Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 162 of 208
Found at i:49510411 original size:23 final size:23
Alignment explanation
Indices: 49510367--49510411 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
49510357 TCTTATTTTG
* *
49510367 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
49510390 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
49510412 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:49510878 original size:2 final size:2
Alignment explanation
Indices: 49510873--49510909 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49510863 TTTCTAATGA
49510873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
49510910 CGCACATGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49516052 original size:14 final size:15
Alignment explanation
Indices: 49516026--49516058 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
49516016 TCCCAAGCTG
49516026 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
49516041 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
49516055 GGAA
1 GGAA
49516059 AAGCGTCGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:49516163 original size:2 final size:2
Alignment explanation
Indices: 49516158--49516184 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49516148 AAAGTAAAAA
49516158 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
49516185 AAAGAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:49517504 original size:44 final size:43
Alignment explanation
Indices: 49517454--49517685 Score: 121
Period size: 44 Copynumber: 5.3 Consensus size: 43
49517444 AGACACTAGC
*
49517454 CTTGCCTCCCTGGGTTGCAGCAGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGAGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
* ** * * ** ** * * *
49517498 CTTGCCTTCCTGCA-CCGACAACGAAGCAGATCGAGGACACCAG-C
1 CTTGCCTCCCTG-AGTTG-CAGCG-AGCAGGTTAAAAATAGCAGAT
*
49517542 CTTGCCTCCCTGGGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGAGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
* * * * ** ** * *
49517586 CTTGCCTTCCTGCACTGGCAGCGAAGCAGATCGAGGACA-CTAG-C
1 CTTGCCTCCCTG-AGTTGCAGCG-AGCAGGTTAAAAATAGC-AGAT
*
49517630 CCTGCCTCCCTGAGTTGCAGCGGAGCAGGTTAAAAATAGCAGAT
1 CTTGCCTCCCTGAGTTGCAGC-GAGCAGGTTAAAAATAGCAGAT
*
49517674 CTTGCCTTCCTG
1 CTTGCCTCCCTG
49517686 CACCGACAGC
Statistics
Matches: 126, Mismatches: 50, Indels: 24
0.63 0.25 0.12
Matches are distributed among these distances:
43 33 0.26
44 61 0.48
45 32 0.25
ACGTcount: A:0.25, C:0.28, G:0.26, T:0.21
Consensus pattern (43 bp):
CTTGCCTCCCTGAGTTGCAGCGAGCAGGTTAAAAATAGCAGAT
Found at i:49518188 original size:88 final size:88
Alignment explanation
Indices: 49517405--49518158 Score: 1148
Period size: 88 Copynumber: 8.6 Consensus size: 88
49517395 GTGAAGATAA
* *
49517405 CAGATCTGGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
49517470 GCAGCAGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* *
49517493 CAGATCTTGCCTTCCTGCACCGACAACGAAGCAGATCGAGGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
49517558 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * * * *
49517581 CAGATCTTGCCTTCCTGCACTGGCAGCGAAGCAGATCGAGGACACTAGCCCTGCCTCCCTGAGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
49517646 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
*
49517669 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCGGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
*
49517734 GCAGCGGAGCAGGTTAAAAATTG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * **
49517757 TAGATATTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCATTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* * * *
49517822 GTAGCGGAGTAAGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
49517845 CAGATATTGCCTTCCTACACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCTTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
* *
49517910 GTAGTGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * *
49517933 CAGATCTTGCTTTCCTGCACTGACGGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
49517998 GCAGCGGAGCAGGTTAAAAATAG
66 GCAGCGGAGCAGGTTAAAAATAG
* * * *
49518021 CAGATCTTGCATTCCTGCACCGACAGCGAAGTAAATCGAAGACACCAGCCTTGCCTCCCTAGGTT
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
** *
49518086 GCAGCAAAGCAGGTTAAAAATAA
66 GCAGCGGAGCAGGTTAAAAATAG
* *
49518109 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGATGACCCCAGCC
1 CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
49518159 CTATCTCCCT
Statistics
Matches: 604, Mismatches: 62, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
88 604 1.00
ACGTcount: A:0.27, C:0.28, G:0.25, T:0.20
Consensus pattern (88 bp):
CAGATCTTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTT
GCAGCGGAGCAGGTTAAAAATAG
Found at i:49518249 original size:44 final size:44
Alignment explanation
Indices: 49518160--49518257 Score: 126
Period size: 44 Copynumber: 2.2 Consensus size: 44
49518150 ACCCCAGCCC
* * *
49518160 TATCTCCCTAGACAACAGTGGAATAGGTTGAAGATTGTAAGTCT
1 TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGTCT
* *
49518204 TATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGCGAA-TCT
1 TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGG-GAAGTCT
*
49518248 TATCTTCCTG
1 TATCTCCCTG
49518258 AAGTTACAGT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 45 0.96
45 2 0.04
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (44 bp):
TATCTCCCTGGACAACAGTGGAATAGGTTGAAGATGGGAAGTCT
Found at i:49518397 original size:84 final size:83
Alignment explanation
Indices: 49518292--49518696 Score: 287
Period size: 89 Copynumber: 4.7 Consensus size: 83
49518282 CCAATAATCA
* * * * *
49518292 TATCTCCCAGAAGTTGTAGTGGAGTGGATTAAAATCACATATCTTATCTCTTTGAAGTTGCAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-ATCTTATCTCTCTGAAGTTGTAGAG
*
49518357 AGCAGATCACATCGAGTCT
65 AGCAGATCACATCTAGTCT
* * * * *
49518376 TATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAA--AGCGAGTCTTATCTCCCTGAAGTTGTA
1 TATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AATCA-C-AATCTTATCTCTCTGAAGTTGTA
* * * * * * *
49518439 GTGGAGCATATTAAAGCCAATAATCA
62 G-AGAGCAGATCACA-TC--TAGTCT
49518465 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGTAGAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-ATCTTATCTCTCTGAAGTTGTAGAG
*
49518530 AGCAGATCGCATCTAGTCT
65 AGCAGATCACATCTAGTCT
* * * * ** *
49518549 TATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAAGCA-AGCCTTATC-CTCCTAAAGTTGTAG
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAA--AATCACAATCTTATCTCT-CTGAAGTTGTAG
* * * * *
49518612 TGAGGCAGACTGAAGATGGCGAATCT
63 AGA-GCAGA-T-CACAT--CTAGTCT
* ** * *
49518638 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTT
1 TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATC-ACAATCTTATCTCTCTGAAGTT
49518697 ACAGTAGAGT
Statistics
Matches: 247, Mismatches: 52, Indels: 39
0.73 0.15 0.12
Matches are distributed among these distances:
83 2 0.01
84 76 0.31
85 29 0.12
86 18 0.07
87 16 0.06
88 26 0.11
89 79 0.32
90 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (83 bp):
TATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACAATCTTATCTCTCTGAAGTTGTAGAGA
GCAGATCACATCTAGTCT
Found at i:49518420 original size:45 final size:44
Alignment explanation
Indices: 49518369--49518922 Score: 313
Period size: 45 Copynumber: 12.7 Consensus size: 44
49518359 CAGATCACAT
*
49518369 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
* * * * *
49518413 GCGAGTCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCAA
1 -CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAA
* * * * *
49518459 -TAATCATATCTCCCTGAAGTTGCAGTGGAGCGGA-TTAA-AATCA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAA--A
* * * * *
49518502 C-AGATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-TC--GCAT
1 CGAG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
* * *
49518542 CTAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGTAAG
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAA
* * * * * **
49518586 CAAGCCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGG
1 CGAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGA-AA
* * * *
49518631 CGAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAA
* * * * ** *
49518676 -TAATCTTATCTCCCTGAAGTTACAGTAGAGTGGA-TTAA-AATCA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAA--A
* * *
49518719 C-AGATCTTATC-CCTCTGAAGTTGCAG-AGAGCAGA-TC--GCAT
1 CGAG-TCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTCAAGAAA
* * * *
49518759 CGGGTCTTATCTCCCTGAAGTTGCAGTAGAGTAGACCCAAGAAA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
49518803 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
1 -CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
* * * * * *
49518848 TCAAGTCTTATCCCCCTGAAATTGCAGTGGGGCA-ACTAAATAAA
1 -CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
* * ** * *
49518892 CAAATCCCATCTCCCTAAAGTTGTAGTGGAG
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAG
49518923 TGGATTAGAA
Statistics
Matches: 394, Mismatches: 83, Indels: 66
0.73 0.15 0.12
Matches are distributed among these distances:
40 40 0.10
41 21 0.05
42 4 0.01
43 53 0.13
44 133 0.34
45 138 0.35
46 5 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAA
Found at i:49518486 original size:44 final size:44
Alignment explanation
Indices: 49518243--49518877 Score: 255
Period size: 44 Copynumber: 14.6 Consensus size: 44
49518233 GAAGATGGCG
* * *
49518243 AATCTTATCTTCCTGAAGTTACAGTGGAGCAAATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * ** **
49518287 AATCATATCTCCCAGAAGTTGTAGTGGAGTGGATTAAAATCACAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
** * * * * *
49518332 -ATCTTATCTCTTTGAAGTTGCAG-AGAGCAGATCACA-TC--G
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * * * *
49518371 AGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAG-AAAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA--T
* * *
49518416 AGTCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * **
49518460 AATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * * *
49518504 GATCTTATCTCTCTGAAGTTGTAG-AGAGCAGA-T--CG-CATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * * * *
49518544 AGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAG-TAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA-T
* * * * * *
49518587 AAGCCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGC--G
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAAT
49518633 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * ** **
49518677 AATCTTATCTCCCTGAAGTTACAGTAGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCA-AT
* * *
49518721 GATCTTATC-CCTCTGAAGTTGCAG-AGAGCAGA-T--CG-C-AT
1 AATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
** * * *** * *
49518759 CGGGTCTTATCTCCCTGAAGTTGCAGTAGAGTAGACCCAAG-AAAGCG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAA--T
* * * *
49518806 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAG-AAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
49518849 CAAGTCTTATCCCCCTGAAATTGCAGTGG
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGG
49518878 GGCAACTAAA
Statistics
Matches: 443, Mismatches: 106, Indels: 83
0.70 0.17 0.13
Matches are distributed among these distances:
37 1 0.00
39 3 0.01
40 59 0.13
41 23 0.05
42 7 0.02
43 29 0.07
44 187 0.42
45 124 0.28
46 8 0.02
47 1 0.00
48 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:49518511 original size:173 final size:172
Alignment explanation
Indices: 49518240--49518705 Score: 555
Period size: 173 Copynumber: 2.7 Consensus size: 172
49518230 GTTGAAGATG
* * ** *
49518240 GCGAATCTTATCTTCCTGAAGTTACAGTGGAGCAAATTAAAGCCAATAATCATATCTCCCAGAAG
1 GCGAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAATAATCATATCTCCCTGAAG
* * * *
49518305 TTGTAGTGGAGTGGATTAAAATCACATATCTTATCTCTTTGAAGTTGCAGAGAGCAGATCACATC
66 TTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
*
49518370 GAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAA
131 GAGTCTTATCTCCCTGAAGTTACAGTGGAACAGACT-AAGAAA
*
49518413 GCGAGTCTTATCTCCCTGAAGTTGTAGTGGAGCATATTAAAGCCAATAATCATATCTCCCTGAAG
1 GCGAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAATAATCATATCTCCCTGAAG
* *
49518478 TTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATC
66 TTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
* * *
49518543 TAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGTAA
131 GAGTCTTATCTCCCTGAAGTTACAGTGGAACAGACTAAGAAA
* * * * * * * *
49518585 GCAAGCCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGC--GAATCTTATCTCCC
1 GCGAGTCTTATCTC-CCTGAAGTTGTAGTGGA-GCA-AATTAA-A-GCCAATAATCATATCTCCC
* ** * * *
49518646 TGAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCTTATCTCCCTGAAGTTACAGTAGAG
61 TGAAGTTGCAGTGGAGCGGATTAAAATCACA-GATCTTATCTCTCTGAAGTTGCAG-AGAG
49518706 TGGATTAAAA
Statistics
Matches: 254, Mismatches: 32, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
171 3 0.01
172 32 0.13
173 212 0.83
174 5 0.02
175 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.28
Consensus pattern (172 bp):
GCGAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAAATTAAAGCCAATAATCATATCTCCCTGAAG
TTGCAGTGGAGCGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCACATC
GAGTCTTATCTCCCTGAAGTTACAGTGGAACAGACTAAGAAA
Found at i:49518906 original size:217 final size:217
Alignment explanation
Indices: 49518369--49518934 Score: 719
Period size: 217 Copynumber: 2.6 Consensus size: 217
49518359 CAGATCACAT
* *
49518369 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAACAGACTCAAGAAAGCGAGTCTTATCTCCCTGAAG
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAG
* * *
49518434 TTGTAGTGGAGCATATTAAAGCCAATAATCATATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAA
66 TTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAA
* * *
49518499 TCACAGATCTTATCTCTCTGAAGTTGTAGAGAGCAGATCGCATCTAGTCTTATCTCCCTGAAGTT
131 TCACAGATCTTATCCCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTT
* * *
49518564 ACAGTGGAGCAGACTAAGTAAG
196 ACAGTAGAGCAGACCAAGAAAG
* * * * * **
49518586 CAAGCCTTATC-CTCCTAAAGTTGTAGT-GAGGCAGACTGAAGATGGCGAA-TCTTATCTCCCTG
1 CGAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAGC-AAGTCTTATCTCCCTG
* * *
49518648 AAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTTACAGTAGAGTGGATTA
63 AAGTTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTA
*
49518713 AAATCACAGATCTTATCCCTCTGAAGTTGCAGAGAGCAGATCGCATCGGGTCTTATCTCCCTGAA
128 AAATCACAGATCTTATCCCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAA
* *
49518778 GTTGCAGTAGAGTAGACCCAAGAAAG
193 GTTACAGTAGAGCAGA-CCAAGAAAG
* * *
49518804 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAATCAAGTCTTATCCCCCTGAAA
1 CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAG
* * ** * ** * * *
49518869 TTGCAGTGGGGCA-ACTAAA-TAAACAAATCCCATCTCCCTAAAGTTGTAGTGGAGTGGATTAGA
66 TTGCAGTGGAGCAGATTAAAGCCAA-TAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
49518932 ATC
130 ATC
49518935 TCTCTGAAAT
Statistics
Matches: 295, Mismatches: 46, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
216 5 0.02
217 220 0.75
218 67 0.23
219 3 0.01
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.26
Consensus pattern (217 bp):
CGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTGAAG
TTGCAGTGGAGCAGATTAAAGCCAATAATCATATCTCCCTGAAGTTGCAGTGGAGTGGATTAAAA
TCACAGATCTTATCCCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTCTTATCTCCCTGAAGTT
ACAGTAGAGCAGACCAAGAAAG
Found at i:49519493 original size:22 final size:22
Alignment explanation
Indices: 49519433--49519490 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 22
49519423 AATCTTCAAG
49519433 GATATGCAATCTT---AGATAT
1 GATATGCAATCTTAGAAGATAT
49519452 GATATGCAATCTTAGAAGATAT
1 GATATGCAATCTTAGAAGATAT
* *
49519474 GATTTTGTAATCTTAGA
1 GA-TATGCAATCTTAGA
49519491 GATTTAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.39
22 8 0.24
23 12 0.36
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
GATATGCAATCTTAGAAGATAT
Found at i:49519718 original size:23 final size:23
Alignment explanation
Indices: 49519674--49519718 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
49519664 TCTTATTTTG
* *
49519674 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
49519697 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
49519719 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:49519763 original size:15 final size:16
Alignment explanation
Indices: 49519737--49519769 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
49519727 TTTTTCCTTA
49519737 TTATTCATTTTCAAAT
1 TTATTCATTTTCAAAT
49519753 TTATT-ATTTTCAAAT
1 TTATTCATTTTCAAAT
49519768 TT
1 TT
49519770 GTTTACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (16 bp):
TTATTCATTTTCAAAT
Found at i:49520182 original size:2 final size:2
Alignment explanation
Indices: 49520177--49520223 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
49520167 TTTCTAATGA
*
49520177 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49520219 AT AT A
1 AT AT A
49520224 CGCACATGTC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:49520297 original size:2 final size:2
Alignment explanation
Indices: 49520277--49520334 Score: 75
Period size: 2 Copynumber: 30.0 Consensus size: 2
49520267 TTTTCAACAC
*
49520277 AT AT AT -T AT A- AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
49520317 AT AT GT AT AT TT AT AT AT
1 AT AT AT AT AT AT AT AT AT
49520335 TTTTCTTTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
1 2 0.04
2 46 0.96
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (2 bp):
AT
Found at i:49524093 original size:15 final size:15
Alignment explanation
Indices: 49524075--49524104 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49524065 ATTTTATAGT
49524075 TAAAAATTAATTTAA
1 TAAAAATTAATTTAA
*
49524090 TAAAATTTAATTTAA
1 TAAAAATTAATTTAA
49524105 AATTAACTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAAAAATTAATTTAA
Found at i:49542919 original size:18 final size:18
Alignment explanation
Indices: 49542852--49542924 Score: 78
Period size: 18 Copynumber: 4.1 Consensus size: 18
49542842 GCGAGCTTTA
* *
49542852 TATAACATGCGAACCATG
1 TATATCATGCGAACCCTG
49542870 TATATCATGCGAACCCTAGG
1 TATATCATGCGAACCCT--G
* *
49542890 TAT-T-ATGTGAACTCTG
1 TATATCATGCGAACCCTG
49542906 TATATCATGCGAACCCTG
1 TATATCATGCGAACCCTG
49542924 T
1 T
49542925 GTTTATTGTG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
16 4 0.09
17 1 0.02
18 35 0.78
19 1 0.02
20 4 0.09
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (18 bp):
TATATCATGCGAACCCTG
Found at i:49543166 original size:22 final size:21
Alignment explanation
Indices: 49543140--49543222 Score: 69
Period size: 22 Copynumber: 3.8 Consensus size: 21
49543130 CAGGTACAAC
49543140 TATGCGAACCCTATGTGTTAT
1 TATGCGAACCCTATGTGTTAT
* *
49543161 TCATGCCAACCCTACATGTGGTA-
1 T-ATGCGAACCCT--ATGTGTTAT
* *
49543184 TATGCGAACCCAATTTGTTGAT
1 TATGCGAACCCTATGTGTT-AT
* *
49543206 TATGCAAACCATATGTG
1 TATGCGAACCCTATGTG
49543223 GGAACCCCTA
Statistics
Matches: 47, Mismatches: 10, Indels: 9
0.71 0.15 0.14
Matches are distributed among these distances:
20 5 0.11
21 2 0.04
22 32 0.68
23 1 0.02
24 7 0.15
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.33
Consensus pattern (21 bp):
TATGCGAACCCTATGTGTTAT
Found at i:49544223 original size:13 final size:14
Alignment explanation
Indices: 49544186--49544226 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 14
49544176 ATTTCAAATG
49544186 CAGATA-ACAGAAT
1 CAGATATACAGAAT
* *
49544199 CAAATATGCAGAA-
1 CAGATATACAGAAT
49544212 CAGATATACAGAAT
1 CAGATATACAGAAT
49544226 C
1 C
49544227 CTACCCCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
13 16 0.73
14 6 0.27
ACGTcount: A:0.51, C:0.17, G:0.15, T:0.17
Consensus pattern (14 bp):
CAGATATACAGAAT
Found at i:49552286 original size:14 final size:14
Alignment explanation
Indices: 49552267--49552296 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49552257 AAAATCAATA
*
49552267 ATATACAGATATAT
1 ATATACACATATAT
49552281 ATATACACATATAT
1 ATATACACATATAT
49552295 AT
1 AT
49552297 GAAAGTATAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.50, C:0.10, G:0.03, T:0.37
Consensus pattern (14 bp):
ATATACACATATAT
Found at i:49554642 original size:44 final size:44
Alignment explanation
Indices: 49554586--49554670 Score: 100
Period size: 44 Copynumber: 1.9 Consensus size: 44
49554576 TCCACCACAA
* *
49554586 CCTCGGGAAGATAGGATTATCGACTTCAATCTGCTCCACTGCAC
1 CCTCGGGAAGATAAGATTATCGACTTCAATCTGCCCCACTGCAC
* ** *
49554630 CCTCAGGG-AGATAAGATTTTCTTCTTCAGTCTGCCCCACTG
1 CCTC-GGGAAGATAAGATTATCGACTTCAATCTGCCCCACTG
49554671 TGACTTCAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
44 31 0.91
45 3 0.09
ACGTcount: A:0.22, C:0.29, G:0.20, T:0.28
Consensus pattern (44 bp):
CCTCGGGAAGATAAGATTATCGACTTCAATCTGCCCCACTGCAC
Found at i:49554680 original size:44 final size:43
Alignment explanation
Indices: 49554615--49555086 Score: 235
Period size: 44 Copynumber: 10.8 Consensus size: 43
49554605 TCGACTTCAA
* *
49554615 TCTGCTCCACTGCACCCTCAGGGAGATAAGATTTTCTTCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTTC-TCAG
* ** *
49554659 TCTGCCCCACTGTGACTTCAGGGGGATAAGACTTGTT-TTCTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TT-TTCTTCTCAG
* * *
49554703 TCTGCTCCACTGCAACTTCAGGGGGATAAGATCTGCTTACTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTT-CTCAG
* *** * * *
49554747 TCTGCTCCGCTGCAACTTCAGGGAGATAAGACCCTATAC-GA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTTCTCAG
** *** * * *
49554788 TCCACTCTGTTGCAACTTCAGAGAGATAAGATCTGTTACTT-TAAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGAT-T-TT-CTTCTCAG
* * * * ** *
49554833 TC-GCTCCACTACAACTCCAGGGAGATAGGATTATCGGCTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTTC-TCAG
* *
49554876 TCTGCTTCACTGTAACTTCAGGGAGATAAGATTTGT-TATCTTC-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTT-TCT-TC-TCAG
* * ** * *
49554920 ATCTGC-CCTACTGCAACTTTAGGGGGATAAGACCTGCTTACTCTG
1 -TCTGCTCC-ACTGCAACTTCAGGGAGATAAGATTTTCTT-CTCAG
* * * * *
49554965 TCTGCTCCGCTGCAACTTCAGGGAGATAAAACCTATTACTT-TAAT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TTTCTTCTCAG
* * * * ** *
49555010 TC-GCTCCACTACAACTTTAGGGAGATAGGATTATCGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTTC-TCAG
* *
49555053 TCTGCTCCACTGCATCGTCAGGGAGATAAGATTT
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTT
49555087 GCCCTCTTCG
Statistics
Matches: 316, Mismatches: 86, Indels: 52
0.70 0.19 0.11
Matches are distributed among these distances:
41 29 0.09
42 4 0.01
43 14 0.04
44 217 0.69
45 46 0.15
46 2 0.01
47 4 0.01
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTTCTTCTCAG
Found at i:49555059 original size:88 final size:88
Alignment explanation
Indices: 49554526--49555084 Score: 342
Period size: 88 Copynumber: 6.4 Consensus size: 88
49554516 ACTTGATGCG
* * * * * * * * *
49554526 ATCTGCTCTACTGCAACTTTAGAGAGATAATATCTATTACTTTAATCCGCTCCACCACAAC-CTC
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTACTTTAATTCGCTCCACTACAACTTTA
49554590 GGGAAGATAGGATTATCGACTTCA
66 GGG-AGATAGGATTATCGACTTCA
* * * * * ***
49554614 ATCTGCTCCACTGCACCCTCAGGGAGATAAGAT-T-TT-CTTCTTCAGTCTGCCCCACTGTGACT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTAC-T-TTAATTC-GCTCCACTACAACT
* * * * ***
49554676 TCAGGGGGATAAGACTTGTTTTC-TCA
63 TTAGGGAGATAGGA-TTATCGACTTCA
* * * * * *
49554702 GTCTGCTCCACTGCAACTTCAGGGGGATAAGATCTGCTTAC--TCAGTCTGCTCCGCTGCAACTT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTG-TTACTTTAATTC-GCTCCACTACAACTT
* * * *
49554765 CAGGGAGATAAGACCCTATACGA-TCCA
64 TAGGGAGATAGGA--TTAT-CGACTTCA
* * **
49554792 CTCTG-T----TGCAACTTCAGAGAGATAAGATCTGTTACTTTAATTCGCTCCACTACAACTCCA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTACTTTAATTCGCTCCACTACAACTTTA
*
49554852 GGGAGATAGGATTATCGGCTTCA
66 GGGAGATAGGATTATCGACTTCA
* * * ** *
49554875 ATCTGCTTCACTGTAACTTCAGGGAGATAAGATTTGTTATCTTCGA-TCTGC-CCTACTGCAACT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTA-CTTTAATTC-GCTCC-ACTACAACT
* * * * * *
49554938 TTAGGGGGATAAGACCT-GCTTAC-TCT
63 TTAGGGAGATAGGA-TTATC-GACTTCA
* * * * *
49554964 GTCTGCTCCGCTGCAACTTCAGGGAGATAAAACCTATTACTTTAATTCGCTCCACTACAACTTTA
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTACTTTAATTCGCTCCACTACAACTTTA
49555029 GGGAGATAGGATTATCGACTTCA
66 GGGAGATAGGATTATCGACTTCA
* *
49555052 ATCTGCTCCACTGCATCGTCAGGGAGATAAGAT
1 ATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
49555085 TTGCCCTCTT
Statistics
Matches: 353, Mismatches: 89, Indels: 58
0.71 0.18 0.12
Matches are distributed among these distances:
82 2 0.01
83 10 0.03
84 5 0.01
85 48 0.14
86 7 0.02
87 8 0.02
88 188 0.53
89 74 0.21
90 8 0.02
91 2 0.01
92 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.19, T:0.30
Consensus pattern (88 bp):
ATCTGCTCCACTGCAACTTCAGGGAGATAAGATCTGTTACTTTAATTCGCTCCACTACAACTTTA
GGGAGATAGGATTATCGACTTCA
Found at i:49555367 original size:43 final size:43
Alignment explanation
Indices: 49555310--49555650 Score: 173
Period size: 43 Copynumber: 7.9 Consensus size: 43
49555300 AGGACTTGTG
* * *
49555310 GCTTAAATTTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCA
* * *
49555353 GCTCAGATCTGTTTCCCTACTCCTAGGGAAGATAAGATTCGTAA
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCG-CA
* * * * * * * * **
49555397 TCTTCA-A-C-CTATCCC-ACTGCTGACTAGGAAGATAGGACTAGTG
1 GCTT-AGATCTGTTTCCCTACTCCTG---GGGAAGATAAGATTCGCA
* * * *
49555440 GCTTAAATCTGTTTCCCTACTTCC-AGGGAATATAAGATTCGCT
1 GCTTAGATCTGTTTCCCTAC-TCCTGGGGAAGATAAGATTCGCA
* *
49555483 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTTGTA
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCA
* * * * * **
49555526 GTCTTCA-A-C-CTATCCC-AC-CGCTGACCAGGG-AGATAGGACTAGTG
1 G-CTT-AGATCTGTTTCCCTACTC-CTG----GGGAAGATAAGATTCGCA
* *** *
49555570 GCTTAAATCTGTTTCCCTACTCCTGAAAAAGATAAGATTCGCC
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCA
*
49555613 GCTTAGATCTGTTTCCCTCCTCCTGGGGAAGATAAGAT
1 GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
49555651 CTGTAATATT
Statistics
Matches: 217, Mismatches: 57, Indels: 48
0.67 0.18 0.15
Matches are distributed among these distances:
40 1 0.00
41 10 0.05
42 15 0.07
43 134 0.62
44 32 0.15
45 15 0.07
46 7 0.03
47 3 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (43 bp):
GCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTCGCA
Found at i:49555405 original size:130 final size:130
Alignment explanation
Indices: 49555263--49555792 Score: 746
Period size: 130 Copynumber: 4.1 Consensus size: 130
49555253 GATAAGACCT
* * * *
49555263 GTAAT-TTCCAACCTATTCAACTGCTG-CTCAGGGAAATAGGACTTGTGGCTTAAATTTGTTTCC
1 GTAATCTT-CAACCTATCCCACTGCTGACT-AGGGAAATAGGACTAGTGGCTTAAATCTGTTTCC
* * *
49555326 CTACTCCTGGGGAAGATAAGATTCGCCGCTCAGATCTGTTTCCCTACTCCTAGGGAAGATAAGAT
64 CTACTCCTGGGAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
49555391 TC
129 TC
49555393 GTAATCTTCAACCTATCCCACTGCTGACTA-GGAAGATAGGACTAGTGGCTTAAATCTGTTTCCC
1 GTAATCTTCAACCTATCCCACTGCTGACTAGGGAA-ATAGGACTAGTGGCTTAAATCTGTTTCCC
* * *
49555457 TACTTCCAGGG-AATATAAGATTCGCTGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
65 TAC-TCCTGGGAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGAT
*
49555521 TT
129 TC
* * * *
49555523 GTAGTCTTCAACCTATCCCACCGCTGACCAGGGAGATAGGACTAGTGGCTTAAATCTGTTTCCCT
1 GTAATCTTCAACCTATCCCACTGCTGACTAGGGAAATAGGACTAGTGGCTTAAATCTGTTTCCCT
** *
49555588 ACTCCTGAAAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTCCTCCTGGGGAAGATAAGA-TC
66 ACTCCTGGGAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTC
* * *
49555652 TGTAATATTCAACCTATCCCACTGCTGACTAGGGAGATAGGACTAGTGGCTTAAATATGTTTCCC
1 -GTAATCTTCAACCTATCCCACTGCTGACTAGGGAAATAGGACTAGTGGCTTAAATCTGTTTCCC
* ** *
49555717 TACTCCTGGGAAAGATAAGATTTGCCGCTTAGATCTGTTTCCCTACTATTGGGGAAGATAAGATC
65 TACTCCTGGGAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATT
49555782 C
130 C
*
49555783 ATAATCTTCA
1 GTAATCTTCA
49555793 TTGATCTGTT
Statistics
Matches: 357, Mismatches: 35, Indels: 16
0.88 0.09 0.04
Matches are distributed among these distances:
129 9 0.03
130 334 0.94
131 14 0.04
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (130 bp):
GTAATCTTCAACCTATCCCACTGCTGACTAGGGAAATAGGACTAGTGGCTTAAATCTGTTTCCCT
ACTCCTGGGAAAGATAAGATTCGCCGCTTAGATCTGTTTCCCTACTCCTGGGGAAGATAAGATTC
Found at i:49557006 original size:22 final size:21
Alignment explanation
Indices: 49556981--49557023 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
49556971 TTAGCCTCTC
*
49556981 CATTTTTACTTTTTCATTTTTT
1 CATTTTTA-ATTTTCATTTTTT
49557003 CATTTTTAATTTTCATTTTTT
1 CATTTTTAATTTTCATTTTTT
49557024 AATCTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTAATTTTCATTTTTT
Found at i:49557036 original size:21 final size:21
Alignment explanation
Indices: 49556982--49557037 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
49556972 TAGCCTCTCC
*
49556982 ATTTTTACTTTTTCATTTTTTC
1 ATTTTTA-TTTTTCATTTTTTA
*
49557004 ATTTTTAATTTTCATTTTTTA
1 ATTTTTATTTTTCATTTTTTA
*
49557025 ATCTTTTTTTTTT
1 AT-TTTTATTTTT
49557038 GTTTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 14 0.48
22 15 0.52
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (21 bp):
ATTTTTATTTTTCATTTTTTA
Found at i:49561901 original size:2 final size:2
Alignment explanation
Indices: 49561888--49561927 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
49561878 AAAATAAATA
* * *
49561888 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AC AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49561928 GAAAGTATAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (2 bp):
AT
Found at i:49561909 original size:12 final size:12
Alignment explanation
Indices: 49561888--49561927 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
49561878 AAAATAAATA
49561888 ATATACATATAT
1 ATATACATATAT
*
49561900 ATATATATATAT
1 ATATACATATAT
*
49561912 ATATACACATAT
1 ATATACATATAT
49561924 ATAT
1 ATAT
49561928 GAAAGTATAC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (12 bp):
ATATACATATAT
Found at i:49566410 original size:13 final size:13
Alignment explanation
Indices: 49566392--49566417 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49566382 AATAAATTAG
49566392 TAAATATAAATAT
1 TAAATATAAATAT
49566405 TAAATATAAATAT
1 TAAATATAAATAT
49566418 ATTATTTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAAATATAAATAT
Found at i:49566481 original size:12 final size:11
Alignment explanation
Indices: 49566452--49566485 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
49566442 ATTTTTAAAA
49566452 AATATTATTTT
1 AATATTATTTT
49566463 AATATTATATTT
1 AATATTAT-TTT
*
49566475 TATATTATTTT
1 AATATTATTTT
49566486 GGTTTTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
AATATTATTTT
Found at i:49566642 original size:13 final size:13
Alignment explanation
Indices: 49566624--49566655 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
49566614 TGAAGTATTG
49566624 TATTTAGGAATAA
1 TATTTAGGAATAA
49566637 TATTTAGGAATAA
1 TATTTAGGAATAA
*
49566650 TTTTTA
1 TATTTA
49566656 AACTCCACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.47
Consensus pattern (13 bp):
TATTTAGGAATAA
Found at i:49566956 original size:7 final size:7
Alignment explanation
Indices: 49566944--49566970 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
49566934 AGCTGACTAA
49566944 AAATAAT
1 AAATAAT
49566951 AAATAAT
1 AAATAAT
49566958 AAATAAT
1 AAATAAT
49566965 AAATAA
1 AAATAA
49566971 AAGAGAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (7 bp):
AAATAAT
Found at i:49576956 original size:28 final size:28
Alignment explanation
Indices: 49576906--49576960 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
49576896 CATAGAAGTA
49576906 TATATAAATAAAAAAATTTAAAAATATAT
1 TATATAAATAAAAAAA-TTAAAAATATAT
**
49576935 TATA-AAATAAAATCATTAAAAATATA
1 TATATAAATAAAAAAATTAAAAATATA
49576961 GACGATATTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 11 0.46
28 9 0.38
29 4 0.17
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (28 bp):
TATATAAATAAAAAAATTAAAAATATAT
Found at i:49577135 original size:3 final size:3
Alignment explanation
Indices: 49577074--49577115 Score: 66
Period size: 3 Copynumber: 14.0 Consensus size: 3
49577064 TGACTACTAC
* *
49577074 AAT AAT AAT AAT AAT CAT AAT AAT AAT AAC AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
49577116 CTAATTAGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:49579014 original size:29 final size:29
Alignment explanation
Indices: 49578906--49579007 Score: 134
Period size: 29 Copynumber: 3.5 Consensus size: 29
49578896 ACTGTTGACA
*
49578906 CCACACGATCGTGTGCCATGCTGTGTAAG
1 CCACACGATCGTGTGCCAGGCTGTGTAAG
** *
49578935 CCACACGA-CTGTGTGCCAGGCCATGTGAG
1 CCACACGATC-GTGTGCCAGGCTGTGTAAG
* *
49578964 CCACATGATCGTGTGTCAGGCTGTGTAAG
1 CCACACGATCGTGTGCCAGGCTGTGTAAG
49578993 CCACACGATCGTGTG
1 CCACACGATCGTGTG
49579008 GTAGGCTAGT
Statistics
Matches: 61, Mismatches: 10, Indels: 4
0.81 0.13 0.05
Matches are distributed among these distances:
28 1 0.02
29 59 0.97
30 1 0.02
ACGTcount: A:0.21, C:0.27, G:0.29, T:0.23
Consensus pattern (29 bp):
CCACACGATCGTGTGCCAGGCTGTGTAAG
Found at i:49580802 original size:24 final size:25
Alignment explanation
Indices: 49580761--49580807 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
49580751 AACTTGTAAA
*
49580761 ATATAATCAACCATTCAAAATATCT
1 ATATAATCAACCAATCAAAATATCT
* *
49580786 ATAT-ATCAAGCAATCAACATAT
1 ATATAATCAACCAATCAAAATAT
49580808 TTGATTTTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (25 bp):
ATATAATCAACCAATCAAAATATCT
Found at i:49583301 original size:20 final size:20
Alignment explanation
Indices: 49583276--49583438 Score: 78
Period size: 21 Copynumber: 7.8 Consensus size: 20
49583266 AAAGTTGAAT
49583276 AGAAGCTCATGAA-AGCTAAA
1 AGAAGCTCAT-AAGAGCTAAA
49583296 AGAAGCTCATAAGAGCTAAA
1 AGAAGCTCATAAGAGCTAAA
* * * * * *
49583316 TAAAAACCCATAAGGGTTGAAC
1 -AGAAGCTCATAAGAGCT-AAA
* *
49583338 AGAAGCTCGTAAGAGCTGAAC
1 AGAAGCTCATAAGAGCT-AAA
* *
49583359 AGAAACTCATAAGAGTTGAACA
1 AGAAGCTCATAAGAGCT-AA-A
* *
49583381 A-AAGCTCGTAAGAGCTGAAC
1 AGAAGCTCATAAGAGCT-AAA
* * * *
49583401 AGAAACTCGTATGAGTTAAA
1 AGAAGCTCATAAGAGCTAAA
* *
49583421 CAAAAGCTCGTAAGAGCT
1 -AGAAGCTCATAAGAGCT
49583439 TAACAGAAAG
Statistics
Matches: 109, Mismatches: 28, Indels: 11
0.74 0.19 0.07
Matches are distributed among these distances:
19 2 0.02
20 20 0.18
21 84 0.77
22 3 0.03
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (20 bp):
AGAAGCTCATAAGAGCTAAA
Found at i:49583357 original size:21 final size:21
Alignment explanation
Indices: 49583333--49583446 Score: 138
Period size: 21 Copynumber: 5.4 Consensus size: 21
49583323 CCATAAGGGT
49583333 TGAACAGAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
* * *
49583354 TGAACAGAAACTCATAAGAGT
1 TGAACAGAAGCTCGTAAGAGC
*
49583375 TGAACAAAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
* * *
49583396 TGAACAGAAACTCGTATGAGT
1 TGAACAGAAGCTCGTAAGAGC
* *
49583417 TAAACAAAAGCTCGTAAGAGC
1 TGAACAGAAGCTCGTAAGAGC
*
49583438 TTAACAGAA
1 TGAACAGAA
49583447 AGTAAACACA
Statistics
Matches: 75, Mismatches: 18, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 75 1.00
ACGTcount: A:0.44, C:0.17, G:0.22, T:0.18
Consensus pattern (21 bp):
TGAACAGAAGCTCGTAAGAGC
Found at i:49583370 original size:42 final size:42
Alignment explanation
Indices: 49583298--49583447 Score: 201
Period size: 42 Copynumber: 3.6 Consensus size: 42
49583288 AAGCTAAAAG
* * * * * * *
49583298 AAGCTCATAAGAGCTAAATAAAAACCCATAAGGGTTGAACAG
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAA
49583340 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAA
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAA
* * *
49583382 AAGCTCGTAAGAGCTGAACAGAAACTCGTATGAGTTAAACAA
1 AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAA
*
49583424 AAGCTCGTAAGAGCTTAACAGAAA
1 AAGCTCGTAAGAGCTGAACAGAAA
49583448 GTAAACACAA
Statistics
Matches: 97, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.45, C:0.17, G:0.21, T:0.17
Consensus pattern (42 bp):
AAGCTCGTAAGAGCTGAACAGAAACTCATAAGAGTTGAACAA
Found at i:49588746 original size:101 final size:98
Alignment explanation
Indices: 49588641--49588985 Score: 400
Period size: 91 Copynumber: 3.6 Consensus size: 98
49588631 TATTATTAAG
49588641 AATTATATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
1 AATTATATGAAATTATATAT-ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
*
49588706 CTCATATAAGAAAATTTATTATCAAT-A----AT
65 TTCATATAAGAAAATTTATTATCAATAATTTTAT
49588735 --TT-TATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
1 AATTATATGAAATTATATAT-ATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
*
49588797 TTCATATAAGAAAATTTATTATCAA-GA----AT
65 TTCATATAAGAAAATTTATTATCAATAATTTTAT
* *
49588826 --TT-TATGAAATTATATATTATTATTAAATTATATTTAATAATAATTATTTTAAATTATACAAA
1 AATTATATGAAATTATATA-TATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAA
* *
49588888 TTCATATAAGAAAATTTATTAGT-TATAATTATTTT
65 TTCATATAAGAAAATTTATTA-TCAATAATT-TTAT
* * * * * *
49588923 AAATTTTATTAAATCATATATTTTAATTAAAATATATTTAATATTAATTATTTCAAATTATAT
1 -AATTATATGAAATTATATATATT-ATTAAATTATATTTAATATTAATTATTTTAAATTATAT
49588986 TTTATAGTAT
Statistics
Matches: 224, Mismatches: 13, Indels: 21
0.87 0.05 0.08
Matches are distributed among these distances:
91 167 0.75
92 5 0.02
97 1 0.00
100 5 0.02
101 46 0.21
ACGTcount: A:0.46, C:0.03, G:0.02, T:0.48
Consensus pattern (98 bp):
AATTATATGAAATTATATATATTATTAAATTATATTTAATATTAATTATTTTAAATTATATAAAT
TCATATAAGAAAATTTATTATCAATAATTTTAT
Found at i:49588927 original size:91 final size:91
Alignment explanation
Indices: 49588611--49588908 Score: 524
Period size: 91 Copynumber: 3.3 Consensus size: 91
49588601 ATGATTTTAG
* * *
49588611 TAAATTCATATAAGAACATTTATTATTAAGAATTATATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
49588676 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
* *
49588702 TAAACTCATATAAGAAAATTTATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
49588767 TTTAATATTAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
49588793 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATTATTATTAAATTATA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
*
49588858 TTTAATAATAATTATTTTAAATTATA
66 TTTAATATTAATTATTTTAAATTATA
*
49588884 CAAATTCATATAAGAAAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
49588909 GTTATAATTA
Statistics
Matches: 197, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 197 1.00
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATCATTATTAAATTATA
TTTAATATTAATTATTTTAAATTATA
Found at i:49589084 original size:15 final size:15
Alignment explanation
Indices: 49589049--49589090 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49589039 TTAAGAATTT
*
49589049 TATTAAATTAT-ATA
1 TATTTAATTATAATA
49589063 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
49589077 TATTTAATAATAAT
1 TATTTAATTATAAT
49589091 TATGTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:49593639 original size:29 final size:29
Alignment explanation
Indices: 49593607--49593675 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 29
49593597 TTAATTTAGT
*
49593607 AATAATAAAATTATATTTTAAT-TCTTAAA
1 AATAATAAAATT-TAATTTAATCTCTTAAA
*
49593636 AATAATAAAAATTTAATTTAATCTTTTAAA
1 AATAAT-AAAATTTAATTTAATCTCTTAAA
*
49593666 AATTATAAAA
1 AATAATAAAA
49593676 GATATAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (29 bp):
AATAATAAAATTTAATTTAATCTCTTAAA
Found at i:49593647 original size:30 final size:30
Alignment explanation
Indices: 49593607--49593675 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
49593597 TTAATTTAGT
*
49593607 AATAAT-AAAATTATATTTTAAT-TCTTAAA
1 AATAATAAAAATT-TAATTTAATCTCTTAAA
*
49593636 AATAATAAAAATTTAATTTAATCTTTTAAA
1 AATAATAAAAATTTAATTTAATCTCTTAAA
*
49593666 AATTATAAAA
1 AATAATAAAA
49593676 GATATAGACT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 14 0.40
30 21 0.60
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
AATAATAAAAATTTAATTTAATCTCTTAAA
Found at i:49604839 original size:44 final size:44
Alignment explanation
Indices: 49604809--49605169 Score: 188
Period size: 44 Copynumber: 8.1 Consensus size: 44
49604799 GGGGCATAGA
*
49604809 ATTAGTAGCTTC-ATCTTGTTCCACTGCAACTTCATGGAGAAAAG
1 ATTAGCAGCTTCAATC-TGTTCCACTGCAACTTCATGGAGAAAAG
* * *
49604853 ATTTGCAGCTTCAATCTGTTCCACTGCAACTTCAAGGAGATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
* * **** ** * * *
49604897 ATTCACTATGGTAGATTCAATCCAACCCACTATAACTTCA-GGGGTATAGG
1 A-T---TA--GCAGCTTCAATCTGTTCCACTGCAACTTCATGGAG-AAAAG
* * ** * * *
49604947 ATTTGTAGCTTCAATCTACTCCACTGTAACTTCAGGGAGATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
* * * *
49604991 ATTCGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGA-AATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAA-AAG
* ** * * * *
49605035 ATTTGTTGCTTCAATCTGCTCCACTGCAATTTCAGGGAGATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
* * * * * * *
49605079 ATTCGTAGCTTCAATCTGCTCCACTGTAACTTTAGGGAGATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
*** * * * * *
49605123 ATTTTTAGCTTTAATCTGCTCCACTGCAATTTCAAGGAGATAAG
1 ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
49605167 ATT
1 ATT
49605170 CGCTATGGTA
Statistics
Matches: 263, Mismatches: 43, Indels: 22
0.80 0.13 0.07
Matches are distributed among these distances:
43 1 0.00
44 221 0.84
45 8 0.03
46 1 0.00
48 1 0.00
49 4 0.02
50 27 0.10
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (44 bp):
ATTAGCAGCTTCAATCTGTTCCACTGCAACTTCATGGAGAAAAG
Found at i:49604883 original size:138 final size:138
Alignment explanation
Indices: 49604680--49605215 Score: 390
Period size: 138 Copynumber: 3.9 Consensus size: 138
49604670 TTGTTGTTGT
* * * * * * * * *
49604680 TTCAATCTAATCCACTGCAACTTTAAGGATATAGGATTTGTAGCCTC-ATCTTGCTCCAC-GACA
1 TTCAATCTACTCCACTGCAACTTCAGGGAGAAAAGATTCGCAGCTTCAATC-TGCTCCACTG-CA
* * *
49604743 ACTTTAGGAAGATAAGATTTGCGACT-GTA-ACTTCATTCTGC-A-CCACTACAACTTTAGGGGC
64 ACTTAAGGAAGATAAGATTTGCGA-TGGTAGA-TTCAATC--CAACCCACTACAACTTCAGGGGC
49604804 ATAGAATTAGTAGC
125 ATAGAATTAGTAGC
** * * *
49604818 TTC-ATCTTGTTCCACTGCAACTTCATGGAGAAAAGATTTGCAGCTTCAATCTGTTCCACTGCAA
1 TTCAATC-TACTCCACTGCAACTTCAGGGAGAAAAGATTCGCAGCTTCAATCTGCTCCACTGCAA
** * * *
49604882 CTTCAAGG-AGATAAGATTCACTATGGTAGATTCAATCCAACCCACTATAACTTCAGGGGTATAG
65 CTT-AAGGAAGATAAGATTTGCGATGGTAGATTCAATCCAACCCACTACAACTTCAGGGGCATAG
* *
49604946 GATTTGTAGC
129 AATTAGTAGC
* * *
49604956 TTCAATCTACTCCACTGTAACTTCAGGGAGATAAGATTCGTAGCTTCAATCTGCTCCACTGCAAC
1 TTCAATCTACTCCACTGCAACTTCAGGGAGAAAAGATTCGCAGCTTCAATCTGCTCCACTGCAAC
* * ** * *
49605021 TTCAGGGAA-ATAAGATTT--G-T--T-GCTTCAAT-CTGCTCCACTGCAATTTCAGGGAG-ATA
66 TT-AAGGAAGATAAGATTTGCGATGGTAGATTCAATCCAAC-CCACTACAACTTCAGGG-GCATA
*
49605077 -AGATTCGTAGC
128 GA-ATTAGTAGC
* * * * *** * *
49605088 TTCAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTTTTAGCTTTAATCTGCTCCACTGCAAT
1 TTCAATCTACTCCACTGCAACTTCAGGGAGAAAAGATTCGCAGCTTCAATCTGCTCCACTGCAAC
* * * * *
49605153 TTCAAGG-AGATAAGATTCGCTATGGTAGATTCAATCTAACCCACTACAACTTTAGGGGTATAG
66 TT-AAGGAAGATAAGATTTGCGATGGTAGATTCAATCCAACCCACTACAACTTCAGGGGCATAG
49605216 GATCTATGGT
Statistics
Matches: 320, Mismatches: 55, Indels: 45
0.76 0.13 0.11
Matches are distributed among these distances:
131 3 0.01
132 105 0.33
133 2 0.01
135 2 0.01
136 1 0.00
137 7 0.02
138 187 0.58
139 13 0.04
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (138 bp):
TTCAATCTACTCCACTGCAACTTCAGGGAGAAAAGATTCGCAGCTTCAATCTGCTCCACTGCAAC
TTAAGGAAGATAAGATTTGCGATGGTAGATTCAATCCAACCCACTACAACTTCAGGGGCATAGAA
TTAGTAGC
Found at i:49605050 original size:88 final size:88
Alignment explanation
Indices: 49604813--49605171 Score: 400
Period size: 88 Copynumber: 4.0 Consensus size: 88
49604803 CATAGAATTA
* * * *
49604813 GTAGCTTC-ATCTTGTTCCACTGCAACTTCATGGAGAA-AAGATTTGCAGCTTCAATCTGTTCCA
1 GTAGCTTCAATC-TGCTCCACTGCAACTTCAGGGA-AATAAGATTTGTAGCTTCAATCTGCTCCA
49604876 CTGCAACTTCAAGGAGATAAGATTCAC
64 CTGCAACTTCAAGGAGATAAGATT--C
* ** ** ** * *
49604903 TATGGTAGATTCAATCCAAC-CCACTATAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTACT
1 ----GTAGCTTCAAT-CTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCT
* *
49604967 CCACTGTAACTTCAGGGAGATAAGATTC
61 CCACTGCAACTTCAAGGAGATAAGATTC
*
49604995 GTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTTGCTTCAATCTGCTCCACT
1 GTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACT
* *
49605060 GCAATTTCAGGGAGATAAGATTC
66 GCAACTTCAAGGAGATAAGATTC
* * * * *
49605083 GTAGCTTCAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTTTTAGCTTTAATCTGCTCCACT
1 GTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACT
*
49605148 GCAATTTCAAGGAGATAAGATTC
66 GCAACTTCAAGGAGATAAGATTC
49605171 G
1 G
49605172 CTATGGTAGA
Statistics
Matches: 227, Mismatches: 34, Indels: 14
0.83 0.12 0.05
Matches are distributed among these distances:
87 2 0.01
88 155 0.68
92 1 0.00
93 1 0.00
94 65 0.29
95 2 0.01
96 1 0.00
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (88 bp):
GTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATTTGTAGCTTCAATCTGCTCCACT
GCAACTTCAAGGAGATAAGATTC
Found at i:49605118 original size:132 final size:134
Alignment explanation
Indices: 49604785--49605214 Score: 458
Period size: 138 Copynumber: 3.2 Consensus size: 134
49604775 TCATTCTGCA
* * * * * *
49604785 CCACTACAACTTTAGGGGCAT-AGAATTAGTAGCTTC-ATCTTGTTCCACTGCAACTTCATGGAG
1 CCACTACAACTTCAGGGGTATAAG-ATTCGTAGCTTCAATC-TGCTCCACTGTAACTTCAGGGAG
* * *
49604848 AAAAGATTTGCAGCTTCAATCTGTTCCACTGCAACTTCAAGGAGATAAGATTCACTATGGTAGAT
64 ATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-T---TATGGTAGAT
49604913 TCAATCCAAC
125 TCAATCCAAC
* * * *
49604923 CCACTATAACTTCAGGGGTATAGGATTTGTAGCTTCAATCTACTCCACTGTAACTTCAGGGAGAT
1 CCACTACAACTTCAGGGGTATAAGATTCGTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGAT
* * * * *
49604988 AAGATTCGTAGCTTCAATCTGCTCCACTGCAACTTCAGGGAAATAAGATT-T-GTTGCTTCAAT-
66 AAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTATGGTAGATTCAATC
**
49605050 CTGC
131 CAAC
* * *
49605054 TCCACTGCAATTTCAGGGAG-ATAAGATTCGTAGCTTCAATCTGCTCCACTGTAACTTTAGGGAG
1 -CCACTACAACTTCAGGG-GTATAAGATTCGTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAG
* * *
49605118 ATAAGATTTTTAGCTTTAATCTGCTCCACTGCAATTTCAAGGAGATAAGATTCGCTATGGTAGAT
64 ATAAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGA-T---TATGGTAGAT
*
49605183 TCAATCTAAC
125 TCAATCCAAC
*
49605193 CCACTACAACTTTAGGGGTATA
1 CCACTACAACTTCAGGGGTATA
49605215 GGATCTATGG
Statistics
Matches: 240, Mismatches: 40, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
131 2 0.01
132 107 0.45
133 3 0.01
134 1 0.00
136 1 0.00
137 3 0.01
138 118 0.49
139 5 0.02
ACGTcount: A:0.30, C:0.21, G:0.18, T:0.31
Consensus pattern (134 bp):
CCACTACAACTTCAGGGGTATAAGATTCGTAGCTTCAATCTGCTCCACTGTAACTTCAGGGAGAT
AAGATTTGTAGCTTCAATCTGCTCCACTGCAACTTCAAGGAGATAAGATTATGGTAGATTCAATC
CAAC
Found at i:49609981 original size:55 final size:55
Alignment explanation
Indices: 49609915--49610025 Score: 213
Period size: 55 Copynumber: 2.0 Consensus size: 55
49609905 GTCATCGATT
*
49609915 CCCATTTGACCTCTCCCTTACTTAGTCTCACTCTTCTCCTTTCTTACTTCTTCTC
1 CCCATTTGACCTCTCCCTCACTTAGTCTCACTCTTCTCCTTTCTTACTTCTTCTC
49609970 CCCATTTGACCTCTCCCTCACTTAGTCTCACTCTTCTCCTTTCTTACTTCTTCTC
1 CCCATTTGACCTCTCCCTCACTTAGTCTCACTCTTCTCCTTTCTTACTTCTTCTC
49610025 C
1 C
49610026 AACTCCTTCT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.11, C:0.41, G:0.04, T:0.44
Consensus pattern (55 bp):
CCCATTTGACCTCTCCCTCACTTAGTCTCACTCTTCTCCTTTCTTACTTCTTCTC
Found at i:49610024 original size:26 final size:26
Alignment explanation
Indices: 49609931--49610018 Score: 72
Period size: 26 Copynumber: 3.3 Consensus size: 26
49609921 TGACCTCTCC
49609931 CTTACTTAGTCTCACTCTTCTCCTTT
1 CTTACTTAGTCTCACTCTTCTCCTTT
** * *
49609957 CTTACTTCTTCTC-CCCATT-TGACCTCTCC
1 CTTACTTAGTCTCACTC-TTCT--CCT-T-T
*
49609986 CTCACTTAGTCTCACTCTTCTCCTTT
1 CTTACTTAGTCTCACTCTTCTCCTTT
49610012 CTTACTT
1 CTTACTT
49610019 CTTCTCCAAC
Statistics
Matches: 45, Mismatches: 10, Indels: 14
0.65 0.14 0.20
Matches are distributed among these distances:
25 3 0.07
26 19 0.42
27 4 0.09
28 4 0.09
29 12 0.27
30 3 0.07
ACGTcount: A:0.11, C:0.39, G:0.03, T:0.47
Consensus pattern (26 bp):
CTTACTTAGTCTCACTCTTCTCCTTT
Found at i:49618312 original size:18 final size:18
Alignment explanation
Indices: 49618289--49618326 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
49618279 TCGTTTTTAT
49618289 TTTCTCTTTTGCTATTTC
1 TTTCTCTTTTGCTATTTC
*
49618307 TTTCTCTTTTGTTATTTC
1 TTTCTCTTTTGCTATTTC
49618325 TT
1 TT
49618327 CTGTTCTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.18, G:0.05, T:0.71
Consensus pattern (18 bp):
TTTCTCTTTTGCTATTTC
Found at i:49619619 original size:14 final size:13
Alignment explanation
Indices: 49619600--49619630 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
49619590 AATGGATTAG
49619600 TATAATTCTTATCA
1 TATAATTCTTAT-A
49619614 TATAATTCTTATA
1 TATAATTCTTATA
49619627 TATA
1 TATA
49619631 TTGTACAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.52
Consensus pattern (13 bp):
TATAATTCTTATA
Found at i:49621572 original size:7 final size:7
Alignment explanation
Indices: 49621560--49621600 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
49621550 TAAAATTACA
*
49621560 ACATTCT
1 ACATTCC
*
49621567 ACATTCT
1 ACATTCC
49621574 ACATTCC
1 ACATTCC
49621581 ACATTCC
1 ACATTCC
49621588 ACATTCC
1 ACATTCC
49621595 ACATTC
1 ACATTC
49621601 ATATATTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.29, C:0.37, G:0.00, T:0.34
Consensus pattern (7 bp):
ACATTCC
Found at i:49622533 original size:15 final size:15
Alignment explanation
Indices: 49622500--49622533 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49622490 AATTTCTTCT
*
49622500 TTTTATTTTTATTTT
1 TTTTATTTTTATTTG
*
49622515 TTTTATTTTTGTTTG
1 TTTTATTTTTATTTG
49622530 TTTT
1 TTTT
49622534 GAATGCAGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.00, G:0.06, T:0.85
Consensus pattern (15 bp):
TTTTATTTTTATTTG
Found at i:49627292 original size:3 final size:3
Alignment explanation
Indices: 49627284--49627312 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
49627274 TGCCTGCTAG
49627284 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
49627313 TGGCAGCAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:49631969 original size:16 final size:17
Alignment explanation
Indices: 49631937--49631969 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
49631927 AACTAACAGT
49631937 TATAAAATTTATATTTA
1 TATAAAATTTATATTTA
49631954 TATAAAATTT-TATTTA
1 TATAAAATTTATATTTA
49631970 AATTATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAAAATTTATATTTA
Found at i:49632264 original size:108 final size:108
Alignment explanation
Indices: 49632072--49632292 Score: 345
Period size: 108 Copynumber: 2.0 Consensus size: 108
49632062 TGTGGTTGAG
* *
49632072 GAGTCTTTCTAGATGTTGAAGATGTACTTAGAAGAATGATAAGAAAAAAAATGGAGGAAGAAGAA
1 GAGTCTTTCTAGATGTCGAAGATATACTTAGAAGAATGATAAGAAAAAAAATGGAGGAAGAAGAA
* * *
49632137 TACCTCTCATTGAAATGGGATAGGAGTATTTATAGGTGGAGGA
66 TACCTATCATTGAAATGGGAGAGGAGTATTTATAGGTAGAGGA
*
49632180 GAGTCTTTCTAGATGTCGAAGATATACTTAGAAGAATGATAAGAAAAAAAGTGGAGGAAGAAGAA
1 GAGTCTTTCTAGATGTCGAAGATATACTTAGAAGAATGATAAGAAAAAAAATGGAGGAAGAAGAA
* * *
49632245 TACCTATCCTT-AAGGTGGGAGAGGAGTATTTGTAGGTAGAGGA
66 TACCTATCATTGAA-ATGGGAGAGGAGTATTTATAGGTAGAGGA
49632288 GAGTC
1 GAGTC
49632293 CACTCTCTCG
Statistics
Matches: 103, Mismatches: 9, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
107 2 0.02
108 101 0.98
ACGTcount: A:0.39, C:0.07, G:0.29, T:0.25
Consensus pattern (108 bp):
GAGTCTTTCTAGATGTCGAAGATATACTTAGAAGAATGATAAGAAAAAAAATGGAGGAAGAAGAA
TACCTATCATTGAAATGGGAGAGGAGTATTTATAGGTAGAGGA
Found at i:49634486 original size:105 final size:105
Alignment explanation
Indices: 49634304--49634514 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
49634294 TTTTCCTATC
49634304 CTATGGCATGCCATCTATATCCTACTCAACCCGATACAGTTAATAGGGTTTCATTTCACTTTTCA
1 CTATGGCATGCCATCTATATCCTACTCAACCCGATACAGTTAATAGGGTTTCATTTCACTTTTCA
49634369 AATACAACCAATATCCAATTCTCATATTTGCACATATATT
66 AATACAACCAATATCCAATTCTCATATTTGCACATATATT
49634409 CTATGGCATGCCATCTATATCCTACTCAACCCGATACAGTTAATAGGGTTTCATTTCACTTTTCA
1 CTATGGCATGCCATCTATATCCTACTCAACCCGATACAGTTAATAGGGTTTCATTTCACTTTTCA
49634474 AATACAACCAATATCCAATTCTCATATTTGCACATATATT
66 AATACAACCAATATCCAATTCTCATATTTGCACATATATT
49634514 C
1 C
49634515 ATTTCAATTT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.31, C:0.25, G:0.09, T:0.35
Consensus pattern (105 bp):
CTATGGCATGCCATCTATATCCTACTCAACCCGATACAGTTAATAGGGTTTCATTTCACTTTTCA
AATACAACCAATATCCAATTCTCATATTTGCACATATATT
Found at i:49635280 original size:14 final size:15
Alignment explanation
Indices: 49635261--49635293 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
49635251 TCTTCTCTGC
49635261 TTTTCTCTC-TTTCT
1 TTTTCTCTCTTTTCT
*
49635275 TTTTCTTTCTTTTCT
1 TTTTCTCTCTTTTCT
49635290 TTTT
1 TTTT
49635294 AATTTGCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (15 bp):
TTTTCTCTCTTTTCT
Found at i:49639142 original size:36 final size:36
Alignment explanation
Indices: 49639095--49639249 Score: 175
Period size: 36 Copynumber: 4.0 Consensus size: 36
49639085 GCTAAGCTAC
49639095 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
*
49639131 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAG
1 CACTTATCACTTTGTCACTTGATCAGATAA--GTA--T--AG
* *
49639173 CTACCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAG
1 ----CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
* *
49639213 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAG
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
49639249 C
1 C
49639250 TAAAGCTACC
Statistics
Matches: 103, Mismatches: 6, Indels: 20
0.80 0.05 0.16
Matches are distributed among these distances:
36 64 0.62
38 3 0.03
40 3 0.03
42 3 0.03
44 2 0.02
46 28 0.27
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (36 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAG
Found at i:49639182 original size:46 final size:46
Alignment explanation
Indices: 49639131--49639285 Score: 204
Period size: 46 Copynumber: 3.6 Consensus size: 46
49639121 ATAAGTATAG
49639131 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
49639177 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AG----
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
49639213 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
49639259 CACTTATCACTTTATCTCTTGATCAGA
1 CACTTATCACTTTTTCACTTGATCAGA
49639286 AGTACTCAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 20
0.78 0.05 0.17
Matches are distributed among these distances:
36 28 0.30
38 2 0.02
39 1 0.01
40 3 0.03
42 3 0.03
43 1 0.01
44 2 0.02
46 53 0.57
ACGTcount: A:0.28, C:0.22, G:0.13, T:0.37
Consensus pattern (46 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:49639190 original size:82 final size:82
Alignment explanation
Indices: 49639052--49639285 Score: 402
Period size: 82 Copynumber: 2.9 Consensus size: 82
49639042 TACGTATGAT
* * *
49639052 CACTTATCA-TTTGTC-CCTGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTTGTCACT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
49639114 TGATCAGATAAGTATAG
66 TGATCAGATAAGTATAG
49639131 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
*
49639196 TGATCAGATAAGTGTAG
66 TGATCAGATAAGTATAG
*
49639213 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTATCTCT
1 CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
49639278 TGATCAGA
66 TGATCAGA
49639286 AGTACTCAAA
Statistics
Matches: 147, Mismatches: 5, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
79 9 0.06
80 5 0.03
81 20 0.14
82 113 0.77
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.36
Consensus pattern (82 bp):
CACTTATCACTTTTTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTTGTCTCT
TGATCAGATAAGTATAG
Found at i:49641175 original size:33 final size:31
Alignment explanation
Indices: 49641084--49641167 Score: 77
Period size: 28 Copynumber: 2.7 Consensus size: 31
49641074 AAAACATGCT
* * *
49641084 GTAACAGTCTGGGCCTGAGCCCTATTCAGTAACA
1 GTAACAGTGTGGGCCTTAGCCC-A-TCAAT-ACA
*
49641118 GT-ATAGTGTGGGCCTTAG-CC--CAATACA
1 GTAACAGTGTGGGCCTTAGCCCATCAATACA
49641145 GTAACAGTGTGGGCCTTAGCCCA
1 GTAACAGTGTGGGCCTTAGCCCA
49641168 ATACAATAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
27 5 0.12
28 18 0.43
29 2 0.05
32 2 0.05
33 13 0.31
34 2 0.05
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.24
Consensus pattern (31 bp):
GTAACAGTGTGGGCCTTAGCCCATCAATACA
Found at i:49641185 original size:33 final size:32
Alignment explanation
Indices: 49641087--49641186 Score: 91
Period size: 33 Copynumber: 3.2 Consensus size: 32
49641077 ACATGCTGTA
* * * * *
49641087 ACAGTCTGGGCCTGAGCCCTATTCAGTAACAGT
1 ACAGTGTGGGCCTTAGCCCAATACA-TAATAGT
* *
49641120 ATAGTGTGGGCCTTAGCCCAATAC--AGTA--
1 ACAGTGTGGGCCTTAGCCCAATACATAATAGT
49641148 ACAGTGTGGGCCTTAGCCCAATACAATAATAGT
1 ACAGTGTGGGCCTTAGCCCAATAC-ATAATAGT
49641181 ACAGTG
1 ACAGTG
49641187 CAATAATGCA
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
28 23 0.43
30 2 0.04
31 3 0.06
33 25 0.47
ACGTcount: A:0.29, C:0.23, G:0.24, T:0.24
Consensus pattern (32 bp):
ACAGTGTGGGCCTTAGCCCAATACATAATAGT
Found at i:49647139 original size:19 final size:19
Alignment explanation
Indices: 49647115--49647154 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
49647105 CAAACCAAAG
49647115 TAAGGTTTTTAGGTCATTA
1 TAAGGTTTTTAGGTCATTA
49647134 TAAGGTTTTTAGGTCATTA
1 TAAGGTTTTTAGGTCATTA
49647153 TA
1 TA
49647155 TTACCCAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.05, G:0.20, T:0.47
Consensus pattern (19 bp):
TAAGGTTTTTAGGTCATTA
Found at i:49649331 original size:35 final size:35
Alignment explanation
Indices: 49649244--49649450 Score: 255
Period size: 35 Copynumber: 6.1 Consensus size: 35
49649234 ATCCAAAAAG
* * *
49649244 AAATAATACATGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
*
49649278 AAATGAT--GTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
49649311 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
49649346 AAATAGTGCGTGAACAGGAGAGATTCCCTGCAA-G
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* *
49649380 AAATGAT--GTGAACAGGAAAGATTCCCTGCAACA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
* * * * *
49649413 GAATAATGCGTGAACAAGAAATATTCCCTGCAAGA
1 AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
49649448 AAA
1 AAA
49649451 GATAAGTGAA
Statistics
Matches: 151, Mismatches: 16, Indels: 11
0.85 0.09 0.06
Matches are distributed among these distances:
32 46 0.30
33 11 0.07
34 11 0.07
35 83 0.55
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (35 bp):
AAATAATGCGTGAACAGGAGAGATTCCCTGCAACA
Found at i:49649391 original size:67 final size:68
Alignment explanation
Indices: 49649241--49649449 Score: 257
Period size: 67 Copynumber: 3.1 Consensus size: 68
49649231 CAGATCCAAA
* *
49649241 AAGAAATAATACATGAACAGGAGAGATTCCCTGCAA-GAAAT-GAT--GTGAACAGGAGAGATTC
1 AAGAAATAAT-CGTGAACAGGAGAGATTCCCTGCAACAAAATAG-TGCGTGAACAGGAGAGATTC
49649302 CCTGC
64 CCTGC
*
49649307 AACAAAATAATGCGTGAACAGGAGAGATTCCCTGCAACAAAATAGTGCGTGAACAGGAGAGATTC
1 AA-GAAATAAT-CGTGAACAGGAGAGATTCCCTGCAACAAAATAGTGCGTGAACAGGAGAGATTC
49649372 CCTGC
64 CCTGC
* * * * * * *
49649377 AAGAAATGAT-GTGAACAGGAAAGATTCCCTGCAACAGAATAATGCGTGAACAAGAAATATTCCC
1 AAGAAATAATCGTGAACAGGAGAGATTCCCTGCAACAAAATAGTGCGTGAACAGGAGAGATTCCC
49649441 TGC
66 TGC
49649444 AAGAAA
1 AAGAAA
49649450 AGATAAGTGA
Statistics
Matches: 126, Mismatches: 12, Indels: 9
0.86 0.08 0.06
Matches are distributed among these distances:
66 2 0.02
67 88 0.70
68 5 0.04
69 7 0.06
70 24 0.19
ACGTcount: A:0.42, C:0.18, G:0.23, T:0.18
Consensus pattern (68 bp):
AAGAAATAATCGTGAACAGGAGAGATTCCCTGCAACAAAATAGTGCGTGAACAGGAGAGATTCCC
TGC
Found at i:49649420 original size:102 final size:102
Alignment explanation
Indices: 49649254--49649450 Score: 340
Period size: 102 Copynumber: 1.9 Consensus size: 102
49649244 AAATAATACA
*
49649254 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAGAGATTCCCTGCAACAAAATAATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAATAATG
* *
49649319 CGTGAACAGGAGAGATTCCCTGCAACAAAATAGTGCG
66 CGTGAACAAGAAAGATTCCCTGCAACAAAATAGTGCG
*
49649356 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACAGAATAATG
1 TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAATAATG
* *
49649421 CGTGAACAAGAAATATTCCCTGCAAGAAAA
66 CGTGAACAAGAAAGATTCCCTGCAACAAAA
49649451 GATAAGTGAA
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 89 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (102 bp):
TGAACAGGAGAGATTCCCTGCAAGAAATGATGTGAACAGGAAAGATTCCCTGCAACAAAATAATG
CGTGAACAAGAAAGATTCCCTGCAACAAAATAGTGCG
Found at i:49650742 original size:22 final size:22
Alignment explanation
Indices: 49650714--49650755 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
49650704 CAAAAGGAGA
49650714 AGCTCACTTATACCACTGGCTT
1 AGCTCACTTATACCACTGGCTT
49650736 AGCTCACTTATACCACTGGC
1 AGCTCACTTATACCACTGGC
49650756 GAAGGTTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.24, C:0.33, G:0.14, T:0.29
Consensus pattern (22 bp):
AGCTCACTTATACCACTGGCTT
Found at i:49657927 original size:70 final size:67
Alignment explanation
Indices: 49657835--49657967 Score: 194
Period size: 70 Copynumber: 1.9 Consensus size: 67
49657825 TCCGAATAAG
* * ** *
49657835 AAAAGGCAAAACTACGTTGTTTTGATAAATGTTTACCTTTTCTAAAGTTAAAAGTCAAAACCATT
1 AAAAGGAAAAACTACGTCGTTTTGATAAATGTTTA-CTCAT-T-AAGTTAAAAGGCAAAACCATT
49657900 AAGTT
63 AAGTT
49657905 AAAAGGAAAAACTACGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
1 AAAAGGAAAAACTACGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTA
49657968 TATTGTTTAT
Statistics
Matches: 58, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
67 21 0.36
68 1 0.02
69 3 0.05
70 33 0.57
ACGTcount: A:0.42, C:0.13, G:0.14, T:0.32
Consensus pattern (67 bp):
AAAAGGAAAAACTACGTCGTTTTGATAAATGTTTACTCATTAAGTTAAAAGGCAAAACCATTAAG
TT
Found at i:49660984 original size:14 final size:14
Alignment explanation
Indices: 49660965--49661004 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
49660955 TTGATTGCCA
49660965 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
49660979 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
49660993 GAAAAATGTTTT
1 GTAAAATGTTTT
49661005 ACTTTTCTGT
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:0.35, C:0.07, G:0.15, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:49663178 original size:369 final size:368
Alignment explanation
Indices: 49662459--49663860 Score: 1458
Period size: 369 Copynumber: 3.8 Consensus size: 368
49662449 CTTTGTAGGA
* * * * *
49662459 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTATTGATACGCGGCCATT-AGTGACCTCATCATAAG
1 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGA-TGACTTCATTATAAG
* * * * ** * * * *
49662523 CTGTGTCATTGACAAGCTTTTCATTGTGATCATGCCCAATATTAAAGAATTCTACGGGGAGCTTT
65 CTATGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTATGGGGAGCTTT
* * * * * *
49662588 ACTTCGTTATGATCAGTTTCAACTATTAATATGTCGCTATTGATGACCTCTTTGTAAGGT-GTGT
130 ACTTCATTATGCTCAGTTTC-ACTACTAATACGTCGCCATTGATGACCTCATTGTAA-GTCGTGT
* * * * * * *
49662652 CAACGACAAGCTTTCTGTTACCATCATGCTCAATATTAAAGGATTCTGTGGGGAGCTTCACTTCG
193 CAACGACAAACTTTCTGTTATCATCATGCCCAACATTAAGGGATTCTCTGGGGAGCTTCGCTTCG
* * * * *
49662717 TTTTGCTCAGTTTCCGCTACTGATATGCCATCACTGATGACTTCATTACAAGATGTGTCAATGAC
258 TTTTGCTCAGTTTCCGCTACTGATATGCCGTCATTGATGACTTCATTATAAGCTGTGTCAATGTC
* * * * * *
49662782 GAAGTTTCCGTTATCATCATACCCAACATTAAGAGATT-TACTGGCG
323 AAACTTTCCATCATCATCATGCCCAACATTAAGAGATTCT-CTGGAG
* * * * * * * * *
49662828 AGCTTTGCTTCTTTTTTCTCAATTTCCGCTACTGATAGGCTGCCATTGGTGACATCATTGTAAGT
1 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * ** ** * * * *
49662893 TGTGTCAAAGACAAGTTTTTGATTATCATCATGCCGAACATTAAGGGATTCTGTGGGGAGCTTTA
66 TATGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTATGGGGAGCTTTA
* *
49662958 CTTCATTATGCTCAGCTTCACTTACTAATACGTCGCCATTGATGATCTCATTGTAAGTCGTGTCA
131 CTTCATTATGCTCAGTTTCAC-TACTAATACGTCGCCATTGATGACCTCATTGTAAGTCGTGTCA
* * * *
49663023 ATGACAAACTTTTTGTTATCGTCATGCCCAACATTAAGGGATTCTCTGGGGAGCTTCGCTACGTT
195 ACGACAAACTTTCTGTTATCATCATGCCCAACATTAAGGGATTCTCTGGGGAGCTTCGCTTCGTT
* * ** * * *
49663088 TTGCTCCA-TTTCCACTATTGATACACCGTCATTCATGACTTCATTATAAGCTGCGTTAATGTCA
260 TTGCT-CAGTTTCCGCTACTGATATGCCGTCATTGATGACTTCATTATAAGCTGTGTCAATGTCA
* * *
49663152 AACTTTCCATCATCATCCTGCCCAACATTGAAG-GATTCTTTGGGG
324 AACTTTCCATCATCATCATGCCCAACATT-AAGAGATTCTCTGGAG
*
49663197 AGCTTTGCTTCATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
1 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * * * *
49663262 TATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGTATTCTCTGGAGAGCTTTG
66 TATGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTATGGGGAGCTTTA
* * * * * * * *
49663327 CTTCGTTTTGCTTAGTTTCCACTACTGATACGCCGTCATTGATGACTTCATTATAAGCTGCGT-T
131 CTTCATTATGCTCAGTTT-CACTACTAATACGTCGCCATTGATGACCTCATTGTAAG-T-CGTGT
* * * ** * * * *
49663391 -GATGTCAAACTTTCCATCATCATCCTGCCCAACATTGAA-GGATTCTTTGGGGAGCTTTGCTTC
193 CAACGACAAACTTTCTGTTATCATCATGCCCAACATT-AAGGGATTCTCTGGGGAGCTTCGCTTC
* * *
49663454 ATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGCTATGTCAATGT
257 GTTTTGCTCAGTTTCCGCTACTGATATGCCGTCATTGATGACTTCATTATAAGCTGTGTCAATGT
49663519 CAAACTTTCCATCATCATCATGCCCAACATTAA-AGTATTCTCTGGAG
322 CAAACTTTCCATCATCATCATGCCCAACATTAAGAG-ATTCTCTGGAG
* *
49663566 AGCTTTGCTTCGTTTTGCTTAGTTTCTGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
1 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * *
49663631 TATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTTTGGGGAGCTTTG
66 TATGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTATGGGGAGCTTTA
* * *
49663696 CTTCGA-TATCCTCAGGTTCAGCTACTAATACGTCGCCATTGATGACCTCATTGTAAGTTGTGTC
131 CTTC-ATTATGCTCAGTTTCA-CTACTAATACGTCGCCATTGATGACCTCATTGTAAGTCGTGTC
* * * * * * * * * * **
49663760 AACGAC-AAGTTTATTTTTATCGTAATGTCCAACATCAAGGGATTTTATGGAGAGCTTTACTTCG
194 AACGACAAACTTT-CTGTTATCATCATGCCCAACATTAAGGGATTCTCTGGGGAGCTTCGCTTCG
** * * * *
49663824 TTCGGCTTAGTTTCCGCTATTGATACGCCGCCATTGA
258 TTTTGCTCAGTTTCCGCTACTGATATGCCGTCATTGA
49663861 CCTCGTTATA
Statistics
Matches: 855, Mismatches: 159, Indels: 38
0.81 0.15 0.04
Matches are distributed among these distances:
367 2 0.00
368 20 0.02
369 817 0.96
370 13 0.02
371 3 0.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (368 bp):
AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
TATGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTATGGGGAGCTTTA
CTTCATTATGCTCAGTTTCACTACTAATACGTCGCCATTGATGACCTCATTGTAAGTCGTGTCAA
CGACAAACTTTCTGTTATCATCATGCCCAACATTAAGGGATTCTCTGGGGAGCTTCGCTTCGTTT
TGCTCAGTTTCCGCTACTGATATGCCGTCATTGATGACTTCATTATAAGCTGTGTCAATGTCAAA
CTTTCCATCATCATCATGCCCAACATTAAGAGATTCTCTGGAG
Found at i:49663794 original size:123 final size:123
Alignment explanation
Indices: 49662459--49663767 Score: 1261
Period size: 123 Copynumber: 10.6 Consensus size: 123
49662449 CTTTGTAGGA
* * * * * *
49662459 AGCTTTGCTTCGTTTTGCTCAGTTTCCGCTATTGATACGCGGCCATT-AGTGACCTCATCATAAG
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGA-TGACTTCATTATAAG
* * * ** * * *
49662523 CTGTGTCATTGACAAGCTTTTCATTGTGATCATGCCCAATATTAAAGAATTCTAC-GGGG
65 CTGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCT-CTGGGG
* * * * * * * * * * * *
49662582 AGCTTTACTTCGTTATGATCAGTTTCAACTATTAATATGTCGCTATTGATGACCTCTTTGTAAGG
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * ** * * * * *
49662647 TGTGTCAACGACAAGCTTTCTGTTACCATCATGCTCAATATTAAAGGATTCTGTGGGG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
** * ** * * *
49662705 AGCTTCACTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCATCACTGATGACTTCATTACAAGA
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * * * * *
49662770 TGTGTCAATGACGAAGTTTCCGTTATCATCATACCCAACATT-AAGAGATT-TACTGGCG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAG-GATTCT-CTGGGG
* * * * * * * * * *
49662828 AGCTTTGCTTCTTTTTTCTCAATTTCCGCTACTGATAGGCTGCCATTGGTGACATCATTGTAAGT
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* ** ** * * * *
49662893 TGTGTCAAAGACAAGTTTTTGATTATCATCATGCCGAACATTAAGGGATTCTGTGGGG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* * * * * * * *
49662951 AGCTTTACTTCATTATGCTCAGCTTCA-CTTACTAATACGTCGCCATTGATGA-TCTCATTGTAA
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGC-TACTGATATGCCGCCATTGATGACT-TCATTATAA
*** * * *
49663014 G-TCGTGTCAATGACAAACTTTTTGTTATCGTCATGCCCAACATTAAGGGATTCTCTGGGG
64 GCT-GTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* * * ** * *
49663074 AGCTTCGCTACGTTTTGCTCCA-TTTCCA-CTATTGATACACCGTCATTCATGACTTCATTATAA
1 AGCTTTGCTTCGTTTTGCT-CAGTTT-CAGCTACTGATATGCCGCCATTGATGACTTCATTATAA
* * * * * *
49663137 GCTGCGTTAATGTCAAACTTTCCATCATCATCCTGCCCAACATTGAAGGATTCTTTGGGG
64 GCTGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* *
49663197 AGCTTTGCTTCATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * * *
49663262 TATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGTATTCTCTGGAG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* * *
49663320 AGCTTTGCTTCGTTTTGCTTAGTTTCCA-CTACTGATACGCCGTCATTGATGACTTCATTATAAG
1 AGCTTTGCTTCGTTTTGCTCAGTTT-CAGCTACTGATATGCCGCCATTGATGACTTCATTATAAG
* ** * * * *
49663384 CTGCGTTGATGTCAAACTTTCCATCATCATCCTGCCCAACATTGAAGGATTCTTTGGGG
65 CTGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* *
49663443 AGCTTTGCTTCATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * * *
49663508 TATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGTATTCTCTGGAG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* *
49663566 AGCTTTGCTTCGTTTTGCTTAGTTTCTGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
* * *
49663631 TATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTTTGGGG
66 TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
* * * * * * * * * *
49663689 AGCTTTGCTTCGATATCCTCAGGTTCAGCTACTAATACGTCGCCATTGATGACCTCATTGTAAGT
1 AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
*
49663754 TGTGTCAACGACAA
66 TGTGTCAATGACAA
49663768 GTTTATTTTT
Statistics
Matches: 977, Mismatches: 192, Indels: 34
0.81 0.16 0.03
Matches are distributed among these distances:
122 10 0.01
123 955 0.98
124 12 0.01
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (123 bp):
AGCTTTGCTTCGTTTTGCTCAGTTTCAGCTACTGATATGCCGCCATTGATGACTTCATTATAAGC
TGTGTCAATGACAAACTTTCCATCATCATCATGCCCAACATTAAAGGATTCTCTGGGG
Found at i:49664044 original size:120 final size:120
Alignment explanation
Indices: 49662631--49664082 Score: 398
Period size: 123 Copynumber: 11.9 Consensus size: 120
49662621 TCGCTATTGA
* * * * * * *
49662631 TGACCTCTTTGTAAGGTGTGTCAACGACAAGCTTTCTGTTACCATCATG-CTCAATATTAAAGGA
1 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCT-AACATTAAGGGA
* * ** * ** *
49662695 TTCTGTGGGGAGCTTCACTTCGTTTTGCTCAGTTTCCGCTACTGATATGCCATCACT
65 TTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* ** * * ** * * * *
49662752 GATGACTTCATTACAAGATGTGTCAATGACGAAG-TTTCCGTTATCATCATACCCAACATTAAGA
1 --TGACCTCATTGTAAGTTGTGTCAACGAC-AAGCTTTTTGTTATCGTCATGCCTAACATTAAGG
* * * * *** * * ** **
49662816 GATT-TACTGGCGAGCTTTGCTTCTTTTTTCTCAATTTCCGCTACTGATAGGCTGCCATT
63 GATTCT-GTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * * *
49662875 GGTGACATCATTGTAAGTTGTGTCAAAGACAAG-TTTTTGATTATCATCATGCCGAACATTAAGG
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTG-TTATCGTCATGCCTAACATTAAGG
* * ** * * * * ** *
49662939 GATTCTGTGGGGAGCTTTACTTCATTATGCTCAGCTTCAC-TTACTAATACGTCGCCATT
63 GATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTC-CGCTATTGATACACCACCA-T
* * * * *
49662998 GATGATCTCATTGTAAGTCGTGTCAATGACAAACTTTTTGTTATCGTCATGCCCAACATTAAGGG
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * ** * ** * **
49663063 ATTCTCTGGGGAGCTTCGCTACGTTTTGCTCCA-TTTCCACTATTGATACACCGTCATT
64 ATTCTGTGGAGAGCTTTACTTCGTTCGGCT-CAGTTTCCGCTATTGATACACCACCA-T
* * * * * * * * *** * * * *
49663121 CATGACTTCATTATAAGCTGCGTTAATGTCAAACTTTCCATCATCATCCTGCCCAACATTGAA-G
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATT-AAGG
* * * * ** * ** *
49663185 GATTCTTTGGGGAGCTTTGCTTCATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATT
63 GATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * * * * * * *** * * * * *
49663244 GATGACTTCATTATAAGCTATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGT
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * ** * * * * **
49663309 ATTCTCTGGAGAGCTTTGCTTCGTTTTGCTTAGTTTCCACTACTGATACGCCGTCATT
64 ATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * * * ** * * * *** * * * *
49663367 GATGACTTCATTATAAGCTGCGTTGATGTCAAACTTTCCATCATCATCCTGCCCAACATTGAA-G
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATT-AAGG
* * * * ** * ** *
49663431 GATTCTTTGGGGAGCTTTGCTTCATTTTGCTCAGTTTCCGCTACTGATATGCCGCCATT
63 GATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * * * * * * *** * * * * *
49663490 GATGACTTCATTATAAGCTATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGT
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * ** * * * ** *
49663555 ATTCTCTGGAGAGCTTTGCTTCGTTTTGCTTAGTTTCTGCTACTGATATGCCGCCATT
64 ATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * * * * * * *** * * * *
49663613 GATGACTTCATTATAAGCTATGTCAATGTCAAACTTTCCATCATCATCATGCCCAACATTAAAGG
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * * * * * * ** *
49663678 ATTCTTTGGGGAGCTTTGCTTCGATATC--CTCAGGTTCAGCTACTAATACGTCGCCATT
64 ATTCTGTGGAGAGCTTTACTTCG-T-TCGGCTCAGTTTCCGCTATTGATACACCACCA-T
* * *
49663736 GATGACCTCATTGTAAGTTGTGTCAACGACAAG-TTTATTTTTATCGTAATGTCC-AACATCAAG
1 --TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTT-TTGTTATCGTCATG-CCTAACATTAAG
* * * * *
49663799 GGATTTTATGGAGAGCTTTACTTCGTTCGGCTTAGTTTCCGCTATTGATACGCCGCCAT
62 GGATTCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCAT
* * * * * * **
49663858 TGACCTCGTTATAAACTT-T-TCCGATGACGAGCTTTTTGTTATCGTCATGCCTAACATTAACCG
1 TGACCTCATTGT-AAGTTGTGT-CAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGG
* * * * *
49663921 ATTCTGTGGAGGGTTTTGCTTTGTTCCGG-TCAG-TTCTCGCTATTGATACACCACCGT
64 ATTCTGTGGAGAGCTTTACTTCGTT-CGGCTCAGTTTC-CGCTATTGATACACCACCAT
** *
49663978 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAATGTTAGGGGAT
1 TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGGAT
* * ** *
49664043 TCTGTGGGGAGCTTTGCTTCGTTATGCTCAGTTTCAGCTA
66 TCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTA
49664083 CTGGCACATC
Statistics
Matches: 1094, Mismatches: 205, Indels: 63
0.80 0.15 0.05
Matches are distributed among these distances:
119 11 0.01
120 151 0.14
121 16 0.01
122 20 0.02
123 874 0.80
124 21 0.02
125 1 0.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (120 bp):
TGACCTCATTGTAAGTTGTGTCAACGACAAGCTTTTTGTTATCGTCATGCCTAACATTAAGGGAT
TCTGTGGAGAGCTTTACTTCGTTCGGCTCAGTTTCCGCTATTGATACACCACCAT
Found at i:49673813 original size:30 final size:33
Alignment explanation
Indices: 49673777--49673836 Score: 90
Period size: 30 Copynumber: 1.9 Consensus size: 33
49673767 TTTTATACTT
49673777 AAACTTTGATT-TGGTGC-AAT-TATACATATG
1 AAACTTTGATTATGGTGCAAATATATACATATG
*
49673807 AAACTTTGATTATGGTTCAAATATATACAT
1 AAACTTTGATTATGGTGCAAATATATACAT
49673837 GAACATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 11 0.42
31 5 0.19
32 3 0.12
33 7 0.27
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.40
Consensus pattern (33 bp):
AAACTTTGATTATGGTGCAAATATATACATATG
Found at i:49674158 original size:16 final size:16
Alignment explanation
Indices: 49674133--49674170 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
49674123 CTACCATACT
*
49674133 TTTTTTTTATTTTTCA
1 TTTTTATTATTTTTCA
49674149 TTTTTATTATTTTTCA
1 TTTTTATTATTTTTCA
49674165 TTTTTA
1 TTTTTA
49674171 ATAAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTTTATTATTTTTCA
Found at i:49675988 original size:36 final size:39
Alignment explanation
Indices: 49675928--49676001 Score: 109
Period size: 36 Copynumber: 2.0 Consensus size: 39
49675918 TAAACACCAA
*
49675928 AAAAATTATTTTAAAAATAAAAAGAATAAAAAGTATTTT
1 AAAAATTATTTTAAAAATAAAAAGAATAAAAAATATTTT
*
49675967 AAAAA-TATTTT-AAAAT-TAAAGAATAAAAAATATTT
1 AAAAATTATTTTAAAAATAAAAAGAATAAAAAATATTT
49676002 ATTTATTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
36 17 0.52
37 5 0.15
38 6 0.18
39 5 0.15
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (39 bp):
AAAAATTATTTTAAAAATAAAAAGAATAAAAAATATTTT
Found at i:49676562 original size:229 final size:229
Alignment explanation
Indices: 49676148--49676698 Score: 935
Period size: 229 Copynumber: 2.4 Consensus size: 229
49676138 GAACACTTCT
* *
49676148 AGTTTAGGGTTTTTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAAGGTTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
*
49676213 TATTTTTTAA-TAAAAATTAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAAAT
66 TATTTTTTAAGAAAAAATTAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAAAT
* *
49676277 TTAAAAATCGGATTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTGTTTTTAAGTTAAGGG
131 TTAAAAATCAGATTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTATTTTTAAGTTAAGGG
49676342 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAG
196 TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAG
49676376 AGTTTAAGGTTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
1 AGTTTAAGGTTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
* *
49676441 TATTTTCTAAGAAAAAATTAATTAAATTAGGGTTTAGGGTTACTTGAGTAATTTAATTAAAAAAT
66 TATTTTTTAAGAAAAAATTAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAAA-
* *
49676506 TTTAAAAATTAGTTTAGGGTTAGGGTTAGGGTTTTTGTTA-GGTTTTGGTATTTTTAAGTTAAGG
130 TTTAAAAATCAGATTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTATTTTTAAGTTAAGG
* *
49676570 GTTTTTAAGGAAAAATCAAATAAGTTAGGGTTTTG
195 GTTTTTAAGGAAAAATCAAATAAATTAGGGTTTAG
* * *
49676605 AGTTTAAGGTTTGTCAATTAAATTATTTACAAATTTTTCAAAATTAGATTAGTTTTCGTGTTTAT
1 AGTTTAAGGTTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
* *
49676670 TATTTTTTAAGAAAATATGAATTAAATTA
66 TATTTTTTAAGAAAAAATTAATTAAATTA
49676699 TAGGGTTTTG
Statistics
Matches: 304, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
228 72 0.24
229 195 0.64
230 37 0.12
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.45
Consensus pattern (229 bp):
AGTTTAAGGTTTGTCAATTAAATTATTTAAAAAATTTTCAAAATTGGATTAGTTTTCGTGTTTAT
TATTTTTTAAGAAAAAATTAATTAAATTAGGGTTTAAGGTTACTTGAGTAATTTAATTAAAAAAT
TTAAAAATCAGATTAGGGTTAGGGTTAGGGTTTTTGTTAGGGTTTTGGTATTTTTAAGTTAAGGG
TTTTTAAGGAAAAATCAAATAAATTAGGGTTTAG
Found at i:49678228 original size:21 final size:21
Alignment explanation
Indices: 49678204--49678247 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
49678194 TCCAGCTTCT
* * *
49678204 GGCGGGGGTTGTGGTTGCTCC
1 GGCGGGGATTCTGGTTCCTCC
49678225 GGCGGGGATTCTGGTTCCTCC
1 GGCGGGGATTCTGGTTCCTCC
49678246 GG
1 GG
49678248 TAGGGTATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.02, C:0.23, G:0.48, T:0.27
Consensus pattern (21 bp):
GGCGGGGATTCTGGTTCCTCC
Found at i:49680400 original size:11 final size:11
Alignment explanation
Indices: 49680381--49680465 Score: 65
Period size: 11 Copynumber: 8.0 Consensus size: 11
49680371 GGATTTAAGA
49680381 GAAATTTGAGAG
1 GAAA-TTGAGAG
49680393 GAAATTGAGAG
1 GAAATTGAGAG
* *
49680404 CAAATTGAGAT
1 GAAATTGAGAG
*
49680415 TAAA-T-AGA-
1 GAAATTGAGAG
*
49680423 G-ATTTGAGA-
1 GAAATTGAGAG
49680432 GAAATTTG-GAAG
1 GAAA-TTGAG-AG
49680444 GAAATTGAGAG
1 GAAATTGAGAG
49680455 GAAATTGAGAG
1 GAAATTGAGAG
49680466 AATAATAGAG
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 7 0.12
10 3 0.05
11 39 0.65
12 9 0.15
ACGTcount: A:0.45, C:0.01, G:0.31, T:0.24
Consensus pattern (11 bp):
GAAATTGAGAG
Found at i:49680427 original size:51 final size:51
Alignment explanation
Indices: 49680365--49680464 Score: 157
Period size: 51 Copynumber: 2.0 Consensus size: 51
49680355 AATAATTAAA
*
49680365 AAATAGGGATTTAAGAGAAATTT-GAGAGGAAATTGAGAGCAAATTGAGATT
1 AAATAGAGATTTAAGAGAAATTTGGA-AGGAAATTGAGAGCAAATTGAGATT
* *
49680416 AAATAGAGATTTGAGAGAAATTTGGAAGGAAATTGAGAGGAAATTGAGA
1 AAATAGAGATTTAAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGAGA
49680465 GAATAATAGA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
51 43 0.96
52 2 0.04
ACGTcount: A:0.46, C:0.01, G:0.29, T:0.24
Consensus pattern (51 bp):
AAATAGAGATTTAAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGAGATT
Found at i:49682037 original size:16 final size:16
Alignment explanation
Indices: 49682016--49682051 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
49682006 TTTGGTTCGC
*
49682016 TGTATTGGATTAGAGG
1 TGTATTGGATTAGACG
49682032 TGTATTGGATTAGACG
1 TGTATTGGATTAGACG
49682048 TGTA
1 TGTA
49682052 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGACG
Found at i:49682403 original size:16 final size:16
Alignment explanation
Indices: 49682366--49682407 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
49682356 NNNNNCATAT
*
49682366 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
49682382 TT-AAATATATTATAA
1 TTAAAATATATTATAA
49682397 TTAAAATATAT
1 TTAAAATATAT
49682408 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:49682414 original size:14 final size:15
Alignment explanation
Indices: 49682375--49682416 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
49682365 TTTAAACATA
*
49682375 ATTATTATTAAATAT
1 ATTATAATTAAATAT
49682390 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
49682404 A-TATAATTTAATA
1 ATTATAATTAAATA
49682417 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:49682534 original size:14 final size:15
Alignment explanation
Indices: 49682485--49682536 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
49682475 GTAAAATATA
49682485 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
49682500 TATTAAATATATTAT
1 AATTAAATATATTAT
49682515 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
49682528 AATTTAATA
1 AATTAAATA
49682537 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:49682587 original size:120 final size:121
Alignment explanation
Indices: 49682364--49682661 Score: 487
Period size: 120 Copynumber: 2.5 Consensus size: 121
49682354 NNNNNNNCAT
*
49682364 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
* *
49682429 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATATTGTAAAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AA
49682486 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
*
49682549 ATTAATATTCTTATATGAATTTACTCAAATCATTATATATGATACTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
* * *
49682605 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATGATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
49682662 TAAAATAATT
Statistics
Matches: 167, Mismatches: 6, Indels: 8
0.92 0.03 0.04
Matches are distributed among these distances:
119 7 0.04
120 155 0.93
121 4 0.02
122 1 0.01
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAATGAAA
Found at i:49682748 original size:24 final size:25
Alignment explanation
Indices: 49682702--49682749 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
49682692 TATGAATTTG
49682702 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
49682728 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
49682750 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:49682753 original size:92 final size:92
Alignment explanation
Indices: 49682657--49682866 Score: 232
Period size: 92 Copynumber: 2.3 Consensus size: 92
49682647 TGATTTAATA
* * *
49682657 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
49682719 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
49682749 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
49682814 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* *
49682839 ATAATTTCATAAAATTCTTAATAATAAA
1 A-AATTTCAAAAAATTCATAATAATAAA
49682867 ATGTTCTTAT
Statistics
Matches: 102, Mismatches: 12, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
90 2 0.02
91 30 0.29
92 62 0.61
93 8 0.08
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:49682874 original size:92 final size:92
Alignment explanation
Indices: 49682692--49682885 Score: 268
Period size: 92 Copynumber: 2.1 Consensus size: 92
49682682 AATTATATTT
* * * *
49682692 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATTAATATTAAATTTCA
1 TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
* *
49682757 TAAAATTCTTGATAATAAATTTTCTTA
66 TAAAATTCTTAATAATAAATGTTCTTA
*
49682784 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAGTG-ATA-TATAATTT
1 TATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAATGAATATTA-AATTT
49682846 CATAAAATTCTTAATAATAAAATGTTCTTA
64 CATAAAATTCTTAATAAT-AAATGTTCTTA
*
49682876 TATCAATTTA
1 TATGAATTTA
49682886 GTAAAATCAA
Statistics
Matches: 91, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
90 2 0.02
91 25 0.27
92 61 0.67
93 3 0.03
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAATGAATATTAAATTTCA
TAAAATTCTTAATAATAAATGTTCTTA
Found at i:49686408 original size:48 final size:47
Alignment explanation
Indices: 49686375--49686557 Score: 312
Period size: 48 Copynumber: 3.8 Consensus size: 47
49686365 ATTTATTGAT
*
49686375 TTTTAATAAAATATTAAAGTCCTTATTTTAAATATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGT-CTTA
49686423 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGT-CTTA
*
49686471 TTTTAATAAAATATTAAAGTCATTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGT-CTTA
*
49686519 TTTTAATGAAATATTAAAGTCCTTATTTTAATTATTGAT
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGAT
49686558 GTAATTATTT
Statistics
Matches: 131, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 131 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (47 bp):
TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCTTA
Found at i:49686415 original size:25 final size:25
Alignment explanation
Indices: 49686387--49686557 Score: 155
Period size: 25 Copynumber: 7.1 Consensus size: 25
49686377 TTAATAAAAT
49686387 ATTAAAGTCCTTATTTTAAATATTG
1 ATTAAAGTCCTTATTTTAAATATTG
* *
49686412 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAA-ATATTG
*
49686435 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAAATATTG
* *
49686460 ATT--AGTCCTTATTTTAATAAAAT-
1 ATTAAAGTCCTTATTTTAA-ATATTG
* *
49686483 ATTAAAGTCATTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAAATATTG
*
49686508 ATT--AGTCCTTATTTT-AATGAAAT-
1 ATTAAAGTCCTTATTTTAAAT--ATTG
*
49686531 ATTAAAGTCCTTATTTTAATTATTG
1 ATTAAAGTCCTTATTTTAAATATTG
49686556 AT
1 AT
49686558 GTAATTATTT
Statistics
Matches: 115, Mismatches: 17, Indels: 28
0.72 0.11 0.17
Matches are distributed among these distances:
22 2 0.02
23 48 0.42
24 13 0.11
25 50 0.43
26 2 0.02
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.50
Consensus pattern (25 bp):
ATTAAAGTCCTTATTTTAAATATTG
Found at i:49686422 original size:23 final size:23
Alignment explanation
Indices: 49686392--49686524 Score: 135
Period size: 23 Copynumber: 5.6 Consensus size: 23
49686382 AAAATATTAA
49686392 AGTCCTTATTTTAAATATTGATT
1 AGTCCTTATTTTAAATATTGATT
* *
49686415 AGTCCTTATTTTAATAAAAT-ATT
1 AGTCCTTATTTTAA-ATATTGATT
*
49686438 AAAGTCCTTATTTTAATTATTGATT
1 --AGTCCTTATTTTAAATATTGATT
* *
49686463 AGTCCTTATTTTAATAAAAT-ATT
1 AGTCCTTATTTTAA-ATATTGATT
* *
49686486 AAAGTCATTATTTTAATTATTGATT
1 --AGTCCTTATTTTAAATATTGATT
49686511 AGTCCTTATTTTAA
1 AGTCCTTATTTTAA
49686525 TGAAATATTA
Statistics
Matches: 89, Mismatches: 13, Indels: 16
0.75 0.11 0.14
Matches are distributed among these distances:
23 47 0.53
24 9 0.10
25 33 0.37
ACGTcount: A:0.35, C:0.08, G:0.07, T:0.50
Consensus pattern (23 bp):
AGTCCTTATTTTAAATATTGATT
Found at i:49687748 original size:23 final size:23
Alignment explanation
Indices: 49687722--49687797 Score: 143
Period size: 23 Copynumber: 3.3 Consensus size: 23
49687712 TAAACAAATT
49687722 CAATTTCCAGCAGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
*
49687745 CAATTTCCAGCAGACAATCATAA
1 CAATTTCCAGCAGACAATCAAAA
49687768 CAATTTCCAGCAGACAATCAAAA
1 CAATTTCCAGCAGACAATCAAAA
49687791 CAATTTC
1 CAATTTC
49687798 AGAACAAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 51 1.00
ACGTcount: A:0.45, C:0.26, G:0.08, T:0.21
Consensus pattern (23 bp):
CAATTTCCAGCAGACAATCAAAA
Found at i:49687825 original size:22 final size:21
Alignment explanation
Indices: 49687783--49687828 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
49687773 TCCAGCAGAC
* *
49687783 AATCAAAACAATTTCAGAACA
1 AATCAAAACAATATCAAAACA
49687804 AATCAAGAACAATATCAAAACA
1 AATCAA-AACAATATCAAAACA
49687826 AAT
1 AAT
49687829 GCAACAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.61, C:0.17, G:0.04, T:0.17
Consensus pattern (21 bp):
AATCAAAACAATATCAAAACA
Found at i:49688762 original size:32 final size:34
Alignment explanation
Indices: 49688721--49688784 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
49688711 CTTTTCGATT
* *
49688721 TTCTTTTAA-GAGAATGGTTTTATAAT-GTGACA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
49688753 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
1 TTCTTTTAAGGAAAATAGTTTTATAATAGTGA
49688785 AATTATTAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 9 0.32
33 15 0.54
34 4 0.14
ACGTcount: A:0.34, C:0.05, G:0.17, T:0.44
Consensus pattern (34 bp):
TTCTTTTAAGGAAAATAGTTTTATAATAGTGACA
Found at i:49689134 original size:17 final size:17
Alignment explanation
Indices: 49689112--49689147 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
49689102 ACTCAAAGGG
*
49689112 AAATAAACAGCAATAGA
1 AAATAAACAACAATAGA
49689129 AAATAAACAACAATAGA
1 AAATAAACAACAATAGA
49689146 AA
1 AA
49689148 CATGCAATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.69, C:0.11, G:0.08, T:0.11
Consensus pattern (17 bp):
AAATAAACAACAATAGA
Found at i:49689884 original size:14 final size:14
Alignment explanation
Indices: 49689865--49689896 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
49689855 TATTGGCTAT
49689865 GCCAATACACCAAA
1 GCCAATACACCAAA
49689879 GCCAATACACCAAA
1 GCCAATACACCAAA
49689893 -CCAA
1 GCCAA
49689897 ACATGCTCTA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.50, C:0.38, G:0.06, T:0.06
Consensus pattern (14 bp):
GCCAATACACCAAA
Found at i:49694530 original size:43 final size:42
Alignment explanation
Indices: 49694479--49694644 Score: 215
Period size: 43 Copynumber: 3.9 Consensus size: 42
49694469 AAAAAGTGCT
* *
49694479 GCTAAAGGTCATGTTCTTTAGCGGTGTTTGTGAGGAAAGCACC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTG-GGAAAGCGCC
*
49694522 GCTAAAGGTCATGTTCTTTAGCGGCATTTGTTGGGAAAGCGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTG-TGGGAAAGCGCC
* * * *
49694565 CCTAAAGGTCATGCTCTATAGCGGCGTTAGTGTGGAAAGCGCC
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTG-GGAAAGCGCC
* * *
49694608 GCTAAATGCCATGTTCTTTAGCAGCGTTTGTGGGAAA
1 GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAA
49694645 AACGTCGCAA
Statistics
Matches: 106, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
42 7 0.07
43 97 0.92
44 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.30, T:0.29
Consensus pattern (42 bp):
GCTAAAGGTCATGTTCTTTAGCGGCGTTTGTGGGAAAGCGCC
Found at i:49698866 original size:6 final size:6
Alignment explanation
Indices: 49698855--49698882 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
49698845 AGGCCACTAT
49698855 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
1 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
49698883 TGGTCACGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
GTGAAA
Found at i:49699012 original size:51 final size:49
Alignment explanation
Indices: 49698886--49699076 Score: 201
Period size: 51 Copynumber: 3.8 Consensus size: 49
49698876 AAAGTGATGG
*
49698886 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A--TGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTGA
* * *
49698932 T-AGGTCGCATGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
1 TCACGT-G--TGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAG-TT-GA
* *
49698985 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGT--TGA
* * * *
49699036 TCACATGTGTAGTACTATGTGCAAGCTACTATGTGAACCGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGG
49699077 TATAATTAAT
Statistics
Matches: 120, Mismatches: 14, Indels: 17
0.79 0.09 0.11
Matches are distributed among these distances:
45 3 0.03
46 2 0.02
48 32 0.27
49 1 0.01
50 1 0.01
51 72 0.60
52 2 0.02
53 4 0.03
54 3 0.03
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (49 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCGGATAGTTGA
Found at i:49699013 original size:99 final size:101
Alignment explanation
Indices: 49698886--49699068 Score: 291
Period size: 99 Copynumber: 1.8 Consensus size: 101
49698876 AAAGTGATGG
*
49698886 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGA-A-TGATAGGTCGCA-TGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGAT-GGTCACAGTGTAGTA
*
49698948 CTATGTGCAGGCTACTATGCGTACCGGATAGCTTCGA
65 CTATGTGCAAGCTACTATGCGTACCGGATAGCTTCGA
* *
49698985 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGGTCACATGTGTAGTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACA-GTGTAGTA
49699050 CTATGTGCAAGCTACTATG
65 CTATGTGCAAGCTACTATG
49699069 TGAACCGGTA
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
99 40 0.53
100 7 0.09
101 4 0.05
102 25 0.33
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.30
Consensus pattern (101 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTACCAGATAGTGATGGTCACAGTGTAGTAC
TATGTGCAAGCTACTATGCGTACCGGATAGCTTCGA
Found at i:49699070 original size:26 final size:26
Alignment explanation
Indices: 49698990--49699070 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
49698980 TTCGATCACG
*
49698990 TGTGTAGTACTATGTGCAGGCTACTA
1 TGTGTAGTACTATGTGCAAGCTACTA
* * * *
49699016 CGTGTA-T-CGGATAGTG-ATGGTCAC-A
1 TGTGTAGTAC-TAT-GTGCAAGCT-ACTA
49699041 TGTGTAGTACTATGTGCAAGCTACTA
1 TGTGTAGTACTATGTGCAAGCTACTA
49699067 TGTG
1 TGTG
49699071 AACCGGTATA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
24 1 0.03
25 17 0.43
26 21 0.52
27 1 0.03
ACGTcount: A:0.23, C:0.15, G:0.28, T:0.33
Consensus pattern (26 bp):
TGTGTAGTACTATGTGCAAGCTACTA
Found at i:49699272 original size:16 final size:16
Alignment explanation
Indices: 49699251--49699282 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49699241 TGATTGAAAG
*
49699251 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
49699267 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
49699283 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:49704068 original size:6 final size:6
Alignment explanation
Indices: 49704057--49704084 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
49704047 AGGCTACTAT
49704057 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
1 GTGAAA GTGAAA GTGAAA GTGAAA GTGA
49704085 TGGTCACGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.36, T:0.18
Consensus pattern (6 bp):
GTGAAA
Found at i:49704143 original size:51 final size:50
Alignment explanation
Indices: 49704088--49704222 Score: 173
Period size: 51 Copynumber: 2.7 Consensus size: 50
49704078 AAAGTGATGG
49704088 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * *
49704139 TCACGTGTGTAATACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGT-ATGA
* *
49704190 TCACATGTGTAGTACTATGTGCAAGCTACTATG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTATG
49704223 TGAACCGGTA
Statistics
Matches: 73, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
50 1 0.01
51 71 0.97
52 1 0.01
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.31
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGTATGA
Found at i:49704469 original size:16 final size:16
Alignment explanation
Indices: 49704448--49704479 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49704438 TGATTGAAAG
*
49704448 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
49704464 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
49704480 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:49710270 original size:25 final size:25
Alignment explanation
Indices: 49710141--49710306 Score: 96
Period size: 25 Copynumber: 6.7 Consensus size: 25
49710131 GCCATGTAAT
** * *
49710141 GGGAAGCTCATTCGAGTTATATAAC
1 GGGAAGCTCATAAGAGCTATATATC
49710166 GGGAAGCTCATAAGAGCTGA-A-ATC
1 GGGAAGCTCATAAGAGCT-ATATATC
* * *
49710190 GGGAAGTTCA-AGCGAGCCA-ATATC
1 GGGAAGCTCATA-AGAGCTATATATC
* **
49710214 GAGAAGCTTCGGAA-AGCTAT-TAATC
1 GGGAAGC-TCATAAGAGCTATAT-ATC
* *
49710239 AGAAAGCTCATAAGAGCTAGT-TATC
1 GGGAAGCTCATAAGAGCTA-TATATC
*
49710264 GGGAAGCTC-TGAAGAGCCATATATC
1 GGGAAGCTCAT-AAGAGCTATATATC
*
49710289 GGGACGCTCATAAGAGCT
1 GGGAAGCTCATAAGAGCT
49710307 GCGGTGTGTC
Statistics
Matches: 107, Mismatches: 22, Indels: 24
0.70 0.14 0.16
Matches are distributed among these distances:
23 3 0.03
24 34 0.32
25 65 0.61
26 5 0.05
ACGTcount: A:0.34, C:0.18, G:0.27, T:0.21
Consensus pattern (25 bp):
GGGAAGCTCATAAGAGCTATATATC
Found at i:49712796 original size:13 final size:13
Alignment explanation
Indices: 49712778--49712803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
49712768 ATATTACATA
49712778 GTCAAATATTTTG
1 GTCAAATATTTTG
49712791 GTCAAATATTTTG
1 GTCAAATATTTTG
49712804 CTATCAACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.15, T:0.46
Consensus pattern (13 bp):
GTCAAATATTTTG
Found at i:49715374 original size:63 final size:63
Alignment explanation
Indices: 49715307--49715449 Score: 151
Period size: 63 Copynumber: 2.3 Consensus size: 63
49715297 GCACCAAAAT
* * *** * *
49715307 AGTGAGTTACACGGTTTGGACACATGGCCGTGTCCCAAGCCCGTGTGACTCTAATCCATAACC
1 AGTGAGTTACACGGTCTAGACACACCCCCGTGTCCCAAGCCCATGTGACTCTAATCCATAAAC
* * * * * * * *
49715370 AGTGAATCACATGGTCTAGACACGCCCCCGTGTCCCTAGCCCATGTGCCTCTAATTCATAAAT
1 AGTGAGTTACACGGTCTAGACACACCCCCGTGTCCCAAGCCCATGTGACTCTAATCCATAAAC
49715433 AGTGAGTTACACGGTCT
1 AGTGAGTTACACGGTCT
49715450 GCCACACGAC
Statistics
Matches: 62, Mismatches: 18, Indels: 0
0.77 0.22 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.25
Consensus pattern (63 bp):
AGTGAGTTACACGGTCTAGACACACCCCCGTGTCCCAAGCCCATGTGACTCTAATCCATAAAC
Found at i:49716914 original size:39 final size:39
Alignment explanation
Indices: 49716760--49716935 Score: 176
Period size: 39 Copynumber: 4.5 Consensus size: 39
49716750 ATTCACTTTT
* * * * *
49716760 AAGCATATATCACATTACACATATAATCACATAGCATTTT
1 AAGCATATATCGCAATACTCATATAATCACATAACA-TTC
* * * *
49716800 AA-CATATATCACAATACTCATATACTTACATAACGTTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* * * *
49716838 AAGCACATAT-GTAATACTCATATATTCACGTAACATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* *
49716876 AAGCATATATCGCAATATTCATATAATCACATATCATTC
1 AAGCATATATCGCAATACTCATATAATCACATAACATTC
* *
49716915 AAGTATATGTCGCAATACTCA
1 AAGCATATATCGCAATACTCA
49716936 AAAACATGTT
Statistics
Matches: 111, Mismatches: 23, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
38 35 0.32
39 74 0.67
40 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (39 bp):
AAGCATATATCGCAATACTCATATAATCACATAACATTC
Found at i:49731799 original size:6 final size:6
Alignment explanation
Indices: 49731785--49731824 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
49731775 TGGTTTGCAA
* *
49731785 AAATGG AAATCG AAATCG AAATGG AAATGG AAATGG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAATGG AAAT
49731825 TATTGCAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.53, C:0.05, G:0.25, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:49731999 original size:27 final size:27
Alignment explanation
Indices: 49731968--49732023 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
49731958 TATTTTCTCG
49731968 AAATTTTACCAAGGGTAAAATTC-TCAA
1 AAATTTTACCAAGGGTAAAA-TCATCAA
*
49731995 AAATTTTACCGAGGGTAAAATCATCAA
1 AAATTTTACCAAGGGTAAAATCATCAA
49732022 AA
1 AA
49732024 TGTTACTGGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.46, C:0.14, G:0.12, T:0.27
Consensus pattern (27 bp):
AAATTTTACCAAGGGTAAAATCATCAA
Found at i:49750879 original size:25 final size:24
Alignment explanation
Indices: 49750851--49750981 Score: 77
Period size: 25 Copynumber: 5.2 Consensus size: 24
49750841 ATTCAAGGGT
49750851 GCTCATTTGAGCACATAATCGAGAA
1 GCTCATTTGAGC-CATAATCGAGAA
* *
49750876 GCTCTCTCTTGAGCCATATAAC-AGGAA
1 GCTC-AT-TTGAGCCATA-ATCGA-GAA
* *
49750903 GCTCATGTGAGCCATTAAT-GGGAA
1 GCTCATTTGAGCCA-TAATCGAGAA
* * * * *
49750927 GCTTATTCGGGCTATATAACGAGAA
1 GCTCATTTGAGCCATA-ATCGAGAA
** *
49750952 GCTCATAAGAGCCATAATCGAAAA
1 GCTCATTTGAGCCATAATCGAGAA
49750976 GCTCAT
1 GCTCAT
49750982 GCGAGCTAAT
Statistics
Matches: 78, Mismatches: 20, Indels: 17
0.68 0.17 0.15
Matches are distributed among these distances:
23 2 0.03
24 25 0.32
25 27 0.35
26 9 0.12
27 15 0.19
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (24 bp):
GCTCATTTGAGCCATAATCGAGAA
Found at i:49751026 original size:48 final size:49
Alignment explanation
Indices: 49750886--49751027 Score: 139
Period size: 49 Copynumber: 2.9 Consensus size: 49
49750876 GCTCTCTCTT
* ** * *
49750886 GAGCCATATAAC-AGGAAGCTCATGTGAGCCATTAATGGGAAGCTTATTC
1 GAGCTATATAACGA-GAAGCTCATAAGAGCCATTAATGGGAAGCTCATGC
* **
49750935 GGGCTATATAACGAGAAGCTCATAAGAGCCA-TAATCGAAAAGCTCATGC
1 GAGCTATATAACGAGAAGCTCATAAGAGCCATTAAT-GGGAAGCTCATGC
* *
49750984 GAGCTA-ATAACGGGTAGCTC-TGAAGAGCCATTAATGGGAAGCTC
1 GAGCTATATAACGAGAAGCTCAT-AAGAGCCATTAATGGGAAGCTC
49751028 CAAATAGCCA
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
47 1 0.01
48 31 0.41
49 43 0.57
50 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (49 bp):
GAGCTATATAACGAGAAGCTCATAAGAGCCATTAATGGGAAGCTCATGC
Found at i:49754789 original size:6 final size:6
Alignment explanation
Indices: 49754778--49754817 Score: 62
Period size: 6 Copynumber: 6.5 Consensus size: 6
49754768 TAGATTTCCA
*
49754778 AAAATG AAAATG AAAATG AAAATG AAAATG GAAATAG AAA
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAAT-G AAA
49754818 CGAGGTCCCA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
6 28 0.90
7 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (6 bp):
AAAATG
Found at i:49755347 original size:21 final size:21
Alignment explanation
Indices: 49755308--49755347 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
49755298 CATTCTAGAC
* *
49755308 TTAACTTTTAAATGGTTTTTA
1 TTAAATTTTAAATGCTTTTTA
*
49755329 TTAAATTTTAATTGCTTTT
1 TTAAATTTTAAATGCTTTT
49755348 GAACTTTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.28, C:0.05, G:0.07, T:0.60
Consensus pattern (21 bp):
TTAAATTTTAAATGCTTTTTA
Found at i:49755384 original size:19 final size:18
Alignment explanation
Indices: 49755355--49755402 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
49755345 TTTGAACTTT
49755355 ATTTAATA-TTTTTATAAA
1 ATTTAATATTTTTTAT-AA
49755373 ATTTAATAATTTTTTATAA
1 ATTTAAT-ATTTTTTATAA
49755392 ATTT-ATATTTT
1 ATTTAATATTTT
49755403 AAAAAAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.18
18 9 0.32
19 7 0.25
20 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATATTTTTTATAA
Done.