Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 99090824
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: 99090824
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 317 characters in sequence are not A, C, G, or T
File 178 of 318
Found at i:55267383 original size:43 final size:43
Alignment explanation
Indices: 55267262--55267383 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
55267252 TGTGTGCGTG
** * *
55267262 TAAGACCATGTCTGGGACGTTGGCATCGATATGTGATTACGTG
1 TAAGACCACATCTGGGACGTTGGCATCGATATGTGACTACGTA
* * *
55267305 TAAGACCACGTCTAGGATGTTGGCATCGATATGTGACT-CTGTA
1 TAAGACCACATCTGGGACGTTGGCATCGATATGTGACTAC-GTA
* *
55267348 TAAGACTACATCTGGGACGTTTGCATCGATATGTGA
1 TAAGACCACATCTGGGACGTTGGCATCGATATGTGA
55267384 TTATGTGTAA
Statistics
Matches: 68, Mismatches: 10, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.25, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TAAGACCACATCTGGGACGTTGGCATCGATATGTGACTACGTA
Found at i:55271583 original size:47 final size:47
Alignment explanation
Indices: 55271529--55271639 Score: 195
Period size: 47 Copynumber: 2.4 Consensus size: 47
55271519 TGCTCAAATT
* *
55271529 ATAAGTTACTTAGTTAAGCTTGTTAAATTTTCCCTTAATATTTCCGG
1 ATAAGTTACTTAGTTAAGCTTGTTAAATTTACCATTAATATTTCCGG
*
55271576 ATAAGTTACTTAGTTAAGCTTGTTAAATTTACCATTATTATTTCCGG
1 ATAAGTTACTTAGTTAAGCTTGTTAAATTTACCATTAATATTTCCGG
55271623 ATAAGTTACTTAGTTAA
1 ATAAGTTACTTAGTTAA
55271640 AGAAAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
47 61 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.44
Consensus pattern (47 bp):
ATAAGTTACTTAGTTAAGCTTGTTAAATTTACCATTAATATTTCCGG
Found at i:55277658 original size:42 final size:43
Alignment explanation
Indices: 55277548--55277677 Score: 149
Period size: 42 Copynumber: 3.0 Consensus size: 43
55277538 AAAGGTCGTA
* ***
55277548 CAATGCCAACGTCCCAGACGTGGTCTTCCATGTAATCAAATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATAT
*
55277591 CAATGCC-ACTGTCCCAGACAG-GGTCTTACACAAAATCAAGTAT
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACAAAATCAAATAT
* * *
55277634 -GATGCCAACGTCCCAGACGTGGTCTTACACAAAAACACATAT
1 CAATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATAT
55277676 CA
1 CA
55277678 GATCCTATGT
Statistics
Matches: 72, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
41 1 0.01
42 35 0.49
43 35 0.49
44 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACACAAAATCAAATAT
Found at i:55280121 original size:40 final size:40
Alignment explanation
Indices: 55280071--55280220 Score: 149
Period size: 40 Copynumber: 3.7 Consensus size: 40
55280061 TAGTGATTCG
*
55280071 CACAATTGCCTTCGGGAATTAGCCCGGATTTAGTAACTAA
1 CACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTAA
* * * * * * **
55280111 CATAAATGCCTTCGGGACTTAACCCAGTTTTGGTAACTCT
1 CACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTAA
* *
55280151 CACAAATGCCTTCGGGAATT-GACCCGGATTTAGTCACTTAG
1 CACAAATGCCTTCGGGAATTAG-CCCGGATTTAGTAAC-TAA
* * *
55280192 CACAAAAGCCTTCGGGACTTAGCCTGGAT
1 CACAAATGCCTTCGGGAATTAGCCCGGAT
55280221 ATCATTCGAA
Statistics
Matches: 86, Mismatches: 21, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
40 60 0.70
41 25 0.29
42 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (40 bp):
CACAAATGCCTTCGGGAATTAGCCCGGATTTAGTAACTAA
Found at i:55284428 original size:13 final size:13
Alignment explanation
Indices: 55284410--55284450 Score: 73
Period size: 13 Copynumber: 3.2 Consensus size: 13
55284400 CTAAACCACC
*
55284410 TCACACGGGCATG
1 TCACACGGCCATG
55284423 TCACACGGCCATG
1 TCACACGGCCATG
55284436 TCACACGGCCATG
1 TCACACGGCCATG
55284449 TC
1 TC
55284451 CTTGTCGAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.22, C:0.37, G:0.24, T:0.17
Consensus pattern (13 bp):
TCACACGGCCATG
Found at i:55290015 original size:39 final size:39
Alignment explanation
Indices: 55289897--55290079 Score: 240
Period size: 39 Copynumber: 4.6 Consensus size: 39
55289887 TCGTTCAAAC
* * ** * **
55289897 GCCTTCGGGACATAGCCCGGTTATGGTAACCCGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* * * *
55289937 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
*
55289977 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55290016 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55290055 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
55290080 CTCGAACATT
Statistics
Matches: 126, Mismatches: 17, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
39 88 0.70
40 38 0.30
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:55296682 original size:39 final size:39
Alignment explanation
Indices: 55296564--55296746 Score: 233
Period size: 39 Copynumber: 4.6 Consensus size: 39
55296554 TCGTTCAAAC
* * ** **
55296564 GCCTTCGGGACATAGCCCGGTTATGGTAAC-CTGCACAAAG
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTC-GCACAATT
* * *
55296604 GCCTTCGGGACTTAACCCGGATATCATAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATT
* *
55296644 GCCTTCGGGCTTAGCCCGGATATCATAACTCACCCAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55296683 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
55296722 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
55296747 CTCGAACATT
Statistics
Matches: 126, Mismatches: 16, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
39 87 0.69
40 39 0.31
ACGTcount: A:0.23, C:0.30, G:0.22, T:0.25
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATT
Found at i:55297959 original size:40 final size:40
Alignment explanation
Indices: 55297897--55298154 Score: 324
Period size: 40 Copynumber: 6.5 Consensus size: 40
55297887 AAGCCAAGTA
* * * * *
55297897 CCTTCGGGATTTA-ACCGGATATAGCT-ACTTGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
55297936 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55297976 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55298016 CCTTCGAGACTTAACCTGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55298056 CCTTCGAGACTTAACCCGGATATAGTAACTCGCATAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
55298096 CCTTCGGGACTTAGCCTGGA-ACTAGTCACTAGCGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
55298136 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
55298155 TTATCATCCG
Statistics
Matches: 195, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
39 13 0.07
40 182 0.93
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55302528 original size:286 final size:286
Alignment explanation
Indices: 55302013--55302553 Score: 850
Period size: 286 Copynumber: 1.9 Consensus size: 286
55302003 GACTCTAAGC
*
55302013 CACATCAGCAAGCATCTCTGCCGAAGTGCACCACCCCTTCATACAGTTTCCCTTGGGACCCCAGG
1 CACATCAGCAAGCAGCTCTGCCGAAGTGCACCACCCCTTCATACAGTTTCCCTTGGGACCCCAGG
*
55302078 AGGAACTATTCCAAATACTACGGGCCCGACCCCTAGGTGTGGGCTGTTGCATTGATTGGACCACC
66 AGGAACTATTCCAAATACTACGGGCCCGACCCCTAGGTGTGGGCCGTTGCATTGATTGGACCACC
* * * ** *
55302143 CTAAAGCAAATCCAACTCACTGACGAAGTGCGAGCTCTCCTGACTACTGACCCATGGGGGCTCTT
131 CTAAAGCAAATCCAACTCACTGACGAAGTCCGAGCTCTCCTGAATACTGACCCATAGGGAATCCT
* * *
55302208 CTTCGAGATCGTCGAGCCAACATATCTAGAGCTCACATTATAACTCTATTCAACCTTCCACCTTC
196 CTTCAAGATCGTCGAGACAACATATCTAGAGCTCACATTAGAACTCTATTCAACCTTCCACCTTC
55302273 AAGCCGTTATGATAGAGTTCAATGAT
261 AAGCCGTTATGATAGAGTTCAATGAT
* * *
55302299 CACATCAGCAAGC-GCATCTGCCGAAGTGCACCACCCCTTCCTACAGTTTCCTTTGGGACCCTAG
1 CACATCAGCAAGCAGC-TCTGCCGAAGTGCACCACCCCTTCATACAGTTTCCCTTGGGACCCCAG
* * *
55302363 GAGGAACTATTCTAGATACTACGGGCCCGACCCCTAGGTGTGGGCCGTTGCATTGATTGGACCTC
65 GAGGAACTATTCCAAATACTACGGGCCCGACCCCTAGGTGTGGGCCGTTGCATTGATTGGACCAC
* * * * *
55302428 CCTAGAGCAGATCCAACTCGCTGACGCAGTCCGGGCTCTCCTGAATACTGACCCATAGGGAATCC
130 CCTAAAGCAAATCCAACTCACTGACGAAGTCCGAGCTCTCCTGAATACTGACCCATAGGGAATCC
* *
55302493 TCTTCAAGATCGTCGAGACAACATATCTCGAGCTCACATTAGAACTCTATTCGACCTTCCA
195 TCTTCAAGATCGTCGAGACAACATATCTAGAGCTCACATTAGAACTCTATTCAACCTTCCA
55302554 TGTAATATCC
Statistics
Matches: 230, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
285 1 0.00
286 229 1.00
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (286 bp):
CACATCAGCAAGCAGCTCTGCCGAAGTGCACCACCCCTTCATACAGTTTCCCTTGGGACCCCAGG
AGGAACTATTCCAAATACTACGGGCCCGACCCCTAGGTGTGGGCCGTTGCATTGATTGGACCACC
CTAAAGCAAATCCAACTCACTGACGAAGTCCGAGCTCTCCTGAATACTGACCCATAGGGAATCCT
CTTCAAGATCGTCGAGACAACATATCTAGAGCTCACATTAGAACTCTATTCAACCTTCCACCTTC
AAGCCGTTATGATAGAGTTCAATGAT
Found at i:55303899 original size:46 final size:46
Alignment explanation
Indices: 55303846--55304021 Score: 232
Period size: 46 Copynumber: 3.8 Consensus size: 46
55303836 TATTTGGGCA
55303846 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* * * *
55303892 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGGCA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---CGA-GCG
*
55303939 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
* *
55303985 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
55304022 GCGGGTTACA
Statistics
Matches: 112, Mismatches: 11, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 67 0.60
47 33 0.29
48 2 0.02
50 4 0.04
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCG
Found at i:55304001 original size:93 final size:93
Alignment explanation
Indices: 55303842--55304013 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
55303832 GGGATATTTG
* *
55303842 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55303907 TTGAGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
*
55303935 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
55304000 TTGAGTCCGAGTTC
66 TTGAGTCCGAGTTC
55304014 ACTTATGGGC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:55310409 original size:71 final size:71
Alignment explanation
Indices: 55310288--55310426 Score: 235
Period size: 71 Copynumber: 2.0 Consensus size: 71
55310278 CGTAGAGTAT
* *
55310288 TTTTCACAATTCGAACATTATCCATAATGTTATAATTACATTTTTGGCAATATCAAACCTTTTAA
1 TTTTCACAATTCGAACATTATACATAATCTTATAATTACATTTTTGGCAATATCAAACCTTTTAA
55310353 CATTCG
66 CATTCG
*
55310359 TTTTCACAATTCGAACATTATACATAATCTTATAATTACATTTTAT-GCAATATCAAAGCTTTTA
1 TTTTCACAATTCGAACATTATACATAATCTTATAATTACATTTT-TGGCAATATCAAACCTTTTA
55310423 ACAT
65 ACAT
55310427 ACTTTTGTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
71 63 0.98
72 1 0.02
ACGTcount: A:0.36, C:0.17, G:0.06, T:0.41
Consensus pattern (71 bp):
TTTTCACAATTCGAACATTATACATAATCTTATAATTACATTTTTGGCAATATCAAACCTTTTAA
CATTCG
Found at i:55317616 original size:40 final size:40
Alignment explanation
Indices: 55317558--55317773 Score: 240
Period size: 40 Copynumber: 5.4 Consensus size: 40
55317548 AAGCCAGGTA
* * * *
55317558 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCGAATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* * * *
55317597 CCTTCAGGACATAGCCCGGATGTAGTAACCCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
55317637 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
55317677 TCTTCGGGACTTAACCCGGATATAGTAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * **
55317717 CCTTCGAGACTTAGCCCGGA-ACTAGTCACTAGTGCAAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCACAAATG
*
55317757 CCTTCGAGACTTAGCCC
1 CCTTCGGGACTTAGCCC
55317774 AGTTATCATC
Statistics
Matches: 151, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
39 12 0.08
40 139 0.92
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:55323322 original size:27 final size:27
Alignment explanation
Indices: 55323263--55323441 Score: 245
Period size: 27 Copynumber: 6.7 Consensus size: 27
55323253 TTTGGTTTAC
55323263 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* ** * *
55323289 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
55323316 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
55323343 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55323370 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55323397 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
55323424 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
55323442 TCGACCTGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 14 0.10
27 121 0.89
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:55323452 original size:81 final size:81
Alignment explanation
Indices: 55323263--55323495 Score: 233
Period size: 81 Copynumber: 2.9 Consensus size: 81
55323253 TTTGGTTTAC
* * ** * *
55323263 AAAATTACCAAAATA-CCC-TGCTTTGTAAAATTA-CTAAAATACCATTGGTTTATAAAATTACC
1 AAAATTACCAAAATACCCCGAGC-CTGTAAAATTATC-AAAATACCCCTAGTTTGTAAAATTACC
*
55323325 AAAATACCCCTAGTTTGT
64 AAAATACCCCTAATTTGT
* **
55323343 AAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
55323408 AATACCCCTAATTTGT
66 AATACCCCTAATTTGT
* ** ** * *
55323424 GAAATTACTGAAATACCCTCGA-CCTGTAAAATTATTGAAATA-CCCTCGACTTGTAAAATTACC
1 AAAATTACCAAAATACCC-CGAGCCTGTAAAATTATCAAAATACCCCTAG-TTTGTAAAATTACC
*
55323487 AAAGTACCC
64 AAAATACCC
55323496 TCGATTTATA
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
80 20 0.15
81 106 0.82
82 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
AATACCCCTAATTTGT
Found at i:55323455 original size:27 final size:27
Alignment explanation
Indices: 55323425--55323499 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55323415 CTAATTTGTG
55323425 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
55323452 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
55323479 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
55323500 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:55323511 original size:54 final size:54
Alignment explanation
Indices: 55323315--55323622 Score: 153
Period size: 54 Copynumber: 5.7 Consensus size: 54
55323305 CATTGGTTTA
* * * * * * *
55323315 TAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTCGA-CTTG
* * * * * * * *
55323369 TAAAATTATCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAATTTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTC-GACTTG
* * ** * * **
55323423 TGAAATTACTGAAA-TACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTG
1 TAAAATTAC-CAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
*** *
55323477 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTG
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
**** *** *
55323531 TAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGTT-
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
* ***
55323583 TACAGAATTACTATTTTACCCTCGATTTATAGAATTACCG
1 TA-A-AATTACCAAAGTACCCTCGATTTATAGAATTACCG
55323623 TTTTACCCCT
Statistics
Matches: 215, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
52 2 0.01
53 7 0.03
54 199 0.93
55 7 0.03
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (54 bp):
TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
Found at i:55323837 original size:27 final size:27
Alignment explanation
Indices: 55323491--55323836 Score: 428
Period size: 27 Copynumber: 12.8 Consensus size: 27
55323481 ATTACCAAAG
*
55323491 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
55323518 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55323545 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
55323572 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
55323599 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55323626 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
55323653 TACCC-CAGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
55323680 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55323707 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
55323734 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55323761 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55323788 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55323815 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
55323837 TAAAATACCC
Statistics
Matches: 287, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
26 2 0.01
27 283 0.99
28 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:55323873 original size:81 final size:81
Alignment explanation
Indices: 55323518--55323880 Score: 223
Period size: 81 Copynumber: 4.5 Consensus size: 81
55323508 ATTACCGTTT
* ** *** * * *
55323518 TACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGA-T
* ***
55323582 TTACAGAATTACTATTT
65 TTACAAAATTACTAAAA
* * * *** * *
55323599 TACCCTCGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTACCATTTTACCC-CAGA
1 TACCCTTGATTTACAAAATTACCGCAATACCCTC-GATTTACAAAATTACCATTTTACCCTC-GA
* **
55323662 TTTACATAATTATCGT--TT
64 TTTACAAAATTA-C-TAAAA
* * *** *
55323680 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
* * ***
55323745 TATAGAATTACTATTT
66 TACAAAATTACTAAAA
* *** * **
55323761 TACCCTTGATTTACAAAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
55323826 TACAAAATTACTAAAA
66 TACAAAATTACTAAAA
* *** *
55323842 TACCCTTGGTTTGTGAAATTACCGCAATACCCTCAATTT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTT
55323881 GTAAAACTAC
Statistics
Matches: 239, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.00
80 3 0.01
81 230 0.96
82 4 0.02
83 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (81 bp):
TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
TACAAAATTACTAAAA
Found at i:55325103 original size:25 final size:25
Alignment explanation
Indices: 55325074--55325121 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55325064 TTATAATATG
* * *
55325074 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55325099 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55325122 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55325190 original size:20 final size:20
Alignment explanation
Indices: 55325165--55325223 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
55325155 TAAATATGGT
55325165 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
55325185 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
55325205 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
55325224 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:55325342 original size:23 final size:24
Alignment explanation
Indices: 55325274--55325439 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
55325264 GAGGAAGTGA
55325274 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55325298 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55325322 AAAAGGGCTTATG-CCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55325345 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
55325368 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
55325392 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
55325416 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55325440 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
23 46 0.35
24 76 0.57
25 11 0.08
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:55325350 original size:47 final size:47
Alignment explanation
Indices: 55325274--55325439 Score: 246
Period size: 47 Copynumber: 3.5 Consensus size: 47
55325264 GAGGAAGTGA
55325274 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
55325321 CAAAAGGGCTTATG-CCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
1 -AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
** *
55325368 AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTA-T
*
55325416 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55325440 ATGATAAAGC
Statistics
Matches: 110, Mismatches: 4, Indels: 7
0.91 0.03 0.06
Matches are distributed among these distances:
46 13 0.12
47 62 0.56
48 24 0.22
49 11 0.10
ACGTcount: A:0.29, C:0.22, G:0.22, T:0.27
Consensus pattern (47 bp):
AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTAT
Found at i:55325666 original size:31 final size:31
Alignment explanation
Indices: 55325631--55325725 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
55325621 CGTTTACAGT
55325631 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55325662 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
55325693 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55325724 AA
1 AA
55325726 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:55328619 original size:27 final size:27
Alignment explanation
Indices: 55328535--55328685 Score: 191
Period size: 27 Copynumber: 5.7 Consensus size: 27
55328525 TTTGGTTTAC
55328535 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * * *
55328561 AAAATTACTAAAATA-CCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
55328587 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55328614 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55328641 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
55328668 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
55328686 TCGACCTGTA
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
26 35 0.32
27 75 0.68
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:55328696 original size:54 final size:54
Alignment explanation
Indices: 55328535--55328757 Score: 204
Period size: 54 Copynumber: 4.2 Consensus size: 54
55328525 TTTGGTTTAC
** * * *
55328535 AAAATTACCAAAATA-CCCTGCTTTGTAAAATTACTAAAATA-CCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
* *
55328587 AAAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACT-AAAATACCCTCGA-TTTGT
* * **
55328641 AAAATTACCAAAATACCCCTAATTTGTGAAATTACTGAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
*** * * * * *
55328695 AAAATTATTGAAATA-CCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTAT
1 AAAATTACCAAAATACCCCT-AATTTGTAAAATTACTAAAATACCCTCGATTTGT
*
55328749 AGAATTACC
1 AAAATTACC
55328758 GTTTTACCCT
Statistics
Matches: 137, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
52 16 0.12
53 26 0.19
54 92 0.67
55 3 0.02
ACGTcount: A:0.40, C:0.21, G:0.09, T:0.31
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
Found at i:55328699 original size:27 final size:27
Alignment explanation
Indices: 55328669--55328743 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55328659 CTAATTTGTG
55328669 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
55328696 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
55328723 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
55328744 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:55329081 original size:27 final size:27
Alignment explanation
Indices: 55328735--55329080 Score: 428
Period size: 27 Copynumber: 12.8 Consensus size: 27
55328725 ATTACCAAAG
*
55328735 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
55328762 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55328789 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
55328816 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
55328843 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55328870 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
55328897 TACCC-CAGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
55328924 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55328951 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
55328978 TACCCTCGATTTATAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55329005 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55329032 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55329059 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
55329081 TAAAATACCC
Statistics
Matches: 287, Mismatches: 28, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
26 2 0.01
27 283 0.99
28 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:55329117 original size:81 final size:81
Alignment explanation
Indices: 55328762--55329124 Score: 223
Period size: 81 Copynumber: 4.5 Consensus size: 81
55328752 ATTACCGTTT
* ** *** * * *
55328762 TACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGA-T
* ***
55328826 TTACAGAATTACTATTT
65 TTACAAAATTACTAAAA
* * * *** * *
55328843 TACCCTCGATTTATAGAATTACCGTTTTACCC-CTAATTTACATAATTACCATTTTACCC-CAGA
1 TACCCTTGATTTACAAAATTACCGCAATACCCTC-GATTTACAAAATTACCATTTTACCCTC-GA
* **
55328906 TTTACATAATTATCGT--TT
64 TTTACAAAATTA-C-TAAAA
* * *** *
55328924 TACCCTCGATTTACAGAATTACCGTTTTACCCTCGATTTACAGAATTACCATTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
* * ***
55328989 TATAGAATTACTATTT
66 TACAAAATTACTAAAA
* *** * **
55329005 TACCCTTGATTTACAAAATTACTGTTTTACCCTTGATTTACAAAATTACTGTTTTACCCTCGATT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
55329070 TACAAAATTACTAAAA
66 TACAAAATTACTAAAA
* *** *
55329086 TACCCTTGGTTTGTGAAATTACCGCAATACCCTCAATTT
1 TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTT
55329125 GTAAAACTAC
Statistics
Matches: 239, Mismatches: 34, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
79 1 0.00
80 3 0.01
81 230 0.96
82 4 0.02
83 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.40
Consensus pattern (81 bp):
TACCCTTGATTTACAAAATTACCGCAATACCCTCGATTTACAAAATTACCATTTTACCCTCGATT
TACAAAATTACTAAAA
Found at i:55330349 original size:25 final size:25
Alignment explanation
Indices: 55330320--55330367 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55330310 TTATAATATG
* * *
55330320 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55330345 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55330368 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55330436 original size:20 final size:20
Alignment explanation
Indices: 55330411--55330469 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
55330401 TAAATATGGT
55330411 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
55330431 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
55330451 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
55330470 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:55330547 original size:24 final size:24
Alignment explanation
Indices: 55330520--55330686 Score: 257
Period size: 24 Copynumber: 7.0 Consensus size: 24
55330510 GAGGAAGTGA
55330520 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55330544 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55330568 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55330592 AAAAGGGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
55330615 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
55330639 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
55330663 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55330687 ATGATAAAGC
Statistics
Matches: 135, Mismatches: 5, Indels: 5
0.93 0.03 0.03
Matches are distributed among these distances:
23 23 0.17
24 101 0.75
25 11 0.08
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:55330637 original size:71 final size:71
Alignment explanation
Indices: 55330520--55330687 Score: 257
Period size: 71 Copynumber: 2.3 Consensus size: 71
55330510 GAGGAAGTGA
55330520 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAAGGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
55330585 AGTTATC
65 AGTTATC
** *
55330592 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCA
1 AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
55330657 GTTATT
66 GTTATC
*
55330663 AAAAGAGGC-TAGGCCTCCAGTTATA
1 AAAAG-GGCTTATGCC-CCAGTTATA
55330688 TGATAAAGCA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
71 54 0.61
72 35 0.39
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.26
Consensus pattern (71 bp):
AAAAGGGCTTATGCCCCAGTTATAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:55330913 original size:31 final size:31
Alignment explanation
Indices: 55330878--55330972 Score: 181
Period size: 31 Copynumber: 3.1 Consensus size: 31
55330868 CGTTTACAGT
55330878 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55330909 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
55330940 AAAGGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55330971 AA
1 AA
55330973 TATGAAAAGG
Statistics
Matches: 63, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:55333835 original size:27 final size:27
Alignment explanation
Indices: 55333776--55333954 Score: 245
Period size: 27 Copynumber: 6.7 Consensus size: 27
55333766 TTTGGTTTAC
55333776 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* ** * *
55333802 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
55333829 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
55333856 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55333883 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
55333910 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* **
55333937 GAAATTACTGAAATACCC
1 AAAATTACCAAAATACCC
55333955 TCGACCTGTA
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
26 14 0.10
27 121 0.89
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:55333965 original size:81 final size:81
Alignment explanation
Indices: 55333776--55334008 Score: 233
Period size: 81 Copynumber: 2.9 Consensus size: 81
55333766 TTTGGTTTAC
* * ** * *
55333776 AAAATTACCAAAATA-CCC-TGCTTTGTAAAATTA-CTAAAATACCATTGGTTTATAAAATTACC
1 AAAATTACCAAAATACCCCGAGC-CTGTAAAATTATC-AAAATACCCCTAGTTTGTAAAATTACC
*
55333838 AAAATACCCCTAGTTTGT
64 AAAATACCCCTAATTTGT
* **
55333856 AAAATTACCAAAATACCCCTAGTTTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
1 AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
55333921 AATACCCCTAATTTGT
66 AATACCCCTAATTTGT
* ** ** * *
55333937 GAAATTACTGAAATACCCTCGA-CCTGTAAAATTATTGAAATA-CCCTCGACTTGTAAAATTACC
1 AAAATTACCAAAATACCC-CGAGCCTGTAAAATTATCAAAATACCCCTAG-TTTGTAAAATTACC
*
55334000 AAAGTACCC
64 AAAATACCC
55334009 TCGATTTATA
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
80 20 0.15
81 106 0.82
82 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (81 bp):
AAAATTACCAAAATACCCCGAGCCTGTAAAATTATCAAAATACCCCTAGTTTGTAAAATTACCAA
AATACCCCTAATTTGT
Found at i:55333968 original size:27 final size:27
Alignment explanation
Indices: 55333938--55334012 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55333928 CTAATTTGTG
55333938 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
55333965 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
55333992 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
55334013 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:55334024 original size:54 final size:54
Alignment explanation
Indices: 55333828--55334135 Score: 153
Period size: 54 Copynumber: 5.7 Consensus size: 54
55333818 CATTGGTTTA
* * * * * * *
55333828 TAAAATTACCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAGTTTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTCGA-CTTG
* * * * * * * *
55333882 TAAAATTATCAAAATACCC-CTAGTTTGTAAAATTACCAAAATACCC-CTAATTTG
1 TAAAATTACCAAAGTACCCTCGA-TTTATAGAATTACCGAAATACCCTC-GACTTG
* * ** * * **
55333936 TGAAATTACTGAAA-TACCCTCGACCTGTAAAATTATTGAAATACCCTCGACTTG
1 TAAAATTAC-CAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
*** *
55333990 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGTTTTACCCTCGATTTG
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
**** *** *
55334044 TAAAATTACCGTTTTACCCTCGATTTATAGAATTACCGTTTTACCCTC-AGTT-
1 TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
* ***
55334096 TACAGAATTACTATTTTACCCTCGATTTATAGAATTACCG
1 TA-A-AATTACCAAAGTACCCTCGATTTATAGAATTACCG
55334136 TTTTACCCCT
Statistics
Matches: 215, Mismatches: 32, Indels: 14
0.82 0.12 0.05
Matches are distributed among these distances:
52 2 0.01
53 7 0.03
54 199 0.93
55 7 0.03
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.34
Consensus pattern (54 bp):
TAAAATTACCAAAGTACCCTCGATTTATAGAATTACCGAAATACCCTCGACTTG
Found at i:55334349 original size:27 final size:27
Alignment explanation
Indices: 55334004--55334348 Score: 419
Period size: 27 Copynumber: 12.8 Consensus size: 27
55333994 ATTACCAAAG
*
55334004 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
55334031 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55334058 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
55334085 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
55334112 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55334139 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
55334166 TACCC-CAGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
55334193 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55334220 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* **
55334247 TACCCTCGATTTA-TGAATTACTATTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55334273 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55334300 TACCCTTGATTTACAAAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55334327 TACCCTCGATTTACAAAATTAC
1 TACCCTCGATTTACAGAATTAC
55334349 TAAAATACCC
Statistics
Matches: 285, Mismatches: 28, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
26 25 0.09
27 258 0.91
28 2 0.01
ACGTcount: A:0.29, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:55335617 original size:25 final size:25
Alignment explanation
Indices: 55335588--55335635 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
55335578 TTATAATATG
* * *
55335588 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
55335613 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
55335636 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:55335704 original size:20 final size:20
Alignment explanation
Indices: 55335679--55335737 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
55335669 TAAATATGGT
55335679 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
55335699 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
55335719 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
55335738 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:55335903 original size:25 final size:24
Alignment explanation
Indices: 55335788--55335907 Score: 170
Period size: 24 Copynumber: 5.0 Consensus size: 24
55335778 GAGGAAGTGA
55335788 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
55335812 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
*
55335836 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
55335860 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
55335884 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
55335908 ATGATAAAGC
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
24 77 0.88
25 11 0.12
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:55336175 original size:30 final size:31
Alignment explanation
Indices: 55336099--55336192 Score: 172
Period size: 31 Copynumber: 3.1 Consensus size: 31
55336089 CGTTTACAGT
55336099 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55336130 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
*
55336161 AAAGGCTT-GGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
55336191 AA
1 AA
55336193 TATGAAAAGG
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
30 23 0.37
31 39 0.63
ACGTcount: A:0.39, C:0.15, G:0.22, T:0.23
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:55339058 original size:27 final size:27
Alignment explanation
Indices: 55338999--55339177 Score: 213
Period size: 27 Copynumber: 6.7 Consensus size: 27
55338989 TTTGGTTTAC
*
55338999 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACTAAAATACCCCTAG-TTTGT
** * *
55339025 AAAATTACTAAAATACCATTGGTTTAT
1 AAAATTACTAAAATACCCCTAGTTTGT
*
55339052 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACTAAAATACCCCTAGTTTGT
55339079 AAAATTA-TCAAAATACCCCTAGTTTGT
1 AAAATTACT-AAAATACCCCTAGTTTGT
55339106 AAAATTA-TCAAAATACCCCTAGTTTGT
1 AAAATTACT-AAAATACCCCTAGTTTGT
* *
55339133 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACTAAAATACCCCTAGTTTGT
* *
55339160 GAAATTACTGAAATACCC
1 AAAATTACTAAAATACCC
55339178 TCGACCTGTA
Statistics
Matches: 134, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
26 14 0.10
27 119 0.89
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACTAAAATACCCCTAGTTTGT
Found at i:55339109 original size:54 final size:55
Alignment explanation
Indices: 55338999--55339231 Score: 228
Period size: 54 Copynumber: 4.3 Consensus size: 55
55338989 TTTGGTTTAC
* ** * *
55338999 AAAATTACCAAAATA-CCCT-GCTTTGTAAAATTA-CTAAAATACCATTGGTTTAT
1 AAAATTACCAAAATACCCCTAGATTTGTAAAATTATC-AAAATACCCCTAGTTTGT
55339052 AAAATTACCAAAATACCCCTAG-TTTGTAAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGATTTGTAAAATTATCAAAATACCCCTAGTTTGT
* * *
55339106 AAAATTATCAAAATACCCCTAG-TTTGTAAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAGATTTGTAAAATTATCAAAATACCCCTAGTTTGT
* ** * ** ** * *
55339160 GAAATTACTGAAATA-CCCTCGACCTGTAAAATTATTGAAATA-CCCTCGACTTGT
1 AAAATTACCAAAATACCCCTAGATTTGTAAAATTATCAAAATACCCCTAG-TTTGT
*
55339214 AAAATTACCAAAGTACCC
1 AAAATTACCAAAATACCC
55339232 TCGATTTATA
Statistics
Matches: 150, Mismatches: 24, Indels: 10
0.82 0.13 0.05
Matches are distributed among these distances:
53 24 0.16
54 122 0.81
55 4 0.03
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (55 bp):
AAAATTACCAAAATACCCCTAGATTTGTAAAATTATCAAAATACCCCTAGTTTGT
Found at i:55339119 original size:81 final size:80
Alignment explanation
Indices: 55338999--55339231 Score: 240
Period size: 81 Copynumber: 2.9 Consensus size: 80
55338989 TTTGGTTTAC
* *
55338999 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCATTGGTTTATAAAATTACCAAA
1 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCACTAGTTTATAAAATTACCAAA
*
55339064 ATACCCCTAGTTTGT
66 ATACCCCTAATTTGT
* * *
55339079 AAAATTATCAAAATACCCCTAG-TTTGTAAAATTA-TCAAAATACCCCTAGTTTGTAAAATTACC
1 AAAATTACCAAAATA-CCCT-GCTTTGTAAAATTACT-AAAATACCACTAGTTTATAAAATTACC
55339142 AAAATACCCCTAATTTGT
63 AAAATACCCCTAATTTGT
* ** * * * * * *
55339160 GAAATTACTGAAATACCCTCGAC-CTGTAAAATTATTGAAATACC-CTCGACTTGTAAAATTACC
1 AAAATTACCAAAATACCCT-G-CTTTGTAAAATTACTAAAATACCACTAG-TTTATAAAATTACC
*
55339223 AAAGTACCC
63 AAAATACCC
55339232 TCGATTTATA
Statistics
Matches: 130, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
80 23 0.18
81 105 0.81
82 2 0.02
ACGTcount: A:0.41, C:0.21, G:0.08, T:0.30
Consensus pattern (80 bp):
AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCACTAGTTTATAAAATTACCAAA
ATACCCCTAATTTGT
Found at i:55339191 original size:27 final size:27
Alignment explanation
Indices: 55339161--55339235 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55339151 CTAATTTGTG
55339161 AAATTACTGAAATACCCTCGACCTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
* *
55339188 AAATTATTGAAATACCCTCGACTTGTA
1 AAATTACTGAAATACCCTCGACCTGTA
*
55339215 AAATTAC-CAAAGTACCCTCGA
1 AAATTACTGAAA-TACCCTCGA
55339236 TTTATAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
26 3 0.07
27 40 0.93
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.27
Consensus pattern (27 bp):
AAATTACTGAAATACCCTCGACCTGTA
Found at i:55339247 original size:54 final size:54
Alignment explanation
Indices: 55339196--55339358 Score: 150
Period size: 54 Copynumber: 3.0 Consensus size: 54
55339186 TAAAATTATT
55339196 GAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
1 GAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
*** * ****
55339250 GTTTTACCCTCGATTTGTAAAATTACCGTTTTACCCTCGATTTATAGAATTACC
1 GAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
*** * * ***
55339304 GTTTTACCCTC-AGTT-TACAGAATTACTATTTTACCCTCGATTTATAGAATTACC
1 GAAATACCCTCGACTTGTA-A-AATTACCAAAGTACCCTCGATTTATAGAATTACC
55339358 G
1 G
55339359 TTTTACCCCT
Statistics
Matches: 96, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
52 2 0.02
53 4 0.04
54 90 0.94
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.36
Consensus pattern (54 bp):
GAAATACCCTCGACTTGTAAAATTACCAAAGTACCCTCGATTTATAGAATTACC
Found at i:55339483 original size:27 final size:27
Alignment explanation
Indices: 55339227--55339483 Score: 331
Period size: 27 Copynumber: 9.5 Consensus size: 27
55339217 ATTACCAAAG
*
55339227 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
** *
55339254 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55339281 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
55339308 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
55339335 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
55339362 TACCC-CTAATTTACATAATTACCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* *
55339389 TACCC-CAGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
55339416 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55339443 TACCCTCGATTTACAGAATTACCATTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
55339470 TACCCTCGTTTTAC
1 TACCCTCGATTTAC
55339484 CATTGTGTAG
Statistics
Matches: 204, Mismatches: 22, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
26 2 0.01
27 200 0.98
28 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:55358770 original size:40 final size:40
Alignment explanation
Indices: 55358726--55358838 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
55358716 TGCTGGAAAT
* * *
55358726 TATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
* * *
55358766 TATATCCGGGCTAAGGCCCGAAGGC-ATTCGTGCGAGTTAT
1 TATATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTGAC
* *
55358806 TCTATCCGGGCTAAGACCCGAAGGCATTTGTGC
1 TATATCCGGGCTAAGACCCGAAGGCAATTGTGC
55358839 ACGTGATTAA
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 3 0.05
40 57 0.92
41 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.29, T:0.25
Consensus pattern (40 bp):
TATATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTGAC
Found at i:55369513 original size:40 final size:40
Alignment explanation
Indices: 55369468--55369634 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
55369458 CGGAATATAA
55369468 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * * *
55369508 CCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
55369548 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
55369588 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
55369627 CCGGATAT
1 CCGGATAT
55369635 CATTCAATTT
Statistics
Matches: 105, Mismatches: 21, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
39 14 0.13
40 91 0.87
ACGTcount: A:0.25, C:0.28, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:55369618 original size:80 final size:79
Alignment explanation
Indices: 55369484--55369634 Score: 198
Period size: 80 Copynumber: 1.9 Consensus size: 79
55369474 ATAATCACGT
*
55369484 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATAACTCGCACGAATGCCTTCGGGCCTTAGCC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGG-CTTAGCC
55369549 CGGATATAGCCACTA
65 CGGATATAGCCACTA
* * ** * *
55369564 GCACAATTGCCTTCGGGTCTTAACCCGGATATAATTTC-CAGCA-TAATTGTCTTCGGGCTTAGC
1 GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTC-GCACGAA-TGCCTTCGGGCTTAGC
55369627 CCGGATAT
64 CCGGATAT
55369635 CATTCAATTT
Statistics
Matches: 62, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
79 17 0.27
80 45 0.73
ACGTcount: A:0.24, C:0.28, G:0.23, T:0.26
Consensus pattern (79 bp):
GCACAAATGCCTTCGGGTCTTAACCCGGATAGAATAACTCGCACGAATGCCTTCGGGCTTAGCCC
GGATATAGCCACTA
Found at i:55372508 original size:26 final size:26
Alignment explanation
Indices: 55372479--55372531 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
55372469 GAAGAGAAAA
55372479 ATGATCACCATGTCATAAAACATAAG
1 ATGATCACCATGTCATAAAACATAAG
55372505 ATGATCACCATGTCATAAAACATAAG
1 ATGATCACCATGTCATAAAACATAAG
55372531 A
1 A
55372532 AAATAGGATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.47, C:0.19, G:0.11, T:0.23
Consensus pattern (26 bp):
ATGATCACCATGTCATAAAACATAAG
Found at i:55376190 original size:13 final size:13
Alignment explanation
Indices: 55376174--55376206 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
55376164 TTTAATTAAA
*
55376174 TTAGTTAATTAGT
1 TTAGATAATTAGT
55376187 TTAGATAATTAGT
1 TTAGATAATTAGT
55376200 TTA-ATAA
1 TTAGATAA
55376207 ACAAACCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:55388844 original size:16 final size:16
Alignment explanation
Indices: 55388823--55388855 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
55388813 AATCGGGTTG
*
55388823 AGAAAATTATTTAATT
1 AGAAAATTAATTAATT
55388839 AGAAAATTAATTAATT
1 AGAAAATTAATTAATT
55388855 A
1 A
55388856 ATTTAAATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (16 bp):
AGAAAATTAATTAATT
Found at i:55390492 original size:25 final size:25
Alignment explanation
Indices: 55390464--55390511 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
55390454 TAATGAATAG
55390464 GAGAGTTTTATCTAATAACTTTATT
1 GAGAGTTTTATCTAATAACTTTATT
55390489 GAGAGTTTTATCTAATAACTTTA
1 GAGAGTTTTATCTAATAACTTTA
55390512 ATGATGGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.33, C:0.08, G:0.12, T:0.46
Consensus pattern (25 bp):
GAGAGTTTTATCTAATAACTTTATT
Found at i:55390629 original size:41 final size:41
Alignment explanation
Indices: 55390578--55390659 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
55390568 TTATAATAAG
55390578 AGATTAATTTAATAGATTGAGCATAATATAAGAAGCACATT
1 AGATTAATTTAATAGATTGAGCATAATATAAGAAGCACATT
*
55390619 AGATTAATTTAATAGATTGAGCATAATATAAGAATCACATT
1 AGATTAATTTAATAGATTGAGCATAATATAAGAAGCACATT
55390660 CTACCTTATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.33
Consensus pattern (41 bp):
AGATTAATTTAATAGATTGAGCATAATATAAGAAGCACATT
Found at i:55391225 original size:58 final size:58
Alignment explanation
Indices: 55391163--55391306 Score: 184
Period size: 58 Copynumber: 2.5 Consensus size: 58
55391153 TTTTAATAAG
* * * *
55391163 ATTATTATTAAATATATTTTAATAAAAATAATAAATAATTTAATCATATTTTT-ACATA
1 ATTATTATTAAATAAAATTTAAT-AAAATAATAAATAATTTAATAACATTTTTAACATA
* *
55391221 ATTATTATTAAATAAAATTTAATAAAATAATATATAATTTAATAACATTTTTAATATA
1 ATTATTATTAAATAAAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
*
55391279 ATTAATATTAAAATAAGAA-TTAATAAAA
1 ATTATTATT-AAATAA-AATTTAATAAAA
55391307 CTTATAATAT
Statistics
Matches: 76, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
57 26 0.34
58 33 0.43
59 15 0.20
60 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (58 bp):
ATTATTATTAAATAAAATTTAATAAAATAATAAATAATTTAATAACATTTTTAACATA
Found at i:55394509 original size:40 final size:40
Alignment explanation
Indices: 55394422--55394572 Score: 123
Period size: 40 Copynumber: 3.8 Consensus size: 40
55394412 AATTGATTGA
* * * **
55394422 TATCCGGGCTAAGCCCCGAAGACAATTATGCTG-GAAATTA-
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC-GAGTCA-TAC
* * *
55394462 TAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGC-TAC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGT--CATAC
*
55394503 -ATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATTC
1 TATCCGGGCTAAGACCCGAAGGCAATT-GTGCGAGTCATAC
* *
55394542 TATCCGGGCTAAGACCCGAAGGTATTTGTGC
1 TATCCGGGCTAAGACCCGAAGGCAATTGTGC
55394573 AAATCGTGAT
Statistics
Matches: 89, Mismatches: 14, Indels: 16
0.75 0.12 0.13
Matches are distributed among these distances:
38 1 0.01
39 5 0.06
40 81 0.91
41 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.27, T:0.23
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCAATTGTGCGAGTCATAC
Found at i:55394586 original size:40 final size:40
Alignment explanation
Indices: 55394503--55394604 Score: 114
Period size: 40 Copynumber: 2.5 Consensus size: 40
55394493 TAGTGGCTAC
* * **
55394503 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* * *
55394543 ATCCGGGCTAAGACCCGAAGGTATTTGTGCAAATCGTGAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* * *
55394583 ATCCGGGTTAAGTCCCGTAGGC
1 ATCCGGGCTAAGACCCGAAGGC
55394605 CTTGGTGCGG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.24
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
Found at i:55396426 original size:28 final size:27
Alignment explanation
Indices: 55396337--55396450 Score: 87
Period size: 27 Copynumber: 4.3 Consensus size: 27
55396327 GAAAATTAGC
* *
55396337 GTGCTTATCGTATTATTTCGCACTTTG
1 GTGCTTATTGTATTATTTTGCACTTTG
**
55396364 GTGCTTATTGT-TGTAAAATTTT-CACTTCA
1 GTGCTTATTGTAT-T---ATTTTGCACTTTG
*
55396393 GAGCTTATTGATATTATTTTGCACTTTG
1 GTGCTTATTG-TATTATTTTGCACTTTG
*
55396421 GTGCTTCTTG--TTA-TTTGCACTTT-
1 GTGCTTATTGTATTATTTTGCACTTTG
55396444 GTGCTTA
1 GTGCTTA
55396451 GTAATATATG
Statistics
Matches: 70, Mismatches: 10, Indels: 18
0.71 0.10 0.18
Matches are distributed among these distances:
23 6 0.09
24 10 0.14
25 3 0.04
26 1 0.01
27 16 0.23
28 13 0.19
29 14 0.20
30 6 0.09
31 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.18, T:0.50
Consensus pattern (27 bp):
GTGCTTATTGTATTATTTTGCACTTTG
Found at i:55398075 original size:5 final size:5
Alignment explanation
Indices: 55398065--55398097 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
55398055 ATGTGTGTTC
55398065 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
55398098 TCACCAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:55400398 original size:54 final size:54
Alignment explanation
Indices: 55400316--55400420 Score: 183
Period size: 54 Copynumber: 1.9 Consensus size: 54
55400306 TTATCTCTTA
*
55400316 AAGACTTTTCCAATAAAGAAAATCAAAAACAGGTGGAGCATCAGAATAATATAG
1 AAGACTCTTCCAATAAAGAAAATCAAAAACAGGTGGAGCATCAGAATAATATAG
* *
55400370 AAGACTCTTCCAATAAAGAAAATCAAAAACAGGTGGAGCATTAGATTAATA
1 AAGACTCTTCCAATAAAGAAAATCAAAAACAGGTGGAGCATCAGAATAATA
55400421 CAGAGTTGAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.50, C:0.13, G:0.16, T:0.21
Consensus pattern (54 bp):
AAGACTCTTCCAATAAAGAAAATCAAAAACAGGTGGAGCATCAGAATAATATAG
Found at i:55404127 original size:23 final size:22
Alignment explanation
Indices: 55404101--55404201 Score: 123
Period size: 23 Copynumber: 4.5 Consensus size: 22
55404091 AGCTTGTAAA
* *
55404101 AGCTTACTGTCTCAGTTCATTGG
1 AGCTTACTGT-TCAGCTCATTAG
55404124 AGCTTACTGATTCAGCTCGA-TAG
1 AGCTTACTG-TTCAGCTC-ATTAG
*
55404147 AGCTTACTGTTCAGCTCAATAG
1 AGCTTACTGTTCAGCTCATTAG
*
55404169 AGCTTACCGTTTCAGCTCATTAG
1 AGCTTACTG-TTCAGCTCATTAG
55404192 AGCTTACTGT
1 AGCTTACTGT
55404202 CCATCAGCTC
Statistics
Matches: 69, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
21 1 0.01
22 20 0.29
23 46 0.67
24 2 0.03
ACGTcount: A:0.23, C:0.23, G:0.20, T:0.35
Consensus pattern (22 bp):
AGCTTACTGTTCAGCTCATTAG
Found at i:55404186 original size:45 final size:46
Alignment explanation
Indices: 55404077--55404228 Score: 157
Period size: 45 Copynumber: 3.3 Consensus size: 46
55404067 CAGCTTGTAT
* * * * *
55404077 GAGCTTACCGATTCAGCTTG-TAAAAGCTTACTGTCTCAGTTCATTG
1 GAGCTTACCGATTCAGCTCGAT-AGAGCTTACTGTCTCAGCTCAATA
*
55404123 GAGCTTACTGATTCAGCTCGATAGAGCTTACTGT-TCAGCTCAATA
1 GAGCTTACCGATTCAGCTCGATAGAGCTTACTGTCTCAGCTCAATA
* **
55404168 GAGCTTACCGTTTCAGCTC-ATTAGAGCTTACTGTCCATCAGCTCAGGA
1 GAGCTTACCGATTCAGCTCGA-TAGAGCTTACTGT-C-TCAGCTCAATA
55404216 GGAGCTTACCGAT
1 -GAGCTTACCGAT
55404229 CATGGCTCGA
Statistics
Matches: 89, Mismatches: 11, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
44 1 0.01
45 38 0.43
46 29 0.33
47 1 0.01
48 9 0.10
49 11 0.12
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (46 bp):
GAGCTTACCGATTCAGCTCGATAGAGCTTACTGTCTCAGCTCAATA
Found at i:55409907 original size:29 final size:29
Alignment explanation
Indices: 55409874--55409938 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
55409864 GTGACGAGAT
55409874 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
55409903 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
55409932 CGGCACT
1 TGGCACT
55409939 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:55410044 original size:2 final size:2
Alignment explanation
Indices: 55410039--55410071 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
55410029 GTGCGTACTC
55410039 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
55410072 CTCCGATCGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55417192 original size:29 final size:29
Alignment explanation
Indices: 55417159--55417223 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
55417149 GTGACGAGAT
55417159 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
55417188 TGGCACTAAGTGTGCATGCTGGAAATATA
1 TGGCACTAAGTGTGCATGCTGGAAATATA
*
55417217 CGGCACT
1 TGGCACT
55417224 GGGTGTGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (29 bp):
TGGCACTAAGTGTGCATGCTGGAAATATA
Found at i:55417335 original size:2 final size:2
Alignment explanation
Indices: 55417330--55417356 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
55417320 ACTCTCTCTC
55417330 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
55417357 CCGATCGAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:55419389 original size:43 final size:43
Alignment explanation
Indices: 55419342--55419583 Score: 267
Period size: 43 Copynumber: 5.7 Consensus size: 43
55419332 TATATGTGTG
55419342 TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACA
1 TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACA
* * **
55419385 TGTAAGACCACGTCTG-GAACATTGGCATCGATATATGACTATG
1 TGTAAGACCACGTCTGAG-ACATTGGCATCGATATGTGATTACA
* * * * * *
55419428 TATAAGACCACATCCGGGACGTTAGCATCGATATGTGATTACA
1 TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACA
* * * * * *
55419471 TGTAAGACCATGTCTGAGACGTTGACATCTATATCTGATTACG
1 TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACA
*
55419514 TGTAAGACC-CTGTCT-AGGACAGTGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGA-GACATTGGCATCGATATGTGATTACA
*
55419557 TGTAAGACCAC-TCTGGGACATTGGCAT
1 TGTAAGACCACGTCTGAGACATTGGCAT
55419584 TGTATAATAT
Statistics
Matches: 161, Mismatches: 32, Indels: 13
0.78 0.16 0.06
Matches are distributed among these distances:
42 15 0.09
43 144 0.89
44 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.28
Consensus pattern (43 bp):
TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACA
Found at i:55419563 original size:129 final size:128
Alignment explanation
Indices: 55419342--55419575 Score: 310
Period size: 129 Copynumber: 1.8 Consensus size: 128
55419332 TATATGTGTG
* * *
55419342 TGTAAGACCACGTCTGAGACATTGGCATCGATATGTGATTACATGTAAGACCACGTCTGGAACAT
1 TGTAAGACCACGTCTGAGACATTGACATCGATATCTGATTACATGTAAGACCACGTCTGGAACAG
**
55419407 TGGCATCGATATATGACTATGTATAAGACCACATCCGGGACGTTAGCATCGATATGTGATTACA
66 TGGCATCGATATATGACTACATATAAGACCAC-TCCGGGACGTTAGCATCGATATGTGATTACA
* * * *
55419471 TGTAAGACCATGTCTGAGACGTTGACATCTATATCTGATTACGTGTAAGACC-CTGTCTAGG-AC
1 TGTAAGACCACGTCTGAGACATTGACATCGATATCTGATTACATGTAAGACCAC-GTCT-GGAAC
* * * *
55419534 AGTGGCATCGATATGTGATTACATGTAAGACCACTCTGGGAC
64 AGTGGCATCGATATATGACTACATATAAGACCACTCCGGGAC
55419576 ATTGGCATTG
Statistics
Matches: 90, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
128 8 0.09
129 80 0.89
130 2 0.02
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (128 bp):
TGTAAGACCACGTCTGAGACATTGACATCGATATCTGATTACATGTAAGACCACGTCTGGAACAG
TGGCATCGATATATGACTACATATAAGACCACTCCGGGACGTTAGCATCGATATGTGATTACA
Found at i:55420298 original size:6 final size:6
Alignment explanation
Indices: 55420270--55420386 Score: 73
Period size: 6 Copynumber: 19.3 Consensus size: 6
55420260 AAGAAACATT
* * *
55420270 ATCAGA A-CTAGA ATCAAA ATCAGA ATCAGA ATTAG- GTGACAGA ATCAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA ATCAGA
* * *
55420319 ATCAGA ATCAGA ATCAGGTA A-CA-A ATCAAA ATCAGA ATCAGT ATCGGTA
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA ATCAGA ATCAG-A
* *
55420368 A-CAGA ATAAAA ATCAGA AT
1 ATCAGA ATCAGA ATCAGA AT
55420387 ATGAATGCAA
Statistics
Matches: 85, Mismatches: 15, Indels: 22
0.70 0.12 0.18
Matches are distributed among these distances:
4 2 0.02
5 6 0.07
6 67 0.79
7 7 0.08
8 3 0.04
ACGTcount: A:0.50, C:0.15, G:0.16, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:55420352 original size:30 final size:31
Alignment explanation
Indices: 55420279--55420386 Score: 157
Period size: 30 Copynumber: 3.5 Consensus size: 31
55420269 TATCAGAACT
* *
55420279 AGAATCAAAATCAGAATCAGAATTAGGTGAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
55420310 AGAATCAGAATCAGAATCAGAATCAGGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
55420341 A-AATCAAAATCAGAATCAGTATC-GGTAAC
1 AGAATCAAAATCAGAATCAGAATCAGGTAAC
*
55420370 AGAATAAAAATCAGAAT
1 AGAATCAAAATCAGAAT
55420387 ATGAATGCAA
Statistics
Matches: 70, Mismatches: 6, Indels: 3
0.89 0.08 0.04
Matches are distributed among these distances:
29 7 0.10
30 34 0.49
31 29 0.41
ACGTcount: A:0.51, C:0.14, G:0.17, T:0.19
Consensus pattern (31 bp):
AGAATCAAAATCAGAATCAGAATCAGGTAAC
Found at i:55420571 original size:27 final size:26
Alignment explanation
Indices: 55420523--55420624 Score: 123
Period size: 27 Copynumber: 3.8 Consensus size: 26
55420513 GCTCAGTTAT
* *
55420523 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
*
55420550 CAGATATTGTGGCGGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
55420576 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
55420604 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
55420625 TTAACAGAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
26 7 0.11
27 51 0.77
28 8 0.12
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:55420811 original size:22 final size:22
Alignment explanation
Indices: 55420783--55420847 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
55420773 GCAAATACGT
*
55420783 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
55420805 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
* *
55420827 TTGACATAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
55420848 AAGGCTTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 2 0.06
22 31 0.89
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:55421332 original size:27 final size:27
Alignment explanation
Indices: 55421300--55421604 Score: 335
Period size: 27 Copynumber: 11.3 Consensus size: 27
55421290 AAGATATCTC
*
55421300 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
* * * *
55421327 AGTAATTCCACCTTATAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTT
* *
55421354 AGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
* * **
55421381 GGTAATTTTACCCTACAAGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTT
* *
55421408 GATAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
**
55421435 GGTAATTCTACCCTACAGGGGTATTCC
1 GGTAATTCTACCCTACAGGGGTATTTT
* *
55421462 GATAATTCTACCCTACAGGGGTATTCT
1 GGTAATTCTACCCTACAGGGGTATTTT
* *
55421489 GGTAATTCTACCCTACAGAGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
**
55421516 GGTAATTCTA-CAAACTAGGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTT
* **
55421543 GGTAATTTTA-CAAACTAGGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTT
* *
55421570 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTT
*
55421597 AGTAATTC
1 GGTAATTC
55421605 CACAATCGAG
Statistics
Matches: 243, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
26 3 0.01
27 237 0.98
28 3 0.01
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTT
Found at i:55421727 original size:81 final size:81
Alignment explanation
Indices: 55421608--55421805 Score: 261
Period size: 81 Copynumber: 2.4 Consensus size: 81
55421598 GTAATTCCAC
* * * * * *
55421608 AATCGAGGGTAAAACGGTAATTTTGTAAACTGAAGGTAAAATGGTAATTTTGTAAATCAAGGGTA
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGATAATTTTGTAAATCAAGGGTA
* *
55421673 AAACGGTAATTTTGTA
66 AAACGGTAATTCTATA
* * * *
55421689 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGATTATTTTTTAAATCGAGGGTG
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGATAATTTTGTAAATCAAGGGTA
55421754 AAACGGTAATTCTATA
66 AAACGGTAATTCTATA
* * *
55421770 AATCAAGGGTAAAATGGTAATTCTACAAATCGAGGG
1 AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGG
55421806 CATTTTAGTA
Statistics
Matches: 102, Mismatches: 15, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 102 1.00
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (81 bp):
AATCGAGGGTAAAATGGTAATTCTATAAATTGAGGGTAAAATGATAATTTTGTAAATCAAGGGTA
AAACGGTAATTCTATA
Found at i:55421792 original size:27 final size:27
Alignment explanation
Indices: 55421608--55421805 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
55421598 GTAATTCCAC
* *
55421608 AATCGAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* *
55421635 AA-CTGAAGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAATGGTAATTTTATA
* * *
55421662 AATCAAGGGTAAAACGGTAATTTTGTA
1 AATCGAGGGTAAAATGGTAATTTTATA
*
55421689 AATCGAGGGTAAAATGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * * *
55421716 AATTGAGGGTAAAATGATTATTTTTTA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * *
55421743 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAATGGTAATTTTATA
* * *
55421770 AATCAAGGGTAAAATGGTAATTCTACA
1 AATCGAGGGTAAAATGGTAATTTTATA
55421797 AATCGAGGG
1 AATCGAGGG
55421806 CATTTTAGTA
Statistics
Matches: 143, Mismatches: 26, Indels: 4
0.83 0.15 0.02
Matches are distributed among these distances:
26 1 0.01
27 141 0.99
28 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.23, T:0.30
Consensus pattern (27 bp):
AATCGAGGGTAAAATGGTAATTTTATA
Found at i:55421820 original size:81 final size:80
Alignment explanation
Indices: 55421645--55421834 Score: 218
Period size: 81 Copynumber: 2.3 Consensus size: 80
55421635 AACTGAAGGT
* * *
55421645 AAAATGGTAATTTTGTAAATCAAGGGTAAAACGGTAATTTTGTAAATCGAGGGTAAAATGGTAAT
1 AAAAT-GTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAATGGTAAT
* * *
55421710 TCTATAAATTGAGGGT
65 TCTACAAATCGAGGGC
* * * *
55421726 AAAATGATTATTTTTTAAATCGAGGGTGAAACGGTAATTCTATAAATCAAGGGTAAAATGGTAAT
1 AAAATG-TAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAATGGTAAT
55421791 TCTACAAATCGAGGGC
65 TCTACAAATCGAGGGC
*** * *
55421807 ATTTTAGTAATTTTGTAAACCAATGGTA
1 AAAAT-GTAATTTTGTAAATCAAGGGTA
55421835 TTTCTATAAT
Statistics
Matches: 88, Mismatches: 19, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
80 1 0.01
81 86 0.98
82 1 0.01
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (80 bp):
AAAATGTAATTTTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCAAGGGTAAAATGGTAATT
CTACAAATCGAGGGC
Found at i:55421945 original size:54 final size:54
Alignment explanation
Indices: 55421784--55422063 Score: 273
Period size: 54 Copynumber: 5.2 Consensus size: 54
55421774 AAGGGTAAAA
* * ** ** **
55421784 TGGTAATTCTACAAATCGAGGGCATTTTAGTAATTTTGTAAACCAATGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
* * ** ** *
55421838 CT-ATAATTTTTAGAAAGTCGAGGGTATTTCTATAATTTTGTAAATCAGGGGTATTT
1 -TGGTAA-TTTTACAAA-TCGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
* * *
55421894 TGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTT
1 TGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
* *
55421948 TGGTAATTTTACAAA-CCAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTT
1 TGGTAATTTTACAAATCGA-GGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
* *
55422002 TGGTAATTTTATAAA-CAAAGGGTATTTAC--TAATTTTACAAACCAGGGGTATTT
1 TGGTAATTTTACAAATC-GAGGGTATTT-CGGTAATTTTACAAACCAGGGGTATTT
55422055 TGGTAATTT
1 TGGTAATTT
55422064 GGTAAACTAA
Statistics
Matches: 191, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
53 34 0.18
54 104 0.54
55 18 0.09
56 35 0.18
ACGTcount: A:0.31, C:0.10, G:0.20, T:0.40
Consensus pattern (54 bp):
TGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTACAAACCAGGGGTATTT
Found at i:55422070 original size:27 final size:27
Alignment explanation
Indices: 55421883--55422063 Score: 249
Period size: 27 Copynumber: 6.7 Consensus size: 27
55421873 TTTTGTAAAT
55421883 CAGGGGTATTTTGGTAATTTTACAAA-
1 CAGGGGTATTTTGGTAATTTTACAAAC
** * *
55421909 TTGAGGGTATTTCGGTAATTTCACAAAC
1 CAG-GGGTATTTTGGTAATTTTACAAAC
*
55421937 CAGTGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
55421964 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
55421991 CAGGGGTATTTTGGTAATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * **
55422018 AAAGGGTA-TTTACTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
55422044 CAGGGGTATTTTGGTAATTT
1 CAGGGGTATTTTGGTAATTT
55422064 GGTAAACTAA
Statistics
Matches: 132, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
26 22 0.17
27 109 0.83
28 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:55424032 original size:6 final size:6
Alignment explanation
Indices: 55424021--55424101 Score: 67
Period size: 6 Copynumber: 13.0 Consensus size: 6
55424011 AACTAGGTGA
* *
55424021 CAGAAT CAGAAT CAGAAT CAGTAT CAGGTAAT -AGAAT CAAAAT CAGAAT
1 CAGAAT CAGAAT CAGAAT CAGAAT CA-G-AAT CAGAAT CAGAAT CAGAAT
* *
55424070 CAGTAT CAAGTAA- CAGAAT CAAAAAT CAGAAT
1 CAGAAT C-AG-AAT CAGAAT C-AGAAT CAGAAT
55424102 GTGAATGCAA
Statistics
Matches: 60, Mismatches: 8, Indels: 14
0.73 0.10 0.17
Matches are distributed among these distances:
5 5 0.08
6 42 0.70
7 10 0.17
8 3 0.05
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (6 bp):
CAGAAT
Found at i:55424065 original size:31 final size:31
Alignment explanation
Indices: 55424020--55424101 Score: 128
Period size: 31 Copynumber: 2.6 Consensus size: 31
55424010 AAACTAGGTG
* *
55424020 ACAGAATCAGAATCAGAATCAGTATCAGGTA
1 ACAGAATCAAAATCAGAATCAGTATCAAGTA
*
55424051 ATAGAATCAAAATCAGAATCAGTATCAAGTA
1 ACAGAATCAAAATCAGAATCAGTATCAAGTA
55424082 ACAGAATCAAAAATCAGAAT
1 ACAGAATC-AAAATCAGAAT
55424102 GTGAATGCAA
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
31 35 0.76
32 11 0.24
ACGTcount: A:0.51, C:0.15, G:0.15, T:0.20
Consensus pattern (31 bp):
ACAGAATCAAAATCAGAATCAGTATCAAGTA
Found at i:55424268 original size:27 final size:26
Alignment explanation
Indices: 55424238--55424339 Score: 132
Period size: 27 Copynumber: 3.8 Consensus size: 26
55424228 ACTCAGTTAT
* *
55424238 CAGATATTGTGACAGAGTCACCAGATA
1 CAGATATTGTGGCAGAGCCACCAGA-A
55424265 CAGATATTGTGGCAGAGCCACCAGAA
1 CAGATATTGTGGCAGAGCCACCAGAA
*
55424291 CAGATATTTGTGGCATAGCCACCAGAAA
1 CAGATA-TTGTGGCAGAGCCACCAG-AA
* *
55424319 CAGATAATGTGGCAAAGCCAC
1 CAGATATTGTGGCAGAGCCAC
55424340 TTAACAGAAT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
26 7 0.10
27 53 0.78
28 8 0.12
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (26 bp):
CAGATATTGTGGCAGAGCCACCAGAA
Found at i:55424526 original size:22 final size:22
Alignment explanation
Indices: 55424498--55424562 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
55424488 GCAAATACGT
*
55424498 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* * *
55424520 TTGGCACAGAGCTAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
55424542 TTGACACAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
55424563 AAGGCTTTAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
21 2 0.06
22 30 0.88
23 2 0.06
ACGTcount: A:0.34, C:0.22, G:0.23, T:0.22
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:55425046 original size:27 final size:27
Alignment explanation
Indices: 55424989--55425317 Score: 355
Period size: 27 Copynumber: 12.3 Consensus size: 27
55424979 GGGGCAAAAT
* * * *
55424989 GGTAATTTTACCCCACA-AGGTATCTC
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
55425015 GGTAATTCCACCCTACAGGGGTATTTT
1 GGTAATTCTACCCTACAGGGGTATTTC
* *
55425042 AGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
55425069 GGTAATTCTACCCTACAGGGGTATTAC
1 GGTAATTCTACCCTACAGGGGTATTTC
**
55425096 AATAATTCTACCCTACA-GGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
55425122 GGTAATTCTACCCTATAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
55425149 GGTAATTCTACCCTACAGGGGTA-TTC
1 GGTAATTCTACCCTACAGGGGTATTTC
55425175 TGGTAATTCTACCCTACAGGGGTA-TTC
1 -GGTAATTCTACCCTACAGGGGTATTTC
* * *
55425202 TGATAATTCTACCCTACAAGGGTATTCC
1 -GGTAATTCTACCCTACAGGGGTATTTC
* ** *
55425230 GGTAATTTTA-CAAACTAGGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTC
* ** *
55425257 GGTAATTTTA-CAAACTAGGGGTATTTT
1 GGTAATTCTACCCTAC-AGGGGTATTTC
*
55425284 GGTAATTCTATCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAGGGGTATTTC
*
55425311 AGTAATT
1 GGTAATT
55425318 TCACAATCGA
Statistics
Matches: 262, Mismatches: 35, Indels: 11
0.85 0.11 0.04
Matches are distributed among these distances:
26 42 0.16
27 215 0.82
28 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.20, T:0.35
Consensus pattern (27 bp):
GGTAATTCTACCCTACAGGGGTATTTC
Found at i:55425368 original size:27 final size:27
Alignment explanation
Indices: 55425322--55425518 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
55425312 GTAATTTCAC
*
55425322 AATCGAGGGTAAAACAGTAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* *
55425349 AA-CTGGGGGTAAAATGGTAATTTTGTA
1 AATC-GAGGGTAAAACGGTAATTTTGTA
* *
55425376 AATCGAGGGCAAAACGATAATTTTGTA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
55425403 AATCAAGGGTAAAATGGTAATTTTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
55425430 AATCGAGGGTAAAACGGTAATTTT-TA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * *
55425456 AATCGAGGGTGAAACGGTAATTCTATA
1 AATCGAGGGTAAAACGGTAATTTTGTA
* * * * **
55425483 AATCAAGGGTGAAATGGTAATTCTACA
1 AATCGAGGGTAAAACGGTAATTTTGTA
55425510 AATCGAGGG
1 AATCGAGGG
55425519 CATTTCAATA
Statistics
Matches: 147, Mismatches: 20, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
26 25 0.17
27 121 0.82
28 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (27 bp):
AATCGAGGGTAAAACGGTAATTTTGTA
Found at i:55425498 original size:80 final size:81
Alignment explanation
Indices: 55425322--55425518 Score: 245
Period size: 80 Copynumber: 2.4 Consensus size: 81
55425312 GTAATTTCAC
* ** * * *
55425322 AATCGAGGGTAAAACAGTAATTTTGTAAA-CTGGGGGTAAAATGGTAATTTTGTAAATCGAGGGC
1 AATCAAGGGTAAAATGGTAATTTTATAAATC-GAGGGTAAAACGGTAATTTTGTAAATCGAGGGC
* *
55425386 AAAACGATAATTTTGTA
65 AAAACGATAATTCTATA
**
55425403 AATCAAGGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTTT-TAAATCGAGGGTG
1 AATCAAGGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGCA
*
55425467 AAACGGTAATTCTATA
66 AAACGATAATTCTATA
* * *
55425483 AATCAAGGGTGAAATGGTAATTCTACAAATCGAGGG
1 AATCAAGGGTAAAATGGTAATTTTATAAATCGAGGG
55425519 CATTTCAATA
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
80 57 0.56
81 43 0.43
82 1 0.01
ACGTcount: A:0.39, C:0.08, G:0.24, T:0.28
Consensus pattern (81 bp):
AATCAAGGGTAAAATGGTAATTTTATAAATCGAGGGTAAAACGGTAATTTTGTAAATCGAGGGCA
AAACGATAATTCTATA
Found at i:55425531 original size:80 final size:81
Alignment explanation
Indices: 55425366--55425538 Score: 213
Period size: 80 Copynumber: 2.1 Consensus size: 81
55425356 GGTAAAATGG
* * * *
55425366 TAATTTTGTAAATCGAGGGCAAAACGATAATTTTGTAAATCAAGGGTAAAATGGTAATTTTATAA
1 TAATTTTGTAAATCGAGGGCAAAACGATAATTCTATAAATCAAGGGTAAAATGGTAATTCTACAA
* **
55425431 ATCGAGGGTAAAACGG
66 ATCGAGGGCAAAACAA
** * *
55425447 TAATTTT-TAAATCGAGGGTGAAACGGTAATTCTATAAATCAAGGGTGAAATGGTAATTCTACAA
1 TAATTTTGTAAATCGAGGGCAAAACGATAATTCTATAAATCAAGGGTAAAATGGTAATTCTACAA
***
55425511 ATCGAGGGCATTTCAA
66 ATCGAGGGCAAAACAA
55425527 TAATTTTGTAAA
1 TAATTTTGTAAA
55425539 CCAGTGATAT
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
80 66 0.86
81 11 0.14
ACGTcount: A:0.39, C:0.09, G:0.21, T:0.31
Consensus pattern (81 bp):
TAATTTTGTAAATCGAGGGCAAAACGATAATTCTATAAATCAAGGGTAAAATGGTAATTCTACAA
ATCGAGGGCAAAACAA
Found at i:55425605 original size:27 final size:27
Alignment explanation
Indices: 55425571--55425776 Score: 108
Period size: 27 Copynumber: 7.7 Consensus size: 27
55425561 TAGAAAGTCA
**
55425571 AGGGTATTTCTGTAATTTTGTAAA-TG
1 AGGGTATTTCTGTAATTTTACAAATTG
55425597 AGGGGTATTT-TGGTAATTTTACAAATTG
1 A-GGGTATTTCT-GTAATTTTACAAATTG
* * **
55425625 AGGGTATTTCGGTAATTTCACAAA-CC
1 AGGGTATTTCTGTAATTTTACAAATTG
**
55425651 AGTGGTATTT-TGATAATTTTACAAA-CC
1 AG-GGTATTTCTG-TAATTTTACAAATTG
***
55425678 AGGGTATTT-TGGTAATTTTACAAACCA
1 AGGGTATTTCT-GTAATTTTACAAATTG
** ***
55425705 AGGGTATTT-TGGTAATTTTATTAACAA
1 AGGGTATTTCT-GTAATTTTACAAATTG
*
55425732 AGGGTATTT-TAGTAATTTTACAAACT-
1 AGGGTATTTCT-GTAATTTTACAAATTG
55425758 AGGGGTATTT-TGGTAATTT
1 A-GGGTATTTCT-GTAATTT
55425777 GGTAAACAAA
Statistics
Matches: 154, Mismatches: 17, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
26 26 0.17
27 125 0.81
28 3 0.02
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AGGGTATTTCTGTAATTTTACAAATTG
Found at i:55425628 original size:110 final size:107
Alignment explanation
Indices: 55425497--55425724 Score: 253
Period size: 110 Copynumber: 2.1 Consensus size: 107
55425487 AAGGGTGAAA
* ***
55425497 TGGTAATTCTACAAATCGAGGGCATTTCAATAATTTTGTAAACCAGTGATATTTCT-ATAACTTT
1 TGGTAATTTTACAAATCGAGGGCATTTCAATAATTTCACAAACCAGTGATATTT-TGATAA-TTT
* ** ** *
55425561 TAGAAAGTCAAGGGTATTTCT-GTAATTTTGTAAATGAGGGGTATTT
64 TACAAA--CAAGGGTATTT-TGGTAATTTTACAAACCAAGGGTATTT
* * ** *
55425607 TGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGATAATTTTA
1 TGGTAATTTTACAAATCGAGGGCATTTCAATAATTTCACAAACCAGTGATATTTTGATAATTTTA
*
55425672 CAAACCAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
66 CAAACAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
55425714 TGGTAATTTTA
1 TGGTAATTTTA
55425725 TTAACAAAGG
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
106 1 0.01
107 41 0.41
109 9 0.09
110 49 0.49
ACGTcount: A:0.32, C:0.10, G:0.19, T:0.39
Consensus pattern (107 bp):
TGGTAATTTTACAAATCGAGGGCATTTCAATAATTTCACAAACCAGTGATATTTTGATAATTTTA
CAAACAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
Found at i:55425692 original size:80 final size:81
Alignment explanation
Indices: 55425570--55425776 Score: 242
Period size: 80 Copynumber: 2.6 Consensus size: 81
55425560 TTAGAAAGTC
** ** ***
55425570 AAGGGTATTTCT-GTAATTTTGTAAATGAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTT
1 AAGGGTATTT-TAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTT
55425634 CGGTAATTTCACAAAC-
65 CGGTAATTTCACAAACA
*
55425650 CAGTGGTATTTT-GATAATTTTACAAACCA-GGGTATTTTGGTAATTTTACAAACCAAGGGTATT
1 AAG-GGTATTTTAG-TAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATT
* * **
55425713 TTGGTAATTTTATTAACA
64 TCGGTAATTTCACAAACA
*
55425731 AAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTT
1 AAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTT
55425777 GGTAAACAAA
Statistics
Matches: 108, Mismatches: 14, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
80 70 0.65
81 38 0.35
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (81 bp):
AAGGGTATTTTAGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTC
GGTAATTTCACAAACA
Found at i:55425783 original size:27 final size:27
Alignment explanation
Indices: 55425597--55425776 Score: 220
Period size: 27 Copynumber: 6.7 Consensus size: 27
55425587 TTTGTAAATG
*
55425597 AGGGGTATTTTGGTAATTTTACAAA-T
1 AGGGGTATTTTGGTAATTTTACAAACC
* * *
55425623 TGAGGGTATTTCGGTAATTTCACAAACC
1 AG-GGGTATTTTGGTAATTTTACAAACC
* *
55425651 AGTGGTATTTTGATAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
55425678 A-GGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACC
* ** *
55425704 AAGGGTATTTTGGTAATTTTATTAACA
1 AGGGGTATTTTGGTAATTTTACAAACC
* * *
55425731 AAGGGTATTTTAGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACC
55425758 AGGGGTATTTTGGTAATTT
1 AGGGGTATTTTGGTAATTT
55425777 GGTAAACAAA
Statistics
Matches: 131, Mismatches: 20, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
26 25 0.19
27 105 0.80
28 1 0.01
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACC
Found at i:55425786 original size:54 final size:54
Alignment explanation
Indices: 55425570--55425776 Score: 238
Period size: 54 Copynumber: 3.9 Consensus size: 54
55425560 TTAGAAAGTC
** ** **
55425570 AAGGGTATTTCT-GTAATTTTGTAAATGAGGGGTATTTTGGTAATTTTACAAATT
1 AAGGGTATTT-TGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACA
* * * * *
55425624 GAGGGTATTTCGGTAATTTCACAAACCAGTGGTATTTTGATAATTTTACAAAC-
1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACA
* * **
55425677 CAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTGGTAATTTTATTAACA
1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACA
* *
55425731 AAGGGTATTTTAGTAATTTTACAAACTAGGGGTATTTTGGTAATTT
1 AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTT
55425777 GGTAAACAAA
Statistics
Matches: 129, Mismatches: 22, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
53 45 0.35
54 84 0.65
ACGTcount: A:0.31, C:0.08, G:0.20, T:0.41
Consensus pattern (54 bp):
AAGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTTACAAACA
Found at i:55434763 original size:129 final size:129
Alignment explanation
Indices: 55434540--55434776 Score: 314
Period size: 129 Copynumber: 1.8 Consensus size: 129
55434530 TATGTGTGTG
* * *
55434540 CGTGTAAGACCACATCTGAGACGTTCACATTGATATCTGATTACGTGTAATACCATGTCTGGGAC
1 CGTGTAAGACCACATCTGAGACGTTCACATCGATATCTGATTACATGTAAGACCATGTCTGGGAC
**
55434605 GTTCGCATCGATATGTGACTATGTATAAGACCACGTCTGGGACGTTGCCATCAATATGTGATTA
66 GTTCGCATCGATATGTGACTACATATAAGACCACGTCTGGGACGTTGCCATCAATATGTGATTA
** * * * * * *
55434669 CGTGTAAGACCATGTCTGGGATGTTGACATCGATATGTGATTACATGTAAGGCCCTGTCTGGGAC
1 CGTGTAAGACCACATCTGAGACGTTCACATCGATATCTGATTACATGTAAGACCATGTCTGGGAC
* * *
55434734 AG-TGGCATCGATATGTGATTACATGTAAGACCACGTCTGGGAC
66 -GTTCGCATCGATATGTGACTACATATAAGACCACGTCTGGGAC
55434777 ATTGGCATTG
Statistics
Matches: 91, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
129 90 0.99
130 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (129 bp):
CGTGTAAGACCACATCTGAGACGTTCACATCGATATCTGATTACATGTAAGACCATGTCTGGGAC
GTTCGCATCGATATGTGACTACATATAAGACCACGTCTGGGACGTTGCCATCAATATGTGATTA
Found at i:55434777 original size:43 final size:43
Alignment explanation
Indices: 55434540--55434784 Score: 269
Period size: 43 Copynumber: 5.7 Consensus size: 43
55434530 TATGTGTGTG
* * ** * *
55434540 CGTGTAAGACCACATCTGAGACGTTCACATTGATATCTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* * * *
55434583 CGTGTAATACCATGTCTGGGACGTTCGCATCGATATGTGACTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* * * *
55434626 TGTATAAGACCACGTCTGGGACGTTGCCATCAATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* * *
55434669 CGTGTAAGACCATGTCTGGGATGTTGACATCGATATGTGATTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
* *
55434712 CATGTAAGGCC-CTGTCTGGGACAG-TGGCATCGATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGATTA
* *
55434755 CATGTAAGACCACGTCTGGGACATTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
55434785 TGTATAATAT
Statistics
Matches: 169, Mismatches: 29, Indels: 8
0.82 0.14 0.04
Matches are distributed among these distances:
43 167 0.99
44 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTA
Found at i:55438534 original size:46 final size:46
Alignment explanation
Indices: 55438467--55438641 Score: 160
Period size: 46 Copynumber: 3.8 Consensus size: 46
55438457 TGTAACCCGC
* *
55438467 CCATAAGTGAACTTGGACTCAACTCAACGAGCTCGGGCGTTTGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* * *
55438513 CCATAAGTGAACTCGGACTCAACTCAAGGAGCTCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG--G-C-ATTTGCAT
* * * * * *
55438563 CTC-T---CGAACTCAGACTCAACTCAACGAGTTCAGACATTCGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
* *
55438606 CCATAAGTGAACTCGGACTCAACTTAACGAGTTCGG
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG
55438642 ATGCCCAAAC
Statistics
Matches: 102, Mismatches: 18, Indels: 18
0.74 0.13 0.13
Matches are distributed among these distances:
42 1 0.01
43 7 0.07
44 1 0.01
46 59 0.58
47 24 0.24
48 1 0.01
49 1 0.01
50 7 0.07
51 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.21, T:0.23
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTTGCAT
Found at i:55441048 original size:30 final size:30
Alignment explanation
Indices: 55441004--55441092 Score: 101
Period size: 30 Copynumber: 3.0 Consensus size: 30
55440994 CAAAGATAAT
55441004 AAGAAAACC-GAATAAAGAAATCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
* *
55441033 GAGAAACCCAGAATAAAGAAATCC-AGAATA
1 AAGAAAACCAGAATAAAGAAATCCAAG-ATA
* * * *
55441063 AAGAGATCCAGGATAAAGAAACCCAAGATA
1 AAGAAAACCAGAATAAAGAAATCCAAGATA
55441093 CGATATTATG
Statistics
Matches: 50, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
29 9 0.18
30 39 0.78
31 2 0.04
ACGTcount: A:0.57, C:0.16, G:0.17, T:0.10
Consensus pattern (30 bp):
AAGAAAACCAGAATAAAGAAATCCAAGATA
Found at i:55441052 original size:15 final size:15
Alignment explanation
Indices: 55441004--55441083 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
55440994 CAAAGATAAT
*
55441004 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
55441018 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
* *
55441033 GAGAAACCCAGAATA
1 AAGAAATCCAGAATA
55441048 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
55441063 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
55441078 AAGAAA
1 AAGAAA
55441084 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
14 9 0.16
15 45 0.82
16 1 0.02
ACGTcount: A:0.59, C:0.14, G:0.17, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55441092 original size:15 final size:15
Alignment explanation
Indices: 55441015--55441092 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
55441005 AGAAAACCGA
55441015 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
* *
55441030 ATAGAGAAA-CCCAG
1 ATAAAGAAATCCAAG
55441044 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
55441059 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
55441075 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
55441090 ATA
1 ATA
55441093 CGATATTATG
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
14 4 0.08
15 45 0.87
16 3 0.06
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:55444117 original size:45 final size:46
Alignment explanation
Indices: 55444053--55444225 Score: 216
Period size: 45 Copynumber: 3.8 Consensus size: 46
55444043 ATGTAACCCG
*
55444053 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
*
55444098 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C--GTTCGCAT
* *
55444148 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGAC--TCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
55444189 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55444226 TGCCCAAATC
Statistics
Matches: 111, Mismatches: 7, Indels: 21
0.80 0.05 0.15
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 1 0.01
43 2 0.02
44 30 0.27
45 35 0.32
47 29 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGTTCGCAT
Found at i:55444217 original size:91 final size:91
Alignment explanation
Indices: 55444061--55444229 Score: 304
Period size: 91 Copynumber: 1.8 Consensus size: 91
55444051 CGCCATAAGT
55444061 GAACTCGGACTCAACTCAACGAGCTCGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGGCG-TCGCATCCATAAGTGAACTCGGACTCAACTCAAC
55444126 GAGTTCGGATGCCTAGTTACATCTCAC
65 GAGTTCGGATGCCTAGTTACATCTCAC
*
55444153 GAACTCGGACTCAACTCAACGAGTTCGGAC-TCGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 GAACTCGGACTCAACTCAACGAGCTCGG-CGTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
55444217 GAGTTCGGATGCC
65 GAGTTCGGATGCC
55444230 CAAATCCAGT
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
91 47 0.63
92 27 0.36
93 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (91 bp):
GAACTCGGACTCAACTCAACGAGCTCGGCGTCGCATCCATAAGTGAACTCGGACTCAACTCAACG
AGTTCGGATGCCTAGTTACATCTCAC
Found at i:55446281 original size:29 final size:29
Alignment explanation
Indices: 55446244--55446327 Score: 100
Period size: 29 Copynumber: 2.9 Consensus size: 29
55446234 GATAACAAGA
*
55446244 AAACC-GAATAAAGAAATCCAAGATAGAG
1 AAACCAGAATAAAGAAATCCAAGATAAAG
55446272 AAACCAGAATAAAGAAATCC-AGAATAAAG
1 AAACCAGAATAAAGAAATCCAAG-ATAAAG
* * *
55446301 AGATCCAGGATAAAGAAACCCAAGATA
1 A-AACCAGAATAAAGAAATCCAAGATA
55446328 CGATACTATG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.15
29 20 0.42
30 19 0.40
31 2 0.04
ACGTcount: A:0.57, C:0.15, G:0.17, T:0.11
Consensus pattern (29 bp):
AAACCAGAATAAAGAAATCCAAGATAAAG
Found at i:55446293 original size:15 final size:15
Alignment explanation
Indices: 55446240--55446318 Score: 92
Period size: 15 Copynumber: 5.4 Consensus size: 15
55446230 CAAAGATAAC
*
55446240 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
55446254 AAGAAATCCA-AGATA
1 AAGAAATCCAGA-ATA
*
55446269 GAGAAA-CCAGAATA
1 AAGAAATCCAGAATA
55446283 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
55446298 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
55446313 AAGAAA
1 AAGAAA
55446319 CCCAAGATAC
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
14 20 0.36
15 35 0.64
ACGTcount: A:0.59, C:0.13, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:55446327 original size:15 final size:15
Alignment explanation
Indices: 55446251--55446327 Score: 79
Period size: 15 Copynumber: 5.2 Consensus size: 15
55446241 AGAAAACCGA
55446251 ATAAAGAAATCCAAG
1 ATAAAGAAATCCAAG
*
55446266 ATAGAGAAA-CC-AG
1 ATAAAGAAATCCAAG
55446279 AATAAAGAAATCC-AG
1 -ATAAAGAAATCCAAG
* *
55446294 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
55446310 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
55446325 ATA
1 ATA
55446328 CGATACTATG
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
13 2 0.04
14 10 0.19
15 39 0.75
16 1 0.02
ACGTcount: A:0.57, C:0.14, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:55449339 original size:92 final size:93
Alignment explanation
Indices: 55449228--55449398 Score: 308
Period size: 92 Copynumber: 1.8 Consensus size: 93
55449218 GCCCATAAGT
* *
55449228 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55449293 CGAG-TCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
55449320 GAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
55449385 CGAGTTCGGATGCC
66 CGAGTTCGGATGCC
55449399 CAAATATCCA
Statistics
Matches: 75, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
92 66 0.88
93 9 0.12
ACGTcount: A:0.27, C:0.30, G:0.22, T:0.20
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACGCTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:55449394 original size:46 final size:46
Alignment explanation
Indices: 55449220--55449394 Score: 223
Period size: 46 Copynumber: 3.8 Consensus size: 46
55449210 TGTAACCCGC
* * *
55449220 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
* *
55449266 CCATAAGTGAACTCGGACTCAACTCAACGAG-TCGGATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACG-CTCG---CAT
* *
55449315 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
55449358 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
55449395 TGCCCAAATA
Statistics
Matches: 111, Mismatches: 10, Indels: 16
0.81 0.07 0.12
Matches are distributed among these distances:
43 3 0.03
44 1 0.01
45 7 0.06
46 88 0.79
47 8 0.07
48 1 0.01
49 3 0.03
ACGTcount: A:0.29, C:0.30, G:0.22, T:0.20
Consensus pattern (46 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGACGCTCGCAT
Found at i:55453044 original size:40 final size:40
Alignment explanation
Indices: 55452995--55453093 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
55452985 TAACCGGGTT
*
55452995 GACCCGAAGGCAATTGTGCTAGTGGC-TAC-ATCCGGGCTAA
1 GACCCGAAGGCAATTGTGCGAGT--CATACTATCCGGGCTAA
*
55453035 GACCCGAAGGC-ATTCGTGCGAGTCATTCTATCCGGGCTAA
1 GACCCGAAGGCAATT-GTGCGAGTCATACTATCCGGGCTAA
*
55453075 GACCCGAAGGCATTTGTGC
1 GACCCGAAGGCAATTGTGC
55453094 AAATCGTGAT
Statistics
Matches: 52, Mismatches: 3, Indels: 8
0.83 0.05 0.13
Matches are distributed among these distances:
38 1 0.02
39 5 0.10
40 44 0.85
41 2 0.04
ACGTcount: A:0.23, C:0.26, G:0.29, T:0.21
Consensus pattern (40 bp):
GACCCGAAGGCAATTGTGCGAGTCATACTATCCGGGCTAA
Found at i:55453107 original size:40 final size:40
Alignment explanation
Indices: 55453024--55453125 Score: 123
Period size: 40 Copynumber: 2.5 Consensus size: 40
55453014 TAGTGGCTAC
* * **
55453024 ATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATTCT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* *
55453064 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGTGAT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
* * *
55453104 ATCCGGGTTAAGTCCCGTAGGC
1 ATCCGGGCTAAGACCCGAAGGC
55453126 CTTGGTGCGG
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 53 1.00
ACGTcount: A:0.24, C:0.25, G:0.28, T:0.23
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAATCATGAT
Found at i:55460460 original size:40 final size:39
Alignment explanation
Indices: 55460295--55460478 Score: 138
Period size: 40 Copynumber: 4.6 Consensus size: 39
55460285 AAATTGAATG
* * *
55460295 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAAT--T
1 ATATCCGGGCTAAGACCCGAAGGC-ATT-TG-TGCAAATCGT
* * * * * *
55460335 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-T
* * * * *
55460375 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATC-GT
*
55460415 CTATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
* * *
55460454 GATATCCGGGTTAAGTCCCGTAGGC
1 -ATATCCGGGCTAAGACCCGAAGGC
55460479 CTTGGTGCGG
Statistics
Matches: 113, Mismatches: 26, Indels: 10
0.76 0.17 0.07
Matches are distributed among these distances:
37 4 0.04
38 2 0.02
39 3 0.03
40 104 0.92
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (39 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCGT
Found at i:55460503 original size:80 final size:81
Alignment explanation
Indices: 55460335--55460523 Score: 186
Period size: 80 Copynumber: 2.4 Consensus size: 81
55460325 GCTGGAAATT
* * * *
55460335 ATAACCGGGTTAAGACCCGAAGGCAATTGTGCTAGTGGCTACATCCGGGCTAAGACCCGAAGGCA
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
*
55460400 TTCGTGCGAGTCATTC
66 TTCGTGCGAGTCATCC
* * * * * *
55460416 -TATCCGGGCTAAGACCCGAAGGCATTTGTGCAAATCG-TGATATCCGGGTTAAGTCCCGTAGGC
1 ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCT-ACATCCGGGCTAAGACCCGAAGGC
* * * *
55460479 CTTGGTGCGGGTTA-CC
65 ATTCGTGCGAGTCATCC
* * *
55460495 ATAACCGGGCTATGTCCCGAAGGCGATTG
1 ATAACCGGGCTAAGACCCGAAGGCAATTG
55460524 ATCGAGTAGC
Statistics
Matches: 86, Mismatches: 20, Indels: 5
0.77 0.18 0.05
Matches are distributed among these distances:
79 2 0.02
80 84 0.98
ACGTcount: A:0.23, C:0.24, G:0.30, T:0.23
Consensus pattern (81 bp):
ATAACCGGGCTAAGACCCGAAGGCAATTGTGCAAATCGCTACATCCGGGCTAAGACCCGAAGGCA
TTCGTGCGAGTCATCC
Found at i:55464917 original size:8 final size:8
Alignment explanation
Indices: 55464900--55464942 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
55464890 GTAGATCGGT
55464900 AAAAGCTG
1 AAAAGCTG
*
55464908 AAATGCTG
1 AAAAGCTG
*
55464916 AAAAGCCG
1 AAAAGCTG
* *
55464924 AAATGCCG
1 AAAAGCTG
55464932 AAAAGCTG
1 AAAAGCTG
55464940 AAA
1 AAA
55464943 GTTTGGCTAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (8 bp):
AAAAGCTG
Found at i:55464921 original size:16 final size:16
Alignment explanation
Indices: 55464900--55464942 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
55464890 GTAGATCGGT
*
55464900 AAAAGCTGAAATGCTG
1 AAAAGCTGAAATGCCG
*
55464916 AAAAGCCGAAATGCCG
1 AAAAGCTGAAATGCCG
55464932 AAAAGCTGAAA
1 AAAAGCTGAAA
55464943 GTTTGGCTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (16 bp):
AAAAGCTGAAATGCCG
Found at i:55465200 original size:28 final size:29
Alignment explanation
Indices: 55465160--55465267 Score: 132
Period size: 28 Copynumber: 3.8 Consensus size: 29
55465150 GACTGTAAAC
55465160 GTGATTTGGGCCTAAT-GGCCATATGAAT
1 GTGATTTGGGCCTAATAGGCCATATGAAT
* * *
55465188 GTGATTTGGGCCTAATGGGCCACATAAAT
1 GTGATTTGGGCCTAATAGGCCATATGAAT
*
55465217 GTGA-TTGGGCCTAATAGGCCATAAGAAT
1 GTGATTTGGGCCTAATAGGCCATATGAAT
* * *
55465245 G-AAATTGGGCCTAGTAGGCCATA
1 GTGATTTGGGCCTAATAGGCCATA
55465268 AGCATGTATG
Statistics
Matches: 70, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
27 1 0.01
28 55 0.79
29 14 0.20
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.27
Consensus pattern (29 bp):
GTGATTTGGGCCTAATAGGCCATATGAAT
Found at i:55474990 original size:19 final size:19
Alignment explanation
Indices: 55474962--55474998 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
55474952 TACATATTAA
*
55474962 CCTACTGTTTATTGAAGCG
1 CCTACCGTTTATTGAAGCG
55474981 CCTACCGTTTATTGAAGC
1 CCTACCGTTTATTGAAGC
55474999 ACTTTCGCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.35
Consensus pattern (19 bp):
CCTACCGTTTATTGAAGCG
Found at i:55482476 original size:28 final size:28
Alignment explanation
Indices: 55482444--55482547 Score: 138
Period size: 28 Copynumber: 3.7 Consensus size: 28
55482434 GCCTGTAAAA
55482444 GTGATTTGGGCCTAAT-GGCCATATGAAT
1 GTGA-TTGGGCCTAATGGGCCATATGAAT
* *
55482472 GTGATTTGGGCCTAATGGGCCACATAAAT
1 GTGA-TTGGGCCTAATGGGCCATATGAAT
*
55482501 GTGATTAGGCCTAATGGGCCATATGAAT
1 GTGATTGGGCCTAATGGGCCATATGAAT
* *
55482529 GAGATTGGGCCTAGTGGGC
1 GTGATTGGGCCTAATGGGC
55482548 AATAAGCATG
Statistics
Matches: 67, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
28 53 0.79
29 14 0.21
ACGTcount: A:0.25, C:0.15, G:0.32, T:0.28
Consensus pattern (28 bp):
GTGATTGGGCCTAATGGGCCATATGAAT
Found at i:55496071 original size:27 final size:28
Alignment explanation
Indices: 55496040--55496104 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 28
55496030 CTACGGATCA
* * *
55496040 AGTCAAATGAATATATCGTC-GATCCAG
1 AGTCAAATAAATAAATCATCTGATCCAG
* *
55496067 AGTCAAATAAATAAATCATCTTATTCAG
1 AGTCAAATAAATAAATCATCTGATCCAG
55496095 AGTCAAATAA
1 AGTCAAATAA
55496105 CAAGTGAAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (28 bp):
AGTCAAATAAATAAATCATCTGATCCAG
Found at i:55496532 original size:19 final size:19
Alignment explanation
Indices: 55496508--55496545 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
55496498 TTACAATTTA
55496508 AATTTTT-ATTTTATTTTCT
1 AATTTTTCA-TTTATTTTCT
55496527 AATTTTTCATTTATTTTCT
1 AATTTTTCATTTATTTTCT
55496546 TCTGACATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
AATTTTTCATTTATTTTCT
Found at i:55501461 original size:18 final size:19
Alignment explanation
Indices: 55501438--55501474 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
55501428 TAGGCCCAAC
55501438 AGCCTA-TCGGGCCCATTT
1 AGCCTATTCGGGCCCATTT
*
55501456 AGCCTATTCTGGCCCATTT
1 AGCCTATTCGGGCCCATTT
55501475 GGCCAAATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.16, C:0.32, G:0.19, T:0.32
Consensus pattern (19 bp):
AGCCTATTCGGGCCCATTT
Found at i:55504172 original size:16 final size:17
Alignment explanation
Indices: 55504144--55504182 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
55504134 ACAATGAAAG
55504144 TTTGGGATTTCGGGATT
1 TTTGGGATTTCGGGATT
55504161 TTTGGG-TTTCGGGATT
1 TTTGGGATTTCGGGATT
55504177 TTTGGG
1 TTTGGG
55504183 GGGTCACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.08, C:0.05, G:0.38, T:0.49
Consensus pattern (17 bp):
TTTGGGATTTCGGGATT
Done.