Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007926.1 Hibiscus syriacus cultivar Beakdansim tig00110332_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: 10075380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 11 of 42
Found at i:2299622 original size:25 final size:25
Alignment explanation
Indices: 2299578--2299625 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
2299568 TATTTTAAAT
2299578 TTAAAATAAAAATTATTCAAAAAAA
1 TTAAAATAAAAATTATTCAAAAAAA
*
2299603 TTAAATATTAAAATTA-TCAAAAA
1 TTAAA-ATAAAAATTATTCAAAAA
2299626 TAAAAGTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (25 bp):
TTAAAATAAAAATTATTCAAAAAAA
Found at i:2303003 original size:84 final size:83
Alignment explanation
Indices: 2302791--2303409 Score: 538
Period size: 84 Copynumber: 7.4 Consensus size: 83
2302781 GGTAGATAAT
* * * * ** * *
2302791 CCTTCTAGCCTTGAGTTATTCTGCAAAAGATGTGTCTTTAAGCTGAGTGTAATCGAACTCAAAAG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTC-GAAG
* *
2302856 GTCTTTTGTTGACAGATAAC
65 GT-ATTTGTTGACAGATAGC
* * * * * * *
2302876 CCTTCTAGCCTTGAGTTATGATGAAAATGACGTGTCTTGGAGCTGAATAAAATCGAATCTCGAAG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAA-CTCGAAG
* *
2302941 GTATTTGATGAAAGATAGC
65 GTATTTGTTGACAGATAGC
* * * * * * * * *
2302960 TCTTCTCGACTTAAGCTATACTGCAAATGATATGTCTTTGAGCTGAATATAATCGAACTCGAAGG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
* * *
2303025 TCTTTTGTTGACATATAAC
66 T-ATTTGTTGACAGATAGC
* * * * * *
2303044 CCTTCTAGCCTTAAGTTATGTTGTAAATGACGTGCCTTGGAGTTGAGTGTAGTCGAACTCGAAGG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
*
2303109 TATTTGGTTGGCAGATAGC
66 TATTT-GTTGACAGATAGC
* * * * ** *
2303128 CCTTCTAGCCTTGAGTTATGCTACAAATAACGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
* * *
2303193 TCTTTGGTTGGCAGTTAGC
66 TATTT-GTTGACAGATAGC
* * * * * * *
2303212 ACTTCTCGACTTAAGCTATACTACAAATGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
* *
2303277 TATTTTGTTGATAGATAAC
66 TA-TTTGTTGACAGATAGC
* * * * *
2303296 CCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
* *
2303361 TCTTTTGTT-AGCAGATAAC
66 T-ATTTGTTGA-CAGATAGC
* * * *
2303380 CCTTCTTGCCTTGAGCTAAGCTGCAAATGA
1 CCTTCTAGCCTTAAGTTATGCTGCAAATGA
2303410 GCACGATATC
Statistics
Matches: 435, Mismatches: 93, Indels: 13
0.80 0.17 0.02
Matches are distributed among these distances:
83 13 0.03
84 364 0.84
85 55 0.13
86 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.33
Consensus pattern (83 bp):
CCTTCTAGCCTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGTATAATCGAACTCGAAGG
TATTTGTTGACAGATAGC
Found at i:2303046 original size:168 final size:167
Alignment explanation
Indices: 2302791--2303391 Score: 695
Period size: 168 Copynumber: 3.6 Consensus size: 167
2302781 GGTAGATAAT
* * * *
2302791 CCTTCTAGCCTTGAGTTATTCTGCAAAAGATGTGTCTTTAAGCTGAGTGTAATCGAACTCAAAAG
1 CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTC-GAAG
* *
2302856 GTCTTTTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGAAAATGACGTGTCTTGGAGCTG
65 GTCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGATGAAAATGACGTGCCTTGGAGCTG
* * *
2302921 AATAAAATCGAATCTCGAAGGTATTTGATGAAAGATAGC
130 AGTATAATCGAA-CTCGAAGGTATTTGTTGAAAGATAGC
* * * * * * * * *
2302960 TCTTCTCGACTTAAGCTATACTGCAAATGATATGTCTTTGAGCTGAATATAATCGAACTCGAAGG
1 CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * *
2303025 TCTTTTGTTGACATATAACCCTTCTAGCCTTAAGTTATGTTGTAAATGACGTGCCTTGGAGTTGA
66 TCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGATGAAAATGACGTGCCTTGGAGCTGA
* * **
2303090 GTGTAGTCGAACTCGAAGGTATTTGGTTGGCAGATAGC
131 GTATAATCGAACTCGAAGGTATTT-GTTGAAAGATAGC
* * * * * * *
2303128 CCTTCTAGCCTTGAGTTATGCTACAAATAACGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGG
1 CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
* * * * * * * * * *
2303193 TCTTTGGTTGGCAGTTAGCACTTCTCGACTTAAGCTAT-ACT-ACAAATGATGTGCCTTTGAGCT
66 TCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGA-TGA-AAATGACGTGCCTTGGAGCT
* *
2303256 GAGTATAATCGAACTCGAAGGTATTTTGTTGATAGATAAC
129 GAGTATAATCGAACTCGAAGGTA-TTTGTTGAAAGATAGC
*
2303296 CCTTCTAGCCTTGAGTTATGTTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
1 CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
*
2303361 TCTTTTGTT-AGCAGATAACCCTTCTTGCCTT
66 TCTTTTGTTGA-CAGATAACCCTTCTAGCCTT
2303392 GAGCTAAGCT
Statistics
Matches: 352, Mismatches: 75, Indels: 11
0.80 0.17 0.03
Matches are distributed among these distances:
167 13 0.04
168 287 0.82
169 52 0.15
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.33
Consensus pattern (167 bp):
CCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGG
TCTTTTGTTGACAGATAACCCTTCTAGCCTTAAGTTATGATGAAAATGACGTGCCTTGGAGCTGA
GTATAATCGAACTCGAAGGTATTTGTTGAAAGATAGC
Found at i:2303219 original size:252 final size:252
Alignment explanation
Indices: 2302733--2303394 Score: 792
Period size: 252 Copynumber: 2.6 Consensus size: 252
2302723 ACCATGCGGT
* * * * * * ** *
2302733 TGATATGCCTCTGAGATGAATGA-AATCGAACTCAAAAGTCTTGATGTTGGTAGATAATCCTTCT
1 TGATATGCCTTTGAGCTGAAT-ATAATCGAACTCGAAGGTATT-TTGTTGACAGATAACCCTTCT
* * * * ** *
2302797 AGCCTTGAGTTAT-TCTGCAAAAGATGTGTCTTTAAGCTGAGTGTAATCGAACTCAAAAGGTCTT
64 AGCCTTAAGTTATGT-TGCAAATGACGTGCCTTGGAGCTGAGTGTAATCGAACTC-GAAGGTCTT
* * * *
2302861 TTGTTGACAGATAACCCTTCTAGCCTTGAGTTATGATGAAAATGACGTGTCTTGGAGCTGAATAA
127 TTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGATGAAAATAACGTGCCTTGGAGCTGAACAA
* *
2302926 AATCGAATCTCGAAGGTATTTGATGAAAGATAGCTCTTCTCGACTTAAGCTATACTGCAAA
192 AATCGAATCTCGAAGGTATTTGATGAAAGATAGCACTTCTCGACTTAAGCTATACTACAAA
* * *
2302987 TGATATGTCTTTGAGCTGAATATAATCGAACTCGAAGGTCTTTTGTTGACATATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTAG
* * * * *
2303052 CCTTAAGTTATGTTGTAAATGACGTGCCTTGGAGTTGAGTGTAGTCGAACTCGAAGGTATTTGGT
66 CCTTAAGTTATGTTGCAAATGACGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
* * * ** *
2303117 TGGCAGATAGCCCTTCTAGCCTTGAGTTATGCT-ACAAATAACGTGCCTTGGAGCTGAGCGTAGT
131 TGGCAGATAACCCTTCTAGCCTTGAGTTATGATGA-AAATAACGTGCCTTGGAGCTGAACAAAAT
* * ** *
2303181 CGAA-CTCGAAGGTCTTTGGTTGGCAGTTAGCACTTCTCGACTTAAGCTATACTACAAA
195 CGAATCTCGAAGGTATTT-GATGAAAGATAGCACTTCTCGACTTAAGCTATACTACAAA
* * *
2303239 TGATGTGCCTTTGAGCTGAGTATAATCGAACTCGAAGGTATTTTGTTGATAGATAACCCTTCTAG
1 TGATATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTAG
* * * *
2303304 CCTTGAGTTATGTTGCAAATGATGTGTCTTTGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
66 CCTTAAGTTATGTTGCAAATGACGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
* *
2303369 TAGCAGATAACCCTTCTTGCCTTGAG
131 TGGCAGATAACCCTTCTAGCCTTGAG
2303395 CTAAGCTGCA
Statistics
Matches: 347, Mismatches: 57, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
251 13 0.04
252 238 0.69
253 60 0.17
254 36 0.10
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (252 bp):
TGATATGCCTTTGAGCTGAATATAATCGAACTCGAAGGTATTTTGTTGACAGATAACCCTTCTAG
CCTTAAGTTATGTTGCAAATGACGTGCCTTGGAGCTGAGTGTAATCGAACTCGAAGGTCTTTTGT
TGGCAGATAACCCTTCTAGCCTTGAGTTATGATGAAAATAACGTGCCTTGGAGCTGAACAAAATC
GAATCTCGAAGGTATTTGATGAAAGATAGCACTTCTCGACTTAAGCTATACTACAAA
Found at i:2303628 original size:121 final size:121
Alignment explanation
Indices: 2303414--2303631 Score: 337
Period size: 121 Copynumber: 1.8 Consensus size: 121
2303404 AAATGAGCAC
* *
2303414 GATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATTGTGAAGTTGAGCCTCGAATT
1 GATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAACCTCGAATT
*
2303479 GGATATCCTTCATCGTGAAGTTGAAATCCAAGGGTTGCATTGTTACTGGTGGACAT
66 GGATATCCTTCATCGAGAAGTTGAAATCCAAGGGTTGCATTGTTACTGGTGGACAT
* * * * * *
2303535 GATATCCTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCTTCGTCGTGAAGTTGAACCTTGAATT
1 GATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAACCTCGAATT
* *
2303600 GGATATCTTTCGTCGAGAAGTTGAAATCCAAG
66 GGATATCCTTCATCGAGAAGTTGAAATCCAAG
2303632 TTAAGTTGCA
Statistics
Matches: 86, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
121 86 1.00
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (121 bp):
GATATCCTTCATCGTGAAGTTGAAATCGTGAATGACCCATTCATCGTGAAGTTGAACCTCGAATT
GGATATCCTTCATCGAGAAGTTGAAATCCAAGGGTTGCATTGTTACTGGTGGACAT
Found at i:2303853 original size:43 final size:44
Alignment explanation
Indices: 2303798--2303907 Score: 143
Period size: 43 Copynumber: 2.5 Consensus size: 44
2303788 GATTCCCTTT
* * *
2303798 GTCATGAAGTTGAAACCGTGGATGT-GTGGGCATGATATCCTCC
1 GTCATGGAGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCC
* * * *
2303841 GTTATGGAGTTGAAATCATGGAT-TCGTGGGTACGATATCCTCT
1 GTCATGGAGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCC
2303884 GTCATGGAGTTGAAATCGTGGATG
1 GTCATGGAGTTGAAATCGTGGATG
2303908 GCTCATTCGT
Statistics
Matches: 56, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
42 1 0.02
43 55 0.98
ACGTcount: A:0.24, C:0.15, G:0.31, T:0.31
Consensus pattern (44 bp):
GTCATGGAGTTGAAATCGTGGATGTCGTGGGCACGATATCCTCC
Found at i:2304274 original size:64 final size:64
Alignment explanation
Indices: 2304205--2304328 Score: 196
Period size: 64 Copynumber: 1.9 Consensus size: 64
2304195 TTGTGAGTTT
* *
2304205 AATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAA-TTGTTTGTTGAGTAC
1 AATATCCTTCACCGTGAAGTTGAAATTGACTCTGAATGAAA-TGGAAAAGTTGTTTGTTGAGTAC
* *
2304269 AATATCCTTCACCGTGAAGTTGAAATTGACTCTGAATGATATTGAAAAGTTGTTTGTTGA
1 AATATCCTTCACCGTGAAGTTGAAATTGACTCTGAATGAAATGGAAAAGTTGTTTGTTGA
2304329 CAGCCACTCC
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
63 6 0.11
64 49 0.89
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (64 bp):
AATATCCTTCACCGTGAAGTTGAAATTGACTCTGAATGAAATGGAAAAGTTGTTTGTTGAGTAC
Found at i:2304623 original size:32 final size:32
Alignment explanation
Indices: 2304582--2304654 Score: 92
Period size: 32 Copynumber: 2.3 Consensus size: 32
2304572 TTCGCATCAT
*
2304582 GATGTTGAATCCCCAAACATGCCCCAATATTC
1 GATGTTGAATCCCCAAACATGCCCCAACATTC
* * * *
2304614 GATGTTGAATCTCGAAAGATGCCCCAACATTT
1 GATGTTGAATCCCCAAACATGCCCCAACATTC
*
2304646 GATATTGAA
1 GATGTTGAA
2304655 AAGATGCCCT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (32 bp):
GATGTTGAATCCCCAAACATGCCCCAACATTC
Found at i:2308531 original size:22 final size:20
Alignment explanation
Indices: 2308488--2308537 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
2308478 TAAATTCAAA
*
2308488 AAATTAAAATAACAGTGGCT
1 AAATTAAAATAACAGTGACT
*
2308508 AAATTAAAAGTTAATAGTGACT
1 AAATTAAAA--TAACAGTGACT
*
2308530 AAAATAAA
1 AAATTAAA
2308538 GGAAATGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 9 0.36
22 16 0.64
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.26
Consensus pattern (20 bp):
AAATTAAAATAACAGTGACT
Found at i:2309036 original size:2 final size:2
Alignment explanation
Indices: 2309029--2309054 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2309019 ACCCCTTTTC
2309029 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
2309055 TGAAAGCATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2315330 original size:13 final size:13
Alignment explanation
Indices: 2315297--2315330 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2315287 CTATTCTAAA
2315297 CATTCATCGAAAC
1 CATTCATCGAAAC
*
2315310 CAATTCATCGAAAT
1 C-ATTCATCGAAAC
2315324 CATTCAT
1 CATTCAT
2315331 TGTACTAGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 7 0.37
14 12 0.63
ACGTcount: A:0.38, C:0.26, G:0.06, T:0.29
Consensus pattern (13 bp):
CATTCATCGAAAC
Found at i:2316448 original size:31 final size:31
Alignment explanation
Indices: 2316413--2316479 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2316403 GGAGAAATAT
**
2316413 TCTCTAATGTTATCGA-TCTATT-GGATTTTAG
1 TCTCTAACATTATCGATTC-ATTCGG-TTTTAG
2316444 TCTCTAACATTATCGATTCATTCGGTTTTAG
1 TCTCTAACATTATCGATTCATTCGGTTTTAG
2316475 TCTCT
1 TCTCT
2316480 TAGCTGTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 28 0.88
32 4 0.12
ACGTcount: A:0.21, C:0.18, G:0.13, T:0.48
Consensus pattern (31 bp):
TCTCTAACATTATCGATTCATTCGGTTTTAG
Found at i:2318541 original size:21 final size:21
Alignment explanation
Indices: 2318506--2318578 Score: 128
Period size: 21 Copynumber: 3.4 Consensus size: 21
2318496 TTGGAGCGTG
2318506 GGGGAAATCGATACCCCCTCAT
1 GGGG-AATCGATACCCCCTCAT
*
2318528 GGGGAATCGGTACCCCCTCAT
1 GGGGAATCGATACCCCCTCAT
2318549 GGGGAATCGATACCCCCTCAT
1 GGGGAATCGATACCCCCTCAT
2318570 GGGGAATCG
1 GGGGAATCG
2318579 GTCCCCTAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
21 45 0.92
22 4 0.08
ACGTcount: A:0.23, C:0.30, G:0.29, T:0.18
Consensus pattern (21 bp):
GGGGAATCGATACCCCCTCAT
Found at i:2318640 original size:20 final size:20
Alignment explanation
Indices: 2318615--2318673 Score: 91
Period size: 20 Copynumber: 3.0 Consensus size: 20
2318605 TCGTTAGACA
2318615 GGGGGAATCGGTACCCCTTG
1 GGGGGAATCGGTACCCCTTG
* * *
2318635 GGGGGAATCTGTTCCCATTG
1 GGGGGAATCGGTACCCCTTG
2318655 GGGGGAATCGGTACCCCTT
1 GGGGGAATCGGTACCCCTT
2318674 AGACATTCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.15, C:0.24, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGGTACCCCTTG
Found at i:2318733 original size:22 final size:21
Alignment explanation
Indices: 2318708--2318749 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
2318698 AAAACCTGCA
*
2318708 GGGGAAATCTATACCCCCTGG
1 GGGGGAATCTATACCCCCTGG
*
2318729 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTATACCCCCTGG
2318750 ACAATCTGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
GGGGGAATCTATACCCCCTGG
Found at i:2318889 original size:34 final size:34
Alignment explanation
Indices: 2318841--2318934 Score: 161
Period size: 34 Copynumber: 2.8 Consensus size: 34
2318831 ATTAGTGAAA
*
2318841 CTAGGGAAAGGTTCTAGCTTATCCCGTGTAAAAG
1 CTAGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAG
*
2318875 CTAGTGAAAGGTTCTAGCTTAGCCCGTGTAAAAG
1 CTAGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAG
*
2318909 CTAGGGAAAGGTTCTAGTTTAGCCCG
1 CTAGGGAAAGGTTCTAGCTTAGCCCG
2318935 GAAAAACTAG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.27
Consensus pattern (34 bp):
CTAGGGAAAGGTTCTAGCTTAGCCCGTGTAAAAG
Found at i:2319823 original size:19 final size:19
Alignment explanation
Indices: 2319799--2319845 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
2319789 ACGATTTTCC
*
2319799 TTTGAAAACAAAAATAGAT
1 TTTGAAAACAAAAATAAAT
* *
2319818 TTTGAAAGCCAAAATTAAAT
1 TTTGAAA-ACAAAAATAAAT
2319838 TTTGAAAA
1 TTTGAAAA
2319846 AGGATTTAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (19 bp):
TTTGAAAACAAAAATAAAT
Found at i:2321318 original size:20 final size:20
Alignment explanation
Indices: 2321280--2321319 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
2321270 ACAGAATGTT
2321280 CAGGGAGTACAGATTCCCCC
1 CAGGGAGTACAGATTCCCCC
*
2321300 CAGGG-GTACCGATTCCCCC
1 CAGGGAGTACAGATTCCCCC
2321319 C
1 C
2321320 TGTCTAACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.40, G:0.25, T:0.15
Consensus pattern (20 bp):
CAGGGAGTACAGATTCCCCC
Found at i:2325863 original size:57 final size:58
Alignment explanation
Indices: 2325695--2325891 Score: 283
Period size: 58 Copynumber: 3.4 Consensus size: 58
2325685 TTTTAATTTG
* *
2325695 GTAAGGAAAATAAATAT-TTGAATTTAATTCCTTGAGAATCTTGAATGATTCTAACTTT
1 GTAAAGAAAATAAAT-TGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTT
* * *
2325753 GTAAGGAAAATAAATTGTTAAATTTATTTCCTTGAGAATCTTGAATTATTCTAACTTT
1 GTAAAGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTT
* *
2325811 GTAAAGAAAA-AAATTGTTGAATTTATTTTCC-TGAGAATCTTAAATGACTCTAACTTT
1 GTAAAGAAAATAAATTGTTGAATTTA-TTTCCTTGAGAATCTTGAATGATTCTAACTTT
*
2325868 GTAAAGAAAATAAATAGTTGAATT
1 GTAAAGAAAATAAATTGTTGAATT
2325892 AAGAATCTTG
Statistics
Matches: 127, Mismatches: 9, Indels: 6
0.89 0.06 0.04
Matches are distributed among these distances:
57 48 0.38
58 79 0.62
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (58 bp):
GTAAAGAAAATAAATTGTTGAATTTATTTCCTTGAGAATCTTGAATGATTCTAACTTT
Found at i:2325986 original size:107 final size:106
Alignment explanation
Indices: 2325787--2325994 Score: 246
Period size: 107 Copynumber: 2.0 Consensus size: 106
2325777 TATTTCCTTG
*
2325787 AGAATCTTGAATTATTCTAACTTTGTAAAGAAAAAAATTGTTGAATTTATTTTCCTGAGAATCTT
1 AGAATCTTGAATTATTCTAACTTTGTAAAAAAAAAAATTGTTGAATTTATTTTCCTGAGAATCTT
* *
2325852 AAATGACTCTAACTTTGTAAAGAAAATAAATAGTTGAATTA
66 AAAGGACTCTAACTTTGAAAAGAAAATAAATAGTTGAATTA
* *
2325893 AGAATCTTGAATTATTCT-ATTTTGTAAAAATAAATAAATTGGTT-AATTTATTTT-CTTAGGAA
1 AGAATCTTGAATTATTCTAACTTTGTAAAAA-AAA-AAATT-GTTGAATTTATTTTCCTGA-GAA
* * * *
2325955 TCTTGAAGGA-TCTTA-TTATGCAAAAGGAAATAAATCGTTG
62 TCTTAAAGGACTCTAACTT-TG-AAAAGAAAATAAATAGTTG
2325995 GATTTCTTGT
Statistics
Matches: 87, Mismatches: 9, Indels: 11
0.81 0.08 0.10
Matches are distributed among these distances:
105 12 0.14
106 30 0.34
107 42 0.48
108 3 0.03
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (106 bp):
AGAATCTTGAATTATTCTAACTTTGTAAAAAAAAAAATTGTTGAATTTATTTTCCTGAGAATCTT
AAAGGACTCTAACTTTGAAAAGAAAATAAATAGTTGAATTA
Found at i:2326214 original size:39 final size:37
Alignment explanation
Indices: 2326165--2326300 Score: 118
Period size: 39 Copynumber: 3.6 Consensus size: 37
2326155 GAAATAAATT
*
2326165 GAAACAAATCGTTTGATTTATTTTCCTGTTTTGTAAAAA
1 GAAATAAATCGTTT-ATTTATTTT-CTGTTTTGTAAAAA
* * * *
2326204 GAAGTAAATCGTTTA--T-TTCTCAGTTTTAT-AAAA
1 GAAATAAATCGTTTATTTATTTTCTGTTTTGTAAAAA
* *
2326237 GAAAATAAATCGTTGGATTTATTTTTCTGTTTTGTAAAAG
1 G-AAATAAATCGTT-TATTTA-TTTTCTGTTTTGTAAAAA
*
2326277 GAAATAAATTGTTATATTTATTTT
1 GAAATAAATCGTT-TATTTATTTT
2326301 TGGGAATCTT
Statistics
Matches: 76, Mismatches: 14, Indels: 15
0.72 0.13 0.14
Matches are distributed among these distances:
33 5 0.07
34 18 0.24
35 4 0.05
36 1 0.01
37 1 0.01
38 5 0.07
39 38 0.50
40 4 0.05
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.46
Consensus pattern (37 bp):
GAAATAAATCGTTTATTTATTTTCTGTTTTGTAAAAA
Found at i:2328332 original size:30 final size:30
Alignment explanation
Indices: 2328296--2328367 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2328286 CCCGCAGGAC
*
2328296 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
2328326 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
2328356 CTGTCCATAGGT
1 CTATCCAGAGGT
2328368 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:2328392 original size:31 final size:30
Alignment explanation
Indices: 2328354--2328600 Score: 229
Period size: 31 Copynumber: 7.9 Consensus size: 30
2328344 GATCCTCGGC
* *
2328354 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
2328384 GAACTGTCCATATGTTCC-ATAGAACATAGGT
1 -AACTGTCCATATGTTCCGA-AGAACATAGGT
2328415 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
2328446 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
2328478 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
2328509 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
2328541 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
* * *
2328572 AATTTTGTCCAGATGTTCCGTAGAACATA
1 AA--CTGTCCATATGTTCCGAAGAACATA
2328601 TGTACCATCG
Statistics
Matches: 184, Mismatches: 9, Indels: 45
0.77 0.04 0.19
Matches are distributed among these distances:
30 14 0.08
31 95 0.52
32 64 0.35
33 11 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:2328464 original size:63 final size:63
Alignment explanation
Indices: 2328387--2328600 Score: 401
Period size: 63 Copynumber: 3.4 Consensus size: 63
2328377 CCTAGGTGAA
*
2328387 CTGTCCATATGTTCCATAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2328450 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2328513 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
* *
2328576 TTGTCCAGATGTTCCGTAGAACATA
1 CTGTCCATATGTTCCGTAGAACATA
2328601 TGTACCATCG
Statistics
Matches: 148, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 148 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (63 bp):
CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
Found at i:2328548 original size:94 final size:94
Alignment explanation
Indices: 2328355--2328571 Score: 250
Period size: 94 Copynumber: 2.3 Consensus size: 94
2328345 ATCCTCGGCA
* * *
2328355 ACTGTCCATAGGTTCCGAAGAACCTAGGTGAACTGTCCATATGTTCCATAGAACATAGGTATACT
1 ACTGTCCATATGTTCCGAAGAACATAGGTGAACTGTCCATATGTTCCAAAGAACATAGGTATACT
2328420 GTCCATATGTCTCGAAAGACATAGGTAAT
66 GTCCATATGTCTCGAAAGACATAGGTAAT
* * *
2328449 TCTGTCCATATGTTCCGTAGAACATAGGT-ATACTGTCCATATGTCTCGAAAG-ACATAGGTAAT
1 ACTGTCCATATGTTCCGAAGAACATAGGTGA-ACTGTCCATATGT-TCCAAAGAACATAGGT-AT
* *
2328512 TCTGTCCATATGT-TCCG-TAGAACATAGGT-AT
63 ACTGTCCATATGTCT-CGAAAG-ACATAGGTAAT
2328543 ACTGTCCATATG-TCTCGAA-AGACATAGGT
1 ACTGTCCATATGTTC-CGAAGA-ACATAGGT
2328572 AATTTTGTCC
Statistics
Matches: 106, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
93 4 0.04
94 73 0.69
95 29 0.27
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.30
Consensus pattern (94 bp):
ACTGTCCATATGTTCCGAAGAACATAGGTGAACTGTCCATATGTTCCAAAGAACATAGGTATACT
GTCCATATGTCTCGAAAGACATAGGTAAT
Found at i:2333467 original size:30 final size:30
Alignment explanation
Indices: 2333431--2333502 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
2333421 CCCGCAGGAC
*
2333431 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
2333461 CTATCCAGAGGTCATAAAGATCCTCGGCAA
1 CTATCCAGAGGTCATAAAGATCCTCGGCAA
* *
2333491 CTGTCCATAGGT
1 CTATCCAGAGGT
2333503 TCCGAAGAAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGCAA
Found at i:2333527 original size:31 final size:30
Alignment explanation
Indices: 2333489--2333739 Score: 235
Period size: 31 Copynumber: 8.0 Consensus size: 30
2333479 GATCCTCGGC
* *
2333489 AACTGTCCATAGGTTCCGAAGAACCTAGGT
1 AACTGTCCATATGTTCCGAAGAACATAGGT
**
2333519 GAACTGTCCATATGTTCCTTAGAACATAGGT
1 -AACTGTCCATATGTTCCGAAGAACATAGGT
2333550 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
2333581 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
2333613 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
* * *
2333644 AATTTTGTCCATATGTTCCGTAGAACATAAGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
2333676 ATACTGTCCATATG-TCTCGAA-AGACATAGGT
1 A-ACTGTCCATATGTTC-CGAAGA-ACATAGGT
*
2333707 AATTCTGTCCATATGTTCCGTAGAACATAGGT
1 AA--CTGTCCATATGTTCCGAAGAACATAGGT
2333739 A
1 A
2333740 CCCTCGACTC
Statistics
Matches: 184, Mismatches: 15, Indels: 41
0.77 0.06 0.17
Matches are distributed among these distances:
30 13 0.07
31 93 0.51
32 67 0.36
33 11 0.06
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (30 bp):
AACTGTCCATATGTTCCGAAGAACATAGGT
Found at i:2333594 original size:32 final size:31
Alignment explanation
Indices: 2333542--2333722 Score: 208
Period size: 32 Copynumber: 5.7 Consensus size: 31
2333532 GTTCCTTAGA
2333542 ACATAGGTATACTGTCCATATGTCTCGAAAG
1 ACATAGGTATACTGTCCATATGTCTCGAAAG
* *
2333573 ACATAGGTAATTCTGTCCATATGT-TCCG-TAG
1 ACATAGGT-ATACTGTCCATATGTCT-CGAAAG
2333604 AACATAGGTATACTGTCCATATGTCTCGAAAG
1 -ACATAGGTATACTGTCCATATGTCTCGAAAG
** *
2333636 ACATAGGTAATTTTGTCCATATGT-TCCG-TAG
1 ACATAGGT-ATACTGTCCATATGTCT-CGAAAG
*
2333667 AACATAAGTATACTGTCCATATGTCTCGAAAG
1 -ACATAGGTATACTGTCCATATGTCTCGAAAG
*
2333699 ACATAGGTAATTCTGTCCATATGT
1 ACATAGGT-ATACTGTCCATATGT
2333723 TCCGTAGAAC
Statistics
Matches: 126, Mismatches: 13, Indels: 21
0.79 0.08 0.13
Matches are distributed among these distances:
31 60 0.48
32 66 0.52
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (31 bp):
ACATAGGTATACTGTCCATATGTCTCGAAAG
Found at i:2333599 original size:63 final size:63
Alignment explanation
Indices: 2333522--2333739 Score: 409
Period size: 63 Copynumber: 3.5 Consensus size: 63
2333512 CCTAGGTGAA
*
2333522 CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2333585 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
* *
2333648 TTGTCCATATGTTCCGTAGAACATAAGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
2333711 CTGTCCATATGTTCCGTAGAACATAGGTA
1 CTGTCCATATGTTCCGTAGAACATAGGTA
2333740 CCCTCGACTC
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 150 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (63 bp):
CTGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCTCGAAAGACATAGGTAATT
Found at i:2339815 original size:6 final size:6
Alignment explanation
Indices: 2339804--2339830 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2339794 TAGACTTGTT
2339804 TCCCAA TCCCAA TCCCAA TCCCAA TCC
1 TCCCAA TCCCAA TCCCAA TCCCAA TCC
2339831 GAACATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.52, G:0.00, T:0.19
Consensus pattern (6 bp):
TCCCAA
Found at i:2343322 original size:19 final size:18
Alignment explanation
Indices: 2343281--2343318 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
2343271 AATAAAAAAC
2343281 TTAAACGCTAAAAAATAA
1 TTAAACGCTAAAAAATAA
*
2343299 TTAAACGCTAAAAATTAA
1 TTAAACGCTAAAAAATAA
2343317 TT
1 TT
2343319 TAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (18 bp):
TTAAACGCTAAAAAATAA
Found at i:2347963 original size:34 final size:35
Alignment explanation
Indices: 2347920--2347987 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 35
2347910 ATTGTACAGG
2347920 GGGAACAGATTCCCCCT-GGGGGTATCGATTCCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
*
2347954 GGGAACAGATTCCTCCTGGGGGGTATCGATTCCC
1 GGGAACAGATTCCCCCTGGGGGGTATCGATTCCC
2347988 TCTAAATGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 16 0.50
35 16 0.50
ACGTcount: A:0.18, C:0.29, G:0.31, T:0.22
Consensus pattern (35 bp):
GGGAACAGATTCCCCCTGGGGGGTATCGATTCCCC
Found at i:2349094 original size:24 final size:24
Alignment explanation
Indices: 2349001--2349094 Score: 88
Period size: 23 Copynumber: 4.0 Consensus size: 24
2348991 CAATCTTATA
*
2349001 TGGCACTACGGTGCAA-TTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
**
2349024 TGGCACTTAAGTGC-ATTTCTACG
1 TGGCACTTCGGTGCAATTTCTACG
* *
2349047 CGGTC-CTTCGG-GACAAATTCTACG
1 TGG-CACTTCGGTG-CAATTTCTACG
*
2349071 TGGCACTTCGGTGCAATTTATACG
1 TGGCACTTCGGTGCAATTTCTACG
2349095 AGCTGTGATG
Statistics
Matches: 55, Mismatches: 10, Indels: 11
0.72 0.13 0.14
Matches are distributed among these distances:
22 2 0.04
23 26 0.47
24 26 0.47
25 1 0.02
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
TGGCACTTCGGTGCAATTTCTACG
Found at i:2350760 original size:22 final size:22
Alignment explanation
Indices: 2350734--2350798 Score: 103
Period size: 22 Copynumber: 3.0 Consensus size: 22
2350724 TTCTGGGCTA
2350734 GGGGAATCGGTACCCATTCAAG
1 GGGGAATCGGTACCCATTCAAG
2350756 GGGGAATCGGTACCCATTCAAG
1 GGGGAATCGGTACCCATTCAAG
* * *
2350778 GGGGAACCGATACCCCTTCAA
1 GGGGAATCGGTACCCATTCAA
2350799 ACGAACAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (22 bp):
GGGGAATCGGTACCCATTCAAG
Found at i:2351532 original size:2 final size:2
Alignment explanation
Indices: 2351525--2351578 Score: 99
Period size: 2 Copynumber: 26.5 Consensus size: 2
2351515 ATAGTTAAGG
2351525 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
2351567 AT AT AT GAT AT A
1 AT AT AT -AT AT A
2351579 AAAAACATAG
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 49 0.96
3 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2355674 original size:23 final size:23
Alignment explanation
Indices: 2355648--2355735 Score: 90
Period size: 23 Copynumber: 3.8 Consensus size: 23
2355638 CAATCTTATA
*
2355648 TGGCACTACGGTGCAATTCTACG
1 TGGCACTTCGGTGCAATTCTACG
* *
2355671 TGGCACTTCGGTGCATTTCTATG
1 TGGCACTTCGGTGCAATTCTACG
* *
2355694 CGGTC-CTTCGG-GATAAATTCTACG
1 TGG-CACTTCGGTG--CAATTCTACG
2355718 TGGCACTTCGGTGCAATT
1 TGGCACTTCGGTGCAATT
2355736 TATACGAGCT
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
22 1 0.02
23 33 0.65
24 16 0.31
25 1 0.02
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
TGGCACTTCGGTGCAATTCTACG
Found at i:2360308 original size:22 final size:22
Alignment explanation
Indices: 2360264--2360328 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
2360254 ATATGAAATT
* * *
2360264 TGTCCCGAAAGATCTCATTTATA
1 TGTCCCGAATGACCT-ATGTATA
2360287 TGTCCCGAA-GAACCTATGTATA
1 TGTCCCGAATG-ACCTATGTATA
2360309 TGTCCCGAATGACCTATGTA
1 TGTCCCGAATGACCTATGTA
2360329 ACCCTCAACT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
22 25 0.66
23 13 0.34
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (22 bp):
TGTCCCGAATGACCTATGTATA
Found at i:2375754 original size:24 final size:22
Alignment explanation
Indices: 2375710--2375761 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
2375700 TAACTTTAAC
2375710 TGAACAAACGAACGAACAAACA
1 TGAACAAACGAACGAACAAACA
2375732 TGAACAAAC--ACGAAC-AAC-
1 TGAACAAACGAACGAACAAACA
*
2375750 TAAACAAACGAA
1 TGAACAAACGAA
2375762 ATTTATTATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 8 0.30
19 3 0.11
20 7 0.26
22 9 0.33
ACGTcount: A:0.60, C:0.23, G:0.12, T:0.06
Consensus pattern (22 bp):
TGAACAAACGAACGAACAAACA
Found at i:2375866 original size:14 final size:14
Alignment explanation
Indices: 2375849--2375875 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2375839 GAACACAAAT
2375849 GAACAAACATAAAC
1 GAACAAACATAAAC
2375863 GAACAAACATAAA
1 GAACAAACATAAA
2375876 ATTAATTGGG
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:0.67, C:0.19, G:0.07, T:0.07
Consensus pattern (14 bp):
GAACAAACATAAAC
Found at i:2376084 original size:14 final size:14
Alignment explanation
Indices: 2376065--2376115 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
2376055 ATAAATGAAT
2376065 ATAAATGAACAAAC
1 ATAAATGAACAAAC
* *
2376079 ATAAATTAACTAAC
1 ATAAATGAACAAAC
*
2376093 ATAAATGAACCAAC
1 ATAAATGAACAAAC
2376107 ATAAATGAA
1 ATAAATGAA
2376116 TGAATTATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.20
Consensus pattern (14 bp):
ATAAATGAACAAAC
Found at i:2384605 original size:17 final size:18
Alignment explanation
Indices: 2384585--2384623 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
2384575 ATTATATAAG
2384585 TAAAATA-TTAAATAAAT
1 TAAAATACTTAAATAAAT
2384602 TAAAATACTTAAATAAAT
1 TAAAATACTTAAATAAAT
2384620 TAAA
1 TAAA
2384624 TAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TAAAATACTTAAATAAAT
Found at i:2384641 original size:22 final size:23
Alignment explanation
Indices: 2384585--2384650 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 23
2384575 ATTATATAAG
2384585 TAAAATATTAAATAAATTAAAATACT
1 TAAAA-ATTAAATAAA--AAAATACT
2384611 TAAATAAATTAAATAAAAAAATA-T
1 T-AA-AAATTAAATAAAAAAATACT
2384635 TAAAAA-TATAATAAAA
1 TAAAAATTA-AATAAAA
2384651 TATACCTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
21 2 0.05
22 10 0.27
23 2 0.05
24 2 0.05
25 6 0.16
26 1 0.03
27 12 0.32
28 2 0.05
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
TAAAAATTAAATAAAAAAATACT
Found at i:2384686 original size:10 final size:10
Alignment explanation
Indices: 2384663--2384712 Score: 64
Period size: 10 Copynumber: 5.0 Consensus size: 10
2384653 TACCTTAAAC
* *
2384663 AGAGAATATA
1 AGAGAATTTG
*
2384673 AGAGTATTTG
1 AGAGAATTTG
*
2384683 AGAGAAGTTG
1 AGAGAATTTG
2384693 AGAGAATTTG
1 AGAGAATTTG
2384703 AGAGAATTTG
1 AGAGAATTTG
2384713 GTGTGATGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 34 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (10 bp):
AGAGAATTTG
Found at i:2386114 original size:25 final size:25
Alignment explanation
Indices: 2386080--2386128 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
2386070 ATCTATTATA
*
2386080 CGTTGTCAATGACCGACAAAGAATG
1 CGTTGTCAATAACCGACAAAGAATG
*
2386105 CGTTGTCAATAACCGAGAAAGAAT
1 CGTTGTCAATAACCGACAAAGAAT
2386129 ATGAACATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (25 bp):
CGTTGTCAATAACCGACAAAGAATG
Found at i:2386939 original size:139 final size:139
Alignment explanation
Indices: 2386689--2386968 Score: 456
Period size: 139 Copynumber: 2.0 Consensus size: 139
2386679 AAAAAGAGAG
* * *
2386689 TTGTTCTCCTTTAAGGTCTTGAGTTCGAGCAACGGTGTCAGTAGGGTATGTGTATGTTAAGAAAG
1 TTGTTCTCCTTTAAGGTATTGAGTTCAAGCAACGGTGTCAGTAGGGTATGTGTATGTTAAAAAAG
* *
2386754 ATTATGAACAAATAGTATCTTGTAATCACCCATACTATTCAGAAAATAATAATTCATATCAATAA
66 ATTACGAACAAATAGTATCTTGTAATAACCCATACTATTCAGAAAATAATAATTCATATCAATAA
*
2386819 AACTTTCTA
131 AACTTCCTA
*
2386828 TTGTTCTCCTTTAAGGTATTGAGTTCAAGCAGA-TGTGTCCA-TAGGGTATGTGTATGTTAAAAA
1 TTGTTCTCCTTTAAGGTATTGAGTTCAAGCA-ACGGTGT-CAGTAGGGTATGTGTATGTTAAAAA
*
2386891 AGATTACGAACAAATAGTATCTTTTAATAACCCATACTATTCAGAAAATAATAATTCATATCAAT
64 AGATTACGAACAAATAGTATCTTGTAATAACCCATACTATTCAGAAAATAATAATTCATATCAAT
2386956 AAAACTTCCTA
129 AAAACTTCCTA
2386967 TT
1 TT
2386969 TCTAGGAAGA
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
139 128 0.98
140 3 0.02
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (139 bp):
TTGTTCTCCTTTAAGGTATTGAGTTCAAGCAACGGTGTCAGTAGGGTATGTGTATGTTAAAAAAG
ATTACGAACAAATAGTATCTTGTAATAACCCATACTATTCAGAAAATAATAATTCATATCAATAA
AACTTCCTA
Found at i:2390647 original size:23 final size:23
Alignment explanation
Indices: 2390610--2390673 Score: 83
Period size: 23 Copynumber: 2.8 Consensus size: 23
2390600 CAGCTCGTAT
*
2390610 AAATGCACCGGAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * *
2390633 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
*
2390656 AAATGCACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
2390674 TATAAGATGT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.31, C:0.27, G:0.27, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:2391436 original size:2 final size:2
Alignment explanation
Indices: 2391429--2391456 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2391419 ACTTATAAAC
2391429 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
2391457 TACTTAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2396115 original size:81 final size:81
Alignment explanation
Indices: 2396015--2396180 Score: 278
Period size: 81 Copynumber: 2.0 Consensus size: 81
2396005 ACCAGCCTCT
* *
2396015 TGTACAACCGGCTCGGTAGCTTCCTGCTCTACACCTCTATGAGAGCTTGTTGCTCCGCCATTTCG
1 TGTACAACCAGCTCGGTAGCTTCCTACTCTACACCTCTATGAGAGCTTGTTGCTCCGCCATTTCG
2396080 TGTGCGAACCATTCTC
66 TGTGCGAACCATTCTC
* * *
2396096 TGTACAATCAGCTCGGTAGCTTCCTACTCTACACCTCTGTGAGAGCTTGTTGCTCTGCCATTTCG
1 TGTACAACCAGCTCGGTAGCTTCCTACTCTACACCTCTATGAGAGCTTGTTGCTCCGCCATTTCG
*
2396161 TGTGCGAGCCATTCTC
66 TGTGCGAACCATTCTC
2396177 TGTA
1 TGTA
2396181 ATTTGCTGCC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.16, C:0.30, G:0.21, T:0.33
Consensus pattern (81 bp):
TGTACAACCAGCTCGGTAGCTTCCTACTCTACACCTCTATGAGAGCTTGTTGCTCCGCCATTTCG
TGTGCGAACCATTCTC
Found at i:2396358 original size:28 final size:28
Alignment explanation
Indices: 2396326--2396391 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
2396316 CGAGAGCTAA
2396326 CACCTCTGTGTAGCTAAAAGTGATTGAG
1 CACCTCTGTGTAGCTAAAAGTGATTGAG
2396354 CACCTCTGTGTAGCTAAAAGTGATTGAG
1 CACCTCTGTGTAGCTAAAAGTGATTGAG
*
2396382 CACCTATGTG
1 CACCTCTGTG
2396392 CTTCAATCGG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (28 bp):
CACCTCTGTGTAGCTAAAAGTGATTGAG
Found at i:2396427 original size:55 final size:55
Alignment explanation
Indices: 2396354--2396668 Score: 312
Period size: 55 Copynumber: 5.7 Consensus size: 55
2396344 AGTGATTGAG
* * * *
2396354 CACCTCTGTGTAGCTAAAAGTGATTGAGCACCTATGTGCTTCAATCGGGAACTGA
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
* * * ** * *
2396409 CACCTCTGTGCAGTTAAAAATAACTGAGCACCTCTGTGCTTCAGCCAAGAGCTGA
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
* ** *
2396464 CACCTCTGTGTAGCTAAAACGGATTGAGCACCTCTATGCTTCAATCGAGAACTGA
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
** * * * *
2396519 CACCTCTGTGCAATTAAAAATGACTGAGCACCTCTGTGCATCAGTCGAGAGCTGA
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
* * * * * * *
2396574 CACCTCTGTGTAGCTAAAATTGATTGAGCACATTTGTGCTTTAATCTAGGATA-TGG
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGA-GA-ACTGA
* **
2396630 CACCTCTGTGCA--TTAGGATGATTGAGCACCTCTGTGCTT
1 CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTT
2396669 TTACAAACGA
Statistics
Matches: 206, Mismatches: 52, Indels: 5
0.78 0.20 0.02
Matches are distributed among these distances:
54 21 0.10
55 170 0.83
56 15 0.07
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (55 bp):
CACCTCTGTGCAGCTAAAAATGATTGAGCACCTCTGTGCTTCAATCGAGAACTGA
Found at i:2396446 original size:28 final size:26
Alignment explanation
Indices: 2396402--2396559 Score: 88
Period size: 28 Copynumber: 5.8 Consensus size: 26
2396392 CTTCAATCGG
2396402 GAACTGACACCTCTGTGCAGTTAAAAA
1 GAACTGACACCTCTGTGCA-TTAAAAA
* **
2396429 TAACTGAGCACCTCTGTGC-TTCAGCCAA
1 GAACTGA-CACCTCTGTGCATT-A-AAAA
* * * *
2396457 GAGCTGACACCTCTGTGTAGCTAAAAC
1 GAACTGACACCTCTGTGCA-TTAAAAA
* * * **
2396484 GGATTGAGCACCTCTATGC-TTCAATCGA
1 GAACTGA-CACCTCTGTGCATT-AA-AAA
2396512 GAACTGACACCTCTGTGCAATTAAAAA
1 GAACTGACACCTCTGTGC-ATTAAAAA
2396539 TG-ACTGAGCACCTCTGTGCAT
1 -GAACTGA-CACCTCTGTGCAT
2396560 CAGTCGAGAG
Statistics
Matches: 95, Mismatches: 24, Indels: 24
0.66 0.17 0.17
Matches are distributed among these distances:
26 3 0.03
27 42 0.44
28 47 0.49
29 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (26 bp):
GAACTGACACCTCTGTGCATTAAAAA
Found at i:2396489 original size:110 final size:108
Alignment explanation
Indices: 2396354--2396668 Score: 409
Period size: 110 Copynumber: 2.9 Consensus size: 108
2396344 AGTGATTGAG
2396354 CACCTCTGTGTAGCTAAAAGTGATTGAGCACCTATGTGCTTCAATCGGGAACTGACACCTCTGTG
1 CACCTCTGTGTAGCTAAAAG-GATTGAGCACCTATGTGCTTCAATCGGGAACTGACACCTCTGTG
*
2396419 CAGTTAAAAATAACTGAGCACCTCTGTGCTTCAGCCAAGAGCTGA
65 CA-TTAAAAATGACTGAGCACCTCTGTGCTTCAGCCAAGAGCTGA
* * *
2396464 CACCTCTGTGTAGCTAAAACGGATTGAGCACCTCTATGCTTCAATCGAGAACTGACACCTCTGTG
1 CACCTCTGTGTAGCTAAAA-GGATTGAGCACCTATGTGCTTCAATCGGGAACTGACACCTCTGTG
* * *
2396529 CAATTAAAAATGACTGAGCACCTCTGTGCATCAGTCGAGAGCTGA
65 C-ATTAAAAATGACTGAGCACCTCTGTGCTTCAGCCAAGAGCTGA
* * * * * *
2396574 CACCTCTGTGTAGCTAAAATTGATTGAGCACATTTGTGCTTTAATCTAGGATA-TGGCACCTCTG
1 CACCTCTGTGTAGCTAAAA-GGATTGAGCACCTATGTGCTTCAATC-GGGA-ACTGACACCTCTG
** *
2396638 TGCATT-AGGATGATTGAGCACCTCTGTGCTT
63 TGCATTAAAAATGACTGAGCACCTCTGTGCTT
2396669 TTACAAACGA
Statistics
Matches: 181, Mismatches: 20, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
109 21 0.12
110 142 0.78
111 17 0.09
112 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (108 bp):
CACCTCTGTGTAGCTAAAAGGATTGAGCACCTATGTGCTTCAATCGGGAACTGACACCTCTGTGC
ATTAAAAATGACTGAGCACCTCTGTGCTTCAGCCAAGAGCTGA
Found at i:2412658 original size:16 final size:17
Alignment explanation
Indices: 2412639--2412671 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2412629 AAAATTAGGT
*
2412639 TTAATAAAA-AATAAAA
1 TTAAGAAAATAATAAAA
2412655 TTAAGAAAATAATAAAA
1 TTAAGAAAATAATAAAA
2412672 ATAACTATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (17 bp):
TTAAGAAAATAATAAAA
Found at i:2414426 original size:33 final size:33
Alignment explanation
Indices: 2414330--2414426 Score: 104
Period size: 33 Copynumber: 2.9 Consensus size: 33
2414320 AATTCACCAA
* * *
2414330 TATTATAGTAATAAATATGTACTAGATTTGATAT
1 TATTATAGTAATAAATATATACTAGATTT-AAAC
* * * *
2414364 TATTATAATAATAAATATAAATTATATTTAAAC
1 TATTATAGTAATAAATATATACTAGATTTAAAC
* *
2414397 TGTTATAGTAATAAATCTATACTAGATTTA
1 TATTATAGTAATAAATATATACTAGATTTA
2414427 TTTGTCTAAT
Statistics
Matches: 50, Mismatches: 13, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
33 26 0.52
34 24 0.48
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (33 bp):
TATTATAGTAATAAATATATACTAGATTTAAAC
Found at i:2415552 original size:37 final size:38
Alignment explanation
Indices: 2415462--2415568 Score: 162
Period size: 38 Copynumber: 2.8 Consensus size: 38
2415452 TGCTAATGAT
* *
2415462 TTTTGAAAAATTATATAATATATGGTTTTTAAAAAAATA
1 TTTTG-AAAACTATATAATATATGGTTTTTAAAAAAACA
* *
2415501 TTTTAAAAACTATATAATATATAGTTTTTAAAAAAACA
1 TTTTGAAAACTATATAATATATGGTTTTTAAAAAAACA
2415539 TTTTGAAAA-TATATAATATATGGTTTTTAA
1 TTTTGAAAACTATATAATATATGGTTTTTAA
2415569 TATTTTAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
37 20 0.32
38 38 0.61
39 4 0.06
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.44
Consensus pattern (38 bp):
TTTTGAAAACTATATAATATATGGTTTTTAAAAAAACA
Found at i:2415611 original size:70 final size:71
Alignment explanation
Indices: 2415462--2415605 Score: 184
Period size: 70 Copynumber: 1.9 Consensus size: 71
2415452 TGCTAATGAT
2415462 TTTTGAAAAATTATATAATATATGGTTTTTAAAAAAATATTTTAAAAACTATATAATATATAGTT
1 TTTTG-AAAA-TATATAATATATGGTTTTT----AAATATTTTAAAAACTATATAATATATAGTT
2415527 TTTAAAAAAACA
60 TTTAAAAAAACA
* *
2415539 TTTTGAAAATATATAATATATGGTTTTT-AATATTTTAAAAA-TCATATATTATATAAGTTTTCA
1 TTTTGAAAATATATAATATATGGTTTTTAAATATTTTAAAAACT-ATATAATATAT-AGTTTTTA
2415602 AAAA
64 AAAA
2415606 TCATTTGCAA
Statistics
Matches: 63, Mismatches: 2, Indels: 10
0.84 0.03 0.13
Matches are distributed among these distances:
69 1 0.02
70 23 0.37
71 11 0.17
75 19 0.30
76 4 0.06
77 5 0.08
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.44
Consensus pattern (71 bp):
TTTTGAAAATATATAATATATGGTTTTTAAATATTTTAAAAACTATATAATATATAGTTTTTAAA
AAAACA
Found at i:2415629 original size:2 final size:2
Alignment explanation
Indices: 2415618--2415649 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2415608 ATTTGCAAAC
2415618 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2415650 GAAATTCGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2415716 original size:2 final size:2
Alignment explanation
Indices: 2415709--2415741 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2415699 CTTTTTACAT
2415709 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2415742 TCAAAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2415944 original size:17 final size:19
Alignment explanation
Indices: 2415930--2416000 Score: 62
Period size: 18 Copynumber: 3.9 Consensus size: 19
2415920 AATTTATATT
2415930 TATT-ATAAATATATATAA
1 TATTAATAAATATATATAA
*
2415948 TATTAATATATATATATATA
1 TATTAATAAATATATATA-A
2415968 TATGT-AT--ATATATA-AA
1 TAT-TAATAAATATATATAA
* *
2415984 TATCAATAATTATATAT
1 TATTAATAAATATATAT
2416001 TTAACAATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 13
0.73 0.05 0.22
Matches are distributed among these distances:
16 6 0.14
17 1 0.02
18 17 0.40
19 12 0.28
20 6 0.14
21 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (19 bp):
TATTAATAAATATATATAA
Found at i:2416000 original size:2 final size:2
Alignment explanation
Indices: 2415924--2415986 Score: 62
Period size: 2 Copynumber: 33.5 Consensus size: 2
2415914 TCATAAAATT
* *
2415924 TA TA TT TA T- TA TA AA TA TA TA TA -A TA T- TA -A 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
* *
2415962 TA TA TA TA TG TA TA TA TA TA AA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
2415987 CAATAATTAT
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
1 4 0.08
2 45 0.92
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2416424 original size:2 final size:2
Alignment explanation
Indices: 2416417--2416452 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2416407 CACATATACC
2416417 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
2416453 CTCATAAGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2416735 original size:19 final size:20
Alignment explanation
Indices: 2416692--2416775 Score: 116
Period size: 20 Copynumber: 4.2 Consensus size: 20
2416682 TGCGATTTTC
* *
2416692 CAAATTCGCACCGCGGAAGT
1 CAAATTCGCAACGCGAAAGT
* *
2416712 TAAATTCGCAACAC-AAAGT
1 CAAATTCGCAACGCGAAAGT
*
2416731 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
2416751 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
2416771 CAAAT
1 CAAAT
2416776 GTTTTTACGC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.29
20 39 0.71
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:2416736 original size:39 final size:40
Alignment explanation
Indices: 2416692--2416775 Score: 118
Period size: 39 Copynumber: 2.1 Consensus size: 40
2416682 TGCGATTTTC
* *
2416692 CAAATTCGCACCGCGGA-AGTTAAATTCGCAACAC-AAAGT
1 CAAATTCGCAACGC-GATAGTCAAATTCGCAACACGAAAGT
*
2416731 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
2416771 CAAAT
1 CAAAT
2416776 GTTTTTACGC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 2 0.05
39 28 0.70
40 10 0.25
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.18
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACACGAAAGT
Found at i:2419408 original size:21 final size:20
Alignment explanation
Indices: 2419382--2419437 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
2419372 TAAGCCCGAT
2419382 GCACCTATCATCATTCAAGAG
1 GCACCT-TCATCATTCAAGAG
* *
2419403 GCACCTCCTATCGTTCAAGAG
1 GCACCTTC-ATCATTCAAGAG
*
2419424 GCCCCTCTCATCAT
1 GCACCT-TCATCAT
2419438 CGAAGAAGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
20 1 0.04
21 26 0.93
22 1 0.04
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (20 bp):
GCACCTTCATCATTCAAGAG
Found at i:2419464 original size:21 final size:21
Alignment explanation
Indices: 2419395--2419486 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 21
2419385 CCTATCATCA
* *
2419395 TTCAAGAGGCACCTCCTATCG
1 TTCAAGAGGCCCCTCCTACCG
*
2419416 TTCAAGAGGCCCCT-CTCATC-
1 TTCAAGAGGCCCCTCCT-ACCG
* *
2419436 ATCGAAGAAGCCCCTCCTACCG
1 TTC-AAGAGGCCCCTCCTACCG
* *
2419458 TTCAAGAGGTCCCGCCTACCG
1 TTCAAGAGGCCCCTCCTACCG
*
2419479 TTTAAGAG
1 TTCAAGAG
2419487 CCCGATTCAT
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
20 4 0.07
21 50 0.86
22 4 0.07
ACGTcount: A:0.24, C:0.35, G:0.20, T:0.22
Consensus pattern (21 bp):
TTCAAGAGGCCCCTCCTACCG
Found at i:2420943 original size:61 final size:62
Alignment explanation
Indices: 2420841--2420980 Score: 194
Period size: 66 Copynumber: 2.2 Consensus size: 62
2420831 TTTTACATTG
2420841 AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTA-TTTT-TTGATTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTATTTTTATTGATTAATTGATTTGTA
* * * *
2420901 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTACTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAA-AATT-TATTTTTA-TTGATTAATTGATTTGT
2420966 A
62 A
2420967 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
2420981 GTTTCTAAAA
Statistics
Matches: 70, Mismatches: 4, Indels: 6
0.88 0.05 0.08
Matches are distributed among these distances:
60 17 0.24
61 13 0.19
62 4 0.06
63 1 0.01
64 4 0.06
66 31 0.44
ACGTcount: A:0.32, C:0.01, G:0.16, T:0.51
Consensus pattern (62 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAAATTTATTTTTATTGATTAATTGATTTGTA
Found at i:2421348 original size:39 final size:39
Alignment explanation
Indices: 2421293--2421379 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
2421283 TCAAGTTGTA
*
2421293 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTT
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
* *
2421332 GATTTTGATTTTCTTTTGCTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
2421371 GATTTTGAT
1 GATTTTGAT
2421380 GAGCATCGGA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.49
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
Found at i:2421713 original size:18 final size:18
Alignment explanation
Indices: 2421690--2421726 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2421680 CGAAATTTAT
2421690 ATTGAAATTCAAACTCAA
1 ATTGAAATTCAAACTCAA
* *
2421708 ATTGAAATTTAAATTCAA
1 ATTGAAATTCAAACTCAA
2421726 A
1 A
2421727 CTCCAATTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.51, C:0.11, G:0.05, T:0.32
Consensus pattern (18 bp):
ATTGAAATTCAAACTCAA
Found at i:2422249 original size:20 final size:20
Alignment explanation
Indices: 2422185--2422241 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
2422175 AAATAAGCGT
*
2422185 TGCGATAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
*
2422205 CGCGAAAGTCAAATTCGCAA
1 TGCGAAAGTCAAATTCGCAA
2422225 TGCGAAAGTCAAATTCG
1 TGCGAAAGTCAAATTCG
2422242 GTTTGCGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.37, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TGCGAAAGTCAAATTCGCAA
Found at i:2422634 original size:12 final size:12
Alignment explanation
Indices: 2422619--2422659 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
2422609 AAGCCGGTTG
*
2422619 TGATTGGGATTT
1 TGATTGCGATTT
**
2422631 TGATTTTGATTT
1 TGATTGCGATTT
2422643 TGATTGCGATTT
1 TGATTGCGATTT
2422655 TGATT
1 TGATT
2422660 TCCTTTTGCT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.17, C:0.02, G:0.24, T:0.56
Consensus pattern (12 bp):
TGATTGCGATTT
Found at i:2422635 original size:6 final size:6
Alignment explanation
Indices: 2422626--2422660 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
2422616 TTGTGATTGG
**
2422626 GATTTT GATTTT GATTTT GATTGC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
2422661 CCTTTTGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.17, C:0.03, G:0.20, T:0.60
Consensus pattern (6 bp):
GATTTT
Found at i:2425115 original size:12 final size:12
Alignment explanation
Indices: 2425098--2425131 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2425088 GGTTGTGGGT
*
2425098 TTTGATATTTTG
1 TTTGATATTGTG
2425110 TTTGATATTGTG
1 TTTGATATTGTG
*
2425122 TTTGGTATTG
1 TTTGATATTG
2425132 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.24, T:0.62
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:2425718 original size:14 final size:15
Alignment explanation
Indices: 2425684--2425721 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
2425674 GAAATCATTG
2425684 AAAAATTATATAGAA
1 AAAAATTATATAGAA
2425699 ATAAAATTATATA-AA
1 A-AAAATTATATAGAA
2425714 AAAAATTA
1 AAAAATTA
2425722 GAGATGTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 7 0.32
15 4 0.18
16 11 0.50
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:2426057 original size:20 final size:20
Alignment explanation
Indices: 2425989--2426059 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
2425979 GAAATTAAAT
*
2425989 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCGAATTTGACTA
* * *
2426009 TTGTGTTACGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
2426029 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
*
2426049 TCGCATTGCGA
1 TCGCGTTGCGA
2426060 TTTACAAATT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:2426072 original size:20 final size:20
Alignment explanation
Indices: 2426049--2426090 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
2426039 AATTTGACTA
2426049 TCGCATTGCGATTTACAAAT
1 TCGCATTGCGATTTACAAAT
* *
2426069 TCGCGTTGCGATTTACAGAT
1 TCGCATTGCGATTTACAAAT
2426089 TC
1 TC
2426091 ACGTTGCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.36
Consensus pattern (20 bp):
TCGCATTGCGATTTACAAAT
Found at i:2426073 original size:40 final size:42
Alignment explanation
Indices: 2425985--2426079 Score: 108
Period size: 40 Copynumber: 2.4 Consensus size: 42
2425975 TTGTGAAATT
* * **
2425985 AAATTCGCGTTGCGAATTTGACTTTTGTGTTACGAATTTGAC
1 AAATTCGCGTTGCGAATTTGACTATCGCATTACGAATTTGAC
* *
2426027 -TA-TCGCGTTGCGAATTTGACTATCGCATTGCG-ATTT-AC
1 AAATTCGCGTTGCGAATTTGACTATCGCATTACGAATTTGAC
2426065 AAATTCGCGTTGCGA
1 AAATTCGCGTTGCGA
2426080 TTTACAGATT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
38 2 0.05
39 5 0.11
40 36 0.82
41 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.22, T:0.37
Consensus pattern (42 bp):
AAATTCGCGTTGCGAATTTGACTATCGCATTACGAATTTGAC
Found at i:2426095 original size:20 final size:20
Alignment explanation
Indices: 2426054--2426097 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
2426044 GACTATCGCA
*
2426054 TTGCGATTTACAAATTCGCG
1 TTGCGATTTACAAATTCACG
*
2426074 TTGCGATTTACAGATTCACG
1 TTGCGATTTACAAATTCACG
2426094 TTGC
1 TTGC
2426098 AAAATTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACAAATTCACG
Found at i:2429769 original size:58 final size:58
Alignment explanation
Indices: 2429693--2429802 Score: 175
Period size: 58 Copynumber: 1.9 Consensus size: 58
2429683 TTGATGCGAC
* *
2429693 ATGTGCCATGCTACCCAAAGTGATAGACTTGGCATGTGTCGTGTCACCCAAAGTGGTG
1 ATGTGCCATGCTACCCAAAGTGATAAACTTGACATGTGTCGTGTCACCCAAAGTGGTG
* * *
2429751 ATGTGTCATGTTACCCAAAGTGATAAACTTGACATGTGTTGTGTCACCCAAA
1 ATGTGCCATGCTACCCAAAGTGATAAACTTGACATGTGTCGTGTCACCCAAA
2429803 ATGATAACAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
58 47 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (58 bp):
ATGTGCCATGCTACCCAAAGTGATAAACTTGACATGTGTCGTGTCACCCAAAGTGGTG
Found at i:2429788 original size:33 final size:32
Alignment explanation
Indices: 2429751--2429822 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 32
2429741 CAAAGTGGTG
* * *
2429751 ATGTGTCATGTTACCCAAAGTGATAAACTTGAC
1 ATGTGTCATGTCACCCAAAATGAT-AACATGAC
**
2429784 ATGTGTTGTGTCACCCAAAATGATAACATGAC
1 ATGTGTCATGTCACCCAAAATGATAACATGAC
*
2429816 ATATGTC
1 ATGTGTC
2429823 GCATCACTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (32 bp):
ATGTGTCATGTCACCCAAAATGATAACATGAC
Found at i:2442040 original size:20 final size:20
Alignment explanation
Indices: 2442015--2442059 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
2442005 CAAATACAAT
*
2442015 ATAATTAAAGTTACAAATCC
1 ATAATTAAAATTACAAATCC
*
2442035 ATAATTAAAATTACAAGTCC
1 ATAATTAAAATTACAAATCC
2442055 ATAAT
1 ATAAT
2442060 ATAGTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (20 bp):
ATAATTAAAATTACAAATCC
Found at i:2442118 original size:6 final size:6
Alignment explanation
Indices: 2442107--2442132 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
2442097 TAAACGAGAT
2442107 ATAAAC ATAAAC ATAAAC ATAAAC AT
1 ATAAAC ATAAAC ATAAAC ATAAAC AT
2442133 CCGATGAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.00, T:0.19
Consensus pattern (6 bp):
ATAAAC
Found at i:2444559 original size:5 final size:5
Alignment explanation
Indices: 2444543--2444577 Score: 52
Period size: 5 Copynumber: 7.0 Consensus size: 5
2444533 AAGTTTTACC
* *
2444543 CGGGT CGAGT CGGGT CGGGT CGAGT CGGGT CGGGT
1 CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT CGGGT
2444578 AGAGTTATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.06, C:0.20, G:0.54, T:0.20
Consensus pattern (5 bp):
CGGGT
Found at i:2444563 original size:15 final size:15
Alignment explanation
Indices: 2444543--2444582 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
2444533 AAGTTTTACC
2444543 CGGGTCGAGTCGGGT
1 CGGGTCGAGTCGGGT
2444558 CGGGTCGAGTCGGGT
1 CGGGTCGAGTCGGGT
*
2444573 CGGGTAGAGT
1 CGGGTCGAGT
2444583 TATTTTAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.10, C:0.17, G:0.53, T:0.20
Consensus pattern (15 bp):
CGGGTCGAGTCGGGT
Found at i:2449865 original size:32 final size:31
Alignment explanation
Indices: 2449829--2449891 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 31
2449819 GAACAAAAAA
*
2449829 ACTAATGTCAACATTTCAATAAGCACAAAATG
1 ACTAATGTCAACATTTCAATAAG-AAAAAATG
** *
2449861 ACTAATGTGGACATTTCACTAAGAAAAAATG
1 ACTAATGTCAACATTTCAATAAGAAAAAATG
2449892 GAGTTAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
31 7 0.26
32 20 0.74
ACGTcount: A:0.46, C:0.16, G:0.13, T:0.25
Consensus pattern (31 bp):
ACTAATGTCAACATTTCAATAAGAAAAAATG
Found at i:2451361 original size:14 final size:14
Alignment explanation
Indices: 2451329--2451362 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2451319 TTTGTTTCAC
*
2451329 GAAAATAGATTCTG
1 GAAAATAGATTCCG
2451343 GAAAATAGATTCCG
1 GAAAATAGATTCCG
*
2451357 TAAAAT
1 GAAAAT
2451363 GAATTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.09, G:0.18, T:0.26
Consensus pattern (14 bp):
GAAAATAGATTCCG
Found at i:2451602 original size:35 final size:38
Alignment explanation
Indices: 2451554--2451681 Score: 97
Period size: 40 Copynumber: 3.4 Consensus size: 38
2451544 TCAATATTAT
* *
2451554 TATTAAAATATTATATCTATAATTTTC-T-AAATAAAAA
1 TATTATAA-ATTATATATATAATTTTCTTAAAATAAAAA
* * *
2451591 TATTAT-GATTAT-TATATACTTTTCTTAAAATAAAAC
1 TATTATAAATTATATATATAATTTTCTTAAAATAAAAA
* * *
2451627 TATTATAAATTATAT-TGATTATTTAT-TAAAAAGAATAATA
1 TATTATAAATTATATAT-ATAATTT-TCTTAAAATAA-AA-A
2451667 TATTATAAATTATAT
1 TATTATAAATTATAT
2451682 TGATTATTTG
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
34 10 0.14
35 6 0.08
36 14 0.19
37 11 0.15
38 13 0.18
39 3 0.04
40 15 0.21
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (38 bp):
TATTATAAATTATATATATAATTTTCTTAAAATAAAAA
Found at i:2451676 original size:40 final size:40
Alignment explanation
Indices: 2451627--2451719 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
2451617 AAAATAAAAC
2451627 TATTATAAATTATATTGATTATTTATTAAAAAGAATAATA
1 TATTATAAATTATATTGATTATTTATTAAAAAGAATAATA
* * *
2451667 TATTATAAATTATATTGATTATTTGTTAAAAGGAATAATT
1 TATTATAAATTATATTGATTATTTATTAAAAAGAATAATA
*
2451707 TATTATTAATTAT
1 TATTATAAATTAT
2451720 TTATTAAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 49 1.00
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.48
Consensus pattern (40 bp):
TATTATAAATTATATTGATTATTTATTAAAAAGAATAATA
Found at i:2451954 original size:21 final size:21
Alignment explanation
Indices: 2451930--2451998 Score: 56
Period size: 21 Copynumber: 3.3 Consensus size: 21
2451920 GTTATAACAA
2451930 TAAAATATAATATTATATTAT
1 TAAAATATAATATTATATTAT
* *
2451951 TAAAATTATCAATA-AATATAATT
1 TAAAA-TAT-AATATTATATTA-T
2451974 TAATAAT-TAATATT-T-TTAT
1 TAA-AATATAATATTATATTAT
2451993 TAAAAT
1 TAAAAT
2451999 GATACTATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
18 3 0.08
19 4 0.10
20 2 0.05
21 10 0.26
22 9 0.23
23 9 0.23
24 2 0.05
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
TAAAATATAATATTATATTAT
Found at i:2452587 original size:23 final size:24
Alignment explanation
Indices: 2452541--2452588 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
2452531 AGGCTTATTT
*
2452541 ATTTAAAAAATACAAATATTTTAA
1 ATTTAAAAAATACAAATATATTAA
2452565 ATTTAAAAATATA-AAA-ATATTAA
1 ATTTAAAAA-ATACAAATATATTAA
2452588 A
1 A
2452589 AAGTTAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 7 0.32
24 12 0.55
25 3 0.14
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
ATTTAAAAAATACAAATATATTAA
Found at i:2452595 original size:25 final size:24
Alignment explanation
Indices: 2452543--2452596 Score: 63
Period size: 25 Copynumber: 2.2 Consensus size: 24
2452533 GCTTATTTAT
* ** *
2452543 TTAAAAAATACAAATATTTTAAAT
1 TTAAAAAATAAAAATATTAAAAAG
2452567 TTAAAAATATAAAAATATTAAAAAG
1 TTAAAAA-ATAAAAATATTAAAAAG
2452592 TTAAA
1 TTAAA
2452597 TATAGTTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
24 7 0.28
25 18 0.72
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (24 bp):
TTAAAAAATAAAAATATTAAAAAG
Found at i:2453926 original size:56 final size:56
Alignment explanation
Indices: 2453814--2453919 Score: 185
Period size: 56 Copynumber: 1.9 Consensus size: 56
2453804 AGATAAGAGG
* *
2453814 TATGTTGTTTGAATTAAATGTAAGAATTTCATTTATATGATATGATAATAGTACTT
1 TATGTTGCTTGAATTAAATGTAAGAATTTCATTTATATGACATGATAATAGTACTT
*
2453870 TATGTTGCTTGAATTAAATGTAAGAATTTTATTTATATGACATGATAATA
1 TATGTTGCTTGAATTAAATGTAAGAATTTCATTTATATGACATGATAATA
2453920 TAACTTTCTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
56 47 1.00
ACGTcount: A:0.37, C:0.04, G:0.14, T:0.45
Consensus pattern (56 bp):
TATGTTGCTTGAATTAAATGTAAGAATTTCATTTATATGACATGATAATAGTACTT
Found at i:2453973 original size:32 final size:33
Alignment explanation
Indices: 2453937--2454021 Score: 109
Period size: 32 Copynumber: 2.6 Consensus size: 33
2453927 CTTTTTATGT
2453937 TAACATTTATTTGAACATAATATTTAATA-AAA
1 TAACATTTATTTGAACATAATATTTAATATAAA
* ** *
2453969 TAACATTTATTCGAACATAATATTTTTTATATA
1 TAACATTTATTTGAACATAATATTTAATATAAA
* *
2454002 TAATATTTATTTGAATATAA
1 TAACATTTATTTGAACATAA
2454022 CTTCTATAAT
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
32 26 0.58
33 19 0.42
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (33 bp):
TAACATTTATTTGAACATAATATTTAATATAAA
Found at i:2454021 original size:17 final size:17
Alignment explanation
Indices: 2453941--2454021 Score: 71
Period size: 17 Copynumber: 4.9 Consensus size: 17
2453931 TTATGTTAAC
2453941 ATTTATTTGAACATAAT
1 ATTTATTTGAACATAAT
* * *
2453958 ATTTA-AT-AAAATAAC
1 ATTTATTTGAACATAAT
*
2453973 ATTTATTCGAACATAAT
1 ATTTATTTGAACATAAT
*
2453990 ATTT-TTT-ATATATAAT
1 ATTTATTTGA-ACATAAT
*
2454006 ATTTATTTGAATATAA
1 ATTTATTTGAACATAA
2454022 CTTCTATAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 10
0.72 0.13 0.14
Matches are distributed among these distances:
15 12 0.24
16 13 0.26
17 24 0.48
18 1 0.02
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (17 bp):
ATTTATTTGAACATAAT
Found at i:2455518 original size:17 final size:18
Alignment explanation
Indices: 2455481--2455520 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
2455471 CCTTCAAAAA
2455481 TTTAAATTTTTATATAGT
1 TTTAAATTTTTATATAGT
* * *
2455499 TTTAATTTTTTTTATATT
1 TTTAAATTTTTATATAGT
2455517 TTTA
1 TTTA
2455521 TTGATAATCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (18 bp):
TTTAAATTTTTATATAGT
Found at i:2456062 original size:22 final size:22
Alignment explanation
Indices: 2456034--2456076 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2456024 GCCAAGTTCA
2456034 TAAAAAAA-TTGAAAATTTTATT
1 TAAAAAAATTTG-AAATTTTATT
2456056 TAAAAAAATTTGAAATTTTAT
1 TAAAAAAATTTGAAATTTTAT
2456077 ATATGTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 17 0.85
23 3 0.15
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (22 bp):
TAAAAAAATTTGAAATTTTATT
Found at i:2460879 original size:2 final size:2
Alignment explanation
Indices: 2460872--2460906 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2460862 TCAAATAATG
2460872 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2460907 AAGTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2461044 original size:17 final size:18
Alignment explanation
Indices: 2460987--2461051 Score: 96
Period size: 18 Copynumber: 3.7 Consensus size: 18
2460977 TATTTCTGAG
*
2460987 GGAATTGGAATCTGTGAA
1 GGAATTGGAATCTGTAAA
*
2461005 GGAATTGAAATCTGTAAA
1 GGAATTGGAATCTGTAAA
*
2461023 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTAAA
2461040 GGAATTGGAATC
1 GGAATTGGAATC
2461052 CAATTACATA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
17 13 0.30
18 30 0.70
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.28
Consensus pattern (18 bp):
GGAATTGGAATCTGTAAA
Found at i:2461836 original size:266 final size:253
Alignment explanation
Indices: 2461411--2462031 Score: 835
Period size: 266 Copynumber: 2.4 Consensus size: 253
2461401 CCTCCACCGA
2461411 GACCCGACCCGACCAAAATAAAGTTTCACCCAACCCGACCCGACCCGAATATATGAATTAGAAAC
1 GACCCGA-CCGACCAAAATAAAGTTT----C-ACCCGACCCGACCCGAATATATGAATTAGAAAC
* * *
2461476 CCGACCCGACCCGAAATAATAAAAAAA-A-ATTATTAAATAAAAACATTGACTTAATTGAAAAAA
60 CCGACCC-ACCCGAAATAATAAAAAAATATTTTATTCAATAAAAACAGTGACTTAATTGAAAAAA
*
2461539 ATTATATATAGAGGGGTATTATTATAATTATTCCTAAATAGATAAGGTAAAATTATATATTTTTT
124 ATTATATATAGAGGGGTATTATTATAATTATTCCTAAATAGATAAGGTAAAATTATATA--TATT
2461604 GGGTAGGGTTGGGTCAGGTATTTTTCACCCTAAACCCAAACCCA-A-CCGACCCGAATATCACAC
187 ---T----TTGGGTC-GGTATTTTTCACCCTAAACCCAAA-CCAGACCCGACCCGAATATCACAC
2461667 TTAAAAAAACCC
243 TTAAAAAAA-CC
* * *
2461679 GACCCGATCCGACCAAAATAAAGTTTCACCTGACCTGACCCGAATATATAAATTAGAAACCCGAC
1 GACCCGA-CCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
2461744 CCTATCCGAAATAATAAAAAAATATTTTAATTCAATAAAAACAGTGACTTAATTGAAAAAAATTA
65 CC-ACCCGAAATAATAAAAAAATATTTT-ATTCAATAAAAACAGTGACTTAATTGAAAAAAATTA
* *
2461809 TATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTTGGG
128 TATATAGAGGGGTATTATTATAATTATTCCTAAATAGATAAGGTAAAATTATATATATTTTTGGG
* * * *
2461874 TCGGTATTTTTCACTCTAAACCCGAACTAGACCCGACCCGAATATTACACTTAAAAAAACC
193 TCGGTATTTTTCACCCTAAACCCAAACCAGACCCGACCCGAATATCACACTTAAAAAAACC
2461935 GACCCGACCTGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCC-A-
1 GACCCGACC-GACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGAC
*
2461998 --ACCCGAAATAATAAAAATATATTTTTATTCAATA
65 CCACCCGAAATAATAAAAAAATA-TTTTATTCAATA
2462032 TATAAATAAG
Statistics
Matches: 325, Mismatches: 21, Indels: 31
0.86 0.06 0.08
Matches are distributed among these distances:
251 27 0.08
252 4 0.01
255 5 0.02
256 81 0.25
257 33 0.10
261 1 0.00
263 55 0.17
264 5 0.02
265 2 0.01
266 87 0.27
268 25 0.08
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.26
Consensus pattern (253 bp):
GACCCGACCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCCGACC
CACCCGAAATAATAAAAAAATATTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATAT
ATAGAGGGGTATTATTATAATTATTCCTAAATAGATAAGGTAAAATTATATATATTTTTGGGTCG
GTATTTTTCACCCTAAACCCAAACCAGACCCGACCCGAATATCACACTTAAAAAAACC
Found at i:2464660 original size:44 final size:44
Alignment explanation
Indices: 2464587--2464671 Score: 134
Period size: 44 Copynumber: 1.9 Consensus size: 44
2464577 AAGAAAGACA
*
2464587 ACTAACACTTGGTTGCCTAAAAATGATAGCTAGTCCAATAAGTG
1 ACTAACACTTGGTTGCCTAAAAATGATAGCTACTCCAATAAGTG
* * *
2464631 ACTAACACTTGGTTGCCTGAAAGTTATAGCTACTCCAATAA
1 ACTAACACTTGGTTGCCTAAAAATGATAGCTACTCCAATAA
2464672 ATTTATACAT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 37 1.00
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (44 bp):
ACTAACACTTGGTTGCCTAAAAATGATAGCTACTCCAATAAGTG
Found at i:2465309 original size:77 final size:77
Alignment explanation
Indices: 2465182--2465335 Score: 308
Period size: 77 Copynumber: 2.0 Consensus size: 77
2465172 TTTACATCAT
2465182 AAAATATTTTTTTTATGGGTGGTGAAAATAGAAATGGAATACACTTTATATGTGAATGGATATAT
1 AAAATATTTTTTTTATGGGTGGTGAAAATAGAAATGGAATACACTTTATATGTGAATGGATATAT
2465247 AGGGTTGTGCAA
66 AGGGTTGTGCAA
2465259 AAAATATTTTTTTTATGGGTGGTGAAAATAGAAATGGAATACACTTTATATGTGAATGGATATAT
1 AAAATATTTTTTTTATGGGTGGTGAAAATAGAAATGGAATACACTTTATATGTGAATGGATATAT
2465324 AGGGTTGTGCAA
66 AGGGTTGTGCAA
2465336 TCTTTCACTT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 77 1.00
ACGTcount: A:0.36, C:0.04, G:0.23, T:0.36
Consensus pattern (77 bp):
AAAATATTTTTTTTATGGGTGGTGAAAATAGAAATGGAATACACTTTATATGTGAATGGATATAT
AGGGTTGTGCAA
Found at i:2467605 original size:2 final size:2
Alignment explanation
Indices: 2467600--2467634 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
2467590 ATCTTGTAGT
2467600 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2467635 TAAGAAAAGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2468822 original size:12 final size:12
Alignment explanation
Indices: 2468805--2468834 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
2468795 ATTTAAAAAC
2468805 AAAATAATTTAA
1 AAAATAATTTAA
2468817 AAAAT-ATTTAA
1 AAAATAATTTAA
2468828 AAAATAA
1 AAAATAA
2468835 AATATCACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (12 bp):
AAAATAATTTAA
Found at i:2468870 original size:17 final size:17
Alignment explanation
Indices: 2468850--2468885 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2468840 CACAAGTTAT
* *
2468850 AATAATAAATTATTAAA
1 AATAAAAAAGTATTAAA
2468867 AATAAAAAAGTATTAAA
1 AATAAAAAAGTATTAAA
2468884 AA
1 AA
2468886 CTTTGAACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
AATAAAAAAGTATTAAA
Found at i:2469553 original size:26 final size:26
Alignment explanation
Indices: 2469523--2469573 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
2469513 TTAATTTTAA
* * *
2469523 AATTTTAAGAATTTAAGAATTTATCT
1 AATTTTAAAAATTTAAAAATCTATCT
2469549 AATTTTAAAAATTTAAAAATCTATC
1 AATTTTAAAAATTTAAAAATCTATC
2469574 GTTATAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (26 bp):
AATTTTAAAAATTTAAAAATCTATCT
Found at i:2473757 original size:37 final size:37
Alignment explanation
Indices: 2473684--2473758 Score: 98
Period size: 37 Copynumber: 2.0 Consensus size: 37
2473674 GTTGGAAAAT
* * *
2473684 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATAATTTCTTTAAAAAATTGAAAATCATAAA
*
2473721 ATTTATATAATTTCTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATATAATTTC-TTTAAAAAATTGAAAATCATAAA
2473758 A
1 A
2473759 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 19 0.58
38 14 0.42
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATAATTTCTTTAAAAAATTGAAAATCATAAA
Found at i:2473760 original size:38 final size:38
Alignment explanation
Indices: 2473679--2473760 Score: 96
Period size: 38 Copynumber: 2.2 Consensus size: 38
2473669 AACAAGTTGG
* * *
2473679 AAAATATTTATATATTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATAATTTCTTTAAAAAATTGAAAATCAT
*
2473718 -AAAATTTATATAATTTCTTTTACAAAATTGAAAAT-AT
1 AAAAATTTATATAATTTC-TTTAAAAAATTGAAAATCAT
2473755 AAAAAT
1 AAAAAT
2473761 GTTTAATGAA
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
37 15 0.41
38 22 0.59
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATAATTTCTTTAAAAAATTGAAAATCAT
Found at i:2474854 original size:2 final size:2
Alignment explanation
Indices: 2474847--2474981 Score: 158
Period size: 2 Copynumber: 71.0 Consensus size: 2
2474837 TCGGGCCGGG
* * *
2474847 TA TA TA TA TT TA AA T- TA AA 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
2474888 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
2474929 TA TA -A TT TA AA T- TA AA TT TA T- TA -A TA T- 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
2474966 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
2474982 ATTTTTAATA
Statistics
Matches: 112, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
1 7 0.06
2 105 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2475473 original size:60 final size:59
Alignment explanation
Indices: 2475405--2475545 Score: 156
Period size: 60 Copynumber: 2.3 Consensus size: 59
2475395 AAAAGTTTGG
** * * *
2475405 AACTAATTTAAAATGAAGGTCATAATTTGGAGATGAAAATGAAATGTTAAAAAATTTAAA
1 AACTAATTTAAAAT-AAGGTCATAATTTAAAGATGAAAATAAAATATTAAAAAATCTAAA
* * * * *
2475465 GACTAATTTAAAATAATAGTCATAGTTTAAAGATGAAATTAAAATATTAAAAAGTCTAAA
1 AACTAATTTAAAATAA-GGTCATAATTTAAAGATGAAAATAAAATATTAAAAAATCTAAA
*
2475525 AACTAATTTGAAATAAAGGTC
1 AACTAATTTAAAAT-AAGGTC
2475546 GGCATGCATT
Statistics
Matches: 66, Mismatches: 13, Indels: 4
0.80 0.16 0.05
Matches are distributed among these distances:
59 2 0.03
60 62 0.94
61 2 0.03
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (59 bp):
AACTAATTTAAAATAAGGTCATAATTTAAAGATGAAAATAAAATATTAAAAAATCTAAA
Found at i:2481464 original size:21 final size:21
Alignment explanation
Indices: 2481440--2481496 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2481430 TTTCCAATAT
2481440 TAACATTTTCGGTAGAAAAAA
1 TAACATTTTCGGTAGAAAAAA
2481461 TAACATTTTCGGTAGAAAAAA
1 TAACATTTTCGGTAGAAAAAA
*
2481482 TAACATTTTAGGTAG
1 TAACATTTTCGGTAG
2481497 CGCTTGATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.32
Consensus pattern (21 bp):
TAACATTTTCGGTAGAAAAAA
Found at i:2484139 original size:24 final size:24
Alignment explanation
Indices: 2484080--2484135 Score: 69
Period size: 23 Copynumber: 2.3 Consensus size: 24
2484070 AATATTTTGG
*
2484080 ATTTTTTAAATAATAATAATTTTAA
1 ATTTTTTTAA-AATAATAATTTTAA
* *
2484105 ATATTTTTAAAATAA-AATTTTTA
1 ATTTTTTTAAAATAATAATTTTAA
2484128 ATTTTTTT
1 ATTTTTTT
2484136 TAAACATGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 14 0.52
24 5 0.19
25 8 0.30
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTTTAAAATAATAATTTTAA
Found at i:2490055 original size:42 final size:42
Alignment explanation
Indices: 2490008--2490089 Score: 155
Period size: 42 Copynumber: 2.0 Consensus size: 42
2489998 CATTCCGGGA
2490008 GGAATTATACTGTACGACAGTCTTATATACGGTTAATAAACC
1 GGAATTATACTGTACGACAGTCTTATATACGGTTAATAAACC
*
2490050 GGAATTCTACTGTACGACAGTCTTATATACGGTTAATAAA
1 GGAATTATACTGTACGACAGTCTTATATACGGTTAATAAA
2490090 ATGTGTTACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (42 bp):
GGAATTATACTGTACGACAGTCTTATATACGGTTAATAAACC
Found at i:2494372 original size:2 final size:2
Alignment explanation
Indices: 2494365--2494408 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
2494355 GAAAAGGGGA
2494365 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
2494407 AT
1 AT
2494409 TCTTCTTCTT
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):
AT
Found at i:2496264 original size:24 final size:24
Alignment explanation
Indices: 2496221--2496331 Score: 71
Period size: 24 Copynumber: 4.3 Consensus size: 24
2496211 AACATAAACC
* * *
2496221 AAAAATATAATTCGATTATAACAT
1 AAAAATTTAATTCAAATATAACAT
*
2496245 AAAAATTTAATTCAAATATAATATTAAAT
1 AAAAATTTAATTC-AA-AT-ATA--ACAT
2496274 ACACGAAATTTAATTCAAATATAACAT
1 A-A--AAATTTAATTCAAATATAACAT
* *
2496301 AAAAATTTATATTAAAAT-TAATAT
1 AAAAATTTA-ATTCAAATATAACAT
*
2496325 AACAATT
1 AAAAATT
2496332 AAAAATAAAA
Statistics
Matches: 70, Mismatches: 8, Indels: 18
0.73 0.08 0.19
Matches are distributed among these distances:
24 30 0.43
25 8 0.11
26 2 0.03
27 7 0.10
29 7 0.10
30 3 0.04
31 2 0.03
32 11 0.16
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAAATTTAATTCAAATATAACAT
Found at i:2497042 original size:12 final size:12
Alignment explanation
Indices: 2497025--2497050 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2497015 TTATCAACGT
2497025 ATAAATTTATGA
1 ATAAATTTATGA
2497037 ATAAATTTATGA
1 ATAAATTTATGA
2497049 AT
1 AT
2497051 GTGATTCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.08, T:0.42
Consensus pattern (12 bp):
ATAAATTTATGA
Found at i:2504583 original size:22 final size:21
Alignment explanation
Indices: 2504539--2504589 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 21
2504529 ATTTTCGTCT
*
2504539 TCTTTATTTTTCTCTTTTCCC
1 TCTTTATTCTTCTCTTTTCCC
2504560 TCTTTATTCTTCTTCTTCTT-CC
1 TCTTTATTCTTC-TCTT-TTCCC
2504582 TCTTTATT
1 TCTTTATT
2504590 TTTTTGATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 11 0.41
22 14 0.52
23 2 0.07
ACGTcount: A:0.06, C:0.27, G:0.00, T:0.67
Consensus pattern (21 bp):
TCTTTATTCTTCTCTTTTCCC
Found at i:2505658 original size:5 final size:5
Alignment explanation
Indices: 2505648--2505674 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
2505638 AATTATATTT
2505648 AATAA AATAA AATAA AATAA AATAA AA
1 AATAA AATAA AATAA AATAA AATAA AA
2505675 ATATTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:2506695 original size:19 final size:19
Alignment explanation
Indices: 2506671--2506714 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
2506661 GTCTAAAAAA
*
2506671 TATTATATTATATTATTAT
1 TATTATATTATATCATTAT
* *
2506690 TATTATCTTATATCATTGT
1 TATTATATTATATCATTAT
2506709 TATTAT
1 TATTAT
2506715 TAATTTATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (19 bp):
TATTATATTATATCATTAT
Found at i:2508145 original size:6 final size:6
Alignment explanation
Indices: 2508134--2508182 Score: 53
Period size: 6 Copynumber: 7.8 Consensus size: 6
2508124 TTATTCAGAT
* * *
2508134 TTTTTA TTTTTA TTTATTA TTATTA TTATTA TTATTA TTTTTA TCTTTT
1 TTTTTA TTTTTA TTT-TTA TTTTTA TTTTTA TTTTTA TTTTTA T-TTTT
2508183 TTAATTTAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
6 30 0.77
7 9 0.23
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTTA
Found at i:2508155 original size:3 final size:3
Alignment explanation
Indices: 2508137--2508177 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
2508127 TTCAGATTTT
* *
2508137 TTA TTT TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTT TTA T
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
2508178 CTTTTTTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 30 0.91
4 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:2508314 original size:13 final size:13
Alignment explanation
Indices: 2508298--2508327 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
2508288 TGAATTGGGT
2508298 TTTTAAATTTTAA
1 TTTTAAATTTTAA
*
2508311 TTTTAATTTTTAA
1 TTTTAAATTTTAA
2508324 TTTT
1 TTTT
2508328 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTAAATTTTAA
Done.