Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397262.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_67.0, whole genome shotgun sequence
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: 8984705
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 112788 characters in sequence are not A, C, G, or T
File 16 of 20
Found at i:6197159 original size:86 final size:86
Alignment explanation
Indices: 6197053--6197213 Score: 268
Period size: 86 Copynumber: 1.9 Consensus size: 86
6197043 AACTAATTAA
* * * *
6197053 TCAATACATGTATTAAGTTTAATGTTTGGAAAATAAATAAATTCAATGTTTTGTTAATAAATTTA
1 TCAATACATGCATTAAGTTTAATGTTTGGAAAAAAAATAAATTAAATGTTTCGTTAATAAATTTA
6197118 TTTTAATTAACATGAAATTTT
66 TTTTAATTAACATGAAATTTT
* *
6197139 TCAATATATGCATTAAGTTTAATGTTTTGAAAAAAAATAAATTAAATGTTTCGTTAATAAATTTA
1 TCAATACATGCATTAAGTTTAATGTTTGGAAAAAAAATAAATTAAATGTTTCGTTAATAAATTTA
6197204 TTTTAATTAA
66 TTTTAATTAA
6197214 TGTTTAAAAA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
86 69 1.00
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (86 bp):
TCAATACATGCATTAAGTTTAATGTTTGGAAAAAAAATAAATTAAATGTTTCGTTAATAAATTTA
TTTTAATTAACATGAAATTTT
Found at i:6197287 original size:82 final size:82
Alignment explanation
Indices: 6197182--6197346 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
6197172 AAAATAAATT
6197182 AAATGTTTCGTTAATAAATTTATTTTAATTAATGTTTAAAAAATGAAAGAAAAAGACTATTTAAA
1 AAATGTTTCGTTAATAAATTTATTTTAATTAATGTTTAAAAAATGAAAGAAAAAGACTATTTAAA
6197247 AAGAAGAAAAAAGAATG
66 AAGAAGAAAAAAGAATG
*
6197264 AAATGTTTTGTTAATAAATTTATTTTAATTAATGTTTAAAAAATGAAAGAAAAAGACTATTTAAA
1 AAATGTTTCGTTAATAAATTTATTTTAATTAATGTTTAAAAAATGAAAGAAAAAGACTATTTAAA
* **
6197329 AGGAAGCGAAAAGAATG
66 AAGAAGAAAAAAGAATG
6197346 A
1 A
6197347 TTGGAAGAAA
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.32
Consensus pattern (82 bp):
AAATGTTTCGTTAATAAATTTATTTTAATTAATGTTTAAAAAATGAAAGAAAAAGACTATTTAAA
AAGAAGAAAAAAGAATG
Found at i:6210586 original size:125 final size:124
Alignment explanation
Indices: 6210247--6210620 Score: 491
Period size: 124 Copynumber: 3.0 Consensus size: 124
6210237 AGTGGCCCAC
* * *
6210247 TGTTTCCTCCTGATTCCAGGTATCAAGGGCCTAAACCCAAACCAAAAGTAATAGCAACATTAAAA
1 TGTTTCCTTCTGATTCCAGGTATCAAAGGCCTAAACCCAAACCAAAAGTAATAGCAACACTAAAA
* * * * *
6210312 TCAGGCACTGTTCCTCTTACCAAGTCTAGTAGCGTGATACTCCACCATTCCTCCACTTT
66 TCAGGGAATGTTCCTGTTACCAAGTCTAGTAGCCTGATACTCCACCATTCCTCCAATTT
* * * * * * *
6210371 TG-TTCGCATCTGATTCCACGTATCAATGGCCTATACGCAAACCCAAAGTAATAGCAACACTAAC
1 TGTTTC-CTTCTGATTCCAGGTATCAAAGGCCTAAACCCAAACCAAAAGTAATAGCAACACTAAA
* * * * *
6210435 ATCAGGGAACGTTCCTGTTACCAAGTCTTGTAGCCTGATGCTGCACTATTCCTCCAATTT
65 ATCAGGGAATGTTCCTGTTACCAAGTCTAGTAGCCTGATACTCCACCATTCCTCCAATTT
* * *
6210495 TGTTTCCTTTTGACTCCAGGTATCAAAGGCCTAAACCCAAGCCAAAAAGTAATAGCAACACTAAA
1 TGTTTCCTTCTGATTCCAGGTATCAAAGGCCTAAACCCAAACC-AAAAGTAATAGCAACACTAAA
*
6210560 ATCAGGGAATGTTCCTGTTACCAAGTCTAGTAGCCTGATAC-CACACCATTCCTCCACTTT
65 ATCAGGGAATGTTCCTGTTACCAAGTCTAGTAGCCTGATACTC-CACCATTCCTCCAATTT
6210620 T
1 T
6210621 TCAATTTATT
Statistics
Matches: 211, Mismatches: 35, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
123 3 0.01
124 132 0.63
125 76 0.36
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (124 bp):
TGTTTCCTTCTGATTCCAGGTATCAAAGGCCTAAACCCAAACCAAAAGTAATAGCAACACTAAAA
TCAGGGAATGTTCCTGTTACCAAGTCTAGTAGCCTGATACTCCACCATTCCTCCAATTT
Found at i:6227381 original size:20 final size:21
Alignment explanation
Indices: 6227358--6227397 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
6227348 AAACAAGCAA
6227358 TGCAAATACAAGTC-ATTAGT
1 TGCAAATACAAGTCAATTAGT
* *
6227378 TGCATATACAGGTCAATTAG
1 TGCAAATACAAGTCAATTAG
6227398 AGGCCCAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (21 bp):
TGCAAATACAAGTCAATTAGT
Found at i:6233834 original size:21 final size:20
Alignment explanation
Indices: 6233799--6233847 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
6233789 ATAAAAATCA
* *
6233799 GAGAGAGAGAGAGAACAGAAG
1 GAGAGAGGGAAAGAACAG-AG
*
6233820 GAGAGAGGGAAAGAAGAGAG
1 GAGAGAGGGAAAGAACAGAG
6233840 GA-AGAGGG
1 GAGAGAGGG
6233848 CGTGAAAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 6 0.24
20 4 0.16
21 15 0.60
ACGTcount: A:0.49, C:0.02, G:0.49, T:0.00
Consensus pattern (20 bp):
GAGAGAGGGAAAGAACAGAG
Found at i:6237573 original size:87 final size:87
Alignment explanation
Indices: 6237427--6237601 Score: 323
Period size: 87 Copynumber: 2.0 Consensus size: 87
6237417 CGATGCATCA
*
6237427 ACAGCAACTAGCTATGCTAGCACAGCAACAGTCTCTTCTCATGGCTGCTGCTGCTAAATCTGCTC
1 ACAGCAACTAGCTATGCTAGCACAGCAACAGTCTCTTCTCATGGCTGCTGCAGCTAAATCTGCTC
* *
6237492 CTGGAAGTACTCAACTGCCTGC
66 CTGGAAATACTCAACAGCCTGC
6237514 ACAGCAACTAGCTATGCTAGCACAGCAACAGTCTCTTCTCATGGCTGCTGCAGCTAAATCTGCTC
1 ACAGCAACTAGCTATGCTAGCACAGCAACAGTCTCTTCTCATGGCTGCTGCAGCTAAATCTGCTC
6237579 CTGGAAATACTCAACAGCCTGC
66 CTGGAAATACTCAACAGCCTGC
6237601 A
1 A
6237602 TCCAACGGCT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
87 85 1.00
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.24
Consensus pattern (87 bp):
ACAGCAACTAGCTATGCTAGCACAGCAACAGTCTCTTCTCATGGCTGCTGCAGCTAAATCTGCTC
CTGGAAATACTCAACAGCCTGC
Found at i:6256912 original size:84 final size:84
Alignment explanation
Indices: 6256766--6256934 Score: 311
Period size: 84 Copynumber: 2.0 Consensus size: 84
6256756 AAATGTGATA
6256766 ACTTTAACATTTTTAGATTAAGGAGGAATAAGCAGAACTCAGAACTCGTAGAAACATGCCCAATA
1 ACTTTAACATTTTTAGATTAAGGAGGAATAAGCAGAACTCAGAACTCGTAGAAACATGCCCAATA
6256831 TATACTCGTTTAAAGTTTG
66 TATACTCGTTTAAAGTTTG
* * *
6256850 ACTTTAATATTTTTAGATTAAGGAGGAATAAGCAGAACTCAGAACTTGTAGAAACATTCCCAATA
1 ACTTTAACATTTTTAGATTAAGGAGGAATAAGCAGAACTCAGAACTCGTAGAAACATGCCCAATA
6256915 TATACTCGTTTAAAGTTTG
66 TATACTCGTTTAAAGTTTG
6256934 A
1 A
6256935 AGCCATAGGT
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.31
Consensus pattern (84 bp):
ACTTTAACATTTTTAGATTAAGGAGGAATAAGCAGAACTCAGAACTCGTAGAAACATGCCCAATA
TATACTCGTTTAAAGTTTG
Found at i:6261247 original size:2 final size:2
Alignment explanation
Indices: 6261240--6261267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6261230 AAGAAGCCAT
6261240 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
6261268 GATAACCACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:6270200 original size:29 final size:28
Alignment explanation
Indices: 6270168--6270222 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
6270158 ATCTAAGAAA
6270168 ATTTAAATAAATTTTTAAT-TTTTTATTAC
1 ATTTAAATAAA--TTTAATATTTTTATTAC
*
6270197 ATTTAATTAAATTTAATATTTTTATT
1 ATTTAAATAAATTTAATATTTTTATT
6270223 TTAGATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 8 0.33
29 10 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTAAATAAATTTAATATTTTTATTAC
Found at i:6270841 original size:11 final size:10
Alignment explanation
Indices: 6270825--6270854 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
6270815 AATTTCAAAC
*
6270825 AAAAAAAATA
1 AAAAAAAAGA
6270835 AAAAAAAAGA
1 AAAAAAAAGA
6270845 AAAAAAAAGA
1 AAAAAAAAGA
6270855 CCCACAGACC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.90, C:0.00, G:0.07, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:6286301 original size:25 final size:26
Alignment explanation
Indices: 6286252--6286301 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
6286242 AAACCATCGG
* *
6286252 TAAAATATTGGTAAAAAAATGTTTTGC
1 TAAAATAGTGGT-AAAAAATATTTTGC
6286279 TAAAATAGTGGT-AAAAATATTTT
1 TAAAATAGTGGTAAAAAATATTTT
6286302 TTTTAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
27 11 0.52
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (26 bp):
TAAAATAGTGGTAAAAAATATTTTGC
Found at i:6292419 original size:2 final size:2
Alignment explanation
Indices: 6292412--6292439 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6292402 TAAAAGTGTA
6292412 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6292440 CAAATATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6297980 original size:22 final size:23
Alignment explanation
Indices: 6297948--6297990 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
6297938 TTTTTTTTCA
*
6297948 AAAAATTATAAATAAT-TGAAGG
1 AAAAATGATAAATAATCTGAAGG
6297970 AAAAATGATAAATAATCTGAA
1 AAAAATGATAAATAATCTGAA
6297991 AATAAAATCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.60, C:0.02, G:0.12, T:0.26
Consensus pattern (23 bp):
AAAAATGATAAATAATCTGAAGG
Found at i:6297997 original size:23 final size:22
Alignment explanation
Indices: 6297947--6297998 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
6297937 TTTTTTTTTC
*
6297947 AAAAAATTATAAATAATTGAAG
1 AAAAAATGATAAATAATTGAAG
*
6297969 GAAAAATGATAAATAATCTGAA-
1 AAAAAATGATAAATAAT-TGAAG
6297991 AATAAAAT
1 AA-AAAAT
6297999 CGACCTAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.10, T:0.25
Consensus pattern (22 bp):
AAAAAATGATAAATAATTGAAG
Found at i:6302492 original size:2 final size:2
Alignment explanation
Indices: 6302485--6302517 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
6302475 TTATTATGTT
6302485 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 T
6302518 TTTGAAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6310674 original size:28 final size:29
Alignment explanation
Indices: 6310637--6310711 Score: 98
Period size: 28 Copynumber: 2.6 Consensus size: 29
6310627 TTTAAAAAAT
6310637 TTTAAATAAATTTTTAT-TTTTTATTATA
1 TTTAAATAAATTTTTATATTTTTATTATA
* * *
6310665 TTTAATTAAAATTTTATATTTTTATTTTA
1 TTTAAATAAATTTTTATATTTTTATTATA
*
6310694 TATCAAATAAATTTTTAT
1 T-TTAAATAAATTTTTAT
6310712 GATTAATGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
28 15 0.38
29 11 0.28
30 13 0.33
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (29 bp):
TTTAAATAAATTTTTATATTTTTATTATA
Found at i:6310710 original size:30 final size:28
Alignment explanation
Indices: 6310640--6310711 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 28
6310630 AAAAAATTTT
*
6310640 AAATAAATTTTTATTTTTTATTATATTT
1 AAATAAATTTTTATTTTTTATTATATTC
* * *
6310668 AATTAAAATTTTATATTTTTATTTTATATC
1 AAATAAATTTTTAT-TTTTTATTATAT-TC
6310698 AAATAAATTTTTAT
1 AAATAAATTTTTAT
6310712 GATTAATGAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 12 0.33
29 11 0.31
30 13 0.36
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (28 bp):
AAATAAATTTTTATTTTTTATTATATTC
Found at i:6315772 original size:54 final size:53
Alignment explanation
Indices: 6315691--6315797 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 53
6315681 AAATCTAAGG
6315691 GTCATGATGCATGAATTAATCTTCTTGAAAACCATGCACTATATCCATTGAAT
1 GTCATGATGCATGAATTAATCTTCTTGAAAACCATGCACTATATCCATTGAAT
* *
6315744 GTCATGATGCAATGAATTAATCTTCTTGAAAATCATTCACTATATCCATTGAAT
1 GTCATGATGC-ATGAATTAATCTTCTTGAAAACCATGCACTATATCCATTGAAT
6315798 AAGGCAAGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
53 10 0.20
54 41 0.80
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.36
Consensus pattern (53 bp):
GTCATGATGCATGAATTAATCTTCTTGAAAACCATGCACTATATCCATTGAAT
Found at i:6325036 original size:15 final size:16
Alignment explanation
Indices: 6325013--6325045 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
6325003 TATACTCATC
6325013 GTATCTTTTT-TTTTT
1 GTATCTTTTTGTTTTT
*
6325028 GTATTTTTTTGTTTTT
1 GTATCTTTTTGTTTTT
6325044 GT
1 GT
6325046 CAGTGGACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.06, C:0.03, G:0.12, T:0.79
Consensus pattern (16 bp):
GTATCTTTTTGTTTTT
Found at i:6328230 original size:56 final size:56
Alignment explanation
Indices: 6328116--6328266 Score: 169
Period size: 56 Copynumber: 2.7 Consensus size: 56
6328106 ACGCGATGGG
* * *
6328116 TATTGTAATTGACGAAATAACTTTACTGTTATGATTTATAATTAACACATTATAAA
1 TATTGTAAGTGACGGAATAACTTTACTGTTATGATTTATAATTAACACATAATAAA
* * * * *
6328172 TATTGTAAGTGACGGAATAATTTTACTGTTATGATTTATAATTGATATGA-AATGAA
1 TATTGTAAGTGACGGAATAACTTTACTGTTATGATTTATAATTAACA-CATAATAAA
* * ** *
6328228 TATTATAAGTGACAGAATGGCTTTACTGTGATGATTTAT
1 TATTGTAAGTGACGGAATAACTTTACTGTTATGATTTAT
6328267 TAAGATTCAA
Statistics
Matches: 80, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
56 79 0.99
57 1 0.01
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (56 bp):
TATTGTAAGTGACGGAATAACTTTACTGTTATGATTTATAATTAACACATAATAAA
Found at i:6330700 original size:26 final size:26
Alignment explanation
Indices: 6330655--6330708 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
6330645 ATTTTTTTAA
* *
6330655 TTATATTTAATATGTATTAATA-ATAT
1 TTATATATAATATATATTAA-AGATAT
*
6330681 TTATATATAATATATTTTAAAGATAT
1 TTATATATAATATATATTAAAGATAT
6330707 TT
1 TT
6330709 TGAGATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.54
Consensus pattern (26 bp):
TTATATATAATATATATTAAAGATAT
Found at i:6334672 original size:3 final size:3
Alignment explanation
Indices: 6334664--6334694 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6334654 TGAAGCAGCT
6334664 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
6334695 GACAAAGCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:6338903 original size:158 final size:158
Alignment explanation
Indices: 6338335--6338926 Score: 539
Period size: 158 Copynumber: 3.8 Consensus size: 158
6338325 TTACTTGGAT
* ** *
6338335 ACAAAACCAAGTGCTTATGTTACAGATTTATATTTCTAATATACTTAATAAATG-GAGGAAAGTT
1 ACAAAACCAAGTGCTTATGTTACAGATTTATGTTTCTAATATACTTAATAGGTGATAGGAAAGTT
** *
6338399 TATATTTATATATCCAAA-ACTCATTTCA----TT-TCCATGTAATATTTGTCAATAATTTAGTA
66 TATATTTATATA-CCAAAGACTCATTTCATCTCTTATTGATGTAATATTTGTCAATAGTTTAG-A
* * *
6338458 -AAAGCTACCTTTTTTTCCTTTTATTTT-AGAC
129 GAAAGTTACC--TTTCTCTTTTTATTTTGA-AC
* * * * * *
6338489 ACAAAACCAAGTGTTTATGTTACAAATTTATGTTTTTAATATACTTAATAGGTG-TGGGAAAATC
1 ACAAAACCAAGTGCTTATGTTACAGATTTATGTTTCTAATATACTTAATAGGTGATAGGAAAGTT
* * * * * *
6338553 TATATTTATATACCCAAGACTCATTTCCTATGTTTTA-AGAATGTGACATTTGTCAATAGTTTAG
66 TATATTTATATACCAAAGACTCATTT-C-ATCTCTTATTG-ATGTAATATTTGTCAATAGTTTAG
*
6338617 -GAAAAGTTACCTTTCTCCTTTTTATTTTGGAC
128 AG-AAAGTTACCTTTCT-CTTTTTATTTTGAAC
* ** * * * *
6338649 ACAAAACTAAGTGCTTATGCGATAGATTTAGGTTTCTGATGTACTTAATAGGTGA-AGGAAAGTT
1 ACAAAACCAAGTGCTTATGTTACAGATTTATGTTTCTAATATACTTAATAGGTGATAGGAAAGTT
* * * * *
6338713 TATATTTATATACCCAACACTTATCTT-GTCTCTTATTGATGTAATATCTGTCAATAGTTTAGAG
66 TATATTTATATACCAAAGACTCAT-TTCATCTCTTATTGATGTAATATTTGTCAATAGTTTAGAG
* * *
6338777 AAAGTTACCATTCACATTTTTATTTTGAAA
130 AAAGTTACCTTTCTC-TTTTTATTTTGAAC
* * * * * *
6338807 ACAAAACCAAGTGCTTGTGTTACATACTCACGTTTCCAATATACTTAATAGG-GATAGGAAAGTT
1 ACAAAACCAAGTGCTTATGTTACAGATTTATGTTTCTAATATACTTAATAGGTGATAGGAAAGTT
* * * *
6338871 TATATTTATATATCAAAGACTCATTTCATCTCTTATTAATGTGATATTTGCCAATA
66 TATATTTATATACCAAAGACTCATTTCATCTCTTATTGATGTAATATTTGTCAATA
6338927 ATTTTTATTT
Statistics
Matches: 351, Mismatches: 67, Indels: 36
0.77 0.15 0.08
Matches are distributed among these distances:
153 4 0.01
154 74 0.21
155 1 0.00
156 1 0.00
157 5 0.01
158 143 0.41
159 6 0.02
160 86 0.25
161 31 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.40
Consensus pattern (158 bp):
ACAAAACCAAGTGCTTATGTTACAGATTTATGTTTCTAATATACTTAATAGGTGATAGGAAAGTT
TATATTTATATACCAAAGACTCATTTCATCTCTTATTGATGTAATATTTGTCAATAGTTTAGAGA
AAGTTACCTTTCTCTTTTTATTTTGAAC
Found at i:6339053 original size:135 final size:134
Alignment explanation
Indices: 6338792--6339061 Score: 301
Period size: 135 Copynumber: 2.0 Consensus size: 134
6338782 TACCATTCAC
* * *
6338792 ATTTTTATTTTGAAAACAAAACCAAGTGCTTGTGTTACATACTCACGTTTCCAATATACTTAATA
1 ATTTTTATTTTGAAAACAAAACCAAGTGCTTATATTACATACTCACATTTCCAATATACTTAATA
** * * *
6338857 GGGATAGGAAAGTTTATATTTATATATCAAAGACTCATTTCATCTCTTATTAATGTGATATTTGC
66 GGGA-AGGAAAGTTTATATTTATATATCAAAGACTCATCCCATCTCTTACTAATATAATATTTGC
6338922 CAATA
130 CAATA
* * * * * * * *
6338927 ATTTTTATTTTGGATACAAAATCAAGTGTTTATATTACATATTTACATTTCTAATATATTTAATA
1 ATTTTTATTTTGAAAACAAAACCAAGTGCTTATATTACATACTCACATTTCCAATATACTTAAT-
* * * *
6338992 AGTGG-AGGAAAGTTTATATTTATGTATTC-AAGATTCATCCCATTTGTTACTAATATAATATTT
65 AG-GGAAGGAAAGTTTATATTTATATA-TCAAAGACTCATCCCATCTCTTACTAATATAATATTT
*
6339055 GTCAATA
128 GCCAATA
6339062 GGTAAGGGAA
Statistics
Matches: 111, Mismatches: 21, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
135 105 0.95
136 4 0.04
137 2 0.02
ACGTcount: A:0.35, C:0.11, G:0.11, T:0.42
Consensus pattern (134 bp):
ATTTTTATTTTGAAAACAAAACCAAGTGCTTATATTACATACTCACATTTCCAATATACTTAATA
GGGAAGGAAAGTTTATATTTATATATCAAAGACTCATCCCATCTCTTACTAATATAATATTTGCC
AATA
Found at i:6339321 original size:158 final size:157
Alignment explanation
Indices: 6338929--6339469 Score: 422
Period size: 158 Copynumber: 3.4 Consensus size: 157
6338919 TGCCAATAAT
* * * * * * * *
6338929 TTTTATTTTGGATACAAAATCAAGTGTTTATATTACATATTTACATTTCTAATATATTTAATAAG
1 TTTTATTTTGGACACAAAATCAAGTGCTTATGTTACATATTTACGTTTTTTATATACTTAATAGG
** ** * * * * * * * * * * ** * * *
6338994 TGGAGGAAAGTTTATATTTATGTATTCAAGATTCATCCCATTTGTTACTAATATAATATTTGTCA
66 TATACAAAAGTTTATATTCATATATCCAAAACTCAGCTCGTCTCTTACCGATATGATACTTGCCA
** *
6339059 ATAGGTAAGGGAAAGTTACCTTTTTCCC
131 ATAATTAA-AGAAAGTTACCTTTTTCCC
* * * * * * * * * *
6339087 TTTAATTTTAGACACAAAATCAAGTGTTTAAGTTATAGATTTTCGTTTCTCATATACTTAATAGA
1 TTTTATTTTGGACACAAAATCAAGTGCTTATGTTACATATTTACGTTTTTTATATACTTAATAGG
* * * * * *
6339152 TATAGAAAAGTTTATATTTATATA-CTAGAAACTTAGCTCGTCTCTTACCGATGTGATACTTGCT
66 TATACAAAAGTTTATATTCATATATCCA-AAACTCAGCTCGTCTCTTACCGATATGATACTTGCC
*
6339216 AATAGTATAAAGAAAGTTACCTTTTTCCC
130 AATAAT-TAAAGAAAGTTACCTTTTTCCC
* * *
6339245 TTTTATTTTGGATACAAAATTAAGTGCTTATGTTACATATTTACATTTTTTATATACTTAATAGG
1 TTTTATTTTGGACACAAAATCAAGTGCTTATGTTACATATTTACGTTTTTTATATACTTAATAGG
* ** ** *
6339310 TGA-ACATAAGTTTATATTCATATATCCAAAACTCATTTCGTCTCTTATTGATATGATATTTGCC
66 T-ATACAAAAGTTTATATTCATATATCCAAAACTCAGCTCGTCTCTTACCGATATGATACTTGCC
* *
6339374 AATAATTTAAGAAAAATTA-CTTTTCTCCC
130 AATAATTAAAG-AAAGTTACCTTTT-TCCC
* * * * * * *
6339403 TCTTATTTTGGGCACAAAACCAAGTGCTTATATCACATGTTTACGTTTTTTATGTACTTAATAGG
1 TTTTATTTTGGACACAAAATCAAGTGCTTATGTTACATATTTACGTTTTTTATATACTTAATAGG
6339468 TA
66 TA
6339470 GAGGAAGATG
Statistics
Matches: 303, Mismatches: 74, Indels: 13
0.78 0.19 0.03
Matches are distributed among these distances:
157 11 0.04
158 286 0.94
159 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (157 bp):
TTTTATTTTGGACACAAAATCAAGTGCTTATGTTACATATTTACGTTTTTTATATACTTAATAGG
TATACAAAAGTTTATATTCATATATCCAAAACTCAGCTCGTCTCTTACCGATATGATACTTGCCA
ATAATTAAAGAAAGTTACCTTTTTCCC
Found at i:6339486 original size:609 final size:606
Alignment explanation
Indices: 6338329--6339500 Score: 1263
Period size: 609 Copynumber: 1.9 Consensus size: 606
6338319 TCCTTTTTAC
* *
6338329 TTGGATACAAAACCAAGTGCTTATGTTACAGATTTATATTTCTAATATACTTAATAAATGGAGGA
1 TTGGATACAAAACCAAGTGCTTATATTACAGATTTACATTTCTAATATACTTAATAAATGGAGGA
** * * * * *
6338394 AAGTTTATATTTATATATCCAAAACTCATTTCATTTCCATGTAATATTTGTCAATAATTTAGTAA
66 AAGTTTATATTTATATATCCAAAACTCATCCCATTTCAATATAATATTTGTCAATAAGTAAGGAA
* * *
6338459 AAGCTACCTTTTTTTCCTTTTATTTTAGACACAAAACCAAGTGTTTATGTTACAAATTTATGTTT
131 AAGCTACCTTTTTTCCCTTTAATTTTAGACACAAAACCAAGTGTTTAAGTTACAAATTTATGTTT
* * * * ** * *
6338524 TTAATATACTTAATAGGTGTGGGAAAATCTATATTTATATACCCAAGACTCATTTCCTATGTTTT
196 CTAATATACTTAATAGATATGAGAAAATCTATATTTATATA-CCAAGAAACATTACCTACGTTTT
* * * *
6338589 AAGAATGTGACATTTGTCAATAGTTTAGGAAAAGTTACCTTTCTCCTTTTTATTTTGGACACAAA
260 AAGAATGTGACACTTGTCAATAGTTAAAGAAAAGTTACCTTTCTCCCTTTTATTTTGGACACAAA
* ** * *
6338654 ACTAAGTGCTTATGCGATAGATTTAGGTTTCTGATGTACTTAATAGGTGAAGGAAAGTTTATATT
325 ACTAAGTGCTTATGCGACAGATTTACATTTCTGATATACTTAATAGGTGAAGCAAAGTTTATATT
* * * * * * *
6338719 TATATACCCAACACTTATCTTGTCTCTTATTGATGTAATATCTGTCAATAGTTTAGAGAAAGTTA
390 CATATACCCAAAACTCATCTTGTCTCTTATTGATATAATATCTGCCAATAATTTAGAGAAAATTA
* * * * *
6338784 CCATTCACATTTTTATTTTGAAAACAAAACCAAGTGCTTGTGTTACATACTCACGTTTCCAATAT
455 CCATTCACACTCTTATTTTGAAAACAAAACCAAGTGCTTATATCACATACTCACGTTTCCAATAT
* * *
6338849 ACTTAATAGGGATAGGAAAGTTTATATTTATATATCAAAGACTCATTTCATCTCTTATTAATGTG
520 ACTTAATAGGGAGAGGAAAGTGTATATTTATATAACAAAGACTCATTTCATCTCTTATTAATGTG
6338914 ATATTTGCCAATAATTTTTATT
585 ATATTTGCCAATAATTTTTATT
* * * * *
6338936 TTGGATACAAAATCAAGTGTTTATATTACATATTTACATTTCTAATATATTTAATAAGTGGAGGA
1 TTGGATACAAAACCAAGTGCTTATATTACAGATTTACATTTCTAATATACTTAATAAATGGAGGA
* * * * *
6339001 AAGTTTATATTTATGTATTCAAGATTCATCCCATTTGTTACTAATATAATATTTGTCAATAGGTA
66 AAGTTTATATTTATATATCCAAAACTCATCCCA--T-TT-C-AATATAATATTTGTCAATAAGTA
* * * * *
6339066 AGGGAAAGTTACC-TTTTTCCCTTTAATTTTAGACACAAAATCAAGTGTTTAAGTTATAGATTT-
126 AGGAAAAGCTACCTTTTTTCCCTTTAATTTTAGACACAAAACCAAGTGTTTAAGTTACAAATTTA
* * * *
6339129 TCGTTTCTCATATACTTAATAGATAT-AGAAAAGTTTATATTTATATA-CTAGAAAC-TTAGCT-
191 T-GTTTCTAATATACTTAATAGATATGAGAAAA-TCTATATTTATATACCAAGAAACATTACCTA
* * *
6339190 CGTCTCTTACCG-ATGTGATACTTG-CTAATAGTATAAAG-AAAGTTACCTTTTTCCCTTTTATT
254 CGT-T-TTA-AGAATGTGACACTTGTC-AATAGT-TAAAGAAAAGTTACCTTTCTCCCTTTTATT
* * ** * * *
6339252 TTGGATACAAAATTAAGTGCTTATGTTACATATTTACATTTTTTATATACTTAATAGGTGAA-CA
314 TTGGACACAAAACTAAGTGCTTATGCGACAGATTTACATTTCTGATATACTTAATAGGTGAAGCA
* * *
6339316 TAAGTTTATATTCATATATCCAAAACTCAT-TTCGTCTCTTATTGATATGATATTTGCCAATAAT
379 -AAGTTTATATTCATATACCCAAAACTCATCTT-GTCTCTTATTGATATAATATCTGCCAATAAT
** * * *** **
6339380 TTA-AGAAAAATTACTTTTCTCCCTCTTATTTTGGGCACAAAACCAAGTGCTTATATCACATGTT
442 TTAGAG-AAAATTACCATTCACACTCTTATTTTGAAAACAAAACCAAGTGCTTATATCACATACT
* *** * * * *
6339444 TACGTTTTTTATGTACTTAATAGGTAGAGG-AAGATGTATATTTGTATAACCAAGACT
506 CACGTTTCCAATATACTTAATAGGGAGAGGAAAG-TGTATATTTATATAACAAAGACT
6339501 TATGTTACAT
Statistics
Matches: 456, Mismatches: 93, Indels: 30
0.79 0.16 0.05
Matches are distributed among these distances:
607 87 0.19
608 14 0.03
609 237 0.52
610 12 0.03
611 78 0.17
612 28 0.06
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.41
Consensus pattern (606 bp):
TTGGATACAAAACCAAGTGCTTATATTACAGATTTACATTTCTAATATACTTAATAAATGGAGGA
AAGTTTATATTTATATATCCAAAACTCATCCCATTTCAATATAATATTTGTCAATAAGTAAGGAA
AAGCTACCTTTTTTCCCTTTAATTTTAGACACAAAACCAAGTGTTTAAGTTACAAATTTATGTTT
CTAATATACTTAATAGATATGAGAAAATCTATATTTATATACCAAGAAACATTACCTACGTTTTA
AGAATGTGACACTTGTCAATAGTTAAAGAAAAGTTACCTTTCTCCCTTTTATTTTGGACACAAAA
CTAAGTGCTTATGCGACAGATTTACATTTCTGATATACTTAATAGGTGAAGCAAAGTTTATATTC
ATATACCCAAAACTCATCTTGTCTCTTATTGATATAATATCTGCCAATAATTTAGAGAAAATTAC
CATTCACACTCTTATTTTGAAAACAAAACCAAGTGCTTATATCACATACTCACGTTTCCAATATA
CTTAATAGGGAGAGGAAAGTGTATATTTATATAACAAAGACTCATTTCATCTCTTATTAATGTGA
TATTTGCCAATAATTTTTATT
Found at i:6347658 original size:91 final size:91
Alignment explanation
Indices: 6347404--6347663 Score: 239
Period size: 91 Copynumber: 2.8 Consensus size: 91
6347394 AGAAAAATGA
* *
6347404 ATAAAAAAACGCAAAA-ATAAGCTAAGAAATCT-TCAAATGCGCGATTT-TCTTTGATTTTTTCC
1 ATAAACAAACGCAAAAGA-AA-CTCA-AAATCTCTCAAATGCGCGATTTCTCTTTG--TTTTT-C
* * *
6347466 CCTCGCTTTTCCTCTCCTCTGTTAGAAAACCG
60 CCTCGCTTTTTCTCTCCTCTGTCACAAAACCG
* * ** ** *
6347498 ATAAACAAACGCAAAATAAGCTCAAAATCTCTCAAAATGCTTGATTTCTCTACGTTTTTCCTTCG
1 ATAAACAAACGCAAAAGAAACTCAAAATCTCTC-AAATGCGCGATTTCTCTTTGTTTTTCCCTCG
6347563 -TTTTTCTCTCCTC-GATCACAAAA-CG
65 CTTTTTCTCTCCTCTG-TCACAAAACCG
* *
6347588 AATAAA-AGAACGGCAAAAGAAACTCAAAAT-TCTCAAATGCGCGCTTTCTCTTTGCTTTTCCCT
1 -ATAAACA-AAC-GCAAAAGAAACTCAAAATCTCTCAAATGCGCGATTTCTCTTTGTTTTTCCCT
6347651 CGCTTTTTCTCTC
63 CGCTTTTTCTCTC
6347664 TCAAACGATA
Statistics
Matches: 137, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
90 28 0.20
91 40 0.29
92 27 0.20
93 10 0.07
94 27 0.20
95 5 0.04
ACGTcount: A:0.31, C:0.25, G:0.11, T:0.33
Consensus pattern (91 bp):
ATAAACAAACGCAAAAGAAACTCAAAATCTCTCAAATGCGCGATTTCTCTTTGTTTTTCCCTCGC
TTTTTCTCTCCTCTGTCACAAAACCG
Found at i:6351340 original size:2 final size:2
Alignment explanation
Indices: 6351333--6351357 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6351323 CAGCAGCCAG
6351333 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
6351358 GCTACCATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:6354174 original size:20 final size:22
Alignment explanation
Indices: 6354146--6354185 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
6354136 CATGCTTTGG
6354146 TATAAGTGT-TAT-TATATAAA
1 TATAAGTGTATATATATATAAA
*
6354166 TATATGTGTATATATATATA
1 TATAAGTGTATATATATATA
6354186 CACATATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 3 0.18
22 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.47
Consensus pattern (22 bp):
TATAAGTGTATATATATATAAA
Found at i:6359412 original size:20 final size:20
Alignment explanation
Indices: 6359387--6359429 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
6359377 GCATATTTAT
6359387 TCACTTCGAAAATTAATGCG
1 TCACTTCGAAAATTAATGCG
6359407 TCACTTCGAAAATTAATGCG
1 TCACTTCGAAAATTAATGCG
6359427 TCA
1 TCA
6359430 TTCTAAATCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (20 bp):
TCACTTCGAAAATTAATGCG
Found at i:6365913 original size:22 final size:22
Alignment explanation
Indices: 6365871--6365913 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
6365861 ACTTCTTCTC
* *
6365871 TTTTTTCACTGTAATATTAATA
1 TTTTTTCAATGTAATAATAATA
6365893 TTTTTTCAAT-TAATCAATAAT
1 TTTTTTCAATGTAAT-AATAAT
6365914 CTTGTAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTTCAATGTAATAATAATA
Found at i:6376793 original size:22 final size:23
Alignment explanation
Indices: 6376765--6376807 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
6376755 GAAGAGGAAA
6376765 AGGAAAG-AAAAGAAAGGGGATG
1 AGGAAAGCAAAAGAAAGGGGATG
* *
6376787 AGGAAAGCAAAGGAAATGGGA
1 AGGAAAGCAAAAGAAAGGGGA
6376808 GGAAAGAGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.53, C:0.02, G:0.40, T:0.05
Consensus pattern (23 bp):
AGGAAAGCAAAAGAAAGGGGATG
Found at i:6382843 original size:2 final size:2
Alignment explanation
Indices: 6382836--6382864 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
6382826 GTCATAGTCC
6382836 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6382865 CACACACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6391923 original size:30 final size:30
Alignment explanation
Indices: 6391889--6391947 Score: 118
Period size: 30 Copynumber: 2.0 Consensus size: 30
6391879 GATAAATAGG
6391889 GCATGTTTGTATAGTATGATCTATACAGCC
1 GCATGTTTGTATAGTATGATCTATACAGCC
6391919 GCATGTTTGTATAGTATGATCTATACAGC
1 GCATGTTTGTATAGTATGATCTATACAGC
6391948 TGATACCATG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (30 bp):
GCATGTTTGTATAGTATGATCTATACAGCC
Found at i:6395028 original size:3 final size:3
Alignment explanation
Indices: 6395020--6395050 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
6395010 CACTTCTTTC
6395020 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
6395051 TTAAGTTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:6396940 original size:24 final size:25
Alignment explanation
Indices: 6396913--6396968 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 25
6396903 CTCTTCTTCC
*
6396913 TCTTCCTCCTCC-TCCTCTTCATAA
1 TCTTCCTCCTCCATCCTCGTCATAA
* * *
6396937 TCTT-CTTCTCCATCTTCGTCATAC
1 TCTTCCTCCTCCATCCTCGTCATAA
6396961 TCTTCCTC
1 TCTTCCTC
6396969 GGATGACTCT
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
23 6 0.24
24 17 0.68
25 2 0.08
ACGTcount: A:0.11, C:0.43, G:0.02, T:0.45
Consensus pattern (25 bp):
TCTTCCTCCTCCATCCTCGTCATAA
Found at i:6397278 original size:22 final size:22
Alignment explanation
Indices: 6397253--6397299 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
6397243 CACTTCTTCA
6397253 TTCTT-TTCTTCACTGCTTTGCT
1 TTCTTCTT-TTCACTGCTTTGCT
* *
6397275 TTCTTCTTTTCTCTGCTTTTCT
1 TTCTTCTTTTCACTGCTTTGCT
6397297 TTC
1 TTC
6397300 ACTTTTCCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.02, C:0.28, G:0.06, T:0.64
Consensus pattern (22 bp):
TTCTTCTTTTCACTGCTTTGCT
Found at i:6397796 original size:2 final size:2
Alignment explanation
Indices: 6397789--6397816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
6397779 ATCCTTTTTC
6397789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6397817 TATTATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6398786 original size:19 final size:19
Alignment explanation
Indices: 6398762--6398802 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
6398752 TCTAATTACT
*
6398762 TTATAT-TTCATTTATTTAA
1 TTATATGTTAATTTA-TTAA
6398781 TTATATGTTAATTTATTAA
1 TTATATGTTAATTTATTAA
6398800 TTA
1 TTA
6398803 CTTTATCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTATATGTTAATTTATTAA
Found at i:6398808 original size:24 final size:22
Alignment explanation
Indices: 6398754--6398808 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 22
6398744 CAGTTTAATC
*
6398754 TAATTACTTTATATTTCATTTA
1 TAATTACTTTATATTTAATTTA
*
6398776 T--TTA-ATTATATGTTAATTTA
1 TAATTACTTTATAT-TTAATTTA
6398796 TTAATTACTTTAT
1 -TAATTACTTTAT
6398809 CCATACTTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
19 6 0.24
20 10 0.40
21 1 0.04
22 1 0.04
23 3 0.12
24 4 0.16
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (22 bp):
TAATTACTTTATATTTAATTTA
Found at i:6400665 original size:2 final size:2
Alignment explanation
Indices: 6400658--6400683 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6400648 TAGCTAGCTA
6400658 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6400684 TGCATGCATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6401003 original size:2 final size:2
Alignment explanation
Indices: 6400996--6401020 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6400986 ACTTTATAAA
6400996 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
6401021 CATTTTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6402152 original size:10 final size:10
Alignment explanation
Indices: 6402137--6402168 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
6402127 GAAGATATTA
6402137 AGAGACAGAG
1 AGAGACAGAG
6402147 AGAGACAGAG
1 AGAGACAGAG
*
6402157 AGAGAGAGAG
1 AGAGACAGAG
6402167 AG
1 AG
6402169 GAAGAGAAGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.44, T:0.00
Consensus pattern (10 bp):
AGAGACAGAG
Found at i:6402376 original size:3 final size:3
Alignment explanation
Indices: 6402370--6402395 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
6402360 AAACAACAAA
6402370 GAT GAT GAT GAT GAT GAT GAT GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GA
6402396 AGAAGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (3 bp):
GAT
Found at i:6416811 original size:31 final size:31
Alignment explanation
Indices: 6416776--6416837 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
6416766 TAGCAATGGT
6416776 TTGCAGATCAAAAGAGAAGTGCATTATTGCC
1 TTGCAGATCAAAAGAGAAGTGCATTATTGCC
6416807 TTGCAGATCAAAAGAGAAGTGCATTATTGCC
1 TTGCAGATCAAAAGAGAAGTGCATTATTGCC
6416838 ATGGAAAAAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (31 bp):
TTGCAGATCAAAAGAGAAGTGCATTATTGCC
Found at i:6416845 original size:26 final size:28
Alignment explanation
Indices: 6416785--6416847 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 28
6416775 TTTGCAGATC
*
6416785 AAAAGAGAAGTGCATTATTGCCTTGCAGA
1 AAAAGAGAAGTGCATTATTGCCATG-AGA
6416814 TCAAAAGAGAAGTGCATTATTGCCATG-GA
1 --AAAAGAGAAGTGCATTATTGCCATGAGA
6416843 AAAAG
1 AAAAG
6416848 CGCTTTGGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 5 0.16
29 2 0.06
31 24 0.77
ACGTcount: A:0.41, C:0.13, G:0.24, T:0.22
Consensus pattern (28 bp):
AAAAGAGAAGTGCATTATTGCCATGAGA
Found at i:6422528 original size:31 final size:32
Alignment explanation
Indices: 6422493--6422554 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
6422483 TTAATTTAAT
6422493 CAATTAAAATTAAATTAAT-ATTT-TTTATTTG
1 CAATTAAAATTAAA-TAATAATTTATTTATTTG
* *
6422524 CAATTATACTTAAATAATAATTTATTTATTT
1 CAATTAAAATTAAATAATAATTTATTTATTT
6422555 AATTATAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 4 0.15
31 16 0.59
32 7 0.26
ACGTcount: A:0.42, C:0.05, G:0.02, T:0.52
Consensus pattern (32 bp):
CAATTAAAATTAAATAATAATTTATTTATTTG
Found at i:6422559 original size:30 final size:30
Alignment explanation
Indices: 6422492--6422561 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 30
6422482 TTTAATTTAA
* *
6422492 TCAATTAAAATTAAATTAATATTTTTTATT
1 TCAATTATACTTAAATTAATATTTTTTATT
6422522 TGCAATTATACTTAAA-TAATAATTTATTTATT
1 T-CAATTATACTTAAATTAAT-ATTT-TTTATT
6422554 T-AATTATA
1 TCAATTATA
6422562 ATTACTAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
30 12 0.34
31 16 0.46
32 7 0.20
ACGTcount: A:0.43, C:0.04, G:0.01, T:0.51
Consensus pattern (30 bp):
TCAATTATACTTAAATTAATATTTTTTATT
Found at i:6460346 original size:40 final size:40
Alignment explanation
Indices: 6460282--6460359 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
6460272 TGAAGCATAT
* * *
6460282 CTTTTAAATGTTCATTTTTTATACTGTGTAAGGGCATTAC
1 CTTTTAAATGTGCAGTTTTCATACTGTGTAAGGGCATTAC
* *
6460322 CTTTTAAATGTGCAGTTTTCATACTGTTTTAGGGCATT
1 CTTTTAAATGTGCAGTTTTCATACTGTGTAAGGGCATT
6460360 TTACTTGTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (40 bp):
CTTTTAAATGTGCAGTTTTCATACTGTGTAAGGGCATTAC
Found at i:6462809 original size:8 final size:8
Alignment explanation
Indices: 6462796--6462823 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
6462786 TTTGAAAATT
6462796 ATTAACTA
1 ATTAACTA
6462804 ATTAACTA
1 ATTAACTA
6462812 ATTAACTA
1 ATTAACTA
6462820 ATTA
1 ATTA
6462824 TTGCCGCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATTAACTA
Found at i:6468311 original size:16 final size:15
Alignment explanation
Indices: 6468287--6468325 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
6468277 AACAGTCCAT
6468287 ATTAA-ATAAATATA
1 ATTAATATAAATATA
*
6468301 ATATAATATAAATTTA
1 AT-TAATATAAATATA
6468317 ATTAATATA
1 ATTAATATA
6468326 TAAATATTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 2 0.09
15 10 0.45
16 10 0.45
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATTAATATAAATATA
Found at i:6503020 original size:84 final size:83
Alignment explanation
Indices: 6502930--6503109 Score: 252
Period size: 84 Copynumber: 2.2 Consensus size: 83
6502920 TGATATGATG
* ** * * *
6502930 ATGATTTATGAGATAAGATATGAAATGTATGCCATGAGATGTGTGTGTTGAAAATATCGTGTACA
1 ATGATTTATGAGATAAAATATGAAATGTATGCCATGAGATGCATGTATTGAAAAT-TCATATACA
* *
6502995 CTATAGGCTAGGCATGAGA
65 CAATAGGCTAAGCATGAGA
*
6503014 ATGATTTATGAGATAAAATATGAAATGTATGCCATGAGATGCATGTATTGAGAATTCATATACAC
1 ATGATTTATGAGATAAAATATGAAATGTATGCCATGAGATGCATGTATTGAAAATTCATATACAC
6503079 AATAGGCTAAGCATGAGA
66 AATAGGCTAAGCATGAGA
* *
6503097 ATGAATGATGAGA
1 ATGATTTATGAGA
6503110 ATGATTTTAC
Statistics
Matches: 85, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
83 35 0.41
84 50 0.59
ACGTcount: A:0.38, C:0.08, G:0.24, T:0.29
Consensus pattern (83 bp):
ATGATTTATGAGATAAAATATGAAATGTATGCCATGAGATGCATGTATTGAAAATTCATATACAC
AATAGGCTAAGCATGAGA
Found at i:6504713 original size:39 final size:39
Alignment explanation
Indices: 6504670--6504845 Score: 155
Period size: 39 Copynumber: 4.5 Consensus size: 39
6504660 TCAGTATTCA
* *
6504670 TCATATGAATAAACCAAAACATTTGTGAATCAATCTTTG
1 TCATATGAATAAACCAAAACATTTATAAATCAATCTTTG
* *
6504709 TCATATTAAT-AACTCAAAAC-TTTCATAAATCAATTTTTAG
1 TCATATGAATAAAC-CAAAACATTT-ATAAATCAATCTTT-G
* * **
6504749 -CATATGAATAAACCAAAGCATTCAT-AATCAATCTTCA
1 TCATATGAATAAACCAAAACATTTATAAATCAATCTTTG
* * * *
6504786 TCATATGGATGAACTAAAACATTTGA-AAATCATTCTTTG
1 TCATATGAATAAACCAAAACATTT-ATAAATCAATCTTTG
6504825 TCATATGAATACACACCAAAA
1 TCATATGAATA-A-ACCAAAA
6504846 AAGATAATAA
Statistics
Matches: 106, Mismatches: 21, Indels: 18
0.73 0.14 0.12
Matches are distributed among these distances:
38 33 0.31
39 60 0.57
40 7 0.07
41 6 0.06
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (39 bp):
TCATATGAATAAACCAAAACATTTATAAATCAATCTTTG
Found at i:6504816 original size:77 final size:78
Alignment explanation
Indices: 6504670--6504845 Score: 191
Period size: 77 Copynumber: 2.2 Consensus size: 78
6504660 TCAGTATTCA
** ** *
6504670 TCATATGAATAAACCAAAACATTTGTGAATCAATCTTTGTCATATTAATAACTCAAAACTTTCAT
1 TCATATGAATAAACCAAAACATTCATGAATCAATCTTCATCATATGAATAACTCAAAACTTTCAT
6504735 AAATCAATT-TTTAG
66 AAATC-ATTCTTT-G
* * *
6504749 -CATATGAATAAACCAAAGCATTCAT-AATCAATCTTCATCATATGGATGAACT-AAAACATTTG
1 TCATATGAATAAACCAAAACATTCATGAATCAATCTTCATCATATGAAT-AACTCAAAAC-TTTC
6504811 A-AAATCATTCTTTG
64 ATAAATCATTCTTTG
6504825 TCATATGAATACACACCAAAA
1 TCATATGAATA-A-ACCAAAA
6504846 AAGATAATAA
Statistics
Matches: 82, Mismatches: 9, Indels: 12
0.80 0.09 0.12
Matches are distributed among these distances:
76 4 0.05
77 41 0.50
78 31 0.38
79 6 0.07
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.32
Consensus pattern (78 bp):
TCATATGAATAAACCAAAACATTCATGAATCAATCTTCATCATATGAATAACTCAAAACTTTCAT
AAATCATTCTTTG
Found at i:6506715 original size:83 final size:85
Alignment explanation
Indices: 6506574--6506749 Score: 257
Period size: 83 Copynumber: 2.1 Consensus size: 85
6506564 CCTTTGGAGA
* * *
6506574 AGCCACGACCTACCCTTTCCATTTTTTTTTTGAGGCTGCGACCATTGTCATGGTAAGTTCAAAAG
1 AGCCACGACCAACCCTTTCCA-TTTTTTTTTAAGGCTGCGACCAGTGTCATGGTAAGTTCAAAAG
6506639 GCTGTGGCCTCCCCT-GTGGG
65 GCTGTGGCCTCCCCTAGTGGG
* * * **
6506659 AGCCACGACCAACCTTTTCCA-TTTTTTTTAAGGCTGCGGCCAGTGTCATGGTAAGTTTAGGAGG
1 AGCCACGACCAACCCTTTCCATTTTTTTTTAAGGCTGCGACCAGTGTCATGGTAAGTTCAAAAGG
6506723 CTGTGGCCTCCCCTAGTGGG
66 CTGTGGCCTCCCCTAGTGGG
6506743 AGCCACG
1 AGCCACG
6506750 GCCTACCCCC
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
83 51 0.62
84 12 0.15
85 19 0.23
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.30
Consensus pattern (85 bp):
AGCCACGACCAACCCTTTCCATTTTTTTTTAAGGCTGCGACCAGTGTCATGGTAAGTTCAAAAGG
CTGTGGCCTCCCCTAGTGGG
Found at i:6510773 original size:29 final size:29
Alignment explanation
Indices: 6510739--6510796 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
6510729 TATAGAAAAT
*
6510739 TGTCAGAAGACCTACCATTTTCTAGGAGC
1 TGTCAGAAGACCTACCATTTGCTAGGAGC
* *
6510768 TGTCAGTAGACCTATCATTTGCTAGGAGC
1 TGTCAGAAGACCTACCATTTGCTAGGAGC
6510797 ATTCTGTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (29 bp):
TGTCAGAAGACCTACCATTTGCTAGGAGC
Found at i:6512292 original size:32 final size:32
Alignment explanation
Indices: 6512219--6512293 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
6512209 CATCCACTCC
* * *
6512219 TTTTACAGCTATATTCACCTAAGTTAACTTCA
1 TTTTACAACAATATTCACCTAAGGTAACTTCA
* * * *
6512251 TTTTCCAACAATATTCACCTACGGTAATTTCG
1 TTTTACAACAATATTCACCTAAGGTAACTTCA
6512283 TTTTACAACAA
1 TTTTACAACAA
6512294 AACCGAGAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.39
Consensus pattern (32 bp):
TTTTACAACAATATTCACCTAAGGTAACTTCA
Found at i:6512960 original size:14 final size:14
Alignment explanation
Indices: 6512937--6512967 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
6512927 AATATGAGTA
6512937 TTTGGATTAATCAC
1 TTTGGATTAATCAC
*
6512951 TTTGGGTTAATCAC
1 TTTGGATTAATCAC
6512965 TTT
1 TTT
6512968 TAATATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.48
Consensus pattern (14 bp):
TTTGGATTAATCAC
Found at i:6517388 original size:12 final size:12
Alignment explanation
Indices: 6517371--6517399 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
6517361 TAAACTCAAA
6517371 CTCTCAAATTTT
1 CTCTCAAATTTT
6517383 CTCTC-AATTTT
1 CTCTCAAATTTT
6517394 CTCTCA
1 CTCTCA
6517400 TTCACACTCC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCTCAAATTTT
Found at i:6522577 original size:31 final size:32
Alignment explanation
Indices: 6522542--6522606 Score: 105
Period size: 32 Copynumber: 2.1 Consensus size: 32
6522532 CACAACTGCA
* *
6522542 GACTTTGAAAATT-CGCTTGCGTAACGCAGGG
1 GACTTTGAAAATTCCCCTTGAGTAACGCAGGG
6522573 GACTTTGAAAATTCCCCTTGAGTAACGCAGGG
1 GACTTTGAAAATTCCCCTTGAGTAACGCAGGG
6522605 GA
1 GA
6522607 ATTCTGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 13 0.42
32 18 0.58
ACGTcount: A:0.28, C:0.20, G:0.28, T:0.25
Consensus pattern (32 bp):
GACTTTGAAAATTCCCCTTGAGTAACGCAGGG
Found at i:6529896 original size:84 final size:83
Alignment explanation
Indices: 6529807--6529964 Score: 253
Period size: 84 Copynumber: 1.9 Consensus size: 83
6529797 TGATATGACG
* * * * *
6529807 ATGATTTATGAGATAAGATATGAAATGTATGCCATGAGATGTATGTGTTGAAAATATCGTGTACA
1 ATGATTTATAAGATAAAATATGAAATGTATGCCATGAGATGTATGTATTGAAAAT-TCATATACA
6529872 CTATAGGCTAGACATAAGA
65 CTATAGGCTAGACATAAGA
*
6529891 ATGATTTATAAGATAAAATATGAAATGTATGCCATGAGATGTATGTATTGAGAATTCATATACAC
1 ATGATTTATAAGATAAAATATGAAATGTATGCCATGAGATGTATGTATTGAAAATTCATATACAC
6529956 TATAGGCTA
66 TATAGGCTA
6529965 AGCATGATAA
Statistics
Matches: 68, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
83 17 0.25
84 51 0.75
ACGTcount: A:0.39, C:0.08, G:0.20, T:0.32
Consensus pattern (83 bp):
ATGATTTATAAGATAAAATATGAAATGTATGCCATGAGATGTATGTATTGAAAATTCATATACAC
TATAGGCTAGACATAAGA
Found at i:6530820 original size:26 final size:26
Alignment explanation
Indices: 6530784--6530837 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
6530774 GTCCACTCAT
6530784 AGATTTATGAATGACATGTGATTACA
1 AGATTTATGAATGACATGTGATTACA
*
6530810 AGATTTATGAATGATATGTGATTACA
1 AGATTTATGAATGACATGTGATTACA
6530836 AG
1 AG
6530838 TACATGCTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (26 bp):
AGATTTATGAATGACATGTGATTACA
Found at i:6531762 original size:38 final size:38
Alignment explanation
Indices: 6531620--6531805 Score: 120
Period size: 39 Copynumber: 4.8 Consensus size: 38
6531610 GATTTCATCT
* * * * * *
6531620 CATTCATCAATTAGTATTCATCACATGAACAAACCATAA
1 CATTCAT-AATTAATCTTCATCATATGAATAAACTAAAA
** * * * *
6531659 CATTTGTAAATCAATCTTCGTCATATTAATAAACCAAAA
1 CATTCAT-AATTAATCTTCATCATATGAATAAACTAAAA
* * * ** *
6531698 CTTTCATAAATTAATTTTTAAGATATGAATAAACTAAAG
1 CATTCAT-AATTAATCTTCATCATATGAATAAACTAAAA
*
6531737 CATTCATAATTAATCTTCATCATATGAATGAACTAAAA
1 CATTCATAATTAATCTTCATCATATGAATAAACTAAAA
** * * *
6531775 CATTTGTAAATCATCCTTCTTCATATGAATA
1 CATTCATAATTAAT-CTTCATCATATGAATA
6531806 CACACCAAAA
Statistics
Matches: 110, Mismatches: 36, Indels: 2
0.74 0.24 0.01
Matches are distributed among these distances:
38 35 0.32
39 75 0.68
ACGTcount: A:0.42, C:0.17, G:0.06, T:0.35
Consensus pattern (38 bp):
CATTCATAATTAATCTTCATCATATGAATAAACTAAAA
Found at i:6535368 original size:3 final size:3
Alignment explanation
Indices: 6535360--6535387 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
6535350 TTCTGCCTTT
6535360 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6535388 ACTCTAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:6542890 original size:20 final size:20
Alignment explanation
Indices: 6542865--6542913 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
6542855 GAACCAGAGT
6542865 AAATGTATCGATACATTGCC
1 AAATGTATCGATACATTGCC
6542885 AAATGTATCGATACATTGCC
1 AAATGTATCGATACATTGCC
6542905 AAATGTATC
1 AAATGTATC
6542914 AATCATGCAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (20 bp):
AAATGTATCGATACATTGCC
Found at i:6552329 original size:27 final size:27
Alignment explanation
Indices: 6552299--6552362 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
6552289 AACTTAAAAT
6552299 TTCAGCTGTCCTACTGTCATAACCATG
1 TTCAGCTGTCCTACTGTCATAACCATG
*
6552326 TTCAGCTGTCCTACTGTTATAACCATG
1 TTCAGCTGTCCTACTGTCATAACCATG
6552353 TTCAGCTGTC
1 TTCAGCTGTC
6552363 TTTGGAGATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.20, C:0.28, G:0.16, T:0.36
Consensus pattern (27 bp):
TTCAGCTGTCCTACTGTCATAACCATG
Found at i:6562523 original size:2 final size:2
Alignment explanation
Indices: 6562504--6562540 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
6562494 ACGAGAACAA
* *
6562504 AT AT AC AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6562541 GTATTACAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:6577689 original size:52 final size:52
Alignment explanation
Indices: 6577623--6577727 Score: 192
Period size: 52 Copynumber: 2.0 Consensus size: 52
6577613 TAATTTCTAC
*
6577623 TAATATGGTTATAATTTAATTAGCTGGGATTAATATAATAATTCAGAAAATA
1 TAATATGGTGATAATTTAATTAGCTGGGATTAATATAATAATTCAGAAAATA
*
6577675 TAATATGGTGATAATTTAATTATCTGGGATTAATATAATAATTCAGAAAATA
1 TAATATGGTGATAATTTAATTAGCTGGGATTAATATAATAATTCAGAAAATA
6577727 T
1 T
6577728 TGCTAATGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.39
Consensus pattern (52 bp):
TAATATGGTGATAATTTAATTAGCTGGGATTAATATAATAATTCAGAAAATA
Found at i:6593306 original size:18 final size:17
Alignment explanation
Indices: 6593277--6593310 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
6593267 ATATTACATG
6593277 ATTAATTATCATGTCAA
1 ATTAATTATCATGTCAA
6593294 ATTAATATATCATGTCA
1 ATTAAT-TATCATGTCA
6593311 TCATCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.41
Consensus pattern (17 bp):
ATTAATTATCATGTCAA
Found at i:6593465 original size:30 final size:30
Alignment explanation
Indices: 6593431--6593500 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
6593421 ATAATTAGTT
* *
6593431 ATAAAGGCTTATTT-GATTCAAAATAAAAAC
1 ATAAAAGCTTATTTAG-CTCAAAATAAAAAC
*
6593461 ATAAAAGCTTATTTAGCTCAAAATAAAAAT
1 ATAAAAGCTTATTTAGCTCAAAATAAAAAC
*
6593491 ATAAGAGCTT
1 ATAAAAGCTT
6593501 GATTGAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 34 0.97
31 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.10, T:0.30
Consensus pattern (30 bp):
ATAAAAGCTTATTTAGCTCAAAATAAAAAC
Found at i:6594661 original size:29 final size:29
Alignment explanation
Indices: 6594628--6594692 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
6594618 TGATCTCCTA
* *
6594628 TTTCAAAAATCTACTTTTTGAGATGTTGG
1 TTTCAAAAATCTACTTCTTAAGATGTTGG
6594657 TTTCAAAAATCTACTTCTTAAGATGTTGG
1 TTTCAAAAATCTACTTCTTAAGATGTTGG
6594686 TTTCAAA
1 TTTCAAA
6594693 CTTTCTTGTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (29 bp):
TTTCAAAAATCTACTTCTTAAGATGTTGG
Found at i:6603103 original size:17 final size:17
Alignment explanation
Indices: 6603081--6603115 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
6603071 ATTCTATCGC
6603081 TTGTTATGACTCAAATT
1 TTGTTATGACTCAAATT
*
6603098 TTGTTATGATTCAAATT
1 TTGTTATGACTCAAATT
6603115 T
1 T
6603116 CCTTGTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (17 bp):
TTGTTATGACTCAAATT
Found at i:6603123 original size:20 final size:18
Alignment explanation
Indices: 6603080--6603124 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
6603070 AATTCTATCG
6603080 CTTGTTATGACTCAAATT
1 CTTGTTATGACTCAAATT
*
6603098 -TTGTTATGATTCAAATTT
1 CTTGTTATGACTCAAA-TT
6603116 CCTTGTTAT
1 -CTTGTTAT
6603125 TTTTTAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
17 14 0.61
18 2 0.09
20 7 0.30
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.51
Consensus pattern (18 bp):
CTTGTTATGACTCAAATT
Found at i:6614423 original size:15 final size:15
Alignment explanation
Indices: 6614403--6614432 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6614393 TGTAATGCTA
6614403 AATATAACAAAGTTT
1 AATATAACAAAGTTT
*
6614418 AATATAATAAAGTTT
1 AATATAACAAAGTTT
6614433 GCTTTTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.03, G:0.07, T:0.37
Consensus pattern (15 bp):
AATATAACAAAGTTT
Found at i:6640447 original size:2 final size:2
Alignment explanation
Indices: 6640440--6640468 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6640430 ATTTTAGGTG
6640440 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6640469 TAAACAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6646857 original size:3 final size:3
Alignment explanation
Indices: 6646851--6646879 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
6646841 TTGATGTTGT
6646851 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
6646880 TTAGGTGATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:6647785 original size:20 final size:18
Alignment explanation
Indices: 6647743--6647779 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
6647733 TGTAAGGTAA
6647743 AGTAATAAGTAATTATAT
1 AGTAATAAGTAATTATAT
6647761 AGTAATAAGTAATTATAT
1 AGTAATAAGTAATTATAT
6647779 A
1 A
6647780 AGGTAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.51, C:0.00, G:0.11, T:0.38
Consensus pattern (18 bp):
AGTAATAAGTAATTATAT
Found at i:6657149 original size:22 final size:22
Alignment explanation
Indices: 6657119--6657267 Score: 167
Period size: 22 Copynumber: 6.8 Consensus size: 22
6657109 TTTTAACTAG
* * *
6657119 TGCGAGATTGATTTTTAAGTAT
1 TGCGTGATTGCTTTTTAAGCAT
* * *
6657141 TACGTGATTAG--TTATAAGTAT
1 TGCGTGATT-GCTTTTTAAGCAT
*
6657162 TGCGTGATTGCTTTTTAGGCAT
1 TGCGTGATTGCTTTTTAAGCAT
*
6657184 TGCGTGATTGCTTTTTAAACAT
1 TGCGTGATTGCTTTTTAAGCAT
*
6657206 TGCGTGATTGCTTTTTAAACAT
1 TGCGTGATTGCTTTTTAAGCAT
*
6657228 TGCGTGATTGCTTTTTAAGTAT
1 TGCGTGATTGCTTTTTAAGCAT
**
6657250 TGCGTGATTAATTTTTAA
1 TGCGTGATTGCTTTTTAA
6657268 CTAATACCTA
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
20 1 0.01
21 17 0.15
22 92 0.83
23 1 0.01
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.46
Consensus pattern (22 bp):
TGCGTGATTGCTTTTTAAGCAT
Found at i:6657393 original size:21 final size:21
Alignment explanation
Indices: 6657350--6657399 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
6657340 AAAATAAGTT
* * *
6657350 ACGCAATATTCAAAGTCAGTC
1 ACGCAATATACAAAGTAAATC
*
6657371 ACTCAATATACAAAGTAAATC
1 ACGCAATATACAAAGTAAATC
6657392 ACGCAATA
1 ACGCAATA
6657400 CTTAAAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.46, C:0.22, G:0.10, T:0.22
Consensus pattern (21 bp):
ACGCAATATACAAAGTAAATC
Found at i:6658468 original size:18 final size:18
Alignment explanation
Indices: 6658435--6658469 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6658425 TCCATCCAAA
**
6658435 GAACCCGGATGGGAACCT
1 GAACCCGGATCCGAACCT
6658453 GAACCCGGATCCGAACC
1 GAACCCGGATCCGAACC
6658470 CGAGAAGCTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.34, G:0.29, T:0.09
Consensus pattern (18 bp):
GAACCCGGATCCGAACCT
Found at i:6671391 original size:14 final size:13
Alignment explanation
Indices: 6671362--6671400 Score: 55
Period size: 11 Copynumber: 3.1 Consensus size: 13
6671352 AATTAGATTA
6671362 ATATAACTTTA-T
1 ATATAACTTTATT
6671374 -TATAACTTTCATT
1 ATATAACTTT-ATT
6671387 ATATAACTTTATT
1 ATATAACTTTATT
6671400 A
1 A
6671401 GATTAATACA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 9 0.38
12 1 0.04
13 5 0.21
14 9 0.38
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (13 bp):
ATATAACTTTATT
Found at i:6671401 original size:44 final size:44
Alignment explanation
Indices: 6671353--6671455 Score: 134
Period size: 44 Copynumber: 2.3 Consensus size: 44
6671343 TACAACTTCA
* **
6671353 ATTAGATTAATATAACTTTATTATAACTTTCATTATATAACTTT
1 ATTAGATTAATATAACTTGAACATAACTTTCATTATATAACTTT
* * *
6671397 ATTAGATTAATACAACTTGAACATAAGTTTCGTTATATAACTTT
1 ATTAGATTAATATAACTTGAACATAACTTTCATTATATAACTTT
*
6671441 AGTTAGCTTAATATA
1 A-TTAGATTAATATA
6671456 GGAGATCCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
44 39 0.78
45 11 0.22
ACGTcount: A:0.39, C:0.10, G:0.07, T:0.45
Consensus pattern (44 bp):
ATTAGATTAATATAACTTGAACATAACTTTCATTATATAACTTT
Found at i:6680896 original size:20 final size:20
Alignment explanation
Indices: 6680871--6680910 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
6680861 TGCTTCAAAA
6680871 TCAGCTGTTTCAATTTGAAG
1 TCAGCTGTTTCAATTTGAAG
**
6680891 TCAGCTGTTTTGATTTGAAG
1 TCAGCTGTTTCAATTTGAAG
6680911 CACTATTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.12, G:0.23, T:0.42
Consensus pattern (20 bp):
TCAGCTGTTTCAATTTGAAG
Found at i:6683670 original size:5 final size:5
Alignment explanation
Indices: 6683662--6683690 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
6683652 AATAGTTTCC
6683662 TTTAG TTTAG TTTAG TTTAG TTTAG TTTA
1 TTTAG TTTAG TTTAG TTTAG TTTAG TTTA
6683691 TGGTTGTTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.17, T:0.62
Consensus pattern (5 bp):
TTTAG
Found at i:6683674 original size:15 final size:15
Alignment explanation
Indices: 6683654--6683690 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
6683644 GTTAATAAAA
*
6683654 TAGTTTCCTTTAGTT
1 TAGTTTACTTTAGTT
*
6683669 TAGTTTAGTTTAGTT
1 TAGTTTACTTTAGTT
6683684 TAGTTTA
1 TAGTTTA
6683691 TGGTTGTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.19, C:0.05, G:0.16, T:0.59
Consensus pattern (15 bp):
TAGTTTACTTTAGTT
Found at i:6690819 original size:11 final size:11
Alignment explanation
Indices: 6690803--6690832 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6690793 TCTATGGCTT
6690803 TTATTTTTTTA
1 TTATTTTTTTA
6690814 TTATTTTTTTA
1 TTATTTTTTTA
*
6690825 TTCTTTTT
1 TTATTTTT
6690833 AGTTGACAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.13, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTATTTTTTTA
Found at i:6699734 original size:18 final size:18
Alignment explanation
Indices: 6699699--6699737 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
6699689 TTCCCACCAG
* * *
6699699 AAAAAGAAACAAATAAAA
1 AAAAAAAAAAAAAGAAAA
6699717 AAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAGAAAA
6699735 AAA
1 AAA
6699738 TAAGGTTCTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.90, C:0.03, G:0.05, T:0.03
Consensus pattern (18 bp):
AAAAAAAAAAAAAGAAAA
Found at i:6701124 original size:39 final size:39
Alignment explanation
Indices: 6701070--6701151 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 39
6701060 ATAGAATGTT
* *
6701070 AATGTTTATGTGCATTAAAAGATGCTACTCCATGAAGAA
1 AATGTTTATGCGCATTAAAAGATGCTACTCCACGAAGAA
6701109 AATGTTTATGCGCATTAAAAGATGCTACTCCACGAAGAA
1 AATGTTTATGCGCATTAAAAGATGCTACTCCACGAAGAA
6701148 AATG
1 AATG
6701152 ATCAAAGTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (39 bp):
AATGTTTATGCGCATTAAAAGATGCTACTCCACGAAGAA
Found at i:6712871 original size:28 final size:28
Alignment explanation
Indices: 6712817--6712872 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
6712807 TTTTTTATGA
*
6712817 AAATATTCATCAATATAAATTTAAAATT
1 AAATATTCATCAATATAAATTAAAAATT
6712845 AAATATTTCATCAA-A-AAATTAAGAAATT
1 AAATA-TTCATCAATATAAATTAA-AAATT
6712873 TATATGAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 11 0.44
29 8 0.32
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (28 bp):
AAATATTCATCAATATAAATTAAAAATT
Found at i:6714408 original size:25 final size:25
Alignment explanation
Indices: 6714380--6714433 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
6714370 CCATGCATTA
6714380 AATTAAGAGTCATCGTGTTCCTTTT
1 AATTAAGAGTCATCGTGTTCCTTTT
*
6714405 AATTAAGAGTCATCTTGTTCCTTTT
1 AATTAAGAGTCATCGTGTTCCTTTT
6714430 AATT
1 AATT
6714434 TATACAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (25 bp):
AATTAAGAGTCATCGTGTTCCTTTT
Found at i:6722196 original size:1 final size:1
Alignment explanation
Indices: 6722190--6722223 Score: 68
Period size: 1 Copynumber: 34.0 Consensus size: 1
6722180 ATCCCACGTT
6722190 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
6722224 AGGTGAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.00, G:1.00, T:0.00
Consensus pattern (1 bp):
G
Found at i:6731140 original size:22 final size:22
Alignment explanation
Indices: 6731112--6731154 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
6731102 AATAGGTTAA
6731112 GGCAAAGCATAGCAGACATAAT
1 GGCAAAGCATAGCAGACATAAT
6731134 GGCAAAGCATAGCAGACATAA
1 GGCAAAGCATAGCAGACATAA
6731155 GGGTCTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.12
Consensus pattern (22 bp):
GGCAAAGCATAGCAGACATAAT
Found at i:6733769 original size:6 final size:6
Alignment explanation
Indices: 6733760--6733793 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
6733750 TATAGTTTAC
* *
6733760 GGGTTT GGGTCT GGGTCT GGGTCT GGGACT GGGT
1 GGGTCT GGGTCT GGGTCT GGGTCT GGGTCT GGGT
6733794 TCCGGTTCCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.03, C:0.12, G:0.53, T:0.32
Consensus pattern (6 bp):
GGGTCT
Found at i:6738618 original size:16 final size:17
Alignment explanation
Indices: 6738594--6738631 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
6738584 GTTTGTTTAG
* *
6738594 ATATATTTGTGT-CTAT
1 ATATGTTTGTGTAATAT
6738610 ATATGTTTGTGTAATAT
1 ATATGTTTGTGTAATAT
6738627 ATATG
1 ATATG
6738632 AGATTGAGCG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.53
Consensus pattern (17 bp):
ATATGTTTGTGTAATAT
Found at i:6739391 original size:2 final size:2
Alignment explanation
Indices: 6739384--6739427 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
6739374 TTACTTCAAA
* *
6739384 AT AT AT AT GT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6739426 AT
1 AT
6739428 TGTGTCACAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6740102 original size:15 final size:15
Alignment explanation
Indices: 6740078--6740108 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
6740068 ATTTATTTTA
6740078 AAAAAAAAAAGAAAG
1 AAAAAAAAAAGAAAG
*
6740093 AAAAAGAAAAGAAAG
1 AAAAAAAAAAGAAAG
6740108 A
1 A
6740109 GGAGGATGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGAAAG
Found at i:6740678 original size:41 final size:41
Alignment explanation
Indices: 6740633--6740710 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
6740623 TCAAGCGGTA
*
6740633 TTTCATATGATTATTCATGTTAACTATTATATCACATAATC
1 TTTCATATGATCATTCATGTTAACTATTATATCACATAATC
*
6740674 TTTCATATGATCATTCATGTTAACTATTATGTCACAT
1 TTTCATATGATCATTCATGTTAACTATTATATCACAT
6740711 GATCAAATTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.32, C:0.15, G:0.06, T:0.46
Consensus pattern (41 bp):
TTTCATATGATCATTCATGTTAACTATTATATCACATAATC
Found at i:6740704 original size:22 final size:22
Alignment explanation
Indices: 6740638--6740704 Score: 52
Period size: 22 Copynumber: 3.2 Consensus size: 22
6740628 CGGTATTTCA
*
6740638 TATGATTATTCATGTTAACTAT
1 TATGATCATTCATGTTAACTAT
* * * *
6740660 TAT-ATCACATAATCTT-TC-A-
1 TATGATCA-TTCATGTTAACTAT
6740679 TATGATCATTCATGTTAACTAT
1 TATGATCATTCATGTTAACTAT
6740701 TATG
1 TATG
6740705 TCACATGATC
Statistics
Matches: 31, Mismatches: 9, Indels: 10
0.62 0.18 0.20
Matches are distributed among these distances:
19 8 0.26
20 6 0.19
21 5 0.16
22 12 0.39
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.46
Consensus pattern (22 bp):
TATGATCATTCATGTTAACTAT
Found at i:6745634 original size:2 final size:2
Alignment explanation
Indices: 6745627--6745663 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6745617 AAAGCTTGAG
*
6745627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6745664 AGAGACTAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6753020 original size:20 final size:21
Alignment explanation
Indices: 6752997--6753039 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
6752987 TTTTTTATTA
6752997 TTAAA-AATATAAAATTATAT
1 TTAAATAATATAAAATTATAT
* *
6753017 TTAAATATTATAAATTTATAT
1 TTAAATAATATAAAATTATAT
6753038 TT
1 TT
6753040 TCAATTCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TTAAATAATATAAAATTATAT
Found at i:6791283 original size:29 final size:30
Alignment explanation
Indices: 6791226--6791292 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 30
6791216 ATAAACAAAA
6791226 TTTTTAAAATTTTCTATTTTGTATTTATAT
1 TTTTTAAAATTTTCTATTTTGTATTTATAT
6791256 TTTTTAAAATTTT-T-TTGTT-TATTATATAT
1 TTTTTAAAATTTTCTATT-TTGTATT-TATAT
*
6791285 ATTTTAAA
1 TTTTTAAA
6791293 TGAACTTTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 6 0.18
29 15 0.44
30 13 0.38
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (30 bp):
TTTTTAAAATTTTCTATTTTGTATTTATAT
Found at i:6805670 original size:2 final size:2
Alignment explanation
Indices: 6805663--6805688 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
6805653 TGGCTTATCA
6805663 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
6805689 CGCACATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6819826 original size:10 final size:10
Alignment explanation
Indices: 6819803--6819847 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
6819793 TAAAAATATA
6819803 AAATTTTATTT
1 AAATTTT-TTT
6819814 AAATTTTTTT
1 AAATTTTTTT
** *
6819824 AAATAATTTA
1 AAATTTTTTT
6819834 AAATTTTTTT
1 AAATTTTTTT
6819844 AAAT
1 AAAT
6819848 ATTATATCAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
10 21 0.75
11 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
AAATTTTTTT
Found at i:6819839 original size:20 final size:19
Alignment explanation
Indices: 6819810--6819848 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
6819800 ATAAAATTTT
6819810 ATTTAAATTTTTTTAAATA
1 ATTTAAATTTTTTTAAATA
6819829 ATTTAAAATTTTTTTAAATA
1 ATTT-AAATTTTTTTAAATA
6819849 TTATATCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.21
20 15 0.79
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATTTAAATTTTTTTAAATA
Found at i:6826936 original size:2 final size:2
Alignment explanation
Indices: 6826925--6826959 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
6826915 AAGAATTTAA
6826925 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
6826960 TTAGCAACTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:6829040 original size:2 final size:2
Alignment explanation
Indices: 6829028--6829063 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6829018 AAAGACAGTA
6829028 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6829064 CTTACATAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:6831754 original size:24 final size:24
Alignment explanation
Indices: 6831727--6831772 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
6831717 TTGGTATCAC
6831727 AATCAAATTGAG-TCGAAAAGGGTG
1 AATCAAATTGAGAT-GAAAAGGGTG
6831751 AATCAAATTGAGATGAAAAGGG
1 AATCAAATTGAGATGAAAAGGG
6831773 CGAGTTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.46, C:0.07, G:0.28, T:0.20
Consensus pattern (24 bp):
AATCAAATTGAGATGAAAAGGGTG
Found at i:6834666 original size:44 final size:44
Alignment explanation
Indices: 6834587--6834671 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 44
6834577 CGAACGACAA
* *
6834587 CTGGCAGTACCTCAGCGAAGGAATAAACGCATGGCTAAAGGCAG
1 CTGGCAGTACCTCAGAGAAGGAATAAACACATGGCTAAAGGCAG
* * *
6834631 CTGGCAGTACCTCAGAGTATGG-ATAGACACCTGGCTAAAGG
1 CTGGCAGTACCTCAGAG-AAGGAATAAACACATGGCTAAAGG
6834672 ACACATGTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
44 32 0.91
45 3 0.09
ACGTcount: A:0.32, C:0.22, G:0.29, T:0.16
Consensus pattern (44 bp):
CTGGCAGTACCTCAGAGAAGGAATAAACACATGGCTAAAGGCAG
Found at i:6836466 original size:13 final size:14
Alignment explanation
Indices: 6836443--6836471 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
6836433 AATCACTAGC
6836443 TTTTTATTTTTATT
1 TTTTTATTTTTATT
6836457 TTTTTA-TTTTATT
1 TTTTTATTTTTATT
6836470 TT
1 TT
6836472 ATTTTTTAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (14 bp):
TTTTTATTTTTATT
Found at i:6841202 original size:1 final size:1
Alignment explanation
Indices: 6841196--6841257 Score: 79
Period size: 1 Copynumber: 62.0 Consensus size: 1
6841186 AAACAAGGTA
* ** * *
6841196 CCCCCCCCCCCCACCCCCCCCCCTTCCCCCCCCCCCCCCCCCCGCCCTCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
6841258 AACTAGCTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.02, C:0.92, G:0.02, T:0.05
Consensus pattern (1 bp):
C
Found at i:6841228 original size:23 final size:23
Alignment explanation
Indices: 6841196--6841257 Score: 97
Period size: 23 Copynumber: 2.6 Consensus size: 23
6841186 AAACAAGGTA
*
6841196 CCCCCCCCCCCCACCCCCCCCCCTT
1 CCCCCCCCCCCC-CCCCCCGCCC-T
6841221 CCCCCCCCCCCCCCCCCCGCCCT
1 CCCCCCCCCCCCCCCCCCGCCCT
6841244 CCCCCCCCCCCCCC
1 CCCCCCCCCCCCCC
6841258 AACTAGCTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
23 15 0.42
24 9 0.25
25 12 0.33
ACGTcount: A:0.02, C:0.92, G:0.02, T:0.05
Consensus pattern (23 bp):
CCCCCCCCCCCCCCCCCCGCCCT
Found at i:6841229 original size:24 final size:24
Alignment explanation
Indices: 6841196--6841257 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
6841186 AAACAAGGTA
6841196 CCCCCCCCCCCCACCCCCCC-CCCT
1 CCCCCCCCCCCC-CCCCCCCGCCCT
*
6841220 TCCCCCCCCCCCCCCCCCCGCCCT
1 CCCCCCCCCCCCCCCCCCCGCCCT
6841244 CCCCCCCCCCCCCC
1 CCCCCCCCCCCCCC
6841258 AACTAGCTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
23 7 0.20
24 28 0.80
ACGTcount: A:0.02, C:0.92, G:0.02, T:0.05
Consensus pattern (24 bp):
CCCCCCCCCCCCCCCCCCCGCCCT
Found at i:6846520 original size:129 final size:129
Alignment explanation
Indices: 6846240--6846496 Score: 514
Period size: 129 Copynumber: 2.0 Consensus size: 129
6846230 ATGCATGAAT
6846240 GTATAATTAATAAGTTTCTGAATAATGCTAATGAGATCAAGCATATTTGTTTCACAAGGTTTAGT
1 GTATAATTAATAAGTTTCTGAATAATGCTAATGAGATCAAGCATATTTGTTTCACAAGGTTTAGT
6846305 CAAATTATTGTTTTTCCTTTTTTTTTATGCACTGAATTTTGTTTCTGGGGGTCTTTTCAATTGA
66 CAAATTATTGTTTTTCCTTTTTTTTTATGCACTGAATTTTGTTTCTGGGGGTCTTTTCAATTGA
6846369 GTATAATTAATAAGTTTCTGAATAATGCTAATGAGATCAAGCATATTTGTTTCACAAGGTTTAGT
1 GTATAATTAATAAGTTTCTGAATAATGCTAATGAGATCAAGCATATTTGTTTCACAAGGTTTAGT
6846434 CAAATTATTGTTTTTCCTTTTTTTTTATGCACTGAATTTTGTTTCTGGGGGTCTTTTCAATTG
66 CAAATTATTGTTTTTCCTTTTTTTTTATGCACTGAATTTTGTTTCTGGGGGTCTTTTCAATTG
6846497 GTTTCCTTTT
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
129 128 1.00
ACGTcount: A:0.26, C:0.11, G:0.16, T:0.47
Consensus pattern (129 bp):
GTATAATTAATAAGTTTCTGAATAATGCTAATGAGATCAAGCATATTTGTTTCACAAGGTTTAGT
CAAATTATTGTTTTTCCTTTTTTTTTATGCACTGAATTTTGTTTCTGGGGGTCTTTTCAATTGA
Found at i:6853544 original size:3 final size:3
Alignment explanation
Indices: 6853536--6853565 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
6853526 AACTGAAGTC
6853536 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT
6853566 TCCACCTCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.33, G:0.33, T:0.33
Consensus pattern (3 bp):
GCT
Found at i:6855412 original size:4 final size:4
Alignment explanation
Indices: 6855398--6855443 Score: 74
Period size: 4 Copynumber: 11.5 Consensus size: 4
6855388 GGTCTTATCA
* *
6855398 ATAT GTAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ACAT AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT AT
6855444 TGTACATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (4 bp):
ATAT
Found at i:6855412 original size:6 final size:6
Alignment explanation
Indices: 6855398--6855443 Score: 74
Period size: 6 Copynumber: 7.7 Consensus size: 6
6855388 GGTCTTATCA
* *
6855398 ATATGT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAC ATAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATAT
6855444 TGTACATAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 38 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (6 bp):
ATATAT
Found at i:6862525 original size:15 final size:15
Alignment explanation
Indices: 6862505--6862534 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6862495 AAAAGTTGAG
*
6862505 CCACCACTATCACCA
1 CCACCACTACCACCA
6862520 CCACCACTACCACCA
1 CCACCACTACCACCA
6862535 TTAGCTCCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.57, G:0.00, T:0.10
Consensus pattern (15 bp):
CCACCACTACCACCA
Found at i:6864069 original size:21 final size:20
Alignment explanation
Indices: 6864021--6864070 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 20
6864011 TCATAAACTC
* *
6864021 ATATTTTTAATTTAAAAAAT
1 ATATTATTAAGTTAAAAAAT
6864041 ATACTTATTAAGTTAAAAAAT
1 ATA-TTATTAAGTTAAAAAAT
6864062 ATTATTATT
1 A-TATTATT
6864071 TATAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 3 0.12
21 21 0.81
22 2 0.08
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (20 bp):
ATATTATTAAGTTAAAAAAT
Found at i:6869645 original size:22 final size:22
Alignment explanation
Indices: 6869622--6869664 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
6869612 TAATAATGTT
6869622 AATTTAATTATTAATTATATTTA
1 AATTT-ATTATTAATTATATTTA
* *
6869645 AATTTTTTATTATTTATATT
1 AATTTATTATTAATTATATT
6869665 GATATAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (22 bp):
AATTTATTATTAATTATATTTA
Found at i:6878490 original size:36 final size:33
Alignment explanation
Indices: 6878450--6878527 Score: 93
Period size: 36 Copynumber: 2.3 Consensus size: 33
6878440 TTCCTCCTGA
* **
6878450 ACCTCCTGCCCCAATTAGGGCCGGTCCTCATCCACC
1 ACCTCCTGCCCCAAGTAGGGCCAAT-C-C-TCCACC
*
6878486 ACCTCCTGTCCCAAGTAGGGCCAATCCTCCACC
1 ACCTCCTGCCCCAAGTAGGGCCAATCCTCCACC
6878519 ACCTCCTGC
1 ACCTCCTGC
6878528 TCCACCTCCC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
33 14 0.38
34 1 0.03
35 1 0.03
36 21 0.57
ACGTcount: A:0.18, C:0.47, G:0.15, T:0.19
Consensus pattern (33 bp):
ACCTCCTGCCCCAAGTAGGGCCAATCCTCCACC
Done.