Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 149 of 199
Found at i:49338289 original size:26 final size:26
Alignment explanation
Indices: 49338231--49338299 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 26
49338221 TAATTATATA
49338231 TGCTCACACGAGCTGTGAAATGGGCC
1 TGCTCACACGAGCTGTGAAATGGGCC
** * * *
49338257 TAATCACATGAGTTGTGAAATGGGCT
1 TGCTCACACGAGCTGTGAAATGGGCC
49338283 TGCTCACACGAGCTGTG
1 TGCTCACACGAGCTGTG
49338300 GGTCGGGCTG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 34 1.00
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (26 bp):
TGCTCACACGAGCTGTGAAATGGGCC
Found at i:49342027 original size:16 final size:17
Alignment explanation
Indices: 49342003--49342043 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
49341993 TTGTTAAATG
*
49342003 TACTCTTTCATAA-TTT
1 TACTTTTTCATAACTTT
49342019 TACTTTTTC-TAACTTT
1 TACTTTTTCATAACTTT
49342035 T-CTTTTTCA
1 TACTTTTTCA
49342044 CTGATCAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.61
Consensus pattern (17 bp):
TACTTTTTCATAACTTT
Found at i:49345509 original size:26 final size:25
Alignment explanation
Indices: 49345477--49345552 Score: 89
Period size: 26 Copynumber: 3.0 Consensus size: 25
49345467 ATGAATTTTC
49345477 TCAAAATTTTACCAAGGGTAAAATTG
1 TCAAAATTTTA-CAAGGGTAAAATTG
* * **
49345503 TCGAAATTATATCGCGGGTAAAATTG
1 TCAAAATTTTA-CAAGGGTAAAATTG
*
49345529 TCAAAATTTTACTAGGGTAAAATT
1 TCAAAATTTTACAAGGGTAAAATT
49345553 AGGGTGAAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
25 11 0.27
26 30 0.73
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (25 bp):
TCAAAATTTTACAAGGGTAAAATTG
Found at i:49346553 original size:12 final size:12
Alignment explanation
Indices: 49346538--49346579 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
49346528 ATCGAGCTAC
49346538 AAATATTTTTAT
1 AAATATTTTTAT
**
49346550 AAATA--TTCGT
1 AAATATTTTTAT
49346560 AAATATTTTTAT
1 AAATATTTTTAT
49346572 AAATATTT
1 AAATATTT
49346580 ACAGAGCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
10 8 0.33
12 16 0.67
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (12 bp):
AAATATTTTTAT
Found at i:49352691 original size:20 final size:20
Alignment explanation
Indices: 49352658--49352702 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
49352648 TAAATTCACA
49352658 TAATTAAAACAAGACAC-AAT
1 TAATTAAAACAAGAC-CTAAT
**
49352678 TAATTAAATTAAGACCTAAT
1 TAATTAAAACAAGACCTAAT
49352698 TAATT
1 TAATT
49352703 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:49353807 original size:18 final size:18
Alignment explanation
Indices: 49353784--49353818 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49353774 TAAGAACAAA
49353784 AAGCATCAAAATAGTTTC
1 AAGCATCAAAATAGTTTC
*
49353802 AAGCATGAAAATAGTTT
1 AAGCATCAAAATAGTTT
49353819 GGCACATCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (18 bp):
AAGCATCAAAATAGTTTC
Found at i:49358448 original size:65 final size:63
Alignment explanation
Indices: 49358357--49358479 Score: 160
Period size: 65 Copynumber: 1.9 Consensus size: 63
49358347 GAGAATCATT
* * *
49358357 AGAAAAGCTGGTGTTATTTTAGCA-TTTTATGTTGTTTTTAAGTATGTTTTGTTTTCTTGCATGA
1 AGAAAAGCTGGTGTTATTTTAGCATTTTTATGTT-ATTTTAAATATG-TTTATTTTCTTGCATGA
*
49358421 AGAATAAGTTGGTGTTATTTT-GTCATTTTTATGTTATTTTAAATATGTTTATTTTCTTG
1 AGAA-AAGCTGGTGTTATTTTAG-CATTTTTATGTTATTTTAAATATGTTTATTTTCTTG
49358480 ATTCAAAAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
64 16 0.31
65 27 0.52
66 9 0.17
ACGTcount: A:0.23, C:0.05, G:0.18, T:0.54
Consensus pattern (63 bp):
AGAAAAGCTGGTGTTATTTTAGCATTTTTATGTTATTTTAAATATGTTTATTTTCTTGCATGA
Found at i:49358492 original size:65 final size:65
Alignment explanation
Indices: 49358365--49358492 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 65
49358355 TTAGAAAAGC
* * * * *
49358365 TGGTGTTATTTTAGCATTTTATGTTGTTTTTAAGTATGTTTTGTTTTCTTGCATGAAGAATAAGT
1 TGGTGTTATTTTAGCATTTTATGTTGATTTTAAATATGTTTTATTTTCTTGCATAAAAAATAAGT
49358430 TGGTGTTATTTT-GTCATTTTTATGTT-ATTTTAAATATG-TTTATTTTCTTG-ATTCAAAAAAT
1 TGGTGTTATTTTAG-CA-TTTTATGTTGATTTTAAATATGTTTTATTTTCTTGCA-T-AAAAAAT
49358491 AA
62 AA
49358493 AAAAAAGTAT
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
63 1 0.02
64 13 0.24
65 31 0.57
66 9 0.17
ACGTcount: A:0.25, C:0.05, G:0.16, T:0.55
Consensus pattern (65 bp):
TGGTGTTATTTTAGCATTTTATGTTGATTTTAAATATGTTTTATTTTCTTGCATAAAAAATAAGT
Found at i:49363411 original size:40 final size:40
Alignment explanation
Indices: 49363351--49363572 Score: 365
Period size: 40 Copynumber: 5.6 Consensus size: 40
49363341 CAAGCTCAAT
* * * * *
49363351 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
49363391 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49363431 TGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* *
49363470 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49363510 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49363550 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
49363573 GTATTCAAAT
Statistics
Matches: 170, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 38 0.22
40 132 0.78
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:49363539 original size:119 final size:120
Alignment explanation
Indices: 49363351--49363572 Score: 383
Period size: 119 Copynumber: 1.9 Consensus size: 120
49363341 CAAGCTCAAT
* *
49363351 TGCCTTCGGGTCTTAACCCGGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
*
49363416 ATCAACTTGCACAATTGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAA
66 ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* * *
49363470 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
49363535 ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGAT
66 ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGAT
49363573 GTATTCAAAT
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
119 81 0.84
120 15 0.16
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (120 bp):
TGCCTTCGGGTCTTAACCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:49371771 original size:40 final size:40
Alignment explanation
Indices: 49371688--49371908 Score: 365
Period size: 40 Copynumber: 5.6 Consensus size: 40
49371678 CAAGCTCAAT
* * * *
49371688 TGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCACGAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
*
49371727 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAT
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49371767 TGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* *
49371806 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49371846 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
1 TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
49371886 TGCCTTCGGGTCTTAGCCCGGAT
1 TGCCTTCGGGTCTTAGCCCGGAT
49371909 GTATTCAAAT
Statistics
Matches: 170, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
39 58 0.34
40 112 0.66
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (40 bp):
TGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:49371797 original size:79 final size:80
Alignment explanation
Indices: 49371684--49371908 Score: 373
Period size: 79 Copynumber: 2.8 Consensus size: 80
49371674 ACCACAAGCT
* * * *
49371684 CAATTGCCTTCGGGTCTTAACCCGG-TATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGG
1 CAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
*
49371748 ATATATCAACTTGCA
66 ATATATCAACTCGCA
*
49371763 CAATTGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGT
1 CAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
49371827 ATATATCAACTCGCA
66 ATATATCAACTCGCA
*
49371842 CAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
1 CAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
49371907 AT
66 AT
49371909 GTATTCAAAT
Statistics
Matches: 136, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
78 12 0.09
79 70 0.51
80 54 0.40
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (80 bp):
CAATTGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGG
ATATATCAACTCGCA
Found at i:49371875 original size:119 final size:119
Alignment explanation
Indices: 49371688--49371908 Score: 381
Period size: 119 Copynumber: 1.9 Consensus size: 119
49371678 CAAGCTCAAT
* *
49371688 TGCCTTCGGGTCTTAACCCGGTATAGCAACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATATA
1 TGCCTTCGGGTCTTAACCCGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
*
49371753 TCAACTTGCACAATTGCCTTC-GGTCTTAGCCCGGATATATCAACTTGCACAAA
66 TCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
* *
49371806 TGCCTTCGGGTCTTAGCCCGTATATATCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
1 TGCCTTCGGGTCTTAACCCG-ATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATAT
49371871 ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGAT
65 ATCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGAT
49371909 GTATTCAAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
118 19 0.20
119 62 0.65
120 15 0.16
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.28
Consensus pattern (119 bp):
TGCCTTCGGGTCTTAACCCGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATA
TCAACTTGCACAAATGCCTTCGGGTCTTAGCCCGGATATATCAACTTGCACAAA
Found at i:49388408 original size:25 final size:24
Alignment explanation
Indices: 49388340--49388408 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
49388330 TAATAATCAG
*
49388340 TCATACAATAAGATAAAT-ATATT
1 TCATATAATAAGATAAATAATATT
* * *
49388363 TCAAAT-TTAA-ACAAATGAATATT
1 TCATATAATAAGATAAAT-AATATT
49388386 TACATATAATAAGATAAATAATA
1 T-CATATAATAAGATAAATAATA
49388409 ATGATAAAAT
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
21 5 0.15
22 3 0.09
23 10 0.29
24 4 0.12
25 7 0.21
26 5 0.15
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.33
Consensus pattern (24 bp):
TCATATAATAAGATAAATAATATT
Found at i:49389445 original size:47 final size:47
Alignment explanation
Indices: 49389376--49389469 Score: 179
Period size: 47 Copynumber: 2.0 Consensus size: 47
49389366 ATTTTGCAGG
*
49389376 GTTAGAGCAGTGGGGGGGACGTGACGAGGCAGAGGAGGTGATAGGAT
1 GTTAGAGCAGTGGAGGGGACGTGACGAGGCAGAGGAGGTGATAGGAT
49389423 GTTAGAGCAGTGGAGGGGACGTGACGAGGCAGAGGAGGTGATAGGAT
1 GTTAGAGCAGTGGAGGGGACGTGACGAGGCAGAGGAGGTGATAGGAT
49389470 AGGGCAGCCT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.27, C:0.09, G:0.50, T:0.15
Consensus pattern (47 bp):
GTTAGAGCAGTGGAGGGGACGTGACGAGGCAGAGGAGGTGATAGGAT
Found at i:49389459 original size:22 final size:22
Alignment explanation
Indices: 49389390--49389460 Score: 63
Period size: 22 Copynumber: 3.1 Consensus size: 22
49389380 GAGCAGTGGG
49389390 GGGGACGTGACGAGGCAGAGGA
1 GGGGACGTGACGAGGCAGAGGA
* * * *
49389412 GGTGATAG-GATGTTAGAGCAGTGGA
1 GGGGA-CGTGACG--AG-GCAGAGGA
49389437 GGGGACGTGACGAGGCAGAGGA
1 GGGGACGTGACGAGGCAGAGGA
49389459 GG
1 GG
49389461 TGATAGGATA
Statistics
Matches: 36, Mismatches: 8, Indels: 10
0.67 0.15 0.19
Matches are distributed among these distances:
22 16 0.44
23 3 0.08
24 3 0.08
25 14 0.39
ACGTcount: A:0.27, C:0.10, G:0.52, T:0.11
Consensus pattern (22 bp):
GGGGACGTGACGAGGCAGAGGA
Found at i:49390191 original size:129 final size:129
Alignment explanation
Indices: 49390054--49390349 Score: 380
Period size: 129 Copynumber: 2.3 Consensus size: 129
49390044 TAAGATTTGC
* * * *
49390054 GGTTTTAATCCGCTCCATTACAACTTCAGGGAGATAGGATTGAATTCTTTTGTCTACTCCACTGT
1 GGTTTTAATCCACTCCACTACAACTTCAGGGAGATAAGATTGAATTCTTTTGTCTACTCCACTGC
* * *
49390119 AACTTCAGGGAGATAAGACTGGATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTAT
66 AACTTCAGGGAGATAAGACTGAATGCGATCTGCACTACTACAACTTCAGAGAGATAAGATCTAT
* * ** *
49390183 GGTTTTAATCCACTCTACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCTGCTCCACTGC
1 GGTTTTAATCCACTCCACTACAACTTCAGGGAGATAAGATTGAATTCTTTTGTCTACTCCACTGC
* * * *
49390248 AACTTCAGGGAGATAAGACTGAATGTGATCTGCAGTACTATAACTTCAGAGAGATAAGATCTGT
66 AACTTCAGGGAGATAAGACTGAATGCGATCTGCACTACTACAACTTCAGAGAGATAAGATCTAT
** **
49390312 AATCTTTAA-CCTACTCCACTACTGC-TCAGGGAGATAAG
1 GGT-TTTAATCC-ACTCCACTACAACTTCAGGGAGATAAG
49390350 GCTGGATGCG
Statistics
Matches: 143, Mismatches: 22, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
129 129 0.90
130 14 0.10
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (129 bp):
GGTTTTAATCCACTCCACTACAACTTCAGGGAGATAAGATTGAATTCTTTTGTCTACTCCACTGC
AACTTCAGGGAGATAAGACTGAATGCGATCTGCACTACTACAACTTCAGAGAGATAAGATCTAT
Found at i:49390247 original size:44 final size:44
Alignment explanation
Indices: 49390065--49390265 Score: 180
Period size: 44 Copynumber: 4.6 Consensus size: 44
49390055 GTTTTAATCC
* * * *
49390065 GCTCCATTACAACTTCAGGGAGATAGGATTGAATTCTTTTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGATTCTTTTGTCT
* * * *
49390109 ACTCCACTGTAACTTCAGGGAGATAAGACTGGATGC----GATCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGATTCTTTTG-TCT
* * ** * *
49390150 GCTCTACTGCAACTTCAGAGAGATAAGATCT--ATGGTTTTAATCC
1 GCTCCACTGCAACTTCAGGGAGATAAGAT-TGGATTCTTTT-GTCT
* * *
49390194 ACTCTACTGCAACTTCAGGGAGATAAGATTGGTTTCTTTTGTCT
1 GCTCCACTGCAACTTCAGGGAGATAAGATTGGATTCTTTTGTCT
49390238 GCTCCACTGCAACTTCAGGGAGATAAGA
1 GCTCCACTGCAACTTCAGGGAGATAAGA
49390266 CTGAATGTGA
Statistics
Matches: 123, Mismatches: 25, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
40 4 0.03
41 27 0.22
42 1 0.01
43 1 0.01
44 85 0.69
45 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.31
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGGGAGATAAGATTGGATTCTTTTGTCT
Found at i:49390472 original size:258 final size:256
Alignment explanation
Indices: 49390208--49390998 Score: 793
Period size: 258 Copynumber: 3.1 Consensus size: 256
49390198 TACTGCAACT
* ** *** * *
49390208 TCAGGGAGATAAGATTGGTTTCTTTTGTCTGCTCCACTGCAACTTCAGGG-AGATAAGACTGAAT
1 TCAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACT-CAACTTC-GGGAAGACAAGATTGAAT
* * ** *
49390272 GTGATCTGCAGTACTA-TAACTTCAGAGAGATAAGATCTGTAATCTTTAACCTACTCCACTACTG
64 GTGATCTGCACTACTACT-ACTTCAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTG
*
49390336 CTCAGGGAGATAAGG-CTGGAT-GC-GATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCC
128 CTCAGGGAGAT-AGGACTGG-TGGCTAATCTGCTT-CCTACTACCTTGGGAAGATAAGATTCGCC
* *
49390398 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAACTACAATCTTCAACCTACTCCACTGC
190 GTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC-ACCTACTCCACTAC
49390463 TGC
254 TGC
* * * *
49390466 TCAGGGAGATAGGACTAGTGGCTTAAATCTGCTTCCTACT-ATC-TCGGGAAGACAAGATTTGCC
1 TCAGGGAGATAAGACTGGTGGCTTAAATCTGC-TCC-ACTCAACTTCGGGAAGACAAGA-TTG-A
* * * * * * *
49390529 GTCTTCGATCTGCTCCACTACTGCTT-AGGGAGATAAGAACTACAATCTTCAACCTACTCCACTG
62 AT-GT-GATCTGCACTACTACTACTTCAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTG
* * * * *
49390593 GTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCTATTATCTCGGGAAGACAAGATTCG
125 CTGCTCAGGGAGATAGGACTGGTGGC-T-AATCTGCTTCCTACTACCTTGGGAAGATAAGATTCG
* * *
49390658 CCGTCTTCAATCTGCTCCGCTACTGCTTAGGGAGATAAGATCTACAATTTTCA---ACTCCACTA
188 CCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCACCTACTCCACTA
49390720 CTGC
253 CTGC
** * * * **
49390724 TCAAAGAGATAGGACTGGTGGCTTAAATCTGCTTCCTAC-C-ATTTCGGGAAGACAAGATTCACC
1 TCAGGGAGATAAGACTGGTGGCTTAAATCTGC-TCC-ACTCAACTTCGGGAAGACAAGATTGAAT
**
49390787 GTCTTC-G-ATCTACTCCACTACTGCTCAGGGAGATAAGATCTACAATCTTTAACCTACTCCACT
64 GTGATCTGCA-CTACT--ACTACT--TCAGGGAGATAAGATCTACAATCTTTAACCTACTCCACT
* * * *
49390850 GCTGCTCAGGGAGATAGGACTGGTGGCTTAAATATGCTTCTTACTACCTTAGGAAGATAAGATCC
124 GCTGCTCAGGGAGATAGGACTGGTGGC-T-AATCTGCTTCCTACTACCTTGGGAAGATAAGATTC
* *
49390915 GCTGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCGACCTACTCTAC
187 GCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTC-ACCTACTCCAC
*
49390980 TATTGC
251 TACTGC
49390986 TCAGGGAGATAAG
1 TCAGGGAGATAAG
49390999 GCTTGGTATG
Statistics
Matches: 438, Mismatches: 70, Indels: 46
0.79 0.13 0.08
Matches are distributed among these distances:
253 5 0.01
254 2 0.00
255 6 0.01
256 3 0.01
257 12 0.03
258 230 0.53
259 9 0.02
260 55 0.13
261 15 0.03
262 93 0.21
263 8 0.02
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (256 bp):
TCAGGGAGATAAGACTGGTGGCTTAAATCTGCTCCACTCAACTTCGGGAAGACAAGATTGAATGT
GATCTGCACTACTACTACTTCAGGGAGATAAGATCTACAATCTTTAACCTACTCCACTGCTGCTC
AGGGAGATAGGACTGGTGGCTAATCTGCTTCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTC
GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTACAATCTTCACCTACTCCACTACTGC
Found at i:49390548 original size:131 final size:131
Alignment explanation
Indices: 49390298--49390996 Score: 966
Period size: 131 Copynumber: 5.4 Consensus size: 131
49390288 TAACTTCAGA
** *
49390298 GAGATAAGATCTGTAATCTTTAACCTACTCCACTACTGCTCAGGGAGATAAGG-CTGGAT-GC--
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGAT-AGGACTGG-TGGCTT
* * * *
49390359 -GATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
64 AAATCTGCTT-CCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT
49390423 TAGG
128 TAGG
* * *
49390427 GAGATAAGAACTACAATCTTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTAGTGGCTTAA
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAA
*
49390492 ATCTGCTTCCTACTATCTCGGGAAGACAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAG
66 ATCTGCTTCCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
49390557 G
131 G
* **
49390558 GAGATAAGAACTACAATCTTCAACCTACTCCACTGGTGCTCAGGGAGATAGGACTGGTGGCTTAA
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAA
* * *
49390623 ATCTGCTTCCTATTATCTCGGGAAGACAAGATTCGCCGTCTTCAATCTGCTCCGCTACTGCTTAG
66 ATCTGCTTCCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
49390688 G
131 G
* **
49390689 GAGATAAGATCTACAATTTTC-A---ACTCCACTACTGCTCAAAGAGATAGGACTGGTGGCTTAA
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAA
* * * * *
49390750 ATCTGCTTCCTACCATTTCGGGAAGACAAGATTCACCGTCTTCGATCTACTCCACTACTGCTCAG
66 ATCTGCTTCCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
49390815 G
131 G
* *
49390816 GAGATAAGATCTACAATCTTTAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAA
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAA
* * * ** * * *
49390881 ATATGCTTCTTACTACCTTAGGAAGATAAGATCCGCTGTCTTCGATCTGCTCCACTACTGCTTAG
66 ATCTGCTTCCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
49390946 G
131 G
* * *
49390947 GAGATAAGATCTACAATCTTCGACCTACTCTACTATTGCTCAGGGAGATA
1 GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATA
49390997 AGGCTTGGTA
Statistics
Matches: 507, Mismatches: 54, Indels: 16
0.88 0.09 0.03
Matches are distributed among these distances:
127 112 0.22
128 5 0.01
129 49 0.10
130 1 0.00
131 332 0.65
132 8 0.02
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.28
Consensus pattern (131 bp):
GAGATAAGATCTACAATCTTCAACCTACTCCACTACTGCTCAGGGAGATAGGACTGGTGGCTTAA
ATCTGCTTCCTACTATCTCGGGAAGACAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAG
G
Found at i:49390698 original size:44 final size:44
Alignment explanation
Indices: 49390384--49390956 Score: 153
Period size: 44 Copynumber: 13.2 Consensus size: 44
49390374 TACCTTGGGA
*
49390384 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *
49390428 AGATAAGA-ACTACAATCTTCAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
49390472 AGATAGGACTAG-TGGCTTAAATCTGCTTCCTACTA-T-C-TCGGG
1 AGATAAGATTCGCCGTCTTCAATCTGC-TCC-ACTACTGCTTAGGG
* * *
49390514 AAGACAAGATTTGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 -AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * ** *
49390559 AGATAAGA-ACTACAATCTTCAACCTACTCCACTGGTGCTCAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *
49390603 AGATAGGACT-GGTGGCTTAAATCTGCTTCCTATTA-T-C-TCGGG
1 AGATAAGATTCGCCGTCTTCAATCTGC-TCC-ACTACTGCTTAGGG
* *
49390645 AAGACAAGATTCGCCGTCTTCAATCTGCTCCGCTACTGCTTAGGG
1 -AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * **
49390690 AGATAAGA-TCTACAATTTTCAA----CTCCACTACTGCTCAAAG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * *** *
49390730 AGATAGGACT-GGTGGCTTAAATCTGCTTC-CTACCATTTCGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * *
49390772 AAGACAAGATTCACCGTCTTCGATCTACTCCACTACTGCTCAGGG
1 -AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
49390817 AGATAAGA-TCTACAATCTTTAACCTACTCCACTGCTGCTCAGGG
1 AGATAAGATTC-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
49390861 AGATAGGACT-GGTGGCTTAAATATGCTTCTTACTAC--CTTAGGA
1 AGATAAGATTCGCCGTCTTCAATCTGC-TC-CACTACTGCTTAGGG
* * *
49390904 AGATAAGATCCGCTGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
49390948 AGATAAGAT
1 AGATAAGAT
49390957 CTACAATCTT
Statistics
Matches: 356, Mismatches: 139, Indels: 68
0.63 0.25 0.12
Matches are distributed among these distances:
39 4 0.01
40 21 0.06
41 1 0.00
42 23 0.06
43 77 0.22
44 204 0.57
45 26 0.07
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
AGATAAGATTCGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:49391642 original size:46 final size:45
Alignment explanation
Indices: 49391541--49391643 Score: 109
Period size: 45 Copynumber: 2.3 Consensus size: 45
49391531 AGCAAAGCTC
* * *
49391541 AAAATGAATGAATCAATCAAGATAGCAAATTTTGCTAGAATACAA
1 AAAATGAATAAATCAATCAAGATAGCAAATTTTGCAAAAATACAA
* * * **
49391586 AATGA-GAATAAATTAATCAAGATGGCGTATTTTGTCAAAAATACAA
1 AA-AATGAATAAATCAATCAAGATAGCAAATTTTG-CAAAAATACAA
49391632 AAAATGAATAAA
1 AAAATGAATAAA
49391644 ATGGAAATAG
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
45 27 0.59
46 19 0.41
ACGTcount: A:0.52, C:0.09, G:0.14, T:0.25
Consensus pattern (45 bp):
AAAATGAATAAATCAATCAAGATAGCAAATTTTGCAAAAATACAA
Found at i:49395551 original size:3 final size:3
Alignment explanation
Indices: 49395539--49395730 Score: 92
Period size: 3 Copynumber: 64.3 Consensus size: 3
49395529 ATATAGGAAT
* * * * *
49395539 ATA ATAA ATA ATA ATG ATA GTA GTG ATA ATA TTA ATA ATA A-A AGTA
1 ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA
* * * *
49395585 ATA CTA GTA ATA AT- ATCA ATA ATA ACA AAA ATA ATA ATA ATA A-A
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * ** *
49395629 AGTA ATA A-A GATA ATA ATA CT- ATA GTA ATG ATG ACG TTA ATA ATA
1 A-TA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
49395674 ATA ATA TTA ATA AT- ATAA ATA ATA ATA CTA CTA ATA ATA AAA ATA
1 ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
49395719 ATG ATA A-A ATA A
1 ATA ATA ATA ATA A
49395731 CAAATATATG
Statistics
Matches: 144, Mismatches: 32, Indels: 26
0.71 0.16 0.13
Matches are distributed among these distances:
2 12 0.08
3 120 0.83
4 12 0.08
ACGTcount: A:0.59, C:0.04, G:0.07, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:49397398 original size:25 final size:24
Alignment explanation
Indices: 49397365--49397422 Score: 82
Period size: 23 Copynumber: 2.4 Consensus size: 24
49397355 TGTATTTATT
*
49397365 TTTAAAATTTTTTAAATAATATATA
1 TTTATAATTTTTTAAA-AATATATA
49397390 TTTATAA-TTTTTAAAAATATATA
1 TTTATAATTTTTTAAAAATATATA
49397413 TTTACTAATT
1 TTTA-TAATT
49397423 AAATCAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.40
24 11 0.37
25 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTATAATTTTTTAAAAATATATA
Found at i:49397408 original size:23 final size:25
Alignment explanation
Indices: 49397373--49397422 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
49397363 TTTTTAAAAT
49397373 TTTTTAAATAATATATATTTA-TAA
1 TTTTTAAATAATATATATTTACTAA
49397397 TTTTTAAA-AATATATATTTACTAA
1 TTTTTAAATAATATATATTTACTAA
49397421 TT
1 TT
49397423 AAATCAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTAAATAATATATATTTACTAA
Found at i:49406844 original size:10 final size:10
Alignment explanation
Indices: 49406829--49406872 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
49406819 AACTAGTACG
49406829 AAACAGAACA
1 AAACAGAACA
*
49406839 AAACAGAATA
1 AAACAGAACA
* *
49406849 GAACAGAACC
1 AAACAGAACA
*
49406859 AAACAAAACA
1 AAACAGAACA
49406869 AAAC
1 AAAC
49406873 GAAACAGAAC
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.68, C:0.20, G:0.09, T:0.02
Consensus pattern (10 bp):
AAACAGAACA
Found at i:49409340 original size:30 final size:30
Alignment explanation
Indices: 49409306--49409364 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
49409296 TACGAGCTTT
49409306 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
1 GGGGCAAAAGTGTAAATATGCAAAAGTTTA
* * * *
49409336 GGGGCAAAATTGTAATTTTGCCAAAGTTT
1 GGGGCAAAAGTGTAAATATGCAAAAGTTT
49409365 GAGTCAAGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.29
Consensus pattern (30 bp):
GGGGCAAAAGTGTAAATATGCAAAAGTTTA
Found at i:49409857 original size:23 final size:23
Alignment explanation
Indices: 49409813--49409884 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
49409803 AGTGTTATTG
49409813 ATCAGTGGTAGCTT-GGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
49409835 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
49409858 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
49409881 ATCA
1 ATCA
49409885 ATGTGGCACT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
22 14 0.30
23 32 0.70
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:49410059 original size:38 final size:37
Alignment explanation
Indices: 49410017--49410089 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
49410007 ATGTGTGGAA
* *
49410017 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
49410055 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
49410090 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:49413111 original size:45 final size:40
Alignment explanation
Indices: 49413013--49413091 Score: 131
Period size: 40 Copynumber: 2.0 Consensus size: 40
49413003 GGACTTTAAT
*
49413013 TTTAATAAACTCATCTTAGTTAATAAATGAGTTGTTGGAA
1 TTTATTAAACTCATCTTAGTTAATAAATGAGTTGTTGGAA
* *
49413053 TTTATTAAACTCATCTTAGTTAGTAATTGAGTTGTTGGA
1 TTTATTAAACTCATCTTAGTTAATAAATGAGTTGTTGGA
49413092 CTTTCTTTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.16, T:0.43
Consensus pattern (40 bp):
TTTATTAAACTCATCTTAGTTAATAAATGAGTTGTTGGAA
Found at i:49419917 original size:28 final size:28
Alignment explanation
Indices: 49419877--49419931 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
49419867 TATCAAAGAT
49419877 AGTTTACTCCAGGAATGCTCTTGGGCCA
1 AGTTTACTCCAGGAATGCTCTTGGGCCA
*
49419905 AGTTTACTCCAGGAATGCTTTTGGGCC
1 AGTTTACTCCAGGAATGCTCTTGGGCC
49419932 TCAATGTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.25, T:0.31
Consensus pattern (28 bp):
AGTTTACTCCAGGAATGCTCTTGGGCCA
Found at i:49423916 original size:17 final size:17
Alignment explanation
Indices: 49423894--49423932 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
49423884 TGAGAGAAAG
*
49423894 AAAGAAATTTTAAGAGA
1 AAAGAAAATTTAAGAGA
49423911 AAAGAAAATTTAAGAGA
1 AAAGAAAATTTAAGAGA
49423928 AAAGA
1 AAAGA
49423933 GGAGAGAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AAAGAAAATTTAAGAGA
Found at i:49430233 original size:40 final size:40
Alignment explanation
Indices: 49430174--49430385 Score: 268
Period size: 40 Copynumber: 5.3 Consensus size: 40
49430164 CATTTGAATG
* * *
49430174 ATATCCGGGCTAAGTCCCGAAGGTAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* * *
49430214 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* * *
49430254 ATACCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
* *
49430294 TTATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-T
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAG-TGATT
* *
49430334 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
49430374 ATATCC-GGCTAA
1 ATATCCGGGCTAA
49430386 ATTCCGAAGA
Statistics
Matches: 147, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 10 0.07
40 132 0.90
41 5 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.28
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGTGATT
Found at i:49430311 original size:80 final size:80
Alignment explanation
Indices: 49430178--49430385 Score: 328
Period size: 80 Copynumber: 2.6 Consensus size: 80
49430168 TGAATGATAT
* *
49430178 CCGGGCTAAGTCCCGAAGGTAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
49430243 TGCGAGTTGCTATAC
66 TGCGAGTTGATATAC
*
49430258 CCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
*
49430323 TGCGAGTTGATATAT
66 TGCGAGTTGATATAC
* * * *
49430338 CCGGGCTAAGACCCGAAGGCATTTGTGCTTGTGGTTATATCC-GGCTAA
1 CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAA
49430386 ATTCCGAAGA
Statistics
Matches: 118, Mismatches: 10, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
79 6 0.05
80 112 0.95
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (80 bp):
CCGGGCTAAGACCCGAAGGCAATTGTGCTAGTGATTTTATCCGGGCTAAGACCCGAAGGCATTTG
TGCGAGTTGATATAC
Found at i:49432619 original size:29 final size:29
Alignment explanation
Indices: 49432556--49432623 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
49432546 TAATCAACCA
49432556 CGCACACTTAGTGCCATGCACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
49432585 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
49432614 CGCACACTTA
1 CGCACACTTA
49432624 CCTTTTCCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 3 0.09
29 31 0.91
ACGTcount: A:0.28, C:0.31, G:0.13, T:0.28
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:49432736 original size:174 final size:173
Alignment explanation
Indices: 49432445--49432772 Score: 550
Period size: 174 Copynumber: 1.9 Consensus size: 173
49432435 AACTCAAGGT
* *
49432445 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
49432510 GAAAATATATATGGGTTGCACGCACATAATGTTTAGTAATCAACCACGCACACTTAGTGCCATGC
66 GAAAATATATATGGGTTGCAC-CACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGC
49432575 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
130 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
49432619 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
* *
49432684 GAAAATATATATTGGGTTCGCA-CACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATG
66 GAAAATATATA-TGGGTT-GCACCACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATG
* *
49432748 TACTTTAAACTCGCACACTTAGTGC
129 CACTTTAAACTCACACACTTAGTGC
49432773 TGTACAATTT
Statistics
Matches: 144, Mismatches: 8, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
174 135 0.94
175 6 0.04
176 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (173 bp):
ACTTACCTTTTCCGCTGTCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATGGGTTGCACCACATAATGCTTAATAATCAACCACGCACACTTAGTGCCATGCA
CTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:49432764 original size:29 final size:30
Alignment explanation
Indices: 49432725--49432803 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
49432715 CTTAATAATC
49432725 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
49432755 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
49432784 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
49432804 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:49489767 original size:20 final size:20
Alignment explanation
Indices: 49489742--49489780 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
49489732 TACTTTATTC
49489742 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
49489762 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
49489781 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:49490108 original size:50 final size:49
Alignment explanation
Indices: 49489986--49490112 Score: 132
Period size: 49 Copynumber: 2.6 Consensus size: 49
49489976 AATAACATGC
* *
49489986 CAAA-GCCATGTCCCAGACATGGTCTTACATGGGATGTTTCCTGTACTG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATGTACTG
* * * **
49490034 CAAATGCCATATCCTAGATATGGTCTTACATGAGA-GTTCTCATAGTGGTG
1 CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTT-TCAT-GTACTG
** *
49490084 CCCATGCCATGTCCCAAACATGGTCTTAC
1 CAAATGCCATGTCCCAGACATGGTCTTAC
49490113 GAGGGACCTC
Statistics
Matches: 63, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
48 7 0.11
49 29 0.46
50 27 0.43
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.29
Consensus pattern (49 bp):
CAAATGCCATGTCCCAGACATGGTCTTACATGAGATGTTTCATGTACTG
Found at i:49494251 original size:15 final size:15
Alignment explanation
Indices: 49494233--49494261 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
49494223 GATGTTTTAT
49494233 TTGACCATGTTAAAC
1 TTGACCATGTTAAAC
49494248 TTGACCATGTTAAA
1 TTGACCATGTTAAA
49494262 GAGGGCGAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (15 bp):
TTGACCATGTTAAAC
Found at i:49509844 original size:21 final size:22
Alignment explanation
Indices: 49509766--49509844 Score: 58
Period size: 25 Copynumber: 3.6 Consensus size: 22
49509756 ACTAAATATC
* *
49509766 ATAAACAAAATAAAAT-AA-AA
1 ATAAACATAATAAATTAAATAA
49509786 ATAAAGCATAA-AAATTAAATAA
1 ATAAA-CATAATAAATTAAATAA
* *
49509808 ATAACCATATGAATAAATTAATTAA
1 ATAA--ACAT-AATAAATTAAATAA
49509833 ATAAA-ATAATAA
1 ATAAACATAATAA
49509845 TAATAATAAT
Statistics
Matches: 48, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
20 9 0.19
21 11 0.23
22 8 0.17
23 3 0.06
24 3 0.06
25 14 0.29
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (22 bp):
ATAAACATAATAAATTAAATAA
Found at i:49514998 original size:12 final size:12
Alignment explanation
Indices: 49514983--49515016 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
49514973 TAATTTGTAT
49514983 AATTAAGAATAA
1 AATTAAGAATAA
49514995 AATTAAGAATAA
1 AATTAAGAATAA
49515007 AATTAA-AATA
1 AATTAAGAATA
49515017 TGTTACTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 4 0.18
12 18 0.82
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (12 bp):
AATTAAGAATAA
Found at i:49522473 original size:17 final size:17
Alignment explanation
Indices: 49522440--49522473 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49522430 AGGTTTCGAT
**
49522440 GCCTCACATTCCTCAAG
1 GCCTCACATTCAGCAAG
49522457 GCCTCACATTCAGCAAG
1 GCCTCACATTCAGCAAG
49522474 AAAACTCTGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.38, G:0.15, T:0.21
Consensus pattern (17 bp):
GCCTCACATTCAGCAAG
Found at i:49527232 original size:18 final size:18
Alignment explanation
Indices: 49527192--49527226 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
49527182 CCAGGTGCGT
*
49527192 ATCCTAGCCCTTATATGC
1 ATCCTAACCCTTATATGC
49527210 ATCCTAACCCTTATATG
1 ATCCTAACCCTTATATG
49527227 TTTCCTTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
ATCCTAACCCTTATATGC
Found at i:49527737 original size:8 final size:9
Alignment explanation
Indices: 49527721--49527750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
49527711 TGAATAAGGC
49527721 AATATTTTT
1 AATATTTTT
49527730 AATATTTTT
1 AATATTTTT
49527739 -ATATTTTT
1 AATATTTTT
49527747 AATA
1 AATA
49527751 AAATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (9 bp):
AATATTTTT
Found at i:49531237 original size:19 final size:20
Alignment explanation
Indices: 49531213--49531250 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
49531203 ACTACAATTC
49531213 TTCAAA-AG-TGTAATGTTGT
1 TTCAAATAGTTGTAA-GTTGT
49531232 TTCAAATAGTTGTAAGTTG
1 TTCAAATAGTTGTAAGTTG
49531251 GATTCGGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 6 0.35
20 6 0.35
21 5 0.29
ACGTcount: A:0.32, C:0.05, G:0.21, T:0.42
Consensus pattern (20 bp):
TTCAAATAGTTGTAAGTTGT
Found at i:49534094 original size:14 final size:15
Alignment explanation
Indices: 49534064--49534096 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
49534054 GTTGTTATGA
49534064 TAGTTAGTAGTTAGG
1 TAGTTAGTAGTTAGG
*
49534079 TAGTTAG-AGTTTGG
1 TAGTTAGTAGTTAGG
49534093 TAGT
1 TAGT
49534097 GAAGGTAGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.42
Consensus pattern (15 bp):
TAGTTAGTAGTTAGG
Found at i:49534760 original size:13 final size:12
Alignment explanation
Indices: 49534731--49534773 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
49534721 CCATTTTTTT
49534731 ATTTTTTATATA
1 ATTTTTTATATA
*
49534743 A-TTTTAATATA
1 ATTTTTTATATA
49534754 ATTTTTTTATATAA
1 A-TTTTTTATAT-A
49534768 ATTTTT
1 ATTTTT
49534774 CACCTGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 10 0.38
12 1 0.04
13 13 0.50
14 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
ATTTTTTATATA
Found at i:49535405 original size:25 final size:26
Alignment explanation
Indices: 49535346--49535406 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
49535336 TGAAAACAGA
49535346 GTGAACAAAACAAAACCACGAAAACT
1 GTGAACAAAACAAAACCACGAAAACT
* * *
49535372 GT-AGGCAAAACAAAATCAC-AAAATT
1 GTGA-ACAAAACAAAACCACGAAAACT
49535397 GTGAACAAAA
1 GTGAACAAAA
49535407 TTACGATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
25 13 0.45
26 16 0.55
ACGTcount: A:0.57, C:0.18, G:0.13, T:0.11
Consensus pattern (26 bp):
GTGAACAAAACAAAACCACGAAAACT
Found at i:49537694 original size:2 final size:2
Alignment explanation
Indices: 49537689--49537752 Score: 74
Period size: 2 Copynumber: 32.0 Consensus size: 2
49537679 TATATATATA
** * *
49537689 TG TG TG TG TG TG TG CA TG TG TG TG TG TG TG TG TG TG TG CG CG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
* *
49537731 TG CG TG CG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG
49537753 CGTGGCTTAG
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.02, C:0.08, G:0.48, T:0.42
Consensus pattern (2 bp):
TG
Found at i:49545866 original size:16 final size:15
Alignment explanation
Indices: 49545847--49545893 Score: 55
Period size: 16 Copynumber: 3.2 Consensus size: 15
49545837 ACAGATAAAT
49545847 GATATATCAGATATCA
1 GATATATCAGATA-CA
49545863 G--ATAT-AGATACA
1 GATATATCAGATACA
49545875 GATCATATCAGATACA
1 GAT-ATATCAGATACA
49545891 GAT
1 GAT
49545894 GAAGATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
12 3 0.11
13 5 0.19
14 4 0.15
15 4 0.15
16 11 0.41
ACGTcount: A:0.45, C:0.13, G:0.15, T:0.28
Consensus pattern (15 bp):
GATATATCAGATACA
Found at i:49545871 original size:29 final size:29
Alignment explanation
Indices: 49545828--49545893 Score: 91
Period size: 29 Copynumber: 2.3 Consensus size: 29
49545818 GTTACAAGAT
49545828 ATATCAGATACAGATAAATGAT-ATATCAG
1 ATATCAGATACAGATAAA-GATCATATCAG
* *
49545857 ATATCAGATATAGATACAGATCATATCAG
1 ATATCAGATACAGATAAAGATCATATCAG
49545886 ATA-CAGAT
1 ATATCAGAT
49545894 GAAGATTTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 8 0.24
29 26 0.76
ACGTcount: A:0.47, C:0.12, G:0.14, T:0.27
Consensus pattern (29 bp):
ATATCAGATACAGATAAAGATCATATCAG
Found at i:49545872 original size:22 final size:22
Alignment explanation
Indices: 49545771--49545866 Score: 131
Period size: 22 Copynumber: 4.3 Consensus size: 22
49545761 AAATACATAA
* *
49545771 ACAGAAACAAGATATATCATAT
1 ACAGATACAAGATATATCAGAT
*
49545793 ACAGTTACAAGATATATCAGAT
1 ACAGATACAAGATATATCAGAT
*
49545815 ACAGTTACAAGATATATCAGAT
1 ACAGATACAAGATATATCAGAT
49545837 ACAGATA-AATGATATATCAGAT
1 ACAGATACAA-GATATATCAGAT
49545859 ATCAGATA
1 A-CAGATA
49545867 TAGATACAGA
Statistics
Matches: 68, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
21 2 0.03
22 60 0.88
23 6 0.09
ACGTcount: A:0.49, C:0.12, G:0.12, T:0.26
Consensus pattern (22 bp):
ACAGATACAAGATATATCAGAT
Found at i:49551380 original size:56 final size:56
Alignment explanation
Indices: 49551314--49551420 Score: 144
Period size: 56 Copynumber: 1.9 Consensus size: 56
49551304 TTATACATAC
* * **
49551314 ATATGTGTTTTATATTCTATAACT-TTAATATATATATGTACATACATTCTTATAAT
1 ATATGTGTTTTACATTCTATAACTCCT-ATATATATACATACATACATTCTTATAAT
* *
49551370 ATATGTGTTTTACATTTTATAACTCCTATATATATACATACATATATTCTT
1 ATATGTGTTTTACATTCTATAACTCCTATATATATACATACATACATTCTT
49551421 TTTTTGTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
56 43 0.98
57 1 0.02
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.50
Consensus pattern (56 bp):
ATATGTGTTTTACATTCTATAACTCCTATATATATACATACATACATTCTTATAAT
Found at i:49551479 original size:26 final size:26
Alignment explanation
Indices: 49551450--49551503 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
49551440 ATCTTAAAAT
* *
49551450 ATACGTATACTTATATACATTTTATA
1 ATACATATACTTACATACATTTTATA
* *
49551476 ATACATATATTTACATATATTTTATA
1 ATACATATACTTACATACATTTTATA
49551502 AT
1 AT
49551504 TTATATACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (26 bp):
ATACATATACTTACATACATTTTATA
Found at i:49554899 original size:7 final size:7
Alignment explanation
Indices: 49554889--49554919 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
49554879 GTTTTTGGAT
49554889 TTTAGGG
1 TTTAGGG
49554896 TTTAGGG
1 TTTAGGG
49554903 TTTAGGG
1 TTTAGGG
49554910 TTTAGGG
1 TTTAGGG
49554917 TTT
1 TTT
49554920 TTAGGATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.13, C:0.00, G:0.39, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:49554938 original size:8 final size:8
Alignment explanation
Indices: 49554878--49554940 Score: 60
Period size: 7 Copynumber: 8.0 Consensus size: 8
49554868 CTGACTTGTA
*
49554878 GGTTTTTG
1 GGTTTTAG
*
49554886 GATTTTAG
1 GGTTTTAG
49554894 GG-TTTAG
1 GGTTTTAG
49554901 GG-TTTAG
1 GGTTTTAG
49554908 GG-TTTAG
1 GGTTTTAG
49554915 GGTTTTTAG
1 GG-TTTTAG
*
49554924 GATTTTTAG
1 G-GTTTTAG
49554933 GGTTTTAG
1 GGTTTTAG
49554941 AGAAAAAAGT
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
7 21 0.45
8 13 0.28
9 13 0.28
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (8 bp):
GGTTTTAG
Found at i:49558634 original size:100 final size:100
Alignment explanation
Indices: 49558456--49558654 Score: 326
Period size: 100 Copynumber: 2.0 Consensus size: 100
49558446 TATAGTTCGC
* * *
49558456 AAGGTTGCAGAAGGATTAAACCATGGAAGCGACTTTTGGGGCTATTTGTTTGATAAGGCTTAATT
1 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGGCTATTTGTTTGATAAGGCTTAATT
* * *
49558521 GTCATGTGTTTCCTGTGATTAATTTACGATTAAGG
66 GTCAGGTGGTTCCTATGATTAATTTACGATTAAGG
49558556 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGGCTATTTGTTTGATAAGGCTTAATT
1 AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGGCTATTTGTTTGATAAGGCTTAATT
* *
49558621 GTTAGGTGGTTCCTATGGTTAATTTACGATTAAG
66 GTCAGGTGGTTCCTATGATTAATTTACGATTAAG
49558655 AAAAAATTGG
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.35
Consensus pattern (100 bp):
AAGGTTCCAGAAGGATTAAACCATGGAAGCGAATTTCGGGGCTATTTGTTTGATAAGGCTTAATT
GTCAGGTGGTTCCTATGATTAATTTACGATTAAGG
Found at i:49565057 original size:86 final size:84
Alignment explanation
Indices: 49564848--49565097 Score: 288
Period size: 86 Copynumber: 2.9 Consensus size: 84
49564838 TAATATCGAT
* * * * * *
49564848 AAAATCTTGTTAAATGGCGGGAATAAATCCCGAAATAAATTTTATTTAATTCAA-TTTGAATTTG
1 AAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTAATTTTCATTTTG
* *
49564912 GAAAAAAATAAAATAAAAG
66 GCAAAAAATCAAATAAAAG
* * *
49564931 AAAATCTTGTTAAACGATAGGAATAAATCCCGAAATAGATTTTATTTTATTTAATTTCTCATTTC
1 AAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTAATTT-TCATTT-
*
49564996 TGGCAAAAAATCAAATACAA-
64 TGGCAAAAAATCAAATAAAAG
* * * *
49565016 TAAATCTTTATTAAACGGTGGGAATAAATCCTGAAACAGATTTTATTTAATTTAATTTTTCATTT
1 AAAATC-TTGTTAAACGGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTAA-TTTTCA-TT
49565081 TTGGCAACAAAATCAAA
63 TTGGCAA-AAAATCAAA
49565098 ATGTAATAAT
Statistics
Matches: 141, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
83 47 0.33
84 2 0.01
85 9 0.06
86 68 0.48
87 15 0.11
ACGTcount: A:0.43, C:0.10, G:0.11, T:0.35
Consensus pattern (84 bp):
AAAATCTTGTTAAACGGTGGGAATAAATCCCGAAATAGATTTTATTTAATTTAATTTTCATTTTG
GCAAAAAATCAAATAAAAG
Found at i:49565211 original size:79 final size:78
Alignment explanation
Indices: 49565125--49565300 Score: 237
Period size: 79 Copynumber: 2.2 Consensus size: 78
49565115 ATGGTAGGAG
* *
49565125 TCAATCCCGAAATTGATTTTATTTTACTCGTTTTTGGAAATAAAACAAAATTTGGAATAACATCG
1 TCAATCCCGAAATTGATTTTATTTTACTCATTTTTGGAAATAAAA-AAAATTTGGAATAAAATCG
49565190 TTGAAC-AGCGGGAA
65 TTGAACGA-CGGGAA
** * * *
49565204 TCAATCCCGAAACGGATTTTATTTTACTCATTTTTTGAAATAAAAATATTTTGGAATAAAATCGT
1 TCAATCCCGAAATTGATTTTATTTTACTCATTTTTGGAAATAAAAAAAATTTGGAATAAAATCGT
*
49565269 TGAACGATGGGAA
66 TGAACGACGGGAA
*
49565282 TCAATCCCAAAATGTGATT
1 TCAATCCCGAAAT-TGATT
49565301 GTGTGCCACT
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
78 38 0.45
79 46 0.55
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (78 bp):
TCAATCCCGAAATTGATTTTATTTTACTCATTTTTGGAAATAAAAAAAATTTGGAATAAAATCGT
TGAACGACGGGAA
Found at i:49567040 original size:22 final size:21
Alignment explanation
Indices: 49567008--49567049 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
49566998 CCAAATCAGG
*
49567008 CTTTTAACGGCGCTTTTTTAGA
1 CTTTTAACGGC-ATTTTTTAGA
*
49567030 CTTTTAGCGGCATTTTTTAG
1 CTTTTAACGGCATTTTTTAG
49567050 CGACGCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.17, C:0.17, G:0.19, T:0.48
Consensus pattern (21 bp):
CTTTTAACGGCATTTTTTAGA
Found at i:49567200 original size:43 final size:43
Alignment explanation
Indices: 49567141--49567494 Score: 417
Period size: 43 Copynumber: 8.3 Consensus size: 43
49567131 TTTTAGAAAT
* * *
49567141 AAACGCCGCTAAAGATCAGGACCTTTAGCGACGCTTTTCTCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
*
49567184 AAACGCCACTATAGATCAAGACCTTTAGCGACGC-TTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
* *
49567226 AAACGCCGCTATAGATCAAGACCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
* * * *
49567269 AAACGCCGCTATAGATTAGGACCTTTAGCGACGCTTTTTCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
* * * *
49567312 AAACGCCACTATAGATCAAGACCTTTCGCAACACTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
** * * *
49567355 AAATTCCGCTATAGATCAGGACCTTTAGTGACACTTTTCCCAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
* * * * *
49567398 AAAAGCCACTATAGATCAAGACCGTTAGCGACGCTTCTCCTAC
1 AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
* * **
49567441 GAACGCCGCTATAGATCATA-ACTTTTAGC-AGCGCTTTTTTCAC
1 AAACGCCGCTATAGATCA-AGACCTTTAGCGA-CGCTTTTCCCAC
49567484 AAACGCCGCTA
1 AAACGCCGCTA
49567495 AAAGTGCCAT
Statistics
Matches: 261, Mismatches: 47, Indels: 6
0.83 0.15 0.02
Matches are distributed among these distances:
42 39 0.15
43 221 0.85
44 1 0.00
ACGTcount: A:0.29, C:0.30, G:0.16, T:0.25
Consensus pattern (43 bp):
AAACGCCGCTATAGATCAAGACCTTTAGCGACGCTTTTCCCAC
Found at i:49571340 original size:57 final size:57
Alignment explanation
Indices: 49571227--49571340 Score: 160
Period size: 57 Copynumber: 2.0 Consensus size: 57
49571217 CTCCACTCCA
**
49571227 ACATTTACAATTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTGTGCTGC
1 ACATTTACAATTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
* *
49571284 ACATTTA-AAGTTTCACCTCCATTTATTTGAACAGAAGACAG-GCTTTTCTTCAGCTGC
1 ACATTTACAA-TTTCACCTCCATTTATTTGAACAGAAG-CAGAGCTCTTATTCAGCTGC
49571341 TCTTCAACGA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
56 2 0.04
57 46 0.90
58 3 0.06
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (57 bp):
ACATTTACAATTTCACCTCCATTTATTTGAACAGAAGCAGAGCTCTTATTCAGCTGC
Found at i:49571794 original size:15 final size:16
Alignment explanation
Indices: 49571760--49571794 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
49571750 GAAATTAGGG
49571760 ATTTTAGGGGGGAAAT
1 ATTTTAGGGGGGAAAT
49571776 ATTTTAGGGGGGAAA-
1 ATTTTAGGGGGGAAAT
49571791 ATTT
1 ATTT
49571795 ATAAATGGCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
ATTTTAGGGGGGAAAT
Found at i:49573007 original size:26 final size:26
Alignment explanation
Indices: 49572972--49573041 Score: 88
Period size: 26 Copynumber: 2.7 Consensus size: 26
49572962 ACTAATTAAT
* *
49572972 CTAAAT-CCTAAACCTTAACCTGACC
1 CTAAATCCCTAAACCCTAACCTAACC
*
49572997 CTGAATCCCTAAACCCTAACCTAACC
1 CTAAATCCCTAAACCCTAACCTAACC
* *
49573023 CTAAATCTCTAACCCCTAA
1 CTAAATCCCTAAACCCTAA
49573042 ATATTATTTA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
25 5 0.13
26 33 0.87
ACGTcount: A:0.36, C:0.39, G:0.03, T:0.23
Consensus pattern (26 bp):
CTAAATCCCTAAACCCTAACCTAACC
Found at i:49573115 original size:108 final size:107
Alignment explanation
Indices: 49572819--49573148 Score: 287
Period size: 108 Copynumber: 3.0 Consensus size: 107
49572809 ATATAAGAAC
* * *
49572819 TTATTTAGTATATAAATTAAAAAATACTAATTAATCTAAA-CTCTAACCCCT-AACCTGATCCTA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATC-CTAA-ACCTGAACCTGA-CC--
* * * * *
49572882 AATCTCTAAACCCTAAATCACTAACTCTTAATCTCAAACCCCTAACCCCTAAACC
61 -A--T-GAAACCCTAAATCCCTAA--C-TAACCT-AAACCTCTAACCCCTAAACA
* *
49572937 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCTTAACCTGACCCTGAA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCTGAACCTGACCATGAA
* * *
49573002 TCCCTAAA-CCCTAACCTAACCCTAAATCTCTAACCCCTAAATA
66 ACCCTAAATCCCTAA-CTAA-CCTAAACCTCTAACCCCTAAACA
* *
49573045 TTATTTAATATATAAATTAAAACACACTAATTAATCTAAA-CC-ATAACCTGACACC-GAATTCA
1 TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTA-AACCTGA-ACCTG-A-CCA
* *
49573107 T-AAACCCTAAATCCCTAACTAATCTTAACCTCTAACCCCTAA
62 TGAAACCCTAAATCCCTAACTAACCTAAACCTCTAACCCCTAA
49573149 CCCATAAACC
Statistics
Matches: 183, Mismatches: 21, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
106 1 0.01
107 26 0.14
108 75 0.41
109 11 0.06
110 5 0.03
111 9 0.05
112 1 0.01
117 5 0.03
118 49 0.27
119 1 0.01
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.29
Consensus pattern (107 bp):
TTATTTAATATATAAATTAAAAAACACTAATTAATCTAAATCCTAAACCTGAACCTGACCATGAA
ACCCTAAATCCCTAACTAACCTAAACCTCTAACCCCTAAACA
Found at i:49573194 original size:7 final size:7
Alignment explanation
Indices: 49573182--49573212 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
49573172 CTTAAATCAG
49573182 AATCCCT
1 AATCCCT
49573189 AATCCCT
1 AATCCCT
49573196 AATCCCT
1 AATCCCT
49573203 AATCCCT
1 AATCCCT
49573210 AAT
1 AAT
49573213 TCCATAATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.32, C:0.39, G:0.00, T:0.29
Consensus pattern (7 bp):
AATCCCT
Found at i:49574198 original size:82 final size:81
Alignment explanation
Indices: 49574049--49574204 Score: 242
Period size: 81 Copynumber: 1.9 Consensus size: 81
49574039 TTTTATTATT
* * *
49574049 ATTAGCGGCGCTTTTTCAAAAATGCCACTAAAGGTCGAGCATTAGCGGCGCTTCTTTAAAAACGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCACTAAAGGCCGAGCATTAGCGGCGCTTCTTTAAAAACGC
49574114 CGCTAAAGGAAAGAGC
66 CGCTAAAGGAAAGAGC
*
49574130 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTAGCGGCGCTT-TTTCAAAAAC
1 ATTAGCGGCGCTTCTTCAAAAACGCCACTAAAGGCC-GAGCATTAGCGGCGCTTCTTT-AAAAAC
*
49574194 GCCGCTTAAGG
64 GCCGCTAAAGG
49574205 CCCCAAAAAC
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 35 0.51
82 33 0.49
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (81 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCACTAAAGGCCGAGCATTAGCGGCGCTTCTTTAAAAACGC
CGCTAAAGGAAAGAGC
Found at i:49574205 original size:41 final size:41
Alignment explanation
Indices: 49574049--49574206 Score: 230
Period size: 41 Copynumber: 3.9 Consensus size: 41
49574039 TTTTATTATT
* * *
49574049 ATTAGCGGCGCTTTTTCAAAAATGCCACTAAAGGTC-GAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
**
49574089 ATTAGCGGCGCTTCTTT-AAAAACGCCGCTAAAGGAAAGAGC
1 ATTAGCGGCGCTT-TTTCAAAAACGCCGCTAAAGGCCAGAGC
*
49574130 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
*
49574171 ATTAGCGGCGCTTTTTCAAAAACGCCGCTTAAGGCC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCC
49574207 CCAAAAACTC
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
40 30 0.28
41 76 0.72
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:49576720 original size:77 final size:77
Alignment explanation
Indices: 49576623--49576830 Score: 283
Period size: 77 Copynumber: 2.7 Consensus size: 77
49576613 GGGAGGATTT
* * * *
49576623 AATCTCGAAACAAAATTATTTAATTAAATCTTGTTTGGAAATAAAACCAAAATAAAATATGTTAA
1 AATCTCGAAATAGAATTATTTAATTAAATCTTGTTTGGAAACAAAACCAAAATAAAATATATTAA
*
49576688 ACGATGAGAATA
66 ACGAGGAGAATA
* * * *
49576700 AATAC-CGAAATAGAATTATTTGATTAAATCTTGTTTCGAAACAAAACCAAAATTAAATCTATTA
1 AAT-CTCGAAATAGAATTATTTAATTAAATCTTGTTTGGAAACAAAACCAAAATAAAATATATTA
*
49576764 AACGAGGGGAATA
65 AACGAGGAGAATA
* *
49576777 AATCTCGAAATAGAATTATTTAATTAAATTTTTGTTTGGAAACAAAATCAAAAT
1 AATCTCGAAATAGAATTATTTAATTAAA-TCTTGTTTGGAAACAAAACCAAAAT
49576831 TGACTAAAAT
Statistics
Matches: 114, Mismatches: 14, Indels: 5
0.86 0.11 0.04
Matches are distributed among these distances:
76 1 0.01
77 90 0.79
78 23 0.20
ACGTcount: A:0.48, C:0.10, G:0.11, T:0.31
Consensus pattern (77 bp):
AATCTCGAAATAGAATTATTTAATTAAATCTTGTTTGGAAACAAAACCAAAATAAAATATATTAA
ACGAGGAGAATA
Found at i:49576922 original size:82 final size:82
Alignment explanation
Indices: 49576695--49577129 Score: 407
Period size: 82 Copynumber: 5.4 Consensus size: 82
49576685 TAAACGATGA
* * ** * * * * *
49576695 GAATAAATACCGAAATAGAATTATTTGATTAAATCTTGTTTCGAAACAAAA-C--CAA--AATTA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAAAGGAATAA
* *
49576755 AATCTATTAAACGAGGG
66 AATCTATTGAACGACGG
* * * * * * ** *
49576772 GAATAAATCTCGAAATAGAATTATTTAATTAAATTTTTGTTTGGAAACAAAATCAAAATTGACTA
1 GAATAAATCCCGAAACAGAATTATTCAATT-AATTCTCGTTTAGAAACAAAATCAAAAAGGAATA
* ** * **
49576837 AAATTTGCTGAATGGTGG
65 AAATCTATTGAACGACGG
* * *
49576855 GAATAAATCCCGAAACAGATTTATTCAATTAATTCTCGTTTGGAAACAAAATCAAAATGGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAAAGGAATAA
* * *
49576920 AATCTGTTGAATGGCGG
66 AATCTATTGAACGACGG
** * *
49576937 GAATAAATCTTGAAACAGAATTATTCAATTAATTCTCGTTTAGAAA-AGAATAAAAAAGGAATAA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAAAGGAATAA
*
49577001 AATCTATTGAACGATGG
66 AATCTATTGAACGACGG
* * * *
49577018 GAATAAATACCGAAACAAAATTATTCAATTAATTCTCATTTAGAAACAAAATGAAAAAGGAA-AA
1 GAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAAAGGAATAA
49577082 AATCTATTGAACGACGG
66 AATCTATTGAACGACGG
* * *
49577099 GAATAACTCCCGAAATAGATTTTATTCAATT
1 GAATAAATCCCGAAACAGA-ATTATTCAATT
49577130 TTAATTTTTA
Statistics
Matches: 298, Mismatches: 52, Indels: 11
0.83 0.14 0.03
Matches are distributed among these distances:
77 27 0.09
78 18 0.06
79 1 0.00
81 103 0.35
82 110 0.37
83 39 0.13
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (82 bp):
GAATAAATCCCGAAACAGAATTATTCAATTAATTCTCGTTTAGAAACAAAATCAAAAAGGAATAA
AATCTATTGAACGACGG
Found at i:49577044 original size:163 final size:165
Alignment explanation
Indices: 49576673--49577129 Score: 464
Period size: 163 Copynumber: 2.8 Consensus size: 165
49576663 ATAAAACCAA
* * * ** * * *
49576673 AATAAAATATGTTAAACGATGAGAATAAATACCGAAATAGAATTATTTGATTAAATCTTGTTTCG
1 AATAAAATATGTTGAACGATGGGAATAAATACCGAAACAGAATTATTCAATTAATTCTCGTTTAG
* * *
49576738 AAACAAAACCAAAAT----T-AAATCTATTAAACGAG-GGGAATAAATCTCGAAATAGAATTATT
66 AAACAAAATCAAAATGGAATAAAATCTATTGAACG-GCGGGAATAAATCTCGAAACAGAATTATT
* * * * * **
49576797 TAATTAAATTTTTGTTTGGAAACAAAATCAAAATTG
130 CAATTAAATTCTCGTTTAGAAACAAAATAAAAAAGG
* * * * * * * *
49576833 ACTAAAATTTGCTGAATGGTGGGAATAAATCCCGAAACAGATTTATTCAATTAATTCTCGTTTGG
1 AATAAAATATGTTGAACGATGGGAATAAATACCGAAACAGAATTATTCAATTAATTCTCGTTTAG
* * *
49576898 AAACAAAATCAAAATGGAATAAAATCTGTTGAATGGCGGGAATAAATCTTGAAACAGAATTATTC
66 AAACAAAATCAAAATGGAATAAAATCTATTGAACGGCGGGAATAAATCTCGAAACAGAATTATTC
*
49576963 AATT-AATTCTCGTTTAGAAA-AGAATAAAAAAGG
131 AATTAAATTCTCGTTTAGAAACAAAATAAAAAAGG
* * * *
49576996 AATAAAATCTATTGAACGATGGGAATAAATACCGAAACAAAATTATTCAATTAATTCTCATTTAG
1 AATAAAATATGTTGAACGATGGGAATAAATACCGAAACAGAATTATTCAATTAATTCTCGTTTAG
* * * * * * *
49577061 AAACAAAATGAAAAAGGAA-AAAATCTATTGAACGACGGGAATAACTCCCGAAATAGATTTTATT
66 AAACAAAATCAAAATGGAATAAAATCTATTGAACGGCGGGAATAAATCTCGAAACAGA-ATTATT
49577125 CAATT
130 CAATT
49577130 TTAATTTTTA
Statistics
Matches: 240, Mismatches: 50, Indels: 11
0.80 0.17 0.04
Matches are distributed among these distances:
160 64 0.27
162 31 0.13
163 90 0.38
164 15 0.06
165 40 0.17
ACGTcount: A:0.46, C:0.11, G:0.14, T:0.29
Consensus pattern (165 bp):
AATAAAATATGTTGAACGATGGGAATAAATACCGAAACAGAATTATTCAATTAATTCTCGTTTAG
AAACAAAATCAAAATGGAATAAAATCTATTGAACGGCGGGAATAAATCTCGAAACAGAATTATTC
AATTAAATTCTCGTTTAGAAACAAAATAAAAAAGG
Found at i:49581430 original size:25 final size:25
Alignment explanation
Indices: 49581380--49581430 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
49581370 TTAATTTTCA
*
49581380 TATATATATATACTTTATATCTTAT
1 TATATATATATACTTTATATCGTAT
49581405 TATATATATAT-CTTTATATACGTAT
1 TATATATATATACTTTATAT-CGTAT
49581430 T
1 T
49581431 TTTAATTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 8 0.33
25 16 0.67
ACGTcount: A:0.35, C:0.08, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATATATATACTTTATATCGTAT
Found at i:49589196 original size:21 final size:22
Alignment explanation
Indices: 49589172--49589222 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
49589162 TAATGTGTTT
49589172 TGTGTTTAATATG-AGTTTAAA
1 TGTGTTTAATATGTAGTTTAAA
* *
49589193 TGTGATTAATATGTTTGTTTAAA
1 TGTGTTTAATATG-TAGTTTAAA
49589216 TGTGTTT
1 TGTGTTT
49589223 GATTGCAGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 12 0.48
23 13 0.52
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (22 bp):
TGTGTTTAATATGTAGTTTAAA
Found at i:49589206 original size:11 final size:11
Alignment explanation
Indices: 49589172--49589222 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 11
49589162 TAATGTGTTT
49589172 TGTGTTTAATA
1 TGTGTTTAATA
*
49589183 TGAGTTTAA-A
1 TGTGTTTAATA
*
49589193 TGTGATTAATA
1 TGTGTTTAATA
49589204 TGTTTGTTTAA-A
1 TG--TGTTTAATA
49589216 TGTGTTT
1 TGTGTTT
49589223 GATTGCAGGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 13 0.39
11 11 0.33
12 3 0.09
13 6 0.18
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (11 bp):
TGTGTTTAATA
Found at i:49592596 original size:42 final size:43
Alignment explanation
Indices: 49592494--49592603 Score: 134
Period size: 42 Copynumber: 2.6 Consensus size: 43
49592484 CAACGGCAAC
* * * *
49592494 GTCCCAGATAGGGTCTTATATGTAATCAAATAACGATGTCACA
1 GTCCCAGACAGGGTCTTACACGTAATCAAATAACGACGTCACA
* *
49592537 CTCCCAGACAGGGTCTTACACGTAATCATAT-ACGACGTCA-A
1 GTCCCAGACAGGGTCTTACACGTAATCAAATAACGACGTCACA
*
49592578 TGTCCCAGACATGGTCTTACACGTAA
1 -GTCCCAGACAGGGTCTTACACGTAA
49592604 ATATTAAATC
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 1 0.02
42 31 0.53
43 26 0.45
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (43 bp):
GTCCCAGACAGGGTCTTACACGTAATCAAATAACGACGTCACA
Found at i:49607089 original size:20 final size:20
Alignment explanation
Indices: 49607064--49607102 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
49607054 TACTTTCTTC
49607064 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
49607084 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
49607103 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:49607448 original size:50 final size:50
Alignment explanation
Indices: 49607394--49607500 Score: 128
Period size: 50 Copynumber: 2.1 Consensus size: 50
49607384 ACATGTGTGT
*
49607394 TCTCATAT-AGGTGACC-ATGCCATGTCCTAGACCTAGTCTTACGGGGGACC
1 TCTCATATCA-GT-ACCAATGCCATGTCCCAGACCTAGTCTTACGGGGGACC
* * * *
49607444 TCTCATCTCAGTACCAATGCCATGTCCCAGACTTGGTCTTACGTGGGACC
1 TCTCATATCAGTACCAATGCCATGTCCCAGACCTAGTCTTACGGGGGACC
*
49607494 CCTCATA
1 TCTCATA
49607501 ACCTCAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
49 3 0.06
50 44 0.92
51 1 0.02
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.27
Consensus pattern (50 bp):
TCTCATATCAGTACCAATGCCATGTCCCAGACCTAGTCTTACGGGGGACC
Found at i:49613899 original size:292 final size:293
Alignment explanation
Indices: 49613341--49613916 Score: 967
Period size: 292 Copynumber: 2.0 Consensus size: 293
49613331 ACCGTTTTTA
**
49613341 GAGTCGAGCACGAGGCATTACCTGACTTAACTTACTAATTCAGATTATAAAAATTTACTTTTAAA
1 GAGTCGAGCACGAGGCATTACCTGACTTAACTTACTAATTCAGAGCATAAAAATTTACTTTTAAA
*
49613406 ATTAATTCACTCACGTTCAATCAATATGTTCCTAAAAAAGACCCTCGAGACCCTAAAACATGCAA
66 ATTAATTCACTCACGTTCAATCAATATGTCCCTAAAAAAGACCCTCGAGACCCTAAAACATGCAA
49613471 CAAAAACAGTTCGGGTCCAAACCGGGAACATTAAAAAAATTTAAATACTTAAATAAATCAAAATA
131 CAAAAACAGTTCGGGTCCAAACCGGGAACATTAAAAAAATTTAAATACTTAAATAAATCAAAATA
* *
49613536 ATTTATTTCACTATTCAAAATAAAATTGTCCACTTGCGTGACAATCACTAATTTAATTATAACTC
196 ATTTATTTCACTATTCAAAATAAAACTGTCCACTTGCGTGACAATCACTAATTTAATTATAAATC
49613601 GAGTTACAAAACTCAAAATTTAGACCATTGCCG
261 GAGTTACAAAACTCAAAATTTAGACCATTGCCG
* * *
49613634 GAGTCGAGCATGAGGCGTTACCTGACTTAACTTACTAATTCAGAGCATAAAAATTTGCTTTTAAA
1 GAGTCGAGCACGAGGCATTACCTGACTTAACTTACTAATTCAGAGCATAAAAATTTACTTTTAAA
*
49613699 ATTAATTCACTCACGTTCAATCAATATGTCCCT-AAAAAGACCCTCGAGACCCTCAAACATGCAA
66 ATTAATTCACTCACGTTCAATCAATATGTCCCTAAAAAAGACCCTCGAGACCCTAAAACATGCAA
* * ** * *
49613763 CGAAAACGGTTCGGGTCCAAACCGGGAACATTAAAAATTTTCTGAATACTTAATTAAATCAAAAT
131 CAAAAACAGTTCGGGTCCAAACCGGGAACATTAAAAAAATT-TAAATACTTAAATAAATCAAAAT
*
49613828 AATTTA-TTCACTATTCACAATAAAACTGTCCACTTGCGTGACAATCACTAATTTAATTATAAAT
195 AATTTATTTCACTATTCAAAATAAAACTGTCCACTTGCGTGACAATCACTAATTTAATTATAAAT
* *
49613892 TGAGTTACGAAACTCAAAATTTAGA
260 CGAGTTACAAAACTCAAAATTTAGA
49613917 TCCGTAAATT
Statistics
Matches: 264, Mismatches: 18, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
292 145 0.55
293 119 0.45
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.29
Consensus pattern (293 bp):
GAGTCGAGCACGAGGCATTACCTGACTTAACTTACTAATTCAGAGCATAAAAATTTACTTTTAAA
ATTAATTCACTCACGTTCAATCAATATGTCCCTAAAAAAGACCCTCGAGACCCTAAAACATGCAA
CAAAAACAGTTCGGGTCCAAACCGGGAACATTAAAAAAATTTAAATACTTAAATAAATCAAAATA
ATTTATTTCACTATTCAAAATAAAACTGTCCACTTGCGTGACAATCACTAATTTAATTATAAATC
GAGTTACAAAACTCAAAATTTAGACCATTGCCG
Found at i:49618267 original size:87 final size:86
Alignment explanation
Indices: 49618090--49618398 Score: 268
Period size: 87 Copynumber: 3.6 Consensus size: 86
49618080 TGAGTAAAAC
* * ** ** * *
49618090 AAAATCTGTTTCGGGATTGATTCCCACCATTCAACGA-ATTTATTACATTTTGATTTTGTTGCCA
1 AAAATCTGTTTCGGGATTTATTCCCACCATTTAAAAAGATTTATTTGA-TTTGATTATATTGCCA
*
49618154 AAAATGAGAAATTAAATTAAAT
65 AAAACGAGAAATTAAATTAAAT
* *
49618176 AAAATCTATTTCGGGATTTATTCCCACCATTTAATAAAGATTTATTTGATTTGATTATATTGCTA
1 AAAATCTGTTTCGGGATTTATTCCCACCATTTAA-AAAGATTTATTTGATTTGATTATATTGCCA
*
49618241 GAAACGAGAAATTAAATTAAAT
65 AAAACGAGAAATTAAATTAAAT
* * * * * * * *
49618263 AAAATTTGTTTCGAGATTTATTCCCGCCGTTTAAGAAGATTTTATTTGATTTTATT-TTTTTCCA
1 AAAATCTGTTTCGGGATTTATTCCCACCATTTAAAAAGA-TTTATTTGATTTGATTATATTGCCA
**
49618327 AATTC--G-AATTAAATTAAAT
65 AAAACGAGAAATTAAATTAAAT
* * * * ** * *
49618346 AAAAATCTATGTCAGGATTTATTCCCGCTGTTTAACAAGATTTTATTCGATTT
1 -AAAATCTGTTTCGGGATTTATTCCCACCATTTAAAAAGA-TTTATTTGATTT
49618399 TGTTTTAATT
Statistics
Matches: 186, Mismatches: 33, Indels: 10
0.81 0.14 0.04
Matches are distributed among these distances:
83 13 0.07
84 45 0.24
86 42 0.23
87 78 0.42
88 8 0.04
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (86 bp):
AAAATCTGTTTCGGGATTTATTCCCACCATTTAAAAAGATTTATTTGATTTGATTATATTGCCAA
AAACGAGAAATTAAATTAAAT
Found at i:49618379 original size:84 final size:83
Alignment explanation
Indices: 49618160--49618481 Score: 255
Period size: 87 Copynumber: 3.8 Consensus size: 83
49618150 GCCAAAAATG
* *
49618160 AGAAATTAAATTAAATAAAATCTATTTCGGGATTTATTCCCACCATTTAATAAAGA-TTTATTTG
1 AGAAATTAAATTAAATAAAATCTATTTC-GGATTTATTCCCGCCGTTTAA-AAAGATTTTATTTG
* * * *
49618224 ATTTGATTATATTGCTAGAAAC
64 ATTTTATT-TTTTTCCA-AAAC
* * *
49618246 GAGAAATTAAATTAAATAAAATTTGTTTCGAGATTTATTCCCGCCGTTTAAGAAGATTTTATTTG
1 -AGAAATTAAATTAAATAAAATCTATTTCG-GATTTATTCCCGCCGTTTAAAAAGATTTTATTTG
*
49618311 ATTTTATTTTTTTCCAAATTC
64 ATTTTATTTTTTTCCAAA-AC
* * * *
49618332 -G-AATTAAATTAAATAAAAATCTATGTCAGGATTTATTCCCGCTGTTTAACAAGATTTTATTCG
1 AGAAATTAAATTAAAT-AAAATCTATTTC-GGATTTATTCCCGCCGTTTAAAAAGATTTTATTTG
* *
49618395 ATTTTGTTTTAATTCC-AAAC
64 ATTTTATTTT-TTTCCAAAAC
* * * * * * *
49618415 A-AAGACGT-AATCAAAT-AATTCTGTTACGGGATTTATTCTCGCCGTTT-AATAGATTTTAATT
1 AGAA-A-TTAAATTAAATAAAATCTATTTC-GGATTTATTCCCGCCGTTTAAAAAGATTTT-ATT
49618476 TGATTT
62 TGATTT
49618482 AATGATATAA
Statistics
Matches: 193, Mismatches: 31, Indels: 26
0.77 0.12 0.10
Matches are distributed among these distances:
82 8 0.04
83 46 0.24
84 53 0.27
85 15 0.08
86 12 0.06
87 59 0.31
ACGTcount: A:0.35, C:0.11, G:0.12, T:0.42
Consensus pattern (83 bp):
AGAAATTAAATTAAATAAAATCTATTTCGGATTTATTCCCGCCGTTTAAAAAGATTTTATTTGAT
TTTATTTTTTTCCAAAAC
Found at i:49620980 original size:49 final size:48
Alignment explanation
Indices: 49620920--49621158 Score: 149
Period size: 50 Copynumber: 4.7 Consensus size: 48
49620910 GATAATAACA
* *
49620920 TGCCAAAGCCATGTCGCAGACATGGTCTTACATGAGATGTT-TCTTATAC-
1 TGCCAATGCCATGTC-CAGACATGGTCTTACATGAGA-GTTCTCATAT-CG
* * *
49620969 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAATGCCATGTCC-AGACATGGTCTTACATGAGAGTTCTCATATC-G
* ** * ** * *
49621019 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCACATCTCGG
1 TGCCAATGCCATGT-CCAGACATGGTCTTACATGAGAGTTCTCATATC-G
* * * ** *
49621069 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGT-CCAGACATGGTCTTACATGAGAGTTCTCAT-A--TC----G
49621125 TGCCAATGCCATGTCCTAGACATGGTCTTACATG
1 TGCCAATGCCATGTCC-AGACATGGTCTTACATG
49621159 GGACCTCTCA
Statistics
Matches: 153, Mismatches: 25, Indels: 17
0.78 0.13 0.09
Matches are distributed among these distances:
48 5 0.03
49 36 0.24
50 77 0.50
51 2 0.01
53 2 0.01
55 2 0.01
56 29 0.19
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.27
Consensus pattern (48 bp):
TGCCAATGCCATGTCCAGACATGGTCTTACATGAGAGTTCTCATATCG
Found at i:49621045 original size:50 final size:50
Alignment explanation
Indices: 49620919--49621222 Score: 243
Period size: 56 Copynumber: 5.9 Consensus size: 50
49620909 TGATAATAAC
* * * ** * *
49620919 ATGCCAAAGCCATGTCGCAGACATGGTCTTACATGAGATGTTTCTTAT--
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * **
49620967 ACTGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCG
1 A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * ** * *
49621018 GTGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCACATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * *
49621068 GTGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---G
*
49621124 ATGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---G
* * *
49621180 ATGCTAATGCCATGTCCCACACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
49621223 TCACCCAAAT
Statistics
Matches: 209, Mismatches: 38, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
48 1 0.00
49 37 0.18
50 79 0.38
53 2 0.01
56 90 0.43
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:49621137 original size:56 final size:56
Alignment explanation
Indices: 49621069--49621222 Score: 245
Period size: 56 Copynumber: 2.8 Consensus size: 56
49621059 CACATCTCGG
*
49621069 TGCCAACGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
* * *
49621125 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATGA
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
* * *
49621181 TGCTAATGCCATGTCCCACACATGGTCTTACATGGGATCTCT
1 TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCT
49621223 TCACCCAAAT
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 90 1.00
ACGTcount: A:0.27, C:0.30, G:0.17, T:0.27
Consensus pattern (56 bp):
TGCCAATGCCATGTCCCAAACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
Found at i:49621594 original size:30 final size:30
Alignment explanation
Indices: 49621560--49621617 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49621550 CCTCGACTCT
49621560 AACTTTTACAAAATTACAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* * *
49621590 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
49621618 AAAGCTCGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.31, C:0.26, G:0.05, T:0.38
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:49626856 original size:20 final size:21
Alignment explanation
Indices: 49626819--49626860 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
49626809 GAAAATATAC
49626819 TCAATAAAAAATCTATAAATA
1 TCAATAAAAAATCTATAAATA
* *
49626840 TCAATTAAAACTC-ATAAATA
1 TCAATAAAAAATCTATAAATA
49626860 T
1 T
49626861 TTTTGTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.31
Consensus pattern (21 bp):
TCAATAAAAAATCTATAAATA
Found at i:49627808 original size:50 final size:50
Alignment explanation
Indices: 49627747--49627841 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 50
49627737 GATAAAAACA
* * *
49627747 TGCCAAAGCCATGTCCCAAACATGGTCTTACGGGGGACCTTTCATCTCGG
1 TGCCAAAGCCATATCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
49627797 TGCCAACGCCATATCCCAGACATGGTCTTACATGGGACCTCTCAT
1 TGCCAAAGCCATATCCCAAACATGGTCTTACAGGGGACCTCTCAT
49627842 AACCTCAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 39 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (50 bp):
TGCCAAAGCCATATCCCAAACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:49628266 original size:30 final size:30
Alignment explanation
Indices: 49628232--49628289 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
49628222 CCTCGACTCT
49628232 AACTTTGACAAAATTACAATTTTGCCCCTA
1 AACTTTGACAAAATTACAATTTTGCCCCTA
* * *
49628262 AACTTTTACATAATTACACTTTTGCCCC
1 AACTTTGACAAAATTACAATTTTGCCCC
49628290 AAAGCTCAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.36
Consensus pattern (30 bp):
AACTTTGACAAAATTACAATTTTGCCCCTA
Found at i:49631746 original size:12 final size:11
Alignment explanation
Indices: 49631722--49631773 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
49631712 TTTATAAATC
49631722 ATTTTATTTAT
1 ATTTTATTTAT
49631733 ATTTTATTTCAT
1 ATTTTATTT-AT
49631745 ATGTATTTATTTAT
1 A--T-TTTATTTAT
*
49631759 AATTTATTTAT
1 ATTTTATTTAT
49631770 -TTTT
1 ATTTT
49631774 TTCGCTAATG
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 3 0.09
11 18 0.51
12 3 0.09
14 4 0.11
15 7 0.20
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (11 bp):
ATTTTATTTAT
Found at i:49633018 original size:24 final size:24
Alignment explanation
Indices: 49632991--49633043 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
49632981 TGAAATCTTT
*
49632991 ATATGTTAA-ATTGTAATGTTAATG
1 ATAT-TTAATATTGAAATGTTAATG
* *
49633015 ATATTTAATATTGAAATTTTAATT
1 ATATTTAATATTGAAATGTTAATG
49633039 ATATT
1 ATATT
49633044 ATTATTAACG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (24 bp):
ATATTTAATATTGAAATGTTAATG
Found at i:49637920 original size:21 final size:21
Alignment explanation
Indices: 49637895--49637938 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
49637885 ATCTTCGAAG
49637895 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
49637916 ATATGCAATCTTAGATATGAT
1 ATATGCAATCTTAGATATGAT
49637937 AT
1 AT
49637939 GTAATCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (21 bp):
ATATGCAATCTTAGATATGAT
Found at i:49637944 original size:19 final size:19
Alignment explanation
Indices: 49637894--49637949 Score: 85
Period size: 21 Copynumber: 2.8 Consensus size: 19
49637884 AATCTTCGAA
49637894 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
49637913 GATATATGCAATCTTAGATAT
1 G--ATATGCAATCTTAGATAT
*
49637934 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
49637950 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.44
21 19 0.56
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:49637956 original size:22 final size:23
Alignment explanation
Indices: 49637907--49637972 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
49637897 ATGCAATCTT
*
49637907 AGATATGATATATGCAATCTT---
1 AGATATGAT-TATGTAATCTTAGA
49637928 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
*
49637950 AGATATGATTTTGTAATCTTAGA
1 AGATATGATTATGTAATCTTAGA
49637973 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
19 10 0.26
21 8 0.21
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (23 bp):
AGATATGATTATGTAATCTTAGA
Found at i:49637982 original size:22 final size:23
Alignment explanation
Indices: 49637938--49637982 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
49637928 AGATATGATA
*
49637938 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
49637961 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
49637983 GTAGGTACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:49638536 original size:44 final size:44
Alignment explanation
Indices: 49638485--49638573 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
49638475 TTTATTTGCA
49638485 TATTTTCCCCCAGATTTTTCATATTCAGTTCAATTTAGTTTTTT
1 TATTTTCCCCCAGATTTTTCATATTCAGTTCAATTTAGTTTTTT
49638529 TATTTTCCCCCAGATTTTTCATATTCAGTTCAATTTAGTTTTTT
1 TATTTTCCCCCAGATTTTTCATATTCAGTTCAATTTAGTTTTTT
49638573 T
1 T
49638574 TCTTTTTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.20, C:0.18, G:0.07, T:0.55
Consensus pattern (44 bp):
TATTTTCCCCCAGATTTTTCATATTCAGTTCAATTTAGTTTTTT
Found at i:49642922 original size:25 final size:25
Alignment explanation
Indices: 49642894--49642960 Score: 118
Period size: 25 Copynumber: 2.7 Consensus size: 25
49642884 AGCCAATATT
49642894 CTTTCATTCTTTTCGAATAATTATA
1 CTTTCATTCTTTTCGAATAATTATA
*
49642919 CTTTCATTTTTTTCGAATAATTATA
1 CTTTCATTCTTTTCGAATAATTATA
49642944 CTTTCATTC-TTTCGAAT
1 CTTTCATTCTTTTCGAAT
49642961 CTTCTTCCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
24 8 0.20
25 32 0.80
ACGTcount: A:0.25, C:0.16, G:0.04, T:0.54
Consensus pattern (25 bp):
CTTTCATTCTTTTCGAATAATTATA
Found at i:49643695 original size:16 final size:15
Alignment explanation
Indices: 49643677--49643717 Score: 55
Period size: 16 Copynumber: 2.7 Consensus size: 15
49643667 AAAATATAAA
49643677 AAAAAGAAAAAAAAG
1 AAAAAGAAAAAAAAG
* *
49643692 AAAAAGTGATAAAAAG
1 AAAAAG-AAAAAAAAG
49643708 AAAAAGAAAA
1 AAAAAGAAAA
49643718 GGGAAATGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (15 bp):
AAAAAGAAAAAAAAG
Found at i:49645216 original size:132 final size:132
Alignment explanation
Indices: 49644979--49645391 Score: 682
Period size: 132 Copynumber: 3.1 Consensus size: 132
49644969 GTGAAACACT
* * * **
49644979 AAGCCTTGTCTCCCTGAGCAACAGCGGAGTAAGTTGAGGACCGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* *
49645044 TAGTGGAGTAGATCGAGGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
49645109 CC
131 CC
* *
49645111 AAGCCTTGTCTCCTTGAGCGGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
** *
49645176 TAGTGGAGAAGATTAAAGACGACAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
66 TAGTGGAGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
49645241 CC
131 CC
*
49645243 AAGCCTTGTCCCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
* * *
49645308 TAGTGGAGCAGATCGAAGACGGCAAATCATATCTTTCCAAGATAGTGGGAAACAGATTTAAGCCA
66 TAGTGGAGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
49645373 CC
131 CC
49645375 AAGCCTTGTCTCCCTGA
1 AAGCCTTGTCTCCCTGA
49645392 AGTTGCAGTG
Statistics
Matches: 259, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
132 259 1.00
ACGTcount: A:0.29, C:0.22, G:0.25, T:0.24
Consensus pattern (132 bp):
AAGCCTTGTCTCCCTGAGCAGCAGCGGAGTAGGTTGAAGATTGTAGATCTTATCTCCCTAAGCAG
TAGTGGAGAAGATCGAAGACGGCAAATCTTATCTTTCCAAGATAGTGGGAAGCAGATTTAAGCCA
CC
Found at i:49645758 original size:217 final size:217
Alignment explanation
Indices: 49645383--49645927 Score: 826
Period size: 217 Copynumber: 2.5 Consensus size: 217
49645373 CCAAGCCTTG
* * *
49645383 TCTCCCTGAAGTTGCAGTGGAGCAGATTAAAACCTTGGATCTTATCTTTCTGAAGTTGCAGAGAG
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGAATCTTATCTCTCTGAAGTTGCAGAGAG
49645448 CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC
66 CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC
* * * *
49645513 CTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGGCAAACCTTATCTCTCTGAGGTTGCAGTGGAG
131 CTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAACCTTATCTCCCTGAAGTTGCAGTGGAA
*
49645578 CAGATTAAAGCTGATAATCCTA
196 CAGATTAAAGCCGATAATCCTA
* * *** * **
49645600 TCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAAATCTTATCTCTCTAAAGTTTTAGAGAG
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGAATCTTATCTCTCTGAAGTTGCAGAGAG
* *
49645665 CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAATCAAGTCTTATC
66 CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC
*
49645730 CTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAGTGGAA
131 CTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAACCTTATCTCCCTGAAGTTGCAGTGGAA
*
49645795 CAGGTTAAAGCCGATAATCCTA
196 CAGATTAAAGCCGATAATCCTA
* *
49645817 TCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTTGAATCTTATCTCTCTGAAG-TGCAGAGAG
1 TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGAATCTTATCTCTCTGAAGTTGCAGAGAG
* * *
49645881 CAGATCGCATCAAGTCTTATC-CTCTTGAAGTTGTAGT-GAGGCAGACT
66 CAGATCGCATCTAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT
49645928 GAAGATGGTA
Statistics
Matches: 292, Mismatches: 34, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
215 3 0.01
216 45 0.15
217 244 0.84
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.29
Consensus pattern (217 bp):
TCTCCCTGAAGTTGCAGTGGAGCGGATTAAAACCTTGAATCTTATCTCTCTGAAGTTGCAGAGAG
CAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATC
CTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAACCTTATCTCCCTGAAGTTGCAGTGGAA
CAGATTAAAGCCGATAATCCTA
Found at i:49645899 original size:172 final size:173
Alignment explanation
Indices: 49645717--49646134 Score: 589
Period size: 172 Copynumber: 2.4 Consensus size: 173
49645707 AGACTAAGTA
*
49645717 ATCAAGTCTTATCCTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGA
1 ATCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGA
* * *
49645782 AGTTGCAGTGGAACAGGTTAAAGCCGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAA
66 AGTTGCAGTGGAACAAGTTAAAGCCGATAATCCTATCTTCCTGAAATTACAGTGGAGTGGATTAA
* *
49645847 AACCTT-GAATCTTATCTCTCTGAAG-TGCAGAGAGCAGATCGC
131 AACCTTAG-ATCTTACCTCTCTGAAGTTGCAGAGAGCAGATCAC
* **
49645889 ATCAAGTCTTATCCTCTTGAAGTTGTAGTGAGGCAGACTGAAGATGGTAAATCTTATCTCCCTGA
1 ATCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGA
* * *
49645954 AGTTGTAGTGGAGCAAGTTAAAGTCGATAATCCTATCTTCCTGAAATTACAGTGGAGTGGATTAA
66 AGTTGCAGTGGAACAAGTTAAAGCCGATAATCCTATCTTCCTGAAATTACAGTGGAGTGGATTAA
49646019 AACCTTAGATCTTACCTCTCTGAAGTTGCAGAGAGCAGATCAC
131 AACCTTAGATCTTACCTCTCTGAAGTTGCAGAGAGCAGATCAC
* * * *
49646062 ATCTAGTCTTAT-CTCCCTGAAGTTGCAGTG-GAGCAGACT-AAG-TAATCAAGTCTTATC-CTC
1 ATCAAGTCTTATCCT-CTTGAAGTTGCAGTGAG-GCAGACTGAAGATGA-CAAATCTTATCTC-C
*
49646122 TTGAAGTTGCAGT
62 CTGAAGTTGCAGT
49646135 AAGGCAGACT
Statistics
Matches: 219, Mismatches: 21, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
171 2 0.01
172 169 0.77
173 48 0.22
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (173 bp):
ATCAAGTCTTATCCTCTTGAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGA
AGTTGCAGTGGAACAAGTTAAAGCCGATAATCCTATCTTCCTGAAATTACAGTGGAGTGGATTAA
AACCTTAGATCTTACCTCTCTGAAGTTGCAGAGAGCAGATCAC
Found at i:49645926 original size:389 final size:390
Alignment explanation
Indices: 49645462--49646355 Score: 1128
Period size: 389 Copynumber: 2.3 Consensus size: 390
49645452 TCGCATCTAG
* * * * * *
49645462 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAGCAAGTCTTATCCTCTTAAAGTTGCA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCA--CATCAAGTCTTATCCTCTTGAAGTTGCA
* *
49645527 GTGAGGCAGACTGAAGATGGCAAACCTTATCTCTCTGAGGTTGCAGTGGAGC-AGATTAAAG-CT
63 GTGAGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAG-TTAAAGTC-
* * * *
49645590 GATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAATCACAAATCTTATCTCTCTAAAG
126 GATAATCCTATCTCCCTGAAATTACAGTAGAGCGGATTAAAACCACAAATCTTACCTCTCTAAAG
** * *
49645655 TTTTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAATC
191 TTGCAGAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATC
*
49645720 AAGTCTTATCCTCTTAAAGTTGCAGTGAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGT
256 AAGTCTTATCCTCTTAAAGTTGCAGTAAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGT
** * **
49645785 TGCAGT-GG-A-AC-AGGTTAAAGCCGATAATCCTATCTTCC-TGAAGTTGCAGTGGAGTGGATT
321 TGCAGTGGGTATACTA-AATAAA--C-A-AATCCTATC-TCCTTAAAGTTGCAGTGGAGCAGATT
*
49645845 AAAACC-TTGAA
380 AAAACCATAG-A
* *
49645856 TCTTATCTCTCTGAAG-TGCAG-AGAGCAGATCGCATCAAGTCTTATCCTCTTGAAGTTGTAGTG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAGTCTTATCCTCTTGAAGTTGCAGTG
* * *
49645919 AGGCAGACTGAAGATGGTAAATCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTAAAGTCGATAA
66 AGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGTCGATAA
* * * ** * *
49645984 TCCTATCTTCCTGAAATTACAGTGGAGTGGATTAAAACCTTAGATCTTACCTCTCTGAAGTTGCA
131 TCCTATCTCCCTGAAATTACAGTAGAGCGGATTAAAACCACAAATCTTACCTCTCTAAAGTTGCA
49646049 GAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTC
196 GAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTC
* * *
49646114 TTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGAAGTTGCAG
261 TTATCCTCTTAAAGTTGCAGTAAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAG
*
49646179 TGGGGTATACTAAATAAACAAATCCTGTCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACCATAG
326 T-GGGTATACTAAATAAACAAATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACCATAG
49646244 A
390 A
* * *
49646245 TCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATCGAGTCTTAT-CTCCCTGAAGTTGCAGT
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAGTCTTATCCT-CTTGAAGTTGCAGT
* * ** * * *
49646309 G-GAGCAGACTAAAAAAAGCAAGCCTTATCCCCCTGAAATTGCAGTGG
65 GAG-GCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGG
49646356 GGCATACTAA
Statistics
Matches: 433, Mismatches: 54, Indels: 29
0.84 0.10 0.06
Matches are distributed among these distances:
388 3 0.01
389 309 0.71
390 14 0.03
391 72 0.17
392 8 0.02
393 11 0.03
394 16 0.04
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (390 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCACATCAAGTCTTATCCTCTTGAAGTTGCAGTG
AGGCAGACTGAAGATGGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGTCGATAA
TCCTATCTCCCTGAAATTACAGTAGAGCGGATTAAAACCACAAATCTTACCTCTCTAAAGTTGCA
GAGAGCAGATCACATCTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAATCAAGTC
TTATCCTCTTAAAGTTGCAGTAAGGCAGACTGAAGATGACAAATCTTATCTCCCTGAAGTTGCAG
TGGGTATACTAAATAAACAAATCCTATCTCCTTAAAGTTGCAGTGGAGCAGATTAAAACCATAGA
Found at i:49646125 original size:217 final size:218
Alignment explanation
Indices: 49645889--49646320 Score: 629
Period size: 217 Copynumber: 2.0 Consensus size: 218
49645879 AGCAGATCGC
* * *
49645889 ATCAAGTCTTATCCTCTTGAAGTTGTAGTGAGGCAGACTGAAGATGGTAAATCTTATCTCCCTGA
1 ATCAAGTCTTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
* * ** * **
49645954 AGTTGTAGTGGAGCA-AGTTAAAGTCGA-TAATCCTATCTTCCTGAAA-TTACAGTGGAGTGGAT
66 AGTTGCAGTGGAGCATA-CTAAA-TAAACAAATCCTATC-TCCTGAAAGTTACAGTGGAGCAGAT
* *
49646016 TAAAACCTTAGATCTTACCTCTCTGAAGTTGCAG-AGAGCAGATCACATCTAGTCTTATCTCCCT
128 TAAAACCATAGATCTTACCTCTCTGAAGTTGCAGTAGAGCAGATCACATCGAGTCTTATCTCCCT
49646080 GAAGTTGCAGTGGAGCAGACTAAGTA
193 GAAGTTGCAGTGGAGCAGACTAAGTA
*
49646106 ATCAAGTCTTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCGAATCTTATCTCCCTGA
1 ATCAAGTCTTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
* * * * *
49646171 AGTTGCAGTGGGGTATACTAAATAAACAAATCCTGTCTCCTTAAAGTTGCAGTGGAGCAGATTAA
66 AGTTGCAGTGGAGCATACTAAATAAACAAATCCTATCTCCTGAAAGTTACAGTGGAGCAGATTAA
* *
49646236 AACCATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATCACATCGAGTCTTATCTCCCTGAA
131 AACCATAGATCTTACCTCTCTGAAGTTGCAGTAGAGCAGATCACATCGAGTCTTATCTCCCTGAA
49646301 GTTGCAGTGGAGCAGACTAA
196 GTTGCAGTGGAGCAGACTAA
49646321 AAAAAGCAAG
Statistics
Matches: 191, Mismatches: 20, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
216 9 0.05
217 130 0.68
218 52 0.27
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (218 bp):
ATCAAGTCTTATCCTCTTGAAGTTGCAGTAAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
AGTTGCAGTGGAGCATACTAAATAAACAAATCCTATCTCCTGAAAGTTACAGTGGAGCAGATTAA
AACCATAGATCTTACCTCTCTGAAGTTGCAGTAGAGCAGATCACATCGAGTCTTATCTCCCTGAA
GTTGCAGTGGAGCAGACTAAGTA
Found at i:49646127 original size:44 final size:42
Alignment explanation
Indices: 49645374--49646366 Score: 390
Period size: 44 Copynumber: 23.0 Consensus size: 42
49645364 TTTAAGCCAC
* * * *
49645374 CAAGCCTTGTCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAC
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
** ** * ***
49645416 CTTGGATCTTATCTTTCTGAAGTTGCAG-AGAGCAGA-TCGCAT
1 C-AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* *
49645458 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAT
* * *
49645502 CAAGTCTTATC-CTCTTAAAGTTGCAGT-GAGGCAGACTGAAGAT
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAAT
** * * * *
49645545 GGCAAACCTTATCTCTCTGAGGTTGCAGTGGAGCAGATTAAAGCT
1 --CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA-AT
* * * * * *
49645590 GATAATCCTATCTCCCTGAAGTTGCAGTAGAGCGGATTAAAAT
1 CA-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* * * ** * ***
49645633 CACAAATCTTATCTCTCTAAAGTTTTAG-AGAGCAGA-TCGCAT
1 --CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* *
49645675 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAGTAAT
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAT
* * *
49645719 CAAGTCTTATC-CTCTTAAAGTTGCAGT-GAGGCAGACTGAAGAT
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAAT
* * ** **
49645762 GACAAATCTTATCTCCCTGAAGTTGCAGTGGAACAGGTTAAAGC
1 --CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* * * ** *
49645806 CGATAATCCTATCTTCCTGAAGTTGCAGTGGAGTGGATTAAAACCTT
1 C-A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAA---T
* * * ***
49645853 GAA-TCTTATCTCTCTGAAG-TGCAG-AGAGCAGA-TCGCAT
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* * *
49645891 CAAGTCTTATC-CTCTTGAAGTTGTAGT-GAGGCAGACTGAAGAT
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAAT
* * * * *
49645934 GGTAAATCTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTAAAGT
1 --CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAAAT
* * * * * ** * *
49645978 CGATAATCCTATCTTCCTGAAATTACAGTGGAGTGGATTAAAAC
1 C-A-AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* * * * * *
49646022 CTTAGATCTTACCTCTCTGAAGTTGCAG-AGAGCAGA-TCACAT
1 C-AAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
*
49646064 CTAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGTAAT
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAA--AAT
* * *
49646108 CAAGTCTTATC-CTCTTGAAGTTGCAGT-AAGGCAGACTGAAGAT
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAAAT
* * * *
49646151 GGCGAA-TCTTATCTCCCTGAAGTTGCAGTGGGGTATACTAAATAAA
1 --C-AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AA-AAT
* * * * * * *
49646197 CAAATCCTGTCTCCTTAAAGTTGCAGTGGAGCAGATTAAAAC
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* * * * *
49646239 CATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTAGA-TCACAT
1 CA-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
* *
49646282 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAAAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT---AAAAT
* * * * *
49646327 CAAGCCTTATCCCCCTGAAATTGCAGTGGGGCATACTAAA
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAA
49646367 TAAACAAATC
Statistics
Matches: 700, Mismatches: 182, Indels: 138
0.69 0.18 0.14
Matches are distributed among these distances:
38 4 0.01
39 12 0.02
40 66 0.09
41 60 0.09
42 32 0.05
43 54 0.08
44 310 0.44
45 148 0.21
46 14 0.02
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (42 bp):
CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAAT
Found at i:49646734 original size:19 final size:19
Alignment explanation
Indices: 49646710--49646763 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
49646700 AATCTTCGAA
49646710 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
49646729 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
49646748 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
49646764 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:49646789 original size:22 final size:22
Alignment explanation
Indices: 49646723--49646786 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 22
49646713 ATGCAATCTT
*
49646723 AGATATGATATGCAATCTT---
1 AGATATGATATGTAATCTTAGA
49646742 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
49646764 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
49646787 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.46
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:49646796 original size:22 final size:23
Alignment explanation
Indices: 49646752--49646796 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
49646742 AGATATGATA
*
49646752 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
49646775 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
49646797 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:49650753 original size:10 final size:9
Alignment explanation
Indices: 49650724--49650800 Score: 70
Period size: 10 Copynumber: 8.4 Consensus size: 9
49650714 TTAAAAAAAC
*
49650724 TTTTATAACA
1 TTTTATAA-T
*
49650734 TTTTAAAAT
1 TTTTATAAT
49650743 TTTCTATAAT
1 TTT-TATAAT
49650753 TTTTAT-AT
1 TTTTATAAT
49650761 TTTTA-ATAT
1 TTTTATA-AT
49650770 TTTTATAAT
1 TTTTATAAT
49650779 TATTTATAAT
1 T-TTTATAAT
*
49650789 TATT-TAAT
1 TTTTATAAT
49650797 TTTT
1 TTTT
49650801 TTATGATTTT
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
8 14 0.25
9 18 0.32
10 25 0.44
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (9 bp):
TTTTATAAT
Found at i:49650762 original size:18 final size:17
Alignment explanation
Indices: 49650741--49650800 Score: 61
Period size: 17 Copynumber: 3.4 Consensus size: 17
49650731 ACATTTTAAA
49650741 ATTTTCTATAATTTTTAT
1 ATTTT-TATAATTTTTAT
49650759 ATTTTTA-ATATTTTTAT
1 ATTTTTATA-ATTTTTAT
49650776 AATTATTTATAATTATTTA-
1 -ATT-TTTATAATT-TTTAT
49650795 ATTTTT
1 ATTTTT
49650801 TTATGATTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
16 1 0.03
17 13 0.35
18 11 0.30
19 7 0.19
20 5 0.14
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
ATTTTTATAATTTTTAT
Found at i:49650894 original size:3 final size:3
Alignment explanation
Indices: 49650886--49650910 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
49650876 AAACTCTCAT
49650886 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
49650911 ATGAATTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:49653790 original size:15 final size:14
Alignment explanation
Indices: 49653766--49653822 Score: 53
Period size: 15 Copynumber: 3.9 Consensus size: 14
49653756 TTTATTAAAA
*
49653766 AAAGTTAAAAAATT
1 AAAGTGAAAAAATT
49653780 CAAAGTGAAAAAA-T
1 -AAAGTGAAAAAATT
49653794 AAGAGTTGAAAAAATTT
1 AA-AG-TGAAAAAA-TT
*
49653811 GAAGTGAAAAAA
1 AAAGTGAAAAAA
49653823 AATATTGTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
13 2 0.06
14 3 0.08
15 27 0.75
16 2 0.06
17 2 0.06
ACGTcount: A:0.61, C:0.02, G:0.16, T:0.21
Consensus pattern (14 bp):
AAAGTGAAAAAATT
Found at i:49671421 original size:27 final size:27
Alignment explanation
Indices: 49671367--49671522 Score: 183
Period size: 27 Copynumber: 5.9 Consensus size: 27
49671357 CAAAATAGTC
* *
49671367 TTTTACCC-ATCA-GGGAATTACGATCA
1 TTTTACCCTA-CAGGGGTATTACGGTCA
* *
49671393 TTTTATCCTACAGGGGTATTACGGACA
1 TTTTACCCTACAGGGGTATTACGGTCA
* * * * *
49671420 TTTTTCCTTATAGAGATATTACGGTCA
1 TTTTACCCTACAGGGGTATTACGGTCA
*
49671447 TTTTACCCTACAAGGGTATTACGGTCA
1 TTTTACCCTACAGGGGTATTACGGTCA
*
49671474 TTTT-CCCTACAGGGGTATTACGTTCA
1 TTTTACCCTACAGGGGTATTACGGTCA
49671500 TTTTACCCTACAGGGGTATTACG
1 TTTTACCCTACAGGGGTATTACG
49671523 ATTATTATAC
Statistics
Matches: 108, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
26 33 0.31
27 75 0.69
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.36
Consensus pattern (27 bp):
TTTTACCCTACAGGGGTATTACGGTCA
Found at i:49671501 original size:53 final size:54
Alignment explanation
Indices: 49671383--49671522 Score: 192
Period size: 53 Copynumber: 2.6 Consensus size: 54
49671373 CCATCAGGGA
* * *
49671383 ATTACGATCATTTTATCCTACAGGGGTATTACGGACATTTTTCCTTATAGAGAT
1 ATTACGATCATTTTACCCTACAGGGGTATTACGGACATTTTTCCCTACAGAGAT
* * * * *
49671437 ATTACGGTCATTTTACCCTACAAGGGTATTACGGTCA-TTTTCCCTACAGGGGT
1 ATTACGATCATTTTACCCTACAGGGGTATTACGGACATTTTTCCCTACAGAGAT
*
49671490 ATTACGTTCATTTTACCCTACAGGGGTATTACG
1 ATTACGATCATTTTACCCTACAGGGGTATTACG
49671523 ATTATTATAC
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
53 43 0.57
54 33 0.43
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (54 bp):
ATTACGATCATTTTACCCTACAGGGGTATTACGGACATTTTTCCCTACAGAGAT
Found at i:49673745 original size:21 final size:21
Alignment explanation
Indices: 49673721--49673760 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49673711 ACTTTTAAAT
*
49673721 ATCAATCAACATTTCAAATTC
1 ATCAATCAACATTTAAAATTC
* *
49673742 ATCATTTAACATTTAAAAT
1 ATCAATCAACATTTAAAAT
49673761 CACAAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.45, C:0.17, G:0.00, T:0.38
Consensus pattern (21 bp):
ATCAATCAACATTTAAAATTC
Found at i:49683036 original size:50 final size:53
Alignment explanation
Indices: 49682924--49683071 Score: 194
Period size: 50 Copynumber: 2.8 Consensus size: 53
49682914 ATTTGGCTAA
* * *
49682924 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGGTTATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-T-AGG-TATG
49682980 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCA-A-G-ATG
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATG
** *
49683030 AGAGGTCCTCCGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCA
49683072 TGTTATTATC
Statistics
Matches: 86, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
50 42 0.49
52 1 0.01
53 1 0.01
56 42 0.49
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (53 bp):
AGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCATAGGTATG
Found at i:49690022 original size:15 final size:16
Alignment explanation
Indices: 49689999--49690034 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
49689989 TAAAATTTTA
49689999 ATAAA-TAAAAAAAAT
1 ATAAATTAAAAAAAAT
49690014 -TAAATTAAAAAAAAT
1 ATAAATTAAAAAAAAT
49690029 ATAAAT
1 ATAAAT
49690035 ATTTTATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 4 0.21
15 10 0.53
16 5 0.26
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (16 bp):
ATAAATTAAAAAAAAT
Found at i:49690081 original size:28 final size:28
Alignment explanation
Indices: 49690010--49690081 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
49690000 TAAATAAAAA
*
49690010 AAATTAAATTAAAAAAAATATAAATATT
1 AAATTAAATTAAAAATAATATAAATATT
** * **
49690038 TTA-TAATTTTTTAAATAATATAAATATT
1 AAATTAA-ATTAAAAATAATATAAATATT
49690066 AAATTAAATTAAAAAT
1 AAATTAAATTAAAAAT
49690082 TTATTAATAT
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
27 3 0.10
28 25 0.81
29 3 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATTAAATTAAAAATAATATAAATATT
Found at i:49691501 original size:11 final size:10
Alignment explanation
Indices: 49691470--49691504 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
49691460 ACTACTAACT
49691470 ACTCTATTGA
1 ACTCTATTGA
*
49691480 ACTCTACTGA
1 ACTCTATTGA
49691490 ACATCTATTGA
1 AC-TCTATTGA
49691501 ACTC
1 ACTC
49691505 CCCTTAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.31, C:0.26, G:0.09, T:0.34
Consensus pattern (10 bp):
ACTCTATTGA
Found at i:49692923 original size:17 final size:18
Alignment explanation
Indices: 49692893--49692928 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
49692883 GTTGATCTCG
*
49692893 AATTGGTTATTTGATAGA
1 AATTGGTTAATTGATAGA
49692911 AATT-GTTAATTGATAGA
1 AATTGGTTAATTGATAGA
49692928 A
1 A
49692929 CTATATGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.39, C:0.00, G:0.19, T:0.42
Consensus pattern (18 bp):
AATTGGTTAATTGATAGA
Found at i:49700696 original size:34 final size:35
Alignment explanation
Indices: 49700635--49700702 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
49700625 GTGGGAACAG
* *
49700635 GGGGTGCGGGGGCAGAGCCCCCGCGGTATGAACCA
1 GGGGTGCGAGGGCAGAGCCCCCGCGGTACGAACCA
*
49700670 GGGGTGCGAGGGCGGAG-CCCCGCGGTACGAACC
1 GGGGTGCGAGGGCAGAGCCCCCGCGGTACGAACC
49700703 GCATACCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 15 0.50
35 15 0.50
ACGTcount: A:0.16, C:0.29, G:0.47, T:0.07
Consensus pattern (35 bp):
GGGGTGCGAGGGCAGAGCCCCCGCGGTACGAACCA
Found at i:49715474 original size:23 final size:23
Alignment explanation
Indices: 49715420--49715475 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
49715410 AATTATAAAG
*
49715420 TATATAAAAAAAATATTTGCATT
1 TATATAAAAAAAATATTTGCATA
*
49715443 TTTA-AAAAATAAATATGTT-CATA
1 TATATAAAAA-AAATAT-TTGCATA
49715466 TATATAAAAA
1 TATATAAAAA
49715476 TTAGTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
22 5 0.19
23 15 0.56
24 7 0.26
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (23 bp):
TATATAAAAAAAATATTTGCATA
Done.