Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 16 of 210
Found at i:5651910 original size:87 final size:86
Alignment explanation
Indices: 5651731--5651911 Score: 197
Period size: 87 Copynumber: 2.1 Consensus size: 86
5651721 TCAAAGGGCA
* *
5651731 TTTTTGATGCATTTTGGCATATCAAGTACCCAATTGAGGGAAAAAAAGCAGGGGCTTAATTGTTT
1 TTTTT-ATGCATTTTGGCATATCAAGTACCCAATTGAGGAAAAAAAAGCAGCGGCTTAATTGTTT
**** * **
5651796 TTTTTTTTAAGTTTGAGAGCATT
65 TTTTGAAAAAGTTGGAGAG-AGG
*
5651819 TTTTTATGCATTTTGGCAGT-TCAAGTACCCAATTGAGTTAAAAAAAGAGCAGCGGCTTAATTGG
1 TTTTTATGCATTTTGGCA-TATCAAGTACCCAATTGAG-GAAAAAAA-AGCAGCGGCTTAATT-G
5651883 TTTTTTTGAAAAAGTTGGA-AG-GG
62 TTTTTTTGAAAAAGTTGGAGAGAGG
5651906 TTTTTA
1 TTTTTA
5651912 CACCATTAAG
Statistics
Matches: 79, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
87 36 0.46
88 12 0.15
89 16 0.20
90 15 0.19
ACGTcount: A:0.29, C:0.10, G:0.22, T:0.39
Consensus pattern (86 bp):
TTTTTATGCATTTTGGCATATCAAGTACCCAATTGAGGAAAAAAAAGCAGCGGCTTAATTGTTTT
TTTGAAAAAGTTGGAGAGAGG
Found at i:5652257 original size:20 final size:20
Alignment explanation
Indices: 5652224--5652261 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5652214 ACGGTATAGT
5652224 TAATGGTTGATTAATTAAAC
1 TAATGGTTGATTAATTAAAC
5652244 TAAT-GTTGATTTAATTAA
1 TAATGGTTGA-TTAATTAA
5652262 CAAAAACCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.03, G:0.13, T:0.45
Consensus pattern (20 bp):
TAATGGTTGATTAATTAAAC
Found at i:5663407 original size:17 final size:19
Alignment explanation
Indices: 5663368--5663410 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 19
5663358 TATCTTAAAA
5663368 ATTTAAAAATTCAAAAACT
1 ATTTAAAAATTCAAAAACT
*
5663387 -TTTAAAAA-T-AAAAATT
1 ATTTAAAAATTCAAAAACT
5663403 ATTTAAAA
1 ATTTAAAA
5663411 GTTTATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 8 0.36
18 8 0.36
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTTAAAAATTCAAAAACT
Found at i:5664121 original size:14 final size:14
Alignment explanation
Indices: 5664102--5664149 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
5664092 TCATTATCTT
5664102 AAAACTAAAATATA
1 AAAACTAAAATATA
5664116 AAAACT-AAAT-TA
1 AAAACTAAAATATA
5664128 AAAA--AAATATATA
1 AAAACTAAA-ATATA
*
5664141 AAGACTAAA
1 AAAACTAAA
5664150 TCTTAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 9
0.74 0.03 0.24
Matches are distributed among these distances:
11 2 0.07
12 8 0.29
13 9 0.32
14 6 0.21
15 3 0.11
ACGTcount: A:0.71, C:0.06, G:0.02, T:0.21
Consensus pattern (14 bp):
AAAACTAAAATATA
Found at i:5664125 original size:13 final size:13
Alignment explanation
Indices: 5664102--5664150 Score: 50
Period size: 12 Copynumber: 3.8 Consensus size: 13
5664092 TCATTATCTT
5664102 AAAACTAAAATATA
1 AAAACT-AAATATA
5664116 AAAACTAAAT-TA
1 AAAACTAAATATA
5664128 AAAA--AAATATA
1 AAAACTAAATATA
5664139 TAAAGACTAAAT
1 -AAA-ACTAAAT
5664151 CTTAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
10 4 0.13
11 2 0.07
12 9 0.30
13 5 0.17
14 6 0.20
15 4 0.13
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (13 bp):
AAAACTAAATATA
Found at i:5671797 original size:6 final size:6
Alignment explanation
Indices: 5671786--5671903 Score: 173
Period size: 6 Copynumber: 19.7 Consensus size: 6
5671776 CGTGCAAAGC
5671786 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
* * * *
5671834 AAAACG AAAACG AAAACG AAAACG AAAATG AAAATG AAAATG AAAATG
1 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
* * *
5671882 AAAATG AAAATG AAAATG AAAA
1 AAAACG AAAACG AAAACG AAAA
5671904 TGACAATGAC
Statistics
Matches: 111, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
6 111 1.00
ACGTcount: A:0.68, C:0.10, G:0.16, T:0.06
Consensus pattern (6 bp):
AAAACG
Found at i:5671904 original size:6 final size:6
Alignment explanation
Indices: 5671786--5671948 Score: 164
Period size: 6 Copynumber: 27.2 Consensus size: 6
5671776 CGTGCAAAGC
* * * * * * * *
5671786 AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG AAAACG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* * * *
5671834 AAAACG AAAACG AAAACG AAAACG AAAATG AAAATG AAAATG AAAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* * * *
5671882 AAAATG AAAATG AAAATG AAAATG ACAATG ACAATG ACAATG ACAATG
1 AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG AAAATG
* *
5671930 ACAATG ACAATG AAAATG A
1 AAAATG AAAATG AAAATG A
5671949 CGTGGAAATG
Statistics
Matches: 154, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 154 1.00
ACGTcount: A:0.63, C:0.11, G:0.17, T:0.09
Consensus pattern (6 bp):
AAAATG
Found at i:5675776 original size:27 final size:27
Alignment explanation
Indices: 5675735--5675788 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5675725 AATGAAGGTG
*
5675735 TTAGAATATAGACATCTACATTTATAT
1 TTAGAATATAAACATCTACATTTATAT
5675762 TTAGAATATAAACATCTACATTTATAT
1 TTAGAATATAAACATCTACATTTATAT
5675789 ATTTGTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.41
Consensus pattern (27 bp):
TTAGAATATAAACATCTACATTTATAT
Found at i:5676702 original size:13 final size:11
Alignment explanation
Indices: 5676674--5676716 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
5676664 AGTTAAATAT
5676674 TATTTTATTAA
1 TATTTTATTAA
5676685 TATTTTACTTAGA
1 TATTTTA-TTA-A
*
5676698 TA-TTTATTAT
1 TATTTTATTAA
5676708 TATTTTATT
1 TATTTTATT
5676717 TAGAAAATGG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 2 0.07
11 16 0.57
12 7 0.25
13 3 0.11
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (11 bp):
TATTTTATTAA
Found at i:5676703 original size:23 final size:23
Alignment explanation
Indices: 5676677--5676720 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5676667 TAAATATTAT
5676677 TTTATTAATATTTTACTTAGATA
1 TTTATTAATATTTTACTTAGATA
* *
5676700 TTTATTATTATTTTATTTAGA
1 TTTATTAATATTTTACTTAGA
5676721 AAATGGTAGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (23 bp):
TTTATTAATATTTTACTTAGATA
Found at i:5681742 original size:17 final size:18
Alignment explanation
Indices: 5681709--5681744 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
5681699 AACTTGATGA
5681709 AAAACATATAGTCTTTCC
1 AAAACATATAGTCTTTCC
*
5681727 AAAACATAT-TTCTTTCC
1 AAAACATATAGTCTTTCC
5681744 A
1 A
5681745 CATTCAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (18 bp):
AAAACATATAGTCTTTCC
Found at i:5694970 original size:27 final size:26
Alignment explanation
Indices: 5694940--5694990 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 26
5694930 ATGCCATTCT
5694940 TACAAA-CAATATAATTGAATAGCAATA
1 TACAAAGCAA-ATAA-TGAATAGCAATA
*
5694967 TACAAAGCAAATGATGAATAGCAA
1 TACAAAGCAAATAATGAATAGCAA
5694991 ACTAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 9 0.41
28 3 0.14
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.22
Consensus pattern (26 bp):
TACAAAGCAAATAATGAATAGCAATA
Found at i:5696736 original size:4 final size:4
Alignment explanation
Indices: 5696625--5696667 Score: 61
Period size: 4 Copynumber: 10.8 Consensus size: 4
5696615 GAGAAGGGGT
*
5696625 TTTA TTTA TTTA TTTA -ATA TTTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA TTTA TTTA TTTA TTT
5696668 GTAACTTCTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 2 0.06
4 31 0.89
5 2 0.06
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:5697895 original size:17 final size:17
Alignment explanation
Indices: 5697873--5697905 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5697863 TAGAATGAGG
*
5697873 TTGAGAAAATGATTTAA
1 TTGAGAAAATAATTTAA
5697890 TTGAGAAAATAATTTA
1 TTGAGAAAATAATTTA
5697906 TTTAAATTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.00, G:0.15, T:0.36
Consensus pattern (17 bp):
TTGAGAAAATAATTTAA
Found at i:5702812 original size:33 final size:33
Alignment explanation
Indices: 5702774--5702848 Score: 105
Period size: 33 Copynumber: 2.3 Consensus size: 33
5702764 CTCCTGTTAA
5702774 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
1 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
* * * * *
5702807 TCCTCCATCAGCATTGGTGCCGCCTATCGTCAG
1 CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
5702840 CCCTCCACC
1 CCCTCCACC
5702849 CCGCCTGAAC
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.16, C:0.47, G:0.19, T:0.19
Consensus pattern (33 bp):
CCCTCCACCAGCACTGGTGCCGCCAATCGCCAG
Found at i:5704809 original size:34 final size:34
Alignment explanation
Indices: 5704756--5704821 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
5704746 AAATACTAAT
* *
5704756 ATGTTTAAAATTTTCATCTTAATCTTTTACTTAA
1 ATGTTTAAAATTTTCATCTTAATATTCTACTTAA
* *
5704790 ATGTTTAAATTTTTTATCTTAATATTCTACTT
1 ATGTTTAAAATTTTCATCTTAATATTCTACTT
5704822 CAATCCATCG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.30, C:0.11, G:0.03, T:0.56
Consensus pattern (34 bp):
ATGTTTAAAATTTTCATCTTAATATTCTACTTAA
Found at i:5712361 original size:23 final size:23
Alignment explanation
Indices: 5712330--5712386 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
5712320 TTTATCTACA
*
5712330 TATGTATATATATT-TATATTTTT
1 TATGAATAT-TATTCTATATTTTT
*
5712353 TATGAATATTTTTCTATATTTTT
1 TATGAATATTATTCTATATTTTT
*
5712376 TAATAAATATT
1 T-ATGAATATT
5712387 TTTGTATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.10
23 18 0.62
24 8 0.28
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (23 bp):
TATGAATATTATTCTATATTTTT
Found at i:5712388 original size:23 final size:23
Alignment explanation
Indices: 5712344--5712389 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
5712334 TATATATATT
*
5712344 TATATTTTTTATGAATATTTTTC
1 TATATTTTTTATAAATATTTTTC
5712367 TATATTTTTTAATAAATATTTTT
1 TATATTTTTT-ATAAATATTTTT
5712390 GTATTTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (23 bp):
TATATTTTTTATAAATATTTTTC
Found at i:5712786 original size:15 final size:15
Alignment explanation
Indices: 5712763--5712797 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5712753 TTTTTATGCC
*
5712763 ATTGATGTATTTATT
1 ATTGTTGTATTTATT
5712778 ATTGTTGTATTTATT
1 ATTGTTGTATTTATT
5712793 ATTGT
1 ATTGT
5712798 AGCATTTGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (15 bp):
ATTGTTGTATTTATT
Found at i:5712804 original size:15 final size:15
Alignment explanation
Indices: 5712771--5712804 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5712761 CCATTGATGT
* *
5712771 ATTTATTATTGTTGT
1 ATTTATTATTGTAGC
5712786 ATTTATTATTGTAGC
1 ATTTATTATTGTAGC
5712801 ATTT
1 ATTT
5712805 GTACATACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.24, C:0.03, G:0.12, T:0.62
Consensus pattern (15 bp):
ATTTATTATTGTAGC
Found at i:5724646 original size:131 final size:131
Alignment explanation
Indices: 5724359--5724988 Score: 958
Period size: 131 Copynumber: 4.8 Consensus size: 131
5724349 GCTAAAAAAT
* * *
5724359 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * * *
5724424 TTGGTAGGAAATGCATTGAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCAAAG
66 TTGGTAGGAAGTGGATCGAAGAT-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
5724489 AA
130 AA
* *
5724491 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTTTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
5724556 TTGGTAGGAAGTGGATCGAAGA-CTAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGATC-AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
5724620 AA
130 AA
5724622 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * * *
5724687 TTGGTAGGAAGCGGATCGAAG-GCTAGGTCTTGTCTTCCCATATTAGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGATC-AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
5724751 AA
130 AA
* * * *
5724753 AGCAAATCTTGTCTTCATGTATTGGTGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
5724818 TTGGTAGGAAATGGATGGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGAT-CAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
5724883 AA
130 AA
* *
5724885 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* *
5724950 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGCCTTCC
66 TTGGTAGGAAGTGGATCGAAG-ATCAGATCTTGTCTTCC
5724989 TGCACCGACA
Statistics
Matches: 454, Mismatches: 39, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
130 1 0.00
131 241 0.53
132 210 0.46
133 2 0.00
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (131 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGATCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAGA
A
Found at i:5724868 original size:263 final size:262
Alignment explanation
Indices: 5724359--5724988 Score: 985
Period size: 263 Copynumber: 2.4 Consensus size: 262
5724349 GCTAAAAAAT
* * *
5724359 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * *
5724424 TTGGTAGGAAATGCATTGAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCAAAG
66 TTGGTAGGAAGTGGATCGAAGA-GCAGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCAAAG
* * * *
5724489 AAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTTTCTTCCTA
130 AAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
* * *
5724554 TATTGGTAGGAAGTGGATCGAAGACTAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCGAA
195 TATTGGTAGGAAATGGATCGAAGACTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAA
5724619 GAA
260 GAA
5724622 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * * *
5724687 TTGGTAGGAAGCGGATCGAAG-GCTAGGTCTTGTCTTCCCATATTAGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGAGC-AGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCAAAG
*
5724751 AAAGCAAATCTTGTCTTCATGTATTGGTGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
130 AAAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTA
*
5724816 TATTGGTAGGAAATGGATGGAAGA-TGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
195 TATTGGTAGGAAATGGATCGAAGACT--AGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
5724880 AAGAA
258 AAGAA
* *
5724885 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
*
5724950 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGCCTTCC
66 TTGGTAGGAAGTGGATCGAAG-AGCAGATCTTGTCTTCC
5724989 TGCACCGACA
Statistics
Matches: 336, Mismatches: 26, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
261 3 0.01
262 117 0.35
263 202 0.60
264 12 0.04
265 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.25, T:0.30
Consensus pattern (262 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGAGCAGATCTTGTCTTCCCATACTAGTAGCGAAGTAGATCAAAGA
AAGCAAATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTAT
ATTGGTAGGAAATGGATCGAAGACTAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
AA
Found at i:5725003 original size:132 final size:131
Alignment explanation
Indices: 5724359--5725015 Score: 899
Period size: 132 Copynumber: 5.0 Consensus size: 131
5724349 GCTAAAAAAT
* * *
5724359 AGCAGATCTTGTCTTCATGTATTGACGTGAAGTAGATCGAAGATAACAGATCTTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * * * * *
5724424 TTGGTAGGAAATGCATTGAAGATGCAGATCTTGTCTTCCCATACTGGTAGCGAAGTAGATCAAAG
66 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGTCTTCCC-CACTGGTGGCGAAGTAGATCGAAG
5724489 AA
130 AA
* *
5724491 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTTTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
** *
5724556 TTGGTAGGAAGTGGATCGAAG-A-CTAGATCTTGTCTTTCCATATTGGTGGCGAAGTAGATCGAA
66 TTGGTAGGAAGTGGATCGAAGAAGC-AGATCTTGTC-TTCCCCACTGGTGGCGAAGTAGATCGAA
5724619 GAA
129 GAA
5724622 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * * *
5724687 TTGGTAGGAAGCGGATCGAAG--GCTAGGTCTTGTCTTCCCATATTAGTGGCGAAGTAGATCGAA
66 TTGGTAGGAAGTGGATCGAAGAAGC-AGATCTTGTCTTCCC-CACTGGTGGCGAAGTAGATCGAA
5724750 GAA
129 GAA
* * * *
5724753 AGCAAATCTTGTCTTCATGTATTGGTGTGAAGTAGATCAAAGATAGCAGATCCTATCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * *
5724818 TTGGTAGGAAATGGATGGAAGATGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGTCTTCCC-CACTGGTGGCGAAGTAGATCGAAG
5724883 AA
130 AA
* *
5724885 AGTAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGTAGATCCTGTCTTCCTATA
1 AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
* * * ***
5724950 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAG
66 TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGTCTTCC-CCACTGGTGGCGAAGTAGATCGAAG
5725015 A
130 A
5725016 CATCAGTCTT
Statistics
Matches: 473, Mismatches: 45, Indels: 14
0.89 0.08 0.03
Matches are distributed among these distances:
130 5 0.01
131 231 0.49
132 235 0.50
133 2 0.00
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (131 bp):
AGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCGAAGATAGCAGATCCTGTCTTCCTATA
TTGGTAGGAAGTGGATCGAAGAAGCAGATCTTGTCTTCCCCACTGGTGGCGAAGTAGATCGAAGA
A
Found at i:5725341 original size:44 final size:44
Alignment explanation
Indices: 5725293--5725615 Score: 186
Period size: 44 Copynumber: 7.5 Consensus size: 44
5725283 TCCTATATCC
* *
5725293 CTGAAGTTGTAGTGGAGCGGATTAAAATCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
* * *** * *
5725337 CTGAAGTTGCAG-AGAGCATA-TCGCATC-TAG-TCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
* * *
5725377 CTGAAGTTGTAGTGGAGCAGACTAAGTAAGCA-AG-TCTTATC-CT
1 CTGAAGTTGCAGTGGAGCAGATTAA--AATCACAGATCTTATCTCT
* * **
5725420 CCTGAAGTTGCAAT-GAGCCAGATTGAAGATGGC-GAATCTTATCTCT
1 -CTGAAGTTGCAGTGGAG-CAGATT-AAAATCACAG-ATCTTATCTCT
* ** * * *
5725466 CTGACGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCCTATCTCA
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCACA-GATCTTATCTCT
** * *
5725510 CTGAAGTTGCAGTGGAGTGGATTAAAACCACAGATCTTATCTTT
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
* * ** * * * *
5725554 CTGAAGGTGCAGTAGAATAGA-TCATAT--CGGGTCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
5725595 CTGAAGTTGCAGTGGAGCAGA
1 CTGAAGTTGCAGTGGAGCAGA
5725616 CTCAAGAAAG
Statistics
Matches: 207, Mismatches: 56, Indels: 35
0.69 0.19 0.12
Matches are distributed among these distances:
40 20 0.10
41 36 0.17
42 5 0.02
43 14 0.07
44 100 0.48
45 27 0.13
46 5 0.02
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCT
Found at i:5725487 original size:45 final size:44
Alignment explanation
Indices: 5725293--5725660 Score: 176
Period size: 44 Copynumber: 8.5 Consensus size: 44
5725283 TCCTATATCC
* * *
5725293 CTGAAGTTGTAGTGGAGCGGATTAA--AATCACAGATCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCA-AG-TCTTATCTCT
* * * * * * *
5725337 CTGAAGTTGCAG-AGAGCATA-T-CG-CATCTAGTCTTATCTCC
1 CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCAAGTCTTATCTCT
* *
5725377 CTGAAGTTGTAGTGGAGCAGACTAAGTAAGCAAGTCTTATC-CT
1 CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCAAGTCTTATCTCT
* *
5725420 CCTGAAGTTGCAAT-GAGCCAGATTGAAG-ATGGCGAA-TCTTATCTCT
1 -CTGAAGTTGCAGTGGAG-CAGATT-AAGTA-AGC-AAGTCTTATCTCT
* * * * *
5725466 CTGACGTTGCAGTGGAGCAGATTAAAGCCAA-TAA-TCCTATCTCA
1 CTGAAGTTGCAGTGGAGCAGATT-AAG-TAAGCAAGTCTTATCTCT
** * *
5725510 CTGAAGTTGCAGTGGAGTGGATTAA--AACCACAGATCTTATCTTT
1 CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCA-AG-TCTTATCTCT
* * ** * * **
5725554 CTGAAGGTGCAGTAGAATAGA-TCA-T-ATCGGGTCTTATCTCT
1 CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCAAGTCTTATCTCT
* * * *
5725595 CTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCCCC
1 CTGAAGTTGCAGTGGAGCAGA-TTAAGTAAGCAAGTCTTATCTCT
* *
5725640 CTGAAATTGCAGTGGGGCAGA
1 CTGAAGTTGCAGTGGAGCAGA
5725661 CCCAAGAAAT
Statistics
Matches: 244, Mismatches: 57, Indels: 45
0.71 0.16 0.13
Matches are distributed among these distances:
40 22 0.09
41 35 0.14
42 7 0.03
43 17 0.07
44 93 0.38
45 62 0.25
46 7 0.03
47 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (44 bp):
CTGAAGTTGCAGTGGAGCAGATTAAGTAAGCAAGTCTTATCTCT
Found at i:5725661 original size:45 final size:45
Alignment explanation
Indices: 5725584--5725701 Score: 130
Period size: 45 Copynumber: 2.6 Consensus size: 45
5725574 ATCATATCGG
* * * *
5725584 GTCTTATCTCTCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAA
1 GTCTTATCCCCCTGAAATTGCAGTGGAGCAGACCCAAGAAAGCAA
* *
5725629 GTCTTATCCCCCTGAAATTGCAGTGGGGCAGACCCAAGAAATCAA
1 GTCTTATCCCCCTGAAATTGCAGTGGAGCAGACCCAAGAAAGCAA
* * * *
5725674 ATCCTA-CCTCCCTGACATTACAGTGGAG
1 GTCTTATCC-CCCTGAAATTGCAGTGGAG
5725702 TAGATTGAAG
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 2 0.03
45 59 0.97
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (45 bp):
GTCTTATCCCCCTGAAATTGCAGTGGAGCAGACCCAAGAAAGCAA
Found at i:5727235 original size:22 final size:24
Alignment explanation
Indices: 5727183--5727229 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5727173 TATATATAAT
* *
5727183 TATATTTTTTTATGAATATTTTTC
1 TATATTTTTTAATAAATATTTTTC
5727207 TATATTTTTTAATAAATATTTTT
1 TATATTTTTTAATAAATATTTTT
5727230 GTATTTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (24 bp):
TATATTTTTTAATAAATATTTTTC
Found at i:5729034 original size:8 final size:8
Alignment explanation
Indices: 5729020--5729049 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
5729010 TGTCCTACTT
5729020 ATATCAGA
1 ATATCAGA
*
5729028 CTATCAGA
1 ATATCAGA
5729036 ATATCAGA
1 ATATCAGA
5729044 ATATCA
1 ATATCA
5729050 TATCACACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.10, T:0.27
Consensus pattern (8 bp):
ATATCAGA
Found at i:5729177 original size:18 final size:18
Alignment explanation
Indices: 5729154--5729188 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5729144 AAATCTTGGA
*
5729154 CCCACATGCTCGTGTGGT
1 CCCACACGCTCGTGTGGT
5729172 CCCACACGCTCGTGTGG
1 CCCACACGCTCGTGTGG
5729189 CCTACACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.37, G:0.29, T:0.23
Consensus pattern (18 bp):
CCCACACGCTCGTGTGGT
Found at i:5735718 original size:11 final size:11
Alignment explanation
Indices: 5735702--5735739 Score: 58
Period size: 11 Copynumber: 3.3 Consensus size: 11
5735692 TATTTCATTT
5735702 GAAAAAAAAAA
1 GAAAAAAAAAA
5735713 GAAAAAAAAAA
1 GAAAAAAAAAA
5735724 GAAAAGAAAAGAA
1 GAAAA-AAAA-AA
5735737 GAA
1 GAA
5735740 CTAAAAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 16 0.64
12 4 0.16
13 5 0.20
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (11 bp):
GAAAAAAAAAA
Found at i:5735728 original size:16 final size:15
Alignment explanation
Indices: 5735703--5735733 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
5735693 ATTTCATTTG
5735703 AAAAAAAAAAGAAAA
1 AAAAAAAAAAGAAAA
5735718 AAAAAAGAAAAGAAAA
1 AAAAAA-AAAAGAAAA
5735734 GAAGAACTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAA
Found at i:5735733 original size:22 final size:22
Alignment explanation
Indices: 5735704--5735751 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
5735694 TTTCATTTGA
5735704 AAAAAAAAAGAA-AAAAAAAAG
1 AAAAAAAAAGAAGAAAAAAAAG
* **
5735725 AAAAGAAAAGAAGAACTAAAAG
1 AAAAAAAAAGAAGAAAAAAAAG
5735747 AAAAA
1 AAAAA
5735752 GGAGAGGCCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.02
Consensus pattern (22 bp):
AAAAAAAAAGAAGAAAAAAAAG
Found at i:5737992 original size:18 final size:18
Alignment explanation
Indices: 5737966--5738000 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5737956 AGGTGTGTTT
*
5737966 CCTAGCCCTTATATGTAC
1 CCTAACCCTTATATGTAC
5737984 CCTAACCCTTATATGTA
1 CCTAACCCTTATATGTA
5738001 TCCTTTTCCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.31, G:0.09, T:0.34
Consensus pattern (18 bp):
CCTAACCCTTATATGTAC
Found at i:5738573 original size:29 final size:29
Alignment explanation
Indices: 5738534--5738792 Score: 245
Period size: 29 Copynumber: 8.9 Consensus size: 29
5738524 AACCTAATTT
* *
5738534 AACCCTAAACCCTAACCTAAATTAATTATA
1 AACCCT-AACCCTAACCTAATTTAATTAAA
* **
5738564 AACCCTAACCCCTAACCTAAATTAATTGCA
1 AACCCTAA-CCCTAACCTAATTTAATTAAA
5738594 AACCCTAACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
**
5738623 AACCCTAACCCTAACCCTAACCTAATTTAATTA
1 AACCCTAACCCTAA-CCTAATTTAA-TTAA--A
5738656 AA----AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
*
5738681 AACCCT-A----AACC---CTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
5738702 AACCCTAACGCTAAAACTAACCTAATTTAATTAAA
1 AACCCTAAC-C-----CTAACCTAATTTAATTAAA
*
5738737 AACCCTAACCTTAACCTAATTTAATTAAA
1 AACCCTAACCCTAACCTAATTTAATTAAA
5738766 AACCCTAACCCTAACCTAATTTAATTA
1 AACCCTAACCCTAACCTAATTTAATTA
5738793 NNNNNNNNNN
Statistics
Matches: 193, Mismatches: 13, Indels: 47
0.76 0.05 0.19
Matches are distributed among these distances:
21 15 0.08
22 1 0.01
24 4 0.02
25 3 0.02
27 4 0.02
28 9 0.05
29 86 0.45
30 41 0.21
31 4 0.02
32 4 0.02
33 3 0.02
34 1 0.01
35 18 0.09
ACGTcount: A:0.45, C:0.27, G:0.01, T:0.27
Consensus pattern (29 bp):
AACCCTAACCCTAACCTAATTTAATTAAA
Found at i:5738665 original size:23 final size:23
Alignment explanation
Indices: 5738635--5738715 Score: 114
Period size: 23 Copynumber: 3.6 Consensus size: 23
5738625 CCCTAACCCT
5738635 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
5738658 AACCCTAACCTAATTTAATTAAA
1 AACCCTAACCTAATTTAATTAAA
*
5738681 AACCCTAAACC---CTTAATTAAA
1 AACCCT-AACCTAATTTAATTAAA
5738702 AACCCTAACGCTAA
1 AACCCTAAC-CTAA
5738716 AACTAACCTA
Statistics
Matches: 52, Mismatches: 1, Indels: 9
0.84 0.02 0.15
Matches are distributed among these distances:
20 3 0.06
21 16 0.31
23 29 0.56
24 4 0.08
ACGTcount: A:0.47, C:0.26, G:0.01, T:0.26
Consensus pattern (23 bp):
AACCCTAACCTAATTTAATTAAA
Found at i:5738698 original size:21 final size:22
Alignment explanation
Indices: 5738649--5738709 Score: 81
Period size: 21 Copynumber: 2.8 Consensus size: 22
5738639 CTAACCTAAT
*
5738649 TTAATTAAAAACCCT-AACCTAAT
1 TTAATTAAAAACCCTAAACC--AC
5738672 TTAATTAAAAACCCTAAACC-C
1 TTAATTAAAAACCCTAAACCAC
5738693 TTAATTAAAAACCCTAA
1 TTAATTAAAAACCCTAA
5738710 CGCTAAAACT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
21 17 0.47
23 15 0.42
24 4 0.11
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (22 bp):
TTAATTAAAAACCCTAAACCAC
Found at i:5738776 original size:35 final size:35
Alignment explanation
Indices: 5738594--5738782 Score: 160
Period size: 35 Copynumber: 5.3 Consensus size: 35
5738584 ATTAATTGCA
*
5738594 AACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTTAACCTAATTTAATTAAAAACCCT
*
5738629 AACCCTAACCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTTAACCTAATTTAATTAAAAACCCT
** *
5738664 AA-CCTAATTTAATTAAAAACCCTAAACCCTTAATTAAAAACCCT
1 AACCCTAA---CCTT---AA-CCT-AA--TTTAATTAAAAACCCT
* *
5738708 AACGCTAAAAC-TAACCTAATTTAATT--AAA----
1 AACCCT-AACCTTAACCTAATTTAATTAAAAACCCT
5738737 AACCCTAACCTTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTTAACCTAATTTAATTAAAAACCCT
5738772 AACCCTAACCT
1 AACCCTAACCT
5738783 AATTTAATTA
Statistics
Matches: 126, Mismatches: 9, Indels: 38
0.73 0.05 0.22
Matches are distributed among these distances:
28 3 0.02
29 20 0.16
31 3 0.02
33 3 0.02
34 5 0.04
35 54 0.43
37 3 0.02
38 3 0.02
39 2 0.02
40 2 0.02
41 3 0.02
42 3 0.02
43 1 0.01
44 17 0.13
45 2 0.02
46 2 0.02
ACGTcount: A:0.45, C:0.28, G:0.01, T:0.26
Consensus pattern (35 bp):
AACCCTAACCTTAACCTAATTTAATTAAAAACCCT
Found at i:5742035 original size:124 final size:126
Alignment explanation
Indices: 5741878--5742229 Score: 527
Period size: 124 Copynumber: 2.8 Consensus size: 126
5741868 CCCAAACATG
*
5741878 CTACTGTAGCAAAAGCGCG-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
1 CTACTGTAGCAAAAGAGCGCTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
* *
5741942 CTAGAAGCGATTTTATATTATTTGCTCAGAAACATCAAAAAAAT-TTATTTCTTAC-ATGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATATTATTTCTT-CTATGAC
* * *
5742002 CTACTGTAGCAAAAGAGCGCT-GACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAAGAGCGCTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
5742066 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTTCTGTGAC
66 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAT-ATTATTTCTTCTATGAC
* * *
5742128 CTACTGTAGCAAAA-A-CGCTTCTACGAGGGCGCGATTTCACAAATTCTTCACAAATACCATCCT
1 CTACTGTAGCAAAAGAGCGC-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCT
**
5742191 GCTAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
65 GCTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
5742230 CTCGAAATTA
Statistics
Matches: 208, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
124 103 0.50
125 4 0.02
126 101 0.49
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (126 bp):
CTACTGTAGCAAAAGAGCGCTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATATTATTTCTTCTATGAC
Found at i:5742189 original size:126 final size:123
Alignment explanation
Indices: 5741878--5742229 Score: 519
Period size: 126 Copynumber: 2.8 Consensus size: 123
5741868 CCCAAACATG
*
5741878 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAACGC-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* *
5741943 TAGAAGCGATTTTATATTATTTGCTCAGAAACATCAAAAAAATTTATTTCTTACATGAC
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATGAC
* * *
5742002 CTACTGTAGCAAAAGAGCGCT-GACGAGGCCGCGATTTCACAAATTCTTCTCAAATAGCATCCTA
1 CTACTGTAGCAAAA-A-CGCTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTG
*
5742066 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATAATTATTTCTT-CTGTGAC
64 CTAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAT--TTATTTCTTAC-ATGAC
* * *
5742128 CTACTGTAGCAAAAACGCTTCTACGAGGGCGCGATTTCACAAATTCTTCACAAATACCATCCTGC
1 CTACTGTAGCAAAAACGC-TCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
**
5742193 TAGAAGCGATTTTATACTATTTTATCAGAAACGTCAA
65 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA
5742230 CTCGAAATTA
Statistics
Matches: 207, Mismatches: 14, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
124 99 0.48
125 4 0.02
126 104 0.50
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.29
Consensus pattern (123 bp):
CTACTGTAGCAAAAACGCTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGCT
AGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAATTTATTTCTTACATGAC
Found at i:5756789 original size:21 final size:21
Alignment explanation
Indices: 5756748--5756790 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5756738 AATAAAGTAG
*
5756748 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
*
5756769 ATTATATTTTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
5756790 A
1 A
5756791 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:5756827 original size:34 final size:32
Alignment explanation
Indices: 5756782--5756845 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 32
5756772 ATATTTTATG
5756782 ATTTTAGTAAATTCATATAATAATTTTATTAAGA
1 ATTTTAGTAAATT-ATAT-ATAATTTTATTAAGA
* *
5756816 ATTTTATTAAATTATATATTATTTTATTAA
1 ATTTTAGTAAATTATATATAATTTTATTAA
5756846 ATTATATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 12 0.43
33 4 0.14
34 12 0.43
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (32 bp):
ATTTTAGTAAATTATATATAATTTTATTAAGA
Found at i:5757075 original size:44 final size:46
Alignment explanation
Indices: 5757026--5757117 Score: 136
Period size: 44 Copynumber: 2.0 Consensus size: 46
5757016 TACAACATCG
*
5757026 TTCCATTCAACCAAACACA-AGAA-TACT-ATTACAGTTCTATTCCA
1 TTCCATTCAACCAAACA-ATAGAATTACTGATTACAGCTCTATTCCA
*
5757070 TTCCATTCAACCAAACAATTGAATTACTGATTACAGCTCTATTCCA
1 TTCCATTCAACCAAACAATAGAATTACTGATTACAGCTCTATTCCA
5757116 TT
1 TT
5757118 ACAGCTCTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
43 1 0.02
44 20 0.47
45 4 0.09
46 18 0.42
ACGTcount: A:0.36, C:0.26, G:0.05, T:0.33
Consensus pattern (46 bp):
TTCCATTCAACCAAACAATAGAATTACTGATTACAGCTCTATTCCA
Found at i:5757120 original size:16 final size:16
Alignment explanation
Indices: 5757099--5757169 Score: 99
Period size: 16 Copynumber: 4.4 Consensus size: 16
5757089 TGAATTACTG
* *
5757099 ATTACAGCTCTATTCC
1 ATTACAGCCCTATTCA
*
5757115 ATTACAGCTCTATTCA
1 ATTACAGCCCTATTCA
5757131 ATTACAGCCCTATTCA
1 ATTACAGCCCTATTCA
5757147 ATTACAGCCCTATTTC-
1 ATTACAGCCCTA-TTCA
5757163 ATTACAG
1 ATTACAG
5757170 TGAACCAAAC
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 49 0.94
17 3 0.06
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.35
Consensus pattern (16 bp):
ATTACAGCCCTATTCA
Found at i:5758327 original size:27 final size:27
Alignment explanation
Indices: 5758292--5758360 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
5758282 AATAATAAAA
5758292 ATCCTCCCAAACACACCAGTATATTAT
1 ATCCTCCCAAACACACCAGTATATTAT
5758319 ATCCTCCCAAACACACCAGTATATTAT
1 ATCCTCCCAAACACACCAGTATATTAT
5758346 ATCCTCCCAAACACA
1 ATCCTCCCAAACACA
5758361 TCAATAAGGC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.38, C:0.36, G:0.03, T:0.23
Consensus pattern (27 bp):
ATCCTCCCAAACACACCAGTATATTAT
Found at i:5758941 original size:22 final size:24
Alignment explanation
Indices: 5758899--5758942 Score: 74
Period size: 22 Copynumber: 1.9 Consensus size: 24
5758889 TAACTAAACT
5758899 TACTTACTTTTCTAACTTAATTCA
1 TACTTACTTTTCTAACTTAATTCA
5758923 TACTT-CTTTTCT-ACTTAATT
1 TACTTACTTTTCTAACTTAATT
5758943 TCTTGCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.40
23 7 0.35
24 5 0.25
ACGTcount: A:0.25, C:0.20, G:0.00, T:0.55
Consensus pattern (24 bp):
TACTTACTTTTCTAACTTAATTCA
Found at i:5759324 original size:22 final size:22
Alignment explanation
Indices: 5759291--5759337 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
5759281 TCTTTCCCTA
5759291 TTTTCGTCTCTT-TCTCTGTTTC
1 TTTTCGTCTCTTCT-TCTGTTTC
*
5759313 TTTTCTGT-TCTTCTTTTGTTTC
1 TTTTC-GTCTCTTCTTCTGTTTC
5759335 TTT
1 TTT
5759338 GTCTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
22 19 0.86
23 3 0.14
ACGTcount: A:0.00, C:0.21, G:0.09, T:0.70
Consensus pattern (22 bp):
TTTTCGTCTCTTCTTCTGTTTC
Found at i:5759541 original size:5 final size:5
Alignment explanation
Indices: 5759533--5759589 Score: 57
Period size: 5 Copynumber: 11.6 Consensus size: 5
5759523 TTAGTTTATT
* *
5759533 TAATA TAATA TAATA TAACA TAATA TATTATA TTATA TAATA -AA-A TAATA
1 TAATA TAATA TAATA TAATA TAATA TA--ATA TAATA TAATA TAATA TAATA
5759583 T-ATA TAA
1 TAATA TAA
5759590 AACATAAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
3 1 0.02
4 8 0.19
5 30 0.70
7 4 0.09
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:5761878 original size:13 final size:13
Alignment explanation
Indices: 5761860--5761885 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5761850 ATAAAATAAG
5761860 AAAGTGATTTGAA
1 AAAGTGATTTGAA
5761873 AAAGTGATTTGAA
1 AAAGTGATTTGAA
5761886 TTTTGTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (13 bp):
AAAGTGATTTGAA
Found at i:5765673 original size:6 final size:6
Alignment explanation
Indices: 5765662--5765695 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
5765652 AGTATCCATC
5765662 TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA TTCC
1 TTCCCA TTCCCA TTCCCA TTCCCA TTCCCA TTCC
5765696 TATTGTAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.15, C:0.50, G:0.00, T:0.35
Consensus pattern (6 bp):
TTCCCA
Found at i:5766468 original size:15 final size:15
Alignment explanation
Indices: 5766450--5766485 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
5766440 CGGGTCGGGT
5766450 GGCGCCTGTCAAGTA
1 GGCGCCTGTCAAGTA
5766465 GGCGCCTGTCAAGTA
1 GGCGCCTGTCAAGTA
5766480 GGCGCC
1 GGCGCC
5766486 AATGAAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.17, C:0.31, G:0.36, T:0.17
Consensus pattern (15 bp):
GGCGCCTGTCAAGTA
Found at i:5766906 original size:19 final size:19
Alignment explanation
Indices: 5766859--5766915 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
5766849 TTTAAATTTT
* *
5766859 TTGTATGAATATTATAATTT
1 TTGTATGAATATTGTAA-TG
*
5766879 TTTTATGAATATTGTAATG
1 TTGTATGAATATTGTAATG
5766898 TTGTATGAATATTGTAAT
1 TTGTATGAATATTGTAAT
5766916 TATTTTATAA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (19 bp):
TTGTATGAATATTGTAATG
Found at i:5766987 original size:19 final size:21
Alignment explanation
Indices: 5766835--5767169 Score: 245
Period size: 22 Copynumber: 15.1 Consensus size: 21
5766825 TAGATTAGAA
*
5766835 TTTTGTATGAATATTTTAAATT
1 TTTTGTATGAATATTGT-AATT
*
5766857 TTTTGTATGAATATTATAATT
1 TTTTGTATGAATATTGTAATT
5766878 TTTT-TATGAATATTGTAA--
1 TTTTGTATGAATATTGTAATT
*
5766896 TGTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
* *
5766917 ATTTTATAATTAA-ATTTGT-ATT
1 -TTTTGT-ATGAATA-TTGTAATT
* * * * *
5766939 TATAGTTTTGGAT-TAGTAATT
1 TTTTG-TATGAATATTGTAATT
5766960 TTTTGTATGAATATTGTAA-T
1 TTTTGTATGAATATTGTAATT
*
5766980 TTTT-TATGAATATTATAAATT
1 TTTTGTATGAATATTGT-AATT
5767001 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
5767026 AGTTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
5767050 TTTTGTATGAATATTGTAATTTTGT
1 TTTTGTATGAATATTGTAA---T-T
* *
5767075 AATTTTGTATGAATATTATATTT
1 --TTTTGTATGAATATTGTAATT
5767098 TTTTGTATGAATATTGTAATATTAT
1 TTTTGTATGAATATTGT-A-A-T-T
*
5767123 AATTTTGTATGAATATTGCAATTT
1 --TTTTGTATGAATATTGTAA-TT
5767147 TTTTGTATGAATATTGTAATT
1 TTTTGTATGAATATTGTAATT
5767168 TT
1 TT
5767170 GTAATTTTGT
Statistics
Matches: 256, Mismatches: 28, Indels: 59
0.75 0.08 0.17
Matches are distributed among these distances:
18 3 0.01
19 25 0.10
20 28 0.11
21 48 0.19
22 75 0.29
23 10 0.04
24 7 0.03
25 9 0.04
26 2 0.01
27 49 0.19
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (21 bp):
TTTTGTATGAATATTGTAATT
Found at i:5767022 original size:49 final size:49
Alignment explanation
Indices: 5766969--5767246 Score: 359
Period size: 49 Copynumber: 5.7 Consensus size: 49
5766959 TTTTTGTATG
* * *
5766969 AATATTGTAATTTTTTATGAATATTATAAATTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* * *
5767018 AATATTATAGTTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* *
5767067 AATTTTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* *
5767115 AATATTATAATTTTGTATGAATATTGCAATTTTTTTGTATGAATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
* * ** *
5767164 AATTTTGTAATTTTGTATGAATATTGTAA--TGTGGGGAT--ATATTGT
1 AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
*
5767209 AATATTGTAATTTTTTGTATGAATATTGTAATTATTTT
1 AATATTGTAA--TTTTGTATGAATATTGTAATTTTTTT
5767247 ATAATTAATT
Statistics
Matches: 197, Mismatches: 27, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
45 16 0.08
47 24 0.12
48 44 0.22
49 113 0.57
ACGTcount: A:0.31, C:0.01, G:0.14, T:0.54
Consensus pattern (49 bp):
AATATTGTAATTTTGTATGAATATTGTAATTTTTTTGTATGAATATTGT
Found at i:5767037 original size:27 final size:25
Alignment explanation
Indices: 5766969--5767193 Score: 215
Period size: 27 Copynumber: 9.1 Consensus size: 25
5766959 TTTTTGTATG
* *
5766969 AATATTGTAATTTTTTATGAATATTAT
1 AATATT-T-ATTTTGTATGAATATTGT
5766996 AA-A-TT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
5767018 AATATTATAGTTTTGTATGAATATTG-
1 AATATT-TA-TTTTGTATGAATATTGT
*
5767044 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
5767067 AATTTTGTAATTTTGTATGAATA-T-T
1 AATATT-T-ATTTTGTATGAATATTGT
5767092 -ATATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
5767115 AATATTATAATTTTGTATGAATATTG-
1 AATATT-T-ATTTTGTATGAATATTGT
*
5767141 CA-ATTT-TTTTGTATGAATATTGT
1 AATATTTATTTTGTATGAATATTGT
*
5767164 AATTTTGTAATTTTGTATGAATATTGT
1 AATATT-T-ATTTTGTATGAATATTGT
5767191 AAT
1 AAT
5767194 GTGGGGATAT
Statistics
Matches: 168, Mismatches: 9, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
21 13 0.08
22 50 0.30
23 5 0.03
24 17 0.10
25 12 0.07
26 4 0.02
27 67 0.40
ACGTcount: A:0.32, C:0.01, G:0.12, T:0.55
Consensus pattern (25 bp):
AATATTTATTTTGTATGAATATTGT
Found at i:5767131 original size:97 final size:98
Alignment explanation
Indices: 5766973--5767188 Score: 398
Period size: 97 Copynumber: 2.2 Consensus size: 98
5766963 TGTATGAATA
* *
5766973 TTGTAATTTTTTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAGTTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
5767038 ATATTGCAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGTATGAATATTGTAATT
*
5767071 TTGTAATTTTGTATGAATATTAT-ATTTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
1 TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
5767135 ATATTGCAATTTTTTTGTATGAATATTGTAATT
66 ATATTGCAATTTTTTTGTATGAATATTGTAATT
5767168 TTGTAATTTTGTATGAATATT
1 TTGTAATTTTGTATGAATATT
5767189 GTAATGTGGG
Statistics
Matches: 115, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
97 93 0.81
98 22 0.19
ACGTcount: A:0.31, C:0.01, G:0.12, T:0.56
Consensus pattern (98 bp):
TTGTAATTTTGTATGAATATTATAAATTTTTTGTATGAATATTGTAATATTATAATTTTGTATGA
ATATTGCAATTTTTTTGTATGAATATTGTAATT
Found at i:5767618 original size:15 final size:16
Alignment explanation
Indices: 5767580--5767618 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
5767570 TAACTCATTT
5767580 AATTTTATATAATGTA
1 AATTTTATATAATGTA
*
5767596 ACTTTTATATAAT-TA
1 AATTTTATATAATGTA
5767611 AATTTTAT
1 AATTTTAT
5767619 TTGATTTGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (16 bp):
AATTTTATATAATGTA
Found at i:5769256 original size:6 final size:6
Alignment explanation
Indices: 5769245--5769288 Score: 61
Period size: 6 Copynumber: 7.3 Consensus size: 6
5769235 TCATGCACCG
* * *
5769245 GAGCCA GAGCCA GAGCCA GAGCCG GAGCCA GACCCA GACCCA GA
1 GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GAGCCA GA
5769289 ACTACATTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.36, G:0.32, T:0.00
Consensus pattern (6 bp):
GAGCCA
Found at i:5769274 original size:24 final size:24
Alignment explanation
Indices: 5769242--5769288 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
5769232 GCATCATGCA
* *
5769242 CCGGAGCCAGAGCCAGAGCCAGAG
1 CCGGAGCCAGACCCAGACCCAGAG
5769266 CCGGAGCCAGACCCAGACCCAGA
1 CCGGAGCCAGACCCAGACCCAGA
5769289 ACTACATTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.30, C:0.38, G:0.32, T:0.00
Consensus pattern (24 bp):
CCGGAGCCAGACCCAGACCCAGAG
Found at i:5772597 original size:22 final size:21
Alignment explanation
Indices: 5772558--5772602 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
5772548 TACCTAATTT
* *
5772558 TTTTCTTCTTTTCCTTCCTTC
1 TTTTCTTCTCTTCATTCCTTC
5772579 TTTTCTTCTGCTTCATTCCTTC
1 TTTTCTTCT-CTTCATTCCTTC
5772601 TT
1 TT
5772603 ATTTCTTTCG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.02, C:0.31, G:0.02, T:0.64
Consensus pattern (21 bp):
TTTTCTTCTCTTCATTCCTTC
Found at i:5772706 original size:27 final size:28
Alignment explanation
Indices: 5772668--5772743 Score: 95
Period size: 27 Copynumber: 2.8 Consensus size: 28
5772658 AAAATAACAG
* *
5772668 CATTGACGCCTCTCAGAAT-GGCACCAC
1 CATTGGCGCCTCCCAGAATAGGCACCAC
*
5772695 CATTGGCGCCTCCCA-AGTAGGCACCAC
1 CATTGGCGCCTCCCAGAATAGGCACCAC
*
5772722 CATTGGCACCTCCCAG-ATAGGC
1 CATTGGCGCCTCCCAGAATAGGC
5772744 GCCAATACTA
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 2 0.05
27 40 0.95
ACGTcount: A:0.24, C:0.38, G:0.21, T:0.17
Consensus pattern (28 bp):
CATTGGCGCCTCCCAGAATAGGCACCAC
Found at i:5773491 original size:5 final size:5
Alignment explanation
Indices: 5773481--5773512 Score: 55
Period size: 5 Copynumber: 6.2 Consensus size: 5
5773471 GATTCATTTG
5773481 TTTAT TTTAT TTTAT TTTAT TTTAT TATTAT T
1 TTTAT TTTAT TTTAT TTTAT TTTAT T-TTAT T
5773513 GTTTTTTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 21 0.81
6 5 0.19
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:5797669 original size:12 final size:12
Alignment explanation
Indices: 5797652--5797676 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5797642 AACGAGCAAC
5797652 ATAATATAAATG
1 ATAATATAAATG
5797664 ATAATATAAATG
1 ATAATATAAATG
5797676 A
1 A
5797677 AAGCACAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:5797927 original size:2 final size:2
Alignment explanation
Indices: 5797920--5797960 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
5797910 CAAAATACTA
*
5797920 AT AT AT AT AT AC AT 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 AT AT AT AT AT AT AT A
5797961 CGAGAATAGG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5799816 original size:132 final size:132
Alignment explanation
Indices: 5799530--5800451 Score: 1422
Period size: 132 Copynumber: 7.0 Consensus size: 132
5799520 TAGGATTGTC
* * *
5799530 GGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACTGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* *
5799595 TGCTTTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCGCTACTGCTTAGGGAGACAAGGCT
66 TGC-TTAGGGAGATAAGATCT-TCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCT
*
5799659 TAGT
129 TGGT
* *
5799663 GGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* * * * * * * *
5799728 TGCTTAGGGAGATAATATCTACATTCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5799793 GT
131 GT
* * * **
5799795 AGCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGATT--CTGTCTTCGATCTATTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* * *
5799858 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTTCTCAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5799923 GT
131 GT
**
5799925 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTTCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* * * * *
5799990 TGCTTAGGGAGATAAGATCTTCAATCTTCAAACTTTTCCACTGCTGCTCAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5800055 GT
131 GT
* *
5800057 GGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATT--CTGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* *
5800120 TACTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGGGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5800185 GT
131 GT
*
5800187 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAT
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* *
5800252 TGCTTAGGGAGACAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAGGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5800317 GT
131 GT
*
5800319 GGCCTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
* *
5800384 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTACTCAGAGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5800449 GT
131 GT
5800451 G
1 G
5800452 TTTCACTGGT
Statistics
Matches: 725, Mismatches: 59, Indels: 11
0.91 0.07 0.01
Matches are distributed among these distances:
130 240 0.33
132 422 0.58
133 63 0.09
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (132 bp):
GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
GT
Found at i:5799913 original size:262 final size:263
Alignment explanation
Indices: 5799530--5800451 Score: 1472
Period size: 262 Copynumber: 3.5 Consensus size: 263
5799520 TAGGATTGTC
*
5799530 GGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACTGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC-CTGTCTTCGATCTGCTCCACTAC
* * *
5799595 TGCTTTAGGGAGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTTAGGGAGACAAGGCTT
65 TGC-TTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTT
* * *
5799660 AGTGGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCAC
129 GGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCAC
* * *
5799725 TACTGCTTAGGGAGATAATATCTACATTCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGGC
194 TACTGCTTAGGGAGATAAGATCTTCAATCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGGC
5799790 TTGGT
259 TTGGT
* * **
5799795 AGCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGATT-CTGTCTTCGATCTATTCCACTACT
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCCTGTCTTCGATCTGCTCCACTACT
* *
5799859 GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTTCTCAGGGAGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTGG
**
5799924 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTTCCGTCTTCGATCTGCTCCACTA
131 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTA
5799989 CTGCTTAGGGAGATAAGATCTTCAATCTTCAA-ACTTTTCCACTGCTGCTCAGGGAGACAAGGCT
196 CTGCTTAGGGAGATAAGATCTTCAATCTTCAACA-TTTTCCACTGCTGCTCAGGGAGACAAGGCT
5800053 TGGT
260 TGGT
*
5800057 GGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATT-CTGTCTTCGATCTGCTCCACTACT
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCCTGTCTTCGATCTGCTCCACTACT
* * *
5800121 ACTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGGGACAAGGCTTGG
66 GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTGG
5800186 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTA
131 TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTA
* * * * * * * *
5800251 TTGCTTAGGGAGACAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAGGGCTT
196 CTGCTTAGGGAGATAAGATCTTCAATCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGGCTT
5800316 GGT
261 GGT
* *
5800319 GGCCTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTC-CTGTCTTCGATCTGCTCCACTAC
* * *
5800384 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTACTCAGAGAGACAAGGCTTG
65 TGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTG
5800449 GTG
130 GTG
5800452 TTTCACTGGT
Statistics
Matches: 609, Mismatches: 44, Indels: 9
0.92 0.07 0.01
Matches are distributed among these distances:
261 1 0.00
262 461 0.76
263 24 0.04
264 86 0.14
265 37 0.06
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (263 bp):
GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCCTGTCTTCGATCTGCTCCACTACT
GCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTTGG
TGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTA
CTGCTTAGGGAGATAAGATCTTCAATCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGGCTT
GGT
Found at i:5800003 original size:44 final size:44
Alignment explanation
Indices: 5799560--5800428 Score: 192
Period size: 44 Copynumber: 19.8 Consensus size: 44
5799550 TATCTTGGAA
** * *
5799560 AGATAAGATTCACTGTCTTCGATCTGCTCCACTACTGCTTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGC-TTAGGG
* * * * *
5799605 AGATAAGATCTAT-AATCTTCAACCTTCTCCGCTACTGCTTAGGG
1 AGATAAGAT-TTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
5799649 AGACAAG-GCTT-AGTGGCTTAAATCTACTTCTCACTA-T-CTT-GGAA
1 AGATAAGATTTTCAGT--CTTCAATCTGC-TC-CACTACTGCTTAGG-G
** * *
5799693 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * ** * *
5799737 AGATAATATCTACATTCTTCAA-CATTTTCCACTGCTGCTCAGGG
1 AGATAAGATTTTCAGTCTTCAATC-TGCTCCACTACTGCTTAGGG
* * * * * *
5799781 AGACAAGGCTTGGT-AG-CTTAAATTTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATT-TTCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * **
5799825 AGATAAGA--TTCTGTCTTCGATCTATTCCACTACTGCTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * * * *
5799867 AGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTTCTCAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** *** * * *
5799911 AGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTTCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
5799955 AGATAAGATTTTCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * *
5799999 AGATAAGATCTTCAATCTTCAAACTTTTCCACTGCTGCTCAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** *** * * *
5800043 AGACAAGGCTTGGTGGCTTAAATCTGCTTCTCACTA-T-CTT-GGAA
1 AGATAAGATTTTCAGTCTTCAATCTGC-TC-CACTACTGCTTAGG-G
* * *
5800087 AGATAAGA--TTCTGTCTTCGATCTGCTCCACTACTACTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * *
5800129 AGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** *** * * *
5800173 GGACAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTTCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** * * *
5800217 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTATTGCTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * * * * * *
5800261 AGACAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** *** * * * *
5800305 AGACAGGGCTTGGTGGCCTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTTCAGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
** * *
5800349 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * *
5800393 AGATAAGATCTTCAATCTTCAACCTTCTCCACTACT
1 AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACT
5800429 ACTCAGAGAG
Statistics
Matches: 557, Mismatches: 216, Indels: 103
0.64 0.25 0.12
Matches are distributed among these distances:
40 12 0.02
41 6 0.01
42 66 0.12
43 27 0.05
44 364 0.65
45 52 0.09
46 30 0.05
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (44 bp):
AGATAAGATTTTCAGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:5800237 original size:394 final size:393
Alignment explanation
Indices: 5799530--5800451 Score: 1452
Period size: 394 Copynumber: 2.3 Consensus size: 393
5799520 TAGGATTGTC
* *
5799530 GGCTTTAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACTGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
* *
5799595 TGCTTTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCGCTACTGCTTAGGGAGACAAGGCT
66 TGC-TTAGGGAGATAAGATCT-TCAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCT
*
5799659 TAGTGGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCA
129 TGGTGGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTC-CCGTCTTCGATCTGCTCCA
* * * * * *
5799724 CTACTGCTTAGGGAGATAATATCTACATTCTTCAACATTTTCCACTGCTGCTCAGGGAGACAAGG
193 CTACTACTTAGGGAGATAAGATCTACAATCTTCAACATTCTCCACTACTACTCAGGGAGACAAGG
* * *
5799789 CTTGGTAGCTTAAATTTGCTTCCCACTATCTTGGAAAGATAAGATTCTGTCTTCGATCTATTCCA
258 CTTGGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCCGTCTTCGATCTACTCCA
* * *
5799854 CTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTTCTCCGCTGCTTCTCAGGGAGACAAGG
323 CTACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGG
5799919 CTTGGT
388 CTTGGT
**
5799925 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTTCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
* * *
5799990 TGCTTAGGGAGATAAGATCTTCAATCTTCAAACTTTTCCACTGCTGCTCAGGGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTG
* *
5800055 GTGGCTTAAATCTGCTTCTCACTATCTTGGAAAGATAAGATT-CTGTCTTCGATCTGCTCCACTA
131 GTGGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTCCCGTCTTCGATCTGCTCCACTA
* * * *
5800119 CTACTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGGGACAAGGCTT
196 CTACTTAGGGAGATAAGATCTACAATCTTCAACATTCTCCACTACTACTCAGGGAGACAAGGCTT
* *
5800184 GGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCAC
261 GGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATT--CCGTCTTCGATCTACTCCAC
* * *
5800249 TATTGCTTAGGGAGACAAGATCTTCAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAGGGC
324 TACTGCTTAGGGAGACAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGC
5800314 TTGGT
389 TTGGT
* *
5800319 GGCCTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTAC
1 GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
* *
5800384 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTACTCAGAGAGACAAGGCTTG
66 TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTG
5800449 GTG
131 GTG
5800452 TTTCACTGGT
Statistics
Matches: 483, Mismatches: 41, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
392 117 0.24
393 1 0.00
394 301 0.62
395 64 0.13
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (393 bp):
GGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCACCGTCTTCGATCTGCTCCACTAC
TGCTTAGGGAGATAAGATCTTCAATCTTCAACCTTCTCCACTACTGCTCAGGGAGACAAGGCTTG
GTGGCTTAAATCTACTTCTCACTATCTTGGAAAGATAAGATTCCCGTCTTCGATCTGCTCCACTA
CTACTTAGGGAGATAAGATCTACAATCTTCAACATTCTCCACTACTACTCAGGGAGACAAGGCTT
GGTAGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCCGTCTTCGATCTACTCCACTA
CTGCTTAGGGAGACAAGATCTACAATCTTCAACCTTCTCCGCTACTACTCAGGGAGACAAGGCTT
GGT
Found at i:5814687 original size:12 final size:12
Alignment explanation
Indices: 5814670--5814694 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5814660 AACGAGCAAC
5814670 ATAATATAAATG
1 ATAATATAAATG
5814682 ATAATATAAATG
1 ATAATATAAATG
5814694 A
1 A
5814695 AAGCACAACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATAATATAAATG
Found at i:5814946 original size:2 final size:2
Alignment explanation
Indices: 5814939--5814985 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
5814929 AAAAATACTA
*
5814939 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5814981 AT AT A
1 AT AT A
5814986 CGAGAATAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5823542 original size:13 final size:13
Alignment explanation
Indices: 5823524--5823549 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5823514 TATTATACTT
5823524 TAGAAATTAATTC
1 TAGAAATTAATTC
5823537 TAGAAATTAATTC
1 TAGAAATTAATTC
5823550 AAGTTAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
TAGAAATTAATTC
Found at i:5825254 original size:41 final size:41
Alignment explanation
Indices: 5825169--5825254 Score: 136
Period size: 41 Copynumber: 2.1 Consensus size: 41
5825159 TAGAAAATCC
*
5825169 TTTTCCTAATTATATAAGGAGTAGATTATAAATTAAACTCG
1 TTTTCCTAATTATATAAGGAGTAGATTATAAATTAAACTAG
* * *
5825210 TTTTCCTAATTATATAAGGAGTGGATTATAAATTATATTAG
1 TTTTCCTAATTATATAAGGAGTAGATTATAAATTAAACTAG
5825251 TTTT
1 TTTT
5825255 TAGTTTTTAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.36, C:0.07, G:0.13, T:0.44
Consensus pattern (41 bp):
TTTTCCTAATTATATAAGGAGTAGATTATAAATTAAACTAG
Found at i:5826840 original size:25 final size:26
Alignment explanation
Indices: 5826789--5826842 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
5826779 AACACACCAA
5826789 TATCGCAGCAAAACTGCCAGTAATAG
1 TATCGCAGCAAAACTGCCAGTAATAG
* *
5826815 TATCGCAGCAAAGCTG-CAGTAGTAG
1 TATCGCAGCAAAACTGCCAGTAATAG
5826840 TAT
1 TAT
5826843 ACTTCCTCCA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
25 11 0.42
26 15 0.58
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.22
Consensus pattern (26 bp):
TATCGCAGCAAAACTGCCAGTAATAG
Found at i:5831161 original size:23 final size:24
Alignment explanation
Indices: 5831121--5831166 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
5831111 CTCGATTCTC
5831121 AAATACACCAAGATATCG-TCTAT
1 AAATACACCAAGATATCGATCTAT
*
5831144 AAATACCACCACGA-ATCGATCTA
1 AAATA-CACCAAGATATCGATCTA
5831167 GGTAGGGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.43, C:0.26, G:0.09, T:0.22
Consensus pattern (24 bp):
AAATACACCAAGATATCGATCTAT
Found at i:5840120 original size:18 final size:18
Alignment explanation
Indices: 5840093--5840128 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
5840083 CTCATTGTTG
5840093 CCATCCTGAACGAATCAA
1 CCATCCTGAACGAATCAA
*
5840111 CCATCTTGAACGAATCAA
1 CCATCCTGAACGAATCAA
5840129 TCTGCGGAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.31, G:0.11, T:0.19
Consensus pattern (18 bp):
CCATCCTGAACGAATCAA
Found at i:5842331 original size:22 final size:22
Alignment explanation
Indices: 5842296--5842338 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5842286 TTACTTTTAG
* *
5842296 TTTTTTTTATTAATTTTTAATA
1 TTTTTATTAATAATTTTTAATA
5842318 TTTTTATTAATAATTTTTAAT
1 TTTTTATTAATAATTTTTAAT
5842339 TAAATGGGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (22 bp):
TTTTTATTAATAATTTTTAATA
Found at i:5842877 original size:42 final size:42
Alignment explanation
Indices: 5842830--5842920 Score: 121
Period size: 42 Copynumber: 2.2 Consensus size: 42
5842820 CTAACTTTAG
* * * *
5842830 ACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAAATCA-A
1 ACCTTTAGCGACGCTTCTCCCAAAAACGCCGCTAAAAAT-ATA
*
5842872 ACCTTTAGCGACGCTTCTCGCAAAAACGCCGCTAAAAATATA
1 ACCTTTAGCGACGCTTCTCCCAAAAACGCCGCTAAAAATATA
5842914 ACCTTTA
1 ACCTTTA
5842921 AAAAAATTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (42 bp):
ACCTTTAGCGACGCTTCTCCCAAAAACGCCGCTAAAAATATA
Found at i:5843920 original size:24 final size:24
Alignment explanation
Indices: 5843891--5843944 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
5843881 TTGATGAAAG
* *
5843891 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
5843915 ATGAACCGTTCAACACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
5843939 A-GAACT
1 ATGAACT
5843945 TACTTTTCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 4 0.16
24 21 0.84
ACGTcount: A:0.46, C:0.19, G:0.15, T:0.20
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:5848173 original size:41 final size:41
Alignment explanation
Indices: 5848111--5848456 Score: 339
Period size: 41 Copynumber: 8.8 Consensus size: 41
5848101 AGATTTTATT
5848111 ATTAGCGGCGCTTTT-TCAAAAACGCCGCTAAAGGTACGAGC
1 ATTAGCGGCGCTTTTCT-AAAAACGCCGCTAAAGGTACGAGC
* * ** * *
5848152 ATTAGCGGCGCTTTTCTAAAAATGCTGCTAAAGGCCCAAGA
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
* *
5848193 ATTAGCAGTGCTTTT-TCAAAAACGCCGCTAAAGGTACGAGC
1 ATTAGCGGCGCTTTTCT-AAAAACGCCGCTAAAGGTACGAGC
* *
5848234 ATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGTACGAGC
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
* * ** **
5848275 ATTAGCGGCGATTTTCCAAAAACGCCATTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
*
5848316 ATTGGCGGCGCTTTT-T--AAA----G------GTACGAGC
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
* **
5848344 ATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
* *
5848385 ATTAGCGGCACTTTTCCAAAAACGCCGCTAAAGG-ATCGAGC
1 ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTA-CGAGC
5848426 ATTAGCGGCGCTTTT-TCAAAAACGCCGCTAA
1 ATTAGCGGCGCTTTTCT-AAAAACGCCGCTAA
5848457 TGCTTAATTT
Statistics
Matches: 249, Mismatches: 38, Indels: 36
0.77 0.12 0.11
Matches are distributed among these distances:
28 20 0.08
31 3 0.01
35 1 0.00
38 3 0.01
40 1 0.00
41 220 0.88
42 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.22
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTCTAAAAACGCCGCTAAAGGTACGAGC
Found at i:5848342 original size:28 final size:28
Alignment explanation
Indices: 5848302--5848358 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
5848292 AAAAACGCCA
* *
5848302 TTAAAGGCCCGAGCATTGGCGGCGCTTT
1 TTAAAGGCACGAGCATTAGCGGCGCTTT
*
5848330 TTAAAGGTACGAGCATTAGCGGCGCTTT
1 TTAAAGGCACGAGCATTAGCGGCGCTTT
5848358 T
1 T
5848359 CCAAAAACGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.28
Consensus pattern (28 bp):
TTAAAGGCACGAGCATTAGCGGCGCTTT
Found at i:5848376 original size:69 final size:69
Alignment explanation
Indices: 5848262--5848399 Score: 231
Period size: 69 Copynumber: 2.0 Consensus size: 69
5848252 AAAACGCCGC
* * *
5848262 TAAAGGTACGAGCATTAGCGGCGATTTTCCAAAAACGCCATTAAAGGCCCGAGCATTGGCGGCGC
1 TAAAGGTACGAGCATTAGCGGCGATTTTCCAAAAACGCCACTAAAGGCCCGAGCATTAGCGGCAC
5848327 TTTT
66 TTTT
* *
5848331 TAAAGGTACGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGCAC
1 TAAAGGTACGAGCATTAGCGGCGATTTTCCAAAAACGCCACTAAAGGCCCGAGCATTAGCGGCAC
5848396 TTTT
66 TTTT
5848400 CCAAAAACGC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 64 1.00
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (69 bp):
TAAAGGTACGAGCATTAGCGGCGATTTTCCAAAAACGCCACTAAAGGCCCGAGCATTAGCGGCAC
TTTT
Found at i:5848417 original size:110 final size:110
Alignment explanation
Indices: 5848221--5848441 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 110
5848211 AAAACGCCGC
*
5848221 TAAAGGTACGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCGA
1 TAAAGGTACGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCACGAGCATTAGCGGCGA
* * *
5848286 TTTTCCAAAAACGCCATTAAAGGCCCGAGCATTGGCGGCGCTTTT
66 TTTTCCAAAAACGCCACTAAAGGACCGAGCATTAGCGGCGCTTTT
* *
5848331 TAAAGGTACGAGCATTAGCGGCGCTTTTCCAAAAACGCCGCTAAAGGCCCGAGCATTAGCGGC-A
1 TAAAGGTACGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCACGAGCATTAGCGGCGA
* *
5848395 CTTTTCCAAAAACGCCGCTAAAGGATCGAGCATTAGCGGCGCTTTT
66 -TTTTCCAAAAACGCCACTAAAGGACCGAGCATTAGCGGCGCTTTT
5848441 T
1 T
5848442 CAAAAACGCC
Statistics
Matches: 102, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
109 1 0.01
110 101 0.99
ACGTcount: A:0.28, C:0.26, G:0.25, T:0.21
Consensus pattern (110 bp):
TAAAGGTACGAGCATTAGCGGCGCTTTCCCAAAAACGCCGCTAAAGGCACGAGCATTAGCGGCGA
TTTTCCAAAAACGCCACTAAAGGACCGAGCATTAGCGGCGCTTTT
Found at i:5848558 original size:40 final size:39
Alignment explanation
Indices: 5848427--5848558 Score: 115
Period size: 40 Copynumber: 3.4 Consensus size: 39
5848417 GGATCGAGCA
* * *
5848427 TTAGCGGCGCTTTTTCAAAAACGCCGCTAATGCTT-AATT
1 TTAGCGGCG-TTTTTCCAAAATGCCGCTAATGCTTGATTT
* * *
5848466 TTAGCGGCG-TTTTCCAAAATGCGCTCTAATGCTCGATCT
1 TTAGCGGCGTTTTTCCAAAATGC-CGCTAATGCTTGATTT
* * * **
5848505 GTAGCGACATTTTTGTAAAAGTGCCGCTAATGCTTGATTT
1 TTAGCGGCGTTTTTCCAAAA-TGCCGCTAATGCTTGATTT
*
5848545 TTAGTGGCGTTTTT
1 TTAGCGGCGTTTTT
5848559 TTATCCAAAC
Statistics
Matches: 71, Mismatches: 18, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 11 0.15
38 9 0.13
39 17 0.24
40 31 0.44
41 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (39 bp):
TTAGCGGCGTTTTTCCAAAATGCCGCTAATGCTTGATTT
Found at i:5848933 original size:2 final size:2
Alignment explanation
Indices: 5848926--5848954 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5848916 TCTAAAATAC
5848926 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 T
5848955 CAATATTTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5848934 original size:22 final size:22
Alignment explanation
Indices: 5848892--5848934 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
5848882 TTTTTTAATA
* *
5848892 GATCTAATATCTCTATCATATT
1 GATCTAAAATCTATATCATATT
5848914 GATCTAAAATACTATAT-ATAT
1 GATCTAAAAT-CTATATCATAT
5848935 ATATATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (22 bp):
GATCTAAAATCTATATCATATT
Found at i:5849501 original size:19 final size:19
Alignment explanation
Indices: 5849474--5849510 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5849464 TAGTAATACA
*
5849474 TTAACATATTATTAAAATT
1 TTAACATATTAATAAAATT
*
5849493 TTAATATATTAATAAAAT
1 TTAACATATTAATAAAAT
5849511 ATTATTTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAACATATTAATAAAATT
Found at i:5852463 original size:4 final size:4
Alignment explanation
Indices: 5852446--5852476 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
5852436 TTAATTGGTT
*
5852446 TAAA TAAT TAAA TAAA TAAA TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA
5852477 TTTCTTTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
TAAA
Found at i:5854564 original size:38 final size:38
Alignment explanation
Indices: 5854513--5854592 Score: 160
Period size: 38 Copynumber: 2.1 Consensus size: 38
5854503 TGTAACATGT
5854513 TGTACTAAAAAGATTGATGTTAGATATGCCACAATCTA
1 TGTACTAAAAAGATTGATGTTAGATATGCCACAATCTA
5854551 TGTACTAAAAAGATTGATGTTAGATATGCCACAATCTA
1 TGTACTAAAAAGATTGATGTTAGATATGCCACAATCTA
5854589 TGTA
1 TGTA
5854593 GTGGGATATG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (38 bp):
TGTACTAAAAAGATTGATGTTAGATATGCCACAATCTA
Found at i:5858189 original size:40 final size:39
Alignment explanation
Indices: 5858145--5858283 Score: 147
Period size: 40 Copynumber: 3.5 Consensus size: 39
5858135 ACACAACAGT
5858145 TTGGCACCCAATGCCTCATCGGATAATTCGAAGTAATAAA
1 TTGGCACCCAATGCCTCATCGGATAATTCGAAGT-ATAAA
* * * *
5858185 TTGGCACCCAGTGTCTCATCGGCTAAATCGAAG--TAAA
1 TTGGCACCCAATGCCTCATCGGATAATTCGAAGTATAAA
* * * *
5858222 TTGGCACCTAGTGCCTCATCGAATTAATTCGAAATAGTAAA
1 TTGGCACCCAATGCCTCATCGGA-TAATTCGAAGTA-TAAA
* *
5858263 TTGACACCCAATGTCTCATCG
1 TTGGCACCCAATGCCTCATCG
5858284 ACTCGAAGTC
Statistics
Matches: 81, Mismatches: 14, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
37 23 0.28
38 8 0.10
40 29 0.36
41 21 0.26
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (39 bp):
TTGGCACCCAATGCCTCATCGGATAATTCGAAGTATAAA
Found at i:5858487 original size:24 final size:24
Alignment explanation
Indices: 5858442--5858488 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5858432 TATATATACC
5858442 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
5858466 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
5858489 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:5861423 original size:10 final size:10
Alignment explanation
Indices: 5861410--5861474 Score: 60
Period size: 10 Copynumber: 6.4 Consensus size: 10
5861400 TTATTATTTT
5861410 TAATTTTTAA
1 TAATTTTTAA
*
5861420 TAATTTTTTA
1 TAATTTTTAA
* *
5861430 CAATTTTTTA
1 TAATTTTTAA
* *
5861440 CAATTTCTAA
1 TAATTTTTAA
5861450 TAAATTTTATAA
1 T-AATTTT-TAA
5861462 -AATTTTTAA
1 TAATTTTTAA
5861471 TAAT
1 TAAT
5861475 AATTATTTTT
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
9 3 0.07
10 35 0.76
11 5 0.11
12 3 0.07
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (10 bp):
TAATTTTTAA
Found at i:5861451 original size:30 final size:31
Alignment explanation
Indices: 5861411--5861468 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
5861401 TATTATTTTT
* * *
5861411 AATTTTTAAT-AATTTTTTACAATTTTTTAC
1 AATTTCTAATAAATTTTATAAAATTTTTTAC
5861441 AATTTCTAATAAATTTTATAAAATTTTT
1 AATTTCTAATAAATTTTATAAAATTTTT
5861469 AATAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
30 9 0.38
31 15 0.62
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (31 bp):
AATTTCTAATAAATTTTATAAAATTTTTTAC
Found at i:5861455 original size:21 final size:21
Alignment explanation
Indices: 5861431--5861473 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5861421 AATTTTTTAC
* *
5861431 AATTTTTTACAATTTCTAATA
1 AATTTTATAAAATTTCTAATA
*
5861452 AATTTTATAAAATTTTTAATA
1 AATTTTATAAAATTTCTAATA
5861473 A
1 A
5861474 TAATTATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTTTATAAAATTTCTAATA
Found at i:5861469 original size:30 final size:30
Alignment explanation
Indices: 5861411--5861469 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
5861401 TATTATTTTT
* * *
5861411 AATTTTTAATAATTTTTTACAATTTTTTAC
1 AATTTCTAATAATTTTATACAAATTTTTAC
5861441 AATTTCTAATAAATTTTATA-AAATTTTTA
1 AATTTCTAAT-AATTTTATACAAATTTTTA
5861470 ATAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (30 bp):
AATTTCTAATAATTTTATACAAATTTTTAC
Found at i:5882643 original size:4 final size:4
Alignment explanation
Indices: 5882634--5882847 Score: 414
Period size: 4 Copynumber: 54.0 Consensus size: 4
5882624 ACTAAAATCT
5882634 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5882682 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5882730 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5882778 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
5882826 --AC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC
5882848 TTAAATGCCA
Statistics
Matches: 208, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.01
4 206 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:5886266 original size:27 final size:25
Alignment explanation
Indices: 5886224--5886277 Score: 72
Period size: 27 Copynumber: 2.1 Consensus size: 25
5886214 TATAGCAAGG
5886224 TTTTTATTTAAAAAAAACTATATAT
1 TTTTTATTTAAAAAAAACTATATAT
* *
5886249 TTTTTTTTATAAATAAAAATTATATAT
1 TTTTTATT-TAAA-AAAAACTATATAT
5886276 TT
1 TT
5886278 ACTTTGTTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.28
26 4 0.16
27 14 0.56
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (25 bp):
TTTTTATTTAAAAAAAACTATATAT
Found at i:5889298 original size:42 final size:42
Alignment explanation
Indices: 5889244--5889383 Score: 192
Period size: 42 Copynumber: 3.3 Consensus size: 42
5889234 TAGATAAAAC
5889244 ATTTGCAGATAAAATTGCTACTGGGTTGTGGATGCACAACAT
1 ATTTGCAGATAAAATTGCTACTGGGTTGTGGATGCACAACAT
* * * *
5889286 ATTTGTAGATAAAATTGCAACTAGGTGGTGGATGCACAACAT
1 ATTTGCAGATAAAATTGCTACTGGGTTGTGGATGCACAACAT
* * * *
5889328 ATTTGCAAATAAAACTG-TCATTGGGTTATGGATGCACAACAT
1 ATTTGCAGATAAAATTGCT-ACTGGGTTGTGGATGCACAACAT
5889370 ATTTGCAGATAAAA
1 ATTTGCAGATAAAA
5889384 CGGCCACTCT
Statistics
Matches: 84, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 84 1.00
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (42 bp):
ATTTGCAGATAAAATTGCTACTGGGTTGTGGATGCACAACAT
Found at i:5891335 original size:91 final size:88
Alignment explanation
Indices: 5891161--5891380 Score: 225
Period size: 91 Copynumber: 2.5 Consensus size: 88
5891151 CACTCCATTT
* * * *** *
5891161 TGTGGATGAACCACTAGTGTTGCAGGTTAATACGCTGTTAGTAGTTATGAATACACAACTGGTTT
1 TGTGGATAAACCACTAGTGTTGCAAGTTAATACACTACCAGTAGTTATGAATACACAACAGGTTT
* *
5891226 GCAGATAATAATTGCCAGT-ATAAAA
66 GCAGATAATAACTACCAGTGAT---A
* *
5891251 TGTGGATAAACCACTAGTGCTTGCAAGTTAATACACTACCAGTAGTTGTGAATTCACAACAGGTT
1 TGTGGATAAACCACTAGTG-TTGCAAGTTAATACACTACCAGTAGTTATGAATACACAACAGGTT
*
5891316 TGCAGATAA-AAGCTACCAGTGATT
65 TGCAGATAATAA-CTACCAGTGATA
* *
5891340 TATGGATAAACCACCAGTGTTTGC-AGTTAA-A-ACTACCAGTA
1 TGTGGATAAACCACTAGTG-TTGCAAGTTAATACACTACCAGTA
5891381 CTTCCTCCTT
Statistics
Matches: 112, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
86 10 0.09
87 1 0.01
88 6 0.05
89 21 0.19
90 20 0.18
91 52 0.46
92 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.29
Consensus pattern (88 bp):
TGTGGATAAACCACTAGTGTTGCAAGTTAATACACTACCAGTAGTTATGAATACACAACAGGTTT
GCAGATAATAACTACCAGTGATA
Found at i:5902822 original size:29 final size:30
Alignment explanation
Indices: 5902787--5902844 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 30
5902777 GTATTAAAAA
5902787 ATTAAATAAATAAAATAATAT-ATA-AAATT
1 ATTAAAT-AATAAAATAATATCATATAAATT
*
5902816 ATTAAATATTAAAATAATATCATATAAAT
1 ATTAAATAATAAAATAATATCATATAAAT
5902845 ATTTTTAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 12 0.46
29 10 0.38
30 4 0.15
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (30 bp):
ATTAAATAATAAAATAATATCATATAAATT
Found at i:5909880 original size:114 final size:114
Alignment explanation
Indices: 5909680--5909907 Score: 438
Period size: 114 Copynumber: 2.0 Consensus size: 114
5909670 TGGATGGAAG
5909680 TGCAAATAGCTCTATCATAGATAGTATCTGAACAGTTAGGGAATTCCCAAACATATTTCCCGAAG
1 TGCAAATAGCTCTATCATAGATAGTATCTGAACAGTTAGGGAATTCCCAAACATATTTCCCGAAG
*
5909745 AGCTACTAGGGTTACCTCCAGATCGTAAGGTAGAATTCAGAACTAAACT
66 AGCTACCAGGGTTACCTCCAGATCGTAAGGTAGAATTCAGAACTAAACT
5909794 TGCAAATAGCTCTATCATAGATAGTATCTGAACAGTTAGGGAATTCCCAAACATATTTCCCGAAG
1 TGCAAATAGCTCTATCATAGATAGTATCTGAACAGTTAGGGAATTCCCAAACATATTTCCCGAAG
*
5909859 AGCTACCAGGGTTACCTCCAGATCGTGAGGTAGAATTCAGAACTAAACT
66 AGCTACCAGGGTTACCTCCAGATCGTAAGGTAGAATTCAGAACTAAACT
5909908 ATCGCTATGA
Statistics
Matches: 112, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.26
Consensus pattern (114 bp):
TGCAAATAGCTCTATCATAGATAGTATCTGAACAGTTAGGGAATTCCCAAACATATTTCCCGAAG
AGCTACCAGGGTTACCTCCAGATCGTAAGGTAGAATTCAGAACTAAACT
Found at i:5910751 original size:170 final size:170
Alignment explanation
Indices: 5910469--5910813 Score: 636
Period size: 170 Copynumber: 2.0 Consensus size: 170
5910459 AAAGAGTTTG
* *
5910469 TGGTGTACAATAATGCATCTTACATTAAAATTGGATGTGTGTATGCAAGGCGAAAAAGTAGTTGT
1 TGGTGTACAATAATGCATCTTACACTAAAATTGGATGTGTGTATGCAAGGCGAAAAAGTAATTGT
*
5910534 TTACGCATTGAGGCAGTTGAAATAGCATGAATGCAACTATCTAACACATGACTTGGAGTTGGCAT
66 TTACGCATTGAGGCAGTTGAAATAGCATGAATACAACTATCTAACACATGACTTGGAGTTGGCAT
5910599 TAGTGGTATTCGCAATAAAAATCTAGATACACTACTTATA
131 TAGTGGTATTCGCAATAAAAATCTAGATACACTACTTATA
*
5910639 TGGTGTACAATAATGCATCTTACACTAACATTGGATGTGTGTATGCAAGGCGAAAAAGTAATTGT
1 TGGTGTACAATAATGCATCTTACACTAAAATTGGATGTGTGTATGCAAGGCGAAAAAGTAATTGT
*
5910704 TTACGCGTTGAGGCAGTTGAAATAGCATGAATACAACTATCTAACACATGACTTGGAGTTGGCAT
66 TTACGCATTGAGGCAGTTGAAATAGCATGAATACAACTATCTAACACATGACTTGGAGTTGGCAT
*
5910769 TAGTGGTATTCGCAATAAAAATCTAGATACGCTACTTATA
131 TAGTGGTATTCGCAATAAAAATCTAGATACACTACTTATA
5910809 TGGTG
1 TGGTG
5910814 AGAGGTGCTA
Statistics
Matches: 169, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
170 169 1.00
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.30
Consensus pattern (170 bp):
TGGTGTACAATAATGCATCTTACACTAAAATTGGATGTGTGTATGCAAGGCGAAAAAGTAATTGT
TTACGCATTGAGGCAGTTGAAATAGCATGAATACAACTATCTAACACATGACTTGGAGTTGGCAT
TAGTGGTATTCGCAATAAAAATCTAGATACACTACTTATA
Found at i:5915338 original size:17 final size:17
Alignment explanation
Indices: 5915316--5915362 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
5915306 TAATTAGAAT
5915316 TTTCTTTCCTCTCCCTA
1 TTTCTTTCCTCTCCCTA
* * *
5915333 TTTCTTCCCTCT-CTTT
1 TTTCTTTCCTCTCCCTA
5915349 TTTCTTTCCTCTCC
1 TTTCTTTCCTCTCC
5915363 TTTACATCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 13 0.52
17 12 0.48
ACGTcount: A:0.02, C:0.40, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTCTTTCCTCTCCCTA
Found at i:5915365 original size:17 final size:17
Alignment explanation
Indices: 5915315--5915365 Score: 68
Period size: 17 Copynumber: 3.1 Consensus size: 17
5915305 CTAATTAGAA
*
5915315 TTTTCTTTCCTCTCCCT
1 TTTTCTTTCCTCTCCTT
* *
5915332 ATTTCTTCCCTCT-CTT
1 TTTTCTTTCCTCTCCTT
5915348 TTTTCTTTCCTCTCCTT
1 TTTTCTTTCCTCTCCTT
5915365 T
1 T
5915366 ACATCATATT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
16 13 0.46
17 15 0.54
ACGTcount: A:0.02, C:0.37, G:0.00, T:0.61
Consensus pattern (17 bp):
TTTTCTTTCCTCTCCTT
Found at i:5922595 original size:5 final size:5
Alignment explanation
Indices: 5922585--5922609 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5922575 GATATTTGAA
5922585 ATTGC ATTGC ATTGC ATTGC ATTGC
1 ATTGC ATTGC ATTGC ATTGC ATTGC
5922610 CTTCATAAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
ATTGC
Found at i:5932543 original size:45 final size:45
Alignment explanation
Indices: 5932474--5932576 Score: 134
Period size: 45 Copynumber: 2.2 Consensus size: 45
5932464 ATGTTAACCA
* ** *
5932474 AGTTCATTGCCACAACGTACTAGCAGGTTTTATCTACACTGATGGAT
1 AGTTCA-T-CCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
*
5932521 AGTTCATCCACAACGTATTAGCAGCTTTTATCTACACAAACGGAT
1 AGTTCATCCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
*
5932566 GGTTCATCCAC
1 AGTTCATCCAC
5932577 CAATATATTT
Statistics
Matches: 50, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
45 43 0.86
46 1 0.02
47 6 0.12
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (45 bp):
AGTTCATCCACAACGTACTAGCAGCTTTTATCTACACAAACGGAT
Found at i:5932631 original size:21 final size:21
Alignment explanation
Indices: 5932592--5932631 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
5932582 TATTTTTATC
**
5932592 ATTAGAAGTTCATTTACAATG
1 ATTAGAAGTTCATCCACAATG
*
5932613 ATTAGTAGTTCATCCACAA
1 ATTAGAAGTTCATCCACAA
5932632 AGTAGTGTAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (21 bp):
ATTAGAAGTTCATCCACAATG
Found at i:5934605 original size:16 final size:15
Alignment explanation
Indices: 5934586--5934621 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5934576 TCAAAAACCT
5934586 TTTTCCTTTTTCTTCA
1 TTTTCCTTTTT-TTCA
*
5934602 TTTTCCTTTTTTTCT
1 TTTTCCTTTTTTTCA
5934617 TTTTC
1 TTTTC
5934622 TACTCAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTCCTTTTTTTCA
Found at i:5934954 original size:48 final size:49
Alignment explanation
Indices: 5934883--5934981 Score: 182
Period size: 48 Copynumber: 2.0 Consensus size: 49
5934873 AAATAAATAC
5934883 ATTCTTTCTTAGTCCATTTTCTCTTTTTC-TTCTCTCTCTTTAACTCAA
1 ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTCTCTCTCTTTAACTCAA
5934931 ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTTCTCTCTCTTTAACTCAA
1 ATTCTTTCTTAGTCCATTTTCTCTTTTTC-TTTCTCTCTCTTTAACTCAA
5934981 A
1 A
5934982 AGACTCTGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
48 29 0.59
50 20 0.41
ACGTcount: A:0.15, C:0.26, G:0.02, T:0.57
Consensus pattern (49 bp):
ATTCTTTCTTAGTCCATTTTCTCTTTTTCTTTCTCTCTCTTTAACTCAA
Found at i:5937061 original size:24 final size:24
Alignment explanation
Indices: 5937034--5937085 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
5937024 TTCTAGAAGT
*
5937034 TTTAGTATTTATTAGTATA-TTATA
1 TTTAGCATTTATTAGTATAGTT-TA
5937058 TTTAGCATTTATTAGTATAGTTTA
1 TTTAGCATTTATTAGTATAGTTTA
5937082 TTTA
1 TTTA
5937086 ACTCACTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.10, T:0.58
Consensus pattern (24 bp):
TTTAGCATTTATTAGTATAGTTTA
Found at i:5938814 original size:20 final size:20
Alignment explanation
Indices: 5938750--5938814 Score: 55
Period size: 20 Copynumber: 3.3 Consensus size: 20
5938740 TATTTTTACA
5938750 ATTTTTAATAGATTTATTAAGT
1 ATTTTTAATA-ATTTATTAA-T
* *
5938772 -TGTTT-ATAGTTT-TTAAT
1 ATTTTTAATAATTTATTAAT
* *
5938789 AATTTTAATATTTTATTAAT
1 ATTTTTAATAATTTATTAAT
5938809 ATTTTT
1 ATTTTT
5938815 CTAGTAATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.03
18 7 0.21
19 9 0.26
20 13 0.38
21 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
ATTTTTAATAATTTATTAAT
Found at i:5938938 original size:18 final size:18
Alignment explanation
Indices: 5938917--5939034 Score: 72
Period size: 18 Copynumber: 6.7 Consensus size: 18
5938907 TTTTGAATTT
5938917 ATAATAATTTTATTTTTA
1 ATAATAATTTTATTTTTA
* *
5938935 ATAAAAATTTTAAGTCTTCT-
1 ATAATAATTTT-A-T-TTTTA
5938955 AT-A-AATTTTATTTTTA
1 ATAATAATTTTATTTTTA
**
5938971 ATTTTTAA-TTTATTTTTA
1 A-TAATAATTTTATTTTTA
* *
5938989 AT-AT-TTTTTGA-ATTT-
1 ATAATAATTTT-ATTTTTA
5939004 ATAATAATTTTATTTTTA
1 ATAATAATTTTATTTTTA
5939022 ATAATGAATTTTA
1 ATAAT-AATTTTA
5939035 GTTTGGGTTT
Statistics
Matches: 77, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
15 5 0.06
16 12 0.16
17 11 0.14
18 32 0.42
19 11 0.14
20 3 0.04
21 3 0.04
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.59
Consensus pattern (18 bp):
ATAATAATTTTATTTTTA
Found at i:5939012 original size:87 final size:88
Alignment explanation
Indices: 5938839--5939034 Score: 313
Period size: 87 Copynumber: 2.2 Consensus size: 88
5938829 ATTTTTAGTA
* * *
5938839 ATTTTTATTAAAAATTTTAAGTCTTCTATAAATTTTATTTTTTTTATTTTTAATTTCTTTCTAAT
1 ATTTTTAATAAAAATTTTAAGTCTTCTATAAATTTTA-TTTTTTAATTTTTAATTTATTTCTAAT
5938904 AGTTTTTGAATTTATAATAATTTT
65 AGTTTTTGAATTTATAATAATTTT
*
5938928 ATTTTTAATAAAAATTTTAAGTCTTCTATAAATTTTA-TTTTTAATTTTTAATTTATTTTTAATA
1 ATTTTTAATAAAAATTTTAAGTCTTCTATAAATTTTATTTTTTAATTTTTAATTTATTTCTAATA
*
5938992 TTTTTTGAATTTATAATAATTTT
66 GTTTTTGAATTTATAATAATTTT
*
5939015 ATTTTTAATAATGAATTTTA
1 ATTTTTAATAA-AAATTTTA
5939035 GTTTGGGTTT
Statistics
Matches: 100, Mismatches: 6, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
87 57 0.57
88 7 0.07
89 36 0.36
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (88 bp):
ATTTTTAATAAAAATTTTAAGTCTTCTATAAATTTTATTTTTTAATTTTTAATTTATTTCTAATA
GTTTTTGAATTTATAATAATTTT
Found at i:5940825 original size:19 final size:19
Alignment explanation
Indices: 5940779--5940825 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
5940769 ATATGTTTGT
*
5940779 AAAATATTATGAAATTTAAA
1 AAAATATTAT-AAATCTAAA
5940799 AAAA-ATTAT-AATCTAAA
1 AAAATATTATAAATCTAAA
5940816 ATAAATATTA
1 A-AAATATTA
5940826 AAACTAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 8 0.33
18 3 0.12
19 9 0.38
20 4 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (19 bp):
AAAATATTATAAATCTAAA
Found at i:5944530 original size:2 final size:2
Alignment explanation
Indices: 5944523--5944559 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5944513 TAAAGTTTAT
5944523 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5944560 GCGTTCATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5947588 original size:22 final size:23
Alignment explanation
Indices: 5947540--5947589 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
5947530 CAAAGAAAAT
* * *
5947540 ATAATCATCTAAAAGCTTGTTAT
1 ATAATCATCTAAAAGATTCTTAG
*
5947563 ATAATCATC-AAAAGATTCTTCG
1 ATAATCATCTAAAAGATTCTTAG
5947585 ATAAT
1 ATAAT
5947590 AATTTACTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (23 bp):
ATAATCATCTAAAAGATTCTTAG
Found at i:5953204 original size:20 final size:20
Alignment explanation
Indices: 5953179--5953219 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
5953169 TTTGGGGTTA
5953179 TTTGCAATTTATGTCCCTCC
1 TTTGCAATTTATGTCCCTCC
5953199 TTTGCAATTTATGTCCCTCC
1 TTTGCAATTTATGTCCCTCC
5953219 T
1 T
5953220 CATTTCACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.29, G:0.10, T:0.46
Consensus pattern (20 bp):
TTTGCAATTTATGTCCCTCC
Found at i:5954943 original size:22 final size:24
Alignment explanation
Indices: 5954893--5954943 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
5954883 TTGCAATGCT
5954893 TTTATATTTTAATAATTGAGTATTA
1 TTTATATTTTAAT-ATTGAGTATTA
5954918 -TTATATATTTAAT-TTGA-T-TTA
1 TTTATAT-TTTAATATTGAGTATTA
5954939 TTTAT
1 TTTAT
5954944 TTATAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
21 3 0.12
22 5 0.21
23 4 0.17
24 6 0.25
25 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (24 bp):
TTTATATTTTAATATTGAGTATTA
Found at i:5958708 original size:13 final size:13
Alignment explanation
Indices: 5958692--5958744 Score: 79
Period size: 13 Copynumber: 4.1 Consensus size: 13
5958682 TTTAAACCAA
5958692 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
5958705 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
* *
5958718 ACTTTTCTATAGC
1 ACTTTTCAAAAGC
5958731 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
5958744 A
1 A
5958745 ATGAAGAACT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:5961028 original size:16 final size:16
Alignment explanation
Indices: 5961009--5961050 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
5960999 GCTTTTTGAG
5961009 TTCAGGTTTTTTCAGA
1 TTCAGGTTTTTTCAGA
*
5961025 TTCA-GTTCTTTTCAGG
1 TTCAGGTT-TTTTCAGA
*
5961041 TTCAGATTTT
1 TTCAGGTTTT
5961051 ATCGGGTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.14
16 17 0.77
17 2 0.09
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (16 bp):
TTCAGGTTTTTTCAGA
Found at i:5962383 original size:3 final size:3
Alignment explanation
Indices: 5962375--5962404 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
5962365 TAGTCTTTTG
*
5962375 TTC TTC TTC TTC TTC ATC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
5962405 CATGTAACAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.03, C:0.33, G:0.00, T:0.63
Consensus pattern (3 bp):
TTC
Found at i:5965456 original size:28 final size:30
Alignment explanation
Indices: 5965401--5965458 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 30
5965391 TCATAACTTT
5965401 CTAAAATTGAGTAACCAATATATAAACATA
1 CTAAAATTGAGTAACCAATATATAAACATA
*
5965431 CTAATAATTTAGTAA-C-ATAT-TAAACATA
1 CTAA-AATTGAGTAACCAATATATAAACATA
5965459 TGTATTAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 8 0.31
29 4 0.15
30 5 0.19
31 9 0.35
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (30 bp):
CTAAAATTGAGTAACCAATATATAAACATA
Done.