Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008532.1 Hibiscus syriacus cultivar Beakdansim tig00111410_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: 857509
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:391546 original size:27 final size:27
Alignment explanation
Indices: 391478--391539 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
391468 TTAGTCAAAT
*
391478 AACAAACGCCACAAAAAGCAGCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
391505 AACAAACGCCACAAAAAGCACCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
391532 AACAAACG
1 AACAAACG
391540 TCGCAAATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.53, C:0.31, G:0.13, T:0.03
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGCACCACTGA
Found at i:391755 original size:44 final size:44
Alignment explanation
Indices: 391685--391776 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
391675 TTTGTGAGGT
391685 TTTG-TCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
* * * * * *
391728 TTTGTTCCGAAAAACGCCGCTATATGTTATGTCATATAGTGGCT
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
391772 TTTGT
1 TTTGT
391777 GAATGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.35
Consensus pattern (44 bp):
TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
Found at i:392015 original size:21 final size:21
Alignment explanation
Indices: 391991--392052 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
391981 TAAACTAGAC
* *
391991 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTAAA
* *
392012 ATCCATAACAAGAAACTTAAA
1 ATCCATAATAACAAACTTAAA
*
392033 ATCCATAATAATAAA-TTAAA
1 ATCCATAATAACAAACTTAAA
392053 GTTTACATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
20 5 0.14
21 30 0.86
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (21 bp):
ATCCATAATAACAAACTTAAA
Found at i:393360 original size:16 final size:16
Alignment explanation
Indices: 393339--393378 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
393329 CATGAAACGA
393339 AGTTCCCCAATTGCTC
1 AGTTCCCCAATTGCTC
*
393355 AGTTCCCCAATTGCTT
1 AGTTCCCCAATTGCTC
393371 AGTTCCCC
1 AGTTCCCC
393379 TAACTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.17, C:0.38, G:0.12, T:0.33
Consensus pattern (16 bp):
AGTTCCCCAATTGCTC
Found at i:394100 original size:21 final size:23
Alignment explanation
Indices: 394075--394121 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
394065 TCTATAAAAA
*
394075 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
394096 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
394119 TAA
1 TAA
394122 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:394136 original size:23 final size:22
Alignment explanation
Indices: 394075--394137 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
394065 TCTATAAAAA
* *
394075 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
394096 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
394119 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
394138 TAATAACTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:395055 original size:69 final size:69
Alignment explanation
Indices: 394924--395064 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 69
394914 AGCAGCAAAT
* *
394924 GAGTTTGGGTAAATGACGGGAATGAAATAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
394989 G-GC
66 GCGC
* *
394992 GAGTTTGGGTAAACGATGGGAATGGAAAAAAATAGGTCAAGGGG-AAAAATGAAAAAGGGTTAAA
1 GAGTTTGGGTAAACGACGGGAAT-G-AAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAA
395056 GGGCGC
64 GGGCGC
395062 GAG
1 GAG
395065 ACTTAGAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
68 21 0.32
69 24 0.36
70 21 0.32
ACGTcount: A:0.43, C:0.04, G:0.36, T:0.16
Consensus pattern (69 bp):
GAGTTTGGGTAAACGACGGGAATGAAAAAATAGGTAAAGGGGAAAAAATGAAAAAGGGTTAAAGG
GCGC
Found at i:395152 original size:41 final size:41
Alignment explanation
Indices: 395101--395222 Score: 147
Period size: 41 Copynumber: 3.0 Consensus size: 41
395091 TTGTAAACAT
* *
395101 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACTCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
395142 AAACTCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACTCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * *
395183 AAA-TGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATA
1 AAACT-CCACTAAAGTACGAGTCTATAGCGACGTTTGTATA
395223 CAATCGCCAC
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 1 0.01
41 67 0.99
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (41 bp):
AAACTCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:395232 original size:41 final size:41
Alignment explanation
Indices: 395104--395240 Score: 143
Period size: 41 Copynumber: 3.3 Consensus size: 41
395094 TAAACATAAA
* * *
395104 CGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAA
1 CGCCACTAAATTACGAGTCTATAGCGACGTTTGTATAAAAT
* * *
395145 CTCCACT-AATGTACGAGTCTATAGCGACATTTATATAAAAAT
1 CGCCACTAAAT-TACGAGTCTATAGCGACGTTTGTAT-AAAAT
* * * *
395187 -GCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATACAAT
1 CGCCACTAAATTACGAGTCTATAGCGACGTTTGTATAAAAT
*
395227 CGCCACTAATTTAC
1 CGCCACTAAATTAC
395241 TGATAAATTG
Statistics
Matches: 77, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
40 6 0.08
41 64 0.83
42 7 0.09
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (41 bp):
CGCCACTAAATTACGAGTCTATAGCGACGTTTGTATAAAAT
Found at i:396174 original size:3 final size:3
Alignment explanation
Indices: 396168--396216 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
396158 TAATATATGC
396168 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
396216 T
1 T
396217 ATCTCGGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:399646 original size:23 final size:22
Alignment explanation
Indices: 399586--399647 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
399576 TCTATAAAAA
*
399586 TAAAAGTA-TTAT-ATATATTT
1 TAAAATTATTTATAATATATTT
*
399606 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
399629 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
399648 TATTAGACCA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 7 0.21
21 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:400554 original size:69 final size:69
Alignment explanation
Indices: 400432--400567 Score: 213
Period size: 69 Copynumber: 2.0 Consensus size: 69
400422 AACAAATGAC
*
400432 TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG-GCG
1 TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTGCG
400496 AGTT
66 AGTT
* *
400500 TGGGTAAATGGCGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAATGAAAAAGGGTTAAAGGGTG
1 TGGGTAAACGGAGGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTG
400564 CGAG
64 CGAG
400568 ACATAGAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 4
0.90 0.04 0.06
Matches are distributed among these distances:
68 17 0.27
69 23 0.37
70 22 0.35
ACGTcount: A:0.45, C:0.04, G:0.36, T:0.15
Consensus pattern (69 bp):
TGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGGGTGCG
AGTT
Found at i:400652 original size:41 final size:41
Alignment explanation
Indices: 400604--400995 Score: 167
Period size: 41 Copynumber: 9.6 Consensus size: 41
400594 TTGTAAACAT
*
400604 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * *
400645 AAACGCCACTAATGTACGAGTGTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * *
400686 AAATGCCACTAAATTATGAGTCTTTAGCGACGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * ** * * * *
400727 AATCACCTCTAATA-TACTGA-TAAATTGTGACATTTAT-TCAAA
1 AAACGCCACTAA-AGTAC-GAGTCTATAGCGACGTTTGTAT--AA
* * * * * * *
400769 AAATGCCATTACAA-TATGAATCTCTTA-CAACGTTT-TTTCAA
1 AAACGCCACTA-AAGTACGAGTCT-ATAGCGACGTTTGTAT-AA
* * * * **
400810 AAATGCCATTATA-TATGTTTCCTATTA-CGGA-GTTTGTATAA
1 AAACGCCACTAAAGTACGAGT-CTA-TAGC-GACGTTTGTATAA
* * * * *
400851 AAACGCCACTAAATTACGAGTCTTTA-CTAGCATTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGA-CGTTTGTATAA
* * * * * *
400892 AAACGACACTAATGTACGAGTCTTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
** * * *
400933 AAACGCCACTAAAGTACTTGTCTATAGAGACTTTTTTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
*
400973 AAACGCCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCT
400996 GTGTCGGTGT
Statistics
Matches: 257, Mismatches: 78, Indels: 33
0.70 0.21 0.09
Matches are distributed among these distances:
39 1 0.00
40 30 0.12
41 196 0.76
42 28 0.11
43 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.32
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:401664 original size:3 final size:3
Alignment explanation
Indices: 401658--401694 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
401648 TAATATATGC
401658 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
401695 CTCGGTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:407516 original size:26 final size:27
Alignment explanation
Indices: 407466--407533 Score: 93
Period size: 26 Copynumber: 2.6 Consensus size: 27
407456 TTAGTCAAAT
* * *
407466 AACAAATGCCACAAAAAGTAGCACTGA
1 AACAAACGCCACAAAAAGAACCACTGA
407493 AACAAACGCCACAAAAA-AACCACTGA
1 AACAAACGCCACAAAAAGAACCACTGA
*
407519 AACAAACGCCGCAAA
1 AACAAACGCCACAAA
407534 TGGTAGCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 21 0.57
27 16 0.43
ACGTcount: A:0.54, C:0.28, G:0.12, T:0.06
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGAACCACTGA
Found at i:407749 original size:44 final size:44
Alignment explanation
Indices: 407678--407761 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
407668 AGGTTGTCCC
*
407678 AAAAACGCCACTAAAAGTTCTGACATATAATGGCGTTTGTTCCG
1 AAAAACGCCACTAAAAGTTATGACATATAATGGCGTTTGTTCCG
* * * * *
407722 AAAAACGCCGCTATATGTTATGTCATATAGTGGCGTTTGT
1 AAAAACGCCACTAAAAGTTATGACATATAATGGCGTTTGT
407762 GAATGTAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
AAAAACGCCACTAAAAGTTATGACATATAATGGCGTTTGTTCCG
Found at i:408001 original size:21 final size:21
Alignment explanation
Indices: 407977--408029 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
407967 TAAACTAGAC
*
407977 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* * *
407998 ATCCATAACAAGAAACTTGAA
1 ATCCATAATAACAAACTTCAA
408019 ATCCATAATAA
1 ATCCATAATAA
408030 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:410079 original size:23 final size:21
Alignment explanation
Indices: 410035--410097 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 21
410025 TCTATAAAAA
*
410035 TAAAATTATTATATTATATTT
1 TAAAATTATTATAATATATTT
410056 TAAAATTATTAATAAATATATTT
1 TAAAATTATT-AT-AATATATTT
*
410079 TAAGGAATTTTTATAATAT
1 TAA--AATTATTATAATAT
410098 TATTAGACTA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 10 0.28
22 2 0.06
23 16 0.44
24 2 0.06
25 6 0.17
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
TAAAATTATTATAATATATTT
Found at i:411019 original size:68 final size:69
Alignment explanation
Indices: 410889--411024 Score: 199
Period size: 68 Copynumber: 2.0 Consensus size: 69
410879 AGCAAATGAG
*
410889 TTTGGGTAAATGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGG-G
1 TTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGGTG
410953 CGAC
66 CGAC
*
410957 TTTGGGTAAACGGCGGGAATGGAAAAAAAATAGGTCAAGGGG-AAAAATG-AAAAGGGTT-AAGG
1 TTTGGGTAAACGACGGGAAT-G--AAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
411019 GTGCGA
63 GTGCGA
411025 GACTTAGAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
68 23 0.37
69 14 0.23
70 7 0.11
71 18 0.29
ACGTcount: A:0.43, C:0.06, G:0.35, T:0.16
Consensus pattern (69 bp):
TTTGGGTAAACGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGGGTG
CGAC
Found at i:411110 original size:41 final size:41
Alignment explanation
Indices: 411062--411201 Score: 154
Period size: 41 Copynumber: 3.4 Consensus size: 41
411052 TTGTAAACAT
*
411062 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * *
411103 AAACGCCACTAATGTATGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
411144 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
411185 AATCGCCATTAATGTAC
1 AAACGCCACTAAAGTAC
411202 TGGTAAATTA
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.30
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:412136 original size:3 final size:3
Alignment explanation
Indices: 412130--412166 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
412120 TAATATATGC
412130 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
412167 ATCTCGGGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:414988 original size:20 final size:21
Alignment explanation
Indices: 414959--415002 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
414949 TCTATAAAAA
*
414959 TAAAAGTATT-ATATATATTT
1 TAAAAGTATTAATAAATATTT
*
414979 TAAAATTATTAATAAATATTT
1 TAAAAGTATTAATAAATATTT
415000 TAA
1 TAA
415003 GGAATTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
TAAAAGTATTAATAAATATTT
Found at i:415017 original size:21 final size:20
Alignment explanation
Indices: 414967--415019 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
414957 AATAAAAGTA
414967 TTATATATATTTTAAAATTAT
1 TTATA-ATATTTTAAAATTAT
*
414988 TAATAAATATTTTAAGGAATT-T
1 TTAT-AATATTTTAA--AATTAT
415010 TTATAATATT
1 TTATAATATT
415020 ATTAGACTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 18 0.67
22 5 0.19
23 4 0.15
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (20 bp):
TTATAATATTTTAAAATTAT
Found at i:415921 original size:68 final size:68
Alignment explanation
Indices: 415801--415939 Score: 228
Period size: 68 Copynumber: 2.0 Consensus size: 68
415791 AGCAACAAAT
* *
415801 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAATGGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAATGAAAAAGGGTTAAAGGG
415866 -GC
66 TGC
415868 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAATAGGTCAAGGAGAAAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGGA-GGGAATG-AAAAAATAGGTCAAGGAGAAAAATGAAAAAGGGTTAAAG
415932 GGTGC
64 GGTGC
415937 GAG
1 GAG
415940 ACTTAGAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
66 2 0.03
67 21 0.31
68 39 0.58
69 5 0.07
ACGTcount: A:0.43, C:0.05, G:0.36, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAATGAAAAAGGGTTAAAGGG
TGC
Found at i:416024 original size:41 final size:41
Alignment explanation
Indices: 415976--416356 Score: 165
Period size: 41 Copynumber: 9.4 Consensus size: 41
415966 TTGTAAACAT
*
415976 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
416017 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
416057 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * ** * * * *
416098 AATCGCCTCTAATGTACTGA-TAAATTGTGACATTTAT-TCAA
1 AAACGCCACTAAAGTAC-GAGTCTATAGCGACGTTTGTAT-AA
* * * * * *
416139 AAATGCCATTACAA-TATGAATCTCTTA-C-AGCGTTT-TTTCAA
1 AAACGCCACTA-AAGTACGAGTCT-ATAGCGA-CGTTTGTAT-AA
* * * * ** **
416180 AAATGCCATTATA-TATGTTTCCTATTTCGGA-GTTTGTATAA
1 AAACGCCACTAAAGTACGAGT-CTATAGC-GACGTTTGTATAA
* * * * * *
416221 AAACGCCACTAAATTATGAGTCTTTA-CTAGCATTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGA-CGTTTGTATAA
* * * * * *
416262 AAACGACACTAATGTACGAGTCTTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
** *
416303 AAACGCCACTAAAGTACTTGTCTATAGCGAC-TTTTTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
416342 AAACGCCACTAAAGT
1 AAACGCCACTAAAGT
416357 TTGAGTATGT
Statistics
Matches: 250, Mismatches: 73, Indels: 36
0.70 0.20 0.10
Matches are distributed among these distances:
39 16 0.06
40 51 0.20
41 170 0.68
42 12 0.05
43 1 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:416130 original size:81 final size:81
Alignment explanation
Indices: 415980--416134 Score: 186
Period size: 81 Copynumber: 1.9 Consensus size: 81
415970 AAACATAAAC
* **
415980 GCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
416045 GACATTTATATAAAAT
66 GACATTTATATAAAAT
* * * * * * * *
416061 GCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATACAATCGCCTCTAATGTACTGA-TAAATTG
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTAC-GAGTAAATAG
*
416125 TGACATTTAT
65 CGACATTTAT
416135 TCAAAAATGC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
81 59 0.97
82 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Consensus pattern (81 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
GACATTTATATAAAAT
Found at i:417007 original size:3 final size:3
Alignment explanation
Indices: 417001--417053 Score: 92
Period size: 3 Copynumber: 18.3 Consensus size: 3
416991 TAATATATGC
417001 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
417048 TT- TTA T
1 TTA TTA T
417054 CTCGGTTTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:421255 original size:21 final size:23
Alignment explanation
Indices: 421231--421277 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
421221 TCTATAAAAA
*
421231 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
421252 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
421275 TAA
1 TAA
421278 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:421292 original size:23 final size:22
Alignment explanation
Indices: 421231--421293 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
421221 TCTATAAAAA
* *
421231 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
421252 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
421275 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
421294 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:422209 original size:70 final size:68
Alignment explanation
Indices: 422069--422209 Score: 205
Period size: 70 Copynumber: 2.0 Consensus size: 68
422059 AGCAACAAAT
* *
422069 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAATGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
422134 GGC
66 GGC
*
422137 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAGTGAAAAAGGGTTAA
1 GAGTTTGGGTAAACGGA-GGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAA
422200 AGGGTGC
63 AGGG-GC
422207 GAG
1 GAG
422210 ACTTAGAAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
67 2 0.03
68 21 0.32
69 21 0.32
70 22 0.33
ACGTcount: A:0.43, C:0.05, G:0.36, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
GGC
Found at i:422294 original size:41 final size:41
Alignment explanation
Indices: 422246--422385 Score: 163
Period size: 41 Copynumber: 3.4 Consensus size: 41
422236 TTGTAAACAT
*
422246 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
422287 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
422328 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
422369 AATCGCCTCTAATGTAC
1 AAACGCCACTAAAGTAC
422386 TGATAAATTG
Statistics
Matches: 80, Mismatches: 19, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:422401 original size:82 final size:82
Alignment explanation
Indices: 422250--422418 Score: 189
Period size: 82 Copynumber: 2.0 Consensus size: 82
422240 AAACATAAAC
* **
422250 GCCACTAAAGTACGATTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAGC
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
422315 GACATTTA-TATAAAAAT
66 GACATTTATTA-AAAAAT
* * * * * * * *
422332 GCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATACAATCGCCTCTAATGTACTGA-TAAATTG
1 GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTAC-GAGTAAATAG
*
422396 TGACATTTATTCAAAAAAT
65 CGACATTTATT-AAAAAAT
422415 GCCA
1 GCCA
422419 TTACAATATG
Statistics
Matches: 72, Mismatches: 12, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
82 58 0.81
83 13 0.18
84 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (82 bp):
GCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTAAATAGC
GACATTTATTAAAAAAT
Found at i:422601 original size:40 final size:40
Alignment explanation
Indices: 422528--422627 Score: 103
Period size: 40 Copynumber: 2.5 Consensus size: 40
422518 CTAGCATTTG
* * * *
422528 TATACAAACGACACTAATGTACGAGTCTTTAGCGGC-GTTA
1 TATA-AAACGCCACTAAAGTACGAGTCTATAGCGACTGTTA
** * *
422568 TATAGAAACGCCACTAAAGTACTTGTCTATAGCGACTTTTT
1 TATA-AAACGCCACTAAAGTACGAGTCTATAGCGACTGTTA
422609 TATAAAACGCCACTAAAGT
1 TATAAAACGCCACTAAAGT
422628 TTGAGTCTGT
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
40 44 0.88
41 6 0.12
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (40 bp):
TATAAAACGCCACTAAAGTACGAGTCTATAGCGACTGTTA
Found at i:423277 original size:3 final size:3
Alignment explanation
Indices: 423269--423325 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
423259 TAATATATGC
423269 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
423317 TTA TT- TTA T
1 TTA TTA TTA T
423326 CTCGGTTTAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:431740 original size:27 final size:27
Alignment explanation
Indices: 431709--431777 Score: 111
Period size: 27 Copynumber: 2.6 Consensus size: 27
431699 TTAGTCAAAT
* *
431709 AACAAACGCCACAAAAAGTAGCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
431736 AACAAACGCCACAAAAAGCACCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
*
431763 AACAAACGCCGCAAA
1 AACAAACGCCACAAA
431778 TGGTAGCGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.52, C:0.30, G:0.13, T:0.04
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGCACCACTGA
Found at i:431986 original size:44 final size:44
Alignment explanation
Indices: 431916--432007 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
431906 TTTGTGAGGT
*
431916 TTTG-TCCCAAAAACGCCACTAAATGTTCTGACATATAATGGCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
* * * * *
431959 TTTGTTCCGAAAAACGCCGCTATATGTTATGTCATATAGTGGCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
432003 TTTGT
1 TTTGT
432008 GAATGTAAAA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 4 0.10
44 38 0.90
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.34
Consensus pattern (44 bp):
TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
Found at i:432248 original size:21 final size:21
Alignment explanation
Indices: 432224--432276 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
432214 TAAACTAGAC
*
432224 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* * *
432245 ATCCATAACAAGAAACTTGAA
1 ATCCATAATAACAAACTTCAA
432266 ATCCATAATAA
1 ATCCATAATAA
432277 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:434339 original size:21 final size:23
Alignment explanation
Indices: 434314--434360 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
434304 TCTATAAAAA
*
434314 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
434335 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
434358 TAA
1 TAA
434361 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:434375 original size:23 final size:22
Alignment explanation
Indices: 434314--434376 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
434304 TCTATAAAAA
* *
434314 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
434335 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
434358 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
434377 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:434550 original size:21 final size:23
Alignment explanation
Indices: 434517--434558 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
434507 AGAATATAAT
434517 AGTATCATATATTATAATAATTG
1 AGTATCATATATTATAATAATTG
*
434540 AGTAT-AT-TATTGTAATAAT
1 AGTATCATATATTATAATAAT
434559 ATTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 11 0.61
22 2 0.11
23 5 0.28
ACGTcount: A:0.43, C:0.02, G:0.10, T:0.45
Consensus pattern (23 bp):
AGTATCATATATTATAATAATTG
Found at i:435380 original size:41 final size:41
Alignment explanation
Indices: 435332--435555 Score: 215
Period size: 41 Copynumber: 5.6 Consensus size: 41
435322 TTGTAAACAT
* *
435332 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAA
* *
435373 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAA
* * *
435414 AAATGCCACTAAATTACGAGTCTTTA-CTGACATTTGTAT-A
1 AAACGCCACTAAAGTACGAGTCTATAGC-GACATTTGTATAA
* * * * * *
435454 AAACGACACTAATGTACGAGTCTTTAGCGGC-GTT-TATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAA
** * ** *
435493 AAACGCCACTAAAGTACTTGTCTATAGTGATTTTTTTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAA
* *
435534 AAA-GTCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCT
435556 TTGCCGGCGT
Statistics
Matches: 148, Mismatches: 30, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
38 3 0.02
39 25 0.17
40 43 0.29
41 77 0.52
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACATTTGTATAA
Found at i:435554 original size:79 final size:79
Alignment explanation
Indices: 435332--435567 Score: 226
Period size: 79 Copynumber: 2.9 Consensus size: 79
435322 TTGTAAACAT
* * *
435332 AAACGCCACTAAAGTACGAT-TCTATAGCGACGTTTGTATAAAAACGCCACTAATGTACGAGTCT
1 AAACGCCACTAAAGTAC-ATGTCTATAGTGACATTTGTATAAAAA-GACACTAATGTACGAGTCT
* * *
435396 ATAGCGACATTTATATAA
64 TTAGCGGC-GTT-TATAA
* * * * *
435414 AAATGCCACTAAATTACGA-GTCTTTACTGACATTTGTATAAAACGACACTAATGTACGAGTCTT
1 AAACGCCACTAAAGTAC-ATGTCTATAGTGACATTTGTATAAAAAGACACTAATGTACGAGTCTT
*
435478 TAGCGGCGTTTATAG
65 TAGCGGCGTTTATAA
* ** * * * *
435493 AAACGCCACTAAAGTACTTGTCTATAGTGATTTTTTTATAAAAAGTCACTAAAGTTCGAGTCTTT
1 AAACGCCACTAAAGTACATGTCTATAGTGACATTTGTATAAAAAGACACTAATGTACGAGTCTTT
435558 -GCCGGCGTTT
66 AG-CGGCGTTT
435568 TTGCTTAAAA
Statistics
Matches: 127, Mismatches: 24, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
78 1 0.01
79 64 0.50
80 2 0.02
81 24 0.19
82 36 0.28
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.31
Consensus pattern (79 bp):
AAACGCCACTAAAGTACATGTCTATAGTGACATTTGTATAAAAAGACACTAATGTACGAGTCTTT
AGCGGCGTTTATAA
Found at i:436235 original size:3 final size:3
Alignment explanation
Indices: 436229--436268 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
436219 ATATATATGC
436229 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
436269 CTCGGGTTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:440395 original size:21 final size:23
Alignment explanation
Indices: 440371--440417 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
440361 TCTATAAAAA
*
440371 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
440392 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
440415 TAA
1 TAA
440418 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:440432 original size:23 final size:22
Alignment explanation
Indices: 440371--440433 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
440361 TCTATAAAAA
* *
440371 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
440392 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
440415 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
440434 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:440596 original size:13 final size:13
Alignment explanation
Indices: 440566--440662 Score: 51
Period size: 13 Copynumber: 7.6 Consensus size: 13
440556 TTAAAATAAG
*
440566 AATATAATAGTAT
1 AATATATTAGTAT
* *
440579 CATATATTATTAT
1 AATATATTAGTAT
440592 AATATAATTGAGTAT
1 AATAT-ATT-AGTAT
440607 -AT-TATT-GTAT
1 AATATATTAGTAT
*
440617 AATATTATTATTAT
1 AATA-TATTAGTAT
* * *
440631 ATTAAATTATTA-
1 AATATATTAGTAT
* *
440643 AAAATATTAATA-
1 AATATATTAGTAT
440655 AATATATT
1 AATATATT
440663 TTAATTATGT
Statistics
Matches: 65, Mismatches: 13, Indels: 13
0.71 0.14 0.14
Matches are distributed among these distances:
10 4 0.06
11 2 0.03
12 18 0.28
13 26 0.40
14 11 0.17
15 4 0.06
ACGTcount: A:0.47, C:0.01, G:0.04, T:0.47
Consensus pattern (13 bp):
AATATATTAGTAT
Found at i:441360 original size:70 final size:68
Alignment explanation
Indices: 441220--441360 Score: 214
Period size: 69 Copynumber: 2.0 Consensus size: 68
441210 AGCAACAAAT
* *
441220 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAATGG
1 GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
441285 GGC
66 GGC
441288 GAGTTTGGGTAAAC-GACGGGAATGAAAAAAAATAGGTCAAGGAG-AAAAATGAAAAAGGGTTAA
1 GAGTTTGGGTAAACGGA-GGGAATG--AAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAA
441351 AGGGTGC
63 AGGG-GC
441358 GAG
1 GAG
441361 ACTTAGAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
67 2 0.03
68 21 0.31
69 22 0.33
70 22 0.33
ACGTcount: A:0.44, C:0.05, G:0.35, T:0.16
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGAGGGAATGAAAAAATAGGTCAAGGAGAAAAAATGAAAAAGGGTTAAAGG
GGC
Found at i:441445 original size:41 final size:41
Alignment explanation
Indices: 441381--441518 Score: 168
Period size: 41 Copynumber: 3.3 Consensus size: 41
441371 TGTAAACTTA
* *
441381 CGACATTTGTAAACATAAACGCCACTAAAGTACGATTCTATAG
1 CGACATTTGTATA-A-AAACGCCACTAAAGTACGAGTCTATAG
* *
441424 CGACGTTTGTATAAAAACGCCACTAATGTACGAGTCTATAG
1 CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
* * * * *
441465 CGACATTTATATAAAAATGCCACTAAACTATGAGTCTTTAG
1 CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
*
441506 CGGCATTTGTATA
1 CGACATTTGTATA
441519 CAATCGCCTC
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
41 70 0.85
42 1 0.01
43 11 0.13
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.29
Consensus pattern (41 bp):
CGACATTTGTATAAAAACGCCACTAAAGTACGAGTCTATAG
Found at i:441680 original size:41 final size:42
Alignment explanation
Indices: 441635--441778 Score: 111
Period size: 41 Copynumber: 3.5 Consensus size: 42
441625 TATTTCGGAG
*
441635 TTTGTATAAAAACGCCACTAAAT-TATGAGTCTTTA-CTAGCA
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGC-AGCA
* ** * *
441676 TTTGTATACAAACGAAACT-AATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
* * ** * *
441717 TTTATATAGAAACGCCACTAAA-GTACTTGTCTATAGC-GACT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAG-CA
*
441758 TTTTTAT-AAAACGCCACTAAA
1 TTTGTATAAAAACGCCACTAAA
441779 GTTTGAGTCT
Statistics
Matches: 83, Mismatches: 16, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
40 17 0.20
41 63 0.76
42 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCAGCA
Found at i:452212 original size:44 final size:44
Alignment explanation
Indices: 452162--452256 Score: 104
Period size: 44 Copynumber: 2.2 Consensus size: 44
452152 TTTTCTTTTG
*
452162 TGGCGTTTTG-TCCCAAAAACGCCACTAAATGTTCTGACATATAA
1 TGGCGTTTTGTTCCCAAAAACGCCACTAAATGTTATGACAT-TAA
** * * * *
452206 TGGCG-TTTGTTCTGAAAAACGCCTCTATATGTTATGCCATTAG
1 TGGCGTTTTGTTCCCAAAAACGCCACTAAATGTTATGACATTAA
452249 TGGCGTTT
1 TGGCGTTT
452257 GTGAATGTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
43 11 0.26
44 31 0.74
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (44 bp):
TGGCGTTTTGTTCCCAAAAACGCCACTAAATGTTATGACATTAA
Found at i:452254 original size:43 final size:44
Alignment explanation
Indices: 452176--452258 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
452166 GTTTTGTCCC
*
452176 AAAAACGCCACTAAATGTTCTGACATATAATGGCGTTTGTTCTG
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTTCTG
* * * *
452220 AAAAACGCCTCTATATGTTATGCCAT-TAGTGGCGTTTGT
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGT
452259 GAATGTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
43 12 0.35
44 22 0.65
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (44 bp):
AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTTCTG
Found at i:452269 original size:44 final size:44
Alignment explanation
Indices: 452176--452270 Score: 102
Period size: 44 Copynumber: 2.2 Consensus size: 44
452166 GTTTTGTCCC
* **
452176 AAAAACGCCACTAAATGTTCTGACATATAATGGCGTTTGTTCTG
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTAATG
* * * *
452220 AAAAACGCCTCTATATGTTATGCCAT-TAGTGGCGTTTGTGAATG
1 AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGT-AATG
*
452264 TAAAACG
1 AAAAACG
452271 TCGCTATTGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
43 12 0.29
44 30 0.71
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (44 bp):
AAAAACGCCACTAAATGTTATGACATATAATGGCGTTTGTAATG
Found at i:452422 original size:14 final size:15
Alignment explanation
Indices: 452396--452436 Score: 66
Period size: 15 Copynumber: 2.8 Consensus size: 15
452386 TTATACAATT
452396 AAAACTAATTTTTCA
1 AAAACTAATTTTTCA
452411 AAAACTAATTTTTCA
1 AAAACTAATTTTTCA
*
452426 AATACT-ATTTT
1 AAAACTAATTTT
452437 CTACTCTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 5 0.20
15 20 0.80
ACGTcount: A:0.44, C:0.12, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAACTAATTTTTCA
Found at i:452513 original size:21 final size:21
Alignment explanation
Indices: 452489--452538 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
452479 TAAACTAGAC
*
452489 ATCCGTAACAACAAACTTCAA
1 ATCCATAACAACAAACTTCAA
* *
452510 ATCCATAACAAGAAACTTGAA
1 ATCCATAACAACAAACTTCAA
452531 ATCCATAA
1 ATCCATAA
452539 TAATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAACTTCAA
Found at i:453821 original size:16 final size:15
Alignment explanation
Indices: 453795--453824 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
453785 TCCCCCCAAC
453795 TAAAAAAGAAGAAAA
1 TAAAAAAGAAGAAAA
453810 TAAAAGAAGAAGAAA
1 TAAAA-AAGAAGAAA
453825 CATGGTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.77, C:0.00, G:0.17, T:0.07
Consensus pattern (15 bp):
TAAAAAAGAAGAAAA
Found at i:455459 original size:68 final size:69
Alignment explanation
Indices: 455344--455483 Score: 239
Period size: 68 Copynumber: 2.0 Consensus size: 69
455334 ATCAGCAATT
* *
455344 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACGACGAGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
455409 G-GC
66 GTGC
455412 GAGTTTGGGTAAACGACGAGAATGAAAAAAATAGGTCAAGGGG-AAAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGACGAGAATG-AAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAG
455476 GGTGC
65 GGTGC
455481 GAG
1 GAG
455484 ACTTAGAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
68 45 0.66
69 23 0.34
ACGTcount: A:0.44, C:0.06, G:0.36, T:0.15
Consensus pattern (69 bp):
GAGTTTGGGTAAACGACGAGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
GTGC
Found at i:455568 original size:41 final size:41
Alignment explanation
Indices: 455520--455614 Score: 145
Period size: 41 Copynumber: 2.3 Consensus size: 41
455510 TTGTAAAAAT
* * *
455520 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
*
455561 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
*
455602 AAATGCCACTAAA
1 AAACGCCACTAAA
455615 TTATGAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 48 1.00
ACGTcount: A:0.40, C:0.20, G:0.15, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACATTTATATAA
Found at i:461727 original size:20 final size:20
Alignment explanation
Indices: 461697--461734 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
461687 TGTCTTCTAG
461697 TTTCTATATAGTTATGAATGT
1 TTTCTATATAGTT-TGAATGT
461718 TTTCTA-ATAGTTTGAAT
1 TTTCTATATAGTTTGAAT
461735 AAGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTATATAGTTTGAATGT
Found at i:464415 original size:32 final size:31
Alignment explanation
Indices: 464342--464417 Score: 80
Period size: 31 Copynumber: 2.4 Consensus size: 31
464332 CTAATGTGAC
* * *
464342 TCTTAGGTAGGCTCTGCGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
** **
464373 TCTCGGGTAGGCCCTGCGACCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGACCCTAAGAT-CAT
464405 TCTTAGGTAGGCC
1 TCTTAGGTAGGCC
464418 GCACGGCCCA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
31 23 0.66
32 12 0.34
ACGTcount: A:0.16, C:0.26, G:0.30, T:0.28
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGACCCTAAGATCAT
Found at i:467962 original size:21 final size:21
Alignment explanation
Indices: 467938--467983 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
467928 AACAATTCTC
*
467938 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAACCCT
* * *
467959 TTCATGTAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAACCCT
467980 TTCA
1 TTCA
467984 CCGAAAGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TTCATGAAAAGATTAAACCCT
Found at i:477925 original size:15 final size:15
Alignment explanation
Indices: 477905--477937 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
477895 TGTAACCGGG
477905 AAAACCAAATTAGTC
1 AAAACCAAATTAGTC
477920 AAAACCAAATTAGTC
1 AAAACCAAATTAGTC
477935 AAA
1 AAA
477938 TAACAAACGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.58, C:0.18, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAACCAAATTAGTC
Found at i:478048 original size:41 final size:41
Alignment explanation
Indices: 478002--478082 Score: 110
Period size: 41 Copynumber: 2.0 Consensus size: 41
477992 TTTGTCGTTT
** *
478002 ACAAACG-CAACTAAAGGTTACGTTTTTTAGCGGCATTTTTA
1 ACAAACGTC-ACTAAAGGTTACAATATTTAGCGGCATTTTTA
*
478043 ACAAACGTCACTAAAGGTTATAATATTTAGCGGCATTTTT
1 ACAAACGTCACTAAAGGTTACAATATTTAGCGGCATTTTT
478083 TCCAAACACC
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
41 34 0.97
42 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Consensus pattern (41 bp):
ACAAACGTCACTAAAGGTTACAATATTTAGCGGCATTTTTA
Found at i:478450 original size:21 final size:21
Alignment explanation
Indices: 478426--478475 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
478416 TAAACTAGAC
*
478426 ATCCGTAACAACAAACTTCAA
1 ATCCATAACAACAAACTTCAA
* * *
478447 ATCCATTACAAGAAACTTGAA
1 ATCCATAACAACAAACTTCAA
478468 ATCCATAA
1 ATCCATAA
478476 TAATAAATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.22
Consensus pattern (21 bp):
ATCCATAACAACAAACTTCAA
Found at i:480395 original size:22 final size:22
Alignment explanation
Indices: 480352--480403 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
480342 AAATATAAAA
* *
480352 TATAATAAATAATATTATTTAT
1 TATAAAAAATAAAATTATTTAT
480374 TATAAAAACATAAAATTA-TTAT
1 TATAAAAA-ATAAAATTATTTAT
*
480396 TTTAAAAA
1 TATAAAAA
480404 TATTAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 18 0.69
23 8 0.31
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAAAAATAAAATTATTTAT
Found at i:480635 original size:26 final size:26
Alignment explanation
Indices: 480589--480645 Score: 64
Period size: 26 Copynumber: 2.2 Consensus size: 26
480579 ACTAGTTGTA
*
480589 AATATAATAGTATCATATATTATTAT
1 AATATAATAGTATCATATATTATAAT
*
480615 AATATAATTGAGTAT-AT-TATTGTAAT
1 AATATAA-T-AGTATCATATATTATAAT
480641 AATAT
1 AATAT
480646 TATTATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 19 0.70
27 3 0.11
28 5 0.19
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.46
Consensus pattern (26 bp):
AATATAATAGTATCATATATTATAAT
Found at i:480651 original size:17 final size:16
Alignment explanation
Indices: 480629--480666 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
480619 TAATTGAGTA
480629 TATTATTGTAATAATAT
1 TATTATTGTAATAA-AT
*
480646 TATTATTGTATTAAAT
1 TATTATTGTAATAAAT
480662 TATTA
1 TATTA
480667 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TATTATTGTAATAAAT
Found at i:481336 original size:68 final size:69
Alignment explanation
Indices: 481220--481359 Score: 248
Period size: 68 Copynumber: 2.0 Consensus size: 69
481210 AGTAGCAAAT
481220 GAGTTTGGGTAAACAACGGGAATGAAAAAATAGGTCAAGGGGATAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACAACGGGAATGAAAAAATAGGTCAAGGGGATAAAATGAAAAAGGGTTAAAGG
481285 G-GC
66 GTGC
*
481288 GAGTTTGGGTAAACGACGGGAATGAAAAAAATAGGTCAAGGGGA-AAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACAACGGGAATG-AAAAAATAGGTCAAGGGGATAAAATGAAAAAGGGTTAAAG
481352 GGTGC
65 GGTGC
481357 GAG
1 GAG
481360 ACTTAAAAAT
Statistics
Matches: 69, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
68 45 0.65
69 24 0.35
ACGTcount: A:0.44, C:0.06, G:0.35, T:0.16
Consensus pattern (69 bp):
GAGTTTGGGTAAACAACGGGAATGAAAAAATAGGTCAAGGGGATAAAATGAAAAAGGGTTAAAGG
GTGC
Found at i:481500 original size:41 final size:41
Alignment explanation
Indices: 481400--481480 Score: 108
Period size: 41 Copynumber: 2.0 Consensus size: 41
481390 AAACATAAAT
* * * * *
481400 GCCACTAAAGTACGATTCTATAGCGACGGTTGTATAAAAAC
1 GCCACGAATGTACGAGTCTATAGCGACAGTTATATAAAAAC
*
481441 GCCACGAATGTACGAGTCTATAGCGACATTTATATAAAAA
1 GCCACGAATGTACGAGTCTATAGCGACAGTTATATAAAAA
481481 TTCCACTAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.25
Consensus pattern (41 bp):
GCCACGAATGTACGAGTCTATAGCGACAGTTATATAAAAAC
Found at i:481679 original size:41 final size:42
Alignment explanation
Indices: 481634--481772 Score: 135
Period size: 41 Copynumber: 3.4 Consensus size: 42
481624 TATTACGGAG
481634 TTTGTATAAAAACGCCACTAAAT-TACGAGTCTTTA-CTGACA
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGC-GACA
* * *
481675 TTTGTATAAAAACGGCACT-AATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGACA
* * ** * **
481716 TTTATATAGAAACGCCACTAAA-GTACTTGTCTATAGCGATT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGACA
*
481757 TTTTTAT-AAAACGCCA
1 TTTGTATAAAAACGCCA
481773 TAAGAGTTTG
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
40 11 0.14
41 67 0.83
42 3 0.04
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGACA
Found at i:485266 original size:21 final size:21
Alignment explanation
Indices: 485242--485287 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
485232 AACAATTCTC
*
485242 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAACCCT
* * *
485263 TTCATGGAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAACCCT
485284 TTCA
1 TTCA
485288 CCGAAAGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (21 bp):
TTCATGAAAAGATTAAACCCT
Found at i:487028 original size:20 final size:21
Alignment explanation
Indices: 486998--487039 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
486988 TGAGTTTCAA
486998 CTTTGACTATTTATATAGTAC
1 CTTTGACTATTTATATAGTAC
487019 CTTT-ACTATTTATATAGTAC
1 CTTTGACTATTTATATAGTAC
487039 C
1 C
487040 ACCTTTACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.29, C:0.17, G:0.07, T:0.48
Consensus pattern (21 bp):
CTTTGACTATTTATATAGTAC
Found at i:490791 original size:27 final size:27
Alignment explanation
Indices: 490760--490828 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 27
490750 TTAGTCAAAT
*
490760 AACAAACGCCACAAAAAGCAGCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
490787 AACAAACGCCACAAAAAGCACCACTGA
1 AACAAACGCCACAAAAAGCACCACTGA
*
490814 AACAAACGCCGCAAA
1 AACAAACGCCACAAA
490829 TGGTAGCAGT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.52, C:0.32, G:0.13, T:0.03
Consensus pattern (27 bp):
AACAAACGCCACAAAAAGCACCACTGA
Found at i:491037 original size:44 final size:44
Alignment explanation
Indices: 490967--491058 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
490957 TTTGTGAGGT
*
490967 TTTG-TCCCAAAAACGCCACTAAATGTTCTGACATATAATGCCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGCCG
* * * * * *
491010 TTTGTTCCGAAAAACGCCGCTACATGTTATGTCATATAGTGGCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGCCG
491054 TTTGT
1 TTTGT
491059 GAATGTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 4 0.10
44 37 0.90
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (44 bp):
TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGCCG
Found at i:491297 original size:21 final size:21
Alignment explanation
Indices: 491273--491325 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
491263 TAAACTAGAC
*
491273 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* *
491294 ATCCATAACAAGAAACTTCAA
1 ATCCATAATAACAAACTTCAA
*
491315 ATTCATAATAA
1 ATCCATAATAA
491326 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:493397 original size:21 final size:23
Alignment explanation
Indices: 493367--493413 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
493357 TCTATAAATA
*
493367 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
493388 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
493411 TAA
1 TAA
493414 TGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:493428 original size:23 final size:22
Alignment explanation
Indices: 493367--493429 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
493357 TCTATAAATA
* *
493367 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
493388 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
493411 TAATGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
493430 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.51
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:494341 original size:69 final size:69
Alignment explanation
Indices: 494214--494354 Score: 216
Period size: 69 Copynumber: 2.0 Consensus size: 69
494204 AGCAGCAAAT
* *
494214 GAGTTTGGGTAAATGACGTGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAAAGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
494279 G-GC
66 GCGC
494282 GAGTTTGGGTAAACAGA-GGGAATGGAAAAAAATAGGTCAAGGGG-AAAAATGAAAAAGGGTTAA
1 GAGTTTGGGTAAA-AGACGGGAAT-G-AAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAA
494345 AGGGCGC
63 AGGGCGC
494352 GAG
1 GAG
494355 ACTTAGAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
68 18 0.27
69 26 0.39
70 23 0.34
ACGTcount: A:0.44, C:0.05, G:0.35, T:0.16
Consensus pattern (69 bp):
GAGTTTGGGTAAAAGACGGGAATGAAAAAATAGGTCAAGGGGAAAAAATGAAAAAGGGTTAAAGG
GCGC
Found at i:494439 original size:41 final size:41
Alignment explanation
Indices: 494391--494782 Score: 162
Period size: 41 Copynumber: 9.6 Consensus size: 41
494381 TTGTAAACAT
* *
494391 AAACGCCACTAAAGTACGATTCAATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * *
494432 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* * * * * *
494473 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTGTATAC
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
** * ** * *
494514 ACTCGCCACTAATGTACTGA-TAAATTA-CGGCGTTTAT-TCAAA
1 AAACGCCACTAAAGTAC-GAGTCTA-TAGCGACGTTTGTAT--AA
* * * * *
494556 AAATGCCATTACAA-TATGAATATCT-TA-C-AGCGTTT-TTTCAA
1 AAACGCCACTA-AAGTACG-A-GTCTATAGCGA-CGTTTGTAT-AA
* * * * ** *
494597 AAATGCCATTATA-TATGTTTCCTATTA-CGAAGTTTGTATAA
1 AAACGCCACTAAAGTACGAGT-CTA-TAGCGACGTTTGTATAA
* * * *
494638 AAATGCCACTAAATTACGAGTCTTTA-CTGACATTTGTATAA
1 AAACGCCACTAAAGTACGAGTCTATAGC-GACGTTTGTATAA
* * * * * *
494679 AAACGGCACTAATGTACGAGTCTTTAGCGGCGTTTATATAG
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
* ** *
494720 AAACGCCACTAAAGTAC-ATGTCTATAGTGATTTTTTTATAA
1 AAACGCCACTAAAGTACGA-GTCTATAGCGACGTTTGTATAA
* *
494761 AAA-GTCACTAAAGTTCGAGTCT
1 AAACGCCACTAAAGTACGAGTCT
494783 TTGCCGGCGT
Statistics
Matches: 264, Mismatches: 67, Indels: 41
0.71 0.18 0.11
Matches are distributed among these distances:
38 1 0.00
39 2 0.01
40 25 0.09
41 202 0.77
42 32 0.12
43 1 0.00
44 1 0.00
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATAA
Found at i:495465 original size:3 final size:3
Alignment explanation
Indices: 495459--495507 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
495449 TAATATATGC
495459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
495507 T
1 T
495508 ATCTCGGGTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:498327 original size:734 final size:736
Alignment explanation
Indices: 496919--498389 Score: 2714
Period size: 734 Copynumber: 2.0 Consensus size: 736
496909 AACTAGCTGA
*
496919 TGCTTTGATCAAAATATGGTAAAATATATGATGATCCTCCTATTATTAGAGAGGATGAGAAAACG
1 TGCTTTGATCAAAATATGGTAAAATATATGATGATCCTCCTATTATTAGAAAGGATGAGAAAACG
*
496984 TTGTTTCCATATCCACCGTTGTTGAAAATTTGGAAAGATTTTGACTTTTGATGGAGGAACTATAT
66 TTGTTTCCATATCCACCGTTGTTGAAAATTTGGAAAGATTTTGACTTTCGATGGAGGAACTATAT
* *
497049 TTTGAATGGATTGTCTGATACATTATATTAAGTATATAGTATCCATAAGACTACTAAATAATTAA
131 TTTGAATGGATTGTCGGATACATTATATTAAGTATATAGTATCCATAAGACTACTAAAGAATTAA
497114 GAATGACATTTGGTCATGTTCTGAGTTGTCACAAAATATGTGGGAGAAACTGTTTTATAAGCAAA
196 GAATGACATTTGGTCATGTTCTGAGTTGTCACAAAATATGTGGGAGAAACTGTTTTATAAGCAAA
*
497179 TTACCTTTAAATAAGGTAACGCACAAGAAAATGGACAAGACATCATATGAGTTATGGAAATGGAA
261 TTACCTTTAAATAAGGTAACACACAAGAAAATGGACAAGACATCATATGAGTTATGGAAATGGAA
497244 TAGAAGAAAACCTTACTACAACTACATAAAAGTGTAGGGTGTCTTGTATAATGTATAATGACATG
326 TAGAAGAAAACCTTACTACAACTACATAAAAGTGTAGGGTGTCTTGTATAATGTATAATGACATG
*
497309 TCGAGACACATGAGTTGTCGACATAATACCTTTAGATAACTGAGCTCAATTAGAGTTATCTTCAT
391 TCGAGACACATGAGTTGTCGACATAATACCTTCAGATAACTGAGCTCAATTAGAGTTATCTTCAT
* *
497374 TGGTTTTTTAAGATCAAAAGATATATTGCGGATCTGCTATCCAATGATTTGAGTCGAGATCAAGT
456 TGGTTTTTTAAGATCAAAAGATATATTGCGGATCTGCTATCCAATGAGTTGAATCGAGATCAAGT
* *
497439 TGATAAAGATCTAACGGAAGTGACCCAAGCACATAAATATTTAAGGCTCTATGTGAAGGAATACC
521 TGATAAAGATCTAAAGGAAGTGACCCAAGCACATAAATATTTAAGGCGCTATGTGAAGGAATACC
*
497504 CAACCTAGTTGACTAGAGATGCCAAGATCTAGGTTCAATTGGGACAACCTACTTACATAGACCTT
586 CAACCTAGTTGACTAGAGATGCCAAGACCTAGGTTCAATTGGGACAACCTACTTACATAGACCTT
497569 GTTAGGTCACTATATGGGTTCTTATCCCAAGTCCATCCCTATGATGAAAACAATGACTAAAATGT
651 GTTAGGTCACTATATGGGTTCTTATCCCAAGTCCATCCCTATGATGAAAACAATGACTAAAATGT
497634 GGAAAAT-TTAAGCAATGCTT
716 GGAAAATGTTAAGCAATGCTT
*
497654 TGCTTTGATCAAAATATGGTCAAATATATGATGATCCTCCTATTATTAGAAAGGATGAGAAAACG
1 TGCTTTGATCAAAATATGGTAAAATATATGATGATCCTCCTATTATTAGAAAGGATGAGAAAACG
497719 TTGTTTCCATATCCACCGTTGTTGAAAATTTGGAAAGATTTTGA-TTTCGATGGAGGAACTATAT
66 TTGTTTCCATATCCACCGTTGTTGAAAATTTGGAAAGATTTTGACTTTCGATGGAGGAACTATAT
*
497783 TTTGAATGGATTGTCGGATACATTGTATTAAGTATATAGTATCCATAAGACTACTAAAGAATTAA
131 TTTGAATGGATTGTCGGATACATTATATTAAGTATATAGTATCCATAAGACTACTAAAGAATTAA
*
497848 GAATGACATTTGGTCATGTTCTGAGTTGTCACAAAATATGTGGGAGAAACTGTTTTATCAGCAAA
196 GAATGACATTTGGTCATGTTCTGAGTTGTCACAAAATATGTGGGAGAAACTGTTTTATAAGCAAA
497913 TTACCTTTAAATAAGGTAACACACAAGAAAATGGACAAGACATCATATGAGTTATGGAAATGGAA
261 TTACCTTTAAATAAGGTAACACACAAGAAAATGGACAAGACATCATATGAGTTATGGAAATGGAA
497978 TAGAAGAAAACCTTACTACAACTACATAAAAGTGTAGGGTGTCTTGTATAATGTATAATGACATG
326 TAGAAGAAAACCTTACTACAACTACATAAAAGTGTAGGGTGTCTTGTATAATGTATAATGACATG
*
498043 TCGAGACACATGAGTTGT-GACATAATACCTTCAGATAACTTAGCTCAATTAGAGTTATCTTCAT
391 TCGAGACACATGAGTTGTCGACATAATACCTTCAGATAACTGAGCTCAATTAGAGTTATCTTCAT
*
498107 TGGTTTTTTAAGATCAAAAGATAATATTGCGGATCTGCTATCCAATGAGTTGAATCTAGATCAAG
456 TGGTTTTTTAAGATCAAAAGAT-ATATTGCGGATCTGCTATCCAATGAGTTGAATCGAGATCAAG
*
498172 TTGATAAATATCTAAAGGAAGTGACCCAAGCACATAAATATTTAAGGCGCTATGTGAAGGAATAC
520 TTGATAAAGATCTAAAGGAAGTGACCCAAGCACATAAATATTTAAGGCGCTATGTGAAGGAATAC
* * *
498237 CCAACCTAGTTGACTGGAGATGCCAAGACCTAGGTTCAATTGGGATAACCTACTTACATAGAGCT
585 CCAACCTAGTTGACTAGAGATGCCAAGACCTAGGTTCAATTGGGACAACCTACTTACATAGACCT
* *
498302 TGTTAGGTCACTGTATGGGTTCTTATCCCAATTCCATCCCTATGATGAAAACAATGACTAAAATG
650 TGTTAGGTCACTATATGGGTTCTTATCCCAAGTCCATCCCTATGATGAAAACAATGACTAAAATG
498367 TGGAAAATGTTAAGCAATGCTT
715 TGGAAAATGTTAAGCAATGCTT
498389 T
1 T
498390 TAATGACAAC
Statistics
Matches: 712, Mismatches: 22, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
733 66 0.09
734 525 0.74
735 121 0.17
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (736 bp):
TGCTTTGATCAAAATATGGTAAAATATATGATGATCCTCCTATTATTAGAAAGGATGAGAAAACG
TTGTTTCCATATCCACCGTTGTTGAAAATTTGGAAAGATTTTGACTTTCGATGGAGGAACTATAT
TTTGAATGGATTGTCGGATACATTATATTAAGTATATAGTATCCATAAGACTACTAAAGAATTAA
GAATGACATTTGGTCATGTTCTGAGTTGTCACAAAATATGTGGGAGAAACTGTTTTATAAGCAAA
TTACCTTTAAATAAGGTAACACACAAGAAAATGGACAAGACATCATATGAGTTATGGAAATGGAA
TAGAAGAAAACCTTACTACAACTACATAAAAGTGTAGGGTGTCTTGTATAATGTATAATGACATG
TCGAGACACATGAGTTGTCGACATAATACCTTCAGATAACTGAGCTCAATTAGAGTTATCTTCAT
TGGTTTTTTAAGATCAAAAGATATATTGCGGATCTGCTATCCAATGAGTTGAATCGAGATCAAGT
TGATAAAGATCTAAAGGAAGTGACCCAAGCACATAAATATTTAAGGCGCTATGTGAAGGAATACC
CAACCTAGTTGACTAGAGATGCCAAGACCTAGGTTCAATTGGGACAACCTACTTACATAGACCTT
GTTAGGTCACTATATGGGTTCTTATCCCAAGTCCATCCCTATGATGAAAACAATGACTAAAATGT
GGAAAATGTTAAGCAATGCTT
Found at i:500573 original size:68 final size:67
Alignment explanation
Indices: 500452--500584 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 67
500442 AGCAGCAATT
500452 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGGG
1 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGGG
500517 GC
66 GC
500519 GAGTTTGGGTAAACGGCGGGAATGAAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACGGCGGGAATG-AAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGG
500584 G
65 G
500585 TGCAAGACTT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 24 0.37
68 41 0.63
ACGTcount: A:0.43, C:0.05, G:0.37, T:0.15
Consensus pattern (67 bp):
GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAAAGGG
GC
Found at i:500675 original size:41 final size:41
Alignment explanation
Indices: 500627--500721 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
500617 TTGTAAAAAT
* * *
500627 AAACGCCACTAAAGTACAATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGACATTTATATAA
* *
500668 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACAAGTCTATAGCGACATTTATATAA
*
500709 AAATGCCACTAAA
1 AAACGCCACTAAA
500722 TTATGAGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAGTACAAGTCTATAGCGACATTTATATAA
Found at i:504630 original size:32 final size:31
Alignment explanation
Indices: 504556--504677 Score: 88
Period size: 31 Copynumber: 3.9 Consensus size: 31
504546 CTAATGTGAC
* *
504556 TCTTAGGTAGGCTCTACGGCCCTGAGATCAT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
** *
504587 TCTCGGGTAGGCCCTGCGGCCCTAAGAT-ATGT
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCA--T
* * * *
504619 TCTTAGGTAGGCCCCATGGCCCCAAAATC-T
1 TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
* *
504649 ATCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 -TCTTAGGTAGGCCCTAC-GGCCCTAAGAT
504678 TCTCCCTTAG
Statistics
Matches: 68, Mismatches: 18, Indels: 10
0.71 0.19 0.10
Matches are distributed among these distances:
30 2 0.03
31 44 0.65
32 22 0.32
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTACGGCCCTAAGATCAT
Found at i:506840 original size:20 final size:20
Alignment explanation
Indices: 506810--506847 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
506800 TGTCTTCTGG
506810 TTTCTATATAGTTATGAATGT
1 TTTCTATATAGTT-TGAATGT
506831 TTTCTA-ATAGTTTGAAT
1 TTTCTATATAGTTTGAAT
506848 AAGATTTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.53
Consensus pattern (20 bp):
TTTCTATATAGTTTGAATGT
Found at i:510472 original size:41 final size:42
Alignment explanation
Indices: 510422--510529 Score: 125
Period size: 41 Copynumber: 2.6 Consensus size: 42
510412 TATTTCAGAG
510422 TTTGTATAAAAATGCCACTAAAT-TACGAGTCTTTA-CTGGCA
1 TTTGTATAAAAATGCCACTAAATGTACGAGTCTTTAGC-GGCA
* * **
510463 TTTGTATAAAAACGACACT-AATGTACGAGTCTTTAGCGGTG
1 TTTGTATAAAAATGCCACTAAATGTACGAGTCTTTAGCGGCA
* *
510504 TTTATATAGAAATGCCACTAAA-GTAC
1 TTTGTATAAAAATGCCACTAAATGTAC
510530 TTGTCTATAG
Statistics
Matches: 56, Mismatches: 8, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
40 3 0.05
41 50 0.89
42 3 0.05
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (42 bp):
TTTGTATAAAAATGCCACTAAATGTACGAGTCTTTAGCGGCA
Found at i:513520 original size:21 final size:21
Alignment explanation
Indices: 513496--513541 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
513486 AACAATTCTC
*
513496 TTCATGAAAAGATTAAATCCT
1 TTCATGAAAAGATTAAACCCT
* * *
513517 TTCATGTAAAGGTTAAGCCCT
1 TTCATGAAAAGATTAAACCCT
513538 TTCA
1 TTCA
513542 CCGAAAGGTC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (21 bp):
TTCATGAAAAGATTAAACCCT
Found at i:523663 original size:44 final size:44
Alignment explanation
Indices: 523593--523684 Score: 114
Period size: 44 Copynumber: 2.1 Consensus size: 44
523583 TTTGTGGCAT
* *
523593 TTTG-TCCCAAAAACGCCACTAAATGTTCTGACATATAATGGTG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
* * * * *
523636 TTTGTTCCGAAAAACGCCGCTATATGTTATGTCATATAGTGGCG
1 TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
523680 TTTGT
1 TTTGT
523685 GAATGTAAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
43 4 0.10
44 37 0.90
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (44 bp):
TTTGTTCCCAAAAACGCCACTAAATGTTATGACATATAATGGCG
Found at i:523923 original size:21 final size:21
Alignment explanation
Indices: 523899--523948 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
523889 TAAACTAGAC
*
523899 ATCCGTAACAACAAACTTCAA
1 ATCCATAACAACAAACTTCAA
* *
523920 ATCCATAACAAGAAACTTTAA
1 ATCCATAACAACAAACTTCAA
523941 ATCCATAA
1 ATCCATAA
523949 TAATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.04, T:0.22
Consensus pattern (21 bp):
ATCCATAACAACAAACTTCAA
Found at i:525989 original size:26 final size:26
Alignment explanation
Indices: 525958--526014 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
525948 ACTAGTTGTA
*
525958 AATATAA-T-AGTATCATATATTGTTAT
1 AATATAATTGAGTAT-AT-TATTGTAAT
525984 AATATAATTGAGTATATTATTGTAAT
1 AATATAATTGAGTATATTATTGTAAT
526010 AATAT
1 AATAT
526015 TATTATTGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 20 0.71
27 3 0.11
28 5 0.18
ACGTcount: A:0.44, C:0.02, G:0.09, T:0.46
Consensus pattern (26 bp):
AATATAATTGAGTATATTATTGTAAT
Found at i:526020 original size:17 final size:16
Alignment explanation
Indices: 525998--526035 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
525988 TAATTGAGTA
525998 TATTATTGTAATAATAT
1 TATTATTGTAATAA-AT
*
526015 TATTATTGTATTAAAT
1 TATTATTGTAATAAAT
526031 TATTA
1 TATTA
526036 AAAATATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (16 bp):
TATTATTGTAATAAAT
Found at i:526736 original size:69 final size:67
Alignment explanation
Indices: 526612--526742 Score: 226
Period size: 69 Copynumber: 1.9 Consensus size: 67
526602 CAGCAGCAAA
*
526612 TGAGTTTGGGTAAACAACGGGAATGAAAAAATAGGTCAAGGGGAAAAATGAAAAAGGGTTAATGG
1 TGAGTTTGGGTAAACAACGGGAATGAAAAAATAGATCAAGGGGAAAAATGAAAAAGGGTTAATGG
526677 GG
66 GG
*
526679 TGAGTTTGGGTAAACGACGGGAATGAAAAAAAATAGATCAAGGGGAAAAATGAAAAAGGGTTAA
1 TGAGTTTGGGTAAACAACGGGAATG--AAAAAATAGATCAAGGGGAAAAATGAAAAAGGGTTAA
526743 AGGGCGCGAG
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 24 0.40
69 36 0.60
ACGTcount: A:0.46, C:0.05, G:0.32, T:0.18
Consensus pattern (67 bp):
TGAGTTTGGGTAAACAACGGGAATGAAAAAATAGATCAAGGGGAAAAATGAAAAAGGGTTAATGG
GG
Found at i:526836 original size:41 final size:41
Alignment explanation
Indices: 526790--526884 Score: 129
Period size: 41 Copynumber: 2.3 Consensus size: 41
526780 TTGTAAACAT
* * *
526790 AAATGCCACT-ATAGAACGATTCTATAGCGACGTTTGTATAA
1 AAATGCCACTAAT-GAACGAGTCTATAGCGACATTTATATAA
* *
526831 AAATGCCACGAATGTACGAGTCTATAGCGACATTTATATAA
1 AAATGCCACTAATGAACGAGTCTATAGCGACATTTATATAA
526872 AAATGCCACTAAT
1 AAATGCCACTAAT
526885 TTATGAGTCT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (41 bp):
AAATGCCACTAATGAACGAGTCTATAGCGACATTTATATAA
Found at i:526893 original size:41 final size:41
Alignment explanation
Indices: 526805--526899 Score: 127
Period size: 41 Copynumber: 2.3 Consensus size: 41
526795 CCACTATAGA
* * *
526805 ACGATTCTATAGCGACGTTTGTATAAAAATGCCACGAATGT
1 ACGAGTCTATAGCGACATTTATATAAAAATGCCACGAATGT
* *
526846 ACGAGTCTATAGCGACATTTATATAAAAATGCCACTAATTT
1 ACGAGTCTATAGCGACATTTATATAAAAATGCCACGAATGT
* *
526887 ATGAGTCTTTAGC
1 ACGAGTCTATAGC
526900 AGTGTTTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 47 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.32
Consensus pattern (41 bp):
ACGAGTCTATAGCGACATTTATATAAAAATGCCACGAATGT
Found at i:527073 original size:41 final size:41
Alignment explanation
Indices: 527028--527126 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
527018 TATTACGGAG
*
527028 TTTGTATAAAAACGCCACTAAAT-TATGAGTCTTTA-CTGGCA
1 TTTGTATAAAAACGCCACT-AATGTACGAGTCTTTAGC-GGCA
** *
527069 TTTGTATAAAAACAACACTAATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAATGTACGAGTCTTTAGCGGCA
* *
527110 TTTATATAGAAACGCCA
1 TTTGTATAAAAACGCCA
527127 GCGATTTTTT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 3 0.06
41 44 0.92
42 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.31
Consensus pattern (41 bp):
TTTGTATAAAAACGCCACTAATGTACGAGTCTTTAGCGGCA
Found at i:527846 original size:3 final size:3
Alignment explanation
Indices: 527840--527869 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
527830 TAATATATGC
527840 TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
527870 CTCGGGTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:531112 original size:3 final size:3
Alignment explanation
Indices: 531106--531130 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
531096 TAATATATGT
531106 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
531131 ATGAGATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:536783 original size:44 final size:44
Alignment explanation
Indices: 536712--536795 Score: 123
Period size: 44 Copynumber: 1.9 Consensus size: 44
536702 ATTTTGACCC
* *
536712 AAAAACGCCACTAAATGTTCTGACATATAATGGCGTTTGTTCCG
1 AAAAACGCCACTAAATGGTATGACATATAATGGCGTTTGTTCCG
* * *
536756 AAAAACGCCACTATATGGTATGTCATATAGTGGCGTTTGT
1 AAAAACGCCACTAAATGGTATGACATATAATGGCGTTTGT
536796 GAATGTAAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 35 1.00
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (44 bp):
AAAAACGCCACTAAATGGTATGACATATAATGGCGTTTGTTCCG
Found at i:537035 original size:21 final size:21
Alignment explanation
Indices: 537011--537063 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
537001 TAAACTAGAC
*
537011 ATCCGTAATAACAAACTTCAA
1 ATCCATAATAACAAACTTCAA
* * *
537032 ATCCATAACAAGAAACTTGAA
1 ATCCATAATAACAAACTTCAA
537053 ATCCATAATAA
1 ATCCATAATAA
537064 TAAATTAAAG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.51, C:0.21, G:0.06, T:0.23
Consensus pattern (21 bp):
ATCCATAATAACAAACTTCAA
Found at i:538879 original size:22 final size:22
Alignment explanation
Indices: 538853--538904 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
538843 AAATATAAAA
*
538853 TATAAAAA-ATAATATTATTTAT
1 TATAAAAACATAAAATTA-TTAT
*
538875 TATAAAAACTTAAAATTATTAT
1 TATAAAAACATAAAATTATTAT
*
538897 TTTAAAAA
1 TATAAAAA
538905 TATTAGAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TATAAAAACATAAAATTATTAT
Found at i:540013 original size:68 final size:69
Alignment explanation
Indices: 539898--540037 Score: 194
Period size: 68 Copynumber: 2.0 Consensus size: 69
539888 AGCAACAAAT
* * * *
539898 GAGTTTGGGTAAATGGCGGGAATGAAAAAATAGGTCAAGGGAAAAAAATGAAAAAGGGTTAAAGG
1 GAGTTTGGGTAAACGACGGGAATGAAAAAATAGCTCAAGGGAAAAAAATGAAAAAAGGTTAAAGG
539963 G-GC
66 GTGC
* * *
539966 GAGTTTGGGTAAACGACGGGAATGAAAAAAATAGCTCATGGG-GAAAAATGAAAAAATGTTAAAG
1 GAGTTTGGGTAAACGACGGGAATG-AAAAAATAGCTCAAGGGAAAAAAATGAAAAAAGGTTAAAG
540030 GGTGC
65 GGTGC
540035 GAG
1 GAG
540038 ACTTAGAAAT
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
68 43 0.68
69 20 0.32
ACGTcount: A:0.44, C:0.06, G:0.34, T:0.17
Consensus pattern (69 bp):
GAGTTTGGGTAAACGACGGGAATGAAAAAATAGCTCAAGGGAAAAAAATGAAAAAAGGTTAAAGG
GTGC
Found at i:540122 original size:41 final size:40
Alignment explanation
Indices: 540074--540213 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 40
540064 TTGTAAACAT
*
540074 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTGTATGA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTAT-A
* * *
540115 AAACGCCACTAATGTACGAGTCTATAGCGACATTTATATAA
1 AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTAT-A
* * * *
540156 AAATGCCACTAAATTATGAGTCTTTAGCGGA-GTTTGTATA
1 AAACGCCACTAAAGTACGAGTCTATAGC-GACGTTTGTATA
* *
540196 CAATCGCCACTAATGTAC
1 -AAACGCCACTAAAGTAC
540214 TGATAAATTG
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
40 1 0.01
41 77 0.96
42 2 0.03
ACGTcount: A:0.35, C:0.19, G:0.17, T:0.29
Consensus pattern (40 bp):
AAACGCCACTAAAGTACGAGTCTATAGCGACGTTTGTATA
Found at i:540361 original size:41 final size:42
Alignment explanation
Indices: 540311--540466 Score: 126
Period size: 41 Copynumber: 3.8 Consensus size: 42
540301 TATTACGGAG
* *
540311 TTTGCATAAAAACGCCACTAAAT-TACGATTCTTTA-CTGGCA
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGC-GGCA
* *
540352 TTTGTATAAAAACGTCACT-AATGTACGAGTCTTTAGCGGCG
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGGCA
* * ** * * *
540393 TTTATATAGAAACGCCACTAAA-GTACTTGTCTATAGCGACT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGGCA
* * * *
540434 TTTTTAT-AAAATGCCACTAGA-GTTCGAGTCTTT
1 TTTGTATAAAAACGCCACTAAATGTACGAGTCTTT
540467 GCCGACGTTT
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
40 22 0.24
41 67 0.73
42 3 0.03
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Consensus pattern (42 bp):
TTTGTATAAAAACGCCACTAAATGTACGAGTCTTTAGCGGCA
Found at i:549876 original size:21 final size:21
Alignment explanation
Indices: 549852--549901 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
549842 TAAACTAGAC
*
549852 ATCCGTAACAACAAACTTCAA
1 ATCCATAACAACAAACTTCAA
* *
549873 ATCCATAACAAGAAACTTGAA
1 ATCCATAACAACAAACTTCAA
549894 ATCCATAA
1 ATCCATAA
549902 TAATAAATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.50, C:0.24, G:0.06, T:0.20
Consensus pattern (21 bp):
ATCCATAACAACAAACTTCAA
Found at i:551981 original size:21 final size:23
Alignment explanation
Indices: 551957--552003 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
551947 TCTATAAAAG
*
551957 TAAAAGTATT-AT-ATTATATTT
1 TAAAAGTATTAATAAATATATTT
*
551978 TAAAATTATTAATAAATATATTT
1 TAAAAGTATTAATAAATATATTT
552001 TAA
1 TAA
552004 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TAAAAGTATTAATAAATATATTT
Found at i:552018 original size:23 final size:22
Alignment explanation
Indices: 551957--552019 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
551947 TCTATAAAAG
* *
551957 TAAAAGTA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
551978 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
552001 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
552020 TATTAGACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:552948 original size:69 final size:68
Alignment explanation
Indices: 552809--552944 Score: 213
Period size: 68 Copynumber: 2.0 Consensus size: 68
552799 AGCAGCAAAT
*
552809 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGTTCAAGGGGAAAAAATGAAAAAGGGATAAAGA
1 GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGCTCAAGGGGAAAAAATGAAAAAGGGATAAAGA
552874 GGC
66 GGC
* * *
552877 GAGTTTGGGTAAACGGTGGGACTGAAAAAAATAGCTCAAGGGG-AAAAATGAAAAAGGGTTAAAG
1 GAGTTTGGGTAAACGGCGGGAATG-AAAAAATAGCTCAAGGGGAAAAAATGAAAAAGGGATAAAG
552941 -GGC
65 AGGC
552944 G
1 G
552945 CGAGACTTAG
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
67 4 0.06
68 42 0.67
69 17 0.27
ACGTcount: A:0.43, C:0.07, G:0.35, T:0.15
Consensus pattern (68 bp):
GAGTTTGGGTAAACGGCGGGAATGAAAAAATAGCTCAAGGGGAAAAAATGAAAAAGGGATAAAGA
GGC
Found at i:553033 original size:41 final size:41
Alignment explanation
Indices: 552985--553124 Score: 147
Period size: 41 Copynumber: 3.4 Consensus size: 41
552975 TTGTAAACAT
* *
552985 AAACGCCACTAAAGTACAATTCTATAGCGACGTTTGTATAA
1 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTATATAA
*
553026 AAACGCCACTAATA-TACGATTCTATAGCGACATTTATATAA
1 AAACGCCACTAA-AGTACGATTCTATAGCGACGTTTATATAA
* * * * * * * *
553067 AAATGCCACTAAATTATGAGTCTTTAGCGGCGTTTCTATAC
1 AAACGCCACTAAAGTACGATTCTATAGCGACGTTTATATAA
* *
553108 AATCGCCACTAATGTAC
1 AAACGCCACTAAAGTAC
553125 TGATAAATTG
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 1 0.01
41 79 0.98
42 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (41 bp):
AAACGCCACTAAAGTACGATTCTATAGCGACGTTTATATAA
Found at i:553268 original size:41 final size:40
Alignment explanation
Indices: 552966--553348 Score: 138
Period size: 41 Copynumber: 9.3 Consensus size: 40
552956 AATTGTAAAC
* * ** *
552966 TTACGGCATTTGTAAACATAAACGCCACTAAAGTACAATTCT
1 TTACGGCATTTGTATA-A-AAACGCCACTAAATTATGAGTCT
* * * * *
553008 ATAGCGACGTTTGTATAAAAACGCCACT-AATATACGATTCT
1 TTA-CGGCATTTGTATAAAAACGCCACTAAAT-TATGAGTCT
* * * *
553049 ATAGCGACATTTATATAAAAATGCCACTAAATTATGAGTCT
1 TTA-CGGCATTTGTATAAAAACGCCACTAAATTATGAGTCT
* * * * **
553090 TTAGCGGCGTTTCTATACAATCGCCACT-AATGTACTGA-TAAA
1 TTA-CGGCATTTGTATAAAAACGCCACTAAAT-TA-TGAGT-CT
* * * * * *
553132 TTGCGGCGTTTAT-TCAAAAAATGCCATTACAA-TATGAATCT
1 TTACGGCATTTGTAT--AAAAACGCCACTA-AATTATGAGTCT
* * * * * **
553173 CTTACGGCGTTT-TTTCAAAAATGCCATTATA-TATGTTTCCT
1 -TTACGGCATTTGTAT-AAAAACGCCACTAAATTATGAGT-CT
553214 ATTACGG-AGTTTGTATAAAAACGCCACTAAATTATGAGTCT
1 -TTACGGCA-TTTGTATAAAAACGCCACTAAATTATGAGTCT
* *
553255 TTACTGGCATTTGTATAAAAACGACACT-AATGTACGAGTCT
1 TTAC-GGCATTTGTATAAAAACGCCACTAAAT-TATGAGTCT
* * * *
553296 TTAGCGGCGTTTATATAGAAACGCCACTAGAGTT-TGAGTCT
1 TTA-CGGCATTTGTATAAAAACGCCACTA-AATTATGAGTCT
*
553337 TTGCCGGCATTT
1 TT-ACGGCATTT
553349 TTGCTTAAAA
Statistics
Matches: 266, Mismatches: 51, Indels: 49
0.73 0.14 0.13
Matches are distributed among these distances:
40 19 0.07
41 190 0.71
42 43 0.16
43 12 0.05
44 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (40 bp):
TTACGGCATTTGTATAAAAACGCCACTAAATTATGAGTCT
Found at i:554014 original size:3 final size:3
Alignment explanation
Indices: 554008--554046 Score: 62
Period size: 3 Copynumber: 13.3 Consensus size: 3
553998 TAATATATGC
*
554008 TTA TTA TTA TTA TTA TTA ATA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
554047 CTCGGGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:561367 original size:21 final size:21
Alignment explanation
Indices: 561343--561400 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
561333 AACAATTCTC
* *
561343 TTCATGAAAAGATTGAATCCT
1 TTCATGTAAAGATTAAATCCT
561364 TTCATGTAAAGATTAAATCCT
1 TTCATGTAAAGATTAAATCCT
*
561385 TTCATGTAAAGGTTAA
1 TTCATGTAAAGATTAA
561401 GCACTTTCAC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.38, C:0.12, G:0.14, T:0.36
Consensus pattern (21 bp):
TTCATGTAAAGATTAAATCCT
Found at i:561407 original size:21 final size:21
Alignment explanation
Indices: 561343--561409 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
561333 AACAATTCTC
* * *
561343 TTCATGAAAAGATTGAATCCT
1 TTCATGTAAAGATTAAAGCCT
*
561364 TTCATGTAAAGATTAAATCCT
1 TTCATGTAAAGATTAAAGCCT
*
561385 TTCATGTAAAGGTT-AAGCACT
1 TTCATGTAAAGATTAAAGC-CT
561406 TTCA
1 TTCA
561410 CCGAAAGGTC
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 3 0.07
21 38 0.93
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (21 bp):
TTCATGTAAAGATTAAAGCCT
Found at i:563932 original size:29 final size:29
Alignment explanation
Indices: 563886--564116 Score: 225
Period size: 29 Copynumber: 7.9 Consensus size: 29
563876 GACCCGACCC
* *
563886 GGTGACATTCTAGGAAATATTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* *
563915 GGTTACATTCTGGGAAATATTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
*
563944 GGTGACATTCTGGAAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* * *
563973 TGTGACATTCTAGAAAATATTTTGAAAAAA
1 GGTGACATTCTGGGAAATATTTTG-AAAAA
* * * *
564003 AGTTACATTC-GGGAATTATTTAGAATAAAA
1 GGTGACATTCTGGGAAATATTTTG-A-AAAA
* * * *
564033 GGTGACATTTTGGGTATTATTTTGAGAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
*
564062 GGTGACATTCTGGGAATTATTTTGAAAAAAA
1 GGTGACATTCTGGGAAATATTTTG--AAAAA
* *
564093 AGTGACATTTTGGG-AAT-TTTTGAA
1 GGTGACATTCTGGGAAATATTTTGAA
564117 TTTAGACTAT
Statistics
Matches: 172, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
27 2 0.01
29 116 0.67
30 27 0.16
31 27 0.16
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (29 bp):
GGTGACATTCTGGGAAATATTTTGAAAAA
Found at i:564057 original size:60 final size:60
Alignment explanation
Indices: 563932--564106 Score: 167
Period size: 60 Copynumber: 3.0 Consensus size: 60
563922 TTCTGGGAAA
* * * * * * * * ** *
563932 TATTTTGAAATAGGTGACATTCTGGAAAATATTTTG--AAAAATGTGACATTCTAGAAAA
1 TATTTTGAAAAAAGTGACATTCTGGGAATTATTTAGAAAAAAAAGTGACATTTTGGGTAT
* * *
563990 TATTTTGAAAAAAAGTTACATTC-GGGAATTATTTAGAATAAAAGGTGACATTTTGGGTAT
1 TATTTTG-AAAAAAGTGACATTCTGGGAATTATTTAGAAAAAAAAGTGACATTTTGGGTAT
* * *
564050 TATTTTGAGAAAGGTGACATTCTGGGAATTATTTTGAAAAAAAAGTGACATTTTGGG
1 TATTTTGAAAAAAGTGACATTCTGGGAATTATTTAGAAAAAAAAGTGACATTTTGGG
564107 AATTTTTGAA
Statistics
Matches: 94, Mismatches: 19, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
58 17 0.18
59 24 0.26
60 53 0.56
ACGTcount: A:0.38, C:0.06, G:0.21, T:0.35
Consensus pattern (60 bp):
TATTTTGAAAAAAGTGACATTCTGGGAATTATTTAGAAAAAAAAGTGACATTTTGGGTAT
Found at i:565100 original size:63 final size:63
Alignment explanation
Indices: 564998--565121 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
564988 TTAATGTGAC
** * *
564998 TCTTAGATAGGCCCTGCGGCCCTGAGATCATTCTCGGGTAGGCCCTGC-GGCCCTAGGATGTGT
1 TCTTAGATAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* * * *
565061 TCTTAGGTAGGCCCCACGGCTCTGAAATC-TATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGATAGGCCCCACGGCCCTGAAATCAT-TCTCGGGTAGGCCCTCAGGCCCTAAGATGT
565122 TCCCTTAGGG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGATAGGCCCCACGGCCCTGAAATCATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:565191 original size:26 final size:26
Alignment explanation
Indices: 565138--565191 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
565128 AGGGTAACTC
*
565138 TTTTATGAGATTTACTGCAGTATAAT
1 TTTTATGAGATTTACTGCACTATAAT
* *
565164 TTTTATGAGATTTACTGGACTATGAT
1 TTTTATGAGATTTACTGCACTATAAT
565190 TT
1 TT
565192 GTTTAGTGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.48
Consensus pattern (26 bp):
TTTTATGAGATTTACTGCACTATAAT
Found at i:573171 original size:18 final size:18
Alignment explanation
Indices: 573145--573179 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
573135 TCGAAAGGAC
*
573145 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
573163 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
573180 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:576309 original size:22 final size:22
Alignment explanation
Indices: 576284--576338 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
576274 TGACCGGTAT
*
576284 GACCCGACCCGACCCGTTGATC
1 GACCCGACCCGACCCGTTGACC
*
576306 GACCCGACACGACCCGTTGACC
1 GACCCGACCCGACCCGTTGACC
576328 GACCCGACCCG
1 GACCCGACCCG
576339 GTGACATTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.47, G:0.24, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCCGTTGACC
Found at i:576329 original size:17 final size:17
Alignment explanation
Indices: 576309--576343 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
576299 GTTGATCGAC
*
576309 CCGACACGACCCGTTGA
1 CCGACACGACCCGGTGA
*
576326 CCGACCCGACCCGGTGA
1 CCGACACGACCCGGTGA
576343 C
1 C
576344 ATTCTGGGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.20, C:0.46, G:0.26, T:0.09
Consensus pattern (17 bp):
CCGACACGACCCGGTGA
Found at i:576382 original size:29 final size:29
Alignment explanation
Indices: 576338--576557 Score: 271
Period size: 29 Copynumber: 7.6 Consensus size: 29
576328 GACCCGACCC
*
576338 GGTGACATTCTGGGAAATATTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* * * *
576367 TGTGACATTCTAGGAAATTTTTTGAAATA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* **
576396 GGTGACATTCTGAGAAATATTTAAAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
*
576425 GGTGACATTCTGGAAAATATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
* *
576454 AGTTACATTCTGGGAAATATTTTGAAACAA
1 GGTGACATTCTGGGAAATATTTTGAAA-AA
* *
576484 -GTGATATTCTGGGAATTATTTTGAAAAA
1 GGTGACATTCTGGGAAATATTTTGAAAAA
*
576512 GGTGACATTCTGGGAATTATTTTGAAAAAA
1 GGTGACATTCTGGGAAATATTTTG-AAAAA
* *
576542 AGTGACATTTTGGGAA
1 GGTGACATTCTGGGAA
576558 TTTTCGAATT
Statistics
Matches: 165, Mismatches: 23, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
28 2 0.01
29 142 0.86
30 21 0.13
ACGTcount: A:0.38, C:0.07, G:0.21, T:0.34
Consensus pattern (29 bp):
GGTGACATTCTGGGAAATATTTTGAAAAA
Found at i:581990 original size:15 final size:15
Alignment explanation
Indices: 581970--582017 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
581960 TGTAACCGGG
581970 AAAACCAAATTAGTC
1 AAAACCAAATTAGTC
*
581985 AAAACCAAATTAATC
1 AAAACCAAATTAGTC
582000 AAAACCAAATTAGTC
1 AAAACCAAATTAGTC
582015 AAA
1 AAA
582018 TAACAAACGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.58, C:0.19, G:0.04, T:0.19
Consensus pattern (15 bp):
AAAACCAAATTAGTC
Done.