Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr6
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: 44797108
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 921406 characters in sequence are not A, C, G, or T
File 133 of 144
Found at i:41224203 original size:36 final size:36
Alignment explanation
Indices: 41224163--41224243 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
41224153 TGACTCATTT
* *
41224163 GTTGGTAATATGAAACGCAAGAAATGCATACTATCC
1 GTTGGTAATATAAAACGCAAGAAATACATACTATCC
** * **
41224199 GTTGGCGATATAAAACGTAAGAAATATGTACTATCC
1 GTTGGTAATATAAAACGCAAGAAATACATACTATCC
41224235 GTTGCGTAA
1 GTTG-GTAA
41224244 GAAATACAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
36 33 0.94
37 2 0.06
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (36 bp):
GTTGGTAATATAAAACGCAAGAAATACATACTATCC
Found at i:41230001 original size:20 final size:20
Alignment explanation
Indices: 41229978--41230015 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
41229968 ATATATTCTT
*
41229978 TAAATTTTTTAAAATTTATG
1 TAAATATTTTAAAATTTATG
41229998 TAAATATTTTAAAATTTA
1 TAAATATTTTAAAATTTA
41230016 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (20 bp):
TAAATATTTTAAAATTTATG
Found at i:41250622 original size:18 final size:19
Alignment explanation
Indices: 41250598--41250640 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41250588 TTACAATAAT
41250598 AAACCCAAAAT-ACAACCC
1 AAACCCAAAATCACAACCC
* *
41250616 TAACCCAAAATCACTACCC
1 AAACCCAAAATCACAACCC
41250635 AAACCC
1 AAACCC
41250641 GAATCTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.42, G:0.00, T:0.09
Consensus pattern (19 bp):
AAACCCAAAATCACAACCC
Found at i:41254917 original size:18 final size:18
Alignment explanation
Indices: 41254896--41254931 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
41254886 GGAAAAAGGA
41254896 AAAAAGAAA-ATAAAAAAC
1 AAAAAGAAACA-AAAAAAC
41254914 AAAAAGAAACAAAAAAAC
1 AAAAAGAAACAAAAAAAC
41254932 CTCTATCAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.83, C:0.08, G:0.06, T:0.03
Consensus pattern (18 bp):
AAAAAGAAACAAAAAAAC
Found at i:41255456 original size:6 final size:6
Alignment explanation
Indices: 41255442--41255475 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
41255432 AGATGTGAAG
*
41255442 AAATAA AAATGA AAATGA AAAGTGA AAATGA AAA
1 AAATGA AAATGA AAATGA AAA-TGA AAATGA AAA
41255476 AGTAAAAGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:41255462 original size:13 final size:13
Alignment explanation
Indices: 41255442--41255476 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
41255432 AGATGTGAAG
41255442 AAAT-AAAAATGA
1 AAATGAAAAATGA
*
41255454 AAATGAAAAGTGA
1 AAATGAAAAATGA
41255467 AAATGAAAAA
1 AAATGAAAAA
41255477 GTAAAAGTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 4 0.20
13 16 0.80
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.14
Consensus pattern (13 bp):
AAATGAAAAATGA
Found at i:41256880 original size:132 final size:132
Alignment explanation
Indices: 41256643--41257241 Score: 977
Period size: 132 Copynumber: 4.5 Consensus size: 132
41256633 ACTTCAGCCT
* * * *
41256643 TATCTCCTTGGACAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAGTGGTGG
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* ** *
41256708 AGTAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
66 AGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
41256773 TC
131 TC
* *
41256775 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTAGTGG
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
* *
41256840 AGCAGATTAAGGATGGCGGATTTTACCTCCCTTAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
66 AGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
*
41256905 TT
131 TC
* *
41256907 TATCTCCCTAGGTAGCAGTGGAATAGATT-AAGGATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAA-GATTACAGATCTTATCTCCCTAAGCAGTAGTG
41256971 GAGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
65 GAGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
*
41257036 TTT
130 TTC
*
41257039 TATCTCCCTAGGCAGCAGTGGAATAGATT-AAGGATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAA-GATTACAGATCTTATCTCCCTAAGCAGTAGTG
*
41257103 GAGCAGATTAAAGATGGCGGATTTTATCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
65 GAGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAA
41257168 TTC
130 TTC
* * *
41257171 TATCTCCCTGGGCAGCAGTGGAATTGATTGAAGATTACAGATCTTATCTCCCAAAACAGTAGTGG
1 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
41257236 AGCAGA
66 AGCAGA
41257242 CGGAAGAAAG
Statistics
Matches: 439, Mismatches: 26, Indels: 4
0.94 0.06 0.01
Matches are distributed among these distances:
131 2 0.00
132 435 0.99
133 2 0.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (132 bp):
TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAAT
TC
Found at i:41257069 original size:88 final size:85
Alignment explanation
Indices: 41256686--41257067 Score: 252
Period size: 88 Copynumber: 4.4 Consensus size: 85
41256676 ATTACAGATC
** *
41256686 TTATCTCCCTAGGCAGTGGTGGAGTAGATCGAAGATGGCAGATTTTACCTCCCTGAGGTTACAGT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATGGCAGATTTTACCTCCCTGAGG-TACAGT
41256751 GGAGTACATTGAAGCCAGTAATT
65 GGAGTACATT-AAG-CAGTAATT
* * * ** * ** *
41256774 CTATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGT--AG
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATGGCAGATTTTACCTCCCTGAG--GTACAG
* * * **
41256837 TGGAGCAGATTAAGGATGGCGGATT
64 TGGAGTACATTAAGCA--G-TAATT
* * * *** * *
41256862 TTACCTCCCTTAGGTTA-CAGTGGAGTACATTGAAGCCAGTA-ATTTTATCTCCCT-AGGTAGCA
1 TTATCTCCC-TAGG-CAGCAGTGGAGTAGATTGAAGATGGCAGATTTTACCTCCCTGAGGTA-CA
* * * * *
41256924 GTGGAATAGATTAAGGATTACAGATC
63 GTGGAGTACATTAAGCAGT--A-ATT
* * * * *
41256950 TTATCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATGGCGGATTTTACCTCCCTGAGGTTACAGT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATGGCAGATTTTACCTCCCTGAGG-TACAGT
41257015 GGAGTACATTGAAGCCAGTAATT
65 GGAGTACATT-AAG-CAGTAATT
*
41257038 TTATCTCCCTAGGCAGCAGTGGAATAGATT
1 TTATCTCCCTAGGCAGCAGTGGAGTAGATT
41257068 AAGGATTACA
Statistics
Matches: 217, Mismatches: 58, Indels: 38
0.69 0.19 0.12
Matches are distributed among these distances:
85 3 0.01
86 4 0.02
87 32 0.15
88 132 0.61
89 37 0.17
90 7 0.03
91 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (85 bp):
TTATCTCCCTAGGCAGCAGTGGAGTAGATTGAAGATGGCAGATTTTACCTCCCTGAGGTACAGTG
GAGTACATTAAGCAGTAATT
Found at i:41257127 original size:88 final size:88
Alignment explanation
Indices: 41256775--41257135 Score: 236
Period size: 88 Copynumber: 4.1 Consensus size: 88
41256765 CCAGTAATTC
* *
41256775 TATCTCCCTGGGCAGCAGTGGAATAGATTGAA-GATTTCAGATCTTGTCTCCCTAAGCAGTAGTG
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAAGGA-TTCAGATCTTATCTCCCTAAGCAGTAGTG
*
41256839 GAGCAGATTAAGGATGGCGGATTT
65 GAGCAGATTAAAGATGGCGGATTT
* * * * * * * * * *
41256863 TACCTCCCTTAGGTTA-CAGTGGAGTACATTGAAGCCAGT-A-ATTTTATCTCCCTAGGTAGCAG
1 TATCTCCC-TAGG-CAGCAGTGGAATAGATTGAAG-GATTCAGATCTTATCTCCCTAAGCAGTAG
** * ** * *
41256925 TGGAATAGATTAAGGATTACAGATCT
63 TGGAGCAGATTAAAGATGGCGGATTT
* * ** * * * * * *
41256951 TATCTCCCTAAGCAGTAGTGGAGCAGATT-AAAGATGGCGGATTTTACCTCCCTGAG--GTTACA
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAAGGAT-TCAGATCTTATCTCCCTAAGCAG-T--A
* * * *** **
41257013 GTGGAGTACATTGAAGCCAG-TAATTT
62 GTGGAGCAGATTAAAGATGGCGGATTT
41257039 TATCTCCCTAGGCAGCAGTGGAATAGATT-AAGGATTACAGATCTTATCTCCCTAAGCAGTAGTG
1 TATCTCCCTAGGCAGCAGTGGAATAGATTGAAGGATT-CAGATCTTATCTCCCTAAGCAGTAGTG
41257103 GAGCAGATTAAAGATGGCGGATTT
65 GAGCAGATTAAAGATGGCGGATTT
41257127 TATCTCCCT
1 TATCTCCCT
41257136 GAGGTTACAG
Statistics
Matches: 196, Mismatches: 62, Indels: 30
0.68 0.22 0.10
Matches are distributed among these distances:
85 1 0.01
86 4 0.02
87 29 0.15
88 125 0.64
89 33 0.17
90 3 0.02
91 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (88 bp):
TATCTCCCTAGGCAGCAGTGGAATAGATTGAAGGATTCAGATCTTATCTCCCTAAGCAGTAGTGG
AGCAGATTAAAGATGGCGGATTT
Found at i:41257191 original size:88 final size:86
Alignment explanation
Indices: 41256821--41257192 Score: 212
Period size: 88 Copynumber: 4.2 Consensus size: 86
41256811 TCAGATCTTG
* * * *
41256821 TCTCCCTAAGCAGTAGTGGAGCAGATTAAGGATGGCGGATTTTACCTCCCTTAGGTTACAGTGGA
1 TCTCCCTAGGCAGCAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCC-TAGG-TACAGTGGA
*
41256886 GTACATTGAAGCCAGTAATTTTA
64 GTACATTGAAGCCAGTAATTCTA
* ** * ** * * * * *
41256909 TCTCCCTAGGTAGCAGTGGAATAGATTAAGGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TCTCCCTAGGCAGCAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCCTAGGTA-CAGTGGAG
* * * *** ** *
41256974 CAGATTAAAGATGGCGGATTTTA
65 TACATTGAAGCCAG-TAATTCTA
* * * * * *** ** *
41256997 CCTCCCTGAGGTTA-CAGTGGAGTACATTGAAGCCAG-TAATTTTATCTCCCTAGGCAGCAGTGG
1 TCTCCCT-AGG-CAGCAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCCTAGGTA-CAGTGG
* * * * *
41257060 AATAGATT-AAG-GATTACAGATCTTA
63 AGTACATTGAAGCCAGTA-A-TTC-TA
* *
41257085 TCTCCCTAAGCAGTAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCCTGAGGTTACAGTGGA
1 TCTCCCTAGGCAGCAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCCT-AGG-TACAGTGGA
41257150 GTACATTGAAGCCAGTAATTCTA
64 GTACATTGAAGCCAGTAATTCTA
*
41257173 TCTCCCTGGGCAGCAGTGGA
1 TCTCCCTAGGCAGCAGTGGA
41257193 ATTGATTGAA
Statistics
Matches: 206, Mismatches: 65, Indels: 26
0.69 0.22 0.09
Matches are distributed among these distances:
86 3 0.01
87 39 0.19
88 120 0.58
89 34 0.17
90 7 0.03
91 3 0.01
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (86 bp):
TCTCCCTAGGCAGCAGTGGAGCAGATTAAAGATGGCGGATTTTATCTCCCTAGGTACAGTGGAGT
ACATTGAAGCCAGTAATTCTA
Found at i:41258414 original size:14 final size:13
Alignment explanation
Indices: 41258395--41258472 Score: 59
Period size: 14 Copynumber: 5.7 Consensus size: 13
41258385 AGTCCTTAAA
41258395 TTTATTTATTTATT
1 TTTA-TTATTTATT
*
41258409 TTTATTAGCTTATT
1 TTTATTA-TTTATT
*
41258423 TTTATTATGTTGTT
1 TTTATTAT-TTATT
*
41258437 TTTATTGTTTATT
1 TTTATTATTTATT
* *
41258450 ATTA-TAATTATT
1 TTTATTATTTATT
41258462 ATATTATTATT
1 -T-TTATTATT
41258473 GTATGTACAG
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
12 6 0.12
13 10 0.20
14 30 0.61
15 3 0.06
ACGTcount: A:0.24, C:0.01, G:0.05, T:0.69
Consensus pattern (13 bp):
TTTATTATTTATT
Found at i:41259919 original size:89 final size:86
Alignment explanation
Indices: 41259704--41259919 Score: 242
Period size: 85 Copynumber: 2.5 Consensus size: 86
41259694 AGATCAGTGA
* * * *
41259704 AGATCGAAAACAAAACCTTGCCTCCATC-GGTTGCAGTAGAGTTGGTTAAAGAAGCAGATATTGC
1 AGATCGAAAACAAATCCTTGCCTCCCTCAGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGC
*
41259768 CTTCCTGCAGATCAGCGAAGC
66 CTTCCTGCAGAACAGCGAAGC
* *
41259789 AGATCGAAAACAAATCCTTGCCTCCTTCA-GTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTG
1 AGATCGAAAACAAATCCTTGCCTCCCTCAGGTTGCAGTGGAGCTGGTTAAAGA-AGCAGATATTG
* *
41259853 CCTTCCTGC-GTTAACAGTGGAGC
65 CCTTCCTGCAG--AACAGCGAAGC
* ** *
41259876 AGATCGAAGACGCAAAT-CTTTTCTCCCTGAGGTTGCAGTGGAGC
1 AGATCGAA-A-ACAAATCCTTGCCTCCCTCAGGTTGCAGTGGAGC
41259920 AGATTGAAGT
Statistics
Matches: 111, Mismatches: 13, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
85 48 0.43
86 19 0.17
87 16 0.14
88 10 0.09
89 18 0.16
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.25
Consensus pattern (86 bp):
AGATCGAAAACAAATCCTTGCCTCCCTCAGGTTGCAGTGGAGCTGGTTAAAGAAGCAGATATTGC
CTTCCTGCAGAACAGCGAAGC
Found at i:41259945 original size:44 final size:44
Alignment explanation
Indices: 41259867--41260406 Score: 295
Period size: 44 Copynumber: 12.3 Consensus size: 44
41259857 CCTGCGTTAA
* * * * *
41259867 CAGTGGAGCAGATCGAAGACGCA-AATCTTTTCTCCCTGAGGTTG
1 CAGTGGAGCAGATTGAAGTC-AATAATCTTATCTCCCTGAAGTTG
* * *
41259911 CAGTGGAGCAGATTGAAGTCAATAACCCTATCTCCCTGAAGCTG
1 CAGTGGAGCAGATTGAAGTCAATAATCTTATCTCCCTGAAGTTG
* * * *
41259955 TAGTGGAG-AGGATTAAAGT-AATAGATCTTATCTCTCTGAAGTTA
1 CAGTGGAGCA-GATTGAAGTCAATA-ATCTTATCTCCCTGAAGTTG
* ** * * ** *
41259999 CAGTAGAGTGGATCGCAG-C-A-GGTCTTATCTCGACTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAATAATCTTATCTC-CCTGAAGTTG
* * ** *
41260041 CAGT-GAGGCAGATCGAAGATGACCAATCTTATCTCCCTGAAGTTA
1 CAGTGGA-GCAGATTGAAG-TCAATAATCTTATCTCCCTGAAGTTG
* * *
41260086 TAGTGGAGCAGATTGAATTCAATAATCCTATCTCCCTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAATAATCTTATCTCCCTGAAGTTG
* * * *
41260130 TAGTGGAGCGGATTAAAGT-AATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAATA-ATCTTATCTCCCTGAAGTTG
* * * * *
41260174 CAGT--AG-AG--TGGA-TCACATCAGGTCTTACCTCCCTAAAGTTA
1 CAGTGGAGCAGATTGAAGTCA-AT-A-ATCTTATCTCCCTGAAGTTG
* * * * *
41260215 CAGTGGAGCAAACT-AAGT-AAGCAGGTCTTATCTCGACTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAA-TA-ATCTTATCTC-CCTGAAGTTG
* * * ** *
41260260 CAGTGGGGCAGATCGAAGATGACCAATCTTATCTCCCTGAAGTTA
1 CAGTGGAGCAGATTGAAG-TCAATAATCTTATCTCCCTGAAGTTG
* * * *
41260305 CAGTGGAGCATATTGAAGCCGATAATCCTATCTCCCTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAATAATCTTATCTCCCTGAAGTTG
* * * * *
41260349 TAGTGGAACGGATTAAAGT-AATAGATCTTATCTCTCTGAAGTTG
1 CAGTGGAGCAGATTGAAGTCAATA-ATCTTATCTCCCTGAAGTTG
*
41260393 CAGTAAGAGCAGAT
1 CAGT-GGAGCAGAT
41260407 CGCATCAAGT
Statistics
Matches: 373, Mismatches: 94, Indels: 57
0.71 0.18 0.11
Matches are distributed among these distances:
38 1 0.00
39 3 0.01
40 2 0.01
41 33 0.09
42 22 0.06
43 16 0.04
44 199 0.53
45 68 0.18
46 25 0.07
47 3 0.01
48 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
CAGTGGAGCAGATTGAAGTCAATAATCTTATCTCCCTGAAGTTG
Found at i:41260198 original size:175 final size:174
Alignment explanation
Indices: 41259874--41260200 Score: 528
Period size: 175 Copynumber: 1.9 Consensus size: 174
41259864 TAACAGTGGA
* * *
41259874 GCAGATCGAAGACGCAAATCTTTTCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCAATAACCC
1 GCAGATCGAAGACGCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCAATAACCC
41259939 TATCTCCCTGAAGCTGTAGTGGAGAGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTA
66 TATCTCCCTGAAGCTGTAGTGGAGAGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTA
*
41260004 GAGTGGATCGCAGCAGGTCTTATCTCGACTGAAGTTGCAGTGAG
131 GAGTGGATCACAGCAGGTCTTATCTCGACTGAAGTTGCAGTGAG
* * * * *
41260048 GCAGATCGAAGATGACCAATCTTATCTCCCTGAAGTTATAGTGGAGCAGATTGAATTCAATAATC
1 GCAGATCGAAGACG-CAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCAATAACC
* * *
41260113 CTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGT
65 CTATCTCCCTGAAGCTGTAGTGGAGAGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGT
*
41260178 AGAGTGGATCACATCAGGTCTTA
130 AGAGTGGATCACAGCAGGTCTTA
41260201 CCTCCCTAAA
Statistics
Matches: 139, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
174 13 0.09
175 126 0.91
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (174 bp):
GCAGATCGAAGACGCAAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTGAAGTCAATAACCC
TATCTCCCTGAAGCTGTAGTGGAGAGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTA
GAGTGGATCACAGCAGGTCTTATCTCGACTGAAGTTGCAGTGAG
Found at i:41260295 original size:175 final size:175
Alignment explanation
Indices: 41259890--41260313 Score: 478
Period size: 175 Copynumber: 2.4 Consensus size: 175
41259880 CGAAGACGCA
* * * * * * * * *
41259890 AATCTTTTCTCCCTGAGGTTGCAGTGGAGCAGATTGAAGTCAATAACCCTATCTCCCTGAAGCTG
1 AATCTTATCTCACTGAAGTTACAGTGGAGCAGATCGAAATCAACAATCCTATCTCCCTGAAGTTG
* *
41259955 TAGTGGAGAGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCGCAGCAG
66 TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCACAGCAG
* * * * *
41260020 GTCTTATCTCGACTGAAGTTGCAGTGAGGCAGATCGAAGATGACC
131 GTCTTACCTCGACTAAAGTTACAGTGAGGCAGAACGAAGATAACC
* * * * *
41260065 AATCTTATCTCCCTGAAGTTATAGTGGAGCAGATTGAATTCAATAATCCTATCTCCCTGAAGTTG
1 AATCTTATCTCACTGAAGTTACAGTGGAGCAGATCGAAATCAACAATCCTATCTCCCTGAAGTTG
* *
41260130 TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTGCAGTAGAGTGGATCACATCAG
66 TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCACAGCAG
* * *
41260195 GTCTTACCTC-CCTAAAGTTACAGTG-GAGCA-AACTAAG-TAAGC
131 GTCTTACCTCGACTAAAGTTACAGTGAG-GCAGAACGAAGATAACC
* * * * * *
41260237 AGGTCTTATCTCGACTGAAGTTGCAGTGGGGCAGATCGAAGATGACCAATCTTATCTCCCTGAAG
1 A-ATCTTATCTC-ACTGAAGTTACAGTGGAGCAGATCGAA-ATCAACAATCCTATCTCCCTGAAG
**
41260302 TTACAGTGGAGC
63 TTGTAGTGGAGC
41260314 ATATTGAAGC
Statistics
Matches: 213, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
172 4 0.02
173 15 0.07
174 37 0.17
175 157 0.74
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (175 bp):
AATCTTATCTCACTGAAGTTACAGTGGAGCAGATCGAAATCAACAATCCTATCTCCCTGAAGTTG
TAGTGGAGCGGATTAAAGTAATAGATCTTATCTCTCTGAAGTTACAGTAGAGTGGATCACAGCAG
GTCTTACCTCGACTAAAGTTACAGTGAGGCAGAACGAAGATAACC
Found at i:41260757 original size:18 final size:19
Alignment explanation
Indices: 41260733--41260775 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
41260723 TTACAATAAT
41260733 AAACCCAAAAT-ACAACCC
1 AAACCCAAAATCACAACCC
* *
41260751 TAACCCAAAATCACTACCC
1 AAACCCAAAATCACAACCC
41260770 AAACCC
1 AAACCC
41260776 GAATCTAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.49, C:0.42, G:0.00, T:0.09
Consensus pattern (19 bp):
AAACCCAAAATCACAACCC
Found at i:41270058 original size:48 final size:49
Alignment explanation
Indices: 41269987--41270085 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
41269977 CCCATGATAA
41269987 TTATAATTCTTTTTGGAAAGAATATAACAT-TTTAATACTTTCCATATG
1 TTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATATG
*
41270035 TTATAATTCTTTTTGGAAAGAATATAACATGTTTAATGCTTTCCATATG
1 TTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATATG
41270084 TT
1 TT
41270086 TTCTATAAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 30 0.61
49 19 0.39
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (49 bp):
TTATAATTCTTTTTGGAAAGAATATAACATGTTTAATACTTTCCATATG
Found at i:41286180 original size:5 final size:5
Alignment explanation
Indices: 41286166--41286222 Score: 60
Period size: 5 Copynumber: 11.2 Consensus size: 5
41286156 AACCTAAATT
* * * *
41286166 AGAAA TGAAA AGAAA AGAAA AGGAA AGAAA AGAAA AGGAAA ATAAA ATAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A-GAAA AGAAA AGAAA
*
41286217 ATAAA A
1 AGAAA A
41286223 TAAATCCCTA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
5 41 0.89
6 5 0.11
ACGTcount: A:0.75, C:0.00, G:0.18, T:0.07
Consensus pattern (5 bp):
AGAAA
Found at i:41292402 original size:132 final size:131
Alignment explanation
Indices: 41292154--41292408 Score: 357
Period size: 132 Copynumber: 1.9 Consensus size: 131
41292144 AAAGGAAGAT
* *** **
41292154 GAGAATGAGACTTTCTTTCCATCCACTTTAGCCTATAACACTTAACATATTTTTTTCATTGTTAA
1 GAGAATGAGACTCTCTTTCCATCCACTTTAGCCTATAACACTTAACATATAAATTTCATCATTAA
* * *
41292219 ATGAAAACTAACAGGTGTTTCCACTAAACATTGACACAACTGGTACAACCATTCAAGANCATCAG
66 ATGAAAACTAACAGGTGTTTCCACTAAACATTGACACAACTAGAACAACCATGCAAGA-CATCAG
41292284 AC
130 AC
*
41292286 GAGAATGAGACTCTCTTTCCATCCACTTTAGCCTATAACACTTAACATCTAAATTTCATCATTAA
1 GAGAATGAGACTCTCTTTCCATCCACTTTAGCCTATAACACTTAACATATAAATTTCATCATTAA
* * * * * *
41292351 ATGAAAATTAACATGTGTTTTCGCTAAACATTGACACAGCTAGAACTACCATGCAAGA
66 ATGAAAACTAACAGGTGTTTCCACTAAACATTGACACAACTAGAACAACCATGCAAGA
41292409 GCGGTTGTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
132 107 1.00
ACGTcount: A:0.36, C:0.22, G:0.11, T:0.31
Consensus pattern (131 bp):
GAGAATGAGACTCTCTTTCCATCCACTTTAGCCTATAACACTTAACATATAAATTTCATCATTAA
ATGAAAACTAACAGGTGTTTCCACTAAACATTGACACAACTAGAACAACCATGCAAGACATCAGA
C
Found at i:41300423 original size:13 final size:13
Alignment explanation
Indices: 41300407--41300433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
41300397 AGAATTCTCG
41300407 ATAAAAATTTTCC
1 ATAAAAATTTTCC
41300420 ATAAAAATTTTCC
1 ATAAAAATTTTCC
41300433 A
1 A
41300434 AGGCACCGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAAAATTTTCC
Found at i:41301457 original size:8 final size:8
Alignment explanation
Indices: 41301444--41301519 Score: 62
Period size: 8 Copynumber: 9.0 Consensus size: 8
41301434 TTTTAGTTCT
41301444 TTTATATA
1 TTTATATA
*
41301452 TTTATACATT
1 TTTAT--ATA
*
41301462 TTTATAAA
1 TTTATATA
*
41301470 TTTATAAA
1 TTTATATA
*
41301478 TTTATAAA
1 TTTATATA
*
41301486 TTTATAGTTT
1 TTTATA--TA
41301496 TTTATATA
1 TTTATATA
41301504 TTTATATA
1 TTTATATA
*
41301512 TTTTTATA
1 TTTATATA
41301520 AAATTATAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 44 0.77
10 13 0.23
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.61
Consensus pattern (8 bp):
TTTATATA
Found at i:41301463 original size:26 final size:25
Alignment explanation
Indices: 41301434--41301515 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
41301424 TAGATATGCT
*
41301434 TTTTAGTTCTTTTATATATTTATACAT
1 TTTTAGTT-TTTTATATATTTATA-AA
** *
41301461 TTTTA-TAAATTTATAAATTTATAAA
1 TTTTAGT-TTTTTATATATTTATAAA
*
41301486 TTTATAGTTTTTTATATATTTATATA
1 TTT-TAGTTTTTTATATATTTATAAA
41301512 TTTT
1 TTTT
41301516 TATAAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
25 5 0.11
26 33 0.75
27 6 0.14
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (25 bp):
TTTTAGTTTTTTATATATTTATAAA
Found at i:41301466 original size:18 final size:17
Alignment explanation
Indices: 41301443--41301528 Score: 93
Period size: 18 Copynumber: 4.9 Consensus size: 17
41301433 TTTTTAGTTC
*
41301443 TTTTATATATTTATACAT
1 TTTTATAAATTTATA-AT
41301461 TTTTATAAATTTATAA-
1 TTTTATAAATTTATAAT
* *
41301477 ATTTATAAATTTATAGTT
1 TTTTATAAATTTATA-AT
*
41301495 TTTTATATATTTATATAT
1 TTTTATAAATTTATA-AT
*
41301513 TTTTATAAAATTATAA
1 TTTTATAAATTTATAA
41301529 AATTTTTATT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
16 14 0.25
17 2 0.04
18 41 0.72
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (17 bp):
TTTTATAAATTTATAAT
Found at i:41301526 original size:26 final size:26
Alignment explanation
Indices: 41301444--41301527 Score: 89
Period size: 26 Copynumber: 3.2 Consensus size: 26
41301434 TTTTAGTTCT
*
41301444 TTTATATATTTATACATTTTTATAAA
1 TTTATATATTTATAAATTTTTATAAA
* * **
41301470 TTTATAAATTTATAAATTTATAGT-TT
1 TTTATATATTTATAAATTTTTA-TAAA
*
41301496 TTTATATATTTATATATTTTTATAAA
1 TTTATATATTTATAAATTTTTATAAA
*
41301522 ATTATA
1 TTTATA
41301528 AAATTTTTAT
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
25 1 0.02
26 43 0.96
27 1 0.02
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTATATATTTATAAATTTTTATAAA
Found at i:41303579 original size:40 final size:40
Alignment explanation
Indices: 41303535--41303618 Score: 141
Period size: 40 Copynumber: 2.1 Consensus size: 40
41303525 GGATTTTCAT
*
41303535 TTGTATTGAATCGAATTAACAGAGATTTAGTTAGGTTTAC
1 TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
* *
41303575 TTGTATTGAATCAAATTAACATAGATTTAGTTAGGTTTAT
1 TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
41303615 TTGT
1 TTGT
41303619 GCTAATTAGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (40 bp):
TTGTATTGAATCAAATTAACAGAGATTTAGTTAGGTTTAC
Found at i:41314359 original size:24 final size:24
Alignment explanation
Indices: 41314331--41314380 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
41314321 TTGAGGTTGT
* * * *
41314331 TCTTCTACCTTTATATTTGACTTA
1 TCTTCGACCTCTATAATCGACTTA
41314355 TCTTCGACCTCTATAATCGACTTA
1 TCTTCGACCTCTATAATCGACTTA
41314379 TC
1 TC
41314381 GATTGGAGGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.22, C:0.26, G:0.06, T:0.46
Consensus pattern (24 bp):
TCTTCGACCTCTATAATCGACTTA
Found at i:41314500 original size:21 final size:23
Alignment explanation
Indices: 41314476--41314526 Score: 54
Period size: 22 Copynumber: 2.3 Consensus size: 23
41314466 TTAATTTAAA
41314476 TTTAATTTCG-TTTT-ACTTATT
1 TTTAATTTCGCTTTTCACTTATT
* *
41314497 TTT-ATTTTGCTTTTCATTTATT
1 TTTAATTTCGCTTTTCACTTATT
*
41314519 TTAAATTT
1 TTTAATTT
41314527 AAATTTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 5 0.21
21 7 0.29
22 8 0.33
23 4 0.17
ACGTcount: A:0.20, C:0.08, G:0.04, T:0.69
Consensus pattern (23 bp):
TTTAATTTCGCTTTTCACTTATT
Found at i:41317259 original size:17 final size:18
Alignment explanation
Indices: 41317227--41317260 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
41317217 CAAATCAGAA
41317227 ATAAATAAACAAAAATAT
1 ATAAATAAACAAAAATAT
*
41317245 ATAAA-AAATAAAAATA
1 ATAAATAAACAAAAATA
41317261 AAAACAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.76, C:0.03, G:0.00, T:0.21
Consensus pattern (18 bp):
ATAAATAAACAAAAATAT
Found at i:41321770 original size:16 final size:15
Alignment explanation
Indices: 41321749--41321786 Score: 53
Period size: 14 Copynumber: 2.6 Consensus size: 15
41321739 TAAATTTTTT
41321749 TTCGAATTTCGAGTTA
1 TTCGAATTT-GAGTTA
41321765 TTCGAA-TTGAGTTA
1 TTCGAATTTGAGTTA
41321779 TTC-AATTT
1 TTCGAATTT
41321787 TTTCAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 2 0.10
14 11 0.52
15 2 0.10
16 6 0.29
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (15 bp):
TTCGAATTTGAGTTA
Found at i:41323510 original size:18 final size:18
Alignment explanation
Indices: 41323489--41323540 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
41323479 CAATAAATAA
41323489 ATTAAAAATTATAAAAAT-
1 ATTAAAAA-TATAAAAATC
*
41323507 ATTAAAAAATAAAAAAATC
1 ATT-AAAAATATAAAAATC
*
41323526 AATAAAAATATAAAA
1 ATTAAAAATATAAAA
41323541 GTTCATAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 22 0.76
19 7 0.24
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (18 bp):
ATTAAAAATATAAAAATC
Found at i:41325464 original size:109 final size:109
Alignment explanation
Indices: 41325161--41325471 Score: 396
Period size: 109 Copynumber: 2.9 Consensus size: 109
41325151 AAGATTCAAG
* * * *
41325161 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAACACATTAGGGCACG-TTCCTC
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * *
41325223 GAATTTCCAAACGCTAAATATTGCATTGTTTTGAAATTTTTAAA
66 GAATTTCCAAACGCTAAATATTGCCTTATTTTAAAATTTTTAAA
* *
41325267 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * * * *
41325332 AAATTACCAAACACAAAACATTGCCTTATTTTAAAATTTTTAAA
66 GAATTTCCAAACGCTAAATATTGCCTTATTTTAAAATTTTTAAA
* * * *
41325376 AGGATACTTAGTTATTTGGTTGAACGAGAAAAATCAAAACCCAGCATATTATGGCACGTTTTCC-
1 AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACG-TTTCCT
* * *
41325440 CGTATTTCCAAATGCTAAATATTGCCTCATTT
65 CGAATTTCCAAACGCTAAATATTGCCTTATTT
41325472 AGAAAAAATT
Statistics
Matches: 177, Mismatches: 24, Indels: 5
0.86 0.12 0.02
Matches are distributed among these distances:
106 27 0.15
108 27 0.15
109 118 0.67
110 5 0.03
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (109 bp):
AGGATACTTAGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTTCCAAACGCTAAATATTGCCTTATTTTAAAATTTTTAAA
Found at i:41325601 original size:4 final size:4
Alignment explanation
Indices: 41325592--41325618 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41325582 ATATCATAAC
41325592 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
41325619 CTGAAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:41325765 original size:14 final size:13
Alignment explanation
Indices: 41325742--41325799 Score: 50
Period size: 12 Copynumber: 4.6 Consensus size: 13
41325732 GTAAGATAAA
41325742 ATATAATATATAT
1 ATATAATATATAT
*
41325755 ATATAA-ATATAC
1 ATATAATATATAT
**
41325767 ATATTTTA-ATAT
1 ATATAATATATAT
*
41325779 ATA-AAAATATAT
1 ATATAATATATAT
41325791 ATATGAATA
1 ATAT-AATA
41325800 AGTATACACA
Statistics
Matches: 33, Mismatches: 8, Indels: 7
0.69 0.17 0.15
Matches are distributed among these distances:
11 1 0.03
12 22 0.67
13 7 0.21
14 3 0.09
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (13 bp):
ATATAATATATAT
Found at i:41325978 original size:15 final size:15
Alignment explanation
Indices: 41325960--41325990 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
41325950 AAGTAACAAT
*
41325960 AATATAAATAATAAA
1 AATAAAAATAATAAA
41325975 AATAAAAATAATAAA
1 AATAAAAATAATAAA
41325990 A
1 A
41325991 TTACTGAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (15 bp):
AATAAAAATAATAAA
Found at i:41327645 original size:45 final size:44
Alignment explanation
Indices: 41327542--41327664 Score: 158
Period size: 45 Copynumber: 2.8 Consensus size: 44
41327532 CTGGATGTGC
* *
41327542 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATCCTTTTAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTATCCTTTTAA
* * * *
41327586 GCCGCTCTACTGCAACTTCAGGGAGATAGGATTTACTGGC-TTTAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTA-T-CCTTTTAA
*
41327631 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTT
41327665 GCCACCTTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
44 30 0.45
45 36 0.54
46 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.31
Consensus pattern (44 bp):
TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTATCCTTTTAA
Found at i:41327678 original size:45 final size:44
Alignment explanation
Indices: 41327542--41327678 Score: 148
Period size: 45 Copynumber: 3.1 Consensus size: 44
41327532 CTGGATGTGC
* * * *
41327542 TCTGCTCTACTGCAACTTCAGAGAGATAAGATCTATCCTTTTAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTACCCCTTTAA
* * * **
41327586 GCCGCTCTACTGCAACTTCAGGGAGATAGGATTTACTGGCTTTAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTAC-CCCTTTAA
* * *
41327631 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCCACCTTCAA
1 TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTACC-CCTTTAA
41327676 TCT
1 TCT
41327679 ACTTCGCTGC
Statistics
Matches: 74, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
44 30 0.41
45 44 0.59
ACGTcount: A:0.26, C:0.25, G:0.18, T:0.31
Consensus pattern (44 bp):
TCTGCTCTACTGCAACTTCAGGGAGATAAGATTTACCCCTTTAA
Found at i:41327976 original size:89 final size:89
Alignment explanation
Indices: 41327822--41328231 Score: 658
Period size: 89 Copynumber: 4.6 Consensus size: 89
41327812 CTGCAAACTA
* * * * * * * *
41327822 TGGTGTCTTTGATCTGCTTCACTGCCAGTACAGGAAGGCAAGATCTACTATCTTCAATCTGCTCC
1 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTGCTCC
*
41327887 GCTGTCAGTACAGGAAGGCAAGGC
66 GCTGTCAGTACAGGAAGGCAAGAC
* * * *
41327911 TGGTGTCTTCGATCTGCTTCGCTGCCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTACTCC
1 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTGCTCC
41327976 GCTGTCAGTACAGGAAGGCAAGAC
66 GCTGTCAGTACAGGAAGGCAAGAC
* *
41328000 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGACATGATCTACTATCTCTAGTCTGCTCC
1 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTGCTCC
41328065 GCTGTCAGTACAGGAAGGCAAGAC
66 GCTGTCAGTACAGGAAGGCAAGAC
*
41328089 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTGCTATCTTTAGTCTGCTCC
1 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTGCTCC
*
41328154 GCTGTCAGTACAGGAAGGTAAGAC
66 GCTGTCAGTACAGGAAGGCAAGAC
*
41328178 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCAAGATCTACTATCTT
1 TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTT
41328232 CATTGATCTG
Statistics
Matches: 302, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 302 1.00
ACGTcount: A:0.22, C:0.25, G:0.24, T:0.29
Consensus pattern (89 bp):
TGGTTTCTTCGATCTGCTTCGCCGTCAGTACAGGAAGGCATGATCTACTATCTTTAGTCTGCTCC
GCTGTCAGTACAGGAAGGCAAGAC
Found at i:41329460 original size:17 final size:16
Alignment explanation
Indices: 41329427--41329483 Score: 78
Period size: 17 Copynumber: 3.4 Consensus size: 16
41329417 TTGGCCTCTC
*
41329427 CTTTTCTCTTTTTCTT
1 CTTTTTTCTTTTTCTT
*
41329443 CTTTTTTCTGTTTCCTT
1 CTTTTTTCT-TTTTCTT
41329460 CTTTTTTCTTTTTTCTT
1 CTTTTTTC-TTTTTCTT
41329477 CTTTTTT
1 CTTTTTT
41329484 TTGAAATATT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
16 8 0.22
17 27 0.75
18 1 0.03
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.77
Consensus pattern (16 bp):
CTTTTTTCTTTTTCTT
Found at i:41334002 original size:109 final size:109
Alignment explanation
Indices: 41333795--41334101 Score: 451
Period size: 108 Copynumber: 2.9 Consensus size: 109
41333785 AAGATTCAAG
*
41333795 AGGATATTTGGCTATTTGGTTAAACGAG--AAATCGAAACCCAGCACATTAGGGCACG-TTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * *
41333857 GAATTTCCAAACGCTAAATATTGCATTGTTTTGAAATTTTTAAA
66 GAATTTCCAAATGCTAAATATTGCCTTATTTTGAAATTTTTAAA
*
41333901 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCTAGCACATTAGGGCACGTTTCCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
* * *
41333966 GAATTACCAAATGCAAAACATTGCCTTATTTTGAAATTTTTAAA
66 GAATTTCCAAATGCTAAATATTGCCTTATTTTGAAATTTTTAAA
* * * * * *
41334010 AGGATACTTAG-TTTTTAGTTGAACGAGAAAAATTGAAACCCAGCACATTAGGGCACGTTTTCTC
1 AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
*
41334074 GTATTTCCAAATGCTAAATATTGCCTTA
66 GAATTTCCAAATGCTAAATATTGCCTTA
41334102 GTTAGAAAAA
Statistics
Matches: 179, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
106 27 0.15
108 99 0.55
109 53 0.30
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.32
Consensus pattern (109 bp):
AGGATATTTGGCTATTTGGTTGAACGAGAAAAATCGAAACCCAGCACATTAGGGCACGTTTCCTC
GAATTTCCAAATGCTAAATATTGCCTTATTTTGAAATTTTTAAA
Found at i:41336554 original size:25 final size:25
Alignment explanation
Indices: 41336526--41336617 Score: 73
Period size: 25 Copynumber: 3.6 Consensus size: 25
41336516 CTTATGAGTG
*
41336526 TCCCGATATATGGCTCTTCGGAACT
1 TCCCGATATATGGCTCTTCGGAGCT
*
41336551 TCCCGAT-TAAAGGCTCTTTCATGG-GCT
1 TCCCGATAT-ATGGCTC-TTC--GGAGCT
** *
41336578 TCTTGATATATGGCTCTCCGGAGCT
1 TCCCGATATATGGCTCTTCGGAGCT
*
41336603 TCCTGATAT-TGGCTC
1 TCCCGATATATGGCTC
41336618 GCATGAGCTT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
24 9 0.17
25 24 0.44
26 5 0.09
27 13 0.24
28 3 0.06
ACGTcount: A:0.17, C:0.26, G:0.22, T:0.35
Consensus pattern (25 bp):
TCCCGATATATGGCTCTTCGGAGCT
Found at i:41336625 original size:24 final size:25
Alignment explanation
Indices: 41336570--41336627 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
41336560 AAGGCTCTTT
* * *
41336570 CATGGGCTTCTTGATATATGGCTCT
1 CATGAGCTTCCTGATATATGGCTCG
**
41336595 CCGGAGCTTCCTGATAT-TGGCTCG
1 CATGAGCTTCCTGATATATGGCTCG
41336619 CATGAGCTT
1 CATGAGCTT
41336628 TCAGTTATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.16, C:0.24, G:0.26, T:0.34
Consensus pattern (25 bp):
CATGAGCTTCCTGATATATGGCTCG
Found at i:41338736 original size:12 final size:12
Alignment explanation
Indices: 41338719--41338757 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
41338709 GAAATCTAGG
41338719 TGGATTCTTTCC
1 TGGATTCTTTCC
*
41338731 TGGATTTTTTCC
1 TGGATTCTTTCC
41338743 TGGATTCTTTCC
1 TGGATTCTTTCC
41338755 TGG
1 TGG
41338758 GTATTGTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.08, C:0.21, G:0.21, T:0.51
Consensus pattern (12 bp):
TGGATTCTTTCC
Found at i:41345775 original size:6 final size:7
Alignment explanation
Indices: 41345756--41345780 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
41345746 GAGCATGTGG
41345756 GGAAAAA
1 GGAAAAA
41345763 GGAAAAA
1 GGAAAAA
41345770 GGAAAAA
1 GGAAAAA
41345777 GGAA
1 GGAA
41345781 TCCAACTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (7 bp):
GGAAAAA
Found at i:41354540 original size:22 final size:22
Alignment explanation
Indices: 41354508--41354558 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
41354498 TTTCACTTTT
41354508 TCAATTCATTCTCAA-CTCTCTC
1 TCAATTCATTCTCAATC-CTCTC
*
41354530 TCAATTTATTCTCAATCCTCTC
1 TCAATTCATTCTCAATCCTCTC
*
41354552 TTAATTC
1 TCAATTC
41354559 TCGCTCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 24 0.96
23 1 0.04
ACGTcount: A:0.24, C:0.31, G:0.00, T:0.45
Consensus pattern (22 bp):
TCAATTCATTCTCAATCCTCTC
Found at i:41354781 original size:18 final size:19
Alignment explanation
Indices: 41354760--41354803 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
41354750 AAAATAATGT
41354760 TATTTATAA-AACTCAAAA
1 TATTTATAACAACTCAAAA
*
41354778 TATTTATAACAACTCTAAA
1 TATTTATAACAACTCAAAA
41354797 -ATTTATA
1 TATTTATA
41354804 CTTTTCACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (19 bp):
TATTTATAACAACTCAAAA
Found at i:41362633 original size:31 final size:31
Alignment explanation
Indices: 41362597--41362666 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
41362587 CCGTAAAATA
* *
41362597 ACTAAAATTTACAACTTATTTAA-TAGAAGTG
1 ACTAAAATTGACAACTTATCTAACT-GAAGTG
* *
41362628 ACTAAAATTGACAATTTATCTAACTGGAGTG
1 ACTAAAATTGACAACTTATCTAACTGAAGTG
41362659 ACTAAAAT
1 ACTAAAAT
41362667 AATCAAATAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 33 0.97
32 1 0.03
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.33
Consensus pattern (31 bp):
ACTAAAATTGACAACTTATCTAACTGAAGTG
Found at i:41364434 original size:31 final size:29
Alignment explanation
Indices: 41364381--41364442 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
41364371 TTATAACTTG
*
41364381 TTGTTAATATTTTAATATATAAAATATAAA
1 TTGTAAATATTTTAATATAT-AAATATAAA
*
41364411 TTGTAAATATTTTTAAGTA-ATAAATATTAA
1 TTGTAAATA-TTTTAA-TATATAAATATAAA
41364441 TT
1 TT
41364443 ATTTATAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 18 0.64
31 8 0.29
32 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (29 bp):
TTGTAAATATTTTAATATATAAATATAAA
Found at i:41365139 original size:20 final size:17
Alignment explanation
Indices: 41365115--41365167 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 17
41365105 AAAAGTTTAG
41365115 TATTTTTATATTTTTATAA
1 TATTTTT-TATTTTTAT-A
*
41365134 TAATTTTTGTAATTTTATA
1 T-ATTTTT-TATTTTTATA
41365153 TATTTTTTATTTTTA
1 TATTTTTTATTTTTA
41365168 ATAAGTTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 7 0.23
18 6 0.20
19 3 0.10
20 14 0.47
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (17 bp):
TATTTTTTATTTTTATA
Found at i:41366520 original size:379 final size:379
Alignment explanation
Indices: 41365821--41366555 Score: 1240
Period size: 379 Copynumber: 1.9 Consensus size: 379
41365811 TACGTTGTAA
*
41365821 CTGTCGAAACCATTTTTTTGATAAAAGGAGTGTCGACTTGGATTTTAAAAATAAAAATGAATACG
1 CTGTCGAAACCATTTTTTTGATAAAAGGAGTGTCGACTTAGATTTTAAAAATAAAAATGAATACG
*
41365886 AGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCAAGCCACTTTGAAAAGTGGTTGTTTTTAA
66 AGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCAAGCCACCTTGAAAAGTGGTTGTTTTTAA
* *
41365951 TAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCATGAAATTCAGAAAAATGAGTTCGGGA
131 TAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAAAATGAGTTCGGGA
* *
41366016 GTCGGTTACGTACGAGGAATGATTAGTACCCTTGTAACGCCCAAAATTGATACCTAGTTGATTAA
196 GTCGGTTACGTACGAGGAATGATTAGCACCCTCGTAACGCCCAAAATTGATACCTAGTTGATTAA
*
41366081 TTAATGTCTGAGTGTCGAAGATTGAAAACTTTAAAGAGATTTAAAATACGATCCTTTATTGAAAT
261 TTAATGTCTGAGTGTCAAAGATTGAAAACTTTAAAGAGATTTAAAATACGATCCTTTATTGAAAT
* *
41366146 GTTTAGAATTTTCGGGAAAAT-GACATATTTTGGGTCCCCACCGGAGTCGCCAAG
326 GATGAGAATTTTCGGGAAAATAG-CATATTTTGGGTCCCCACCGGAGTCGCCAAG
** * *
41366200 CTGTCGAAATTATTTTTTTGATAAAAGGGGTGTCGACTTAGATTTTAAAAATGAAAATGAATACG
1 CTGTCGAAACCATTTTTTTGATAAAAGGAGTGTCGACTTAGATTTTAAAAATAAAAATGAATACG
* **
41366265 GGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCCGGCCACCTTGAAAAGTGGTTGTTTTTAA
66 AGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCAAGCCACCTTGAAAAGTGGTTGTTTTTAA
* *
41366330 TAAACAATTTAATTTTATTAAAACAACGATTTTGGTCTACGAAATTCAAAAAAATGGGTTCGGGA
131 TAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAAAATGAGTTCGGGA
* * *
41366395 GTCGGTTACGTAGGAGGAA-GAATTAGCACTCTCGTAATGCCCAAAATTGATACCTAGTTGATTA
196 GTCGGTTACGTACGAGGAATG-ATTAGCACCCTCGTAACGCCCAAAATTGATACCTAGTTGATTA
*
41366459 ATTAATGTCTTAGTGTCAAAGATTGAAAACTTTAAAGAGATTTAAAATACGATCCTTTATTGAAA
260 ATTAATGTCTGAGTGTCAAAGATTGAAAACTTTAAAGAGATTTAAAATACGATCCTTTATTGAAA
41366524 TGATGAGAATTTTCGGGAAAATAGCATATTTT
325 TGATGAGAATTTTCGGGAAAATAGCATATTTT
41366556 ACGTTAATCG
Statistics
Matches: 332, Mismatches: 22, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
378 1 0.00
379 330 0.99
380 1 0.00
ACGTcount: A:0.34, C:0.13, G:0.20, T:0.33
Consensus pattern (379 bp):
CTGTCGAAACCATTTTTTTGATAAAAGGAGTGTCGACTTAGATTTTAAAAATAAAAATGAATACG
AGAGTCGCCACCAATCCTTTTTGATAAGGTGTGATCAAGCCACCTTGAAAAGTGGTTGTTTTTAA
TAAACAATTTAATTTTATTAAAACAACGATTTTGGTCCACGAAATTCAAAAAAATGAGTTCGGGA
GTCGGTTACGTACGAGGAATGATTAGCACCCTCGTAACGCCCAAAATTGATACCTAGTTGATTAA
TTAATGTCTGAGTGTCAAAGATTGAAAACTTTAAAGAGATTTAAAATACGATCCTTTATTGAAAT
GATGAGAATTTTCGGGAAAATAGCATATTTTGGGTCCCCACCGGAGTCGCCAAG
Found at i:41366827 original size:73 final size:73
Alignment explanation
Indices: 41366682--41366818 Score: 238
Period size: 73 Copynumber: 1.9 Consensus size: 73
41366672 TCTAAAAATA
* * **
41366682 GGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCTGAGATCGTTTAAAACTTGAGA
1 GGATCATGCACAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAACTTGAGA
41366747 GAAAAAAG
66 GAAAAAAG
41366755 GGATCATGCACAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAACTTGAG
1 GGATCATGCACAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAACTTGAG
41366819 TTTGAAAAGA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (73 bp):
GGATCATGCACAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAACTTGAGA
GAAAAAAG
Found at i:41367228 original size:28 final size:28
Alignment explanation
Indices: 41367196--41367361 Score: 97
Period size: 28 Copynumber: 5.7 Consensus size: 28
41367186 AAAGAGATAT
41367196 ATATGTATGTATATATATAAATTAAAAA
1 ATATGTATGTATATATATAAATTAAAAA
*** ** * *
41367224 ATATGTATGTATATGCGTGTA-T-ATAT
1 ATATGTATGTATATATATAAATTAAAAA
*
41367250 ATATGTATATATATAAAGTATAAAGTATAAATAA
1 ATATGTATGTATAT--A-TATAAA-T-TAAA-AA
41367284 TATATAGGTATGTATATATATAAATTAAAAAA
1 -ATAT--GTATGTATATATATAAATT-AAAAA
* * *
41367316 AAAT-TATGTATGTATATATATTATAAAA
1 ATATGTATGTATATATATAAATTA-AAAA
*
41367344 A-ATGTATGTATGTATATA
1 ATATGTATGTATATATATA
41367362 TACATAACAA
Statistics
Matches: 105, Mismatches: 19, Indels: 28
0.69 0.12 0.18
Matches are distributed among these distances:
26 15 0.14
27 4 0.04
28 51 0.49
29 2 0.02
31 3 0.03
32 4 0.04
33 5 0.05
34 7 0.07
35 5 0.05
37 9 0.09
ACGTcount: A:0.48, C:0.01, G:0.11, T:0.40
Consensus pattern (28 bp):
ATATGTATGTATATATATAAATTAAAAA
Found at i:41367329 original size:32 final size:30
Alignment explanation
Indices: 41367291--41367363 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 30
41367281 TAATATATAG
41367291 GTATGTATATATATAAATTAAAAAAAAAT-TAT
1 GTATGTATATATAT--ATT-AAAAAAAATGTAT
*
41367323 GTATG--TATATATATTATAAAAAATGTAT
1 GTATGTATATATATATTAAAAAAAATGTAT
41367351 GTATGTATATATA
1 GTATGTATATATA
41367364 CATAACAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
27 8 0.22
28 11 0.30
30 13 0.35
32 5 0.14
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (30 bp):
GTATGTATATATATATTAAAAAAAATGTAT
Found at i:41367362 original size:28 final size:29
Alignment explanation
Indices: 41367291--41367363 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
41367281 TAATATATAG
* *
41367291 GTATGTATATATATAAATTAAAAAAAAAT
1 GTATGTATGTATATATATTAAAAAAAAAT
*
41367320 -TATGTATGTATATATATT-ATAAAAAAT
1 GTATGTATGTATATATATTAAAAAAAAAT
41367347 GTATGTATGTATATATA
1 GTATGTATGTATATATA
41367364 CATAACAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (29 bp):
GTATGTATGTATATATATTAAAAAAAAAT
Found at i:41367373 original size:28 final size:27
Alignment explanation
Indices: 41367313--41367375 Score: 92
Period size: 28 Copynumber: 2.3 Consensus size: 27
41367303 ATAAATTAAA
*
41367313 AAAAAATTATGTATGTATATATATTAT
1 AAAAAATTATGTATGTATATATATCAT
41367340 AAAAAATGTATGTATGTATATATA-CAT
1 AAAAAAT-TATGTATGTATATATATCAT
41367367 AACAAAATT
1 AA-AAAATT
41367376 TGAAATTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
27 12 0.36
28 21 0.64
ACGTcount: A:0.51, C:0.03, G:0.08, T:0.38
Consensus pattern (27 bp):
AAAAAATTATGTATGTATATATATCAT
Found at i:41369123 original size:138 final size:138
Alignment explanation
Indices: 41368923--41369181 Score: 374
Period size: 138 Copynumber: 1.9 Consensus size: 138
41368913 GGTTTTAGTT
* *
41368923 TGCTCCACTGCAACGTCAGGGAGATAAGACTTGTCATGGTAAATTTAACCCGACCTACTGCAACT
1 TGCTCCACTGCAACGTCAAGGAGATAAGACTTATCATGGTAAATTTAACCCGACCTACTGCAACT
* * * * *
41368988 TCAGAGGTATAGGATTCATCATTTTAATCCGCTTCACTGTAACTTTAGGGTGATAGAATTAGTAG
66 TCAGAGGTATAGGATTCATCATTTTAATCAGCTCCACTGCAACTTGAGGGAGATAGAATTAGTAG
41369053 CTTCAATC
131 CTTCAATC
* * * * * *
41369061 TGCTCCACTGCAACTTCAAGGAGATAAGACTTATTATGGTAGATTTAATCCGGCCTGCTGCAACT
1 TGCTCCACTGCAACGTCAAGGAGATAAGACTTATCATGGTAAATTTAACCCGACCTACTGCAACT
* * *
41369126 TTAGAGGTATAGGATTTATCATTTTAATTAGCTCCACTGCAACTTGAGGGAGATAG
66 TCAGAGGTATAGGATTCATCATTTTAATCAGCTCCACTGCAACTTGAGGGAGATAG
41369182 GACTTGTCGT
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 105 1.00
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (138 bp):
TGCTCCACTGCAACGTCAAGGAGATAAGACTTATCATGGTAAATTTAACCCGACCTACTGCAACT
TCAGAGGTATAGGATTCATCATTTTAATCAGCTCCACTGCAACTTGAGGGAGATAGAATTAGTAG
CTTCAATC
Found at i:41369838 original size:44 final size:44
Alignment explanation
Indices: 41369788--41369957 Score: 157
Period size: 45 Copynumber: 3.8 Consensus size: 44
41369778 TAGTAACTTT
41369788 AATCTGCTCCACTGCAACTTTAGGGAGATAAGA-TTGGTTTAG-TC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTT-G-TTAGCTC
* * *
41369832 AGTCTGCTCCACTACAACTTTAGGGAGATAAGACTTGTTGGCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTAGC-TC
* * * * * *
41369877 AATCTGCTCTACTGCAACTTTAAGGAGATAAAATTTGTCATCTTC
1 AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTAGC-TC
* * * *
41369922 AGTCTACCCCACTGCAACTTCAGAGG-GATAAGACTT
1 AATCTGCTCCACTGCAACTTTAG-GGAGATAAGACTT
41369958 ACTTTCTTCA
Statistics
Matches: 102, Mismatches: 20, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
43 3 0.03
44 32 0.31
45 65 0.64
46 2 0.02
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (44 bp):
AATCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTTAGCTC
Found at i:41369922 original size:45 final size:44
Alignment explanation
Indices: 41369695--41369954 Score: 184
Period size: 44 Copynumber: 5.9 Consensus size: 44
41369685 AAGTCTGGTG
* * * * ***
41369695 TCTTCAATCTACTCCATTACAACTTCAGGGAGATAAGATCCATCA
1 TCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGT-A
* * * * * * *
41369740 T-TTTAATCCGCTCCACTGCAACTTCAGGGAGGTAGGGTTAGTA
1 TCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTA
* * * *
41369783 ACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTT
1 TCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTA
** * * *
41369827 TAGTCAGTCTGCTCCACTACAACTTTAGGGAGATAAGACTTGT-
1 TCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTA
* * *
41369870 TGGCTTCAATCTGCTCTACTGCAACTTTAAGGAGATAAAATTTGTCA
1 T--CTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGT-A
* * * *
41369917 TCTTCAGTCTACCCCACTGCAACTTCAGAGG-GATAAGA
1 TCTTCAATCTGCTCCACTGCAACTTTAG-GGAGATAAGA
41369955 CTTACTTTCT
Statistics
Matches: 167, Mismatches: 42, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
43 2 0.01
44 100 0.60
45 62 0.37
46 2 0.01
47 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (44 bp):
TCTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTTGTA
Found at i:41369969 original size:90 final size:89
Alignment explanation
Indices: 41369788--41369957 Score: 207
Period size: 89 Copynumber: 1.9 Consensus size: 89
41369778 TAGTAACTTT
* * * * * *
41369788 AATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTTAGTCAGTCTGCTCCACTACAACTTT
1 AATCTGCTCCACTGCAACTTTAAGGAGATAAAATTGGTATAGTCAGTCTACCCCACTACAACTTC
*
41369853 AGGGAGATAAGACTTGTTGGCTTC
66 AGGGAGATAAGACTTCTTGGCTTC
* * ** *
41369877 AATCTGCTCTACTGCAACTTTAAGGAGATAAAATTTGTCATCTTCAGTCTACCCCACTGCAACTT
1 AATCTGCTCCACTGCAACTTTAAGGAGATAAAATTGGT-ATAGTCAGTCTACCCCACTACAACTT
41369942 CAGAGG-GATAAGACTT
65 CAG-GGAGATAAGACTT
41369958 ACTTTCTTCA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
89 34 0.50
90 32 0.47
91 2 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (89 bp):
AATCTGCTCCACTGCAACTTTAAGGAGATAAAATTGGTATAGTCAGTCTACCCCACTACAACTTC
AGGGAGATAAGACTTCTTGGCTTC
Found at i:41370124 original size:404 final size:404
Alignment explanation
Indices: 41369302--41370227 Score: 1175
Period size: 404 Copynumber: 2.3 Consensus size: 404
41369292 ATGCAATTTG
* * * *
41369302 CTCTACTGCAACTTCAGAGAGATAAGATTCATCATTTTAATCCGCTTCACTGCAGCTTCAGGGAG
1 CTCTACTGCAACTTCAGGGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAG
* * * * * *
41369367 ATAGGACTAGTAACTTCAATTTGTTCCACTGCAACTTTAGGGAAATAAGATTGGAATAGTCAGTT
66 GTAGGATTAGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGAATAGTCAGTC
* * * *
41369432 TGCTTCACTGCAACTTCAGAGAGATAAGACTTGTTAGCTTTAATCTGCTCCACCGCAACTTCAGG
131 TGCTCCACTACAACTTCAGAGAGATAAGACTTGTTAGCTTCAATCTGCTCCACCGCAACTTCAAG
* * * ** * * *
41369497 GAGATAATATTTGCTATCTTCAGTTTGCCCCGTTGTAACTTTAGGGGGATAAGACTTACTTTCTT
196 GAGATAAAATTTGCTATCTTCAGTCTACCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTT
41369562 CAATTTTAACGTCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAATGCCA
261 CAATTTTAACGTCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAATGCCA
* * *
41369627 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCCACTATAACGCCAATGAGATAAGTCTG
326 GGGAAACAAGATTCGCTACATTTAGCTTTAATATGTTCCACTATAACGCCAAGGAGATAAGTCTG
* *
41369692 GTGTCTTCAATCTA
391 CTATCTTCAATCTA
* * *
41369706 CTCCATTACAACTTCAGGGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAG
1 CTCTACTGCAACTTCAGGGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAG
* * **
41369771 GTAGGGTTAGTAACTTTAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGTTTAGTCAGTC
66 GTAGGATTAGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGAATAGTCAGTC
* * * * * *
41369836 TGCTCCACTACAACTTTAGGGAGATAAGACTTGTTGGCTTCAATCTGCTCTACTGCAACTTTAAG
131 TGCTCCACTACAACTTCAGAGAGATAAGACTTGTTAGCTTCAATCTGCTCCACCGCAACTTCAAG
41369901 GAGATAAAATTTG-TCATCTTCAGTCTACCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCT
196 GAGATAAAATTTGCT-ATCTTCAGTCTACCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCT
* * *
41369965 TCAATTTTAATG-CTAGGGAGATAAGATTTGTTGCCTTCAGCTTTAATCTGCTCCGCTGCAATG-
260 TCAATTTTAACGTC-AGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAATGC
* * * * *
41370028 CAGGGAAACAAGATTCGCTACATTTAGCTTTAATATGTTCCACTGTCATGCCAAGGGGATAGGAT
324 CAGGGAAACAAGATTCGCTACATTTAGCTTTAATATGTTCCACTATAACGCCAAGGAGATAAG-T
* *
41370093 -TCGCTATCTTCAGTCTT
388 CT-GCTATCTTCAATCTA
* * * * *
41370110 CTCTACTGCAACTTCAGGGAGATAAGA-CTTAGTACGA--TCAATCTGCCCCACTGCAACTTTA-
1 CTCTACTGCAACTTCAGGGAGATAAGATC-CA-T-C-ATTTTAATCCGCTCCACTGCAACTTCAG
* * * * *
41370171 GGAGGATAAGATTAGTGACTTCAATCTACCCCACTGCAACTTTAGGAAGATAAGATT
62 GGAGG-TAGGATTAGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATT
41370228 CGCCATGACG
Statistics
Matches: 448, Mismatches: 65, Indels: 17
0.85 0.12 0.03
Matches are distributed among these distances:
403 59 0.13
404 322 0.72
405 65 0.15
406 1 0.00
407 1 0.00
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (404 bp):
CTCTACTGCAACTTCAGGGAGATAAGATCCATCATTTTAATCCGCTCCACTGCAACTTCAGGGAG
GTAGGATTAGTAACTTCAATCTGCTCCACTGCAACTTTAGGGAGATAAGATTGGAATAGTCAGTC
TGCTCCACTACAACTTCAGAGAGATAAGACTTGTTAGCTTCAATCTGCTCCACCGCAACTTCAAG
GAGATAAAATTTGCTATCTTCAGTCTACCCCACTGCAACTTCAGAGGGATAAGACTTACTTTCTT
CAATTTTAACGTCAGGGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCCGCTGCAATGCCA
GGGAAACAAGATTCGCTACATTTAGCTTTAATATGTTCCACTATAACGCCAAGGAGATAAGTCTG
CTATCTTCAATCTA
Found at i:41370203 original size:44 final size:44
Alignment explanation
Indices: 41370114--41370227 Score: 151
Period size: 44 Copynumber: 2.6 Consensus size: 44
41370104 AGTCTTCTCT
* *
41370114 ACTGCAACTTCAGG-GAGATAAGACTTAGTACGATCAATCTGCCCC
1 ACTGCAACTTTAGGAG-GATAAGA-TTAGTACGATCAATCTACCCC
*
41370159 ACTGCAACTTTAGGAGGATAAGATTAGTGAC-TTCAATCTACCCC
1 ACTGCAACTTTAGGAGGATAAGATTAGT-ACGATCAATCTACCCC
*
41370203 ACTGCAACTTTAGGAAGATAAGATT
1 ACTGCAACTTTAGGAGGATAAGATT
41370228 CGCCATGACG
Statistics
Matches: 63, Mismatches: 4, Indels: 5
0.88 0.06 0.07
Matches are distributed among these distances:
44 40 0.63
45 22 0.35
46 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.25
Consensus pattern (44 bp):
ACTGCAACTTTAGGAGGATAAGATTAGTACGATCAATCTACCCC
Found at i:41370371 original size:51 final size:51
Alignment explanation
Indices: 41370257--41370390 Score: 160
Period size: 51 Copynumber: 2.6 Consensus size: 51
41370247 TTAACGCTAG
* ** *
41370257 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTGCTGCAATGCCAG
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACACCAA
* * * * * *
41370308 GGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAA
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACACCAA
* *
41370359 GGAGATAGGATTCGCTGCCTTCATCTTTAATC
1 GGAGATAAGATTCGCTGCCTTCAGCTTTAATC
41370391 CACTCCACTT
Statistics
Matches: 67, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 67 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.31
Consensus pattern (51 bp):
GGAGATAAGATTCGCTGCCTTCAGCTTTAATCTGCTCTACTGCAACACCAA
Found at i:41370482 original size:51 final size:51
Alignment explanation
Indices: 41370402--41370503 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
41370392 ACTCCACTTC
* * * * *
41370402 AGCTTTAATGTATTCTACTACAATGCTAGGGAAACAAGATTCGCTATCTTT
1 AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
* * * *
41370453 AGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCTTT
1 AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
41370504 GATCTGCTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (51 bp):
AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
Found at i:41370497 original size:123 final size:123
Alignment explanation
Indices: 41370275--41370498 Score: 306
Period size: 123 Copynumber: 1.8 Consensus size: 123
41370265 GATTCGCTGC
* * *
41370275 CTTCAGCTTTAATCTGCTCTGCTGCAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCTACTACAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* * * * *
41370340 TGTTCTACTGTAACACCAAGGAGATAGGATTCGCTGCCTTCATCTTTAATCCACTCCA
66 TGTTCCACTGCAACACCAAGGAAATAAGAGTCGCTGCCTTCATCTTTAATCCACTCCA
* * * *
41370398 CTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAACAAGATTCGCTATCTTTAGCTTTAATC
1 CTTCAGCTTTAATCTACTCTACTACAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
* *
41370463 TGTTCCACTGCAA-AGCTAGGAAAATAAGAGTCGCTG
66 TGTTCCACTGCAACACCAAGG-AAATAAGAGTCGCTG
41370499 TCTTTGATCT
Statistics
Matches: 86, Mismatches: 14, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
122 5 0.06
123 81 0.94
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.32
Consensus pattern (123 bp):
CTTCAGCTTTAATCTACTCTACTACAATGCCAGGGAAACAAGATTCGCTACCTTTAGCTTTAATC
TGTTCCACTGCAACACCAAGGAAATAAGAGTCGCTGCCTTCATCTTTAATCCACTCCA
Found at i:41370559 original size:44 final size:44
Alignment explanation
Indices: 41370505--41370706 Score: 115
Period size: 44 Copynumber: 4.6 Consensus size: 44
41370495 GCTGTCTTTG
* *
41370505 ATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * * ***** *
41370549 ATCTACTCCACTGCTACTAAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * * **
41370592 ATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCGTCTTCA
1 ATCTAC-TCCACTACT-GCTTAGGG-AGACAGGATCT-ACAATCTTCA
* * *
41370637 ATCTACTCCACAACTGCTTAAGGAGGCAGGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * *
41370681 ACCTACTCTACTGCTGCTCAGGGAGA
1 ATCTACTCCACTACTGCTTAGGGAGA
41370707 TAGAATTGGT
Statistics
Matches: 112, Mismatches: 38, Indels: 16
0.67 0.23 0.10
Matches are distributed among these distances:
43 18 0.16
44 77 0.69
45 17 0.15
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.27
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
Found at i:41370704 original size:132 final size:131
Alignment explanation
Indices: 41370505--41370757 Score: 380
Period size: 132 Copynumber: 1.9 Consensus size: 131
41370495 GCTGTCTTTG
* * * * *
41370505 ATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACTAAG
1 ATCTACTCCACAACTGCTTAAGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTACTAAG
* * *
41370570 GGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGTCTT
66 GGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAA-ACAAGATTCACCGTCTT
41370635 CA
130 CA
* * * *
41370637 ATCTACTCCACAACTGCTTAAGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTGCTCAG
1 ATCTACTCCACAACTGCTTAAGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTACTAAG
*
41370702 GGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTC
66 GGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTC
41370758 GCTACCTTTA
Statistics
Matches: 108, Mismatches: 13, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
131 8 0.07
132 100 0.93
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (131 bp):
ATCTACTCCACAACTGCTTAAGGAGACAGGATCTACAATCTTCAACCTACTCCACTGCTACTAAG
GGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTCACCGTCTTC
A
Found at i:41370804 original size:437 final size:437
Alignment explanation
Indices: 41370307--41371631 Score: 2533
Period size: 437 Copynumber: 3.0 Consensus size: 437
41370297 TGCAATGCCA
41370307 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
1 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
41370372 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
66 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
41370437 AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
131 AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
41370502 TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
196 TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
41370567 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
261 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
* * *
41370632 CTTCAATCTACTCCACAACTGCTTAAGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
326 CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
41370697 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
391 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
41370744 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
1 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
41370809 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
66 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
41370874 AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
131 AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
41370939 TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
196 TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
41371004 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
261 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
41371069 CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
326 CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
41371134 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
391 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
41371181 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
1 GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
* *
41371246 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATATATTCTACTACAATGCCAGGGAAAC
66 GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
* * *
41371311 AATATTCACTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCCAGGAAAATAAGAGTCGCTGTCT
131 AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
*
41371376 TTGATCTGCTCCACTTCTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
196 TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
* *
41371441 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTAGTACCTTGGGAAGATAGGATTCACCGT
261 AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
41371506 CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
326 CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
41371571 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
391 CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
*
41371618 GGGAAGATAAGATT
1 GGGAA-ACAAGATT
41371632 TGTCGTCTTT
Statistics
Matches: 875, Mismatches: 12, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
437 868 0.99
438 7 0.01
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (437 bp):
GGGAAACAAGATTCGCTACCTTTAGCTTTAATCTGTTCTACTGTAACACCAAGGAGATAGGATTC
GCTGCCTTCATCTTTAATCCACTCCACTTCAGCTTTAATGTATTCTACTACAATGCTAGGGAAAC
AAGATTCGCTATCTTTAGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCT
TTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGCTACT
AAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCACCGT
CTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGCTG
CTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTT
Found at i:41370919 original size:51 final size:51
Alignment explanation
Indices: 41370839--41370940 Score: 123
Period size: 51 Copynumber: 2.0 Consensus size: 51
41370829 ACTCCACTTC
* * * * *
41370839 AGCTTTAATGTATTCTACTACAATGCTAGGGAAACAAGATTCGCTATCTTT
1 AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
* * * *
41370890 AGCTTTAATCTGTTCCACTGCAAAGCTAGGAAAATAAGAGTCGCTGTCTTT
1 AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
41370941 GATCTGCTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (51 bp):
AGCTTTAATCTATTCCACTACAAAGCTAGGAAAACAAGAGTCGCTATCTTT
Found at i:41370996 original size:44 final size:44
Alignment explanation
Indices: 41370942--41371143 Score: 124
Period size: 44 Copynumber: 4.6 Consensus size: 44
41370932 GCTGTCTTTG
* *
41370942 ATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * * ***** *
41370986 ATCTACTCCACTGCTACTAAGGGAGATAGGA-CTGGTGGCTTAA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * * ** *
41371029 ATCTGCTTCC-CTACTACCTT-GGGAAGATAAGAT-TCACCGTCTTCG
1 ATCTAC-TCCACTACT-GCTTAGGG-AGACAGGATCT-ACAATCTTCA
*
41371074 ATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCA
1 ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
* * * *
41371118 ACCTACTCTACTGCTGCTCAGGGAGA
1 ATCTACTCCACTACTGCTTAGGGAGA
41371144 TAGAATTGGT
Statistics
Matches: 114, Mismatches: 36, Indels: 16
0.69 0.22 0.10
Matches are distributed among these distances:
43 18 0.16
44 78 0.68
45 18 0.16
ACGTcount: A:0.26, C:0.27, G:0.20, T:0.28
Consensus pattern (44 bp):
ATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCA
Found at i:41371141 original size:132 final size:131
Alignment explanation
Indices: 41370935--41371194 Score: 403
Period size: 132 Copynumber: 2.0 Consensus size: 131
41370925 AAGAGTCGCT
* * * *
41370935 GTCTTTGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCTTCAATCTACTCCACTGC
1 GTCTTCGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
* * *
41371000 TACTAAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAGATTCA
66 TACTAAGGGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAA-ACAAGATTCA
41371065 CC
130 CC
* *
41371067 GTCTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCTTCAACCTACTCTACTGC
1 GTCTTCGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
* * *
41371132 TGCTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTC
66 TACTAAGGGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTC
41371195 GCTACCTTTA
Statistics
Matches: 116, Mismatches: 12, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
131 8 0.07
132 108 0.93
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.29
Consensus pattern (131 bp):
GTCTTCGATCTACTCCACTACTGCTTAGGGAGACAGGATCTACAATCTTCAACCTACTCCACTGC
TACTAAGGGAGATAGAACTGGTGGCCTAAATCTGCTTCCCTACTACCTTGGGAAACAAGATTCAC
C
Found at i:41371578 original size:132 final size:132
Alignment explanation
Indices: 41371355--41371987 Score: 856
Period size: 132 Copynumber: 4.8 Consensus size: 132
41371345 TGCAAAGCCA
* * * * *
41371355 GGAAAATAAGAGTCGCTGTCTTTGATCTGCTCCACTTCTGCTTAGGGAGACATGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCT
* * * *
41371420 TCAATCTACTCCACTGCTACTAAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTAGTACCT
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
41371485 TG
131 TG
* * * * *
41371487 GGAAGATAGGATTCACCGTCTTCGATCTACTCCACTACTGCTTAGGGAGGCAGGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCT
* * * *
41371552 TCAACCTACTCTACTGCTGCTCAGGGAGATAGAATTGGTGGCCTAAATCTGCTTCCCTACTACCT
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
41371617 TG
131 TG
* * * *
41371619 GGAAGATAAGATTTGTCGTCTTTGATCTGCTCTACTACTGCTTAGGGAGACATGATCTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCT
* * * *
41371684 TTAATCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCAGTTTCCCTACTACCT
66 TCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
41371749 TG
131 TG
* * *
41371751 GGAAGATAAGATTTGCCGTATTCGATCTGCTCCACTACTG-TCTAGGGAGACAGGATCTACAATC
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCT-TAGGGAGACATGATCTACAATC
* * * * * *
41371815 TTCAACCTACTCTACTGTTGCTCAAGGAGATAAGACTGGTGGCTTAAATCTGCTTCCTTATTACC
65 TTCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACC
41371880 TTG
130 TTG
* * * * *
41371883 AGAAGATAATATTCGTCGTCTTCGATCTACTCCACTACTGCTTAGGGAGACATGATTTACAATCT
1 GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCT
**
41371948 TCAACCTACTCCACTATTGCTCAGGGAGATAAGG-CTGGTG
66 TCAACCTACTCCACTGCTGCTCAGGGAGAT-AGGACTGGTG
41371988 CTTTTGATCT
Statistics
Matches: 436, Mismatches: 62, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
131 1 0.00
132 432 0.99
133 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (132 bp):
GGAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGACATGATCTACAATCT
TCAACCTACTCCACTGCTGCTCAGGGAGATAGGACTGGTGGCTTAAATCTGCTTCCCTACTACCT
TG
Found at i:41376483 original size:73 final size:73
Alignment explanation
Indices: 41376331--41376474 Score: 261
Period size: 73 Copynumber: 2.0 Consensus size: 73
41376321 TCTCGGATTT
* * *
41376331 AAAAAAGGGATCATGCCCAGTAAGTTAGGACACGATCTTTTCTTAATTCCCGAGATCGTTTAAAA
1 AAAAAAGGGACCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
41376396 CTTGAGAG
66 CTTGAGAG
41376404 AAAAAAGGGACCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
1 AAAAAAGGGACCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
41376469 CTTGAG
66 CTTGAG
41376475 TTTGAAAAGA
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.26
Consensus pattern (73 bp):
AAAAAAGGGACCATGCCCAGTAAGTTAGGACACGATCTCTTCTTAATTCCCAAGATCGTTTAAAA
CTTGAGAG
Found at i:41377013 original size:8 final size:8
Alignment explanation
Indices: 41377000--41377033 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
41376990 ATTATAAAAA
41377000 ATGTATAT
1 ATGTATAT
*
41377008 ATGTATGT
1 ATGTATAT
*
41377016 ATGTATGT
1 ATGTATAT
41377024 ATGTATAT
1 ATGTATAT
41377032 AT
1 AT
41377034 ACATAACAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (8 bp):
ATGTATAT
Found at i:41377017 original size:12 final size:12
Alignment explanation
Indices: 41377000--41377033 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
41376990 ATTATAAAAA
41377000 ATGTATATATGT
1 ATGTATATATGT
*
41377012 ATGTATGTATGT
1 ATGTATATATGT
41377024 ATGTATATAT
1 ATGTATATAT
41377034 ACATAACAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (12 bp):
ATGTATATATGT
Found at i:41377034 original size:4 final size:4
Alignment explanation
Indices: 41377000--41377029 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
41376990 ATTATAAAAA
*
41377000 ATGT ATAT ATGT ATGT ATGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
41377030 ATATACATAA
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:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:41381246 original size:10 final size:10
Alignment explanation
Indices: 41381231--41381257 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
41381221 TCTCCTTTCT
41381231 CTTCTTCAAC
1 CTTCTTCAAC
41381241 CTTCTTCAAC
1 CTTCTTCAAC
41381251 CTTCTTC
1 CTTCTTC
41381258 TGTTATCTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.41, G:0.00, T:0.44
Consensus pattern (10 bp):
CTTCTTCAAC
Found at i:41384040 original size:14 final size:15
Alignment explanation
Indices: 41384018--41384094 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
41384008 CAATCAAACA
41384018 CCAGAAAAT-ATTTT
1 CCAGAAAATCATTTT
*
41384032 CCAGTAAATCATTTT
1 CCAGAAAATCATTTT
*
41384047 ACAGAAAAGTAAAACATTTT
1 CCAGAAAA-T----CATTTT
41384067 CCAG-AAATCATTTT
1 CCAGAAAATCATTTT
* *
41384081 ACGGAAAA-CATTTT
1 CCAGAAAATCATTTT
41384095 ACTGGCAATC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 22 0.44
15 14 0.28
16 1 0.02
18 1 0.02
19 3 0.06
20 9 0.18
ACGTcount: A:0.43, C:0.16, G:0.09, T:0.32
Consensus pattern (15 bp):
CCAGAAAATCATTTT
Found at i:41384059 original size:20 final size:20
Alignment explanation
Indices: 41384034--41384073 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41384024 AATATTTTCC
*
41384034 AGTAAATCATTTTACAGAAA
1 AGTAAAACATTTTACAGAAA
*
41384054 AGTAAAACATTTTCCAGAAA
1 AGTAAAACATTTTACAGAAA
41384074 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.10, T:0.28
Consensus pattern (20 bp):
AGTAAAACATTTTACAGAAA
Found at i:41384079 original size:34 final size:35
Alignment explanation
Indices: 41384022--41384088 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
41384012 CAAACACCAG
*
41384022 AAAATATTTTCCAGTAAATCATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
*
41384057 AAAACATTTTCCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
41384089 CATTTTACTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.46, C:0.13, G:0.09, T:0.31
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:41384095 original size:14 final size:14
Alignment explanation
Indices: 41384057--41384096 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
41384047 ACAGAAAAGT
*
41384057 AAAACATTTTCCAG
1 AAAACATTTTACAG
* *
41384071 AAATCATTTTACGG
1 AAAACATTTTACAG
41384085 AAAACATTTTAC
1 AAAACATTTTAC
41384097 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.33
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:41384477 original size:23 final size:23
Alignment explanation
Indices: 41384450--41384496 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
41384440 AAAAAATATT
41384450 AAATATATATA-TTTTTTATTTTA
1 AAATATA-ATAGTTTTTTATTTTA
41384473 AAATATAATAGTTTTTTATTTTA
1 AAATATAATAGTTTTTTATTTTA
41384496 A
1 A
41384497 GTTTATTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 3 0.13
23 20 0.87
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
AAATATAATAGTTTTTTATTTTA
Found at i:41384605 original size:9 final size:9
Alignment explanation
Indices: 41384591--41384618 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41384581 TTTTGTTACA
41384591 ACAATTAAT
1 ACAATTAAT
41384600 ACAATTAAT
1 ACAATTAAT
41384609 ACAATTAAT
1 ACAATTAAT
41384618 A
1 A
41384619 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41384640 original size:68 final size:68
Alignment explanation
Indices: 41384561--41384770 Score: 370
Period size: 68 Copynumber: 3.1 Consensus size: 68
41384551 TCAAGTTTGT
*
41384561 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41384626 AAA
66 AAA
*
41384629 TTTACTAATCAAATGTTAGATTTTATTATAACAATTAATACAATTAATACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
41384694 AAA
66 AAA
*
41384697 TTGACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATTTGAT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
*
41384760 AAT
66 AAA
41384763 TTTACTAA
1 TTTACTAA
41384771 CAATTAATTT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
66 26 0.19
67 1 0.01
68 109 0.80
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (68 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATTTGAT
AAA
Found at i:41384671 original size:9 final size:9
Alignment explanation
Indices: 41384659--41384686 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41384649 TTTTATTATA
41384659 ACAATTAAT
1 ACAATTAAT
41384668 ACAATTAAT
1 ACAATTAAT
41384677 ACAATTAAT
1 ACAATTAAT
41384686 A
1 A
41384687 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41384780 original size:16 final size:16
Alignment explanation
Indices: 41384759--41384800 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41384749 AATAATTTGA
*
41384759 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41384775 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41384791 TAGTTTTAAT
1 TAATTTTAAT
41384801 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41386385 original size:11 final size:11
Alignment explanation
Indices: 41386371--41386402 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41386361 TATTATATTT
41386371 CTGTTATTTTG
1 CTGTTATTTTG
41386382 CTGTTATTTTG
1 CTGTTATTTTG
*
41386393 TTGTTATTTT
1 CTGTTATTTT
41386403 ATTGTTGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.09, C:0.06, G:0.16, T:0.69
Consensus pattern (11 bp):
CTGTTATTTTG
Found at i:41386407 original size:11 final size:11
Alignment explanation
Indices: 41386372--41386414 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
41386362 ATTATATTTC
**
41386372 TGTTATTTTGC
1 TGTTATTTTAT
*
41386383 TGTTATTTTGT
1 TGTTATTTTAT
41386394 TGTTATTTTAT
1 TGTTATTTTAT
*
41386405 TGTTGTTTTA
1 TGTTATTTTA
41386415 CTACCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 29 1.00
ACGTcount: A:0.12, C:0.02, G:0.16, T:0.70
Consensus pattern (11 bp):
TGTTATTTTAT
Found at i:41386408 original size:22 final size:22
Alignment explanation
Indices: 41386354--41386413 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
41386344 ATAGATCAGC
* *
41386354 ATTTTACTATTATATTT-CTGTT
1 ATTTTACTGTTAT-TTTGTTGTT
*
41386376 ATTTTGCTGTTATTTTGTTGTT
1 ATTTTACTGTTATTTTGTTGTT
* *
41386398 ATTTTATTGTTGTTTT
1 ATTTTACTGTTATTTT
41386414 ACTACCATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 3 0.10
22 28 0.90
ACGTcount: A:0.15, C:0.05, G:0.12, T:0.68
Consensus pattern (22 bp):
ATTTTACTGTTATTTTGTTGTT
Found at i:41389998 original size:26 final size:26
Alignment explanation
Indices: 41389969--41390023 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
41389959 CTCGATTTAT
41389969 AGACATAAGAAGTATAAATGAAGTAG
1 AGACATAAGAAGTATAAATGAAGTAG
41389995 AGACATAAGAAGTATAAATGAAGTAG
1 AGACATAAGAAGTATAAATGAAGTAG
41390021 AGA
1 AGA
41390024 TCCACTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.18
Consensus pattern (26 bp):
AGACATAAGAAGTATAAATGAAGTAG
Found at i:41390187 original size:16 final size:17
Alignment explanation
Indices: 41390151--41390205 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
41390141 GTGCACTTTT
* *
41390151 AAAACCTTACTAAGATA
1 AAAACCTTAGTAAGAAA
41390168 AAAACCTT-GTAAGAAA
1 AAAACCTTAGTAAGAAA
*
41390184 AAAATCTTAGTGAAGAAA
1 AAAACCTTAGT-AAGAAA
41390202 AAAA
1 AAAA
41390206 ATACACATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 13 0.39
17 10 0.30
18 10 0.30
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (17 bp):
AAAACCTTAGTAAGAAA
Found at i:41403538 original size:22 final size:23
Alignment explanation
Indices: 41403491--41403538 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
41403481 AGGTCTTCTG
*
41403491 TTTTCATCAAATTTAATGTGTAT
1 TTTTCATCAAATTTAATGTCTAT
*
41403514 TTTTCAT-AAATTTCATGTCT-T
1 TTTTCATCAAATTTAATGTCTAT
41403535 TTTT
1 TTTT
41403539 GTTTATCTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 5 0.22
22 11 0.48
23 7 0.30
ACGTcount: A:0.25, C:0.10, G:0.06, T:0.58
Consensus pattern (23 bp):
TTTTCATCAAATTTAATGTCTAT
Found at i:41406748 original size:19 final size:19
Alignment explanation
Indices: 41406724--41406777 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
41406714 GAAAATAAAT
41406724 ATAATTTTAATAATTTT-TA
1 ATAA-TTTAATAATTTTGTA
*
41406743 ATAATTTATTAATTTTGTA
1 ATAATTTAATAATTTTGTA
** *
41406762 ATTGTTAAATAATTTT
1 ATAATTTAATAATTTT
41406778 AAAAACTTCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 11 0.38
19 18 0.62
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (19 bp):
ATAATTTAATAATTTTGTA
Found at i:41406756 original size:27 final size:27
Alignment explanation
Indices: 41406725--41406776 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
41406715 AAAATAAATA
*
41406725 TAATTTTAATAATT-TTTAATAATTTAT
1 TAATTTT-ATAATTGTTAAATAATTTAT
*
41406752 TAATTTTGTAATTGTTAAATAATTT
1 TAATTTTATAATTGTTAAATAATTT
41406777 TAAAAACTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
TAATTTTATAATTGTTAAATAATTTAT
Found at i:41406913 original size:21 final size:22
Alignment explanation
Indices: 41406889--41406942 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
41406879 CACCGCTGTT
*
41406889 TCTAATCTCACTGCTACAGT-A
1 TCTAATCTCACCGCTACAGTAA
41406910 TCTAATCTCACCGCTACAGTAA
1 TCTAATCTCACCGCTACAGTAA
41406932 T-TAATCTCACC
1 TCTAATCTCACC
41406943 TCCACCGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 29 0.94
22 2 0.06
ACGTcount: A:0.30, C:0.31, G:0.07, T:0.31
Consensus pattern (22 bp):
TCTAATCTCACCGCTACAGTAA
Found at i:41412237 original size:18 final size:17
Alignment explanation
Indices: 41412208--41412271 Score: 56
Period size: 18 Copynumber: 3.5 Consensus size: 17
41412198 AAGAAAATGT
41412208 TTTGAAATTGAATAACGA
1 TTTGAAA-TGAATAACGA
* *
41412226 TTTGTAAATGAATAATGT
1 TTTG-AAATGAATAACGA
*
41412244 TTTGGAAACGAATGAAACGA
1 TTT-GAAATGAAT--AACGA
41412264 TTTGAAAT
1 TTTGAAAT
41412272 TAACATAAGA
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
18 22 0.61
19 8 0.22
20 6 0.17
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (17 bp):
TTTGAAATGAATAACGA
Found at i:41413906 original size:17 final size:17
Alignment explanation
Indices: 41413868--41413903 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
41413858 ATATCTAGAG
41413868 AAATATTAAATTAAATT
1 AAATATTAAATTAAATT
*
41413885 TAATATTAAATT-AATT
1 AAATATTAAATTAAATT
41413901 AAA
1 AAA
41413904 ATAATATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAATATTAAATTAAATT
Found at i:41425396 original size:745 final size:745
Alignment explanation
Indices: 41423966--41425455 Score: 2980
Period size: 745 Copynumber: 2.0 Consensus size: 745
41423956 ATAAGCCCTT
41423966 ATAAGAGACAAAATGCATGTGTTAGAAAAGTTTTAAATTTGACAAAATTTTAAGCCCGGTAATGC
1 ATAAGAGACAAAATGCATGTGTTAGAAAAGTTTTAAATTTGACAAAATTTTAAGCCCGGTAATGC
41424031 CTCTTACCCTGTTCTGGTGTTGGATACGAGTAATGAGTGTTACAGTGTAGGGTTGGATGGAGATG
66 CTCTTACCCTGTTCTGGTGTTGGATACGAGTAATGAGTGTTACAGTGTAGGGTTGGATGGAGATG
41424096 GTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTGCATTCTTTATCTGATATGGGCC
131 GTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTGCATTCTTTATCTGATATGGGCC
41424161 AAGGCCCTACTGTATTTCTGAGACTGTATCTGAATGGATTAAAACCCAAATTGATTCTGTGATGG
196 AAGGCCCTACTGTATTTCTGAGACTGTATCTGAATGGATTAAAACCCAAATTGATTCTGTGATGG
41424226 GCACAGGCCCCAGACTGTATCTAACTGAATTTTTTTGATTATCTGTATGCATGTGTAACGCCTCA
261 GCACAGGCCCCAGACTGTATCTAACTGAATTTTTTTGATTATCTGTATGCATGTGTAACGCCTCA
41424291 AAATTTTAATTTTGGGTATTGTGAATGTGTGACACAGAATATCTATCTATTTTAGTCGTTATGTG
326 AAATTTTAATTTTGGGTATTGTGAATGTGTGACACAGAATATCTATCTATTTTAGTCGTTATGTG
41424356 TTCTGGGTGTGTTTAGGAGGTCCCAAGTTCAAGTTAGGACTTGGGCAAATTTTGGTATTTTTATG
391 TTCTGGGTGTGTTTAGGAGGTCCCAAGTTCAAGTTAGGACTTGGGCAAATTTTGGTATTTTTATG
41424421 AATAAGCCCTATCTTTGGTCAGTAGGTTTTTAAGTAAAAGTTGGCAAATTATTAACAGAATGTGC
456 AATAAGCCCTATCTTTGGTCAGTAGGTTTTTAAGTAAAAGTTGGCAAATTATTAACAGAATGTGC
41424486 CTGCTGGTCTAGTGGATAAGTGGAGTGTTGGTGTGAAGGAGGTCATTTGTTTGAATCTTGGTGTG
521 CTGCTGGTCTAGTGGATAAGTGGAGTGTTGGTGTGAAGGAGGTCATTTGTTTGAATCTTGGTGTG
41424551 GGCATTATTTTTGCTCGTGTGTCTAGGAGAGTTTTATATGAACTAAAAATCTGAGTAGTGGATTT
586 GGCATTATTTTTGCTCGTGTGTCTAGGAGAGTTTTATATGAACTAAAAATCTGAGTAGTGGATTT
41424616 CGTGGGGAGTTTGATGGAGAGAAATAAGGGATTGGGGTGATTATCAAATATTTTGTTCATCTTTT
651 CGTGGGGAGTTTGATGGAGAGAAATAAGGGATTGGGGTGATTATCAAATATTTTGTTCATCTTTT
41424681 TTTCTTTCCCCAAAATCCCTCCACCTTTCC
716 TTTCTTTCCCCAAAATCCCTCCACCTTTCC
41424711 ATAAGAGACAAAATGCATGTGTTAGAAAAGTTTTAAATTTGACAAAATTTTAAGCCCGGTAATGC
1 ATAAGAGACAAAATGCATGTGTTAGAAAAGTTTTAAATTTGACAAAATTTTAAGCCCGGTAATGC
41424776 CTCTTACCCTGTTCTGGTGTTGGATACGAGTAATGAGTGTTACAGTGTAGGGTTGGATGGAGATG
66 CTCTTACCCTGTTCTGGTGTTGGATACGAGTAATGAGTGTTACAGTGTAGGGTTGGATGGAGATG
41424841 GTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTGCATTCTTTATCTGATATGGGCC
131 GTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTGCATTCTTTATCTGATATGGGCC
41424906 AAGGCCCTACTGTATTTCTGAGACTGTATCTGAATGGATTAAAACCCAAATTGATTCTGTGATGG
196 AAGGCCCTACTGTATTTCTGAGACTGTATCTGAATGGATTAAAACCCAAATTGATTCTGTGATGG
41424971 GCACAGGCCCCAGACTGTATCTAACTGAATTTTTTTGATTATCTGTATGCATGTGTAACGCCTCA
261 GCACAGGCCCCAGACTGTATCTAACTGAATTTTTTTGATTATCTGTATGCATGTGTAACGCCTCA
41425036 AAATTTTAATTTTGGGTATTGTGAATGTGTGACACAGAATATCTATCTATTTTAGTCGTTATGTG
326 AAATTTTAATTTTGGGTATTGTGAATGTGTGACACAGAATATCTATCTATTTTAGTCGTTATGTG
41425101 TTCTGGGTGTGTTTAGGAGGTCCCAAGTTCAAGTTAGGACTTGGGCAAATTTTGGTATTTTTATG
391 TTCTGGGTGTGTTTAGGAGGTCCCAAGTTCAAGTTAGGACTTGGGCAAATTTTGGTATTTTTATG
41425166 AATAAGCCCTATCTTTGGTCAGTAGGTTTTTAAGTAAAAGTTGGCAAATTATTAACAGAATGTGC
456 AATAAGCCCTATCTTTGGTCAGTAGGTTTTTAAGTAAAAGTTGGCAAATTATTAACAGAATGTGC
41425231 CTGCTGGTCTAGTGGATAAGTGGAGTGTTGGTGTGAAGGAGGTCATTTGTTTGAATCTTGGTGTG
521 CTGCTGGTCTAGTGGATAAGTGGAGTGTTGGTGTGAAGGAGGTCATTTGTTTGAATCTTGGTGTG
41425296 GGCATTATTTTTGCTCGTGTGTCTAGGAGAGTTTTATATGAACTAAAAATCTGAGTAGTGGATTT
586 GGCATTATTTTTGCTCGTGTGTCTAGGAGAGTTTTATATGAACTAAAAATCTGAGTAGTGGATTT
41425361 CGTGGGGAGTTTGATGGAGAGAAATAAGGGATTGGGGTGATTATCAAATATTTTGTTCATCTTTT
651 CGTGGGGAGTTTGATGGAGAGAAATAAGGGATTGGGGTGATTATCAAATATTTTGTTCATCTTTT
41425426 TTTCTTTCCCCAAAATCCCTCCACCTTTCC
716 TTTCTTTCCCCAAAATCCCTCCACCTTTCC
41425456 GTTTTTCTCT
Statistics
Matches: 745, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
745 745 1.00
ACGTcount: A:0.25, C:0.13, G:0.25, T:0.36
Consensus pattern (745 bp):
ATAAGAGACAAAATGCATGTGTTAGAAAAGTTTTAAATTTGACAAAATTTTAAGCCCGGTAATGC
CTCTTACCCTGTTCTGGTGTTGGATACGAGTAATGAGTGTTACAGTGTAGGGTTGGATGGAGATG
GTGTGTAGAGGCTGGTGGGTAGGATTCTGATTTACTGTATCTGCATTCTTTATCTGATATGGGCC
AAGGCCCTACTGTATTTCTGAGACTGTATCTGAATGGATTAAAACCCAAATTGATTCTGTGATGG
GCACAGGCCCCAGACTGTATCTAACTGAATTTTTTTGATTATCTGTATGCATGTGTAACGCCTCA
AAATTTTAATTTTGGGTATTGTGAATGTGTGACACAGAATATCTATCTATTTTAGTCGTTATGTG
TTCTGGGTGTGTTTAGGAGGTCCCAAGTTCAAGTTAGGACTTGGGCAAATTTTGGTATTTTTATG
AATAAGCCCTATCTTTGGTCAGTAGGTTTTTAAGTAAAAGTTGGCAAATTATTAACAGAATGTGC
CTGCTGGTCTAGTGGATAAGTGGAGTGTTGGTGTGAAGGAGGTCATTTGTTTGAATCTTGGTGTG
GGCATTATTTTTGCTCGTGTGTCTAGGAGAGTTTTATATGAACTAAAAATCTGAGTAGTGGATTT
CGTGGGGAGTTTGATGGAGAGAAATAAGGGATTGGGGTGATTATCAAATATTTTGTTCATCTTTT
TTTCTTTCCCCAAAATCCCTCCACCTTTCC
Found at i:41425597 original size:18 final size:18
Alignment explanation
Indices: 41425545--41425597 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
41425535 GTGTTGCTCC
*
41425545 ACGTTTGTCTGCGATCAT
1 ACGTTTGTCTGCGATCGT
* *
41425563 ACGTTTGTTTACGATCGT
1 ACGTTTGTCTGCGATCGT
*
41425581 ACGTTTGTCTGTGATCG
1 ACGTTTGTCTGCGATCG
41425598 CTCGGTAAGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.15, C:0.19, G:0.25, T:0.42
Consensus pattern (18 bp):
ACGTTTGTCTGCGATCGT
Found at i:41430261 original size:16 final size:16
Alignment explanation
Indices: 41430240--41430281 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
41430230 TGTTATTCAA
41430240 GCTTTGTGCCTAGCAG
1 GCTTTGTGCCTAGCAG
*
41430256 GCTTTGTGCTTAGCAG
1 GCTTTGTGCCTAGCAG
41430272 GCTTTGTGCC
1 GCTTTGTGCC
41430282 GGTGTTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.31, T:0.36
Consensus pattern (16 bp):
GCTTTGTGCCTAGCAG
Found at i:41430336 original size:22 final size:22
Alignment explanation
Indices: 41430269--41430341 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
41430259 TTGTGCTTAG
41430269 CAGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCCGGTGTTATT
* *
41430291 CAAGCTTTGCT-CC-----TAGT
1 CAGGCTTTG-TGCCGGTGTTATT
41430308 -AGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCCGGTGTTATT
41430329 CAGGCTTTGTGCC
1 CAGGCTTTGTGCC
41430342 TAGCAAGCTT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
15 1 0.03
16 9 0.23
17 3 0.08
21 3 0.08
22 22 0.56
23 1 0.03
ACGTcount: A:0.11, C:0.22, G:0.29, T:0.38
Consensus pattern (22 bp):
CAGGCTTTGTGCCGGTGTTATT
Found at i:41430344 original size:38 final size:38
Alignment explanation
Indices: 41430253--41430362 Score: 150
Period size: 38 Copynumber: 2.9 Consensus size: 38
41430243 TTGTGCCTAG
*
41430253 CAGGCTTTGTGCTTAGCAGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATT
* *
41430291 CAAGCTTTGCT-CCTAGTAGGCTTTGTGCCGGTGTTATT
1 CAGGCTTTG-TGCCTAGCAGGCTTTGTGCCGGTGTTATT
* * *
41430329 CAGGCTTTGTGCCTAGCAAGCTTAGTGCCAGTGT
1 CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGT
41430363 ATTAAAAGTT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
37 1 0.02
38 60 0.97
39 1 0.02
ACGTcount: A:0.14, C:0.21, G:0.29, T:0.36
Consensus pattern (38 bp):
CAGGCTTTGTGCCTAGCAGGCTTTGTGCCGGTGTTATT
Found at i:41431271 original size:50 final size:51
Alignment explanation
Indices: 41431212--41431325 Score: 115
Period size: 51 Copynumber: 2.2 Consensus size: 51
41431202 TTTATAAAGT
* * * *
41431212 CATGTATTATAAAA-CTCTCATGTTAGTT-AAGATTGCATCATAAATTATGA
1 CATGCATTATAAAACCT-TCATGATAGTTAAAGATTGCATCATAAATGAAGA
** * * *
41431262 CATGCATTATGTAACCTTCATGATAGTTAAAGTTTGCATCTTAAATGAAGT
1 CATGCATTATAAAACCTTCATGATAGTTAAAGATTGCATCATAAATGAAGA
41431313 CATGCATTTATAA
1 CATGCA-TTATAA
41431326 CTCATTTGTT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
50 21 0.42
51 25 0.50
52 4 0.08
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (51 bp):
CATGCATTATAAAACCTTCATGATAGTTAAAGATTGCATCATAAATGAAGA
Found at i:41439266 original size:22 final size:22
Alignment explanation
Indices: 41439238--41439312 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
41439228 TTGTGCCTAG
* *
41439238 CAGGCTTCGTGCCGGTGTTAAT
1 CAGGCTTTGTGCCGGTGTTATT
*
41439260 CAGGCTTTGTGCTGGTGTTATT
1 CAGGCTTTGTGCCGGTGTTATT
*
41439282 CTA-GCTTTGTGCCGATGTTATT
1 C-AGGCTTTGTGCCGGTGTTATT
41439304 CAGGCTTTG
1 CAGGCTTTG
41439313 CTCCTAGCAG
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 44 0.96
23 1 0.02
ACGTcount: A:0.12, C:0.19, G:0.29, T:0.40
Consensus pattern (22 bp):
CAGGCTTTGTGCCGGTGTTATT
Found at i:41439266 original size:38 final size:38
Alignment explanation
Indices: 41439215--41439373 Score: 133
Period size: 38 Copynumber: 4.0 Consensus size: 38
41439205 TGAATTATAT
* *
41439215 TGTTATTCAGGCTTTGTGCCTAGCAGGCTTCGTGCCGG
1 TGTTAATCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
* * *
41439253 TGTTAATCAGGCTTTGTGCTGGTGTTATTCTA-GCTTTGTGCCGA
1 TGTTAATCAGGCTTTGTGC-----CTA-GC-AGGCTTTGTGCCGG
* *
41439297 TGTTATTCAGGCTTTGCT-CCTAGCAGGCTTTGTGCCAG
1 TGTTAATCAGGCTTTG-TGCCTAGCAGGCTTTGTGCCGG
* * * *
41439335 TGTTGATCAGGCTTTGTGCCTAGAAAGCTTAGTGCCGG
1 TGTTAATCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
41439373 T
1 T
41439374 TTATTAAAAG
Statistics
Matches: 95, Mismatches: 16, Indels: 20
0.73 0.12 0.15
Matches are distributed among these distances:
37 2 0.02
38 60 0.63
39 2 0.02
43 2 0.02
44 27 0.28
45 2 0.02
ACGTcount: A:0.14, C:0.20, G:0.29, T:0.37
Consensus pattern (38 bp):
TGTTAATCAGGCTTTGTGCCTAGCAGGCTTTGTGCCGG
Found at i:41439925 original size:42 final size:42
Alignment explanation
Indices: 41439841--41439930 Score: 110
Period size: 42 Copynumber: 2.1 Consensus size: 42
41439831 AATTCAGACT
* * * **
41439841 GTTACACTGCCTAGCACACGGGCGTGTGTGGCTATTTCGAGA
1 GTTACACGGCCTAGCACACGGGCGTGTGTGCCCAACTCGAGA
*
41439883 GTTACACGGCCTGGCACACGGGCGTGTG-GCCCAACTCAGAGA
1 GTTACACGGCCTAGCACACGGGCGTGTGTGCCCAACTC-GAGA
41439925 GTTACA
1 GTTACA
41439931 GGGGCACGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
41 5 0.12
42 36 0.88
ACGTcount: A:0.21, C:0.27, G:0.31, T:0.21
Consensus pattern (42 bp):
GTTACACGGCCTAGCACACGGGCGTGTGTGCCCAACTCGAGA
Found at i:41449189 original size:19 final size:18
Alignment explanation
Indices: 41449152--41449204 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
41449142 AAATTATTTT
* *
41449152 TTTTATAAATGTGATAAA
1 TTTTATAAATGTAAAAAA
41449170 TTTTATAAATAGTAAAAAA
1 TTTTATAAAT-GTAAAAAA
*
41449189 TATTTA-AAATGGAAAA
1 T-TTTATAAATGTAAAA
41449205 TTTGATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 15 0.50
19 11 0.37
20 4 0.13
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (18 bp):
TTTTATAAATGTAAAAAA
Found at i:41451476 original size:22 final size:22
Alignment explanation
Indices: 41451448--41451491 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
41451438 AAACACTTAA
41451448 TCAAAATTGTACCTTTTCGATT
1 TCAAAATTGTACCTTTTCGATT
41451470 TCAAAATTGTACCTTTTCGATT
1 TCAAAATTGTACCTTTTCGATT
41451492 CGTCTAGGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.09, T:0.45
Consensus pattern (22 bp):
TCAAAATTGTACCTTTTCGATT
Found at i:41451859 original size:21 final size:21
Alignment explanation
Indices: 41451815--41451860 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
41451805 AATATTAAAT
*
41451815 TTAATCTAATATTTATCTTGA
1 TTAATCTAATATTAATCTTGA
*
41451836 TTAATTTAATATTAAATCTT-A
1 TTAATCTAATATT-AATCTTGA
41451857 TTAA
1 TTAA
41451861 AATAGTAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.52
Consensus pattern (21 bp):
TTAATCTAATATTAATCTTGA
Found at i:41453602 original size:19 final size:21
Alignment explanation
Indices: 41453570--41453608 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
41453560 TAATATTTGT
41453570 TTGTCACAAATTTT-CTATGA
1 TTGTCACAAATTTTACTATGA
41453590 TTGTCAC-AATTTTACTATG
1 TTGTCACAAATTTTACTATG
41453609 CATGCAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (21 bp):
TTGTCACAAATTTTACTATGA
Found at i:41458648 original size:26 final size:26
Alignment explanation
Indices: 41458616--41458748 Score: 156
Period size: 26 Copynumber: 5.3 Consensus size: 26
41458606 TGATGACGAT
41458616 AAAATTAGATATTATAGTGTGAGATA
1 AAAATTAGATATTATAGTGTGAGATA
*
41458642 AAAATTAG-T-GTA-AGTGATGACGAT-
1 AAAATTAGATATTATAGTG-TGA-GATA
41458666 AAAATTAGATATTATAGTGTGAGATA
1 AAAATTAGATATTATAGTGTGAGATA
*
41458692 AAAATTAG-T-GTA-AGTGATGACGAT-
1 AAAATTAGATATTATAGTG-TGA-GATA
41458716 AAAATTAGATATTATAGTGTGAGATA
1 AAAATTAGATATTATAGTGTGAGATA
41458742 AAAATTA
1 AAAATTA
41458749 AATTAAATGT
Statistics
Matches: 91, Mismatches: 4, Indels: 24
0.76 0.03 0.20
Matches are distributed among these distances:
23 8 0.09
24 26 0.29
25 16 0.18
26 33 0.36
27 8 0.09
ACGTcount: A:0.46, C:0.02, G:0.20, T:0.32
Consensus pattern (26 bp):
AAAATTAGATATTATAGTGTGAGATA
Found at i:41458670 original size:50 final size:50
Alignment explanation
Indices: 41458595--41458748 Score: 308
Period size: 50 Copynumber: 3.1 Consensus size: 50
41458585 TACATGTGCG
41458595 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
1 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
41458645 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
1 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
41458695 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
1 ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
41458745 ATTA
1 ATTA
41458749 AATTAAATGT
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 104 1.00
ACGTcount: A:0.44, C:0.02, G:0.21, T:0.32
Consensus pattern (50 bp):
ATTAGTGTAAGTGATGACGATAAAATTAGATATTATAGTGTGAGATAAAA
Found at i:41458673 original size:24 final size:24
Alignment explanation
Indices: 41458595--41458723 Score: 140
Period size: 24 Copynumber: 5.2 Consensus size: 24
41458585 TACATGTGCG
41458595 ATTAGTGTAAGTGATGACGATAAA
1 ATTAGTGTAAGTGATGACGATAAA
*
41458619 ATTAGATATTATAGTG-TGA-GATAAAA
1 ATTAG-T-GTA-AGTGATGACGAT-AAA
41458645 ATTAGTGTAAGTGATGACGATAAA
1 ATTAGTGTAAGTGATGACGATAAA
*
41458669 ATTAGATATTATAGTG-TGA-GATAAAA
1 ATTAG-T-GTA-AGTGATGACGAT-AAA
41458695 ATTAGTGTAAGTGATGACGATAAA
1 ATTAGTGTAAGTGATGACGATAAA
41458719 ATTAG
1 ATTAG
41458724 ATATTATAGT
Statistics
Matches: 89, Mismatches: 4, Indels: 24
0.76 0.03 0.21
Matches are distributed among these distances:
23 8 0.09
24 31 0.35
25 16 0.18
26 26 0.29
27 8 0.09
ACGTcount: A:0.43, C:0.02, G:0.22, T:0.32
Consensus pattern (24 bp):
ATTAGTGTAAGTGATGACGATAAA
Found at i:41464519 original size:20 final size:20
Alignment explanation
Indices: 41464496--41464533 Score: 62
Period size: 18 Copynumber: 2.0 Consensus size: 20
41464486 TATATATATG
41464496 TATATAT-AAAT-TATGAAA
1 TATATATAAAATATATGAAA
41464514 TATATATAAAATATATGAAA
1 TATATATAAAATATATGAAA
41464534 GTGTTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 4 0.22
20 7 0.39
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (20 bp):
TATATATAAAATATATGAAA
Found at i:41465980 original size:23 final size:24
Alignment explanation
Indices: 41465953--41466001 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
41465943 GGTGTAATTT
* *
41465953 GGGTTTTGGG-TTAGGTTTAGTTG
1 GGGTTTTGGGCTGAGGGTTAGTTG
41465976 GGGTTTTGGGCTGAGGGTTAGTTG
1 GGGTTTTGGGCTGAGGGTTAGTTG
41466000 GG
1 GG
41466002 CCCTGGGCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.08, C:0.02, G:0.49, T:0.41
Consensus pattern (24 bp):
GGGTTTTGGGCTGAGGGTTAGTTG
Found at i:41466516 original size:20 final size:20
Alignment explanation
Indices: 41466485--41466530 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
41466475 ATTTAATAAA
* *
41466485 TAAAAATAAAAATCCTAAAAC
1 TAAAACTAAAAGT-CTAAAAC
41466506 TAAAACTAAAAGTCTAAAAC
1 TAAAACTAAAAGTCTAAAAC
41466526 TAAAA
1 TAAAA
41466531 ATCACGACAG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.65, C:0.13, G:0.02, T:0.20
Consensus pattern (20 bp):
TAAAACTAAAAGTCTAAAAC
Found at i:41467791 original size:12 final size:12
Alignment explanation
Indices: 41467754--41467804 Score: 52
Period size: 12 Copynumber: 4.3 Consensus size: 12
41467744 TATCATAGTT
41467754 CTTACTT-CTT-
1 CTTACTTGCTTA
* *
41467764 CTTTACTTACTCA
1 C-TTACTTGCTTA
*
41467777 CTTACTTGTTTA
1 CTTACTTGCTTA
41467789 CTTACTTGCTTA
1 CTTACTTGCTTA
41467801 CTTA
1 CTTA
41467805 AACAACTTAT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
10 1 0.03
11 6 0.18
12 25 0.76
13 1 0.03
ACGTcount: A:0.18, C:0.25, G:0.04, T:0.53
Consensus pattern (12 bp):
CTTACTTGCTTA
Found at i:41468166 original size:50 final size:50
Alignment explanation
Indices: 41468006--41468300 Score: 231
Period size: 50 Copynumber: 5.8 Consensus size: 50
41467996 TGATAATAAC
* * * *
41468006 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGT-TTCTTG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * ** * *
41468053 TACTGCCAATGCCATATCCCAGATATGATC-TACATGAGAGTTTTCATATCG
1 -A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * * * **
41468104 GTGCCCATGCCATGTCCTATACATGGTCTTACGGGGGACCTCTCATCTC-
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
*
41468153 AGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCG
1 A-TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* *
41468204 ATGCCAACGCCATGCCCCAGACATGGTCTTACATGAGACCTCTCATAATCTCAATAATG
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC------G
*
41468263 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA
1 ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
41468301 TCTTATTTCC
Statistics
Matches: 194, Mismatches: 37, Indels: 21
0.77 0.15 0.08
Matches are distributed among these distances:
48 9 0.05
49 44 0.23
50 96 0.49
51 4 0.02
53 5 0.03
59 36 0.19
ACGTcount: A:0.25, C:0.28, G:0.20, T:0.27
Consensus pattern (50 bp):
ATGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:41477084 original size:17 final size:17
Alignment explanation
Indices: 41477062--41477096 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
41477052 AGTGATTCAT
*
41477062 TACTTTAATTCAATTAA
1 TACTTTAACTCAATTAA
*
41477079 TACTTTAACTCAGTTAA
1 TACTTTAACTCAATTAA
41477096 T
1 T
41477097 TTTTATACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (17 bp):
TACTTTAACTCAATTAA
Found at i:41478264 original size:27 final size:27
Alignment explanation
Indices: 41478234--41478375 Score: 83
Period size: 27 Copynumber: 5.3 Consensus size: 27
41478224 GAAACCAATA
41478234 TAGTCTACTGGAACAGTAAACACGAGG
1 TAGTCTACTGGAACAGTAAACACGAGG
* ** * *
41478261 TAGTCCACCAGTACAATAAACACGAGG
1 TAGTCTACTGGAACAGTAAACACGAGG
* * * * *
41478288 TAGTCCACTGGGATAATAAACACGGGG
1 TAGTCTACTGGAACAGTAAACACGAGG
* ** ** *
41478315 TAGACTGTTAGG-ACAGTATTCACGGGG
1 TAGTCTACT-GGAACAGTAAACACGAGG
* *
41478342 TAGT-TCACCGAAACAGTAAACACGAGG
1 TAGTCT-ACTGGAACAGTAAACACGAGG
41478369 -AGTCTAC
1 TAGTCTAC
41478376 CAAGACAGTA
Statistics
Matches: 85, Mismatches: 26, Indels: 9
0.71 0.22 0.08
Matches are distributed among these distances:
26 7 0.08
27 76 0.89
28 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.19
Consensus pattern (27 bp):
TAGTCTACTGGAACAGTAAACACGAGG
Found at i:41484102 original size:16 final size:16
Alignment explanation
Indices: 41484078--41484108 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
41484068 CGCTGTCATG
41484078 GAATAGAGTTGTAATA
1 GAATAGAGTTGTAATA
*
41484094 GAATTGAGTTGTAAT
1 GAATAGAGTTGTAAT
41484109 CAGTAATTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.00, G:0.26, T:0.35
Consensus pattern (16 bp):
GAATAGAGTTGTAATA
Found at i:41487718 original size:22 final size:23
Alignment explanation
Indices: 41487651--41487749 Score: 89
Period size: 22 Copynumber: 4.4 Consensus size: 23
41487641 AGTGAACAGG
* * *
41487651 AAATATTCTCTAGCGTGAACAGT
1 AAATATTCTCTGGCATGAATAGT
** *
41487674 AGAA-A-TCTCTGGCAAAAACAGT
1 A-AATATTCTCTGGCATGAATAGT
41487696 AAGAT-TT-TCTGGCATGAATAGT
1 AA-ATATTCTCTGGCATGAATAGT
41487718 AAATATTCTCTGGCATGAATAGT
1 AAATATTCTCTGGCATGAATAGT
*
41487741 GAATATTCT
1 AAATATTCT
41487750 TTGTAGTTTG
Statistics
Matches: 62, Mismatches: 8, Indels: 12
0.76 0.10 0.15
Matches are distributed among these distances:
21 3 0.05
22 31 0.50
23 26 0.42
24 2 0.03
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (23 bp):
AAATATTCTCTGGCATGAATAGT
Done.