Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr6
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 47432654
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2298022 characters in sequence are not A, C, G, or T
File 121 of 136
Found at i:41171356 original size:27 final size:27
Alignment explanation
Indices: 41171324--41171377 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
41171314 CCAGCTTAAA
*
41171324 AAAGTAAAGAACTTCTGATGTTCAGGT
1 AAAGTAAAGAACTTATGATGTTCAGGT
41171351 AAAGTAAAGAACTTATGATGTTCAGGT
1 AAAGTAAAGAACTTATGATGTTCAGGT
41171378 TCAATGTTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.09, G:0.22, T:0.30
Consensus pattern (27 bp):
AAAGTAAAGAACTTATGATGTTCAGGT
Found at i:41181642 original size:6 final size:6
Alignment explanation
Indices: 41181631--41181667 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
41181621 TTTGTCAAAG
41181631 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT G
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTTT G
41181668 TTGGATCATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.19, T:0.65
Consensus pattern (6 bp):
GATTTT
Found at i:41206987 original size:73 final size:72
Alignment explanation
Indices: 41206903--41207071 Score: 171
Period size: 73 Copynumber: 2.3 Consensus size: 72
41206893 CCGGGCTGTA
* * * * * *
41206903 TAATAGGAAGCTCATAAGAGCCATATTTAGA-AAGCTT-ATGTGAGCCAATAACGGGTAGCTCTG
1 TAATAGGAAGCTCAAAAGAGCCAGATATAGAGAAG-TTCAAGCGAGCC-ATAACGGGAAGCTCTG
41206966 AAGAGCCAT
64 AAGAGCCAT
** * * * *
41206975 TAATCAGGAAGCTCCGAATAGCCAGATATCGAGAAGTTCAAGCGAGCCATATCGGGAAGCTCTGG
1 TAAT-AGGAAGCTCAAAAGAGCCAGATATAGAGAAGTTCAAGCGAGCCATAACGGGAAGCTCTGA
41207040 AGAGCCAT
65 AGAGCCAT
41207048 TAATTAGGAAGCTCACAAAGAGCC
1 TAA-TAGGAAGCTCA-AAAGAGCC
41207072 TTTAATTGGG
Statistics
Matches: 78, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
72 4 0.05
73 57 0.73
74 17 0.22
ACGTcount: A:0.36, C:0.20, G:0.25, T:0.20
Consensus pattern (72 bp):
TAATAGGAAGCTCAAAAGAGCCAGATATAGAGAAGTTCAAGCGAGCCATAACGGGAAGCTCTGAA
GAGCCAT
Found at i:41207060 original size:25 final size:26
Alignment explanation
Indices: 41207029--41207121 Score: 93
Period size: 26 Copynumber: 3.7 Consensus size: 26
41207019 AGCCATATCG
*
41207029 GGAAGCTC-TGGAGAGCCATTAATTA
1 GGAAGCTCATGAAGAGCCATTAATTA
** * *
41207054 GGAAGCTCACAAAGAGCCTTTAATTG
1 GGAAGCTCATGAAGAGCCATTAATTA
*
41207080 GGAAGCTCATGAAGAGCC-GTATATTA
1 GGAAGCTCATGAAGAGCCATTA-ATTA
*
41207106 GGACGCTCAT-AAGAGC
1 GGAAGCTCATGAAGAGC
41207122 TGCGGTGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 16 0.29
26 40 0.71
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (26 bp):
GGAAGCTCATGAAGAGCCATTAATTA
Found at i:41207504 original size:21 final size:21
Alignment explanation
Indices: 41207480--41207519 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41207470 GTAAATTTAG
*
41207480 CTCAATTTAATACAATTCATA
1 CTCAATTCAATACAATTCATA
*
41207501 CTCAATTCAATCCAATTCA
1 CTCAATTCAATACAATTCA
41207520 CATCTTAGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.25, G:0.00, T:0.35
Consensus pattern (21 bp):
CTCAATTCAATACAATTCATA
Found at i:41209152 original size:21 final size:22
Alignment explanation
Indices: 41209128--41209176 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 22
41209118 ACCTAGTTGT
41209128 TACCTAAATTTGTACAAAAA-G
1 TACCTAAATTTGTACAAAAAGG
41209149 TACCTAAATTTGTACAAAAAGG
1 TACCTAAATTTGTACAAAAAGG
41209171 TACCTA
1 TACCTA
41209177 GTTACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.74
22 7 0.26
ACGTcount: A:0.45, C:0.16, G:0.10, T:0.29
Consensus pattern (22 bp):
TACCTAAATTTGTACAAAAAGG
Found at i:41215942 original size:26 final size:26
Alignment explanation
Indices: 41215913--41215963 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
41215903 GCCAAAAGTT
41215913 CTAATTGTACATGAAACCCAAATTTA
1 CTAATTGTACATGAAACCCAAATTTA
*
41215939 CTAATTGTACATGAAACTCAAATTT
1 CTAATTGTACATGAAACCCAAATTT
41215964 CTTTTCATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.41, C:0.18, G:0.08, T:0.33
Consensus pattern (26 bp):
CTAATTGTACATGAAACCCAAATTTA
Found at i:41216639 original size:313 final size:314
Alignment explanation
Indices: 41216071--41216697 Score: 1247
Period size: 313 Copynumber: 2.0 Consensus size: 314
41216061 AAATTTCATC
41216071 ACTTCTTTACCCAAACAAAGAACAAACAATTAATTTAATTAATTGTGATGGTTTTTCATTGTTTT
1 ACTTCTTTACCCAAACAAAGAACAAACAATTAATTTAATTAATTGTGATGGTTTTTCATTGTTTT
41216136 TAACTTAGTACGAAATATTCGAGATTATATAATCAAAAGAAATTTAAGTTTAATTTAACAATGAT
66 TAACTTAGTACGAAATATTCGAGATTATATAATCAAAAGAAATTTAAGTTTAATTTAACAATGAT
41216201 TAAATATAAGTTATCGAGTTGACTGCATTAAAAATAATATGAAAACATAAAATAAAATTTTAAAA
131 TAAATATAAGTTATCGAGTTGACTGCATTAAAAATAATATGAAAACATAAAATAAAATTTTAAAA
41216266 CTTAGAAAGAGATTAATTTAATTAATTTTAATATTATAGTAACAAATCGGTTAACATTATATTTT
196 CTTAGAAAGAGATTAATTTAATTAATTTTAATATTATAGTAACAAATCGGTTAACATTATATTTT
41216331 GAAATTTAAAATTTTAAGGGATAAAAAATTTTTAACAATTTA-TGAATTGATTT
261 GAAATTTAAAATTTTAAGGGATAAAAAATTTTTAACAATTTATTGAATTGATTT
41216384 ACTTCTTTACCCAAACAAAGAACAAACAATTAATTTAATTAATTGTGATGGTTTTTCATTGTTTT
1 ACTTCTTTACCCAAACAAAGAACAAACAATTAATTTAATTAATTGTGATGGTTTTTCATTGTTTT
41216449 TAACTTAGTACGAAATATTCGAGATTATATAATCAAAAGAAATTTAAGTTTAATTTAACAATGAT
66 TAACTTAGTACGAAATATTCGAGATTATATAATCAAAAGAAATTTAAGTTTAATTTAACAATGAT
41216514 TAAATATAAGTTATCGAGTTGACTGCATTAAAAATAATATGAAAACATAAAATAAAATTTTAAAA
131 TAAATATAAGTTATCGAGTTGACTGCATTAAAAATAATATGAAAACATAAAATAAAATTTTAAAA
41216579 CTTAGAAAGAGATTAATTTAATTAATTTTAATATTATAGTAACAAATCGGTTAACATTATATTTT
196 CTTAGAAAGAGATTAATTTAATTAATTTTAATATTATAGTAACAAATCGGTTAACATTATATTTT
41216644 GAAATTTAAAATTTTAAGGGATAAAAAATTTTTAACAATTTATTGAATTGATTT
261 GAAATTTAAAATTTTAAGGGATAAAAAATTTTTAACAATTTATTGAATTGATTT
41216698 TCATTTTTTG
Statistics
Matches: 313, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
313 302 0.96
314 11 0.04
ACGTcount: A:0.44, C:0.07, G:0.10, T:0.38
Consensus pattern (314 bp):
ACTTCTTTACCCAAACAAAGAACAAACAATTAATTTAATTAATTGTGATGGTTTTTCATTGTTTT
TAACTTAGTACGAAATATTCGAGATTATATAATCAAAAGAAATTTAAGTTTAATTTAACAATGAT
TAAATATAAGTTATCGAGTTGACTGCATTAAAAATAATATGAAAACATAAAATAAAATTTTAAAA
CTTAGAAAGAGATTAATTTAATTAATTTTAATATTATAGTAACAAATCGGTTAACATTATATTTT
GAAATTTAAAATTTTAAGGGATAAAAAATTTTTAACAATTTATTGAATTGATTT
Found at i:41224518 original size:114 final size:114
Alignment explanation
Indices: 41224370--41224599 Score: 442
Period size: 114 Copynumber: 2.0 Consensus size: 114
41224360 TCTTCAGTTT
*
41224370 ATCGGATCTTATCTCCTTTTAAATGTTAACTTTTTAAATACTAAATTTTTATTAAGTTAAATATT
1 ATCGGATCTTATCTCCTTTTAAATGTTAACTTTTTAAATACTAAATTTTTATTAAGTTAAATATA
41224435 ATATATTTATTTTATGATATAACAATAAAAAAATATAATTGTAAAATAA
66 ATATATTTATTTTATGATATAACAATAAAAAAATATAATTGTAAAATAA
*
41224484 ATCGGGTCTTATCTCCTTTTAAATGTTAACTTTTTAAATACTAAATTTTTATTAAGTTAAATATA
1 ATCGGATCTTATCTCCTTTTAAATGTTAACTTTTTAAATACTAAATTTTTATTAAGTTAAATATA
41224549 ATATATTTATTTTATGATATAACAATAAAAAAATATAATTGTAAAATAA
66 ATATATTTATTTTATGATATAACAATAAAAAAATATAATTGTAAAATAA
41224598 AT
1 AT
41224600 AAAAAATATA
Statistics
Matches: 114, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.44
Consensus pattern (114 bp):
ATCGGATCTTATCTCCTTTTAAATGTTAACTTTTTAAATACTAAATTTTTATTAAGTTAAATATA
ATATATTTATTTTATGATATAACAATAAAAAAATATAATTGTAAAATAA
Found at i:41227816 original size:28 final size:27
Alignment explanation
Indices: 41227778--41227853 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 27
41227768 CTTTCTTTCT
41227778 AAATTCTTAATCTTCAATTTTCAATC-CC
1 AAATT-TTAAT-TTCAATTTTCAATCTCC
* * *
41227806 CAATTTCTAATTTTATATTTTCAATCTCT
1 AAATTT-TAATTTCA-ATTTTCAATCTCC
41227835 AAATTTTAATTTTCAATTT
1 AAATTTTAA-TTTCAATTT
41227854 CGAATTTTCA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
27 4 0.10
28 25 0.64
29 10 0.26
ACGTcount: A:0.32, C:0.17, G:0.00, T:0.51
Consensus pattern (27 bp):
AAATTTTAATTTCAATTTTCAATCTCC
Found at i:41227830 original size:21 final size:20
Alignment explanation
Indices: 41227806--41227861 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 20
41227796 TTTCAATCCC
41227806 CAATTTCTAATTTTATATTTT
1 CAATTTCTAATTTTA-ATTTT
*
41227827 CAATCTCTAAATTTTAATTTT
1 CAATTTCT-AATTTTAATTTT
*
41227848 CAATTTCGAATTTT
1 CAATTTCTAATTTT
41227862 CAATCCTCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.19
21 18 0.58
22 7 0.23
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (20 bp):
CAATTTCTAATTTTAATTTT
Found at i:41227853 original size:35 final size:36
Alignment explanation
Indices: 41227809--41227882 Score: 84
Period size: 35 Copynumber: 2.1 Consensus size: 36
41227799 CAATCCCCAA
*
41227809 TTTCTAATTT-TATATTTTCAAT-CTCTAAAT-TTTAAT
1 TTTCTAATTTCGA-ATTTTCAATCCTC-AAATATTT-AT
41227845 TTTC-AATTTCGAATTTTCAATCCTCAAATATTTAT
1 TTTCTAATTTCGAATTTTCAATCCTCAAATATTTAT
41227880 TTT
1 TTT
41227883 AATATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
35 23 0.68
36 11 0.32
ACGTcount: A:0.30, C:0.14, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTCTAATTTCGAATTTTCAATCCTCAAATATTTAT
Found at i:41227871 original size:21 final size:20
Alignment explanation
Indices: 41227793--41227871 Score: 50
Period size: 21 Copynumber: 3.8 Consensus size: 20
41227783 CTTAATCTTC
* *
41227793 AATTTTCAATCCCCAATTTCT
1 AATTTT-AATCCTCAATTTCA
** *
41227814 AATTTTATATTTTCAATCTCTA
1 AATTTTA-ATCCTCAATTTC-A
** *
41227836 AATTTTAATTTTCAATTTCG
1 AATTTTAATCCTCAATTTCA
41227856 AATTTTCAATCCTCAA
1 AATTTT-AATCCTCAA
41227872 ATATTTATTT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
20 7 0.15
21 32 0.70
22 7 0.15
ACGTcount: A:0.32, C:0.19, G:0.01, T:0.48
Consensus pattern (20 bp):
AATTTTAATCCTCAATTTCA
Found at i:41229481 original size:20 final size:20
Alignment explanation
Indices: 41229458--41229496 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
41229448 GTCCAATATA
41229458 TTAAAAAGTTTACCAAAATT
1 TTAAAAAGTTTACCAAAATT
** *
41229478 TTAAAGGGTTTATCAAAAT
1 TTAAAAAGTTTACCAAAAT
41229497 AACTAAGGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (20 bp):
TTAAAAAGTTTACCAAAATT
Found at i:41229561 original size:20 final size:19
Alignment explanation
Indices: 41229507--41229580 Score: 58
Period size: 20 Copynumber: 3.8 Consensus size: 19
41229497 AACTAAGGAT
* * *
41229507 TTACCAAACTTTCTATTGTT
1 TTACCAAAATTTCTA-AGAT
* * *
41229527 TTACCAATATATCTAATAGT
1 TTACCAAAATTTCTAAGA-T
* *
41229547 TTATCAAATTTTCTAAGAT
1 TTACCAAAATTTCTAAGAT
41229566 TTACCAAAATTTCTA
1 TTACCAAAATTTCTA
41229581 CCCTTTTGCC
Statistics
Matches: 40, Mismatches: 13, Indels: 3
0.71 0.23 0.05
Matches are distributed among these distances:
19 14 0.35
20 26 0.65
ACGTcount: A:0.35, C:0.16, G:0.04, T:0.45
Consensus pattern (19 bp):
TTACCAAAATTTCTAAGAT
Found at i:41229707 original size:20 final size:20
Alignment explanation
Indices: 41229684--41229770 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
41229674 ATTTAGGGAT
*
41229684 TTACCAAAATATCTAACAAG
1 TTACCAATATATCTAACAAG
* * *
41229704 TTACCAATATATTTAACGAT
1 TTACCAATATATCTAACAAG
* * *
41229724 TTACCAATATTTCTAAGAAC
1 TTACCAATATATCTAACAAG
41229744 TTACCAATATATCTAACAAG
1 TTACCAATATATCTAACAAG
*
41229764 TTGCCAA
1 TTACCAA
41229771 AATTTCTATC
Statistics
Matches: 54, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.32
Consensus pattern (20 bp):
TTACCAATATATCTAACAAG
Found at i:41229708 original size:40 final size:40
Alignment explanation
Indices: 41229664--41229778 Score: 122
Period size: 40 Copynumber: 2.9 Consensus size: 40
41229654 TTCTATAATT
* ** *
41229664 TTACCAAAATATTTAGGGATTTACCAAAATATCTAACAAG
1 TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
* * *
41229704 TTACCAATATATTTAACGATTTACCAATATTTCTAAGAAC
1 TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
* * * * *
41229744 TTACCAATATATCTAACAAGTTGCCAAAATTTCTA
1 TTACCAATATATTTAACGATTTACCAAAATATCTA
41229779 TCTTTTTATC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.34
Consensus pattern (40 bp):
TTACCAATATATTTAACGATTTACCAAAATATCTAACAAC
Found at i:41229792 original size:60 final size:60
Alignment explanation
Indices: 41229684--41229813 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
41229674 ATTTAGGGAT
* * *
41229684 TTACCAAAATATCTAACAAGTTACCAATATATTTAACGATTTACCAATATTTCTAAGA-A
1 TTACCAATATATCTAACAAGTTACCAAAATATTTAACGATTTACCAATATTTATAAGACA
* * ** * *
41229743 CTTACCAATATATCTAACAAGTTGCCAAAAT-TTCTATCTTTTTATCAATATTTATGAGACA
1 -TTACCAATATATCTAACAAGTTACCAAAATATT-TAACGATTTACCAATATTTATAAGACA
41229804 TTACCAATAT
1 TTACCAATAT
41229814 TCCCAAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
59 2 0.03
60 56 0.95
61 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.05, T:0.37
Consensus pattern (60 bp):
TTACCAATATATCTAACAAGTTACCAAAATATTTAACGATTTACCAATATTTATAAGACA
Found at i:41229914 original size:20 final size:20
Alignment explanation
Indices: 41229891--41229935 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41229881 TTTATGAGAC
* *
41229891 TTTACCAATATTTCTAAAGA
1 TTTACCAAAATATCTAAAGA
*
41229911 TTTACCAAAATATCTAACGA
1 TTTACCAAAATATCTAAAGA
41229931 TTTAC
1 TTTAC
41229936 TGGTATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (20 bp):
TTTACCAAAATATCTAAAGA
Found at i:41230013 original size:19 final size:20
Alignment explanation
Indices: 41229970--41230016 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
41229960 TTTTTAAAGT
41229970 TTTACCAAAACATCTAACAA
1 TTTACCAAAACATCTAACAA
* *
41229990 TTTACTAAAATATCTAAC-A
1 TTTACCAAAACATCTAACAA
41230009 TTTACCAA
1 TTTACCAA
41230017 TATTTATGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 8 0.33
20 16 0.67
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (20 bp):
TTTACCAAAACATCTAACAA
Found at i:41230055 original size:20 final size:19
Alignment explanation
Indices: 41230032--41230070 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
41230022 ATGAGACTTA
41230032 ACCAAAATTTCCAACATTTT
1 ACCAAAATTTCCAA-ATTTT
* *
41230052 ACCAATATTTTCAAATTTT
1 ACCAAAATTTCCAAATTTT
41230071 CTAAACCCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.38, C:0.21, G:0.00, T:0.41
Consensus pattern (19 bp):
ACCAAAATTTCCAAATTTT
Found at i:41230191 original size:20 final size:20
Alignment explanation
Indices: 41230118--41230192 Score: 62
Period size: 20 Copynumber: 3.8 Consensus size: 20
41230108 TCTATAAATA
* **
41230118 TACCAAAATATCTATGGATTT
1 TACCAATATATCTAAAGA-TT
* **
41230139 TA-CAATATATCGAACTATT
1 TACCAATATATCTAAAGATT
* *
41230158 TCCCAATATTTCTAAAGATT
1 TACCAATATATCTAAAGATT
41230178 TACCAATATATCTAA
1 TACCAATATATCTAA
41230193 CGACCAAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 3
0.73 0.21 0.05
Matches are distributed among these distances:
19 3 0.07
20 36 0.88
21 2 0.05
ACGTcount: A:0.40, C:0.17, G:0.05, T:0.37
Consensus pattern (20 bp):
TACCAATATATCTAAAGATT
Found at i:41230371 original size:20 final size:20
Alignment explanation
Indices: 41230348--41230426 Score: 90
Period size: 20 Copynumber: 3.9 Consensus size: 20
41230338 TTACAAAAAC
*
41230348 TTCTATGAGTTTACCAATAT
1 TTCTATGAATTTACCAATAT
41230368 TTCTAAT-AATTTTACCAA-ATT
1 TTCT-ATGAA-TTTACCAATA-T
*
41230389 TTATATGAATTTACCAATAT
1 TTCTATGAATTTACCAATAT
*
41230409 TTCTATCAATTTACCAAT
1 TTCTATGAATTTACCAAT
41230427 TTTTATATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 33 0.66
21 17 0.34
ACGTcount: A:0.35, C:0.15, G:0.04, T:0.46
Consensus pattern (20 bp):
TTCTATGAATTTACCAATAT
Found at i:41230396 original size:41 final size:40
Alignment explanation
Indices: 41230319--41230435 Score: 128
Period size: 41 Copynumber: 2.9 Consensus size: 40
41230309 TTTTTGACTG
* * * * ** * *
41230319 TACCAAAATTTCTAACTATTTACAAAAACTTCTATGAGTT
1 TACCAATATTTCTATCAATTTACCAAATTTTATATGAATT
41230359 TACCAATATTTCTAAT-AATTTTACCAAATTTTATATGAATT
1 TACCAATATTTCT-ATCAA-TTTACCAAATTTTATATGAATT
*
41230400 TACCAATATTTCTATCAATTTACCAATTTTTATATG
1 TACCAATATTTCTATCAATTTACCAAATTTTATATG
41230436 GATATTTTAC
Statistics
Matches: 65, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 32 0.49
41 33 0.51
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.44
Consensus pattern (40 bp):
TACCAATATTTCTATCAATTTACCAAATTTTATATGAATT
Found at i:41230538 original size:20 final size:20
Alignment explanation
Indices: 41230513--41230566 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
41230503 TTGATTTATT
41230513 AAATATCTAAAATTTTACCA
1 AAATATCTAAAATTTTACCA
** *
41230533 AAATATCTAGTATATTACCA
1 AAATATCTAAAATTTTACCA
41230553 AAAT-TCTTAAAATT
1 AAATATC-TAAAATT
41230567 AAACCCAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 2 0.07
20 25 0.93
ACGTcount: A:0.48, C:0.13, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATATCTAAAATTTTACCA
Found at i:41230763 original size:24 final size:24
Alignment explanation
Indices: 41230731--41230777 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41230721 GACGTCCTTG
41230731 TCAATGAAATCCTAACAGTTTTAT
1 TCAATGAAATCCTAACAGTTTTAT
*
41230755 TCAATGAAATCCTAACGGTTTTA
1 TCAATGAAATCCTAACAGTTTTA
41230778 CCTTTTCATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (24 bp):
TCAATGAAATCCTAACAGTTTTAT
Found at i:41235898 original size:17 final size:16
Alignment explanation
Indices: 41235870--41235901 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
41235860 AAAAGAGTAA
41235870 GCCCGAGCCCGGCCCG
1 GCCCGAGCCCGGCCCG
41235886 GCCCGACGCCCGGCCC
1 GCCCGA-GCCCGGCCC
41235902 ATTTTTTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.06, C:0.59, G:0.34, T:0.00
Consensus pattern (16 bp):
GCCCGAGCCCGGCCCG
Found at i:41236267 original size:18 final size:18
Alignment explanation
Indices: 41236244--41236305 Score: 54
Period size: 18 Copynumber: 3.3 Consensus size: 18
41236234 CGTCCATATT
41236244 ATTTTTTAATTTTTTTTA
1 ATTTTTTAATTTTTTTTA
*
41236262 ATTTTTT-ATATTATTTTA
1 ATTTTTTAAT-TTTTTTTA
* * *
41236280 ATATTTAATAATTTTATATA
1 AT-TTT-TTAATTTTTTTTA
41236300 ATTTTT
1 ATTTTT
41236306 ATTTATTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 2 0.06
18 16 0.47
19 6 0.18
20 8 0.24
21 2 0.06
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (18 bp):
ATTTTTTAATTTTTTTTA
Found at i:41236278 original size:28 final size:27
Alignment explanation
Indices: 41236243--41236329 Score: 77
Period size: 28 Copynumber: 3.1 Consensus size: 27
41236233 CCGTCCATAT
* ** *
41236243 TATTTTTTAATTTTTTTTAATTTTTTA
1 TATTTTTTAATATTTAATAATTTTATA
41236270 TATTATTTTAATATTTAATAATTTTATA
1 TATT-TTTTAATATTTAATAATTTTATA
* * *
41236298 TAATTTTTATTTATTGAA-AATTTTTATA
1 TATTTTTTA-ATATTTAATAA-TTTTATA
41236326 TATT
1 TATT
41236330 CATCTTAACA
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
27 11 0.22
28 38 0.78
ACGTcount: A:0.32, C:0.00, G:0.01, T:0.67
Consensus pattern (27 bp):
TATTTTTTAATATTTAATAATTTTATA
Found at i:41240783 original size:27 final size:27
Alignment explanation
Indices: 41240745--41240835 Score: 139
Period size: 27 Copynumber: 3.4 Consensus size: 27
41240735 GGAGGGTTTT
*
41240745 TGATTGGCGGCACCAAAGGTGCC-TAAC
1 TGATTGGCGGCACCAATGGTGCCAT-AC
*
41240772 TGATTGGCGGCACCGATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
*
41240799 TGGTTGGCGGCACCAATGGTGCCATAC
1 TGATTGGCGGCACCAATGGTGCCATAC
41240826 TGATTGGCGG
1 TGATTGGCGG
41240836 GACTACTCGT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
27 57 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.24, G:0.34, T:0.22
Consensus pattern (27 bp):
TGATTGGCGGCACCAATGGTGCCATAC
Found at i:41241255 original size:36 final size:34
Alignment explanation
Indices: 41241189--41241255 Score: 89
Period size: 36 Copynumber: 1.9 Consensus size: 34
41241179 GTTAGTTAGT
* *
41241189 TATTATTTTTAGTAAAATTAATAATTTTATTGTG
1 TATTATTTTGAGTAAAATTAATAATATTATTGTG
*
41241223 TATTATTTTGAGTATAAAATTATTAATATTATT
1 TATTATTTTGAG--TAAAATTAATAATATTATT
41241256 ATTGTGTTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 11 0.39
36 17 0.61
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.55
Consensus pattern (34 bp):
TATTATTTTGAGTAAAATTAATAATATTATTGTG
Found at i:41247106 original size:220 final size:220
Alignment explanation
Indices: 41246724--41247165 Score: 848
Period size: 220 Copynumber: 2.0 Consensus size: 220
41246714 ACGAGTTAGA
*
41246724 GCCACATATTTTTCGGCAAACAATGATCCTACTTGAGAGTGACATGGAGGGGCAGACAAACACAT
1 GCCACATATTTTTCGACAAACAATGATCCTACTTGAGAGTGACATGGAGGGGCAGACAAACACAT
41246789 CTTTCTGACAATGGTTGGGCACAATGGAGCCGGGGCAGTAGGCTCAAAGTTTTGACGAAGGCTTT
66 CTTTCTGACAATGGTTGGGCACAATGGAGCCGGGGCAGTAGGCTCAAAGTTTTGACGAAGGCTTT
41246854 CGTTATGGCCAAATGACCACAAACTTAGTCGAAGGGATCAACGCTGTCTTGTTGAAAACACGTCA
131 CGTTATGGCCAAATGACCACAAACTTAGTCGAAGGGATCAACGCTGTCTTGTTGAAAACACGTCA
41246919 TCTTTCGATTGCATCTGTATTTTCT
196 TCTTTCGATTGCATCTGTATTTTCT
41246944 GCCACATATTTTTCGACAAACAATGATCCTACTTGAGAGTGACATGGAGGGGCAGACAAACACAT
1 GCCACATATTTTTCGACAAACAATGATCCTACTTGAGAGTGACATGGAGGGGCAGACAAACACAT
*
41247009 CTTTCTGACAATGGTTGGGCACAATGGAGCCGTGGCAGTAGGCTCAAAGTTTTGACGAAGGCTTT
66 CTTTCTGACAATGGTTGGGCACAATGGAGCCGGGGCAGTAGGCTCAAAGTTTTGACGAAGGCTTT
* *
41247074 CGTTATGGCCAAATGACCACACACTTAGTCGAAGGGATTAACGCTGTCTTGTTGAAAACACGTCA
131 CGTTATGGCCAAATGACCACAAACTTAGTCGAAGGGATCAACGCTGTCTTGTTGAAAACACGTCA
41247139 TCTTTCGATTGCATCTGTATTTTCT
196 TCTTTCGATTGCATCTGTATTTTCT
41247164 GC
1 GC
41247166 TACTTTCTAC
Statistics
Matches: 218, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
220 218 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (220 bp):
GCCACATATTTTTCGACAAACAATGATCCTACTTGAGAGTGACATGGAGGGGCAGACAAACACAT
CTTTCTGACAATGGTTGGGCACAATGGAGCCGGGGCAGTAGGCTCAAAGTTTTGACGAAGGCTTT
CGTTATGGCCAAATGACCACAAACTTAGTCGAAGGGATCAACGCTGTCTTGTTGAAAACACGTCA
TCTTTCGATTGCATCTGTATTTTCT
Found at i:41247905 original size:11 final size:11
Alignment explanation
Indices: 41247889--41247913 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
41247879 GCTTATGCTT
41247889 AAATTGTATCC
1 AAATTGTATCC
41247900 AAATTGTATCC
1 AAATTGTATCC
41247911 AAA
1 AAA
41247914 CTAAGTTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.16, G:0.08, T:0.32
Consensus pattern (11 bp):
AAATTGTATCC
Found at i:41250561 original size:158 final size:152
Alignment explanation
Indices: 41250125--41250589 Score: 417
Period size: 160 Copynumber: 2.9 Consensus size: 152
41250115 GCAAGTTGAA
*
41250125 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTCTCTCCGTATTTTATTA
1 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCT-CG-ATTTTATTA
41250190 TTTTAGAAAATATTATAATTTTTTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTG-AA
64 TTTTAGAAAATATTATAA-TTTTTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
* *
41250254 -ATTTATTAATTTAGTGTGTTTTTT
128 TATTTATTAATTTAGTCTGATTTTT
* * * * * * * * * *
41250278 AAATTAATTTGGTGTAAGAAAAAAAAC-CATTA-TCCCTGCCCTTTGCTCGTATTATTTTATCGA
1 AAA-AAAGTT--TGT-----AATACACTC-TTACT-TCGGCCATTTGTTCGTATTTTTTTCTCGA
* * * *
41250341 TTTTTATTACTTTAAATA-AAAATATT-TTATTTTCGTATTTTATTATTTTATATTATTCCAGTG
56 -TTTTATTA-TTT---TAGAAAATATTATAATTTT--TATTTTATAATTTTACATTATTTCAGTG
** *
41250404 CATTTTGTTTGAAATATTTGTATTAA-TTATTTCTGAATTTTT
114 CATAATGTTTGAAATA-TT-TATTAATTTA-GTCTG-ATTTTT
*
41250446 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCATATTTTTTTCTCTGCATTTTATTA
1 AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTC-G-ATTTTATTA
* *
41250511 TTTTAGAAAATATTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTG-AA
64 TTTTAGAAAATATTATAA-TTTTTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAA
41250575 -ATTTATTAATTTAGT
128 TATTTATTAATTTAGT
41250590 ATGTTTTAAA
Statistics
Matches: 241, Mismatches: 40, Indels: 61
0.70 0.12 0.18
Matches are distributed among these distances:
153 3 0.01
154 11 0.05
155 5 0.02
156 4 0.02
157 4 0.02
158 40 0.17
159 3 0.01
160 47 0.20
161 45 0.19
162 3 0.01
163 42 0.17
164 4 0.02
165 4 0.02
166 5 0.02
167 13 0.05
168 8 0.03
ACGTcount: A:0.30, C:0.10, G:0.09, T:0.51
Consensus pattern (152 bp):
AAAAAAGTTTGTAATACACTCTTACTTCGGCCATTTGTTCGTATTTTTTTCTCGATTTTATTATT
TTAGAAAATATTATAATTTTTATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATAT
TTATTAATTTAGTCTGATTTTT
Found at i:41250585 original size:40 final size:39
Alignment explanation
Indices: 41250537--41250670 Score: 108
Period size: 40 Copynumber: 3.3 Consensus size: 39
41250527 AAGTTTTAAT
41250537 TTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
1 TTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
* * * * ** * * *
41250576 TTTATTAATTTAGTATGT-TTTAAATTAATTTTTATAAGTTTTAAT
1 TTTA-TAATTTTGCAT-TATTTCAGTGCA----TA-ATGTTTGAAA
41250621 TTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
1 TTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
41250660 TTTATTAATTT
1 TTTA-TAATTT
41250671 AGTATGTTTT
Statistics
Matches: 68, Mismatches: 18, Indels: 17
0.66 0.17 0.17
Matches are distributed among these distances:
39 15 0.22
40 23 0.34
41 1 0.01
43 1 0.01
44 17 0.25
45 11 0.16
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (39 bp):
TTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAA
Found at i:41250650 original size:84 final size:85
Alignment explanation
Indices: 41250523--41250692 Score: 324
Period size: 84 Copynumber: 2.0 Consensus size: 85
41250513 TTAGAAAATA
41250523 TTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTA
1 TTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTA
41250588 GTATG-TTTTAAATTAATTT
66 GTATGTTTTTAAATTAATTT
41250607 TTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTA
1 TTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTA
41250672 GTATGTTTTTTAAATTAATTT
66 GTATG-TTTTTAAATTAATTT
41250693 GGTGTAAGAA
Statistics
Matches: 84, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
84 70 0.83
86 14 0.17
ACGTcount: A:0.32, C:0.04, G:0.09, T:0.55
Consensus pattern (85 bp):
TTATAAGTTTTAATTTTATAATTTTGCATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTA
GTATGTTTTTAAATTAATTT
Found at i:41251387 original size:5 final size:5
Alignment explanation
Indices: 41251361--41251579 Score: 86
Period size: 5 Copynumber: 44.2 Consensus size: 5
41251351 TCCTTCCCTC
*
41251361 TTCTT CTTC-T TTCTT TTTTT TTCTT TTCTCAT TTCCTT TTC-T TTCTT
1 TTCTT -TTCTT TTCTT TTCTT TTCTT TTCT--T TT-CTT TTCTT TTCTT
* * *
41251408 TCCTT CT-TT TTCTT TTCTTT TTCTT TTCTCCT TTCCTT TTCTT TCCTT
1 TTCTT TTCTT TTCTT TTC-TT TTCTT TTCT--T TT-CTT TTCTT TTCTT
* * * * *
41251456 CT-TT TTC-T TTCTT TT-TT GTTCTT CTCATT TCCTT TTCTT TCCTT CT-TT
1 TTCTT TTCTT TTCTT TTCTT -TTCTT TTC-TT TTCTT TTCTT TTCTT TTCTT
* * * * * * * * *
41251504 TTC-T TTCTT TCCTC TCCTC TCCTT TTC-T TTCTT TCCTC TCCTT TCCTT
1 TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT TTCTT
41251552 TTC-T TTC-T TTC-T TTC-T TTCTT CTTCTT T
1 TTCTT TTCTT TTCTT TTCTT TTCTT -TTCTT T
41251580 CCCTCTCCTT
Statistics
Matches: 167, Mismatches: 26, Indels: 41
0.71 0.11 0.18
Matches are distributed among these distances:
4 46 0.28
5 87 0.52
6 24 0.14
7 6 0.04
8 4 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (5 bp):
TTCTT
Found at i:41251402 original size:18 final size:16
Alignment explanation
Indices: 41251361--41251581 Score: 83
Period size: 14 Copynumber: 13.9 Consensus size: 16
41251351 TCCTTCCCTC
*
41251361 TTCTTCTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
*
41251376 TT-TTTTTCTTTTCTCAT
1 TTCTTTTTC-TTTC-CTT
*
41251393 TTCCTTTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
* *
41251408 TCCTTCTT-TTT-CTT
1 TTCTTTTTCTTTCCTT
*
41251422 TTCTTTTTCTTTTCTCCT
1 TTCTTTTTC-TTTC-CTT
*
41251440 TTCCTTTTCTTTCC--
1 TTCTTTTTCTTTCCTT
41251454 TTCTTTTTCTTT-CTT
1 TTCTTTTTCTTTCCTT
* *
41251469 TT-TTGTTC-TTCTCAT
1 TTCTTTTTCTTTC-CTT
*
41251484 TTCCTTTTCTTTCCTT
1 TTCTTTTTCTTTCCTT
*
41251500 CTTTTTCTTTCTTTCCTCT
1 -TTCTT-TTTCTTTCCT-T
*
41251519 CCTCTCCTTTTCTTT-C-T
1 --T-TCTTTTTCTTTCCTT
* * *
41251536 TTCCTCTCCTTTCCTT
1 TTCTTTTTCTTTCCTT
41251552 TTCTTTCTTTCTTT-C-T
1 TTC-TT-TTTCTTTCCTT
*
41251568 TTCTTCTTCTTTCC
1 TTCTTTTTCTTTCC
41251582 CTCTCCTTCT
Statistics
Matches: 155, Mismatches: 27, Indels: 48
0.67 0.12 0.21
Matches are distributed among these distances:
13 3 0.02
14 48 0.31
15 23 0.15
16 18 0.12
17 20 0.13
18 30 0.19
19 2 0.01
20 9 0.06
21 2 0.01
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (16 bp):
TTCTTTTTCTTTCCTT
Found at i:41251407 original size:36 final size:35
Alignment explanation
Indices: 41251327--41251425 Score: 103
Period size: 36 Copynumber: 2.8 Consensus size: 35
41251317 TTAATAAAAA
* *
41251327 TTTCTTTTTTTCTTTTTTTTTC-CTTC-CTTCCCT
1 TTTCTTTCTTTCTTTTTTTTTCTTTTCTCTTCCCT
* *
41251360 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCT
1 TTTC-T-TTCTTTCTTTTTTTTTCTTTTCTC-TTCCCT
* *
41251398 TTTCTTTCTTTCCTTCTTTTTCTTTTCT
1 TTTCTTTCTTTCTTTTTTTTTCTTTTCT
41251426 TTTTCTTTTC
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
33 3 0.06
34 1 0.02
35 16 0.30
36 24 0.44
37 2 0.04
38 8 0.15
ACGTcount: A:0.01, C:0.26, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTCTTTCTTTCTTTTTTTTTCTTTTCTCTTCCCT
Found at i:41251414 original size:44 final size:43
Alignment explanation
Indices: 41251363--41251561 Score: 199
Period size: 44 Copynumber: 4.6 Consensus size: 43
41251353 CTTCCCTCTT
41251363 CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
41251406 TTTCCTTCTTTTTCTTTTCTTTTTCTTTTCTCCTTTCCTTTTCTTTC
1 CTT-CTTC--TTTCTTTT-TTTTTCTTTTCTCATTTCCTTTTCTTTC
*
41251453 CTTCTT-TTTCTTTCTTTTTTGTTCTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTTCTTT-TTTTTTCTT-TTCTCATTTCCTTTTCTTTC
** ** * *
41251497 CTTCTT-TTTCTTTCTTTCCTCTCCTCTCCTTTTC-TTTCTTTC
1 CTTCTTCTTTCTTT-TTTTTTCTTTTCTCATTTCCTTTTCTTTC
* * *
41251539 C-TCTCCTTTCCTTTTCTTTCTTT
1 CTTCTTCTTTCTTTTTTTTTCTTT
41251562 CTTTCTTTCT
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
41 8 0.06
42 15 0.12
43 24 0.18
44 43 0.33
46 11 0.08
47 29 0.22
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (43 bp):
CTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
Found at i:41251414 original size:47 final size:46
Alignment explanation
Indices: 41251360--41251513 Score: 224
Period size: 47 Copynumber: 3.4 Consensus size: 46
41251350 TTCCTTCCCT
41251360 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
41251406 TTTCCTTCTT-TTTCTTTTCTTTTTCTTTTCTCCTTTCCTTTTCTTTC
1 CTT-CTTCTTCTTTCTTTT-TTTTTCTTTTCTCATTTCCTTTTCTTTC
* *
41251453 CTTCTTTTTCTTTCTTTTTTGTTC--TTCTCATTTCCTTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
*
41251497 CTTCTTTTTCTTTCTTT
1 CTTCTTCTTCTTTCTTT
41251514 CCTCTCCTCT
Statistics
Matches: 99, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
44 36 0.36
46 20 0.20
47 43 0.43
ACGTcount: A:0.01, C:0.26, G:0.01, T:0.72
Consensus pattern (46 bp):
CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
Found at i:41251505 original size:87 final size:89
Alignment explanation
Indices: 41251360--41251540 Score: 235
Period size: 87 Copynumber: 2.0 Consensus size: 89
41251350 TTCCTTCCCT
*
41251360 CTTCTTCTTCTTTCTTTTTTTTTCTTTTCTCATTTCCTTTTCTTTCTTTCCTTCTTTTTCTTTTC
1 CTTCTTCTTCTTTCTTTTTTGTTC-TTTCTCATTTCC--TTCTTTCTTTCCTTCTTTTTC-TTTC
* **
41251425 TTT-TTCTTTTCTCCTTTCCTTTTCTTTC
62 TTTCCTCTCCTCTCCTTTCC-TTTCTTTC
*
41251453 CTTCTTTTTCTTTCTTTTTTGTTC-TTCTCATTTCC-T-TTTCTTTCCTTCTTTTTCTTTCTTTC
1 CTTCTTCTTCTTTCTTTTTTGTTCTTTCTCATTTCCTTCTTTCTTTCCTTCTTTTTCTTTCTTTC
*
41251515 CTCTCCTCTCCTTTTCTTTCTTTC
66 CTCTCCTCTCCTTTCCTTTCTTTC
41251539 CT
1 CT
41251541 CTCCTTTCCT
Statistics
Matches: 81, Mismatches: 6, Indels: 9
0.84 0.06 0.09
Matches are distributed among these distances:
86 17 0.21
87 30 0.37
88 1 0.01
91 11 0.14
93 22 0.27
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.70
Consensus pattern (89 bp):
CTTCTTCTTCTTTCTTTTTTGTTCTTTCTCATTTCCTTCTTTCTTTCCTTCTTTTTCTTTCTTTC
CTCTCCTCTCCTTTCCTTTCTTTC
Found at i:41251510 original size:24 final size:23
Alignment explanation
Indices: 41251360--41251580 Score: 140
Period size: 24 Copynumber: 9.6 Consensus size: 23
41251350 TTCCTTCCCT
*
41251360 CTTCTTCTTCTTTCTTTT-TTT-
1 CTTCTTTTTCTTTCTTTTCTTTC
41251381 -TTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTTTT-TC-TTT-CTTTTCTTTC
* *
41251406 TTTCCTTCTT-TTTCTTTTCTTT-
1 CTT-CTTTTTCTTTCTTTTCTTTC
*
41251428 -TTCTTTTCTCCTTTCCTTTTCTTTC
1 CTTC-TTT-TTCTTT-CTTTTCTTTC
41251453 CTTCTTTTTCTTTC-TTT-TTT-
1 CTTCTTTTTCTTTCTTTTCTTTC
* *
41251473 GTTC-TTCTCATTTCCTTTTCTTTC
1 CTTCTTTTTC-TTT-CTTTTCTTTC
* *
41251497 CTTCTTTTTCTTTCTTTCCTCTC
1 CTTCTTTTTCTTTCTTTTCTTTC
* * *
41251520 CTCTCCTTTTCTTTCTTTCCTCTC
1 CT-TCTTTTTCTTTCTTTTCTTTC
*
41251544 CTTTCCTTTTCTTTC-TTTCTTTC
1 C-TTCTTTTTCTTTCTTTTCTTTC
* *
41251567 TTTCTTCTTCTTTC
1 CTTCTTTTTCTTTC
41251581 CCTCTCCTTC
Statistics
Matches: 162, Mismatches: 17, Indels: 41
0.74 0.08 0.19
Matches are distributed among these distances:
19 4 0.02
20 13 0.08
21 10 0.06
22 21 0.13
23 37 0.23
24 59 0.36
25 8 0.05
26 6 0.04
27 4 0.02
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.69
Consensus pattern (23 bp):
CTTCTTTTTCTTTCTTTTCTTTC
Found at i:41251675 original size:27 final size:26
Alignment explanation
Indices: 41251629--41251696 Score: 84
Period size: 27 Copynumber: 2.5 Consensus size: 26
41251619 TATAAGGGCA
41251629 GTGCCGCCAACCTCA-TTGGCACCATCG
1 GTGCCGCCAA--TCAGTTGGCACCATCG
* *
41251656 GTGCCGCCAATCAGTATGGCACCTTTG
1 GTGCCGCCAATCAGT-TGGCACCATCG
41251683 GTGCCGCCAATCAG
1 GTGCCGCCAATCAG
41251697 AAACCCGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
25 3 0.08
26 1 0.03
27 33 0.89
ACGTcount: A:0.19, C:0.35, G:0.25, T:0.21
Consensus pattern (26 bp):
GTGCCGCCAATCAGTTGGCACCATCG
Found at i:41261561 original size:9 final size:9
Alignment explanation
Indices: 41261549--41261612 Score: 58
Period size: 9 Copynumber: 6.9 Consensus size: 9
41261539 TTTAATTAAT
41261549 TTTTAAAAA
1 TTTTAAAAA
41261558 TTTTAAAAA
1 TTTTAAAAA
**
41261567 TTCAAAAAA
1 TTTTAAAAA
*
41261576 TTATAAAACCA
1 TTTTAAAA--A
*
41261587 TTTTTAAAA
1 TTTTAAAAA
41261596 -TTTAAAAA
1 TTTTAAAAA
41261604 TTGTTAAAA
1 TT-TTAAAA
41261613 TTATTAAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
8 7 0.16
9 24 0.55
10 6 0.14
11 7 0.16
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.39
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:41262288 original size:47 final size:45
Alignment explanation
Indices: 41262237--41262404 Score: 141
Period size: 47 Copynumber: 3.6 Consensus size: 45
41262227 TATTTAATAT
*
41262237 TAATTATTTTAAATTGTATAAATTCATATAAGAAAAATTATTATCAA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTAT-AA
* * **
41262284 TAATT-TTATGAAA-TTATATATT-AT-T-ATTAAATTATATGTAATAA
1 TAATTATT-TTAAATTTATAAATTCATATAAGAAAATT-TAT-T-ATAA
* *
41262328 TAATTATTTTAAATTATACAAATTCATATAAGAAAATTTATTAGTTA
1 TAATTATTTTAAATT-TATAAATTCATATAAGAAAATTTATTA-TAA
41262375 TAATTATTTTAAATTTTATTAAA-TCATATA
1 TAATTATTTTAAA-TTTA-TAAATTCATATA
41262405 TTTTAATTAA
Statistics
Matches: 96, Mismatches: 12, Indels: 26
0.72 0.09 0.19
Matches are distributed among these distances:
42 5 0.05
43 4 0.04
44 14 0.15
45 12 0.12
46 10 0.10
47 36 0.38
48 9 0.09
49 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.47
Consensus pattern (45 bp):
TAATTATTTTAAATTTATAAATTCATATAAGAAAATTTATTATAA
Found at i:41262331 original size:44 final size:43
Alignment explanation
Indices: 41262201--41262345 Score: 116
Period size: 44 Copynumber: 3.2 Consensus size: 43
41262191 AAGAATTTTA
* *
41262201 TGAAATTATATATCATTATTAAATTATATTTAATATTAATTATT
1 TGAAATTATATATAATTATTAAATTATA-TTAATAATAATTATT
* * * *
41262245 TTAAATTGTATA-AATTCATATAAGA-AAAATTATTATCAATAATT-TT
1 TGAAATTATATATAATT-AT-TAA-ATTATATTA--AT-AATAATTATT
*
41262291 ATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATT
1 -TGAAATTATATATAATTATTAAATTATAT-TAATAATAATTATT
*
41262336 TTAAATTATA
1 TGAAATTATA
41262346 CAAATTCATA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
43 3 0.04
44 31 0.40
45 10 0.13
46 11 0.14
47 20 0.26
48 3 0.04
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.48
Consensus pattern (43 bp):
TGAAATTATATATAATTATTAAATTATATTAATAATAATTATT
Found at i:41262339 original size:26 final size:28
Alignment explanation
Indices: 41262285--41262345 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
41262275 TATTATCAAT
* *
41262285 AATTTTATGAAATTATATATTATTATTA
1 AATTATATGAAATAATATATTATTATTA
*
41262313 AATTATATGTAATAATA-ATTATT-TTA
1 AATTATATGAAATAATATATTATTATTA
41262339 AATTATA
1 AATTATA
41262346 CAAATTCATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (28 bp):
AATTATATGAAATAATATATTATTATTA
Found at i:41262389 original size:91 final size:91
Alignment explanation
Indices: 41262185--41262370 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 91
41262175 ACCTCCAATG
* * * *
41262185 ATTATTAAGAATTTTATGAAATTATATATCATTATTAAATTATATTTAATATTAATTATTTTAAA
1 ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
* *
41262250 TTGTATAAATTCATATAAGAAAAATT
66 TTATACAAATTCATATAAGAAAAATT
*
41262276 ATTATCAATAATTTTATGAAATTATATATTATTATTAAATTATATGTAATAATAATTATTTTAAA
1 ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
*
41262341 TTATACAAATTCATATAAGAAAATTT
66 TTATACAAATTCATATAAGAAAAATT
41262367 ATTA
1 ATTA
41262371 GTTATAATTA
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 87 1.00
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.47
Consensus pattern (91 bp):
ATTATCAATAATTTTATGAAATTATATATCATTATTAAATTATATGTAATAATAATTATTTTAAA
TTATACAAATTCATATAAGAAAAATT
Found at i:41262507 original size:16 final size:15
Alignment explanation
Indices: 41262486--41262515 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
41262476 TAAATTCATA
41262486 TAAGAATTTTGATTAT
1 TAAGAATTTT-ATTAT
41262502 TAAGAATTTTATTA
1 TAAGAATTTTATTA
41262516 AATTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (15 bp):
TAAGAATTTTATTAT
Found at i:41262511 original size:120 final size:120
Alignment explanation
Indices: 41262386--41262799 Score: 683
Period size: 120 Copynumber: 3.5 Consensus size: 120
41262376 AATTATTTTA
* * *
41262386 AATTTTATTAAATCATATATTTTAATTAAAATATTTTTAATATTAATTACT-TCAAATTATATTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTA-TGTTAAATTATATTT
* *
41262450 TATAGTATCATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
*
41262506 AATTTTATTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
41262571 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
66 ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* *
41262626 AATTTTATT-AAGCTGTATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTT
1 AATTTTATTAAATC-ATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTT
41262690 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAG
65 TATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
* * *
41262745 AA-TTTATTAAATTATATATTTTAATTATAATATATTTAATAATTATTATGTTAAA
1 AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAA
41262800 ATATGATTAA
Statistics
Matches: 277, Mismatches: 14, Indels: 8
0.93 0.05 0.03
Matches are distributed among these distances:
118 45 0.16
119 22 0.08
120 210 0.76
ACGTcount: A:0.42, C:0.02, G:0.06, T:0.49
Consensus pattern (120 bp):
AATTTTATTAAATCATATATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTT
ATAGTATCATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAG
Found at i:41262523 original size:59 final size:60
Alignment explanation
Indices: 41262459--41262764 Score: 186
Period size: 59 Copynumber: 5.1 Consensus size: 60
41262449 TTATAGTATC
*
41262459 ATATATTATGATTTTAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAATT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAA-T
* * * * * * * * * *
41262520 ATATATTTTAATTAAAATATATTTA-ATAATAATTATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATT--ATTAAGAATTTTATTA-AAT
* * *
41262578 CATATATTATGATTTGAGTAAATTCATATAAGAATATTGATTATTAAGAATTTTATTAAGCT
1 -ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAA-AT
* * * * * * * * * * *
41262640 GTATATTTTAATTAAAATATATTTA-ATAATAATTATG-TTAAATT-A-TATTTTA-TAGTAT
1 ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATT--ATTAAGAATTTTATTA-AAT
* *
41262698 CATATATTATGATTTGAGTAAATTCATATAAG-ATATTGATTATTAAGAA-TTTATTAAATT
1 -ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAA-T
41262758 ATATATT
1 ATATATT
41262765 TTAATTATAA
Statistics
Matches: 174, Mismatches: 51, Indels: 42
0.65 0.19 0.16
Matches are distributed among these distances:
58 9 0.05
59 72 0.41
60 41 0.24
61 49 0.28
62 3 0.02
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (60 bp):
ATATATTATGATTTAAGTAAATTCATATAAGAATTTTGATTATTAAGAATTTTATTAAAT
Found at i:41262535 original size:18 final size:17
Alignment explanation
Indices: 41262507--41262541 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41262497 ATTATTAAGA
*
41262507 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
41262524 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
41262542 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:41277157 original size:24 final size:25
Alignment explanation
Indices: 41277130--41277177 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
41277120 AGAAGAAAGT
41277130 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
41277154 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
41277178 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:41277590 original size:19 final size:19
Alignment explanation
Indices: 41277568--41277612 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
41277558 AGTTTTTAAG
*
41277568 TTTTAAATATTTTTTGGAT
1 TTTTAAATATTTTTTGAAT
*
41277587 TTTTAAATATTTTTTTAAT
1 TTTTAAATATTTTTTGAAT
41277606 TTTTAAA
1 TTTTAAA
41277613 CGAATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.64
Consensus pattern (19 bp):
TTTTAAATATTTTTTGAAT
Found at i:41278284 original size:26 final size:26
Alignment explanation
Indices: 41278255--41278304 Score: 91
Period size: 26 Copynumber: 1.9 Consensus size: 26
41278245 CTTAAACTAA
41278255 ACTTTTTAAAAATATTTCTCAAAATC
1 ACTTTTTAAAAATATTTCTCAAAATC
*
41278281 ACTTTTTAAAAGTATTTCTCAAAA
1 ACTTTTTAAAAATATTTCTCAAAA
41278305 GTAATATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.14, G:0.02, T:0.42
Consensus pattern (26 bp):
ACTTTTTAAAAATATTTCTCAAAATC
Found at i:41280887 original size:21 final size:21
Alignment explanation
Indices: 41280861--41280911 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
41280851 CTCATTCTTT
**
41280861 CTTGGCAGTAGATTTAGTGGC
1 CTTGGCACCAGATTTAGTGGC
*
41280882 CTTGGCACCCGATTTAGTGGC
1 CTTGGCACCAGATTTAGTGGC
41280903 CTTGGCACC
1 CTTGGCACC
41280912 GTTGGATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.29
Consensus pattern (21 bp):
CTTGGCACCAGATTTAGTGGC
Found at i:41281321 original size:8 final size:8
Alignment explanation
Indices: 41281311--41281357 Score: 58
Period size: 8 Copynumber: 5.8 Consensus size: 8
41281301 TATATACATT
*
41281311 TTTTTATT
1 TTTTTATA
41281319 TTTTTATA
1 TTTTTATA
41281327 TTTTTATA
1 TTTTTATA
41281335 TTTTTAATA
1 TTTTT-ATA
* *
41281344 ATTTTAAA
1 TTTTTATA
41281352 TTTTTA
1 TTTTTA
41281358 ATTAATTGCT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
8 27 0.79
9 7 0.21
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTTATA
Found at i:41281338 original size:17 final size:17
Alignment explanation
Indices: 41281311--41281359 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
41281301 TATATACATT
*
41281311 TTTTTAT-TTTTTTATA
1 TTTTTATATTTTTAATA
41281327 TTTTTATATTTTTAATA
1 TTTTTATATTTTTAATA
* *
41281344 ATTTTAAATTTTTAAT
1 TTTTTATATTTTTAAT
41281360 TAATTGCTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
16 7 0.24
17 22 0.76
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTATATTTTTAATA
Found at i:41288474 original size:2 final size:2
Alignment explanation
Indices: 41288467--41288493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41288457 CGCATTAACA
41288467 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 A
41288494 AAGAGAGAAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41288579 original size:2 final size:2
Alignment explanation
Indices: 41288572--41288598 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41288562 CGCATTAACA
41288572 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 A
41288599 AAGAGAGAAA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41288580 original size:105 final size:106
Alignment explanation
Indices: 41288413--41288624 Score: 408
Period size: 105 Copynumber: 2.0 Consensus size: 106
41288403 CTGCAAAGAT
41288413 TCCTCTATTATTGATATCACTGTCAAACATTGCAATCTTGCTGACGCATTAACAATATATATATA
1 TCCTCTATTATTGATATCACTGTCAAACATTGCAATCTTGCTGACGCATTAACAATATATATATA
41288478 TATATATATATATATAAAGAGAGAAAAACC-GGATTGATGG
66 TATATATATATATATAAAGAGAGAAAAACCAGGATTGATGG
41288518 TCCTCTATTATTGATATCACTGTCAAACATTGCAATCTTGCTGACGCATTAACAATATATATATA
1 TCCTCTATTATTGATATCACTGTCAAACATTGCAATCTTGCTGACGCATTAACAATATATATATA
41288583 TATATATATATATATAAAGAGAGAAAAACCATGGATTGATGG
66 TATATATATATATATAAAGAGAGAAAAACCA-GGATTGATGG
41288625 ATGTGGCAAG
Statistics
Matches: 105, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
105 95 0.90
107 10 0.10
ACGTcount: A:0.39, C:0.14, G:0.13, T:0.33
Consensus pattern (106 bp):
TCCTCTATTATTGATATCACTGTCAAACATTGCAATCTTGCTGACGCATTAACAATATATATATA
TATATATATATATATAAAGAGAGAAAAACCAGGATTGATGG
Found at i:41288911 original size:6 final size:6
Alignment explanation
Indices: 41288892--41288930 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
41288882 CCGCATTTGC
* *
41288892 TCAT-G TCATAG TCATGG TCATGG TCATGG TCTTGG TCAT
1 TCATGG TCATGG TCATGG TCATGG TCATGG TCATGG TCAT
41288931 ACAAGGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.38
Consensus pattern (6 bp):
TCATGG
Found at i:41293396 original size:24 final size:24
Alignment explanation
Indices: 41293363--41293443 Score: 85
Period size: 24 Copynumber: 3.4 Consensus size: 24
41293353 ATGCTGAGGA
*
41293363 TGCTCATCTACCTTGGTTGGAAAC
1 TGCTCCTCTACCTTGGTTGGAAAC
* *
41293387 TGCTCCTCTACTTTGGTAGGAAGA-
1 TGCTCCTCTACCTTGGTTGGAA-AC
* *
41293411 TCCT-CTGCTACCTTGGTTGGAACC
1 TGCTCCT-CTACCTTGGTTGGAAAC
41293435 TGCTCCTCT
1 TGCTCCTCT
41293444 TTCTTAGTTG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
23 2 0.04
24 40 0.89
25 3 0.07
ACGTcount: A:0.16, C:0.28, G:0.21, T:0.35
Consensus pattern (24 bp):
TGCTCCTCTACCTTGGTTGGAAAC
Found at i:41308337 original size:16 final size:17
Alignment explanation
Indices: 41308305--41308340 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
41308295 ATTATGTTAA
41308305 TAATTTATTTAAAATTT
1 TAATTTATTTAAAATTT
*
41308322 TAATTT-TTTTAAATTT
1 TAATTTATTTAAAATTT
41308338 TAA
1 TAA
41308341 AAAAATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.67
17 6 0.33
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
TAATTTATTTAAAATTT
Found at i:41309290 original size:6 final size:6
Alignment explanation
Indices: 41309279--41309305 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
41309269 ATTAAGAAGC
41309279 AAAAGG AAAAGG AAAAGG AAAAGG AAA
1 AAAAGG AAAAGG AAAAGG AAAAGG AAA
41309306 CAAACTTAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:41312770 original size:46 final size:46
Alignment explanation
Indices: 41312656--41312774 Score: 118
Period size: 46 Copynumber: 2.6 Consensus size: 46
41312646 ACTGCTACAT
* * *
41312656 TGCTCTTAAACACAAACTT-AATCTGTTTA-CACAAAATAAATGATGA
1 TGCTCTTAAGCACAAGCTTAAAT-TGTTCATC-CAAAATAAATGATGA
** *
41312702 TGCTCTTAAGCATGAGCTTAAATTGTTCATCCAAAATAAATGATGT
1 TGCTCTTAAGCACAAGCTTAAATTGTTCATCCAAAATAAATGATGA
* *
41312748 TGTTCTTAAGTACAAG-TATAAATTGTT
1 TGCTCTTAAGCACAAGCT-TAAATTGTT
41312775 TATATATATA
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
45 1 0.02
46 55 0.92
47 4 0.07
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (46 bp):
TGCTCTTAAGCACAAGCTTAAATTGTTCATCCAAAATAAATGATGA
Found at i:41314152 original size:21 final size:21
Alignment explanation
Indices: 41314119--41314163 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
41314109 TACCTAATTT
41314119 TATATTATAAAATT-ATTTGA
1 TATATTATAAAATTAATTTGA
41314139 TATATTACTAAAATTAGATTTGA
1 TATATTA-TAAAATTA-ATTTGA
41314162 TA
1 TA
41314164 ACATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 7 0.32
21 7 0.32
23 8 0.36
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
TATATTATAAAATTAATTTGA
Found at i:41314211 original size:26 final size:25
Alignment explanation
Indices: 41314154--41314222 Score: 77
Period size: 26 Copynumber: 2.7 Consensus size: 25
41314144 TACTAAAATT
* *
41314154 AGATTTGATAACATTTTTTTAAGTA
1 AGATTTGATAATACTTTTTTAAGTA
* *
41314179 AGTTTTGGTAATACATTTTTTAAGGTA
1 AGATTTGATAATAC-TTTTTTAA-GTA
41314206 A-ATTTGATAATACTTTT
1 AGATTTGATAATACTTTT
41314223 AATTATACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
25 14 0.39
26 18 0.50
27 4 0.11
ACGTcount: A:0.33, C:0.04, G:0.13, T:0.49
Consensus pattern (25 bp):
AGATTTGATAATACTTTTTTAAGTA
Found at i:41314772 original size:25 final size:25
Alignment explanation
Indices: 41314742--41314795 Score: 90
Period size: 25 Copynumber: 2.2 Consensus size: 25
41314732 ATAAAAAAAA
41314742 TTAAAATTAATTCCATATATTTTAG
1 TTAAAATTAATTCCATATATTTTAG
* *
41314767 TTAAAATTGATTTCATATATTTTAG
1 TTAAAATTAATTCCATATATTTTAG
41314792 TTAA
1 TTAA
41314796 TATGAGGGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.50
Consensus pattern (25 bp):
TTAAAATTAATTCCATATATTTTAG
Found at i:41317447 original size:3 final size:3
Alignment explanation
Indices: 41317439--41317475 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41317429 TTTAAATGAA
41317439 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
41317476 TCAACTCATG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:41331777 original size:104 final size:104
Alignment explanation
Indices: 41331597--41331804 Score: 407
Period size: 104 Copynumber: 2.0 Consensus size: 104
41331587 CTAATTGATG
41331597 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
1 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
41331662 GTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
66 GTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
41331701 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
1 ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
*
41331766 TTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
66 GTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
41331805 CAAACATAAC
Statistics
Matches: 103, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 103 1.00
ACGTcount: A:0.25, C:0.17, G:0.20, T:0.38
Consensus pattern (104 bp):
ATGTCTTTCATTGAATCGTTGTTGGATCCTATTCCATCCTAGATGGGGATTTGTTGGAAAATAAA
GTACAATGATGCTTCTTTGATACTGATGCGTCCATTCCA
Found at i:41334821 original size:58 final size:58
Alignment explanation
Indices: 41334748--41334871 Score: 221
Period size: 58 Copynumber: 2.1 Consensus size: 58
41334738 CCAAATTTGT
*
41334748 TCAGTAAAGGCTGAAGGGGTATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
1 TCAG-AAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
*
41334807 TCAGAAAGGCTGAAGGGGGATTAGGTATGAAGGAATCGGAGAGCTGGAATAGAGCTCA
1 TCAGAAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
41334865 TCAGAAA
1 TCAGAAA
41334872 CATACTTGCT
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
58 59 0.94
59 4 0.06
ACGTcount: A:0.36, C:0.10, G:0.35, T:0.19
Consensus pattern (58 bp):
TCAGAAAGGCTGAAGGGGGATTAGGTATGAAAGAATCGGAGAGCTGGAATAGAGCTCA
Found at i:41339368 original size:31 final size:29
Alignment explanation
Indices: 41339303--41339371 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
41339293 TTGTCCAAGA
***
41339303 GTAAATACTCAAAATTTGAAGGGTTAAAGT
1 GTAAATA-TCAAAATTTGAAGGACCAAAGT
41339333 GTAAATATCAAAAATTTGAAGGACCAATAGT
1 GTAAATATC-AAAATTTGAAGGACCAA-AGT
41339364 GTAAATAT
1 GTAAATAT
41339372 TTTAAGGATG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 2 0.06
30 21 0.62
31 11 0.32
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (29 bp):
GTAAATATCAAAATTTGAAGGACCAAAGT
Found at i:41341604 original size:90 final size:90
Alignment explanation
Indices: 41341444--41341659 Score: 256
Period size: 90 Copynumber: 2.4 Consensus size: 90
41341434 CTCCTTGGTT
* * * * * * *
41341444 TTAATGAGTTCATAGCCTAAAGTTTGGGTGGTCCTGCTAAGATGGACTTGATGAATTCATCGAAT
1 TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTCATCAAAT
* *
41341509 ATATAGGATGAACTACTAGATGCTC
66 ATATAGGATGAACCACTAAATGCTC
* *
41341534 TTAATGAGTTCATAACCTAGAGTTTGGGTGATCCTATTAAGACGAACTTGATGAAC-CTATCAAA
1 TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTC-ATCAAA
* *
41341598 TTTATAGGATGAGCCACTAAATGCTC
65 TATATAGGATGAACCACTAAATGCTC
* * *
41341624 TTAATGAATTCATATCCCAG-GTTTTGGGTGGTCCTA
1 TTAATGAGTTCATAACCTAGAG-TTTGGGTGGTCCTA
41341660 GTGAGATGGG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
89 2 0.02
90 105 0.98
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (90 bp):
TTAATGAGTTCATAACCTAGAGTTTGGGTGGTCCTACTAAGACGAACTTGATGAACTCATCAAAT
ATATAGGATGAACCACTAAATGCTC
Found at i:41341690 original size:90 final size:89
Alignment explanation
Indices: 41341444--41341690 Score: 250
Period size: 90 Copynumber: 2.7 Consensus size: 89
41341434 CTCCTTGGTT
* * * *
41341444 TTAATGAGTTCATAGCCTAAAGTTTGGGTGGTCCT-GCTAAGATGGACTTGATGAATTCATCGAA
1 TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAG-TAAGATGGACTTGATGAATTCAT-GAA
* * *
41341508 TATATAGGATGAACTACTAGATGCTC
64 TTTATAGGATGAACCACTAAATGCTC
* * * * * *
41341534 TTAATGAGTTCATAACCTAGAGTTTGGGTGATCCTATTAAGACGAACTTGATGAACCTATCA--A
1 TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAGTAAGATGGACTTGATGAA--T-TCATGA
*
41341597 ATTTATAGGATGAGCCACTAAATGCTC
63 ATTTATAGGATGAACCACTAAATGCTC
* * *
41341624 TTAATGAATTCATATCCCAG-GTTTTGGGTGGTCCTAGTGAGATGGGCTTGATGAATTCACTGAA
1 TTAATGAATTCATAACCCAGAG-TTTGGGTGGTCCTAGTAAGATGGACTTGATGAATTCA-TGAA
41341688 TTT
64 TTT
41341691 TTAAACTGAA
Statistics
Matches: 130, Mismatches: 19, Indels: 16
0.79 0.12 0.10
Matches are distributed among these distances:
87 3 0.02
88 1 0.01
89 1 0.01
90 121 0.93
92 1 0.01
93 3 0.02
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (89 bp):
TTAATGAATTCATAACCCAGAGTTTGGGTGGTCCTAGTAAGATGGACTTGATGAATTCATGAATT
TATAGGATGAACCACTAAATGCTC
Found at i:41342327 original size:14 final size:14
Alignment explanation
Indices: 41342310--41342338 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
41342300 TTACTAAAAT
41342310 TACATTAGATGAAA
1 TACATTAGATGAAA
41342324 TACATTAGATGAAA
1 TACATTAGATGAAA
41342338 T
1 T
41342339 TTTGTCTAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (14 bp):
TACATTAGATGAAA
Found at i:41343576 original size:27 final size:28
Alignment explanation
Indices: 41343532--41343591 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 28
41343522 AATAATTCAA
*
41343532 AAAAATTTATAAAAAATACT-TAAAATTT
1 AAAAATTTATAAAAAATA-TATAAAATTG
* *
41343560 AAAAATTTA-GAATAATATATAAAATTG
1 AAAAATTTATAAAAAATATATAAAATTG
41343587 AAAAA
1 AAAAA
41343592 AGTATTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 1 0.04
27 18 0.64
28 9 0.32
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (28 bp):
AAAAATTTATAAAAAATATATAAAATTG
Found at i:41343611 original size:28 final size:29
Alignment explanation
Indices: 41343580--41343634 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
41343570 AATAATATAT
*
41343580 AAAATTG-AAAAAAGTA-TTTAAATTTTAG
1 AAAATTGTAAAAAA-AACTTTAAATTTTAG
41343608 AAAATTGTAAAAAAAACTTTAAATTTT
1 AAAATTGTAAAAAAAACTTTAAATTTT
41343635 CAAAAACATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 16 0.67
ACGTcount: A:0.55, C:0.02, G:0.07, T:0.36
Consensus pattern (29 bp):
AAAATTGTAAAAAAAACTTTAAATTTTAG
Found at i:41343821 original size:21 final size:21
Alignment explanation
Indices: 41343797--41343837 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
41343787 AAAAAAGTCA
41343797 AAATATA-TAGATTTTTTAAAT
1 AAATATAGTA-ATTTTTTAAAT
*
41343818 AAATTTAGTAATTTTTTAAA
1 AAATATAGTAATTTTTTAAA
41343838 GAATTACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (21 bp):
AAATATAGTAATTTTTTAAAT
Found at i:41357720 original size:23 final size:23
Alignment explanation
Indices: 41357693--41357747 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 23
41357683 AAACTAATCC
41357693 TCTCTCAAATTTCC-TCTC-AATT
1 TCTCTCAAATTTCCTTC-CAAATT
41357715 TGCTCTCAAA-TTCCTTCCAAATT
1 T-CTCTCAAATTTCCTTCCAAATT
41357738 TCTCTCAAAT
1 TCTCTCAAAT
41357748 CCATATTTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
22 14 0.48
23 15 0.52
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (23 bp):
TCTCTCAAATTTCCTTCCAAATT
Found at i:41357742 original size:22 final size:21
Alignment explanation
Indices: 41357693--41357747 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
41357683 AAACTAATCC
41357693 TCTCTCAAATTTCCTCTCAATT
1 TCTCTCAAA-TTCCTCTCAATT
41357715 TGCTCTCAAATTCCT-TCCAAATT
1 T-CTCTCAAATTCCTCT-C-AATT
41357738 TCTCTCAAAT
1 TCTCTCAAAT
41357748 CCATATTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.03
22 16 0.53
23 13 0.43
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (21 bp):
TCTCTCAAATTCCTCTCAATT
Found at i:41359921 original size:16 final size:15
Alignment explanation
Indices: 41359891--41359919 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41359881 TCTCTTAATT
41359891 TTTTTAAAATATTTA
1 TTTTTAAAATATTTA
41359906 TTTTTAAAATATTT
1 TTTTTAAAATATTT
41359920 TACAATATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTTAAAATATTTA
Found at i:41360656 original size:15 final size:13
Alignment explanation
Indices: 41360619--41360653 Score: 54
Period size: 12 Copynumber: 2.7 Consensus size: 13
41360609 TTTCTTTTTT
41360619 ATTTTATTTAATA
1 ATTTTATTTAATA
41360632 A-TTTATTTAATA
1 ATTTTATTTAATA
41360644 ATTTTTATTT
1 A-TTTTATTT
41360654 TAAATAGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 12 0.60
13 1 0.05
14 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (13 bp):
ATTTTATTTAATA
Found at i:41369539 original size:4 final size:4
Alignment explanation
Indices: 41369532--41369569 Score: 76
Period size: 4 Copynumber: 9.5 Consensus size: 4
41369522 TTATATATAT
41369532 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG AT
41369570 TATTTAAGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (4 bp):
ATAG
Found at i:41377020 original size:931 final size:931
Alignment explanation
Indices: 41375218--41377060 Score: 3686
Period size: 931 Copynumber: 2.0 Consensus size: 931
41375208 TGCGTTTACT
41375218 TGAGTTTAGTATAAAAATAGCGGTAGCGGTGAGATTAGATACTGTAGTGATACTGTAGCGTGAGA
1 TGAGTTTAGTATAAAAATAGCGGTAGCGGTGAGATTAGATACTGTAGTGATACTGTAGCGTGAGA
41375283 CAAAAAGTAAGCTAAACGCACCGCACCCAATCACCCATCTAAACCCACCCTTGGTATTCCTGCCT
66 CAAAAAGTAAGCTAAACGCACCGCACCCAATCACCCATCTAAACCCACCCTTGGTATTCCTGCCT
41375348 GAGTATTAACCTTCAACTACACAAACATTACACAATTTCATAAATATTATTTAATTTATTATCAT
131 GAGTATTAACCTTCAACTACACAAACATTACACAATTTCATAAATATTATTTAATTTATTATCAT
41375413 AGCATTGATAATGTTGAATTCACTGGTTGGATAAAAAATCAATAGATATTTCGATTTTTTTAAAA
196 AGCATTGATAATGTTGAATTCACTGGTTGGATAAAAAATCAATAGATATTTCGATTTTTTTAAAA
41375478 AATTAAATAGATTGAGTCACAAATTAATATTAATTGATTCAAATTAAAAATTTGATTAAATTAAA
261 AATTAAATAGATTGAGTCACAAATTAATATTAATTGATTCAAATTAAAAATTTGATTAAATTAAA
41375543 AGTTGAACTAATTTTCAATATATAATTTTATTAATAATTTCTTTAATCAAATTATCCAAATCAAT
326 AGTTGAACTAATTTTCAATATATAATTTTATTAATAATTTCTTTAATCAAATTATCCAAATCAAT
41375608 TAAACCAATAATCTTATCATTGATCCAATTCTTAAAATTCTAATAAACCACTGGGCTACATGAAG
391 TAAACCAATAATCTTATCATTGATCCAATTCTTAAAATTCTAATAAACCACTGGGCTACATGAAG
41375673 CCCTTCGCAAGAGATTGGAGTAACTCTTGCTGTTTTAAATGATGAGTTATAATTAGCTTTTTTTT
456 CCCTTCGCAAGAGATTGGAGTAACTCTTGCTGTTTTAAATGATGAGTTATAATTAGCTTTTTTTT
41375738 TCTTCCTGTTTAATCAAGGGTAAGAGACCCGAGATTTGGTGGCCTTGTAAGGTTACTGGTAGCAA
521 TCTTCCTGTTTAATCAAGGGTAAGAGACCCGAGATTTGGTGGCCTTGTAAGGTTACTGGTAGCAA
41375803 ATGGAATGGTTTGTACCCCGAAAAAGAAAAGAAATGATGGGCAACAATTGGACCATCCAGCATGT
586 ATGGAATGGTTTGTACCCCGAAAAAGAAAAGAAATGATGGGCAACAATTGGACCATCCAGCATGT
41375868 CACGATCACATAATAACCAACCATTTGCCATCAGAATCAGATTTCAAAACTTCACCATATGCAAC
651 CACGATCACATAATAACCAACCATTTGCCATCAGAATCAGATTTCAAAACTTCACCATATGCAAC
41375933 ACATTTATGGAGTGGACCCATATAATTCCCTAGTTCTGACCTTTACAGTTTTGACCATCAAACTT
716 ACATTTATGGAGTGGACCCATATAATTCCCTAGTTCTGACCTTTACAGTTTTGACCATCAAACTT
41375998 GTGGATTCTACTCATTTTGCACTCTTCACAATGTCATAATAACCAAACTATTCGGAATCCCAAAA
781 GTGGATTCTACTCATTTTGCACTCTTCACAATGTCATAATAACCAAACTATTCGGAATCCCAAAA
41376063 TTGATTACAACATATCAACCTGTGCAACACATCAGTGGGGTGGAGATATGGACGTAACTCTTTTA
846 TTGATTACAACATATCAACCTGTGCAACACATCAGTGGGGTGGAGATATGGACGTAACTCTTTTA
41376128 TCAACCTGTGCAACACATCAG
911 TCAACCTGTGCAACACATCAG
41376149 TGAGTTTAGTATAAAAATAGCGGTAGCGGTGAGATTAGATACTGTAGTGATACTGTAGCGTGAGA
1 TGAGTTTAGTATAAAAATAGCGGTAGCGGTGAGATTAGATACTGTAGTGATACTGTAGCGTGAGA
41376214 CAAAAAGTAAGCTAAACGCACCGCACCCAATCACCCATCTAAACCCACCCTTGGTATTCCTGCCT
66 CAAAAAGTAAGCTAAACGCACCGCACCCAATCACCCATCTAAACCCACCCTTGGTATTCCTGCCT
41376279 GAGTATTAACCTTCAACTACACAAACATTACACAATTTCATAAATATTATTTAATTTATTATCAT
131 GAGTATTAACCTTCAACTACACAAACATTACACAATTTCATAAATATTATTTAATTTATTATCAT
41376344 AGCATTGATAATGTTGAATTCACTGGTTGGATAAAAAATCAATAGATATTTCGATTTTTTTAAAA
196 AGCATTGATAATGTTGAATTCACTGGTTGGATAAAAAATCAATAGATATTTCGATTTTTTTAAAA
41376409 AATTAAATAGATTGAGTCACAAATTAATATTAATTGATTCAAATTAAAAATTTGATTAAATTAAA
261 AATTAAATAGATTGAGTCACAAATTAATATTAATTGATTCAAATTAAAAATTTGATTAAATTAAA
41376474 AGTTGAACTAATTTTCAATATATAATTTTATTAATAATTTCTTTAATCAAATTATCCAAATCAAT
326 AGTTGAACTAATTTTCAATATATAATTTTATTAATAATTTCTTTAATCAAATTATCCAAATCAAT
41376539 TAAACCAATAATCTTATCATTGATCCAATTCTTAAAATTCTAATAAACCACTGGGCTACATGAAG
391 TAAACCAATAATCTTATCATTGATCCAATTCTTAAAATTCTAATAAACCACTGGGCTACATGAAG
41376604 CCCTTCGCAAGAGATTGGAGTAACTCTTGCTGTTTTAAATGATGAGTTATAATTAGCTTTTTTTT
456 CCCTTCGCAAGAGATTGGAGTAACTCTTGCTGTTTTAAATGATGAGTTATAATTAGCTTTTTTTT
41376669 TCTTCCTGTTTAATCAAGGGTAAGAGACCCGAGATTTGGTGGCCTTGTAAGGTTACTGGTAGCAA
521 TCTTCCTGTTTAATCAAGGGTAAGAGACCCGAGATTTGGTGGCCTTGTAAGGTTACTGGTAGCAA
41376734 ATGGAATGGTTTGTACCCCGAAAAAGAAAAGAAATGATGGGCAACAATTGGACCATCCAGCATGT
586 ATGGAATGGTTTGTACCCCGAAAAAGAAAAGAAATGATGGGCAACAATTGGACCATCCAGCATGT
41376799 CACGATCACATAATAACCAACCATTTGCCATCAGAATCAGATTTCAAAACTTCACCATATGCAAC
651 CACGATCACATAATAACCAACCATTTGCCATCAGAATCAGATTTCAAAACTTCACCATATGCAAC
41376864 ACATTTATGGAGTGGACCCATATAATTCCCTAGTTCTGACCTTTACAGTTTTGACCATCAAACTT
716 ACATTTATGGAGTGGACCCATATAATTCCCTAGTTCTGACCTTTACAGTTTTGACCATCAAACTT
41376929 GTGGATTCTACTCATTTTGCACTCTTCACAATGTCATAATAACCAAACTATTCGGAATCCCAAAA
781 GTGGATTCTACTCATTTTGCACTCTTCACAATGTCATAATAACCAAACTATTCGGAATCCCAAAA
41376994 TTGATTACAACATATCAACCTGTGCAACACATCAGTGGGGTGGAGATATGGACGTAACTCTTTTA
846 TTGATTACAACATATCAACCTGTGCAACACATCAGTGGGGTGGAGATATGGACGTAACTCTTTTA
41377059 TC
911 TC
41377061 TATGCAACTT
Statistics
Matches: 912, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
931 912 1.00
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.32
Consensus pattern (931 bp):
TGAGTTTAGTATAAAAATAGCGGTAGCGGTGAGATTAGATACTGTAGTGATACTGTAGCGTGAGA
CAAAAAGTAAGCTAAACGCACCGCACCCAATCACCCATCTAAACCCACCCTTGGTATTCCTGCCT
GAGTATTAACCTTCAACTACACAAACATTACACAATTTCATAAATATTATTTAATTTATTATCAT
AGCATTGATAATGTTGAATTCACTGGTTGGATAAAAAATCAATAGATATTTCGATTTTTTTAAAA
AATTAAATAGATTGAGTCACAAATTAATATTAATTGATTCAAATTAAAAATTTGATTAAATTAAA
AGTTGAACTAATTTTCAATATATAATTTTATTAATAATTTCTTTAATCAAATTATCCAAATCAAT
TAAACCAATAATCTTATCATTGATCCAATTCTTAAAATTCTAATAAACCACTGGGCTACATGAAG
CCCTTCGCAAGAGATTGGAGTAACTCTTGCTGTTTTAAATGATGAGTTATAATTAGCTTTTTTTT
TCTTCCTGTTTAATCAAGGGTAAGAGACCCGAGATTTGGTGGCCTTGTAAGGTTACTGGTAGCAA
ATGGAATGGTTTGTACCCCGAAAAAGAAAAGAAATGATGGGCAACAATTGGACCATCCAGCATGT
CACGATCACATAATAACCAACCATTTGCCATCAGAATCAGATTTCAAAACTTCACCATATGCAAC
ACATTTATGGAGTGGACCCATATAATTCCCTAGTTCTGACCTTTACAGTTTTGACCATCAAACTT
GTGGATTCTACTCATTTTGCACTCTTCACAATGTCATAATAACCAAACTATTCGGAATCCCAAAA
TTGATTACAACATATCAACCTGTGCAACACATCAGTGGGGTGGAGATATGGACGTAACTCTTTTA
TCAACCTGTGCAACACATCAG
Found at i:41378338 original size:29 final size:29
Alignment explanation
Indices: 41378296--41378353 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
41378286 CAAAGAATAG
41378296 TTACATTATAGCCAGTTTAGCTCCCCACA
1 TTACATTATAGCCAGTTTAGCTCCCCACA
41378325 TTACATTATAGCCAGTTTAGCTCCCCACA
1 TTACATTATAGCCAGTTTAGCTCCCCACA
41378354 ATATATTACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.31, G:0.10, T:0.31
Consensus pattern (29 bp):
TTACATTATAGCCAGTTTAGCTCCCCACA
Found at i:41378361 original size:29 final size:29
Alignment explanation
Indices: 41378297--41378361 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
41378287 AAAGAATAGT
*
41378297 TACATTATAGCCAGTTTAGCTCCCCACAT
1 TACATTATAGCCAGTTTAGCTCCCCACAA
41378326 TACATTATAGCCAGTTTAGCTCCCCACAA
1 TACATTATAGCCAGTTTAGCTCCCCACAA
*
41378355 TATATTA
1 TACATTA
41378362 CTGCTCCTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.28, G:0.09, T:0.32
Consensus pattern (29 bp):
TACATTATAGCCAGTTTAGCTCCCCACAA
Found at i:41395664 original size:9 final size:9
Alignment explanation
Indices: 41395652--41395679 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41395642 TTTTATTACA
41395652 ACAATTAAT
1 ACAATTAAT
41395661 ACAATTAAT
1 ACAATTAAT
41395670 ACAATTAAT
1 ACAATTAAT
41395679 A
1 A
41395680 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41395727 original size:68 final size:68
Alignment explanation
Indices: 41395618--41395831 Score: 405
Period size: 68 Copynumber: 3.2 Consensus size: 68
41395608 GTAAAAATAT
41395618 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
1 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
41395683 TGA
66 TGA
41395686 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
1 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
41395751 TGA
66 TGA
41395754 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATT-A-ACAATTAATAATT
1 TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
41395817 TGA
66 TGA
*
41395820 TAATTTTACTAA
1 TAAATTTACTAA
41395832 CAATTAATTT
Statistics
Matches: 145, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
66 27 0.19
67 1 0.01
68 117 0.81
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (68 bp):
TAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATACAATTAATAATT
TGA
Found at i:41395732 original size:9 final size:9
Alignment explanation
Indices: 41395720--41395747 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
41395710 TTTTATTACA
41395720 ACAATTAAT
1 ACAATTAAT
41395729 ACAATTAAT
1 ACAATTAAT
41395738 ACAATTAAT
1 ACAATTAAT
41395747 A
1 A
41395748 ATTTGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (9 bp):
ACAATTAAT
Found at i:41395841 original size:16 final size:16
Alignment explanation
Indices: 41395820--41395861 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
41395810 AATAATTTGA
*
41395820 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
41395836 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
41395852 TAGTTTTAAT
1 TAATTTTAAT
41395862 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:41395845 original size:22 final size:23
Alignment explanation
Indices: 41395835--41395890 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
41395825 TTACTAACAA
* * *
41395835 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
41395857 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
41395880 TTAATTTTAAT
1 TTAATTTTAAT
41395891 TTTAGTTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:41405609 original size:28 final size:28
Alignment explanation
Indices: 41405555--41405624 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
41405545 TTTGATATAT
* *
41405555 TTTTAT-AATTTTTACATTATTTGTAAG
1 TTTTATGAATTTTTAAATTATTTATAAG
41405582 TTTTATGAATTTTTAAATCT-TTTATAAG
1 TTTTATGAATTTTTAAAT-TATTTATAAG
*
41405610 ATTT-TGAATGTTTTA
1 TTTTATGAAT-TTTTA
41405625 GTAATTTATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.30
28 25 0.68
29 1 0.03
ACGTcount: A:0.30, C:0.03, G:0.09, T:0.59
Consensus pattern (28 bp):
TTTTATGAATTTTTAAATTATTTATAAG
Found at i:41406114 original size:3 final size:3
Alignment explanation
Indices: 41406106--41406142 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
41406096 TATAATTAAA
41406106 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
41406143 TTCCCTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:41417909 original size:24 final size:24
Alignment explanation
Indices: 41417849--41417909 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
41417839 TGCTGCAGTC
* *
41417849 GATGGTGAGGATGGTAATGGTGAT
1 GATGGTGACGATGGTAATGATGAT
* * *
41417873 GACGGTGATGATGGTATTGATGAT
1 GATGGTGACGATGGTAATGATGAT
*
41417897 GATGATGACGATG
1 GATGGTGACGATG
41417910 ACGATGAAGC
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.26, C:0.03, G:0.41, T:0.30
Consensus pattern (24 bp):
GATGGTGACGATGGTAATGATGAT
Found at i:41430618 original size:16 final size:17
Alignment explanation
Indices: 41430588--41430619 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41430578 TATTTTAAAA
41430588 TTTCTTTTACAATTTTT
1 TTTCTTTTACAATTTTT
41430605 TTTCTTTT-CAATTTT
1 TTTCTTTTACAATTTT
41430620 AGAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.16, C:0.12, G:0.00, T:0.72
Consensus pattern (17 bp):
TTTCTTTTACAATTTTT
Found at i:41432245 original size:25 final size:27
Alignment explanation
Indices: 41432174--41432238 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
41432164 CCTATCAGGT
*
41432174 AGGCGCCAATGAAGGTGCCTGATAGAG
1 AGGCGCCAATGAATGTGCCTGATAGAG
41432201 AGGCGCCAATGAATGTGCCTGATAGAG
1 AGGCGCCAATGAATGTGCCTGATAGAG
41432228 AGGCGCCAATG
1 AGGCGCCAATG
41432239 GTGGCCTTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.20, G:0.35, T:0.15
Consensus pattern (27 bp):
AGGCGCCAATGAATGTGCCTGATAGAG
Found at i:41432384 original size:3 final size:3
Alignment explanation
Indices: 41432378--41432430 Score: 83
Period size: 3 Copynumber: 18.3 Consensus size: 3
41432368 GAGAGAAAGG
*
41432378 AGA AGA AG- AGA AGG AGA AGA AGA AGA AGA AG- AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
41432424 AGA AGA A
1 AGA AGA A
41432431 AAAAAGGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:41432404 original size:23 final size:23
Alignment explanation
Indices: 41432378--41432430 Score: 97
Period size: 23 Copynumber: 2.3 Consensus size: 23
41432368 GAGAGAAAGG
*
41432378 AGAAGAAGAGAAGGAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
41432401 AGAAGAAGAGAAGAAGAAGAAGA
1 AGAAGAAGAGAAGAAGAAGAAGA
41432424 AGAAGAA
1 AGAAGAA
41432431 AAAAAGGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (23 bp):
AGAAGAAGAGAAGAAGAAGAAGA
Found at i:41432515 original size:12 final size:12
Alignment explanation
Indices: 41432498--41432523 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
41432488 GTTTGTGAAT
41432498 TTTTAGAAGATA
1 TTTTAGAAGATA
41432510 TTTTAGAAGATA
1 TTTTAGAAGATA
41432522 TT
1 TT
41432524 GTGAATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
TTTTAGAAGATA
Found at i:41432636 original size:21 final size:21
Alignment explanation
Indices: 41432592--41432777 Score: 163
Period size: 22 Copynumber: 9.0 Consensus size: 21
41432582 TAGATTAGAA
*
41432592 TTTTGTATGAATATTCTAACTT
1 TTTTGTATGAATATTGTAA-TT
41432614 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
*
41432635 TTTTTTATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
* *
41432654 TGTTGTCTGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
41432675 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
41432697 TATAGTTTTGGAT-TAGTAA--
1 TTTTG-TATGAATATTGTAATT
41432716 -TTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
41432736 TTTTGTATGAATATTGTAATTT
1 TTTTGTATGAATATTGTAA-TT
41432758 TTTTGTATGAATATTGTAAT
1 TTTTGTATGAATATTGTAAT
41432778 ATTATAGTTT
Statistics
Matches: 130, Mismatches: 21, Indels: 27
0.73 0.12 0.15
Matches are distributed among these distances:
17 5 0.04
18 7 0.05
19 16 0.12
20 3 0.02
21 44 0.34
22 48 0.37
23 7 0.05
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.55
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:41432790 original size:27 final size:22
Alignment explanation
Indices: 41432716--41432800 Score: 118
Period size: 22 Copynumber: 3.7 Consensus size: 22
41432706 GGATTAGTAA
41432716 TTTGTATGAATATTGTAA-TTT
1 TTTGTATGAATATTGTAATTTT
41432737 TTTGTATGAATATTGTAATTTT
1 TTTGTATGAATATTGTAATTTT
41432759 TTTGTATGAATATTGTAATATTATAGT
1 TTTGTATGAATATTGT-A-ATT-T--T
41432786 TTTGTATGAATATTG
1 TTTGTATGAATATTG
41432801 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
21 18 0.31
22 19 0.33
23 1 0.02
24 3 0.05
25 1 0.02
27 16 0.28
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.55
Consensus pattern (22 bp):
TTTGTATGAATATTGTAATTTT
Found at i:41434906 original size:6 final size:6
Alignment explanation
Indices: 41434895--41434935 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
41434885 GCATCATGCA
* * *
41434895 CCAGAG CCAGAG CCTGAG CCAGAG CTAGAG CCAGAG ACAGA
1 CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGAG CCAGA
41434936 ACTATATTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.34, C:0.29, G:0.32, T:0.05
Consensus pattern (6 bp):
CCAGAG
Found at i:41438286 original size:21 final size:21
Alignment explanation
Indices: 41438260--41438311 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
41438250 AATACCTTAT
*
41438260 TTTTTTCTTCT-TTTCCTTCC
1 TTTTTTCTTCTGCTTCCTTCC
41438280 TTCTTTTCTTCTGCTTCCTTCC
1 TT-TTTTCTTCTGCTTCCTTCC
*
41438302 TTATTTCTTC
1 TTTTTTCTTC
41438312 CGTTTCTGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 16 0.57
22 10 0.36
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.65
Consensus pattern (21 bp):
TTTTTTCTTCTGCTTCCTTCC
Found at i:41440394 original size:11 final size:11
Alignment explanation
Indices: 41440380--41440419 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
41440370 TGTTTTCTCC
41440380 CTATTTTGCTA
1 CTATTTTGCTA
*
41440391 CTATTTTACTA
1 CTATTTTGCTA
* *
41440402 TTATGTTGCTA
1 CTATTTTGCTA
41440413 CTATTTT
1 CTATTTT
41440420 TGTTGGTATT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.20, C:0.15, G:0.07, T:0.57
Consensus pattern (11 bp):
CTATTTTGCTA
Found at i:41440520 original size:30 final size:30
Alignment explanation
Indices: 41440461--41440520 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
41440451 TATTTTATTA
*
41440461 TTAATTTTGTTATTATTTTAAAGGCATTTG
1 TTAATTTTGTTATTATTTTAAAGGAATTTG
41440491 TTAATTTTGTTATTATTTTAGAA-GAATTTG
1 TTAATTTTGTTATTATTTTA-AAGGAATTTG
41440521 CTTGTTAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.28, C:0.02, G:0.13, T:0.57
Consensus pattern (30 bp):
TTAATTTTGTTATTATTTTAAAGGAATTTG
Found at i:41443882 original size:7 final size:7
Alignment explanation
Indices: 41443870--41443902 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
41443860 TCCAGCAAAA
41443870 ATGAAAT
1 ATGAAAT
41443877 ATGAAAT
1 ATGAAAT
41443884 ATGAAAT
1 ATGAAAT
41443891 ATGAAAT
1 ATGAAAT
*
41443898 GTGAA
1 ATGAA
41443903 TGGTATGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.55, C:0.00, G:0.18, T:0.27
Consensus pattern (7 bp):
ATGAAAT
Found at i:41458380 original size:12 final size:12
Alignment explanation
Indices: 41458342--41458381 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
41458332 ATTATTTATG
41458342 TCTTTT-ATAAA
1 TCTTTTAATAAA
41458353 T-TTTTAAT-AA
1 TCTTTTAATAAA
*
41458363 TATTTTAATAAA
1 TCTTTTAATAAA
41458375 TCTTTTA
1 TCTTTTA
41458382 TATCATTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 7 0.28
11 10 0.40
12 8 0.32
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (12 bp):
TCTTTTAATAAA
Found at i:41458440 original size:18 final size:18
Alignment explanation
Indices: 41458417--41458453 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
41458407 AATCTTAAAT
41458417 ATTGAAACTTGAATCTTC
1 ATTGAAACTTGAATCTTC
41458435 ATTGAAACTTGAATCTTC
1 ATTGAAACTTGAATCTTC
41458453 A
1 A
41458454 GAGTTCGGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (18 bp):
ATTGAAACTTGAATCTTC
Found at i:41466401 original size:14 final size:14
Alignment explanation
Indices: 41466382--41466409 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
41466372 ACTCGGCATA
41466382 AGACTTGGCAAAAT
1 AGACTTGGCAAAAT
41466396 AGACTTGGCAAAAT
1 AGACTTGGCAAAAT
41466410 TCAGACATGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (14 bp):
AGACTTGGCAAAAT
Found at i:41467731 original size:152 final size:153
Alignment explanation
Indices: 41467455--41467759 Score: 603
Period size: 152 Copynumber: 2.0 Consensus size: 153
41467445 TGGAACAAAT
41467455 GCGAATATTTATCAGATTTGAGAGATTAATTAATTAGCCAAATGACATGGATTGCAAATAATTCA
1 GCGAATATTTATCAGATTTGAGAGATTAATTAATTAGCCAAATGACATGGATTGCAAATAATTCA
41467520 CCATTTACAATTTGCTAACCAACTGAACAGTATTTTTTTTTTTTTGGTTTTATAGTAATTTAAAA
66 CCATTTACAATTTGCTAACCAACTGAACAGTATTTTTTTTTTTTTGGTTTTATAGTAATTTAAAA
41467585 TTTTACTGAAGT-ATAAAAAGTA
131 TTTTACTGAAGTAATAAAAAGTA
41467607 GCGAATATTTATCAGATTTGAGAGATTAATTAATTAGCCAAATGACATGGATTGCAAATAATTCA
1 GCGAATATTTATCAGATTTGAGAGATTAATTAATTAGCCAAATGACATGGATTGCAAATAATTCA
41467672 CCATTTACAATTTGCTAACCAACTGAACAGTATTTTTTTTTTTTTGGTTTTATAGTAATTTAAAA
66 CCATTTACAATTTGCTAACCAACTGAACAGTATTTTTTTTTTTTTGGTTTTATAGTAATTTAAAA
41467737 TTTTACTGAAGTAATAAAAAGTA
131 TTTTACTGAAGTAATAAAAAGTA
41467760 AATGAAAAAA
Statistics
Matches: 152, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
152 142 0.93
153 10 0.07
ACGTcount: A:0.37, C:0.10, G:0.13, T:0.39
Consensus pattern (153 bp):
GCGAATATTTATCAGATTTGAGAGATTAATTAATTAGCCAAATGACATGGATTGCAAATAATTCA
CCATTTACAATTTGCTAACCAACTGAACAGTATTTTTTTTTTTTTGGTTTTATAGTAATTTAAAA
TTTTACTGAAGTAATAAAAAGTA
Found at i:41467850 original size:22 final size:22
Alignment explanation
Indices: 41467821--41467873 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
41467811 ATATATATAT
* * *
41467821 AATT-AATAGAATTGATTTTAA
1 AATTAAATAAAATTAATTTCAA
*
41467842 AGTTAAATAAAATTAATTTCAA
1 AATTAAATAAAATTAATTTCAA
41467864 AATTAAATAA
1 AATTAAATAA
41467874 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.55, C:0.02, G:0.06, T:0.38
Consensus pattern (22 bp):
AATTAAATAAAATTAATTTCAA
Found at i:41476602 original size:71 final size:73
Alignment explanation
Indices: 41476461--41476610 Score: 187
Period size: 71 Copynumber: 2.1 Consensus size: 73
41476451 ACTTTTGGTT
* **
41476461 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTTATGTCACTTGGC
1 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
*
41476526 CATTAACC
66 CATTAACA
* * * * * *
41476534 AAGAGTTGTCAC-ATTTATAGTGATGAGTTATGTCTCTTG-TTACCAAAAGTCATGTCATTTAAT
1 AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
*
41476597 TATTAACA
66 CATTAACA
41476605 AAGAGT
1 AAGAGT
41476611 CATAATTATT
Statistics
Matches: 66, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
71 30 0.45
72 24 0.36
73 12 0.18
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (73 bp):
AAGAGTTGTCACTATTTATAGTGATAAATTAGGTCTCTTGAATACCAAAAGTCATGTCACTTAAC
CATTAACA
Found at i:41482150 original size:22 final size:21
Alignment explanation
Indices: 41482107--41482150 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
41482097 TACGCGTGTG
*
41482107 TTTTTAGATATTATCTTCTAA
1 TTTTTAGATATTATATTCTAA
* *
41482128 TTTTTATATATTTATATTTTAA
1 TTTTTAGATA-TTATATTCTAA
41482150 T
1 T
41482151 GCGGATTGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.30, C:0.05, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTTAGATATTATATTCTAA
Found at i:41493772 original size:27 final size:27
Alignment explanation
Indices: 41493734--41493789 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
41493724 ATTATAATAT
41493734 AAAATACTAATAGAATAG-AAGAAGAAG
1 AAAATACTAATAGAATAGAAAGAA-AAG
*
41493761 AAAATACTAATATAATAGAAAGAAAAG
1 AAAATACTAATAGAATAGAAAGAAAAG
41493788 AA
1 AA
41493790 TTGTCTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 22 0.81
28 5 0.19
ACGTcount: A:0.66, C:0.04, G:0.14, T:0.16
Consensus pattern (27 bp):
AAAATACTAATAGAATAGAAAGAAAAG
Found at i:41494966 original size:12 final size:12
Alignment explanation
Indices: 41494951--41494975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41494941 TCTCTCTCTC
41494951 TCTCTCGTTCTA
1 TCTCTCGTTCTA
41494963 TCTCTCGTTCTA
1 TCTCTCGTTCTA
41494975 T
1 T
41494976 GGATGGAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.32, G:0.08, T:0.52
Consensus pattern (12 bp):
TCTCTCGTTCTA
Found at i:41502597 original size:95 final size:96
Alignment explanation
Indices: 41502434--41502628 Score: 383
Period size: 95 Copynumber: 2.0 Consensus size: 96
41502424 GATAATTGTC
41502434 AATTTCGAAAATGAACAAATTGATATCTCTCAATAAAAAATATAAAAAAAATTCAAAATATTTAT
1 AATTTCGAAAATGAACAAATTGATATCTCTCAATAAAAAATATAAAAAAAATTCAAAATATTTAT
41502499 AAAATTTCCAAATTTAATATAA-ATTTTTAA
66 AAAATTTCCAAATTTAATATAATATTTTTAA
41502529 AATTTCGAAAATGAACAAATTGATATCTCTCAATAAAAAATATAAAAAAAATTCAAAATATTTAT
1 AATTTCGAAAATGAACAAATTGATATCTCTCAATAAAAAATATAAAAAAAATTCAAAATATTTAT
41502594 AAAATTTCCAAATTTAATATAATATTTTTAA
66 AAAATTTCCAAATTTAATATAATATTTTTAA
41502625 AATT
1 AATT
41502629 ATTCTAAAAA
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 87 0.88
96 12 0.12
ACGTcount: A:0.53, C:0.08, G:0.03, T:0.35
Consensus pattern (96 bp):
AATTTCGAAAATGAACAAATTGATATCTCTCAATAAAAAATATAAAAAAAATTCAAAATATTTAT
AAAATTTCCAAATTTAATATAATATTTTTAA
Found at i:41502867 original size:22 final size:22
Alignment explanation
Indices: 41502824--41502868 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
41502814 TGTAACAAGA
***
41502824 TTTTAATTTAACACGTTTAATT
1 TTTTAATTTAACACGAACAATT
*
41502846 TTTTAATTTAACTCGAACAATT
1 TTTTAATTTAACACGAACAATT
41502868 T
1 T
41502869 CACTCGATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.51
Consensus pattern (22 bp):
TTTTAATTTAACACGAACAATT
Found at i:41507452 original size:16 final size:16
Alignment explanation
Indices: 41507415--41507454 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
41507405 TTGATAAAAT
* *
41507415 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
41507431 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
41507447 TAAAATTA
1 TAAAATTA
41507455 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Done.