Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A04
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: 81554553
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2322942 characters in sequence are not A, C, G, or T
File 167 of 253
Found at i:54239656 original size:39 final size:40
Alignment explanation
Indices: 54239611--54239835 Score: 233
Period size: 40 Copynumber: 5.7 Consensus size: 40
54239601 GCTCCTCGTT
* * * *
54239611 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
*
54239651 C-AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* *
54239690 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * * *
54239730 CAAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCA
1 CAAATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCA
** * * * *
54239770 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
54239811 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
54239836 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 22, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.24
40 105 0.67
41 14 0.09
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:54239844 original size:41 final size:41
Alignment explanation
Indices: 54239767--54239844 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54239757 CTTGTATCTC
* * *
54239767 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54239808 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54239845 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54246915 original size:39 final size:40
Alignment explanation
Indices: 54246872--54246978 Score: 126
Period size: 39 Copynumber: 2.7 Consensus size: 40
54246862 TCCTCGTTCA
* * *
54246872 AATGCCTTCGGGACATAGCCCAGTTTTAGTAACCCACAC-
1 AATGCCTTCGGGACATAACCCAGATTTAATAACCCACACG
* * * *
54246911 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACATAACCCAGATTTAATAACCCACACG
* *
54246951 AATGCCTTCGGGACTTAACCCGGATTTA
1 AATGCCTTCGGGACATAACCCAGATTTA
54246979 GTATCTCGCA
Statistics
Matches: 60, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
39 32 0.53
40 28 0.47
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.25
Consensus pattern (40 bp):
AATGCCTTCGGGACATAACCCAGATTTAATAACCCACACG
Found at i:54246966 original size:40 final size:39
Alignment explanation
Indices: 54246872--54247094 Score: 198
Period size: 40 Copynumber: 5.6 Consensus size: 39
54246862 TCCTCGTTCA
* * * * * *
54246872 AATGCCTTCGGGACATAGCCCAGTTTTAGTAACCCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
54246911 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
54246950 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * * *
54246990 AAAGGCCTTCGGGGCTTAACCCGGAACTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
54247030 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
54247071 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
54247095 CAGCATTCAA
Statistics
Matches: 153, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
39 36 0.24
40 106 0.69
41 11 0.07
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:54247103 original size:41 final size:41
Alignment explanation
Indices: 54247026--54247103 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
54247016 CTTGTATCTC
* * *
54247026 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
54247067 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
54247104 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:54250353 original size:35 final size:35
Alignment explanation
Indices: 54250304--54250462 Score: 149
Period size: 35 Copynumber: 4.5 Consensus size: 35
54250294 GTATATACAT
54250304 ATGTGATGATATATTGAACTTGTATATTTGGCTAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCTAC
* * * * * *
54250339 ATGTCATGTTATATTAAACTTGAACATTTGACTAC
1 ATGTGATGATATATTGAACTTGTATATTTGGCTAC
* * * * *
54250374 ATGTGATGTTTTATTGAGCTTGTATA-TTCGCTCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCT-AC
* * * * *
54250409 ATATAATGATATATTGTACTTGTATATTTGGCCAT
1 ATGTGATGATATATTGAACTTGTATATTTGGCTAC
*
54250444 ATGTGATGATATAATGAAC
1 ATGTGATGATATATTGAAC
54250463 CTTGAGTATT
Statistics
Matches: 95, Mismatches: 27, Indels: 4
0.75 0.21 0.03
Matches are distributed among these distances:
34 4 0.04
35 87 0.92
36 4 0.04
ACGTcount: A:0.30, C:0.10, G:0.17, T:0.43
Consensus pattern (35 bp):
ATGTGATGATATATTGAACTTGTATATTTGGCTAC
Found at i:54254231 original size:29 final size:30
Alignment explanation
Indices: 54254178--54254235 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
54254168 CGGAAGTTTT
54254178 GGCACTAAGTGTGCGATTTAAACTAGCTTG
1 GGCACTAAGTGTGCGATTTAAACTAGCTTG
54254208 GGCACTAAGTGTGCGATTT-AACTAGCTT
1 GGCACTAAGTGTGCGATTTAAACTAGCTT
54254236 CGGCTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.32
30 19 0.68
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (30 bp):
GGCACTAAGTGTGCGATTTAAACTAGCTTG
Found at i:54262299 original size:37 final size:38
Alignment explanation
Indices: 54262217--54262299 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 38
54262207 GCAGAGGATA
* * *
54262217 GCTCAACCCTTTGAAGCATCCCAATGGTGGGAAGATTT
1 GCTCAACCCTGTGAAGCATCCAAATGATGGGAAGATTT
*
54262255 GCTCAACCCTGTGGAGCAT-CAAGATGATGGG-AGATTT
1 GCTCAACCCTGTGAAGCATCCAA-ATGATGGGAAGATTT
54262292 GCTCAACC
1 GCTCAACC
54262300 TTTCGGAGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
37 16 0.40
38 24 0.60
ACGTcount: A:0.27, C:0.24, G:0.25, T:0.24
Consensus pattern (38 bp):
GCTCAACCCTGTGAAGCATCCAAATGATGGGAAGATTT
Found at i:54263371 original size:10 final size:10
Alignment explanation
Indices: 54263356--54263380 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
54263346 TGTAAAGTTG
54263356 ATAATTAAAA
1 ATAATTAAAA
54263366 ATAATTAAAA
1 ATAATTAAAA
54263376 ATAAT
1 ATAAT
54263381 AGTATTGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (10 bp):
ATAATTAAAA
Found at i:54263926 original size:21 final size:20
Alignment explanation
Indices: 54263891--54263945 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 20
54263881 CTTCAATCCC
*
54263891 CAATTTCAAATTTTATATTTT
1 CAATTTCAAA-TTTAAATTTT
54263912 CAATCTTCAAATTTAAATTTT
1 CAAT-TTCAAATTTAAATTTT
*
54263933 CAATTTCGAATTT
1 CAATTTCAAATTT
54263946 TCGATCCTCA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 8 0.26
21 17 0.55
22 6 0.19
ACGTcount: A:0.35, C:0.13, G:0.02, T:0.51
Consensus pattern (20 bp):
CAATTTCAAATTTAAATTTT
Found at i:54263938 original size:28 final size:28
Alignment explanation
Indices: 54263867--54263938 Score: 69
Period size: 28 Copynumber: 2.6 Consensus size: 28
54263857 ATTCTCGATC
* * *
54263867 TTTC-AATCTTCAATCTTCAATCCCCAA
1 TTTCAAATTTTCAATTTTCAATCCCAAA
*
54263894 TTTCAAATTTT-ATATTTTCAATCTTCAAA
1 TTTCAAATTTTCA-ATTTTCAATC-CCAAA
54263923 TTT-AAATTTTCAATTT
1 TTTCAAATTTTCAATTT
54263939 CGAATTTTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
27 5 0.14
28 25 0.68
29 7 0.19
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (28 bp):
TTTCAAATTTTCAATTTTCAATCCCAAA
Found at i:54267271 original size:32 final size:31
Alignment explanation
Indices: 54267202--54267271 Score: 76
Period size: 32 Copynumber: 2.3 Consensus size: 31
54267192 CTCCCTTTTC
54267202 TCTCTT-TTGCTACCGATTTCCCTTCGCCTA
1 TCTCTTGTTGCTACCGATTTCCCTTCGCCTA
*
54267232 T-TTTTGTTGCTACCGAAATTTCCCTT-GCCT-
1 TCTCTTGTTGCTACCG--ATTTCCCTTCGCCTA
54267262 TCCTCTTGTT
1 T-CTCTTGTT
54267272 TGTTTTATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
29 3 0.09
30 11 0.33
31 4 0.12
32 15 0.45
ACGTcount: A:0.10, C:0.31, G:0.11, T:0.47
Consensus pattern (31 bp):
TCTCTTGTTGCTACCGATTTCCCTTCGCCTA
Found at i:54267878 original size:31 final size:31
Alignment explanation
Indices: 54267840--54267918 Score: 104
Period size: 31 Copynumber: 2.5 Consensus size: 31
54267830 TTTTTGGGCC
* * *
54267840 AGGGCGTGTGGGCCCATACGGGCAGGTCACA
1 AGGGCGTGTGGGCCCATACAGGCAAGCCACA
* *
54267871 AGGGCGTGTGGGCCCAAATAGGCAAGCCACA
1 AGGGCGTGTGGGCCCATACAGGCAAGCCACA
*
54267902 TGGGCGTGTGGGCCCAT
1 AGGGCGTGTGGGCCCAT
54267919 TTTTTTGAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.20, C:0.25, G:0.41, T:0.14
Consensus pattern (31 bp):
AGGGCGTGTGGGCCCATACAGGCAAGCCACA
Found at i:54270433 original size:41 final size:41
Alignment explanation
Indices: 54270384--54270488 Score: 124
Period size: 41 Copynumber: 2.6 Consensus size: 41
54270374 TTATACCCTA
* *
54270384 AATTGCACATA-AGTGCCACTGTTTGTACTTCGGTACCCCCG
1 AATTGCACATACA-TACCACTATTTGTACTTCGGTACCCCCG
* * *
54270425 AATTGCACATACATACCCCTATTTGTACTTTGGTACCCCTG
1 AATTGCACATACATACCACTATTTGTACTTCGGTACCCCCG
* *
54270466 AATAGCACATACAT-GCACTATTT
1 AATTGCACATACATACCACTATTT
54270489 ACACTCTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
40 7 0.13
41 47 0.85
42 1 0.02
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (41 bp):
AATTGCACATACATACCACTATTTGTACTTCGGTACCCCCG
Found at i:54282866 original size:40 final size:40
Alignment explanation
Indices: 54282788--54282867 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 40
54282778 TGGATAGTAC
** *
54282788 TTGAGTAAGGGACGAGATGTATAAAGTATGTATGAATGAA
1 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
54282828 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
1 TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
54282868 AGGAAGAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.42, C:0.04, G:0.28, T:0.26
Consensus pattern (40 bp):
TTGAGTAAGGGACGAGATGTATAAAGTATACATAAATGAA
Found at i:54283863 original size:22 final size:21
Alignment explanation
Indices: 54283838--54283879 Score: 75
Period size: 22 Copynumber: 2.0 Consensus size: 21
54283828 GCCTAAATGG
54283838 TCACACAGGCGTGTTGCCCCTC
1 TCACACAGGCGTG-TGCCCCTC
54283860 TCACACAGGCGTGTGCCCCT
1 TCACACAGGCGTGTGCCCCT
54283880 ATGTTAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.14, C:0.40, G:0.24, T:0.21
Consensus pattern (21 bp):
TCACACAGGCGTGTGCCCCTC
Found at i:54285923 original size:31 final size:31
Alignment explanation
Indices: 54285888--54285947 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
54285878 AACAGCCTAT
54285888 TGACTTAAATAG-AAACGTTT-GAATAGTTTGG
1 TGACTT-AATAGAAAAC-TTTCGAATAGTTTGG
*
54285919 TGACTTAATTGAAAACTTTCGAATAGTTT
1 TGACTTAATAGAAAACTTTCGAATAGTTT
54285948 AATGATAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
30 7 0.27
31 19 0.73
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.38
Consensus pattern (31 bp):
TGACTTAATAGAAAACTTTCGAATAGTTTGG
Found at i:54290434 original size:40 final size:40
Alignment explanation
Indices: 54290364--54290531 Score: 149
Period size: 40 Copynumber: 4.2 Consensus size: 40
54290354 CGGGGTTTAG
** * *
54290364 CCGGATATAACCACTCGCAC-AAGGCCTTCGGGTCTTAAC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * *
54290403 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * **
54290443 CCGGATATAGTCGCTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * * *
54290483 CCAGATGTAGTCGCTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGATATAGTCAC-TAGCACAAATGCCTTCGGGTCTTAAC
*
54290524 CCAGATAT
1 CCGGATAT
54290532 CATTCGAGTA
Statistics
Matches: 106, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
39 15 0.14
40 62 0.58
41 29 0.27
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.24
Consensus pattern (40 bp):
CCGGATATAGTCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:54290514 original size:41 final size:40
Alignment explanation
Indices: 54290387--54290531 Score: 175
Period size: 40 Copynumber: 3.6 Consensus size: 40
54290377 CTCGCACAAG
* * * * * *
54290387 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
*
54290427 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
* * *
54290467 GCCTTC-GGATCTTAGTCCAGATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCAGATATAGTCGC-TAGCACAAAT
54290508 GCCTTCGGGACTTAGCCCAGATAT
1 GCCTTCGGGACTTAGCCCAGATAT
54290532 CATTCGAGTA
Statistics
Matches: 91, Mismatches: 11, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
39 3 0.03
40 58 0.64
41 27 0.30
42 3 0.03
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCAGATATAGTCGCTAGCACAAAT
Found at i:54291764 original size:38 final size:40
Alignment explanation
Indices: 54291718--54291795 Score: 142
Period size: 38 Copynumber: 2.0 Consensus size: 40
54291708 CAAGAACTCC
54291718 TTCCTCCTTCCTTAGAATTTT-GG-CCAAAAGAAATGAAA
1 TTCCTCCTTCCTTAGAATTTTCGGACCAAAAGAAATGAAA
54291756 TTCCTCCTTCCTTAGAATTTTCGGACCAAAAGAAATGAAA
1 TTCCTCCTTCCTTAGAATTTTCGGACCAAAAGAAATGAAA
54291796 AAGGATGAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
38 21 0.55
39 2 0.05
40 15 0.39
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.31
Consensus pattern (40 bp):
TTCCTCCTTCCTTAGAATTTTCGGACCAAAAGAAATGAAA
Found at i:54298477 original size:39 final size:40
Alignment explanation
Indices: 54298432--54298542 Score: 98
Period size: 40 Copynumber: 2.8 Consensus size: 40
54298422 CGGGGTTTAG
* * *
54298432 CCGGATATAACCACTCGCA-CAAGGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
*** * *
54298471 CCGGATATGGTCACTAGCATAAATGCCTTCGGGACTTAGC
1 CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
** * * *
54298511 CCGGATATAGTCGCTAGCACAAATGCCTTCGG
1 CCGGATATAACCACTAGCATAAAGGCCTTCGG
54298543 ATCTTAGTCC
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
39 15 0.25
40 45 0.75
ACGTcount: A:0.25, C:0.29, G:0.23, T:0.23
Consensus pattern (40 bp):
CCGGATATAACCACTAGCATAAAGGCCTTCGGGACTTAAC
Found at i:54298502 original size:40 final size:40
Alignment explanation
Indices: 54298455--54298598 Score: 184
Period size: 40 Copynumber: 3.6 Consensus size: 40
54298445 CTCGCACAAG
* * * * *
54298455 GCCTTCGGGTCTTAACCCGGATATGGTCACTAGCATAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
54298495 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
1 GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
* * *
54298535 GCCTTC-GGATCTTAGTCC-GATGTAGTCGCTTAGCACAAAA
1 GCCTTCGGGA-CTTAGCCCGGATATAGTCGC-TAGCACAAAT
54298575 GCCTTCGGGACTTAGCCCGGATAT
1 GCCTTCGGGACTTAGCCCGGATAT
54298599 CATTCGAGTA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
39 13 0.14
40 70 0.78
41 7 0.08
ACGTcount: A:0.24, C:0.26, G:0.24, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAAT
Found at i:54299829 original size:38 final size:38
Alignment explanation
Indices: 54299787--54299862 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
54299777 CAAGAACTCC
*
54299787 TTCCTCCTTCCTTAGAATTTTCGGCCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGACCAAAAGAAATGAA
54299825 TTCCTCCTTCCTTAGAATTTTCGACCAAAAGAAATGAA
1 TTCCTCCTTCCTTAGAATTTTCGACCAAAAGAAATGAA
54299863 AAAGGATGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.32
Consensus pattern (38 bp):
TTCCTCCTTCCTTAGAATTTTCGACCAAAAGAAATGAA
Found at i:54309254 original size:24 final size:24
Alignment explanation
Indices: 54309227--54309276 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
54309217 GCTTAGTAAG
54309227 TAAGTACGTAAATAATTATCAATA
1 TAAGTACGTAAATAATTATCAATA
54309251 TAAGTACGTAAATAATTATCAATA
1 TAAGTACGTAAATAATTATCAATA
54309275 TA
1 TA
54309277 TTAACAAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.34
Consensus pattern (24 bp):
TAAGTACGTAAATAATTATCAATA
Found at i:54313153 original size:6 final size:6
Alignment explanation
Indices: 54313144--54313190 Score: 57
Period size: 6 Copynumber: 8.5 Consensus size: 6
54313134 TTGAAATTGA
*
54313144 TATATG TATA-- TATATG TATATA TATATG TATATG --TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
54313188 TAT
1 TAT
54313191 GTTTGAGTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
4 8 0.23
6 27 0.77
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:54313168 original size:22 final size:22
Alignment explanation
Indices: 54313143--54313186 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
54313133 ATTGAAATTG
54313143 ATATATGTATATATATGTATAT
1 ATATATGTATATATATGTATAT
*
54313165 ATATATGTATATGTATGTATAT
1 ATATATGTATATATATGTATAT
54313187 GTATGTTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
ATATATGTATATATATGTATAT
Found at i:54313191 original size:10 final size:10
Alignment explanation
Indices: 54313144--54313192 Score: 66
Period size: 10 Copynumber: 5.1 Consensus size: 10
54313134 TTGAAATTGA
*
54313144 TATATGTATA
1 TATATGTATG
54313154 TATATGTA--
1 TATATGTATG
*
54313162 TATATATATG
1 TATATGTATG
54313172 TATATGTATG
1 TATATGTATG
54313182 TATATGTATG
1 TATATGTATG
54313192 T
1 T
54313193 TTGAGTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
8 7 0.20
10 28 0.80
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (10 bp):
TATATGTATG
Found at i:54314864 original size:25 final size:25
Alignment explanation
Indices: 54314836--54315018 Score: 123
Period size: 25 Copynumber: 7.3 Consensus size: 25
54314826 ATCTAGGAAA
*
54314836 CCTTTATGGCTAATCTTGTGAAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
* *
54314861 CCTTTGTGACGTATTATCTAG-G--AAG
1 CCTTTGTGGC-TA--ATCTTGTGAAAAG
54314886 CCTTTGTGGCTAATCTTGTGAAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
*
54314911 CCCTTGTTGTG-TATTATCTTG-G--AAG
1 CCTTTG-TG-GCTA--ATCTTGTGAAAAG
* *
54314936 CCATTGTGGCTAATCTTGT-AAGAAA
1 CCTTTGTGGCTAATCTTGTGAA-AAG
* **
54314961 CCTTTGTGGCATATTCTT-TGGCAAG
1 CCTTTGTGGC-TAATCTTGTGAAAAG
* *
54314986 CCTTTGTGGCTAATGTTGTGGAAAG
1 CCTTTGTGGCTAATCTTGTGAAAAG
54315011 CCTTTGTG
1 CCTTTGTG
54315019 CCATATTATT
Statistics
Matches: 124, Mismatches: 16, Indels: 36
0.70 0.09 0.20
Matches are distributed among these distances:
22 11 0.09
23 2 0.02
24 11 0.09
25 74 0.60
26 12 0.10
27 3 0.02
28 11 0.09
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (25 bp):
CCTTTGTGGCTAATCTTGTGAAAAG
Found at i:54314900 original size:50 final size:50
Alignment explanation
Indices: 54314825--54315099 Score: 259
Period size: 50 Copynumber: 5.5 Consensus size: 50
54314815 AACATGACAC
* * * *
54314825 TATCTAGGAAACCTTTATGGCTAATCTTGTGAAAAGCCTTTGTGACGTAT
1 TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCATAT
* * **
54314875 TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAAAAGCCCTTGTTGTGTAT
1 TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCATAT
* * *
54314925 TATCTTGGAAGCCATTGTGGCTAATCTTGT-AAGAAACCTTTGTGGCATAT
1 TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAA-AAGCCTTTGTGGCATAT
* * * * *
54314975 TCT-TTGGCAAGCCTTTGTGGCTAATGTTGTGGAAAGCCTTTGTGCCATAT
1 TATCTAGG-AAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCATAT
* * ** * * * * *
54315025 TAT-TTGACAATTCTTTGTGACTTATCTTATGAAAAGCCCTTGTGGTATAT
1 TATCTAG-GAAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCATAT
* *
54315075 TATCTAGGAAACCTTTGTGTCTAAT
1 TATCTAGGAAGCCTTTGTGGCTAAT
54315100 TTTTTAAGAA
Statistics
Matches: 183, Mismatches: 37, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
49 6 0.03
50 174 0.95
51 3 0.02
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (50 bp):
TATCTAGGAAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGCATAT
Found at i:54320710 original size:25 final size:25
Alignment explanation
Indices: 54320684--54320864 Score: 99
Period size: 25 Copynumber: 7.2 Consensus size: 25
54320674 GAAGTCTGTA
*
54320684 TGGCTAATCTTGTGAAAAGCCTTTA
1 TGGCTAATCTTGTGAAAAGCCTTTG
* * * ***
54320709 TGGC-ATATTTTCT-ATTAAGCCTGCA
1 TGGCTA-ATCTTGTGA-AAAGCCTTTG
* * *
54320734 TGGCTAATCTTGTTAAAAACATTTG
1 TGGCTAATCTTGTGAAAAGCCTTTG
*
54320759 TGGCGTATTATC-T-T-AGAAGCCTTTG
1 TGGC-TA--ATCTTGTGAAAAGCCTTTG
* * *
54320784 TGGATAATCTTATGAAAAGACTTTG
1 TGGCTAATCTTGTGAAAAGCCTTTG
*
54320809 TGGCGTATTATC-TG-G-GAAGCCTTTG
1 TGGC-TA--ATCTTGTGAAAAGCCTTTG
54320834 TGGCTAATCTTGTGAAAAGCCTTTG
1 TGGCTAATCTTGTGAAAAGCCTTTG
54320859 TGGCTA
1 TGGCTA
54320865 GTATTTTGAA
Statistics
Matches: 116, Mismatches: 24, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
22 6 0.05
23 3 0.03
24 8 0.07
25 83 0.72
26 8 0.07
27 2 0.02
28 6 0.05
ACGTcount: A:0.25, C:0.15, G:0.22, T:0.38
Consensus pattern (25 bp):
TGGCTAATCTTGTGAAAAGCCTTTG
Found at i:54320779 original size:50 final size:50
Alignment explanation
Indices: 54320674--54320862 Score: 184
Period size: 50 Copynumber: 3.8 Consensus size: 50
54320664 TAATATCTCG
* * * * *
54320674 GAAGTCTGTATGGCTAATCTTGTGAAAAGCCTTTATGGCATATTTTC-TA
1 GAAGCCTGTATGGCTAATCTTGTGAAAAACCTTTGTGGCGTATTATCTTA
* * * *
54320723 TTAAGCCTGCATGGCTAATCTTGTTAAAAACATTTGTGGCGTATTATCTTA
1 -GAAGCCTGTATGGCTAATCTTGTGAAAAACCTTTGTGGCGTATTATCTTA
* * * * **
54320774 GAAGCCTTTGTGGATAATCTTATGAAAAGA-CTTTGTGGCGTATTATCTGG
1 GAAGCCTGTATGGCTAATCTTGTGAAAA-ACCTTTGTGGCGTATTATCTTA
* * *
54320824 GAAGCCTTTGTGGCTAATCTTGTGAAAAGCCTTTGTGGC
1 GAAGCCTGTATGGCTAATCTTGTGAAAAACCTTTGTGGC
54320863 TAGTATTTTG
Statistics
Matches: 114, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
50 111 0.97
51 3 0.03
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (50 bp):
GAAGCCTGTATGGCTAATCTTGTGAAAAACCTTTGTGGCGTATTATCTTA
Found at i:54320887 original size:50 final size:49
Alignment explanation
Indices: 54320684--54320913 Score: 150
Period size: 50 Copynumber: 4.6 Consensus size: 49
54320674 GAAGTCTGTA
* * * *
54320684 TGGCTAATCTTGTGAAAAGCCTTTATGGCA-TATTTTCTATTAAG-CCTGCA
1 TGGCTAATCTTGTGAAAAGCCTTTGTGGCAGTATTTT-GA-GAAGCCCTG-G
* * * * * *
54320734 TGGCTAATCTTGTTAAAAACATTTGTGGC-GTATTATCTTAGAAGCCTTTG
1 TGGCTAATCTTGTGAAAAGCCTTTGTGGCAGTATT-T-TGAGAAGCCCTGG
* * * * * *
54320784 TGGATAATCTTATGAAAAGACTTTGTGGC-GTATTATCTGGGAAGCCTTTG
1 TGGCTAATCTTGTGAAAAGCCTTTGTGGCAGTATT-T-TGAGAAGCCCTGG
* *
54320834 TGGCTAATCTTGTGAAAAGCCTTTGTGGCTAGTATTTTGAAAATCCCTGG
1 TGGCTAATCTTGTGAAAAGCCTTTGTGGC-AGTATTTTGAGAAGCCCTGG
54320884 TGGCGTATTATC-TGTG--AAGCCTTTGTGGCA
1 TGGC-TA--ATCTTGTGAAAAGCCTTTGTGGCA
54320914 AAGTATTAGA
Statistics
Matches: 147, Mismatches: 24, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
49 1 0.01
50 125 0.85
51 8 0.05
52 10 0.07
53 3 0.02
ACGTcount: A:0.24, C:0.15, G:0.23, T:0.37
Consensus pattern (49 bp):
TGGCTAATCTTGTGAAAAGCCTTTGTGGCAGTATTTTGAGAAGCCCTGG
Found at i:54320911 original size:25 final size:25
Alignment explanation
Indices: 54320755--54320912 Score: 91
Period size: 25 Copynumber: 6.3 Consensus size: 25
54320745 GTTAAAAACA
54320755 TTTGTGGCGTATTATCT-TAGAAGCC
1 TTTGTGGCGTATTATCTGT-GAAGCC
* * *
54320780 TTTGT-G-G-ATAATCTTATGAAAAGAC
1 TTTGTGGCGTATTATC-TGTG--AAGCC
*
54320805 TTTGTGGCGTATTATCTGGGAAGCC
1 TTTGTGGCGTATTATCTGTGAAGCC
54320830 TTTGTGGC-TA--ATCTTGTGAAAAGCC
1 TTTGTGGCGTATTATC-TGTG--AAGCC
** *
54320855 TTTGTGGCTAGTATT-T-TGAAAATCC
1 TTTGTGGC--GTATTATCTGTGAAGCC
* *
54320880 CTGGTGGCGTATTATCTGTGAAGCC
1 TTTGTGGCGTATTATCTGTGAAGCC
54320905 TTTGTGGC
1 TTTGTGGC
54320913 AAAGTATTAG
Statistics
Matches: 99, Mismatches: 17, Indels: 34
0.66 0.11 0.23
Matches are distributed among these distances:
22 8 0.08
23 11 0.11
24 5 0.05
25 61 0.62
26 1 0.01
27 5 0.05
28 7 0.07
29 1 0.01
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.38
Consensus pattern (25 bp):
TTTGTGGCGTATTATCTGTGAAGCC
Found at i:54334310 original size:18 final size:18
Alignment explanation
Indices: 54334273--54334312 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
54334263 TTGGAAATCA
*
54334273 AAATTATTAAAAGATGAT
1 AAATTATTAAAAGATAAT
54334291 AAATTATTAAATAGA-AAT
1 AAATTATTAAA-AGATAAT
54334309 AAAT
1 AAAT
54334313 ATCATTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 17 0.85
19 3 0.15
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (18 bp):
AAATTATTAAAAGATAAT
Found at i:54342550 original size:21 final size:21
Alignment explanation
Indices: 54342510--54342550 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54342500 CCTCTAGCAT
**
54342510 GGGCATGTCCCTGGGTCACAA
1 GGGCATGTCCCTGGACCACAA
*
54342531 GGGCATGTCCCTTGACCACA
1 GGGCATGTCCCTGGACCACA
54342551 TGAGCTTGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.20
Consensus pattern (21 bp):
GGGCATGTCCCTGGACCACAA
Found at i:54343769 original size:19 final size:19
Alignment explanation
Indices: 54343726--54343770 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
54343716 GATATTCTCG
* *
54343726 TTGAACACTTGGAATATTA
1 TTGAACACTTGGAAAAATA
* *
54343745 TCGAACACTTGGAAAAATC
1 TTGAACACTTGGAAAAATA
54343764 TTGAACA
1 TTGAACA
54343771 TAAGTGTCAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.16, G:0.16, T:0.29
Consensus pattern (19 bp):
TTGAACACTTGGAAAAATA
Found at i:54349765 original size:11 final size:11
Alignment explanation
Indices: 54349749--54349776 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
54349739 TTGGATAAGT
54349749 ATAAGTTTGTA
1 ATAAGTTTGTA
54349760 ATAAGTTTGTA
1 ATAAGTTTGTA
54349771 ATAAGT
1 ATAAGT
54349777 ATAAGTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.43
Consensus pattern (11 bp):
ATAAGTTTGTA
Found at i:54351736 original size:12 final size:12
Alignment explanation
Indices: 54351719--54351743 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54351709 GTACTTAGTA
54351719 GATTTGGAAGTT
1 GATTTGGAAGTT
54351731 GATTTGGAAGTT
1 GATTTGGAAGTT
54351743 G
1 G
54351744 GAAATGGATA
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:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (12 bp):
GATTTGGAAGTT
Found at i:54356921 original size:10 final size:10
Alignment explanation
Indices: 54356906--54356936 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
54356896 TCAACTAACA
54356906 CATCTCTAGC
1 CATCTCTAGC
54356916 CATCTCTAGC
1 CATCTCTAGC
*
54356926 CATCTTTAGC
1 CATCTCTAGC
54356936 C
1 C
54356937 TCAACTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.39, G:0.10, T:0.32
Consensus pattern (10 bp):
CATCTCTAGC
Found at i:54356944 original size:20 final size:21
Alignment explanation
Indices: 54356893--54356944 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
54356883 TTAGAAATTT
*
54356893 GCCTCAACTAACACATCTCTA
1 GCCTCAACTAGCACATCTCTA
* *
54356914 GCCATC-TCTAGC-CATCTTTA
1 GCC-TCAACTAGCACATCTCTA
54356934 GCCTCAACTAG
1 GCCTCAACTAG
54356945 ATATTTATCC
Statistics
Matches: 25, Mismatches: 4, Indels: 5
0.74 0.12 0.15
Matches are distributed among these distances:
19 2 0.08
20 14 0.56
21 7 0.28
22 2 0.08
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.27
Consensus pattern (21 bp):
GCCTCAACTAGCACATCTCTA
Found at i:54359304 original size:40 final size:40
Alignment explanation
Indices: 54359244--54359320 Score: 127
Period size: 40 Copynumber: 1.9 Consensus size: 40
54359234 TTAACAATTA
*
54359244 TAATAATTCAAATATGGTTTAAAGTAACTAAGAATCTATT
1 TAATAATTCAAATATGGTTTAAAGCAACTAAGAATCTATT
* *
54359284 TAATAATTCAAATATTGTTTATAGCAACTAAGAATCT
1 TAATAATTCAAATATGGTTTAAAGCAACTAAGAATCT
54359321 GTAAAGCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (40 bp):
TAATAATTCAAATATGGTTTAAAGCAACTAAGAATCTATT
Found at i:54360129 original size:18 final size:18
Alignment explanation
Indices: 54360093--54360139 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
54360083 AGGTTTTTCT
54360093 ATTAAATT-ATTTATATA
1 ATTAAATTAATTTATATA
*
54360110 ATATAAGTTAATTT-TATA
1 AT-TAAATTAATTTATATA
54360128 ATTAAATTAATT
1 ATTAAATTAATT
54360140 ATTAAGTTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 11 0.42
18 11 0.42
19 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
ATTAAATTAATTTATATA
Found at i:54360503 original size:13 final size:12
Alignment explanation
Indices: 54360465--54360508 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
54360455 GAAAATTTAT
54360465 TTAATTGGAAAA
1 TTAATTGGAAAA
54360477 TTAATT-GATTAAA
1 TTAATTGGA--AAA
54360490 TTTAATTGGAAAA
1 -TTAATTGGAAAA
54360503 TTAATT
1 TTAATT
54360509 TAATAAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 2 0.07
12 12 0.43
13 6 0.21
14 6 0.21
15 2 0.07
ACGTcount: A:0.45, C:0.00, G:0.11, T:0.43
Consensus pattern (12 bp):
TTAATTGGAAAA
Found at i:54360515 original size:26 final size:26
Alignment explanation
Indices: 54360463--54360516 Score: 90
Period size: 26 Copynumber: 2.1 Consensus size: 26
54360453 TTGAAAATTT
*
54360463 ATTTAATTGGAAAATTAATTGATTAA
1 ATTTAATTGGAAAATTAATTGAATAA
*
54360489 ATTTAATTGGAAAATTAATTTAATAA
1 ATTTAATTGGAAAATTAATTGAATAA
54360515 AT
1 AT
54360517 AGTATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (26 bp):
ATTTAATTGGAAAATTAATTGAATAA
Found at i:54363987 original size:19 final size:20
Alignment explanation
Indices: 54363952--54363999 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
54363942 AGAAATAATT
* *
54363952 TTAAAATTTAAACATAAATA
1 TTAAAATGTAAACATAAAAA
54363972 TTAAAATGTAAA-ATAAAAA
1 TTAAAATGTAAACATAAAAA
*
54363991 TAAAAATGT
1 TTAAAATGT
54364000 TACCAAGACG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (20 bp):
TTAAAATGTAAACATAAAAA
Found at i:54366382 original size:11 final size:11
Alignment explanation
Indices: 54366366--54366401 Score: 63
Period size: 11 Copynumber: 3.2 Consensus size: 11
54366356 TTGGTGAAAG
54366366 TGAAAATTTTT
1 TGAAAATTTTT
54366377 TGAAAATTTTTT
1 TGAAAA-TTTTT
54366389 TGAAAATTTTT
1 TGAAAATTTTT
54366400 TG
1 TG
54366402 TATAAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 13 0.54
12 11 0.46
ACGTcount: A:0.33, C:0.00, G:0.11, T:0.56
Consensus pattern (11 bp):
TGAAAATTTTT
Found at i:54366389 original size:12 final size:12
Alignment explanation
Indices: 54366366--54366400 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
54366356 TTGGTGAAAG
54366366 TGAAAA-TTTTT
1 TGAAAATTTTTT
54366377 TGAAAATTTTTT
1 TGAAAATTTTTT
54366389 TGAAAATTTTTT
1 TGAAAATTTTTT
54366401 GTATAAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 6 0.26
12 17 0.74
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (12 bp):
TGAAAATTTTTT
Found at i:54367709 original size:31 final size:32
Alignment explanation
Indices: 54367661--54367727 Score: 93
Period size: 31 Copynumber: 2.1 Consensus size: 32
54367651 GAAATTTTAG
*
54367661 ATTTTAATTTCTGTATTTTTTTTA-TTTTTAAA
1 ATTTTAATTTCTGTA-TTTTTTTAGATTTTAAA
*
54367693 ATTTTAATTT-TTTATTTTTTTAGATTTTAAA
1 ATTTTAATTTCTGTATTTTTTTAGATTTTAAA
54367724 ATTT
1 ATTT
54367728 ATGTTTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
30 8 0.25
31 14 0.44
32 10 0.31
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (32 bp):
ATTTTAATTTCTGTATTTTTTTAGATTTTAAA
Found at i:54374525 original size:47 final size:47
Alignment explanation
Indices: 54374466--54375105 Score: 1068
Period size: 47 Copynumber: 13.6 Consensus size: 47
54374456 TATTTGAATA
* * *
54374466 AATGAGAAAGTGTATATATGTGATAAGGCCGAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374513 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54374562 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54374609 AATGTGAAAATGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374656 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54374703 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374750 -ATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54374798 AATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374844 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54374891 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374938 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54374985 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
54375032 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54375079 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54375106 TCCCGAAGGG
Statistics
Matches: 562, Mismatches: 25, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
46 56 0.10
47 416 0.74
48 34 0.06
49 56 0.10
ACGTcount: A:0.33, C:0.08, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54375300 original size:36 final size:36
Alignment explanation
Indices: 54375223--54375323 Score: 166
Period size: 36 Copynumber: 2.8 Consensus size: 36
54375213 CCGAGCTCTA
54375223 AAGACCCGATGACTACGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATT-TGTCCGGGT
*
54375260 AAGACCCGATGACTACGTGTGGAGATTTTTCCGGGT
1 AAGACCCGATGACTACGTGTGGAGATTTGTCCGGGT
* *
54375296 AAGACCCGATAACTTCGTGTGGAGATTT
1 AAGACCCGATGACTACGTGTGGAGATTT
54375324 CGTCTGAGCT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
36 34 0.56
37 27 0.44
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (36 bp):
AAGACCCGATGACTACGTGTGGAGATTTGTCCGGGT
Found at i:54376649 original size:40 final size:40
Alignment explanation
Indices: 54376595--54376876 Score: 399
Period size: 40 Copynumber: 7.1 Consensus size: 40
54376585 AGAATTGAGA
*
54376595 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTA
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* *
54376635 GTGATATATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTA
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
** *
54376675 GTGATGCATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
*
54376715 GTGTTATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* * *
54376754 GTGTTATATCCGGGCTAGGTCCCGAAGAGCATTCGAGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* * * *
54376794 GTGTTATATCCGGGCTAGGTCCCAAAGAGCATTCGAGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
* *
54376834 GTG-T-TATCCGGGCTAAGTCTCGAAGAGCATTCATGCTG
1 GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
54376872 GTGAT
1 GTGAT
54376877 GTGTATTCGG
Statistics
Matches: 224, Mismatches: 16, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
38 32 0.14
39 39 0.17
40 153 0.68
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (40 bp):
GTGATATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTG
Found at i:54376727 original size:80 final size:78
Alignment explanation
Indices: 54376601--54376874 Score: 388
Period size: 79 Copynumber: 3.5 Consensus size: 78
54376591 GAGAGTGATA
* * *
54376601 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGAGCA
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCA
*
54376666 TTCGTGCTAGTGAT
66 TTCGTGCTGGTG-T
* *
54376680 GCATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGT-CCGAAGAGC
1 -TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
54376744 ATTCGTGCTGGTGTT
65 ATTCGTGCTGGTG-T
* * * *
54376759 ATATCCGGGCTAGGTCCCGAAGAGCATTCGAGCTGGTGTTATATCCGGGCTAGGTCCCAAAGAGC
1 -TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGC
*
54376824 ATTCGAGCTGGTGT
65 ATTCGTGCTGGTGT
* *
54376838 TATCCGGGCTAAGTCTCGAAGAGCATTCATGCTGGTG
1 TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTG
54376875 ATGTGTATTC
Statistics
Matches: 174, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
78 33 0.19
79 71 0.41
80 70 0.40
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.26
Consensus pattern (78 bp):
TATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAAGTCCCGAAGAGCA
TTCGTGCTGGTGT
Found at i:54376816 original size:119 final size:118
Alignment explanation
Indices: 54376599--54376876 Score: 396
Period size: 119 Copynumber: 2.3 Consensus size: 118
54376589 TTGAGAGTGA
* *
54376599 TATATCCGGGCTAAGTCCCGAAGAGCATTCGTGCTAGTGATATATCCGGGCTAAGTCCCGAGGAG
1 TATATCCGGGCTAAGT-CCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAG
* * * * *
54376664 CATTCGTGCTAGTGATGCATCCGGGCTAAGTCCCGAGGAGCATTCGTGCTGGTG
65 CATTCGAGCTAGTGATACATCCGGGCTAAGTCCCAAAGAGCATTCGAGCTGGTG
* *
54376718 TTATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGTTATATCCGGGCTAGGTCCCGAAGAG
1 -TATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAG
* * * *
54376783 CATTCGAGCTGGTGTTATATCCGGGCTAGGTCCCAAAGAGCATTCGAGCTGGTG
65 CATTCGAGCTAGTGATACATCCGGGCTAAGTCCCAAAGAGCATTCGAGCTGGTG
*
54376837 T-TATCCGGGCTAAGTCTCGAAGAGCATTCATGCTGGTGAT
1 TATATCCGGGCTAAGTC-CGAAGAGCATTCGTGCTGGTGAT
54376877 GTGTATTCGG
Statistics
Matches: 142, Mismatches: 15, Indels: 4
0.88 0.09 0.02
Matches are distributed among these distances:
117 15 0.11
118 22 0.15
119 89 0.63
120 16 0.11
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (118 bp):
TATATCCGGGCTAAGTCCGAAGAGCATTCGTGCTGGTGATATATCCGGGCTAAGTCCCGAAGAGC
ATTCGAGCTAGTGATACATCCGGGCTAAGTCCCAAAGAGCATTCGAGCTGGTG
Found at i:54380572 original size:47 final size:47
Alignment explanation
Indices: 54380518--54381249 Score: 1315
Period size: 47 Copynumber: 15.6 Consensus size: 47
54380508 TATTTGAATA
*
54380518 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380565 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380614 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380661 AATGTGAAA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380707 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54380754 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380801 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54380848 AATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380894 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
*
54380941 AATGTGAAAGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380988 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54381035 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54381082 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54381129 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* * * * * *
54381176 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
* *
54381223 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
54381250 TCCCGAAGGG
Statistics
Matches: 662, Mismatches: 19, Indels: 8
0.96 0.03 0.01
Matches are distributed among these distances:
46 91 0.14
47 525 0.79
49 46 0.07
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54380659 original size:22 final size:22
Alignment explanation
Indices: 54380631--54380705 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 22
54380621 AAGTGTATAT
54380631 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
* *** ****
54380653 ATGTGATGAATGTGAAATGTATAT
1 ATGTGAT-AAGGCCTAATG-GCCG
54380677 ATGTGATAAGGCCTAATGGCCG
1 ATGTGATAAGGCCTAATGGCCG
54380699 ATGTGAT
1 ATGTGAT
54380706 GAATGTGAAA
Statistics
Matches: 35, Mismatches: 16, Indels: 4
0.64 0.29 0.07
Matches are distributed among these distances:
22 14 0.40
23 14 0.40
24 7 0.20
ACGTcount: A:0.31, C:0.11, G:0.29, T:0.29
Consensus pattern (22 bp):
ATGTGATAAGGCCTAATGGCCG
Found at i:54380837 original size:187 final size:188
Alignment explanation
Indices: 54380518--54381249 Score: 1315
Period size: 187 Copynumber: 3.9 Consensus size: 188
54380508 TATTTGAATA
*
54380518 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCAATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTG--TATA
*
54380583 TATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
64 TATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAAT
54380648 GGCCGATGTGATGAATGTGAAA-TGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
129 GGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380707 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
*
54380772 TGTGATAAGGCCTAATAGCCGACGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
66 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
*
54380837 CCGATGTGATGAATGTGAAAGTGTATATAT-TGATAAGGCCTAATAGCCGATGTGATG
131 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54380894 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
54380959 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
66 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
54381024 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
131 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
54381082 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
1 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
* * * * *
54381147 TGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGG
66 TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
* * * *
54381212 CCAACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
131 CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAG
54381250 TCCCGAAGGG
Statistics
Matches: 526, Mismatches: 15, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
187 274 0.52
188 194 0.37
189 58 0.11
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (188 bp):
AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAAAGTGTATATA
TGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGG
CCGATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
Found at i:54381419 original size:37 final size:37
Alignment explanation
Indices: 54381369--54381468 Score: 182
Period size: 37 Copynumber: 2.7 Consensus size: 37
54381359 CGAGCTCTAT
54381369 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
54381406 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
54381443 AGACCCGATAACTTCGTGTGGAGATT
1 AGACCCGATGACTACGTGTGGAGATT
54381469 TCGTCTGAGC
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 61 1.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
Found at i:54386272 original size:19 final size:20
Alignment explanation
Indices: 54386248--54386285 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54386238 GGTACCACCA
54386248 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
54386267 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
54386286 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:54386626 original size:93 final size:93
Alignment explanation
Indices: 54386515--54386685 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
54386505 GCCCCTAAGT
* *
54386515 GAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54386580 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * * *
54386608 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54386673 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54386686 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (93 bp):
GAACTCAGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54386682 original size:46 final size:46
Alignment explanation
Indices: 54386510--54386682 Score: 199
Period size: 46 Copynumber: 3.7 Consensus size: 46
54386500 AACCCGCCCC
* * * * *
54386510 TAAGTGAACTCAGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
54386556 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
54386604 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
54386649 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54386683 TGCTCAACCA
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 59 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:54393393 original size:19 final size:20
Alignment explanation
Indices: 54393369--54393406 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
54393359 GGTTCCACCA
54393369 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
54393388 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
54393407 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:54393746 original size:93 final size:93
Alignment explanation
Indices: 54393636--54393806 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
54393626 GCCCCTAAGT
* *
54393636 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAATGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54393701 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* * *
54393729 GAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
54393794 CGAGTTCGGATGC
66 CGAGTTCGGATGC
54393807 TCAACCATCC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAATGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:54393803 original size:46 final size:46
Alignment explanation
Indices: 54393631--54393803 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
54393621 AACCCGCCCC
* * * *
54393631 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
* * *
54393677 TAAATGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-ATTTGCATCCA
* *
54393725 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
54393770 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
54393804 TGCTCAACCA
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
44 2 0.02
45 2 0.02
46 60 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 4 0.04
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
Found at i:54403786 original size:52 final size:52
Alignment explanation
Indices: 54403719--54403890 Score: 213
Period size: 52 Copynumber: 3.2 Consensus size: 52
54403709 GATATGACAT
* * *
54403719 TGTGCTAAGTAAAATAATACTATGACATTTAAGTGAAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAATACCATGGCATTTAAGTGAAATAAGTCCATGGCAA
* * *
54403771 TGTGCTAAGTGAAATAAGACCATGGCATCTAAGTGTAATAAGTCCATGGCAA
1 TGTGCTAAGTGAAATAATACCATGGCATTTAAGTGAAATAAGTCCATGGCAA
54403823 TGTGCTAAGTGAAATAAGT-CCATGGCAATGTGCTAAGTGAAATAAGTCCATGGC-A
1 TGTGCTAAGTGAAATAA-TACCATGGC-AT-T--TAAGTGAAATAAGTCCATGGCAA
*
54403878 TGGTGTTAAGTGA
1 T-GTGCTAAGTGA
54403891 GAAATTTCCT
Statistics
Matches: 104, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
52 70 0.67
53 2 0.02
55 2 0.02
56 30 0.29
ACGTcount: A:0.37, C:0.13, G:0.23, T:0.27
Consensus pattern (52 bp):
TGTGCTAAGTGAAATAATACCATGGCATTTAAGTGAAATAAGTCCATGGCAA
Found at i:54403788 original size:28 final size:28
Alignment explanation
Indices: 54403748--54403890 Score: 215
Period size: 28 Copynumber: 5.2 Consensus size: 28
54403738 CTATGACATT
54403748 TAAGTGAAATAAGTCCATGGCAATGTGC
1 TAAGTGAAATAAGTCCATGGCAATGTGC
*
54403776 TAAGTGAAATAAGACCATGGC-A--T-C
1 TAAGTGAAATAAGTCCATGGCAATGTGC
*
54403800 TAAGTGTAATAAGTCCATGGCAATGTGC
1 TAAGTGAAATAAGTCCATGGCAATGTGC
54403828 TAAGTGAAATAAGTCCATGGCAATGTGC
1 TAAGTGAAATAAGTCCATGGCAATGTGC
*
54403856 TAAGTGAAATAAGTCCATGGC-ATGGTGT
1 TAAGTGAAATAAGTCCATGGCAAT-GTGC
54403884 TAAGTGA
1 TAAGTGA
54403891 GAAATTTCCT
Statistics
Matches: 105, Mismatches: 5, Indels: 10
0.88 0.04 0.08
Matches are distributed among these distances:
24 20 0.19
25 2 0.02
27 4 0.04
28 79 0.75
ACGTcount: A:0.36, C:0.13, G:0.25, T:0.26
Consensus pattern (28 bp):
TAAGTGAAATAAGTCCATGGCAATGTGC
Found at i:54404032 original size:101 final size:102
Alignment explanation
Indices: 54403914--54404111 Score: 321
Period size: 101 Copynumber: 2.0 Consensus size: 102
54403904 TGAACCTTAG
54403914 GAATAAAATAGCTTTTGACAAAAGTGTGGTACTATGTGAAAGCCACTTTGTGAATAAAATAGCTT
1 GAATAAAATAGCTTTTGACAAAAGTGTGGTACTATGTGAAAGCCACTTTGTGAATAAAATAGCTT
54403979 TGG--ACACAAGTGTGGTACTATGTAAAGGCCACTTTGT
66 TGGCTACA-AAG-GTGGTACTATGTAAAGGCCACTTTGT
* * *
54404016 GAATAAAATAG-TTTTGACACAAGTGTGGTACTATGTGAAGGCGACTTTGTGAATAAAATAGCTT
1 GAATAAAATAGCTTTTGACAAAAGTGTGGTACTATGTGAAAGCCACTTTGTGAATAAAATAGCTT
*
54404080 TGGCTACAAAGGTGGTACTATGTGAAGGCCAC
66 TGGCTACAAAGGTGGTACTATGTAAAGGCCAC
54404112 CGTGTATCCG
Statistics
Matches: 90, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
101 73 0.81
102 14 0.16
103 3 0.03
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (102 bp):
GAATAAAATAGCTTTTGACAAAAGTGTGGTACTATGTGAAAGCCACTTTGTGAATAAAATAGCTT
TGGCTACAAAGGTGGTACTATGTAAAGGCCACTTTGT
Found at i:54404057 original size:50 final size:51
Alignment explanation
Indices: 54403914--54404111 Score: 303
Period size: 51 Copynumber: 3.9 Consensus size: 51
54403904 TGAACCTTAG
* *
54403914 GAATAAAATAGCTTTTGACAAAAGTGTGGTACTATGTGAAAGCCACTTTGT
1 GAATAAAATAGCTTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
* *
54403965 GAATAAAATAGCTTTGGACACAAGTGTGGTACTATGTAAAGGCCACTTTGT
1 GAATAAAATAGCTTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
54404016 GAATAAAATAG-TTTTGACACAAGTGTGGTACTATGTGAAGGCGACTTTGT
1 GAATAAAATAGCTTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
*
54404066 GAATAAAATAGC-TTTGGCTACAAAG-GTGGTACTATGTGAAGGCCAC
1 GAATAAAATAGCTTTTGAC-AC-AAGTGTGGTACTATGTGAAGGCCAC
54404112 CGTGTATCCG
Statistics
Matches: 135, Mismatches: 9, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
50 52 0.39
51 80 0.59
52 3 0.02
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (51 bp):
GAATAAAATAGCTTTTGACACAAGTGTGGTACTATGTGAAGGCCACTTTGT
Found at i:54408312 original size:24 final size:25
Alignment explanation
Indices: 54408271--54408328 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
54408261 AAGCTCCTCC
* *
54408271 TGAGCTGATAAACAGTAAGCTTTAT
1 TGAGCTGAAAAACAGTAAGCTCTAT
*
54408296 TGAGCT-AAAAACGGTAAGCTCTAT
1 TGAGCTGAAAAACAGTAAGCTCTAT
54408320 TGAGCTGAA
1 TGAGCTGAA
54408329 TAGTAAGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 21 0.72
25 8 0.28
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (25 bp):
TGAGCTGAAAAACAGTAAGCTCTAT
Found at i:54408337 original size:22 final size:22
Alignment explanation
Indices: 54408279--54408339 Score: 68
Period size: 24 Copynumber: 2.7 Consensus size: 22
54408269 CCTGAGCTGA
* *
54408279 TAAACAGTAAGCTTTATTGAGC
1 TAAAAAGTAAGCTCTATTGAGC
54408301 TAAAAACGGTAAGCTCTATTGAGC
1 TAAAAA--GTAAGCTCTATTGAGC
* *
54408325 TGAATAGTAAGCTCT
1 TAAAAAGTAAGCTCT
54408340 TTCGAGATAC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 14 0.42
24 19 0.58
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.30
Consensus pattern (22 bp):
TAAAAAGTAAGCTCTATTGAGC
Found at i:54410095 original size:15 final size:17
Alignment explanation
Indices: 54410061--54410097 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
54410051 TCAAATCATA
54410061 ATAATTAACCAAATATT
1 ATAATTAACCAAATATT
*
54410078 ATAATT-ACCATA-ATT
1 ATAATTAACCAAATATT
54410093 ATAAT
1 ATAAT
54410098 AATATTTGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 5 0.26
17 6 0.32
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (17 bp):
ATAATTAACCAAATATT
Found at i:54410169 original size:38 final size:38
Alignment explanation
Indices: 54410075--54410175 Score: 114
Period size: 38 Copynumber: 2.7 Consensus size: 38
54410065 TTAACCAAAT
*
54410075 ATTATAATTACCATAATTATAATAATATTTGAAAAAAA
1 ATTATAATTACAATAATTATAATAATATTTGAAAAAAA
* * ****
54410113 ATTAAAATTATAGA-AATTATAATAATATTTGATCCTAA
1 ATTATAATTACA-ATAATTATAATAATATTTGAAAAAAA
*
54410151 ATTATTATTACAATAATTATAATAA
1 ATTATAATTACAATAATTATAATAA
54410176 AGATTTCGGT
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
37 1 0.02
38 49 0.96
39 1 0.02
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.40
Consensus pattern (38 bp):
ATTATAATTACAATAATTATAATAATATTTGAAAAAAA
Found at i:54410235 original size:27 final size:27
Alignment explanation
Indices: 54410170--54410224 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
54410160 ACAATAATTA
54410170 TAATAAAGATTTCGGTAAATTATTTTT
1 TAATAAAGATTTCGGTAAATTATTTTT
54410197 TAATAAAGATTTCGGTAAATTATTTTT
1 TAATAAAGATTTCGGTAAATTATTTTT
54410224 T
1 T
54410225 TAGTTAAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.11, T:0.49
Consensus pattern (27 bp):
TAATAAAGATTTCGGTAAATTATTTTT
Found at i:54413841 original size:33 final size:33
Alignment explanation
Indices: 54413799--54413871 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
54413789 CTTGATCTAT
* *
54413799 ATATATTATCAAATTTAGTACATTCAGTATTCA
1 ATATATTATCAAATTTAATACATTCAGCATTCA
54413832 ATATATTATCAAATTTAATACATTCAGCATTCA
1 ATATATTATCAAATTTAATACATTCAGCATTCA
*
54413865 ATCTATT
1 ATATATT
54413872 CAATTTAGCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.40, C:0.14, G:0.04, T:0.42
Consensus pattern (33 bp):
ATATATTATCAAATTTAATACATTCAGCATTCA
Found at i:54421713 original size:28 final size:28
Alignment explanation
Indices: 54421655--54421722 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
54421645 GTTCTTAGAA
* * * * *
54421655 ACTCTTTCCTGAAGAATAGTCCTTGCGG
1 ACTCTTGCTTGAAGAATAGTCCCTACAG
*
54421683 ACTCTTGCTTGAAGTATAGTCCCTACAG
1 ACTCTTGCTTGAAGAATAGTCCCTACAG
*
54421711 ACTTTTGCTTGA
1 ACTCTTGCTTGA
54421723 GAGATGGTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (28 bp):
ACTCTTGCTTGAAGAATAGTCCCTACAG
Found at i:54421741 original size:28 final size:28
Alignment explanation
Indices: 54421670--54421785 Score: 110
Period size: 28 Copynumber: 4.1 Consensus size: 28
54421660 TTCCTGAAGA
*
54421670 ATAGTCCT-TGCGGACTCTTGCTTG-AAG
1 ATAGT-CTATGCGGACTCTTACTTGAAAG
** * * * * *
54421697 TATAGTCCCTACAGACTTTTGCTTGAGAG
1 -ATAGTCTATGCGGACTCTTACTTGAAAG
*
54421726 ATGGTCTATGCGGACTCTTACTTGAAAG
1 ATAGTCTATGCGGACTCTTACTTGAAAG
*
54421754 ATAGTCTATGGGGACTCTTACTTGAAAG
1 ATAGTCTATGCGGACTCTTACTTGAAAG
54421782 ATAG
1 ATAG
54421786 CCCATGGAGA
Statistics
Matches: 71, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
27 1 0.01
28 68 0.96
29 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.33
Consensus pattern (28 bp):
ATAGTCTATGCGGACTCTTACTTGAAAG
Found at i:54421792 original size:28 final size:28
Alignment explanation
Indices: 54421737--54421800 Score: 101
Period size: 28 Copynumber: 2.3 Consensus size: 28
54421727 TGGTCTATGC
* *
54421737 GGACTCTTACTTGAAAGATAGTCTATGG
1 GGACTCTTACTTGAAAGATAGCCCATGG
54421765 GGACTCTTACTTGAAAGATAGCCCATGG
1 GGACTCTTACTTGAAAGATAGCCCATGG
*
54421793 AGACTCTT
1 GGACTCTT
54421801 GCTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 33 1.00
ACGTcount: A:0.28, C:0.19, G:0.23, T:0.30
Consensus pattern (28 bp):
GGACTCTTACTTGAAAGATAGCCCATGG
Found at i:54423610 original size:41 final size:41
Alignment explanation
Indices: 54423565--54423669 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
54423555 AGCGGCGGCA
*
54423565 TTTTACCAAAAACGCTGCTAAAAA-CAGAGCAATAGCGGCTT
1 TTTTA-CAAAAACGCCGCTAAAAACCAGAGCAATAGCGGCTT
** *
54423606 TTTTAGTAAAACGCCGCTAAAAACCAGAGCATTAGCGACGC-T
1 TTTTACAAAAACGCCGCTAAAAACCAGAGCAATAGCG--GCTT
**
54423648 TTCGA-AAAAACGCCGCTAAAAA
1 TTTTACAAAAACGCCGCTAAAAA
54423670 TCATATAATC
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
40 15 0.28
41 33 0.61
42 4 0.07
43 2 0.04
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.20
Consensus pattern (41 bp):
TTTTACAAAAACGCCGCTAAAAACCAGAGCAATAGCGGCTT
Found at i:54423760 original size:17 final size:17
Alignment explanation
Indices: 54423738--54423772 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
54423728 CTAAAACACT
*
54423738 AAACCCCTAAATCCTAA
1 AAACCCCTAAATACTAA
54423755 AAACCCCTAAATACTAA
1 AAACCCCTAAATACTAA
54423772 A
1 A
54423773 CTATAACCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.51, C:0.31, G:0.00, T:0.17
Consensus pattern (17 bp):
AAACCCCTAAATACTAA
Found at i:54429201 original size:43 final size:42
Alignment explanation
Indices: 54429099--54429372 Score: 377
Period size: 43 Copynumber: 6.4 Consensus size: 42
54429089 TATATATGGT
* ** * *
54429099 CTTTAGTGGCGTTTTTGGGGAAAGCATCGCTAAAGATCATGT
1 CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
* * * * * *
54429141 CTTTAGTGGCATTTTTGGGAAAAGCACCGTTAAATGTCATGA
1 CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
*
54429183 GCTTTAGCGGCGTTTTTGGGGAAAGTGCCGCTAAAGGTCATGA
1 -CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
*
54429226 TCTTTAGCGGCATTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
1 -CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
54429269 CTTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
1 C-TTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
*
54429312 CTTTTAGCGGTGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
1 C-TTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
54429355 CCTTTAGCGGCGTTTTTG
1 -CTTTAGCGGCGTTTTTG
54429373 AGAAAAAAAC
Statistics
Matches: 209, Mismatches: 20, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
42 36 0.17
43 172 0.82
44 1 0.00
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (42 bp):
CTTTAGCGGCGTTTTTGGGGAAAGCGCCGCTAAAGGTCATGA
Found at i:54429651 original size:7 final size:7
Alignment explanation
Indices: 54429639--54429739 Score: 175
Period size: 7 Copynumber: 14.1 Consensus size: 7
54429629 ATATACATCG
54429639 GCTTTTA
1 GCTTTTA
54429646 GCTTTTA
1 GCTTTTA
54429653 GCTTTTA
1 GCTTTTA
54429660 GCTTTTA
1 GCTTTTA
54429667 GCTTTTA
1 GCTTTTA
54429674 GCTTTTA
1 GCTTTTA
54429681 GCTTTTA
1 GCTTTTA
54429688 GCTTTTA
1 GCTTTTA
54429695 GCTTTTA
1 GCTTTTA
*
54429702 GCTATTA
1 GCTTTTA
54429709 GCTATTTA
1 GCT-TTTA
54429717 GCTTTTA
1 GCTTTTA
54429724 GCTATTTA
1 GCT-TTTA
54429732 GCTTTTA
1 GCTTTTA
54429739 G
1 G
54429740 ATATAAGGTT
Statistics
Matches: 90, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
7 77 0.86
8 13 0.14
ACGTcount: A:0.17, C:0.14, G:0.15, T:0.54
Consensus pattern (7 bp):
GCTTTTA
Found at i:54432985 original size:46 final size:46
Alignment explanation
Indices: 54432935--54433107 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
54432925 TGGTTGACCA
*
54432935 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
54432981 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
* * * *
54433028 TCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATACGAACA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* *
54433074 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
54433108 GGGGCGGGTT
Statistics
Matches: 107, Mismatches: 13, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 3 0.03
46 62 0.58
47 29 0.27
48 3 0.03
50 4 0.04
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:54433092 original size:93 final size:93
Alignment explanation
Indices: 54432933--54433102 Score: 277
Period size: 93 Copynumber: 1.8 Consensus size: 93
54432923 GATGGTTGAC
* ***
54432933 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAGTT
54432998 GAGTCCGAGTTCGTGAGATGTAACTAGG
66 GAGTCCGAGTTCGTGAGATGTAACTAGG
* * *
54433026 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATACGAACACCCGAGCTCGTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAGTT
54433091 GAGTCCGAGTTC
66 GAGTCCGAGTTC
54433103 ACTTAGGGGC
Statistics
Matches: 70, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATACAAACACCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAGG
Found at i:54449145 original size:26 final size:26
Alignment explanation
Indices: 54449116--54449223 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54449106 TGGTAAAAAT
54449116 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* * *
54449142 TGATAATGGATTAGGTAAATATTCTA
1 TGATAATGGGTTAGGTAAATGTTCCA
54449168 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
54449194 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54449220 TGAT
1 TGAT
54449224 GGGCATTTCA
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 75 1.00
ACGTcount: A:0.32, C:0.06, G:0.24, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54456335 original size:370 final size:370
Alignment explanation
Indices: 54455654--54456766 Score: 2172
Period size: 370 Copynumber: 3.0 Consensus size: 370
54455644 CAGAAATTGA
*
54455654 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTT
1 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
54455719 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
66 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
* *
54455784 TGGGAGCCAGAAGAGGAGATGCAACAACAATACCTTCATCTGTTTAGATCAGGTAAATTTCGAGG
131 TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
54455849 ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
196 ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
54455914 CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
261 CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
54455979 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
326 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
54456024 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
1 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
54456089 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
66 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
54456154 TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
131 TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
54456219 ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
196 ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
54456284 CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
261 CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
54456349 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
326 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
54456394 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
1 AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
54456459 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
66 TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
54456524 TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
131 TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
* *
54456589 ACGAAATTTCTTTAAAGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
196 ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
*
54456654 CAAAATTTCATGCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
261 CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
54456719 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
326 GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
54456764 AGT
1 AGT
54456767 GCAAAATAGG
Statistics
Matches: 737, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
370 737 1.00
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (370 bp):
AGTTCAGACTAATTTGACCTTTGAGGAGGAGCCTGTGCAAATATTGGCTCGAGATGTTAAGGTTC
TCAGAAGGAAATCTGTCCCATTAGTGAAAGTGCTTTGGCGTAATCATGGCAGAGAGGAAGCCACT
TGGGAGCCAGAAGAGGAGATGCAACAGCAATACCCTCATCTGTTTAGATCAGGTAAATTTCGAGG
ATGAAATTTCTTTAAGGAGGGTAGAGTTGTAACGCCCCAATTTTCAGGAATTCTGTGAATGTTGG
CAAAATTTCATTCTTTGATTTTGTCATTTGTGAGTGAAATTATGAAATAGGACCTATGTGAAAAT
GTTTGAAAATGCTATAGGCTAATTTGTAGTGGCCAAATAAATAGT
Found at i:54456906 original size:26 final size:26
Alignment explanation
Indices: 54456877--54456984 Score: 180
Period size: 26 Copynumber: 4.2 Consensus size: 26
54456867 TGGTACAAAT
54456877 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
54456903 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54456929 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
**
54456955 TGATAATGATTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
54456981 TGAT
1 TGAT
54456985 GGGCATTTCA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 76 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:54460276 original size:53 final size:53
Alignment explanation
Indices: 54460194--54460402 Score: 222
Period size: 53 Copynumber: 3.9 Consensus size: 53
54460184 TTTTCCTTTT
* * * * * *
54460194 TGAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGCATCGTTGCCTTA
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* *
54460247 TGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGTA-CCTTTTCCTTATA
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCC-TTGCC-T-TA
* * * * *
54460302 TTAACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTA
1 TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
* * * *
54460355 TAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATGATATCCTT
1 T-GAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
54460403 ATCTTACCAA
Statistics
Matches: 131, Mismatches: 20, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
52 1 0.01
53 43 0.33
54 43 0.33
55 42 0.32
56 2 0.02
ACGTcount: A:0.22, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAACTCACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTA
Found at i:54460392 original size:109 final size:107
Alignment explanation
Indices: 54460181--54460394 Score: 304
Period size: 108 Copynumber: 2.0 Consensus size: 107
54460171 TTACTCGGGA
* * * * *
54460181 ACCTTTTCCTTTTTGAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGCATCGTTGCCTT
1 ACCTTTTCCTTTTTGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGACATCCTTGCCTT
54460246 ATGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGT
66 ATGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGT
* **
54460288 ACCTTTTCCTTATATT-AACTCATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCC
1 ACCTTTTCCTT-T-TTGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGACATCCTTGCC
* *
54460352 TTATAGAACTTATCAATGCCATGCCTTGGCATGGTCTTACATG
64 TTAT-GAACTCACCAATGCCATGCCTTGGCATGGTCTTACATG
54460395 ATATCCTTAT
Statistics
Matches: 94, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
107 11 0.12
108 45 0.48
109 38 0.40
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.37
Consensus pattern (107 bp):
ACCTTTTCCTTTTTGAACTCACCAATGCCATGTCTTGACATGGTCTTACATGACATCCTTGCCTT
ATGAACTCACCAATGCCATGCCTTGGCATGGTCTTACATGGT
Found at i:54460436 original size:47 final size:47
Alignment explanation
Indices: 54460381--54460502 Score: 208
Period size: 47 Copynumber: 2.6 Consensus size: 47
54460371 CATGCCTTGG
*
54460381 CATGGTCTTACATGATATCCTTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
* *
54460428 CATGGTCTTATATGGTATCATTATCTTACCAAATGCCATGTTCCAAA
1 CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
*
54460475 CATGGTCTTACATGGTATCCTTGTCTTA
1 CATGGTCTTACATGGTATCCTTATCTTA
54460503 GTGCCAATGC
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (47 bp):
CATGGTCTTACATGGTATCCTTATCTTACCAAATGCCATGTTCCAAA
Found at i:54473058 original size:24 final size:24
Alignment explanation
Indices: 54473009--54473059 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
54472999 TTCGTAGGTC
* *
54473009 AAATAAATTATGCTAATAAATGCT
1 AAATAAATTATACTAATAAATACT
* *
54473033 AAATATATTATACTAATAAGTACT
1 AAATAAATTATACTAATAAATACT
54473057 AAA
1 AAA
54473060 CCCTCTAGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.53, C:0.08, G:0.06, T:0.33
Consensus pattern (24 bp):
AAATAAATTATACTAATAAATACT
Found at i:54474376 original size:46 final size:46
Alignment explanation
Indices: 54474302--54474478 Score: 177
Period size: 46 Copynumber: 3.8 Consensus size: 46
54474292 AGGTTATTTG
* * *
54474302 TGTGCTAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTCGAGA
1 TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGACCTCGAGA
*
54474346 TGTAAGCCAGTGTAAGA-CATGTCTGAGACAT-GCATCTA-CTACGAGA
1 TGT--GCCAGTGTAAGACCATGTCTGAGACATGGCATCGACCT-CGAGA
* **
54474392 TGTGTCAGTGTAAGACCATGTCT-AGGACATGGCATCGACACGTATAGA
1 TGTGCCAGTGTAAGACCATGTCTGA-GACATGGCATCGAC-C-TCGAGA
* *
54474440 GGTGCCAGTGTAAGACCATGTCTGGGACATGGCATCGAC
1 TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGAC
54474479 ATAGATATGT
Statistics
Matches: 112, Mismatches: 11, Indels: 16
0.81 0.08 0.12
Matches are distributed among these distances:
44 15 0.13
45 14 0.12
46 43 0.38
48 39 0.35
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (46 bp):
TGTGCCAGTGTAAGACCATGTCTGAGACATGGCATCGACCTCGAGA
Found at i:54474643 original size:49 final size:48
Alignment explanation
Indices: 54474504--54474702 Score: 192
Period size: 49 Copynumber: 4.1 Consensus size: 48
54474494 CTAGTGTAAG
*
54474504 TCGGCCTCGATTTTGATAGT-AGTGTAAGACCATGTCTAGGACATGGCA
1 TCGGCCTCGA-TTTGATAGTCAGTGTAAGACCATGTCTGGGACATGGCA
* * * *
54474552 TCGGCAC-AGATATGTGAGAG-CTAGTGTAAGACCATGTTTGGGACATGGCG
1 TCGGC-CTCGAT-T-TGATAGTC-AGTGTAAGACCATGTCTGGGACATGGCA
*
54474602 TCTGCCTCGATTTCGATAGTCAGTGTAAGACCATGTCTGGGACATGGCA
1 TCGGCCTCGATTT-GATAGTCAGTGTAAGACCATGTCTGGGACATGGCA
* * ** * *
54474651 TCGACCT-GA-TGGATGAACCAGTGTAAGACTATGTCTGGGATATGGCA
1 TCGGCCTCGATTTGAT-AGTCAGTGTAAGACCATGTCTGGGACATGGCA
54474698 TCGGC
1 TCGGC
54474703 ATTATACCCT
Statistics
Matches: 124, Mismatches: 18, Indels: 19
0.77 0.11 0.12
Matches are distributed among these distances:
46 3 0.02
47 34 0.27
48 11 0.09
49 43 0.35
50 33 0.27
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (48 bp):
TCGGCCTCGATTTGATAGTCAGTGTAAGACCATGTCTGGGACATGGCA
Found at i:54476358 original size:40 final size:42
Alignment explanation
Indices: 54476314--54476393 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
54476304 AAGGTTTTTA
*
54476314 GACACGGGCTA-GGACAC-GA-GTGTGTCATGGCCGTGTGAGG
1 GACACGGGCAATGGACACGGATGTGTGTCA-GGCCGTGTGAGG
*
54476354 GACACGGGCAATGGGCACGGATGTGTGTCAGGCCGTGTGA
1 GACACGGGCAATGGACACGGATGTGTGTCAGGCCGTGTGA
54476394 AAACCCCTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 10 0.29
41 5 0.14
42 12 0.34
43 8 0.23
ACGTcount: A:0.20, C:0.20, G:0.42, T:0.17
Consensus pattern (42 bp):
GACACGGGCAATGGACACGGATGTGTGTCAGGCCGTGTGAGG
Found at i:54478406 original size:55 final size:53
Alignment explanation
Indices: 54478219--54478410 Score: 189
Period size: 53 Copynumber: 3.7 Consensus size: 53
54478209 ACACGGGTAC
* * * * *
54478219 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTATCC-T---TT-TGAAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATG-AA
* * *
54478268 CTTACCATTGCCATGTCTTGACATGGTCTTACATAGTATCCTTGCCTTATGAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
* * * *
54478321 CTCACCAATGCCATGCCTTGGCATGGTCTTACATGGGA-CCTTTGCCTTGTAGTAA
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCC-TTGCCTTAT-G-AA
*
54478376 CTTATCAATGCCATGTCTTGACATGGTCTTACATG
1 CTTACCAATGCCATGTCTTGACATGGTCTTACATG
54478411 ATTTCCTTAC
Statistics
Matches: 120, Mismatches: 15, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
49 37 0.31
50 1 0.01
52 2 0.02
53 44 0.37
54 3 0.03
55 33 0.28
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.36
Consensus pattern (53 bp):
CTTACCAATGCCATGTCTTGACATGGTCTTACATGGGATCCTTGCCTTATGAA
Found at i:54485536 original size:16 final size:16
Alignment explanation
Indices: 54485517--54485547 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
54485507 CTTCTTCACT
54485517 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
54485533 TACTTACTTACTTAA
1 TACTCACTTACTTAA
54485548 TCAAATTTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:54485553 original size:20 final size:20
Alignment explanation
Indices: 54485514--54485553 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
54485504 AAACTTCTTC
* *
54485514 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
54485534 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
54485554 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:54485919 original size:55 final size:52
Alignment explanation
Indices: 54485736--54485985 Score: 233
Period size: 55 Copynumber: 4.7 Consensus size: 52
54485726 ACACGGGTAC
* * * * *
54485736 CTTACCATTGCCATGACTTGTCATGGTCTTACGTGGTA---T-CCTTTTGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTTAG-AA
* *
54485785 CTTACCATTGCCATGTCTTGACATGGTCTTACATGGTATCCTTGCC-TTATGAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTA-CCTTGCCTTTA-GAA
* * * *
54485838 CTCACCAATGCCATGCCTTGGCATGGTCTGACATGGGACCTTTGCCTTGTAGTAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACC-TTGCCTT-TAG-AA
* * *
54485893 CTTATCAATGCCATGTCTTGACATGGTCTTACATGAGTTCCTTGCC-TTAGAAA
1 CTTACCAATGCCATGCCTTGACATGGTCTTACATG-GTACCTTGCCTTTAG-AA
*
54485946 CCTTACCAATTGCCATGCCTTGGCATGGTCTTACATGGTA
1 -CTTACCAA-TGCCATGCCTTGACATGGTCTTACATGGTA
54485986 TCCCTAAACC
Statistics
Matches: 166, Mismatches: 22, Indels: 21
0.79 0.11 0.10
Matches are distributed among these distances:
49 35 0.21
52 2 0.01
53 47 0.28
54 15 0.09
55 64 0.39
56 3 0.02
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.35
Consensus pattern (52 bp):
CTTACCAATGCCATGCCTTGACATGGTCTTACATGGTACCTTGCCTTTAGAA
Found at i:54485927 original size:108 final size:110
Alignment explanation
Indices: 54485783--54485983 Score: 320
Period size: 108 Copynumber: 1.8 Consensus size: 110
54485773 ATCCTTTTGA
*
54485783 AACTTACCATTGCCATGTCTTGACATGGTCTTACATG-GTATCCTTGCCTTATG-AA-CTCACCA
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGAGT-TCCTTGCCTTA-GAAACCTCACCA
54485845 A-TGCCATGCCTTGGCATGGTCTGACATGGGACCTTTGCCTTGTAGT
64 ATTGCCATGCCTTGGCATGGTCTGACATGGGACCTTTGCCTTGTAGT
* *
54485891 AACTTATCAATGCCATGTCTTGACATGGTCTTACATGAGTTCCTTGCCTTAGAAACCTTACCAAT
1 AACTTACCAATGCCATGTCTTGACATGGTCTTACATGAGTTCCTTGCCTTAGAAACCTCACCAAT
*
54485956 TGCCATGCCTTGGCATGGTCTTACATGG
66 TGCCATGCCTTGGCATGGTCTGACATGG
54485984 TATCCCTAAA
Statistics
Matches: 85, Mismatches: 4, Indels: 6
0.89 0.04 0.06
Matches are distributed among these distances:
107 1 0.01
108 48 0.56
109 9 0.11
110 27 0.32
ACGTcount: A:0.22, C:0.25, G:0.19, T:0.33
Consensus pattern (110 bp):
AACTTACCAATGCCATGTCTTGACATGGTCTTACATGAGTTCCTTGCCTTAGAAACCTCACCAAT
TGCCATGCCTTGGCATGGTCTGACATGGGACCTTTGCCTTGTAGT
Found at i:54487362 original size:20 final size:21
Alignment explanation
Indices: 54487337--54487375 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
54487327 CTCCTATGAC
*
54487337 CAAGTTGCCTTCG-CTCCAAA
1 CAAGTTGACTTCGACTCCAAA
54487357 CAAGTTGACTTCGACTCCA
1 CAAGTTGACTTCGACTCCA
54487376 TAATAGACGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.26, C:0.33, G:0.15, T:0.26
Consensus pattern (21 bp):
CAAGTTGACTTCGACTCCAAA
Found at i:54498756 original size:21 final size:21
Alignment explanation
Indices: 54498709--54498761 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
54498699 TCCTAGGGTG
*
54498709 TAAATTGAATTCAATTGAATAT
1 TAAA-TGAATTAAATTGAATAT
*
54498731 GAAATGAATTAAATTG-ATGAT
1 TAAATGAATTAAATTGAAT-AT
*
54498752 TAAATTAATT
1 TAAATGAATT
54498762 TATATAGATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 2 0.08
21 21 0.81
22 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.11, T:0.40
Consensus pattern (21 bp):
TAAATGAATTAAATTGAATAT
Found at i:54504690 original size:40 final size:40
Alignment explanation
Indices: 54504646--54504797 Score: 234
Period size: 40 Copynumber: 3.8 Consensus size: 40
54504636 GAATATAGCC
* *
54504646 ACTCGCTCAAATGCCTTCGGGACTTAACCCGG-ATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAAT-TAGTA
*
54504686 ACTCGCACAAATACCTTCGGGACTTAGCCCGGAATTAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
* *
54504726 ACTCGCACAAATGCCTTCTGGACTTAGCCCGGAATTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
*
54504766 ACTAGCACAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
54504798 TTATCATCCG
Statistics
Matches: 103, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
40 101 0.98
41 2 0.02
ACGTcount: A:0.27, C:0.29, G:0.21, T:0.23
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATTAGTA
Found at i:54511540 original size:47 final size:47
Alignment explanation
Indices: 54511428--54511601 Score: 191
Period size: 47 Copynumber: 3.7 Consensus size: 47
54511418 GGTCAGACAT
* *
54511428 CGATGCCATGTCCCAGACATGGTCTTACACT-GAC--ACATCTCGTACC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAG-CTTACGTCTCG-AGC
54511474 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTTACGTCTCGAGGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACGTCTCGA-GC
* * * *
54511520 CGATGCCATGTCCCAAACAT-GTCTTACACTAGCACT-CGTCCCAATGC
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGC-TTACGTCTCGA-GC
*
54511567 CGATGCCATGTCCCAGACATGGTTTTACACTAGCT
1 CGATGCCATGTCCCAGACATGGTCTTACACTAGCT
54511602 CCCATAATGT
Statistics
Matches: 111, Mismatches: 10, Indels: 13
0.83 0.07 0.10
Matches are distributed among these distances:
44 11 0.10
45 16 0.14
46 18 0.16
47 53 0.48
48 13 0.12
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.25
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTAGCTTACGTCTCGAGC
Found at i:54511624 original size:94 final size:93
Alignment explanation
Indices: 54511473--54511646 Score: 226
Period size: 94 Copynumber: 1.9 Consensus size: 93
54511463 CATCTCGTAC
* * * *
54511473 CCGATGCATGTCCCAGACATGTCTTACACTAGCTTACGTCTCGAGGCCGATGCCATGTCCCAAAC
1 CCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATATCGAGGCCAATGCCATGTCCCAAAC
54511538 ATGTCTTACACTAGCACTCGTCCCAATG
66 ATGTCTTACACTAGCACTCGTCCCAATG
* * * *
54511566 CCGATGCCATGTCCCAGACATGGTTTTACACTAGCTCCCATAAT-GTGGCCAATG-CATGTTCCA
1 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACAT-ATCGAGGCCAATGCCATGTCCCA
*
54511629 GACATGTCTTACACTAGC
63 AACATGTCTTACACTAGC
54511647 TCACACAAGT
Statistics
Matches: 69, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
93 6 0.09
94 39 0.57
95 23 0.33
96 1 0.01
ACGTcount: A:0.24, C:0.32, G:0.18, T:0.26
Consensus pattern (93 bp):
CCGATGCATGTCCCAGACATGTCTTACACTAGCTCACATATCGAGGCCAATGCCATGTCCCAAAC
ATGTCTTACACTAGCACTCGTCCCAATG
Found at i:54523225 original size:46 final size:46
Alignment explanation
Indices: 54523172--54523339 Score: 155
Period size: 46 Copynumber: 3.6 Consensus size: 46
54523162 ATTGTCAGCT
* * *
54523172 AGTGTAAGACATGTCGGGGACATGCATCGGCCACATTATGAGGGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCC
* * * * *
54523218 AGTGTAAGACCATGTTTAGGACATGGCATTGG-CA-GTGAGATGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCACAT--GATGAGAGCC
* * *
54523266 AATGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCAC-ATGATG-AGAGCC
54523312 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
54523340 CGCTACGAGT
Statistics
Matches: 97, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
46 49 0.51
47 27 0.28
48 21 0.22
ACGTcount: A:0.29, C:0.18, G:0.30, T:0.23
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCACATGATGAGAGCC
Found at i:54524528 original size:22 final size:21
Alignment explanation
Indices: 54524503--54524543 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
54524493 TCGAATTGGT
54524503 CACACGGGCGTGTTGCCCCTCC
1 CACACGGGCGTGTT-CCCCTCC
54524525 CACACGGGCGTGTTCCCCT
1 CACACGGGCGTGTTCCCCT
54524544 GTGTCTAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.10, C:0.44, G:0.27, T:0.20
Consensus pattern (21 bp):
CACACGGGCGTGTTCCCCTCC
Found at i:54528518 original size:18 final size:18
Alignment explanation
Indices: 54528495--54528530 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
54528485 ACTATGACTC
*
54528495 GAGAAAATAGTTTAACCA
1 GAGAAAATAGCTTAACCA
54528513 GAGAAAATAGCTTAACCA
1 GAGAAAATAGCTTAACCA
54528531 AAATATGAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (18 bp):
GAGAAAATAGCTTAACCA
Found at i:54529682 original size:2 final size:2
Alignment explanation
Indices: 54529675--54529713 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
54529665 AAGGGGTGTT
54529675 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
54529714 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:54534718 original size:18 final size:20
Alignment explanation
Indices: 54534692--54534738 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
54534682 ATAAATACAA
*
54534692 TATCGATAACTTT-TTTT-G
1 TATCGATAAATTTATTTTGG
*
54534710 TATCAATAAATTTATTTTGG
1 TATCGATAAATTTATTTTGG
54534730 TATCGATAA
1 TATCGATAA
54534739 TGTTAGTTCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.46
19 4 0.17
20 9 0.38
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
TATCGATAAATTTATTTTGG
Found at i:54539947 original size:43 final size:42
Alignment explanation
Indices: 54539897--54540054 Score: 140
Period size: 43 Copynumber: 3.7 Consensus size: 42
54539887 ATATGTGTTC
* *
54539897 TCGTGTAAGACCACATCTGGGACATTGGCATCGATCTTTGAT
1 TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGAT
* * * * *
54539939 TATGTGTAAGACCATGTTTGGGACATCGGTATCG-TATTTGAT
1 T-CGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGAT
* * **
54539981 TCGTGTAAGACC-CTGTCTGGGGCAGTGGCATCGATATGAGAT
1 TCGTGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGAT
* * * *
54540023 AGCATGTAAGACCACGTTTGGGACGTTGGCAT
1 -TCGTGTAAGACCACGTCTGGGACATTGGCAT
54540055 TGTTTGATAT
Statistics
Matches: 89, Mismatches: 22, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
41 24 0.27
42 15 0.17
43 49 0.55
44 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.30
Consensus pattern (42 bp):
TCGTGTAAGACCACGTCTGGGACATTGGCATCGATATTTGAT
Found at i:54542731 original size:19 final size:19
Alignment explanation
Indices: 54542707--54542746 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
54542697 TAACCACAAC
54542707 GGTTGGAAATCAATTGAAG
1 GGTTGGAAATCAATTGAAG
*
54542726 GGTTGGGAATCAATTGAAG
1 GGTTGGAAATCAATTGAAG
54542745 GG
1 GG
54542747 CATAAATACC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.05, G:0.38, T:0.25
Consensus pattern (19 bp):
GGTTGGAAATCAATTGAAG
Found at i:54545460 original size:56 final size:57
Alignment explanation
Indices: 54545336--54545480 Score: 145
Period size: 58 Copynumber: 2.5 Consensus size: 57
54545326 TATATTAGTC
* *
54545336 GTCACTTAATTATTAATATTTTTTTTAGTCACCTAATTATAAAAATGTTGTAAAATA
1 GTCACTCAATTATTAATATTTTTTTTAGTCAACTAATTATAAAAATGTTGTAAAATA
* * *
54545393 GTCACTTAATTATTAGTAATTTTTTTTAGTCAACTAGA-TAT-GAAA-GTT-TCAAAATA
1 GTCACTCAATTATTAAT-ATTTTTTTTAGTCAACTA-ATTATAAAAATGTTGT-AAAATA
* *
54545449 GTCCCTCAATTATTCAATTTTGTCTTTTTAGT
1 GTCACTCAATTATT-AATATT-T-TTTTTAGT
54545481 GACTCAACTA
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
55 1 0.01
56 23 0.31
57 22 0.29
58 28 0.37
59 1 0.01
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (57 bp):
GTCACTCAATTATTAATATTTTTTTTAGTCAACTAATTATAAAAATGTTGTAAAATA
Found at i:54546520 original size:12 final size:12
Alignment explanation
Indices: 54546491--54546520 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
54546481 ACTTGAATTC
54546491 TTTTTTCTTTTT
1 TTTTTTCTTTTT
*
54546503 CTTTTTCTTTTT
1 TTTTTTCTTTTT
54546515 TTTTTT
1 TTTTTT
54546521 TAACTTGGGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTCTTTTT
Found at i:54549146 original size:32 final size:33
Alignment explanation
Indices: 54549105--54549168 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 33
54549095 AATCTTTAAA
*
54549105 AAGCTTAAAAGAT-AAAAATTA-CAAAAAAAAG
1 AAGCTTAAAACATAAAAAATTATCAAAAAAAAG
*
54549136 AAGCTTTAAAACATAAAAAATTATTAAAAAAAA
1 AAGC-TTAAAACATAAAAAATTATCAAAAAAAA
54549169 TCATTTTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
31 4 0.14
32 8 0.29
33 8 0.29
34 8 0.29
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.20
Consensus pattern (33 bp):
AAGCTTAAAACATAAAAAATTATCAAAAAAAAG
Found at i:54558791 original size:41 final size:41
Alignment explanation
Indices: 54558724--54558929 Score: 214
Period size: 41 Copynumber: 5.0 Consensus size: 41
54558714 AAGTATATCG
* * *
54558724 AGGGTTACCTAAGTACAAATAGGGGCACCTCTGTGTAATTC
1 AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
*
54558765 AGGAGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
1 AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
* * * * *
54558806 AGGGGTACCAAAGTAGAAATAGGGGAACGTCTATGCAATTT
1 AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
* * * * * * *
54558847 AGGGGTACCGAAGTAGAAACAGGGGCGCGTATGTACAATTC
1 AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
* ** * * *
54558888 AGAGGTACTGAAGTACAAACAGGGTCACGTCTGTGCAATTC
1 AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
54558929 A
1 A
54558930 TTATTATTCT
Statistics
Matches: 140, Mismatches: 25, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 140 1.00
ACGTcount: A:0.33, C:0.18, G:0.28, T:0.21
Consensus pattern (41 bp):
AGGGGTACCAAAGTACAAATAGGGGCACCTCTGTGCAATTC
Found at i:54566055 original size:41 final size:41
Alignment explanation
Indices: 54565937--54566056 Score: 127
Period size: 41 Copynumber: 3.0 Consensus size: 41
54565927 GTACATCTAG
* *
54565937 GGGTACCGAAGTAC-AA-AGGGGAACATCTGTGCAATTTAA
1 GGGTACCGAAGTACAAACAGGGGCACATCTGTGCAATTCAA
* * * *
54565976 GGGTACCGAAGTACAAATAGGGGCACATATGTGTAATTCAG
1 GGGTACCGAAGTACAAACAGGGGCACATCTGTGCAATTCAA
** * * *
54566017 GGGTATTGAAGTACAAACATGGTCACGTCTGTGCAATTCA
1 GGGTACCGAAGTACAAACAGGGGCACATCTGTGCAATTCA
54566057 TCATTATTCT
Statistics
Matches: 66, Mismatches: 13, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.21
40 2 0.03
41 50 0.76
ACGTcount: A:0.33, C:0.16, G:0.28, T:0.23
Consensus pattern (41 bp):
GGGTACCGAAGTACAAACAGGGGCACATCTGTGCAATTCAA
Found at i:54567059 original size:13 final size:13
Alignment explanation
Indices: 54567041--54567067 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
54567031 GAAGTAATCG
54567041 CACACGGGCGTGT
1 CACACGGGCGTGT
54567054 CACACGGGCGTGT
1 CACACGGGCGTGT
54567067 C
1 C
54567068 CCTGCTGAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.33, G:0.37, T:0.15
Consensus pattern (13 bp):
CACACGGGCGTGT
Found at i:54570818 original size:28 final size:28
Alignment explanation
Indices: 54570786--54570856 Score: 101
Period size: 28 Copynumber: 2.5 Consensus size: 28
54570776 AATGAGATTG
54570786 GCACTAAGTGTGCGAGTTT-AAT-TGTATA
1 GCACTAAGTGTGCGAGTTTGAATAT-TA-A
*
54570814 GCACTAAGTGTGCGAGTTTGACTATTAA
1 GCACTAAGTGTGCGAGTTTGAATATTAA
54570842 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
54570857 CTTACTATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 35 0.88
29 4 0.10
30 1 0.03
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGAATATTAA
Found at i:54582657 original size:23 final size:22
Alignment explanation
Indices: 54582631--54582694 Score: 69
Period size: 23 Copynumber: 2.9 Consensus size: 22
54582621 GAAATATTTA
54582631 TTTTATTATTTTATATTTTTAAT
1 TTTTATTATTTTAT-TTTTTAAT
***
54582654 TTTTATTCAAACTATTTTTTAAT
1 TTTTATT-ATTTTATTTTTTAAT
54582677 TTTTA--ATTTTATTTTTTA
1 TTTTATTATTTTATTTTTTA
54582695 GTAGATTTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
20 10 0.29
23 20 0.59
24 4 0.12
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTATTATTTTATTTTTTAAT
Found at i:54593429 original size:48 final size:48
Alignment explanation
Indices: 54593358--54593544 Score: 232
Period size: 48 Copynumber: 3.9 Consensus size: 48
54593348 CATTAGGGAA
* * *
54593358 TTCATTGATTTGGCTTCGGGCCATTATATTGGTACTTCGGGTGTAAGC
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGTGAGC
** *
54593406 TTCATTGATTTGGCTTTAGGCCATGATATTGGAACTTCGGGTGTGAG-
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGTGAGC
* * ** *
54593453 TTACATTGATTTAGCTTCGGACCATGATATCAGCACTTCGGGTGCGAGC
1 TT-CATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGTGAGC
* * *
54593502 TTCTTTGATTTGGCTTCGGGACATGATATTGGCACTTAGGGTG
1 TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTG
54593545 CGAGACTCCC
Statistics
Matches: 117, Mismatches: 20, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
47 2 0.02
48 113 0.97
49 2 0.02
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (48 bp):
TTCATTGATTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGTGAGC
Found at i:54597673 original size:17 final size:17
Alignment explanation
Indices: 54597651--54597687 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
54597641 ATGCACTAAC
**
54597651 ATGAAAATGTGATGACA
1 ATGAAAATGAAATGACA
54597668 ATGAAAATGAAATGACA
1 ATGAAAATGAAATGACA
54597685 ATG
1 ATG
54597688 TATACTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (17 bp):
ATGAAAATGAAATGACA
Found at i:54603880 original size:47 final size:47
Alignment explanation
Indices: 54603822--54604263 Score: 767
Period size: 47 Copynumber: 9.4 Consensus size: 47
54603812 CAGCCAAGAC
*
54603822 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54603869 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
54603916 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54603963 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
54604010 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
*
54604057 AGTGTATATATGTGATAAGGCCTAATAGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54604104 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
54604151 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* * * * * * *
54604198 AGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATGGATGTGAA
1 AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
* *
54604245 AGTGCATAAATGTGATAAG
1 AGTGTATATATGTGATAAG
54604264 TCCCGAAGGG
Statistics
Matches: 379, Mismatches: 16, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 379 1.00
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.29
Consensus pattern (47 bp):
AGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATGAATGTGAA
Done.