Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 73 of 103
Found at i:27392283 original size:82 final size:83
Alignment explanation
Indices: 27392046--27392283 Score: 262
Period size: 82 Copynumber: 2.8 Consensus size: 83
27392036 GGAAGAAAAA
* * * * *
27392046 GAAAAAAGAAGAAGGAATGAGGGAACGACGACTGAAAGAGAGGTCAGGCGGCAAGGGAGAAAGGC
1 GAAAAAAAAAGAAGGAATGAGGGAACGTCGACTGGAAGAGAGG-CCGGCGGCAAGGGAGAAAGCC
27392111 GAGCAAGAGAAAGGGAAAG
65 GAGCAAGAGAAAGGGAAAG
* * * * * * *
27392130 AAAAGAAAAAAGAAAAAGGAATGAGGGAACATCGGCTGGAAGAGAGGTCGGCGACAAGGCAAAAA
1 GAAA-AAAAAAG---AAGGAATGAGGGAACGTCGACTGGAAGAGAGGCCGGCGGCAAGGGAGAAA
** *
27392195 ATCGAGCAAGAGAGAGGG-AAG
62 GCCGAGCAAGAGAAAGGGAAAG
* * *
27392216 GAAAAAAAAAGAAGGAATAAGGGAATGTCGACTGGAAGAGAGGCCGACGGCAAGGGAGAAAGCCG
1 GAAAAAAAAAGAAGGAATGAGGGAACGTCGACTGGAAGAGAGGCCGGCGGCAAGGGAGAAAGCCG
27392281 AGC
66 AGC
27392284 CTGTTGTGGA
Statistics
Matches: 124, Mismatches: 26, Indels: 10
0.77 0.16 0.06
Matches are distributed among these distances:
82 46 0.37
84 3 0.02
85 13 0.10
86 6 0.05
87 28 0.23
88 28 0.23
ACGTcount: A:0.47, C:0.11, G:0.37, T:0.05
Consensus pattern (83 bp):
GAAAAAAAAAGAAGGAATGAGGGAACGTCGACTGGAAGAGAGGCCGGCGGCAAGGGAGAAAGCCG
AGCAAGAGAAAGGGAAAG
Found at i:27393303 original size:2 final size:2
Alignment explanation
Indices: 27393292--27393388 Score: 121
Period size: 2 Copynumber: 50.0 Consensus size: 2
27393282 TTACATTTTC
27393292 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
27393333 GT CT -T GT CT AT -T ANT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
27393373 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
27393389 GCTTGCTATA
Statistics
Matches: 86, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
1 4 0.05
2 81 0.94
3 1 0.01
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (2 bp):
AT
Found at i:27399682 original size:54 final size:54
Alignment explanation
Indices: 27399600--27399702 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
27399590 AGAACATTAG
*
27399600 AAATAAAGTTTTTAATTGGCATCAGAACAA-TCATAGTTT-AGATTTAAAACCTTA
1 AAATAAAGTTTTTAAGTGGCATCAGAACAACT-ATAGTTTGA-ATTTAAAACCTTA
*
27399654 AAATAAAGTTTTTAAGTGGTATCAGAACAACTATAGTTTGAATTTAAAA
1 AAATAAAGTTTTTAAGTGGCATCAGAACAACTATAGTTTGAATTTAAAA
27399703 TCCTAAGAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
54 43 0.96
55 2 0.04
ACGTcount: A:0.44, C:0.09, G:0.13, T:0.35
Consensus pattern (54 bp):
AAATAAAGTTTTTAAGTGGCATCAGAACAACTATAGTTTGAATTTAAAACCTTA
Found at i:27400325 original size:2 final size:2
Alignment explanation
Indices: 27400318--27400366 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
27400308 TGTAAAACTA
27400318 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27400360 AT AT AT A
1 AT AT AT A
27400367 ATGTATATGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27407417 original size:32 final size:33
Alignment explanation
Indices: 27407363--27407424 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
27407353 ATGTTTTCTA
27407363 TTGTTTGGATAAACTGTGG-AAAATATTTTTCG
1 TTGTTTGGATAAACTGTGGAAAAATATTTTTCG
* * * *
27407395 TTGTTTGGATCATCTTTTGAAAAATATTTT
1 TTGTTTGGATAAACTGTGGAAAAATATTTT
27407425 CCCCCATCAC
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 15 0.60
33 10 0.40
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (33 bp):
TTGTTTGGATAAACTGTGGAAAAATATTTTTCG
Found at i:27407778 original size:34 final size:34
Alignment explanation
Indices: 27407735--27407813 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
27407725 CAAAATAATA
* *
27407735 AAACCTACTAATAATATAATTAATCATTCTACAT
1 AAACTTACTAATAATATAATTAATCATCCTACAT
* *
27407769 AAACTTACTAGTAATATAATTAATCATCCTTCAT
1 AAACTTACTAATAATATAATTAATCATCCTACAT
*
27407803 AAGCCTTACTA
1 AA-ACTTACTA
27407814 TGGTTCCTAC
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
34 32 0.82
35 7 0.18
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (34 bp):
AAACTTACTAATAATATAATTAATCATCCTACAT
Found at i:27407872 original size:78 final size:78
Alignment explanation
Indices: 27407790--27407951 Score: 324
Period size: 78 Copynumber: 2.1 Consensus size: 78
27407780 TAATATAATT
27407790 AATCATCCTTCATAAGCCTTACTATGGTTCCTACATATATAATTAAGCATCCTATAAATATCCAA
1 AATCATCCTTCATAAGCCTTACTATGGTTCCTACATATATAATTAAGCATCCTATAAATATCCAA
27407855 CATATATCTTGCA
66 CATATATCTTGCA
27407868 AATCATCCTTCATAAGCCTTACTATGGTTCCTACATATATAATTAAGCATCCTATAAATATCCAA
1 AATCATCCTTCATAAGCCTTACTATGGTTCCTACATATATAATTAAGCATCCTATAAATATCCAA
27407933 CATATATCTTGCA
66 CATATATCTTGCA
27407946 AATCAT
1 AATCAT
27407952 AAAATCTAAT
Statistics
Matches: 84, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 84 1.00
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.35
Consensus pattern (78 bp):
AATCATCCTTCATAAGCCTTACTATGGTTCCTACATATATAATTAAGCATCCTATAAATATCCAA
CATATATCTTGCA
Found at i:27412638 original size:54 final size:52
Alignment explanation
Indices: 27412572--27412674 Score: 152
Period size: 54 Copynumber: 1.9 Consensus size: 52
27412562 AGTATACAAA
27412572 TTTAGATCACTAAATCAACTTGACTAAGAAAAAAAATAAAACACTTACATGCAT
1 TTTAGATCACTAAATCAACTTGACTAAG-AAAAAAA-AAAACACTTACATGCAT
* ** *
27412626 TTTAGATTACTAAATCAACTTGACTGTGAAAAAGAAAAACACTTACATG
1 TTTAGATCACTAAATCAACTTGACTAAGAAAAAAAAAAACACTTACATG
27412675 TATATGGGCG
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
52 14 0.31
53 6 0.13
54 25 0.56
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.27
Consensus pattern (52 bp):
TTTAGATCACTAAATCAACTTGACTAAGAAAAAAAAAAACACTTACATGCAT
Found at i:27412731 original size:39 final size:39
Alignment explanation
Indices: 27412688--27412764 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
27412678 ATGGGCGTCC
* *
27412688 TATTTAAGTTAATAAATAATCTCATGTAAGCTTTTTACT
1 TATTTAAATTAATAAATAATCTAATGTAAGCTTTTTACT
*
27412727 TATTTAAATTAATAAATAATCTAATGTAAGTTTTTTAC
1 TATTTAAATTAATAAATAATCTAATGTAAGCTTTTTAC
27412765 AGTAGATTGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (39 bp):
TATTTAAATTAATAAATAATCTAATGTAAGCTTTTTACT
Found at i:27412992 original size:14 final size:14
Alignment explanation
Indices: 27412973--27413026 Score: 63
Period size: 14 Copynumber: 3.6 Consensus size: 14
27412963 ACTAATGTTC
27412973 TAGATTTTTCTTAT
1 TAGATTTTTCTTAT
* *
27412987 TAGATTTTTTTTTCCT
1 TAGA-TTTTTCTT-AT
27413003 CTAGATTTTTCTTAT
1 -TAGATTTTTCTTAT
27413018 TAGATTTTT
1 TAGATTTTT
27413027 TTCCTCCCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
14 13 0.39
15 8 0.24
16 8 0.24
17 4 0.12
ACGTcount: A:0.19, C:0.09, G:0.07, T:0.65
Consensus pattern (14 bp):
TAGATTTTTCTTAT
Found at i:27413231 original size:92 final size:92
Alignment explanation
Indices: 27413128--27413336 Score: 278
Period size: 92 Copynumber: 2.3 Consensus size: 92
27413118 GTCTCATATC
* * * * *
27413128 ATTTTTTAGTGTTAAATGTAACTAATGT-AAATAAGTGCATATCAGCTAGCTAAAGATAAGATTT
1 ATTTTTAAGTGTTAAATGTAACTAATGTAAAAT-AGTGCAAATCAACTACCTAAAAATAAGATTT
* *
27413192 TGAGAGATATTAAGTTATTACATATTCT
65 AGAGAGAGATTAAGTTATTACATATTCT
* * *
27413220 ATTTTTAAGTGTTAAATGTAACTGATGTAAAATGGTGCAAATCAACTACCTAAAAATAGGATTTA
1 ATTTTTAAGTGTTAAATGTAACTAATGTAAAATAGTGCAAATCAACTACCTAAAAATAAGATTTA
*
27413285 GAGAGAGATTGAGTTATTACATATTCT
66 GAGAGAGATTAAGTTATTACATATTCT
* *
27413312 A-TTTTCAGTGTTAAATATAACTAAT
1 ATTTTTAAGTGTTAAATGTAACTAAT
27413337 AAAAAGTGAT
Statistics
Matches: 102, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
91 21 0.21
92 77 0.75
93 4 0.04
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (92 bp):
ATTTTTAAGTGTTAAATGTAACTAATGTAAAATAGTGCAAATCAACTACCTAAAAATAAGATTTA
GAGAGAGATTAAGTTATTACATATTCT
Found at i:27413382 original size:91 final size:92
Alignment explanation
Indices: 27413128--27413391 Score: 259
Period size: 92 Copynumber: 2.9 Consensus size: 92
27413118 GTCTCATATC
* * * * * *
27413128 ATTTTTTAGTGTTAAATGTAACTAATGTAAATAA-G-TGCATATCAGCTAGCTAAAGATAAGATT
1 ATTTTTAAGTGTTAAATATAACTAATG-AAA-AATGATACAAATCAACTAACTAAAGATAAGATT
* * *
27413191 TTGAGAGATATTAAGTTATTACATATTCT
64 TTAAGAGAGATTGAGTTATTACATATTCT
* * * * * * * *
27413220 ATTTTTAAGTGTTAAATGTAACTGATGTAAAATGGTGCAAATCAACTACCTAAAAATAGGA-TTT
1 ATTTTTAAGTGTTAAATATAACTAATGAAAAATGATACAAATCAACTAACTAAAGATAAGATTTT
27413284 AGAGAGAGATTGAGTTATTACATATTCT
66 A-AGAGAGATTGAGTTATTACATATTCT
* * * * *
27413312 A-TTTTCAGTGTTAAATATAACTAAT-AAAAAGTGATACAGATCAATTAATTAAAGATAAAATTT
1 ATTTTTAAGTGTTAAATATAACTAATGAAAAA-TGATACAAATCAACTAACTAAAGATAAGATTT
27413375 TAAGAGAGATTGAGTTA
65 TAAGAGAGATTGAGTTA
27413392 CTACCCATTC
Statistics
Matches: 143, Mismatches: 24, Indels: 11
0.80 0.13 0.06
Matches are distributed among these distances:
90 6 0.04
91 62 0.43
92 75 0.52
ACGTcount: A:0.41, C:0.07, G:0.16, T:0.36
Consensus pattern (92 bp):
ATTTTTAAGTGTTAAATATAACTAATGAAAAATGATACAAATCAACTAACTAAAGATAAGATTTT
AAGAGAGATTGAGTTATTACATATTCT
Found at i:27426587 original size:21 final size:22
Alignment explanation
Indices: 27426555--27426595 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
27426545 TTATATTTAA
*
27426555 TTTATTCAATTTGCTATTTCTC
1 TTTATTCAATTTGCAATTTCTC
27426577 TTTATTC-ATTTGCAATTTC
1 TTTATTCAATTTGCAATTTC
27426596 CACTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.59
Consensus pattern (22 bp):
TTTATTCAATTTGCAATTTCTC
Found at i:27426853 original size:11 final size:12
Alignment explanation
Indices: 27426823--27426855 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27426813 CCCCTTGATT
*
27426823 TATTTATTATCA
1 TATTTATTACCA
27426835 TATTTATTACCA
1 TATTTATTACCA
27426847 T-TTTATTAC
1 TATTTATTAC
27426856 ATGCTAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.30, C:0.12, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTTATTACCA
Found at i:27432044 original size:2 final size:2
Alignment explanation
Indices: 27432037--27432074 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
27432027 NNNNNNNNNN
27432037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27432075 GTACTGAGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:27435372 original size:25 final size:25
Alignment explanation
Indices: 27435336--27435389 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
27435326 CTTTTTAAAC
*
27435336 TAATGTTTATTTATT-CTATAAAGAT
1 TAATGTTAATTTATTGC-ATAAAGAT
*
27435361 TAATGTTAATTTATTGCATGAAGAT
1 TAATGTTAATTTATTGCATAAAGAT
27435386 TAAT
1 TAAT
27435390 ATTATTAATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
25 25 0.96
26 1 0.04
ACGTcount: A:0.37, C:0.04, G:0.11, T:0.48
Consensus pattern (25 bp):
TAATGTTAATTTATTGCATAAAGAT
Found at i:27441833 original size:55 final size:54
Alignment explanation
Indices: 27441742--27441927 Score: 210
Period size: 55 Copynumber: 3.4 Consensus size: 54
27441732 TGAAGAGTTA
* * * *
27441742 TTTTAGCGTGTCATGGCTATTACTGGCATGTTGTGGGTTAACTAGTTATTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTTGTGGGTTAACTAGTT-TTTGGGT
* * * * * *
27441797 TGTTAGCGTGTCACGGCTGTTCCTGGGGTGTGGTGGGTTAATTGAATTTATGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTTGTGGGTTAACT-AGTTTTTGGGT
* * *
27441852 TTTTGGCGTGTCATGGCTGTTCCTGGCGTGTTGTGGGTTAACTGGTTTTTTGGGT
1 TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTTGTGGGTTAACTAG-TTTTTGGGT
* *
27441907 TTTTAGCATGTCACGGATGTT
1 TTTTAGCGTGTCACGGCTGTT
27441928 GGTGTAACCA
Statistics
Matches: 106, Mismatches: 23, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
55 103 0.97
56 3 0.03
ACGTcount: A:0.12, C:0.12, G:0.33, T:0.42
Consensus pattern (54 bp):
TTTTAGCGTGTCACGGCTGTTCCTGGCGTGTTGTGGGTTAACTAGTTTTTGGGT
Found at i:27441989 original size:31 final size:31
Alignment explanation
Indices: 27441954--27442035 Score: 112
Period size: 31 Copynumber: 2.6 Consensus size: 31
27441944 AATTACAGTG
*
27441954 ATGCATGGCGTGTCACGACATTTGAC-TTGAT
1 ATGCATGGCGTGTCACAACATTTGACGTT-AT
* *
27441985 ATGCATGGCGTGTTACAACATTTTACGTTAT
1 ATGCATGGCGTGTCACAACATTTGACGTTAT
*
27442016 ATGCATGGCGTGTGACAACA
1 ATGCATGGCGTGTCACAACA
27442036 CGATTGACAA
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
31 44 0.96
32 2 0.04
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (31 bp):
ATGCATGGCGTGTCACAACATTTGACGTTAT
Found at i:27445127 original size:82 final size:82
Alignment explanation
Indices: 27444990--27445152 Score: 299
Period size: 82 Copynumber: 2.0 Consensus size: 82
27444980 CGAAGCATCC
*
27444990 CCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAGTCACTTC
1 CCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAATCACTTC
*
27445055 CCTCATTTTCCAAGCTT
66 CCTCATCTTCCAAGCTT
*
27445072 CCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAATCCCTTC
1 CCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAATCACTTC
27445137 CCTCATCTTCCAAGCT
66 CCTCATCTTCCAAGCT
27445153 CCTGGGCGGA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.22, C:0.39, G:0.18, T:0.21
Consensus pattern (82 bp):
CCCCCCCTTCACTCGGCAAGAGGTGCACTTCACTCCGGATCACGAAGCAACGGAGCAATCACTTC
CCTCATCTTCCAAGCTT
Found at i:27445310 original size:42 final size:42
Alignment explanation
Indices: 27445252--27445374 Score: 201
Period size: 42 Copynumber: 2.9 Consensus size: 42
27445242 ACGGAGGCAA
* * *
27445252 CAACAGCTTATGTGCACTCCCACTCACACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
*
27445294 CAACGGCTTATGTGCACTCTTACTCGCACATAGCCGGGTCAG
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
*
27445336 CAACGGCTTATGTGCACTCCTACTCGCACATAACCGGGT
1 CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGT
27445375 TCAAATCAAC
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.22
Consensus pattern (42 bp):
CAACGGCTTATGTGCACTCCTACTCGCACATAGCCGGGTCAG
Found at i:27448650 original size:31 final size:31
Alignment explanation
Indices: 27448598--27448905 Score: 271
Period size: 31 Copynumber: 9.9 Consensus size: 31
27448588 AATAAGGAAT
* *
27448598 AAATG-TGAGACACACCATGCATAACAAATA
1 AAATGTTGTGACACGCCATGCATAACAAATA
* *
27448628 AAATGTTGTGACACGCCGTGCATATCAAATA
1 AAATGTTGTGACACGCCATGCATAACAAATA
* * *
27448659 AAATATTGTAACACGCCATTCATAACAAGA-A
1 AAATGTTGTGACACGCCATGCATAACAA-ATA
*** *
27448690 AAATGAAATGACACGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAATA
*
27448721 AAATATTGTGACACGCCATGCATAACAAGATA
1 AAATGTTGTGACACGCCATGCATAACAA-ATA
* * * * **
27448753 AACT-TGGTGACACGCCAAGGATAACAAGCA
1 AAATGTTGTGACACGCCATGCATAACAAATA
* * * *
27448783 AAATGTTCTAACATGCCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATAACAAATA
* * * *
27448814 AAAGGTTATGACACGCCATGCATATAACAAGTT
1 AAATGTTGTGACACGCCATGC--ATAACAAATA
* * *
27448847 AAACGTTGTGACATGCCATGCATAACAATTA
1 AAATGTTGTGACACGCCATGCATAACAAATA
* * *
27448878 AATTGTTCTGACTCGCCATGCATAACAA
1 AAATGTTGTGACACGCCATGCATAACAA
27448906 GTTCTGGTAT
Statistics
Matches: 221, Mismatches: 50, Indels: 13
0.78 0.18 0.05
Matches are distributed among these distances:
30 9 0.04
31 179 0.81
32 6 0.03
33 27 0.12
ACGTcount: A:0.42, C:0.20, G:0.16, T:0.22
Consensus pattern (31 bp):
AAATGTTGTGACACGCCATGCATAACAAATA
Found at i:27448766 original size:93 final size:92
Alignment explanation
Indices: 27448606--27448907 Score: 327
Period size: 93 Copynumber: 3.2 Consensus size: 92
27448596 ATAAATGTGA
* * * * * *
27448606 GACACACCATGCATAACAAATAAAATGTTGTGACACGCCGTGCATATCAA-ATAAAATATTGTAA
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGAT-AAA-CTTGTGA
* ***
27448670 CACGCCATTCATAACAAGAAAAATGAAAT
64 CACGCCATGCATAACAAGAAAAATGTTCT
*
27448699 GACACGCCATGCATAACAAGTAAAATATTGTGACACGCCATGCATAACAAGATAAACTTGGTGAC
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAACTT-GTGAC
* * *
27448764 ACGCCAAGGATAACAAGCAAAATGTTCT
65 ACGCCATGCATAACAAGAAAAATGTTCT
* * * * *
27448792 AACATGCCATGCATAACAAGTAAAAGGTTATGACACGCCATGCATATAACAAGTTAAACGTTGTG
1 GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGC--ATAACAAGATAAAC-TTGTG
* ** *
27448857 ACATGCCATGCATAACAATTAAATTGTTCT
63 ACACGCCATGCATAACAAGAAAAATGTTCT
*
27448887 GACTCGCCATGCATAACAAGT
1 GACACGCCATGCATAACAAGT
27448908 TCTGGTATGT
Statistics
Matches: 175, Mismatches: 29, Indels: 8
0.83 0.14 0.04
Matches are distributed among these distances:
92 2 0.01
93 111 0.63
94 2 0.01
95 58 0.33
96 2 0.01
ACGTcount: A:0.41, C:0.21, G:0.16, T:0.22
Consensus pattern (92 bp):
GACACGCCATGCATAACAAGTAAAATGTTGTGACACGCCATGCATAACAAGATAAACTTGTGACA
CGCCATGCATAACAAGAAAAATGTTCT
Found at i:27449518 original size:19 final size:21
Alignment explanation
Indices: 27449472--27449513 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
27449462 TCTTGGTATC
27449472 AAATTAATTGTGTATAGGCAAAA
1 AAATTAATTGTGTAT--GCAAAA
27449495 AAATTAATTGTGTAT-CAAA
1 AAATTAATTGTGTATGCAAA
27449514 TAATTGGACA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.21
23 15 0.79
ACGTcount: A:0.48, C:0.05, G:0.14, T:0.33
Consensus pattern (21 bp):
AAATTAATTGTGTATGCAAAA
Found at i:27449579 original size:14 final size:15
Alignment explanation
Indices: 27449560--27449620 Score: 63
Period size: 14 Copynumber: 4.1 Consensus size: 15
27449550 TATATATTTT
*
27449560 TACAATGAAT-TGTA
1 TACAATAAATGTGTA
27449574 TACAATAAATTGTGTA
1 TACAATAAA-TGTGTA
*
27449590 TACAAAAAATGTGTA
1 TACAATAAATGTGTA
* *
27449605 TAAAATGAAT-TGTA
1 TACAATAAATGTGTA
27449619 TA
1 TA
27449621 AAAAAATTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
14 14 0.35
15 14 0.35
16 12 0.30
ACGTcount: A:0.48, C:0.05, G:0.13, T:0.34
Consensus pattern (15 bp):
TACAATAAATGTGTA
Found at i:27449591 original size:16 final size:16
Alignment explanation
Indices: 27449570--27449617 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
27449560 TACAATGAAT
27449570 TGTATACAATAAATTG
1 TGTATACAATAAATTG
*
27449586 TGTATACAA-AAAATG
1 TGTATACAATAAATTG
* *
27449601 TGTATAAAATGAATTG
1 TGTATACAATAAATTG
27449617 T
1 T
27449618 ATAAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
15 13 0.48
16 14 0.52
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (16 bp):
TGTATACAATAAATTG
Found at i:27449614 original size:45 final size:45
Alignment explanation
Indices: 27449563--27449652 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
27449553 ATATTTTTAC
* *
27449563 AATGAATTGTATACAATAAA-TTGTGTATAC-AAAAAATGTGTATAA
1 AATGAATTGTATA-AAAAAATTTATGTATACAAAAAAAT-TGTATAA
27449608 AATGAATTGTATAAAAAAATTTATGTATACTAAAAAAATTGTATA
1 AATGAATTGTATAAAAAAATTTATGTATAC-AAAAAAATTGTATA
27449653 GACAAAGGCC
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
44 5 0.12
45 22 0.55
46 6 0.15
47 7 0.17
ACGTcount: A:0.51, C:0.03, G:0.11, T:0.34
Consensus pattern (45 bp):
AATGAATTGTATAAAAAAATTTATGTATACAAAAAAATTGTATAA
Found at i:27449621 original size:14 final size:15
Alignment explanation
Indices: 27449570--27449627 Score: 59
Period size: 14 Copynumber: 3.9 Consensus size: 15
27449560 TACAATGAAT
*
27449570 TGTATACAATAAATTG
1 TGTATAAAATAAA-TG
27449586 TGTATACAAA-AAATG
1 TGTATA-AAATAAATG
*
27449601 TGTATAAAATGAAT-
1 TGTATAAAATAAATG
27449615 TGTATAAAA-AAAT
1 TGTATAAAATAAAT
27449628 TTATGTATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
13 3 0.08
14 12 0.32
15 11 0.30
16 9 0.24
17 2 0.05
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (15 bp):
TGTATAAAATAAATG
Found at i:27451139 original size:31 final size:31
Alignment explanation
Indices: 27451101--27451430 Score: 220
Period size: 31 Copynumber: 10.6 Consensus size: 31
27451091 CCATAAATAG
*
27451101 TAAAATGTTGTGACACG-CAGTGCATACCAAC
1 TAAAATGTTGTGACACGCCA-TGCATAACAAC
* * * *
27451132 TAAAATGTTGTCACACGTCATGCAAAACAAG
1 TAAAATGTTGTGACACGCCATGCATAACAAC
* * *
27451163 TAAAATATCGTGACACGCCATGCATAACAAGA
1 TAAAATGTTGTGACACGCCATGCATAACAA-C
* * * * ** *
27451195 TAAACT-TGGTGACACGCCAAGGATAATGAG
1 TAAAATGTTGTGACACGCCATGCATAACAAC
* * * *
27451225 GAAAATATTGTGACACACCATGCATAACAAGA
1 TAAAATGTTGTGACACGCCATGCATAACAA-C
* * * * * *
27451257 TAAACT-TGGTGACACGCCAAGGATAACGAG
1 TAAAATGTTGTGACACGCCATGCATAACAAC
* * * *
27451287 GAAAATGTTGTGACACACCATGCAAAACAAT
1 TAAAATGTTGTGACACGCCATGCATAACAAC
*
27451318 TAAAATGTTGTGACACGCCA-ACGATAACAAGC
1 TAAAATGTTGTGACACGCCATGC-ATAACAA-C
* * * *
27451350 -AAAATGTTTCTGACACGCTATGCATATCAAAA
1 TAAAATG-TTGTGACACGCCATGCATAAC-AAC
* * * *
27451382 TCAAACGTTGTGACACGCCATGAATAACAAG
1 TAAAATGTTGTGACACGCCATGCATAACAAC
27451413 TAAAATGTTGTGACACGC
1 TAAAATGTTGTGACACGC
27451431 TAAAGCTGAC
Statistics
Matches: 226, Mismatches: 62, Indels: 22
0.73 0.20 0.07
Matches are distributed among these distances:
30 9 0.04
31 167 0.74
32 43 0.19
33 7 0.03
ACGTcount: A:0.40, C:0.20, G:0.19, T:0.21
Consensus pattern (31 bp):
TAAAATGTTGTGACACGCCATGCATAACAAC
Found at i:27451210 original size:62 final size:62
Alignment explanation
Indices: 27451157--27451430 Score: 266
Period size: 62 Copynumber: 4.4 Consensus size: 62
27451147 CGTCATGCAA
* * *
27451157 AACAAGTAAAATATCGTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGGAT
1 AACAAGGAAAATATTGTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGCAT
** * *
27451219 AATGAGGAAAATATTGTGACACACCATGCATAACAAGATAAACTTGGTGACACGCCAAGGAT
1 AACAAGGAAAATATTGTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGCAT
* * * * * * *
27451281 AACGAGGAAAATGTTGTGACACACCATGCAAAACAA-TTAAAATGTTGTGACACGCCAA-CGAT
1 AACAAGGAAAATATTGTGACACGCCATGCATAACAAGATAAACT-TGGTGACACGCCAAGC-AT
* * * * * * * *
27451343 AACAAGCAAAATGTTTCTGACACGCTATGCATATCAAAATCAAACGTT-GTGACACGCCATGAAT
1 AACAAGGAAAAT-ATTGTGACACGCCATGCATAACAAGAT-AAAC-TTGGTGACACGCCAAGCAT
* *
27451407 AACAAGTAAAATGTTGTGACACGC
1 AACAAGGAAAATATTGTGACACGC
27451431 TAAAGCTGAC
Statistics
Matches: 178, Mismatches: 27, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
61 5 0.03
62 115 0.65
63 28 0.16
64 25 0.14
65 4 0.02
66 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (62 bp):
AACAAGGAAAATATTGTGACACGCCATGCATAACAAGATAAACTTGGTGACACGCCAAGCAT
Found at i:27453593 original size:31 final size:30
Alignment explanation
Indices: 27453555--27453756 Score: 190
Period size: 31 Copynumber: 6.5 Consensus size: 30
27453545 AATAAGGAAT
27453555 AAATGTTGTGACACGCCATGCATTGCAA-TCA
1 AAATGTTGTGACACGCCATGCATT-CAAGT-A
* * *
27453586 AAATGTTGTGACATGTCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCAT-TCAAGTA
* * *
27453617 AAATGTTGTGACACGCCATGCCTAACAAGTT
1 AAATGTTGTGACACGCCATGCAT-TCAAGTA
** *
27453648 AAACATTGTGACACGCCATGCATATCAAGTT
1 AAATGTTGTGACACGCCATGCAT-TCAAGTA
* *
27453679 AAACGTTATGACACGCCATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCAT-TCAAGTA
* * *
27453710 AAATGTTGTCACATGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCAT-TCAAGTA
* *
27453741 AAATGCTGTCACACGC
1 AAATGTTGTGACACGC
27453757 TAATAACTAA
Statistics
Matches: 148, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
31 147 0.99
32 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (30 bp):
AAATGTTGTGACACGCCATGCATTCAAGTA
Found at i:27453631 original size:62 final size:60
Alignment explanation
Indices: 27453555--27453756 Score: 217
Period size: 62 Copynumber: 3.3 Consensus size: 60
27453545 AATAAGGAAT
*
27453555 AAATGTTGTGACACGCCATGCATTGCAA-TCAAAATGTTGTGACATGTCATGCATAACAAGTA
1 AAATGTTGTGACACGCCATGCATT-CAAGT-AAAATGTTGTGACATG-CATGCATATCAAGTA
* * * ** * *
27453617 AAATGTTGTGACACGCCATGCCTAACAAGTTAAACATTGTGACACGCCATGCATATCAAGTT
1 AAATGTTGTGACACGCCATGCAT-TCAAGTAAAATGTTGTGACATG-CATGCATATCAAGTA
* * *
27453679 AAACGTTATGACACGCCATGCATATCAAGTAAAATGTTGTCACATGCTATGCATATCAAGTA
1 AAATGTTGTGACACGCCATGCAT-TCAAGTAAAATGTTGTGACATGC-ATGCATATCAAGTA
* *
27453741 AAATGCTGTCACACGC
1 AAATGTTGTGACACGC
27453757 TAATAACTAA
Statistics
Matches: 114, Mismatches: 23, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
61 1 0.01
62 112 0.98
63 1 0.01
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (60 bp):
AAATGTTGTGACACGCCATGCATTCAAGTAAAATGTTGTGACATGCATGCATATCAAGTA
Found at i:27453739 original size:93 final size:93
Alignment explanation
Indices: 27453560--27453739 Score: 229
Period size: 93 Copynumber: 1.9 Consensus size: 93
27453550 GGAATAAATG
* * * *
27453560 TTGTGACACGCCATGCATTGCAATCAAAATGTTGTGACATGTCATGCATAACAAGTAAAATGTTG
1 TTGTGACACGCCATGCATTGCAATCAAAACGTTATGACACGCCATGCATAACAAGTAAAATGTTG
* *
27453625 TGACACGCCATGCCTAACAAGTTAAACA
66 TCACACGCCATGCATAACAAGTTAAACA
* *
27453653 TTGTGACACGCCATGCATAT-CAAGT-TAAACGTTATGACACGCCATGCATATCAAGTAAAATGT
1 TTGTGACACGCCATGCAT-TGCAA-TCAAAACGTTATGACACGCCATGCATAACAAGTAAAATGT
* * *
27453716 TGTCACATGCTATGCATATCAAGT
64 TGTCACACGCCATGCATAACAAGT
27453740 AAAATGCTGT
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
93 72 0.97
94 2 0.03
ACGTcount: A:0.34, C:0.21, G:0.18, T:0.27
Consensus pattern (93 bp):
TTGTGACACGCCATGCATTGCAATCAAAACGTTATGACACGCCATGCATAACAAGTAAAATGTTG
TCACACGCCATGCATAACAAGTTAAACA
Found at i:27454403 original size:47 final size:46
Alignment explanation
Indices: 27454330--27454629 Score: 293
Period size: 47 Copynumber: 6.4 Consensus size: 46
27454320 CTAAACATGA
* *
27454330 CCATGGCGTGTCACCAACT-TTGAACTCTAGCATGTCACAGATTTCCT
1 CCATGGCGTGTCACCAACTCTT-AACTCT-GCGTGTCACAGATTCCCT
* **
27454377 CCATGGCGTGTCACCAACTCTTAACTCTGACGTCTCACAGATTCAAT
1 CCATGGCGTGTCACCAACTCTTAACTCTG-CGTGTCACAGATTCCCT
* * * * * *
27454424 CCATGGCATCTCACCAACCCTGAA-TGTTGGCATGTCACAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACT-CT-GCGTGTCACAGATTCCCT
* *
27454471 CCATGCCGTGTCACCAACTCTTAA-TCTGGCGTGTCATAGATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCT-GCGTGTCACAGATTCCCT
* * * * *
27454517 CCATGGCGTCTTACCAACTCTGAACGCTGTCGTGTCACACATTCCCAT
1 CCATGGCGTGTCACCAACTCTTAACTCTG-CGTGTCACAGATTCCC-T
* * *
27454565 -CATAGCGTGTCACCAACTCTTAACTCTAGCGTCTCACAAATTCCCT
1 CCATGGCGTGTCACCAACTCTTAACTCT-GCGTGTCACAGATTCCCT
*
27454611 CCATGGCGTCTCACCAACT
1 CCATGGCGTGTCACCAACT
27454630 TTGAGCGGTG
Statistics
Matches: 206, Mismatches: 38, Indels: 18
0.79 0.15 0.07
Matches are distributed among these distances:
46 42 0.20
47 159 0.77
48 5 0.02
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.28
Consensus pattern (46 bp):
CCATGGCGTGTCACCAACTCTTAACTCTGCGTGTCACAGATTCCCT
Found at i:27454457 original size:94 final size:94
Alignment explanation
Indices: 27454330--27454628 Score: 361
Period size: 94 Copynumber: 3.2 Consensus size: 94
27454320 CTAAACATGA
* ** * * *
27454330 CCATGGCGTGTCACCAACTTTGAACTCTAGCATGTCACAGATTTCCTCCATGGCGTGTCACCAAC
1 CCATGGCGTCTCACCAACCCTGAACGCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACCAAC
**
27454395 TCTTAACTCTGACGTCTCACAGATTCAAT
66 TCTTAACTCTGACGTCTCACAGATTCCCT
* * * *
27454424 CCATGGCATCTCACCAACCCTGAATGTTGGCATGTCACAGATTCCCTCCATGCCGTGTCACCAAC
1 CCATGGCGTCTCACCAACCCTGAACGCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACCAAC
* * *
27454489 TCTTAA-TCTGGCGTGTCATAGATTCCCT
66 TCTTAACTCTGACGTCTCACAGATTCCCT
* * * * * *
27454517 CCATGGCGTCTTACCAACTCTGAACGCTGTCGTGTCACACATTCCCAT-CATAGCGTGTCACCAA
1 CCATGGCGTCTCACCAACCCTGAACGCTGGCATGTCACAGATTCCC-TCCATGGCGTGTCACCAA
*
27454581 CTCTTAACTCT-AGCGTCTCACAAATTCCCT
65 CTCTTAACTCTGA-CGTCTCACAGATTCCCT
27454611 CCATGGCGTCTCACCAAC
1 CCATGGCGTCTCACCAAC
27454629 TTTGAGCGGT
Statistics
Matches: 172, Mismatches: 30, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
93 76 0.44
94 96 0.56
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (94 bp):
CCATGGCGTCTCACCAACCCTGAACGCTGGCATGTCACAGATTCCCTCCATGGCGTGTCACCAAC
TCTTAACTCTGACGTCTCACAGATTCCCT
Found at i:27454677 original size:94 final size:93
Alignment explanation
Indices: 27454330--27454687 Score: 335
Period size: 94 Copynumber: 3.8 Consensus size: 93
27454320 CTAAACATGA
* * * * * * ** *
27454330 CCATGGCGTGTCACCAACTTTGAACTCTAG-CATGTCACAGATTTCCTCCATGGCGTGTCACCAA
1 CCATGGCGTCTCACCAACTCTGAACGCT-GCCGTGTCACACATTCCCAACATGACGTGTCACCAA
**
27454394 CTCTTAACTCTGACGTCTCACAGATTCAAT
65 CTCTTAACTCTG-CGTCTCACAGATTCCCT
* * * * * * * ** *
27454424 CCATGGCATCTCACCAACCCTGAATGTTGGCATGTCACAGATTCCCTCCATGCCGTGTCACCAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAACATGACGTGTCACCAAC
* *
27454489 TCTTAA-TCTGGCGTGTCATAGATTCCCT
66 TCTTAACTCT-GCGTCTCACAGATTCCCT
* * *
27454517 CCATGGCGTCTTACCAACTCTGAACGCTGTCGTGTCACACATTCCCATCAT-AGCGTGTCACCAA
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAACATGA-CGTGTCACCAA
*
27454581 CTCTTAACTCTAGCGTCTCACAAATTCCCT
65 CTCTTAACTCT-GCGTCTCACAGATTCCCT
* * * * * *
27454611 CCATGGCGTCTCACCAACTTTGAGCGGTGCCGTATCACACATTCCCAACATGACGTTTCACGAAC
1 CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAACATGACGTGTCACCAAC
* *
27454676 TCTAAACCCTGC
66 TCTTAACTCTGC
27454688 CCTGCGACAG
Statistics
Matches: 220, Mismatches: 39, Indels: 11
0.81 0.14 0.04
Matches are distributed among these distances:
93 78 0.35
94 141 0.64
95 1 0.00
ACGTcount: A:0.23, C:0.34, G:0.16, T:0.27
Consensus pattern (93 bp):
CCATGGCGTCTCACCAACTCTGAACGCTGCCGTGTCACACATTCCCAACATGACGTGTCACCAAC
TCTTAACTCTGCGTCTCACAGATTCCCT
Found at i:27456775 original size:15 final size:15
Alignment explanation
Indices: 27456757--27456824 Score: 50
Period size: 15 Copynumber: 4.3 Consensus size: 15
27456747 TTAATTTATT
27456757 TTTAAATATTAATAA
1 TTTAAATATTAATAA
27456772 TTTATAATTTATTTAA-AA
1 TTTA-AA--TA-TTAATAA
27456790 TATTCAAAT-TTAATAA
1 T-TT-AAATATTAATAA
* *
27456806 TTTAAATAGTAATAT
1 TTTAAATATTAATAA
27456821 TTTA
1 TTTA
27456825 TTTTTAATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
14 4 0.09
15 19 0.44
16 5 0.12
17 1 0.02
18 5 0.12
19 8 0.19
20 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (15 bp):
TTTAAATATTAATAA
Found at i:27456775 original size:26 final size:25
Alignment explanation
Indices: 27456745--27456824 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 25
27456735 GATTATTTAC
*
27456745 TTTTAATTTATTTTTAAATATTAATAA
1 TTTTAATTTA-TTTAAAATATTAA-AA
*
27456772 TTTATAATTTATTTAAAATATTCAAA
1 TTT-TAATTTATTTAAAATATTAAAA
* * *
27456798 -TTTAA-TAATTT-AAATAGTAATA
1 TTTTAATTTATTTAAAATATTAAAA
27456820 TTTTA
1 TTTTA
27456825 TTTTTAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
22 8 0.18
23 9 0.20
24 3 0.07
25 2 0.04
26 2 0.04
27 14 0.31
28 7 0.16
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (25 bp):
TTTTAATTTATTTAAAATATTAAAA
Found at i:27456805 original size:27 final size:28
Alignment explanation
Indices: 27456748--27456809 Score: 83
Period size: 27 Copynumber: 2.2 Consensus size: 28
27456738 TATTTACTTT
*
27456748 TAATTTATTTTTAAATATTAATAATTTA
1 TAATTTATTTTAAAATATTAATAATTTA
*
27456776 TAATTTA-TTTAAAATATTCA-AATTTAA
1 TAATTTATTTTAAAATATTAATAATTT-A
27456803 TAATTTA
1 TAATTTA
27456810 AATAGTAATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
26 5 0.16
27 19 0.61
28 7 0.23
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATTTATTTTAAAATATTAATAATTTA
Found at i:27456916 original size:154 final size:151
Alignment explanation
Indices: 27456652--27457217 Score: 385
Period size: 160 Copynumber: 3.7 Consensus size: 151
27456642 TTATTTTATT
* * * *
27456652 TTTAAATATTAATATTTTATTTACAATTTAATCATTAATATTATAAAATACTACTATTTTATTTA
1 TTTAAATAGTAATATTTTATTTACAATTTAATCATTAACATTATAAAATACTAATATTTAATTTA
*
27456717 TAATTTAAATGATATTATGATTATTTACTTTTAATTTATTTTTAAATATTAATAATTTATAATTT
66 TAATTT--ATGATATTATGATTATTTA-TTTTAATTTATTTTTAAAAATTAATAATTTATAATTT
27456782 ATTTAAAATATTCAAATTTAATAA
128 ATTTAAAATATTCAAATTTAATAA
** *
27456806 TTTAAATAGTAATATTTTATTTTTAATTTAATCA-TAACATTATAAAATATTAATATTTAATTTA
1 TTTAAATAGTAATATTTTATTTACAATTTAATCATTAACATTATAAAATACTAATATTTAATTTA
* *** * ** *
27456870 TAA-TT-TGTTATTATGATTACAAATTTT-TTTTATTTTTTTAAATTAAAAATTTATAATTTATT
66 TAATTTATGATATTATGATTATTTATTTTAATTTATTTTTAAAAATTAATAATTTATAATTTATT
*
27456932 TATAAT-TT--AATCATTAAT--
131 TAAAATATTCAAAT--TTAATAA
* * * ** * * ** * ** *
27456950 TTTAAAATATTAATATTTTATTTATAATTTAAAT-GTTATTATGATTATTTATTTTTATTTTATT
1 TTT-AAATAGTAATATTTTATTTACAATTT-AATCATTAACATTATAAAATACTAATATTTAATT
* * * * *
27457014 T-T-ATTTTTCA-A--AT-ATTAATGATTTATAATTTA--TTTAAAACATTAATAATTGATAATT
64 TATAATTTATGATATTATGATTATTTATTT-TAATTTATTTTTAAAA-ATTAATAATTTATAATT
* *
27457071 TAAATATTAATATTTCATTTATAATTTAATTATTAACA
127 T--AT-TTAA-A-AT-ATTCA-AATTT-A--A-T-A-A
* * *
27457109 TTATAAAATACTAATATTTTATTTATAATTTAATCATTAACATTATAAAATACTAATATTTTATT
1 TT-T-AAATAGTAATATTTTATTTACAATTTAATCATTAACATTATAAAATACTAATATTTAATT
* *
27457174 TATAATTTAAATGTTATTATGATTATTTATTTTTATTTTATTTT
64 TATAATTT--ATGATATTATGATTATTTA-TTTTAATTTATTTT
27457218 NNNNNNNNNN
Statistics
Matches: 313, Mismatches: 58, Indels: 66
0.72 0.13 0.15
Matches are distributed among these distances:
142 13 0.04
143 19 0.06
144 11 0.04
145 30 0.10
146 34 0.11
147 36 0.12
148 5 0.02
149 14 0.04
150 2 0.01
151 2 0.01
152 3 0.01
153 32 0.10
154 32 0.10
155 1 0.00
159 5 0.02
160 48 0.15
161 1 0.00
162 4 0.01
164 1 0.00
165 1 0.00
167 2 0.01
168 12 0.04
169 3 0.01
170 2 0.01
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (151 bp):
TTTAAATAGTAATATTTTATTTACAATTTAATCATTAACATTATAAAATACTAATATTTAATTTA
TAATTTATGATATTATGATTATTTATTTTAATTTATTTTTAAAAATTAATAATTTATAATTTATT
TAAAATATTCAAATTTAATAA
Found at i:27457005 original size:105 final size:102
Alignment explanation
Indices: 27456821--27457010 Score: 258
Period size: 105 Copynumber: 1.8 Consensus size: 102
27456811 ATAGTAATAT
*
27456821 TTTATTTTTAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGA
1 TTTATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGA
27456886 TTACAAATTTTTTTTATTTTTTTAAATTAAAAATTTATAA
66 TT---AATTTTTTTTATTTTTTTAAATTAAAAATTTATAA
* * *
27456926 TTTATTTATAATTTAATCATTA-ATTTTAAAATATTAATATTTTATTTATAATTTAAATGTTATT
1 TTTATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAA-TT---TGTTATT
27456990 ATGATT-ATTTATTTTTATTTT
62 ATGATTAATTT-TTTTTATTTT
27457011 ATTTTATTTT
Statistics
Matches: 76, Mismatches: 4, Indels: 10
0.84 0.04 0.11
Matches are distributed among these distances:
104 31 0.41
105 32 0.42
108 13 0.17
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (102 bp):
TTTATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGA
TTAATTTTTTTTATTTTTTTAAATTAAAAATTTATAA
Found at i:27457038 original size:105 final size:105
Alignment explanation
Indices: 27456824--27457045 Score: 245
Period size: 105 Copynumber: 2.1 Consensus size: 105
27456814 GTAATATTTT
*
27456824 ATTTTTAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGATTA
1 ATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGATTA
* * * *
27456889 CAAATTTTTTTTATTTTTTTAAATTAAAAATTTATAATTT
66 CAAATTTTTATTATTATTTTAAATTAAAAATATATAATTG
* * *
27456929 ATTTATAATTTAATCATTA-ATTTTAAAATATTAATATTTTATTTATAATTTAAATGTTATTATG
1 ATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAA-TT---TGTTATTATG
*** ** **
27456993 ATTATTTATTTTTATT-TTATTTTATTTTTCAAATAT-TAA-TG
62 ATTACAAATTTTTATTATTATTTTAAATTAAAAATATATAATTG
27457034 ATTTATAATTTA
1 ATTTATAATTTA
27457046 TTTAAAACAT
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
104 27 0.28
105 32 0.33
106 3 0.03
107 14 0.14
108 22 0.22
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.57
Consensus pattern (105 bp):
ATTTATAATTTAATCATAACATTATAAAATATTAATATTTAATTTATAATTTGTTATTATGATTA
CAAATTTTTATTATTATTTTAAATTAAAAATATATAATTG
Found at i:27457118 original size:42 final size:42
Alignment explanation
Indices: 27457072--27457183 Score: 197
Period size: 42 Copynumber: 2.7 Consensus size: 42
27457062 TTGATAATTT
* * *
27457072 AAATATTAATATTTCATTTATAATTTAATTATTAACATTATA
1 AAATACTAATATTTTATTTATAATTTAATCATTAACATTATA
27457114 AAATACTAATATTTTATTTATAATTTAATCATTAACATTATA
1 AAATACTAATATTTTATTTATAATTTAATCATTAACATTATA
27457156 AAATACTAATATTTTATTTATAATTTAA
1 AAATACTAATATTTTATTTATAATTTAA
27457184 ATGTTATTAT
Statistics
Matches: 67, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 67 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (42 bp):
AAATACTAATATTTTATTTATAATTTAATCATTAACATTATA
Found at i:27457127 original size:118 final size:115
Alignment explanation
Indices: 27456892--27457132 Score: 252
Period size: 118 Copynumber: 2.1 Consensus size: 115
27456882 ATGATTACAA
** * * * *
27456892 ATTTT-TTTTATTTTTTTAAATTAAAAATTTATAATTTATTTATAATTTAATCATTAATTTTAAA
1 ATTTTATTTTATTTTTCAAAATTAAAAATTTATAATTTATTTAAAAATTAATAATTAAATTTAAA
* * ** * ** * **
27456956 ATATTAATATTTTATTTATAATTTAAATGTTATTATGATTATTTATTTTT
66 ATATTAATATTTCATTTATAATTTAAATATTAACATGATAAAATACTAAT
**
27457006 ATTTTATTTTATTTTTCAAATATTAATGATTTATAATTTATTTAAAACATTAATAATTGATAATT
1 ATTTTATTTTATTTTTCAAA-ATTAAAAATTTATAATTTATTTAAAA-ATTAATAATT-A-AATT
* *
27457071 T-AAATATTAATATTTCATTTATAATTTAATTATTAACATTATAAAATACTAAT
62 TAAAATATTAATATTTCATTTATAATTTAAATATTAACATGATAAAATACTAAT
27457124 ATTTTATTT
1 ATTTTATTT
27457133 ATAATTTAAT
Statistics
Matches: 102, Mismatches: 20, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
114 5 0.05
115 12 0.12
116 23 0.23
117 8 0.08
118 50 0.49
119 4 0.04
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.56
Consensus pattern (115 bp):
ATTTTATTTTATTTTTCAAAATTAAAAATTTATAATTTATTTAAAAATTAATAATTAAATTTAAA
ATATTAATATTTCATTTATAATTTAAATATTAACATGATAAAATACTAAT
Found at i:27457134 original size:22 final size:22
Alignment explanation
Indices: 27457109--27457178 Score: 67
Period size: 22 Copynumber: 3.3 Consensus size: 22
27457099 ATTATTAACA
27457109 TTATAAAATACTAATATTTTAT
1 TTATAAAATACTAATATTTTAT
* * *
27457131 TTAT--AAT-TTAATCA-TTAACA
1 TTATAAAATACTAAT-ATTTTA-T
27457151 TTATAAAATACTAATATTTTAT
1 TTATAAAATACTAATATTTTAT
27457173 TTATAA
1 TTATAA
27457179 TTTAAATGTT
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
19 7 0.19
20 8 0.22
22 14 0.39
23 7 0.19
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (22 bp):
TTATAAAATACTAATATTTTAT
Found at i:27460268 original size:2 final size:2
Alignment explanation
Indices: 27460261--27460312 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
27460251 TCCTTTACAC
27460261 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27460303 AT AT AT AT AT
1 AT AT AT AT AT
27460313 CTTCATTGTA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:27478467 original size:3 final size:3
Alignment explanation
Indices: 27478459--27478487 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
27478449 TTTTAAGCTT
27478459 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
27478488 GCATAAGATT
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:27483098 original size:14 final size:14
Alignment explanation
Indices: 27483079--27483116 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
27483069 CAAGTAGCTT
27483079 ATTTATAAAAA-AGA
1 ATTTATAAAAATA-A
27483093 ATTTATAAAAATAA
1 ATTTATAAAAATAA
27483107 ATTTATAAAA
1 ATTTATAAAA
27483117 TAGATTTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 22 0.96
15 1 0.04
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
ATTTATAAAAATAA
Found at i:27483116 original size:13 final size:13
Alignment explanation
Indices: 27483079--27483124 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
27483069 CAAGTAGCTT
*
27483079 ATTTATAAAAAAGA
1 ATTTATAAAATA-A
27483093 ATTTATAAAAATAA
1 ATTTAT-AAAATAA
*
27483107 ATTTATAAAATAG
1 ATTTATAAAATAA
27483120 ATTTA
1 ATTTA
27483125 GAGCTTGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
13 11 0.38
14 13 0.45
15 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (13 bp):
ATTTATAAAATAA
Found at i:27483975 original size:27 final size:27
Alignment explanation
Indices: 27483920--27483976 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
27483910 ATAAACACTT
*
27483920 AATTTTAAAATTATTATTTTTAATAAA
1 AATTTTAAAATTATTATTTTAAATAAA
*
27483947 AATTTTATAATTAATT-TTTTAAATTAAA
1 AATTTTAAAATT-ATTATTTTAAA-TAAA
27483975 AA
1 AA
27483977 AATCAAATCA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 17 0.65
28 9 0.35
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTTTAAAATTATTATTTTAAATAAA
Found at i:27495281 original size:33 final size:33
Alignment explanation
Indices: 27495239--27495327 Score: 115
Period size: 37 Copynumber: 2.6 Consensus size: 33
27495229 TATCATTAGC
*
27495239 TAAGTAGCATGAATACCTTTTCTTTTTTGAAAA
1 TAAGTAGCATGAACACCTTTTCTTTTTTGAAAA
*
27495272 TAAGTAGCATGAACACCTTTTTTTTTTTTTTTGAAAA
1 TAAGTAGCATGAACACC----TTTTCTTTTTTGAAAA
*
27495309 TAAGCAGCATGAACACCTT
1 TAAGTAGCATGAACACCTT
27495328 AACAAAAAGG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
33 18 0.37
37 31 0.63
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (33 bp):
TAAGTAGCATGAACACCTTTTCTTTTTTGAAAA
Found at i:27495311 original size:37 final size:37
Alignment explanation
Indices: 27495256--27495327 Score: 126
Period size: 37 Copynumber: 1.9 Consensus size: 37
27495246 CATGAATACC
*
27495256 TTTTCTTTTTTGAAAATAAGTAGCATGAACACCTTTT
1 TTTTCTTTTTTGAAAATAAGCAGCATGAACACCTTTT
*
27495293 TTTTTTTTTTTGAAAATAAGCAGCATGAACACCTT
1 TTTTCTTTTTTGAAAATAAGCAGCATGAACACCTT
27495328 AACAAAAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.44
Consensus pattern (37 bp):
TTTTCTTTTTTGAAAATAAGCAGCATGAACACCTTTT
Found at i:27497963 original size:42 final size:41
Alignment explanation
Indices: 27497886--27497973 Score: 99
Period size: 42 Copynumber: 2.1 Consensus size: 41
27497876 ATTGATAGTC
*
27497886 ATCTCAGACTATGAAAGAGAAGATAGTTTTAGAAATTC-AGTA
1 ATCTCAGACTATGAAAGAGAACATA-TTTTAGAAATTCGA-TA
* *
27497928 ATCTCATACTATGAAAGAGAACAT-TTCTCTGGAAATTCGATA
1 ATCTCAGACTATGAAAGAGAACATATT-T-TAGAAATTCGATA
27497970 ATCT
1 ATCT
27497974 GCACTGGTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
40 2 0.05
41 1 0.03
42 36 0.90
43 1 0.03
ACGTcount: A:0.40, C:0.14, G:0.16, T:0.31
Consensus pattern (41 bp):
ATCTCAGACTATGAAAGAGAACATATTTTAGAAATTCGATA
Found at i:27499050 original size:3 final size:3
Alignment explanation
Indices: 27499044--27499071 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
27499034 TCATTATCCC
27499044 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
27499072 CAAAACATTT
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:27504088 original size:102 final size:103
Alignment explanation
Indices: 27503923--27504138 Score: 353
Period size: 102 Copynumber: 2.1 Consensus size: 103
27503913 GTTATAGATC
* * * *
27503923 ATATTTATTGAGTAAAATTTTATCATTATACTTTTTTAATTTAATTAAAAAATAATATAAAATCC
1 ATATTTAATGACTAAAATGTTATCATTATACTCTTTTAATTTAATTAAAAAATAATATAAAATCC
*
27503988 TATCCATTTAAAATAAGTAGTAAATTTTATTTATTGAA
66 TATCCATTTAAAATAAGTACTAAATTTTATTTATTGAA
* *
27504026 ATATTTAATGACTAAAATGTTATCATTATAC-CTTTTAATTTAATTCAAAAATAATATAAAATCG
1 ATATTTAATGACTAAAATGTTATCATTATACTCTTTTAATTTAATTAAAAAATAATATAAAATCC
27504090 TATCCATTTAAAATAAGTACTAAATTTTATTTATTGAA
66 TATCCATTTAAAATAAGTACTAAATTTTATTTATTGAA
*
27504128 ATATTCAATGA
1 ATATTTAATGA
27504139 TATTTTATTA
Statistics
Matches: 105, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
102 77 0.73
103 28 0.27
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (103 bp):
ATATTTAATGACTAAAATGTTATCATTATACTCTTTTAATTTAATTAAAAAATAATATAAAATCC
TATCCATTTAAAATAAGTACTAAATTTTATTTATTGAA
Found at i:27515458 original size:120 final size:118
Alignment explanation
Indices: 27515294--27515531 Score: 458
Period size: 120 Copynumber: 2.0 Consensus size: 118
27515284 ATTTTTATAT
27515294 TTTTATTTTACTAAATAAGTTTTTTATCATTAATAGTTGATTAATAATTATTAATAAAAATATCA
1 TTTTATTTTACTAAATAAGTTTTTTATCATTAATAGTTGATTAATAATTATTAATAAAAATATCA
27515359 TTTGTCATTTTATATCATATGACATTGACATGATATGTTGATATGTCATAATA
66 TTTGTCATTTTATATCATATGACATTGACATGATATGTTGATATGTCATAATA
27515412 NTTTTATTTTAACTAAATAAGTTTTTTATCATTAATAGTTGATTAATAATTATTAATAAAAATAT
1 -TTTTATTTT-ACTAAATAAGTTTTTTATCATTAATAGTTGATTAATAATTATTAATAAAAATAT
27515477 CATTTGTCATTTTATATCATATGACATTGACATGATATGTTGATATGTCATAATA
64 CATTTGTCATTTTATATCATATGACATTGACATGATATGTTGATATGTCATAATA
27515532 GATGATGATA
Statistics
Matches: 118, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
119 9 0.08
120 109 0.92
ACGTcount: A:0.37, C:0.07, G:0.08, T:0.47
Consensus pattern (118 bp):
TTTTATTTTACTAAATAAGTTTTTTATCATTAATAGTTGATTAATAATTATTAATAAAAATATCA
TTTGTCATTTTATATCATATGACATTGACATGATATGTTGATATGTCATAATA
Found at i:27518346 original size:21 final size:21
Alignment explanation
Indices: 27518307--27518354 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
27518297 ATTATTTATT
27518307 TTTAAAAATTACAAATTTAAA
1 TTTAAAAATTACAAATTTAAA
*
27518328 TTTAAAAATTA-ATATTTTAAA
1 TTTAAAAATTACA-AATTTAAA
27518349 -TTAAAA
1 TTTAAAA
27518355 TATAAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 7 0.28
21 18 0.72
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (21 bp):
TTTAAAAATTACAAATTTAAA
Found at i:27518395 original size:16 final size:16
Alignment explanation
Indices: 27518376--27518406 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27518366 TAATATTTTT
*
27518376 ATATTTTAATTATAAC
1 ATATTTAAATTATAAC
27518392 ATATTTAAATTATAA
1 ATATTTAAATTATAA
27518407 ATAAAAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTTAAATTATAAC
Found at i:27518438 original size:15 final size:15
Alignment explanation
Indices: 27518420--27518450 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
27518410 AAAAATTAGT
27518420 ATTTTTAAAATATTA
1 ATTTTTAAAATATTA
*
27518435 ATTTTTAAATTATTA
1 ATTTTTAAAATATTA
27518450 A
1 A
27518451 GTGAAATTTA
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTTAAAATATTA
Found at i:27518624 original size:11 final size:11
Alignment explanation
Indices: 27518597--27518638 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
27518587 ATAATAATAT
*
27518597 TTAAATTTAAA
1 TTAAAATTAAA
27518608 TT-AAATTAAA
1 TTAAAATTAAA
*
27518618 TTAAAATAAAA
1 TTAAAATTAAA
*
27518629 TAAAAATTAA
1 TTAAAATTAA
27518639 GTTTTAATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TTAAAATTAAA
Found at i:27518811 original size:23 final size:23
Alignment explanation
Indices: 27518754--27518827 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
27518744 TAAATTACAA
* * *
27518754 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
27518776 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
27518799 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
27518823 A-AAAT
1 ATAAAT
27518828 AAAATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:27518824 original size:22 final size:21
Alignment explanation
Indices: 27518752--27518828 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
27518742 ATTAAATTAC
*
27518752 AAATAAAATATTAATACTTAA
1 AAATAAAATATTAATATTTAA
* *
27518773 ATAATCAACTATTAATATTTAA
1 A-AATAAAATATTAATATTTAA
27518795 AAATATAAATTATTAATATTTAA
1 AAATA-AAA-TATTAATATTTAA
27518818 AAGATAAAATA
1 AA-ATAAAATA
27518829 AAATAAAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:27546643 original size:102 final size:102
Alignment explanation
Indices: 27546521--27546714 Score: 325
Period size: 102 Copynumber: 1.9 Consensus size: 102
27546511 ACAGCCAAAA
* * * *
27546521 AGAAGAAGAACAACAGGTCAAATCTAAAACACACATGCTGCTAACCAAATTTCGATAATAAGCTG
1 AGAAGAAGAACAACAAGTCAAATCTAAAACACACATGCTGCTAACCAAATATCAATAATAAACTG
27546586 CTTACCCAGATATGTCTATAAGAAGAATGGTTGGCTC
66 CTTACCCAGATATGTCTATAAGAAGAATGGTTGGCTC
* *
27546623 AGAAGAAGAAGAAGAAGTCAAATCTAAAACACACATGCTGCTAACCAAATATCAATAATAAACTG
1 AGAAGAAGAACAACAAGTCAAATCTAAAACACACATGCTGCTAACCAAATATCAATAATAAACTG
*
27546688 CTTACCCAGCTATGTCTATAAGAAGAA
66 CTTACCCAGATATGTCTATAAGAAGAA
27546715 GGGTGGGTTC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
102 85 1.00
ACGTcount: A:0.44, C:0.19, G:0.16, T:0.21
Consensus pattern (102 bp):
AGAAGAAGAACAACAAGTCAAATCTAAAACACACATGCTGCTAACCAAATATCAATAATAAACTG
CTTACCCAGATATGTCTATAAGAAGAATGGTTGGCTC
Found at i:27548037 original size:2 final size:2
Alignment explanation
Indices: 27548030--27548055 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
27548020 TCTTTCTTTT
27548030 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
27548056 GGTGGGTGGG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:27559367 original size:15 final size:15
Alignment explanation
Indices: 27559349--27559466 Score: 66
Period size: 15 Copynumber: 7.9 Consensus size: 15
27559339 AAAATTTAAA
27559349 ATATTAATATTTTAT
1 ATATTAATATTTTAT
** *
27559364 ATA-TAAT-TTAAAC
1 ATATTAATATTTTAT
*
27559377 ATTATTAATA-TTAAT
1 A-TATTAATATTTTAT
* * *
27559392 ATGATTAAAATGTTAA
1 AT-ATTAATATTTTAT
*
27559408 ATATTAATATTTTAA
1 ATATTAATATTTTAT
*
27559423 ACTATTAATGTTTTAT
1 A-TATTAATATTTTAT
*
27559439 TTATTAA-ATTATTAAT
1 ATATTAATATT-TT-AT
27559455 ATATTAA-ATTTT
1 ATATTAATATTTT
27559467 TAATGAATAT
Statistics
Matches: 79, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
13 4 0.05
14 9 0.11
15 39 0.49
16 27 0.34
ACGTcount: A:0.44, C:0.02, G:0.03, T:0.52
Consensus pattern (15 bp):
ATATTAATATTTTAT
Found at i:27559468 original size:31 final size:31
Alignment explanation
Indices: 27559377--27559470 Score: 81
Period size: 31 Copynumber: 3.1 Consensus size: 31
27559367 TAATTTAAAC
* *
27559377 ATTATT-AA-TATTAATATGATTAAAATGTTA
1 ATTATTAAATTATTAATAT-ATTAAATTTTTA
*
27559407 AATATTAATATT-TTAA-ACTATT-AATGTTTTA
1 ATTATTAA-ATTATTAATA-TATTAAAT-TTTTA
*
27559438 TTTATTAAATTATTAATATATTAAATTTTTA
1 ATTATTAAATTATTAATATATTAAATTTTTA
27559469 AT
1 AT
27559471 GAATATAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 15
0.70 0.08 0.21
Matches are distributed among these distances:
30 10 0.20
31 29 0.58
32 10 0.20
33 1 0.02
ACGTcount: A:0.44, C:0.01, G:0.03, T:0.52
Consensus pattern (31 bp):
ATTATTAAATTATTAATATATTAAATTTTTA
Found at i:27559469 original size:16 final size:16
Alignment explanation
Indices: 27559387--27559470 Score: 61
Period size: 16 Copynumber: 5.3 Consensus size: 16
27559377 ATTATTAATA
* *
27559387 TTAATATGATTAAAATG
1 TTAATAT-ATTAAATTT
27559404 TTAA-ATATT-AATATT
1 TTAATATATTAAAT-TT
27559419 TTAA-ACTATT-AATGTT
1 TTAATA-TATTAAAT-TT
* *
27559435 TT-ATTTATTAAATTA
1 TTAATATATTAAATTT
27559450 TTAATATATTAAATTT
1 TTAATATATTAAATTT
27559466 TTAAT
1 TTAAT
27559471 GAATATAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 2 0.04
15 17 0.31
16 32 0.58
17 4 0.07
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (16 bp):
TTAATATATTAAATTT
Found at i:27559518 original size:23 final size:23
Alignment explanation
Indices: 27559479--27559542 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
27559469 ATGAATATAA
27559479 AAAT-AAAAT-TTATTAATATT-T
1 AAATAAAAATATTATTAAT-TTAT
* * *
27559500 TAATAATATTATTATTAATTTAT
1 AAATAAAAATATTATTAATTTAT
27559523 AAATAAAAATATTATTAATT
1 AAATAAAAATATTATTAATT
27559543 AAAATATTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 3 0.09
22 5 0.15
23 26 0.76
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
AAATAAAAATATTATTAATTTAT
Found at i:27559521 original size:20 final size:20
Alignment explanation
Indices: 27559488--27559551 Score: 51
Period size: 23 Copynumber: 3.1 Consensus size: 20
27559478 AAAATAAAAT
* *
27559488 TTATTAATATTTTAATAATA
1 TTATTATTAATTTAATAATA
*
27559508 TTATTATTAATTTATAAATAAAA
1 TTATTATTAA-TT-T-AATAATA
*
27559531 ATATTATTAA-TTAA-AATA
1 TTATTATTAATTTAATAATA
27559549 TTA
1 TTA
27559552 GTAATTAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 5 0.14
19 2 0.06
20 9 0.26
21 3 0.09
22 1 0.03
23 15 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTATTATTAATTTAATAATA
Found at i:27559599 original size:40 final size:41
Alignment explanation
Indices: 27559499--27559608 Score: 100
Period size: 40 Copynumber: 2.7 Consensus size: 41
27559489 TATTAATATT
*
27559499 TTAATAATATT-ATTATTAATTTATAAATAAAAATATTATTAA
1 TTAA-AATATTAATTATTAAATTAT-AATAAAAATATTATTAA
* * * *
27559541 TTAAAATATTAGTAATTAAATTAT-ATTAAAATATTGA-TAT
1 TTAAAATATTAATTATTAAATTATAATAAAAATATT-ATTAA
* *
27559581 TTAAATTATTAATTATTAATATTTTAAT
1 TTAAAATATTAATTATTAA-ATTATAAT
27559609 TAATTATAAA
Statistics
Matches: 55, Mismatches: 9, Indels: 8
0.76 0.12 0.11
Matches are distributed among these distances:
40 28 0.51
41 11 0.20
42 16 0.29
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (41 bp):
TTAAAATATTAATTATTAAATTATAATAAAAATATTATTAA
Found at i:27560019 original size:12 final size:12
Alignment explanation
Indices: 27560002--27560026 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
27559992 AGGAGGAGTG
27560002 AAAAAAAAAAGA
1 AAAAAAAAAAGA
27560014 AAAAAAAAAAGA
1 AAAAAAAAAAGA
27560026 A
1 A
27560027 TATGAGGGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAGA
Found at i:27560748 original size:20 final size:21
Alignment explanation
Indices: 27560709--27560749 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27560699 GGTGAATCCT
27560709 TTATTAAGCATCGAACATAAC
1 TTATTAAGCATCGAACATAAC
* *
27560730 TTATTTAGCAT-GTACATAAC
1 TTATTAAGCATCGAACATAAC
27560750 CTAATGTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.39, C:0.17, G:0.10, T:0.34
Consensus pattern (21 bp):
TTATTAAGCATCGAACATAAC
Found at i:27566131 original size:42 final size:42
Alignment explanation
Indices: 27566073--27566154 Score: 146
Period size: 42 Copynumber: 2.0 Consensus size: 42
27566063 TGGGCAGACA
27566073 AAAAATGAAGTTTGGCTTACAAATAAAAAACAAAAAGAAAGC
1 AAAAATGAAGTTTGGCTTACAAATAAAAAACAAAAAGAAAGC
* *
27566115 AAAAATGAAGTTTGGCTTACAAATGAAAAACAAGAAGAAA
1 AAAAATGAAGTTTGGCTTACAAATAAAAAACAAAAAGAAA
27566155 AAAGGGTTCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.59, C:0.09, G:0.16, T:0.17
Consensus pattern (42 bp):
AAAAATGAAGTTTGGCTTACAAATAAAAAACAAAAAGAAAGC
Found at i:27576984 original size:42 final size:42
Alignment explanation
Indices: 27576935--27577017 Score: 157
Period size: 42 Copynumber: 2.0 Consensus size: 42
27576925 AAAAATTATA
*
27576935 CACTATCACTGTATCAAATATCTATAACTATATAAAAAGGAG
1 CACTATCACTATATCAAATATCTATAACTATATAAAAAGGAG
27576977 CACTATCACTATATCAAATATCTATAACTATATAAAAAGGA
1 CACTATCACTATATCAAATATCTATAACTATATAAAAAGGA
27577018 AGCCTCATGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.47, C:0.17, G:0.07, T:0.29
Consensus pattern (42 bp):
CACTATCACTATATCAAATATCTATAACTATATAAAAAGGAG
Found at i:27577006 original size:19 final size:19
Alignment explanation
Indices: 27576946--27577009 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
27576936 ACTATCACTG
27576946 TATCAAATATCTATAACTA
1 TATCAAATATCTATAACTA
* * * *
27576965 TATAAAAAGGAGCACTATCACTA
1 TAT-CAAA-TA--TCTATAACTA
27576988 TATCAAATATCTATAACTA
1 TATCAAATATCTATAACTA
27577007 TAT
1 TAT
27577010 AAAAAGGAAG
Statistics
Matches: 33, Mismatches: 8, Indels: 8
0.67 0.16 0.16
Matches are distributed among these distances:
19 14 0.42
20 3 0.09
21 2 0.06
22 3 0.09
23 11 0.33
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (19 bp):
TATCAAATATCTATAACTA
Found at i:27578037 original size:25 final size:24
Alignment explanation
Indices: 27578008--27578078 Score: 85
Period size: 23 Copynumber: 3.0 Consensus size: 24
27577998 TAACTACTTA
*
27578008 ATCTTGATCATGAACTTTCTTTGAT
1 ATCTTGATCATGAACTTTCGTTG-T
*
27578033 ATCTTGATCACGAAC-TTCGTTGT
1 ATCTTGATCATGAACTTTCGTTGT
27578056 -TGCTTGATCATGAA-TTTCGTTGT
1 AT-CTTGATCATGAACTTTCGTTGT
27578079 CGTTTGATCT
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
22 1 0.02
23 20 0.49
24 6 0.15
25 14 0.34
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.45
Consensus pattern (24 bp):
ATCTTGATCATGAACTTTCGTTGT
Found at i:27578065 original size:23 final size:23
Alignment explanation
Indices: 27578035--27578087 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
27578025 TCTTTGATAT
*
27578035 CTTGATCACGAACTTCGTTGTTG
1 CTTGATCACGAACTTCGTTGTCG
* *
27578058 CTTGATCATGAATTTCGTTGTCG
1 CTTGATCACGAACTTCGTTGTCG
*
27578081 TTTGATC
1 CTTGATC
27578088 TTCACTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (23 bp):
CTTGATCACGAACTTCGTTGTCG
Found at i:27578897 original size:28 final size:28
Alignment explanation
Indices: 27578866--27578974 Score: 112
Period size: 28 Copynumber: 3.7 Consensus size: 28
27578856 TATGATCTTG
*
27578866 GAAGATGTATATTGCAATTAAACTATTT
1 GAAGAAGTATATTGCAATTAAACTATTT
*
27578894 GAAGAAGTATATTGCAA-TAAGGCTATAATTTT
1 GAAGAAGTATATTGCAATTAA-AC--T-A-TTT
*
27578926 GAAAGAAGTATATTGCAATAAAACTATTT
1 G-AAGAAGTATATTGCAATTAAACTATTT
* *
27578955 AAAGAAATATATTGCAATTA
1 GAAGAAGTATATTGCAATTA
27578975 GGATTACATT
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
27 3 0.04
28 34 0.51
29 3 0.04
30 2 0.03
31 2 0.03
32 4 0.06
33 17 0.25
34 2 0.03
ACGTcount: A:0.45, C:0.06, G:0.15, T:0.34
Consensus pattern (28 bp):
GAAGAAGTATATTGCAATTAAACTATTT
Found at i:27579865 original size:35 final size:35
Alignment explanation
Indices: 27579809--27579908 Score: 146
Period size: 35 Copynumber: 2.9 Consensus size: 35
27579799 TGTTGTACAG
* *
27579809 AGAACAACTTGAACAAGTGAAGTGCTACTTCACGC
1 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
* * *
27579844 AGAATAACTAGAACAAGTGAAGCGCTACTTTATGC
1 AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
*
27579879 AGAATAACTAGAACAAGTGAAGTACTACTT
1 AGAATAACTAGAACAAGTGAAGTGCTACTT
27579909 AAAGTAGAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.41, C:0.18, G:0.19, T:0.22
Consensus pattern (35 bp):
AGAATAACTAGAACAAGTGAAGTGCTACTTCACGC
Found at i:27579926 original size:35 final size:35
Alignment explanation
Indices: 27579809--27579931 Score: 138
Period size: 35 Copynumber: 3.5 Consensus size: 35
27579799 TGTTGTACAG
* * *
27579809 AGAACAACTTGAACAAGTGAAGTGCTACTTCACGC
1 AGAACAACTAGAACAAGTGAAGTGCTACTTAAAGC
* * * *
27579844 AGAATAACTAGAACAAGTGAAGCGCTACTTTATGC
1 AGAACAACTAGAACAAGTGAAGTGCTACTTAAAGC
* * *
27579879 AGAATAACTAGAACAAGTGAAGTACTACTTAAAGT
1 AGAACAACTAGAACAAGTGAAGTGCTACTTAAAGC
* *
27579914 AGAACAATTAGAATAAGT
1 AGAACAACTAGAACAAGT
27579932 AAAGCATTAC
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 75 1.00
ACGTcount: A:0.44, C:0.15, G:0.19, T:0.22
Consensus pattern (35 bp):
AGAACAACTAGAACAAGTGAAGTGCTACTTAAAGC
Found at i:27580305 original size:29 final size:29
Alignment explanation
Indices: 27580186--27580305 Score: 123
Period size: 29 Copynumber: 4.1 Consensus size: 29
27580176 CCTATTCATG
* * **
27580186 TACAGCTTATTCTCTTGTACCTATTCTTG
1 TACAACTTCTTCTCTTGTACCTATTCTCA
* * *
27580215 TACAGCTTCTTCTCTTGTACTTCTTCTCA
1 TACAACTTCTTCTCTTGTACCTATTCTCA
* * *
27580244 CACAACTTCTTCTCTTGTACATATTCTCG
1 TACAACTTCTTCTCTTGTACCTATTCTCA
* * *
27580273 TACAACTTTTTCTCTTGTACCTTTTCTTA
1 TACAACTTCTTCTCTTGTACCTATTCTCA
27580302 TACA
1 TACA
27580306 CTTATTTTCT
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.18, C:0.28, G:0.07, T:0.47
Consensus pattern (29 bp):
TACAACTTCTTCTCTTGTACCTATTCTCA
Found at i:27581076 original size:36 final size:35
Alignment explanation
Indices: 27580999--27581168 Score: 164
Period size: 36 Copynumber: 4.6 Consensus size: 35
27580989 AATTTAAAGT
27580999 GGTGCTCTTTATAATAGCACGTAATTTATTATCCTTGAAG
1 GGTGCTCTTTATAATAGCAC-----TTATTATCCTTGAAG
27581039 GGTGCTCTTTATAATAGCACTTATTGATCCTTGAAG
1 GGTGCTCTTTATAATAGCACTTATT-ATCCTTGAAG
* * * *
27581075 GGTGCTCTTCATAATAGTACAATTTATTATCC-TCAGTG
1 GGTGCTCTTTATAATAG--C-ACTTATTATCCTTGA-AG
*
27581113 GGTGCTCTTTATAATAGCACTTGTTGATCCTTGGAA-
1 GGTGCTCTTTATAATAGCACTTATT-ATCCTT-GAAG
*
27581149 GGTGCTCTTTAAAATAGCAC
1 GGTGCTCTTTATAATAGCAC
27581169 ACAATTTATT
Statistics
Matches: 112, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
35 10 0.09
36 50 0.45
37 3 0.03
38 23 0.21
39 6 0.05
40 20 0.18
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (35 bp):
GGTGCTCTTTATAATAGCACTTATTATCCTTGAAG
Found at i:27581122 original size:74 final size:74
Alignment explanation
Indices: 27580999--27581180 Score: 242
Period size: 74 Copynumber: 2.4 Consensus size: 74
27580989 AATTTAAAGT
*
27580999 GGTGCTCTTTATAATAGCACGTAATTTATTATCCTTGAAGGGTGCTCTTTATAATAGCACTTATT
1 GGTGCTCTTTATAATAGCAC--AATTTATTATCCTAGAAGGGTGCTCTTTATAATAGCACTTATT
27581064 GATCCTT-GAA
64 GATCCTTGGAA
* * * *
27581074 GGGTGCTCTTCATAATAGTACAATTTATTATCCTCAG-TGGGTGCTCTTTATAATAGCACTTGTT
1 -GGTGCTCTTTATAATAGCACAATTTATTATCCT-AGAAGGGTGCTCTTTATAATAGCACTTATT
27581138 GATCCTTGGAA
64 GATCCTTGGAA
*
27581149 GGTGCTCTTTAAAATAGCACACAATTTATTAT
1 GGTGCTCTTTATAATAG--CACAATTTATTAT
27581181 TATACTTCAA
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
74 60 0.64
75 4 0.04
76 30 0.32
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (74 bp):
GGTGCTCTTTATAATAGCACAATTTATTATCCTAGAAGGGTGCTCTTTATAATAGCACTTATTGA
TCCTTGGAA
Found at i:27582230 original size:13 final size:13
Alignment explanation
Indices: 27582212--27582236 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
27582202 TGTTACCAAC
27582212 CGGTTATGGAGAT
1 CGGTTATGGAGAT
27582225 CGGTTATGGAGA
1 CGGTTATGGAGA
27582237 CAAAAGAGAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.08, G:0.40, T:0.28
Consensus pattern (13 bp):
CGGTTATGGAGAT
Found at i:27582632 original size:34 final size:34
Alignment explanation
Indices: 27582579--27582682 Score: 106
Period size: 34 Copynumber: 3.0 Consensus size: 34
27582569 GTGGCTGCTT
27582579 ATTTTTGGAGGAAGAATAGAGCAGCTTAGCTACTG
1 ATTTTT-GAGGAAGAATAGAGCAGCTTAGCTACTG
* *
27582614 ATTTTTGAGGAA-ACATAGAGCAGCTTGGCTGCTG
1 ATTTTTGAGGAAGA-ATAGAGCAGCTTAGCTACTG
* * *
27582648 A-TTTTGAGG-TGGATATGAGCAGCTTTGGCTACTG
1 ATTTTTGAGGAAGAATA-GAGCAGC-TTAGCTACTG
27582682 A
1 A
27582683 AAATTTTTGG
Statistics
Matches: 60, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.05
33 16 0.27
34 35 0.58
35 6 0.10
ACGTcount: A:0.27, C:0.12, G:0.30, T:0.31
Consensus pattern (34 bp):
ATTTTTGAGGAAGAATAGAGCAGCTTAGCTACTG
Found at i:27582859 original size:5 final size:5
Alignment explanation
Indices: 27582851--27582890 Score: 57
Period size: 5 Copynumber: 8.4 Consensus size: 5
27582841 ACGGGAAAGG
*
27582851 AAGAA AAGAA AAGAA GAGAA AAGAA AAG-A AAGAA AA-AA AA
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA AA
27582891 AATATATATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
4 8 0.25
5 24 0.75
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:27582872 original size:15 final size:14
Alignment explanation
Indices: 27582846--27582890 Score: 65
Period size: 15 Copynumber: 3.2 Consensus size: 14
27582836 AAGGAACGGG
*
27582846 AAAGGAAGAAAAGA
1 AAAGAAAGAAAAGA
27582860 AAAGAAGAGAAAAGA
1 AAAGAA-AGAAAAGA
27582875 AAAGAAAGAAAA-A
1 AAAGAAAGAAAAGA
27582888 AAA
1 AAA
27582891 AATATATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 4 0.14
14 11 0.38
15 14 0.48
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAAGA
Found at i:27583040 original size:14 final size:14
Alignment explanation
Indices: 27583013--27583050 Score: 60
Period size: 14 Copynumber: 2.7 Consensus size: 14
27583003 AGAAAAGGNG
27583013 GAGAAAAGAAAAGAA
1 GAGAAAA-AAAAGAA
27583028 GAGAAAAAAAAGAA
1 GAGAAAAAAAAGAA
27583042 GA-AAAAAAA
1 GAGAAAAAAA
27583051 TAAATGGGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 7 0.30
14 9 0.39
15 7 0.30
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
GAGAAAAAAAAGAA
Found at i:27583041 original size:157 final size:156
Alignment explanation
Indices: 27582857--27583167 Score: 554
Period size: 156 Copynumber: 2.0 Consensus size: 156
27582847 AAGGAAGAAA
* *
27582857 AGAAAAGAAGAGAAAAGAAAAGAAAGAA-AAAAAAAATATATATGGGCATAGCTCAATAAGAAGA
1 AGAAAAGAAAAGAAAAGAAAAAAAAGAAGAAAAAAAATA-A-ATGGGCATAGCTCAATAAGAAGA
27582921 GAGTGGGCATGACCCAATAGGAAGAAATTGGAAGAGCCCATGGAAAGGGCCCAAT-TGCAATAAG
64 GAGTGGGCATGACCCAATAGGAAGAAATTGGAAGAGCCCATGGAAAGGGCCCAATGTGCAATAAG
27582985 AAAAGAAAAGTCCAAAAGAGAAAAGGNGG
129 AAAAGAAAAGTCCAAAAGAGAAAAGG-GG
*
27583014 AGAAAAGAAAAGAAGAGAAAAAAAAGAAGAAAAAAAATAAATGGGCATAGCTCAATAAGAAGAGA
1 AGAAAAGAAAAGAAAAGAAAAAAAAGAAGAAAAAAAATAAATGGGCATAGCTCAATAAGAAGAGA
27583079 GTGGGCATGACCCAATAGGAAGAAATTGGAAGAGCCCATGGAAAGGGCCCAATGTGCAATAAGAA
66 GTGGGCATGACCCAATAGGAAGAAATTGGAAGAGCCCATGGAAAGGGCCCAATGTGCAATAAGAA
27583144 AAGAAAAGTCCAAAAGAGAAAAGG
131 AAGAAAAGTCCAAAAGAGAAAAGG
27583168 AAGGTTGAGA
Statistics
Matches: 149, Mismatches: 3, Indels: 4
0.96 0.02 0.03
Matches are distributed among these distances:
156 78 0.52
157 61 0.41
158 10 0.07
ACGTcount: A:0.53, C:0.10, G:0.26, T:0.10
Consensus pattern (156 bp):
AGAAAAGAAAAGAAAAGAAAAAAAAGAAGAAAAAAAATAAATGGGCATAGCTCAATAAGAAGAGA
GTGGGCATGACCCAATAGGAAGAAATTGGAAGAGCCCATGGAAAGGGCCCAATGTGCAATAAGAA
AAGAAAAGTCCAAAAGAGAAAAGGGG
Found at i:27585282 original size:25 final size:25
Alignment explanation
Indices: 27585245--27585292 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
27585235 ATATATATAT
27585245 ATGGGCATAGCCCAATAAGAAGAGA
1 ATGGGCATAGCCCAATAAGAAGAGA
* *
27585270 ATGGGCATGGCCCAATAGGAAGA
1 ATGGGCATAGCCCAATAAGAAGA
27585293 AATTGGAGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.40, C:0.17, G:0.31, T:0.12
Consensus pattern (25 bp):
ATGGGCATAGCCCAATAAGAAGAGA
Found at i:27586353 original size:34 final size:34
Alignment explanation
Indices: 27586285--27586420 Score: 98
Period size: 34 Copynumber: 3.9 Consensus size: 34
27586275 CCAAAAATTT
* * *
27586285 TCAGCAGCCATAGCTGCTC-ATATCTACCT-CAAAA
1 TCAGCAGCCA-AGCTGCTCTAT-TTTTCCTAAAAAA
*
27586319 TCAGTAGCCAAGCTGCTCTATTTTTCCTAAAAAA
1 TCAGCAGCCAAGCTGCTCTATTTTTCCTAAAAAA
* * * * *
27586353 TCAACAACTAAGCTGCTCTATTCTTCCTCCAAAAA
1 TCAGCAGCCAAGCTGCTCTATTTTTCCT-AAAAAA
* *
27586388 TAAGCAGCCACAGTTGCT-TATTTCTTCCCTAAA
1 TCAGCAGCCA-AGCTGCTCTATTT-TT-CCTAAA
27586421 TGGCAGCAAA
Statistics
Matches: 79, Mismatches: 17, Indels: 10
0.75 0.16 0.09
Matches are distributed among these distances:
33 13 0.16
34 38 0.48
35 15 0.19
36 10 0.13
37 3 0.04
ACGTcount: A:0.32, C:0.29, G:0.10, T:0.29
Consensus pattern (34 bp):
TCAGCAGCCAAGCTGCTCTATTTTTCCTAAAAAA
Found at i:27587484 original size:19 final size:17
Alignment explanation
Indices: 27587460--27587498 Score: 60
Period size: 19 Copynumber: 2.2 Consensus size: 17
27587450 AATTTTTAAT
27587460 ATTATTTTATTAATAAAAA
1 ATTATTTTATT--TAAAAA
27587479 ATTATTTTATTTAAAAA
1 ATTATTTTATTTAAAAA
27587496 ATT
1 ATT
27587499 TCCTCGTCTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
19 11 0.55
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
ATTATTTTATTTAAAAA
Found at i:27588727 original size:65 final size:65
Alignment explanation
Indices: 27588649--27588843 Score: 285
Period size: 60 Copynumber: 3.1 Consensus size: 65
27588639 ACGTAGTTCA
* * *
27588649 TTTTTTTTGCCTTAACTTTTGCCTAAGTCGTCCTGTTAAGCATTTTCAACTTAGCAGGCTTCTTT
1 TTTTTTTTGCCTTAACTTTTGCCTAAGTCATCATGTTAAGGATTTTCAACTTAGCAGGCTTCTTT
* *
27588714 TTTTTTTTGCCTTAACTTTTGCCTAAGTCTTCTTGTTAAGGATTTTCAACTTAGCAGG---C--T
1 TTTTTTTTGCCTTAACTTTTGCCTAAGTCATCATGTTAAGGATTTTCAACTTAGCAGGCTTCTTT
* *
27588774 TTTTTTTTGTCTTAACTTTTGCCTAAGTCATCATCTTAAGGATTTTCAACTTAGCAGGCTT-TTT
1 TTTTTTTTGCCTTAACTTTTGCCTAAGTCATCATGTTAAGGATTTTCAACTTAGCAGGCTTCTTT
27588838 TTTTTT
1 TTTTTT
27588844 GGATGCAGTT
Statistics
Matches: 118, Mismatches: 7, Indels: 11
0.87 0.05 0.08
Matches are distributed among these distances:
60 55 0.47
62 1 0.01
64 7 0.06
65 55 0.47
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.50
Consensus pattern (65 bp):
TTTTTTTTGCCTTAACTTTTGCCTAAGTCATCATGTTAAGGATTTTCAACTTAGCAGGCTTCTTT
Found at i:27596037 original size:49 final size:49
Alignment explanation
Indices: 27595958--27596072 Score: 149
Period size: 49 Copynumber: 2.3 Consensus size: 49
27595948 AGACTTAGTG
* * * *
27595958 TTGATCATGAACTTGCTTGATCTTCGCTTCAAGGGTCTTGATGACATAATC
1 TTGATCATGAAC--ACTTGATATTAGCTTCAAAGGTCTTGATGACATAATC
* *
27596009 TTGATCATGAACACTTGATATTAGCTTCAAAGGTCTTGATGACTTAATT
1 TTGATCATGAACACTTGATATTAGCTTCAAAGGTCTTGATGACATAATC
*
27596058 TTGATCACGAACACT
1 TTGATCATGAACACT
27596073 ATATCTTGGT
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 45 0.79
51 12 0.21
ACGTcount: A:0.28, C:0.18, G:0.17, T:0.37
Consensus pattern (49 bp):
TTGATCATGAACACTTGATATTAGCTTCAAAGGTCTTGATGACATAATC
Found at i:27596110 original size:25 final size:25
Alignment explanation
Indices: 27596073--27596166 Score: 83
Period size: 23 Copynumber: 3.9 Consensus size: 25
27596063 CACGAACACT
* *
27596073 ATATCTTGGTCACAAACTTCGTTTG
1 ATATCTTGATCACGAACTTCGTTTG
27596098 ATATCTTGATCACGAA-TTC-TGTTG
1 ATATCTTGATCACGAACTTCGT-TTG
27596122 -T-TGCTTGATCACGAACTTCG-TTG
1 ATAT-CTTGATCACGAACTTCGTTTG
***
27596145 -CCGCTTGATCACGAACTTCGTT
1 ATATCTTGATCACGAACTTCGTT
27596167 GCCGCTTGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
22 1 0.02
23 34 0.58
24 10 0.17
25 14 0.24
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.38
Consensus pattern (25 bp):
ATATCTTGATCACGAACTTCGTTTG
Found at i:27596130 original size:23 final size:23
Alignment explanation
Indices: 27596102--27596177 Score: 118
Period size: 23 Copynumber: 3.3 Consensus size: 23
27596092 CGTTTGATAT
**
27596102 CTTGATCACGAA-TTCTGTTGTTG
1 CTTGATCACGAACTTC-GTTGCCG
27596125 CTTGATCACGAACTTCGTTGCCG
1 CTTGATCACGAACTTCGTTGCCG
27596148 CTTGATCACGAACTTCGTTGCCG
1 CTTGATCACGAACTTCGTTGCCG
27596171 CTTGATC
1 CTTGATC
27596178 TTCACTTTAG
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
23 47 0.94
24 3 0.06
ACGTcount: A:0.17, C:0.26, G:0.21, T:0.36
Consensus pattern (23 bp):
CTTGATCACGAACTTCGTTGCCG
Found at i:27596546 original size:57 final size:57
Alignment explanation
Indices: 27596432--27596546 Score: 128
Period size: 57 Copynumber: 2.0 Consensus size: 57
27596422 AATTTAGATA
* ** **
27596432 TTATCTCTAAATTATCTTAATATATTTAGAGATAAATTAAATAATTAAATTTGATTT
1 TTATCTCTAAATTATCATAATATATTTAGAGATAAATTAAATAACAAAATTAAATTT
*
27596489 TTATCTCTAAATTAGT-ATAAT-TA-TTAGAGGTAAATTAAATAACCAATAATTAAATTT
1 TTATCTCTAAATTA-TCATAATATATTTAGAGATAAATTAAATAA-CAA-AATTAAATTT
27596546 T
1 T
27596547 GATTGGTCAA
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
55 18 0.37
56 3 0.06
57 27 0.55
58 1 0.02
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (57 bp):
TTATCTCTAAATTATCATAATATATTTAGAGATAAATTAAATAACAAAATTAAATTT
Found at i:27596615 original size:81 final size:80
Alignment explanation
Indices: 27596489--27596735 Score: 345
Period size: 81 Copynumber: 3.1 Consensus size: 80
27596479 AATTTGATTT
* * * * ** *
27596489 TTATCTCTAAATTAGTAT-AATTA-TTAGAGGTAAATTAAATAACCAATAATTAAATTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAA-TAAATTTTGATTG
27596552 GTCAAAAATATGAATA
65 GTCAAAAATATGAATA
*
27596568 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAACAAATTTTTGATTG
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAATAAA-TTTTGATTG
*
27596633 GTCAAAAATATAAATA
65 GTCAAAAATATGAATA
* * *
27596649 TTATCTCTAAATTATTTTGATTTATTTGGAGATAAATTGGATGACCAATAACTAATTTTTGATTA
1 TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAA-TAAATTTTGATTG
27596714 GTCAAAAATATGAATA
65 GTCAAAAATATGAATA
27596730 TTATCT
1 TTATCT
27596736 ACCAATAGGT
Statistics
Matches: 150, Mismatches: 14, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
79 16 0.11
80 7 0.05
81 125 0.83
82 2 0.01
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (80 bp):
TTATCTCTAAATTATTTTGATTTATTTAGAGATAAATTGGATGACCAATAATAAATTTTGATTGG
TCAAAAATATGAATA
Found at i:27605547 original size:5 final size:5
Alignment explanation
Indices: 27605539--27605569 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
27605529 TTTTAATATA
*
27605539 ATTTT ATTTT ATTTT ATTTT ATTTT ACTTT A
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT A
27605570 AAAAGAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (5 bp):
ATTTT
Found at i:27618288 original size:47 final size:44
Alignment explanation
Indices: 27618174--27618308 Score: 128
Period size: 48 Copynumber: 2.9 Consensus size: 44
27618164 ATTTTCTAAT
* *
27618174 ATTTTATAATTTCTAAAAA-TAAAAATTATTTCTATTTTTTATC
1 ATTTTAGAATTTCTAAAAATTAAAAATTATTTTTATTTTTTATC
* * * * *
27618217 ATTCTAGAATTTTTTTAATAATTAAAAATTATTTTTGGTTTTTTAAATT
1 ATTTTAGAA--TTTCTAAAAATTAAAAATTATTTTT-ATTTTTT--ATC
*
27618266 TTTTTAGAATTTCTAAAAATTAAAAAATTATTTTTATGTTTTT
1 ATTTTAGAATTTCTAAAAATT-AAAAATTATTTTTAT-TTTTT
27618309 CAAAATTTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 11
0.76 0.13 0.12
Matches are distributed among these distances:
43 7 0.10
45 8 0.11
46 13 0.18
47 17 0.24
48 18 0.25
49 9 0.12
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.56
Consensus pattern (44 bp):
ATTTTAGAATTTCTAAAAATTAAAAATTATTTTTATTTTTTATC
Found at i:27618380 original size:19 final size:17
Alignment explanation
Indices: 27618349--27618387 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
27618339 AAAACATTTC
27618349 TAATTTTTTAATTTCTT
1 TAATTTTTTAATTTCTT
*
27618366 TAATGTTTTTAAATTTTTT
1 TAAT-TTTTT-AATTTCTT
27618385 TAA
1 TAA
27618388 AGTGATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 4 0.21
18 5 0.26
19 10 0.53
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
TAATTTTTTAATTTCTT
Found at i:27619304 original size:76 final size:76
Alignment explanation
Indices: 27619174--27619316 Score: 189
Period size: 76 Copynumber: 1.9 Consensus size: 76
27619164 AGTGCCACGA
*
27619174 AGGACAATGCATCCTTATTAGATGACAATACATTATAGCTGCAACTATAAAAAAGAGTGGTATCA
1 AGGACAATGCATCCTTATTAGAGGACAATACATTATAGCTGCAACTATAAAAAAGAGTGGTATCA
27619239 AAGTGCCATTG
66 AAGTGCCATTG
** * * * * * *
27619250 AGGACAATGGGTCCTTATTGGGGGACAATACCTTGTAG-TCGCAATTATAGAAAAGAGTGGTATC
1 AGGACAATGCATCCTTATTAGAGGACAATACATTATAGCT-GCAACTATAAAAAAGAGTGGTATC
27619314 AAA
65 AAA
27619317 ATAGACTTTG
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
75 1 0.02
76 56 0.98
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (76 bp):
AGGACAATGCATCCTTATTAGAGGACAATACATTATAGCTGCAACTATAAAAAAGAGTGGTATCA
AAGTGCCATTG
Found at i:27620185 original size:15 final size:15
Alignment explanation
Indices: 27620165--27620206 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
27620155 AACATTACAG
27620165 AATTATAACTTATAA
1 AATTATAACTTATAA
27620180 AATTATTAA-TTATAA
1 AATTA-TAACTTATAA
*
27620195 TATATATAACTT
1 AAT-TATAACTT
27620207 TGTTTATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
15 16 0.70
16 7 0.30
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTATAACTTATAA
Found at i:27620229 original size:15 final size:15
Alignment explanation
Indices: 27620171--27620237 Score: 57
Period size: 15 Copynumber: 4.4 Consensus size: 15
27620161 ACAGAATTAT
* *
27620171 AACTTATAAAATTATT
1 AACTTATAATA-TATA
27620187 AA-TTATAATATATA
1 AACTTATAATATATA
**
27620201 TAACTT-TGTTTATATA
1 -AACTTAT-AATATATA
27620217 AACTTATAATATATA
1 AACTTATAATATATA
27620232 AACTTA
1 AACTTA
27620238 AAGAGAAGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
14 3 0.07
15 27 0.66
16 11 0.27
ACGTcount: A:0.48, C:0.06, G:0.01, T:0.45
Consensus pattern (15 bp):
AACTTATAATATATA
Found at i:27620443 original size:2 final size:2
Alignment explanation
Indices: 27620438--27620464 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
27620428 ATATATATGA
27620438 GT GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT GT G
27620465 CCTGTGTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:27620789 original size:366 final size:366
Alignment explanation
Indices: 27620111--27620802 Score: 1059
Period size: 366 Copynumber: 1.9 Consensus size: 366
27620101 TTTTTAGTAT
* * * *
27620111 ATATATACTTTACATATAAATATATTTACTTTTTATTTTATGTTAACATTACAGAATTATAACTT
1 ATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAATTATAACTC
* * *
27620176 ATAAAATTATTAATTATAATATATATAACTTTGTTTATATAAACTTATAATATATAAACTTAAAG
66 ATAAAATTATTAATTACAATATATAGAACTTTGTTTATATAAACTTATAACATATAAACTTAAAG
27620241 AGAAGTTGTGAAATTAGAATAATTCTGAAATGTAATTATTATTTTTAATTTAATGTAATTAAGAA
131 AGAAGTTGTGAAATTAGAATAATTCTGAAATGTAATTATTATTTTTAATTTAATGTAATTAAGAA
* *
27620306 CAAACTTGTATAGTTAATTAAATTAATTCATGAAACTATAATTATTAATTAACTTGTAATGTCTT
196 CAAACTTATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAATGTCTT
* * *
27620371 TTAATATATATACTTTGTATATATTAAGTTCATTTATAAGGAATACAATTACTA-TATATATATA
261 TTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATTATATATATA
27620435 TGAGTGTGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTATAA
326 TGAGTGTGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTATAA
* *
27620476 ATATGTACTTTAAATATAAACATATTTACTTTTTATTTTGTGTTAACATTACAAAAATTATAACT
1 ATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTAC-AAAATTATAACT
*
27620541 CATAAAATTATTAATTACAATATATAGACCTTTGTTTATATAAACTTATAACATATAAA-TCTAA
65 CATAAAATTATTAATTACAATATATAGAACTTTGTTTATATAAACTTATAACATATAAACT-TAA
* * * * **
27620605 AGAGAAGTTGTGAGATTAGAATAGTT-TGGAAACT-TAGTTATTTTTTTTAATTTCTTGTAATTA
129 AGAGAAGTTGTGAAATTAGAATAATTCT-GAAA-TGTAATTATTATTTTTAATTTAATGTAATTA
* * * * *
27620668 AGGATAAACTTATATAGTTAATTAAATTAATTAATGAAAGTATGATTATTAATTGACTTGTAATG
192 AGAACAAACTTATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAATG
** *
27620733 TCTTTTAATATATATACTTTATATACATTGGGTTCATTTATAAGAAATATAATTACTATTATATA
257 TCTTTTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATTATATA
27620798 TATAT
322 TATAT
27620803 TAAAATACTT
Statistics
Matches: 293, Mismatches: 29, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
365 50 0.17
366 231 0.79
367 12 0.04
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.44
Consensus pattern (366 bp):
ATATATACTTTAAATATAAACATATTTACTTTTTATTTTATGTTAACATTACAAAATTATAACTC
ATAAAATTATTAATTACAATATATAGAACTTTGTTTATATAAACTTATAACATATAAACTTAAAG
AGAAGTTGTGAAATTAGAATAATTCTGAAATGTAATTATTATTTTTAATTTAATGTAATTAAGAA
CAAACTTATATAGTTAATTAAATTAATTAATGAAACTATAATTATTAATTAACTTGTAATGTCTT
TTAATATATATACTTTATATACATTAAGTTCATTTATAAGAAATACAATTACTATTATATATATA
TGAGTGTGTGTGTGTGTGTGTGTGTGTGTGCCTGTGTATAA
Found at i:27638962 original size:2 final size:2
Alignment explanation
Indices: 27638955--27639005 Score: 63
Period size: 2 Copynumber: 27.0 Consensus size: 2
27638945 AATGGTATGA
*
27638955 AT AT AT AT AT AT AT AT AT AT AT A- AT -T AT AT AA AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
27638994 AT AT AT AC AT AT
1 AT AT AT AT AT AT
27639006 GCATAAGCAT
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
1 3 0.07
2 39 0.93
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:27642138 original size:37 final size:38
Alignment explanation
Indices: 27642097--27642179 Score: 105
Period size: 37 Copynumber: 2.2 Consensus size: 38
27642087 CACATTAACG
* *
27642097 TTGCCTAGAAAGTGGGACAAAAATACCATT-ATTAATA
1 TTGCCTAAAAAGTGGGACAAAAATACCATTCACTAATA
****
27642134 TTGCCTAAAAAGTGGGTTTGAAATACCATTCACTAATA
1 TTGCCTAAAAAGTGGGACAAAAATACCATTCACTAATA
27642172 TTGCCTAA
1 TTGCCTAA
27642180 GTAGCGGGAC
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
37 25 0.64
38 14 0.36
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.30
Consensus pattern (38 bp):
TTGCCTAAAAAGTGGGACAAAAATACCATTCACTAATA
Found at i:27642196 original size:38 final size:37
Alignment explanation
Indices: 27642097--27642196 Score: 94
Period size: 37 Copynumber: 2.7 Consensus size: 37
27642087 CACATTAACG
* * * *
27642097 TTGCCTAGAAAGTGGGACAAAAATACCATTATTAATA
1 TTGCCTAAAAAGCGGGACATAAATACCATTACTAATA
* **
27642134 TTGCCTAAAAAGTGGG-TTTGAAATACCATTCACTAATA
1 TTGCCTAAAAAGCGGGACAT-AAATACCATT-ACTAATA
**
27642172 TTGCCTAAGTAGCGGGACATAAATA
1 TTGCCTAAAAAGCGGGACATAAATA
27642197 ACAATACCTC
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
37 25 0.50
38 24 0.48
39 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (37 bp):
TTGCCTAAAAAGCGGGACATAAATACCATTACTAATA
Found at i:27642437 original size:18 final size:19
Alignment explanation
Indices: 27642414--27642458 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
27642404 TATTTACATG
* *
27642414 ATTAACAC-GATTGATATA
1 ATTAACACAGATTAATACA
27642432 ATTAACACATGATTAATACA
1 ATTAACACA-GATTAATACA
27642452 ATTAACA
1 ATTAACA
27642459 TAATTAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 8 0.35
20 15 0.65
ACGTcount: A:0.49, C:0.13, G:0.07, T:0.31
Consensus pattern (19 bp):
ATTAACACAGATTAATACA
Found at i:27642442 original size:29 final size:29
Alignment explanation
Indices: 27642409--27642465 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
27642399 TAACCTATTT
* * *
27642409 ACATGATTAACACGATTGATATAATTAAC
1 ACATGATTAACACAATTAACATAATTAAC
*
27642438 ACATGATTAATACAATTAACATAATTAA
1 ACATGATTAACACAATTAACATAATTAA
27642466 AATAATTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.49, C:0.12, G:0.07, T:0.32
Consensus pattern (29 bp):
ACATGATTAACACAATTAACATAATTAAC
Found at i:27642477 original size:14 final size:16
Alignment explanation
Indices: 27642460--27642498 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
27642450 CAATTAACAT
27642460 AATTAAAATAAT-TA-
1 AATTAAAATAATGTAC
27642474 AATTAAAAT-ATGTAC
1 AATTAAAATAATGTAC
27642489 AATTAAAATA
1 AATTAAAATA
27642499 TAATTCTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 11 0.50
15 9 0.41
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.33
Consensus pattern (16 bp):
AATTAAAATAATGTAC
Found at i:27642976 original size:37 final size:38
Alignment explanation
Indices: 27642917--27643000 Score: 118
Period size: 38 Copynumber: 2.2 Consensus size: 38
27642907 TTAAATACCT
*
27642917 TTAATGTTGCCTAAAAAGTGGGGTAG-AATACCACTCA
1 TTAATATTGCCTAAAAAGTGGGGTAGAAATACCACTCA
* *
27642954 TTAATATTGCTTAAGAAA-TGGGGTTGAAATACCACTCA
1 TTAATATTGCCTAA-AAAGTGGGGTAGAAATACCACTCA
27642992 TTAATATTG
1 TTAATATTG
27643001 TCGATATAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
37 19 0.45
38 23 0.55
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (38 bp):
TTAATATTGCCTAAAAAGTGGGGTAGAAATACCACTCA
Found at i:27647548 original size:27 final size:27
Alignment explanation
Indices: 27647522--27647597 Score: 75
Period size: 27 Copynumber: 2.9 Consensus size: 27
27647512 CTGTTAGGTA
* *
27647522 AAAG-TATTCATCCATTTCTAGTGGGT
1 AAAGATATCCATCCACTTCTAGTGGGT
**
27647548 AAAGATATCCATCCACTTCTAGTAAGT
1 AAAGATATCCATCCACTTCTAGTGGGT
* * *
27647575 AAAGTTA-CCATTCACCTCTAGTG
1 AAAGATATCCATCCACTTCTAGTG
27647598 ATGGGTAAAG
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
26 17 0.41
27 24 0.59
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Consensus pattern (27 bp):
AAAGATATCCATCCACTTCTAGTGGGT
Found at i:27647594 original size:26 final size:27
Alignment explanation
Indices: 27647546--27647596 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
27647536 TTTCTAGTGG
*
27647546 GTAAAGATATCCATCCACTTCTAGTAA
1 GTAAAGATATCCATCCACCTCTAGTAA
* *
27647573 GTAAAGTTA-CCATTCACCTCTAGT
1 GTAAAGATATCCATCCACCTCTAGT
27647597 GATGGGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 13 0.62
27 8 0.38
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (27 bp):
GTAAAGATATCCATCCACCTCTAGTAA
Found at i:27648959 original size:37 final size:37
Alignment explanation
Indices: 27648878--27648959 Score: 155
Period size: 37 Copynumber: 2.2 Consensus size: 37
27648868 TAATGTTGTG
*
27648878 TGATGATATTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
27648915 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
27648952 TGATGATG
1 TGATGATG
27648960 ATATTGCATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 44 1.00
ACGTcount: A:0.28, C:0.10, G:0.37, T:0.26
Consensus pattern (37 bp):
TGATGATGTTGAAGTGTGCGAGTAGGGAGTGCACACA
Found at i:27649028 original size:2 final size:2
Alignment explanation
Indices: 27649018--27649070 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
27649008 GTATATACAA
*
27649018 AT AT GT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
27649060 AT AT AT AT AT A
1 AT AT AT AT AT A
27649071 NGATGTGGGA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27649396 original size:71 final size:70
Alignment explanation
Indices: 27649291--27649464 Score: 204
Period size: 71 Copynumber: 2.5 Consensus size: 70
27649281 TGCAACGAGG
* * ** * * *
27649291 TTCATTTTTACTGCAGCAAGAAACTCGAGAGTTTTGGGGGTCACACTAGTCTGGTTCTCACTGCA
1 TTCATTTTCACTGCAGCGAGAAACTCTCGGGTTTTGGAGGTCACACTAGCCTGGTTCT-ACTGCA
27649356 GCAAGA
65 GCAAGA
* *
27649362 TTCATTTTCACTGCAGCGAGAAACTCTCGGGTTTTGGAGGTCACACTAGCCTGGTTCTGCTGTAG
1 TTCATTTTCACTGCAGCGAGAAACTCTCGGGTTTTGGAGGTCACACTAGCCTGGTTCTACTGCAG
**
27649427 TGAGA
66 CAAGA
* * * *
27649432 TTTATTCTCATTGAAGCGAGAAACTCTCGGGTT
1 TTCATTTTCACTGCAGCGAGAAACTCTCGGGTT
27649465 CTAGTGCAGT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
70 37 0.42
71 51 0.58
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (70 bp):
TTCATTTTCACTGCAGCGAGAAACTCTCGGGTTTTGGAGGTCACACTAGCCTGGTTCTACTGCAG
CAAGA
Found at i:27650518 original size:27 final size:27
Alignment explanation
Indices: 27650488--27650541 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
27650478 TCTTCACTAC
* *
27650488 TCATCTATTTCTAATGGGTAAAAGTAT
1 TCATCCATTTCTAATGAGTAAAAGTAT
*
27650515 TCATCCATTTCTAGTGAGTAAAAGTAT
1 TCATCCATTTCTAATGAGTAAAAGTAT
27650542 CTATCAACCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (27 bp):
TCATCCATTTCTAATGAGTAAAAGTAT
Found at i:27650564 original size:30 final size:31
Alignment explanation
Indices: 27650528--27650611 Score: 111
Period size: 30 Copynumber: 2.8 Consensus size: 31
27650518 TCCATTTCTA
*
27650528 GTGAGTAAAAG-TATCTATCAACCTTTGACC
1 GTGAGTAAAAGTTATCCATCAACCTTTGACC
*
27650558 GTGAGT-AAAGTTATCCATCCACCTTTGACC
1 GTGAGTAAAAGTTATCCATCAACCTTTGACC
* *
27650588 GTGGGT-AAAGTTATCCATCCACCT
1 GTGAGTAAAAGTTATCCATCAACCT
27650612 CTAATGGGTA
Statistics
Matches: 50, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
29 4 0.08
30 46 0.92
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (31 bp):
GTGAGTAAAAGTTATCCATCAACCTTTGACC
Found at i:27650629 original size:27 final size:27
Alignment explanation
Indices: 27650562--27650677 Score: 142
Period size: 27 Copynumber: 4.2 Consensus size: 27
27650552 TTGACCGTGA
* * *
27650562 GTAAAGTTATCCATCCACCTTTGACCGTGG
1 GTAAAGGTATCCATCCACCTCT-A--ATGG
*
27650592 GTAAAGTTATCCATCCACCTCTAATGG
1 GTAAAGGTATCCATCCACCTCTAATGG
*
27650619 GTAAAGGTATCCATCCACCTCTAGTGG
1 GTAAAGGTATCCATCCACCTCTAATGG
* *
27650646 GTAAAGGTATCAATCTACCTCTAATGG
1 GTAAAGGTATCCATCCACCTCTAATGG
27650673 GTAAA
1 GTAAA
27650678 AGCATTGATC
Statistics
Matches: 79, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
27 57 0.72
29 1 0.01
30 21 0.27
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.28
Consensus pattern (27 bp):
GTAAAGGTATCCATCCACCTCTAATGG
Done.