Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr3
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: 100348136
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 3062571 characters in sequence are not A, C, G, or T
File 85 of 290
Found at i:28362912 original size:43 final size:42
Alignment explanation
Indices: 28362850--28362952 Score: 109
Period size: 43 Copynumber: 2.4 Consensus size: 42
28362840 TCCCAAATGT
* * * * *
28362850 GGTCTTACATGTAACCAAATATCGTTGC-CACTGTCCCTGACAG
1 GGTCTTACACGAAATCAAATAT-GATGCTCA-TGTCCCAGACAG
* *
28362893 GGTCTTACACGAAATCAAATATGATGCTGATGTCCCAGACAT
1 GGTCTTACACGAAATCAAATATGATGCTCATGTCCCAGACAG
28362935 GGTCTTACACGTAAATCA
1 GGTCTTACACG-AAATCA
28362953 TAAGTTGATG
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
42 25 0.49
43 26 0.51
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.27
Consensus pattern (42 bp):
GGTCTTACACGAAATCAAATATGATGCTCATGTCCCAGACAG
Found at i:28362973 original size:44 final size:42
Alignment explanation
Indices: 28362883--28362992 Score: 105
Period size: 44 Copynumber: 2.6 Consensus size: 42
28362873 GTTGCCACTG
* * ** **
28362883 TCCCTGACAGGGTCTTACACGAAATCAAATATGATGCTGATG
1 TCCCAGACACGGTCTTACACGAAATCAAATATGATGCCAACA
*
28362925 TCCCAGACATGGTCTTACACGTAAATCATAAGT-TGATGCCAACA
1 TCCCAGACACGGTCTTACACG-AAATCA-AA-TATGATGCCAACA
* *
28362969 TCCCAGACGCGGTCTTACATGAAA
1 TCCCAGACACGGTCTTACACGAAA
28362993 ACACTTATCA
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
42 19 0.34
43 9 0.16
44 27 0.48
45 1 0.02
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.25
Consensus pattern (42 bp):
TCCCAGACACGGTCTTACACGAAATCAAATATGATGCCAACA
Found at i:28364536 original size:24 final size:22
Alignment explanation
Indices: 28364493--28364536 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
28364483 AGGAATTTAG
*
28364493 ATAGTTTTTTTTATTTTGTTGT
1 ATAGTTTTTTATATTTTGTTGT
*
28364515 ATAGTGTTTTTATCTTTATGTT
1 ATAGT-TTTTTATATTT-TGTT
28364537 TTTATTTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 9 0.50
24 4 0.22
ACGTcount: A:0.16, C:0.02, G:0.14, T:0.68
Consensus pattern (22 bp):
ATAGTTTTTTATATTTTGTTGT
Found at i:28366475 original size:95 final size:98
Alignment explanation
Indices: 28366366--28366593 Score: 279
Period size: 95 Copynumber: 2.4 Consensus size: 98
28366356 CGACCACATT
*
28366366 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-CTTG-ATATG-G-GTCAATGTAA
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAATATGAGAGTCAATGTAA
*
28366427 GACCATGTCTGGGACATGGCATCGACACCGATAG
66 GACCATGTCTGGGACATAGCATCGACACCGAT-G
* * * *
28366461 ATGAGAGCCAGTGTAAGGCCATGTC-GTGGACATGGCATTAGCCTCGATATATGAGAGTTAGTGT
1 ATGAGAGCCAGTGTAAGACCATGTCTG-GGACATGGCATCAGCCTCGA-ATATGAGAGTCAATGT
* ***
28366525 AAGAGCATGTCTGGGACATAGCATCGACTTTGATG
64 AAGACCATGTCTGGGACATAGCATCGACACCGATG
* *
28366560 -TGTGAGCCAGTGTAACACCATGTCTGGGACATGG
1 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGG
28366594 TGTCGACATC
Statistics
Matches: 113, Mismatches: 13, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
94 1 0.01
95 37 0.33
96 3 0.03
98 34 0.30
99 3 0.03
100 35 0.31
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (98 bp):
ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCTCGAATATGAGAGTCAATGTAA
GACCATGTCTGGGACATAGCATCGACACCGATG
Found at i:28366497 original size:50 final size:47
Alignment explanation
Indices: 28366365--28366593 Score: 198
Period size: 50 Copynumber: 4.8 Consensus size: 47
28366355 TCGACCACAT
**
28366365 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCTTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCCGA
* *
28366412 TATG-G-GTCAATGTAAGACCATGTCTGGGACATGGCATC-GACACCGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-C-CCGA
* *
28366458 TAGATGAGAGCCAGTGTAAGGCCATGTC-GTGGACATGGCATTAGCCTCGATA
1 T--ATGAGAGCCAGTGTAAGACCATGTCTG-GGACATGGCATCAGCC-CG--A
** * * **
28366510 TATGAGAGTTAGTGTAAGAGCATGTCTGGGACATAGCATC-GACTTTGA
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAG-C-CCGA
* * *
28366558 TGTGTGAGCCAGTGTAACACCATGTCTGGGACATGG
1 TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGG
28366594 TGTCGACATC
Statistics
Matches: 145, Mismatches: 23, Indels: 27
0.74 0.12 0.14
Matches are distributed among these distances:
44 1 0.01
45 32 0.22
46 4 0.03
47 4 0.03
48 33 0.23
49 4 0.03
50 63 0.43
51 2 0.01
52 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (47 bp):
TATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCAGCCCGA
Found at i:28373451 original size:13 final size:13
Alignment explanation
Indices: 28373433--28373457 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28373423 TTACTCGCAC
28373433 ATCACATATCGAA
1 ATCACATATCGAA
28373446 ATCACATATCGA
1 ATCACATATCGA
28373458 TGGCAACATA
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:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (13 bp):
ATCACATATCGAA
Found at i:28373451 original size:101 final size:101
Alignment explanation
Indices: 28373323--28373548 Score: 296
Period size: 101 Copynumber: 2.2 Consensus size: 101
28373313 AGACAGGGTT
* * * *
28373323 TTACTCGCATA-CATATATCAGAATCACATTTTGATGCCAACATATAAAACGTGGACTTACTCGC
1 TTACTCGCACATCACATATCAGAATCACATATCGATGCCAACATATAAAACGTGGACTTACTCGC
** * *
28373387 ACACATATATCA-GAATCACATGTCGATGCCATGGTC
66 ACACATATAT-AGGAATCACACATCGATGCCATAGTA
* * *
28373423 TTACTCGCACATCACATATC-GAAATCACATATCGATGGCAACATATTAAACGTGGTCTTACTCG
1 TTACTCGCACATCACATATCAG-AATCACATATCGATGCCAACATATAAAACGTGGACTTACTCG
*
28373487 CGCACATATATAGGAATCACACATCGATGCCATAGTA
65 CACACATATATAGGAATCACACATCGATGCCATAGTA
*
28373524 TTACTCACACATCACATATCAGAAT
1 TTACTCGCACATCACATATCAGAAT
28373549 TCATATGTCG
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
100 12 0.11
101 96 0.88
102 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.13, T:0.27
Consensus pattern (101 bp):
TTACTCGCACATCACATATCAGAATCACATATCGATGCCAACATATAAAACGTGGACTTACTCGC
ACACATATATAGGAATCACACATCGATGCCATAGTA
Found at i:28376420 original size:3 final size:3
Alignment explanation
Indices: 28376412--28376440 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28376402 GAAAACACAC
28376412 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
28376441 TTTTTAGAAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:28386769 original size:44 final size:44
Alignment explanation
Indices: 28386667--28386787 Score: 156
Period size: 44 Copynumber: 2.7 Consensus size: 44
28386657 GAAATCTGAA
* * * *
28386667 CTCGTTGAGTTGG-CCTAAGTTCATGATATGTATGAGA-CATCTGAG
1 CTCGTTGAGTTGGTCC-GAGTTCAT--TATGGATGCGAGCATCCGAG
*
28386712 CTCGTTGAGTTGGTTCGAGTTCATTATGGATGCGAGCATCCGAG
1 CTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGAGCATCCGAG
28386756 CTCGTTGAGTTGGTCCGAGTTCATTATGGATG
1 CTCGTTGAGTTGGTCCGAGTTCATTATGGATG
28386788 TGATACATGT
Statistics
Matches: 68, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
43 9 0.13
44 38 0.56
45 20 0.29
46 1 0.01
ACGTcount: A:0.20, C:0.17, G:0.30, T:0.34
Consensus pattern (44 bp):
CTCGTTGAGTTGGTCCGAGTTCATTATGGATGCGAGCATCCGAG
Found at i:28389425 original size:39 final size:40
Alignment explanation
Indices: 28389380--28389564 Score: 178
Period size: 40 Copynumber: 4.7 Consensus size: 40
28389370 GCTCCTCGTT
* * *
28389380 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
**
28389420 C-AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
28389459 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * * * * *
28389499 CAAAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCA
1 CAAATGCCTTCGGGA-CATAACCCGGATTTAGTAAC-TCGCA
* *
28389540 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACATAACCCGGA
28389565 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
39 37 0.30
40 74 0.61
41 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28389480 original size:40 final size:39
Alignment explanation
Indices: 28389347--28389564 Score: 165
Period size: 40 Copynumber: 5.5 Consensus size: 39
28389337 AAATCACGTA
* * **
28389347 CCTTCGGGATTTAA-CCGGATATAGCTCCTCGTTCA-AATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCG--CACAATG
* * * * *
28389386 CCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
* *
28389425 CCTTCGGGACATAACCCGGATTTAACAACTCGCACGAATG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * *
28389465 CCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGG
1 CCTTCGGGACTTAACCCGGATTTAGCAACTCGCAC-AATG
* * * * *
28389505 CCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCACAAAG
1 CCTTCGGGA-CTTAACCCGGATTTA-GCAAC-TCGCACAATG
*
28389545 CCTTCGGGACTTAGCCCGGA
1 CCTTCGGGACTTAACCCGGA
28389565 CAGCATTCAA
Statistics
Matches: 143, Mismatches: 29, Indels: 13
0.77 0.16 0.07
Matches are distributed among these distances:
38 2 0.01
39 48 0.34
40 85 0.59
41 8 0.06
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.26
Consensus pattern (39 bp):
CCTTCGGGACTTAACCCGGATTTAGCAACTCGCACAATG
Found at i:28395517 original size:830 final size:830
Alignment explanation
Indices: 28393919--28395579 Score: 3178
Period size: 830 Copynumber: 2.0 Consensus size: 830
28393909 GTAATTCTTC
28393919 CGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGT
1 CGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGT
28393984 CATCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCT
66 CATCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCT
28394049 GATATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCA
131 GATATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCA
28394114 CCTCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAAC
196 CCTCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAAC
28394179 CAAGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGA
261 CAAGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGA
28394244 ATTTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACAC
326 ATTTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACAC
28394309 CCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGT
391 CCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGT
28394374 AAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCG
456 AAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCG
28394439 GTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACG
521 GTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACG
28394504 GGCTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTC
586 GGCTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTC
* * *
28394569 CAGATGGTCTACCTCGAGCAGTGGTAGCACCCGGTTTCCCACTCTGATTTTCATTCTGTTCAAAC
651 CAGATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAAC
* *
28394634 AACCTCGGGCAATCTTTAATGAAGTGGTCCACTGATCCGCATTTGTAACAGGAGCGGTCAGGAAA
716 AACCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAA
*
28394699 TCTACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTTCTGT
781 TCTACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTGT
28394749 CGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGT
1 CGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGT
28394814 CATCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCT
66 CATCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCT
28394879 GATATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCA
131 GATATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCA
*
28394944 CCTCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAACC
196 CCTCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAAC
28395009 CAAGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGA
261 CAAGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGA
28395074 ATTTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACAC
326 ATTTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACAC
28395139 CCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGT
391 CCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGT
* *
28395204 AGGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGGGTGAATGTACCG
456 AAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCG
28395269 GTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACG
521 GTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACG
* *
28395334 GGCTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACTAGCATTGCCCGTATTTC
586 GGCTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTC
**
28395399 CAGATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCCGAC
651 CAGATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAAC
*
28395464 AACCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGGAA
716 AACCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAA
* *
28395529 TCTACAACTCCCCGAATGCCATTTACCGCAATATCGGCATTTCGTCCTGT
781 TCTACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTGT
28395579 C
1 C
28395580 TCGACGTTCA
Statistics
Matches: 815, Mismatches: 16, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
830 815 1.00
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (830 bp):
CGGAAAAACATCCGGGTATTCACAAACCACCGGCACAGATTCGGGTTTCTTTTCTAATTCTTTGT
CATCAAGCACATATGCAAGGTATGCTTCGCACCCTTTTCTTACATATTTCTGTGCCAACATTGCT
GATATTACAGCTGGCATCCCCTCCAAGTCCGCAGACTCAATTCGGACTACTTCGTTATTTGCGCA
CCTCAAATCAATAGTCTTGCTCTTGCAATTCACAATCGCATCATGCGCGGTCAACCAATCCAAAC
CAAGGATAACATCAAATTCATCAAACGGCAAAAGCATCAAGTCCGCCGGAAAACAGGAACCTCGA
ATTTCCAGGGGACATTTCTTACACACTTTGTCGACAAGCACGTAACGACCCAAGGGATTTGACAC
CCGAATTACGAACTCAGTAGACTCAATAGGTAAAGTCTTACTGGATGCTAAGGTTTCACATATGT
AAGAATGAGTAGAACCGGGGTCAATCAAAGCAATTACATTAGTATCAAAGAGAGTGAATGTACCG
GTAATAACATCAGGCGAAGAAGCATCCTCGCGGGCACGTATAGCATAAGCTCTAGCAGGCGCACG
GGCTTCGGATCTGGTTATATCATCTCTAGATCCTCTCTGACCACCACCAGCATTGCCCATATTTC
CAGATGGTCTACCTCGAGCAGTGGTAGCACCCGGTCTCCCACTCTGATTTGCATTCTGTCCAAAC
AACCTCGGGCAATCTTTAATGAAGTGGTCAACTGATCCGCACTTGTAACAGGAGCGGTCAGGAAA
TCTACAACTCCCCGAATGCCATTTACCGCAATATCGACATTCCGTCCTGT
Found at i:28398176 original size:40 final size:39
Alignment explanation
Indices: 28398078--28398340 Score: 278
Period size: 40 Copynumber: 6.6 Consensus size: 39
28398068 TCCTCGTTCA
* * * *
28398078 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28398117 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28398156 GAATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28398196 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28398236 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28398276 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28398317 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28398341 CAGCATTCAA
Statistics
Matches: 197, Mismatches: 21, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
39 40 0.20
40 145 0.74
41 12 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28398300 original size:120 final size:119
Alignment explanation
Indices: 28398078--28398340 Score: 307
Period size: 120 Copynumber: 2.2 Consensus size: 119
28398068 TCCTCGTTCA
* * *
28398078 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGGATT
1 AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
* * *
28398143 TAATAACTCGCACGAATGCCTTCGGGACTTAACCCGGATTTAATAAC-TCGCAC
66 TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
* * * * *
28398196 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGGA
1 -AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACAC-AAGGCCTTCGGGACATAACCCGG-
* * ** * *
28398261 ATTT-GTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
63 ATTTAATAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAATAACTTAGCAC
*
28398317 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
28398341 CAGCATTCAA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 37 0.31
120 75 0.62
121 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.25
Consensus pattern (119 bp):
AATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCACACAAGGCCTTCGGGACATAACCCGGATT
TAATAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAATAACTTAGCAC
Found at i:28398349 original size:41 final size:41
Alignment explanation
Indices: 28398272--28398349 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28398262 TTTGTATCTC
* * *
28398272 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28398313 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28398350 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28413418 original size:48 final size:48
Alignment explanation
Indices: 28413306--28413560 Score: 327
Period size: 48 Copynumber: 5.3 Consensus size: 48
28413296 ATGAGATTTT
* * * *
28413306 GTGTAAGA-CATTTTCTGGGACATGGCATTGGC-ATCTGAGATATGTGCCT
1 GTGTAAGACCA-TGTCTGGGACATGGCATCGGCGA--TGATATATGTGCCA
* * * *
28413355 GTGTAAGACCGTGTCTGGGACATTGCATCGGCGATAATGTATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
* *
28413403 GTGTAAAACTATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
* *
28413451 GTGTAAGACCATGTCTGCGACATGGCATCAGC-AGTGATATATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGA-TGATATATGTGCCA
*
28413499 GTGTAAGACCATGTCTGGGACATGGCATTGGCGATGATATATGTGCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
*
28413547 ATGTAAGACCATGT
1 GTGTAAGACCATGT
28413561 GTAACACCCC
Statistics
Matches: 180, Mismatches: 22, Indels: 9
0.85 0.10 0.04
Matches are distributed among these distances:
47 1 0.01
48 150 0.83
49 27 0.15
50 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.29, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGCGATGATATATGTGCCA
Found at i:28417464 original size:25 final size:25
Alignment explanation
Indices: 28417436--28417507 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
28417426 GCTTTATCAT
** *
28417436 ATAACTTGAGGCCTAGCCTTTTTTA
1 ATAACTTGAGGCAAAGCCCTTTTTA
*
28417461 ATAAC-TGGGGCAAAGCCCTTTTTA
1 ATAACTTGAGGCAAAGCCCTTTTTA
*
28417485 ATAAC-TGGGGCATAAGCCCTTTT
1 ATAACTTGAGGCA-AAGCCCTTTT
28417508 GCACTTCCTC
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
24 27 0.64
25 15 0.36
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.33
Consensus pattern (25 bp):
ATAACTTGAGGCAAAGCCCTTTTTA
Found at i:28417482 original size:24 final size:25
Alignment explanation
Indices: 28417450--28417507 Score: 100
Period size: 24 Copynumber: 2.4 Consensus size: 25
28417440 CTTGAGGCCT
*
28417450 AGCCTTTTTTAATAACTGGGGCA-A
1 AGCCCTTTTTAATAACTGGGGCATA
28417474 AGCCCTTTTTAATAACTGGGGCATA
1 AGCCCTTTTTAATAACTGGGGCATA
28417499 AGCCCTTTT
1 AGCCCTTTT
28417508 GCACTTCCTC
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 22 0.69
25 10 0.31
ACGTcount: A:0.26, C:0.21, G:0.19, T:0.34
Consensus pattern (25 bp):
AGCCCTTTTTAATAACTGGGGCATA
Found at i:28417579 original size:9 final size:9
Alignment explanation
Indices: 28417565--28417621 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
28417555 ATCTCGTGTG
28417565 CATATCATA
1 CATATCATA
*
28417574 CATATCATGTG
1 CATATCA--TA
28417585 CATATCATA
1 CATATCATA
* *
28417594 CATGTCATGTG
1 CATATCA--TA
28417605 CATATCATA
1 CATATCATA
28417614 CATATCAT
1 CATATCAT
28417622 GTTTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:28417584 original size:20 final size:20
Alignment explanation
Indices: 28417561--28417623 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
28417551 GAACATCTCG
28417561 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
28417581 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
28417601 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
28417621 TGT
1 TGT
28417624 TTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:28417688 original size:25 final size:25
Alignment explanation
Indices: 28417660--28417707 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
28417650 ATATATAAAC
* * *
28417660 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
28417685 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
28417708 CATATTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:28424649 original size:44 final size:43
Alignment explanation
Indices: 28424573--28424679 Score: 139
Period size: 44 Copynumber: 2.5 Consensus size: 43
28424563 CCAAATAGGA
* *
28424573 TCTTACACGAAA--TCAGATACGATG-CCTATGTCCCAGACATGG
1 TCTTACACGAAATCTCAAAT-CGA-GACCTATGTCCCAGACACGG
28424615 TCTTACACGTAAATCTCAAATCGAGACCTATGTCCCAGACACGG
1 TCTTACACG-AAATCTCAAATCGAGACCTATGTCCCAGACACGG
*
28424659 TCTTACACGATATCTCAAATC
1 TCTTACACGAAATCTCAAATC
28424680 AATGTCAACG
Statistics
Matches: 58, Mismatches: 3, Indels: 7
0.85 0.04 0.10
Matches are distributed among these distances:
42 9 0.16
43 15 0.26
44 29 0.50
45 5 0.09
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (43 bp):
TCTTACACGAAATCTCAAATCGAGACCTATGTCCCAGACACGG
Found at i:28434657 original size:67 final size:67
Alignment explanation
Indices: 28434581--28434716 Score: 236
Period size: 67 Copynumber: 2.0 Consensus size: 67
28434571 GGGAGATAAA
*
28434581 GTATTTTTGAAAGTATCCCCATGGAGAAAGGTTTAAAGATTTGGTAGGAAAGGCAAGTTGAGTCC
1 GTATTTTTGAAAGTATCCCCATGGAGAAAGGTTTAAAGATTCGGTAGGAAAGGCAAGTTGAGTCC
28434646 TC
66 TC
* **
28434648 GTATTTTTGAAAGTATCCCTATGGAGAAAGGTTTGGAGATTCGGTAGGAAAGGCAAGTTGAGTCC
1 GTATTTTTGAAAGTATCCCCATGGAGAAAGGTTTAAAGATTCGGTAGGAAAGGCAAGTTGAGTCC
28434713 TC
66 TC
28434715 GT
1 GT
28434717 TTCATAGGAC
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 65 1.00
ACGTcount: A:0.29, C:0.12, G:0.29, T:0.30
Consensus pattern (67 bp):
GTATTTTTGAAAGTATCCCCATGGAGAAAGGTTTAAAGATTCGGTAGGAAAGGCAAGTTGAGTCC
TC
Found at i:28438024 original size:94 final size:94
Alignment explanation
Indices: 28437838--28438025 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 94
28437828 TGATTGTTCC
* *
28437838 TTTCGATAAGTGATTAAATGTTAATCATGATGTTATGGCCTATTCGGTTTTATGTTTTTACTGTT
1 TTTCGATAAGTGATTAAATATTAAGCATGATGTTATGGCCTATTCGGTTTTATGTTTTTACTGTT
28437903 AACTTTAAGAAATCTGTGATGAAGTAGGA
66 AACTTTAAGAAATCTGTGATGAAGTAGGA
28437932 TTTCGATAAGTGATTAAATATTAAGCATGATGTTATGGCCTATTCGGTTTTATGTTTTTACTGTT
1 TTTCGATAAGTGATTAAATATTAAGCATGATGTTATGGCCTATTCGGTTTTATGTTTTTACTGTT
28437997 AACTTTAAGAAATCTGTGATGAAGTAGGA
66 AACTTTAAGAAATCTGTGATGAAGTAGGA
28438026 GTGGCATTTA
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
94 92 1.00
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (94 bp):
TTTCGATAAGTGATTAAATATTAAGCATGATGTTATGGCCTATTCGGTTTTATGTTTTTACTGTT
AACTTTAAGAAATCTGTGATGAAGTAGGA
Found at i:28444829 original size:48 final size:48
Alignment explanation
Indices: 28444719--28444939 Score: 230
Period size: 48 Copynumber: 4.6 Consensus size: 48
28444709 ATGAGATTTC
* * * *
28444719 GTGTAAGACCATGTCTGGGACATGGCATCAGTATATGAGATATGTACCT
1 GTGTAAGACCATGTCTGGGACATGGCATCGGT-GATGATATATGTACCA
* * * *
28444768 GTATAAGACCATGTTTGGGACATGGAATCGGTGATGATATATGTCCCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATATGTACCA
* * * * *
28444816 GTGTAAGACCATGTCTGGGACATGGCATTGGCGTTGATATATGTGCTA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATATGTACCA
* * * * *
28444864 GTGTAAGACCATGTCTAGAACATGGCATCGG-GAATGACATATGGATTCA
1 GTGTAAGACCATGTCTGGGACATGGCATCGGTG-ATGATATATGTA-CCA
*
28444913 -TGTAAGACCATGTCGGGGACATGGCAT
1 GTGTAAGACCATGTCTGGGACATGGCAT
28444940 TCGTACTTTA
Statistics
Matches: 142, Mismatches: 28, Indels: 5
0.81 0.16 0.03
Matches are distributed among these distances:
47 1 0.01
48 112 0.79
49 29 0.20
ACGTcount: A:0.28, C:0.16, G:0.29, T:0.28
Consensus pattern (48 bp):
GTGTAAGACCATGTCTGGGACATGGCATCGGTGATGATATATGTACCA
Found at i:28446241 original size:19 final size:18
Alignment explanation
Indices: 28446209--28446245 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
28446199 TACACAGCTT
28446209 GGGGACACGAGCGTGTCA
1 GGGGACACGAGCGTGTCA
*
28446227 GGGGAACACGGGCGTGTCA
1 GGGG-ACACGAGCGTGTCA
28446246 TGTGTCCACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.22, G:0.46, T:0.11
Consensus pattern (18 bp):
GGGGACACGAGCGTGTCA
Found at i:28448934 original size:28 final size:28
Alignment explanation
Indices: 28448893--28448948 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
28448883 CTCGAACCTG
* *
28448893 TTAGAATGGTACGGGCGTGTGTTCTACC
1 TTAGAATGGCACGGCCGTGTGTTCTACC
28448921 TTAGAATGGCACGGCCGTGTGTTCTACC
1 TTAGAATGGCACGGCCGTGTGTTCTACC
28448949 CGTGTGAGTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.30, T:0.30
Consensus pattern (28 bp):
TTAGAATGGCACGGCCGTGTGTTCTACC
Found at i:28449758 original size:24 final size:24
Alignment explanation
Indices: 28449728--28449775 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
28449718 AAAAGATTTA
28449728 ATCATCACTTGCATACAACAGAGC
1 ATCATCACTTGCATACAACAGAGC
28449752 ATCATCACTTGCATACAACAGAGC
1 ATCATCACTTGCATACAACAGAGC
28449776 TTCTTCTCAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (24 bp):
ATCATCACTTGCATACAACAGAGC
Found at i:28451620 original size:55 final size:55
Alignment explanation
Indices: 28451550--28451671 Score: 131
Period size: 55 Copynumber: 2.2 Consensus size: 55
28451540 TATGTAGTCC
* * * * *
28451550 CACGCCCATGGTAATTTAATAGGTTCGACCA-TGTTTGC-TTGACACGGGCGTGTCG
1 CACGCCCGTGTTAATTTAACAGGTTCGACCACGGTTT-CAATG-CACGGGCGTGTCG
* * * *
28451605 CACGCTCGTGTTAATTTGACAGGTTTGGCCACGGTTTCAATGCACGGGCGTGTCG
1 CACGCCCGTGTTAATTTAACAGGTTCGACCACGGTTTCAATGCACGGGCGTGTCG
28451660 CACGCCCGTGTT
1 CACGCCCGTGTT
28451672 GTTTTGGCAG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
55 49 0.89
56 6 0.11
ACGTcount: A:0.17, C:0.25, G:0.29, T:0.29
Consensus pattern (55 bp):
CACGCCCGTGTTAATTTAACAGGTTCGACCACGGTTTCAATGCACGGGCGTGTCG
Found at i:28456268 original size:48 final size:46
Alignment explanation
Indices: 28456187--28456312 Score: 168
Period size: 48 Copynumber: 2.7 Consensus size: 46
28456177 ACTCGTAGCT
28456187 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGT-CTCAAT-GCC
1 GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTACT--ATGGCC
* *
28456233 GATGCCATGTCCC-GAACATGGTCTTACACTGGCTCTCGTACTGTGGCC
1 GATG-CATGTCCCAG-ACAT-GTCTTACACTAGCTCTCGTACTATGGCC
28456281 GATGCATGTCCCAGACATGTCTTACACTAGCT
1 GATGCATGTCCCAGACATGTCTTACACTAGCT
28456313 TACAATAGTC
Statistics
Matches: 71, Mismatches: 3, Indels: 12
0.83 0.03 0.14
Matches are distributed among these distances:
46 18 0.25
47 25 0.35
48 26 0.37
49 2 0.03
ACGTcount: A:0.21, C:0.31, G:0.21, T:0.28
Consensus pattern (46 bp):
GATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTACTATGGCC
Found at i:28456306 original size:94 final size:92
Alignment explanation
Indices: 28456142--28456312 Score: 263
Period size: 94 Copynumber: 1.8 Consensus size: 92
28456132 TAAGATGCTA
* * *
28456142 ATGCCATGTCCTGGACATGGTCTTACACTAGCTTTACTCGTAGCTGATGCATGTCCCAGACATGT
1 ATGCCATGTCCCGAACATGGTCTTACACTAGCTTTACTCGTAGCCGATGCATGTCCCAGACATGT
28456207 CTTACACTAGCTCTCGTCTCAATGCCG
66 CTTACACTAGCTCTCGTCTCAATGCCG
* *
28456234 ATGCCATGTCCCGAACATGGTCTTACACTGGCTCTCGTACT-GTGGCCGATGCATGTCCCAGACA
1 ATGCCATGTCCCGAACATGGTCTTACACTAGCT-T--TACTCGTAGCCGATGCATGTCCCAGACA
28456298 TGTCTTACACTAGCT
63 TGTCTTACACTAGCT
28456313 TACAATAGTC
Statistics
Matches: 71, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
92 30 0.42
93 1 0.01
94 36 0.51
95 4 0.06
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.29
Consensus pattern (92 bp):
ATGCCATGTCCCGAACATGGTCTTACACTAGCTTTACTCGTAGCCGATGCATGTCCCAGACATGT
CTTACACTAGCTCTCGTCTCAATGCCG
Found at i:28459961 original size:32 final size:32
Alignment explanation
Indices: 28459916--28459987 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
28459906 TTACTCTTTA
*
28459916 ACTCTTAGCTGATAGTAACCAGACCTCAAATC
1 ACTCTTAGCTGATAATAACCAGACCTCAAATC
*
28459948 ACTCTTAGTTGATAATAACCAGACCTCAAATC
1 ACTCTTAGCTGATAATAACCAGACCTCAAATC
*
28459980 AATCTTAG
1 ACTCTTAG
28459988 AAAACATAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.25, G:0.11, T:0.28
Consensus pattern (32 bp):
ACTCTTAGCTGATAATAACCAGACCTCAAATC
Found at i:28476804 original size:29 final size:29
Alignment explanation
Indices: 28476765--28476831 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
28476755 AGCAACGAGT
28476765 TGAAGTAAGTGAGGAAAAGGAGGACCTTGA
1 TGAAG-AAGTGAGGAAAAGGAGGACCTTGA
*
28476795 TGAAGAAGTGAGGAATAGGAGGACCTTGA
1 TGAAGAAGTGAGGAAAAGGAGGACCTTGA
28476824 TGAAGAAG
1 TGAAGAAG
28476832 AAGATCCCAC
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.40, C:0.06, G:0.37, T:0.16
Consensus pattern (29 bp):
TGAAGAAGTGAGGAAAAGGAGGACCTTGA
Found at i:28485336 original size:43 final size:44
Alignment explanation
Indices: 28485246--28485392 Score: 147
Period size: 43 Copynumber: 3.4 Consensus size: 44
28485236 ATCGAGATGT
* * * * *
28485246 GATTACATGTAAGACCATGTCTGGGACATTGTCAT-TTTATTGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATGC
*
28485289 GATTACGTATAAGACCATGTCTGGGACATTGGCATCGTTAAT-C
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATGC
* * * * * *
28485332 GATTATGTGTAAGACCCTGTCTGGGATAGTGGCATCGAT-ATGT
1 GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATGC
* *
28485375 GATAACATGTAAGACCAT
1 GATTACGTGTAAGACCAT
28485393 ATATGGGATA
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 2 0.02
43 79 0.93
44 4 0.05
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (44 bp):
GATTACGTGTAAGACCATGTCTGGGACATTGGCATCGTTAATGC
Found at i:28488005 original size:46 final size:46
Alignment explanation
Indices: 28487879--28488038 Score: 146
Period size: 46 Copynumber: 3.4 Consensus size: 46
28487869 TGTGTTACTC
* * * * * *
28487879 TAAGACATGTCTAGGACATGCATTGGCCAC-ATTATGAGAGCCAGTG
1 TAAGACATGTCTGGGACATGCATCGACCTCGA-GATGAGAGCTAGTG
* *
28487925 TAAGACATG-CTTGGGACATGCATCGACTTTGAGATGAGAGCTAGTG
1 TAAGACATGTC-TGGGACATGCATCGACCTCGAGATGAGAGCTAGTG
* * *
28487971 TAAGACATGTCTGGGACATGTATC-AGCCTCGAGATATACAAGCTAGTG
1 TAAGACATGTCTGGGACATGCATCGA-CCTCGAGAT-GA-GAGCTAGTG
*
28488019 TAAGACCTGTCTGGGACATG
1 TAAGACATGTCTGGGACATG
28488039 GCGTCAGCTT
Statistics
Matches: 94, Mismatches: 14, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
45 2 0.02
46 62 0.66
47 3 0.03
48 27 0.29
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.25
Consensus pattern (46 bp):
TAAGACATGTCTGGGACATGCATCGACCTCGAGATGAGAGCTAGTG
Found at i:28488114 original size:49 final size:49
Alignment explanation
Indices: 28487966--28488188 Score: 158
Period size: 49 Copynumber: 4.7 Consensus size: 49
28487956 AGATGAGAGC
* * * * *
28487966 TAGTGTAAGACATGTCTGGGACAT-GTATC-AGCCTCGAGATAT-ACAAGC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGA-CCTCGATAAATGA-AAGT
* * * ***
28488014 TAGTGTAAGACCTGTCTGGGACATGGCGTC-AGCT---T-ATTGTGTGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAAATGAAAGT
* * * *
28488058 TAGTGTAAGACATGTCCGGGACATGGCATTGACACT-GATAAATGAGAGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGAC-CTCGATAAATGAAAGT
* * * *
28488107 TAGTGTAAGACCTATCTGGGACACGGCATCGGCCTCGATATATGAAAGT
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAAATGAAAGT
* * *
28488156 CAGTGTAAGACCTGTTTGGGACATGGCAACGAC
1 TAGTGTAAGACCTGTCTGGGACATGGCATCGAC
28488189 TTTGATGTGC
Statistics
Matches: 134, Mismatches: 33, Indels: 15
0.74 0.18 0.08
Matches are distributed among these distances:
44 28 0.21
45 1 0.01
46 2 0.01
48 28 0.21
49 75 0.56
ACGTcount: A:0.28, C:0.18, G:0.28, T:0.26
Consensus pattern (49 bp):
TAGTGTAAGACCTGTCTGGGACATGGCATCGACCTCGATAAATGAAAGT
Found at i:28505567 original size:43 final size:42
Alignment explanation
Indices: 28505420--28505589 Score: 189
Period size: 43 Copynumber: 4.0 Consensus size: 42
28505410 TAGGATTCCG
* * * * *
28505420 ATATATGATTTCGTGTAAGACCACGTCTCGTACATTGGCATC
1 ATATTTGATTACGTGTAAGACCATGTCTGGGACATTGGCATC
*
28505462 A-ATTTGAGATTTACGTGTAAGACCATGTCTGGGACATTAGCATC
1 ATATTT--GA-TTACGTGTAAGACCATGTCTGGGACATTGGCATC
* ** * *
28505506 ATATTTTATTTTGTGTAAGACCCTGTCTGGGACAGTGGCATC
1 ATATTTGATTACGTGTAAGACCATGTCTGGGACATTGGCATC
*
28505548 GATATTTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
1 -ATATTTGATTACGTGTAAGACCATGTCTGGGACATTGGCAT
28505590 TATACGAGTT
Statistics
Matches: 105, Mismatches: 18, Indels: 9
0.80 0.14 0.07
Matches are distributed among these distances:
41 3 0.03
42 30 0.29
43 38 0.36
44 30 0.29
45 4 0.04
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
ATATTTGATTACGTGTAAGACCATGTCTGGGACATTGGCATC
Found at i:28509945 original size:39 final size:40
Alignment explanation
Indices: 28509844--28510028 Score: 209
Period size: 40 Copynumber: 4.7 Consensus size: 40
28509834 TTGAATGATG
* * * *
28509844 TCCGGGCTAAGTCCCGAAGGCTTTTG-GCTAAGTGAC-CAT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTAAT
* *
28509883 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATACTAAT
1 -TCCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAAT
*
28509924 TCCGGGCTAAG-CCCGAAGGCATTTGTGCGAGTTACTAAA
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
*
28509963 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACT-AT
1 TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
* *
28510002 AACCGGGCTATGTCCCGAAGGCATTTG
1 -TCCGGGCTAAGTCCCGAAGGCATTTG
28510029 AACGAGTAGC
Statistics
Matches: 125, Mismatches: 14, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
39 36 0.29
40 84 0.67
41 5 0.04
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAT
Found at i:28509980 original size:79 final size:80
Alignment explanation
Indices: 28509844--28510028 Score: 225
Period size: 79 Copynumber: 2.3 Consensus size: 80
28509834 TTGAATGATG
* *
28509844 TCCGGGCTAAGTCCCGAAGGCTTTTGGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATTT
1 TCCGGGCTAAGTCCCGAAGGCATTTGGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
28509909 GTGCGAGATACTA-A
66 GTGCGAGATACTATA
* * * **
28509923 TTCCGGGCTAAG-CCCGAAGGCATTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTTG-GCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
*
28509985 TTTGTGCGAGTTACTATA
63 TTTGTGCGAGATACTATA
* *
28510003 ACCGGGCTATGTCCCGAAGGCATTTG
1 TCCGGGCTAAGTCCCGAAGGCATTTG
28510029 AACGAGTAGC
Statistics
Matches: 91, Mismatches: 10, Indels: 8
0.83 0.09 0.07
Matches are distributed among these distances:
78 1 0.01
79 62 0.68
80 28 0.31
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGCTAAGTCCCGAAGGCATTTGGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATTT
GTGCGAGATACTATA
Found at i:28510050 original size:79 final size:79
Alignment explanation
Indices: 28509897--28510061 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
28509887 GGACTAAGAT
* **
28509897 CCGAAGGCATTTGTGCGAGATACTAATTCCGGGCTAAGCCCGAAGGCATTTGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
*
28509962 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
28509976 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGATACTAAT-ACCGGGCTAAG-CCCGAAGGCATTTGAACGAGTTA-C
* *
28510039 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
28510055 CCGAAGG
1 CCGAAGG
28510062 TACGTGATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 48 0.64
80 25 0.33
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATACTAATACCGGGCTAAGCCCGAAGGCATTTGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:28515452 original size:39 final size:39
Alignment explanation
Indices: 28515237--28515459 Score: 218
Period size: 40 Copynumber: 5.6 Consensus size: 39
28515227 TTGAATGCTG
* * * * *
28515237 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
28515277 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
28515316 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
28515357 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* *
28515397 TCCGGGTTAAGTCCCGAAGGCATTGTGTGAGCTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
28515436 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
28515460 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 19, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 38 0.24
40 104 0.67
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.25
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28515479 original size:79 final size:80
Alignment explanation
Indices: 28515317--28515494 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 80
28515307 AGATACAAAT
* * * *
28515317 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
28515382 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * *
28515397 TCCGGGTTAAGTCCCGAAGG-CATTGTGTGAGCTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
28515461 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
28515476 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
28515495 TACGTGATTT
Statistics
Matches: 83, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
78 16 0.19
79 48 0.58
80 19 0.23
ACGTcount: A:0.26, C:0.22, G:0.28, T:0.24
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:28523231 original size:40 final size:39
Alignment explanation
Indices: 28523200--28523409 Score: 242
Period size: 40 Copynumber: 5.3 Consensus size: 39
28523190 GGACTAAGAT
* *
28523200 CCGAAGGCATTTGTGCGAGATACAAATTCCGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGATACAAA-TCCGGGTTAAGTC
* *
28523240 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
* *
28523280 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * *
28523320 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTC
1 CCGAAGGCATTCGTGCGAGATA-CAAATCCGGGTTAAGTC
* * * * *
28523360 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGATAC-AAATCCGGGTTAAGTC
28523399 CCGAAGGCATT
1 CCGAAGGCATT
28523410 TGAACGAGGA
Statistics
Matches: 156, Mismatches: 11, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
39 34 0.22
40 119 0.76
41 3 0.02
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGAAGGCATTCGTGCGAGATACAAATCCGGGTTAAGTC
Found at i:28523363 original size:120 final size:120
Alignment explanation
Indices: 28523147--28523409 Score: 309
Period size: 120 Copynumber: 2.2 Consensus size: 120
28523137 TTGAATGCTG
* *
28523147 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
* *
28523211 TGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
66 CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACTAAA
* * * * **
28523267 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAATCCGGGTTAAG-TCCCGAAGGCAT
1 TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGAT-CCGAAGGCAT
* * * * * *
28523330 TCGTGCGAGTTATTAAA-TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
65 TCGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
* *
28523386 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
28523410 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 19, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
119 38 0.31
120 74 0.61
121 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.27, T:0.26
Consensus pattern (120 bp):
TCCGGGCTAAGTCCCGAAGGCATTCGTGCTAAGTGAATAAATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGATACAAATTCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:28523429 original size:79 final size:80
Alignment explanation
Indices: 28523148--28523444 Score: 230
Period size: 80 Copynumber: 3.7 Consensus size: 80
28523138 TGAATGCTGT
* ** * * * **
28523148 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATTCGAAC-GAGTGACTAAATCCGGGTTAAG-TCCCGAAGGCATT
* * *
28523211 TGTGCGAGATAC-AAATT
64 CGTGCGAGTTACTAAA-A
* * * * **
28523228 CCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGAT-ACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAG-TGACTAAATCCGGGTTAAGTCCCGAAGGCATTC
* *
28523292 GTGCGAGTTATTAAAT
65 GTGCGAGTTACTAAAA
* ** * * *
28523308 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATT-G
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
*
28523372 TGTGAGTTACTAAAA
66 TGCGAGTTACTAAAA
* * * *
28523387 CCGGGCTATGTCCCGAAGGCATTTGAACGAG-GAGCTATATCC-GGTTAAATCCCGAAGG
1 CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGA-CTAAATCCGGGTTAAGTCCCGAAGG
28523445 TACGTGATTT
Statistics
Matches: 183, Mismatches: 28, Indels: 14
0.81 0.12 0.06
Matches are distributed among these distances:
78 15 0.08
79 47 0.26
80 110 0.60
81 11 0.06
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (80 bp):
CCGGGCTAAGTCCCGAAGGCATTCGAACGAGTGACTAAATCCGGGTTAAGTCCCGAAGGCATTCG
TGCGAGTTACTAAAA
Found at i:28527586 original size:43 final size:43
Alignment explanation
Indices: 28527416--28527587 Score: 163
Period size: 43 Copynumber: 4.0 Consensus size: 43
28527406 CATAGGATTC
* * *
28527416 CGATATGTGATTTCATGTAAGACCACGTCTGGGATGTTGGCAT
1 CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
* ** * * *
28527459 CGAT-TTGAGAGTTATGTGTAAGACCATGTCTGGGACATCGGCAT
1 CGATATT-TGA-TTACATGTAAGACCACGTCTGGGACGTTGGCAT
*** *
28527503 CG-TATTTGATTTTGTGTAAGACC-CTATCTGGGACAG-TGGCAT
1 CGATATTTGATTACATGTAAGACCAC-GTCTGGGAC-GTTGGCAT
28527545 CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
28527588 TGTACGAGTT
Statistics
Matches: 102, Mismatches: 19, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
42 30 0.29
43 41 0.40
44 31 0.30
ACGTcount: A:0.24, C:0.17, G:0.27, T:0.32
Consensus pattern (43 bp):
CGATATTTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
Found at i:28532669 original size:45 final size:44
Alignment explanation
Indices: 28532619--28532707 Score: 151
Period size: 45 Copynumber: 2.0 Consensus size: 44
28532609 AAAACATGTG
*
28532619 TCACATATATCATGAACTCAGACCACAACTCAATGAGTTCAGATC
1 TCACATATATCATGAACTCAAACCACAACTC-ATGAGTTCAGATC
*
28532664 TCACATATATCATGAACTCAAATCACAACTCATGAGTTCAGATC
1 TCACATATATCATGAACTCAAACCACAACTCATGAGTTCAGATC
28532708 ACATATTTCC
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 13 0.31
45 29 0.69
ACGTcount: A:0.38, C:0.26, G:0.10, T:0.26
Consensus pattern (44 bp):
TCACATATATCATGAACTCAAACCACAACTCATGAGTTCAGATC
Found at i:28532708 original size:20 final size:20
Alignment explanation
Indices: 28532636--28532710 Score: 60
Period size: 20 Copynumber: 3.5 Consensus size: 20
28532626 TATCATGAAC
*
28532636 TCAGACCACAACTCAATGAGT
1 TCAGATCACAACTC-ATGAGT
* **
28532657 TCAGATCTCACATATATCATGAAC
1 TCAGA--TCACA-A-CTCATGAGT
*
28532681 TCAAATCACAACTCATGAGT
1 TCAGATCACAACTCATGAGT
28532701 TCAGATCACA
1 TCAGATCACA
28532711 TATTTCCTAG
Statistics
Matches: 41, Mismatches: 9, Indels: 9
0.69 0.15 0.15
Matches are distributed among these distances:
20 15 0.37
21 6 0.15
22 5 0.12
23 4 0.10
24 9 0.22
25 2 0.05
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.24
Consensus pattern (20 bp):
TCAGATCACAACTCATGAGT
Found at i:28539219 original size:42 final size:43
Alignment explanation
Indices: 28539158--28539262 Score: 115
Period size: 42 Copynumber: 2.5 Consensus size: 43
28539148 TGAGATTTAT
** *
28539158 GTGTAAGACCATGTCTGGGATATTGGCATCG-TATCT-AATTTC
1 GTGTAAGACCATGTCTGGGATAGAGGCATCGATA-CTGAATTAC
* *
28539200 GTGTAAGACCTTGTTTGGGATAGAGGCATCGATACTGAATTAC
1 GTGTAAGACCATGTCTGGGATAGAGGCATCGATACTGAATTAC
* * *
28539243 ATGTAAGACCACGTCCGGGA
1 GTGTAAGACCATGTCTGGGA
28539263 CGTCGGCATT
Statistics
Matches: 51, Mismatches: 10, Indels: 3
0.80 0.16 0.05
Matches are distributed among these distances:
42 29 0.57
43 22 0.43
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
GTGTAAGACCATGTCTGGGATAGAGGCATCGATACTGAATTAC
Found at i:28541812 original size:39 final size:39
Alignment explanation
Indices: 28541758--28541835 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
28541748 AATAGGAAGA
28541758 CTTAGAAAATTTTCTTGATTTGGAGAGTCACATGCCCGT
1 CTTAGAAAATTTTCTTGATTTGGAGAGTCACATGCCCGT
28541797 CTTAGAAAATTTTCTTGATTTGGAGAGTCACATGCCCGT
1 CTTAGAAAATTTTCTTGATTTGGAGAGTCACATGCCCGT
28541836 GTGGGCAGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (39 bp):
CTTAGAAAATTTTCTTGATTTGGAGAGTCACATGCCCGT
Found at i:28552123 original size:16 final size:16
Alignment explanation
Indices: 28552082--28552124 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
28552072 AAAAACTTGC
*
28552082 CAAAAGTAAAGAAAAA
1 CAAAAGTAAATAAAAA
28552098 -AAATAGTAAATAAAAA
1 CAAA-AGTAAATAAAAA
*
28552114 CAAAATTAAAT
1 CAAAAGTAAAT
28552125 TGCAACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 3 0.13
16 17 0.74
17 3 0.13
ACGTcount: A:0.72, C:0.05, G:0.07, T:0.16
Consensus pattern (16 bp):
CAAAAGTAAATAAAAA
Found at i:28553303 original size:30 final size:30
Alignment explanation
Indices: 28553261--28553337 Score: 104
Period size: 30 Copynumber: 2.6 Consensus size: 30
28553251 CACACGGGTG
*
28553261 TGTGG-TCTACCCGTGTGTCACGCACAGG-CT
1 TGTGGATC-ACCCGTGTGTCACACAC-GGACT
28553291 TGTGGATCACCCGTGTGTCACACACGGACT
1 TGTGGATCACCCGTGTGTCACACACGGACT
*
28553321 TGTGGATCACACGTGTG
1 TGTGGATCACCCGTGTG
28553338 GAAGTGCCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
29 2 0.05
30 39 0.91
31 2 0.05
ACGTcount: A:0.17, C:0.27, G:0.30, T:0.26
Consensus pattern (30 bp):
TGTGGATCACCCGTGTGTCACACACGGACT
Found at i:28557657 original size:48 final size:47
Alignment explanation
Indices: 28557584--28557908 Score: 273
Period size: 50 Copynumber: 6.7 Consensus size: 47
28557574 AGGGTAAGAT
*
28557584 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACATCAAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAC-TCAAG
* * *
28557632 GTCGATGCCATGTCCCAGATATGGTCTTACACTGGCTCTCA-TATATTGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACT-CA---AG
* * ** *
28557682 GCTGATGCCATGTCACAGACATGGTCTTACACTGGCTCTCACTTGTTGAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAC---TCAAG
* * * * * *
28557732 GTCAATGCCATGTCCTAGACATGGTCTTACACTAGCTTTCATATCTCGAG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTC--A-CTCAAG
* * *
28557782 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCATCTCAAT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CTCAAG
* * * * *
28557830 GCCTATGCCATGTTCTAGACATGGTATTACACTGGCTCTTA-T-AATGTG
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTCAA---G
28557878 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
28557909 AGCACACATG
Statistics
Matches: 229, Mismatches: 34, Indels: 30
0.78 0.12 0.10
Matches are distributed among these distances:
45 2 0.01
46 11 0.05
47 13 0.06
48 86 0.38
50 113 0.49
52 1 0.00
53 2 0.01
54 1 0.00
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (47 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTCAAG
Found at i:28557774 original size:100 final size:99
Alignment explanation
Indices: 28557584--28557908 Score: 385
Period size: 100 Copynumber: 3.3 Consensus size: 99
28557574 AGGGTAAGAT
* * * *
28557584 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACAC-ATCAAGGTCGATGCCATGTCCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTATCAATGTCAATGCCATGTCCT
* *
28557648 AGATATGGTCTTACACTGGCTCTCATATATTGAG
66 AGACATGGTCTTACACTGGCTTTCATATATTGAG
* * * **
28557682 GCTGATGCCATGTCACAGACATGGTCTTACACTGGCTCTCACTTGTTGATGTCAATGCCATGTCC
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAC-TATCAATGTCAATGCCATGTCC
* * *
28557747 TAGACATGGTCTTACACTAGCTTTCATATCTCGAG
65 TAGACATGGTCTTACACTGGCTTTCATATATTGAG
* * * * * *
28557782 GCCGATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCA-TCTCAATGCCTATGCCATGTTCT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTATCAATGTCAATGCCATGTCCT
* *
28557846 AGACATGGTATTACACTGGCTCTT-ATA-A-TGTG
66 AGACATGGTCTTACACTGGCT-TTCATATATTGAG
28557878 GCCGATG-CATGTCCCAGACAT-GTCTTACACT
1 GCCGATGCCATGTCCCAGACATGGTCTTACACT
28557909 AGCACACATG
Statistics
Matches: 194, Mismatches: 30, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
94 10 0.05
95 13 0.07
96 9 0.05
98 78 0.40
99 2 0.01
100 82 0.42
ACGTcount: A:0.23, C:0.27, G:0.20, T:0.30
Consensus pattern (99 bp):
GCCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACTATCAATGTCAATGCCATGTCCT
AGACATGGTCTTACACTGGCTTTCATATATTGAG
Found at i:28561500 original size:57 final size:57
Alignment explanation
Indices: 28561407--28561518 Score: 206
Period size: 57 Copynumber: 2.0 Consensus size: 57
28561397 ATGCATATGA
*
28561407 CATAACTTTCATCATCATAACGACACCATCACAATCATGTCATTCATTTCAGGAAGG
1 CATAACTTTCATCATCATAACGACACCATCACAATCATATCATTCATTTCAGGAAGG
*
28561464 CATAACTTTCATCATCATAACGACACCATCATAATCATATCATTCATTTCAGGAA
1 CATAACTTTCATCATCATAACGACACCATCACAATCATATCATTCATTTCAGGAA
28561519 AATTATCGTT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.37, C:0.26, G:0.08, T:0.29
Consensus pattern (57 bp):
CATAACTTTCATCATCATAACGACACCATCACAATCATATCATTCATTTCAGGAAGG
Found at i:28564395 original size:48 final size:48
Alignment explanation
Indices: 28564321--28564595 Score: 213
Period size: 48 Copynumber: 5.7 Consensus size: 48
28564311 AGGGTAAGAT
* *
28564321 GCTGATGCCATGTCTCAGACATGGTCTTACACTGGCTCACACATCAAG
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACATCGAG
** * *
28564369 G-TCGATGCCATGTCCCAGACATGGTCTTACACTAACTCTCATATATCGAG
1 GCT-GATGCCATGTCCCAGACATGGTCTTACACT--GGCTCACACATCGAG
* *
28564419 GCTGA-GCCATGTCCCA-ACATGGTCTTACACTGGCTCACATCTGTTG-G
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACA-C-ATCGAG
* * * * * * *
28564466 TGCTAATGTCATGTCCTAAACATGGTCTTACACTAGCTTTCATATATCGAG
1 -GCTGATGCCATGTCCCAGACATGGTCTTACACTGGC--TCACACATCGAG
* * * * * *
28564517 GCTGATGCCATATCCCAGAGATAGTCTTACACTGGCTCTCATAAT-GTG
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACA-CATCGAG
* *
28564565 GCCGATG-CATGTCCCAGACAT-ATCTTACACT
1 GCTGATGCCATGTCCCAGACATGGTCTTACACT
28564596 AGCACACATG
Statistics
Matches: 178, Mismatches: 36, Indels: 28
0.74 0.15 0.12
Matches are distributed among these distances:
46 14 0.08
47 14 0.08
48 62 0.35
49 22 0.12
50 60 0.34
51 2 0.01
52 4 0.02
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (48 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACATCGAG
Found at i:28564495 original size:98 final size:98
Alignment explanation
Indices: 28564321--28564554 Score: 303
Period size: 98 Copynumber: 2.4 Consensus size: 98
28564311 AGGGTAAGAT
* *
28564321 GCTGATGCCATGTCTCAGACATGGTCTTACACTGGCTCACACATCAAGGTCGATGCCATGTCCCA
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACATCAAGGTCAATGCCATGTCCCA
*
28564386 GACATGGTCTTACACTAACTCTCATATATCGAG
66 AACATGGTCTTACACTAACTCTCATATATCGAG
*** *
28564419 GCTGA-GCCATGTCCCA-ACATGGTCTTACACTGGCTCACATC-TGTTGGTGCTAATGTCATGTC
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACA-CATCAAGGT-C-AATGCCATGTC
* * *
28564481 CTAAACATGGTCTTACACTAGCTTTCATATATCGAG
63 CCAAACATGGTCTTACACTAACTCTCATATATCGAG
* * *
28564517 GCTGATGCCATATCCCAGAGATAGTCTTACACTGGCTC
1 GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTC
28564555 TCATAATGTG
Statistics
Matches: 118, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
96 27 0.23
97 12 0.10
98 51 0.43
99 10 0.08
100 18 0.15
ACGTcount: A:0.24, C:0.27, G:0.20, T:0.29
Consensus pattern (98 bp):
GCTGATGCCATGTCCCAGACATGGTCTTACACTGGCTCACACATCAAGGTCAATGCCATGTCCCA
AACATGGTCTTACACTAACTCTCATATATCGAG
Found at i:28564593 original size:146 final size:146
Alignment explanation
Indices: 28564339--28564604 Score: 326
Period size: 146 Copynumber: 1.8 Consensus size: 146
28564329 CATGTCTCAG
* * *
28564339 ACATGGTCTTACACTGGCTCACACATCAAGGTCGATGCCATGTCCCAGACATGGTCTTACACTAA
1 ACATGGTCTTACACTAGCTCACACATCAAGGTCGATGCCATATCCCAGACATAGTCTTACACTAA
* * * *
28564404 CTCTCATATATCGAGGCTGAGCCATGTCCCAACATGGTCTTACACTGGCTCACATCTGTTGGTGC
66 CTCTCATATATCGAGGCCGAGCCATGTCCCAACATGATCTTACACTAGCACACATCTGTTGGTGC
28564469 TAATGTCATGTCCTAA
131 TAATGTCATGTCCTAA
* * * *
28564485 ACATGGTCTTACACTAGCTTTCATATATCGAGG-CTGATGCCATATCCCAGAGATAGTCTTACAC
1 ACATGGTCTTACACTAGC--TCACACATCAAGGTC-GATGCCATATCCCAGACATAGTCTTACAC
** *
28564549 TGGCTCTCATA-AT-GTGGCCGATG-CATGTCCCAGACAT-ATCTTACACTAGCACACAT
63 TAACTCTCATATATCGAGGCCGA-GCCATGTCCCA-ACATGATCTTACACTAGCACACAT
28564605 GTCCCCCAAA
Statistics
Matches: 101, Mismatches: 14, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
146 48 0.48
147 8 0.08
148 45 0.45
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.28
Consensus pattern (146 bp):
ACATGGTCTTACACTAGCTCACACATCAAGGTCGATGCCATATCCCAGACATAGTCTTACACTAA
CTCTCATATATCGAGGCCGAGCCATGTCCCAACATGATCTTACACTAGCACACATCTGTTGGTGC
TAATGTCATGTCCTAA
Found at i:28570210 original size:563 final size:563
Alignment explanation
Indices: 28569133--28570252 Score: 1875
Period size: 563 Copynumber: 2.0 Consensus size: 563
28569123 AAGGAGGAAG
* * *
28569133 TGTTTTGTATGGTGATCATTACCTATCATCTGGCAGCTAGGCTACACATTATCTGATATGTGTCG
1 TGTTTTGTATGGTGATCATCACCTATCATCTGGCAACTAGGCTACACATTATCTGATATGTGTCA
* * *
28569198 TATGGACACTATGTGGTGTGTAAGGATGGGTGGGTGTTTTTAACCCCACATGGTGTGATGGGATG
66 CATCGACACTATGTGGTGTGTAAGGATGGGTGGGTGTTTTTAACCCCACATGGTGTGATGGGATA
28569263 GACGGAGATGGTGTGTAGAGATGGAGGTAGGACTCACTGTATTTGTTCTGTATATTTGCATAACT
131 GACGGAGATGGTGTGTAGAGATGGAGGTAGGACTCACTGTATTTGTTCTGTATATTTGCATAACT
* * ** *
28569328 ATTTTTTTTATTTGTATCTGAAATGGACATAAGTCTGAATCTACATCTGACTGTATATGAGATTA
196 ATTTCTGTTAGCTATATCTGAAATGGACATAAGTCTGAATCTACATCTGACTGTATATGAGATTA
* * **
28569393 CTGTATGTTTTTCGCGTCAATTTCTGTTGGGTTACACACTGAGTTTTCGTAAATTCACTTTTGTT
261 CTATATGTTTTTCACGTCAATTTCTGTTGGGTTACACACTGAGTTTTCGTAAACCCACTTTTGTT
* * *
28569458 TGTCTATTTTGTACAGGTAATCCACAGACTTAGGCGGATCGGTGTAATAGAGTCTTACGATGACC
326 TGTCTACTTTGTACAGGTAATCCACAGACTTAGGCGGATCGGTGCAACAGAGTCTTACGATGACC
*
28569523 ATTAGTCTACGAATTGATTTTAATTAAAGGTTTAATTATTCAAGGTTTATTTCTAAGAGTTTTGT
391 ATTAGTCTACGAACTGATTTTAATTAAAGGTTTAATTATTCAAGGTTTATTTCTAAGAGTTTTGT
* * **
28569588 ATTAATTGGACTCTCCGTACTGTTGATTTAAATTTTGGGATTTGGATTTTTTGTTTAATAATTTA
456 ATTAATTGGACTCTCCATACTGTTGACTTAAATTTTGGGATTTGGATTTTTCATTTAATAATTTA
* *
28569653 TTAGGACGACTAGCTAAAAACATG-GTTTTTACTAAACCGTAC
521 TTAGGACGACTAGCTAAAAACACGAATTTTTACTAAACCGTAC
* *
28569695 TGTTTTTTATGGTGATCATCGCCTATCATCTGGCAACTAGGCTACACATTATCTGATATGTGTCA
1 TGTTTTGTATGGTGATCATCACCTATCATCTGGCAACTAGGCTACACATTATCTGATATGTGTCA
28569760 CATCGACACTATGTGGTGTGTAAGGATGGGTGGGTGTTTTTAACCCCACATGGTGTGATGGGATA
66 CATCGACACTATGTGGTGTGTAAGGATGGGTGGGTGTTTTTAACCCCACATGGTGTGATGGGATA
* *
28569825 GACGGAGATGGTGTGTAGAGGATGGGGGTAGGACTCACTGTATTTGTTCTGTGTATTTGCATAAC
131 GACGGAGATGGTGTGTAGA-GATGGAGGTAGGACTCACTGTATTTGTTCTGTATATTTGCATAAC
* * *
28569890 TGTTTCTGTTAGCTATATCTGAAATGGACATAAGTTTGAATCTGCATCTGACTGTATATGAGATT
195 TATTTCTGTTAGCTATATCTGAAATGGACATAAGTCTGAATCTACATCTGACTGTATATGAGATT
28569955 ACTATATGTTTTGT-ACGTCAATTTCTGTTGGGTTACACACTGAGTTTTCGTAAACCCACTTTTG
260 ACTATATGTTTT-TCACGTCAATTTCTGTTGGGTTACACACTGAGTTTTCGTAAACCCACTTTTG
* * * *
28570019 TTTGTCTGCTTTGTACAGGTAATCCACAGACTTAGGCGGATCGGTGCAGCGGAGTCTTGCGATGA
324 TTTGTCTACTTTGTACAGGTAATCCACAGACTTAGGCGGATCGGTGCAACAGAGTCTTACGATGA
*
28570084 CCATTAGTCTACGAACTGATTTTAATTAAAGGTTTTATTATTCAAGGTTTATTTCTAAGAGTTTT
389 CCATTAGTCTACGAACTGATTTTAATTAAAGGTTTAATTATTCAAGGTTTATTTCTAAGAGTTTT
28570149 GTATTAATTGGACTCTCCATACTGTTGACTTAAATTTTGGGATTTGGATTTTTCATTTAATAATT
454 GTATTAATTGGACTCTCCATACTGTTGACTTAAATTTTGGGATTTGGATTTTTCATTTAATAATT
28570214 TATTAGGACGACTAGCTAAAAACACGAATTTTTACTAAA
519 TATTAGGACGACTAGCTAAAAACACGAATTTTTACTAAA
28570253 ACAAAGGTTT
Statistics
Matches: 518, Mismatches: 37, Indels: 4
0.93 0.07 0.01
Matches are distributed among these distances:
562 141 0.27
563 365 0.70
564 12 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.39
Consensus pattern (563 bp):
TGTTTTGTATGGTGATCATCACCTATCATCTGGCAACTAGGCTACACATTATCTGATATGTGTCA
CATCGACACTATGTGGTGTGTAAGGATGGGTGGGTGTTTTTAACCCCACATGGTGTGATGGGATA
GACGGAGATGGTGTGTAGAGATGGAGGTAGGACTCACTGTATTTGTTCTGTATATTTGCATAACT
ATTTCTGTTAGCTATATCTGAAATGGACATAAGTCTGAATCTACATCTGACTGTATATGAGATTA
CTATATGTTTTTCACGTCAATTTCTGTTGGGTTACACACTGAGTTTTCGTAAACCCACTTTTGTT
TGTCTACTTTGTACAGGTAATCCACAGACTTAGGCGGATCGGTGCAACAGAGTCTTACGATGACC
ATTAGTCTACGAACTGATTTTAATTAAAGGTTTAATTATTCAAGGTTTATTTCTAAGAGTTTTGT
ATTAATTGGACTCTCCATACTGTTGACTTAAATTTTGGGATTTGGATTTTTCATTTAATAATTTA
TTAGGACGACTAGCTAAAAACACGAATTTTTACTAAACCGTAC
Found at i:28574258 original size:16 final size:16
Alignment explanation
Indices: 28574239--28574269 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28574229 CTTCTTCACT
28574239 TACTCACTTACTTAAA
1 TACTCACTTACTTAAA
*
28574255 TACTTACTTACTTAA
1 TACTCACTTACTTAA
28574270 TCAAATTTAT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (16 bp):
TACTCACTTACTTAAA
Found at i:28574275 original size:20 final size:20
Alignment explanation
Indices: 28574236--28574275 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
28574226 AAACTTCTTC
* *
28574236 ACTTACTCACTTACTTAAAT
1 ACTTACTCACTTAATCAAAT
*
28574256 ACTTACTTACTTAATCAAAT
1 ACTTACTCACTTAATCAAAT
28574276 TTATTAATAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (20 bp):
ACTTACTCACTTAATCAAAT
Found at i:28575343 original size:2 final size:2
Alignment explanation
Indices: 28575336--28575378 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
28575326 AAAGGAAAAT
28575336 TG TG TG TG TG TG TG TG 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 TG TG TG TG TG TG TG TG
28575378 T
1 T
28575379 CATATTGGAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:28575931 original size:39 final size:39
Alignment explanation
Indices: 28575845--28576106 Score: 393
Period size: 39 Copynumber: 6.7 Consensus size: 39
28575835 TAATTAAAGA
* * * * *
28575845 TTATAACCGGGCTAAGACCCGCAGGCCTT-GTG-TGAGAG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTG-GTG
*
28575883 TTATGTCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
28575922 TTATATCCGGGCTAATTCCTGAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
* *
28575961 TTATATCCGAGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
28576000 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
*
28576039 TTATATCCGGGCTAAGTCCCGAAGGTATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
28576078 TTATATCCGGGCTAAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCGAAGGCATT
28576107 TGTGTTGGAA
Statistics
Matches: 207, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
38 24 0.12
39 181 0.87
40 2 0.01
ACGTcount: A:0.19, C:0.22, G:0.30, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCGAAGGCATTCGTGCTGGTG
Found at i:28580117 original size:39 final size:40
Alignment explanation
Indices: 28580072--28580243 Score: 222
Period size: 40 Copynumber: 4.3 Consensus size: 40
28580062 GCTCCTCGTT
* * *
28580072 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
*
28580112 C-AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * *
28580151 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
* * * *
28580191 CAAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCA
1 CAAATGCCTTCGGGACATAACCCGG-ATTTAGTAACTCGCA
28580231 CAAATGCCTTCGG
1 CAAATGCCTTCGG
28580244 ATCTTAGTCC
Statistics
Matches: 119, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
39 35 0.29
40 80 0.67
41 4 0.03
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACATAACCCGGATTTAGTAACTCGCA
Found at i:28580172 original size:40 final size:39
Alignment explanation
Indices: 28580074--28580296 Score: 216
Period size: 40 Copynumber: 5.6 Consensus size: 39
28580064 TCCTCGTTCA
* * * *
28580074 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* *
28580113 AATGCCTTCGGGACATAACCCGGATTTAATAACTCGCAC
1 AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
*
28580152 GAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
* * *
28580192 AAAGGCCTTCGGGGCTTAACCCGGAATTT-GTATCTCGCAC
1 -AATGCCTTCGGGACTTAACCCGG-ATTTAGTAACTCGCAC
** * * * *
28580232 AAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCAC
1 -AATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCAC
* *
28580273 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
28580297 CAGCATTCAA
Statistics
Matches: 157, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
39 40 0.25
40 105 0.67
41 12 0.08
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.26
Consensus pattern (39 bp):
AATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCAC
Found at i:28580256 original size:80 final size:79
Alignment explanation
Indices: 28580072--28580296 Score: 240
Period size: 80 Copynumber: 2.8 Consensus size: 79
28580062 GCTCCTCGTT
* * * * *
28580072 CAAATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACACAATGCCTTCGGGACATAACCCGG-
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGT-ACTCGCACAAAGCCTTCGGGACTTAACCCGGA
28580136 ATTTAATAACTCGCA
65 ATTTAATAACTCGCA
* * *
28580151 CGAATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACAAAGGCCTTCGGGGCTTAACCCGG
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTA-CTCGCACAAA-GCCTTCGGGACTTAACCCGG
* *
28580216 AATTT-GTATCTCGCA
64 AATTTAATAACTCGCA
* * * * *
28580231 CAAATGCCTTC-GGATCTTAGTCCGGATATATTCACTTAGCACAAAGCCTTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGT-AC-TCGCACAAAGCCTTCGGGACTTAACCCG
28580295 GA
63 GA
28580297 CAGCATTCAA
Statistics
Matches: 122, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
78 1 0.01
79 39 0.32
80 69 0.57
81 13 0.11
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (79 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTACTCGCACAAAGCCTTCGGGACTTAACCCGGAA
TTTAATAACTCGCA
Found at i:28580305 original size:41 final size:41
Alignment explanation
Indices: 28580228--28580305 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
28580218 TTTGTATCTC
* * *
28580228 GCACAAATGCCTTCGGATCTTAGTCCGGATATATTCACTTA
1 GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
28580269 GCACAAA-GCCTTCGGGA-CTTAGCCCGGACAGCATTCA
1 GCACAAATGCCTTC-GGATCTTAGCCCGGACA-CATTCA
28580306 ATTAATCATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 17 0.53
41 15 0.47
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (41 bp):
GCACAAATGCCTTCGGATCTTAGCCCGGACACATTCACTTA
Found at i:28584872 original size:31 final size:32
Alignment explanation
Indices: 28584814--28584873 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 32
28584804 TGGTCAAATA
* *
28584814 TAACCGAACATAAGCAAAATGACCAAGCCTTG
1 TAACCGAACATAAGCAAAATAAACAAGCCTTG
*
28584846 TAACCGAACTTAA-CAAAATAAACAAGCC
1 TAACCGAACATAAGCAAAATAAACAAGCC
28584874 ATCTTCGCAT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.48, C:0.25, G:0.12, T:0.15
Consensus pattern (32 bp):
TAACCGAACATAAGCAAAATAAACAAGCCTTG
Found at i:28585612 original size:56 final size:56
Alignment explanation
Indices: 28585532--28585765 Score: 396
Period size: 56 Copynumber: 4.2 Consensus size: 56
28585522 TCCCAAACAG
*
28585532 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACAT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* * * *
28585588 GGTCTTACTCGCACACATATATCAGGATCACATATCAATGCCAACATTTTAAATGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
* *
28585644 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACGTACTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
*
28585700 GGTCTTACTCGCACACGTATATCAGAATCACATATCGATGCCAACATATTAAACGT
1 GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
28585756 GGTCTTACTC
1 GGTCTTACTC
28585766 ATGATCACAA
Statistics
Matches: 164, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 164 1.00
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGCACACATATATCAGAATCACATATCGATGCCAACATATTAAACGT
Found at i:28588220 original size:43 final size:42
Alignment explanation
Indices: 28588151--28588272 Score: 133
Period size: 43 Copynumber: 2.9 Consensus size: 42
28588141 TACTGTACCA
* * *
28588151 ATGCCATATCCCAGATATGGTCTTACAC-ATGATCTCGTATCG
1 ATGCCATATCCCAAATATGGTCTTACACGAAG-TCTCATATCG
*
28588193 ATGCCA-ATAGCCAAACTATGGTCTTACACGAAGTCTCATATCG
1 ATGCCATAT-CCCAAA-TATGGTCTTACACGAAGTCTCATATCG
* *
28588236 ATTCCATATCCCATATATGGTCTTACACGTAA-TCTCA
1 ATGCCATATCCCAAATATGGTCTTACACG-AAGTCTCA
28588273 GTAACCTTAA
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
41 2 0.03
42 29 0.43
43 33 0.49
44 4 0.06
ACGTcount: A:0.30, C:0.26, G:0.14, T:0.30
Consensus pattern (42 bp):
ATGCCATATCCCAAATATGGTCTTACACGAAGTCTCATATCG
Found at i:28588733 original size:13 final size:13
Alignment explanation
Indices: 28588715--28588741 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28588705 TTCATGCTTA
28588715 TAACAGCCCACAT
1 TAACAGCCCACAT
28588728 TAACAGCCCACAT
1 TAACAGCCCACAT
28588741 T
1 T
28588742 TTCCATTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.37, G:0.07, T:0.19
Consensus pattern (13 bp):
TAACAGCCCACAT
Found at i:28591512 original size:40 final size:43
Alignment explanation
Indices: 28591468--28591558 Score: 134
Period size: 44 Copynumber: 2.2 Consensus size: 43
28591458 ACGAATTGAT
28591468 ATAGCTTTGGTTT-A-TG-TGGCACTAAGTGTGCGATATCGAG
1 ATAGCTTTGGTTTAAGTGATGGCACTAAGTGTGCGATATCGAG
**
28591508 ATAGCTTTGGTTTAATGTGATGGCACTAAGTGTGCGATATCGTT
1 ATAGCTTTGGTTTAA-GTGATGGCACTAAGTGTGCGATATCGAG
28591552 ATAGCTT
1 ATAGCTT
28591559 CAGCTAAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 13 0.29
41 1 0.02
43 2 0.04
44 29 0.64
ACGTcount: A:0.23, C:0.12, G:0.27, T:0.37
Consensus pattern (43 bp):
ATAGCTTTGGTTTAAGTGATGGCACTAAGTGTGCGATATCGAG
Found at i:28595532 original size:23 final size:24
Alignment explanation
Indices: 28595486--28595532 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
28595476 AGACCGTATC
* * *
28595486 TAGATCGATTTTTTGTTATGTTCA
1 TAGATCGATATTTTGATATATTCA
28595510 TAGAT-GATATTTTGATATATTCA
1 TAGATCGATATTTTGATATATTCA
28595533 AATGATGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 15 0.75
24 5 0.25
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (24 bp):
TAGATCGATATTTTGATATATTCA
Found at i:28618906 original size:27 final size:27
Alignment explanation
Indices: 28618876--28619053 Score: 187
Period size: 27 Copynumber: 6.6 Consensus size: 27
28618866 ATATTGAGCC
* * * *
28618876 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* * *
28618903 CGCACACTTAGTGCCACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
*
28618930 CGCACACTTAGTGCTACATAGTCAGACT
1 CGCACACTTAGTGCTACATAGTCA-AAT
** * *
28618958 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
28618985 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
28619012 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
28619039 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
28619054 GTACAATTTA
Statistics
Matches: 127, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
27 103 0.81
28 24 0.19
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:28619015 original size:82 final size:81
Alignment explanation
Indices: 28618897--28619052 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
28618887 TGCTATATAA
* * *
28618897 TCAACTCGCACACTTAGTGCCACGTAATCAAATCGCACACTTAGTGCTACATAGTCAGACTCGCA
1 TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCA-AATCGCA
28618962 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
28618979 TCAATTCGCACACTTAGTG-CATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCCA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
28619043 CACTTAGTGC
65 CACTTAGTGC
28619053 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.27
82 48 0.73
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCCACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:28625123 original size:22 final size:22
Alignment explanation
Indices: 28625098--28625141 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
28625088 AATTATTAAC
*
28625098 ATAATGAATTTTAATTAATTTT
1 ATAATAAATTTTAATTAATTTT
*
28625120 ATAATAAATTTTGATTAATTTT
1 ATAATAAATTTTAATTAATTTT
28625142 GATTATTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
ATAATAAATTTTAATTAATTTT
Found at i:28632062 original size:43 final size:43
Alignment explanation
Indices: 28632001--28632085 Score: 161
Period size: 43 Copynumber: 2.0 Consensus size: 43
28631991 TTTTCAAATG
28632001 GCCATTTACGACACACGGTCATGTTACACGGCCGTGTGTCTCA
1 GCCATTTACGACACACGGTCATGTTACACGGCCGTGTGTCTCA
*
28632044 GCCATTTACGACACACGGTCATGTTACATGGCCGTGTGTCTC
1 GCCATTTACGACACACGGTCATGTTACACGGCCGTGTGTCTC
28632086 CTAGGCTACC
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.20, C:0.29, G:0.24, T:0.27
Consensus pattern (43 bp):
GCCATTTACGACACACGGTCATGTTACACGGCCGTGTGTCTCA
Found at i:28639417 original size:22 final size:19
Alignment explanation
Indices: 28639389--28639430 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
28639379 TGATAATCTT
28639389 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
28639411 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
28639430 T
1 T
28639431 CAACTTTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:28642885 original size:27 final size:27
Alignment explanation
Indices: 28642832--28642896 Score: 71
Period size: 28 Copynumber: 2.4 Consensus size: 27
28642822 ATATATAAAT
* *
28642832 ATTATAAAATAATTATTTTGTACTTAA
1 ATTATAAAATAATTAATTTGTAATTAA
*
28642859 ATTATTAACATAATTAATTT-TAATT-A
1 ATTA-TAAAATAATTAATTTGTAATTAA
*
28642885 ATTTTAAAATAA
1 ATTATAAAATAA
28642897 AATTTGATTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
25 7 0.22
26 4 0.12
27 8 0.25
28 13 0.41
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.48
Consensus pattern (27 bp):
ATTATAAAATAATTAATTTGTAATTAA
Found at i:28650355 original size:46 final size:45
Alignment explanation
Indices: 28650206--28650472 Score: 166
Period size: 47 Copynumber: 5.7 Consensus size: 45
28650196 TTATGTAAGT
* * *
28650206 CAGTGTAAGACATGTTTGGGACATGCATCAGCCAC-ATTATGAGAGC
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGA-GATGA-AGC
* * * * * *
28650252 CAGTGTAAGGCCATGTCCGGGACATGGCATTAGCATTGAGA-CAAGTGC
1 CAGTGTAA-GACATGTCTGGGACAT-GCATCAGCCTCGAGATGAA--GC
* * *
28650300 TAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGTAAGC
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATG-AAGC
* * ** *
28650346 CAGTGTAAGACATGTCTGGGACTTGCAT-TGGTTACGAGATGATAGT
1 CAGTGTAAGACATGTCTGGGACATGCATCAGCCT-CGAGATGA-AGC
* * *
28650392 CAGTGTAAGATCATGTCTGGGACAAGGCATCTA--CTTGAGATGTGAGC
1 CAGTGTAAGA-CATGTCTGGGAC-ATGCATC-AGCCTCGAGATG-AAGC
* *
28650439 CAGTGTAAGACCGTGTTTGGGACATGGCATCAGC
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCAGC
28650473 ACCTTACCCA
Statistics
Matches: 169, Mismatches: 35, Indels: 32
0.72 0.15 0.14
Matches are distributed among these distances:
45 3 0.02
46 68 0.40
47 73 0.43
48 24 0.14
49 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.30, T:0.24
Consensus pattern (45 bp):
CAGTGTAAGACATGTCTGGGACATGCATCAGCCTCGAGATGAAGC
Found at i:28660238 original size:46 final size:46
Alignment explanation
Indices: 28660090--28660307 Score: 165
Period size: 46 Copynumber: 4.7 Consensus size: 46
28660080 TTATATGAGT
* * * *
28660090 CAGTGTAAGACATGTCTGGGACATGTATCGGCCAC-ATTATGAGAGC
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGA-GACGAGAGC
* * * ** *
28660136 CAGTGTAAGGCCATGTCCGGGACATGGCATCAGTATTGAGACGA-ATGC
1 CAGTGTAA-GACATGTCTGGGACAT-GCATCGGCCTCGAGACGAGA-GC
* * *
28660184 TAGTGTAAGACATGTCAGGGACATGCTTCGGCCTCGAGACGTA-AGC
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACG-AGAGC
* * * * * *
28660230 CAGTGTAAGACAAGTTTGGGACATGCATC-GACTACGAGATGATAGT
1 CAGTGTAAGACATGTCTGGGACATGCATCGGCCT-CGAGACGAGAGC
28660276 CAGTGTAAGACCATGTCTGGGACATGGCATCG
1 CAGTGTAAGA-CATGTCTGGGACAT-GCATCG
28660308 ACTTGAGATG
Statistics
Matches: 134, Mismatches: 28, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
45 4 0.03
46 64 0.48
47 43 0.32
48 22 0.16
49 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (46 bp):
CAGTGTAAGACATGTCTGGGACATGCATCGGCCTCGAGACGAGAGC
Found at i:28660316 original size:47 final size:45
Alignment explanation
Indices: 28660087--28660356 Score: 149
Period size: 47 Copynumber: 5.8 Consensus size: 45
28660077 CACTTATATG
* * * * *
28660087 AGTCAGTGTAAGACATGTCTGGGACATGTATCGGC-CACATTATGAG
1 AGTCAGTGTAAGACATGTCTGGGACATGCATCGACTC-GA-GATGAT
* * * * *
28660133 AGCCAGTGTAAGGCCATGTCCGGGACATGGCATCAGTA-TTGAGACGA-
1 AGTCAGTGTAA-GACATGTCTGGGACAT-GCATC-G-ACTCGAGATGAT
* * * *
28660180 A-TGCTAGTGTAAGACATGTCAGGGACATGCTTCGGCCTCGAGACG-T
1 AGT-C-AGTGTAAGACATGTCTGGGACATGCATC-GACTCGAGATGAT
* * *
28660226 AAGCCAGTGTAAGACAAGTTTGGGACATGCATCGACTACGAGATGAT
1 -AGTCAGTGTAAGACATGTCTGGGACATGCATCGACT-CGAGATGAT
*
28660273 AGTCAGTGTAAGACCATGTCTGGGACATGGCATCGACTTGAGATG-T
1 AGTCAGTGTAAGA-CATGTCTGGGACAT-GCATCGACTCGAGATGAT
* * *
28660319 GAG-CTAGGGTAGGACCGTGTCTGGGACATGGCATCGAC
1 -AGTC-AGTGTAAGA-CATGTCTGGGACAT-GCATCGAC
28660357 ACCTTACCCA
Statistics
Matches: 177, Mismatches: 30, Indels: 33
0.74 0.12 0.14
Matches are distributed among these distances:
45 3 0.02
46 66 0.37
47 83 0.47
48 23 0.13
49 2 0.01
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (45 bp):
AGTCAGTGTAAGACATGTCTGGGACATGCATCGACTCGAGATGAT
Found at i:28678912 original size:94 final size:94
Alignment explanation
Indices: 28678766--28679069 Score: 338
Period size: 94 Copynumber: 3.2 Consensus size: 94
28678756 GATATAAAAT
*
28678766 ATGTCTGGGACATGCATCGGCCACAATATGAGT-GCTAGTGTAAGACCATGTCTGGGACATGGCA
1 ATGTCTGGGACATGCATCGGCCACGATATGA-TAGCTAGTGTAAGACCATGTCTGGGACATGGCA
28678830 TCGGCGTAGAGATGAGTGCCAGTGTAAGAC
65 TCGGCGTAGAGATGAGTGCCAGTGTAAGAC
* * * *
28678860 ATGTCTGGGAAATGCATCGGCCTCGATGATGATAGCCAGTGTAAGA-CGTGTCTGGGACAT-GCA
1 ATGTCTGGGACATGCATCGGCCACGAT-ATGATAGCTAGTGTAAGACCATGTCTGGGACATGGCA
* *
28678923 TCGGC-TA-AGA-GTTGTGCTAGTGTAAGAC
65 TCGGCGTAGAGATG-AGTGCCAGTGTAAGAC
* * *
28678951 ATGTCTGGGACATGCATCAG-CACGTATATACGAGAGCTAGTGTAAGACCATGTTTGGGACATGG
1 ATGTCTGGGACATGCATCGGCCACG-ATAT--GATAGCTAGTGTAAGACCATGTCTGGGACATGG
*
28679015 CATCGG-GCTCGATGATGA-TAGCCAGTGTAAGACC
63 CATCGGCG-TAGA-GATGAGT-GCCAGTGTAAGA-C
*
28679049 ATGTCTTGGACATGGCATCGG
1 ATGTCTGGGACAT-GCATCGG
28679070 TAACTTATTC
Statistics
Matches: 175, Mismatches: 19, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
90 6 0.03
91 37 0.21
92 16 0.09
93 20 0.11
94 45 0.26
95 16 0.09
96 2 0.01
97 13 0.07
98 14 0.08
99 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (94 bp):
ATGTCTGGGACATGCATCGGCCACGATATGATAGCTAGTGTAAGACCATGTCTGGGACATGGCAT
CGGCGTAGAGATGAGTGCCAGTGTAAGAC
Found at i:28679026 original size:141 final size:141
Alignment explanation
Indices: 28678766--28679069 Score: 386
Period size: 141 Copynumber: 2.1 Consensus size: 141
28678756 GATATAAAAT
28678766 ATGTCTGGGACATGCATCGGCCACAATATGAGTGCTAGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGTCTGGGACATGCATCGGCCACAATAT-AGTGCTAGTGTAAGACCATGTCTGGGACATGGCAT
* * *
28678831 CGGCGTAGAGATGAGTGCCAGTGTAAGACATGTCTGGGAAATGCATCGGCCTCGATGATGATAGC
65 CGACGTAGAGACGAGAGCCAGTGTAAGACATGTCTGGGAAATGCATCGGCCTCGATGATGATAGC
28678896 CAGTGTAAGA-C
130 CAGTGTAAGACC
* *
28678907 GTGTCTGGGACATGCATCGGCTA-AGAGT-T-GTGCTAGTGTAAGA-CATGTCTGGGACAT-GCA
1 ATGTCTGGGACATGCATCGGCCACA-A-TATAGTGCTAGTGTAAGACCATGTCTGGGACATGGCA
* * * * * *
28678967 TCAGCACGTATATACGAGAGCTAGTGTAAGACCATGTTTGGGACATGGCATCGGGCTCGATGATG
64 TC-G-ACGTAGAGACGAGAGCCAGTGTAAGA-CATGTCTGGGAAAT-GCATCGGCCTCGATGATG
28679032 ATAGCCAGTGTAAGACC
125 ATAGCCAGTGTAAGACC
*
28679049 ATGTCTTGGACATGGCATCGG
1 ATGTCTGGGACAT-GCATCGG
28679070 TAACTTATTC
Statistics
Matches: 142, Mismatches: 13, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
137 5 0.04
138 15 0.11
139 34 0.24
140 13 0.09
141 55 0.39
142 13 0.09
143 7 0.05
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (141 bp):
ATGTCTGGGACATGCATCGGCCACAATATAGTGCTAGTGTAAGACCATGTCTGGGACATGGCATC
GACGTAGAGACGAGAGCCAGTGTAAGACATGTCTGGGAAATGCATCGGCCTCGATGATGATAGCC
AGTGTAAGACC
Found at i:28679042 original size:49 final size:46
Alignment explanation
Indices: 28678766--28679069 Score: 273
Period size: 47 Copynumber: 6.4 Consensus size: 46
28678756 GATATAAAAT
* * *
28678766 ATGTCTGGGACATGCATCGGCCACAAT-ATGAGT-GCTAGTGTAAGACC
1 ATGTCTGGGACATGCATCGG-CTCGATGATGA-TAGCCAGTGTAAGA-C
*
28678813 ATGTCTGGGACATGGCATCGGCGTAGA-GATGAGT-GCCAGTGTAAGAC
1 ATGTCTGGGACAT-GCATCGGC-TCGATGATGA-TAGCCAGTGTAAGAC
*
28678860 ATGTCTGGGAAATGCATCGGCCTCGATGATGATAGCCAGTGTAAGAC
1 ATGTCTGGGACATGCATCGG-CTCGATGATGATAGCCAGTGTAAGAC
* * * *
28678907 GTGTCTGGGACATGCATCGGCTAAGA-GTTG-T-GCTAGTGTAAGAC
1 ATGTCTGGGACATGCATCGGCT-CGATGATGATAGCCAGTGTAAGAC
* * * *
28678951 ATGTCTGGGACATGCATCAGCACGTAT-ATACGAGAGCTAGTGTAAGACC
1 ATGTCTGGGACATGCATCGGCTCG-ATGAT--GATAGCCAGTGTAAGA-C
*
28679000 ATGTTTGGGACATGGCATCGGGCTCGATGATGATAGCCAGTGTAAGACC
1 ATGTCTGGGACAT-GCATC-GGCTCGATGATGATAGCCAGTGTAAGA-C
*
28679049 ATGTCTTGGACATGGCATCGG
1 ATGTCTGGGACAT-GCATCGG
28679070 TAACTTATTC
Statistics
Matches: 216, Mismatches: 24, Indels: 33
0.79 0.09 0.12
Matches are distributed among these distances:
43 1 0.00
44 33 0.15
45 1 0.00
46 17 0.08
47 66 0.31
48 39 0.18
49 46 0.21
50 7 0.03
51 6 0.03
ACGTcount: A:0.26, C:0.19, G:0.31, T:0.24
Consensus pattern (46 bp):
ATGTCTGGGACATGCATCGGCTCGATGATGATAGCCAGTGTAAGAC
Found at i:28685663 original size:50 final size:50
Alignment explanation
Indices: 28685617--28685815 Score: 181
Period size: 50 Copynumber: 4.0 Consensus size: 50
28685607 TGCCACATAT
* *
28685617 GTAGCAAAACTATCTGGTACGCATAGTAGCCTGCACTTAGTACCACACA-
1 GTAGCAAAATTATCTGGTACACATAGTAGCCTGCACTTAGTACCACACAC
* * * *
28685666 -T-GCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTAGTACTACACAC
1 GTAGC-A-AAATTATCTGGTACACATAGTAGCCTGCACTTAGTACCACACAC
** * * *
28685716 GT-GACCTAATTATCTGATACACGTAGTAGCCTGCACTTAGTACTACACAC
1 GTAG-CAAAATTATCTGGTACACATAGTAGCCTGCACTTAGTACCACACAC
* * * * * *
28685766 GTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACTTAGTACTACACA
1 GT-AGCAAAATTATCTGGTACACATAGTAGCCTGCACTTAGTACCACACA
28685816 TGCGACCTAG
Statistics
Matches: 125, Mismatches: 18, Indels: 12
0.81 0.12 0.08
Matches are distributed among these distances:
47 2 0.02
48 2 0.02
49 37 0.30
50 43 0.34
51 40 0.32
52 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.19, T:0.25
Consensus pattern (50 bp):
GTAGCAAAATTATCTGGTACACATAGTAGCCTGCACTTAGTACCACACAC
Found at i:28685805 original size:101 final size:99
Alignment explanation
Indices: 28685640--28685824 Score: 271
Period size: 101 Copynumber: 1.8 Consensus size: 99
28685630 CTGGTACGCA
* *
28685640 TAGTAGCCTGCACTTAGTACCACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACTTA
1 TAGTAGCCTGCACTTAGTACCACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
*
28685705 GTACTACACACGTGACCTAATTATCTGATACACG
66 GTACTACACACGCGACCTAATTATCTGATACACG
* * * * *
28685739 TAGTAGCCTGCACTTAGTACTACACACGTGATCGAAGTTATCGGGTACGCATAGTAGCCTGCACT
1 TAGTAGCCTGCACTTAGTACCACACACGCGA-CCAA-TTATCCGGTACACATAGTAGCCTGCACT
*
28685804 TAGTACTACACATGCGACCTA
64 TAGTACTACACACGCGACCTA
28685825 GCTACATATA
Statistics
Matches: 75, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
99 28 0.37
100 3 0.04
101 44 0.59
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (99 bp):
TAGTAGCCTGCACTTAGTACCACACACGCGACCAATTATCCGGTACACATAGTAGCCTGCACTTA
GTACTACACACGCGACCTAATTATCTGATACACG
Found at i:28686459 original size:30 final size:30
Alignment explanation
Indices: 28686425--28686485 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28686415 TCCTTAACTC
28686425 AAACTTTGGAAAAATTACAATTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
* * * * *
28686455 AAACTTTTGCATATTTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTACAATTTTGCCCCT
28686485 A
1 A
28686486 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTACAATTTTGCCCCT
Found at i:28690930 original size:18 final size:18
Alignment explanation
Indices: 28690907--28690944 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
28690897 CTTGGCCCAT
28690907 TGCAGTAATAGTAAACAG
1 TGCAGTAATAGTAAACAG
*
28690925 TGCAGTAATAGTAATCAG
1 TGCAGTAATAGTAAACAG
28690943 TG
1 TG
28690945 TAATAACAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.26
Consensus pattern (18 bp):
TGCAGTAATAGTAAACAG
Found at i:28691322 original size:27 final size:27
Alignment explanation
Indices: 28691285--28691501 Score: 213
Period size: 27 Copynumber: 8.0 Consensus size: 27
28691275 AAATATACAT
* **
28691285 CACATAGGGGCAAAATAGTCATCCTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* *
28691312 CATATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* * * * *
28691339 CTCATAAGAGAAAAATCGTCATTTCAC
1 CACATAAGGGCAAAATAGTCATTTTAC
*
28691366 CACATAAGGGCAAAACT-GTCATTTTAA
1 CACATAAGGGCAAAA-TAGTCATTTTAC
*
28691393 CACATAAGGGCAAAACAGTCATTTTAC
1 CACATAAGGGCAAAATAGTCATTTTAC
* ** *
28691420 CACATAAGAGCAAAACCGTCATTTTAT
1 CACATAAGGGCAAAATAGTCATTTTAC
* * * *
28691447 CACATAAAGGAAAAATCGTCATTTTAA
1 CACATAAGGGCAAAATAGTCATTTTAC
*
28691474 CACATAAGGGCAAAA-AGGTTATTTTAC
1 CACATAAGGGCAAAATA-GTCATTTTAC
28691501 C
1 C
28691502 TTACAGGGGT
Statistics
Matches: 155, Mismatches: 32, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
27 154 0.99
28 1 0.01
ACGTcount: A:0.41, C:0.20, G:0.14, T:0.24
Consensus pattern (27 bp):
CACATAAGGGCAAAATAGTCATTTTAC
Found at i:28691403 original size:81 final size:81
Alignment explanation
Indices: 28691315--28691502 Score: 272
Period size: 81 Copynumber: 2.3 Consensus size: 81
28691305 ATCCTACCAT
* * *
28691315 ATAAGGGCAAAACAGTCATTTTACCTCATAAGAGAAAAATCGTCATTTCACCACATAAGGGCAAA
1 ATAAGGGCAAAACAGTCATTTTACCTCATAAGAGAAAAACCGTCATTTCACCACATAAAGGAAAA
28691380 A-CTGTCATTTTAACAC
66 ATC-GTCATTTTAACAC
* * * *
28691396 ATAAGGGCAAAACAGTCATTTTACCACATAAGAGCAAAACCGTCATTTTATCACATAAAGGAAAA
1 ATAAGGGCAAAACAGTCATTTTACCTCATAAGAGAAAAACCGTCATTTCACCACATAAAGGAAAA
28691461 ATCGTCATTTTAACAC
66 ATCGTCATTTTAACAC
*
28691477 ATAAGGGCAAAA-AGGTTATTTTACCT
1 ATAAGGGCAAAACA-GTCATTTTACCT
28691503 TACAGGGGTA
Statistics
Matches: 96, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
80 1 0.01
81 94 0.98
82 1 0.01
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (81 bp):
ATAAGGGCAAAACAGTCATTTTACCTCATAAGAGAAAAACCGTCATTTCACCACATAAAGGAAAA
ATCGTCATTTTAACAC
Found at i:28691524 original size:27 final size:27
Alignment explanation
Indices: 28691494--28691635 Score: 178
Period size: 27 Copynumber: 5.3 Consensus size: 27
28691484 CAAAAAGGTT
* * *
28691494 ATTTTACCTTACAGGGGTATTACAGTC
1 ATTTTACCCTACAGGGGTATTTCGGTC
* *
28691521 ATTTTACCTTACAGGGGTATTTTGGTC
1 ATTTTACCCTACAGGGGTATTTCGGTC
* *
28691548 ATTTTACCCTA-TGAGGGTATTTTGGTC
1 ATTTTACCCTACAG-GGGTATTTCGGTC
* *
28691575 ATTTTACCCTATAAGGGTATTTCGGTC
1 ATTTTACCCTACAGGGGTATTTCGGTC
*
28691602 ATTTTACCCTATAGGGGTATTTCGGTC
1 ATTTTACCCTACAGGGGTATTTCGGTC
28691629 ATTTTAC
1 ATTTTAC
28691636 AAGTAAATAA
Statistics
Matches: 104, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
26 1 0.01
27 103 0.99
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.42
Consensus pattern (27 bp):
ATTTTACCCTACAGGGGTATTTCGGTC
Found at i:28691549 original size:81 final size:82
Alignment explanation
Indices: 28691464--28691634 Score: 184
Period size: 81 Copynumber: 2.1 Consensus size: 82
28691454 AGGAAAAATC
* * *
28691464 GTCATTTTAACAC-ATAAGGGCAAAAAGGTTATTTTACCTTACAGGGGTATTACAGTCATTTTAC
1 GTCATTTTAACACTATAAGGGCAAAAAGGTCATTTTACCCTACAAGGGTATTACAGTCATTTTAC
* *
28691528 CTTACAGGGGTATTTTG
66 CCTACAGGGGTATTTCG
* * * **** * * *
28691545 GTCATTTT-ACCCTATGAGGGTATTTTGGTCATTTTACCCTATAAGGGTATTTCGGTCATTTTAC
1 GTCATTTTAACACTATAAGGGCAAAAAGGTCATTTTACCCTACAAGGGTATTACAGTCATTTTAC
*
28691609 CCTATAGGGGTATTTCG
66 CCTACAGGGGTATTTCG
28691626 GTCATTTTA
1 GTCATTTTA
28691635 CAAGTAAATA
Statistics
Matches: 72, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
80 3 0.04
81 69 0.96
ACGTcount: A:0.25, C:0.16, G:0.20, T:0.40
Consensus pattern (82 bp):
GTCATTTTAACACTATAAGGGCAAAAAGGTCATTTTACCCTACAAGGGTATTACAGTCATTTTAC
CCTACAGGGGTATTTCG
Found at i:28692045 original size:16 final size:16
Alignment explanation
Indices: 28692024--28692058 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
28692014 ACAACCCACT
28692024 TTTCGGCTTTTCAACC
1 TTTCGGCTTTTCAACC
*
28692040 TTTCGGCTTTTCAGCC
1 TTTCGGCTTTTCAACC
28692056 TTT
1 TTT
28692059 ACAGTTTCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.09, C:0.29, G:0.14, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCAACC
Found at i:28695347 original size:38 final size:38
Alignment explanation
Indices: 28695305--28695381 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
28695295 TTCCAAATTA
* * * *
28695305 ACATGTGTAACCGTGGCGTATCCATTTAGCACCACGTT
1 ACATGTGTAACCATGGCATATCCACTTAGCACCAAGTT
* **
28695343 ACATGTTTAACCATGTTATATCCACTTAGCACCAAGTT
1 ACATGTGTAACCATGGCATATCCACTTAGCACCAAGTT
28695381 A
1 A
28695382 ATGAATCGAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (38 bp):
ACATGTGTAACCATGGCATATCCACTTAGCACCAAGTT
Found at i:28695466 original size:48 final size:48
Alignment explanation
Indices: 28695350--28695483 Score: 162
Period size: 48 Copynumber: 2.8 Consensus size: 48
28695340 GTTACATGTT
* * * *
28695350 TAACCATGTTATATCCACTTAGCACCAAGTTA-ATGAATCGATATAAG
1 TAACCGTGGTATATCCACTTAGCACCAAGTTACATGTATCAATATAAG
* * **
28695397 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCAAGTTACATGTATCAATATAAG
* * *
28695445 TAATCGTGGTATATCCACTTAGCACCATGTTACACGTAT
1 TAACCGTGGTATATCCACTTAGCACCAAGTTACATGTAT
28695484 AACCGTGGTA
Statistics
Matches: 74, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 28 0.38
48 46 0.62
ACGTcount: A:0.32, C:0.22, G:0.15, T:0.31
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCAAGTTACATGTATCAATATAAG
Found at i:28699358 original size:27 final size:27
Alignment explanation
Indices: 28699328--28699387 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
28699318 CCCCGATTTT
* * *
28699328 TAAAATTACTAAAATACCCTTGTAGTG
1 TAAAATTACTAAAATACCCCTATAGGG
*
28699355 TAAAATTACTGAAATACCCCTATAGGG
1 TAAAATTACTAAAATACCCCTATAGGG
28699382 TAAAAT
1 TAAAAT
28699388 GATTGTTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (27 bp):
TAAAATTACTAAAATACCCCTATAGGG
Found at i:28700863 original size:54 final size:54
Alignment explanation
Indices: 28700658--28700863 Score: 202
Period size: 54 Copynumber: 3.8 Consensus size: 54
28700648 TTTCTTTTTA
* * *
28700658 AACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATCCTTGCCTTAT-G
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * * * * *
28700711 AACTCACCATTACCATGCC-TGCGCATGGTCTTACATGGGAT-TTTGCCTTATAG
1 AACTTACCAATGCCATGCCTTG-ACATGGTCTTACATGGTATCCTTGCCTTATAG
** * * * * *
28700764 TAGTTTATCAATGCCATGTCTTGACATGGTCTTACATGATTTCCTTGCCTTGTAG
1 -AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
* * *
28700819 AACTTACCAATGTCATGCCTTGGCATGGTCTTACTTGGTATCCTT
1 AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTT
28700864 AAACCCTAAT
Statistics
Matches: 119, Mismatches: 29, Indels: 9
0.76 0.18 0.06
Matches are distributed among these distances:
52 11 0.09
53 33 0.28
54 63 0.53
55 12 0.10
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.37
Consensus pattern (54 bp):
AACTTACCAATGCCATGCCTTGACATGGTCTTACATGGTATCCTTGCCTTATAG
Found at i:28706821 original size:113 final size:113
Alignment explanation
Indices: 28706623--28706849 Score: 445
Period size: 113 Copynumber: 2.0 Consensus size: 113
28706613 ACTAACTGTA
*
28706623 ACGGGCCTTTCACTACTATCTGGTGGCACCGTCCTTTCTGTGGGAGCGGGTGCGTTACTTTCAAC
1 ACGGGCCTTTCACTACTATCTGGTGGCACCATCCTTTCTGTGGGAGCGGGTGCGTTACTTTCAAC
28706688 ATCACCTGCACCAACTCGTTCAGGATCCATAACTATAAAATCGTCAGG
66 ATCACCTGCACCAACTCGTTCAGGATCCATAACTATAAAATCGTCAGG
28706736 ACGGGCCTTTCACTACTATCTGGTGGCACCATCCTTTCTGTGGGAGCGGGTGCGTTACTTTCAAC
1 ACGGGCCTTTCACTACTATCTGGTGGCACCATCCTTTCTGTGGGAGCGGGTGCGTTACTTTCAAC
28706801 ATCACCTGCACCAACTCGTTCAGGATCCATAACTATAAAATCGTCAGG
66 ATCACCTGCACCAACTCGTTCAGGATCCATAACTATAAAATCGTCAGG
28706849 A
1 A
28706850 GTCGTCACAC
Statistics
Matches: 113, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 113 1.00
ACGTcount: A:0.23, C:0.28, G:0.22, T:0.27
Consensus pattern (113 bp):
ACGGGCCTTTCACTACTATCTGGTGGCACCATCCTTTCTGTGGGAGCGGGTGCGTTACTTTCAAC
ATCACCTGCACCAACTCGTTCAGGATCCATAACTATAAAATCGTCAGG
Found at i:28707500 original size:16 final size:16
Alignment explanation
Indices: 28707479--28707511 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28707469 ATGAAAGTAG
28707479 ACTCATTAAGGAATCT
1 ACTCATTAAGGAATCT
28707495 ACTCATTAAGGAATCT
1 ACTCATTAAGGAATCT
28707511 A
1 A
28707512 AAAATAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.30
Consensus pattern (16 bp):
ACTCATTAAGGAATCT
Found at i:28719773 original size:33 final size:35
Alignment explanation
Indices: 28719707--28719782 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 35
28719697 TTTAGCCCCT
*
28719707 CTTTCAGTAGCAGTAGCAGTCTAGGCCTGAGCCCA
1 CTTTCAGTAACAGTAGCAGTCTAGGCCTGAGCCCA
* *
28719742 -TTTCAGTAACAGTGGCAGTCT-GGCCTTAGCCCA
1 CTTTCAGTAACAGTAGCAGTCTAGGCCTGAGCCCA
28719775 CTTT-AGTA
1 CTTTCAGTA
28719783 TAGTATGCAA
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
33 15 0.41
34 22 0.59
ACGTcount: A:0.22, C:0.26, G:0.24, T:0.28
Consensus pattern (35 bp):
CTTTCAGTAACAGTAGCAGTCTAGGCCTGAGCCCA
Found at i:28724227 original size:25 final size:25
Alignment explanation
Indices: 28724182--28724229 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
28724172 AGCACATAAT
*
28724182 CAGGAAGCTCATGTGAGCCATGTAA
1 CAGGAAGCTCATGAGAGCCATGTAA
28724207 CAGGAAGCTCATGAGAGCCATGT
1 CAGGAAGCTCATGAGAGCCATGT
28724230 CGGGAAGCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (25 bp):
CAGGAAGCTCATGAGAGCCATGTAA
Found at i:28724235 original size:23 final size:24
Alignment explanation
Indices: 28724182--28724238 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
28724172 AGCACATAAT
*
28724182 CAGGAAGCTCATGTGAGCCATGTAA
1 CAGGAAGCTCATGAGAGCCATGT-A
28724207 CAGGAAGCTCATGAGAGCCATGT-
1 CAGGAAGCTCATGAGAGCCATGTA
*
28724230 CGGGAAGCT
1 CAGGAAGCT
28724239 AGTGCAAGCC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 8 0.27
25 22 0.73
ACGTcount: A:0.30, C:0.21, G:0.32, T:0.18
Consensus pattern (24 bp):
CAGGAAGCTCATGAGAGCCATGTA
Found at i:28724368 original size:26 final size:26
Alignment explanation
Indices: 28724265--28724395 Score: 82
Period size: 26 Copynumber: 5.2 Consensus size: 26
28724255 GGGTAACTTG
*
28724265 AAGAGTCAT-TAAT-GGGAAGCTC-T
1 AAGAGCCATGTAATCGGGAAGCTCAT
* * *
28724288 AGATAGCCATAT-ATCGGGAAGTTCA-
1 A-AGAGCCATGTAATCGGGAAGCTCAT
* *
28724313 AGTGAGCCAT-T-ATCGGGAAGCTCACA
1 A-AGAGCCATGTAATCGGGAAGCTCA-T
* *
28724339 AAGAGTC-TTTAATCGGGAAGCTCAT
1 AAGAGCCATGTAATCGGGAAGCTCAT
*
28724364 GAAGAGCCATGTAAT-GGGATGCTCAT
1 -AAGAGCCATGTAATCGGGAAGCTCAT
28724390 AAGAGC
1 AAGAGC
28724396 TAAGGTATGT
Statistics
Matches: 86, Mismatches: 12, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
23 1 0.01
24 22 0.26
25 28 0.33
26 30 0.35
27 5 0.06
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.23
Consensus pattern (26 bp):
AAGAGCCATGTAATCGGGAAGCTCAT
Found at i:28726066 original size:7 final size:7
Alignment explanation
Indices: 28726054--28726080 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
28726044 AATAAATCAC
28726054 AATAAAG
1 AATAAAG
28726061 AATAAAG
1 AATAAAG
28726068 AATAAAG
1 AATAAAG
28726075 AATAAA
1 AATAAA
28726081 TTTGTAGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (7 bp):
AATAAAG
Found at i:28731907 original size:46 final size:46
Alignment explanation
Indices: 28731857--28732032 Score: 216
Period size: 46 Copynumber: 3.8 Consensus size: 46
28731847 TGGTTGAGCA
28731857 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28731903 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
*
28731948 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
28731996 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28732033 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 10, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 63 0.57
47 29 0.26
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:28732013 original size:93 final size:93
Alignment explanation
Indices: 28731854--28732025 Score: 317
Period size: 93 Copynumber: 1.8 Consensus size: 93
28731844 GGATGGTTGA
* *
28731854 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28731919 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
28731947 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
28732012 TGAGTCCGAGTTCG
66 TGAGTCCGAGTTCG
28732026 CTTATGGGCG
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 76 1.00
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:28733372 original size:92 final size:92
Alignment explanation
Indices: 28733215--28733399 Score: 361
Period size: 92 Copynumber: 2.0 Consensus size: 92
28733205 TGACTGTGAT
28733215 GCAAGTAGCTTAAAAGCTGTGAATGTAGAAATAAATAATCCAAAGTTCTAAATATGTTAAATTAA
1 GCAAGTAGCTTAAAAGCTGTGAATGTAGAAATAAATAATCCAAAGTTCTAAATATGTTAAATTAA
28733280 GCTTAGTAACACCTCATACTCGACTCC
66 GCTTAGTAACACCTCATACTCGACTCC
28733307 GCAAGTAGCTTAAAAGCTGTGAATGTAGAAATAAATAATCCAAAGTTCTAAATATGTTAAATTAA
1 GCAAGTAGCTTAAAAGCTGTGAATGTAGAAATAAATAATCCAAAGTTCTAAATATGTTAAATTAA
*
28733372 GCTTAGTAACACTTCATACTCGACTCC
66 GCTTAGTAACACCTCATACTCGACTCC
28733399 G
1 G
28733400 GCAACGGTCT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
92 92 1.00
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (92 bp):
GCAAGTAGCTTAAAAGCTGTGAATGTAGAAATAAATAATCCAAAGTTCTAAATATGTTAAATTAA
GCTTAGTAACACCTCATACTCGACTCC
Found at i:28734742 original size:43 final size:42
Alignment explanation
Indices: 28734620--28734742 Score: 131
Period size: 43 Copynumber: 2.9 Consensus size: 42
28734610 AGTACCGTAC
* * * * *
28734620 CAATGTCATATCCCAGATATGGTCTTACATGTAATCTCGTAT
1 CAATGCCATATCCCACATATGGTCTTACACGTAGTCTCATAT
* * * *
28734662 CGATGCCAATAGCCAAGC-TATGGTCTTACACGAAGTCTCATAT
1 CAATGCC-ATATCCCA-CATATGGTCTTACACGTAGTCTCATAT
28734705 CAATGCCATATCCCACATATGGTCTTACACGTTAGTCT
1 CAATGCCATATCCCACATATGGTCTTACACG-TAGTCT
28734743 TAGTGACCCT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 25 0.39
43 38 0.59
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.31
Consensus pattern (42 bp):
CAATGCCATATCCCACATATGGTCTTACACGTAGTCTCATAT
Found at i:28745049 original size:27 final size:27
Alignment explanation
Indices: 28745019--28745073 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
28745009 AAAAAACTAA
*
28745019 ATACAATTAAACATTATTTTATAATAT
1 ATACAATTAAACATTATATTATAATAT
*
28745046 ATACAATTAAATATTATATTATAATAT
1 ATACAATTAAACATTATATTATAATAT
28745073 A
1 A
28745074 CAAATTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (27 bp):
ATACAATTAAACATTATATTATAATAT
Found at i:28745387 original size:22 final size:22
Alignment explanation
Indices: 28745348--28745389 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28745338 AGTTAGACCT
*
28745348 TTTTTTCTGTTTGTTTTATTCA
1 TTTTTTCTATTTGTTTTATTCA
28745370 TTTTTTCTATTT-TCTTTATT
1 TTTTTTCTATTTGT-TTTATT
28745390 TTTCCCAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.10, C:0.10, G:0.05, T:0.76
Consensus pattern (22 bp):
TTTTTTCTATTTGTTTTATTCA
Found at i:28754085 original size:30 final size:30
Alignment explanation
Indices: 28754051--28754111 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
28754041 TTCTTAATAC
*
28754051 AAACTTTGGAAAAATTAAATTTTTGCCCCT
1 AAACTTTGGAAAAATTAAACTTTTGCCCCT
* * * *
28754081 AAACTTTTGCATAATTACACTTTTGCCCCT
1 AAACTTTGGAAAAATTAAACTTTTGCCCCT
28754111 A
1 A
28754112 GGCTCGGGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.38
Consensus pattern (30 bp):
AAACTTTGGAAAAATTAAACTTTTGCCCCT
Found at i:28760575 original size:16 final size:16
Alignment explanation
Indices: 28760556--28760591 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
28760546 ACTGTCTTTC
28760556 TGCTCGTCAATGTTAA
1 TGCTCGTCAATGTTAA
**
28760572 TGCTTTTCAATGTTAA
1 TGCTCGTCAATGTTAA
28760588 TGCT
1 TGCT
28760592 TGGATTCTCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (16 bp):
TGCTCGTCAATGTTAA
Found at i:28760592 original size:16 final size:16
Alignment explanation
Indices: 28760562--28760592 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28760552 TTTCTGCTCG
28760562 TCAATGTTAATGCTTT
1 TCAATGTTAATGCTTT
28760578 TCAATGTTAATGCTT
1 TCAATGTTAATGCTT
28760593 GGATTCTCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.13, G:0.13, T:0.48
Consensus pattern (16 bp):
TCAATGTTAATGCTTT
Found at i:28763548 original size:28 final size:28
Alignment explanation
Indices: 28763515--28763570 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
28763505 AAATTAATTA
*
28763515 AATTATGAATTAATACACATTTCTGGAC
1 AATTATGAATTAATACACATTACTGGAC
28763543 AATTATGAATTAATACACATTACTGGAC
1 AATTATGAATTAATACACATTACTGGAC
28763571 CGTCTTAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (28 bp):
AATTATGAATTAATACACATTACTGGAC
Found at i:28763714 original size:22 final size:21
Alignment explanation
Indices: 28763684--28763725 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
28763674 TGTCGAAAAT
28763684 AGTAAAAATTAA-TCAAAATTA
1 AGTAAAAATTAACT-AAAATTA
28763705 AGTATAAAATTAACTAAAATT
1 AGTA-AAAATTAACTAAAATT
28763726 CACCATTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 4 0.21
22 14 0.74
23 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (21 bp):
AGTAAAAATTAACTAAAATTA
Found at i:28764832 original size:51 final size:51
Alignment explanation
Indices: 28764755--28764851 Score: 142
Period size: 51 Copynumber: 1.9 Consensus size: 51
28764745 CGGATACACG
*
28764755 GTGGCCTTCACATAGCACCACCCTTGTAG-CCAAACCTATTTTATTCTCAAA
1 GTGGCCTTCACATAGCACCACACTTGT-GTCCAAACCTATTTTATTCTCAAA
* **
28764806 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGCACCACACTTGTGTCCAAACCTATTTTATTC
28764852 CTAAGGTTCA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.02
51 40 0.98
ACGTcount: A:0.26, C:0.28, G:0.13, T:0.33
Consensus pattern (51 bp):
GTGGCCTTCACATAGCACCACACTTGTGTCCAAACCTATTTTATTCTCAAA
Found at i:28764931 original size:52 final size:52
Alignment explanation
Indices: 28764875--28765003 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
28764865 GGAAAATTTC
28764875 TCACTTAGCACCA-TGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
1 TCACTTAGCA-CATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
* *
28764927 TCACTTAGCACATTGCCATGGTCTTATTTCACTTAGATGCCATGGTCTTATT
1 TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
28764979 TCACTTAGCACATTGCCATGGACTT
1 TCACTTAGCACATTGCCATGGACTT
28765004 TAGAATAACC
Statistics
Matches: 73, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
51 2 0.03
52 71 0.97
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (52 bp):
TCACTTAGCACATTGCCATGGACTTATTTCACTTAGATGCCATGGACTTATT
Found at i:28764944 original size:28 final size:27
Alignment explanation
Indices: 28764875--28765003 Score: 171
Period size: 24 Copynumber: 4.9 Consensus size: 27
28764865 GGAAAATTTC
28764875 TCACTTAGCACCATGCCATGGACTTATT
1 TCACTTAGCA-CATGCCATGGACTTATT
28764903 TCACTTAG---ATGCCATGGACTTATT
1 TCACTTAGCACATGCCATGGACTTATT
*
28764927 TCACTTAGCACATTGCCATGGTCTTATT
1 TCACTTAGCACA-TGCCATGGACTTATT
*
28764955 TCACTTAG---ATGCCATGGTCTTATT
1 TCACTTAGCACATGCCATGGACTTATT
28764979 TCACTTAGCACATTGCCATGGACTT
1 TCACTTAGCACA-TGCCATGGACTT
28765004 TAGAATAACC
Statistics
Matches: 91, Mismatches: 2, Indels: 16
0.83 0.02 0.15
Matches are distributed among these distances:
24 47 0.52
25 1 0.01
27 2 0.02
28 41 0.45
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (27 bp):
TCACTTAGCACATGCCATGGACTTATT
Found at i:28767658 original size:51 final size:51
Alignment explanation
Indices: 28767600--28767696 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 51
28767590 CGGATACACG
*
28767600 GTGGCCTTCACATAGTACCACCCTTGTAG-CCAAACCTATTTTATTCTCAAA
1 GTGGCCTTCACATAGTACCACACTTGT-GTCCAAACCTATTTTATTCTCAAA
**
28767651 GTGGCCTTCACATAGTACCACACTTGTGTCCAAAGTTATTTTATTC
1 GTGGCCTTCACATAGTACCACACTTGTGTCCAAACCTATTTTATTC
28767697 CTAAGGTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
50 1 0.02
51 41 0.98
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (51 bp):
GTGGCCTTCACATAGTACCACACTTGTGTCCAAACCTATTTTATTCTCAAA
Done.