Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A08
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: 123748673
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 5630000 characters in sequence are not A, C, G, or T
File 131 of 373
Found at i:43294855 original size:43 final size:43
Alignment explanation
Indices: 43294756--43294872 Score: 123
Period size: 42 Copynumber: 2.7 Consensus size: 43
43294746 TCTAAGATGT
* * * * *
43294756 TGGCATCGACT-TATGATTTACGTGTAAGACCATGTCTGGGGCAT
1 TGGCATCGA-TATTTGATTT-CATGTAAGACCATGTCTAGGACAG
* *
43294800 TGGCATCG-TATTTGATTTCATGTAAGACCCTGTTTAGGACAG
1 TGGCATCGATATTTGATTTCATGTAAGACCATGTCTAGGACAG
43294842 TGGCATCGATATTTGATTAT-ATGTAAGACCA
1 TGGCATCGATATTTGATT-TCATGTAAGACCA
43294873 CGTTTGTTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
42 27 0.44
43 26 0.42
44 9 0.15
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (43 bp):
TGGCATCGATATTTGATTTCATGTAAGACCATGTCTAGGACAG
Found at i:43297772 original size:33 final size:33
Alignment explanation
Indices: 43297735--43297805 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
43297725 AACAGCGCAT
* * *
43297735 ACAGTAACGGTCTGGGCCTAA-CCCTATTCATTA
1 ACAGT-ACAGTCTGGGCCTAAGCCCTATGCAGTA
* *
43297768 ACAGTACAGTCTTGGCCTAAGTCCTATGCAGTA
1 ACAGTACAGTCTGGGCCTAAGCCCTATGCAGTA
43297801 ACAGT
1 ACAGT
43297806 GTGGGCCTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (33 bp):
ACAGTACAGTCTGGGCCTAAGCCCTATGCAGTA
Found at i:43297967 original size:23 final size:23
Alignment explanation
Indices: 43297940--43298003 Score: 92
Period size: 23 Copynumber: 2.8 Consensus size: 23
43297930 ACCAATATCG
*
43297940 CAGCATAGCTGCTAATAGTAACA
1 CAGCAAAGCTGCTAATAGTAACA
* *
43297963 TAGCAAAGCTGCTAATAGTAACG
1 CAGCAAAGCTGCTAATAGTAACA
*
43297986 CAGCAAAGCTACTAATAG
1 CAGCAAAGCTGCTAATAG
43298004 CAGTAAACGT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (23 bp):
CAGCAAAGCTGCTAATAGTAACA
Found at i:43304689 original size:9 final size:9
Alignment explanation
Indices: 43304670--43304706 Score: 58
Period size: 9 Copynumber: 4.1 Consensus size: 9
43304660 TGAGTTTTTG
43304670 AATTCGAAT
1 AATTCGAAT
43304679 AACTT-GAAT
1 AA-TTCGAAT
43304688 AATTCGAAT
1 AATTCGAAT
43304697 AATTCGAAT
1 AATTCGAAT
43304706 A
1 A
43304707 TCAAACTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 2 0.08
9 22 0.85
10 2 0.08
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:43304814 original size:31 final size:31
Alignment explanation
Indices: 43304748--43304809 Score: 101
Period size: 29 Copynumber: 2.1 Consensus size: 31
43304738 AACTTCCAAA
*
43304748 CCTTCTTACTTTTTACCTCAAAACTTTTACT
1 CCTTCTTACTTTCTACCTCAAAACTTTTACT
43304779 CCTTCTTACTTTCT-CC-CAAAACTTTTACT
1 CCTTCTTACTTTCTACCTCAAAACTTTTACT
43304808 CC
1 CC
43304810 CCTTCCATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 15 0.50
30 2 0.07
31 13 0.43
ACGTcount: A:0.21, C:0.34, G:0.00, T:0.45
Consensus pattern (31 bp):
CCTTCTTACTTTCTACCTCAAAACTTTTACT
Found at i:43305945 original size:44 final size:44
Alignment explanation
Indices: 43305891--43306040 Score: 184
Period size: 43 Copynumber: 3.5 Consensus size: 44
43305881 TATGAGTTCT
*
43305891 CATGTAAGACCACGTCTGGGACTTTGGCATCGAT-TTATGATTTA
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATT-TGATTTA
* * *
43305935 CTTGTAAGACCATGTCTGGGACATTGACATCG-TATTTGATTT-
1 CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
* *
43305977 CATGTAAGACC-CTGTCTGGGACAGTGGCATTGATATTTGA-TTA
1 CATGTAAGACCAC-GTCTGGGACATTGGCATCGATATTTGATTTA
*
43306020 CATGTAAGACTACGTCTGGGA
1 CATGTAAGACCACGTCTGGGA
43306041 TGTTGGTATT
Statistics
Matches: 91, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
42 28 0.31
43 32 0.35
44 31 0.34
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (44 bp):
CATGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTTA
Found at i:43306014 original size:43 final size:43
Alignment explanation
Indices: 43305890--43306029 Score: 169
Period size: 44 Copynumber: 3.3 Consensus size: 43
43305880 ATATGAGTTC
*
43305890 TCATGTAAGACCAC-GTCTGGGACTTTGGCATCGAT-TTATGATT
1 TCATGTAAGACC-CTGTCTGGGACATTGGCATCGATATT-TGATT
* * *
43305933 TACTTGTAAGACCATGTCTGGGACATTGACATCG-TATTTGATT
1 T-CATGTAAGACCCTGTCTGGGACATTGGCATCGATATTTGATT
* *
43305976 TCATGTAAGACCCTGTCTGGGACAGTGGCATTGATATTTGATT
1 TCATGTAAGACCCTGTCTGGGACATTGGCATCGATATTTGATT
*
43306019 ACATGTAAGAC
1 TCATGTAAGAC
43306030 TACGTCTGGG
Statistics
Matches: 83, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
42 27 0.33
43 27 0.33
44 29 0.35
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (43 bp):
TCATGTAAGACCCTGTCTGGGACATTGGCATCGATATTTGATT
Found at i:43309430 original size:27 final size:27
Alignment explanation
Indices: 43309400--43309533 Score: 169
Period size: 27 Copynumber: 5.0 Consensus size: 27
43309390 ATAGTCATTT
* ** *
43309400 TACCCTCCAGGGGTAAATCAGTAGTTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* * *
43309427 TACCTTACAAGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
43309454 TACCCTACAGGGGTATTTCGGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
*
43309481 TACCCTATAGGGGTATTTCAGTAATTC
1 TACCCTACAGGGGTATTTCAGTAATTC
* *
43309508 TACCCTACAGGGTTATTTGAGTAATT
1 TACCCTACAGGGGTATTTCAGTAATT
43309534 TTTTAAATCG
Statistics
Matches: 93, Mismatches: 14, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 93 1.00
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.34
Consensus pattern (27 bp):
TACCCTACAGGGGTATTTCAGTAATTC
Found at i:43309586 original size:27 final size:27
Alignment explanation
Indices: 43309528--43309625 Score: 119
Period size: 27 Copynumber: 3.6 Consensus size: 27
43309518 GGTTATTTGA
* *
43309528 GTAATTTTTTAAATCGAAGGTAAAACT-
1 GTAATTCTGTAAATCGAAGGTAAAA-TG
* *
43309555 ATAATTCTGTAAATCGATGGTAAAATG
1 GTAATTCTGTAAATCGAAGGTAAAATG
*
43309582 GTAATTCTATAAATC-AAGGGTAAAATG
1 GTAATTCTGTAAATCGAA-GGTAAAATG
43309609 GTAATTCTGTAAATCGA
1 GTAATTCTGTAAATCGA
43309626 CTGTAAATCG
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
26 2 0.03
27 57 0.95
28 1 0.02
ACGTcount: A:0.41, C:0.08, G:0.17, T:0.34
Consensus pattern (27 bp):
GTAATTCTGTAAATCGAAGGTAAAATG
Found at i:43309665 original size:65 final size:65
Alignment explanation
Indices: 43309561--43309690 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
43309551 AACTATAATT
* *
43309561 CTGTAAATCGATGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTGTAAATCGA
1 CTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTATAAATCGA
43309626 CTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTATAAATCGA
1 CTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTATAAATCGA
43309691 GGGTACTTTG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.41, C:0.09, G:0.20, T:0.30
Consensus pattern (65 bp):
CTGTAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGGTAAAATGGTAATTCTATAAATCGA
Found at i:43309670 original size:38 final size:38
Alignment explanation
Indices: 43309591--43309670 Score: 115
Period size: 38 Copynumber: 2.1 Consensus size: 38
43309581 GGTAATTCTA
* * *
43309591 TAAATCAAGGGTAAAATGGTAATTCTGTAAATCGACTG
1 TAAATCAAGGGTAAAATGGTAATTCTATAAATCAACGG
* *
43309629 TAAATCGAGGGTAAAATGGTAATTCTATAAATCAAGGG
1 TAAATCAAGGGTAAAATGGTAATTCTATAAATCAACGG
43309667 TAAA
1 TAAA
43309671 ATGGTAATTC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.42, C:0.09, G:0.21, T:0.28
Consensus pattern (38 bp):
TAAATCAAGGGTAAAATGGTAATTCTATAAATCAACGG
Found at i:43309706 original size:27 final size:27
Alignment explanation
Indices: 43309629--43309695 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
43309619 AAATCGACTG
43309629 TAAATCGAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
*
43309656 TAAATCAAGGGTAAAATGGTAATTCTA
1 TAAATCGAGGGTAAAATGGTAATTCTA
43309683 TAAATCGAGGGTA
1 TAAATCGAGGGTA
43309696 CTTTGGTAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.42, C:0.07, G:0.22, T:0.28
Consensus pattern (27 bp):
TAAATCGAGGGTAAAATGGTAATTCTA
Found at i:43312391 original size:43 final size:42
Alignment explanation
Indices: 43312336--43312490 Score: 129
Period size: 43 Copynumber: 3.7 Consensus size: 42
43312326 ATATCGTACA
* * * *
43312336 ATGCCAAC-GTCCCAAACATGGTCTTATATGTAATCATATCTCG
1 ATGCC-ACTGTCCCAAACATGGTCTTACACGTAATCAAAT-ACG
* *
43312379 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAATACG
1 ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATACG
* * *
43312420 ATGGCGA-TGTCCCAAACATGGTCTTACACGTAATCACATATCA
1 AT-GCCACTGTCCCAAACATGGTCTTACACGTAATCAAATA-CG
* * *
43312463 ATGCCAAC-GTCCCAGACCTAGTCTTACA
1 ATGCC-ACTGTCCCAAACATGGTCTTACA
43312491 TGAATACACA
Statistics
Matches: 91, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
41 25 0.27
42 22 0.24
43 44 0.48
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (42 bp):
ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATACG
Found at i:43312443 original size:41 final size:43
Alignment explanation
Indices: 43312336--43312455 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 43
43312326 ATATCGTACA
* * * *
43312336 ATGCCAAC-GTCCCAAACATGGTCTTATATGTAATCATATCTCG
1 ATGCC-ACTGTCCCAAACATGGTCTTACACGTAATCAAATCACG
* *
43312379 ATGCCACTGTCCCAGACAGGGTCTTACACG-AATCAAAT-ACG
1 ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATCACG
*
43312420 ATGGCGA-TGTCCCAAACATGGTCTTACACGTAATCA
1 AT-GCCACTGTCCCAAACATGGTCTTACACGTAATCA
43312456 CATATCAATG
Statistics
Matches: 65, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
41 25 0.38
42 17 0.26
43 23 0.35
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (43 bp):
ATGCCACTGTCCCAAACATGGTCTTACACGTAATCAAATCACG
Found at i:43317067 original size:24 final size:24
Alignment explanation
Indices: 43317040--43317137 Score: 115
Period size: 24 Copynumber: 4.0 Consensus size: 24
43317030 AAGGCTGTTA
43317040 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
43317064 GGAGAGGATTTAGGGGTTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * * *
43317088 GGACAGGATTTAGAAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
*
43317112 GGAGAAGATTTAGGAGTTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
43317137 G
1 G
43317138 AGCAAGAGTT
Statistics
Matches: 60, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
24 57 0.95
25 3 0.05
ACGTcount: A:0.36, C:0.04, G:0.38, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:43319993 original size:40 final size:40
Alignment explanation
Indices: 43319895--43320237 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
43319885 TCCTCGTTCA
* * * * *
43319895 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
43319934 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43319974 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43320014 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43320054 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43320094 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
43320134 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
43320174 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
43320214 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43320238 CAGCATTCAA
Statistics
Matches: 278, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.13
40 233 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:43327426 original size:40 final size:40
Alignment explanation
Indices: 43327328--43327670 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
43327318 TCCTCGTTCA
* * * * *
43327328 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* *
43327367 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43327407 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
*
43327447 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43327487 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
43327527 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * *
43327567 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
* * * * * *
43327607 AAGGCCTTC-GGATCTTAATCCGGATATATTCACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTAATAAC-TCGCACG
* *
43327647 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
43327671 CAGCATTCAA
Statistics
Matches: 278, Mismatches: 22, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 37 0.13
40 233 0.84
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
Found at i:43329236 original size:27 final size:26
Alignment explanation
Indices: 43329196--43329306 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
43329186 AGGAAGCATC
* *
43329196 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
43329223 CTGGTGGCTCTGCCACATACATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
43329250 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* **
43329277 CTGGTGACTCTATCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
43329303 CTGG
1 CTGG
43329307 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 16 0.21
27 57 0.76
28 2 0.03
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:43329280 original size:54 final size:53
Alignment explanation
Indices: 43329196--43329306 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
43329186 AGGAAGCATC
* *
43329196 CTGGTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATACATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACAT-CATCTGTT
* * * *
43329250 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACTCTATCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATCATCTGTT
43329303 CTGG
1 CTGG
43329307 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 11 0.22
54 40 0.78
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTACCACATCATCTGTT
Found at i:43329402 original size:21 final size:18
Alignment explanation
Indices: 43329369--43329407 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 18
43329359 CTCCCCACAT
43329369 GGTGAAAGGTTGGTATGGG
1 GGTGAAAGGTTGG-ATGGG
43329388 GGTGAATATGGTTGGATGGG
1 GGTGAA-A-GGTTGGATGGG
43329408 TTTCGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.33
20 6 0.33
21 6 0.33
ACGTcount: A:0.21, C:0.00, G:0.51, T:0.28
Consensus pattern (18 bp):
GGTGAAAGGTTGGATGGG
Found at i:43330304 original size:15 final size:16
Alignment explanation
Indices: 43330264--43330303 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
43330254 TTAGAATGGG
43330264 TTTACAAAAACAAAGA
1 TTTACAAAAACAAAGA
*
43330280 TTTTCAAAAACAAA-A
1 TTTACAAAAACAAAGA
43330295 TTTA-AAAAA
1 TTTACAAAAA
43330304 AAACTTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
14 5 0.23
15 4 0.18
16 13 0.59
ACGTcount: A:0.62, C:0.10, G:0.03, T:0.25
Consensus pattern (16 bp):
TTTACAAAAACAAAGA
Found at i:43334146 original size:32 final size:32
Alignment explanation
Indices: 43334105--43334168 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
43334095 GGAGAGGGTA
* *
43334105 ACCATGGACTTTGTGAGTGGGTTGCCTTTGAC
1 ACCATGGACTTTGTGAGTGGATTGACTTTGAC
43334137 ACCATGGACTTTGTGAGTGGATTGACTTTGAC
1 ACCATGGACTTTGTGAGTGGATTGACTTTGAC
43334169 TTTGTGAGTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.19, C:0.17, G:0.30, T:0.34
Consensus pattern (32 bp):
ACCATGGACTTTGTGAGTGGATTGACTTTGAC
Found at i:43335615 original size:24 final size:24
Alignment explanation
Indices: 43335588--43335685 Score: 133
Period size: 24 Copynumber: 4.0 Consensus size: 24
43335578 AAGGCTGTCA
43335588 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
43335612 GGAGAGGATTTAGGGGTTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
43335636 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
*
43335660 GGAGAAGATTTAGGAGTTGATCAAG
1 GGAGAAGATTTAGGAGCTGAT-AAG
43335685 G
1 G
43335686 AGCAAGAGTT
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
24 61 0.95
25 3 0.05
ACGTcount: A:0.35, C:0.03, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:43335664 original size:48 final size:49
Alignment explanation
Indices: 43335588--43335685 Score: 153
Period size: 48 Copynumber: 2.0 Consensus size: 49
43335578 AAGGCTGTCA
* * *
43335588 GGAGAAGATTTAGGAGCTGATAAGGGAGAGGATTTAGGGGTTGAT-AAG
1 GGAGAAGATTTAGGAGCTGATAAAGGAGAAGATTTAGGAGTTGATCAAG
*
43335636 GGAGAGGATTTAGGAGCTGATAAAGGAGAAGATTTAGGAGTTGATCAAG
1 GGAGAAGATTTAGGAGCTGATAAAGGAGAAGATTTAGGAGTTGATCAAG
43335685 G
1 G
43335686 AGCAAGAGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
48 41 0.91
49 4 0.09
ACGTcount: A:0.35, C:0.03, G:0.40, T:0.22
Consensus pattern (49 bp):
GGAGAAGATTTAGGAGCTGATAAAGGAGAAGATTTAGGAGTTGATCAAG
Found at i:43337117 original size:27 final size:26
Alignment explanation
Indices: 43337077--43337187 Score: 132
Period size: 27 Copynumber: 4.2 Consensus size: 26
43337067 AGGAAGCGTC
* *
43337077 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
43337104 CTGGTGGCTCTGCCACATACATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
43337131 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* * * *
43337158 CTAGTGACTCTGTCACATTATCTATT
1 CTGGTGGCTCTGCCACATTATCTGTT
43337184 CTGG
1 CTGG
43337188 CAGCCATGCT
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
26 14 0.19
27 57 0.78
28 2 0.03
ACGTcount: A:0.18, C:0.25, G:0.21, T:0.36
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:43343432 original size:24 final size:24
Alignment explanation
Indices: 43343399--43343488 Score: 126
Period size: 24 Copynumber: 3.8 Consensus size: 24
43343389 AAGGTTATCA
43343399 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* * *
43343423 GGAGAGGATTTAGGGGGTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
43343447 GGAGAGGATTTAGGAGCTGATAAA
1 GGAGAAGATTTAGGAGCTGATAAG
*
43343471 GGATAAGATTTAGGAGCT
1 GGAGAAGATTTAGGAGCT
43343489 AATCAAGGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.34, C:0.03, G:0.40, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:43344976 original size:54 final size:53
Alignment explanation
Indices: 43344892--43345002 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 53
43344882 AGGAAGCGTC
* *
43344892 CTGGTGGCTATGCCACAATTATTTGATCTGGTGGCTCTGCCACATACATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-CATCTGTT
* * * *
43344946 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATCATCTGTT
43344999 CTGG
1 CTGG
43345003 CAGCCATGCT
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
53 11 0.22
54 40 0.78
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATCATCTGTT
Found at i:43344999 original size:26 final size:26
Alignment explanation
Indices: 43344892--43345002 Score: 141
Period size: 27 Copynumber: 4.2 Consensus size: 26
43344882 AGGAAGCGTC
* * *
43344892 CTGGTGGCTATGCCACAATTATTTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
*
43344919 CTGGTGGCTCTGCCACATACATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
43344946 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* *
43344973 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
43344999 CTGG
1 CTGG
43345003 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 7, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
26 16 0.21
27 57 0.76
28 2 0.03
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:43347358 original size:27 final size:27
Alignment explanation
Indices: 43347328--43347505 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43347318 ATATTGAGTC
* * * *
43347328 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43347355 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43347382 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43347410 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43347437 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43347464 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43347491 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43347506 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43347467 original size:82 final size:81
Alignment explanation
Indices: 43347349--43347504 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43347339 TGCTATATAA
* *
43347349 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43347414 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43347431 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43347495 CACTTAGTGC
65 CACTTAGTGC
43347505 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43347998 original size:12 final size:12
Alignment explanation
Indices: 43347981--43348006 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43347971 ATGGCATACT
43347981 TATGTATATATA
1 TATGTATATATA
43347993 TATGTATATATA
1 TATGTATATATA
43348005 TA
1 TA
43348007 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:43355258 original size:27 final size:27
Alignment explanation
Indices: 43355228--43355405 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
43355218 ATATTGAGTC
* * * *
43355228 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
43355255 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43355282 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
43355310 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
43355337 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
43355364 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
43355391 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
43355406 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:43355367 original size:82 final size:81
Alignment explanation
Indices: 43355249--43355404 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
43355239 TGCTATATAA
* *
43355249 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
43355314 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
43355331 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
43355395 CACTTAGTGC
65 CACTTAGTGC
43355405 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:43355897 original size:12 final size:12
Alignment explanation
Indices: 43355880--43355905 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
43355870 ATGGCATACT
43355880 TATGTATATATA
1 TATGTATATATA
43355892 TATGTATATATA
1 TATGTATATATA
43355904 TA
1 TA
43355906 CTTCGGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (12 bp):
TATGTATATATA
Found at i:43358894 original size:39 final size:41
Alignment explanation
Indices: 43358851--43358962 Score: 124
Period size: 40 Copynumber: 2.8 Consensus size: 41
43358841 AGATTTAGTT
* *
43358851 GCATTAGCGGCGTTTTTTTAAAAAGCGCCGCTAATA-A-TG-
1 GCATTAGCGGCGCTTTTTCAAAAA-CGCCGCTAATAGATTGA
* *
43358890 GCATTAGCGGCGCTTTGTCAAAAACGCTGC-AATAGATTGA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAATAGATTGA
* * *
43358930 GTATTAGCGGCGCTTTTTGAAAAATGCCGCTAA
1 GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAA
43358963 AGCTCAATAA
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
37 4 0.07
38 6 0.10
39 23 0.38
40 25 0.42
41 2 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (41 bp):
GCATTAGCGGCGCTTTTTCAAAAACGCCGCTAATAGATTGA
Found at i:43359018 original size:13 final size:14
Alignment explanation
Indices: 43359000--43359032 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
43358990 GATTAATATG
*
43359000 GGTTTAGGGTTG-T
1 GGTTTAGGATTGAT
43359013 GGTTTAGGATTGAT
1 GGTTTAGGATTGAT
43359027 GGTTTA
1 GGTTTA
43359033 TGTTTTATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.15, C:0.00, G:0.39, T:0.45
Consensus pattern (14 bp):
GGTTTAGGATTGAT
Found at i:43359286 original size:6 final size:6
Alignment explanation
Indices: 43359275--43359308 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
43359265 AAATAAAGTC
43359275 TTATTT TTATTT TTATTT TTA-TT TTA-TT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
43359309 GATCATATCT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.37
6 17 0.63
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (6 bp):
TTATTT
Found at i:43359499 original size:16 final size:17
Alignment explanation
Indices: 43359465--43359508 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
43359455 ATGATTTTAT
43359465 CTAAACCC-T-AACGCA
1 CTAAACCCTTAAACGCA
43359480 CTAAACCCTTAAAC-CA
1 CTAAACCCTTAAACGCA
*
43359496 CTAAACCTTTAAA
1 CTAAACCCTTAAA
43359509 ACCTTAAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 8 0.31
16 15 0.58
17 3 0.12
ACGTcount: A:0.43, C:0.34, G:0.02, T:0.20
Consensus pattern (17 bp):
CTAAACCCTTAAACGCA
Found at i:43359644 original size:21 final size:21
Alignment explanation
Indices: 43359614--43359658 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
43359604 CCTAAATCTC
*
43359614 AAACCTTAAAT-ATAAACCCT
1 AAACCTTAAATCAAAAACCCT
43359634 AAACTCTTAAATCAAAAACCCT
1 AAAC-CTTAAATCAAAAACCCT
43359656 AAA
1 AAA
43359659 ATATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.18
21 7 0.32
22 11 0.50
ACGTcount: A:0.53, C:0.24, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCTTAAATCAAAAACCCT
Found at i:43359665 original size:22 final size:21
Alignment explanation
Indices: 43359619--43359671 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
43359609 ATCTCAAACC
* * *
43359619 TTAAATATAAACCCTAAACTC
1 TTAAATAAAAACCCTAAAATA
43359640 TTAAATCAAAAACCCTAAAATA
1 TTAAAT-AAAAACCCTAAAATA
43359662 TTAAA-AAAAA
1 TTAAATAAAAA
43359672 TTAATATAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 5 0.18
21 6 0.21
22 17 0.61
ACGTcount: A:0.58, C:0.17, G:0.00, T:0.25
Consensus pattern (21 bp):
TTAAATAAAAACCCTAAAATA
Found at i:43360200 original size:7 final size:7
Alignment explanation
Indices: 43360159--43360231 Score: 62
Period size: 7 Copynumber: 10.1 Consensus size: 7
43360149 TTAGGGCATT
43360159 GGGTTTA
1 GGGTTTA
43360166 GGGATTTA
1 GGG-TTTA
43360174 GGGTATT-
1 GGGT-TTA
43360181 GGGTATTA
1 GGGT-TTA
*
43360189 -TGTTTA
1 GGGTTTA
43360195 GGGTTTA
1 GGGTTTA
*
43360202 -GCTTATA
1 GGGTT-TA
43360209 GGGTTTA
1 GGGTTTA
43360216 GGGTATTA
1 GGGT-TTA
43360224 GGGTTTA
1 GGGTTTA
43360231 G
1 G
43360232 TCTATTGGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
6 6 0.11
7 30 0.55
8 19 0.35
ACGTcount: A:0.19, C:0.01, G:0.37, T:0.42
Consensus pattern (7 bp):
GGGTTTA
Found at i:43363767 original size:3 final size:3
Alignment explanation
Indices: 43363761--43363794 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
43363751 ATTATTATTA
*
43363761 TTG TTG TTG TTG TTG TTG TTT TTG TTG TTTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG -TTG TTG
43363795 ATTCGAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.00, C:0.00, G:0.29, T:0.71
Consensus pattern (3 bp):
TTG
Found at i:43364252 original size:36 final size:36
Alignment explanation
Indices: 43364211--43364329 Score: 139
Period size: 36 Copynumber: 3.1 Consensus size: 36
43364201 ACCCACATAA
*
43364211 TACATAAATATATATCATATCATAAGTTACATAACT
1 TACATAAATATATATCATATCATAACTTACATAACT
*
43364247 TACATAGTACATAAATATATGTCATATCATAACTTACATACCT
1 TACATA--A-AT--ATATA--TCATATCATAACTTACATAACT
* *
43364290 TACATAAATGTATATCATAACATAACTTACATAACT
1 TACATAAATATATATCATATCATAACTTACATAACT
43364326 TACA
1 TACA
43364330 AAACTTACGT
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
36 30 0.42
38 5 0.07
39 2 0.03
40 2 0.03
41 6 0.08
43 26 0.37
ACGTcount: A:0.45, C:0.17, G:0.03, T:0.34
Consensus pattern (36 bp):
TACATAAATATATATCATATCATAACTTACATAACT
Found at i:43364266 original size:43 final size:42
Alignment explanation
Indices: 43364205--43364329 Score: 154
Period size: 43 Copynumber: 3.1 Consensus size: 42
43364195 TACTTAACCC
*
43364205 ACATAATACATAAATATATATCATATCATAAGTTACATAACTT
1 ACAT-ATACATAAATATATATCATATCATAACTTACATAACTT
*
43364248 ACATAGTACATAAATATATGTCATATCATAACTTACAT-AC--
1 ACATA-TACATAAATATATATCATATCATAACTTACATAACTT
* *
43364288 -C-T-TACATAAATGTATATCATAACATAACTTACATAACTT
1 ACATATACATAAATATATATCATATCATAACTTACATAACTT
43364327 ACA
1 ACA
43364330 AAACTTACGT
Statistics
Matches: 71, Mismatches: 5, Indels: 14
0.79 0.06 0.16
Matches are distributed among these distances:
36 29 0.41
37 2 0.03
38 1 0.01
39 1 0.01
40 1 0.01
42 3 0.04
43 34 0.48
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (42 bp):
ACATATACATAAATATATATCATATCATAACTTACATAACTT
Found at i:43364286 original size:9 final size:9
Alignment explanation
Indices: 43364274--43364337 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
43364264 TATGTCATAT
43364274 CATAACTTA
1 CATAACTTA
*
43364283 CATACCTTA
1 CATAACTTA
*
43364292 CATAAATGTA
1 CATAACT-TA
* * *
43364302 TATCA-TAA
1 CATAACTTA
43364310 CATAACTTA
1 CATAACTTA
43364319 CATAACTTA
1 CATAACTTA
*
43364328 CAAAACTTA
1 CATAACTTA
43364337 C
1 C
43364338 GTAATACATA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
8 4 0.09
9 34 0.79
10 5 0.12
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (9 bp):
CATAACTTA
Found at i:43369448 original size:13 final size:14
Alignment explanation
Indices: 43369432--43369460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43369422 TTATAAATAT
43369432 TTATAAT-GTTTAA
1 TTATAATAGTTTAA
43369445 TTATAATAGTTTAA
1 TTATAATAGTTTAA
43369459 TT
1 TT
43369461 CGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATAATAGTTTAA
Found at i:43369899 original size:21 final size:21
Alignment explanation
Indices: 43369867--43369918 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43369857 ACAACTTAGA
*
43369867 GCAGAGGCAGCAG-AGAGGGAG
1 GCAGAGGTAGCAGCA-AGGGAG
*
43369888 GCAGCGGTAGCAGCAAGGGAG
1 GCAGAGGTAGCAGCAAGGGAG
43369909 GCAGAGGTAG
1 GCAGAGGTAG
43369919 TAGTGATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.50, T:0.04
Consensus pattern (21 bp):
GCAGAGGTAGCAGCAAGGGAG
Found at i:43370368 original size:43 final size:43
Alignment explanation
Indices: 43370318--43370409 Score: 130
Period size: 43 Copynumber: 2.1 Consensus size: 43
43370308 CGGCTAAAAG
* * *
43370318 TGACTTTTAGCGGCGCTTTTCCAACAAACACCGCTAAAAGCTA
1 TGACTTTTAGCGACACTTTTCCAACAAACACCGCTAAAAGCCA
** *
43370361 TGACTTTTAGCGACACTTTTTTAACAAACGCCGCTAAAAGCCA
1 TGACTTTTAGCGACACTTTTCCAACAAACACCGCTAAAAGCCA
43370404 TGACTT
1 TGACTT
43370410 ATAGTGGCTG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (43 bp):
TGACTTTTAGCGACACTTTTCCAACAAACACCGCTAAAAGCCA
Found at i:43376309 original size:40 final size:40
Alignment explanation
Indices: 43376226--43376568 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
43376216 TTGAATGCTG
* * * * * *
43376226 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
43376266 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
43376306 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
43376346 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
43376386 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
43376426 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
43376466 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
43376506 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
43376545 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43376569 TGAACGAGGA
Statistics
Matches: 279, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.13
40 236 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:43383742 original size:40 final size:40
Alignment explanation
Indices: 43383659--43384001 Score: 476
Period size: 40 Copynumber: 8.6 Consensus size: 40
43383649 TTGAATGCTG
* * * * * *
43383659 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGC-GAGTTATTAAA
* * * * *
43383699 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTAAG-TCCCGAAGGCATTCGTGCGAGTTATTAAA
43383739 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
43383779 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
43383819 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
43383859 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
*
43383899 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
43383939 TCCGGGTTATGTCCCGAAGGCATT-GTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
* * *
43383978 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
43384002 TGAACGAGGA
Statistics
Matches: 279, Mismatches: 21, Indels: 7
0.91 0.07 0.02
Matches are distributed among these distances:
39 35 0.13
40 236 0.85
41 8 0.03
ACGTcount: A:0.24, C:0.20, G:0.28, T:0.27
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
Found at i:43386268 original size:19 final size:19
Alignment explanation
Indices: 43386241--43386277 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43386231 TTAGTAAAAA
*
43386241 ATGTTTATCACACATCAAG
1 ATGTGTATCACACATCAAG
43386260 ATGTGTATCACACATCAA
1 ATGTGTATCACACATCAA
43386278 ACATTCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (19 bp):
ATGTGTATCACACATCAAG
Found at i:43396463 original size:24 final size:25
Alignment explanation
Indices: 43396419--43396468 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
43396409 ACTCTTCTCA
* *
43396419 TCTCTTCAATTCTCTCTCATTTTTC
1 TCTCTTCAATTCCCTCTCATTGTTC
43396444 TCTCTTC-ATTCCCT-TCCATTGTTC
1 TCTCTTCAATTCCCTCT-CATTGTTC
43396468 T
1 T
43396469 TCACTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.10, C:0.34, G:0.02, T:0.54
Consensus pattern (25 bp):
TCTCTTCAATTCCCTCTCATTGTTC
Found at i:43399396 original size:17 final size:18
Alignment explanation
Indices: 43399374--43399408 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
43399364 TCACATTGAA
43399374 GTGTTTT-ATTGAAAACC
1 GTGTTTTCATTGAAAACC
43399391 GTGTTTTCATTGAAAACC
1 GTGTTTTCATTGAAAACC
43399409 CTTCTTTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (18 bp):
GTGTTTTCATTGAAAACC
Found at i:43400319 original size:26 final size:27
Alignment explanation
Indices: 43400290--43400342 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43400280 ATAAATCTTA
43400290 CATTC-AACACATAGGGGTATTTTAGT
1 CATTCTAACACATAGGGGTATTTTAGT
* * *
43400316 CATTCTCACCCTTAGGGGTATTTTAGT
1 CATTCTAACACATAGGGGTATTTTAGT
43400343 AATTTCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
CATTCTAACACATAGGGGTATTTTAGT
Found at i:43400685 original size:28 final size:28
Alignment explanation
Indices: 43400653--43400707 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
43400643 ATACATGCAT
*
43400653 ATGGCTCACTAGG-CCCAATCACATTCAA
1 ATGGCCCA-TAGGCCCCAATCACATTCAA
*
43400681 ATGGCCCATCGGCCCCAATCACATTCA
1 ATGGCCCATAGGCCCCAATCACATTCA
43400708 TAGTCATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.29, C:0.36, G:0.15, T:0.20
Consensus pattern (28 bp):
ATGGCCCATAGGCCCCAATCACATTCAA
Found at i:43403588 original size:27 final size:27
Alignment explanation
Indices: 43403554--43403745 Score: 215
Period size: 27 Copynumber: 7.1 Consensus size: 27
43403544 TGGATAAGTT
* *
43403554 GTAGAATTATCGAAATACCCCTGTAAG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
43403581 GTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
** *
43403608 GTAGAATTATTGAAATACCCCTCTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
43403635 GTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * ** * *
43403662 ATAGAATTATCGAAATATTCTTGTTGG
1 GTAGAATTACCGAAATACCCCTGTAGG
*
43403689 GTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTACCGAAATACCCCTGTAGG
* * * *
43403716 GTAGGACTACC-AATTTACCCCTGAAGG
1 GTAGAATTACCGAA-ATACCCCTGTAGG
43403743 GTA
1 GTA
43403746 AACTGACTAT
Statistics
Matches: 137, Mismatches: 27, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
26 2 0.01
27 135 0.99
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (27 bp):
GTAGAATTACCGAAATACCCCTGTAGG
Found at i:43403629 original size:54 final size:54
Alignment explanation
Indices: 43403554--43403719 Score: 242
Period size: 54 Copynumber: 3.1 Consensus size: 54
43403544 TGGATAAGTT
* *
43403554 GTAGAATTATCGAAATACCCCTGTAAGGTAGAATTACCGAAATACCCTTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
* *
43403608 GTAGAATTATTGAAATACCCCTCTAGGGTAGAATTACCGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
* ** * * *
43403662 ATAGAATTATCGAAATATTCTTGTTGGGTAGAAATACCGAAATACCCCTGTAGG
1 GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
43403716 GTAG
1 GTAG
43403720 GACTACCAAT
Statistics
Matches: 99, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.27
Consensus pattern (54 bp):
GTAGAATTATCGAAATACCCCTGTAGGGTAGAATTACCGAAATACCCCTGTAGG
Found at i:43410620 original size:40 final size:40
Alignment explanation
Indices: 43410576--43410825 Score: 342
Period size: 40 Copynumber: 6.3 Consensus size: 40
43410566 GGACTAAGAT
* * * * *
43410576 CCGAAGGCATTTGTGCGAGATA-CAAATTCTGGGTTAAGCC
1 CCGAAGGCATTCGTGCGAGTTATTAAA-TCCGGGTTAAGTC
* * * *
43410616 CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43410656 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43410696 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
*
43410736 CCGAAGGCATTCGTGCGAGTTATTAAATCTGGGTTAAGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
* * * * *
43410776 CCGAAGGCATT-GTGTGAGTTACTAAAACCGGGCTATGTC
1 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
43410815 CCGAAGGCATT
1 CCGAAGGCATT
43410826 TGAACGAGGA
Statistics
Matches: 194, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
39 33 0.17
40 158 0.81
41 3 0.02
ACGTcount: A:0.26, C:0.20, G:0.28, T:0.26
Consensus pattern (40 bp):
CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTC
Found at i:43410660 original size:80 final size:80
Alignment explanation
Indices: 43410523--43410825 Score: 362
Period size: 80 Copynumber: 3.8 Consensus size: 80
43410513 TTGAATGCTG
* * * * * **
43410523 TCTGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCAT
1 TCTGGGTTAAGTCCCGAAGGCCTTTGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCAT
* * *
43410586 TTGTGCGAGATA-CAAA
64 TCGTGCGAGTTATTAAA
* *
43410602 TTCTGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATT
1 -TCTGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
43410667 CGTGCGAGTTATTAAA
65 CGTGCGAGTTATTAAA
* * * *
43410683 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCTGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
43410748 GTGCGAGTTATTAAA
66 GTGCGAGTTATTAAA
* * * * *
43410763 TCTGGGTTAAGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TCTGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATT
43410826 TGAACGAGGA
Statistics
Matches: 193, Mismatches: 27, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
79 36 0.19
80 146 0.76
81 11 0.06
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (80 bp):
TCTGGGTTAAGTCCCGAAGGCCTTTGTGCGAGTTACTAAATCCGGGTTAAGTCCCGAAGGCATTC
GTGCGAGTTATTAAA
Found at i:43410743 original size:120 final size:119
Alignment explanation
Indices: 43410530--43410825 Score: 344
Period size: 120 Copynumber: 2.5 Consensus size: 119
43410520 CTGTCTGGGC
* * * * * * * *
43410530 TAAGTCCCGAAGGCTTTGTGCTAAGTGAATATATCCGGACTAAGAT-CCGAAGGCATTTGTGCGA
1 TAAGTCCCGAAGGCATTGTGC-GAGTTACTAAAACCGGGCTAAG-TCCCGAAGGCATTCGTGCGA
* * *
43410594 GATACAAATTCTGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGT
64 GATACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGT
* * *
43410650 TAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTAAGTCCCGAAGGCATTCGTGCGAG
1 TAAGTCCCGAAGGCATT-GTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGTGCGAG
* * * * * *
43410715 TTATTAAA-TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAATCTGGGT
65 ATA-CAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGT
* *
43410770 TAAGTCCCGAAGGCATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATT
1 TAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATT
43410826 TGAACGAGGA
Statistics
Matches: 151, Mismatches: 22, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
119 35 0.23
120 109 0.72
121 7 0.05
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.27
Consensus pattern (119 bp):
TAAGTCCCGAAGGCATTGTGCGAGTTACTAAAACCGGGCTAAGTCCCGAAGGCATTCGTGCGAGA
TACAAATTCCGGGTTAAGCCCCGAAGGCATTCGTGCGAGATACTAAATCCGGGT
Found at i:43422783 original size:26 final size:26
Alignment explanation
Indices: 43422754--43422809 Score: 103
Period size: 26 Copynumber: 2.2 Consensus size: 26
43422744 TGGCGTAAAA
*
43422754 CCATAATCAGAATAATTGGCTTTAAG
1 CCATAATCAGAATAATTGGCATTAAG
43422780 CCATAATCAGAATAATTGGCATTAAG
1 CCATAATCAGAATAATTGGCATTAAG
43422806 CCAT
1 CCAT
43422810 CGGCAGCTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (26 bp):
CCATAATCAGAATAATTGGCATTAAG
Found at i:43422998 original size:41 final size:41
Alignment explanation
Indices: 43422929--43423052 Score: 176
Period size: 41 Copynumber: 3.0 Consensus size: 41
43422919 CTTAAAAGCC
* * *
43422929 ACCGGTAGATCCACGGTCATCAAGCAACCATGCAATCCTTA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
* * * *
43422970 ATCGGTGGATCCACGATCGTCAAACAACCATGCAATTCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
*
43423011 ACCCGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
1 ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
43423052 A
1 A
43423053 TTTCTTCCTC
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.31, C:0.32, G:0.18, T:0.19
Consensus pattern (41 bp):
ACCGGTGGATCCACGGTCGTCAAGCAACCATGCAATCCTCA
Found at i:43423380 original size:27 final size:27
Alignment explanation
Indices: 43423317--43423472 Score: 154
Period size: 27 Copynumber: 5.7 Consensus size: 27
43423307 ATCTACAAAC
*
43423317 CAAGGGTATTTCTGTAATTTTTTGAAAGT
1 CAAGGGTATTTCTGTAATTTTCT-AAA-T
* *
43423346 CAAGGGTATTTCTATAATTTTGTAAAT
1 CAAGGGTATTTCTGTAATTTTCTAAAT
*
43423373 C-AGTGGTATTTCTGTAATTTTCCAAAT
1 CAAG-GGTATTTCTGTAATTTTCTAAAT
* *
43423400 CAAGGGTATTTCGGTAATTTTAC-AAGT
1 CAAGGGTATTTCTGTAATTTT-CTAAAT
* * * * *
43423427 CGAGAGTATTTCGGTAATTTTGTAAAC
1 CAAGGGTATTTCTGTAATTTTCTAAAT
*
43423454 CAAGGGTATTTCAGTAATT
1 CAAGGGTATTTCTGTAATT
43423473 CTACCTTACA
Statistics
Matches: 108, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
26 2 0.02
27 79 0.73
28 6 0.06
29 21 0.19
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.41
Consensus pattern (27 bp):
CAAGGGTATTTCTGTAATTTTCTAAAT
Found at i:43423462 original size:81 final size:82
Alignment explanation
Indices: 43423312--43423472 Score: 202
Period size: 81 Copynumber: 2.0 Consensus size: 82
43423302 GGTAAATCTA
* * * *
43423312 CAAACCAAGGGTATTTCTGTAATTTTTTGAAAGTCAAGGGTATTTCTATAATTTTGTAAATCAGT
1 CAAACCAAGGGTATTTCGGTAA-TTTTTGAAAGTCAAGAGTATTTCGATAATTTTGTAAACCAGT
*
43423377 GGTATTTCTGTAATTTTC
65 GGTATTTCAGTAATTTTC
* * *
43423395 CAAATCAAGGGTATTTCGGTAA-TTTT-ACAAGTCGAGAGTATTTCGGTAATTTTGTAAACCAAG
1 CAAACCAAGGGTATTTCGGTAATTTTTGA-AAGTCAAGAGTATTTCGATAATTTTGTAAACC-AG
43423458 -GGTATTTCAGTAATT
64 TGGTATTTCAGTAATT
43423473 CTACCTTACA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
80 1 0.01
81 45 0.66
82 2 0.03
83 20 0.29
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (82 bp):
CAAACCAAGGGTATTTCGGTAATTTTTGAAAGTCAAGAGTATTTCGATAATTTTGTAAACCAGTG
GTATTTCAGTAATTTTC
Found at i:43423485 original size:81 final size:81
Alignment explanation
Indices: 43423312--43423498 Score: 191
Period size: 81 Copynumber: 2.3 Consensus size: 81
43423302 GGTAAATCTA
* * * * *
43423312 CAAACCAAGGGTATTTCTGTAATTTTTTGAAAGTCAAGGGTATTTCTATAATTTTGTAAATCAGT
1 CAAATCAAGGGTATTTCAGTAA--TTTTGAAAGTCAAGAGTATTTCGATAATTTTGTAAACCAGT
* *
43423377 GGTATTTCTGTAATTTTC
64 GGTATTTCAGTAATTTAC
* * *
43423395 CAAATCAAGGGTATTTCGGTAATTTT-ACAAGTCGAGAGTATTTCGGTAATTTTGTAAACCAAG-
1 CAAATCAAGGGTATTTCAGTAATTTTGA-AAGTCAAGAGTATTTCGATAATTTTGTAAACC-AGT
43423458 GGTATTTCAGTAATTCTAC
64 GGTATTTCAGTAATT-TAC
** *
43423477 CTTA-CAAGGGCATTTCAGTAAT
1 CAAATCAAGGGTATTTCAGTAAT
43423499 ATTAGCCTAC
Statistics
Matches: 88, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
80 1 0.01
81 61 0.69
82 6 0.07
83 20 0.23
ACGTcount: A:0.30, C:0.13, G:0.18, T:0.39
Consensus pattern (81 bp):
CAAATCAAGGGTATTTCAGTAATTTTGAAAGTCAAGAGTATTTCGATAATTTTGTAAACCAGTGG
TATTTCAGTAATTTAC
Found at i:43427837 original size:34 final size:35
Alignment explanation
Indices: 43427793--43427861 Score: 113
Period size: 34 Copynumber: 2.0 Consensus size: 35
43427783 TCTACCCCTC
43427793 AATGGAGCACTACTTGCCTTTACTTCTTG-TTTTT
1 AATGGAGCACTACTTGCCTTTACTTCTTGCTTTTT
* *
43427827 AATGGGGCACTACTTTCCTTTACTTCTTGCTTTTT
1 AATGGAGCACTACTTGCCTTTACTTCTTGCTTTTT
43427862 CTCTCCCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 27 0.84
35 5 0.16
ACGTcount: A:0.16, C:0.22, G:0.14, T:0.48
Consensus pattern (35 bp):
AATGGAGCACTACTTGCCTTTACTTCTTGCTTTTT
Found at i:43429371 original size:22 final size:21
Alignment explanation
Indices: 43429340--43429380 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
43429330 CACTTGACAC
*
43429340 AGGGGAACACACCTATGTGGA
1 AGGGGAACACACCCATGTGGA
*
43429361 AGGGGCAACACGCCCATGTG
1 AGGGG-AACACACCCATGTG
43429381 ATCAATTTGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.29, C:0.24, G:0.34, T:0.12
Consensus pattern (21 bp):
AGGGGAACACACCCATGTGGA
Found at i:43429570 original size:41 final size:41
Alignment explanation
Indices: 43429515--43429619 Score: 160
Period size: 41 Copynumber: 2.6 Consensus size: 41
43429505 ACGGCTTGGC
* *
43429515 ACACGCCC-TTTCCATGGCCCGTGTCATTCACATAGCCATG
1 ACACGCCCGTGTCCATGGCCCGTGTCATTCACACAGCCATG
43429555 ACACGCCCGTGTCCATGGCCCGTGTCATTCACACAGCCATG
1 ACACGCCCGTGTCCATGGCCCGTGTCATTCACACAGCCATG
* *
43429596 ACACGCCCGTG-CCCTAGCCCGTGT
1 ACACGCCCGTGTCCATGGCCCGTGT
43429620 GGAAAAACCT
Statistics
Matches: 60, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
40 19 0.32
41 41 0.68
ACGTcount: A:0.18, C:0.40, G:0.21, T:0.21
Consensus pattern (41 bp):
ACACGCCCGTGTCCATGGCCCGTGTCATTCACACAGCCATG
Found at i:43430680 original size:46 final size:46
Alignment explanation
Indices: 43430629--43430751 Score: 133
Period size: 46 Copynumber: 2.6 Consensus size: 46
43430619 CCTAGCCCAC
* * *
43430629 GCATGTCCCAGACATGTCTTACGCTAGCTTAC-GTCTCGAGGCCGAT
1 GCATGTCCCAGACATGTCTTACACTAGC-TACTGTCTCAAGACCGAT
* * * *
43430675 GCATGTCCCAAACATGTATTACACTAGC-ACTTGTCTCAATATCGAT
1 GCATGTCCCAGACATGTCTTACACTAGCTAC-TGTCTCAAGACCGAT
43430721 GCAATGTCCCAGACATGGTCTTACACTAGCT
1 GC-ATGTCCCAGACAT-GTCTTACACTAGCT
43430752 CACACAAATG
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
44 2 0.03
46 37 0.59
47 12 0.19
48 12 0.19
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (46 bp):
GCATGTCCCAGACATGTCTTACACTAGCTACTGTCTCAAGACCGAT
Found at i:43433404 original size:13 final size:14
Alignment explanation
Indices: 43433388--43433416 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
43433378 TTATAAATAT
43433388 TTATAAT-GTTTAA
1 TTATAATAGTTTAA
43433401 TTATAATAGTTTAA
1 TTATAATAGTTTAA
43433415 TT
1 TT
43433417 CGTCATTAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (14 bp):
TTATAATAGTTTAA
Found at i:43433855 original size:21 final size:21
Alignment explanation
Indices: 43433823--43433874 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
43433813 ACAACTTAGA
*
43433823 GCAGAGGCAGCAG-AGAGGGAG
1 GCAGAGGTAGCAGCA-AGGGAG
*
43433844 GCAGCGGTAGCAGCAAGGGAG
1 GCAGAGGTAGCAGCAAGGGAG
43433865 GCAGAGGTAG
1 GCAGAGGTAG
43433875 TAGTGATGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.31, C:0.15, G:0.50, T:0.04
Consensus pattern (21 bp):
GCAGAGGTAGCAGCAAGGGAG
Found at i:43434325 original size:43 final size:43
Alignment explanation
Indices: 43434274--43434365 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
43434264 CGGCTAAAAG
* * *
43434274 TGACTTTTAGCGGCGCTTTTCCAACAAACACCACTAAAAGCTA
1 TGACTTTTAGCGACACTTTTCCAACAAACACCACTAAAAGCCA
** * *
43434317 TGACTTTTAGCGACACTTTTTTAACAAACGCCGCTAAAAGCCA
1 TGACTTTTAGCGACACTTTTCCAACAAACACCACTAAAAGCCA
43434360 TGACTT
1 TGACTT
43434366 ATAGTGGCTG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (43 bp):
TGACTTTTAGCGACACTTTTCCAACAAACACCACTAAAAGCCA
Found at i:43439561 original size:19 final size:19
Alignment explanation
Indices: 43439534--43439570 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
43439524 TTAGTAAAAA
*
43439534 ATGTTTATCACACATCAAG
1 ATGTGTATCACACATCAAG
43439553 ATGTGTATCACACATCAA
1 ATGTGTATCACACATCAA
43439571 ACATTCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.11, T:0.30
Consensus pattern (19 bp):
ATGTGTATCACACATCAAG
Found at i:43449621 original size:13 final size:13
Alignment explanation
Indices: 43449596--43449630 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
43449586 TCAAGTTAAC
43449596 AAAGAAT-AAATA
1 AAAGAATAAAATA
43449608 AAAGAATAAAATA
1 AAAGAATAAAATA
*
43449621 AAAGGATAAA
1 AAAGAATAAA
43449631 GAAATTGCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 7 0.33
13 14 0.67
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.14
Consensus pattern (13 bp):
AAAGAATAAAATA
Found at i:43456023 original size:24 final size:25
Alignment explanation
Indices: 43455979--43456028 Score: 59
Period size: 24 Copynumber: 2.0 Consensus size: 25
43455969 ACTCTTCTCA
* *
43455979 TCTCTTCAATTCTCTCTCATTTTTC
1 TCTCTTCAATTCCCTCTCATTGTTC
43456004 TCTCTTC-ATTCCCT-TCCATTGTTC
1 TCTCTTCAATTCCCTCT-CATTGTTC
43456028 T
1 T
43456029 TCACTTTCTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.10, C:0.34, G:0.02, T:0.54
Consensus pattern (25 bp):
TCTCTTCAATTCCCTCTCATTGTTC
Found at i:43457563 original size:31 final size:31
Alignment explanation
Indices: 43457511--43457590 Score: 117
Period size: 31 Copynumber: 2.5 Consensus size: 31
43457501 CTCAACTTGT
43457511 ACTGGGCC-ATAGCACTTTTCATATTTCATAAC
1 ACTGGGCCGA-AGC-CTTTTCATATTTCATAAC
**
43457543 ACTGGGCCGAAGCCTTTTCATATTTCATATT
1 ACTGGGCCGAAGCCTTTTCATATTTCATAAC
43457574 ACTGGGCCGAAGCCTTT
1 ACTGGGCCGAAGCCTTT
43457591 ACTGTAAATG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
31 33 0.73
32 11 0.24
33 1 0.02
ACGTcount: A:0.24, C:0.25, G:0.17, T:0.34
Consensus pattern (31 bp):
ACTGGGCCGAAGCCTTTTCATATTTCATAAC
Found at i:43457835 original size:24 final size:24
Alignment explanation
Indices: 43457784--43457904 Score: 156
Period size: 25 Copynumber: 5.0 Consensus size: 24
43457774 ACTTTATCAT
*
43457784 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
43457809 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
43457833 ATAACTGTGGCATAAGCCC-TTTA
1 ATAACTGGGGCATAAGCCCTTTTA
* *
43457856 ATGACTGGGGCATAAGCCCTTTATC
1 ATAACTGGGGCATAAGCCCTTT-TA
43457881 ATAACTGGGGCATAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
43457905 CACTTCCTCC
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
23 21 0.25
24 29 0.35
25 34 0.40
ACGTcount: A:0.28, C:0.22, G:0.21, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:43457862 original size:23 final size:23
Alignment explanation
Indices: 43457805--43457902 Score: 142
Period size: 23 Copynumber: 4.1 Consensus size: 23
43457795 CCTAGCCTCT
*
43457805 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
43457828 TTTTAATAACTGTGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
*
43457852 TTTAATGACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
43457875 TTTATCATAACTGGGGCATAAGCCC
1 TTTA--ATAACTGGGGCATAAGCCC
43457900 TTT
1 TTT
43457903 TACACTTCCT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
23 25 0.37
24 21 0.31
25 21 0.31
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:43457978 original size:20 final size:20
Alignment explanation
Indices: 43457953--43458019 Score: 116
Period size: 20 Copynumber: 3.4 Consensus size: 20
43457943 TTATGATTAC
43457953 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
43457973 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
43457993 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
43458013 ACCATGT
1 ATCATGT
43458020 TTATCAAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:43457984 original size:11 final size:11
Alignment explanation
Indices: 43457953--43458008 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
43457943 TTATGATTAC
43457953 ATCATGTGCAT
1 ATCATGTGCAT
*
43457964 ATCA--TACAT
1 ATCATGTGCAT
43457973 ATCATGTGCAT
1 ATCATGTGCAT
*
43457984 ATCA--TACAT
1 ATCATGTGCAT
*
43457993 GTCATGTGCAT
1 ATCATGTGCAT
43458004 ATCAT
1 ATCAT
43458009 ACATACCATG
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
9 15 0.43
11 20 0.57
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (11 bp):
ATCATGTGCAT
Found at i:43458088 original size:25 final size:25
Alignment explanation
Indices: 43458056--43458103 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
43458046 ATACATAAAC
* * *
43458056 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
43458081 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
43458104 CATTTTATAA
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:43464068 original size:17 final size:18
Alignment explanation
Indices: 43464046--43464079 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43464036 TCACATTGAA
43464046 GTGTTTT-ATTGAAAACT
1 GTGTTTTCATTGAAAACT
43464063 GTGTTTTCATTGAAAAC
1 GTGTTTTCATTGAAAAC
43464080 CCTTCTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.29, C:0.09, G:0.18, T:0.44
Consensus pattern (18 bp):
GTGTTTTCATTGAAAACT
Found at i:43464991 original size:26 final size:27
Alignment explanation
Indices: 43464962--43465014 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
43464952 ATAAATCTTA
43464962 CATTC-AACACATAGGGGTATTTTAGT
1 CATTCTAACACATAGGGGTATTTTAGT
* * *
43464988 CATTCTCACCCTTAGGGGTATTTTAGT
1 CATTCTAACACATAGGGGTATTTTAGT
43465015 AATTTCTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (27 bp):
CATTCTAACACATAGGGGTATTTTAGT
Found at i:43465357 original size:28 final size:28
Alignment explanation
Indices: 43465325--43465379 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
43465315 ATACATGCAT
*
43465325 ATGGCTCACTAGG-CCCAATCACATTCAA
1 ATGGCCCA-TAGGCCCCAATCACATTCAA
*
43465353 ATGGCCCATCGGCCCCAATCACATTCA
1 ATGGCCCATAGGCCCCAATCACATTCA
43465380 TAGTCATGCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 3 0.12
28 21 0.88
ACGTcount: A:0.29, C:0.36, G:0.15, T:0.20
Consensus pattern (28 bp):
ATGGCCCATAGGCCCCAATCACATTCAA
Found at i:43469019 original size:40 final size:41
Alignment explanation
Indices: 43468972--43469242 Score: 345
Period size: 40 Copynumber: 6.7 Consensus size: 41
43468962 AATTTTTATT
* * *
43468972 CGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGATTTTATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATTATATC
*
43469012 CGGGCTAAGACCCGAAGGCATTTGTGCGAGTTGA-TATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATTATATC
* *
43469052 CGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGAT-TATATC
* *
43469094 CGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGAT-TATATC
* **
43469136 TGGGCTAAGACCCGAAGGCAATTGTGAAAGTTGA-TATATC
1 CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATTATATC
* **
43469176 CGGGCTAAGACCCGAAGGC-ATTCGTGCGAGTTG-CTATGCC
1 CGGGCTAAGACCCGAAGGCAATT-GTGCGAGTTGATTATATC
*
43469216 CGGGTTAAGACCCGAAGGCAATTGTGC
1 CGGGCTAAGACCCGAAGGCAATTGTGC
43469243 TTGTGGTAAT
Statistics
Matches: 209, Mismatches: 16, Indels: 12
0.88 0.07 0.05
Matches are distributed among these distances:
39 3 0.01
40 123 0.59
41 6 0.03
42 77 0.37
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (41 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCGAGTTGATTATATC
Found at i:43469113 original size:82 final size:82
Alignment explanation
Indices: 43468972--43469242 Score: 370
Period size: 82 Copynumber: 3.3 Consensus size: 82
43468962 AATTTTTATT
* * *
43468972 CGGGCTAAGTCCCGAAGGCAATTGTGCTAG-TGAT-TTTATCCGGGCTAAGACCCGAAGGCATTT
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGCATTT
43469035 GTGCGAGTTGATATATC
66 GTGCGAGTTGATATATC
* * * *
43469052 CGGGCTAAGACCCGCAGGCATTTGTGCGAGTTGATATATATCCGGGCTAAGACCCGCAGGCATTT
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGCATTT
43469117 GTGCGAGTTGATATATATC
66 GTGCGAGTTG--ATATATC
* * *
43469136 TGGGCTAAGACCCGAAGGCAATTGTGAAAGTTG--ATATATCCGGGCTAAGACCCGAAGGCATTC
1 CGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGCATTT
* **
43469199 GTGCGAGTTGCTATGCC
66 GTGCGAGTTGATATATC
*
43469216 CGGGTTAAGACCCGAAGGCAATTGTGC
1 CGGGCTAAGACCCGAAGGCAATTGTGC
43469243 TTGTGGTAAT
Statistics
Matches: 168, Mismatches: 19, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
80 54 0.32
81 4 0.02
82 75 0.45
84 35 0.21
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.25
Consensus pattern (82 bp):
CGGGCTAAGACCCGAAGGCAATTGTGCAAGTTGATATATATCCGGGCTAAGACCCGAAGGCATTT
GTGCGAGTTGATATATC
Found at i:43477399 original size:40 final size:40
Alignment explanation
Indices: 43477344--43477651 Score: 493
Period size: 40 Copynumber: 7.8 Consensus size: 40
43477334 GCATTTGTAT
43477344 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
43477384 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
43477424 ATATATCCGGGCTAAGACCCG-A-GCA-TTGTGCG-GTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
43477460 ATATAT-CGGGCTAAGA-CCGAAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
43477498 ATATATCCGGGCTAAGACCCGCAGGCATTTGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* *
43477538 ATATATCCGGGCTAAGACCCGAAGGCAATTGTGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
*
43477578 ATATATCCGGGCTAAGACCCGAAGGCATTCGTGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
* ** * *
43477618 CTATGCCCGGGCTAAGGCCCGAAGGCAATTGTGC
1 ATATATCCGGGCTAAGACCCGAAGGCATTTGTGC
43477652 TTGTGGTAAT
Statistics
Matches: 249, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
34 3 0.01
35 11 0.04
36 13 0.05
37 14 0.06
38 13 0.05
39 11 0.04
40 184 0.74
ACGTcount: A:0.25, C:0.21, G:0.30, T:0.24
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG
Found at i:43483557 original size:40 final size:40
Alignment explanation
Indices: 43483498--43483604 Score: 196
Period size: 40 Copynumber: 2.7 Consensus size: 40
43483488 ATTTGAATGA
*
43483498 TATCCGGGCTAAGTTCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
43483538 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
*
43483578 TATCCGGGCTAAGACCCGAAGGCATTT
1 TATCCGGGCTAAGTCCCGAAGGCATTT
43483605 GTGCGAGTTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 65 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (40 bp):
TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
Found at i:43483625 original size:40 final size:40
Alignment explanation
Indices: 43483498--43483668 Score: 193
Period size: 40 Copynumber: 4.3 Consensus size: 40
43483488 ATTTGAATGA
**
43483498 TATCCGGGCTAAGTTCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
*
43483538 TATCCGGGCTAAGTCCCGAAGGCATTTATGCTAGTGATTT
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
* * * *
43483578 TATCCGGGCTAAGACCCGAAGGCATTTGTGCGAGTTG-CTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAG-TGATTT
* * * * * * *
43483618 TACCCGGGTTAAGACCCGAAGGCAATTGTGCTTGTGGTTA
1 TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
43483658 TATCC-GGCTAA
1 TATCCGGGCTAA
43483669 ATTCCGAAGA
Statistics
Matches: 115, Mismatches: 14, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
39 7 0.06
40 106 0.92
41 2 0.02
ACGTcount: A:0.23, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
TATCCGGGCTAAGACCCGAAGGCATTTATGCTAGTGATTT
Found at i:43488508 original size:40 final size:40
Alignment explanation
Indices: 43488443--43488686 Score: 337
Period size: 40 Copynumber: 6.1 Consensus size: 40
43488433 TGGGAGTTAA
** * * *
43488443 CCGGATATAGCCACTCGCTCGAATGCCTTCGGGACATAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* *
43488483 CCAGATATAGTAACTCGCACCAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
** *
43488523 CCGGATATAGTAACTCGCACAAATGCCTTCGAAACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
*
43488563 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAAC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
43488603 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
1 CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
* * * *
43488643 CC-GAAACTAGTCACTAGCGCAAATGCCTTCGGGACTTAGC
1 CCGGATA-TAGTAACTCGCACAAATGCCTTCGGGACTTAGC
43488683 CCGG
1 CCGG
43488687 TTATCATCCG
Statistics
Matches: 184, Mismatches: 18, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
39 3 0.02
40 180 0.98
41 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.21, T:0.21
Consensus pattern (40 bp):
CCGGATATAGTAACTCGCACAAATGCCTTCGGGACTTAGC
Found at i:43499242 original size:40 final size:40
Alignment explanation
Indices: 43499180--43499304 Score: 169
Period size: 40 Copynumber: 3.1 Consensus size: 40
43499170 GATTTAGCCA
* * * *
43499180 GATATAGCAACTCGCACAAATGCCTTCAGGTCTTAGCCCG
1 GATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
* **
43499220 GATATAGTCACTAGCATGAATGCCTTCGGGACTTAGCCCG
1 GATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
* *
43499260 GATATAGTAACTTGCACAAATGCCTTTGGGACTTAGCCCG
1 GATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
43499300 GATAT
1 GATAT
43499305 CATCCGAATA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 73 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.26
Consensus pattern (40 bp):
GATATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCG
Found at i:43506140 original size:40 final size:40
Alignment explanation
Indices: 43506073--43506249 Score: 225
Period size: 40 Copynumber: 4.5 Consensus size: 40
43506063 ACCCAAGTAT
*
43506073 CTTCGGGAT-TTAG-CCGGATATAACAACTCGCACAAATGC
1 CTTCGGG-TCTTAGCCCGGATATAGCAACTCGCACAAATGC
43506112 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* * * *
43506152 CTTCGGGTCTTAGCCCGGATATAATC-ACTAGCATAAATTC
1 CTTCGGGTCTTAGCCCGGATAT-AGCAACTCGCACAAATGC
* * *
43506192 CTTCGGGACATAGCCCGGATATAGCAACTCGCACGAATGC
1 CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
* *
43506232 CTTCGGATCTTAGTCCGG
1 CTTCGGGTCTTAGCCCGG
43506250 TTATCATCCG
Statistics
Matches: 118, Mismatches: 16, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
38 1 0.01
39 13 0.11
40 102 0.86
41 2 0.02
ACGTcount: A:0.26, C:0.28, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGTCTTAGCCCGGATATAGCAACTCGCACAAATGC
Found at i:43514410 original size:40 final size:40
Alignment explanation
Indices: 43514352--43514519 Score: 223
Period size: 40 Copynumber: 4.2 Consensus size: 40
43514342 TCTTTGGGAT
*
43514352 TTAG-CCGGATATAACAACTCGCACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
*
43514391 TTAGCCCGGATATAGCAACTCGTACAAATGCCTTCGGGTC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
* * * *
43514431 TTAGCCCGGATATAATC-ACTAGCATAAATGCCTTCGGGAC
1 TTAGCCCGGATAT-AGCAACTCGCACAAATGCCTTCGGGTC
* * *
43514471 ATAGCCCGGATATAGCAACTCGCACGAATGCCTTCGGATC
1 TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
*
43514511 TTAGTCCGG
1 TTAGCCCGG
43514520 TTATCATCCG
Statistics
Matches: 110, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
39 6 0.05
40 102 0.93
41 2 0.02
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
TTAGCCCGGATATAGCAACTCGCACAAATGCCTTCGGGTC
Found at i:43527762 original size:40 final size:41
Alignment explanation
Indices: 43527718--43527811 Score: 111
Period size: 40 Copynumber: 2.3 Consensus size: 41
43527708 TCTTGTTATT
*
43527718 GCACACTTAGTGCCTA-ATATAGCCGAAGCTATTCCAATTC
1 GCACACTTAGTGCCTATATATAGCCGAAGCTATTCCAAATC
* * ** *
43527758 GCACACTTAGTG-CTATTTATTGCCGGTGCTATTTCAAATC
1 GCACACTTAGTGCCTATATATAGCCGAAGCTATTCCAAATC
*
43527798 GAACACTTAGTGCC
1 GCACACTTAGTGCC
43527812 GAACATAGTC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
39 3 0.07
40 41 0.91
41 1 0.02
ACGTcount: A:0.27, C:0.26, G:0.17, T:0.31
Consensus pattern (41 bp):
GCACACTTAGTGCCTATATATAGCCGAAGCTATTCCAAATC
Found at i:43531264 original size:28 final size:28
Alignment explanation
Indices: 43531227--43531301 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
43531217 AATATATAGT
* *
43531227 AACTCCGCACACTTAGTGCT-TAGTAGTCA
1 AACT-CGCACACTTAGTGCTATA-CAATCA
* *
43531256 AACTCGCACATTTAGTGCTATACAATTA
1 AACTCGCACACTTAGTGCTATACAATCA
43531284 AACTCGCACACTTAGTGC
1 AACTCGCACACTTAGTGC
43531302 CAATCTCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 34 0.85
29 6 0.15
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (28 bp):
AACTCGCACACTTAGTGCTATACAATCA
Found at i:43539027 original size:28 final size:28
Alignment explanation
Indices: 43538990--43539064 Score: 89
Period size: 28 Copynumber: 2.6 Consensus size: 28
43538980 AATATATAGT
* *
43538990 AACTCCGCACACTTAGTGCT-TAGTAGTCA
1 AACT-CGCACACTTAGTGCTATA-CAATCA
* *
43539019 AACTCGCACATTTAGTGCTATACAATTA
1 AACTCGCACACTTAGTGCTATACAATCA
43539047 AACTCGCACACTTAGTGC
1 AACTCGCACACTTAGTGC
43539065 CAATCTCATT
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
28 34 0.85
29 6 0.15
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.28
Consensus pattern (28 bp):
AACTCGCACACTTAGTGCTATACAATCA
Found at i:43547139 original size:49 final size:49
Alignment explanation
Indices: 43547083--43547307 Score: 279
Period size: 49 Copynumber: 4.5 Consensus size: 49
43547073 CTAGTACGCA
* * * *
43547083 TAGTAGCCTACACATAGTACTACACATGCGACCAATTATCCGGTACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
* *
43547132 TAGTAGCCTGCACTTAGTACTACACACGTGACCGATTATCCGGAACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
** * *
43547181 TAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACG
1 TAGTAGCCTGCACTTAGTACTACACACGTGACC-AATTATCCGGTACACG
* * * * * *
43547231 TAGTAGCCTGCACTGAGTACTACACACGTGATCACAGTTTTCGGGTACGCA
1 TAGTAGCCTGCACTTAGTACTACACACGTGA-C-CAATTATCCGGTACACG
43547282 TAGTAGCCTGCACTTAGTACTACACA
1 TAGTAGCCTGCACTTAGTACTACACA
43547308 TGCGACCTCA
Statistics
Matches: 151, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
49 76 0.50
50 40 0.26
51 34 0.23
52 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (49 bp):
TAGTAGCCTGCACTTAGTACTACACACGTGACCAATTATCCGGTACACG
Found at i:43547253 original size:99 final size:100
Alignment explanation
Indices: 43547081--43547314 Score: 294
Period size: 99 Copynumber: 2.4 Consensus size: 100
43547071 ATCTAGTACG
* * * ** *
43547081 CATAGTAGCCTACACATAGTACTACACATGCGACCAATTATCCGGTACACGTAGTAGCCTGCACT
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAGTAGCCTGCACT
*
43547146 TAGTACTACACACGTGA-C-C-GATTATCCGGAACA
66 GAGTACTACACACGTGATCACAG-TTATCCGGAACA
* * *
43547179 CGTAGTAGCCTGCACTTAGTACTACACACGTGACCTAACCATCTGATACACGTAGTAGCCTGCAC
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC-AACCATCCGATACACGTAGTAGCCTGCAC
* * * *
43547244 TGAGTACTACACACGTGATCACAGTTTTCGGGTACG
65 TGAGTACTACACACGTGATCACAGTTATCCGGAACA
*
43547280 CATAGTAGCCTGCACTTAGTACTACACATGCGACC
1 CATAGTAGCCTGCACTTAGTACTACACACGCGACC
43547315 TCACAATAGA
Statistics
Matches: 115, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
98 30 0.26
99 42 0.37
100 1 0.01
101 41 0.36
102 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.24
Consensus pattern (100 bp):
CATAGTAGCCTGCACTTAGTACTACACACGCGACCAACCATCCGATACACGTAGTAGCCTGCACT
GAGTACTACACACGTGATCACAGTTATCCGGAACA
Found at i:43549816 original size:48 final size:48
Alignment explanation
Indices: 43549648--43549831 Score: 190
Period size: 48 Copynumber: 3.8 Consensus size: 48
43549638 ATCCATTAAT
* * ** *
43549648 TCGATGCCATGTCCCGAACATGGTCTTACACTAACTATCAAAATCAAG-G
1 TCGATGCCATGTCCCAAACATGGTCTTACACTAAC-ACCACTAT-ATGTG
** * * *
43549697 TCGACACCATGTCCCAAACATGGTCTTACACTAGCTCTCACATATTTGTG
1 TCGATGCCATGTCCCAAACATGGTCTTACACTAACAC-CAC-TATATGTG
* * * *
43549747 CCGATGCCATGTCCTAGACATGGTCTTACACTAACACCTCTATATGTG
1 TCGATGCCATGTCCCAAACATGGTCTTACACTAACACCACTATATGTG
*
43549795 TCGATGCCATGTCCCAAACATGCTCTTACACTAACAC
1 TCGATGCCATGTCCCAAACATGGTCTTACACTAACAC
43549832 ATCTCGTAGC
Statistics
Matches: 109, Mismatches: 23, Indels: 7
0.78 0.17 0.05
Matches are distributed among these distances:
48 40 0.37
49 36 0.33
50 33 0.30
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (48 bp):
TCGATGCCATGTCCCAAACATGGTCTTACACTAACACCACTATATGTG
Found at i:43549882 original size:46 final size:45
Alignment explanation
Indices: 43549796--43549962 Score: 140
Period size: 46 Copynumber: 3.6 Consensus size: 45
43549786 CTATATGTGT
* * ** *
43549796 CGATGCCATGTCCCAAACATGCTCTTACACTAAC-ACATCTCGTA-GC
1 CGATG-CATGTCCTAGACATGC-CTTACACTGGCTACATCTC-AAGGC
43549842 CGATGCATGTCCTAGACATGCCTTACACTGGCTTACATCTCAAGGC
1 CGATGCATGTCCTAGACATGCCTTACACTGGC-TACATCTCAAGGC
* * * * * *
43549888 CGATGCATGTCTTAGACATGTCTTACACTGGCTCTCGTCTCCATGC
1 CGATGCATGTCCTAGACATGCCTTACACTGGCT-ACATCTCAAGGC
* *
43549934 CGATGCCATGTTCTAGACATTGTCTTACA
1 CGATG-CATGTCCTAGACA-TGCCTTACA
43549963 TTAGCTCTCA
Statistics
Matches: 102, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
44 9 0.09
45 16 0.16
46 57 0.56
47 11 0.11
48 9 0.09
ACGTcount: A:0.23, C:0.31, G:0.17, T:0.29
Consensus pattern (45 bp):
CGATGCATGTCCTAGACATGCCTTACACTGGCTACATCTCAAGGC
Found at i:43550386 original size:30 final size:30
Alignment explanation
Indices: 43550302--43550386 Score: 125
Period size: 30 Copynumber: 2.8 Consensus size: 30
43550292 ATGATTTGGG
* * * *
43550302 CAAAATGACCATTATGCCCTTAAACTTTCA
1 CAAAATGACTATTTTACCCTTAGACTTTCA
43550332 CAAAATGACTATTTTACCCTTAGACTTTCA
1 CAAAATGACTATTTTACCCTTAGACTTTCA
*
43550362 CAAAATGACTATTTTACCCCTAGAC
1 CAAAATGACTATTTTACCCTTAGAC
43550387 CTAAAAATCA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 50 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.32
Consensus pattern (30 bp):
CAAAATGACTATTTTACCCTTAGACTTTCA
Found at i:43555795 original size:27 final size:27
Alignment explanation
Indices: 43555757--43555811 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
43555747 GCAAATCCAG
43555757 TAAATCAGGATCCTACTCCTCGTACTA
1 TAAATCAGGATCCTACTCCTCGTACTA
43555784 TAAATCAGGATCCTACTCCTCGTACTA
1 TAAATCAGGATCCTACTCCTCGTACTA
43555811 T
1 T
43555812 GTATGATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.29, C:0.29, G:0.11, T:0.31
Consensus pattern (27 bp):
TAAATCAGGATCCTACTCCTCGTACTA
Found at i:43558278 original size:13 final size:13
Alignment explanation
Indices: 43558262--43558288 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
43558252 ATAAATAAGC
43558262 GCTATACGGCCGT
1 GCTATACGGCCGT
43558275 GCTATACGGCCGT
1 GCTATACGGCCGT
43558288 G
1 G
43558289 TCCCTGTCGA
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:0.15, C:0.30, G:0.33, T:0.22
Consensus pattern (13 bp):
GCTATACGGCCGT
Found at i:43559072 original size:36 final size:36
Alignment explanation
Indices: 43559025--43559095 Score: 142
Period size: 36 Copynumber: 2.0 Consensus size: 36
43559015 CTATCGTAAT
43559025 CTTAGTTAATTAGATAATTAGTCTTAGTTTAAAACA
1 CTTAGTTAATTAGATAATTAGTCTTAGTTTAAAACA
43559061 CTTAGTTAATTAGATAATTAGTCTTAGTTTAAAAC
1 CTTAGTTAATTAGATAATTAGTCTTAGTTTAAAAC
43559096 TTCTCTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.42
Consensus pattern (36 bp):
CTTAGTTAATTAGATAATTAGTCTTAGTTTAAAACA
Found at i:43561313 original size:21 final size:21
Alignment explanation
Indices: 43561296--43561344 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
43561286 GGCACACGGT
* *
43561296 CGTGTGGAAGGGTAACACCCC
1 CGTGTGGAAGGGCAACACGCC
43561317 CGTGTGGAAGGGCAACACGCC
1 CGTGTGGAAGGGCAACACGCC
43561338 CGTGTGG
1 CGTGTGG
43561345 TCATTATAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.27, G:0.39, T:0.14
Consensus pattern (21 bp):
CGTGTGGAAGGGCAACACGCC
Found at i:43562774 original size:46 final size:47
Alignment explanation
Indices: 43562498--43562812 Score: 177
Period size: 48 Copynumber: 6.7 Consensus size: 47
43562488 TATAATGTCA
* * * * *
43562498 ATGCCATGTCCCAGACATGGTCTTACACTGGCT-CGTCCATCAAGTCG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGCTACATCTAT-ACGCCG
* * * ** * *
43562545 ATTCCATGTCCCAGA-ATGGTCTTACACTGACTATCA-AAATTGAGGCTG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGCTA-CATCTA-T-ACGCCG
* * * * * *
43562593 ATGCCATGTCCTAGACATGGTCTTACACTAGCTCTCA-CATATTCGTGCTG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGCT-ACATC-TATAC--GCCG
* * *
43562643 ATGCCATGCCCCAAACATGGTCTTACACT-GATACATCTATACGTTCTG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGCTACATCTATACG--CCG
* * *
43562691 ATGCCATGTCCTAGACATGGTCTTACACTGAC-ACATCTCATA-GCCG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGCTACATCT-ATACGCCG
*
43562737 ATG-CATGCCCCAGACAT-GTCTTACACTGGCTTACATCT-TAAGGCCG
1 ATGCCATGCCCCAGACATGGTCTTACACTGGC-TACATCTAT-ACGCCG
* * *
43562783 ATG-CATGTCCCATAC-TGTTCTTACACTGGC
1 ATGCCATGCCCCAGACATGGTCTTACACTGGC
43562813 CCTCGTCTCA
Statistics
Matches: 214, Mismatches: 36, Indels: 37
0.75 0.13 0.13
Matches are distributed among these distances:
44 13 0.06
45 14 0.07
46 57 0.27
47 15 0.07
48 60 0.28
49 24 0.11
50 31 0.14
ACGTcount: A:0.24, C:0.29, G:0.18, T:0.29
Consensus pattern (47 bp):
ATGCCATGCCCCAGACATGGTCTTACACTGGCTACATCTATACGCCG
Found at i:43565872 original size:40 final size:40
Alignment explanation
Indices: 43565804--43566050 Score: 300
Period size: 40 Copynumber: 6.2 Consensus size: 40
43565794 CGGAATTTAG
* * * *
43565804 CCGGATATAACCACAAGCACAATTGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * * * * *
43565844 CCGGGT-ATAGCAACTCGTACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
* * *
43565884 CCGGAT-ATATCAACTCGCACAAATGCCTTCGGGTCTTAGC
1 CCGGATAAAATC-ACTAGCACAAATGCCTTCGGGTCTTAAC
43565924 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
*
43565964 CCGGATAAAATCACTAGCATAAATGCCTTCGGGTCTTAAC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
* * **
43566004 CCGGATAAAATCACTAGCATAAATGCCTTCGGGACTTGTC
1 CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
43566044 CCGGATA
1 CCGGATA
43566051 TCATTCAAAT
Statistics
Matches: 186, Mismatches: 19, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
39 2 0.01
40 180 0.97
41 4 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
CCGGATAAAATCACTAGCACAAATGCCTTCGGGTCTTAAC
Found at i:43580040 original size:46 final size:48
Alignment explanation
Indices: 43579968--43580072 Score: 142
Period size: 46 Copynumber: 2.2 Consensus size: 48
43579958 GACAGGACAG
* * *
43579968 GACAGAAATGAGCCATGTAAGTCCATATCAG-T-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
*
43580014 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAG--ATATATATGGCATTGGA
43580064 GACAGGAAT
1 GACAGGAAT
43580073 AATTCATGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 28 0.55
49 1 0.02
50 22 0.43
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
Found at i:43584383 original size:46 final size:48
Alignment explanation
Indices: 43584311--43584415 Score: 142
Period size: 46 Copynumber: 2.2 Consensus size: 48
43584301 GACAGGACAG
* * *
43584311 GACAGAAATGAGCCATGTAAGTCCATATCAG-T-TATATGGCTTTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
*
43584357 GACAGGAATGAGCCATGTAAGCCCATATTAGATATATATATGGCATTGGA
1 GACAGGAATGAGCCATGTAAGCCCATATCAG--ATATATATGGCATTGGA
43584407 GACAGGAAT
1 GACAGGAAT
43584416 AATTCACGTA
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
46 28 0.55
49 1 0.02
50 22 0.43
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (48 bp):
GACAGGAATGAGCCATGTAAGCCCATATCAGATATATATGGCATTGGA
Found at i:43586241 original size:25 final size:25
Alignment explanation
Indices: 43586203--43586250 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
43586193 TTATAATATG
** *
43586203 AAAATGACTGTTTTGCCCATAGGTA
1 AAAATGACCATTTTACCCATAGGTA
*
43586228 AAAATGACCATTTTACCCCTAGG
1 AAAATGACCATTTTACCCATAGG
43586251 GTTTAATTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.33, C:0.21, G:0.17, T:0.29
Consensus pattern (25 bp):
AAAATGACCATTTTACCCATAGGTA
Found at i:43586313 original size:11 final size:11
Alignment explanation
Indices: 43586297--43586334 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
43586287 ACATTAATTG
43586297 ACATGATATGC
1 ACATGATATGC
43586308 ACATGATATG-
1 ACATGATATGC
*
43586318 -TATGATATGC
1 ACATGATATGC
43586328 ACATGAT
1 ACATGAT
43586335 GTATTCATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
9 8 0.35
11 15 0.65
ACGTcount: A:0.37, C:0.13, G:0.18, T:0.32
Consensus pattern (11 bp):
ACATGATATGC
Found at i:43586433 original size:25 final size:25
Alignment explanation
Indices: 43586381--43586469 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
43586371 GAGGAAGTGC
43586381 AAAAGGG-TTATGCCCCAG-TTACCG
1 AAAAGGGCTT-TGCCCCAGTTTACCG
43586405 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
* *
43586430 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCG
43586455 AAAAGGGCTTTGCCC
1 AAAAGGGCTTTGCCC
43586470 TAGTGATTAA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
24 15 0.25
25 46 0.75
ACGTcount: A:0.27, C:0.26, G:0.24, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:43586729 original size:31 final size:31
Alignment explanation
Indices: 43586694--43586777 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
43586684 TTGTTACAGT
43586694 AAAGGCTTCGGCCCAGTGATATGAATAATAA
1 AAAGGCTTCGGCCCAGTGATATGAATAATAA
* **
43586725 AAAGGCTTCGGCCTAGTGATATGAATAATGC
1 AAAGGCTTCGGCCCAGTGATATGAATAATAA
*
43586756 AAAGGCTTCAGCCCAGT-ATATG
1 AAAGGCTTCGGCCCAGTGATATG
43586778 CTGAGATTGA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
30 5 0.10
31 43 0.90
ACGTcount: A:0.35, C:0.18, G:0.24, T:0.24
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGATATGAATAATAA
Found at i:43592530 original size:46 final size:46
Alignment explanation
Indices: 43592463--43592634 Score: 190
Period size: 46 Copynumber: 3.7 Consensus size: 46
43592453 AACCCGCCCC
*
43592463 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATGCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATGCA
*
43592509 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACATG--
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATGCA
* * * * *
43592557 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATGCA
* *
43592602 TAAGTGAACTCGGACTCCACTCAACGACTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
43592635 ATGCTCAACC
Statistics
Matches: 105, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 1 0.01
45 2 0.02
46 58 0.55
47 28 0.27
48 3 0.03
49 1 0.01
50 4 0.04
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATGCA
Found at i:43592575 original size:93 final size:93
Alignment explanation
Indices: 43592468--43592638 Score: 288
Period size: 93 Copynumber: 1.8 Consensus size: 93
43592458 GCCCCTAAGT
* * *
43592468 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATGCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
*
43592533 CGAGTTCGGATGCCTAGTTACATGTCAC
66 CGACTTCGGATGCCTAGTTACATGTCAC
* *
43592561 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCCACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
43592626 CGACTTCGGATGC
66 CGACTTCGGATGC
43592639 TCAACCATCC
Statistics
Matches: 72, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGACTTCGGATGCCTAGTTACATGTCAC
Found at i:43596024 original size:47 final size:47
Alignment explanation
Indices: 43595948--43596148 Score: 296
Period size: 47 Copynumber: 4.3 Consensus size: 47
43595938 CTTCGGGACT
* * * * * *
43595948 TATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGCCC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
43595995 TGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGG-CC
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
* *
43596041 TCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGCCT
1 T-ATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
*
43596089 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCT
1 TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
43596136 TATCACATATATA
1 TATCACATATATA
43596149 TACACTTTAT
Statistics
Matches: 141, Mismatches: 11, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
46 3 0.02
47 136 0.96
48 2 0.01
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (47 bp):
TATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCC
Found at i:43596168 original size:116 final size:116
Alignment explanation
Indices: 43596048--43596264 Score: 398
Period size: 116 Copynumber: 1.9 Consensus size: 116
43596038 GCCTCATCAC
*
43596048 ATATATACACTTTCACATTCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
43596113 TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTATCACAT
66 TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTATCACAT
* *
43596164 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
*
43596229 TCATCACATCGGCTATTAGGCCTTATCACATATATA
66 TCATCACATCGGCCATTAGGCCTTATCACATATATA
43596265 CACTTTCACA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
116 97 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (116 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATACACTTTCACAT
TCATCACATCGGCCATTAGGCCTTATCACATATATATACACTTTATCACAT
Found at i:43596170 original size:69 final size:67
Alignment explanation
Indices: 43596088--43596217 Score: 224
Period size: 69 Copynumber: 1.9 Consensus size: 67
43596078 CTATTAGGCC
43596088 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
1 TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
43596153 CT
66 CT
* *
43596155 TTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATA
1 TTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATA
43596218 CACTTTCACA
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
67 7 0.12
69 52 0.88
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.35
Consensus pattern (67 bp):
TTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTTATCACATATATATACA
CT
Found at i:43596181 original size:18 final size:20
Alignment explanation
Indices: 43596135--43596176 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
43596125 CCATTAGGCC
43596135 TTATCACATATATATACACT
1 TTATCACATATATATACACT
43596155 TTATCACATATATATACACT
1 TTATCACATATATATACACT
43596175 TT
1 TT
43596177 CACATTCATC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.00, T:0.43
Consensus pattern (20 bp):
TTATCACATATATATACACT
Found at i:43596271 original size:163 final size:163
Alignment explanation
Indices: 43596001--43596319 Score: 611
Period size: 163 Copynumber: 2.0 Consensus size: 163
43595991 GCCCTGTCAC
43596001 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACAT
43596066 TCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
66 TCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
43596131 GGCCTTATCACATATATATACACTTTATCACAT
131 GGCCTTATCACATATATATACACTTTATCACAT
* * *
43596164 ATATATACACTTTCACATTCATCACATTGGCCATTCGGCCTTATCACATATATACACTTTCACAT
1 ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACAT
43596229 TCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
66 TCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
43596294 GGCCTTATCACATATATATACACTTT
131 GGCCTTATCACATATATATACACTTT
43596320 CACATTCATC
Statistics
Matches: 153, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
163 153 1.00
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.34
Consensus pattern (163 bp):
ATATATACACTTTCACATTCATCACATCGGCCATTAGGCCTCATCACATATATACACTTTCACAT
TCATCACATCGGCTATTAGGCCTTATCACATATATACACTTTCACATTCATCACATCGGCCATTA
GGCCTTATCACATATATATACACTTTATCACAT
Done.