Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 149 of 335
Found at i:43745295 original size:15 final size:15
Alignment explanation
Indices: 43745253--43745300 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
43745243 AATTTGATTA
43745253 TTTTTAGTTTTTATAT
1 TTTTTAG-TTTTATAT
*
43745269 TTTTTA-TATTTATTT
1 TTTTTAGT-TTTATAT
*
43745284 TTTTTAGTTTTAAAT
1 TTTTTAGTTTTATAT
43745299 TT
1 TT
43745301 ATTATTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
14 1 0.04
15 19 0.70
16 7 0.26
ACGTcount: A:0.21, C:0.00, G:0.04, T:0.75
Consensus pattern (15 bp):
TTTTTAGTTTTATAT
Found at i:43745295 original size:30 final size:32
Alignment explanation
Indices: 43745234--43745294 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
43745224 TTACTGCAGC
* *
43745234 TATTTTTCAAATTTGATTATTTTTAGTTTTTA
1 TATTTTTTATATTTGATTATTTTTAGTTTTTA
*
43745266 TATTTTTTATATTT-ATTTTTTTTAGTTTT
1 TATTTTTTATATTTGATTATTTTTAGTTTT
43745295 AAATTTATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 14 0.54
32 12 0.46
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (32 bp):
TATTTTTTATATTTGATTATTTTTAGTTTTTA
Found at i:43746089 original size:17 final size:17
Alignment explanation
Indices: 43746078--43746110 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
43746068 AATAAATATG
43746078 AAAA-AAATATAAAAAT
1 AAAATAAATATAAAAAT
43746094 AAAATAAATA-AAAAAT
1 AAAATAAATATAAAAAT
43746110 A
1 A
43746111 CAAAGAAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (17 bp):
AAAATAAATATAAAAAT
Found at i:43751642 original size:19 final size:19
Alignment explanation
Indices: 43751618--43751656 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
43751608 TTAGCAAGAT
43751618 AAATTGTCTTAATCGCATG
1 AAATTGTCTTAATCGCATG
*
43751637 AAATTGTCTTAATTGCATG
1 AAATTGTCTTAATCGCATG
43751656 A
1 A
43751657 TCTGAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (19 bp):
AAATTGTCTTAATCGCATG
Found at i:43759911 original size:33 final size:33
Alignment explanation
Indices: 43759874--43759943 Score: 131
Period size: 33 Copynumber: 2.1 Consensus size: 33
43759864 TCACCTATTT
43759874 TTTTACTTTAAAAATATATAATTTTTGTATATG
1 TTTTACTTTAAAAATATATAATTTTTGTATATG
*
43759907 TTTTACTTTGAAAATATATAATTTTTGTATATG
1 TTTTACTTTAAAAATATATAATTTTTGTATATG
43759940 TTTT
1 TTTT
43759944 TTTTTTATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (33 bp):
TTTTACTTTAAAAATATATAATTTTTGTATATG
Found at i:43762151 original size:19 final size:20
Alignment explanation
Indices: 43762122--43762159 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
43762112 AGAGACTAAA
43762122 ATGTATAAATTTTGAAATTG
1 ATGTATAAATTTTGAAATTG
*
43762142 ATGT-TAAATTTTGTAATT
1 ATGTATAAATTTTGAAATT
43762160 ATAGATAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 13 0.76
20 4 0.24
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (20 bp):
ATGTATAAATTTTGAAATTG
Found at i:43766651 original size:27 final size:27
Alignment explanation
Indices: 43766586--43766737 Score: 209
Period size: 27 Copynumber: 5.7 Consensus size: 27
43766576 TTTGGTTTAC
43766586 AAAATTACCAAAATA-CCCT-GCTTTGT
1 AAAATTACCAAAATACCCCTAG-TTTGT
* * * *
43766612 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAGTTTGT
43766639 AAAATTACCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
43766666 AAAATTATCAAAATACCCCTAGTTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
*
43766693 AAAATTACCAAAATACCCCTAATTTGT
1 AAAATTACCAAAATACCCCTAGTTTGT
* *
43766720 GAAATTACTAAAATACCC
1 AAAATTACCAAAATACCC
43766738 TCGACCTGTA
Statistics
Matches: 112, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
26 14 0.12
27 97 0.87
28 1 0.01
ACGTcount: A:0.42, C:0.20, G:0.07, T:0.31
Consensus pattern (27 bp):
AAAATTACCAAAATACCCCTAGTTTGT
Found at i:43766706 original size:81 final size:80
Alignment explanation
Indices: 43766586--43766809 Score: 227
Period size: 81 Copynumber: 2.8 Consensus size: 80
43766576 TTTGGTTTAC
* * * *
43766586 AAAATTACCAAAATACCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTATAAAATTACCAAA
1 AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
**
43766651 ATACCCCTAG-TTTGT
66 ATA-CCCTAGACCTGT
* * * * *
43766666 AAAATTATCAAAATACCCCT-AGTTTGTAAAATTACCAAAATACCCCTAATTTGTGAAATTACTA
1 AAAATTATCAAAATA-CCCTGA-TTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCA
*
43766730 AAATACCCTCGACCTGT
64 AAATACCCTAGACCTGT
** **** *
43766747 AAAATTATTGAAATACCCTCGATTTGTAAAATTACCGTTTTACCCTTGATTTATAGAATTACC
1 AAAATTATCAAAATACCCT-GATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACC
43766810 GTTTTACCCT
Statistics
Matches: 115, Mismatches: 24, Indels: 9
0.78 0.16 0.06
Matches are distributed among these distances:
80 23 0.20
81 91 0.79
82 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.08, T:0.33
Consensus pattern (80 bp):
AAAATTATCAAAATACCCTGATTTGTAAAATTACCAAAATACCCTTGATTTATAAAATTACCAAA
ATACCCTAGACCTGT
Found at i:43766748 original size:54 final size:54
Alignment explanation
Indices: 43766586--43766781 Score: 211
Period size: 54 Copynumber: 3.6 Consensus size: 54
43766576 TTTGGTTTAC
** * * *
43766586 AAAATTACCAAAATA-CCCTGCTTTGTAAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
* *
43766639 AAAATTACCAAAATACCCCTAGTTTGTAAAATTA-TCAAAATACCC-CTAGTTTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACT-AAAATACCCTCGA-TTTGT
* **
43766693 AAAATTACCAAAATACCCCTAATTTGTGAAATTACTAAAATACCCTCGACCTGT
1 AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
*** *
43766747 AAAATTATTGAAATA-CCCTCGATTTGTAAAATTAC
1 AAAATTACCAAAATACCCCT-AATTTGTAAAATTAC
43766782 CGTTTTACCC
Statistics
Matches: 121, Mismatches: 16, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
53 20 0.17
54 98 0.81
55 3 0.02
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (54 bp):
AAAATTACCAAAATACCCCTAATTTGTAAAATTACTAAAATACCCTCGATTTGT
Found at i:43766751 original size:27 final size:27
Alignment explanation
Indices: 43766586--43766781 Score: 186
Period size: 27 Copynumber: 7.3 Consensus size: 27
43766576 TTTGGTTTAC
* *
43766586 AAAATTACCAAAATACCCT-GCTTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* * *
43766612 AAAATTACTAAAATACCCTTGGTTTAT
1 AAAATTACTAAAATACCCTCGATTTGT
* *
43766639 AAAATTACCAAAATACCC-CTAGTTTGT
1 AAAATTACTAAAATACCCTCGA-TTTGT
*
43766666 AAAATTA-TCAAAATACCC-CTAGTTTGT
1 AAAATTACT-AAAATACCCTCGA-TTTGT
* *
43766693 AAAATTACCAAAATACCC-CTAATTTGT
1 AAAATTACTAAAATACCCTC-GATTTGT
* **
43766720 GAAATTACTAAAATACCCTCGACCTGT
1 AAAATTACTAAAATACCCTCGATTTGT
* *
43766747 AAAATTATTGAAATACCCTCGATTTGT
1 AAAATTACTAAAATACCCTCGATTTGT
43766774 AAAATTAC
1 AAAATTAC
43766782 CGTTTTACCC
Statistics
Matches: 142, Mismatches: 22, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
26 18 0.13
27 122 0.86
28 2 0.01
ACGTcount: A:0.41, C:0.20, G:0.08, T:0.32
Consensus pattern (27 bp):
AAAATTACTAAAATACCCTCGATTTGT
Found at i:43766790 original size:27 final size:27
Alignment explanation
Indices: 43766760--43767134 Score: 461
Period size: 27 Copynumber: 13.9 Consensus size: 27
43766750 ATTATTGAAA
** *
43766760 TACCCTCGATTTGTAAAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
43766787 TACCCTTGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
**
43766814 TACCCTC-AGTTTACAGAATTACTATTT
1 TACCCTCGA-TTTACAGAATTACCGTTT
*
43766841 TACCCTCGATTTATAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
43766868 TACCC-CTAATTTACATAATTACCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
* * *
43766895 TACCC-CTGATTTACATAATTATCATTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
43766922 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* * *
43766949 TACCCACAATTTACATAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
43766976 TACCC-CTGATTTACATAATTATCGTTT
1 TACCCTC-GATTTACAGAATTACCGTTT
*
43767003 TACCCTCGACTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
43767030 TACCCTCGATTTACAGAATTACCGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
43767057 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
* *
43767084 TACCCTTGATTTACAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACCGTTT
*
43767111 TACCCTCGATTTACAAAATTACCG
1 TACCCTCGATTTACAGAATTACCG
43767135 AAATACCCTC
Statistics
Matches: 305, Mismatches: 37, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
26 3 0.01
27 299 0.98
28 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.09, T:0.40
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACCGTTT
Found at i:43767176 original size:27 final size:27
Alignment explanation
Indices: 43767113--43767210 Score: 83
Period size: 27 Copynumber: 3.6 Consensus size: 27
43767103 TACTGTTTTA
* *
43767113 CCCTCGATTTACAAAATTACCGAAATA-
1 CCCT-GATTTATAAAATTACCAAAATAC
* *
43767140 CCCTCAATTTGTAAAATTACCAAAATAC
1 CCCT-GATTTATAAAATTACCAAAATAC
*
43767168 CCCTGATTTATAAAGTTA-CAGAAATAC
1 CCCTGATTTATAAAATTACCA-AAATAC
* *
43767195 CCTTGACTTTTTAAAA
1 CCCTGA-TTTATAAAA
43767211 ATTATAGAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
26 2 0.03
27 45 0.78
28 11 0.19
ACGTcount: A:0.40, C:0.22, G:0.07, T:0.31
Consensus pattern (27 bp):
CCCTGATTTATAAAATTACCAAAATAC
Found at i:43767251 original size:27 final size:26
Alignment explanation
Indices: 43767204--43767259 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
43767194 CCCTTGACTT
*
43767204 TTTAAAAATTATAGAAGTACCATTGG
1 TTTAAAAATTATAGAAATACCATTGG
*
43767230 TTTACAAAATTACT-GAAATACCTTTGG
1 TTTA-AAAATTA-TAGAAATACCATTGG
43767257 TTT
1 TTT
43767260 GTTGATTTAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 21 0.81
28 1 0.04
ACGTcount: A:0.38, C:0.11, G:0.12, T:0.39
Consensus pattern (26 bp):
TTTAAAAATTATAGAAATACCATTGG
Found at i:43767377 original size:27 final size:27
Alignment explanation
Indices: 43767313--43767377 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
43767303 ACCCCTAAAA
*
43767313 GGTAAAAAGACCGTAAAGCCCCTGTAG
1 GGTAAAATGACCGTAAAGCCCCTGTAG
* *
43767340 GGTAAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAATGACCGTAA-AGCCCCTGTAG
43767367 GGTAAAATGAC
1 GGTAAAATGAC
43767378 GAATATGCCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 32 0.97
28 1 0.03
ACGTcount: A:0.35, C:0.20, G:0.25, T:0.20
Consensus pattern (27 bp):
GGTAAAATGACCGTAAAGCCCCTGTAG
Found at i:43768563 original size:25 final size:25
Alignment explanation
Indices: 43768534--43768581 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43768524 TTATAATATG
* * *
43768534 AAAATGACCGTTTTGCCCCTAGGTA
1 AAAATGACCATTATACCCCTAGGTA
43768559 AAAATGACCATTATACCCCTAGG
1 AAAATGACCATTATACCCCTAGG
43768582 GTTTATGTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.33, C:0.25, G:0.17, T:0.25
Consensus pattern (25 bp):
AAAATGACCATTATACCCCTAGGTA
Found at i:43768650 original size:20 final size:20
Alignment explanation
Indices: 43768625--43768683 Score: 100
Period size: 20 Copynumber: 3.0 Consensus size: 20
43768615 TAAATATGGT
43768625 ATGTATGATATGCACATGAA
1 ATGTATGATATGCACATGAA
* *
43768645 ATGTATGCTATGCACATGAT
1 ATGTATGATATGCACATGAA
43768665 ATGTATGATATGCACATGA
1 ATGTATGATATGCACATGA
43768684 GGTAATCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.32
Consensus pattern (20 bp):
ATGTATGATATGCACATGAA
Found at i:43768817 original size:23 final size:24
Alignment explanation
Indices: 43768734--43768899 Score: 248
Period size: 24 Copynumber: 7.0 Consensus size: 24
43768724 GAGGAAGTGA
43768734 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43768758 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43768782 AAAAGGGCTTATGCCCCAGTTATC
1 AAAAGGGCTTATGCCCCAGTTATC
43768806 AAAA-GGCTTATGCCCCAGTTAT-
1 AAAAGGGCTTATGCCCCAGTTATC
*
43768828 AAAAGGGCTTATGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
* * *
43768852 GAAAGGGCTTTTGCCCCAGTTATT
1 AAAAGGGCTTATGCCCCAGTTATC
*
43768876 AAAAGAGGC-TAGGCCTCCAGTTAT
1 AAAAG-GGCTTATGCC-CCAGTTAT
43768900 ATGATAAAGC
Statistics
Matches: 133, Mismatches: 5, Indels: 7
0.92 0.03 0.05
Matches are distributed among these distances:
22 4 0.03
23 36 0.27
24 82 0.62
25 11 0.08
ACGTcount: A:0.29, C:0.23, G:0.22, T:0.27
Consensus pattern (24 bp):
AAAAGGGCTTATGCCCCAGTTATC
Found at i:43768857 original size:70 final size:71
Alignment explanation
Indices: 43768734--43768880 Score: 242
Period size: 70 Copynumber: 2.1 Consensus size: 71
43768724 GAGGAAGTGA
43768734 AAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
1 AAAA-GGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCC
43768799 AGTTATC
65 AGTTATC
** *
43768806 AAAAGGCTTATGCCCCAGTTAT-AAAAGGGCTTATGCCCCAGTTATTGAAAGGGCTTTTGCCCCA
1 AAAAGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
*
43768870 GTTATT
66 GTTATC
43768876 AAAAG
1 AAAAG
43768881 AGGCTAGGCC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
70 49 0.69
71 18 0.25
72 4 0.06
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (71 bp):
AAAAGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCAGTTATCAAAAGGGCTTATGCCCCA
GTTATC
Found at i:43769127 original size:31 final size:31
Alignment explanation
Indices: 43769091--43769185 Score: 163
Period size: 31 Copynumber: 3.1 Consensus size: 31
43769081 CGTTTACAGT
*
43769091 AAAGGCTTCGGCCTAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
43769122 AAAGGCTTCGGCCCAGTAATATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
* *
43769153 AAATGCTTCGGCCCAGTATTATGAAATATGA
1 AAAGGCTTCGGCCCAGTAATATGAAATATGA
43769184 AA
1 AA
43769186 TATGAAAAGG
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 61 1.00
ACGTcount: A:0.39, C:0.15, G:0.21, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTAATATGAAATATGA
Found at i:43773985 original size:23 final size:23
Alignment explanation
Indices: 43773940--43773987 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
43773930 GAGTAAACCA
*
43773940 TTTTATTTTTTTATTTCATTTAG
1 TTTTATTTTTTTATTTCAATTAG
*
43773963 TTTTCTTTTTTTAATTT-AATTAG
1 TTTTATTTTTTT-ATTTCAATTAG
43773986 TT
1 TT
43773988 AAAGTTGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 18 0.82
24 4 0.18
ACGTcount: A:0.19, C:0.04, G:0.04, T:0.73
Consensus pattern (23 bp):
TTTTATTTTTTTATTTCAATTAG
Found at i:43778453 original size:27 final size:28
Alignment explanation
Indices: 43778423--43778494 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 28
43778413 ACACGTCAAG
*
43778423 AAAGAAAGA-CCTTTATGGCGAACTCTA
1 AAAGAAAGAGCCTTTATGGAGAACTCTA
* *
43778450 AAAGAAA-AGCCTTTTTGGAGAACTCTG
1 AAAGAAAGAGCCTTTATGGAGAACTCTA
*
43778477 GAAG-AAGAGCCTTTATGG
1 AAAGAAAGAGCCTTTATGG
43778495 TGAATTCTGT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
26 3 0.08
27 35 0.92
ACGTcount: A:0.38, C:0.15, G:0.24, T:0.24
Consensus pattern (28 bp):
AAAGAAAGAGCCTTTATGGAGAACTCTA
Found at i:43778503 original size:27 final size:27
Alignment explanation
Indices: 43778422--43778503 Score: 85
Period size: 27 Copynumber: 3.0 Consensus size: 27
43778412 AACACGTCAA
*
43778422 GAAAGAA-AGACCTTTATGGCGAACTCT
1 GAAAGAAGAG-CCTTTATGGAGAACTCT
* * *
43778449 AAAAGAAAAGCCTTTTTGGAGAACTCT
1 GAAAGAAGAGCCTTTATGGAGAACTCT
* * *
43778476 GGAAGAAGAGCCTTTATGGTGAATTCT
1 GAAAGAAGAGCCTTTATGGAGAACTCT
43778503 G
1 G
43778504 TATGGACTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
27 43 0.96
28 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.26
Consensus pattern (27 bp):
GAAAGAAGAGCCTTTATGGAGAACTCT
Found at i:43778729 original size:35 final size:35
Alignment explanation
Indices: 43778647--43778739 Score: 98
Period size: 35 Copynumber: 2.7 Consensus size: 35
43778637 TTCATGATGT
* *
43778647 CACTTCGTAGAGCCAATAGATCATTTTCGTAATGC
1 CACTCCGTAGAGCCAATAGATCATTTTCGTAATAC
** * * *
43778682 TGCTCCAG-AGAGCTAATAGATCATTTTTGTGATAC
1 CACTCC-GTAGAGCCAATAGATCATTTTCGTAATAC
*
43778717 CACTCCGTAGAGCCAGTAGATCA
1 CACTCCGTAGAGCCAATAGATCA
43778740 ATCTTCCAAC
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
34 1 0.02
35 43 0.96
36 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.29
Consensus pattern (35 bp):
CACTCCGTAGAGCCAATAGATCATTTTCGTAATAC
Found at i:43782963 original size:9 final size:9
Alignment explanation
Indices: 43782949--43782973 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
43782939 TTTTATTTTC
43782949 AATTAATTA
1 AATTAATTA
43782958 AATTAATTA
1 AATTAATTA
43782967 AATTAAT
1 AATTAAT
43782974 AATTAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
AATTAATTA
Found at i:43784630 original size:3 final size:3
Alignment explanation
Indices: 43784622--43784658 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
43784612 CTTTTTAAGC
43784622 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
43784659 ACACCACCGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:43794500 original size:14 final size:15
Alignment explanation
Indices: 43794483--43794511 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
43794473 TCCTCTCCCA
43794483 TTTCTT-TTTTCTTT
1 TTTCTTCTTTTCTTT
43794497 TTTCTTCTTTTCTTT
1 TTTCTTCTTTTCTTT
43794512 CTGTTATAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTCTTCTTTTCTTT
Found at i:43820837 original size:20 final size:20
Alignment explanation
Indices: 43820808--43820891 Score: 89
Period size: 20 Copynumber: 4.2 Consensus size: 20
43820798 GAATTATTGC
*
43820808 ACTTATGTGCCCCTGTTTGT
1 ACTTACGTGCCCCTGTTTGT
*
43820828 ACTTACGTGCCCCTATTTGT
1 ACTTACGTGCCCCTGTTTGT
* * * *
43820848 ACTT-CGATACCTCTGATTGC
1 ACTTACG-TGCCCCTGTTTGT
*
43820868 ACTTATGTGCCCCTGTTTGT
1 ACTTACGTGCCCCTGTTTGT
43820888 ACTT
1 ACTT
43820892 CGATACCCCT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
19 2 0.04
20 47 0.94
21 1 0.02
ACGTcount: A:0.14, C:0.27, G:0.17, T:0.42
Consensus pattern (20 bp):
ACTTACGTGCCCCTGTTTGT
Found at i:43820900 original size:20 final size:20
Alignment explanation
Indices: 43820817--43820902 Score: 77
Period size: 20 Copynumber: 4.3 Consensus size: 20
43820807 CACTTATGTG
*
43820817 CCCCTGTTTGTACTTACGTG
1 CCCCTGTTTGTACTTACGTA
*
43820837 CCCCTATTTGTACTT-CGATA
1 CCCCTGTTTGTACTTACG-TA
* * * * *
43820857 CCTCTGATTGCACTTATGTG
1 CCCCTGTTTGTACTTACGTA
43820877 CCCCTGTTTGTACTT-CGATA
1 CCCCTGTTTGTACTTACG-TA
43820897 CCCCTG
1 CCCCTG
43820903 AATGCATATC
Statistics
Matches: 50, Mismatches: 13, Indels: 6
0.72 0.19 0.09
Matches are distributed among these distances:
19 3 0.06
20 46 0.92
21 1 0.02
ACGTcount: A:0.14, C:0.31, G:0.16, T:0.38
Consensus pattern (20 bp):
CCCCTGTTTGTACTTACGTA
Found at i:43820919 original size:40 final size:40
Alignment explanation
Indices: 43820828--43820908 Score: 126
Period size: 40 Copynumber: 2.0 Consensus size: 40
43820818 CCCTGTTTGT
* * * *
43820828 ACTTACGTGCCCCTATTTGTACTTCGATACCTCTGATTGC
1 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
43820868 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
1 ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
43820908 A
1 A
43820909 TATCTGTGCC
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (40 bp):
ACTTATGTGCCCCTGTTTGTACTTCGATACCCCTGAATGC
Found at i:43824948 original size:70 final size:70
Alignment explanation
Indices: 43824834--43824974 Score: 255
Period size: 70 Copynumber: 2.0 Consensus size: 70
43824824 AGGCATTGAC
*
43824834 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAGATTATTGCATTTTAAAGTTTATACG
1 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
43824899 AGCTT
66 AGCTT
* *
43824904 ATATGGTTATTTACAACTTATAAAGTTGTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
1 ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
43824969 AGCTT
66 AGCTT
43824974 A
1 A
43824975 CTAAGCATTC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.36, C:0.08, G:0.13, T:0.43
Consensus pattern (70 bp):
ATATGGTTATTTACAACATATAAAGTTCTTATTGAAATAAATTATTGCATTTTAAAGTTTATACG
AGCTT
Found at i:43829015 original size:18 final size:18
Alignment explanation
Indices: 43828965--43829015 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
43828955 TCTTCCAGGG
43828965 TTAGGGTTTTTA-TTTTA
1 TTAGGGTTTTTATTTTTA
**
43828982 TTAGGG-TTAGAGTTTTTA
1 TTAGGGTTTTTA-TTTTTA
43829000 TTAGGGTTTTTATTTT
1 TTAGGGTTTTTATTTT
43829016 GGGTTTAGAG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 3 0.11
17 6 0.22
18 15 0.56
19 3 0.11
ACGTcount: A:0.18, C:0.00, G:0.22, T:0.61
Consensus pattern (18 bp):
TTAGGGTTTTTATTTTTA
Found at i:43830693 original size:19 final size:18
Alignment explanation
Indices: 43830665--43830707 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 18
43830655 TTTAAAAACA
* *
43830665 AGAGACTTGAGAGGGTTTG
1 AGAGAATTGAGAGAG-TTG
43830684 AGAGAATTGAGAGAGTTG
1 AGAGAATTGAGAGAGTTG
43830702 AGAGAA
1 AGAGAA
43830708 GGATGTGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 9 0.41
19 13 0.59
ACGTcount: A:0.37, C:0.02, G:0.40, T:0.21
Consensus pattern (18 bp):
AGAGAATTGAGAGAGTTG
Found at i:43837993 original size:18 final size:19
Alignment explanation
Indices: 43837970--43838006 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
43837960 GTTTCTTTTC
43837970 ACTTTCCCCA-TTTTTCCT
1 ACTTTCCCCACTTTTTCCT
*
43837988 ACTTTCTCCACTTTTTCCT
1 ACTTTCCCCACTTTTTCCT
43838007 TCACGTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.11, C:0.38, G:0.00, T:0.51
Consensus pattern (19 bp):
ACTTTCCCCACTTTTTCCT
Found at i:43840993 original size:47 final size:47
Alignment explanation
Indices: 43840930--43841271 Score: 558
Period size: 47 Copynumber: 7.3 Consensus size: 47
43840920 CCCTTCGGGA
* *
43840930 CTTATCACATTTATACACTTTCACATCCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* * * * *
43840977 CTTATCACATATATACACCTTCACATCCATCACATCGGCCATTAGGT
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43841024 CTTATCTCATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43841071 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
* *
43841118 CTTGTCACATATATACACTTTCACATTCACCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43841165 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
*
43841212 CTTGTCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
43841259 CTTATCACATATA
1 CTTATCACATATA
43841272 CATATCTTGT
Statistics
Matches: 271, Mismatches: 24, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
47 271 1.00
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATTGGCCATTCGGC
Found at i:43841196 original size:25 final size:25
Alignment explanation
Indices: 43841122--43841199 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
43841112 TTAGGCCTTG
43841122 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
* ** * * *
43841147 CCACAT-T-GGC-CATTCGGCCTT-A
1 TCACATATATACACTTTC-ACATTCA
43841169 TCACATATATACACTTTCACATTCA
1 TCACATATATACACTTTCACATTCA
43841194 TCACAT
1 TCACAT
43841200 TGGCCATTAG
Statistics
Matches: 36, Mismatches: 12, Indels: 10
0.62 0.21 0.17
Matches are distributed among these distances:
22 10 0.28
23 5 0.14
24 5 0.14
25 16 0.44
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (25 bp):
TCACATATATACACTTTCACATTCA
Found at i:43849027 original size:29 final size:29
Alignment explanation
Indices: 43848985--43849040 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
43848975 GAAATAACAA
43848985 CAAATATGTGCTATAATAGGGTTCCAAAT
1 CAAATATGTGCTATAATAGGGTTCCAAAT
43849014 CAAATATGTGCTATAATAGGGTTCCAA
1 CAAATATGTGCTATAATAGGGTTCCAA
43849041 CTAATTCGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (29 bp):
CAAATATGTGCTATAATAGGGTTCCAAAT
Found at i:43850600 original size:44 final size:44
Alignment explanation
Indices: 43850551--43850641 Score: 173
Period size: 44 Copynumber: 2.1 Consensus size: 44
43850541 TTTGAAAATG
*
43850551 GTTTGAAGGTGATTTGGTAAGTATATGTTATGTAAGTTAACTAT
1 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
43850595 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
1 GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
43850639 GTT
1 GTT
43850642 GGTACATTTG
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 46 1.00
ACGTcount: A:0.29, C:0.03, G:0.25, T:0.43
Consensus pattern (44 bp):
GTTTGAAGGTGATTTGGTAAGTATACGTTATGTAAGTTAACTAT
Found at i:43851718 original size:2 final size:2
Alignment explanation
Indices: 43851711--43851748 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
43851701 AAGGTATGTG
43851711 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
43851749 GCATGAATTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43852167 original size:46 final size:47
Alignment explanation
Indices: 43852055--43852169 Score: 128
Period size: 46 Copynumber: 2.5 Consensus size: 47
43852045 CTGCACTATC
* * **
43852055 TAGTGGTTTAA-C-CATATATCTATTCTGGCAGCTTGGTTGCAATTA
1 TAGTGGCTTAACCACATATATCTGTTCTGGCAGCTTGACTGCAATTA
* * * *
43852100 TAGTGGCTTAACCACACATATCTGTTTTGGTAGCTTGACTGCAA-TG
1 TAGTGGCTTAACCACATATATCTGTTCTGGCAGCTTGACTGCAATTA
*
43852146 TAGTGGCTTGACCACATATATCTG
1 TAGTGGCTTAACCACATATATCTG
43852170 ATAAATCGTA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
45 10 0.17
46 24 0.41
47 24 0.41
ACGTcount: A:0.24, C:0.18, G:0.21, T:0.37
Consensus pattern (47 bp):
TAGTGGCTTAACCACATATATCTGTTCTGGCAGCTTGACTGCAATTA
Found at i:43871517 original size:55 final size:55
Alignment explanation
Indices: 43871398--43871519 Score: 156
Period size: 55 Copynumber: 2.2 Consensus size: 55
43871388 CGAAATGACA
* * * *
43871398 GTGGGCGAACCTGCCAAAACAACACGGGCGTTCGACACGCCCGTGTCTAGAACCC
1 GTGGCCGAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCAAGAACCC
* * *
43871453 ATGGCCGAACCTGTCAAATCAACACGGGCGTGCGACACGCCCGTGCCAAGCAA-CC
1 GTGGCCGAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCAAG-AACCC
*
43871508 GTGGTCGAACCT
1 GTGGCCGAACCT
43871520 ATTAAACTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
55 55 0.96
56 2 0.04
ACGTcount: A:0.25, C:0.34, G:0.27, T:0.13
Consensus pattern (55 bp):
GTGGCCGAACCTGCCAAAACAACACGGGCGTGCGACACGCCCGTGCCAAGAACCC
Found at i:43871532 original size:55 final size:55
Alignment explanation
Indices: 43871414--43871539 Score: 141
Period size: 55 Copynumber: 2.3 Consensus size: 55
43871404 GAACCTGCCA
* * * *
43871414 AAAC-AACACGGGCGTTCGACACGCCCGTGTCTAGAACCCATGGCCGAACCTGTC
1 AAACTAACACGGGCGTGCGACACGCCCGTGCCAAGAACCCATGGCCGAACCTATC
* * *
43871468 AAA-TCAACACGGGCGTGCGACACGCCCGTGCCAAGCAA-CCGTGGTCGAACCTATT
1 AAACT-AACACGGGCGTGCGACACGCCCGTGCCAAG-AACCCATGGCCGAACCTATC
*
43871523 AAACTAACACAGGCGTG
1 AAACTAACACGGGCGTG
43871540 GGCATACATA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
54 3 0.05
55 54 0.90
56 3 0.05
ACGTcount: A:0.29, C:0.33, G:0.25, T:0.14
Consensus pattern (55 bp):
AAACTAACACGGGCGTGCGACACGCCCGTGCCAAGAACCCATGGCCGAACCTATC
Found at i:43871954 original size:16 final size:16
Alignment explanation
Indices: 43871935--43871979 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
43871925 TTATTAACAC
43871935 TATTTTTTATTATTTT
1 TATTTTTTATTATTTT
* *
43871951 TATTTTTTA-GACTTT
1 TATTTTTTATTATTTT
43871966 TATTTTATTATTAT
1 TATTTT-TTATTAT
43871980 CAATATCGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
15 10 0.43
16 12 0.52
17 1 0.04
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.73
Consensus pattern (16 bp):
TATTTTTTATTATTTT
Found at i:43875063 original size:37 final size:37
Alignment explanation
Indices: 43875022--43875094 Score: 137
Period size: 37 Copynumber: 2.0 Consensus size: 37
43875012 CGAAAATCAT
43875022 GATCACTCTGCTGACACTTTTCTGACCCACTCAAATC
1 GATCACTCTGCTGACACTTTTCTGACCCACTCAAATC
*
43875059 GATCACTCTGCTGACACTTTTTTGACCCACTCAAAT
1 GATCACTCTGCTGACACTTTTCTGACCCACTCAAAT
43875095 TTAACATCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.32
Consensus pattern (37 bp):
GATCACTCTGCTGACACTTTTCTGACCCACTCAAATC
Found at i:43878391 original size:39 final size:43
Alignment explanation
Indices: 43878341--43878454 Score: 119
Period size: 44 Copynumber: 2.7 Consensus size: 43
43878331 CTGTACACAA
* **
43878341 CACTTAGTGTGTGA-ATTGAAATAGCTTTGGTTC-A-TG-TGG
1 CACTAAGTGTGTGATACCGAAATAGCTTTGGTTCAAGTGATGG
*
43878380 CACTAAGTGTGTGATACCGAGATAGCTTTGGTTCAATGTGATGG
1 CACTAAGTGTGTGATACCGAAATAGCTTTGGTTCAA-GTGATGG
* * **
43878424 CACTAAGTGTGCGATATCGCTATAGCTTTGG
1 CACTAAGTGTGTGATACCGAAATAGCTTTGG
43878455 CTAAACATTT
Statistics
Matches: 62, Mismatches: 8, Indels: 5
0.83 0.11 0.07
Matches are distributed among these distances:
39 13 0.21
40 16 0.26
41 1 0.02
43 2 0.03
44 30 0.48
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (43 bp):
CACTAAGTGTGTGATACCGAAATAGCTTTGGTTCAAGTGATGG
Found at i:43878405 original size:40 final size:43
Alignment explanation
Indices: 43878361--43878454 Score: 122
Period size: 44 Copynumber: 2.2 Consensus size: 43
43878351 GTGAATTGAA
*
43878361 ATAGCTTTGGTTC-A-TG-TGGCACTAAGTGTGTGATACCGAG
1 ATAGCTTTGGTTCAAGTGATGGCACTAAGTGTGCGATACCGAG
* **
43878401 ATAGCTTTGGTTCAATGTGATGGCACTAAGTGTGCGATATCGCT
1 ATAGCTTTGGTTCAA-GTGATGGCACTAAGTGTGCGATACCGAG
43878445 ATAGCTTTGG
1 ATAGCTTTGG
43878455 CTAAACATTT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
40 13 0.28
41 1 0.02
43 2 0.04
44 30 0.65
ACGTcount: A:0.22, C:0.15, G:0.29, T:0.34
Consensus pattern (43 bp):
ATAGCTTTGGTTCAAGTGATGGCACTAAGTGTGCGATACCGAG
Found at i:43878638 original size:40 final size:40
Alignment explanation
Indices: 43878603--43878681 Score: 140
Period size: 40 Copynumber: 2.0 Consensus size: 40
43878593 TTGATACTAT
*
43878603 GTGTATGAAACTTGATGAAATGGTATATACATGATAAATC
1 GTGTATAAAACTTGATGAAATGGTATATACATGATAAATC
*
43878643 GTGTATAAAACTTGATGAAATGGTTTATACATGATAAAT
1 GTGTATAAAACTTGATGAAATGGTATATACATGATAAAT
43878682 GGTTATGAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.41, C:0.06, G:0.19, T:0.34
Consensus pattern (40 bp):
GTGTATAAAACTTGATGAAATGGTATATACATGATAAATC
Found at i:43878683 original size:18 final size:19
Alignment explanation
Indices: 43878615--43878685 Score: 65
Period size: 19 Copynumber: 3.7 Consensus size: 19
43878605 GTATGAAACT
*
43878615 TGATGAAATGGTATATACA
1 TGATGAAATGGTTTATACA
* * *
43878634 TGAT-AAATCGTGTATAAAACT
1 TGATGAAAT-G-GT-TTATACA
43878655 TGATGAAATGGTTTATACA
1 TGATGAAATGGTTTATACA
43878674 TGAT-AAATGGTT
1 TGATGAAATGGTT
43878686 ATGAATTAGA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
18 12 0.29
19 13 0.32
20 4 0.10
21 8 0.20
22 4 0.10
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (19 bp):
TGATGAAATGGTTTATACA
Found at i:43882507 original size:32 final size:32
Alignment explanation
Indices: 43882466--43882531 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
43882456 TATTTGATCG
43882466 AAGCTCCAGTGTTAGTTCAGCTAGAACCAGGA
1 AAGCTCCAGTGTTAGTTCAGCTAGAACCAGGA
*
43882498 AAGCTCCAGTGTTTGTTCAGCTAGAACCAGGA
1 AAGCTCCAGTGTTAGTTCAGCTAGAACCAGGA
43882530 AA
1 AA
43882532 AGAATTTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (32 bp):
AAGCTCCAGTGTTAGTTCAGCTAGAACCAGGA
Found at i:43886283 original size:17 final size:17
Alignment explanation
Indices: 43886261--43886295 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
43886251 TAGAAATGGT
43886261 AAGTTTTATGTCATATA
1 AAGTTTTATGTCATATA
43886278 AAGTTTTATGTCATATA
1 AAGTTTTATGTCATATA
43886295 A
1 A
43886296 TAGGTGTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.37, C:0.06, G:0.11, T:0.46
Consensus pattern (17 bp):
AAGTTTTATGTCATATA
Found at i:43887845 original size:28 final size:28
Alignment explanation
Indices: 43887812--43887867 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
43887802 CACTTAACAT
43887812 GCATAACTAATACATTTATGCATTCATA
1 GCATAACTAATACATTTATGCATTCATA
43887840 GCATAACTAATACATTTATGCATTCATA
1 GCATAACTAATACATTTATGCATTCATA
43887868 CTCAAATACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (28 bp):
GCATAACTAATACATTTATGCATTCATA
Found at i:43887875 original size:24 final size:27
Alignment explanation
Indices: 43887820--43887882 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 27
43887810 ATGCATAACT
*
43887820 AATACATTTATGCATTCATAGCATAACT
1 AATACATTTATGCATTCATAGCAT-ACA
43887848 AATACATTTATGCATTCATA-C-T-CA
1 AATACATTTATGCATTCATAGCATACA
43887872 AATACCATTTA
1 AATA-CATTTA
43887883 ATCACAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
24 5 0.15
25 6 0.18
26 1 0.03
27 1 0.03
28 20 0.61
ACGTcount: A:0.40, C:0.19, G:0.05, T:0.37
Consensus pattern (27 bp):
AATACATTTATGCATTCATAGCATACA
Found at i:43897487 original size:19 final size:20
Alignment explanation
Indices: 43897463--43897500 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
43897453 GGTACCACCA
43897463 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
43897482 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
43897501 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:43897829 original size:46 final size:46
Alignment explanation
Indices: 43897724--43897848 Score: 207
Period size: 46 Copynumber: 2.7 Consensus size: 46
43897714 AACCCGCCCC
* *
43897724 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
* *
43897769 TAAATGAACTCGGACTCAACTCAACGAGTTCGGACATTTGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
43897815 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
43897849 TGCTCAACCA
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
45 31 0.42
46 43 0.58
ACGTcount: A:0.30, C:0.27, G:0.21, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
Found at i:43897867 original size:46 final size:45
Alignment explanation
Indices: 43897726--43897867 Score: 137
Period size: 46 Copynumber: 3.1 Consensus size: 45
43897716 CCCGCCCCTA
* * *
43897726 AGTGAACTCGGACTCAACTCAACGAGCTCGG-CGTTC-GCATCCAT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
* ** **
43897770 AAATGAACTCGGACTCAACTCAACGAGTTCGGACATT-TGCATCCAT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCC-T
*
43897816 AAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTC-ACCATCCT
43897863 AGTGA
1 AGTGA
43897868 CATGTCACTT
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
45 29 0.35
46 49 0.58
47 1 0.01
48 5 0.06
ACGTcount: A:0.30, C:0.28, G:0.20, T:0.22
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGTTCACCATCCT
Found at i:43902180 original size:28 final size:28
Alignment explanation
Indices: 43902135--43902231 Score: 178
Period size: 28 Copynumber: 3.5 Consensus size: 28
43902125 CTTAAAACCC
*
43902135 TAGGGGT-ATATCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
43902162 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
43902190 TAGGGGTAATTTCGGTAATTTTGCTCTT
1 TAGGGGTAATTTCGGTAATTTTGCTCTT
43902218 TAGGGGTAATTTCG
1 TAGGGGTAATTTCG
43902232 TGATCTACGC
Statistics
Matches: 68, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
27 7 0.10
28 61 0.90
ACGTcount: A:0.19, C:0.10, G:0.27, T:0.44
Consensus pattern (28 bp):
TAGGGGTAATTTCGGTAATTTTGCTCTT
Found at i:43904083 original size:19 final size:18
Alignment explanation
Indices: 43904046--43904089 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43904036 ATACATACAG
43904046 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
43904063 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
43904082 TACTAATT
1 TAATAATT
43904090 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:43906509 original size:19 final size:19
Alignment explanation
Indices: 43906485--43906532 Score: 78
Period size: 21 Copynumber: 2.4 Consensus size: 19
43906475 GGGGTATATC
43906485 GGTAATTTTGCTCTTTAGG
1 GGTAATTTTGCTCTTTAGG
43906504 GGTAATTTTTTGCTCTTTAGG
1 GGTAA--TTTTGCTCTTTAGG
43906525 GGTAATTT
1 GGTAATTT
43906533 CGGTAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 8 0.30
21 19 0.70
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (19 bp):
GGTAATTTTGCTCTTTAGG
Found at i:43906516 original size:21 final size:21
Alignment explanation
Indices: 43906490--43906532 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
43906480 ATATCGGTAA
43906490 TTTTGCTCTTTAGGGGTAATT
1 TTTTGCTCTTTAGGGGTAATT
43906511 TTTTGCTCTTTAGGGGTAATT
1 TTTTGCTCTTTAGGGGTAATT
43906532 T
1 T
43906533 CGGTAATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.14, C:0.09, G:0.23, T:0.53
Consensus pattern (21 bp):
TTTTGCTCTTTAGGGGTAATT
Found at i:43908406 original size:19 final size:18
Alignment explanation
Indices: 43908369--43908412 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
43908359 ATACATACAG
43908369 TAAT-ATTTTTCTAATAA
1 TAATAATTTTTCTAATAA
*
43908386 TAATAATTTTATCTCATAA
1 TAATAATTTT-TCTAATAA
*
43908405 TACTAATT
1 TAATAATT
43908413 AAAATTTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 4 0.17
18 5 0.22
19 14 0.61
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATAATTTTTCTAATAA
Found at i:43912620 original size:19 final size:20
Alignment explanation
Indices: 43912596--43912633 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
43912586 GGTACCACCA
43912596 AAACAT-ATATCA-CATCTTT
1 AAACATCAT-TCATCATCTTT
43912615 AAACATCATTCATCATCTT
1 AAACATCATTCATCATCTT
43912634 ACCACCTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.24, G:0.00, T:0.37
Consensus pattern (20 bp):
AAACATCATTCATCATCTTT
Found at i:43916734 original size:46 final size:49
Alignment explanation
Indices: 43916551--43916734 Score: 150
Period size: 46 Copynumber: 3.9 Consensus size: 49
43916541 GGGAAAGTGT
* * * * * *
43916551 CGATGCCATGTCCCAAACGTGGTCTTACACTAGCTCTCGCCT-ATCCGT-GT
1 CGATGCCATGTCCCAGACATAGTCTTACACTAG--CTCACATAAT-CGTAGC
* * * *
43916601 CGATGCCATGTCCCAGACATGGTCTTACACTA--ACACA-ACTCTTAGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTAGCTCACATAATCGTAGC
* * ** *
43916647 CGATGCCATGTCCCAGGCATAGTCTTACACTGGCTTTCATAAT-GTGGC
1 CGATGCCATGTCCCAGACATAGTCTTACACTAGCTCACATAATCGTAGC
43916695 CGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCACATAA
1 CGATGCCATGTCCCAGACATAGTCTTACACTAGCTCACATAA
43916735 GTGACCCAAA
Statistics
Matches: 108, Mismatches: 21, Indels: 14
0.76 0.15 0.10
Matches are distributed among these distances:
45 2 0.02
46 51 0.47
47 13 0.12
48 10 0.09
49 2 0.02
50 30 0.28
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (49 bp):
CGATGCCATGTCCCAGACATAGTCTTACACTAGCTCACATAATCGTAGC
Found at i:43923025 original size:22 final size:23
Alignment explanation
Indices: 43922983--43923025 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
43922973 TGGGTAGGAA
43922983 GTTTTCTAGAAAATTTGCATTTT
1 GTTTTCTAGAAAATTTGCATTTT
43923006 GTTTTCT--AAAATATTGCATT
1 GTTTTCTAGAAAAT-TTGCATT
43923026 AGCATAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 7 0.37
23 7 0.37
ACGTcount: A:0.28, C:0.09, G:0.12, T:0.51
Consensus pattern (23 bp):
GTTTTCTAGAAAATTTGCATTTT
Found at i:43923698 original size:30 final size:29
Alignment explanation
Indices: 43923662--43923719 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
43923652 GTAATTTCTG
*
43923662 AAAATTGAATC-AAATCAAATTTTCATGTAT
1 AAAATTGAA-CAAAATCAAA-GTTCATGTAT
*
43923692 AAAATTGCACAAAATCAAAGTTCATGTA
1 AAAATTGAACAAAATCAAAGTTCATGTA
43923720 CGACATTGCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 9 0.36
30 16 0.64
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (29 bp):
AAAATTGAACAAAATCAAAGTTCATGTAT
Found at i:43923716 original size:29 final size:30
Alignment explanation
Indices: 43923673--43923750 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
43923663 AAATTGAATC
* *
43923673 AAATCAAATTTTCATGTATAAAATTGCACA-
1 AAATCAAA-GTTCATGTACAAAATTGCACAT
* * *
43923703 AAATCAAAGTTCATGTACGACATTGCATATT
1 AAATCAAAGTTCATGTACAAAATTGCACA-T
43923734 AAATCAAAGTTCATGTA
1 AAATCAAAGTTCATGTA
43923751 GATATTCATC
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 16 0.39
30 8 0.20
31 17 0.41
ACGTcount: A:0.44, C:0.14, G:0.10, T:0.32
Consensus pattern (30 bp):
AAATCAAAGTTCATGTACAAAATTGCACAT
Found at i:43925943 original size:12 final size:12
Alignment explanation
Indices: 43925926--43925958 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
43925916 CTCGTATGTC
43925926 AGGCCGTGTGCT
1 AGGCCGTGTGCT
43925938 AGGCCGTGTGCT
1 AGGCCGTGTGCT
43925950 AGGCCGTGT
1 AGGCCGTGT
43925959 AACTGCCTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.09, C:0.24, G:0.42, T:0.24
Consensus pattern (12 bp):
AGGCCGTGTGCT
Found at i:43927001 original size:19 final size:19
Alignment explanation
Indices: 43926979--43927037 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
43926969 TAAGTGCTTA
43926979 AGGGGTACCGAAGTACAAC
1 AGGGGTACCGAAGTACAAC
* *
43926998 AGGGGCA-CGTAAGTACATTC
1 AGGGGTACCG-AAGTACA-AC
*
43927018 AGGGGTACCAAAGTACAAC
1 AGGGGTACCGAAGTACAAC
43927037 A
1 A
43927038 AAGGCACGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
18 2 0.06
19 15 0.47
20 14 0.44
21 1 0.03
ACGTcount: A:0.37, C:0.20, G:0.29, T:0.14
Consensus pattern (19 bp):
AGGGGTACCGAAGTACAAC
Found at i:43927022 original size:20 final size:20
Alignment explanation
Indices: 43926962--43927022 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
43926952 AGTACAACAA
* *
43926962 GGGCACGTAAGTGC-TTAAG
1 GGGCACGTAAGTACATTCAG
* *
43926981 GGGTACCG-AAGTACA-ACAG
1 GGGCA-CGTAAGTACATTCAG
43927000 GGGCACGTAAGTACATTCAG
1 GGGCACGTAAGTACATTCAG
43927020 GGG
1 GGG
43927023 TACCAAAGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
18 2 0.06
19 22 0.69
20 8 0.25
ACGTcount: A:0.30, C:0.18, G:0.36, T:0.16
Consensus pattern (20 bp):
GGGCACGTAAGTACATTCAG
Found at i:43927033 original size:39 final size:39
Alignment explanation
Indices: 43926939--43927071 Score: 187
Period size: 39 Copynumber: 3.4 Consensus size: 39
43926929 AAAAGTACTA
* *
43926939 TCAGGAGTACTGAAGTACAACAAGGGCACGTAAGTGC-T
1 TCAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCAT
* * *
43926977 TAAGGGGTACCGAAGTACAACAGGGGCACGTAAGTACAT
1 TCAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCAT
* * *
43927016 TCAGGGGTACCAAAGTACAACAAAGGCACGTACGTGCAT
1 TCAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCAT
43927055 TCAGGGGTACCGAAGTA
1 TCAGGGGTACCGAAGTA
43927072 AAAAATTTTT
Statistics
Matches: 82, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
38 32 0.39
39 50 0.61
ACGTcount: A:0.35, C:0.20, G:0.29, T:0.17
Consensus pattern (39 bp):
TCAGGGGTACCGAAGTACAACAAGGGCACGTAAGTGCAT
Found at i:43932965 original size:40 final size:40
Alignment explanation
Indices: 43932920--43933086 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
43932910 CGGAATATAA
43932920 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
43932960 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
43933000 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
43933040 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
43933079 CCGGATAT
1 CCGGATAT
43933087 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:43940959 original size:40 final size:40
Alignment explanation
Indices: 43940914--43941080 Score: 185
Period size: 40 Copynumber: 4.2 Consensus size: 40
43940904 CGGAATATAA
43940914 CCGGATATAATCACGT-GCACAAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCAC-TAGCACAAATGCCTTCGGGTCTTAGC
* * * *
43940954 CCGGATAGAATAACTCGCACGAATGCCTTCGGGTCTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * *
43940994 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
** * * * *
43941034 CCGGATATAATTTCCAGCATAATTGTCTTCGGG-CTTAGC
1 CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
43941073 CCGGATAT
1 CCGGATAT
43941081 CATTCAATTT
Statistics
Matches: 107, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 14 0.13
40 93 0.87
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (40 bp):
CCGGATATAATCACTAGCACAAATGCCTTCGGGTCTTAGC
Found at i:43946373 original size:20 final size:20
Alignment explanation
Indices: 43946348--43946388 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
43946338 AATGAATGTC
43946348 TATATGAATTCTCAATTAAT
1 TATATGAATTCTCAATTAAT
43946368 TATATGAATTCTCAATTAAT
1 TATATGAATTCTCAATTAAT
43946388 T
1 T
43946389 TTCGTATCAT
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:0.39, C:0.10, G:0.05, T:0.46
Consensus pattern (20 bp):
TATATGAATTCTCAATTAAT
Found at i:43952292 original size:37 final size:37
Alignment explanation
Indices: 43952233--43952415 Score: 294
Period size: 37 Copynumber: 4.9 Consensus size: 37
43952223 AGCTCAGACG
* * * *
43952233 AAATCTCCACATGAAGTTATCGGGTCTTACTCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43952270 AAATCTCCACACGTAGTCATCGGGTCTTAGCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
* *
43952307 TAATCTCCACACGTAGTCATCGGGTCTTACCCAGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
43952344 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
*
43952381 TAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
1 AAATCTCCACACGTAGTCATCGGGTCTTACCCGGA
43952416 ATATATTTCC
Statistics
Matches: 135, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 135 1.00
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.24
Consensus pattern (37 bp):
AAATCTCCACACGTAGTCATCGGGTCTTACCCGGACA
Found at i:43952629 original size:46 final size:46
Alignment explanation
Indices: 43952561--43952651 Score: 119
Period size: 46 Copynumber: 2.0 Consensus size: 46
43952551 TATATATACA
* ** *
43952561 CATCTCATACATATCTCACATTAGCCATTTGGCTTTACCACATATC
1 CATCTCATACACATCTCACATTAGCCATTCAGCCTTACCACATATC
* * *
43952607 CATCTCATACACGTTTCGCATTAGCCATTCAGCCTTACCACATAT
1 CATCTCATACACATCTCACATTAGCCATTCAGCCTTACCACATAT
43952652 ATTCATGTTC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
46 38 1.00
ACGTcount: A:0.27, C:0.32, G:0.08, T:0.33
Consensus pattern (46 bp):
CATCTCATACACATCTCACATTAGCCATTCAGCCTTACCACATATC
Found at i:43952689 original size:47 final size:47
Alignment explanation
Indices: 43952625--43953060 Score: 611
Period size: 47 Copynumber: 9.1 Consensus size: 47
43952615 ACACGTTTCG
* * * * ** *
43952625 CATTAGCCATTCAGCCTTACCACATATATTCATGTTCATATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* * *
43952672 CATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
43952719 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
43952766 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
* ** *
43952813 CATTGGCCATTCGGCCTTATCACGCATATATATATACAGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCA--C----ACATACGCATGTTCACATTCATCA
43952866 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
***
43952913 CATTGGCCATTCGGCCTTATCACACATATATATACGGGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCAT----GTTCACATTCATCA
*
43952964 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATCCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
*
43953011 CACTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
1 CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
43953058 CAT
1 CAT
43953061 AAAATCCTAA
Statistics
Matches: 352, Mismatches: 27, Indels: 20
0.88 0.07 0.05
Matches are distributed among these distances:
47 264 0.75
49 1 0.00
51 45 0.13
53 42 0.12
ACGTcount: A:0.26, C:0.30, G:0.12, T:0.31
Consensus pattern (47 bp):
CATTGGCCATTCGGCCTTATCACACATACGCATGTTCACATTCATCA
Found at i:43952892 original size:100 final size:99
Alignment explanation
Indices: 43952648--43953038 Score: 596
Period size: 98 Copynumber: 4.0 Consensus size: 99
43952638 GCCTTACCAC
* * * * * *
43952648 ATATATTCATGTTCATATTCATCACATTGGCCATTCGGCCTTATCTCATATATGCATGTTCACAT
1 ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
43952713 TCATCACATTGGCCATTCGGCCTTATCA-C----
66 TCATCACATTGGCCATTCGGCCTTATCACCATAT
* ** *
43952742 ACATACGCATGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
1 ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
43952807 TCATCACATTGGCCATTCGGCCTTATCACGCATAT
66 TCATCACATTGGCCATTCGGCCTTATCAC-CATAT
43952842 ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
1 ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
*
43952907 TCATCACATTGGCCATTCGGCCTTATCA-CACAT
66 TCATCACATTGGCCATTCGGCCTTATCACCATAT
*
43952940 ATATATACGGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
1 ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
* *
43953005 CCATCACACTGGCCATTCGGCCTTATCACACATA
66 TCATCACATTGGCCATTCGGCCTTATCAC-CATA
43953039 CGCATGTTCA
Statistics
Matches: 273, Mismatches: 16, Indels: 10
0.91 0.05 0.03
Matches are distributed among these distances:
94 86 0.32
96 1 0.00
98 94 0.34
100 92 0.34
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (99 bp):
ATATATACAGGTTCACATTCATCACATTGGCCATTCGGCCTTATCACACATACGCATGTTCACAT
TCATCACATTGGCCATTCGGCCTTATCACCATAT
Found at i:43953057 original size:25 final size:25
Alignment explanation
Indices: 43952982--43953059 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
43952972 ATTCGGCCTT
*
43952982 ATCACACATACGCATGTTCACATCC
1 ATCACACATACGCATGTTCACATTC
* * *
43953007 ATCACAC-T-GGCCA--TTCGGCCTT-
1 ATCACACATACG-CATGTTC-ACATTC
43953029 ATCACACATACGCATGTTCACATTC
1 ATCACACATACGCATGTTCACATTC
43953054 ATCACA
1 ATCACA
43953060 TAAAATCCTA
Statistics
Matches: 39, Mismatches: 7, Indels: 14
0.65 0.12 0.23
Matches are distributed among these distances:
22 10 0.26
23 6 0.15
24 7 0.18
25 16 0.41
ACGTcount: A:0.29, C:0.35, G:0.10, T:0.26
Consensus pattern (25 bp):
ATCACACATACGCATGTTCACATTC
Found at i:43958501 original size:18 final size:18
Alignment explanation
Indices: 43958480--43958518 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
43958470 AATAAAAATT
43958480 TAAAAATCAAATTTAAAC
1 TAAAAATCAAATTTAAAC
*
43958498 TAAAGATCAAATTTAAAC
1 TAAAAATCAAATTTAAAC
43958516 TAA
1 TAA
43958519 TTACAGGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (18 bp):
TAAAAATCAAATTTAAAC
Found at i:43958595 original size:29 final size:29
Alignment explanation
Indices: 43958552--43958615 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
43958542 AAATAATATG
**
43958552 ATCTTTATCTGGCCAA-TTTCAAATCTTTA
1 ATCTTTATCCAGCCAACTTT-AAATCTTTA
43958581 ATCTTTATCCAGCCAACTTTAAATCTTTA
1 ATCTTTATCCAGCCAACTTTAAATCTTTA
43958610 ATCTTT
1 ATCTTT
43958616 CAATCTACCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 29 0.91
30 3 0.09
ACGTcount: A:0.28, C:0.22, G:0.05, T:0.45
Consensus pattern (29 bp):
ATCTTTATCCAGCCAACTTTAAATCTTTA
Found at i:43964733 original size:21 final size:21
Alignment explanation
Indices: 43964717--43964779 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
43964707 GCCCATTTAG
43964717 AGGCCACACACGCCCATGTGA
1 AGGCCACACACGCCCATGTGA
* * * *
43964738 AGGCCACACATGCTCGTGTGG
1 AGGCCACACACGCCCATGTGA
* *
43964759 AGGGCACACACGCCCGTGTGA
1 AGGCCACACACGCCCATGTGA
43964780 GCACTCATGT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.24, C:0.33, G:0.30, T:0.13
Consensus pattern (21 bp):
AGGCCACACACGCCCATGTGA
Found at i:43966025 original size:43 final size:43
Alignment explanation
Indices: 43965977--43966146 Score: 184
Period size: 43 Copynumber: 4.0 Consensus size: 43
43965967 GTTACTGAGA
43965977 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* *
43966020 TGTGATTACATGTAAGACCATGTCTGCGACATTGGCATTGTTAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTG-TAT
* * * * * * * *
43966064 T-CGATTTCGTGTAAGACCCTGTCTAGGAAAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
* * *
43966105 ATGTGATAACATGTAAGACCATATCTGGGATA-TGGCATTGTA
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTA
43966147 CGAGCTATAT
Statistics
Matches: 102, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
41 1 0.01
42 8 0.08
43 90 0.88
44 3 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.32
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATTGTAT
Found at i:43966992 original size:47 final size:47
Alignment explanation
Indices: 43966934--43967026 Score: 125
Period size: 47 Copynumber: 2.0 Consensus size: 47
43966924 ACCGTGTGCG
* * *
43966934 ACACACTGTCATGT-TACACGGCCGTGTGTCCCCTGGGGTAGCCCTTT
1 ACACACGGTCAT-TCTACACAGCCATGTGTCCCCTGGGGTAGCCCTTT
* *
43966981 ACACACGGTCATTCTACATAGCCATGTGTCCCTTGGGGTAGCCCTT
1 ACACACGGTCATTCTACACAGCCATGTGTCCCCTGGGGTAGCCCTT
43967027 CGAATTTAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.17, C:0.31, G:0.24, T:0.28
Consensus pattern (47 bp):
ACACACGGTCATTCTACACAGCCATGTGTCCCCTGGGGTAGCCCTTT
Found at i:43968260 original size:19 final size:18
Alignment explanation
Indices: 43968227--43968292 Score: 64
Period size: 19 Copynumber: 3.6 Consensus size: 18
43968217 TAAAAATACC
43968227 ATAAAATAAATAACATAA
1 ATAAAATAAATAACATAA
*
43968245 ATAAATATATATAACATAAA
1 ATAAA-ATAAATAACAT-AA
43968265 ATAATAATAAA-AACA-AA
1 ATAA-AATAAATAACATAA
*
43968282 ACTCAAATAAA
1 A-TAAAATAAA
43968293 ATTAATTCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
17 9 0.22
18 7 0.17
19 14 0.34
20 10 0.24
21 1 0.02
ACGTcount: A:0.70, C:0.08, G:0.00, T:0.23
Consensus pattern (18 bp):
ATAAAATAAATAACATAA
Found at i:43971407 original size:18 final size:20
Alignment explanation
Indices: 43971361--43971399 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
43971351 GTCATGTTCT
*
43971361 AAGCCACACGGGCGTGTGCC
1 AAGCCACATGGGCGTGTGCC
43971381 AAGCCACATGGGCGTGTGC
1 AAGCCACATGGGCGTGTGC
43971400 GACCACATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.21, C:0.31, G:0.36, T:0.13
Consensus pattern (20 bp):
AAGCCACATGGGCGTGTGCC
Found at i:43977710 original size:40 final size:40
Alignment explanation
Indices: 43977583--43977750 Score: 171
Period size: 40 Copynumber: 4.2 Consensus size: 40
43977573 CGGAATATAA
* *
43977583 CCGGATATAACCACGT-GCACAAATGCCTTCAGGTCTTAGC
1 CCGGATATAACCAC-TAGCACAATTGCCTTCGGGTCTTAGC
* **
43977623 CCGGATAGAATGACTCA-CACGAA-TGCCTTCGGGTCTTAGC
1 CCGGATATAACCACT-AGCAC-AATTGCCTTCGGGTCTTAGC
*
43977663 CCGGATATAGCCACTAGCACAATTGCCTTCGGGTCTTAGC
1 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAGC
*** * * * *
43977703 CCGGATATAATTTCCAGCATAATTGTCTTCGGGGCTTAGC
1 CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAGC
43977743 CCGGATAT
1 CCGGATAT
43977751 CATTCAATTT
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
39 4 0.04
40 101 0.94
41 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (40 bp):
CCGGATATAACCACTAGCACAATTGCCTTCGGGTCTTAGC
Found at i:43977733 original size:80 final size:80
Alignment explanation
Indices: 43977583--43977750 Score: 207
Period size: 80 Copynumber: 2.1 Consensus size: 80
43977573 CGGAATATAA
43977583 CCGGATATAACCACGTGCACAAATGCCTTCAGGTCTTAGCCCGGATAGAATGACTCACACGAATG
1 CCGGATATAACCACGTGCACAAATGCCTTCAGGTCTTAGCCCGGATAGAATGACTCACACGAATG
*
43977648 CCTTCGGGTCTTAGC
66 CCTTCGGGGCTTAGC
* * * * ** *
43977663 CCGGATATAGCCAC-TAGCACAATTGCCTTCGGGTCTTAGCCCGGATATAATTTC-CAGCA-TAA
1 CCGGATATAACCACGT-GCACAAATGCCTTCAGGTCTTAGCCCGGATAGAATGACTCA-CACGAA
*
43977725 TTGTCTTCGGGGCTTAGC
64 -TGCCTTCGGGGCTTAGC
43977743 CCGGATAT
1 CCGGATAT
43977751 CATTCAATTT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
79 5 0.07
80 71 0.93
ACGTcount: A:0.24, C:0.27, G:0.23, T:0.26
Consensus pattern (80 bp):
CCGGATATAACCACGTGCACAAATGCCTTCAGGTCTTAGCCCGGATAGAATGACTCACACGAATG
CCTTCGGGGCTTAGC
Found at i:43985203 original size:35 final size:35
Alignment explanation
Indices: 43985152--43985222 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
43985142 ACTTATCTGA
* *
43985152 TGATCTATTTCTTGGAAATGCGCTTCAGCCTTTTG
1 TGATATATTTCTTGGAAATGCGCTTCAGCCCTTTG
*
43985187 TGATATATTTCTTGGAAATGCGTTTCAGCCCTTTG
1 TGATATATTTCTTGGAAATGCGCTTCAGCCCTTTG
43985222 T
1 T
43985223 TGGAACTTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (35 bp):
TGATATATTTCTTGGAAATGCGCTTCAGCCCTTTG
Found at i:43985761 original size:15 final size:15
Alignment explanation
Indices: 43985741--43985769 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
43985731 TGGAAGTAAC
43985741 CCCTCATAGAAATAA
1 CCCTCATAGAAATAA
43985756 CCCTCATAGAAATA
1 CCCTCATAGAAATA
43985770 CTGTAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.28, G:0.07, T:0.21
Consensus pattern (15 bp):
CCCTCATAGAAATAA
Found at i:43988655 original size:19 final size:21
Alignment explanation
Indices: 43988600--43988656 Score: 73
Period size: 22 Copynumber: 2.7 Consensus size: 21
43988590 AGATTTATTT
43988600 TATTCATGTTAATTCAATAAGA
1 TATT-ATGTTAATTCAATAAGA
43988622 TGATTATGTTAATTCAATAAGA
1 T-ATTATGTTAATTCAATAAGA
*
43988644 T-TTAT-TTTATTCA
1 TATTATGTTAATTCA
43988657 TGTTTAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
22 19 0.58
23 3 0.09
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (21 bp):
TATTATGTTAATTCAATAAGA
Found at i:43989475 original size:18 final size:18
Alignment explanation
Indices: 43989454--43989492 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
43989444 AATCAAAATT
*
43989454 TAAAAATCAAATTTGAAC
1 TAAAAATCAAATTTAAAC
* *
43989472 TAAAGATTAAATTTAAAC
1 TAAAAATCAAATTTAAAC
43989490 TAA
1 TAA
43989493 TTACAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.08, G:0.05, T:0.31
Consensus pattern (18 bp):
TAAAAATCAAATTTAAAC
Found at i:43989559 original size:29 final size:29
Alignment explanation
Indices: 43989526--43989589 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
43989516 AAATAATTTG
**
43989526 ATCTTTATCCAGCCAA-TTTCAAATCTTTA
1 ATCTTTATCCAGCCAACTTT-AAATCTCCA
*
43989555 ATCTTTTTCCAGCCAACTTTAAATCTCCA
1 ATCTTTATCCAGCCAACTTTAAATCTCCA
43989584 ATCTTT
1 ATCTTT
43989590 CAATCTACCC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
29 28 0.90
30 3 0.10
ACGTcount: A:0.28, C:0.27, G:0.03, T:0.42
Consensus pattern (29 bp):
ATCTTTATCCAGCCAACTTTAAATCTCCA
Found at i:43990388 original size:26 final size:25
Alignment explanation
Indices: 43990358--43990433 Score: 71
Period size: 26 Copynumber: 2.9 Consensus size: 25
43990348 TAGGTGTAGC
*
43990358 AGGCTTTGTGTCAGTGTATATTTAGT
1 AGGCTTTGAG-CAGTGTATATTTAGT
* * *
43990384 AGGCTTCGAGCTATTATATATTTAGT
1 AGGCTTTGAGC-AGTGTATATTTAGT
* *
43990410 AAGCTTTGAGCCGGTGTATATTTA
1 AGGCTTTGAG-CAGTGTATATTTA
43990434 CCAAGCTTTG
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
25 1 0.03
26 37 0.95
27 1 0.03
ACGTcount: A:0.24, C:0.11, G:0.24, T:0.42
Consensus pattern (25 bp):
AGGCTTTGAGCAGTGTATATTTAGT
Found at i:43996221 original size:16 final size:16
Alignment explanation
Indices: 43996200--43996230 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
43996190 TCTGTCTCTT
*
43996200 TTCTTTTATTTTGTTC
1 TTCTTTAATTTTGTTC
43996216 TTCTTTAATTTTGTT
1 TTCTTTAATTTTGTT
43996231 TAAATTTAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.10, G:0.06, T:0.74
Consensus pattern (16 bp):
TTCTTTAATTTTGTTC
Found at i:43997862 original size:35 final size:35
Alignment explanation
Indices: 43997811--43997880 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
43997801 CTTTCTGAGC
43997811 CTGTGAATATCCGTAAGTCTGTTACACTGTTGAAT
1 CTGTGAATATCCGTAAGTCTGTTACACTGTTGAAT
* *
43997846 CTGTGAATATCTGTAAGTCTGTTGCACTGTTGAAT
1 CTGTGAATATCCGTAAGTCTGTTACACTGTTGAAT
43997881 TAAATTATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.24, C:0.16, G:0.21, T:0.39
Consensus pattern (35 bp):
CTGTGAATATCCGTAAGTCTGTTACACTGTTGAAT
Found at i:44001135 original size:68 final size:64
Alignment explanation
Indices: 44001028--44001182 Score: 152
Period size: 68 Copynumber: 2.4 Consensus size: 64
44001018 TCATAGTACA
* * * *
44001028 GACCTAGCTACATATATCCTGTAGCTCTATTGTCTACATGGTGTACACATAGTATCACCCATGC
1 GACCTAGCTACATATATCCTGTAGCTCTATTGTCTACATGATGTACACATAGCACCACACATGC
* * * * *
44001092 GACCTAGCTACATCATAATGTCTTGTAGCTCTCTTGTAC-ACATGATGTGCACTTAGCACCATAC
1 GACCTAGCTACAT-AT-A--TCCTGTAGCTCTATTGT-CTACATGATGTACACATAGCACCACAC
*
44001156 ATGT
61 ATGC
44001160 GACCTAGCTACATACTAT-CTGTA
1 GACCTAGCTACATA-TATCCTGTA
44001183 TCATCCAATC
Statistics
Matches: 74, Mismatches: 11, Indels: 12
0.76 0.11 0.12
Matches are distributed among these distances:
64 17 0.23
65 3 0.04
66 1 0.01
67 2 0.03
68 50 0.68
69 1 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.32
Consensus pattern (64 bp):
GACCTAGCTACATATATCCTGTAGCTCTATTGTCTACATGATGTACACATAGCACCACACATGC
Found at i:44003794 original size:14 final size:14
Alignment explanation
Indices: 44003775--44003805 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
44003765 GTTTTAAGGC
44003775 TCCACACGCCCGTG
1 TCCACACGCCCGTG
*
44003789 TCCACACGCCCTTG
1 TCCACACGCCCGTG
44003803 TCC
1 TCC
44003806 CAAAGTCGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.13, C:0.52, G:0.16, T:0.19
Consensus pattern (14 bp):
TCCACACGCCCGTG
Found at i:44012503 original size:31 final size:31
Alignment explanation
Indices: 44012465--44012574 Score: 148
Period size: 31 Copynumber: 3.5 Consensus size: 31
44012455 TTTAACGGTT
* *
44012465 ACTGGGCCGAATCCTTTTAATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
*
44012496 ACTGGGCCGAAGCCTTATCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* * *
44012527 ACTAGGCCAAAGCCTTCTCATAAATCATATC
1 ACTGGGCCGAAGCCTTTTCATAAATCATATC
* *
44012558 ATTGGACCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
44012575 ACTGTAAACG
Statistics
Matches: 68, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.15, T:0.28
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATAAATCATATC
Found at i:44012823 original size:25 final size:25
Alignment explanation
Indices: 44012795--44012864 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
44012785 CTCTTTTAAT
* *
44012795 AACTGGGGAAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
44012820 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGATA
*
44012845 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
44012865 AGCACTTCCT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGATA
Found at i:44013714 original size:27 final size:27
Alignment explanation
Indices: 44013677--44013755 Score: 124
Period size: 27 Copynumber: 2.9 Consensus size: 27
44013667 TATTCACCAT
*
44013677 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGGTCAC
44013704 TTTACCCTACAGGGGCTTTACGGTCAC
1 TTTACCCTACAGGGGCTTTACGGTCAC
*
44013731 TTCACCCTACAGGGGCTTTACGGTC
1 TTTACCCTACAGGGGCTTTACGGTC
44013756 TTTTTACCTA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
27 48 0.98
28 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.23, T:0.29
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGGTCAC
Found at i:44013847 original size:27 final size:27
Alignment explanation
Indices: 44013794--44014180 Score: 206
Period size: 27 Copynumber: 14.3 Consensus size: 27
44013784 TTTCATCCTA
* * * * *
44013794 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
44013821 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44013848 CAATGGTATTTCTA-TAATTTTTAGAAAGG
1 CAAGGGTATTT-TAGTAA-TTTTATAAA-C
* * * *
44013877 CAAGGGTATTTTTGTAACTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
44013904 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
** * * *
44013931 TGAGGGTATTTCAGTAATTTCACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
44013958 C-AGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTAGTAATTTTATAAAC
* * * *
44013985 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
44014012 CAGGGGTATTTTAGCAATTTTACAGAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44014039 C-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTTA-TAAAC
** * *
44014065 TGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44014092 CAAGGGTATTTTAGTAGTTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
**** * *
44014119 CAAGGGTAAAACAGTAATTCTATAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
*** * *
44014146 CAAGGGTAAAATAGTAATTCTATAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
*
44014173 TAAGGGTA
1 CAAGGGTA
44014181 AAACGGTAAT
Statistics
Matches: 288, Mismatches: 63, Indels: 18
0.78 0.17 0.05
Matches are distributed among these distances:
26 22 0.08
27 237 0.82
28 16 0.06
29 13 0.05
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTATAAAC
Found at i:44013999 original size:81 final size:79
Alignment explanation
Indices: 44013879--44014102 Score: 252
Period size: 81 Copynumber: 2.8 Consensus size: 79
44013869 TAGAAAGGCA
* * ** **
44013879 AGGGTATTTTTGTAACTTTGTAAATCAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTC
1 AGGGTATTTTGGTAATTTTACAAAT-AGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTC
*
44013943 AGTAATTTCACAAACC
64 AGCAATTTCACAAACC
*
44013959 AGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTT
1 AG-GGTATTTTGGTAATTTTACAAA-TAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTC
* *
44014024 AGCAATTTTACAGACC
64 AGCAATTTCACAAACC
** * ** *
44014040 AGGGTATTTTGGTAATTTTACTGATTGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTT
1 AGGGTATTTTGGTAATTTTACAAATAG-GGGTATTTTGGTAATTTTACAAACCAGGGGTATTT
44014103 TAGTAGTTTT
Statistics
Matches: 124, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
79 2 0.02
80 54 0.44
81 66 0.53
82 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.41
Consensus pattern (79 bp):
AGGGTATTTTGGTAATTTTACAAATAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCAG
CAATTTCACAAACC
Found at i:44014092 original size:80 final size:81
Alignment explanation
Indices: 44013905--44014105 Score: 255
Period size: 80 Copynumber: 2.5 Consensus size: 81
44013895 TTTGTAAATC
** * *
44013905 AGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCAGTAATTTCACAAACCAGTGGTATTT
1 AGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTTAGCAATTTCACAAACCAGTGGTATTT
44013969 TGGTAATTTTACAAACT
65 TGGTAATTTTACAAACT
* *
44013986 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAGACCAG-GGTATTTT
1 AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTCACAAACCAGTGGTATTTT
**
44014050 GGTAATTTTACTGA-T
66 GGTAATTTTACAAACT
* ** *
44014065 TGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAG
1 AG-GGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAG
44014106 TAGTTTTGTA
Statistics
Matches: 106, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
79 2 0.02
80 55 0.52
81 48 0.45
82 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.40
Consensus pattern (81 bp):
AGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTCACAAACCAGTGGTATTTT
GGTAATTTTACAAACT
Found at i:44014125 original size:54 final size:54
Alignment explanation
Indices: 44013794--44014126 Score: 251
Period size: 54 Copynumber: 6.1 Consensus size: 54
44013784 TTTCATCCTA
* * * * *
44013794 CAAGGGTGTTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAAT
* * * * * *
44013848 CAATGGTATTTCT-ATAATTTTTAGAAAGGCAAGGGTATTTTTGTAACTTTGTAAAT
1 CAAGGGTATTT-TGGTAA-TTTTACAAA-CCAAGGGTATTTTAGTAATTTTGTAAAT
* *** * ***
44013904 CAGGGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCAGTAATTTCACAAA-
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAAT
* * * * ** *
44013957 CCAGTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAAT
* * * * * * *
44014012 CAGGGGTATTTTAGCAATTTTACAGACC-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTT-GTAAAT
** ** *
44014065 TGAGGGTATTTTGGTAATTTTGTAAACCAAGGGTATTTTAGTAGTTTTGTAAAT
1 CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAAT
44014119 CAAGGGTA
1 CAAGGGTA
44014127 AAACAGTAAT
Statistics
Matches: 213, Mismatches: 57, Indels: 18
0.74 0.20 0.06
Matches are distributed among these distances:
53 42 0.20
54 118 0.55
55 18 0.08
56 35 0.16
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.39
Consensus pattern (54 bp):
CAAGGGTATTTTGGTAATTTTACAAACCAAGGGTATTTTAGTAATTTTGTAAAT
Found at i:44014136 original size:54 final size:54
Alignment explanation
Indices: 44014078--44014315 Score: 199
Period size: 54 Copynumber: 4.4 Consensus size: 54
44014068 GGGTATTTTG
* *** * * *
44014078 GTAATTTTGTAAACCAAGGGTATTTTAGTAGTTTTGTAAATCAAGGGTAAAACA
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
* * * *
44014132 GTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATTAAGGGTAAAACG
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
*** * * * **
44014186 GTAATTCTGTAAATTGAGGGTAAAATAGTAATTCTGTAAGTCGAGGGTAAAATG
1 GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
* * * * * * *
44014240 GTAATTCTATAAATCGAGGGTAAAA-CGATAATTCTGTAAATCGAGGGTAAAACG
1 GTAATTCTGTAAACCAAGGGTAAAATAG-TAATTCTATAAATCAAGGGTAAAACA
* * *
44014294 GTAATTCTATAAATCGAGGGTA
1 GTAATTCTGTAAACCAAGGGTA
44014316 CTTTGGTAAT
Statistics
Matches: 159, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
53 1 0.01
54 158 0.99
ACGTcount: A:0.40, C:0.08, G:0.21, T:0.31
Consensus pattern (54 bp):
GTAATTCTGTAAACCAAGGGTAAAATAGTAATTCTATAAATCAAGGGTAAAACA
Found at i:44014181 original size:27 final size:27
Alignment explanation
Indices: 44014114--44014315 Score: 253
Period size: 27 Copynumber: 7.5 Consensus size: 27
44014104 AGTAGTTTTG
*
44014114 TAAATCAAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
* *
44014141 TAAATCAAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
** * *
44014168 TAAATTAAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
* * *
44014195 TAAATTGAGGGTAAAATAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
* **
44014222 TAAGTCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
44014249 TAAATCGAGGGTAAAAC-GATAATTCTG
1 TAAATCGAGGGTAAAACAG-TAATTCTA
*
44014276 TAAATCGAGGGTAAAACGGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
44014303 TAAATCGAGGGTA
1 TAAATCGAGGGTA
44014316 CTTTGGTAAT
Statistics
Matches: 157, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
26 1 0.01
27 155 0.99
28 1 0.01
ACGTcount: A:0.42, C:0.08, G:0.21, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACAGTAATTCTA
Found at i:44014326 original size:54 final size:54
Alignment explanation
Indices: 44014103--44014315 Score: 293
Period size: 54 Copynumber: 3.9 Consensus size: 54
44014093 AAGGGTATTT
* * * *
44014103 TAGTAGTTTTGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAA
1 TAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
* * * *
44014157 TAGTAATTCTATAAATTAAGGGTAAAACGGTAATTCTGTAAATTGAGGGTAAAA
1 TAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
* * *
44014211 TAGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAGGGTAAAA
1 TAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
* *
44014265 -CGATAATTCTGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 TAG-TAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
44014316 CTTTGGTAAT
Statistics
Matches: 140, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.01
54 139 0.99
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (54 bp):
TAGTAATTCTGTAAATCAAGGGTAAAACGGTAATTCTATAAATCGAGGGTAAAA
Found at i:44014340 original size:81 final size:81
Alignment explanation
Indices: 44014112--44014315 Score: 309
Period size: 81 Copynumber: 2.5 Consensus size: 81
44014102 TTAGTAGTTT
* * * *
44014112 TGTAAATCAAGGGTAAAACAGTAATTCTATAAATCAAGGGTAAAATAGTAATTCTATAAATTAAG
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAG
*
44014177 GGTAAAACGGTAATTC
66 GGTAAAACGATAATTC
* * * * *
44014193 TGTAAATTGAGGGTAAAATAGTAATTCTGTAAGTCGAGGGTAAAATGGTAATTCTATAAATCGAG
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAG
44014258 GGTAAAACGATAATTC
66 GGTAAAACGATAATTC
*
44014274 TGTAAATCGAGGGTAAAACGGTAATTCTATAAATCGAGGGTA
1 TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTA
44014316 CTTTGGTAAT
Statistics
Matches: 108, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 108 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (81 bp):
TGTAAATCGAGGGTAAAACAGTAATTCTATAAATCGAGGGTAAAATGGTAATTCTATAAATTGAG
GGTAAAACGATAATTC
Found at i:44016634 original size:31 final size:31
Alignment explanation
Indices: 44016588--44016702 Score: 171
Period size: 31 Copynumber: 3.8 Consensus size: 31
44016578 TTAGTCTTGA
44016588 CATAT-ACTGGGCCGAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
44016618 CATATCACTGGACCGAAGCCTTATCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
*
44016649 CATATCACTGGGCCAAAGCCTTTTCATAAAT
1 CATATCACTGGGCCGAAGCCTTTTCATAAAT
* *
44016680 GATATCATTGGGCCGAAG-CTTTT
1 CATATCACTGGGCCGAAGCCTTTT
44016703 ATTGTAAATG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
30 10 0.13
31 66 0.87
ACGTcount: A:0.30, C:0.23, G:0.17, T:0.30
Consensus pattern (31 bp):
CATATCACTGGGCCGAAGCCTTTTCATAAAT
Found at i:44016950 original size:25 final size:25
Alignment explanation
Indices: 44016922--44017016 Score: 163
Period size: 25 Copynumber: 3.8 Consensus size: 25
44016912 CTCTTTTAAT
* *
44016922 AACTGGGGCAAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTCGGTA
44016947 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
44016972 AACTGGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTCGGTA
*
44016997 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
44017017 AGCACTTCCT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 67 1.00
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.26
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTCGGTA
Found at i:44018167 original size:27 final size:27
Alignment explanation
Indices: 44018127--44018200 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
44018117 TATTCGTAAT
* *
44018127 TTTACCATACAGGGG-TATTACGGTCAC
1 TTTACCCTACAGGGGCT-TTACGATCAC
*
44018154 TTTACCCTATAGGGGCTTTACGATCAC
1 TTTACCCTACAGGGGCTTTACGATCAC
* *
44018181 TTCACCCTACAGGGTCTTTA
1 TTTACCCTACAGGGGCTTTA
44018201 TGGTCTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
27 39 0.98
28 1 0.03
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (27 bp):
TTTACCCTACAGGGGCTTTACGATCAC
Found at i:44018297 original size:27 final size:27
Alignment explanation
Indices: 44018244--44018576 Score: 172
Period size: 27 Copynumber: 12.3 Consensus size: 27
44018234 TTTCATCCTA
* * * * *
44018244 CAAGGGTGTTTTGGTAAATCTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* *
44018271 CAAGGGTATTTCAGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44018298 CAATGGTATTTCTA-TAATTTTTAGAAAGT
1 CAAGGGTATTT-TAGTAA-TTTTATAAA-C
* * *
44018327 CAAGGGTATTTCTA-TAACTTTGTAAAT
1 CAAGGGTATTT-TAGTAATTTTATAAAC
* * * *
44018354 CAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
** ** * *
44018381 TGAGGGTATTTCGGTAATTTCACAAA-
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44018407 CTAGTGGTATTTTGGTAATTTTACAAAC
1 CAAG-GGTATTTTAGTAATTTTATAAAC
* * * *
44018435 TAGGGGTATTTTGGTAATTTTACAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
44018462 CAGGGGTATTTTAGCAATTTTACAGAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * *
44018489 C-AGGGTATTTTGGTAATTTTACT-GAT
1 CAAGGGTATTTTAGTAATTTTA-TAAAC
* * *
44018515 CGAGGGTATTTTGGTAATTTTGTAAAC
1 CAAGGGTATTTTAGTAATTTTATAAAC
* * * *
44018542 CGAGGGTATTTTAGTAGTTTTGTAAAT
1 CAAGGGTATTTTAGTAATTTTATAAAC
*
44018569 CGAGGGTA
1 CAAGGGTA
44018577 AAACAGTAAT
Statistics
Matches: 249, Mismatches: 48, Indels: 18
0.79 0.15 0.06
Matches are distributed among these distances:
26 24 0.10
27 194 0.78
28 15 0.06
29 16 0.06
ACGTcount: A:0.30, C:0.10, G:0.22, T:0.39
Consensus pattern (27 bp):
CAAGGGTATTTTAGTAATTTTATAAAC
Found at i:44018416 original size:54 final size:51
Alignment explanation
Indices: 44018357--44018535 Score: 196
Period size: 54 Copynumber: 3.4 Consensus size: 51
44018347 TGTAAATCAG
* * *
44018357 GGGTATTTTGGTAATTTTACAAATTGAGGGTATTTCGGTAATTTCACAAACTA
1 GGGTATTTTGGTAATTTTACAAA-T-AGGGTATTTTGGTAATTTTACAAACCA
44018410 GTGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTACAAACCA
1 G-GGTATTTTGGTAATTTTACAAA-TA-GGGTATTTTGGTAATTTTACAAACCA
* * ** * * *
44018464 GGGGTATTTTAGCAATTTTACAGACCAGGGTATTTTGGTAATTTTACTGATCGA
1 -GGGTATTTTGGTAATTTTACA-AATAGGGTATTTTGGTAATTTTAC-AAACCA
44018518 GGGTATTTTGGTAATTTT
1 GGGTATTTTGGTAATTTT
44018536 GTAAACCGAG
Statistics
Matches: 108, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
53 38 0.35
54 68 0.63
55 2 0.02
ACGTcount: A:0.27, C:0.09, G:0.22, T:0.41
Consensus pattern (51 bp):
GGGTATTTTGGTAATTTTACAAATAGGGTATTTTGGTAATTTTACAAACCA
Found at i:44018450 original size:81 final size:79
Alignment explanation
Indices: 44018350--44018552 Score: 221
Period size: 80 Copynumber: 2.5 Consensus size: 79
44018340 ATAACTTTGT
** * * *
44018350 AAATCAGGGGTATTTTGGTAATTTTACAAA-TTGAGGGTATTTCGGTAATTTCACAAACTAGTGG
1 AAAT-AGGGGTATTTTGGTAATTTTACAAACCAG-GGGTATTTCAGCAATTTCACAAACCAG-GG
44018414 TATTTTGGTAATTTTAC
63 TATTTTGGTAATTTTAC
* * *
44018431 AAACTAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGCAATTTTACAGACCAGGGTA
1 AAA-TAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCAGCAATTTCACAAACCAGGGTA
44018496 TTTTGGTAATTTTAC
65 TTTTGGTAATTTTAC
** * **
44018511 TGATCGAGGGTATTTTGGTAATTTTGTAAACC-GAGGGTATTT
1 AAATAG-GGGTATTTTGGTAATTTTACAAACCAG-GGGTATTT
44018553 TAGTAGTTTT
Statistics
Matches: 105, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
79 3 0.03
80 51 0.49
81 49 0.47
82 2 0.02
ACGTcount: A:0.29, C:0.09, G:0.23, T:0.39
Consensus pattern (79 bp):
AAATAGGGGTATTTTGGTAATTTTACAAACCAGGGGTATTTCAGCAATTTCACAAACCAGGGTAT
TTTGGTAATTTTAC
Found at i:44018584 original size:27 final size:27
Alignment explanation
Indices: 44018564--44018765 Score: 278
Period size: 27 Copynumber: 7.5 Consensus size: 27
44018554 AGTAGTTTTG
*
44018564 TAAATCGAGGGTAAAACAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
44018591 TAAATCAAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
*
44018618 TAAATTGAGGGTAAAACAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
* ** *
44018645 TAAATTGAGGGTAAAATGGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
* **
44018672 TAAGTCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
* *
44018699 TAAATCGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTA
* *
44018726 TAAGTCGAGGGTAAAATAGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTA
44018753 TAAATCGAGGGTA
1 TAAATCGAGGGTA
44018766 CTTTGGTAAT
Statistics
Matches: 157, Mismatches: 18, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 157 1.00
ACGTcount: A:0.41, C:0.08, G:0.23, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAACAGTAATTCTA
Found at i:44021286 original size:71 final size:71
Alignment explanation
Indices: 44021200--44021363 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
44021190 CGATTTGTCT
44021200 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
44021265 CTTTCA
66 CTTTCA
44021271 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
44021336 CTTTCA
66 CTTTCA
44021342 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
44021364 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:44021401 original size:71 final size:70
Alignment explanation
Indices: 44021200--44021397 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
44021190 CGATTTGTCT
* * * *
44021200 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
44021265 CTTTCA
65 CTTTCA
* * * *
44021271 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
44021336 CTTTCA
65 CTTTCA
* *
44021342 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
44021398 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:44028856 original size:71 final size:71
Alignment explanation
Indices: 44028770--44028933 Score: 328
Period size: 71 Copynumber: 2.3 Consensus size: 71
44028760 CGATTTGTCT
44028770 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
44028835 CTTTCA
66 CTTTCA
44028841 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
44028906 CTTTCA
66 CTTTCA
44028912 CGTAGCTCTCTTGTCTACATGG
1 CGTAGCTCTCTTGTCTACATGG
44028934 GATACATCTC
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 93 1.00
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (71 bp):
CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
CTTTCA
Found at i:44028971 original size:71 final size:70
Alignment explanation
Indices: 44028770--44028967 Score: 258
Period size: 71 Copynumber: 2.8 Consensus size: 70
44028760 CGATTTGTCT
* * * *
44028770 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
44028835 CTTTCA
65 CTTTCA
* * * *
44028841 CGTAGCTCTCTTGTCTACATGGTGTCCTTCACTTGGAATCACGCATGCGACCTAGCTACATTTAT
1 CGTAGCTCTCTTGTCTACATGGTGTACAT-ACTTCGAATCACACATGCGACCTAGCTACATTTAT
44028906 CTTTCA
65 CTTTCA
* *
44028912 CGTAGCTCTCTTGTCTACATGG-GATACAT-C-TCGTATCACACATGTGACCTAGCTAC
1 CGTAGCTCTCTTGTCTACATGGTG-TACATACTTCGAATCACACATGCGACCTAGCTAC
44028968 TACAGGGTGT
Statistics
Matches: 120, Mismatches: 6, Indels: 5
0.92 0.05 0.04
Matches are distributed among these distances:
68 22 0.18
69 1 0.01
70 1 0.01
71 96 0.80
ACGTcount: A:0.21, C:0.28, G:0.17, T:0.34
Consensus pattern (70 bp):
CGTAGCTCTCTTGTCTACATGGTGTACATACTTCGAATCACACATGCGACCTAGCTACATTTATC
TTTCA
Found at i:44030466 original size:29 final size:30
Alignment explanation
Indices: 44030432--44030492 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
44030422 TAAGTAGTCG
* *
44030432 AAGCTAG-TTAAATCGCATACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
44030461 AAGCTAGTTTAAATCACACACTTAGTGCCA
1 AAGCTAGTTTAAATCACACACTTAGTGCCA
44030491 AA
1 AA
44030493 ACTTCCATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 7 0.24
30 22 0.76
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (30 bp):
AAGCTAGTTTAAATCACACACTTAGTGCCA
Found at i:44040128 original size:6 final size:6
Alignment explanation
Indices: 44040119--44040160 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
44040109 GAAGTCTAAG
**
44040119 AAAATA AAAATA ATCATA AAAATA AAAAT- AAAAT- AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AAAATA AA
44040161 TGGACTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:44041740 original size:16 final size:16
Alignment explanation
Indices: 44041721--44041759 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
44041711 TAATAAAGAG
44041721 AAAAT-AAAATAAAATA
1 AAAATAAAAAT-AAATA
44041737 AAAATAAAAATAAATA
1 AAAATAAAAATAAATA
*
44041753 ATAATAA
1 AAAATAA
44041760 TAATGAGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAAATAAATA
Done.