Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 144 of 206
Found at i:44053384 original size:181 final size:180
Alignment explanation
Indices: 44053020--44053478 Score: 598
Period size: 181 Copynumber: 2.5 Consensus size: 180
44053010 GGATTAGTAG
* * * * * * *
44053020 CTTCAATCTGCTCCACTACAACTTTTGGGAGATAAGATTGGTATCTTCAACCTGCTCCACTACAA
1 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAA
* * * *
44053085 CTTCAGGGAGATAAGGTTTGTGGCT-TCGATCTGATCCACTGTAACTTCAGGGAGATAAGATCTG
66 CTTCAGGGAGATAAGGTTT-T--ATAT-GATCTGATCCACTGCAACTTCAGAGAGATAAGATCTA
* * *
44053149 CAATTTATAGCTTCAATCCATTCCACTACAATTTCAGGGAAATAAGATTCGCTAT
127 CAATTAATAGCTTCAA-CCATTCCACTACAACTTAAGGGAAATAAGATTCGCTAT
* * * *
44053204 GTTCAGTTTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTACTCCATTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAA
* * *
44053269 CTTCAAGGAGATAAGGTTTTATATGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACAAT
66 CTTCAGGGAGATAAGGTTTTATATGATCTGATCCACTGCAACTTCAGAGAGATAAGATCTACAAT
*
44053334 TAATAGCTTCAA-CATGTTCCACTGCAACTTAAGGGAAATAAGATTCGCTAT
131 TAATAGCTTCAACCA--TTCCACTACAACTTAAGGGAAATAAGATTCGCTAT
* * *
44053385 CTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGCTCCACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAA
* *
44053450 CTTTAGGGAGATAAGGTTTGATATGATCT
66 CTTCAGGGAGATAAGGTTTTATATGATCT
44053479 TCAATCCATC
Statistics
Matches: 240, Mismatches: 32, Indels: 9
0.85 0.11 0.03
Matches are distributed among these distances:
179 2 0.01
181 164 0.68
182 1 0.00
183 1 0.00
184 72 0.30
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (180 bp):
CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTGCTCCACTGCAA
CTTCAGGGAGATAAGGTTTTATATGATCTGATCCACTGCAACTTCAGAGAGATAAGATCTACAAT
TAATAGCTTCAACCATTCCACTACAACTTAAGGGAAATAAGATTCGCTAT
Found at i:44053411 original size:96 final size:92
Alignment explanation
Indices: 44053114--44053421 Score: 285
Period size: 96 Copynumber: 3.3 Consensus size: 92
44053104 GTGGCTTCGA
* * *
44053114 TCTGATCCACTGTAACTTCAGGGAGATAAGATCTGCAATTTATAGCTTCAATCCA-TTCCACTAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-CAA-TTATAGCTTCAA--CATTTCCACTGC
* *
44053178 AATTTCAGGGAAATAAGATTCGCTATGTTCAG
62 AACTTAAGGGAAATAAGATTCGCTAT-TTCAG
* * * * * *
44053210 TTTGCTCCACTGCAACTTTAGGGAGATAAGA-CT--AGTA-A-CTTCAACCTACTCCATTGCAAC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCAATTATAGCTTCAACAT-TTCCACTGCAAC
* * * * *
44053270 TTCAA-GGAGATAAGGTT--TTATATGA-
65 TT-AAGGGAAATAAGATTCGCTATTTCAG
* *
44053295 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTACAATTAATAGCTTCAACATGTTCCACTGCA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATCT-CAATT-ATAGCTTCAACAT-TTCCACTGCA
44053360 ACTTAAGGGAAATAAGATTCGCTATCTTCAG
63 ACTTAAGGGAAATAAGATTCGCTAT-TTCAG
44053391 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
44053422 CTTGTAACTT
Statistics
Matches: 165, Mismatches: 32, Indels: 30
0.73 0.14 0.13
Matches are distributed among these distances:
85 27 0.16
86 4 0.02
87 4 0.02
89 28 0.17
90 3 0.02
91 5 0.03
92 31 0.19
94 3 0.02
95 4 0.02
96 56 0.34
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (92 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATCTCAATTATAGCTTCAACATTTCCACTGCAACT
TAAGGGAAATAAGATTCGCTATTTCAG
Found at i:44053448 original size:44 final size:43
Alignment explanation
Indices: 44052987--44053464 Score: 225
Period size: 44 Copynumber: 10.6 Consensus size: 43
44052977 TTTAATCCGA
** * *
44052987 TCCACTGCAACTTCACAGAGATAGGATTAGTAGCTTCAA-TCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GTAACTTCAACT-TGC
* ** * *
44053031 TCCACTACAACTTTTGGGAGATAAGATTGGTATCTTCAACCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-GTAACTTCAACTTGC
* * ** * *
44053075 TCCACTACAACTTCAGGGAGATAAGGTTTGTGGCTTCGA-TCTGA
1 TCCACTGCAACTTCAGGGAGATAA-GATTGTAACTTCAACT-TGC
* *
44053119 TCCACTGTAACTTCAGGGAGATAAGATCTGCAATTTATAGCTTCAA--TCC
1 TCCACTGCAACTTCAGGGAGATAAGAT-TG-----TA-A-CTTCAACTTGC
* * * ** **
44053168 ATTCCACTACAATTTCAGGGAAATAAGATTCGCTATGTTCAGTTTGC
1 --TCCACTGCAACTTCAGGGAGATAAGATT-G-TAACTTCAACTTGC
* * * *
44053215 TCCACTGCAACTTTAGGGAGATAAGACTAGTAACTTCAACCTAC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTCAACTTGC
* * * * * *
44053259 TCCATTGCAACTTCAAGGAGATAAGGTT-TTA-TATGATC-TGC
1 TCCACTGCAACTTCAGGGAGATAAGATTGTAACT-TCAACTTGC
* * * * *
44053300 TCTACTGCAACTTCAGAGAGATAAGATCTACAATTAATAGCTTCAACATGT
1 TCCACTGCAACTTCAGGGAGATAAGAT-T----GT-A-A-CTTCAACTTGC
* * * *
44053351 TCCACTGCAACTTAAGGGAAATAAGATTCGCTATCTTC-AGTCTGC
1 TCCACTGCAACTTCAGGGAGATAAGATT-G-TAACTTCAACT-TGC
44053396 TCCACTGCAACTTCAGGGAGATAAGACTTGTAACTTCAACTTGC
1 TCCACTGCAACTTCAGGGAGATAAGA-TTGTAACTTCAACTTGC
*
44053440 TCCACTGCAACTTTAGGGAGATAAG
1 TCCACTGCAACTTCAGGGAGATAAG
44053465 GTTTGATATG
Statistics
Matches: 323, Mismatches: 78, Indels: 66
0.69 0.17 0.14
Matches are distributed among these distances:
41 25 0.08
42 6 0.02
43 3 0.01
44 153 0.47
45 63 0.20
46 3 0.01
47 6 0.02
48 1 0.00
49 3 0.01
50 5 0.02
51 55 0.17
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (43 bp):
TCCACTGCAACTTCAGGGAGATAAGATTGTAACTTCAACTTGC
Found at i:44053452 original size:89 final size:88
Alignment explanation
Indices: 44053170--44053464 Score: 276
Period size: 89 Copynumber: 3.3 Consensus size: 88
44053160 TTCAATCCAT
* * * * *
44053170 TCCACTACAATTTCAGGGAAATAAGATTCGCTATGTTCAGTTTGCTCCACTGCAACTTTAGGGAG
1 TCCACTGCAACTTAAGGGAAATAAGATTCGCTAT-TTCAGTCTGCTCCACTGCAACTTCAGGGAG
* * *
44053235 ATAAGACTAGTAACTTCAACCTAC
65 ATAAGACTTGTAACTTCAACATGC
* * * * * * * *
44053259 TCCATTGCAACTTCAA-GGAGATAAGGTT--TTATATGA-TCTGCTCTACTGCAACTTCAGAGAG
1 TCCACTGCAACTT-AAGGGAAATAAGATTCGCTATTTCAGTCTGCTCCACTGCAACTTCAGGGAG
*
44053320 ATAAGATCTACAAT-TAATAGCTTCAACATGT
65 ATAAGA-CT----TGT-A-A-CTTCAACATGC
44053351 TCCACTGCAACTTAAGGGAAATAAGATTCGCTATCTTCAGTCTGCTCCACTGCAACTTCAGGGAG
1 TCCACTGCAACTTAAGGGAAATAAGATTCGCTAT-TTCAGTCTGCTCCACTGCAACTTCAGGGAG
*
44053416 ATAAGACTTGTAACTTCAACTTGC
65 ATAAGACTTGTAACTTCAACATGC
* *
44053440 TCCACTGCAACTTTAGGGAGATAAG
1 TCCACTGCAACTTAAGGGAAATAAG
44053465 GTTTGATATG
Statistics
Matches: 162, Mismatches: 29, Indels: 30
0.73 0.13 0.14
Matches are distributed among these distances:
85 27 0.17
86 4 0.02
87 3 0.02
89 53 0.33
90 3 0.02
91 5 0.03
92 31 0.19
94 3 0.02
95 4 0.02
96 29 0.18
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.29
Consensus pattern (88 bp):
TCCACTGCAACTTAAGGGAAATAAGATTCGCTATTTCAGTCTGCTCCACTGCAACTTCAGGGAGA
TAAGACTTGTAACTTCAACATGC
Found at i:44054366 original size:5 final size:5
Alignment explanation
Indices: 44054350--44054403 Score: 60
Period size: 5 Copynumber: 10.8 Consensus size: 5
44054340 GGGCTCTCTT
44054350 TTTTC -TTT- TTTTC TTTTC TTTTTC TTCTT- TTTTC TTTTTC TTTTC
1 TTTTC TTTTC TTTTC TTTTC -TTTTC TT-TTC TTTTC -TTTTC TTTTC
44054395 TTTTC TTTT
1 TTTTC TTTT
44054404 TTATTTTATG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
4 8 0.19
5 23 0.53
6 12 0.28
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:44054380 original size:22 final size:22
Alignment explanation
Indices: 44054348--44054405 Score: 75
Period size: 21 Copynumber: 2.6 Consensus size: 22
44054338 TTGGGCTCTC
44054348 TTTTTTCTTTTTTTC-TTTTCT
1 TTTTTTCTTTTTTTCTTTTTCT
44054369 TTTTCTTC-TTTTTTCTTTTTCTT
1 TTTT-TTCTTTTTTTCTTTTTC-T
44054392 TTCTTTTCTTTTTT
1 TT-TTTTCTTTTTT
44054406 ATTTTATGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
21 11 0.34
22 8 0.25
23 6 0.19
24 7 0.22
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (22 bp):
TTTTTTCTTTTTTTCTTTTTCT
Found at i:44054384 original size:16 final size:16
Alignment explanation
Indices: 44054346--44054404 Score: 81
Period size: 16 Copynumber: 3.9 Consensus size: 16
44054336 CCTTGGGCTC
44054346 TCTTTTTTCTTTTT-T
1 TCTTTTTTCTTTTTCT
44054361 TC--TTTTCTTTTTCT
1 TCTTTTTTCTTTTTCT
44054375 TCTTTTTTCTTTTTCT
1 TCTTTTTTCTTTTTCT
44054391 T-TTCTTTTCTTTTT
1 TCTT-TTTTCTTTTT
44054405 TATTTTATGA
Statistics
Matches: 40, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.25
14 3 0.08
15 4 0.10
16 23 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TCTTTTTTCTTTTTCT
Found at i:44054399 original size:32 final size:29
Alignment explanation
Indices: 44054346--44054405 Score: 92
Period size: 27 Copynumber: 2.2 Consensus size: 29
44054336 CCTTGGGCTC
44054346 TCTTTTTTCTTTTTTTCTTTTCTTTTTCT
1 TCTTTTTTCTTTTTTTCTTTTCTTTTTCT
44054375 TCTTTTTTC--TTTTTCTTTTC-TTTTCT
1 TCTTTTTTCTTTTTTTCTTTTCTTTTTCT
44054401 T-TTTT
1 TCTTTT
44054406 ATTTTATGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.13
26 7 0.23
27 11 0.35
29 9 0.29
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (29 bp):
TCTTTTTTCTTTTTTTCTTTTCTTTTTCT
Found at i:44054410 original size:22 final size:21
Alignment explanation
Indices: 44054348--44054410 Score: 72
Period size: 22 Copynumber: 2.9 Consensus size: 21
44054338 TTGGGCTCTC
*
44054348 TTTTTTCTTTTTTTCTTTTCTT
1 TTTTTTC-TTTTTTATTTTCTT
* *
44054370 TTTCTTCTTTTTTCTTTTTCTT
1 TTTTTTCTTTTTT-ATTTTCTT
44054392 TTCTTTTCTTTTTTATTTT
1 TT-TTTTCTTTTTTATTTT
44054411 ATGAAATATT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
21 6 0.17
22 19 0.54
23 10 0.29
ACGTcount: A:0.02, C:0.14, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTCTTTTTTATTTTCTT
Found at i:44054514 original size:14 final size:15
Alignment explanation
Indices: 44054491--44054523 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
44054481 ATCAACGCTT
*
44054491 TTCCAGATAAGG-CC
1 TTCCACATAAGGTCC
44054505 TTCCACATAAGGTCC
1 TTCCACATAAGGTCC
44054520 TTCC
1 TTCC
44054524 CTATTTGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.24, C:0.33, G:0.15, T:0.27
Consensus pattern (15 bp):
TTCCACATAAGGTCC
Found at i:44059891 original size:125 final size:125
Alignment explanation
Indices: 44059664--44059912 Score: 408
Period size: 125 Copynumber: 2.0 Consensus size: 125
44059654 AAGGTTTTTA
* * *
44059664 GGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTATAAAATCGCTTTTACCAG
1 GGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAG
* * *
44059729 GATGATTTATGAGAAGAATTTGTTAAATCGCGTCCACGTGGACGCACTTTTGCTACAGTT
66 GAAGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGTT
* *
44059789 GGTCCTGGAAGAAATAATTTTGAGTTGACATTTCTGAGCAAATAGTATAAAATTGCTTCTACCAG
1 GGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAG
* *
44059854 GAAGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
66 GAAGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGT
44059913 AGCATGTTTG
Statistics
Matches: 114, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
125 114 1.00
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (125 bp):
GGTCCTGGAAGAAATAATTTCGAGTTGACATTTCTGAGCAAATAGTATAAAATCGCTTCTACCAG
GAAGATTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCACTTTTGCTACAGTT
Found at i:44060254 original size:41 final size:41
Alignment explanation
Indices: 44060187--44060424 Score: 298
Period size: 41 Copynumber: 5.8 Consensus size: 41
44060177 CTTTCGGGGT
* * *
44060187 TTTAGCGGCATTTTTTGAGAAAGCGCCGCTAATGATCAGGCC
1 TTTAGCGGC-GTTTTTGAAAAAGCGCCGCTAATGATCAGGGC
*
44060229 TTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGATCAGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGGGC
* * *
44060270 TTTAGCGGCGTTTTTGGAAAAGCGCTGCTAATGATCAGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGGGC
** *
44060311 TTTAGCGGCGTTTTTGGGAAAGCGCCGCTAATGATCAGGGA
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGGGC
* *** *
44060352 TTTAGCAGCGTTTTTGGGGAAGCGCTGCTAAT-ACTCAGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGA-TCAGGGC
**
44060393 TTTAGCGGCGTTTTTGAAGTAGCGCCGCTAAT
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
44060425 TCTCTATTTT
Statistics
Matches: 177, Mismatches: 18, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
40 1 0.01
41 167 0.94
42 9 0.05
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGATCAGGGC
Found at i:44060417 original size:123 final size:124
Alignment explanation
Indices: 44060187--44060424 Score: 329
Period size: 123 Copynumber: 1.9 Consensus size: 124
44060177 CTTTCGGGGT
* * *
44060187 TTTAGCGGCATTTTTTGAGAAAGCGCCGCTAATGATCAGGCCTTTAGCGGCATTTTTGAAAAAGC
1 TTTAGCGGCAGTTTTTGAGAAAGCGCCGCTAATGATCAGGCATTTAGCAGCATTTTTGAAAAAGC
*
44060252 GCCGCTAATGATCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCTGCTAATGATCAGGGA
66 GCCGCTAATGATCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGATCAGGGA
* * * ***
44060311 TTTAGCGGC-GTTTTTGGGAAAGCGCCGCTAATGATCAGGGATTTAGCAGCGTTTTTGGGGAAGC
1 TTTAGCGGCAGTTTTTGAGAAAGCGCCGCTAATGATCAGGCATTTAGCAGCATTTTTGAAAAAGC
* *
44060375 GCTGCTAAT-ACTCAGGGCTTTAGCGGCGTTTTT-GAAGTAGCGCCGCTAAT
66 GCCGCTAATGA-TCAGGGCTTTAGCGGCGTTTTTGGAA-AAGCGCCGCTAAT
44060425 TCTCTATTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 5
0.85 0.10 0.04
Matches are distributed among these distances:
122 4 0.04
123 87 0.87
124 9 0.09
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (124 bp):
TTTAGCGGCAGTTTTTGAGAAAGCGCCGCTAATGATCAGGCATTTAGCAGCATTTTTGAAAAAGC
GCCGCTAATGATCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGATCAGGGA
Found at i:44062280 original size:13 final size:13
Alignment explanation
Indices: 44062256--44062280 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
44062246 CTGCAAGAAA
44062256 AGGGGGAAAGATG
1 AGGGGGAAAGATG
44062269 AGGGGGAAAGAT
1 AGGGGGAAAGAT
44062281 ATTTCAACAA
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:0.40, C:0.00, G:0.52, T:0.08
Consensus pattern (13 bp):
AGGGGGAAAGATG
Found at i:44063523 original size:32 final size:33
Alignment explanation
Indices: 44063487--44063551 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
44063477 CTGGAATTTG
*
44063487 TTTATTTGTAATTTGTTAT-TTTTCTGTGTTTT
1 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
44063519 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
1 TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
44063552 GCTTATAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 19 0.61
33 12 0.39
ACGTcount: A:0.12, C:0.03, G:0.15, T:0.69
Consensus pattern (33 bp):
TTTATTTGTAATTTGTTATGTTTTCTGGGTTTT
Found at i:44066103 original size:86 final size:85
Alignment explanation
Indices: 44065963--44066192 Score: 247
Period size: 86 Copynumber: 2.7 Consensus size: 85
44065953 AGTTATGCTT
* *
44065963 TTTAGTGGCGTTTGT-GAAAAAGCGTCGCTAAAAGT-TAATGTTATAGCGGCGTTTTTA-ATAGA
1 TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCT-ATGTTATAGCGGCGTTTTTAGAGA-A
* *
44066025 GGTGCCGCTAAAGGTCATGAG-C
64 AGCGCCGCTAAAGGTCATG-GTC
* *
44066047 TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCT-TGTTCTTTAGCGGCGTTTTTAGGGAA
1 TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTATG-T-TATAGCGGCGTTTTTAGAGAA
*
44066111 AGCGCCGCTAAAGGTCCTGGTC
64 AGCGCCGCTAAAGGTCATGGTC
* * * * * *
44066133 TTTAGCGGCGTTTGTGGGAAAAGCGCCGCTAAAGGTC-CTGGTATTAGTGGCGTTTTTAGA
1 TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTATGTTA-TAGCGGCGTTTTTAGA
44066193 AAAAAAACGC
Statistics
Matches: 124, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
84 18 0.15
85 35 0.28
86 70 0.56
87 1 0.01
ACGTcount: A:0.23, C:0.15, G:0.31, T:0.31
Consensus pattern (85 bp):
TTTAGTGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCTATGTTATAGCGGCGTTTTTAGAGAAAG
CGCCGCTAAAGGTCATGGTC
Found at i:44066185 original size:42 final size:43
Alignment explanation
Indices: 44066028--44066187 Score: 200
Period size: 43 Copynumber: 3.7 Consensus size: 43
44066018 TAATAGAGGT
* * *
44066028 GCCGCTAAAGGTCATGAG-CTTTAGTGGCGTTTGTGGAAAAAGC
1 GCCGCTAAAGGTCCTG-GTCTTTAGCGGCGTTTGTGGGAAAAGC
* * * *
44066071 GTCGCTAAAGGTCTTGTTCTTTAGCGGCGTTTTTAGGG-AAAGC
1 GCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGT-GGGAAAAGC
44066114 GCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
1 GCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
* *
44066157 GCCGCTAAAGGTCCTGGT-ATTAGTGGCGTTT
1 GCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTT
44066188 TTAGAAAAAA
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
42 14 0.14
43 86 0.84
44 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.33, T:0.29
Consensus pattern (43 bp):
GCCGCTAAAGGTCCTGGTCTTTAGCGGCGTTTGTGGGAAAAGC
Found at i:44067235 original size:25 final size:25
Alignment explanation
Indices: 44067207--44067390 Score: 173
Period size: 25 Copynumber: 7.9 Consensus size: 25
44067197 TCGTATAATC
44067207 TCTATTTTATTACATCAAATAAACT
1 TCTATTTTATTACATCAAATAAACT
44067232 TCTATTTTATTACATCAAAT-AA-T
1 TCTATTTTATTACATCAAATAAACT
** * *
44067255 ATC-A--AAATAAC-TCAAA-AAAAT
1 -TCTATTTTATTACATCAAATAAACT
44067276 TCTATTTTATTACATCAAATAAACT
1 TCTATTTTATTACATCAAATAAACT
44067301 TCTATTTTATTACATCAAAT-AA-T
1 TCTATTTTATTACATCAAATAAACT
** * *
44067324 ATC-A--AAATAAC-TC-AA-AAATT
1 -TCTATTTTATTACATCAAATAAACT
44067344 TCTATTTTATTACATCAAATAAACT
1 TCTATTTTATTACATCAAATAAACT
44067369 TCTATTTTATTACATCAAATAA
1 TCTATTTTATTACATCAAATAA
44067391 TATCAAAATA
Statistics
Matches: 128, Mismatches: 14, Indels: 34
0.73 0.08 0.19
Matches are distributed among these distances:
19 6 0.05
20 13 0.10
21 10 0.08
22 4 0.03
23 10 0.08
24 15 0.12
25 70 0.55
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (25 bp):
TCTATTTTATTACATCAAATAAACT
Found at i:44067318 original size:69 final size:69
Alignment explanation
Indices: 44067207--44067434 Score: 395
Period size: 69 Copynumber: 3.3 Consensus size: 69
44067197 TCGTATAATC
44067207 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAA
1 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAA
*
44067272 AAAT
66 AATT
44067276 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTC-AAA
1 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAA
44067340 AATT
66 AATT
*
44067344 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAT
1 TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAA
**
44067409 TTTT
66 AATT
* *
44067413 TTTATTTTATTACATAAAATAA
1 TCTATTTTATTACATCAAATAA
44067435 TATCAAAATA
Statistics
Matches: 152, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
68 67 0.44
69 85 0.56
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (69 bp):
TCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCAAAA
AATT
Found at i:44069858 original size:11 final size:11
Alignment explanation
Indices: 44069844--44069907 Score: 51
Period size: 11 Copynumber: 5.7 Consensus size: 11
44069834 TTAAATATGG
44069844 ATTTGAGAGAA
1 ATTTGAGAGAA
*
44069855 ATTTG-GAAGGA
1 ATTTGAG-AGAA
*
44069866 ATTTGAAAGAA
1 ATTTGAGAGAA
*
44069877 AATTGAGAGGAA
1 ATTTGAGA-GAA
*
44069889 ATTT-AAAGGAA
1 ATTTGAGA-GAA
44069900 ATTTGAGA
1 ATTTGAGA
44069908 AAGGATTAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
10 1 0.02
11 32 0.78
12 8 0.20
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:44069887 original size:22 final size:23
Alignment explanation
Indices: 44069844--44069907 Score: 71
Period size: 22 Copynumber: 2.8 Consensus size: 23
44069834 TTAAATATGG
*
44069844 ATTTGAGAGAAATTTG-GAAGG-A
1 ATTTGAAAGAAATTTGAG-AGGAA
*
44069866 ATTTGAAAGAAAATTGAGAGGAA
1 ATTTGAAAGAAATTTGAGAGGAA
44069889 ATTT-AAAGGAAATTTGAGA
1 ATTTGAAA-GAAATTTGAGA
44069908 AAGGATTAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
22 20 0.56
23 16 0.44
ACGTcount: A:0.47, C:0.00, G:0.27, T:0.27
Consensus pattern (23 bp):
ATTTGAAAGAAATTTGAGAGGAA
Found at i:44070401 original size:25 final size:24
Alignment explanation
Indices: 44070314--44070415 Score: 84
Period size: 25 Copynumber: 4.2 Consensus size: 24
44070304 TAAATGATTT
*
44070314 ATAAGAACAATTCAAAATAAAT--A
1 ATAA-AACAATTTAAAATAAATAAA
* * *
44070337 ATAAAA-AGTTTCAAATAAACAAA
1 ATAAAACAATTTAAAATAAATAAA
* * *
44070360 ATATAAATAACTAAAAATAAATAACA
1 ATA-AAACAATTTAAAATAAATAA-A
*
44070386 ATAAAACAATTTAAAATAAATAAT
1 ATAAAACAATTTAAAATAAATAAA
44070410 ATAAAA
1 ATAAAA
44070416 AATAACATAT
Statistics
Matches: 61, Mismatches: 13, Indels: 9
0.73 0.16 0.11
Matches are distributed among these distances:
21 10 0.16
22 2 0.03
23 8 0.13
24 9 0.15
25 28 0.46
26 4 0.07
ACGTcount: A:0.68, C:0.07, G:0.02, T:0.24
Consensus pattern (24 bp):
ATAAAACAATTTAAAATAAATAAA
Found at i:44070416 original size:25 final size:25
Alignment explanation
Indices: 44070297--44070416 Score: 70
Period size: 25 Copynumber: 4.9 Consensus size: 25
44070287 TAAATAATAG
* *
44070297 TTTAAAATAAATGATTTATAAGAACAA
1 TTTAAAATAAAT-A-ATATAAAAACAA
* *
44070324 TTCAAAATAAAT-A-AT-AAAA-AG
1 TTTAAAATAAATAATATAAAAACAA
* * * * *
44070345 TTTCAAATAAACAAAATATAAATAA
1 TTTAAAATAAATAATATAAAAACAA
* * *
44070370 CTAAAAATAAATAACA-ATAAAACAA
1 TTTAAAATAAATAATATA-AAAACAA
44070395 TTTAAAATAAATAATATAAAAA
1 TTTAAAATAAATAATATAAAAA
44070417 ATAACATATA
Statistics
Matches: 68, Mismatches: 19, Indels: 14
0.67 0.19 0.14
Matches are distributed among these distances:
21 10 0.15
22 4 0.06
23 4 0.06
24 4 0.06
25 34 0.50
26 1 0.01
27 11 0.16
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.27
Consensus pattern (25 bp):
TTTAAAATAAATAATATAAAAACAA
Found at i:44070449 original size:37 final size:38
Alignment explanation
Indices: 44070378--44070456 Score: 110
Period size: 37 Copynumber: 2.1 Consensus size: 38
44070368 AACTAAAAAT
44070378 AAATAACAATAAAACAATTTAAAATAAATAATATA-AA
1 AAATAACAATAAAACAATTTAAAATAAATAATATATAA
*
44070415 AAATAACATATAAAAC-ATTTTAAA-AAATATATATATAA
1 AAATAACA-ATAAAACAATTTAAAATAAATA-ATATATAA
44070453 AAAT
1 AAAT
44070457 TTGAAAGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
36 5 0.13
37 20 0.53
38 13 0.34
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (38 bp):
AAATAACAATAAAACAATTTAAAATAAATAATATATAA
Found at i:44070456 original size:38 final size:37
Alignment explanation
Indices: 44070362--44070455 Score: 118
Period size: 38 Copynumber: 2.4 Consensus size: 37
44070352 TAAACAAAAT
*
44070362 ATAAATAACTAAAAATAAATAACAATAAAACAATTTAAA
1 ATAAATAA-TATAAA-AAATAACAATAAAACAATTTAAA
*
44070401 ATAAATAATATAAAAAATAACATATAAAACATTTTAAA
1 ATAAATAATATAAAAAATAACA-ATAAAACAATTTAAA
44070439 A-AATATATATATAAAAA
1 ATAA-ATA-ATATAAAAA
44070456 TTTGAAAGAT
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
37 10 0.20
38 23 0.46
39 17 0.34
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (37 bp):
ATAAATAATATAAAAAATAACAATAAAACAATTTAAA
Found at i:44070467 original size:23 final size:23
Alignment explanation
Indices: 44070401--44070556 Score: 109
Period size: 23 Copynumber: 6.3 Consensus size: 23
44070391 ACAATTTAAA
* *
44070401 ATAAATAATATAAAAAATA-ACAT
1 ATAAA-AATTTAAAAAATATATAT
44070424 ATAAAACATTTTAAAAAATATATAT
1 ATAAAA-A-TTTAAAAAATATATAT
* *
44070449 ATAAAAATTTGAAAGATATATAT
1 ATAAAAATTTAAAAAATATATAT
*
44070472 ATAATAATTTACAATAAATAATATAT
1 ATAAAAATTTA-AA-AAAT-ATATAT
*
44070498 AAAAGAAATTTAAATAAATA-ATAT
1 ATAA-AAATTTAAA-AAATATATAT
* *
44070522 GTAAAGCAACTTAAAATAAATAATATAT
1 ATAAA--AA-TTTAAA-AAAT-ATATAT
44070550 ATAAAAA
1 ATAAAAA
44070557 CTAAAAATAA
Statistics
Matches: 108, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
22 1 0.01
23 30 0.28
24 19 0.18
25 15 0.14
26 28 0.26
27 7 0.06
28 8 0.07
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (23 bp):
ATAAAAATTTAAAAAATATATAT
Found at i:44070495 original size:26 final size:26
Alignment explanation
Indices: 44070433--44070553 Score: 112
Period size: 26 Copynumber: 4.8 Consensus size: 26
44070423 TATAAAACAT
44070433 TTTAAA-AAAT-ATATATATAA-AAA
1 TTTAAATAAATAATATATATAAGAAA
* * *
44070456 TTTGAA-AGAT-ATATATATAA-TAA
1 TTTAAATAAATAATATATATAAGAAA
*
44070479 TTTACAATAAATAATATATAAAAGAAA
1 TTTA-AATAAATAATATATATAAGAAA
* *
44070506 TTTAAATAAATAATATGTA-AAGCAAC
1 TTTAAATAAATAATATATATAAG-AAA
*
44070532 TTAAAATAAATAATATATATAA
1 TTTAAATAAATAATATATATAA
44070554 AAACTAAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
23 23 0.28
24 2 0.02
25 6 0.07
26 42 0.52
27 8 0.10
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (26 bp):
TTTAAATAAATAATATATATAAGAAA
Found at i:44070558 original size:26 final size:25
Alignment explanation
Indices: 44070415--44070568 Score: 100
Period size: 26 Copynumber: 6.2 Consensus size: 25
44070405 ATAATATAAA
* * * *
44070415 AAATAACATATAAAACATTTTAAA-
1 AAATAATATATAAAAAACTTAAAAT
* * *
44070439 AAAT-ATATATATAAAAATTTGAAAG
1 AAATAATATATA-AAAAACTTAAAAT
* * * *
44070464 ATAT-ATATAT-AATAATTTACAAT
1 AAATAATATATAAAAAACTTAAAAT
* *
44070487 AAATAATATATAAAAGAAATTTAAAT
1 AAATAATATATAAAA-AACTTAAAAT
* *
44070513 AAATAATATGTAAAGCAACTTAAAAT
1 AAATAATATATAAA-AAACTTAAAAT
*
44070539 AAATAATATATATAAAAACTAAAAAT
1 AAATAATATATA-AAAAACTTAAAAT
44070565 AAAT
1 AAAT
44070569 GATGATAAAA
Statistics
Matches: 103, Mismatches: 20, Indels: 12
0.76 0.15 0.09
Matches are distributed among these distances:
23 18 0.17
24 20 0.19
25 11 0.11
26 52 0.50
27 2 0.02
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (25 bp):
AAATAATATATAAAAAACTTAAAAT
Found at i:44071346 original size:16 final size:16
Alignment explanation
Indices: 44071303--44071354 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 16
44071293 TTCTCTTTAA
44071303 AAAATAAAAATAAATAA-
1 AAAA-AAAAATAAA-AAG
*
44071320 ATAAAACAAAATGAAAAG
1 A-AAAA-AAAATAAAAAG
44071338 AAAAAAAAATAAAAAG
1 AAAAAAAAATAAAAAG
44071354 A
1 A
44071355 CCACCTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
16 11 0.37
17 8 0.27
18 11 0.37
ACGTcount: A:0.81, C:0.02, G:0.06, T:0.12
Consensus pattern (16 bp):
AAAAAAAAATAAAAAG
Found at i:44091579 original size:29 final size:29
Alignment explanation
Indices: 44091547--44091674 Score: 141
Period size: 29 Copynumber: 4.4 Consensus size: 29
44091537 CAATTAACAT
* * * *
44091547 AGATAGCCATAAAAGTGTTCTTTTAAGAA
1 AGATAGCCACAAAGGTGTTCCTTTAAGAG
* * *
44091576 AGATAGCCACAAAGGCGTTCCATTAACAG
1 AGATAGCCACAAAGGTGTTCCTTTAAGAG
* *
44091605 AGATAGCCACAAAGGTGTCCCTTTAATAG
1 AGATAGCCACAAAGGTGTTCCTTTAAGAG
* * *
44091634 AGGTAGCCACAAAGGTGTT-CTTTTACAG
1 AGATAGCCACAAAGGTGTTCCTTTAAGAG
44091662 AGATAGCCACAAA
1 AGATAGCCACAAA
44091675 TTCCTCTATT
Statistics
Matches: 83, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
28 19 0.23
29 64 0.77
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (29 bp):
AGATAGCCACAAAGGTGTTCCTTTAAGAG
Found at i:44091674 original size:57 final size:58
Alignment explanation
Indices: 44091523--44091674 Score: 180
Period size: 58 Copynumber: 2.6 Consensus size: 58
44091513 TTAGAGTATT
* * * * * *
44091523 GCCACAAAGGCATTCAATTAACATAGATAGCCATAAAAGTGTTCTTTTAAGAAAGATA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAAGTGTCCCTTTAAGAAAGATA
* * * *
44091581 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAGGTGTCCCTTTAATAGAGGTA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAAGTGTCCCTTTAAGAAAGATA
* * *
44091639 GCCACAAAGGTGTT-CTTTTACAGAGATAGCCACAAA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAA
44091675 TTCCTCTATT
Statistics
Matches: 81, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
57 20 0.25
58 61 0.75
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (58 bp):
GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAAGTGTCCCTTTAAGAAAGATA
Found at i:44091687 original size:57 final size:57
Alignment explanation
Indices: 44091523--44091706 Score: 176
Period size: 58 Copynumber: 3.2 Consensus size: 57
44091513 TTAGAGTATT
* * * * * * * *
44091523 GCCACAAAGGCATTCAATTAACATAGATAGCCATAAAAGTGTTCTTTTAAGAAAGATA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCA-CAAAGTGTCCCTTTAACAGAGATA
* *
44091581 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAGGTGTCCCTTTAATAGAGGTA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAA-GTGTCCCTTTAACAGAGATA
* * *
44091639 GCCACAAAGGTGTT-CTTTTACAGAGATAGCCACAAA-T-TCCTCTATTTAACAGAGATA
1 GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAGTGTCC-C--TTTAACAGAGATA
*
44091696 TCCACAAAGGC
1 GCCACAAAGGC
44091707 TCACTTTTAT
Statistics
Matches: 106, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
54 3 0.03
55 2 0.02
57 43 0.41
58 58 0.55
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (57 bp):
GCCACAAAGGCGTTCCATTAACAGAGATAGCCACAAAGTGTCCCTTTAACAGAGATA
Found at i:44091715 original size:29 final size:29
Alignment explanation
Indices: 44091523--44091715 Score: 114
Period size: 29 Copynumber: 6.7 Consensus size: 29
44091513 TTAGAGTATT
** *
44091523 GCCACAAAGGCAT-TCAATTAACATAGATA
1 GCCACAAAGGC-TCTCTTTTAACAGAGATA
* * *
44091552 GCCATAAAAGTG-T-TCTTTTAAGAAAGATA
1 GCCA-CAAAG-GCTCTCTTTTAACAGAGATA
**
44091581 GCCACAAAGGCGT-TCCATTAACAGAGATA
1 GCCACAAAGGC-TCTCTTTTAACAGAGATA
* * * *
44091610 GCCACAAAGG-TGTCCCTTTAATAGAGGTA
1 GCCACAAAGGCTCT-CTTTTAACAGAGATA
*
44091639 GCCACAAAGG-TGTTCTTTT-ACAGAGATA
1 GCCACAAAGGCT-CTCTTTTAACAGAGATA
**
44091667 GCCACAAATTC-CTCTATTTAACAGAGATA
1 GCCACAAAGGCTCTCT-TTTAACAGAGATA
* *
44091696 TCCACAAAGGCTCACTTTTA
1 GCCACAAAGGCTCTCTTTTA
44091716 TGAAAATTGG
Statistics
Matches: 129, Mismatches: 24, Indels: 22
0.74 0.14 0.13
Matches are distributed among these distances:
27 5 0.04
28 23 0.18
29 92 0.71
30 8 0.06
31 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.17, T:0.25
Consensus pattern (29 bp):
GCCACAAAGGCTCTCTTTTAACAGAGATA
Found at i:44098188 original size:18 final size:17
Alignment explanation
Indices: 44098151--44098189 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
44098141 ATTATTATGT
* *
44098151 ATTAAATGGTTAATTGA
1 ATTAAATGATTAAGTGA
44098168 ATTAAATGATTAAAGTGA
1 ATTAAATGATT-AAGTGA
44098186 ATTA
1 ATTA
44098190 TTGATGAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.38
Consensus pattern (17 bp):
ATTAAATGATTAAGTGA
Found at i:44102252 original size:43 final size:43
Alignment explanation
Indices: 44102203--44102505 Score: 323
Period size: 43 Copynumber: 7.1 Consensus size: 43
44102193 AAAACAGGCT
* *
44102203 TTTAGCGGCGCTTTTCCAAGAAACGCCGCTAAAAACCATGACC
1 TTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATGACC
* * * *
44102246 TTTAGCGACGCTTTTCCCACAAACGCCGCGAAAGACCATAACC
1 TTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATGACC
* * *
44102289 TTTAGCGGCGC-TTTCCCACAAACGCCGTTAAAGACCACGACC
1 TTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATGACC
* *
44102331 TTTAGCGGCGCTTTTCTC-ACAAGCGTCGCTAAAGACCATGACC
1 TTTAGCGGCGCTTTTC-CAACAAACGCCGCTAAAGACCATGACC
*
44102374 TTTAGCGGCGCTTTTCCCAA-AAACGCCGCTAAAGAACATGACC
1 TTTAGCGGCGCTTTT-CCAACAAACGCCGCTAAAGACCATGACC
* * * * * *
44102417 TTTAGCGGTGCTTTTTGTC-ACCAACGCCGCTATAGATCA-AACC
1 TTTAGCGGCGC-TTTT-CCAACAAACGCCGCTAAAGACCATGACC
* * *
44102460 TTTAGCGGCGCTTCTCGCAA-AAACGCCGCTAAA-AACATAACC
1 TTTAGCGGCGCTTTTC-CAACAAACGCCGCTAAAGACCATGACC
44102502 TTTA
1 TTTA
44102506 AAAAAATATT
Statistics
Matches: 220, Mismatches: 31, Indels: 19
0.81 0.11 0.07
Matches are distributed among these distances:
41 3 0.01
42 61 0.28
43 133 0.60
44 23 0.10
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (43 bp):
TTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATGACC
Found at i:44102503 original size:128 final size:126
Alignment explanation
Indices: 44102203--44102505 Score: 365
Period size: 128 Copynumber: 2.4 Consensus size: 126
44102193 AAAACAGGCT
*
44102203 TTTAGCGGCGCTTTTCCAAGAAACGCCGCTAAAAACCATGACCTTTAGCGACGCTTTTCCCACAA
1 TTTAGCGGCGCTTTTCCAA-AAACGCCGCTAAAAA-CATGACCTTTAGCGACGCTTTTCCCAAAA
* * *
44102268 ACGCCGCGAAAGACCATAACCTTTAGCGGCGCTTTCCCACAAACGCCGTTAAAGACCACGACC
64 ACGCCGCGAAAGAACATAACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCACAACC
* * * * *
44102331 TTTAGCGGCGCTTTTCTCACAAGCGTCGCTAAAGACCATGACCTTTAGCGGCGCTTTTCCCAAAA
1 TTTAGCGGCGCTTTTC-CAAAAACGCCGCTAAA-AACATGACCTTTAGCGACGCTTTTCCCAAAA
* * * ** * * *
44102396 ACGCCGCTAAAGAACATGACCTTTAGCGGTGCTTTTTGTCACCAACGCCGCTATAGATCA-AACC
64 ACGCCGCGAAAGAACATAACCTTTAGCGGCGC--TTTCCCACAAACGCCGCTAAAGACCACAACC
* *
44102460 TTTAGCGGCGCTTCTCGCAAAAACGCCGCTAAAAACATAACCTTTA
1 TTTAGCGGCGCTTTTC-CAAAAACGCCGCTAAAAACATGACCTTTA
44102506 AAAAAATATT
Statistics
Matches: 147, Mismatches: 24, Indels: 8
0.82 0.13 0.04
Matches are distributed among these distances:
128 93 0.63
129 34 0.23
130 20 0.14
ACGTcount: A:0.28, C:0.31, G:0.18, T:0.23
Consensus pattern (126 bp):
TTTAGCGGCGCTTTTCCAAAAACGCCGCTAAAAACATGACCTTTAGCGACGCTTTTCCCAAAAAC
GCCGCGAAAGAACATAACCTTTAGCGGCGCTTTCCCACAAACGCCGCTAAAGACCACAACC
Found at i:44104572 original size:17 final size:17
Alignment explanation
Indices: 44104543--44104585 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
44104533 ATATTATAAT
44104543 ATTATATATTAATTTTGC
1 ATTATA-ATTAATTTTGC
44104561 ATTATAATTAATTTTGC
1 ATTATAATTAATTTTGC
44104578 ATTATAAT
1 ATTATAAT
44104586 ATTATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 19 0.76
18 6 0.24
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.53
Consensus pattern (17 bp):
ATTATAATTAATTTTGC
Found at i:44108293 original size:14 final size:14
Alignment explanation
Indices: 44108274--44108300 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
44108264 TAACTTGACC
44108274 CCTAAATCCCTAAA
1 CCTAAATCCCTAAA
44108288 CCTAAATCCCTAA
1 CCTAAATCCCTAA
44108301 CTCTTAACCC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.37, G:0.00, T:0.22
Consensus pattern (14 bp):
CCTAAATCCCTAAA
Found at i:44108920 original size:41 final size:41
Alignment explanation
Indices: 44108764--44108919 Score: 249
Period size: 41 Copynumber: 3.8 Consensus size: 41
44108754 AAATGTTTTT
*
44108764 GCGGCGCTTTTTCAAAAACGCCGCTAAAAGGCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCT-AAAGGCCAGAGCATTA
* *
44108806 GCGGCGCTTCTTCAAAAACTCCGATAAAGGCCAGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
* *
44108847 GTGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGAGCATTA
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
*
44108888 GCGGCGCTTCTTCAAAAGCGCCGCTAAAGGCC
1 GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCC
44108920 CCAAAAACTC
Statistics
Matches: 105, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
41 83 0.79
42 22 0.21
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (41 bp):
GCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCAGAGCATTA
Found at i:44109080 original size:40 final size:39
Alignment explanation
Indices: 44108968--44109089 Score: 111
Period size: 40 Copynumber: 3.1 Consensus size: 39
44108958 TTTGCGGCAC
** * * *
44108968 TTTTCAAAAAATGCCGCTAATTCTT-ATTTTTAGCAGCAT
1 TTTTCAAAAAGCGCCACTAATGCTTGATTTTTAGCAGC-G
* * **
44109007 TTTTCAAAAAGCGCCGCTAATGCTCGACCTTTAGCAGCG
1 TTTTCAAAAAGCGCCACTAATGCTTGATTTTTAGCAGCG
* **
44109046 TTTTGATAAAAGCGCCACTAATGCTTGATTTTTAGTGGCG
1 TTTTCA-AAAAGCGCCACTAATGCTTGATTTTTAGCAGCG
44109086 TTTT
1 TTTT
44109090 TTTTCCAAAC
Statistics
Matches: 67, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
39 26 0.39
40 41 0.61
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (39 bp):
TTTTCAAAAAGCGCCACTAATGCTTGATTTTTAGCAGCG
Found at i:44109670 original size:23 final size:23
Alignment explanation
Indices: 44109640--44109687 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
44109630 TGTACATTGG
44109640 GGACAATGTGCAAAATAAAGTGT
1 GGACAATGTGCAAAATAAAGTGT
44109663 GGACAATGTGCAAAATAAAGTGT
1 GGACAATGTGCAAAATAAAGTGT
44109686 GG
1 GG
44109688 GGTGACATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.42, C:0.08, G:0.29, T:0.21
Consensus pattern (23 bp):
GGACAATGTGCAAAATAAAGTGT
Found at i:44116017 original size:27 final size:27
Alignment explanation
Indices: 44115967--44116019 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
44115957 AGACAATTTC
* *
44115967 TTCATAGATTGTCACAAAGGCTTCCTT
1 TTCATAGATTGCCACAAAGCCTTCCTT
44115994 TTCATAGATTAGCCAC-AAGCCTTCCT
1 TTCATAGATT-GCCACAAAGCCTTCCT
44116020 GCATTTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (27 bp):
TTCATAGATTGCCACAAAGCCTTCCTT
Found at i:44117978 original size:17 final size:17
Alignment explanation
Indices: 44117956--44117989 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
44117946 ATTGCAAGGG
*
44117956 AGAAAAGGGAAAAGAAA
1 AGAAAAGAGAAAAGAAA
*
44117973 AGAAAAGAGAAGAGAAA
1 AGAAAAGAGAAAAGAAA
44117990 CATGATGCTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (17 bp):
AGAAAAGAGAAAAGAAA
Found at i:44118372 original size:28 final size:28
Alignment explanation
Indices: 44118341--44118459 Score: 134
Period size: 28 Copynumber: 4.3 Consensus size: 28
44118331 AGTCCTTACC
44118341 GACTATCTTTCAAGCAAGTGTCTGCATG
1 GACTATCTTTCAAGCAAGTGTCTGCATG
* *
44118369 GACTAT-TTTCAAGCAATTGTCCGCATG
1 GACTATCTTTCAAGCAAGTGTCTGCATG
* * * **
44118396 GACTATCTTTCAAGAAAGAGTCTGGAAA
1 GACTATCTTTCAAGCAAGTGTCTGCATG
* *
44118424 GACTAT-TCTTCAAGCAAGTGCCTGTATG
1 GACTATCT-TTCAAGCAAGTGTCTGCATG
44118452 GACTATCT
1 GACTATCT
44118460 GTAACACCTC
Statistics
Matches: 73, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
27 26 0.36
28 46 0.63
29 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (28 bp):
GACTATCTTTCAAGCAAGTGTCTGCATG
Found at i:44118428 original size:55 final size:56
Alignment explanation
Indices: 44118341--44118459 Score: 152
Period size: 55 Copynumber: 2.1 Consensus size: 56
44118331 AGTCCTTACC
* * ** *
44118341 GACTATCTTTCAAGCAAGTGTCTGCATGGACTATT-TTCAAGCAATTGTCC-GCATG
1 GACTATCTTTCAAGAAAGAGTCTGCAAAGACTATTCTTCAAGCAAGTG-CCTGCATG
* *
44118396 GACTATCTTTCAAGAAAGAGTCTGGAAAGACTATTCTTCAAGCAAGTGCCTGTATG
1 GACTATCTTTCAAGAAAGAGTCTGCAAAGACTATTCTTCAAGCAAGTGCCTGCATG
44118452 GACTATCT
1 GACTATCT
44118460 GTAACACCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
55 32 0.58
56 23 0.42
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (56 bp):
GACTATCTTTCAAGAAAGAGTCTGCAAAGACTATTCTTCAAGCAAGTGCCTGCATG
Found at i:44120267 original size:20 final size:20
Alignment explanation
Indices: 44120244--44120286 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
44120234 ACACTAGAAA
44120244 GCATCAAAATGCCA-ACAGAG
1 GCATCAAAATG-CATACAGAG
* *
44120264 GCATCGAAGTGCATACAGAG
1 GCATCAAAATGCATACAGAG
44120284 GCA
1 GCA
44120287 CTAAAGTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (20 bp):
GCATCAAAATGCATACAGAG
Found at i:44127465 original size:12 final size:12
Alignment explanation
Indices: 44127448--44127478 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
44127438 CTATAAATAA
44127448 GAACTATGCGTT
1 GAACTATGCGTT
*
44127460 GAACTATGTGTT
1 GAACTATGCGTT
44127472 GAACTAT
1 GAACTAT
44127479 TTCAACACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.29, C:0.13, G:0.23, T:0.35
Consensus pattern (12 bp):
GAACTATGCGTT
Found at i:44131895 original size:76 final size:76
Alignment explanation
Indices: 44131754--44131905 Score: 189
Period size: 76 Copynumber: 2.0 Consensus size: 76
44131744 ATTATATTGA
* * * *
44131754 TATTCAGGATTTGTGCCTAGCAGGCTTTGTGCTGGTGTTATTCAGGCTTTATTCCTAGTAGGCTT
1 TATTCAGGATTTGTGCCTAACAGGCTTTGTGCTAGTGTTATTCAGGCTTTATGCCTAGCAGGCTT
*
44131819 AGTGCCGGTGT
66 AGTGCCAGTGT
* * * * * *
44131830 TATTTAGGCTTTGTGCCTAATAGGCTTTGTG-TCAGTGTTATTTAGGCTTTGTGCCTAGCATGCT
1 TATTCAGGATTTGTGCCTAACAGGCTTTGTGCT-AGTGTTATTCAGGCTTTATGCCTAGCAGGCT
44131894 TAGTGCCAGTGT
65 TAGTGCCAGTGT
44131906 ATTAAAAAGT
Statistics
Matches: 64, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
75 1 0.02
76 63 0.98
ACGTcount: A:0.15, C:0.16, G:0.28, T:0.41
Consensus pattern (76 bp):
TATTCAGGATTTGTGCCTAACAGGCTTTGTGCTAGTGTTATTCAGGCTTTATGCCTAGCAGGCTT
AGTGCCAGTGT
Found at i:44131904 original size:38 final size:38
Alignment explanation
Indices: 44131754--44131905 Score: 169
Period size: 38 Copynumber: 4.0 Consensus size: 38
44131744 ATTATATTGA
* * **
44131754 TATTCAGGATTTGTGCCTAGCAGGCTTTGTGCTGGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGT
* * * *
44131792 TATTCAGGCTTTATTCCTAGTAGGCTTAGTGCCGGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGT
* ** * *
44131830 TATTTAGGCTTTGTGCCTAATAGGCTTTGTGTCAGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGT
* *
44131868 TATTTAGGCTTTGTGCCTAGCATGCTTAGTGCCAGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGT
44131906 ATTAAAAAGT
Statistics
Matches: 96, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 96 1.00
ACGTcount: A:0.15, C:0.16, G:0.28, T:0.41
Consensus pattern (38 bp):
TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGT
Found at i:44134340 original size:79 final size:79
Alignment explanation
Indices: 44134209--44134368 Score: 311
Period size: 79 Copynumber: 2.0 Consensus size: 79
44134199 CTACTATAGA
44134209 CCCTTTATTTTTAAGCTAATTGGTTAAAGTTAGCAATATGATGAAAATCTTCAGGATAACAATGC
1 CCCTTTATTTTTAAGCTAATTGGTTAAAGTTAGCAATATGATGAAAATCTTCAGGATAACAATGC
*
44134274 CACGATAATAATCC
66 CACCATAATAATCC
44134288 CCCTTTATTTTTAAGCTAATTGGTTAAAGTTAGCAATATGATGAAAATCTTCAGGATAACAATGC
1 CCCTTTATTTTTAAGCTAATTGGTTAAAGTTAGCAATATGATGAAAATCTTCAGGATAACAATGC
44134353 CACCATAATAATCC
66 CACCATAATAATCC
44134367 CC
1 CC
44134369 TTAATTCATC
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (79 bp):
CCCTTTATTTTTAAGCTAATTGGTTAAAGTTAGCAATATGATGAAAATCTTCAGGATAACAATGC
CACCATAATAATCC
Found at i:44135154 original size:15 final size:15
Alignment explanation
Indices: 44135134--44135163 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44135124 GCGGGAATGG
*
44135134 AATTTTTATAATTTT
1 AATTTTTAAAATTTT
44135149 AATTTTTAAAATTTT
1 AATTTTTAAAATTTT
44135164 TAAATTAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
AATTTTTAAAATTTT
Found at i:44135236 original size:30 final size:32
Alignment explanation
Indices: 44135190--44135250 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
44135180 AATTTGTCCT
44135190 TTTAACTCTTCTAAAAATAATAAA-ATTTTAA
1 TTTAACTCTTCTAAAAATAATAAAGATTTTAA
* *
44135221 TTTAA-TCTTTTAAAAATTATAAAGATTTTA
1 TTTAACTCTTCTAAAAATAATAAAGATTTTA
44135251 GCCCCTAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 16 0.59
31 11 0.41
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.46
Consensus pattern (32 bp):
TTTAACTCTTCTAAAAATAATAAAGATTTTAA
Found at i:44145595 original size:18 final size:19
Alignment explanation
Indices: 44145574--44145609 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
44145564 TTCTTATAAT
44145574 TATAT-ATAAAATTTAAAA
1 TATATAATAAAATTTAAAA
*
44145592 TATATAATAAGATTTAAA
1 TATATAATAAAATTTAAA
44145610 CTCAATACAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (19 bp):
TATATAATAAAATTTAAAA
Found at i:44149017 original size:8 final size:9
Alignment explanation
Indices: 44148989--44149096 Score: 60
Period size: 9 Copynumber: 11.4 Consensus size: 9
44148979 ATAGGTAATT
44148989 AATTTCTAAA
1 AATTT-TAAA
44148999 AATTTTAAA
1 AATTTTAAA
44149008 AATTTTAAA
1 AATTTTAAA
*
44149017 AATATATAAA
1 AAT-TTTAAA
*
44149027 TTATTTTAAA
1 -AATTTTAAA
*
44149037 AA-ATTAAA
1 AATTTTAAA
44149045 AATTATTTAAA
1 AA-T-TTTAAA
* *
44149056 AA--GTACA
1 AATTTTAAA
*
44149063 AATTATAAA
1 AATTTTAAA
*
44149072 TATATATTTTAA
1 -A-AT-TTTAAA
44149084 AATTTTAAA
1 AATTTTAAA
44149093 AATT
1 AATT
44149097 AATTAATTGC
Statistics
Matches: 75, Mismatches: 13, Indels: 21
0.69 0.12 0.19
Matches are distributed among these distances:
7 5 0.07
8 7 0.09
9 29 0.39
10 18 0.24
11 12 0.16
12 4 0.05
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.42
Consensus pattern (9 bp):
AATTTTAAA
Found at i:44149018 original size:19 final size:19
Alignment explanation
Indices: 44148989--44149057 Score: 52
Period size: 19 Copynumber: 3.6 Consensus size: 19
44148979 ATAGGTAATT
44148989 AATTTCTAAAAATTTT-AAA
1 AATTT-TAAAAATTTTAAAA
* *
44149008 AATTTTAAAAATATATAAAT
1 AATTTTAAAAAT-TTTAAAA
* *
44149028 TATTTTAAAAA-ATTAAAA
1 AATTTTAAAAATTTTAAAA
*
44149046 ATTATTTAAAAA
1 AAT-TTTAAAAA
44149058 GTACAAATTA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
18 12 0.31
19 15 0.38
20 12 0.31
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (19 bp):
AATTTTAAAAATTTTAAAA
Found at i:44149034 original size:20 final size:20
Alignment explanation
Indices: 44149009--44149057 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
44148999 AATTTTAAAA
*
44149009 ATTTT-AAAAATATATAAATT
1 ATTTTAAAAAAT-TAAAAATT
44149029 ATTTTAAAAAATTAAAAATT
1 ATTTTAAAAAATTAAAAATT
44149049 A-TTTAAAAA
1 ATTTTAAAAA
44149058 GTACAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 8 0.30
20 13 0.48
21 6 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
ATTTTAAAAAATTAAAAATT
Found at i:44151513 original size:42 final size:43
Alignment explanation
Indices: 44151394--44151534 Score: 117
Period size: 43 Copynumber: 3.3 Consensus size: 43
44151384 CATAGGATTC
* * ** *
44151394 CGATATGTGATTTCGTGTAAGACCACATCTGGGAC-GTTGGCAT
1 CGATATATGATTTTGTGTAAGACCATGTCTGGGACAG-TGACAT
* ** * *
44151437 CGATTTGA-GATTTACATGTAAGACCATGTTTGGGACATTGACAT
1 CGATAT-ATGATTT-TGTGTAAGACCATGTCTGGGACAGTGACAT
* *
44151481 C-ATATATGATTTTGTGTAAGACCCTGTCTGGGATAGTGACAT
1 CGATATATGATTTTGTGTAAGACCATGTCTGGGACAGTGACAT
*
44151523 CGATATTTGATT
1 CGATATATGATT
44151535 ACATGTAAGA
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
42 26 0.34
43 27 0.35
44 24 0.31
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (43 bp):
CGATATATGATTTTGTGTAAGACCATGTCTGGGACAGTGACAT
Found at i:44151545 original size:43 final size:42
Alignment explanation
Indices: 44151448--44151546 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 42
44151438 GATTTGAGAT
* *
44151448 TTACATGTAAGACCATGTTTGGGACATTGACATCATATATGA
1 TTACATGTAAGACCATGTCTGGGACAGTGACATCATATATGA
*** * * *
44151490 TTTTGTGTAAGACCCTGTCTGGGATAGTGACATCGATATTTGA
1 TTACATGTAAGACCATGTCTGGGACAGTGACATC-ATATATGA
44151533 TTACATGTAAGACC
1 TTACATGTAAGACC
44151547 TCATCTAGGA
Statistics
Matches: 45, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
42 27 0.60
43 18 0.40
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.34
Consensus pattern (42 bp):
TTACATGTAAGACCATGTCTGGGACAGTGACATCATATATGA
Found at i:44159548 original size:20 final size:20
Alignment explanation
Indices: 44159518--44159568 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
44159508 TGGTCTTTTG
44159518 GGTTTTT-GATCAAACGTTCA
1 GGTTTTTCGATCAAACGTT-A
44159538 -GTTTTTCGATCAAACGTTA
1 GGTTTTTCGATCAAACGTTA
44159557 GGTTTTTC-ATCA
1 GGTTTTTCGATCA
44159569 TCTAAGGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 11 0.38
20 18 0.62
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (20 bp):
GGTTTTTCGATCAAACGTTA
Found at i:44163493 original size:28 final size:27
Alignment explanation
Indices: 44163428--44163497 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 27
44163418 TTTAACAGTA
*
44163428 ACAGTACAGTATGGGCCTTAGCCTATT
1 ACAGTACAGTATGGGCCTGAGCCTATT
* * *
44163455 ACAGAAACAGTGTGGGCCTGAGCTTGA-T
1 ACAG-TACAGTATGGGCCTGAGCCT-ATT
44163483 ACAGTATCAGTATGG
1 ACAGTA-CAGTATGG
44163498 TGCAAGTATG
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
27 5 0.15
28 28 0.82
29 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (27 bp):
ACAGTACAGTATGGGCCTGAGCCTATT
Found at i:44163739 original size:32 final size:32
Alignment explanation
Indices: 44163678--44163880 Score: 234
Period size: 32 Copynumber: 6.4 Consensus size: 32
44163668 GAATGGTTGC
* *
44163678 AAGCCATAAGT-ACAGTAATATGATTGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
44163709 AAGTCATCAGTAGCAGTGATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * ** *
44163741 CAGCCATTAGTAATGGTAATATGATCGGTACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
44163773 AAGCCATCAGTAAC-GATAATATGATCGGCACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
*
44163805 AAGCCATCAGTAACGAG-AATATGATCGGTACA
1 AAGCCATCAGTAAC-AGTAATATGATCGGCACA
* *
44163837 AAGCCATCAGTAAC-GATATTATGATCGACACA
1 AAGCCATCAGTAACAG-TAATATGATCGGCACA
44163869 AAGCCATCAGTA
1 AAGCCATCAGTA
44163881 GCATCGCAGC
Statistics
Matches: 145, Mismatches: 21, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
30 1 0.01
31 10 0.07
32 133 0.92
34 1 0.01
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:44163795 original size:64 final size:65
Alignment explanation
Indices: 44163678--44163880 Score: 263
Period size: 64 Copynumber: 3.2 Consensus size: 65
44163668 GAATGGTTGC
* * * * * *
44163678 AAGCCATAAGT-AC-AGTAATATGATTGGCACAAAGTCATCAGTAGC-AGTGATATGATCGGCAC
1 AAGCCATCAGTAACGAGTAATATGATCGGTACAAAGCCATCAGTAACGA-TAATATGATCGGCAC
44163740 A
65 A
* * *
44163741 CAGCCATTAGTAATG-GTAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGGCACA
1 AAGCCATCAGTAACGAGTAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGGCACA
* *
44163805 AAGCCATCAGTAACGAG-AATATGATCGGTACAAAGCCATCAGTAACGATATTATGATCGACACA
1 AAGCCATCAGTAACGAGTAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGGCACA
44163869 AAGCCATCAGTA
1 AAGCCATCAGTA
44163881 GCATCGCAGC
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
63 9 0.07
64 112 0.91
65 2 0.02
ACGTcount: A:0.39, C:0.19, G:0.20, T:0.22
Consensus pattern (65 bp):
AAGCCATCAGTAACGAGTAATATGATCGGTACAAAGCCATCAGTAACGATAATATGATCGGCACA
Found at i:44164079 original size:24 final size:23
Alignment explanation
Indices: 44164052--44164110 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 23
44164042 CCATGCTCAG
44164052 AATTAGTCATTCAAATCACAGACA
1 AATTAGTCATTCAAA-CACAGACA
*
44164076 AATTAGTCATACCAAACACAGACA
1 AATTAGTCAT-TCAAACACAGACA
*
44164100 AATCAGTCATT
1 AATTAGTCATT
44164111 TGACCTCGAG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 27 0.87
25 4 0.13
ACGTcount: A:0.46, C:0.22, G:0.08, T:0.24
Consensus pattern (23 bp):
AATTAGTCATTCAAACACAGACA
Found at i:44164187 original size:27 final size:27
Alignment explanation
Indices: 44164150--44164543 Score: 457
Period size: 27 Copynumber: 14.6 Consensus size: 27
44164140 CCACCAGGGC
* * *
44164150 ATTACAGTCATTTTACCCTACAAGAGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
44164177 ACTATGGTCATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
44164204 ATTATGGTCATTTTACCCTACAAGAGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
44164231 GTTACGGTCATTTTACCGTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
44164258 ATTACGGTCATTTTACCCTATAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * *
44164285 ATTACAGTTATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * *
44164312 ACTATGGTCATTTTACCCTATAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
*
44164339 ATTACGGTCATTTTACCCTACAAGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* * * * * *
44164366 ATTATGATTATTTTACCTTACATGGCT
1 ATTACGGTCATTTTACCCTACAGGGGT
*
44164393 ATTACGGTCATTTTACCCTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
44164420 ATTATGGTAATTTTACCCTACAGGGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
44164447 ATTACGGTCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
44164474 ATTACGGTCATTTTACCTTACAGGGGC
1 ATTACGGTCATTTTACCCTACAGGGGT
* *
44164501 ATTACAGTCATTTTACCTTACA-GGGT
1 ATTACGGTCATTTTACCCTACAGGGGT
44164527 CATTACGGTCATTTTAC
1 -ATTACGGTCATTTTAC
44164544 AACCTTTTCG
Statistics
Matches: 311, Mismatches: 55, Indels: 2
0.85 0.15 0.01
Matches are distributed among these distances:
26 3 0.01
27 308 0.99
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (27 bp):
ATTACGGTCATTTTACCCTACAGGGGT
Found at i:44176155 original size:28 final size:28
Alignment explanation
Indices: 44176115--44176174 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
44176105 AAAAATTAAG
44176115 TTATTTTCTAGAAATTATTTTTCGAAAA
1 TTATTTTCTAGAAATTATTTTTCGAAAA
* *
44176143 TTATTTTCTAGAAATTATTTTTTGAAAG
1 TTATTTTCTAGAAATTATTTTTCGAAAA
44176171 TTAT
1 TTAT
44176175 ATTCAGTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.08, T:0.53
Consensus pattern (28 bp):
TTATTTTCTAGAAATTATTTTTCGAAAA
Found at i:44176174 original size:14 final size:14
Alignment explanation
Indices: 44176115--44176163 Score: 73
Period size: 14 Copynumber: 3.5 Consensus size: 14
44176105 AAAAATTAAG
44176115 TTATTTTCTAGAAA
1 TTATTTTCTAGAAA
*
44176129 TTATTTT-TCGAAAA
1 TTATTTTCTAG-AAA
44176143 TTATTTTCTAGAAA
1 TTATTTTCTAGAAA
44176157 TTATTTT
1 TTATTTT
44176164 TTGAAAGTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
13 2 0.06
14 27 0.87
15 2 0.06
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTTTCTAGAAA
Found at i:44180208 original size:18 final size:18
Alignment explanation
Indices: 44180171--44180206 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
44180161 TTGATTAAAA
*
44180171 TAAAAATAATAGAGAATT
1 TAAAAATAATAGACAATT
44180189 TAAAAATAATA-ACAATT
1 TAAAAATAATAGACAATT
44180206 T
1 T
44180207 TATTTAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (18 bp):
TAAAAATAATAGACAATT
Found at i:44180476 original size:2 final size:2
Alignment explanation
Indices: 44180463--44180507 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
44180453 TTAAATAAAA
*
44180463 AT AT AG AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44180505 AT A
1 AT A
44180508 ATTTATGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:44183738 original size:52 final size:51
Alignment explanation
Indices: 44183665--44183763 Score: 146
Period size: 52 Copynumber: 1.9 Consensus size: 51
44183655 TGCTCATACG
* *
44183665 AGCTATGAATCGGTATGCTCTCACGAGCTGAAAATCAGAAAGCTCATAAGAA
1 AGCTAAGAATCAGTATGCTCTCACGAGCTG-AAATCAGAAAGCTCATAAGAA
*
44183717 AGCTAAGAATCAGTA-GCCTCTCACGAGCTGAAATCAGTAAGCTCATA
1 AGCTAAGAATCAGTATG-CTCTCACGAGCTGAAATCAGAAAGCTCATA
44183764 TGAGCTGTGG
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
51 17 0.40
52 26 0.60
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.21
Consensus pattern (51 bp):
AGCTAAGAATCAGTATGCTCTCACGAGCTGAAATCAGAAAGCTCATAAGAA
Found at i:44183768 original size:24 final size:24
Alignment explanation
Indices: 44183689--44183770 Score: 60
Period size: 24 Copynumber: 3.2 Consensus size: 24
44183679 ATGCTCTCAC
*
44183689 GAGCTGAAAATCAGAAAGCTCATAA
1 GAGCTG-AAATCAGTAAGCTCATAA
* *
44183714 GAAAGCTAAGAATCAGT-AGCCTC-TCAC
1 G--AGCTGA-AATCAGTAAG-CTCAT-AA
*
44183741 GAGCTGAAATCAGTAAGCTCATAT
1 GAGCTGAAATCAGTAAGCTCATAA
44183765 GAGCTG
1 GAGCTG
44183771 TGGTGTGCCC
Statistics
Matches: 45, Mismatches: 5, Indels: 15
0.69 0.08 0.23
Matches are distributed among these distances:
24 17 0.38
25 9 0.20
26 4 0.09
27 15 0.33
ACGTcount: A:0.39, C:0.20, G:0.22, T:0.20
Consensus pattern (24 bp):
GAGCTGAAATCAGTAAGCTCATAA
Found at i:44185337 original size:25 final size:28
Alignment explanation
Indices: 44185281--44185348 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
44185271 GTTTCTGTTA
*
44185281 AAGGAATGTCTTTGTGGTAAATCTCTGAT
1 AAGGAATGCCTTTGTGGTAAA-CTCTGAT
*
44185310 AAGGAATACCTTTGTGGT-AA-TCT-AT
1 AAGGAATGCCTTTGTGGTAAACTCTGAT
44185335 AAGGAGATGCCTTT
1 AAGGA-ATGCCTTT
44185349 ATGGCACAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
25 7 0.20
26 10 0.29
28 2 0.06
29 16 0.46
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (28 bp):
AAGGAATGCCTTTGTGGTAAACTCTGAT
Found at i:44185522 original size:29 final size:29
Alignment explanation
Indices: 44185388--44185528 Score: 140
Period size: 29 Copynumber: 4.9 Consensus size: 29
44185378 TCAATTTTCA
* * *
44185388 TAAAACAATGCCTTTGTGGTGATCTCTAT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTAT
* *
44185417 TAAAAGGAAGCCTTTGTGACGATCTCTAT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTAT
* * * *
44185446 TAAAAGGAAGCTTTTGTGACGATCTCTGT
1 TAAAAGAAAGCCTTTGTGGCGATCTCTAT
* * * *
44185475 TAAAATG-AAGCATTTGTGGCAATATCTTT
1 TAAAA-GAAAGCCTTTGTGGCGATCTCTAT
*
44185504 TAAAAGAAAGCCTTTGTGGCAATCT
1 TAAAAGAAAGCCTTTGTGGCGATCT
44185529 TTGTCAAAGG
Statistics
Matches: 96, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
28 1 0.01
29 94 0.98
30 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (29 bp):
TAAAAGAAAGCCTTTGTGGCGATCTCTAT
Found at i:44188127 original size:43 final size:43
Alignment explanation
Indices: 44188079--44188164 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
44188069 TCAAATGAAA
44188079 GAAGAGAATTGAATTTTACACTAAGGAAAATCTTCATAATTGT
1 GAAGAGAATTGAATTTTACACTAAGGAAAATCTTCATAATTGT
44188122 GAAGAGAATTGAATTTTACACTAAGGAAAATCTTCATAATTGT
1 GAAGAGAATTGAATTTTACACTAAGGAAAATCTTCATAATTGT
44188165 TTTCCTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.42, C:0.09, G:0.16, T:0.33
Consensus pattern (43 bp):
GAAGAGAATTGAATTTTACACTAAGGAAAATCTTCATAATTGT
Found at i:44199751 original size:21 final size:20
Alignment explanation
Indices: 44199722--44199763 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
44199712 GTGTCTTGAT
44199722 GGTGTGGTGCGA-TAGGCAAG
1 GGTGTGGTGCGAGTA-GCAAG
44199742 GGTGTTGGTGCGAGTAGCAAG
1 GGTG-TGGTGCGAGTAGCAAG
44199763 G
1 G
44199764 CAGCAGCGGC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 14 0.70
22 2 0.10
ACGTcount: A:0.19, C:0.10, G:0.50, T:0.21
Consensus pattern (20 bp):
GGTGTGGTGCGAGTAGCAAG
Found at i:44200345 original size:16 final size:15
Alignment explanation
Indices: 44200320--44200353 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
44200310 AAAGTTGATA
*
44200320 ATAATTAATATATATT
1 ATAATAAATATA-ATT
44200336 ATAATAAATATAATT
1 ATAATAAATATAATT
44200351 ATA
1 ATA
44200354 TACTAGTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAATAAATATAATT
Found at i:44212525 original size:14 final size:14
Alignment explanation
Indices: 44212506--44212536 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44212496 TGAAAATTTT
*
44212506 TTAACAGAAAAGTG
1 TTAACACAAAAGTG
44212520 TTAACACAAAAGTG
1 TTAACACAAAAGTG
44212534 TTA
1 TTA
44212537 TTGCAGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (14 bp):
TTAACACAAAAGTG
Found at i:44225723 original size:22 final size:21
Alignment explanation
Indices: 44225692--44225733 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
44225682 ATAAACTAAA
44225692 ACTAAATAAAAACCCTAAAACT
1 ACTAAAT-AAAACCCTAAAACT
*
44225714 ACTAACTAAAACCCTAAAAC
1 ACTAAATAAAACCCTAAAAC
44225734 GAATTGGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.57, C:0.26, G:0.00, T:0.17
Consensus pattern (21 bp):
ACTAAATAAAACCCTAAAACT
Found at i:44227961 original size:18 final size:18
Alignment explanation
Indices: 44227938--44227996 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
44227928 AGGCAAAATG
*
44227938 ATTGTAAGAATCTTATTA
1 ATTGTAAGAATCTTAATA
* ** *
44227956 ATTGT-AGAAGCAAAATG
1 ATTGTAAGAATCTTAATA
*
44227973 ATTGTAAGAATCTTAGTA
1 ATTGTAAGAATCTTAATA
44227991 ATTGTA
1 ATTGTA
44227997 GAAGGTTTTA
Statistics
Matches: 30, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
17 12 0.40
18 18 0.60
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (18 bp):
ATTGTAAGAATCTTAATA
Found at i:44227976 original size:35 final size:35
Alignment explanation
Indices: 44227930--44228000 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
44227920 GAGTAGTAAG
*
44227930 GCAAAATGATTGTAAGAATCTTATTAATTGTAGAA
1 GCAAAATGATTGTAAGAATCTTAGTAATTGTAGAA
44227965 GCAAAATGATTGTAAGAATCTTAGTAATTGTAGAA
1 GCAAAATGATTGTAAGAATCTTAGTAATTGTAGAA
44228000 G
1 G
44228001 GTTTTATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.42, C:0.06, G:0.20, T:0.32
Consensus pattern (35 bp):
GCAAAATGATTGTAAGAATCTTAGTAATTGTAGAA
Found at i:44236129 original size:14 final size:14
Alignment explanation
Indices: 44236110--44236137 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
44236100 TACATCATTT
44236110 TTTTAATTATATTG
1 TTTTAATTATATTG
44236124 TTTTAATTATATTG
1 TTTTAATTATATTG
44236138 CTCTCAAGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (14 bp):
TTTTAATTATATTG
Found at i:44239674 original size:20 final size:22
Alignment explanation
Indices: 44239634--44239676 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
44239624 TTTAAAAAAG
*
44239634 TTAAAAATTCAAAAAATTATTT
1 TTAAAAAATCAAAAAATTATTT
44239656 TTAAAAAAT-AAAAAA-TATTT
1 TTAAAAAATCAAAAAATTATTT
44239676 T
1 T
44239677 GATTATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 6 0.30
22 8 0.40
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTAAAAAATCAAAAAATTATTT
Found at i:44247720 original size:46 final size:46
Alignment explanation
Indices: 44247661--44247838 Score: 241
Period size: 46 Copynumber: 3.9 Consensus size: 46
44247651 AGGATATTTG
* *
44247661 TTGTGTAGGTTCAACCCTAACGGGTGACCAGACACTATTATTTGAT
1 TTGTGTAGGTTCAACCCTAATGGGTGACCAAACACTATTATTTGAT
* * * *
44247707 TCGTGTATGTTCAACCCTAATGGGTGACAAAATACTATTATTTGAT
1 TTGTGTAGGTTCAACCCTAATGGGTGACCAAACACTATTATTTGAT
* *
44247753 TTGTGTAGGTTCAACCCTAATGGGTGACGAAACACTATTATTCGAT
1 TTGTGTAGGTTCAACCCTAATGGGTGACCAAACACTATTATTTGAT
* * *
44247799 TTGTGTAGGTTTAA-CCTAAATGGGTAACCAGACACTATTA
1 TTGTGTAGGTTCAACCCT-AATGGGTGACCAAACACTATTA
44247839 CTTTCACCTA
Statistics
Matches: 116, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
45 3 0.03
46 113 0.97
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (46 bp):
TTGTGTAGGTTCAACCCTAATGGGTGACCAAACACTATTATTTGAT
Found at i:44249652 original size:28 final size:28
Alignment explanation
Indices: 44249612--44249665 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
44249602 GCCAATTGTA
*
44249612 TCCCACCAATTTTGCTAATAATATTTTG
1 TCCCACCAATTTTGATAATAATATTTTG
*
44249640 TCCCACCAATTTTGATAATCATATTT
1 TCCCACCAATTTTGATAATAATATTT
44249666 AAAGTTGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.30, C:0.22, G:0.06, T:0.43
Consensus pattern (28 bp):
TCCCACCAATTTTGATAATAATATTTTG
Found at i:44252054 original size:12 final size:12
Alignment explanation
Indices: 44252029--44252067 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
44252019 ACTCGCTTCT
* *
44252029 TTACTTACTCAC
1 TTACTTGCTTAC
*
44252041 TTACTTGTTTAC
1 TTACTTGCTTAC
44252053 TTACTTGCTTAC
1 TTACTTGCTTAC
44252065 TTA
1 TTA
44252068 AATAACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.21, C:0.23, G:0.05, T:0.51
Consensus pattern (12 bp):
TTACTTGCTTAC
Found at i:44252384 original size:50 final size:50
Alignment explanation
Indices: 44252316--44252604 Score: 337
Period size: 50 Copynumber: 5.7 Consensus size: 50
44252306 TTTTCTGTTT
* * ** ** *
44252316 TGCCAATGCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATAACAG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
44252366 TGCCCATGCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC-ATGGGACCTCTCATCTCGG
* * *
44252416 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
**
44252466 TGCCAATGCCATGTCCCAGATGTGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * * **
44252516 TGCCAACGCCATGGCCGAGACATGGTCTTACATGAGACCTCTCATAATCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC---GG
44252572 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
44252605 TGGATCTCAT
Statistics
Matches: 203, Mismatches: 28, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
49 1 0.00
50 166 0.82
51 1 0.00
53 5 0.02
56 30 0.15
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.26
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:44252500 original size:150 final size:149
Alignment explanation
Indices: 44252267--44252614 Score: 385
Period size: 150 Copynumber: 2.3 Consensus size: 149
44252257 TGATAATACA
* * ** **
44252267 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTTCTGTTTTGCCAATGCCATATCC
1 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCTCATCTGTGGTGCCAATGCCATATCC
** * * *
44252332 CAGATATGGTCTTACATGGGAGTTCTCATAACAGTGCCCATGCCATGTCCCAGACATGGTCTTAC
66 CAGATATGGTCTTACATGGGACCTCTCATAACAGTGCCAACGCCATGGCCCAGACATGGTCTTAC
*
44252397 GA-GGGACCTCTCATCTCGG
131 -ATGAGACCTCTCATCTCGG
* *
44252416 TGCCAACGCCATGTCCCAGACATAGTCTTACATGGGACCTCTCATCT-TGGTGCCAATGCCATGT
1 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGA--TCTCATCTGTGGTGCCAATGCCATAT
* ** * *
44252480 CCCAGATGTGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGGCCGAGACATGGTCTT
64 CCCAGATATGGTCTTACATGGGACCTCTCATAACAGTGCCAACGCCATGGCCCAGACATGGTCTT
**
44252545 ACATGAGACCTCTCATAATCTCAATAA
129 ACATGAGACCTCTC---ATCTC---GG
* * *
44252572 TGCCAATGCCATGTCCCAGACATGGTCTTACATTGGATCTCAT
1 TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCTCAT
44252615 TCCCTTAATG
Statistics
Matches: 166, Mismatches: 24, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
149 36 0.22
150 80 0.48
151 5 0.03
153 5 0.03
154 6 0.04
156 34 0.20
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (149 bp):
TGCCAAAGCCATGTCCCAGACATAGTCTTACATGGGATCTCATCTGTGGTGCCAATGCCATATCC
CAGATATGGTCTTACATGGGACCTCTCATAACAGTGCCAACGCCATGGCCCAGACATGGTCTTAC
ATGAGACCTCTCATCTCGG
Found at i:44252965 original size:13 final size:13
Alignment explanation
Indices: 44252947--44252972 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
44252937 GCCCAAACGT
44252947 CGAAATTTTCTCA
1 CGAAATTTTCTCA
44252960 CGAAATTTTCTCA
1 CGAAATTTTCTCA
44252973 AAATCATTCC
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:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (13 bp):
CGAAATTTTCTCA
Found at i:44254117 original size:21 final size:20
Alignment explanation
Indices: 44254081--44254119 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
44254071 ATATACCATG
44254081 CAATACTTTACATTTCAATC
1 CAATACTTTACATTTCAATC
*
44254101 CAATACATTTCCATTTCAA
1 CAATAC-TTTACATTTCAA
44254120 AACTACCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.36, C:0.26, G:0.00, T:0.38
Consensus pattern (20 bp):
CAATACTTTACATTTCAATC
Found at i:44254169 original size:2 final size:2
Alignment explanation
Indices: 44254145--44254191 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
44254135 TCACATTAGT
* * *
44254145 TA TA CA TA TA CA TA TA CA 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 TA TA
44254187 TA TA T
1 TA TA T
44254192 GATCACATAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.06, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:44256452 original size:60 final size:61
Alignment explanation
Indices: 44256308--44256434 Score: 152
Period size: 61 Copynumber: 2.1 Consensus size: 61
44256298 AGAACAACCA
* * * **
44256308 TTGTGGAAAAATTTTGGAAA-GAAATGCCTTTGTGGTGAGTATTAAATGTGAAGTAACGCCT
1 TTGTGGAAAAACTCTGAAAAGGAAA-GCCTTTGTGGTGAGTATTAAATGAAAAGTAACGCCT
* *
44256369 TTGTGGAAAAACTCTGAAAAGGAAAGCCTTTGTGGTGAGTACTT-AATGAAAAG-GATGCCT
1 TTGTGGAAAAACTCTGAAAAGGAAAGCCTTTGTGGTGAGTA-TTAAATGAAAAGTAACGCCT
44256429 TTGTGG
1 TTGTGG
44256435 CAATCTCTAG
Statistics
Matches: 57, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
60 11 0.19
61 40 0.70
62 6 0.11
ACGTcount: A:0.32, C:0.09, G:0.28, T:0.31
Consensus pattern (61 bp):
TTGTGGAAAAACTCTGAAAAGGAAAGCCTTTGTGGTGAGTATTAAATGAAAAGTAACGCCT
Found at i:44256457 original size:28 final size:27
Alignment explanation
Indices: 44256365--44256491 Score: 83
Period size: 28 Copynumber: 4.4 Consensus size: 27
44256355 GTGAAGTAAC
* *
44256365 GCCTTTGTGGAAAAACTCTGAAAAGGAAA
1 GCCTTTGTGG-CAATCTCTGAAAAGG-AA
* * * *
44256394 GCCTTTGTGGTGAGTACTTAATGAAAAGGAT
1 GCCTTTGTGG-CAAT-C-T-CTGAAAAGGAA
*
44256425 GCCTTTGTGGCAATCTCTAGATAAGGAA
1 GCCTTTGTGGCAATCTCT-GAAAAGGAA
* **
44256453 GCCTTTATGGTTATCTCTGAAAAGGAA
1 GCCTTTGTGGCAATCTCTGAAAAGGAA
*
44256480 TGCCTTCGTGGC
1 -GCCTTTGTGGC
44256492 GCCATCTAAA
Statistics
Matches: 75, Mismatches: 18, Indels: 11
0.72 0.17 0.11
Matches are distributed among these distances:
27 9 0.12
28 31 0.41
29 12 0.16
30 3 0.04
31 12 0.16
32 8 0.11
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.29
Consensus pattern (27 bp):
GCCTTTGTGGCAATCTCTGAAAAGGAA
Found at i:44259604 original size:16 final size:16
Alignment explanation
Indices: 44259583--44259614 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44259573 ATTTTGTTGT
*
44259583 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
44259599 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
44259615 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:44259831 original size:44 final size:46
Alignment explanation
Indices: 44259744--44259833 Score: 114
Period size: 46 Copynumber: 2.0 Consensus size: 46
44259734 AACAGATACA
* *
44259744 CGGTGGATTCAGCACACATCAACCACCCTTTGTAATCAATGATATC
1 CGGTGGATTCAGCACACAGCAACCACCCTTTATAATCAATGATATC
* *
44259790 CGGTGGGA-TCAGCACATAGCAACCA-CC-TTATAATTAATGATATC
1 CGGT-GGATTCAGCACACAGCAACCACCCTTTATAATCAATGATATC
44259834 GGTTCACATA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
44 15 0.38
45 2 0.05
46 19 0.49
47 3 0.08
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.26
Consensus pattern (46 bp):
CGGTGGATTCAGCACACAGCAACCACCCTTTATAATCAATGATATC
Found at i:44259900 original size:51 final size:51
Alignment explanation
Indices: 44259842--44260032 Score: 224
Period size: 51 Copynumber: 3.8 Consensus size: 51
44259832 TCGGTTCACA
* * * * *
44259842 TAGTAGCCTTCACATAGTACTACACATGTGACCATCACTATCCGCTACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
* ** * *
44259893 TAGTAGCCTGCACATAGTACTACACACGTGATCAAAACTATCTGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
* * * * *
44259944 TAGTAGACTTCACATAGTACTACACATGCGACCTATCA-T-TTTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTACACG
44259994 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
44260033 TTCACTTTCA
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
49 4 0.04
50 38 0.33
51 70 0.61
52 2 0.02
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
Found at i:44260021 original size:101 final size:102
Alignment explanation
Indices: 44259840--44260024 Score: 293
Period size: 101 Copynumber: 1.8 Consensus size: 102
44259830 TATCGGTTCA
* * *
44259840 CATAGTAGCCTTCACATAGTACTACACATGTGACCATCACTATCCGCTACATGTAGTAGCCTGCA
1 CATAGTAGACTTCACATAGTACTACACATGCGACCATCACTATCCGCTACACGTAGTAGCCTGCA
44259905 CATAGTACTACACACGTGATCAAAACTATCTGGTACG
66 CATAGTACTACACACGTGATCAAAACTATCTGGTACG
** *
44259942 CATAGTAGACTTCACATAGTACTACACATGCGACCTATCA-T-TTTGGTACACGTAGTAGCCTGC
1 CATAGTAGACTTCACATAGTACTACACATGCGACC-ATCACTATCCGCTACACGTAGTAGCCTGC
44260005 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
44260025 CCATCACTTT
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
101 38 0.50
102 34 0.45
103 4 0.05
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.26
Consensus pattern (102 bp):
CATAGTAGACTTCACATAGTACTACACATGCGACCATCACTATCCGCTACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCAAAACTATCTGGTACG
Found at i:44260047 original size:101 final size:102
Alignment explanation
Indices: 44259835--44260048 Score: 270
Period size: 101 Copynumber: 2.1 Consensus size: 102
44259825 AATGATATCG
* * *
44259835 GTTCACATAGTAGCCTTCACATAGTACTACACATGTGACCATCACTATCCGCTACATGTAGTAGC
1 GTTCACATAGTAGACTTCACATAGTACTACACATGCGACCATCACTATCCGCTACACGTAGTAGC
* **
44259900 CTGCACATAGTACTACACACGTGATCAAAACTATCTG
66 CTGCACATAGTACTACACACGTGACCAAAACTATCAC
* * ** *
44259937 GTACGCATAGTAGACTTCACATAGTACTACACATGCGACCTATCA-T-TTTGGTACACGTAGTAG
1 GTTCACATAGTAGACTTCACATAGTACTACACATGCGACC-ATCACTATCCGCTACACGTAGTAG
** *
44260000 CCTGCACATAGTACTACACACGTGACCATCACTTTCAC
65 CCTGCACATAGTACTACACACGTGACCAAAACTATCAC
*
44260038 TTTCACATAGT
1 GTTCACATAGT
44260049 GGCCTACACA
Statistics
Matches: 94, Mismatches: 17, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
101 53 0.56
102 37 0.39
103 4 0.04
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (102 bp):
GTTCACATAGTAGACTTCACATAGTACTACACATGCGACCATCACTATCCGCTACACGTAGTAGC
CTGCACATAGTACTACACACGTGACCAAAACTATCAC
Found at i:44270999 original size:35 final size:35
Alignment explanation
Indices: 44270933--44271022 Score: 108
Period size: 35 Copynumber: 2.6 Consensus size: 35
44270923 ATCACTGTGA
* * * *
44270933 CATGTTTAACATGTGAGTCAGAATCAAAATAATGG
1 CATGCTTAACATGCGAATCAGAATCAAAATAATAG
* * *
44270968 CATGCTTAACATGCGAATCATAATTAGAATAATAG
1 CATGCTTAACATGCGAATCAGAATCAAAATAATAG
*
44271003 CATGCTCAACATGCGAATCA
1 CATGCTTAACATGCGAATCA
44271023 AAATATCAAT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 47 1.00
ACGTcount: A:0.40, C:0.17, G:0.17, T:0.27
Consensus pattern (35 bp):
CATGCTTAACATGCGAATCAGAATCAAAATAATAG
Found at i:44271034 original size:35 final size:35
Alignment explanation
Indices: 44270960--44271034 Score: 98
Period size: 35 Copynumber: 2.1 Consensus size: 35
44270950 TCAGAATCAA
* * * *
44270960 AATAATGGCATGCTTAACATGCGAATCATAATTAG
1 AATAATAGCATGCTCAACATGCGAATCAAAATTAC
44270995 AATAATAGCATGCTCAACATGCGAATCAAAA-TATC
1 AATAATAGCATGCTCAACATGCGAATCAAAATTA-C
44271030 AATAA
1 AATAA
44271035 ATCAATATCA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 2 0.06
35 33 0.94
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (35 bp):
AATAATAGCATGCTCAACATGCGAATCAAAATTAC
Found at i:44286508 original size:21 final size:21
Alignment explanation
Indices: 44286467--44286508 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
44286457 TTAACAATGC
* **
44286467 TTTTATCTCAAACGTGTTTTT
1 TTTTATCTCAAAAGTCCTTTT
44286488 TTTTATCTCAAAAGTCCTTTT
1 TTTTATCTCAAAAGTCCTTTT
44286509 GAAAAGCTAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (21 bp):
TTTTATCTCAAAAGTCCTTTT
Found at i:44292543 original size:20 final size:20
Alignment explanation
Indices: 44292518--44292587 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
44292508 TACAAAAATA
44292518 CAAAAACTTTTAAAATGTAT
1 CAAAAACTTTTAAAATGTAT
** * * *
44292538 CAAAAAGGCCCTTAAACCTTTTAA
1 CAAAAA--CTTTTAAA--ATGTAT
44292562 CAAAAACTTTTAAAATGTAT
1 CAAAAACTTTTAAAATGTAT
44292582 CAAAAA
1 CAAAAA
44292588 GACTCTTAAA
Statistics
Matches: 36, Mismatches: 10, Indels: 8
0.67 0.19 0.15
Matches are distributed among these distances:
20 15 0.42
22 12 0.33
24 9 0.25
ACGTcount: A:0.50, C:0.16, G:0.06, T:0.29
Consensus pattern (20 bp):
CAAAAACTTTTAAAATGTAT
Found at i:44292566 original size:44 final size:44
Alignment explanation
Indices: 44292517--44292603 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
44292507 ATACAAAAAT
*
44292517 ACAAAAACTTTTAAAATGTATCAAAAAGGCCCTTAAACCTTTTA
1 ACAAAAACTTTTAAAATGTATCAAAAAGACCCTTAAACCTTTTA
*
44292561 ACAAAAACTTTTAAAATGTATCAAAAAGACTCTTAAACCTTTT
1 ACAAAAACTTTTAAAATGTATCAAAAAGACCCTTAAACCTTTT
44292604 CAAAAATAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (44 bp):
ACAAAAACTTTTAAAATGTATCAAAAAGACCCTTAAACCTTTTA
Found at i:44292596 original size:22 final size:22
Alignment explanation
Indices: 44292519--44292597 Score: 56
Period size: 22 Copynumber: 3.6 Consensus size: 22
44292509 ACAAAAATAC
*
44292519 AAAA-ACTTTTAAAATGTATCA
1 AAAAGACTCTTAAAATGTATCA
* * * *
44292540 AAAAGGCCCTTAAACCT-T-TTA
1 AAAAGACTCTTAAA-ATGTATCA
* *
44292561 ACAAAAACTTTTAAAATGTATCA
1 A-AAAGACTCTTAAAATGTATCA
44292584 AAAAGACTCTTAAA
1 AAAAGACTCTTAAA
44292598 CCTTTTCAAA
Statistics
Matches: 40, Mismatches: 13, Indels: 9
0.65 0.21 0.15
Matches are distributed among these distances:
21 8 0.20
22 28 0.70
23 4 0.10
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29
Consensus pattern (22 bp):
AAAAGACTCTTAAAATGTATCA
Found at i:44292606 original size:22 final size:22
Alignment explanation
Indices: 44292537--44292609 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
44292527 TTAAAATGTA
* *
44292537 TCAAAAAGGCCCTTAAACCTTT
1 TCAAAAAGACTCTTAAACCTTT
* * * *
44292559 T-AACAAAAACTTTTAAA-ATGTA
1 TCAA-AAAGACTCTTAAACCT-TT
44292581 TCAAAAAGACTCTTAAACCTTT
1 TCAAAAAGACTCTTAAACCTTT
44292603 TCAAAAA
1 TCAAAAA
44292610 TAAAAGCAAT
Statistics
Matches: 37, Mismatches: 10, Indels: 8
0.67 0.18 0.15
Matches are distributed among these distances:
21 3 0.08
22 31 0.84
23 3 0.08
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.29
Consensus pattern (22 bp):
TCAAAAAGACTCTTAAACCTTT
Found at i:44292840 original size:20 final size:20
Alignment explanation
Indices: 44292770--44292843 Score: 62
Period size: 20 Copynumber: 3.7 Consensus size: 20
44292760 AAAAAATTAT
* * *
44292770 AAAATTTTATAAAGTCGTAAG
1 AAAATTATA-AAAATCGTAAA
44292791 AAAATTATACAAAAT-GTAAA
1 AAAATTATA-AAAATCGTAAA
* **
44292811 GAAA-TATAAATTTCGTAAA
1 AAAATTATAAAAATCGTAAA
44292830 AAAATTATAAAAAT
1 AAAATTATAAAAAT
44292844 TATCGTATCA
Statistics
Matches: 41, Mismatches: 10, Indels: 5
0.73 0.18 0.09
Matches are distributed among these distances:
18 3 0.07
19 12 0.29
20 14 0.34
21 12 0.29
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (20 bp):
AAAATTATAAAAATCGTAAA
Found at i:44293170 original size:21 final size:21
Alignment explanation
Indices: 44293117--44293170 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
44293107 TACAGTTCTA
* *
44293117 TTTC-TTTCTTTTTTTGCTGT
1 TTTCTTTTCTTTTGTTGCTAT
*
44293137 TTT-TTATTATTTTGTTGCTAT
1 TTTCTT-TTCTTTTGTTGCTAT
44293158 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
44293171 CTTTTGACTA
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
20 4 0.15
21 21 0.78
22 2 0.07
ACGTcount: A:0.06, C:0.11, G:0.07, T:0.76
Consensus pattern (21 bp):
TTTCTTTTCTTTTGTTGCTAT
Found at i:44293637 original size:19 final size:19
Alignment explanation
Indices: 44293609--44293665 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 19
44293599 GTCGCTAATT
*
44293609 TTTTATAATTTTTATAAAA
1 TTTTACAATTTTTATAAAA
* ***
44293628 TTTTACAATTTTTTTACTT
1 TTTTACAATTTTTATAAAA
*
44293647 TTTTACGATTTTTATAAAA
1 TTTTACAATTTTTATAAAA
44293666 AAAATTCTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (19 bp):
TTTTACAATTTTTATAAAA
Found at i:44294869 original size:26 final size:27
Alignment explanation
Indices: 44294839--44294896 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 27
44294829 ATATTAAAAT
*
44294839 TATTTATATAATTT-TATTATATATTA
1 TATTTATAAAATTTGTATTATATATTA
* *
44294865 TATTT-TAAAATTTGTATTTTCTATTA
1 TATTTATAAAATTTGTATTATATATTA
*
44294891 TTTTTA
1 TATTTA
44294897 ATGGTGTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
25 7 0.27
26 19 0.73
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTATAAAATTTGTATTATATATTA
Found at i:44299399 original size:94 final size:95
Alignment explanation
Indices: 44299237--44299443 Score: 287
Period size: 94 Copynumber: 2.2 Consensus size: 95
44299227 CTTGTTAAAA
*
44299237 CTCACTCTACGTGTTCCTTTGAGAATATGAGCTTTTGTGAGCCTCACTTTGCGTGCTCCTTGAGA
1 CTCACTCTACGTGTTCCTTTGAGAACATGAGCTTTTGTGAGCCTCACTTTGCGTGCTCCTTGAGA
* *
44299302 GCATGGGATTTTTTGAGTTTTGTGATAAGT
66 GCATGGGATTTTGTGAGATTTGTGATAAGT
** *
44299332 CTCACTCTGTGTGTTCCTTTGA-AACATGAG-TATTTGTGAGCCTCACTTTGTGTGCTCCTTGAG
1 CTCACTCTACGTGTTCCTTTGAGAACATGAGCT-TTTGTGAGCCTCACTTTGCGTGCTCCTTGAG
*
44299395 AGCATGGGCTTTTGTGAGATTTGT-ATATA-T
65 AGCATGGGATTTTGTGAGATTTGTGATA-AGT
* *
44299425 CTCATTCTACGTGCTCCTT
1 CTCACTCTACGTGTTCCTT
44299444 GCGAGCTACG
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
93 20 0.20
94 59 0.60
95 20 0.20
ACGTcount: A:0.17, C:0.19, G:0.23, T:0.41
Consensus pattern (95 bp):
CTCACTCTACGTGTTCCTTTGAGAACATGAGCTTTTGTGAGCCTCACTTTGCGTGCTCCTTGAGA
GCATGGGATTTTGTGAGATTTGTGATAAGT
Found at i:44306492 original size:18 final size:19
Alignment explanation
Indices: 44306459--44306494 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
44306449 ATCATTAATT
*
44306459 GAATTTTTTATCAAAAATC
1 GAATATTTTATCAAAAATC
44306478 GAATATTTT-TCAAAAAT
1 GAATATTTTATCAAAAAT
44306495 AAAATATTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (19 bp):
GAATATTTTATCAAAAATC
Found at i:44306500 original size:18 final size:19
Alignment explanation
Indices: 44306464--44306502 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
44306454 TAATTGAATT
**
44306464 TTTTATCAAAAATCGAATA
1 TTTTATCAAAAATAAAATA
44306483 TTTT-TCAAAAATAAAATA
1 TTTTATCAAAAATAAAATA
44306501 TT
1 TT
44306503 CTCAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (19 bp):
TTTTATCAAAAATAAAATA
Found at i:44317792 original size:2 final size:2
Alignment explanation
Indices: 44317785--44317828 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
44317775 TATTTCCAAT
44317785 TA TA 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 TA TA
44317827 TA
1 TA
44317829 CTATCATTTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44330038 original size:23 final size:23
Alignment explanation
Indices: 44329995--44330038 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
44329985 ATTCCTTCTT
*
44329995 TCCTTGTTTTCTCCTCTTTTCAC
1 TCCTTGTTTTCTCCTCATTTCAC
*
44330018 TCCTTTTTTTC-CCTCCATTTC
1 TCCTTGTTTTCTCCT-CATTTC
44330039 CTTTCTTCTC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.17
23 15 0.83
ACGTcount: A:0.05, C:0.36, G:0.02, T:0.57
Consensus pattern (23 bp):
TCCTTGTTTTCTCCTCATTTCAC
Found at i:44338087 original size:21 final size:22
Alignment explanation
Indices: 44338063--44338103 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
44338053 GCTCTATACT
44338063 TATAA-ACCATAAA-CAAATCTA
1 TATAATACCA-AAACCAAATCTA
44338084 TATAATACCAAAACCAAATC
1 TATAATACCAAAACCAAATC
44338104 ACACCATACA
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:0.56, C:0.22, G:0.00, T:0.22
Consensus pattern (22 bp):
TATAATACCAAAACCAAATCTA
Found at i:44339159 original size:43 final size:44
Alignment explanation
Indices: 44339036--44339148 Score: 135
Period size: 43 Copynumber: 2.6 Consensus size: 44
44339026 AGCTCGTACA
* * *
44339036 ATGCCAGCGTCCCAGACGTGGTCTTACATGTGATCAC-AGATCG
1 ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACAAGATCG
* *
44339079 ATGCC-ACTGTCCCAAATAG-GGTCTTACATGTAAACACAAG-TCG
1 ATGCCAAC-GTCCCAGA-CGTGGTCTTACATGTAAACACAAGATCG
44339122 ATGCCAACGTCCCAGACGTGGTCTTAC
1 ATGCCAACGTCCCAGACGTGGTCTTAC
44339149 TCGAAAACAC
Statistics
Matches: 58, Mismatches: 7, Indels: 10
0.77 0.09 0.13
Matches are distributed among these distances:
42 2 0.03
43 51 0.88
44 5 0.09
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (44 bp):
ATGCCAACGTCCCAGACGTGGTCTTACATGTAAACACAAGATCG
Found at i:44360097 original size:51 final size:50
Alignment explanation
Indices: 44359970--44360155 Score: 241
Period size: 51 Copynumber: 3.7 Consensus size: 50
44359960 ATTATCATTC
* * *
44359970 GGTACACGTAGTAGCCTTCACATAATACTACACACGTGATC-AAGTTTTAT
1 GGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTTTT-T
*
44360020 GGTTCACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGCTTTTT
1 GGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAG-TTTTT
* * * *
44360071 GGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATTA-TTTATC
1 GGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCA-AAGTTT-TT
*
44360122 GATACACGTAGTAGCCTTCACATAGTACTACACA
1 GGTACACGTAGTAGCCTTCACATAGTACTACACA
44360156 CGTGTTCATC
Statistics
Matches: 120, Mismatches: 12, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
50 40 0.33
51 75 0.62
52 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (50 bp):
GGTACACGTAGTAGCCTTCACATAGTACTACACATGTGACCAAAGTTTTT
Found at i:44360105 original size:26 final size:26
Alignment explanation
Indices: 44360073--44360155 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
44360063 AGCTTTTTGG
44360073 TACACATAGTAGCCTTCACTTAGTAC
1 TACACATAGTAGCCTTCACTTAGTAC
*
44360099 TACACAT-GT-GACCATT-ATTTA-T-C
1 TACACATAGTAG-CC-TTCACTTAGTAC
* *
44360122 GATACACGTAGTAGCCTTCACATAGTAC
1 --TACACATAGTAGCCTTCACTTAGTAC
44360150 TACACA
1 TACACA
44360156 CGTGTTCATC
Statistics
Matches: 43, Mismatches: 5, Indels: 18
0.65 0.08 0.27
Matches are distributed among these distances:
23 1 0.02
24 2 0.05
25 16 0.37
26 21 0.49
27 2 0.05
28 1 0.02
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (26 bp):
TACACATAGTAGCCTTCACTTAGTAC
Found at i:44360120 original size:101 final size:102
Alignment explanation
Indices: 44359970--44360155 Score: 277
Period size: 101 Copynumber: 1.8 Consensus size: 102
44359960 ATTATCATTC
* * *
44359970 GGTACACGTAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTAT-GGTTCACGTAGTAG
1 GGTACACATAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTATCGATACACGTAGTAG
44360034 CCTTCACATAGTACTACACATGTGACCAAAGCTTTTT
66 CCTTCACATAGTACTACACATGTGACCAAAGCTTTTT
* * * * *
44360071 GGTACACATAGTAGCCTTCACTTAGTACTACACATGTGA-CCATTATTTATCGATACACGTAGTA
1 GGTACACATAGTAGCCTTCACATAATACTACACACGTGATCAAGT-TTTATCGATACACGTAGTA
44360135 GCCTTCACATAGTACTACACA
65 GCCTTCACATAGTACTACACA
44360156 CGTGTTCATC
Statistics
Matches: 75, Mismatches: 8, Indels: 3
0.87 0.09 0.03
Matches are distributed among these distances:
100 3 0.04
101 40 0.53
102 32 0.43
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (102 bp):
GGTACACATAGTAGCCTTCACATAATACTACACACGTGATCAAGTTTTATCGATACACGTAGTAG
CCTTCACATAGTACTACACATGTGACCAAAGCTTTTT
Found at i:44361428 original size:3 final size:3
Alignment explanation
Indices: 44361420--44361446 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
44361410 CCATAAAAAT
44361420 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
44361447 TTTTTCCTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:44367727 original size:101 final size:102
Alignment explanation
Indices: 44367605--44367797 Score: 264
Period size: 101 Copynumber: 1.9 Consensus size: 102
44367595 ACTATTATCA
* * *
44367605 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACATGATCAAGT-TTTACAG-TTCGCGTA
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACATGA-CAAGTATTTACAGATACACGTA
44367668 GTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
65 GTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
* * * ** * * *
44367706 TTCGGTACACATAGTAGCCTTCACTTAGTACTATACATGTGACCATTATTTATAGATACACGTAG
1 TTCGATACACATAGTAGCCTTCACATAGTACTACACACATGACAAGTATTTACAGATACACGTAG
44367771 TAGCCTTCACATAGTACTACACACGTG
66 TAGCCTTCACATAGTACTACACACGTG
44367798 TTCATCGATA
Statistics
Matches: 79, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
100 3 0.04
101 42 0.53
102 34 0.43
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (102 bp):
TTCGATACACATAGTAGCCTTCACATAGTACTACACACATGACAAGTATTTACAGATACACGTAG
TAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
Found at i:44367748 original size:51 final size:50
Alignment explanation
Indices: 44367605--44367797 Score: 221
Period size: 51 Copynumber: 3.8 Consensus size: 50
44367595 ACTATTATCA
* *
44367605 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACATGATC-AAGTT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
* *
44367654 TTAC-AGTTCGCGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGCTT
1 TT-CGA-TACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAG-TT
* * * * * *
44367706 TTCGGTACACATAGTAGCCTTCACTTAGTACTATACATGTGACCATTA-TT
1 TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCA-AAGTT
*
44367756 TATAGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
1 T-TCGATACACGTAGTAGCCTTCACATAGTACTACACACGTG
44367798 TTCATCGATA
Statistics
Matches: 119, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
49 3 0.03
50 39 0.33
51 72 0.61
52 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.30
Consensus pattern (50 bp):
TTCGATACACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGTT
Done.