Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 161 of 226
Found at i:51795701 original size:20 final size:20
Alignment explanation
Indices: 51795653--51795701 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
51795643 GTTGTTAAAT
*
51795653 AAATTTATAATTTATAACTA
1 AAATTTTTAATTTATAACTA
* * *
51795673 AAATATTTAATTTTTTACTA
1 AAATTTTTAATTTATAACTA
*
51795693 TAATTTTTA
1 AAATTTTTA
51795702 TTCTTAATTA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTTTAATTTATAACTA
Found at i:51796257 original size:24 final size:24
Alignment explanation
Indices: 51796230--51796281 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
51796220 ACCAAAAATA
51796230 TTCAAAGACTTGACATGTAAATTT
1 TTCAAAGACTTGACATGTAAATTT
** *
51796254 TTCATTGACTTGATATGTAAATTT
1 TTCAAAGACTTGACATGTAAATTT
51796278 TTCA
1 TTCA
51796282 TTTTGATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (24 bp):
TTCAAAGACTTGACATGTAAATTT
Found at i:51796282 original size:24 final size:24
Alignment explanation
Indices: 51796236--51796283 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
51796226 AATATTCAAA
51796236 GACTTGACATGTAAATTTTTCATT
1 GACTTGACATGTAAATTTTTCATT
*
51796260 GACTTGATATGTAAATTTTTCATT
1 GACTTGACATGTAAATTTTTCATT
51796284 TTGATTAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.29, C:0.10, G:0.12, T:0.48
Consensus pattern (24 bp):
GACTTGACATGTAAATTTTTCATT
Found at i:51801160 original size:14 final size:14
Alignment explanation
Indices: 51801135--51801172 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
51801125 TAACATTATG
51801135 TTAAAA-ATTAAAA
1 TTAAAATATTAAAA
51801148 TTAAAATATTAAAA
1 TTAAAATATTAAAA
*
51801162 TTTAAAT-TTAA
1 TTAAAATATTAA
51801173 GCTGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 10 0.43
14 13 0.57
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTAAAATATTAAAA
Found at i:51802993 original size:20 final size:19
Alignment explanation
Indices: 51802948--51802993 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
51802938 TTCCAAACTT
*
51802948 GAGTTGTTCTCAATATAAA
1 GAGTTGTTCTAAATATAAA
*
51802967 G-GTTGTTCTAAATAATTAA
1 GAGTTGTTCTAAAT-ATAAA
51802986 GAGTTGTT
1 GAGTTGTT
51802994 TTGTGGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 11 0.48
19 6 0.26
20 6 0.26
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.41
Consensus pattern (19 bp):
GAGTTGTTCTAAATATAAA
Found at i:51805742 original size:31 final size:31
Alignment explanation
Indices: 51805678--51805742 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
51805668 GGTTTCTATA
* * *
51805678 TTTGGCTTGAATGTTTAATTTGGTGCCTGAG
1 TTTGGCTTCAATGTTCAATTTGGTGCCTAAG
51805709 TTTGGCTTCAATGTTCAATTTGGTGCCTAAG
1 TTTGGCTTCAATGTTCAATTTGGTGCCTAAG
51805740 TTT
1 TTT
51805743 TTTCAAATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.17, C:0.12, G:0.25, T:0.46
Consensus pattern (31 bp):
TTTGGCTTCAATGTTCAATTTGGTGCCTAAG
Found at i:51810805 original size:24 final size:24
Alignment explanation
Indices: 51810760--51810805 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
51810750 AACACGTGTG
* *
51810760 TATGTACTATCCATTTTGAATTTA
1 TATGTACTATCCAATTTAAATTTA
**
51810784 TATGTACTATGTAATTTAAATT
1 TATGTACTATCCAATTTAAATT
51810806 GTCTCCTATG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (24 bp):
TATGTACTATCCAATTTAAATTTA
Found at i:51812603 original size:19 final size:18
Alignment explanation
Indices: 51812579--51812644 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 18
51812569 ATGATAAAAA
51812579 ATAAAAATCAATAAAATTT
1 ATAAAAAT-AATAAAATTT
*
51812598 ATAAAAATGAATAAATTTT
1 ATAAAAAT-AATAAAATTT
* *
51812617 AAAAAAATATTTAAAATTT
1 ATAAAAATA-ATAAAATTT
*
51812636 ATTAAAATA
1 ATAAAAATA
51812645 TAGAATAAAA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 1 0.03
19 38 0.97
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (18 bp):
ATAAAAATAATAAAATTT
Found at i:51812717 original size:20 final size:18
Alignment explanation
Indices: 51812667--51812725 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
51812657 ATAAAAATCG
51812667 TAAAAATTGT-AAAATATA
1 TAAAAA-TGTAAAAATATA
* *
51812685 TAGAACTGTAAAAATATA
1 TAAAAATGTAAAAATATA
*
51812703 TAAAAATGTAAAAAAATA
1 TAAAAATGTAAAAATATA
51812721 TAAAA
1 TAAAA
51812726 TTATTCCCAC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
17 3 0.09
18 32 0.91
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.27
Consensus pattern (18 bp):
TAAAAATGTAAAAATATA
Found at i:51813035 original size:20 final size:20
Alignment explanation
Indices: 51813010--51813052 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
51813000 TTTATAAAAG
51813010 TTTACAATCTTTATAATTTT
1 TTTACAATCTTTATAATTTT
*
51813030 TTTACAATTTTTATAATTTT
1 TTTACAATCTTTATAATTTT
51813050 TTT
1 TTT
51813053 GTCACACGTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (20 bp):
TTTACAATCTTTATAATTTT
Found at i:51815684 original size:38 final size:37
Alignment explanation
Indices: 51815601--51815686 Score: 104
Period size: 38 Copynumber: 2.3 Consensus size: 37
51815591 CTCTGTACAA
51815601 CCTGTAGATAATCATTTCATGGTGTCACTTCGTAAAG
1 CCTGTAGATAATCATTTCATGGTGTCACTTCGTAAAG
* * *
51815638 CTTATAGATAATCATTTTCATGGTGTCGC-TC-TATAGAG
1 CCTGTAGATAATCA-TTTCATGGTGTCACTTCGTA-A-AG
51815676 CCTGTAGATAA
1 CCTGTAGATAA
51815687 CCATACCACG
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 2 0.05
37 15 0.37
38 24 0.59
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (37 bp):
CCTGTAGATAATCATTTCATGGTGTCACTTCGTAAAG
Found at i:51817595 original size:41 final size:41
Alignment explanation
Indices: 51817515--51817749 Score: 380
Period size: 41 Copynumber: 5.7 Consensus size: 41
51817505 ATATAACACT
** * * *
51817515 GGCATAAAGCCTGCTAGGCACCAAGCCCGATACATTTCACC
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* * *
51817556 GGCACAAAGCCTGCTAGACATAAAGTCTGATATAATTCACC
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
51817597 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
* *
51817638 GGCATAAAGCCTGCTAGGCATAAAGCCTAACATAATTCACC
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
51817679 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
51817720 GGCATAAAGCCTGCTAGGCATAAAGCCTGA
1 GGCATAAAGCCTGCTAGGCATAAAGCCTGA
51817750 ACTTACAAAA
Statistics
Matches: 179, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 179 1.00
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (41 bp):
GGCATAAAGCCTGCTAGGCATAAAGCCTGATATAATTCACC
Found at i:51818930 original size:16 final size:17
Alignment explanation
Indices: 51818909--51818940 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
51818899 AAATATGCAA
51818909 TCACATAA-TTCATATT
1 TCACATAACTTCATATT
51818925 TCACATAACTTCATAT
1 TCACATAACTTCATAT
51818941 CATCAATTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.22, G:0.00, T:0.41
Consensus pattern (17 bp):
TCACATAACTTCATATT
Found at i:51819190 original size:41 final size:41
Alignment explanation
Indices: 51819102--51819256 Score: 127
Period size: 41 Copynumber: 3.7 Consensus size: 41
51819092 GGCTCGTACA
* ** * *
51819102 ATGCCAACGTCCCAGAC-GTGGTCTTACATGTAATCACATATG
1 ATGCCAATGTCCCAGACAG-GGTCTTACA-CAAATCAAATACG
* *
51819144 ATGCCACTGTCCCAGAGAGGGTCTTACACAAATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATACG
* * **
51819185 ATGCCAATGTCCCGGACATGGTCTTACACGTATACACAAGT-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACAAAT-CA-AA-TACG
*
51819228 ATGCCAACGTCCCAGAC-GTGGTCTTACAC
1 ATGCCAATGTCCCAGACAG-GGTCTTACAC
51819257 GAAAATACAT
Statistics
Matches: 92, Mismatches: 16, Indels: 9
0.79 0.14 0.08
Matches are distributed among these distances:
41 36 0.39
42 25 0.27
43 30 0.33
44 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.23
Consensus pattern (41 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACAAATCAAATACG
Found at i:51820109 original size:28 final size:31
Alignment explanation
Indices: 51820070--51820128 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 31
51820060 CCTTTCCTTT
51820070 TTATTATAATAAC-ATTAT-AATA-TATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
* *
51820098 TTATTATTATAACTTTTATAAATAGTATAAA
1 TTATTATAATAACTATTATAAATAGTATAAA
51820129 AACTATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
28 12 0.46
29 4 0.15
30 4 0.15
31 6 0.23
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (31 bp):
TTATTATAATAACTATTATAAATAGTATAAA
Found at i:51829351 original size:23 final size:21
Alignment explanation
Indices: 51829316--51829383 Score: 57
Period size: 24 Copynumber: 3.0 Consensus size: 21
51829306 ATCTTTATAT
51829316 TCTC-TTATATTTTAAATTTAA
1 TCTCTTTAT-TTTTAAATTTAA
*
51829337 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-A-AATTTAA
*
51829362 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTA-TTTTTAAATTTAA
51829384 AAATTTAGGT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
21 4 0.11
22 6 0.16
23 8 0.21
24 10 0.26
25 10 0.26
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (21 bp):
TCTCTTTATTTTTAAATTTAA
Found at i:51829360 original size:25 final size:22
Alignment explanation
Indices: 51829316--51829383 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 22
51829306 ATCTTTATAT
51829316 TCTC-TTATATTTTA-AATTTAA
1 TCTCTTTAT-TTTTAGAATTTAA
*
51829337 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-AGAATTTAA
*
51829362 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTATTTTTAGAATTTAA
51829384 AAATTTAGGT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
21 4 0.10
22 7 0.18
23 13 0.33
24 5 0.13
25 10 0.26
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (22 bp):
TCTCTTTATTTTTAGAATTTAA
Found at i:51829379 original size:22 final size:22
Alignment explanation
Indices: 51829316--51829383 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 22
51829306 ATCTTTATAT
* *
51829316 TCTC-TTATATTTTAAATTTAA
1 TCTCTTTATTTTTTGAATTTAA
* *
51829337 TCTCTATTTATTTTTAAGAATTTAG
1 TCTC--TTTATTTTT-TGAATTTAA
51829362 TCTCTTTATTTTTTGAATTTAA
1 TCTCTTTATTTTTTGAATTTAA
51829384 AAATTTAGGT
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
21 4 0.11
22 7 0.19
23 9 0.24
24 7 0.19
25 10 0.27
ACGTcount: A:0.28, C:0.09, G:0.04, T:0.59
Consensus pattern (22 bp):
TCTCTTTATTTTTTGAATTTAA
Found at i:51840332 original size:45 final size:45
Alignment explanation
Indices: 51840235--51840337 Score: 163
Period size: 46 Copynumber: 2.3 Consensus size: 45
51840225 TAATTTTGTA
*
51840235 AAGAAAACCATACTAAGTTGTGAAATGTAGGTATGGTATTTCAGT
1 AAGAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
*
51840280 AATGAAAATCATACTAAGTTGTGAAAAGTAGGT-TGGTATTTCAGT
1 AA-GAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
51840325 GAAGAAAACCATA
1 -AAGAAAACCATA
51840338 TTGAGTTATA
Statistics
Matches: 53, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
45 23 0.43
46 30 0.57
ACGTcount: A:0.41, C:0.09, G:0.21, T:0.29
Consensus pattern (45 bp):
AAGAAAACCATACTAAGTTGTGAAAAGTAGGTATGGTATTTCAGT
Found at i:51841188 original size:93 final size:93
Alignment explanation
Indices: 51841023--51841234 Score: 236
Period size: 93 Copynumber: 2.3 Consensus size: 93
51841013 AAAAGTTTTT
* ** * *
51841023 AAACTGTTTCAAAAAAAAGTAATTAAG--TCTATGTTTTTTTTTTTGCATTCAATTGGGTACTTA
1 AAACTTTTTCAAAAAAAAACAATTAAGCTTCTATGTTTTTTTTTTGGCATTCAATTAGGTACTTA
** * *
51841086 ATTTTCAAAATGCATCAAAAAGGACTTC
66 AGCTGCAAAATGCATCAAAAAGGACGTC
*
51841114 AAATTTTTTCAAAAAAAAACAATTAAGCTTCTACT-TTTTTTTTTTGGCACTT-AATTAGGTACT
1 AAACTTTTTCAAAAAAAAACAATTAAGCTTCTA-TGTTTTTTTTTTGGCA-TTCAATTAGGTACT
* * *
51841177 TGAGCTGCAAAATGCATGAAAAAGGCCGTC
64 TAAGCTGCAAAATGCATCAAAAAGGACGTC
* *
51841207 GAACTTTTTC-AAAAAAACCAATTAAGCT
1 AAACTTTTTCAAAAAAAAACAATTAAGCT
51841235 CCAGCTTTTT
Statistics
Matches: 101, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
91 23 0.23
92 17 0.17
93 58 0.57
94 3 0.03
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.36
Consensus pattern (93 bp):
AAACTTTTTCAAAAAAAAACAATTAAGCTTCTATGTTTTTTTTTTGGCATTCAATTAGGTACTTA
AGCTGCAAAATGCATCAAAAAGGACGTC
Found at i:51841516 original size:19 final size:19
Alignment explanation
Indices: 51841494--51841579 Score: 95
Period size: 19 Copynumber: 4.4 Consensus size: 19
51841484 ATGATAAAAA
51841494 ATAAAAATGAATAAAATTT
1 ATAAAAATGAATAAAATTT
*
51841513 ATAAAAATGAATAAATTTT
1 ATAAAAATGAATAAAATTT
*
51841532 AATAAAAAT-ATTTAAAATTT
1 -ATAAAAATGA-ATAAAATTT
*
51841552 ATTAAAAATAGAATAAAA-CT
1 A-TAAAAAT-GAATAAAATTT
51841572 ATAAAAAT
1 ATAAAAAT
51841580 TGTAAAATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
19 27 0.47
20 24 0.42
21 5 0.09
22 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAAAATGAATAAAATTT
Found at i:51841536 original size:20 final size:20
Alignment explanation
Indices: 51841493--51841569 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
51841483 AATGATAAAA
51841493 AATAAAAATGAATAAAATTT
1 AATAAAAATGAATAAAATTT
*
51841513 -ATAAAAATGAATAAATTTT
1 AATAAAAATGAATAAAATTT
*
51841532 AATAAAAAT-ATTTAAAATTT
1 AATAAAAATGA-ATAAAATTT
*
51841552 ATTAAAAATAGAATAAAA
1 AATAAAAAT-GAATAAAA
51841570 CTATAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
19 19 0.40
20 23 0.48
21 5 0.10
22 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (20 bp):
AATAAAAATGAATAAAATTT
Found at i:51841576 original size:39 final size:38
Alignment explanation
Indices: 51841505--51841627 Score: 105
Period size: 39 Copynumber: 3.3 Consensus size: 38
51841495 TAAAAATGAA
** *
51841505 TAAAATTTATAAAAATGAATAAATTTTAATAAAAATATT
1 TAAAATTTATAAAAATGAATAAATACTAATAAAAAT-TG
51841544 TAAAATTTATTAAAAATAGAATAAA-ACT-ATAAAAATTG
1 TAAAATTTA-TAAAAAT-GAATAAATACTAATAAAAATTG
* * *
51841582 TAAAATATATAGAACTGTAA-AAATA-T-ATAAAAA-TG
1 TAAAATTTATAAAAATG-AATAAATACTAATAAAAATTG
*
51841617 TAAAATATATA
1 TAAAATTTATA
51841628 TATAAAATTA
Statistics
Matches: 74, Mismatches: 6, Indels: 12
0.80 0.07 0.13
Matches are distributed among these distances:
35 13 0.18
36 12 0.16
37 8 0.11
38 9 0.12
39 17 0.23
40 8 0.11
41 7 0.09
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (38 bp):
TAAAATTTATAAAAATGAATAAATACTAATAAAAATTG
Found at i:51841600 original size:17 final size:17
Alignment explanation
Indices: 51841571--51841627 Score: 78
Period size: 18 Copynumber: 3.2 Consensus size: 17
51841561 AGAATAAAAC
51841571 TATAAAAATTGTAAAATA
1 TATAAAAA-TGTAAAATA
* *
51841589 TATAGAACTGTAAAAATA
1 TATAAAAATGT-AAAATA
51841607 TATAAAAATGTAAAATA
1 TATAAAAATGTAAAATA
51841624 TATA
1 TATA
51841628 TATAAAATTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
17 13 0.38
18 21 0.62
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.32
Consensus pattern (17 bp):
TATAAAAATGTAAAATA
Found at i:51841703 original size:19 final size:20
Alignment explanation
Indices: 51841671--51841727 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
51841661 TTATAAAGTA
*
51841671 GTAAGAAAATTATAAAAAAT
1 GTAAAAAAATTATAAAAAAT
* **
51841691 GTAAAGAAA-TATAAAATTT
1 GTAAAAAAATTATAAAAAAT
51841710 GTAAAAAAATTATAAAAA
1 GTAAAAAAATTATAAAAA
51841728 TTATCTTACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAAAT
Found at i:51841932 original size:28 final size:28
Alignment explanation
Indices: 51841901--51841968 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
51841891 TTTGATACGT
*
51841901 TTTATATTTTTTATGATTTTTATAAAAG
1 TTTATATTTTTTATAATTTTTATAAAAG
* * * * * *
51841929 TTTACAATCTTTATAATTTTTTTACAAT
1 TTTATATTTTTTATAATTTTTATAAAAG
51841957 TTTATATTTTTT
1 TTTATATTTTTT
51841969 TTTCTCACAC
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.63
Consensus pattern (28 bp):
TTTATATTTTTTATAATTTTTATAAAAG
Found at i:51841971 original size:20 final size:20
Alignment explanation
Indices: 51841929--51841969 Score: 68
Period size: 18 Copynumber: 2.1 Consensus size: 20
51841919 TTTATAAAAG
51841929 TTTACAATCTTTATAATTTT
1 TTTACAATCTTTATAATTTT
51841949 TTTACAAT-TTTAT-ATTTT
1 TTTACAATCTTTATAATTTT
51841967 TTT
1 TTT
51841970 TTCTCACACG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 8 0.38
19 5 0.24
20 8 0.38
ACGTcount: A:0.27, C:0.07, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTACAATCTTTATAATTTT
Found at i:51845896 original size:38 final size:38
Alignment explanation
Indices: 51845854--51845942 Score: 124
Period size: 38 Copynumber: 2.3 Consensus size: 38
51845844 CTGTACAGCT
* * * *
51845854 TGTAGATAATCATTTTTATGGTGTCGCTTCGTAGAGCC
1 TGTAGATAACCATTTTCATGGTGTCGCTCCATAGAGCC
51845892 TGTAGATAACCATTTTCATGGTGTCGCTCCATAGAGCC
1 TGTAGATAACCATTTTCATGGTGTCGCTCCATAGAGCC
**
51845930 CATAGATAACCAT
1 TGTAGATAACCAT
51845943 ACCACAATGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (38 bp):
TGTAGATAACCATTTTCATGGTGTCGCTCCATAGAGCC
Found at i:51849294 original size:22 final size:22
Alignment explanation
Indices: 51849264--51849306 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51849254 ACACCAAAAC
*
51849264 AAGCTTTTAGCGGCGCTTTTTT
1 AAGCCTTTAGCGGCGCTTTTTT
51849286 AAGCCTTTAGCGGCGCTTTTT
1 AAGCCTTTAGCGGCGCTTTTT
51849307 AGCGCCGCAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.14, C:0.21, G:0.23, T:0.42
Consensus pattern (22 bp):
AAGCCTTTAGCGGCGCTTTTTT
Found at i:51849583 original size:43 final size:43
Alignment explanation
Indices: 51849465--51849625 Score: 145
Period size: 43 Copynumber: 3.8 Consensus size: 43
51849455 AGAGTAAGAC
* * *
51849465 CTTTAGCGGTGCTTTCCCCTA-AAACGCCGC-AATAG-CCTCTGAT
1 CTTTAGCGGCGCTTTCTCC-ACAAACGCCGCTAA-AGACC-ATGAT
*
51849508 CTGTAGCGGCGCTTTCT-CACAAACG-CGACTAAAGACCATGAT
1 CTTTAGCGGCGCTTTCTCCACAAACGCCG-CTAAAGACCATGAT
* * * *
51849550 CTTTAGTGGCGCTTTTTCCACAAACGCCGCTAAAGACCCTTAT
1 CTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATGAT
** *
51849593 CTTTAGCGGCGCTTTGACCA-AAACGCCACTAAA
1 CTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAA
51849626 TTTGGCAGAT
Statistics
Matches: 99, Mismatches: 13, Indels: 13
0.79 0.10 0.10
Matches are distributed among these distances:
41 3 0.03
42 39 0.39
43 55 0.56
44 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.25
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTCTCCACAAACGCCGCTAAAGACCATGAT
Found at i:51849977 original size:21 final size:21
Alignment explanation
Indices: 51849935--51850026 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
51849925 TTTGACGCTG
**
51849935 CTCTGCTTCCCTCGCTTTAGC
1 CTCTGCTTCCCTCGCTGCAGC
51849956 CTCTGCTTCCCTCGCTGCAGC
1 CTCTGCTTCCCTCGCTGCAGC
* * * *
51849977 CTGTACTTCTCTCACTGCCA-C
1 CTCTGCTTCCCTCGCTG-CAGC
* * *
51849998 CTCTGCTTCTCTTGCTGCCGC
1 CTCTGCTTCCCTCGCTGCAGC
*
51850019 ATCTGCTT
1 CTCTGCTT
51850027 TAAGCTGCTG
Statistics
Matches: 57, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
20 1 0.02
21 54 0.95
22 2 0.04
ACGTcount: A:0.07, C:0.42, G:0.15, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCGCTGCAGC
Found at i:51850072 original size:66 final size:66
Alignment explanation
Indices: 51849996--51850143 Score: 192
Period size: 66 Copynumber: 2.2 Consensus size: 66
51849986 TCTCACTGCC
* * *
51849996 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGCTCTTCATA-CTTTCGT
1 ACCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTG-TAGCTGGAGCTCTTCATATCTTT-GT
51850059 TGA
64 TGA
* * * * *
51850062 ACCTCAGCTTCTCTCGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTTTTTG
1 ACCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGCTCTTCATATCTTTGTTG
51850127 A
66 A
51850128 ACCTCAGCTTCTCTCG
1 ACCTCAGCTTCTCTCG
51850144 ATGTTGCCTC
Statistics
Matches: 72, Mismatches: 8, Indels: 4
0.86 0.10 0.05
Matches are distributed among these distances:
65 1 0.01
66 67 0.93
67 4 0.06
ACGTcount: A:0.14, C:0.30, G:0.18, T:0.39
Consensus pattern (66 bp):
ACCTCAGCTTCTCTCGCTGCCGCATCTACTTTAAGCTGTAGCTGGAGCTCTTCATATCTTTGTTG
A
Found at i:51850159 original size:66 final size:66
Alignment explanation
Indices: 51849996--51850166 Score: 184
Period size: 66 Copynumber: 2.6 Consensus size: 66
51849986 TCTCACTGCC
* * * * ** *
51849996 ACCTCTGCTTCTCTTGCTGCCGCATCTGCTTTAAGCTGCT-GCTGGAGCTCTTCATACTTTCGTT
1 ACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTG-TAGCTGGAGCTCTTCATACTTTCGTT
51850060 GA
65 GA
* * * * *
51850062 ACCTCAGCTTCTCTCGCTGCTGCATCTACTTTCAGTTGTAGCTGGAGTTCTTCATATCTTT-TTT
1 ACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGTAGCTGGAGCTCTTCATA-CTTTCGTT
51850126 GA
65 GA
* *
51850128 ACCTCAGCTTCTCTCGATGTTGCCTCCACTTTAAGTTGT
1 ACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGT
51850167 GTAATTTGCT
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 85 0.94
67 4 0.04
ACGTcount: A:0.14, C:0.29, G:0.18, T:0.40
Consensus pattern (66 bp):
ACCTCAGCTTCTCTCGATGCTGCATCCACTTTAAGTTGTAGCTGGAGCTCTTCATACTTTCGTTG
A
Found at i:51858529 original size:17 final size:17
Alignment explanation
Indices: 51858507--51858540 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
51858497 GTGACTTGTT
* *
51858507 TAAAAAATTCAGAAAAA
1 TAAAAAAATAAGAAAAA
51858524 TAAAAAAATAAGAAAAA
1 TAAAAAAATAAGAAAAA
51858541 AATCAATTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (17 bp):
TAAAAAAATAAGAAAAA
Found at i:51858889 original size:106 final size:106
Alignment explanation
Indices: 51858746--51859116 Score: 697
Period size: 106 Copynumber: 3.5 Consensus size: 106
51858736 AGGGGAAGTC
* *
51858746 ATTATCACTGACATTAGTAGGCCAAACCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
1 ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
51858811 ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
66 ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
*
51858852 ATTATTACTGACATTAGTAGGTCAACCCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
1 ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
51858917 ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
66 ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
*
51858958 ATTATTACTGACATTAGTAGGCCAACCCTCAGCTAATTTCTTCCAAATAATAAGGTGAAGTTATT
1 ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
*
51859023 ATGACTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
66 ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
51859064 ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAA
1 ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAA
51859117 CTATTTGCAT
Statistics
Matches: 258, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
106 258 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (106 bp):
ATTATTACTGACATTAGTAGGCCAACCCTCAACTAATTTCTTCCAAATAATAAGGTGAAGTTATT
ATGATTGACATTAGTAGGACAACCCTCAACTCATATCAGTT
Found at i:51861761 original size:65 final size:64
Alignment explanation
Indices: 51861638--51861761 Score: 180
Period size: 65 Copynumber: 2.0 Consensus size: 64
51861628 AAGGTAAGGG
* *
51861638 GAAGTTATTATCACCGACATTAGTAGGCCAACCCTCAAATTCGTATATCTTCCAAATAATAAGAT
1 GAAGTTATTATCACCGACAGTAGTAGGCCAACCCTCAAACTCG-ATATCTTCCAAATAATAAGAT
* * *
51861703 GAAGTTATTATGACTGACAGTAGTAGGCCAACCCTC-AACTC-ATTTCTTCCAAATAATAA
1 GAAGTTATTATCACCGACAGTAGTAGGCCAACCCTCAAACTCGATATCTTCCAAATAATAA
51861762 CTATTTGCAG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
62 17 0.31
64 4 0.07
65 33 0.61
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
GAAGTTATTATCACCGACAGTAGTAGGCCAACCCTCAAACTCGATATCTTCCAAATAATAAGAT
Found at i:51866875 original size:14 final size:14
Alignment explanation
Indices: 51866856--51866883 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
51866846 GATGGATGAA
51866856 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
51866870 TATTAAGCAGTTAG
1 TATTAAGCAGTTAG
51866884 AAAGTTGTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (14 bp):
TATTAAGCAGTTAG
Found at i:51872807 original size:22 final size:20
Alignment explanation
Indices: 51872782--51872821 Score: 62
Period size: 22 Copynumber: 1.9 Consensus size: 20
51872772 ATTAAATTTT
51872782 AATATTATTTTCATAAAATAAC
1 AATATTATTTT-A-AAAATAAC
51872804 AATATTATTTTAAAAATA
1 AATATTATTTTAAAAATA
51872822 TTTTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 1 0.06
22 11 0.61
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
AATATTATTTTAAAAATAAC
Found at i:51880703 original size:9 final size:9
Alignment explanation
Indices: 51880689--51880833 Score: 90
Period size: 9 Copynumber: 16.3 Consensus size: 9
51880679 AGTATATATG
51880689 AGTTATGTA
1 AGTTATGTA
51880698 AGTTATGT-
1 AGTTATGTA
*
51880706 A-TTACGTA
1 AGTTATGTA
*
51880714 AGTTAT-TT
1 AGTTATGTA
*
51880722 AGTTATGTG
1 AGTTATGTA
*
51880731 AGTTACGTATA
1 AGTTA--TGTA
*
51880742 ATATTATGTA
1 A-GTTATGTA
*
51880752 ACGTATTATGTT
1 A-G--TTATGTA
51880764 A-TTATGTA
1 AGTTATGTA
51880772 AGTTATGT-
1 AGTTATGTA
51880780 A-TTATGTA
1 AGTTATGTA
51880788 AGTTATGTA
1 AGTTATGTA
51880797 AGTTATGTA
1 AGTTATGTA
* *
51880806 AATTAAGT-
1 AGTTATGTA
*
51880814 A-TTATATA
1 AGTTATGTA
*
51880822 AGTTATGCA
1 AGTTATGTA
51880831 AGT
1 AGT
51880834 CCGACAAGTT
Statistics
Matches: 105, Mismatches: 18, Indels: 26
0.70 0.12 0.17
Matches are distributed among these distances:
7 15 0.14
8 20 0.19
9 53 0.50
10 4 0.04
11 3 0.03
12 10 0.10
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (9 bp):
AGTTATGTA
Found at i:51880714 original size:16 final size:16
Alignment explanation
Indices: 51880691--51880828 Score: 105
Period size: 16 Copynumber: 7.9 Consensus size: 16
51880681 TATATATGAG
51880691 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
* *
51880707 TTACGTAAGTTATTTA
1 TTATGTAAGTTATGTA
* *
51880723 GTTATGTGAGTTACGTATAATA
1 -TTATGTAAG-T---TAT-GTA
51880745 TTATGTAACGTATTATGTTA
1 TTATGTAA-G--TTATG-TA
51880765 TTATGTAAGTTATGTA
1 TTATGTAAGTTATGTA
51880781 TTATGTAAGTTATGTAA
1 TTATGTAAGTTATGT-A
* *
51880798 GTTATGTAAATTAAGTA
1 -TTATGTAAGTTATGTA
*
51880815 TTATATAAGTTATG
1 TTATGTAAGTTATG
51880829 CAAGTCCGAC
Statistics
Matches: 98, Mismatches: 13, Indels: 22
0.74 0.10 0.17
Matches are distributed among these distances:
16 42 0.43
17 14 0.14
18 14 0.14
19 1 0.01
20 13 0.13
21 10 0.10
22 3 0.03
23 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.47
Consensus pattern (16 bp):
TTATGTAAGTTATGTA
Found at i:51880718 original size:25 final size:25
Alignment explanation
Indices: 51880689--51880833 Score: 98
Period size: 25 Copynumber: 5.5 Consensus size: 25
51880679 AGTATATATG
*
51880689 AGTTATGTAAGTTATGTATTACGTA
1 AGTTATGTAAGTTATGTATTATGTA
* *
51880714 AGTTAT-TTAGTTATGTGAGTTACGTATA
1 AGTTATGTAAGTTATGT-A-TTA--TGTA
*
51880742 ATATTATGTAACGTATTATGTTATTATGTA
1 A-GTTATGTAA-G--TTATG-TATTATGTA
51880772 AGTTATGT-A-TTATGTAAGTTATGTA
1 AGTTATGTAAGTTATGT-A-TTATGTA
* * *
51880797 AGTTATGTAAATTAAGTATTATATA
1 AGTTATGTAAGTTATGTATTATGTA
*
51880822 AGTTATGCAAGT
1 AGTTATGTAAGT
51880834 CCGACAAGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 28
0.71 0.08 0.21
Matches are distributed among these distances:
23 1 0.01
24 15 0.16
25 38 0.40
26 5 0.05
27 5 0.05
28 4 0.04
29 10 0.11
30 6 0.06
31 1 0.01
32 3 0.03
33 6 0.06
34 1 0.01
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.46
Consensus pattern (25 bp):
AGTTATGTAAGTTATGTATTATGTA
Found at i:51880898 original size:22 final size:22
Alignment explanation
Indices: 51880868--51880910 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
51880858 ACACCAAAAC
*
51880868 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
51880890 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
51880911 AGCGCCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:51881156 original size:129 final size:129
Alignment explanation
Indices: 51881004--51881317 Score: 502
Period size: 129 Copynumber: 2.4 Consensus size: 129
51880994 TTTTATAAAT
* * * *
51881004 AAACGTCGCTAAAGATCATGACCTTTAGCGGCGCATTTCTCACAAACGCCGCTAAAGAACAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACAAGAC
*
51881069 CTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCAC
66 CTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTAACCAC
*
51881133 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACAAGAC
* * * * **
51881198 CTTTAGCGGTGCTTTAACCACAAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCAC
66 CTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTAACCAC
* *
51881262 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTATCACAAACGCCGCTAAA
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAA
51881318 AGTACAACTC
Statistics
Matches: 171, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 171 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (129 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGAACAAGAC
CTTTAGCGGCGCTTTAACCACAAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTAACCAC
Found at i:51881334 original size:43 final size:43
Alignment explanation
Indices: 51881004--51881317 Score: 452
Period size: 43 Copynumber: 7.3 Consensus size: 43
51880994 TTTTATAAAT
* * * *
51881004 AAACGTCGCTAAAGATCATGACCTTTAGCGGCGCATTT-CTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTAC-CAC
* *
51881047 AAACGCCGCTAAAGAACAAGACCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
*
51881090 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
51881133 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTT-CTCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTAC-CAC
* *
51881176 AAACGCCGCTAAAGACCAAGACCTTTAGCGGTGCTTTAACCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* * * * *
51881219 AAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
* *
51881262 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTTATCAC
1 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
51881305 AAACGCCGCTAAA
1 AAACGCCGCTAAA
51881318 AGTACAACTC
Statistics
Matches: 245, Mismatches: 23, Indels: 6
0.89 0.08 0.02
Matches are distributed among these distances:
42 1 0.00
43 242 0.99
44 2 0.01
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.20
Consensus pattern (43 bp):
AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTACCAC
Found at i:51882315 original size:40 final size:40
Alignment explanation
Indices: 51882252--51882336 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
51882242 TAGCTTGAAC
* * *
51882252 ATCAACACTTCAATATTTAATATGTAAGGAATTATCAAAA
1 ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
* *
51882292 ATCAACATTTCAATAATTT-ATATGCAAGAAATTAACACAA
1 ATCAACACTTCAAT-ATTTAATATGCAAGAAATTAACAAAA
51882332 ATCAA
1 ATCAA
51882337 TCTTACAACA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 35 0.90
41 4 0.10
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.31
Consensus pattern (40 bp):
ATCAACACTTCAATATTTAATATGCAAGAAATTAACAAAA
Found at i:51882509 original size:86 final size:85
Alignment explanation
Indices: 51882412--51882599 Score: 268
Period size: 86 Copynumber: 2.2 Consensus size: 85
51882402 GGCATTAGGG
* ** * *
51882412 CTAAATCTTCAATTTCTATAATGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTC
1 CTAAATTTTCAATTT-TATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
* *
51882477 ATGTATTTACCAAAAATCAGA
65 ATGCATTTACCAAAAAGCAGA
* *
51882498 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTC
1 CTAAATTTTCAAT-TTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
*
51882563 ATGCATTTACCAACAAGCAGA
65 ATGCATTTACCAAAAAGCAGA
51882584 CTAAATTTTCAATTTT
1 CTAAATTTTCAATTTT
51882600 CAATTTTTAA
Statistics
Matches: 90, Mismatches: 11, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
85 3 0.03
86 85 0.94
87 2 0.02
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (85 bp):
CTAAATTTTCAATTTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTCA
TGCATTTACCAAAAAGCAGA
Found at i:51882864 original size:86 final size:87
Alignment explanation
Indices: 51882690--51882864 Score: 217
Period size: 86 Copynumber: 2.0 Consensus size: 87
51882680 TCATCATTTC
* * * * * *
51882690 AACAATTTACATGCAAAAAATTAGCAAAAATTAACAATTCATGTATAATGTATTTACCAAAAACC
1 AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
* *
51882755 GGACCAACTTGTCAATTTTTAT
66 AGACCAAATTGTCAATTTTTAT
* * * *
51882777 AACATTTTAAATGCAACAAATTAACACAAATTAACAATACAAGT-TCATATATTCACCAAAAACC
1 AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
* *
51882841 AGACTAAATTTTCAATTTTTAT
66 AGACCAAATTGTCAATTTTTAT
51882863 AA
1 AA
51882865 AATAAGAGAT
Statistics
Matches: 74, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
86 37 0.50
87 37 0.50
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.31
Consensus pattern (87 bp):
AACAATTTAAATGCAAAAAATTAACAAAAATTAACAATACAAGTATAATATATTCACCAAAAACC
AGACCAAATTGTCAATTTTTAT
Found at i:51888235 original size:22 final size:22
Alignment explanation
Indices: 51888207--51888359 Score: 225
Period size: 22 Copynumber: 7.0 Consensus size: 22
51888197 TGTTGATAGT
*
51888207 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
51888229 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
51888251 ACGTACTAAGCTCTCATGTTTA
1 ACGTACTAAGCTCTCATGTTTA
* * * **
51888273 ACGAACTAAACCCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
**
51888295 ACGTACTAAGCTCTCATGGCTA
1 ACGTACTAAGCTCTCATGTTTA
*
51888317 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTA
51888339 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
51888360 GAACAATAAA
Statistics
Matches: 119, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 119 1.00
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTA
Found at i:51888505 original size:14 final size:14
Alignment explanation
Indices: 51888486--51888515 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51888476 AACCCATAAA
51888486 CCTTAAATCACAAT
1 CCTTAAATCACAAT
*
51888500 CCTTAAATCAGAAT
1 CCTTAAATCACAAT
51888514 CC
1 CC
51888516 CTGATCCATA
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:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (14 bp):
CCTTAAATCACAAT
Found at i:51888630 original size:21 final size:20
Alignment explanation
Indices: 51888595--51888633 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
51888585 CTAAATTAAC
*
51888595 TATATATATACCCTAAACCA
1 TATATATAAACCCTAAACCA
51888615 TATATATTAAACCCTAAAC
1 TATATA-TAAACCCTAAAC
51888634 TATAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (20 bp):
TATATATAAACCCTAAACCA
Found at i:51889043 original size:40 final size:41
Alignment explanation
Indices: 51888999--51889135 Score: 127
Period size: 40 Copynumber: 3.4 Consensus size: 41
51888989 TCGGCTTAGG
* *
51888999 TTTTTTGCGGCGTTTTTCCAAAAAATGCCGCTAATGCT-AA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
* *** *
51889039 TTTTTAGCGGCG-CTTTCCTGGAAACGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
* * ** * *
51889079 TCTTTAGCGGCG-TTTTACGTAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
*
51889119 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGTTTTT
51889136 TGTCCAAACG
Statistics
Matches: 79, Mismatches: 16, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
39 20 0.25
40 55 0.70
41 4 0.05
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTTCCAAAAAACGCCGCTAATGCTCAA
Found at i:51889262 original size:16 final size:16
Alignment explanation
Indices: 51889241--51889288 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
51889231 CTTATTATCT
51889241 TATTATGTAAGTTATG
1 TATTATGTAAGTTATG
*
51889257 TATTATGTAAGTTAAG
1 TATTATGTAAGTTATG
**
51889273 TATTACATAAGTTATG
1 TATTATGTAAGTTATG
51889289 CAAGTCCGAC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.35, C:0.02, G:0.17, T:0.46
Consensus pattern (16 bp):
TATTATGTAAGTTATG
Found at i:51889404 original size:19 final size:18
Alignment explanation
Indices: 51889380--51889456 Score: 62
Period size: 19 Copynumber: 4.5 Consensus size: 18
51889370 TTACGTAACT
51889380 TATTATGTAATAAGTTATG
1 TATTATGT-ATAAGTTATG
51889399 TATTATG--TAAG-T-T-
1 TATTATGTATAAGTTATG
51889412 TA-TA--TATAAGTTATGTG
1 TATTATGTATAAGTTA--TG
51889429 TATTATGTCATAAGTTATG
1 TATTATGT-ATAAGTTATG
51889448 TATTATGTA
1 TATTATGTA
51889457 AGTTTATATA
Statistics
Matches: 47, Mismatches: 0, Indels: 23
0.67 0.00 0.33
Matches are distributed among these distances:
12 6 0.13
13 3 0.06
14 1 0.02
15 1 0.02
16 5 0.11
17 2 0.04
18 3 0.06
19 17 0.36
20 1 0.02
21 8 0.17
ACGTcount: A:0.34, C:0.01, G:0.16, T:0.49
Consensus pattern (18 bp):
TATTATGTATAAGTTATG
Found at i:51889418 original size:52 final size:49
Alignment explanation
Indices: 51889349--51889472 Score: 176
Period size: 49 Copynumber: 2.5 Consensus size: 49
51889339 ATGCAAGTTG
* * *
51889349 TTATATAAGTTTCTATATAAGTTACGTAACTTATTATGTAATAAGTTATGTA
1 TTATGTAAGTTTATATATAAGTTACGT---GTATTATGTAATAAGTTATGTA
* *
51889401 TTATGTAAGTTTATATATAAGTTATGTGTATTATGTCATAAGTTATGTA
1 TTATGTAAGTTTATATATAAGTTACGTGTATTATGTAATAAGTTATGTA
51889450 TTATGTAAGTTTATATATAAGTT
1 TTATGTAAGTTTATATATAAGTT
51889473 GTTATATAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
49 43 0.64
52 24 0.36
ACGTcount: A:0.35, C:0.03, G:0.14, T:0.48
Consensus pattern (49 bp):
TTATGTAAGTTTATATATAAGTTACGTGTATTATGTAATAAGTTATGTA
Found at i:51889427 original size:21 final size:22
Alignment explanation
Indices: 51889401--51889449 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
51889391 AAGTTATGTA
51889401 TTATGTAAGT-TTATAT-ATAAG
1 TTATGT-AGTATTATATCATAAG
*
51889422 TTATGT-GTATTATGTCATAAG
1 TTATGTAGTATTATATCATAAG
51889443 TTATGTA
1 TTATGTA
51889450 TTATGTAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 2 0.08
20 5 0.21
21 17 0.71
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TTATGTAGTATTATATCATAAG
Found at i:51889634 original size:24 final size:23
Alignment explanation
Indices: 51889607--51889704 Score: 60
Period size: 24 Copynumber: 4.2 Consensus size: 23
51889597 TTTATTATTG
51889607 AAAATATAGATGTTAATATTTAGA
1 AAAATATAGAT-TTAATATTTAGA
* **
51889631 AAAATA-ACATTTACAATTATTTCTA
1 AAAATATAGATTT--AA-TATTTAGA
* * *
51889656 AAATTATAAAATTTATTA-TT-G-
1 AAAATAT-AGATTTAATATTTAGA
51889677 AAAATATAGATGTTAATATTTAGA
1 AAAATATAGAT-TTAATATTTAGA
51889701 AAAA
1 AAAA
51889705 AACATTTACA
Statistics
Matches: 55, Mismatches: 10, Indels: 18
0.66 0.12 0.22
Matches are distributed among these distances:
20 3 0.05
21 11 0.20
22 4 0.07
23 6 0.11
24 14 0.25
25 12 0.22
27 5 0.09
ACGTcount: A:0.51, C:0.03, G:0.07, T:0.39
Consensus pattern (23 bp):
AAAATATAGATTTAATATTTAGA
Found at i:51889764 original size:55 final size:55
Alignment explanation
Indices: 51889697--51889808 Score: 215
Period size: 55 Copynumber: 2.0 Consensus size: 55
51889687 TGTTAATATT
51889697 TAGAAAAAAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATA
1 TAGAAAAAAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATA
*
51889752 TAGAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATA
1 TAGAAAAAAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATA
51889807 TA
1 TA
51889809 CATGTTAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (55 bp):
TAGAAAAAAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATA
Found at i:51889767 original size:69 final size:70
Alignment explanation
Indices: 51889565--51889755 Score: 366
Period size: 70 Copynumber: 2.7 Consensus size: 70
51889555 CTGAATTATG
*
51889565 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
1 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
51889630 AAAAA
66 AAAAA
51889635 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
1 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
51889700 AAAAA
66 AAAAA
51889705 -AACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGA
1 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGA
51889756 AAATAACATT
Statistics
Matches: 120, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
69 51 0.43
70 69 0.57
ACGTcount: A:0.48, C:0.05, G:0.05, T:0.41
Consensus pattern (70 bp):
TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
AAAAA
Found at i:51889771 original size:124 final size:125
Alignment explanation
Indices: 51889631--51889880 Score: 459
Period size: 124 Copynumber: 2.0 Consensus size: 125
51889621 AATATTTAGA
* *
51889631 AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATAT
1 AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAAT
51889696 TTAGAAAAA-AACATTTACAATTATTTCTAAAATTATAAA-ATTTATTATTGAAAATATAG
66 TTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATA-TTATTATTGAAAATATAG
51889755 AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAAT
1 AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAAT
51889820 TTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAG
66 TTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAG
51889880 A
1 A
51889881 TGTTAATATT
Statistics
Matches: 122, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
124 72 0.59
125 49 0.40
126 1 0.01
ACGTcount: A:0.50, C:0.05, G:0.04, T:0.40
Consensus pattern (125 bp):
AAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAAT
TTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAG
Found at i:51889841 original size:70 final size:70
Alignment explanation
Indices: 51889746--51889922 Score: 279
Period size: 70 Copynumber: 2.5 Consensus size: 70
51889736 TTTATTATTG
*
51889746 AAAATATAG-AAAATAACATTTACAATTATTTCTAAAATTATAAA-ATTTATTATTGAAAATATA
1 AAAATTTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATA-TTATTATTGAAAATATA
51889809 CATGTT
65 CATGTT
*
51889815 AAAATTTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAG
1 AAAATTTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAC
51889880 ATGTT
66 ATGTT
* *
51889885 AATATTTAGAAAAATAACATGTACAATTAGTTT-TAAAA
1 AAAATTTAGAAAAATAACATTTACAATTA-TTTCTAAAA
51889923 ATTTCTAGAA
Statistics
Matches: 101, Mismatches: 4, Indels: 5
0.92 0.04 0.05
Matches are distributed among these distances:
69 8 0.08
70 89 0.88
71 4 0.04
ACGTcount: A:0.51, C:0.05, G:0.06, T:0.38
Consensus pattern (70 bp):
AAAATTTAGAAAAATAACATTTACAATTATTTCTAAAATTATAAATATTATTATTGAAAATATAC
ATGTT
Found at i:51889894 original size:194 final size:195
Alignment explanation
Indices: 51889565--51889922 Score: 641
Period size: 194 Copynumber: 1.8 Consensus size: 195
51889555 CTGAATTATG
* * *
51889565 TAACATTTACAATTCTTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATATTTAG
1 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAATTTAG
51889630 AAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATA
66 AAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATA
*
51889695 TTTAGAAAAA-AACATTTACAATTA-TTTCTAAAATTATAAAATTTATTATTGAAAATATAGAAA
131 TTTAGAAAAATAACATGTACAATTAGTTT-TAAAATTATAAAATTTATTATTGAAAATATAGAAA
51889758 A
195 A
51889759 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAATTTAG
1 TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAATTTAG
51889824 AAAAATAACATTTACAATTATTTCTAAAATTAT-AAATATTATTATTGAAAATATAGATGTTAAT
66 AAAAATAACATTTACAATTATTTCTAAAATTATAAAAT-TTATTATTGAAAATATAGATGTTAAT
51889888 ATTTAGAAAAATAACATGTACAATTAGTTTTAAAA
130 ATTTAGAAAAATAACATGTACAATTAGTTTTAAAA
51889923 ATTTCTAGAA
Statistics
Matches: 157, Mismatches: 4, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
193 4 0.03
194 132 0.84
195 18 0.11
196 3 0.02
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (195 bp):
TAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATACATGTTAAAATTTAG
AAAAATAACATTTACAATTATTTCTAAAATTATAAAATTTATTATTGAAAATATAGATGTTAATA
TTTAGAAAAATAACATGTACAATTAGTTTTAAAATTATAAAATTTATTATTGAAAATATAGAAAA
Found at i:51891800 original size:12 final size:12
Alignment explanation
Indices: 51891783--51891839 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
51891773 TTCTAGAATT
*
51891783 GGGGGATTTTTG
1 GGGGGAATTTTG
* *
51891795 GGGGGAAATTCG
1 GGGGGAATTTTG
51891807 GGGGGAATTTTG
1 GGGGGAATTTTG
**
51891819 GGGATAA-TTTG
1 GGGGGAATTTTG
51891830 GGGGGAATTT
1 GGGGGAATTT
51891840 CGGCTAAGTG
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 9 0.26
12 26 0.74
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (12 bp):
GGGGGAATTTTG
Found at i:51891821 original size:23 final size:24
Alignment explanation
Indices: 51891783--51891839 Score: 73
Period size: 23 Copynumber: 2.4 Consensus size: 24
51891773 TTCTAGAATT
*
51891783 GGGGGATTTTTGGGGGGA-AATTCG
1 GGGGGAATTTT-GGGGGATAATTCG
*
51891807 GGGGGAATTTT-GGGGATAATTTG
1 GGGGGAATTTTGGGGGATAATTCG
51891830 GGGGGAATTT
1 GGGGGAATTT
51891840 CGGCTAAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
22 5 0.17
23 15 0.50
24 10 0.33
ACGTcount: A:0.19, C:0.02, G:0.47, T:0.32
Consensus pattern (24 bp):
GGGGGAATTTTGGGGGATAATTCG
Found at i:51893879 original size:86 final size:84
Alignment explanation
Indices: 51893772--51893933 Score: 261
Period size: 86 Copynumber: 1.9 Consensus size: 84
51893762 CTTTAAAACC
*
51893772 AAACGCCGCTAAGTACATTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCACCAAT
1 AAACGCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCC-CCAA-
51893837 CAAATAGCGGCGCTATGATAG
64 CAAATAGCGGCGCTATGATAG
* * * *
51893858 AAACGCCGCTAAATACCTTAACATTAGTGGCGATTGACCAGAACACGCCACTATCACCCTCAACC
1 AAACGCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACA
51893923 AATAGCGGCGC
66 AATAGCGGCGC
51893934 ATACATAAAA
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
84 12 0.17
85 3 0.04
86 56 0.79
ACGTcount: A:0.35, C:0.30, G:0.17, T:0.18
Consensus pattern (84 bp):
AAACGCCGCTAAATACATTAACATTAGTGGCGATTGACCAAAACACGCCACTATCACCCCCAACA
AATAGCGGCGCTATGATAG
Found at i:51895837 original size:13 final size:13
Alignment explanation
Indices: 51895819--51895844 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51895809 AAAGTGCGAG
51895819 CCTGTTGAAGACA
1 CCTGTTGAAGACA
51895832 CCTGTTGAAGACA
1 CCTGTTGAAGACA
51895845 ATATGCAAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (13 bp):
CCTGTTGAAGACA
Found at i:51898165 original size:90 final size:90
Alignment explanation
Indices: 51898065--51898312 Score: 233
Period size: 89 Copynumber: 2.8 Consensus size: 90
51898055 GACATCAAAT
*
51898065 TTTTTCAAAAAAAGCAATTAAGCTTCTACTTTTTTTTTTGCACTCAATTGGGTACTTGAGCTGCA
1 TTTTTCAAAAAAAGCAATTAAGCTTCTACTTTTTTTTTTGCACTCAATTGGGTACTTGAACTGCA
* **
51898130 AAATGCATGAAA-AAGGCGGTC-GAAC
66 AAATGCAT-AAAGAAGACCCTCAG-AC
* * * * * * *
51898155 TTTTTCAAAAAAAACCAATTAAGCTCCAAC--TTATTTCT-CACTTAATTGGGTACTTGAACTAT
1 TTTTTC-AAAAAAAGCAATTAAGCTTCTACTTTTTTTTTTGCACTCAATTGGGTACTTGAACT-G
51898217 CAAAATGCATAAAGAAGACCCTCAGAC
64 CAAAATGCATAAAGAAGACCCTCAGAC
**** *
51898244 TTAAAAAAAAAAAAGCAATTAAGCTT-T--TTTTTGTTTTTGCACTCAATTGAGTACTTGAACTG
1 TT-TTTCAAAAAAAGCAATTAAGCTTCTACTTTTT-TTTTTGCACTCAATTGGGTACTTGAACTG
51898306 CTAAAAT
64 C-AAAAT
51898313 ATATAAAAAA
Statistics
Matches: 125, Mismatches: 23, Indels: 20
0.74 0.14 0.12
Matches are distributed among these distances:
88 25 0.20
89 48 0.38
90 32 0.26
91 20 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (90 bp):
TTTTTCAAAAAAAGCAATTAAGCTTCTACTTTTTTTTTTGCACTCAATTGGGTACTTGAACTGCA
AAATGCATAAAGAAGACCCTCAGAC
Found at i:51899848 original size:38 final size:38
Alignment explanation
Indices: 51899762--51899854 Score: 132
Period size: 38 Copynumber: 2.4 Consensus size: 38
51899752 TGCTTTGTAG
* * * *
51899762 AGCCTGTAGATAATCATTTTCATGGTGTCGCTTCATAG
1 AGCCTGTAGATAACCATTTTCATGGTGTCACTCCATAA
*
51899800 AGCCTATAGATAACCATTTTCATGGTGTCACTCCATAA
1 AGCCTGTAGATAACCATTTTCATGGTGTCACTCCATAA
*
51899838 AGCCCGTAGATAACCAT
1 AGCCTGTAGATAACCAT
51899855 ACCACAATGC
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 48 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (38 bp):
AGCCTGTAGATAACCATTTTCATGGTGTCACTCCATAA
Found at i:51906317 original size:18 final size:17
Alignment explanation
Indices: 51906283--51906321 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
51906273 TTTGCAAGCG
51906283 AAAATCTAAGCGAAATC
1 AAAATCTAAGCGAAATC
* *
51906300 AAAATCCTAATCGGAATC
1 AAAAT-CTAAGCGAAATC
51906318 AAAA
1 AAAA
51906322 AGCGAGGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.54, C:0.18, G:0.10, T:0.18
Consensus pattern (17 bp):
AAAATCTAAGCGAAATC
Found at i:51910481 original size:6 final size:6
Alignment explanation
Indices: 51910470--51910495 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
51910460 ATAAAATTTA
51910470 TTAAAT TTAAAT TTAAAT TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TTAAAT TT
51910496 TTAGACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:51910940 original size:19 final size:19
Alignment explanation
Indices: 51910903--51910940 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
51910893 CAAATTTTAT
*
51910903 ATTTTTAAAAAATTATAAA
1 ATTTTTAAAAAAATATAAA
*
51910922 ATTTTTAAAAAAATCTAAA
1 ATTTTTAAAAAAATATAAA
51910941 GAATATATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTTTAAAAAAATATAAA
Found at i:51911213 original size:2 final size:2
Alignment explanation
Indices: 51911206--51911249 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
51911196 TGTGGATCAT
51911206 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51911248 TA
1 TA
51911250 NNNNNNNNNN
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51918711 original size:11 final size:11
Alignment explanation
Indices: 51918697--51918723 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
51918687 TATTTTTTAA
51918697 TTTTAAAATAT
1 TTTTAAAATAT
51918708 TTTTAAAATAT
1 TTTTAAAATAT
51918719 TTTTA
1 TTTTA
51918724 TTTTTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:51918740 original size:31 final size:31
Alignment explanation
Indices: 51918705--51918763 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
51918695 AATTTTAAAA
*
51918705 TATTTTTAAAATAT-TTTTATTTTTATTTTTT
1 TATTTTTAAAATATATTTT-TTTGTATTTTTT
51918736 TATTTTTAAAATATATTTTTTTGTATTT
1 TATTTTTAAAATATATTTTTTTGTATTT
51918764 ATTAAAAATC
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (31 bp):
TATTTTTAAAATATATTTTTTTGTATTTTTT
Found at i:51919965 original size:14 final size:14
Alignment explanation
Indices: 51919946--51919977 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
51919936 TATGTCAAAA
51919946 ATTAAAATTTAAAT
1 ATTAAAATTTAAAT
51919960 ATTAAAATTTAAAT
1 ATTAAAATTTAAAT
51919974 -TTAA
1 ATTAA
51919978 GCTGAATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.22
14 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAAATTTAAAT
Found at i:51921504 original size:45 final size:40
Alignment explanation
Indices: 51921407--51921493 Score: 106
Period size: 39 Copynumber: 2.1 Consensus size: 40
51921397 TATATGCAAG
* *
51921407 TATATATATATATATATATGAAGATTAGAAATATATAAAA
1 TATATAAATATATATATATGAAAATTAGAAATATATAAAA
*
51921447 TATA-AAATATATATTTATGAAAATTA-AAATGCATATAAAA
1 TATATAAATATATATATATGAAAATTAGAAAT--ATATAAAA
51921487 TGATATA
1 T-ATATA
51921494 TAAATAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 4 0.10
39 19 0.47
40 13 0.32
41 3 0.08
42 1 0.03
ACGTcount: A:0.55, C:0.01, G:0.07, T:0.37
Consensus pattern (40 bp):
TATATAAATATATATATATGAAAATTAGAAATATATAAAA
Found at i:51930530 original size:24 final size:25
Alignment explanation
Indices: 51930503--51930549 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
51930493 CTTTATATTC
*
51930503 TTATATTTCA-AATTTAATCTCTAT
1 TTATATTTAAGAATTTAATCTCTAT
* *
51930527 TTATTTTTAAGAATTTAGTCTCT
1 TTATATTTAAGAATTTAATCTCT
51930550 TTATTTTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.55
Consensus pattern (25 bp):
TTATATTTAAGAATTTAATCTCTAT
Found at i:51933902 original size:16 final size:16
Alignment explanation
Indices: 51933850--51933904 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
51933840 TTATTTTGAC
*
51933850 TTGTTCCAAA-AGTGAG
1 TTGTTCCAAATA-AGAG
51933866 TTGTTCTCAATATAA-AGG
1 TTGTTC-CAA-ATAAGA-G
51933884 TTGTTCCAAATAAGAG
1 TTGTTCCAAATAAGAG
51933900 TTGTT
1 TTGTT
51933905 TTGTGGTGAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
16 16 0.48
17 8 0.24
18 8 0.24
19 1 0.03
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.38
Consensus pattern (16 bp):
TTGTTCCAAATAAGAG
Found at i:51934272 original size:16 final size:16
Alignment explanation
Indices: 51934253--51934285 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51934243 TAAAATTTTG
51934253 AAAAAATAAAAAATAC
1 AAAAAATAAAAAATAC
*
51934269 AAAAAATAAAAATTAC
1 AAAAAATAAAAAATAC
51934285 A
1 A
51934286 TTTTGGCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAAAATAC
Found at i:51934324 original size:29 final size:30
Alignment explanation
Indices: 51934278--51934406 Score: 154
Period size: 29 Copynumber: 4.4 Consensus size: 30
51934268 CAAAAAATAA
* * *
51934278 AAATTACATTTTGGCCCCTGAACTTT-TCT
1 AAATTACATTTCGACCCCTAAACTTTCTCT
* *
51934307 AAATTACATTTCAACCCCTAAACTTTCTCA
1 AAATTACATTTCGACCCCTAAACTTTCTCT
*
51934337 AAATTACATTTCTACCCCTAAACTTT-TCT
1 AAATTACATTTCGACCCCTAAACTTTCTCT
* * * *
51934366 AAATTTCATTTGGGCCCCTAAACTTTCTAT
1 AAATTACATTTCGACCCCTAAACTTTCTCT
51934396 AAATTACATTT
1 AAATTACATTT
51934407 TAGCTACATA
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
29 46 0.54
30 39 0.46
ACGTcount: A:0.31, C:0.25, G:0.05, T:0.40
Consensus pattern (30 bp):
AAATTACATTTCGACCCCTAAACTTTCTCT
Found at i:51934355 original size:59 final size:58
Alignment explanation
Indices: 51934277--51934407 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 58
51934267 ACAAAAAATA
* *
51934277 AAAATTACATTTTGGCCCCTGAACTTTTCTAAATTACATTTCAACCCCTAAACTTTCT
1 AAAATTACATTTTGACCCCTAAACTTTTCTAAATTACATTTCAACCCCTAAACTTTCT
* ***
51934335 CAAAATTACATTTCT-ACCCCTAAACTTTTCTAAATTTCATTTGGGCCCCTAAACTTTCT
1 -AAAATTACATTT-TGACCCCTAAACTTTTCTAAATTACATTTCAACCCCTAAACTTTCT
51934394 ATAAATTACATTTT
1 A-AAATTACATTTT
51934408 AGCTACATAT
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
58 2 0.03
59 61 0.95
60 1 0.02
ACGTcount: A:0.31, C:0.24, G:0.05, T:0.40
Consensus pattern (58 bp):
AAAATTACATTTTGACCCCTAAACTTTTCTAAATTACATTTCAACCCCTAAACTTTCT
Found at i:51935034 original size:13 final size:13
Alignment explanation
Indices: 51935012--51935050 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
51935002 AGAAGAAGGG
51935012 AGAAAGAAAGAAAA
1 AGAAA-AAAGAAAA
51935026 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
51935039 A-AAAATAAGAAA
1 AGAAAA-AAGAAA
51935051 GATAGCAGGC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 4 0.17
13 15 0.62
14 5 0.21
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:51935051 original size:17 final size:17
Alignment explanation
Indices: 51935012--51935052 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
51935002 AGAAGAAGGG
*
51935012 AGAAAGAAAGAAAAAGA
1 AGAAAGAAAAAAAAAGA
* *
51935029 AAAAAGAAAAAAAAATA
1 AGAAAGAAAAAAAAAGA
51935046 AGAAAGA
1 AGAAAGA
51935053 TAGCAGGCCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (17 bp):
AGAAAGAAAAAAAAAGA
Found at i:51935791 original size:17 final size:16
Alignment explanation
Indices: 51935745--51935793 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
51935735 TAAAGAAAAA
51935745 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAA-TTT
* *
51935762 TCATGACTTCAAAATTT
1 TCGTG-TTTCAAAATTT
51935779 CTCGTGTTTCAAAAT
1 -TCGTGTTTCAAAAT
51935794 AATAATAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.29, C:0.16, G:0.12, T:0.43
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:51936056 original size:18 final size:19
Alignment explanation
Indices: 51936028--51936083 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
51936018 TGTTTCTAAT
51936028 ATTCTCGTATTTCAAAAAA
1 ATTCTCGTATTTCAAAAAA
*
51936047 ATTC-CGTATTTAAAAAAAA
1 ATTCTCGTATTT-CAAAAAA
51936066 ATTCTCGTATTTCAAAAA
1 ATTCTCGTATTTCAAAAA
51936084 TTTTTGTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.21
19 19 0.58
20 7 0.21
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (19 bp):
ATTCTCGTATTTCAAAAAA
Found at i:51936084 original size:17 final size:17
Alignment explanation
Indices: 51936028--51936144 Score: 76
Period size: 17 Copynumber: 6.5 Consensus size: 17
51936018 TGTTTCTAAT
51936028 ATTCTCGTATTTCAAAAAA
1 ATTCTCGTATTTC--AAAA
*
51936047 ATTC-CGTATTTAAAAAAAA
1 ATTCTCGTATTT---CAAAA
51936066 ATTCTCGTATTTCAAAA
1 ATTCTCGTATTTCAAAA
* * *
51936083 ATTTTTGTGTTTCAAAA
1 ATTCTCGTATTTCAAAA
* *
51936100 ATTTTCGTGCTTTCAAGAA
1 ATTCTCGT-ATTTCAA-AA
*
51936119 ATTAC-CGTGTCTTCAAAA
1 ATT-CTCGTAT-TTCAAAA
51936137 ATTCTCGT
1 ATTCTCGT
51936145 TTTTTTAAAC
Statistics
Matches: 80, Mismatches: 9, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
17 26 0.32
18 22 0.28
19 25 0.31
20 7 0.09
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.40
Consensus pattern (17 bp):
ATTCTCGTATTTCAAAA
Found at i:51936100 original size:18 final size:17
Alignment explanation
Indices: 51936062--51936144 Score: 85
Period size: 17 Copynumber: 4.7 Consensus size: 17
51936052 GTATTTAAAA
* *
51936062 AAAAATTCTCGTATTTC
1 AAAAATTTTCGTGTTTC
*
51936079 AAAAATTTTTGTGTTTC
1 AAAAATTTTCGTGTTTC
51936096 AAAAATTTTCGTGCTTTC
1 AAAAATTTTCGTG-TTTC
**
51936114 AAGAAATTACCGTGTCTTC
1 AA-AAATTTTCGTGT-TTC
*
51936133 AAAAATTCTCGT
1 AAAAATTTTCGT
51936145 TTTTTTAAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
17 26 0.47
18 15 0.27
19 14 0.25
ACGTcount: A:0.33, C:0.16, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAAATTTTCGTGTTTC
Found at i:51947136 original size:11 final size:10
Alignment explanation
Indices: 51947122--51947176 Score: 76
Period size: 10 Copynumber: 5.5 Consensus size: 10
51947112 TAAAAAAGAG
51947122 AAAAAACAACA
1 AAAAAACAA-A
51947133 AAAAAACAAA
1 AAAAAACAAA
51947143 AAAAAACAAA
1 AAAAAACAAA
*
51947153 AAAAAA-ACA
1 AAAAAACAAA
*
51947162 AAAAAGCAAA
1 AAAAAACAAA
51947172 AAAAA
1 AAAAA
51947177 GTAAAAAAAG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
9 7 0.17
10 24 0.60
11 9 0.22
ACGTcount: A:0.87, C:0.11, G:0.02, T:0.00
Consensus pattern (10 bp):
AAAAAACAAA
Found at i:51947146 original size:21 final size:21
Alignment explanation
Indices: 51947122--51947166 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
51947112 TAAAAAAGAG
*
51947122 AAAAAACAACAAAAAAACAAA
1 AAAAAACAAAAAAAAAACAAA
51947143 AAAAAACAAAAAAAAAACAAA
1 AAAAAACAAAAAAAAAACAAA
51947164 AAA
1 AAA
51947167 GCAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.89, C:0.11, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAACAAAAAAAAAACAAA
Found at i:51947155 original size:29 final size:29
Alignment explanation
Indices: 51947113--51947185 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
51947103 TATTATGCCT
* *
51947113 AAAAAAGAGAAAAAACAACAAAAAAACAAA
1 AAAAAACA-AAAAAAAAACAAAAAAACAAA
*
51947143 AAAAAACAAAAAAAAAACAAAAAAGCAAA
1 AAAAAACAAAAAAAAAACAAAAAAACAAA
**
51947172 AAAAAGTAAAAAAA
1 AAAAAACAAAAAAA
51947186 GAAGAAGAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
29 31 0.82
30 7 0.18
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.01
Consensus pattern (29 bp):
AAAAAACAAAAAAAAAACAAAAAAACAAA
Found at i:51947177 original size:10 final size:10
Alignment explanation
Indices: 51947113--51947185 Score: 64
Period size: 10 Copynumber: 7.5 Consensus size: 10
51947103 TATTATGCCT
*
51947113 AAAAAAG-AG
1 AAAAAAGCAA
51947122 AAAAAA-CAA
1 AAAAAAGCAA
*
51947131 CAAAAAAACAA
1 -AAAAAAGCAA
*
51947142 AAAAAAACAA
1 AAAAAAGCAA
51947152 AAAAAA--AA
1 AAAAAAGCAA
51947160 CAAAAAAGCAA
1 -AAAAAAGCAA
*
51947171 AAAAAAGTAA
1 AAAAAAGCAA
51947181 AAAAA
1 AAAAA
51947186 GAAGAAGAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
8 2 0.04
9 13 0.23
10 36 0.64
11 5 0.09
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.01
Consensus pattern (10 bp):
AAAAAAGCAA
Found at i:51948402 original size:154 final size:152
Alignment explanation
Indices: 51948061--51948522 Score: 530
Period size: 154 Copynumber: 3.0 Consensus size: 152
51948051 AAGAATTATA
* * *
51948061 TTTTTC-AATTTTTGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGTCG
1 TTTTTCAAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTC-
*
51948125 TACGCTGAGG--TTTTTTAAATTTCTGTTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTT
65 -ACGCTGAGGTATTTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTT
* ** *
51948186 GAGCCTCGAGTCACATCAAGGTA-
129 GAGCCTCGGGTCACGCCGAGGTAT
* * *
51948209 TTTTTCAATTTCTATTTTTTTTAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGG
1 TTTTTCAAATT-T-TTGTTTTT-CAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGG
* * *
51948274 TCATGCCGAGGTATTTCTTTTAAATTT-TCGTTTTTCAAAAAATCAACTCATAATAC-AGAGGTG
63 TCACGCTGAGGTA-TT-TTTTAAATTTCT-GTTTTTCAAAAAATCAACTCATAATGCGAGAGGTG
*
51948337 AGTTGAGCCTCGGGTCATGCCGAGGTAT
125 AGTTGAGCCTCGGGTCACGCCGAGGTAT
* *
51948365 TTCTTTCAAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGATGGTTTGAGCCTCGGGTC
1 TT-TTTCAAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTC
* * *
51948430 ACGCTGAGGTA--TTTTCAATTTCTGTTTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTGA
65 ACGCTGAGGTATTTTTTAAATTTCTG-TTTTTC---AAAAAATCAACTCATAATGCGAGAGGTGA
* * *
51948493 GTTGAGTCTCGGGTTACGCTGAGGTAT
126 GTTGAGCCTCGGGTCACGCCGAGGTAT
51948520 TTT
1 TTT
51948523 CAATATCTAT
Statistics
Matches: 266, Mismatches: 29, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
148 6 0.02
149 3 0.01
150 18 0.07
151 14 0.05
152 40 0.15
153 3 0.01
154 87 0.33
155 68 0.26
156 19 0.07
157 8 0.03
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (152 bp):
TTTTTCAAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCGGGTCA
CGCTGAGGTATTTTTTAAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGA
GCCTCGGGTCACGCCGAGGTAT
Found at i:51948477 original size:232 final size:228
Alignment explanation
Indices: 51948062--51948521 Score: 606
Period size: 232 Copynumber: 2.0 Consensus size: 228
51948052 AGAATTATAT
* * *
51948062 TTTTCAATTTTTGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGTCGTA
1 TTTTAAATTTTCGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCG-A
* * *
51948127 CGCTGAGGTTTTTTAAATTTCTGTTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
65 CGCCGAGGTTTTTTAAATTTCTGTTTTTCAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCT
** *
51948192 CGAGTCACATCAAGGTATTTTTCAATTTCTATTTTTTTTAAAAAAATCAACTCATAATGCGAGAG
130 CGAGTCACATCAAGGTATTTTTCAATTTCTATTTTTTAAAAAAAAATCAACTCATAATGCGAGAA
* *
51948257 GTGGGTTGAGCCTCGGGTCATGCCGAGGTATTTC
195 GTGAGTTGAGCCTCGGGTCACGCCGAGGTATTTC
51948291 TTTTAAATTTTCGTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC-A
1 TTTTAAATTTTCGTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCGA
* *
51948354 TGCCGAGGTATTTCTTTCAAATTTTTGTTTTTCAAAAATCAACTCATAATGCGAGAGATG-GTTT
65 CGCCGAGG--TTT-TTT-AAATTTCTGTTTTTC-AAAATCAACTCATAATGCGAGAGATGAG-TT
* * * *
51948418 GAGCCTCGGGTCAC-GCTGAGGTA-TTTTCAATTTCTGTTTTTTCAAAAAAAAATCAACTCATAA
124 GAGCCTCGAGTCACATC-AAGGTATTTTTCAATTTCTATTTTTT-AAAAAAAAATCAACTCATAA
* * * *
51948481 TGCTAGAAGTGAGTTGAGTCTCGGGTTACGCTGAGGTATTT
187 TGCGAGAAGTGAGTTGAGCCTCGGGTCACGCCGAGGTATTT
51948522 TCAATATCTA
Statistics
Matches: 201, Mismatches: 21, Indels: 15
0.85 0.09 0.06
Matches are distributed among these distances:
227 7 0.03
229 42 0.21
230 22 0.11
231 34 0.17
232 96 0.48
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (228 bp):
TTTTAAATTTTCGTTTTTCAAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTCGGGTCGAC
GCCGAGGTTTTTTAAATTTCTGTTTTTCAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTC
GAGTCACATCAAGGTATTTTTCAATTTCTATTTTTTAAAAAAAAATCAACTCATAATGCGAGAAG
TGAGTTGAGCCTCGGGTCACGCCGAGGTATTTC
Found at i:51948522 original size:78 final size:75
Alignment explanation
Indices: 51948059--51948570 Score: 501
Period size: 78 Copynumber: 6.7 Consensus size: 75
51948049 TCAAGAATTA
* * *
51948059 TATTTTTCAATTTTTGTTTTTC-AAAAATCAACTCATAATACGAGAGGTGAGTTGAGCCTTGGGT
1 TATTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
51948123 CGTACGCTGAGG
66 C--ACGCTGAGG
* * *
51948135 T-TTTTTAAATTTCTGTTTTTC--AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGT
1 TATTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
* *
51948197 CAC-ATCAAGG
66 CACGCT-GAGG
* * *
51948207 TATTTTTCAATTTCTATTTTTTTTAAAAAAATCAACTCATAATGCGAGAGGTGGGTTGAGCCTCG
1 TATTTTTCAATTTC---TGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCG
* *
51948272 GGTCATGCCGAGG
63 GGTCACGCTGAGG
* *
51948285 TATTTCTTTTAAATTT-TCGTTTTTCAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTC
1 TA--T-TTTTCAATTTCT-GTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
* *
51948348 GGGTCATGCCGAGG
62 GGGTCACGCTGAGG
* *
51948362 TATTTCTTTCAAATTTTTGTTTTTC-AAAAATCAACTCATAATGCGAGAGATG-GTTTGAGCCTC
1 TA-TT-TTTC-AATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAG-TTGAGCCTC
51948425 GGGTCACGCTGAGG
62 GGGTCACGCTGAGG
* * *
51948439 TA-TTTTCAATTTCTGTTTTTTCAAAAAAAAATCAACTCATAATGCTAGAAGTGAGTTGAGTCTC
1 TATTTTTCAATTTCTG-TTTTTC---AAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC
*
51948503 GGGTTACGCTGAGG
62 GGGTCACGCTGAGG
* * ** * *
51948517 TA-TTTTCAATATCTATTTTTC-AAAGGTCAACTCACAAT-CTGAGAAGTGAGTTGA
1 TATTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGC-GAGAGGTGAGTTGA
51948571 ACTTCGGATC
Statistics
Matches: 372, Mismatches: 40, Indels: 51
0.80 0.09 0.11
Matches are distributed among these distances:
71 1 0.00
72 7 0.02
73 45 0.12
74 48 0.13
75 20 0.05
76 31 0.08
77 81 0.22
78 128 0.34
79 1 0.00
80 1 0.00
81 9 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (75 bp):
TATTTTTCAATTTCTGTTTTTCAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGG
Found at i:51948887 original size:16 final size:16
Alignment explanation
Indices: 51948868--51948900 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
51948858 TAAAATTTTG
51948868 AAAAAATAAAAAATAC
1 AAAAAATAAAAAATAC
*
51948884 AAAAAATAAAAATTAC
1 AAAAAATAAAAAATAC
51948900 A
1 A
51948901 TTTTGGCCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAAAATAAAAAATAC
Found at i:51948998 original size:29 final size:30
Alignment explanation
Indices: 51948893--51949020 Score: 118
Period size: 29 Copynumber: 4.4 Consensus size: 30
51948883 CAAAAAATAA
* * *
51948893 AAATTACATTTTGGCCCCTGAACTTT-TCT
1 AAATTACATTTCGACCCCTAAACTTTATCT
* * * *
51948922 AAATTACATTTCAACCCTTAAATTTTATCA
1 AAATTACATTTCGACCCCTAAACTTTATCT
*
51948952 AAATTACATTTCTACCCCTAAACTTT-TCT
1 AAATTACATTTCGACCCCTAAACTTTATCT
* * * * *
51948981 AAATTGCATTTGGGCCCCT-AACTTTCTAT
1 AAATTACATTTCGACCCCTAAACTTTATCT
51949010 AAATTACATTT
1 AAATTACATTT
51949021 TAGCCACATA
Statistics
Matches: 80, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
28 6 0.08
29 49 0.61
30 25 0.31
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (30 bp):
AAATTACATTTCGACCCCTAAACTTTATCT
Found at i:51949650 original size:13 final size:13
Alignment explanation
Indices: 51949628--51949666 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
51949618 AGAAGAAGGG
51949628 AGAAAGAAAGAAAA
1 AGAAA-AAAGAAAA
51949642 AGAAAAAAGAAAA
1 AGAAAAAAGAAAA
*
51949655 AAAAAAAAGAAA
1 AGAAAAAAGAAA
51949667 GATAGCAGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AGAAAAAAGAAAA
Found at i:51949650 original size:17 final size:17
Alignment explanation
Indices: 51949628--51949668 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
51949618 AGAAGAAGGG
*
51949628 AGAAAGAAAGAAAAAGAA
1 AGAAAGAAA-AAAAAAAA
51949646 A-AAAGAAAAAAAAAAA
1 AGAAAGAAAAAAAAAAA
51949662 AGAAAGA
1 AGAAAGA
51949669 TAGCAGGCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
16 8 0.38
17 12 0.57
18 1 0.05
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AGAAAGAAAAAAAAAAA
Found at i:51950231 original size:20 final size:20
Alignment explanation
Indices: 51950206--51950243 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
51950196 AAAAATATTC
51950206 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
51950226 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
51950244 TTAGAATCCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:51950405 original size:17 final size:16
Alignment explanation
Indices: 51950359--51950407 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 16
51950349 TAAAGAAAAA
51950359 TCGTGTTTCAAAAGTTT
1 TCGTGTTTCAAAA-TTT
*
51950376 TCATGTCTTCAAAATTT
1 TCGTGT-TTCAAAATTT
51950393 CTCGTGTTTCAAAAT
1 -TCGTGTTTCAAAAT
51950408 AATAATAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 16 0.57
18 12 0.43
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (16 bp):
TCGTGTTTCAAAATTT
Found at i:51950678 original size:17 final size:19
Alignment explanation
Indices: 51950643--51950695 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 19
51950633 TGTTTCTAAT
51950643 ATTCTCGTATTTCAAAAAA
1 ATTCTCGTATTTCAAAAAA
51950662 ATTC-CGTATTT--AAAAA
1 ATTCTCGTATTTCAAAAAA
51950678 ATTCTCGTATTTCAAAAA
1 ATTCTCGTATTTCAAAAA
51950696 TTGTTATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 9 0.29
17 7 0.23
18 7 0.23
19 8 0.26
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.38
Consensus pattern (19 bp):
ATTCTCGTATTTCAAAAAA
Found at i:51950732 original size:18 final size:17
Alignment explanation
Indices: 51950711--51951050 Score: 112
Period size: 18 Copynumber: 18.9 Consensus size: 17
51950701 ATGTTTAGAA
51950711 AAAAATTT-GTTGTGTTTC
1 AAAAATTTCG-TGT-TTTC
51950729 AAAAATCTTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
* * *
51950747 AAAAATTCCGACG----A
1 AAAAATTTCG-TGTTTTC
51950761 AAAAATTTTCCGTGTTTTC
1 AAAAA-TTT-CGTGTTTTC
*
51950780 TAAAAATTT-ATGTTTTTC
1 -AAAAATTTCGTG-TTTTC
* *
51950798 ATAAATTTTCGTGTTCTC
1 A-AAAATTTCGTGTTTTC
* *
51950816 AAAAATTCCGATG--ATC
1 AAAAATTTCG-TGTTTTC
*
51950832 AAAATTTTTTTTCGTGTTTTC
1 AAAA---ATT-TCGTGTTTTC
* *
51950853 TAAAAACTTCCATG-TTTC
1 -AAAAA-TTTCGTGTTTTC
51950871 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
*
51950889 AAAAATTTTCGTGATTTC
1 AAAAA-TTTCGTGTTTTC
*
51950907 AACAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
* *
51950924 ATAAATTTTCGCG-TTTC
1 A-AAAATTTCGTGTTTTC
**
51950941 AAAAAAAATCGTGTTTTC
1 -AAAAATTTCGTGTTTTC
*
51950959 AAAAAAAAATTCTCGT-ATTTC
1 ----AAAAATT-TCGTGTTTTC
*
51950980 AAAAATTT-TTGTGTTTC
1 AAAAATTTCGTGT-TTTC
*
51950997 AAAAATTTTCATGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
51951015 AAGAAATTGCCGTGTCTTC
1 AA-AAATT-TCGTGTTTTC
51951034 AAAAATTCTCGTGTTTT
1 AAAAATT-TCGTGTTTT
51951051 TTTAAAACAA
Statistics
Matches: 242, Mismatches: 43, Indels: 74
0.67 0.12 0.21
Matches are distributed among these distances:
14 5 0.02
15 4 0.02
16 9 0.04
17 61 0.25
18 101 0.42
19 32 0.13
20 10 0.04
21 12 0.05
22 8 0.03
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:51950732 original size:20 final size:20
Alignment explanation
Indices: 51950691--51950733 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
51950681 CTCGTATTTC
*
51950691 AAAAATTGTTATGTTTAGAA
1 AAAAATTGTTATGTTTACAA
*
51950711 AAAAATTTGTTGTGTTT-CAA
1 AAAAA-TTGTTATGTTTACAA
51950731 AAA
1 AAA
51950734 TCTTCGTGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 10 0.50
21 10 0.50
ACGTcount: A:0.44, C:0.02, G:0.14, T:0.40
Consensus pattern (20 bp):
AAAAATTGTTATGTTTACAA
Found at i:51950877 original size:73 final size:67
Alignment explanation
Indices: 51950723--51950895 Score: 211
Period size: 73 Copynumber: 2.5 Consensus size: 67
51950713 AAATTTGTTG
*
51950723 TGTTTCAAAAATCTTCGTGTTTTCAAAAATTCCGACGAAAAAATTTTCCGTGTTTTCTAAAAATT
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAATTCCGACGAAAAAATTTTCCGTGTTTTCTAAAAATT
*
51950788 TA
66 CA
* * * * *
51950790 TGTTTTTCATAAATTTTCGTGTTCTCAAAAATTCCGATGATCAAAATTTTTTTTCGTGTTTTCTA
1 TG--TTTCAAAAATTTTCGTGTTTTCAAAAATTCCGACGA--AAAA--ATTTTCCGTGTTTTCTA
51950855 AAAACTTCCA
60 AAAA-TT-CA
51950865 TGTTTCAAAAATTTTCGTGTTTTCAAAAATT
1 TGTTTCAAAAATTTTCGTGTTTTCAAAAATT
51950896 TTCGTGATTT
Statistics
Matches: 89, Mismatches: 9, Indels: 10
0.82 0.08 0.09
Matches are distributed among these distances:
67 2 0.02
69 32 0.36
71 4 0.04
73 46 0.52
74 2 0.02
75 3 0.03
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (67 bp):
TGTTTCAAAAATTTTCGTGTTTTCAAAAATTCCGACGAAAAAATTTTCCGTGTTTTCTAAAAATT
CA
Found at i:51950885 original size:17 final size:17
Alignment explanation
Indices: 51950594--51951049 Score: 181
Period size: 17 Copynumber: 25.2 Consensus size: 17
51950584 TTTTCGCGTT
51950594 TTTCAAATAATTTTCGTG
1 TTTCAAA-AATTTTCGTG
51950612 TTCTCAAAAAATTTATTTTCGTG
1 TT-TC--AAAA---ATTTTCGTG
* * * *
51950635 TTTCTAATATTCTCGTA
1 TTTCAAAAATTTTCGTG
* * *
51950652 TTTCAAAAAAATTCCGTA
1 TTTC-AAAAATTTTCGTG
* * *
51950670 TTTAAAAAATTCTCGTA
1 TTTCAAAAATTTTCGTG
*
51950687 TTTCAAAAATTGTT-ATG
1 TTTCAAAAATT-TTCGTG
* *
51950704 TTTAGAAAAAAATTTGTTGTG
1 TTT---CAAAAATTT-TCGTG
*
51950725 TTTCAAAAATCTTCGTG
1 TTTCAAAAATTTTCGTG
* *
51950742 TTTTCAAAAA-TTCCGACG
1 -TTTCAAAAATTTTCG-TG
*
51950760 ---AAAAAATTTTCCGTG
1 TTTCAAAAATTTT-CGTG
*
51950775 TTTTCTAAAAATTTAT-GTT
1 -TTTC-AAAAATTT-TCGTG
*
51950794 TTTCATAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
*
51950811 TTCTCAAAAA-TTCCGATG
1 TT-TCAAAAATTTTCG-TG
* *
51950829 -ATCAAAATTTTTTTTCGTG
1 TTTCAAAA---ATTTTCGTG
* * *
51950848 TTTTCTAAAAACTTCCATG
1 -TTTC-AAAAATTTTCGTG
51950867 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTTTCGTG
51950884 TTTTCAAAAATTTTCGTG
1 -TTTCAAAAATTTTCGTG
* *
51950902 ATTTCAACAATTCTCGTG
1 -TTTCAAAAATTTTCGTG
* *
51950920 TTTCATAAATTTTCGCG
1 TTTCAAAAATTTTCGTG
***
51950937 TTTCAAAAAAAATCGTG
1 TTTCAAAAATTTTCGTG
* *
51950954 TTTTCAAAAAAAAATTCTCGTA
1 -TTTC----AAAAATTTTCGTG
*
51950976 TTTCAAAAATTTTTGTG
1 TTTCAAAAATTTTCGTG
*
51950993 TTTCAAAAATTTTCATG
1 TTTCAAAAATTTTCGTG
**
51951010 TTTTCAAGAAATTGCCGTG
1 -TTTCAA-AAATTTTCGTG
*
51951029 TCTTCAAAAATTCTCGTG
1 T-TTCAAAAATTTTCGTG
51951047 TTT
1 TTT
51951050 TTTTAAAACA
Statistics
Matches: 325, Mismatches: 71, Indels: 85
0.68 0.15 0.18
Matches are distributed among these distances:
14 5 0.02
15 3 0.01
16 9 0.03
17 119 0.37
18 100 0.31
19 25 0.08
20 23 0.07
21 15 0.05
22 15 0.05
23 11 0.03
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTTTCGTG
Found at i:51950953 original size:34 final size:35
Alignment explanation
Indices: 51950879--51950963 Score: 91
Period size: 35 Copynumber: 2.4 Consensus size: 35
51950869 TCAAAAATTT
* * ***
51950879 TCGTGTTTTCAAAAATTTTCGTGATTTCAACAATTC
1 TCGTG-TTTCAAAAATTTTCGCGATTTCAAAAAAAA
*
51950915 TCGTGTTTCATAAATTTTCGCG-TTTCAAAAAAAA
1 TCGTGTTTCAAAAATTTTCGCGATTTCAAAAAAAA
51950949 TCGTGTTTTCAAAAA
1 TCGTG-TTTCAAAAA
51950964 AAAATTCTCG
Statistics
Matches: 41, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
34 13 0.32
35 23 0.56
36 5 0.12
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.41
Consensus pattern (35 bp):
TCGTGTTTCAAAAATTTTCGCGATTTCAAAAAAAA
Found at i:51958440 original size:46 final size:46
Alignment explanation
Indices: 51958366--51958503 Score: 199
Period size: 46 Copynumber: 3.0 Consensus size: 46
51958356 CGTGGCAAAG
*
51958366 TGTGGAACGTAGGTATGGTAATTT-AGTAAAGAAAACCATACTGAGT
1 TGTGAAACGTAGGTATGGT-ATTTCAGTAAAGAAAACCATACTGAGT
* *
51958412 TGTGAAACGTAGGTATGGTATTTCAGTAATGAAAATCATACTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
* * *
51958458 TGTGAAAAGTAGGT-TGGTATTTCAATAAAGAAAACCATATTGAGT
1 TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
51958503 T
1 T
51958504 ATAGCATTGT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
45 32 0.39
46 51 0.61
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (46 bp):
TGTGAAACGTAGGTATGGTATTTCAGTAAAGAAAACCATACTGAGT
Found at i:51959345 original size:91 final size:90
Alignment explanation
Indices: 51959192--51959358 Score: 221
Period size: 91 Copynumber: 1.8 Consensus size: 90
51959182 AAAATTTTTC
* * ** *
51959192 AAAAAAAAGTAATTAAGTCTATGTTTTTTTTTTTGCATTCAATTAGGTACTTAATTTTCAAAATG
1 AAAAAAAAGCAATTAAGTCTATCTTTTTTTTTTTGCATTCAATTAGGTACTTAAGCTGCAAAATG
51959257 CATCAAAAAGGACTTCAAATTAAAA
66 CATCAAAAAGGACTTCAAATTAAAA
* *
51959282 AAAAAAAAGCAATTAAGCTTCTA-CTTTTTTTTTTTGCACTT-GATTAGGTACTTGAGCTGCAAA
1 AAAAAAAAGCAATTAAG--TCTATCTTTTTTTTTTTGCA-TTCAATTAGGTACTTAAGCTGCAAA
*
51959345 ATGCATGAAAAAGG
63 ATGCATCAAAAAGG
51959359 CCGTCGAACT
Statistics
Matches: 66, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
90 16 0.24
91 44 0.67
92 6 0.09
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.36
Consensus pattern (90 bp):
AAAAAAAAGCAATTAAGTCTATCTTTTTTTTTTTGCATTCAATTAGGTACTTAAGCTGCAAAATG
CATCAAAAAGGACTTCAAATTAAAA
Found at i:51959768 original size:17 final size:16
Alignment explanation
Indices: 51959748--51959800 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 16
51959738 AAAAATCGTA
51959748 AAAATTGTAAAATATAT
1 AAAA-TGTAAAATATAT
51959765 AAAACTGTAAAAATATAT
1 AAAA-TGT-AAAATATAT
*
51959783 AGAAATGTAAAAAATAT
1 A-AAATGTAAAATATAT
51959800 A
1 A
51959801 TATATAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
17 16 0.50
18 13 0.41
19 3 0.09
ACGTcount: A:0.62, C:0.02, G:0.08, T:0.28
Consensus pattern (16 bp):
AAAATGTAAAATATAT
Found at i:51959792 original size:35 final size:35
Alignment explanation
Indices: 51959728--51959800 Score: 87
Period size: 35 Copynumber: 2.1 Consensus size: 35
51959718 AAAAAATTGA
* *
51959728 ATAAAACTATAAAAATCGTAAAAATTGTAAAATAT
1 ATAAAACTATAAAAATCATAAAAATTGTAAAAAAT
*
51959763 ATAAAACTGTAAAAAT-ATATAGAAA-TGTAAAAAAT
1 ATAAAACTATAAAAATCATA-A-AAATTGTAAAAAAT
51959798 ATA
1 ATA
51959801 TATATAAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 2 0.06
35 28 0.85
36 3 0.09
ACGTcount: A:0.62, C:0.04, G:0.07, T:0.27
Consensus pattern (35 bp):
ATAAAACTATAAAAATCATAAAAATTGTAAAAAAT
Found at i:51959797 original size:19 final size:18
Alignment explanation
Indices: 51959728--51959802 Score: 75
Period size: 18 Copynumber: 4.2 Consensus size: 18
51959718 AAAAAATTGA
* *
51959728 ATAAAACTATAAAAATCGT
1 ATAAAACTGTAAAAAT-AT
*
51959747 A-AAAATTGT-AAAATAT
1 ATAAAACTGTAAAAATAT
51959763 ATAAAACTGTAAAAATAT
1 ATAAAACTGTAAAAATAT
51959781 ATAGAAA-TGTAAAAAATAT
1 ATA-AAACTGT-AAAAATAT
51959800 ATA
1 ATA
51959803 TATAAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.04
17 12 0.25
18 19 0.40
19 15 0.31
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
ATAAAACTGTAAAAATAT
Found at i:51959859 original size:20 final size:18
Alignment explanation
Indices: 51959836--51959902 Score: 55
Period size: 20 Copynumber: 3.4 Consensus size: 18
51959826 TTATAAAATT
51959836 TTATAAAAGTAGTAAGAAAA
1 TTATAAAA-TAGTAA-AAAA
*
51959856 TTATAAAAAATGTAAAGAAA
1 TTATAAAATA-GTAAA-AAA
*
51959876 -TATAAAATTTGTAAAAAAA
1 TTATAAAA-TAGT-AAAAAA
51959895 TTATAAAA
1 TTATAAAA
51959903 ATTATCTTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (18 bp):
TTATAAAATAGTAAAAAA
Found at i:51959881 original size:19 final size:20
Alignment explanation
Indices: 51959847--51959903 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
51959837 TATAAAAGTA
*
51959847 GTAAGAAAATTATAAAAAAT
1 GTAAAAAAATTATAAAAAAT
* **
51959867 GTAAAGAAA-TATAAAATTT
1 GTAAAAAAATTATAAAAAAT
51959886 GTAAAAAAATTATAAAAA
1 GTAAAAAAATTATAAAAA
51959904 TTATCTTACC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.65, C:0.00, G:0.09, T:0.26
Consensus pattern (20 bp):
GTAAAAAAATTATAAAAAAT
Found at i:51960120 original size:28 final size:27
Alignment explanation
Indices: 51960087--51960154 Score: 109
Period size: 28 Copynumber: 2.5 Consensus size: 27
51960077 TTTTATATTT
*
51960087 TTTTATGATTTTTATAAAAGTTTACAA
1 TTTTATAATTTTTATAAAAGTTTACAA
51960114 TCTTTATAATTTTTATAAAAGTTTACAA
1 T-TTTATAATTTTTATAAAAGTTTACAA
*
51960142 TTTTAAAATTTTT
1 TTTTATAATTTTT
51960155 TTTACAATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
27 12 0.32
28 26 0.68
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.54
Consensus pattern (27 bp):
TTTTATAATTTTTATAAAAGTTTACAA
Found at i:51960160 original size:20 final size:21
Alignment explanation
Indices: 51960135--51960177 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51960125 TTTATAAAAG
51960135 TTTACAA-TTTTAAAATTTTT
1 TTTACAATTTTTAAAATTTTT
*
51960155 TTTACAATTTTTATAATTTTT
1 TTTACAATTTTTAAAATTTTT
51960176 TT
1 TT
51960178 GTCACATGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTACAATTTTTAAAATTTTT
Found at i:51964551 original size:17 final size:19
Alignment explanation
Indices: 51964523--51964557 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
51964513 ATGTCATTAA
51964523 TTGGGTTTGGGTT-GGTTT
1 TTGGGTTTGGGTTAGGTTT
51964541 TTGGG-TTGGGTTAGGTT
1 TTGGGTTTGGGTTAGGTT
51964558 AGATAATTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.03, C:0.00, G:0.46, T:0.51
Consensus pattern (19 bp):
TTGGGTTTGGGTTAGGTTT
Found at i:51965132 original size:14 final size:15
Alignment explanation
Indices: 51965105--51965134 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
51965095 ATAACCTTCT
51965105 AAATATTTATTATTA
1 AAATATTTATTATTA
51965120 AAATATTTA-TATTA
1 AAATATTTATTATTA
51965134 A
1 A
51965135 TCAAAATGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
AAATATTTATTATTA
Found at i:51965513 original size:11 final size:9
Alignment explanation
Indices: 51965465--51965509 Score: 54
Period size: 9 Copynumber: 4.7 Consensus size: 9
51965455 TTTTGAGCAA
51965465 TTTAATTTT
1 TTTAATTTT
*
51965474 TTTATGTTTAT
1 TTTA-ATTT-T
51965485 ATTTAATTTT
1 -TTTAATTTT
51965495 TTTAATTTT
1 TTTAATTTT
51965504 TTTAAT
1 TTTAAT
51965510 ATTTCCCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 19 0.61
10 4 0.13
11 4 0.13
12 4 0.13
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTAATTTT
Found at i:51968326 original size:15 final size:15
Alignment explanation
Indices: 51968306--51968337 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
51968296 CGCTACCGTA
51968306 AATTAAATTGATAAT
1 AATTAAATTGATAAT
51968321 AATTAAATTGATAAT
1 AATTAAATTGATAAT
51968336 AA
1 AA
51968338 GAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (15 bp):
AATTAAATTGATAAT
Found at i:51973337 original size:31 final size:29
Alignment explanation
Indices: 51973302--51973377 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 29
51973292 ATCTCAAAAT
* *
51973302 TATACGTGAACTTTGATTTAACGTGCAATTG
1 TATACGTGAACTTT-ATTTAA-GTACAATTA
** *
51973333 TATACACGAACTTTATTTTAGTACAATTA
1 TATACGTGAACTTTATTTAAGTACAATTA
*
51973362 TATGCGTGAAACTTTA
1 TATACGTG-AACTTTA
51973378 ATTGTGGTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
29 12 0.33
30 12 0.33
31 12 0.33
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (29 bp):
TATACGTGAACTTTATTTAAGTACAATTA
Found at i:51975124 original size:20 final size:20
Alignment explanation
Indices: 51975099--51975137 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
51975089 TAATAGAAAA
51975099 TATCTTT-TTTTATTATTTTG
1 TATCTTTATTTT-TTATTTTG
51975119 TATCTTTATTTTTTATTTT
1 TATCTTTATTTTTTATTTT
51975138 TCGGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.15, C:0.05, G:0.03, T:0.77
Consensus pattern (20 bp):
TATCTTTATTTTTTATTTTG
Done.