Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr5
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: 65570391
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1216948 characters in sequence are not A, C, G, or T
File 126 of 203
Found at i:40031962 original size:22 final size:20
Alignment explanation
Indices: 40031926--40031971 Score: 74
Period size: 22 Copynumber: 2.2 Consensus size: 20
40031916 ACAAATATGA
40031926 ATATAAATAAATAAATATTT
1 ATATAAATAAATAAATATTT
40031946 ATATAAAATAAAATAAATATTT
1 ATAT-AAAT-AAATAAATATTT
40031968 ATAT
1 ATAT
40031972 TTAGAATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 4 0.17
21 4 0.17
22 16 0.67
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATAAATAAATAAATATTT
Found at i:40032427 original size:20 final size:20
Alignment explanation
Indices: 40032399--40032437 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40032389 AGTCATTAAA
*
40032399 TCAATTTGATTAAAATCAAC
1 TCAAATTGATTAAAATCAAC
*
40032419 TCAAATTGATTAGAATCAA
1 TCAAATTGATTAAAATCAA
40032438 ATAAAATCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (20 bp):
TCAAATTGATTAAAATCAAC
Found at i:40032444 original size:20 final size:20
Alignment explanation
Indices: 40032404--40032444 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
40032394 TTAAATCAAT
* *
40032404 TTGATTAAAATCAACTCAAA
1 TTGATTAAAATCAAATAAAA
*
40032424 TTGATTAGAATCAAATAAAA
1 TTGATTAAAATCAAATAAAA
40032444 T
1 T
40032445 CAAGATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.51, C:0.10, G:0.07, T:0.32
Consensus pattern (20 bp):
TTGATTAAAATCAAATAAAA
Found at i:40033287 original size:377 final size:376
Alignment explanation
Indices: 40032436--40034198 Score: 2196
Period size: 377 Copynumber: 4.7 Consensus size: 376
40032426 GATTAGAATC
* * * * *
40032436 AAATAAAATCAAGATAAAAT-TCCTTTTATAAATAGATTCTT-TATGTTTGCTGAGAAAAATTAA
1 AAATCAAATCAAGAT-AAATGTCCTTTTAAAAACAGATT-TTGTATGTTTGTTGAGAAAAAATAA
* * * * ** *
40032499 CTTTCGTGCTGGGCTAAAATATCTGCAGGCCCATTTTGCGCCCGACTAGTCTAGACATTTCGCAT
64 CTTTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCGT
*
40032564 CGCCCACGTTGTGCTGGTGCACCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAAG
129 CGCCCACGTTGTGC-GGTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAAG
* * *
40032629 GCAATGTTTCGAGCTTAGTCATTCAATCACTCTTCAAGTGGATTCTCATATATATTTGTGTTTTT
193 GCAAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGATTCTCATATATATTTGTGTTTTT
*
40032694 TTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGATATTTTGGAAATTTC
258 TTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTTC
* *
40032759 CATGAATAAAGATACAAAATCTGCAATAAATAAGTCATTAAATCAATTTGATTA
323 CATGAATAAAGATACAAAATCTGCATTAAATGAGTCATTAAATCAATTTGATTA
*
40032813 CAATCAAATCAAGATAAATGT-CTATTTAAAAACAGATTCTT-TATGTTTGTTGAGAAAAAATAA
1 AAATCAAATCAAGATAAATGTCCT-TTTAAAAACAGATT-TTGTATGTTTGTTGAGAAAAAATAA
* * * * ** * * *
40032876 CTTTCGTGCTGGGCTAAAATATTCGCATGCCCATTTTGTGCTTGACCGGTCCAGACGTTTCGCGT
64 CTTTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCGT
* *
40032941 CGCCCACGTTGTGCTGGTGCACCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGTGCAAG
129 CGCCCACGTTGTGC-GGTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAAG
*
40033006 GCAAGGTTTCAAGCTTAGTCATTCAATCACTCTTCAAGTGGATTCTCATATATATTTGTGTTTTT
193 GCAAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGATTCTCATATATATTTGTG-TTTT
40033071 TTTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTT
257 TTTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTT
* * * *
40033136 CCATGAATAAAGATAGAAAATCTGCATTAAAGGAGCCATTGAATCAATTTGATTA
322 CCATGAATAAAGATACAAAATCTGCATTAAATGAGTCATTAAATCAATTTGATTA
*
40033191 AAATCAAATCAAGATAAATGTCCTTTTAAAAACAGATTTTGTATGTTTGCTGAGAAAAAATAACT
1 AAATCAAATCAAGATAAATGTCCTTTTAAAAACAGATTTTGTATGTTTGTTGAGAAAAAATAACT
* * * ** * * * *
40033256 TTCGTGTTGGGCT-AACTACCCGTAGGCCCATTTTGGGCTAGATTGGTCTGGACATTTCGAGTTG
66 TTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCGTCG
* * * *
40033320 CCTATGTCGTGCGAGTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCTCAAGGC
131 CCCACGTTGTGCG-GTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAAGGC
* * * * * *
40033385 AGGGTTTCAAGCTTAGTCATTCAATCACCTTTCAAGTGGGTTCTTATATATATTGGGGTTCTTTC
195 AAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGATTCTCATATATATTTGTGTT-TTT-
** * * * *
40033450 TTAAAATTCTGAAGGACTCTTTAGGCTTTTATAGGTATTCAATATGGAGGTATTTTGGAAATTTC
258 TTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTTC
* * *
40033515 TATGAATAAAGATACAAAATTTGCATTAAATGAGTCATTAAATCAATTTCATTA
323 CATGAATAAAGATACAAAATCTGCATTAAATGAGTCATTAAATCAATTTGATTA
* *
40033569 AAATCAAATCAAGATAAATGTCCTTTTAAAAATAGATTATGTATGTTTGTTGAGAAAAAAATAAC
1 AAATCAAATCAAGATAAATGTCCTTTTAAAAACAGATTTTGTATGTTTGTTGAG-AAAAAATAAC
* * * * ** * * * *
40033634 TTTCGTGTTGGGATAAAATATCCGTAGGCCTATTTTTGGCCTAACCGTTCCGGACATTTCCCATC
65 TTTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCGTC
* * ** * * * * *
40033699 ACCTATATCGTTCGAGTGCGCCCCAACCCTGATAGGTTTGGATTTGC-ACCCCCTGA-GCGCGAA
130 GCCCACGTTGTGCG-GTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCT-ACGCGC-AA
* * *
40033762 -GCAAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGGTTCTCGTATATATTAGTGTTTT
192 GGCAAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGATTCTCATATATATTTGTGTTTT
* * * *
40033826 TTTTT-ATTCTGAGGAATTCTTTAGGCTTTTATAGACATTGAATATGGAGGTATTTTGGAAATTT
257 TTTTTAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTT
* * * * *
40033890 TCATGAATAAATATACAAAATATGAATTAAATGAGTCATTAAATCAAATTGATTTGAA
322 CCATGAATAAAGATACAAAATCTGCATTAAATGAGTCATTAAATCAATTTGA-TT--A
* *
40033948 TTAAATAAAATCAAGATAAATGTCCTTTTAAAAACAGATTATGTATGTTTGTTGAGAAAAAAATA
1 --AAATCAAATCAAGATAAATGTCCTTTTAAAAACAGATTTTGTATGTTTGTTGAG-AAAAAATA
* * * * * * *
40034013 ACTTTCGTGTTGGGCTAAAATATTCGCAAGCCCAATTTGGGCCCGATTAGTTCGGACATTTTGCG
63 ACTTTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCG
* * * * * **
40034078 TCGCCCACATTGTGCGGGTGCGCTCCAACCCCGATGGGTTTGGATTTGTAACCCCCAACGCGTGA
128 TCGCCCACGTTGTGC-GGTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAA
* ** *
40034143 GGTAAAATTTCAAGCTTAGTTATTCAATCACCCTTCAAGTTGG-TTCTCATATATAT
192 GGCAAGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAG-TGGATTCTCATATATAT
40034199 AAACATCTCA
Statistics
Matches: 1211, Mismatches: 153, Indels: 39
0.86 0.11 0.03
Matches are distributed among these distances:
376 107 0.09
377 379 0.31
378 346 0.29
379 92 0.08
380 79 0.07
381 149 0.12
382 56 0.05
383 3 0.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (376 bp):
AAATCAAATCAAGATAAATGTCCTTTTAAAAACAGATTTTGTATGTTTGTTGAGAAAAAATAACT
TTCGTGTTGGGCTAAAATATCCGCAGGCCCATTTTGGGCCCGACTGGTCCGGACATTTCGCGTCG
CCCACGTTGTGCGGTGCGCCCCAACCCCGATGGGTTTGGATCTGCAACCCCCTACGCGCAAGGCA
AGGTTTCAAGCTTAGTCATTCAATCACCCTTCAAGTGGATTCTCATATATATTTGTGTTTTTTTT
TAATTCTGAAGAATTCTTTAGGCTTTTATAGGCATTCAATATGAAGGTATTTTGGAAATTTCCAT
GAATAAAGATACAAAATCTGCATTAAATGAGTCATTAAATCAATTTGATTA
Found at i:40035290 original size:4 final size:4
Alignment explanation
Indices: 40035283--40035312 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
40035273 TATTTTAGAT
*
40035283 AGAA AGAA AGAG AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
40035313 TGAGAATCAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:40037036 original size:34 final size:34
Alignment explanation
Indices: 40036975--40037165 Score: 168
Period size: 34 Copynumber: 5.6 Consensus size: 34
40036965 GCAATATGGA
* * * * *
40036975 ATGCTTATGATAGATTAATACGATAGCATTTAAT
1 ATGCTTATAACAGATCAATACGGTAGCAATTAAT
* * * *
40037009 ATGCTTATAATAGTTCAATATGGTAGCAAATAAT
1 ATGCTTATAACAGATCAATACGGTAGCAATTAAT
* * * *
40037043 ATACTTATAACGGATCAATACGTTAGTAATTAAT
1 ATGCTTATAACAGATCAATACGGTAGCAATTAAT
* ** * *
40037077 ATGCTTATAACAGATCAATAAGGTAAAAACTAAC
1 ATGCTTATAACAGATCAATACGGTAGCAATTAAT
* *
40037111 ATGCTTATAACAGATCAATGCGGT-GCCAAATAAT
1 ATGCTTATAACAGATCAATACGGTAG-CAATTAAT
* *
40037145 ATGTTTATAACAAATCAATAC
1 ATGCTTATAACAGATCAATAC
40037166 AATAGAAAAA
Statistics
Matches: 124, Mismatches: 32, Indels: 2
0.78 0.20 0.01
Matches are distributed among these distances:
34 124 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.32
Consensus pattern (34 bp):
ATGCTTATAACAGATCAATACGGTAGCAATTAAT
Found at i:40045885 original size:33 final size:33
Alignment explanation
Indices: 40045843--40045912 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
40045833 CAATTATGTG
40045843 TGATTAATTCTTGGTTTTATATTTCTAGACTAT
1 TGATTAATTCTTGGTTTTATATTTCTAGACTAT
40045876 TGATTAATTCTTGGTTTTATATTTCTAGACTAT
1 TGATTAATTCTTGGTTTTATATTTCTAGACTAT
40045909 TGAT
1 TGAT
40045913 CCATGTTTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (33 bp):
TGATTAATTCTTGGTTTTATATTTCTAGACTAT
Found at i:40048664 original size:67 final size:67
Alignment explanation
Indices: 40048509--40048695 Score: 198
Period size: 67 Copynumber: 2.8 Consensus size: 67
40048499 TGCTTACGAC
* * * * * * *
40048509 AGATCAATACGATAACATTTAATATGCTTATAACAATTCGACATAGTAGCAAATAATATGATCAT
1 AGATCAATACGGTAACAATTAATATACTTATAACAAATCAATATAGTAGC-AATAACATGATCAT
40048574 AAT
65 AAT
* *** *
40048577 GGATCAATACGGTGGTAATTAATATACTTATAACAGAAT-AATA-AGTTAGCAATAACATGATTA
1 AGATCAATACGGTAACAATTAATATACTTATAACA-AATCAATATAG-TAGCAATAACATGATCA
40048640 TAAT
64 TAAT
* **
40048644 AGATCAATGCGGTAACAATTAATATGTTTATAACAAATCAATATAGTAGCAA
1 AGATCAATACGGTAACAATTAATATACTTATAACAAATCAATATAGTAGCAA
40048696 AAGACATGCT
Statistics
Matches: 96, Mismatches: 19, Indels: 9
0.77 0.15 0.07
Matches are distributed among these distances:
66 3 0.03
67 55 0.57
68 36 0.38
69 2 0.02
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.30
Consensus pattern (67 bp):
AGATCAATACGGTAACAATTAATATACTTATAACAAATCAATATAGTAGCAATAACATGATCATA
AT
Found at i:40050996 original size:7 final size:7
Alignment explanation
Indices: 40050984--40051009 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
40050974 TCAAATATAT
40050984 TAAAATG
1 TAAAATG
40050991 TAAAATG
1 TAAAATG
40050998 TAAAATG
1 TAAAATG
40051005 TAAAA
1 TAAAA
40051010 AATATTCACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.27
Consensus pattern (7 bp):
TAAAATG
Found at i:40052404 original size:22 final size:22
Alignment explanation
Indices: 40052374--40052427 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
40052364 GTTTAGCAGT
* *
40052374 TTTG-TGCTCTCTGTTCAGCAC
1 TTTGCTGCTCTCTATGCAGCAC
40052395 TTCTGC-GCTCTCTATGCAGCAC
1 TT-TGCTGCTCTCTATGCAGCAC
40052417 TTTGCTGCTCT
1 TTTGCTGCTCT
40052428 TTGCTTAGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 5 0.18
22 23 0.82
ACGTcount: A:0.09, C:0.31, G:0.19, T:0.41
Consensus pattern (22 bp):
TTTGCTGCTCTCTATGCAGCAC
Found at i:40066535 original size:20 final size:20
Alignment explanation
Indices: 40066512--40066549 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
40066502 GCCTAGGTCG
*
40066512 CATTCTATTAGCCTTTGTGA
1 CATTATATTAGCCTTTGTGA
*
40066532 CATTATGTTAGCCTTTGT
1 CATTATATTAGCCTTTGT
40066550 AGTGTACTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.47
Consensus pattern (20 bp):
CATTATATTAGCCTTTGTGA
Found at i:40072899 original size:26 final size:26
Alignment explanation
Indices: 40072826--40072885 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
40072816 ATATTTTCTA
* *
40072826 AAAATTTTACC-GAAGGCAAAATCATC
1 AAAATTTTACCAG-GGGTAAAATCATC
40072852 AAAATTTTACCAGGGGTAAAATCATC
1 AAAATTTTACCAGGGGTAAAATCATC
40072878 AAAATTTT
1 AAAATTTT
40072886 GATGAGGGTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
26 30 0.97
27 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (26 bp):
AAAATTTTACCAGGGGTAAAATCATC
Found at i:40076234 original size:27 final size:27
Alignment explanation
Indices: 40076204--40076280 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
40076194 AATGCACCAG
*
40076204 AGTGCCAATATCAATGATTTGCATTGA
1 AGTGCCAATATCAATGATTTGCATCGA
*
40076231 AGTGCCAATATCATTG-TGTTGCATCGA
1 AGTGCCAATATCAATGAT-TTGCATCGA
* * *
40076258 AGGGCCAATATCACTAATTTGCA
1 AGTGCCAATATCAATGATTTGCA
40076281 GCAAATCCCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
26 1 0.02
27 41 0.95
28 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.31
Consensus pattern (27 bp):
AGTGCCAATATCAATGATTTGCATCGA
Found at i:40077642 original size:11 final size:11
Alignment explanation
Indices: 40077626--40077668 Score: 59
Period size: 11 Copynumber: 3.7 Consensus size: 11
40077616 CCTAAAATAC
40077626 ATAAAATATTA
1 ATAAAATATTA
40077637 ATAAAATATCTTA
1 ATAAAATA--TTA
40077650 ATAAAATATTA
1 ATAAAATATTA
*
40077661 TTAAAATA
1 ATAAAATA
40077669 ATTTCACCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 18 0.62
13 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
ATAAAATATTA
Found at i:40081979 original size:13 final size:13
Alignment explanation
Indices: 40081961--40081986 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40081951 TATCATGTGG
40081961 CATGTTTTATATA
1 CATGTTTTATATA
40081974 CATGTTTTATATA
1 CATGTTTTATATA
40081987 TCAATTCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
CATGTTTTATATA
Found at i:40082679 original size:22 final size:22
Alignment explanation
Indices: 40082624--40082681 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
40082614 AGTGTTTAAA
**
40082624 CAATAGGCACCAAAATGCTGAG
1 CAATAGGCACCGTAATGCTGAG
*
40082646 CAATAGGCACCGTAATG-TGAAT
1 CAATAGGCACCGTAATGCTG-AG
40082668 CAATAGGCACCGTA
1 CAATAGGCACCGTA
40082682 GTGCAAATCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
21 2 0.06
22 30 0.94
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (22 bp):
CAATAGGCACCGTAATGCTGAG
Found at i:40082690 original size:22 final size:22
Alignment explanation
Indices: 40082646--40082690 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
40082636 AAATGCTGAG
**
40082646 CAATAGGCACCGTAATGTGAAT
1 CAATAGGCACCGTAATGCAAAT
*
40082668 CAATAGGCACCGTAGTGCAAAT
1 CAATAGGCACCGTAATGCAAAT
40082690 C
1 C
40082691 CTGTAAAAGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (22 bp):
CAATAGGCACCGTAATGCAAAT
Found at i:40083704 original size:19 final size:21
Alignment explanation
Indices: 40083680--40083719 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
40083670 ATTTCAAAGT
40083680 TTTAATGT-T-GGTATCGATA
1 TTTAATGTCTAGGTATCGATA
*
40083699 TTTAATTTCTAGGTATCGATA
1 TTTAATGTCTAGGTATCGATA
40083720 CTATATCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.28, C:0.07, G:0.17, T:0.47
Consensus pattern (21 bp):
TTTAATGTCTAGGTATCGATA
Found at i:40100869 original size:20 final size:20
Alignment explanation
Indices: 40100844--40100881 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40100834 TAAAGAAATT
40100844 AAATGC-AATGGAAAATAATG
1 AAATGCAAAT-GAAAATAATG
40100864 AAATGCAAATGAAAATAA
1 AAATGCAAATGAAAATAA
40100882 CAAAACTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.61, C:0.05, G:0.16, T:0.18
Consensus pattern (20 bp):
AAATGCAAATGAAAATAATG
Found at i:40105671 original size:51 final size:49
Alignment explanation
Indices: 40105609--40105721 Score: 138
Period size: 51 Copynumber: 2.2 Consensus size: 49
40105599 TTCCAAGTCA
*
40105609 TTTTCATTTTCATTTTGGAGAAAA-CTACACTCATTTCGAAATGTTTTCAT
1 TTTTCATTTTCATTTTGAAGAAAATC-ACACTCATTTCGAAATG-TTTCAT
* * *
40105659 TTTTCTATTTTCATTTTTAAGAAAATCACATTCATTTCTAAATGTTTCAT
1 TTTTC-ATTTTCATTTTGAAGAAAATCACACTCATTTCGAAATGTTTCAT
*
40105709 TTCTCCATTTTCA
1 TT-TTCATTTTCA
40105722 CCATTTCTAT
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
50 20 0.36
51 34 0.62
52 1 0.02
ACGTcount: A:0.27, C:0.17, G:0.06, T:0.50
Consensus pattern (49 bp):
TTTTCATTTTCATTTTGAAGAAAATCACACTCATTTCGAAATGTTTCAT
Found at i:40112764 original size:21 final size:22
Alignment explanation
Indices: 40112728--40112771 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
40112718 CCTAATTTCC
*
40112728 AATTTTATATTTTCAATCTTCA
1 AATTTTATACTTTCAATCTTCA
*
40112750 AATTTTA-ACTTTCAATTTTCA
1 AATTTTATACTTTCAATCTTCA
40112771 A
1 A
40112772 TTTCAAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.14, G:0.00, T:0.52
Consensus pattern (22 bp):
AATTTTATACTTTCAATCTTCA
Found at i:40112768 original size:13 final size:13
Alignment explanation
Indices: 40112721--40112777 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
40112711 TTCAATCCCT
* *
40112721 AATTTCCAATTTT
1 AATTTTCAATTTC
40112734 ATATTTTCAATCTTC
1 A-ATTTTCAAT-TTC
40112749 AAATTTT-AACTTTC
1 -AATTTTCAA-TTTC
40112763 AATTTTCAATTTC
1 AATTTTCAATTTC
40112776 AA
1 AA
40112778 AATTTCAATC
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 13 0.35
14 15 0.41
15 8 0.22
16 1 0.03
ACGTcount: A:0.33, C:0.16, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTTTCAATTTC
Found at i:40112783 original size:14 final size:13
Alignment explanation
Indices: 40112738--40112786 Score: 53
Period size: 14 Copynumber: 3.5 Consensus size: 13
40112728 AATTTTATAT
40112738 TTTCAATCTTCAAA
1 TTTCAAT-TTCAAA
* *
40112752 TTTTAACTTTCAAT
1 TTTCAA-TTTCAAA
40112766 TTTCAATTTCAAAA
1 TTTCAATTTC-AAA
40112780 TTTCAAT
1 TTTCAAT
40112787 CATCAATTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
13 4 0.14
14 24 0.83
15 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.00, T:0.49
Consensus pattern (13 bp):
TTTCAATTTCAAA
Found at i:40112792 original size:28 final size:28
Alignment explanation
Indices: 40112736--40112794 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
40112726 CCAATTTTAT
* *
40112736 ATTTTCAATCTTCAAATTTTAACTTTCA
1 ATTTTCAATCTTCAAATTTCAACTATCA
40112764 ATTTTCAAT-TTCAAAATTTCAA-TCATCA
1 ATTTTCAATCTTC-AAATTTCAACT-ATCA
40112792 ATT
1 ATT
40112795 ATTTTTTTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
27 4 0.15
28 23 0.85
ACGTcount: A:0.36, C:0.17, G:0.00, T:0.47
Consensus pattern (28 bp):
ATTTTCAATCTTCAAATTTCAACTATCA
Found at i:40112815 original size:14 final size:13
Alignment explanation
Indices: 40112791--40112826 Score: 63
Period size: 13 Copynumber: 2.7 Consensus size: 13
40112781 TTCAATCATC
40112791 AATTATTTTTTTA
1 AATTATTTTTTTA
40112804 AATTATTTTTTTA
1 AATTATTTTTTTA
40112817 AATTTATTTT
1 AA-TTATTTT
40112827 CTTCGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
AATTATTTTTTTA
Found at i:40114577 original size:63 final size:62
Alignment explanation
Indices: 40114481--40114650 Score: 191
Period size: 63 Copynumber: 2.7 Consensus size: 62
40114471 TTTTTTTTGT
* * * ** *
40114481 CACAATCATCACAACAGCACAC-TCATTCCCTGCATTATCACCTTCAA-TTTCGGTTTATTTTA
1 CACAACCACCACAACA-CACACATCATTCCCTGCATTAACACCTTCAACACT-AGTTTATTTTA
*
40114543 CACAACCACCACAACACACACAATCATTCCCTGCATTAACACATTCAACACTAGTTTATTTTA
1 CACAACCACCACAACACACAC-ATCATTCCCTGCATTAACACCTTCAACACTAGTTTATTTTA
* * * *
40114606 CACAAGCACCACAACACGCCCCATCATTCCCTGTATTAACACCTT
1 CACAACCACCACAACAC-ACACATCATTCCCTGCATTAACACCTT
40114651 TTCTATGGAT
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
61 5 0.05
62 14 0.15
63 70 0.76
64 3 0.03
ACGTcount: A:0.33, C:0.35, G:0.05, T:0.27
Consensus pattern (62 bp):
CACAACCACCACAACACACACATCATTCCCTGCATTAACACCTTCAACACTAGTTTATTTTA
Found at i:40119627 original size:41 final size:41
Alignment explanation
Indices: 40119570--40119710 Score: 140
Period size: 41 Copynumber: 3.4 Consensus size: 41
40119560 ATTATACTTA
* * *
40119570 AATTGCACATACGTGCCCTTGTTTGTTCTTCGATACCCATG
1 AATTGAACATACGTGCCCCTGTTTGTACTTCGATACCCATG
* * *
40119611 AATTGAACATATGTGCCCCTGTTTGTACTTCGATACCCTTA
1 AATTGAACATACGTGCCCCTGTTTGTACTTCGATACCCATG
** * * * * * *
40119652 AATTTCATATACGTTCCCCAGTTTATACTTCGGTACCCTTG
1 AATTGAACATACGTGCCCCTGTTTGTACTTCGATACCCATG
40119693 AATT-ACACATACGTGCCC
1 AATTGA-ACATACGTGCCC
40119711 TAATTCAGTT
Statistics
Matches: 81, Mismatches: 18, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
41 81 1.00
ACGTcount: A:0.23, C:0.27, G:0.14, T:0.35
Consensus pattern (41 bp):
AATTGAACATACGTGCCCCTGTTTGTACTTCGATACCCATG
Found at i:40122221 original size:41 final size:41
Alignment explanation
Indices: 40122164--40122539 Score: 430
Period size: 41 Copynumber: 9.2 Consensus size: 41
40122154 TAATTATACT
* *
40122164 TGAATTACACATACGTGCCCCTATTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
40122205 TGAATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCA
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
40122246 TAAATTGCAGATACGTGCCCTTGTTTGTACTTCGATGCCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* *
40122287 TGAATTGCATATTCGTGCCCCTGTTTGTACTTCGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * *
40122328 TAAATTGCACATACGTGCCCTTGTTTGTACTTTGATACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * *
40122369 TGAATTGCATATTCGTGCCCCTGTTTGTACTTTGGTACCCC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * *
40122410 TAAATTTCACATACGTGCCCCTATTTATACTTCGGTACCTC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* ** *
40122451 TGAATTGCACATACGTGCCCCTATTTGTACTAGGGTA-CTC
1 TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
* * * * * * *
40122491 TGTATAGCACTTACGTGCCCCTGTTTATACATTTGGTAACCT
1 TGAATTGCACATACGTGCCCCTGTTTGTAC-TTCGGTACCCC
40122533 TGAATTG
1 TGAATTG
40122540 AATAATATAT
Statistics
Matches: 283, Mismatches: 50, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
40 28 0.10
41 249 0.88
42 6 0.02
ACGTcount: A:0.20, C:0.27, G:0.17, T:0.35
Consensus pattern (41 bp):
TGAATTGCACATACGTGCCCCTGTTTGTACTTCGGTACCCC
Found at i:40122305 original size:21 final size:21
Alignment explanation
Indices: 40122276--40122391 Score: 64
Period size: 21 Copynumber: 5.6 Consensus size: 21
40122266 TTGTTTGTAC
40122276 TTCGATGCCCCTGAATTGCATA
1 TTCG-TGCCCCTGAATTGCATA
*
40122298 TTCGTGCCCCTG-TTTG--TA
1 TTCGTGCCCCTGAATTGCATA
* * *
40122316 CTTCGGTACCCCTAAATTGCACA
1 -TTC-GTGCCCCTGAATTGCATA
* * *
40122339 TACGTGCCCTTG-TTTG--TA
1 TTCGTGCCCCTGAATTGCATA
* *
40122357 CTTTGATACCCCTGAATTGCATA
1 -TTCG-TGCCCCTGAATTGCATA
40122380 TTCGTGCCCCTG
1 TTCGTGCCCCTG
40122392 TTTGTACTTT
Statistics
Matches: 66, Mismatches: 18, Indels: 21
0.63 0.17 0.20
Matches are distributed among these distances:
18 3 0.05
19 5 0.08
20 19 0.29
21 27 0.41
22 9 0.14
23 3 0.05
ACGTcount: A:0.17, C:0.29, G:0.18, T:0.35
Consensus pattern (21 bp):
TTCGTGCCCCTGAATTGCATA
Found at i:40134597 original size:6 final size:6
Alignment explanation
Indices: 40134586--40134632 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
40134576 AGCCAAAAAA
* * *
40134586 AAATAT AAATAT AAATAA AAATTT ATATAT AAA-AT AAAATAT AAATA
1 AAATAT AAATAT AAATAT AAATAT AAATAT AAATAT -AAATAT AAATA
40134633 GCATAATTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
5 2 0.06
6 29 0.88
7 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
AAATAT
Found at i:40134605 original size:18 final size:17
Alignment explanation
Indices: 40134581--40134632 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 17
40134571 ATGTTAGCCA
40134581 AAAAAAAATATAAATAT
1 AAAAAAAATATAAATAT
* *
40134598 AAATAAAAATTTATATAT
1 AAA-AAAAATATAAATAT
40134616 AAAATAAAATATAAATA
1 AAAA-AAAATATAAATA
40134633 GCATAATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 4 0.14
18 25 0.86
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAAAAATATAAATAT
Found at i:40139665 original size:22 final size:22
Alignment explanation
Indices: 40139621--40139736 Score: 90
Period size: 22 Copynumber: 5.1 Consensus size: 22
40139611 CCCACAAAAT
* *
40139621 ACAACCAAACATAGCCTCTAAAC
1 ACAA-CAAACATACCCTCCAAAC
* **
40139644 ACAACTAATTTACCCTCCAAAC
1 ACAACAAACATACCCTCCAAAC
40139666 ACAACCAAACATACCCTCC-AAC
1 ACAA-CAAACATACCCTCCAAAC
* * *
40139688 ACAACCAAATATAGCCTCCAAGC
1 ACAA-CAAACATACCCTCCAAAC
* * *
40139711 ACCACCAAATATACCCTTCAAAC
1 A-CAACAAACATACCCTCCAAAC
40139734 ACA
1 ACA
40139737 TCCATTTAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 7
0.77 0.15 0.07
Matches are distributed among these distances:
22 39 0.52
23 34 0.45
24 2 0.03
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (22 bp):
ACAACAAACATACCCTCCAAAC
Found at i:40139684 original size:23 final size:23
Alignment explanation
Indices: 40139621--40139736 Score: 128
Period size: 23 Copynumber: 5.1 Consensus size: 23
40139611 CCCACAAAAT
* * *
40139621 ACAACCAAACATAGCCTCTAAAC
1 ACAACCAAATATACCCTCCAAAC
* *
40139644 ACAA-CTAATTTACCCTCCAAAC
1 ACAACCAAATATACCCTCCAAAC
*
40139666 ACAACCAAACATACCCTCC-AAC
1 ACAACCAAATATACCCTCCAAAC
* *
40139688 ACAACCAAATATAGCCTCCAAGC
1 ACAACCAAATATACCCTCCAAAC
* *
40139711 ACCACCAAATATACCCTTCAAAC
1 ACAACCAAATATACCCTCCAAAC
40139734 ACA
1 ACA
40139737 TCCATTTAAA
Statistics
Matches: 75, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
22 37 0.49
23 38 0.51
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (23 bp):
ACAACCAAATATACCCTCCAAAC
Found at i:40139706 original size:45 final size:44
Alignment explanation
Indices: 40139621--40139736 Score: 133
Period size: 45 Copynumber: 2.6 Consensus size: 44
40139611 CCCACAAAAT
* * *
40139621 ACAACCAAACATAGCCTCTAAACACAACTAATTTACCCTCCAAAC
1 ACAACCAAACATACCCTC-AAACACAACAAATATACCCTCCAAAC
* * *
40139666 ACAACCAAACATACCCTCCAACACAACCAAATATAGCCTCCAAGC
1 ACAACCAAACATACCCTCAAACACAA-CAAATATACCCTCCAAAC
* *
40139711 ACCACCAAATATACCCTTCAAACACA
1 ACAACCAAACATACCC-TCAAACACA
40139737 TCCATTTAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 3
0.83 0.12 0.04
Matches are distributed among these distances:
44 7 0.12
45 45 0.75
46 8 0.13
ACGTcount: A:0.45, C:0.38, G:0.03, T:0.15
Consensus pattern (44 bp):
ACAACCAAACATACCCTCAAACACAACAAATATACCCTCCAAAC
Found at i:40145935 original size:40 final size:41
Alignment explanation
Indices: 40145885--40145974 Score: 101
Period size: 40 Copynumber: 2.2 Consensus size: 41
40145875 CAAGAGCTAC
* * * * *
40145885 CAATACATTCCCAAAGACACCTAGTGCTTTGGAGAACTAT-
1 CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
* *
40145925 CAATAAATTCCCACAGGCACCCAATGCTCTAGAGAACTATA
1 CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
40145966 CAATGAAAT
1 CAAT-AAAT
40145975 ACAACAAGTG
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
40 33 0.80
41 4 0.10
42 4 0.10
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.22
Consensus pattern (41 bp):
CAATAAATTCCCAAAGACACCCAATGCTCTAGAGAACTATA
Found at i:40147646 original size:231 final size:231
Alignment explanation
Indices: 40147243--40147707 Score: 876
Period size: 231 Copynumber: 2.0 Consensus size: 231
40147233 TCAGAGTAAG
*
40147243 AATTAAGAATGCTTAGTAAGTTCAAATGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
*
40147308 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTG
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
40147373 CATGTCAACATTATCAACTAAATAAGTTAGCCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGCCACTTTTACAAATCATGAGAAATATCTAAGACAT
40147438 TAAGGCACTTCAATACTTATCACATATCACATATCA
196 TAAGGCACTTCAATACTTATCACATATCACATATCA
40147474 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
1 AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
40147539 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
66 GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
*
40147604 CATGTCAACATTATCAACTAAATAAGTTAGTCACTTTTACAAATCATGAGAAATATCTAAGACAT
131 CATGTCAACATTATCAACTAAATAAGTTAGCCACTTTTACAAATCATGAGAAATATCTAAGACAT
* * *
40147669 TAAGGTAGTTCAATACTTATCACATATCACATGTCA
196 TAAGGCACTTCAATACTTATCACATATCACATATCA
40147705 AAT
1 AAT
40147708 ATAAAACATA
Statistics
Matches: 228, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
231 228 1.00
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.31
Consensus pattern (231 bp):
AATTAAGAATGCTTAGTAAGTTCAAACGGAGTTATTAAACTTACCTTGATCCATTAAAGCATAAA
GAAAATGTCATACATCTTGGCATTCAAAAATGGCCATTCTTGGCACATATTGGCACATCTAAGTA
CATGTCAACATTATCAACTAAATAAGTTAGCCACTTTTACAAATCATGAGAAATATCTAAGACAT
TAAGGCACTTCAATACTTATCACATATCACATATCA
Found at i:40150883 original size:25 final size:25
Alignment explanation
Indices: 40150854--40150920 Score: 71
Period size: 25 Copynumber: 2.7 Consensus size: 25
40150844 AACTGTTTTT
*
40150854 GATAGTATATCCTAAAACTACTATA
1 GATAGTATATACTAAAACTACTATA
* * * *
40150879 TATAGTGTATACTGAGACTACTATA
1 GATAGTATATACTAAAACTACTATA
**
40150904 GATAGGCTATACTAAAA
1 GATAGTATATACTAAAA
40150921 ACACTCAAGT
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (25 bp):
GATAGTATATACTAAAACTACTATA
Found at i:40155089 original size:50 final size:50
Alignment explanation
Indices: 40155035--40155406 Score: 326
Period size: 50 Copynumber: 7.6 Consensus size: 50
40155025 GATCCTTTAA
* *
40155035 ACTGCAATGTCAGGGAAGTAAGATACGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * ** * * **
40155085 ACTGCAATGCCTGGGAAGTAAGATTCACCATTGTGGCTTCAATCTTTTGA
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
*
40155135 ACTGCAATGTCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * * * * * * **
40155185 GCTGC-ATCCCTA--AAAGTAAGATCCGCCGTTGTGGCTTCGATCTTTTAA
1 ACTGCAATGCC-AGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * *
40155233 ATTGCAATGTCGGGGAAGTGAGATTCGCTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * * * * **
40155283 ACTGCATTGCCA--GAAGTAAGATTCGCCGTTATGGCTTCTATCTTTTAA
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* * * * *
40155331 ATTGCAATGTCGGGGAAGTGAGATTCACTGTTGTAGCTTCAATCTGTTCC
1 ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
* *
40155381 GCTGCATTGCCA--GAAGTAAGATTCGC
1 ACTGCAATGCCAGGGAAGTAAGATTCGC
40155407 CATTGTGGCT
Statistics
Matches: 240, Mismatches: 76, Indels: 14
0.73 0.23 0.04
Matches are distributed among these distances:
48 79 0.33
49 6 0.03
50 155 0.65
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (50 bp):
ACTGCAATGCCAGGGAAGTAAGATTCGCTGTTGTAGCTTCAATCTGTTCC
Found at i:40155258 original size:98 final size:98
Alignment explanation
Indices: 40155003--40155432 Score: 610
Period size: 98 Copynumber: 4.4 Consensus size: 98
40154993 GCCGAGGAAA
* * * *
40155003 TAAGATTCTCCATTGTGGCTTCGATCCTTTAAACTGCAATGTCAGGGAAGTAAGATACGCTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
* *
40155068 TAGCTTCAATCTGTTCCACTGCAATGCCTGGGAAG
66 TAGCTTCAATCTGTTCCACTGCATTGCC--AGAAG
* * * *
40155103 TAAGATTCACCATTGTGGCTTCAATCTTTTGAACTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
* * *
40155168 TAGCTTCAATCTGTTCCGCTGCA-TCCCTAAAAG
66 TAGCTTCAATCTGTTCCACTGCATTGCC-AGAAG
* * * *
40155201 TAAGATCCGCCGTTGTGGCTTCGATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCGCTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
40155266 TAGCTTCAATCTGTTCCACTGCATTGCCAGAAG
66 TAGCTTCAATCTGTTCCACTGCATTGCCAGAAG
* * * * * *
40155299 TAAGATTCGCCGTTATGGCTTCTATCTTTTAAATTGCAATGTCGGGGAAGTGAGATTCACTGTTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
*
40155364 TAGCTTCAATCTGTTCCGCTGCATTGCCAGAAG
66 TAGCTTCAATCTGTTCCACTGCATTGCCAGAAG
40155397 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTG
1 TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTG
40155433 GAAACTATGG
Statistics
Matches: 300, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
98 212 0.71
99 6 0.02
100 82 0.27
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.33
Consensus pattern (98 bp):
TAAGATTCGCCATTGTGGCTTCGATCTTTTAAATTGCAATGTCAGGGAAGTAAGATTCGCTGTTG
TAGCTTCAATCTGTTCCACTGCATTGCCAGAAG
Found at i:40160679 original size:21 final size:21
Alignment explanation
Indices: 40160653--40160694 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
40160643 GGCACAGCTC
*
40160653 CTTTCCCAACTGTCATTTGTA
1 CTTTCCCAACTGACATTTGTA
40160674 CTTTCCCAACTGACATTTGTA
1 CTTTCCCAACTGACATTTGTA
40160695 GTCCCATCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.10, T:0.40
Consensus pattern (21 bp):
CTTTCCCAACTGACATTTGTA
Found at i:40185830 original size:8 final size:8
Alignment explanation
Indices: 40185817--40185843 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40185807 TGGACTATCG
40185817 ATTCAATC
1 ATTCAATC
40185825 ATTCAATC
1 ATTCAATC
40185833 ATTCAATC
1 ATTCAATC
40185841 ATT
1 ATT
40185844 TAAACCAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTCAATC
Found at i:40192896 original size:74 final size:74
Alignment explanation
Indices: 40192775--40192923 Score: 289
Period size: 74 Copynumber: 2.0 Consensus size: 74
40192765 AATAGTTGCA
40192775 ACTAGATCCAGCTAACTCGTATCTTCACTTTCAAAACTGTCAAACATTTCTAAAGTTCTCATTAA
1 ACTAGATCCAGCTAACTCGTATCTTCACTTTCAAAACTGTCAAACATTTCTAAAGTTCTCATTAA
40192840 TGTTAACTG
66 TGTTAACTG
*
40192849 ACTAGGTCCAGCTAACTCGTATCTTCACTTTCAAAACTGTCAAACATTTCTAAAGTTCTCATTAA
1 ACTAGATCCAGCTAACTCGTATCTTCACTTTCAAAACTGTCAAACATTTCTAAAGTTCTCATTAA
40192914 TGTTAACTG
66 TGTTAACTG
40192923 A
1 A
40192924 AGTTTTTGAA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.32, C:0.23, G:0.10, T:0.35
Consensus pattern (74 bp):
ACTAGATCCAGCTAACTCGTATCTTCACTTTCAAAACTGTCAAACATTTCTAAAGTTCTCATTAA
TGTTAACTG
Found at i:40195303 original size:24 final size:24
Alignment explanation
Indices: 40195272--40195319 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
40195262 AATGCATTCA
* *
40195272 TTTGAATTT-TGGAAATTTTATGT
1 TTTGAATTTATGAAAATTGTATGT
40195295 TTTGCAATTTATGAAAATTGTATGT
1 TTTG-AATTTATGAAAATTGTATGT
40195320 GACTATAGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 4 0.19
24 5 0.24
25 12 0.57
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTTGAATTTATGAAAATTGTATGT
Found at i:40200340 original size:6 final size:6
Alignment explanation
Indices: 40200326--40200440 Score: 86
Period size: 6 Copynumber: 19.2 Consensus size: 6
40200316 CCAGAGACAA
* * **
40200326 ATACAG ATGCAG ATGCAG ATACAG ACCCAG ATACAG ATACAG ATACAG
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG
* * * * * * * * *
40200374 ATGCAG ATACAG ATGCAA ACACAA ATTCAG ATACAA ATGCAG ACACAG
1 ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG ATACAG
* * *
40200422 ATTCAG TTACAG ATGCAG A
1 ATACAG ATACAG ATACAG A
40200441 CACCAATCCT
Statistics
Matches: 82, Mismatches: 27, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
6 82 1.00
ACGTcount: A:0.44, C:0.20, G:0.19, T:0.17
Consensus pattern (6 bp):
ATACAG
Found at i:40200344 original size:12 final size:12
Alignment explanation
Indices: 40200329--40200440 Score: 116
Period size: 12 Copynumber: 9.3 Consensus size: 12
40200319 GAGACAAATA
*
40200329 CAGATGCAGATG
1 CAGATACAGATG
**
40200341 CAGATACAGACC
1 CAGATACAGATG
*
40200353 CAGATACAGATA
1 CAGATACAGATG
40200365 CAGATACAGATG
1 CAGATACAGATG
40200377 CAGATACAGATG
1 CAGATACAGATG
* * * *
40200389 CAAACACAAATT
1 CAGATACAGATG
*
40200401 CAGATACAAATG
1 CAGATACAGATG
* *
40200413 CAGACACAGATT
1 CAGATACAGATG
*
40200425 CAGTTACAGATG
1 CAGATACAGATG
40200437 CAGA
1 CAGA
40200441 CACCAATCCT
Statistics
Matches: 80, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
12 80 1.00
ACGTcount: A:0.44, C:0.21, G:0.20, T:0.16
Consensus pattern (12 bp):
CAGATACAGATG
Found at i:40200344 original size:24 final size:24
Alignment explanation
Indices: 40200317--40200443 Score: 119
Period size: 24 Copynumber: 5.3 Consensus size: 24
40200307 GATGCAATTC
* * *
40200317 CAGAGACAAATACAGATGCAGATG
1 CAGACACAGATACAGATACAGATG
* ** *
40200341 CAGATACAGACCCAGATACAGATA
1 CAGACACAGATACAGATACAGATG
* *
40200365 CAGATACAGATGCAGATACAGATG
1 CAGACACAGATACAGATACAGATG
* * * *
40200389 CAAACACAAATTCAGATACAAATG
1 CAGACACAGATACAGATACAGATG
* *
40200413 CAGACACAGATTCAGTTACAGATG
1 CAGACACAGATACAGATACAGATG
40200437 CAGACAC
1 CAGACAC
40200444 CAATCCTACC
Statistics
Matches: 85, Mismatches: 18, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 85 1.00
ACGTcount: A:0.45, C:0.21, G:0.19, T:0.15
Consensus pattern (24 bp):
CAGACACAGATACAGATACAGATG
Found at i:40203584 original size:8 final size:8
Alignment explanation
Indices: 40203567--40203607 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
40203557 AGATACAATA
*
40203567 TTTTTCAT
1 TTTTTAAT
40203575 TTTTTAAT
1 TTTTTAAT
40203583 TTTTTAA-
1 TTTTTAAT
40203590 TTTTT-AT
1 TTTTTAAT
40203597 TTGTTTAAT
1 TT-TTTAAT
40203606 TT
1 TT
40203608 ATTTTAAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 1 0.03
7 7 0.24
8 17 0.59
9 4 0.14
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (8 bp):
TTTTTAAT
Found at i:40203593 original size:15 final size:15
Alignment explanation
Indices: 40203575--40203607 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
40203565 TATTTTTCAT
40203575 TTTTTAATTT-TTTAA
1 TTTTT-ATTTGTTTAA
40203590 TTTTTATTTGTTTAA
1 TTTTTATTTGTTTAA
40203605 TTT
1 TTT
40203608 ATTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (15 bp):
TTTTTATTTGTTTAA
Found at i:40209126 original size:32 final size:32
Alignment explanation
Indices: 40209086--40209209 Score: 158
Period size: 32 Copynumber: 3.9 Consensus size: 32
40209076 ATAAGTATAA
* *
40209086 TAATATGATTGGCACAAAGCCATCAGTAGCAG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* * * **
40209118 TGATATGATCAGCACACAGCCATCAGTAATGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
* *
40209150 TAATATGATCGGTACAAAGCCATCAGTAACGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAG
*
40209182 TAATATAATCGGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTA
40209210 GCATCGTAGA
Statistics
Matches: 78, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 78 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (32 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAG
Found at i:40209172 original size:64 final size:64
Alignment explanation
Indices: 40209086--40209209 Score: 176
Period size: 64 Copynumber: 1.9 Consensus size: 64
40209076 ATAAGTATAA
* * * * *
40209086 TAATATGATTGGCACAAAGCCATCAGTAGCAGTGATATGATCAGCACACAGCCATCAGTAATGG
1 TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTAATGG
* * *
40209150 TAATATGATCGGTACAAAGCCATCAGTAACGGTAATATAATCGGCACAAAGCCATCAGTA
1 TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTA
40209210 GCATCGTAGA
Statistics
Matches: 52, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
64 52 1.00
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (64 bp):
TAATATGATCGGCACAAAGCCATCAGTAACAGTAATATAATCAGCACAAAGCCATCAGTAATGG
Found at i:40209404 original size:11 final size:11
Alignment explanation
Indices: 40209388--40209433 Score: 56
Period size: 11 Copynumber: 4.0 Consensus size: 11
40209378 CAGAATCAGT
40209388 CATACAAATCA
1 CATACAAATCA
40209399 CATACAAATCA
1 CATACAAATCA
*
40209410 GTCATACTAATCA
1 --CATACAAATCA
*
40209423 CAGACAAATCA
1 CATACAAATCA
40209434 ATCATTTACA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 20 0.67
13 10 0.33
ACGTcount: A:0.50, C:0.26, G:0.04, T:0.20
Consensus pattern (11 bp):
CATACAAATCA
Found at i:40209413 original size:24 final size:24
Alignment explanation
Indices: 40209381--40209438 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
40209371 CCATGCTCAG
*
40209381 AATCAGTCATACAAATCACATACA
1 AATCAGTCATACAAATCACAGACA
*
40209405 AATCAGTCATACTAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
40209429 AATCAATCAT
1 AATCAGTCAT
40209439 TTACATCACG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.22
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:40209415 original size:13 final size:13
Alignment explanation
Indices: 40209381--40209422 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
40209371 CCATGCTCAG
40209381 AATCAGTCATACA
1 AATCAGTCATACA
40209394 AATCA--CATACA
1 AATCAGTCATACA
*
40209405 AATCAGTCATACT
1 AATCAGTCATACA
40209418 AATCA
1 AATCA
40209423 CAGACAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 11 0.42
13 15 0.58
ACGTcount: A:0.48, C:0.24, G:0.05, T:0.24
Consensus pattern (13 bp):
AATCAGTCATACA
Found at i:40209446 original size:24 final size:24
Alignment explanation
Indices: 40209395--40209467 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
40209385 AGTCATACAA
* * *
40209395 ATCACATACAAATCAGTCATACTA-
1 ATCACAGACAAATCAATCAT-TTAC
40209419 ATCACAGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* *
40209443 ATCACGGACAAATAAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
40209467 A
1 A
40209468 CTCGAGGGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.47, C:0.23, G:0.05, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:40209516 original size:27 final size:27
Alignment explanation
Indices: 40209482--40209841 Score: 174
Period size: 27 Copynumber: 13.4 Consensus size: 27
40209472 AGGGGAAAAA
*
40209482 GTCA-TTTACCCTTCAAGGGCATTACG
1 GTCATTTTACCCTTCAAGGGTATTACG
* *
40209508 GTAATTTTA-CCTT-ACAGTGGTATTTCG
1 GTCATTTTACCCTTCA-AG-GGTATTACG
* *
40209535 GTCATTTAACCC-T-ATGGGGTATTACG
1 GTCATTTTACCCTTCA-AGGGTATTACG
* * *
40209561 GTCATTTTACCCTAC-AGAGGCATTACA
1 GTCATTTTACCCTTCAAG-GGTATTACG
* ** * *
40209588 GTTATTTTACCCTAT-GGGGGTTTTTCG
1 GTCATTTTACCCT-TCAAGGGTATTACG
*
40209615 GT-ATTTTACCCTACAAGGGTATTACG
1 GTCATTTTACCCTTCAAGGGTATTACG
**
40209641 GTCATTTTA-CCTATCAAGGGTATTTTG
1 GTCATTTTACCCT-TCAAGGGTATTACG
* * * * *
40209668 ATAATTTTACCCATCGAGGGTATTTCG
1 GTCATTTTACCCTTCAAGGGTATTACG
* * **
40209695 GTCATTTTACCCATCAGGGGTATTTTG
1 GTCATTTTACCCTTCAAGGGTATTACG
* * * * *
40209722 ATAATTATACCCATCGAGGGTATTTTAC-
1 GTCATTTTACCCTTCAAGGGTA--TTACG
* * *
40209750 -TCATTTTACCCATCGAGGATAATT-CG
1 GTCATTTTACCCTTCAAGGGT-ATTACG
*
40209776 GTCATTTTACCCTTCAAGGGTAATT-CA
1 GTCATTTTACCCTTCAAGGGT-ATTACG
* * *
40209803 ATCATTTTACCCTACGAGGGTAATTTA--
1 GTCATTTTACCCTTCAAGGGT-A-TTACG
40209830 GTCATTTTACCC
1 GTCATTTTACCC
40209842 CCTCGGGGGT
Statistics
Matches: 258, Mismatches: 56, Indels: 39
0.73 0.16 0.11
Matches are distributed among these distances:
25 2 0.01
26 54 0.21
27 192 0.74
28 8 0.03
29 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (27 bp):
GTCATTTTACCCTTCAAGGGTATTACG
Found at i:40209570 original size:80 final size:79
Alignment explanation
Indices: 40209482--40209706 Score: 217
Period size: 80 Copynumber: 2.8 Consensus size: 79
40209472 AGGGGAAAAA
*
40209482 GTCA-TTTACCCTTCAAGGGCATTACGGTAATTTTACCTTACAGTGGTATTTCGGTCATTTAACC
1 GTCATTTTACCCTTCAAGGGCATTACGGTAATTTTACC-TACAG-GGTATTTCGGTCATTTTACC
**
40209546 CTA-TGGGGTATTACG
64 CTACAAGGGTATTACG
* * * ** *
40209561 GTCATTTTACCCTAC-AGAGGCATTACAGTTATTTTACCCTATGGGGGTTTTTCGGT-ATTTTAC
1 GTCATTTTACCCTTCAAG-GGCATTACGGTAATTTTA-CCTA-CAGGGTATTTCGGTCATTTTAC
40209624 CCTACAAGGGTATTACG
63 CCTACAAGGGTATTACG
* ** * *
40209641 GTCATTTTA-CCTATCAAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGGTCATTTTAC
1 GTCATTTTACCCT-TCAAGGGCATTACGGTAATTTTACCTA-C-AGGGTATTTCGGTCATTTTAC
40209705 CC
63 CC
40209707 ATCAGGGGTA
Statistics
Matches: 117, Mismatches: 20, Indels: 16
0.76 0.13 0.10
Matches are distributed among these distances:
79 23 0.20
80 80 0.68
81 14 0.12
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.38
Consensus pattern (79 bp):
GTCATTTTACCCTTCAAGGGCATTACGGTAATTTTACCTACAGGGTATTTCGGTCATTTTACCCT
ACAAGGGTATTACG
Found at i:40209600 original size:53 final size:53
Alignment explanation
Indices: 40209502--40209651 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 53
40209492 CTTCAAGGGC
* * * *
40209502 ATTACGGTAATTTTACCTTACAGTGGTATTTCGGTCATTTAACCCTAT-GGGGT
1 ATTACGGT-ATTTTACCCTACAGAGGTATTACGGTCATTTTACCCTATGGGGGT
* * *
40209555 ATTACGGTCATTTTACCCTACAGAGGCATTACAGTTATTTTACCCTATGGGGGT
1 ATTACGGT-ATTTTACCCTACAGAGGTATTACGGTCATTTTACCCTATGGGGGT
* *
40209609 TTTTCGGTATTTTACCCTACA-AGGGTATTACGGTCATTTTACC
1 ATTACGGTATTTTACCCTACAGA-GGTATTACGGTCATTTTACC
40209652 TATCAAGGGT
Statistics
Matches: 82, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
52 1 0.01
53 70 0.85
54 11 0.13
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (53 bp):
ATTACGGTATTTTACCCTACAGAGGTATTACGGTCATTTTACCCTATGGGGGT
Found at i:40209688 original size:54 final size:54
Alignment explanation
Indices: 40209617--40209763 Score: 201
Period size: 54 Copynumber: 2.7 Consensus size: 54
40209607 GTTTTTCGGT
* *
40209617 ATTTTACCC-TACAAGGGTATTACGGTCATTTTACCTATCAAGGGTATTTTGATA
1 ATTTTACCCAT-CGAGGGTATTACGGTCATTTTACCCATCAAGGGTATTTTGATA
* *
40209671 ATTTTACCCATCGAGGGTATTTCGGTCATTTTACCCATCAGGGGTATTTTGATA
1 ATTTTACCCATCGAGGGTATTACGGTCATTTTACCCATCAAGGGTATTTTGATA
*
40209725 ATTATACCCATCGAGGGTATTTTAC--TCATTTTACCCATC
1 ATTTTACCCATCGAGGGTA--TTACGGTCATTTTACCCATC
40209764 GAGGATAATT
Statistics
Matches: 84, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
54 80 0.95
55 1 0.01
56 3 0.04
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (54 bp):
ATTTTACCCATCGAGGGTATTACGGTCATTTTACCCATCAAGGGTATTTTGATA
Found at i:40209787 original size:54 final size:54
Alignment explanation
Indices: 40209642--40209864 Score: 198
Period size: 54 Copynumber: 4.1 Consensus size: 54
40209632 GGTATTACGG
* * * * * **
40209642 TCATTTTACCTATCAAGGGTATTTTGATAATTTTACCCATCGAGGGTATTTCGG
1 TCATTTTACCCATCGAGGGTAATTTGGTCATTTTACCCATCGAGGGTATTTCAA
* * * * * *
40209696 TCATTTTACCCATC-AGGGGTATTTTGATAATTATACCCATCGAGGGTATTTTAC
1 TCATTTTACCCATCGA-GGGTAATTTGGTCATTTTACCCATCGAGGGTATTTCAA
* * * * *
40209750 TCATTTTACCCATCGAGGATAATTCGGTCATTTTACCCTTCAAGGGTAATTCAA
1 TCATTTTACCCATCGAGGGTAATTTGGTCATTTTACCCATCGAGGGTATTTCAA
* * * * *
40209804 TCATTTTACCC-TACGAGGGTAATTTAGTCATTTTACCCCCTCGGGGGTAATTCGA
1 TCATTTTACCCAT-CGAGGGTAATTTGGTCATTTTA-CCCATCGAGGGTATTTCAA
40209859 TCATTT
1 TCATTT
40209865 AACAAATATT
Statistics
Matches: 142, Mismatches: 23, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
53 2 0.01
54 118 0.83
55 22 0.15
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (54 bp):
TCATTTTACCCATCGAGGGTAATTTGGTCATTTTACCCATCGAGGGTATTTCAA
Found at i:40209814 original size:81 final size:80
Alignment explanation
Indices: 40209611--40209864 Score: 271
Period size: 81 Copynumber: 3.1 Consensus size: 80
40209601 ATGGGGGTTT
* * * * *
40209611 TTCGGT-ATTTTACCCTACAAGGGT-ATTACGGTCATTTTACCTATCAAGGGTATTTTGATAATT
1 TTCGGTCATTTTACCCTTCAAGGGTAATT-CGATCATTTTACCCATCGAGGGTATTTT-ATCATT
*
40209674 TTACCCATCGAGGGTAT
64 TTACCCATCGAGGGTAA
* * * * * *
40209691 TTCGGTCATTTTACCCATCAGGGGTATTTTGATAATTATACCCATCGAGGGTATTTTACTCATTT
1 TTCGGTCATTTTACCCTTCAAGGGTAATTCGATCATTTTACCCATCGAGGGTATTTTA-TCATTT
*
40209756 TACCCATCGAGGATAA
65 TACCCATCGAGGGTAA
* *
40209772 TTCGGTCATTTTACCCTTCAAGGGTAATTCAATCATTTTACCC-TACGAGGGTAATTTAGTCATT
1 TTCGGTCATTTTACCCTTCAAGGGTAATTCGATCATTTTACCCAT-CGAGGGTATTTTA-TCATT
* *
40209836 TTACCCCCTCGGGGGTAA
64 TTA-CCCATCGAGGGTAA
*
40209854 TTCGATCATTT
1 TTCGGTCATTT
40209865 AACAAATATT
Statistics
Matches: 143, Mismatches: 26, Indels: 8
0.81 0.15 0.05
Matches are distributed among these distances:
80 8 0.06
81 112 0.78
82 23 0.16
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (80 bp):
TTCGGTCATTTTACCCTTCAAGGGTAATTCGATCATTTTACCCATCGAGGGTATTTTATCATTTT
ACCCATCGAGGGTAA
Found at i:40209865 original size:27 final size:27
Alignment explanation
Indices: 40209736--40209864 Score: 109
Period size: 27 Copynumber: 4.7 Consensus size: 27
40209726 TTATACCCAT
* * *
40209736 CGAGGGTATTTTACTCATTTTACCC-A
1 CGAGGGTAATTCAATCATTTTACCCTA
* ** *
40209762 TCGAGGATAATTCGGTCATTTTACCCTT
1 -CGAGGGTAATTCAATCATTTTACCCTA
*
40209790 CAAGGGTAATTCAATCATTTTACCCTA
1 CGAGGGTAATTCAATCATTTTACCCTA
* *
40209817 CGAGGGTAATTTAGTCATTTTACCCCCT-
1 CGAGGGTAATTCAATCATTTTA--CCCTA
* *
40209845 CGGGGGTAATTCGATCATTT
1 CGAGGGTAATTCAATCATTT
40209865 AACAAATATT
Statistics
Matches: 81, Mismatches: 18, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
27 61 0.75
28 16 0.20
29 4 0.05
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (27 bp):
CGAGGGTAATTCAATCATTTTACCCTA
Found at i:40212292 original size:41 final size:41
Alignment explanation
Indices: 40212276--40212429 Score: 290
Period size: 41 Copynumber: 3.8 Consensus size: 41
40212266 CTTATAGCTT
* *
40212276 GATTCAGATCACCGGCACGTAGCCTGCTAGGTTTATAACCT
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
40212317 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
40212358 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
1 GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
40212399 GATTCAAATCACCGGCACGTAGCCTGCTAGG
1 GATTCAAATCACCGGCACGTAGCCTGCTAGG
40212430 NNNNNNNNNN
Statistics
Matches: 111, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 111 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (41 bp):
GATTCAAATCACCGGCACGTAGCCTGCTAGGTTTATAACCC
Found at i:40221757 original size:41 final size:41
Alignment explanation
Indices: 40221520--40221747 Score: 381
Period size: 41 Copynumber: 5.6 Consensus size: 41
40221510 TGATTCAGTA
40221520 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40221561 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40221602 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
40221643 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* * *
40221684 CACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
40221725 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
40221748 GTAACGTCTG
Statistics
Matches: 180, Mismatches: 4, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 173 0.96
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:40223035 original size:16 final size:19
Alignment explanation
Indices: 40223000--40223038 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
40222990 TATGTTTTGT
40223000 TTTATTATATTATACATTA
1 TTTATTATATTATACATTA
40223019 TTTATTA-ATT-TAC-TTA
1 TTTATTATATTATACATTA
40223035 TTTA
1 TTTA
40223039 ACCTTTAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.35
17 3 0.15
18 3 0.15
19 7 0.35
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATTATATTATACATTA
Found at i:40223494 original size:41 final size:41
Alignment explanation
Indices: 40223375--40223517 Score: 137
Period size: 41 Copynumber: 3.5 Consensus size: 41
40223365 GGTTGTTACA
* ** *
40223375 GCCTAGCAGGCTTTATGCCGGTGAATTATAGCAGGCTTTAT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
** * * *
40223416 GCCTAGCAGGCTTCGTGCCGGTGTATCAT-ATCTAGCTTTGT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAAT-AAGCTTTAT
* *
40223457 GCCTAGAAGGCTTTATGCCGGTGTATTTTAATAAGCTTTAT
1 GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
* *
40223498 ACATCA-CAGGCTTTATGCCG
1 GCCT-AGCAGGCTTTATGCCG
40223518 ATGTGGTATC
Statistics
Matches: 80, Mismatches: 19, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
41 77 0.96
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.24, T:0.34
Consensus pattern (41 bp):
GCCTAGCAGGCTTTATGCCGGTGTATTATAATAAGCTTTAT
Found at i:40227569 original size:41 final size:41
Alignment explanation
Indices: 40227508--40227669 Score: 193
Period size: 41 Copynumber: 4.0 Consensus size: 41
40227498 TGAAAATAAG
* *
40227508 ATGTTTCAGACTTTACGTCTAAG-AGGCTTGATGCCGATGAA
1 ATGTTTCAGACTTTATGTCT-AGCAGGCTTGATGCCGGTGAA
40227549 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
* **
40227590 TTACTTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAA
1 ATGTTTCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTGAA
* * * * * *
40227631 ATGTATCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
40227670 TTTTATACAA
Statistics
Matches: 104, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
40 4 0.04
41 97 0.93
42 3 0.03
ACGTcount: A:0.20, C:0.19, G:0.27, T:0.34
Consensus pattern (41 bp):
ATGTTTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAA
Found at i:40231572 original size:46 final size:46
Alignment explanation
Indices: 40231487--40231574 Score: 115
Period size: 46 Copynumber: 1.9 Consensus size: 46
40231477 AAATATGCAG
* * * *
40231487 TGTGGGCCTTAGCCCATTACAGTATCAGAATTAGAAATAGAATACA
1 TGTGGGCCTAAGCCCAATACAGTATCAAAATCAGAAATAGAATACA
*
40231533 TGTGGGCCTAAGCCCAATACAGTGA-CAAAATCAGTAATAGAA
1 TGTGGGCCTAAGCCCAATACAGT-ATCAAAATCAGAAATAGAA
40231575 ATGCAACAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
46 35 0.97
47 1 0.03
ACGTcount: A:0.39, C:0.18, G:0.20, T:0.23
Consensus pattern (46 bp):
TGTGGGCCTAAGCCCAATACAGTATCAAAATCAGAAATAGAATACA
Found at i:40231845 original size:32 final size:32
Alignment explanation
Indices: 40231790--40231928 Score: 163
Period size: 32 Copynumber: 4.4 Consensus size: 32
40231780 GAATGGCTAC
* **
40231790 AAGCCATAAGT-ACAGTAATATGATTAGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* * *
40231821 AAGCCATCAGTAGCAGTGATATGATCGACACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
* ** * *
40231853 CAGCCATCAGTAATGGTAATATGATCGGTACG
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
*
40231885 AAGCCATCAGTAACGGTAATATGATCGGCACA
1 AAGCCATCAGTAACAGTAATATGATCGGCACA
40231917 AAGCCATCAGTA
1 AAGCCATCAGTA
40231929 GCATCGCAGC
Statistics
Matches: 89, Mismatches: 18, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
31 10 0.11
32 79 0.89
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.21
Consensus pattern (32 bp):
AAGCCATCAGTAACAGTAATATGATCGGCACA
Found at i:40232101 original size:24 final size:24
Alignment explanation
Indices: 40232073--40232130 Score: 91
Period size: 24 Copynumber: 2.4 Consensus size: 24
40232063 ACATTTTCAG
*
40232073 AATCAGTCATACGAATCACAGAA-A
1 AATCAGTCATACCAATCACA-AACA
40232097 AATCAGTCATACCAATCACAAACA
1 AATCAGTCATACCAATCACAAACA
40232121 AATCAGTCAT
1 AATCAGTCAT
40232131 TTAAATCATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 2 0.06
24 30 0.94
ACGTcount: A:0.48, C:0.24, G:0.09, T:0.19
Consensus pattern (24 bp):
AATCAGTCATACCAATCACAAACA
Found at i:40232137 original size:24 final size:24
Alignment explanation
Indices: 40232086--40232163 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
40232076 CAGTCATACG
***
40232086 AATCACAGAA-AAATCAGTCATACC
1 AATCACA-AACAAATCAGTCATTTA
40232110 AATCACAAACAAATCAGTCATTTA
1 AATCACAAACAAATCAGTCATTTA
* * *
40232134 AATCATAGACAAATCAATCATTTA
1 AATCACAAACAAATCAGTCATTTA
*
40232158 CATCAC
1 AATCAC
40232164 GGACAAATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
23 2 0.04
24 43 0.96
ACGTcount: A:0.49, C:0.23, G:0.05, T:0.23
Consensus pattern (24 bp):
AATCACAAACAAATCAGTCATTTA
Found at i:40232168 original size:24 final size:24
Alignment explanation
Indices: 40232111--40232183 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
40232101 AGTCATACCA
* * *
40232111 ATCACAAACAAATCAGTCATTTAA
1 ATCACAGACAAATCAATCATTTAC
*
40232135 ATCATAGACAAATCAATCATTTAC
1 ATCACAGACAAATCAATCATTTAC
* * *
40232159 ATCACGGACAAATAAATCACTTAC
1 ATCACAGACAAATCAATCATTTAC
40232183 A
1 A
40232184 CTCGAAAGGT
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.48, C:0.22, G:0.05, T:0.25
Consensus pattern (24 bp):
ATCACAGACAAATCAATCATTTAC
Found at i:40232257 original size:27 final size:27
Alignment explanation
Indices: 40232227--40232507 Score: 145
Period size: 27 Copynumber: 10.4 Consensus size: 27
40232217 GGCATTACGG
* * *
40232227 TCATTTTACCTTATAGTGGAATTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* * *
40232254 TCATTTAACCCTATGGGGGTTTTTCGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* *
40232281 TCATTTTACCCTACAGGGGTATTACGA
1 TCATTTTACCCTATAGGGGTATTTCGA
* *
40232308 TTATTTTA-CCTATCGAGGGTATTTC-A
1 TCATTTTACCCTATAG-GGGTATTTCGA
* * *
40232334 TTAATTTTA-CCTATCGAGGGTATTTCAA
1 -TCATTTTACCCTATAG-GGGTATTTCGA
* *
40232362 TCATTTTACCC-ATCGAGGGTATTT-TA
1 TCATTTTACCCTATAG-GGGTATTTCGA
* * *
40232388 GTCATTTTACCC-ATCGAGGGTATTTTGG
1 -TCATTTTACCCTATAG-GGGTATTTCGA
* * *
40232416 TAATTTTACCC-ATCGAGGGTAATTC-A
1 TCATTTTACCCTATAG-GGGTATTTCGA
* *
40232442 GTCATTTTACCCT-TCAGAGGTAATTTAG-
1 -TCATTTTACCCTAT-AGGGGT-ATTTCGA
* *
40232470 TCATTTTACCCTA-CGAGGGTAATTT-GG
1 TCATTTTACCCTATAG-GGGT-ATTTCGA
40232497 TCATTTTACCC
1 TCATTTTACCC
40232508 CTCGAGGGTA
Statistics
Matches: 209, Mismatches: 31, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
26 9 0.04
27 193 0.92
28 7 0.03
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTATAGGGGTATTTCGA
Found at i:40232341 original size:54 final size:55
Alignment explanation
Indices: 40232226--40232517 Score: 225
Period size: 54 Copynumber: 5.4 Consensus size: 55
40232216 GGGCATTACG
* * * * * *
40232226 GTCATTTTACCTTAT--AGTGGAATTTCGATCATTTAACCCTAT-GGGGGTTTTTC-
1 GTCATTTTACCCTATCGAG-GGTATTTCGATAATTTTACCC-ATCGAGGGTATTTCA
* * *
40232279 GATCATTTTACCCTA-C-AGGGGTATTACGATTATTTTACCTATCGAGGGTATTTCA
1 G-TCATTTTACCCTATCGA-GGGTATTTCGATAATTTTACCCATCGAGGGTATTTCA
* * * * *
40232334 TTAATTTTA-CCTATCGAGGGTATTTCAATCATTTTACCCATCGAGGGTATTTTA
1 GTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCA
* * *
40232388 GTCATTTTACCC-ATCGAGGGTATTTTGGTAATTTTACCCATCGAGGGTAATTCA
1 GTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCA
* * *
40232442 GTCATTTTACCCT-TC-AGAGGTAATTTAG-TCATTTTACCC-TACGAGGGTAATTT-G
1 GTCATTTTACCCTATCGAG-GGT-ATTTCGATAATTTTACCCAT-CGAGGGT-ATTTCA
*
40232496 GTCATTTTACCC-CTCGAGGGTA
1 GTCATTTTACCCTATCGAGGGTA
40232518 ATTCAGTCAT
Statistics
Matches: 197, Mismatches: 27, Indels: 30
0.78 0.11 0.12
Matches are distributed among these distances:
53 11 0.06
54 172 0.87
55 14 0.07
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (55 bp):
GTCATTTTACCCTATCGAGGGTATTTCGATAATTTTACCCATCGAGGGTATTTCA
Found at i:40232365 original size:81 final size:80
Alignment explanation
Indices: 40232270--40232529 Score: 260
Period size: 81 Copynumber: 3.2 Consensus size: 80
40232260 AACCCTATGG
* * * *
40232270 GGGTTTTTCGATCATTTTACCCTACAGGGGTA-TTACGATTATTTTACCTATCGAGGGTATTTCA
1 GGGTATTTCAATCATTTTACCCTACAGGGGTATTTA-G-TCATTTTACCCATCGAGGGTATTTCA
* *
40232334 TTAATTTTACCTATCGA
64 GTAATTTTACCCATCGA
*
40232351 GGGTATTTCAATCATTTTACCC-ATC-GAGGGTATTTTAGTCATTTTACCCATCGAGGGTATTTT
1 GGGTATTTCAATCATTTTACCCTA-CAG-GGGTA-TTTAGTCATTTTACCCATCGAGGGTATTTC
*
40232414 GGTAATTTTACCCATCGA
63 AGTAATTTTACCCATCGA
* * * *
40232432 GGGTAATTCAGTCATTTTACCCTTCAGAGGTAATTTAGTCATTTTACCC-TACGAGGGTAATTT-
1 GGGTATTTCAATCATTTTACCCTACAGGGGT-ATTTAGTCATTTTACCCAT-CGAGGGT-ATTTC
* * *
40232495 GGTCATTTTACCCCTCGA
63 AGTAATTTTACCCATCGA
* *
40232513 GGGTAATTCAGTCATTT
1 GGGTATTTCAATCATTT
40232530 AACAAATATT
Statistics
Matches: 156, Mismatches: 14, Indels: 18
0.83 0.07 0.10
Matches are distributed among these distances:
80 3 0.02
81 143 0.92
82 7 0.04
83 3 0.02
ACGTcount: A:0.23, C:0.18, G:0.18, T:0.40
Consensus pattern (80 bp):
GGGTATTTCAATCATTTTACCCTACAGGGGTATTTAGTCATTTTACCCATCGAGGGTATTTCAGT
AATTTTACCCATCGA
Found at i:40232513 original size:27 final size:27
Alignment explanation
Indices: 40232310--40232529 Score: 250
Period size: 27 Copynumber: 8.1 Consensus size: 27
40232300 TATTACGATT
* * *
40232310 ATTTTACCTATCGAGGGT-ATTTCATTA
1 ATTTTACCCATCGAGGGTAATTT-AGTC
* *
40232337 ATTTTACCTATCGAGGGT-ATTTCAATC
1 ATTTTACCCATCGAGGGTAATTT-AGTC
*
40232364 ATTTTACCCATCGAGGGTATTTTAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
* * *
40232391 ATTTTACCCATCGAGGGTATTTTGGTA
1 ATTTTACCCATCGAGGGTAATTTAGTC
*
40232418 ATTTTACCCATCGAGGGTAATTCAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
*
40232445 ATTTTACCCTTC-AGAGGTAATTTAGTC
1 ATTTTACCCATCGAG-GGTAATTTAGTC
*
40232472 ATTTTACCC-TACGAGGGTAATTTGGTC
1 ATTTTACCCAT-CGAGGGTAATTTAGTC
* *
40232499 ATTTTACCCCTCGAGGGTAATTCAGTC
1 ATTTTACCCATCGAGGGTAATTTAGTC
40232526 ATTT
1 ATTT
40232530 AACAAATATT
Statistics
Matches: 172, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
26 3 0.02
27 163 0.95
28 6 0.03
ACGTcount: A:0.24, C:0.19, G:0.18, T:0.40
Consensus pattern (27 bp):
ATTTTACCCATCGAGGGTAATTTAGTC
Found at i:40240376 original size:159 final size:159
Alignment explanation
Indices: 40240136--40240447 Score: 484
Period size: 159 Copynumber: 2.0 Consensus size: 159
40240126 AAAGATACAT
* * * *
40240136 AATTTAAAACATTATGGTTCTAAAGGACCTAAGTGAATATGTGCATACCATGTTTTAATTACAAG
1 AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
*
40240201 TTTTATATGCTTGATGATAAGAATATA-ACATTGTTTATTTATTGAAATTATCGTACGTAGTTAA
66 TTTTATATGCTTGATGATAAGAATA-ACACATTGTTTATTTATTGAAATTATCATACGTAGTTAA
* *
40240265 AATCGATGCCATTCTATTGAAAGATGTGAG
130 AATCGATGCCAGTCTATCGAAAGATGTGAG
* * *
40240295 AATTTAGAACATTACGGTTCTAAAATAACTAAGTGAATATGTGCATACCATGTTTTAAATA-TAG
1 AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
* *
40240359 TTTTTATATGCTTGATGATGAGAATAACACATTGTTTCTTTATTGAAATTATCATACGTAGTTAA
66 -TTTTATATGCTTGATGATAAGAATAACACATTGTTTATTTATTGAAATTATCATACGTAGTTAA
40240424 AATCGATGCCAGTCTATCGAAAGA
130 AATCGATGCCAGTCTATCGAAAGA
40240448 CAAAGGGAAA
Statistics
Matches: 139, Mismatches: 12, Indels: 4
0.90 0.08 0.03
Matches are distributed among these distances:
158 3 0.02
159 136 0.98
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (159 bp):
AATTTAAAACATTACGGTTCTAAAAGAACTAAGTGAATATGTGCATACCATGTTTTAAATACAAG
TTTTATATGCTTGATGATAAGAATAACACATTGTTTATTTATTGAAATTATCATACGTAGTTAAA
ATCGATGCCAGTCTATCGAAAGATGTGAG
Found at i:40242211 original size:13 final size:13
Alignment explanation
Indices: 40242193--40242256 Score: 110
Period size: 13 Copynumber: 4.9 Consensus size: 13
40242183 AGTTCTTCAT
40242193 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
40242206 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
* *
40242219 TGTTTTTCAGAAG
1 TGCTTTTGAGAAG
40242232 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
40242245 TGCTTTTGAGAA
1 TGCTTTTGAGAA
40242257 ATTTGAGTGT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 47 1.00
ACGTcount: A:0.23, C:0.08, G:0.28, T:0.41
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:40242515 original size:8 final size:8
Alignment explanation
Indices: 40242502--40242537 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
40242492 TAATTAGAAT
40242502 ATATTTAA
1 ATATTTAA
40242510 ATATTTAA
1 ATATTTAA
40242518 ATATTTAA
1 ATATTTAA
40242526 ATATTTAA
1 ATATTTAA
40242534 ATAT
1 ATAT
40242538 AAAAATTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
ATATTTAA
Found at i:40242543 original size:16 final size:16
Alignment explanation
Indices: 40242508--40242543 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
40242498 GAATATATTT
**
40242508 AAATATTTAAATATTT
1 AAATATTTAAATATAA
40242524 AAATATTTAAATATAA
1 AAATATTTAAATATAA
40242540 AAAT
1 AAAT
40242544 TAAATATTTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
AAATATTTAAATATAA
Found at i:40245188 original size:32 final size:32
Alignment explanation
Indices: 40245147--40245208 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
40245137 AAGGTTAACA
40245147 TATTTAATATTTATATATAAATATAGGATAGT
1 TATTTAATATTTATATATAAATATAGGATAGT
40245179 TATTTAATATTTATATATAAATATAGGATA
1 TATTTAATATTTATATATAAATATAGGATA
40245209 ATCATGGGTC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.08, T:0.47
Consensus pattern (32 bp):
TATTTAATATTTATATATAAATATAGGATAGT
Found at i:40248039 original size:143 final size:143
Alignment explanation
Indices: 40247781--40248069 Score: 517
Period size: 143 Copynumber: 2.0 Consensus size: 143
40247771 TAAATACGTA
40247781 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
*
40247846 CCACTGGCTGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
66 CCACTGGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
*
40247911 GCTCGAAACCAAG
131 ACTCGAAACCAAG
40247924 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
1 GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
* * *
40247989 CCA-TGGGCCGAGTTACGTGGGAGTACCTGACGATTTGGAAAACGTTAGGCTGCTGTTAGATCAA
66 CCACT-GGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAA
40248053 TACTCGAAACCAAG
130 TACTCGAAACCAAG
40248067 GTT
1 GTT
40248070 AATTACCTAT
Statistics
Matches: 140, Mismatches: 5, Indels: 2
0.95 0.03 0.01
Matches are distributed among these distances:
142 1 0.01
143 139 0.99
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (143 bp):
GTTTGTGCAGTAAATGTTTTTATTTATCATATGTTTTGACTAATATATAGCTTGTACAGGTGGAA
CCACTGGCCGAGTTACGTGGGAGTACCTGACGAGTTGGAAAACATTAGGCTACTGTTAGATCAAT
ACTCGAAACCAAG
Found at i:40254415 original size:3 final size:3
Alignment explanation
Indices: 40254407--40254456 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
40254397 GGACTAGATG
40254407 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
40254455 TA
1 TA
40254457 GAAAAAAACA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:40262618 original size:26 final size:26
Alignment explanation
Indices: 40262584--40262644 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
40262574 CCTTAAATAT
* *
40262584 AATTAAAATAT-ATTAAATTATTTAAC
1 AATTTAAATATGATAAAATT-TTTAAC
*
40262610 AATTTAAATATGATAAAATTTTTAAT
1 AATTTAAATATGATAAAATTTTTAAC
40262636 AATATTAAA
1 AAT-TTAAA
40262645 AAAATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 18 0.60
27 12 0.40
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
AATTTAAATATGATAAAATTTTTAAC
Found at i:40265035 original size:23 final size:22
Alignment explanation
Indices: 40264965--40265049 Score: 104
Period size: 21 Copynumber: 4.0 Consensus size: 22
40264955 CCTGATCAGT
40264965 ATACGACACAT-AAGTGCCTA-
1 ATACGACACATAAAGTGCCTAG
* ** *
40264985 AAACGACACACGAGGTGCCT-G
1 ATACGACACATAAAGTGCCTAG
40265006 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCT-AG
40265029 ATACGACACATAAAGTGCCTA
1 ATACGACACATAAAGTGCCTA
40265050 ATTGGCAAAG
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
22 1 0.02
23 21 0.39
ACGTcount: A:0.39, C:0.25, G:0.20, T:0.16
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTAG
Found at i:40266070 original size:51 final size:50
Alignment explanation
Indices: 40265990--40266327 Score: 317
Period size: 51 Copynumber: 6.7 Consensus size: 50
40265980 GATGAACACG
*
40265990 TGTGTAGTACTGTGTGAAGGCTACTATGTGTATCGATAAATAATTGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAAT-ATTGTCACA
* * * * * * *
40266041 TGTCTAGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCT-TTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAA-ATATT-GTCACA
* * * *
40266092 TGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACA
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAAT-ATTGTCACA
* * *
40266143 TGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGTTTTGGTCACG
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAA-TATT-GTCACA
* * * * *
40266194 TGTGTAGTACTATGTGAAGGCTAGTACGTGAACCG-TAAAAACTTGATCACA
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAATA-TTG-TCACA
* * * *
40266245 TGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCACG
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAATA-TTG-TCACA
* *
40266295 TGTGTAGTACTATGTGGAGGCTACTACGTGTAT
1 TGTGTAGTACTATGTGAAGGCTACTATGTGTAT
40266328 TGAATGATAA
Statistics
Matches: 239, Mismatches: 39, Indels: 19
0.80 0.13 0.06
Matches are distributed among these distances:
50 48 0.20
51 189 0.79
52 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (50 bp):
TGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAATATTGTCACA
Found at i:40266162 original size:102 final size:101
Alignment explanation
Indices: 40265986--40266324 Score: 441
Period size: 102 Copynumber: 3.3 Consensus size: 101
40265976 TATCGATGAA
* * * * *
40265986 CACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTATCGATAAATAATTGTCACATGTCTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
*
40266051 TAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCGA-AAGCTTTGGT
* *
40266088 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATGATGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
* *
40266153 TAAGTGAAGGCTACTATGTGTATCGAAAAGTTTTGGT
66 TAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
* * *
40266190 CACGTGTGTAGTACTATGTGAAGGCTAGTACGTGAACCG-TAAA-AACTTGATCACATGTGTAGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAA--TGGTCACATGTGTAGT
* * * * *
40266253 ACTATGTGAAGGCTACTACGTGAACCGTAAAAC-TTGAT
64 ACTAAGTGAAGGCTACTATGTGTACCG-AAAGCTTTGGT
*
40266291 CACGTGTGTAGTACTATGTGGAGGCTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
40266325 TATTGAATGA
Statistics
Matches: 211, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
100 1 0.00
101 40 0.19
102 169 0.80
103 1 0.00
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (101 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCGAAAGCTTTGGT
Found at i:40266249 original size:153 final size:152
Alignment explanation
Indices: 40265981--40266327 Score: 412
Period size: 153 Copynumber: 2.3 Consensus size: 152
40265971 TAAGGTATCG
* * *
40265981 ATGAACACGTGTGTAGTACTGTGTGAAGGCTACTATGTGTATCGATAAATAATTGTCACATGTCT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAATAATTGTCACATGTCT
* * * * * * *
40266046 AGTACTAAGTGAAGGCTACAATGTGTACCGAGAAGCTTTGGTCACGTGTGTAGTACTGTGTGAAG
66 AGTACTAAGTGAAGGCTACAACGTGAACCGAAAAACTTTGATCACATGTGTAGTACTATGTGAAG
* **
40266111 GCTACTACGTGAATCGATAAATG
131 GCTACTACGTGAACCG-TAAAAC
* * * *
40266134 ATGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTATCGA-AAAGT-TTTGGTCACGTGT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAA-TAATT-GTCACATGT
* * **
40266197 GTAGTACTATGTGAAGGCTAGTACGTGAACCGTAAAAAC-TTGATCACATGTGTAGTACTATGTG
64 CTAGTACTAAGTGAAGGCTACAACGTGAACCG-AAAAACTTTGATCACATGTGTAGTACTATGTG
40266261 AAGGCTACTACGTGAACCGTAAAAC
128 AAGGCTACTACGTGAACCGTAAAAC
* * * *
40266286 TTGATCACGTGTGTAGTACTATGTGGAGGCTACTACGTGTAT
1 ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTAT
40266328 TGAATGATAA
Statistics
Matches: 164, Mismatches: 27, Indels: 7
0.83 0.14 0.04
Matches are distributed among these distances:
152 45 0.27
153 115 0.70
154 4 0.02
ACGTcount: A:0.29, C:0.15, G:0.26, T:0.30
Consensus pattern (152 bp):
ATGATCACATGTGTAGTACTATGTGAAGGCTACTATGTGTATCGATAAATAATTGTCACATGTCT
AGTACTAAGTGAAGGCTACAACGTGAACCGAAAAACTTTGATCACATGTGTAGTACTATGTGAAG
GCTACTACGTGAACCGTAAAAC
Found at i:40268177 original size:23 final size:22
Alignment explanation
Indices: 40268106--40268191 Score: 97
Period size: 21 Copynumber: 4.0 Consensus size: 22
40268096 CCTGATCAGT
40268106 ATACGACACAT-AAGTGCCTGA
1 ATACGACACATAAAGTGCCTGA
** *
40268127 A-ACGACACACGAGGTGCCT-A
1 ATACGACACATAAAGTGCCTGA
*
40268147 ATACGACACATAAAGTGTCTGA
1 ATACGACACATAAAGTGCCTGA
*
40268169 GATACGACACATAAAGTGTCTGA
1 -ATACGACACATAAAGTGCCTGA
40268192 TCGGCAAAGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
20 10 0.18
21 22 0.40
22 1 0.02
23 22 0.40
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (22 bp):
ATACGACACATAAAGTGCCTGA
Found at i:40269144 original size:30 final size:28
Alignment explanation
Indices: 40269073--40269155 Score: 78
Period size: 30 Copynumber: 2.9 Consensus size: 28
40269063 ATTTTCCCTC
* **
40269073 TTTCTTTTCTTTCCCTTTTTCTTCCCCTGT
1 TTTCTTTTCTTTCTC-TTTTCTT-TTCTGT
* *
40269103 TTTCGTCTCTTTCTCTGTTTCTTTTCTGT
1 TTTCTTTTCTTTCTCT-TTTCTTTTCTGT
40269132 TCTTCTTTTCTTTCT-TTTTCTTTT
1 T-TTCTTTTCTTTCTCTTTTCTTTT
40269156 TTTTTTGTTT
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
28 8 0.18
29 7 0.16
30 29 0.66
ACGTcount: A:0.00, C:0.27, G:0.05, T:0.69
Consensus pattern (28 bp):
TTTCTTTTCTTTCTCTTTTCTTTTCTGT
Found at i:40269404 original size:30 final size:27
Alignment explanation
Indices: 40269364--40269428 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 27
40269354 TTTCCTATAA
* *
40269364 TATATTATTTTAATCTTAATTAATATAATT
1 TATAATATTTTAAT-TTAA-CAATAT-ATT
*
40269394 TATAATATTTTAATTTAACAATATTTT
1 TATAATATTTTAATTTAACAATATATT
40269421 TATAATAT
1 TATAATAT
40269429 AAATCAAGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 10 0.31
28 5 0.16
29 4 0.12
30 13 0.41
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (27 bp):
TATAATATTTTAATTTAACAATATATT
Found at i:40271718 original size:21 final size:20
Alignment explanation
Indices: 40271685--40271724 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
40271675 ATTTTTACGA
40271685 TTTTAAATATAAAATATTAG
1 TTTTAAATATAAAATATTAG
*
40271705 TTTTATATCATAAAATATTA
1 TTTTAAAT-ATAAAATATTA
40271725 AAATTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTTAAATATAAAATATTAG
Found at i:40271988 original size:49 final size:49
Alignment explanation
Indices: 40271931--40272027 Score: 194
Period size: 49 Copynumber: 2.0 Consensus size: 49
40271921 GATACATGCC
40271931 GTTATCCACTATTCACACCCAAATCCAAGTACCATTGCTGACCAGGAGG
1 GTTATCCACTATTCACACCCAAATCCAAGTACCATTGCTGACCAGGAGG
40271980 GTTATCCACTATTCACACCCAAATCCAAGTACCATTGCTGACCAGGAG
1 GTTATCCACTATTCACACCCAAATCCAAGTACCATTGCTGACCAGGAG
40272028 CCGAGTAAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (49 bp):
GTTATCCACTATTCACACCCAAATCCAAGTACCATTGCTGACCAGGAGG
Found at i:40275838 original size:20 final size:20
Alignment explanation
Indices: 40275815--40275852 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40275805 AAAAATAGAA
40275815 AAAAATAAG-AAAAATAATGT
1 AAAAA-AAGTAAAAATAATGT
*
40275835 AAAAAAAGTAAAAGTAAT
1 AAAAAAAGTAAAAATAAT
40275853 AAAAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (20 bp):
AAAAAAAGTAAAAATAATGT
Found at i:40279276 original size:30 final size:29
Alignment explanation
Indices: 40279145--40279278 Score: 78
Period size: 30 Copynumber: 4.5 Consensus size: 29
40279135 TTTTTCTTAC
* * *
40279145 CATTTTATAATTAATGTTAACA-TATTTT
1 CATTATATAATTAATGTAAACACGATTTT
* *
40279173 CA-TAGTATAGTTAATGTAAACATACACATTTT
1 CATTA-TATAATTAATGTAAAC--AC-GATTTT
* * * *
40279205 CATAATATAATTGATGTATAA-ATGCTTTCT
1 CATTATATAATTAATGTA-AACACGATTT-T
*
40279235 CA-TAGTTTAATTAATGTAAACACGATTTCT
1 CATTA-TATAATTAATGTAAACACGATTT-T
40279265 CATTATATAATTAA
1 CATTATATAATTAA
40279279 GCTAAAAATC
Statistics
Matches: 79, Mismatches: 16, Indels: 20
0.69 0.14 0.17
Matches are distributed among these distances:
27 1 0.01
28 16 0.20
29 6 0.08
30 33 0.42
31 2 0.03
32 18 0.23
33 3 0.04
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.43
Consensus pattern (29 bp):
CATTATATAATTAATGTAAACACGATTTT
Found at i:40281391 original size:41 final size:41
Alignment explanation
Indices: 40281245--40281377 Score: 239
Period size: 41 Copynumber: 3.2 Consensus size: 41
40281235 ACTGGCACTT
* *
40281245 AGCCTGCTAGACATAAAGTCTGAAATGTTTCACCGGCATCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
*
40281286 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCATCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
40281327 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
1 AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
40281368 AGCCTGCTAG
1 AGCCTGCTAG
40281378 GCACCGAGCC
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 88 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (41 bp):
AGCCTGCTAGACTTAAAGTCTGAAATGTTTCACCGGCGTCA
Found at i:40282226 original size:288 final size:288
Alignment explanation
Indices: 40281710--40282262 Score: 1061
Period size: 288 Copynumber: 1.9 Consensus size: 288
40281700 ATAAACTTAT
40281710 CTATACATACCTTTCGATTAATAACCAAGAATTTATACATAAGCCATATTCATTCTTCAACTAAA
1 CTATACATACCTTTCGATTAATAACCAAGAATTTATACATAAGCCATATTCATTCTTCAACTAAA
40281775 TTCAAGAGCTTACATATATCTGTATACATATATGTATATTCGAACATTAATCATATATTTATATA
66 TTCAAGAGCTTACATATATCTGTATACATATATGTATATTCGAACATTAATCATATATTTATATA
*
40281840 TATACATATTATTTTTACTTTGACTAAATTCAAGCTATATACTTTCAATTTGAGCTCATCCAAAT
131 TATACATATCATTTTTACTTTGACTAAATTCAAGCTATATACTTTCAATTTGAGCTCATCCAAAT
* * *
40281905 GCAATATATATATGTATATATATATATATTAATTAATAACATTAAATTGCTAGTTGACTTACCTC
196 ACAATAGATATATATATATATATATATATTAATTAATAACATTAAATTGCTAGTTGACTTACCTC
40281970 GGACGCAAACCTTATATATATATATACA
261 GGACGCAAACCTTATATATATATATACA
40281998 CTATACATACCTTTCGATTAATAACCAAGAATTTATACATAAGCCATATTCATTCTTCAACTAAA
1 CTATACATACCTTTCGATTAATAACCAAGAATTTATACATAAGCCATATTCATTCTTCAACTAAA
*
40282063 TTCAAGAGCTTACATATATGTGTATACATATATGTATATTCGAACATTAATCATATATTTATATA
66 TTCAAGAGCTTACATATATCTGTATACATATATGTATATTCGAACATTAATCATATATTTATATA
40282128 TATACATATCATTTTTACTTTGACTAAATTCAAGCTATATACTTTCAATTTGAGCTCATCCAAAT
131 TATACATATCATTTTTACTTTGACTAAATTCAAGCTATATACTTTCAATTTGAGCTCATCCAAAT
40282193 ACAATAGATATATATATATATATATATATTAATTAATAACATTAAATTGCTAGTTGACTTACCTC
196 ACAATAGATATATATATATATATATATATTAATTAATAACATTAAATTGCTAGTTGACTTACCTC
40282258 GGACG
261 GGACG
40282263 GTGAAAAATT
Statistics
Matches: 260, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
288 260 1.00
ACGTcount: A:0.39, C:0.16, G:0.07, T:0.39
Consensus pattern (288 bp):
CTATACATACCTTTCGATTAATAACCAAGAATTTATACATAAGCCATATTCATTCTTCAACTAAA
TTCAAGAGCTTACATATATCTGTATACATATATGTATATTCGAACATTAATCATATATTTATATA
TATACATATCATTTTTACTTTGACTAAATTCAAGCTATATACTTTCAATTTGAGCTCATCCAAAT
ACAATAGATATATATATATATATATATATTAATTAATAACATTAAATTGCTAGTTGACTTACCTC
GGACGCAAACCTTATATATATATATACA
Found at i:40282958 original size:28 final size:26
Alignment explanation
Indices: 40282925--40282976 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
40282915 TTTTTAATGT
40282925 TTATTATAACATAATAATATATTATACC
1 TTATTATAACAT-AT-ATATATTATACC
40282953 TTATTATAACATATATATATTATA
1 TTATTATAACATATATATATTATA
40282977 TTAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 10 0.42
27 2 0.08
28 12 0.50
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATTATAACATATATATATTATACC
Found at i:40285681 original size:24 final size:23
Alignment explanation
Indices: 40285654--40285700 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
40285644 CCCTTTGCAT
40285654 GTTTATTTCCTGTTTTTAGTTTTA
1 GTTTATTTCCTGTTTTTA-TTTTA
**
40285678 GTTTATTTTTTGTTTTTATTTTA
1 GTTTATTTCCTGTTTTTATTTTA
40285701 TTTTGGGTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.13, C:0.04, G:0.11, T:0.72
Consensus pattern (23 bp):
GTTTATTTCCTGTTTTTATTTTA
Found at i:40287310 original size:20 final size:20
Alignment explanation
Indices: 40287280--40287317 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
40287270 TATAGATACA
40287280 ATTTTTAATTTTTGTTTAGTT
1 ATTTTTAATTTTT-TTTAGTT
40287301 ATTTTT-ATTTTTTTTAG
1 ATTTTTAATTTTTTTTAG
40287318 GTCATGTATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 6 0.35
21 6 0.35
ACGTcount: A:0.18, C:0.00, G:0.08, T:0.74
Consensus pattern (20 bp):
ATTTTTAATTTTTTTTAGTT
Found at i:40290345 original size:25 final size:28
Alignment explanation
Indices: 40290316--40290367 Score: 83
Period size: 25 Copynumber: 2.0 Consensus size: 28
40290306 TATATTAGTA
40290316 AAGGTTAATATA-GTA-AAT-TAACAAT
1 AAGGTTAATATATGTATAATATAACAAT
40290341 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAATATATGTATAATATAACAA
40290368 ATTAAAATGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 12 0.50
26 3 0.12
27 3 0.12
28 6 0.25
ACGTcount: A:0.52, C:0.04, G:0.12, T:0.33
Consensus pattern (28 bp):
AAGGTTAATATATGTATAATATAACAAT
Found at i:40297519 original size:25 final size:28
Alignment explanation
Indices: 40297491--40297542 Score: 74
Period size: 25 Copynumber: 2.0 Consensus size: 28
40297481 TATATTAGTA
40297491 AAGGTTAACATA-GTA-AAT-TAACAAT
1 AAGGTTAACATATGTATAATATAACAAT
*
40297516 AAGGTTAATATATGTATAATATAACAA
1 AAGGTTAACATATGTATAATATAACAA
40297543 ATTAAAATGC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 11 0.48
26 3 0.13
27 3 0.13
28 6 0.26
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.31
Consensus pattern (28 bp):
AAGGTTAACATATGTATAATATAACAAT
Found at i:40299458 original size:41 final size:40
Alignment explanation
Indices: 40299429--40299545 Score: 162
Period size: 41 Copynumber: 2.9 Consensus size: 40
40299419 GTGAATTAAT
*
40299429 TCAGACTTTAAGTCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAG-CTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
40299470 TCAGGTTATAAACCTAGCAGGCTACGTGCCGGTGATCTGAA
1 TCAGCTT-TAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
* *
40299511 TCAGGCTATAAGCCTAGCAGGCTAAGTGCCGGTGA
1 TCA-GCTTTAAGCCTAGCAGGCTACGTGCCGGTGA
40299546 ATATGTTAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
40 2 0.03
41 63 0.94
42 2 0.03
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (40 bp):
TCAGCTTTAAGCCTAGCAGGCTACGTGCCGGTGATCTGAA
Found at i:40312515 original size:18 final size:18
Alignment explanation
Indices: 40312486--40312529 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
40312476 TGAGTCATGG
* *
40312486 AAGGAAGATGAAA-ATGA
1 AAGGAGGATGAAACATCA
40312503 AAGCGAGGATGAAACATCA
1 AAG-GAGGATGAAACATCA
40312522 AAGGAGGA
1 AAGGAGGA
40312530 AGACGAGGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 3 0.13
18 14 0.61
19 6 0.26
ACGTcount: A:0.52, C:0.07, G:0.32, T:0.09
Consensus pattern (18 bp):
AAGGAGGATGAAACATCA
Found at i:40312623 original size:25 final size:25
Alignment explanation
Indices: 40312577--40312624 Score: 71
Period size: 24 Copynumber: 1.9 Consensus size: 25
40312567 ATTTCTTGTC
*
40312577 TTTAGTTTTTATTTCTTTTTAGATG
1 TTTAGTTTTTATTTCTTGTTAGATG
40312602 TTTA-TTTTTATTTCTTAGTTAGA
1 TTTAGTTTTTATTTCTT-GTTAGA
40312625 ATTTTGCTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 12 0.57
25 9 0.43
ACGTcount: A:0.19, C:0.04, G:0.10, T:0.67
Consensus pattern (25 bp):
TTTAGTTTTTATTTCTTGTTAGATG
Found at i:40320134 original size:118 final size:118
Alignment explanation
Indices: 40319958--40320192 Score: 470
Period size: 118 Copynumber: 2.0 Consensus size: 118
40319948 TCTTTTCATC
40319958 ACATTACATCTCAACTACGAACTTATCATTTCATTACCTATTTTCACCCATTTCATTTGCATAAC
1 ACATTACATCTCAACTACGAACTTATCATTTCATTACCTATTTTCACCCATTTCATTTGCATAAC
40320023 ATACAAGGCATAAACATAACATTAACCATAGCCACAAGCTAGTGCATTTAAGT
66 ATACAAGGCATAAACATAACATTAACCATAGCCACAAGCTAGTGCATTTAAGT
40320076 ACATTACATCTCAACTACGAACTTATCATTTCATTACCTATTTTCACCCATTTCATTTGCATAAC
1 ACATTACATCTCAACTACGAACTTATCATTTCATTACCTATTTTCACCCATTTCATTTGCATAAC
40320141 ATACAAGGCATAAACATAACATTAACCATAGCCACAAGCTAGTGCATTTAAG
66 ATACAAGGCATAAACATAACATTAACCATAGCCACAAGCTAGTGCATTTAAG
40320193 CATAACCCTT
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
118 117 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.31
Consensus pattern (118 bp):
ACATTACATCTCAACTACGAACTTATCATTTCATTACCTATTTTCACCCATTTCATTTGCATAAC
ATACAAGGCATAAACATAACATTAACCATAGCCACAAGCTAGTGCATTTAAGT
Found at i:40320883 original size:44 final size:44
Alignment explanation
Indices: 40320812--40320954 Score: 155
Period size: 45 Copynumber: 3.2 Consensus size: 44
40320802 GATCGAAGTG
* * *
40320812 TGCCATGGTGTCTTTTAATCATGGTCTTATTTATTCTCTTCTTGA
1 TGCCATAGTGTC-TTTAACCATGGTCTTATTTATTCTCTTCGTGA
* *
40320857 TGCCATAGTGTCTTTAACCATGGTCTTATTCATTCTCTATCGTGT
1 TGCCATAGTGTCTTTAACCATGGTCTTATTTATTCTCT-TCGTGA
** *
40320902 TGTAATAGTGTCTTTCAACCATGGTCTT-TTTCATT-TGATTCGTGA
1 TGCCATAGTGTCTTT-AACCATGGTCTTATTT-ATTCT-CTTCGTGA
40320947 TGCCATAG
1 TGCCATAG
40320955 CATCTTTCAG
Statistics
Matches: 82, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
44 24 0.29
45 42 0.51
46 16 0.20
ACGTcount: A:0.18, C:0.19, G:0.17, T:0.46
Consensus pattern (44 bp):
TGCCATAGTGTCTTTAACCATGGTCTTATTTATTCTCTTCGTGA
Found at i:40320992 original size:45 final size:45
Alignment explanation
Indices: 40320943--40321105 Score: 231
Period size: 45 Copynumber: 3.6 Consensus size: 45
40320933 CATTTGATTC
* *
40320943 GTGATGCCATAGCATCTTTCAG-CTATGGTTTTACTCGATAGAATT
1 GTGATGCCATAACATCTTTCAGTC-ATGGTCTTACTCGATAGAATT
* * *
40320988 GTGATGCCATAACGTCTTTTAGTCATGGTCTTGCTCGATAGAATT
1 GTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAATT
*
40321033 GTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAATC
1 GTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAATT
* *
40321078 GTGATGCCATAACGTCTTTCGGT-ATGGT
1 GTGATGCCATAACATCTTTCAGTCATGGT
40321106 GCCATAGTGT
Statistics
Matches: 106, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 5 0.05
45 100 0.94
46 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (45 bp):
GTGATGCCATAACATCTTTCAGTCATGGTCTTACTCGATAGAATT
Found at i:40321005 original size:90 final size:90
Alignment explanation
Indices: 40320911--40321097 Score: 245
Period size: 90 Copynumber: 2.1 Consensus size: 90
40320901 TTGTAATAGT
** * * *
40320911 GTCTTTCAACCATGGTCTTTTTC-ATTTG-ATTCGTGATGCCATAGCATCTTTCAG-CTATGGTT
1 GTCTTTCAACCATGGTCTTGCTCGA-TAGAATT-GTGATGCCATAACATCTTTCAGTC-ATGGTC
*
40320973 TTACTCGATAGAATTGTGATGCCATAAC
63 TTACTCGATAGAATCGTGATGCCATAAC
* **
40321001 GTCTTTTAGTCATGGTCTTGCTCGATAGAATTGTGATGCCATAACATCTTTCAGTCATGGTCTTA
1 GTCTTTCAACCATGGTCTTGCTCGATAGAATTGTGATGCCATAACATCTTTCAGTCATGGTCTTA
40321066 CTCGATAGAATCGTGATGCCATAAC
66 CTCGATAGAATCGTGATGCCATAAC
40321091 GTCTTTC
1 GTCTTTC
40321098 GGTATGGTGC
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
90 79 0.94
91 5 0.06
ACGTcount: A:0.22, C:0.20, G:0.19, T:0.39
Consensus pattern (90 bp):
GTCTTTCAACCATGGTCTTGCTCGATAGAATTGTGATGCCATAACATCTTTCAGTCATGGTCTTA
CTCGATAGAATCGTGATGCCATAAC
Found at i:40321975 original size:56 final size:56
Alignment explanation
Indices: 40321889--40322008 Score: 231
Period size: 56 Copynumber: 2.1 Consensus size: 56
40321879 ACAAGGGATG
40321889 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
*
40321945 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAGAATAAAATAAGAAGC
1 ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
40322001 ATGGGCAA
1 ATGGGCAA
40322009 TAAACTAATA
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 63 1.00
ACGTcount: A:0.45, C:0.09, G:0.23, T:0.23
Consensus pattern (56 bp):
ATGGGCAAAACATGTCATGAAACATGTTGTGTTAATGGAAAAATAAAATAAGAAGC
Found at i:40323276 original size:39 final size:40
Alignment explanation
Indices: 40323177--40323320 Score: 145
Period size: 40 Copynumber: 3.6 Consensus size: 40
40323167 CGAATGATGT
* * *
40323177 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTA-AGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGA-T-ACTATAA
* * *
40323217 CCAGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGATACTATA-A
*
40323257 CCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTATAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
*
40323296 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
40323321 AACGAGTAGC
Statistics
Matches: 88, Mismatches: 9, Indels: 14
0.79 0.08 0.13
Matches are distributed among these distances:
39 34 0.39
40 43 0.49
41 10 0.11
42 1 0.01
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGATACTATAA
Found at i:40323334 original size:40 final size:39
Alignment explanation
Indices: 40323229--40323327 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 39
40323219 AGACTAAGAT
** * *
40323229 CCGAAGGCATTTGTGCGAGATACTA-ATTCCGGGCTAAGC
1 CCGAAGGCATTTGAACGAGTTACTATA-ACCGGGCTAAGC
** *
40323268 CCGAAGGCATTTGTGCGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAG-C
40323308 CCGAAGGCATTTGAACGAGT
1 CCGAAGGCATTTGAACGAGT
40323328 AGCTATATCC
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
39 33 0.62
40 20 0.38
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
CCGAAGGCATTTGAACGAGTTACTATAACCGGGCTAAGC
Found at i:40323339 original size:79 final size:80
Alignment explanation
Indices: 40323176--40323326 Score: 182
Period size: 79 Copynumber: 1.9 Consensus size: 80
40323166 TCGAATGATG
*
40323176 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATATCCAGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
**
40323241 GTGCGAGATACTAAT
66 GAACGAGATACTAAT
* * * * * *
40323256 TCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTATAACCGGGCTATG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAACCAGACTAAGAT-CCGAAGGCAT
40323318 TTGAACGAG
64 TTGAACGAG
40323327 TAGCTATATC
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.02
79 41 0.68
80 18 0.30
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACCATAACCAGACTAAGATCCGAAGGCATTT
GAACGAGATACTAAT
Found at i:40341600 original size:23 final size:23
Alignment explanation
Indices: 40341574--40341629 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
40341564 GATTAAGATC
40341574 GCACCGAAGTGCAAG-GAACAGGA
1 GCACCGAAGTGCAAGAG-ACAGGA
*
40341597 GCACTGAAGTGCAAGAGACAGGA
1 GCACCGAAGTGCAAGAGACAGGA
* *
40341620 GTACCAAAGT
1 GCACCGAAGT
40341630 ATAAATCAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 27 0.96
24 1 0.04
ACGTcount: A:0.39, C:0.20, G:0.32, T:0.09
Consensus pattern (23 bp):
GCACCGAAGTGCAAGAGACAGGA
Found at i:40348866 original size:639 final size:639
Alignment explanation
Indices: 40347648--40348925 Score: 2414
Period size: 639 Copynumber: 2.0 Consensus size: 639
40347638 TTCCTAACTT
40347648 CTGGTACATAATATACATCATTTAAGGTTAAAACCTTTCCAGAAGTGAATTGTAGTTCAACAGAC
1 CTGGTACATAATATACATCATTTAAGGTTAAAACCTTTCCAGAAGTGAATTGTAGTTCAACAGAC
40347713 CCTTTGCCTTTAATTGTTGCGGTGGAAGAATTTCCCATGTACAAGACATTGTCATTTTCACATTG
66 CCTTTGCCTTTAATTGTTGCGGTGGAAGAATTTCCCATGTACAAGACATTGTCATTTTCACATTG
40347778 TGTGAAATTTATGAACATGCTTTTTGTCTTTGCACACATGTTTGGTTGCTCCAGTATCAATCCAC
131 TGTGAAATTTATGAACATGCTTTTTGTCTTTGCACACATGTTTGGTTGCTCCAGTATCAATCCAC
40347843 CATGTATTATCATCTTGTGCCATATTAATTTCAGATATCATTGCAACAAACTTTTCGTTATTATC
196 CATGTATTATCATCTTGTGCCATATTAATTTCAGATATCATTGCAACAAACTTTTCGTTATTATC
40347908 AGTCTTAGAAGATGATTTCTTCTTTAAAAATCGGCATTCATTCTTGAAATGTCCCGACTTTTCAC
261 AGTCTTAGAAGATGATTTCTTCTTTAAAAATCGGCATTCATTCTTGAAATGTCCCGACTTTTCAC
40347973 AATGATAGCATAAGCCCTTTTGTTTCTTTTTGAACTTAGGTGCTCTATCAGTCTGATTGAACTTT
326 AATGATAGCATAAGCCCTTTTGTTTCTTTTTGAACTTAGGTGCTCTATCAGTCTGATTGAACTTT
* * *
40348038 CTCTTGAATGGTTTAGTAGTCTGTACTTCCTCCGTAACATGTACTTTGGCATTTTCAGAATTTAG
391 CTCTTGAATGGTTTAGTAGTCTATACTTCCTCCGTAACATGCACTTTGGCATTTTCAAAATTTAG
* *
40348103 GTTCTGATCTTGTTTTCGATACTCTTCTTCAATACGAAGATGATTTGCCAAAGCCTCAAGAGATA
456 GTTCTGATCTTATTTTCGATACTCTTCTTCAATACGAAGATGATTTACCAAAGCCTCAAGAGATA
*
40348168 TTTCCTCTTTCTTATGTTTTAGACTTCTTTTAAAGTCTTTCCAAGATGGAGGAAGTTTGTCTATT
521 TTTCCTCTTTCTTATGTTTTAGACTTCTTTTAAAGTCTTCCCAAGATGGAGGAAGTTTGTCTATT
*
40348233 ATGGAGGATACCACAATCATTTCATCCATTTTCATATCATATTGCTTAAATTGA
586 ATGGAGGATACAACAATCATTTCATCCATTTTCATATCATATTGCTTAAATTGA
*
40348287 CTGGTACATAATATACTTCATTTAAGGTTAAAACCTTTCCAGAAGTGAATTGTAGTTCAACAGAC
1 CTGGTACATAATATACATCATTTAAGGTTAAAACCTTTCCAGAAGTGAATTGTAGTTCAACAGAC
* * *
40348352 CCTTTGCCTTTGATTGTTGCGGTGGAAGAATTTCTCATGTATAAGACATTGTCATTTTCACATTG
66 CCTTTGCCTTTAATTGTTGCGGTGGAAGAATTTCCCATGTACAAGACATTGTCATTTTCACATTG
40348417 TGTGAAATTTATGAACATGCTTTTTGTCTTTGCACACATGTTTGGTTGCTCCAGTATCAATCCAC
131 TGTGAAATTTATGAACATGCTTTTTGTCTTTGCACACATGTTTGGTTGCTCCAGTATCAATCCAC
40348482 CATGTATTATCATCTTGTGCCATATTAATTTCAGATATCATTGCAACAAACTTTTCGTTATTATC
196 CATGTATTATCATCTTGTGCCATATTAATTTCAGATATCATTGCAACAAACTTTTCGTTATTATC
40348547 AGTCTTAGAAGATGATTTCTTCTTTAAAAATCGGCATTCATTCTTGAAATGTCCCGACTTTTCAC
261 AGTCTTAGAAGATGATTTCTTCTTTAAAAATCGGCATTCATTCTTGAAATGTCCCGACTTTTCAC
40348612 AATGATAGCATAAGCCCTTTTGTTTCTTTTTGAACTTAGGTGCTCTATCAGTCT-ATTTGAACTT
326 AATGATAGCATAAGCCCTTTTGTTTCTTTTTGAACTTAGGTGCTCTATCAGTCTGA-TTGAACTT
40348676 TCTCTTGAATGGTTTAGTAGTCTATACTTCCTCCGTAACATGCACTTTGGCATTTTCAAAATTTA
390 TCTCTTGAATGGTTTAGTAGTCTATACTTCCTCCGTAACATGCACTTTGGCATTTTCAAAATTTA
*
40348741 GGTTCTGATCTTATTTTCGATATTCTTCTTCAATACGAAGATGATTTACCAAAGCCTCAAGAGAT
455 GGTTCTGATCTTATTTTCGATACTCTTCTTCAATACGAAGATGATTTACCAAAGCCTCAAGAGAT
*
40348806 ATTTCCTCTTTCTTATGTTTTAGACTTCTTTTAAAGTCTTCCCAAGATGGAGGAAGTTTGTTTAT
520 ATTTCCTCTTTCTTATGTTTTAGACTTCTTTTAAAGTCTTCCCAAGATGGAGGAAGTTTGTCTAT
*
40348871 TATGGAGGATACAACAATCATTTCATCCATTTTCATATCATATTGCTTGAATTGA
585 TATGGAGGATACAACAATCATTTCATCCATTTTCATATCATATTGCTTAAATTGA
40348926 TTCAACATCT
Statistics
Matches: 624, Mismatches: 14, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
638 1 0.00
639 623 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (639 bp):
CTGGTACATAATATACATCATTTAAGGTTAAAACCTTTCCAGAAGTGAATTGTAGTTCAACAGAC
CCTTTGCCTTTAATTGTTGCGGTGGAAGAATTTCCCATGTACAAGACATTGTCATTTTCACATTG
TGTGAAATTTATGAACATGCTTTTTGTCTTTGCACACATGTTTGGTTGCTCCAGTATCAATCCAC
CATGTATTATCATCTTGTGCCATATTAATTTCAGATATCATTGCAACAAACTTTTCGTTATTATC
AGTCTTAGAAGATGATTTCTTCTTTAAAAATCGGCATTCATTCTTGAAATGTCCCGACTTTTCAC
AATGATAGCATAAGCCCTTTTGTTTCTTTTTGAACTTAGGTGCTCTATCAGTCTGATTGAACTTT
CTCTTGAATGGTTTAGTAGTCTATACTTCCTCCGTAACATGCACTTTGGCATTTTCAAAATTTAG
GTTCTGATCTTATTTTCGATACTCTTCTTCAATACGAAGATGATTTACCAAAGCCTCAAGAGATA
TTTCCTCTTTCTTATGTTTTAGACTTCTTTTAAAGTCTTCCCAAGATGGAGGAAGTTTGTCTATT
ATGGAGGATACAACAATCATTTCATCCATTTTCATATCATATTGCTTAAATTGA
Found at i:40353104 original size:22 final size:22
Alignment explanation
Indices: 40353079--40353134 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
40353069 CAAGGGAGCC
40353079 TTGTCTCGAGACA-ATCAAAAAA
1 TTGTCTCGAGACATAT-AAAAAA
* **
40353101 TTGTCTCAAGACATATAGCAAA
1 TTGTCTCGAGACATATAAAAAA
40353123 TTGTCTCGAGAC
1 TTGTCTCGAGAC
40353135 CTTAGGCTCC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 27 0.93
23 2 0.07
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
TTGTCTCGAGACATATAAAAAA
Found at i:40361784 original size:23 final size:23
Alignment explanation
Indices: 40361740--40361785 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
40361730 TCGTGTTGTG
* *
40361740 GTGACGTCGTATGTCTCCTCGTC
1 GTGACATCGTATGTCGCCTCGTC
* *
40361763 GTGACATCTTATGTCGCGTCGTC
1 GTGACATCGTATGTCGCCTCGTC
40361786 AGGACGTCAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.11, C:0.28, G:0.26, T:0.35
Consensus pattern (23 bp):
GTGACATCGTATGTCGCCTCGTC
Found at i:40363271 original size:40 final size:38
Alignment explanation
Indices: 40363227--40363324 Score: 99
Period size: 40 Copynumber: 2.4 Consensus size: 38
40363217 AATATTTAAT
* *
40363227 TATTTTTAAAATTTTTAAAA-ATTCAAAAATATTATAAAAA
1 TATTTTTAAAA--ATTAAAATATTAAAAAATATTA-AAAAA
40363267 TATTTTTAAAAATTAAAATTATTAAAAAATATTAAAAAA
1 TATTTTTAAAAATTAAAA-TATTAAAAAATATTAAAAAA
*
40363306 TTAAAATTTTAAAAATTAA
1 -T--ATTTTTAAAAATTAA
40363325 TTAAATGTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
38 6 0.12
39 5 0.10
40 25 0.50
42 14 0.28
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (38 bp):
TATTTTTAAAAATTAAAATATTAAAAAATATTAAAAAA
Found at i:40363275 original size:31 final size:29
Alignment explanation
Indices: 40363237--40363320 Score: 102
Period size: 31 Copynumber: 2.9 Consensus size: 29
40363227 TATTTTTAAA
40363237 ATTTTTAAAAATTCAAAAATATTATAAAAAT
1 ATTTTTAAAAATT-AAAAATATTA-AAAAAT
*
40363268 ATTTTTAAAAATTAAAATTATTAAAAAAT
1 ATTTTTAAAAATTAAAAATATTAAAAAAT
* *
40363297 A--TTAAAAAATT-AAAATTTTAAAAA
1 ATTTTTAAAAATTAAAAATATTAAAAA
40363321 TTAATTAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
26 11 0.22
27 9 0.18
29 7 0.14
30 9 0.18
31 13 0.27
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (29 bp):
ATTTTTAAAAATTAAAAATATTAAAAAAT
Found at i:40363299 original size:10 final size:10
Alignment explanation
Indices: 40363251--40363306 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
40363241 TTAAAAATTC
40363251 AAAAATATTA
1 AAAAATATTA
*
40363261 TAAAAATATTTT
1 -AAAAATA-TTA
*
40363273 TAAAA-ATT-
1 AAAAATATTA
*
40363281 AAAATTATTA
1 AAAAATATTA
40363291 AAAAATATTA
1 AAAAATATTA
40363301 AAAAAT
1 AAAAAT
40363307 TAAAATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
8 3 0.08
9 5 0.14
10 16 0.43
11 11 0.30
12 2 0.05
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATATTA
Found at i:40363304 original size:27 final size:27
Alignment explanation
Indices: 40363234--40363329 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 27
40363224 AATTATTTTT
* * *
40363234 AAAATTTTTAAAAATTCAAAAATATTATA
1 AAAATATTAAAAAATT-AAAATTATTA-A
*
40363263 AAAATATTTTTAAAAATTAAAATTATTAA
1 AAAATA--TTAAAAAATTAAAATTATTAA
40363292 AAAATATTAAAAAATTAAAATT-TTAA
1 AAAATATTAAAAAATTAAAATTATTAA
*
40363318 AAATTAATTAAA
1 AAAAT-ATTAAA
40363330 TGTTGATATA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
26 8 0.13
27 21 0.35
29 12 0.20
30 9 0.15
31 10 0.17
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (27 bp):
AAAATATTAAAAAATTAAAATTATTAA
Done.