Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 142 of 427
Found at i:38380998 original size:27 final size:27
Alignment explanation
Indices: 38380968--38381019 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
38380958 AACATCAGGG
*
38380968 TATGATGAA-AAATAAATAAAGGAATGA
1 TATG-TGAATAAACAAATAAAGGAATGA
*
38380995 TATGTGAATAAACAAATAAATGAAT
1 TATGTGAATAAACAAATAAAGGAAT
38381020 AAATGTAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.58, C:0.02, G:0.15, T:0.25
Consensus pattern (27 bp):
TATGTGAATAAACAAATAAAGGAATGA
Found at i:38381067 original size:16 final size:16
Alignment explanation
Indices: 38380998--38381074 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 16
38380988 GGAATGATAT
*
38380998 GTGAATAAACAAATAA
1 GTGAATAAATAAATAA
*
38381014 ATGAATAAATGTAAAGAATAA
1 GTGAATAAA--T--A-AATAA
**
38381035 -TGAATAAATAACCAA
1 GTGAATAAATAAATAA
38381050 GTGAATAAATAAATAA
1 GTGAATAAATAAATAA
*
38381066 GTAAATAAA
1 GTGAATAAA
38381075 AGGATTAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
15 3 0.06
16 30 0.62
18 1 0.02
20 9 0.19
21 5 0.10
ACGTcount: A:0.62, C:0.04, G:0.12, T:0.22
Consensus pattern (16 bp):
GTGAATAAATAAATAA
Found at i:38382326 original size:15 final size:16
Alignment explanation
Indices: 38382278--38382319 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
38382268 AATGGATTGT
*
38382278 TTATTTGGATTTATTA
1 TTATTTGGTTTTATTA
38382294 TTATTTGGTTTTATTA
1 TTATTTGGTTTTATTA
38382310 TT-TTTGGTTT
1 TTATTTGGTTT
38382320 CTATATTGCC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 8 0.32
16 17 0.68
ACGTcount: A:0.17, C:0.00, G:0.14, T:0.69
Consensus pattern (16 bp):
TTATTTGGTTTTATTA
Found at i:38382606 original size:44 final size:45
Alignment explanation
Indices: 38382524--38382640 Score: 134
Period size: 44 Copynumber: 2.6 Consensus size: 45
38382514 CTTCGATCTG
38382524 CTCCACTGCAACTTCATGA-AGATAAGA-TCTGTAGCTTTAATCCA
1 CTCCACTGCAACTTCA-GAGAGATAAGATTCTGTAGCTTTAATCCA
**
38382568 CTCCACTGCAACTTCAGAGAGATAAGATTC-GT-GACTTTAATCTG
1 CTCCACTGCAACTTCAGAGAGATAAGATTCTGTAG-CTTTAATCCA
* * * *
38382612 CTTCGCTGCAACCTCAGGGAGATAAGATT
1 CTCCACTGCAACTTCAGAGAGATAAGATT
38382641 AGCCATTTAC
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
43 3 0.05
44 59 0.92
45 2 0.03
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (45 bp):
CTCCACTGCAACTTCAGAGAGATAAGATTCTGTAGCTTTAATCCA
Found at i:38384141 original size:40 final size:39
Alignment explanation
Indices: 38384083--38384250 Score: 203
Period size: 39 Copynumber: 4.3 Consensus size: 39
38384073 CGTTCAAACA
* * * * * *
38384083 CCTTCGGGGCATAGCCCGGTTATGATACCCCGCACAAATG
1 CCTTC-GGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
38384123 CCTTCGGGACTTAACCCGGATATCACAACTCGCACAATTG
1 CCTTCGGG-CTTAGCCCGGATATCATAACTCGCACAATTG
*
38384163 CCTTC-GGCTTAGCCCGGATATCATAACTGGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
* *
38384201 CCTTCGGGCTTAGCCCGGATATCACAATTCGCACAATTG
1 CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
*
38384240 CCTACGGGCTT
1 CCTTCGGGCTT
38384251 TGTAACACCC
Statistics
Matches: 111, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
38 33 0.30
39 45 0.41
40 33 0.30
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTG
Found at i:38384222 original size:39 final size:39
Alignment explanation
Indices: 38384113--38384250 Score: 206
Period size: 39 Copynumber: 3.5 Consensus size: 39
38384103 TATGATACCC
* *
38384113 CGCACAAATGCCTTCGGGACTTAACCCGGATATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
*
38384153 CGCACAATTGCCTTC-GGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
* *
38384191 GGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38384230 CGCACAATTGCCTACGGGCTT
1 CGCACAATTGCCTTCGGGCTT
38384251 TGTAACACCC
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
38 33 0.37
39 42 0.47
40 14 0.16
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:38385770 original size:80 final size:80
Alignment explanation
Indices: 38385686--38385834 Score: 183
Period size: 80 Copynumber: 1.9 Consensus size: 80
38385676 TATGGTAACC
* * * *
38385686 CGCACCAAGGCCTACGGGACTTAACCCGGATATCA-CGATTTGCACAAATGCCTTCGGGTCTTAG
1 CGCACCAAGGCCTACGGGACTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAA
38385750 CCCGGATAGAATGACT
65 CCCGGATAGAATGACT
* * * * * * *
38385766 CGCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
38385831 CCGG
66 CCGG
38385835 TTATAATTTC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
79 1 0.02
80 56 0.98
ACGTcount: A:0.23, C:0.30, G:0.25, T:0.22
Consensus pattern (80 bp):
CGCACCAAGGCCTACGGGACTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAAC
CCGGATAGAATGACT
Found at i:38385776 original size:40 final size:38
Alignment explanation
Indices: 38385727--38385834 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 38
38385717 ATCACGATTT
*
38385727 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATG-ACTC
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGAT-GAA-GCACTA
*
38385767 GCACGAATGCCTTCGGGTCTTAGCCCGGATGTAGCCACTA
1 GCAC-AATGCCTTCGGGTCTTAGCCCGGATGAAG-CACTA
*
38385807 GCACAATTGCCTTCGGGTCTTAACCCGG
1 GCACAA-TGCCTTCGGGTCTTAGCCCGG
38385835 TTATAATTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
38 1 0.02
39 4 0.07
40 56 0.92
ACGTcount: A:0.21, C:0.30, G:0.26, T:0.23
Consensus pattern (38 bp):
GCACAATGCCTTCGGGTCTTAGCCCGGATGAAGCACTA
Found at i:38395497 original size:78 final size:78
Alignment explanation
Indices: 38395412--38395592 Score: 265
Period size: 78 Copynumber: 2.3 Consensus size: 78
38395402 TCGTTCAAAC
* * * * *
38395412 GCCTTCGGGCATAGCCCGGTTTTGAT-ACCCGCACAAATGCCTTCGGGACTTAACCCGGGTATCA
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAATGCCTTCGGG-CTTAACCCGGATATCA
38395476 CAACTCGCACAATT
65 CAACTCGCACAATT
* * *
38395490 GCCTTCGGGCTTAGCCCGGATATCATAACTCGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCAC
*
38395555 AATTCGCACAATT
66 AACTCGCACAATT
38395568 GCCTTCGGGCTTAGCCCGGATATCA
1 GCCTTCGGGCTTAGCCCGGATATCA
38395593 CTCGAACATT
Statistics
Matches: 93, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
78 74 0.80
79 19 0.20
ACGTcount: A:0.22, C:0.31, G:0.22, T:0.24
Consensus pattern (78 bp):
GCCTTCGGGCTTAGCCCGGATATCATAACCCGCACAAATGCCTTCGGGCTTAACCCGGATATCAC
AACTCGCACAATT
Found at i:38395520 original size:39 final size:39
Alignment explanation
Indices: 38395441--38395593 Score: 252
Period size: 39 Copynumber: 3.9 Consensus size: 39
38395431 TTTTGATACC
* * *
38395441 CGCACAAATGCCTTCGGGACTTAACCCGGGTATCACAACT
1 CGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACT
*
38395481 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
*
38395520 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
38395559 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
1 CGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38395594 TCGAACATTC
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
39 90 0.84
40 17 0.16
ACGTcount: A:0.24, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
CGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACT
Found at i:38403513 original size:39 final size:39
Alignment explanation
Indices: 38403435--38403586 Score: 232
Period size: 39 Copynumber: 3.9 Consensus size: 39
38403425 TTGATACCCT
* * *
38403435 GCACAAATGCCTTCGGGACTTAACCCGGGTATCACAACTC
1 GCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAACTC
*
38403475 GCACAATTGCCTTCGGGCTTAGCCCGGATATCATAACTC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
* *
38403514 GCACAATTGCCTTCGGGCTTAGCCTGGATATCACAATTC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
*
38403553 GCACAATTGCCTTCGGGCTTCGCCCGGATATCAC
1 GCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
38403587 TCGAACATTC
Statistics
Matches: 103, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
39 87 0.84
40 16 0.16
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (39 bp):
GCACAATTGCCTTCGGGCTTAGCCCGGATATCACAACTC
Found at i:38405427 original size:95 final size:95
Alignment explanation
Indices: 38405302--38405489 Score: 252
Period size: 95 Copynumber: 2.0 Consensus size: 95
38405292 GGTTCGTGGC
* * * ** * *
38405302 TTTAATCTACTCCACTGCAACTTTAGGGAGATAA-GATTCACCATGATAACTTCAATCCATCTTA
1 TTTAACCTACTCCACTGCAACTTCAAGGAGATAAGGCCT-ACCATAATAACTTCAATCCATCCTA
*
38405366 CTGCAACTTTAGGGGTATAGGATTTGTAACT
65 CTGCAACTTCAGGGGTATAGGATTTGTAACT
* * * *
38405397 TTTAACCTGCTCCACTGTAACTTCAAGGAGATAAGGCCTGCCATAATAACTTCAATCCGTCCTAC
1 TTTAACCTACTCCACTGCAACTTCAAGGAGATAAGGCCTACCATAATAACTTCAATCCATCCTAC
38405462 TGCAACTTCAGGGGTATAGGATTTGTAA
66 TGCAACTTCAGGGGTATAGGATTTGTAA
38405490 TTTGTAGCTT
Statistics
Matches: 80, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
95 78 0.98
96 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (95 bp):
TTTAACCTACTCCACTGCAACTTCAAGGAGATAAGGCCTACCATAATAACTTCAATCCATCCTAC
TGCAACTTCAGGGGTATAGGATTTGTAACT
Found at i:38418834 original size:93 final size:93
Alignment explanation
Indices: 38418675--38418847 Score: 247
Period size: 93 Copynumber: 1.9 Consensus size: 93
38418665 GGGATATTTG
* * * * *
38418675 GGCATCCGAACTCGTTGAGTTGAGTCTGGGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACGCGTTGAG
*
38418740 TTGGGTCCGAGTTCGTGAGATGTAACTA
66 TTGAGTCCGAGTTCGTGAGATGTAACTA
* * * *
38418768 GGCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACGCCCTAGCGCGTTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACGCGTTGAG
*
38418833 TTGAGTCTGAGTTCG
66 TTGAGTCCGAGTTCG
38418848 CTTATGGGTG
Statistics
Matches: 69, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
93 69 1.00
ACGTcount: A:0.19, C:0.20, G:0.32, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACGCGTTGAG
TTGAGTCCGAGTTCGTGAGATGTAACTA
Found at i:38426335 original size:49 final size:49
Alignment explanation
Indices: 38426263--38426450 Score: 232
Period size: 49 Copynumber: 3.8 Consensus size: 49
38426253 TAGCCGAAGC
*
38426263 TATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * * * * *
38426312 TATCTGGTACACGTAGTAGCCTGCGCTTAGTATTACACACGTGATCGAAGT
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGA-CCAA-T
* * * *
38426363 TATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAAC
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
* * *
38426412 AATCTGGTACACGTAGTAGCCTGCACTTAGCACTACACA
1 TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACA
38426451 CGTGACCTCA
Statistics
Matches: 114, Mismatches: 23, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
49 71 0.62
50 6 0.05
51 37 0.32
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (49 bp):
TATCTGGTACACATAGTAGCCTGCACTTAGTACTACACATGCGACCAAT
Found at i:38426430 original size:100 final size:100
Alignment explanation
Indices: 38426257--38426455 Score: 326
Period size: 100 Copynumber: 2.0 Consensus size: 100
38426247 CACTTGTAGC
* * **
38426257 CGAAGCTATCTGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCAATTATCTGGTAC
1 CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAACAATCTGGTAC
* * *
38426322 ACGTAGTAGCCTGCGCTTAGTATTACACACGTGAT
66 ACGTAGTAGCCTGCACTTAGCACTACACACGTGAT
*
38426357 CGAAGTTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAACAATCTGGTAC
1 CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAACAATCTGGTAC
38426422 ACGTAGTAGCCTGCACTTAGCACTACACACGTGA
66 ACGTAGTAGCCTGCACTTAGCACTACACACGTGA
38426456 CCTCACAATA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
100 91 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (100 bp):
CGAAGCTATCAGGTACGCATAGTAGCCTACACTTAGTACTACACATGCGACCAACAATCTGGTAC
ACGTAGTAGCCTGCACTTAGCACTACACACGTGAT
Found at i:38429768 original size:29 final size:29
Alignment explanation
Indices: 38429735--38429795 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
38429725 CAGCTACAAG
*
38429735 ATGTGTCAGTGTAAGACTATGTCTGGGAC
1 ATGTGCCAGTGTAAGACTATGTCTGGGAC
38429764 ATGTGCCAGTGTAAGACTATGTCTGGGAC
1 ATGTGCCAGTGTAAGACTATGTCTGGGAC
38429793 ATG
1 ATG
38429796 GAATCAGCAC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.30
Consensus pattern (29 bp):
ATGTGCCAGTGTAAGACTATGTCTGGGAC
Found at i:38436500 original size:3 final size:3
Alignment explanation
Indices: 38436482--38436528 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
38436472 TAAATAGATG
*
38436482 AAT AGAT AAT AA- AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38436527 AA
1 AA
38436529 AGGCACAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38436689 original size:16 final size:16
Alignment explanation
Indices: 38436663--38436707 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38436653 AAATGTAAAG
38436663 AATAA-TGAATAAAT-
1 AATAAGTGAATAAATA
38436677 AATCAAGTGAATAAATA
1 AAT-AAGTGAATAAATA
*
38436694 AATAAGTAAATAAA
1 AATAAGTGAATAAA
38436708 AGGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 19 0.70
17 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (16 bp):
AATAAGTGAATAAATA
Found at i:38436808 original size:86 final size:88
Alignment explanation
Indices: 38436705--38436879 Score: 318
Period size: 86 Copynumber: 2.0 Consensus size: 88
38436695 ATAAGTAAAT
*
38436705 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAACAAAGGGACTAAAAT-AAAAAAA-ATTCGT
1 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAACATTCGT
38436768 AAAAATAAATAATTTAGGAAGAA
66 AAAAATAAATAATTTAGGAAGAA
38436791 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAAACATTCG
1 AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAAT-AAAAAAAACATTCG
38436856 TAAAAATAAATAATTTAGGAAGAA
65 TAAAAATAAATAATTTAGGAAGAA
38436880 TCCAAAATAA
Statistics
Matches: 85, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
86 49 0.58
88 7 0.08
89 29 0.34
ACGTcount: A:0.65, C:0.05, G:0.13, T:0.18
Consensus pattern (88 bp):
AAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAACATTCGT
AAAAATAAATAATTTAGGAAGAA
Found at i:38438108 original size:16 final size:16
Alignment explanation
Indices: 38438087--38438120 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
38438077 AATGGACTGT
38438087 TTATTTGGA-TTTATTA
1 TTATTT-GATTTTATTA
38438103 TTATTTGATTTTATTA
1 TTATTTGATTTTATTA
38438119 TT
1 TT
38438121 TTAGGTTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 2 0.12
16 15 0.88
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (16 bp):
TTATTTGATTTTATTA
Found at i:38442477 original size:10 final size:10
Alignment explanation
Indices: 38442464--38442505 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
38442454 GATCCAATTT
*
38442464 AAAAATTATT
1 AAAAATTATA
38442474 AAAAATT-TA
1 AAAAATTATA
*
38442483 AAAAATAATA
1 AAAAATTATA
38442493 AAAAATTA-A
1 AAAAATTATA
38442502 AAAA
1 AAAA
38442506 TCCGATTCAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 12 0.43
10 16 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAAATTATA
Found at i:38442482 original size:18 final size:18
Alignment explanation
Indices: 38442459--38442506 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
38442449 CAATCGATCC
* *
38442459 AATTTAAAAATTATTAAA
1 AATTTAAAAAATAATAAA
38442477 AATTTAAAAAATAATAAA
1 AATTTAAAAAATAATAAA
*
38442495 AAATTAAAAAAT
1 AATTTAAAAAAT
38442507 CCGATTCAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTTAAAAAATAATAAA
Found at i:38444216 original size:24 final size:24
Alignment explanation
Indices: 38444163--38444219 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 24
38444153 ATTTTCATAA
* *
38444163 TCAGATACATATGCGCATTCAAAT
1 TCAGATACAAATGCGCATACAAAT
* *
38444187 TTAGATACAAATGCAG-ATACAGAT
1 TCAGATACAAATGC-GCATACAAAT
38444211 TCAGATACA
1 TCAGATACA
38444220 GATGTAGTCA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 26 0.96
25 1 0.04
ACGTcount: A:0.42, C:0.18, G:0.14, T:0.26
Consensus pattern (24 bp):
TCAGATACAAATGCGCATACAAAT
Found at i:38444220 original size:12 final size:12
Alignment explanation
Indices: 38444189--38444223 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
38444179 ATTCAAATTT
*
38444189 AGATACAAATGC
1 AGATACAGATGC
*
38444201 AGATACAGATTC
1 AGATACAGATGC
38444213 AGATACAGATG
1 AGATACAGATG
38444224 TAGTCATAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.46, C:0.14, G:0.20, T:0.20
Consensus pattern (12 bp):
AGATACAGATGC
Found at i:38448932 original size:39 final size:39
Alignment explanation
Indices: 38448884--38448987 Score: 156
Period size: 39 Copynumber: 2.7 Consensus size: 39
38448874 ATGTTTGGGC
* * *
38448884 TAAAGTCCCGTAAGCTTCGAGCTGGTATTATAGCGGGTT
1 TAAATTCCCGCAAGCTTCGAGCTGGTATTATACCGGGTT
38448923 TAAATTCCCGCAAGCTTCGAGCTGGTATTATACCGGGTT
1 TAAATTCCCGCAAGCTTCGAGCTGGTATTATACCGGGTT
* *
38448962 TAAATTCCCGCAGGCTT-GTGCTGGTA
1 TAAATTCCCGCAAGCTTCGAGCTGGTA
38448988 ATTGGTTTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
38 8 0.13
39 52 0.87
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.31
Consensus pattern (39 bp):
TAAATTCCCGCAAGCTTCGAGCTGGTATTATACCGGGTT
Found at i:38457105 original size:2 final size:2
Alignment explanation
Indices: 38457098--38457128 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38457088 AAGAAGAACG
38457098 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 T
38457129 GATTGATGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38465203 original size:25 final size:25
Alignment explanation
Indices: 38465174--38465221 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
38465164 TTATAATATG
* * *
38465174 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
38465199 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
38465222 GTTTATATAT
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:38465413 original size:23 final size:24
Alignment explanation
Indices: 38465334--38465477 Score: 204
Period size: 24 Copynumber: 6.0 Consensus size: 24
38465324 GAGGAAGTGC
38465334 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38465358 AAAAGGGCTTATGCCCCAGTCATT
1 AAAAGGGCTTATGCCCCAGTTATT
38465382 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
*
38465406 -AAAGGGCTTATGCCTCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATT
38465429 AAAAAAGGGCTT-TGCCCCAGTTATT
1 --AAAAGGGCTTATGCCCCAGTTATT
*
38465454 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
38465478 ATGATAAAGC
Statistics
Matches: 109, Mismatches: 5, Indels: 11
0.87 0.04 0.09
Matches are distributed among these distances:
23 28 0.26
24 52 0.48
25 20 0.18
26 9 0.08
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATT
Found at i:38465705 original size:31 final size:31
Alignment explanation
Indices: 38465670--38465729 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
38465660 CGTTTACAGT
38465670 AAAGGCTTCGGCCCAGTAATATGAATTATAA
1 AAAGGCTTCGGCCCAGTAATATGAATTATAA
**
38465701 AAAGGCTTCGGCCCAGTGTTATGAATTAT
1 AAAGGCTTCGGCCCAGTAATATGAATTAT
38465730 GAAATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAATTATAA
Found at i:38467015 original size:48 final size:48
Alignment explanation
Indices: 38466944--38467172 Score: 164
Period size: 48 Copynumber: 4.9 Consensus size: 48
38466934 TAGGGTTAAG
* * * *
38466944 TGTGATCCCATGTAAGACTATGTCTAGGACATGGCATTGGTACCGATA
1 TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCACCGATA
* *
38466992 TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCATCGATG
1 TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCACCGATA
* ** * * * *
38467040 TGTAATTTCGTGTAAGACCATAG-CT-GGGC-T---ATCGGCATCGAAA
1 TGTGATCCCGTGTAAGACCAT-GTCTAGGACATGACATTGGCACCGATA
* * * * * * * *
38467083 TATGATCCCATATAAGACCATGTTTGGGACATGGCATTGGCATCGTTA
1 TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCACCGATA
* * * * * *
38467131 TGTGATCCCATGTAATACCATATCCAGGATATGCCATTGGCA
1 TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCA
38467173 TCTTACTATG
Statistics
Matches: 141, Mismatches: 33, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
42 1 0.01
43 26 0.18
44 3 0.02
45 1 0.01
46 1 0.01
47 3 0.02
48 105 0.74
49 1 0.01
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (48 bp):
TGTGATCCCGTGTAAGACCATGTCTAGGACATGACATTGGCACCGATA
Found at i:38470343 original size:15 final size:13
Alignment explanation
Indices: 38470326--38470378 Score: 63
Period size: 13 Copynumber: 3.9 Consensus size: 13
38470316 AGTTTCCATC
38470326 TATTATTATATTAT
1 TATTA-TATATTAT
38470340 CTATTTATATATTAT
1 -TA-TTATATATTAT
*
38470355 TTTTATATATTAT
1 TATTATATATTAT
38470368 TA-TATATATTA
1 TATTATATATTA
38470379 AACCCTTAGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
12 9 0.26
13 12 0.34
14 1 0.03
15 10 0.29
16 3 0.09
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (13 bp):
TATTATATATTAT
Found at i:38470352 original size:23 final size:25
Alignment explanation
Indices: 38470326--38470378 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
38470316 AGTTTCCATC
38470326 TATTA-TTATAT-TATCTATT-TATA
1 TATTATTTATATATAT-TATTATATA
*
38470349 TATTATTTTTATATATTATTATATA
1 TATTATTTATATATATTATTATATA
38470374 TATTA
1 TATTA
38470379 AACCCTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 5 0.19
24 9 0.35
25 12 0.46
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
TATTATTTATATATATTATTATATA
Found at i:38478347 original size:19 final size:19
Alignment explanation
Indices: 38478319--38478355 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38478309 CAAGGAAGGA
*
38478319 AGAGATAAGAAAAAGAAAG
1 AGAGAAAAGAAAAAGAAAG
*
38478338 AGAGAAAAGAAGAAGAAA
1 AGAGAAAAGAAAAAGAAA
38478356 TAATTCAGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (19 bp):
AGAGAAAAGAAAAAGAAAG
Found at i:38481508 original size:30 final size:30
Alignment explanation
Indices: 38481468--38481527 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38481458 TAAAATTCAC
* *
38481468 GTCTTAGGTAAAATGATCATTTTGCCCCTA
1 GTCTTAGGTAAAATAACCATTTTGCCCCTA
*
38481498 GTCTTTGGTAAAATAACCATTTTGCCCCTA
1 GTCTTAGGTAAAATAACCATTTTGCCCCTA
38481528 TGCTCGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.37
Consensus pattern (30 bp):
GTCTTAGGTAAAATAACCATTTTGCCCCTA
Found at i:38482526 original size:3 final size:3
Alignment explanation
Indices: 38482508--38482554 Score: 69
Period size: 3 Copynumber: 15.7 Consensus size: 3
38482498 TAAATAGATG
*
38482508 AAT AGAT AAT AA- AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
38482553 AA
1 AA
38482555 AGAAACAAAC
Statistics
Matches: 40, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:38482715 original size:16 final size:16
Alignment explanation
Indices: 38482689--38482733 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
38482679 AAATGTAAAG
38482689 AATAA-TGAATAAAT-
1 AATAAGTGAATAAATA
38482703 AATCAAGTGAATAAATA
1 AAT-AAGTGAATAAATA
*
38482720 AATAAGTAAATAAA
1 AATAAGTGAATAAA
38482734 AAGATTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
14 3 0.11
15 2 0.07
16 19 0.70
17 3 0.11
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.24
Consensus pattern (16 bp):
AATAAGTGAATAAATA
Found at i:38482837 original size:85 final size:87
Alignment explanation
Indices: 38482731--38482903 Score: 298
Period size: 85 Copynumber: 2.0 Consensus size: 87
38482721 ATAAGTAAAT
*
38482731 AAAAAGATTAAAGTAAGAACAAATAAAATAAATAATAAAGGGACTAAAAT-AAAAAAA-ATT-GT
1 AAAAAGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAATATTCGT
38482793 AAAAACAAATAATTTAGGAAGA
66 AAAAACAAATAATTTAGGAAGA
38482815 AAAAAGGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAATATTCG
1 AAAAA-GATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAATATTCG
*
38482880 TAAAAATAAATAATTTAGGAAGA
65 TAAAAACAAATAATTTAGGAAGA
38482903 A
1 A
38482904 TCCAAAATAA
Statistics
Matches: 83, Mismatches: 2, Indels: 4
0.93 0.02 0.04
Matches are distributed among these distances:
84 5 0.06
85 44 0.53
86 7 0.08
87 3 0.04
88 24 0.29
ACGTcount: A:0.65, C:0.03, G:0.12, T:0.19
Consensus pattern (87 bp):
AAAAAGATTAAAGTAAGAACAAATAAAATAAATAAAAAAGGGACTAAAATAAAAAAAATATTCGT
AAAAACAAATAATTTAGGAAGA
Found at i:38482976 original size:30 final size:27
Alignment explanation
Indices: 38482907--38482978 Score: 72
Period size: 30 Copynumber: 2.6 Consensus size: 27
38482897 GGAAGAATCC
*
38482907 AAAATAAATAAAAAAGGGCTAAATTGA
1 AAAATAAATAAAAAAGGGATAAATTGA
* ** *
38482934 CATTTAAGTAAAATAGGAGGGATAAATTGA
1 AAAATAAATAAAA-A--AGGGATAAATTGA
38482964 AAAATAAATAAAAAA
1 AAAATAAATAAAAAA
38482979 TACGGGCTAA
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
27 10 0.30
28 1 0.03
29 1 0.03
30 21 0.64
ACGTcount: A:0.61, C:0.03, G:0.15, T:0.21
Consensus pattern (27 bp):
AAAATAAATAAAAAAGGGATAAATTGA
Found at i:38498047 original size:47 final size:47
Alignment explanation
Indices: 38497974--38498103 Score: 152
Period size: 47 Copynumber: 2.8 Consensus size: 47
38497964 GTGCAAATAA
* * * *
38497974 TACCTTGATTTGGCTACGGGCCATGGTATAGGTATTCAGAGAGGAGT
1 TACCTTGATTTGGTTATGGGCCATGGTATAGGTACTCAGAGAGAAGT
* * * * *
38498021 TACCTTTATTTGGTTATGGGCTATGGTATAGGTACTCCGGGATAAGT
1 TACCTTGATTTGGTTATGGGCCATGGTATAGGTACTCAGAGAGAAGT
* **
38498068 TACCTTGATTTGGTTTTGAACCATGGTATAGGTACT
1 TACCTTGATTTGGTTATGGGCCATGGTATAGGTACT
38498104 TATCGATTCA
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
47 69 1.00
ACGTcount: A:0.22, C:0.14, G:0.28, T:0.36
Consensus pattern (47 bp):
TACCTTGATTTGGTTATGGGCCATGGTATAGGTACTCAGAGAGAAGT
Found at i:38499731 original size:22 final size:22
Alignment explanation
Indices: 38499706--38499758 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
38499696 ATTTATTTAA
*
38499706 TTATTT-TTAGGTCATTAGGAAT
1 TTATTTCTTACGTCATTAGG-AT
*
38499728 TTATTTCTTTCGTCATTAGGAT
1 TTATTTCTTACGTCATTAGGAT
38499750 TTAATTTCT
1 TT-ATTTCT
38499759 CCATAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.23, C:0.09, G:0.13, T:0.55
Consensus pattern (22 bp):
TTATTTCTTACGTCATTAGGAT
Found at i:38502246 original size:12 final size:13
Alignment explanation
Indices: 38502214--38502251 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
38502204 TGTGTAAATA
38502214 ATGCATTTAATTAGG
1 ATGCATTTAATT--G
38502229 ATGCATTTAATT-
1 ATGCATTTAATTG
38502241 ATGCATTTAAT
1 ATGCATTTAAT
38502252 ATTAGATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 11 0.48
15 12 0.52
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (13 bp):
ATGCATTTAATTG
Found at i:38502594 original size:48 final size:48
Alignment explanation
Indices: 38502402--38502597 Score: 170
Period size: 48 Copynumber: 4.2 Consensus size: 48
38502392 GTTATGTGTT
* * * *
38502402 ATCCCATGTAAGACTATGTCTGGGACATGGCATTGGTAGCGATATGAG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
* * * *
38502450 ATCCCATGTAAGACCATGTCTAGGACATGACATTGGCATCGATGTGTA
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
** * * * * *
38502498 ATTTCGTGTAAGACCATAG-CTGGG-C-T---ATCGACATCGAAATATG
1 ATCCCATGTAAGACCAT-GTCTGGGACATGGCATTGGCATCGATATGTG
* * * *
38502541 ATCCCATGTAAGACTATGTTTGGGACATGGCATTGGCATTGTTATGTG
1 ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
38502589 ATCCCATGT
1 ATCCCATGT
38502598 TATACCATAT
Statistics
Matches: 112, Mismatches: 29, Indels: 14
0.72 0.19 0.09
Matches are distributed among these distances:
42 1 0.01
43 28 0.25
44 1 0.01
45 1 0.01
46 1 0.01
47 1 0.01
48 78 0.70
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (48 bp):
ATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCGATATGTG
Found at i:38505870 original size:15 final size:15
Alignment explanation
Indices: 38505850--38505881 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
38505840 TCTAGTTTCC
38505850 ATCTATTATTATATT
1 ATCTATTATTATATT
38505865 ATCTATTATTATATT
1 ATCTATTATTATATT
38505880 AT
1 AT
38505882 TTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.59
Consensus pattern (15 bp):
ATCTATTATTATATT
Found at i:38505896 original size:21 final size:23
Alignment explanation
Indices: 38505853--38505905 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 23
38505843 AGTTTCCATC
* *
38505853 TATTATTATATTATCTATTATTA
1 TATTATTATATTATATATCATTA
38505876 TATTATT-T-TTATATATCATTA
1 TATTATTATATTATATATCATTA
38505897 TATATATTA
1 TAT-TATTA
38505906 AACCCTTAGT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 14 0.54
22 5 0.19
23 7 0.27
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATTATTATATTATATATCATTA
Found at i:38520071 original size:29 final size:29
Alignment explanation
Indices: 38520031--38520133 Score: 120
Period size: 29 Copynumber: 3.6 Consensus size: 29
38520021 TAATCGATCA
* *
38520031 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATATAATTTAAGCT
* * *
38520060 CGTACACATAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATATAATTTAAGCT
38520089 CGCACACTTAGTGCCATACT--TTTCAAGCT
1 CGCACACTTAGTGCCATA-TAATTT-AAGCT
*
38520118 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
38520134 ATCTTGTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
28 3 0.05
29 59 0.94
30 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.17, T:0.31
Consensus pattern (29 bp):
CGCACACTTAGTGCCATATAATTTAAGCT
Found at i:38528134 original size:29 final size:28
Alignment explanation
Indices: 38528100--38528202 Score: 127
Period size: 29 Copynumber: 3.6 Consensus size: 28
38528090 TAATCGATCA
*
38528100 CGCACACTTAGTGCCATGTGATTTAAGCT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
* *
38528129 CGCACACATAGTGCCATATAATTTAAGTT
1 CGCACACTTAGTGCCATAT-ATTTAAGCT
38528158 CGCACACTTAGTGCCATACT-TTTCAAGCT
1 CGCACACTTAGTGCCATA-TATTT-AAGCT
*
38528187 TGCACACTTAGTGCCA
1 CGCACACTTAGTGCCA
38528203 ATCTTGTCAC
Statistics
Matches: 65, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
28 3 0.05
29 61 0.94
30 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.30
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTTAAGCT
Found at i:38528972 original size:29 final size:31
Alignment explanation
Indices: 38528936--38528998 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
38528926 AAGAAGGAGG
38528936 GATTTTTGCTCCA-TTT-TTGGTTTAGAAGA
1 GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
* *
38528965 GATTTTTGCTTCATTTTCTTTGTTTAGAAGA
1 GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
38528996 GAT
1 GAT
38528999 CTAGAAGGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.40
30 3 0.10
31 15 0.50
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.51
Consensus pattern (31 bp):
GATTTTTGCTCCATTTTCTTGGTTTAGAAGA
Found at i:38530274 original size:38 final size:40
Alignment explanation
Indices: 38530151--38530332 Score: 158
Period size: 40 Copynumber: 4.6 Consensus size: 40
38530141 TCGAATGATG
* * *
38530151 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGC-AAGTTACTAAA
* * * *
38530191 TCCGGACTAGGAT-CCGAAGGCATTCGTGCGAGTTAATAAA
1 TCCGGGCTAAG-TCCCGAAGGCATTCGTGCAAGTTACTAAA
*
38530231 TCCGGGCTAA-TCCCGAAGGC-TTTGTGCAAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
* * * * **
38530269 CCCGGGTTAAGTGCCAAAGGCATTCGTGCAAGTCGCTATAA
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTA-AA
**
38530310 -CCGGGCTTCGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
38530333 TGAGCGAGTC
Statistics
Matches: 112, Mismatches: 24, Indels: 12
0.76 0.16 0.08
Matches are distributed among these distances:
38 24 0.21
39 16 0.14
40 63 0.56
41 9 0.08
ACGTcount: A:0.25, C:0.24, G:0.27, T:0.24
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCAAGTTACTAAA
Found at i:38530316 original size:78 final size:79
Alignment explanation
Indices: 38530151--38530302 Score: 191
Period size: 78 Copynumber: 1.9 Consensus size: 79
38530141 TCGAATGATG
* * * *
38530151 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATATCCGGACTAGGATCCGAAGGCATTC
1 TCCGGGCTAA-TCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCAAAGGCATTC
* *
38530216 GTGCGAGTTAATAAA
65 GTGCAAGTCAATAAA
* **
38530231 TCCGGGCTAATCCCGAAGGCTTTGTGC-AAGTTACTAAACCCGGGTTAAG-TGCCAAAGGCATTC
1 TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGAT-CCAAAGGCATTC
38530294 GTGCAAGTC
65 GTGCAAGTC
38530303 GCTATAACCG
Statistics
Matches: 62, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
77 1 0.02
78 34 0.55
79 17 0.27
80 10 0.16
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (79 bp):
TCCGGGCTAATCCCGAAGGCTTTGTGCTAAGTGACTAAACCCGGACTAAGATCCAAAGGCATTCG
TGCAAGTCAATAAA
Found at i:38532405 original size:30 final size:30
Alignment explanation
Indices: 38532369--38532499 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
38532359 GACAAGATTG
* * * * *
38532369 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
38532399 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
38532427 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
38532457 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
38532486 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38532500 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:38532460 original size:58 final size:58
Alignment explanation
Indices: 38532369--38532499 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
38532359 GACAAGATTG
* * * * * *
38532369 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
38532427 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
38532486 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38532500 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:38540369 original size:30 final size:30
Alignment explanation
Indices: 38540333--38540463 Score: 171
Period size: 30 Copynumber: 4.5 Consensus size: 30
38540323 GACAAGATTG
* * * * *
38540333 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
*
38540363 GCACTAAGTGTGCGAGTTTG---ATTATATA
1 GCACTAAGTGTGCGAG-CTGAAAATTATATA
38540391 GCACTAAGTGTGCGAGCTGAAAATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
38540421 GCACTAAGTGTGCGAGCTGAAAA-TATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATATA
38540450 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38540464 GATTCACTAT
Statistics
Matches: 92, Mismatches: 5, Indels: 9
0.87 0.05 0.08
Matches are distributed among these distances:
27 2 0.02
28 22 0.24
29 20 0.22
30 46 0.50
31 2 0.02
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGCTGAAAATTATATA
Found at i:38540424 original size:58 final size:58
Alignment explanation
Indices: 38540333--38540463 Score: 174
Period size: 58 Copynumber: 2.2 Consensus size: 58
38540323 GACAAGATTG
* * * * * *
38540333 GCACTAAGTGTGCGGGTTTAAAATTGTACAGCACTAAGTGTGCGAGTTTG-ATTATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAG-CTGAAATATATA
*
38540391 GCACTAAGTGTGCGAGCTGAAAATTATATAGCACTAAGTGTGCGAGCTGAAAATATATA
1 GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTG-AAATATATA
38540450 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38540464 GATTCACTAT
Statistics
Matches: 64, Mismatches: 7, Indels: 3
0.86 0.09 0.04
Matches are distributed among these distances:
57 2 0.03
58 41 0.64
59 21 0.33
ACGTcount: A:0.32, C:0.14, G:0.26, T:0.28
Consensus pattern (58 bp):
GCACTAAGTGTGCGAGCTGAAAATTATACAGCACTAAGTGTGCGAGCTGAAATATATA
Found at i:38547324 original size:16 final size:17
Alignment explanation
Indices: 38547303--38547335 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
38547293 CACATTGAAG
38547303 TGTTTT-TTGAAAACCT
1 TGTTTTATTGAAAACCT
38547319 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
38547336 CTTCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.45
Consensus pattern (17 bp):
TGTTTTATTGAAAACCT
Found at i:38552652 original size:9 final size:9
Alignment explanation
Indices: 38552640--38552696 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
38552630 TTTGATAAAC
38552640 ATGATATGT
1 ATGATATGT
*
38552649 ATGATATGCAC
1 ATGATATG--T
*
38552660 ATGACATGT
1 ATGATATGT
*
38552669 ATGATATGCAC
1 ATGATATG--T
38552680 ATGATATGT
1 ATGATATGT
38552689 ATGATATG
1 ATGATATG
38552697 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:38552663 original size:20 final size:20
Alignment explanation
Indices: 38552638--38552708 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
38552628 ATTTTGATAA
38552638 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
38552658 ACATGACATGTATGATATGC
1 ACATGATATGTATGATATGC
38552678 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
38552698 ACATGAGATGT
1 ACATGATATGT
38552709 TCATAAATGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:38552685 original size:11 final size:11
Alignment explanation
Indices: 38552649--38552703 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
38552639 CATGATATGT
38552649 ATGATATGCAC
1 ATGATATGCAC
* *
38552660 ATGACATG--T
1 ATGATATGCAC
38552669 ATGATATGCAC
1 ATGATATGCAC
*
38552680 ATGATATG--T
1 ATGATATGCAC
38552689 ATGATATGCAC
1 ATGATATGCAC
38552700 ATGA
1 ATGA
38552704 GATGTTCATA
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
9 15 0.44
11 19 0.56
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.31
Consensus pattern (11 bp):
ATGATATGCAC
Found at i:38552966 original size:24 final size:24
Alignment explanation
Indices: 38552753--38552942 Score: 321
Period size: 24 Copynumber: 8.0 Consensus size: 24
38552743 GGAGGAAGTG
38552753 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
*
38552777 -TAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
38552800 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
38552824 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
38552848 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
* *
38552872 TAAAAGGGCTTTTGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
38552896 CAAAAGGGCTTATGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
38552920 CAAAAGGGCTT-TGCCCCAGTTAT
1 CAAAAGGGCTTATGCCCCAGTTAT
38552943 TAAAGAGGCT
Statistics
Matches: 159, Mismatches: 6, Indels: 3
0.95 0.04 0.02
Matches are distributed among these distances:
23 34 0.21
24 125 0.79
ACGTcount: A:0.27, C:0.24, G:0.21, T:0.28
Consensus pattern (24 bp):
CAAAAGGGCTTATGCCCCAGTTAT
Found at i:38553213 original size:30 final size:31
Alignment explanation
Indices: 38553160--38553222 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 31
38553150 CGTTTACAGT
38553160 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* ** *
38553191 AAAGGCTTCTG-CCAGTGTTATGAATTATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
38553221 AA
1 AA
38553223 TATGAAAAGG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 18 0.64
31 10 0.36
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:38559587 original size:18 final size:17
Alignment explanation
Indices: 38559564--38559597 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
38559554 TAGCTGTGCC
38559564 GTTTTCTCTTCTGTATTA
1 GTTTTCTCTTCT-TATTA
38559582 GTTTTCTCTTCTTATT
1 GTTTTCTCTTCTTATT
38559598 TTCTTCCGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.09, C:0.18, G:0.09, T:0.65
Consensus pattern (17 bp):
GTTTTCTCTTCTTATTA
Found at i:38560750 original size:25 final size:24
Alignment explanation
Indices: 38560717--38560764 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
38560707 TTATAACATG
* *
38560717 AAAATGACCATTTTTCCCCTAGGT
1 AAAATGACCATTATACCCCTAGGT
38560741 AAAAGTGACCATTATACCCCTAGG
1 AAAA-TGACCATTATACCCCTAGG
38560765 GTTTATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (24 bp):
AAAATGACCATTATACCCCTAGGT
Found at i:38560815 original size:9 final size:9
Alignment explanation
Indices: 38560803--38560859 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
38560793 TTTGATAAAC
38560803 ATGATATGT
1 ATGATATGT
*
38560812 ATGATATGCAC
1 ATGATATG--T
*
38560823 ATGACATGT
1 ATGATATGT
*
38560832 ATGATATGACA
1 ATGATATG--T
38560843 ATGATATGT
1 ATGATATGT
38560852 ATGATATG
1 ATGATATG
38560860 CACATGAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.37, C:0.07, G:0.21, T:0.35
Consensus pattern (9 bp):
ATGATATGT
Found at i:38560826 original size:20 final size:20
Alignment explanation
Indices: 38560801--38560871 Score: 108
Period size: 20 Copynumber: 3.5 Consensus size: 20
38560791 ATTTTGATAA
38560801 ACATGATATGTATGATATGC
1 ACATGATATGTATGATATGC
*
38560821 ACATGACATGTATGATATG-
1 ACATGATATGTATGATATGC
38560840 ACAATGATATGTATGATATGC
1 AC-ATGATATGTATGATATGC
*
38560861 ACATGAGATGT
1 ACATGATATGT
38560872 TCATAAATGC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
19 2 0.04
20 42 0.91
21 2 0.04
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.32
Consensus pattern (20 bp):
ACATGATATGTATGATATGC
Found at i:38560977 original size:32 final size:32
Alignment explanation
Indices: 38560918--38560978 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
38560908 AGGAAGTGCA
*
38560918 AAAGGGCTTATGCCCCAGTTATTAAAGGGATT
1 AAAGGGCTTATGCCCCAGTTATAAAAGGGATT
38560950 AAAGGGCTTATG-CCCAGTTATCAAAAGGG
1 AAAGGGCTTATGCCCCAGTTAT-AAAAGGG
38560979 CTTATGCCCC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (32 bp):
AAAGGGCTTATGCCCCAGTTATAAAAGGGATT
Found at i:38560994 original size:24 final size:24
Alignment explanation
Indices: 38560950--38561138 Score: 285
Period size: 24 Copynumber: 7.9 Consensus size: 24
38560940 TAAAGGGATT
38560950 AAAGGGCTTATG-CCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATCA
38560973 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATCA
*
38560997 AAAGGGCTTATGCCCCAGTTATTA
1 AAAGGGCTTATGCCCCAGTTATCA
* *
38561021 AAAGGGCTTTTGCCCCAGTTATTA
1 AAAGGGCTTATGCCCCAGTTATCA
*
38561045 AAAGGGCTTTTGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATCA
38561069 AAAGGGCTTATGCCCCAGTTATCA
1 AAAGGGCTTATGCCCCAGTTATCA
*
38561093 AAAGGGCTT-TGCCCCAGTTATTA
1 AAAGGGCTTATGCCCCAGTTATCA
*
38561116 AAAGAGGC-TAGGCCTCCAGTTAT
1 AAAG-GGCTTATGCC-CCAGTTAT
38561139 ATGATAAAGC
Statistics
Matches: 156, Mismatches: 6, Indels: 6
0.93 0.04 0.04
Matches are distributed among these distances:
23 30 0.19
24 118 0.76
25 8 0.05
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Consensus pattern (24 bp):
AAAGGGCTTATGCCCCAGTTATCA
Found at i:38570034 original size:30 final size:30
Alignment explanation
Indices: 38570000--38570059 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
38569990 GACACAGCCA
38570000 TGACACACGGGTGTGTAG-TCTACCCGTGTG
1 TGACACACGGGTGTGTAGATC-ACCCGTGTG
*
38570030 TGACACACGGGTGTGTGGATCACCCGTGTG
1 TGACACACGGGTGTGTAGATCACCCGTGTG
38570060 GAAGTGCCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.17, C:0.23, G:0.35, T:0.25
Consensus pattern (30 bp):
TGACACACGGGTGTGTAGATCACCCGTGTG
Found at i:38570768 original size:30 final size:30
Alignment explanation
Indices: 38570725--38570784 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
38570715 TAAAATTCAC
*
38570725 GTCTTAGGCAAAATGATCATTTTGCCCCTA
1 GTCTTAGGCAAAATGACCATTTTGCCCCTA
* *
38570755 GTCTTTGGTAAAATGACCATTTTGCCCCTA
1 GTCTTAGGCAAAATGACCATTTTGCCCCTA
38570785 TGCTCGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (30 bp):
GTCTTAGGCAAAATGACCATTTTGCCCCTA
Found at i:38571062 original size:16 final size:16
Alignment explanation
Indices: 38571041--38571071 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38571031 CTAAACCCTT
38571041 AATCATTTTACAAAAC
1 AATCATTTTACAAAAC
*
38571057 AATCATTTTGCAAAA
1 AATCATTTTACAAAA
38571072 TAGACCCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.32
Consensus pattern (16 bp):
AATCATTTTACAAAAC
Found at i:38572207 original size:55 final size:55
Alignment explanation
Indices: 38572143--38572253 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
38572133 AATTTAATCT
38572143 AATATTTATCTAATATTACTTTAATGTTTATTTTAATAAGTGTAATTATAGTTGA
1 AATATTTATCTAATATTACTTTAATGTTTATTTTAATAAGTGTAATTATAGTTGA
* *
38572198 AATATTTATCTAATATTATTTTAATGTTTATTTTAATAAGTTTAATTATAGTTGA
1 AATATTTATCTAATATTACTTTAATGTTTATTTTAATAAGTGTAATTATAGTTGA
38572253 A
1 A
38572254 CTCTTTGAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.37, C:0.03, G:0.08, T:0.52
Consensus pattern (55 bp):
AATATTTATCTAATATTACTTTAATGTTTATTTTAATAAGTGTAATTATAGTTGA
Found at i:38572384 original size:26 final size:26
Alignment explanation
Indices: 38572333--38572383 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
38572323 AGTTGTAGCG
*
38572333 AGAAAATTTTCTGAAGAGATTATTTT
1 AGAAAATTTTCTAAAGAGATTATTTT
*
38572359 AGAAAA-TTTCTAAAGATATTATTTT
1 AGAAAATTTTCTAAAGAGATTATTTT
38572384 TGATTCACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 17 0.74
26 6 0.26
ACGTcount: A:0.41, C:0.04, G:0.12, T:0.43
Consensus pattern (26 bp):
AGAAAATTTTCTAAAGAGATTATTTT
Found at i:38575737 original size:39 final size:39
Alignment explanation
Indices: 38575680--38575779 Score: 137
Period size: 39 Copynumber: 2.6 Consensus size: 39
38575670 CACGTTTTTT
* * * *
38575680 AGTATTGCAATATATGCTTGAACATTATGTGATTATATG
1 AGTATTGCGATATATGCTTAAACATTATGTAATTATACG
*
38575719 AGTATTGCGATATGTGCTTAAACATTATGTAATTATACG
1 AGTATTGCGATATATGCTTAAACATTATGTAATTATACG
* *
38575758 TGTAATGCGATATATGCTTAAA
1 AGTATTGCGATATATGCTTAAA
38575780 AGTGAATATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 53 1.00
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (39 bp):
AGTATTGCGATATATGCTTAAACATTATGTAATTATACG
Found at i:38586025 original size:31 final size:31
Alignment explanation
Indices: 38586002--38586075 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
38585992 ATAGTGAATC
**
38586002 CGCACACTTAGTGCTATATATATATTCAGCT
1 CGCACACTTAGTGCTATATATATATGAAGCT
38586033 CGCACACTTAGTGCTATATA-ATCA--AA-CT
1 CGCACACTTAGTGCTATATATAT-ATGAAGCT
38586061 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
38586076 GTACAATTTT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 17 0.41
29 1 0.02
30 2 0.05
31 21 0.51
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.31
Consensus pattern (31 bp):
CGCACACTTAGTGCTATATATATATGAAGCT
Found at i:38586097 original size:30 final size:29
Alignment explanation
Indices: 38586001--38586104 Score: 111
Period size: 28 Copynumber: 3.5 Consensus size: 29
38585991 TATAGTGAAT
* *
38586001 CCGCACACTTAGTGCTATATATATATTCAGC
1 CCGCACACTTAGTGCTATATA-AT-TTAAAC
* *
38586032 TCGCACACTTAGTGCTATATAA-TCAAAC
1 CCGCACACTTAGTGCTATATAATTTAAAC
* * *
38586060 TCGCACACTTAGTGCTGTACAATTTTAAAC
1 CCGCACACTTAGTGCTATATAA-TTTAAAC
38586090 CCGCACACTTAGTGC
1 CCGCACACTTAGTGC
38586105 CAATCTTGTC
Statistics
Matches: 63, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
28 23 0.37
30 20 0.32
31 20 0.32
ACGTcount: A:0.30, C:0.27, G:0.13, T:0.30
Consensus pattern (29 bp):
CCGCACACTTAGTGCTATATAATTTAAAC
Found at i:38586585 original size:2 final size:2
Alignment explanation
Indices: 38586578--38586602 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
38586568 TAAGGGCCGA
38586578 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
38586603 CAATGTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38602538 original size:29 final size:29
Alignment explanation
Indices: 38602505--38602606 Score: 150
Period size: 29 Copynumber: 3.5 Consensus size: 29
38602495 TGACGAGATC
38602505 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
38602534 GGCACTAAGTGTGCGTGCTGGAAATATAT
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
** * *
38602563 GGCACTAAGTGTGCAAGCTGGAAAAATAC
1 GGCACTAAGTGTGCGTGCTGGAAATATAT
**
38602592 GGCACTGGGTGTGCG
1 GGCACTAAGTGTGCG
38602607 AGCTCGGAGG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.27, C:0.16, G:0.33, T:0.24
Consensus pattern (29 bp):
GGCACTAAGTGTGCGTGCTGGAAATATAT
Found at i:38604710 original size:17 final size:18
Alignment explanation
Indices: 38604673--38604711 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38604663 TGCAAAACAA
38604673 AAGAAAAAAGAGCAAGAG
1 AAGAAAAAAGAGCAAGAG
* *
38604691 AAGAAACAAGAG-AGGAG
1 AAGAAAAAAGAGCAAGAG
38604708 AAGA
1 AAGA
38604712 GCGCGTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.64, C:0.05, G:0.31, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAGCAAGAG
Found at i:38610120 original size:92 final size:90
Alignment explanation
Indices: 38609970--38610681 Score: 288
Period size: 92 Copynumber: 7.8 Consensus size: 90
38609960 CACAAACCTT
* * * * * * *
38609970 ATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATTTCTCTTAAGTTGCAGTG
1 ATCTCCCTGAAGTTGCAGTAGAGAAGA-T-AA-ACA-CAAACCTTATCTCTCTGAAGTTGCAGTG
*
38610035 GAACAAATTGAAGCTATAAACCACAGATCTC
62 GAACAGATTGAAGC-ATAAACCACA-ATCTC
* * * *
38610066 ATCTCTCTGAAGTTACAGTAGAGAAGATCAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAGC
1 ATCTCCCTGAAGTTGCAGTAGAGAAGATAAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAAC
* * * *
38610131 AGACTAAAG-AT--AGCA-AATCTT
66 AGATTGAAGCATAAACCACAATCTC
* * * *
38610152 ATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTT
1 ATCTCCCTGAAGTTGCAGT-----AGA--GAAG--ATAAA-CACAAACCTTATCTCTCTGAAGTT
* * * * *
38610217 GTAGTAGAGCAGA-TCAA-CACAAA--AC--T-T-
56 GCAGTGGAACAGATTGAAGCATAAACCACAATCTC
* * * * *
38610244 ATCTCCCTGAAGTTGCAGTAGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTG
1 ATCTCCCTGAAGTTGCAGTAGAGAAGA-T-AA-ACA-CAAACCTTATCTCTCTGAAGTTGCAGTG
*
38610309 GAACAGATTGAAGCTATAAACCACCGATCTC
62 GAACAGATTGAAGC-ATAAACCA-CAATCTC
** * * * **
38610340 ATCTCTTTGAAGCTGCAGTAGAGTAGATCAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAGT
1 ATCTCCCTGAAGTTGCAGTAGAGAAGATAAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAAC
* * * *
38610405 AGACTAAAG-AT--AGCA-AATCTT
66 AGATTGAAGCATAAACCACAATCTC
* * * * * *
38610426 ATTTCCCTGAAGTTGCAGTGGAACAGATTGGAGCTATAAACCACAGATCTCATCTCTTTGAAGTT
1 ATCTCCCTGAAGTTGCAGT-----AGA--GAAG--ATAAA-CACAAACCTTATCTCTCTGAAGTT
* * * *
38610491 GCAGTAGAGCAGA-TCAA-CACAAA-C-C--T-T-
56 GCAGTGGAACAGATTGAAGCATAAACCACAATCTC
* * * * * *
38610518 ATCTCCCTGAAGTTCCAGTGGAGTAGACTAAAGATAGCAAATCTTATTTC-CTTGAAGTTGCAGT
1 ATCTCCCTGAAGTTGCAGTAGAGAAGA-T-AA-ACA-CAAACCTTATCTCTC-TGAAGTTGCAGT
*
38610582 GGAACAGATTGAAGCTATAAACCACCGATCTC
61 GGAACAGATTGAAGC-ATAAACCA-CAATCTC
* * * ** * *
38610614 ATATCTCTGAAGTTGCAGTAGAGCAGATCAAA-ACAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
1 ATCTCCCTGAAGTTGCAGTAGAGAAGAT-AAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAA
38610678 CAGA
65 CAGA
38610682 CTAAAGATAG
Statistics
Matches: 467, Mismatches: 91, Indels: 120
0.69 0.13 0.18
Matches are distributed among these distances:
83 2 0.00
84 2 0.00
85 12 0.03
86 97 0.21
87 12 0.03
88 8 0.02
89 8 0.02
90 5 0.01
91 7 0.01
92 134 0.29
93 15 0.03
94 7 0.01
95 24 0.05
96 132 0.28
97 2 0.00
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (90 bp):
ATCTCCCTGAAGTTGCAGTAGAGAAGATAAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAAC
AGATTGAAGCATAAACCACAATCTC
Found at i:38610952 original size:137 final size:137
Alignment explanation
Indices: 38609679--38610951 Score: 1981
Period size: 137 Copynumber: 9.3 Consensus size: 137
38609669 TCAGCGGAGT
** * *
38609679 AGATCAACACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACTAAAGATAGAAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
** *
38609744 TCCCTGAAGTTATAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTTTCTGAAGTTGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
* * *
38609809 GAAAAGT
131 GTAGAGC
** * *
38609816 AGATCAACACAAGTCTTATTTCCATGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
*
38609881 TCCCTGAAGTTGCAGTGGAACAGATGGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
38609946 GTAGAGC
131 GTAGAGC
*
38609953 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCGAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* * * *
38610018 TCTCTTAAGTTGCAGTGGAACAAATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTACA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
*
38610083 GTAGAGA
131 GTAGAGC
*
38610090 AGATCAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
*
38610155 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGTA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
38610220 GTAGAGC
131 GTAGAGC
* *
38610227 AGATCAACACAAAACTTATCTCCCTGAAGTTGCAGTAGAGCAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* * *
38610292 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACCGATCTCATCTCTTTGAAGCTGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
*
38610357 GTAGAGT
131 GTAGAGC
* *
38610364 AGATCAACACAAACCTTATCTCTCTGAAGTTGCAGTGGAGTAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* *
38610429 TCCCTGAAGTTGCAGTGGAACAGATTGGAGCTATAAACCACAGATCTCATCTCTTTGAAGTTGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
38610494 GTAGAGC
131 GTAGAGC
* *
38610501 AGATCAACACAAACCTTATCTCCCTGAAGTTCCAGTGGAGTAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* * *
38610566 TCCTTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACCGATCTCATATCTCTGAAGTTGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
38610631 GTAGAGC
131 GTAGAGC
* **
38610638 AGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* * * *
38610703 TCCCTAAAGTTGCAGTGGAATAGATTGAAGCTATAAATCACAGATCTCATCTCTCTGAAGTTACA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
**
38610768 GTA-ATAA
131 GTAGA-GC
* * * * * *
38610775 AGATCAAAACAAACCCTATCTCCCTAAAGTTGCAGTGGAGTAAACTAAAAATAGCAAATCTTATT
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
* *
38610840 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATCACAGATCTCATCTCTCTGAAGTCGCA
66 TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
*
38610905 GTGGAGC
131 GTAGAGC
* * ** *
38610912 TGATCAAAACAAACCCCATCTCCCTGAAGTTACAGTGGAG
1 AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAG
38610952 TGGATCACAG
Statistics
Matches: 1049, Mismatches: 85, Indels: 4
0.92 0.07 0.00
Matches are distributed among these distances:
136 1 0.00
137 1047 1.00
138 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (137 bp):
AGATCAACACAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGATAGCAAATCTTATT
TCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAACCACAGATCTCATCTCTCTGAAGTTGCA
GTAGAGC
Found at i:38613079 original size:132 final size:132
Alignment explanation
Indices: 38612854--38613095 Score: 306
Period size: 132 Copynumber: 1.8 Consensus size: 132
38612844 ATGAAGGTGA
* * * * *
38612854 TGTTCGATGTTTGGAAATTCGGGAAATCGTGCCCTACCGTGCTGGGTTGCAATTTCTCGTTTACT
1 TGTTCGATGTTTAGAAATTCGGGAAATAGTGCCCTACCGTGCTGGGTTGCAATCTCCCATTTACT
* * * * * *
38612919 CAAAATAATTGAGTGTCTCTTTAAAATTTCACTCATGTTTTCTAAAAACTTTTTAAAACAAAGGA
66 CAAAATAATCGAATATCCCTTCAAAATTTCACACATGTTTTCTAAAAACTTTTTAAAACAAAGGA
38612984 AG
131 AG
* * * **
38612986 TGTTCGATGTTTAGCAATTCGTGG-GATAGTGCCCTATCGTGCTGGGTTGCAATCTCCCATTTGT
1 TGTTCGATGTTTAGAAATTCG-GGAAATAGTGCCCTACCGTGCTGGGTTGCAATCTCCCATTTAC
* *
38613050 TCAAAATAATCGAATATCCCTTCAGAATTTCACACGTGTTTTCTAA
65 TCAAAATAATCGAATATCCCTTCAAAATTTCACACATGTTTTCTAA
38613096 GGCAAAGAAA
Statistics
Matches: 91, Mismatches: 18, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
132 89 0.98
133 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (132 bp):
TGTTCGATGTTTAGAAATTCGGGAAATAGTGCCCTACCGTGCTGGGTTGCAATCTCCCATTTACT
CAAAATAATCGAATATCCCTTCAAAATTTCACACATGTTTTCTAAAAACTTTTTAAAACAAAGGA
AG
Found at i:38625587 original size:11 final size:11
Alignment explanation
Indices: 38625567--38625597 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
38625557 TCAAATCATC
*
38625567 AAGAATAAATT
1 AAGAACAAATT
38625578 AAGAACAAATT
1 AAGAACAAATT
38625589 AAGAACAAA
1 AAGAACAAA
38625598 ACTAGATGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.10, T:0.16
Consensus pattern (11 bp):
AAGAACAAATT
Found at i:38630706 original size:6 final size:6
Alignment explanation
Indices: 38630691--38630756 Score: 73
Period size: 6 Copynumber: 10.8 Consensus size: 6
38630681 CTTCTATTTC
*
38630691 AAAAA- AAAAAGG AAAAAG AAAAGAA AAAAAG AAAAAG AAAAAG AAAAAAG
1 AAAAAG AAAAA-G AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG -AAAAAG
*
38630741 AGAAA- AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAA
38630757 AAATAGAGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
5 9 0.17
6 27 0.52
7 16 0.31
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:38630719 original size:19 final size:18
Alignment explanation
Indices: 38630691--38630757 Score: 84
Period size: 18 Copynumber: 3.6 Consensus size: 18
38630681 CTTCTATTTC
38630691 AAAA-AAAAAAGGAAAAAG
1 AAAAGAAAAAA-GAAAAAG
38630709 AAAAGAAAAAAAGAAAAAG
1 AAAAG-AAAAAAGAAAAAG
38630728 AAAAAGAAAAAAGAGAAAA-
1 -AAAAGAAAAAAGA-AAAAG
38630747 AAAAGAAAAAA
1 AAAAGAAAAAA
38630758 AATAGAGAGG
Statistics
Matches: 45, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
18 15 0.33
19 15 0.33
20 15 0.33
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (18 bp):
AAAAGAAAAAAGAAAAAG
Found at i:38630719 original size:20 final size:19
Alignment explanation
Indices: 38630694--38630758 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
38630684 CTATTTCAAA
38630694 AAAAAAAGGAAAAAGAAAAG
1 AAAAAAA-GAAAAAGAAAAG
38630714 AAAAAAAGAAAAAGAAAA-
1 AAAAAAAGAAAAAGAAAAG
38630732 AGAAAAAAGAGAAAA-AAAAG
1 A-AAAAAAGA-AAAAGAAAAG
38630752 AAAAAAA
1 AAAAAAA
38630759 ATAGAGAGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
18 1 0.02
19 29 0.69
20 12 0.29
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAAG
Found at i:38630725 original size:25 final size:24
Alignment explanation
Indices: 38630691--38630756 Score: 89
Period size: 24 Copynumber: 2.7 Consensus size: 24
38630681 CTTCTATTTC
*
38630691 AAAAAAAAAAGGAAAAAGAAAAGA
1 AAAAAAAAAAAGAAAAAGAAAAGA
38630715 AAAAAAGAAAAAGAAAAAGAAAA-A
1 AAAAAA-AAAAAGAAAAAGAAAAGA
*
38630739 AGAGAAAAAAAAGAAAAA
1 A-AAAAAAAAAAGAAAAA
38630757 AAATAGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
24 19 0.50
25 19 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (24 bp):
AAAAAAAAAAAGAAAAAGAAAAGA
Found at i:38630759 original size:20 final size:19
Alignment explanation
Indices: 38630691--38630759 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 19
38630681 CTTCTATTTC
38630691 AAAAAAAAAAG-GAAAAAGA
1 AAAAAAAAAAGAGAAAAA-A
38630710 AAAGAAAAAAAGA-AAAAGAA
1 AAA-AAAAAAAGAGAAAA-AA
*
38630730 AAAGAAAAAAGAGAAAAAA
1 AAAAAAAAAAGAGAAAAAA
38630749 AAGAAAAAAAA
1 AA-AAAAAAAA
38630760 TAGAGAGGCC
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
19 15 0.35
20 27 0.63
21 1 0.02
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAGAAAAAA
Found at i:38632028 original size:207 final size:207
Alignment explanation
Indices: 38631673--38633038 Score: 2077
Period size: 207 Copynumber: 6.7 Consensus size: 207
38631663 GTAGATCTGG
* ** * *
38631673 CTGAAGCAAGATCCAAGATGGTTTGGAATCCTTGTGCTTGTAAGGAACAAATTGAAAACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
38631738 GATTTGGCTTTGACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * * *
38631803 AGAACAAATCGAAGTTTGGTGCCTCCATATTCGACAGAGAGCAGACACATAGCAGATCTAGCCTT
131 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
*
38631868 TAGATGTTTATA
196 CAGATGTTTATA
*
38631880 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGTT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* * *
38631945 GATTTGGCTTTCATGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTATATTGTTAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
38632010 AGAACAAATCAAAGTTTGGCGTCTTCATATTCAACGGAGAGCAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
*
38632075 CAGATGTTAATA
196 CAGATGTTTATA
38632087 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* * *
38632152 AATTGGGCTTTCACATGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
38632217 AGAACAAATCAAA-TTTGGGCGTCTCCATATTCGACGGAGAGCATACACATAGCAAATCTGGCCT
131 AGAACAAATCAAAGTTT-GGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCT
*
38632281 TCAAATGTTTATA
195 TCAGATGTTTATA
* *
38632294 CTGAAGCAAGATCCAAGATGGTTTAGCATCCTTGTGCTTACAAGGAACAAATCAAAGACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* *
38632359 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAATATGATTTGGCATCTTTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* *
38632424 AGAACAAATCGAAGTTTGGCATCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
131 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
38632489 CAGATGTTTATA
196 CAGATGTTTATA
* * * *
38632501 CTGAAGTAAAATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGTAACAAATCGAAGACATAACT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
*
38632566 GATTTGGTTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
* * * *
38632631 AGAACAAATCGAAGTTTGGCGTCTCCATATTAGACGGAAAGCAGACACATAGCAGATTTGGCCTT
131 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
38632696 CAGATGTTTATA
196 CAGATGTTTATA
*
38632708 CTGAAGCAAGATCCAAGATGATTTGGCATCCTTGTGCTTACAAGGAACAAATCGAA-ACATAGCT
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* *
38632772 GATTTGGCTTTCACGTGCTTACGATAAAGCAAATCTAAGATGATTTGGGATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
38632837 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGATCAGAC-CTATAGCAGATCTGGCCT
131 AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACAC-ATAGCAGATCTGGCCT
38632901 TCAGATGATTT-TA
195 TCAGATG-TTTATA
* * * * *
38632914 CTAAAGC-AGATCCAAGA-----T-G-AT--TTG-G----CAAGGAGCAAATCGAAGACACAACA
1 CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
* * * * *
38632964 GATTTGGCTTTCACATGTTTATGCTGAAGCAGATCTAAGATGATTTGGCATCTCTGTATTGTCAG
66 GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
*
38633029 AAAACAAATC
131 AGAACAAATC
38633039 GAAGAAACAG
Statistics
Matches: 1071, Mismatches: 83, Indels: 25
0.91 0.07 0.02
Matches are distributed among these distances:
191 15 0.01
192 72 0.07
195 1 0.00
196 3 0.00
198 2 0.00
199 1 0.00
200 1 0.00
205 11 0.01
206 144 0.13
207 818 0.76
208 3 0.00
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.28
Consensus pattern (207 bp):
CTGAAGCAAGATCCAAGATGGTTTGGCATCCTTGTGCTTACAAGGAACAAATCGAAGACATAGCT
GATTTGGCTTTCACGTGCTTACGATGAAGCAAATCTAAGATGATTTGGCATCTCTGTATTGTCAG
AGAACAAATCAAAGTTTGGCGTCTCCATATTCGACGGAGAGCAGACACATAGCAGATCTGGCCTT
CAGATGTTTATA
Found at i:38633441 original size:17 final size:17
Alignment explanation
Indices: 38633421--38633475 Score: 92
Period size: 17 Copynumber: 3.1 Consensus size: 17
38633411 CTTTAAGGAT
38633421 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATATG
38633438 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATATG
38633455 ATATGCAATCTTAGATATG
1 --ATGCAATCTTAGATATG
38633474 AT
1 AT
38633476 AGGCAATCTA
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
17 19 0.53
19 17 0.47
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.36
Consensus pattern (17 bp):
ATGCAATCTTAGATATG
Found at i:38633462 original size:19 final size:19
Alignment explanation
Indices: 38633418--38633484 Score: 111
Period size: 19 Copynumber: 3.6 Consensus size: 19
38633408 AATCTTTAAG
38633418 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38633437 G--ATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
38633454 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
38633473 GATAGGCAATCT
1 GATATGCAATCT
38633485 AGAAGATATG
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
17 17 0.38
19 28 0.62
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:38639061 original size:7 final size:7
Alignment explanation
Indices: 38639043--38639083 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
38639033 AAAAACAATG
38639043 GAAAAAA
1 GAAAAAA
38639050 GAAAAGAA
1 GAAAA-AA
*
38639058 -AAAAGA
1 GAAAAAA
38639064 GAAAAAA
1 GAAAAAA
38639071 GAAAAAA
1 GAAAAAA
38639078 GAAAAA
1 GAAAAA
38639084 TTGAGAGGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 1 0.03
7 27 0.90
8 2 0.07
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Found at i:38639072 original size:16 final size:15
Alignment explanation
Indices: 38639051--38639083 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
38639041 TGGAAAAAAG
38639051 AAAAGAAAAAAGAGAA
1 AAAAGAAAAAAGA-AA
38639067 AAAAGAAAAAAGAAA
1 AAAAGAAAAAAGAAA
38639082 AA
1 AA
38639084 TTGAGAGGCC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAGAAA
Found at i:38640173 original size:84 final size:83
Alignment explanation
Indices: 38640032--38640505 Score: 615
Period size: 84 Copynumber: 5.6 Consensus size: 83
38640022 AAAATTCAAT
* * * * ** *
38640032 GCCTTAATCCCCTATGCAATAGGGTAATAGGCTAAAATTGTAGATCTTATCTCCCTAAGCAGTTG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
38640097 TGGAGTAGATCGAAGACTC
66 TGGAGTAGATCGAAGA-TC
* * *
38640116 GCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTGCAGATCTTATCTCCCTAAGTAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
** *
38640181 CAGAGCAGATCGAAGATGATGC
66 TGGAGTAGATCG-A-A-GAT-C
* *
38640203 GCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* *
38640268 TGGAGTGGATTGAAGACTC
66 TGGAGTAGATCGAAGA-TC
38640287 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* *
38640352 CGGAGCAGATCGGAGATGATGC
66 TGGAGTAGATC-GA-A-GAT-C
*
38640374 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
* *
38640439 TGGAGTGGATTGAAGATC
66 TGGAGTAGATCGAAGATC
* * *
38640457 GCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTAAGATATAGCAGATCT
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAAT-TA-CAGATCT
38640506 GACCTTCAGA
Statistics
Matches: 345, Mismatches: 34, Indels: 21
0.86 0.09 0.05
Matches are distributed among these distances:
83 36 0.10
84 146 0.42
85 12 0.03
86 7 0.02
87 144 0.42
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (83 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATCTTATCTCCCTAAGCAGTAG
TGGAGTAGATCGAAGATC
Found at i:38640321 original size:171 final size:171
Alignment explanation
Indices: 38640032--38640505 Score: 761
Period size: 171 Copynumber: 2.8 Consensus size: 171
38640022 AAAATTCAAT
* * * * ** * *
38640032 GCCTTAATCCCCTATGCAATAGGGTAATAGGCTAAAATTGTAGATCTTATCTCCCTAAGCAGTTG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
* *
38640097 TGGAGTAGATCGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTGCAGATC
66 TGGAGTGGATTGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTGCAGATC
*
38640162 TTATCTCCCTAAGTAGTAGCAGAGCAGATCGAAGATGATGC
131 TTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGATGATGC
*
38640203 GCCTTAACCCCCTAAGTAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
* *
38640268 TGGAGTGGATTGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAGATC
66 TGGAGTGGATTGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTGCAGATC
* *
38640333 TTATCTCCCTAAGCAGTAGCGGAGCAGATCGGAGATGATGC
131 TTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGATGATGC
38640374 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
1 GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
* *
38640439 TGGAGTGGATTGAAGA-TCGCCTTAACTCCCTAAGCAGTAGGGTAATAGGCTAAGATATAGCAGA
66 TGGAGTGGATTGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAA-A-ATTGCAGA
38640503 TCT
129 TCT
38640506 GACCTTCAGA
Statistics
Matches: 280, Mismatches: 21, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
170 35 0.12
171 236 0.84
172 9 0.03
ACGTcount: A:0.32, C:0.22, G:0.22, T:0.24
Consensus pattern (171 bp):
GCCTTAACCCCCTAAGCAGTAGGGTAACAGGCTAAAATTACAAATCTTATCTCCCTAAGCAGTAG
TGGAGTGGATTGAAGACTCGCCTTAACCCCCTAAGCAGTAGGGTAATAGGCTAAAATTGCAGATC
TTATCTCCCTAAGCAGTAGCAGAGCAGATCGAAGATGATGC
Found at i:38640657 original size:92 final size:92
Alignment explanation
Indices: 38640495--38640766 Score: 350
Period size: 92 Copynumber: 3.0 Consensus size: 92
38640485 AGGCTAAGAT
* * * *
38640495 ATAGCAGATCTGACCTTCAGATGTTTACATCGAAGTAGATCCAAGATGACAGATTTGGCATCTTT
1 ATAGTAGATCTGACCTTCAGATGTTTACATCGAAGCAAATCCAAGATGACAGATTTGGCATCTCT
*
38640560 GTATTAGATGGGGAGCAGATCGAAAAC
66 GTATTAGACGGGGAGCAGATCGAAAAC
* * *
38640587 ATAGTAGATCTGACCTTCAGGTGTTTACATTGAAGCAAATCTAAGATGACAGATTTGGCATCTCT
1 ATAGTAGATCTGACCTTCAGATGTTTACATCGAAGCAAATCCAAGATGACAGATTTGGCATCTCT
* * *
38640652 GTATTAGACGGGGGGCAGATCGGAGAC
66 GTATTAGACGGGGAGCAGATCGAAAAC
* ** * *
38640679 ATAGTAGATCTGATCTTCATTTGTTTACATCGAAGCGAATCCAAGATAGA-ATATTTGGCATCTC
1 ATAGTAGATCTGACCTTCAGATGTTTACATCGAAGCAAATCCAAGAT-GACAGATTTGGCATCTC
* * *
38640743 TGTATT-GTCAGAGAGCAGATCGAA
65 TGTATTAGACGGGGAGCAGATCGAA
38640767 GATAGCAGAT
Statistics
Matches: 156, Mismatches: 23, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
91 13 0.08
92 141 0.90
93 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (92 bp):
ATAGTAGATCTGACCTTCAGATGTTTACATCGAAGCAAATCCAAGATGACAGATTTGGCATCTCT
GTATTAGACGGGGAGCAGATCGAAAAC
Found at i:38640787 original size:44 final size:44
Alignment explanation
Indices: 38640721--38641039 Score: 305
Period size: 44 Copynumber: 7.3 Consensus size: 44
38640711 AAGCGAATCC
* * *
38640721 AAGATAGAATATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
1 AAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCG
* * * *
38640765 AAGATAGCAGATTTGGCGTCTCTATATTATCAGGGAGCGGATCG
1 AAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCG
* *
38640809 AAGATAGTAGATTTAGCGTCTCTGTATTGTCAGAG-GACAGATCG
1 AAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAG-CAGATCG
*
38640853 AAGATAGCAGATTTGGCATCTCTGTATTGTCAGAGAGCAGATCG
1 AAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCG
* * *
38640897 AAGATAGCAGATTTGGCTTTCACGTGT-TTACG-CTGA-AGCAGATC-
1 AAGATAGCAGATTTGGC-GTCTC-TGTATT--GTCAGAGAGCAGATCG
* * * * *
38640941 TA-ATA-C-GATTTGGCGTCTCTGTATTAGACGGGGAACAGATCG
1 AAGATAGCAGATTTGGCGTCTCTGTATT-GTCAGAGAGCAGATCG
* * * *
38640983 AAGATAACAGATTTGGCGTCTCTGTATTAGAC-GGGAAGCAGATCA
1 AAGATAGCAGATTTGGCGTCTCTGTATT-GTCAGAG-AGCAGATCG
38641028 AAGATAGCAGAT
1 AAGATAGCAGAT
38641040 ATCGCCTTCC
Statistics
Matches: 231, Mismatches: 30, Indels: 27
0.80 0.10 0.09
Matches are distributed among these distances:
39 4 0.02
40 7 0.03
41 15 0.06
42 2 0.01
43 7 0.03
44 134 0.58
45 55 0.24
46 6 0.03
47 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.27, T:0.28
Consensus pattern (44 bp):
AAGATAGCAGATTTGGCGTCTCTGTATTGTCAGAGAGCAGATCG
Found at i:38640997 original size:45 final size:45
Alignment explanation
Indices: 38640947--38641039 Score: 152
Period size: 45 Copynumber: 2.1 Consensus size: 45
38640937 GATCTAATAC
*
38640947 GATTTGGCGTCTCTGTATTAGACGGGGAA-CAGATCGAAGATAACA
1 GATTTGGCGTCTCTGTATTAGAC-GGGAAGCAGATCAAAGATAACA
*
38640992 GATTTGGCGTCTCTGTATTAGACGGGAAGCAGATCAAAGATAGCA
1 GATTTGGCGTCTCTGTATTAGACGGGAAGCAGATCAAAGATAACA
38641037 GAT
1 GAT
38641040 ATCGCCTTCC
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 5 0.11
45 40 0.89
ACGTcount: A:0.31, C:0.15, G:0.29, T:0.25
Consensus pattern (45 bp):
GATTTGGCGTCTCTGTATTAGACGGGAAGCAGATCAAAGATAACA
Found at i:38641064 original size:130 final size:129
Alignment explanation
Indices: 38640818--38641069 Score: 298
Period size: 130 Copynumber: 1.9 Consensus size: 129
38640808 GAAGATAGTA
* * *
38640818 GATTTAGCGTCTCTGTATTGTCAGAGGACAGATCGAAGATAGCAGATTTGGCATCTCTGTATTGT
1 GATTTAGCGTCTCTGTATTGACAGAGGACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGA
* * * * * *
38640883 CAGAGAGCAGATCGAAGATAGCAGATTTGGCTTTCACGTGTTTACGCTGAAGCAGATCTAATAC
66 CAGAGAGCAGATCAAAGATAGCAGATATCGCCTTCACGAGTTCACGCTGAAGCAGATCTAATAC
* * *
38640947 GATTTGGCGTCTCTGTATTAGAC-GGGGAACAGATCGAAGATAACAGATTTGGCGTCTCTGTATT
1 GATTTAGCGTCTCTGTATT-GACAGAGG-ACAGATCGAAGATAACAGATTTGGCATCTCTGTATT
*
38641011 AGAC-GGGAAGCAGATCAAAGATAGCAGATATCGCCTTC-CTGAGTTGCA-G-TGAAGCAGAT
64 -GACAGAG-AGCAGATCAAAGATAGCAGATATCGCCTTCAC-GAGTT-CACGCTGAAGCAGAT
38641070 TGAAGCCGTC
Statistics
Matches: 104, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
129 21 0.20
130 49 0.47
131 33 0.32
132 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.27, T:0.27
Consensus pattern (129 bp):
GATTTAGCGTCTCTGTATTGACAGAGGACAGATCGAAGATAACAGATTTGGCATCTCTGTATTGA
CAGAGAGCAGATCAAAGATAGCAGATATCGCCTTCACGAGTTCACGCTGAAGCAGATCTAATAC
Found at i:38641408 original size:19 final size:19
Alignment explanation
Indices: 38641383--38641455 Score: 123
Period size: 19 Copynumber: 3.9 Consensus size: 19
38641373 ATAATCTTCA
38641383 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
38641402 GTGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
38641421 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
38641438 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
38641456 AGATATGATT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
17 17 0.34
19 33 0.66
ACGTcount: A:0.37, C:0.11, G:0.16, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:38641423 original size:14 final size:15
Alignment explanation
Indices: 38641404--38641441 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
38641394 TCTTAGATGT
38641404 GATATG-CAATCTTA
1 GATATGACAATCTTA
38641418 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
38641435 GATATGA
1 GATATGA
38641442 TATGCAATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 1 0.05
17 14 0.67
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.34
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:38641481 original size:22 final size:22
Alignment explanation
Indices: 38641383--38641478 Score: 79
Period size: 19 Copynumber: 4.8 Consensus size: 22
38641373 ATAATCTTCA
38641383 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
38641402 GTGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
38641421 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
38641438 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
38641460 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
38641479 GATTTAATTT
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
17 17 0.25
19 30 0.45
22 8 0.12
23 12 0.18
ACGTcount: A:0.36, C:0.09, G:0.17, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:38641792 original size:16 final size:17
Alignment explanation
Indices: 38641761--38641793 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
38641751 TTGATTTTTA
*
38641761 ATTTTCTTTTATAATTT
1 ATTTTCTTTAATAATTT
38641778 ATTTT-TTTAATAATTT
1 ATTTTCTTTAATAATTT
38641794 TAGTATTATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTCTTTAATAATTT
Found at i:38643602 original size:16 final size:16
Alignment explanation
Indices: 38643581--38643611 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38643571 AATTAAATTA
*
38643581 AATTAATTAATTTTTC
1 AATTAAATAATTTTTC
38643597 AATTAAATAATTTTT
1 AATTAAATAATTTTT
38643612 TAACCCAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (16 bp):
AATTAAATAATTTTTC
Found at i:38645768 original size:34 final size:34
Alignment explanation
Indices: 38645725--38645792 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
38645715 TTATGCAAAG
38645725 ATTGATTCAAAGAATAGAACACAACCTTCTGTAT
1 ATTGATTCAAAGAATAGAACACAACCTTCTGTAT
38645759 ATTGATTCAAAGAATAGAACACAACCTTCTGTAT
1 ATTGATTCAAAGAATAGAACACAACCTTCTGTAT
38645793 CAAACTTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (34 bp):
ATTGATTCAAAGAATAGAACACAACCTTCTGTAT
Found at i:38650211 original size:19 final size:21
Alignment explanation
Indices: 38650174--38650216 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
38650164 ATTTTGGGAC
*
38650174 TTTTTGGACTTTGGGATTTTA
1 TTTTTGGACTTTGGGATTTGA
38650195 TTTTTGGA-TTT-GGATTTGA
1 TTTTTGGACTTTGGGATTTGA
38650214 TTT
1 TTT
38650217 GAGACTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 8 0.38
ACGTcount: A:0.14, C:0.02, G:0.23, T:0.60
Consensus pattern (21 bp):
TTTTTGGACTTTGGGATTTGA
Found at i:38663792 original size:46 final size:45
Alignment explanation
Indices: 38663725--38663894 Score: 175
Period size: 46 Copynumber: 3.7 Consensus size: 45
38663715 TAACCCGCCC
*
38663725 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTT-GCATCCA
* *
38663771 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT--T
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTGCATCCA
* * ***
38663819 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGATATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG-GCGTTGCATCCA
*
38663864 TAAGTGAACTCGGACTCCACTCAACGAGTTC
1 TAAGTGAACTCGGACTCAACTCAACGAGTTC
38663895 AGATGCTCAA
Statistics
Matches: 102, Mismatches: 14, Indels: 16
0.77 0.11 0.12
Matches are distributed among these distances:
43 5 0.05
45 2 0.02
46 57 0.56
47 28 0.27
48 3 0.03
49 1 0.01
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.24
Consensus pattern (45 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTGCATCCA
Found at i:38663842 original size:93 final size:93
Alignment explanation
Indices: 38663730--38663900 Score: 279
Period size: 93 Copynumber: 1.8 Consensus size: 93
38663720 CGCCCTAAGT
* *
38663730 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
38663795 CGAGTTCGGATGCCTAGTTACATTTCAC
66 CGAGTTCAGATGCCTAGTTACATTTCAC
* * * *
38663823 GAACTCGGACTCAACTCAACGAGTTCGGATATTTGCATCCATAAGTGAACTCGGACTCCACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
38663888 CGAGTTCAGATGC
66 CGAGTTCAGATGC
38663901 TCAACCATCC
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 71 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCAGATGCCTAGTTACATTTCAC
Found at i:38670323 original size:66 final size:68
Alignment explanation
Indices: 38670247--38670433 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
38670237 TAGTACCACT
*
38670247 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
38670309 CACG
65 CACG
38670313 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
38670378 ATCACG
63 ATCACG
38670384 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
38670434 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:38670358 original size:71 final size:71
Alignment explanation
Indices: 38670270--38670433 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
38670260 CGATTTGTCT
38670270 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
38670335 CTTTCA
66 CTTTCA
38670341 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
38670406 CTTTCA
66 CTTTCA
38670412 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
38670434 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:38670471 original size:71 final size:70
Alignment explanation
Indices: 38670270--38670467 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
38670260 CGATTTGTCT
* * *
38670270 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
38670335 CTTTCA
65 CTTTCA
* * *
38670341 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
38670406 CTTTCA
65 CTTTCA
* *
38670412 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
38670468 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:38677891 original size:66 final size:68
Alignment explanation
Indices: 38677815--38678001 Score: 281
Period size: 71 Copynumber: 2.7 Consensus size: 68
38677805 TAGTACCACT
*
38677815 CATGCGACCTAGC-CGATTTGTC-T-CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
1 CATGCGACCTAGCAC-ATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAAT
38677877 CACG
65 CACG
38677881 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGA
38677946 ATCACG
63 ATCACG
38677952 CATGCGACCTAGCTACATTTATCTTTCACGTAGCTCTCTTGTCTACATGG
1 CATGCGACCTAGC-ACATTTATC-TT-ACGTAGCTCTCTTGTCTACATGG
38678002 GATACATCTC
Statistics
Matches: 114, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
66 13 0.11
67 6 0.05
68 1 0.01
69 1 0.01
71 93 0.82
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (68 bp):
CATGCGACCTAGCACATTTATCTTACGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATC
ACG
Found at i:38677926 original size:71 final size:71
Alignment explanation
Indices: 38677838--38678001 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
38677828 CGATTTGTCT
38677838 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
38677903 CTTTCA
66 CTTTCA
38677909 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
38677974 CTTTCA
66 CTTTCA
38677980 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
38678002 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:38678039 original size:71 final size:70
Alignment explanation
Indices: 38677838--38678035 Score: 276
Period size: 71 Copynumber: 2.8 Consensus size: 70
38677828 CGATTTGTCT
* * *
38677838 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
38677903 CTTTCA
65 CTTTCA
* * *
38677909 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACGCATGCGACCTAGCTACATTTAT
38677974 CTTTCA
65 CTTTCA
* *
38677980 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACGCATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACGCATGCGACCTAGCTAC
38678036 TACAGGGTGT
Statistics
Matches: 121, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
68 23 0.19
69 1 0.01
70 1 0.01
71 96 0.79
ACGTcount: A:0.20, C:0.28, G:0.18, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACGCATGCGACCTAGCTACATTTATC
TTTCA
Found at i:38680320 original size:51 final size:51
Alignment explanation
Indices: 38680244--38680347 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
38680234 TTTTGTGCAT
38680244 AATTGGTCAATTTTACCCTTTTAAGTGAGAGTGAGAAACTATTCCTTCGTG
1 AATTGGTCAATTTTACCCTTTTAAGTGAGAGTGAGAAACTATTCCTTCGTG
*
38680295 AATTGGTCAATTTTACCCTTTTAAGTGGGAGTGAGAAACTATTCCTTCGTG
1 AATTGGTCAATTTTACCCTTTTAAGTGAGAGTGAGAAACTATTCCTTCGTG
38680346 AA
1 AA
38680348 GTCTTCACCT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (51 bp):
AATTGGTCAATTTTACCCTTTTAAGTGAGAGTGAGAAACTATTCCTTCGTG
Found at i:38682705 original size:30 final size:30
Alignment explanation
Indices: 38682669--38682771 Score: 120
Period size: 28 Copynumber: 3.5 Consensus size: 30
38682659 GACAAGATTG
* * *
38682669 GCACTAAGTGTGCGGGTTTAAAATTGTACA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
*
38682699 GCACTAAGTGTGCGAGTTT--GATTATATA
1 GCACTAAGTGTGCGAGTTTAAAATTATATA
* * *
38682727 GCACTAAGTGTGCGAGCTGAATATATATATA
1 GCACTAAGTGTGCGAGTTTAAAAT-TATATA
38682758 GCACTAAGTGTGCG
1 GCACTAAGTGTGCG
38682772 GATTCACTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.37
30 20 0.32
31 20 0.32
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (30 bp):
GCACTAAGTGTGCGAGTTTAAAATTATATA
Found at i:38682759 original size:31 final size:28
Alignment explanation
Indices: 38682698--38682771 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 28
38682688 AAAATTGTAC
*
38682698 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGAGTATGATTATAT
38682726 AGCACTAAGTGTGCGAGCTGAAT-ATATATAT
1 AGCACTAAGTGTGCGAG-T--ATGAT-TATAT
38682757 AGCACTAAGTGTGCG
1 AGCACTAAGTGTGCG
38682772 GATTCACTAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
28 17 0.41
29 1 0.02
30 2 0.05
31 21 0.51
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.30
Consensus pattern (28 bp):
AGCACTAAGTGTGCGAGTATGATTATAT
Found at i:38693632 original size:89 final size:88
Alignment explanation
Indices: 38693463--38693962 Score: 500
Period size: 88 Copynumber: 5.7 Consensus size: 88
38693453 GCGAATCTTG
* * * ** * * * *
38693463 TCTCCCTAAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTATCTCCTTGAAGTTGCAGTCGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTGCAGTGGA
*** **
38693528 GCA-AGTTAAAATTACAAGTCTTA
66 GCAGA-TTAAAGCCACAAACCTTA
* * *
38693551 TCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGG
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCTAAAGTTGCAGTGG
* ** **
38693616 AGCAGATTGAAGTTACAAGTCTTA
65 AGCAGATTAAAGCCACAAACCTTA
* * * * *
38693640 TCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATATTATCTCCCAAAAGTTGCAATGG
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATA-CAAATCTTATCTCCCTAAAGTTGCAGTGG
* *
38693705 AGTAGATTGAAGCCACAAACCTTA
65 AGCAGATTAAAGCCACAAACCTTA
* * * *
38693729 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATAACAAATCTTATCTTCCTAAAGTTGTAGCGG
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGAT-ACAAATCTTATCTCCCTAAAGTTGCAGTGG
38693793 AGCAGATTAAAGCCACAAACCTTA
65 AGCAGATTAAAGCCACAAACCTTA
* * * * * * * *
38693817 TCCCCCTGAAGTTGTAGTGGGGCAGGTTGAAGTTACAATTCTTATCTCTCTGAAGTTGCAGTGGA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTGCAGTGGA
*
38693882 GTAGATTAAAGCCACAAACCTTA
66 GCAGATTAAAGCCACAAACCTTA
* * * * * * * *
38693905 TCCCCCTGAAGTTGCAGTGGGGTAGGTTGAAGTTACGATTCTTATCTCCTTAAAGTTG
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTG
38693963 TAGTAGAGTG
Statistics
Matches: 357, Mismatches: 51, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
88 202 0.57
89 154 0.43
90 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.28
Consensus pattern (88 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATACAAATCTTATCTCCCTAAAGTTGCAGTGGA
GCAGATTAAAGCCACAAACCTTA
Found at i:38693905 original size:44 final size:44
Alignment explanation
Indices: 38693463--38693924 Score: 417
Period size: 44 Copynumber: 10.5 Consensus size: 44
38693453 GCGAATCTTG
* * * *
38693463 TCTCCCTAAAGTTGTAGTGGAGTAGATTGAAGCCACAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
* * * ** **
38693507 TCTCCTTGAAGTTGCAGTCGAGCA-AGTTAAAATTACAAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGA-TTGAAGCTACAAACCTTA
* * *
38693551 TCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCC-TA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CAAA-CCTTA
* * **
38693596 TCTCCCTAAAGTTGCAGTGGAGCAGATTGAAGTTACAAGTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
* * * **
38693640 TCTTCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATATTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTA-CAAACCTTA
** * * *
38693685 TCTCCCAAAAGTTGCAATGGAGTAGATTGAAGCCACAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
* * *
38693729 TCTCCCTGAAGTTGCAGTGGAGCAGGTTGAA-ATAACAAATCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCT-ACAAACCTTA
* * * * * *
38693773 TCTTCCTAAAGTTGTAGCGGAGCAGATTAAAGCCACAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
* * * * * **
38693817 TCCCCCTGAAGTTGTAGTGGGGCAGGTTGAAGTTACAATTCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
* * * *
38693861 TCTCTCTGAAGTTGCAGTGGAGTAGATTAAAGCCACAAACCTTA
1 TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
*
38693905 TCCCCCTGAAGTTGCAGTGG
1 TCTCCCTGAAGTTGCAGTGG
38693925 GGTAGGTTGA
Statistics
Matches: 327, Mismatches: 83, Indels: 16
0.77 0.19 0.04
Matches are distributed among these distances:
43 2 0.01
44 253 0.77
45 71 0.22
46 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (44 bp):
TCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGCTACAAACCTTA
Found at i:38693981 original size:88 final size:88
Alignment explanation
Indices: 38693555--38694013 Score: 429
Period size: 88 Copynumber: 5.2 Consensus size: 88
38693545 GTCTTATCTT
* ** * * * * * *
38693555 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATCCTATCTCCCTAAAGTTGCAGTGGAGCA
1 CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTA-CAATTCTTATCTCCTTAAAGTTGTAGTGGAGTA
* ** ** **
38693620 GATTGAAGTTACAAGTCTTATCTT
65 GATTAAAGCCACAAACCTTATCCC
* ** * * * ** * *
38693644 CCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCAAATATTATCTCCCAAAAGTTGCAATGGAGTA
1 CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTA-CAATTCTTATCTCCTTAAAGTTGTAGTGGAGTA
* *
38693709 GATTGAAGCCACAAACCTTATCTC
65 GATTAAAGCCACAAACCTTATCCC
* * * * * *
38693733 CCTGAAGTTGCAGTGGAGCAGGTTGAAATAACAAATCTTATCTTCC-TAAAGTTGTAGCGGAGCA
1 CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAATTCTTATC-TCCTTAAAGTTGTAGTGGAGTA
38693797 GATTAAAGCCACAAACCTTATCCC
65 GATTAAAGCCACAAACCTTATCCC
* * *
38693821 CCTGAAGTTGTAGTGGGGCAGGTTGAAGTTACAATTCTTATCT-CTCTGAAGTTGCAGTGGAGTA
1 CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAATTCTTATCTCCT-TAAAGTTGTAGTGGAGTA
38693885 GATTAAAGCCACAAACCTTATCCC
65 GATTAAAGCCACAAACCTTATCCC
* * * *
38693909 CCTGAAGTTGCAGTGGGGTAGGTTGAAGTTACGATTCTTATCTCCTTAAAGTTGTAGTAGAGTGG
1 CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAATTCTTATCTCCTTAAAGTTGTAGTGGAGTAG
** * * *
38693974 AGCAAAGCAACAATTCC-TATACC
66 ATTAAAGCCACAA-ACCTTATCCC
*
38693997 CCTGAAGATGCAGTGGG
1 CCTGAAGTTGCAGTGGG
38694014 ATGGAATGAG
Statistics
Matches: 320, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
86 1 0.00
87 1 0.00
88 206 0.64
89 112 0.35
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (88 bp):
CCTGAAGTTGCAGTGGGGCAGGTTGAAGTTACAATTCTTATCTCCTTAAAGTTGTAGTGGAGTAG
ATTAAAGCCACAAACCTTATCCC
Found at i:38695978 original size:5 final size:5
Alignment explanation
Indices: 38695968--38696009 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
38695958 AAATGTTACA
**
38695968 TTTAT TTTAT TTTAT TTTAT TTTAT ACTAT TTT-T TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TTT
38696010 TTAAAATTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 4 0.12
5 28 0.88
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTAT
Found at i:38697946 original size:7 final size:7
Alignment explanation
Indices: 38697934--38697959 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
38697924 GAATGAGGTA
38697934 TTGAATG
1 TTGAATG
38697941 TTGAATG
1 TTGAATG
38697948 TTGAATG
1 TTGAATG
38697955 TTGAA
1 TTGAA
38697960 ATGAATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.27, T:0.42
Consensus pattern (7 bp):
TTGAATG
Found at i:38699960 original size:22 final size:21
Alignment explanation
Indices: 38699912--38699969 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
38699902 AATAATTCAA
* *
38699912 TCTTCTCTATTTTTTTCCTTC
1 TCTTCTTTATTTTTTTTCTTC
38699933 -C-T-TTTATTTTATTTTCTTC
1 TCTTCTTTATTTT-TTTTCTTC
38699952 TCTTCTTTATTTTCTTTT
1 TCTTCTTTATTTT-TTTT
38699970 GTTTAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 7 0.23
19 8 0.27
20 2 0.07
21 1 0.03
22 12 0.40
ACGTcount: A:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (21 bp):
TCTTCTTTATTTTTTTTCTTC
Done.