Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 159 of 172
Found at i:52051566 original size:25 final size:25
Alignment explanation
Indices: 52051538--52051658 Score: 125
Period size: 25 Copynumber: 4.6 Consensus size: 25
52051528 TCAAAATCAA
* *
52051538 AATCAGAATTAGAATTAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
* *
52051563 AATCAAAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
52051588 AATCAGAACCAGAATCAGAATTAGGTAACAG
1 AAT------CAGAATCAGAATCAGGTAACAG
*
52051619 AATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGGTAACAG
*
52051644 AATTAGAATCAGAAT
1 AATCAGAATCAGAAT
52051659 GTGAATGCAA
Statistics
Matches: 79, Mismatches: 11, Indels: 12
0.77 0.11 0.12
Matches are distributed among these distances:
25 57 0.72
31 22 0.28
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.21
Consensus pattern (25 bp):
AATCAGAATCAGAATCAGGTAACAG
Found at i:52051592 original size:56 final size:56
Alignment explanation
Indices: 52051532--52051658 Score: 209
Period size: 56 Copynumber: 2.3 Consensus size: 56
52051522 ATAGAATCAA
* *
52051532 AATCAAAATCAGAATTAGAATTAGGTAACAGAATCAAAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGAATTAGGTAACAGAATCAAAATCAGTATCAGGTAACAG
* *
52051588 AATCAGAACCAGAATCAGAATTAGGTAACAGAATCAGAATCAGTATCAGGTAACAG
1 AATCAGAATCAGAATCAGAATTAGGTAACAGAATCAAAATCAGTATCAGGTAACAG
*
52051644 AATTAGAATCAGAAT
1 AATCAGAATCAGAAT
52051659 GTGAATGCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 65 1.00
ACGTcount: A:0.49, C:0.13, G:0.17, T:0.20
Consensus pattern (56 bp):
AATCAGAATCAGAATCAGAATTAGGTAACAGAATCAAAATCAGTATCAGGTAACAG
Found at i:52051652 original size:31 final size:30
Alignment explanation
Indices: 52051561--52051658 Score: 107
Period size: 31 Copynumber: 3.4 Consensus size: 30
52051551 ATTAGGTAAC
*
52051561 AGAATCAAAATCAGTATCAGGTAACAGAAT
1 AGAATCAGAATCAGTATCAGGTAACAGAAT
* * *
52051591 CAGAACCAGAATCAGAATTAGGTAAC-----
1 -AGAATCAGAATCAGTATCAGGTAACAGAAT
52051617 AGAATCAGAATCAGTATCAGGTAACAGAATT
1 AGAATCAGAATCAGTATCAGGTAACAGAA-T
52051648 AGAATCAGAAT
1 AGAATCAGAAT
52051659 GTGAATGCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 12
0.74 0.10 0.16
Matches are distributed among these distances:
25 22 0.41
31 32 0.59
ACGTcount: A:0.48, C:0.14, G:0.18, T:0.19
Consensus pattern (30 bp):
AGAATCAGAATCAGTATCAGGTAACAGAAT
Found at i:52051855 original size:31 final size:32
Alignment explanation
Indices: 52051796--52051859 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
52051786 TGACGAAGTC
* *
52051796 AACAGATACAGATATTGTGGCTAGGCCACCAG
1 AACAGATACAGATATTGTGGCGAAGCCACCAG
* *
52051828 AACAGATATATATA-TGTGGCGAAGCCACCAG
1 AACAGATACAGATATTGTGGCGAAGCCACCAG
52051859 A
1 A
52051860 TTGCAGCGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.19
Consensus pattern (32 bp):
AACAGATACAGATATTGTGGCGAAGCCACCAG
Found at i:52052191 original size:27 final size:28
Alignment explanation
Indices: 52052161--52052219 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
52052151 AACACCCTAG
52052161 GGGTAAAAT-GGTAATTTTACCCCACAA
1 GGGTAAAATCGGTAATTTTACCCCACAA
** *
52052188 GGGT-ATCTCGGTAATTTTACCCTACAA
1 GGGTAAAATCGGTAATTTTACCCCACAA
52052215 GGGTA
1 GGGTA
52052220 TTTCAATAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 2 0.07
27 25 0.93
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.29
Consensus pattern (28 bp):
GGGTAAAATCGGTAATTTTACCCCACAA
Found at i:52052220 original size:27 final size:27
Alignment explanation
Indices: 52052171--52052285 Score: 124
Period size: 27 Copynumber: 4.3 Consensus size: 27
52052161 GGGTAAAATG
* * *
52052171 GTAATTTTACCCCACAAGGGTATCTCG
1 GTAATTTTACCCTACAAGGGTATTTCA
52052198 GTAATTTTACCCTACAAGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTCA
* * *
52052225 ATAATTCTACCCTACAGGGGTATTTCA
1 GTAATTTTACCCTACAAGGGTATTTCA
* ** *
52052252 GTAATTTCA-CAAATCAGGGGTATTTCA
1 GTAATTTTACCCTA-CAAGGGTATTTCA
52052279 GTAATTT
1 GTAATTT
52052286 CACAAATCAG
Statistics
Matches: 76, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
26 2 0.03
27 74 0.97
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.35
Consensus pattern (27 bp):
GTAATTTTACCCTACAAGGGTATTTCA
Found at i:52052286 original size:27 final size:27
Alignment explanation
Indices: 52052239--52052705 Score: 538
Period size: 27 Copynumber: 17.3 Consensus size: 27
52052229 TTCTACCCTA
** * *
52052239 CAGGGGTATTTCAGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
** * *
52052266 CAGGGGTATTTCAGTAATTTCACAAAT
1 CAGGGGTATTTTGGTAATTTTACAAAC
52052293 CAGGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
52052320 TAGGGGTATTTTGATAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
52052347 CATGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* **
52052374 TAGGGGTATTTTGGTAATTTTATGAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* ** *
52052401 AAAAGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * **
52052428 CAGGGATTTTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
*
52052455 CAAGGGTATTTTGGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * *
52052482 TAGGGGTATTTTGGTGATTTTATAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
52052509 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
**
52052536 CAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
52052563 CAAGGGTATTTTGTTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * * *
52052590 CAGAGGTATTTTGGTGATTTTATAGAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* * *
52052617 CAAGGGTATTCTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* **
52052644 TAGGGGTATTTTGGTAATTTTGTAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
* *
52052671 CAAGGGTATTTTAGTAATTTTACAAAC
1 CAGGGGTATTTTGGTAATTTTACAAAC
52052698 CAGGGGTA
1 CAGGGGTA
52052706 AATGGATGAG
Statistics
Matches: 366, Mismatches: 74, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 366 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (27 bp):
CAGGGGTATTTTGGTAATTTTACAAAC
Found at i:52052354 original size:108 final size:107
Alignment explanation
Indices: 52052242--52052705 Score: 624
Period size: 108 Copynumber: 4.3 Consensus size: 107
52052232 TACCCTACAG
* * ** * * * * *
52052242 GGGTATTTCAGTAATTTCACAAATCAGGGGTATTTCAGTAATTTCACAAATCAGGGGTATTTTGG
1 GGGTATTTTAGTAATTTTACAAA-CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAG
* * ** *
52052307 TAATTTTACAAACTAGGGGTATTTTGATAATTTTACAAACCAT
65 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
* * * *
52052350 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTAATTTTATGAACAAAAGGTATTTTAG
1 GGGTATTTTAGTAATTTTACAAAC-AGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAG
* *
52052415 TAATTTTACAAACCAGGGATTTTTTGGTAATTTTGTAAACCAA
65 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
* *
52052458 GGGTATTTTGGTAATTTTACAAACTAGGGGTATTTTGGTGATTTTATAAACCAAGGGTATTTTAG
1 GGGTATTTTAGTAATTTTACAAAC-AGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAG
52052523 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
65 TAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
* * * *
52052566 GGGTATTTT-GTTAATTTTACAAACCAGAGGTATTTTGGTGATTTTATAGACCAAGGGTATTCTA
1 GGGTATTTTAG-TAATTTTACAAA-CAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTA
*
52052630 GTAATTTTACAAACTAGGGGTATTTTGGTAATTTTGTAAACCAA
64 GTAATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
52052674 GGGTATTTTAGTAATTTTACAAACCAGGGGTA
1 GGGTATTTTAGTAATTTTACAAA-CAGGGGTA
52052706 AATGGATGAG
Statistics
Matches: 321, Mismatches: 31, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
107 2 0.01
108 317 0.99
109 2 0.01
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.39
Consensus pattern (107 bp):
GGGTATTTTAGTAATTTTACAAACAGGGGTATTTTGGTAATTTTATAAACCAAGGGTATTTTAGT
AATTTTACAAACCAGGGGTATTTTGGTAATTTTGTAAACCAA
Found at i:52053971 original size:33 final size:33
Alignment explanation
Indices: 52053934--52054000 Score: 134
Period size: 33 Copynumber: 2.0 Consensus size: 33
52053924 GAGAGCTAAT
52053934 ACATTTGGCCAATTGAAAATGACACAAAACTCA
1 ACATTTGGCCAATTGAAAATGACACAAAACTCA
52053967 ACATTTGGCCAATTGAAAATGACACAAAACTCA
1 ACATTTGGCCAATTGAAAATGACACAAAACTCA
52054000 A
1 A
52054001 AAGCAAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.46, C:0.21, G:0.12, T:0.21
Consensus pattern (33 bp):
ACATTTGGCCAATTGAAAATGACACAAAACTCA
Found at i:52054710 original size:46 final size:46
Alignment explanation
Indices: 52054595--52054768 Score: 174
Period size: 46 Copynumber: 3.7 Consensus size: 46
52054585 ACACAATAAG
* * *
52054595 CTGATGCCATGTCCCAGACAGGTCTTACACTAGCT-T-GTACATCGTGA
1 CTGATG-CATGTCCCAGACATGTCTTACACTAGCTCTCATACA--ATGA
** * *
52054642 GGCCAATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTTTCAATG-
1 --CTGATGCATGTCCCAGACATGTCTTACACTAGCTCTC-ATACAATGA
* **
52054690 CTGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATACTGTGA
1 CTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATACAATGA
*
52054736 CTGATGTATGTCCCAGACATGTCTTACACTAGC
1 CTGATGCATGTCCCAGACATGTCTTACACTAGC
52054769 ACACATATCA
Statistics
Matches: 106, Mismatches: 15, Indels: 11
0.80 0.11 0.08
Matches are distributed among these distances:
45 4 0.04
46 65 0.61
48 27 0.25
49 7 0.07
51 3 0.03
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (46 bp):
CTGATGCATGTCCCAGACATGTCTTACACTAGCTCTCATACAATGA
Found at i:52054749 original size:92 final size:94
Alignment explanation
Indices: 52054594--52054768 Score: 241
Period size: 92 Copynumber: 1.9 Consensus size: 94
52054584 CACACAATAA
*
52054594 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCTTGTACATCGTGAGGCCAATGCATGTCCCA
1 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCTTATACATCGTGA-GCCAATGCATGTCCCA
52054659 GACATGTCTTACACTAGCTCTCGTTTCAAT
65 GACATGTCTTACACTAGCTCTCGTTTCAAT
* * ** *
52054689 GCTGATG-CATGTCCCAGACATGTCTTACACTGGCTCTCATAC-T-GTGA-CTGATGTATGTCCC
1 GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCT-T-ATACATCGTGAGCCAATGCATGTCCC
52054750 AGACATGTCTTACACTAGC
64 AGACATGTCTTACACTAGC
52054769 ACACATATCA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
92 30 0.42
94 30 0.42
95 9 0.12
96 3 0.04
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (94 bp):
GCTGATGCCATGTCCCAGACAGGTCTTACACTAGCTTATACATCGTGAGCCAATGCATGTCCCAG
ACATGTCTTACACTAGCTCTCGTTTCAAT
Found at i:52055955 original size:27 final size:27
Alignment explanation
Indices: 52055922--52055977 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
52055912 TTCAAAAGTT
52055922 TTTTTCAAATTTCCTTTCTATGCGTTC
1 TTTTTCAAATTTCCTTTCTATGCGTTC
52055949 TTTTTCAAATTTCCTTTCTATGCGTTC
1 TTTTTCAAATTTCCTTTCTATGCGTTC
52055976 TT
1 TT
52055978 AGTTTAGTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.14, C:0.21, G:0.07, T:0.57
Consensus pattern (27 bp):
TTTTTCAAATTTCCTTTCTATGCGTTC
Found at i:52057395 original size:109 final size:109
Alignment explanation
Indices: 52057204--52057423 Score: 370
Period size: 109 Copynumber: 2.0 Consensus size: 109
52057194 TGGCAAGTTA
* *
52057204 TAAGGACAAAGTCGATGAAAGCAGTCGGTGATTTCAACCTCGATGCGATTATTATGCTATCTAAC
1 TAAGGACAAAGCCGACGAAAGCAGTCGGTGATTTCAACCTCGATGCGATTATTATGCTATCTAAC
52057269 CAAGTAGAACTCTTAAATAAAAAGATTGATGATTTGAGTGGTTC
66 CAAGTAGAACTCTTAAATAAAAAGATTGATGATTTGAGTGGTTC
* *
52057313 TAAGGACAAAGCCGACGAAAGCAG-CTGGTGTTTTCAACCTCGCTGCGATTATTATGCTATCTAA
1 TAAGGACAAAGCCGACGAAAGCAGTC-GGTGATTTCAACCTCGATGCGATTATTATGCTATCTAA
* *
52057377 CCAGGTAGAACTCTTAAATAAAAAGATTGATGATTTGTGTGGTTC
65 CCAAGTAGAACTCTTAAATAAAAAGATTGATGATTTGAGTGGTTC
52057422 TA
1 TA
52057424 CTCAGGCACA
Statistics
Matches: 104, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
108 1 0.01
109 103 0.99
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.30
Consensus pattern (109 bp):
TAAGGACAAAGCCGACGAAAGCAGTCGGTGATTTCAACCTCGATGCGATTATTATGCTATCTAAC
CAAGTAGAACTCTTAAATAAAAAGATTGATGATTTGAGTGGTTC
Found at i:52063253 original size:18 final size:18
Alignment explanation
Indices: 52063232--52063269 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
52063222 AATAAAATTG
* *
52063232 AAATGAAAATAAAAAGAA
1 AAATCAAAAGAAAAAGAA
52063250 AAATCAAAAGAAAAAGAA
1 AAATCAAAAGAAAAAGAA
52063268 AA
1 AA
52063270 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.79, C:0.03, G:0.11, T:0.08
Consensus pattern (18 bp):
AAATCAAAAGAAAAAGAA
Found at i:52063303 original size:20 final size:19
Alignment explanation
Indices: 52063261--52063307 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
52063251 AATCAAAAGA
*
52063261 AAAAGAAAATAAATTAAATT
1 AAAA-AAAATAAAATAAATT
52063281 AAATAAAAATAAGAATAAA-T
1 AAA-AAAAATAA-AATAAATT
52063301 AAAAAAA
1 AAAAAAA
52063308 TAGGAGGATT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 14 0.58
21 6 0.25
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAAAAAATAAAATAAATT
Found at i:52081506 original size:47 final size:46
Alignment explanation
Indices: 52081455--52081592 Score: 177
Period size: 46 Copynumber: 3.0 Consensus size: 46
52081445 AATTATGAGG
*
52081455 CATCCGAACTCGTTGACTTGTGTTCCGAGTTCACTTATGGATGAAAA
1 CATCCGAACTCGTTGAGTTGTGTTCCGAGTTCA-TTATGGATGAAAA
* * **
52081502 CATCCCAACTCGTTGAGTTGTATTCCGAGTTCATTATGGATGTGAA
1 CATCCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGAAAA
* * * * *
52081548 CATCTGAGCTCGTTGAGTTGCGTTCTGAGTTCATTATGGGTGAAA
1 CATCCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGAAA
52081593 TTATGATAGT
Statistics
Matches: 77, Mismatches: 14, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
46 47 0.61
47 30 0.39
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (46 bp):
CATCCGAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGAAAA
Found at i:52088972 original size:47 final size:47
Alignment explanation
Indices: 52088880--52089053 Score: 194
Period size: 47 Copynumber: 3.7 Consensus size: 47
52088870 ATTGAGATCT
* * * * * *
52088880 GAACTCGTTGAGTTGCGTTCCGAGTTCGTGA-GAATTATGAGGCATCC
1 GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGA-TGTCAAGCATCC
*
52088927 GAACTCTTTGAGTTGCGTTCCGAGTTCACTTATGGATG-CAAGCATCC
1 GAACTCGTTGAGTTGCGTTCCGAGTTCA-TTATGGATGTCAAGCATCC
* *
52088974 GAACTCGTTGAGTTGTGTTCCGAGTTCATTATGGATGTGAA-CA-CC
1 GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAGCATCC
* *
52089019 TGAGCTCGTTGAGTTGCGTTCCGAGTTTATTATGG
1 -GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGG
52089054 GTGAAATTAT
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
45 2 0.02
46 42 0.38
47 61 0.55
48 3 0.03
49 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.33
Consensus pattern (47 bp):
GAACTCGTTGAGTTGCGTTCCGAGTTCATTATGGATGTCAAGCATCC
Found at i:52090435 original size:49 final size:49
Alignment explanation
Indices: 52090333--52090455 Score: 149
Period size: 49 Copynumber: 2.5 Consensus size: 49
52090323 ATGCCGACGC
* * * * *
52090333 CATGTCCCAGACATGGTCTTACACTGGCTTTCATATAGCGAGGTCGATTT
1 CATGTCCCAGACA-GGTCTTACACTAGCTCTCATATAGCGAGATCAATGT
* *
52090383 CATGTCCCAGACAGGTCTTACACTAGCTCTCATCTATCG-GTATCAATGT
1 CATGTCCCAGACAGGTCTTACACTAGCTCTCATATAGCGAG-ATCAATGT
*
52090432 CATGTCTCAGACAGGTCTTACACT
1 CATGTCCCAGACAGGTCTTACACT
52090456 GACACACAAC
Statistics
Matches: 64, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 1 0.02
49 50 0.78
50 13 0.20
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.31
Consensus pattern (49 bp):
CATGTCCCAGACAGGTCTTACACTAGCTCTCATATAGCGAGATCAATGT
Found at i:52096761 original size:16 final size:15
Alignment explanation
Indices: 52096736--52096779 Score: 65
Period size: 13 Copynumber: 3.0 Consensus size: 15
52096726 AATACTTAAG
52096736 TATATAATATAATAA
1 TATATAATATAATAA
52096751 TATATTAATATAAT-A
1 TATA-TAATATAATAA
52096766 -ATATAATATAATAA
1 TATATAATATAATAA
52096780 AACATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
13 9 0.33
14 4 0.15
15 5 0.19
16 9 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
TATATAATATAATAA
Found at i:52096779 original size:8 final size:8
Alignment explanation
Indices: 52096739--52096773 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
52096729 ACTTAAGTAT
52096739 ATAATATA
1 ATAATATA
52096747 ATAATATA
1 ATAATATA
*
52096755 TTAATATA
1 ATAATATA
52096763 ATAATATA
1 ATAATATA
52096771 ATA
1 ATA
52096774 TAATAAAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
ATAATATA
Found at i:52097724 original size:6 final size:6
Alignment explanation
Indices: 52097713--52097744 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
52097703 CTCTGTACCG
52097713 TACTGT TACTGT TACTGT TACTGT TACTGT TA
1 TACTGT TACTGT TACTGT TACTGT TACTGT TA
52097745 TTTTTCGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.16, T:0.50
Consensus pattern (6 bp):
TACTGT
Found at i:52111855 original size:128 final size:126
Alignment explanation
Indices: 52111627--52112010 Score: 583
Period size: 128 Copynumber: 3.0 Consensus size: 126
52111617 AAGAAGGTAA
* * *
52111627 ATCGTTGCAGCTCATCATTATCAGTGATATTATAATGTGCCTTGGGTTTTATGAGATCAGGCTAG
1 ATCGTTGCAGCTCATCATTATCAGTGATATTGTAATGTGCCTTAGGTTTTATGAGATCATGCTAG
52111692 CCAATTGAAAGTCAAATAAAGATCATTAGCCTTGGTGATATTATCAACAATTTTCTATTTAGT
66 CCAATTGAAAGTCAAAT-AAGATCATTAGCCTTGGTGATATTATCAAC-ATTTTCTATTTAGT
* * **
52111755 ATCGTTGCAGCTCGTCATTATCAGTGATATTGTAATGTACCTTAATTTTTATGAGATCATGCTAG
1 ATCGTTGCAGCTCATCATTATCAGTGATATTGTAATGTGCCTTAGGTTTTATGAGATCATGCTAG
* * **
52111820 CCAATTGAAAGTTAAATAGAGATCATTAGCCTTGGTGATATTATCAGCATCACTCTATTTAGT
66 CCAATTGAAAGTCAAATA-AGATCATTAGCCTTGGTGATATTATCAACAT-TTTCTATTTAGT
* *
52111883 ATTGTTGCAGCTCATCATTATCAGTGATATTGTAATGTGCCTTAGGTTTTATAAGATCATGCTAG
1 ATCGTTGCAGCTCATCATTATCAGTGATATTGTAATGTGCCTTAGGTTTTATGAGATCATGCTAG
*
52111948 CCAATTGAAGGTCAAAT-A-ATCATTAGCCTTGGTGATATTATCAACATTATTCTATTTAGT
66 CCAATTGAAAGTCAAATAAGATCATTAGCCTTGGTGATATTATCAACATT-TTCTATTTAGT
52112008 ATC
1 ATC
52112011 ATCAATATAA
Statistics
Matches: 230, Mismatches: 23, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
125 40 0.17
126 1 0.00
127 3 0.01
128 186 0.81
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (126 bp):
ATCGTTGCAGCTCATCATTATCAGTGATATTGTAATGTGCCTTAGGTTTTATGAGATCATGCTAG
CCAATTGAAAGTCAAATAAGATCATTAGCCTTGGTGATATTATCAACATTTTCTATTTAGT
Found at i:52123203 original size:44 final size:43
Alignment explanation
Indices: 52123131--52123290 Score: 159
Period size: 42 Copynumber: 3.7 Consensus size: 43
52123121 TGGTATTGAC
* *
52123131 CTGAA-TTATCGTGTAAGACCGTGCCTGGGACACAGGCATCGAT
1 CTGAATTTA-CGTGTAAGACCATGTCTGGGACACAGGCATCGAT
*
52123174 TTGAAATTTACGTGTAAGACCATGTCTGGGACATC-GGCATCGTAT
1 CTG-AATTTACGTGTAAGACCATGTCTGGGACA-CAGGCATCG-AT
* * * *
52123219 CT--ATTTTCGTATAAGACCCTGTCTGGGACAGAGGCATCGAT
1 CTGAATTTACGTGTAAGACCATGTCTGGGACACAGGCATCGAT
* *
52123260 ACTGAA-TTACATGTAAGACCACGTCTGGGAC
1 -CTGAATTTACGTGTAAGACCATGTCTGGGAC
52123291 GTCGACATTG
Statistics
Matches: 96, Mismatches: 13, Indels: 16
0.77 0.10 0.13
Matches are distributed among these distances:
41 2 0.02
42 34 0.35
43 22 0.23
44 31 0.32
45 7 0.07
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (43 bp):
CTGAATTTACGTGTAAGACCATGTCTGGGACACAGGCATCGAT
Found at i:52123762 original size:12 final size:13
Alignment explanation
Indices: 52123745--52123776 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52123735 GCAAATGTTA
52123745 AGTTTTG-TGCAT
1 AGTTTTGATGCAT
52123757 AGTTTTGATGCAT
1 AGTTTTGATGCAT
52123770 -GTTTTGA
1 AGTTTTGA
52123777 AATGTGTTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.19, C:0.06, G:0.25, T:0.50
Consensus pattern (13 bp):
AGTTTTGATGCAT
Found at i:52133134 original size:14 final size:15
Alignment explanation
Indices: 52133117--52133149 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
52133107 TAATAATTGT
*
52133117 TAAATGGTAAAA-TA
1 TAAATGCTAAAACTA
52133131 TAAATGCTAAAACTA
1 TAAATGCTAAAACTA
52133146 TAAA
1 TAAA
52133150 AATTTAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.27
Consensus pattern (15 bp):
TAAATGCTAAAACTA
Found at i:52137361 original size:14 final size:14
Alignment explanation
Indices: 52137344--52137380 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
52137334 AACAGTGTAC
52137344 TTTTTGTTCTTA-TT
1 TTTTTGTT-TTAGTT
52137358 TTTTTGTTTTAGTT
1 TTTTTGTTTTAGTT
52137372 TTTTT-TTTT
1 TTTTTGTTTT
52137381 CCTGTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 7 0.32
14 15 0.68
ACGTcount: A:0.05, C:0.03, G:0.08, T:0.84
Consensus pattern (14 bp):
TTTTTGTTTTAGTT
Found at i:52138858 original size:14 final size:14
Alignment explanation
Indices: 52138839--52138866 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52138829 TGTTTCAAAA
52138839 CCATTTGCAATTTT
1 CCATTTGCAATTTT
52138853 CCATTTGCAATTTT
1 CCATTTGCAATTTT
52138867 TTGGCTAAAT
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:0.21, C:0.21, G:0.07, T:0.50
Consensus pattern (14 bp):
CCATTTGCAATTTT
Found at i:52150581 original size:266 final size:266
Alignment explanation
Indices: 52150105--52150607 Score: 670
Period size: 266 Copynumber: 1.9 Consensus size: 266
52150095 AGAAATATGA
* * *
52150105 AAAAATCAGTGGTGCCAAATTATATCCCAGGAAACTCCTAAAACCAACTCTATGCCTCTTGTTTT
1 AAAAATCAGTCGTGCCAAATTATATCCCAGGAAACTCCTAAAACCAACTCTAAGCCTCTCGTTTT
*
52150170 TGTATTTTCTAAGTAAACTACTTATATAACAAGCATGCAATTATAAGTTTTCGAAACCCAAGAAG
66 TGTATTTTCTAAGTAAACTACTTATATAACAAGCATGCAATTATAAGTTTGCGAAACCCAAGAAG
* ** * *
52150235 CATTTTTGGTAACATAAACCCAGGAAACCTTGCATGAACTATTATGCAGATTTCCTACCATAGCT
131 CATTTTTGGTAACATAAACCCAGAAAACCTTGCATGAACTACAATACAGATTTCCTACCAAAGCT
* *
52150300 ATGTTTTCTTATTGTGGGTCAAAAATTGAGAG-TTTTGCAATTCCAGAAACTTGAAAATGCAAAA
196 ATGTTTTCTTATTGTGGATAAAAAATTGAGAGATTTTGCAATTCCAGAAACTTGAAAATGCAAAA
52150364 ACATGG
261 ACATGG
*
52150370 AAAAATCAG-CGTG-CAAACTTATATCCCAGGAAACTCCTAAAACCAAGTCTAAGCCTCTCGTTT
1 AAAAATCAGTCGTGCCAAA-TTATATCCCAGGAAACTCCTAAAACCAACTCTAAGCCTCTCGTTT
52150433 TTGTATGTTT-TAAGTAAACTACTTGCATA-ACTACAAG-AGTG-AGATTATAAG-TTGCGAAAC
65 TTGTAT-TTTCTAAGTAAACTACTT--ATATA--ACAAGCA-TGCA-ATTATAAGTTTGCGAAAC
* * *
52150493 CCAAGAAGC-TTTATTGGTAACATAAACCCA-AAAAGCGTTGCATGGACTACAATACCGATTT-C
123 CCAAGAAGCATTT-TTGGTAACATAAACCCAGAAAA-CCTTGCATGAACTACAATACAGATTTCC
*
52150555 T-CAGAAAGCTATGTTTTTCTTATTGTGGATAAAAAATTGAGAGATTTTGCAAT
186 TAC-CAAAGCTATG-TTTTCTTATTGTGGATAAAAAATTGAGAGATTTTGCAAT
52150608 GCAGACCCGC
Statistics
Matches: 209, Mismatches: 16, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
263 4 0.02
264 66 0.32
265 29 0.14
266 86 0.41
267 24 0.11
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.31
Consensus pattern (266 bp):
AAAAATCAGTCGTGCCAAATTATATCCCAGGAAACTCCTAAAACCAACTCTAAGCCTCTCGTTTT
TGTATTTTCTAAGTAAACTACTTATATAACAAGCATGCAATTATAAGTTTGCGAAACCCAAGAAG
CATTTTTGGTAACATAAACCCAGAAAACCTTGCATGAACTACAATACAGATTTCCTACCAAAGCT
ATGTTTTCTTATTGTGGATAAAAAATTGAGAGATTTTGCAATTCCAGAAACTTGAAAATGCAAAA
ACATGG
Found at i:52157210 original size:34 final size:34
Alignment explanation
Indices: 52157167--52157277 Score: 181
Period size: 34 Copynumber: 3.3 Consensus size: 34
52157157 ATTGAAAGTT
52157167 TTGAAGACACCAATGAAGTAATAAGAGTTATATG
1 TTGAAGACACCAATGAAGTAATAAGAGTTATATG
52157201 TTGAAGACACCAATGAAGTAATAAGAGTTATATG
1 TTGAAGACACCAATGAAGTAATAAGAGTTATATG
* *
52157235 TTGAAGACACCAATGAAGT-ATTAGAG-TACTCTG
1 TTGAAGACACCAATGAAGTAATAAGAGTTA-TATG
52157268 TTGAAGACAC
1 TTGAAGACAC
52157278 TTTCAAGTTA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
32 2 0.03
33 19 0.26
34 53 0.72
ACGTcount: A:0.41, C:0.12, G:0.21, T:0.26
Consensus pattern (34 bp):
TTGAAGACACCAATGAAGTAATAAGAGTTATATG
Found at i:52163104 original size:3 final size:3
Alignment explanation
Indices: 52163096--52163125 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
52163086 TTTTCTCCTT
52163096 ATA ATA ATA ATA ATA ATA ATA ATA GATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT
52163126 TTCATGAGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:52164742 original size:155 final size:155
Alignment explanation
Indices: 52164534--52164843 Score: 584
Period size: 155 Copynumber: 2.0 Consensus size: 155
52164524 AATTCATTGC
52164534 TTATTAAATCAAACTTTTAATATTAGCTATGAGCTCGAGCTTCGTCAAAAATCTAAACACCTTTC
1 TTATTAAATCAAACTTTTAATATTAGCTATGAGCTCGAGCTTCGTCAAAAATCTAAACACCTTTC
52164599 TTCTTATCTGAAACCATTTTAGTTAGAAAATTTATATATTTATTTTCTTCTCTAAAAACATGCAT
66 TTCTTATCTGAAACCATTTTAGTTAGAAAATTTATATATTTATTTTCTTCTCTAAAAACATGCAT
52164664 TAACCTTAATTGTACAATACGCTTT
131 TAACCTTAATTGTACAATACGCTTT
52164689 TTATTAAATCAAACTTTTAATATTAGCTATGAGCTCGAGCTTCGTCAAAAATCTAAACACCTTTC
1 TTATTAAATCAAACTTTTAATATTAGCTATGAGCTCGAGCTTCGTCAAAAATCTAAACACCTTTC
* * * *
52164754 TTCTTATCTGAAACCATTTTAGTTAGGAAATTTATATATTTATTTTCTTCTTTAGAAATATGCAT
66 TTCTTATCTGAAACCATTTTAGTTAGAAAATTTATATATTTATTTTCTTCTCTAAAAACATGCAT
52164819 TAACCTTAATTGTACAATACGCTTT
131 TAACCTTAATTGTACAATACGCTTT
52164844 AAAACTTGAA
Statistics
Matches: 151, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (155 bp):
TTATTAAATCAAACTTTTAATATTAGCTATGAGCTCGAGCTTCGTCAAAAATCTAAACACCTTTC
TTCTTATCTGAAACCATTTTAGTTAGAAAATTTATATATTTATTTTCTTCTCTAAAAACATGCAT
TAACCTTAATTGTACAATACGCTTT
Found at i:52172380 original size:21 final size:21
Alignment explanation
Indices: 52172354--52172396 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
52172344 CTCTACATTT
52172354 ACTAGATTATAACAAACTCAC
1 ACTAGATTATAACAAACTCAC
*
52172375 ACTAGATTATAACACACTCAC
1 ACTAGATTATAACAAACTCAC
52172396 A
1 A
52172397 AATTCGGTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.23
Consensus pattern (21 bp):
ACTAGATTATAACAAACTCAC
Found at i:52176029 original size:196 final size:196
Alignment explanation
Indices: 52175803--52176174 Score: 656
Period size: 196 Copynumber: 1.9 Consensus size: 196
52175793 ATATTTTATT
52175803 TTAGCATATCGATTTTTTTTTACTTTACGTCCAACCTCTCCCCCCTTTTTCCATCTATATTCCCT
1 TTAGCATATCGATTTTTTTTTACTTTACGTCCAACCTCTCCCCCCTTTTTCCATCTATATTCCCT
*
52175868 TTTTTTTCATTTCAGGGCCGAATTACGCCTGTTTTCACATCTAGGATTTACATATACAACATATA
66 TTTTTTTCATTTCAGGGCCGAATTACGCCTGTTTACACATCTAGGATTTACATATACAACATATA
* *
52175933 TTACTGTCAAGGGTGAATTTCTTATTTTATTGAGCTTATAATATATTATATAATTTATATTAGAT
131 TTACTGTCAAGGATGAATTTCTTATTTTATTGAGCTTATAACATATTATATAATTTATATTAGAT
52175998 G
196 G
* *
52175999 TTAGACATATCGA-TTTTTTTTACTTTACGTCCAACCTCTCCCCCTTTTTTCCATCTATATTCCT
1 TTAG-CATATCGATTTTTTTTTACTTTACGTCCAACCTCTCCCCCCTTTTTCCATCTATATTCCC
* *
52176063 TTTTTTTTCATTTCAGGGCCGAATTATGCCTGTTTACACATCTAGGATTTACATATTCAACATAT
65 TTTTTTTTCATTTCAGGGCCGAATTACGCCTGTTTACACATCTAGGATTTACATATACAACATAT
*
52176128 ATTACTGTCAATGATGAATTTCTTATTTTATTGAGCTTATAACATAT
130 ATTACTGTCAAGGATGAATTTCTTATTTTATTGAGCTTATAACATAT
52176175 AGTTTATATT
Statistics
Matches: 167, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
196 159 0.95
197 8 0.05
ACGTcount: A:0.25, C:0.20, G:0.10, T:0.45
Consensus pattern (196 bp):
TTAGCATATCGATTTTTTTTTACTTTACGTCCAACCTCTCCCCCCTTTTTCCATCTATATTCCCT
TTTTTTTCATTTCAGGGCCGAATTACGCCTGTTTACACATCTAGGATTTACATATACAACATATA
TTACTGTCAAGGATGAATTTCTTATTTTATTGAGCTTATAACATATTATATAATTTATATTAGAT
G
Found at i:52176223 original size:15 final size:14
Alignment explanation
Indices: 52176202--52176244 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
52176192 AGAATATTAA
52176202 TTCTATTATATATT
1 TTCTATTATATATT
* *
52176216 TATCTATTCTATATA
1 T-TCTATTATATATT
*
52176231 TTCTAATATATATT
1 TTCTATTATATATT
52176245 AGTATTATTT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.33, C:0.09, G:0.00, T:0.58
Consensus pattern (14 bp):
TTCTATTATATATT
Found at i:52176945 original size:45 final size:45
Alignment explanation
Indices: 52176881--52176970 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
52176871 CTTTTTGAAG
52176881 AAGGTTCTATTACTAACATGTTTACTTCCATTATGGGTAATGTAT
1 AAGGTTCTATTACTAACATGTTTACTTCCATTATGGGTAATGTAT
*
52176926 AAGGTTCTGTTACTAACATGTTTACTTCCATTATGGGTAATGTAT
1 AAGGTTCTATTACTAACATGTTTACTTCCATTATGGGTAATGTAT
52176971 TTGGGTTCAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (45 bp):
AAGGTTCTATTACTAACATGTTTACTTCCATTATGGGTAATGTAT
Found at i:52177851 original size:12 final size:13
Alignment explanation
Indices: 52177834--52177865 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
52177824 ATAGCACATT
52177834 TCAAAAC-ATGCA
1 TCAAAACTATGCA
52177846 TCAAAACTATGCA
1 TCAAAACTATGCA
52177859 -CAAAACT
1 TCAAAACT
52177866 TAACATTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 14 0.74
13 5 0.26
ACGTcount: A:0.50, C:0.25, G:0.06, T:0.19
Consensus pattern (13 bp):
TCAAAACTATGCA
Found at i:52178466 original size:86 final size:85
Alignment explanation
Indices: 52178314--52178473 Score: 207
Period size: 86 Copynumber: 1.9 Consensus size: 85
52178304 GACAAGTACA
* * * *
52178314 ATGCCGACGTCCCAGACGTGGTCTTACATGTAATTCAGTATCGATGCCTCTGTCCCAGACAGGGT
1 ATGCCGACGTCCCAGACATGGTATTACATGTAATTCAGAATCGATGCCTCTGTCCCAGACACGGT
*
52178379 CTTATACGAAAACAGATACG
66 CTTACACGAAAACAGATACG
* * *
52178399 ATGCCGATGTCCCAGACATGGTATTACACT-TAAATTTCA-AATCGATGCTTGTGTCCCAGACAC
1 ATGCCGACGTCCCAGACATGGTATTACA-TGT-AA-TTCAGAATCGATGCCTCTGTCCCAGACAC
52178462 GGTCTTACACGA
63 GGTCTTACACGA
52178474 TAATTCAGGT
Statistics
Matches: 64, Mismatches: 8, Indels: 5
0.83 0.10 0.06
Matches are distributed among these distances:
85 26 0.41
86 34 0.53
87 4 0.06
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (85 bp):
ATGCCGACGTCCCAGACATGGTATTACATGTAATTCAGAATCGATGCCTCTGTCCCAGACACGGT
CTTACACGAAAACAGATACG
Found at i:52179045 original size:22 final size:23
Alignment explanation
Indices: 52179020--52179077 Score: 82
Period size: 25 Copynumber: 2.5 Consensus size: 23
52179010 ATCACAAAAC
*
52179020 TCATGATATC-AACAATGGTATT
1 TCATGAAATCTAACAATGGTATT
52179042 TCATGAAATCTTTAACAATGGTATT
1 TCATGAAATC--TAACAATGGTATT
52179067 TCATGAAATCT
1 TCATGAAATCT
52179078 TTAACAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 9 0.28
23 1 0.03
25 22 0.69
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.38
Consensus pattern (23 bp):
TCATGAAATCTAACAATGGTATT
Found at i:52179060 original size:25 final size:25
Alignment explanation
Indices: 52179030--52179083 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
52179020 TCATGATATC
52179030 AACAATGGTATTTCATGAAATCTTT
1 AACAATGGTATTTCATGAAATCTTT
52179055 AACAATGGTATTTCATGAAATCTTT
1 AACAATGGTATTTCATGAAATCTTT
52179080 AACA
1 AACA
52179084 GAAATAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (25 bp):
AACAATGGTATTTCATGAAATCTTT
Found at i:52181033 original size:21 final size:21
Alignment explanation
Indices: 52181009--52181073 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
52180999 AAGTCTAGCT
*
52181009 GAAGCACATAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
*
52181030 GAAGC-C-CGAAG-GCT-AACT
1 GAAGCACAC-AAGTGCTAAACG
52181048 GAAGCACACAAGTGCTAAACG
1 GAAGCACACAAGTGCTAAACG
52181069 GAAGC
1 GAAGC
52181074 CCGAAGGCTA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
18 8 0.22
19 7 0.19
20 8 0.22
21 13 0.36
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (21 bp):
GAAGCACACAAGTGCTAAACG
Found at i:52181050 original size:39 final size:39
Alignment explanation
Indices: 52180992--52181091 Score: 173
Period size: 39 Copynumber: 2.6 Consensus size: 39
52180982 TCGTGATATA
* * *
52180992 AAGCCCGAAGTCTAGCTGAAGCACATAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
52181031 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
1 AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
52181070 AAGCCCGAAGGCTAACTGAAGC
1 AAGCCCGAAGGCTAACTGAAGC
52181092 TCATCAGAGC
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 58 1.00
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (39 bp):
AAGCCCGAAGGCTAACTGAAGCACACAAGTGCTAAACGG
Found at i:52186513 original size:15 final size:15
Alignment explanation
Indices: 52186493--52186522 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52186483 ATAATCCTAA
*
52186493 TAATTATCTTAATAT
1 TAATTATCCTAATAT
52186508 TAATTATCCTAATAT
1 TAATTATCCTAATAT
52186523 AAATAAAATG
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:0.40, C:0.10, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATTATCCTAATAT
Found at i:52192186 original size:3 final size:3
Alignment explanation
Indices: 52192178--52192226 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
52192168 TTACTTCACT
*
52192178 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC GTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
52192226 T
1 T
52192227 CCTATCTCTC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.00, C:0.33, G:0.02, T:0.65
Consensus pattern (3 bp):
TTC
Found at i:52196657 original size:55 final size:55
Alignment explanation
Indices: 52196592--52196704 Score: 208
Period size: 55 Copynumber: 2.1 Consensus size: 55
52196582 TCACAATTTC
* *
52196592 AAAATTTAATTTATATTATTACTGTTTAAATTTTAAATATCACACAGATACCTAA
1 AAAATTTAATTTATATTAGTACCGTTTAAATTTTAAATATCACACAGATACCTAA
52196647 AAAATTTAATTTATATTAGTACCGTTTAAATTTTAAATATCACACAGATACCTAA
1 AAAATTTAATTTATATTAGTACCGTTTAAATTTTAAATATCACACAGATACCTAA
52196702 AAA
1 AAA
52196705 TATTAAGATA
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 56 1.00
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (55 bp):
AAAATTTAATTTATATTAGTACCGTTTAAATTTTAAATATCACACAGATACCTAA
Found at i:52196710 original size:28 final size:28
Alignment explanation
Indices: 52196619--52196710 Score: 73
Period size: 28 Copynumber: 3.3 Consensus size: 28
52196609 ATTACTGTTT
*
52196619 AAATTTTAAATATCACACAGATACCTAA
1 AAATATTAAATATCACACAGATACCTAA
* * * * **
52196647 AAA-ATTTAAT-TTATATTAG-TACCGTTT
1 AAATATTAAATATCACA-CAGATACC-TAA
*
52196674 AAATTTTAAATATCACACAGATACCTAA
1 AAATATTAAATATCACACAGATACCTAA
52196702 AAATATTAA
1 AAATATTAA
52196711 GATACTATAA
Statistics
Matches: 44, Mismatches: 15, Indels: 10
0.64 0.22 0.14
Matches are distributed among these distances:
26 7 0.16
27 11 0.25
28 19 0.43
29 7 0.16
ACGTcount: A:0.48, C:0.13, G:0.04, T:0.35
Consensus pattern (28 bp):
AAATATTAAATATCACACAGATACCTAA
Found at i:52202790 original size:17 final size:18
Alignment explanation
Indices: 52202768--52202831 Score: 67
Period size: 19 Copynumber: 3.6 Consensus size: 18
52202758 ATTCCAAGAT
52202768 ATTTTTAAAAT-TTTTAA
1 ATTTTTAAAATATTTTAA
*
52202785 ATTTTTACAATATTTTATA
1 ATTTTTAAAATATTTTA-A
* **
52202804 ATTTCTATTATATTTTAA
1 ATTTTTAAAATATTTTAA
*
52202822 ATTCTTAAAA
1 ATTTTTAAAA
52202832 AAATATAACA
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 10 0.27
18 12 0.32
19 15 0.41
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (18 bp):
ATTTTTAAAATATTTTAA
Found at i:52204366 original size:14 final size:15
Alignment explanation
Indices: 52204338--52204367 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
52204328 TAGTCTTTGG
52204338 TTTTGGTTTTGGTTT
1 TTTTGGTTTTGGTTT
52204353 TTTTGGTTTT-GTTT
1 TTTTGGTTTTGGTTT
52204367 T
1 T
52204368 AGATAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.33
15 10 0.67
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (15 bp):
TTTTGGTTTTGGTTT
Found at i:52207037 original size:13 final size:13
Alignment explanation
Indices: 52207019--52207044 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52207009 TCCACTTCGC
52207019 CTTGTGGGGCAAT
1 CTTGTGGGGCAAT
52207032 CTTGTGGGGCAAT
1 CTTGTGGGGCAAT
52207045 GTCCGCCACC
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:0.15, C:0.15, G:0.38, T:0.31
Consensus pattern (13 bp):
CTTGTGGGGCAAT
Found at i:52209453 original size:16 final size:16
Alignment explanation
Indices: 52209432--52209463 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52209422 TAATGTGTTT
52209432 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
52209448 TGCTGCTGTTGTTTAA
1 TGCTGCTGTTGTTTAA
52209464 ATGCAGAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.25, T:0.50
Consensus pattern (16 bp):
TGCTGCTGTTGTTTAA
Found at i:52209645 original size:45 final size:45
Alignment explanation
Indices: 52209577--52209680 Score: 154
Period size: 45 Copynumber: 2.3 Consensus size: 45
52209567 AAGAGGTGGA
**
52209577 CAACATCATGCATAATTTGTGGAACAAATTAAGGAAGCATTTGAC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
* * * *
52209622 CAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGC
1 CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
52209667 CAACATCATGCATA
1 CAACATCATGCATA
52209681 TGAGGAAGCA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 53 1.00
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.26
Consensus pattern (45 bp):
CAACATCATGCATAATTCATGGAACAAATTAAGGAAGCATTTGAC
Found at i:52209686 original size:30 final size:30
Alignment explanation
Indices: 52209651--52209710 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
52209641 TGGAAGAATT
*
52209651 TGAGGAAGCATTTGGCCAACATCATGCATA
1 TGAGGAAGCATTTGACCAACATCATGCATA
52209681 TGAGGAAGCATTTGACCAACATCATGCATA
1 TGAGGAAGCATTTGACCAACATCATGCATA
52209711 ATTCATGGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.20, G:0.22, T:0.23
Consensus pattern (30 bp):
TGAGGAAGCATTTGACCAACATCATGCATA
Found at i:52209693 original size:75 final size:75
Alignment explanation
Indices: 52209608--52209755 Score: 287
Period size: 75 Copynumber: 2.0 Consensus size: 75
52209598 GAACAAATTA
*
52209608 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTGAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGCCAACAT
52209673 CATGCATATG
66 CATGCATATG
52209683 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGCCAACAT
1 AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGCCAACAT
52209748 CATGCATA
66 CATGCATA
52209756 ATTTAAGGAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.37, C:0.18, G:0.20, T:0.25
Consensus pattern (75 bp):
AGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATTTAAGGAAGCATTTGGCCAACAT
CATGCATATG
Found at i:52209777 original size:45 final size:45
Alignment explanation
Indices: 52209681--52209780 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
52209671 ATCATGCATA
* * *
52209681 TGAGGAAGCATTTGACCAACATCATGCATAATTCATGGAAGAATT
1 TGAGGAAGCATTTGACCAACATCATGCATAATTCAAGGAACAAAT
* * *
52209726 TAAGGAAGCATTTGGCCAACATCATGCATAATTTAAGGAACAAAT
1 TGAGGAAGCATTTGACCAACATCATGCATAATTCAAGGAACAAAT
52209771 TGAGGAAGCA
1 TGAGGAAGCA
52209781 CCATGGCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
45 48 1.00
ACGTcount: A:0.40, C:0.15, G:0.21, T:0.24
Consensus pattern (45 bp):
TGAGGAAGCATTTGACCAACATCATGCATAATTCAAGGAACAAAT
Found at i:52209929 original size:45 final size:45
Alignment explanation
Indices: 52209880--52210053 Score: 249
Period size: 45 Copynumber: 3.9 Consensus size: 45
52209870 TCGGCCATGG
* * * *
52209880 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* *
52209925 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
*
52209970 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
* * * *
52210015 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTG
52210054 TCCACCTCTT
Statistics
Matches: 117, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 117 1.00
ACGTcount: A:0.25, C:0.19, G:0.16, T:0.40
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATAAATTATGCATGATGTTGGTCAAA
Found at i:52210188 original size:45 final size:46
Alignment explanation
Indices: 52210078--52210280 Score: 374
Period size: 46 Copynumber: 4.5 Consensus size: 46
52210068 GCCGTCCATG
*
52210078 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCAT
1 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCAT
52210124 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCA-
1 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCAT
*
52210169 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCAT
1 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCAT
52210215 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCA-
1 TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCAT
52210260 TGGAAGAATTTGAGGAAGCAT
1 TGGAAGAATTTGAGGAAGCAT
52210281 CACGGCCGAA
Statistics
Matches: 153, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
45 65 0.42
46 88 0.58
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (46 bp):
TGGAAGAATTTGAGGAAGCATTTGACCAACATCATGCATAATTCAT
Found at i:52210233 original size:91 final size:91
Alignment explanation
Indices: 52210078--52210280 Score: 406
Period size: 91 Copynumber: 2.2 Consensus size: 91
52210068 GCCGTCCATG
52210078 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATTGGAAGAATTTGAGGAAGC
1 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATTGGAAGAATTTGAGGAAGC
52210143 ATTTGACCAACATCATGCATAATTCA
66 ATTTGACCAACATCATGCATAATTCA
52210169 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATTGGAAGAATTTGAGGAAGC
1 TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATTGGAAGAATTTGAGGAAGC
52210234 ATTTGACCAACATCATGCATAATTCA
66 ATTTGACCAACATCATGCATAATTCA
52210260 TGGAAGAATTTGAGGAAGCAT
1 TGGAAGAATTTGAGGAAGCAT
52210281 CACGGCCGAA
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
91 112 1.00
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (91 bp):
TGGAAGAATTTGAGGAAGCATTTGGCCAACATCATGCATAATTCATTGGAAGAATTTGAGGAAGC
ATTTGACCAACATCATGCATAATTCA
Found at i:52220037 original size:43 final size:43
Alignment explanation
Indices: 52219976--52220083 Score: 135
Period size: 43 Copynumber: 2.5 Consensus size: 43
52219966 AAAGCGTCGT
* * *
52219976 TAAAAAACGTGACCTTTAGCGGCACTTTCCATACAAACGCCGC
1 TAAAGAACGTGACCTTTAGCGGCACTTTCCATACAAACACCAC
* * * *
52220019 TAAAGAACGTGACTTTTAGCGCCACTTTTCATACAAACACCAT
1 TAAAGAACGTGACCTTTAGCGGCACTTTCCATACAAACACCAC
**
52220062 TAAAGAATATGACCTTTAGCGG
1 TAAAGAACGTGACCTTTAGCGG
52220084 TGCTTTTACA
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 54 1.00
ACGTcount: A:0.34, C:0.25, G:0.16, T:0.25
Consensus pattern (43 bp):
TAAAGAACGTGACCTTTAGCGGCACTTTCCATACAAACACCAC
Found at i:52220923 original size:13 final size:14
Alignment explanation
Indices: 52220897--52220925 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
52220887 ACTAACGGAG
52220897 AATTAAACCATTAT
1 AATTAAACCATTAT
52220911 AATTAAA-CATTAT
1 AATTAAACCATTAT
52220924 AA
1 AA
52220926 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:52222960 original size:27 final size:27
Alignment explanation
Indices: 52222930--52222981 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
52222920 TTTGCTATGT
*
52222930 TTGGCACACTATATCATTTTTCCATGA
1 TTGGCACACTATATCACTTTTCCATGA
*
52222957 TTGGCACACTTTATCACTTTTCCAT
1 TTGGCACACTATATCACTTTTCCAT
52222982 AGTTCAACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.23, C:0.25, G:0.10, T:0.42
Consensus pattern (27 bp):
TTGGCACACTATATCACTTTTCCATGA
Found at i:52223114 original size:31 final size:30
Alignment explanation
Indices: 52223071--52223156 Score: 109
Period size: 31 Copynumber: 2.8 Consensus size: 30
52223061 CTTGTCACTT
* *
52223071 GTAGCCGAAGCTATCACTATTCACTGATCAG
1 GTAGCCGAAGCTA-CACTTTTCACTAATCAG
* *
52223102 GTAGCTGGAGCTACTACTTTTCACTAATCAG
1 GTAGCCGAAGCTAC-ACTTTTCACTAATCAG
52223133 GTAGCCGAAGCTACCACTTTTCAC
1 GTAGCCGAAGCTA-CACTTTTCAC
52223157 ATTGTACACA
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 1 0.02
31 45 0.96
32 1 0.02
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (30 bp):
GTAGCCGAAGCTACACTTTTCACTAATCAG
Found at i:52223233 original size:33 final size:33
Alignment explanation
Indices: 52223149--52223262 Score: 142
Period size: 33 Copynumber: 3.5 Consensus size: 33
52223139 GAAGCTACCA
* *
52223149 CTTTTCACA-TTGTACACACAAGGCGTACATTTC
1 CTTTTCA-AGTTGTACACACAAAGTGTACATTTC
*
52223182 CTTTTCAAG-TGTACACACAAAGTGTACGTTTC
1 CTTTTCAAGTTGTACACACAAAGTGTACATTTC
* * *
52223214 TTTTTTAAGTTGTACACACACAGTGTACATTTC
1 CTTTTCAAGTTGTACACACAAAGTGTACATTTC
*
52223247 CTTTTCCAGTTGTACA
1 CTTTTCAAGTTGTACA
52223263 TTTTAGGTAC
Statistics
Matches: 69, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
32 28 0.41
33 41 0.59
ACGTcount: A:0.26, C:0.23, G:0.13, T:0.38
Consensus pattern (33 bp):
CTTTTCAAGTTGTACACACAAAGTGTACATTTC
Found at i:52225755 original size:29 final size:29
Alignment explanation
Indices: 52225713--52225768 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
52225703 TAAATTTAAC
52225713 ATTACTTTGAATTTTTGCAGGCTCATCGG
1 ATTACTTTGAATTTTTGCAGGCTCATCGG
52225742 ATTACTTTGAATTTTTGCAGGCTCATC
1 ATTACTTTGAATTTTTGCAGGCTCATC
52225769 AGGTGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
ATTACTTTGAATTTTTGCAGGCTCATCGG
Found at i:52229123 original size:29 final size:29
Alignment explanation
Indices: 52229081--52229136 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
52229071 TAAATTTAAC
52229081 ATTACTTTGAATTTTTGCAGGCTCATCGG
1 ATTACTTTGAATTTTTGCAGGCTCATCGG
52229110 ATTACTTTGAATTTTTGCAGGCTCATC
1 ATTACTTTGAATTTTTGCAGGCTCATC
52229137 AGGTGTTTCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.43
Consensus pattern (29 bp):
ATTACTTTGAATTTTTGCAGGCTCATCGG
Found at i:52235749 original size:18 final size:18
Alignment explanation
Indices: 52235723--52235758 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
52235713 TAGGGATTTT
*
52235723 GATTTGGGAAAATTTAGG
1 GATTAGGGAAAATTTAGG
52235741 GATTAGGGAAAATTTAGG
1 GATTAGGGAAAATTTAGG
52235759 AAATTGGGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (18 bp):
GATTAGGGAAAATTTAGG
Found at i:52235771 original size:18 final size:17
Alignment explanation
Indices: 52235726--52235773 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
52235716 GGATTTTGAT
*
52235726 TTGGGAAAATTTAGGGA
1 TTGGGAAAATTTAGGAA
52235743 TTAGGGAAAATTTAGGAAA
1 TT-GGGAAAATTTAGG-AA
*
52235762 TTGGGGAAATTT
1 TTGGGAAAATTT
52235774 TGTTGGGGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 2 0.07
18 22 0.81
19 3 0.11
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
TTGGGAAAATTTAGGAA
Found at i:52237682 original size:61 final size:60
Alignment explanation
Indices: 52237600--52237719 Score: 222
Period size: 61 Copynumber: 2.0 Consensus size: 60
52237590 ATTTCTAACA
*
52237600 TTTTTTTATAAAATTGCCCATAAAATTTTACTTTTATTCAATTTAGTCCATGAGCCTAAG
1 TTTTTTTACAAAATTGCCCATAAAATTTTACTTTTATTCAATTTAGTCCATGAGCCTAAG
52237660 TTTTCTTTACAAAATTGCCCATAAAATTTTACTTTTATTCAATTTAGTCCATGAGCCTAA
1 TTTT-TTTACAAAATTGCCCATAAAATTTTACTTTTATTCAATTTAGTCCATGAGCCTAA
52237720 AACATACAAA
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
60 4 0.07
61 54 0.93
ACGTcount: A:0.32, C:0.17, G:0.07, T:0.44
Consensus pattern (60 bp):
TTTTTTTACAAAATTGCCCATAAAATTTTACTTTTATTCAATTTAGTCCATGAGCCTAAG
Found at i:52241641 original size:22 final size:23
Alignment explanation
Indices: 52241614--52241658 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
52241604 ACCTGATAAG
52241614 AATACGACACAT-AAGTGCCTGA
1 AATACGACACATAAAGTGCCTGA
*
52241636 AATACGACACATAAAGTGTCTGA
1 AATACGACACATAAAGTGCCTGA
52241659 TCAGTAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (23 bp):
AATACGACACATAAAGTGCCTGA
Found at i:52241918 original size:29 final size:29
Alignment explanation
Indices: 52241844--52241923 Score: 108
Period size: 28 Copynumber: 2.8 Consensus size: 29
52241834 CACCAAAATG
* * * *
52241844 TCCAACCAAAACACACCAGTATCATATAA
1 TCCATCCAAAACACACCAGAATAATACAA
*
52241873 TCC-TCCCAAACACACCAGAATAATACAA
1 TCCATCCAAAACACACCAGAATAATACAA
52241901 TCCATCCAAAACACACCAGAATA
1 TCCATCCAAAACACACCAGAATA
52241924 GCACAAAGTG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
28 23 0.52
29 21 0.48
ACGTcount: A:0.47, C:0.34, G:0.04, T:0.15
Consensus pattern (29 bp):
TCCATCCAAAACACACCAGAATAATACAA
Found at i:52252379 original size:17 final size:15
Alignment explanation
Indices: 52252351--52252391 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
52252341 AATGTTTTTG
*
52252351 TTCTAAACAATAATTA
1 TTCTAAATAAT-ATTA
52252367 TTCTTAAATAATATTA
1 TTC-TAAATAATATTA
52252383 TTCTAAATA
1 TTCTAAATA
52252392 GAAGTTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
15 6 0.26
16 10 0.43
17 7 0.30
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (15 bp):
TTCTAAATAATATTA
Found at i:52253272 original size:50 final size:51
Alignment explanation
Indices: 52253218--52253320 Score: 172
Period size: 50 Copynumber: 2.0 Consensus size: 51
52253208 CTTGTTATTT
*
52253218 CTTTCCTTAGAAAATACCATTAATTTTATCTAAAAT-ATAAATTAGTATAA
1 CTTTCCCTAGAAAATACCATTAATTTTATCTAAAATAATAAATTAGTATAA
*
52253268 CTTTCCCTAGAAAATACCATTACTTTTATCTAAAATAAATAAATTAGTATAA
1 CTTTCCCTAGAAAATACCATTAATTTTATCTAAAAT-AATAAATTAGTATAA
52253320 C
1 C
52253321 GCAATTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 34 0.69
52 15 0.31
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (51 bp):
CTTTCCCTAGAAAATACCATTAATTTTATCTAAAATAATAAATTAGTATAA
Found at i:52263477 original size:76 final size:76
Alignment explanation
Indices: 52263384--52263543 Score: 266
Period size: 76 Copynumber: 2.1 Consensus size: 76
52263374 TAGTAGTTTT
* * * **
52263384 TAAAATTAAAATACTATTCAAAATATAATTTTTAAAATATTGTTAATTATTAAACAAATCATTAC
1 TAAAATTAAAATACTATTAAAAATAAAAATTTTAAAATATTGTTAATTAAGAAACAAATCATTAC
52263449 TATTCTTCTAA
66 TATTCTTCTAA
52263460 TAAAATTAAAATACTATTAAAAATAAAAATTTTAAAATATTGTTAATTAAGAAACAAATCATTAC
1 TAAAATTAAAATACTATTAAAAATAAAAATTTTAAAATATTGTTAATTAAGAAACAAATCATTAC
52263525 TATTCTTCTAA
66 TATTCTTCTAA
52263536 TAATAATT
1 TAA-AATT
52263544 TTAAAAATAT
Statistics
Matches: 78, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
76 74 0.95
77 4 0.05
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (76 bp):
TAAAATTAAAATACTATTAAAAATAAAAATTTTAAAATATTGTTAATTAAGAAACAAATCATTAC
TATTCTTCTAA
Found at i:52263698 original size:20 final size:19
Alignment explanation
Indices: 52263660--52263704 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
52263650 AAATATTGTT
*
52263660 AAATATATTTAACAGTTTA
1 AAATATATTTAAAAGTTTA
*
52263679 AAATCATATTTAAAATTTTA
1 AAAT-ATATTTAAAAGTTTA
*
52263699 ATATAT
1 AAATAT
52263705 TGTTATGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (19 bp):
AAATATATTTAAAAGTTTA
Found at i:52265768 original size:41 final size:41
Alignment explanation
Indices: 52265572--52265758 Score: 315
Period size: 41 Copynumber: 4.6 Consensus size: 41
52265562 TGATTCAGTA
52265572 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
52265613 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
52265654 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* * *
52265695 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATACT-T
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAAT-GTAT
52265736 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
52265759 GTAACGTCTG
Statistics
Matches: 141, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
40 2 0.01
41 138 0.98
42 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:52273438 original size:41 final size:41
Alignment explanation
Indices: 52273201--52273428 Score: 390
Period size: 41 Copynumber: 5.6 Consensus size: 41
52273191 TGATTCAGTA
52273201 CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCA-TTAAGCCTGCTAGACATATAGTCTGAAATGTAT
52273242 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
52273283 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
52273324 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
* *
52273365 CACCGGCATTAAGCCTGCTAGACTTAAAGTCTG-AAT-TACTT
1 CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA--T
52273406 CACCGGCATTAAGCCTGCTAGAC
1 CACCGGCATTAAGCCTGCTAGAC
52273429 GTAACGTCTG
Statistics
Matches: 182, Mismatches: 2, Indels: 6
0.96 0.01 0.03
Matches are distributed among these distances:
39 2 0.01
40 5 0.03
41 175 0.96
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
CACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTAT
Found at i:52301778 original size:23 final size:23
Alignment explanation
Indices: 52301737--52301780 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
52301727 CTAGAAAATG
*
52301737 AAAACCCTTTCCCTCTTTCTCCC
1 AAAACCCTTGCCCTCTTTCTCCC
* *
52301760 AAAACCCTTGGCCTTTTTCTC
1 AAAACCCTTGCCCTCTTTCTC
52301781 TACGATGATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.18, C:0.41, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAACCCTTGCCCTCTTTCTCCC
Found at i:52308384 original size:91 final size:92
Alignment explanation
Indices: 52308271--52308544 Score: 399
Period size: 92 Copynumber: 3.0 Consensus size: 92
52308261 ATAATTCACG
* * ** *
52308271 TTGCAATTTCACTACTTAATAAATTTTGTCG-GAAAGTGGCTTTTATTTTTAGCATTGCATTA-T
1 TTGCAATTTCACTACTTAATAAATCTTGTCGAG-AAGTCGCACTTATTTTTAGCATTGCACTATT
* *
52308334 CTAAGTTGTTTTGGTTTTTTGAAACTTA
65 TTAAGTTGTTTTGATTTTTTGAAACTTA
* * *
52308362 TTGCGATTTCACTACTTAATAAATCTTGTCAAGAAGTTGCACTTATTTTTAGCATTGCACTATTT
1 TTGCAATTTCACTACTTAATAAATCTTGTCGAGAAGTCGCACTTATTTTTAGCATTGCACTATTT
* *
52308427 TAAGTTGTTTTGATTTCTTGAAACTTG
66 TAAGTTGTTTTGATTTTTTGAAACTTA
*
52308454 TTGCAATTTCACTACTTAATAAATCTTGGCGAGAAGTCGCACTTATTTTTAGCATTGCACTATTT
1 TTGCAATTTCACTACTTAATAAATCTTGTCGAGAAGTCGCACTTATTTTTAGCATTGCACTATTT
*
52308519 TAAGTTATTTTGATTTTTTGAAACTT
66 TAAGTTGTTTTGATTTTTTGAAACTT
52308545 GTTTTGGGTT
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
91 53 0.32
92 111 0.68
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.46
Consensus pattern (92 bp):
TTGCAATTTCACTACTTAATAAATCTTGTCGAGAAGTCGCACTTATTTTTAGCATTGCACTATTT
TAAGTTGTTTTGATTTTTTGAAACTTA
Found at i:52320087 original size:232 final size:227
Alignment explanation
Indices: 52319616--52320118 Score: 582
Period size: 232 Copynumber: 2.2 Consensus size: 227
52319606 ATTAATTATT
* * * *
52319616 ACTTATGGCATCAAAGAAGAGCTTTATAAGAAAGAAACAAAAGAGGACTGAGTGCGATACTTAAT
1 ACTTATGGCATCAAAGAAGAGCCTTATAAAAAAGAAACAAAAGAGCACTGAGTGCGATACTCAAT
* * * * *
52319681 TACCATTTGATCAAATTACCTTTGTTGGTGCAAAATGATTATGGGTATTTGTTTCCATTGGTAAG
66 TACCATTTGATCAAATTACCCTTGTTGGTGAAAAATGATTATCGGTATTTGTCTCAATTGGTAAG
* * *
52319746 ATTCTTCATTTTTTTTAAAAGAAACGAATATTGTTGTGTACTTGTAATTGTTGATTTGGGGAAAT
131 ATTCTTCATTTTTTTTAAAAGAAAAGAATATTGTTGTGTACTTGTAATAGTTGATTTGGAGAAAT
* * *
52319811 ATTTACTTGATTGATGAGATTTATTAATGCTC
196 ATTTACTTGATTGATAAGATTTATTAAAGATC
* * * * * *
52319843 ATTTAAGGCATCAAA-AAAAGGCCTTATAAAAAAGAAACAAATGA-CATTGAGTGCAATATACTC
1 ACTTATGGCATCAAAGAAGA-GCCTTATAAAAAAGAAACAAAAGAGCACTGAGTGC--GATACTC
* *
52319906 GATTATCATTTGATCAAAATTACCCTTGTTGGTGAAAGAAT-ATTATCGGTATTTG-CTCAATTG
63 AATTACCATTTGATC-AAATTACCCTTGTTGGTGAAA-AATGATTATCGGTATTTGTCTCAATTG
* *** * *
52319969 GTAATATTCTTGCATTTCTTTTTCTTGAGAAAAGAGTATTGTTGTGTACTTATTAATAGTTGATT
126 GTAAGATTCTT-CATTT-TTTTT-AAAAGAAAAGAATATTGTTGTGTACTT-GTAATAGTTGATT
* * * *
52320034 TTGAGAAATATTTACTTGGTTGATAATATTTTTTAAAGATC
187 TGGAGAAATATTTACTTGATTGATAAGATTTATTAAAGATC
* *
52320075 ACTTATGGCATCAAAGAAGAGTCTTATAACAAAGAAACAAAAGA
1 ACTTATGGCATCAAAGAAGAGCCTTATAAAAAAGAAACAAAAGA
52320119 TAATTAAGTG
Statistics
Matches: 227, Mismatches: 39, Indels: 15
0.81 0.14 0.05
Matches are distributed among these distances:
226 11 0.05
227 34 0.15
228 34 0.15
229 37 0.16
230 8 0.04
231 22 0.10
232 78 0.34
233 3 0.01
ACGTcount: A:0.35, C:0.11, G:0.17, T:0.37
Consensus pattern (227 bp):
ACTTATGGCATCAAAGAAGAGCCTTATAAAAAAGAAACAAAAGAGCACTGAGTGCGATACTCAAT
TACCATTTGATCAAATTACCCTTGTTGGTGAAAAATGATTATCGGTATTTGTCTCAATTGGTAAG
ATTCTTCATTTTTTTTAAAAGAAAAGAATATTGTTGTGTACTTGTAATAGTTGATTTGGAGAAAT
ATTTACTTGATTGATAAGATTTATTAAAGATC
Found at i:52323203 original size:13 final size:13
Alignment explanation
Indices: 52323185--52323217 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
52323175 TTTCCTCACC
52323185 TCTGTTTCA-GTA
1 TCTGTTTCATGTA
52323197 TTCTGTTTCATGTA
1 -TCTGTTTCATGTA
52323211 TCTGTTT
1 TCTGTTT
52323218 GATGACGGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 16 0.84
14 3 0.16
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (13 bp):
TCTGTTTCATGTA
Found at i:52336827 original size:30 final size:31
Alignment explanation
Indices: 52336791--52336859 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
52336781 AATCAAAAAA
52336791 ATCTAAAACAAG-T-CAAAGAGTTATGATTAT
1 ATCTAAAACAAGTTACAAA-AGTTATGATTAT
** **
52336821 ATCTAAAATTAGTTACTTAAGTTATGATTAT
1 ATCTAAAACAAGTTACAAAAGTTATGATTAT
52336852 ATCTAAAA
1 ATCTAAAA
52336860 TTAGTTAGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
30 10 0.30
31 21 0.64
32 2 0.06
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (31 bp):
ATCTAAAACAAGTTACAAAAGTTATGATTAT
Found at i:52338346 original size:29 final size:29
Alignment explanation
Indices: 52338313--52338371 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
52338303 AAGTAAAAGC
52338313 AAAGTGTTAATATATATGGAGAGAGGGAG
1 AAAGTGTTAATATATATGGAGAGAGGGAG
52338342 AAAGTGTTAATATATATGGAGAGAGGGAG
1 AAAGTGTTAATATATATGGAGAGAGGGAG
52338371 A
1 A
52338372 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.00, G:0.34, T:0.24
Consensus pattern (29 bp):
AAAGTGTTAATATATATGGAGAGAGGGAG
Found at i:52353663 original size:205 final size:206
Alignment explanation
Indices: 52353152--52353733 Score: 832
Period size: 204 Copynumber: 2.8 Consensus size: 206
52353142 TAGGCTGCAG
* * *
52353152 CATAGCAGATC-CAACCTTCAGATGTTTATACTGAAGTAGATCCAAGATGGTTTGGTATCCTTGT
1 CATAGCAGATCTC-ACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGT
* * * *
52353216 GTTTACAAGGAACAAATTGAAGACATAGCTGATTTGGTTTTCACGTACTTACGTTGAAGCAAATC
65 GTTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATC
* * *
52353281 TAAGATGATTTGGCATCTCTGTATTGTCAGGGAACAAATCAAAGTCTTGCATCTCCATATTCGAC
130 TAAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATATTCGAC
52353346 AGAGAGCAGATA
195 AGAGAGCAGATA
* * * *
52353358 CATAACAGA--TCACGTTCAGATGTTTATACCGAAGAAGATCCAAGATGATTTGGCATCCTTGTA
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
* * * * * * * *
52353421 CTTACAAGGAGCGAATAAAAAACATAGCTGATTTGGCTTTCACGTGTTTACGATAAAGCAAATGT
66 TTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCT
* *
52353486 ATGATGATTTGGCATCTCTGTATTG-CTAGAGAACAAATCGAAGTCTGGCATCTCCA-CTTCGAC
131 AAGATGATTTGGCATCTCTGTATTGTC-AGAGAACAAATCGAAGTCTGGCATCTCCATATTCGAC
* *
52353549 GGGGAGCAGATA
195 AGAGAGCAGATA
* * *
52353561 CATTGCAGATCTCACCTTCAGATGATTATACTGAAGAAGATCCAAGATGATTTGGCATTCTTGTG
1 CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
* *
52353626 TTTACAAGGAACAAATCGAAGACGTAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCT
66 TTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCT
52353691 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
131 AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAG
52353734 AAGCAAATTT
Statistics
Matches: 327, Mismatches: 44, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
203 24 0.07
204 149 0.46
205 145 0.44
206 9 0.03
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Consensus pattern (206 bp):
CATAGCAGATCTCACCTTCAGATGTTTATACTGAAGAAGATCCAAGATGATTTGGCATCCTTGTG
TTTACAAGGAACAAATAGAAGACATAGCTGATTTGGCTTTCACGTGCTTACGATGAAGCAAATCT
AAGATGATTTGGCATCTCTGTATTGTCAGAGAACAAATCGAAGTCTGGCATCTCCATATTCGACA
GAGAGCAGATA
Found at i:52355384 original size:22 final size:21
Alignment explanation
Indices: 52355334--52355384 Score: 50
Period size: 20 Copynumber: 2.4 Consensus size: 21
52355324 TATTCATCAC
52355334 ATATTATATTTTACTATATTT
1 ATATTATATTTTACTATATTT
* * **
52355355 -CATGATATTTTTTTATATATT
1 ATATTATATTTTACTATAT-TT
52355376 ATATTATAT
1 ATATTATAT
52355385 ACATTATATT
Statistics
Matches: 22, Mismatches: 6, Indels: 3
0.71 0.19 0.10
Matches are distributed among these distances:
20 14 0.64
21 2 0.09
22 6 0.27
ACGTcount: A:0.33, C:0.04, G:0.02, T:0.61
Consensus pattern (21 bp):
ATATTATATTTTACTATATTT
Found at i:52355390 original size:14 final size:14
Alignment explanation
Indices: 52355368--52355399 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
52355358 GATATTTTTT
*
52355368 TATATATTATATTA
1 TATACATTATATTA
52355382 TATACATTATATTA
1 TATACATTATATTA
52355396 TATA
1 TATA
52355400 TTTTCATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (14 bp):
TATACATTATATTA
Found at i:52366722 original size:19 final size:19
Alignment explanation
Indices: 52366694--52366751 Score: 66
Period size: 19 Copynumber: 3.1 Consensus size: 19
52366684 GTGTTAACAT
52366694 TTTATT-ATTTTTTAAAAA
1 TTTATTAATTTTTTAAAAA
***
52366712 TTTATTAATTTTTTTTGAA
1 TTTATTAATTTTTTAAAAA
52366731 TTT-TTAAATTTTTTAAAAA
1 TTTATT-AATTTTTTAAAAA
52366750 TT
1 TT
52366752 AACTAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
TTTATTAATTTTTTAAAAA
Found at i:52367434 original size:3 final size:3
Alignment explanation
Indices: 52367426--52367483 Score: 107
Period size: 3 Copynumber: 19.3 Consensus size: 3
52367416 TTTCCACACC
*
52367426 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT ATT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT
52367474 CTT CTT CTT C
1 CTT CTT CTT C
52367484 AAATTCTTTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.66
Consensus pattern (3 bp):
CTT
Found at i:52373551 original size:2 final size:2
Alignment explanation
Indices: 52373540--52373576 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
52373530 AATATATATG
*
52373540 GA GA GG GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
52373577 TCACAATGGC
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:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52373913 original size:25 final size:25
Alignment explanation
Indices: 52373864--52373914 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52373854 AAATAGAAAA
* *
52373864 TATATATAAGTATAATTTCATCACT
1 TATATATAAATATAATTTCAGCACT
*
52373889 TATATATAAATATAATTTGAGCACT
1 TATATATAAATATAATTTCAGCACT
52373914 T
1 T
52373915 TGAAAAGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (25 bp):
TATATATAAATATAATTTCAGCACT
Found at i:52374532 original size:3 final size:3
Alignment explanation
Indices: 52374518--52374552 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
52374508 TAGCTATTCA
*
52374518 CTT CTA CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CT
52374553 CTTGGATGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.63
Consensus pattern (3 bp):
CTT
Found at i:52376024 original size:15 final size:15
Alignment explanation
Indices: 52376006--52376039 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
52375996 TAATGTGTGT
52376006 TTTGTCCAACAAAAG
1 TTTGTCCAACAAAAG
*
52376021 TTTGTCCAACTAAAG
1 TTTGTCCAACAAAAG
52376036 TTTG
1 TTTG
52376040 GTAATGTGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (15 bp):
TTTGTCCAACAAAAG
Found at i:52376242 original size:12 final size:12
Alignment explanation
Indices: 52376225--52376253 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
52376215 AAAGTTTATC
52376225 AAATCTTATGAT
1 AAATCTTATGAT
52376237 AAATCTTATGAT
1 AAATCTTATGAT
52376249 AAATC
1 AAATC
52376254 ATCCAAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (12 bp):
AAATCTTATGAT
Found at i:52383370 original size:55 final size:55
Alignment explanation
Indices: 52383263--52383399 Score: 141
Period size: 55 Copynumber: 2.5 Consensus size: 55
52383253 TGGTCGTGAG
* ** * * * *
52383263 CGAAACTGCCAAAACAACACGAGAGTGCGACACGCCCGTGCCTTGAAACTGTGG-
1 CGAAACTGTCAAATTAACACGGGCGTGCGACACCCCCGTGCCTAGAAACTGTGGT
* * *
52383317 CTGAAACTGTCAAATTAACACGGGCGTGCGACACCCCCGTGTCTAGCACCTGTGGT
1 C-GAAACTGTCAAATTAACACGGGCGTGCGACACCCCCGTGCCTAGAAACTGTGGT
* * *
52383373 CGAACCTGTTAAATTACCACGGGCGTG
1 CGAAACTGTCAAATTAACACGGGCGTG
52383400 GGCCTACATA
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
54 1 0.01
55 66 0.97
56 1 0.01
ACGTcount: A:0.27, C:0.29, G:0.26, T:0.18
Consensus pattern (55 bp):
CGAAACTGTCAAATTAACACGGGCGTGCGACACCCCCGTGCCTAGAAACTGTGGT
Found at i:52389845 original size:30 final size:30
Alignment explanation
Indices: 52389769--52389855 Score: 102
Period size: 30 Copynumber: 2.9 Consensus size: 30
52389759 ACGGTCATGA
* * *
52389769 CACACGAACGTGTGGTCTGCCTGTGTGCCT
1 CACACGGACGTGTGGTTTGCCCGTGTGCCT
*
52389799 TACACGGACGTGTGGTTTGCCCGTGTGCCT
1 CACACGGACGTGTGGTTTGCCCGTGTGCCT
* * * *
52389829 CATACGGGCGTGTGGTTTACCCATGTG
1 CACACGGACGTGTGGTTTGCCCGTGTG
52389856 GAAGTGCCTA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.13, C:0.26, G:0.32, T:0.29
Consensus pattern (30 bp):
CACACGGACGTGTGGTTTGCCCGTGTGCCT
Found at i:52393827 original size:6 final size:6
Alignment explanation
Indices: 52393800--52393869 Score: 54
Period size: 6 Copynumber: 11.7 Consensus size: 6
52393790 TAATTTAGCC
* * * * *
52393800 ATTTTT ATTTCT ATTATA ATTTTT A-TTTT ATTTTT AGTTTA ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
*
52393847 ATTTTCT AATTTTT -CTTTT ATTT
1 ATTTT-T -ATTTTT ATTTTT ATTT
52393870 ACTTTTGTCA
Statistics
Matches: 48, Mismatches: 12, Indels: 8
0.71 0.18 0.12
Matches are distributed among these distances:
5 9 0.19
6 32 0.67
7 2 0.04
8 5 0.10
ACGTcount: A:0.21, C:0.04, G:0.01, T:0.73
Consensus pattern (6 bp):
ATTTTT
Found at i:52393828 original size:23 final size:23
Alignment explanation
Indices: 52393802--52393851 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
52393792 ATTTAGCCAT
52393802 TTTTATTTCTA-TTATAATTTTTA
1 TTTTATTTCTAGTT-TAATTTTTA
*
52393825 TTTTATTTTTAGTTTAATTTTTA
1 TTTTATTTCTAGTTTAATTTTTA
52393848 TTTT
1 TTTT
52393852 CTAATTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 23 0.92
24 2 0.08
ACGTcount: A:0.22, C:0.02, G:0.02, T:0.74
Consensus pattern (23 bp):
TTTTATTTCTAGTTTAATTTTTA
Found at i:52399687 original size:70 final size:70
Alignment explanation
Indices: 52399607--52399749 Score: 277
Period size: 70 Copynumber: 2.0 Consensus size: 70
52399597 GCGTAATATC
52399607 CTCCACTTTAGGGAGTGGGGAGAGATTTGGATAGTTTAAACATTGTATAAAAGACAGTATTCAAA
1 CTCCACTTTAGGGAGTGGGGAGAGATTTGGATAGTTTAAACATTGTATAAAAGACAGTATTCAAA
52399672 TCAAA
66 TCAAA
*
52399677 CTCCACTTTAGGGATTGGGGAGAGATTTGGATAGTTTAAACATTGTATAAAAGACAGTATTCAAA
1 CTCCACTTTAGGGAGTGGGGAGAGATTTGGATAGTTTAAACATTGTATAAAAGACAGTATTCAAA
52399742 TCAAA
66 TCAAA
52399747 CTC
1 CTC
52399750 ATCATAGCTC
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (70 bp):
CTCCACTTTAGGGAGTGGGGAGAGATTTGGATAGTTTAAACATTGTATAAAAGACAGTATTCAAA
TCAAA
Found at i:52402076 original size:22 final size:22
Alignment explanation
Indices: 52402051--52402095 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
52402041 TTTAATAAAG
52402051 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
52402073 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
52402095 A
1 A
52402096 CACTCCCCCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:52405851 original size:22 final size:22
Alignment explanation
Indices: 52405826--52405870 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
52405816 TTTAATAAAG
52405826 AAAATATCTACAAAATATTCCT
1 AAAATATCTACAAAATATTCCT
* *
52405848 AAAATATTTACAGAATATTCCT
1 AAAATATCTACAAAATATTCCT
52405870 A
1 A
52405871 CAATTACACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.02, T:0.33
Consensus pattern (22 bp):
AAAATATCTACAAAATATTCCT
Found at i:52408401 original size:6 final size:6
Alignment explanation
Indices: 52408390--52408414 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52408380 AATAATTTTA
52408390 TTGTGG TTGTGG TTGTGG TTGTGG T
1 TTGTGG TTGTGG TTGTGG TTGTGG T
52408415 CTGTTGCACG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (6 bp):
TTGTGG
Found at i:52411650 original size:2 final size:2
Alignment explanation
Indices: 52411643--52411672 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52411633 GTTCATACAC
52411643 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
52411673 CAAATGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:52412265 original size:15 final size:15
Alignment explanation
Indices: 52412245--52412276 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
52412235 TAGTAGAGTC
52412245 ATGATGGTGGTGATG
1 ATGATGGTGGTGATG
52412260 ATGATGGTGGTGATG
1 ATGATGGTGGTGATG
52412275 AT
1 AT
52412277 AAGAGCAAAT
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:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
ATGATGGTGGTGATG
Found at i:52413382 original size:81 final size:80
Alignment explanation
Indices: 52413297--52413447 Score: 198
Period size: 81 Copynumber: 1.9 Consensus size: 80
52413287 TGTCCCTCAC
* * *** *
52413297 AAAAATAA-TTTCAATTCAA-TCTTTTTATAAATAGTTAAATTATAAATTAATATTATAGTAAAA
1 AAAAAAAATTTTCAATTCAATTC-TCTTATAAATAAAGAAATCATAAATTAATA-TATAGTAAAA
52413360 TTACACTTCGACCTCCT
64 TTACACTTCGACCTCCT
* *
52413377 AAAAAAAATTTTCAATTCAGTTCTCTTATAAATAAAGAAATCATAATTTAATATATAGTAAAATT
1 AAAAAAAATTTTCAATTCAATTCTCTTATAAATAAAGAAATCATAAATTAATATATAGTAAAATT
52413442 ACACTT
66 ACACTT
52413448 TAGTCCCTTT
Statistics
Matches: 61, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
80 25 0.41
81 34 0.56
82 2 0.03
ACGTcount: A:0.46, C:0.11, G:0.04, T:0.38
Consensus pattern (80 bp):
AAAAAAAATTTTCAATTCAATTCTCTTATAAATAAAGAAATCATAAATTAATATATAGTAAAATT
ACACTTCGACCTCCT
Found at i:52413996 original size:17 final size:19
Alignment explanation
Indices: 52413967--52414012 Score: 53
Period size: 17 Copynumber: 2.6 Consensus size: 19
52413957 TATTATAAGC
*
52413967 AATATGAAA-AATAAATT-
1 AATATAAAATAATAAATTA
*
52413984 AATA-AAAATAATATATTA
1 AATATAAAATAATAAATTA
52414002 AATATAAAATA
1 AATATAAAATA
52414013 GTCAAATAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 3 0.12
17 11 0.46
18 4 0.17
19 6 0.25
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AATATAAAATAATAAATTA
Found at i:52415915 original size:23 final size:23
Alignment explanation
Indices: 52415885--52415932 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
52415875 CTCACTTGCC
52415885 TTAGTAAAGTAGATGAGTCATGT
1 TTAGTAAAGTAGATGAGTCATGT
52415908 TTAGTAAAGTAGATGAGTCATGT
1 TTAGTAAAGTAGATGAGTCATGT
52415931 TT
1 TT
52415933 CACATTCTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.33, C:0.04, G:0.25, T:0.38
Consensus pattern (23 bp):
TTAGTAAAGTAGATGAGTCATGT
Found at i:52416141 original size:14 final size:14
Alignment explanation
Indices: 52416106--52416133 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52416096 CTTTTAGGTT
52416106 TAGCTATATTCGCA
1 TAGCTATATTCGCA
52416120 TAGCTATATTCGCA
1 TAGCTATATTCGCA
52416134 CTGTTATACT
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:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (14 bp):
TAGCTATATTCGCA
Found at i:52418557 original size:10 final size:10
Alignment explanation
Indices: 52418542--52418590 Score: 71
Period size: 10 Copynumber: 4.9 Consensus size: 10
52418532 TATTTTAGCT
52418542 TTTATCTTTA
1 TTTATCTTTA
52418552 TTTATCTTTA
1 TTTATCTTTA
* *
52418562 ATTATATTTA
1 TTTATCTTTA
*
52418572 TTTATCTATA
1 TTTATCTTTA
52418582 TTTATCTTT
1 TTTATCTTT
52418591 TAGAATTTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:52420992 original size:23 final size:23
Alignment explanation
Indices: 52420904--52420992 Score: 123
Period size: 23 Copynumber: 4.0 Consensus size: 23
52420894 ACATGATCAG
52420904 TATACGACACAT-AAGTGCCTG-
1 TATACGACACATAAAGTGCCTGA
**
52420925 -ATACGACACA-CGAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
*
52420946 AATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
52420969 TATACGACACATAAAGTGCCTGA
1 TATACGACACATAAAGTGCCTGA
52420992 T
1 T
52420993 CGGCAAAGCC
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
20 18 0.30
22 10 0.17
23 32 0.53
ACGTcount: A:0.37, C:0.24, G:0.19, T:0.20
Consensus pattern (23 bp):
TATACGACACATAAAGTGCCTGA
Found at i:52421587 original size:27 final size:28
Alignment explanation
Indices: 52421545--52421601 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
52421535 TTTCATAACT
*
52421545 TTATATCATATTCATA-ATCCAAAA-CA
1 TTATATCATATTCATACAACCAAAATCA
52421571 TTATAATCAT-TTACATACAACCAAAATCA
1 TTAT-ATCATATT-CATACAACCAAAATCA
52421600 TT
1 TT
52421602 TAACTTAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
26 6 0.23
27 9 0.35
28 7 0.27
29 4 0.15
ACGTcount: A:0.46, C:0.19, G:0.00, T:0.35
Consensus pattern (28 bp):
TTATATCATATTCATACAACCAAAATCA
Found at i:52423058 original size:26 final size:28
Alignment explanation
Indices: 52423027--52423083 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
52423017 ATGCTTTCTG
*
52423027 TTTTCTTT-TCTCTA-TTCTTTTGTTT-C
1 TTTTCTTTAT-TCTATTTCTTTTATTTGC
52423053 TTTTCTTTATTCTATTTCTTTTATTTGC
1 TTTTCTTTATTCTATTTCTTTTATTTGC
52423081 TTT
1 TTT
52423084 AGTTACTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
26 12 0.44
27 11 0.41
28 4 0.15
ACGTcount: A:0.07, C:0.16, G:0.04, T:0.74
Consensus pattern (28 bp):
TTTTCTTTATTCTATTTCTTTTATTTGC
Found at i:52423108 original size:13 final size:13
Alignment explanation
Indices: 52423090--52423128 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
52423080 CTTTAGTTAC
52423090 TAATAATATATTA
1 TAATAATATATTA
*
52423103 TAATAATTTATTTA
1 TAATAATATA-TTA
52423117 TATATAATATAT
1 TA-ATAATATAT
52423129 AAATATCTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 9 0.41
14 6 0.27
15 7 0.32
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
TAATAATATATTA
Found at i:52428091 original size:14 final size:15
Alignment explanation
Indices: 52428067--52428095 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52428057 GAATGGCTTC
52428067 TGCTATTCTTTCTTT
1 TGCTATTCTTTCTTT
52428082 TGCT-TTCTTTCTTT
1 TGCTATTCTTTCTTT
52428096 ATTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.03, C:0.21, G:0.07, T:0.69
Consensus pattern (15 bp):
TGCTATTCTTTCTTT
Found at i:52428164 original size:12 final size:12
Alignment explanation
Indices: 52428135--52428190 Score: 58
Period size: 12 Copynumber: 4.5 Consensus size: 12
52428125 ATATATTAGT
* *
52428135 TAATAATGATAA
1 TAATAATAATTA
*
52428147 TGATAATAATTA
1 TAATAATAATTA
52428159 TAATAATAATTA
1 TAATAATAATTA
*
52428171 TAATAAATATATTT
1 TAAT-AATA-ATTA
52428185 TAATAA
1 TAATAA
52428191 CACATATTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 24 0.65
13 6 0.16
14 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (12 bp):
TAATAATAATTA
Found at i:52428803 original size:20 final size:19
Alignment explanation
Indices: 52428757--52428803 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
52428747 AACCCTTTTT
*
52428757 CCTAATTTCTCTTAATTAAG
1 CCTAA-TTCACTTAATTAAG
52428777 -CTAAATTCACTTAATTAAAG
1 CCT-AATTCACTTAATT-AAG
52428797 CCTAATT
1 CCTAATT
52428804 AAACAAACAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
19 12 0.52
20 9 0.39
21 2 0.09
ACGTcount: A:0.36, C:0.19, G:0.04, T:0.40
Consensus pattern (19 bp):
CCTAATTCACTTAATTAAG
Found at i:52432670 original size:17 final size:18
Alignment explanation
Indices: 52432648--52432681 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
52432638 TTTTAGGGAT
52432648 TAAATTGAA-GGCAAAAG
1 TAAATTGAAGGGCAAAAG
*
52432665 TAAATTTAAGGGCAAAA
1 TAAATTGAAGGGCAAAA
52432682 AGCGTGAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.21
Consensus pattern (18 bp):
TAAATTGAAGGGCAAAAG
Found at i:52437884 original size:47 final size:47
Alignment explanation
Indices: 52437775--52437885 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
52437765 CCGGGATAAG
*
52437775 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACATTATAGTA
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
* * *
52437822 CACAAAGTACTTCATCGGAACAAATCCGGAACTTTAACAGTAGTCG-A
1 CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTA-TAGTA
52437869 CACATAGTG-TCTCATCG
1 CACATAGTGCT-TCATCG
52437886 ACTCAATGTC
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
46 1 0.02
47 53 0.95
48 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.16, T:0.25
Consensus pattern (47 bp):
CACATAGTGCTTCATCGGAACAAATCCGGAACTTTAACAGTATAGTA
Found at i:52438536 original size:26 final size:26
Alignment explanation
Indices: 52438500--52438553 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
52438490 CTAAAAATTC
52438500 ACTAGTTTTCTTCATTTTAACCTCAT
1 ACTAGTTTTCTTCATTTTAACCTCAT
52438526 ACTAGTTTTCTTCATTTTAACCTCAT
1 ACTAGTTTTCTTCATTTTAACCTCAT
52438552 AC
1 AC
52438554 ATGTAGAACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.24, C:0.24, G:0.04, T:0.48
Consensus pattern (26 bp):
ACTAGTTTTCTTCATTTTAACCTCAT
Found at i:52441850 original size:36 final size:37
Alignment explanation
Indices: 52441803--52441874 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 37
52441793 TATACTTATT
*
52441803 TAGCTCAAGAGCAAGGGGATACAAA-TTGGATAGGGA
1 TAGCTCAAGAGCAAGGGGAAACAAAGTTGGATAGGGA
52441839 TAGCTCAAGAGCAAGGGGAAACAAAGTTGGATAGGG
1 TAGCTCAAGAGCAAGGGGAAACAAAGTTGGATAGGG
52441875 GAAAAGAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
36 24 0.71
37 10 0.29
ACGTcount: A:0.39, C:0.11, G:0.35, T:0.15
Consensus pattern (37 bp):
TAGCTCAAGAGCAAGGGGAAACAAAGTTGGATAGGGA
Found at i:52442117 original size:36 final size:36
Alignment explanation
Indices: 52442046--52442133 Score: 106
Period size: 36 Copynumber: 2.3 Consensus size: 36
52442036 GTAAAAGAAG
*
52442046 AAATCCGGACTTAAAGTCCGCAGGCTATATACTGGAAT
1 AAATCCGG--TTAAAGTCCGCAGGCTATATACTGGAAA
*
52442084 AAATCCGGTTAAAGTCCGCAGGCTA-AGTGCTGGAAA
1 AAATCCGGTTAAAGTCCGCAGGCTATA-TACTGGAAA
52442120 AATATCCGGGTTAA
1 AA-ATCC-GGTTAA
52442134 GGACCCGCAG
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
35 1 0.02
36 26 0.58
37 4 0.09
38 14 0.31
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (36 bp):
AAATCCGGTTAAAGTCCGCAGGCTATATACTGGAAA
Found at i:52443618 original size:18 final size:19
Alignment explanation
Indices: 52443597--52443636 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
52443587 AAGCATAAAT
*
52443597 ATCATTCATATCAAA-ACA
1 ATCATCCATATCAAATACA
*
52443615 ATCATCCATTTCAAATACA
1 ATCATCCATATCAAATACA
52443634 ATC
1 ATC
52443637 TTACTTTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (19 bp):
ATCATCCATATCAAATACA
Found at i:52447987 original size:18 final size:19
Alignment explanation
Indices: 52447936--52447989 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
52447926 AAAAAAATAT
*
52447936 TAAAATATAACAA-ATTCA
1 TAAAGTATAACAATATTCA
52447954 TAAAGTAATTAA-AATATTC-
1 TAAAGT-A-TAACAATATTCA
52447973 TAAAGTATAACAATATT
1 TAAAGTATAACAATATT
52447990 AAAGTTAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
17 3 0.10
18 12 0.39
19 9 0.29
20 7 0.23
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (19 bp):
TAAAGTATAACAATATTCA
Found at i:52448010 original size:18 final size:17
Alignment explanation
Indices: 52447942--52448010 Score: 52
Period size: 18 Copynumber: 3.8 Consensus size: 17
52447932 ATATTAAAAT
52447942 ATAACAAATTCATAAAGTA
1 ATAA-AAATT-ATAAAGTA
*
52447961 ATTAAAATATTCTAAAGT-
1 A-TAAAA-ATTATAAAGTA
*
52447979 ATAACAA-TATTAAAGTTA
1 ATAAAAATTA-TAAAG-TA
52447997 ATAAAAATTATAAA
1 ATAAAAATTATAAA
52448011 TTATTTACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 13
0.70 0.07 0.23
Matches are distributed among these distances:
15 1 0.03
16 6 0.15
17 5 0.12
18 11 0.28
19 11 0.28
20 6 0.15
ACGTcount: A:0.58, C:0.06, G:0.04, T:0.32
Consensus pattern (17 bp):
ATAAAAATTATAAAGTA
Done.