Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A08
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: 119882356
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2655529 characters in sequence are not A, C, G, or T
File 129 of 362
Found at i:42877850 original size:24 final size:23
Alignment explanation
Indices: 42877833--42877890 Score: 98
Period size: 24 Copynumber: 2.5 Consensus size: 23
42877823 AAAAAGAAAA
42877833 AATAAAAAAAAAATAAAAAATAT
1 AATAAAAAAAAAATAAAAAATAT
*
42877856 AATAAAAAATATAATAAAAAATAT
1 AATAAAAAA-AAAATAAAAAATAT
42877880 AATAAAAAAAA
1 AATAAAAAAAA
42877891 GAAGAAAGGA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 10 0.31
24 22 0.69
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (23 bp):
AATAAAAAAAAAATAAAAAATAT
Found at i:42877852 original size:12 final size:12
Alignment explanation
Indices: 42877817--42877890 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 12
42877807 TTCACTTTCG
*
42877817 AAAAAGAAAAAGA
1 AAAAATAAAAA-A
42877830 AAAAAT-AAAAA
1 AAAAATAAAAAA
42877841 AAAAATAAAAAA
1 AAAAATAAAAAA
* *
42877853 TATAATAAAAAA
1 AAAAATAAAAAA
* *
42877865 TATAATAAAAAA
1 AAAAATAAAAAA
* *
42877877 TATAATAAAAAA
1 AAAAATAAAAAA
42877889 AA
1 AA
42877891 GAAGAAAGGA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
11 7 0.12
12 44 0.79
13 5 0.09
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:42879387 original size:135 final size:133
Alignment explanation
Indices: 42879137--42879549 Score: 396
Period size: 135 Copynumber: 3.1 Consensus size: 133
42879127 GTGAATTCAC
** * * **
42879137 AGATCTTATCTCCCTGAAATAACAAGTGGAGTAGATCAAAGACGAG-AAATCTTATCCTT-TTGA
1 AGATCTTATCTCCCT-AAGCAGCAAGTGGAGTAGATCAAAGACG-GCGAATCTTAT-CTTCCCGA
* * * *
42879200 GATAGCACGGGAGGAGATTCT-AGCCACTAGCCTTATCTTCCTGAGGTAGCAAGGAAGCAGGTTG
63 GGTAGCAGGGGA-GAGATT-TAAGCCACCAGCCTTATCTTCCTGAAGTAGCAAGGAAGCAGGTTG
42879264 AAAATTGT
126 AAAATTGT
* * *
42879272 AGAT-TTCGTCTCCTTAAAGTAGCAAGTGGAGTAGATCAAAGACGGCGAATCTTATCTTCCCGAG
1 AGATCTT-ATCTCCCT-AAGCAGCAAGTGGAGTAGATCAAAGACGGCGAATCTTATCTTCCCGAG
* * * ***
42879336 GTAGTAGGGGAGTAGATTTAAGCCACCAGTCTTATCTTCCTGAAGTAGCAAGGAAGTAAACTGAA
64 GTAGCAGGGGAG-AGATTTAAGCCACCAGCCTTATCTTCCTGAAGTAGCAAGGAAGCAGGTTGAA
*
42879401 GATTGT
128 AATTGT
* * * * *
42879407 AGATCTTATCTCCCTAAGCAG-TAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCGAAGT
1 AGATCTTATCTCCCTAAGCAGCAAGTGGAGTAGATCAAAGACGGCGAATCTTATCTTCCCGAGGT
* *
42879471 AGCAGGGGAAGAGATTTCAA-CCATCAGCCTTAT-TTCTCTGAAGTAGTAAGGGAA-CAGGTT-A
66 AGCAGGGG-AGAGATTT-AAGCCACCAGCCTTATCTTC-CTGAAGTAGCAA-GGAAGCAGGTTGA
42879532 AAGATTGT
127 AA-ATTGT
42879540 AG-TCTTATCT
1 AGATCTTATCT
42879550 TCTTGAGGTA
Statistics
Matches: 231, Mismatches: 36, Indels: 25
0.79 0.12 0.09
Matches are distributed among these distances:
132 13 0.06
133 82 0.35
134 21 0.09
135 113 0.49
136 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (133 bp):
AGATCTTATCTCCCTAAGCAGCAAGTGGAGTAGATCAAAGACGGCGAATCTTATCTTCCCGAGGT
AGCAGGGGAGAGATTTAAGCCACCAGCCTTATCTTCCTGAAGTAGCAAGGAAGCAGGTTGAAAAT
TGT
Found at i:42879681 original size:178 final size:177
Alignment explanation
Indices: 42879363--42879801 Score: 411
Period size: 178 Copynumber: 2.5 Consensus size: 177
42879353 TTAAGCCACC
* * * *
42879363 AGTCTTATCTTCCTGAAGTAGCAAGGAAGTAAACTGAAGATTGTAGATCTTATCTCCCTAAGCAG
1 AGTCTTATCTTCCTGAAGTAGCAAGGAAGAAAACTGAAGATTATAGATCTTATCTCCCGAAGCAA
* * *
42879428 TAGTGGAGCAGATCGAAGACGACGAATCTTATCTTCCCGAAGTAGCAGGGGAAGAGATTTCAACC
66 CAGTGGAGAAGATCGAAAACGACGAATCTTATCTTCCCGAAGTAGCAGGGGAAGAGATTTCAACC
* * *
42879493 ATCAGCCTTATTTCTCTGAAGTAGTAAGGGAACAGGTTAAAGATTGT
131 ATCAGCCTTATCTCCCTGAAGTAGCAAGGGAACAGGTTAAAGATTGT
* * * * *
42879540 AGTCTTATCTTCTTGAGGTAGCAAGGGAGAAAACTGAAGATTATAGATCTTGTCTCCTCG-AGAT
1 AGTCTTATCTTCCTGAAGTAGCAAGGAAGAAAACTGAAGATTATAGATCTTATCTCC-CGAAG-C
* * * ** * *
42879604 AACAGTGGGGAAGATCGAAAATGGCGAATCTTATCTTCTTGAGGTAGCAGGGG-AGCAGATTTTA
64 AACAGTGGAGAAGATCGAAAACGACGAATCTTATCTTCCCGAAGTAGCAGGGGAAG-AGATTTCA
* * * * ** * * * *
42879668 GCTATTAGCCTTATCTCCCTGAGGTAGCAAGGGAGTAGGCTGAAGATAGC
128 ACCATCAGCCTTATCTCCCTGAAGTAGCAAGGGAACAGGTTAAAGATTGT
* * * * * *
42879718 AGGACTTATCTCCCTGAAGTTGC-AGTGGAGCAGACTGAAGA-TAGTAGATCTTATCTCCCTGAA
1 A-GTCTTATCTTCCTGAAGTAGCAAG-GAAGAAAACTGAAGATTA-TAGATCTTATCTCCC-GAA
**
42879781 GTTACAGTGGA-ATAGATCGAA
62 GCAACAGTGGAGA-AGATCGAA
42879802 GATAGCAAAC
Statistics
Matches: 211, Mismatches: 42, Indels: 16
0.78 0.16 0.06
Matches are distributed among these distances:
177 55 0.26
178 95 0.45
179 59 0.28
180 2 0.01
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.27
Consensus pattern (177 bp):
AGTCTTATCTTCCTGAAGTAGCAAGGAAGAAAACTGAAGATTATAGATCTTATCTCCCGAAGCAA
CAGTGGAGAAGATCGAAAACGACGAATCTTATCTTCCCGAAGTAGCAGGGGAAGAGATTTCAACC
ATCAGCCTTATCTCCCTGAAGTAGCAAGGGAACAGGTTAAAGATTGT
Found at i:42879756 original size:45 final size:45
Alignment explanation
Indices: 42879676--42879892 Score: 201
Period size: 45 Copynumber: 4.8 Consensus size: 45
42879666 TAGCTATTAG
* * ** *
42879676 CCTTATCTCCCTGAGGTAGCAAG-GGAGTAGGCTGAAGATAGCAGGA
1 CCTTATCTCCCTGAAGTTGC-AGTGGAACAGACTGAAGATAGCA-GA
* *
42879722 -CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAGA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAGA
* * * *
42879766 TCTTATCTCCCTGAAGTTACAGTGGAATAGA-TCGAAGATAGCAAA
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGACT-GAAGATAGCAGA
* * * **
42879811 CCTTATCTCTCTAAAGTTGCAGTAGAACAGGTTGAAG-TAGCA-A
1 CCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAGA
* *
42879854 GTCTTATCTCCCTGAAGTTGTAGTGGAACAGACTGAAGA
1 -CCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGA
42879893 CCACAAATCT
Statistics
Matches: 141, Mismatches: 24, Indels: 13
0.79 0.13 0.07
Matches are distributed among these distances:
43 1 0.01
44 40 0.28
45 99 0.70
46 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.25
Consensus pattern (45 bp):
CCTTATCTCCCTGAAGTTGCAGTGGAACAGACTGAAGATAGCAGA
Found at i:42879905 original size:89 final size:90
Alignment explanation
Indices: 42879722--42879918 Score: 206
Period size: 89 Copynumber: 2.2 Consensus size: 90
42879712 GATAGCAGGA
* * * *
42879722 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGTAGATCTTATCTCCCTGAAGTTACA
1 CTTATCTCCCTAAAGTTGCAGTAGAACAGACTGAAGATAGAAGATCTTATCTCCCTGAAGTTACA
* *
42879787 GTGGAATAGATCGAAGATAGCAAAC
66 GTGGAACAGATCGAAGACAGCAAAC
* ** **
42879812 CTTATCTCTCTAAAGTTGCAGTAGAACAGGTTGAAG-TAGCAAG-TCTTATCTCCCTGAAGTTGT
1 CTTATCTCCCTAAAGTTGCAGTAGAACAGACTGAAGATAG-AAGATCTTATCTCCCTGAAGTTAC
*
42879875 AGTGGAACAGA-CTGAAGACCA-CAAAT
65 AGTGGAACAGATC-GAAGA-CAGCAAAC
*
42879901 CTTAT-TCCCCTGAAGTTG
1 CTTATCT-CCCTAAAGTTG
42879919 TAGTGGGATG
Statistics
Matches: 89, Mismatches: 14, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
88 2 0.02
89 54 0.61
90 33 0.37
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (90 bp):
CTTATCTCCCTAAAGTTGCAGTAGAACAGACTGAAGATAGAAGATCTTATCTCCCTGAAGTTACA
GTGGAACAGATCGAAGACAGCAAAC
Found at i:42880003 original size:91 final size:91
Alignment explanation
Indices: 42879895--42880173 Score: 398
Period size: 91 Copynumber: 3.1 Consensus size: 91
42879885 ACTGAAGACC
* *
42879895 ACAAATCTTATTCCCCTGAAGTTGTAGTGGGATGGATTGAAGTTATAATATCATATCTTATCTCT
1 ACAAATCTTATTCCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATAATATCAGATCTTATCTCT
42879960 CTGAAGTTGCAGTAGAGTAGATCAAA
66 CTGAAGTTGCAGTAGAGTAGATCAAA
* * *
42879986 ACAAATCTTATTCCCCTGAAGTTGCAGTAGGATGAATTGAAGTTATAATATCAGATTTTATCTCT
1 ACAAATCTTATTCCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATAATATCAGATCTTATCTCT
* * * *
42880051 CTGAATTTGCAGAAGAGCATATCAAA
66 CTGAAGTTGCAGTAGAGTAGATCAAA
* * * *
42880077 ATAAATCATATTCCCCTGAAGTTGCAGTGGGACGGATTGAAGCTATAA-ATTACAGATCTTATCT
1 ACAAATCTTATTCCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATAATA-T-CAGATCTTATCT
* *
42880141 CTCTGAAGTTGTAGTGGAGTAGATCAAA
64 CTCTGAAGTTGCAGTAGAGTAGATCAAA
42880169 ACAAA
1 ACAAA
42880174 CCCTATTTTC
Statistics
Matches: 163, Mismatches: 23, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
90 1 0.01
91 125 0.77
92 37 0.23
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (91 bp):
ACAAATCTTATTCCCCTGAAGTTGCAGTGGGATGGATTGAAGTTATAATATCAGATCTTATCTCT
CTGAAGTTGCAGTAGAGTAGATCAAA
Found at i:42880597 original size:13 final size:13
Alignment explanation
Indices: 42880579--42880606 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
42880569 GTTCAATTAA
42880579 CACCCCACTAAAC
1 CACCCCACTAAAC
42880592 CACCCCACTAAAC
1 CACCCCACTAAAC
42880605 CA
1 CA
42880607 ACTACTAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.54, G:0.00, T:0.07
Consensus pattern (13 bp):
CACCCCACTAAAC
Found at i:42880779 original size:24 final size:24
Alignment explanation
Indices: 42880730--42880805 Score: 116
Period size: 24 Copynumber: 3.1 Consensus size: 24
42880720 TTTGGAGAAA
**
42880730 AAAAGGAGAGAGGTTCGAATACAAG
1 AAAAGGAGAGACTTTC-AATACAAG
42880755 AAAAGGAGAGACTTTCAATACAAG
1 AAAAGGAGAGACTTTCAATACAAG
*
42880779 AAAAGAAGAGACTTTCAATACAAG
1 AAAAGGAGAGACTTTCAATACAAG
42880803 AAA
1 AAA
42880806 TACACGAGAT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
24 34 0.71
25 14 0.29
ACGTcount: A:0.53, C:0.11, G:0.22, T:0.14
Consensus pattern (24 bp):
AAAAGGAGAGACTTTCAATACAAG
Found at i:42881222 original size:21 final size:21
Alignment explanation
Indices: 42881196--42881243 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
42881186 TCATATCTTG
42881196 AGTTTCACAACTCAGA-AAATA
1 AGTTTCACAACTC-GATAAATA
*
42881217 AGTTTCACAAGTCGATAAATA
1 AGTTTCACAACTCGATAAATA
42881238 AGTTTC
1 AGTTTC
42881244 GTGATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.29
Consensus pattern (21 bp):
AGTTTCACAACTCGATAAATA
Found at i:42882467 original size:27 final size:27
Alignment explanation
Indices: 42882437--42882587 Score: 178
Period size: 27 Copynumber: 5.6 Consensus size: 27
42882427 ATATTGAGTC
* * *
42882437 CGCACACTCAGTGCTATATAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42882464 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
42882492 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
42882519 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
42882546 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
42882573 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
42882588 GTACAATTTA
Statistics
Matches: 106, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
27 82 0.77
28 24 0.23
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:42882549 original size:82 final size:81
Alignment explanation
Indices: 42882437--42882586 Score: 230
Period size: 82 Copynumber: 1.8 Consensus size: 81
42882427 ATATTGAGTC
*
42882437 CGCACACTCAGTGCTATATAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCACACTTA
1 CGCACACTCAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCACACTTA
42882502 GTGCCGCATGGTCAATT
65 GTGCCGCATGGTCAATT
* * **
42882519 CGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
1 CGCACACTCAGTGCTAT-ATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTA
42882583 GTGC
65 GTGC
42882587 TGTACAATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 17 0.27
82 45 0.73
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
CGCACACTCAGTGCTATATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCACACTTAG
TGCCGCATGGTCAATT
Found at i:42890370 original size:23 final size:21
Alignment explanation
Indices: 42890344--42890405 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
42890334 ATATTGAGTC
* *
42890344 CGCACACTCAGTGATATAATACT
1 CGCACACTTAGTGATACAA-A-T
*
42890367 CGCACACTTAGTGCTACAAAT
1 CGCACACTTAGTGATACAAAT
*
42890388 CGCACACTTAGTGCTACA
1 CGCACACTTAGTGATACA
42890406 TAGTCAAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.53
22 1 0.03
23 16 0.44
ACGTcount: A:0.32, C:0.29, G:0.15, T:0.24
Consensus pattern (21 bp):
CGCACACTTAGTGATACAAAT
Found at i:42890392 original size:21 final size:21
Alignment explanation
Indices: 42890366--42890405 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
42890356 GATATAATAC
42890366 TCGCACACTTAGTGCTACAAA
1 TCGCACACTTAGTGCTACAAA
42890387 TCGCACACTTAGTGCTACA
1 TCGCACACTTAGTGCTACA
42890406 TAGTCAAACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.25
Consensus pattern (21 bp):
TCGCACACTTAGTGCTACAAA
Found at i:42890453 original size:27 final size:27
Alignment explanation
Indices: 42890387--42890482 Score: 111
Period size: 27 Copynumber: 3.5 Consensus size: 27
42890377 GTGCTACAAA
* *
42890387 TCGCACACTTAGTGCTACATAGTCAAAC
1 TCGCACACTTAGTGCAACATAGTC-AAT
** *
42890415 TCGCACACTTAGTGCCGCATGGTCAAT
1 TCGCACACTTAGTGCAACATAGTCAAT
* * *
42890442 TCGCACACTTAGTGCATCATATTCATT
1 TCGCACACTTAGTGCAACATAGTCAAT
42890469 TCGCACACTTAGTG
1 TCGCACACTTAGTG
42890483 GTCAAAACAT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
27 38 0.64
28 21 0.36
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (27 bp):
TCGCACACTTAGTGCAACATAGTCAAT
Found at i:42892174 original size:3 final size:3
Alignment explanation
Indices: 42892166--42892449 Score: 82
Period size: 3 Copynumber: 94.3 Consensus size: 3
42892156 TTAACTTTAA
* * * * * * *
42892166 TAT TAT TAT TGT TAT TAC TAG TAT TAT TAT AAA TAT TAT TCT TAT TTT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
42892214 TAT TAT TAC TAT TTT CTAT TTT TTT TAC TAT TAT TAT TAT T-T TCAT
1 TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT
** * * * * *
42892260 TAT TAT TCAT ATAT TAT TAT T-T GCT TTT TTT TAT TGT CAT TAT TGT
1 TAT TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
42892306 TAACG TAT CAT TAT TTT TAT TTT TAT TAT TTT TAT TAT CT-T CTA- CAT
1 T-A-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT -TAT TAT
* * * * * *
42892353 TTT TAT TAT TAG TGT TAT T-T CAT TAT TAT TAT ATGT TAC TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* * * * *
42892397 CAT TCAT TTT TTT TAT T-T T-T TAT TCT T-T TAT TAA TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
42892440 TAC TAT TAT T
1 TAT TAT TAT T
42892450 TTTTACTATT
Statistics
Matches: 200, Mismatches: 64, Indels: 34
0.67 0.21 0.11
Matches are distributed among these distances:
2 12 0.06
3 171 0.86
4 15 0.08
5 2 0.01
ACGTcount: A:0.26, C:0.07, G:0.03, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:42892256 original size:19 final size:19
Alignment explanation
Indices: 42892219--42892256 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
42892209 ATTTTTATTA
*
42892219 TTACTATTTTCTATTTTTT
1 TTACTATTATCTATTTTTT
*
42892238 TTACTATTAT-TATTATTT
1 TTACTATTATCTATTTTTT
42892256 T
1 T
42892257 CATTATTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (19 bp):
TTACTATTATCTATTTTTT
Found at i:42894119 original size:19 final size:19
Alignment explanation
Indices: 42894097--42894135 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42894087 TTTTATCATT
42894097 TTTACTCTTTTTGATACAA
1 TTTACTCTTTTTGATACAA
42894116 TTTACTCTTTTTGATACAA
1 TTTACTCTTTTTGATACAA
42894135 T
1 T
42894136 GACAAAACCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.05, T:0.54
Consensus pattern (19 bp):
TTTACTCTTTTTGATACAA
Found at i:42901388 original size:48 final size:48
Alignment explanation
Indices: 42901332--42901464 Score: 180
Period size: 48 Copynumber: 2.8 Consensus size: 48
42901322 TTCAATCGAT
* * *
42901332 AAGTACCTATACCATGGCCCGTAGTCAAATCAAGGTAACTTATCC-CC-
1 AAGTACCTATACCATGGCCCGAAGACAAATCAAGGCAACTTA-CCTCCG
*
42901379 AGAGTACCTATACCATGGCCCGAAGACAAATCAAGGCAATTTACCTCCG
1 A-AGTACCTATACCATGGCCCGAAGACAAATCAAGGCAACTTACCTCCG
* *
42901428 AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCA
1 AAGTACCTATACCATGGCCCGAAGACAAATCAAGGCA
42901465 TAACTCGCAC
Statistics
Matches: 77, Mismatches: 6, Indels: 5
0.88 0.07 0.06
Matches are distributed among these distances:
47 3 0.04
48 73 0.95
49 1 0.01
ACGTcount: A:0.34, C:0.29, G:0.18, T:0.19
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGAAGACAAATCAAGGCAACTTACCTCCG
Found at i:42901499 original size:50 final size:48
Alignment explanation
Indices: 42901332--42901505 Score: 167
Period size: 48 Copynumber: 3.6 Consensus size: 48
42901322 TTCAATCGAT
* * * * *
42901332 AAGTACCTATACCATGGCCCGTAGTCAAATCAAGG-TAACTTATCCCC-
1 AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCAAAC-TACCCCCG
* * ** *
42901379 AGAGTACCTATACCATGGCCCGAAGACAAATCAAGGCAATTTACCTCCG
1 A-AGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCAAACTACCCCCG
42901428 AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCATAACT-CGCACCCG
1 AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCA-AACTAC-C-CCCG
*
42901478 AAGTG-CTGATATCATGGCCCGAAGCCAA
1 AAGTGCCT-ATACCATGGCCCGAAGCCAA
42901506 CTTAATACTC
Statistics
Matches: 107, Mismatches: 13, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
47 1 0.01
48 72 0.67
49 7 0.07
50 27 0.25
ACGTcount: A:0.33, C:0.30, G:0.19, T:0.18
Consensus pattern (48 bp):
AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGGCAAACTACCCCCG
Found at i:42902395 original size:26 final size:26
Alignment explanation
Indices: 42902366--42902421 Score: 112
Period size: 26 Copynumber: 2.2 Consensus size: 26
42902356 TAAGACTTAT
42902366 TTTAACTTTGTTTTATCTATTATATG
1 TTTAACTTTGTTTTATCTATTATATG
42902392 TTTAACTTTGTTTTATCTATTATATG
1 TTTAACTTTGTTTTATCTATTATATG
42902418 TTTA
1 TTTA
42902422 TTAACATTTT
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:0.23, C:0.07, G:0.07, T:0.62
Consensus pattern (26 bp):
TTTAACTTTGTTTTATCTATTATATG
Found at i:42911022 original size:38 final size:38
Alignment explanation
Indices: 42910961--42911147 Score: 223
Period size: 38 Copynumber: 4.8 Consensus size: 38
42910951 ATTTGATGTG
*
42910961 TATCCGGGCTTAAAGACCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGG-TTAAA-TCCCGCAGGCTTCGTGCTGGTAATA
42911001 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* *
42911039 TATCCGGGTTAAATTCCGCAGGCTTCGTGCTAG-AATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAA-TA
* * * *
42911077 TGTCCGGGTTAAATCCCGCAGGCCTAGTGCTGGTATTA
1 TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
* * * *
42911115 TATCTGAGCTTAAAATCCTGCAGGCTTAGTGCT
1 TATCCG-GGTT-AAATCCCGCAGGCTTCGTGCT
42911148 AGTGACTGGA
Statistics
Matches: 129, Mismatches: 14, Indels: 8
0.85 0.09 0.05
Matches are distributed among these distances:
37 2 0.02
38 91 0.71
39 9 0.07
40 27 0.21
ACGTcount: A:0.22, C:0.23, G:0.26, T:0.29
Consensus pattern (38 bp):
TATCCGGGTTAAATCCCGCAGGCTTCGTGCTGGTAATA
Found at i:42912545 original size:47 final size:48
Alignment explanation
Indices: 42912484--42912613 Score: 183
Period size: 48 Copynumber: 2.7 Consensus size: 48
42912474 TTCAATAGAT
* * *
42912484 AAGTACCTATACCATGGCCCGTAGGCAAATCAAGGTAACTTATCCT-CG
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGG-AAATTATCCTCCG
* *
42912532 GAGTACCTA-ACCATGGCCCGAAGCCAAATCAAGGAAATTTTCCTCCG
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGAAATTATCCTCCG
*
42912579 AAGTGCCTATACCATGGCCCGAAGCCAAATCAAGG
1 AAGTACCTATACCATGGCCCGAAGCCAAATCAAGG
42912614 CATAACTCGC
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
46 8 0.11
47 32 0.44
48 33 0.45
ACGTcount: A:0.32, C:0.28, G:0.20, T:0.19
Consensus pattern (48 bp):
AAGTACCTATACCATGGCCCGAAGCCAAATCAAGGAAATTATCCTCCG
Found at i:42917048 original size:40 final size:40
Alignment explanation
Indices: 42917011--42917196 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
42917001 GCTACTCGTT
* * *
42917011 CAAATGCCTTCGGGACATAGCCCAG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
42917051 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
42917091 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
42917131 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
* *
42917172 CAAA-ACCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
42917197 CATCATTCAA
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
39 3 0.02
40 115 0.88
41 13 0.10
ACGTcount: A:0.27, C:0.27, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:42921336 original size:17 final size:19
Alignment explanation
Indices: 42921239--42921329 Score: 152
Period size: 19 Copynumber: 4.9 Consensus size: 19
42921229 ATAATCTTCA
42921239 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
42921258 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
42921277 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
*
42921294 ATGAT-TACAATCTTAGAT
1 ATGATATGCAATCTTAGAT
42921312 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
42921330 AGATATGATT
Statistics
Matches: 68, Mismatches: 1, Indels: 6
0.91 0.01 0.08
Matches are distributed among these distances:
17 16 0.24
18 16 0.24
19 36 0.53
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:42921355 original size:22 final size:22
Alignment explanation
Indices: 42921239--42921352 Score: 87
Period size: 19 Copynumber: 5.8 Consensus size: 22
42921229 ATAATCTTCA
42921239 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
42921258 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
42921277 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
*
42921294 ATGAT-TACAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
42921312 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
42921334 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
42921353 GATTTAATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 33 0.39
22 8 0.09
23 12 0.14
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Found at i:42921645 original size:18 final size:17
Alignment explanation
Indices: 42921622--42921655 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
42921612 TTTCCCTGAT
*
42921622 TTTTTTTATATATTTTAA
1 TTTTTTAATA-ATTTTAA
42921640 TTTTTTAATAATTTTA
1 TTTTTTAATAATTTTA
42921656 GTATCATGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTTTAATAATTTTAA
Found at i:42923197 original size:40 final size:40
Alignment explanation
Indices: 42923148--42923344 Score: 280
Period size: 40 Copynumber: 5.1 Consensus size: 40
42923138 CGGATGTAAC
* *
42923148 AACCAGCACGAATTCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
*
42923188 AACCCGCACGAATACCTTCGAGACTTAA------TATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
**
42923222 AACCCGCACGAATACCTTCAAGACTTAACCCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
*
42923262 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
* *
42923302 AACCCGCACGAATGCCCTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
42923342 AAC
1 AAC
42923345 TAGCACAATT
Statistics
Matches: 143, Mismatches: 8, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
34 33 0.23
40 110 0.77
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (40 bp):
AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
Found at i:42923274 original size:74 final size:75
Alignment explanation
Indices: 42923148--42923344 Score: 270
Period size: 74 Copynumber: 2.6 Consensus size: 75
42923138 CGGATGTAAC
* *
42923148 AACCAGCACGAATTCCTTCGGGACTTAACCCGGTTATAATAACCCGCACGAATACCTTCGAGACT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAATAACCCGCACGAATACCTTCGAGACT
42923213 TAA-TATAAT
66 TAACTATAAT
** * *
42923222 AACCCGCACGAATACCTTCAAGACTTAACCCGGTTATAATAACCCGCACGAATGCCTTCGGGACT
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAATAACCCGCACGAATACCTTCGAGACT
42923287 TAACCCGGTTATAAT
66 TAA--C---TATAAT
* *
42923302 AACCCGCACGAATGCCCTCGGGACTTAACCCGGTTATAATAAC
1 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAATAAC
42923345 TAGCACAATT
Statistics
Matches: 107, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
74 62 0.58
80 45 0.42
ACGTcount: A:0.32, C:0.29, G:0.16, T:0.22
Consensus pattern (75 bp):
AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAATAACCCGCACGAATACCTTCGAGACT
TAACTATAAT
Found at i:42923396 original size:80 final size:80
Alignment explanation
Indices: 42923138--42923402 Score: 240
Period size: 80 Copynumber: 3.4 Consensus size: 80
42923128 GAATTTGGCT
* * * * * * *
42923138 CGGATGTAACAACCAGCACGAATTCCTTCGGGACTTAACCCGGTTATAATAACCCGCACGAATAC
1 CGGATATAATAACCAGCACAAATGCCCTCGGGACTTAACCCGGTTATAATAACCAGCACGAATGC
*
42923203 CTTCGAGACTT-A--
66 CTTCGGGACTTAACC
* * * * ** *
42923215 ---ATATAATAACCCGCACGAATACCTTCAAGACTTAACCCGGTTATAATAACCCGCACGAATGC
1 CGGATATAATAACCAGCACAAATGCCCTCGGGACTTAACCCGGTTATAATAACCAGCACGAATGC
42923277 CTTCGGGACTTAACC
66 CTTCGGGACTTAACC
* * * *
42923292 CGGTTATAATAACCCGCACGAATGCCCTCGGGACTTAACCCGGTTATAATAACTAGCAC-AATTG
1 CGGATATAATAACCAGCACAAATGCCCTCGGGACTTAACCCGGTTATAATAACCAGCACGAA-TG
**
42923356 CCTTC-GGATCTTAGTC
65 CCTTCGGGA-CTTAACC
* * *
42923372 CGGATATAGTAACTAGCACAAATGCCTTCGG
1 CGGATATAATAACCAGCACAAATGCCCTCGG
42923403 ATCTTAGTCC
Statistics
Matches: 157, Mismatches: 23, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
74 65 0.41
75 1 0.01
79 5 0.03
80 86 0.55
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (80 bp):
CGGATATAATAACCAGCACAAATGCCCTCGGGACTTAACCCGGTTATAATAACCAGCACGAATGC
CTTCGGGACTTAACC
Found at i:42923398 original size:40 final size:40
Alignment explanation
Indices: 42923251--42923418 Score: 160
Period size: 40 Copynumber: 4.2 Consensus size: 40
42923241 AAGACTTAAC
* ** * **
42923251 CCGGTTATAATAACCCGCACGAATGCCTTCGGGA-CTTAAC
1 CCGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGT
* ** * * **
42923291 CCGGTTATAATAACCCGCACGAATGCCCTCGGGA-CTTAAC
1 CCGGATATAATAACTAGCACAAATGCCTTC-GGATCTTAGT
* *
42923331 CCGGTTATAATAACTAGCACAATTGCCTTCGGATCTTAGT
1 CCGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGT
*
42923371 CCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGT
42923411 CCGGATAT
1 CCGGATAT
42923419 CATCAGAATA
Statistics
Matches: 116, Mismatches: 11, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
39 3 0.03
40 113 0.97
ACGTcount: A:0.28, C:0.27, G:0.20, T:0.26
Consensus pattern (40 bp):
CCGGATATAATAACTAGCACAAATGCCTTCGGATCTTAGT
Found at i:42930791 original size:40 final size:39
Alignment explanation
Indices: 42930681--42930816 Score: 181
Period size: 39 Copynumber: 3.5 Consensus size: 39
42930671 CGGATGTAAC
* *
42930681 AACCAGCACGAATGCCTTC-GGACTTAACCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAACCGGTTATAAT
42930719 AA-CCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATACCTTCGGGACTTAA-CCGGTTATAAT
42930758 AACCCGCACGAATAACCTTCGGGACTTAACCGGTTAT-AT
1 AACCCGCACGAAT-ACCTTCGGGACTTAACCGGTTATAAT
** *
42930797 AACTAGCAC-AATGCCTTCGG
1 AACCCGCACGAATACCTTCGG
42930817 ATCTTAGTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
37 21 0.24
38 13 0.15
39 22 0.25
40 18 0.20
41 15 0.17
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (39 bp):
AACCCGCACGAATACCTTCGGGACTTAACCGGTTATAAT
Found at i:42930839 original size:39 final size:39
Alignment explanation
Indices: 42930787--42930872 Score: 147
Period size: 40 Copynumber: 2.2 Consensus size: 39
42930777 CGGGACTTAA
*
42930787 CCGGTTATATAACTAGCAC-AATGCCTTCGGATCTTAGT
1 CCGGATATATAACTAGCACAAATGCCTTCGGATCTTAGT
42930825 CCGGATATAGTAACTAGCACAAATGCCTTCGGATCTTAGT
1 CCGGATATA-TAACTAGCACAAATGCCTTCGGATCTTAGT
42930865 CCGGATAT
1 CCGGATAT
42930873 CATCCGAATA
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 8 0.18
39 10 0.22
40 27 0.60
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (39 bp):
CCGGATATATAACTAGCACAAATGCCTTCGGATCTTAGT
Found at i:42938188 original size:40 final size:40
Alignment explanation
Indices: 42938130--42938390 Score: 355
Period size: 40 Copynumber: 6.5 Consensus size: 40
42938120 CGGATGTAAC
*
42938130 AACCAGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
* * * *
42938170 AACCCGCATGAATACCTTCGGGACTTAACTCGATTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
*
42938210 AACCCGCACGAATACCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
42938250 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
42938290 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
1 AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
** ** * *
42938330 AACTAGCAC-AATTGCCTTC-GGATCTTAGTCCGGATATAGT
1 AACCCGCACGAA-TGCCTTCGGGA-CTTAACCCGGTTATAAT
** *
42938370 AACTAGCACAAATGCCTTCGG
1 AACCCGCACGAATGCCTTCGG
42938391 ATCTTAGTCC
Statistics
Matches: 202, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
39 5 0.02
40 194 0.96
41 3 0.01
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.24
Consensus pattern (40 bp):
AACCCGCACGAATGCCTTCGGGACTTAACCCGGTTATAAT
Found at i:42941679 original size:40 final size:40
Alignment explanation
Indices: 42941624--42941761 Score: 120
Period size: 37 Copynumber: 3.5 Consensus size: 40
42941614 ACCAGTTTGG
*
42941624 CACCCAGTGTCTCATCGAATAATTCAAAGTAGTAAATTGA
1 CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
** ** * *
42941664 CACCCAATGTCTCATCGGTTAA---ACCGAAGTAAATTGG
1 CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
* * * *
42941701 CACCCAATGCCTCATCGAATAAATTCGAAGTAATAAACTGA
1 CACCCAATGTCTCATCGAAT-AATTCAAAGTAGTAAATTGA
***
42941742 CACCTTGTGTCTCATCGAAT
1 CACCCAATGTCTCATCGAAT
42941762 CGAAGTCGAA
Statistics
Matches: 73, Mismatches: 21, Indels: 7
0.72 0.21 0.07
Matches are distributed among these distances:
37 28 0.38
38 2 0.03
40 19 0.26
41 24 0.33
ACGTcount: A:0.35, C:0.24, G:0.15, T:0.26
Consensus pattern (40 bp):
CACCCAATGTCTCATCGAATAATTCAAAGTAGTAAATTGA
Found at i:42942184 original size:16 final size:14
Alignment explanation
Indices: 42942128--42942194 Score: 57
Period size: 16 Copynumber: 4.6 Consensus size: 14
42942118 GTCTTTCTCC
42942128 TTTC-TTTCTTTC-
1 TTTCTTTTCTTTCT
*
42942140 TTTCTTTCCTTTCT
1 TTTCTTTTCTTTCT
*
42942154 GTTTCGTTTTTTTTCT
1 -TTTC-TTTTCTTTCT
42942170 ATTTCTATTTCTTTCT
1 -TTTCT-TTTCTTTCT
42942186 TCTTCTTTT
1 T-TTCTTTT
42942195 TTTTTAAATT
Statistics
Matches: 44, Mismatches: 5, Indels: 9
0.76 0.09 0.16
Matches are distributed among these distances:
12 4 0.09
13 7 0.16
15 9 0.20
16 24 0.55
ACGTcount: A:0.03, C:0.21, G:0.03, T:0.73
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:42942184 original size:32 final size:31
Alignment explanation
Indices: 42942140--42942199 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
42942130 TCTTTCTTTC
42942140 TTTCTTTCCTTTCTGT-TTCGTTTTTTTTCTA
1 TTTCTTTCCTTTCT-TCTTCGTTTTTTTTCTA
* *
42942171 TTTCTATTTCTTTCTTCTTCTTTTTTTTT
1 TTTCT-TTCCTTTCTTCTTCGTTTTTTTT
42942200 AAATTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 6 0.24
32 19 0.76
ACGTcount: A:0.03, C:0.18, G:0.03, T:0.75
Consensus pattern (31 bp):
TTTCTTTCCTTTCTTCTTCGTTTTTTTTCTA
Found at i:42942191 original size:22 final size:23
Alignment explanation
Indices: 42942132--42942191 Score: 54
Period size: 22 Copynumber: 2.7 Consensus size: 23
42942122 TTCTCCTTTC
* *
42942132 TTTCTTTCTTTCTT-TCCTTTCTG
1 TTTCTTTC-TTCTTCTCATTTCTA
*
42942155 TTTCGTTT-TTTTTCT-ATTTCTA
1 TTTC-TTTCTTCTTCTCATTTCTA
42942177 TTTCTTTCTTCTTCT
1 TTTCTTTCTTCTTCT
42942192 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 3 0.10
22 19 0.63
23 5 0.17
24 3 0.10
ACGTcount: A:0.03, C:0.22, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTCTTTCTTCTTCTCATTTCTA
Found at i:42943360 original size:19 final size:19
Alignment explanation
Indices: 42943323--42943361 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
42943313 AAATGTTAAC
**
42943323 ATCAATTTTCAATGGTTGT
1 ATCAATTTTCAATAATTGT
42943342 ATCAATTTTCAATAATTGT
1 ATCAATTTTCAATAATTGT
42943361 A
1 A
42943362 CCATCCTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.10, T:0.46
Consensus pattern (19 bp):
ATCAATTTTCAATAATTGT
Found at i:42943735 original size:28 final size:28
Alignment explanation
Indices: 42943704--42943778 Score: 80
Period size: 28 Copynumber: 2.7 Consensus size: 28
42943694 GAATATTTTA
*
42943704 TAATATTTTTAAATTTTTTTATAAATTT
1 TAATAATTTTAAATTTTTTTATAAATTT
* * *
42943732 TAATAACTTTTGAA-TTTCTTATATATTT
1 TAATAA-TTTTAAATTTTTTTATAAATTT
**
42943760 TTTTAATTTTAAATTTTTT
1 TAATAATTTTAAATTTTTT
42943779 GAATTTTTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
27 6 0.16
28 25 0.68
29 6 0.16
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.64
Consensus pattern (28 bp):
TAATAATTTTAAATTTTTTTATAAATTT
Found at i:42943742 original size:21 final size:21
Alignment explanation
Indices: 42943699--42943742 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
42943689 ATTTTGAATA
* *
42943699 TTTTATAATATTTTTAAATTT
1 TTTTATAATATTTTAAAACTT
42943720 TTTTATAA-ATTTTAATAACTT
1 TTTTATAATATTTTAA-AACTT
42943741 TT
1 TT
42943743 GAATTTCTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (21 bp):
TTTTATAATATTTTAAAACTT
Found at i:42944779 original size:20 final size:20
Alignment explanation
Indices: 42944741--42944779 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
42944731 TGGAGCAAAA
* * *
42944741 ATATCGATACCTTAGGAAAT
1 ATATCAATACCCTAAGAAAT
42944761 ATATCAATACCCTAAGAAA
1 ATATCAATACCCTAAGAAA
42944780 AGTATCGATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (20 bp):
ATATCAATACCCTAAGAAAT
Found at i:42945175 original size:33 final size:33
Alignment explanation
Indices: 42945128--42945193 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 33
42945118 GAATAGATTA
*
42945128 CTCCCCCTTAATAAAAGTCATTTTCAATTTAAG
1 CTCCCCCTTAATAAAAATCATTTTCAATTTAAG
42945161 CTCCCCC-TATATAAAAATCATTTTCAATTTAAG
1 CTCCCCCTTA-ATAAAAATCATTTTCAATTTAAG
42945194 GCATAAAGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 2 0.06
33 29 0.94
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.36
Consensus pattern (33 bp):
CTCCCCCTTAATAAAAATCATTTTCAATTTAAG
Found at i:42948049 original size:17 final size:17
Alignment explanation
Indices: 42948003--42948041 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
42947993 CATATTCGGG
42948003 TATCTGTTATTCTATTA
1 TATCTGTTATTCTATTA
42948020 TATCTGTTATTCTATTA
1 TATCTGTTATTCTATTA
42948037 TATCT
1 TATCT
42948042 AGTTTTCTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.13, G:0.05, T:0.59
Consensus pattern (17 bp):
TATCTGTTATTCTATTA
Found at i:42948641 original size:18 final size:19
Alignment explanation
Indices: 42948618--42948666 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
42948608 TGATAAAACG
*
42948618 GTTTTTATGAAAA-TGATT
1 GTTTTTATGAAAATTAATT
*
42948636 GTTTTTCT-AAAATTAATT
1 GTTTTTATGAAAATTAATT
*
42948654 GTTTTTAAGAAAA
1 GTTTTTATGAAAA
42948667 CAAACCCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
17 4 0.16
18 17 0.68
19 4 0.16
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (19 bp):
GTTTTTATGAAAATTAATT
Found at i:42954520 original size:38 final size:38
Alignment explanation
Indices: 42954468--42954543 Score: 118
Period size: 38 Copynumber: 2.0 Consensus size: 38
42954458 GTAATAGAAA
*
42954468 ATGTTAATGAGTGACTAATTTG-CAACTTTTTGATAACG
1 ATGTTAATGAGTGACTAATTTGTC-ACTTTTCGATAACG
*
42954506 ATGTTAATGGGTGACTAATTTGTCACTTTTCGATAACG
1 ATGTTAATGAGTGACTAATTTGTCACTTTTCGATAACG
42954544 TTAGTGACTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
38 34 0.97
39 1 0.03
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (38 bp):
ATGTTAATGAGTGACTAATTTGTCACTTTTCGATAACG
Found at i:42954906 original size:5 final size:5
Alignment explanation
Indices: 42954896--42954938 Score: 52
Period size: 5 Copynumber: 8.4 Consensus size: 5
42954886 TAAATTTTAA
*
42954896 TTATT TTATT TTATT TTATT TCTATCT TTATT TT-TT CTATT TT
1 TTATT TTATT TTATT TTATT T-TAT-T TTATT TTATT TTATT TT
42954939 TGCTTTCATC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
4 3 0.09
5 22 0.67
6 6 0.18
7 2 0.06
ACGTcount: A:0.16, C:0.07, G:0.00, T:0.77
Consensus pattern (5 bp):
TTATT
Found at i:42957797 original size:21 final size:22
Alignment explanation
Indices: 42957771--42957811 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
42957761 ATTTTGCTTG
*
42957771 CTGTGTTGCGACATC-CAAGCT
1 CTGTGTTGCAACATCACAAGCT
42957792 CTGTGTTGCAACATCACAAG
1 CTGTGTTGCAACATCACAAG
42957812 TAGTCCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.24, C:0.27, G:0.22, T:0.27
Consensus pattern (22 bp):
CTGTGTTGCAACATCACAAGCT
Found at i:42963293 original size:40 final size:43
Alignment explanation
Indices: 42963209--42963327 Score: 108
Period size: 42 Copynumber: 2.9 Consensus size: 43
42963199 GACACAGGGG
*
42963209 AAATCTTTAGAAATTTTGGTAAATTCTTTAGAAATATATATAT
1 AAATCCTTAGAAATTTTGGTAAATTCTTTAGAAATATATATAT
* * *
42963252 -AA-CCTTAGAGAA-TTTGGTAAA-TGTTTAGATAT-TTTAGTAT
1 AAATCCTTAGA-AATTTTGGTAAATTCTTTAGAAATATATA-TAT
* *
42963292 AAATCCTTAG-AATTATTGATAAA-TATTTAGAAATAT
1 AAATCCTTAGAAATT-TTGGTAAATTCTTTAGAAATAT
42963328 TGTTACAAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 14
0.75 0.08 0.17
Matches are distributed among these distances:
39 3 0.05
40 14 0.23
41 18 0.29
42 26 0.42
43 1 0.02
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.42
Consensus pattern (43 bp):
AAATCCTTAGAAATTTTGGTAAATTCTTTAGAAATATATATAT
Found at i:42963315 original size:20 final size:20
Alignment explanation
Indices: 42963290--42963329 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42963280 ATATTTTAGT
* *
42963290 ATAAATCCTTAGAATTATTG
1 ATAAATACTTAGAAATATTG
*
42963310 ATAAATATTTAGAAATATTG
1 ATAAATACTTAGAAATATTG
42963330 TTACAAACTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (20 bp):
ATAAATACTTAGAAATATTG
Found at i:42965305 original size:19 final size:19
Alignment explanation
Indices: 42965291--42965327 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42965281 CTTTTTTTTT
42965291 ATAATTTTTTATTTTTTAA
1 ATAATTTTTTATTTTTTAA
*
42965310 ATTATTTTTTATTTTTTA
1 ATAATTTTTTATTTTTTA
42965328 TTTTTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
ATAATTTTTTATTTTTTAA
Found at i:42965324 original size:6 final size:7
Alignment explanation
Indices: 42965294--42965336 Score: 54
Period size: 7 Copynumber: 6.4 Consensus size: 7
42965284 TTTTTTTATA
42965294 ATTTTTT
1 ATTTTTT
42965301 ATTTTTT
1 ATTTTTT
**
42965308 A--AATT
1 ATTTTTT
42965313 ATTTTTT
1 ATTTTTT
42965320 ATTTTTT
1 ATTTTTT
42965327 ATTTTTT
1 ATTTTTT
42965334 ATT
1 ATT
42965337 AAGGCCTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 3 0.10
7 27 0.90
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (7 bp):
ATTTTTT
Found at i:42965348 original size:42 final size:42
Alignment explanation
Indices: 42965302--42965392 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
42965292 TAATTTTTTA
* **
42965302 TTTTTTAAATT-ATT-TTTTATTTTTTATTTTTTATTAAGGCC
1 TTTTTTAAATTGATTGATTT-TTTTAAATTTTTTATTAAGGCC
*
42965343 TTTTTTAATTTGATTGATTTTTTTAAATTTTTTATTAAGGCC
1 TTTTTTAAATTGATTGATTTTTTTAAATTTTTTATTAAGGCC
42965385 TTTTTTAA
1 TTTTTTAA
42965393 TTTGTTATTA
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
41 10 0.23
42 31 0.70
43 3 0.07
ACGTcount: A:0.23, C:0.04, G:0.07, T:0.66
Consensus pattern (42 bp):
TTTTTTAAATTGATTGATTTTTTTAAATTTTTTATTAAGGCC
Found at i:42965353 original size:23 final size:23
Alignment explanation
Indices: 42965321--42965413 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 23
42965311 TTATTTTTTA
42965321 TTTTTT-ATTTTTTATTAAGGCC
1 TTTTTTAATTTTTTATTAAGGCC
* **
42965343 TTTTTTAA--TTTGATT---GAT
1 TTTTTTAATTTTTTATTAAGGCC
42965361 TTTTTTAAATTTTTTATTAAGGCC
1 TTTTTT-AATTTTTTATTAAGGCC
*
42965385 TTTTTTAATTTGTTATTAAGGCC
1 TTTTTTAATTTTTTATTAAGGCC
42965408 TTTTTT
1 TTTTTT
42965414 TTTACCCTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 13
0.74 0.09 0.17
Matches are distributed among these distances:
18 7 0.12
19 2 0.04
21 12 0.21
22 6 0.11
23 23 0.40
24 7 0.12
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.63
Consensus pattern (23 bp):
TTTTTTAATTTTTTATTAAGGCC
Found at i:42965416 original size:42 final size:40
Alignment explanation
Indices: 42965323--42965416 Score: 100
Period size: 42 Copynumber: 2.2 Consensus size: 40
42965313 ATTTTTTATT
* ***
42965323 TTTTATTTTTTATTAAGGCCTTTTTTAATTTGATTGATTT
1 TTTTATTTTTTATTAAGGCCTTTTTTAATTTGATTAAGCC
42965363 TTTTAAATTTTTTATTAAGGCCTTTTTTAATTTGTTATTAAGGCC
1 TTTT--ATTTTTTATTAAGGCCTTTTTTAATTTG--ATTAA-GCC
42965408 TTTT-TTTTT
1 TTTTATTTTT
42965417 ACCCTTTAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
40 4 0.09
42 33 0.73
44 4 0.09
45 4 0.09
ACGTcount: A:0.20, C:0.06, G:0.10, T:0.64
Consensus pattern (40 bp):
TTTTATTTTTTATTAAGGCCTTTTTTAATTTGATTAAGCC
Found at i:42973486 original size:24 final size:24
Alignment explanation
Indices: 42973458--42973511 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
42973448 TCAAAGAGTT
* *
42973458 ACACGGCCTGGCACATGACCTGTG
1 ACACGGCCTAGCACACGACCTGTG
*
42973482 ACACGGCCTAGCATACGACCTGTG
1 ACACGGCCTAGCACACGACCTGTG
42973506 ACACGG
1 ACACGG
42973512 TCGTCTGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.28, T:0.15
Consensus pattern (24 bp):
ACACGGCCTAGCACACGACCTGTG
Found at i:42974330 original size:56 final size:55
Alignment explanation
Indices: 42974263--42974411 Score: 217
Period size: 56 Copynumber: 2.7 Consensus size: 55
42974253 GTTACATATG
*
42974263 AATCAAATTGCTAAAAGATAATATTGCATAATAATATTCTATAATATCCCATTAGA
1 AATCAAATTGCTAAAA-ATAATATCGCATAATAATATTCTATAATATCCCATTAGA
* * *
42974319 AATCAAATTGCTAAGAAATAATATCGCATTATAATATTCTATAATATCTCATTAGG
1 AATCAAATTGCTAA-AAATAATATCGCATAATAATATTCTATAATATCCCATTAGA
* *
42974375 AATCAAATTGCTAAAATATAATATCCCATACTAATAT
1 AATCAAATTGCTAAAA-ATAATATCGCATAATAATAT
42974412 GCTAACATAA
Statistics
Matches: 84, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
55 2 0.02
56 80 0.95
57 2 0.02
ACGTcount: A:0.46, C:0.13, G:0.07, T:0.34
Consensus pattern (55 bp):
AATCAAATTGCTAAAAATAATATCGCATAATAATATTCTATAATATCCCATTAGA
Found at i:42975449 original size:22 final size:21
Alignment explanation
Indices: 42975414--42975466 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
42975404 TCTTTTTTCT
42975414 ATTTTTAAACATTTTAATTTTA
1 ATTTTTAAACA-TTTAATTTTA
*
42975436 ATTTTTCAAA-ATTTATTTTTAA
1 ATTTTT-AAACATTTAATTTT-A
42975458 GATTTTTAA
1 -ATTTTTAA
42975467 TTAAACATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
21 8 0.30
22 10 0.37
23 9 0.33
ACGTcount: A:0.36, C:0.04, G:0.02, T:0.58
Consensus pattern (21 bp):
ATTTTTAAACATTTAATTTTA
Found at i:42975917 original size:21 final size:21
Alignment explanation
Indices: 42975891--42975933 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
42975881 GGTTCGCTGT
*
42975891 ATTGGATTAGAGGTGTATTGG
1 ATTGGATTAGAGGTGTAATGG
42975912 ATTGGATTAGAGGTGTAATGG
1 ATTGGATTAGAGGTGTAATGG
42975933 A
1 A
42975934 ATAGAGGTGT
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:0.28, C:0.00, G:0.37, T:0.35
Consensus pattern (21 bp):
ATTGGATTAGAGGTGTAATGG
Found at i:42975933 original size:16 final size:16
Alignment explanation
Indices: 42975914--42975946 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
42975904 TGTATTGGAT
*
42975914 TGGATTAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42975930 TGGAATAGAGGTGTAA
1 TGGAATAGAGGTGTAA
42975946 T
1 T
42975947 AGCAAATCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.36, T:0.30
Consensus pattern (16 bp):
TGGAATAGAGGTGTAA
Found at i:42975991 original size:45 final size:44
Alignment explanation
Indices: 42975925--42976019 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
42975915 GGATTAGAGG
* *
42975925 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAAC-ACTGTTTGGTTGAA
* **
42975970 TGTAATGGAATAGAGGCGTAATAGTAAAACTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
42976014 TGTAAT
1 TGTAAT
42976020 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 18 0.40
45 27 0.60
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGCAAAACACTGTTTGGTTGAA
Found at i:42976202 original size:18 final size:17
Alignment explanation
Indices: 42976181--42976215 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42976171 TTATTATTTA
*
42976181 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42976199 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42976216 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42976209 original size:28 final size:27
Alignment explanation
Indices: 42976139--42976211 Score: 76
Period size: 27 Copynumber: 2.7 Consensus size: 27
42976129 TTTATTATCA
*
42976139 AAAATAAATAATTTAATCATATTTAAAC
1 AAAATATATAATTTAAT-ATATTTAAAC
* * **
42976167 ATAAT-TATTATTTAATATATTTTAATT
1 AAAATATATAATTTAATATA-TTTAAAC
42976194 AAAATATATAATTTAATA
1 AAAATATATAATTTAATA
42976212 AAATTCTTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 4
0.77 0.15 0.09
Matches are distributed among these distances:
26 3 0.08
27 18 0.50
28 15 0.42
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (27 bp):
AAAATATATAATTTAATATATTTAAAC
Found at i:42976328 original size:144 final size:147
Alignment explanation
Indices: 42976100--42976371 Score: 487
Period size: 144 Copynumber: 1.9 Consensus size: 147
42976090 ATGATTATTG
42976100 TTATTGTTATTTAAATTTTAATAAGATTATTTATTATCAAAAATAAATAATTTAATCATATTTAA
1 TTATTGTTATTTAAATTTTAATAAGATTA--TATTATCAAAAATAAATAATTTAATCATATTTAA
*
42976165 ACATAATTATTATTTAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
64 ACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGC
42976230 AGAAATTTGTTTTGGTAAA
129 AGAAATTTGTTTTGGTAAA
*
42976249 TTATT-TTATTTAAATTTTAATAAGATTA-A-TATCAATAATAAATAATTTAATCATATTTAAAC
1 TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
42976311 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
66 ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTA
42976372 ATATTCTTAT
Statistics
Matches: 121, Mismatches: 2, Indels: 5
0.95 0.02 0.04
Matches are distributed among these distances:
144 92 0.76
145 1 0.01
148 23 0.19
149 5 0.04
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (147 bp):
TTATTGTTATTTAAATTTTAATAAGATTATATTATCAAAAATAAATAATTTAATCATATTTAAAC
ATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAGCAG
AAATTTGTTTTGGTAAA
Found at i:42976346 original size:18 final size:17
Alignment explanation
Indices: 42976325--42976359 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42976315 TTATTATTAA
*
42976325 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42976343 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42976360 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42976403 original size:54 final size:54
Alignment explanation
Indices: 42976345--42976523 Score: 128
Period size: 55 Copynumber: 3.1 Consensus size: 54
42976335 ATTAAAATAT
*
42976345 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
** * * * * *
42976399 ATAATATATGATACTGTAAAATAT-AAAATAACATAATTATTATTAAATAT-AATATAATTAAAA
1 ATAAT-T-T-A-A---TAAAAT-TCTTAATAA-TTAA-TATTCTT--ATATGAAT-TTACTCAAA
*
42976462 TAT
53 -AC
*
42976465 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATC
1 ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
42976519 ATAAT
1 ATAAT
42976524 ATATGATTAT
Statistics
Matches: 91, Mismatches: 18, Indels: 32
0.65 0.13 0.23
Matches are distributed among these distances:
54 10 0.11
55 11 0.12
56 4 0.04
57 7 0.08
58 5 0.05
59 11 0.12
61 11 0.12
62 5 0.05
63 7 0.08
64 4 0.04
65 11 0.12
66 5 0.05
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (54 bp):
ATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAAAC
Found at i:42976405 original size:61 final size:61
Alignment explanation
Indices: 42976340--42976527 Score: 190
Period size: 61 Copynumber: 3.1 Consensus size: 61
42976330 TTTTAATTAA
*
42976340 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAACCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * *
42976401 AATATATGATACT-GTAAAA-T-ATAA-AATAACATAATTATTAT-TAAATATAAT-ATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAATTA-AT-ATTCTTATATGAATTTACTCA-AATCAT
42976460 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
42976521 AATATAT
1 AATATAT
42976528 GATTATAACT
Statistics
Matches: 94, Mismatches: 23, Indels: 20
0.69 0.17 0.15
Matches are distributed among these distances:
58 6 0.06
59 29 0.31
60 16 0.17
61 37 0.39
62 6 0.06
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
Found at i:42976438 original size:120 final size:120
Alignment explanation
Indices: 42976308--42976530 Score: 419
Period size: 120 Copynumber: 1.9 Consensus size: 120
42976298 ATCATATTTA
* *
42976308 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
42976373 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
42976428 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
42976493 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 TATTCTTATATGAATTTACTCAAACCATAATATATGAT
42976531 TATAACTAAT
Statistics
Matches: 100, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
120 100 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATAATATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAACCATAATATATGATACTGTAAAATATAAAAT
Found at i:42976466 original size:18 final size:17
Alignment explanation
Indices: 42976445--42976479 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42976435 TTATTATTAA
42976445 ATATAATATAATTAAAAT
1 ATATAATATAA-TAAAAT
*
42976463 ATATAATTTAATAAAAT
1 ATATAATATAATAAAAT
42976480 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
ATATAATATAATAAAAT
Found at i:42976542 original size:17 final size:16
Alignment explanation
Indices: 42976520--42976566 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
42976510 ACTCAAATCA
42976520 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
42976537 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
42976551 TAAATATATGATTTAA
1 T-AATATATGATTTAA
42976567 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:42976567 original size:17 final size:17
Alignment explanation
Indices: 42976539--42976572 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
42976529 ATTATAACTA
*
42976539 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
42976556 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
42976573 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:42976715 original size:93 final size:92
Alignment explanation
Indices: 42976605--42976799 Score: 286
Period size: 93 Copynumber: 2.1 Consensus size: 92
42976595 GATTATAGTT
* * *
42976605 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATT-TAATAATAATATATAATTTC
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTAT-ATAATAATATATAATTTC
* *
42976668 ATAAAATTCTTGATAATAAAAATTTTCTTA
64 ATAAAATTCTTAATAAT-AAAATGTTCTTA
* *
42976698 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAGTGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
42976763 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
42976790 TATGAATTTA
1 TATGAATTTA
42976800 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
92 21 0.23
93 68 0.73
94 4 0.04
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTATATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:42983082 original size:21 final size:20
Alignment explanation
Indices: 42983040--42983079 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
42983030 GATTTAGGGT
*
42983040 TTAAAACATTTTTTAAATAA
1 TTAAAACATGTTTTAAATAA
* *
42983060 TTAAAATATGTTTTAGATAA
1 TTAAAACATGTTTTAAATAA
42983080 ATTGAAAGTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (20 bp):
TTAAAACATGTTTTAAATAA
Found at i:42987550 original size:16 final size:16
Alignment explanation
Indices: 42987529--42987562 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
42987519 AATTGAGATG
* *
42987529 AGAAAATTATTTAATT
1 AGAAAACTAGTTAATT
42987545 AGAAAACTAGTTAATT
1 AGAAAACTAGTTAATT
42987561 AG
1 AG
42987563 TTTAAATCAA
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:0.50, C:0.03, G:0.12, T:0.35
Consensus pattern (16 bp):
AGAAAACTAGTTAATT
Found at i:42989287 original size:33 final size:32
Alignment explanation
Indices: 42989249--42989355 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 32
42989239 AGATTACTTT
42989249 ATATTTTATATATTATTATATTAAATTATTTAA
1 ATATTTTAT-TATTATTATATTAAATTATTTAA
* **
42989282 ATATTTCATGTACCATTATATTAAATTATTTAA
1 ATATTTTAT-TATTATTATATTAAATTATTTAA
*
42989315 AT-TTATT-TTATTATTATATTTAAGTT-TTTAAA
1 ATATT-TTATTATTATTATA-TTAAATTATTT-AA
42989347 ATATTTTAT
1 ATATTTTAT
42989356 GTGTCATTAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 11 0.18
32 15 0.25
33 35 0.57
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (32 bp):
ATATTTTATTATTATTATATTAAATTATTTAA
Found at i:42991285 original size:10 final size:10
Alignment explanation
Indices: 42991270--42991298 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
42991260 AACACCCCCC
42991270 TTTCTTTTCT
1 TTTCTTTTCT
42991280 TTTCTTTTC-
1 TTTCTTTTCT
42991289 TTTCTTTTCT
1 TTTCTTTTCT
42991299 CCCTGTTTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTTCT
Found at i:42991292 original size:4 final size:5
Alignment explanation
Indices: 42991270--42991298 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
42991260 AACACCCCCC
42991270 TTTCT TTTCT TTTCT TTTC- TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT
42991299 CCCTGTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 19 0.83
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (5 bp):
TTTCT
Found at i:42995897 original size:6 final size:6
Alignment explanation
Indices: 42995886--42995913 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
42995876 CATTGTTATA
42995886 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAA
42995914 GCAAATGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:42998579 original size:15 final size:15
Alignment explanation
Indices: 42998524--42998580 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
42998514 TTTATACTAC
42998524 AAAATATTTATTATT
1 AAAATATTTATTATT
** *
42998539 AGTATATTTATAATTGT
1 AAAATATTTATTA-T-T
42998556 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
42998573 AAAATATT
1 AAAATATT
42998581 AATATTGAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:43010140 original size:11 final size:11
Alignment explanation
Indices: 43010124--43010158 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
43010114 GCTCGAGAAG
*
43010124 GTTGGAATATC
1 GTTGGAGTATC
*
43010135 GTTGGAGCATC
1 GTTGGAGTATC
43010146 GTTGGAGTATC
1 GTTGGAGTATC
43010157 GT
1 GT
43010159 CACACTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.20, C:0.11, G:0.34, T:0.34
Consensus pattern (11 bp):
GTTGGAGTATC
Found at i:43018240 original size:25 final size:25
Alignment explanation
Indices: 43018208--43018256 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
43018198 TATTCATGTC
43018208 ATATATCATATATCAACTATATTAT
1 ATATATCATATATCAACTATATTAT
*
43018233 ATATATCATATATCAATTATATTA
1 ATATATCATATATCAACTATATTA
43018257 CATACTATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATCATATATCAACTATATTAT
Found at i:43027240 original size:58 final size:57
Alignment explanation
Indices: 43027091--43027240 Score: 135
Period size: 57 Copynumber: 2.6 Consensus size: 57
43027081 ATTGTATAAC
** * * * *
43027091 AGGATTACCGGTCCAGGCTAAATCCTTTATATAACGTATGCTCAGAGGAGCTCGATT
1 AGGATTACCCATCCAGGCTAAATCCTTTCTATAACGTATACTCAGAGGAACTAGATT
* * * * *
43027148 AGGATTA-CCAGTCCACGCTAAACCCTAATC-ATAACGTATACTC-GAGAGATATTATATT
1 AGGATTACCCA-TCCAGGCTAAATCCT-TTCTATAACGTATACTCAGAG-GA-ACTAGATT
*
43027206 GGGATTACCCATCCAGGCTAAATCCTTTCTATAAC
1 AGGATTACCCATCCAGGCTAAATCCTTTCTATAAC
43027241 AAGGTTATTG
Statistics
Matches: 72, Mismatches: 15, Indels: 11
0.73 0.15 0.11
Matches are distributed among these distances:
56 4 0.06
57 36 0.50
58 29 0.40
59 3 0.04
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (57 bp):
AGGATTACCCATCCAGGCTAAATCCTTTCTATAACGTATACTCAGAGGAACTAGATT
Found at i:43037190 original size:42 final size:42
Alignment explanation
Indices: 43037131--43037245 Score: 142
Period size: 43 Copynumber: 2.7 Consensus size: 42
43037121 TTATGATTTA
* *
43037131 CATGTAAGACCCCGTCTGGGACGTTGGCATCG-TATTTGGTTT
1 CATGTAAGA-CCCGTCTGGGACGTTGGCATCGATATTTGATTG
* **
43037173 CGTGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGATTG
1 CATGTAAGACCC-GTCTGGGACGTTGGCATCGATATTTGATTG
*
43037216 CATGTAAGACCACGCCTGGGACGTTGGCAT
1 CATGTAAGACC-CGTCTGGGACGTTGGCAT
43037246 TGTACGATCT
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 3 0.05
42 25 0.41
43 32 0.52
44 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.29
Consensus pattern (42 bp):
CATGTAAGACCCGTCTGGGACGTTGGCATCGATATTTGATTG
Found at i:43037224 original size:43 final size:42
Alignment explanation
Indices: 43037131--43037237 Score: 133
Period size: 42 Copynumber: 2.5 Consensus size: 42
43037121 TTATGATTTA
** * *
43037131 CATGTAAGACCCCGTCTGGGACGTTGGCATCGTATTTGGTTT
1 CATGTAAGACCCCGTCTGGGACAATGGCATCGTATTTGATTG
* *
43037173 CGTGTAAGACCCTGTCTGGGACAATGGCATCGATATTTGATTG
1 CATGTAAGACCCCGTCTGGGACAATGGCATCG-TATTTGATTG
* *
43037216 CATGTAAGACCACGCCTGGGAC
1 CATGTAAGACCCCGTCTGGGAC
43037238 GTTGGCATTG
Statistics
Matches: 54, Mismatches: 10, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
42 28 0.52
43 26 0.48
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.28
Consensus pattern (42 bp):
CATGTAAGACCCCGTCTGGGACAATGGCATCGTATTTGATTG
Found at i:43039563 original size:20 final size:21
Alignment explanation
Indices: 43039538--43039576 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43039528 CTCTTGAAAC
*
43039538 AGGGC-ACACGCCCGTGTGGA
1 AGGGCAACAAGCCCGTGTGGA
43039558 AGGGCAACAAGCCCGTGTG
1 AGGGCAACAAGCCCGTGTG
43039577 TTCATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.23, C:0.28, G:0.38, T:0.10
Consensus pattern (21 bp):
AGGGCAACAAGCCCGTGTGGA
Found at i:43040666 original size:57 final size:57
Alignment explanation
Indices: 43040598--43040714 Score: 216
Period size: 57 Copynumber: 2.1 Consensus size: 57
43040588 CGTCAGCCAT
*
43040598 TACATTTCATATTTCATAAATTGAGCCCACATCTCATACATTTAAAATAGGTACCTG
1 TACATTCCATATTTCATAAATTGAGCCCACATCTCATACATTTAAAATAGGTACCTG
*
43040655 TACATTCCATATTTCATACATTGAGCCCACATCTCATACATTTAAAATAGGTACCTG
1 TACATTCCATATTTCATAAATTGAGCCCACATCTCATACATTTAAAATAGGTACCTG
43040712 TAC
1 TAC
43040715 CACTCATCAC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
57 58 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (57 bp):
TACATTCCATATTTCATAAATTGAGCCCACATCTCATACATTTAAAATAGGTACCTG
Found at i:43040935 original size:49 final size:49
Alignment explanation
Indices: 43040831--43040956 Score: 146
Period size: 49 Copynumber: 2.6 Consensus size: 49
43040821 AGATGCCGAC
* *
43040831 ACCATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGTTAAT
1 ACCATGTCCCAGACA-GGTCTTACACTGGCTCTCATATAGCGAGGTCAAT
* * * *
43040881 GCCATGTCCCAGACAGGTCTTACACTGGCTCTCATCTATCG-GTGTCGAT
1 ACCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAG-GTCAAT
* * *
43040930 ACCATGTCCTAGACATGTATTACACTG
1 ACCATGTCCCAGACAGGTCTTACACTG
43040957 ATACACAACA
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.77
50 14 0.22
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (49 bp):
ACCATGTCCCAGACAGGTCTTACACTGGCTCTCATATAGCGAGGTCAAT
Found at i:43041137 original size:46 final size:48
Alignment explanation
Indices: 43041015--43041139 Score: 130
Period size: 48 Copynumber: 2.6 Consensus size: 48
43041005 GTATATCGCG
* *
43041015 AGGCCAATGCATGTGCCAGACATGTCTTACACTGGCTTAAATATCTCA
1 AGGCCAATGCATGTCCCAGACATGTCTTACAATGGCTTAAATATCTCA
* * ** * *
43041063 AGGCCGATGCATGTCCTAGACACATCTTACAATGGCTCT-CATA-CT-G
1 AGGCCAATGCATGTCCCAGACATGTCTTACAATGGCT-TAAATATCTCA
* *
43041109 TGGCTAATGCATGTCCCAGACATGTCTTACA
1 AGGCCAATGCATGTCCCAGACATGTCTTACA
43041140 CTAGCACACA
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
46 25 0.40
47 2 0.03
48 34 0.55
49 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.27
Consensus pattern (48 bp):
AGGCCAATGCATGTCCCAGACATGTCTTACAATGGCTTAAATATCTCA
Found at i:43047593 original size:46 final size:46
Alignment explanation
Indices: 43047526--43047651 Score: 216
Period size: 46 Copynumber: 2.7 Consensus size: 46
43047516 AACCCGCCCC
* * *
43047526 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCATTCGTATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
43047572 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
43047618 TAGGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43047652 TGCTCAACTA
Statistics
Matches: 76, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:43048107 original size:30 final size:30
Alignment explanation
Indices: 43048073--43048132 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43048063 ATTTAATACG
43048073 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
43048103 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43048133 GGCTCGGGAG
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:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43055159 original size:93 final size:93
Alignment explanation
Indices: 43055052--43055222 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
43055042 GCCCCTAAGT
* *
43055052 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43055117 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
*
43055145 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43055210 CGAGTTCGGATGC
66 CGAGTTCGGATGC
43055223 TCAACCATCC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:43055219 original size:46 final size:46
Alignment explanation
Indices: 43055047--43055219 Score: 219
Period size: 46 Copynumber: 3.7 Consensus size: 46
43055037 AACCCGCCCC
* * *
43055047 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
*
43055093 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCATCCA
* *
43055141 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
43055186 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43055220 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 61 0.56
47 29 0.27
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:43055676 original size:30 final size:30
Alignment explanation
Indices: 43055642--43055701 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
43055632 ATTTAATACG
43055642 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
43055672 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
43055702 GGCTCGGGAA
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:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Found at i:43061625 original size:42 final size:42
Alignment explanation
Indices: 43061515--43061675 Score: 166
Period size: 43 Copynumber: 3.8 Consensus size: 42
43061505 ATCCGATATG
* *
43061515 TGATATCGTGTAAGACCATGTCTGGGATGTTGGCATCG-ACTTA
1 TGATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGTA--TA
*
43061558 TGATTTACGTGTAAGACCATGTCTGGGACGTTGGCATCGTATC
1 TGATTT-CGTGTAAGACCATGTCTGGGACGTTGGCATCGTATA
*
43061601 TGATTTCGTGTAAGACC-TGATCTGGGACAG-TGGCATCGATATT
1 TGATTTCGTGTAAGACCATG-TCTGGGAC-GTTGGCATCG-TATA
* * * * *
43061644 TGATTACATGTAAAACCACGTCTGAGACGTTG
1 TGATTTCGTGTAAGACCATGTCTGGGACGTTG
43061676 ACATTGTACG
Statistics
Matches: 102, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
41 2 0.02
42 28 0.27
43 39 0.38
44 32 0.31
45 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (42 bp):
TGATTTCGTGTAAGACCATGTCTGGGACGTTGGCATCGTATA
Found at i:43061638 original size:86 final size:85
Alignment explanation
Indices: 43061515--43061675 Score: 202
Period size: 86 Copynumber: 1.9 Consensus size: 85
43061505 ATCCGATATG
* * * *
43061515 TGATATCGTGTAAGACCATGTCTGGGATGTTGGCATCGACT-TATGATTTACGTGTAAGACCATG
1 TGATATCGTGTAAGACCATGTCTGGGAAGTTGGCATCGA-TATATGA-TTACATGTAAAACCACG
*
43061579 TCTGGGACGTTGGCATCGTATC
64 TCTGAGACGTTGGCATCGTATC
* *
43061601 TGATTTCGTGTAAGACC-TGATCTGGGACAG-TGGCATCGATATTTGATTACATGTAAAACCACG
1 TGATATCGTGTAAGACCATG-TCTGGGA-AGTTGGCATCGATATATGATTACATGTAAAACCACG
43061664 TCTGAGACGTTG
64 TCTGAGACGTTG
43061676 ACATTGTACG
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
85 28 0.43
86 36 0.55
87 1 0.02
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (85 bp):
TGATATCGTGTAAGACCATGTCTGGGAAGTTGGCATCGATATATGATTACATGTAAAACCACGTC
TGAGACGTTGGCATCGTATC
Found at i:43066464 original size:21 final size:22
Alignment explanation
Indices: 43066440--43066480 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
43066430 CGCTAGACAC
*
43066440 AGGGGC-ACACGCCTGTGTGGG
1 AGGGGCAACACGCCCGTGTGGG
43066461 AGGGGCAACACGCCCGTGTG
1 AGGGGCAACACGCCCGTGTG
43066481 ACCAATTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.17, C:0.27, G:0.44, T:0.12
Consensus pattern (22 bp):
AGGGGCAACACGCCCGTGTGGG
Found at i:43067430 original size:42 final size:42
Alignment explanation
Indices: 43067383--43067467 Score: 154
Period size: 42 Copynumber: 2.0 Consensus size: 42
43067373 TGAAGCTTAG
43067383 TAAGTTGCATA-AAAATAAATATAATGACATCTTTACCATTCA
1 TAAGTTGCA-AGAAAATAAATATAATGACATCTTTACCATTCA
43067425 TAAGTTGCAAGAAAATAAATATAATGACATCTTTACCATTCA
1 TAAGTTGCAAGAAAATAAATATAATGACATCTTTACCATTCA
43067467 T
1 T
43067468 CATCATGCTC
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.45, C:0.14, G:0.08, T:0.33
Consensus pattern (42 bp):
TAAGTTGCAAGAAAATAAATATAATGACATCTTTACCATTCA
Found at i:43067887 original size:46 final size:46
Alignment explanation
Indices: 43067837--43068010 Score: 201
Period size: 46 Copynumber: 3.7 Consensus size: 46
43067827 ACATCATGTA
*
43067837 GCCGATGCATGTCCCAAACATGTCTTACACTGGCT-TACATCAAGAG
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CATCAAGAG
* * * *
43067883 GCCGATGCATGTCCCAAACATGTCTTACACTAACTCTCGTCTCA-AT
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATC-AAGAG
* * *
43067929 GCCGATGTCATGTCCCAGACATGATCTTATACTAGCTCTCAT-AATGTG
1 GCCGATG-CATGTCCCAAACATG-TCTTACACTAGCTCTCATCAA-GAG
*
43067977 GCCGATGCATGTCCCAGACATGTCTTACACTAGC
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGC
43068011 ACACAAACAT
Statistics
Matches: 109, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
46 56 0.51
47 31 0.28
48 22 0.20
ACGTcount: A:0.26, C:0.29, G:0.18, T:0.27
Consensus pattern (46 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATCAAGAG
Found at i:43067957 original size:94 final size:92
Alignment explanation
Indices: 43067837--43068008 Score: 249
Period size: 94 Copynumber: 1.8 Consensus size: 92
43067827 ACATCATGTA
*
43067837 GCCGATGCATGTCCCAAACATGTCTTACACTGGCT-TACATCAA-GAGGCCGATGCATGTCCCAA
1 GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCT-CAT-AATGAGGCCGATGCATGTCCCAA
43067900 ACATGTCTTACACTAACTCTCGTCTCAAT
64 ACATGTCTTACACTAACTCTCGTCTCAAT
* * * *
43067929 GCCGATGTCATGTCCCAGACATGATCTTATACTAGCTCTCATAATGTGGCCGATGCATGTCCCAG
1 GCCGATG-CATGTCCCAAACATG-TCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAA
43067994 ACATGTCTTACACTA
64 ACATGTCTTACACTA
43068009 GCACACAAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
92 7 0.10
93 16 0.23
94 47 0.66
95 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.17, T:0.27
Consensus pattern (92 bp):
GCCGATGCATGTCCCAAACATGTCTTACACTAGCTCTCATAATGAGGCCGATGCATGTCCCAAAC
ATGTCTTACACTAACTCTCGTCTCAAT
Found at i:43067998 original size:140 final size:140
Alignment explanation
Indices: 43067749--43068007 Score: 342
Period size: 140 Copynumber: 1.8 Consensus size: 140
43067739 AAGTCGATAC
* **
43067749 CATGTCCCAAACATGGTCTTACACTGACTCCCACGTATCCGTGCCAACGCCATATCCCAGACATG
1 CATGTCCCAAACATGGTCTTACACTAACT-CCACGTATCAATGCCAACGCCATATCCCAGACATG
* *
43067814 GTCTTATACTGACACATCATGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCA
65 ATCTTATACTGACACATAATGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCA
43067879 AGAGGCCGATG
130 AGAGGCCGATG
* * * * * *
43067890 CATGTCCCAAACAT-GTCTTACACTAACT-CTCGTCTCAATGCCGATGTCATGTCCCAGACATGA
1 CATGTCCCAAACATGGTCTTACACTAACTCCACGTATCAATGCCAACGCCATATCCCAGACATGA
* * * *
43067953 TCTTATACTAGCTCTCATAATGTGGCCGATGCATGTCCCAGACATGTCTTACACT
66 TCTTATACT-G-ACACATAATGTAGCCGATGCATGTCCCAAACATGTCTTACACT
43068008 AGCACACAAA
Statistics
Matches: 101, Mismatches: 15, Indels: 5
0.83 0.12 0.04
Matches are distributed among these distances:
138 35 0.35
139 1 0.01
140 51 0.50
141 14 0.14
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.27
Consensus pattern (140 bp):
CATGTCCCAAACATGGTCTTACACTAACTCCACGTATCAATGCCAACGCCATATCCCAGACATGA
TCTTATACTGACACATAATGTAGCCGATGCATGTCCCAAACATGTCTTACACTGGCTTACATCAA
GAGGCCGATG
Found at i:43073981 original size:47 final size:48
Alignment explanation
Indices: 43073907--43074173 Score: 166
Period size: 47 Copynumber: 5.7 Consensus size: 48
43073897 GGTATAAATA
* *
43073907 CCGATGCCATATCCCAGACATGTTCTTACACTAG-CTCTCACGTTAAG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGACTCTCACGTTAAG
* * * **
43073954 TCGATGCCATGTCCCAGACATGGTCTTACACT-GACTCCCACATATTCGTG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGACTCTCAC--GTT-AAG
* * * * * *
43074004 CTGATGCAATGTCCCAGACATGGTCTTATA-TTGACACATCATG-T-AG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGACTC-TCACGTTAAG
* * * ** * *
43074050 CCGAT-ACATGTCCCAAACAT-GTCTTACACTGGTTTACATCAAG--AGG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGACT-C-TCACGTTAAG
43074096 CCGATG-CATGTCCCAGACAT-GTCTTACACTAG-CTCT--CGTCTCAATG
1 CCGATGCCATGTCCCAGACATGGTCTTACACTAGACTCTCACGT-T-AA-G
*
43074142 CCAATGCCATGTCCCAGACATGGTCTTACACT
1 CCGATGCCATGTCCCAGACATGGTCTTACACT
43074174 GGCTCCATAA
Statistics
Matches: 170, Mismatches: 33, Indels: 33
0.72 0.14 0.14
Matches are distributed among these distances:
41 1 0.01
43 1 0.01
44 8 0.05
45 16 0.09
46 48 0.28
47 49 0.29
48 11 0.06
49 3 0.02
50 31 0.18
51 2 0.01
ACGTcount: A:0.25, C:0.30, G:0.17, T:0.28
Consensus pattern (48 bp):
CCGATGCCATGTCCCAGACATGGTCTTACACTAGACTCTCACGTTAAG
Found at i:43074106 original size:46 final size:45
Alignment explanation
Indices: 43074006--43074218 Score: 157
Period size: 46 Copynumber: 4.6 Consensus size: 45
43073996 TATTCGTGCT
* * * * *
43074006 GATGCAATGTCCCAGACATGGTCTTATA-TTGACACATCATGTA-GCC
1 GATGC-ATGTCCCAGACAT-GTCTTACACTGGTCTCATCAAG-AGGCC
* * *
43074052 GATACATGTCCCAAACATGTCTTACACTGGTTTACATCAAGAGGCC
1 GATGCATGTCCCAGACATGTCTTACACTGGTCT-CATCAAGAGGCC
* * * *
43074098 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTCTCA-ATGCC
1 GATGCATGTCCCAGACATGTCTTACACT-GGTCTCATC-AAGAGGCC
* * *
43074144 AATGCCATGTCCCAGACATGGTCTTACACTGG-CTCCAT-AATGTGGCT
1 GATG-CATGTCCCAGACAT-GTCTTACACTGGTCT-CATCAA-GAGGCC
*
43074191 GATGCATGTCCCATACATGTCTTACACT
1 GATGCATGTCCCAGACATGTCTTACACT
43074219 AGCACACAAA
Statistics
Matches: 133, Mismatches: 24, Indels: 21
0.75 0.13 0.12
Matches are distributed among these distances:
44 7 0.05
45 26 0.20
46 64 0.48
47 26 0.20
48 10 0.08
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGTCTCATCAAGAGGCC
Found at i:43077420 original size:47 final size:48
Alignment explanation
Indices: 43077359--43077452 Score: 147
Period size: 47 Copynumber: 2.0 Consensus size: 48
43077349 AACGATATAT
*
43077359 AAATATATACATATATGTATT-AAAATATATACGTAATAATAAAAATAA
1 AAATATATACATATA-GTATTAAAAATATATACATAATAATAAAAATAA
*
43077407 AAAT-TATATATATAGTATTAAAAATATATACATAATAATAAAAATA
1 AAATATATACATATAGTATTAAAAATATATACATAATAATAAAAATA
43077453 CAATATTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 5 0.12
47 34 0.79
48 4 0.09
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (48 bp):
AAATATATACATATAGTATTAAAAATATATACATAATAATAAAAATAA
Found at i:43077434 original size:20 final size:20
Alignment explanation
Indices: 43077397--43077452 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
43077387 ATACGTAATA
* *
43077397 ATAAAAATAAAAATTATATAT
1 ATAATAATAAAAA-TATATAC
* *
43077418 ATAGTATTAAAAATATATAC
1 ATAATAATAAAAATATATAC
43077438 ATAATAATAAAAATA
1 ATAATAATAAAAATA
43077453 CAATATTAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
20 19 0.66
21 10 0.34
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (20 bp):
ATAATAATAAAAATATATAC
Found at i:43078076 original size:19 final size:19
Alignment explanation
Indices: 43078054--43078093 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
43078044 ATACTAATGC
43078054 TAATAAATAAT-AAATATAA
1 TAAT-AATAATAAAATATAA
*
43078073 TAATAGTAATAAAATATAA
1 TAATAATAATAAAATATAA
43078092 TA
1 TA
43078094 GTATATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (19 bp):
TAATAATAATAAAATATAA
Found at i:43078091 original size:25 final size:28
Alignment explanation
Indices: 43078054--43078105 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 28
43078044 ATACTAATGC
43078054 TAATAAATAATAA-A-TATA-ATAATAG
1 TAATAAATAATAATAGTATATATAATAG
43078079 TAATAAA-ATATAATAGTATATATAATA
1 TAATAAATA-ATAATAGTATATATAATA
43078106 TTAAAATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
24 1 0.04
25 11 0.48
26 1 0.04
27 4 0.17
28 6 0.26
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (28 bp):
TAATAAATAATAATAGTATATATAATAG
Found at i:43078659 original size:13 final size:13
Alignment explanation
Indices: 43078643--43078672 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
43078633 CCGCCGTCTT
*
43078643 CCGTCGCCGGCCA
1 CCGTCACCGGCCA
43078656 CCGTCACCGGCCA
1 CCGTCACCGGCCA
43078669 CCGT
1 CCGT
43078673 GGACGGTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.53, G:0.27, T:0.10
Consensus pattern (13 bp):
CCGTCACCGGCCA
Found at i:43079662 original size:17 final size:17
Alignment explanation
Indices: 43079642--43079677 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
43079632 AACTAAAATT
43079642 AAAAATTAAAAATAACG
1 AAAAATTAAAAATAACG
* *
43079659 AAAATTTTAAAATAACG
1 AAAAATTAAAAATAACG
43079676 AA
1 AA
43079678 TTACCATTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.06, G:0.06, T:0.22
Consensus pattern (17 bp):
AAAAATTAAAAATAACG
Found at i:43079844 original size:10 final size:10
Alignment explanation
Indices: 43079829--43079869 Score: 64
Period size: 10 Copynumber: 4.1 Consensus size: 10
43079819 TTAAATAAAA
43079829 AGTTTGAGAG
1 AGTTTGAGAG
43079839 AGTTTGAGAG
1 AGTTTGAGAG
**
43079849 AGTTAAAGAG
1 AGTTTGAGAG
43079859 AGTTTGAGAG
1 AGTTTGAGAG
43079869 A
1 A
43079870 ATGATGTGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.37, C:0.00, G:0.37, T:0.27
Consensus pattern (10 bp):
AGTTTGAGAG
Found at i:43080656 original size:17 final size:17
Alignment explanation
Indices: 43080634--43080667 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
43080624 ATTATGGGTA
*
43080634 TGATATTTCAAATATTT
1 TGATATGTCAAATATTT
*
43080651 TGATATGTGAAATATTT
1 TGATATGTCAAATATTT
43080668 CAAATATCAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TGATATGTCAAATATTT
Found at i:43080858 original size:8 final size:8
Alignment explanation
Indices: 43080856--43080883 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
43080846 TTAAAAAAAT
43080856 AAATTAAA
1 AAATTAAA
43080864 AAATTAAA
1 AAATTAAA
43080872 AAATTAAA
1 AAATTAAA
43080880 AAAT
1 AAAT
43080884 ATATTTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAATTAAA
Found at i:43080884 original size:28 final size:28
Alignment explanation
Indices: 43080826--43080882 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 28
43080816 GCTTGATTTT
* **
43080826 ATAAATAAAAAATTTATTAATTAAAAAA
1 ATAAATAAAAAATTAAAAAATTAAAAAA
43080854 ATAAATTAAAAAATTAAAAAATTAAAAAA
1 ATAAA-TAAAAAATTAAAAAATTAAAAAA
43080883 TATATTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 5 0.20
29 20 0.80
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (28 bp):
ATAAATAAAAAATTAAAAAATTAAAAAA
Found at i:43082768 original size:35 final size:36
Alignment explanation
Indices: 43082729--43082798 Score: 133
Period size: 36 Copynumber: 2.0 Consensus size: 36
43082719 TTTTTATCAA
43082729 ATAAAATGA-TTTTTTTTATCTTTCCTTTATTTCCC
1 ATAAAATGATTTTTTTTTATCTTTCCTTTATTTCCC
43082764 ATAAAATGATTTTTTTTTATCTTTCCTTTATTTCC
1 ATAAAATGATTTTTTTTTATCTTTCCTTTATTTCC
43082799 TTTTATGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 9 0.26
36 25 0.74
ACGTcount: A:0.23, C:0.16, G:0.03, T:0.59
Consensus pattern (36 bp):
ATAAAATGATTTTTTTTTATCTTTCCTTTATTTCCC
Found at i:43086066 original size:21 final size:21
Alignment explanation
Indices: 43086029--43086068 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
43086019 AAGTTGAATT
*
43086029 AATTTAATAATAGTACAAATA
1 AATTTAATAATAATACAAATA
43086050 AATTTAAT-ATGAATACAAA
1 AATTTAATAAT-AATACAAA
43086069 GTGTGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (21 bp):
AATTTAATAATAATACAAATA
Found at i:43087272 original size:76 final size:75
Alignment explanation
Indices: 43087178--43087317 Score: 208
Period size: 76 Copynumber: 1.9 Consensus size: 75
43087168 ATACACTCAG
* * * * * *
43087178 ACTATAAATACTATATTAAATTTTCTGTTTGGGGAGTTAATTTTAGGGTTTTCGCTTGTAGTTTA
1 ACTATAAATACTACATTAAACTATCAGTTTGGGGAGTTAATTTTAGGGTTCTAGCTTGTA-TTTA
43087243 ATTGGACTTAA
65 ATTGGACTTAA
*
43087254 ACTATAAATACTACATTAAACTATCAGTTTGGGGAGTTCATTTTAGGGTTCTAGCTTGTATTTA
1 ACTATAAATACTACATTAAACTATCAGTTTGGGGAGTTAATTTTAGGGTTCTAGCTTGTATTTA
43087318 GTTAGCTTTC
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
75 4 0.07
76 53 0.93
ACGTcount: A:0.29, C:0.10, G:0.18, T:0.44
Consensus pattern (75 bp):
ACTATAAATACTACATTAAACTATCAGTTTGGGGAGTTAATTTTAGGGTTCTAGCTTGTATTTAA
TTGGACTTAA
Found at i:43090393 original size:20 final size:20
Alignment explanation
Indices: 43090368--43090412 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
43090358 AGGGACTAAA
*
43090368 ATGAAAAGTTATAAAATTTG
1 ATGAAAAATTATAAAATTTG
* *
43090388 ATGAAAAATTATGAAATTTT
1 ATGAAAAATTATAAAATTTG
43090408 ATGAA
1 ATGAA
43090413 TACATGTGCT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (20 bp):
ATGAAAAATTATAAAATTTG
Found at i:43092583 original size:20 final size:20
Alignment explanation
Indices: 43092558--43092616 Score: 84
Period size: 20 Copynumber: 3.0 Consensus size: 20
43092548 TTGTAAGGGA
*
43092558 TTGCACTTCGGTACCTCTGG
1 TTGCACTTCGGTGCCTCTGG
43092578 TTGCACTTCGGTGCCTCT-G
1 TTGCACTTCGGTGCCTCTGG
*
43092597 TAAGCACTTCGGTGCCTCTG
1 T-TGCACTTCGGTGCCTCTG
43092617 TTACAATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 2 0.06
20 33 0.94
ACGTcount: A:0.10, C:0.31, G:0.25, T:0.34
Consensus pattern (20 bp):
TTGCACTTCGGTGCCTCTGG
Found at i:43097206 original size:42 final size:42
Alignment explanation
Indices: 43097155--43097264 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 42
43097145 GTTGAGAATA
* **
43097155 CGTGTAAGACCATATCTGGGATATGGCATCGATATGAGATTT
1 CGTGTAAGACCATATCTGGGATATGGCACCGATATGAGATCC
* *
43097197 CGTGTAAGACCATAGCTGGGCTATTGGCACCGATATGAGATCC
1 CGTGTAAGACCATATCTGGGATA-TGGCACCGATATGAGATCC
*
43097240 CATGTAAGACCATATCTGGGATATG
1 CGTGTAAGACCATATCTGGGATATG
43097265 ACATTGGTAT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 23 0.39
43 36 0.61
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCATATCTGGGATATGGCACCGATATGAGATCC
Found at i:43099188 original size:24 final size:26
Alignment explanation
Indices: 43099144--43099192 Score: 75
Period size: 24 Copynumber: 1.9 Consensus size: 26
43099134 CAAGGTAAGT
43099144 TTGTATGTTAAATAAGCTTTAATATAA
1 TTGTATGTTAAAT-AGCTTTAATATAA
43099171 TTGTAT-TTAAAT-GCTTTAATAT
1 TTGTATGTTAAATAGCTTTAATAT
43099193 TGCATGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.45
26 6 0.27
27 6 0.27
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.49
Consensus pattern (26 bp):
TTGTATGTTAAATAGCTTTAATATAA
Found at i:43103363 original size:41 final size:42
Alignment explanation
Indices: 43103318--43103470 Score: 141
Period size: 41 Copynumber: 3.6 Consensus size: 42
43103308 AGATTACATG
43103318 TAAGACCATATCTGGGATATGGCATT-AGTATGAGACTTCG-A
1 TAAGACCATATCTGGGATATGGCATTGA-TATGAGACTTCGTA
* * * *
43103359 TAAGACCATATCTGGCATATGGCATTGATATGAGATTTTGTG
1 TAAGACCATATCTGGGATATGGCATTGATATGAGACTTCGTA
* * * * * * * *
43103401 TAAGACCATAGCTGGGCTATTGACATCGATACGGGA-TTACATG
1 TAAGACCATATCTGGGATA-TGGCATTGATATGAGACTT-CGTA
*
43103444 TAAGACCATATCTAGGATATGGCATTG
1 TAAGACCATATCTGGGATATGGCATTG
43103471 GTACAGTACC
Statistics
Matches: 90, Mismatches: 18, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
41 35 0.39
42 25 0.28
43 30 0.33
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (42 bp):
TAAGACCATATCTGGGATATGGCATTGATATGAGACTTCGTA
Done.