Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
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: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 139 of 410
Found at i:42045412 original size:28 final size:28
Alignment explanation
Indices: 42045343--42045443 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42045333 GACAAGATTG
* * * *
42045343 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
42045373 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42045401 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
42045430 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42045444 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42053333 original size:28 final size:28
Alignment explanation
Indices: 42053264--42053364 Score: 114
Period size: 28 Copynumber: 3.5 Consensus size: 28
42053254 GACAAGATTG
* * * *
42053264 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTT--GATTATATA
42053294 GCACTAAGTGTGCGAGTTTGATTATATA
1 GCACTAAGTGTGCGAGTTTGATTATATA
*
42053322 GCACTAAGTGTGCGAG-TTGAATACATATA
1 GCACTAAGTGTGCGAGTTTG-AT-TATATA
42053351 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42053365 GATTCACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.05
28 24 0.38
29 19 0.30
30 18 0.28
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.30
Consensus pattern (28 bp):
GCACTAAGTGTGCGAGTTTGATTATATA
Found at i:42060998 original size:40 final size:40
Alignment explanation
Indices: 42060953--42061120 Score: 167
Period size: 40 Copynumber: 4.2 Consensus size: 40
42060943 CGGAATATAA
42060953 CCGGATATAACCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
42060993 CCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42061033 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
*** * * * * *
42061073 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
42061113 CCGGATAT
1 CCGGATAT
42061121 CATTCAATTT
Statistics
Matches: 104, Mismatches: 23, Indels: 2
0.81 0.18 0.02
Matches are distributed among these distances:
39 1 0.01
40 103 0.99
ACGTcount: A:0.23, C:0.27, G:0.24, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42061103 original size:80 final size:80
Alignment explanation
Indices: 42060969--42061118 Score: 196
Period size: 80 Copynumber: 1.9 Consensus size: 80
42060959 ATAACCACGT
* *
42060969 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
42061034 CGGATGTAGCCACTA
66 CGGATGTAGCCACTA
* * ** * *
42061049 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGGCTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTC-GCACGAA-TGCCTTCGGGGCTTAG
42061112 CCCGGAT
64 CCCGGAT
42061119 ATCATTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
79 3 0.05
80 57 0.95
ACGTcount: A:0.22, C:0.27, G:0.25, T:0.26
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATGACTCGCACGAATGCCTTCGGGGCTTAGCC
CGGATGTAGCCACTA
Found at i:42063321 original size:43 final size:44
Alignment explanation
Indices: 42063166--42063322 Score: 171
Period size: 43 Copynumber: 3.6 Consensus size: 44
42063156 TGTGTTTTCT
* * *
42063166 TGTAAGACCATGTCTGGGACGTTGGCATCGACT-TATGATTTACG
1 TGTAAGACCATGTCTGGGACGTTGGCATC-AATATTTGATTTACA
* *
42063210 TGTAAGACCATGTCTGGGACATCGGCATC-ATATTTGATTT-CA
1 TGTAAGACCATGTCTGGGACGTTGGCATCAATATTTGATTTACA
* *
42063252 TGTAAGACCTTGTCTGGGATAG-TGGCATCAATATTTG-TTTACA
1 TGTAAGACCATGTCTGGGA-CGTTGGCATCAATATTTGATTTACA
* * *
42063295 TGTAAGACCACGTCTAGGATGTTGGCAT
1 TGTAAGACCATGTCTGGGACGTTGGCAT
42063323 TATACGAGCT
Statistics
Matches: 95, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
42 30 0.32
43 38 0.40
44 27 0.28
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (44 bp):
TGTAAGACCATGTCTGGGACGTTGGCATCAATATTTGATTTACA
Found at i:42063630 original size:17 final size:17
Alignment explanation
Indices: 42063608--42063643 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
42063598 TTTGATGATA
42063608 TTTTCAAGTTTTGAATG
1 TTTTCAAGTTTTGAATG
*
42063625 TTTTCATGTTTTGAATG
1 TTTTCAAGTTTTGAATG
42063642 TT
1 TT
42063644 AAGTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.06, G:0.17, T:0.58
Consensus pattern (17 bp):
TTTTCAAGTTTTGAATG
Found at i:42066019 original size:45 final size:44
Alignment explanation
Indices: 42065862--42066035 Score: 188
Period size: 45 Copynumber: 3.8 Consensus size: 44
42065852 ATTTGGGCAT
42065862 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * * *
42065907 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCAT
1 -CCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
42065955 CCGAGCTCATTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* *
42066000 CCGAGCTCGTTGAGTTGAGTCCGGGTTCACTTATGG
1 CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42066036 CGGGTTACAT
Statistics
Matches: 106, Mismatches: 16, Indels: 13
0.79 0.12 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 35 0.33
46 32 0.30
47 30 0.28
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (44 bp):
CCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42070937 original size:46 final size:45
Alignment explanation
Indices: 42070870--42071045 Score: 185
Period size: 46 Copynumber: 3.8 Consensus size: 45
42070860 TATTTGGGCA
*
42070870 TCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
*** * *
42070916 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAG-GCA-
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-ACTTATG-GA-T-GCGAAG
* *
42070963 TCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-G
* * *
42071009 CCCGAGCTCGTTGAGTTGAGTCCGGGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42071046 GCGGGTTACA
Statistics
Matches: 109, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 1 0.01
44 3 0.03
45 1 0.01
46 67 0.61
47 32 0.29
48 1 0.01
49 3 0.03
50 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.29
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAG
Found at i:42071025 original size:93 final size:93
Alignment explanation
Indices: 42070866--42071037 Score: 281
Period size: 93 Copynumber: 1.8 Consensus size: 93
42070856 AGGATATTTG
* * *
42070866 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAGTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
42070931 TTGAGTCCGAGTTCGAGAGATGTAACTA
66 TTGAGTCCGAGTTCGAGAGATGTAACTA
* * *
42070959 GGCATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
*
42071024 TTGAGTCCGGGTTC
66 TTGAGTCCGAGTTC
42071038 ACTTATGGGC
Statistics
Matches: 72, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.20, C:0.20, G:0.31, T:0.28
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGAGAGATGTAACTA
Found at i:42078618 original size:2 final size:2
Alignment explanation
Indices: 42078611--42078646 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
42078601 ATTGAAAGGG
* *
42078611 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42078647 GTGTTGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:42084835 original size:27 final size:26
Alignment explanation
Indices: 42084787--42084846 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
42084777 GCGAGGCTGC
*
42084787 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
42084814 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
42084840 TAGATAT
1 CAGATAT
42084847 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42085210 original size:8 final size:8
Alignment explanation
Indices: 42085199--42085229 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
42085189 GGGCCCGTTA
42085199 GCCCATTG
1 GCCCATTG
*
42085207 GCCCGTTG
1 GCCCATTG
42085215 GCCCATTG
1 GCCCATTG
42085223 GCCCATT
1 GCCCATT
42085230 TTCGGCTCAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.10, C:0.39, G:0.26, T:0.26
Consensus pattern (8 bp):
GCCCATTG
Found at i:42085211 original size:16 final size:16
Alignment explanation
Indices: 42085190--42085226 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
42085180 TACCAAAGTG
42085190 GGCCCGTTAGCCCATT
1 GGCCCGTTAGCCCATT
*
42085206 GGCCCGTTGGCCCATT
1 GGCCCGTTAGCCCATT
42085222 GGCCC
1 GGCCC
42085227 ATTTTCGGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.08, C:0.41, G:0.30, T:0.22
Consensus pattern (16 bp):
GGCCCGTTAGCCCATT
Found at i:42087859 original size:43 final size:43
Alignment explanation
Indices: 42087811--42087896 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
42087801 CGTATAAGGG
42087811 GCGATATGCATATGTATAAATGAATTTGATTTGAACGAAATTT
1 GCGATATGCATATGTATAAATGAATTTGATTTGAACGAAATTT
42087854 GCGATATGCATATGTATAAATGAATTTGATTTGAACGAAATTT
1 GCGATATGCATATGTATAAATGAATTTGATTTGAACGAAATTT
42087897 TATGATCTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (43 bp):
GCGATATGCATATGTATAAATGAATTTGATTTGAACGAAATTT
Found at i:42101980 original size:27 final size:26
Alignment explanation
Indices: 42101932--42101991 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
42101922 GCGAGGCTGC
*
42101932 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
42101959 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
42101985 CAGATAT
1 CAGATAT
42101992 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:42114606 original size:46 final size:46
Alignment explanation
Indices: 42114556--42114731 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
42114546 TGGTTGAGCA
*
42114556 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
42114602 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
42114649 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
42114695 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42114732 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 64 0.58
47 29 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:42114712 original size:93 final size:93
Alignment explanation
Indices: 42114553--42114724 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42114543 GGATGGTTGA
* *
42114553 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42114618 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
42114646 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42114711 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42114725 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42117501 original size:29 final size:29
Alignment explanation
Indices: 42117415--42117498 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
42117405 CATAGTATCG
* * * *
42117415 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTCTGG-TTTCTC
42117445 TAT-TCTGGATTTCTTTATTCTGGTTTCTC
1 TATCT-TGGATTTCTTTATTCTGGTTTCTC
42117474 TATCTTGGATTTCTTTATTC-GGTTT
1 TATCTTGGATTTCTTTATTCTGGTTT
42117499 TCTTGTTATC
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 5 0.10
29 23 0.48
30 20 0.42
ACGTcount: A:0.11, C:0.17, G:0.15, T:0.57
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCTGGTTTCTC
Found at i:42117502 original size:14 final size:15
Alignment explanation
Indices: 42117424--42117502 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
42117414 GTATCTTGGG
*
42117424 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
42117439 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
42117454 TTTCTTTATTCTGG-
1 TTTCTTTATTCTGGA
*
42117468 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
42117483 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
42117497 TTTCTT
1 TTTCTT
42117503 GTTATCTTTG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
13 2 0.04
14 18 0.33
15 33 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:42119933 original size:46 final size:46
Alignment explanation
Indices: 42119883--42120058 Score: 214
Period size: 46 Copynumber: 3.8 Consensus size: 46
42119873 TGGTTGAGCA
*
42119883 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * * *
42119929 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--A--CG
*
42119976 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
* * *
42120022 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
42120059 GCGGGTTACA
Statistics
Matches: 110, Mismatches: 13, Indels: 14
0.80 0.09 0.10
Matches are distributed among these distances:
43 6 0.05
45 3 0.03
46 64 0.58
47 29 0.26
48 3 0.03
50 5 0.05
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACG
Found at i:42120039 original size:93 final size:93
Alignment explanation
Indices: 42119880--42120051 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
42119870 GGATGGTTGA
* *
42119880 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42119945 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
42119973 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
42120038 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
42120052 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:42129220 original size:20 final size:20
Alignment explanation
Indices: 42129192--42129229 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42129182 CTAAGAACTA
42129192 TGTGATCTGAGCTCATGAGT
1 TGTGATCTGAGCTCATGAGT
* *
42129212 TGTGGTCTGAGTTCATGA
1 TGTGATCTGAGCTCATGA
42129230 TATATGTGAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.32, T:0.37
Consensus pattern (20 bp):
TGTGATCTGAGCTCATGAGT
Found at i:42135551 original size:49 final size:49
Alignment explanation
Indices: 42135498--42135813 Score: 477
Period size: 47 Copynumber: 6.6 Consensus size: 49
42135488 GATTTTATGC
* *
42135498 GATGAATGTGAATGTGTATATATATGAGATAAGGCCGAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
*
42135547 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
*
42135596 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
*
42135645 GATGAATGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
*
42135692 GATGAATGTG-AAG-GTATATATATGTGATAAGGCCGAATGGCCAATGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
* * * *
42135739 GATGAATGTGAAAGTG--TATATATGTGATAGGGCCGAGTGGCCAACGT
1 GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
*
42135786 GATGGATGTGAAAGTGTATA-A-ATGTGAT
1 GATGAATGTGAAAGTGTATATATATGTGAT
42135814 GAATCCCGAA
Statistics
Matches: 252, Mismatches: 9, Indels: 14
0.92 0.03 0.05
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
47 130 0.52
48 4 0.02
49 114 0.45
ACGTcount: A:0.33, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
GATGAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGT
Found at i:42137285 original size:40 final size:40
Alignment explanation
Indices: 42137236--42137447 Score: 334
Period size: 40 Copynumber: 5.3 Consensus size: 40
42137226 ACATGAGAAT
*
42137236 TGCTTGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
1 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
42137276 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
1 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
42137316 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
1 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
* *
42137356 TGCTAGTGATGTAACCGGACTAAGTCCCGAAGAGCATTCG
1 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
* * * * * *
42137396 TGCTAGTGATGTATTCGGGCTAGGTCCCGAAGAGCAATCA
1 TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
*
42137436 TGCTGGTGATGT
1 TGCTAGTGATGT
42137448 GTATTCGGGC
Statistics
Matches: 162, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 162 1.00
ACGTcount: A:0.24, C:0.20, G:0.29, T:0.27
Consensus pattern (40 bp):
TGCTAGTGATGTATCCGGACTAAGTTCCGAAGAGCATTCG
Found at i:42141223 original size:49 final size:49
Alignment explanation
Indices: 42141170--42141580 Score: 595
Period size: 49 Copynumber: 8.6 Consensus size: 49
42141160 TTTATGCGAC
* * *
42141170 GAATGTGAATGTGTATATATATGGGATAAGGCCGAATGGCTGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
* * *
42141219 GAATGTGAATGTGTATATATATGAGATAAGGCCGAATGACCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
*
42141268 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
*
42141317 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
*
42141366 GAATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
* *
42141415 GAACGTGAAAGTG--TATATATGTGATAAGGCCTAATGGCCGATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
* * *
42141462 GAATGTG-AAG-GTGTATCTATGTGATAAGGCCGAATGGCCAATGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
* * * *
42141509 GAATGTGAAAGTG--TATATATGTGATAGGGCCGAGTGGCCAACGTGAT
1 GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
*
42141556 GGATGTGAAAGTGTATA-A-ATGTGAT
1 GAATGTGAAAGTGTATATATATGTGAT
42141581 GAATCCCGAA
Statistics
Matches: 339, Mismatches: 17, Indels: 14
0.92 0.05 0.04
Matches are distributed among these distances:
45 1 0.00
46 3 0.01
47 127 0.37
48 4 0.01
49 204 0.60
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (49 bp):
GAATGTGAAAGTGTATATATATGTGATAAGGCCGAATGGCCGATGTGAT
Found at i:42144762 original size:29 final size:29
Alignment explanation
Indices: 42144672--42144831 Score: 180
Period size: 29 Copynumber: 5.5 Consensus size: 29
42144662 ACTCGATTTC
* * **
42144672 GCACACTTAGTGCCATGTGATTT-AAGCCC
1 GCACACTTAGTGCCATAT-ATTTCCAGCAT
* *** *
42144701 GCACACATAGTGCCATACCCTTCGAGC-T
1 GCACACTTAGTGCCATATATTTCCAGCAT
** *
42144729 CGCACACCCAGTGCCGTATATTTCCAGCAT
1 -GCACACTTAGTGCCATATATTTCCAGCAT
42144759 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
42144788 GCACACTTAGTGCCATATATTTCCAGCAT
1 GCACACTTAGTGCCATATATTTCCAGCAT
42144817 GCACACTTAGTGCCA
1 GCACACTTAGTGCCA
42144832 ATCTCGTCAC
Statistics
Matches: 111, Mismatches: 17, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
28 2 0.02
29 108 0.97
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
GCACACTTAGTGCCATATATTTCCAGCAT
Found at i:42151978 original size:60 final size:60
Alignment explanation
Indices: 42151878--42152016 Score: 176
Period size: 60 Copynumber: 2.3 Consensus size: 60
42151868 AACTGTGTTA
*
42151878 ATATGGGCAAGGCCCAATATATCTCGACTTGTAATAGGGCTACGACCCAGATTAATACTG
1 ATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGACCCAGATTAATACTG
* * * *
42151938 ATATGGGCTAGGCCCAATATA-CTCTGA-TACTGTAA-GGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCTAGGCCCAATATATCTC-GACT--TGTAATAGGGCTACGACCCAGATTAATACTG
42151998 ATATGGGCTAAGGCCCAAT
1 ATATGGGCT-AGGCCCAAT
42152017 TAACACTTAT
Statistics
Matches: 70, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
59 4 0.06
60 52 0.74
61 14 0.20
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (60 bp):
ATATGGGCTAGGCCCAATATATCTCGACTTGTAATAGGGCTACGACCCAGATTAATACTG
Found at i:42154057 original size:17 final size:19
Alignment explanation
Indices: 42154015--42154058 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
42154005 ATGAAATTTT
*
42154015 AATTAGTATTATGAGATAA
1 AATTATTATTATGAGATAA
*
42154034 AATTATTATTATTAGA-AA
1 AATTATTATTATGAGATAA
42154052 AA-TATTA
1 AATTATTA
42154059 CTGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 5 0.22
18 4 0.17
19 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (19 bp):
AATTATTATTATGAGATAA
Found at i:42156700 original size:60 final size:60
Alignment explanation
Indices: 42156624--42156758 Score: 177
Period size: 60 Copynumber: 2.2 Consensus size: 60
42156614 AACTGTGTTA
42156624 ATATGGGCAAGGCCCAATATA-TCTCA-ACTTGTAATAGGGCTACGGCCCAGATTAATACTG
1 ATATGGGCAAGGCCCAATATACTCTCATAC-TGTAA-AGGGCTACGGCCCAGATTAATACTG
* * * *
42156684 ATATGGG-ATAGGCCCAATATACTCTGATACTGTAAGGGGCTATGGCCCAGATTAATATTG
1 ATATGGGCA-AGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
42156744 ATATGGGCTAAGGCC
1 ATATGGGC-AAGGCC
42156759 AAGTAACACT
Statistics
Matches: 66, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
59 1 0.02
60 48 0.73
61 14 0.21
62 3 0.05
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (60 bp):
ATATGGGCAAGGCCCAATATACTCTCATACTGTAAAGGGCTACGGCCCAGATTAATACTG
Found at i:42164111 original size:30 final size:30
Alignment explanation
Indices: 42164075--42164234 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42164065 GACAAGATTG
* * * * *
42164075 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
42164105 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
42164133 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42164162 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42164192 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42164221 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42164235 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:42164203 original size:59 final size:57
Alignment explanation
Indices: 42164075--42164234 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42164065 GACAAGATTG
* * * * * *
42164075 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
42164133 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
42164192 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
42164235 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:42172134 original size:29 final size:29
Alignment explanation
Indices: 42172040--42172198 Score: 205
Period size: 29 Copynumber: 5.5 Consensus size: 29
42172030 GACAAGATTG
* * * * *
42172040 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATA
* * *
42172070 GCACTAAGTGTGCGAGTTTG--ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATATATA
42172098 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
*
42172127 GCACTAAGTGTGCGAGCTGAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
42172156 GCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATA
42172185 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42172199 GATTCACTAT
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
27 2 0.02
28 21 0.18
29 77 0.66
30 15 0.13
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (29 bp):
GCACTAAGTGTGCGAGCTGAAAATATATA
Found at i:42180064 original size:28 final size:28
Alignment explanation
Indices: 42179995--42180116 Score: 134
Period size: 28 Copynumber: 4.5 Consensus size: 28
42179985 AAAATTGTAC
* *
42179995 AGCACTAAGTGTGCGAGTTG---ATTAT
1 AGCACTAAGTGTGCGAGCTGAAAATAAT
42180020 A-CAGCTAAGTGTGCGAGCTGAAAATAAT
1 AGCA-CTAAGTGTGCGAGCTGAAAATAAT
*
42180048 AGCACTAAGTGTGCGAGCTGAAATTATAT
1 AGCACTAAGTGTGCGAGCTGAAAATA-AT
42180077 AGCACTAAGT-TGCGA-CTGAAAAT-AT
1 AGCACTAAGTGTGCGAGCTGAAAATAAT
42180102 AAGCACT-AGTGTGCG
1 -AGCACTAAGTGTGCG
42180117 GATTCACTAT
Statistics
Matches: 85, Mismatches: 4, Indels: 15
0.82 0.04 0.14
Matches are distributed among these distances:
24 2 0.02
25 21 0.25
26 10 0.12
27 7 0.08
28 31 0.36
29 14 0.16
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGCTGAAAATAAT
Found at i:42180074 original size:55 final size:52
Alignment explanation
Indices: 42179995--42180116 Score: 151
Period size: 55 Copynumber: 2.3 Consensus size: 52
42179985 AAAATTGTAC
*
42179995 AGCACTAAGTGTGCGAGTTGATTATACAG-CTAAGTGTGCGAGCTGAAAATA-A
1 AGCACTAAGTGTGCGAGCTGATTATACAGACTAAGT-TGCGA-CTGAAAATATA
*
42180047 TAGCACTAAGTGTGCGAGCTGAAATTATATAGCACTAAGTTGCGACTGAAAATATA
1 -AGCACTAAGTGTGCGAGCTG--ATTATACAG-ACTAAGTTGCGACTGAAAATATA
42180103 AGCACT-AGTGTGCG
1 AGCACTAAGTGTGCG
42180117 GATTCACTAT
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
53 19 0.31
54 8 0.13
55 23 0.37
56 6 0.10
57 6 0.10
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.25
Consensus pattern (52 bp):
AGCACTAAGTGTGCGAGCTGATTATACAGACTAAGTTGCGACTGAAAATATA
Found at i:42182645 original size:30 final size:30
Alignment explanation
Indices: 42182609--42182768 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42182599 GACAAGATTG
* * * * *
42182609 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
42182639 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
42182667 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42182696 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42182726 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42182755 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42182769 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:42182737 original size:59 final size:57
Alignment explanation
Indices: 42182609--42182768 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42182599 GACAAGATTG
* * * * * *
42182609 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
42182667 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
42182726 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
42182769 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:42190596 original size:30 final size:30
Alignment explanation
Indices: 42190560--42190719 Score: 213
Period size: 29 Copynumber: 5.5 Consensus size: 30
42190550 GACAAGATTG
* * * * *
42190560 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
* *
42190590 GCACTAAGTGTGCGAGTTTG---ATTATACA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
42190618 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42190647 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42190677 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
42190706 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
42190720 GATTCACTAT
Statistics
Matches: 120, Mismatches: 5, Indels: 11
0.88 0.04 0.08
Matches are distributed among these distances:
27 2 0.02
28 23 0.19
29 48 0.40
30 45 0.38
31 2 0.02
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:42190688 original size:59 final size:57
Alignment explanation
Indices: 42190560--42190719 Score: 214
Period size: 59 Copynumber: 2.8 Consensus size: 57
42190550 GACAAGATTG
* * * * * *
42190560 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATACA
1 GCACTAAGTGTGCGAGCTGAAAA-TATATAGCACTAAGTGTGCGAGTCTGATTATACA
*
42190618 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAG-CTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTG---ATTATACA
42190677 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
1 GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCG
42190720 GATTCACTAT
Statistics
Matches: 92, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
56 2 0.02
57 20 0.22
58 20 0.22
59 50 0.54
ACGTcount: A:0.33, C:0.14, G:0.26, T:0.27
Consensus pattern (57 bp):
GCACTAAGTGTGCGAGCTGAAAATATATAGCACTAAGTGTGCGAGTCTGATTATACA
Found at i:42193551 original size:37 final size:36
Alignment explanation
Indices: 42193501--42193618 Score: 200
Period size: 37 Copynumber: 3.2 Consensus size: 36
42193491 TACGAAGTCT
*
42193501 TACCCGGACATAATCTCCACACGTAGTCATCGGGTC
1 TACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
42193537 ATACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
42193574 TTACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
1 -TACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
42193611 TCACCCGG
1 T-ACCCGG
42193619 AACATATTCC
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
36 1 0.01
37 77 0.99
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.24
Consensus pattern (36 bp):
TACCCGGTCATAATCTCCACACGTAGTCATCGGGTC
Found at i:42193775 original size:49 final size:49
Alignment explanation
Indices: 42193720--42194029 Score: 527
Period size: 49 Copynumber: 6.4 Consensus size: 49
42193710 TTTTACATTA
*
42193720 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
42193769 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
42193818 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATC-
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
42193866 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
42193915 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
** * * *
42193964 GCCATTAGGCCTTATCACACGT--ATGCACTTTCACATTCATCACATTG
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
*
42194011 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
42194030 CATATATGTA
Statistics
Matches: 253, Mismatches: 7, Indels: 4
0.96 0.03 0.02
Matches are distributed among these distances:
47 41 0.16
48 48 0.19
49 164 0.65
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (49 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCG
Found at i:42193913 original size:97 final size:98
Alignment explanation
Indices: 42193720--42194029 Score: 527
Period size: 97 Copynumber: 3.2 Consensus size: 98
42193710 TTTTACATTA
*
42193720 GCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
42193785 ACATATACATACACTTTCACATTCACCACATCG
66 ACATATACATACACTTTCACATTCACCACATCG
42193818 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATC-GCCATTAGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
42193882 ACATATACATACACTTTCACATTCACCACATCG
66 ACATATACATACACTTTCACATTCACCACATCG
*
42193915 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATC
1 GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
** * * *
42193980 ACACGT--ATGCACTTTCACATTCATCACATTG
66 ACATATACATACACTTTCACATTCACCACATCG
*
42194011 GCCATTCGGCCTTATCACA
1 GCCATTAGGCCTTATCACA
42194030 CATATATGTA
Statistics
Matches: 203, Mismatches: 8, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
96 40 0.20
97 96 0.47
98 67 0.33
ACGTcount: A:0.29, C:0.32, G:0.09, T:0.30
Consensus pattern (98 bp):
GCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATC
ACATATACATACACTTTCACATTCACCACATCG
Found at i:42193929 original size:146 final size:145
Alignment explanation
Indices: 42193714--42194029 Score: 526
Period size: 146 Copynumber: 2.2 Consensus size: 145
42193704 CATATATTTT
* *
42193714 ACATTAGCCATTAGGCCTTATCACATATATATACACTTTCACATTCACCACATCGGCCATTAGGC
1 ACATTCGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGC
*
42193779 CTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACATATACAT
66 CTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACACAT--AT
42193844 ACACTTTCACATTCACC
129 ACACTTTCACATTCACC
42193861 ACA-TCGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGC
1 ACATTCGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGC
* * *
42193925 CTTATCACATATACATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACACGTATGC
66 CTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACACATATAC
*
42193990 ACTTTCACATTCATC
131 ACTTTCACATTCACC
* *
42194005 ACATTGGCCATTCGGCCTTATCACA
1 ACATTCGCCATTAGGCCTTATCACA
42194030 CATATATGTA
Statistics
Matches: 159, Mismatches: 9, Indels: 4
0.92 0.05 0.02
Matches are distributed among these distances:
144 20 0.13
145 19 0.12
146 117 0.74
147 3 0.02
ACGTcount: A:0.30, C:0.32, G:0.09, T:0.30
Consensus pattern (145 bp):
ACATTCGCCATTAGGCCTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGC
CTTATCACATATACATACACTTTCACATTCACCACATCGGCCATTAGGCCTTATCACACATATAC
ACTTTCACATTCACC
Found at i:42199418 original size:27 final size:27
Alignment explanation
Indices: 42199343--42199422 Score: 88
Period size: 27 Copynumber: 3.0 Consensus size: 27
42199333 AAACATACAT
* **
42199343 CACATAGGGGCAAAACAGTCAGCTTAC
1 CACATAAGGGCAAAACAGTCATTTTAC
* * * * *
42199370 CATATAAGAGAAAAATAGTCATTTTGC
1 CACATAAGGGCAAAACAGTCATTTTAC
42199397 CACATAAGGGCAAAACAGTCATTTTA
1 CACATAAGGGCAAAACAGTCATTTTA
42199423 TCATATTGGG
Statistics
Matches: 40, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 40 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (27 bp):
CACATAAGGGCAAAACAGTCATTTTAC
Found at i:42207082 original size:15 final size:16
Alignment explanation
Indices: 42207059--42207092 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42207049 TCATTTTTAT
*
42207059 TATATTTTTATGG-TC
1 TATAGTTTTATGGATC
42207074 TATAGTTTTATGGATC
1 TATAGTTTTATGGATC
42207090 TAT
1 TAT
42207093 TTTGTGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.24, C:0.06, G:0.15, T:0.56
Consensus pattern (16 bp):
TATAGTTTTATGGATC
Found at i:42211579 original size:13 final size:13
Alignment explanation
Indices: 42211561--42211587 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42211551 GAAGTAATCA
42211561 CACACGGGCGTGT
1 CACACGGGCGTGT
42211574 CACACGGGCGTGT
1 CACACGGGCGTGT
42211587 C
1 C
42211588 CTTACCGAGC
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:42219274 original size:40 final size:40
Alignment explanation
Indices: 42219229--42219396 Score: 162
Period size: 40 Copynumber: 4.2 Consensus size: 40
42219219 CGGAATATAA
42219229 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * *
42219269 CCGGATAGAAT-ATCTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCA-CTAGCACAAATGCCTTCGGGTCTTAGC
* ** * *
42219309 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42219349 CCGGATATAATTTCCAGCATAATTGTCTTCGGGAT-TTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGG-TCTTAGC
42219389 CCGGATAT
1 CCGGATAT
42219397 CATTCAATTT
Statistics
Matches: 105, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
39 2 0.02
40 101 0.96
41 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.27
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42219379 original size:80 final size:80
Alignment explanation
Indices: 42219245--42219394 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 80
42219235 ATAATCACGT
*
42219245 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATATCTCGCACGAATGCCTTCGGG-TCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGAT-TTAGC
42219309 CCGGATGTAGCCACTA
65 CCGGATGTAGCCACTA
* * * * *
42219325 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGATTTAG
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTC-GCACGAA-TGCCTTCGGGATTTAG
42219388 CCCGGAT
64 CCCGGAT
42219395 ATCATTCAAT
Statistics
Matches: 61, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
79 3 0.05
80 57 0.93
81 1 0.02
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (80 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATATCTCGCACGAATGCCTTCGGGATTTAGCC
CGGATGTAGCCACTA
Found at i:42232170 original size:29 final size:29
Alignment explanation
Indices: 42232137--42232268 Score: 165
Period size: 29 Copynumber: 4.6 Consensus size: 29
42232127 GTGACGAGAT
*
42232137 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
*
42232166 TGGCACTAAGTGTGCGTGCTGGAAATATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* *
42232195 AGGCACTAAGTGTGCATGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* * **
42232224 TGACACTATGTGTGCAAGCTGGAAAAATA
1 TGGCACTAAGTGTGCGTGCTGGAAAAATA
* **
42232253 CGGCACTGGGTGTGCG
1 TGGCACTAAGTGTGCG
42232269 AGCTCGAAGG
Statistics
Matches: 91, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 91 1.00
ACGTcount: A:0.30, C:0.15, G:0.31, T:0.24
Consensus pattern (29 bp):
TGGCACTAAGTGTGCGTGCTGGAAAAATA
Found at i:42237797 original size:22 final size:22
Alignment explanation
Indices: 42237771--42237815 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
42237761 ATTATGTGTA
42237771 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
42237793 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
42237815 T
1 T
42237816 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:42242316 original size:27 final size:27
Alignment explanation
Indices: 42242271--42242332 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
42242261 GTAAACAGTC
* * ** *
42242271 ATTTTACCCTACAGGGGTATTTTGGTA
1 ATTTTACACTACAAGGGTAGCTTAGTA
*
42242298 ATTTTACACTACAATGGTAGCTTAGTA
1 ATTTTACACTACAAGGGTAGCTTAGTA
42242325 ATTTTACA
1 ATTTTACA
42242333 AATTGAGGTC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTAGCTTAGTA
Found at i:42245568 original size:29 final size:29
Alignment explanation
Indices: 42245505--42245611 Score: 128
Period size: 29 Copynumber: 3.7 Consensus size: 29
42245495 TTCACATACC
* * * *
42245505 TGTATCTGGCCCACTAAGCCC-AATCATA
1 TGTATATGGCCCATTAGGCCCAAATCACA
*
42245533 T-TCATATGGCCCATTAGGCCCAAATCACC
1 TGT-ATATGGCCCATTAGGCCCAAATCACA
42245562 TGTATATGGCCCATTAGGCCCAAATCACA
1 TGTATATGGCCCATTAGGCCCAAATCACA
* *
42245591 TTTATATGGCCCGTTAGGCCC
1 TGTATATGGCCCATTAGGCCC
42245612 GGTCACATTC
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
27 1 0.01
28 16 0.24
29 50 0.74
30 1 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (29 bp):
TGTATATGGCCCATTAGGCCCAAATCACA
Found at i:42245610 original size:58 final size:57
Alignment explanation
Indices: 42245502--42245611 Score: 157
Period size: 58 Copynumber: 1.9 Consensus size: 57
42245492 AATTTCACAT
* *
42245502 ACCTGTATCTGGCCCACTAAGCCCAATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCACTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
42245559 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCCCGTTAGGCCC
1 ACCTGTATATGGCCCACTAAGCCC-AATCACATTCATATGGCCCATTAGGCCC
42245612 GGTCACATTC
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
57 21 0.46
58 25 0.54
ACGTcount: A:0.26, C:0.32, G:0.16, T:0.25
Consensus pattern (57 bp):
ACCTGTATATGGCCCACTAAGCCCAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:42247639 original size:40 final size:40
Alignment explanation
Indices: 42247583--42247840 Score: 369
Period size: 40 Copynumber: 6.5 Consensus size: 40
42247573 TGGATGATAA
* *
42247583 CCGGGCTAAGTCCCGAAGGCATTTGTGCTAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
*
42247623 TCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42247663 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42247703 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42247743 CCGGGCTAACTCCCGAAGGCATTAGTGTGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42247783 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
42247823 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42247841 TACTTGGCTT
Statistics
Matches: 200, Mismatches: 16, Indels: 5
0.90 0.07 0.02
Matches are distributed among these distances:
39 17 0.09
40 183 0.92
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.27
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42254036 original size:80 final size:80
Alignment explanation
Indices: 42253952--42254100 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42253942 TATGGTAACC
* * * *
42253952 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42254016 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42254032 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42254097 CCGG
66 CCGG
42254101 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42254042 original size:40 final size:38
Alignment explanation
Indices: 42253993--42254100 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42253983 ATCACGATTT
*
42253993 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42254033 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42254073 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42254101 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42259133 original size:80 final size:80
Alignment explanation
Indices: 42259049--42259197 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42259039 TATGGTAACC
* * * *
42259049 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42259113 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42259129 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42259194 CCGG
66 CCGG
42259198 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42259139 original size:40 final size:38
Alignment explanation
Indices: 42259090--42259197 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42259080 ATCACGATTT
*
42259090 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42259130 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42259170 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42259198 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42261625 original size:28 final size:29
Alignment explanation
Indices: 42261583--42261696 Score: 126
Period size: 29 Copynumber: 4.0 Consensus size: 29
42261573 TACCTGTATC
* * *
42261583 TGGCCTATTAAGCCC-AATCATATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
*
42261611 TGGCCCATTAGGCCCAAATCACCTGT-ATA
1 TGGCCCATTAGGCCCAAATCACAT-TCATA
*
42261640 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
* * *
42261669 TGGCTCGTTAGGCCC-AGTCACATTCATA
1 TGGCCCATTAGGCCCAAATCACATTCATA
42261697 ATCATGCTCA
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
28 25 0.34
29 48 0.65
30 1 0.01
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (29 bp):
TGGCCCATTAGGCCCAAATCACATTCATA
Found at i:42261644 original size:57 final size:58
Alignment explanation
Indices: 42261574--42261684 Score: 152
Period size: 58 Copynumber: 1.9 Consensus size: 58
42261564 AATTTCACAT
* * *
42261574 ACCTGTATCTGGCCTATTAAGCCC-AATCATATTCATATGGCCCATTAGGCCCAAATC
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
* * * *
42261631 ACCTGTATATGGCCCATTAGGCCCAAATCACATTTATATGGCTCGTTAGGCCCA
1 ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCA
42261685 GTCACATTCA
Statistics
Matches: 46, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
57 21 0.46
58 25 0.54
ACGTcount: A:0.27, C:0.29, G:0.16, T:0.28
Consensus pattern (58 bp):
ACCTGTATATGGCCCATTAAGCCCAAATCACATTCATATGGCCCATTAGGCCCAAATC
Found at i:42263893 original size:32 final size:32
Alignment explanation
Indices: 42263855--42263921 Score: 98
Period size: 32 Copynumber: 2.1 Consensus size: 32
42263845 CAAACCATCA
* *
42263855 CAATATCAATTGGGCCTAGCCCATCTCAAAAT
1 CAATATCAATTAGGCCTAGCCCATATCAAAAT
* *
42263887 CAATATCAGTTAGGCCTAGCCCATATCAGAAT
1 CAATATCAATTAGGCCTAGCCCATATCAAAAT
42263919 CAA
1 CAA
42263922 ACCCATATGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.36, C:0.27, G:0.13, T:0.24
Consensus pattern (32 bp):
CAATATCAATTAGGCCTAGCCCATATCAAAAT
Found at i:42264263 original size:27 final size:27
Alignment explanation
Indices: 42264231--42264292 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
42264221 GTAAACAGTC
* * * *
42264231 ATTTTACCCTACAGGGGTATTTTGGTA
1 ATTTTACACTACAAGGGTAGTTTAGTA
*
42264258 ATTTTACACTACAATGGTAGTTTAGTA
1 ATTTTACACTACAAGGGTAGTTTAGTA
42264285 ATTTTACA
1 ATTTTACA
42264293 AACTGAGGTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (27 bp):
ATTTTACACTACAAGGGTAGTTTAGTA
Found at i:42271382 original size:121 final size:120
Alignment explanation
Indices: 42271191--42271413 Score: 320
Period size: 121 Copynumber: 1.9 Consensus size: 120
42271181 CACAACAACA
* * *
42271191 ATGAGAATGAGAATAGAAATGTAATGGGTATGAGGTTTTCCTAATCTCAATTTAACACGAAACGT
1 ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTGTTCCTAAACTCAATTTAACACGAAACGT
* *
42271256 ATGATAACTAACCTAGGAATTCAAATTAAATGATAGACATTGGCATGGTAATAGC
66 ATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGTAATAGC
* * * * ** *
42271311 ATGAGAATAAGTATAGTAATGTCATGGTTATGAGGTGTTCCTATAACTTGATTTAACACGAAATG
1 ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTGTTCCTA-AACTCAATTTAACACGAAACG
*
42271376 TATGATAACTAACCTAAGAATGCAAATTAAGTGATAGA
65 TATGATAACTAACCTAAGAATGCAAATTAAATGATAGA
42271414 AAAATGAAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
120 37 0.42
121 52 0.58
ACGTcount: A:0.40, C:0.11, G:0.20, T:0.30
Consensus pattern (120 bp):
ATGAGAATAAGAATAGAAATGTAATGGGTATGAGGTGTTCCTAAACTCAATTTAACACGAAACGT
ATGATAACTAACCTAAGAATGCAAATTAAATGATAGACATTGGCATGGTAATAGC
Found at i:42280086 original size:22 final size:22
Alignment explanation
Indices: 42280058--42280113 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
42280048 AATGCCTAGT
*
42280058 AGGCTTAGTGCCAGTGCTATTC
1 AGGCTTAGTGCCAGTGCTATAC
* *
42280080 AGGCTTAGTGCCGGTGTTATAC
1 AGGCTTAGTGCCAGTGCTATAC
*
42280102 AGGCTTAATGCC
1 AGGCTTAGTGCC
42280114 TAGTAGGCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.20, C:0.21, G:0.29, T:0.30
Consensus pattern (22 bp):
AGGCTTAGTGCCAGTGCTATAC
Found at i:42280088 original size:60 final size:60
Alignment explanation
Indices: 42280015--42280151 Score: 186
Period size: 60 Copynumber: 2.3 Consensus size: 60
42280005 AGTGAGGTGT
* *
42280015 TATTCAGGTTTAGTGCTAGTGTTATCCAAGCTTAATGCCTAGTAGGCTTAG-TGCCAGTGC
1 TATTCAGGCTTAGTGCTAGTGTTATACAAGCTTAATGCCTAGTAGGCTTAGTTG-CAGTGC
** * * *
42280075 TATTCAGGCTTAGTGCCGGTGTTATACAGGCTTAATGCCTAGTAGGCTTAGTTGCGGTGT
1 TATTCAGGCTTAGTGCTAGTGTTATACAAGCTTAATGCCTAGTAGGCTTAGTTGCAGTGC
*
42280135 TATTCAGGCTTAATGCT
1 TATTCAGGCTTAGTGCT
42280152 TAGTAGGCTT
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
60 65 0.97
61 2 0.03
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (60 bp):
TATTCAGGCTTAGTGCTAGTGTTATACAAGCTTAATGCCTAGTAGGCTTAGTTGCAGTGC
Found at i:42280122 original size:38 final size:38
Alignment explanation
Indices: 42280080--42280161 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
42280070 AGTGCTATTC
42280080 AGGCTTAG-TGCCGGTGTTATACAGGCTTAATGCCTAGT
1 AGGCTTAGTTG-CGGTGTTATACAGGCTTAATGCCTAGT
* *
42280118 AGGCTTAGTTGCGGTGTTATTCAGGCTTAATGCTTAGT
1 AGGCTTAGTTGCGGTGTTATACAGGCTTAATGCCTAGT
42280156 AGGCTT
1 AGGCTT
42280162 GATGCCGATG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
38 39 0.95
39 2 0.05
ACGTcount: A:0.20, C:0.16, G:0.29, T:0.35
Consensus pattern (38 bp):
AGGCTTAGTTGCGGTGTTATACAGGCTTAATGCCTAGT
Found at i:42281927 original size:40 final size:39
Alignment explanation
Indices: 42281882--42282010 Score: 127
Period size: 40 Copynumber: 3.3 Consensus size: 39
42281872 CGGAACATAA
42281882 CCGGATATAACCATGTGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAACCAT-TGCACAAATGCCTTCGGGTCTTAGC
* * * *
42281922 CCGGATAGAATGTC-TCGCACGAATGCCTT-GGGTCTTAGC
1 CCGGATATAA--CCATTGCACAAATGCCTTCGGGTCTTAGC
* * * * *
42281961 CCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAACCA-TTGCACAAATGCCTTCGGGTCTTAGC
42282001 CCGGATATAA
1 CCGGATATAA
42282011 TTTCCAGCAT
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
37 1 0.01
39 29 0.41
40 38 0.54
41 1 0.01
42 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.25
Consensus pattern (39 bp):
CCGGATATAACCATTGCACAAATGCCTTCGGGTCTTAGC
Found at i:42282025 original size:40 final size:40
Alignment explanation
Indices: 42281898--42282048 Score: 139
Period size: 40 Copynumber: 3.8 Consensus size: 40
42281888 ATAACCATGT
* * *
42281898 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGTCTC-
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTC-CA
* ** * *
42281938 GCACGAA-TGCCTT-GGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42281977 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTCCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
* *
42282017 GCATAATTGTCTTCGGGAT-TTAGCCCGGATAT
1 GCACAATTGCCTTCGGG-TCTTAGCCCGGATAT
42282049 CATTCAATTT
Statistics
Matches: 89, Mismatches: 17, Indels: 10
0.77 0.15 0.09
Matches are distributed among these distances:
38 2 0.02
39 28 0.31
40 56 0.63
41 3 0.03
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAATCTCCA
Found at i:42285591 original size:19 final size:19
Alignment explanation
Indices: 42285569--42285608 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
42285559 AATGAAATTA
42285569 TATGTGATGTTGATGAACC
1 TATGTGATGTTGATGAACC
42285588 TATGTGATGTTGATGAACC
1 TATGTGATGTTGATGAACC
42285607 TA
1 TA
42285609 CTCAATTGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.28, C:0.10, G:0.25, T:0.38
Consensus pattern (19 bp):
TATGTGATGTTGATGAACC
Found at i:42286922 original size:2 final size:2
Alignment explanation
Indices: 42286915--42286946 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42286905 AAAGGAATTG
42286915 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42286947 GTTATTATAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42287422 original size:25 final size:25
Alignment explanation
Indices: 42287392--42287439 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
42287382 ATGATGGTAC
*
42287392 ATGATATAT-TGATATATTGAAATGG
1 ATGATATATGT-ATATAATGAAATGG
42287417 ATGATATATGTATATAATGAAAT
1 ATGATATATGTATATAATGAAAT
42287440 AATAAGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 20 0.95
26 1 0.05
ACGTcount: A:0.44, C:0.00, G:0.17, T:0.40
Consensus pattern (25 bp):
ATGATATATGTATATAATGAAATGG
Found at i:42290880 original size:30 final size:30
Alignment explanation
Indices: 42290846--42290906 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
42290836 TCCTTAACTC
42290846 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
42290876 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
42290906 A
1 A
42290907 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:42293850 original size:20 final size:20
Alignment explanation
Indices: 42293825--42293862 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42293815 GTCACATATA
42293825 TCATGAACTCAGACCACAAC
1 TCATGAACTCAGACCACAAC
* *
42293845 TCATGAGCTCAGATCACA
1 TCATGAACTCAGACCACA
42293863 TAGTTCCTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.32, G:0.13, T:0.18
Consensus pattern (20 bp):
TCATGAACTCAGACCACAAC
Found at i:42299048 original size:27 final size:27
Alignment explanation
Indices: 42299014--42299105 Score: 103
Period size: 27 Copynumber: 3.4 Consensus size: 27
42299004 ATGCAAAACA
* *
42299014 GTCATTTTACCCTATAGGGGTATGTCG
1 GTCATTTTACACTACAGGGGTATGTCG
*
42299041 GTCATTTTACACTACAGGGGTATTTCG
1 GTCATTTTACACTACAGGGGTATGTCG
* * * *
42299068 GTAATTATACACTACAAGGGTATTTCG
1 GTCATTTTACACTACAGGGGTATGTCG
* *
42299095 ATAATTTTACA
1 GTCATTTTACA
42299106 AATCGAGGGT
Statistics
Matches: 57, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (27 bp):
GTCATTTTACACTACAGGGGTATGTCG
Found at i:42299114 original size:27 final size:27
Alignment explanation
Indices: 42299058--42299558 Score: 581
Period size: 27 Copynumber: 18.6 Consensus size: 27
42299048 TACACTACAG
* * * *
42299058 GGGTATTTCGGTAATTATAC-ACTACAA
1 GGGTATTTCGATAATTTTACAAAT-CGA
42299085 GGGTATTTCGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* * *
42299112 GGGTGTTTCAATAATTTTACAAATTGA
1 GGGTATTTCGATAATTTTACAAATCGA
*
42299139 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* *
42299166 GCGTATTTC-AGTTATTTTACAAATCGA
1 GGGTATTTCGA-TAATTTTACAAATCGA
*
42299193 GGGTATTT-TAGTAATTTTACAAATCGA
1 GGGTATTTCGA-TAATTTTACAAATCGA
* * *
42299220 GGGTGTTTCAATAATTTTACAAATTGA
1 GGGTATTTCGATAATTTTACAAATCGA
*
42299247 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* * *
42299274 GCGTATTTCGGTTATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
*
42299301 GGGTATTTC-AGTAATTTTACAAATCAA
1 GGGTATTTCGA-TAATTTTACAAATCGA
* * *
42299328 TGGTGTTTTGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* *
42299355 GGGTGTTTCGGTAATTTTACAAAGT-GA
1 GGGTATTTCGATAATTTTACAAA-TCGA
*
42299382 GGGTATTTTGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
* *
42299409 GGGTGTTTCGATAATTTCACAAATCG-
1 GGGTATTTCGATAATTTTACAAATCGA
* *
42299435 GGGTATTTCGAAAACTTTACAAAAT-GA
1 GGGTATTTCGATAATTTTAC-AAATCGA
*
42299462 GGGTATTTC-AGTAATTTCAC-AATCGA
1 GGGTATTTCGA-TAATTTTACAAATCGA
*
42299488 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
42299515 GGGTATTTCGATAATTTTACAAATCGA
1 GGGTATTTCGATAATTTTACAAATCGA
42299542 GGGTATTTC-AGTAATTT
1 GGGTATTTCGA-TAATTT
42299559 CTCTTTATTA
Statistics
Matches: 407, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
25 3 0.01
26 39 0.10
27 360 0.88
28 5 0.01
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (27 bp):
GGGTATTTCGATAATTTTACAAATCGA
Found at i:42299208 original size:108 final size:109
Alignment explanation
Indices: 42299060--42299558 Score: 640
Period size: 108 Copynumber: 4.6 Consensus size: 109
42299050 CACTACAGGG
* * * *
42299060 GTATTTCGGTAATTATAC-ACTACAAGGGTA-TTTCGATAATTTTACAAATCGAGGGTGTTTCAA
1 GTATTTCGGTAATTTTACAAAT-CGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTCAA
42299123 TAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
65 TAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
* *
42299168 GTATTTCAGTTATTTTACAAATCGAGGGTATTTTAG-TAATTTTACAAATCGAGGGTGTTTCAAT
1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTCAAT
42299232 AATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
66 AATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
* * * * **
42299276 GTATTTCGGTTATTTTACAAATCGAGGGTATTTCAG-TAATTTTACAAATCAATGGTGTTTTGAT
1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTCAAT
* * *
42299340 AATTTTACAAATCGAGGGTGTTTCGGTAATTTTACAAAGT-GAGG
66 AATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAA-TCGAGC
* * * * * *
42299384 GTATTTTGATAATTTTACAAATCGAGGGT-GTTTCGATAATTTCACAAATCG-GGGTATTTCGAA
1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTC-AA
* * * * *
42299447 -AACTTTACAAAATGAGGGTATTTCAGTAATTTCAC-AATCGAGG
65 TAATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
* * *
42299490 GTATTTCGGTAATTTTACAAATCGAGGGTA-TTTCGATAATTTTACAAATCGAGGGTATTTCAGT
1 GTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTCAAT
42299554 AATTT
66 AATTT
42299559 CTCTTTATTA
Statistics
Matches: 344, Mismatches: 38, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
105 1 0.00
106 54 0.16
107 51 0.15
108 231 0.67
109 7 0.02
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.38
Consensus pattern (109 bp):
GTATTTCGGTAATTTTACAAATCGAGGGTATTTTAGATAATTTTACAAATCGAGGGTGTTTCAAT
AATTTTACAAATTGAGGGTATTTCGGTAATTTTACAAATCGAGC
Found at i:42300275 original size:27 final size:27
Alignment explanation
Indices: 42300241--42300317 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
42300231 ATGCAAAACA
*
42300241 GTCATTTTACCCTACAGGGGTATGTCG
1 GTCATTTTACACTACAGGGGTATGTCG
*
42300268 GTCATTTTACACTACAGGGGTATTTCG
1 GTCATTTTACACTACAGGGGTATGTCG
* * * *
42300295 GTAATTATAAACTACAAGGGTAT
1 GTCATTTTACACTACAGGGGTAT
42300318 TTCAATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (27 bp):
GTCATTTTACACTACAGGGGTATGTCG
Found at i:42300784 original size:27 final size:27
Alignment explanation
Indices: 42300285--42300784 Score: 545
Period size: 27 Copynumber: 18.6 Consensus size: 27
42300275 TACACTACAG
* * * *
42300285 GGGTATTTCGGTAATTATA-AACTACAA
1 GGGTATTTCAGTAATTTTACAAAT-CGA
*
42300312 GGGTATTTCAATAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* * *
42300339 GGGTGTTTCAATAATTTTACAAATTGA
1 GGGTATTTCAGTAATTTTACAAATCGA
*
42300366 GGGTATTTCGGTAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
42300393 GCGTATTTCAGTTATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
*
42300420 GGGTATTTCAGTAATTTTACAAATCAA
1 GGGTATTTCAGTAATTTTACAAATCGA
*
42300447 TGGTGT-TTTGA-TAATTTTACAAATCGA
1 -GG-GTATTTCAGTAATTTTACAAATCGA
* * *
42300474 GGGTGTTTCGGTAATTTTACAAAGCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* * *
42300501 GGGTGTTTCAGTAATTTCACAAATCGG
1 GGGTATTTCAGTAATTTTACAAATCGA
*
42300528 GGGTATTTCAATAATTTTACAAATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
42300555 GGGTATTTAAGTAATTTCAC-AATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
42300581 GGGTATTTTAGTAATTTTACAAATCAA
1 GGGTATTTCAGTAATTTTACAAATCGA
* *
42300608 GGGTATTT-TGATAATTTTACAAATCAA
1 GGGTATTTCAG-TAATTTTACAAATCGA
* *
42300635 GGGTGTTTC-GATAATTTCACAAATC-A
1 GGGTATTTCAG-TAATTTTACAAATCGA
* * *
42300661 GGGGTATTTC-GAAAACTTTACAAAACGA
1 -GGGTATTTCAG-TAATTTTACAAATCGA
* *
42300689 GGGTATTTTAGTAATTTCAC-AATCGA
1 GGGTATTTCAGTAATTTTACAAATCGA
*
42300715 GGGTATTTCGGTAATTTTACAAATCG-
1 GGGTATTTCAGTAATTTTACAAATCGA
42300741 GGGTATTTC-GATAATTTTACAAATCGA
1 GGGTATTTCAG-TAATTTTACAAATCGA
42300768 GGGTATTTCAGTAATTT
1 GGGTATTTCAGTAATTT
42300785 CTCTTTATTA
Statistics
Matches: 406, Mismatches: 52, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
25 3 0.01
26 77 0.19
27 312 0.77
28 12 0.03
29 2 0.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (27 bp):
GGGTATTTCAGTAATTTTACAAATCGA
Found at i:42304034 original size:27 final size:27
Alignment explanation
Indices: 42303955--42304048 Score: 118
Period size: 27 Copynumber: 3.5 Consensus size: 27
42303945 CAATGCAAAA
* * * *
42303955 CAGTTATTTTACCCTACAGGGGTATGT
1 CAGTAATTTTACACTACAAGGGTATTT
*
42303982 CAGTCATTTTACACTACAAGGGTATTT
1 CAGTAATTTTACACTACAAGGGTATTT
*
42304009 CAGTAATTTTACACTACAAGGGTATTG
1 CAGTAATTTTACACTACAAGGGTATTT
42304036 C-GATAATTTTACA
1 CAG-TAATTTTACA
42304049 AATCGGGGGT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
26 1 0.02
27 59 0.98
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.36
Consensus pattern (27 bp):
CAGTAATTTTACACTACAAGGGTATTT
Found at i:42304058 original size:27 final size:27
Alignment explanation
Indices: 42304000--42304286 Score: 272
Period size: 27 Copynumber: 10.7 Consensus size: 27
42303990 TTACACTACA
* * *
42304000 AGGGTATTTCAGTAATTTTAC-ACTACA
1 AGGGTATTTCGGTAATTTTACAAAT-CG
* *
42304027 AGGGTATTGCGATAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
42304054 GGGGTGTTTTGGTAATTTTACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
42304081 AGGGTATTTTGGTAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCG
* * * *
42304108 AGGGTGTTTCGATAATTTTAAAAATTG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
42304135 AAGGTGTTTCGGTAATTTTAAAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
** * * *
42304162 AGAATGTTTTGGTAATTTCACAAATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* * *
42304189 GGGGTATTTCGATAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCG
42304216 AGGGTATTTCGGTAATTTTAC-AATCG
1 AGGGTATTTCGGTAATTTTACAAATCG
* ** *
42304242 ATGGTATTTTAGTAATTTTACAAATCA
1 AGGGTATTTCGGTAATTTTACAAATCG
* *
42304269 AAGGTATTTCAGTAATTT
1 AGGGTATTTCGGTAATTT
42304287 CTCTTTATTA
Statistics
Matches: 213, Mismatches: 45, Indels: 4
0.81 0.17 0.02
Matches are distributed among these distances:
26 22 0.10
27 189 0.89
28 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCGGTAATTTTACAAATCG
Found at i:42304096 original size:81 final size:81
Alignment explanation
Indices: 42304000--42304286 Score: 337
Period size: 81 Copynumber: 3.6 Consensus size: 81
42303990 TTACACTACA
* * * * *
42304000 AGGGTATTTCAGTAATTTTAC-ACTACAAGGGTATTGCGATAATTTTACAAATCGGGGGTGTTTT
1 AGGGTATTTTAGTAATTTTACAAAT-CAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTC
42304064 GGTAATTTTACAAATCG
65 GGTAATTTTACAAATCG
* * * * *
42304081 AGGGTATTTTGGTAATTTTACAAATCAAGGGTGTTTCGATAATTTTAAAAATTGAAGGTGTTTCG
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
*
42304146 GTAATTTTAAAAATCG
66 GTAATTTTACAAATCG
** * * * ** * *
42304162 AGAATGTTTTGGTAATTTCACAAATCGGGGGTATTTCGATAATTTTACAAATCAAGGGTATTTCG
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
42304227 GTAATTTTAC-AATCG
66 GTAATTTTACAAATCG
* *
42304242 ATGGTATTTTAGTAATTTTACAAATCAAAGGTATTTC-AGTAATTT
1 AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGA-TAATTT
42304287 CTCTTTATTA
Statistics
Matches: 171, Mismatches: 33, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
79 1 0.01
80 39 0.23
81 129 0.75
82 2 0.01
ACGTcount: A:0.32, C:0.09, G:0.20, T:0.39
Consensus pattern (81 bp):
AGGGTATTTTAGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATCGAGGGTGTTTCG
GTAATTTTACAAATCG
Found at i:42304633 original size:28 final size:28
Alignment explanation
Indices: 42304593--42304665 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
42304583 CTTATTCATT
* * * *
42304593 TGGCCCTTTAGGCCCAATCTCGTTCACA
1 TGGCCCATCAGGCCCAATCACATTCACA
*
42304621 TGGCCCATCAGGCCCAATCACATTCATA
1 TGGCCCATCAGGCCCAATCACATTCACA
42304649 TGGCCCATCAGGCCCAA
1 TGGCCCATCAGGCCCAA
42304666 CTACTTCCCA
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (28 bp):
TGGCCCATCAGGCCCAATCACATTCACA
Found at i:42308640 original size:42 final size:42
Alignment explanation
Indices: 42308594--42308679 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
42308584 ATATGTACAT
42308594 AGTCCTTTATTTGGGTCTACGAAACTCAAATCATACTTTAGA
1 AGTCCTTTATTTGGGTCTACGAAACTCAAATCATACTTTAGA
42308636 AGTCCTTTATTTGGGTCTACGAAACTCAAATCATACTTTAGA
1 AGTCCTTTATTTGGGTCTACGAAACTCAAATCATACTTTAGA
42308678 AG
1 AG
42308680 GGTTCGGGAC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.35
Consensus pattern (42 bp):
AGTCCTTTATTTGGGTCTACGAAACTCAAATCATACTTTAGA
Found at i:42319240 original size:28 final size:29
Alignment explanation
Indices: 42319173--42319273 Score: 125
Period size: 28 Copynumber: 3.5 Consensus size: 29
42319163 ATAGTGAATC
*
42319173 CGCACACTTAGTGCTATATACATTC-AGCT
1 CGCACACTTAGTGCTATATA-ATTCAAACT
42319202 CGCACACTTAGTGCTATATAA-TCAAACT
1 CGCACACTTAGTGCTATATAATTCAAACT
* * * *
42319230 CGCACACTTAGTGCTGTACAATTTTAAACC
1 CGCACACTTAGTGCTATATAA-TTCAAACT
42319260 CGCACACTTAGTGC
1 CGCACACTTAGTGC
42319274 CAATCTTGTC
Statistics
Matches: 64, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
27 2 0.03
28 23 0.36
29 20 0.31
30 19 0.30
ACGTcount: A:0.30, C:0.28, G:0.14, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCTATATAATTCAAACT
Found at i:42322100 original size:31 final size:31
Alignment explanation
Indices: 42322054--42322132 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
42322044 TTTAACGGCT
*
42322054 ACTGGGCTGAAGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
42322085 ACTGGGTCGACGCCTTTTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
42322116 ATTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
42322133 ACTGTAAACG
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:42323229 original size:27 final size:26
Alignment explanation
Indices: 42323199--42323300 Score: 80
Period size: 27 Copynumber: 3.8 Consensus size: 26
42323189 GGGCATATTC
42323199 GTCATTTTACCATACAAGGGTATTACA
1 GTCATTTTACC-TACAAGGGTATTACA
* * *
42323226 GTCACTTTACCCTACAGGGGCT-TTACG
1 GTCATTTTA-CCTACAAGGG-TATTACA
* * **
42323253 GTCTTTTTACCTATTAAGGGTATTTTA
1 GTCATTTTACCTA-CAAGGGTATTACA
*
42323280 GTCATTTCATCCTACAAGGGT
1 GTCATTTTA-CCTACAAGGGT
42323301 GTTTTGGTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 10
0.71 0.16 0.12
Matches are distributed among these distances:
26 5 0.09
27 45 0.79
28 7 0.12
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.37
Consensus pattern (26 bp):
GTCATTTTACCTACAAGGGTATTACA
Found at i:42323347 original size:27 final size:27
Alignment explanation
Indices: 42323321--42323626 Score: 192
Period size: 27 Copynumber: 11.3 Consensus size: 27
42323311 ATCTACAAAC
* *
42323321 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*
42323348 CAATGGTATTTCTA-TAACTTTTAG-AAAGT
1 CAAGGGTATTT-TAGTAA-TTTT-GTAAA-T
*
42323377 CAAGGGTATTTTTGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* **
42323404 C-AGTGGTATTTTGGTAATTTTACAAA-
1 CAAG-GGTATTTTAGTAATTTTGTAAAT
* * **
42323430 CTAGGGGTATTTTGGTAATTTTACAAAT
1 C-AAGGGTATTTTAGTAATTTTGTAAAT
** ** ** *
42323458 TGAGGGTATTTCGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
** *
42323485 CAAGGGTATTTTAGTAATTTTACAGA-
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* * * *
42323511 CTAGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTT-GTAAAT
* * *
42323538 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTGTAAAT
*
42323565 CAATGGTATTTTAGTAATTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
* **** *
42323592 CGAGGGTAAAACAGTAATTCTGTAAAT
1 CAAGGGTATTTTAGTAATTTTGTAAAT
42323619 CAAGGGTA
1 CAAGGGTA
42323627 AAACAGTAAT
Statistics
Matches: 227, Mismatches: 39, Indels: 26
0.78 0.13 0.09
Matches are distributed among these distances:
26 25 0.11
27 171 0.75
28 17 0.07
29 14 0.06
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.40
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTGTAAAT
Found at i:42323554 original size:80 final size:81
Alignment explanation
Indices: 42323317--42323585 Score: 301
Period size: 80 Copynumber: 3.3 Consensus size: 81
42323307 GTAAATCTAC
* ** * ** * * *
42323317 AAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTATTTCT-ATAACTTTTAGAAAGTCAAG
1 AAACCAAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTT-TGGTAA-TTTTACAAA-TCGAG
*
42323381 GGTATTTTTGTAATTTTGT
63 GGTATTTTGGTAATTTTGT
* * *
42323400 AAATC-AGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATTGAGGG
1 AAACCAAG-GGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATCGAGGG
* **
42323464 TATTTCGGTAATTTTAC
65 TATTTTGGTAATTTTGT
* **
42323481 AAACCAAGGGTATTTTAGTAATTTTACAGACTA-GGGTATTTTGGTAATTTTACTGATCGAGGGT
1 AAACCAAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATCGAGGGT
42323545 ATTTTGGTAATTTTGT
66 ATTTTGGTAATTTTGT
*
42323561 AAACCAATGGTATTTTAGTAATTTT
1 AAACCAAGGGTATTTTAGTAATTTT
42323586 GTAAATCGAG
Statistics
Matches: 157, Mismatches: 26, Indels: 9
0.82 0.14 0.05
Matches are distributed among these distances:
80 65 0.41
81 45 0.29
82 13 0.08
83 34 0.22
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.42
Consensus pattern (81 bp):
AAACCAAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAATCGAGGGT
ATTTTGGTAATTTTGT
Found at i:42323594 original size:54 final size:54
Alignment explanation
Indices: 42323302--42323599 Score: 251
Period size: 54 Copynumber: 5.5 Consensus size: 54
42323292 TACAAGGGTG
* * * *
42323302 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
* * * * *
42323356 TTTCT-ATAACTTTTAGAAAGTCAAGGGTATTTTTGTAATTTTGTAAATCAGTGGTA
1 TTT-TGGTAA-TTTTACAAA-TCAAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
* * ** *** *
42323412 TTTTGGTAATTTTACAAA-CTAGGGGTATTTTGGTAATTTTACAAATTGAGGGTA
1 TTTTGGTAATTTTACAAATC-AAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
* * ** * * *
42323466 TTTCGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTACAGA-CTAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
** * *
42323519 TTTTGGTAATTTTACTGATCGAGGGTATTTTGGTAATTTTGTAAACCAATGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
* ** *
42323573 TTTTAGTAATTTTGTAAATCGAGGGTA
1 TTTTGGTAATTTTACAAATCAAGGGTA
42323600 AAACAGTAAT
Statistics
Matches: 196, Mismatches: 41, Indels: 14
0.78 0.16 0.06
Matches are distributed among these distances:
53 43 0.22
54 99 0.51
55 17 0.09
56 37 0.19
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (54 bp):
TTTTGGTAATTTTACAAATCAAGGGTATTTTAGTAATTTTGTAAACCAATGGTA
Found at i:42323715 original size:27 final size:27
Alignment explanation
Indices: 42323379--42323721 Score: 235
Period size: 27 Copynumber: 12.7 Consensus size: 27
42323369 TAGAAAGTCA
* *
42323379 AGGGTATTTTTGTAATTTTGTAAATC-
1 AGGGTATTTTGGTAATTTTATAAATCG
* *
42323405 AGTGGTATTTTGGTAATTTTACAAA-CT
1 AG-GGTATTTTGGTAATTTTATAAATCG
* *
42323432 AGGGGTATTTTGGTAATTTTACAAATTG
1 A-GGGTATTTTGGTAATTTTATAAATCG
* * * *
42323460 AGGGTATTTCGGTAATTTTACAAACCA
1 AGGGTATTTTGGTAATTTTATAAATCG
* * * *
42323487 AGGGTATTTTAGTAATTTTACAGA-CT
1 AGGGTATTTTGGTAATTTTATAAATCG
*
42323513 AGGGTATTTTGGTAATTTTACT-GATCG
1 AGGGTATTTTGGTAATTTTA-TAAATCG
* * *
42323540 AGGGTATTTTGGTAATTTTGTAAACCA
1 AGGGTATTTTGGTAATTTTATAAATCG
* * *
42323567 ATGGTATTTTAGTAATTTTGTAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
***** * * *
42323594 AGGGTAAAACAGTAATTCTGTAAATCA
1 AGGGTATTTTGGTAATTTTATAAATCG
***** *
42323621 AGGGTAAAACAGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
*** *
42323648 AGGGTAAAATGGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
**** *
42323675 AGGGTAAAACGGTAATTCTATAAATCG
1 AGGGTATTTTGGTAATTTTATAAATCG
42323702 AGGGTATTTTGGTAATTTTA
1 AGGGTATTTTGGTAATTTTA
42323722 CAATTTGAGG
Statistics
Matches: 269, Mismatches: 41, Indels: 13
0.83 0.13 0.04
Matches are distributed among these distances:
26 26 0.10
27 241 0.90
28 2 0.01
ACGTcount: A:0.33, C:0.08, G:0.21, T:0.38
Consensus pattern (27 bp):
AGGGTATTTTGGTAATTTTATAAATCG
Found at i:42326833 original size:40 final size:39
Alignment explanation
Indices: 42326802--42326901 Score: 128
Period size: 39 Copynumber: 2.5 Consensus size: 39
42326792 TGGACTAGGA
42326802 TCCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAG
1 TCCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAG
* * * * * * *
42326841 CCCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAG
1 TCCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAG
42326880 TCCCGAAGGCATTCGTGCGAGT
1 T-CCGAAGGCATTCGTGCGAGT
42326902 CACTATAACC
Statistics
Matches: 50, Mismatches: 10, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 32 0.64
40 18 0.36
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (39 bp):
TCCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAG
Found at i:42326850 original size:39 final size:40
Alignment explanation
Indices: 42326803--42326941 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 40
42326793 GGACTAGGAT
* *
42326803 CCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAG-C
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
* * * *
42326842 CCGAAGGCATTTGTGCAAGTTACTAAACCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
* * **
42326882 CCGAAGGCATTCGTGCGAGTCACTATAA-CCGGGCTTCGTC
1 CCGAAGGCATTCGTGCGAGTTAATA-AACCCGGGCTAAGTC
* *
42326922 CCGAAGGCATTTGAGCGAGT
1 CCGAAGGCATTCGTGCGAGT
42326942 CGTTATATCC
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
39 32 0.38
40 50 0.60
41 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTAATAAACCCGGGCTAAGTC
Found at i:42326965 original size:79 final size:79
Alignment explanation
Indices: 42326802--42326967 Score: 174
Period size: 79 Copynumber: 2.1 Consensus size: 79
42326792 TGGACTAGGA
* * * *
42326802 TCCGAAGGCATTCGTGCGAGTTAATAAATCTGGGCTAAGCCCGAAGGCATTTGTGCAAGTTACTA
1 TCCGAAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTA
*
42326867 AACCCGGGTTAAGT
66 AACCCGGGTTAAAT
* * ** * **
42326881 CCCGAAGGCATTCGTGCGAGTCACTATAA-CCGGGCTTCGTCCCGAAGGCATTTGAGCGAGTCGT
1 TCCGAAGGCATTCGTGCGAGTCAATA-AATCCGGGCTAAG-CCCGAAGGCATTTGAGCAAGTCAC
* *
42326945 TATATCC-GGTTAAAT
64 TAAACCCGGGTTAAAT
42326960 TCCGAAGG
1 TCCGAAGG
42326968 TACGTGATTC
Statistics
Matches: 70, Mismatches: 15, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
79 44 0.63
80 26 0.37
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (79 bp):
TCCGAAGGCATTCGTGCGAGTCAATAAATCCGGGCTAAGCCCGAAGGCATTTGAGCAAGTCACTA
AACCCGGGTTAAAT
Found at i:42328596 original size:42 final size:42
Alignment explanation
Indices: 42328447--42328602 Score: 134
Period size: 42 Copynumber: 3.6 Consensus size: 42
42328437 GGGTGCCAAA
* * * * *
42328447 GCCATGTCCCAGACATGGTCTTACATCGGACCACACATAGAT
1 GCCATATCCCAGACATGGTCTTATATCAGACCACATATCGAT
* * * *
42328489 GCCATATCCCAGATATGGTCTTATA-CGAAGCCTCAAATCAGTGCCGAC
1 GCCATATCCCAGACATGGTCTTATATC--AGAC-CACAT-A-T--CGAT
**
42328537 GCCATGCCCCAGACATGGTCTTATATCAGACCACATATCGAT
1 GCCATATCCCAGACATGGTCTTATATCAGACCACATATCGAT
*
42328579 GCCATATCCCTGACATGGTCTTAT
1 GCCATATCCCAGACATGGTCTTAT
42328603 TCAAAATCAC
Statistics
Matches: 88, Mismatches: 18, Indels: 16
0.72 0.15 0.13
Matches are distributed among these distances:
41 1 0.01
42 46 0.52
43 2 0.02
44 4 0.05
45 2 0.02
46 5 0.06
47 3 0.03
48 24 0.27
49 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.24
Consensus pattern (42 bp):
GCCATATCCCAGACATGGTCTTATATCAGACCACATATCGAT
Found at i:42328631 original size:90 final size:90
Alignment explanation
Indices: 42328442--42328651 Score: 231
Period size: 90 Copynumber: 2.3 Consensus size: 90
42328432 AAATAGGGTG
* *
42328442 CCAAAGCCATGTCCCAGACATGGTCTTACATCGGACCACACATAGATGCCATATCCCAGATATGG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATCAGACCACACATAGATGCCATATCCCAGACATGG
* * * * *
42328507 TCTTATACGAAGCCTCAAATCAGTG
66 TCTTATACAAAACCACAAATCAATA
* * * * * * *
42328532 CCGACGCCATGCCCCAGACATGGTCTTATATCAGACCACATATCGATGCCATATCCCTGACATGG
1 CCAAAGCCATGTCCCAGACATGGTCTTACATCAGACCACACATAGATGCCATATCCCAGACATGG
* * **
42328597 TCTTATTCAAAATCACTTATCAATA
66 TCTTATACAAAACCACAAATCAATA
* * *
42328622 CCAAAGCCATATCCCTGATATGGTCTTACA
1 CCAAAGCCATGTCCCAGACATGGTCTTACA
42328652 CGGGATCGCG
Statistics
Matches: 95, Mismatches: 25, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
90 95 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (90 bp):
CCAAAGCCATGTCCCAGACATGGTCTTACATCAGACCACACATAGATGCCATATCCCAGACATGG
TCTTATACAAAACCACAAATCAATA
Found at i:42339495 original size:25 final size:29
Alignment explanation
Indices: 42339441--42339505 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 29
42339431 TTATTTTCAC
42339441 TTTTATCTTTATTTATCTTCTTTAAGTACT-
1 TTTTAT-TTTATTTATC-TCTTTAAGTACTA
42339471 TTTTATTTTATTT-TC-CTTTAA-TACTA
1 TTTTATTTTATTTATCTCTTTAAGTACTA
*
42339497 TTTCATTTT
1 TTTTATTTT
42339506 TAGGTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 4 0.12
26 14 0.42
28 2 0.06
29 7 0.21
30 6 0.18
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (29 bp):
TTTTATTTTATTTATCTCTTTAAGTACTA
Found at i:42345583 original size:40 final size:40
Alignment explanation
Indices: 42345528--42345703 Score: 248
Period size: 40 Copynumber: 4.4 Consensus size: 40
42345518 GATGATAACT
*
42345528 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACAATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
42345568 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* *
42345608 GGGCTAAGTCCCGAAGGCATTGGTGCAAGTTACTATATCC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
* * *
42345648 GGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATA-CC
1 GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATATCC
* * *
42345687 CGGTTAAATCCCGAAGG
1 GGGCTAAGTCCCGAAGG
42345704 TACTTGGCTT
Statistics
Matches: 124, Mismatches: 11, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
39 17 0.14
40 107 0.86
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.24
Consensus pattern (40 bp):
GGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATATCC
Found at i:42353362 original size:39 final size:40
Alignment explanation
Indices: 42353243--42353458 Score: 280
Period size: 39 Copynumber: 5.5 Consensus size: 40
42353233 TGGATGATAA
*
42353243 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAGT-T
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-TAT
* * *
42353283 CCGGGCTAAGTCCGGAAGGCATTTGTGTGAGTTACAATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
42353323 CCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
42353362 CCGGGCTAAGTCCCGAAGGCATTGGTGC-AGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
* * *
42353401 CCGGGCTATGTCCCGAAGGCATTCGAGCGAG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
* * *
42353441 -CTGGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
42353459 TACTTGGCTT
Statistics
Matches: 157, Mismatches: 15, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
39 90 0.57
40 67 0.43
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:42353380 original size:79 final size:79
Alignment explanation
Indices: 42353243--42353432 Score: 278
Period size: 79 Copynumber: 2.4 Consensus size: 79
42353233 TGGATGATAA
*
42353243 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAGTTCCGGGCTAAGTCCGGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCA-TTG
42353308 TGTG-AGTTACAATAT
65 -GTGCAGTTACAATAT
*
42353323 CCGGGCTAAGTCCCGAAGGC-TTTGTGCGAGTTACTA-TATCCGGGCTAAGTCCCGAAGGCATTG
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAGT-TCCGGGCTAAGTCCCGAAGGCATTG
*
42353386 GTGCAGTTACTATAT
65 GTGCAGTTACAATAT
* * *
42353401 CCGGGCTATGTCCCGAAGGCATTCGAGCGAGT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGT
42353433 AGCTATATCT
Statistics
Matches: 101, Mismatches: 6, Indels: 7
0.89 0.05 0.06
Matches are distributed among these distances:
77 3 0.03
78 33 0.33
79 45 0.45
80 20 0.20
ACGTcount: A:0.22, C:0.23, G:0.31, T:0.25
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTGACTAGTTCCGGGCTAAGTCCCGAAGGCATTGG
TGCAGTTACAATAT
Found at i:42355306 original size:47 final size:48
Alignment explanation
Indices: 42355231--42355362 Score: 187
Period size: 48 Copynumber: 2.8 Consensus size: 48
42355221 CTCAATCGAT
* * * *
42355231 AAGTACCTATACCATGGCCTGTAACCAAATCAATGTAAC-CTATC-CTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCT-TCTCCA
*
42355278 GAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCTTCTCCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCTTCTCCA
*
42355326 AAATACCTATACCATGGCCCGTAGCCAAATCAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
42355363 TAAATTGCAC
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
47 37 0.49
48 39 0.51
ACGTcount: A:0.34, C:0.29, G:0.14, T:0.23
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCTTCTCCA
Found at i:42355500 original size:21 final size:21
Alignment explanation
Indices: 42355474--42355531 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
42355464 TTTCCAATAC
42355474 CAAATCATAGTCGAATCATT-T
1 CAAATCAT-GTCGAATCATTGT
*
42355495 CAAATCACTGTTGAATCATTGT
1 CAAATCA-TGTCGAATCATTGT
*
42355517 CCAATCATGGTCGAA
1 CAAATCAT-GTCGAA
42355532 CAAGTTCATA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
21 18 0.58
22 13 0.42
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.31
Consensus pattern (21 bp):
CAAATCATGTCGAATCATTGT
Found at i:42357310 original size:48 final size:45
Alignment explanation
Indices: 42357222--42357368 Score: 140
Period size: 44 Copynumber: 3.3 Consensus size: 45
42357212 GAAAAACTCT
* * * *
42357222 CACACTTAGTGCCAAATA-A-ATAG-TCGAAGCTATATGAATCTCG
1 CACACTAAGTGCTAAATATATATAGCT-GAAGCTATCTCAATCTCG
* *
42357265 CACACCAAGTGCCAATATATATATATAGCTGAAGCTATCTCAATCTCG
1 CACACTAAGTG-C--TAAATATATATAGCTGAAGCTATCTCAATCTCG
* ** *
42357313 CACACTAAGTG-TAAATATATATAGTTGAAGCTATCTTGATTTCG
1 CACACTAAGTGCTAAATATATATAGCTGAAGCTATCTCAATCTCG
42357357 CACACTAAGTGC
1 CACACTAAGTGC
42357369 ACATAATTAG
Statistics
Matches: 85, Mismatches: 12, Indels: 12
0.78 0.11 0.11
Matches are distributed among these distances:
43 9 0.11
44 40 0.47
46 4 0.05
47 1 0.01
48 30 0.35
49 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (45 bp):
CACACTAAGTGCTAAATATATATAGCTGAAGCTATCTCAATCTCG
Found at i:42357893 original size:21 final size:21
Alignment explanation
Indices: 42357869--42357908 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
42357859 ATTTGTATAA
*
42357869 CTATCATCAAACATTCAAAAT
1 CTATCATCAAACATCCAAAAT
* *
42357890 CTATGATTAAACATCCAAA
1 CTATCATCAAACATCCAAA
42357909 TACTCATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.47, C:0.23, G:0.03, T:0.28
Consensus pattern (21 bp):
CTATCATCAAACATCCAAAAT
Found at i:42360807 original size:18 final size:18
Alignment explanation
Indices: 42360784--42360839 Score: 67
Period size: 18 Copynumber: 3.1 Consensus size: 18
42360774 CTGGATGGGT
42360784 CTGCACTGATTACTGTTA
1 CTGCACTGATTACTGTTA
* *
42360802 CTGCACCGATTACTATTA
1 CTGCACTGATTACTGTTA
* * *
42360820 CTACACTGTTTATTGTTA
1 CTGCACTGATTACTGTTA
42360838 CT
1 CT
42360840 ATAATGGGCC
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (18 bp):
CTGCACTGATTACTGTTA
Found at i:42365657 original size:40 final size:40
Alignment explanation
Indices: 42365612--42365778 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
42365602 CGGAATATAA
42365612 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
42365652 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
42365692 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
42365732 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
42365771 CCGGATAT
1 CCGGATAT
42365779 TATTCAATTT
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:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:42371922 original size:32 final size:32
Alignment explanation
Indices: 42371885--42371948 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
42371875 ATGATCTTGA
42371885 ATGTGTTTTGAAGTATTTGATGGATTATTAAT
1 ATGTGTTTTGAAGTATTTGATGGATTATTAAT
42371917 ATGTGTTTTGAAGTATTTGATGGATTATTAAT
1 ATGTGTTTTGAAGTATTTGATGGATTATTAAT
42371949 CTTAGTTGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (32 bp):
ATGTGTTTTGAAGTATTTGATGGATTATTAAT
Found at i:42373797 original size:24 final size:24
Alignment explanation
Indices: 42373769--42373829 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
42373759 AACCGTATTT
* *
42373769 GCACACATAGTGCTA-ATTACACTC
1 GCACACATAGTGCCATAGTACAC-C
*
42373793 GCACACATAGTGCCATAGTATACC
1 GCACACATAGTGCCATAGTACACC
42373817 GCACACATAGTGC
1 GCACACATAGTGC
42373830 ATTGGATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 28 0.85
25 5 0.15
ACGTcount: A:0.33, C:0.30, G:0.16, T:0.21
Consensus pattern (24 bp):
GCACACATAGTGCCATAGTACACC
Found at i:42384696 original size:38 final size:38
Alignment explanation
Indices: 42384546--42384689 Score: 207
Period size: 38 Copynumber: 3.8 Consensus size: 38
42384536 TCAAATGCAG
*
42384546 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGTGCCAA
1 TGTTATTCAAGCTTAATGCCTAGCAGGCTTAGTGCCAA
* *
42384584 TGTTATTCAAGCTTAGTGCCTAGCAGGCTTAGAGCCAA
1 TGTTATTCAAGCTTAATGCCTAGCAGGCTTAGTGCCAA
* * *
42384622 TGTTATTCAGGCTTAATGCCTAGCAAGCTTAGTGCCGA
1 TGTTATTCAAGCTTAATGCCTAGCAGGCTTAGTGCCAA
* * *
42384660 TCTTATTCAGGCTTAATGCCTAGTAGGCTT
1 TGTTATTCAAGCTTAATGCCTAGCAGGCTT
42384690 GATGCCGGTG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 97 1.00
ACGTcount: A:0.24, C:0.21, G:0.23, T:0.33
Consensus pattern (38 bp):
TGTTATTCAAGCTTAATGCCTAGCAGGCTTAGTGCCAA
Found at i:42385232 original size:21 final size:23
Alignment explanation
Indices: 42385192--42385234 Score: 63
Period size: 21 Copynumber: 1.9 Consensus size: 23
42385182 ATGAATAAGG
42385192 ATGTTTGAAATGAAATATTTAGGT
1 ATGTTTGAAATG-AATATTTAGGT
42385216 ATGTTTG-AATG-ATATTTAG
1 ATGTTTGAAATGAATATTTAG
42385235 ATCCCTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (23 bp):
ATGTTTGAAATGAATATTTAGGT
Found at i:42389915 original size:39 final size:39
Alignment explanation
Indices: 42389861--42389940 Score: 142
Period size: 39 Copynumber: 2.1 Consensus size: 39
42389851 GAAGCATAAA
*
42389861 GAGTTGCTAGAGTTGAAACAAACCTGGATGACTGTCACT
1 GAGTTGCTAGAGTTGAAACAAACCGGGATGACTGTCACT
*
42389900 GAGTTGCTAGAGTTGAAACAAGCCGGGATGACTGTCACT
1 GAGTTGCTAGAGTTGAAACAAACCGGGATGACTGTCACT
42389939 GA
1 GA
42389941 TTATGAAATA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.30, C:0.17, G:0.29, T:0.24
Consensus pattern (39 bp):
GAGTTGCTAGAGTTGAAACAAACCGGGATGACTGTCACT
Found at i:42393716 original size:15 final size:17
Alignment explanation
Indices: 42393696--42393728 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42393686 ATACATAATG
42393696 TGTTTC-ATG-TATCAA
1 TGTTTCGATGATATCAA
42393711 TGTTTCGATGATATCAA
1 TGTTTCGATGATATCAA
42393728 T
1 T
42393729 CCGGCCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 3 0.19
17 7 0.44
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.45
Consensus pattern (17 bp):
TGTTTCGATGATATCAA
Found at i:42400728 original size:16 final size:16
Alignment explanation
Indices: 42400702--42400746 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 16
42400692 TATGAATCGA
*
42400702 CAAAA-GCCGAAATAC
1 CAAAATGCCGAAAAAC
*
42400717 CGAAATGCCGAAAAAC
1 CAAAATGCCGAAAAAC
*
42400733 TAAAATGCCGAAAA
1 CAAAATGCCGAAAA
42400747 GCCGAAAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
15 4 0.16
16 21 0.84
ACGTcount: A:0.53, C:0.22, G:0.16, T:0.09
Consensus pattern (16 bp):
CAAAATGCCGAAAAAC
Found at i:42401019 original size:29 final size:29
Alignment explanation
Indices: 42400964--42401050 Score: 97
Period size: 29 Copynumber: 3.0 Consensus size: 29
42400954 GTGAGCATGA
* * *
42400964 ATATGAATGTGA-ATGGGCCTAACGGGCT
1 ATATAAATGTGATTTGGGCCTAATGGGCT
*
42400992 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATAAATGTGATTTGGGCCTAATGGGCT
* *
42401021 ATATGAAA-GTGATTGGGGCCTAATGAGCT
1 ATAT-AAATGTGATTTGGGCCTAATGGGCT
42401050 A
1 A
42401051 GATACAGGTA
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
28 11 0.22
29 36 0.72
30 3 0.06
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.28
Consensus pattern (29 bp):
ATATAAATGTGATTTGGGCCTAATGGGCT
Found at i:42405770 original size:80 final size:80
Alignment explanation
Indices: 42405674--42405860 Score: 196
Period size: 80 Copynumber: 2.3 Consensus size: 80
42405664 TCGATCAATC
* * *
42405674 GCCTTCGGGACATAGCCCGGTTATAGTAACCCGCACCAAGGCCTACGGGACTTAACCCGGATATC
1 GCCTTCGGGTCTTAGCCCGGTTATAATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATAT-
* * *
42405739 A-CGATTTGCACAAAT
65 AGCCACTAGCACAAAT
* * * * * * * * * *
42405754 GCCTTCGGGTCTTAGCCCGGATAGAATGACTCGCACGAATGCCTTCGGGTCTTAGCCCGGATGTA
1 GCCTTCGGGTCTTAGCCCGGTTATAATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATATA
*
42405819 GCCACTAGCACAATT
66 GCCACTAGCACAAAT
*
42405834 GCCTTCGGGTCTTAACCCGGTTATAAT
1 GCCTTCGGGTCTTAGCCCGGTTATAAT
42405861 TTCCAGCATA
Statistics
Matches: 86, Mismatches: 20, Indels: 2
0.80 0.19 0.02
Matches are distributed among these distances:
79 1 0.01
80 85 0.99
ACGTcount: A:0.24, C:0.29, G:0.24, T:0.24
Consensus pattern (80 bp):
GCCTTCGGGTCTTAGCCCGGTTATAATAACCCGCACCAAGGCCTACGGGACTTAACCCGGATATA
GCCACTAGCACAAAT
Found at i:42405795 original size:40 final size:38
Alignment explanation
Indices: 42405746--42405853 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42405736 ATCACGATTT
*
42405746 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42405786 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42405826 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42405854 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42408163 original size:17 final size:18
Alignment explanation
Indices: 42408121--42408169 Score: 50
Period size: 17 Copynumber: 2.8 Consensus size: 18
42408111 AGTTGAAAAG
42408121 GAGCATGATTGTCATACTT
1 GAGCATGA-TGTCATACTT
*
42408140 G-GCCATGATG-CATTCTT
1 GAG-CATGATGTCATACTT
42408157 GAGCATGAT-TCAT
1 GAGCATGATGTCAT
42408170 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:42409057 original size:40 final size:40
Alignment explanation
Indices: 42408991--42409157 Score: 169
Period size: 40 Copynumber: 4.2 Consensus size: 40
42408981 AAATTGAATG
* * *
42408991 ATATCCGGGCTAAG-CCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* * **
42409030 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
* *
42409070 ATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGC-GAGTTATT
1 ATATCCGGGCTAAGACCCGAAGGCAATT-GTGCTG-GTAATT
* * ** *
42409110 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCACGTGATT
1 ATATCCGGGCTAAGACCCGAAGGCAATTGTGCTGGTAATT
42409150 ATATCCGG
1 ATATCCGG
42409158 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:42419555 original size:80 final size:80
Alignment explanation
Indices: 42419471--42419619 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
42419461 TATGGTAACC
* * * *
42419471 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
42419535 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
42419551 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
42419616 CCGG
66 CCGG
42419620 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:42419561 original size:40 final size:38
Alignment explanation
Indices: 42419512--42419619 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
42419502 ATCACGATTT
*
42419512 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
42419552 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
42419592 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
42419620 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:42421468 original size:47 final size:45
Alignment explanation
Indices: 42421366--42421470 Score: 113
Period size: 48 Copynumber: 2.2 Consensus size: 45
42421356 TCTTGAGGCT
* * *
42421366 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCAATGCC
1 GATGCATGTCCCAAACATGTCTTACACTAGCTCTCATAT-AATGCC
* *
42421412 AATGCCATGTCCCAAACATGGTCTTACACTGGCTCTCATA-ATATGGCC
1 GATG-CATGTCCCAAACAT-GTCTTACACTAGCTCTCATATA-AT-GCC
42421460 GATGCATGTCC
1 GATGCATGTCC
42421471 TGCACATTGC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
46 4 0.08
47 22 0.45
48 23 0.47
ACGTcount: A:0.24, C:0.30, G:0.18, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAAACATGTCTTACACTAGCTCTCATATAATGCC
Found at i:42423007 original size:68 final size:68
Alignment explanation
Indices: 42422860--42423015 Score: 149
Period size: 68 Copynumber: 2.2 Consensus size: 68
42422850 AGCCGATTTG
* * * * *
42422860 TCTCGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATT
1 TCTCGTAGCTCTCTTGTCTACATGGTGTACATCAC-TCGAATCACACATGCGACCTAGCTACATA
*
42422925 TATC
65 TATA
* *
42422929 TCTCACGTAGCTCTCTTGTCTACATGG-GATACATC-C-CGTATCACACATGTGACCTAGCTACT
1 TCT--CGTAGCTCTCTTGTCTACATGGTG-TACATCACTCGAATCACACATGCGACCTAGCTAC-
42422991 ATATAGTA
62 ATATA-TA
42422999 TCTCGTAGC-CTTCTTGT
1 TCTCGTAGCTC-TCTTGT
42423016 ACACATGATG
Statistics
Matches: 73, Mismatches: 8, Indels: 13
0.78 0.09 0.14
Matches are distributed among these distances:
67 1 0.01
68 33 0.45
69 7 0.10
70 6 0.08
71 26 0.36
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.35
Consensus pattern (68 bp):
TCTCGTAGCTCTCTTGTCTACATGGTGTACATCACTCGAATCACACATGCGACCTAGCTACATAT
ATA
Done.