Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 166 of 279
Found at i:55099803 original size:86 final size:86
Alignment explanation
Indices: 55099713--55099979 Score: 527
Period size: 86 Copynumber: 3.1 Consensus size: 86
55099703 AATATAATTG
55099713 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
55099778 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
55099799 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
55099864 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
55099885 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
1 TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
55099950 TGTTAAGTATTAATGTTGATA
66 TGTTAAGTATTAATGTTGATA
55099971 TAATT-TTAT
1 TAATTATTAT
55099980 GTGGAGAGAA
Statistics
Matches: 181, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
85 4 0.02
86 177 0.98
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.47
Consensus pattern (86 bp):
TAATTATTATAATTTTTATCTTTAATATTAATAATTTGAAATTAATAATAAACATGAAACCTGTT
TGTTAAGTATTAATGTTGATA
Found at i:55102459 original size:92 final size:91
Alignment explanation
Indices: 55102302--55102510 Score: 269
Period size: 92 Copynumber: 2.3 Consensus size: 91
55102292 TTGATTTTAG
** *
55102302 TAAATTCATATAAGAACAATTTATTATTGAGAATTTTATGAAATTATATATCACTATTAAATTAT
1 TAAATTCATATAAGAA-AATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTAT
*
55102367 ATTTAAT-ATTAATTATTTTAAATTATA
65 ATGTAATAATT-ATTATTTTAAATTATA
* *
55102394 TAAATTCATATAAGAAAATTTATTATCAAGTATTTTATGAAATT-TAATATTAATTATTAAATTA
1 TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTAT-ATA-TAACTATTAAATTA
*
55102458 TATGTAATAATTATTATTTTAGATTATA
64 TATGTAATAATTATTATTTTAAATTATA
* * * *
55102486 CAAATTCATAAAATATAATTTATTA
1 TAAATTCATATAAGAAAATTTATTA
55102511 GTTATAATTA
Statistics
Matches: 103, Mismatches: 11, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
90 1 0.01
91 28 0.27
92 71 0.69
93 3 0.03
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (91 bp):
TAAATTCATATAAGAAAATTTATTATCAAGAATTTTATGAAATTATATATAACTATTAAATTATA
TGTAATAATTATTATTTTAAATTATA
Found at i:55102674 original size:120 final size:120
Alignment explanation
Indices: 55102533--55103058 Score: 955
Period size: 120 Copynumber: 4.4 Consensus size: 120
55102523 TTAAATTATT
* * * * * *
55102533 TTAAATCATATATTATAATTAAAATATATTTAATATTAATTAT-TTCAAATTATCTTTTATAGTA
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT-AATTTATATTTTACAGTA
*
55102597 TCATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
65 TCATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
* *
55102653 TTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
55102718 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
55102773 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
55102838 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
55102893 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
55102958 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
66 CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
55103013 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
1 TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTT
55103059 TAAATATGAT
Statistics
Matches: 394, Mismatches: 11, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
120 392 0.99
121 2 0.01
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
TTAAATTATATATTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTAT
CATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTA
Found at i:55102795 original size:18 final size:17
Alignment explanation
Indices: 55102767--55102801 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55102757 ATTATTAAGA
*
55102767 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55102784 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55102802 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55102915 original size:18 final size:17
Alignment explanation
Indices: 55102887--55102921 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55102877 ATTATTAAGA
*
55102887 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55102904 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55102922 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55103035 original size:18 final size:17
Alignment explanation
Indices: 55103007--55103041 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
55102997 ATTATTAAGA
*
55103007 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
55103024 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
55103042 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:55103255 original size:44 final size:45
Alignment explanation
Indices: 55103206--55103296 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
55103196 ACCTCTATTC
* * *
55103206 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
55103250 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
55103295 CA
1 CA
55103297 CCTCTAATCC
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.37, C:0.29, G:0.07, T:0.27
Consensus pattern (45 bp):
CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
Found at i:55103298 original size:16 final size:16
Alignment explanation
Indices: 55103277--55103345 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
55103267 GATTAGCTAT
55103277 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
55103293 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
55103310 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
55103326 TACGCCTCTAATCCAA
1 TACACCTCTAATCCAA
55103342 TACA
1 TACA
55103346 GCGAATCAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
16 34 0.68
17 16 0.32
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:55103319 original size:33 final size:32
Alignment explanation
Indices: 55103277--55103345 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
55103267 GATTAGCTAT
55103277 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
*
55103310 TACACCTCTAATCCAATACGCCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
55103342 TACA
1 TACA
55103346 GCGAATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 8 0.23
33 27 0.77
ACGTcount: A:0.36, C:0.38, G:0.01, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:55107654 original size:13 final size:13
Alignment explanation
Indices: 55107636--55107660 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55107626 ATATGAAATA
55107636 ATTAATAGAATCG
1 ATTAATAGAATCG
55107649 ATTAATAGAATC
1 ATTAATAGAATC
55107661 ATTTAGTTAA
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:0.48, C:0.08, G:0.12, T:0.32
Consensus pattern (13 bp):
ATTAATAGAATCG
Found at i:55118557 original size:17 final size:16
Alignment explanation
Indices: 55118535--55118568 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
55118525 GGGATCAATA
55118535 AATTTTACTCAATGAAT
1 AATTTTACTCAAT-AAT
*
55118552 AATTTTATTCAATAAT
1 AATTTTACTCAATAAT
55118568 A
1 A
55118569 TTAATCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (16 bp):
AATTTTACTCAATAAT
Found at i:55119027 original size:16 final size:16
Alignment explanation
Indices: 55119006--55119041 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
55118996 AAATTAAGTT
*
55119006 AAATATTGTTAAATAA
1 AAATATTGGTAAATAA
*
55119022 AAATATTGGTATATAA
1 AAATATTGGTAAATAA
55119038 AAAT
1 AAAT
55119042 TCACACGTAA
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:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (16 bp):
AAATATTGGTAAATAA
Found at i:55119461 original size:23 final size:26
Alignment explanation
Indices: 55119394--55119462 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 26
55119384 GTAGATGGCT
* *
55119394 TTTTCTTTTTTGTATTTTAAATGCTCA
1 TTTT-TTTTTTGAATTTTTAATGCTCA
* *
55119421 TTTTTTTTTTTAA-ATTTAATG-T-A
1 TTTTTTTTTTGAATTTTTAATGCTCA
55119444 -TTTTTTTTTGAATTTTTAA
1 TTTTTTTTTTGAATTTTTAA
55119463 AATTCTTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
22 11 0.31
23 6 0.17
24 1 0.03
25 6 0.17
26 7 0.20
27 4 0.11
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.68
Consensus pattern (26 bp):
TTTTTTTTTTGAATTTTTAATGCTCA
Found at i:55138407 original size:24 final size:24
Alignment explanation
Indices: 55138349--55138407 Score: 57
Period size: 24 Copynumber: 2.5 Consensus size: 24
55138339 ATATTATTTC
*
55138349 AATACAATAATTAAACTTTATATA
1 AATAAAATAATTAAACTTTATATA
* * * *
55138373 AATATATTAATTATATTTTAT-TA
1 AATAAAATAATTAAACTTTATATA
55138396 AATAAAAATAAT
1 AAT-AAAATAAT
55138408 CTTTAATTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.42
Consensus pattern (24 bp):
AATAAAATAATTAAACTTTATATA
Found at i:55141510 original size:2 final size:2
Alignment explanation
Indices: 55141503--55141537 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
55141493 ACAAAGCCTT
55141503 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
55141538 TCTTTCTATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:55146242 original size:78 final size:78
Alignment explanation
Indices: 55146113--55146271 Score: 291
Period size: 78 Copynumber: 2.0 Consensus size: 78
55146103 ACCATTTGTC
* *
55146113 TACACAGTGGTGAAAGTATGATCGTATAGAGAGTCTTACGGTTAAAGAGGTTTGGTAAGTTTTGG
1 TACACAGTGGTAAAAGTATGATCGTATAGAAAGTCTTACGGTTAAAGAGGTTTGGTAAGTTTTGG
55146178 ATCAAAAGAGTCT
66 ATCAAAAGAGTCT
*
55146191 TACACAGTGGTAAAAGTATGATTGTATAGAAAGTCTTACGGTTAAAGAGGTTTGGTAAGTTTTGG
1 TACACAGTGGTAAAAGTATGATCGTATAGAAAGTCTTACGGTTAAAGAGGTTTGGTAAGTTTTGG
55146256 ATCAAAAGAGTCT
66 ATCAAAAGAGTCT
55146269 TAC
1 TAC
55146272 TTCCCTATGG
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 78 1.00
ACGTcount: A:0.33, C:0.09, G:0.26, T:0.31
Consensus pattern (78 bp):
TACACAGTGGTAAAAGTATGATCGTATAGAAAGTCTTACGGTTAAAGAGGTTTGGTAAGTTTTGG
ATCAAAAGAGTCT
Found at i:55150062 original size:28 final size:28
Alignment explanation
Indices: 55149998--55150068 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
55149988 TTCTATAATA
55149998 GTTTCTGAAAAAATAAATTAGAGAAGAC
1 GTTTCTGAAAAAATAAATTAGAGAAGAC
* *
55150026 GTATT-TGAAAAAATAATTTTA-AGAAGAT
1 GT-TTCTGAAAAAATAA-ATTAGAGAAGAC
*
55150054 GTTTCTGAACAAATA
1 GTTTCTGAAAAAATA
55150069 GTGTCAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
27 2 0.05
28 30 0.81
29 5 0.14
ACGTcount: A:0.48, C:0.06, G:0.15, T:0.31
Consensus pattern (28 bp):
GTTTCTGAAAAAATAAATTAGAGAAGAC
Found at i:55155566 original size:22 final size:21
Alignment explanation
Indices: 55155541--55155582 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
55155531 AAAATTAAAA
*
55155541 AGAACTTTAAGAGGAATTTGAG
1 AGAAATTTAAGA-GAATTTGAG
*
55155563 AGAAATTTGAGAGAATTTGA
1 AGAAATTTAAGAGAATTTGA
55155583 AAGGATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.43, C:0.02, G:0.26, T:0.29
Consensus pattern (21 bp):
AGAAATTTAAGAGAATTTGAG
Found at i:55155954 original size:6 final size:6
Alignment explanation
Indices: 55155943--55155976 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
55155933 TGAGTGAGGC
* *
55155943 CTACGA CTACGA CTACGA CTACTA CTACTA CTAC
1 CTACGA CTACGA CTACGA CTACGA CTACGA CTAC
55155977 ACTCTTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.32, C:0.35, G:0.09, T:0.24
Consensus pattern (6 bp):
CTACGA
Found at i:55156848 original size:3 final size:3
Alignment explanation
Indices: 55156840--55156868 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55156830 GCCTCATTCG
55156840 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
55156869 ATTGCTCATT
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:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:55159014 original size:52 final size:52
Alignment explanation
Indices: 55158931--55159041 Score: 170
Period size: 52 Copynumber: 2.1 Consensus size: 52
55158921 ACATTAAGCT
* * *
55158931 TTGACAGTGAAATAATAACAGCTTGTTTGATTCATTGTAATGTAATAGAGCC
1 TTGATAGTGAAATAATAACAGCTTGTTTGATTCATTGTAACGCAATAGAGCC
*
55158983 TTGATAGTGAAATAATAACAG-TATGTTTGATTCATTGTAACGCAATAGAGCT
1 TTGATAGTGAAATAATAACAGCT-TGTTTGATTCATTGTAACGCAATAGAGCC
55159035 TTGATAG
1 TTGATAG
55159042 ACGTAAGCAT
Statistics
Matches: 54, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
51 1 0.02
52 53 0.98
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (52 bp):
TTGATAGTGAAATAATAACAGCTTGTTTGATTCATTGTAACGCAATAGAGCC
Found at i:55159426 original size:49 final size:49
Alignment explanation
Indices: 55159354--55159453 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
55159344 TACGTCCAAC
55159354 TGAGAATCCCCATTTTCTGAAAAGAAAAACCCGGAGATGAATAATCGCT
1 TGAGAATCCCCATTTTCTGAAAAGAAAAACCCGGAGATGAATAATCGCT
55159403 TGAGAATCCCCATTTTCTGAAAAGAAAAACCCGGAGATGAATAATCGCT
1 TGAGAATCCCCATTTTCTGAAAAGAAAAACCCGGAGATGAATAATCGCT
55159452 TG
1 TG
55159454 GCTTTGCAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (49 bp):
TGAGAATCCCCATTTTCTGAAAAGAAAAACCCGGAGATGAATAATCGCT
Found at i:55162264 original size:80 final size:78
Alignment explanation
Indices: 55162164--55162441 Score: 398
Period size: 76 Copynumber: 3.5 Consensus size: 78
55162154 GTTAGAAAAT
* * *
55162164 AAATAAAAAAAGTGTAATAAATGGTAATCCTAGTAACATTTTTCTATAAAAAGTAATTTCCTTCC
1 AAAT-AAATAAGTGTAATAAATGGTAATCCTAATAACATTTTTCTATAAAAAGTCATTTCCTTCC
*
55162229 GAATTAAAGTTAAAAA
65 CAATTAAAGTT--AAA
* *
55162245 AAATAAATAAGTGTAATAAATGGTAATCCTAATAATATTTTTCTATAAAAAGTCATTTCCTTCCT
1 AAATAAATAAGTGTAATAAATGGTAATCCTAATAACATTTTTCTATAAAAAGTCATTTCCTTCCC
55162310 AATTAAAGTT-AA
66 AATTAAAGTTAAA
* *
55162322 AAA-AAATAAGCGTAATAAATGGTAATCCTAATAACATTTTTCTATAAAAAGTCATTTCCTCCCC
1 AAATAAATAAGTGTAATAAATGGTAATCCTAATAACATTTTTCTATAAAAAGTCATTTCCTTCCC
*
55162386 AATTGAAGTTAAA
66 AATTAAAGTTAAA
* * *
55162399 AAATAGATAAGTGTAATAAATGATAATCTTAATAACAATTTTT
1 AAATAAATAAGTGTAATAAATGGTAATCCTAATAAC-ATTTTT
55162442 TATCCTTCCC
Statistics
Matches: 180, Mismatches: 14, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
76 66 0.37
77 10 0.06
78 28 0.16
79 6 0.03
80 66 0.37
81 4 0.02
ACGTcount: A:0.46, C:0.11, G:0.09, T:0.34
Consensus pattern (78 bp):
AAATAAATAAGTGTAATAAATGGTAATCCTAATAACATTTTTCTATAAAAAGTCATTTCCTTCCC
AATTAAAGTTAAA
Found at i:55162473 original size:7 final size:7
Alignment explanation
Indices: 55162461--55162486 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
55162451 CTTAAAGATA
55162461 AAAAAAT
1 AAAAAAT
55162468 AAAAAAT
1 AAAAAAT
55162475 AAAAAAT
1 AAAAAAT
55162482 AAAAA
1 AAAAA
55162487 GGTGTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:55169923 original size:3 final size:3
Alignment explanation
Indices: 55169915--55169941 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
55169905 GGTGAGCCAA
55169915 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
55169942 TTCACCTTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:55170572 original size:28 final size:29
Alignment explanation
Indices: 55170541--55170614 Score: 82
Period size: 28 Copynumber: 2.7 Consensus size: 29
55170531 ATTTTTTAAA
55170541 ATTTGAAAAA-ATTAAAAAAATGAAAATT
1 ATTTGAAAAATATTAAAAAAATGAAAATT
** *
55170569 ATTT-AAAAATATTAAAACTATTAAAATT
1 ATTTGAAAAATATTAAAAAAATGAAAATT
* *
55170597 ATTAGAAAAGTA-TAAAAA
1 ATTTGAAAAATATTAAAAA
55170615 TTATAAAGAT
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
27 5 0.13
28 27 0.71
29 6 0.16
ACGTcount: A:0.62, C:0.01, G:0.05, T:0.31
Consensus pattern (29 bp):
ATTTGAAAAATATTAAAAAAATGAAAATT
Found at i:55170590 original size:9 final size:9
Alignment explanation
Indices: 55170546--55170615 Score: 54
Period size: 9 Copynumber: 7.7 Consensus size: 9
55170536 TTAAAATTTG
55170546 AAAAA-ATT
1 AAAAATATT
* *
55170554 AAAAAAATG
1 AAAAATATT
*
55170563 AAAATTATTT
1 AAAAATA-TT
55170573 AAAAATATT
1 AAAAATATT
*
55170582 AAAACTATT
1 AAAAATATT
*
55170591 AAAATTATT
1 AAAAATATT
55170600 AGAAAAGTA-T
1 A-AAAA-TATT
55170610 AAAAAT
1 AAAAAT
55170616 TATAAAGATT
Statistics
Matches: 50, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
8 6 0.12
9 30 0.60
10 12 0.24
11 2 0.04
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.30
Consensus pattern (9 bp):
AAAAATATT
Found at i:55170592 original size:18 final size:18
Alignment explanation
Indices: 55170551--55170600 Score: 55
Period size: 19 Copynumber: 2.7 Consensus size: 18
55170541 ATTTGAAAAA
* * *
55170551 ATTAAAAAAATGAAAATT
1 ATTAAAAATATTAAAACT
55170569 ATTTAAAAATATTAAAACT
1 A-TTAAAAATATTAAAACT
*
55170588 ATTAAAATTATTA
1 ATTAAAAATATTA
55170601 GAAAAGTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (18 bp):
ATTAAAAATATTAAAACT
Found at i:55173881 original size:33 final size:33
Alignment explanation
Indices: 55173844--55173908 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
55173834 TTTTAAAAAA
*
55173844 TTCAAAGAAATAT-ATAAAAAATATATAAATATT
1 TTCAAAAAAATATAATAAAAAATATA-AAATATT
* *
55173877 TTCAAAAAAATATAATAATAAATTTAAAATAT
1 TTCAAAAAAATATAATAAAAAATATAAAATAT
55173909 ATATACAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 18 0.64
34 10 0.36
ACGTcount: A:0.62, C:0.03, G:0.02, T:0.34
Consensus pattern (33 bp):
TTCAAAAAAATATAATAAAAAATATAAAATATT
Found at i:55175069 original size:28 final size:30
Alignment explanation
Indices: 55175034--55175091 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
55175024 ATTGACTGAC
55175034 AAACAC-AATTTTT-GTCATAATTTTACTT
1 AAACACAAATTTTTGGTCATAATTTTACTT
55175062 AAACACAAATTTTTGGTCATAATTTTACTT
1 AAACACAAATTTTTGGTCATAATTTTACTT
55175092 CAATTGTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 6 0.21
29 7 0.25
30 15 0.54
ACGTcount: A:0.36, C:0.14, G:0.05, T:0.45
Consensus pattern (30 bp):
AAACACAAATTTTTGGTCATAATTTTACTT
Found at i:55195163 original size:54 final size:54
Alignment explanation
Indices: 55195045--55195148 Score: 142
Period size: 51 Copynumber: 2.0 Consensus size: 54
55195035 TGACCCATGG
* *
55195045 AAATTCTTTTTATCACTTAATTATATATATATTTTAAATTCATCATTCAATTATA
1 AAATT-TTTTTATCACTCAATTATATATATATTTTAAATTCATCATCCAATTATA
* *
55195100 AAATTTTTTTATCACTCAATTATAT-T-T-TTTTTAATTTATCATCCAATTA
1 AAATTTTTTTATCACTCAATTATATATATATTTTAAATTCATCATCCAATTA
55195149 ATAGAGATTG
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
51 19 0.42
52 1 0.02
53 1 0.02
54 19 0.42
55 5 0.11
ACGTcount: A:0.36, C:0.12, G:0.00, T:0.53
Consensus pattern (54 bp):
AAATTTTTTTATCACTCAATTATATATATATTTTAAATTCATCATCCAATTATA
Found at i:55198353 original size:18 final size:18
Alignment explanation
Indices: 55198330--55198379 Score: 59
Period size: 16 Copynumber: 2.8 Consensus size: 18
55198320 AAAAAATTAC
55198330 ATTTAAAAATTATATAAT
1 ATTTAAAAATTATATAAT
*
55198348 ATTT--AAATTACATAAT
1 ATTTAAAAATTATATAAT
*
55198364 AGTTTAAAAAATATAT
1 A-TTTAAAAATTATAT
55198380 TAATCTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 12 0.46
17 3 0.12
18 4 0.15
19 7 0.27
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
ATTTAAAAATTATATAAT
Found at i:55200079 original size:16 final size:15
Alignment explanation
Indices: 55200054--55200086 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
55200044 TTATGTTGAA
55200054 ATAATTTTATAATTC
1 ATAATTTTATAATTC
55200069 ATAATTATTATAATTC
1 ATAATT-TTATAATTC
55200085 AT
1 AT
55200087 GAAAAGCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (15 bp):
ATAATTTTATAATTC
Found at i:55204239 original size:24 final size:25
Alignment explanation
Indices: 55204211--55204257 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
55204201 AAATTTAATC
*
55204211 TTTAATGTTTATATT-TTTTGTTAA
1 TTTAATATTTATATTGTTTTGTTAA
*
55204235 TTTAATATTTATTTTGTTTTGTT
1 TTTAATATTTATATTGTTTTGTT
55204258 TTTTAAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.70
Consensus pattern (25 bp):
TTTAATATTTATATTGTTTTGTTAA
Found at i:55207134 original size:35 final size:35
Alignment explanation
Indices: 55207079--55207153 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
55207069 AAACAATTAC
* **
55207079 GGACCACTTTTACGAATTAGGACATTACTCGTTAT
1 GGACCACTTTAACGAATTAGGACAACACTCGTTAT
* * *
55207114 GGACCACTTTAAGGACTTAGGACAACACTTGTTAT
1 GGACCACTTTAACGAATTAGGACAACACTCGTTAT
55207149 GGACC
1 GGACC
55207154 GCACTCACAC
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (35 bp):
GGACCACTTTAACGAATTAGGACAACACTCGTTAT
Found at i:55216451 original size:17 final size:17
Alignment explanation
Indices: 55216429--55216464 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55216419 TTTATTTTGG
55216429 TGCATAAATTTATTATA
1 TGCATAAATTTATTATA
55216446 TGCATAAATTTATTATA
1 TGCATAAATTTATTATA
55216463 TG
1 TG
55216465 AGTATCAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (17 bp):
TGCATAAATTTATTATA
Found at i:55221771 original size:29 final size:28
Alignment explanation
Indices: 55221720--55221774 Score: 74
Period size: 29 Copynumber: 1.9 Consensus size: 28
55221710 TAAATTCTGG
55221720 AATTATTATAAATATTTTGAATTTTAAA
1 AATTATTATAAATATTTTGAATTTTAAA
* * *
55221748 AATTATATATATATTTTTTTAATTTTA
1 AATTAT-TATAAATATTTTGAATTTTA
55221775 GTTGTGAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
AATTATTATAAATATTTTGAATTTTAAA
Found at i:55226281 original size:20 final size:21
Alignment explanation
Indices: 55226256--55226294 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
55226246 TATCCCATTG
55226256 TTGAAATTAT-TTTTTCAATA
1 TTGAAATTATATTTTTCAATA
*
55226276 TTGAAATTTTATTTTTCAA
1 TTGAAATTATATTTTTCAA
55226295 ATTTCAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TTGAAATTATATTTTTCAATA
Found at i:55231617 original size:22 final size:22
Alignment explanation
Indices: 55231589--55231634 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
55231579 ACTAAAATGA
55231589 AAGCGCCTTAAAAGTTTTGGGC
1 AAGCGCCTTAAAAGTTTTGGGC
55231611 AAGCGCCTTAAAAGTTTTGGGC
1 AAGCGCCTTAAAAGTTTTGGGC
55231633 AA
1 AA
55231635 CTAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.17, G:0.26, T:0.26
Consensus pattern (22 bp):
AAGCGCCTTAAAAGTTTTGGGC
Found at i:55237767 original size:24 final size:24
Alignment explanation
Indices: 55237740--55237787 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
55237730 TGTAGGAATG
*
55237740 TCCATCCATGGTGGACCTAATGCC
1 TCCATCCATGATGGACCTAATGCC
55237764 TCCATCCATGATGGACCTAATGCC
1 TCCATCCATGATGGACCTAATGCC
55237788 ACCTTAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.23, C:0.33, G:0.19, T:0.25
Consensus pattern (24 bp):
TCCATCCATGATGGACCTAATGCC
Found at i:55248648 original size:21 final size:20
Alignment explanation
Indices: 55248620--55248664 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
55248610 ATTTTAACAG
55248620 AACTGCTGATGTAGCAAGTT
1 AACTGCTGATGTAGCAAGTT
* *
55248640 AACTAGCTGATGTGGCCAGTT
1 AACT-GCTGATGTAGCAAGTT
55248661 AACT
1 AACT
55248665 TGTCACGTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.29
Consensus pattern (20 bp):
AACTGCTGATGTAGCAAGTT
Found at i:55252503 original size:21 final size:20
Alignment explanation
Indices: 55252477--55252521 Score: 72
Period size: 21 Copynumber: 2.2 Consensus size: 20
55252467 CTATGTGGCA
55252477 AGTTAACTGGCCACATCAGC
1 AGTTAACTGGCCACATCAGC
*
55252497 TAGTTAACTTGCCACATCAGC
1 -AGTTAACTGGCCACATCAGC
55252518 AGTT
1 AGTT
55252522 CTGTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTTAACTGGCCACATCAGC
Found at i:55252617 original size:30 final size:31
Alignment explanation
Indices: 55252552--55252617 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
55252542 ACTGTTAATC
* *
55252552 AGTGACTGTTTTGTCACTTTTTTATAACGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
*
55252583 AGTGACTGTTTTGTTA-TTTTTCA-AAAGTT
1 AGTGACTGTTTTGTCACTTTTTCATAAAGTT
55252612 AAGTGA
1 -AGTGA
55252618 TTGAAATGAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 5 0.16
30 11 0.35
31 15 0.48
ACGTcount: A:0.24, C:0.09, G:0.18, T:0.48
Consensus pattern (31 bp):
AGTGACTGTTTTGTCACTTTTTCATAAAGTT
Found at i:55252783 original size:35 final size:35
Alignment explanation
Indices: 55252739--55252805 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
55252729 ATTATTAAAA
* *
55252739 TTTATTTTTCACAAATTAATAAGAATTACATACAT
1 TTTAATTTTCACAAATTAACAAGAATTACATACAT
55252774 TTTAATTTTCACAAATTAACAAGAATTACATA
1 TTTAATTTTCACAAATTAACAAGAATTACATA
55252806 TGACAGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (35 bp):
TTTAATTTTCACAAATTAACAAGAATTACATACAT
Found at i:55253755 original size:16 final size:16
Alignment explanation
Indices: 55253734--55253787 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
55253724 GGCTTGACCC
*
55253734 ATTTTAAATTTATAAT
1 ATTTTATATTTATAAT
*
55253750 ATTTTATA-TTATATT
1 ATTTTATATTTATAAT
55253765 ATTTTTATATATTAT-AT
1 A-TTTTATAT-TTATAAT
55253782 ATTTTA
1 ATTTTA
55253788 GAAGACATTA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 7 0.22
16 19 0.59
17 2 0.06
18 4 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATTTTATATTTATAAT
Found at i:55260839 original size:2 final size:2
Alignment explanation
Indices: 55260832--55260890 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
55260822 GCAGAAAAGA
*
55260832 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
55260874 AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG A
55260891 ATAATTATAA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:55264803 original size:15 final size:15
Alignment explanation
Indices: 55264783--55264813 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55264773 TTTGCACTAT
55264783 GTTAGTTCTTTTATA
1 GTTAGTTCTTTTATA
55264798 GTTAGTTCTTTTATA
1 GTTAGTTCTTTTATA
55264813 G
1 G
55264814 ATACTGTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (15 bp):
GTTAGTTCTTTTATA
Found at i:55267687 original size:18 final size:18
Alignment explanation
Indices: 55267645--55267701 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
55267635 AATTATAAAA
**
55267645 ATATATTTTAACGTTTTT
1 ATATATTTTAAAATTTTT
*
55267663 CAAATATTTTAAAATTTTT
1 -ATATATTTTAAAATTTTT
55267682 ATATATTTTAAAATTTTT
1 ATATATTTTAAAATTTTT
55267700 AT
1 AT
55267702 CGAAGTACAC
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.37, C:0.04, G:0.02, T:0.58
Consensus pattern (18 bp):
ATATATTTTAAAATTTTT
Found at i:55272233 original size:44 final size:44
Alignment explanation
Indices: 55272183--55272270 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
55272173 TTGTGGTGAG
55272183 ATGTTGAGTAGGAGAAGAAAGCATTGATTTTAGGATGGATTCAA
1 ATGTTGAGTAGGAGAAGAAAGCATTGATTTTAGGATGGATTCAA
55272227 ATGTTGAGTAGGAGAAGAAAGCATTGATTTTAGGATGGATTCAA
1 ATGTTGAGTAGGAGAAGAAAGCATTGATTTTAGGATGGATTCAA
55272271 TCTGTCAAGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.30, T:0.30
Consensus pattern (44 bp):
ATGTTGAGTAGGAGAAGAAAGCATTGATTTTAGGATGGATTCAA
Found at i:55276764 original size:35 final size:35
Alignment explanation
Indices: 55276713--55276839 Score: 121
Period size: 35 Copynumber: 3.6 Consensus size: 35
55276703 CATGGCAAAG
* * * *
55276713 TGTGAAACATAGGTATGGTATTAACCATACTGAGT
1 TGTGAAACGTAAGTATGATATTATCCATACTGAGT
55276748 TGTGAAACGTAAGTATGATATTATCCATACTGAGT
1 TGTGAAACGTAAGTATGATATTATCCATACTGAGT
** ** * * *
55276783 TAAGAAACGT-AGATATGGCATTTTTCATACGGAGT
1 TGTGAAACGTAAG-TATGATATTATCCATACTGAGT
* *
55276818 TGTGAAATGTAGGTATGATATT
1 TGTGAAACGTAAGTATGATATT
55276840 TCAATGAGGA
Statistics
Matches: 73, Mismatches: 17, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
34 2 0.03
35 70 0.96
36 1 0.01
ACGTcount: A:0.34, C:0.09, G:0.23, T:0.34
Consensus pattern (35 bp):
TGTGAAACGTAAGTATGATATTATCCATACTGAGT
Found at i:55280504 original size:18 final size:20
Alignment explanation
Indices: 55280462--55280498 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
55280452 ATATTTTATG
*
55280462 ATTA-TTTAATTAGATATAT
1 ATTATTTTAATGAGATATAT
55280481 ATTATTTTAATGAGATAT
1 ATTATTTTAATGAGATAT
55280499 TTTATTATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
ATTATTTTAATGAGATATAT
Found at i:55282812 original size:429 final size:429
Alignment explanation
Indices: 55282005--55282867 Score: 1692
Period size: 429 Copynumber: 2.0 Consensus size: 429
55281995 ACCCTAAGGG
*
55282005 CGAA-ATCGTCATTAATTAAAAGTTAAGGGCAAAATGATAATTTTACCTAGATCATTAATTAAAT
1 CGAAGATCATCATTAATTAAAAGTTAAGGGCAAAATGATAATTTTACCTAGATCATTAATTAAAT
55282069 GCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGACGACTCAA
66 GCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGACGACTCAA
55282134 ATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTACTGAAATTATAAACACAAACAAGCA
131 ATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTACTGAAATTATAAACACAAACAAGCA
55282199 ATGAGGTAAGTTCATGTAACTTGAATTATATTCTTAAATGCTTGAAATGCATGTTTTTGATATGA
196 ATGAGGTAAGTTCATGTAACTTGAATTATATTCTTAAATGCTTGAAATGCATGTTTTTGATATGA
*
55282264 ATATGATTTGAATGTTCATTATATGAAATTTTATGAAACATTGACATATTTGATAAAAGAGGAAG
261 ATATGATTTGAATGTTCATTATATGAAATTTTATGAAACATTGACATATTTGATAAAAGAGAAAG
55282329 AAATCCCGGTTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGAT
326 AAATCCCGGTTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGAT
55282394 CTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCC
391 CTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCC
55282433 CGAAGATCATCATTAATTAAAAGTTAAGGGCAAAATGATAATTTTACCTAGATCATTAATTAAAT
1 CGAAGATCATCATTAATTAAAAGTTAAGGGCAAAATGATAATTTTACCTAGATCATTAATTAAAT
55282498 GCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGACGACTCAA
66 GCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGACGACTCAA
55282563 ATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTACTGAAATTATAAACACAAACAAGCA
131 ATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTACTGAAATTATAAACACAAACAAGCA
55282628 ATGAGGTAAGTTCATGTAACTTGAATTATATTCTTAAATGCTTGAAATGCATGTTTTTGATATGA
196 ATGAGGTAAGTTCATGTAACTTGAATTATATTCTTAAATGCTTGAAATGCATGTTTTTGATATGA
*
55282693 ATATGATTTGAATGTTCATTATATGGAATTTTATGAAACATTGACATATTTGATAAAAGAGAAAG
261 ATATGATTTGAATGTTCATTATATGAAATTTTATGAAACATTGACATATTTGATAAAAGAGAAAG
55282758 AAATCCCGGTTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGAT
326 AAATCCCGGTTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGAT
55282823 CTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCC
391 CTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCC
55282862 CGAAGA
1 CGAAGA
55282868 ATACGTGTAA
Statistics
Matches: 431, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
428 4 0.01
429 427 0.99
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (429 bp):
CGAAGATCATCATTAATTAAAAGTTAAGGGCAAAATGATAATTTTACCTAGATCATTAATTAAAT
GCATTAGAATATGAAATGAATGAAAATGATGATCAAATTTATTTATAAAGATCCGGACGACTCAA
ATATGAGACTTGATCGTGGAAAAGAAAAGATATCGGATTACTGAAATTATAAACACAAACAAGCA
ATGAGGTAAGTTCATGTAACTTGAATTATATTCTTAAATGCTTGAAATGCATGTTTTTGATATGA
ATATGATTTGAATGTTCATTATATGAAATTTTATGAAACATTGACATATTTGATAAAAGAGAAAG
AAATCCCGGTTGAATGAAAGGAAAATTCGATGGATCTCTGAAAAGGAATTGACGGTAAAAAGGAT
CTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCC
Found at i:55283085 original size:46 final size:46
Alignment explanation
Indices: 55283038--55283266 Score: 278
Period size: 46 Copynumber: 5.0 Consensus size: 46
55283028 GCTCTCTGAT
* * * *
55283038 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAGCCTGAT
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
*
55283084 ATGAAATGTGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * *
55283130 GGGAAATAAATAAGACCATGGTTGAAAGATACCATGGCAGCGTGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
* *
55283176 ATGAAATGAATAAGACCATGGTTGAAAGACACCATGGCAACATGAC
1 ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
** * * * *
55283222 AAAAAAATGAGTAAGACCATAGTTGAAAGACACTATGGCATCATG
1 -ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATG
55283267 TCAAAGATAA
Statistics
Matches: 160, Mismatches: 22, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
46 122 0.76
47 38 0.24
ACGTcount: A:0.41, C:0.15, G:0.24, T:0.20
Consensus pattern (46 bp):
ATGAAATGAGTAAGACCATGGTTGAAAGATACCATGGCAACATGAC
Found at i:55303732 original size:37 final size:37
Alignment explanation
Indices: 55303674--55303819 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
55303664 TACGTATGAT
* *
55303674 CACTTATCA-TTTG-TCCCTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55303709 CACCTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55303746 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
*
55303783 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
55303820 TAAAGCTATC
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 8 0.08
36 4 0.04
37 92 0.88
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (37 bp):
CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
Found at i:55303836 original size:46 final size:46
Alignment explanation
Indices: 55303783--55304051 Score: 331
Period size: 46 Copynumber: 5.6 Consensus size: 46
55303773 TAAGTGTAGC
* **
55303783 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* *
55303829 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55303875 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
*
55303927 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
* ** * *
55303973 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGGTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
55304025 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
55304052 AGTACTCAAA
Statistics
Matches: 198, Mismatches: 13, Indels: 24
0.84 0.06 0.10
Matches are distributed among these distances:
46 112 0.57
48 1 0.01
49 2 0.01
50 1 0.01
52 82 0.41
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
Found at i:55303902 original size:52 final size:52
Alignment explanation
Indices: 55303826--55304045 Score: 290
Period size: 52 Copynumber: 4.3 Consensus size: 52
55303816 TAGCTAAAGC
* *
55303826 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTATCACT
1 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55303879 TATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
*
55303931 TATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
* * ** * *
55303977 TATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGGTACCACT
1 TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
55304029 TATCACTTTGTCACTTG
1 TATCACTTT-TCACTTG
55304046 ATCAGAAGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 14
0.84 0.07 0.08
Matches are distributed among these distances:
46 43 0.29
49 1 0.01
52 85 0.58
53 18 0.12
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (52 bp):
TATCACTTTTCACTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATCACT
Found at i:55303948 original size:98 final size:98
Alignment explanation
Indices: 55303783--55304051 Score: 448
Period size: 98 Copynumber: 2.7 Consensus size: 98
55303773 TAAGTGTAGC
* * *
55303783 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACT
55303848 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
**
55303882 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
*
55303947 GATCAGATAAGTATAGCCGAAGCTATTACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* * *
55303980 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGGTACCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
55304045 GATCAGA
66 GATCAGA
55304052 AGTACTCAAA
Statistics
Matches: 159, Mismatches: 11, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
98 150 0.94
99 9 0.06
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:55307233 original size:49 final size:50
Alignment explanation
Indices: 55307178--55307381 Score: 241
Period size: 49 Copynumber: 4.0 Consensus size: 50
55307168 TTCGTTTTCT
*
55307178 CGATGCCATAGTCCAACTATGGTCTTACACGTAATCACA-AATCACATAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* * *
55307227 CGATGCCATAGCCCAACTATGGTCTTACACGAAATCACA-TATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
* *
55307276 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATATCACACATATCACTTAC
1 CGATGCCATAGCCCAACTATGGTCTTACAC-G--T---A-ATCACACA-ATCACATAC
* * *
55307334 CGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCACAT
1 CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACAT
55307382 GTTCACATGT
Statistics
Matches: 136, Mismatches: 10, Indels: 17
0.83 0.06 0.10
Matches are distributed among these distances:
49 74 0.54
50 7 0.05
51 7 0.05
52 1 0.01
55 1 0.01
56 6 0.04
57 1 0.01
58 39 0.29
ACGTcount: A:0.32, C:0.30, G:0.14, T:0.24
Consensus pattern (50 bp):
CGATGCCATAGCCCAACTATGGTCTTACACGTAATCACACAATCACATAC
Found at i:55307348 original size:58 final size:59
Alignment explanation
Indices: 55307262--55307380 Score: 231
Period size: 58 Copynumber: 2.0 Consensus size: 59
55307252 TACACGAAAT
55307262 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACAT-ATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
55307320 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
1 CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
55307379 CA
1 CA
55307381 TGTTCACATG
Statistics
Matches: 60, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
58 54 0.90
59 6 0.10
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (59 bp):
CACATATCACTTACCGATGCCATAGCCCAGCTATGGTCTTACACGGAATCACATAATCA
Found at i:55307361 original size:28 final size:28
Alignment explanation
Indices: 55307271--55307361 Score: 80
Period size: 28 Copynumber: 3.2 Consensus size: 28
55307261 TCACATATCA
55307271 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
* * **
55307299 CTTACACGGAAT-CACATATCACA-CATAT-CA
1 CTTAC-C-G-ATGC-CATAGCCCAGC-TATGGT
55307329 CTTACCGATGCCATAGCCCAGCTATGGT
1 CTTACCGATGCCATAGCCCAGCTATGGT
55307357 CTTAC
1 CTTAC
55307362 ACGGAATCAC
Statistics
Matches: 47, Mismatches: 8, Indels: 16
0.66 0.11 0.23
Matches are distributed among these distances:
27 12 0.26
28 13 0.28
29 2 0.04
30 8 0.17
31 12 0.26
ACGTcount: A:0.27, C:0.32, G:0.15, T:0.25
Consensus pattern (28 bp):
CTTACCGATGCCATAGCCCAGCTATGGT
Found at i:55308757 original size:37 final size:37
Alignment explanation
Indices: 55308700--55308804 Score: 160
Period size: 37 Copynumber: 2.9 Consensus size: 37
55308690 TATGATCACT
*
55308700 TATCACT-TGTC-CCTGATCAGATAAGTGTAGCCACC
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
* * *
55308735 TATCACTTTGTTTCTTGATCAGATAAGTGTAGCCACT
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
55308772 TATCACTCTGTCTCTTGATCAGATAAGTGTAGC
1 TATCACTCTGTCTCTTGATCAGATAAGTGTAGC
55308805 TAAAGCTATC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
35 7 0.11
36 3 0.05
37 53 0.84
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (37 bp):
TATCACTCTGTCTCTTGATCAGATAAGTGTAGCCACC
Found at i:55308847 original size:52 final size:52
Alignment explanation
Indices: 55308768--55309179 Score: 475
Period size: 52 Copynumber: 8.2 Consensus size: 52
55308758 TAAGTGTAGC
* * *
55308768 CACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTAT
1 CACTTTTCACT-TGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
*
55308821 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55308873 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55308919 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55308971 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55309017 CACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55309069 CAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
* * *
55309115 CACTTTCCACTTGTCACTT-ATCAGATAAGTGTAGCTAAAGCTACCACTTAT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
55309166 CACTTTGTCACTTG
1 CACTTT-TCACTTG
55309180 ATCAGAAGTA
Statistics
Matches: 303, Mismatches: 37, Indels: 39
0.80 0.10 0.10
Matches are distributed among these distances:
46 123 0.41
49 1 0.00
51 33 0.11
52 136 0.45
53 10 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (52 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCAAAGCTATCACTTAT
Found at i:55308890 original size:46 final size:46
Alignment explanation
Indices: 55308818--55309185 Score: 416
Period size: 46 Copynumber: 7.7 Consensus size: 46
55308808 AGCTATCACT
*
55308818 TATCACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
55308863 TATCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
55308909 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* *
55308961 TACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
55309007 TATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* *
55309059 TACCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGC
1 TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
* **
55309105 TATTACTTATCACTTTCCACTTGTCACTT-ATCAGATAAGTGTAGCTAAAGC
1 TATCACTTATCAC--T----TTGTCACTTGATCAGATAAGTGTAGCCGAAGC
*
55309156 TACCACTTATCACTTTGTCACTTGATCAGA
1 TATCACTTATCACTTTGTCACTTGATCAGA
55309186 AGTACTCAAA
Statistics
Matches: 275, Mismatches: 28, Indels: 39
0.80 0.08 0.11
Matches are distributed among these distances:
45 21 0.08
46 129 0.47
48 3 0.01
49 1 0.00
50 2 0.01
51 30 0.11
52 89 0.32
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (46 bp):
TATCACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCCGAAGC
Found at i:55308934 original size:98 final size:98
Alignment explanation
Indices: 55308767--55309185 Score: 741
Period size: 98 Copynumber: 4.3 Consensus size: 98
55308757 ATAAGTGTAG
* * * ** * *
55308767 CCACTTATCACTCTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTTCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
**
55308832 TGTCACTTGATCAGATAAGTGTAGCCGAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
*
55308865 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
55308930 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
55308963 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
55309028 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
55309061 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
55309126 TGTCACTT-ATCAGATAAGTGTAGCTAAAGCTA
66 TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
55309158 CCACTTATCACTTTGTCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
55309186 AGTACTCAAA
Statistics
Matches: 310, Mismatches: 11, Indels: 1
0.96 0.03 0.00
Matches are distributed among these distances:
97 52 0.17
98 258 0.83
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (98 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACT
TGTCACTTGATCAGATAAGTGTAGCTAAAGCTA
Found at i:55312410 original size:30 final size:30
Alignment explanation
Indices: 55312349--55312410 Score: 72
Period size: 31 Copynumber: 2.1 Consensus size: 30
55312339 TTAATAGGGT
**
55312349 ATTCAAATCACTTTTCAAATTTCACTTTCA
1 ATTCAAATCACTTTTCAAATTTCACAATCA
* *
55312379 ATTCAAAATCACTTTTCCATTTTCA-AATCA
1 ATTC-AAATCACTTTTCAAATTTCACAATCA
55312409 AT
1 AT
55312411 ATACAATTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 9 0.33
31 18 0.67
ACGTcount: A:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTCAAATCACTTTTCAAATTTCACAATCA
Found at i:55313201 original size:11 final size:10
Alignment explanation
Indices: 55313178--55313271 Score: 52
Period size: 10 Copynumber: 9.2 Consensus size: 10
55313168 TTTTCTATGC
55313178 TTTGTTTCTT
1 TTTGTTTCTT
55313188 TTTGTTTCCTT
1 TTTGTTT-CTT
*
55313199 TTTCTTTCTT
1 TTTGTTTCTT
*
55313209 TTAT-TTGAGCTT
1 TT-TGTT--TCTT
*
55313221 TCTGTTTCTT
1 TTTGTTTCTT
* *
55313231 TTCT-ATGC--
1 TT-TGTTTCTT
55313239 TTTGTTTCTT
1 TTTGTTTCTT
55313249 TTTGTTTCCTT
1 TTTGTTT-CTT
*
55313260 TTTCTTTCTT
1 TTTGTTTCTT
55313270 TT
1 TT
55313272 ATTTGAGCTT
Statistics
Matches: 64, Mismatches: 10, Indels: 20
0.68 0.11 0.21
Matches are distributed among these distances:
7 1 0.02
8 4 0.06
10 32 0.50
11 21 0.33
12 6 0.09
ACGTcount: A:0.03, C:0.16, G:0.09, T:0.72
Consensus pattern (10 bp):
TTTGTTTCTT
Found at i:55313228 original size:22 final size:21
Alignment explanation
Indices: 55313203--55313292 Score: 71
Period size: 22 Copynumber: 4.3 Consensus size: 21
55313193 TTCCTTTTTC
55313203 TTTCTTTTATTTGAGCTTTCTG
1 TTTCTTTTATTT-AGCTTTCTG
* *
55313225 TTTCTTTTCTAT-GC-TT-TG
1 TTTCTTTTATTTAGCTTTCTG
** * *
55313243 TTTCTTTT-TGTTTCCTTTTTC
1 TTTCTTTTAT-TTAGCTTTCTG
55313264 TTTCTTTTATTTGAGCTTTCTG
1 TTTCTTTTATTT-AGCTTTCTG
55313286 TTTCTTT
1 TTTCTTT
55313293 CCTTTTGTTT
Statistics
Matches: 53, Mismatches: 9, Indels: 12
0.72 0.12 0.16
Matches are distributed among these distances:
17 1 0.02
18 11 0.21
19 3 0.06
20 4 0.08
21 11 0.21
22 23 0.43
ACGTcount: A:0.06, C:0.16, G:0.10, T:0.69
Consensus pattern (21 bp):
TTTCTTTTATTTAGCTTTCTG
Found at i:55313236 original size:61 final size:61
Alignment explanation
Indices: 55313165--55313311 Score: 258
Period size: 61 Copynumber: 2.4 Consensus size: 61
55313155 GCTTCTGTTC
55313165 TTCTTTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGT
1 TTCTTTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGT
55313226 TTCTTTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGT
1 TTCTTTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGT
* * *
55313287 TTCTTTCCTTTTGTTTTGTTTCTTT
1 TTCTTTTC-TATGCTTTGTTTCTTT
55313312 ATTTTACTTT
Statistics
Matches: 82, Mismatches: 3, Indels: 1
0.95 0.03 0.01
Matches are distributed among these distances:
61 68 0.83
62 14 0.17
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (61 bp):
TTCTTTTCTATGCTTTGTTTCTTTTTGTTTCCTTTTTCTTTCTTTTATTTGAGCTTTCTGT
Found at i:55313340 original size:3 final size:3
Alignment explanation
Indices: 55313332--55313357 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55313322 ATGTTTTGTT
55313332 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
55313358 TATTATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:55313362 original size:3 final size:3
Alignment explanation
Indices: 55313356--55313380 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
55313346 AATAATAATA
55313356 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
55313381 CTACTACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:55313489 original size:3 final size:3
Alignment explanation
Indices: 55313481--55313506 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
55313471 TGTCTTTATT
55313481 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
55313507 TATCATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:55314925 original size:40 final size:40
Alignment explanation
Indices: 55314870--55314949 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
55314860 CTCCTCATAA
55314870 CCATAATAGAAAAGTATAGGGTGTTTATGCCCTGTAATTT
1 CCATAATAGAAAAGTATAGGGTGTTTATGCCCTGTAATTT
55314910 CCATAATAGAAAAGTATAGGGTGTTTATGCCCTGTAATTT
1 CCATAATAGAAAAGTATAGGGTGTTTATGCCCTGTAATTT
55314950 TTACAGCATC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.12, G:0.20, T:0.35
Consensus pattern (40 bp):
CCATAATAGAAAAGTATAGGGTGTTTATGCCCTGTAATTT
Found at i:55323627 original size:14 final size:15
Alignment explanation
Indices: 55323608--55323667 Score: 54
Period size: 14 Copynumber: 4.1 Consensus size: 15
55323598 TTTTGTTTCC
*
55323608 TTTTGTTCCTTT-TT
1 TTTTGTTTCTTTATT
* *
55323622 TTTTG-TGCTTTCTAT
1 TTTTGTTTCTTTAT-T
*
55323637 TTTTGTTTCTTT-TC
1 TTTTGTTTCTTTATT
55323651 TTTTGTTTCTTTATT
1 TTTTGTTTCTTTATT
55323666 TT
1 TT
55323668 ACGTTATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
13 5 0.13
14 18 0.47
15 10 0.26
16 5 0.13
ACGTcount: A:0.03, C:0.12, G:0.08, T:0.77
Consensus pattern (15 bp):
TTTTGTTTCTTTATT
Found at i:55323821 original size:3 final size:3
Alignment explanation
Indices: 55323807--55323873 Score: 57
Period size: 3 Copynumber: 22.7 Consensus size: 3
55323797 ATTTATATAC
* * * * *
55323807 TAA TAC TAA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TCAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
*
55323853 TAG T-A TAA TAA T-A TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
55323874 TATCATAAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
2 3 0.05
3 50 0.91
4 2 0.04
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:55324427 original size:15 final size:14
Alignment explanation
Indices: 55324384--55324427 Score: 52
Period size: 15 Copynumber: 3.0 Consensus size: 14
55324374 TAGGAAATTC
*
55324384 TATTTTAAGTTTAT
1 TATTTTAATTTTAT
*
55324398 TTTTTTAATTATTAT
1 TATTTTAATT-TTAT
55324413 TATTTTAGATTTTAT
1 TATTTTA-ATTTTAT
55324428 ATTAATTTTC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 8 0.32
15 14 0.56
16 3 0.12
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (14 bp):
TATTTTAATTTTAT
Found at i:55325340 original size:19 final size:19
Alignment explanation
Indices: 55325316--55325354 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55325306 TATTTTGTTA
55325316 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
55325335 TTTATTTTTATTTCATCTT
1 TTTATTTTTATTTCATCTT
55325354 T
1 T
55325355 AACTTTTTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTATTTTTATTTCATCTT
Found at i:55325361 original size:19 final size:19
Alignment explanation
Indices: 55325319--55325363 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
55325309 TTTGTTATTT
*
55325319 ATTTTTATTTCATCTTTTT
1 ATTTTTATTTCATCTTTTA
55325338 ATTTTTATTTCATC-TTTA
1 ATTTTTATTTCATCTTTTA
55325356 ACTTTTTA
1 A-TTTTTA
55325364 CTTTTTACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.20, C:0.11, G:0.00, T:0.69
Consensus pattern (19 bp):
ATTTTTATTTCATCTTTTA
Found at i:55329863 original size:34 final size:34
Alignment explanation
Indices: 55329820--55329888 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
55329810 ATGTAACAAA
55329820 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
1 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
55329854 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
1 TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
55329888 T
1 T
55329889 ACTTGGGTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.42
Consensus pattern (34 bp):
TGAATAAGTCTATAAAAAGTTCTAGTATTTATTC
Found at i:55332201 original size:42 final size:42
Alignment explanation
Indices: 55332140--55332252 Score: 172
Period size: 42 Copynumber: 2.7 Consensus size: 42
55332130 TCGTTTTCTC
** * *
55332140 GATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAAT
1 GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
* *
55332182 GATGCCATAGCCCAGCTATGGTCTTACACATATTCATATATT
1 GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
55332224 GATGCCATAGCCCAGCTATGGTCTTACAC
1 GATGCCATAGCCCAGCTATGGTCTTACAC
55332253 GAATCATATA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 65 1.00
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (42 bp):
GATGCCATAGCCCAGCTATGGTCTTACACATATTCACATAAT
Found at i:55332290 original size:46 final size:47
Alignment explanation
Indices: 55332181--55332342 Score: 156
Period size: 47 Copynumber: 3.6 Consensus size: 47
55332171 CTTCACATAA
* * * **
55332181 TGATGCCATAGCCCAGCTATGGTCTTACACATATTCATATAT-----
1 TGATGCCATATCCCAGATATGGTCTTACACAGAAGCATATATCACAC
* * * *
55332223 TGATGCCATAGCCCAGCTATGGTCTTACAC-GAATCATATATCTCAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGAAGCATATATCACAC
* * *
55332269 TGATGCCATATCCCAAATATGGTCTTATACAGTAGCATATATCACAC
1 TGATGCCATATCCCAGATATGGTCTTACACAGAAGCATATATCACAC
* *
55332316 CGATGCCATATCTCAGATATGGTCTTA
1 TGATGCCATATCCCAGATATGGTCTTA
55332343 TACGGATATC
Statistics
Matches: 102, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
41 9 0.09
42 30 0.29
46 26 0.25
47 37 0.36
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.31
Consensus pattern (47 bp):
TGATGCCATATCCCAGATATGGTCTTACACAGAAGCATATATCACAC
Found at i:55332399 original size:31 final size:31
Alignment explanation
Indices: 55332364--55332574 Score: 341
Period size: 31 Copynumber: 6.8 Consensus size: 31
55332354 CTTGTCACTT
* *
55332364 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
55332395 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
55332426 GTAGCCGGAGCTACCAATTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
55332457 GTAGCCGGAGCTACCAATTTTCATTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
* *
55332488 GTAGCAGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
55332519 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGGAGCTACCACTTTTCACTGATCAG
*
55332550 GTAGCCGAAGCTACCACTTTTCACT
1 GTAGCCGGAGCTACCACTTTTCACT
55332575 TGTCATTTGT
Statistics
Matches: 169, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 169 1.00
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (31 bp):
GTAGCCGGAGCTACCACTTTTCACTGATCAG
Found at i:55332655 original size:50 final size:50
Alignment explanation
Indices: 55332550--55332726 Score: 266
Period size: 50 Copynumber: 3.5 Consensus size: 50
55332540 CACTGATCAG
* * * *
55332550 GTAGCCGAAGCTACCACTTTTCACTTGTCATTTGTCCCTGATCAGATAGGT
1 GTAGCCGAAGCTATCACTTATCACTT-TCATTTGTCCTTGATCAGATAAGT
* *
55332601 GTAGCAGAAGCTATCACTTATCACTTTCACTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
55332651 GTAGCCGAAGCTA-CTACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATC-ACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
*
55332701 GTAGCCGAAGCGATCACTTATCACTT
1 GTAGCCGAAGCTATCACTTATCACTT
55332727 ATTTCCATGG
Statistics
Matches: 115, Mismatches: 9, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
49 1 0.01
50 90 0.78
51 24 0.21
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (50 bp):
GTAGCCGAAGCTATCACTTATCACTTTCATTTGTCCTTGATCAGATAAGT
Found at i:55335163 original size:46 final size:46
Alignment explanation
Indices: 55335105--55335274 Score: 177
Period size: 46 Copynumber: 3.7 Consensus size: 46
55335095 TGTAACCCGC
55335105 CCATAAGCGAACTCGGACTCAACTCAACGAGCTAGGGCATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTAGGGCATTCGCAT
* * *
55335151 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTAGG--G-C-A-TTCGCAT
* * * * *
55335201 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTTGGACTTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGCTAGGGCATTCGCAT
**
55335244 CCATAAATGAACTCGGACTCAACTCAACGAG
1 CCATAAGCGAACTCGGACTCAACTCAACGAG
55335275 TTCGGATGCC
Statistics
Matches: 103, Mismatches: 12, Indels: 18
0.77 0.09 0.14
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 2 0.02
46 57 0.55
47 26 0.25
48 3 0.03
49 2 0.02
50 4 0.04
51 2 0.02
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGCTAGGGCATTCGCAT
Found at i:55335224 original size:93 final size:93
Alignment explanation
Indices: 55335112--55335284 Score: 292
Period size: 93 Copynumber: 1.9 Consensus size: 93
55335102 CGCCCATAAG
* *
55335112 CGAACTCGGACTCAACTCAACGAGCTAGGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTAGGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
55335177 ACGAGCTCGGATGCCTAGTTACATCTCA
66 ACGAGCTCGGATGCCTAGTTACATCTCA
* * *
55335205 CGAACTCGGACTCAACTCAACGAGTTTGGACTTTCGCATCCATAAATGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTAGGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
*
55335270 ACGAGTTCGGATGCC
66 ACGAGCTCGGATGCC
55335285 CAAATATCCC
Statistics
Matches: 74, Mismatches: 6, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTAGGACATTCGCATCCATAAATGAACTCGGACTCAACTCA
ACGAGCTCGGATGCCTAGTTACATCTCA
Found at i:55338649 original size:18 final size:18
Alignment explanation
Indices: 55338624--55338683 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
55338614 AGATGTTCGA
55338624 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
* * *
55338642 CATGGATTTC-CCAGAGAT
1 CTTGGATTTCTCC-GAAAC
55338660 CTTGGATTTCTCCGAAAC
1 CTTGGATTTCTCCGAAAC
55338678 CTTGGA
1 CTTGGA
55338684 GATCCTCGGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 2 0.06
18 30 0.88
19 2 0.06
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.32
Consensus pattern (18 bp):
CTTGGATTTCTCCGAAAC
Found at i:55338721 original size:30 final size:30
Alignment explanation
Indices: 55338685--55338742 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
55338675 AACCTTGGAG
55338685 ATCCTCGGTCTCACAGATTATTGGAAACTT
1 ATCCTCGGTCTCACAGATTATTGGAAACTT
55338715 ATCCTCGGTCTCACAGATTATTGGAAAC
1 ATCCTCGGTCTCACAGATTATTGGAAAC
55338743 GGCTTGACTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (30 bp):
ATCCTCGGTCTCACAGATTATTGGAAACTT
Found at i:55338774 original size:18 final size:18
Alignment explanation
Indices: 55338751--55338787 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
55338741 ACGGCTTGAC
55338751 TGTTCCGGTTATTTGGTT
1 TGTTCCGGTTATTTGGTT
55338769 TGTTCCGGTTATTTGGTT
1 TGTTCCGGTTATTTGGTT
55338787 T
1 T
55338788 ATGAAATGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.05, C:0.11, G:0.27, T:0.57
Consensus pattern (18 bp):
TGTTCCGGTTATTTGGTT
Found at i:55340857 original size:43 final size:43
Alignment explanation
Indices: 55340809--55340891 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
55340799 TTAATTGGGA
55340809 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAAGT
1 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAAGT
* * *
55340852 AAATAGTTCCCTTATTCTAGTAAACTACTAACAGATAAAA
1 AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA
55340892 TAAAAATATT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.47, C:0.17, G:0.06, T:0.30
Consensus pattern (43 bp):
AAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAAGT
Found at i:55340899 original size:43 final size:43
Alignment explanation
Indices: 55340807--55340899 Score: 134
Period size: 43 Copynumber: 2.2 Consensus size: 43
55340797 TCTTAATTGG
55340807 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
* * * *
55340850 GTAAATAGTTCCCTTATTCTAGTAAACTACTAACAGATAAAATA
1 GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAA-A
55340894 -AAAATA
1 GAAAATA
55340900 TTTCTAGAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
43 43 0.98
44 1 0.02
ACGTcount: A:0.49, C:0.15, G:0.06, T:0.29
Consensus pattern (43 bp):
GAAAATAGTTCCCTTATTCTAATAAACTACTAAAACATAAAAA
Found at i:55340943 original size:19 final size:18
Alignment explanation
Indices: 55340921--55340960 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
55340911 TGAATAAAAC
55340921 TTATCTACCCAAATAAGAT
1 TTATCTACCCAAATAA-AT
*
55340940 TTATCTACCTAAATAAAT
1 TTATCTACCCAAATAAAT
55340958 TTA
1 TTA
55340961 AAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (18 bp):
TTATCTACCCAAATAAAT
Found at i:55343503 original size:36 final size:36
Alignment explanation
Indices: 55343463--55343534 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
55343453 AAATATTTGA
55343463 AAGAGAAATTTAGCTGCAGACTAATTAGTTAAGATG
1 AAGAGAAATTTAGCTGCAGACTAATTAGTTAAGATG
55343499 AAGAGAAATTTAGCTGCAGACTAATTAGTTAAGATG
1 AAGAGAAATTTAGCTGCAGACTAATTAGTTAAGATG
55343535 GTATCTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (36 bp):
AAGAGAAATTTAGCTGCAGACTAATTAGTTAAGATG
Found at i:55345797 original size:12 final size:12
Alignment explanation
Indices: 55345780--55345813 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
55345770 CAACATCTAC
55345780 GCCGCCGCAGCT
1 GCCGCCGCAGCT
*
55345792 GCCGCCGCTGCT
1 GCCGCCGCAGCT
*
55345804 GCCTCCGCAG
1 GCCGCCGCAG
55345814 ACCGTCGTGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.06, C:0.50, G:0.32, T:0.12
Consensus pattern (12 bp):
GCCGCCGCAGCT
Found at i:55345985 original size:18 final size:18
Alignment explanation
Indices: 55345959--55346031 Score: 65
Period size: 18 Copynumber: 4.1 Consensus size: 18
55345949 ATGATGATCC
* *
55345959 TAACGAAAATAATATTAG
1 TAACAAAAATAATAATAG
* *
55345977 TAACAAAAATCATAATAT
1 TAACAAAAATAATAATAG
* * * *
55345995 TAATATAAATAATCATAT
1 TAACAAAAATAATAATAG
*
55346013 TAATAAAAATAATAATAG
1 TAACAAAAATAATAATAG
55346031 T
1 T
55346032 GGAAACGAGA
Statistics
Matches: 44, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 44 1.00
ACGTcount: A:0.59, C:0.05, G:0.04, T:0.32
Consensus pattern (18 bp):
TAACAAAAATAATAATAG
Found at i:55362839 original size:24 final size:24
Alignment explanation
Indices: 55362807--55362860 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
55362797 CATAGCTGGC
55362807 TGTTTAGTTCATTAGTCACCCTAA
1 TGTTTAGTTCATTAGTCACCCTAA
55362831 TGTTTAGTTCATTAGTCACCCTAA
1 TGTTTAGTTCATTAGTCACCCTAA
*
55362855 TTTTTA
1 TGTTTA
55362861 ACAGTAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.11, T:0.46
Consensus pattern (24 bp):
TGTTTAGTTCATTAGTCACCCTAA
Found at i:55366802 original size:20 final size:20
Alignment explanation
Indices: 55366779--55366816 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55366769 TAAATATAAG
55366779 AAACTGAAA-AATTTTAATGA
1 AAACT-AAACAATTTTAATGA
*
55366799 AAACTAAACCATTTTAAT
1 AAACTAAACAATTTTAAT
55366817 ACAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.53, C:0.11, G:0.05, T:0.32
Consensus pattern (20 bp):
AAACTAAACAATTTTAATGA
Found at i:55383339 original size:31 final size:30
Alignment explanation
Indices: 55383304--55383368 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 30
55383294 AAAGAGAATT
*
55383304 TTTTAAAA-ATTTGAAGGGTCATAATTAAAA
1 TTTTAAAATATTTGAAGGGT-ATAATGAAAA
* *
55383334 GTTTTAAAATTTTTTAAGGGTATAATGAAAA
1 -TTTTAAAATATTTGAAGGGTATAATGAAAA
55383365 TTTT
1 TTTT
55383369 CCTAATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
30 4 0.13
31 17 0.57
32 9 0.30
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.43
Consensus pattern (30 bp):
TTTTAAAATATTTGAAGGGTATAATGAAAA
Found at i:55385327 original size:3 final size:3
Alignment explanation
Indices: 55385319--55385351 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
55385309 CAATAAATAC
55385319 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
55385352 TCCATGTGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:55385932 original size:29 final size:31
Alignment explanation
Indices: 55385874--55385937 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 31
55385864 ATAATTCTAA
* **
55385874 CATTTTTAAAGGGTTTAAACTGAATTTTTTT
1 CATTTTTAAAGGGTCTAAACTGAAAATTTTT
55385905 CATTTTT-AAGGG-CTAAACTGAAAATTTTT
1 CATTTTTAAAGGGTCTAAACTGAAAATTTTT
55385934 -ATTT
1 CATTT
55385938 ATATTAATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 4 0.13
29 14 0.47
30 5 0.17
31 7 0.23
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.48
Consensus pattern (31 bp):
CATTTTTAAAGGGTCTAAACTGAAAATTTTT
Found at i:55391171 original size:3 final size:3
Alignment explanation
Indices: 55391163--55391190 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
55391153 TTTATAAGTA
55391163 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
55391191 GATTATGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55391563 original size:22 final size:23
Alignment explanation
Indices: 55391526--55391569 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 23
55391516 GTTCTATTAT
55391526 TAGCACGTTAAGTGCTCTCTGTA
1 TAGCACGTTAAGTGCTCTCTGTA
*
55391549 TAGCAC-TTTAGTGCTCTCTGT
1 TAGCACGTTAAGTGCTCTCTGT
55391570 TCGCTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (23 bp):
TAGCACGTTAAGTGCTCTCTGTA
Found at i:55393021 original size:17 final size:17
Alignment explanation
Indices: 55392992--55393025 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
55392982 TTAATAATTT
55392992 TATTTGTTTTTTGAAAA
1 TATTTGTTTTTTGAAAA
55393009 TATTT-TTTATTTGAAAA
1 TATTTGTTT-TTTGAAAA
55393026 ACCAGTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 3 0.19
17 13 0.81
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.59
Consensus pattern (17 bp):
TATTTGTTTTTTGAAAA
Found at i:55402887 original size:6 final size:6
Alignment explanation
Indices: 55402876--55402903 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
55402866 GTGGTGCTCG
55402876 TCGTCT TCGTCT TCGTCT TCGTCT TCGT
1 TCGTCT TCGTCT TCGTCT TCGTCT TCGT
55402904 ACACGTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.32, G:0.18, T:0.50
Consensus pattern (6 bp):
TCGTCT
Found at i:55404266 original size:20 final size:20
Alignment explanation
Indices: 55404230--55404268 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
55404220 AAATTAAAAA
*
55404230 GATTAAGAAAAGCAAAAAGT
1 GATTAAGAAAAGAAAAAAGT
55404250 GATTGAAGAAAA-AAAAAAG
1 GATT-AAGAAAAGAAAAAAG
55404269 ATGGTGATCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.64, C:0.03, G:0.21, T:0.13
Consensus pattern (20 bp):
GATTAAGAAAAGAAAAAAGT
Found at i:55412179 original size:20 final size:20
Alignment explanation
Indices: 55412154--55412195 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
55412144 GGAAAGTACA
55412154 TAGATTGAAAATGATCAAAT
1 TAGATTGAAAATGATCAAAT
55412174 TAGATTGAAAATGATCAAAT
1 TAGATTGAAAATGATCAAAT
55412194 TA
1 TA
55412196 AAATATATGA
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:0.50, C:0.05, G:0.14, T:0.31
Consensus pattern (20 bp):
TAGATTGAAAATGATCAAAT
Found at i:55420677 original size:130 final size:131
Alignment explanation
Indices: 55420480--55420728 Score: 383
Period size: 130 Copynumber: 1.9 Consensus size: 131
55420470 AAGATATGAA
* * *
55420480 TGAAATTTTGAAGGGATAGTCGATTATTTTGAGCAAATGCGAAATTGCAACCCAACACGTTAGGG
1 TGAAATTTCGAAGGGATAGTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGG
* * * *
55420545 CACGATTCCGCGAATTGCCAAATATCGGATCTCATCTTCGTTTTGAAGAATTTTAAGAGACATGC
66 CACGATTCCGCGAATTGCCAAACATCGAATCCCATCTTCGATTTGAAGAATTTTAAGAGACATGC
55420610 G
131 G
* * *
55420611 TGAAATTTCGAAGTGATATTCGATTA-TTCGAGCAAACGCGGAATTGCAACCCAACACGTTAGGG
1 TGAAATTTCGAAGGGATAGTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGG
* *
55420675 CACGATTCCGCGAATTGCCAAACATCGAATCCCGTCTTCGATTTGAATAATTTT
66 CACGATTCCGCGAATTGCCAAACATCGAATCCCATCTTCGATTTGAAGAATTTT
55420729 TGAATGAATG
Statistics
Matches: 106, Mismatches: 12, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
130 83 0.78
131 23 0.22
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (131 bp):
TGAAATTTCGAAGGGATAGTCGATTATTTCGAGCAAACGCGAAATTGCAACCCAACACGTTAGGG
CACGATTCCGCGAATTGCCAAACATCGAATCCCATCTTCGATTTGAAGAATTTTAAGAGACATGC
G
Found at i:55422750 original size:14 final size:15
Alignment explanation
Indices: 55422731--55422760 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
55422721 GACAAAAGAG
55422731 AAAAGAAAA-GAAAA
1 AAAAGAAAATGAAAA
55422745 AAAAGAAAATGAAAA
1 AAAAGAAAATGAAAA
55422760 A
1 A
55422761 TCATTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (15 bp):
AAAAGAAAATGAAAA
Found at i:55424006 original size:15 final size:15
Alignment explanation
Indices: 55423968--55424006 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
55423958 ATAAGAAAAG
*
55423968 AAAAGAAAAAGTGGA
1 AAAAGAAAAAGAGGA
*
55423983 AAAGGAAAAAGAGGA
1 AAAAGAAAAAGAGGA
55423998 AAAA-AAAAA
1 AAAAGAAAAA
55424007 CAAAAAAAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 5 0.24
15 16 0.76
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.03
Consensus pattern (15 bp):
AAAAGAAAAAGAGGA
Found at i:55425613 original size:24 final size:23
Alignment explanation
Indices: 55425579--55425628 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
55425569 CAAAACTCAA
* *
55425579 AACCTTGAAAAATAAATTAATCCT
1 AACCTTAAAAAATAAA-AAATCCT
*
55425603 AACCTTAAAAATTAAAAAATCCT
1 AACCTTAAAAAATAAAAAATCCT
55425626 AAC
1 AAC
55425629 TCTAGAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 9 0.39
24 14 0.61
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (23 bp):
AACCTTAAAAAATAAAAAATCCT
Found at i:55425623 original size:23 final size:24
Alignment explanation
Indices: 55425579--55425628 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
55425569 CAAAACTCAA
*
55425579 AACCTTGAAAAATAAATTAATCCT
1 AACCTTGAAAAATAAATAAATCCT
55425603 AACCTT-AAAAATTAAA-AAATCCT
1 AACCTTGAAAAA-TAAATAAATCCT
55425626 AAC
1 AAC
55425629 TCTAGAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 14 0.58
24 10 0.42
ACGTcount: A:0.54, C:0.18, G:0.02, T:0.26
Consensus pattern (24 bp):
AACCTTGAAAAATAAATAAATCCT
Found at i:55426645 original size:21 final size:21
Alignment explanation
Indices: 55426621--55426661 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55426611 TAAACATAAC
55426621 AATTTATATGTATTT-TATATT
1 AATTTATATG-ATTTATATATT
*
55426642 AATTTTTATGATTTATATAT
1 AATTTATATGATTTATATAT
55426662 ATATTTGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (21 bp):
AATTTATATGATTTATATATT
Found at i:55427533 original size:33 final size:33
Alignment explanation
Indices: 55427494--55427569 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
55427484 ATATGCACAG
55427494 ATAGGGTTTTATTGAACTTCCATTGTTAACCAA
1 ATAGGGTTTTATTGAACTTCCATTGTTAACCAA
*
55427527 ATAGGGTTTTATTGAACTTCCATTGTTAACTAA
1 ATAGGGTTTTATTGAACTTCCATTGTTAACCAA
55427560 ATAGGGTTTT
1 ATAGGGTTTT
55427570 GTTATATACA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (33 bp):
ATAGGGTTTTATTGAACTTCCATTGTTAACCAA
Found at i:55433119 original size:6 final size:6
Alignment explanation
Indices: 55433108--55433132 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55433098 TAAAATGAAT
55433108 AAAATA AAAATA AAAATA AAAATA A
1 AAAATA AAAATA AAAATA AAAATA A
55433133 TATATTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:55439428 original size:40 final size:40
Alignment explanation
Indices: 55439384--55439466 Score: 166
Period size: 40 Copynumber: 2.1 Consensus size: 40
55439374 TTGTCAACTA
55439384 GATTCATTTTGGTCCTTAAACTTGGGTTCTGTTAAGATTT
1 GATTCATTTTGGTCCTTAAACTTGGGTTCTGTTAAGATTT
55439424 GATTCATTTTGGTCCTTAAACTTGGGTTCTGTTAAGATTT
1 GATTCATTTTGGTCCTTAAACTTGGGTTCTGTTAAGATTT
55439464 GAT
1 GAT
55439467 GATGTGATCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.47
Consensus pattern (40 bp):
GATTCATTTTGGTCCTTAAACTTGGGTTCTGTTAAGATTT
Found at i:55440065 original size:26 final size:26
Alignment explanation
Indices: 55440035--55440087 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
55440025 GAGTTTTTGA
55440035 ATGATTAGCTAATGTATTTGGTATTT
1 ATGATTAGCTAATGTATTTGGTATTT
55440061 ATGATTAGCTAATGTATTTGGTATTT
1 ATGATTAGCTAATGTATTTGGTATTT
55440087 A
1 A
55440088 CTTTTTTCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.04, G:0.19, T:0.49
Consensus pattern (26 bp):
ATGATTAGCTAATGTATTTGGTATTT
Found at i:55450009 original size:12 final size:12
Alignment explanation
Indices: 55449992--55450016 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
55449982 TGATTTTTAG
55449992 AAAGAATCTACC
1 AAAGAATCTACC
55450004 AAAGAATCTACC
1 AAAGAATCTACC
55450016 A
1 A
55450017 CATCCATGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.24, G:0.08, T:0.16
Consensus pattern (12 bp):
AAAGAATCTACC
Found at i:55452962 original size:12 final size:13
Alignment explanation
Indices: 55452932--55452964 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
55452922 TTTTACTTTT
55452932 AATTAAAACTATA
1 AATTAAAACTATA
55452945 AATTAAAA-TATA
1 AATTAAAACTATA
*
55452957 ATTTAAAA
1 AATTAAAA
55452965 ATTATCAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (13 bp):
AATTAAAACTATA
Found at i:55453047 original size:21 final size:19
Alignment explanation
Indices: 55452991--55453047 Score: 53
Period size: 21 Copynumber: 2.8 Consensus size: 19
55452981 TATTATTAAA
55452991 TATTTAATTAAAATAATTTT
1 TATTTAA-TAAAATAATTTT
*
55453011 TA-TTAAAAATATATAATCTTT
1 TATTTAATAA-A-ATAAT-TTT
55453032 TATTTAATAAAGATAA
1 TATTTAATAAA-ATAA
55453048 ATTCATAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
18 2 0.07
19 5 0.17
20 7 0.23
21 10 0.33
22 6 0.20
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TATTTAATAAAATAATTTT
Found at i:55462367 original size:6 final size:6
Alignment explanation
Indices: 55462361--55462405 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
55462351 CAACTCTTCT
* *
55462361 TCCTCT TCCTCG TCCTCG TCCTCG TCCTCG TCCTCT TCCTC- TCCT
1 TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG TCCTCG TCCT
55462406 TCTGGGTCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
5 4 0.11
6 33 0.89
ACGTcount: A:0.00, C:0.51, G:0.09, T:0.40
Consensus pattern (6 bp):
TCCTCG
Found at i:55467446 original size:19 final size:19
Alignment explanation
Indices: 55467422--55467474 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 19
55467412 GATGTTGATT
*
55467422 TAAAAAATTTAAAAATGTA
1 TAAAAAATTTAAAAATATA
* *
55467441 TAAAAATTTTAAAATTATA
1 TAAAAAATTTAAAAATATA
* *
55467460 TGAAAAATTCAAAAA
1 TAAAAAATTTAAAAA
55467475 GCATATATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (19 bp):
TAAAAAATTTAAAAATATA
Found at i:55469573 original size:20 final size:21
Alignment explanation
Indices: 55469548--55469593 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
55469538 AGAAATATAC
* *
55469548 TATACAT-AATATTCGAAATA
1 TATACATAAATAGTCAAAATA
55469568 TATACATGAAATAGTCAAAATA
1 TATACAT-AAATAGTCAAAATA
55469590 TATA
1 TATA
55469594 TACTACTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 7 0.32
22 15 0.68
ACGTcount: A:0.52, C:0.09, G:0.07, T:0.33
Consensus pattern (21 bp):
TATACATAAATAGTCAAAATA
Done.