Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009267.1 Hibiscus syriacus cultivar Beakdansim tig00112925_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: 1725308
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 10
Found at i:215483 original size:23 final size:23
Alignment explanation
Indices: 215417--215484 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
215407 TCTTGATTTA
*
215417 ATTTTTTTCCTTTTTTCCT-TTTT
1 ATTTTTTT-CTTTTTTCCTCTTTC
* * *
215440 GTTTTTTTATTTTTAT-TTCTTTC
1 ATTTTTTTCTTTTT-TCCTCTTTC
215463 ATTTTTTTCTTTTTTCCTCTTT
1 ATTTTTTTCTTTTTTCCTCTTT
215485 TTTTCTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
22 7 0.20
23 28 0.80
ACGTcount: A:0.06, C:0.15, G:0.01, T:0.78
Consensus pattern (23 bp):
ATTTTTTTCTTTTTTCCTCTTTC
Found at i:215485 original size:18 final size:18
Alignment explanation
Indices: 215464--215498 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
215454 ATTTCTTTCA
215464 TTTTTTTCTTTTTTCCTC
1 TTTTTTTCTTTTTTCCTC
215482 TTTTTTTCTTTTTTCCT
1 TTTTTTTCTTTTTTCCT
215499 TTCTTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTTTTCTTTTTTCCTC
Found at i:215514 original size:27 final size:26
Alignment explanation
Indices: 215484--215537 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
215474 TTTTCCTCTT
215484 TTTTTCTTTTTTCCTTTCTTTGATGGA
1 TTTTTCTTTTTT-CTTTCTTTGATGGA
*
215511 TTTTTCTTTTTTCTTTCTTTGCTGGA
1 TTTTTCTTTTTTCTTTCTTTGATGGA
215537 T
1 T
215538 GAGTATAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.06, C:0.15, G:0.11, T:0.69
Consensus pattern (26 bp):
TTTTTCTTTTTTCTTTCTTTGATGGA
Found at i:215829 original size:2 final size:2
Alignment explanation
Indices: 215824--215876 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
215814 ACAAAAAAGG
215824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
215866 AT AT AT AT AT A
1 AT AT AT AT AT A
215877 AAAGGATAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:217607 original size:7 final size:8
Alignment explanation
Indices: 217589--217627 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
217579 ATAAATGTAT
217589 AAATGCAA
1 AAATGCAA
217597 AAATG-AA
1 AAATGCAA
217604 AAATGCAA
1 AAATGCAA
*
217612 AGATGC-A
1 AAATGCAA
217619 AAATGCAA
1 AAATGCAA
217627 A
1 A
217628 TGTATGTATG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
7 13 0.48
8 14 0.52
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (8 bp):
AAATGCAA
Found at i:217609 original size:15 final size:15
Alignment explanation
Indices: 217589--217627 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
217579 ATAAATGTAT
217589 AAATGCAAAAATGAA
1 AAATGCAAAAATGAA
* *
217604 AAATGCAAAGATGCA
1 AAATGCAAAAATGAA
217619 AAATGCAAA
1 AAATGCAAA
217628 TGTATGTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.15, T:0.13
Consensus pattern (15 bp):
AAATGCAAAAATGAA
Found at i:219160 original size:19 final size:18
Alignment explanation
Indices: 219119--219174 Score: 62
Period size: 19 Copynumber: 3.1 Consensus size: 18
219109 ATTAATACCT
219119 TAATAAAATAA-AAAAATA
1 TAATAAAATAATAAAAA-A
219137 TTAATAAAATAATATAAAAA
1 -TAATAAAATAATA-AAAAA
*
219157 TAAT-AAGTAATAAAAAA
1 TAATAAAATAATAAAAAA
219174 T
1 T
219175 TTGAAAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 15 0.44
20 2 0.06
21 4 0.12
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
TAATAAAATAATAAAAAA
Found at i:219684 original size:27 final size:27
Alignment explanation
Indices: 219649--219703 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 27
219639 ATTTCAAAAT
219649 TATAATTATGAAA-AAAATATTAATTTA
1 TATAATTAT-AAATAAAATATTAATTTA
* *
219676 TATATTTATAAATAAAATATTTATTTA
1 TATAATTATAAATAAAATATTAATTTA
219703 T
1 T
219704 TTAGAAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 3 0.12
27 22 0.88
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
TATAATTATAAATAAAATATTAATTTA
Found at i:219798 original size:20 final size:19
Alignment explanation
Indices: 219759--219809 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
219749 TTTCTTCGAT
219759 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
219778 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
219798 ATTTAAAAAATA
1 A-TTAAAAAATA
219810 GGATATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 7 0.26
20 14 0.52
21 6 0.22
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:219989 original size:18 final size:16
Alignment explanation
Indices: 219958--219992 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
219948 GAATAAACAA
219958 ATATTATTTATTATAT
1 ATATTATTTATTATAT
219974 ATATATATTTATT-TAT
1 ATAT-TATTTATTATAT
219990 ATA
1 ATA
219993 AATAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 10 0.56
17 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTTATTATAT
Found at i:220008 original size:12 final size:11
Alignment explanation
Indices: 219993--220041 Score: 53
Period size: 12 Copynumber: 4.2 Consensus size: 11
219983 TATTTATATA
219993 AATAATAAAAAT
1 AATAAT-AAAAT
220005 AATAATAAAAT
1 AATAATAAAAT
*
220016 AATATTGAAAAT
1 AATAAT-AAAAT
*
220028 AATGATTAAAAT
1 AAT-AATAAAAT
220040 AA
1 AA
220042 AAGGAATTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
11 10 0.29
12 21 0.62
13 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:220040 original size:29 final size:29
Alignment explanation
Indices: 220008--220088 Score: 85
Period size: 29 Copynumber: 2.8 Consensus size: 29
219998 TAAAAATAAT
*
220008 AATAAAATAATATTGAAAATAATG-ATTAA
1 AATAAAA-AATATTAAAAATAATGTATTAA
* *
220037 AATAAAAGGA-ATTAAAAATATTGTATTAA
1 AATAAAA-AATATTAAAAATAATGTATTAA
*
220066 AATATAAAATATTAAAAAATAAT
1 AATAAAAAATATT-AAAAATAAT
220089 AATCAAAAAT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
28 12 0.29
29 22 0.52
30 8 0.19
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (29 bp):
AATAAAAAATATTAAAAATAATGTATTAA
Found at i:221345 original size:3 final size:3
Alignment explanation
Indices: 221339--221400 Score: 53
Period size: 3 Copynumber: 22.0 Consensus size: 3
221329 ATTATTTATT
* * *
221339 TAA TAA TAA TAA T-A TAA T-A TAA TAA CAA TAT TAA -AA CAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
221383 TAA TAA TAA CTAA -AA TAA
1 TAA TAA TAA -TAA TAA TAA
221401 ATGAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 12
0.75 0.06 0.18
Matches are distributed among these distances:
2 10 0.20
3 36 0.73
4 3 0.06
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:221361 original size:19 final size:19
Alignment explanation
Indices: 221339--221391 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
221329 ATTATTTATT
* *
221339 TAATAATAATAATATAATA
1 TAATAATAATAATAAAACA
* *
221358 TAATAACAATATTAAAACA
1 TAATAATAATAATAAAACA
*
221377 AAATAATAATAATAA
1 TAATAATAATAATAA
221392 CTAAAATAAA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (19 bp):
TAATAATAATAATAAAACA
Found at i:221402 original size:22 final size:21
Alignment explanation
Indices: 221339--221402 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 21
221329 ATTATTTATT
*
221339 TAATAATAATAATATAATATAA
1 TAATAATAATAAAATAA-ATAA
* * *
221361 TAACAATATTAAAACAAAATAA
1 TAATAATAATAAAA-TAAATAA
221383 TAATAATAACTAAAATAAAT
1 TAATAATAA-TAAAATAAAT
221403 GAAATAAAAA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
22 26 0.79
23 7 0.21
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.30
Consensus pattern (21 bp):
TAATAATAATAAAATAAATAA
Found at i:222773 original size:27 final size:27
Alignment explanation
Indices: 222735--222798 Score: 101
Period size: 27 Copynumber: 2.4 Consensus size: 27
222725 TTGAAACCTC
*
222735 TAGAGATAATAATCATCCATTTAACTA
1 TAGAGATAATAACCATCCATTTAACTA
*
222762 TAGAGATAATAACCATCTATTTAACTA
1 TAGAGATAATAACCATCCATTTAACTA
*
222789 TCGAGATAAT
1 TAGAGATAAT
222799 TTGGTTCTCC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (27 bp):
TAGAGATAATAACCATCCATTTAACTA
Found at i:227597 original size:43 final size:43
Alignment explanation
Indices: 227538--227697 Score: 171
Period size: 43 Copynumber: 3.7 Consensus size: 43
227528 ACAAAAAACA
* * * *
227538 CCGCAATAAGTATTGATGTTTAGCGGCGTTTGTGTGACAAATG
1 CCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTGACAAATG
* * * *
227581 CCGTAATAGGTGTTGATATTTAGTGGCGTTTGTCAGAAAAATG
1 CCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTGACAAATG
* *
227624 CCGCAATAGGTGTTGATATTTAGCGGCGTTT-TTTAGACAAACG
1 CCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCT-GACAAATG
* * *
227667 TCGCAATAGGT-TATGATGTTTAGCGACGTTT
1 CCGCAATAGGTGT-TGATATTTAGCGGCGTTT
227698 TTCTCTAAAA
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
42 2 0.02
43 96 0.98
ACGTcount: A:0.26, C:0.13, G:0.27, T:0.34
Consensus pattern (43 bp):
CCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCTGACAAATG
Found at i:227714 original size:86 final size:85
Alignment explanation
Indices: 227531--227768 Score: 217
Period size: 86 Copynumber: 2.8 Consensus size: 85
227521 TTTTTTAACA
* * *
227531 AAAAACACCGCAATAAGTATTGATGTTTAGCGGCGTTTGTGTGACAAATGCCGTAATAGGTGTTG
1 AAAAACACCGCAATAAGTGTTGATGTTTAGCGGCGTTT-TGTGACAAACGCCGCAATAGGTGTTG
* * *
227596 ATATTTAGTGGCGTTTGTCAG
65 ATATTTAGCGACGTTTGTCAC
** * * * *
227617 AAAAATGCCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACGTCGCAATAGGT-TAT
1 AAAAACACCGCAATAAGTGTTGATGTTTAGCGGCGTTTTGT-GACAAACGCCGCAATAGGTGT-T
* * *
227681 GATGTTTAGCGACGTTTTTCTC
64 GATATTTAGCGACGTTTGTCAC
* * * * *** * * *
227703 TAAAACACCGCAGTAAATGTTGATGTTTTGCGGCGTTTTCCCATAAACACCGCAATAGGTGCTGA
1 AAAAACACCGCAATAAGTGTTGATGTTTAGCGGCGTTTTGTGACAAACGCCGCAATAGGTGTTGA
227768 T
66 T
227769 GTTTTGTGGC
Statistics
Matches: 119, Mismatches: 30, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
85 22 0.18
86 97 0.82
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (85 bp):
AAAAACACCGCAATAAGTGTTGATGTTTAGCGGCGTTTTGTGACAAACGCCGCAATAGGTGTTGA
TATTTAGCGACGTTTGTCAC
Found at i:227755 original size:42 final size:42
Alignment explanation
Indices: 227624--227868 Score: 179
Period size: 43 Copynumber: 5.8 Consensus size: 42
227614 CAGAAAAATG
* * * *** *
227624 CCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACG
1 CCGCAGTAGGTGTTGATGTTTTGCGGCG-TTTTCCCACAAACA
* * * * *
227667 TCGCAATAGGT-TATGATGTTTAGCGACGTTTTTCTCTA-AAACA
1 CCGCAGTAGGTGT-TGATGTTTTGCGGCG-TTTTC-CCACAAACA
** *
227710 CCGCAGTAAATGTTGATGTTTTGCGGCGTTTTCCCATAAACA
1 CCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCCCACAAACA
* * * *
227752 CCGCAATAGGTGCTGATGTTTTGTGGCGTTTTCCCACAAACG
1 CCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCCCACAAACA
* * * * * *
227794 TCGTAGTAGGTTTTGATGTTTTGCAGCGTTTTTCTCACAAACG
1 CCGCAGTAGGTGTTGATGTTTTGCGGCG-TTTTCCCACAAACA
* * *
227837 CTGCAGTAGGTATTGATGTTTTACGGCGTTTT
1 CCGCAGTAGGTGTTGATGTTTTGCGGCGTTTT
227869 TGCTAAAAAC
Statistics
Matches: 162, Mismatches: 35, Indels: 11
0.78 0.17 0.05
Matches are distributed among these distances:
41 2 0.01
42 71 0.44
43 87 0.54
44 2 0.01
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (42 bp):
CCGCAGTAGGTGTTGATGTTTTGCGGCGTTTTCCCACAAACA
Found at i:227824 original size:127 final size:128
Alignment explanation
Indices: 227624--227868 Score: 298
Period size: 127 Copynumber: 1.9 Consensus size: 128
227614 CAGAAAAATG
* * *
227624 CCGCAATAGGTGTTGATATTTAGCGGCGTTTTTTAGACAAACGTCGCAATAGGTTATGATGTTTA
1 CCGCAATAGGTGCTGATATTTAGCGGCGTTTTTCACACAAACGTCGCAATAGGTTATGATGTTTA
* *
227689 GCGACGTTTTTCTCTA-AAACACCGCAGTAAATGTTGATGTTTTGCGGCGTTTTCCCATAAACA
66 GCGACGTTTTTCTC-ACAAACACCGCAGTAAATATTGATGTTTTACGGCGTTTTCCCATAAACA
* * * * * * * *
227752 CCGCAATAGGTGCTGATGTTTTGTGGCG-TTTTCCCACAAACGTCGTAGTAGGTTTTGATGTTTT
1 CCGCAATAGGTGCTGATATTTAGCGGCGTTTTTCACACAAACGTCGCAATAGGTTATGATGTTTA
* * **
227816 GC-AGCGTTTTTCTCACAAACGCTGCAGTAGGTATTGATGTTTTACGGCGTTTT
66 GCGA-CGTTTTTCTCACAAACACCGCAGTAAATATTGATGTTTTACGGCGTTTT
227869 TGCTAAAAAC
Statistics
Matches: 98, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
126 2 0.02
127 72 0.73
128 24 0.24
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (128 bp):
CCGCAATAGGTGCTGATATTTAGCGGCGTTTTTCACACAAACGTCGCAATAGGTTATGATGTTTA
GCGACGTTTTTCTCACAAACACCGCAGTAAATATTGATGTTTTACGGCGTTTTCCCATAAACA
Found at i:227879 original size:43 final size:43
Alignment explanation
Indices: 227798--227880 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
227788 CAAACGTCGT
* * *
227798 AGTAGGTTTTGATGTTTTGCAGCGTTTTTCTCACAAACGCTGC
1 AGTAGGTATTGATGTTTTACAGCGTTTTTCTCAAAAACGCTGC
*
227841 AGTAGGTATTGATGTTTTACGGCGTTTTTGCT-AAAAACGC
1 AGTAGGTATTGATGTTTTACAGCGTTTTT-CTCAAAAACGC
227881 CAGTAAAGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
43 33 0.94
44 2 0.06
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.39
Consensus pattern (43 bp):
AGTAGGTATTGATGTTTTACAGCGTTTTTCTCAAAAACGCTGC
Found at i:237247 original size:41 final size:41
Alignment explanation
Indices: 237189--237272 Score: 125
Period size: 41 Copynumber: 2.0 Consensus size: 41
237179 TATTGCGACA
* * *
237189 TTTTTTATAAACGCCGCTAAAG-AACATGGATATTACGGCGT
1 TTTTTTACAAACACCGCTAAAGTAA-ATGGATATTACGACGT
237230 TTTTTTACAAACACCGCTAAAGTAAATGGATATTACGACGT
1 TTTTTTACAAACACCGCTAAAGTAAATGGATATTACGACGT
237271 TT
1 TT
237273 AATCACAAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (41 bp):
TTTTTTACAAACACCGCTAAAGTAAATGGATATTACGACGT
Found at i:237281 original size:41 final size:41
Alignment explanation
Indices: 237197--237282 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 41
237187 CATTTTTTAT
* * ** *
237197 AAACGCCGCTAAAGAACATGGATATTACGGCGTTTTTTTAC
1 AAACACCGCTAAAGAACATGGATATTACGACGTTTAATCAC
237238 AAACACCGCTAAAGTAA-ATGGATATTACGACGTTTAATCAC
1 AAACACCGCTAAAG-AACATGGATATTACGACGTTTAATCAC
237279 AAAC
1 AAAC
237283 GCCAGATAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 37 0.95
42 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (41 bp):
AAACACCGCTAAAGAACATGGATATTACGACGTTTAATCAC
Found at i:239375 original size:166 final size:164
Alignment explanation
Indices: 239083--239385 Score: 362
Period size: 166 Copynumber: 1.8 Consensus size: 164
239073 TTATAAAAAC
* **
239083 GACACGATAAACAACATATTACGGCGTTTATGGGATAAACGCCGCTAAATTATTACTCTATTACG
1 GACACGATAAACAACATATTACGGCGTTTAT--GAAAAACGCCGCTAAATTACCACTCTATTACG
* * * * * * *
239148 GCGTTTTTTTGCACAAACGCCACTATAAACAACCCTTTTGCGACGTTTGTTTGATAAACGCCGCT
64 GCGATTTGTTGAAAAAACGCCACTATAAACAACCCTATTGCGACGTTTGTCTGACAAACGCCGCT
239213 AAATTACTTCTCAATAGCGTCGTTTGTTGAACAAAG
129 AAATTACTTCTCAATAGCGTCGTTTGTTGAACAAAG
* *
239249 GACACTATAAACAACACTATTACGGCGCTTGTAT-AAAAACGCCGCTAAATTTACCACTCTATTG
1 GACACGATAAACAACA-TATTACGGCG-TT-TATGAAAAACGCCGCTAAA-TTACCACTCTATTA
* * *
239313 CGGC-ATTTGTTGAAAAAATGCCACTATAAACAACTCTATTGCGGCGTTTAAG-CT-ACAAACGC
62 CGGCGATTTGTTGAAAAAACGCCACTATAAACAACCCTATTGCGACGTTT--GTCTGACAAACGC
*
239375 CGGTAAATTAC
125 CGCTAAATTAC
239386 CACTCTATTG
Statistics
Matches: 115, Mismatches: 16, Indels: 12
0.80 0.11 0.08
Matches are distributed among these distances:
166 83 0.72
167 26 0.23
168 3 0.03
169 3 0.03
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (164 bp):
GACACGATAAACAACATATTACGGCGTTTATGAAAAACGCCGCTAAATTACCACTCTATTACGGC
GATTTGTTGAAAAAACGCCACTATAAACAACCCTATTGCGACGTTTGTCTGACAAACGCCGCTAA
ATTACTTCTCAATAGCGTCGTTTGTTGAACAAAG
Found at i:239405 original size:83 final size:81
Alignment explanation
Indices: 239077--239416 Score: 274
Period size: 83 Copynumber: 4.1 Consensus size: 81
239067 GCGATTTTAT
* * * * * **
239077 AAAAACGACACGATAAACAACA-TATTACGGCGTTTATGGGATAAACGCCGCTAAATTATTACTC
1 AAAAACGCCACTATAAACAACACTATTGCGGCGTTTA--GTAAAAACGCCGCTAAATTACCACTC
* * *
239141 TATTACGGCGTTTTTTTGC
64 TATTGCGGCG-TTTGTTGA
* * * * * **
239160 ACAAACGCCACTATAAACAACCCTTTTGCGACGTTT-GTTTGATAAACGCCGCTAAATTACTTCT
1 AAAAACGCCACTATAAACAACACTATTGCGGCGTTTAG--T-AAAAACGCCGCTAAATTACCACT
* * *
239224 CAATAGCGTCGTTTGTTGA
63 CTATTGCGGCGTTTGTTGA
* * * *
239243 ACAAAGGACACTATAAACAACACTATTACGGCGCTTGTA-TAAAAACGCCGCTAAATTTACCACT
1 AAAAACGCCACTATAAACAACACTATTGCGGCG-TT-TAGTAAAAACGCCGCTAAA-TTACCACT
*
239307 CTATTGCGGCATTTGTTGA
63 CTATTGCGGCGTTTGTTGA
* * * *
239326 AAAAATGCCACTATAAACAACTCTATTGCGGCGTTTAAGCTACAAACGCCGGTAAATTACCACTC
1 AAAAACGCCACTATAAACAACACTATTGCGGCGTTT-AG-TAAAAACGCCGCTAAATTACCACTC
* *
239391 TATTGCGGTGTTTGTT-T
64 TATTGCGGCGTTTGTTGA
239408 AAAAACGCC
1 AAAAACGCC
239417 GCTAAAGTAT
Statistics
Matches: 206, Mismatches: 40, Indels: 23
0.77 0.15 0.09
Matches are distributed among these distances:
81 2 0.01
82 25 0.12
83 124 0.60
84 54 0.26
85 1 0.00
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (81 bp):
AAAAACGCCACTATAAACAACACTATTGCGGCGTTTAGTAAAAACGCCGCTAAATTACCACTCTA
TTGCGGCGTTTGTTGA
Found at i:244235 original size:15 final size:15
Alignment explanation
Indices: 244217--244246 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
244207 CCACGGTGCT
244217 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
244232 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
244247 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:253920 original size:19 final size:19
Alignment explanation
Indices: 253885--253932 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
253875 ACCCCTTTGA
*
253885 AAATACGTGATTTTTAATG
1 AAATACATGATTTTTAATG
253904 ATAATACATGA-TTTTAATG
1 A-AATACATGATTTTTAATG
253923 AAGATACATG
1 AA-ATACATG
253933 CTCTTGGCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 1 0.04
19 17 0.65
20 8 0.31
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.38
Consensus pattern (19 bp):
AAATACATGATTTTTAATG
Found at i:255467 original size:24 final size:24
Alignment explanation
Indices: 255422--255467 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
255412 TTTGAATGAT
* *
255422 CATGTCCCTTGGCATCCTAAAAGA
1 CATGTCCATTGGCATCATAAAAGA
255446 CATGTCCATTGG-ATCATGAAAA
1 CATGTCCATTGGCATCAT-AAAA
255468 TTCACAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.26
Consensus pattern (24 bp):
CATGTCCATTGGCATCATAAAAGA
Found at i:258149 original size:19 final size:20
Alignment explanation
Indices: 258110--258161 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
258100 GAAACCCCTT
258110 TGAAAATACATGACTTTTTAA
1 TGAAAATACATGAC-TTTTAA
258131 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGACTTTTAA
*
258150 TGAAGATACATG
1 TGAAAATACATG
258162 CTCTTGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 17 0.57
21 13 0.43
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGACTTTTAA
Found at i:266059 original size:21 final size:21
Alignment explanation
Indices: 266030--266105 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
266020 CGAGGCGTGC
*
266030 ATCGGTGCATCTTCATGATGT
1 ATCGATGCATCTTCATGATGT
* *
266051 ATCGATGCATATTCATAGGGATGC
1 ATCGATGCATCTTCAT---GATGT
*
266075 ATCGATGCACCTTCAT-AGTGT
1 ATCGATGCATCTTCATGA-TGT
266096 ATCGATGCAT
1 ATCGATGCAT
266106 TATGCACAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
20 1 0.02
21 25 0.57
24 18 0.41
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (21 bp):
ATCGATGCATCTTCATGATGT
Found at i:266078 original size:24 final size:24
Alignment explanation
Indices: 266046--266092 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
266036 GCATCTTCAT
* *
266046 GATGTATCGATGCATATTCATAGG
1 GATGCATCGATGCACATTCATAGG
*
266070 GATGCATCGATGCACCTTCATAG
1 GATGCATCGATGCACATTCATAG
266093 TGTATCGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (24 bp):
GATGCATCGATGCACATTCATAGG
Found at i:272076 original size:65 final size:66
Alignment explanation
Indices: 271922--272085 Score: 183
Period size: 65 Copynumber: 2.5 Consensus size: 66
271912 AAAATAGCTT
* * * ** * *
271922 GAGTGCATCGATGCATAG-CTTGTGCATCGGTGCATTAAATGCATTCGATGTTTCTATTTGTTCA
1 GAGTGCATCGATGCATAGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAATTTATTCA
271986 A
66 A
* * *
271987 GGGTGCATCGATGCATAGA-GAGTGCATTGGTACACTAAATGCATTCGA-AATTCAATTTAATT-
1 GAGTGCATCGATGCATAGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAATTT-ATTC
*
272049 GA
65 AA
*
272051 GAGTGCATCGATGCATGGACTAGTGCATCGGTACA
1 GAGTGCATCGATGCATAGACTAGTGCATCGGTACA
272086 TCTCTTTGAA
Statistics
Matches: 81, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
64 25 0.31
65 56 0.69
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.31
Consensus pattern (66 bp):
GAGTGCATCGATGCATAGACTAGTGCATCGGTACACTAAATGCATTCGATAATTCAATTTATTCA
A
Found at i:279096 original size:21 final size:21
Alignment explanation
Indices: 279070--279109 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
279060 CCCCCTTTGA
*
279070 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
279091 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
279110 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:283687 original size:31 final size:31
Alignment explanation
Indices: 283629--283690 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
283619 CTCGACCATA
*
283629 ACTGAAATGACGATGATTCTATGGATGTAAT
1 ACTGAAATGACGAGGATTCTATGGATGTAAT
* * * *
283660 ACTGAAATGACTAGGCTTTTATTGATGTAAT
1 ACTGAAATGACGAGGATTCTATGGATGTAAT
283691 GTTCATTTCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.35
Consensus pattern (31 bp):
ACTGAAATGACGAGGATTCTATGGATGTAAT
Found at i:289884 original size:22 final size:21
Alignment explanation
Indices: 289845--289903 Score: 57
Period size: 22 Copynumber: 2.6 Consensus size: 21
289835 CATGTTGTCT
*
289845 TTTATTATTATTATTTTAATTA
1 TTTATTATTATTAATTT-ATTA
289867 TTTATTATT-TGTAATTTATTA
1 TTTATTATTAT-TAATTTATTA
289888 TTAATATATATTATTA
1 TT--TAT-TATTATTA
289904 GAATACATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
21 7 0.23
22 14 0.45
23 3 0.10
24 6 0.19
25 1 0.03
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTATTATTATTAATTTATTA
Found at i:291155 original size:21 final size:21
Alignment explanation
Indices: 291130--291184 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
291120 TGGTCGGGTC
*
291130 TGGATCTGGGCTTCCGGGTTT
1 TGGATCTGGGCCTCCGGGTTT
*
291151 TGGATCTGGGCCTCCGGGTTC
1 TGGATCTGGGCCTCCGGGTTT
* *
291172 TAGTTCTGGGCCT
1 TGGATCTGGGCCT
291185 ATAAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.05, C:0.24, G:0.36, T:0.35
Consensus pattern (21 bp):
TGGATCTGGGCCTCCGGGTTT
Found at i:291626 original size:137 final size:137
Alignment explanation
Indices: 291477--291812 Score: 469
Period size: 137 Copynumber: 2.5 Consensus size: 137
291467 CAAAAGGTTA
*
291477 AACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGATTTCTTCTCATTATGAACTCC
1 AACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
* * *
291542 TTCTAGAAATACTGACCCTCAAAAGA-GGTGTCATTGATTCAACTTCATATATGATGAATTAAAG
66 TTCTAGAAATACTGACCCTCAAAAGATGG-GTCATTAATTCAACTTCATATATAACGAATTAAAG
291606 CAACGTTG
130 CAACGTTG
*
291614 AACAAGTTCTTCTTATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
1 AACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
* ** * ** *** * *
291679 TTCTGGAAATGTTGACCCTCAAAATATGGGTTGTTAATTTGGCTTCATATGTAACGAATTAAGGC
66 TTCTAGAAATACTGACCCTCAAAAGATGGGTCATTAATTCAACTTCATATATAACGAATTAAAGC
*
291744 AAGGTTG
131 AACGTTG
* *
291751 AACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTAAGATGAGTTCTTCTCATTATGAAC
1 AACAAGTTCTTCTCATTATGAATTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTATGAAC
291813 ACTTCTGGAA
Statistics
Matches: 177, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
136 3 0.02
137 172 0.97
138 2 0.01
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.39
Consensus pattern (137 bp):
AACAAGTTCTTCTCATTATGAATTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTATGAACTCC
TTCTAGAAATACTGACCCTCAAAAGATGGGTCATTAATTCAACTTCATATATAACGAATTAAAGC
AACGTTG
Found at i:292025 original size:123 final size:123
Alignment explanation
Indices: 291744--292311 Score: 671
Period size: 123 Copynumber: 4.7 Consensus size: 123
291734 GAATTAAGGC
*
291744 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTAAGATGAGTTCTTCTCATTA
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
** * * * *
291808 TGAAC-ACTTCTGGAAATGTTAATGTTGATCTATCTACTTCTGTGATAGAGTCATAC-A
65 TGAACTTTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* * * **
291865 AAGGTTGAACAAGCTCTTCTGATTATGAACTTCTTCTTCCTCTTCAGATAAGTTCTTCTTGTTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
291930 GAACTTTTTCTGGAAAAGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
66 GAACTTTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* * *
291988 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTTTCAGATAAGTTCTTCTTATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* * * *
292053 GAACTTTCTCTAGAAAAGTTGATGTTGATCTATCTCATTCTGTGATAGAGTCATGTAA
66 GAACTTTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
* *
292111 AAGGTTGAACAAGTTCTTCTCATTATGAACTTGTTTTTCCTCTTCAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
* ** * * ** * * *
292176 GAACTCTACCTGG--CA----ATGTTGATCCA--T-C-GAT-TGATAAATTTGA-GCAA
66 GAACTTTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGA-GTCATGCAA
*
292223 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTG
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATTA
* ** *
292288 TGAACTCTACCTGGAAATGTTGAT
65 TGAACTTTTTCTGGAAAAGTTGAT
292312 CTATTGAATG
Statistics
Matches: 391, Mismatches: 45, Indels: 24
0.85 0.10 0.05
Matches are distributed among these distances:
112 47 0.12
113 40 0.10
115 1 0.00
117 10 0.03
119 2 0.01
121 60 0.15
122 47 0.12
123 184 0.47
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
GAACTTTTTCTGGAAAAGTTGATGTTGATCTATCTCCTTCTGTGATAGAGTCATGCAA
Found at i:292563 original size:22 final size:22
Alignment explanation
Indices: 292502--292563 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
292492 AAATCCAATA
* * *
292502 AATCTTTCTTCTTTGAAAAGAG
1 AATCTATCATCTTTGAAGAGAG
292524 AATCTATCATCTTTGAAGAGAG
1 AATCTATCATCTTTGAAGAGAG
292546 AATCTATCATCTTTGAAG
1 AATCTATCATCTTTGAAG
292564 TGATATAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAGAGAG
Found at i:292943 original size:20 final size:20
Alignment explanation
Indices: 292896--292943 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
292886 TGATCGCAAC
*
292896 ATTGGTTTAGCACCATAATT
1 ATTGGTTCAGCACCATAATT
** *
292916 GCTAGTTCAGCACCATAATT
1 ATTGGTTCAGCACCATAATT
292936 ATTGGTTC
1 ATTGGTTC
292944 TTAAAACATT
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.38
Consensus pattern (20 bp):
ATTGGTTCAGCACCATAATT
Found at i:293594 original size:10 final size:10
Alignment explanation
Indices: 293579--293633 Score: 69
Period size: 10 Copynumber: 5.4 Consensus size: 10
293569 ATTATTATTA
293579 TTTTTCATTT
1 TTTTTCATTT
293589 TTTTTCA-TT
1 TTTTTCATTT
293598 TTTTTCATTT
1 TTTTTCATTT
293608 CATTTTTC-TTT
1 --TTTTTCATTT
293619 CTTTTTCATTT
1 -TTTTTCATTT
293630 TTTT
1 TTTT
293634 CTTCAAGCAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 9 0.22
10 19 0.47
11 6 0.15
12 6 0.15
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.78
Consensus pattern (10 bp):
TTTTTCATTT
Found at i:300895 original size:12 final size:13
Alignment explanation
Indices: 300880--300943 Score: 66
Period size: 12 Copynumber: 5.3 Consensus size: 13
300870 TTAAAATATA
300880 TATTATAT-TTAT
1 TATTATATATTAT
*
300892 TATTATATACTA-
1 TATTATATATTAT
* *
300904 TAGTAT-GATTAT
1 TATTATATATTAT
300916 TATTAT-TATTAT
1 TATTATATATTAT
300928 TATTAT-TATTAT
1 TATTATATATTAT
300940 TATT
1 TATT
300944 TTACAATATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
11 3 0.07
12 39 0.89
13 2 0.05
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:300896 original size:3 final size:3
Alignment explanation
Indices: 300888--300943 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
300878 TATATTATAT
* * *
300888 TTA TTA TTA TATA CTA -TA GTA TGA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
300933 TTA TTA TTA TT
1 TTA TTA TTA TT
300944 TTACAATATT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.91
4 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.04, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:303880 original size:30 final size:30
Alignment explanation
Indices: 303846--303928 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
303836 TTGTAAATAA
*
303846 TATTTTAGTCATTTGAGTTTTTGTTTACT-T
1 TATTTTAGTCCTTTGAGTTTTTGTTT-CTGT
* *
303876 TA-TTTAGGTCCTTTGAGTTTCTGTTTTTGT
1 TATTTTA-GTCCTTTGAGTTTTTGTTTCTGT
* *
303906 TATTTTTGTCCTTTAAGTTTTTG
1 TATTTTAGTCCTTTGAGTTTTTG
303929 AAATTACTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 5 0.11
30 36 0.82
31 3 0.07
ACGTcount: A:0.13, C:0.08, G:0.16, T:0.63
Consensus pattern (30 bp):
TATTTTAGTCCTTTGAGTTTTTGTTTCTGT
Found at i:304043 original size:30 final size:30
Alignment explanation
Indices: 303967--304070 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 30
303957 TGTTTTTGCC
*
303967 ATTTTAGTCTTTTAAATTTCATCTTGTGAT
1 ATTTTAGTCTTTTAAATTTCATATTGTGAT
* ** * *
303997 A-TTTGGTCTTCAAAATTT-ATATTTTTACT
1 ATTTTAGTCTTTTAAATTTCATATTGTGA-T
*
304026 ATTTTAGTCTTTTAAATTTC-TGTTTGTG-T
1 ATTTTAGTCTTTTAAATTTCAT-ATTGTGAT
*
304055 CATTTTAGTCCTTTAA
1 -ATTTTAGTCTTTTAA
304071 TTTTTTTAAT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 6 0.11
29 17 0.30
30 30 0.54
31 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.57
Consensus pattern (30 bp):
ATTTTAGTCTTTTAAATTTCATATTGTGAT
Found at i:309124 original size:12 final size:12
Alignment explanation
Indices: 309077--309155 Score: 56
Period size: 12 Copynumber: 6.5 Consensus size: 12
309067 CAAAAAGAGG
309077 GAAAAA-ATAAA
1 GAAAAATATAAA
309088 -AAAAAT-TAAA
1 GAAAAATATAAA
**
309098 GCAAGGATAATAAA
1 G-AAAAAT-ATAAA
309112 GAAAAATATAAA
1 GAAAAATATAAA
* *
309124 GAAAAAAAAACAAA
1 G--AAAAATATAAA
*
309138 GAAAAAAATAAA
1 GAAAAATATAAA
309150 GAAAAA
1 GAAAAA
309156 GGGACGAGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
10 9 0.17
12 26 0.48
13 4 0.07
14 15 0.28
ACGTcount: A:0.77, C:0.03, G:0.10, T:0.10
Consensus pattern (12 bp):
GAAAAATATAAA
Found at i:309130 original size:14 final size:13
Alignment explanation
Indices: 309106--309155 Score: 59
Period size: 12 Copynumber: 3.9 Consensus size: 13
309096 AAGCAAGGAT
309106 AATAAAG-AAAAA
1 AATAAAGAAAAAA
*
309118 TATAAAGAAAAAAA
1 AATAAAG-AAAAAA
*
309132 AACAAAG-AAAAA
1 AATAAAGAAAAAA
309144 AATAAAGAAAAA
1 AATAAAGAAAAA
309156 GGGACGAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
12 17 0.55
13 4 0.13
14 10 0.32
ACGTcount: A:0.82, C:0.02, G:0.08, T:0.08
Consensus pattern (13 bp):
AATAAAGAAAAAA
Found at i:310216 original size:32 final size:32
Alignment explanation
Indices: 310168--310398 Score: 363
Period size: 32 Copynumber: 7.2 Consensus size: 32
310158 AAGCAATAGA
* *
310168 GGGCATCTTTGAAGATTCAACATCACATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
310200 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
310232 GGGTATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
*
310264 GGGCATCTTTGGAGATTCAACATCAAATGATG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
310296 GGGCATCTTTGGAGATTCAACATCAAATGTTG
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
310328 GGGCATCTTTGGAGATTCAACATCAAAATGTTG
1 GGGCATCTTTGGAGATTCAACATC-AAATGTTG
* * * * *
310361 GGGCATCTATGGAGATTCAATATCGAATATTA
1 GGGCATCTTTGGAGATTCAACATCAAATGTTG
310393 GGGCAT
1 GGGCAT
310399 TCAATATCCT
Statistics
Matches: 187, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
32 157 0.84
33 30 0.16
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (32 bp):
GGGCATCTTTGGAGATTCAACATCAAATGTTG
Found at i:310615 original size:39 final size:37
Alignment explanation
Indices: 310516--310643 Score: 134
Period size: 36 Copynumber: 3.4 Consensus size: 37
310506 TTTGTCTCCA
* * *
310516 TTGAAAC-AAATTTTGTCTCTCTTGAGACGGTTTCCC
1 TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCAC
*
310552 TTGAAAC-AAATTTTGTCTCCCTTGAGACAATTTCAC
1 TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCAC
* * *
310588 TTGAAACAAAAGATTTTATCTCGCTTGAGATAGTTTCAC
1 TTGAAAC-AAA-ATTTTGTCTCCCTTGAGACAGTTTCAC
*
310627 TCGAAACACAATATTTT
1 TTGAAACA-AA-ATTTT
310644 TAGAAACTAA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
36 39 0.50
38 3 0.04
39 36 0.46
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCAC
Found at i:310713 original size:43 final size:43
Alignment explanation
Indices: 310665--310904 Score: 230
Period size: 43 Copynumber: 5.3 Consensus size: 43
310655 CCTGATTTTC
*
310665 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
** **
310708 AGGGGTTTCTTGATGAAAAGCTTGAGGGACTGTCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
* ** *
310751 AGGGGTTCCTTGATGACAAATTTGATGACAAACTTGAAGGACCATCGTGATATAT
1 AGGGGTTTCTTGATGA-AAAGCT--TG----A---GAA--ACCATCGTGATATGT
* *
310806 AGGGG-TTCTTTGAGGACAAGCTTGAGAAACCATCGTGATATGT
1 AGGGGTTTC-TTGATGAAAAGCTTGAGAAACCATCGTGATATGT
**
310849 AGGGGTTTCTTGATGAAAAGCTTGAGGGACCATCGTGATATGT
1 AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
*
310892 AGGGGTTCCTTGA
1 AGGGGTTTCTTGA
310905 AGACAAATTT
Statistics
Matches: 159, Mismatches: 24, Indels: 28
0.75 0.11 0.13
Matches are distributed among these distances:
43 114 0.72
44 7 0.04
45 3 0.02
46 2 0.01
48 1 0.01
50 1 0.01
52 2 0.01
53 1 0.01
54 5 0.03
55 23 0.14
ACGTcount: A:0.28, C:0.12, G:0.30, T:0.30
Consensus pattern (43 bp):
AGGGGTTTCTTGATGAAAAGCTTGAGAAACCATCGTGATATGT
Found at i:310801 original size:55 final size:53
Alignment explanation
Indices: 310717--310964 Score: 203
Period size: 43 Copynumber: 5.0 Consensus size: 53
310707 TAGGGGTTTC
**
310717 TTGATGAAAAGCTTGAGGGACTGTCGTGATATGTAGGGGTTCCTTGATGACAAA
1 TTGATGAAAA-CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
* * * *
310771 TTTGATGACAAACTTGAAGGACCATCGTGATATATAGGGGTTCTTTGAGGAC--A
1 -TTGATGA-AAACTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
** *
310824 ---A-G----CTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATG--AAA
1 TTGATGAAAACTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
*
310867 ---A-G----CTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAA
1 TTGATGAAAACTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
* * *
310912 TTTGATGAACACTTGAGGGACCAACGTGATATGTAGGGGTTCCTTGGTGACAA
1 -TTGATGAAAACTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAA
310965 TTTAGAAACT
Statistics
Matches: 159, Mismatches: 20, Indels: 29
0.76 0.10 0.14
Matches are distributed among these distances:
43 68 0.43
45 3 0.02
48 1 0.01
49 2 0.01
50 1 0.01
53 1 0.01
54 39 0.25
55 41 0.26
56 3 0.02
ACGTcount: A:0.29, C:0.13, G:0.29, T:0.29
Consensus pattern (53 bp):
TTGATGAAAACTTGAGGGACCATCGTGATATGTAGGGGTTCCTTGATGACAAA
Found at i:310854 original size:141 final size:141
Alignment explanation
Indices: 310665--310957 Score: 475
Period size: 141 Copynumber: 2.1 Consensus size: 141
310655 CCTGATTTTC
310665 AGGGGTT-TCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
1 AGGGGTTCTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
** *
310729 TTGAGGGACTGTCGTGATATGTAGGGGTTCCTTGATGACAAATTTGATGACAAACTTGAAGGACC
66 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGA-AAACTTGAAGGACC
*
310794 ATCGTGATATAT
130 AACGTGATATAT
* *
310806 AGGGGTTCT-TTGAGGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
1 AGGGGTTCTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
* *
310870 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGAACACTTGAGGGACCA
66 TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGAAAACTTGAAGGACCA
*
310935 ACGTGATATGT
131 ACGTGATATAT
310946 AGGGGTTC-CTTG
1 AGGGGTTCTCTTG
310958 GTGACAATTT
Statistics
Matches: 141, Mismatches: 9, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
140 33 0.23
141 107 0.76
142 1 0.01
ACGTcount: A:0.28, C:0.13, G:0.30, T:0.29
Consensus pattern (141 bp):
AGGGGTTCTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGC
TTGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGAAAACTTGAAGGACCA
ACGTGATATAT
Found at i:311022 original size:140 final size:140
Alignment explanation
Indices: 310665--311001 Score: 412
Period size: 141 Copynumber: 2.4 Consensus size: 140
310655 CCTGATTTTC
* * * * * *
310665 AGGGGTTTCTTGAAGAAAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCT
1 AGGGGTTCCTTGAGGACAA-CTTGAGAAACCAGCGTGATATGTAAGAGTTTCTTGATGAAAAGCT
** *
310730 TGAGGGACTGTCGTGATATGTAGGGGTTCCTTGATGACAAATTTGATGACAAACTTGAAGGACCA
65 TGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGACAAACTTGAAGGACCA
*
310795 TCGTGATATAT
130 ACGTGATATAT
* * * *
310806 AGGGGTTCTTTGAGGACAAGCTTGAGAAACCATCGTGATATGTAGGGGTTTCTTGATGAAAAGCT
1 AGGGGTTCCTTGAGGACAA-CTTGAGAAACCAGCGTGATATGTAAGAGTTTCTTGATGAAAAGCT
* *
310871 TGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGA-ACACTTGAGGGACCA
65 TGAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGACAAACTTGAAGGACCA
*
310935 ACGTGATATGT
130 ACGTGATATAT
* * * *
310946 AGGGGTTCCTTG-GTGACAA-TTTAGAAACTGAGCTTGAT-TTTCAAGAGTTTCTTGAT
1 AGGGGTTCCTTGAG-GACAACTTGAGAAAC-CAGCGTGATATGT-AAGAGTTTCTTGAT
311002 TTTTAAGTCC
Statistics
Matches: 174, Mismatches: 19, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
138 10 0.06
139 19 0.11
140 38 0.22
141 107 0.61
ACGTcount: A:0.28, C:0.13, G:0.28, T:0.30
Consensus pattern (140 bp):
AGGGGTTCCTTGAGGACAACTTGAGAAACCAGCGTGATATGTAAGAGTTTCTTGATGAAAAGCTT
GAGGGACCATCGTGATATGTAGGGGTTCCTTGAAGACAAATTTGATGACAAACTTGAAGGACCAA
CGTGATATAT
Found at i:311126 original size:90 final size:90
Alignment explanation
Indices: 310992--311393 Score: 655
Period size: 90 Copynumber: 4.5 Consensus size: 90
310982 ATTTTCAAGA
*
310992 GTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
311057 GATCTAAGAAACTGAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
* *
311082 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCGTAAGACCTTCAGTGCAGGATATTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
*
311147 GATTTAAGAAACTGAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
* * * *
311172 GTTTCTT-ATTTTTTTAGTCTTTCGGGCCATCCATAAGACCTTCAGTGCATGATGTTTTCAAATG
1 GTTTCTTGA-TTTTTAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATG
311236 AGATCTAAGAAACTGAGCCTTCGGGG
65 AGATCTAAGAAACTGAGCCTTCGGGG
** *
311262 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCTGTAAGACCTTCAGTGCATGATGTTTTCAAATGA
1 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
* *
311327 GATTTAAGAAACTAAGCCTTCGGGG
66 GATCTAAGAAACTGAGCCTTCGGGG
*
311352 GTTTCTTGATTTTTAAGTCCTTCAGG-CAACCATAAGACCTTC
1 GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTC
311394 GGGCAAAATG
Statistics
Matches: 289, Mismatches: 21, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
89 14 0.05
90 274 0.95
91 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (90 bp):
GTTTCTTGATTTTTAAGTCCTTCAGGCCATCCATAAGACCTTCAGTGCAGGATGTTTTCAAATGA
GATCTAAGAAACTGAGCCTTCGGGG
Found at i:314573 original size:30 final size:30
Alignment explanation
Indices: 314539--314621 Score: 89
Period size: 30 Copynumber: 2.8 Consensus size: 30
314529 TTGTAAATAA
* *
314539 TATTTTAGTCATTTGAGTTTTTGTTTAT-TT
1 TATTTTAGTCCTTTGAGTTTTTGTTT-TCGT
*
314569 TA-TTTAGGTCCTTTGAGTTTCTGTTTTCGT
1 TATTTTA-GTCCTTTGAGTTTTTGTTTTCGT
* *
314599 TATTTTTGTCCTTTAAGTTTTTG
1 TATTTTAGTCCTTTGAGTTTTTG
314622 AAATTACTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
29 5 0.11
30 36 0.82
31 3 0.07
ACGTcount: A:0.13, C:0.08, G:0.16, T:0.63
Consensus pattern (30 bp):
TATTTTAGTCCTTTGAGTTTTTGTTTTCGT
Found at i:314736 original size:30 final size:30
Alignment explanation
Indices: 314660--314763 Score: 81
Period size: 30 Copynumber: 3.5 Consensus size: 30
314650 TGTTTTTGCC
*
314660 ATTTTAGTCTTTTAAATTTCATCTTGTGAT
1 ATTTTAGTCTTTTAAATTTCATATTGTGAT
* ** * *
314690 A-TTTGGTCTTCAAAATTT-ATATTTTTACT
1 ATTTTAGTCTTTTAAATTTCATATTGTGA-T
*
314719 ATTTTAGTCTTTTAAATTTC-TGTTTGTG-T
1 ATTTTAGTCTTTTAAATTTCAT-ATTGTGAT
*
314748 CATTTTAGTCCTTTAA
1 -ATTTTAGTCTTTTAA
314764 TTTTTTAATT
Statistics
Matches: 56, Mismatches: 13, Indels: 10
0.71 0.16 0.13
Matches are distributed among these distances:
28 6 0.11
29 17 0.30
30 30 0.54
31 3 0.05
ACGTcount: A:0.23, C:0.11, G:0.10, T:0.57
Consensus pattern (30 bp):
ATTTTAGTCTTTTAAATTTCATATTGTGAT
Found at i:314783 original size:30 final size:30
Alignment explanation
Indices: 314660--314783 Score: 76
Period size: 30 Copynumber: 4.2 Consensus size: 30
314650 TGTTTTTGCC
* *
314660 ATTTTAGTCTTTTAAATTTC-ATCTTGTGAT
1 ATTTTAGTCCTTTAAATTTCTAT-TTGTGTT
* * * * **
314690 A-TTTGGT-CTTCAAAATTTATATTTTTACT
1 ATTTTAGTCCTT-TAAATTTCTATTTGTGTT
* * *
314719 ATTTTAGTCTTTTAAATTTCTGTTTGTGTC
1 ATTTTAGTCCTTTAAATTTCTATTTGTGTT
* *
314749 ATTTTAGTCCTTTAATTTTTTAATTT-TGTT
1 ATTTTAGTCCTTTAAATTTCT-ATTTGTGTT
314779 ATTTT
1 ATTTT
314784 GATTCTTAAG
Statistics
Matches: 68, Mismatches: 21, Indels: 10
0.69 0.21 0.10
Matches are distributed among these distances:
28 2 0.03
29 16 0.24
30 45 0.66
31 5 0.07
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.60
Consensus pattern (30 bp):
ATTTTAGTCCTTTAAATTTCTATTTGTGTT
Found at i:315372 original size:14 final size:16
Alignment explanation
Indices: 315355--315386 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
315345 TATTATTTTT
315355 TGAAT-TTTAT-TTAA
1 TGAATGTTTATCTTAA
315369 TGAATGTTTATCTTAA
1 TGAATGTTTATCTTAA
315385 TG
1 TG
315387 TAAAATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.31
15 5 0.31
16 6 0.38
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.53
Consensus pattern (16 bp):
TGAATGTTTATCTTAA
Found at i:319953 original size:16 final size:15
Alignment explanation
Indices: 319905--319956 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 15
319895 TTTATTATTA
319905 TTATT-TTAAT-TAT
1 TTATTATTAATATAT
**
319918 TTATTATTTGTA-AT
1 TTATTATTAATATAT
319932 TTATTATTAATATAT
1 TTATTATTAATATAT
319947 ATTATTATTA
1 -TTATTATTA
319957 GAATACATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 5 0.16
14 15 0.48
15 2 0.06
16 9 0.29
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (15 bp):
TTATTATTAATATAT
Found at i:321277 original size:20 final size:21
Alignment explanation
Indices: 321209--321289 Score: 112
Period size: 21 Copynumber: 4.0 Consensus size: 21
321199 GGTGTTGGGT
*
321209 CGGG-TCTAGATCTGGGCTTC
1 CGGGTTCTAGATCTGGGCCTC
* *
321229 CGGGTTTTGGATCTGGGCCTC
1 CGGGTTCTAGATCTGGGCCTC
321250 CGGGTTCTAGATCTGGGCCT-
1 CGGGTTCTAGATCTGGGCCTC
*
321270 CTGGTTCTAGATCTGGGCCT
1 CGGGTTCTAGATCTGGGCCT
321290 ATAAAATTAA
Statistics
Matches: 54, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 23 0.43
21 31 0.57
ACGTcount: A:0.09, C:0.25, G:0.35, T:0.32
Consensus pattern (21 bp):
CGGGTTCTAGATCTGGGCCTC
Found at i:321283 original size:41 final size:41
Alignment explanation
Indices: 321209--321289 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
321199 GGTGTTGGGT
* * *
321209 CGGGTCTAGATCTGGGCTTCCGGGTTTTGGATCTGGGCCTC
1 CGGGTCTAGATCTGGGCCTCCGGGTTCTAGATCTGGGCCTC
*
321250 CGGGTTCTAGATCTGGGCCT-CTGGTTCTAGATCTGGGCCT
1 CGGG-TCTAGATCTGGGCCTCCGGGTTCTAGATCTGGGCCT
321290 ATAAAATTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 21 0.60
42 14 0.40
ACGTcount: A:0.09, C:0.25, G:0.35, T:0.32
Consensus pattern (41 bp):
CGGGTCTAGATCTGGGCCTCCGGGTTCTAGATCTGGGCCTC
Found at i:324003 original size:21 final size:21
Alignment explanation
Indices: 323979--324031 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
323969 TAATAAAGGT
323979 AGTACCGATACTCCCTTTAGG
1 AGTACCGATACTCCCTTTAGG
*
324000 AGTACTGATACTCCCTTTAGG
1 AGTACCGATACTCCCTTTAGG
*
324021 AGTACCAATAC
1 AGTACCGATAC
324032 CCTCTGTACT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (21 bp):
AGTACCGATACTCCCTTTAGG
Found at i:324092 original size:21 final size:20
Alignment explanation
Indices: 324066--324106 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
324056 TGCAGATATT
*
324066 TCATCCCCAAATGGTTAGAAA
1 TCAT-CCCAAATGGCTAGAAA
*
324087 TCATCCCTAATGGCTAGAAA
1 TCATCCCAAATGGCTAGAAA
324107 CGGCCACAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.37, C:0.24, G:0.15, T:0.24
Consensus pattern (20 bp):
TCATCCCAAATGGCTAGAAA
Found at i:325875 original size:19 final size:18
Alignment explanation
Indices: 325842--325890 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
325832 AATGATTTGG
325842 TTTTGAAATAAAAAATTG-A
1 TTTTGAAA-AAAAAA-TGAA
325861 TTTTGAAAAACAAAATGAAA
1 TTTTGAAAAA-AAAATG-AA
325881 TTTTGAAAAA
1 TTTTGAAAAA
325891 TGATTTGCAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 4 0.15
19 12 0.44
20 11 0.41
ACGTcount: A:0.55, C:0.02, G:0.10, T:0.33
Consensus pattern (18 bp):
TTTTGAAAAAAAAATGAA
Found at i:327603 original size:20 final size:21
Alignment explanation
Indices: 327566--327606 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
327556 TGCAAAGATT
*
327566 TCATCTCCAAATGGCTAGAAA
1 TCATCCCCAAATGGCTAGAAA
327587 TCATCCCCAAA-GGCTAGAAA
1 TCATCCCCAAATGGCTAGAAA
327607 CGGACACAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.39, C:0.27, G:0.15, T:0.20
Consensus pattern (21 bp):
TCATCCCCAAATGGCTAGAAA
Found at i:328481 original size:60 final size:60
Alignment explanation
Indices: 328364--328481 Score: 157
Period size: 60 Copynumber: 2.0 Consensus size: 60
328354 TCGGGTTACA
* * * *
328364 ATTTTATAAATTTTAATAGTTGAGAGACTCAACAAAGCAATATCCTATAATTAAGGGATT
1 ATTTTATAAATTTTAATAGTAGAGAGACTCAACAAAACAACATCCTATAATCAAGGGATT
* * *
328424 ATTTTATAACTTTTAATAGTCAG-GAGACTCAACAAAACAACGTCCTATAATCGAGGGA
1 ATTTTATAAATTTTAATAGT-AGAGAGACTCAACAAAACAACATCCTATAATCAAGGGA
328482 CTTTAGCCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
60 49 0.98
61 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (60 bp):
ATTTTATAAATTTTAATAGTAGAGAGACTCAACAAAACAACATCCTATAATCAAGGGATT
Found at i:329601 original size:43 final size:43
Alignment explanation
Indices: 329551--329656 Score: 203
Period size: 43 Copynumber: 2.5 Consensus size: 43
329541 CTGTAGTTTT
329551 CATTTGTAGTTCAATGAAATGACTAGACTTTTTCTGTACTCTC
1 CATTTGTAGTTCAATGAAATGACTAGACTTTTTCTGTACTCTC
*
329594 CATTTGTAGTTCAATGAAATGATTAGACTTTTTCTGTACTCTC
1 CATTTGTAGTTCAATGAAATGACTAGACTTTTTCTGTACTCTC
329637 CATTTGTAGTTCAATGAAAT
1 CATTTGTAGTTCAATGAAAT
329657 ATCACAATTT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 62 1.00
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.42
Consensus pattern (43 bp):
CATTTGTAGTTCAATGAAATGACTAGACTTTTTCTGTACTCTC
Found at i:330677 original size:24 final size:20
Alignment explanation
Indices: 330619--330666 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
330609 GATCAATTAA
*
330619 TATCATACTAAATAACTAGC
1 TATCATTCTAAATAACTAGC
*
330639 TATCATTCTAAATAACTTGC
1 TATCATTCTAAATAACTAGC
330659 TATCATTC
1 TATCATTC
330667 ATAATCGATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.04, T:0.38
Consensus pattern (20 bp):
TATCATTCTAAATAACTAGC
Found at i:331339 original size:48 final size:48
Alignment explanation
Indices: 331275--331403 Score: 125
Period size: 48 Copynumber: 2.6 Consensus size: 48
331265 AGTACTTTAA
* * **
331275 CACCACCATCACACAGACGTCAGACACGTGCTAAGTACC-TATTGGTAG
1 CACCACCGTCACACAGACGTCAGACACGTGCAAAGTACCATA-TAATAG
* * * * *
331323 CATCACCGTCACACAGAAGTTAGACACATGCAAAGTATCATATAATAG
1 CACCACCGTCACACAGACGTCAGACACGTGCAAAGTACCATATAATAG
*
331371 CACCACCGTCATACAAGTTACGTCAGACACGTG
1 CACCACCGTCACAC-AG--ACGTCAGACACGTG
331404 TTATAAGTAT
Statistics
Matches: 63, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
48 48 0.76
49 4 0.06
51 11 0.17
ACGTcount: A:0.35, C:0.29, G:0.17, T:0.19
Consensus pattern (48 bp):
CACCACCGTCACACAGACGTCAGACACGTGCAAAGTACCATATAATAG
Found at i:334545 original size:28 final size:28
Alignment explanation
Indices: 334502--334586 Score: 143
Period size: 28 Copynumber: 3.0 Consensus size: 28
334492 TCCTAAACAA
* *
334502 ACAAGATTTTTGCACGGTTGATTTTAAC
1 ACAAGATTTCTACACGGTTGATTTTAAC
334530 ACAAGATTTCTACACGGTTGATTTTAAC
1 ACAAGATTTCTACACGGTTGATTTTAAC
*
334558 ACAAGATTTCTACACGGTTGATTCTAAC
1 ACAAGATTTCTACACGGTTGATTTTAAC
334586 A
1 A
334587 TTCCACCTCA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 54 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (28 bp):
ACAAGATTTCTACACGGTTGATTTTAAC
Found at i:335703 original size:27 final size:27
Alignment explanation
Indices: 335671--335739 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
335661 TTAGGGTTTA
335671 TTGAGGTTTGATGGATTTGGATTTAAT
1 TTGAGGTTTGATGGATTTGGATTTAAT
335698 TTGAGGTTTGATGGATTTGGATTTAAT
1 TTGAGGTTTGATGGATTTGGATTTAAT
*
335725 TTGATGTTGTGATGG
1 TTGAGGTT-TGATGG
335740 TTGAAACAAC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 34 0.85
28 6 0.15
ACGTcount: A:0.20, C:0.00, G:0.32, T:0.48
Consensus pattern (27 bp):
TTGAGGTTTGATGGATTTGGATTTAAT
Found at i:336320 original size:28 final size:27
Alignment explanation
Indices: 336268--336321 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 27
336258 AAGACTAGGG
336268 AAAAGTAAGGATGAAATTGCAAGTATTT
1 AAAAGTAAGGATGAAATTG-AAGTATTT
*
336296 AAAAGTTAAGGTATGAGATTG-AGTAT
1 AAAAG-TAAGG-ATGAAATTGAAGTAT
336322 GTTATTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
28 10 0.43
29 5 0.22
30 8 0.35
ACGTcount: A:0.44, C:0.02, G:0.24, T:0.30
Consensus pattern (27 bp):
AAAAGTAAGGATGAAATTGAAGTATTT
Found at i:339291 original size:24 final size:24
Alignment explanation
Indices: 339262--339403 Score: 189
Period size: 24 Copynumber: 5.9 Consensus size: 24
339252 AACATAATTC
339262 ATGTCAAGTATCAGATCAGAATCT
1 ATGTCAAGTATCAGATCAGAATCT
*
339286 AGGTCAAGTATCAGATCAGAATCT
1 ATGTCAAGTATCAGATCAGAATCT
* *
339310 AAGTCAAGTATCAGATCAGAATCC
1 ATGTCAAGTATCAGATCAGAATCT
* ** *
339334 ATTTC-AGATATCTTATCAGAATCC
1 ATGTCAAG-TATCAGATCAGAATCT
339358 ATGTCAAGTATCAGATCAGAAT-T
1 ATGTCAAGTATCAGATCAGAATCT
339381 CATGTCAAGTATCAGATCAGAAT
1 -ATGTCAAGTATCAGATCAGAAT
339404 TCAAATCAAA
Statistics
Matches: 104, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
23 2 0.02
24 100 0.96
25 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.16, T:0.28
Consensus pattern (24 bp):
ATGTCAAGTATCAGATCAGAATCT
Found at i:339418 original size:24 final size:24
Alignment explanation
Indices: 339367--339418 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
339357 CATGTCAAGT
** **
339367 ATCAGATCAGAATTCATGTCAAGT
1 ATCAGATCAGAATTCAAATCAAAA
339391 ATCAGATCAGAATTCAAATCAAAA
1 ATCAGATCAGAATTCAAATCAAAA
339415 ATCA
1 ATCA
339419 TATAAAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.25
Consensus pattern (24 bp):
ATCAGATCAGAATTCAAATCAAAA
Found at i:340215 original size:19 final size:19
Alignment explanation
Indices: 340191--340229 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
340181 GTCGAACACG
340191 CATTCAAGTGACATCTATA
1 CATTCAAGTGACATCTATA
340210 CATTCAAGTGACATCTATA
1 CATTCAAGTGACATCTATA
340229 C
1 C
340230 CGTTCTGGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.23, G:0.10, T:0.31
Consensus pattern (19 bp):
CATTCAAGTGACATCTATA
Found at i:344271 original size:24 final size:24
Alignment explanation
Indices: 344241--344407 Score: 201
Period size: 24 Copynumber: 7.0 Consensus size: 24
344231 AAACATAATT
* *
344241 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
344265 TAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
* *
344289 CAAGTCAAGTATCAGATCATAATC
1 CATGTCAAGTATCAGATCAGAATC
* * *
344313 GAAGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCAGATCAGAATC
*
344337 CATGTC-AGATATCATATCAGAATC
1 CATGTCAAG-TATCAGATCAGAATC
* * *
344361 CATGTCAAATATCAGATCAAAATT
1 CATGTCAAGTATCAGATCAGAATC
344385 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
344408 TCAAATCAAA
Statistics
Matches: 123, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
23 2 0.02
24 120 0.98
25 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.27
Consensus pattern (24 bp):
CATGTCAAGTATCAGATCAGAATC
Found at i:344404 original size:72 final size:72
Alignment explanation
Indices: 344237--344407 Score: 229
Period size: 72 Copynumber: 2.4 Consensus size: 72
344227 TTTAAAACAT
* * *
344237 AATTCATGTCAAGTATCATATCAAAATCTAGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATC
1 AATTCATGTCAAGTATCATATCAGAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAATATC
*
344302 AGATCAT
66 AGATCAA
* * * *
344309 AA-TCGAAGTCAAGTATCATATCAGAATCCATGTC-AGATATCATATCAGAATCCATGTCAAATA
1 AATTC-ATGTCAAGTATCATATCAGAATCCAGGTCAAG-TATCAGATCAGAATCCAAGTCAAATA
344372 TCAGATCAA
64 TCAGATCAA
*
344381 AATTCATGTCAAGTATCAGATCAGAAT
1 AATTCATGTCAAGTATCATATCAGAAT
344408 TCAAATCAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
71 4 0.05
72 80 0.93
73 2 0.02
ACGTcount: A:0.41, C:0.18, G:0.13, T:0.27
Consensus pattern (72 bp):
AATTCATGTCAAGTATCATATCAGAATCCAGGTCAAGTATCAGATCAGAATCCAAGTCAAATATC
AGATCAA
Found at i:346809 original size:21 final size:22
Alignment explanation
Indices: 346785--346832 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
346775 CCCAGTCAAA
346785 GTCAAAGGTC-GGTCAACGCTG
1 GTCAAAGGTCTGGTCAACGCTG
* *
346806 GTCAAAGTTCTGGTCAACGGTG
1 GTCAAAGGTCTGGTCAACGCTG
346828 GTCAA
1 GTCAA
346833 CGGTTAACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.25, C:0.21, G:0.31, T:0.23
Consensus pattern (22 bp):
GTCAAAGGTCTGGTCAACGCTG
Found at i:349070 original size:48 final size:48
Alignment explanation
Indices: 348998--349164 Score: 219
Period size: 48 Copynumber: 3.5 Consensus size: 48
348988 AAACATAATT
* * *
348998 CATGTCAAGTATCATATCAAAATCTAGGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCTAAGTCAAGTATCAGATCAGAATC
* * *
349046 CAAGTCAACTATCATATCAGAATCTAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCAGATCAGAATCTAAGTCAAGTATCAGATCAGAATC
* * * * *
349094 CATGACATA-TATCAGATCAGAATCCATGTCAAGTATTAGATCAGAATT
1 CATGTCA-AGTATCAGATCAGAATCTAAGTCAAGTATCAGATCAGAATC
349142 CATGTCAAGTATCAGATCAGAAT
1 CATGTCAAGTATCAGATCAGAAT
349165 TCAAATCAAA
Statistics
Matches: 105, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
47 1 0.01
48 103 0.98
49 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (48 bp):
CATGTCAAGTATCAGATCAGAATCTAAGTCAAGTATCAGATCAGAATC
Found at i:349173 original size:24 final size:24
Alignment explanation
Indices: 349001--349182 Score: 195
Period size: 24 Copynumber: 7.6 Consensus size: 24
348991 CATAATTCAT
* * * *
349001 GTCAAGTATCATATCAAAATCTAG
1 GTCAAGTATCAGATCAGAATCCAA
349025 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* * *
349049 GTCAACTATCATATCAGAATCTAA
1 GTCAAGTATCAGATCAGAATCCAA
*
349073 GTCAAGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
* *
349097 GACATA-TATCAGATCAGAATCCAT
1 GTCA-AGTATCAGATCAGAATCCAA
* * *
349121 GTCAAGTATTAGATCAGAATTCAT
1 GTCAAGTATCAGATCAGAATCCAA
*
349145 GTCAAGTATCAGATCAGAATTCAA
1 GTCAAGTATCAGATCAGAATCCAA
* **
349169 ATCAAAAATCAGAT
1 GTCAAGTATCAGAT
349183 AAAATATTCA
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
23 1 0.01
24 134 0.99
25 1 0.01
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:353420 original size:35 final size:34
Alignment explanation
Indices: 353381--353446 Score: 123
Period size: 35 Copynumber: 1.9 Consensus size: 34
353371 GATACGAGAC
353381 ACAGAATATGATATTATTAATTTTAAAATTAGATA
1 ACAGAATATGATATTATTAATTTT-AAATTAGATA
353416 ACAGAATATGATATTATTAATTTTAAATTAG
1 ACAGAATATGATATTATTAATTTTAAATTAG
353447 GGAACTCCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 7 0.23
35 24 0.77
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (34 bp):
ACAGAATATGATATTATTAATTTTAAATTAGATA
Found at i:353943 original size:25 final size:23
Alignment explanation
Indices: 353898--353943 Score: 56
Period size: 25 Copynumber: 1.9 Consensus size: 23
353888 ACTTTAATAC
* *
353898 ATATATTTATAAATAACTATAAA
1 ATATATTTATAAAGAAATATAAA
353921 ATATATTTTATTAAAGAAATATA
1 ATATA-TTTA-TAAAGAAATATA
353944 TTTATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 5 0.26
24 4 0.21
25 10 0.53
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATATTTATAAAGAAATATAAA
Found at i:355204 original size:82 final size:83
Alignment explanation
Indices: 355053--355206 Score: 206
Period size: 82 Copynumber: 1.9 Consensus size: 83
355043 CAGGTCTATA
* * * * *
355053 TATAGTGGCGTTTTTTCAATAAACGCCGCAACATATTAGTACTTTAGCGGCGTTTTTATACAAAC
1 TATAGTGGCGTTTTTTAAATAAACGCCACAACAAATTAGTACTTTAGCGGAGTTTTGATACAAAC
355118 GCCGCAATAGGGTTCACT
66 GCCGCAATAGGGTTCACT
*
355136 TATAGTGGCG-TTTTTAAATAAACGCCACAA-AAATTA-TAACTTTAGCGGAGTTTTGGTAGCAA
1 TATAGTGGCGTTTTTTAAATAAACGCCACAACAAATTAGT-ACTTTAGCGGAGTTTTGATA-CAA
*
355198 ATGCCGCAA
64 ACGCCGCAA
355207 ATGAATCGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
80 1 0.02
81 22 0.35
82 29 0.47
83 10 0.16
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (83 bp):
TATAGTGGCGTTTTTTAAATAAACGCCACAACAAATTAGTACTTTAGCGGAGTTTTGATACAAAC
GCCGCAATAGGGTTCACT
Found at i:355224 original size:82 final size:81
Alignment explanation
Indices: 355053--355258 Score: 202
Period size: 82 Copynumber: 2.5 Consensus size: 81
355043 CAGGTCTATA
* * * *
355053 TATAGTGGCGTTTTTTCAATAAACGCCGCAACATATTAGT-ACTTTAGCGGCGTTTTTATACAAA
1 TATAGTGGCG-TTTTTAAATAAACGCCGCAA-AAATTA-TAACTTTAGCGGAGTTTTGATACAAA
**
355117 CGCCGCAATAGGGTTCACT
63 CGCCGCAATAGGAATCACT
* * *
355136 TATAGTGGCGTTTTTAAATAAACGCCACAAAAATTATAACTTTAGCGGAGTTTTGGTAGCAAATG
1 TATAGTGGCGTTTTTAAATAAACGCCGCAAAAATTATAACTTTAGCGGAGTTTTGATA-CAAACG
*
355201 CCGCAA-ATGAATCGAACT
65 CCGCAATAGGAATC--ACT
* *
355219 T-TAGTGGTGTTTTTACAAAAAACGCCGCAATAAAATTATA
1 TATAGTGGCGTTTTTA-AATAAACGCCGC-A-AAAATTATA
355259 TATGGTGGCG
Statistics
Matches: 103, Mismatches: 13, Indels: 12
0.80 0.10 0.09
Matches are distributed among these distances:
80 1 0.01
81 26 0.25
82 42 0.41
83 24 0.23
84 1 0.01
85 9 0.09
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.31
Consensus pattern (81 bp):
TATAGTGGCGTTTTTAAATAAACGCCGCAAAAATTATAACTTTAGCGGAGTTTTGATACAAACGC
CGCAATAGGAATCACT
Found at i:358310 original size:30 final size:30
Alignment explanation
Indices: 358274--358347 Score: 139
Period size: 30 Copynumber: 2.5 Consensus size: 30
358264 ACTACGGCGT
358274 TGAATGTGGAGCAGCGTAACACCTCGGTTC
1 TGAATGTGGAGCAGCGTAACACCTCGGTTC
358304 TGAATGTGGAGCAGCGTAACACCTCGGTTC
1 TGAATGTGGAGCAGCGTAACACCTCGGTTC
*
358334 TGAATGTTGAGCAG
1 TGAATGTGGAGCAG
358348 AAAAATGCAG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (30 bp):
TGAATGTGGAGCAGCGTAACACCTCGGTTC
Found at i:358755 original size:43 final size:42
Alignment explanation
Indices: 358657--358881 Score: 220
Period size: 43 Copynumber: 5.2 Consensus size: 42
358647 AAGGAAATTA
*
358657 GCGGCGTTTGTATCCAAAAAAACGCCGCTATATATCTGA-TCTTTT
1 GCGGCGTTTGT-T-C-AAAAAACGCCGCTATAGATCTGACT-TTTT
* *
358702 ACGGTG-TTGTTCAAAAAAACGCCGCTATAGATCTGACTTTTT
1 GCGGCGTTTGTTC-AAAAAACGCCGCTATAGATCTGACTTTTT
* * *
358744 GCGGCGTTTGTTCCAAAAACGCCGCTATAGACCTCAACTTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACTTTTT
* * * *
358787 GCGGCGTTTGTTCTAAAAACGCCGCTATAAATCTCAACCTTTT
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCT-GACTTTTT
* * * * * *
358830 GCGGCATTTATTCCAAAAACGCCGCTATAGATCTTGACCTATA
1 GCGGCGTTTGTTCAAAAAACGCCGCTATAGATC-TGACTTTTT
358873 GCGGCGTTT
1 GCGGCGTTT
358882 TTTGTTCTCA
Statistics
Matches: 156, Mismatches: 20, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
42 51 0.33
43 96 0.62
44 5 0.03
45 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.32
Consensus pattern (42 bp):
GCGGCGTTTGTTCAAAAAACGCCGCTATAGATCTGACTTTTT
Found at i:358877 original size:86 final size:86
Alignment explanation
Indices: 358674--358881 Score: 244
Period size: 86 Copynumber: 2.4 Consensus size: 86
358664 TTGTATCCAA
* * *
358674 AAAAACGCCGCTATATATC-TGATCTTTTA-CGGTG-TTGTTCAAAAAAACGCCGCTATAGATCT
1 AAAAACGCCGCTATAGATCTTGA-CTTTTAGCGGCGTTTGTTCAAAAAAACGCCGCTATAAATCT
* * * *
358736 GACTTTTTGCGGCGTTTGTTCC
65 AACCTTTTGCGGCATTTATTCC
* ** * *
358758 AAAAACGCCGCTATAGACCTCAACTTTTTGCGGCGTTTGTTC-TAAAAACGCCGCTATAAATCTC
1 AAAAACGCCGCTATAGATCTTGACTTTTAGCGGCGTTTGTTCAAAAAAACGCCGCTATAAATCT-
358822 AACCTTTTGCGGCATTTATTCC
65 AACCTTTTGCGGCATTTATTCC
* *
358844 AAAAACGCCGCTATAGATCTTGACCTATAGCGGCGTTT
1 AAAAACGCCGCTATAGATCTTGACTTTTAGCGGCGTTT
358882 TTTGTTCTCA
Statistics
Matches: 102, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
84 22 0.22
85 24 0.24
86 56 0.55
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (86 bp):
AAAAACGCCGCTATAGATCTTGACTTTTAGCGGCGTTTGTTCAAAAAAACGCCGCTATAAATCTA
ACCTTTTGCGGCATTTATTCC
Found at i:360022 original size:42 final size:43
Alignment explanation
Indices: 359936--360028 Score: 143
Period size: 42 Copynumber: 2.2 Consensus size: 43
359926 AATATATATA
**
359936 TATATTTATCAGATATAACTTAATTTAATTTGAAATAAATTTT
1 TATATTTATCAGATATAACTTAAGCTAATTTGAAATAAATTTT
* *
359979 TATATTTATCAGGTATAAC-TAAGCTGATTTGAAATAAATTTT
1 TATATTTATCAGATATAACTTAAGCTAATTTGAAATAAATTTT
360021 TATATTTA
1 TATATTTA
360029 AAAAATAGAT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 28 0.61
43 18 0.39
ACGTcount: A:0.40, C:0.05, G:0.08, T:0.47
Consensus pattern (43 bp):
TATATTTATCAGATATAACTTAAGCTAATTTGAAATAAATTTT
Found at i:360450 original size:12 final size:12
Alignment explanation
Indices: 360433--360466 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
360423 AACGAAACTT
360433 TTAAATTTTAAA
1 TTAAATTTTAAA
360445 TTAAA-TTTAAA
1 TTAAATTTTAAA
*
360456 TTAAATGTTAA
1 TTAAATTTTAA
360467 TATTTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TTAAATTTTAAA
Found at i:360967 original size:24 final size:24
Alignment explanation
Indices: 360940--360991 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
360930 CGTTCATTTA
* *
360940 CGTTCGTGAACGTTCGGTTATGTT
1 CGTTCATGAACGTTCGATTATGTT
* **
360964 CGTTTATGTTCGTTCGATTATGTT
1 CGTTCATGAACGTTCGATTATGTT
360988 CGTT
1 CGTT
360992 TATGTTCATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.15, G:0.25, T:0.48
Consensus pattern (24 bp):
CGTTCATGAACGTTCGATTATGTT
Found at i:360978 original size:14 final size:14
Alignment explanation
Indices: 360961--360991 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
360951 GTTCGGTTAT
*
360961 GTTCGTTTATGTTC
1 GTTCGATTATGTTC
360975 GTTCGATTATGTTC
1 GTTCGATTATGTTC
360989 GTT
1 GTT
360992 TATGTTCATT
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:0.10, C:0.13, G:0.23, T:0.55
Consensus pattern (14 bp):
GTTCGATTATGTTC
Found at i:360992 original size:24 final size:24
Alignment explanation
Indices: 360950--361011 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
360940 CGTTCGTGAA
*
360950 CGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
360974 CGTTCGATTATGTTCGTTTATGTT
1 CGTTCGATTATGTTCGTTTATGTT
*
360998 CATTC-ATTTATGTT
1 CGTTCGA-TTATGTT
361012 TAACACAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 1 0.03
24 34 0.97
ACGTcount: A:0.13, C:0.13, G:0.19, T:0.55
Consensus pattern (24 bp):
CGTTCGATTATGTTCGTTTATGTT
Found at i:361749 original size:10 final size:10
Alignment explanation
Indices: 361734--361792 Score: 57
Period size: 10 Copynumber: 5.7 Consensus size: 10
361724 GGGTCTCCAA
361734 CGTTTATGTT
1 CGTTTATGTT
361744 CGTTTATGTT
1 CGTTTATGTT
361754 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
361765 ATGTTCGTGTT
1 -CGTTTATGTT
361776 CGTTTATGTT
1 CGTTTATGTT
361786 CGTTTAT
1 CGTTTAT
361793 TTATTAAATG
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 28 0.72
11 7 0.18
12 4 0.10
ACGTcount: A:0.10, C:0.12, G:0.20, T:0.58
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:361765 original size:16 final size:16
Alignment explanation
Indices: 361740--361796 Score: 82
Period size: 16 Copynumber: 3.7 Consensus size: 16
361730 CCAACGTTTA
*
361740 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
361756 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
*
361772 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
361788 T-TT-ATTTAT
1 TGTTCATTTAT
361797 TAAATGAACG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
14 5 0.13
15 2 0.05
16 31 0.82
ACGTcount: A:0.11, C:0.11, G:0.19, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:361878 original size:16 final size:16
Alignment explanation
Indices: 361857--361889 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
361847 AAAAAAAAAT
361857 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
361873 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
361889 T
1 T
361890 TTATTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:362138 original size:2 final size:2
Alignment explanation
Indices: 362133--362182 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
362123 CTTCATATGT
362133 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
362174 TA CA TA TA T
1 TA TA TA TA T
362183 GAGATACTCG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:365647 original size:5 final size:5
Alignment explanation
Indices: 365639--365678 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
365629 AAATAAAATG
*
365639 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAGAA GAAAA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA GAAAA
365679 AACAGATTAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:369933 original size:18 final size:18
Alignment explanation
Indices: 369907--369942 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
369897 ATGTGAGCTA
* *
369907 GGAAGATGAAGGAGAGAG
1 GGAAAATGAAGGAAAGAG
369925 GGAAAATGAAGGAAAGAG
1 GGAAAATGAAGGAAAGAG
369943 TAATCTGGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.44, T:0.06
Consensus pattern (18 bp):
GGAAAATGAAGGAAAGAG
Found at i:375841 original size:25 final size:27
Alignment explanation
Indices: 375795--375844 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
375785 TCAAAAACCT
*
375795 CTTTATATCAAAAATTCTTTTCTAAAC
1 CTTTATATCAAAAATTCCTTTCTAAAC
*
375822 CTTTA-AT-AAAATTTCCTTTCTAA
1 CTTTATATCAAAAATTCCTTTCTAA
375845 TTATCTCTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 14 0.67
26 2 0.10
27 5 0.24
ACGTcount: A:0.36, C:0.18, G:0.00, T:0.46
Consensus pattern (27 bp):
CTTTATATCAAAAATTCCTTTCTAAAC
Found at i:383958 original size:20 final size:20
Alignment explanation
Indices: 383933--383971 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
383923 AGTTGTGGCC
383933 ATTTCTAGCCGTTAGGGATG
1 ATTTCTAGCCGTTAGGGATG
*
383953 ATTTCTAGCCGTTTGGGAT
1 ATTTCTAGCCGTTAGGGAT
383972 TGAAATCTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (20 bp):
ATTTCTAGCCGTTAGGGATG
Found at i:385639 original size:23 final size:23
Alignment explanation
Indices: 385613--385681 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
385603 CACCACAACT
*
385613 CGTATAAATGCACCGAAGTGCCA
1 CGTATAAATGCACCAAAGTGCCA
* * *
385636 CGTATAATTGTACCAAAGTGCCG
1 CGTATAAATGCACCAAAGTGCCA
*
385659 CGTAGAAATGCACCAAAGTGCCA
1 CGTATAAATGCACCAAAGTGCCA
385682 TATAAAATGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.35, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
CGTATAAATGCACCAAAGTGCCA
Found at i:386199 original size:2 final size:2
Alignment explanation
Indices: 386192--386242 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
386182 ACTCATAGTC
386192 AT AT AT AT -T 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
386233 AT AT AT AT AT
1 AT AT AT AT AT
386243 CATTTACCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:393047 original size:578 final size:584
Alignment explanation
Indices: 391954--393486 Score: 2753
Period size: 578 Copynumber: 2.6 Consensus size: 584
391944 CGATTATGTC
*
391954 AACTATTAATCTTCCTTTGGGCCGATCAATAC-GAACATATCCTAAGTTACATATGCATAACCTT
1 AACTATTAATCTTCCTTTGGGCCGATCAATACTG-ACATATCCTAAGTTACATATACATAACCTT
* * *
392018 CATATTTTAAAACTAAAATATTTTCCACAATAGAGGACTCTTTAAAGACTTAATGCATTAATTAA
65 CATATTTTAAAACTAAAATATTTTCCACAATAAAGGTCTATTTAAAGACTTAATGCATTAATTAA
* * * *
392083 GTCCTCTTAAAATAAATATCAGTACTCAAATTTAATATTTCTATATCAATCAAAGTTTAAAATTG
130 GTCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTG
* * * *
392148 AAATTTTTTATTGCACTACAGTATCCAAAATAACCCAAAATAT-G-TTCCTAAATGGTGCTATAA
195 AAATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGCTATAA
*
392211 AAAATCGAAAATTCAAGTTTTGATTGTTTCTGGAAAAATTTCTTAAACATTCATTTAATTCATAA
260 AAAATCGAAAATTCAAGTTTTGATTGTTTCTGGAAAATTTTCTTAAACATTCATTTAATTCATAA
392276 CTTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTTTAAAACTAAAATATCCTA
325 CTTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTTTAAAACTAAAATATCCTA
*
392341 AGTTACATATCCTTTGGGCCGATCAATACTAACATATCCTAAGTTACATATACATAACCTTCTTA
390 AGTTACATATCCTTTGGGCCGATCAATACTAACATATCCTAAGTTACATATACATAACCTTCATA
392406 TATTAAAACTAAAATATTTTCCACAATAGAGATCTCTTTAAAGACTTAATAAACTATTAATCTTC
455 TATTAAAACTAAAATATTTTCCACAATAGAGATCTCTTTAAAGACTTAATAAACTATTAATCTTC
*
392471 CTCTAAGCCGATC-T-T-AC-TAT-CTAAG-TACATATGCATAACCGAATTTAAAATACTTTATA
520 CTCTAAGCCGATCTTATAACATATCCTAAGTTACATATGCATAACCGAATTCAAAATACTTTATA
392530 AACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACATAACCTTC
1 AACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACATAACCTTC
392595 ATATTTTAAAACTAAAATATTTTCCACAATAAAGGTCTATTTAAAGACTTAATGCATTAATTAAG
66 ATATTTTAAAACTAAAATATTTTCCACAATAAAGGTCTATTTAAAGACTTAATGCATTAATTAAG
392660 TCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTGA
131 TCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTGA
392725 AATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGCTATAAA
196 AATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGCTATAAA
392790 AAATCGAAAATTCAAGTTTTGATTGTTTCTGGAAAATTTTCTTAAACATTCATTTAATTCATAAC
261 AAATCGAAAATTCAAGTTTTGATTGTTTCTGGAAAATTTTCTTAAACATTCATTTAATTCATAAC
392855 TTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTTTAAAACTAAAATATCCTAA
326 TTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTTTAAAACTAAAATATCCTAA
392920 GTTACATATCCTTTGGGCCGATCAATACTAACATATCCTAAGTTACATATACATAACCTTCATAT
391 GTTACATATCCTTTGGGCCGATCAATACTAACATATCCTAAGTTACATATACATAACCTTCATAT
*
392985 TTTAAAACTAAAATATTTTCCACAATAGAGATCTCTTTAAAGACTTAATAAACTATTAATCTTCC
456 ATTAAAACTAAAATATTTTCCACAATAGAGATCTCTTTAAAGACTTAATAAACTATTAATCTTCC
393050 TCTAAGCCGATCTTACTAACATATCCTAAGTTACATATGCATAACCGAATTCAAAATACTTTATA
521 TCTAAGCCGATCTTA-TAACATATCCTAAGTTACATATGCATAACCGAATTCAAAATACTTTATA
393115 AACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACATAACCTTC
1 AACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACATAACCTTC
* *
393180 ATATTTTAAAACTAAAATATTTTTCACAATAAAGGTCTATTTAAAGACTTAATTCATTAATTAAG
66 ATATTTTAAAACTAAAATATTTTCCACAATAAAGGTCTATTTAAAGACTTAATGCATTAATTAAG
393245 TCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTGA
131 TCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTGA
*
393310 AATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGTTATAAA
196 AATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGCTAT-AA
* * *
393375 AAAACCGAAAACTT-AAATTTTGATTGTTTTTGGAAAATTTTCTTAAACATTCATTTAATTCATA
260 AAAATCGAAAA-TTCAAGTTTTGATTGTTTCTGGAAAATTTTCTTAAACATTCATTTAATTCATA
*
393439 ACTTTATAAATTACCAAAGGCAAATCGAATTCAAAATAATCAATATTT
324 ACTTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTT
393487 AACTAAAAAT
Statistics
Matches: 922, Mismatches: 23, Indels: 14
0.96 0.02 0.01
Matches are distributed among these distances:
576 223 0.24
577 2 0.00
578 289 0.31
579 1 0.00
581 1 0.00
582 2 0.00
583 3 0.00
584 5 0.01
585 287 0.31
586 107 0.12
587 2 0.00
ACGTcount: A:0.41, C:0.17, G:0.08, T:0.35
Consensus pattern (584 bp):
AACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACATAACCTTC
ATATTTTAAAACTAAAATATTTTCCACAATAAAGGTCTATTTAAAGACTTAATGCATTAATTAAG
TCCTCTTAAAATAAATATCAGTATTCAAATTTAATATTTCTAAATCAACCAAAGGTTAAAATTGA
AATTTCTGATTGAACTACAATATCCAAAATAACCCAAAATATGGTTTCCTAAATGGTGCTATAAA
AAATCGAAAATTCAAGTTTTGATTGTTTCTGGAAAATTTTCTTAAACATTCATTTAATTCATAAC
TTTATAAATTACCAAAGGCAAACCGAATTCAAAATAATCAATATTTTAAAACTAAAATATCCTAA
GTTACATATCCTTTGGGCCGATCAATACTAACATATCCTAAGTTACATATACATAACCTTCATAT
ATTAAAACTAAAATATTTTCCACAATAGAGATCTCTTTAAAGACTTAATAAACTATTAATCTTCC
TCTAAGCCGATCTTATAACATATCCTAAGTTACATATGCATAACCGAATTCAAAATACTTTATA
Found at i:393175 original size:81 final size:80
Alignment explanation
Indices: 393027--393176 Score: 228
Period size: 80 Copynumber: 1.9 Consensus size: 80
393017 CTCTTTAAAG
* *
393027 ACTTAATAAACTATTAATCTTCCTCTAAGCCGATCTTACTAACATATCCTAAGTTACATATGCAT
1 ACTTAATAAACTATTAATCTTCCTCTAAGCCGATCATACTAACATATCCTAAGTTACATATACAT
393092 AACCGAATTCAAAAT
66 AACCGAATTCAAAAT
* * ** *
393107 ACTTTATAAACTATTAATCTTCCTTTGGGCCGATCAATACTGACATATCCTAAGTTACATATACA
1 ACTTAATAAACTATTAATCTTCCTCTAAGCCGATC-ATACTAACATATCCTAAGTTACATATACA
393172 TAACC
65 TAACC
393177 TTCATATTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
80 31 0.50
81 31 0.50
ACGTcount: A:0.37, C:0.23, G:0.07, T:0.33
Consensus pattern (80 bp):
ACTTAATAAACTATTAATCTTCCTCTAAGCCGATCATACTAACATATCCTAAGTTACATATACAT
AACCGAATTCAAAAT
Found at i:395379 original size:29 final size:28
Alignment explanation
Indices: 395318--395375 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
395308 TTTATTACTT
* *
395318 AAAT-ATATCATTCTAAATTATTTAATA
1 AAATAATATCATTCAAAACTATTTAATA
*
395345 ATATAATATCATTCAAAAACTATTT-ATA
1 AAATAATATCATTC-AAAACTATTTAATA
395373 AAA
1 AAA
395376 ATAACATTTC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
27 3 0.12
28 14 0.56
29 8 0.32
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.40
Consensus pattern (28 bp):
AAATAATATCATTCAAAACTATTTAATA
Found at i:399378 original size:64 final size:64
Alignment explanation
Indices: 399297--399426 Score: 224
Period size: 64 Copynumber: 2.0 Consensus size: 64
399287 TGGTTGTTGG
* * *
399297 TTGTATAGTAGCCGTTAACTTGTTGTTTATGTGGTAAGCTGGTTTCTTGTAGCATGTTTCCTGC
1 TTGTATAGTAGCCGTTAACTTGTTGTTTACGTAGTAAACTGGTTTCTTGTAGCATGTTTCCTGC
*
399361 TTGTATAGTAGTCGTTAACTTGTTGTTTACGTAGTAAACTGGTTTCTTGTAGCATGTTTCCTGC
1 TTGTATAGTAGCCGTTAACTTGTTGTTTACGTAGTAAACTGGTTTCTTGTAGCATGTTTCCTGC
399425 TT
1 TT
399427 TCTTAGGTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
64 62 1.00
ACGTcount: A:0.17, C:0.14, G:0.23, T:0.46
Consensus pattern (64 bp):
TTGTATAGTAGCCGTTAACTTGTTGTTTACGTAGTAAACTGGTTTCTTGTAGCATGTTTCCTGC
Found at i:415388 original size:374 final size:373
Alignment explanation
Indices: 414674--415426 Score: 1422
Period size: 373 Copynumber: 2.0 Consensus size: 373
414664 TGGTGTTTGT
*
414674 TTTATGTACGGGGTCGATATCTGGATGTATTTTGGTGTTCTTATGTTCAATGAAATCCTAAGGCA
1 TTTATGTAAGGGGTCGATATCTGGATGTATTTTGGTG-T-TTATGTTCAATGAAATCCTAAGGCA
414739 CTCTTTTCCTCCTTCGCTGATTAAGGAGCTTCTCTTTAAGTCTCTAATCAAGAAAGAGGTTTTTA
64 CTCTTTTCCTCCTTCGCTGATTAAGGAGCTTCTCTTTAAGTCTCTAATCAAGAAAGAGGTTTTTA
414804 ATGAGGCCTTCAATTCCTATAAAAAAAAAGAATAGAAATTCAAGGCACAACTTATTTTAACACTT
129 ATGAGGCCTTCAATTCCTATAAAAAAAAAGAATAGAAATTCAAGGCACAACTTATTTTAACACTT
414869 GGGATGCACAAGGAATTGAAATTTCAGTAAAACCCCTAGTGAATCAAAATAATTTCAGATATTAG
194 GGGATGCACAAGGAATTGAAATTTCAGTAAAACCCCTAGTGAATCAAAATAATTTCAGATATTAG
414934 ATCCCAATAAATATGACACATGGATGTCTTAAACATCTCAAGTCTCACTATCACATTAGCATTAC
259 ATCCCAATAAATATGACACATGGATGTCTTAAACATCTCAAGTCTCACTATCACATTAGCATTAC
414999 TTTAGGTGCACGATAAACCTTCAGCCAGAAGCTTGACCAAGAAAT-TTCA
324 TTTAGGTGCACGATAAACCTTCAGCCAGAAGCTTGACCAAGAAATATTCA
415048 TTTATGTAAGGGGTCGATATCTGGATGTATTTTGGTG-TTATGTTCAATGAAATCCTAAGGCACT
1 TTTATGTAAGGGGTCGATATCTGGATGTATTTTGGTGTTTATGTTCAATGAAATCCTAAGGCACT
415112 CTTTTCCTCCTTCCGCTGATTAAGGAGCTTCTCTTTAAGTCTCTCTAATCAAGAAAGAGGTTTTT
66 CTTTTCCTCCTT-CGCTGATTAAGGAGCTTCTCTTTAAG--TCTCTAATCAAGAAAGAGGTTTTT
415177 AATGAGGCCTTCAATTCCTAT-AAAAAAAAGAATAGAAATTCAAGGCACAACTTATTTTAACACT
128 AATGAGGCCTTCAATTCCTATAAAAAAAAAGAATAGAAATTCAAGGCACAACTTATTTTAACACT
415241 TGGGATGCACAAGGAATTGAAATTTCAGTAAAACCCCTAGTGAATCAAAATAATTTCAGATATTA
193 TGGGATGCACAAGGAATTGAAATTTCAGTAAAACCCCTAGTGAATCAAAATAATTTCAGATATTA
415306 GATCCCAATAAATATGACACATGGATGTCTTAAACATCTCAAGTCTCAACTATCACATTAGCATT
258 GATCCCAATAAATATGACACATGGATGTCTTAAACATCTCAAGTCTC-ACTATCACATTAGCATT
415371 ACTTTAGGTGCACGATAAACCTTCAGCCAGAAGCTTGACCAAGAAATATTCA
322 ACTTTAGGTGCACGATAAACCTTCAGCCAGAAGCTTGACCAAGAAATATTCA
415423 TTTA
1 TTTA
415427 CTTGACACAA
Statistics
Matches: 373, Mismatches: 1, Indels: 9
0.97 0.00 0.02
Matches are distributed among these distances:
371 39 0.10
372 26 0.07
373 155 0.42
374 145 0.39
375 8 0.02
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (373 bp):
TTTATGTAAGGGGTCGATATCTGGATGTATTTTGGTGTTTATGTTCAATGAAATCCTAAGGCACT
CTTTTCCTCCTTCGCTGATTAAGGAGCTTCTCTTTAAGTCTCTAATCAAGAAAGAGGTTTTTAAT
GAGGCCTTCAATTCCTATAAAAAAAAAGAATAGAAATTCAAGGCACAACTTATTTTAACACTTGG
GATGCACAAGGAATTGAAATTTCAGTAAAACCCCTAGTGAATCAAAATAATTTCAGATATTAGAT
CCCAATAAATATGACACATGGATGTCTTAAACATCTCAAGTCTCACTATCACATTAGCATTACTT
TAGGTGCACGATAAACCTTCAGCCAGAAGCTTGACCAAGAAATATTCA
Found at i:422130 original size:78 final size:78
Alignment explanation
Indices: 422034--422193 Score: 311
Period size: 78 Copynumber: 2.1 Consensus size: 78
422024 AATAATTAAA
422034 AATTATGAATTAGACTCATGAATTTTTTTGATCGTGTTGTCTTCGTTAAAATACTTGTATCTTGA
1 AATTATGAATTAGACTCATGAATTTTTTTGATCGTGTTGTCTTCGTTAAAATACTTGTATCTTGA
422099 GTTCCCAACTTTT
66 GTTCCCAACTTTT
*
422112 AATTATGAATTAGACTCATGAATTTTTTTGATCGTGTTGTCTTCGTTAAAATAGTTGTATCTTGA
1 AATTATGAATTAGACTCATGAATTTTTTTGATCGTGTTGTCTTCGTTAAAATACTTGTATCTTGA
422177 GTTCCCAACTTTT
66 GTTCCCAACTTTT
422190 AATT
1 AATT
422194 TAGACTTTTT
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 81 1.00
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (78 bp):
AATTATGAATTAGACTCATGAATTTTTTTGATCGTGTTGTCTTCGTTAAAATACTTGTATCTTGA
GTTCCCAACTTTT
Found at i:423142 original size:22 final size:21
Alignment explanation
Indices: 423111--423153 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 21
423101 TCAATGAGAT
423111 TAATTTAAAC-AATATTATAAA
1 TAATTTAAACTAA-ATTATAAA
423132 TAATATTAAACTAAATTATAAA
1 TAAT-TTAAACTAAATTATAAA
423154 ATTAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 14 0.70
23 2 0.10
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
TAATTTAAACTAAATTATAAA
Found at i:423738 original size:8 final size:8
Alignment explanation
Indices: 423725--423749 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
423715 GTAGCGCTTC
423725 TTTCTTTT
1 TTTCTTTT
423733 TTTCTTTT
1 TTTCTTTT
423741 TTTCTTTT
1 TTTCTTTT
423749 T
1 T
423750 CTTTAGAGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (8 bp):
TTTCTTTT
Found at i:424796 original size:24 final size:23
Alignment explanation
Indices: 424730--424788 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
424720 CTTTTTTAAA
* *
424730 TTTGTTTTTATGA-ATTTTTTCC
1 TTTGTCTTTATGACGTTTTTTCC
**
424752 TTTGTCTTTATGGTGTATTTTT-C
1 TTTGTCTTTATGACGT-TTTTTCC
424775 TTTGTCTTTATGAC
1 TTTGTCTTTATGAC
424789 ACGTTTTTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 11 0.37
23 14 0.47
24 5 0.17
ACGTcount: A:0.12, C:0.10, G:0.14, T:0.64
Consensus pattern (23 bp):
TTTGTCTTTATGACGTTTTTTCC
Found at i:426099 original size:44 final size:45
Alignment explanation
Indices: 426036--426121 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
426026 CGTCGTCATT
*
426036 ATCATCATCATCCAACA-CCCCTCCGAGACCAGAAATGCCCCATC
1 ATCATCATCATCCAACACCCCCTCCGAGACCAGAAACGCCCCATC
* *
426080 ATCATCATCATCCACCACCCCCTCCGAGACTAGAAACGCCCC
1 ATCATCATCATCCAACACCCCCTCCGAGACCAGAAACGCCCC
426122 CTCTGAGACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 16 0.42
45 22 0.58
ACGTcount: A:0.30, C:0.45, G:0.09, T:0.15
Consensus pattern (45 bp):
ATCATCATCATCCAACACCCCCTCCGAGACCAGAAACGCCCCATC
Found at i:426121 original size:21 final size:21
Alignment explanation
Indices: 426097--426179 Score: 121
Period size: 21 Copynumber: 4.0 Consensus size: 21
426087 TCATCCACCA
426097 CCCCCTCCGAGACTAGAAACG
1 CCCCCTCCGAGACTAGAAACG
*
426118 CCCCCTCTGAGACTAGAAACG
1 CCCCCTCCGAGACTAGAAACG
* *
426139 CCCCCTCCGATACTTGAAACG
1 CCCCCTCCGAGACTAGAAACG
* *
426160 CCCCCTCTGAGACCAGAAAC
1 CCCCCTCCGAGACTAGAAAC
426180 ATCATCATCA
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 54 1.00
ACGTcount: A:0.28, C:0.42, G:0.17, T:0.13
Consensus pattern (21 bp):
CCCCCTCCGAGACTAGAAACG
Found at i:426158 original size:42 final size:42
Alignment explanation
Indices: 426097--426179 Score: 139
Period size: 42 Copynumber: 2.0 Consensus size: 42
426087 TCATCCACCA
*
426097 CCCCCTCCGAGACTAGAAACGCCCCCTCTGAGACTAGAAACG
1 CCCCCTCCGAGACTAGAAACGCCCCCTCTGAGACCAGAAACG
* *
426139 CCCCCTCCGATACTTGAAACGCCCCCTCTGAGACCAGAAAC
1 CCCCCTCCGAGACTAGAAACGCCCCCTCTGAGACCAGAAAC
426180 ATCATCATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.42, G:0.17, T:0.13
Consensus pattern (42 bp):
CCCCCTCCGAGACTAGAAACGCCCCCTCTGAGACCAGAAACG
Found at i:427221 original size:2 final size:2
Alignment explanation
Indices: 427214--427297 Score: 168
Period size: 2 Copynumber: 42.0 Consensus size: 2
427204 AGGGAGAACT
427214 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
427256 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
427298 ATTATGGGAG
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 82 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:427354 original size:22 final size:22
Alignment explanation
Indices: 427323--427364 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
427313 TAAGGTAGTA
* *
427323 TATTTTACAAAAAACTTTCAAC
1 TATTTGACAAAAAACGTTCAAC
*
427345 TATTTGACAATAAACGTTCA
1 TATTTGACAAAAAACGTTCA
427365 TACTCCTGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (22 bp):
TATTTGACAAAAAACGTTCAAC
Found at i:428014 original size:28 final size:28
Alignment explanation
Indices: 427974--428036 Score: 126
Period size: 28 Copynumber: 2.2 Consensus size: 28
427964 TAAACATTAA
427974 TGTTTAAGATACTAAAGTTTTGTAGGAT
1 TGTTTAAGATACTAAAGTTTTGTAGGAT
428002 TGTTTAAGATACTAAAGTTTTGTAGGAT
1 TGTTTAAGATACTAAAGTTTTGTAGGAT
428030 TGTTTAA
1 TGTTTAA
428037 AATAAATATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (28 bp):
TGTTTAAGATACTAAAGTTTTGTAGGAT
Found at i:429798 original size:58 final size:58
Alignment explanation
Indices: 429727--429839 Score: 154
Period size: 58 Copynumber: 1.9 Consensus size: 58
429717 TTCTAATTAA
* * * *
429727 AATTATAACCAAATTAATAGAATGTATAAATAATAAAGATCAAATGTGTTATTATCCT
1 AATTATAACCAAATTAATAAAATATATAAATAATAAAGACCAAATGTATTATTATCCT
* * * *
429785 AATTATGACCAAATTGATAAAATATATAAATAATGAGGACCAAATGTATTATTAT
1 AATTATAACCAAATTAATAAAATATATAAATAATAAAGACCAAATGTATTATTAT
429840 ATAAATTTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.49, C:0.08, G:0.10, T:0.34
Consensus pattern (58 bp):
AATTATAACCAAATTAATAAAATATATAAATAATAAAGACCAAATGTATTATTATCCT
Found at i:435778 original size:24 final size:24
Alignment explanation
Indices: 435751--435799 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
435741 TGCATGACAT
435751 TGTAAATAGATGTTATATACATCA
1 TGTAAATAGATGTTATATACATCA
* *
435775 TGTACATAGATGTTTTATACATCA
1 TGTAAATAGATGTTATATACATCA
435799 T
1 T
435800 CAAGAAGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (24 bp):
TGTAAATAGATGTTATATACATCA
Found at i:436976 original size:16 final size:16
Alignment explanation
Indices: 436936--436976 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
436926 AAATAACTGG
* *
436936 TATCAACCCGACCTGT
1 TATCAACCTGACCTAT
436952 TATCAACCTGACCTAT
1 TATCAACCTGACCTAT
436968 TATCAACCT
1 TATCAACCT
436977 AACATGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.29, C:0.34, G:0.07, T:0.29
Consensus pattern (16 bp):
TATCAACCTGACCTAT
Done.