Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 124041150
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 124041150
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 335 characters in sequence are not A, C, G, or T
File 62 of 410
Found at i:16984316 original size:32 final size:32
Alignment explanation
Indices: 16984275--16984353 Score: 158
Period size: 32 Copynumber: 2.5 Consensus size: 32
16984265 GTGCCCCAAG
16984275 CCACACGGGCGTGTGCAACCACACGGCCCCAC
1 CCACACGGGCGTGTGCAACCACACGGCCCCAC
16984307 CCACACGGGCGTGTGCAACCACACGGCCCCAC
1 CCACACGGGCGTGTGCAACCACACGGCCCCAC
16984339 CCACACGGGCGTGTG
1 CCACACGGGCGTGTG
16984354 ACTCACTAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 47 1.00
ACGTcount: A:0.20, C:0.44, G:0.28, T:0.08
Consensus pattern (32 bp):
CCACACGGGCGTGTGCAACCACACGGCCCCAC
Found at i:16996380 original size:42 final size:43
Alignment explanation
Indices: 16996303--16996402 Score: 121
Period size: 42 Copynumber: 2.3 Consensus size: 43
16996293 CAGACGTGGT
* * *
16996303 CTTACATGTAATCAAATGTCGATGCCACTGTCCCAAACAGGGG
1 CTTACATGAAATCAAATGACGATGCCAATGTCCCAAACAGGGG
* * *
16996346 CTTACATGAAATCATAT-ACGATGCCAATGTCCCAAACATGGT
1 CTTACATGAAATCAAATGACGATGCCAATGTCCCAAACAGGGG
*
16996388 CTTACACGTAAATCA
1 CTTACATG-AAATCA
16996403 CAAATCGATG
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 28 0.57
43 21 0.43
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
CTTACATGAAATCAAATGACGATGCCAATGTCCCAAACAGGGG
Found at i:16998490 original size:44 final size:44
Alignment explanation
Indices: 16998427--16998513 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
16998417 CTATATATAT
16998427 ATATATATAGCTGAAGCTAT-TTCGATCTT-GCACACTAAGTGCAA
1 ATATATATAGCTGAAGCTATCTT-GAT-TTCGCACACTAAGTGCAA
*
16998471 ATATATATAGTTGAAGCTATCTTGATTTCGCACACTAAGTGCA
1 ATATATATAGCTGAAGCTATCTTGATTTCGCACACTAAGTGCA
16998514 CATAATTAGT
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
43 2 0.05
44 36 0.90
45 2 0.05
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Consensus pattern (44 bp):
ATATATATAGCTGAAGCTATCTTGATTTCGCACACTAAGTGCAA
Found at i:17016230 original size:32 final size:32
Alignment explanation
Indices: 17016189--17016257 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
17016179 TAGTCTCAAA
17016189 GTTGGGTTTCAAAGGATAAAAATTTCATCATG
1 GTTGGGTTTCAAAGGATAAAAATTTCATCATG
17016221 GTTGGGTTTCAAAGGATAAAAATTTCATCATG
1 GTTGGGTTTCAAAGGATAAAAATTTCATCATG
17016253 GTTGG
1 GTTGG
17016258 CTTCAAAAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.35
Consensus pattern (32 bp):
GTTGGGTTTCAAAGGATAAAAATTTCATCATG
Found at i:17018251 original size:25 final size:24
Alignment explanation
Indices: 17018192--17018255 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 24
17018182 ATTTTCTCAA
* *
17018192 AAATATAAAATTTTAATAATTCAAT
1 AAAT-TAAAATTTAAATAATTAAAT
**
17018217 AGTTTGAAAATTTAAATAATTAAATT
1 AAATT-AAAATTTAAATAATTAAA-T
17018243 AAATTAAAATTTA
1 AAATTAAAATTTA
17018256 GGAGAAAATT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
24 1 0.03
25 26 0.84
26 4 0.13
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (24 bp):
AAATTAAAATTTAAATAATTAAAT
Found at i:17018822 original size:17 final size:18
Alignment explanation
Indices: 17018795--17018828 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
17018785 AATTAAATAT
17018795 ATGCATATTAAATTATTA
1 ATGCATATTAAATTATTA
*
17018813 ATGC-TATTAATTTATT
1 ATGCATATTAAATTATT
17018829 TAAAAATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (18 bp):
ATGCATATTAAATTATTA
Found at i:17019017 original size:22 final size:22
Alignment explanation
Indices: 17018983--17019024 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
17018973 AGTTGATAAT
17018983 AATTAATATATATT-ATAATGG
1 AATTAATATATATTAATAATGG
17019004 AATTAATTATATATTAATAAT
1 AATTAA-TATATATTAATAAT
17019025 TATAATCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.32
22 8 0.42
23 5 0.26
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
AATTAATATATATTAATAATGG
Found at i:17019133 original size:29 final size:30
Alignment explanation
Indices: 17019076--17019133 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
17019066 CTTTTGAAAA
* * *
17019076 TACTTACAAAAAGAGGCATCTAATTTTTAT
1 TACTTACAAAAAGAGGCAACCAAATTTTAT
17019106 TACTTACAAAAAGA-GCAACCAAATTTTA
1 TACTTACAAAAAGAGGCAACCAAATTTTA
17019134 AAAATACTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.45, C:0.16, G:0.09, T:0.31
Consensus pattern (30 bp):
TACTTACAAAAAGAGGCAACCAAATTTTAT
Found at i:17023908 original size:26 final size:27
Alignment explanation
Indices: 17023879--17023932 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
17023869 TCACACAAGT
*
17023879 TAGTCATTT-ACGCACGAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
* *
17023905 TAGTCATTTAACACCCTAGGGGCAAAA
1 TAGTCATTTAACACACGAGGGGCAAAA
17023932 T
1 T
17023933 GGTAATTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (27 bp):
TAGTCATTTAACACACGAGGGGCAAAA
Found at i:17023992 original size:27 final size:27
Alignment explanation
Indices: 17023934--17023997 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
17023924 GGGCAAAATG
*
17023934 GTAATTTTACCCCACAAGGGTATCTTA
1 GTAATTCTACCCCACAAGGGTATCTTA
* * *
17023961 GTAATTCTACCCTACAGGGGTAT-TTC
1 GTAATTCTACCCCACAAGGGTATCTTA
17023987 GATAATTCTAC
1 G-TAATTCTAC
17023998 AACTTATCCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 3 0.09
27 29 0.91
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (27 bp):
GTAATTCTACCCCACAAGGGTATCTTA
Found at i:17029147 original size:40 final size:40
Alignment explanation
Indices: 17029073--17029214 Score: 167
Period size: 40 Copynumber: 3.5 Consensus size: 40
17029063 CCGCACCAAG
* * * * * *
17029073 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
17029113 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
17029153 GCCTTCGGGTCTTAGCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
17029193 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
17029215 GTAATTTTCA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 87 1.00
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:17029233 original size:40 final size:40
Alignment explanation
Indices: 17029105--17029256 Score: 155
Period size: 40 Copynumber: 3.8 Consensus size: 40
17029095 ATCACGATTT
* * * * *
17029105 GCACAAATGCCTTCGGGTCTTAGCCCGGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
17029145 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
* * * **
17029185 GCACAATTGCCTTCGGGTCTTAACCCGGATGTA-ATTTTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACT-A
* * *
17029225 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
17029257 CATTCAATTT
Statistics
Matches: 95, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
39 4 0.04
40 89 0.94
41 2 0.02
ACGTcount: A:0.22, C:0.26, G:0.23, T:0.29
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
Found at i:17037250 original size:40 final size:40
Alignment explanation
Indices: 17037176--17037316 Score: 158
Period size: 40 Copynumber: 3.5 Consensus size: 40
17037166 CCGCACCAAG
* * * * * *
17037176 GCCTACGGGACTTAACCCGGATATCACGATTTGCACAAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* *
17037216 GCCTTCGGGTCTTAGCCCGGATTTAACAACTTGCACGAAT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
* * * *
17037256 GCCTTCGGGTCTT-GCCCGGATATAGCTACTAGCACAATT
1 GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
*
17037295 GCCTTCGGGTCTTAACCCGGAT
1 GCCTTCGGGTCTTAGCCCGGAT
17037317 GTAATTTTCA
Statistics
Matches: 85, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
39 33 0.39
40 52 0.61
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCCTTCGGGTCTTAGCCCGGATATAACAACTTGCACAAAT
Found at i:17039087 original size:39 final size:39
Alignment explanation
Indices: 17039044--17039180 Score: 141
Period size: 40 Copynumber: 3.5 Consensus size: 39
17039034 GGCTGTCACA
*
17039044 GAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAG-CCC
1 GAAGGCATTCGTGCGAGTTACTAAA-CCGGGCTAAGTCCC
* * * *
17039083 GAAGGCATTTGTGCAAGTTACTAAACCCAGGTTAAGTCCC
1 GAAGGCATTCGTGCGAGTTACTAAA-CCGGGCTAAGTCCC
* * **
17039123 GAAGGCATTCGTGTGAGTCACTATAACCGGGCTTCGTCCC
1 GAAGGCATTCGTGCGAGTTACTA-AACCGGGCTAAGTCCC
* *
17039163 GAAGGCATTTGAGCGAGT
1 GAAGGCATTCGTGCGAGT
17039181 CGTTATATCC
Statistics
Matches: 79, Mismatches: 17, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
39 30 0.38
40 47 0.59
41 2 0.03
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (39 bp):
GAAGGCATTCGTGCGAGTTACTAAACCGGGCTAAGTCCC
Found at i:17039130 original size:40 final size:39
Alignment explanation
Indices: 17039044--17039135 Score: 121
Period size: 39 Copynumber: 2.3 Consensus size: 39
17039034 GGCTGTCACA
* * *
17039044 GAAGGCATTCGTGCGAGTTAATAAATCCGGGCTAAGCCC
1 GAAGGCATTCGTGCAAGTTAATAAACCCAGGCTAAGCCC
* * *
17039083 GAAGGCATTTGTGCAAGTTACTAAACCCAGGTTAAGTCCC
1 GAAGGCATTCGTGCAAGTTAATAAACCCAGGCTAAG-CCC
17039123 GAAGGCATTCGTG
1 GAAGGCATTCGTG
17039136 TGAGTCACTA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
39 30 0.67
40 15 0.33
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.23
Consensus pattern (39 bp):
GAAGGCATTCGTGCAAGTTAATAAACCCAGGCTAAGCCC
Found at i:17045334 original size:27 final size:26
Alignment explanation
Indices: 17045286--17045345 Score: 75
Period size: 27 Copynumber: 2.3 Consensus size: 26
17045276 GCGAGGCTAC
*
17045286 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
17045313 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
17045339 CAGATAT
1 CAGATAT
17045346 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.28
27 21 0.72
ACGTcount: A:0.35, C:0.20, G:0.23, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:17045349 original size:2 final size:2
Alignment explanation
Indices: 17045342--17045369 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17045332 ACCAGAACAG
17045342 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17045370 GTGGCGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17050144 original size:40 final size:40
Alignment explanation
Indices: 17050087--17050347 Score: 377
Period size: 40 Copynumber: 6.5 Consensus size: 40
17050077 CTAACGGGGT
* * *
17050087 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
17050127 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
17050167 TAAGTCCCGAAGGCATTTGTG-TGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCT-AGTTACTAATTCCGGGC
*
17050207 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
*
17050247 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAAT-TCCGGGC
** *
17050287 TAAGTCCCGAAGGCATTTGTGCTAGCGAC-CATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCTAGTTACTAAT-TCCGGGC
* *
17050327 TAAGACCCGACGGC-TTTGTGC
1 TAAGTCCCGAAGGCATTTGTGC
17050348 GAGTGGTTAT
Statistics
Matches: 208, Mismatches: 9, Indels: 9
0.92 0.04 0.04
Matches are distributed among these distances:
39 10 0.05
40 198 0.95
ACGTcount: A:0.23, C:0.23, G:0.27, T:0.28
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTTACTAATTCCGGGC
Found at i:17054527 original size:71 final size:71
Alignment explanation
Indices: 17054411--17054552 Score: 275
Period size: 71 Copynumber: 2.0 Consensus size: 71
17054401 TGAAACGAGA
17054411 CATTTCCAATTTTGTTTCGAAGTGTTTAATATGTCAGCAAGTGAAGGCGGAACATCAAGTGCCTA
1 CATTTCCAATTTTGTTTCGAAGTGTTTAATATGTCAGCAAGTGAAGGCGGAACATCAAGTGCCTA
*
17054476 CGGGTT
66 CAGGTT
17054482 CATTTCCAATTTTGTTTCGAAGTGTTTAATATGTCAGCAAGTGAAGGCGGAACATCAAGTGCCTA
1 CATTTCCAATTTTGTTTCGAAGTGTTTAATATGTCAGCAAGTGAAGGCGGAACATCAAGTGCCTA
17054547 CAGGTT
66 CAGGTT
17054553 TACTTCAGCC
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (71 bp):
CATTTCCAATTTTGTTTCGAAGTGTTTAATATGTCAGCAAGTGAAGGCGGAACATCAAGTGCCTA
CAGGTT
Found at i:17057583 original size:40 final size:40
Alignment explanation
Indices: 17057380--17057561 Score: 285
Period size: 40 Copynumber: 4.5 Consensus size: 40
17057370 CTAACGGGGT
* * * *
17057380 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
*
17057420 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCTGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
* *
17057460 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTTCGGAC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
17057500 TAAGTCCCGAAGGCATTTGTGCGAGTTACT-ATATCCGGGC
1 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT-TCCGGGC
17057540 TAAGTCCCGAAGGCATTTGTGC
1 TAAGTCCCGAAGGCATTTGTGC
17057562 TAGCGACCAT
Statistics
Matches: 131, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
39 2 0.02
40 129 0.98
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (40 bp):
TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTCCGGGC
Found at i:17057583 original size:80 final size:80
Alignment explanation
Indices: 17057380--17057629 Score: 301
Period size: 80 Copynumber: 3.1 Consensus size: 80
17057370 CTAACGGGGT
* *
17057380 TAAGTCCCGAAGACATTTGTGCTAGTGATTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
*
17057445 TTACTA-ATTCTGGGC
66 TTACTATA-TCCGGGC
* * * *
17057460 TAAGTCCCGAAGGCATTTGTGCGAGTTACTAATTTCGGACTAAGTCCCGAAGGCATTTGTGCGAG
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
17057525 TTACTATATCCGGGC
66 TTACTATATCCGGGC
* * * * * *
17057540 TAAGTCCCGAAGGCATTTGTGCTAGCGAC-CATATCCGGGCTAAGACCTGACGGC-CTTGTGCGA
1 TAAGTCCCGAAGGCATTTGTGCTAGTGACTAAT-TCCGGGCTAAGTCCCGAAGGCATTTGTGCGA
***
17057603 GTGGTTATATCC-GGC
65 GTTACTATATCCGGGC
*
17057618 TAAATCCCGAAG
1 TAAGTCCCGAAG
17057630 ATAATTGGTT
Statistics
Matches: 147, Mismatches: 21, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
78 14 0.10
79 19 0.13
80 113 0.77
81 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.27, T:0.27
Consensus pattern (80 bp):
TAAGTCCCGAAGGCATTTGTGCTAGTGACTAATTCCGGGCTAAGTCCCGAAGGCATTTGTGCGAG
TTACTATATCCGGGC
Found at i:17062792 original size:28 final size:27
Alignment explanation
Indices: 17062730--17062798 Score: 120
Period size: 27 Copynumber: 2.5 Consensus size: 27
17062720 TAGTGAGTCT
17062730 GCACACTTAGTGCTATATAATCAACTC
1 GCACACTTAGTGCTATATAATCAACTC
*
17062757 GCACACTTAGTGCTATATGATCAAACTC
1 GCACACTTAGTGCTATATAATC-AACTC
17062785 GCACACTTAGTGCT
1 GCACACTTAGTGCT
17062799 GTACAAGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.29
Consensus pattern (27 bp):
GCACACTTAGTGCTATATAATCAACTC
Found at i:17071678 original size:99 final size:96
Alignment explanation
Indices: 17071560--17071738 Score: 252
Period size: 96 Copynumber: 1.8 Consensus size: 96
17071550 TACAAGATGT
* * *
17071560 GTCAGTGTAAGACCATGTCTAGGACATGGCATCGACACGGATATGTGA-GAGCTAGTGTAAGACC
1 GTCAATGTAAGACCATGTCTAGGACATGGCATCGAC-CGG--ATG-GATGAGCCAGTGTAAAACC
17071624 ATGTCTGGGACATGGCATTGGCCTCGATTTCGATA
62 ATGTCTGGGACATGGCATTGGCCTCGATTTCGATA
* **
17071659 GTCAATGTAAGACCATGTCTGGGACATGGCATCGACTTGATGGATGAGCCAGTGTAAAACCATGT
1 GTCAATGTAAGACCATGTCTAGGACATGGCATCGACCGGATGGATGAGCCAGTGTAAAACCATGT
*
17071724 CTGGGACCTGGCATT
66 CTGGGACATGGCATT
17071739 AGCATTATAC
Statistics
Matches: 72, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
95 2 0.03
96 35 0.49
98 1 0.01
99 34 0.47
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.25
Consensus pattern (96 bp):
GTCAATGTAAGACCATGTCTAGGACATGGCATCGACCGGATGGATGAGCCAGTGTAAAACCATGT
CTGGGACATGGCATTGGCCTCGATTTCGATA
Found at i:17074331 original size:50 final size:49
Alignment explanation
Indices: 17074166--17074387 Score: 282
Period size: 49 Copynumber: 4.5 Consensus size: 49
17074156 CTGGTACGCA
* * * *
17074166 TAGTAGCCTGCACATAGTACTACACATGCGACCAATTATCCGGTACATG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
*
17074215 TAGTAGCCTACACTTAGTACTACACACGTGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * *
17074264 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAAACATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * * *
17074314 TAGTGGCCTGCACTTAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
17074365 TAGTAGCCTGCACTTAGTACTAC
1 TAGTAGCCTGCACTTAGTACTAC
17074388 GCATGCGACC
Statistics
Matches: 150, Mismatches: 20, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
49 76 0.51
50 42 0.28
51 31 0.21
52 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.26
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:17074398 original size:101 final size:99
Alignment explanation
Indices: 17074153--17074398 Score: 314
Period size: 101 Copynumber: 2.5 Consensus size: 99
17074143 TAGCCAAAGC
* * ** * *
17074153 TATCTGGTACGCATAGTAGCCTGCACATAGTACTACACATGCGACC-AATTATCCGGTACATGTA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAACATCCGATACACGTA
17074217 GTAGCCTACACTTAGTACTACACACGTGACCAAT
66 GTAGCCTACACTTAGTACTACACACGTGACCAAT
* * * * *
17074251 TATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAAACATCTGATACACGTA
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAACATCCGATACACGTA
* * *
17074316 GTGGCCTGCACTTAGTACTACACACGTGATCACAGT
66 GTAGCCTACACTTAGTACTACACACGTGA-C-CAAT
* * *
17074352 TTTCGGGTACGCATAGTAGCCTGCACTTAGTACTACGCATGCGACCT
1 TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCT
17074399 CACAATAGAT
Statistics
Matches: 124, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
98 40 0.32
99 40 0.32
100 1 0.01
101 43 0.35
ACGTcount: A:0.28, C:0.27, G:0.19, T:0.26
Consensus pattern (99 bp):
TATCCGGTACGCATAGTAGCCTGCACTTAGTACTACACATGCGACCTAAACATCCGATACACGTA
GTAGCCTACACTTAGTACTACACACGTGACCAAT
Found at i:17075546 original size:28 final size:28
Alignment explanation
Indices: 17075511--17075565 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
17075501 CACGGGTTGA
*
17075511 GACACGGG-TGTGTCGAGGCCGTGTGAGT
1 GACACGGGATGTG-CCAGGCCGTGTGAGT
17075539 GACACGGGCATGTGCCAGGCCGTGTGA
1 GACACGGG-ATGTGCCAGGCCGTGTGA
17075566 AAAGCCTTGT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 8 0.33
29 12 0.50
30 4 0.17
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (28 bp):
GACACGGGATGTGCCAGGCCGTGTGAGT
Found at i:17078083 original size:26 final size:24
Alignment explanation
Indices: 17078042--17078094 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
17078032 TATGACCAAT
*
17078042 TTTTGTAAACATTTCACACAACCA
1 TTTTGTAAACAATTCACACAACCA
* *
17078066 TTTTGTATAACCAATTCATATAACCA
1 TTTTGTA-AA-CAATTCACACAACCA
17078092 TTT
1 TTT
17078095 GTCATTTGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 2 0.08
26 15 0.62
ACGTcount: A:0.36, C:0.21, G:0.04, T:0.40
Consensus pattern (24 bp):
TTTTGTAAACAATTCACACAACCA
Found at i:17078242 original size:46 final size:46
Alignment explanation
Indices: 17078182--17078528 Score: 335
Period size: 46 Copynumber: 7.8 Consensus size: 46
17078172 TTCGACACGA
* * *
17078182 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGT
* * * * *
17078228 TGCCATGGTATCTTTCAACCATGGACTTATTCATTTCCCCGTTATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-TCTGTCATGT
* * * *
17078275 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT-TCTGTCATGT
*
17078322 TGCCATGGTATCTTTCAACCATGG-----C-C---TTATG-CA--T
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGT
* * *
17078356 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTCTC-GTTATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGT
* * * *
17078401 TGCCATGGTATCTTTCAACCATGGTTTTATTC-TTTTCATGTTACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTC-TGTCATGT
* * * * *
17078447 GGCCATGGTATCTTTCAACCATGGTCTTGCACATTTTGTATCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGT
*
17078493 TGCCATGGTATCTTTCAACCATGGTCTTACACATTT
1 TGCCATGGTATCTTTCAACCATGGTCTTACTCATTT
17078529 CATTTCAGAA
Statistics
Matches: 251, Mismatches: 34, Indels: 32
0.79 0.11 0.10
Matches are distributed among these distances:
34 25 0.10
36 2 0.01
37 1 0.00
38 1 0.00
40 1 0.00
42 1 0.00
43 2 0.01
44 4 0.02
45 32 0.13
46 103 0.41
47 79 0.31
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACTCATTTTCTGTCATGT
Found at i:17078285 original size:47 final size:47
Alignment explanation
Indices: 17078182--17078356 Score: 244
Period size: 47 Copynumber: 3.7 Consensus size: 47
17078172 TTCGACACGA
* * * * * *
17078182 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTT-TCTGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGTCATGT
* *
17078228 TGCCATGGTATCTTTCAACCATGGACTTATTCATTTCCCCGTTATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGTCATGT
*
17078275 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCCGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGTCATGT
* *
17078322 TGCCATGGTATCTTTCAACCATGGCCTTATGCATT
1 TGCCATGGTATCTTTCAACCATGGTCTTATTCATT
17078357 GCCATGGTAT
Statistics
Matches: 114, Mismatches: 14, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
46 31 0.27
47 83 0.73
ACGTcount: A:0.18, C:0.25, G:0.15, T:0.42
Consensus pattern (47 bp):
TGCCATGGTATCTTTCAACCATGGTCTTATTCATTTCCCCGTCATGT
Found at i:17078342 original size:94 final size:93
Alignment explanation
Indices: 17078182--17078521 Score: 305
Period size: 94 Copynumber: 3.8 Consensus size: 93
17078172 TTCGACACGA
* * * *
17078182 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTCTGTCATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
*
17078247 CATGGACTTATTCATTTCCCCGTTATGT
66 CATGGACTTATGCATTTCCCCGTTATGT
* * *
17078275 TGCCATGGTATCTTTCAACCATGGTCTTATTTATTTCCCCGTCATGTTGCCATGGTATCTTTCAA
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTT-CCCGTCATGTTGCCATGGTATCTTTCAA
*
17078340 CCATGGCCTTATG--------C---A--T
65 CCATGGACTTATGCATTTCCCCGTTATGT
* * * *
17078356 TGCCATGGTATCTTTCAACCATGGTCTTATTCA-TTCTCGTTATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
** * * ** *
17078420 CATGGTTTTATTC-TTTTCATGTTACGT
66 CATGGACTTATGCATTTCCCCGTTATGT
* * * * ****
17078447 GGCCATGGTATCTTTCAACCATGGTCTTGCACATTTTGTATCATGTTGCCATGGTATCTTTCAAC
1 TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
*
17078512 CATGGTCTTA
66 CATGGACTTA
17078522 CACATTTCAT
Statistics
Matches: 207, Mismatches: 26, Indels: 29
0.79 0.10 0.11
Matches are distributed among these distances:
79 36 0.17
80 2 0.01
81 33 0.16
83 1 0.00
86 1 0.00
89 1 0.00
91 30 0.14
92 35 0.17
93 31 0.15
94 37 0.18
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (93 bp):
TGCCATAGTATCTTTCAACCATGGTCTTACTCATTTCCCGTCATGTTGCCATGGTATCTTTCAAC
CATGGACTTATGCATTTCCCCGTTATGT
Found at i:17078364 original size:34 final size:34
Alignment explanation
Indices: 17078321--17078390 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
17078311 CCCCGTCATG
17078321 TTGCCATGGTATCTTTCAACCATGGCCTTATGCA
1 TTGCCATGGTATCTTTCAACCATGGCCTTATGCA
* *
17078355 TTGCCATGGTATCTTTCAACCATGGTCTTATTCA
1 TTGCCATGGTATCTTTCAACCATGGCCTTATGCA
17078389 TT
1 TT
17078391 CTCGTTATGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (34 bp):
TTGCCATGGTATCTTTCAACCATGGCCTTATGCA
Found at i:17080654 original size:11 final size:11
Alignment explanation
Indices: 17080638--17080685 Score: 60
Period size: 11 Copynumber: 4.2 Consensus size: 11
17080628 CTTTATATAC
17080638 TAATAAAATAA
1 TAATAAAATAA
17080649 TAATAAAATATA
1 TAATAAAATA-A
* *
17080661 TTATTAAAATAT
1 -TAATAAAATAA
17080673 TAATAAAATAA
1 TAATAAAATAA
17080684 TA
1 TA
17080686 TTTATCTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
11 21 0.68
12 1 0.03
13 9 0.29
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
TAATAAAATAA
Found at i:17080668 original size:24 final size:24
Alignment explanation
Indices: 17080632--17080687 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
17080622 TTCTTTCTTT
*
17080632 ATATACTAATAAAATAATAATAAA
1 ATATATTAATAAAATAATAATAAA
* *
17080656 ATATATTATTAAAATATTAATAAA
1 ATATATTAATAAAATAATAATAAA
17080680 ATAATATT
1 AT-ATATT
17080688 TATCTAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 23 0.82
25 5 0.18
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATATTAATAAAATAATAATAAA
Found at i:17084922 original size:26 final size:27
Alignment explanation
Indices: 17084893--17084965 Score: 67
Period size: 26 Copynumber: 2.7 Consensus size: 27
17084883 ACCAATAACA
17084893 CAGCAAAGCTGCCAGTAATAAT-AATG
1 CAGCAAAGCTGCCAGTAATAATAAATG
** * *
17084919 CAGCATTGCTGCCAGAAATAGTAAATG
1 CAGCAAAGCTGCCAGTAATAATAAATG
** **
17084946 TGGCAAAGCCACCAGTAATA
1 CAGCAAAGCTGCCAGTAATA
17084966 GTGAATCTGA
Statistics
Matches: 35, Mismatches: 11, Indels: 1
0.74 0.23 0.02
Matches are distributed among these distances:
26 18 0.51
27 17 0.49
ACGTcount: A:0.40, C:0.21, G:0.21, T:0.19
Consensus pattern (27 bp):
CAGCAAAGCTGCCAGTAATAATAAATG
Found at i:17085656 original size:16 final size:17
Alignment explanation
Indices: 17085635--17085670 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17085625 CTCCTTAAGC
*
17085635 TCCCAACCTACAATC-G
1 TCCCAACATACAATCAG
17085651 TCCCAACATACAATCAG
1 TCCCAACATACAATCAG
17085668 TCC
1 TCC
17085671 ATCATTTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.33, C:0.42, G:0.06, T:0.19
Consensus pattern (17 bp):
TCCCAACATACAATCAG
Found at i:17098027 original size:22 final size:20
Alignment explanation
Indices: 17097982--17098030 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
17097972 TTTTGTTTTT
* *
17097982 TTTTCTATTCTTCCTACCGA
1 TTTTCTTTTCTTCCTACCAA
17098002 -TTTCTTTTCTTCTCTACACAA
1 TTTTCTTTTCTTC-CTAC-CAA
17098023 TTTTCTTT
1 TTTTCTTT
17098031 GTTTCACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 11 0.46
20 4 0.17
21 2 0.08
22 7 0.29
ACGTcount: A:0.14, C:0.27, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTTCTTTTCTTCCTACCAA
Found at i:17099720 original size:39 final size:39
Alignment explanation
Indices: 17099642--17099755 Score: 183
Period size: 39 Copynumber: 2.9 Consensus size: 39
17099632 TATGGTAACC
** *
17099642 TGCACAAAGGCCTTCGGGACTTAACCCGGATATCACAATT
1 TGCACAATTGCCTTCGGG-CTTAGCCCGGATATCACAATT
17099682 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
1 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
*
17099721 TGCACAATTGCCTTTGGGCTTAGCCCGGATATCAC
1 TGCACAATTGCCTTCGGGCTTAGCCCGGATATCAC
17099756 TCGAACATTC
Statistics
Matches: 70, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
39 54 0.77
40 16 0.23
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
TGCACAATTGCCTTCGGGCTTAGCCCGGATATCACAATT
Found at i:17107780 original size:39 final size:39
Alignment explanation
Indices: 17107654--17107795 Score: 225
Period size: 39 Copynumber: 3.7 Consensus size: 39
17107644 CCGCACAAAG
*
17107654 GCCTTCGGGACTTAACCCGGATATCACAATTTGCACAATT
1 GCCTTCGGG-CTTAGCCCGGATATCACAATTTGCACAATT
* * *
17107694 GCCTTCGGGCTTAG-CCGGATATCATAACTCGC-CAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
17107731 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
1 GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
17107770 GCCTTCGGGCTTAGCCCGGATATCAC
1 GCCTTCGGGCTTAGCCCGGATATCAC
17107796 TCGAACATTC
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
37 19 0.20
38 30 0.32
39 35 0.38
40 9 0.10
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
GCCTTCGGGCTTAGCCCGGATATCACAATTTGCACAATT
Found at i:17114071 original size:39 final size:39
Alignment explanation
Indices: 17114025--17114203 Score: 207
Period size: 39 Copynumber: 4.5 Consensus size: 39
17114015 TGAATGATAC
*
17114025 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATATAT
*
17114064 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGA-TATAT
** * *
17114104 CC-GGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATATAT
* * * * *
17114143 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGA-TATAT
**
17114183 CCGGATTAAGACCCGAAGGCA
1 CCGGGCTAAGACCCGAAGGCA
17114204 ATTGTGCTTG
Statistics
Matches: 123, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
39 66 0.54
40 57 0.46
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATATAT
Found at i:17114161 original size:40 final size:39
Alignment explanation
Indices: 17114025--17114224 Score: 206
Period size: 40 Copynumber: 5.1 Consensus size: 39
17114015 TGAATGATAC
* *
17114025 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGTTATAT
*
17114064 CCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTG-TTATAT
** *
17114104 CC-GGCTAAGACCCGAAGGCATTCGTGCGAGTTGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGTTATAT
* * * *
17114143 CCGGGCTAAGACCCGAAGGCATTTGTGCAAGT-TACCAAAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGT--TATAT
** * * *
17114183 CCGGATTAAGACCCGAAGGCAATTGTGCTTGTGGTTATAT
1 CCGGGCTAAGACCCGAAGGCATTTATGCTAGT-GTTATAT
17114223 CC
1 CC
17114225 TGCTAAATTC
Statistics
Matches: 138, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 66 0.48
40 70 0.51
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.26, T:0.27
Consensus pattern (39 bp):
CCGGGCTAAGACCCGAAGGCATTTATGCTAGTGTTATAT
Found at i:17114230 original size:79 final size:78
Alignment explanation
Indices: 17114028--17114224 Score: 225
Period size: 79 Copynumber: 2.5 Consensus size: 78
17114018 ATGATACCCG
* * * * * *
17114028 GGCTAAGTCCCGAAGGCATTTATGCTAGTGATATATCCGGGCTAAGTCCCGAAGGCATTTATGCT
1 GGCTAAGACCCGAAGGCAATTGTGCTAGTGTTATATCCGGGCTAAGACCCGAAGGCATTTATGCA
** *
17114093 AGTGATTATATCC
66 AGTGACCAAATCC
* *
17114106 GGCTAAGACCCGAAGGC-ATTCGTGCGAGTTGTTATATCCGGGCTAAGACCCGAAGGCATTTGTG
1 GGCTAAGACCCGAAGGCAATT-GTGCTAG-TGTTATATCCGGGCTAAGACCCGAAGGCATTTATG
*
17114170 CAAGTTACCAAATCC
64 CAAGTGACCAAATCC
* *
17114185 GGATTAAGACCCGAAGGCAATTGTGCTTGTGGTTATATCC
1 GG-CTAAGACCCGAAGGCAATTGTGCTAGT-GTTATATCC
17114225 TGCTAAATTC
Statistics
Matches: 99, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
77 2 0.02
78 21 0.21
79 45 0.45
80 28 0.28
81 3 0.03
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (78 bp):
GGCTAAGACCCGAAGGCAATTGTGCTAGTGTTATATCCGGGCTAAGACCCGAAGGCATTTATGCA
AGTGACCAAATCC
Found at i:17119722 original size:40 final size:40
Alignment explanation
Indices: 17119678--17119777 Score: 110
Period size: 40 Copynumber: 2.5 Consensus size: 40
17119668 ACTTCGGTGT
*
17119678 CCCTGATTGCACATTTGTGCCACTGAATGCACTCTGAAGC
1 CCCTGATTGCACATTCGTGCCACTGAATGCACTCTGAAGC
*** * * **
17119718 CCCTGACAACACATTCGTGCCCCTGAATGTACTCTGGTGC
1 CCCTGATTGCACATTCGTGCCACTGAATGCACTCTGAAGC
* *
17119758 CCCTAATTGCACACTCGTGC
1 CCCTGATTGCACATTCGTGC
17119778 TCTTGATTAC
Statistics
Matches: 47, Mismatches: 13, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (40 bp):
CCCTGATTGCACATTCGTGCCACTGAATGCACTCTGAAGC
Found at i:17119777 original size:20 final size:20
Alignment explanation
Indices: 17119678--17119777 Score: 53
Period size: 20 Copynumber: 5.0 Consensus size: 20
17119668 ACTTCGGTGT
* * *
17119678 CCCTGATTGCACATTTGTGC
1 CCCTGAATGCACACTCGTGC
* * *
17119698 CACTGAATGCACTCT-GAAGC
1 CCCTGAATGCACACTCG-TGC
* *
17119718 CCCTGACA-ACACATTCGTGC
1 CCCTGA-ATGCACACTCGTGC
* * *
17119738 CCCTGAATGTACTCTGGTGC
1 CCCTGAATGCACACTCGTGC
17119758 CCCT-AATTGCACACTCGTGC
1 CCCTGAA-TGCACACTCGTGC
17119778 TCTTGATTAC
Statistics
Matches: 57, Mismatches: 18, Indels: 10
0.67 0.21 0.12
Matches are distributed among these distances:
19 4 0.07
20 51 0.89
21 2 0.04
ACGTcount: A:0.21, C:0.34, G:0.19, T:0.26
Consensus pattern (20 bp):
CCCTGAATGCACACTCGTGC
Found at i:17122014 original size:26 final size:26
Alignment explanation
Indices: 17121965--17122162 Score: 116
Period size: 26 Copynumber: 7.9 Consensus size: 26
17121955 CACAAATGCA
*
17121965 GCTCTTTGTGAGCTTTCC-GTTTAAAG
1 GCTCTTTGTGAGC-TTCCTGATTAAAG
* *
17121991 GCTCTTCGTGAGCTTCCTGATTAAAA
1 GCTCTTTGTGAGCTTCCTGATTAAAG
** * * * *
17122017 ATTCTATATGAACTTCCTGATT-ATG
1 GCTCTTTGTGAGCTTCCTGATTAAAG
*
17122042 GCTCTATGTGAGCTTCCTG-TTATATA-
1 GCTCTTTGTGAGCTTCCTGATTA-A-AG
** *
17122068 GC-C-CAGATAAGCTTCCTGA-T--AG
1 GCTCTTTG-TGAGCTTCCTGATTAAAG
*
17122090 GCTCTTTGTGAGCTTCTTGA-T--AG
1 GCTCTTTGTGAGCTTCCTGATTAAAG
*
17122113 GCTCTTTTTGTGAGCTTCCTGATTAATG
1 GCTC--TTTGTGAGCTTCCTGATTAAAG
17122141 GCTCTTTGTGAGCTTCCT-ATTA
1 GCTCTTTGTGAGCTTCCTGATTA
17122163 TATGGATTGA
Statistics
Matches: 133, Mismatches: 25, Indels: 29
0.71 0.13 0.16
Matches are distributed among these distances:
21 1 0.01
22 2 0.02
23 18 0.14
24 4 0.03
25 51 0.38
26 52 0.39
28 5 0.04
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.40
Consensus pattern (26 bp):
GCTCTTTGTGAGCTTCCTGATTAAAG
Found at i:17122057 original size:25 final size:25
Alignment explanation
Indices: 17122019--17122163 Score: 106
Period size: 25 Copynumber: 5.9 Consensus size: 25
17122009 GATTAAAAAT
* *
17122019 TCTATATGAACTTCCTGATTATGGC
1 TCTATGTGAGCTTCCTGATTATGGC
* *
17122044 TCTATGTGAGCTTCCTGTTATATAGC
1 TCTATGTGAGCTTCCTGAT-TATGGC
* *
17122070 -CCA-GATAAGCTTCCTGA-TA-GGC
1 TCTATG-TGAGCTTCCTGATTATGGC
* *
17122092 TCTTTGTGAGCTTCTTGA-TA-GGC
1 TCTATGTGAGCTTCCTGATTATGGC
*
17122115 TCTTTTTGTGAGCTTCCTGATTAATGGC
1 TC--TATGTGAGCTTCCTGATT-ATGGC
*
17122143 TCTTTGTGAGCTTCCT-ATTAT
1 TCTATGTGAGCTTCCTGATTAT
17122164 ATGGATTGAG
Statistics
Matches: 98, Mismatches: 13, Indels: 19
0.75 0.10 0.15
Matches are distributed among these distances:
22 2 0.02
23 20 0.20
24 4 0.04
25 46 0.47
26 20 0.20
27 1 0.01
28 5 0.05
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (25 bp):
TCTATGTGAGCTTCCTGATTATGGC
Found at i:17122110 original size:23 final size:23
Alignment explanation
Indices: 17122077--17122158 Score: 110
Period size: 23 Copynumber: 3.3 Consensus size: 23
17122067 AGCCCAGATA
17122077 AGCTTCCTGATAGGCTCTTTGTG
1 AGCTTCCTGATAGGCTCTTTGTG
*
17122100 AGCTTCTTGATAGGCTCTTTTTGTG
1 AGCTTCCTGATAGGCTC--TTTGTG
17122125 AGCTTCCTGATTAATGGCTCTTTGTG
1 AGCTTCCTGA-T-A-GGCTCTTTGTG
17122151 AGCTTCCT
1 AGCTTCCT
17122159 ATTATATGGA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
23 16 0.31
25 15 0.29
26 15 0.29
27 1 0.02
28 5 0.10
ACGTcount: A:0.13, C:0.21, G:0.23, T:0.43
Consensus pattern (23 bp):
AGCTTCCTGATAGGCTCTTTGTG
Found at i:17124146 original size:22 final size:22
Alignment explanation
Indices: 17124120--17124165 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
17124110 TTATTCTATG
17124120 AATTG-ATATATGTTTATAAATT
1 AATTGAATAT-TGTTTATAAATT
* *
17124142 AATTGAATATTTTTTCTAAATT
1 AATTGAATATTGTTTATAAATT
17124164 AA
1 AA
17124166 GATAAATTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.50
Consensus pattern (22 bp):
AATTGAATATTGTTTATAAATT
Found at i:17126440 original size:27 final size:27
Alignment explanation
Indices: 17126392--17126539 Score: 165
Period size: 27 Copynumber: 5.5 Consensus size: 27
17126382 TAAAGTACAT
*
17126392 CACAAAGGCATTCC-CTTCATAGATTGC
1 CACAAAGGC-TTCCTTTTCATAGATTGC
* * * *
17126419 CATAGAGGCTTCCTTTTTATAGATAGC
1 CACAAAGGCTTCCTTTTCATAGATTGC
*
17126446 CACAAAGGCTTCCTTTTAATAGATTGC
1 CACAAAGGCTTCCTTTTCATAGATTGC
* * *
17126473 CAC-AAGGACTTTCTTTTCATAAATCGC
1 CACAAAGG-CTTCCTTTTCATAGATTGC
*
17126500 CACAAAGGCTTCCTTTTCATAGATCGC
1 CACAAAGGCTTCCTTTTCATAGATTGC
*
17126527 AACAAAGGCTTCC
1 CACAAAGGCTTCC
17126540 ATTTACTAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
26 8 0.08
27 90 0.88
28 4 0.04
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (27 bp):
CACAAAGGCTTCCTTTTCATAGATTGC
Found at i:17142230 original size:11 final size:11
Alignment explanation
Indices: 17142214--17142247 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
17142204 GGCTATAACA
17142214 TCCATTTCATT
1 TCCATTTCATT
17142225 TCCATTTCCATT
1 TCCATTT-CATT
*
17142237 TTCATTTCATT
1 TCCATTTCATT
17142248 CTTATTTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.18, C:0.26, G:0.00, T:0.56
Consensus pattern (11 bp):
TCCATTTCATT
Found at i:17143496 original size:21 final size:21
Alignment explanation
Indices: 17143472--17143514 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
17143462 ACCTTTTCTA
17143472 AAGTTAAAAGTCAAAACAATT
1 AAGTTAAAAGTCAAAACAATT
*
17143493 AAGTTAAAAGTCAAAACCATT
1 AAGTTAAAAGTCAAAACAATT
17143514 A
1 A
17143515 TATTGTTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.56, C:0.12, G:0.09, T:0.23
Consensus pattern (21 bp):
AAGTTAAAAGTCAAAACAATT
Found at i:17143780 original size:45 final size:45
Alignment explanation
Indices: 17143716--17143806 Score: 164
Period size: 45 Copynumber: 2.0 Consensus size: 45
17143706 CACCTAAAAT
*
17143716 TTTAGGTCAGATTGCATGGTAGTAAACACACGGGTAGAGACACGG
1 TTTAGGTCAGATTGCATGGTAGCAAACACACGGGTAGAGACACGG
*
17143761 TTTAGGTTAGATTGCATGGTAGCAAACACACGGGTAGAGACACGG
1 TTTAGGTCAGATTGCATGGTAGCAAACACACGGGTAGAGACACGG
17143806 T
1 T
17143807 CATGAGTCTT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (45 bp):
TTTAGGTCAGATTGCATGGTAGCAAACACACGGGTAGAGACACGG
Found at i:17145018 original size:2 final size:2
Alignment explanation
Indices: 17145011--17145055 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17145001 ATGTAGATTT
17145011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17145053 TA T
1 TA T
17145056 CCAAGTTAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17146371 original size:50 final size:50
Alignment explanation
Indices: 17146312--17146748 Score: 346
Period size: 50 Copynumber: 8.7 Consensus size: 50
17146302 ACTTATTCAT
17146312 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
* * * * * * *
17146362 CACATAGTAGCTTGTACTTAGTTCTACACACT-TGACTTATCCATTTGATA
1 CACATAGTAGCCTGCACTTAGTACTACACA-TGTGACCTATCAATCTGGTA
* * * ** * *
17146412 CACGTAGTAGCCTGCACTTAGTACTACACACGTAATCGAAGTTAAT-GGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTA-TCAATCTGGTA
* * * * * *
17146463 CGCGTAGTAGCTTGCACTTAGTGCTACACATGCGACCTATCAATCCGGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
* * * **
17146513 CACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTAATA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
* * ** * *
17146563 CACGTAGTAGCCTGCACTTAGTACTACACACGTGATCAAAACTATC-GAGTA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGA-CCTATCAATCTG-GTA
* * * *
17146614 CATATAATAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGT-
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
* * * * * * * *
17146663 CACGTAGTGGCCCGCACTCAGAACTACACACGTGACCTA--AAACTGTTTTAAA
1 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTG--GT--A
* *
17146715 CACATAGTAGCCTGCACATAGTACTATACATGTG
1 CACATAGTAGCCTGCACTTAGTACTACACATGTG
17146749 TTCACACAAC
Statistics
Matches: 301, Mismatches: 73, Indels: 24
0.76 0.18 0.06
Matches are distributed among these distances:
47 5 0.02
49 35 0.12
50 157 0.52
51 75 0.25
52 29 0.10
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.27
Consensus pattern (50 bp):
CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTA
Found at i:17146490 original size:101 final size:100
Alignment explanation
Indices: 17146312--17146643 Score: 285
Period size: 101 Copynumber: 3.3 Consensus size: 100
17146302 ACTTATTCAT
* * * * *
17146312 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACATAGTAGCTTGT
1 CACATAGTAGCCTGCACTTAGTACTACACACGTAACCAATCAATCGGGTACACATAGTAGCTTGC
* * * * **
17146377 ACTTAGTTCTACACACT-TGACTTATCCATTTGATA
66 ACTTAGTGCTACACA-TGCGACCTATCAATCCGATA
* * * * *
17146412 CACGTAGTAGCCTGCACTTAGTACTACACACGTAATCGAAGTTAAT-GGGTACGCGTAGTAGCTT
1 CACATAGTAGCCTGCACTTAGTACTACACACGTAA-CCAA-TCAATCGGGTACACATAGTAGCTT
*
17146476 GCACTTAGTGCTACACATGCGACCTATCAATCCGGTA
64 GCACTTAGTGCTACACATGCGACCTATCAATCCGATA
* * *** * *
17146513 CACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAA-CCATCTAATACACGTAGTAGCCTG
1 CACATAGTAGCCTGCACTTAGTACTACACACGTAACC-AATCAATCGGGTACACATAGTAGCTTG
* * * ** * *
17146577 CACTTAGTACTACACACGTGATCAAAACTAT-CGAGTA
65 CACTTAGTGCTACACATGCGA-CCTATCAATCCGA-TA
* *
17146614 CATATAATAGCCTGCACTTAGTACTACACA
1 CACATAGTAGCCTGCACTTAGTACTACACA
17146644 TGCGACCTAA
Statistics
Matches: 188, Mismatches: 37, Indels: 13
0.79 0.16 0.05
Matches are distributed among these distances:
99 2 0.01
100 68 0.36
101 114 0.61
102 4 0.02
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (100 bp):
CACATAGTAGCCTGCACTTAGTACTACACACGTAACCAATCAATCGGGTACACATAGTAGCTTGC
ACTTAGTGCTACACATGCGACCTATCAATCCGATA
Found at i:17146590 original size:151 final size:151
Alignment explanation
Indices: 17146312--17146702 Score: 516
Period size: 151 Copynumber: 2.6 Consensus size: 151
17146302 ACTTATTCAT
* * *
17146312 CACATAGTAGCCTGCACTTAGTACTACACATGTGACCTATCAATCTGGTACACATAGTAGCTTGT
1 CACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAGCCTGC
* * * * * *
17146377 ACTTAGTTCTACACACTTGACTTATCCATTTGATACACGTAGTAGCCTGCACTTAGTACTACACA
66 ACTTAGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACA
* ** *
17146442 CGTAATCGAAGTTAAT-GGGTA
131 CGTAATCAAAACT-ATCGAGTA
* * * * *
17146463 CGCGTAGTAGCTTGCACTTAGTGCTACACATGCGACCTATCAATCCGGTACACATAGTAGCCTGC
1 CACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAGCCTGC
17146528 ACTTAGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACA
66 ACTTAGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACA
*
17146593 CGTGATCAAAACTATCGAGTA
131 CGTAATCAAAACTATCGAGTA
* * * * * *
17146614 CATATAATAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGT-CACGTAGTGGCCCGC
1 CACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAGCCTGC
* *
17146678 ACTCAGAACTACACACGTGACCTAA
66 ACTTAGTACTACACACGTGACCTAA
17146703 AACTGTTTTA
Statistics
Matches: 207, Mismatches: 32, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
150 37 0.18
151 170 0.82
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.26
Consensus pattern (151 bp):
CACATAGTAGCCTGCACTTAGTACTACACATGCGACCTATCAATCTGGTACACATAGTAGCCTGC
ACTTAGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTGCACTTAGTACTACACA
CGTAATCAAAACTATCGAGTA
Found at i:17146726 original size:101 final size:101
Alignment explanation
Indices: 17146512--17146746 Score: 276
Period size: 101 Copynumber: 2.3 Consensus size: 101
17146502 TCAATCCGGT
* * * *
17146512 ACACATAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTAATACACGTAGTAGCCTG
1 ACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTAATACACGTAGTAGCCCG
* * * *
17146577 CACTTAGTACTACACACGTGATCAAAACTATCGAGT
66 CACTCAGAACTACACACGTGACCAAAACTATCGAGA
* * ** *
17146613 ACATATAATAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTGGT-CACGTAGTGGCCCG
1 ACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTAATACACGTAGTAGCCCG
* **
17146677 CACTCAGAACTACACACGTGACCTAAAACTGTTTTA-A
66 CACTCAGAACTACACACGTGACC-AAAACT-ATCGAGA
* *
17146714 ACACATAGTAGCCTGCACATAGTACTATACATG
1 ACACATAGTAGCCTGCACTTAGTACTACACATG
17146747 TGTTCACACA
Statistics
Matches: 112, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
100 32 0.29
101 78 0.70
102 2 0.02
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.24
Consensus pattern (101 bp):
ACACATAGTAGCCTGCACTTAGTACTACACATGCGACCTAACAATCTAATACACGTAGTAGCCCG
CACTCAGAACTACACACGTGACCAAAACTATCGAGA
Found at i:17152725 original size:28 final size:28
Alignment explanation
Indices: 17152589--17152730 Score: 171
Period size: 29 Copynumber: 5.0 Consensus size: 28
17152579 GTGAGCATGA
* * *
17152589 ATATGAATGTGACTGGGCCTAACGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
* *
17152617 ATATAAATGTGATTTGGGCCTAATGGGCC
1 ATATGAATATGA-TTGGGCCTAATGGGCC
* *
17152646 AT-TTACAGATGATTTGGGCCTAATGGGCC
1 ATATGA-ATATGA-TTGGGCCTAATGGGCC
17152675 ATATGAATAT-ATTGGGCCTAATGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
*
17152702 ATATGAATATGATTGGGCTTAATGGGCC
1 ATATGAATATGATTGGGCCTAATGGGCC
17152730 A
1 A
17152731 GATACAAGTA
Statistics
Matches: 101, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
27 26 0.26
28 31 0.31
29 42 0.42
30 2 0.02
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (28 bp):
ATATGAATATGATTGGGCCTAATGGGCC
Found at i:17156057 original size:32 final size:31
Alignment explanation
Indices: 17155967--17156081 Score: 178
Period size: 31 Copynumber: 3.7 Consensus size: 31
17155957 CAATCTCAGT
*
17155967 ATAT-ACTGGGCCGAAGCCTTTACATTATTC
1 ATATCACTGGGCCGAAGCCTTTTCATTATTC
* *
17155997 ATATCACTGGGCTGAAGCCTTTTCATTATTA
1 ATATCACTGGGCCGAAGCCTTTTCATTATTC
17156028 ATATCACTGGGCCGAAGCCTTTTTCATTATTC
1 ATATCACTGGGCCGAAGCC-TTTTCATTATTC
*
17156060 ATATCACTAGGCCGAAGCCTTT
1 ATATCACTGGGCCGAAGCCTTT
17156082 ACTGTAACAG
Statistics
Matches: 77, Mismatches: 6, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
30 4 0.05
31 44 0.57
32 29 0.38
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (31 bp):
ATATCACTGGGCCGAAGCCTTTTCATTATTC
Found at i:17156337 original size:26 final size:25
Alignment explanation
Indices: 17156301--17156396 Score: 140
Period size: 26 Copynumber: 3.8 Consensus size: 25
17156291 CTCTTTTAAT
* *
17156301 AACTGGGGCAAAAGCCCTTTTTGATA
1 AACTGGGGC-AAAGCCCTTTTCGGTA
17156327 AACTGGGGCAAAAGCCCTTTTCGGTA
1 AACTGGGGC-AAAGCCCTTTTCGGTA
17156353 AACTGGGGCAAAGCCCTTTTCGGT-
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
17156377 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
17156397 GCACTTCCTC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
24 19 0.28
25 15 0.22
26 33 0.49
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:17156461 original size:17 final size:18
Alignment explanation
Indices: 17156439--17156474 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
17156429 GCATAAATGA
17156439 ATAC-ATCATGTGCATAT
1 ATACAATCATGTGCATAT
17156456 ATACATATCATGTGCATAT
1 ATACA-ATCATGTGCATAT
17156475 CGTATCAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.36
Consensus pattern (18 bp):
ATACAATCATGTGCATAT
Found at i:17159979 original size:16 final size:16
Alignment explanation
Indices: 17159958--17159988 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17159948 GTAACGCCCT
*
17159958 AAAAATCCCGAAATCC
1 AAAAATCCCAAAATCC
17159974 AAAAATCCCAAAATC
1 AAAAATCCCAAAATC
17159989 TTGAATTTTT
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:0.55, C:0.29, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAATCCCAAAATCC
Found at i:17161045 original size:15 final size:16
Alignment explanation
Indices: 17161027--17161059 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17161017 GCAAAACCTG
17161027 AAATA-CCGAAATGCC
1 AAATAGCCGAAATGCC
*
17161042 AAATAGCTGAAATGCC
1 AAATAGCCGAAATGCC
17161058 AA
1 AA
17161060 GAAGCTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.48, C:0.21, G:0.15, T:0.15
Consensus pattern (16 bp):
AAATAGCCGAAATGCC
Found at i:17161055 original size:16 final size:16
Alignment explanation
Indices: 17161034--17161069 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
17161024 CTGAAATACC
17161034 GAAATGCCAA-ATAGCT
1 GAAATGCCAAGA-AGCT
17161050 GAAATGCCAAGAAGCT
1 GAAATGCCAAGAAGCT
17161066 GAAA
1 GAAA
17161070 GTTTGGCTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (16 bp):
GAAATGCCAAGAAGCT
Found at i:17161392 original size:28 final size:28
Alignment explanation
Indices: 17161279--17161421 Score: 137
Period size: 28 Copynumber: 5.0 Consensus size: 28
17161269 ATGAGCATGA
* * *
17161279 ATATGAATGTGACTGGGCCTAACGAGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
* *
17161307 ATATAAATGTTATTTGGGCCTAATGGGCC
1 ATATGAATGTGA-TTGGGCCTAATGGGCC
* *
17161336 ATAT-ACAGGTGATTTTGGCCTAATGGGCC
1 ATATGA-ATGTGA-TTGGGCCTAATGGGCC
* *
17161365 ATATGAATATGATTGGGCCTAATAGGCC
1 ATATGAATGTGATTGGGCCTAATGGGCC
* *
17161393 ATACGAATATGATT-GGCCTTAATGGGCC
1 ATATGAATGTGATTGGGCC-TAATGGGCC
17161421 A
1 A
17161422 GATACAAGTA
Statistics
Matches: 97, Mismatches: 14, Indels: 8
0.82 0.12 0.07
Matches are distributed among these distances:
27 4 0.04
28 47 0.48
29 45 0.46
30 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (28 bp):
ATATGAATGTGATTGGGCCTAATGGGCC
Found at i:17161469 original size:27 final size:27
Alignment explanation
Indices: 17161439--17161492 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
17161429 GTATGTGAAT
17161439 TTGTTTGGGTGTTGTAAGGGGTTTTGG
1 TTGTTTGGGTGTTGTAAGGGGTTTTGG
17161466 TTGTTTGGGTGTTGTAAGGGGTTTTGG
1 TTGTTTGGGTGTTGTAAGGGGTTTTGG
17161493 GCCTAGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.07, C:0.00, G:0.44, T:0.48
Consensus pattern (27 bp):
TTGTTTGGGTGTTGTAAGGGGTTTTGG
Found at i:17164197 original size:23 final size:23
Alignment explanation
Indices: 17164167--17164212 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
17164157 CCAAGATTGT
17164167 AACGTGAATCTCGAATCTCTGTC
1 AACGTGAATCTCGAATCTCTGTC
17164190 AACGTGAATCTCGAATCTCTGTC
1 AACGTGAATCTCGAATCTCTGTC
17164213 TGGCACTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (23 bp):
AACGTGAATCTCGAATCTCTGTC
Found at i:17168569 original size:22 final size:23
Alignment explanation
Indices: 17168536--17168594 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 23
17168526 TCCTTTATCA
*
17168536 AAATT-AAGCACAGAAAC-ACAC
1 AAATTAAATCACAGAAACTACAC
*
17168557 AAATTAAATCACAGAAACTTCAC
1 AAATTAAATCACAGAAACTACAC
17168580 AAATATAAATTCACA
1 AAAT-TAAA-TCACA
17168595 CATCACAGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 5 0.16
22 11 0.34
23 7 0.22
24 4 0.12
25 5 0.16
ACGTcount: A:0.56, C:0.20, G:0.05, T:0.19
Consensus pattern (23 bp):
AAATTAAATCACAGAAACTACAC
Found at i:17176288 original size:30 final size:30
Alignment explanation
Indices: 17176238--17176309 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 30
17176228 CAGGTATATA
17176238 TATATGAAATACATGGAAAT-GAT-ATTACATG
1 TATATG-AA-ACATGGAAATGGATGA-TACATG
17176269 ATATATTGAAACAT-GAAATGGATGATACATG
1 -TATA-TGAAACATGGAAATGGATGATACATG
17176300 TATATGAAAC
1 TATATGAAAC
17176310 TTGCTTAGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
29 6 0.16
30 9 0.24
31 13 0.35
32 7 0.19
33 2 0.05
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.31
Consensus pattern (30 bp):
TATATGAAACATGGAAATGGATGATACATG
Found at i:17178769 original size:14 final size:14
Alignment explanation
Indices: 17178750--17178779 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17178740 TAGGAGTGTC
17178750 ATAAGAAAATTCTA
1 ATAAGAAAATTCTA
*
17178764 ATAAGAAAATTTTA
1 ATAAGAAAATTCTA
17178778 AT
1 AT
17178780 TACGAATAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.33
Consensus pattern (14 bp):
ATAAGAAAATTCTA
Found at i:17184982 original size:20 final size:21
Alignment explanation
Indices: 17184957--17184995 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
17184947 CATAACTATA
17184957 TATGTATGCATGAT-TGTATT
1 TATGTATGCATGATATGTATT
*
17184977 TATGTATGGATGATATGTA
1 TATGTATGCATGATATGTA
17184996 AAGAAATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.28, C:0.03, G:0.23, T:0.46
Consensus pattern (21 bp):
TATGTATGCATGATATGTATT
Found at i:17190879 original size:18 final size:18
Alignment explanation
Indices: 17190856--17190903 Score: 69
Period size: 18 Copynumber: 2.6 Consensus size: 18
17190846 TCGAGTTAAA
17190856 TTAATCGAATTATTCGAG
1 TTAATCGAATTATTCGAG
*
17190874 TTAATCGAGTTATTCGAG
1 TTAATCGAATTATTCGAG
*
17190892 TCAACTCGAATT
1 TTAA-TCGAATT
17190904 TTTTTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 20 0.77
19 6 0.23
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.38
Consensus pattern (18 bp):
TTAATCGAATTATTCGAG
Found at i:17192062 original size:23 final size:22
Alignment explanation
Indices: 17192019--17192063 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
17192009 GTTAATTTGA
**
17192019 ATTGTATGTATATGATTGTATT
1 ATTGTATGTATATGAAAGTATT
17192041 ATTGTGATGTATATGAAAGTATT
1 ATTGT-ATGTATATGAAAGTATT
17192064 CACATATCCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (22 bp):
ATTGTATGTATATGAAAGTATT
Found at i:17198348 original size:43 final size:43
Alignment explanation
Indices: 17198301--17198443 Score: 179
Period size: 43 Copynumber: 3.3 Consensus size: 43
17198291 GAGATGTGGC
*
17198301 TACATGTAAGACCATGTCTGGGACATTGGCATTGTATTGTGAT
1 TACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGTGAT
17198344 TACATGTAAGACCATGTCTGGGACATTGGCATCGTTATT-TGAT
1 TACATGTAAGACCATGTCTGGGACATTGGCATCG-TATTGTGAT
* *
17198387 TTCATGTAA-ACCATAG-CTGGG-CAATCGGCATCG-ATATGTGAT
1 TACATGTAAGACCAT-GTCTGGGAC-ATTGGCATCGTAT-TGTGAT
*
17198429 AACATGTAAGACCAT
1 TACATGTAAGACCAT
17198444 ATCTAGGATA
Statistics
Matches: 89, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
40 2 0.02
41 2 0.02
42 30 0.34
43 51 0.57
44 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.23, T:0.31
Consensus pattern (43 bp):
TACATGTAAGACCATGTCTGGGACATTGGCATCGTATTGTGAT
Found at i:17198740 original size:20 final size:20
Alignment explanation
Indices: 17198715--17198755 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
17198705 ATTCATGAGA
17198715 TAGTTTTATCTGTATATGGC
1 TAGTTTTATCTGTATATGGC
*
17198735 TAGTTTTATTTGTATATGGC
1 TAGTTTTATCTGTATATGGC
17198755 T
1 T
17198756 TACTAAGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.20, C:0.07, G:0.20, T:0.54
Consensus pattern (20 bp):
TAGTTTTATCTGTATATGGC
Found at i:17202602 original size:40 final size:40
Alignment explanation
Indices: 17202543--17202684 Score: 124
Period size: 40 Copynumber: 3.5 Consensus size: 40
17202533 AAATTGAATG
* * *
17202543 ATATCCGGGCTAAGCCCCGAAGACAATTATGCTGGAAATT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ***
17202583 ATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGCT
1 ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
* * * ** *
17202623 ATATCCGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTCATT
1 ATATCCGGGCTAAGACCCGAAGACAATT-ATGCTAGAAACT
*
17202663 CTATCCGGGCTAAGACCCGAAG
1 ATATCCGGGCTAAGACCCGAAG
17202685 GCATTTGTGC
Statistics
Matches: 85, Mismatches: 16, Indels: 2
0.83 0.16 0.02
Matches are distributed among these distances:
39 3 0.04
40 82 0.96
ACGTcount: A:0.27, C:0.25, G:0.27, T:0.21
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGACAATTATGCTAGAAACT
Found at i:17202708 original size:40 final size:39
Alignment explanation
Indices: 17202581--17202710 Score: 147
Period size: 40 Copynumber: 3.3 Consensus size: 39
17202571 ATGCTGGAAA
* * *
17202581 TTATATCCGGGTTAAGACCCGAAGGCAATTGTGCTAGCGGC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGC-A-CAGC
* *
17202622 -TATATCCGGGCTAAGACCCGAAGGCATTCGTGC-GAGTC
1 TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAG-C
*
17202660 ATTCTATCCGGGCTAAGACCCGAAGGCATTTGTGCACATGC
1 -TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACA-GC
17202701 TTATATCCGG
1 TTATATCCGG
17202711 TTATATTCCG
Statistics
Matches: 75, Mismatches: 9, Indels: 11
0.79 0.09 0.12
Matches are distributed among these distances:
37 1 0.01
38 1 0.01
40 70 0.93
41 2 0.03
42 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.25
Consensus pattern (39 bp):
TTATATCCGGGCTAAGACCCGAAGGCATTTGTGCACAGC
Found at i:17206053 original size:23 final size:22
Alignment explanation
Indices: 17206010--17206054 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
17206000 GTTAATTTGA
* **
17206010 ATTGTATGTATGTGATTGTATT
1 ATTGTATGTATATGAAAGTATT
17206032 ATTGTCATGTATATGAAAGTATT
1 ATTGT-ATGTATATGAAAGTATT
17206055 CACATACCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.29, C:0.02, G:0.20, T:0.49
Consensus pattern (22 bp):
ATTGTATGTATATGAAAGTATT
Found at i:17206430 original size:26 final size:26
Alignment explanation
Indices: 17206401--17206478 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
17206391 CTGGAGGTCT
17206401 TGATTAAAGGCTCTTTGTGAGCTTCC
1 TGATTAAAGGCTCTTTGTGAGCTTCC
* * *
17206427 TGATTAAA-ACTTCTTCGTGAGCCTCC
1 TGATTAAAGGC-TCTTTGTGAGCTTCC
* *
17206453 TGATT-ATGGCTC-TTATGAGCTTCC
1 TGATTAAAGGCTCTTTGTGAGCTTCC
17206477 TG
1 TG
17206479 TTATATAGCC
Statistics
Matches: 42, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
24 11 0.26
25 4 0.10
26 27 0.64
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (26 bp):
TGATTAAAGGCTCTTTGTGAGCTTCC
Found at i:17213993 original size:13 final size:13
Alignment explanation
Indices: 17213977--17214009 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
17213967 GCCCGTGTAA
17213977 GGCACACGGCCTG
1 GGCACACGGCCTG
17213990 GGCACACGGCCTG
1 GGCACACGGCCTG
17214003 GGCACAC
1 GGCACAC
17214010 AGGCATGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.39, G:0.36, T:0.06
Consensus pattern (13 bp):
GGCACACGGCCTG
Found at i:17221096 original size:28 final size:29
Alignment explanation
Indices: 17221065--17221166 Score: 79
Period size: 30 Copynumber: 3.5 Consensus size: 29
17221055 ATCTTATTAT
17221065 ATTAATTATATTAATAA-TAAAT-TATATG
1 ATTAA-TATATTAATAATTAAATATATATG
* *
17221093 ATTAA-ATATAAATAATTAAATATGTATG
1 ATTAATATATTAATAATTAAATATATATG
* * *
17221121 TTTAATAATATTTATAACTATAACAT-TTTAT-
1 ATTAAT-ATATTAATAA-T-TAA-ATATATATG
17221152 ATTAATATATTAATA
1 ATTAATATATTAATA
17221167 TTTTAAAAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
26 9 0.15
27 5 0.08
28 14 0.24
30 16 0.27
31 6 0.10
32 7 0.12
33 2 0.03
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (29 bp):
ATTAATATATTAATAATTAAATATATATG
Found at i:17227578 original size:9 final size:9
Alignment explanation
Indices: 17227560--17227625 Score: 73
Period size: 9 Copynumber: 7.2 Consensus size: 9
17227550 GTTAATAAAT
17227560 AATT-TTAA
1 AATTATTAA
17227568 AATTATTAA
1 AATTATTAA
17227577 AATTATTATA
1 AATTATTA-A
*
17227587 TTAATTTTTAA
1 --AATTATTAA
*
17227598 AAATA-TAA
1 AATTATTAA
17227606 AATTATTAA
1 AATTATTAA
17227615 AATTATTAA
1 AATTATTAA
17227624 AA
1 AA
17227626 CTTTAATTTC
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
8 11 0.22
9 29 0.59
10 1 0.02
11 1 0.02
12 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
AATTATTAA
Found at i:17227783 original size:28 final size:28
Alignment explanation
Indices: 17227751--17227810 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
17227741 ATTGAACTTA
**
17227751 AAAACCTGGGTTTTTGAAAGTTGTTTTT
1 AAAACCTGGGTTTTTGAAACCTGTTTTT
* *
17227779 AAAACTTGTGTTTTTGAAACCTGTTTTT
1 AAAACCTGGGTTTTTGAAACCTGTTTTT
17227807 AAAA
1 AAAA
17227811 ATCAGCCTTC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.30, C:0.08, G:0.17, T:0.45
Consensus pattern (28 bp):
AAAACCTGGGTTTTTGAAACCTGTTTTT
Found at i:17228443 original size:46 final size:47
Alignment explanation
Indices: 17228360--17228448 Score: 135
Period size: 46 Copynumber: 1.9 Consensus size: 47
17228350 AGTGGGACTC
*
17228360 GGGGAGGAGGAGGATGAACAATGGAAAGAAACAATGGATATGACTTG
1 GGGGAGGAGGAGGATGAACAATGGAAAGAAACAATGGAGATGACTTG
* * *
17228407 GGGGAGGAGGATGATGAA-GATGGAAAGAAATAATGGAGATGA
1 GGGGAGGAGGAGGATGAACAATGGAAAGAAACAATGGAGATGA
17228449 TGATGATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 21 0.55
47 17 0.45
ACGTcount: A:0.42, C:0.03, G:0.40, T:0.15
Consensus pattern (47 bp):
GGGGAGGAGGAGGATGAACAATGGAAAGAAACAATGGAGATGACTTG
Found at i:17231925 original size:18 final size:18
Alignment explanation
Indices: 17231902--17231938 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
17231892 AGTGAGTGTC
17231902 TAAATGCTTTAATACTTG
1 TAAATGCTTTAATACTTG
17231920 TAAATGCTTTAATACTTG
1 TAAATGCTTTAATACTTG
17231938 T
1 T
17231939 GTTAAATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (18 bp):
TAAATGCTTTAATACTTG
Found at i:17232693 original size:22 final size:22
Alignment explanation
Indices: 17232635--17232693 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 22
17232625 TCTTAAAAAG
*
17232635 ATTTTTTTAGAAAAGGGAATTA
1 ATTTTTTTAGAAAAAGGAATTA
* * *
17232657 TTTTTTTTAGTAAAAGTAATTA
1 ATTTTTTTAGAAAAAGGAATTA
*
17232679 ATTTTTTTAAAAAAA
1 ATTTTTTTAGAAAAA
17232694 TTAAACAACA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
ATTTTTTTAGAAAAAGGAATTA
Found at i:17237736 original size:2 final size:2
Alignment explanation
Indices: 17237729--17237755 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17237719 GAGACTAGTC
17237729 AT 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 AT A
17237756 CATGTCATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17240961 original size:40 final size:40
Alignment explanation
Indices: 17240902--17241109 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 40
17240892 CAATTGAATG
* * * *
17240902 ATATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
17240942 ATATCCGGGTTAAGACCCGAAGGCCA-TTGTGCTAGTGACC
1 ATATCCGGGCTAAGACCCGAAGG-CATTTGTGCAAGTAATT
* * **
17240982 ACATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * **
17241022 AAATCCGGGCTAATACCCGAAGGCATTTGTGCAAGTCGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
* * * **
17241062 CTATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTT
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
17241102 ATATCCGG
1 ATATCCGG
17241110 TTGTATTCCG
Statistics
Matches: 140, Mismatches: 26, Indels: 4
0.82 0.15 0.02
Matches are distributed among these distances:
39 2 0.01
40 136 0.97
41 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTAATT
Found at i:17241040 original size:80 final size:80
Alignment explanation
Indices: 17240904--17241109 Score: 236
Period size: 80 Copynumber: 2.6 Consensus size: 80
17240894 ATTGAATGAT
* * ** * * *
17240904 ATCCGGGCTAAGTCCCGAAGACATTTATGCTAGTAATTATATCCGGGTTAAGACCCGAAGGCCA-
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGG-CAT
*
17240968 TTGTGCTAGT-GACCAC
65 TTGTGCAAGTCGACC-C
* * *
17240984 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTTGTTAAATCCGGGCTAATACCCGAAGGCATT
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
** *
17241049 TGTGCAAGTCGTTCT
66 TGTGCAAGTCGACCC
* *
17241064 ATCCGGGCTAAGACCCGAAGGCATTCGTGCATGTGGTTATATCCGG
1 ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGG
17241110 TTGTATTCCG
Statistics
Matches: 107, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
79 2 0.02
80 103 0.96
81 2 0.02
ACGTcount: A:0.25, C:0.24, G:0.26, T:0.25
Consensus pattern (80 bp):
ATCCGGGCTAAGACCCGAAGGCATTCGTGCAAGTAGTTATATCCGGGCTAAGACCCGAAGGCATT
TGTGCAAGTCGACCC
Found at i:17243925 original size:2 final size:2
Alignment explanation
Indices: 17243914--17243947 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
17243904 CTCAAATGAT
17243914 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17243948 GTTTACAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17245465 original size:27 final size:27
Alignment explanation
Indices: 17245399--17245467 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
17245389 AGCTTGTTAG
* *
17245399 GCCCACTAGCGAACACCTCTTCACCAA
1 GCCCACTGGCGATCACCTCTTCACCAA
*
17245426 GCCCACTGGCGATC-CCTTCTTCGCCAA
1 GCCCACTGGCGATCACC-TCTTCACCAA
17245453 GCCCACTGGCGATCA
1 GCCCACTGGCGATCA
17245468 TGGTTCGCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.05
27 35 0.95
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.17
Consensus pattern (27 bp):
GCCCACTGGCGATCACCTCTTCACCAA
Found at i:17248130 original size:46 final size:47
Alignment explanation
Indices: 17248002--17248162 Score: 163
Period size: 46 Copynumber: 3.4 Consensus size: 47
17247992 ATGTTGATTC
* *
17248002 CATGTCCCAAACATGGTCTTACACTAGCTCTCACATCTCCGT-GTCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCT-T-ACATCT-CGTAGTCGATG
* *
17248051 CCATGTCCCGGACATGGTCTTACACTGAC--ACATCTCGTAGTCGATG
1 -CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGTCGATG
* * *
17248097 TATGTCCCAGACAT-GTCTTACACTGGCTTACATCTTG-AGGCCGATG
1 CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTA-GTCGATG
*
17248143 CATGTCCCCGACAT-GTCTTA
1 CATGTCCCAGACATGGTCTTA
17248163 AACTAGCTCT
Statistics
Matches: 96, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
44 12 0.12
45 16 0.17
46 44 0.46
50 24 0.25
ACGTcount: A:0.22, C:0.30, G:0.19, T:0.29
Consensus pattern (47 bp):
CATGTCCCAGACATGGTCTTACACTGGCTTACATCTCGTAGTCGATG
Found at i:17250734 original size:79 final size:79
Alignment explanation
Indices: 17250590--17250808 Score: 257
Period size: 79 Copynumber: 2.7 Consensus size: 79
17250580 GAATCACATA
* * * * *
17250590 CCTTCGGAATTTAACCGGATATAGCTACTCGCTCAAATGCCTTCGGGACATAGCCCGG-TTATAG
1 CCTTCGGGACTTAACCGGATATAG-TACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAG
17250654 TAACTCGCACAAATG
65 TAACTCGCACAAATG
* *
17250669 CCTTCGGGACTTAACCCGGATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGCCCGGAAT-TA
1 CCTTCGGGACTTAA-CCGGATATAGT-ACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATA
17250732 GTAACTCGCACAAATG
64 GTAACTCGCACAAATG
* * *
17250748 CCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGCCCGGA
1 CCTTCGGGA-CTTA-ACCGGATATAGT-AC-TCGCACAAATGCCTTCGGGACTTAGCCCGGA
17250809 TATCATTCGA
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
78 3 0.03
79 61 0.51
80 45 0.38
81 11 0.09
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CCTTCGGGACTTAACCGGATATAGTACTCGCACAAATGCCTTCGGGACTTAGCCCGGAATATAGT
AACTCGCACAAATG
Found at i:17250737 original size:39 final size:41
Alignment explanation
Indices: 17250604--17250808 Score: 237
Period size: 40 Copynumber: 5.1 Consensus size: 41
17250594 CGGAATTTAA
* *
17250604 CCGG-ATATAGCT-ACTCGCTCAAATGCCTTCGGGACATAGC
1 CCGGAATATAG-TAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17250644 CCGG-TTATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
17250684 CCGG-ATTTAGTAACTCGCACCAATGCCTTCGGG-CTTAGC
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
17250723 CCGGAAT-TAGTAACTCGCACAAATGCCTTC-GGATCTTAGT
1 CCGGAATATAGTAACTCGCACAAATGCCTTCGGGA-CTTAGC
* * *
17250763 CCGG-ATATAGTCACTTAGCACAAAAGCCTTCGGGACTTAGC
1 CCGGAATATAGTAAC-TCGCACAAATGCCTTCGGGACTTAGC
17250804 CCGGA
1 CCGGA
17250809 TATCATTCGA
Statistics
Matches: 143, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 34 0.24
40 81 0.57
41 23 0.16
42 3 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (41 bp):
CCGGAATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:17251525 original size:2 final size:2
Alignment explanation
Indices: 17251518--17251543 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17251508 TCATGTGCAA
17251518 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
17251544 GCAAGAGCCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17257419 original size:27 final size:27
Alignment explanation
Indices: 17257389--17257588 Score: 265
Period size: 27 Copynumber: 7.4 Consensus size: 27
17257379 TGGATAAGTT
* *
17257389 GTAGAATTACCAAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
17257416 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
17257443 GTAGAATTATTGAAGTACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* *
17257470 GTAGAATTACCGAAATACTCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
17257497 ATAGAATTACCGAAATACCCTTTTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
17257524 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * *
17257551 GTAGAATTACCGAGATACCCTTGTGGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
17257578 GTAAAATTACC
1 GTAGAATTACC
17257589 ATTTTGCCTC
Statistics
Matches: 149, Mismatches: 24, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 149 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:17258326 original size:27 final size:26
Alignment explanation
Indices: 17258274--17258332 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
17258264 CCACATATAT
*
17258274 ATATCTGTTCTGGTGGCCTAGCCACA
1 ATATCTGTTCTGGTGACCTAGCCACA
* * *
17258300 ATATCTGTATCTGGTGACTTCGTCACA
1 ATATCTGT-TCTGGTGACCTAGCCACA
17258327 ATATCT
1 ATATCT
17258333 AGCAGCCTCG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 8 0.29
27 20 0.71
ACGTcount: A:0.22, C:0.24, G:0.19, T:0.36
Consensus pattern (26 bp):
ATATCTGTTCTGGTGACCTAGCCACA
Found at i:17259973 original size:40 final size:40
Alignment explanation
Indices: 17259895--17260118 Score: 283
Period size: 40 Copynumber: 5.5 Consensus size: 40
17259885 ACCCAAGTAT
* *
17259895 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* **
17259934 CTTCGGGTCTTAGCCCGGATATAGTCACTAGCATGAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
17259974 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
17260014 CTTCGGGACTTAGCGCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* * *
17260057 CTTCTGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
17260097 CTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
17260119 CATCCGAATA
Statistics
Matches: 160, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
39 12 0.08
40 113 0.71
41 1 0.01
43 34 0.21
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:17260080 original size:83 final size:80
Alignment explanation
Indices: 17259895--17260118 Score: 290
Period size: 83 Copynumber: 2.8 Consensus size: 80
17259885 ACCCAAGTAT
* * * *
17259895 CTTCGGGATTTAG-CCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
**
17259959 CACTAGCATGAATGC
66 CACTAGCACAAATGC
** * *
17259974 CTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGCCTTCGGGACTTAGCGCGGGTATAG-
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
17260038 CAACTACTCGCACAAATGC
66 C-ACTA---GCACAAATGC
* *
17260057 CTTCTGGACTTAGCCCGGATATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
17260119 CATCCGAATA
Statistics
Matches: 124, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
79 13 0.10
80 47 0.38
83 64 0.52
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (80 bp):
CTTCGGGACTTAGCCCGGATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGT
CACTAGCACAAATGC
Found at i:17260096 original size:123 final size:119
Alignment explanation
Indices: 17259895--17260118 Score: 340
Period size: 123 Copynumber: 1.8 Consensus size: 119
17259885 ACCCAAGTAT
* * *
17259895 CTTCGGGATTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGTCTTAGCCCGGATATAGTC
1 CTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
**
17259960 ACTAGCATGAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
66 ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
* *
17260014 CTTCGGGACTTAGCGCGGGTATAGCAACTACTCGCACAAATGCCTTCTGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGC-CGGATATAGC-A--ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATAT
*
17260079 AGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGGATAT
62 AGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGATAT
17260119 CATCCGAATA
Statistics
Matches: 93, Mismatches: 8, Indels: 4
0.89 0.08 0.04
Matches are distributed among these distances:
119 13 0.14
120 9 0.10
121 1 0.01
123 70 0.75
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.25
Consensus pattern (119 bp):
CTTCGGGACTTAGCCGGATATAGCAACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
ACTAGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTCGCTAGCACAAATGC
Found at i:17267643 original size:41 final size:41
Alignment explanation
Indices: 17267598--17267715 Score: 98
Period size: 41 Copynumber: 3.1 Consensus size: 41
17267588 TGAAAGATAA
17267598 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
* * * * *
17267639 ATGTAGAC-AAG-AG-A-GC-T-A---C--GTGAAAGATA-A
1 ATGTAG-CTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17267669 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
1 ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
17267710 ATGTAG
1 ATGTAG
17267716 ACAAGAGAGC
Statistics
Matches: 54, Mismatches: 10, Indels: 26
0.60 0.11 0.29
Matches are distributed among these distances:
29 1 0.02
30 8 0.15
31 9 0.17
32 1 0.02
33 3 0.06
34 1 0.02
35 1 0.02
36 1 0.02
37 1 0.02
38 3 0.06
39 1 0.02
40 9 0.17
41 14 0.26
42 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.29, T:0.21
Consensus pattern (41 bp):
ATGTAGCTAGGTCGCATGCGTGATTCCAAGTGAAGGACACC
Found at i:17267654 original size:71 final size:71
Alignment explanation
Indices: 17267566--17267729 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
17267556 GAGATGTATC
17267566 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17267631 AGGACA
66 AGGACA
17267637 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
1 CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
17267702 AGGACA
66 AGGACA
17267708 CCATGTAGACAAGAGAGCTACG
1 CCATGTAGACAAGAGAGCTACG
17267730 AGACAAATCG
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:0.35, C:0.18, G:0.28, T:0.19
Consensus pattern (71 bp):
CCATGTAGACAAGAGAGCTACGTGAAAGATAAATGTAGCTAGGTCGCATGCGTGATTCCAAGTGA
AGGACA
Found at i:17278402 original size:28 final size:29
Alignment explanation
Indices: 17278292--17278393 Score: 145
Period size: 29 Copynumber: 3.6 Consensus size: 29
17278282 TAATCAGCCG
** *
17278292 CGCACACTTAGTGCCATATACTTT-AAACT
1 CGCACACTTAGTGCCATGCA-TTTCAAGCT
17278321 CGCACACTTAGTGCCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
17278350 CGCACACTTAGT-CCATGCATTTCAAGCT
1 CGCACACTTAGTGCCATGCATTTCAAGCT
*
17278378 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
17278394 ATCTCTCAAC
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
28 30 0.45
29 37 0.55
ACGTcount: A:0.26, C:0.32, G:0.15, T:0.26
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCATTTCAAGCT
Found at i:17280396 original size:15 final size:15
Alignment explanation
Indices: 17280361--17280398 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
17280351 AACTCTTAAA
17280361 CCATAAA-CCATAAT
1 CCATAAACCCATAAT
17280375 CTC-TAAACCCATAAT
1 C-CATAAACCCATAAT
17280390 CCATAAACC
1 CCATAAACC
17280399 TTAAAATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (15 bp):
CCATAAACCCATAAT
Found at i:17280403 original size:22 final size:20
Alignment explanation
Indices: 17280355--17280403 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
17280345 AACCCCAACT
*
17280355 CTTAAACCATAAACCATAAT
1 CTTAAACCATAAACCATAAC
*
17280375 CTCTAAACCCATAATCCATAAAC
1 CT-TAAA-CCATAAACCAT-AAC
17280398 CTTAAA
1 CTTAAA
17280404 ATGTTTAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 2 0.08
21 4 0.17
22 14 0.58
23 4 0.17
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (20 bp):
CTTAAACCATAAACCATAAC
Found at i:17282528 original size:16 final size:16
Alignment explanation
Indices: 17282507--17282540 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17282497 ATGTGCAAAC
17282507 CCATGTTATATGCGAA
1 CCATGTTATATGCGAA
* *
17282523 CCATGTTGTATGTGAA
1 CCATGTTATATGCGAA
17282539 CC
1 CC
17282541 TGGGTTATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (16 bp):
CCATGTTATATGCGAA
Found at i:17282627 original size:17 final size:18
Alignment explanation
Indices: 17282587--17282633 Score: 53
Period size: 17 Copynumber: 2.7 Consensus size: 18
17282577 CCATGTTATA
*
17282587 ACCATGTGTGAACCCATT
1 ACCATGTGAGAACCCATT
* *
17282605 A-TATGTGCGAACCCA-T
1 ACCATGTGAGAACCCATT
17282621 ACCATGTGAGAAC
1 ACCATGTGAGAAC
17282634 TCATGTTGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
16 2 0.08
17 21 0.88
18 1 0.04
ACGTcount: A:0.32, C:0.26, G:0.19, T:0.23
Consensus pattern (18 bp):
ACCATGTGAGAACCCATT
Found at i:17290904 original size:25 final size:25
Alignment explanation
Indices: 17290876--17290937 Score: 70
Period size: 25 Copynumber: 2.5 Consensus size: 25
17290866 GTCACCCATT
**
17290876 TCAGCTCTTATGAGCTTCCCAATAC
1 TCAGCTCGCATGAGCTTCCCAATAC
* * *
17290901 TCAGCTCGCGTGAGCTTCCCATTAT
1 TCAGCTCGCATGAGCTTCCCAATAC
*
17290926 TCAGCTCACATG
1 TCAGCTCGCATG
17290938 TAATGCCCCA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.21, C:0.32, G:0.16, T:0.31
Consensus pattern (25 bp):
TCAGCTCGCATGAGCTTCCCAATAC
Found at i:17291298 original size:26 final size:26
Alignment explanation
Indices: 17291269--17291324 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
17291259 TGATAAAAAT
17291269 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17291295 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17291321 TGAT
1 TGAT
17291325 GGGCATTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.07, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17306753 original size:49 final size:49
Alignment explanation
Indices: 17306597--17306780 Score: 200
Period size: 49 Copynumber: 3.8 Consensus size: 49
17306587 CCATCAAAGT
* * *
17306597 CGATGCCATGT-CTCAGACATGGTCTTACACTGGCTCTCATCTATTGGTGC
1 CGATGCCATGTCCT-AAACATGGTCTTACACTAGCTCTTATCTA-TGGTGC
* * * * *
17306647 CGATGTCATGTCCTAGACATGGTCTTACACT-GATACATATC-A--AT-C
1 CGATGCCATGTCCTAAACATGGTCTTACACTAGCT-CTTATCTATGGTGC
* *
17306692 CGATTCCATGTCCTAAAGATGGTCTTACACTAGCTCTTATCTATGGTGC
1 CGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTTATCTATGGTGC
*
17306741 CGATGCCATGTCCCAAACATGGTCTTACACTAGCTCTTAT
1 CGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTTAT
17306781 ATCTCCCTAG
Statistics
Matches: 112, Mismatches: 15, Indels: 15
0.79 0.11 0.11
Matches are distributed among these distances:
45 33 0.29
46 4 0.04
48 1 0.01
49 41 0.37
50 31 0.28
51 2 0.02
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (49 bp):
CGATGCCATGTCCTAAACATGGTCTTACACTAGCTCTTATCTATGGTGC
Found at i:17313648 original size:43 final size:42
Alignment explanation
Indices: 17313600--17313754 Score: 181
Period size: 43 Copynumber: 3.7 Consensus size: 42
17313590 TGTGTTCTCA
*
17313600 TGTAAGACCACATCTGGGACGTTGGCATCGATATGTGATTACG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATT-CG
* * * * *
17313643 TGTAAGACCATGTCTAGGACATTGACATCG-TATTTGATTCG
1 TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTCG
* *
17313684 TGTAAGACC-CTGTCTGGGACAG-TGGCATCGATATGTGATGGCA
1 TGTAAGACCAC-GTCTGGGAC-GTTGGCATCGATATGTGAT-TCG
17313727 TGTAAGACCACGTCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACGTTGGCAT
17313755 TGTACAATAA
Statistics
Matches: 93, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
41 26 0.28
42 16 0.17
43 50 0.54
44 1 0.01
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACGTTGGCATCGATATGTGATTCG
Found at i:17313957 original size:18 final size:19
Alignment explanation
Indices: 17313923--17313960 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
17313913 GATGCAAAAT
17313923 ATATATGATGTAAATGAAA
1 ATATATGATGTAAATGAAA
*
17313942 ATATATG-TGTATATGAAA
1 ATATATGATGTAAATGAAA
17313960 A
1 A
17313961 GTACATTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (19 bp):
ATATATGATGTAAATGAAA
Found at i:17318261 original size:39 final size:39
Alignment explanation
Indices: 17318207--17318350 Score: 234
Period size: 39 Copynumber: 3.7 Consensus size: 39
17318197 GAATGTTCGA
17318207 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
* * *
17318246 GTGATACCCGGGCTAAGCCCGAAGGCAATTGTGCGAGTT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
17318285 ATGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
1 GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
*
17318324 GTGATATCCGGGTTAAGTCCCGAAGGC
1 GTGATATCCGGGCTAAG-CCCGAAGGC
17318351 CTTTGTGCGG
Statistics
Matches: 95, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
39 86 0.91
40 9 0.09
ACGTcount: A:0.26, C:0.22, G:0.30, T:0.22
Consensus pattern (39 bp):
GTGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATT
Found at i:17318297 original size:78 final size:79
Alignment explanation
Indices: 17318208--17318390 Score: 269
Period size: 78 Copynumber: 2.3 Consensus size: 79
17318198 AATGTTCGAG
17318208 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC
17318272 AATTGTGCGAGTTA
66 AATTGTGCGAGTTA
* *
17318286 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC
** *
17318351 CTTTGTGCGGGTTA
66 AATTGTGCGAGTTA
** * *
17318365 CCATAACCGGGCTATGTCCCGAAGGC
1 TGATATCCGGGCTAAG-CCCGAAGGC
17318391 GTTTGAACGA
Statistics
Matches: 94, Mismatches: 9, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
78 53 0.56
79 32 0.34
80 9 0.10
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCAAATTGTGATACCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGTTA
Found at i:17323149 original size:24 final size:24
Alignment explanation
Indices: 17323122--17323169 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
17323112 AAACATCTCT
17323122 AAATA-AATCATAG-TTAGACTAGGA
1 AAATATAA-CATAGTTTA-ACTAGGA
17323146 AAATATAACATAGTTTAACTAGGA
1 AAATATAACATAGTTTAACTAGGA
17323170 GAAGAAACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 17 0.77
25 5 0.23
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (24 bp):
AAATATAACATAGTTTAACTAGGA
Found at i:17325483 original size:29 final size:29
Alignment explanation
Indices: 17325439--17325533 Score: 95
Period size: 29 Copynumber: 3.2 Consensus size: 29
17325429 GTTAATAATT
*
17325439 TATA-AAAATTAGAT-AAATCAAAATTTCA
1 TATATAAAATTACATAAAATCAAAA-TTCA
*
17325467 TATATAAAATTACATAAAATTAAAATTCA
1 TATATAAAATTACATAAAATCAAAATTCA
* * *
17325496 TATATATAATTATATATTAAATCATAATTCA
1 TATATAAAATTACATA--AAATCAAAATTCA
*
17325527 TGTATAA
1 TATATAA
17325534 TTTTAATATT
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
28 4 0.07
29 27 0.49
30 8 0.15
31 16 0.29
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (29 bp):
TATATAAAATTACATAAAATCAAAATTCA
Found at i:17325525 original size:31 final size:30
Alignment explanation
Indices: 17325451--17325533 Score: 96
Period size: 29 Copynumber: 2.7 Consensus size: 30
17325441 TAAAAATTAG
17325451 ATAAATCAAAATTTCATATATAAAATTACAT
1 ATAAATCAAAA-TTCATATATAAAATTACAT
* * *
17325482 A-AAATTAAAATTCATATATATAATTATAT
1 ATAAATCAAAATTCATATATAAAATTACAT
* *
17325511 ATTAAATCATAATTCATGTATAA
1 A-TAAATCAAAATTCATATATAA
17325534 TTTTAATATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 18 0.42
30 8 0.19
31 17 0.40
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (30 bp):
ATAAATCAAAATTCATATATAAAATTACAT
Found at i:17326528 original size:44 final size:44
Alignment explanation
Indices: 17326469--17326557 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
17326459 TTCAAAAAGT
17326469 ATAAGAACTTATGACATATTTTCACCTTTATAATATATAGCAAA
1 ATAAGAACTTATGACATATTTTCACCTTTATAATATATAGCAAA
17326513 ATAAGAACTTATGACATATTTTCACCTTTATAATATATAGCAAA
1 ATAAGAACTTATGACATATTTTCACCTTTATAATATATAGCAAA
17326557 A
1 A
17326558 ACCTTACATG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.44, C:0.13, G:0.07, T:0.36
Consensus pattern (44 bp):
ATAAGAACTTATGACATATTTTCACCTTTATAATATATAGCAAA
Found at i:17330186 original size:25 final size:26
Alignment explanation
Indices: 17330092--17330200 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
17330082 TAATACAAAT
*
17330092 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17330118 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17330144 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
17330170 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
17330195 TGATAA
1 TGATAA
17330201 GAATTTCATG
Statistics
Matches: 81, Mismatches: 2, Indels: 1
0.96 0.02 0.01
Matches are distributed among these distances:
25 24 0.30
26 57 0.70
ACGTcount: A:0.33, C:0.06, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:17331708 original size:25 final size:26
Alignment explanation
Indices: 17331680--17331731 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
17331670 TTTACAGTTT
17331680 TACCCCTAGAGATAAATT-ACCGAAA
1 TACCCCTAGAGATAAATTGACCGAAA
* * *
17331705 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGAGATAAATTGACCGAAA
17331731 T
1 T
17331732 GCATGTTTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 16 0.70
26 7 0.30
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.25
Consensus pattern (26 bp):
TACCCCTAGAGATAAATTGACCGAAA
Found at i:17335884 original size:26 final size:26
Alignment explanation
Indices: 17335848--17335956 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
17335838 TGATACAAAT
17335848 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17335874 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
17335900 TGATAATGGGTTAGGTAAATGTT-CA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
17335925 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
17335951 TGATAA
1 TGATAA
17335957 GAATTTCATG
Statistics
Matches: 81, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
25 25 0.31
26 56 0.69
ACGTcount: A:0.34, C:0.06, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Done.