Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 133 of 295
Found at i:40688202 original size:239 final size:238
Alignment explanation
Indices: 40687779--40688256 Score: 728
Period size: 239 Copynumber: 2.0 Consensus size: 238
40687769 TAAACCTATG
*
40687779 ATGATTATAGTGTTTGTCACTCTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAAACTAAAAGAT
1 ATGATTATAATGTTTGTCACTCTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAAACTAAAAGAT
* * *
40687844 ACCACCTAGGTTCTCCCTCGGTCTCACCTAGGCATATAGATATCCTCTTGGTTTCACTATTAGAC
66 ACAACCTAGGTTCTCCCTCGGTCTCACCTAGGCATATAGATATCCTCTTGATCTCACTATTAGAC
* * *
40687909 ACAAGTGTATCAAAGTCCTACACGATAGAGTCTCTTCTCAGTCTCATCTATCTAAAT-TTTCCAC
131 ACAAGTGTAACAAAGTCCTACACGATAGAATCTCCTCTCAGTCTCATCTATCTAAATATTT-CAC
*
40687973 TAGAGGAGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
195 TAGAAGAGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
* *
40688017 ATGATTATAATGTTTGTCACTCTTAGCTAAGAATCT-CTTCTCAGTCTCATCTTAGACTAAAAGA
1 ATGATTATAATGTTTGTCACTCTTAGCTAAGAATCTCCTT-TCAGTCTCATCCTAAACTAAAAGA
* *
40688081 TTCAACCTAGGTTCTCCTCTCGGTCTCACCTAGGCATATAGATCTCCTCTTGATCTCACTATTCA
65 TACAACCTAGGTTCTCC-CTCGGTCTCACCTAGGCATATAGATATCCTCTTGATCTCACTATT-A
* * * *
40688146 -ACACAAGTGTAACAAAGTCCTACATGATAGAATCTCCTCTTAGTCTCGTTTATCTAAATATTTC
128 GACACAAGTGTAACAAAGTCCTACACGATAGAATCTCCTCTCAGTCTCATCTATCTAAATATTTC
* **
40688210 ATTAGAAGTTTCAATTCTAGTATAATATGCAATTTAATACACTTGA
193 ACTAGAAGAGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
40688256 A
1 A
40688257 CAAACAACCA
Statistics
Matches: 217, Mismatches: 19, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
237 3 0.01
238 72 0.33
239 138 0.64
240 4 0.02
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.35
Consensus pattern (238 bp):
ATGATTATAATGTTTGTCACTCTTAGCTAAGAATCTCCTTTCAGTCTCATCCTAAACTAAAAGAT
ACAACCTAGGTTCTCCCTCGGTCTCACCTAGGCATATAGATATCCTCTTGATCTCACTATTAGAC
ACAAGTGTAACAAAGTCCTACACGATAGAATCTCCTCTCAGTCTCATCTATCTAAATATTTCACT
AGAAGAGTCAATTCTAGTATAATATGCAATTTAATACACTTGA
Found at i:40693223 original size:55 final size:54
Alignment explanation
Indices: 40693140--40693251 Score: 188
Period size: 55 Copynumber: 2.1 Consensus size: 54
40693130 CCAAAGTAGG
* *
40693140 AAAAATATTAAGTTAGGAGATATATAATAGCAGAGGAAAGGAATGAAGGATTATA
1 AAAAACATTAAGTTAGGAGAAATATAATAGCAGAGGAAAGGAATGAAGGATTA-A
*
40693195 AAAAACATTAAGTTAGGAGAAATATAATAGTAGAGGAAAGGAATGAAGGATTAA
1 AAAAACATTAAGTTAGGAGAAATATAATAGCAGAGGAAAGGAATGAAGGATTAA
40693249 AAA
1 AAA
40693252 GAAATTTAAC
Statistics
Matches: 54, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
54 4 0.07
55 50 0.93
ACGTcount: A:0.54, C:0.02, G:0.23, T:0.21
Consensus pattern (54 bp):
AAAAACATTAAGTTAGGAGAAATATAATAGCAGAGGAAAGGAATGAAGGATTAA
Found at i:40701371 original size:25 final size:23
Alignment explanation
Indices: 40701343--40701417 Score: 82
Period size: 22 Copynumber: 3.3 Consensus size: 23
40701333 AGCTTAGCGC
40701343 GCTCTCCGATTATTAGCACATTAGT
1 GCTCTCCG--TATTAGCACATTAGT
* *
40701368 GCTCTCCGT-TTAGCAGATTCGT
1 GCTCTCCGTATTAGCACATTAGT
* *
40701390 GCTCTCTGTA-TAGCACTTTAGT
1 GCTCTCCGTATTAGCACATTAGT
40701412 GCTCTC
1 GCTCTC
40701418 TGTTCAATAG
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
22 34 0.79
23 1 0.02
25 8 0.19
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (23 bp):
GCTCTCCGTATTAGCACATTAGT
Found at i:40701418 original size:22 final size:22
Alignment explanation
Indices: 40701356--40701420 Score: 85
Period size: 22 Copynumber: 3.0 Consensus size: 22
40701346 CTCCGATTAT
* *
40701356 TAGCACATTAGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCTGTA
* *
40701378 TAGCAGATTCGTGCTCTCTGTA
1 TAGCACATTAGTGCTCTCTGTA
*
40701400 TAGCACTTTAGTGCTCTCTGT
1 TAGCACATTAGTGCTCTCTGT
40701421 TCAATAGTGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.20, T:0.38
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTCTGTA
Found at i:40712138 original size:32 final size:32
Alignment explanation
Indices: 40712084--40712149 Score: 87
Period size: 32 Copynumber: 2.1 Consensus size: 32
40712074 GGCCCATACA
* * *
40712084 GCCCAATTGGTCGAGCCCGTGTCTCGCACACG
1 GCCCAATTGGTCGAACACGTGTCTCACACACG
* *
40712116 GCCCAATTGGTCGAACATGTGTCTCATACACG
1 GCCCAATTGGTCGAACACGTGTCTCACACACG
40712148 GC
1 GC
40712150 TTTGCTTATC
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.20, C:0.33, G:0.26, T:0.21
Consensus pattern (32 bp):
GCCCAATTGGTCGAACACGTGTCTCACACACG
Found at i:40714480 original size:4 final size:4
Alignment explanation
Indices: 40714471--40714505 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
40714461 TATTTGTTAA
*
40714471 ATAC ATAC ATAC ATAC ATAC ATAC ATGC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
40714506 TATATATAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.49, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:40714784 original size:24 final size:24
Alignment explanation
Indices: 40714726--40714784 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 24
40714716 CTTTATTTTT
40714726 TATATAATTTAAAATAAACTAAAA
1 TATATAATTTAAAATAAACTAAAA
40714750 TAT-TACTATTTAAAACT-AA-TAAAA
1 TATATA--ATTTAAAA-TAAACTAAAA
40714774 TATATAGATTT
1 TATATA-ATTT
40714785 TTAATATTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
23 2 0.07
24 15 0.50
25 12 0.40
26 1 0.03
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (24 bp):
TATATAATTTAAAATAAACTAAAA
Found at i:40716324 original size:31 final size:30
Alignment explanation
Indices: 40716236--40716324 Score: 72
Period size: 31 Copynumber: 2.9 Consensus size: 30
40716226 CTGTATATAT
* * *
40716236 AAATTTTAA-TTTGATGTAATTATACACGTA
1 AAATTTTAATTTTAATTTAA-TATATACGTA
* * * * *
40716266 AAACTCTAATTGTAATTTAAATGTATACTTA
1 AAATTTTAATTTTAATTT-AATATATACGTA
40716297 AAATTTTAATTTTAATTTAATCATATAC
1 AAATTTTAATTTTAATTTAAT-ATATAC
40716325 ATTTAAATAA
Statistics
Matches: 44, Mismatches: 12, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
30 10 0.23
31 32 0.73
32 2 0.05
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (30 bp):
AAATTTTAATTTTAATTTAATATATACGTA
Found at i:40716553 original size:3 final size:3
Alignment explanation
Indices: 40716545--40716574 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
40716535 ATTTATCCTG
40716545 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40716575 ATTTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:40719576 original size:20 final size:19
Alignment explanation
Indices: 40719527--40719577 Score: 57
Period size: 20 Copynumber: 2.6 Consensus size: 19
40719517 GCCCATTAAG
40719527 CCCCCCCAAAAAAACCTAA
1 CCCCCCCAAAAAAACCTAA
****
40719546 CCCAAAAAAAAAATACCTAA
1 CCCCCCCAAAAAA-ACCTAA
40719566 CCCCCCCAAAAA
1 CCCCCCCAAAAA
40719578 GCCAAGAAAC
Statistics
Matches: 23, Mismatches: 8, Indels: 1
0.72 0.25 0.03
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.53, C:0.41, G:0.00, T:0.06
Consensus pattern (19 bp):
CCCCCCCAAAAAAACCTAA
Found at i:40720754 original size:24 final size:24
Alignment explanation
Indices: 40720700--40720754 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 24
40720690 GTTGTTAATT
*
40720700 TATTACTTTATTTTGATATCTTTAT
1 TATTA-TTTATTTTGATATCTTTAA
*
40720725 TA-TATTTACTTTTTATAT-TTTAA
1 TATTATTTA-TTTTGATATCTTTAA
40720748 TATTATT
1 TATTATT
40720755 ATTATCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.38
24 14 0.54
25 2 0.08
ACGTcount: A:0.27, C:0.05, G:0.02, T:0.65
Consensus pattern (24 bp):
TATTATTTATTTTGATATCTTTAA
Found at i:40720831 original size:22 final size:23
Alignment explanation
Indices: 40720794--40720836 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
40720784 ATTTTATTTA
40720794 TTTATATATATATATGTATATGT
1 TTTATATATATATATGTATATGT
*
40720817 TTTA-ATATATTTATGTATAT
1 TTTATATATATATATGTATAT
40720837 ACTTATGTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (23 bp):
TTTATATATATATATGTATATGT
Found at i:40720961 original size:24 final size:25
Alignment explanation
Indices: 40720920--40720975 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
40720910 TATGTATATC
*
40720920 TATATATTTTTCGTATATAT-TATG-
1 TATATATTTTTCGAATAT-TGTATGT
40720944 TATATATGTTTTC-AATATTGTATGT
1 TATATAT-TTTTCGAATATTGTATGT
40720969 TATATAT
1 TATATAT
40720976 ATTATTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 15 0.54
25 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (25 bp):
TATATATTTTTCGAATATTGTATGT
Found at i:40721251 original size:24 final size:24
Alignment explanation
Indices: 40721224--40721269 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40721214 ATATTTTTTT
*
40721224 ATATCATCTTATGTACATATATAA
1 ATATCATCTTATATACATATATAA
* *
40721248 ATATTATGTTATATACATATAT
1 ATATCATCTTATATACATATAT
40721270 GTAATATGCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATCATCTTATATACATATATAA
Found at i:40721463 original size:37 final size:35
Alignment explanation
Indices: 40721398--40721467 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
40721388 TTATATATAG
40721398 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
40721435 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
40721468 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:40721602 original size:25 final size:24
Alignment explanation
Indices: 40721574--40721629 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
40721564 GTTATATTTT
*
40721574 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
40721599 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
40721622 CACTATTA
1 CACTATTA
40721630 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:40728607 original size:16 final size:17
Alignment explanation
Indices: 40728575--40728607 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40728565 TTTATAAGTA
*
40728575 TATATCAATCGTTTCAT
1 TATATCAATCATTTCAT
40728592 TATATCAAT-ATTTCAT
1 TATATCAATCATTTCAT
40728608 GTTTCATCAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.33, C:0.15, G:0.03, T:0.48
Consensus pattern (17 bp):
TATATCAATCATTTCAT
Found at i:40728953 original size:46 final size:46
Alignment explanation
Indices: 40728893--40729158 Score: 343
Period size: 46 Copynumber: 6.0 Consensus size: 46
40728883 TTTGACATGA
* * * * * *
40728893 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
** * * *
40728939 TGCCATGGTATCTTTCAACCATGGTCTTATTCTTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
* *
40728985 TGCGATGGTATCTTTCAACCATGGTCTTACACATCTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
40729031 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
40729077 TGCCATGGTATCTTTCAACCATGGTCTT--ACA---C--A-CAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
40729115 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
40729159 AGAGCACACT
Statistics
Matches: 196, Mismatches: 15, Indels: 18
0.86 0.07 0.08
Matches are distributed among these distances:
38 33 0.17
39 1 0.01
40 3 0.02
41 1 0.01
43 1 0.01
44 3 0.02
45 5 0.03
46 149 0.76
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:40729123 original size:38 final size:38
Alignment explanation
Indices: 40729072--40729147 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
40729062 CATTTCATAT
40729072 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
40729110 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
1 CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
40729148 TTTCATATCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (38 bp):
CAGGTTGCCATGGTATCTTTCAACCATGGTCTTACACA
Found at i:40737388 original size:73 final size:73
Alignment explanation
Indices: 40737296--40738576 Score: 970
Period size: 74 Copynumber: 16.8 Consensus size: 73
40737286 TCAATTTTTG
* *
40737296 TTCAATTTATGTTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
40737361 GAGGTATT
66 GAGGTAAT
* * *
40737369 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGGCACGCT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
40737434 GAGGT-AT
66 GAGGTAAT
* * **
40737441 TGTCAATTTTTGTGTTTCAATCTATTTTTCAAAAATCAACTCATATTACGAGAAATGAGTTGAGC
1 T-TCAA---------TT---TCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
40737506 CTCAGGACACGCTGAGGTAAT
53 CTCAGGACACGCTGAGGTAAT
* * *
40737527 CTCAATTTCTGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGG-CACGT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGC
40737591 TGAGGTAAT
65 TGAGGTAAT
* * ** *** * ** * * * * *
40737600 TTCAATTCCTGCTTTTCAATTTGTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAG-T
1 TTCAATTTCTGTTTTTCAA-----A--AATCAACTCATAT-TGC-GAGA--G-GTGAGTTGAGCC
* ** * * * *
40737664 TGAGCCTCAGGAC--ACGCTGAG
54 TCAG-GACACG-CTGA-GGTAAT
* * ** *
40737685 GT-AATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAG
1 TTCAATTTC--TGT-T-TT-TC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG
* *
40737749 ACATGCTGAGGTATT
59 ACACGCTGAGGTAAT
* * * *
40737764 TTCAATTTTTGTCTTTCAAAAAATCAACTCATACTGCGAGATGTGAGTTGAGCCTCAAGG-CACG
1 TTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACG
*
40737828 TTGAGGTAAT
64 CTGAGGTAAT
* * * * ** * * * * * *
40737838 TTCAATTTCCGCTTCTCAATTTATATTTTTCAA-AAAAATTCAACTCATATTGCGAGAGGTGAGT
1 TTCAATTTCTGTTTTTCAA---A-A---ATCAACTCATATT--GC-GAGA--G-GTGAGTTGAG-
40737902 TGAACCTCAGGACACGCTGAGGTAAT
52 ----CCTCAGGACACGCTGAGGTAAT
* ** * *
40737928 TTCAATTTCTG-TTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATG
1 TTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACG
*
40737992 CTGAGGTATT
64 CTGAGGTAAT
* * *
40738002 TTCAATTTTTGTCTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
1 TTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
40738067 TGAGGTAAT
65 TGAGGTAAT
** **
40738076 TTCAATTTCTGTTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGC
1 TTCAATTTCTGTT-TTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
40738141 TGAGGTAAT
65 TGAGGTAAT
* ** * *
40738150 TTCAATTTCTG-TTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
40738214 GAGGTATT
66 GAGGTAAT
*
40738222 TTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGAC
1 TTCAATTTCTGTTTTTC-----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGAC
40738287 ACGCTGAGGTAAT
61 ACGCTGAGGTAAT
* * * * *
40738300 TTCAATTTCTG-TTTTCAAAAATTAACTCATATTGCAAGAGGTGAGTTAAGCTTCGGGACACGCT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
40738364 GAGGTAAT
66 GAGGTAAT
* * ** * *
40738372 TTCAATTTCTG-TTTTCAAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTT
1 TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
*
40738436 GAGGTATT
66 GAGGTAAT
*
40738444 TTCAATTTCTG-TTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTCCACA
1 TTCAATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACA
* *
40738507 TGCTGAGGTATT
62 CGCTGAGGTAAT
* *
40738519 TTCAATTTCTGTCTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTCAATTTCTGTTTTTCAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
40738577 ATCACACACT
Statistics
Matches: 956, Mismatches: 172, Indels: 156
0.74 0.13 0.12
Matches are distributed among these distances:
72 196 0.21
73 181 0.19
74 217 0.23
75 38 0.04
76 40 0.04
77 7 0.01
78 64 0.07
79 23 0.02
80 19 0.02
81 2 0.00
82 10 0.01
83 4 0.00
84 19 0.02
85 87 0.09
86 4 0.00
87 2 0.00
88 3 0.00
89 9 0.01
90 27 0.03
91 4 0.00
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (73 bp):
TTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCT
GAGGTAAT
Found at i:40737720 original size:74 final size:73
Alignment explanation
Indices: 40737633--40738576 Score: 1036
Period size: 74 Copynumber: 12.6 Consensus size: 73
40737623 TATTTTTCAA
40737633 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
40737698 CTGTTGTC
66 CTGTTTTC
** * * *
40737706 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
40737771 TTTGTCTTTC
65 TCTGT-TTTC
* * *
40737781 AAAAAATCAACTCATACTGCGAGATGTGAGTTGAGCCTCAAGG-CACGTTGAGGTAATTTCAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGACACGCTGAGGTAATTTCAATT
* *
40737845 TCCGCTTCTC
65 TCTG-TTTTC
** ** * * * * * *
40737855 AATTTATATTTTTCAA-AAAAATTCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGC
1 AA---A-A--AATCAACTCATATT--GC-GAGA--G-GTGAGTTGAG-----CCTCAGGACACGC
*
40737919 TGAGGTAATTTCAATTTCTGTTGTC
49 TGAGGTAATTTCAATTTCTGTTTTC
** * * *
40737944 AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATT
*
40738009 TTTGTCTTTC
65 TCTGT-TTTC
*
40738019 AAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
*
40738084 CTGTTGTTA
66 CTGTT-TTC
**
40738093 AAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
40738158 CTGTTTTC
66 CTGTTTTC
* ** * * *
40738166 -AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
40738230 CTGTTTTTC
66 CTG-TTTTC
*
40738239 AAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
1 ----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
40738304 ATTTCTGTTTTC
62 ATTTCTGTTTTC
* * * * *
40738316 -AAAAATTAACTCATATTGCAAGAGGTGAGTTAAGCTTCGGGACACGCTGAGGTAATTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
40738380 CTGTTTTC
66 CTGTTTTC
* * ** * * *
40738388 -AAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
40738452 CTGTTTTC
66 CTGTTTTC
* * *
40738460 AAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTCCACATGCTGAGGTATTTTCAA
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAATTTCAA
40738524 TTTCTGTCTTTC
63 TTTCTGT-TTTC
* *
40738536 AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
40738577 ATCACACACT
Statistics
Matches: 734, Mismatches: 99, Indels: 71
0.81 0.11 0.08
Matches are distributed among these distances:
72 192 0.26
73 41 0.06
74 285 0.39
75 34 0.05
76 40 0.05
77 7 0.01
78 61 0.08
79 10 0.01
80 4 0.01
81 1 0.00
82 4 0.01
83 1 0.00
84 4 0.01
85 12 0.02
86 1 0.00
87 1 0.00
89 7 0.01
90 29 0.04
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTT
CTGTTTTC
Found at i:40737844 original size:238 final size:220
Alignment explanation
Indices: 40737613--40738576 Score: 1312
Period size: 238 Copynumber: 4.3 Consensus size: 220
40737603 AATTCCTGCT
* *
40737613 TTTCAATTTGTATTTTTCAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTCAATTTCTGTTTTTC-AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACA
40737678 CGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
65 CGCTGAGGTAATTTCAATTTCTGTTGTC--AAAAATCAACTCATATTGCGAGAAATGAGTTGAGC
* * *
40737743 CTCAAGACATGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAATCAACTCATACTGCGAGATGT
128 CTCAAGACATGCTGAGGTATTTTCAATTTCTGT-TTTCAAAAAATCAACTCATATTGCGAGAGGT
*
40737808 GAGTTGAGCCTCAAGG-CACGTTGAGGTAA
192 GAGTTGAGCCTC-AGGACACGCTGAGGTAA
*
40737837 TTTCAATTTCCGCTTCTCAATTTATATTTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGT
1 TTTCAA-------TT-TC------TGTTTTTCAAAAAAA-TCAACTCATATTGCGAGAGGTGAGT
*
40737902 TGAACCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAAATCAACTCATATTGCGA
51 TGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTC--AAAAATCAACTCATATTGCGA
*
40737967 GAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTTTGTCTTTCAAAAAATCAACTC
114 GAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTCAATTTCTGT-TTTCAAAAAATCAACTC
*
40738032 ATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
178 ATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAA
* **
40738075 TTTCAATTTCTGTTGTT-AAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* *
40738139 GCTGAGGTAATTTCAATTTCTGTTTTCAAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTC
66 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
*
40738204 AAGACATGCTGAGGTATTTTCAATTTCTGTTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGG
131 AAGACATGCTGAGGTATTTTCAATTTCTG-TTTTC----AAAAAATCAACTCATATTGCGAGAGG
40738269 TGAGTTGAGCCTCAGGACACGCTGAGGTAA
191 TGAGTTGAGCCTCAGGACACGCTGAGGTAA
* * * * *
40738299 TTTCAATTTCTG-TTTTC--AAAAATTAACTCATATTGCAAGAGGTGAGTTAAGCTTCGGGACAC
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
* * *
40738361 GCTGAGGTAATTTCAATTTCTGTTTTCAAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTC
66 GCTGAGGTAATTTCAATTTCTGTTGTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
* * *
40738426 AAGACACGTTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGT
131 AAGACATGCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGT
* *
40738491 TGAGCCTC-GGTCCACATGCTGAGGTAT
196 TGAGCCTCAGG---ACACGCTGAGGTAA
* * *
40738518 TTTCAATTTCTGTCTTTC-AAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
40738577 ATCACACACT
Statistics
Matches: 678, Mismatches: 35, Indels: 57
0.88 0.05 0.07
Matches are distributed among these distances:
216 2 0.00
217 37 0.05
219 24 0.04
220 73 0.11
221 41 0.06
222 192 0.28
223 10 0.01
224 77 0.11
230 2 0.00
231 4 0.01
232 1 0.00
237 10 0.01
238 205 0.30
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (220 bp):
TTTCAATTTCTGTTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACAC
GCTGAGGTAATTTCAATTTCTGTTGTCAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTC
AAGACATGCTGAGGTATTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGT
TGAGCCTCAGGACACGCTGAGGTAA
Found at i:40738216 original size:72 final size:73
Alignment explanation
Indices: 40737864--40738576 Score: 948
Period size: 72 Copynumber: 9.6 Consensus size: 73
40737854 CAATTTATAT
*
40737864 TTTTCAAAAAAATTCAACTCATATTGCGAGAGGTGAGTTGAACCTCAGGACACGCTGAGGTAATT
1 TTTTC-AAAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATT
40737929 TCAATTTCTG
64 TCAATTTCTG
* ** * * *
40737939 TTGTCAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTT
1 TTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
*
40738004 CAATTTTTG
65 CAATTTCTG
*
40738013 TCTTTCAAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 T-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
40738078 CAATTTCTG
65 CAATTTCTG
* **
40738087 TTGTTAAAAAAATCAACTCATATTGCGAGAAATGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
1 TT-TTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTT
40738152 CAATTTCTG
65 CAATTTCTG
* ** * * *
40738161 TTTTC-AAAATTCAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACATGCTGAGGTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
40738225 AATTTCTG
66 AATTTCTG
*
40738233 TTTTTCAAAAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
1 -TTTTC----AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTA
40738298 ATTTCAATTTCTG
61 ATTTCAATTTCTG
* * * * *
40738311 TTTTC-AAAAATTAACTCATATTGCAAGAGGTGAGTTAAGCTTCGGGACACGCTGAGGTAATTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
40738375 AATTTCTG
66 AATTTCTG
* * ** * * *
40738383 TTTTC-AAAATTTAACTCATATTGCGAGAAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTC
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
40738447 AATTTCTG
66 AATTTCTG
* * *
40738455 TTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTCCACATGCTGAGGTATT
1 TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTAAT
40738519 TTCAATTTCTG
63 TTCAATTTCTG
* *
40738530 TCTTTCAAAAAGTCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 T-TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
40738577 ATCACACACT
Statistics
Matches: 565, Mismatches: 59, Indels: 26
0.87 0.09 0.04
Matches are distributed among these distances:
72 192 0.34
73 41 0.07
74 187 0.33
75 39 0.07
76 40 0.07
77 6 0.01
78 60 0.11
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTC
AATTTCTG
Found at i:40740689 original size:27 final size:23
Alignment explanation
Indices: 40740649--40740715 Score: 64
Period size: 27 Copynumber: 2.7 Consensus size: 23
40740639 TCATGATTAC
*
40740649 TATATATTAGTGTATATTTTATTTA
1 TATATATTA-TGTATATGTT-TTTA
40740674 TTTATATATATATGTATATGTTTTTA
1 --TATATAT-TATGTATATGTTTTTA
40740700 -ATATATTTATGTATAT
1 TATATA-TTATGTATAT
40740716 ACTTATGTAG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
23 14 0.38
24 1 0.03
26 4 0.11
27 16 0.43
28 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (23 bp):
TATATATTATGTATATGTTTTTA
Found at i:40740840 original size:24 final size:25
Alignment explanation
Indices: 40740799--40740854 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 25
40740789 TATGTATATC
*
40740799 TATATATTTTTCGTATATAT-TATG-
1 TATATATTTTTCGAATAT-TGTATGT
40740823 TATATATGTTTTC-AATATTGTATGT
1 TATATAT-TTTTCGAATATTGTATGT
40740848 TATATAT
1 TATATAT
40740855 ATTATTGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 1 0.04
24 15 0.54
25 12 0.43
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (25 bp):
TATATATTTTTCGAATATTGTATGT
Found at i:40740909 original size:10 final size:11
Alignment explanation
Indices: 40740867--40740917 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
40740857 TATTGTGTAT
40740867 ATATTTTA-AC
1 ATATTTTATAC
40740877 ATTATTAGTTATAC
1 A-TATT--TTATAC
*
40740891 ATCTTTTATAC
1 ATATTTTATAC
40740902 -TATTTTATAC
1 ATATTTTATAC
40740912 ATATTT
1 ATATTT
40740918 CTAATATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
10 10 0.29
11 15 0.44
13 6 0.18
14 3 0.09
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.55
Consensus pattern (11 bp):
ATATTTTATAC
Found at i:40741345 original size:37 final size:35
Alignment explanation
Indices: 40741280--40741349 Score: 81
Period size: 37 Copynumber: 1.9 Consensus size: 35
40741270 TTATATATAG
40741280 TATTATTTTCATACATTATCATATTTATTATTATACC
1 TATTATTTTCATA-ATTATCATATTTATT-TTATACC
40741317 TATTATTTTCACT-ATTATCACT-TATTATTTTAT
1 TATTATTTTCA-TAATTATCA-TAT-TTATTTTAT
40741350 TTTAATATTA
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
36 12 0.40
37 17 0.57
38 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.00, T:0.57
Consensus pattern (35 bp):
TATTATTTTCATAATTATCATATTTATTTTATACC
Found at i:40741485 original size:25 final size:24
Alignment explanation
Indices: 40741457--40741512 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
40741447 GTTATATTTT
*
40741457 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
40741482 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
40741505 CACTATTA
1 CACTATTA
40741513 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:40744364 original size:28 final size:28
Alignment explanation
Indices: 40744332--40744546 Score: 306
Period size: 28 Copynumber: 7.7 Consensus size: 28
40744322 ACTTGATATT
40744332 TCGCACACTAAGTGCCATAC-CAAATGTC
1 TCGCACACTAAGTGCCATACTC-AATGTC
* *
40744360 TCGCACACTAAGTGTCATATTCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
*
40744388 TCGCACACTAAGTGCCATACTCAACGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
*
40744416 TTGCACACTAAGTGCCATACTCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* *
40744444 TCTCACACTAAGTGCCATACTCAATGTA
1 TCGCACACTAAGTGCCATACTCAATGTC
40744472 TCGCACACTAAGTGCCATACTCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
* ***
40744500 TTGCACACTAAGTGTTGTACTCAATGTC
1 TCGCACACTAAGTGCCATACTCAATGTC
**
40744528 TCATACACTAAGTGCCATA
1 TCGCACACTAAGTGCCATA
40744547 TATAGTCGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
28 163 0.99
29 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.27
Consensus pattern (28 bp):
TCGCACACTAAGTGCCATACTCAATGTC
Found at i:40744592 original size:40 final size:40
Alignment explanation
Indices: 40744532--40744622 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
40744522 AATGTCTCAT
*
40744532 ACACTAAGTGCCATATATAGTCGAAGCTATCTTAAATCGC
1 ACACTAAGTGCCATATATAGTCAAAGCTATCTTAAATCGC
* *
40744572 ACACAAAGTGCCGTATATAGTCAAAGCTATCTTAAATCGC
1 ACACTAAGTGCCATATATAGTCAAAGCTATCTTAAATCGC
40744612 ACACTAAGTGC
1 ACACTAAGTGC
40744623 TAAACATAGC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.25
Consensus pattern (40 bp):
ACACTAAGTGCCATATATAGTCAAAGCTATCTTAAATCGC
Found at i:40745787 original size:10 final size:10
Alignment explanation
Indices: 40745768--40745817 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
40745758 TTAAATTCTA
40745768 AAAGATAAAT
1 AAAGATAAAT
40745778 ATAA-ATAAAT
1 A-AAGATAAAT
*
40745788 AAAGATAATT
1 AAAGATAAAT
40745798 AAAGATAAAT
1 AAAGATAAAT
40745808 GAAA-ATAAAT
1 -AAAGATAAAT
40745818 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40748968 original size:21 final size:21
Alignment explanation
Indices: 40748928--40748968 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40748918 TGGGGATGAT
* *
40748928 GAGCCGTGCGACGGAGAGGAG
1 GAGCCGTGCGACGAAAAGGAG
*
40748949 GAGCCGTGCGATGAAAAGGA
1 GAGCCGTGCGACGAAAAGGA
40748969 AGAAGAGGAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.46, T:0.07
Consensus pattern (21 bp):
GAGCCGTGCGACGAAAAGGAG
Found at i:40749437 original size:7 final size:6
Alignment explanation
Indices: 40749415--40749456 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
40749405 AAGAAGAGAT
*
40749415 AAAAT- AAAATA AAAATGA AAAATAA AAAATA AAAGTA AAAAT
1 AAAATA AAAATA AAAAT-A AAAAT-A AAAATA AAAATA AAAAT
40749457 TGGGTTGCCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
5 5 0.16
6 15 0.47
7 12 0.38
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:40749438 original size:13 final size:12
Alignment explanation
Indices: 40749415--40749456 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
40749405 AAGAAGAGAT
40749415 AAAAT-AAAATA
1 AAAATAAAAATA
40749426 AAAATGAAAAATAA
1 AAAAT-AAAAAT-A
*
40749440 AAAATAAAAGTA
1 AAAATAAAAATA
40749452 AAAAT
1 AAAAT
40749457 TGGGTTGCCT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
11 5 0.19
12 6 0.22
13 10 0.37
14 6 0.22
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.17
Consensus pattern (12 bp):
AAAATAAAAATA
Found at i:40755832 original size:10 final size:10
Alignment explanation
Indices: 40755813--40755862 Score: 59
Period size: 10 Copynumber: 5.0 Consensus size: 10
40755803 TTAAATTTTA
40755813 AAAGATAAAT
1 AAAGATAAAT
40755823 ACAA-ATAAAT
1 A-AAGATAAAT
*
40755833 AAAGATAATT
1 AAAGATAAAT
40755843 AAAGATAAAT
1 AAAGATAAAT
40755853 GAAA-ATAAAT
1 -AAAGATAAAT
40755863 CCTAAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
9 2 0.06
10 28 0.80
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.08, T:0.22
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:40761827 original size:21 final size:21
Alignment explanation
Indices: 40761801--40761843 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
40761791 TTAAAGTGTC
40761801 TTAGCTACTACACGTTTTAAA
1 TTAGCTACTACACGTTTTAAA
*
40761822 TTAGCTCCTACACGTTTTAAA
1 TTAGCTACTACACGTTTTAAA
40761843 T
1 T
40761844 GTGTCCTAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.21, G:0.09, T:0.40
Consensus pattern (21 bp):
TTAGCTACTACACGTTTTAAA
Found at i:40765264 original size:19 final size:20
Alignment explanation
Indices: 40765223--40765266 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
40765213 GTGAGAGTGC
*
40765223 AAAAGAAAAGAAAACCAAGA
1 AAAAGAAAAGAAAAACAAGA
* *
40765243 AAAAGAAAGGAAAAATAA-A
1 AAAAGAAAAGAAAAACAAGA
40765262 AAAAG
1 AAAAG
40765267 GGAATGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (20 bp):
AAAAGAAAAGAAAAACAAGA
Found at i:40768443 original size:27 final size:27
Alignment explanation
Indices: 40768421--40768489 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
40768411 TTTTAATGCT
*
40768421 TGTTTTTAATATGTCATAGTTAATACA
1 TGTTATTAATATGTCATAGTTAATACA
* * *
40768448 TGTTATTAATTTGTCTTAGTCTATTACA
1 TGTTATTAATATGTCATAGT-TAATACA
* *
40768476 TATTTTTAATATGT
1 TGTTATTAATATGT
40768490 TCTAGCTTCA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 17 0.50
28 17 0.50
ACGTcount: A:0.29, C:0.07, G:0.10, T:0.54
Consensus pattern (27 bp):
TGTTATTAATATGTCATAGTTAATACA
Found at i:40768484 original size:28 final size:27
Alignment explanation
Indices: 40768423--40768489 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 27
40768413 TTAATGCTTG
*
40768423 TTTTTAATATGTCATAGTTAATACATG
1 TTTTTAATATGTCATAGTTAATACATA
* * * *
40768450 TTATTAATTTGTCTTAGTCTATTACATA
1 TTTTTAATATGTCATAGT-TAATACATA
40768478 TTTTTAATATGT
1 TTTTTAATATGT
40768490 TCTAGCTTCA
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
27 15 0.47
28 17 0.53
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.54
Consensus pattern (27 bp):
TTTTTAATATGTCATAGTTAATACATA
Found at i:40769963 original size:23 final size:23
Alignment explanation
Indices: 40769937--40770009 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
40769927 GCTCGATTCA
* *
40769937 TTTAGCGTTTGTGAACATGTTCG
1 TTTAGTGTTCGTGAACATGTTCG
*
40769960 TTTAGTGTTCGCGAACATGTTCG
1 TTTAGTGTTCGTGAACATGTTCG
* *
40769983 TTTAGTGTTCGTCAACATGTTCA
1 TTTAGTGTTCGTGAACATGTTCG
40770006 TTTA
1 TTTA
40770010 TATTCACGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.19, C:0.15, G:0.22, T:0.44
Consensus pattern (23 bp):
TTTAGTGTTCGTGAACATGTTCG
Found at i:40777094 original size:30 final size:31
Alignment explanation
Indices: 40777058--40777115 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
40777048 ACTTAACAAG
40777058 CAAATGCCTCTAAAATAATAA-AAAATTTAA
1 CAAATGCCTCTAAAATAATAACAAAATTTAA
*
40777088 CAAATGCCTTTAAAATAATAACAAAATT
1 CAAATGCCTCTAAAATAATAACAAAATT
40777116 AGTAATAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.55, C:0.14, G:0.03, T:0.28
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAACAAAATTTAA
Found at i:40780338 original size:29 final size:29
Alignment explanation
Indices: 40780279--40780338 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 29
40780269 TATGGTTTAA
* *
40780279 TGTGCAAGTGTATACATGAACTTTGATTT
1 TGTGCAAGTGTATACATGAAATTTGAATT
* * * *
40780308 TGTGCAATTTTATCCATGAAATTTTAATT
1 TGTGCAAGTGTATACATGAAATTTGAATT
40780337 TG
1 TG
40780339 ATCCAATTCT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (29 bp):
TGTGCAAGTGTATACATGAAATTTGAATT
Found at i:40787606 original size:21 final size:21
Alignment explanation
Indices: 40787577--40787617 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
40787567 TGCTGGACAG
*
40787577 GAGCCGGAATGGGAGTGTTTA
1 GAGCCGGAATGAGAGTGTTTA
*
40787598 GAGCTGGAATGAGAGTGTTT
1 GAGCCGGAATGAGAGTGTTT
40787618 GGTTGCTGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.07, G:0.41, T:0.27
Consensus pattern (21 bp):
GAGCCGGAATGAGAGTGTTTA
Found at i:40794151 original size:21 final size:20
Alignment explanation
Indices: 40794110--40794152 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
40794100 TTTAAAAGTT
40794110 AAAAATTATTAAAATTCTAA
1 AAAAATTATTAAAATTCTAA
* * *
40794130 AAAACATTTTTAATATTTTAA
1 AAAA-ATTATTAAAATTCTAA
40794151 AA
1 AA
40794153 TTTTAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATTATTAAAATTCTAA
Found at i:40795937 original size:26 final size:25
Alignment explanation
Indices: 40795895--40795943 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
40795885 TTTTATAAAT
40795895 AAAAAATTTATTTATTAAAAACAAA
1 AAAAAATTTATTTATTAAAAACAAA
*
40795920 AAAAAATATT-TTTAATTATAAACA
1 AAAAAAT-TTATTT-ATTAAAAACA
40795944 TTAATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 10 0.48
26 11 0.52
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (25 bp):
AAAAAATTTATTTATTAAAAACAAA
Found at i:40798236 original size:45 final size:45
Alignment explanation
Indices: 40798169--40798466 Score: 257
Period size: 45 Copynumber: 6.6 Consensus size: 45
40798159 TTAAAGGATA
* * * *
40798169 CCATAGCGTCTTTCAACCATGGTCTTATTAATTTCCGACAT-GATG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAG-TG
*
40798214 CCATAGTGTCTTTCAACTATGGTCTTTTTCATTTCCG-TCAT-GTTG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGAT-ATAG-TG
* * * *
40798259 -CATAATATCTTTCAATTATAGTCTTATTCATTTCC-AGTATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGA-TATAGTG
* * * * *
40798303 TCATGGTGTCTTTCAACTATGATCTTATTCATTTTCGGTATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAGTG
* ** * *
40798348 TCATAGTGTCTTTCAACTATGGTAGTATTCATTTCTGGTATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAGTG
* * * *
40798393 CCAAAGTTTCTTTCAACTATGGTTTTATTCATTTTC-AGTATAGTG
1 CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGA-TATAGTG
* * * * *
40798438 TCACAATGTCTTTTAACTATGGTTTTATT
1 CCATAGTGTCTTTCAACTATGGTCTTATT
40798467 TGTTTTTCAA
Statistics
Matches: 208, Mismatches: 38, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
44 34 0.16
45 174 0.84
ACGTcount: A:0.23, C:0.17, G:0.15, T:0.45
Consensus pattern (45 bp):
CCATAGTGTCTTTCAACTATGGTCTTATTCATTTCCGATATAGTG
Found at i:40798466 original size:135 final size:134
Alignment explanation
Indices: 40798215--40798458 Score: 314
Period size: 135 Copynumber: 1.8 Consensus size: 134
40798205 GACATGATGC
** * *
40798215 CATAGTGTCTTTCAACTATGGTCTTTTTCATTTCCGTCATGTTGCATAATATCTTTCAATTATAG
1 CATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCATGTTGCATAATATCTTTCAACTATAG
***
40798280 TCTTATTCATTTCCAGTATAGTGTCATGGTGTCTTTCAACTATGATCTTATTCATTTTCGGTATA
66 TCTTATTCATTTCCAGTATAGTGTCACAATGTCTTTCAACTATGATCTTATTCATTTTCGGTATA
40798345 GTGT
131 GTGT
* *
40798349 CATAGTGTCTTTCAACTATGGTAGTATTCATTTCTGGT-ATAG-TGCCA-AAGTTTCTTTCAACT
1 CATAGTGTCTTTCAACTATGGTAGTATTCATTTC-CGTCAT-GTTG-CATAA-TATCTTTCAACT
* * * *
40798411 ATGGTTTTATTCATTTTCAGTATAGTGTCACAATGTCTTTTAACTATG
62 ATAGTCTTATTCATTTCCAGTATAGTGTCACAATGTCTTTCAACTATG
40798459 GTTTTATTTG
Statistics
Matches: 93, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
134 37 0.40
135 56 0.60
ACGTcount: A:0.23, C:0.16, G:0.15, T:0.46
Consensus pattern (134 bp):
CATAGTGTCTTTCAACTATGGTAGTATTCATTTCCGTCATGTTGCATAATATCTTTCAACTATAG
TCTTATTCATTTCCAGTATAGTGTCACAATGTCTTTCAACTATGATCTTATTCATTTTCGGTATA
GTGT
Found at i:40801355 original size:73 final size:73
Alignment explanation
Indices: 40801236--40801437 Score: 260
Period size: 73 Copynumber: 2.8 Consensus size: 73
40801226 CAGACATATT
** ** *
40801236 AATTGCTTGTCTGAGCTGAACATATAATCATGTCAAGTTACCCGTTTGGGCTAAACCTTTATGTC
1 AATTGCTCATCTGAGCTGAACATATAATCATGTCAAGTTACCCGTTTGGGCTAAAAATTTATATC
*
40801301 ACTACATC
66 AATACATC
*
40801309 AATTGCTCATCTGAGCTGACCATATAATCATGTCAAGTTACCCGTTTGGGCTAAAAATTTATATC
1 AATTGCTCATCTGAGCTGAACATATAATCATGTCAAGTTACCCGTTTGGGCTAAAAATTTATATC
40801374 AATACATC
66 AATACATC
* * * ** * * **
40801382 AGTTGCTCATTTGAACTGAACATATAATTGTGTCAGGTTACCTGTCCGGGCTAAAA
1 AATTGCTCATCTGAGCTGAACATATAATCATGTCAAGTTACCCGTTTGGGCTAAAA
40801438 CTTAATGTAG
Statistics
Matches: 112, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
73 112 1.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (73 bp):
AATTGCTCATCTGAGCTGAACATATAATCATGTCAAGTTACCCGTTTGGGCTAAAAATTTATATC
AATACATC
Found at i:40805386 original size:8 final size:8
Alignment explanation
Indices: 40805363--40805409 Score: 60
Period size: 9 Copynumber: 5.8 Consensus size: 8
40805353 TAGCTAATTG
40805363 TTTTATTT
1 TTTTATTT
40805371 TATTTATTT
1 T-TTTATTT
*
40805380 CTTTA-TT
1 TTTTATTT
40805387 TTTTATTT
1 TTTTATTT
40805395 TTTTACTTT
1 TTTTA-TTT
40805404 TTTTAT
1 TTTTAT
40805410 AAATTAATCA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
7 6 0.18
8 13 0.38
9 15 0.44
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (8 bp):
TTTTATTT
Found at i:40805392 original size:19 final size:19
Alignment explanation
Indices: 40805363--40805407 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
40805353 TAGCTAATTG
*
40805363 TTTTATTTTATTTATTT-C
1 TTTTTTTTTATTTATTTAC
*
40805381 TTTATTTTTTATTTTTTTAC
1 TTT-TTTTTTATTTATTTAC
40805401 TTTTTTT
1 TTTTTTT
40805408 ATAAATTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 3 0.13
19 16 0.70
20 4 0.17
ACGTcount: A:0.13, C:0.04, G:0.00, T:0.82
Consensus pattern (19 bp):
TTTTTTTTTATTTATTTAC
Found at i:40805393 original size:15 final size:16
Alignment explanation
Indices: 40805373--40805406 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
40805363 TTTTATTTTA
40805373 TTTATTTCTTTA-TTT
1 TTTATTTCTTTACTTT
*
40805388 TTTATTTTTTTACTTT
1 TTTATTTCTTTACTTT
40805404 TTT
1 TTT
40805407 TATAAATTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.12, C:0.06, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTATTTCTTTACTTT
Found at i:40805393 original size:24 final size:24
Alignment explanation
Indices: 40805363--40805409 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
40805353 TAGCTAATTG
40805363 TTTTATTTTATTTA-TTTCTTTATT
1 TTTTATTTT-TTTACTTTCTTTATT
*
40805387 TTTTATTTTTTTACTTTTTTTAT
1 TTTTATTTTTTTACTTTCTTTAT
40805410 AAATTAATCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.81
Consensus pattern (24 bp):
TTTTATTTTTTTACTTTCTTTATT
Found at i:40813235 original size:62 final size:62
Alignment explanation
Indices: 40813094--40813244 Score: 198
Period size: 62 Copynumber: 2.4 Consensus size: 62
40813084 CACACAGTCG
* * * *
40813094 GGGCACACGCCCATGTCCCTAGTCGTGTGGCTTTGCGCCACAGATAGTGAGTTACACAGCTT
1 GGGCACACGCCCATGTCCCTGGCCGTGTGGCTTTGCACCACAAATAGTGAGTTACACAGCTT
* * *
40813156 GGGCACACAG-TCGTGTCCCTGGCCGTGTGG-TCTTGTACCACAAATAGTGAGTTACACAGCTT
1 GGGCACAC-GCCCATGTCCCTGGCCGTGTGGCT-TTGCACCACAAATAGTGAGTTACACAGCTT
*
40813218 GGGCACACGCCCCTGTCCCTGGCCGTG
1 GGGCACACGCCCATGTCCCTGGCCGTG
40813245 AGAACTCTGC
Statistics
Matches: 77, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
61 2 0.03
62 74 0.96
63 1 0.01
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.23
Consensus pattern (62 bp):
GGGCACACGCCCATGTCCCTGGCCGTGTGGCTTTGCACCACAAATAGTGAGTTACACAGCTT
Found at i:40816459 original size:21 final size:21
Alignment explanation
Indices: 40816433--40816594 Score: 180
Period size: 21 Copynumber: 7.7 Consensus size: 21
40816423 AGCTCGAAAC
* * *
40816433 CTGAACAGAAGCTCATAAAAG
1 CTGAACAAAAGCTCGTAAGAG
* *
40816454 CTGAACAAAAACTCATAAGAG
1 CTGAACAAAAGCTCGTAAGAG
* *
40816475 TTGAACAGAAGCTCGTAAGAG
1 CTGAACAAAAGCTCGTAAGAG
* * *
40816496 CTAAACAAAAACTCATAAGAG
1 CTGAACAAAAGCTCGTAAGAG
* *
40816517 TTGAACAAAAGCTTGTAAGAG
1 CTGAACAAAAGCTCGTAAGAG
* *
40816538 CTAAACAAAAGCTTGTAAGAG
1 CTGAACAAAAGCTCGTAAGAG
* *
40816559 CTAAACAAAAGCTTGTAAGAG
1 CTGAACAAAAGCTCGTAAGAG
40816580 CTGAACAAAAGCTCG
1 CTGAACAAAAGCTCG
40816595 AAAGTGTTAA
Statistics
Matches: 120, Mismatches: 21, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 120 1.00
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (21 bp):
CTGAACAAAAGCTCGTAAGAG
Found at i:40816606 original size:42 final size:42
Alignment explanation
Indices: 40816452--40816612 Score: 189
Period size: 42 Copynumber: 3.8 Consensus size: 42
40816442 AGCTCATAAA
* * * *
40816452 AGCTGAACAAAAACTCATAAGAGTTGAACAGAAGCTCGTAAG
1 AGCTAAACAAAAACTCATAAGAGTTAAACAAAAGCTTGTAAG
*
40816494 AGCTAAACAAAAACTCATAAGAGTTGAACAAAAGCTTGTAAG
1 AGCTAAACAAAAACTCATAAGAGTTAAACAAAAGCTTGTAAG
* ** *
40816536 AGCTAAACAAAAGCTTGTAAGAGCTAAACAAAAGCTTGTAAG
1 AGCTAAACAAAAACTCATAAGAGTTAAACAAAAGCTTGTAAG
* * *
40816578 AGCTGAACAAAAGCTCGA-AAGTGTTAAACAGAAAG
1 AGCTAAACAAAAACTC-ATAAGAGTTAAACA-AAAG
40816613 TAAAACACGA
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
42 100 0.96
43 4 0.04
ACGTcount: A:0.48, C:0.15, G:0.20, T:0.17
Consensus pattern (42 bp):
AGCTAAACAAAAACTCATAAGAGTTAAACAAAAGCTTGTAAG
Found at i:40816606 original size:63 final size:63
Alignment explanation
Indices: 40816444--40816612 Score: 196
Period size: 63 Copynumber: 2.7 Consensus size: 63
40816434 TGAACAGAAG
* * * *
40816444 CTCATAAAAGCTGAACAAAAACTC-ATAAGAGTTGAACAGAAGCTCGTAAGAGCTAAACAAAAA
1 CTCATAAGAGCTGAACAAAAGCTCGA-AAGAGTTAAACAAAAGCTCGTAAGAGCTAAACAAAAA
* * * * * *
40816507 CTCATAAGAGTTGAACAAAAGCTTGTAAGAGCTAAACAAAAGCTTGTAAGAGCTAAACAAAAG
1 CTCATAAGAGCTGAACAAAAGCTCGAAAGAGTTAAACAAAAGCTCGTAAGAGCTAAACAAAAA
** *
40816570 CTTGTAAGAGCTGAACAAAAGCTCGAAAGTGTTAAACAGAAAG
1 CTCATAAGAGCTGAACAAAAGCTCGAAAGAGTTAAACA-AAAG
40816613 TAAAACACGA
Statistics
Matches: 87, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
63 83 0.95
64 4 0.05
ACGTcount: A:0.48, C:0.15, G:0.19, T:0.18
Consensus pattern (63 bp):
CTCATAAGAGCTGAACAAAAGCTCGAAAGAGTTAAACAAAAGCTCGTAAGAGCTAAACAAAAA
Found at i:40816607 original size:21 final size:21
Alignment explanation
Indices: 40816436--40816612 Score: 165
Period size: 21 Copynumber: 8.4 Consensus size: 21
40816426 TCGAAACCTG
* * * *
40816436 AACAGAAGCTCATAAAAGCTG
1 AACAAAAGCTCGTAAGAGCTA
* * * *
40816457 AACAAAAACTCATAAGAGTTG
1 AACAAAAGCTCGTAAGAGCTA
*
40816478 AACAGAAGCTCGTAAGAGCTA
1 AACAAAAGCTCGTAAGAGCTA
* * * *
40816499 AACAAAAACTCATAAGAGTTG
1 AACAAAAGCTCGTAAGAGCTA
*
40816520 AACAAAAGCTTGTAAGAGCTA
1 AACAAAAGCTCGTAAGAGCTA
*
40816541 AACAAAAGCTTGTAAGAGCTA
1 AACAAAAGCTCGTAAGAGCTA
* *
40816562 AACAAAAGCTTGTAAGAGCTG
1 AACAAAAGCTCGTAAGAGCTA
* * *
40816583 AACAAAAGCTCGAAAGTGTTA
1 AACAAAAGCTCGTAAGAGCTA
40816604 AACAGAAAG
1 AACA-AAAG
40816613 TAAAACACGA
Statistics
Matches: 130, Mismatches: 25, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
21 126 0.97
22 4 0.03
ACGTcount: A:0.49, C:0.15, G:0.19, T:0.17
Consensus pattern (21 bp):
AACAAAAGCTCGTAAGAGCTA
Found at i:40818127 original size:6 final size:6
Alignment explanation
Indices: 40818116--40818153 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
40818106 GTTTTAATGT
40818116 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
40818154 TTTGAAAAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.16, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
TTAGGG
Found at i:40818175 original size:28 final size:28
Alignment explanation
Indices: 40818140--40818215 Score: 109
Period size: 28 Copynumber: 2.7 Consensus size: 28
40818130 AGGGTTAGGG
40818140 TTAGGG-TTAGGGTTTTTGAAAAAATAAA
1 TTAGGGTTTAGGGTTTTT-AAAAAATAAA
* *
40818168 TTAGGGTTTATGGTTTTTAAAAATTAAA
1 TTAGGGTTTAGGGTTTTTAAAAAATAAA
*
40818196 TTTGGGTTTAGGGTTTTTAA
1 TTAGGGTTTAGGGTTTTTAA
40818216 TAGGTAAGTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
28 33 0.77
29 10 0.23
ACGTcount: A:0.32, C:0.00, G:0.24, T:0.45
Consensus pattern (28 bp):
TTAGGGTTTAGGGTTTTTAAAAAATAAA
Found at i:40818511 original size:126 final size:126
Alignment explanation
Indices: 40818281--40818710 Score: 596
Period size: 126 Copynumber: 3.4 Consensus size: 126
40818271 TTTTTGTATA
* * * * *
40818281 GTCAACAAAAGTACTG-AAAAAGCTCTCAACTAGACACTCTTTTTGTACATTAGTTTCTTAAAAA
1 GTCAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTAGTTTATGAAAAA
* * *
40818345 GTAATTTTGAGAAGATAGTTCTAAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
66 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
* * * * **
40818406 GTCAACAAAAGTACTGAAAAAAGCTTCTAGCTGGACACTCTTTTTGTATAGTAAATTATGAAAAA
1 GTCAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTAGTTTATGAAAAA
* * * *
40818471 ATAATTTTGAGAAGATGGTTCTGAAAAAGTAGG-TCAAAAA-ATGCTTCAAGTAAGATACACT
66 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACAT--TTCAAGTAGGATGCACT
* * * * *
40818532 GTCAGCAAAAGTATTGAAAAAAGCTCCCAGCTGGACACTCTTTTTGAACAGTAGTTTTTGAAAAA
1 GTCAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTAGTTTATGAAAAA
40818597 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
66 ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
* *
40818658 ATCAGCAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTA
1 GTCAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTA
40818711 CATTCTGCTT
Statistics
Matches: 265, Mismatches: 35, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
124 2 0.01
125 22 0.08
126 233 0.88
127 6 0.02
128 2 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (126 bp):
GTCAACAAAAGTACTGAAAAAAGCTCCCAGCTAGACACTCTTTTTGTACAGTAGTTTATGAAAAA
ATAATTTTGAGAAGATGGTTCTGAAAAAATAGGTTGAAAAACATTTCAAGTAGGATGCACT
Found at i:40818807 original size:25 final size:25
Alignment explanation
Indices: 40818778--40818850 Score: 85
Period size: 25 Copynumber: 2.9 Consensus size: 25
40818768 TTACATCAAG
40818778 AGAAATTGAAGAAGTTTAGAAGGAT
1 AGAAATTGAAGAAGTTTAGAAGGAT
* * * *
40818803 AGAAATTAAAGAAGTTCAAAAGAAT
1 AGAAATTGAAGAAGTTTAGAAGGAT
*
40818828 AAAAATTGAAGAA-TTTGAGAAGG
1 AGAAATTGAAGAAGTTT-AGAAGG
40818851 TATAAGTTGA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
24 2 0.05
25 36 0.95
ACGTcount: A:0.53, C:0.01, G:0.23, T:0.22
Consensus pattern (25 bp):
AGAAATTGAAGAAGTTTAGAAGGAT
Found at i:40821947 original size:60 final size:59
Alignment explanation
Indices: 40821881--40822008 Score: 161
Period size: 60 Copynumber: 2.2 Consensus size: 59
40821871 TGTATTACCT
* *
40821881 TATTCAAAAGAACTTCTATTTTATTAAAT-ATGACAAAATATACAAATAATTTATACAAA-A
1 TATTCAAAACAACTTCTATTTTATTAAATGAT-AC--AATATAAAAATAATTTATACAAATA
* * *
40821941 TATTCAAAACAACTTTTGTTTTATTAAATGATACAATATAAAAATAATTTGTACAAATA
1 TATTCAAAACAACTTCTATTTTATTAAATGATACAATATAAAAATAATTTATACAAATA
*
40822000 TATTAAAAA
1 TATTCAAAA
40822009 AATAAATGCA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 21 0.35
59 9 0.15
60 28 0.47
61 2 0.03
ACGTcount: A:0.51, C:0.09, G:0.04, T:0.37
Consensus pattern (59 bp):
TATTCAAAACAACTTCTATTTTATTAAATGATACAATATAAAAATAATTTATACAAATA
Found at i:40825633 original size:21 final size:20
Alignment explanation
Indices: 40825600--40825641 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 20
40825590 GATTCAAAAT
40825600 AACTCTAAAGGTGCAATGTC
1 AACTCTAAAGGTGCAATGTC
*
40825620 AACTCCTAGAGGTGCAATGTC
1 AACT-CTAAAGGTGCAATGTC
40825641 A
1 A
40825642 TCTGAATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AACTCTAAAGGTGCAATGTC
Found at i:40832430 original size:32 final size:32
Alignment explanation
Indices: 40832389--40832451 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
40832379 TCAAAACCTT
*
40832389 TCATCGTAACATTATCATATTTGGCCATAACG
1 TCATCGTAACATTATCATATTCGGCCATAACG
*
40832421 TCATTGTAACATTATCATATTCGGCCATAAC
1 TCATCGTAACATTATCATATTCGGCCATAAC
40832452 ATCTGGGCTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (32 bp):
TCATCGTAACATTATCATATTCGGCCATAACG
Found at i:40832710 original size:33 final size:33
Alignment explanation
Indices: 40832670--40832737 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
40832660 GGTTTATGTT
*
40832670 TTTTCAATTTGTACAAGCTCGAGGGAGTTTTTG
1 TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
*
40832703 TTTTCAATTTGTACAAACTTGAGGGAGTTTTTG
1 TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
40832736 TT
1 TT
40832738 CCCTATGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.22, C:0.10, G:0.22, T:0.46
Consensus pattern (33 bp):
TTTTCAATTTGTACAAACTCGAGGGAGTTTTTG
Found at i:40834720 original size:41 final size:41
Alignment explanation
Indices: 40834579--40834940 Score: 455
Period size: 41 Copynumber: 8.9 Consensus size: 41
40834569 TATAAAACAT
* * **
40834579 AGAGCAATAGTGGCGTTTTTGGTAAAACATCGCTAAAAA-C
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* *
40834619 AGAGCAATAGCGACGTTTTTGGTAAAACGCCGCTAAAAA-C
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
*
40834659 AGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * *
40834700 AGAGCAATAGAGGTGCTTTTGGTAAAATGCCGCTAAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCT-AAAAACC
*
40834742 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAGAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * *
40834783 AGAGCATTAGCAGCGCTTTTGGTAAAA---CGCTAGAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * * * *
40834821 GGTGTATTAGCGGCGCTTTTGGTAAAACGCCGTTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
*
40834862 AGAGCATTAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
* * * * *
40834903 GGAGTATTAGCGGCACTTTTGATAAAACGCCGCTAAAA
1 AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA
40834941 GTCATATAAC
Statistics
Matches: 288, Mismatches: 29, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
38 34 0.12
40 74 0.26
41 142 0.49
42 38 0.13
ACGTcount: A:0.34, C:0.20, G:0.24, T:0.22
Consensus pattern (41 bp):
AGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACC
Found at i:40834884 original size:120 final size:119
Alignment explanation
Indices: 40834579--40834932 Score: 422
Period size: 120 Copynumber: 2.9 Consensus size: 119
40834569 TATAAAACAT
* * ** * * *
40834579 AGAGCAATAGTGGCGTTTTTGGTAAAACATCGCTAAAAA-CAGAGCAATAGCGACGTTTTTGGTA
1 AGAGCAATAGAGGCGCTTTTGGTAAAACGCCGTTAAAAACCAGAGCAATAGCGGCGCTTTTGGTA
* * *
40834643 AAACGCCGCTAAAAACAGAGCAATAGCGGCGTTTTTGGTAAAACGCCGCTAAAAACC
66 AAACGCCGCTAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAA---CGCTAAAAACC
* * *
40834700 AGAGCAATAGAGGTGCTTTTGGTAAAATGCCGCTAAAAAACCAGAGCAATAGCGGCGCTTTTGGT
1 AGAGCAATAGAGGCGCTTTTGGTAAAACGCCG-TTAAAAACCAGAGCAATAGCGGCGCTTTTGGT
* *
40834765 AAAACGCCGCTAGAAACCAGAGCATTAGCAGCGCTTTTGGTAAAACGCTAGAAACC
65 AAAACGCCGCTA-AAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTAAAAACC
* * * * * *
40834821 GGTGTATTAGCGGCGCTTTTGGTAAAACGCCGTTAAAAACCAGAGCATTAGCGGCGCTTTTGGTA
1 AGAGCAATAGAGGCGCTTTTGGTAAAACGCCGTTAAAAACCAGAGCAATAGCGGCGCTTTTGGTA
* * * *
40834886 AAACGCCGCTAAAAACCGGAGTATTAGCGGCACTTTTGATAAAACGC
66 AAACGCCGCT-AAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGC
40834933 CGCTAAAAGT
Statistics
Matches: 200, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
120 71 0.35
121 62 0.31
122 5 0.03
123 34 0.17
124 28 0.14
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (119 bp):
AGAGCAATAGAGGCGCTTTTGGTAAAACGCCGTTAAAAACCAGAGCAATAGCGGCGCTTTTGGTA
AAACGCCGCTAAAACCAGAGCATTAGCGGCGCTTTTGGTAAAACGCTAAAAACC
Found at i:40835029 original size:23 final size:22
Alignment explanation
Indices: 40834982--40835029 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
40834972 AAAAAATCAT
* *
40834982 AAACACTAATCTATAATCCTTA
1 AAACACTAAACTATAAACCTTA
*
40835004 AAACACTAAACTCCTAAACCTTA
1 AAACACTAAACT-ATAAACCTTA
40835027 AAA
1 AAA
40835030 AATCTTAAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (22 bp):
AAACACTAAACTATAAACCTTA
Found at i:40835374 original size:14 final size:14
Alignment explanation
Indices: 40835352--40835399 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
40835342 TTAATTATCA
*
40835352 TTATAGTTTAAGGT
1 TTATGGTTTAAGGT
*
40835366 TTATGGTTTAAGCT
1 TTATGGTTTAAGGT
*
40835380 ATATGGGTTTAAGGT
1 TTAT-GGTTTAAGGT
40835395 TTATG
1 TTATG
40835400 AGTTAACTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.25, C:0.02, G:0.25, T:0.48
Consensus pattern (14 bp):
TTATGGTTTAAGGT
Found at i:40835399 original size:15 final size:15
Alignment explanation
Indices: 40835357--40835399 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
40835347 TATCATTATA
40835357 GTTTAAGGTTTAT-G
1 GTTTAAGGTTTATGG
* *
40835371 GTTTAAGCTATATGG
1 GTTTAAGGTTTATGG
40835386 GTTTAAGGTTTATG
1 GTTTAAGGTTTATG
40835400 AGTTAACTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
14 11 0.46
15 13 0.54
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (15 bp):
GTTTAAGGTTTATGG
Found at i:40835457 original size:21 final size:21
Alignment explanation
Indices: 40835424--40835487 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
40835414 TAAAGGTGGT
*
40835424 TTAAGGGT-TGGGGTTTAAGG
1 TTAAGGGTGAGGGGTTTAAGG
*
40835444 TT-AGGTGTTAGGGG-TTAAGGG
1 TTAAGG-GTGAGGGGTTTAA-GG
*
40835465 TTAAGGGTGAGGGGTTTATGG
1 TTAAGGGTGAGGGGTTTAAGG
40835486 TT
1 TT
40835488 TAGGATTTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.08
20 8 0.22
21 19 0.53
22 6 0.17
ACGTcount: A:0.19, C:0.00, G:0.45, T:0.36
Consensus pattern (21 bp):
TTAAGGGTGAGGGGTTTAAGG
Found at i:40835520 original size:14 final size:14
Alignment explanation
Indices: 40835476--40835539 Score: 60
Period size: 14 Copynumber: 4.5 Consensus size: 14
40835466 TAAGGGTGAG
40835476 GGGTTT-ATGGTTTA
1 GGGTTTAAT-GTTTA
*
40835490 GGATTT-ATGTTTTA
1 GGGTTTAATG-TTTA
40835504 GGGTTTAATGTTTA
1 GGGTTTAATGTTTA
* *
40835518 GGGATTAAGAGTTTA
1 GGGTTTAA-TGTTTA
40835533 GGGTTTA
1 GGGTTTA
40835540 GATTAGTTAG
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
13 1 0.02
14 27 0.64
15 14 0.33
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (14 bp):
GGGTTTAATGTTTA
Found at i:40835540 original size:7 final size:7
Alignment explanation
Indices: 40835421--40835540 Score: 50
Period size: 7 Copynumber: 17.0 Consensus size: 7
40835411 GTTTAAAGGT
40835421 GGTTTAAG
1 GGTTT-AG
*
40835429 GG-TTGG
1 GGTTTAG
*
40835435 GGTTTAA
1 GGTTTAG
40835442 GG-TTA-
1 GGTTTAG
40835447 GGTGTTAGG
1 GGT-TTA-G
*
40835456 GGTTAAG
1 GGTTTAG
*
40835463 GGTTAAG
1 GGTTTAG
*
40835470 GG-TGAGG
1 GGTTTA-G
*
40835477 GGTTTAT
1 GGTTTAG
40835484 GGTTTAG
1 GGTTTAG
* *
40835491 GATTTAT
1 GGTTTAG
*
40835498 GTTTTAG
1 GGTTTAG
*
40835505 GGTTTAA
1 GGTTTAG
*
40835512 TGTTTAG
1 GGTTTAG
*
40835519 GGATTAAG
1 GG-TTTAG
*
40835527 AGTTTAG
1 GGTTTAG
40835534 GGTTTAG
1 GGTTTAG
40835541 ATTAGTTAGT
Statistics
Matches: 83, Mismatches: 21, Indels: 17
0.69 0.17 0.14
Matches are distributed among these distances:
5 2 0.02
6 8 0.10
7 59 0.71
8 11 0.13
9 3 0.04
ACGTcount: A:0.21, C:0.00, G:0.39, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:40835714 original size:22 final size:22
Alignment explanation
Indices: 40835689--40835731 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
40835679 GAGTTATTAT
40835689 TTTAAGGCTTATGGA-TTATGGG
1 TTTAAGGCTTAT-GATTTATGGG
* *
40835711 TTTAGGGTTTATGATTTATGG
1 TTTAAGGCTTATGATTTATGG
40835732 TTATGTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.21, C:0.02, G:0.30, T:0.47
Consensus pattern (22 bp):
TTTAAGGCTTATGATTTATGGG
Found at i:40836115 original size:8 final size:8
Alignment explanation
Indices: 40836102--40836144 Score: 61
Period size: 8 Copynumber: 5.5 Consensus size: 8
40836092 TAATTCTTCA
40836102 AAAAAATT
1 AAAAAATT
40836110 AAAAAATT
1 AAAAAATT
40836118 -AAAAATT
1 AAAAAATT
*
40836125 AAAAACTT
1 AAAAAATT
*
40836133 AAAAACTT
1 AAAAAATT
40836141 AAAA
1 AAAA
40836145 TTTTAATATT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
7 7 0.21
8 26 0.79
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (8 bp):
AAAAAATT
Found at i:40836123 original size:15 final size:15
Alignment explanation
Indices: 40836103--40836144 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
40836093 AATTCTTCAA
40836103 AAAAATTAAAAAATT
1 AAAAATTAAAAAATT
*
40836118 AAAAATTAAAAACTT
1 AAAAATTAAAAAATT
40836133 AAAAACTTAAAA
1 AAAAA-TTAAAA
40836145 TTTTAATATT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATTAAAAAATT
Found at i:40838845 original size:17 final size:17
Alignment explanation
Indices: 40838823--40838859 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
40838813 CTTGATCCTC
40838823 TGTTAAATGTAATTAAA
1 TGTTAAATGTAATTAAA
40838840 TGTTAAATGTAATTAAA
1 TGTTAAATGTAATTAAA
40838857 TGT
1 TGT
40838860 AATTAATATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (17 bp):
TGTTAAATGTAATTAAA
Found at i:40838874 original size:10 final size:10
Alignment explanation
Indices: 40838825--40838871 Score: 64
Period size: 10 Copynumber: 4.9 Consensus size: 10
40838815 TGATCCTCTG
40838825 TTAAATGTAA
1 TTAAATGTAA
40838835 TTAAATG---
1 TTAAATGTAA
40838842 TTAAATGTAA
1 TTAAATGTAA
40838852 TTAAATGTAA
1 TTAAATGTAA
40838862 TTAATATGTA
1 TTAA-ATGTA
40838872 TTACAATTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
7 7 0.21
10 21 0.64
11 5 0.15
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (10 bp):
TTAAATGTAA
Found at i:40838881 original size:16 final size:15
Alignment explanation
Indices: 40838860--40838889 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40838850 AATTAAATGT
40838860 AATTAATATGTATTAC
1 AATTAATATG-ATTAC
40838876 AATTAATATGATTA
1 AATTAATATGATTA
40838890 ACTTAATCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (15 bp):
AATTAATATGATTAC
Found at i:40838882 original size:20 final size:20
Alignment explanation
Indices: 40838825--40838871 Score: 64
Period size: 17 Copynumber: 2.5 Consensus size: 20
40838815 TGATCCTCTG
40838825 TTAAATGTAATTAAATG---
1 TTAAATGTAATTAAATGTAA
40838842 TTAAATGTAATTAAATGTAA
1 TTAAATGTAATTAAATGTAA
40838862 TTAATATGTA
1 TTAA-ATGTA
40838872 TTACAATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 17 0.65
20 4 0.15
21 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.43
Consensus pattern (20 bp):
TTAAATGTAATTAAATGTAA
Found at i:40841633 original size:43 final size:43
Alignment explanation
Indices: 40841559--40841657 Score: 155
Period size: 43 Copynumber: 2.3 Consensus size: 43
40841549 AATTTTTATG
40841559 ACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTGA
1 ACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCT-A
* * *
40841603 A-CTTTAGCGGCGTTTGTGGGATAAGTGCCGCTAAAGGTCCTA
1 ACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTA
40841645 ACCTTTAGCGGCG
1 ACCTTTAGCGGCG
40841658 CATCTATAGA
Statistics
Matches: 51, Mismatches: 3, Indels: 3
0.89 0.05 0.05
Matches are distributed among these distances:
42 2 0.04
43 48 0.94
44 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.25
Consensus pattern (43 bp):
ACCTTTAGCGGCGTTTGTGGAAAAAGCGCCGCTAAAGGTCCTA
Found at i:40843674 original size:2 final size:2
Alignment explanation
Indices: 40843667--40843692 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40843657 TAATAAACAA
40843667 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
40843693 GCTACACCAA
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:40851922 original size:15 final size:14
Alignment explanation
Indices: 40851898--40851928 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
40851888 ATTTAGTTAA
40851898 TACCTTAATCGAAT
1 TACCTTAATCGAAT
40851912 TACCATTAATCGAAT
1 TACC-TTAATCGAAT
40851927 TA
1 TA
40851929 ACTGAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (14 bp):
TACCTTAATCGAAT
Found at i:40853925 original size:12 final size:12
Alignment explanation
Indices: 40853908--40853934 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40853898 TTGTAAAAAT
40853908 AATATTAGATTA
1 AATATTAGATTA
40853920 AATATTAGATTA
1 AATATTAGATTA
40853932 AAT
1 AAT
40853935 TTAATACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (12 bp):
AATATTAGATTA
Found at i:40854078 original size:37 final size:37
Alignment explanation
Indices: 40854016--40854086 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
40854006 GATAATCACT
*
40854016 TTAATATTAAATTAATAAAATACTATTAAGATAAGTC
1 TTAATATTAAATTAATAAAATACTATTAAAATAAGTC
*
40854053 TTAA-ATTAAATTTAATATTAA-ACTATTAAAATAA
1 TTAATATTAAA-TTAATA-AAATACTATTAAAATAA
40854087 TACTATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 6 0.20
37 22 0.73
38 2 0.07
ACGTcount: A:0.54, C:0.04, G:0.03, T:0.39
Consensus pattern (37 bp):
TTAATATTAAATTAATAAAATACTATTAAAATAAGTC
Found at i:40860255 original size:30 final size:30
Alignment explanation
Indices: 40860220--40860277 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
40860210 AACAGGGGAC
* *
40860220 ACACGCCCATGTGGCTAGGCCGTGTGTCAG
1 ACACGCCCATATGGCCAGGCCGTGTGTCAG
*
40860250 ACACGCCCGTATGGCCAGGCCGTGTGTC
1 ACACGCCCATATGGCCAGGCCGTGTGTC
40860278 TCACACAGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.19
Consensus pattern (30 bp):
ACACGCCCATATGGCCAGGCCGTGTGTCAG
Found at i:40863383 original size:20 final size:18
Alignment explanation
Indices: 40863333--40863384 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 18
40863323 CTTGTGGATA
40863333 AATATTAAATTAA-ACTT
1 AATATTAAATTAATACTT
40863350 AATATTAAGA-TAATCACTTT
1 AATATTAA-ATTAAT-AC-TT
40863370 AATATTAAATTAATA
1 AATATTAAATTAATA
40863385 AAATACTACT
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
17 11 0.37
18 1 0.03
19 4 0.13
20 14 0.47
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (18 bp):
AATATTAAATTAATACTT
Found at i:40874655 original size:27 final size:27
Alignment explanation
Indices: 40874625--40874802 Score: 196
Period size: 27 Copynumber: 6.6 Consensus size: 27
40874615 ATATTGAGTC
* * *
40874625 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAAAT
*
40874652 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
*
40874679 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATCAAA-T
** ** *
40874707 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAAAT
* **
40874734 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAAAT
* *
40874761 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAATCAAAT
40874788 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40874803 GTATAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAAAT
Found at i:40874764 original size:82 final size:81
Alignment explanation
Indices: 40874646--40874801 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40874636 TGCTATATAA
* *
40874646 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40874711 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40874728 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40874792 CACTTAGTGC
65 CACTTAGTGC
40874802 TGTATAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40881756 original size:45 final size:45
Alignment explanation
Indices: 40881698--40881829 Score: 194
Period size: 45 Copynumber: 2.9 Consensus size: 45
40881688 AATCAAATAC
* * * *
40881698 GATGCCGATGTCCCAGATATGGTCTTACACGTAACCACATATATT
1 GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATATT
*
40881743 GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATTTATT
1 GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATATT
*
40881788 GATGCCAACGTCCCAGACGTGGTCTTACACG-AGAACACATAT
1 GATGCCAACGTCCCAGACATGGTCTTACACGTA-AACACATAT
40881830 TAGATCCTAT
Statistics
Matches: 79, Mismatches: 7, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
44 1 0.01
45 78 0.99
ACGTcount: A:0.30, C:0.27, G:0.18, T:0.25
Consensus pattern (45 bp):
GATGCCAACGTCCCAGACATGGTCTTACACGTAAACACATATATT
Found at i:40891316 original size:148 final size:148
Alignment explanation
Indices: 40891055--40891349 Score: 527
Period size: 148 Copynumber: 2.0 Consensus size: 148
40891045 GTACTGAGCT
* * *
40891055 GATTTCTTCTATAGTTGAAAAACATGGCTGGAAAATATTTTTCCTTCATCCCGGCGATGTTCTCA
1 GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
*
40891120 CAAAGGTTGTAATGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
66 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
40891185 GTATGGTTTACCTGAGGC
131 GTATGGTTTACCTGAGGC
*
40891203 GATTTCTTCTATAGTTGAAAAACATGACTGGCAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
1 GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
*
40891268 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTTTCCAGATGATGTACTCCATCAACGCACA
66 CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
*
40891333 GTATGGTTTACTTGAGG
131 GTATGGTTTACCTGAGG
40891350 TCTAGATGAA
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
148 140 1.00
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (148 bp):
GATTTCTTCTATAGTTGAAAAACATGACTGGAAAATATTTTGCCTTCATCCCGGCAATGTTCTCA
CAAAGGTTGTAAAGGAATTTTATGCCCACTTAACCTCTCCAGATGATGTACTCCATCAACGCACA
GTATGGTTTACCTGAGGC
Found at i:40892661 original size:18 final size:18
Alignment explanation
Indices: 40892638--40892673 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
40892628 TTGGGGGTGT
40892638 GTTGTACTTATTGTATGC
1 GTTGTACTTATTGTATGC
40892656 GTTGTACTTATTGTATGC
1 GTTGTACTTATTGTATGC
40892674 ATTAGATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.11, G:0.22, T:0.50
Consensus pattern (18 bp):
GTTGTACTTATTGTATGC
Found at i:40896412 original size:12 final size:12
Alignment explanation
Indices: 40896395--40896419 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40896385 TTTTAATAAT
40896395 ATTTAATATTAA
1 ATTTAATATTAA
40896407 ATTTAATATTAA
1 ATTTAATATTAA
40896419 A
1 A
40896420 GTGATTAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTTAATATTAA
Found at i:40899052 original size:17 final size:19
Alignment explanation
Indices: 40899025--40899059 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
40899015 TTCTCCTCCT
40899025 CTAAGGGGAAAC-AGAAAG
1 CTAAGGGGAAACAAGAAAG
40899043 CTAA-GGGAAACAAGAAA
1 CTAAGGGGAAACAAGAAA
40899060 CTGACTAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.11, G:0.29, T:0.06
Consensus pattern (19 bp):
CTAAGGGGAAACAAGAAAG
Found at i:40900486 original size:20 final size:21
Alignment explanation
Indices: 40900449--40900488 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40900439 AAGGGCTATT
40900449 TTGTAAAGTTTGTAAAATAAG
1 TTGTAAAGTTTGTAAAATAAG
*
40900470 TTGTAAA-TTTGTGAAATAA
1 TTGTAAAGTTTGTAAAATAA
40900489 TTAAAATTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.40
Consensus pattern (21 bp):
TTGTAAAGTTTGTAAAATAAG
Found at i:40901265 original size:48 final size:46
Alignment explanation
Indices: 40901152--40901269 Score: 166
Period size: 46 Copynumber: 2.5 Consensus size: 46
40901142 TATGTGTGCT
* *
40901152 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAAAGCC
*
40901198 AGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATAT-ACAAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-A-ATATGA-AAGCC
*
40901246 AGTGTAAGACATGCCTGGGACATG
1 AGTGTAAGACATGTCTGGGACATG
40901270 GCGTCAACTT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
46 33 0.51
47 2 0.03
48 30 0.46
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACAATATGAAAGCC
Found at i:40901397 original size:143 final size:145
Alignment explanation
Indices: 40901189--40901457 Score: 379
Period size: 143 Copynumber: 1.9 Consensus size: 145
40901179 CGGCCACATT
40901189 ATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCCAGTGTAAG
1 ATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCCAGTGTAAG
* * *
40901254 A-CATGCCTGGGACATGGCGTCAAC-TTGTTGTG-T-GTCAGTGTAAGACC-TATCTGGGACACG
66 ATC-TGCCTGGGACATGGCATCAACTTTGATGTGCTAGCCAGTGTAAGACCATATCTGGGACACG
40901314 GCATTGACACCGATAG
130 GCATTGACACCGATAG
* **
40901330 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGTATCGGCCTCGAGATATGA-AAGTTAGTGT
1 ATGAGAGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATAT-ACAAGCCAGTGT
* * *
40901394 AAGATCTGTCTGGGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCTGGGAC
63 AAGATCTGCCTGGGACATGGCATCAACTTTGATGTGCTAGCCAGTGTAAGACCATATCTGGGAC
40901458 TTGGCATCGG
Statistics
Matches: 111, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
141 18 0.16
142 14 0.13
143 47 0.42
144 9 0.08
145 1 0.01
146 13 0.12
147 9 0.08
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (145 bp):
ATGAGAGCCAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGATATACAAGCCAGTGTAAG
ATCTGCCTGGGACATGGCATCAACTTTGATGTGCTAGCCAGTGTAAGACCATATCTGGGACACGG
CATTGACACCGATAG
Found at i:40901407 original size:99 final size:97
Alignment explanation
Indices: 40901290--40901468 Score: 241
Period size: 97 Copynumber: 1.8 Consensus size: 97
40901280 GTTGTGTGTC
*
40901290 AGTGTAAGACCTATCTGGGACACGGCATTGACACCGATAGATGAGAGCCAGTGTAAGACCATGTC
1 AGTGTAAGACCTATCTGGGACACGGCATCGACACCGAT-G-TGAGAGCCAGTGTAAGACCATGTC
*
40901355 TGGGACATGGTATCGGCCTCGAGATATGAAAGTT
64 TGGGACATGGCATCGGCCTCGAGATATGAAAGTT
* * * *** **
40901389 AGTGTAAGATCTGTCTGGGACATGGCATCGACTTTGATGTGCTAGCCAGTGTAAGACCATGTCTG
1 AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATGTGAGAGCCAGTGTAAGACCATGTCTG
*
40901454 GGACTTGGCATCGGC
66 GGACATGGCATCGGC
40901469 ATCGTATCCC
Statistics
Matches: 69, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
97 37 0.54
98 1 0.01
99 31 0.45
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.25
Consensus pattern (97 bp):
AGTGTAAGACCTATCTGGGACACGGCATCGACACCGATGTGAGAGCCAGTGTAAGACCATGTCTG
GGACATGGCATCGGCCTCGAGATATGAAAGTT
Found at i:40901463 original size:48 final size:49
Alignment explanation
Indices: 40901152--40901466 Score: 210
Period size: 48 Copynumber: 6.6 Consensus size: 49
40901142 TATGTGTGCT
* * *
40901152 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-C-ACATTATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGA-TATGAAAGCC
*
40901198 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGATAT-ACAAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGAGATATGA-AAGCC
* * * * *** *
40901246 AGTGTAAGA-CATGCCTGGGACATGGCGTCAACT--TG-T-TGTGTGTC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGATATGAAAGCC
* * * * * * *
40901290 AGTGTAAGACC-TATCTGGGACACGGCATTGACACCGATAGATGAGAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGAC-TCGAGATATGAAAGCC
* * **
40901339 AGTGTAAGACCATGTCTGGGACATGGTATCGGCCTCGAGATATGAAAGTT
1 AGTGTAAGACCATGTCTGGGACATGGCATC-GACTCGAGATATGAAAGCC
* ** * **
40901389 AGTGTAAGATC-TGTCTGGGACATGGCATCGACT-TTGATGTGCTAGCC
1 AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGATATGAAAGCC
*
40901436 AGTGTAAGACCATGTCTGGGACTTGGCATCG
1 AGTGTAAGACCATGTCTGGGACATGGCATCG
40901467 GCATCGTATC
Statistics
Matches: 206, Mismatches: 48, Indels: 28
0.73 0.17 0.10
Matches are distributed among these distances:
44 27 0.13
45 2 0.01
46 29 0.14
47 20 0.10
48 53 0.26
49 39 0.19
50 34 0.17
51 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.30, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCGACTCGAGATATGAAAGCC
Found at i:40902889 original size:39 final size:39
Alignment explanation
Indices: 40902834--40902922 Score: 160
Period size: 39 Copynumber: 2.3 Consensus size: 39
40902824 GTTTAATGTT
*
40902834 TATGACGTGATTATGTTTGTTTGCCATTCTTGGTTGGTAA
1 TATGACATG-TTATGTTTGTTTGCCATTCTTGGTTGGTAA
40902874 TATGACATGTTATGTTTGTTTGCCATTCTTGGTTGGTAA
1 TATGACATGTTATGTTTGTTTGCCATTCTTGGTTGGTAA
40902913 TATGACATGT
1 TATGACATGT
40902923 GTGTTGGATG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 40 0.83
40 8 0.17
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (39 bp):
TATGACATGTTATGTTTGTTTGCCATTCTTGGTTGGTAA
Found at i:40904623 original size:56 final size:50
Alignment explanation
Indices: 40904509--40904629 Score: 149
Period size: 51 Copynumber: 2.4 Consensus size: 50
40904499 AGGATTAGAA
40904509 TTAATCATATTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
1 TTAAT-AT-TTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
* * * *
40904561 TAAATATTTAATATTAATATTAATAAAATATTATCTAA-ATAAATATTTAAT
1 TTAATATTTAATATTAA-ATTAATAAAATATTATC-AAGATAAAAAATAAAT
40904612 TT-A-ATTTAATATTAAATT
1 TTAATATTTAATATTAAATT
40904630 TGTTAAAGTA
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
48 3 0.05
49 12 0.19
50 11 0.18
51 30 0.48
52 6 0.10
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (50 bp):
TTAATATTTAATATTAAATTAATAAAATATTATCAAGATAAAAAATAAAT
Found at i:40918347 original size:30 final size:29
Alignment explanation
Indices: 40918293--40918352 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
40918283 TTCCCGAGCC
40918293 TAGGGGAAAAAGTGTAAATATGCAAAAGTT
1 TAGGGGAAAAAGTGTAAATATGC-AAAGTT
* *
40918323 TAGGGGAAAAA-TGTAATTTTTGCAAAGTT
1 TAGGGGAAAAAGTGTAA-ATATGCAAAGTT
40918352 T
1 T
40918353 GAGTAAAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.30
Consensus pattern (29 bp):
TAGGGGAAAAAGTGTAAATATGCAAAGTT
Found at i:40933700 original size:42 final size:40
Alignment explanation
Indices: 40933644--40933755 Score: 197
Period size: 42 Copynumber: 2.8 Consensus size: 40
40933634 GCTACTTGCT
40933644 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
40933684 CAAATGTGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
1 CAAA--TGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
*
40933726 CAAATGCCTTCGGGACTTAGCCCGGATATA
1 CAAATGCCTTCGGGACTTAGCCCGGTTATA
40933756 ACTCACAACC
Statistics
Matches: 69, Mismatches: 1, Indels: 4
0.93 0.01 0.05
Matches are distributed among these distances:
40 29 0.42
42 40 0.58
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTCGCA
Found at i:40947659 original size:54 final size:54
Alignment explanation
Indices: 40947567--40947674 Score: 162
Period size: 54 Copynumber: 2.0 Consensus size: 54
40947557 AAAGAGTTAG
* * * * *
40947567 AAGATAAATTTGGTGTTTCTTCGAAGTCTGACTAGCGTGCTTCCGTTCCTTCCT
1 AAGACAAATCTGGTGTTTCTTCAAAGTCTGACTAGCGTGCATCCATTCCTTCCT
*
40947621 AAGACAAATCTGGTGTTTCTTCAAAGTTTGACTAGCGTGCATCCATTCCTTCCT
1 AAGACAAATCTGGTGTTTCTTCAAAGTCTGACTAGCGTGCATCCATTCCTTCCT
40947675 TTTCCTTTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (54 bp):
AAGACAAATCTGGTGTTTCTTCAAAGTCTGACTAGCGTGCATCCATTCCTTCCT
Found at i:40948864 original size:3 final size:3
Alignment explanation
Indices: 40948856--40948881 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
40948846 TTATAAAAAT
40948856 ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC AT
40948882 GTTCTCAGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.35
Consensus pattern (3 bp):
ATC
Found at i:40954435 original size:49 final size:49
Alignment explanation
Indices: 40954380--40954600 Score: 215
Period size: 49 Copynumber: 4.6 Consensus size: 49
40954370 TGTGTGTGTC
* * *
40954380 AGTGTAAAACCTGTCTAGGACATGACATCGACACAGATAAGTGAGAGCC
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACACAGATAAGTGAGAGCT
* * *
40954429 AGTGTAAAACCTGTCTAGGACATGGCATCGGCCTCAAGAT-A-TGCA-AGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATC-GACAC-AGATAAGTG-AGAGCT
* * * *** *
40954478 AGTGTAAGACCTGTCTAGGACATGGCATCG--GC--TTGAG-GTTTGTT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACACAGATAAGTGAGAGCT
* *
40954522 AGTGTAAGACCTGTTTAGGACATGGCATCAACACAGATAAGTGAGAGCT
1 AGTGTAAGACCTGTCTAGGACATGGCATCGACACAGATAAGTGAGAGCT
*
40954571 AGTGTAAGACCTGTCTGGGACATGGCATCG
1 AGTGTAAGACCTGTCTAGGACATGGCATCG
40954601 GCCTTGACGT
Statistics
Matches: 139, Mismatches: 22, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
43 1 0.01
44 32 0.23
46 2 0.01
48 4 0.03
49 91 0.65
50 5 0.04
51 4 0.03
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.24
Consensus pattern (49 bp):
AGTGTAAGACCTGTCTAGGACATGGCATCGACACAGATAAGTGAGAGCT
Found at i:40954546 original size:93 final size:94
Alignment explanation
Indices: 40954429--40954607 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 94
40954419 AGTGAGAGCC
** *
40954429 AGTGTAAAACCTGTCTAGGACATGGCATCGGCCTCAAGAT-A-TGCA-AGCTAGTGTAAGACCTG
1 AGTGTAAAACCTGTCTAGGACATGGCATC-AACAC-AGATAAGTG-AGAGCTAGTGTAAGACCTG
40954491 TCTAGGACATGGCATCGG-CTTGAGGTTTGTT
63 TCTAGGACATGGCATCGGCCTTGAGGTTTGTT
* *
40954522 AGTGTAAGACCTGTTTAGGACATGGCATCAACACAGATAAGTGAGAGCTAGTGTAAGACCTGTCT
1 AGTGTAAAACCTGTCTAGGACATGGCATCAACACAGATAAGTGAGAGCTAGTGTAAGACCTGTCT
*
40954587 GGGACATGGCATCGGCCTTGA
66 AGGACATGGCATCGGCCTTGA
40954608 CGTATGTAAG
Statistics
Matches: 76, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
91 4 0.05
92 4 0.05
93 63 0.83
94 5 0.07
ACGTcount: A:0.27, C:0.19, G:0.28, T:0.25
Consensus pattern (94 bp):
AGTGTAAAACCTGTCTAGGACATGGCATCAACACAGATAAGTGAGAGCTAGTGTAAGACCTGTCT
AGGACATGGCATCGGCCTTGAGGTTTGTT
Found at i:40954624 original size:49 final size:46
Alignment explanation
Indices: 40954379--40954648 Score: 174
Period size: 49 Copynumber: 5.7 Consensus size: 46
40954369 ATGTGTGTGT
* * * * *
40954379 CAGTGTAAAACCTGTCTAGGACATGACATCGACACAGA-TAAGTGAGAG
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGGC-CTGAGTATGT-A-AG
* * *
40954427 CCAGTGTAAAACCTGTCTAGGACATGGCATCGGCCTCAAGATATGCAAG
1 -CAGTGTAAGACCTGTCTAGGACATGGCATCGGCCT-GAG-TATGTAAG
* *
40954476 CTAGTGTAAGACCTGTCTAGGACATGGCATCGGCTTGAGGTTTGT---
1 C-AGTGTAAGACCTGTCTAGGACATGGCATCGGCCTGA-GTATGTAAG
* * ** * *
40954521 TAGTGTAAGACCTGTTTAGGACATGGCATCAACACAGA-TAAGTGAGAG
1 CAGTGTAAGACCTGTCTAGGACATGGCATCGGC-CTGAGTATGT-A-AG
*
40954569 CTAGTGTAAGACCTGTCTGGGACATGGCATCGGCCTTGACGTATGTAAG
1 C-AGTGTAAGACCTGTCTAGGACATGGCATCGGCC-TGA-GTATGTAAG
** * *
40954618 TCAGTGTAA-TTCTATCTGGGACATGGCATCG
1 -CAGTGTAAGACCTGTCTAGGACATGGCATCG
40954649 ATTTAGATGT
Statistics
Matches: 176, Mismatches: 29, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
43 3 0.02
44 29 0.16
45 2 0.01
48 26 0.15
49 106 0.60
50 3 0.02
51 7 0.04
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (46 bp):
CAGTGTAAGACCTGTCTAGGACATGGCATCGGCCTGAGTATGTAAG
Found at i:40969872 original size:5 final size:5
Alignment explanation
Indices: 40969862--40969886 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
40969852 TATTGGGGTT
40969862 GACAG GACAG GACAG GACAG GACAG
1 GACAG GACAG GACAG GACAG GACAG
40969887 AAATGAGCCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.40, C:0.20, G:0.40, T:0.00
Consensus pattern (5 bp):
GACAG
Found at i:40982595 original size:20 final size:21
Alignment explanation
Indices: 40982570--40982609 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
40982560 TGTAACTTAG
40982570 AAAATTTATTTATGT-TTCGA
1 AAAATTTATTTATGTGTTCGA
*
40982590 AAAATTTTTTTATGTGTTCG
1 AAAATTTATTTATGTGTTCG
40982610 GTTTGGTCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.30, C:0.05, G:0.12, T:0.53
Consensus pattern (21 bp):
AAAATTTATTTATGTGTTCGA
Found at i:40983368 original size:17 final size:17
Alignment explanation
Indices: 40983348--40983382 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
40983338 CAAATGAAGC
40983348 CTCACTAACACCTCTAT
1 CTCACTAACACCTCTAT
40983365 CTCACTAACACCTCTAT
1 CTCACTAACACCTCTAT
40983382 C
1 C
40983383 AAGGCCACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (17 bp):
CTCACTAACACCTCTAT
Found at i:40984012 original size:10 final size:11
Alignment explanation
Indices: 40983992--40984024 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
40983982 AATATTTTGT
40983992 TTTTCTTTTTTC
1 TTTT-TTTTTTC
40984004 TTTTTTTTTTC
1 TTTTTTTTTTC
40984015 TTTTTTTTTT
1 TTTTTTTTTT
40984025 TTGAGGGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 17 0.81
12 4 0.19
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (11 bp):
TTTTTTTTTTC
Found at i:40984012 original size:18 final size:17
Alignment explanation
Indices: 40983986--40984026 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
40983976 GTACGTAATA
*
40983986 TTTTGTTTTTCTTTTTT
1 TTTTTTTTTTCTTTTTT
40984003 CTTTTTTTTTTCTTTTTT
1 -TTTTTTTTTTCTTTTTT
40984021 TTTTTT
1 TTTTTT
40984027 GAGGGGTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.00, C:0.07, G:0.02, T:0.90
Consensus pattern (17 bp):
TTTTTTTTTTCTTTTTT
Found at i:40984847 original size:17 final size:18
Alignment explanation
Indices: 40984814--40984847 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40984804 ATTGTAATCA
*
40984814 AAAATAAAAATTTCCCAC
1 AAAATAAAAATTACCCAC
40984832 AAAATAAAAA-TACCCA
1 AAAATAAAAATTACCCA
40984848 TTACCTTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.62, C:0.21, G:0.00, T:0.18
Consensus pattern (18 bp):
AAAATAAAAATTACCCAC
Found at i:40986149 original size:15 final size:15
Alignment explanation
Indices: 40986129--40986158 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40986119 ATTGAATTAA
40986129 TTTTATTTTTAAAAT
1 TTTTATTTTTAAAAT
40986144 TTTTATTTTTAAAAT
1 TTTTATTTTTAAAAT
40986159 AAATAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTATTTTTAAAAT
Found at i:40987308 original size:23 final size:21
Alignment explanation
Indices: 40987278--40987326 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
40987268 ATTTATTACA
*
40987278 GTTTTTAAATTAAGGTTTTAGT
1 GTTTTT-AATTAAGGGTTTAGT
*
40987300 GTTTATTAATTAGGGGTTTAGT
1 GTTT-TTAATTAAGGGTTTAGT
40987322 GTTTT
1 GTTTT
40987327 AGGGTTTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 21 0.88
23 2 0.08
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.55
Consensus pattern (21 bp):
GTTTTTAATTAAGGGTTTAGT
Found at i:40987320 original size:8 final size:8
Alignment explanation
Indices: 40987309--40987366 Score: 50
Period size: 8 Copynumber: 7.4 Consensus size: 8
40987299 TGTTTATTAA
*
40987309 TTAGGGGT
1 TTAGGGTT
*
40987317 TTAGTGTT
1 TTAGGGTT
40987325 TTAGGGTT
1 TTAGGGTT
40987333 TTA---TT
1 TTAGGGTT
*
40987338 ATTAGGCTT
1 -TTAGGGTT
40987347 TTAGGGTTT
1 TTAGGG-TT
40987356 TTAGGGTT
1 TTAGGGTT
40987364 TTA
1 TTA
40987367 AAGTTAGGGT
Statistics
Matches: 41, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 2 0.05
6 3 0.07
8 26 0.63
9 10 0.24
ACGTcount: A:0.16, C:0.02, G:0.29, T:0.53
Consensus pattern (8 bp):
TTAGGGTT
Found at i:40987350 original size:30 final size:31
Alignment explanation
Indices: 40987291--40987387 Score: 96
Period size: 30 Copynumber: 3.2 Consensus size: 31
40987281 TTTAAATTAA
* *
40987291 GGTTTTAGTG-TTTATTAATTAGGGGTTTAG
1 GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
* *
40987321 TGTTTTAGGGTTTTATT-ATTAGGCTTTTAG
1 GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
*
40987351 GGTTTTTAGGGTTTTA--AAGTTAGG-GTTTAT
1 GG-TTTTAGGGTTTTATTAA-TTAGGCGTTTAG
40987381 GGTTTTA
1 GGTTTTA
40987388 ATTGATTAAA
Statistics
Matches: 56, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
29 5 0.09
30 27 0.48
31 24 0.43
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.53
Consensus pattern (31 bp):
GGTTTTAGGGTTTTATTAATTAGGCGTTTAG
Found at i:40991016 original size:7 final size:7
Alignment explanation
Indices: 40991006--40991034 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
40990996 CAAAATTAAA
40991006 AATGTCC
1 AATGTCC
40991013 AATGTCC
1 AATGTCC
40991020 AATGTCC
1 AATGTCC
40991027 AA-GTCC
1 AATGTCC
40991033 AA
1 AA
40991035 CCAAAATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (7 bp):
AATGTCC
Found at i:40994077 original size:15 final size:15
Alignment explanation
Indices: 40994057--40994086 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
40994047 TTATGCATGC
*
40994057 AAAATATAAAAGACA
1 AAAATACAAAAGACA
40994072 AAAATACAAAAGACA
1 AAAATACAAAAGACA
40994087 TAATAGTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.10, G:0.07, T:0.10
Consensus pattern (15 bp):
AAAATACAAAAGACA
Done.