Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008826.1 Hibiscus syriacus cultivar Beakdansim tig00112000_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 3884024
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3420804 original size:29 final size:28
Alignment explanation
Indices: 3420772--3420925 Score: 168
Period size: 29 Copynumber: 5.4 Consensus size: 28
3420762 AATTTTACAG
* * *
3420772 AAATAACACCCTTTTTAAAATAATTACCA
1 AAATAGCACCCTTTTTGAATTAATT-CCA
3420801 AAATAGCACCCTTTTTGAATTAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATT-CCA
* **
3420830 AAATAACATTCTTTTTGAATTAATTCCAA
1 AAATAGCACCCTTTTTGAATTAATTCC-A
3420859 AAATAGCA-CCTTTTTGAATTAATTTCCA
1 AAATAGCACCCTTTTTGAATTAA-TTCCA
* * *
3420887 AAATAGCACCCATTTCGAATAAATTCCCA
1 AAATAGCACCCTTTTTGAATTAATT-CCA
3420916 AAATA-CACCC
1 AAATAGCACCC
3420926 GATCAACGGT
Statistics
Matches: 109, Mismatches: 12, Indels: 9
0.84 0.09 0.07
Matches are distributed among these distances:
28 31 0.28
29 78 0.72
ACGTcount: A:0.41, C:0.22, G:0.05, T:0.32
Consensus pattern (28 bp):
AAATAGCACCCTTTTTGAATTAATTCCA
Found at i:3420912 original size:57 final size:57
Alignment explanation
Indices: 3420800--3420924 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 57
3420790 AATAATTACC
** * * *
3420800 AAAATAGCACCCTTTTTGAATTAATTCCCAAAATAACATTCTTTTTGAATTAATTCCA
1 AAAATAGCA-CCTTTTTGAATTAATTCCCAAAATAACACCCATTTCGAATAAATTCCA
* * *
3420858 AAAATAGCACCTTTTTGAATTAATTTCCAAAATAGCACCCATTTCGAATAAATTCCC
1 AAAATAGCACCTTTTTGAATTAATTCCCAAAATAACACCCATTTCGAATAAATTCCA
3420915 AAAATA-CACC
1 AAAATAGCACC
3420925 CGATCAACGG
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
56 4 0.07
57 46 0.78
58 9 0.15
ACGTcount: A:0.40, C:0.22, G:0.06, T:0.33
Consensus pattern (57 bp):
AAAATAGCACCTTTTTGAATTAATTCCCAAAATAACACCCATTTCGAATAAATTCCA
Found at i:3420955 original size:17 final size:18
Alignment explanation
Indices: 3420933--3420966 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
3420923 CCCGATCAAC
3420933 GGTCAAC-GGTCGGGTCG
1 GGTCAACGGGTCGGGTCG
3420950 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
3420967 AAAACCGGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.12, C:0.24, G:0.47, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCG
Found at i:3420961 original size:13 final size:13
Alignment explanation
Indices: 3420943--3420968 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3420933 GGTCAACGGT
3420943 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
3420956 CGGGTCGGGTCAA
1 CGGGTCGGGTCAA
3420969 AACCGGTCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
CGGGTCGGGTCAA
Found at i:3431468 original size:45 final size:45
Alignment explanation
Indices: 3431393--3431482 Score: 126
Period size: 45 Copynumber: 2.0 Consensus size: 45
3431383 AAATATGAGA
* *
3431393 CTTATGAAATAAGTTGGGTAATATCAGTAATAGCTCCAACATAGT
1 CTTAGGAAATAAGTTGGGTAATATCAGTAATAGCCCCAACATAGT
* * **
3431438 CTTAGGAAATTAGTTGGGTAATGTTGGTAATAGCCCCAACATAGT
1 CTTAGGAAATAAGTTGGGTAATATCAGTAATAGCCCCAACATAGT
3431483 GAGAGAAATA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.31
Consensus pattern (45 bp):
CTTAGGAAATAAGTTGGGTAATATCAGTAATAGCCCCAACATAGT
Found at i:3437095 original size:3 final size:3
Alignment explanation
Indices: 3437087--3437127 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
3437077 TCATTTCGTT
*
3437087 TTA TTA TTA TTA TTA ATA TTA -TA TATA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TT
3437128 TAATAAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:3437140 original size:21 final size:24
Alignment explanation
Indices: 3437092--3437140 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 24
3437082 TCGTTTTATT
* *
3437092 ATTATTATTAATATTATATATATT
1 ATTATTATTAATATTATATAAATA
3437116 ATTATTATT-AT-TTA-ATAAATA
1 ATTATTATTAATATTATATAAATA
3437137 ATTA
1 ATTA
3437141 CAAAGACCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 3 0.13
23 2 0.09
24 9 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTATTATTAATATTATATAAATA
Found at i:3437642 original size:13 final size:13
Alignment explanation
Indices: 3437624--3437648 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3437614 AAAAGAAGAA
3437624 CGGTGGTCGGCGG
1 CGGTGGTCGGCGG
3437637 CGGTGGTCGGCG
1 CGGTGGTCGGCG
3437649 CCGGAACAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.60, T:0.16
Consensus pattern (13 bp):
CGGTGGTCGGCGG
Found at i:3446445 original size:27 final size:27
Alignment explanation
Indices: 3446415--3446476 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
3446405 GAACTGAGTT
*
3446415 TTCATCTATTTTGTTTATCATGTGCGA
1 TTCATCTATTTGGTTTATCATGTGCGA
*
3446442 TTCATCTATTTGGTTTATCATGTGCGT
1 TTCATCTATTTGGTTTATCATGTGCGA
3446469 TTCATCTA
1 TTCATCTA
3446477 CAACAGCAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.15, T:0.52
Consensus pattern (27 bp):
TTCATCTATTTGGTTTATCATGTGCGA
Found at i:3447238 original size:22 final size:22
Alignment explanation
Indices: 3447210--3447288 Score: 140
Period size: 22 Copynumber: 3.6 Consensus size: 22
3447200 ACATCTACAT
3447210 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
3447232 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3447254 TCTTCAAAGATGATAGATTCTT
1 TCTTCAAAGATGATAGATTCTC
*
3447276 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3447289 AAACTTTATT
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 55 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:3448000 original size:45 final size:45
Alignment explanation
Indices: 3447936--3448341 Score: 659
Period size: 45 Copynumber: 9.0 Consensus size: 45
3447926 CTATTTCTCA
3447936 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * * *
3447981 CATCTATAAGACCTTCAGTGCATGATGTTATCAAAACATTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3448026 CATCTGTAAGCCTTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
3448071 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTTGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
3448116 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
3448161 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3448206 CATTTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
3448251 CATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCGGGT
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * *
3448296 CATCTATAAGACCTGCAGTGCAGGATGTTTTCAAGAAGCCTTCGGG
1 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAA-AA-CCTTCGGG
3448342 AGCTTTTTGA
Statistics
Matches: 335, Mismatches: 24, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 325 0.97
46 2 0.01
47 8 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:3448358 original size:75 final size:74
Alignment explanation
Indices: 3448273--3448414 Score: 223
Period size: 75 Copynumber: 1.9 Consensus size: 74
3448263 CTTCAGTGCA
*
3448273 TGATGCTTTCAAAACCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATGTTTTCAAGAAGCCTT
1 TGATGCTTTCAAAACCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATGCTTTCAA-AA-CCTT
3448338 CGGGAGCTTTT
64 CGGGAGCTTTT
* * *
3448349 TGATG-TTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATGCTTTCAAAACCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATGCTTTCAAAACCTTCG
3448413 GG
66 GG
3448415 TCATCTGTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
73 8 0.13
74 2 0.03
75 47 0.76
76 5 0.08
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (74 bp):
TGATGCTTTCAAAACCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATGCTTTCAAAACCTTCG
GGAGCTTTT
Found at i:3448403 original size:45 final size:45
Alignment explanation
Indices: 3448349--3448551 Score: 309
Period size: 45 Copynumber: 4.5 Consensus size: 45
3448339 GGGAGCTTTT
3448349 TGATG-TTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
1 TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
3448393 TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* *
3448438 TAATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
* ** *
3448483 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCA
1 TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
*
3448528 TGATGTTTTCAAAAAGCCTTCGGG
1 TGATGCTTTC-AAAA-CCTTCGGG
3448552 ATCTTTTTGA
Statistics
Matches: 148, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
44 5 0.03
45 131 0.89
46 4 0.03
47 8 0.05
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (45 bp):
TGATGCTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCA
Found at i:3448448 original size:120 final size:119
Alignment explanation
Indices: 3448228--3448459 Score: 367
Period size: 120 Copynumber: 1.9 Consensus size: 119
3448218 CTTCAGTGCA
*
3448228 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCG
* *
3448293 GGTCATCTATAAGACCTGCAGTGCAGGATGTTTTCAAGAAGCCTTCGGGAGCTTTT
66 GGTCATCTATAAGACCTGCAGTGCAGAATGCTTTCAA-AA-CCTTCGGGAGCTTTT
*
3448349 TGATG-TTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCG
* * * *
3448413 GGTCATCTGTAAGCCCTTCAGTGCATAATGCTTTCAAAACCTTCGGG
66 GGTCATCTATAAGACCTGCAGTGCAGAATGCTTTCAAAACCTTCGGG
3448460 TCATCTGTAA
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
118 8 0.08
119 2 0.02
120 88 0.85
121 5 0.05
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (119 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCG
GGTCATCTATAAGACCTGCAGTGCAGAATGCTTTCAAAACCTTCGGGAGCTTTT
Found at i:3448506 original size:210 final size:210
Alignment explanation
Indices: 3448138--3448672 Score: 863
Period size: 210 Copynumber: 2.5 Consensus size: 210
3448128 CTTCAGTGCA
3448138 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATG-TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* *
3448203 GGTCATTTGTAAACCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCA
65 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCA
* *
3448268 GTGCATGATGCTTTCAAAACCTTCGGGTCATCTATAAGACCTGCAGTGCAGGATGTTTTCAAGAA
130 GTGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAA
3448333 GCCTTCGGGAGCTTTT
195 GCCTTCGGGAGCTTTT
* *
3448349 TGATGTTTCAAAACCTTCGGGTCATCTGTAAGACCTTCAGTGCATGATGCTTTCAAAACCTTCGG
1 TGATGTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
* * *
3448414 GTCATCTGTAAGCCCTTCAGTGCATAATGCTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
66 GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAG
* *
3448479 TGCATGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAG
131 TGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAG
*
3448544 CCTTCGGGATCTTTT
196 CCTTCGGGAGCTTTT
* * *
3448559 TGATATTTTCAAAACCTTCTGGTCATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTCG
1 TGAT-GTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
* * * *
3448624 GGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGG
65 GGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAA-CCTTCGGG
3448673 AGCTTTTTGA
Statistics
Matches: 298, Mismatches: 23, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
210 197 0.66
211 89 0.30
212 4 0.01
213 8 0.03
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (210 bp):
TGATGTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGG
GTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCATCTATAAGCCCTTCAG
TGCATGATGCTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCAGGATGTTTTCAAAAAG
CCTTCGGGAGCTTTT
Found at i:3448570 original size:76 final size:74
Alignment explanation
Indices: 3448483--3448625 Score: 205
Period size: 76 Copynumber: 1.9 Consensus size: 74
3448473 CTTCAGTGCA
*
3448483 TGATGTTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTT
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTC-AAAA-CCTT
3448548 CGGGATCTTTT
64 CGGGATCTTTT
* ** * * *
3448559 TGATATTTTCAAAACCTTCTGGTCATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTCG
1 TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAACCTTCG
3448624 GG
66 GG
3448626 TCATCTATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 48 0.80
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (74 bp):
TGATATTTTCAAAACCTTCGGGTCATCCATAAGACCTGCAGTGCATGATGTTTTCAAAACCTTCG
GGATCTTTT
Found at i:3448613 original size:45 final size:45
Alignment explanation
Indices: 3448559--3448672 Score: 147
Period size: 45 Copynumber: 2.5 Consensus size: 45
3448549 GGGATCTTTT
* * * * * *
3448559 TGATATTTTCAAAACCTTCTGGTCATCTGTAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
3448604 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
*
3448649 GGATGTTTTCAAAAAGCCTTCGGG
1 TGATGTTTTC-AAAA-CCTTCGGG
3448673 AGCTTTTTGA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
45 48 0.80
46 4 0.07
47 8 0.13
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCA
Found at i:3448658 original size:121 final size:121
Alignment explanation
Indices: 3448444--3448774 Score: 572
Period size: 121 Copynumber: 2.7 Consensus size: 121
3448434 TGCATAATGC
3448444 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
* * * *
3448509 CCATAAGACCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGATCTTTTTGATAT
66 CTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAT
* *
3448565 TTTCAAAACCTTCTGGTCATCTGTAAGCCCTTCAGTGTATGATGTTTTCAAAACCTTCGGGTCAT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
*
3448630 CTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGT
66 CTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAT
* *
3448686 TTTCAAAACCTTCGGGTCGTTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
1 TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
*
3448751 CTGTAAGACCTACAGTGCAGGATG
66 CTATAAGACCTACAGTGCAGGATG
3448775 ATAGGACCTC
Statistics
Matches: 198, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
121 198 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (121 bp):
TTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGTCAT
CTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATAT
Found at i:3448684 original size:76 final size:74
Alignment explanation
Indices: 3448604--3448746 Score: 214
Period size: 76 Copynumber: 1.9 Consensus size: 74
3448594 CTTCAGTGTA
3448604 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAAAGCCTT
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTC-AAAA-CCTT
3448669 CGGGAGCTTTT
64 CGGGAGCTTTT
* * * * * *
3448680 TGATGTTTTCAAAACCTTCGGGTCGTTTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCG
1 TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
3448745 GG
66 GG
3448747 TCATCTGTAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
74 8 0.13
75 4 0.07
76 49 0.80
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (74 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTATAAGACCTACAGTGCAGGATGTTTTCAAAACCTTCG
GGAGCTTTT
Found at i:3448729 original size:45 final size:45
Alignment explanation
Indices: 3448680--3448774 Score: 145
Period size: 45 Copynumber: 2.1 Consensus size: 45
3448670 GGGAGCTTTT
* * * *
3448680 TGATGTTTTCAAAACCTTCGGGTCGTTTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
3448725 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
1 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
*
3448770 GGATG
1 TGATG
3448775 ATAGGACCTC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 45 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (45 bp):
TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGACCTACAGTGCA
Found at i:3448936 original size:3 final size:3
Alignment explanation
Indices: 3448930--3448992 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
3448920 TCATTTTGTT
** * *
3448930 TTA TTA TTA TTA TTA TTA AAA TTA TTT TTA TTA ATA TTA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
3448976 -TA TATA TTA TTA TTA TT
1 TTA T-TA TTA TTA TTA TT
3448993 TAATAAATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
2 2 0.04
3 41 0.84
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:3453353 original size:24 final size:26
Alignment explanation
Indices: 3453305--3453354 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
3453295 TTTTGATTGA
3453305 TTTCTTCCCTTCATCTTCTAAGTCAAG
1 TTTCTTCCCTT-ATCTTCTAAGTCAAG
*
3453332 TTTCTTCCCTT-T-TTCTATGTCAA
1 TTTCTTCCCTTATCTTCTAAGTCAA
3453355 ATTTGATCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 10 0.45
25 1 0.05
27 11 0.50
ACGTcount: A:0.16, C:0.28, G:0.06, T:0.50
Consensus pattern (26 bp):
TTTCTTCCCTTATCTTCTAAGTCAAG
Found at i:3456346 original size:43 final size:43
Alignment explanation
Indices: 3456283--3456370 Score: 133
Period size: 43 Copynumber: 2.0 Consensus size: 43
3456273 CAAATCTTGA
*
3456283 CTTTTGCGAATGAAGCAAACTGGGTTGAAAGTGTCGCTATTGC
1 CTTTTGCGAATGAAGCAAACTGGGTTGAAAGTGTCGCTATCGC
* *
3456326 CTTTTGCGAAT-AGAGTAAACTGGGTTGAGAGTGTCGCTATCGC
1 CTTTTGCGAATGA-AGCAAACTGGGTTGAAAGTGTCGCTATCGC
3456369 CT
1 CT
3456371 CTGCAATACT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 1 0.02
43 40 0.98
ACGTcount: A:0.24, C:0.17, G:0.28, T:0.31
Consensus pattern (43 bp):
CTTTTGCGAATGAAGCAAACTGGGTTGAAAGTGTCGCTATCGC
Found at i:3456637 original size:89 final size:90
Alignment explanation
Indices: 3456486--3456673 Score: 315
Period size: 89 Copynumber: 2.1 Consensus size: 90
3456476 ATTTTTTAAG
* * *
3456486 TAAATATTTGTTTTATAATTAAATGGAAATTCTATAAAATAAACATATATAAGTCATGGATAATC
1 TAAATATTTGTTTTATAATTAAAAGGAAATTATATAAAATAAACATAAATAAGTCATGGATAATC
*
3456551 GGGTATGATGTGACATGAAAATA-A
66 GGGTATGATGTGACATGAAAAAATA
*
3456575 TAAATATTTGTTTTATAATTAAAAGGAAATTATATAAAATAAACATAAATAAGTCATGGATAATT
1 TAAATATTTGTTTTATAATTAAAAGGAAATTATATAAAATAAACATAAATAAGTCATGGATAATC
*
3456640 GGGTATGATGTGGCATGAAAAAATA
66 GGGTATGATGTGACATGAAAAAATA
3456665 TAAATATTT
1 TAAATATTT
3456674 CATAAATATA
Statistics
Matches: 92, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
89 82 0.89
90 10 0.11
ACGTcount: A:0.46, C:0.04, G:0.14, T:0.35
Consensus pattern (90 bp):
TAAATATTTGTTTTATAATTAAAAGGAAATTATATAAAATAAACATAAATAAGTCATGGATAATC
GGGTATGATGTGACATGAAAAAATA
Found at i:3461221 original size:17 final size:17
Alignment explanation
Indices: 3461188--3461219 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3461178 TTGATTATAG
3461188 TTATTTAATTATATTTA
1 TTATTTAATTATATTTA
3461205 TTATTTAA-TATATTT
1 TTATTTAATTATATTT
3461220 TACCTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TTATTTAATTATATTTA
Found at i:3462294 original size:19 final size:17
Alignment explanation
Indices: 3462249--3462302 Score: 51
Period size: 19 Copynumber: 3.1 Consensus size: 17
3462239 AACTTAATTT
3462249 TTAAGAAA--ATTAGAAA
1 TTAAGAAATTATTA-AAA
3462265 TTAAGAAATTAGTTATAAA
1 TTAAGAAATTA-TTA-AAA
3462284 TTAA-AATATTATTAAAA
1 TTAAGAA-ATTATTAAAA
3462301 TT
1 TT
3462303 TTTAAAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
16 8 0.24
17 5 0.15
18 6 0.18
19 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (17 bp):
TTAAGAAATTATTAAAA
Found at i:3469718 original size:105 final size:105
Alignment explanation
Indices: 3469430--3469718 Score: 307
Period size: 105 Copynumber: 2.7 Consensus size: 105
3469420 TTTATTGTGG
* * * *
3469430 TCACTAAAACAATATTTAGCGTGGCAACATTGATGGTCACAAAATAAATTTTTAGTGTCAAACAA
1 TCACTAAAA-AATA-TTAGTGTGACAACATTGATGGTCACAAAATAAA-TTTTATTGTCAAATAA
* * * * *
3469495 ATTCATCTTAAATTTTATTGATAATAAGGTGACAAATATTTGG
63 ATTCATCATAATTTTTATTGACAATAAGGTGACAAAAATTTGA
* * * * * *
3469538 TCAGTAAAAAATA-TAATATGACAACATTGATAGTGACAAAATAAATTTTTTGTGTCAAATAAAT
1 TCACTAAAAAATATTAGTGTGACAACATTGATGGTCACAAAATAAATTTTAT-TGTCAAATAAAT
* *
3469602 TTATCATAATTTTTATTGACAAT-A-GTGTCAAAAATTTGA
65 TCATCATAATTTTTATTGACAATAAGGTGACAAAAATTTGA
* *
3469641 TCACTAAAAAATACTTAGTGTGACAATATTGATGGTCACGAAAA-ATATTTTCATTGTCAAATAA
1 TCACTAAAAAATA-TTAGTGTGACAACATTGATGGTCAC-AAAATAAATTTT-ATTGTCAAATAA
*
3469705 ATTCATCACAATTT
63 ATTCATCATAATTT
3469719 CTCTTGTTAA
Statistics
Matches: 149, Mismatches: 27, Indels: 13
0.79 0.14 0.07
Matches are distributed among these distances:
103 24 0.16
104 5 0.03
105 103 0.69
106 5 0.03
107 4 0.03
108 8 0.05
ACGTcount: A:0.42, C:0.11, G:0.12, T:0.35
Consensus pattern (105 bp):
TCACTAAAAAATATTAGTGTGACAACATTGATGGTCACAAAATAAATTTTATTGTCAAATAAATT
CATCATAATTTTTATTGACAATAAGGTGACAAAAATTTGA
Found at i:3482428 original size:21 final size:21
Alignment explanation
Indices: 3482402--3482452 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3482392 TCATCATTTC
*
3482402 AGTCAATGTTGTCACCTGTGT
1 AGTCAATGTTGTCACATGTGT
3482423 AGTCAATGTTGTCACATGTGT
1 AGTCAATGTTGTCACATGTGT
3482444 AGTCAATGT
1 AGTCAATGT
3482453 GTTCAGAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.24, C:0.16, G:0.24, T:0.37
Consensus pattern (21 bp):
AGTCAATGTTGTCACATGTGT
Found at i:3482454 original size:11 final size:11
Alignment explanation
Indices: 3482418--3482454 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3482408 TGTTGTCACC
3482418 TGTGTAGTCAA
1 TGTGTAGTCAA
3482429 TGT-T-GTCACA
1 TGTGTAGTCA-A
3482439 TGTGTAGTCAA
1 TGTGTAGTCAA
3482450 TGTGT
1 TGTGT
3482455 TCAGAGCATC
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 4 0.17
10 5 0.22
11 10 0.43
12 4 0.17
ACGTcount: A:0.22, C:0.11, G:0.27, T:0.41
Consensus pattern (11 bp):
TGTGTAGTCAA
Found at i:3483479 original size:16 final size:16
Alignment explanation
Indices: 3483458--3483491 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
3483448 GATGCAAATT
3483458 AATGCAACGTATCCAC
1 AATGCAACGTATCCAC
3483474 AATGCAACGTATCCAC
1 AATGCAACGTATCCAC
3483490 AA
1 AA
3483492 AGACTAGTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.12, T:0.18
Consensus pattern (16 bp):
AATGCAACGTATCCAC
Found at i:3488319 original size:2 final size:2
Alignment explanation
Indices: 3488312--3488341 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3488302 ACGTAATAAC
3488312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3488342 TCTACTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3489021 original size:20 final size:20
Alignment explanation
Indices: 3488992--3489031 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3488982 CAGTGCAATA
* *
3488992 CATAATTTACATGAATGTAC
1 CATAACTTACATGAAAGTAC
*
3489012 CATAACTTACTTGAAAGTAC
1 CATAACTTACATGAAAGTAC
3489032 TCAACTTAAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (20 bp):
CATAACTTACATGAAAGTAC
Found at i:3493871 original size:574 final size:574
Alignment explanation
Indices: 3492658--3494371 Score: 3011
Period size: 574 Copynumber: 3.0 Consensus size: 574
3492648 ACAAATACTA
*
3492658 CTTTGTAATCATCTTAGCTTAATCAAAAATTAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
1 CTTTGTAATCATCTTAGCTTAATCAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
3492723 ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
66 ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
*
3492788 GACGAAAATGAAAATTTTAAAATTTTAGTGGCCAAAGTAGAAACTTAAGAAAAGTTCAAAGACCA
131 GACGAAAATGAAAATTTTAAAATTTTGGTGGCCAAAGTAGAAACTTAAGAAAAGTTCAAAGACCA
*
3492853 AACTGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
196 AAATGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
*
3492918 CTCTATGAAATTTAGATAACATGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATG
261 CTCTATGAAATTTAGATAACAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATG
* * *
3492983 ACAGTATGAGGTTAGTAATATTATTATG-AATTTTTAATAATTAGAATTTAACATTAATCAGTGG
326 ATAGTATGAGGTTAGTAATATTATTCTGAAATTTTTAATCATTAGAATTTAACATTAATCAGTGG
*
3493047 AATTAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAATTTTTTG
391 AATTAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTG
* *
3493112 AAAAAGTACAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAGAGATGA
456 AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
3493177 TAAGGGTGTGTCATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
521 TAAGGGTGTGTCATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
3493231 CTTTGTAATCATCTTAGCTTAATCAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
1 CTTTGTAATCATCTTAGCTTAATCAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
* * * *
3493296 ACTTTTAATATTTCTAAAGAATTAATTAAGTCCCTTTACTTGTACTACCTAAAATTTTGACAAGT
66 ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
* *
3493361 GACCAAAATGAAAATTTTAAAATTTTGGTGGCCAAAGTAGGAACTTAAGAAAAGTTCAAAGACCA
131 GACGAAAATGAAAATTTTAAAATTTTGGTGGCCAAAGTAGAAACTTAAGAAAAGTTCAAAGACCA
3493426 AAATGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
196 AAATGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
* * *
3493491 CTCTATGAAATTTGGATAATAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATA
261 CTCTATGAAATTTAGATAACAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATG
*
3493556 ATAGTATGAGGTTAGTAATGTTATTCTGAAATTTTTAATCATTAGAATTTAACATTAATCAGTGG
326 ATAGTATGAGGTTAGTAATATTATTCTGAAATTTTTAATCATTAGAATTTAACATTAATCAGTGG
* *
3493621 AATCAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTC
391 AATTAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTG
3493686 AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
456 AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
* *
3493751 TATGGGTGTGTTATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
521 TAAGGGTGTGTCATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
* *
3493805 CTTTGTAATCATCTTAACTTAATAAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
1 CTTTGTAATCATCTTAGCTTAATCAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
3493870 ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
66 ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
* * *
3493935 AACGAAAATGAAAATTTTAAAATTTTGATGGCCAAAGTAGAAACTTAAGAAGAGTTCAAAGACCA
131 GACGAAAATGAAAATTTTAAAATTTTGGTGGCCAAAGTAGAAACTTAAGAAAAGTTCAAAGACCA
*
3494000 AAATGGTAATATTCCCAAAAACAAATTTATTCCATAAAT-AATAGTTCATCC-------T---TT
196 AAATGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
*
3494054 CTCTATGAAATTTAGATAACAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGGTG
261 CTCTATGAAATTTAGATAACAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATG
* *
3494119 ATAGTATGAGGTTAGTAATATTATTCTGAAATTTTTAATCATTAGAATTTAAAATTAATTAGTGG
326 ATAGTATGAGGTTAGTAATATTATTCTGAAATTTTTAATCATTAGAATTTAACATTAATCAGTGG
*
3494184 AATTAAGTAGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTG
391 AATTAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTG
3494249 AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
456 AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
* * *
3494314 TAAGGGTATGTCAAGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAATGT
521 TAAGGGTGTGTCATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
3494368 CTTT
1 CTTT
3494372 TAACATAAAA
Statistics
Matches: 1089, Mismatches: 51, Indels: 12
0.95 0.04 0.01
Matches are distributed among these distances:
563 305 0.28
566 1 0.00
573 349 0.32
574 434 0.40
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (574 bp):
CTTTGTAATCATCTTAGCTTAATCAAAAAATAAATAAATCTTCAAACTTTCTAAAAATTGACTTA
ACTCTTAATCTTTCTAAAGAATCAATTAAGTCCCTTTACTTGTACTACTTAAAATTTTGACAAGT
GACGAAAATGAAAATTTTAAAATTTTGGTGGCCAAAGTAGAAACTTAAGAAAAGTTCAAAGACCA
AAATGGTAATATTCCCAAAAAGAAATTTATTCCATAAATAAATAGTTCATCCTTAAAAGTGGATT
CTCTATGAAATTTAGATAACAGGATAATCAGATTGAATTGGAAGTTTACAAAAATTTAAAGGATG
ATAGTATGAGGTTAGTAATATTATTCTGAAATTTTTAATCATTAGAATTTAACATTAATCAGTGG
AATTAAGTGGATTTTCCATGTTAAAGTGGAATAGTGGAATTAAAGTGACTATGTTGAAATTTTTG
AAAAAGTGCAAGGGTAAAGTTGGAAGGTGAAAATTTATTTGTTCATATTTGAATTTGAAAGATGA
TAAGGGTGTGTCATGGTAATTTGGTAATTATCATATTTTTAAAGGGTAAAAGGT
Found at i:3494831 original size:21 final size:20
Alignment explanation
Indices: 3494807--3494847 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
3494797 TGTGATTTTG
*
3494807 GATTGAAATTGATATGGAATT
1 GATTGAAATTG-CATGGAATT
*
3494828 GATTGTAATTGCATGGAATT
1 GATTGAAATTGCATGGAATT
3494848 TAAGTTAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.02, G:0.24, T:0.39
Consensus pattern (20 bp):
GATTGAAATTGCATGGAATT
Found at i:3497299 original size:21 final size:21
Alignment explanation
Indices: 3497275--3497323 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
3497265 ACGATCATGA
*
3497275 CAACACCG-TATACTATCACAT
1 CAACACCGTTA-ACTATAACAT
* *
3497296 CAACATCGTTAACTATAATAT
1 CAACACCGTTAACTATAACAT
3497317 CAACACC
1 CAACACC
3497324 ATAATGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 21 0.91
22 2 0.09
ACGTcount: A:0.41, C:0.31, G:0.04, T:0.24
Consensus pattern (21 bp):
CAACACCGTTAACTATAACAT
Found at i:3498035 original size:76 final size:73
Alignment explanation
Indices: 3497955--3498365 Score: 300
Period size: 76 Copynumber: 5.7 Consensus size: 73
3497945 AATATCGTGT
*
3497955 TTCACTAAGAAATAAGTTATGATTTGGAATGTTAATATTTTTATTTATAAAATGGGTTGTGCCAA
1 TTCACTAAGAAATAGGTTATGATTTGGAATGTT-ATATTTTTA--TATAAAATGGGTTGTGCCAA
3498020 GAATGTCATTG
63 GAATGTCATTG
* * * * *
3498031 TTCACTAAGAAATAGGTTGTGATATGTAATGTTATCATTTTTATTAATAAAATGAGTTGCGCCCA
1 TTCACTAAGAAATAGGTTATGATTTGGAATGTTAT-ATTTTTA-T-ATAAAATGGGTTGTG-CCA
*
3498096 AGAATATCA-TG
62 AGAATGTCATTG
* * * *
3498107 GTCAACTAAGAAATAGGTTGTGATTTGGAATG--------TTA-ATAAAATGAGTTGCGCCAAAG
1 TTC-ACTAAGAAATAGGTTATGATTTGGAATGTTATATTTTTATATAAAATGGGTTGTGCC-AAG
*
3498163 AATGTCATGG
64 AATGTCATTG
* * * *
3498173 GTCACTAAGAAATAGGTAACGATTTGGAATATTAATATTTTTATTAATAAAATGGGTTGTGGCCA
1 TTCACTAAGAAATAGGTTATGATTTGGAATGTT-ATATTTTTA-T-ATAAAATGGGTTGT-GCCA
* *
3498238 ATAATGTCA-TC
62 AGAATGTCATTG
* * * *
3498249 TTAACTAAGAAATAGGTTGTGATTTGGATTG-T-TA---TTA-ATAAAATGGGTTGTTCCCAAGA
1 TTCACTAAGAAATAGGTTATGATTTGGAATGTTATATTTTTATATAAAATGGGTTG-TGCCAAGA
*
3498308 ATGTCATGG
65 ATGTCATTG
* * * * *
3498317 TTCACTAAGTAATAGG-TAGCGATATGGAACGTTAAATTTTTATTATAAA
1 TTCACTAAGAAATAGGTTA-TGATTTGGAATGTTATATTTTTA-TATAAA
3498366 TAATTTGAAA
Statistics
Matches: 266, Mismatches: 40, Indels: 59
0.73 0.11 0.16
Matches are distributed among these distances:
64 2 0.01
65 48 0.18
66 4 0.02
67 25 0.09
68 26 0.10
69 1 0.00
70 4 0.02
73 5 0.02
74 3 0.01
75 10 0.04
76 77 0.29
77 58 0.22
78 3 0.01
ACGTcount: A:0.36, C:0.09, G:0.20, T:0.36
Consensus pattern (73 bp):
TTCACTAAGAAATAGGTTATGATTTGGAATGTTATATTTTTATATAAAATGGGTTGTGCCAAGAA
TGTCATTG
Found at i:3498180 original size:65 final size:65
Alignment explanation
Indices: 3498072--3498209 Score: 206
Period size: 65 Copynumber: 2.1 Consensus size: 65
3498062 TTATCATTTT
* ***
3498072 TATTAATAAAATGAGTTGCGCCCAAGAATATCATGGTCAACTAAGAAATAGGTTGTGATTTGGAA
1 TATTAATAAAATGAGTTGCGCCAAAGAATATCATGGTCAACTAAGAAATAGGTAACGATTTGGAA
* *
3498137 TGTTAATAAAATGAGTTGCGCCAAAGAATGTCATGGGTC-ACTAAGAAATAGGTAACGATTTGGA
1 TATTAATAAAATGAGTTGCGCCAAAGAATATCAT-GGTCAACTAAGAAATAGGTAACGATTTGGA
3498201 A
65 A
3498202 TATTAATA
1 TATTAATA
3498210 TTTTTATTAA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
65 61 0.94
66 4 0.06
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (65 bp):
TATTAATAAAATGAGTTGCGCCAAAGAATATCATGGTCAACTAAGAAATAGGTAACGATTTGGAA
Found at i:3498464 original size:75 final size:70
Alignment explanation
Indices: 3498373--3498508 Score: 209
Period size: 75 Copynumber: 1.9 Consensus size: 70
3498363 AAATAATTTG
*
3498373 AAAGTATGGATACTTTTCCACAAGTATCGATACTTTTGAATTTTTTTAAAAGAACATGGAAAATG
1 AAAGTATGGATACTTTTCCACAAATATCGATACTTTTGAA----TTTAAAA-AACATGGAAAATG
3498438 AGAAGGCTGC
61 AGAAGGCTGC
*
3498448 AAAGTATTGATACTTTTCCACAAATATCGATACTTTTGAATTTAAAAAACATGGAAAATGA
1 AAAGTATGGATACTTTTCCACAAATATCGATACTTTTGAATTTAAAAAACATGGAAAATGA
3498509 TTTTTTGACT
Statistics
Matches: 59, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
70 14 0.24
71 7 0.12
75 38 0.64
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.32
Consensus pattern (70 bp):
AAAGTATGGATACTTTTCCACAAATATCGATACTTTTGAATTTAAAAAACATGGAAAATGAGAAG
GCTGC
Found at i:3499807 original size:23 final size:23
Alignment explanation
Indices: 3499780--3499842 Score: 108
Period size: 23 Copynumber: 2.7 Consensus size: 23
3499770 TACTCCCTTG
*
3499780 GGTATCGGTACTCCCCTTCCAGT
1 GGTATCGATACTCCCCTTCCAGT
3499803 GGTATCGATACTCCCCTTCCAGT
1 GGTATCGATACTCCCCTTCCAGT
*
3499826 GGTATCGATACTTCCCT
1 GGTATCGATACTCCCCT
3499843 AGGTATCGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.33, G:0.19, T:0.32
Consensus pattern (23 bp):
GGTATCGATACTCCCCTTCCAGT
Found at i:3501222 original size:77 final size:77
Alignment explanation
Indices: 3501132--3501315 Score: 237
Period size: 75 Copynumber: 2.4 Consensus size: 77
3501122 GGGCATTACA
*
3501132 ATGACATTCTTGGGTGTAACTCATTTTATTAATAAAAATATTAACATTCCAGATTACAACCTATT
1 ATGACATTCTTGGGTGTAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATT
* * * **
3501197 TTTTAGTGACCC
66 TCTTAATAAAAC
* * * * *
3501209 ATGACATTCTTGGGCGTAAC-C-TATTATTAATAAAAATATTAACATTTCATATCACAACTTATT
1 ATGACATTCTTGGGTGTAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATT
3501272 TCTTAATAAAAC
66 TCTTAATAAAAC
* *
3501284 ATGACATTATTTGGTGTAACTCATTTTATTAA
1 ATGACATTCTTGGGTGTAACTCATTTTATTAA
3501316 CATTCTAAAT
Statistics
Matches: 90, Mismatches: 15, Indels: 4
0.83 0.14 0.04
Matches are distributed among these distances:
75 61 0.68
76 2 0.02
77 27 0.30
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (77 bp):
ATGACATTCTTGGGTGTAACTCATTTTATTAATAAAAATATTAACATTCCAGATCACAACCTATT
TCTTAATAAAAC
Found at i:3501437 original size:77 final size:77
Alignment explanation
Indices: 3501310--3501729 Score: 540
Period size: 77 Copynumber: 5.4 Consensus size: 77
3501300 TAACTCATTT
* * * * * *
3501310 TATTAACATTCTAAATAGAAACATATTTCTTAGTGAACCATGATATTCTTGGGCGTAACCCATTT
1 TATTAACATTCTAGATCGCAACTTATTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTT
3501375 TATTAATAAAAA
66 TATTAATAAAAA
* * * *
3501387 TATTAAGATTCGATATCGCAACTTTTTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTT
1 TATTAACATTCTAGATCGCAACTTATTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTT
3501452 TATTAATAAAAA
66 TATTAATAAAAA
* * * * * * *
3501464 TCATTAACTTTCTAGATAGCAACCTATTGT-TTAGTGAACCATGATACTCTTGGGTGCAAACCAT
1 T-ATTAACATTCTAGATCGCAACTTATT-TCTTAGTGAACCATGACATTCTTGGGCGCAACCCAT
3501528 TTTATTAATAAAAA
64 TTTATTAATAAAAA
* * *
3501542 TATTAACATTCCAGATCGCAACCTATTTCTTAGTGAACCATGACATTCTTGGGTGCAACCCATTT
1 TATTAACATTCTAGATCGCAACTTATTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTT
3501607 TATTAATAAAAA
66 TATTAATAAAAA
* * * * *
3501619 TATTAACATTCTAGATCGCAA-TCTATTTCTTAGTTAACCACGACATTCTT-GACTTCAACCAAT
1 TATTAACATTCTAGATCGCAACT-TATTTCTTAGTGAACCATGACATTCTTGGGC-GCAACCCAT
3501682 TTTATTAATAAAAA
64 TTTATTAATAAAAA
* *
3501696 TATTAACATTCTAGATTGCAACATATTTCTTAGT
1 TATTAACATTCTAGATCGCAACTTATTTCTTAGT
3501730 AAATCCCAAC
Statistics
Matches: 301, Mismatches: 36, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
76 2 0.01
77 234 0.78
78 64 0.21
79 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (77 bp):
TATTAACATTCTAGATCGCAACTTATTTCTTAGTGAACCATGACATTCTTGGGCGCAACCCATTT
TATTAATAAAAA
Found at i:3501593 original size:155 final size:154
Alignment explanation
Indices: 3501310--3501729 Score: 574
Period size: 155 Copynumber: 2.7 Consensus size: 154
3501300 TAACTCATTT
* * * * * *
3501310 TATTAACATTCTAAATAGAAACATATTTCTTAGTGAACCATGATATTCTTGGGCGTAACCCATTT
1 TATTAACATTCTAGATAGCAACCTATTTCTTAGTGAACCATGATATTCTTGGGTGCAAACCATTT
* * * * *
3501375 TATTAATAAAAATATTAAGATTCGATATCGCAACTTTTTTCTTAGTGAACCATGACATTCTTGGG
66 TATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTGGG
3501440 CGCAACCCATTTTATTAATAAAAA
131 CGCAACCCATTTTATTAATAAAAA
* *
3501464 TCATTAACTTTCTAGATAGCAACCTATTGT-TTAGTGAACCATGATACTCTTGGGTGCAAACCAT
1 T-ATTAACATTCTAGATAGCAACCTATT-TCTTAGTGAACCATGATATTCTTGGGTGCAAACCAT
*
3501528 TTTATTAATAAAAATATTAACATTCCAGATCGCAACCTATTTCTTAGTGAACCATGACATTCTTG
64 TTTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTG
*
3501593 GGTGCAACCCATTTTATTAATAAAAA
129 GGCGCAACCCATTTTATTAATAAAAA
* * * * * ** *
3501619 TATTAACATTCTAGATCGCAATCTATTTCTTAGTTAACCACGACATTCTTGACTTC-AACCAATT
1 TATTAACATTCTAGATAGCAACCTATTTCTTAGTGAACCATGATATTCTTGGGTGCAAACC-ATT
* *
3501683 TTATTAATAAAAATATTAACATTCTAGATTGCAACATATTTCTTAGT
65 TTATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGT
3501730 AAATCCCAAC
Statistics
Matches: 235, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
153 5 0.02
154 91 0.39
155 138 0.59
156 1 0.00
ACGTcount: A:0.35, C:0.18, G:0.11, T:0.37
Consensus pattern (154 bp):
TATTAACATTCTAGATAGCAACCTATTTCTTAGTGAACCATGATATTCTTGGGTGCAAACCATTT
TATTAATAAAAATATTAACATTCCAGATCGCAACATATTTCTTAGTGAACCATGACATTCTTGGG
CGCAACCCATTTTATTAATAAAAA
Found at i:3503957 original size:24 final size:21
Alignment explanation
Indices: 3503921--3503965 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 21
3503911 AAATTGATAG
3503921 AATATATAAATATTAATGATTA
1 AATATATAAATATTAAT-ATTA
3503943 AATATATAATTATATTAATATTA
1 AATATATAA--ATATTAATATTA
3503966 TTAACTATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.43
23 4 0.19
24 8 0.38
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATAAATATTAATATTA
Found at i:3507599 original size:106 final size:106
Alignment explanation
Indices: 3507489--3508048 Score: 908
Period size: 106 Copynumber: 5.3 Consensus size: 106
3507479 TGACCCATTC
* * * * * **
3507489 CGAGTCCAATATCC-TCTGCCGTGAAGTTGAAATTGGTTCTGGAACTGGGGAATTATTTGTTGAC
1 CGAGTCCAATATCCTTC-GCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGAC
*
3507553 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* * *
3507595 CGAGTCCAATATCCTTCGCTGTGAAGATGAAATTGGCTCTGAAACAT-GGAAATGGTTTGTTGAC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAAC-TGGGTAATGGTTTGTTGAC
*
3507659 AACCAGCCGTCCCTTCGTCGTGAAGTTGAACGTGTGTTGTCT
65 AACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
3507701 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
3507766 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
*
3507807 CGAGTCCAATATCATTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
*
3507872 ACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* *
3507913 CGAGTCTAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
* *
3507978 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
* *
3508019 GGAGTCCAATATCCTTCGTTGTGAAGTTGA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGA
3508049 ACTTGCGTTG
Statistics
Matches: 427, Mismatches: 24, Indels: 6
0.93 0.05 0.01
Matches are distributed among these distances:
105 1 0.00
106 423 0.99
107 3 0.01
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTGTTGACA
ACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
Found at i:3508049 original size:43 final size:43
Alignment explanation
Indices: 3507988--3508092 Score: 183
Period size: 43 Copynumber: 2.4 Consensus size: 43
3507978 ACCAGCGGTC
*
3507988 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
3508031 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATAT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
*
3508074 CCTTCGCTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
3508093 ATTGGCTCTG
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (43 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:3508090 original size:149 final size:149
Alignment explanation
Indices: 3507890--3508198 Score: 537
Period size: 149 Copynumber: 2.1 Consensus size: 149
3507880 TCCCTTCATC
* * *
3507890 GTGAAGTTGAACTTGTGTTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
* **
3507955 AACTGGGTAATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 AACTGGGAAATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCA
3508020 GAGTCCAATATCCTTCGTT
131 GAGTCCAATATCCTTCGTT
*
3508039 GTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
1 GTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
* *
3508104 AATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCA
66 AACTGGGAAATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCA
3508169 GAGTCCAATATCCTTCGTT
131 GAGTCCAATATCCTTCGTT
3508188 GTGAAGTTGAA
1 GTGAAGTTGAA
3508199 ATTGGCTCTG
Statistics
Matches: 151, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (149 bp):
GTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA
AACTGGGAAATGGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCCA
GAGTCCAATATCCTTCGTT
Found at i:3508129 original size:255 final size:255
Alignment explanation
Indices: 3507776--3508304 Score: 862
Period size: 255 Copynumber: 2.1 Consensus size: 255
3507766 ACCAGCCGTC
* * *
3507776 CCTTCGTCGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAGATT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATT
* * *
3507841 GGCTCTGAAACTGGGTAATGGTTTGTTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGT
66 GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGC
* * *
3507906 GTTGTCTC-GAGTCTAATATCCTTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTT
131 GTTGTC-CAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTT
*
3507970 TATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
195 TATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* *
3508031 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATT
* * * *
3508096 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGC
* * *
3508161 GTTGTCCAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTT
131 GTTGTCCAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTT
*
3508226 ATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTGGAGTCCAATAT
196 ATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
3508286 CCTTCGTTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
3508305 ATTGGGAAAT
Statistics
Matches: 253, Mismatches: 20, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
254 1 0.00
255 252 1.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (255 bp):
CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATT
GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGC
GTTGTCCAGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTT
ATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:3508216 original size:106 final size:106
Alignment explanation
Indices: 3508031--3508408 Score: 573
Period size: 106 Copynumber: 3.7 Consensus size: 106
3508021 AGTCCAATAT
* * *
3508031 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
3508096 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
**
3508137 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCCAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
3508202 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
66 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
* *
3508243 CCTTCATCGTGAAGTTGAACTTGCTTTGTCTGGAGTCCAATATCCTTCG-T-T---G-TG-AA--
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
*
3508299 -G-T-TGAAATTGGGAAATTGTTTATTGACGACCAGCGGTC
66 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
* * *
3508337 CCTTCGTCGTGAAGTTAAACTTACGTTGTCTGGAGTCCAATATCCTTAGTTGTGAAGTTGAAATT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
3508402 GGCTCTG
66 GGCTCTG
3508409 GGTAAAACCT
Statistics
Matches: 246, Mismatches: 14, Indels: 24
0.87 0.05 0.08
Matches are distributed among these distances:
94 79 0.32
95 2 0.01
96 2 0.01
99 3 0.01
100 4 0.02
101 3 0.01
104 2 0.01
105 2 0.01
106 149 0.61
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATT
GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTC
Found at i:3508235 original size:361 final size:349
Alignment explanation
Indices: 3507670--3508398 Score: 1075
Period size: 361 Copynumber: 2.1 Consensus size: 349
3507660 ACCAGCCGTC
* * *
3507670 CCTTCGTCGTGAAGTTGAACGTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAGATT
1 CCTTCGTTGTGAAGTTGAACGTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * *
3507735 GGCTCTGAAACTGGGTAATGGTTTGTTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGT
66 GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGC
* *
3507800 GTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTT
131 GTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTT
* *
3507865 GTTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTG-TGTTGTCTCGAGTCTAATATCCTT
196 ATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGCT-TTGTCTCGAGTCCAATATCCTT
*
3507929 CGCTGTGAAGTTGAGATTGGCTCTGAAACTGGGTAATGGTTTATTGACAACCAGCGGTCCCTTCG
260 CGCTGTGAAGTTGAAATTGG----GAAA-----T--T-GTTTATTGACAACCAGCGGTCCCTTCG
* *
3507994 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
313 TCGTGAAGTTAAACTTACGTTGTCTGGAGTCCAATAT
* *
3508031 CCTTCGTTGTGAAGTTGAACTTGCGTTGTCTTGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
1 CCTTCGTTGTGAAGTTGAACGTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
* * *
3508096 GGCTCTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGC
66 GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGC
* * * *
3508161 GTTGTC-CAGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTT
131 GTTGTCTC-GAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTT
* *
3508225 TATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTGGAGTCCAATATCCTT
195 TATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTCGAGTCCAATATCCTT
* *
3508290 CGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACGACCAGCGGTCCCTTCGTCGTGAAGTTAA
260 CGCTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAA
3508355 ACTTACGTTGTCTGGAGTCCAATAT
325 ACTTACGTTGTCTGGAGTCCAATAT
*
3508380 CCTTAGTTGTGAAGTTGAA
1 CCTTCGTTGTGAAGTTGAA
3508399 ATTGGCTCTG
Statistics
Matches: 339, Mismatches: 27, Indels: 16
0.89 0.07 0.04
Matches are distributed among these distances:
349 79 0.23
350 1 0.00
352 1 0.00
357 4 0.01
360 1 0.00
361 252 0.74
362 1 0.00
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (349 bp):
CCTTCGTTGTGAAGTTGAACGTGCGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATT
GGCTCTGAAACTGGGAAATGGTTTATTGACAACCAGCCGTCCCTTCGTCGTGAAGTTGAACTTGC
GTTGTCTCGAGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATGGTTT
ATTGACAACCAGCCGTCCCTTCATCGTGAAGTTGAACTTGCTTTGTCTCGAGTCCAATATCCTTC
GCTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAA
CTTACGTTGTCTGGAGTCCAATAT
Found at i:3508368 original size:94 final size:94
Alignment explanation
Indices: 3508207--3508403 Score: 340
Period size: 94 Copynumber: 2.1 Consensus size: 94
3508197 AAATTGGCTC
* * *
3508207 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCTTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTAAACTTACGTTGT
*
3508272 CTGGAGTCCAATATCCTTCGTTGTGAAGT
66 CTGGAGTCCAATATCCTTAGTTGTGAAGT
* *
3508301 TGAAATTGGGAAATTGTTTATTGACGACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTACGTTGT
1 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTAAACTTACGTTGT
3508366 CTGGAGTCCAATATCCTTAGTTGTGAAGT
66 CTGGAGTCCAATATCCTTAGTTGTGAAGT
3508395 TGAAATTGG
1 TGAAATTGG
3508404 CTCTGGGTAA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 97 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (94 bp):
TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTCCCTTCATCGTGAAGTTAAACTTACGTTGT
CTGGAGTCCAATATCCTTAGTTGTGAAGT
Found at i:3509095 original size:6 final size:6
Alignment explanation
Indices: 3509079--3509144 Score: 55
Period size: 6 Copynumber: 10.7 Consensus size: 6
3509069 ACCCACCTTA
* * *
3509079 TTTTC- TTTTCT TTTTCTT TTGTTATT TTTTCTT TTTTCT ATTT-T TTCTCT
1 TTTTCT TTTTCT TTTTC-T TT-TT-CT TTTTC-T TTTTCT TTTTCT TTTTCT
3509129 TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTT
3509145 TCAATTTAGG
Statistics
Matches: 49, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
5 8 0.16
6 25 0.51
7 11 0.22
8 5 0.10
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.82
Consensus pattern (6 bp):
TTTTCT
Found at i:3509108 original size:16 final size:16
Alignment explanation
Indices: 3509089--3509126 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
3509079 TTTTCTTTTC
3509089 TTTTTCTTTTGT-TAT
1 TTTTTCTTTTGTCTAT
*
3509104 TTTTTCTTTTTTCTAT
1 TTTTTCTTTTGTCTAT
3509120 TTTTTCT
1 TTTTTCT
3509127 CTTTTTCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.05, C:0.11, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTTCTTTTGTCTAT
Found at i:3509115 original size:7 final size:7
Alignment explanation
Indices: 3509084--3509146 Score: 67
Period size: 7 Copynumber: 8.7 Consensus size: 7
3509074 CCTTATTTTC
3509084 TTTTC-T
1 TTTTCTT
3509090 TTTTCTT
1 TTTTCTT
*
3509097 TTGTTATT
1 TT-TTCTT
3509105 TTTTCTT
1 TTTTCTT
3509112 TTTTCTATT
1 TTTTC--TT
3509121 TTTTCTCT
1 TTTTCT-T
3509129 TTTTC-T
1 TTTTCTT
3509135 TTTTCTT
1 TTTTCTT
3509142 TTTTC
1 TTTTC
3509147 AATTTAGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 11
0.79 0.03 0.18
Matches are distributed among these distances:
6 11 0.22
7 19 0.39
8 12 0.24
9 7 0.14
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:3509138 original size:16 final size:17
Alignment explanation
Indices: 3509079--3509138 Score: 65
Period size: 16 Copynumber: 3.6 Consensus size: 17
3509069 ACCCACCTTA
*
3509079 TTTTCT-TTTCTTTTTCT
1 TTTTCTATTT-TTTCTCT
3509096 TTTGT-TATTTTTTCT-T
1 TTT-TCTATTTTTTCTCT
3509112 TTTTCTATTTTTTCTCT
1 TTTTCTATTTTTTCTCT
3509129 TTTTCT-TTTT
1 TTTTCTATTTT
3509139 CTTTTTTCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
15 1 0.03
16 18 0.47
17 15 0.39
18 4 0.11
ACGTcount: A:0.03, C:0.13, G:0.02, T:0.82
Consensus pattern (17 bp):
TTTTCTATTTTTTCTCT
Found at i:3509145 original size:8 final size:8
Alignment explanation
Indices: 3509089--3509138 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
3509079 TTTTCTTTTC
3509089 TTTTTCTT
1 TTTTTCTT
* *
3509097 TTGTT-AT
1 TTTTTCTT
3509104 TTTTTC-T
1 TTTTTCTT
3509111 TTTTTCTAT
1 TTTTTCT-T
*
3509120 TTTTTCTC
1 TTTTTCTT
3509128 TTTTTCTT
1 TTTTTCTT
3509136 TTT
1 TTT
3509139 CTTTTTTCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
7 12 0.35
8 14 0.41
9 8 0.24
ACGTcount: A:0.04, C:0.12, G:0.02, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:3519889 original size:2 final size:2
Alignment explanation
Indices: 3519882--3519914 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3519872 TAATATACAG
3519882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3519915 ATAAACGACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3523353 original size:17 final size:17
Alignment explanation
Indices: 3523331--3523364 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3523321 AGTTTATAAA
3523331 TATTATATATTTTTATT
1 TATTATATATTTTTATT
3523348 TATTATATATTTTTATT
1 TATTATATATTTTTATT
3523365 AATTTTGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATTATATATTTTTATT
Found at i:3525737 original size:57 final size:57
Alignment explanation
Indices: 3525648--3525772 Score: 214
Period size: 57 Copynumber: 2.2 Consensus size: 57
3525638 GATGACTTAT
*
3525648 CAGAATGCATAAGCCATATAAGAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
* *
3525705 CAGAATACATAAGCCATATAAAAAGCTGGATAGACAAGAAAAATAAGTGTAGAGATG
1 CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
*
3525762 CATAATGCATA
1 CAGAATGCATA
3525773 TATGTTCCCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 63 1.00
ACGTcount: A:0.49, C:0.12, G:0.21, T:0.18
Consensus pattern (57 bp):
CAGAATGCATAAGCCATATAAAAAGCTCGATAGACAAGAAAAATAAGTGTAGAGATG
Found at i:3528164 original size:39 final size:38
Alignment explanation
Indices: 3528115--3528203 Score: 101
Period size: 39 Copynumber: 2.3 Consensus size: 38
3528105 ATGGATTACG
* * *
3528115 GTTTAAGGTTTTAGGATTTAAAG-TTTTAAAGTTTATA
1 GTTTAGGGTTTTAGGATTTAAAGATATTAAAATTTATA
*
3528152 TTGTTTAGGG-TTTAGGGTTTAAAGATATTAAAATTTATA
1 --GTTTAGGGTTTTAGGATTTAAAGATATTAAAATTTATA
*
3528191 GTTTGGGGTTTTA
1 GTTTAGGGTTTTA
3528204 AGATCTATAG
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
37 7 0.16
38 17 0.40
39 19 0.44
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.48
Consensus pattern (38 bp):
GTTTAGGGTTTTAGGATTTAAAGATATTAAAATTTATA
Found at i:3528270 original size:22 final size:21
Alignment explanation
Indices: 3528237--3528305 Score: 66
Period size: 22 Copynumber: 3.2 Consensus size: 21
3528227 AGGTTTAAAT
*
3528237 TTTAAGGCTTAAAGTATTAGGG
1 TTTAAGGTTTAAAGT-TTAGGG
* * * *
3528259 TTTAGGGTTTAAAATTTTGTGA
1 TTTAAGGTTTAAAGTTTAG-GG
*
3528281 TTTAAGGTTTAAAGTTTAGAG
1 TTTAAGGTTTAAAGTTTAGGG
3528302 TTTA
1 TTTA
3528306 CGGTGTTGTG
Statistics
Matches: 36, Mismatches: 10, Indels: 3
0.73 0.20 0.06
Matches are distributed among these distances:
21 7 0.19
22 29 0.81
ACGTcount: A:0.30, C:0.01, G:0.23, T:0.45
Consensus pattern (21 bp):
TTTAAGGTTTAAAGTTTAGGG
Found at i:3531770 original size:34 final size:35
Alignment explanation
Indices: 3531716--3531794 Score: 124
Period size: 34 Copynumber: 2.2 Consensus size: 35
3531706 TATTTATTTT
*
3531716 ATATTTATTTCTTAATGATTATAATTTGAATCTTAA
1 ATATTT-TTTCTTAATGATTATAATTTGAATATTAA
3531752 ATATTTTTTCTT-ATGATTATAATTTGAATATTAA
1 ATATTTTTTCTTAATGATTATAATTTGAATATTAA
3531786 ATTATTTTT
1 A-TATTTTT
3531795 AATGATTTCA
Statistics
Matches: 41, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
34 22 0.54
35 13 0.32
36 6 0.15
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (35 bp):
ATATTTTTTCTTAATGATTATAATTTGAATATTAA
Found at i:3533774 original size:14 final size:14
Alignment explanation
Indices: 3533747--3533792 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
3533737 TAGTATTATT
3533747 TATT-AAAT-AAAA
1 TATTAAAATAAAAA
3533759 TATTAAAATAAAAA
1 TATTAAAATAAAAA
3533773 TATTAAAAATAATAAA
1 TATT-AAAATAA-AAA
3533789 TATT
1 TATT
3533793 TACTATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
12 4 0.13
13 4 0.13
14 8 0.27
15 7 0.23
16 7 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TATTAAAATAAAAA
Found at i:3537342 original size:171 final size:172
Alignment explanation
Indices: 3537052--3537377 Score: 537
Period size: 171 Copynumber: 1.9 Consensus size: 172
3537042 GCAGACCCAG
* *
3537052 TTTTAACCTTTGAGATGAGTTCAATATTTTAATCAGAAATTTCAGTTGAGAATTAAATTTTAATA
1 TTTTAACCTTTGAGATGAGTTCAATATTTTAATAAGAAATTTCAGTTGAGAATTAAATTTGAATA
* * * **
3537117 CTGATATTAATTTTGAGATGACTTAATTAAAGCAATATTTCATTAAAGTGACCTCAAGTATGGAA
66 CCGATATTAATTTTAAGATGACTTAATTAAAGAAATAAGTCATTAAAGTGACCTCAAGTATGGAA
3537182 AATATTTTATA-AGGTTATGTATATTTTAGACCCAAGTTCAA
131 AATATTTTATACAGGTTATGTATATTTTAGACCCAAGTTCAA
* * *
3537223 TTTTGACCTTTGAGATGAGTTCAATATTTTAATAAGAAATTTTAGTTGATAATTAAATTTGAATA
1 TTTTAACCTTTGAGATGAGTTCAATATTTTAATAAGAAATTTCAGTTGAGAATTAAATTTGAATA
*
3537288 CCGATATTAATTTTAAGATGACTTAATTAAAGAAATAAGTCTTTAAAGTGACCTCAAGTATGGAA
66 CCGATATTAATTTTAAGATGACTTAATTAAAGAAATAAGTCATTAAAGTGACCTCAAGTATGGAA
*
3537353 AATATTTTATACATGTTATGTATAT
131 AATATTTTATACAGGTTATGTATAT
3537378 GTAACCTAGG
Statistics
Matches: 142, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
171 130 0.92
172 12 0.08
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.40
Consensus pattern (172 bp):
TTTTAACCTTTGAGATGAGTTCAATATTTTAATAAGAAATTTCAGTTGAGAATTAAATTTGAATA
CCGATATTAATTTTAAGATGACTTAATTAAAGAAATAAGTCATTAAAGTGACCTCAAGTATGGAA
AATATTTTATACAGGTTATGTATATTTTAGACCCAAGTTCAA
Found at i:3538221 original size:24 final size:24
Alignment explanation
Indices: 3538189--3538239 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3538179 ACTAAGATGG
3538189 ATACAAATTGTGATGTTGACATGT
1 ATACAAATTGTGATGTTGACATGT
3538213 ATACAAATTGTGATGTTGACATGT
1 ATACAAATTGTGATGTTGACATGT
3538237 ATA
1 ATA
3538240 AGGCATGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (24 bp):
ATACAAATTGTGATGTTGACATGT
Found at i:3544820 original size:45 final size:45
Alignment explanation
Indices: 3544770--3544902 Score: 187
Period size: 45 Copynumber: 3.0 Consensus size: 45
3544760 ACTAGCATAT
*
3544770 CCAATATACTTACCATTTATCCCATAAGCTCATAAGCTTATTTTA
1 CCAATATACTTACCATTTATACCATAAGCTCATAAGCTTATTTTA
* * * *
3544815 CCAATACACTTACCATTTAAATCATAAGCTCGTAAGCTTATTTTA
1 CCAATATACTTACCATTTATACCATAAGCTCATAAGCTTATTTTA
* * *
3544860 CCAATATACTTGCCA-TTATTCCATAAACTCATAAGCTTATTTT
1 CCAATATACTTACCATTTATACCATAAGCTCATAAGCTTATTTT
3544903 CATGATTACC
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
44 23 0.30
45 53 0.70
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (45 bp):
CCAATATACTTACCATTTATACCATAAGCTCATAAGCTTATTTTA
Found at i:3550050 original size:23 final size:22
Alignment explanation
Indices: 3550020--3550067 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
3550010 AAAGGAAAAC
* *
3550020 AACCCCTAATATAAGGTAGAAT
1 AACCCCTAACATAAAGTAGAAT
*
3550042 AACCACCTAACATAAAGTAGGAT
1 AACC-CCTAACATAAAGTAGAAT
3550065 AAC
1 AAC
3550068 ATCTTTCCCT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 4 0.18
23 18 0.82
ACGTcount: A:0.48, C:0.21, G:0.12, T:0.19
Consensus pattern (22 bp):
AACCCCTAACATAAAGTAGAAT
Found at i:3550162 original size:150 final size:150
Alignment explanation
Indices: 3549922--3550192 Score: 488
Period size: 150 Copynumber: 1.8 Consensus size: 150
3549912 GACGATATCC
3549922 TTCCCTTTTCCAACTAAAGCGGTGAATTGTCGATATTTCTTCTAAAAAAATCTTAAGTTAAATTG
1 TTCCCTTTTCCAACTAAAGCGGTGAATTGTCGATATTTCTTCTAAAAAAATCTTAAGTTAAATTG
* * *
3549987 ATAACTCTTCATCATTTCAAACCAAAGGAAAACAACCCCTAATATAAGGTAGAATAACCACCTAA
66 ACAACACTTCAGCATTTCAAACCAAAGGAAAACAACCCCTAATATAAGGTAGAATAACCACCTAA
3550052 CATAAAGTAGGATAACATCT
131 CATAAAGTAGGATAACATCT
* *
3550072 TTCCCTTTTCCAACTAAAGCGGTGAATTGTCGATATTTCTTCTAAAACAATCTTAAGTTAATTTG
1 TTCCCTTTTCCAACTAAAGCGGTGAATTGTCGATATTTCTTCTAAAAAAATCTTAAGTTAAATTG
*
3550137 ACAACACTTCAGCATTTCAAACCAAAGGAAAACACCCCCTAATATAAGGTAGAATA
66 ACAACACTTCAGCATTTCAAACCAAAGGAAAACAACCCCTAATATAAGGTAGAATA
3550193 TCAATTTTCC
Statistics
Matches: 115, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 115 1.00
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.30
Consensus pattern (150 bp):
TTCCCTTTTCCAACTAAAGCGGTGAATTGTCGATATTTCTTCTAAAAAAATCTTAAGTTAAATTG
ACAACACTTCAGCATTTCAAACCAAAGGAAAACAACCCCTAATATAAGGTAGAATAACCACCTAA
CATAAAGTAGGATAACATCT
Found at i:3552205 original size:30 final size:28
Alignment explanation
Indices: 3552140--3552206 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 28
3552130 TTTTCATAGT
** *
3552140 GACTAAAATATAAGTTTTGAAAGTTTAG
1 GACTAAAATATAAACTTTGAAACTTTAG
*
3552168 TAGCTAAAATATAAACTTTGAAAACTTTAGG
1 GA-CTAAAATATAAACTTTG-AAACTTTA-G
3552199 GACTAAAA
1 GACTAAAA
3552207 ATTTAATTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
28 1 0.03
29 15 0.48
30 13 0.42
31 2 0.06
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.31
Consensus pattern (28 bp):
GACTAAAATATAAACTTTGAAACTTTAG
Found at i:3566738 original size:24 final size:23
Alignment explanation
Indices: 3566710--3566754 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
3566700 TTTTTAAGAT
*
3566710 TCATTAATGGTATTTTCAAATTTA
1 TCATTAATGGAATTTT-AAATTTA
*
3566734 TCATTAATTGAATTTTAAATT
1 TCATTAATGGAATTTTAAATT
3566755 CAATTATATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (23 bp):
TCATTAATGGAATTTTAAATTTA
Found at i:3577748 original size:18 final size:18
Alignment explanation
Indices: 3577695--3577748 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3577685 TAAATAAATG
3577695 AGTAAAATATATAA-AA-A
1 AGTAAAATA-ATAATAATA
**
3577712 AGTAAAAGCAT-ATATATA
1 AGTAAAATAATAATA-ATA
3577730 AGTAAAATAATAATAATA
1 AGTAAAATAATAATAATA
3577748 A
1 A
3577749 AAAAAAGAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
15 1 0.03
16 3 0.10
17 8 0.28
18 14 0.48
19 3 0.10
ACGTcount: A:0.65, C:0.02, G:0.07, T:0.26
Consensus pattern (18 bp):
AGTAAAATAATAATAATA
Found at i:3577810 original size:2 final size:2
Alignment explanation
Indices: 3577798--3577833 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3577788 TAAAATAGGA
3577798 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3577834 ATAACACTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3578284 original size:37 final size:37
Alignment explanation
Indices: 3578243--3578339 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
3578233 GGATCCTATC
* *
3578243 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
* * * * *
3578280 TTTAGGAGTTTGAATCCTAGCAAAATTTTATCCTATT
1 TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
3578317 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCCTAGTAG
3578340 GACGAAAAGG
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCCTAGTAGAACTCTATCATATT
Found at i:3579366 original size:106 final size:106
Alignment explanation
Indices: 3579068--3580332 Score: 1735
Period size: 106 Copynumber: 12.0 Consensus size: 106
3579058 AGCATTGTTC
* * ** *
3579068 TGAGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTATTTGTTGAC
1 TGAGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
* * * *
3579132 AACCAGTC-GTCCCTTCGTTGTGAAGTTAAACTTGTGTTGTAT
65 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3579174 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AA-T--GAAA-T-TTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* * * * ** *
3579233 ATCAGCCGCCCCTTCGTCGTGAAGTTGAGCTTGTATTGCCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * * * *
3579274 TGGGTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTAAAATTAGGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3579339 ACCAGCGGTCCCTTCATCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3579380 TGAGTCCAATATCCTACGCTGTGAAGTTGAAATTAGCTCTGAAATTGGAAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3579445 ACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3579486 TGAGTCCATTATCCTTCACTGTGAAGTTAAAATTGGTTCTGAAATTGGGAAATTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
3579551 ACCAGCGTTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTAT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * * *
3579592 GGAGTCCAATATCCTTCGTTGTAAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
* *
3579657 ACCAGCGGTCCCTTCGTCATAAAGTTGAACTTGCGTTGT-T
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
** *
3579697 TGTAGTCCAATATCCTTTTCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAC
1 TG-AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
3579762 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3579804 GGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3579869 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* *
3579910 GGAGTCCAATATCCTTCGCTGAT-AAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGAC
1 TGAGTCCAATATCCTTCGCTG-TGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC
3579974 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
65 AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * * *
3580016 AGAGTCCAATATCTTTCGCTGTGAAGTTTAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAGA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
3580081 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
* * * *
3580122 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*** * * *
3580187 GTAAGCCG-CCCTTCG-CTGTGAAGTTGAGCTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTC-GTGAAGTTGAACTTGCGTTGTCT
* *
3580227 TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACA
1 TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
*
3580292 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCT
66 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
3580333 GGAGAGAAAC
Statistics
Matches: 1026, Mismatches: 118, Indels: 30
0.87 0.10 0.03
Matches are distributed among these distances:
99 1 0.00
100 75 0.07
101 3 0.00
102 5 0.00
104 4 0.00
105 97 0.09
106 836 0.81
107 5 0.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (106 bp):
TGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACA
ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
Found at i:3580372 original size:21 final size:21
Alignment explanation
Indices: 3580347--3580407 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
3580337 AGAAACTGTC
3580347 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
* *
3580368 TCAAGGAAGAC------TGTC
1 TCAAGGGAGACAAAATTTGTT
3580383 TCAAGGGAGACAAAATTTGTT
1 TCAAGGGAGACAAAATTTGTT
3580404 TCAA
1 TCAA
3580408 AGAAAAACTA
Statistics
Matches: 30, Mismatches: 4, Indels: 12
0.65 0.09 0.26
Matches are distributed among these distances:
15 13 0.43
21 17 0.57
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (21 bp):
TCAAGGGAGACAAAATTTGTT
Found at i:3580388 original size:36 final size:36
Alignment explanation
Indices: 3580341--3580474 Score: 153
Period size: 37 Copynumber: 3.7 Consensus size: 36
3580331 CTGGAGAGAA
*
3580341 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGAAG
1 ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
* * *
3580377 ACTGTCTCAAGGGAGACAAAATTTGTTTCAAAGAAAA
1 ACTGTCTCAAGCGAGACAAAATTTGTTTC-AAGGAAG
* * * *
3580414 ACTATCTCAAGCGAGATAAAATCTTGTTTTAAATG-AG
1 ACTGTCTCAAGCGAGACAAAAT-TTG-TTTCAAGGAAG
*
3580451 ACTGTCTCAAGCAAGACAAAATTT
1 ACTGTCTCAAGCGAGACAAAATTT
3580475 ATATTGGAAA
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
36 31 0.37
37 44 0.53
38 5 0.06
39 3 0.04
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.27
Consensus pattern (36 bp):
ACTGTCTCAAGCGAGACAAAATTTGTTTCAAGGAAG
Found at i:3581247 original size:22 final size:22
Alignment explanation
Indices: 3581221--3581297 Score: 109
Period size: 22 Copynumber: 3.5 Consensus size: 22
3581211 TTGTGTTTGG
3581221 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* * *
3581243 TCAAATGTTTGGTATTTGATGT
1 TCAAAGGTTTGGCATTTGATGC
* *
3581265 TCAAAGGTTTGTCATTTGATTC
1 TCAAAGGTTTGGCATTTGATGC
3581287 TCAAAGGTTTG
1 TCAAAGGTTTG
3581298 ATGGGGTAGC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.23, C:0.10, G:0.23, T:0.43
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:3581933 original size:18 final size:17
Alignment explanation
Indices: 3581899--3581956 Score: 64
Period size: 17 Copynumber: 3.3 Consensus size: 17
3581889 TTTTTGTCCC
*
3581899 TTTTTCTTTTTGATTTTG
1 TTTTTCTTTTT-CTTTTG
3581917 TTCTTTCTTTTTCTTTTG
1 TT-TTTCTTTTTCTTTTG
*
3581935 TTTCTCTTTTT-TCTTTG
1 TTTTTCTTTTTCT-TTTG
3581952 TTTTT
1 TTTTT
3581957 GATTGGATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.03
17 16 0.46
18 9 0.26
19 9 0.26
ACGTcount: A:0.02, C:0.12, G:0.07, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTG
Found at i:3581933 original size:24 final size:25
Alignment explanation
Indices: 3581898--3581960 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
3581888 CTTTTTGTCC
*
3581898 CTTTTTCTTTTTGATTT-TGTTCTTT
1 CTTTTTC-TTTTGATTTCTCTTCTTT
*
3581923 CTTTTTCTTTTG-TTTCTCTTTTTT
1 CTTTTTCTTTTGATTTCTCTTCTTT
*
3581947 CTTTGT-TTTTGATT
1 CTTTTTCTTTTGATT
3581961 GGATCTTCCA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 8 0.24
24 18 0.55
25 7 0.21
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.76
Consensus pattern (25 bp):
CTTTTTCTTTTGATTTCTCTTCTTT
Found at i:3586653 original size:8 final size:8
Alignment explanation
Indices: 3586640--3586685 Score: 56
Period size: 8 Copynumber: 5.6 Consensus size: 8
3586630 ATAAAATAGG
3586640 AAATATAT
1 AAATATAT
3586648 AAATATAT
1 AAATATAT
*
3586656 ATATATAT
1 AAATATAT
*
3586664 ATATATAT
1 AAATATAT
*
3586672 ATATATAT
1 AAATATAT
3586680 ATAATA
1 A-AATA
3586686 ACACTTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
8 32 0.91
9 3 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAATATAT
Found at i:3586655 original size:2 final size:2
Alignment explanation
Indices: 3586642--3586682 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
3586632 AAAATAGGAA
*
3586642 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3586683 ATAACACTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:3587135 original size:37 final size:37
Alignment explanation
Indices: 3587094--3587190 Score: 140
Period size: 37 Copynumber: 2.6 Consensus size: 37
3587084 GGATCCTATC
*
3587094 TTTAGGAGTTTAAATCATAGTAGAACTCTATCATATT
1 TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
* * * *
3587131 TTTAGGAGTTTGAATCATAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
*
3587168 TTTAGGAGTTTGAATCCTAGTAG
1 TTTAGGAGTTTGAATCATAGTAG
3587191 GACGAAAAGG
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 52 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.40
Consensus pattern (37 bp):
TTTAGGAGTTTGAATCATAGTAGAACTCTATCATATT
Found at i:3588013 original size:19 final size:19
Alignment explanation
Indices: 3587984--3588035 Score: 81
Period size: 19 Copynumber: 2.8 Consensus size: 19
3587974 ACTCCCCAGG
3587984 AGTTT-GAAACTTTTCAAT
1 AGTTTCGAAACTTTTCAAT
3588002 AGTTTCGAAACTTTTCAAT
1 AGTTTCGAAACTTTTCAAT
3588021 AGTTTC-AATACTTTT
1 AGTTTCGAA-ACTTTT
3588036 GGGTAGTATG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
18 7 0.22
19 25 0.78
ACGTcount: A:0.31, C:0.13, G:0.10, T:0.46
Consensus pattern (19 bp):
AGTTTCGAAACTTTTCAAT
Found at i:3590939 original size:167 final size:166
Alignment explanation
Indices: 3590640--3591139 Score: 833
Period size: 167 Copynumber: 3.0 Consensus size: 166
3590630 CTTCGTTTTA
* * *
3590640 TTGAGGAGTTCTAGGGGCTGAAA-AATTATGGATAATTCCATTAGAATTACAAAATTCACCACAA
1 TTGAGGGGTTCCATGGGCT-AAACAATTATGGATAATTCCATTAGAATTACAAAATTCACCACAA
* *
3590704 CTAAGATTTTAAAATTCGGTTTCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATT
65 CTAAGATTTTCAAATTCGGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATT
3590769 TTGGTTTATTTTAGAGAAAGTGATGAATTTTTCTAAAG
130 TTGGTTTATTTTAGAGAAAGTGATGAA-TTTTCTAAAG
*
3590807 TTGAGGGGTTCCATGGGCTAAACAATTATGGATAATTCCATCAGAATTACAAAATTCACCACAAC
1 TTGAGGGGTTCCATGGGCTAAACAATTATGGATAATTCCATTAGAATTACAAAATTCACCACAAC
*
3590872 TAAGATTTTCAAATTCAGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATTT
66 TAAGATTTTCAAATTCGGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATTT
*
3590937 TGGTTTATTTTAAAGAAAGTGATGAAATTTTCTAAAG
131 TGGTTTATTTTAGAGAAAGTGATG-AATTTTCTAAAG
* * *
3590974 ATGAGGGGTTCCATGGGAT-AACAAATTATGGATAATTCCATTAGAATTAAAAAATTCACCACAA
1 TTGAGGGGTTCCATGGGCTAAAC-AATTATGGATAATTCCATTAGAATTACAAAATTCACCACAA
*
3591038 CTAAGATTTTCAAATTCGGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACATTTTTCATT
65 CTAAGATTTTCAAATTCGGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATT
*
3591103 TTGGTTTATTTTAGAGAAAGTGGTGAATTTTCTAAAG
130 TTGGTTTATTTTAGAGAAAGTGATGAATTTTCTAAAG
3591140 CTTCATCTTT
Statistics
Matches: 314, Mismatches: 16, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
166 18 0.06
167 294 0.94
168 2 0.01
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Consensus pattern (166 bp):
TTGAGGGGTTCCATGGGCTAAACAATTATGGATAATTCCATTAGAATTACAAAATTCACCACAAC
TAAGATTTTCAAATTCGGTTCCATGGTCACTCCTAACACTTGAAATTGAGTAACCTTTTTCATTT
TGGTTTATTTTAGAGAAAGTGATGAATTTTCTAAAG
Found at i:3599392 original size:5 final size:5
Alignment explanation
Indices: 3599368--3599431 Score: 51
Period size: 5 Copynumber: 12.6 Consensus size: 5
3599358 ATGGTAATTT
** *
3599368 TTTTA TTCTTA TAATA TTTTA TTTTA TTTT- TATT- TTTTA TTTTTA TTTTTA
1 TTTTA TT-TTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA -TTTTA
*
3599419 TTTTG TTTTA TTT
1 TTTTA TTTTA TTT
3599432 AATGTTAGTA
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
4 6 0.12
5 27 0.56
6 15 0.31
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:3599398 original size:6 final size:6
Alignment explanation
Indices: 3599384--3599422 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
3599374 TCTTATAATA
3599384 TTTTA- TTTTAT TTTTATT TTTTAT TTTTAT TTTTAT TTT
1 TTTTAT TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTT
3599423 GTTTTATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTAT
Found at i:3599404 original size:35 final size:30
Alignment explanation
Indices: 3599364--3599431 Score: 75
Period size: 30 Copynumber: 2.1 Consensus size: 30
3599354 AATAATGGTA
*
3599364 ATTTTTTTATTCTTATAATATTTTATTTTATTTT
1 ATTTTTTTATT-TT-T-AT-TTTTATTTTGTTTT
3599398 -TATTTTTTATTTTTATTTTTATTTTGTTTT
1 AT-TTTTTTATTTTTATTTTTATTTTGTTTT
3599428 ATTT
1 ATTT
3599432 AATGTTAGTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
30 15 0.48
31 3 0.10
32 1 0.03
33 3 0.10
34 9 0.29
ACGTcount: A:0.19, C:0.01, G:0.01, T:0.78
Consensus pattern (30 bp):
ATTTTTTTATTTTTATTTTTATTTTGTTTT
Found at i:3599407 original size:13 final size:12
Alignment explanation
Indices: 3599384--3599422 Score: 62
Period size: 13 Copynumber: 3.2 Consensus size: 12
3599374 TCTTATAATA
3599384 TTTTA-TTTTAT
1 TTTTATTTTTAT
3599395 TTTTATTTTTTAT
1 TTTTA-TTTTTAT
3599408 TTTTATTTTTAT
1 TTTTATTTTTAT
3599420 TTT
1 TTT
3599423 GTTTTATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 11 0.42
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTTATTTTTAT
Found at i:3599413 original size:19 final size:18
Alignment explanation
Indices: 3599384--3599422 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 18
3599374 TCTTATAATA
3599384 TTTTATTTTATTTTTATT
1 TTTTATTTTATTTTTATT
3599402 TTTTATTTTTATTTTTATT
1 TTTTA-TTTTATTTTTATT
3599421 TT
1 TT
3599423 GTTTTATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (18 bp):
TTTTATTTTATTTTTATT
Found at i:3603269 original size:37 final size:37
Alignment explanation
Indices: 3603222--3603310 Score: 128
Period size: 37 Copynumber: 2.4 Consensus size: 37
3603212 CTTGGAGATT
3603222 GTTTCTCTTGAAA-AAATGTTTTGTCTCT-CTTGAGACA
1 GTTTCTCTTGAAACAAA-GTTTTGTCT-TGCTTGAGACA
*
3603259 GTTTCTCTTGAAACAAAGTTTTGTCTTGCTTGAGATA
1 GTTTCTCTTGAAACAAAGTTTTGTCTTGCTTGAGACA
*
3603296 GTTTTTCTTGAAACA
1 GTTTCTCTTGAAACA
3603311 TAAACCTTTG
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
36 1 0.02
37 44 0.92
38 3 0.06
ACGTcount: A:0.25, C:0.15, G:0.17, T:0.44
Consensus pattern (37 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTTGCTTGAGACA
Found at i:3603359 original size:67 final size:67
Alignment explanation
Indices: 3603259--3603578 Score: 453
Period size: 67 Copynumber: 4.8 Consensus size: 67
3603249 TCTTGAGACA
* * *
3603259 GTTTCTCTTGAAACAAAGTTTTGTCTTGCTTGAGATAGTTTTTCTTGAAACATAAACCTTTGAGC
1 GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
3603324 TT
66 TT
* * * * *
3603326 GTTTCTCTTGAAACAAAGTTTTGTTTCGCTTGAGACAGTTTATCTTTAAATATAAACCTTTGAGA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
3603391 TT
66 TT
* * *
3603393 TTTTTTCTTGAAACAAAGTTTTGTCTCGCTTGAGACA-TCTTCTCTTGAAACATAAACCTTTGAG
1 GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGT-TTCTCTTGAAACATAAACCTTTGAG
*
3603457 ATC
65 ATT
* * * * *
3603460 ATTTCTCTTGAAACAAAATTTTGTCTCACTTGAGATAATTTCTCTTGAAACATAAAGCTTTGAGA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
*
3603525 AT
66 TT
*
3603527 GTTTCTCATGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACA
1 GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACA
3603579 AAGTTTCATC
Statistics
Matches: 224, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
66 1 0.00
67 222 0.99
68 1 0.00
ACGTcount: A:0.28, C:0.16, G:0.15, T:0.41
Consensus pattern (67 bp):
GTTTCTCTTGAAACAAAGTTTTGTCTCGCTTGAGATAGTTTCTCTTGAAACATAAACCTTTGAGA
TT
Found at i:3603502 original size:37 final size:37
Alignment explanation
Indices: 3603452--3603625 Score: 150
Period size: 37 Copynumber: 4.8 Consensus size: 37
3603442 ACATAAACCT
*
3603452 TTGAGATCATTTCTCTTGAAACAAAATTTTGTCTCAC
1 TTGAGATAATTTCTCTTGAAACAAAATTTTGTCTCAC
3603489 TTGAGATAATTTCTCTTGAAACATAAA----G-CT---
1 TTGAGATAATTTCTCTTGAAACA-AAATTTTGTCTCAC
* * * *
3603519 TTGAGA-ATGTTTCTCATGAAACAAAGTTTTGTCTCGC
1 TTGAGATA-ATTTCTCTTGAAACAAAATTTTGTCTCAC
* * **
3603556 TTGAGATAGTTTCTCTTGAAACAAAGTTTCATCTCAC
1 TTGAGATAATTTCTCTTGAAACAAAATTTTGTCTCAC
* *
3603593 TTGAGATGATTTTCCCTTGAAACACAAATTTTG
1 TTGAGAT-AATTTCTCTTGAAACA-AAATTTTG
3603626 AAATTGTTGC
Statistics
Matches: 111, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
29 3 0.03
30 19 0.17
33 3 0.03
34 3 0.03
37 60 0.54
38 18 0.16
39 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (37 bp):
TTGAGATAATTTCTCTTGAAACAAAATTTTGTCTCAC
Found at i:3603643 original size:104 final size:102
Alignment explanation
Indices: 3603452--3603734 Score: 266
Period size: 104 Copynumber: 2.7 Consensus size: 102
3603442 ACATAAACCT
** * * *
3603452 TTGAGATCA-TTTCTCTTGAAACAAAATTTTGTCTCACTTGAGATAATTTCTCTTGAAACATAAA
1 TTGAGAT-AGTTTCTCTTGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAACACAAA
* * * * * *
3603516 GCTTTGAGAA-TGTTTCTCATGAAACAAAGTTTTGTCTCGC
65 -TTTTGA-AATTGTTGCACATGAAACAAA-ATTAGTCTCAC
*
3603556 TTGAGATAGTTTCTCTTGAAACAAAGTTTCATCTCACTTGAGATGATTTTCCCTTGAAACACAAA
1 TTGAGATAGTTTCTCTTGAAACAAAATTTCATCTCACTTGAGAT-ATTTTCCCTTGAAACACAAA
*
3603621 TTTTGAAATTGTTGCACTTGAAACAAAATTAGTCTCAC
65 TTTTGAAATTGTTGCACATGAAACAAAATTAGTCTCAC
* ** ** ** * *
3603659 TTGAGATTGTTT-TCCTCAAAACAAAAAAATCATCTTGCTTGAGACAATTTTCCCTTGAAACTCA
1 TTGAGATAGTTTCT-CTTGAAAC-AAAATTTCATCTCACTTGAGA-TATTTTCCCTTGAAACACA
*
3603723 AATCTTGAAATT
63 AATTTTGAAATT
3603735 ATTTATCTCA
Statistics
Matches: 149, Mismatches: 24, Indels: 12
0.81 0.13 0.06
Matches are distributed among these distances:
102 1 0.01
103 28 0.19
104 103 0.69
105 17 0.11
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.37
Consensus pattern (102 bp):
TTGAGATAGTTTCTCTTGAAACAAAATTTCATCTCACTTGAGATATTTTCCCTTGAAACACAAAT
TTTGAAATTGTTGCACATGAAACAAAATTAGTCTCAC
Found at i:3604673 original size:3 final size:3
Alignment explanation
Indices: 3604667--3604725 Score: 100
Period size: 3 Copynumber: 19.0 Consensus size: 3
3604657 GATGATGATG
3604667 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT ATT
3604713 ATAT ATT ATT ATT
1 AT-T ATT ATT ATT
3604726 TTTGTATTAC
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
3 48 0.89
4 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:3606523 original size:17 final size:16
Alignment explanation
Indices: 3606472--3606523 Score: 52
Period size: 17 Copynumber: 3.2 Consensus size: 16
3606462 TGGTAATTAT
**
3606472 TTTTTATTTA-TAATA
1 TTTTTATTTACTTTTA
3606487 TTTTTATTTACTTTTAA
1 TTTTTATTTACTTTT-A
*
3606504 TTTTTATTTTCATTTTA
1 TTTTTATTTAC-TTTTA
3606521 TTT
1 TTT
3606524 AATGTTATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
15 10 0.32
16 2 0.06
17 15 0.48
18 4 0.13
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTTATTTACTTTTA
Found at i:3607118 original size:3 final size:3
Alignment explanation
Indices: 3607110--3607152 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3607100 AAACTAGAAT
3607110 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
3607153 GGAAAAAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3608791 original size:19 final size:19
Alignment explanation
Indices: 3608767--3608804 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
3608757 ACCGCAACAC
3608767 AATTTAGT-AGAGTAATATA
1 AATTTAGTCA-AGTAATATA
*
3608786 AATTTATTCAAGTAATATA
1 AATTTAGTCAAGTAATATA
3608805 TATATTTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.47, C:0.03, G:0.11, T:0.39
Consensus pattern (19 bp):
AATTTAGTCAAGTAATATA
Found at i:3613563 original size:13 final size:13
Alignment explanation
Indices: 3613545--3613569 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3613535 TAAAATAAAA
3613545 TAAAATTAATAAT
1 TAAAATTAATAAT
3613558 TAAAATTAATAA
1 TAAAATTAATAA
3613570 AATATCATCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TAAAATTAATAAT
Found at i:3618766 original size:35 final size:34
Alignment explanation
Indices: 3618726--3618792 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 34
3618716 TGTTTTCTTG
3618726 ATTTTCATCATATTCTTCAACTCTTCTTCTTCTCT
1 ATTTTCATCATATTCTTCAACT-TTCTTCTTCTCT
* * **
3618761 ATTTTCATCGTCTTCTTTGACTTTCTTCTTCT
1 ATTTTCATCATATTCTTCAACTTTCTTCTTCT
3618793 GTTTATGTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 10 0.36
35 18 0.64
ACGTcount: A:0.13, C:0.27, G:0.03, T:0.57
Consensus pattern (34 bp):
ATTTTCATCATATTCTTCAACTTTCTTCTTCTCT
Found at i:3621984 original size:23 final size:22
Alignment explanation
Indices: 3621924--3621987 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
3621914 CAGCTCATAT
*
3621924 AATTGCAACGAAGTGCCACGTAG
1 AATTGCACCG-AGTGCCACGTAG
* *
3621947 AATTGCACTAGAGTGCCGCGTAG
1 AATTGCAC-CGAGTGCCACGTAG
3621970 AATTGCACCGCAGTGCCA
1 AATTGCACCG-AGTGCCA
3621988 TATAATAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
22 1 0.03
23 32 0.94
24 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (22 bp):
AATTGCACCGAGTGCCACGTAG
Found at i:3622188 original size:103 final size:103
Alignment explanation
Indices: 3622006--3622220 Score: 367
Period size: 103 Copynumber: 2.1 Consensus size: 103
3621996 TTTCCATAAA
* * * *
3622006 GACCACAAATCATTCCTTAAGAATTATATACATATACTAGGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
3622071 TTCACACATATTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATATTCCAAAGAATACATATATGTCCCGAAG
*
3622109 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
*
3622174 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TTCACACATATTCCAAAGAATACATATATGTCCCGAAG
*
3622212 TACCACATA
1 GACCACATA
3622221 GACCCTCGAC
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.27
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGAC
TTCACACATATTCCAAAGAATACATATATGTCCCGAAG
Found at i:3627659 original size:23 final size:23
Alignment explanation
Indices: 3627633--3627696 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
3627623 CAGCTCATAT
3627633 AATTGCACCGAAGTGCCAAGTAG
1 AATTGCACCGAAGTGCCAAGTAG
* * **
3627656 AATTACACCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCAAGTAG
*
3627679 AATTGCACCGTAGTGCCA
1 AATTGCACCGAAGTGCCA
3627697 TATAATAATG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.19
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCAAGTAG
Found at i:3627900 original size:103 final size:103
Alignment explanation
Indices: 3627721--3627929 Score: 355
Period size: 103 Copynumber: 2.0 Consensus size: 103
3627711 TTTGGACTAT
* * * *
3627721 ATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGATTTGACA
1 ATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACA
3627786 CATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
66 CATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
*
3627824 ATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCACA
1 ATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACA
* *
3627889 CATGTTCCAAAGAATACATATATGTCCTGAAGGATCAC
66 CATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
3627927 ATA
1 ATA
3627930 GACCCTCGAC
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (103 bp):
ATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCACA
CATGTTCCAAAGAATACATATATGTCCCGAAGGACCAC
Found at i:3630258 original size:24 final size:23
Alignment explanation
Indices: 3630229--3630275 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 23
3630219 AAAAATATTA
3630229 TAATCAAATAAAATATAATTAAAT
1 TAATCAAATAAAATA-AATTAAAT
*
3630253 TAATCAAATTAAATAAATTAAAT
1 TAATCAAATAAAATAAATTAAAT
3630276 AAATGAAGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.34
Consensus pattern (23 bp):
TAATCAAATAAAATAAATTAAAT
Found at i:3636925 original size:22 final size:19
Alignment explanation
Indices: 3636876--3636925 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 19
3636866 TTAAGGGCAA
3636876 AAAATAAAAAATATTAAAT
1 AAAATAAAAAATATTAAAT
**
3636895 AAACCAAAAATATATATAAGAT
1 AAAATAAAAA-ATAT-TAA-AT
3636917 AAAATAAAA
1 AAAATAAAA
3636926 TAAAAGGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
19 8 0.33
20 4 0.17
21 3 0.12
22 9 0.38
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (19 bp):
AAAATAAAAAATATTAAAT
Found at i:3638138 original size:3 final size:3
Alignment explanation
Indices: 3638130--3638174 Score: 72
Period size: 3 Copynumber: 14.7 Consensus size: 3
3638120 GTAATTAACA
*
3638130 AAT AAT AAT AAT AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
3638175 ATAAATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3638157 original size:19 final size:19
Alignment explanation
Indices: 3638129--3638174 Score: 76
Period size: 19 Copynumber: 2.5 Consensus size: 19
3638119 TGTAATTAAC
3638129 AAATAATAATAATAATAAT
1 AAATAATAATAATAATAAT
*
3638148 AAATATTAATAATAATAAT
1 AAATAATAATAATAATAAT
3638167 -AATAATAA
1 AAATAATAA
3638175 ATAAATAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
AAATAATAATAATAATAAT
Found at i:3638158 original size:25 final size:25
Alignment explanation
Indices: 3638130--3638177 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
3638120 GTAATTAACA
3638130 AATAATAATAATAATAATAAATATT
1 AATAATAATAATAATAATAAATATT
3638155 AATAATAATAATAATAATAAATA
1 AATAATAATAATAATAATAAATA
3638178 AATAAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AATAATAATAATAATAATAAATATT
Found at i:3638195 original size:25 final size:27
Alignment explanation
Indices: 3638130--3638195 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
3638120 GTAATTAACA
*
3638130 AATAATAATAATAATAATAAATATTAAT
1 AATAATAAAAATAATAATAAATA-TAAT
*
3638158 AATAATAATAATAATAAATAAATA-AAT
1 AATAATAAAAATAAT-AATAAATATAAT
3638185 -ATAA-AAAAATA
1 AATAATAAAAATA
3638196 TTTTTTTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
25 6 0.17
26 4 0.11
27 3 0.08
28 15 0.42
29 8 0.22
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (27 bp):
AATAATAAAAATAATAATAAATATAAT
Found at i:3638280 original size:43 final size:40
Alignment explanation
Indices: 3638203--3638297 Score: 120
Period size: 43 Copynumber: 2.3 Consensus size: 40
3638193 ATATTTTTTT
* **
3638203 AAACTATATAATATAAAATTTTTAAAATGTTTTTTTTCAA
1 AAACTATATAATATAAAATTTTAAAAATGTTTTTTTAAAA
3638243 AAACTATATATTATATATAAATTTTCAAAAATG-TTTTTTAAAA
1 AAACTATATA--ATATA-AAATTTT-AAAAATGTTTTTTTAAAA
3638286 AAACTATATAAT
1 AAACTATATAAT
3638298 TTTCAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
40 10 0.21
41 2 0.04
42 5 0.10
43 25 0.52
44 6 0.12
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (40 bp):
AAACTATATAATATAAAATTTTAAAAATGTTTTTTTAAAA
Found at i:3638345 original size:38 final size:37
Alignment explanation
Indices: 3638236--3638560 Score: 326
Period size: 38 Copynumber: 8.6 Consensus size: 37
3638226 AAAATGTTTT
*
3638236 TTTTCAAAAACTATATATTATATATAAATTTTCAAAAATG
1 TTTT-AAAAACTATATA-T-TATATAAGTTTTCAAAAATG
* *
3638276 TTTTTTAAAA--A-A-ACTATATAA-TTTTCAAAAAATG
1 -TTTTAAAAACTATATATTATATAAGTTTTC-AAAAATG
*
3638310 TTTTCAAAAATTATATATTATATAAGTTTTCAAAAATG
1 TTTT-AAAAACTATATATTATATAAGTTTTCAAAAATG
*
3638348 TTTTCAAAAACTATATATTATATAAGTTTTTAAAAAATG
1 TTTT-AAAAACTATATATTATATAAG-TTTTCAAAAATG
3638387 TTTTAAAAAACTATATATTATATAAGTTTTC-AAAATG
1 TTTT-AAAAACTATATATTATATAAGTTTTCAAAAATG
*
3638424 ATTTTAAAAACTATATATTATATATA-TTTTCTAAAATG
1 -TTTTAAAAACTATATATTATATA-AGTTTTCAAAAATG
* * *
3638462 TTTTAAAAATTATATATTATAT-AGTTTTCTAAAGTG
1 TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
* * *
3638498 TTTTAAAATCTATATATTATATATATATTTTCAAAAAACCG
1 TTTTAAAAACTATATATTATATA-A-GTTTTC-AAAAA-TG
* *
3638539 -TTTACAAACTATATAATATATA
1 TTTTAAAAACTATATATTATATA
3638561 TATAGATATA
Statistics
Matches: 248, Mismatches: 19, Indels: 35
0.82 0.06 0.12
Matches are distributed among these distances:
33 9 0.04
34 18 0.07
35 1 0.00
36 33 0.13
37 53 0.21
38 57 0.23
39 46 0.19
40 26 0.10
41 5 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATAAGTTTTCAAAAATG
Found at i:3639335 original size:84 final size:83
Alignment explanation
Indices: 3639190--3640271 Score: 1213
Period size: 84 Copynumber: 12.9 Consensus size: 83
3639180 TTTGACATGC
** * * * * * * * *
3639190 CCTTGAGCTGAATGTAATCGAAATCGAAGGTC-TTTGATGACAAATAACCCTTCTCGACTTGAGC
1 CCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGT
3639254 TATGCTGCAAATGATGTG
66 TATGCTGCAAATGATGTG
* * * * *
3639272 CCTTGAAGGTGAGCGTAGTCGAACTCGAAGATCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAG
1 CCTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3639337 TTAT-CTGCAAATGATGTA
65 TTATGCTGCAAATGATGTG
* * * * * *
3639355 CCTGGGGGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGGTAACCCTTCTAGCCTTGAG
1 CCT-TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* *
3639420 TTATGTTGCAAATGATATG
65 TTATGCTGCAAATGATGTG
* ** * *
3639439 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTT-TATGGCAGATAGTCTTTCTCGACTTAA
1 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGT-TGGCAGATAACCCTTCTAGACTTAA
*
3639503 GATATGCTGCAAATGATGTG
64 GTTATGCTGCAAATGATGTG
* * * *
3639523 CCTTAGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGATGGCTGATAACCCTTCTCGACTTAAG
1 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3639588 CTATGCTGCAAATGATGTG
65 TTATGCTGCAAATGATGTG
* * * *
3639607 CCTTTGAGCTGAGCGTAATCGAACTCGAAGGACTTTTGTTGGTAGATAACCCTTCTAGCCTTAAG
1 CC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
3639672 TTATACTGTAAATGATGTT
65 TTATGCTGCAAATGATGTG
* * * *
3639691 CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGATGGCAGATAACCCTTATCGACTTAAG
1 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
3639756 ATATGATGAAAATGATGTG
65 TTATGCTGCAAATGATGTG
* *
3639775 CCTTTGAGCTGAGCATAGTCGAACTCGTAA-GTCTTTTGTTGGCAGATAACCCTTCTAG-CATTG
1 CC-TTGAGCTGAGCGTAGTCGAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTAGAC-TTA
* *
3639838 AGTTATGCTACAAATGATATG
63 AGTTATGCTGCAAATGATGTG
* * *
3639859 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAG
1 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3639924 TTATGCTGTAAATGATGTG
65 TTATGCTGCAAATGATGTG
* ** * *
3639943 CCTTTGAGTTGA-CGTAGTCGAACTCGAAGGTCTTTTGACGGCAGATAGCCCTTCTCGACTTAAG
1 CC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3640007 CTATGCTGCAAATGATGTG
65 TTATGCTGCAAATGATGTG
* * * * * * *
3640026 CCTCTGAGCTGAGCATAGTTGAACTCGAAGGTCTTTTGATGGTAGTTAACCCTTCTTGACTTCAG
1 CCT-TGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3640091 TTATGCTGCAAATAATGTG
65 TTATGCTGCAAATGATGTG
* * * * *
3640110 CCTTTGAGCTGAGCGTAGTCAAACTTGAAGGTCTTTTGTTAGCAGATAACCCTTCTAGCCTTGAG
1 CC-TTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
* * *
3640175 TTATGTTACAAATGATATG
65 TTATGCTGCAAATGATGTG
* * * * * *
3640194 CTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCTAGCCTTGAG
1 CCTT-GAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAG
*
3640259 TTATGCTACAAAT
65 TTATGCTGCAAAT
3640272 AAATAAAGAA
Statistics
Matches: 853, Mismatches: 127, Indels: 38
0.84 0.12 0.04
Matches are distributed among these distances:
82 6 0.01
83 181 0.21
84 656 0.77
85 10 0.01
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (83 bp):
CCTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGACTTAAGT
TATGCTGCAAATGATGTG
Found at i:3640047 original size:503 final size:503
Alignment explanation
Indices: 3639162--3640247 Score: 1466
Period size: 503 Copynumber: 2.2 Consensus size: 503
3639152 TTTTTCTCGA
* * * * * *
3639162 CTTAAGCTATACTATAAATTTGACATGCCCTT-GAGCTGAATGTAATCGAAATCGAAGGTC-TTT
1 CTTAAGTTATACTACAAA--TGATATG-CCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTT
* * * * * * * *
3639225 GATGACAAATAACCCTTCTCGACTTGAGCTATGCTGCAAATGATGTGCCTTGAAGGTGAGCGTAG
63 GATGGCAAATAACCCTTATCGACTTAAGATATGATGAAAATGATGTGCCTTGAAGCTGAGCATAG
* * * *
3639290 TCGAACTCGAAGATCTTTTGTTGGTAGATAACCCTTCTAGCCTTGAGTTATCTGCAAATGATGTA
128 TCGAACTCGAAGATCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATCTACAAATGATATA
* * * * *
3639355 CCTGGGGGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGTTGGCAGGTAACCCTTCTAGCCTTGAG
193 CCTGGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAG
* * *
3639420 TTATGTTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTTATGGCAGA
258 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGACGGCAGA
* * *
3639485 TAGTCTTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTAGAGCTGAGCGTAGTTGAACTCG
323 TAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTTGAACTCG
*
3639550 AAGGTCTTTTGATGGCT-GATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTTGA
388 AAGGTCTTTTGATGG-TAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTTGA
* * *
3639614 GCTGAGCGTAATCGAACTCGAAGGACTTTTGTTGGTAGATAACCCTTCTAGC
452 GCTGAGCGTAATCAAACTCGAAGGACTTTTGTTAGCAGATAACCCTTCTAGC
** * *
3639666 CTTAAGTTATACTGTAAATGATGTTCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGAT
1 CTTAAGTTATACTACAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGAT
*
3639731 GGCAGATAACCCTTATCGACTTAAGATATGATGAAAATGATGTGCCTTTG-AGCTGAGCATAGTC
66 GGCAAATAACCCTTATCGACTTAAGATATGATGAAAATGATGTGCC-TTGAAGCTGAGCATAGTC
*
3639795 GAACTCGTAAG-TCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGCTACAAATGATATG
130 GAACTCG-AAGATCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTAT-CTACAAATGATATA
* * * *
3639859 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAG
193 CCTGGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAG
* * * * *
3639924 TTATGCTGTAAATGATGTGCCTTTGAGTTGA-CGTAGTCGAACTCGAAGGTCTTTTGACGGCAGA
258 TTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGACGGCAGA
*
3639988 TAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCT-GAGCTGAGCATAGTTGAACTC
323 TAGCCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCT-TAGAGCTGAGCATAGTTGAACTC
* * * *
3640052 GAAGGTCTTTTGATGGTAGTTAACCCTTCTTGACTTCAGTTATGCTGCAAATAATGTGCCTTTGA
387 GAAGGTCTTTTGATGGTAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTTGA
* * *
3640117 GCTGAGCGTAGTCAAACTTGAAGGTCTTTTGTTAGCAGATAACCCTTCTAGC
452 GCTGAGCGTAATCAAACTCGAAGGACTTTTGTTAGCAGATAACCCTTCTAGC
* ** * * * * *
3640169 CTTGAGTTATGTTACAAATGATATGCTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTT
1 CTTAAGTTATACTACAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGAT
*
3640234 GGCATATAACCCTT
66 GGCAAATAACCCTT
3640248 CTAGCCTTGA
Statistics
Matches: 508, Mismatches: 67, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
501 4 0.01
502 30 0.06
503 358 0.70
504 116 0.23
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (503 bp):
CTTAAGTTATACTACAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGGTCTTTTGAT
GGCAAATAACCCTTATCGACTTAAGATATGATGAAAATGATGTGCCTTGAAGCTGAGCATAGTCG
AACTCGAAGATCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATCTACAAATGATATACCT
GGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAGTTA
TGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTTGACGGCAGATAG
CCCTTCTCGACTTAAGATATGCTGCAAATGATGTGCCTTAGAGCTGAGCATAGTTGAACTCGAAG
GTCTTTTGATGGTAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATAATGTGCCTTTGAGCTG
AGCGTAATCAAACTCGAAGGACTTTTGTTAGCAGATAACCCTTCTAGC
Found at i:3640265 original size:335 final size:334
Alignment explanation
Indices: 3639190--3640249 Score: 1342
Period size: 335 Copynumber: 3.2 Consensus size: 334
3639180 TTTGACATGC
** * * * * *
3639190 CCTT-GAGCTGAATGTAATCGAAATCGAAGGTC-TTTGATGACAAATAACCCTTCTCGACTTGAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCATATAACCCTTCTCGACTTAAG
* *
3639253 CTATGCTGCAAATGATGTGCC-TTGAAGGTGAGCGTAGTCGAACTCGAAGATCTTTTGTTGGTAG
66 CTATGCTGCAAATGATGTGCCTTTG-AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAG
* * * *
3639317 ATAACCCTTCTAGCCTTGAGTTATCTGCAAATGATGTACCTGGGGGCTGAGCGTAGTCAAACTCG
130 ATAACCCTTCTAGCCTTAAGTTATCTGCAAATGATGTACCT-TGAGCTGAGCGTAGTCGAACTCG
* * * * * * *
3639382 AAGGTCTTTTGTTGGCAGGTAACCCTTCTAGCCTTGAGTTATGTTGCAAATGATATGCCTTGGAG
194 AAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATGTGCCTTTGAG
* ** * * * * *
3639447 CTGAGCGTAGTCGAACTCAAAGGTCTTTT-TATGGCAGATAGTCTTTCTCGACTTAAGATATGCT
259 CTGAGCGTAGTCGAACTCGAAGGTCTTTTGT-TGGCAGATAACCCTTCTAGCCTTGAGTTATGCT
* *
3639511 GCAAATGATGTG
323 ACAAATGATATG
* *
3639523 CCTTAGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTTGATGGC-TGATAACCCTTCTCGACTTAA
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCAT-ATAACCCTTCTCGACTTAA
* *
3639587 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAATCGAACTCGAAGGACTTTTGTTGGTAG
65 GCTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAG
* * *
3639652 ATAACCCTTCTAGCCTTAAGTTATACTGTAAATGATGTTCCTTGGAGCTGAGTGTAGTCGAACTC
130 ATAACCCTTCTAGCCTTAAGTTAT-CTGCAAATGATGTACCTT-GAGCTGAGCGTAGTCGAACTC
* * * *
3639717 GAAGGTCTTTTGATGGCAGATAACCCTTATCGACTTAAGATATGATGAAAATGATGTGCCTTTGA
193 GAAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATGTGCCTTTGA
* *
3639782 GCTGAGCATAGTCGAACTCGTAA-GTCTTTTGTTGGCAGATAACCCTTCTAGCATTGAGTTATGC
258 GCTGAGCGTAGTCGAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGC
3639846 TACAAATGATATG
322 TACAAATGATATG
* *
3639859 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCAGATAGCCCTTCTCGACTTAAG
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCATATAACCCTTCTCGACTTAAG
* * * ** *
3639924 TTATGCTGTAAATGATGTGCCTTTGAGTTGA-CGTAGTCGAACTCGAAGGTCTTTTGACGGCAGA
66 CTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGA
* * * * * * *
3639988 TAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTCTGAGCTGAGCATAGTTGAACTCG
131 TAACCCTTCTAGCCTTAAGTTAT-CTGCAAATGATGTACCT-TGAGCTGAGCGTAGTCGAACTCG
* * * * * *
3640053 AAGGTCTTTTGATGGTAGTTAACCCTTCTTGACTTCAGTTATGCTGCAAATAATGTGCCTTTGAG
194 AAGGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATGTGCCTTTGAG
* * * *
3640118 CTGAGCGTAGTCAAACTTGAAGGTCTTTTGTTAGCAGATAACCCTTCTAGCCTTGAGTTATGTTA
259 CTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTA
3640183 CAAATGATATG
324 CAAATGATATG
* * * *
3640194 CTTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCT
1 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCATATAACCCTTCT
3640250 AGCCTTGAGT
Statistics
Matches: 631, Mismatches: 85, Indels: 20
0.86 0.12 0.03
Matches are distributed among these distances:
333 4 0.01
334 25 0.04
335 360 0.57
336 239 0.38
337 3 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (334 bp):
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGATGGCATATAACCCTTCTCGACTTAAG
CTATGCTGCAAATGATGTGCCTTTGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGTAGA
TAACCCTTCTAGCCTTAAGTTATCTGCAAATGATGTACCTTGAGCTGAGCGTAGTCGAACTCGAA
GGTCTTTTGATGGCAGATAACCCTTCTAGACTTAAGTTATGATGCAAATGATGTGCCTTTGAGCT
GAGCGTAGTCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTACA
AATGATATG
Found at i:3641573 original size:95 final size:95
Alignment explanation
Indices: 3641358--3641619 Score: 332
Period size: 95 Copynumber: 2.7 Consensus size: 95
3641348 AGCGAGCTAG
* *
3641358 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTCAAGAGGGACAGCTCAA--TATTATTGTATAGA
1 ATCCATAAAGTCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCT-TTATTG--T--A
* * *
3641421 TATTATAATCACCTTTATCAGGCTAGCTGTATATT
61 TATTATAACCACATTTATCAGGCTAGCTGAATATT
* * *
3641456 ATCCATAAAG-CCGGGACATTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATT
1 ATCCATAAAGTCGGGGA-GTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATT
* *
3641520 ATAACCACATTTATCATGCTAGCTGAATTTT
65 ATAACCACATTTATCAGGCTAGCTGAATATT
* *
3641551 ATCCATAAAGTCGGGGAGTTTAACCAATTGCTCTAGAGGGATAGCTCAAGCTTTATTTTATATAT
1 ATCCATAAAGTCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATAT-T
3641616 ATAA
65 ATAA
3641620 TATTACAATA
Statistics
Matches: 144, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
95 83 0.58
96 10 0.07
97 5 0.03
98 39 0.27
99 6 0.04
100 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (95 bp):
ATCCATAAAGTCGGGGAGTTTAACCAATTGCTCTAGAGGGACAGCTCAAGCTTTATTGTATATTA
TAACCACATTTATCAGGCTAGCTGAATATT
Found at i:3645100 original size:9 final size:10
Alignment explanation
Indices: 3645067--3645100 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
3645057 ATAAATAAAT
3645067 AAAAAGAAAG
1 AAAAAGAAAG
3645077 AAAAAGAAAG
1 AAAAAGAAAG
*
3645087 AAAAA-AAGG
1 AAAAAGAAAG
3645096 AAAAA
1 AAAAA
3645101 TAAATCAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 8 0.35
10 15 0.65
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:3645155 original size:20 final size:22
Alignment explanation
Indices: 3645130--3645169 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
3645120 AAAAAATATA
3645130 AAAAATATAT-TAA-ATAAACC
1 AAAAATATATATAAGATAAACC
3645150 AAAAATATATATAAGATAAA
1 AAAAATATATATAAGATAAA
3645170 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
21 3 0.17
22 5 0.28
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (22 bp):
AAAAATATATATAAGATAAACC
Found at i:3645159 original size:22 final size:21
Alignment explanation
Indices: 3645129--3645169 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
3645119 TAAAAAATAT
3645129 AAAAAATATATTAA-ATAAACC
1 AAAAAATATA-TAAGATAAACC
3645150 AAAAATATATATAAGATAAA
1 AAAAA-ATATATAAGATAAA
3645170 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
AAAAAATATATAAGATAAACC
Found at i:3645175 original size:22 final size:20
Alignment explanation
Indices: 3645130--3645175 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
3645120 AAAAAATATA
*
3645130 AAAAATATATTAAATAAACC
1 AAAAATATATTAAATAAAAC
*
3645150 AAAAATATATATAAGATAAAAT
1 AAAAATATAT-TAA-ATAAAAC
3645172 AAAA
1 AAAA
3645176 TAAAAGGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 10 0.45
21 3 0.14
22 9 0.41
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (20 bp):
AAAAATATATTAAATAAAAC
Found at i:3645234 original size:2 final size:2
Alignment explanation
Indices: 3645227--3645264 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3645217 ATAATAAATG
3645227 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3645265 ATTAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3647153 original size:63 final size:62
Alignment explanation
Indices: 3647046--3647167 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 62
3647036 GTCGAGGGTT
* * *
3647046 TACCTATGTTCTACGGAACATATGGACAGAATTACCTATGTCTTTCGGTACATATGGACATTA
1 TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTT-GGGACATATGGACATTA
* *
3647109 TACCTATGTTCTAAGGAACATATGGACAG-TTTACCTAGGTTCTTTGGGACCTATGGACA
1 TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGG-TCTTTGGGACATATGGACA
3647168 GTTGCTGAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 20 0.38
63 33 0.62
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (62 bp):
TACCTATGTTCTAAGGAACATATGGACAGAATTACCTAGGTCTTTGGGACATATGGACATTA
Done.