Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 148 of 427
Found at i:40469945 original size:31 final size:30
Alignment explanation
Indices: 40469910--40469968 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
40469900 TACACATGAA
*
40469910 ATATATGGAAAT-AATGTTACATGATATATAG
1 ATATAT-GAAATGAATGATACATG-TATATAG
*
40469941 ATATATGAAATGGATGATACATGTATAT
1 ATATATGAAATGAATGATACATGTATAT
40469969 GGAACTTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.44, C:0.03, G:0.17, T:0.36
Consensus pattern (30 bp):
ATATATGAAATGAATGATACATGTATATAG
Found at i:40478118 original size:35 final size:35
Alignment explanation
Indices: 40478072--40478142 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
40478062 ATTATAGGTA
40478072 TGACCACATCTGGGACGTTAGCATTGTACGATGTG
1 TGACCACATCTGGGACGTTAGCATTGTACGATGTG
*
40478107 TGACCATATCTGGGACGTTAGCATTGTACGATGTG
1 TGACCACATCTGGGACGTTAGCATTGTACGATGTG
40478142 T
1 T
40478143 ATGATTATCC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (35 bp):
TGACCACATCTGGGACGTTAGCATTGTACGATGTG
Found at i:40482263 original size:18 final size:18
Alignment explanation
Indices: 40482223--40482265 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
40482213 TATATTGTAA
40482223 GCGAACCCATGTTATTAT
1 GCGAACCCATGTTATTAT
* * *
40482241 ACGAACCCATGTTTTTGT
1 GCGAACCCATGTTATTAT
40482259 GCGAACC
1 GCGAACC
40482266 TTAATATTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.26, C:0.26, G:0.19, T:0.30
Consensus pattern (18 bp):
GCGAACCCATGTTATTAT
Found at i:40483978 original size:31 final size:31
Alignment explanation
Indices: 40483943--40484047 Score: 108
Period size: 31 Copynumber: 3.4 Consensus size: 31
40483933 AATATTAAAT
40483943 TTAATTTAATATTTATCTTGATAGTATTTTA
1 TTAATTTAATATTTATCTTGATAGTATTTTA
* * * * **
40483974 TTAATTTAATACTAAT-GTGAGA-TATTAAA
1 TTAATTTAATATTTATCTTGATAGTATTTTA
*
40484003 TTTGATTTAATATTTATCTTGAT-GATATTTTA
1 -TTAATTTAATATTTATCTTGATAG-TATTTTA
40484035 TTAATTTAATATT
1 TTAATTTAATATT
40484048 AATATAAGTA
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
29 5 0.09
30 17 0.30
31 29 0.52
32 5 0.09
ACGTcount: A:0.35, C:0.03, G:0.08, T:0.54
Consensus pattern (31 bp):
TTAATTTAATATTTATCTTGATAGTATTTTA
Found at i:40484011 original size:61 final size:61
Alignment explanation
Indices: 40483934--40484050 Score: 200
Period size: 61 Copynumber: 1.9 Consensus size: 61
40483924 GATAATTTTA
40483934 ATATTAAATTTAATTTAATATTTATCTTGAT-AGTATTTTATTAATTTAATACTAATGTGAG
1 ATATTAAATTTAATTTAATATTTATCTTGATGA-TATTTTATTAATTTAATACTAATGTGAG
* *
40483995 ATATTAAATTTGATTTAATATTTATCTTGATGATATTTTATTAATTTAATATTAAT
1 ATATTAAATTTAATTTAATATTTATCTTGATGATATTTTATTAATTTAATACTAAT
40484051 ATAAGTAACT
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
61 52 0.98
62 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.53
Consensus pattern (61 bp):
ATATTAAATTTAATTTAATATTTATCTTGATGATATTTTATTAATTTAATACTAATGTGAG
Found at i:40489247 original size:16 final size:16
Alignment explanation
Indices: 40489228--40489266 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
40489218 AATTTTTTTT
40489228 AGTTTAATTTAAATAA
1 AGTTTAATTTAAATAA
* *
40489244 AG-TTCATTTTAATAA
1 AGTTTAATTTAAATAA
40489259 AGTTTAAT
1 AGTTTAAT
40489267 GCTTAATAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.44, C:0.03, G:0.08, T:0.46
Consensus pattern (16 bp):
AGTTTAATTTAAATAA
Found at i:40490406 original size:28 final size:29
Alignment explanation
Indices: 40490371--40490428 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
40490361 TGTTATGCCA
40490371 TGATATGTATAAACCTATTT-ATTCCATT
1 TGATATGTATAAACCTATTTGATTCCATT
*
40490399 TGATATGTATGAACCTATTTGATTCCATT
1 TGATATGTATAAACCTATTTGATTCCATT
40490428 T
1 T
40490429 TTTCAACTCC
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 19 0.68
29 9 0.32
ACGTcount: A:0.29, C:0.14, G:0.10, T:0.47
Consensus pattern (29 bp):
TGATATGTATAAACCTATTTGATTCCATT
Found at i:40496703 original size:42 final size:42
Alignment explanation
Indices: 40496592--40496703 Score: 145
Period size: 43 Copynumber: 2.6 Consensus size: 42
40496582 TACTATACCA
** *
40496592 ATGCCATATCCCAGATATGGTCTTACATGGGATCTTAATTCG
1 ATGCCATATCCCAGATATGGTCTTACATGAAATCTCAATTCG
* * *
40496634 ATACCAATAGCCCAGCTATGGTCTTACATGAAATCTC-ATATCG
1 ATGCC-ATATCCCAGATATGGTCTTACATGAAATCTCAAT-TCG
40496677 ATGCCATATCCCAGATATGGTCTTACA
1 ATGCCATATCCCAGATATGGTCTTACA
40496704 CGTAGACTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
42 26 0.44
43 33 0.56
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAGATATGGTCTTACATGAAATCTCAATTCG
Found at i:40501165 original size:14 final size:14
Alignment explanation
Indices: 40501146--40501175 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40501136 TATCTTATAA
40501146 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
40501160 ATATGCGTTAATCT
1 ATATGCGTGAATCT
40501174 AT
1 AT
40501176 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:40508973 original size:14 final size:14
Alignment explanation
Indices: 40508956--40508985 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40508946 TATCTTATAA
40508956 ATATGCGTGAATCT
1 ATATGCGTGAATCT
*
40508970 ATATGCGTTAATCT
1 ATATGCGTGAATCT
40508984 AT
1 AT
40508986 CTTGAAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.40
Consensus pattern (14 bp):
ATATGCGTGAATCT
Found at i:40515100 original size:17 final size:17
Alignment explanation
Indices: 40515078--40515110 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40515068 CATTTTTGTT
40515078 CTCTTGATGCC-ATTTCC
1 CTCTTG-TGCCGATTTCC
40515095 CTCTTGTGCCGATTTC
1 CTCTTGTGCCGATTTC
40515111 TTTTGGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.33, G:0.15, T:0.42
Consensus pattern (17 bp):
CTCTTGTGCCGATTTCC
Found at i:40522843 original size:17 final size:17
Alignment explanation
Indices: 40522821--40522853 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40522811 CATTTTTGTT
40522821 CTCTTGATGCC-ATTTCC
1 CTCTTG-TGCCGATTTCC
40522838 CTCTTGTGCCGATTTC
1 CTCTTGTGCCGATTTC
40522854 TTTTGGTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.33, G:0.15, T:0.42
Consensus pattern (17 bp):
CTCTTGTGCCGATTTCC
Found at i:40525041 original size:3 final size:3
Alignment explanation
Indices: 40525033--40525084 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
40525023 CAGATAAAAT
40525033 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
40525081 ATA A
1 ATA A
40525085 GTAAATATCT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40529549 original size:24 final size:25
Alignment explanation
Indices: 40529513--40529574 Score: 67
Period size: 24 Copynumber: 2.5 Consensus size: 25
40529503 AAAACCTAAT
*
40529513 AAAAATAAGCTTAAAGA-AAAATAA
1 AAAAATAAGCTTAAACATAAAATAA
40529537 AAAAAT-AGTCTTAAACATAAAATAA
1 AAAAATAAG-CTTAAACATAAAATAA
40529562 TAAATAA-AAGCTT
1 -AAA-AATAAGCTT
40529575 TTAAACATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 2 0.06
24 13 0.41
25 7 0.22
26 6 0.19
27 4 0.12
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.23
Consensus pattern (25 bp):
AAAAATAAGCTTAAACATAAAATAA
Found at i:40535341 original size:28 final size:28
Alignment explanation
Indices: 40535279--40535376 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 28
40535269 TCACAAATTG
** * *
40535279 GCACTAAGTGTGCGGGTTCAAATTATACA
1 GCACTAAGTGTGCAAGTTC-GATTATATA
* *
40535308 GTACTAAGTGTGCAAGTTTGATTATATA
1 GCACTAAGTGTGCAAGTTCGATTATATA
* *
40535336 GCACTAAGTGTGCGAGTTCGACTAT-TAA
1 GCACTAAGTGTGCAAGTTCGATTATAT-A
40535364 GCACTAAGTGTGC
1 GCACTAAGTGTGC
40535377 GGGCTTATTG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
27 1 0.02
28 42 0.72
29 15 0.26
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.31
Consensus pattern (28 bp):
GCACTAAGTGTGCAAGTTCGATTATATA
Found at i:40537327 original size:19 final size:19
Alignment explanation
Indices: 40537290--40537327 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
40537280 ACCTGTCAGA
*
40537290 AGAAAATAAATGAAGAATT
1 AGAAAATAAATGAAAAATT
40537309 AGAAAATAAAAT-AAAAATT
1 AGAAAAT-AAATGAAAAATT
40537328 TAAATTGCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.68, C:0.00, G:0.11, T:0.21
Consensus pattern (19 bp):
AGAAAATAAATGAAAAATT
Found at i:40544686 original size:5 final size:5
Alignment explanation
Indices: 40544676--40544755 Score: 60
Period size: 5 Copynumber: 15.8 Consensus size: 5
40544666 AATTTCTCCT
*
40544676 TTTTC TTTTC TTTTC TTTTC TTCTT- TCTTTC -TTTC TATTTC GTTTC
1 TTTTC TTTTC TTTTC TTTTC TT-TTC T-TTTC TTTTC T-TTTC TTTTC
* *
40544722 TTCTC TGTTTC TTTTTC TTGT- TTTTC -TTTC TTTT
1 TTTTC T-TTTC -TTTTC TTTTC TTTTC TTTTC TTTT
40544756 ATTTGTTCTT
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
4 11 0.18
5 34 0.57
6 14 0.23
7 1 0.02
ACGTcount: A:0.01, C:0.20, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTTC
Found at i:40544706 original size:26 final size:26
Alignment explanation
Indices: 40544677--40544754 Score: 79
Period size: 26 Copynumber: 3.0 Consensus size: 26
40544667 ATTTCTCCTT
40544677 TTTCTTTTCTTTTCTTTTCTTCTTTC
1 TTTCTTTTCTTTTCTTTTCTTCTTTC
* * *
40544703 TTTC-TTTCTATTTCGTTTCTTCTCTG
1 TTTCTTTTCT-TTTCTTTTCTTCTTTC
*
40544729 TTTCTTTTTCTTGT-TTTTCTTTCTTT
1 TTTC-TTTTCTTTTCTTTTC-TTCTTT
40544755 TATTTGTTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 7
0.76 0.11 0.13
Matches are distributed among these distances:
25 5 0.12
26 25 0.60
27 7 0.17
28 5 0.12
ACGTcount: A:0.01, C:0.21, G:0.04, T:0.74
Consensus pattern (26 bp):
TTTCTTTTCTTTTCTTTTCTTCTTTC
Found at i:40544777 original size:21 final size:19
Alignment explanation
Indices: 40544729--40544780 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 19
40544719 TTCTTCTCTG
*
40544729 TTTCTTTT-TCTTGTTTTTC
1 TTTCTTTTAT-TTGTTTTTA
40544748 TTTCTTTTATTTGTTCTTTA
1 TTTCTTTTATTTGTT-TTTA
40544768 TTTCATTTTATTT
1 TTTC-TTTTATTT
40544781 CTTTCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 13 0.45
20 8 0.28
21 8 0.28
ACGTcount: A:0.08, C:0.12, G:0.04, T:0.77
Consensus pattern (19 bp):
TTTCTTTTATTTGTTTTTA
Found at i:40544931 original size:3 final size:3
Alignment explanation
Indices: 40544923--40544968 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
40544913 TTGATAAAAT
40544923 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
40544969 GTAAATATCT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:40548176 original size:43 final size:42
Alignment explanation
Indices: 40548109--40548222 Score: 122
Period size: 43 Copynumber: 2.7 Consensus size: 42
40548099 TACCATACCA
* * * * **
40548109 ATGCCATATCCTAGATATAGTCTTACATGGGATCTCA-ATTTG
1 ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCATA-TTG
* *
40548151 ATGCCAATAGCCGAGCTATGGTCTTACACGAAATCTCATATTG
1 ATGCC-ATAGCCCAGATATGGTCTTACACGAAATCTCATATTG
*
40548194 ATGCCATATCCCAGATATGGTCTTACACG
1 ATGCCATAGCCCAGATATGGTCTTACACG
40548223 TAGACTCAAA
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
42 26 0.43
43 33 0.55
44 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.31
Consensus pattern (42 bp):
ATGCCATAGCCCAGATATGGTCTTACACGAAATCTCATATTG
Found at i:40559472 original size:25 final size:25
Alignment explanation
Indices: 40559444--40559493 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
40559434 TCCCCCAAAT
40559444 CAACTTAAGGTTGGAGACAAAGTGC
1 CAACTTAAGGTTGGAGACAAAGTGC
40559469 CAACTTAAGGTTGGAGACAAAGTGC
1 CAACTTAAGGTTGGAGACAAAGTGC
40559494 TATTAGACAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.16, G:0.28, T:0.20
Consensus pattern (25 bp):
CAACTTAAGGTTGGAGACAAAGTGC
Found at i:40565192 original size:40 final size:40
Alignment explanation
Indices: 40565133--40565301 Score: 164
Period size: 40 Copynumber: 4.2 Consensus size: 40
40565123 CGGGACTTTA
* * *
40565133 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
40565173 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
40565213 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * *
40565253 CCCGGATGT-A-AA-TTTCAGCATAATTGTCTTCGGGGCTTAG
1 CCCGGATATAACAACTTGCA-CA-AA-TGCCTTCGGGTCTTAG
40565293 CCCGGATAT
1 CCCGGATAT
40565302 CATTCAATTT
Statistics
Matches: 104, Mismatches: 22, Indels: 6
0.79 0.17 0.05
Matches are distributed among these distances:
37 3 0.03
38 3 0.03
39 1 0.01
40 97 0.93
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:40573181 original size:40 final size:40
Alignment explanation
Indices: 40573136--40573302 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
40573126 CGGAATATAA
40573136 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
40573176 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
* * *
40573216 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
40573256 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40573295 CCGGATAT
1 CCGGATAT
40573303 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40573286 original size:80 final size:79
Alignment explanation
Indices: 40573136--40573302 Score: 205
Period size: 80 Copynumber: 2.1 Consensus size: 79
40573126 CGGAATATAA
* *
40573136 CCGGATATAATCACGTGCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
40573201 CCTTCGGGCCTTAGC
66 CCTTCGGG-CTTAGC
* * ** *
40573216 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA
*
40573278 TTGTCTTCGGGCTTAGC
64 -TGCCTTCGGGCTTAGC
40573295 CCGGATAT
1 CCGGATAT
40573303 CATTCAATTT
Statistics
Matches: 76, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
79 18 0.24
80 58 0.76
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (79 bp):
CCGGATATAACCACGTGCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATG
CCTTCGGGCTTAGC
Found at i:40574150 original size:17 final size:19
Alignment explanation
Indices: 40574127--40574172 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
40574117 AAGAAGCATG
40574127 AATCATGCTCAAGAATG-C
1 AATCATGCTCAAGAATGAC
*
40574145 -ATCATGGC-CAAGTATGAC
1 AATCAT-GCTCAAGAATGAC
40574163 AATCATGCTC
1 AATCATGCTC
40574173 CTTTTCAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 7
0.74 0.03 0.23
Matches are distributed among these distances:
17 12 0.52
18 5 0.22
19 6 0.26
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.24
Consensus pattern (19 bp):
AATCATGCTCAAGAATGAC
Found at i:40576446 original size:40 final size:40
Alignment explanation
Indices: 40576313--40576557 Score: 293
Period size: 40 Copynumber: 6.2 Consensus size: 40
40576303 TGAATGATAC
*
40576313 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTA-AT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
40576352 CCGGGCTAAG-TCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
*
40576391 -CGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
** *
40576430 CCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG-TTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTATAT
* * * ** *
40576470 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
* * * * *
40576510 CCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
40576550 CC-GGCTAA
1 CCGGGCTAA
40576558 ATTCCGAAGA
Statistics
Matches: 179, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
38 34 0.19
39 46 0.26
40 97 0.54
41 2 0.01
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTATAT
Found at i:40583551 original size:17 final size:18
Alignment explanation
Indices: 40583509--40583557 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
40583499 AGTTGAAAAG
40583509 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
40583528 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
40583545 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
40583558 GCTTCTTGCA
Statistics
Matches: 26, Mismatches: 1, Indels: 8
0.74 0.03 0.23
Matches are distributed among these distances:
17 16 0.62
18 4 0.15
19 6 0.23
ACGTcount: A:0.24, C:0.18, G:0.22, T:0.35
Consensus pattern (18 bp):
GAGCATGATGTCATACTT
Found at i:40584445 original size:40 final size:40
Alignment explanation
Indices: 40584379--40584545 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
40584369 AAATTGAATG
* * *
40584379 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
40584418 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
40584458 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
40584498 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
40584538 ATATCCGG
1 ATATCCGG
40584546 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40588019 original size:29 final size:28
Alignment explanation
Indices: 40587987--40588060 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
40587977 GATTCAAGCC
* *
40587987 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACAC-TAGTGCCATACAGTACAAACT
* *
40588016 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACAC-TAGTGCCATACAGTACAAACT
40588045 CGCACACTCAGTGCCA
1 CGCACACT-AGTGCCA
40588061 ATCTCGTCAC
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
28 1 0.03
29 38 0.97
ACGTcount: A:0.31, C:0.34, G:0.15, T:0.20
Consensus pattern (28 bp):
CGCACACTAGTGCCATACAGTACAAACT
Found at i:40592279 original size:17 final size:17
Alignment explanation
Indices: 40592245--40592279 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40592235 TGTTCTTAAC
**
40592245 TTTTAAAAACTATTATT
1 TTTTAAAAACTAACATT
40592262 TTTTAAAAACTAACATT
1 TTTTAAAAACTAACATT
40592279 T
1 T
40592280 GTTACATATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (17 bp):
TTTTAAAAACTAACATT
Found at i:40598498 original size:19 final size:19
Alignment explanation
Indices: 40598474--40598513 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
40598464 ACATACATGA
40598474 ATTTATTTCAATAATAGCT
1 ATTTATTTCAATAATAGCT
40598493 ATTTATTTCAATAATAGCT
1 ATTTATTTCAATAATAGCT
40598512 AT
1 AT
40598514 AGTGAGGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.47
Consensus pattern (19 bp):
ATTTATTTCAATAATAGCT
Found at i:40598709 original size:17 final size:17
Alignment explanation
Indices: 40598675--40598707 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
40598665 AAGAATAACT
40598675 TAATTAAAATATTAAAA
1 TAATTAAAATATTAAAA
*
40598692 TAATTAGAAT-TTAAAA
1 TAATTAAAATATTAAAA
40598708 ATTAAGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
TAATTAAAATATTAAAA
Found at i:40599860 original size:40 final size:40
Alignment explanation
Indices: 40599816--40599895 Score: 124
Period size: 40 Copynumber: 2.0 Consensus size: 40
40599806 AATTTTGATG
* * *
40599816 ATTGATTTTTTTGCTACTCCATTTTGTGTAAGTAATGGTT
1 ATTGATTTGTTTGCTACTCCATTTCGTGTAAGTAACGGTT
*
40599856 ATTGATTTGTTTGCTATTCCATTTCGTGTAAGTAACGGTT
1 ATTGATTTGTTTGCTACTCCATTTCGTGTAAGTAACGGTT
40599896 TCTTTTATGA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (40 bp):
ATTGATTTGTTTGCTACTCCATTTCGTGTAAGTAACGGTT
Found at i:40609112 original size:44 final size:46
Alignment explanation
Indices: 40609056--40609171 Score: 130
Period size: 44 Copynumber: 2.5 Consensus size: 46
40609046 TGTGCATGCT
*
40609056 GATGCATATCCCAGACATGTCTTACACTAGCACAACTCT-T-A-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGC-CAACTCTGTCAGGCC
* * * ***
40609100 GATGCGTGTCCCAGACACGTCTTACACTGGCTGTCTCTGTCGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTC-AGGCC
40609147 GATGCATGTCCCAGACATGTCTTAC
1 GATGCATGTCCCAGACATGTCTTAC
40609172 TCTGGCACTC
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
43 4 0.07
44 28 0.47
46 1 0.02
47 26 0.44
ACGTcount: A:0.22, C:0.31, G:0.21, T:0.26
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCCAACTCTGTCAGGCC
Found at i:40609202 original size:47 final size:46
Alignment explanation
Indices: 40609151--40609264 Score: 140
Period size: 47 Copynumber: 2.4 Consensus size: 46
40609141 GAGGCCGATG
* * *
40609151 CATGTCCCAGACATGTCTTACTCTGGCACTCA-ACTCTGTGCTAACAC
1 CATGTCCCAGACATGTCTTACACTGGCACTCATAATATG-GCTAA-AC
* * *
40609198 CATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGAAG
1 CATGTCCCAGACAT-GTCTTACACTGGCACTCATAATATGGCTAAAC
40609245 CATGTCCCAGACATGTCTTA
1 CATGTCCCAGACATGTCTTA
40609265 TACTAGCCCT
Statistics
Matches: 59, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
46 6 0.10
47 29 0.49
48 20 0.34
49 4 0.07
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.28
Consensus pattern (46 bp):
CATGTCCCAGACATGTCTTACACTGGCACTCATAATATGGCTAAAC
Found at i:40609328 original size:94 final size:91
Alignment explanation
Indices: 40609002--40609326 Score: 277
Period size: 94 Copynumber: 3.5 Consensus size: 91
40608992 TGGGATATAT
* * * * *
40609002 TGCCGATGCCATGTCCCAGACATGGTTTTACACTGACTCTCATATGTGCATGCTGATGCATATCC
1 TGCCGATGCCATGTCCCAGACACGGTCTTACACTGGCTCTCATATATG---GCTGATGCATGTCC
* ** *
40609067 CAGACATGTCTTACACTAGCACAACTCTTA
63 CAGACATGTCTTATACTAGC-CCTCTCTGA
* * *
40609097 -GCCGATG-CGTGTCCCAGACAC-GTCTTACACTGGCTGTCTC-TGTCGA-GGCCGATGCATGTC
1 TGCCGATGCCATGTCCCAGACACGGTCTTACACTGGC--TCTCATAT--ATGGCTGATGCATGTC
* *
40609157 CCAGACATGTCTTACT-CTGGCACTCAACTCTG-
62 CCAGACATGTCTTA-TACTAGC-C-C-TCTCTGA
** ** * *
40609189 TGCTAACACCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATGGCTGAAGCATGTCCCA
1 TGCCGATGCCATGTCCCAGACACGGTCTTACACTGGCTCTCAT-ATATGGCTGATGCATGTCCCA
40609254 GACATGTCTTATACTAGCCCTCGTCTGGA
65 GACATGTCTTATACTAGCCCTC-TCT-GA
*
40609283 TGCCGATGCCATGTCCCAAACACGGTCTTACACTGGCTCTCATA
1 TGCCGATGCCATGTCCCAGACACGGTCTTACACTGGCTCTCATA
40609327 ATGTGGACAA
Statistics
Matches: 184, Mismatches: 29, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
91 32 0.17
92 15 0.08
93 31 0.17
94 92 0.50
95 14 0.08
ACGTcount: A:0.22, C:0.30, G:0.20, T:0.27
Consensus pattern (91 bp):
TGCCGATGCCATGTCCCAGACACGGTCTTACACTGGCTCTCATATATGGCTGATGCATGTCCCAG
ACATGTCTTATACTAGCCCTCTCTGA
Found at i:40609355 original size:187 final size:184
Alignment explanation
Indices: 40609010--40609363 Score: 403
Period size: 187 Copynumber: 1.9 Consensus size: 184
40609000 ATTGCCGATG
* * *
40609010 CCATGTCCCAGACATGGTTTTACACTGACTCTCATATGTGCATGCTGATGCATATCCCAGACATG
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCATATATG-A-GCTGAAGCATATCCCAGACATG
* * * * *
40609075 TCTTACACTAGCACAACTCTTAGCCGATGCGTGTCCCAGACACGTCTTACACTGGCTGTCTCTGT
64 TCTTACACTAGCACAACTCTGAGCCGATGCATGTCCCAAACACGTCTTACACTGGCTCTCTATGT
* ** * *
40609140 CGAGGCCGATGCATGTCCCAGACATGTCTTACTCTGGCACTCAACTCTGTGCTAACA
129 CGAGACAAAT-CATGTCCAAGACATGTCTTACACTGGCACTCAACTCTGTGCTAACA
* *
40609197 CCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATATG-GCTGAAGCATGTCCCAGACATGT
1 CCATGTCCCAGACATGGTCTTACACTGACTCTCAT-ATATGAGCTGAAGCATATCCCAGACATGT
* **
40609261 CTTATACTAGC-CCTCGTCTGGATGCCGATGCCATGTCCCAAACACGGTCTTACACTGGCTCTCA
65 CTTACACTAGCACAAC-TCT-GA-GCCGATG-CATGTCCCAAACAC-GTCTTACACTGGCTCTC-
*
40609325 TAATGT-G-GACAAAT-ATGTCCAAGGCATGTCTTACACTGG
124 T-ATGTCGAGACAAATCATGTCCAAGACATGTCTTACACTGG
40609364 TGCACAAATC
Statistics
Matches: 140, Mismatches: 19, Indels: 16
0.80 0.11 0.09
Matches are distributed among these distances:
184 2 0.01
185 34 0.24
186 1 0.01
187 62 0.44
188 16 0.11
189 20 0.14
190 2 0.01
191 3 0.02
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.27
Consensus pattern (184 bp):
CCATGTCCCAGACATGGTCTTACACTGACTCTCATATATGAGCTGAAGCATATCCCAGACATGTC
TTACACTAGCACAACTCTGAGCCGATGCATGTCCCAAACACGTCTTACACTGGCTCTCTATGTCG
AGACAAATCATGTCCAAGACATGTCTTACACTGGCACTCAACTCTGTGCTAACA
Found at i:40613703 original size:15 final size:16
Alignment explanation
Indices: 40613678--40613709 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
40613668 ATAAAAATAA
40613678 TAAAAACAAACCAACT
1 TAAAAACAAACCAACT
40613694 TAAAAA-AAACCAACT
1 TAAAAACAAACCAACT
40613709 T
1 T
40613710 TGCAGATGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.62, C:0.22, G:0.00, T:0.16
Consensus pattern (16 bp):
TAAAAACAAACCAACT
Found at i:40614829 original size:26 final size:27
Alignment explanation
Indices: 40614800--40614853 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
40614790 TCACACAAGT
*
40614800 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
40614826 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
40614853 T
1 T
40614854 GTTAATTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:40614902 original size:27 final size:27
Alignment explanation
Indices: 40614863--40615026 Score: 184
Period size: 27 Copynumber: 6.1 Consensus size: 27
40614853 TGTTAATTTA
* * * *
40614863 ACCCCACAAGGGTATCTCGGTAATTCC
1 ACCCTACAGGGGTATTTCGGTAATTCT
* * *
40614890 ACTCTACAGGGGTATTTCAGTATTTCT
1 ACCCTACAGGGGTATTTCGGTAATTCT
* *
40614917 ACCCTACAAGGGTATTTCGATAATTCT
1 ACCCTACAGGGGTATTTCGGTAATTCT
* * * **
40614944 ATCCTATAGGGGTATGTCAATAATTCT
1 ACCCTACAGGGGTATTTCGGTAATTCT
40614971 ACCCTACAGGGGTATTTCGGTAATTCT
1 ACCCTACAGGGGTATTTCGGTAATTCT
* *
40614998 ACCTTACAGGGGTATTTCGCTAATTCT
1 ACCCTACAGGGGTATTTCGGTAATTCT
40615025 AC
1 AC
40615027 AACTTATCCA
Statistics
Matches: 113, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 113 1.00
ACGTcount: A:0.26, C:0.23, G:0.18, T:0.34
Consensus pattern (27 bp):
ACCCTACAGGGGTATTTCGGTAATTCT
Found at i:40621721 original size:33 final size:32
Alignment explanation
Indices: 40621670--40621733 Score: 83
Period size: 33 Copynumber: 2.0 Consensus size: 32
40621660 ACGAAGTCAC
* *
40621670 CAGATACAGATATTGTGGCTAGGCCACCAGAA
1 CAGATACAGATATTGTGGCGAAGCCACCAGAA
* *
40621702 CAGATATATATATATGTGGCGAAGCCACCAGA
1 CAGATACAGATAT-TGTGGCGAAGCCACCAGA
40621734 TTGCAGCGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
32 11 0.41
33 16 0.59
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (32 bp):
CAGATACAGATATTGTGGCGAAGCCACCAGAA
Found at i:40622397 original size:27 final size:27
Alignment explanation
Indices: 40622360--40622514 Score: 220
Period size: 27 Copynumber: 5.7 Consensus size: 27
40622350 AGTCATTTAA
*
40622360 GGGTATCTCGGTAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
40622387 GGGTATTTCGGTATTTCTACCCTACAA
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
40622414 GGGTATTTCGGTCATTCTATCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
**
40622441 GGGTATTTCAATAATTCTACCCTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
* *
40622468 GGGTATTTCGATAATTCTACCTTACAG
1 GGGTATTTCGGTAATTCTACCCTACAG
*
40622495 GGGTATTTCGCTAATTCTAC
1 GGGTATTTCGGTAATTCTAC
40622515 AACTTATCCA
Statistics
Matches: 114, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 114 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.35
Consensus pattern (27 bp):
GGGTATTTCGGTAATTCTACCCTACAG
Found at i:40636398 original size:40 final size:40
Alignment explanation
Indices: 40636353--40636520 Score: 194
Period size: 40 Copynumber: 4.2 Consensus size: 40
40636343 CGGAATATAA
40636353 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
40636393 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** *
40636433 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * * *
40636473 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
40636513 CCGGATAT
1 CCGGATAT
40636521 CATTCAATTT
Statistics
Matches: 109, Mismatches: 18, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
39 1 0.01
40 108 0.99
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:40638948 original size:20 final size:20
Alignment explanation
Indices: 40638923--40638964 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
40638913 TATCATCATG
*
40638923 ATCTGTCCGTTTGGTTAGCA
1 ATCTGTCAGTTTGGTTAGCA
40638943 ATCTGTCAGTTTGGTTAGCA
1 ATCTGTCAGTTTGGTTAGCA
40638963 AT
1 AT
40638965 GTACCTACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.19, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
ATCTGTCAGTTTGGTTAGCA
Found at i:40645701 original size:24 final size:24
Alignment explanation
Indices: 40645656--40645701 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
40645646 TGAAAAAACA
* *
40645656 TTTGAATTTTTATATGAGAATGTG
1 TTTGAATTTTTATAGGAAAATGTG
*
40645680 TTTGAATTTTTATCGGAAAATG
1 TTTGAATTTTTATAGGAAAATG
40645702 CATCTGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (24 bp):
TTTGAATTTTTATAGGAAAATGTG
Found at i:40647906 original size:31 final size:31
Alignment explanation
Indices: 40647865--40647928 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
40647855 CCTTTTCATA
* *
40647865 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGACCGAAGCCT
** *
40647896 TTTCAAATTTCATATTATTGGACCGAAGCCT
1 TTTCAAATTTCATAACACTGGACCGAAGCCT
40647927 TT
1 TT
40647929 GCTGTAAACG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.38
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGACCGAAGCCT
Found at i:40648173 original size:24 final size:24
Alignment explanation
Indices: 40648121--40648310 Score: 269
Period size: 24 Copynumber: 8.0 Consensus size: 24
40648111 GCTTTATCAT
*
40648121 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
* *
40648146 ATAACTGGGGCAAAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTA
*
40648170 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40648193 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
* *
40648217 ATAACTAGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
40648241 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40648265 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
40648288 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40648311 TCACTTCCTC
Statistics
Matches: 152, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
23 44 0.29
24 96 0.63
25 12 0.08
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:40648201 original size:47 final size:48
Alignment explanation
Indices: 40648120--40648311 Score: 273
Period size: 47 Copynumber: 4.0 Consensus size: 48
40648110 TGCTTTATCA
* *
40648120 TATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTT
1 TATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTT
* *
40648169 TATAACTGGGGCATAAGCCC-TTTGATAACTGGGGCGTAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
* * *
40648216 GATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
*
40648264 AATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTT
1 TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
40648311 T
1 T
40648312 CACTTCCTCC
Statistics
Matches: 130, Mismatches: 11, Indels: 6
0.88 0.07 0.04
Matches are distributed among these distances:
47 68 0.52
48 49 0.38
49 13 0.10
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (48 bp):
TATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTT
Found at i:40648222 original size:71 final size:72
Alignment explanation
Indices: 40648121--40648311 Score: 280
Period size: 71 Copynumber: 2.7 Consensus size: 72
40648111 GCTTTATCAT
* *
40648121 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTTATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAA
*
40648185 GCCC-TTTG
64 GCCCTTTTA
* * * *
40648193 ATAACTGGGGCGTAAGCCCTTTTGATAACTAGGGCATAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
40648258 CCTTTTA
66 CCTTTTA
40648265 ATAACTGGGGCATAAGCCC-TTTAATAACTGGGGCATAAGCCCTTTTT
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTT
40648312 CACTTCCTCC
Statistics
Matches: 107, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 74 0.69
72 33 0.31
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (72 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCATAAGCCCTTTTTATAACTGGGGCATAAGC
CCTTTTA
Found at i:40648388 original size:20 final size:20
Alignment explanation
Indices: 40648365--40648407 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
40648355 GAACATCTCG
40648365 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
40648385 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
40648405 TGT
1 TGT
40648408 TTATCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:40648490 original size:25 final size:25
Alignment explanation
Indices: 40648444--40648491 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
40648434 ATATATAAAC
* * * *
40648444 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40648469 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40648492 CATATTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40649762 original size:27 final size:27
Alignment explanation
Indices: 40649733--40650132 Score: 473
Period size: 27 Copynumber: 14.8 Consensus size: 27
40649723 GGGTATTTTA
* * * **
40649733 GTAATTTTGTAAATCAAAGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
40649760 GTAATTCTGTAAATCAAGGGTGAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40649787 GTAATTCTATAAATCGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
40649814 GTAATTCTGTAAA-CTGAGGGTAAAATG
1 GTAATTCTGTAAATC-GAGGGTAAAATG
*
40649841 GTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40649868 GTAATTTTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAATG
*
40649895 GTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
** *
40649922 GTAATTCTGTAAATTAAGGGCAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40649949 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* ** *
40649976 GTAATTTTACAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40650003 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAATG
*
40650030 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAATG
* *
40650057 GTAATTTTGTAAATTGAGGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* * *
40650084 GTAATTATGTAAATCGGGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAATG
* *
40650111 ATAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40650133 CTTTGGTAAT
Statistics
Matches: 324, Mismatches: 43, Indels: 12
0.85 0.11 0.03
Matches are distributed among these distances:
26 3 0.01
27 319 0.98
28 2 0.01
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAATG
Found at i:40650159 original size:27 final size:27
Alignment explanation
Indices: 40650138--40650227 Score: 119
Period size: 27 Copynumber: 3.3 Consensus size: 27
40650128 GGGTACTTTG
*
40650138 GTAATTTTACAAGTCGAAGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
*
40650165 GTAATTTTACAAATCGAGGGTATTTCA
1 GTAATTTTACAAATCGAAGGTATTTCA
* * *
40650192 GTATTTTTACAAA-CTAAGGGTATTTCG
1 GTAATTTTACAAATCGAA-GGTATTTCA
40650219 GTAATTTTA
1 GTAATTTTA
40650228 GTAAACTAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.04
27 53 0.96
ACGTcount: A:0.32, C:0.10, G:0.18, T:0.40
Consensus pattern (27 bp):
GTAATTTTACAAATCGAAGGTATTTCA
Found at i:40650179 original size:54 final size:54
Alignment explanation
Indices: 40650121--40650227 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
40650111 ATAATTCTGT
* * *
40650121 AAATCGGGGGTACTTT-GGTAATTTTACAAGTCGAA-GGTATTTCAGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTACAA-ACGAAGGGTATTTCAGTAATTTTAC
* * *
40650175 AAATCGAGGGTATTTCAGTATTTTTACAAACTAAGGGTATTTCGGTAATTTTA
1 AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTA
40650228 GTAAACTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
53 6 0.13
54 39 0.87
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (54 bp):
AAATCGAGGGTATTTCAGTAATTTTACAAACGAAGGGTATTTCAGTAATTTTAC
Found at i:40650241 original size:27 final size:27
Alignment explanation
Indices: 40650138--40650242 Score: 90
Period size: 27 Copynumber: 3.9 Consensus size: 27
40650128 GGGTACTTTG
* *
40650138 GTAATTTTACAAGTCGAAG-GTATTTCA
1 GTAATTTTACAA-ACTAAGAGTATTTCA
* *
40650165 GTAATTTTACAAA-TCGAGGGTATTTCA
1 GTAATTTTACAAACT-AAGAGTATTTCA
* * *
40650192 GTATTTTTACAAACTAAGGGTATTTCG
1 GTAATTTTACAAACTAAGAGTATTTCA
*
40650219 GTAATTTTAGTAAACTAA-AGTATT
1 GTAATTTTA-CAAACTAAGAGTATT
40650243 CTAAACATGG
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
26 2 0.03
27 55 0.85
28 8 0.12
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (27 bp):
GTAATTTTACAAACTAAGAGTATTTCA
Found at i:40652914 original size:31 final size:31
Alignment explanation
Indices: 40652873--40652936 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40652863 CCTTTTCATA
*
40652873 TTTCATATTTCATAACACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
**
40652904 TTTCAAATTTCATATTACTGGGCCGAAGCCT
1 TTTCAAATTTCATAACACTGGGCCGAAGCCT
40652935 TT
1 TT
40652937 GCTGTAAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCAAATTTCATAACACTGGGCCGAAGCCT
Found at i:40653181 original size:24 final size:24
Alignment explanation
Indices: 40653129--40653294 Score: 239
Period size: 24 Copynumber: 7.0 Consensus size: 24
40653119 GCTTTTTCAT
* *
40653129 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTG
*
40653154 ATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
40653178 ATAACTGGGGCATAAGCCC-TTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40653201 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40653225 ATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTG
*
40653249 ATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTG
40653272 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40653295 TCACTTCCTC
Statistics
Matches: 131, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
23 44 0.34
24 75 0.57
25 12 0.09
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTG
Found at i:40653230 original size:71 final size:71
Alignment explanation
Indices: 40653129--40653294 Score: 253
Period size: 71 Copynumber: 2.3 Consensus size: 71
40653119 GCTTTTTCAT
*
40653129 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
1 ATAACTGG-GGCATAAGCC-CTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAA
*
40653193 GCCCTTTG
64 GCCCTTTA
* * **
40653201 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGC
1 ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
40653266 CCTTTA
66 CCTTTA
40653272 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40653295 TCACTTCCTC
Statistics
Matches: 87, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
71 75 0.86
72 12 0.14
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (71 bp):
ATAACTGGGGCATAAGCCCTTTTAATAACTGGGGCAAAAGCCCTTTTGATAACTGGGGCATAAGC
CCTTTA
Found at i:40653294 original size:47 final size:48
Alignment explanation
Indices: 40653129--40653294 Score: 239
Period size: 47 Copynumber: 3.5 Consensus size: 48
40653119 GCTTTTTCAT
* * *
40653129 ATAACTGGAGGCCT-AGCCTCTTTTAATAACTGGGGCAAAAGCCCTTTTG
1 ATAACTGG-GGCATAAGCC-CTTTTGATAACTGGGGCATAAGCCCTTTTG
*
40653178 ATAACTGGGGCATAAGCCC-TTTGATAACTGGGGCGTAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
* *
40653225 ATAACTGGGGCGTAAGCCCTTTTGATAACTGGGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
40653272 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
40653295 TCACTTCCTC
Statistics
Matches: 107, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
47 68 0.64
48 27 0.25
49 12 0.11
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (48 bp):
ATAACTGGGGCATAAGCCCTTTTGATAACTGGGGCATAAGCCCTTTTG
Found at i:40653367 original size:9 final size:9
Alignment explanation
Indices: 40653353--40653409 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
40653343 ATCTCGTGTG
40653353 CATATCATA
1 CATATCATA
*
40653362 CATATCATGTG
1 CATATCA--TA
40653373 CATATCATA
1 CATATCATA
* *
40653382 CATGTCATGTG
1 CATATCA--TA
40653393 CATATCATA
1 CATATCATA
40653402 CATATCAT
1 CATATCAT
40653410 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:40653372 original size:20 final size:20
Alignment explanation
Indices: 40653349--40653411 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
40653339 GAACATCTCG
40653349 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
40653369 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
40653389 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
40653409 TGT
1 TGT
40653412 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:40653482 original size:25 final size:25
Alignment explanation
Indices: 40653448--40653495 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
40653438 ATATATAAAC
*
40653448 CCTAGGGGCAAAACGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
40653473 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
40653496 CATATTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:40654756 original size:27 final size:27
Alignment explanation
Indices: 40654737--40655135 Score: 509
Period size: 27 Copynumber: 14.8 Consensus size: 27
40654727 GGGTATTTTA
* *
40654737 GTAATTTTGTAAATCGAGGGTAAAACA
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40654764 GTAATTCTGTAAATCAAGGGTGAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
40654791 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40654818 GTAATTTTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
* **
40654845 GTAATTCTGTAAATCAAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40654872 GTAATTTTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
**
40654899 GTAATTCTGTAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
*
40654926 GTAATTCTGTAAATTGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
40654953 GTAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
40654980 GTAATTTTACAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* **
40655007 GTAATTCTATAAATCGAGGGTAAAATA
1 GTAATTCTGTAAATCGAGGGTAAAACG
40655034 GTAATTCTGTAAA-CTGAGGGTAAAACG
1 GTAATTCTGTAAATC-GAGGGTAAAACG
*
40655061 GTAATTTTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40655088 GTAATTATGTAAATCG-GGGTAAAATG
1 GTAATTCTGTAAATCGAGGGTAAAACG
* *
40655114 ATAATTCTGTAAATCGGGGGTA
1 GTAATTCTGTAAATCGAGGGTA
40655136 CTTTGGTAAT
Statistics
Matches: 322, Mismatches: 43, Indels: 14
0.85 0.11 0.04
Matches are distributed among these distances:
26 26 0.08
27 293 0.91
28 3 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.29
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAGGGTAAAACG
Found at i:40655189 original size:27 final size:27
Alignment explanation
Indices: 40655124--40655230 Score: 101
Period size: 27 Copynumber: 4.0 Consensus size: 27
40655114 ATAATTCTGT
* *
40655124 AAATCGGGGGTACTTT-GGTAATTTTAC
1 AAATCGAGGGTA-TTTCAGTAATTTTAC
* * *
40655151 AAGTTGAAGGTATTTCAGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
40655178 AAATCGAGGGTATTTCAATATTTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTAC
* *
40655205 AAA-CTAAGGGTATTTCGGTAATTTTA
1 AAATC-GAGGGTATTTCAGTAATTTTA
40655231 GTAAACTAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
26 4 0.06
27 60 0.94
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AAATCGAGGGTATTTCAGTAATTTTAC
Found at i:40656926 original size:21 final size:21
Alignment explanation
Indices: 40656901--40656950 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
40656891 GGATATTTTG
40656901 TAAAATTTACATTTTAGTCTA
1 TAAAATTTACATTTTAGTCTA
*
40656922 TAAAATTCACATTTTAGTCTA
1 TAAAATTTACATTTTAGTCTA
40656943 TAAAATTT
1 TAAAATTT
40656951 GTTTAGAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (21 bp):
TAAAATTTACATTTTAGTCTA
Found at i:40665265 original size:40 final size:40
Alignment explanation
Indices: 40665157--40665364 Score: 301
Period size: 40 Copynumber: 5.2 Consensus size: 40
40665147 CGGGATTTAA
* * * * *
40665157 CCGGATATAGCGACTCGCACGATTGCCTTCGGGTCATAAC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
* * * * * *
40665197 CCGGATTTGGT-GACTTGCACAAAGGCCTTCGGGTCTTAGC
1 CCGGATAT-ATCAACTCGCACGAATGCCTTCGGGTCTTAGC
40665237 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
40665277 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
40665317 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
40665357 CCGGATAT
1 CCGGATAT
40665365 TTTCAATGTT
Statistics
Matches: 151, Mismatches: 15, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 1 0.01
40 150 0.99
ACGTcount: A:0.22, C:0.29, G:0.25, T:0.25
Consensus pattern (40 bp):
CCGGATATATCAACTCGCACGAATGCCTTCGGGTCTTAGC
Found at i:40668828 original size:39 final size:40
Alignment explanation
Indices: 40668650--40668832 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
40668640 CCGCACCAAG
* * * * * * * *
40668650 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * *
40668690 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAA-T
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCAC-AATT
*
40668730 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* * * *
40668770 GCCTTCGGGTCTTAACCCGGATATAATTTC-AGCATAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
* *
40668809 GTCTTCGGGGCTTAGCCCGGATAT
1 GCCTTCGGGTCTTAGCCCGGATAT
40668833 CATTCAATTT
Statistics
Matches: 122, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 31 0.25
40 89 0.73
41 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACTACTAGCACAATT
Found at i:40676440 original size:40 final size:40
Alignment explanation
Indices: 40676381--40676507 Score: 164
Period size: 40 Copynumber: 3.2 Consensus size: 40
40676371 CGGGACTTTA
* * *
40676381 CCCGGATATCACGATTTGCACAAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* *
40676421 CCCGGATTTAACAACTTGCACGAATGCCTTCGGGTCTTAG
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
* * * * *
40676461 CCCGGATATAGCTACTAGCACAATTGCCTTCGGGTCTTAA
1 CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
40676501 CCCGGAT
1 CCCGGAT
40676508 GTAAATTTCA
Statistics
Matches: 75, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (40 bp):
CCCGGATATAACAACTTGCACAAATGCCTTCGGGTCTTAG
Found at i:40676526 original size:40 final size:40
Alignment explanation
Indices: 40676398--40676549 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
40676388 ATCACGATTT
* * * *
40676398 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
*
40676438 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
* * * *
40676478 GCACAATTGCCTTCGGGTCTTAACCCGGATGTAAAT-TTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACT-A
* * * *
40676518 GCATAATTGTCTTTGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
40676550 CATTCAATTT
Statistics
Matches: 94, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.03
40 89 0.95
41 2 0.02
ACGTcount: A:0.23, C:0.25, G:0.23, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
Found at i:40681387 original size:46 final size:44
Alignment explanation
Indices: 40681293--40681512 Score: 183
Period size: 46 Copynumber: 4.8 Consensus size: 44
40681283 GTAAGTTGCT
* * * * *
40681293 GATGCCATATCCCAGACATGGTCTTACACTGACACATTTCATAGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCATCTCATGGCC
**
40681339 GATGCATGTCCCAGACATGTCTTACACTGGCTTACATCTCGGGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-T-CATCTCATGGCC
* *
40681385 GATGCATGTCCCAGACATGTCTTACATTAGCGCTCGTCTCAAT-GCC
1 GATGCATGTCCCAGACATGTCTTACACT-G-GCTCATCTC-ATGGCC
* * *
40681431 GATGCCATGTCCCAGATATGGTCTTGCACTGGCTC-TCATAATGTGGCC
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGCTCATC-TCA--TGGCC
* * *
40681479 AATGCATGTCCTAGACATGTCTTACACTAGCTCA
1 GATGCATGTCCCAGACATGTCTTACACTGGCTCA
40681513 CACAAATGAC
Statistics
Matches: 142, Mismatches: 20, Indels: 23
0.77 0.11 0.12
Matches are distributed among these distances:
44 12 0.08
45 16 0.11
46 69 0.49
47 29 0.20
48 16 0.11
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (44 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTCATCTCATGGCC
Found at i:40681464 original size:94 final size:92
Alignment explanation
Indices: 40681336--40681509 Score: 235
Period size: 94 Copynumber: 1.9 Consensus size: 92
40681326 ACATTTCATA
* *
40681336 GCCGATGCATGTCCCAGACATGTCTTACACTGGCT-TACAT-CTCGGGGCCGATGCATGTCCCAG
1 GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCT-CATAAT-GGGGCCAATGCATGTCCCAG
*
40681399 ACATGTCTTACATTAGCGCTCGTCTCAAT
64 ACATGTCTTACACTAGCGCTCGTCTCAAT
* * * *
40681428 GCCGATGCCATGTCCCAGATATGGTCTTGCACTGGCTCTCATAATGTGGCCAATGCATGTCCTAG
1 GCCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGGGGCCAATGCATGTCCCAG
40681493 ACATGTCTTACACTAGC
64 ACATGTCTTACACTAGC
40681510 TCACACAAAT
Statistics
Matches: 71, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
92 7 0.10
93 13 0.18
94 49 0.69
95 2 0.03
ACGTcount: A:0.21, C:0.29, G:0.22, T:0.28
Consensus pattern (92 bp):
GCCGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGGGGCCAATGCATGTCCCAGAC
ATGTCTTACACTAGCGCTCGTCTCAAT
Found at i:40691109 original size:54 final size:55
Alignment explanation
Indices: 40691041--40691152 Score: 145
Period size: 55 Copynumber: 2.1 Consensus size: 55
40691031 CGAGCCTGCC
* *
40691041 AAAACAACACGGGCGTGCGACAC-CCCGTGTGGAAGAACTGTGGATGAACCTGTT
1 AAAACAACACGGGCGTGCGACACGCCCGTGTGGAACAACCGTGGATGAACCTGTT
* * * * * *
40691095 AAAACAGCATGGGCGTGCGATACGCCTGTGTGGAACACCCGTGGTTGAACCTGTT
1 AAAACAACACGGGCGTGCGACACGCCCGTGTGGAACAACCGTGGATGAACCTGTT
40691150 AAA
1 AAA
40691153 TTAAAACAGG
Statistics
Matches: 49, Mismatches: 8, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
54 20 0.41
55 29 0.59
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.19
Consensus pattern (55 bp):
AAAACAACACGGGCGTGCGACACGCCCGTGTGGAACAACCGTGGATGAACCTGTT
Found at i:40695847 original size:31 final size:30
Alignment explanation
Indices: 40695781--40695840 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 30
40695771 TTAGGTGGAT
* **
40695781 TTTTCCTTAAGTATTGTCTTAAGTCAATCAA
1 TTTTCCCTAAGTATTGTCTTAACCCAATC-A
40695812 TTTTCCCTAAGGTATTGTCTTAACCCAAT
1 TTTTCCCTAA-GTATTGTCTTAACCCAAT
40695841 TCTTTTCTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 9 0.36
32 16 0.64
ACGTcount: A:0.27, C:0.20, G:0.10, T:0.43
Consensus pattern (30 bp):
TTTTCCCTAAGTATTGTCTTAACCCAATCA
Found at i:40700357 original size:44 final size:44
Alignment explanation
Indices: 40700294--40700382 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
40700284 GGATGATGTT
40700294 TCCATTTATTTCTATTGAAAATAGACTCATTAATAATTTAAACA
1 TCCATTTATTTCTATTGAAAATAGACTCATTAATAATTTAAACA
40700338 TCCATTTATTTCTATTGAAAATAGACTCATTAATAATTTAAACA
1 TCCATTTATTTCTATTGAAAATAGACTCATTAATAATTTAAACA
40700382 T
1 T
40700383 GTAAATTTTA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (44 bp):
TCCATTTATTTCTATTGAAAATAGACTCATTAATAATTTAAACA
Found at i:40709966 original size:12 final size:12
Alignment explanation
Indices: 40709934--40709972 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
40709924 TTGGTTGATA
* *
40709934 GAGAGATTAGAG
1 GAGAGATTTGGG
40709946 GAGAGATTTGGG
1 GAGAGATTTGGG
40709958 GAGAGATTTGGG
1 GAGAGATTTGGG
40709970 GAG
1 GAG
40709973 TGGATTAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.49, T:0.21
Consensus pattern (12 bp):
GAGAGATTTGGG
Found at i:40713724 original size:22 final size:22
Alignment explanation
Indices: 40713679--40713724 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
40713669 ACAAGTTATC
*
40713679 TTAATTTAAAACAAATATTTAA
1 TTAATTTAAAACAAATATTCAA
*
40713701 TTAATTTATAAACATATA-TCAA
1 TTAATTTA-AAACAAATATTCAA
40713723 TT
1 TT
40713725 CATAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAATTTAAAACAAATATTCAA
Found at i:40714995 original size:19 final size:19
Alignment explanation
Indices: 40714946--40714995 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
40714936 GGCTCCGGAA
*
40714946 TGCATTCAAGGGCACGAATG
1 TGCATTC-AGGGCACCAATG
40714966 TGCTATT-AGGGCACCAGA-G
1 TGC-ATTCAGGGCACCA-ATG
40714985 TGCATTCAGGG
1 TGCATTCAGGG
40714996 GCACTTATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
18 3 0.12
19 16 0.62
20 4 0.15
21 3 0.12
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.22
Consensus pattern (19 bp):
TGCATTCAGGGCACCAATG
Found at i:40718027 original size:28 final size:28
Alignment explanation
Indices: 40717995--40718049 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
40717985 ATTGGTTAAG
*
40717995 TTGGATGTCTTTAAAATTGTTATAAAAA
1 TTGGATGTCTTTAAAAGTGTTATAAAAA
40718023 TTGGATGTCTTTAAAAGTGTTATAAAA
1 TTGGATGTCTTTAAAAGTGTTATAAAA
40718050 GTTGAGTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.38, C:0.04, G:0.16, T:0.42
Consensus pattern (28 bp):
TTGGATGTCTTTAAAAGTGTTATAAAAA
Found at i:40718455 original size:49 final size:51
Alignment explanation
Indices: 40718383--40718490 Score: 175
Period size: 49 Copynumber: 2.1 Consensus size: 51
40718373 ACTAGTGACT
40718383 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AGATAGC-TTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCTTTGGTCA
* *
40718432 CAAGTGTGGTACTGTGTGAAGGCCACTTTGTGAAGAAAGATAGCTTTGGTCA
1 CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAG-AAGATAGCTTTGGTCA
40718484 CAAGTGT
1 CAAGTGT
40718491 TGTAACACCC
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
49 33 0.61
51 7 0.13
52 14 0.26
ACGTcount: A:0.28, C:0.14, G:0.31, T:0.28
Consensus pattern (51 bp):
CAAGTGTGGTACTATGTGAAGGCCACTTTGAGAAGAAGATAGCTTTGGTCA
Found at i:40719533 original size:27 final size:27
Alignment explanation
Indices: 40719503--40719792 Score: 323
Period size: 27 Copynumber: 10.7 Consensus size: 27
40719493 TACTGAAATG
** *
40719503 CCCTCGATTTGTAAAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
40719530 CCCTCGATTTACAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* **
40719557 CCCT-TAGTTTACAGAATTACTATTTTA
1 CCCTCGA-TTTACAGAATTACCGTTTTA
* * *
40719584 CCCCCAATTTACAGAATTACCATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
40719611 CCCCCGATTTACATAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
40719638 CCC-CTAATTTACATAATTATCGTTTTA
1 CCCTC-GATTTACAGAATTACCGTTTTA
*
40719665 CCCTCGACTTACAGAATTACCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
*
40719692 CCCTCGATTTACAGAATTATCGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* **
40719719 CCCTCGATTTATAGAATTACTATTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* * *
40719746 CCCTTGATTTATAGAATTACTGTTTTA
1 CCCTCGATTTACAGAATTACCGTTTTA
* *
40719773 CCCTCAATTTACAAAATTAC
1 CCCTCGATTTACAGAATTAC
40719793 TAAAATACCC
Statistics
Matches: 229, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.01
27 225 0.98
28 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
CCCTCGATTTACAGAATTACCGTTTTA
Found at i:40719916 original size:27 final size:27
Alignment explanation
Indices: 40719785--40720022 Score: 210
Period size: 27 Copynumber: 8.7 Consensus size: 27
40719775 CTCAATTTAC
*
40719785 AAAATTACTAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
40719812 AAAATTACCAAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
*
40719839 AAAATTACCAAAATACCCTTGGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
* * * *
40719866 GAAATTACCGAAATACCCTCAATTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
* * **
40719893 AAAATTACCAAAATACCCCTAATTTAC
1 AAAATTACCAAAATACCCTTAGTTTGT
* * * *
40719920 AAAGTTA-TAGAAATACCCTTGACTTTCT
1 AAAATTACCA-AAATACCCTT-AGTTTGT
* * * **
40719948 AAAAATTA-TAGAAATACCATTGGTTTAC
1 -AAAATTACCA-AAATACCCTTAGTTTGT
**
40719976 AAAATTACTGAAATACCCTTAGTTTGT
1 AAAATTACCAAAATACCCTTAGTTTGT
* * *
40720003 AGATTTACCAAAACACCCTT
1 AAAATTACCAAAATACCCTT
40720023 GTAGGATGAA
Statistics
Matches: 172, Mismatches: 35, Indels: 8
0.80 0.16 0.04
Matches are distributed among these distances:
26 1 0.01
27 145 0.84
28 8 0.05
29 18 0.10
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTACCAAAATACCCTTAGTTTGT
Found at i:40720118 original size:27 final size:27
Alignment explanation
Indices: 40720041--40720118 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
40720031 AAATGTCTAA
*
40720041 AATACCCCTAT-TAGGTAAAAAGACCGT
1 AATACCCCTATAT-GGTAAAATGACCGT
* *
40720068 AA-AGCCCCTATAGGGTAAAGTGACCGT
1 AATA-CCCCTATATGGTAAAATGACCGT
*
40720095 AATACCCCTGTATGGTAAAATGAC
1 AATACCCCTATATGGTAAAATGAC
40720119 GAATATGCCC
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 1 0.02
27 40 0.95
28 1 0.02
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (27 bp):
AATACCCCTATATGGTAAAATGACCGT
Found at i:40721381 original size:9 final size:9
Alignment explanation
Indices: 40721369--40721443 Score: 51
Period size: 9 Copynumber: 7.7 Consensus size: 9
40721359 TGATAAACAA
40721369 GATATGTAT
1 GATATGTAT
*
40721378 GATATGCACAT
1 GATATG--TAT
40721389 GATATGTAT
1 GATATGTAT
*
40721398 GATATGCACAT
1 GATATG--TAT
*
40721409 GACATGTAT
1 GATATGTAT
* *
40721418 CATATGCACAT
1 GATATG--TAT
40721429 GATATGTAT
1 GATATGTAT
40721438 GATATG
1 GATATG
40721444 CACACGAGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 12
0.69 0.14 0.17
Matches are distributed among these distances:
9 28 0.56
11 22 0.44
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.35
Consensus pattern (9 bp):
GATATGTAT
Found at i:40721392 original size:11 final size:11
Alignment explanation
Indices: 40721376--40721447 Score: 57
Period size: 11 Copynumber: 7.1 Consensus size: 11
40721366 CAAGATATGT
40721376 ATGATATGCAC
1 ATGATATGCAC
*
40721387 ATGATATG--T
1 ATGATATGCAC
40721396 ATGATATGCAC
1 ATGATATGCAC
* *
40721407 ATGACATG--T
1 ATGATATGCAC
*
40721416 ATCATATGCAC
1 ATGATATGCAC
*
40721427 ATGATATG--T
1 ATGATATGCAC
40721436 ATGATATGCAC
1 ATGATATGCAC
40721447 A
1 A
40721448 CGAGATGTTC
Statistics
Matches: 45, Mismatches: 10, Indels: 12
0.67 0.15 0.18
Matches are distributed among these distances:
9 22 0.49
11 23 0.51
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:40721416 original size:40 final size:40
Alignment explanation
Indices: 40721372--40721460 Score: 144
Period size: 40 Copynumber: 2.2 Consensus size: 40
40721362 TAAACAAGAT
*
40721372 ATGTATGATATGCACATGATATGTATGATATGCACATGAC
1 ATGTATCATATGCACATGATATGTATGATATGCACATGAC
* *
40721412 ATGTATCATATGCACATGATATGTATGATATGCACACGAG
1 ATGTATCATATGCACATGATATGTATGATATGCACATGAC
40721452 ATGT-TCATA
1 ATGTATCATA
40721461 AATGCATTGG
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 5 0.11
40 41 0.89
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (40 bp):
ATGTATCATATGCACATGATATGTATGATATGCACATGAC
Found at i:40721455 original size:20 final size:20
Alignment explanation
Indices: 40721369--40721447 Score: 140
Period size: 20 Copynumber: 4.0 Consensus size: 20
40721359 TGATAAACAA
40721369 GATATGTATGATATGCACAT
1 GATATGTATGATATGCACAT
40721389 GATATGTATGATATGCACAT
1 GATATGTATGATATGCACAT
* *
40721409 GACATGTATCATATGCACAT
1 GATATGTATGATATGCACAT
40721429 GATATGTATGATATGCACA
1 GATATGTATGATATGCACA
40721448 CGAGATGTTC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 55 1.00
ACGTcount: A:0.35, C:0.13, G:0.19, T:0.33
Consensus pattern (20 bp):
GATATGTATGATATGCACAT
Found at i:40721532 original size:23 final size:23
Alignment explanation
Indices: 40721502--40721622 Score: 190
Period size: 23 Copynumber: 5.1 Consensus size: 23
40721492 AGGAAGTGCA
40721502 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
40721525 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT--T
40721550 AAAGGGCTTATGCCCCAGTTATT
1 AAAGGGCTTATGCCCCAGTTATT
*
40721573 AAAGGGCTTATGCCCCAATTATT
1 AAAGGGCTTATGCCCCAGTTATT
40721596 AAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAGGGCTTATGCCCCAGTTATT
40721620 AAA
1 AAA
40721623 AGAGGCTAGG
Statistics
Matches: 92, Mismatches: 2, Indels: 9
0.89 0.02 0.09
Matches are distributed among these distances:
22 3 0.03
23 45 0.49
24 12 0.13
25 32 0.35
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (23 bp):
AAAGGGCTTATGCCCCAGTTATT
Found at i:40721558 original size:25 final size:24
Alignment explanation
Indices: 40721502--40721645 Score: 181
Period size: 23 Copynumber: 6.0 Consensus size: 24
40721492 AGGAAGTGCA
40721502 AAAGGGCTTATGCCCCAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
40721525 AAAGGGCTTATGCCCCAGTTATGAT
1 AAAGGGCTTATGCCCCAGTTAT-AT
40721550 AAAGGGCTTATGCCCCAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
* *
40721573 AAAGGGCTTATGCCCCAATTATTAA
1 AAAGGGCTTATGCCCCAGTTA-TAT
40721598 AAAGGGCTT-TGCCCCAGTTAT-T
1 AAAGGGCTTATGCCCCAGTTATAT
*
40721620 AAAAGAGGC-TAGGCCTCCAGTTATAT
1 -AAAG-GGCTTATGCC-CCAGTTATAT
40721646 GATAAAGCAG
Statistics
Matches: 107, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
23 49 0.46
24 17 0.16
25 40 0.37
26 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATAT
Found at i:40721573 original size:48 final size:48
Alignment explanation
Indices: 40721501--40721622 Score: 210
Period size: 48 Copynumber: 2.6 Consensus size: 48
40721491 GAGGAAGTGC
*
40721501 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAGTTATGA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATGA
* *
40721549 TAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATTA
1 AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATGA
40721597 AAAAGGGCTT-TGCCCCAGTTATTAAA
1 AAAAGGGCTTATGCCCCAGTTATTAAA
40721623 AGAGGCTAGG
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
47 16 0.23
48 54 0.77
ACGTcount: A:0.30, C:0.20, G:0.20, T:0.29
Consensus pattern (48 bp):
AAAAGGGCTTATGCCCCAGTTATTAAAGGGCTTATGCCCCAATTATGA
Found at i:40721872 original size:31 final size:31
Alignment explanation
Indices: 40721837--40721900 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
40721827 CGTTTACCGT
*
40721837 AAAGGCTTCGGCCCAGTAATATGAAATTTGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
**
40721868 AAAGGCTTCGGCCCAGTGTTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
40721899 AA
1 AA
40721901 TATGAAAAGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:40727356 original size:9 final size:9
Alignment explanation
Indices: 40727342--40727366 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
40727332 ATAAATTTTA
40727342 GGAAAATTT
1 GGAAAATTT
40727351 GGAAAATTT
1 GGAAAATTT
40727360 GGAAAAT
1 GGAAAAT
40727367 AGGGGTTGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (9 bp):
GGAAAATTT
Found at i:40728507 original size:40 final size:40
Alignment explanation
Indices: 40728431--40728508 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 40
40728421 GGAGCACAGA
* * ** *
40728431 AGTGCATTTAAGGGCACGAATGTGCTGTCAAGGACATCAG
1 AGTGCATTTAAGGGCACAAATATGCAATCAAAGACATCAG
40728471 AGTGCATTT-AGAGGCACAAATATGCAATCAAAGACATC
1 AGTGCATTTAAG-GGCACAAATATGCAATCAAAGACATC
40728509 GAAGTGTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
39 2 0.06
40 30 0.94
ACGTcount: A:0.36, C:0.18, G:0.24, T:0.22
Consensus pattern (40 bp):
AGTGCATTTAAGGGCACAAATATGCAATCAAAGACATCAG
Found at i:40728554 original size:40 final size:40
Alignment explanation
Indices: 40728510--40728595 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
40728500 AAAGACATCG
*
40728510 AAGTGTTTAAAAGGGCAAATTTGTGCAAACAGGGACACCA
1 AAGTGTTTAAAAGGGCAAAGTTGTGCAAACAGGGACACCA
** * *
40728550 AAGTGTTTGTAAGGGCACAGTTGTGCAAATAGGGACACCA
1 AAGTGTTTAAAAGGGCAAAGTTGTGCAAACAGGGACACCA
40728590 AAGTGT
1 AAGTGT
40728596 ATATAGGGGT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (40 bp):
AAGTGTTTAAAAGGGCAAAGTTGTGCAAACAGGGACACCA
Found at i:40728615 original size:40 final size:40
Alignment explanation
Indices: 40728531--40728617 Score: 111
Period size: 40 Copynumber: 2.2 Consensus size: 40
40728521 AGGGCAAATT
* * *
40728531 TGTGCAAACAGGGACACCAAAGTGTTTGTAAGGGCACAGT
1 TGTGCAAACAGGGACACCAAAGTGTATATAAGGGCACAGA
* * * *
40728571 TGTGCAAATAGGGACACCAAAGTGTATATAGGGGTACTGA
1 TGTGCAAACAGGGACACCAAAGTGTATATAAGGGCACAGA
40728611 TGTGCAA
1 TGTGCAA
40728618 TTAAGGCACT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.30, T:0.22
Consensus pattern (40 bp):
TGTGCAAACAGGGACACCAAAGTGTATATAAGGGCACAGA
Found at i:40734588 original size:40 final size:40
Alignment explanation
Indices: 40734529--40734670 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
40734519 AAATTGAATG
* * *
40734529 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
40734569 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
40734609 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
40734649 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
40734671 GCATTTGTGC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 3 0.03
40 83 0.97
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:40734671 original size:40 final size:39
Alignment explanation
Indices: 40734568--40734696 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
40734558 TGCTGGAAAT
* * *
40734568 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGC-ATTGTGCGAGTGAC
* *
40734608 TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCATT-GTGCGAGTGAC
* *
40734648 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC-ACGTGAT
1 TATATCCGGGCTAAGACCCGAAGGCA-TTGTGCGA-GTGAC
40734688 TATATCCGG
1 TATATCCGG
40734697 TTATATTCCG
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 4 0.05
40 72 0.92
41 2 0.03
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TATATCCGGGCTAAGACCCGAAGGCATTGTGCGAGTGAC
Found at i:40742581 original size:40 final size:40
Alignment explanation
Indices: 40742515--40742681 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
40742505 AAATTGAATG
* * *
40742515 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * ***
40742554 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
*
40742594 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
40742634 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
40742674 ATATCCGG
1 ATATCCGG
40742682 TTATATTCCG
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
39 16 0.15
40 87 0.83
41 2 0.02
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
Found at i:40747934 original size:40 final size:40
Alignment explanation
Indices: 40747879--40748087 Score: 296
Period size: 40 Copynumber: 5.2 Consensus size: 40
40747869 ACATTGGAAA
40747879 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
40747919 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
40747959 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * *
40747999 ATATATCCGGGCTAAGA-CCGAAGGCCTTTGTGCAAG-TC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
* * * * * *
40748037 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
*
40748078 CTATATCCGG
1 ATATATCCGG
40748088 TTAAATCCCG
Statistics
Matches: 149, Mismatches: 17, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
38 2 0.01
39 28 0.19
40 119 0.80
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
Found at i:40748012 original size:80 final size:78
Alignment explanation
Indices: 40747879--40748087 Score: 292
Period size: 79 Copynumber: 2.6 Consensus size: 78
40747869 ACATTGGAAA
40747879 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCCGAAGG
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGA-CCGAAGG
* *
40747944 CATTCGTGCGAGTTG
65 CATTCGTGCAAG-TC
40747959 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
* *
40748024 CTTTGTGCAAGTC
66 ATTCGTGCAAGTC
* * * * * * *
40748037 ACCAAATCCGGGTTATGACCCGAAGGCAATCGTGCGAGTCGCTATATCCGG
1 A-TATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGG
40748088 TTAAATCCCG
Statistics
Matches: 117, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
78 2 0.02
79 58 0.50
80 57 0.49
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (78 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTGATATATCCGGGCTAAGACCGAAGGC
ATTCGTGCAAGTC
Found at i:40754323 original size:47 final size:47
Alignment explanation
Indices: 40754260--40754364 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
40754250 CCCTTCGGGA
* *
40754260 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
40754307 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
40754354 CTTATCACATA
1 CTTATCACATA
40754365 ATTAATACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:40758833 original size:39 final size:40
Alignment explanation
Indices: 40758765--40759075 Score: 551
Period size: 40 Copynumber: 7.9 Consensus size: 40
40758755 GAATACACAT
*
40758765 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
* *
40758805 CATCGGCACGAAT-ACCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
40758844 CACCGGCACGAATGCCCTTC-GGA-TTAG-CCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
40758881 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
40758921 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
40758961 CACCGGCACGAATGCCCTTCGGGA-TTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
40759000 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
*
40759040 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGAT
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGAT
40759076 CATCGTCGAG
Statistics
Matches: 260, Mismatches: 6, Indels: 10
0.94 0.02 0.04
Matches are distributed among these distances:
37 30 0.12
38 7 0.03
39 82 0.32
40 141 0.54
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (40 bp):
CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAA
Found at i:40759006 original size:79 final size:80
Alignment explanation
Indices: 40758765--40759075 Score: 551
Period size: 79 Copynumber: 4.0 Consensus size: 80
40758755 GAATACACAT
* * *
40758765 CACCGGCACGAATGCCCTTCGGGACTTAGCCCGGATATAACATCGGCACGAAT-ACCTTCGGGAT
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAT
40758829 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
40758844 CACCGGCACGAATGCCCTTC-GGA-TTAG-CCGGATATAACACCGGCACGAATGCCCTTCGGGAT
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAT
40758906 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
40758921 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGA-
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAT
40758985 TTAGCCCGGATATAA
66 TTAGCCCGGATATAA
*
40759000 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAC
1 CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAT
40759065 TTAGCCCGGAT
66 TTAGCCCGGAT
40759076 CATCGTCGAG
Statistics
Matches: 225, Mismatches: 2, Indels: 9
0.95 0.01 0.04
Matches are distributed among these distances:
76 22 0.10
77 49 0.22
78 6 0.03
79 103 0.46
80 45 0.20
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (80 bp):
CACCGGCACGAATGCCCTTCGGGATTTAGCCCGGATATAACACCGGCACGAATGCCCTTCGGGAT
TTAGCCCGGATATAA
Found at i:40759202 original size:38 final size:38
Alignment explanation
Indices: 40759116--40759207 Score: 112
Period size: 38 Copynumber: 2.4 Consensus size: 38
40759106 CTCTATATGA
* * * **
40759116 AGCCAGTGGGTCTTAATCCGGACATAATCTCTGTACAT
1 AGCCAGCGGGTCTTTACCCGGACATAATCTCTACACAT
* *
40759154 AGCCATCGGGTCTTTACCCGGACATAATCTCTACATAT
1 AGCCAGCGGGTCTTTACCCGGACATAATCTCTACACAT
*
40759192 AGTCAGCGGGTCTTTA
1 AGCCAGCGGGTCTTTA
40759208 AACTCGGATT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.29
Consensus pattern (38 bp):
AGCCAGCGGGTCTTTACCCGGACATAATCTCTACACAT
Found at i:40761210 original size:47 final size:47
Alignment explanation
Indices: 40761147--40761251 Score: 192
Period size: 47 Copynumber: 2.2 Consensus size: 47
40761137 CCCTTCGGGA
* *
40761147 CTTATCACATTTATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
40761194 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
40761241 CTTATCACATA
1 CTTATCACATA
40761252 ATTAATACTA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 56 1.00
ACGTcount: A:0.28, C:0.30, G:0.08, T:0.34
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATCCATCACATTGGCCATTCGGC
Found at i:40766767 original size:39 final size:39
Alignment explanation
Indices: 40766708--40766886 Score: 218
Period size: 39 Copynumber: 4.5 Consensus size: 39
40766698 TAATGGAGAA
*
40766708 TTATATCCGGGCTAAGTCCCGAAAGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
40766747 TTATATCCGGGCTATA-TCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTA-AGTCCCGAAGGCATTCGTGCTGGTG
* * * *
40766786 CTATATCCGGGCTAACTCTCGAAGGCATTCGTGCTAGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* * * *
40766825 TTATATCTGGGCTAAAGTCCCGTAGGC-TTTGTGCTGGTA
1 TTATATCCGGGCT-AAGTCCCGAAGGCATTCGTGCTGGTG
*
40766864 TTATATCTGGGCTTAAAGTCCCG
1 TTATATCCGGGC-T-AAGTCCCG
40766887 CATGCTTTGT
Statistics
Matches: 124, Mismatches: 12, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
38 1 0.01
39 102 0.82
40 21 0.17
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:40768727 original size:22 final size:22
Alignment explanation
Indices: 40768697--40768739 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
40768687 TTCTGATGCA
*
40768697 TTTATTCTGACTTCATGTTGCC
1 TTTAGTCTGACTTCATGTTGCC
40768719 TTTAGTCTGACTTCATGTTGC
1 TTTAGTCTGACTTCATGTTGC
40768740 TGGTCACATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.16, T:0.49
Consensus pattern (22 bp):
TTTAGTCTGACTTCATGTTGCC
Found at i:40768861 original size:28 final size:27
Alignment explanation
Indices: 40768805--40768862 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
40768795 GTGTTGACTA
* *
40768805 TTTTTTAACATGCATGTAGTGATTATT
1 TTTTTTAACATGCATATAATGATTATT
* *
40768832 TTTTTATAATATGCATATAATGACT-TT
1 TTTTT-TAACATGCATATAATGATTATT
40768859 TTTT
1 TTTT
40768863 AGGGGGCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 11 0.42
28 15 0.58
ACGTcount: A:0.28, C:0.07, G:0.10, T:0.55
Consensus pattern (27 bp):
TTTTTTAACATGCATATAATGATTATT
Found at i:40770966 original size:27 final size:27
Alignment explanation
Indices: 40770948--40771017 Score: 104
Period size: 27 Copynumber: 2.6 Consensus size: 27
40770938 ATAGTGAGTC
40770948 CGCACACTTAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTATATAATCAACT
* *
40770975 CGCACACTTAGTGCTACATGATCAAACT
1 CGCACACTTAGTGCTATATAATC-AACT
*
40771003 CACACACTTAGTGCT
1 CGCACACTTAGTGCT
40771018 GTACAAGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.31, C:0.29, G:0.13, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTATATAATCAACT
Found at i:40771049 original size:29 final size:29
Alignment explanation
Indices: 40771013--40771070 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
40771003 CACACACTTA
40771013 GTGCTGTACAAGTTTTAAACCCGCACACT
1 GTGCTGTACAAGTTTTAAACCCGCACACT
40771042 GTGCTGTACAAGTTTTAAACCCGCACACT
1 GTGCTGTACAAGTTTTAAACCCGCACACT
40771071 TAGTGCCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.28
Consensus pattern (29 bp):
GTGCTGTACAAGTTTTAAACCCGCACACT
Found at i:40772779 original size:21 final size:22
Alignment explanation
Indices: 40772725--40772780 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
40772715 ACACCCCAAC
*
40772725 TCAACAAGCTGCCTCAACTCAG
1 TCAACAAGCTGCCCCAACTCAG
* *
40772747 TCACCTAG-TGCCCCAACTCA-
1 TCAACAAGCTGCCCCAACTCAG
40772767 TCAACAAGCTGCCC
1 TCAACAAGCTGCCC
40772781 TAAGAGAAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 6 0.21
21 16 0.57
22 6 0.21
ACGTcount: A:0.29, C:0.41, G:0.12, T:0.18
Consensus pattern (22 bp):
TCAACAAGCTGCCCCAACTCAG
Found at i:40773215 original size:23 final size:24
Alignment explanation
Indices: 40773184--40773231 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
40773174 TTCTAACATA
*
40773184 TGAGTATTGA-AAAAACAAATGTG
1 TGAGAATTGAGAAAAACAAATGTG
* *
40773207 TGAGAATTGAGAAATACATATGTG
1 TGAGAATTGAGAAAAACAAATGTG
40773231 T
1 T
40773232 TTTTTTCATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 9 0.43
24 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.23, T:0.29
Consensus pattern (24 bp):
TGAGAATTGAGAAAAACAAATGTG
Found at i:40782603 original size:46 final size:46
Alignment explanation
Indices: 40782535--40782803 Score: 181
Period size: 46 Copynumber: 5.8 Consensus size: 46
40782525 TGTAACCCGC
* * *
40782535 CCATAAGCGAACTCGGAGTCAACTCAATGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * *
40782581 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTC-G--GAC--GTTCGCAT
* * * * *
40782631 -C-TCA-CGAACTTGGACTCAACTCAACGAGTTCAGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * * * *
40782674 CCATAAGTGAACTCAGACTCAACTCAACGAGTTCGGATGCCTAG-TT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACG-TTCGCAT
* * * *
40782720 ACATTTCA-CGAACTCGGACTCAACTCAACGAGTTTGGACGTTCGCAT
1 CCA--TAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
* * * * *
40782767 GCATAGGTGAACTCAGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGA
40782804 TGCCCAAATA
Statistics
Matches: 171, Mismatches: 38, Indels: 28
0.72 0.16 0.12
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 3 0.02
45 3 0.02
46 89 0.52
47 58 0.34
48 4 0.02
49 3 0.02
50 3 0.02
51 3 0.02
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGACGTTCGCAT
Found at i:40782651 original size:47 final size:47
Alignment explanation
Indices: 40782589--40782753 Score: 187
Period size: 47 Copynumber: 3.5 Consensus size: 47
40782579 ATCCATAAGT
*
40782589 GAACTCGGACTCAACTCAACGAGCTCAGATGCCTAGTTACATCTCAC
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATCTCAC
* * * *
40782636 GAACTTGGACTCAACTCAACGAGTTCAGA---C-A-TTCGCATCCATAAGT
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTT-ACAT-C-TCA-C
* * *
40782682 GAACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCAC
1 GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATCTCAC
40782729 GAACTCGGACTCAACTCAACGAGTT
1 GAACTCGGACTCAACTCAACGAGTT
40782754 TGGACGTTCG
Statistics
Matches: 96, Mismatches: 13, Indels: 18
0.76 0.10 0.14
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 26 0.27
47 51 0.53
48 2 0.02
49 1 0.01
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (47 bp):
GAACTCGGACTCAACTCAACGAGTTCAGATGCCTAGTTACATCTCAC
Found at i:40782672 original size:93 final size:93
Alignment explanation
Indices: 40782542--40782807 Score: 406
Period size: 93 Copynumber: 2.9 Consensus size: 93
40782532 CGCCCATAAG
* * * * *
40782542 CGAACTCGGAGTCAACTCAATGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
* *
40782607 ACGAGCTCAGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
40782635 CGAACTTGGACTCAACTCAACGAGTTCAGACATTCGCATCCATAAGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
*
40782700 ACGAGTTCGGATGCCTAGTTACATTTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
* * *
40782728 CGAACTCGGACTCAACTCAACGAGTTTGGACGTTCGCATGCATAGGTGAACTCAGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
40782793 ACGAGTTCGGATGCC
66 ACGAGTTCGGATGCC
40782808 CAAATATCCT
Statistics
Matches: 156, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 156 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCATCCATAAGTGAACTCAGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:40785571 original size:30 final size:30
Alignment explanation
Indices: 40785527--40785595 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 30
40785517 TAAAGATAAC
*
40785527 AAGAAAACC-GAATAAAGAAATCCA-AGATA
1 AAGAAACCCAGAATAAAGAAATCCAGA-ATA
*
40785556 GAGAAACCCAGAATAAAGAAATCCAGAATA
1 AAGAAACCCAGAATAAAGAAATCCAGAATA
40785586 AAGAAACCCA
1 AAGAAACCCA
40785596 AGATACGATA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
29 7 0.20
30 27 0.77
31 1 0.03
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.09
Consensus pattern (30 bp):
AAGAAACCCAGAATAAAGAAATCCAGAATA
Found at i:40785575 original size:15 final size:15
Alignment explanation
Indices: 40785527--40785595 Score: 79
Period size: 15 Copynumber: 4.7 Consensus size: 15
40785517 TAAAGATAAC
*
40785527 AAGAAAACC-GAATA
1 AAGAAACCCAGAATA
*
40785541 AAGAAATCCA-AGATA
1 AAGAAACCCAGA-ATA
*
40785556 GAGAAACCCAGAATA
1 AAGAAACCCAGAATA
*
40785571 AAGAAATCCAGAATA
1 AAGAAACCCAGAATA
40785586 AAGAAACCCA
1 AAGAAACCCA
40785596 AGATACGATA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
14 9 0.20
15 36 0.78
16 1 0.02
ACGTcount: A:0.59, C:0.17, G:0.14, T:0.09
Consensus pattern (15 bp):
AAGAAACCCAGAATA
Found at i:40788647 original size:46 final size:46
Alignment explanation
Indices: 40788579--40788745 Score: 173
Period size: 46 Copynumber: 3.6 Consensus size: 46
40788569 TGTAACCCGC
* *
40788579 CCATAAGTGAACTCGGAGTCAACTCAATGAGCTCGGGCATTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
* *
40788625 CCATAAGTGAACTCGGACTCAACTCAACGAGCTTGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-A-TTCGCAT
* * *
40788675 CTCA-CA---AACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
*
40788718 CCATAAGTGAACTCAGACTCAACTCAAC
1 CCATAAGTGAACTCGGACTCAACTCAAC
40788746 AAGTTCGGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 22
0.75 0.08 0.17
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 1 0.01
46 51 0.52
47 25 0.25
48 1 0.01
49 1 0.01
50 6 0.06
51 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.22
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGCAT
Found at i:40788694 original size:47 final size:47
Alignment explanation
Indices: 40788634--40788848 Score: 237
Period size: 47 Copynumber: 4.6 Consensus size: 47
40788624 TCCATAAGTG
40788634 AACTCGGACTCAACTCAACGAGCTT-GGATGCCTAGTTACATCTCACA
1 AACTCGGACTCAACTCAACGAG-TTCGGATGCCTAGTTACATCTCACA
* *
40788681 AACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATC-CATAA
1 AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATCTCA-CA
* * * * *
40788724 GTGAACTCAGACTCAACTCAACAAGTTCGGATGCCTAGTTACATTTGACG
1 ---AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACA
* * *
40788774 AACTCAGACTCAACTCAACGAGTTCGGATGCCTAGTTACATTTCACG
1 AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACA
40788821 AACTCGGACTCAACTCAACGAGTTCGGA
1 AACTCGGACTCAACTCAACGAGTTCGGA
40788849 CGTTCGCATG
Statistics
Matches: 144, Mismatches: 12, Indels: 24
0.80 0.07 0.13
Matches are distributed among these distances:
42 4 0.03
43 6 0.04
44 1 0.01
46 28 0.19
47 97 0.67
49 1 0.01
50 4 0.03
51 3 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (47 bp):
AACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACATCTCACA
Found at i:40788697 original size:93 final size:93
Alignment explanation
Indices: 40788588--40788801 Score: 322
Period size: 93 Copynumber: 2.3 Consensus size: 93
40788578 CCCATAAGTG
* * * * *
40788588 AACTCGGAGTCAACTCAATGAGCTCGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
*
40788653 GAGCTT-GGATGCCTAGTTACATCTCACA
66 AAG-TTCGGATGCCTAGTTACATCTCACA
40788681 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
* * *
40788746 AAGTTCGGATGCCTAGTTACATTTGACG
66 AAGTTCGGATGCCTAGTTACATCTCACA
*
40788774 AACTCAGACTCAACTCAACGAGTTCGGA
1 AACTCGGACTCAACTCAACGAGTTCGGA
40788802 TGCCTAGTTA
Statistics
Matches: 110, Mismatches: 10, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
92 2 0.02
93 108 0.98
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCAGACTCAACTCAAC
AAGTTCGGATGCCTAGTTACATCTCACA
Done.