Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr10
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: 57797951
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 1092422 characters in sequence are not A, C, G, or T
File 97 of 187
Found at i:28360351 original size:13 final size:13
Alignment explanation
Indices: 28360333--28360392 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
28360323 GATCAAGTGG
28360333 AAAATGAATATAT
1 AAAATGAATATAT
*
28360346 AAAATGATTATAT
1 AAAATGAATATAT
* *
28360359 -GAATCGATTATAT
1 AAAAT-GAATATAT
28360372 GGAAAATGAATATAT
1 --AAAATGAATATAT
28360387 AAAATG
1 AAAATG
28360393 GTAATATGAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 3 0.08
13 26 0.67
15 7 0.18
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.13, T:0.32
Consensus pattern (13 bp):
AAAATGAATATAT
Found at i:28360375 original size:41 final size:41
Alignment explanation
Indices: 28360330--28360454 Score: 157
Period size: 41 Copynumber: 3.1 Consensus size: 41
28360320 GTTGATCAAG
28360330 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
* * *
28360371 TGGAAAATGAATATATAAAATGGTAATATGAAT-TAGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGA-TTATA
** * *
28360412 TGG-AAATG-ATATATGGAATGATTATATAAATCGGTTATA
1 TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
28360451 TGGA
1 TGGA
28360455 TAGATATTTA
Statistics
Matches: 71, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
39 26 0.37
40 6 0.08
41 39 0.55
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (41 bp):
TGGAAAATGAATATATAAAATGATTATATGAATCGATTATA
Found at i:28361294 original size:22 final size:22
Alignment explanation
Indices: 28361266--28361311 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
28361256 AATTGGGTAT
28361266 TGAATTCATGGAATGGAAAGTG
1 TGAATTCATGGAATGGAAAGTG
*
28361288 TGAATTCATGGAATGGAAGGTG
1 TGAATTCATGGAATGGAAAGTG
28361310 TG
1 TG
28361312 GTTAACTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.04, G:0.35, T:0.28
Consensus pattern (22 bp):
TGAATTCATGGAATGGAAAGTG
Found at i:28362066 original size:22 final size:22
Alignment explanation
Indices: 28362040--28362083 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
28362030 GTTTAAACAT
28362040 ATTTCTTTTCCCGTCCCCCCAC
1 ATTTCTTTTCCCGTCCCCCCAC
28362062 ATTTCTTTTCCCGTCCCCCCAC
1 ATTTCTTTTCCCGTCCCCCCAC
28362084 TCCCAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.09, C:0.50, G:0.05, T:0.36
Consensus pattern (22 bp):
ATTTCTTTTCCCGTCCCCCCAC
Found at i:28362350 original size:20 final size:20
Alignment explanation
Indices: 28362325--28362365 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
28362315 AAGTTTGTTT
28362325 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
28362345 TATTTTTTCTTTCTCTGATA
1 TATTTTTTCTTTCTCTGATA
28362365 T
1 T
28362366 CCAGTACAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.15, C:0.15, G:0.05, T:0.66
Consensus pattern (20 bp):
TATTTTTTCTTTCTCTGATA
Found at i:28368027 original size:26 final size:26
Alignment explanation
Indices: 28367991--28368042 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
28367981 AGAAGATGAA
28367991 TTAGAAATCTTCTCTCTACTATCACG
1 TTAGAAATCTTCTCTCTACTATCACG
28368017 TTAGAAATCTTCTCTCTACTATCACG
1 TTAGAAATCTTCTCTCTACTATCACG
28368043 CTATCTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.08, T:0.38
Consensus pattern (26 bp):
TTAGAAATCTTCTCTCTACTATCACG
Found at i:28369753 original size:27 final size:27
Alignment explanation
Indices: 28369679--28369755 Score: 77
Period size: 27 Copynumber: 2.9 Consensus size: 27
28369669 CTTCATCCCT
* * *
28369679 ATTTTACCCCTATTAAAA-ATTTAACG
1 ATTTTACCCTTATTAAAATTTTTAACA
** *
28369705 ATTTTACCCTTGA-TAATTTTTTTTACA
1 ATTTTACCCTT-ATTAAAATTTTTAACA
28369732 ATTTTACCCTTATTAAAATTTTTA
1 ATTTTACCCTTATTAAAATTTTTA
28369756 GAAAATATGT
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
26 14 0.36
27 25 0.64
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (27 bp):
ATTTTACCCTTATTAAAATTTTTAACA
Found at i:28378062 original size:30 final size:30
Alignment explanation
Indices: 28378028--28378091 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
28378018 TTCCCATTTT
28378028 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
28378058 GATACATAAATTCCTCTTTTATATATAAAA
1 GATACATAAATTCCTCTTTTATATATAAAA
28378088 GATA
1 GATA
28378092 TAAATATAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (30 bp):
GATACATAAATTCCTCTTTTATATATAAAA
Found at i:28380017 original size:55 final size:55
Alignment explanation
Indices: 28379951--28380060 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
28379941 AACCTTATGG
28379951 TTATTTGCTCAAAAATTTAAATATGCAAGGAATATATGGATTCTAGATAGTTTAA
1 TTATTTGCTCAAAAATTTAAATATGCAAGGAATATATGGATTCTAGATAGTTTAA
28380006 TTATTTGCTCAAAAATTTAAATATGCAAGGAATATATGGATTCTAGATAGTTTAA
1 TTATTTGCTCAAAAATTTAAATATGCAAGGAATATATGGATTCTAGATAGTTTAA
28380061 CCTAAGAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.40, C:0.07, G:0.15, T:0.38
Consensus pattern (55 bp):
TTATTTGCTCAAAAATTTAAATATGCAAGGAATATATGGATTCTAGATAGTTTAA
Found at i:28382610 original size:6 final size:6
Alignment explanation
Indices: 28382601--28382628 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
28382591 TGATGAACTC
28382601 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTT
28382629 TCTTGAGCAG
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:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTCT
Found at i:28385025 original size:59 final size:58
Alignment explanation
Indices: 28384932--28385081 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
28384922 GTACTTGTGG
* *
28384932 CTTGTGA-TTGCGGTTGCTTTTAGTGCCCAAACAAATTCAATCCTTGACATGCTGGTT
1 CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
* * * *
28384989 CTTGTGACTTGTGGTTTACTTTTGGTGCCAAAACAAATTTAATCCTTGACATGCTGGTA
1 CTTGTGACTTGCGG-TTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
* *
28385048 GTTGTGGCTTGCGGTTGCTTTTAGTGCCAAAACA
1 CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACA
28385082 TAGCAACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 7 0.09
58 23 0.29
59 50 0.62
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (58 bp):
CTTGTGACTTGCGGTTGCTTTTAGTGCCAAAACAAATTCAATCCTTGACATGCTGGTA
Found at i:28385176 original size:26 final size:26
Alignment explanation
Indices: 28385123--28385178 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
28385113 AATGTCACAC
* *
28385123 ATTTTGAAGCTTCATTTTCTTTGATT
1 ATTTTGAAGCTTCAATTTCTATGATT
*
28385149 ATTTTGAA-CTTCAATTTCATATGCTT
1 ATTTTGAAGCTTCAATTTC-TATGATT
28385175 ATTT
1 ATTT
28385179 CAGATGTATG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 9 0.35
26 17 0.65
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (26 bp):
ATTTTGAAGCTTCAATTTCTATGATT
Found at i:28385705 original size:120 final size:120
Alignment explanation
Indices: 28385568--28386032 Score: 736
Period size: 120 Copynumber: 3.9 Consensus size: 120
28385558 GTAGTATTAT
*
28385568 ATATATTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTATTAAATTATA
1 ATATATTATGATTTTAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATA
* * * *
28385632 TATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATT
65 TATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATC
* *
28385688 ATATATTATGATTTTAGAAAATTCATATAAGAATATTTAA-TATTAAGAATTTTACTAAATTATA
1 ATATATTATGATTTTAGAAAATTAATATAAGAATA-TTAATTATTAAGAATTTTATTAAATTATA
* * *
28385752 TATTTTTATTAAATTATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
65 TATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATC
* * *
28385808 ATATATTATGATTTGAGTAAATTAATATAAGAATATTAATTATTAAGAATTTCATTAAATTATAT
1 ATATATTATGATTTTAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
* *
28385873 AGTTTAATTAAAATATATTTAATAATAATTATGTTAATTTATATTTTACAGTATC
66 ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATC
* *
28385928 ATATATTATGATTTCAGTAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
1 ATATATTATGATTTTAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
28385993 ATTTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
66 ATTTTAATTAAAATATATTTAATAATAATTATG-TTAAAT
28386033 ATGATTAAAT
Statistics
Matches: 327, Mismatches: 16, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
119 4 0.01
120 318 0.97
121 5 0.02
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (120 bp):
ATATATTATGATTTTAGAAAATTAATATAAGAATATTAATTATTAAGAATTTTATTAAATTATAT
ATTTTAATTAAAATATATTTAATAATAATTATGTTAAATTATATTTTACAGTATC
Found at i:28386004 original size:18 final size:17
Alignment explanation
Indices: 28385976--28386010 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28385966 ATTATTAAGA
*
28385976 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
28385993 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
28386011 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:28386241 original size:44 final size:45
Alignment explanation
Indices: 28386176--28386266 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
28386166 ACCTCTATTC
* * *
28386176 CATTCAACCAAACACAAGATTA-CTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
***
28386220 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTAGCTATTACACCTCTAATCCAATA
28386265 CA
1 CA
28386267 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:28386268 original size:16 final size:16
Alignment explanation
Indices: 28386247--28386315 Score: 129
Period size: 16 Copynumber: 4.2 Consensus size: 16
28386237 GATTAGCTAT
28386247 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28386263 TACACCTCTAATCCCAA
1 TACACCTCTAAT-CCAA
28386280 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28386296 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
28386312 TACA
1 TACA
28386316 GCGAACCAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
16 36 0.69
17 16 0.31
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:28386289 original size:33 final size:32
Alignment explanation
Indices: 28386247--28386315 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 32
28386237 GATTAGCTAT
28386247 TACACCTCTAATCCAATACACCTCTAATCCCAA
1 TACACCTCTAATCCAATACACCTCTAAT-CCAA
28386280 TACACCTCTAATCCAATACACCTCTAATCCAA
1 TACACCTCTAATCCAATACACCTCTAATCCAA
28386312 TACA
1 TACA
28386316 GCGAACCAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 8 0.22
33 28 0.78
ACGTcount: A:0.38, C:0.38, G:0.00, T:0.25
Consensus pattern (32 bp):
TACACCTCTAATCCAATACACCTCTAATCCAA
Found at i:28389446 original size:85 final size:85
Alignment explanation
Indices: 28389352--28389522 Score: 281
Period size: 85 Copynumber: 2.0 Consensus size: 85
28389342 TCTCATGCTA
* *
28389352 ATTGATCATTTGCTCTTTACAATCCTTAAAAATTTCATCCTTAAATCA-CTACTTAATTTAATGA
1 ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATC-ACTTAATTTAATAA
*
28389416 AATTTTGATTTAGTCCCTCAT
65 AATTATGATTTAGTCCCTCAT
* *
28389437 ATTGATCATTTGCCCTTTATAATCCTTAAAAATTTCATCCTTAAATCATCATTTAATTTAATAAA
1 ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATCACTTAATTTAATAAA
28389502 ATTATGATTTAGTCCCTCAT
66 ATTATGATTTAGTCCCTCAT
28389522 A
1 A
28389523 ATTCTTTATT
Statistics
Matches: 80, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
85 79 0.99
86 1 0.01
ACGTcount: A:0.33, C:0.18, G:0.05, T:0.43
Consensus pattern (85 bp):
ATTGATCATTTGCCCTTTACAATCCTTAAAAATTTCATCCTTAAATCATCACTTAATTTAATAAA
ATTATGATTTAGTCCCTCAT
Found at i:28391402 original size:47 final size:47
Alignment explanation
Indices: 28391333--28391425 Score: 186
Period size: 47 Copynumber: 2.0 Consensus size: 47
28391323 AACCATATTT
28391333 AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCTA
1 AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCTA
28391380 AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCT
1 AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCT
28391426 TCTAGTAGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 46 1.00
ACGTcount: A:0.18, C:0.32, G:0.19, T:0.30
Consensus pattern (47 bp):
AAAGTTTGGTTCCGGCACACGTCAGGCGCCACCCTTTCACTTTTCTA
Found at i:28392886 original size:45 final size:44
Alignment explanation
Indices: 28392822--28392914 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
28392812 ATAGAACTGT
*
28392822 AATGGAATAGAGGCGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAGAGACGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
*
28392867 AATGGAATAGA-ACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAGAGAC-GTAATAGTATTCATGTGTTTGGTTGAATGG
28392911 AATG
1 AATG
28392915 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
43 1 0.02
44 24 0.55
45 19 0.43
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.35
Consensus pattern (44 bp):
AATGGAATAGAGACGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:28394801 original size:20 final size:20
Alignment explanation
Indices: 28394776--28394817 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
28394766 AACAAGGATG
28394776 AAAGCATTTGGAACCTTAAT
1 AAAGCATTTGGAACCTTAAT
28394796 AAAGCATTTGGAACCTTAAT
1 AAAGCATTTGGAACCTTAAT
28394816 AA
1 AA
28394818 TTATATCCCT
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:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAGCATTTGGAACCTTAAT
Found at i:28396553 original size:52 final size:51
Alignment explanation
Indices: 28396475--28396578 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 51
28396465 AATAGCGCCT
*
28396475 GAATGGATTCAGGCTGTAATACCATTACAGCCAACCAAATTAATGTTTGGTG
1 GAATGGATTCAGGCTGTAATACCATTACAGCCAA-CAAAATAATGTTTGGTG
28396527 GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
1 GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
28396578 G
1 G
28396579 TGGGCCCACC
Statistics
Matches: 51, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
51 17 0.33
52 34 0.67
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (51 bp):
GAATGGATTCAGGCTGTAATACCATTACAGCCAACAAAATAATGTTTGGTG
Found at i:28398160 original size:46 final size:47
Alignment explanation
Indices: 28398079--28398169 Score: 175
Period size: 46 Copynumber: 2.0 Consensus size: 47
28398069 ATCATGTCAA
28398079 ATATGGTTCGGTACTTCTTCGAATTGACCTTCAGTGGGTTTAATCAC
1 ATATGGTTCGGTACTTCTTCGAATTGACCTTCAGTGGGTTTAATCAC
28398126 ATATGGTTCGGTACTTC-TCGAATTGACCTTCAGTGGGTTTAATC
1 ATATGGTTCGGTACTTCTTCGAATTGACCTTCAGTGGGTTTAATC
28398170 GTGTCTATTC
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 27 0.61
47 17 0.39
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (47 bp):
ATATGGTTCGGTACTTCTTCGAATTGACCTTCAGTGGGTTTAATCAC
Found at i:28400936 original size:27 final size:27
Alignment explanation
Indices: 28400898--28400950 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
28400888 AACTGAGAAG
*
28400898 TGAATAGAAAGCACAGAATATTCTATT
1 TGAATAGAAAGCACAGAATATGCTATT
*
28400925 TGAATAGAAAGCACCGAATATGCTAT
1 TGAATAGAAAGCACAGAATATGCTAT
28400951 AGTTTCAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (27 bp):
TGAATAGAAAGCACAGAATATGCTATT
Found at i:28401967 original size:16 final size:18
Alignment explanation
Indices: 28401928--28401961 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28401918 TAAGTTTATG
28401928 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
28401945 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
28401962 AATTTAGAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:28403271 original size:21 final size:20
Alignment explanation
Indices: 28403242--28403282 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
28403232 CTCTCTCACC
*
28403242 AAAATTTTCAAAAATATTTAT
1 AAAAATTTCAAAAAT-TTTAT
28403263 AAAAATTTCAAAAATTTTAT
1 AAAAATTTCAAAAATTTTAT
28403283 TTTTTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
AAAAATTTCAAAAATTTTAT
Found at i:28403291 original size:14 final size:14
Alignment explanation
Indices: 28403274--28403303 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
28403264 AAAATTTCAA
*
28403274 AAATTTTATTTTTT
1 AAATTATATTTTTT
28403288 AAATTATATTTTTT
1 AAATTATATTTTTT
28403302 AA
1 AA
28403304 GAAAAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
AAATTATATTTTTT
Found at i:28405457 original size:19 final size:19
Alignment explanation
Indices: 28405422--28405459 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
28405412 AAGTTACAAA
*
28405422 AAATAAAAAATATAAATAT
1 AAATAAAAAATAAAAATAT
28405441 AAATAAAATAA-AAAAATAT
1 AAATAAAA-AATAAAAATAT
28405460 TAATTACATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.88
20 2 0.12
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAAAAAATAAAAATAT
Found at i:28407362 original size:40 final size:41
Alignment explanation
Indices: 28407284--28407364 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 41
28407274 AGGAAGCGCT
**
28407284 TGTCCACGTGGACAAAAAACGCTTCCTTGAGGGCGCACTTTG
1 TGTCCACGTGGAC-AAAAACGCTTCCTTGAGGAAGCACTTTG
*
28407326 TGTCCACGTGGAC-AAAGCGCTTCCTTGAGGAAGCACTTT
1 TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTT
28407365 TTCCGTTTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 23 0.64
42 13 0.36
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.25
Consensus pattern (41 bp):
TGTCCACGTGGACAAAAACGCTTCCTTGAGGAAGCACTTTG
Found at i:28407551 original size:96 final size:96
Alignment explanation
Indices: 28407443--28407753 Score: 423
Period size: 97 Copynumber: 3.2 Consensus size: 96
28407433 ATTTTAGGGG
* * * * * * * *
28407443 TTTAAGGAAAAAATTAAATAAATAAGGGTTTAGGGTTTCTTAATTAAATTAATTATAGATTTTAA
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
28407508 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
66 AAAATTAGATTAGGGTTTAGTGTTTATGGTT
28407539 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAATTATTTT
1 TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAA--ATTTT
**
28407604 TTAAAA-TAGATTAGGGTTTAGTG-TT-TGGTT
64 AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
28407634 TTTAAGGGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
1 TTTAA--GAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTT
* * *
28407699 AAAAAAATTAGATTGGGGTTTAGTATTTAGGGTT
64 -AAAAAATTAGATTAGGGTTTAGTGTTTATGGTT
*
28407733 TTTAA-AGAAAAATCAAATAAA
1 TTTAAGAAAAAAATCAAATAAA
28407754 GCTAGTTGTT
Statistics
Matches: 191, Mismatches: 16, Indels: 16
0.86 0.07 0.07
Matches are distributed among these distances:
95 15 0.08
96 71 0.37
97 85 0.45
98 11 0.06
99 9 0.05
ACGTcount: A:0.42, C:0.02, G:0.17, T:0.39
Consensus pattern (96 bp):
TTTAAGAAAAAAATCAAATAAATTAGGGTTTAAGGTTACTTGAGTAAATTAATTATAAATTTTAA
AAAATTAGATTAGGGTTTAGTGTTTATGGTT
Found at i:28408306 original size:11 final size:11
Alignment explanation
Indices: 28408290--28408315 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
28408280 GTTAGACTTA
28408290 ATAAATAATTT
1 ATAAATAATTT
28408301 ATAAATAATTT
1 ATAAATAATTT
28408312 ATAA
1 ATAA
28408316 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
ATAAATAATTT
Found at i:28408315 original size:18 final size:16
Alignment explanation
Indices: 28408294--28408333 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
28408284 GACTTAATAA
28408294 ATAATTTATAAATAATTT
1 ATAATTT-TAAA-AATTT
*
28408312 ATAATTTTTAAAATTT
1 ATAATTTTAAAAATTT
28408328 ATAATT
1 ATAATT
28408334 AATTTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTAAAAATTT
Found at i:28408483 original size:16 final size:16
Alignment explanation
Indices: 28408462--28408513 Score: 104
Period size: 16 Copynumber: 3.2 Consensus size: 16
28408452 TTTGGTTCGC
28408462 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28408478 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28408494 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
28408510 TGTA
1 TGTA
28408514 ATAGCTAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.25, C:0.00, G:0.37, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:28408625 original size:61 final size:60
Alignment explanation
Indices: 28408546--28408734 Score: 206
Period size: 61 Copynumber: 3.1 Consensus size: 60
28408536 ATTTAATAAA
28408546 AATATATAATTTAGTAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTTA-TAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
* * * * * ** ** * *
28408607 AATATATAATACTATAAAA-T-ATAAT-TTAACATAATTATTAT-TAAATATAATTTAATAAA
1 AATATATAAT-TTATAAAATTCTTAATATTAA-AT-ATTCTTATATGAATTTTCTAAAATCAT
28408666 AATATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
1 AATATATAATTT-ATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
28408727 AATATATA
1 AATATATA
28408735 TAATACTACA
Statistics
Matches: 98, Mismatches: 22, Indels: 16
0.72 0.16 0.12
Matches are distributed among these distances:
58 5 0.05
59 32 0.33
60 16 0.16
61 39 0.40
62 6 0.06
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (60 bp):
AATATATAATTTATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCAT
Found at i:28408683 original size:59 final size:59
Alignment explanation
Indices: 28408522--28408707 Score: 171
Period size: 59 Copynumber: 3.1 Consensus size: 59
28408512 TAATAGCTAA
* *
28408522 TATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAATATTAAATAT
1 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAA-TCATAATATTAAATAT
* * * ** ** * * *
28408582 TCTTATATGAATTTTCTAAAATCATAATATATAATACT-ATAAAAT-ATAAT-TTAACATAAT
1 TATTAT-TAAATATAATTTAATAAAAATATATAAT-TTAATAAAATCATAATATTAA-AT-AT
*
28408642 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATAT
1 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAA-TCATAATATTAAATAT
*
28408702 TCTTAT
1 TATTAT
28408708 ATGAATTTTC
Statistics
Matches: 94, Mismatches: 24, Indels: 16
0.70 0.18 0.12
Matches are distributed among these distances:
58 5 0.05
59 32 0.34
60 21 0.22
61 31 0.33
62 5 0.05
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (59 bp):
TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATCATAATATTAAATAT
Found at i:28408732 original size:59 final size:59
Alignment explanation
Indices: 28408549--28408732 Score: 182
Period size: 59 Copynumber: 3.1 Consensus size: 59
28408539 TAATAAAAAT
*
28408549 ATATAATTTAGTAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATA
* * * * * **
28408608 ATAT-ATAATACTATAAAATATAATTTAACA-TAATTATTATTAAATAT-AATTTAATAAAA--A
1 ATATAAT-TTA--ATAAAAT-T--CTTAATATTAAATATTCTT--ATATGAATTTTCTAAAATCA
28408668 T-
58 TA
28408669 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATA
1 ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATA
28408728 ATATA
1 ATATA
28408733 TATAATACTA
Statistics
Matches: 96, Mismatches: 15, Indels: 28
0.69 0.11 0.20
Matches are distributed among these distances:
55 4 0.04
56 15 0.16
57 9 0.09
58 5 0.05
59 18 0.19
61 12 0.12
62 5 0.05
63 9 0.09
64 15 0.16
65 4 0.04
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (59 bp):
ATATAATTTAATAAAATTCTTAATATTAAATATTCTTATATGAATTTTCTAAAATCATA
Found at i:28408781 original size:120 final size:120
Alignment explanation
Indices: 28408522--28408739 Score: 402
Period size: 120 Copynumber: 1.8 Consensus size: 120
28408512 TAATAGCTAA
*
28408522 TATTATTAAATATAATTTAATAAAAATATATAATTTAGTAAAATTCTTAATATTAAATATTCTTA
1 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
* *
28408587 TATGAATTTTCTAAAATCATAATATATAATACTATAAAATATAATTTAACATAAT
66 TATGAATTTTCTAAAATCATAATATATAATAATATAAAATATAACTTAACATAAT
28408642 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
1 TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
28408707 TATGAATTTTCTAAAATCATAATATAT-ATAATA
66 TATGAATTTTCTAAAATCATAATATATAATAATA
28408740 CTACAATACT
Statistics
Matches: 96, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
119 5 0.05
120 91 0.95
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (120 bp):
TATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATTAAATATTCTTA
TATGAATTTTCTAAAATCATAATATATAATAATATAAAATATAACTTAACATAAT
Found at i:28408860 original size:14 final size:15
Alignment explanation
Indices: 28408841--28408873 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
28408831 CTTTATTCTT
*
28408841 AAAATTCAAAAA-TA
1 AAAATTAAAAAACTA
28408855 AAAATTAAAAAACTA
1 AAAATTAAAAAACTA
28408870 AAAA
1 AAAA
28408874 ATTTAAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (15 bp):
AAAATTAAAAAACTA
Found at i:28409343 original size:58 final size:58
Alignment explanation
Indices: 28409220--28409369 Score: 212
Period size: 59 Copynumber: 2.6 Consensus size: 58
28409210 AAAGTTGCTA
* **
28409220 TGTTTTGGCACTAAAAGCAACCGCAAGCCACAACTACCAGCATGTCAAGGATTAAATT
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
* * * *
28409278 TGTTTTGGCACCAAAAGTAAACCACAAGTCACAAGAACCAGCATGTCAAGGATTGAATT
1 TGTTTTGGCACTAAAAG-CAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
*
28409337 TGTTTGGGCACTAAAAGCAACCGCAA-TCACAAG
1 TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAG
28409370 CCACAAGTAC
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
57 7 0.09
58 23 0.29
59 50 0.62
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (58 bp):
TGTTTTGGCACTAAAAGCAACCGCAAGTCACAAGAACCAGCATGTCAAGGATTAAATT
Found at i:28418801 original size:20 final size:21
Alignment explanation
Indices: 28418763--28418802 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
28418753 TACTTTATTT
*
28418763 CATTTTTCTTTATTTTTCTTC
1 CATTTTTCTTTATTATTCTTC
*
28418784 CATTTTT-TTTCTTATTCTT
1 CATTTTTCTTTATTATTCTT
28418803 TCCTTTCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.72
Consensus pattern (21 bp):
CATTTTTCTTTATTATTCTTC
Found at i:28418805 original size:21 final size:21
Alignment explanation
Indices: 28418763--28418818 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
28418753 TACTTTATTT
* * *
28418763 CATTTTTCTTTATTTTTCTTC
1 CATTTTTATTTCTTATTCTTC
28418784 CATTTTT-TTTCTTATTCTTTC
1 CATTTTTATTTCTTATTC-TTC
28418805 C-TTTCTTATTTCTT
1 CATTT-TTATTTCTT
28418819 TTCCTTCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
20 11 0.37
21 13 0.43
22 6 0.20
ACGTcount: A:0.09, C:0.20, G:0.00, T:0.71
Consensus pattern (21 bp):
CATTTTTATTTCTTATTCTTC
Found at i:28418809 original size:15 final size:17
Alignment explanation
Indices: 28418791--28418824 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
28418781 TTCCATTTTT
28418791 TTTCTTA-TTC-TTTCC
1 TTTCTTATTTCTTTTCC
28418806 TTTCTTATTTCTTTTCC
1 TTTCTTATTTCTTTTCC
28418823 TT
1 TT
28418825 CATTCTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 3 0.18
17 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTCTTATTTCTTTTCC
Found at i:28419242 original size:6 final size:6
Alignment explanation
Indices: 28419233--28419261 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
28419223 TTATTCTGTC
28419233 GTGGTT GTGGTT GTGGTT GTGGTT G-GGTT
1 GTGGTT GTGGTT GTGGTT GTGGTT GTGGTT
28419262 TCTTTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (6 bp):
GTGGTT
Found at i:28421095 original size:18 final size:17
Alignment explanation
Indices: 28421074--28421108 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28421064 TTATTATTAA
*
28421074 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28421092 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28421109 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28421116 original size:79 final size:79
Alignment explanation
Indices: 28421033--28421268 Score: 220
Period size: 79 Copynumber: 3.0 Consensus size: 79
28421023 TTATTATCAA
28421033 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
28421098 TTTAATAAAATTCT
66 TTTAATAAAATTCT
* * * * **** * * *
28421112 TAATAATTAGCA-TAAAT-TTGTTTTGGTA-AATTATTATT--GT-TATTGTT-ATTTAAAT-TT
1 TAATAAATA--ATTTAATCATATTTAAACATAATTATTATTAAATATATT-TTAATTAAAATATA
* * **
28421169 TAA-TAAGATTAATATTAA
63 TAATTTA-A-TAAAATTCT
*
28421187 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAA
1 TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
28421252 TTTAATAAAATTCT
66 TTTAATAAAATTCT
28421266 TAA
1 TAA
28421269 AATTAATATT
Statistics
Matches: 112, Mismatches: 31, Indels: 28
0.65 0.18 0.16
Matches are distributed among these distances:
73 3 0.03
74 9 0.08
75 30 0.27
76 13 0.12
78 12 0.11
79 33 0.29
80 9 0.08
81 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (79 bp):
TAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATAA
TTTAATAAAATTCT
Found at i:28421245 original size:16 final size:16
Alignment explanation
Indices: 28421208--28421249 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28421198 TTAATCATAT
*
28421208 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
28421224 TT-AAATATATTATAA
1 TTAAAATATATTATAA
28421239 TTAAAATATAT
1 TTAAAATATAT
28421250 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:28421256 original size:14 final size:15
Alignment explanation
Indices: 28421217--28421258 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
28421207 TTTAAACATA
*
28421217 ATTATTATTAAATAT
1 ATTATAATTAAATAT
28421232 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
28421246 A-TATAATTTAATA
1 ATTATAATTAAATA
28421259 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:28421256 original size:154 final size:155
Alignment explanation
Indices: 28420961--28421273 Score: 558
Period size: 154 Copynumber: 2.0 Consensus size: 155
28420951 TAGAATACCC
28420961 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-TA
*
28421026 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
65 TTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
28421091 TATATAATTTAATAAAATTCTTAATAA
130 TATATAATTTAATAAAATTCTTAA-AA
* *
28421118 TTAGCATAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTA-A-
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
*
28421181 TATTAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
66 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
28421246 ATATAATTTAATAAAATTCTTAAAA
131 ATATAATTTAATAAAATTCTTAAAA
28421271 TTA
1 TTA
28421274 ATATTCTTAT
Statistics
Matches: 152, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
153 5 0.03
154 86 0.57
155 1 0.01
157 60 0.39
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (155 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATAT
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAAT
ATATAATTTAATAAAATTCTTAAAA
Found at i:28421349 original size:154 final size:153
Alignment explanation
Indices: 28421022--28421324 Score: 355
Period size: 154 Copynumber: 2.0 Consensus size: 153
28421012 TAATAAGATT
* * *
28421022 ATTATTATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATT
1 ATTAATATTAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATT
* * * ** * * *
28421087 AAAATATATAATTTAATAAAATTCTTAATAATTAGCATAAATTTGTTTTGGTAAATTATTATTGT
66 AAAATATATAATTTAATAAAATTCTTAATAATTAACATAAATATGATTTACTAAATCATTAATGA
* * **
28421152 TATTGTTATTTAAATTTTAATAAG
131 TATTGATATATAAA-TAGAATAAG
28421176 ATTAATATTAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATT
1 ATTAATATTAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATT
* **
28421241 AAAATATATAATTTAATAAAATTCTTAA-AATTAATATTCTTATATGAATTTACTCAAATCA-TA
66 AAAATATATAATTTAATAAAATTCTTAATAATTAACA-T-AAATATG-ATTTACT-AAATCATTA
28421304 AT-ATA-TGATACTATAAA-AGAA
127 ATGATATTGATA-TATAAATAGAA
28421325 AATTTCAAAT
Statistics
Matches: 126, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
153 8 0.06
154 95 0.75
155 11 0.09
156 7 0.06
157 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (153 bp):
ATTAATATTAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATT
AAAATATATAATTTAATAAAATTCTTAATAATTAACATAAATATGATTTACTAAATCATTAATGA
TATTGATATATAAATAGAATAAG
Found at i:28421362 original size:15 final size:15
Alignment explanation
Indices: 28421342--28421380 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 15
28421332 AATAATTAAT
28421342 ATTAAATATGATTTA
1 ATTAAATATGATTTA
28421357 ATTAAATATATGATTTA
1 ATT-AA-ATATGATTTA
*
28421374 ATAAAAT
1 ATTAAAT
28421381 TTAAAATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 5 0.24
16 4 0.19
17 12 0.57
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (15 bp):
ATTAAATATGATTTA
Found at i:28421367 original size:17 final size:17
Alignment explanation
Indices: 28421347--28421380 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28421337 TTAATATTAA
*
28421347 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
28421364 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
28421381 TTAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:28421527 original size:93 final size:92
Alignment explanation
Indices: 28421412--28421606 Score: 284
Period size: 93 Copynumber: 2.1 Consensus size: 92
28421402 AATTATATTT
* * * **
28421412 TATGAATTTGTATAATTTAAAATAA-TAATTATTACATATAATTTAATAATAATATATAATTTTT
1 TATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAATAATATATAATTTCA
* * *
28421476 TAAAATTCTTGATAATAAAAATTTTTTTA
65 TAAAATTCTTAATAAT-AAAATGTTCTTA
*
28421505 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCAT
28421570 AAAATTCTTAATAATAAAATGTTCTTA
66 AAAATTCTTAATAATAAAATGTTCTTA
28421597 TATGAATTTA
1 TATGAATTTA
28421607 CTAAAATCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
92 20 0.22
93 69 0.75
94 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATTAATATTAAATATAATTTAATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:28421574 original size:47 final size:45
Alignment explanation
Indices: 28421422--28421566 Score: 116
Period size: 46 Copynumber: 3.2 Consensus size: 45
28421412 TATGAATTTG
* *
28421422 TATAA-TTTAAAATAA-TAATTATTACATATAATTTAATAATAATA
1 TATAATTTTAAAATAATTAA-TATTAAATATAATTTAATAATGATA
** * * * ** * *
28421466 TATAATTTTTTAAAATTCTTGATAATAAAAATTTTTTTAT-ATGAATT
1 TATAA--TTTTAAAATAATTAATATTAAATATAATTTAATAATG-ATA
*
28421513 TATACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATA-ATTTTAAAATAATTAATATTAAATATAATTTAATAATGATA
28421559 TATAATTT
1 TATAATTT
28421567 CATAAAATTC
Statistics
Matches: 72, Mismatches: 22, Indels: 13
0.67 0.21 0.12
Matches are distributed among these distances:
44 5 0.07
45 3 0.04
46 32 0.44
47 29 0.40
48 3 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (45 bp):
TATAATTTTAAAATAATTAATATTAAATATAATTTAATAATGATA
Found at i:28421581 original size:47 final size:45
Alignment explanation
Indices: 28421447--28421587 Score: 122
Period size: 47 Copynumber: 3.0 Consensus size: 45
28421437 TAATTATTAC
* *
28421447 ATATAATTTAATAATAATATATAATTTTTTAAAATTCTTGATAATAA
1 ATATAATTTAATAATGATATATAA--TTTTAAAATTCTTAATAATAA
* ** * * * ** *
28421494 AAATTTTTTTAT-ATGAATTTATACAATTTAAAATAATTAATATTAA
1 ATATAATTTAATAATG-ATATATA-ATTTTAAAATTCTTAATAATAA
28421540 ATATAATTTAATAATGATATATAATTTCATAAAATTCTTAATAATAA
1 ATATAATTTAATAATGATATATAATTT--TAAAATTCTTAATAATAA
28421587 A
1 A
28421588 ATGTTCTTAT
Statistics
Matches: 69, Mismatches: 20, Indels: 10
0.70 0.20 0.10
Matches are distributed among these distances:
45 3 0.04
46 32 0.46
47 33 0.48
48 1 0.01
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (45 bp):
ATATAATTTAATAATGATATATAATTTTAAAATTCTTAATAATAA
Found at i:28422773 original size:18 final size:17
Alignment explanation
Indices: 28422752--28422786 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28422742 TTATTATTAA
*
28422752 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28422770 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28422787 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28422916 original size:18 final size:17
Alignment explanation
Indices: 28422895--28422929 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28422885 TTATTATTAA
*
28422895 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28422913 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28422930 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28422996 original size:154 final size:144
Alignment explanation
Indices: 28422705--28423092 Score: 670
Period size: 154 Copynumber: 2.6 Consensus size: 144
28422695 NNNNNNNNNN
28422705 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
1 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
28422770 ATATAATTTAATAAAATTCTT-ATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAAT
66 ATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAAT
28422834 TTTAATAAGATTAA
131 TTTAATAAGATTAA
28422848 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
1 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
*
28422913 ATATAATTTAATAAAATTCTTAATAATTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTG
66 ATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGT--A--A--A---TTATT-
28422978 TTATTTAAATTTTAATAAGATTAA
121 TTATTTAAATTTTAATAAGATTAA
28423002 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
1 TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
28423067 ATATAATTTAATAAAATTCTTAATAA
66 ATATAATTTAATAAAATTCTTAATAA
28423093 ATAAAATTCT
Statistics
Matches: 233, Mismatches: 1, Indels: 11
0.95 0.00 0.04
Matches are distributed among these distances:
143 86 0.37
144 24 0.10
146 1 0.00
148 1 0.00
150 1 0.00
153 5 0.02
154 115 0.49
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (144 bp):
TATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAAT
ATATAATTTAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTTTATTTAAAT
TTTAATAAGATTAA
Found at i:28423070 original size:18 final size:17
Alignment explanation
Indices: 28423049--28423083 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
28423039 TTATTATTAA
*
28423049 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28423067 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28423084 TCTTAATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28423129 original size:61 final size:61
Alignment explanation
Indices: 28423064--28423251 Score: 177
Period size: 61 Copynumber: 3.1 Consensus size: 61
28423054 TTTTAATTAA
*
28423064 AATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTCTATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTATATGAATTTACTCAAATCAT
* * * * * * * * * * * * * *
28423125 AATATATGATACT-GTAAAA-TATAAATTAACATAATTATTAT-TAAATATA-TTATAATTAA
1 AATATATAAT-TTAATAAAATTCTTAATAAATAAAATTCTTATATGAATTTACTCA-AATCAT
* *
28423184 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTATATGAATTTACTCAAATCAT
28423245 AATATAT
1 AATATAT
28423252 GATTATAACT
Statistics
Matches: 90, Mismatches: 31, Indels: 12
0.68 0.23 0.09
Matches are distributed among these distances:
58 3 0.03
59 24 0.27
60 29 0.32
61 31 0.34
62 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (61 bp):
AATATATAATTTAATAAAATTCTTAATAAATAAAATTCTTATATGAATTTACTCAAATCAT
Found at i:28423167 original size:120 final size:120
Alignment explanation
Indices: 28423032--28423254 Score: 410
Period size: 120 Copynumber: 1.9 Consensus size: 120
28423022 ATCATATTTA
*
28423032 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
28423097 AATTCTTCTATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 AATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
*
28423152 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
*
28423217 TATTCTTATATGAATTTACTCAAATCATAATATATGAT
66 AATTCTTATATGAATTTACTCAAATCATAATATATGAT
28423255 TATAACTAAT
Statistics
Matches: 99, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
120 99 1.00
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAAATAA
AATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:28423197 original size:14 final size:15
Alignment explanation
Indices: 28423148--28423199 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
28423138 GTAAAATATA
28423148 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
28423163 TATTAAATATATTAT
1 AATTAAATATATTAT
28423178 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
28423191 AATTTAATA
1 AATTAAATA
28423200 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:28423266 original size:17 final size:16
Alignment explanation
Indices: 28423244--28423290 Score: 53
Period size: 17 Copynumber: 2.9 Consensus size: 16
28423234 ACTCAAATCA
28423244 TAATATATGATTATAAC
1 TAATATATGATT-TAAC
*
28423261 T-A-ATATGATTTAAT
1 TAATATATGATTTAAC
28423275 TAAATATATGATTTAA
1 T-AATATATGATTTAA
28423291 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 4 0.15
15 8 0.31
16 2 0.08
17 12 0.46
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (16 bp):
TAATATATGATTTAAC
Found at i:28423291 original size:17 final size:17
Alignment explanation
Indices: 28423263--28423296 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
28423253 ATTATAACTA
*
28423263 ATATGATTTAATTAAAT
1 ATATGATTTAATAAAAT
28423280 ATATGATTTAATAAAAT
1 ATATGATTTAATAAAAT
28423297 TTAAAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
ATATGATTTAATAAAAT
Found at i:28423489 original size:92 final size:92
Alignment explanation
Indices: 28423328--28423521 Score: 286
Period size: 92 Copynumber: 2.1 Consensus size: 92
28423318 TATTATAGTT
* *
28423328 TATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAATAATATATAATTTCAT
1 TATGAATTTATACAATTTAAAATAATAATTATTACATATAATTTAATAATAATATATAATTTCAT
* *
28423393 AAAATTCTTGATAATAAAAATTTTCTTA
66 AAAATTCTTAATAAT-AAAATGTTCTTA
* *
28423421 TATGAATTTATACAATTTAAAATAATTAA-TATTA-ATATAA-TTATATAGTGATATATAATTTC
1 TATGAATTTATACAATTTAAAATAA-TAATTATTACATATAATTTA-ATAATAATATATAATTTC
28423483 ATAAAATTCTTAATAATAAAATGTTCTTA
64 ATAAAATTCTTAATAATAAAATGTTCTTA
28423512 TATGAATTTA
1 TATGAATTTA
28423522 CTAAAATCAA
Statistics
Matches: 93, Mismatches: 6, Indels: 6
0.89 0.06 0.06
Matches are distributed among these distances:
91 24 0.26
92 38 0.41
93 28 0.30
94 3 0.03
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (92 bp):
TATGAATTTATACAATTTAAAATAATAATTATTACATATAATTTAATAATAATATATAATTTCAT
AAAATTCTTAATAATAAAATGTTCTTA
Found at i:28426984 original size:9 final size:9
Alignment explanation
Indices: 28426970--28426994 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
28426960 TCTGAACTAC
28426970 ATTTATCTT
1 ATTTATCTT
28426979 ATTTATCTT
1 ATTTATCTT
28426988 ATTTATC
1 ATTTATC
28426995 AGCAAATGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.12, G:0.00, T:0.64
Consensus pattern (9 bp):
ATTTATCTT
Found at i:28428807 original size:15 final size:16
Alignment explanation
Indices: 28428787--28428822 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
28428777 TTTAATTTTC
*
28428787 AAATTTTCAAAAA-AA
1 AAATTTTAAAAAATAA
28428802 AAATTTTAAAAAATAA
1 AAATTTTAAAAAATAA
28428818 AAATT
1 AAATT
28428823 GCATTTTGAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTTTAAAAAATAA
Found at i:28428852 original size:30 final size:31
Alignment explanation
Indices: 28428818--28428919 Score: 122
Period size: 30 Copynumber: 3.4 Consensus size: 31
28428808 TAAAAAATAA
*
28428818 AAATTGCATTTTGACCCCTAAACTTTTC-CT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
28428848 AAATTTCATTTTGACCCTTAAAC-TTTCTTT
1 AAATTTCATTTTGACCCCTAAACTTTTCTCT
* *
28428878 AAATTTCACTTAGACCCCTAAAC-TTTCAT-T
1 AAATTTCATTTTGACCCCTAAACTTTTC-TCT
28428908 AAATTTCATTTT
1 AAATTTCATTTT
28428920 AATCCTAAAT
Statistics
Matches: 62, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
29 4 0.06
30 57 0.92
31 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.04, T:0.44
Consensus pattern (31 bp):
AAATTTCATTTTGACCCCTAAACTTTTCTCT
Found at i:28429312 original size:3 final size:3
Alignment explanation
Indices: 28429304--28429350 Score: 58
Period size: 3 Copynumber: 15.0 Consensus size: 3
28429294 GCTAGACTTT
* *
28429304 GAA GAA GAA GAA GGAA GAA GAA GGAA GAA GAA AAA GAG GAA GAA GAA
1 GAA GAA GAA GAA -GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA
28429351 ATAAAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 32 0.84
4 6 0.16
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:28429322 original size:10 final size:10
Alignment explanation
Indices: 28429307--28429335 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
28429297 AGACTTTGAA
28429307 GAAGAAGAAG
1 GAAGAAGAAG
28429317 GAAGAAGAAG
1 GAAGAAGAAG
28429327 GAAGAAGAA
1 GAAGAAGAA
28429336 AAAGAGGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAG
Found at i:28429466 original size:15 final size:13
Alignment explanation
Indices: 28429444--28429482 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
28429434 GCAGCCCAAG
28429444 AAAAAAACAACAAA
1 AAAAAAACAA-AAA
28429458 AACAAAAACAAAAA
1 AA-AAAAACAAAAA
28429472 AAAAGAAACAA
1 AAAA-AAACAA
28429483 GCCCCCTCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 2 0.09
14 13 0.57
15 8 0.35
ACGTcount: A:0.85, C:0.13, G:0.03, T:0.00
Consensus pattern (13 bp):
AAAAAAACAAAAA
Found at i:28429651 original size:15 final size:15
Alignment explanation
Indices: 28429631--28429700 Score: 63
Period size: 15 Copynumber: 4.5 Consensus size: 15
28429621 GGCCCAGCAG
28429631 AGAAAAAAA-AAGAAA
1 AGAAAAAAAGAA-AAA
28429646 AGAAAAAGAAGAAAAA
1 AGAAAAA-AAGAAAAA
* *
28429662 GAGAAGGAAAA-AAGAA
1 -AGAA-AAAAAGAAAAA
*
28429678 GGAAAAAAAGAAAAA
1 AGAAAAAAAGAAAAA
28429693 AGAAAAAA
1 AGAAAAAA
28429701 GAGGTTCAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
14 4 0.09
15 21 0.48
16 9 0.20
17 8 0.18
18 2 0.05
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AGAAAAAAAGAAAAA
Found at i:28429657 original size:14 final size:13
Alignment explanation
Indices: 28429643--28429702 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
28429633 AAAAAAAAAG
28429643 AAAAGAAAAAGAAGA
1 AAAAGAAAAAG-A-A
* *
28429658 AAAAGAGAAGGAA
1 AAAAGAAAAAGAA
**
28429671 AAAAGAAGGA-AA
1 AAAAGAAAAAGAA
28429683 AAAAGAAAAAAGAA
1 AAAAG-AAAAAGAA
28429697 AAAAGA
1 AAAAGA
28429703 GGTTCAATTC
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
12 7 0.20
13 11 0.31
14 8 0.23
15 9 0.26
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAGAA
Found at i:28429673 original size:32 final size:30
Alignment explanation
Indices: 28429636--28429696 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 30
28429626 AGCAGAGAAA
28429636 AAAAAAGAAAAGAAAAAGAAGAAAAAGAGAAGG
1 AAAAAAG-AAAGAAAAA-AAGAAAAA-AGAAGG
*
28429669 AAAAAAGAAGGAAAAAAAGAAAAAAGAA
1 AAAAAAGAAAGAAAAAAAGAAAAAAGAA
28429697 AAAAGAGGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 4 0.15
31 8 0.30
32 8 0.30
33 7 0.26
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (30 bp):
AAAAAAGAAAGAAAAAAAGAAAAAAGAAGG
Found at i:28429870 original size:17 final size:16
Alignment explanation
Indices: 28429837--28429885 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
28429827 TTTATGCATT
28429837 TTTATATTTATATTTTTAA
1 TTTA-ATTTA-ATTTTT-A
28429856 TTTAATTTAATTTTTA
1 TTTAATTTAATTTTTA
* *
28429872 TTTTATTTTATTTT
1 TTTAATTTAATTTT
28429886 AAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 13 0.46
17 6 0.21
18 5 0.18
19 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTAATTTAATTTTTA
Found at i:28430076 original size:20 final size:22
Alignment explanation
Indices: 28430051--28430093 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
28430041 TCGGGTTTCG
28430051 AAATTT-TCGTG-TCTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
*
28430071 AAATTTCTCGTGTTTTTCAAAA
1 AAATTTCTCGTGTTCTTCAAAA
28430093 A
1 A
28430094 TAAGGTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 5 0.25
22 9 0.45
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (22 bp):
AAATTTCTCGTGTTCTTCAAAA
Found at i:28430227 original size:18 final size:18
Alignment explanation
Indices: 28430197--28430549 Score: 189
Period size: 17 Copynumber: 19.9 Consensus size: 18
28430187 TAAAAATCGG
*
28430197 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** *
28430215 AAAAATTCCCGTG-TTGC
1 AAAAATTTTCGTGTTTTC
*
28430232 AAAAATTTTCATGTTTTTC
1 AAAAATTTTCGTG-TTTTC
*
28430251 AAAAATTCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
** ***
28430269 AAAAAAATTCCAATTTTC
1 AAAAATTTTCGTGTTTTC
*
28430287 AAAATTTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
28430305 TAAAAA-CTTC-TGTGTTTC
1 -AAAAATTTTCGTGT-TTTC
28430323 AAAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
28430340 TAAAATTTTCGT-ATTTC
1 AAAAATTTTCGTGTTTTC
*
28430357 AAAAATTTTCTTGTTTTC
1 AAAAATTTTCGTGTTTTC
* * *
28430375 -AAATTTTTCGT-ATTTA
1 AAAAATTTTCGTGTTTTC
**
28430391 AAAAATCCTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
28430409 -AAAA-TTCCAGTG-TTTC
1 AAAAATTTTC-GTGTTTTC
*
28430425 AAAATTTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
** **
28430442 AAAAAAAAATTCCCGTTTTCC
1 --AAAAATTTTCGTGTTTT-C
* *
28430463 AAAAACTTTCGCGTTTT-
1 AAAAATTTTCGTGTTTTC
**
28430480 AAGAAATTGACCGTG-TTTC
1 AA-AAATT-TTCGTGTTTTC
*
28430499 ATAAATTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
28430516 AAAGAAATCTCGTG-TTTC
1 AAA-AATTTTCGTGTTTTC
*
28430534 -AAAATTTTCATGTTTT
1 AAAAATTTTCGTGTTTT
28430550 TTTAAAAAAT
Statistics
Matches: 249, Mismatches: 64, Indels: 45
0.70 0.18 0.13
Matches are distributed among these distances:
16 15 0.06
17 101 0.41
18 83 0.33
19 46 0.18
20 3 0.01
21 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:28430250 original size:36 final size:35
Alignment explanation
Indices: 28430197--28430265 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 35
28430187 TAAAAATCGG
* *
28430197 AAAATTTTTCGTGTTTTCAAAAATTCCCGTGTTGC
1 AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
*
28430232 AAAAATTTTCATGTTTTTCAAAAATTCTCGTGTT
1 AAAAATTTTCATG-TTTTCAAAAATTCCCGTGTT
28430266 TTCAAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 11 0.37
36 19 0.63
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (35 bp):
AAAAATTTTCATGTTTTCAAAAATTCCCGTGTTGC
Found at i:28430602 original size:15 final size:15
Alignment explanation
Indices: 28430550--28430605 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 15
28430540 TTCATGTTTT
28430550 TTTAAAAAATT-GTG
1 TTTAAAAAATTCGTG
** *
28430564 TTTCTAAAATTCTTGTAT
1 TTTAAAAAATTC--GT-G
28430582 TTTAAAAAATTCGTG
1 TTTAAAAAATTCGTG
28430597 TTTAAAAAA
1 TTTAAAAAA
28430606 AAAGGAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 7
0.71 0.13 0.16
Matches are distributed among these distances:
14 9 0.28
15 9 0.28
16 2 0.06
17 2 0.06
18 10 0.31
ACGTcount: A:0.41, C:0.05, G:0.09, T:0.45
Consensus pattern (15 bp):
TTTAAAAAATTCGTG
Found at i:28434957 original size:44 final size:44
Alignment explanation
Indices: 28434901--28435483 Score: 282
Period size: 44 Copynumber: 13.2 Consensus size: 44
28434891 TTGGGGAGGT
*
28434901 AAGACCTG-TATCTTCGATCTACTTCA-CACTAGTATGGAAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGG-AAGAC
* * *
28434944 ACGATCTGCTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * *
28434988 AAGATCCATTATCTTTGATCTACTTCACCACTAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTAT-GGAAGAC
* * *
28435033 AAGATCTGCCATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * *
28435077 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * * *
28435121 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-AAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* * * *
28435165 AAGATCCGCTATCTTCGATATACTTCATGTCAATA-AAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * *
28435209 AAGATCCACTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
*** * *
28435253 AAGATCCATTATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* * *
28435297 AAGATCCGCTATCTTCGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
** * * *
28435341 AAGATCCACTATCTTTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCA--TCACTAGTATGGAAGAC
* *
28435385 AAGATCTGCTATC-TCTGATCTACTTCATGTCAATA-CAT-GAAGAC
1 AAGATCTGCTATCTTC-GATCTACTTCA--TCACTAGTATGGAAGAC
* *** * *
28435429 AATATCCATTATCTTCGATCTACTTCACCACCAGTATGGGAAGAC
1 AAGATCTGCTATCTTCGATCTACTTCATCACTAGTAT-GGAAGAC
28435474 AAGATCTGCT
1 AAGATCTGCT
28435484 GCTTTTTCAC
Statistics
Matches: 467, Mismatches: 53, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
42 7 0.01
43 17 0.04
44 383 0.82
45 48 0.10
46 4 0.01
47 8 0.02
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (44 bp):
AAGATCTGCTATCTTCGATCTACTTCATCACTAGTATGGAAGAC
Found at i:28435177 original size:88 final size:88
Alignment explanation
Indices: 28434939--28435455 Score: 740
Period size: 88 Copynumber: 5.9 Consensus size: 88
28434929 CTAGTATGGA
* * *
28434939 AAGACACGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
* * * *
28435003 TGATCTACTTCA--CCACTAGTATGGG
65 CGATCTACTTCATGTCAATA-CAT--G
* *
28435028 AAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATC-TC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
28435092 TGATCTACTTCATGTCAATACATG
66 -GATCTACTTCATGTCAATACATG
** * *
28435116 AAGACAAGATCCATTATCTTCGATCTACTTCATGTCAATACATAAAGACAAGATCCGCTATCTTC
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
* *
28435181 GATATACTTCATGTCAATAAATG
66 GATCTACTTCATGTCAATACATG
* *
28435204 AAGACAAGATCCACTATC-TCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
28435268 CGATCTACTTCATGTCAATACATG
65 CGATCTACTTCATGTCAATACATG
*
28435292 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTT
1 AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
28435357 GATCTACTTCATGTCAATACATG
66 GATCTACTTCATGTCAATACATG
* * *
28435380 AAGACAAGATCTGCTATC-TCTGATCTACTTCATGTCAATACATGAAGACAATATCCATTATCTT
1 AAGACAAGATCCGCTATCTTC-GATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTT
28435444 CGATCTACTTCA
65 CGATCTACTTCA
28435456 CCACCAGTAT
Statistics
Matches: 392, Mismatches: 28, Indels: 17
0.90 0.06 0.04
Matches are distributed among these distances:
87 4 0.01
88 309 0.79
89 71 0.18
90 4 0.01
91 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (88 bp):
AAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATCCACTATCTTC
GATCTACTTCATGTCAATACATG
Found at i:28435227 original size:132 final size:132
Alignment explanation
Indices: 28434952--28435455 Score: 807
Period size: 132 Copynumber: 3.8 Consensus size: 132
28434942 ACACGATCTG
*
28434952 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTTGATCTACTTCA--
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * * * *
28435015 CCACTAGTATGGGAAGACAAGATCTGCCATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
66 TCAATA-CAT--GAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAG
28435080 ATCCA
128 ATCCA
28435085 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
* * *
28435150 TCAATACATAAAGACAAGATCCGCTATCTTCGATATACTTCATGTCAATAAATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
28435215 CA
131 CA
28435217 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
28435282 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
66 TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
28435347 CA
131 CA
* ***
28435349 CTATCTTTGATCTACTTCATGTCAATACATGAAGACAAGATCTGCTATC-TCTGATCTACTTCAT
1 CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTC-GATCTACTTCAT
* **
28435413 GTCAATACATGAAGACAATATCCATTATCTTCGATCTACTTCA
65 GTCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCA
28435456 CCACCAGTAT
Statistics
Matches: 349, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
131 2 0.01
132 279 0.80
133 62 0.18
134 2 0.01
135 4 0.01
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (132 bp):
CTATCTCTGATCTACTTCATGTCAATACATGAAGACAAGATCCATTATCTTCGATCTACTTCATG
TCAATACATGAAGACAAGATCCGCTATCTTCGATCTACTTCATGTCAATACATGAAGACAAGATC
CA
Found at i:28443535 original size:189 final size:189
Alignment explanation
Indices: 28443215--28443559 Score: 618
Period size: 189 Copynumber: 1.8 Consensus size: 189
28443205 TTGTCCAACT
28443215 GCTCTTGTACTTGTAGCTAAAGTCAGTCTTGCATCTCCTTCTGGTACTGTTCGAGCTTTTCCAAT
1 GCTCTTGTACTTGTAGCTAAAGTCAGTCTTGCATCTCCTTCTGGTACTGTTCGAGCTTTTCCAAT
* *
28443280 CTTTGATCCATGTCTTTTGTCTTTGCTCCTGTGCCGTATCGGTGTTTGGTTGGTTGGTTGGTTTC
66 CTCTGATCCATGTCTTTTGTCTTTGCTCCAGTGCCGTATCGGTGTTTGGTTGGTTGGTTGGTTTC
* *
28443345 CAGGTTGACTGAGAAATGATTTTAATTAATTAAGATCCTTTACCGGTGTTTAATGCACC
131 CAGGTTAACTGAGAAATAATTTTAATTAATTAAGATCCTTTACCGGTGTTTAATGCACC
* *
28443404 GCTCTTGTACTTGTAGCTGAAGTCAGTCTTGCATCTCCTTCTGGTATTGTTCGAGCTTTTCCAAT
1 GCTCTTGTACTTGTAGCTAAAGTCAGTCTTGCATCTCCTTCTGGTACTGTTCGAGCTTTTCCAAT
*
28443469 CTCTGATCCATGTCTTTTGTCTTTGCTCGAGTGCCGTATCGGTGTTTGGTTGGTTGGTTGGTTTC
66 CTCTGATCCATGTCTTTTGTCTTTGCTCCAGTGCCGTATCGGTGTTTGGTTGGTTGGTTGGTTTC
*
28443534 CAGGTTAACTGAGCAATAATTTTAAT
131 CAGGTTAACTGAGAAATAATTTTAAT
28443560 CAGAACCCTC
Statistics
Matches: 148, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
189 148 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.42
Consensus pattern (189 bp):
GCTCTTGTACTTGTAGCTAAAGTCAGTCTTGCATCTCCTTCTGGTACTGTTCGAGCTTTTCCAAT
CTCTGATCCATGTCTTTTGTCTTTGCTCCAGTGCCGTATCGGTGTTTGGTTGGTTGGTTGGTTTC
CAGGTTAACTGAGAAATAATTTTAATTAATTAAGATCCTTTACCGGTGTTTAATGCACC
Found at i:28451943 original size:19 final size:20
Alignment explanation
Indices: 28451910--28451949 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28451900 AAGTAGAAAG
*
28451910 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
28451930 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
28451949 A
1 A
28451950 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:28457695 original size:21 final size:21
Alignment explanation
Indices: 28457666--28457730 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
28457656 AATTTTATTT
28457666 ATTCTAAAACCTTAAATCTAAA
1 ATTC-AAAACCTTAAATCTAAA
* *
28457688 ATTCAAAACCCTAAATCCAAA
1 ATTCAAAACCTTAAATCTAAA
* * *
28457709 ATTTAAAATCTCAAATCCTAAA
1 ATTCAAAACCTTAAAT-CTAAA
28457731 TCTAAACCCG
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
21 27 0.77
22 8 0.23
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTCAAAACCTTAAATCTAAA
Found at i:28457943 original size:119 final size:119
Alignment explanation
Indices: 28457725--28457943 Score: 285
Period size: 119 Copynumber: 1.8 Consensus size: 119
28457715 AATCTCAAAT
* * * *
28457725 CCTAAATCTAAACCCGTAACCCCAAACCATTGAATCTTGAACCCATAACCCCAAACCTTTGAACT
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
***
28457790 GTAACCCAAACAATTAAACATTGAACATTGAACCCTGAGCCCAAATTATGAATC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGAATC
* * **
28457844 CCTAAATCTAAAATCGTAACCCCAAATCATTAAATCTTAAATTCATAACCCCAAACCTTTGAACC
1 CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
** * * * *
28457909 GTAACCTGAACTATTGAATATTGAACCCCAAACCC
66 GTAACCCAAACAATTAAACATTGAACACCAAACCC
28457944 AAATCTTGAA
Statistics
Matches: 83, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
119 83 1.00
ACGTcount: A:0.40, C:0.30, G:0.07, T:0.23
Consensus pattern (119 bp):
CCTAAATCTAAAACCGTAACCCCAAACCATTAAATCTTAAACCCATAACCCCAAACCTTTGAACC
GTAACCCAAACAATTAAACATTGAACACCAAACCCTGAGCCCAAATTATGAATC
Found at i:28462573 original size:20 final size:20
Alignment explanation
Indices: 28462548--28462616 Score: 61
Period size: 20 Copynumber: 3.5 Consensus size: 20
28462538 ACATGATATC
28462548 CTTAGAAATTTTGGTAAAAG
1 CTTAGAAATTTTGGTAAAAG
* * *
28462568 CTTAGAAAATTT-GTTAAAT
1 CTTAGAAATTTTGGTAAAAG
* *
28462587 TTATAGGAATTTTGGTAAATAG
1 CT-TAGAAATTTTGGTAAA-AG
28462609 -TTAGAAAT
1 CTTAGAAAT
28462617 AATTGAAAAT
Statistics
Matches: 37, Mismatches: 9, Indels: 6
0.71 0.17 0.12
Matches are distributed among these distances:
19 6 0.16
20 25 0.68
21 5 0.14
22 1 0.03
ACGTcount: A:0.41, C:0.03, G:0.17, T:0.39
Consensus pattern (20 bp):
CTTAGAAATTTTGGTAAAAG
Found at i:28462729 original size:20 final size:20
Alignment explanation
Indices: 28462706--28462789 Score: 53
Period size: 20 Copynumber: 4.2 Consensus size: 20
28462696 GAAATATTAG
28462706 TAAATTTTTAAAAGTTTTGA
1 TAAATTTTTAAAAGTTTTGA
* ** *
28462726 TAAATTCTTGCAAGTTTTGG
1 TAAATTTTTAAAAGTTTTGA
** * * *
28462746 TAAAAGTGTAGAAGTTCTGA
1 TAAATTTTTAAAAGTTTTGA
* *
28462766 TAAATTATTAGATA-TTTTGA
1 TAAATTTTTA-AAAGTTTTGA
28462786 TAAA
1 TAAA
28462790 CCCTAATGAT
Statistics
Matches: 44, Mismatches: 19, Indels: 2
0.68 0.29 0.03
Matches are distributed among these distances:
20 43 0.98
21 1 0.02
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.43
Consensus pattern (20 bp):
TAAATTTTTAAAAGTTTTGA
Found at i:28470004 original size:13 final size:13
Alignment explanation
Indices: 28469959--28470009 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
28469949 ACATTCTCTC
*
28469959 AAAAT-AATAATG
1 AAAATGAATAAAG
28469971 AAAATGTAAATAAA-
1 AAAATG--AATAAAG
*
28469985 TAAATGAATAAAG
1 AAAATGAATAAAG
28469998 AAAATGAATAAA
1 AAAATGAATAAA
28470010 ATTATAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
12 11 0.34
13 11 0.34
14 5 0.16
15 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.22
Consensus pattern (13 bp):
AAAATGAATAAAG
Found at i:28470252 original size:33 final size:32
Alignment explanation
Indices: 28470209--28470298 Score: 94
Period size: 33 Copynumber: 2.8 Consensus size: 32
28470199 AAAAGTATGT
* *
28470209 ATATATATATAAGTTATAAAAGTATGTACGTGC
1 ATATGTATATAA-TTATAAAAGTATGTACGTAC
* *
28470242 ATATGTATAT-ATTATAAAAATGTATGTATGTAT
1 ATATGTATATAATTAT-AAAA-GTATGTACGTAC
28470275 ATATGTATATAAATTAT-AAAGTAT
1 ATATGTATAT-AATTATAAAAGTAT
28470299 AACAAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
31 4 0.08
32 9 0.18
33 31 0.63
35 5 0.10
ACGTcount: A:0.44, C:0.02, G:0.12, T:0.41
Consensus pattern (32 bp):
ATATGTATATAATTATAAAAGTATGTACGTAC
Found at i:28471479 original size:19 final size:20
Alignment explanation
Indices: 28471446--28471485 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
28471436 AAGTAAAAAG
*
28471446 AATTTAAAATAATGTTGATA
1 AATTTAAAATAATGTGGATA
*
28471466 AATTT-AAATCATGTGGATA
1 AATTTAAAATAATGTGGATA
28471485 A
1 A
28471486 TAATTTAGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (20 bp):
AATTTAAAATAATGTGGATA
Found at i:28488082 original size:26 final size:26
Alignment explanation
Indices: 28488053--28488107 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
28488043 TCAACTTATC
28488053 TTTTAAGTT-AATAAATTCTCATTGAG
1 TTTTAAGTTCAATAAATTCTC-TTGAG
* * *
28488079 TTTTCATTTCAATAATTTCTCTTGAG
1 TTTTAAGTTCAATAAATTCTCTTGAG
28488105 TTT
1 TTT
28488108 ATTTTAGAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.60
27 10 0.40
ACGTcount: A:0.27, C:0.11, G:0.09, T:0.53
Consensus pattern (26 bp):
TTTTAAGTTCAATAAATTCTCTTGAG
Found at i:28489674 original size:96 final size:96
Alignment explanation
Indices: 28489556--28489744 Score: 263
Period size: 96 Copynumber: 2.0 Consensus size: 96
28489546 AAAGGAGGAA
* * * * *
28489556 TACGATTGAGGTATCATCTTTTGTGCGATGTTATTGGTATAGTTCAAAAGATCATAAGGGTTTCC
1 TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
28489621 AATGTCCAATTAAATATCCAAATAGAGAGAC
66 AATGTCCAATTAAATATCCAAATAGAGAGAC
* * * *
28489652 TACGATTGAGATATCA-CATTTTGTGCAATGTTATTGGTGTAATTCAAAATATTACAAGAGTTTT
1 TACGATTGAGATATCATC-TTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTC
* *
28489716 CAATGTCCAGTTAAATATCCAACTAGAGA
65 CAATGTCCAATTAAATATCCAAATAGAGA
28489745 ATAAAGTAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
95 1 0.01
96 80 0.99
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (96 bp):
TACGATTGAGATATCATCTTTTGTGCAATGTTATTGGTATAATTCAAAAGATCACAAGAGTTTCC
AATGTCCAATTAAATATCCAAATAGAGAGAC
Found at i:28493034 original size:23 final size:22
Alignment explanation
Indices: 28492991--28493035 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28492981 ATGAGATAAT
*
28492991 TAAAAATAAAAATATTTTTAAA
1 TAAAAATAAAAATATTATTAAA
28493013 TAAAAATATCAAAA-ATTATTAAA
1 TAAAAATA--AAAATATTATTAAA
28493036 AACGAGAGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 8 0.40
23 8 0.40
24 4 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAATAAAAATATTATTAAA
Found at i:28498751 original size:26 final size:26
Alignment explanation
Indices: 28498706--28498767 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
28498696 ATGGTAATTA
28498706 AATTAAATT-AAATACTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
* **
28498731 GATTAAATTAAAATGTTATATAATGT
1 AATTAAATTAAAATACTATATAATGT
28498757 AATTAAATTAA
1 AATTAAATTAA
28498768 GTTAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
25 8 0.25
26 24 0.75
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (26 bp):
AATTAAATTAAAATACTATATAATGT
Found at i:28500770 original size:3 final size:3
Alignment explanation
Indices: 28500762--28500789 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
28500752 ACGTGAAAGA
28500762 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
28500790 CAACATATAT
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28502409 original size:196 final size:196
Alignment explanation
Indices: 28502075--28502467 Score: 768
Period size: 196 Copynumber: 2.0 Consensus size: 196
28502065 GTAGTAGTTT
28502075 AATTGTTAAGCATTCTCTCTTTTTCCCTTATATCTTAAGTTCGAGTCATGCTAAACTTCTTCATT
1 AATTGTTAAGCATTCTCTCTTTTTCCCTTATATCTTAAGTTCGAGTCATGCTAAACTTCTTCATT
28502140 TTTCCTTTTAATTTCTGTAACACTCTAAACCCGGCCTAGACGTTTAGACCAAGTCCAAAGAGTTA
66 TTTCCTTTTAATTTCTGTAACACTCTAAACCCGGCCTAGACGTTTAGACCAAGTCCAAAGAGTTA
*
28502205 CATTATCGATTCTAAAATCTCATAGTTATAACGCATCAAAATAAAATCATTCATCACATAAAATC
131 CATTATCGATTCTAAAATCTCATAGTTATAACGCATCAAAATAAAACCATTCATCACATAAAATC
28502270 C
196 C
28502271 AATTGTTAAGCATTCTCTCTTTTTCCCTTATATCTTAAGTTCGAGTCATGCTAAACTTCTTCATT
1 AATTGTTAAGCATTCTCTCTTTTTCCCTTATATCTTAAGTTCGAGTCATGCTAAACTTCTTCATT
28502336 TTTCCTTTTAATTTCTGTAACACTCTAAACCCGGCCTAGACGTTTAGACCAAGTCCAAAGAGTTA
66 TTTCCTTTTAATTTCTGTAACACTCTAAACCCGGCCTAGACGTTTAGACCAAGTCCAAAGAGTTA
*
28502401 CATTATCGATTCTAAAATCTCATAGTTATAACGCATCAAAATTAAACCATTCATCACATAAAATC
131 CATTATCGATTCTAAAATCTCATAGTTATAACGCATCAAAATAAAACCATTCATCACATAAAATC
28502466 C
196 C
28502467 A
1 A
28502468 GCACGATAGT
Statistics
Matches: 195, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
196 195 1.00
ACGTcount: A:0.32, C:0.23, G:0.09, T:0.36
Consensus pattern (196 bp):
AATTGTTAAGCATTCTCTCTTTTTCCCTTATATCTTAAGTTCGAGTCATGCTAAACTTCTTCATT
TTTCCTTTTAATTTCTGTAACACTCTAAACCCGGCCTAGACGTTTAGACCAAGTCCAAAGAGTTA
CATTATCGATTCTAAAATCTCATAGTTATAACGCATCAAAATAAAACCATTCATCACATAAAATC
C
Found at i:28503316 original size:172 final size:172
Alignment explanation
Indices: 28503023--28503369 Score: 631
Period size: 172 Copynumber: 2.0 Consensus size: 172
28503013 AATGCAGAGT
*
28503023 ACAAATATCCACAATCTCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
1 ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
*
28503088 ATCAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
66 ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
28503153 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
131 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
* *
28503195 ACAAATGTCCACAATATCTAATCAGTCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
1 ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
* *
28503260 ATAAGAATAAGTATCATAGTATGTATACAATTATGTTATTCATACGTCCATCACAGAGTATCAGA
66 ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
*
28503325 GAGTTTTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
131 GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
28503367 ACA
1 ACA
28503370 TCAATATCAG
Statistics
Matches: 168, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
172 168 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (172 bp):
ACAAATATCCACAATATCTAATCAATCATTCCAAATTGTTTCACAAGTAGATAATACAGCTCAAT
ATAAGAATAAGTATCATAGTATGCATACAATTATGTTATTCATACGCCCATCACAGAGTATCAGA
GAGTTCTCGTATAATCAAATTCAAATCATTCATGTATTGGGG
Found at i:28506389 original size:21 final size:22
Alignment explanation
Indices: 28506364--28506404 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28506354 AGATATGAAA
* *
28506364 TTAAAT-TATATTTAGGATTCT
1 TTAAATCTAAATTGAGGATTCT
28506385 TTAAATCTAAATTGAGGATT
1 TTAAATCTAAATTGAGGATT
28506405 AGAAACGAGA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 6 0.35
22 11 0.65
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (22 bp):
TTAAATCTAAATTGAGGATTCT
Found at i:28510933 original size:13 final size:12
Alignment explanation
Indices: 28510901--28510938 Score: 60
Period size: 11 Copynumber: 3.2 Consensus size: 12
28510891 CCTTTCCCCC
28510901 TCCCTTCTCTC-
1 TCCCTTCTCTCT
28510912 TCCCTTCTCTCT
1 TCCCTTCTCTCT
28510924 TCCCTCTCTCTCT
1 TCCCT-TCTCTCT
28510937 TC
1 TC
28510939 TTTTTTTNNN
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 11 0.44
12 5 0.20
13 9 0.36
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (12 bp):
TCCCTTCTCTCT
Found at i:28521111 original size:21 final size:22
Alignment explanation
Indices: 28521065--28521120 Score: 53
Period size: 21 Copynumber: 2.6 Consensus size: 22
28521055 GTGATAGTCC
*
28521065 TACACGATTGTGTGAATGAGAG
1 TACACGATAGTGTGAATGAGAG
* *
28521087 -ACACGCTAGTGTGACTGA-AG
1 TACACGATAGTGTGAATGAGAG
* *
28521107 TACACAATCGTGTG
1 TACACGATAGTGTG
28521121 GGTAGACCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.30, C:0.16, G:0.29, T:0.25
Consensus pattern (22 bp):
TACACGATAGTGTGAATGAGAG
Found at i:28521628 original size:23 final size:22
Alignment explanation
Indices: 28521581--28521628 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
28521571 CAAACACACT
**
28521581 AACCTATAAGAAAATCAATCTA
1 AACCTATAAGAAAATCAATAGA
28521603 AACCATATATAGAAAATCAA-AGA
1 AACC-TATA-AGAAAATCAATAGA
28521626 AAC
1 AAC
28521629 TGATGTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 8 0.36
24 10 0.45
ACGTcount: A:0.58, C:0.17, G:0.06, T:0.19
Consensus pattern (22 bp):
AACCTATAAGAAAATCAATAGA
Found at i:28521922 original size:3 final size:3
Alignment explanation
Indices: 28521914--28521943 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
28521904 AAAATTAAAT
28521914 ATA ATA ATA A-A ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
28521944 CAACAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:28521936 original size:17 final size:18
Alignment explanation
Indices: 28521901--28521943 Score: 59
Period size: 20 Copynumber: 2.3 Consensus size: 18
28521891 TTTTCTTCTC
28521901 AATAAAATTAAATATAAT
1 AATAAAATTAAATATAAT
*
28521919 AATAAAATAATAATAATAAT
1 AATAAAATTA-AAT-ATAAT
28521939 AATAA
1 AATAA
28521944 CAACAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.41
19 3 0.14
20 10 0.45
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AATAAAATTAAATATAAT
Found at i:28525870 original size:30 final size:30
Alignment explanation
Indices: 28525824--28525917 Score: 143
Period size: 30 Copynumber: 3.1 Consensus size: 30
28525814 TTTTATTATG
*
28525824 CCAATATCTCGATACCCATATCTTTGACTTT
1 CCAATAT-TTGATACCCATATCTTTGACTTT
28525855 CCAATATTTGATACCCATATCTTTGACTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
* * *
28525885 CTATTATTTGATACCCATATCTTTGATTTT
1 CCAATATTTGATACCCATATCTTTGACTTT
28525915 CCA
1 CCA
28525918 TAAATATGGA
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
30 51 0.88
31 7 0.12
ACGTcount: A:0.26, C:0.24, G:0.06, T:0.44
Consensus pattern (30 bp):
CCAATATTTGATACCCATATCTTTGACTTT
Found at i:28525879 original size:15 final size:15
Alignment explanation
Indices: 28525834--28525911 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
28525824 CCAATATCTC
28525834 GATACCCATATCTTT
1 GATACCCATATCTTT
** *
28525849 GACTTTCCA-ATATTT
1 GA-TACCCATATCTTT
28525864 GATACCCATATCTTT
1 GATACCCATATCTTT
** * *
28525879 GACTTTCTAT-TATTT
1 GA-TACCCATATCTTT
28525894 GATACCCATATCTTT
1 GATACCCATATCTTT
28525909 GAT
1 GAT
28525912 TTTCCATAAA
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.26, C:0.22, G:0.08, T:0.45
Consensus pattern (15 bp):
GATACCCATATCTTT
Found at i:28528339 original size:60 final size:60
Alignment explanation
Indices: 28528246--28528358 Score: 181
Period size: 60 Copynumber: 1.9 Consensus size: 60
28528236 CACTATATGA
* *
28528246 TGTGTAGGGATGGGTGAGTGTTTTTAACCCCACATGGTGTGATAAGATGGACGGAGTTGG
1 TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACGGAGTTGG
* **
28528306 TGTGTAGGGATAGGTGGGTGTTTTTAACCCCACATGGTATGATGGGATGGACG
1 TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACG
28528359 AAGATGGACG
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.21, C:0.11, G:0.38, T:0.30
Consensus pattern (60 bp):
TGTGTAGGGATAGGTGAGTGTTTTTAACCCCACATGGTATGATAAGATGGACGGAGTTGG
Found at i:28538375 original size:30 final size:30
Alignment explanation
Indices: 28538285--28538375 Score: 94
Period size: 30 Copynumber: 3.0 Consensus size: 30
28538275 AATGTAATGT
* * * *
28538285 TCACACAAGCTGACAGTATTTTAGGGTTGC
1 TCACACAAGCTGACATTATATTAAGGTTTC
* * * *
28538315 TCACACAAGTTGACATTGTAAT-CGGATTTC
1 TCACACAAGCTGACATTATATTAAGG-TTTC
28538345 TCACACAAGCTGACATTATATTAAGGTTTC
1 TCACACAAGCTGACATTATATTAAGGTTTC
28538375 T
1 T
28538376 TGCACGGGCT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
29 2 0.04
30 44 0.92
31 2 0.04
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.33
Consensus pattern (30 bp):
TCACACAAGCTGACATTATATTAAGGTTTC
Found at i:28542081 original size:12 final size:12
Alignment explanation
Indices: 28542049--28542103 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
28542039 GTCCATATAC
28542049 ATAT-TATAAA-
1 ATATATATAAAT
28542059 AT-TAT-TAAAT
1 ATATATATAAAT
28542069 ATATATATAAAT
1 ATATATATAAAT
*
28542081 ATATATATGTAAGT
1 ATATATA--TAAAT
28542095 ATATATATA
1 ATATATATA
28542104 TATTTACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
9 5 0.13
10 5 0.13
11 3 0.08
12 14 0.37
14 11 0.29
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (12 bp):
ATATATATAAAT
Found at i:28542086 original size:14 final size:14
Alignment explanation
Indices: 28542067--28542105 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
28542057 AAATTATTAA
28542067 ATATATATATAAAT
1 ATATATATATAAAT
* *
28542081 ATATATATGTAAGT
1 ATATATATATAAAT
28542095 ATATATATATA
1 ATATATATATA
28542106 TTTACAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (14 bp):
ATATATATATAAAT
Found at i:28542250 original size:3 final size:3
Alignment explanation
Indices: 28542236--28542306 Score: 63
Period size: 3 Copynumber: 22.7 Consensus size: 3
28542226 TAAATGGGTA
* *
28542236 AAT AAA AAT AAT AAT AAGGT AAGT AAT AAT AAT AACT -AC AAT AAT AAT
1 AAT AAT AAT AAT AAT AA--T AA-T AAT AAT AAT AA-T AAT AAT AAT AAT
* *
28542284 GAC AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AA
28542307 AACTAATTAG
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 48 0.86
4 5 0.09
5 3 0.05
ACGTcount: A:0.63, C:0.04, G:0.06, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:28543905 original size:50 final size:50
Alignment explanation
Indices: 28543831--28544436 Score: 389
Period size: 50 Copynumber: 12.2 Consensus size: 50
28543821 TAACTCGTAA
** ** * * *
28543831 CTTTAATCTGCTTAACTGTGATGTC-GGAGAAGTAAGATTCGCCATTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGG-GAAGCAAGATTCACCGTTGTGG
* * *
28543881 CTTTAATCTTCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** ** * *
28543931 GTTTAATCTGCTCCACTGCACCG-CTAGGAAAGCAAGA--CA-CGCTGTGG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* * * *
28543978 CTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
** ** * * * * * * * * *
28544028 CTTTAATCTGCTCCACTGCATTGCCAGGGAAGTAACACTCGCTGCTATGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* * *
28544078 CTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAGGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** * * * * * * * * *
28544128 CTTTAATCTGTTCCACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTAG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* *
28544178 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** * * * *** *
28544228 CTTTAATCTGTTCCACTGCACCGCCTA-AGAAGTAAGATTCACTACTGTAG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* *
28544278 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
* ** ** * * * * *** *
28544328 CTTTAATCTGTTCCACTGCACCG-CTTGGGAGGTAAGACTCGTTGTTGTAG
1 CTTTAATCTTTTTAACTGCAATGTC-AGGGAAGCAAGATTCACCGTTGTGG
* *
28544378 CTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGG
1 CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
28544428 CTTTAATCT
1 CTTTAATCT
28544437 GTTCCACTGC
Statistics
Matches: 409, Mismatches: 137, Indels: 20
0.72 0.24 0.04
Matches are distributed among these distances:
47 31 0.08
48 3 0.01
49 4 0.01
50 367 0.90
51 4 0.01
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (50 bp):
CTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGG
Found at i:28544123 original size:100 final size:100
Alignment explanation
Indices: 28543880--28544458 Score: 752
Period size: 100 Copynumber: 5.8 Consensus size: 100
28543870 CGCCATTGTG
* * * * *
28543880 GCTTTAATCTTCTTAACTGCAATGTCAGGGAAGCAAGATACACCGTCGTGGGTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
28543945 ACTGCACCGCTAGGAAAGCAAGACACGCTG-TG--
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* * * * *
28543977 GCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAAGATACGCCGTTGTGGCTTTAATCTGCTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
** * * *
28544042 ACTGCATTGCCAGGGAAGTAACACTCGCTGCTATG
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* * *
28544077 GCTTTAGTCTTTTTAACTGCAATGTCGGGGAAGCAGGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
28544142 ACTGCACTGCCTGGGAGGTAAGATTCGCTGCTGTA
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* *
28544177 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAGGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
* * * *
28544242 ACTGCACCGCCTA-AGAAGTAAGATTCACTACTGTA
66 ACTGCACCGCC-AGGGAAGTAAGACTCGCTGCTGTA
* *
28544277 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGCAAGATTCATCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
** * * *
28544342 ACTGCACCGCTTGGGAGGTAAGACTCGTTGTTGTA
66 ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
* *
28544377 GCTTTAATCTTTTTAACTGCAATGTCAGGGAGGGAAGATTCACCGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
28544442 ACTGCACCGCCAGGGAA
66 ACTGCACCGCCAGGGAA
28544459 ACTAAGATCT
Statistics
Matches: 427, Mismatches: 50, Indels: 7
0.88 0.10 0.01
Matches are distributed among these distances:
97 82 0.19
98 1 0.00
100 344 0.81
ACGTcount: A:0.23, C:0.22, G:0.24, T:0.31
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCAGGGAAGCAAGATTCACCGTTGTGGCTTTAATCTGTTCC
ACTGCACCGCCAGGGAAGTAAGACTCGCTGCTGTA
Found at i:28544621 original size:44 final size:44
Alignment explanation
Indices: 28544562--28545089 Score: 387
Period size: 44 Copynumber: 11.8 Consensus size: 44
28544552 CCTTTATTTT
* *
28544562 AATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * ** *
28544606 AATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAATTCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGAT-TACTA-GCTTC
* ** *
28544652 AGTCTATTCCACTGTAATCTCAGGGAGATAA-A--ACCT-GATGT-
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTA-CTAGCT-TC
* * * * * * * *
28544693 GATCTACTCTACTGTAA-CTTCAGAGAGACAAGATCCT-TTA-TTTT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * * * *
28544737 AATCCGCTCCACTTTAATCTCAAGGAGATAGGATTACTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
** * *
28544781 AATCTGCTCTGCTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
28544825 AATCTGCTCTACTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * *
28544869 AATCTGCTCTACTGTAATCTCAGGGAGATAAGATTTCTAACTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* * * * *
28544913 AATCTGATGCGATCTACTCTACTGTAA-CTTCAGAGAGATGAGATCCT-TTA-TTTT
1 AATC---T--G--CT-C-C-ACTGTAATC-TCAGGGAGATAAGAT--TACTAGCTTC
* * *
28544967 AATCCGCTCCACTGTAATCTTAGGGAGATAGGATTACTAGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
* *
28545011 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTTCTGGCTTC
1 AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
28545055 AATCTGCTCCACTGTAA-CATCAGGGAGATAAGATT
1 AATCTGCTCCACTGTAATC-TCAGGGAGATAAGATT
28545090 CACCATTTCC
Statistics
Matches: 387, Mismatches: 65, Indels: 64
0.75 0.13 0.12
Matches are distributed among these distances:
40 1 0.00
41 24 0.06
42 5 0.01
43 5 0.01
44 275 0.71
45 7 0.02
46 32 0.08
47 3 0.01
49 2 0.01
51 2 0.01
52 1 0.00
53 1 0.00
54 26 0.07
55 2 0.01
56 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (44 bp):
AATCTGCTCCACTGTAATCTCAGGGAGATAAGATTACTAGCTTC
Found at i:28544679 original size:173 final size:174
Alignment explanation
Indices: 28544474--28544811 Score: 552
Period size: 175 Copynumber: 1.9 Consensus size: 174
28544464 GATCTGTAAC
* *
28544474 TCTTCAGTCTATTCCACTATAATCTCAGGGAGATAAGACCTGATACGATCTGCTCTACTATAACT
1 TCTTCAGTCTATTCCACTATAATCTCAGGGAGATAAAACCTGATACGATCTACTCTACTATAACT
* * *
28544539 T-TAGAGATAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGC
66 TAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGC
28544603 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAAT
131 TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAAT
* ** *
28544647 TCTTCAGTCTATTCCACTGTAATCTCAGGGAGATAAAACCTGATGTGATCTACTCTACTGTAACT
1 TCTTCAGTCTATTCCACTATAATCTCAGGGAGATAAAACCTGATACGATCTACTCTACTATAACT
* *
28544712 TCAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTTTAATCTCAAGGAGATAGGATTACTGG
66 T-AGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAG
*
28544777 CTTCAATCTGCTCTGCTGTAATCTCAGGGAGATAA
130 CTTCAATCTGCTCCGCTGTAATCTCAGGGAGATAA
28544812 GATTTCTGGC
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
173 60 0.40
175 91 0.60
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (174 bp):
TCTTCAGTCTATTCCACTATAATCTCAGGGAGATAAAACCTGATACGATCTACTCTACTATAACT
TAGAGAGACAAGATCCTTTATTTTAATCCGCTCCACTGTAATCTCAAGGAGATAGGATTACTAGC
TTCAATCTGCTCCGCTGTAATCTCAGGGAGATAATATCTAAAAT
Found at i:28546492 original size:19 final size:18
Alignment explanation
Indices: 28546468--28546512 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
28546458 TTAGCCTCTC
28546468 CATTTTTACTTTCATTTTT
1 CATTTTT-CTTTCATTTTT
*
28546487 CATTTTTTTTTCATTTTT
1 CATTTTTCTTTCATTTTT
28546505 CACTTTTT
1 CA-TTTTT
28546513 TTCCTCAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (18 bp):
CATTTTTCTTTCATTTTT
Found at i:28546498 original size:18 final size:19
Alignment explanation
Indices: 28546477--28546514 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
28546467 CCATTTTTAC
28546477 TTTCATTTTTCA-TTTTTT
1 TTTCATTTTTCACTTTTTT
28546495 TTTCATTTTTCACTTTTTT
1 TTTCATTTTTCACTTTTTT
28546514 T
1 T
28546515 CCTCAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTCATTTTTCACTTTTTT
Found at i:28547386 original size:24 final size:25
Alignment explanation
Indices: 28547340--28547386 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 25
28547330 GACCTTGATA
* * *
28547340 GATTTTTCTTTTTGCTTTTAACTTT
1 GATTTTTCTTTTTGATCTGAACTTT
28547365 GATTTTT-TTTTTGATCTGAACT
1 GATTTTTCTTTTTGATCTGAACT
28547387 CTTGGGATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.15, C:0.11, G:0.11, T:0.64
Consensus pattern (25 bp):
GATTTTTCTTTTTGATCTGAACTTT
Found at i:28551583 original size:24 final size:24
Alignment explanation
Indices: 28551543--28551589 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
28551533 AAAGGGAAAT
*
28551543 AAGAGAAAGTGATGGAAAATGTTG
1 AAGAGAAAGTGAAGGAAAATGTTG
*
28551567 AAGAGAAAG-GAAAGGAAAGTGTT
1 AAGAGAAAGTG-AAGGAAAATGTT
28551590 ATAAATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.49, C:0.00, G:0.34, T:0.17
Consensus pattern (24 bp):
AAGAGAAAGTGAAGGAAAATGTTG
Found at i:28553420 original size:22 final size:22
Alignment explanation
Indices: 28553394--28553438 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
28553384 ATTATGTGTA
28553394 TTAATTCATAATATAA-TTAATT
1 TTAATT-ATAATATAATTTAATT
* *
28553416 TTAATTTTAATCTAATTTAATT
1 TTAATTATAATATAATTTAATT
28553438 T
1 T
28553439 GGGTTAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (22 bp):
TTAATTATAATATAATTTAATT
Found at i:28554902 original size:3 final size:3
Alignment explanation
Indices: 28554894--28554934 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
28554884 TGAGGATCCT
28554894 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
28554935 TCCCACAAAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Done.