTCCAACC
*
41452378 AGCTCATTTGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
41452398 AGCTCATTCGAGCTCAATTT
1 AGCTCATTCGAGCTCAATTT
41452418 AGCT
1 AGCT
41452422 TTCCATCAGC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (20 bp):
AGCTCATTCGAGCTCAATTT
Found at i:41454515 original size:27 final size:26
Alignment explanation
Indices: 41454485--41454539 Score: 67
Period size: 27 Copynumber: 2.1 Consensus size: 26
41454475 TTAAACCTAC
41454485 TTCTAA-AGAAAAAAACTCAAGAGAGAA
1 TTCTAAGAG-AAAAAACTCAA-AGAGAA
**
41454512 TTCTCGGAGAAAAAACTCAAAGAGAA
1 TTCTAAGAGAAAAAACTCAAAGAGAA
41454538 TT
1 TT
41454540 TTCAATCAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 8 0.32
27 15 0.60
28 2 0.08
ACGTcount: A:0.53, C:0.13, G:0.16, T:0.18
Consensus pattern (26 bp):
TTCTAAGAGAAAAAACTCAAAGAGAA
Found at i:41461931 original size:15 final size:15
Alignment explanation
Indices: 41461913--41461944 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
41461903 TTCTTCATTT
41461913 TCTTTTTCTCTCATC
1 TCTTTTTCTCTCATC
*
41461928 TCTTTTTTTCTCATC
1 TCTTTTTCTCTCATC
41461943 TC
1 TC
41461945 GAGTTCGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.62
Consensus pattern (15 bp):
TCTTTTTCTCTCATC
Found at i:41462977 original size:9 final size:9
Alignment explanation
Indices: 41462963--41462996 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
41462953 TTTCACGATT
41462963 TTTTTTTAG
1 TTTTTTTAG
41462972 TTTTTTTAG
1 TTTTTTTAG
*
41462981 TTTTTTT-C
1 TTTTTTTAG
41462989 TTTTTTTA
1 TTTTTTTA
41462997 CGATACCGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.09, C:0.03, G:0.06, T:0.82
Consensus pattern (9 bp):
TTTTTTTAG
Found at i:41466493 original size:39 final size:39
Alignment explanation
Indices: 41466439--41466516 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41466429 CATAAGAATT
41466439 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
*
41466478 TATTCATGAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
41466517 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
Found at i:41469561 original size:43 final size:43
Alignment explanation
Indices: 41469500--41469613 Score: 158
Period size: 43 Copynumber: 2.7 Consensus size: 43
41469490 GTATCGCTAA
* * *
41469500 CTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGACCAGGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
*
41469543 CTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
1 CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
* *
41469586 CTTTAGCGACGC-TTTCTCCAAAAACGCC
1 CTTTAGCGGCGCTTTTC-CCACAAACGCC
41469614 ACTGAAGGTC
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
42 4 0.06
43 59 0.94
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAAACCAAGAC
Found at i:41470540 original size:23 final size:23
Alignment explanation
Indices: 41470506--41470990 Score: 342
Period size: 23 Copynumber: 21.3 Consensus size: 23
41470496 AATGGAAAGT
*
41470506 AGCACTTTAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41470529 AGCGA-TAAAACA-TCTCAATTTGC
1 AGC-ACTTAAACACT-TCAATTTAC
* **
41470552 AACAAC-TAAACACTTCAATTTGT
1 AGC-ACTTAAACACTTCAATTTAC
*
41470575 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41470598 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41470621 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41470643 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
* *
41470666 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
41470689 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* * *
41470712 AGCATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41470735 AGCACTT-AACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41470757 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41470779 AGCAATAAAACA-TCTCAATTT-C
1 AGCACTTAAACACT-TCAATTTAC
*
41470801 TAGCAAC-TAAACACTTCAATTTGC
1 -AGC-ACTTAAACACTTCAATTTAC
41470825 AGCACTTAAACACTTCAATTTAC
1 AGCACTTAAACACTTCAATTTAC
* * *
41470848 AGCATTTAAACACTTAAATTTGC
1 AGCACTTAAACACTTCAATTTAC
*
41470871 AGCACTTAAACA-TATCAATTAAC
1 AGCACTTAAACACT-TCAATTTAC
* * * *
41470894 AACATTTATACACCTCAA-TTAC
1 AGCACTTAAACACTTCAATTTAC
* *
41470916 AGCGA-TAAAACA-TCTCAATTTCC
1 AGC-ACTTAAACACT-TCAATTTAC
* *
41470939 AGCAAC-TAAATACTTCAATTTGC
1 AGC-ACTTAAACACTTCAATTTAC
*
41470962 AGCACTTAAACACTTCAATTTGC
1 AGCACTTAAACACTTCAATTTAC
41470985 AGCACT
1 AGCACT
41470991 ATCAAATTTC
Statistics
Matches: 362, Mismatches: 69, Indels: 62
0.73 0.14 0.13
Matches are distributed among these distances:
21 1 0.00
22 70 0.19
23 284 0.78
24 7 0.02
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (23 bp):
AGCACTTAAACACTTCAATTTAC
Found at i:41470947 original size:137 final size:137
Alignment explanation
Indices: 41470543--41470988 Score: 788
Period size: 137 Copynumber: 3.3 Consensus size: 137
41470533 ATAAAACATC
* ** * *
41470543 TCAATTTGCAACAAC-TAAACACTTCAATTTGTAGCACTTAAACACTTCAATTTGCAGCACTTAA
1 TCAATTTGCAGC-ACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAA
41470607 ACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
65 ACATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAAC
41470672 TAAATACT
130 TAAATACT
41470680 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTT-AA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
* *
41470744 CATATCAATTAACAACATTTATACACCTCAATTACAGCAATAAAACATCTCAATTTCTAGCAACT
66 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
*
41470809 AAACACT
131 AAATACT
41470816 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
41470881 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
66 CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
41470946 AAATACT
131 AAATACT
*
41470953 TCAATTTGCAGCACTTAAACACTTCAATTTGCAGCA
1 TCAATTTGCAGCACTTAAACACTTCAATTTACAGCA
41470989 CTATCAAATT
Statistics
Matches: 295, Mismatches: 12, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
136 135 0.46
137 160 0.54
ACGTcount: A:0.40, C:0.24, G:0.06, T:0.30
Consensus pattern (137 bp):
TCAATTTGCAGCACTTAAACACTTCAATTTACAGCATTTAAACACTTAAATTTGCAGCACTTAAA
CATATCAATTAACAACATTTATACACCTCAATTACAGCGATAAAACATCTCAATTTCCAGCAACT
AAATACT
Found at i:41471408 original size:41 final size:39
Alignment explanation
Indices: 41471325--41471408 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
41471315 GCACGATACA
* **
41471325 ATATAAAAAGCATATATAAATATATGAATGTAGAGGCAT
1 ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
*
41471364 ATATAAAAAGCATATATAAATATATGTATGTCACAGAAACT
1 ATATAAAAAGCATATATAAATATATGAATGT-ACAGAAA-T
41471405 ATAT
1 ATAT
41471409 TCATTTATGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
39 30 0.77
40 4 0.10
41 5 0.13
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (39 bp):
ATATAAAAAGCATATATAAATATATGAATGTACAGAAAT
Found at i:41474177 original size:140 final size:135
Alignment explanation
Indices: 41474029--41474365 Score: 404
Period size: 149 Copynumber: 2.4 Consensus size: 135
41474019 AACGCCGCTA
* * *
41474029 TTTCATTTTGAACAAAATGACACCGTTTTGTTATGCTAAAAATTTTTTATTTTATTTTTTATAAA
1 TTTCATTTTAAACAAAACGACACCGTTTTGCTATGCTAAAAATTTTTTA--TTATTTTTTATAAA
*
41474094 TTGATTTATTTTTTGCGGCGTTTTTATAAAAAAACGCCGCAATTGCTTACCTTTAGAAAAACGCC
64 TTGATTTA--TTTTGCGGCGTTTTTAT-AAAAAACACCGCAATTGCTTACCTTTAGAAAAACGCC
41474159 GCAAAATTTT
126 GCAAAATTTT
* *
41474169 TTTCATTTTAAACAAAACGACGCCGTTTTGCTATTCTAAAAATTTTTTATTATTTTTTATAAATT
1 TTTCATTTTAAACAAAACGACACCGTTTTGCTATGCTAAAAATTTTTTATTATTTTTTATAAATT
*
41474234 GATTTATTTTGCGGCGTTTTTATAAAAAACACCGCTATTGCTTACCTTTAGCGGCGTTTTTCATA
66 GATTTATTTTGCGGCGTTTTTATAAAAAACACCGCAATTGCTTACCTTTA-----G--------A
41474299 AAAACGCCGCAAAATTTTT
118 AAAACGCCGCAAAA-TTTT
** * *
41474318 TTTCATTTTAAACAAAACGACGTCGTTTTTCTATTCTAAAAATTTTTT
1 TTTCATTTTAAACAAAACGACACCGTTTTGCTATGCTAAAAATTTTTT
41474366 TATTTTGTTT
Statistics
Matches: 174, Mismatches: 9, Indels: 19
0.86 0.04 0.09
Matches are distributed among these distances:
135 25 0.14
136 17 0.10
138 22 0.13
140 45 0.26
148 15 0.09
149 50 0.29
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (135 bp):
TTTCATTTTAAACAAAACGACACCGTTTTGCTATGCTAAAAATTTTTTATTATTTTTTATAAATT
GATTTATTTTGCGGCGTTTTTATAAAAAACACCGCAATTGCTTACCTTTAGAAAAACGCCGCAAA
ATTTT
Found at i:41474391 original size:15 final size:15
Alignment explanation
Indices: 41474373--41474402 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41474363 TTTTATTTTG
*
41474373 TTTTTTATATATTAA
1 TTTTTTATAAATTAA
41474388 TTTTTTATAAATTAA
1 TTTTTTATAAATTAA
41474403 AATAAAAAGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTTTTTATAAATTAA
Found at i:41474973 original size:8 final size:8
Alignment explanation
Indices: 41474962--41475048 Score: 96
Period size: 8 Copynumber: 11.5 Consensus size: 8
41474952 CTGAATCCCT
41474962 AACCCTTA
1 AACCCTTA
41474970 AACCCTTA
1 AACCCTTA
41474978 AACCCTTA
1 AACCCTTA
41474986 AACCCTT-
1 AACCCTTA
41474993 AACCCTTA
1 AACCCTTA
41475001 AATCCC-TA
1 AA-CCCTTA
*
41475009 AACCCCT-
1 AACCCTTA
*
41475016 AACCCCTA
1 AACCCTTA
41475024 AA-CCTTA
1 AACCCTTA
*
41475031 AATCC-T-
1 AACCCTTA
41475037 AACCCTTA
1 AACCCTTA
41475045 AACC
1 AACC
41475049 ATAATCCCTA
Statistics
Matches: 70, Mismatches: 2, Indels: 14
0.81 0.02 0.16
Matches are distributed among these distances:
6 4 0.06
7 25 0.36
8 38 0.54
9 3 0.04
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (8 bp):
AACCCTTA
Found at i:41474974 original size:23 final size:23
Alignment explanation
Indices: 41474948--41475046 Score: 89
Period size: 23 Copynumber: 4.4 Consensus size: 23
41474938 CCTTAACTCG
*
41474948 ACCCCTGAATCCCT-AACCCTTAA
1 ACCCCTAAATCCCTAAACCCTT-A
*
41474971 ACCCTTAAA-CCCTTAAACCCTTA
1 ACCCCTAAATCCC-TAAACCCTTA
* *
41474994 ACCCTTAAATCCCTAAACCCCTA
1 ACCCCTAAATCCCTAAACCCTTA
* *
41475017 ACCCCTAAA-CCTTAAATCC-TA
1 ACCCCTAAATCCCTAAACCCTTA
*
41475038 ACCCTTAAA
1 ACCCCTAAA
41475047 CCATAATCCC
Statistics
Matches: 66, Mismatches: 7, Indels: 8
0.81 0.09 0.10
Matches are distributed among these distances:
21 10 0.15
22 11 0.17
23 35 0.53
24 10 0.15
ACGTcount: A:0.35, C:0.40, G:0.01, T:0.23
Consensus pattern (23 bp):
ACCCCTAAATCCCTAAACCCTTA
Found at i:41474983 original size:16 final size:15
Alignment explanation
Indices: 41474958--41475048 Score: 107
Period size: 16 Copynumber: 6.1 Consensus size: 15
41474948 ACCCCTGAAT
41474958 CCCT-AACCCTTAAA
1 CCCTAAACCCTTAAA
41474972 CCCTTAAACCCTTAAA
1 CCC-TAAACCCTTAAA
*
41474988 CCCTTAACCCTTAAA
1 CCCTAAACCCTTAAA
* *
41475003 TCCCTAAACCCCTAAC
1 -CCCTAAACCCTTAAA
41475019 CCCTAAA-CCTTAAA
1 CCCTAAACCCTTAAA
*
41475033 TCCT-AACCCTTAAA
1 CCCTAAACCCTTAAA
41475047 CC
1 CC
41475049 ATAATCCCTA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
13 2 0.03
14 19 0.29
15 19 0.29
16 25 0.38
ACGTcount: A:0.35, C:0.42, G:0.00, T:0.23
Consensus pattern (15 bp):
CCCTAAACCCTTAAA
Found at i:41475063 original size:8 final size:7
Alignment explanation
Indices: 41474958--41475060 Score: 75
Period size: 8 Copynumber: 14.0 Consensus size: 7
41474948 ACCCCTGAAT
41474958 CCCT-AA
1 CCCTAAA
41474964 CCCTTAAA
1 CCC-TAAA
41474972 CCCTTAAA
1 CCC-TAAA
41474980 CCCTTAAA
1 CCC-TAAA
*
41474988 CCCTTAA
1 CCCTAAA
41474995 CCCTTAAA
1 CCC-TAAA
41475003 TCCCTAAA
1 -CCCTAAA
*
41475011 CCCCTAAC
1 -CCCTAAA
41475019 CCCTAAA
1 CCCTAAA
*
41475026 CCTTAAA
1 CCCTAAA
*
41475033 TCCT-AA
1 CCCTAAA
41475039 CCCTTAAA
1 CCC-TAAA
* *
41475047 CCATAAT
1 CCCTAAA
41475054 CCCTAAA
1 CCCTAAA
41475061 TCCATACTCC
Statistics
Matches: 78, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
6 7 0.09
7 30 0.38
8 38 0.49
9 3 0.04
ACGTcount: A:0.37, C:0.40, G:0.00, T:0.23
Consensus pattern (7 bp):
CCCTAAA
Found at i:41475065 original size:15 final size:15
Alignment explanation
Indices: 41475029--41475075 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
41475019 CCCTAAACCT
41475029 TAAATCC-TAA-CCC
1 TAAATCCATAATCCC
41475042 TTAAA-CCATAATCCC
1 -TAAATCCATAATCCC
*
41475057 TAAATCCATACTCCC
1 TAAATCCATAATCCC
41475072 TAAA
1 TAAA
41475076 CCTTAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 2 0.07
14 11 0.38
15 16 0.55
ACGTcount: A:0.40, C:0.34, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:41475293 original size:33 final size:33
Alignment explanation
Indices: 41475227--41475295 Score: 84
Period size: 33 Copynumber: 2.1 Consensus size: 33
41475217 TCTAAACCCA
* ** * *
41475227 AAACCCTAACCTGACCCTGAATCCCTAATCCCT
1 AAACCCTAACCTAACCCAAAATCCATAACCCCT
*
41475260 AAACCCTAACCTAACCCAAAATTCATAACCCCT
1 AAACCCTAACCTAACCCAAAATCCATAACCCCT
41475293 AAA
1 AAA
41475296 TATTATTTAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.39, C:0.39, G:0.03, T:0.19
Consensus pattern (33 bp):
AAACCCTAACCTAACCCAAAATCCATAACCCCT
Found at i:41476219 original size:41 final size:41
Alignment explanation
Indices: 41476151--41476390 Score: 337
Period size: 41 Copynumber: 5.9 Consensus size: 41
41476141 TTTTATTATT
*
41476151 ATTAGCGGCGCTTTTTTC-AAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGC-TTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* *
41476192 ATTAGCGGCGCTT-TCTCAAAAATGCCGCTAAAGATCC-GAGC
1 ATTAGCGGCGCTTCT-TCAAAAACGCCGCTAAAG-GCCAGAGC
*
41476233 ATTAGCGGCGCTTCTTCAAAAACGCCGCT-AAGGCTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
* * *
41476273 ATTAGCGGCGCTACATCAAAAACGCCGCTAAAGCCCAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
41476314 ATTAGCGGCGCTT-TTCAAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTCTTC-AAAAACGCCGCTAAAGGCCAGAGC
*
41476355 ATTAGCGGCGCTTCTTCAAAAACGACGCTAAAGGCC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
41476391 CCAAAAACTC
Statistics
Matches: 178, Mismatches: 13, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
39 2 0.01
40 40 0.22
41 130 0.73
42 6 0.03
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:41476292 original size:81 final size:80
Alignment explanation
Indices: 41476151--41476387 Score: 336
Period size: 81 Copynumber: 2.9 Consensus size: 80
41476141 TTTTATTATT
*
41476151 ATTAGCGGCGCTTTTTTC-AAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTTCTCAAAAAT
1 ATTAGCGGCGC--TTTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGC-TTCTCAAAAAC
*
41476215 GCCGCTAAAGATCC-GAGC
63 GCCGCTAAAG-CCCAGAGC
* *
41476233 ATTAGCGGCGCTTCTTCAAAAACGCCGCT-AAGGCTAGAGCATTAGCGGCGCTACATCAAAAACG
1 ATTAGCGGCGCTT-TTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTC-TCAAAAACG
41476297 CCGCTAAAGCCCAGAGC
64 CCGCTAAAGCCCAGAGC
41476314 ATTAGCGGCGCTTTTCAAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTTCAAAAACG
1 ATTAGCGGCGCTTTTC-AAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTC-TCAAAAACG
*
41476379 ACGCTAAAG
64 CCGCTAAAG
41476388 GCCCCAAAAA
Statistics
Matches: 141, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
80 9 0.06
81 70 0.50
82 62 0.44
ACGTcount: A:0.30, C:0.27, G:0.23, T:0.19
Consensus pattern (80 bp):
ATTAGCGGCGCTTTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTTCTCAAAAACGCC
GCTAAAGCCCAGAGC
Found at i:41476528 original size:40 final size:39
Alignment explanation
Indices: 41476439--41476561 Score: 140
Period size: 40 Copynumber: 3.1 Consensus size: 39
41476429 TTTGCGGCAC
* * *
41476439 TTTTCAAAAAACGCCACTAATGCT-TATTTTTAGCGGCG
1 TTTTTAAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCG
** **
41476477 TTTCCCAAAAAGCGCCGCTAATGCTCTACCTTTAGCGGCG
1 TTT-TTAAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCG
* *
41476517 TTTTTATAAAAGCGCCGCTAATGCTCGATTTTTAGTGGCG
1 TTTTTA-AAAAGCGCCGCTAATGCTCTATTTTTAGCGGCG
41476557 TTTTT
1 TTTTT
41476562 TGTCCAAACG
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
38 3 0.04
39 19 0.27
40 49 0.69
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.35
Consensus pattern (39 bp):
TTTTTAAAAAGCGCCGCTAATGCTCTATTTTTAGCGGCG
Found at i:41478167 original size:20 final size:21
Alignment explanation
Indices: 41478117--41478168 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
41478107 GAAACACGCT
*
41478117 GAAAGTAAGCTAAATTGAGCTC
1 GAAA-TAAGCTGAATTGAGCTC
*
41478139 GAAA-GAGCTGAATTGAGCTC
1 GAAATAAGCTGAATTGAGCTC
41478159 -AAATAAGCTG
1 GAAATAAGCTG
41478169 GTTGGAGCTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 3 0.12
20 19 0.73
22 4 0.15
ACGTcount: A:0.40, C:0.13, G:0.25, T:0.21
Consensus pattern (21 bp):
GAAATAAGCTGAATTGAGCTC
Found at i:41480089 original size:54 final size:56
Alignment explanation
Indices: 41479973--41480089 Score: 204
Period size: 54 Copynumber: 2.1 Consensus size: 56
41479963 ACAAGGGATG
41479973 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41480029 AT-GGCAAAACATGTCATG-AACATGTTGTGTTAATGGAAGAAT-AAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41480082 ATGGGCAA
1 ATGGGCAA
41480090 TAAACTAATA
Statistics
Matches: 59, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
53 13 0.22
54 28 0.47
55 16 0.27
56 2 0.03
ACGTcount: A:0.44, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41482596 original size:27 final size:27
Alignment explanation
Indices: 41482565--41482738 Score: 171
Period size: 27 Copynumber: 6.6 Consensus size: 27
41482555 TAAATTGTAC
41482565 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
41482592 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
41482618 ATGCACTAAGTGTGGCGAATTGACCA-GC
1 A-GCACTAAGTGT-GCGATTTGACTATGT
*
41482646 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
41482674 AGCACTAAGTGTGCGA-TTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41482700 AGCACTAAGTGTGCGA-TTGA-TATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
41482725 AGCACTGA-TGTGCG
1 AGCACTAAGTGTGCG
41482739 GACTCAATAT
Statistics
Matches: 124, Mismatches: 18, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
24 6 0.05
25 10 0.08
26 32 0.26
27 51 0.41
28 25 0.20
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:41482711 original size:81 final size:79
Alignment explanation
Indices: 41482566--41482719 Score: 222
Period size: 81 Copynumber: 1.9 Consensus size: 79
41482556 AAATTGTACA
* *
41482566 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
41482631 GGCGAATTGACCAGCG
66 -GCG-ATTGACCAGCG
* *
41482647 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCG-ATTGATTACG-TAGCACTAAGT
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAGT
41482710 GTGCGATTGA
64 GTGCGATTGA
41482720 TATATAGCAC
Statistics
Matches: 67, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
79 5 0.07
80 4 0.06
81 33 0.49
82 25 0.37
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (79 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAAGTGT
GCGATTGACCAGCG
Found at i:41487485 original size:40 final size:41
Alignment explanation
Indices: 41487437--41487522 Score: 122
Period size: 40 Copynumber: 2.1 Consensus size: 41
41487427 TGTCGAAGCG
* *
41487437 ATTTGTGCGACGTTACTA-AATCCGGGTTAAGT-CCGAAGGC
1 ATTTGTGCGAAGTTACTATAA-CCGGGCTAAGTCCCGAAGGC
*
41487477 ATTTGTGCGAAGTTACTATAACCGGGCTATGTCCCGAAGGC
1 ATTTGTGCGAAGTTACTATAACCGGGCTAAGTCCCGAAGGC
41487518 ATTTG
1 ATTTG
41487523 ATAACGAAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
40 26 0.63
41 15 0.37
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (41 bp):
ATTTGTGCGAAGTTACTATAACCGGGCTAAGTCCCGAAGGC
Found at i:41502953 original size:56 final size:56
Alignment explanation
Indices: 41502867--41502986 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
41502857 ACAAGGGATG
41502867 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
41502923 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
41502979 ATGGGCAA
1 ATGGGCAA
41502987 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:41504200 original size:40 final size:40
Alignment explanation
Indices: 41504116--41504339 Score: 287
Period size: 40 Copynumber: 5.7 Consensus size: 40
41504106 TCGAATGATG
* * * *
41504116 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAA
* * *
41504156 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41504196 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41504235 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
41504275 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
41504316 --CGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
41504340 AACGAGTAGC
Statistics
Matches: 164, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
39 56 0.34
40 98 0.60
41 10 0.06
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:41504252 original size:79 final size:80
Alignment explanation
Indices: 41504116--41504339 Score: 287
Period size: 79 Copynumber: 2.8 Consensus size: 80
41504106 TCGAATGATG
* * * * *
41504116 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGAT-CCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGCTAAG-TCCCGAAGGCAT
*
41504179 TTGTGCGAGATACTAAT
64 TTGTGCGAGATACTAAA
* *
41504196 TCCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
*
41504260 GTGCGAGTTACTAAA
66 GTGCGAGATACTAAA
* *
41504275 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA--CGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AATCCGGGCTAAGTCCCGAAGGCATT
41504338 TG
65 TG
41504340 AACGAGTAGC
Statistics
Matches: 127, Mismatches: 13, Indels: 9
0.85 0.09 0.06
Matches are distributed among these distances:
78 1 0.01
79 82 0.65
80 42 0.33
81 2 0.02
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAATCCGGGCTAAGTCCCGAAGGCATTT
GTGCGAGATACTAAA
Found at i:41504330 original size:119 final size:119
Alignment explanation
Indices: 41504116--41504337 Score: 297
Period size: 119 Copynumber: 1.9 Consensus size: 119
41504106 TCGAATGATG
*
41504116 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
**
41504181 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
66 GTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
* * * * **
41504235 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* *
41504298 TTGTGCGAGTTACT-ATAACGGGCTATGTCCCGAAGGCATT
64 TTGTGCGAGATACTAATAACGGGCTAAG-CCCGAAGGCATT
41504338 TGAACGAGTA
Statistics
Matches: 89, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
118 11 0.12
119 71 0.80
120 7 0.08
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAAA
Found at i:41504346 original size:119 final size:119
Alignment explanation
Indices: 41504116--41504372 Score: 290
Period size: 119 Copynumber: 2.2 Consensus size: 119
41504106 TCGAATGATG
* *
41504116 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
** **
41504181 GTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTA-CTAAA
66 GTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAG-TAGCTAAA
* * * **
41504235 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGTTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCAT
* * * *
41504298 TTGTGCGAGTTACT-ATAACGGGCTATGTCCCGAAGGCATTTGAACGAGTAGCTATA
64 TTGTGCGAGATACTAATAACGGGCTAAG-CCCGAAGGCATTGGAACGAGTAGCTAAA
* *
41504354 TCC-GGTTAAATTCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
41504373 TACGTGATTT
Statistics
Matches: 117, Mismatches: 17, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
118 27 0.23
119 83 0.71
120 7 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (119 bp):
TCCGGGTTAAGTCCCGAAGGCTTTGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTAATAACGGGCTAAGCCCGAAGGCATTGGAACGAGTAGCTAAA
Found at i:41506344 original size:6 final size:6
Alignment explanation
Indices: 41506335--41506430 Score: 72
Period size: 6 Copynumber: 16.5 Consensus size: 6
41506325 TTTTCTTTCG
* ** ** * **
41506335 TTTCTT TTTCAT CATCTT TTTCAA TTTCTT TTTCTT TTTCTT TTGCAA
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
** *
41506383 TTTCTT TTTCTT TTTCAC TTTCTA TTTCTT TTTC-- -TTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
41506428 TTT
1 TTT
41506431 TATTACAACG
Statistics
Matches: 66, Mismatches: 21, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
3 3 0.05
6 63 0.95
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (6 bp):
TTTCTT
Found at i:41506365 original size:24 final size:24
Alignment explanation
Indices: 41506335--41506392 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
41506325 TTTTCTTTCG
*
41506335 TTTCTTTTTCATCATCTTTTTCAA
1 TTTCTTTTTCATCATCTTTTGCAA
* **
41506359 TTTCTTTTTCTTTTTCTTTTGCAA
1 TTTCTTTTTCATCATCTTTTGCAA
41506383 TTTCTTTTTC
1 TTTCTTTTTC
41506393 TTTTTCACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.10, C:0.19, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTCTTTTTCATCATCTTTTGCAA
Found at i:41506370 original size:18 final size:17
Alignment explanation
Indices: 41506335--41506430 Score: 88
Period size: 18 Copynumber: 5.5 Consensus size: 17
41506325 TTTTCTTTCG
*
41506335 TTTCTTTTTCATCATCTT
1 TTTCTTTTTCAT-TTCTT
** *
41506353 TTTCAATTTCTTTTTCTT
1 TTTCTTTTTC-ATTTCTT
*
41506371 TTTCTTTTGCAATTTCTT
1 TTTCTTTTTC-ATTTCTT
*
41506389 TTTCTTTTTCACTTTCTA
1 TTTCTTTTTCA-TTTCTT
41506407 TTTCTTTTTC--TTCTT
1 TTTCTTTTTCATTTCTT
41506422 TTTCTTTTT
1 TTTCTTTTT
41506431 TATTACAACG
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
15 13 0.20
17 1 0.02
18 49 0.77
19 1 0.02
ACGTcount: A:0.08, C:0.19, G:0.01, T:0.72
Consensus pattern (17 bp):
TTTCTTTTTCATTTCTT
Found at i:41506393 original size:24 final size:23
Alignment explanation
Indices: 41506352--41506418 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 23
41506342 TTCATCATCT
41506352 TTTTCAATTTCTTTTTCTTTTTC
1 TTTTCAATTTCTTTTTCTTTTTC
41506375 TTTTGCAATTTCTTTTTCTTTTTC
1 TTTT-CAATTTCTTTTTCTTTTTC
* *
41506399 ACTTTCTATTTCTTTTTCTT
1 -TTTTCAATTTCTTTTTCTT
41506419 CTTTTTCTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
23 4 0.10
24 33 0.82
25 3 0.08
ACGTcount: A:0.09, C:0.18, G:0.01, T:0.72
Consensus pattern (23 bp):
TTTTCAATTTCTTTTTCTTTTTC
Found at i:41508701 original size:20 final size:20
Alignment explanation
Indices: 41508671--41508717 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41508661 AAGCTGAAAG
* *
41508671 TAAGCTAAATTCAGCTCGAA
1 TAAGCTGAATTCAGCTCAAA
* *
41508691 TGAGCTGAATTGAGCTCAAA
1 TAAGCTGAATTCAGCTCAAA
41508711 TAAGCTG
1 TAAGCTG
41508718 GTTGGAGCTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (20 bp):
TAAGCTGAATTCAGCTCAAA
Found at i:41511867 original size:19 final size:20
Alignment explanation
Indices: 41511843--41511893 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
41511833 AAAGGAAGAC
41511843 AGAAAAAGA-AATAAAAAAA
1 AGAAAAAGAGAATAAAAAAA
* *
41511862 AGAAAAAGAGAATGAAAAAG
1 AGAAAAAGAGAATAAAAAAA
41511882 AGCAAAAAGAGA
1 AG-AAAAAGAGA
41511894 TTGAGAGTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 9 0.32
20 10 0.36
21 9 0.32
ACGTcount: A:0.75, C:0.02, G:0.20, T:0.04
Consensus pattern (20 bp):
AGAAAAAGAGAATAAAAAAA
Found at i:41513669 original size:33 final size:34
Alignment explanation
Indices: 41513632--41513703 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
41513622 GAGTTAGTTT
*
41513632 ATTAAATTTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
* * *
41513665 ATTAATTTTATTTCACCTTAAATAAGTGTTAGTA
1 ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
41513699 ATTAA
1 ATTAA
41513704 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (34 bp):
ATTAAATTTAGTTCACCTCAAATAAGTGTTAGTA
Found at i:41516351 original size:18 final size:17
Alignment explanation
Indices: 41516330--41516365 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
41516320 TTTTATTTGA
*
41516330 TTTTGTCTTTTTCTATTT
1 TTTTGACTTTTTCT-TTT
41516348 TTTTGACTTTTTCTTTT
1 TTTTGACTTTTTCTTTT
41516365 T
1 T
41516366 AATATTCTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.78
Consensus pattern (17 bp):
TTTTGACTTTTTCTTTT
Found at i:41517355 original size:12 final size:12
Alignment explanation
Indices: 41517333--41517366 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
41517323 ATCGATTTCA
41517333 CGAAATTTTTTT
1 CGAAATTTTTTT
41517345 -GAAATTTTTTT
1 CGAAATTTTTTT
41517356 CG-AATTTTTTT
1 CGAAATTTTTTT
41517367 ATTTGTTTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 20 0.95
12 1 0.05
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (12 bp):
CGAAATTTTTTT
Found at i:41520968 original size:39 final size:39
Alignment explanation
Indices: 41520914--41520991 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
41520904 CATAGTAATT
41520914 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
*
41520953 TATTCATAAAGTCTAAAAATTAAAACTAAGTATTTAAAG
1 TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
41520992 AATTAAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.53, C:0.08, G:0.08, T:0.32
Consensus pattern (39 bp):
TATTCATAAAGTCTAAAAATTAAAACAAAGTATTTAAAG
Found at i:41521215 original size:9 final size:9
Alignment explanation
Indices: 41521201--41521226 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41521191 TTTCTTGGGC
41521201 CAAGATTTT
1 CAAGATTTT
41521210 CAAGATTTT
1 CAAGATTTT
41521219 CAAGATTT
1 CAAGATTT
41521227 GAAATCTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.42
Consensus pattern (9 bp):
CAAGATTTT
Found at i:41525850 original size:47 final size:47
Alignment explanation
Indices: 41525772--41526718 Score: 1390
Period size: 47 Copynumber: 19.6 Consensus size: 47
41525762 CCCTTCGGGA
* * * * * *
41525772 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41525819 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
41525866 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTACGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41525913 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41525960 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526009 CTTATCACATATATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--------ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41526064 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526111 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41526160 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41526207 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41526254 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526303 CTTATCACATATATATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--------ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41526358 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526405 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41526454 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41526501 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
41526548 ATTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526597 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
41526646 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
41526693 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
41526719 CACAATTATC
Statistics
Matches: 834, Mismatches: 44, Indels: 44
0.90 0.05 0.05
Matches are distributed among these distances:
47 465 0.56
49 275 0.33
55 94 0.11
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:41526011 original size:96 final size:95
Alignment explanation
Indices: 41525772--41526718 Score: 1420
Period size: 96 Copynumber: 9.8 Consensus size: 95
41525762 CCCTTCGGGA
* * * * * * * *
41525772 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
* *
41525836 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATTGGCCATTCGGC
* * *
41525866 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTACGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
* *
41525930 CTTTCACATTCATCACATCGGCCATTAGGC
66 CTTTCACATTCATCACATTGGCCATTCGGC
41525960 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC------A-
41526025 ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
57 ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41526064 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATAC
41526129 ACTTTCACATTCATCACATTGGCCATTCGGC
65 ACTTTCACATTCATCACATTGGCCATTCGGC
*
41526160 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
* * *
41526224 CTTTCACATTCATCACATCGGCTATTAGGC
66 CTTTCACATTCATCACATTGGCCATTCGGC
41526254 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC------A-
41526319 ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
57 ATATATACACTTTCACATTCATCACATTGGCCATTCGGC
41526358 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATAC
41526423 ACTTTCACATTCATCACATTGGCCATTCGGC
65 ACTTTCACATTCATCACATTGGCCATTCGGC
*
41526454 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCAC-ATATATACA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
* * *
41526518 CTTTCACATTCATCACATCGGCTATTAGGC
66 CTTTCACATTCATCACATTGGCCATTCGGC
*
41526548 ATTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATAT
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATAT
41526613 ACACTTTCACATTCATCACATTGGCCATTCGGC
63 ACACTTTCACATTCATCACATTGGCCATTCGGC
41526646 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACA-ATATATAC
41526711 A--TTCACAT
65 ACTTTCACAT
41526719 CACAATTATC
Statistics
Matches: 795, Mismatches: 34, Indels: 48
0.91 0.04 0.05
Matches are distributed among these distances:
94 184 0.23
96 385 0.48
98 43 0.05
102 94 0.12
104 89 0.11
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (95 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACAATATATACA
CTTTCACATTCATCACATTGGCCATTCGGC
Found at i:41526299 original size:294 final size:294
Alignment explanation
Indices: 41525772--41526718 Score: 1698
Period size: 294 Copynumber: 3.3 Consensus size: 294
41525762 CCCTTCGGGA
* * * * * * * *
41525772 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCCTGTCAC--ATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
* * *
41525835 ACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
* *
41525900 TCGGCTATTACGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTAT
131 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
41525965 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
196 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
41526030 TACACTTTCACATTCATCACATTGGCCATTCGGC
261 TACACTTTCACATTCATCACATTGGCCATTCGGC
41526064 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
41526129 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
41526194 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
131 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
41526259 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
196 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
41526324 TACACTTTCACATTCATCACATTGGCCATTCGGC
261 TACACTTTCACATTCATCACATTGGCCATTCGGC
41526358 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
41526423 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
66 ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
*
41526488 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCATTAT
131 TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
41526553 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCAC------ATATATA
196 CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
41526612 TACACTTTCACATTCATCACATTGGCCATTCGGC
261 TACACTTTCACATTCATCACATTGGCCATTCGGC
41526646 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
41526711 A--TTCACAT
66 ACTTTCACAT
41526719 CACAATTATC
Statistics
Matches: 639, Mismatches: 14, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
286 7 0.01
288 107 0.17
292 47 0.07
294 478 0.75
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (294 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATAC
ACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACATTCATCACA
TCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTAT
CACATATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATATATA
TACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:41529557 original size:9 final size:9
Alignment explanation
Indices: 41529543--41529567 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41529533 TAAATAATTC
41529543 AAAAAAAAT
1 AAAAAAAAT
41529552 AAAAAAAAT
1 AAAAAAAAT
41529561 AAAAAAA
1 AAAAAAA
41529568 GGAGATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (9 bp):
AAAAAAAAT
Found at i:41531524 original size:20 final size:20
Alignment explanation
Indices: 41531476--41531515 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
41531466 TAAATAACTA
*
41531476 AATTGAGCTCGAATGAGCTG
1 AATTGAGCTCAAATGAGCTG
41531496 AATTGAGCTCAAATGAGCTG
1 AATTGAGCTCAAATGAGCTG
41531516 GTTGGAGCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (20 bp):
AATTGAGCTCAAATGAGCTG
Found at i:41538747 original size:47 final size:47
Alignment explanation
Indices: 41538695--41539061 Score: 475
Period size: 47 Copynumber: 7.6 Consensus size: 47
41538685 GATAATTGTG
* *
41538695 ATGTGAATGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41538742 ATGTGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
41538789 ATGTGAAAGTGTATATATATATATATGTGATAAGGCCTAATGGCCGATGTGATGA
1 ATGTGAAAGTG--------TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41538844 ATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGACGATGTGATGA
1 ATGTGAAAGTG----TATATATGTGATAAGGCCTAATGGCCGATGTGATGA
*
41538895 ATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* *
41538942 ATGTGAAAGTGTATATATGTGATGAGGCTTAATGGCCGATGTGATGA
1 ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
* * * * * *
41538989 ATGTGAAAGTGTATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGG
1 ATGTGAAAGTGTATATATGTGATAAG-GCCTAATGGCCGATGTGATGA
*
41539036 ATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGAAAGTGTATATATGTGATAAG
41539062 TCCCGAAGGG
Statistics
Matches: 289, Mismatches: 21, Indels: 19
0.88 0.06 0.06
Matches are distributed among these distances:
46 2 0.01
47 190 0.66
48 2 0.01
51 50 0.17
55 45 0.16
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.30
Consensus pattern (47 bp):
ATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGA
Found at i:41538871 original size:153 final size:143
Alignment explanation
Indices: 41538695--41539061 Score: 483
Period size: 153 Copynumber: 2.5 Consensus size: 143
41538685 GATAATTGTG
41538695 ATGTG-AA-TGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
1 ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
*
41538758 ATGTGATAAGGCCGAATGGCCAATGTGATGAATGTGAAAGTGTATATATATATATATGTGATAAG
66 ATGTGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTG--------TATATATGTGATAAG
41538823 GCCTAATGGCCGATGTGATGA
123 GCCTAATGGCCGATGTGATGA
*
41538844 ATGTGAAAGTGTATATATATATGTGATAAGGCCTAATGGACGATGTGATGAATGTGAAAGTGTAT
1 ATGTGAAAGTG--TATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTAT
* * * *
41538909 ATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATGAGGCTTAA
64 ATATGTGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAA
41538974 TGGCCGATGTGATGA
129 TGGCCGATGTGATGA
* * * * * *
41538989 ATGTGAAAGTG--TATATATGTGA-CAGAGCCGAGTGGCCAACGTGATGGATGTGAAAGTGTATA
1 ATGTGAAAGTGTATATATATGTGATAAG-GCCTAATGGCCGATGTGATGAATGTGAAAGTGTATA
*
41539051 AATGTGATAAG
65 TATGTGATAAG
41539062 TCCCGAAGGG
Statistics
Matches: 199, Mismatches: 14, Indels: 18
0.86 0.06 0.08
Matches are distributed among these distances:
140 2 0.01
141 51 0.26
145 45 0.23
149 5 0.03
150 2 0.01
151 2 0.01
153 92 0.46
ACGTcount: A:0.34, C:0.08, G:0.29, T:0.30
Consensus pattern (143 bp):
ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATAT
ATGTGATAAGGCCGAATAGCCAATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATG
GCCGATGTGATGA
Found at i:41556803 original size:161 final size:161
Alignment explanation
Indices: 41556615--41556923 Score: 433
Period size: 161 Copynumber: 1.9 Consensus size: 161
41556605 TTGGACCAAG
* *
41556615 ATTTCCAAGATTTGAAATCTTGATTTTCTTGATTCTTGAAATAGCTCCAAACAACAAAATTAGG-
1 ATTTCCAAGATTTGAAATCTTGATTTTCTTGACTCTTGAAATAGCTCAAAACAACAAAATT-GGA
* * *
41556679 CCAAGATTCGGTTTCCTGATTTTCTTGAAAACAAGAAAGTGAATCTTGATCTTCTCTTT-CTTTC
65 CAAAGATTCAGTTTCCTGAATTTCTTGAAAACAAGAAAGTGAATCTTGATCTTCTCTTTCCTTT-
*
41556743 GCGTACGCATCTAAGGCCTTTGTGACTCGTATC
129 GCATACGCATCTAAGGCCTTTGTGACTCGTATC
* * * ** *
41556776 ATTTCCAAGATTTGAAATTTTGATTTTCTTGACTCTTGAAATCGCTCAAAATAGTAAGATTGGAC
1 ATTTCCAAGATTTGAAATCTTGATTTTCTTGACTCTTGAAATAGCTCAAAACAACAAAATTGGAC
* * * * *
41556841 AAAGATTCAGTTTCTTGAATTTCTTGAAAACAAGATAGTGAATCTTGATTTTCTTTTTCCTTTGT
66 AAAGATTCAGTTTCCTGAATTTCTTGAAAACAAGAAAGTGAATCTTGATCTTCTCTTTCCTTTGC
41556906 ATACGCATCTAAGGCCTT
131 ATACGCATCTAAGGCCTT
41556924 GCTAATGAAG
Statistics
Matches: 129, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
160 2 0.02
161 123 0.95
162 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.39
Consensus pattern (161 bp):
ATTTCCAAGATTTGAAATCTTGATTTTCTTGACTCTTGAAATAGCTCAAAACAACAAAATTGGAC
AAAGATTCAGTTTCCTGAATTTCTTGAAAACAAGAAAGTGAATCTTGATCTTCTCTTTCCTTTGC
ATACGCATCTAAGGCCTTTGTGACTCGTATC
Found at i:41566576 original size:25 final size:25
Alignment explanation
Indices: 41566548--41566596 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
41566538 TAGTGGCAAG
*
41566548 GTGGTGACACAGGTGTGGTAAGGAA
1 GTGGCGACACAGGTGTGGTAAGGAA
* *
41566573 GTGGCGTCATAGGTGTGGTAAGGA
1 GTGGCGACACAGGTGTGGTAAGGA
41566597 GGTCAGAGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.24, C:0.08, G:0.45, T:0.22
Consensus pattern (25 bp):
GTGGCGACACAGGTGTGGTAAGGAA
Found at i:41568086 original size:20 final size:21
Alignment explanation
Indices: 41568063--41568107 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
41568053 AGCTTGTTTT
*
41568063 AGCTCCAA-CCAGCTCATTTG
1 AGCTCCAATCCAGCTCATTCG
*
41568083 AGCT-CAATTCAGCTCATTCG
1 AGCTCCAATCCAGCTCATTCG
41568103 AGCTC
1 AGCTC
41568108 AATTTAGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.27
Consensus pattern (21 bp):
AGCTCCAATCCAGCTCATTCG
Found at i:41568108 original size:20 final size:20
Alignment explanation
Indices: 41568072--41568116 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
41568062 TAGCTCCAAC
*
41568072 CAGCTCATTTGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
41568092 CAGCTCATTCGAGCTCAATT
1 CAGCTCATTCGAGCTCAATT
*
41568112 TAGCT
1 CAGCT
41568117 TTCCATCAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.24, C:0.27, G:0.16, T:0.33
Consensus pattern (20 bp):
CAGCTCATTCGAGCTCAATT
Found at i:41568298 original size:22 final size:22
Alignment explanation
Indices: 41568255--41568303 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
41568245 ATCTAGCCAC
*
41568255 ATTTATTGTTAATTAT-ATTTT
1 ATTTATTGTTAATTATAATTTA
* *
41568276 ATTTATGTGTTTATTTTAATTTA
1 ATTTAT-TGTTAATTATAATTTA
41568299 ATTTA
1 ATTTA
41568304 ATATGTCTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 6 0.26
22 8 0.35
23 9 0.39
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (22 bp):
ATTTATTGTTAATTATAATTTA
Found at i:41576730 original size:26 final size:27
Alignment explanation
Indices: 41576668--41576723 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
41576658 GTCTGTTTCC
*
41576668 TTTTCACTCTCAATCTATTTTTGCTCT
1 TTTTCATTCTCAATCTATTTTTGCTCT
* *
41576695 TTTTCATTCTCATTCTCTTTTT-CT-T
1 TTTTCATTCTCAATCTATTTTTGCTCT
41576720 TTTT
1 TTTT
41576724 GATTTCTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 5 0.19
26 2 0.08
27 19 0.73
ACGTcount: A:0.11, C:0.23, G:0.02, T:0.64
Consensus pattern (27 bp):
TTTTCATTCTCAATCTATTTTTGCTCT
Found at i:41593269 original size:12 final size:12
Alignment explanation
Indices: 41593252--41593276 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41593242 TTTCACTCAT
41593252 CTCTTTTTCAAA
1 CTCTTTTTCAAA
41593264 CTCTTTTTCAAA
1 CTCTTTTTCAAA
41593276 C
1 C
41593277 CCTCTCTCTT
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:0.24, C:0.28, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTTTTTCAAA
Found at i:41593394 original size:21 final size:22
Alignment explanation
Indices: 41593346--41593395 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
41593336 ACTCTCTTTT
*
41593346 TCGATTTCTTGTTCTTTTTCTT
1 TCGATTTCTTGTTCTTTTTCTC
41593368 TC-ATTTCTT-TT-TTTTGTCTC
1 TCGATTTCTTGTTCTTTT-TCTC
41593388 TCGATTTC
1 TCGATTTC
41593396 ATTCCATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 7 0.28
21 12 0.48
22 2 0.08
ACGTcount: A:0.06, C:0.20, G:0.08, T:0.66
Consensus pattern (22 bp):
TCGATTTCTTGTTCTTTTTCTC
Found at i:41594990 original size:18 final size:18
Alignment explanation
Indices: 41594956--41594997 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41594946 ACTCAACATT
*
41594956 TAATTAAGCTGAATTAAC
1 TAATTAAACTGAATTAAC
*
41594974 TAATTAAACT-AACTTAAT
1 TAATTAAACTGAA-TTAAC
41594992 TAATTA
1 TAATTA
41594998 TTCCAGCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 2 0.10
18 19 0.90
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (18 bp):
TAATTAAACTGAATTAAC
Found at i:41596415 original size:20 final size:20
Alignment explanation
Indices: 41596369--41596417 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
41596359 TTTTCCCTTG
*
41596369 CTCTTTTTTTCCCACAATCT
1 CTCTTCTTTTCCCACAATCT
** * *
41596389 CGATTCTTTTCTCTCAATCT
1 CTCTTCTTTTCCCACAATCT
41596409 CTCTTCTTT
1 CTCTTCTTT
41596418 CTTTTCTTTT
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.12, C:0.33, G:0.02, T:0.53
Consensus pattern (20 bp):
CTCTTCTTTTCCCACAATCT
Found at i:41599524 original size:30 final size:30
Alignment explanation
Indices: 41599476--41599547 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 30
41599466 ATGTGCATAT
** *
41599476 GGAGCTGAATTAAAGCATGAATGTGTTTAA
1 GGAGCTGAATGGAAGCATGAATGTATTTAA
* * *
41599506 GGAGCTGAATGGAGGCATGCATGTATTTAG
1 GGAGCTGAATGGAAGCATGAATGTATTTAA
41599536 GGAGCTGAATGG
1 GGAGCTGAATGG
41599548 GGAAGCTAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.31, C:0.08, G:0.35, T:0.26
Consensus pattern (30 bp):
GGAGCTGAATGGAAGCATGAATGTATTTAA
Found at i:41600954 original size:10 final size:10
Alignment explanation
Indices: 41600941--41600966 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
41600931 TTAATTTCTT
41600941 TTTTTTCAAA
1 TTTTTTCAAA
41600951 TTTTTTCAAA
1 TTTTTTCAAA
41600961 TTTTTT
1 TTTTTT
41600967 TTAAACACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (10 bp):
TTTTTTCAAA
Found at i:41604780 original size:18 final size:19
Alignment explanation
Indices: 41604759--41604795 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41604749 AAAGAAAGAT
41604759 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
41604777 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
41604796 GGGAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:41615133 original size:16 final size:16
Alignment explanation
Indices: 41615114--41615152 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
41615104 GGGGAAAAGA
41615114 AAAGAAA-AGAAAAATT
1 AAAGAAACA-AAAAATT
*
41615130 AAAGAAACAAACAATT
1 AAAGAAACAAAAAATT
41615146 AAAGAAA
1 AAAGAAA
41615153 GATATAGGAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 20 0.95
17 1 0.05
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (16 bp):
AAAGAAACAAAAAATT
Found at i:41618171 original size:37 final size:37
Alignment explanation
Indices: 41618121--41618194 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
41618111 TCGAGAAAGA
41618121 TTGCACAACTCCCTTCAAACGGCTCTAATCTCCCCTC
1 TTGCACAACTCCCTTCAAACGGCTCTAATCTCCCCTC
41618158 TTGCACAACTCCCTTCAAACGGCTCTAATCTCCCCTC
1 TTGCACAACTCCCTTCAAACGGCTCTAATCTCCCCTC
41618195 CAATGACGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.43, G:0.08, T:0.27
Consensus pattern (37 bp):
TTGCACAACTCCCTTCAAACGGCTCTAATCTCCCCTC
Found at i:41620407 original size:18 final size:17
Alignment explanation
Indices: 41620384--41620422 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41620374 CTCTTTTTGC
41620384 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
41620402 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
41620420 TCT
1 TCT
41620423 GTCTTCCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:41623358 original size:24 final size:23
Alignment explanation
Indices: 41623310--41623362 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
41623300 TAATATTTGT
*
41623310 TTTTAATATGTCTAGCTACAGCA
1 TTTTAATATGTCTAGCTACAACA
*
41623333 TTTTAATGTGTCTTTAGCTA-AACA
1 TTTTAATATGTC--TAGCTACAACA
41623357 TTTTAA
1 TTTTAA
41623363 ATACAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
23 11 0.42
24 9 0.35
25 6 0.23
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (23 bp):
TTTTAATATGTCTAGCTACAACA
Found at i:41624723 original size:12 final size:12
Alignment explanation
Indices: 41624706--41624735 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
41624696 GTAAGTGTTT
41624706 AAAAAAATTTGA
1 AAAAAAATTTGA
41624718 AAAAAAATTTGA
1 AAAAAAATTTGA
41624730 AAAAAA
1 AAAAAA
41624736 GAAATTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (12 bp):
AAAAAAATTTGA
Found at i:41627960 original size:45 final size:43
Alignment explanation
Indices: 41627911--41628007 Score: 149
Period size: 45 Copynumber: 2.2 Consensus size: 43
41627901 CGAAAAAAAA
* *
41627911 GAAAAAAATTGAGAATAAAAAAAAGAGTATGAAGTAAAAAAATTC
1 GAAAAAAATTGAGAAT-AAAAAAAGAGCACGAAGT-AAAAAATTC
41627956 GAAAAAAAATTGAGAATAAAAAAAGAGCACGAAGTAAAAAATTC
1 G-AAAAAAATTGAGAATAAAAAAAGAGCACGAAGTAAAAAATTC
41628000 GAAAAAAA
1 GAAAAAAA
41628008 AGTGAAGTGT
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
43 7 0.14
44 10 0.20
45 17 0.35
46 15 0.31
ACGTcount: A:0.66, C:0.04, G:0.15, T:0.14
Consensus pattern (43 bp):
GAAAAAAATTGAGAATAAAAAAAGAGCACGAAGTAAAAAATTC
Found at i:41628008 original size:45 final size:46
Alignment explanation
Indices: 41627912--41628008 Score: 162
Period size: 44 Copynumber: 2.2 Consensus size: 46
41627902 GAAAAAAAAG
* *
41627912 AAAAAAATTGAGAATAAAAAAAAGAGTATGAAGTAAAAAAATTCGA
1 AAAAAAATTGAGAATAAAAAAAAGAGCACGAAGTAAAAAAATTCGA
41627958 AAAAAAATTGAGAAT-AAAAAAAGAGCACGAAGT-AAAAAATTCGA
1 AAAAAAATTGAGAATAAAAAAAAGAGCACGAAGTAAAAAAATTCGA
41628002 AAAAAAA
1 AAAAAAA
41628009 GTGAAGTGTT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 18 0.37
45 16 0.33
46 15 0.31
ACGTcount: A:0.67, C:0.04, G:0.14, T:0.14
Consensus pattern (46 bp):
AAAAAAATTGAGAATAAAAAAAAGAGCACGAAGTAAAAAAATTCGA
Found at i:41628743 original size:12 final size:12
Alignment explanation
Indices: 41628714--41628753 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
41628704 AAACAGCATG
41628714 TGAAAAAGAAAA
1 TGAAAAAGAAAA
** *
41628726 ACAAAAAGAAAT
1 TGAAAAAGAAAA
41628738 TGAAAAAGAAAA
1 TGAAAAAGAAAA
41628750 TGAA
1 TGAA
41628754 CATGAACATG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.15, T:0.10
Consensus pattern (12 bp):
TGAAAAAGAAAA
Found at i:41628758 original size:6 final size:6
Alignment explanation
Indices: 41628749--41628783 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
41628739 GAAAAAGAAA
41628749 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAA
1 ATGAAC ATGAAC ATGAAC ATGAAC ATGAAC ATGAA
41628784 AGAAAACAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.17
Consensus pattern (6 bp):
ATGAAC
Found at i:41628759 original size:18 final size:18
Alignment explanation
Indices: 41628738--41628777 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
41628728 AAAAAGAAAT
41628738 TGAAAAAGAAAATGAACA
1 TGAAAAAGAAAATGAACA
* * *
41628756 TGAACATGAACATGAACA
1 TGAAAAAGAAAATGAACA
41628774 TGAA
1 TGAA
41628778 CATGAAAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.17, T:0.15
Consensus pattern (18 bp):
TGAAAAAGAAAATGAACA
Found at i:41628847 original size:33 final size:32
Alignment explanation
Indices: 41628800--41628861 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
41628790 CAATAAATTG
*
41628800 AAAAATAAAATGAGAGTGAGATTGAGAAAAAGA
1 AAAAAGAAAATGAGAGTGAGATTGA-AAAAAGA
* *
41628833 AAAAAGAAATTGAGATTGAGATTGAAAAA
1 AAAAAGAAAATGAGAGTGAGATTGAAAAA
41628862 GGATGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 4 0.15
33 22 0.85
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.18
Consensus pattern (32 bp):
AAAAAGAAAATGAGAGTGAGATTGAAAAAAGA
Found at i:41634730 original size:33 final size:34
Alignment explanation
Indices: 41634679--41634753 Score: 116
Period size: 33 Copynumber: 2.2 Consensus size: 34
41634669 AGATTTAAAC
*
41634679 AAATTAATTACTAACACTTATTTAAGGTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41634713 AAATTAATT-CTAACACTTATTTGAGCTGAACTA
1 AAATTAATTACTAACACTTATTTAAGCTGAACTA
*
41634746 AATTTAAT
1 AAATTAAT
41634754 AAACTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
33 29 0.76
34 9 0.24
ACGTcount: A:0.43, C:0.12, G:0.08, T:0.37
Consensus pattern (34 bp):
AAATTAATTACTAACACTTATTTAAGCTGAACTA
Found at i:41636535 original size:18 final size:17
Alignment explanation
Indices: 41636512--41636550 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41636502 CTCTTTTTGC
41636512 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
41636530 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
41636548 TCT
1 TCT
41636551 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:41637513 original size:18 final size:18
Alignment explanation
Indices: 41637472--41637513 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
41637462 CCGCTGAATA
41637472 TTTTTTTAATTTTTATTT
1 TTTTTTTAATTTTTATTT
* *
41637490 GATTTTTT-ATTTTTCTTT
1 -TTTTTTTAATTTTTATTT
41637508 TTTTTT
1 TTTTTT
41637514 GACTTTTTTG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 5 0.25
18 9 0.45
19 6 0.30
ACGTcount: A:0.12, C:0.02, G:0.02, T:0.83
Consensus pattern (18 bp):
TTTTTTTAATTTTTATTT
Found at i:41655625 original size:17 final size:17
Alignment explanation
Indices: 41655603--41655635 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
41655593 TGGAGGAAAT
41655603 AGACGTTTTTGGGGCAA
1 AGACGTTTTTGGGGCAA
41655620 AGACGTTTTTGGGGCA
1 AGACGTTTTTGGGGCA
41655636 GGGTCGTATC
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:0.21, C:0.12, G:0.36, T:0.30
Consensus pattern (17 bp):
AGACGTTTTTGGGGCAA
Found at i:41657379 original size:30 final size:28
Alignment explanation
Indices: 41657345--41657401 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 28
41657335 TCACTCAACA
41657345 AAAATCTGAA-TTCAATGTAATGTCCTCAAT
1 AAAATCT-AATTTCAATGT-AT-TCCTCAAT
41657375 AAAATCTAATTTCAATGTATTCCTCAA
1 AAAATCTAATTTCAATGTATTCCTCAA
41657402 GTGTAGTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
28 7 0.27
29 4 0.15
30 15 0.58
ACGTcount: A:0.40, C:0.18, G:0.07, T:0.35
Consensus pattern (28 bp):
AAAATCTAATTTCAATGTATTCCTCAAT
Found at i:41661395 original size:18 final size:19
Alignment explanation
Indices: 41661374--41661410 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
41661364 AAAGGAAGAT
41661374 AGAAAAAGA-AATCAAAAA
1 AGAAAAAGAGAATCAAAAA
*
41661392 AGAAAAAGAGAATGAAAAA
1 AGAAAAAGAGAATCAAAAA
41661411 GAGCAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.76, C:0.03, G:0.16, T:0.05
Consensus pattern (19 bp):
AGAAAAAGAGAATCAAAAA
Found at i:41663192 original size:33 final size:34
Alignment explanation
Indices: 41663155--41663226 Score: 101
Period size: 33 Copynumber: 2.1 Consensus size: 34
41663145 GAGTTAGTCT
*
41663155 ATTAAATCTAGTTCAGCTCAAATAAGTGTTAG-A
1 ATTAAATCTAGTTCAACTCAAATAAGTGTTAGTA
* * *
41663188 ATTAATTTTAGTTCAACTTAAATAAGTGTTAGTA
1 ATTAAATCTAGTTCAACTCAAATAAGTGTTAGTA
41663222 ATTAA
1 ATTAA
41663227 TTTGTTTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 28 0.82
34 6 0.18
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.39
Consensus pattern (34 bp):
ATTAAATCTAGTTCAACTCAAATAAGTGTTAGTA
Found at i:41665340 original size:18 final size:17
Alignment explanation
Indices: 41665317--41665355 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
41665307 CCCTTTTTGC
41665317 TCTTTTTCATTCTCTTTT
1 TCTTTTTCATT-TCTTTT
*
41665335 TCTTTTTTGATTTCTTTT
1 TC-TTTTTCATTTCTTTT
41665353 TCT
1 TCT
41665356 GTCTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
17 1 0.05
18 10 0.53
19 8 0.42
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (17 bp):
TCTTTTTCATTTCTTTT
Found at i:41674409 original size:16 final size:17
Alignment explanation
Indices: 41674377--41674409 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41674367 CCATGTCCTC
41674377 CAACTCAACATAATGTTG
1 CAACTCAACA-AATGTTG
41674395 CAACTCAAC-AATGTT
1 CAACTCAACAAATGTT
41674410 AGAAATTTCA
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:0.39, C:0.24, G:0.09, T:0.27
Consensus pattern (17 bp):
CAACTCAACAAATGTTG
Found at i:41676633 original size:29 final size:29
Alignment explanation
Indices: 41676591--41676691 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
41676581 CATGAAATTG
41676591 GCACTAAGTGTGCGGGTTCAAATTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
41676620 GCACTAAGTGTGCGGGTTCAAGTTGTATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
* * *
41676649 GCACTAAGTGTGCGAGTTC-GATTATATA
1 GCACTAAGTGTGCGGGTTCAAATTGTATA
*
41676677 ACACTAAGTGTGCGG
1 GCACTAAGTGTGCGG
41676692 ACTTACTATA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
28 19 0.29
29 46 0.71
ACGTcount: A:0.27, C:0.15, G:0.29, T:0.30
Consensus pattern (29 bp):
GCACTAAGTGTGCGGGTTCAAATTGTATA
Found at i:41678955 original size:27 final size:28
Alignment explanation
Indices: 41678899--41678953 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
41678889 TCGGCTAGAC
* *
41678899 TTAGACATCATTAAAGCTTGTAATAAAA
1 TTAGACATCATTAAAACATGTAATAAAA
41678927 TTAGACA-CATTAATAACATGTAATAAA
1 TTAGACATCATTAA-AACATGTAATAAA
41678954 TTTAAAACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.49, C:0.11, G:0.09, T:0.31
Consensus pattern (28 bp):
TTAGACATCATTAAAACATGTAATAAAA
Found at i:41695926 original size:19 final size:19
Alignment explanation
Indices: 41695902--41695938 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
41695892 GCATCGAAAT
41695902 GTCACATTCGTTGCTGGAG
1 GTCACATTCGTTGCTGGAG
41695921 GTCACATTCGTTGCTGGA
1 GTCACATTCGTTGCTGGA
41695939 TCAACTACAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.22, G:0.30, T:0.32
Consensus pattern (19 bp):
GTCACATTCGTTGCTGGAG
Found at i:41696914 original size:14 final size:15
Alignment explanation
Indices: 41696895--41696924 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
41696885 TAAATCCAAT
41696895 AGCCATAATT-ATCC
1 AGCCATAATTCATCC
41696909 AGCCATAATTCATCC
1 AGCCATAATTCATCC
41696924 A
1 A
41696925 CACATCTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.67
15 5 0.33
ACGTcount: A:0.37, C:0.30, G:0.07, T:0.27
Consensus pattern (15 bp):
AGCCATAATTCATCC
Found at i:41697653 original size:28 final size:28
Alignment explanation
Indices: 41697615--41697726 Score: 98
Period size: 28 Copynumber: 3.6 Consensus size: 28
41697605 GCTCCCTCCA
41697615 TTTCTTTTCTTTTCTGCCCTCTGTTTAT
1 TTTCTTTTCTTTTCTGCCCTCTGTTTAT
* * **
41697643 TTTCTTTTCTTTTCTGCCGATTTGCTCTCTCCG
1 TTTCTTTTCTTTTCTGCC-CTCTG-T-T-T-AT
41697676 TTTCTTTTCTTTTCTTTTCTGCCCTCTGTTTAT
1 TTTCTTTTC---T--TTTCTGCCCTCTGTTTAT
41697709 TTTCTTTTCTTTTCTGCC
1 TTTCTTTTCTTTTCTGCC
41697727 AATTTGCTCC
Statistics
Matches: 66, Mismatches: 8, Indels: 20
0.70 0.09 0.21
Matches are distributed among these distances:
28 26 0.39
29 3 0.05
30 2 0.03
31 1 0.02
32 1 0.02
33 18 0.27
34 1 0.02
35 1 0.02
36 2 0.03
37 3 0.05
38 8 0.12
ACGTcount: A:0.03, C:0.27, G:0.08, T:0.62
Consensus pattern (28 bp):
TTTCTTTTCTTTTCTGCCCTCTGTTTAT
Done.