Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 132 of 438
Found at i:39287284 original size:26 final size:28
Alignment explanation
Indices: 39287247--39287302 Score: 80
Period size: 26 Copynumber: 2.1 Consensus size: 28
39287237 TCACATATAA
* *
39287247 CTTCCTATTTTTTCCTATTTTATT-TTT
1 CTTCCTATTTTTTCCAATTGTATTGTTT
39287274 CTTCCTA-TTTTTCCAATTGTATTGTTT
1 CTTCCTATTTTTTCCAATTGTATTGTTT
39287301 CT
1 CT
39287303 ATTTTCAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.12, C:0.20, G:0.04, T:0.64
Consensus pattern (28 bp):
CTTCCTATTTTTTCCAATTGTATTGTTT
Found at i:39290812 original size:22 final size:23
Alignment explanation
Indices: 39290779--39290823 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
39290769 TTTTACATGA
39290779 ATTTTATATAAAT-T-TATTTTG
1 ATTTTATATAAATATATATTTTG
*
39290800 ATTTATATTTAAATATATATTTTG
1 ATTT-TATATAAATATATATTTTG
39290824 GTTCAATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 8 0.40
23 1 0.05
24 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
ATTTTATATAAATATATATTTTG
Found at i:39292690 original size:29 final size:28
Alignment explanation
Indices: 39292638--39292695 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 28
39292628 TTTGTGTCGA
*
39292638 TGTTTTATTAGCAGGCACTTTGTACCGG
1 TGTTTTATTAGCAGGCACTATGTACCGG
* *
39292666 TGTTTTATTTAGCAGGTACTATGTATCGG
1 TGTTTTA-TTAGCAGGCACTATGTACCGG
39292695 T
1 T
39292696 AATTGATACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.19, C:0.14, G:0.24, T:0.43
Consensus pattern (28 bp):
TGTTTTATTAGCAGGCACTATGTACCGG
Found at i:39295012 original size:104 final size:104
Alignment explanation
Indices: 39294741--39295012 Score: 298
Period size: 104 Copynumber: 2.6 Consensus size: 104
39294731 TATGCCATAC
* * * * * *
39294741 GGCCTGGACACACGCCCATGTCCTTGCCTGTGTGGCTCACACGTCTTGAGCACACGTCCATGCCC
1 GGCCTGGACACACGCCTATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGTCCATGTCC
** * ** * *
39294806 CTTCCCGTATGGTTCTAAATTATAAACAATGAGTTACAC
66 CTAACCATATGGTTCTAAAGCATAAACAATAAGTTACAA
* * * ** *
39294845 GGCCTAGACACACG-CTCATGTCCTTGTCCGTGTGGCTCACATGGTCTGGGCACAAG-CCTATGT
1 GGCCTGGACACACGCCT-ATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGTCC-ATGT
*
39294908 CCCTAACCATATGGTTCTAAAGCATAAACAGTAAGTTACAA
64 CCCTAACCATATGGTTCTAAAGCATAAACAATAAGTTACAA
* *
39294949 GGCCTGGACACACGCCTTTGTCCTTGCCCGTGTGAGC-CACACAACCTGGGCACACGTCCATGTC
1 GGCCTGGACACACGCCTATGTCCTTGCCCGTGTG-GCTCACACGACCTGGGCACACGTCCATGTC
39295013 TTTGCCCACA
Statistics
Matches: 136, Mismatches: 27, Indels: 10
0.79 0.16 0.06
Matches are distributed among these distances:
103 3 0.02
104 127 0.93
105 6 0.04
ACGTcount: A:0.23, C:0.31, G:0.22, T:0.24
Consensus pattern (104 bp):
GGCCTGGACACACGCCTATGTCCTTGCCCGTGTGGCTCACACGACCTGGGCACACGTCCATGTCC
CTAACCATATGGTTCTAAAGCATAAACAATAAGTTACAA
Found at i:39298891 original size:23 final size:25
Alignment explanation
Indices: 39298835--39298891 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 25
39298825 TCAATTATAT
*
39298835 TAATTTTATT-TAATATTAAAATAA
1 TAATATTATTATAATATTAAAATAA
**
39298859 T-ATAAAATTATAAT-TTAAAA-AA
1 TAATATTATTATAATATTAAAATAA
39298881 TAATATTATTA
1 TAATATTATTA
39298892 ATTTCAGGTT
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
22 3 0.12
23 18 0.69
24 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAATATTATTATAATATTAAAATAA
Found at i:39300667 original size:19 final size:19
Alignment explanation
Indices: 39300632--39300691 Score: 77
Period size: 18 Copynumber: 3.2 Consensus size: 19
39300622 GTGTTGATAT
39300632 TGAGATGGGAAAT-GAATA
1 TGAGATGGGAAATGGAATA
39300650 TGAGATGGGAAATGGAATA
1 TGAGATGGGAAATGGAATA
* * *
39300669 TGAAATGATGAAATGAAATA
1 TGAGATG-GGAAATGGAATA
39300689 TGA
1 TGA
39300692 ATATTGAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 13 0.35
19 11 0.30
20 13 0.35
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (19 bp):
TGAGATGGGAAATGGAATA
Found at i:39300701 original size:19 final size:19
Alignment explanation
Indices: 39300640--39300704 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
39300630 ATTGAGATGG
* **
39300640 GAAATG-AATATGAGATGG
1 GAAATGAAATATGAAATAT
*
39300658 GAAATGGAATATGAAATGAT
1 GAAATGAAATATGAAAT-AT
39300678 GAAATGAAATATG-AATATT
1 GAAATGAAATATGAAATA-T
39300697 GAAATGAA
1 GAAATGAA
39300705 TTCATGTACT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
18 7 0.17
19 21 0.52
20 12 0.30
ACGTcount: A:0.51, C:0.00, G:0.25, T:0.25
Consensus pattern (19 bp):
GAAATGAAATATGAAATAT
Found at i:39306383 original size:31 final size:27
Alignment explanation
Indices: 39306325--39306378 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
39306315 AGTTTCCACG
39306325 TAAAATCTGTATGTTCTATTTTTCTTT
1 TAAAATCTGTATGTTCTATTTTTCTTT
39306352 TAAAATCTGTATGTTCTATTTTTCTTT
1 TAAAATCTGTATGTTCTATTTTTCTTT
39306379 CTTTTCTTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.59
Consensus pattern (27 bp):
TAAAATCTGTATGTTCTATTTTTCTTT
Found at i:39329575 original size:28 final size:29
Alignment explanation
Indices: 39329543--39329603 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
39329533 TTGTTGCGTT
39329543 TTTTAACATAAATTT-TA-ATATTTT-AATA
1 TTTTAA-A-AAATTTATATATATTTTAAATA
*
39329571 TTTTAAAAAATTTATATTTATTTTAAATA
1 TTTTAAAAAATTTATATATATTTTAAATA
39329600 TTTT
1 TTTT
39329604 TTAGAATTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 6 0.21
27 3 0.10
28 12 0.41
29 8 0.28
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (29 bp):
TTTTAAAAAATTTATATATATTTTAAATA
Found at i:39331384 original size:40 final size:40
Alignment explanation
Indices: 39331332--39331412 Score: 144
Period size: 40 Copynumber: 2.0 Consensus size: 40
39331322 TTGCAATAGT
* *
39331332 TTAATCATATAAACCTAAAAACTATGCGAGATAATAGAGC
1 TTAATCACATAAACCTAAAAACTATGCAAGATAATAGAGC
39331372 TTAATCACATAAACCTAAAAACTATGCAAGATAATAGAGC
1 TTAATCACATAAACCTAAAAACTATGCAAGATAATAGAGC
39331412 T
1 T
39331413 AACTAAAGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 39 1.00
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (40 bp):
TTAATCACATAAACCTAAAAACTATGCAAGATAATAGAGC
Found at i:39342533 original size:12 final size:13
Alignment explanation
Indices: 39342505--39342537 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
39342495 TTATTTCTTT
39342505 TTCTCCATCTACC
1 TTCTCCATCTACC
*
39342518 TTCTCC-TCTTCC
1 TTCTCCATCTACC
39342530 TTCTCCAT
1 TTCTCCAT
39342538 AGCCGAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
12 11 0.61
13 7 0.39
ACGTcount: A:0.09, C:0.45, G:0.00, T:0.45
Consensus pattern (13 bp):
TTCTCCATCTACC
Found at i:39344746 original size:29 final size:27
Alignment explanation
Indices: 39344712--39344814 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 27
39344702 TACTCAATCA
*
39344712 CGCACACTTAGTGCCATGTGATTCAAGCC
1 CGCACACTTAGTGCCAT-T-ATTCAAGCT
* * *
39344741 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCAT-TA-TTCAAGCT
*
39344770 CGCACACTTAGTGCCATACATTACAAGCT
1 CGCACACTTAGTGCCAT-TATT-CAAGCT
*
39344799 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
39344815 ATCTCGTCAC
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
28 2 0.03
29 60 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (27 bp):
CGCACACTTAGTGCCATTATTCAAGCT
Found at i:39346337 original size:8 final size:8
Alignment explanation
Indices: 39346324--39346353 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
39346314 CTAGATCGGC
39346324 AAAAGCCG
1 AAAAGCCG
39346332 AAAAGCCG
1 AAAAGCCG
*
39346340 AAATGCCG
1 AAAAGCCG
39346348 AAAAGC
1 AAAAGC
39346354 TGGTATTTTG
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:0.50, C:0.23, G:0.23, T:0.03
Consensus pattern (8 bp):
AAAAGCCG
Found at i:39346624 original size:28 final size:28
Alignment explanation
Indices: 39346584--39346672 Score: 153
Period size: 28 Copynumber: 3.2 Consensus size: 28
39346574 TGTACTAGAG
39346584 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
39346612 TACCCCTATGTATGCAAAATTACCATTA
1 TACCCCTATGTATGCAAAATTACCATTA
*
39346640 TACCCCTATGTATGCAAAATGACC-TCTA
1 TACCCCTATGTATGCAAAATTACCAT-TA
39346668 TACCC
1 TACCC
39346673 TTAGGGTTAA
Statistics
Matches: 59, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
27 1 0.02
28 58 0.98
ACGTcount: A:0.34, C:0.28, G:0.08, T:0.30
Consensus pattern (28 bp):
TACCCCTATGTATGCAAAATTACCATTA
Found at i:39346822 original size:28 final size:27
Alignment explanation
Indices: 39346781--39346870 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 27
39346771 AGGAAGCGTC
*
39346781 CTGGTGGCTATGCCACAAATTATCTGTT
1 CTGGTGGCAATGCCACAAA-TATCTGTT
** **
39346809 CTGGTGGCCCTGCCACGTATATCTGTT
1 CTGGTGGCAATGCCACAAATATCTGTT
*
39346836 CTGGTGGCATTGCCACAAAATATCTGTAT
1 CTGGTGGCAATGCCAC-AAATATCTGT-T
39346865 CTGGTG
1 CTGGTG
39346871 ACTCTGTCAC
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
27 22 0.42
28 23 0.44
29 7 0.13
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (27 bp):
CTGGTGGCAATGCCACAAATATCTGTT
Found at i:39346839 original size:27 final size:28
Alignment explanation
Indices: 39346781--39346870 Score: 103
Period size: 27 Copynumber: 3.2 Consensus size: 28
39346771 AGGAAGCGTC
*
39346781 CTGGTGGCTA-TGCCACAAATTATCTGTT
1 CTGGTGGC-ACTGCCACAAAATATCTGTT
* **
39346809 CTGGTGGCCCTGCCAC-GTATATCTGTT
1 CTGGTGGCACTGCCACAAAATATCTGTT
*
39346836 CTGGTGGCATTGCCACAAAATATCTGTAT
1 CTGGTGGCACTGCCACAAAATATCTGT-T
39346865 CTGGTG
1 CTGGTG
39346871 ACTCTGTCAC
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
27 22 0.43
28 22 0.43
29 7 0.14
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.33
Consensus pattern (28 bp):
CTGGTGGCACTGCCACAAAATATCTGTT
Found at i:39346889 original size:55 final size:56
Alignment explanation
Indices: 39346781--39346895 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 56
39346771 AGGAAGCGTC
* * *
39346781 CTGGTGGCTATGCCACAAATTATCTGTTCTGGTGGCCCTGCCACGTATATCTGT-T
1 CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
* * *
39346836 CTGGTGGC-ATTGCCACAAAATATCTGTATCTGGTGACTCTGTCACAT-TTTCTGTAT
1 CTGGTGGCTA-TGCCACAAAATATCTGT-TCTGGTGACCCTGCCACATATATCTGTAT
39346892 CTGG
1 CTGG
39346896 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
54 1 0.02
55 30 0.59
56 20 0.39
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (56 bp):
CTGGTGGCTATGCCACAAAATATCTGTTCTGGTGACCCTGCCACATATATCTGTAT
Found at i:39347360 original size:19 final size:19
Alignment explanation
Indices: 39347336--39347374 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
39347326 TTTTAATTAT
* *
39347336 TTTTATGGTTTTGTTTTAC
1 TTTTATGATTTTATTTTAC
*
39347355 TTTTATTATTTTATTTTAC
1 TTTTATGATTTTATTTTAC
39347374 T
1 T
39347375 ATAATGAAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.15, C:0.05, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTATGATTTTATTTTAC
Found at i:39349355 original size:21 final size:22
Alignment explanation
Indices: 39349329--39349372 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
39349319 ATTTTATTAA
* *
39349329 TAATTAATACTT-ATTGAAATG
1 TAATTAAAACTTAATTAAAATG
39349350 TAATTAAAACTTAATTAAAATG
1 TAATTAAAACTTAATTAAAATG
39349372 T
1 T
39349373 TTATATTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.48, C:0.05, G:0.07, T:0.41
Consensus pattern (22 bp):
TAATTAAAACTTAATTAAAATG
Found at i:39364788 original size:50 final size:48
Alignment explanation
Indices: 39364713--39364855 Score: 196
Period size: 48 Copynumber: 2.9 Consensus size: 48
39364703 ATTGGGTAAG
* *
39364713 GTGCCGATGCCATGTCCCAGACATGGTCTTACACAAGCTCTAGCATATCT
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCT--CATATCA
* * * *
39364763 GTGCCAATGCCGTGTCCCAGACATGGTCTTACACTAGCACTCATCTCA
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
* *
39364811 ATGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCACATA
1 GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATA
39364856 AGTGACCCAA
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
48 44 0.54
50 37 0.46
ACGTcount: A:0.24, C:0.31, G:0.19, T:0.25
Consensus pattern (48 bp):
GTGCCGATGCCATGTCCCAGACATGGTCTTACACTAGCTCTCATATCA
Found at i:39368485 original size:23 final size:23
Alignment explanation
Indices: 39368445--39368629 Score: 137
Period size: 23 Copynumber: 7.9 Consensus size: 23
39368435 GTACTCAACA
* *
39368445 CAGCTCGTTTAGAGCTTATTGTTT
1 CAGCTCG-TAAGAGCTTACTGTTT
39368469 CAGCTCGTAAGAGCTTACTGTTT
1 CAGCTCGTAAGAGCTTACTGTTT
* *
39368492 TAACTCGTAAGAGCTTACTGTTT
1 CAGCTCGTAAGAGCTTACTGTTT
* *
39368515 CAGCTCGTAAGAGTTTACCGATTT
1 CAGCTCGTAAGAGCTTACTG-TTT
** *
39368539 -AGCTCAAAAGAGCTTACT-ATT
1 CAGCTCGTAAGAGCTTACTGTTT
*
39368560 CAGCTC-AATAGAGCTTACCAT-TTT
1 CAGCTCGTA-AGAGCTTA-C-TGTTT
*
39368584 CAGCTC-AATAGAGCTTACTGTTTAT
1 CAGCTCGTA-AGAGCTTACTG-TT-T
* *
39368609 CAGCTCAGGAGGAGCTTACTG
1 CAGCTC-GTAAGAGCTTACTG
39368630 ACCATGACTT
Statistics
Matches: 135, Mismatches: 16, Indels: 18
0.80 0.09 0.11
Matches are distributed among these distances:
21 4 0.03
22 14 0.10
23 67 0.50
24 32 0.24
25 7 0.05
26 10 0.07
27 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (23 bp):
CAGCTCGTAAGAGCTTACTGTTT
Found at i:39368516 original size:46 final size:46
Alignment explanation
Indices: 39368455--39368606 Score: 157
Period size: 46 Copynumber: 3.3 Consensus size: 46
39368445 CAGCTCGTTT
* * * **
39368455 AGAGCTTATTGTTTCAGCTCGTAAGAGCTTACTGTTTTAACTCGTA
1 AGAGCTTACTGTTTCAGCTCGTAAGAGCTTACCGATTTAACTCAAA
* *
39368501 AGAGCTTACTGTTTCAGCTCGTAAGAGTTTACCGATTTAGCTCAAA
1 AGAGCTTACTGTTTCAGCTCGTAAGAGCTTACCGATTTAACTCAAA
* * * *
39368547 AGAGCTTACT-ATTCAGCTC-AATAGAGCTTACC-ATTTTCAGCTCAAT
1 AGAGCTTACTGTTTCAGCTCGTA-AGAGCTTACCGA-TTT-AACTCAAA
39368593 AGAGCTTACTGTTT
1 AGAGCTTACTGTTT
39368607 ATCAGCTCAG
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
44 2 0.02
45 20 0.22
46 66 0.73
47 2 0.02
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (46 bp):
AGAGCTTACTGTTTCAGCTCGTAAGAGCTTACCGATTTAACTCAAA
Found at i:39368590 original size:24 final size:23
Alignment explanation
Indices: 39368501--39368615 Score: 94
Period size: 24 Copynumber: 4.9 Consensus size: 23
39368491 TTAACTCGTA
*
39368501 AGAGCTTA-CTGTTTCAGCTC-GT
1 AGAGCTTACCT-TTTCAGCTCAAT
* * *
39368523 AAGAGTTTACCGATTT-AGCTCAAA
1 -AGAGCTTACC-TTTTCAGCTCAAT
*
39368547 AGAGCTTA-CTATTCAGCTCAAT
1 AGAGCTTACCTTTTCAGCTCAAT
39368569 AGAGCTTACCATTTTCAGCTCAAT
1 AGAGCTTACC-TTTTCAGCTCAAT
*
39368593 AGAGCTTACTGTTTATCAGCTCA
1 AGAGCTTAC-CTTT-TCAGCTCA
39368616 GGAGGAGCTT
Statistics
Matches: 74, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
21 2 0.03
22 16 0.22
23 20 0.27
24 28 0.38
25 8 0.11
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.33
Consensus pattern (23 bp):
AGAGCTTACCTTTTCAGCTCAAT
Found at i:39369352 original size:19 final size:21
Alignment explanation
Indices: 39369311--39369358 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
39369301 TTAAAATTGT
39369311 AACTAAAAATATTAAAATAAA
1 AACTAAAAATATTAAAATAAA
* *
39369332 AA-TAAAAAT-TTAGAATCAA
1 AACTAAAAATATTAAAATAAA
39369351 AACTAAAA
1 AACTAAAA
39369359 TAAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 10 0.42
20 12 0.50
21 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.23
Consensus pattern (21 bp):
AACTAAAAATATTAAAATAAA
Found at i:39372144 original size:22 final size:21
Alignment explanation
Indices: 39372119--39372159 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
39372109 AATTGACTTC
*
39372119 AATATTTTAATTAAAATAATTA
1 AATATATTAATT-AAATAATTA
*
39372141 AATATATTAGTTAAATAAT
1 AATATATTAATTAAATAAT
39372160 ATTATGTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
AATATATTAATTAAATAATTA
Found at i:39372202 original size:13 final size:13
Alignment explanation
Indices: 39372181--39372223 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
39372171 GAATTAAATT
*
39372181 ATATTAATTTTAA
1 ATATAAATTTTAA
39372194 ATATAAATTTTAA
1 ATATAAATTTTAA
*
39372207 ATTTTAAA-TTTAA
1 A-TATAAATTTTAA
39372220 ATAT
1 ATAT
39372224 TGTAGATAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 19 0.73
14 5 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATAAATTTTAA
Found at i:39372508 original size:2 final size:2
Alignment explanation
Indices: 39372501--39372535 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
39372491 CAACCACCGC
39372501 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 T
39372536 CAAATAACAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:39374646 original size:6 final size:6
Alignment explanation
Indices: 39374637--39374697 Score: 77
Period size: 6 Copynumber: 10.2 Consensus size: 6
39374627 TTTCAAAACC
* * *
39374637 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG GAAGGG GAAGGG GAAGGG
1 AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG AAAGGG
* *
39374685 GAAGGG GAAGGG A
1 AAAGGG AAAGGG A
39374698 TCGTATGGGT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (6 bp):
AAAGGG
Found at i:39374654 original size:12 final size:12
Alignment explanation
Indices: 39374637--39374697 Score: 86
Period size: 12 Copynumber: 5.1 Consensus size: 12
39374627 TTTCAAAACC
*
39374637 AAAGGGAAAGGG
1 AAAGGGGAAGGG
*
39374649 AAAGGGAAAGGG
1 AAAGGGGAAGGG
39374661 AAAGGGGAAGGG
1 AAAGGGGAAGGG
*
39374673 GAAGGGGAAGGG
1 AAAGGGGAAGGG
*
39374685 GAAGGGGAAGGG
1 AAAGGGGAAGGG
39374697 A
1 A
39374698 TCGTATGGGT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (12 bp):
AAAGGGGAAGGG
Found at i:39374660 original size:18 final size:18
Alignment explanation
Indices: 39374637--39374697 Score: 86
Period size: 18 Copynumber: 3.4 Consensus size: 18
39374627 TTTCAAAACC
*
39374637 AAAGGGAAAGGGAAAGGG
1 AAAGGGAAAGGGGAAGGG
39374655 AAAGGGAAAGGGGAAGGG
1 AAAGGGAAAGGGGAAGGG
* *
39374673 GAAGGGGAAGGGGAAGGG
1 AAAGGGAAAGGGGAAGGG
*
39374691 GAAGGGA
1 AAAGGGA
39374698 TCGTATGGGT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
AAAGGGAAAGGGGAAGGG
Found at i:39374962 original size:20 final size:20
Alignment explanation
Indices: 39374939--39374986 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
39374929 TTATATTTTA
39374939 TTTTTATTTA-TTATCAATG
1 TTTTTATTTATTTATCAATG
39374958 TTTTTATTTATTTATCAATG
1 TTTTTATTTATTTATCAATG
39374978 TTTTT-TTTA
1 TTTTTATTTA
39374987 AATCTAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.23, C:0.04, G:0.04, T:0.69
Consensus pattern (20 bp):
TTTTTATTTATTTATCAATG
Found at i:39375631 original size:40 final size:39
Alignment explanation
Indices: 39375557--39375641 Score: 100
Period size: 40 Copynumber: 2.2 Consensus size: 39
39375547 TGGGATTTAA
* * * *
39375557 GGTTTAGGGGTTATAGATTAGTGTTTAGGGTTTTTT-TG
1 GGTTTAGGGGTTATAGACTAGTGTCTAGGATTTTTTAGG
*
39375595 GGTTTAGGGGTTATATAGACTAGTGTCTATGATTTTTTAGG
1 GGTTTAGGGG-T-TATAGACTAGTGTCTAGGATTTTTTAGG
39375636 GGTTTA
1 GGTTTA
39375642 AGGTTTAGGG
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
38 10 0.26
39 1 0.03
40 21 0.54
41 7 0.18
ACGTcount: A:0.19, C:0.02, G:0.32, T:0.47
Consensus pattern (39 bp):
GGTTTAGGGGTTATAGACTAGTGTCTAGGATTTTTTAGG
Found at i:39375672 original size:15 final size:16
Alignment explanation
Indices: 39375629--39375670 Score: 77
Period size: 15 Copynumber: 2.7 Consensus size: 16
39375619 GTCTATGATT
39375629 TTTTAGGGGTTTAAGG
1 TTTTAGGGGTTTAAGG
39375645 -TTTAGGGGTTTAAGG
1 TTTTAGGGGTTTAAGG
39375660 TTTTAGGGGTT
1 TTTTAGGGGTT
39375671 AATATTAACC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
15 15 0.60
16 10 0.40
ACGTcount: A:0.17, C:0.00, G:0.38, T:0.45
Consensus pattern (16 bp):
TTTTAGGGGTTTAAGG
Found at i:39375694 original size:7 final size:7
Alignment explanation
Indices: 39375684--39375714 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
39375674 ATTAACCCTG
39375684 AACCCAT
1 AACCCAT
39375691 AACCCAT
1 AACCCAT
39375698 AACCCAT
1 AACCCAT
*
39375705 AACCCCT
1 AACCCAT
39375712 AAC
1 AAC
39375715 TCCTAAACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.42, C:0.45, G:0.00, T:0.13
Consensus pattern (7 bp):
AACCCAT
Found at i:39375793 original size:22 final size:22
Alignment explanation
Indices: 39375736--39375806 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
39375726 AAACCTCAAC
*
39375736 CCTTAAACC-ATAATTCATAAA
1 CCTTAAACCTATAACTCATAAA
*
39375757 CCTTAAA-ATAGTAACTCATAAA
1 CCTTAAACCTA-TAACTCATAAA
* *
39375779 CCTTAAACCTTTAAC-CATATA
1 CCTTAAACCTATAACTCATAAA
*
39375800 CCCTAAA
1 CCTTAAA
39375807 TTGTAAATCC
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
21 19 0.46
22 21 0.51
23 1 0.02
ACGTcount: A:0.45, C:0.25, G:0.01, T:0.28
Consensus pattern (22 bp):
CCTTAAACCTATAACTCATAAA
Found at i:39375939 original size:7 final size:7
Alignment explanation
Indices: 39375919--39376019 Score: 85
Period size: 7 Copynumber: 14.1 Consensus size: 7
39375909 TACTAATTAA
39375919 CTAAACC
1 CTAAACC
39375926 CTAAAACC
1 CT-AAACC
39375934 CTAAACC
1 CTAAACC
39375941 CTAAACC
1 CTAAACC
39375948 CTAAACC
1 CTAAACC
*
39375955 CTAAATC
1 CTAAACC
*
39375962 CTAAAAC
1 CTAAACC
* *
39375969 ATAAACT
1 CTAAACC
* *
39375976 CTTAATC
1 CTAAACC
* *
39375983 ATAGACC
1 CTAAACC
*
39375990 CTTAACCC
1 C-TAAACC
*
39375998 CTAACCC
1 CTAAACC
39376005 CTAAACC
1 CTAAACC
*
39376012 TTAAACC
1 CTAAACC
39376019 C
1 C
39376020 CAACACTTAA
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
7 61 0.84
8 12 0.16
ACGTcount: A:0.42, C:0.38, G:0.01, T:0.20
Consensus pattern (7 bp):
CTAAACC
Found at i:39376030 original size:21 final size:21
Alignment explanation
Indices: 39375989--39376032 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
39375979 AATCATAGAC
*
39375989 CCTTAACCCCTAACCCCTAAA
1 CCTTAACCCCTAACACCTAAA
*
39376010 CCTTAAACCCC-AACACTTAAA
1 CCTT-AACCCCTAACACCTAAA
39376031 CC
1 CC
39376033 ATAATTCCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 14 0.70
22 6 0.30
ACGTcount: A:0.36, C:0.45, G:0.00, T:0.18
Consensus pattern (21 bp):
CCTTAACCCCTAACACCTAAA
Found at i:39376331 original size:54 final size:54
Alignment explanation
Indices: 39376229--39376340 Score: 127
Period size: 54 Copynumber: 2.1 Consensus size: 54
39376219 TGTGATATTT
* **
39376229 TTTAGGGTTTAGGGTTTTATGGGTTATAGTTTAATGTTTAGGA-GTTTTTAGGG
1 TTTAGGGTTTAGGGTTTTAAGGGTTATACATTAATGTTTAGGATGTTTTTAGGG
* * ** * *
39376282 TTTATGGGTTTAGTGTTTTAAGGGTTATACATTAGTGTTTATTATTTTTTTGGGG
1 TTTA-GGGTTTAGGGTTTTAAGGGTTATACATTAATGTTTAGGATGTTTTTAGGG
39376337 TTTA
1 TTTA
39376341 AAGTTTTAGG
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
53 4 0.08
54 32 0.67
55 12 0.25
ACGTcount: A:0.19, C:0.01, G:0.28, T:0.53
Consensus pattern (54 bp):
TTTAGGGTTTAGGGTTTTAAGGGTTATACATTAATGTTTAGGATGTTTTTAGGG
Found at i:39376419 original size:41 final size:41
Alignment explanation
Indices: 39376362--39376499 Score: 199
Period size: 41 Copynumber: 3.4 Consensus size: 41
39376352 GTTATATGAC
39376362 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
* *
39376403 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCCGAT
1 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
* * *
39376444 TTTTAGCGGCGTTTTA-CAAAAAAACGCCGCTATTGCTCT-GT
1 TTTTAGCGGCGTTTTATC--GAAAGCGCCGCTAATGCTCTGGT
39376485 TTTTAGCGGCGTTTT
1 TTTTAGCGGCGTTTT
39376500 TTGTAAAACG
Statistics
Matches: 88, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
40 1 0.01
41 71 0.81
42 16 0.18
ACGTcount: A:0.19, C:0.22, G:0.24, T:0.36
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
Found at i:39376519 original size:40 final size:40
Alignment explanation
Indices: 39376362--39376522 Score: 191
Period size: 41 Copynumber: 4.0 Consensus size: 40
39376352 GTTATATGAC
*
39376362 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTATCGAAAACGCCGCTAATGCTCT-GT
* *
39376403 TTTTAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCCGAT
1 TTTTAGCGGCGTTTTATCGAAAACGCCGCTAATGCTCTG-T
* *
39376444 TTTTAGCGGCGTTTTA-CAAAAAAACGCCGCTATTGCTCTGT
1 TTTTAGCGGCGTTTTATC--GAAAACGCCGCTAATGCTCTGT
* * *
39376485 TTTTAGCGGCGTTTT-TTGTAAAACGCCACTATTGCTCT
1 TTTTAGCGGCGTTTTATCG-AAAACGCCGCTAATGCTCT
39376523 ATGTTTTACA
Statistics
Matches: 107, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
40 20 0.19
41 70 0.65
42 17 0.16
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.35
Consensus pattern (40 bp):
TTTTAGCGGCGTTTTATCGAAAACGCCGCTAATGCTCTGT
Found at i:39388819 original size:36 final size:36
Alignment explanation
Indices: 39388750--39388829 Score: 99
Period size: 36 Copynumber: 2.2 Consensus size: 36
39388740 TGGGTCACAT
* *
39388750 GGCCGTGTTGCAGGTCGTGTGATAGCCTATGTCCTA
1 GGCCGTGTTGCAGGTCGTGTGACAGCCTATGTCCCA
* * *
39388786 GGCTGTGTTGCAGG-CTGTGTGACGGCCTGTGTCCCA
1 GGCCGTGTTGCAGGTC-GTGTGACAGCCTATGTCCCA
39388822 GGCCGTGT
1 GGCCGTGT
39388830 GTGCTCAAAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
35 1 0.03
36 36 0.97
ACGTcount: A:0.10, C:0.24, G:0.38, T:0.29
Consensus pattern (36 bp):
GGCCGTGTTGCAGGTCGTGTGACAGCCTATGTCCCA
Found at i:39395162 original size:27 final size:27
Alignment explanation
Indices: 39395132--39395231 Score: 89
Period size: 27 Copynumber: 3.7 Consensus size: 27
39395122 CTACCTTACA
39395132 AGGGTATTTCTGTAATTTTGTAAATCG
1 AGGGTATTTCTGTAATTTTGTAAATCG
*** * *
39395159 AGGGTAAAACAGTAATTCTGTAAATCG
1 AGGGTATTTCTGTAATTTTGTAAATCG
* *
39395186 AGGGTA-CTCTGATAATTTT-TCAAGTCG
1 AGGGTATTTCTG-TAATTTTGT-AAATCG
39395213 AGGGTATTT-TAGTAATTTT
1 AGGGTATTTCT-GTAATTTT
39395232 ACAAACTAGG
Statistics
Matches: 58, Mismatches: 11, Indels: 8
0.75 0.14 0.10
Matches are distributed among these distances:
26 3 0.05
27 53 0.91
28 2 0.03
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (27 bp):
AGGGTATTTCTGTAATTTTGTAAATCG
Found at i:39395244 original size:27 final size:27
Alignment explanation
Indices: 39395213--39395289 Score: 100
Period size: 27 Copynumber: 2.9 Consensus size: 27
39395203 TTTCAAGTCG
*
39395213 AGGGTATTTTAGTAATTTTACAAACTA
1 AGGGTATTTTAGTAATTTTACAAACCA
* * *
39395240 GGGGTATTTTGGTAATTTTATAAACCA
1 AGGGTATTTTAGTAATTTTACAAACCA
* *
39395267 ATGGTATTTTAGTAATTCTACAA
1 AGGGTATTTTAGTAATTTTACAA
39395290 CTTGTCCACT
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.34, C:0.08, G:0.17, T:0.42
Consensus pattern (27 bp):
AGGGTATTTTAGTAATTTTACAAACCA
Found at i:39395245 original size:54 final size:54
Alignment explanation
Indices: 39395187--39395289 Score: 118
Period size: 54 Copynumber: 1.9 Consensus size: 54
39395177 TGTAAATCGA
** * *
39395187 GGGTACTCTGATAATTTT-TCAAGTCGAGGGTATTTTAGTAATTTTACAAACTAG
1 GGGTACTCTGATAATTTTAT-AAACCAAGGGTATTTTAGTAATTCTACAAACTAG
* * * *
39395241 GGGTATTTTGGTAATTTTATAAACCAATGGTATTTTAGTAATTCTACAA
1 GGGTACTCTGATAATTTTATAAACCAAGGGTATTTTAGTAATTCTACAA
39395290 CTTGTCCACT
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
54 39 0.98
55 1 0.03
ACGTcount: A:0.31, C:0.10, G:0.18, T:0.41
Consensus pattern (54 bp):
GGGTACTCTGATAATTTTATAAACCAAGGGTATTTTAGTAATTCTACAAACTAG
Found at i:39396312 original size:48 final size:48
Alignment explanation
Indices: 39396241--39396506 Score: 196
Period size: 48 Copynumber: 5.6 Consensus size: 48
39396231 GCGGATGAGC
* *
39396241 TCCCATATAAGACCATATCTGGGATATGGCTTCGGCAGT-GATATGTGA
1 TCCCATGTAAGACCATGTCTGGGATATGGCTTCGGCA-TCGATATGTGA
* * *
39396289 TCCCATGTAAAACCATGTCTGGGATATGGCTTTGGCATCGTTATGTGA
1 TCCCATGTAAGACCATGTCTGGGATATGGCTTCGGCATCGATATGTGA
* * * *
39396337 TCCCATGTAAGACCATGT-TCGGGACATGGCATT-AGCA-CCATAATGAGA
1 TCCCATGTAAGACCATGTCT-GGGATATGGC-TTCGGCATCGAT-ATGTGA
* * * * * * *
39396385 -CATCGTGTAAGACCATAG-CTTGGCTATCAG-TT-TG-AT--ATGTGTGA
1 TC-CCATGTAAGACCAT-GTCTGGGATAT-GGCTTCGGCATCGATATGTGA
* *
39396429 TCCCATGTAAGACCATGTCTGGGATATGGCATT-GGCATCGTTATGTGG
1 TCCCATGTAAGACCATGTCTGGGATATGGC-TTCGGCATCGATATGTGA
* *
39396477 TCCCATGTAAGACCATATCTGGGATGTGGC
1 TCCCATGTAAGACCATGTCTGGGATATGGC
39396507 ATTGGCACCC
Statistics
Matches: 171, Mismatches: 31, Indels: 32
0.73 0.13 0.14
Matches are distributed among these distances:
43 2 0.01
44 23 0.13
45 6 0.04
46 3 0.02
47 8 0.05
48 124 0.73
49 5 0.03
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.30
Consensus pattern (48 bp):
TCCCATGTAAGACCATGTCTGGGATATGGCTTCGGCATCGATATGTGA
Found at i:39398499 original size:27 final size:27
Alignment explanation
Indices: 39398444--39398499 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
39398434 AGTTTGTCAG
* * *
39398444 GCCTTCTGGTGAACACTAGCTTGCCAA
1 GCCTTCTAGTGAACACCAGCTCGCCAA
*
39398471 GCCTTCTAGTGAACACCAGCTCGCTAA
1 GCCTTCTAGTGAACACCAGCTCGCCAA
39398498 GC
1 GC
39398500 ATCAAACTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.23
Consensus pattern (27 bp):
GCCTTCTAGTGAACACCAGCTCGCCAA
Found at i:39400367 original size:14 final size:14
Alignment explanation
Indices: 39400348--39400377 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
39400338 GTTTCAACAC
39400348 ATAAATATGTGTTA
1 ATAAATATGTGTTA
*
39400362 ATAAATATGTTTTA
1 ATAAATATGTGTTA
39400376 AT
1 AT
39400378 CTGATTCTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
ATAAATATGTGTTA
Found at i:39404671 original size:31 final size:31
Alignment explanation
Indices: 39404623--39404688 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
39404613 AACCCTTCCT
* *
39404623 GCATTAAATCCATCCAAAAACAGCAAATATA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
*
39404654 GCATGAAATCCAACCAAAAACAGCAAATGTA
1 GCATGAAATCCAACCAAAAACAGCAAATATA
39404685 GCAT
1 GCAT
39404689 AAAAAATACA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.50, C:0.23, G:0.11, T:0.17
Consensus pattern (31 bp):
GCATGAAATCCAACCAAAAACAGCAAATATA
Found at i:39404988 original size:21 final size:21
Alignment explanation
Indices: 39404932--39404995 Score: 65
Period size: 27 Copynumber: 2.8 Consensus size: 21
39404922 TCTGCTGCCA
*
39404932 TCGCTGCTACCTCTGCCTCTC
1 TCGCTGCTGCCTCTGCCTCTC
39404953 TCATTGCTGCAGCTGCCTCTGCCTCTC
1 TC---GCT---GCTGCCTCTGCCTCTC
39404980 TCGCTGCTGCCTCTGC
1 TCGCTGCTGCCTCTGC
39404996 TCTAAGTTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 12
0.73 0.02 0.24
Matches are distributed among these distances:
21 13 0.36
24 6 0.17
27 17 0.47
ACGTcount: A:0.05, C:0.44, G:0.19, T:0.33
Consensus pattern (21 bp):
TCGCTGCTGCCTCTGCCTCTC
Found at i:39405427 original size:13 final size:14
Alignment explanation
Indices: 39405401--39405429 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
39405391 ACTAACGACG
39405401 AATTAAACCATTAT
1 AATTAAACCATTAT
39405415 AATTAAA-CATTAT
1 AATTAAACCATTAT
39405428 AA
1 AA
39405430 ATATTTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:39409171 original size:79 final size:80
Alignment explanation
Indices: 39409028--39409235 Score: 190
Period size: 79 Copynumber: 2.6 Consensus size: 80
39409018 ACCTTCGGAG
* * ** * * * *
39409028 CTTAA-CCGGATATAGCTACTCGTTCAAACGCCTTCGGGACATAGCCCGGATATGGTAACCCGCA
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
39409092 CCAAGGCCTACGGGA
66 CCAAGGCCTACGGGA
* * * *
39409107 CTTAACCCGGATATCA-CGA-TTGCACAAATGCCTTCGGGTCTTAGCCCGGATA-GAATGACTCG
1 CTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATG-ATAACCCG
* * * *
39409169 CACGAATGCCTTCGGGT
64 CACCAAGGCCTACGGGA
* * * *
39409186 CTTAGCCCGGATATAGCCACTAGCACCATTGCCTTCGGGTCTTAACCCGG
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
39409236 TTATAATTTC
Statistics
Matches: 104, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
78 2 0.02
79 65 0.62
80 36 0.35
81 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (80 bp):
CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
CCAAGGCCTACGGGA
Found at i:39409180 original size:40 final size:40
Alignment explanation
Indices: 39409128--39409235 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
39409118 TATCACGATT
** *
39409128 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
39409168 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
39409208 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
39409236 TTATAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:39416465 original size:79 final size:80
Alignment explanation
Indices: 39416322--39416529 Score: 190
Period size: 79 Copynumber: 2.6 Consensus size: 80
39416312 ACCTTCGGAG
* * ** * * * *
39416322 CTTAA-CCGGATATAGCTACTCGTTCAAACGCCTTCGGGACATAGCCCGGATATGGTAACCCGCA
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
39416386 CCAAGGCCTACGGGA
66 CCAAGGCCTACGGGA
* * * *
39416401 CTTAACCCGGATATCA-CGA-TTGCACAAATGCCTTCGGGTCTTAGCCCGGATA-GAATGACTCG
1 CTTAACCCGGATAT-AGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATG-ATAACCCG
* * * *
39416463 CACGAATGCCTTCGGGT
64 CACCAAGGCCTACGGGA
* * * *
39416480 CTTAGCCCGGATATAGCCACTAGCACCATTGCCTTCGGGTCTTAACCCGG
1 CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGG
39416530 TTATAATTTC
Statistics
Matches: 104, Mismatches: 20, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
78 2 0.02
79 65 0.62
80 36 0.35
81 1 0.01
ACGTcount: A:0.24, C:0.30, G:0.24, T:0.22
Consensus pattern (80 bp):
CTTAACCCGGATATAGCCACTAGCACAAATGCCTTCGGGTCTTAGCCCGGATATGATAACCCGCA
CCAAGGCCTACGGGA
Found at i:39416474 original size:40 final size:40
Alignment explanation
Indices: 39416422--39416529 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 40
39416412 TATCACGATT
** *
39416422 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAATGACTC
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
39416462 GCACGAATGCCTTCGGGTCTTAGCCCGGATATAGCCACTA
1 GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
* * *
39416502 GCACCATTGCCTTCGGGTCTTAACCCGG
1 GCACAAATGCCTTCGGGTCTTAGCCCGG
39416530 TTATAATTTC
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 59 1.00
ACGTcount: A:0.21, C:0.31, G:0.25, T:0.23
Consensus pattern (40 bp):
GCACAAATGCCTTCGGGTCTTAGCCCGGATAGAACCACTA
Found at i:39417850 original size:38 final size:39
Alignment explanation
Indices: 39417740--39417901 Score: 245
Period size: 39 Copynumber: 4.2 Consensus size: 39
39417730 TGTGAATGAA
* *
39417740 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAGT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
*
39417779 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39417818 TGTGCGAGCTATGATATCC-GGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39417856 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
39417896 TGTGCG
1 TGTGCG
39417902 GGTTACCATA
Statistics
Matches: 113, Mismatches: 8, Indels: 3
0.91 0.06 0.02
Matches are distributed among these distances:
38 36 0.32
39 60 0.53
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39417868 original size:77 final size:79
Alignment explanation
Indices: 39417751--39417901 Score: 252
Period size: 77 Copynumber: 1.9 Consensus size: 79
39417741 GTGCGAATTG
*
39417751 TGATATCCGGGCTAAGCCCGAAGGCAGTTGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC
39417815 AATTGTGCGAGCTA
66 AATTGTGCGAGCTA
* *
39417829 TGATATCC-GGCTAAGCCCGAAGGCAATTGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC
*
39417893 ATTTGTGCG
66 AATTGTGCG
39417902 GGTTACCATA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
77 43 0.63
78 25 0.37
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCAATTGTGCGAATTGTGATATCCGGGCTAAGTCCCGAAGGC
AATTGTGCGAGCTA
Found at i:39417917 original size:40 final size:39
Alignment explanation
Indices: 39417740--39417931 Score: 233
Period size: 39 Copynumber: 4.9 Consensus size: 39
39417730 TGTGAATGAA
* * *
39417740 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAGT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39417779 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
*
39417818 TGTGCGAGCTATGATATCC-GGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39417856 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCAAT
* ** * *
39417896 TGTGCGGGTTACCATAACCGGGCTATGTCCCGAAGG
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGG
39417932 TGTTTTGAAC
Statistics
Matches: 136, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
38 36 0.26
39 60 0.44
40 40 0.29
ACGTcount: A:0.23, C:0.21, G:0.32, T:0.24
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39425767 original size:39 final size:39
Alignment explanation
Indices: 39425713--39425875 Score: 263
Period size: 39 Copynumber: 4.2 Consensus size: 39
39425703 TGTGAATGAA
*
39425713 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAGT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
39425752 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* *
39425791 TGTGCGAACTATGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
* * *
39425830 TGTGCGAGTTGTGATATCCGGGTTAAGTCCCGAAGGCATT
1 TGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAAT
39425870 TGTGCG
1 TGTGCG
39425876 GGTTACCATA
Statistics
Matches: 115, Mismatches: 8, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
39 98 0.85
40 17 0.15
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
Found at i:39425891 original size:40 final size:40
Alignment explanation
Indices: 39425730--39425905 Score: 160
Period size: 39 Copynumber: 4.5 Consensus size: 40
39425720 ATTGTGATAT
* * *** *
39425730 CCGGGCTAAG-CCCGAAGGCAGTTGTGCGAATTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCATAA
** ** *
39425769 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAACTATGATAT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCATAA
*** *
39425808 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTGTGATAT
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCATAA
* * *
39425847 CCGGGTTAAGTCCCGAAGGCATTTGTGCGGGTTACCATAA
1 CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCATAA
*
39425887 CCGGGCTATGTCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
39425906 TGTTTTGAAC
Statistics
Matches: 121, Mismatches: 15, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
39 81 0.67
40 40 0.33
ACGTcount: A:0.23, C:0.23, G:0.32, T:0.22
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCAATTGTGCGAGTTACCATAA
Found at i:39430102 original size:28 final size:28
Alignment explanation
Indices: 39430040--39430095 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
39430030 GGCCCATGTA
*
39430040 AGAGAACTTTTTCCCATTATACAACCAC
1 AGAGAACTTCTTCCCATTATACAACCAC
39430068 AGAGAACTTCTTCCCATTATACAACCAC
1 AGAGAACTTCTTCCCATTATACAACCAC
39430096 TTCGAACAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.36, C:0.30, G:0.07, T:0.27
Consensus pattern (28 bp):
AGAGAACTTCTTCCCATTATACAACCAC
Found at i:39431600 original size:9 final size:9
Alignment explanation
Indices: 39431586--39431778 Score: 221
Period size: 9 Copynumber: 21.7 Consensus size: 9
39431576 TAACTATAAT
39431586 TAAGTTATG
1 TAAGTTATG
39431595 TAAGTTATG
1 TAAGTTATG
* * *
39431604 ATATGATATA
1 -TAAGTTATG
*
39431614 T-ATTTATG
1 TAAGTTATG
39431622 T-A-TTATG
1 TAAGTTATG
39431629 TAAGTTATG
1 TAAGTTATG
*
39431638 TAAATTATG
1 TAAGTTATG
*
39431647 TAAGTTCTG
1 TAAGTTATG
*
39431656 TAAGTTCTG
1 TAAGTTATG
39431665 TAAGTTATG
1 TAAGTTATG
*
39431674 TGAGTTATG
1 TAAGTTATG
39431683 TAAGTTATG
1 TAAGTTATG
*
39431692 TAAGTTATA
1 TAAGTTATG
39431701 TAAGTTATG
1 TAAGTTATG
*
39431710 TGAGTTATG
1 TAAGTTATG
*
39431719 TGAGTTATG
1 TAAGTTATG
*
39431728 TAAGTAATG
1 TAAGTTATG
*
39431737 TAAGTTATA
1 TAAGTTATG
39431746 TAAGTTATG
1 TAAGTTATG
*
39431755 TAAGTTATA
1 TAAGTTATG
*
39431764 TGAGTTATG
1 TAAGTTATG
39431773 TAAGTT
1 TAAGTT
39431779 CAAGTATATA
Statistics
Matches: 156, Mismatches: 25, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
7 6 0.04
8 6 0.04
9 138 0.88
10 6 0.04
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:39431683 original size:45 final size:45
Alignment explanation
Indices: 39431588--39431778 Score: 253
Period size: 45 Copynumber: 4.3 Consensus size: 45
39431578 ACTATAATTA
* * * *
39431588 AGTTATGTAAGTTATGATATGATATAT-ATTTATGT-A-TTATGTA
1 AGTTATGTAAGTTATG-TAAGTTATATAAGTTATGTAAGTTATGTG
* * * *
39431631 AGTTATGTAAATTATGTAAGTTCTGTAAGTTCTGTAAGTTATGTG
1 AGTTATGTAAGTTATGTAAGTTATATAAGTTATGTAAGTTATGTG
*
39431676 AGTTATGTAAGTTATGTAAGTTATATAAGTTATGTGAGTTATGTG
1 AGTTATGTAAGTTATGTAAGTTATATAAGTTATGTAAGTTATGTG
* *
39431721 AGTTATGTAAGTAATGTAAGTTATATAAGTTATGTAAGTTATATG
1 AGTTATGTAAGTTATGTAAGTTATATAAGTTATGTAAGTTATGTG
39431766 AGTTATGTAAGTT
1 AGTTATGTAAGTT
39431779 CAAGTATATA
Statistics
Matches: 128, Mismatches: 17, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
42 6 0.05
43 21 0.16
44 1 0.01
45 100 0.78
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.45
Consensus pattern (45 bp):
AGTTATGTAAGTTATGTAAGTTATATAAGTTATGTAAGTTATGTG
Found at i:39432083 original size:29 final size:28
Alignment explanation
Indices: 39432050--39432116 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 28
39432040 ATCACATGGA
*
39432050 AAAAAATTATTTTAATTAAATAATATTT
1 AAAAAATTATATTAATTAAATAATATTT
*
39432078 ATAAAAATTATATTAATTTAATAATATTT
1 A-AAAAATTATATTAATTAAATAATATTT
39432107 AAATAAATTA
1 AAA-AAATTA
39432117 ATCCAAATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
28 3 0.09
29 32 0.91
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (28 bp):
AAAAAATTATATTAATTAAATAATATTT
Found at i:39432086 original size:20 final size:20
Alignment explanation
Indices: 39432063--39432167 Score: 56
Period size: 20 Copynumber: 5.3 Consensus size: 20
39432053 AAATTATTTT
39432063 AATTAAATAATATTTATAAA
1 AATTAAATAATATTTATAAA
* * *
39432083 AATTATATTAAT-TTAATAAT
1 AATTA-AATAATATTTATAAA
* * **
39432103 ATTTAAATAA-ATTAATCCA
1 AATTAAATAATATTTATAAA
* * **
39432122 AATTATATTAT-TATTATATT
1 AATTAAATAATAT-TTATAAA
39432142 AATTAAATAATATTTA-AATA
1 AATTAAATAATATTTATAA-A
39432162 AATTAA
1 AATTAA
39432168 TCCAAATTAT
Statistics
Matches: 60, Mismatches: 19, Indels: 12
0.66 0.21 0.13
Matches are distributed among these distances:
19 18 0.30
20 36 0.60
21 6 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTAAATAATATTTATAAA
Found at i:39432128 original size:39 final size:41
Alignment explanation
Indices: 39432081--39432191 Score: 118
Period size: 50 Copynumber: 2.5 Consensus size: 41
39432071 AATATTTATA
39432081 AAAATTATATTAATTT-AATAATATTTAAATAAATTAATCC
1 AAAATTATATTAATTTAAATAATATTTAAATAAATTAATCC
39432121 AAATTATATTATTATTATATTAATTAAATAATATTTAAATAAATTAATCC
1 -AA--A-ATTA-TATTA-A-T--TTAAATAATATTTAAATAAATTAATCC
*
39432171 -AAATTATATTAATTAAAATAA
1 AAAATTATATTAATTTAAATAA
39432192 GATTGAACCT
Statistics
Matches: 60, Mismatches: 1, Indels: 19
0.75 0.01 0.24
Matches are distributed among these distances:
40 7 0.12
41 2 0.03
42 1 0.02
43 2 0.03
44 9 0.15
45 9 0.15
46 2 0.03
47 1 0.02
48 1 0.02
49 2 0.03
50 24 0.40
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (41 bp):
AAAATTATATTAATTTAAATAATATTTAAATAAATTAATCC
Found at i:39432143 original size:50 final size:50
Alignment explanation
Indices: 39432084--39432181 Score: 187
Period size: 50 Copynumber: 2.0 Consensus size: 50
39432074 ATTTATAAAA
*
39432084 ATTATATTAATTTAATAATATTTAAATAAATTAATCCAAATTATATTATT
1 ATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTATT
39432134 ATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTA
1 ATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTA
39432182 ATTAAAATAA
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (50 bp):
ATTATATTAATTAAATAATATTTAAATAAATTAATCCAAATTATATTATT
Found at i:39432174 original size:25 final size:25
Alignment explanation
Indices: 39432097--39432180 Score: 98
Period size: 25 Copynumber: 3.4 Consensus size: 25
39432087 ATATTAATTT
39432097 AATAATATTTAAATAAATTAATCCA
1 AATAATATTTAAATAAATTAATCCA
* * * * *
39432122 AATTATATTATTATTATATTAAT-TA
1 AATAATATT-TAAATAAATTAATCCA
39432147 AATAATATTTAAATAAATTAATCCA
1 AATAATATTTAAATAAATTAATCCA
*
39432172 AATTATATT
1 AATAATATT
39432181 AATTAAAATA
Statistics
Matches: 46, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
24 10 0.22
25 26 0.57
26 10 0.22
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (25 bp):
AATAATATTTAAATAAATTAATCCA
Found at i:39436119 original size:75 final size:75
Alignment explanation
Indices: 39435982--39436127 Score: 176
Period size: 75 Copynumber: 1.9 Consensus size: 75
39435972 TGGCGTTTAT
*
39435982 AAAAGCGCCACTAATAAAAGGCTATAAGACGACAACGTTTTAAAATCTCTTTAGATGTTTTGTGG
1 AAAAGCGCCACTAATAAAAGGCTATAAGACGACAACGTTTTAAAATCTATTTAGATGTTTTGTGG
39436047 CATTTTTCGA
66 CATTTTTCGA
**
39436057 AAAAGCGCCACTAATAACAAGG-TA-ATA-ACGAC-ACTGTTTTGCAATCTATTAATAGATG-TT
1 AAAAGCGCCACTAATAA-AAGGCTATA-AGACGACAAC-GTTTTAAAATCTATT--TAGATGTTT
*
39436117 TGTGGCGTTTT
61 TGTGGCATTTT
39436128 CTAGTGAAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
73 2 0.03
74 18 0.29
75 32 0.52
76 10 0.16
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.32
Consensus pattern (75 bp):
AAAAGCGCCACTAATAAAAGGCTATAAGACGACAACGTTTTAAAATCTATTTAGATGTTTTGTGG
CATTTTTCGA
Found at i:39436211 original size:188 final size:188
Alignment explanation
Indices: 39435853--39436266 Score: 473
Period size: 188 Copynumber: 2.2 Consensus size: 188
39435843 TTAATAAATA
* * * * *
39435853 TTTGTGGCGTTTTT-ATAAAGCGCCACTAATTAGAAGGCTACA-AACGAC-GTAGTTTTTGCAAT
1 TTTGTGGCATTTTTGAAAAAGCGCCACTAATAACAAGG-TA-ATAACGACACT-G-TTTTGCAAT
* * * * **
39435915 CTGTTAATAGATTTTTGTGGCGTTTCTAGTGAAAACGCCAGTATTTCACACCTTTTTTGGCGTTT
62 CTATTAATAGATGTTTGTGGCGTTTCTAGTGAAAACGCCAGTAATTCACACCTATTGCGGCGTTT
*
39435980 ATAAAAGCGCCACTAATAAAAGGCTATAAGACGACAACGTTTTAAAATCTCTT-TAGATG-T
127 ATAAAAGCGCCACTAATAAAAGGATATAAGACGACAACGTTTTAAAATCTCTTATAGATGTT
39436040 TTTGTGGCATTTTTCGAAAAAGCGCCACTAATAACAAGGTAATAACGACACTGTTTTGCAATCTA
1 TTTGTGGCATTTTT-GAAAAAGCGCCACTAATAACAAGGTAATAACGACACTGTTTTGCAATCTA
**
39436105 TTAATAGATGTTTGTGGCGTTTTCTAGTGAAAACGCTGGTAATTCACACCTATTGCGGCGTTTAT
65 TTAATAGATGTTTGTGGCG-TTTCTAGTGAAAACGCCAGTAATTCACACCTATTGCGGCGTTTAT
* * ** * * *
39436170 ATAAGCGCCACTAATAACATA-GATGTAA-ACGACGCCGTTTTACATTCTCTTAATGGATGTT
129 AAAAGCGCCACTAATAA-A-AGGATATAAGACGACAACGTTTTAAAATCTCTT-ATAGATGTT
** **
39436231 TTTGTGGTGTTTTTTTAAAAGCGCCACTAATAACAA
1 TTTGTGGCATTTTTGAAAAAGCGCCACTAATAACAA
39436267 AGCTTCAAAA
Statistics
Matches: 192, Mismatches: 25, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
187 43 0.22
188 83 0.43
189 27 0.14
190 26 0.14
191 13 0.07
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (188 bp):
TTTGTGGCATTTTTGAAAAAGCGCCACTAATAACAAGGTAATAACGACACTGTTTTGCAATCTAT
TAATAGATGTTTGTGGCGTTTCTAGTGAAAACGCCAGTAATTCACACCTATTGCGGCGTTTATAA
AAGCGCCACTAATAAAAGGATATAAGACGACAACGTTTTAAAATCTCTTATAGATGTT
Found at i:39436378 original size:3 final size:3
Alignment explanation
Indices: 39436372--39436442 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
39436362 TTTTTCTCTT
39436372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
39436420 TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT
39436443 TACTATTAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:39436838 original size:21 final size:21
Alignment explanation
Indices: 39436812--39436858 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
39436802 AGTTTAAGGT
**
39436812 TTTATGGTTTTGGATTTAGAG
1 TTTATGGTTTAAGATTTAGAG
*
39436833 TTTATGGTTTAAGATTTAGGG
1 TTTATGGTTTAAGATTTAGAG
39436854 TTTAT
1 TTTAT
39436859 AATTTAGGCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.26, T:0.53
Consensus pattern (21 bp):
TTTATGGTTTAAGATTTAGAG
Found at i:39436864 original size:21 final size:21
Alignment explanation
Indices: 39436824--39436864 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
39436814 TATGGTTTTG
**
39436824 GATTTAGAGTTTATGGTTTAA
1 GATTTAGAGTTTATAATTTAA
*
39436845 GATTTAGGGTTTATAATTTA
1 GATTTAGAGTTTATAATTTA
39436865 GGCCGGTCTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (21 bp):
GATTTAGAGTTTATAATTTAA
Found at i:39436963 original size:29 final size:29
Alignment explanation
Indices: 39436908--39436963 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
39436898 GATTTAGGAA
*
39436908 TCTATATTTAAGGGTTTAAGGGTTTAGTG
1 TCTATATTTAAGGGTTTAAGGGCTTAGTG
* *
39436937 TCTATAGTTT-AGGGTTTTATGGCTTAG
1 TCTATA-TTTAAGGGTTTAAGGGCTTAG
39436964 GATTCAATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.21, C:0.05, G:0.27, T:0.46
Consensus pattern (29 bp):
TCTATATTTAAGGGTTTAAGGGCTTAGTG
Found at i:39436996 original size:21 final size:21
Alignment explanation
Indices: 39436972--39437011 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
39436962 AGGATTCAAT
39436972 GTTTAATA-TTTAGGGTTTAAG
1 GTTT-ATAGTTTAGGGTTTAAG
39436993 GTTTATAGTTTAGGGTTTA
1 GTTTATAGTTTAGGGTTTA
39437012 TTACTAGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (21 bp):
GTTTATAGTTTAGGGTTTAAG
Found at i:39437305 original size:10 final size:10
Alignment explanation
Indices: 39437290--39437316 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
39437280 AGACCTTATT
39437290 TAATTTGTTA
1 TAATTTGTTA
39437300 TAATTTGTTA
1 TAATTTGTTA
39437310 TAATTTG
1 TAATTTG
39437317 GTCATATCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (10 bp):
TAATTTGTTA
Found at i:39437869 original size:153 final size:153
Alignment explanation
Indices: 39437613--39438045 Score: 611
Period size: 152 Copynumber: 2.8 Consensus size: 153
39437603 GTTTTCCATA
* *
39437613 AAGCACCACTAATGCCACTAAAGCTCAATGAAAAACGACGTCGTTCTGTTTAATCTTTTAGCGGC
1 AAGCGCCACTAATGCCACTAAAGCTCAA--AAAAACGACGTCGTTCTCTTTAATCTTTTAGCGGC
*
39437678 ATTTTT-AAAAAGCGCCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATGT
64 ATTTTTAAAAAAGCACCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATGT
39437742 TGGATCTATTGCGCCA-TTTTTTGGG
129 TGGATCTATTGCG-CAGTTTTTTGGG
* * * **
39437767 AAGCGCCACTAATGCCACTGAAGCTCAAAAAAACAACGTTGTTCTCTTTAATCTTTTAGCGGTGT
1 AAGCGCCACTAATGCCACTAAAGCTCAAAAAAACGACGTCGTTCTCTTTAATCTTTTAGCGGCAT
39437832 TTTTAAAAAAGCACCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATGTTG
66 TTTTAAAAAAGCACCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATGTTG
* *
39437897 GATCTATTGTGGAGTTTTTTGGG
131 GATCTATTGCGCAGTTTTTTGGG
* * * * *
39437920 AAACGCCGCTAATGCCACTAAAGCT-AAAAAAATGACGTCGTTCTTTTTAATCTTTTAGCAGCAT
1 AAGCGCCACTAATGCCACTAAAGCTCAAAAAAACGACGTCGTTCTCTTTAATCTTTTAGCGGCAT
* * * * * * * *
39437984 TTTTAAAAATGCACCGCTATAGGTTGATCTATAGCGGCACTTTCTCAATAACGCTGCTAATG
66 TTTTAAAAAAGCACCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATG
39438046 CTCGATCTTT
Statistics
Matches: 249, Mismatches: 28, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
152 123 0.49
153 100 0.40
154 26 0.10
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (153 bp):
AAGCGCCACTAATGCCACTAAAGCTCAAAAAAACGACGTCGTTCTCTTTAATCTTTTAGCGGCAT
TTTTAAAAAAGCACCGCTATAGATCGACCTATAGCGGCGCTTTCTTAAAAACGCCGCTAATGTTG
GATCTATTGCGCAGTTTTTTGGG
Found at i:39438883 original size:34 final size:34
Alignment explanation
Indices: 39438813--39438885 Score: 94
Period size: 34 Copynumber: 2.1 Consensus size: 34
39438803 GCATTATTGT
* *
39438813 TACTGTTACTGTAATGGGCTAAGGCCCACACTGA
1 TACTGATACTGTAATGGGCTAAGGCCCACACAGA
* *
39438847 TACTGATACTGTAATGGGCTATGGCTCTA-ACAGA
1 TACTGATACTGTAATGGGCTAAGGC-CCACACAGA
39438881 TACTG
1 TACTG
39438886 GACTGTCACT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 32 0.94
35 2 0.06
ACGTcount: A:0.27, C:0.21, G:0.23, T:0.29
Consensus pattern (34 bp):
TACTGATACTGTAATGGGCTAAGGCCCACACAGA
Found at i:39439496 original size:17 final size:18
Alignment explanation
Indices: 39439474--39439521 Score: 59
Period size: 17 Copynumber: 2.8 Consensus size: 18
39439464 GGTGTTATAG
39439474 AAGAAAAAGAGAGATG-A
1 AAGAAAAAGAGAGATGAA
39439491 AAGAAAAAGA-A-ATTGAA
1 AAGAAAAAGAGAGA-TGAA
39439508 AAGAAAAA-AGAGAT
1 AAGAAAAAGAGAGAT
39439522 TGAGATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 1 0.04
16 4 0.15
17 21 0.78
18 1 0.04
ACGTcount: A:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (18 bp):
AAGAAAAAGAGAGATGAA
Found at i:39439523 original size:18 final size:18
Alignment explanation
Indices: 39439474--39439524 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
39439464 GGTGTTATAG
39439474 AAGAAAAAGAGAGA-TG-A
1 AAGAAAAA-AGAGATTGAA
*
39439491 AAG-AAAAAGAAATTGAA
1 AAGAAAAAAGAGATTGAA
39439508 AAGAAAAAAGAGATTGA
1 AAGAAAAAAGAGATTGA
39439525 GATTGAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
15 4 0.14
16 6 0.21
17 7 0.24
18 12 0.41
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.10
Consensus pattern (18 bp):
AAGAAAAAAGAGATTGAA
Found at i:39440645 original size:11 final size:11
Alignment explanation
Indices: 39440629--39440653 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
39440619 TCATTTAAGG
39440629 CATCCCTCATT
1 CATCCCTCATT
39440640 CATCCCTCATT
1 CATCCCTCATT
39440651 CAT
1 CAT
39440654 TCACATCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.20, C:0.44, G:0.00, T:0.36
Consensus pattern (11 bp):
CATCCCTCATT
Found at i:39443989 original size:12 final size:14
Alignment explanation
Indices: 39443974--39444005 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
39443964 GTGAGAACAC
39443974 ATGTGTA-G-TACT
1 ATGTGTAGGCTACT
39443986 ATGTGTAGGCTACT
1 ATGTGTAGGCTACT
39444000 ATGTGT
1 ATGTGT
39444006 TTAAAATGGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.39
13 1 0.06
14 10 0.56
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (14 bp):
ATGTGTAGGCTACT
Found at i:39444051 original size:51 final size:50
Alignment explanation
Indices: 39443992--39444103 Score: 127
Period size: 50 Copynumber: 2.2 Consensus size: 50
39443982 TACTATGTGT
** *
39443992 AGGCTACTATGTGTTTAAAATGGTTTTAGGTCAC-TGTGTAGTAAAAAGTGC
1 AGGCTACTATGTGTACAAAATGG--TTAGGTCACATGTGTAGTAAAAAGTAC
* * * **
39444043 AGGCTACTACGTGTACCAAATGGTTAGGTCGCATGTGTAGTACTAAGTAC
1 AGGCTACTATGTGTACAAAATGGTTAGGTCACATGTGTAGTAAAAAGTAC
39444093 AGGCTACTATG
1 AGGCTACTATG
39444104 CGTATCCGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
49 8 0.16
50 24 0.47
51 19 0.37
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (50 bp):
AGGCTACTATGTGTACAAAATGGTTAGGTCACATGTGTAGTAAAAAGTAC
Found at i:39444099 original size:50 final size:51
Alignment explanation
Indices: 39443971--39444198 Score: 151
Period size: 51 Copynumber: 4.5 Consensus size: 51
39443961 GTTGTGAGAA
* * * **
39443971 CACATGTGTAGTACTATGTGTAGGCTACTATGTGTTTAAAATGGTTTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAAATGG-TTTAGGT
** *
39444023 CAC-TGTGTAGTAAAAAGTGCAGGCTACTACGTGTACCAAATGG-TTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAAATGGTTTAGGT
* * * * ** * * * *
39444072 CGCATGTGTAGTACTAAGTACAGGCTACTATGCGTATC-CGATAGCTTCGGC
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTA-CAAAATGGTTTAGGT
* * * *
39444123 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTA-AAAGATAGCTTT-GGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAA-AT-GGTTTAGGT
* * * *
39444174 CACAAGTGTGGTACTATGTGAAGGC
1 CACATGTGTAGTACTAAGTGCAGGC
39444199 CACTTTGTGA
Statistics
Matches: 137, Mismatches: 33, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
49 8 0.06
50 30 0.22
51 94 0.69
52 5 0.04
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTACGTGTACAAAATGGTTTAGGT
Found at i:39444219 original size:51 final size:51
Alignment explanation
Indices: 39444111--39444252 Score: 164
Period size: 51 Copynumber: 2.8 Consensus size: 51
39444101 ATGCGTATCC
* * * *
39444111 GATAGCTTCGGCCACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAA
1 GATAGCTTTGGACACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAA
* * *
39444162 GATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTG-AAGAA
1 GATAGCTTTGGACACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAA-AA
*
39444213 GGTAGCTTT-GACTACAACG-GTGGTACTATGTGCAGGCCAC
1 GATAGCTTTGGAC-ACAA-GTGTGGTACTATGTGCAGGCCAC
39444253 GGGCATCCAT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
50 4 0.05
51 74 0.94
52 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.29, T:0.27
Consensus pattern (51 bp):
GATAGCTTTGGACACAAGTGTGGTACTATGTGCAGGCCACTATGTGTAAAA
Found at i:39450406 original size:52 final size:50
Alignment explanation
Indices: 39450328--39450516 Score: 159
Period size: 50 Copynumber: 3.7 Consensus size: 50
39450318 GTTGTGAGAA
**
39450328 CACATGTGTAGTACTATA-TGCT-GGCTACTATGTGTTTAAAATGGTTTTAGCT
1 CACATGTGTAGTACTA-AGTG-TAGGCTACTATGTGTACAAAATGG--TTAGCT
* * * *
39450380 CACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATGGTTAGGT
1 CACATGTGTAGTACTAAGTGTAGGCTACTATGTGTACAAAATGGTTAGCT
* * * *** *
39450430 CACATGTCTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCAG-T
1 CACATGTGTAGTACTAAGTGTAGGCTACTATGTGTACAAAAT-GGTT-AGCT
* * *
39450481 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTA
1 CACATGTGTAGTACTAAGTGTAGGCTACTATGTGTA
39450517 AAAGATAGCT
Statistics
Matches: 117, Mismatches: 16, Indels: 9
0.82 0.11 0.06
Matches are distributed among these distances:
50 42 0.36
51 38 0.32
52 37 0.32
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (50 bp):
CACATGTGTAGTACTAAGTGTAGGCTACTATGTGTACAAAATGGTTAGCT
Found at i:39450447 original size:50 final size:51
Alignment explanation
Indices: 39450328--39450565 Score: 203
Period size: 51 Copynumber: 4.7 Consensus size: 51
39450318 GTTGTGAGAA
* *** * * * *
39450328 CACATGTGTAGTACTATA-TGCTGGCTACTATGTGTTTAAAATGGTTTTAGCT
1 CACATGTGTAGTACTA-AGTGCAGGCTACTATGTGTACCAGATAG-CTTAGGT
* * *
39450380 CACATGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGAT-GGTTAGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTAGGT
* * *
39450430 CACATGTCTAGTACTAAGTGCAGGCTACTATGCGTACCCGATAGCTTCA-GT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTT-AGGT
* * ** *
39450481 CACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAAGATAGCTTTGGT
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTAGGT
* * * * * *
39450532 CACAAGTGTGGTACTATGTGAAGGCCACTTTGTG
1 CACATGTGTAGTACTAAGTGCAGGCTACTATGTG
39450566 AAGAAGGTAG
Statistics
Matches: 155, Mismatches: 27, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
50 42 0.27
51 79 0.51
52 34 0.22
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.32
Consensus pattern (51 bp):
CACATGTGTAGTACTAAGTGCAGGCTACTATGTGTACCAGATAGCTTAGGT
Found at i:39450577 original size:51 final size:50
Alignment explanation
Indices: 39450469--39450610 Score: 153
Period size: 51 Copynumber: 2.8 Consensus size: 50
39450459 ATGCGTACCC
* * * *
39450469 GATAGCTTCAGTCACATGTGTGGTACTAAGTGCAGGCCACTATGTGTAAAA
1 GATAGCTT-TGTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAAAA
*
39450520 GATAGCTTTGGTCACAAGTGTGGTACTATGTGAAGGCCACTTTGTG-AAGAA
1 GATAGCTTT-GTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAA-AA
* * *
39450571 GGTAGCTTTGACTACAACG-GTGGTACTATGTGTAGGCCAC
1 GATAGCTTTGTC-ACAA-GTGTGGTACTATGTGAAGGCCAC
39450611 CGGGCATCCA
Statistics
Matches: 79, Mismatches: 8, Indels: 8
0.83 0.08 0.08
Matches are distributed among these distances:
50 4 0.05
51 74 0.94
52 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (50 bp):
GATAGCTTTGTCACAAGTGTGGTACTATGTGAAGGCCACTATGTGTAAAA
Found at i:39453627 original size:40 final size:40
Alignment explanation
Indices: 39453581--39453676 Score: 111
Period size: 40 Copynumber: 2.4 Consensus size: 40
39453571 GAAAAAATCG
* * *
39453581 AATAGATGGAGTTTTAACGGCGTTTTTAAAAAAACGCCGC
1 AATAGATCGAGCTTTAACGGCATTTTTAAAAAAACGCCGC
* * *
39453621 AATAGATCGAGCTTTAGCGGCATTTTTGAAAAAGCGCCGC
1 AATAGATCGAGCTTTAACGGCATTTTTAAAAAAACGCCGC
* * *
39453661 TATAGGTCGACCTTTA
1 AATAGATCGAGCTTTA
39453677 GCGGTGTTTT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 47 1.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (40 bp):
AATAGATCGAGCTTTAACGGCATTTTTAAAAAAACGCCGC
Found at i:39453677 original size:40 final size:40
Alignment explanation
Indices: 39453593--39453680 Score: 113
Period size: 40 Copynumber: 2.2 Consensus size: 40
39453583 TAGATGGAGT
* * *
39453593 TTTAACGGCGTTTTTAAAAAAACGCCGCAATAGATCGAGC
1 TTTAGCGGCATTTTTAAAAAAACGCCGCAATAGATCGACC
* * * *
39453633 TTTAGCGGCATTTTTGAAAAAGCGCCGCTATAGGTCGACC
1 TTTAGCGGCATTTTTAAAAAAACGCCGCAATAGATCGACC
39453673 TTTAGCGG
1 TTTAGCGG
39453681 TGTTTTACCA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.27
Consensus pattern (40 bp):
TTTAGCGGCATTTTTAAAAAAACGCCGCAATAGATCGACC
Found at i:39454737 original size:14 final size:13
Alignment explanation
Indices: 39454700--39454760 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
39454690 ATAGGTTTGG
*
39454700 GGGTTATGGGTTTAA
1 GGGTTAT-GATTT-A
39454715 GGGTTATGATTTA
1 GGGTTATGATTTA
39454728 GGGTTGATGATTTA
1 GGGTT-ATGATTTA
**
39454742 TGTTTTATGATTTA
1 -GGGTTATGATTTA
39454756 GGGTT
1 GGGTT
39454761 TGAGGTTTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
13 9 0.23
14 20 0.51
15 10 0.26
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.48
Consensus pattern (13 bp):
GGGTTATGATTTA
Found at i:39454776 original size:28 final size:28
Alignment explanation
Indices: 39454718--39454776 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
39454708 GGTTTAAGGG
**
39454718 TTATGATTTAGGGTTGATGATTTATGTT
1 TTATGATTTAGGGTTGATGATTTATAAT
*
39454746 TTATGATTTAGGGTTTGA-GGTTTATAAT
1 TTATGATTTAGGG-TTGATGATTTATAAT
39454774 TTA
1 TTA
39454777 GAAGGTTAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 23 0.85
29 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTATGATTTAGGGTTGATGATTTATAAT
Found at i:39454870 original size:39 final size:40
Alignment explanation
Indices: 39454781--39454875 Score: 110
Period size: 39 Copynumber: 2.5 Consensus size: 40
39454771 AATTTAGAAG
39454781 GTTAGGGG-TT-TA-GGGTTTAAGGGTTAGTGGTTAGGAT
1 GTTAGGGGTTTATATGGGTTTAAGGGTTAGTGGTTAGGAT
* * * * *
39454818 -TAAGGGATATATATGGGTTTAAGGTTTATTGGTTAGG-T
1 GTTAGGGGTTTATATGGGTTTAAGGGTTAGTGGTTAGGAT
39454856 GTTAGGGGTTTATATGGGTT
1 GTTAGGGGTTTATATGGGTT
39454876 AAGAGGATAG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
36 5 0.11
37 1 0.02
38 3 0.07
39 37 0.80
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (40 bp):
GTTAGGGGTTTATATGGGTTTAAGGGTTAGTGGTTAGGAT
Found at i:39455135 original size:7 final size:7
Alignment explanation
Indices: 39455125--39455180 Score: 58
Period size: 7 Copynumber: 8.0 Consensus size: 7
39455115 TAAGGGTTAA
39455125 TTAGGGT
1 TTAGGGT
39455132 TTAGGGT
1 TTAGGGT
* *
39455139 CTAGTGT
1 TTAGGGT
**
39455146 TCGGGGT
1 TTAGGGT
39455153 TTAGGGT
1 TTAGGGT
39455160 TTAGGGT
1 TTAGGGT
*
39455167 TTATGGT
1 TTAGGGT
*
39455174 ATAGGGT
1 TTAGGGT
39455181 CAGGGTCTTA
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.14, C:0.04, G:0.41, T:0.41
Consensus pattern (7 bp):
TTAGGGT
Found at i:39455321 original size:7 final size:7
Alignment explanation
Indices: 39455277--39455338 Score: 56
Period size: 7 Copynumber: 8.9 Consensus size: 7
39455267 TTTTTAGCGT
39455277 TTTAGGG
1 TTTAGGG
39455284 TGTTAGGG
1 T-TTAGGG
*
39455292 TTTAGAG
1 TTTAGGG
39455299 TTTAGGG
1 TTTAGGG
**
39455306 -TTA-TT
1 TTTAGGG
*
39455311 TTTAGTG
1 TTTAGGG
39455318 TTTAAGGG
1 TTT-AGGG
39455326 TTTAGGG
1 TTTAGGG
39455333 TTTAGG
1 TTTAGG
39455339 AGTATACATG
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
6 6 0.13
7 26 0.58
8 13 0.29
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (7 bp):
TTTAGGG
Found at i:39455449 original size:27 final size:27
Alignment explanation
Indices: 39455419--39455503 Score: 82
Period size: 27 Copynumber: 3.1 Consensus size: 27
39455409 TGGATTGGAT
*
39455419 TTTGTGGTTT-TGGTTTGGGGCTTAGGG
1 TTTG-GGTTTATGGTTTGGGGTTTAGGG
* *
39455446 TTTGGTGTTTATGATTTGAGGTTTAGGG
1 TTTGG-GTTTATGGTTTGGGGTTTAGGG
* * **
39455474 TTAGAGTTTGGGGTTTGGGGTTTAGGG
1 TTTGGGTTTATGGTTTGGGGTTTAGGG
39455501 TTT
1 TTT
39455504 AAGGTTTAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
26 1 0.02
27 28 0.61
28 17 0.37
ACGTcount: A:0.09, C:0.01, G:0.41, T:0.48
Consensus pattern (27 bp):
TTTGGGTTTATGGTTTGGGGTTTAGGG
Found at i:39455501 original size:14 final size:14
Alignment explanation
Indices: 39455430--39455503 Score: 69
Period size: 14 Copynumber: 5.4 Consensus size: 14
39455420 TTGTGGTTTT
*
39455430 GGTTTGGGGCTTAG
1 GGTTTGGGGTTTAG
* *
39455444 GGTTTGGTGTTTAT
1 GGTTTGGGGTTTAG
* *
39455458 GATTTGAGGTTTAG
1 GGTTTGGGGTTTAG
* * *
39455472 GG-TTAGAGTTTGG
1 GGTTTGGGGTTTAG
39455485 GGTTTGGGGTTTAG
1 GGTTTGGGGTTTAG
39455499 GGTTT
1 GGTTT
39455504 AAGGTTTAAT
Statistics
Matches: 44, Mismatches: 15, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
13 9 0.20
14 35 0.80
ACGTcount: A:0.11, C:0.01, G:0.43, T:0.45
Consensus pattern (14 bp):
GGTTTGGGGTTTAG
Found at i:39455504 original size:7 final size:7
Alignment explanation
Indices: 39455430--39455511 Score: 53
Period size: 7 Copynumber: 11.9 Consensus size: 7
39455420 TTGTGGTTTT
*
39455430 GGTTTGG
1 GGTTTAG
*
39455437 GGCTTAG
1 GGTTTAG
39455444 GGTTT-G
1 GGTTTAG
*
39455450 GTGTTTAT
1 G-GTTTAG
*
39455458 GATTT-G
1 GGTTTAG
39455464 AGGTTTAG
1 -GGTTTAG
39455472 GG-TTAG
1 GGTTTAG
* *
39455478 AGTTTGG
1 GGTTTAG
*
39455485 GGTTTGG
1 GGTTTAG
39455492 GGTTTAG
1 GGTTTAG
*
39455499 GGTTTAA
1 GGTTTAG
39455506 GGTTTA
1 GGTTTA
39455512 ATTTTGGAAT
Statistics
Matches: 58, Mismatches: 12, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
6 7 0.12
7 49 0.84
8 2 0.03
ACGTcount: A:0.13, C:0.01, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:39459228 original size:23 final size:23
Alignment explanation
Indices: 39459198--39459247 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
39459188 AACATTAATC
*
39459198 AAATGTATGAATTGTAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
39459221 AAATGTATGAATTGCAGCCCTTT
1 AAATGTATGAATTGCAGCCCTTT
39459244 AAAT
1 AAAT
39459248 AAACTTGAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (23 bp):
AAATGTATGAATTGCAGCCCTTT
Found at i:39459803 original size:241 final size:241
Alignment explanation
Indices: 39459380--39459866 Score: 870
Period size: 241 Copynumber: 2.0 Consensus size: 241
39459370 ATGAATTAAT
* *
39459380 TTTATTACCATATAGCTTGCTTGTCCATTAAAATTACAACAATAGCTGTCCTTCTCTCCAACCTA
1 TTTATTACCATATAACTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTA
*
39459445 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACGGGTTGCCTTATATCGAG
66 ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACAGGTTGCCTTATATCGAG
*
39459510 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTT
131 CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
39459575 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
196 AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
*
39459621 TTTATTACCATGA-AACTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAATCT
1 TTTATTACCAT-ATAACTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCT
* * *
39459685 TATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTGATAGGTTGCCTTATATCGA
65 AATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACAGGTTGCCTTATATCGA
39459750 GCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACAG-CACGTATGATGAATCTTAAAAAAT
130 GCTGTAAGATATAATGGATCCTCCCTAGGTGTAACAAC-GCCACGTATGATGAATCTTAAAAAAT
39459814 TCAAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
194 TCAAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
39459862 TTTAT
1 TTTAT
39459867 ATAACCTTAA
Statistics
Matches: 236, Mismatches: 8, Indels: 4
0.95 0.03 0.02
Matches are distributed among these distances:
241 234 0.99
242 2 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (241 bp):
TTTATTACCATATAACTTGCTTGTCCATTAAAATTACAACAATAGCTGACCTTCTCTCCAACCTA
ATTTTAAATATTTTAAAGATTCAAAGTATATAGGCTGGAAACCTAACAGGTTGCCTTATATCGAG
CTGTAAGATATAATGGATCCTCCCTAGGTGTAACAACGCCACGTATGATGAATCTTAAAAAATTC
AAAAAGACTTGAAAAAAGTTCTATCGAGCTCATTTACTATTGAATA
Found at i:39460344 original size:9 final size:9
Alignment explanation
Indices: 39460332--39460426 Score: 82
Period size: 9 Copynumber: 9.9 Consensus size: 9
39460322 AATAACTCAT
39460332 ATAACTTAC
1 ATAACTTAC
*
39460341 ATAATTTAC
1 ATAACTTAC
*
39460350 ATAACAACTTAT
1 AT---AACTTAC
*
39460362 ATAACTCAC
1 ATAACTTAC
39460371 ATAACTTAC
1 ATAACTTAC
*
39460380 ATAATTTAC
1 ATAACTTAC
*
39460389 ATAACTCAC
1 ATAACTTAC
*
39460398 ATAACGTAC
1 ATAACTTAC
39460407 ATAACAACTTAC
1 AT---AACTTAC
39460419 ATAACTTA
1 ATAACTTA
39460427 ACTAATACAT
Statistics
Matches: 68, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
9 53 0.78
12 15 0.22
ACGTcount: A:0.46, C:0.21, G:0.01, T:0.32
Consensus pattern (9 bp):
ATAACTTAC
Found at i:39460421 original size:30 final size:30
Alignment explanation
Indices: 39460311--39460424 Score: 126
Period size: 30 Copynumber: 3.9 Consensus size: 30
39460301 CATTACTTAA
* * * * *
39460311 ATAAATTACATAATAACTCATATAACTTAC
1 ATAACTTACATAACAACTTACATAACTCAC
* *
39460341 ATAATTTACATAACAACTTATATAACTCAC
1 ATAACTTACATAACAACTTACATAACTCAC
*
39460371 ATAACTTACAT---AATTTACATAACTCAC
1 ATAACTTACATAACAACTTACATAACTCAC
*
39460398 ATAACGTACATAACAACTTACATAACT
1 ATAACTTACATAACAACTTACATAACT
39460425 TAACTAATAC
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
27 24 0.33
30 48 0.67
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (30 bp):
ATAACTTACATAACAACTTACATAACTCAC
Found at i:39466349 original size:43 final size:43
Alignment explanation
Indices: 39466301--39466487 Score: 295
Period size: 43 Copynumber: 4.3 Consensus size: 43
39466291 ACTGGGCAAA
* *
39466301 TTAGCGGCGTTTTTTAAAAAAGCGCCGCTAAAAGTCCAGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCACCGCTAAAAGTCCTGGTCT
*
39466344 TTAGCGGCGTTTTTTAAAAAAGTACCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCACCGCTAAAAGTCCTGGTCT
39466387 TTAGCGGCGTTTTTTAAAATAA-CACCGCTAAAAGTCCTGGTCT
1 TTAGCGGCGTTTTTTAAAA-AAGCACCGCTAAAAGTCCTGGTCT
* * *
39466430 TTAGCGGCATTTTTTAAAAAAGCGCCGCTAAAAGTCTTGGTCT
1 TTAGCGGCGTTTTTTAAAAAAGCACCGCTAAAAGTCCTGGTCT
*
39466473 TTAGCGGCATTTTTT
1 TTAGCGGCGTTTTTT
39466488 TTCAAACAAA
Statistics
Matches: 135, Mismatches: 7, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
42 2 0.01
43 131 0.97
44 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTAAAAAAGCACCGCTAAAAGTCCTGGTCT
Found at i:39470867 original size:24 final size:24
Alignment explanation
Indices: 39470840--39470954 Score: 212
Period size: 24 Copynumber: 4.8 Consensus size: 24
39470830 CTTATTATGT
**
39470840 TCGCACACATAGTGCCATAGCGAA
1 TCGCACACATAGTGCCATAGTAAA
39470864 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
39470888 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
39470912 TCGCACACATAGTGCCATAGTAAA
1 TCGCACACATAGTGCCATAGTAAA
39470936 TCGCACACATAGTGCCATA
1 TCGCACACATAGTGCCATA
39470955 TATTTCCAGC
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
24 89 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (24 bp):
TCGCACACATAGTGCCATAGTAAA
Found at i:39473330 original size:16 final size:15
Alignment explanation
Indices: 39473284--39473330 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
39473274 AGCTAGGATT
*
39473284 AGTTTTAATTTAATCA
1 AGTTTTTATTTAAT-A
*
39473300 A-TTTTTATTTGATA
1 AGTTTTTATTTAATA
39473314 AGTTTTTATCTTAATA
1 AGTTTTTAT-TTAATA
39473330 A
1 A
39473331 ACTAATAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 2 0.08
15 17 0.65
16 7 0.27
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.55
Consensus pattern (15 bp):
AGTTTTTATTTAATA
Found at i:39482006 original size:29 final size:28
Alignment explanation
Indices: 39481972--39482074 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
39481962 TACTCAATCA
*
39481972 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
39482001 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
39482030 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
39482059 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
39482075 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:39489796 original size:29 final size:28
Alignment explanation
Indices: 39489762--39489864 Score: 116
Period size: 29 Copynumber: 3.6 Consensus size: 28
39489752 TACTCAATCA
*
39489762 CGCACACTTAGTGCCATATGATTCAAGCC
1 CGCACACTTAGTGCCATAT-ATTCAAGCT
* * *
39489791 CGCACACATAGTGCCATATAGTCCAAACT
1 CGCACACTTAGTGCCATATA-TTCAAGCT
* *
39489820 CGCACACTTAGTGCCGTACATTACAAGCT
1 CGCACACTTAGTGCCATATATT-CAAGCT
*
39489849 CGCACACTCAGTGCCA
1 CGCACACTTAGTGCCA
39489865 ATCTCGTCAC
Statistics
Matches: 61, Mismatches: 11, Indels: 4
0.80 0.14 0.05
Matches are distributed among these distances:
28 2 0.03
29 59 0.97
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (28 bp):
CGCACACTTAGTGCCATATATTCAAGCT
Found at i:39493433 original size:24 final size:25
Alignment explanation
Indices: 39493401--39493450 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
39493391 GCCGAATCTT
* *
39493401 CATCCTCA-TTCACCTAGCCATTTC
1 CATCATCATTTCACCTAGCCAATTC
*
39493425 CATCATCATTTCACTTAGCCAATTC
1 CATCATCATTTCACCTAGCCAATTC
39493450 C
1 C
39493451 GCCCTTCTCG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.24, C:0.38, G:0.04, T:0.34
Consensus pattern (25 bp):
CATCATCATTTCACCTAGCCAATTC
Found at i:39495681 original size:17 final size:17
Alignment explanation
Indices: 39495661--39495704 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
39495651 TTGTCATCTA
39495661 TTTATTTATTTTT-TATT
1 TTTA-TTATTTTTATATT
*
39495678 TTTATAATTTTTATATT
1 TTTATTATTTTTATATT
*
39495695 TGTATTATTT
1 TTTATTATTT
39495705 ATTAAATCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (17 bp):
TTTATTATTTTTATATT
Found at i:39499331 original size:22 final size:22
Alignment explanation
Indices: 39499306--39499349 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
39499296 CCTGGAGTTC
*
39499306 ACAGAGAATGTCAATACTAGGG
1 ACAGAAAATGTCAATACTAGGG
*
39499328 ACAGAAAATGTCAGTACTAGGG
1 ACAGAAAATGTCAATACTAGGG
39499350 GTAGCGGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.14, G:0.27, T:0.18
Consensus pattern (22 bp):
ACAGAAAATGTCAATACTAGGG
Found at i:39502804 original size:137 final size:137
Alignment explanation
Indices: 39502599--39502874 Score: 534
Period size: 137 Copynumber: 2.0 Consensus size: 137
39502589 CGAAATGTAA
39502599 AACTTTTTCCACAAAATTTAAATGTAACAGCCGTTTTCGGTAAAAATCAGAACAGTGGTTTCGGG
1 AACTTTTTCCACAAAATTTAAATGTAACAGCCGTTTTCGGTAAAAATCAGAACAGTGGTTTCGGG
*
39502664 ACCATAAATTCAAAGTCAAAAAAATTATTTTTATATTATTTTGAGGTCTATAGCATGATAATATT
66 ACCACAAATTCAAAGTCAAAAAAATTATTTTTATATTATTTTGAGGTCTATAGCATGATAATATT
39502729 ATAGTAT
131 ATAGTAT
*
39502736 AACTTTTTCCACAACATTTAAATGTAACAGCCGTTTTCGGTAAAAATCAGAACAGTGGTTTCGGG
1 AACTTTTTCCACAAAATTTAAATGTAACAGCCGTTTTCGGTAAAAATCAGAACAGTGGTTTCGGG
39502801 ACCACAAATTCAAAGTCAAAAAAATTATTTTTATATTATTTTGAGGTCTATAGCATGATAATATT
66 ACCACAAATTCAAAGTCAAAAAAATTATTTTTATATTATTTTGAGGTCTATAGCATGATAATATT
39502866 ATAGTAT
131 ATAGTAT
39502873 AA
1 AA
39502875 AAATTTCGTT
Statistics
Matches: 137, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
137 137 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (137 bp):
AACTTTTTCCACAAAATTTAAATGTAACAGCCGTTTTCGGTAAAAATCAGAACAGTGGTTTCGGG
ACCACAAATTCAAAGTCAAAAAAATTATTTTTATATTATTTTGAGGTCTATAGCATGATAATATT
ATAGTAT
Found at i:39504010 original size:26 final size:25
Alignment explanation
Indices: 39503980--39504058 Score: 60
Period size: 26 Copynumber: 3.2 Consensus size: 25
39503970 AATGTGTGCG
39503980 AGATACATTGAGTTGGCTTCGGGCC
1 AGATACATTGAGTTGGCTTCGGGCC
** *
39504005 ATGAT--ATTG-G--CACTTCGGGTGCG
1 A-GATACATTGAGTTGGCTTC-GG-GCC
39504028 AGATACATTGAGTTGGCTTCGGGCC
1 AGATACATTGAGTTGGCTTCGGGCC
39504053 ACGATA
1 A-GATA
39504059 TTGACACTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 17
0.63 0.10 0.27
Matches are distributed among these distances:
21 4 0.10
22 5 0.13
23 4 0.10
24 8 0.21
25 5 0.13
26 9 0.23
27 4 0.10
ACGTcount: A:0.22, C:0.19, G:0.32, T:0.28
Consensus pattern (25 bp):
AGATACATTGAGTTGGCTTCGGGCC
Found at i:39504046 original size:48 final size:48
Alignment explanation
Indices: 39503929--39504087 Score: 221
Period size: 48 Copynumber: 3.2 Consensus size: 48
39503919 GTCATTAGGG
*
39503929 GATACATTGAGTTGGCTTAGGGCCATGATATTGGCACTTCGAATGTGTGCGA
1 GATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCG---G-GTGCGA
39503981 GATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGA
1 GATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGA
* * * *
39504029 GATACATTGAGTTGGCTTCGGGCCACGATATTGACACTTAGTGTGCGA
1 GATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGA
*
39504077 GATTC-TTGAGT
1 GATACATTGAGT
39504088 ATCCGATATT
Statistics
Matches: 101, Mismatches: 6, Indels: 5
0.90 0.05 0.04
Matches are distributed among these distances:
47 6 0.06
48 54 0.53
49 1 0.01
52 40 0.40
ACGTcount: A:0.21, C:0.17, G:0.31, T:0.31
Consensus pattern (48 bp):
GATACATTGAGTTGGCTTCGGGCCATGATATTGGCACTTCGGGTGCGA
Found at i:39513508 original size:47 final size:46
Alignment explanation
Indices: 39513395--39513748 Score: 282
Period size: 47 Copynumber: 7.7 Consensus size: 46
39513385 TGATTTGTGC
* * * ** * *
39513395 GCCAGAGTAAG-CATGTCTGGGACATGCTTTGGCCACA-TTATGAGA
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGG-CACAGAGATGGGT
* *
39513440 GCCAGTGTAAGACCATATCTGGGACATGGCATCAGCACAGAGATGGGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGAGATGGGT
* * *
39513488 GCCAGAGTAAGACATGTCTGGGACATGCATCGGC-CTCGACA-GAGGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAC-AGAGATG-GGT
* * *
39513534 AGCCAGTGTAAGACGTGTCTGGGACAGGCATCGGCTA-AGAG-T-TGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-ACAGAGATGGGT
* *
39513579 GCTAGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGAGATGGGT
1 GCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCACAGAGATGGGT
* * * *
39513627 GCTAGAGTAAGACATGTCTGGGACATGCATCGGC-CTCGACA-GAGGT
1 GCCAGTGTAAGACATGTCTGGGACATGCATCGGCAC-AGAGATG-GGT
* * *
39513673 AGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTA-AGAG-T-TGT
1 -GCCAGTGTAAGACATGTCTGGGACATGCATCGGC-ACAGAGATGGGT
*
39513718 GCTAGTGTAAGACATGTCTGGGACATGCATC
1 GCCAGTGTAAGACATGTCTGGGACATGCATC
39513749 AGCAAGGATA
Statistics
Matches: 249, Mismatches: 39, Indels: 43
0.75 0.12 0.13
Matches are distributed among these distances:
44 39 0.16
45 30 0.12
46 39 0.16
47 109 0.44
48 32 0.13
ACGTcount: A:0.26, C:0.20, G:0.32, T:0.21
Consensus pattern (46 bp):
GCCAGTGTAAGACATGTCTGGGACATGCATCGGCACAGAGATGGGT
Found at i:39513693 original size:139 final size:139
Alignment explanation
Indices: 39513443--39513752 Score: 561
Period size: 139 Copynumber: 2.2 Consensus size: 139
39513433 TATGAGAGCC
*
39513443 AGTGTAAGACCATATCTGGGACATGGCATCAGCACAGAGATGGGTGCCAGAGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGGGTGCCAGAGTAAGACATGTCTG
*
39513508 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACAGGCATCGGCTAAG
66 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
39513573 AGTTGTGCT
131 AGTTGTGCT
* * *
39513582 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGAGATGGGTGCTAGAGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGGGTGCCAGAGTAAGACATGTCTG
39513647 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
66 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
39513712 AGTTGTGCT
131 AGTTGTGCT
39513721 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCA
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCA
39513753 AGGATATATG
Statistics
Matches: 164, Mismatches: 7, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
137 8 0.05
138 13 0.08
139 143 0.87
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (139 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGGGTGCCAGAGTAAGACATGTCTG
GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
AGTTGTGCT
Found at i:39513735 original size:91 final size:87
Alignment explanation
Indices: 39513443--39513748 Score: 271
Period size: 91 Copynumber: 3.3 Consensus size: 87
39513433 TATGAGAGCC
* * *
39513443 AGTGTAAGACCATATCTGGGACATGGCATCAGC-ACAGAGATGGGTGCCAGAGTAAGACATGTCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-AGAG-T--GTGCCAGTGTAAGACATGTCT
* *
39513507 GGGACATGCATCGGCCTCGACAGAG-GTAGCC
60 GGGACACGCATCGG-CT--ACAGAGTGT-GCT
* * * *
39513538 AGTGTAAGACGTGTCTGGGACAGGCATCGGCTAAGAGTTGTGCTAGTGTAAGACCATGTTTGGGA
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAG-TGTGCCAGTGTAAGA-CATGTCTGGGA
*
39513603 CATGGCATCGGC-ACAGAGATGGGTGCT
64 CA-CGCATCGGCTACAGAG-T--GTGCT
* *
39513630 AGAGTAAGACATGTCTGGGACATGCATCGGCCTCGACAGAG-GTAGCCAGTGTAAGACGTGTCTG
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CT--A-AGAGTGT-GCCAGTGTAAGACATGTCTG
39513694 GGACACGCATCGGCTA-AGAGTTGTGCT
61 GGACACGCATCGGCTACAGAG-TGTGCT
39513721 AGTGTAAGACATGTCTGGGACATGCATC
1 AGTGTAAGACATGTCTGGGACATGCATC
39513749 AGCAAGGATA
Statistics
Matches: 179, Mismatches: 19, Indels: 30
0.79 0.08 0.13
Matches are distributed among these distances:
89 6 0.03
91 44 0.25
92 42 0.23
93 36 0.20
94 26 0.15
95 21 0.12
96 4 0.02
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.21
Consensus pattern (87 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTAAGAGTGTGCCAGTGTAAGACATGTCTGGGACA
CGCATCGGCTACAGAGTGTGCT
Found at i:39513776 original size:139 final size:139
Alignment explanation
Indices: 39513443--39513799 Score: 531
Period size: 139 Copynumber: 2.6 Consensus size: 139
39513433 TATGAGAGCC
* * ** *
39513443 AGTGTAAGACCATATCTGGGACATGGCATCAGCACAGAGATGGGTGCCAGAGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGAACTAGAGTAAGACATGTCTG
*
39513508 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACAGGCATCGGCTAAG
66 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
39513573 AGTTGTGCT
131 AGTTGTGCT
* * * **
39513582 AGTGTAAGACCATGTTTGGGACATGGCATCGGCACAGAGATGGGTGCTAGAGTAAGACATGTCTG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGAACTAGAGTAAGACATGTCTG
39513647 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
66 GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
39513712 AGTTGTGCT
131 AGTTGTGCT
* *
39513721 AGTGTAAGA-CATGTCTGGGACAT-GCATCAGCA-AGGATATATGAGAACTAGTGTAAGACCATG
1 AGTGTAAGACCATGTCTGGGACATGGCATCAGCACA-G--AGATGAGAACTAGAGTAAGA-CATG
39513783 TCTGGGACATGGCATCG
62 TCTGGGACAT-GCATCG
39513800 ACAGTATATC
Statistics
Matches: 201, Mismatches: 12, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
136 1 0.00
137 9 0.04
138 13 0.06
139 158 0.79
140 14 0.07
141 6 0.03
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.21
Consensus pattern (139 bp):
AGTGTAAGACCATGTCTGGGACATGGCATCAGCACAGAGATGAGAACTAGAGTAAGACATGTCTG
GGACATGCATCGGCCTCGACAGAGGTAGCCAGTGTAAGACGTGTCTGGGACACGCATCGGCTAAG
AGTTGTGCT
Found at i:39522578 original size:19 final size:19
Alignment explanation
Indices: 39522548--39522607 Score: 61
Period size: 19 Copynumber: 3.1 Consensus size: 19
39522538 GCCCCCTCCA
*
39522548 TTTCTCTTCTTTCTTTTCTT-
1 TTTCT-TTCTTTC-TCTCTTC
39522568 TTTCTTTCTTTCTCTCTTC
1 TTTCTTTCTTTCTCTCTTC
*
39522587 TTTCCTTCTTTC-CTCATTC
1 TTTCTTTCTTTCTCTC-TTC
39522606 TT
1 TT
39522608 CCCCTTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
18 8 0.22
19 23 0.64
20 5 0.14
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (19 bp):
TTTCTTTCTTTCTCTCTTC
Found at i:39522587 original size:15 final size:15
Alignment explanation
Indices: 39522550--39522595 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
39522540 CCCCTCCATT
39522550 TCTCTTCTTTCTTT-
1 TCTCTTCTTTCTTTC
*
39522564 TCTTTTTCTTTCTTTC
1 TC-TCTTCTTTCTTTC
*
39522580 TCTCTTCTTTCCTTC
1 TCTCTTCTTTCTTTC
39522595 T
1 T
39522596 TTCCTCATTC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 2 0.07
15 23 0.85
16 2 0.07
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (15 bp):
TCTCTTCTTTCTTTC
Found at i:39522607 original size:30 final size:30
Alignment explanation
Indices: 39522550--39522607 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
39522540 CCCCTCCATT
* * *
39522550 TCTCTTCTTTCTTTTCTTTTTCTTTCTTTC
1 TCTCTTCTTTCTCTTCTTTCTCATTCTTTC
39522580 TCTCTTCTTTC-CTTCTTTCCTCATTCTT
1 TCTCTTCTTTCTCTTCTTT-CTCATTCTT
39522608 CCCCTTTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (30 bp):
TCTCTTCTTTCTCTTCTTTCTCATTCTTTC
Found at i:39522645 original size:13 final size:13
Alignment explanation
Indices: 39522603--39522646 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
39522593 TCTTTCCTCA
39522603 TTCTTCCCC-TTT
1 TTCTTCCCCATTT
*
39522615 CTTCTTCCCTCATCT
1 -TTCTTCCC-CATTT
39522630 TTCTTCCCCATTT
1 TTCTTCCCCATTT
39522643 TTCT
1 TTCT
39522647 CTTAACCACC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.59
14 9 0.33
15 2 0.07
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.55
Consensus pattern (13 bp):
TTCTTCCCCATTT
Done.