Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 153 of 172
Found at i:50128005 original size:5 final size:6
Alignment explanation
Indices: 50127953--50128023 Score: 65
Period size: 6 Copynumber: 11.7 Consensus size: 6
50127943 CATATAGTTC
* * * *
50127953 AAAATA TAAAAGA AAAATA AACATA AAAAGA AAAA-A GACACATA AAAATA
1 AAAATA -AAAATA AAAATA AAAATA AAAATA AAAATA -A-AAATA AAAATA
50128003 AAAATA AAAAT- AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAA
50128024 CAAGCGGACT
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
5 6 0.11
6 38 0.72
7 8 0.15
8 1 0.02
ACGTcount: A:0.79, C:0.04, G:0.04, T:0.13
Consensus pattern (6 bp):
AAAATA
Found at i:50134734 original size:3 final size:3
Alignment explanation
Indices: 50134726--50134797 Score: 83
Period size: 3 Copynumber: 24.0 Consensus size: 3
50134716 TTATGTTGTA
* **
50134726 ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT ATT ACC ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
50134774 CTTT ATT ATT -TT CTT ATT ATT ATT
1 -ATT ATT ATT ATT ATT ATT ATT ATT
50134798 CTTTTCATTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
2 2 0.03
3 54 0.93
4 2 0.03
ACGTcount: A:0.28, C:0.06, G:0.01, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:50136360 original size:6 final size:6
Alignment explanation
Indices: 50136345--50136400 Score: 76
Period size: 6 Copynumber: 9.3 Consensus size: 6
50136335 ATTGAGTCCA
* * * *
50136345 TTTATC TTTATG TTTATT TTTATT TCTATT TTTATT TTTATT TTTATG
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
50136393 TTTATT TT
1 TTTATT TT
50136401 GTTTTCCTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.16, C:0.04, G:0.04, T:0.77
Consensus pattern (6 bp):
TTTATT
Found at i:50136378 original size:18 final size:18
Alignment explanation
Indices: 50136357--50136413 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
50136347 TATCTTTATG
50136357 TTTATTTTTATTTCTATT
1 TTTATTTTTATTTCTATT
* *
50136375 TTTATTTTTATTTTTATG
1 TTTATTTTTATTTCTATT
50136393 TTTATTTTGT-TTTCCTATT
1 TTTATTTT-TATTT-CTATT
50136412 TT
1 TT
50136414 GAACTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 27 0.82
19 6 0.18
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (18 bp):
TTTATTTTTATTTCTATT
Found at i:50136426 original size:36 final size:35
Alignment explanation
Indices: 50136345--50136426 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 35
50136335 ATTGAGTCCA
* **
50136345 TTTATCTTTATGTTTATTTTTATTTCTATTTTTATT
1 TTTAT-TTTATGTTTATTTTTATTTCTATTTTGAAC
50136381 TTTATTTTTATGTTTATTTTGT-TTTCCTATTTTGAAC
1 TTTA-TTTTATGTTTATTTT-TATTT-CTATTTTGAAC
50136418 TTTATTTTA
1 TTTATTTTA
50136427 ATTATTATGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
36 26 0.65
37 14 0.35
ACGTcount: A:0.17, C:0.06, G:0.05, T:0.72
Consensus pattern (35 bp):
TTTATTTTATGTTTATTTTTATTTCTATTTTGAAC
Found at i:50139953 original size:6 final size:7
Alignment explanation
Indices: 50139934--50139959 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
50139924 TATGTTAAGA
50139934 AGTTTTT
1 AGTTTTT
50139941 AGTTTTT
1 AGTTTTT
50139948 AGTTTTT
1 AGTTTTT
50139955 AGTTT
1 AGTTT
50139960 CAATTGAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.69
Consensus pattern (7 bp):
AGTTTTT
Found at i:50142029 original size:21 final size:21
Alignment explanation
Indices: 50141981--50142029 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
50141971 ATTAAGGAAC
* *
50141981 CTTTA-AAAATATTGGTGAAT
1 CTTTAGAAAATATTGCTAAAT
*
50142001 CCTT-GAAAATATTGCTAAAT
1 CTTTAGAAAATATTGCTAAAT
50142021 CTTTAGAAA
1 CTTTAGAAA
50142030 TTTTGATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (21 bp):
CTTTAGAAAATATTGCTAAAT
Found at i:50143560 original size:21 final size:21
Alignment explanation
Indices: 50143536--50143576 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
50143526 AGATAAAAAA
50143536 AAATTTAATATATCATAATAC
1 AAATTTAATATATCATAATAC
50143557 AAATTTAATATATCATAATA
1 AAATTTAATATATCATAATA
50143577 GTGTACTAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATTTAATATATCATAATAC
Found at i:50146375 original size:17 final size:18
Alignment explanation
Indices: 50146353--50146389 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
50146343 ATTTTGGATA
*
50146353 TAATTT-TTTAGGTATTT
1 TAATTTATTTAGGCATTT
50146370 TAATTTATTTAGGCATTT
1 TAATTTATTTAGGCATTT
50146388 TA
1 TA
50146390 TGTTTGTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (18 bp):
TAATTTATTTAGGCATTT
Found at i:50155588 original size:23 final size:23
Alignment explanation
Indices: 50155559--50155624 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 23
50155549 CTGATTAATT
50155559 AATTAATAATTTAATTTAATTTC
1 AATTAATAATTTAATTTAATTTC
50155582 AATTAAT-ATTT--TTTAAAATTTC
1 AATTAATAATTTAATTT--AATTTC
50155604 AATT-ATCAA-TTAATTTAATTT
1 AATTAAT-AATTTAATTTAATTT
50155625 AAAATTAGGT
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
20 3 0.08
21 2 0.05
22 21 0.57
23 8 0.22
24 3 0.08
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (23 bp):
AATTAATAATTTAATTTAATTTC
Found at i:50155615 original size:29 final size:27
Alignment explanation
Indices: 50155555--50155630 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 27
50155545 TGGTCTGATT
50155555 AATTAATTAATAATTT--AATTTAATTTC
1 AATTAATT--TAATTTAAAATTTAATTTC
*
50155582 AATTAATATT-TTTTAAAATTTCAATTATC
1 AATTAAT-TTAATTTAAAATTT-AATT-TC
50155611 AATTAATTTAATTTAAAATT
1 AATTAATTTAATTTAAAATT
50155631 AGGTGATTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
25 3 0.07
26 1 0.02
27 12 0.29
28 7 0.17
29 18 0.44
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTAATTTAATTTAAAATTTAATTTC
Found at i:50156626 original size:15 final size:16
Alignment explanation
Indices: 50156606--50156638 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
50156596 ATATATTTTT
50156606 TTATTTT-ATTTTTAA
1 TTATTTTAATTTTTAA
50156621 TTATTTTAAATTTTTAA
1 TTATTTT-AATTTTTAA
50156638 T
1 T
50156639 ATAACCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
17 9 0.56
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTTTAATTTTTAA
Found at i:50156711 original size:21 final size:22
Alignment explanation
Indices: 50156685--50156743 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
50156675 GTTTTAAGAA
*
50156685 TTGTTTTAGTA-TTATTTTTAT
1 TTGTTTTAATATTTATTTTTAT
*
50156706 TTGTTTTAATATTTGTTTTTAT
1 TTGTTTTAATATTTATTTTTAT
* *
50156728 GT-TTTTAA-ATATATTT
1 TTGTTTTAATATTTATTT
50156744 GATTTATTAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 6 0.19
21 16 0.50
22 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (22 bp):
TTGTTTTAATATTTATTTTTAT
Found at i:50156758 original size:26 final size:24
Alignment explanation
Indices: 50156714--50156762 Score: 71
Period size: 26 Copynumber: 2.0 Consensus size: 24
50156704 ATTTGTTTTA
*
50156714 ATATTTGTTTTTATGTTTTTAAAT
1 ATATTTGTTTTTATATTTTTAAAT
50156738 ATATTTGATTTATTATATTTTTAAA
1 ATATTTG-TTT-TTATATTTTTAAA
50156763 CTTTTTTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.32
25 3 0.14
26 12 0.55
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
ATATTTGTTTTTATATTTTTAAAT
Found at i:50157025 original size:41 final size:41
Alignment explanation
Indices: 50156968--50157054 Score: 167
Period size: 41 Copynumber: 2.1 Consensus size: 41
50156958 ATCACCTCTA
50156968 TATATGACCCTAGCTTAATATAATATAAAAAATCATTCTTG
1 TATATGACCCTAGCTTAATATAATATAAAAAATCATTCTTG
50157009 TATATGACCCTAGCTTAATATAATATAAAAAATCATTCTTG
1 TATATGACCCTAGCTTAATATAATATAAAAAATCATTCTTG
50157050 T-TATG
1 TATATG
50157055 TATGAAAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 4 0.09
41 42 0.91
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (41 bp):
TATATGACCCTAGCTTAATATAATATAAAAAATCATTCTTG
Found at i:50165302 original size:13 final size:13
Alignment explanation
Indices: 50165286--50165318 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
50165276 TTTAATTAAA
*
50165286 TTAGTTAATTAGT
1 TTAGATAATTAGT
50165299 TTAGATAATTAGT
1 TTAGATAATTAGT
50165312 TTA-ATAA
1 TTAGATAA
50165319 ACAAACCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (13 bp):
TTAGATAATTAGT
Found at i:50170841 original size:6 final size:6
Alignment explanation
Indices: 50170823--50170861 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
50170813 TCGTTCTATC
* *
50170823 TTTTTA TTCTTA TTTTTA TTTTTA TTTTTA TTTTCA TTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTT
50170862 CAATTTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.15, C:0.05, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:50174610 original size:26 final size:26
Alignment explanation
Indices: 50174574--50174651 Score: 86
Period size: 26 Copynumber: 2.9 Consensus size: 26
50174564 TTTGCAAAAC
*
50174574 TTAAAATCCTAATTATCTTATCTAAA
1 TTAAAACCCTAATTATCTTATCTAAA
* *
50174600 TTAAAACCCTAATTATCCTAAT-TTAA
1 TTAAAACCCTAATTAT-CTTATCTAAA
*
50174626 TTTAAACTCCTAATTATCTTAATCTA
1 TTAAAAC-CCTAATTATCTT-ATCTA
50174652 CACAAAATCT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
26 26 0.62
27 15 0.36
28 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (26 bp):
TTAAAACCCTAATTATCTTATCTAAA
Found at i:50174638 original size:27 final size:28
Alignment explanation
Indices: 50174574--50174651 Score: 90
Period size: 27 Copynumber: 2.9 Consensus size: 28
50174564 TTTGCAAAAC
* *
50174574 TTAAAATCCTAATTAT-CTTATCTAAAT
1 TTAAACTCCTAATTATCCTAATCTAAAT
* *
50174601 TAAAAC-CCTAATTATCCTAAT-TTAAT
1 TTAAACTCCTAATTATCCTAATCTAAAT
*
50174627 TTAAACTCCTAATTATCTTAATCTA
1 TTAAACTCCTAATTATCCTAATCTA
50174652 CACAAAATCT
Statistics
Matches: 41, Mismatches: 7, Indels: 5
0.77 0.13 0.09
Matches are distributed among these distances:
26 18 0.44
27 22 0.54
28 1 0.02
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAACTCCTAATTATCCTAATCTAAAT
Found at i:50178847 original size:38 final size:38
Alignment explanation
Indices: 50178779--50178881 Score: 125
Period size: 38 Copynumber: 2.7 Consensus size: 38
50178769 GCTTTATAAG
* * *
50178779 TAGCAGGCTTCGTGCTGGTGCTATTTAGGCTCAATGCC
1 TAGCAGGCTTCGTGCCGGTGTTATTCAGGCTCAATGCC
* * * *
50178817 TAGCAGGCTTCATACCGGTGTTATTCAGGCTTAGTGCC
1 TAGCAGGCTTCGTGCCGGTGTTATTCAGGCTCAATGCC
* *
50178855 TAGTAGGCTTTGTGCCGGTGTTATTCA
1 TAGCAGGCTTCGTGCCGGTGTTATTCA
50178882 AGCTTAGTGC
Statistics
Matches: 54, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 54 1.00
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (38 bp):
TAGCAGGCTTCGTGCCGGTGTTATTCAGGCTCAATGCC
Found at i:50178887 original size:38 final size:38
Alignment explanation
Indices: 50178813--50178891 Score: 113
Period size: 38 Copynumber: 2.1 Consensus size: 38
50178803 TTAGGCTCAA
*
50178813 TGCCTAGCAGGCTTCATACCGGTGTTATTCAGGCTTAG
1 TGCCTAGCAGGCTTCATACCGGTGTTATTCAAGCTTAG
* ** *
50178851 TGCCTAGTAGGCTTTGTGCCGGTGTTATTCAAGCTTAG
1 TGCCTAGCAGGCTTCATACCGGTGTTATTCAAGCTTAG
50178889 TGC
1 TGC
50178892 TGGTGTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.16, C:0.22, G:0.28, T:0.34
Consensus pattern (38 bp):
TGCCTAGCAGGCTTCATACCGGTGTTATTCAAGCTTAG
Found at i:50178904 original size:60 final size:60
Alignment explanation
Indices: 50178831--50179016 Score: 230
Period size: 60 Copynumber: 3.0 Consensus size: 60
50178821 AGGCTTCATA
*
50178831 CCGGTGTTATTCAGGCTTAGTGCCTAGTAGGCTTTGTGCCGGTGTTATTCAAGCTTAGTG
1 CCGGTGTTATTCAGGCTTAGTGCATAGTAGGCTTTGTGCCGGTGTTATTCAAGCTTAGTG
* * * * *
50178891 CTGGTGTTATTCAGGCTTAGTGCATAGCAAG-TTTCATGCCGATGTTATTCAAGCTTAGTG
1 CCGGTGTTATTCAGGCTTAGTGCATAGTAGGCTTT-GTGCCGGTGTTATTCAAGCTTAGTG
* * * *
50178951 CCGATGAGTTATTCAGGCTTAGTGCTTAGTAGGCTTCGTGCCGGTGTGATATTCAGGCTTAGTG
1 CCG--GTGTTATTCAGGCTTAGTGCATAGTAGGCTTTGTGCCGGTGT--TATTCAAGCTTAGTG
50179015 CC
1 CC
50179017 TAGTAGGCTT
Statistics
Matches: 105, Mismatches: 15, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
59 3 0.03
60 52 0.50
62 32 0.30
63 2 0.02
64 16 0.15
ACGTcount: A:0.18, C:0.18, G:0.28, T:0.35
Consensus pattern (60 bp):
CCGGTGTTATTCAGGCTTAGTGCATAGTAGGCTTTGTGCCGGTGTTATTCAAGCTTAGTG
Found at i:50178943 original size:22 final size:23
Alignment explanation
Indices: 50178927--50178975 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
50178917 GCAAGTTTCA
50178927 TGCCGAT-GTTATTCAAGCTTAG
1 TGCCGATAGTTATTCAAGCTTAG
*
50178949 TGCCGATGAGTTATTCAGGCTTAG
1 TGCCGAT-AGTTATTCAAGCTTAG
50178973 TGC
1 TGC
50178976 TTAGTAGGCT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 7 0.29
24 17 0.71
ACGTcount: A:0.20, C:0.18, G:0.27, T:0.35
Consensus pattern (23 bp):
TGCCGATAGTTATTCAAGCTTAG
Found at i:50178965 original size:24 final size:22
Alignment explanation
Indices: 50178861--50178975 Score: 82
Period size: 22 Copynumber: 5.4 Consensus size: 22
50178851 TGCCTAGTAG
* *
50178861 GCTTTGTGCCGGTGTTATTCAA
1 GCTTAGTGCCGATGTTATTCAA
* * *
50178883 GCTTAGTGCTGGTGTTATTCAG
1 GCTTAGTGCCGATGTTATTCAA
*
50178905 GCTTAGTG-C-A---TA-GCAA
1 GCTTAGTGCCGATGTTATTCAA
*
50178921 GTTTCA-TGCCGATGTTATTCAA
1 GCTT-AGTGCCGATGTTATTCAA
*
50178943 GCTTAGTGCCGATGAGTTATTCAG
1 GCTTAGTGCCGAT--GTTATTCAA
50178967 GCTTAGTGC
1 GCTTAGTGC
50178976 TTAGTAGGCT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
16 7 0.10
17 4 0.06
18 1 0.01
21 3 0.04
22 40 0.56
24 17 0.24
ACGTcount: A:0.19, C:0.17, G:0.27, T:0.37
Consensus pattern (22 bp):
GCTTAGTGCCGATGTTATTCAA
Found at i:50179037 original size:40 final size:40
Alignment explanation
Indices: 50178960--50179037 Score: 120
Period size: 40 Copynumber: 1.9 Consensus size: 40
50178950 GCCGATGAGT
* *
50178960 TATTCAGGCTTAGTGCTTAGTAGGCTTCGTGCCGGTGTGA
1 TATTCAGGCTTAGTGCCTAGTAGGCTTCGAGCCGGTGTGA
* *
50179000 TATTCAGGCTTAGTGCCTAGTAGGCTTTGAGCTGGTGT
1 TATTCAGGCTTAGTGCCTAGTAGGCTTCGAGCCGGTGT
50179038 ATCAAATGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.15, C:0.17, G:0.32, T:0.36
Consensus pattern (40 bp):
TATTCAGGCTTAGTGCCTAGTAGGCTTCGAGCCGGTGTGA
Found at i:50182320 original size:24 final size:24
Alignment explanation
Indices: 50182292--50182344 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
50182282 TTTCTAGAAG
* *
50182292 ATTTAGTATTTATTAGTATAAAAT
1 ATTTAGCATTTATTAGCATAAAAT
*
50182316 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAGCATAAAAT
50182340 ATTTA
1 ATTTA
50182345 ATGTTGATTA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.49
Consensus pattern (24 bp):
ATTTAGCATTTATTAGCATAAAAT
Found at i:50186032 original size:24 final size:24
Alignment explanation
Indices: 50185975--50186026 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
50185965 TTTCTAGTAG
* * * *
50185975 ATTTAGTATTTATTAGTATATTAT
1 ATTTAGCATTTACTAGCATAATAT
50185999 ATTTAGCATTTACTAGCATAATAT
1 ATTTAGCATTTACTAGCATAATAT
50186023 ATTT
1 ATTT
50186027 GACATTGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTACTAGCATAATAT
Found at i:50188463 original size:42 final size:42
Alignment explanation
Indices: 50188400--50188514 Score: 133
Period size: 42 Copynumber: 2.8 Consensus size: 42
50188390 TCTGTTGACT
* * * * * *
50188400 AATATAA-AAATATAGTGAAACATCACATCTACTTTATCACT
1 AATATAACAAACATAATAAAACATCACGTCTAATTTATCACA
* * *
50188441 CATATAACAGACATAATAAAACATCACGTCTAATTTATGACA
1 AATATAACAAACATAATAAAACATCACGTCTAATTTATCACA
*
50188483 AATATAACAAACATAATGAAACATCACGTCTA
1 AATATAACAAACATAATAAAACATCACGTCTA
50188515 GTCACTTTCA
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
41 6 0.10
42 55 0.90
ACGTcount: A:0.49, C:0.18, G:0.06, T:0.27
Consensus pattern (42 bp):
AATATAACAAACATAATAAAACATCACGTCTAATTTATCACA
Found at i:50194847 original size:23 final size:23
Alignment explanation
Indices: 50194821--50194870 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
50194811 TTTAAAGGTT
50194821 AATATCAATAAAA-TAAATAAATA
1 AATA-CAATAAAAGTAAATAAATA
**
50194844 AATACCTTAAAAGTAAATAAATA
1 AATACAATAAAAGTAAATAAATA
50194867 AATA
1 AATA
50194871 AAATCCACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 6 0.25
23 18 0.75
ACGTcount: A:0.66, C:0.06, G:0.02, T:0.26
Consensus pattern (23 bp):
AATACAATAAAAGTAAATAAATA
Found at i:50196799 original size:29 final size:29
Alignment explanation
Indices: 50196760--50196815 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
50196750 ATTAATTATT
*
50196760 TTAATCTTATTACTACTATCATTATATCA
1 TTAATATTATTACTACTATCATTATATCA
* **
50196789 TTAATATTATTATTGTTATCATTATAT
1 TTAATATTATTACTACTATCATTATAT
50196816 TTCCACTCAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.34, C:0.11, G:0.02, T:0.54
Consensus pattern (29 bp):
TTAATATTATTACTACTATCATTATATCA
Found at i:50197037 original size:8 final size:10
Alignment explanation
Indices: 50197014--50197040 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
50197004 ATACTCATAT
50197014 ATATATTGAA
1 ATATATTGAA
50197024 ATATATTGAA
1 ATATATTGAA
50197034 ATATATT
1 ATATATT
50197041 TTTTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.44
Consensus pattern (10 bp):
ATATATTGAA
Found at i:50197052 original size:13 final size:13
Alignment explanation
Indices: 50197034--50197059 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50197024 ATATATTGAA
50197034 ATATATTTTTTAT
1 ATATATTTTTTAT
50197047 ATATATTTTTTAT
1 ATATATTTTTTAT
50197060 CTTATTTTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
ATATATTTTTTAT
Found at i:50197909 original size:109 final size:107
Alignment explanation
Indices: 50197718--50198052 Score: 546
Period size: 109 Copynumber: 3.1 Consensus size: 107
50197708 TACGCATATT
** *
50197718 AATATCCTTAAAAATATTTTAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAA-ATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
50197783 CTAATGTGCTGGGTTTCGATTTTTCTCGTTCGACCAAATAGCCA
65 CTAATGTGCTGGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCA
*
50197827 AATATCCTTTTACAATTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
1 AATATCCTTTTAAAATTTC-AAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCC
* *
50197892 CTAATGTGCTGGGTTTCGATTTTCTTGTTCGACCAAATAGCCG
65 CTAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
* * *
50197935 AATATCCTTTTAAAATTTCGAAATAAGGCAATCTTTTGCGTTTGGAAATTCGAGGAAACGTGCCC
1 AATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
*
50198000 TAATGTGCTGGGTTTCGA-TTTCTCGTTGGACCAAATAGCCA
66 TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
50198041 AATATCCTTTTA
1 AATATCCTTTTA
50198053 TATCTTAATC
Statistics
Matches: 212, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
106 32 0.15
107 61 0.29
108 44 0.21
109 75 0.35
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (107 bp):
AATATCCTTTTAAAATTTCAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCC
TAATGTGCTGGGTTTCGATTTTCTCGTTCGACCAAATAGCCA
Found at i:50200429 original size:107 final size:108
Alignment explanation
Indices: 50200239--50200497 Score: 389
Period size: 107 Copynumber: 2.4 Consensus size: 108
50200229 AGCCTCACAG
50200239 GGGTTTCGATTTTTCTCGTTCGACCAAATAGCCAAATATCCTTTT-AAATTTCAAAAATAAGGCA
1 GGGTTTCGA-TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAAATAAGGCA
*
50200303 ATGTTCTGCGTTTGAAAATTCGAGAAAACGAGTCCTAATATGTT
65 ATGTTCTGCGTTTGAAAATTCGAGAAAACGAGTCCTAATATGCT
* * * *
50200347 GGGTTTCGATTTTCTTGTTTGACCAAATAGTCGAATATCCTTTTAAAATTTC-AAAATAAGGCAA
1 GGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAAATAAGGCAA
* * * * *
50200411 TGTTTTGCGTTTGGAAATTCGAGGAAACGTGTCCTAATGTGCT
66 TGTTCTGCGTTTGAAAATTCGAGAAAACGAGTCCTAATATGCT
*
50200454 GGGTTTCGA-TTTCTCGTTGGACCAAATAGCCAAATATCCTTTTA
1 GGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTA
50200498 TATCTTAATT
Statistics
Matches: 136, Mismatches: 14, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
106 31 0.23
107 89 0.65
108 16 0.12
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (108 bp):
GGGTTTCGATTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAAATAAGGCAA
TGTTCTGCGTTTGAAAATTCGAGAAAACGAGTCCTAATATGCT
Found at i:50203373 original size:7 final size:7
Alignment explanation
Indices: 50203361--50203393 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
50203351 TATAAAAATA
50203361 ATTTTAT
1 ATTTTAT
50203368 ATTTTAT
1 ATTTTAT
50203375 ATTTTAT
1 ATTTTAT
50203382 ATTTTAT
1 ATTTTAT
50203389 ATTTT
1 ATTTT
50203394 CTCATAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTAT
Found at i:50204044 original size:17 final size:16
Alignment explanation
Indices: 50204022--50204059 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
50204012 TTTTAAGAAA
*
50204022 ATTTAAATATTTTATAT
1 ATTTAAATA-GTTATAT
50204039 ATTTAAATAGTTATAT
1 ATTTAAATAGTTATAT
50204055 -TTTAA
1 ATTTAA
50204060 TTTTTTGAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 6 0.30
17 9 0.45
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTTAAATAGTTATAT
Found at i:50204105 original size:21 final size:20
Alignment explanation
Indices: 50204081--50204137 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 20
50204071 CTTATAATTA
50204081 ATTTTAATTTAAAAATTAAAT
1 ATTTTAA-TTAAAAATTAAAT
* *
50204102 ATTTTGA-TAATATAATTTAAT
1 ATTTTAATTAA-A-AATTAAAT
50204123 ATTTTAAATTAAAAA
1 ATTTT-AATTAAAAA
50204138 CTATTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 8
0.73 0.08 0.20
Matches are distributed among these distances:
19 3 0.10
20 1 0.03
21 20 0.69
22 2 0.07
23 3 0.10
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (20 bp):
ATTTTAATTAAAAATTAAAT
Found at i:50210068 original size:16 final size:18
Alignment explanation
Indices: 50210045--50210093 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
50210035 ATCCTCAAGC
50210045 ACATATAATTAAATCT-A
1 ACATATAATTAAATCTAA
*
50210062 A-ATATAATTATAT-TAA
1 ACATATAATTAAATCTAA
*
50210078 ACACATAATTAAATCT
1 ACATATAATTAAATCT
50210094 TGATAAACTT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
15 1 0.04
16 13 0.50
17 11 0.42
18 1 0.04
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.37
Consensus pattern (18 bp):
ACATATAATTAAATCTAA
Found at i:50210106 original size:33 final size:34
Alignment explanation
Indices: 50210049--50210112 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
50210039 TCAAGCACAT
50210049 ATAATTAAATCTAAATATAATTATAT-TAAACAC
1 ATAATTAAATCTAAATATAATTATATGTAAACAC
**
50210082 ATAATTAAATCTTGATA-AACTTATATGTAAA
1 ATAATTAAATCTAAATATAA-TTATATGTAAA
50210113 TTTATGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 2 0.07
33 21 0.78
34 4 0.15
ACGTcount: A:0.52, C:0.08, G:0.03, T:0.38
Consensus pattern (34 bp):
ATAATTAAATCTAAATATAATTATATGTAAACAC
Found at i:50210532 original size:19 final size:19
Alignment explanation
Indices: 50210510--50210549 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
50210500 TTTAGATACA
50210510 TATATATTT-TTTTATAATT
1 TATA-ATTTCTTTTATAATT
*
50210529 TATAATTTCTTTTATATTT
1 TATAATTTCTTTTATAATT
50210548 TA
1 TA
50210550 AGAAATTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (19 bp):
TATAATTTCTTTTATAATT
Found at i:50212344 original size:67 final size:67
Alignment explanation
Indices: 50212251--50212651 Score: 570
Period size: 67 Copynumber: 6.0 Consensus size: 67
50212241 ATGCATTGAA
* *
50212251 TATGC-AATTTGAGTATTTAAATGTATGCATTTAATTAAATCAATTATATATATATGATTTGAGA
1 TATGCGAA-TTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGA
50212315 AAG
65 AAG
* * * * * ** *
50212318 TATGTGAATTGAGTATTTAAAGGTATGTATTTAATTGAATTGATTATATGTGGATAATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
50212383 AG
66 AG
*
50212385 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATGTATATATGATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
50212450 AG
66 AG
* * * * * *
50212452 TATGCGAAGTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTGTATAATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
50212517 AG
66 AG
*
50212519 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATGTGATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
*
50212584 GG
66 AG
* * * * *
50212586 TATGCGAATTGAGTATTTAAATGTATTTATTTAATTGAATAGATTATATATATGTTATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
50212651 A
66 A
50212652 TTGAATTATT
Statistics
Matches: 294, Mismatches: 39, Indels: 2
0.88 0.12 0.01
Matches are distributed among these distances:
67 292 0.99
68 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.42
Consensus pattern (67 bp):
TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
AG
Found at i:50212389 original size:134 final size:134
Alignment explanation
Indices: 50212251--50212634 Score: 653
Period size: 134 Copynumber: 2.9 Consensus size: 134
50212241 ATGCATTGAA
* *
50212251 TATGC-AATTTGAGTATTTAAATGTATGCATTTAATTAAATCAATTATATATATATGATTTGAGA
1 TATGCGAA-TTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGA
* *
50212315 AAGTATGTGAATTGAGTATTTAAAGGTATGTATTTAATTGAATTGATTATATGTGGATAATTTGA
65 AAGTATGCGAATTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTGGATAATTTGA
50212380 GAAAG
130 GAAAG
*
50212385 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATGTATATATGATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
* *
50212450 AGTATGCGAAGTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTGTATAATTTGAG
66 AGTATGCGAATTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTGGATAATTTGAG
50212515 AAAG
131 AAAG
*
50212519 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATGTGATTTGAGAA
1 TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
* * *
50212584 GGTATGCGAATTGAGTATTTAAATGTATTTATTTAATTGAATAGATTATAT
66 AGTATGCGAATTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATAT
50212635 ATATGTTATT
Statistics
Matches: 236, Mismatches: 13, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
134 234 0.99
135 2 0.01
ACGTcount: A:0.37, C:0.02, G:0.18, T:0.42
Consensus pattern (134 bp):
TATGCGAATTGAGTATTTAAATGTATGTATTTAATTAAATCGATTATATATATATGATTTGAGAA
AGTATGCGAATTGAGTATTTAAATGTATGTATTTAATTGAATTGATTATATGTGGATAATTTGAG
AAAG
Found at i:50212906 original size:22 final size:22
Alignment explanation
Indices: 50212858--50212936 Score: 63
Period size: 23 Copynumber: 3.5 Consensus size: 22
50212848 AGTTCATTAG
* *
50212858 AGCTTACTGTTACAGCTCGTATG
1 AGCTTACTGTT-CAGCTCATATA
50212881 AGCTTACTGTTCAGCTCATCA-A
1 AGCTTACTGTTCAGCTCAT-ATA
* *
50212903 AGCTTACCGTTTCAGCCCA-ATA
1 AGCTTACTG-TTCAGCTCATATA
*
50212925 GAGCCTACTGTT
1 -AGCTTACTGTT
50212937 TATCAGCTCA
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
21 1 0.02
22 18 0.39
23 27 0.59
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (22 bp):
AGCTTACTGTTCAGCTCATATA
Found at i:50213131 original size:20 final size:19
Alignment explanation
Indices: 50213106--50213170 Score: 67
Period size: 20 Copynumber: 3.3 Consensus size: 19
50213096 AAGATATGTG
50213106 TTTATATGGATGAATTACTA
1 TTTATATGGATGAATTA-TA
* * *
50213126 TTTATACGGATGAACTATG
1 TTTATATGGATGAATTATA
* *
50213145 GTTATATGAATGAATTATA
1 TTTATATGGATGAATTATA
50213164 GTTTATA
1 -TTTATA
50213171 CGAATATAAA
Statistics
Matches: 35, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 15 0.43
20 20 0.57
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (19 bp):
TTTATATGGATGAATTATA
Found at i:50214898 original size:27 final size:27
Alignment explanation
Indices: 50214849--50214907 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
50214839 CTTTTCTTTT
* *
50214849 AGAGTTTGCCGTACATATTATTCCTT-C
1 AGAGTTTGCCATACATATCATT-CTTCC
**
50214876 AGAGTTTGCCATATTTATCATTCTTCC
1 AGAGTTTGCCATACATATCATTCTTCC
50214903 AGAGT
1 AGAGT
50214908 ACCTATACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 3 0.11
27 24 0.89
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (27 bp):
AGAGTTTGCCATACATATCATTCTTCC
Found at i:50215133 original size:58 final size:58
Alignment explanation
Indices: 50215049--50215212 Score: 177
Period size: 58 Copynumber: 2.8 Consensus size: 58
50215039 TCAAAGATCG
* * *
50215049 CCACAAAGG-TTTCCATATCTAGAGATTTCCATAAAGGCGTCCTTTTCGTTTAGTACTCA
1 CCACAAAGGCTTTCC-T-TTTAGAGATTACCATAAAGGCATCCTTTTCGTTTAGTACTCA
* * * * **
50215108 CGAGAAAGGCTTTCCTTTTAGAGATTACCACAAGGGCATCCTTTTTATTTAGTACTCA
1 CCACAAAGGCTTTCCTTTTAGAGATTACCATAAAGGCATCCTTTTCGTTTAGTACTCA
* * * * *
50215166 CCACAAAGGCTTTCCTTTCAAAGATTGCCATCAAGACATCCTTTTCG
1 CCACAAAGGCTTTCCTTTTAGAGATTACCATAAAGGCATCCTTTTCG
50215213 GGTGTTTTAG
Statistics
Matches: 84, Mismatches: 20, Indels: 3
0.79 0.19 0.03
Matches are distributed among these distances:
58 71 0.85
59 8 0.10
60 5 0.06
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.33
Consensus pattern (58 bp):
CCACAAAGGCTTTCCTTTTAGAGATTACCATAAAGGCATCCTTTTCGTTTAGTACTCA
Found at i:50223409 original size:21 final size:19
Alignment explanation
Indices: 50223375--50223428 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 19
50223365 TTTTTGAAAA
50223375 AAAAAGTTATAAAAAAT-TTT
1 AAAAA-TTA-AAAAAATCTTT
50223395 AAAAATATTAAAAAAATCTTT
1 -AAAA-ATTAAAAAAATCTTT
50223416 AAAAATTAAAAAA
1 AAAAATTAAAAAA
50223429 TATATATATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
19 9 0.29
20 11 0.35
21 10 0.32
22 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATTAAAAAAATCTTT
Found at i:50226418 original size:22 final size:22
Alignment explanation
Indices: 50226390--50226434 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
50226380 TTTTTATTTC
50226390 ATTCCTTCG-GTATATCTCTATA
1 ATTCCTT-GTGTATATCTCTATA
50226412 ATTCCTTGTGTATATCTCTATA
1 ATTCCTTGTGTATATCTCTATA
50226434 A
1 A
50226435 GCTATCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.24, C:0.20, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTCCTTGTGTATATCTCTATA
Found at i:50226590 original size:17 final size:18
Alignment explanation
Indices: 50226565--50226598 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
50226555 ACTTGACATC
*
50226565 ATAATAAAA-TATTATTT
1 ATAACAAAATTATTATTT
50226582 ATAACAAAATTATTATT
1 ATAACAAAATTATTATT
50226599 ATTAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
ATAACAAAATTATTATTT
Found at i:50228957 original size:21 final size:23
Alignment explanation
Indices: 50228931--50228988 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
50228921 AAAATTTATC
50228931 TACAAATCATAT-CTCTAAGA-T
1 TACAAATCATATACTCTAAGATT
* *
50228952 TACAAAATCATATATTCTAATATT
1 TAC-AAATCATATACTCTAAGATT
*
50228976 TACACATCATATA
1 TACAAATCATATA
50228989 TAAGATTCCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 3 0.10
22 9 0.29
23 15 0.48
24 4 0.13
ACGTcount: A:0.45, C:0.17, G:0.02, T:0.36
Consensus pattern (23 bp):
TACAAATCATATACTCTAAGATT
Found at i:50230443 original size:15 final size:15
Alignment explanation
Indices: 50230423--50230454 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
50230413 TGAGGAAGGA
50230423 AAGAAAAAATTTTAG
1 AAGAAAAAATTTTAG
50230438 AAGAAAAAATTTTAG
1 AAGAAAAAATTTTAG
50230453 AA
1 AA
50230455 TTTGTTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (15 bp):
AAGAAAAAATTTTAG
Found at i:50230955 original size:41 final size:41
Alignment explanation
Indices: 50230876--50230958 Score: 130
Period size: 41 Copynumber: 2.0 Consensus size: 41
50230866 CATGGTGGAC
** *
50230876 TAAGCTTTAAACCAACTATTTCATTTGATTTTTTAAACACA
1 TAAGCTTTAAACCAACTATTTCATTTGATTAATCAAACACA
*
50230917 TAAGCTTTGAACCAACTATTTCATTTGATTAATCAAACACA
1 TAAGCTTTAAACCAACTATTTCATTTGATTAATCAAACACA
50230958 T
1 T
50230959 CTCACACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.37, C:0.18, G:0.06, T:0.39
Consensus pattern (41 bp):
TAAGCTTTAAACCAACTATTTCATTTGATTAATCAAACACA
Found at i:50233142 original size:22 final size:22
Alignment explanation
Indices: 50233097--50233160 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
50233087 GTCCCTGGGT
* * *
50233097 CACATGGGT-TGTACCTTCTTC
1 CACAAGGGTGTGTGCCTCCTTC
50233118 CACAAGGGTGTGTGCCTCCTTC
1 CACAAGGGTGTGTGCCTCCTTC
* *
50233140 CACACGGGCGTGTGCC-CCTTC
1 CACAAGGGTGTGTGCCTCCTTC
50233161 ATATGGGCGT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 13 0.35
22 24 0.65
ACGTcount: A:0.12, C:0.34, G:0.25, T:0.28
Consensus pattern (22 bp):
CACAAGGGTGTGTGCCTCCTTC
Found at i:50244224 original size:20 final size:20
Alignment explanation
Indices: 50244201--50244259 Score: 73
Period size: 21 Copynumber: 2.9 Consensus size: 20
50244191 AATTTTCTTG
*
50244201 TAAAACTCAAGTTTTTCCTA
1 TAAAACCCAAGTTTTTCCTA
* *
50244221 TAAAACCCAAGTAATTCCCTA
1 TAAAACCCAAGT-TTTTCCTA
50244242 TAAAATCCCAAGTTTTTC
1 TAAAA-CCCAAGTTTTTC
50244260 TTTCTCTTTT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 11 0.34
21 14 0.44
22 7 0.22
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (20 bp):
TAAAACCCAAGTTTTTCCTA
Found at i:50246603 original size:56 final size:56
Alignment explanation
Indices: 50246536--50246701 Score: 266
Period size: 56 Copynumber: 3.0 Consensus size: 56
50246526 AATTCAATCT
*
50246536 TTAATTTATGAAAAGAGTTGGTTGCATCAACCATTACTAACCCATGAGAA-TCTTTA
1 TTAATTTATGAAAAGAGTTTGTTGCATCAACCATTACTAACCCATGAGAATTC-TTA
* *
50246592 TTAATTTATGAAAAGAGTTTGTTACATCAACCATTACTAACCCATGAGGATTCTTA
1 TTAATTTATGAAAAGAGTTTGTTGCATCAACCATTACTAACCCATGAGAATTCTTA
*
50246648 TTAATTTATGAAAAGAGTTTGCTGCATCAACCATTACTAACCCAT--GAATTCTTA
1 TTAATTTATGAAAAGAGTTTGTTGCATCAACCATTACTAACCCATGAGAATTCTTA
50246702 AAGGATAATC
Statistics
Matches: 103, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
54 8 0.08
56 93 0.90
57 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.13, T:0.35
Consensus pattern (56 bp):
TTAATTTATGAAAAGAGTTTGTTGCATCAACCATTACTAACCCATGAGAATTCTTA
Found at i:50253620 original size:953 final size:958
Alignment explanation
Indices: 50251769--50254079 Score: 3765
Period size: 953 Copynumber: 2.4 Consensus size: 958
50251759 CTTGGATACG
**
50251769 TGTTGGGGTTTTGACAACAAAAAAAGAAGAGAACAAGACAGAGAACAAAGGAGCAAGAAGCTTGA
1 TGTT-GGGTTTTGACAACAGCAAAAGAAGAGAACAAGACAGAGAACAAAGGAGCAAGAAGCTTGA
*
50251834 CATAATTTACTTGCTCACAAATGTGCATCAAGGAAGCAATCTGCTTTACACAACTAATATGCTTT
65 CATAATTTACTTGCTCACAAATGTGCATCAAGGAAGCAATCTGCTTTACACAACTGATATGCTTT
*
50251899 CTCATTCAATATGGAAACAATACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCA
130 CTCATTCAATATGAAAACAATACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCA
50251964 CTAATCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAA
195 CTAATCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAA
* *
50252029 TCATCACTTAAACCCATCAAAACATCAACAATTAAGTTCATTTTCAACCAAACTAAATTACATTG
260 TCATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAACTAAATTACATTG
* * * *
50252094 CAACTAAAATAGAACATATGTTGCTACAACATGCACAATTGCTGTAGCATGCATACAAGCTATAT
325 CAACTAAAACAAAACATATGTTGCTGCAACATGCACAATTGTTGTAGCATGCATACAAGCTATAT
** * *
50252159 GCACTCAACAAAATCATCATAACAGTATGCACTTTAACCAAAAATAACAGTAACATGGTTGGTCA
390 GCACTCAACAAAATCATCATAACAACATGCACTTTAACCAAAAATAACAGCAACATGGTTGGCCA
* * *
50252224 TTTTCAACAGTCCTCCTTGGCCTCCATGTTGAAGATACCAATCATCCATCAAGTTTTTTTTAGCT
455 TTTTCAACACTCCTCCTTGGCCTCCATGTTGAAAATACCAATCATCCATCAAGTATTTTTTAGCT
* *
50252289 TGGCAGTCCCTAGATGCTTTATTTCAAGCTGACTCTGCTCAAGCAATTCATTTTCAACCTTGTCT
520 TGGCAATCCCTAGATGCTTTATTTCAAGCTGACTCTACTCAAGCAATTCATTTTCAACCTTGTCT
*
50252354 TCATTCTCAACCAAATATGACTTACACACTTGATTATCCCATTCTTTTGTGCCAAAGATTTGTTC
585 TCATTCTCAACCAAATATGACTTACACACTTGATTATCCCATTCTTTTGTGCCAAAGAGTTGTTC
* *
50252419 ATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTGGTTGGCAACTTGCCTTCAAACACATCTTGCC
650 ATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTAGTTGGCAACTTGCCTTCAAACACATCTTACC
* *
50252484 TTGTTTCTTTGTTCATTACAGTCATGTTTCTTTTTGCACATACTCCCTCCCGCTGTGGAGTGTCT
715 TTGTTTCTTTGCTCATTACAGTCATGTTTCTTCTTGCACATACTCCCTCCCGCTGTGGAGTGTCT
*
50252549 TCATGCACATACCCCATCAACTCCTCCTTCAGCTTATCTCAAGCTTGTTTAGGAGTCTCACAGGG
780 TCATGCACATACCCCATCAACTCCTCCTTCAGCTTATCCCAAGCTTGTTTAGGAGTCTCACAGGG
* * *
50252614 GTGAGCTGTTGCTCTCTCTTTTACAAGCAGCCCTCAAAGATGACAAGCTTTAACAGCTTCTTGTC
845 GTGAGCTGTTGCTCTATCTTTTACAAACAACCCTCAAAGATGACAAGCTTTAACAGCTTCTTGTC
50252679 TTTCTTAACAAG-AA-A-AAG-A-AAAGACTTGGGCTCATGATACAATT
910 TTTCTTAACAAGCAACAGAAGAATAAAGACTTGGGCTCATGATACAATT
*
50252723 TGTTGGGTTTTGACAACAGCAAAAGAAGAGAACAAGACAGAGAACAAAGGAGTAAGAAGCTTGAC
1 TGTTGGGTTTTGACAACAGCAAAAGAAGAGAACAAGACAGAGAACAAAGGAGCAAGAAGCTTGAC
*
50252788 ATAATTTACTTGCTCACAAATGTGCATCAA-GAAACTAATCTGCTTTACACAACTGATATGCTTT
66 ATAATTTACTTGCTCACAAATGTGCATCAAGGAAGC-AATCTGCTTTACACAACTGATATGCTTT
* **
50252852 CTCATTCAATATGAAAATAGCACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCA
130 CTCATTCAATATGAAAACAATACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCA
*
50252917 CTAGTCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAA
195 CTAATCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAA
*
50252982 TCATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAAATAAATTACATTG
260 TCATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAACTAAATTACATTG
* * * *
50253047 CAACTAAAACAAAACATATGTTACTGCAACATGCACAATTATTGTAGCATGCATACAAGTTGTAT
325 CAACTAAAACAAAACATATGTTGCTGCAACATGCACAATTGTTGTAGCATGCATACAAGCTATAT
* * * *
50253112 GCACTCAACAAAATCATCATAACAACGTGCATTTTAA-CAAAATATAATAGCAGCATGGTTGGCC
390 GCACTCAACAAAATCATCATAACAACATGCACTTTAACCAAAA-ATAACAGCAACATGGTTGGCC
*
50253176 ATTTTCAACACTCCTCCTTGGCCTCCATGTTGAAAATACCAATCATTCATCAAGTATTTTTTAGC
454 ATTTTCAACACTCCTCCTTGGCCTCCATGTTGAAAATACCAATCATCCATCAAGTATTTTTTAGC
* *
50253241 TTGGCAATCCTTAGATGCTTTATTTCAAGTTGACTCTACTCAAGCAATTCATTTTCAACCTTGTC
519 TTGGCAATCCCTAGATGCTTTATTTCAAGCTGACTCTACTCAAGCAATTCATTTTCAACCTTGTC
*
50253306 TTTATTCTCAACCAAATATGACTTACACACTTGATTATCCCATTCTTTTGTGCCAAAGAGTTGTT
584 TTCATTCTCAACCAAATATGACTTACACACTTGATTATCCCATTCTTTTGTGCCAAAGAGTTGTT
50253371 CATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTAGTTGGCAACTTGCCTTCAAACACATCTTAC
649 CATCAAATGGAGTCTTCTCCTCCTTCACAGCCTTAGTTGGCAACTTGCCTTCAAACACATCTTAC
* * * *
50253436 CTTGTTTCTTTGCTCATTATAGTCCTGTTTCTTCTTGCACATACTCCCTCCTGTTGTGGAGTGTC
714 CTTGTTTCTTTGCTCATTACAGTCATGTTTCTTCTTGCACATACTCCCTCCCGCTGTGGAGTGTC
50253501 TTCATGCACATACCCCATCAACTCCTCCTTCAGCTTATCCCAAGCTTGTTTAGGAGTCTCACAGG
779 TTCATGCACATACCCCATCAACTCCTCCTTCAGCTTATCCCAAGCTTGTTTAGGAGTCTCACAGG
* * * *
50253566 GGTGAGTTGTTGCTCTATCTTTTACAAACAACCTTTAAAGTTGACAAGCTTTAACAGCTTCTTGT
844 GGTGAGCTGTTGCTCTATCTTTTACAAACAACCCTCAAAGATGACAAGCTTTAACAGCTTCTTGT
50253631 CTTTCTTAACAAGCAACAGAAGCAAAAAAACAAACCTTTAAAGACTTGGGCTCATGATACAATT
909 CTTTCTTAACAAGCAACAGAAG----------AA----TAAAGACTTGGGCTCATGATACAATT
* *
50253695 TGTTGGGTTTTGACGACAGCAAAAGAAGAGAACAAGACAAAGAACAAAGGAGCAAGAAGCTTGAC
1 TGTTGGGTTTTGACAACAGCAAAAGAAGAGAACAAGACAGAGAACAAAGGAGCAAGAAGCTTGAC
* * * *
50253760 ATAATTTAGTTGCTCACAAATGTACATTAAGGAAGCAATCTACTTTACACAACTGATATGCTTTC
66 ATAATTTACTTGCTCACAAATGTGCATCAAGGAAGCAATCTGCTTTACACAACTGATATGCTTTC
* *
50253825 TCATTCAGTATGAAAACAATACATTTATAATCAAAATACATCACCAAATATTCAAGTAATCCCAC
131 TCATTCAATATGAAAACAATACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCAC
* * * * * *
50253890 TAATTAGCATTAGGAATACTAAAACATTGCTTGTACACATGAATAAGCTGACTTATCAGCTCAAT
196 TAATCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAAT
* *
50253955 CATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAGCTAAATTAAATTGC
261 CATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAACTAAATTACATTGC
50254020 AACTAAAACAGAAA-ATATGTTGCTGCAACATGCACAATTGTTGTAGCATGCATACAAGCT
326 AACTAAAACA-AAACATATGTTGCTGCAACATGCACAATTGTTGTAGCATGCATACAAGCT
50254080 GAACAACAAC
Statistics
Matches: 1253, Mismatches: 81, Indels: 28
0.92 0.06 0.02
Matches are distributed among these distances:
952 9 0.01
953 851 0.68
954 6 0.00
955 1 0.00
956 3 0.00
967 1 0.00
972 375 0.30
973 7 0.01
ACGTcount: A:0.34, C:0.22, G:0.13, T:0.30
Consensus pattern (958 bp):
TGTTGGGTTTTGACAACAGCAAAAGAAGAGAACAAGACAGAGAACAAAGGAGCAAGAAGCTTGAC
ATAATTTACTTGCTCACAAATGTGCATCAAGGAAGCAATCTGCTTTACACAACTGATATGCTTTC
TCATTCAATATGAAAACAATACATTTATAATCAAAATACATCACCAAATATTCAACTAATCCCAC
TAATCAGCATTGGGACTATTAAAACATTGCTTGTACACAAGAATAAGCTGACTTATCAGTTCAAT
CATCACCTAAACCCATCAAAACATCAACAACTAAGTTCATTTTCAACCAAACTAAATTACATTGC
AACTAAAACAAAACATATGTTGCTGCAACATGCACAATTGTTGTAGCATGCATACAAGCTATATG
CACTCAACAAAATCATCATAACAACATGCACTTTAACCAAAAATAACAGCAACATGGTTGGCCAT
TTTCAACACTCCTCCTTGGCCTCCATGTTGAAAATACCAATCATCCATCAAGTATTTTTTAGCTT
GGCAATCCCTAGATGCTTTATTTCAAGCTGACTCTACTCAAGCAATTCATTTTCAACCTTGTCTT
CATTCTCAACCAAATATGACTTACACACTTGATTATCCCATTCTTTTGTGCCAAAGAGTTGTTCA
TCAAATGGAGTCTTCTCCTCCTTCACAGCCTTAGTTGGCAACTTGCCTTCAAACACATCTTACCT
TGTTTCTTTGCTCATTACAGTCATGTTTCTTCTTGCACATACTCCCTCCCGCTGTGGAGTGTCTT
CATGCACATACCCCATCAACTCCTCCTTCAGCTTATCCCAAGCTTGTTTAGGAGTCTCACAGGGG
TGAGCTGTTGCTCTATCTTTTACAAACAACCCTCAAAGATGACAAGCTTTAACAGCTTCTTGTCT
TTCTTAACAAGCAACAGAAGAATAAAGACTTGGGCTCATGATACAATT
Found at i:50254572 original size:21 final size:20
Alignment explanation
Indices: 50254546--50254590 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
50254536 GTAAGTTATG
*
50254546 AATATCAATTAAATCATTTCA
1 AATATCAA-TAAATCATTACA
*
50254567 AATATCTATAAATCATTACA
1 AATATCAATAAATCATTACA
50254587 AATA
1 AATA
50254591 AAAACCAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.51, C:0.13, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATCAATAAATCATTACA
Found at i:50263441 original size:24 final size:23
Alignment explanation
Indices: 50263413--50263465 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
50263403 TAATTAGCAC
*
50263413 ATATATATATTTGA-AATTATAAAA
1 ATATAT-TATTTAATAATTA-AAAA
50263437 ATATATTATTTAATTAATTAAAAA
1 ATATATTATTTAA-TAATTAAAAA
50263461 ATATA
1 ATATA
50263466 AAAAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 6 0.23
24 15 0.58
25 5 0.19
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (23 bp):
ATATATTATTTAATAATTAAAAA
Found at i:50268585 original size:18 final size:18
Alignment explanation
Indices: 50268558--50268650 Score: 125
Period size: 18 Copynumber: 5.2 Consensus size: 18
50268548 TACGATCGTT
50268558 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* * *
50268576 TACGGCACTATTCACATG
1 TACGGTACTATTCACGTA
50268594 TACGGTACTATTCACGT-
1 TACGGTACTATTCACGTA
*
50268611 TAATGGTACTATTCACGTA
1 T-ACGGTACTATTCACGTA
*
50268630 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
50268648 TAC
1 TAC
50268651 AGTAGTTGGG
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
17 1 0.02
18 63 0.97
19 1 0.02
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.33
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:50274676 original size:98 final size:98
Alignment explanation
Indices: 50274502--50274698 Score: 340
Period size: 98 Copynumber: 2.0 Consensus size: 98
50274492 GTACAATAAA
* *
50274502 ACTTTAAAAGAACATACACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGTACGATC
1 ACTTTAAAAGAACATACACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
50274567 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
* *
50274600 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATACACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
50274665 CCTTTAAAATCCCAAACTTGGAATATTTCCTTT
66 CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
50274698 A
1 A
50274699 TCATTTTAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (98 bp):
ACTTTAAAAGAACATACACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:50276464 original size:17 final size:17
Alignment explanation
Indices: 50276442--50276483 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
50276432 CCAAATCTAC
* * *
50276442 TTTGGGCTTCTGTTTGG
1 TTTGGGCCTCAGTTGGG
50276459 TTTGGGCCTCAGTTGGG
1 TTTGGGCCTCAGTTGGG
50276476 TTTGGGCC
1 TTTGGGCC
50276484 ACCTCGGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.17, G:0.38, T:0.43
Consensus pattern (17 bp):
TTTGGGCCTCAGTTGGG
Found at i:50282457 original size:7 final size:7
Alignment explanation
Indices: 50282447--50282511 Score: 53
Period size: 7 Copynumber: 8.9 Consensus size: 7
50282437 CCAAATAAGA
50282447 AATAAAT
1 AATAAAT
50282454 AAT-AA-
1 AATAAAT
50282459 AATAAAGT
1 AATAAA-T
50282467 AATAAAT
1 AATAAAT
*
50282474 AAAGTAAAGA
1 -AA-TAAA-T
*
50282484 AAAATAAT
1 AATA-AAT
50282492 AATAAAT
1 AATAAAT
50282499 AATAAAT
1 AATAAAT
50282506 AATAAA
1 AATAAA
50282512 AATTGGGTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 14
0.72 0.06 0.22
Matches are distributed among these distances:
5 3 0.06
6 4 0.09
7 20 0.43
8 12 0.26
9 8 0.17
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (7 bp):
AATAAAT
Found at i:50282508 original size:17 final size:17
Alignment explanation
Indices: 50282447--50282514 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
50282437 CCAAATAAGA
50282447 AATAAATAATAAAATAAAGT
1 AATAAATAAT--AATAAA-T
* *
50282467 AATAAATAA-AGTAAAG
1 AATAAATAATAATAAAT
50282483 AA-AAATAATAATAAAT
1 AATAAATAATAATAAAT
50282499 AATAAATAATAA-AAAT
1 AATAAATAATAATAAAT
50282515 TGGGTTGCCT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.14
16 13 0.31
17 14 0.33
20 9 0.21
ACGTcount: A:0.72, C:0.00, G:0.04, T:0.24
Consensus pattern (17 bp):
AATAAATAATAATAAAT
Found at i:50286830 original size:22 final size:22
Alignment explanation
Indices: 50286802--50286843 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
50286792 GTAACTTAGT
50286802 CATATTTGAACTAAGTAGGTAG
1 CATATTTGAACTAAGTAGGTAG
* *
50286824 CATATTTGAAGTAATTAGGT
1 CATATTTGAACTAAGTAGGT
50286844 GAAGCCTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.36, C:0.07, G:0.21, T:0.36
Consensus pattern (22 bp):
CATATTTGAACTAAGTAGGTAG
Found at i:50289065 original size:48 final size:48
Alignment explanation
Indices: 50289010--50289106 Score: 185
Period size: 48 Copynumber: 2.0 Consensus size: 48
50289000 TGTGAAGCTA
50289010 AAAGGTTGTGAAGAAGGACATAATTTGATTGAAAATTAGGTCAAGGTT
1 AAAGGTTGTGAAGAAGGACATAATTTGATTGAAAATTAGGTCAAGGTT
*
50289058 AAAGGTTGTGAAGGAGGACATAATTTGATTGAAAATTAGGTCAAGGTT
1 AAAGGTTGTGAAGAAGGACATAATTTGATTGAAAATTAGGTCAAGGTT
50289106 A
1 A
50289107 TAAATGAATT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.39, C:0.04, G:0.28, T:0.29
Consensus pattern (48 bp):
AAAGGTTGTGAAGAAGGACATAATTTGATTGAAAATTAGGTCAAGGTT
Found at i:50300567 original size:21 final size:21
Alignment explanation
Indices: 50300535--50300575 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
50300525 GAACATTTGG
50300535 TGTATAGGCTAAGAA-AGGCCT
1 TGTATAGGCTAA-AACAGGCCT
50300556 TGTAT-GGCCTAAAACAGGCC
1 TGTATAGG-CTAAAACAGGCC
50300576 CCTCGAGCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.32, C:0.20, G:0.27, T:0.22
Consensus pattern (21 bp):
TGTATAGGCTAAAACAGGCCT
Found at i:50303435 original size:16 final size:16
Alignment explanation
Indices: 50303414--50303444 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50303404 CCGTTACCGT
50303414 TACGCATTCGAGTGGC
1 TACGCATTCGAGTGGC
*
50303430 TACGCATTGGAGTGG
1 TACGCATTCGAGTGG
50303445 GCTAATGTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.19, G:0.35, T:0.26
Consensus pattern (16 bp):
TACGCATTCGAGTGGC
Found at i:50310271 original size:21 final size:21
Alignment explanation
Indices: 50310245--50310285 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
50310235 ATCTGCTCAA
* *
50310245 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
50310266 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
50310286 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:50314771 original size:16 final size:16
Alignment explanation
Indices: 50314738--50314771 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
50314728 GGAGATTGTT
* *
50314738 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
50314754 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
50314770 AA
1 AA
50314772 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:50325319 original size:23 final size:22
Alignment explanation
Indices: 50325267--50325319 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
50325257 TCCACGTCTT
*
50325267 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
50325289 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
50325312 TTTCTTTT
1 TTTCTTTT
50325320 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:50328118 original size:114 final size:112
Alignment explanation
Indices: 50327844--50328335 Score: 451
Period size: 114 Copynumber: 4.3 Consensus size: 112
50327834 GACTCGTATC
* * * * *
50327844 AGTTCTGGTCTTGATGTATATTGGCATTAGTGGCGC-TTATGAACAAACGCCGGTAATGTATAGT
1 AGTT-TGGTCTTGATGTATATTAGAATTAGTGGCGCTTTAAGAA-AAACGCCGCTAAAGTATAGT
* * * * *
50327908 ATTAGCGGCGCTTAGCGGAAGCGCCGCAAAAGATGTTAACTAAAACGCAG
64 ATTAGCAGCGCTTAGCGTAAGCGCCGC-AAATATCTTAACCAAAACGCAG
*
50327958 AGTTTGGTCTTGATGTATATT-GCAATTAGTGGCGCTTATAA-AGAAAACGCCGCTAATGTATAG
1 AGTTTGGTCTTGATGTATATTAG-AATTAGTGGCGCTT-TAAGA-AAAACGCCGCTAAAGTATAG
* * * * * *
50328021 TATTAGCGGCGCATAGCGTTAAACGCCACAAGATATCTTAATCAAAACGCAC
63 TATTAGCAGCGCTTAGCG-TAAGCGCCGCAA-ATATCTTAACCAAAACGCAG
* * * * *
50328073 CGTTTTGGTCTTGATGTATACTATAATTAGTGGCG-TTTAAGGAAAACGCCAG-TAAAGGATAGT
1 AG-TTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTTAAGAAAAACGCC-GCTAAAGTATAGT
* * * *
50328136 -TATAGCAGCGTTTGGTGGTAAGCGCCTCCAAATATCTTAACCAAAACGCAG
64 AT-TAGCAGCGCTTAG-CGTAAGCGCC-GCAAATATCTTAACCAAAACGCAG
* * * *
50328187 AGTTTGGTCTTGA-GAAGTATTAGAATTAGTGGCGCTTGATGAAAAACGCCGCTAAAGTATATTA
1 AGTTTGGTCTTGATGTA-TATTAGAATTAGTGGCGCTTTAAGAAAAACGCCGCTAAAGTATAGTA
* * *
50328251 TTAGCAGCG-TTTGTGTAACGCGCCGCAAAGTATCTTAACCAAAACACAG
65 TTAGCAGCGCTTAGCGTAA-GCGCCGCAAA-TATCTTAACCAAAACGCAG
* * *
50328300 CGTTTAGTTCTTGATGTATACTAGAATTAGTGGCGC
1 AGTTT-GGTCTTGATGTATATTAGAATTAGTGGCGC
50328336 ACATGGGAAA
Statistics
Matches: 313, Mismatches: 44, Indels: 42
0.78 0.11 0.11
Matches are distributed among these distances:
112 11 0.04
113 86 0.27
114 151 0.48
115 36 0.12
116 29 0.09
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.28
Consensus pattern (112 bp):
AGTTTGGTCTTGATGTATATTAGAATTAGTGGCGCTTTAAGAAAAACGCCGCTAAAGTATAGTAT
TAGCAGCGCTTAGCGTAAGCGCCGCAAATATCTTAACCAAAACGCAG
Found at i:50328500 original size:18 final size:18
Alignment explanation
Indices: 50328479--50328514 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
50328469 TTATTTTATA
50328479 TGTTT-TTTATATTTAATT
1 TGTTTATTTATA-TTAATT
50328497 TGTTTATTTATATTAATT
1 TGTTTATTTATATTAATT
50328515 AAAATTCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TGTTTATTTATATTAATT
Found at i:50334057 original size:72 final size:72
Alignment explanation
Indices: 50333964--50334127 Score: 206
Period size: 72 Copynumber: 2.3 Consensus size: 72
50333954 AAAATCACAT
* * *
50333964 ATAAACAACTATTAATAAAACTA-ATTTAGTA-AAAAATAAGTGGAACATAAATTCAATATCTAA
1 ATAAACAACTATTAATAAAACTAGA-TTA-CACAAAAATAAGTAGAACATAAATTCAATATCCAA
*
50334027 AGACCAAAC
64 AAACCAAAC
* * *
50334036 ATAAACAACTATTAATTAAACTAGATTACACATAACTAAGTAGAACATAAATTCAATATCCAAAA
1 ATAAACAACTATTAATAAAACTAGATTACACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
*
50334101 ACTAAAC
66 ACCAAAC
* *
50334108 ATAAATAACTATTGATAAAA
1 ATAAACAACTATTAATAAAA
50334128 ACATACTTCG
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
71 1 0.01
72 77 0.97
73 1 0.01
ACGTcount: A:0.55, C:0.13, G:0.05, T:0.26
Consensus pattern (72 bp):
ATAAACAACTATTAATAAAACTAGATTACACAAAAATAAGTAGAACATAAATTCAATATCCAAAA
ACCAAAC
Found at i:50335514 original size:15 final size:14
Alignment explanation
Indices: 50335494--50335525 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
50335484 ATTTGTAATA
50335494 AAATAAGCAGGCGAG
1 AAATAAGCAGGC-AG
50335509 AAATAAGCAGGCAG
1 AAATAAGCAGGCAG
50335523 AAA
1 AAA
50335526 ATTGTGAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.53, C:0.12, G:0.28, T:0.06
Consensus pattern (14 bp):
AAATAAGCAGGCAG
Found at i:50337700 original size:7 final size:7
Alignment explanation
Indices: 50337668--50337699 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
50337658 AGAGGGAACC
50337668 AGCAAAG
1 AGCAAAG
50337675 AGCAAAG
1 AGCAAAG
50337682 AGCAAAG
1 AGCAAAG
*
50337689 AGCAGAG
1 AGCAAAG
50337696 AGCA
1 AGCA
50337700 GTGTAGCAGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.53, C:0.16, G:0.31, T:0.00
Consensus pattern (7 bp):
AGCAAAG
Found at i:50338130 original size:41 final size:41
Alignment explanation
Indices: 50338035--50338137 Score: 102
Period size: 41 Copynumber: 2.5 Consensus size: 41
50338025 TACTTTTTGG
*** *
50338035 AAAAACGCCGCTAAA-AATAGAGCATTAGCAGCGTTTCTTC
1 AAAAACGCCGCTAAAGACCCGAGCATTAGCAGCGCTTCTTC
* * * *
50338075 AAAAGCACCACTAAAGACCCGAGCATTAGCGGCGCTT-TTC
1 AAAAACGCCGCTAAAGACCCGAGCATTAGCAGCGCTTCTTC
*
50338115 TAAAAACGCCGCTAAAGCCCCGA
1 -AAAAACGCCGCTAAAGACCCGA
50338138 AAACTCAAAA
Statistics
Matches: 49, Mismatches: 12, Indels: 3
0.77 0.19 0.05
Matches are distributed among these distances:
40 15 0.31
41 34 0.69
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.17
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGACCCGAGCATTAGCAGCGCTTCTTC
Found at i:50338226 original size:40 final size:39
Alignment explanation
Indices: 50338182--50338303 Score: 154
Period size: 40 Copynumber: 3.1 Consensus size: 39
50338172 TTTGTGGCAC
* * *
50338182 TTTTTGAAAAACGCCGCTAATGCTCATTTTTTGCGGCGT
1 TTTTTTAAAAACGCCGCTAATGCTGATTTTTAGCGGCGT
* * *
50338221 TTTTTTAAAAAGCGCCGCTAATACTAGATCTTTAGCGACGT
1 TTTTTTAAAAA-CGCCGCTAATGCT-GATTTTTAGCGGCGT
*
50338262 TTTTTTAAAAGCGCCGCTAATGCTTGATTTTTAGCGGCGT
1 TTTTTTAAAAACGCCGCTAATGC-TGATTTTTAGCGGCGT
50338302 TT
1 TT
50338304 ATTATCCAAA
Statistics
Matches: 70, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
39 10 0.14
40 38 0.54
41 22 0.31
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.39
Consensus pattern (39 bp):
TTTTTTAAAAACGCCGCTAATGCTGATTTTTAGCGGCGT
Found at i:50339022 original size:13 final size:13
Alignment explanation
Indices: 50339004--50339028 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
50338994 CTATTTCAAA
50339004 GGTCACACGGGTT
1 GGTCACACGGGTT
50339017 GGTCACACGGGT
1 GGTCACACGGGT
50339029 GTGTGGTTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.24, G:0.40, T:0.20
Consensus pattern (13 bp):
GGTCACACGGGTT
Found at i:50339610 original size:44 final size:44
Alignment explanation
Indices: 50339544--50339891 Score: 181
Period size: 44 Copynumber: 7.5 Consensus size: 44
50339534 TACTATAGCG
* *
50339544 AATCTTATCTCCCTGAAATTGCAGTAGAGTAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
*
50339588 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTAC-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAG-TAGATTGAAGCTACA
* * * * * *
50339631 AATACATATATCCTTGAAGTTGCAAT-GAGTCGGAATGAAGCTACAACTACA
1 AAT-CTTATCTCCCTGAAGTTGCAGTGGAGT-AGATTGAAG------CTACA
* * * * *
50339682 AATCCTATAC-CCCTGAAGTTACAGTGG-GTTGGATTGAATTTGTTAGAGCG
1 AATCTTAT-CTCCCTGAAGTTGCAGTGGAG-TAGATTGAA---GCT--A-CA
* *
50339732 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
* * * * * * * *
50339776 AATCCTGAAC-CCCTAAAATTACAGTGGATTGGATTGAATCTACCATAGTA
1 AAT-CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTA-C-----A
* *
50339826 AATCTTATCTCCCTGAAGTTGTAGTGGAGAAGATTGAAGCTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
*
50339870 AATCCTA-C-CCCTGAAGTTGCAG
1 AATCTTATCTCCCTGAAGTTGCAG
50339892 CAGGTCAGAA
Statistics
Matches: 228, Mismatches: 46, Indels: 62
0.68 0.14 0.18
Matches are distributed among these distances:
42 13 0.06
43 9 0.04
44 94 0.41
45 9 0.04
47 3 0.01
49 7 0.03
50 86 0.38
51 6 0.03
53 1 0.00
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGCTACA
Found at i:50339775 original size:94 final size:94
Alignment explanation
Indices: 50339483--50340049 Score: 286
Period size: 94 Copynumber: 6.1 Consensus size: 94
50339473 AACAGATCAG
* * * ** * * * * *
50339483 TGAAGCCACAATTCCTATACCCCTAAAGTTGTAGTGGGTTGGATTGAATTTTACTATAGCGAATC
1 TGAAGCTACAAATCCTATACCCCTGAAGTTACAGTGGATTGGATTGAA-TCTACCAGAGCAAATC
* * *
50339548 TTATCTCCCTGAAATTGCAGTAGAGTAGAT
65 TTATCTCCCTGAAGTTGCAGTGGAGAAGAT
* * *** * *
50339578 TGAAGCTACAAATCTTAT-CTCCCTGAAGTTGCAGTGGAGCAAGA-TGAAGCTA-C--A--ATA-
1 TGAAGCTACAAATCCTATAC-CCCTGAAGTTACAGTGGA-TTGGATTGAATCTACCAGAGCAAAT
* * * *
50339635 CATATATCCTTGAAGTTGCAATGAGTCGGAATGAAGCT
64 CTTATCTCCCTGAAGTTGC----AGT-GG-A-GAAGAT
** * * *** *
50339673 ACAA-CTACAAATCCTATACCCCTGAAGTTACAGTGGGTTGGATTGAATTTGTTAGAGCGAATCT
1 TGAAGCTACAAATCCTATACCCCTGAAGTTACAGTGGATTGGATTGAATCTACCAGAGCAAATCT
50339737 TATCTCCCTGAAGTTGCAGTGGAGCAA-AT
66 TATCTCCCTGAAGTTGCAGTGGAG-AAGAT
* * * *
50339766 TGAAGCTACAAATCCTGA-ACCCCTAAAATTACAGTGGATTGGATTGAATCTACCATAGTAAATC
1 TGAAGCTACAAATCCT-ATACCCCTGAAGTTACAGTGGATTGGATTGAATCTACCAGAGCAAATC
*
50339830 TTATCTCCCTGAAGTTGTAGTGGAGAAGAT
65 TTATCTCCCTGAAGTTGCAGTGGAGAAGAT
* * ** * * * * *
50339860 TGAAGCTACAAATCC--TACCCCTGAAGTTGCAGCAGG-TCAGAATGAAACTACGATAACAAATC
1 TGAAGCTACAAATCCTATACCCCTGAAGTTACAG-TGGATTGGATTGAATCTACCAGAGCAAATC
* * * *
50339922 TTATCTCCTTGAATTTGAAGTGGAGCGAGA-
65 TTATCTCCCTGAAGTTGCAGTGGAG-AAGAT
* * * * * * * * * * *
50339952 TGAAGCTATAGA-CCCACACCTCTAAAGTTGCAGTGGGA-CGGATTGAATTTACCATAGCGAATC
1 TGAAGCTACAAATCCTATACCCCTGAAGTTACAGT-GGATTGGATTGAATCTACCAGAGCAAATC
* * * * *
50340015 TTATCACTCTGAAGTTGTAGTGGAGCATAT
65 TTATCTCCCTGAAGTTGCAGTGGAGAAGAT
50340045 TGAAG
1 TGAAG
50340050 TTGTAAATAT
Statistics
Matches: 356, Mismatches: 87, Indels: 60
0.71 0.17 0.12
Matches are distributed among these distances:
88 15 0.04
89 1 0.00
91 3 0.01
92 69 0.19
93 73 0.21
94 128 0.36
95 44 0.12
96 5 0.01
97 1 0.00
99 1 0.00
100 16 0.04
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (94 bp):
TGAAGCTACAAATCCTATACCCCTGAAGTTACAGTGGATTGGATTGAATCTACCAGAGCAAATCT
TATCTCCCTGAAGTTGCAGTGGAGAAGAT
Found at i:50340049 original size:93 final size:92
Alignment explanation
Indices: 50339732--50340049 Score: 302
Period size: 92 Copynumber: 3.4 Consensus size: 92
50339722 TGTTAGAGCG
* * * *
50339732 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGCTACAAATCCTGA-ACCCCTAAAATT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCC-CACA-CCCTAAAGTT
* * *
50339796 ACAGTGGATTGGATTGAATCTACCATAGTA
64 GCAGTGGA-CGGATTGAATCTACCATAGCA
* * *
50339826 AATCTTATCTCCCTGAAGTTGTAGTGGAGAAGATTGAAGCTACAAATCCTAC-CCCTGAAGTTGC
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCCCACACCCTAAAGTTGC
* * * * * * *
50339890 AGCAGGTCAGAATGAAACTACGATAACA
66 AG-TGGACGGATTGAATCTACCATAGCA
* * * * *
50339918 AATCTTATCTCCTTGAATTTGAAGTGGAGCGAGA-TGAAGCTATAGA-CCCACACCTCTAAAGTT
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGC-AGATTGAAGCTACAAATCCCACACC-CTAAAGTT
* *
50339981 GCAGTGGGACGGATTGAATTTACCATAGCG
64 GCAGT-GGACGGATTGAATCTACCATAGCA
* * *
50340011 AATCTTATCACTCTGAAGTTGTAGTGGAGCATATTGAAG
1 AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAG
50340050 TTGTAAATAT
Statistics
Matches: 178, Mismatches: 39, Indels: 15
0.77 0.17 0.06
Matches are distributed among these distances:
91 4 0.02
92 65 0.37
93 63 0.35
94 46 0.26
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (92 bp):
AATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTGAAGCTACAAATCCCACACCCTAAAGTTGC
AGTGGACGGATTGAATCTACCATAGCA
Found at i:50342786 original size:35 final size:35
Alignment explanation
Indices: 50342740--50342864 Score: 94
Period size: 35 Copynumber: 3.4 Consensus size: 35
50342730 CGCAACCGTC
*
50342740 GGTTAAACCAACTAGCACTGGGTGCAAATATTGTT
1 GGTTAATCCAACTAGCACTGGGTGCAAATATTGTT
* * *
50342775 GGTTAATCCAACTAG-AGCTAGGCT-CATAATTATTATC
1 GGTTAATCCAACTAGCA-CT-GGGTGCA-AA-TATTGTT
* * *
50342812 GTCTGTATAT-CAGACTAGCACTAGGTGTAAATATTGTT
1 G-GT-TA-ATCCA-ACTAGCACTGGGTGCAAATATTGTT
50342850 GGTTAATCCAACTAG
1 GGTTAATCCAACTAG
50342865 AGCTGAGCTC
Statistics
Matches: 68, Mismatches: 11, Indels: 22
0.67 0.11 0.22
Matches are distributed among these distances:
34 1 0.01
35 25 0.37
36 9 0.13
37 7 0.10
38 7 0.10
39 8 0.12
40 10 0.15
41 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.32
Consensus pattern (35 bp):
GGTTAATCCAACTAGCACTGGGTGCAAATATTGTT
Found at i:50347077 original size:30 final size:31
Alignment explanation
Indices: 50347017--50347078 Score: 83
Period size: 30 Copynumber: 2.0 Consensus size: 31
50347007 GAATCTGGTA
*
50347017 GGTGGTTAATGATGGGACTTAGTGGAATGTG
1 GGTGGTTAATGATGGGACTTAATGGAATGTG
*
50347048 GGTGGTTAATTAT-GGACTTAATAGG-ATGTG
1 GGTGGTTAATGATGGGACTTAAT-GGAATGTG
50347078 G
1 G
50347079 ACCGTTAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 14 0.50
31 14 0.50
ACGTcount: A:0.24, C:0.03, G:0.39, T:0.34
Consensus pattern (31 bp):
GGTGGTTAATGATGGGACTTAATGGAATGTG
Found at i:50347823 original size:10 final size:10
Alignment explanation
Indices: 50347807--50347845 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
50347797 TATCCTAGCT
50347807 TTTATCTTTA
1 TTTATCTTTA
*
50347817 ATTATCTTTA
1 TTTATCTTTA
50347827 TTTAT-TTGTA
1 TTTATCTT-TA
50347837 TTTATCTTT
1 TTTATCTTT
50347846 TAGAATTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.08, G:0.03, T:0.69
Consensus pattern (10 bp):
TTTATCTTTA
Found at i:50350836 original size:2 final size:2
Alignment explanation
Indices: 50350829--50350863 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
50350819 GTCTAAAACA
*
50350829 AT AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50350864 GACTTAACCG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:50351718 original size:38 final size:36
Alignment explanation
Indices: 50351638--50351723 Score: 109
Period size: 38 Copynumber: 2.3 Consensus size: 36
50351628 TTGTAATATT
**
50351638 GTTGCTGGTATATTGTTGCGTATGTTGGTATACATG
1 GTTGCTGGTATATTGTTGCGTACATTGGTATACATG
* * *
50351674 GCTGCTGGTATATTGTTGCTTAACATATGTTATACATG
1 GTTGCTGGTATATTGTTGCGT-ACAT-TGGTATACATG
50351712 GTTGCTGGTATA
1 GTTGCTGGTATA
50351724 CATGGCTATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
36 19 0.45
37 2 0.05
38 21 0.50
ACGTcount: A:0.20, C:0.10, G:0.27, T:0.43
Consensus pattern (36 bp):
GTTGCTGGTATATTGTTGCGTACATTGGTATACATG
Found at i:50352444 original size:21 final size:20
Alignment explanation
Indices: 50352377--50352445 Score: 52
Period size: 21 Copynumber: 3.5 Consensus size: 20
50352367 TGTAGGCAAC
*
50352377 TGAGTTGGGGCAGCTTG--T
1 TGAGTTGGGGTAGCTTGTTT
* * * *
50352395 TGAGTTGGGGTACCCTCTTGC
1 TGAGTTGGGGTAGCTTGTT-T
*
50352416 TGATTTGGGGTAGCTTGTTAT
1 TGAGTTGGGGTAGCTTGTT-T
50352437 TGAGTTGGG
1 TGAGTTGGG
50352446 ACACCAACTT
Statistics
Matches: 36, Mismatches: 12, Indels: 3
0.71 0.24 0.06
Matches are distributed among these distances:
18 13 0.36
21 23 0.64
ACGTcount: A:0.12, C:0.12, G:0.39, T:0.38
Consensus pattern (20 bp):
TGAGTTGGGGTAGCTTGTTT
Found at i:50353203 original size:40 final size:39
Alignment explanation
Indices: 50353118--50353214 Score: 149
Period size: 39 Copynumber: 2.5 Consensus size: 39
50353108 AAAGAGTCAT
* *
50353118 TGCATGCATATTAAAAAATAGGCAACACACTAACATCAC
1 TGCATGCATATTAAAAAATAGGCAACACACCAACATCAA
* *
50353157 TACATGCATATTAAAAAATAGTCAACACACCAACAATCAA
1 TGCATGCATATTAAAAAATAGGCAACACACCAAC-ATCAA
50353197 TGCATGCATATTAAAAAA
1 TGCATGCATATTAAAAAA
50353215 AATTCACTAA
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
39 31 0.60
40 21 0.40
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.22
Consensus pattern (39 bp):
TGCATGCATATTAAAAAATAGGCAACACACCAACATCAA
Found at i:50355481 original size:28 final size:28
Alignment explanation
Indices: 50355413--50355482 Score: 81
Period size: 28 Copynumber: 2.5 Consensus size: 28
50355403 TAAATAAGGT
*
50355413 ATAA-AGCAATTTAAGAATAATAATATTA
1 ATAATAGCAA-TTAAGAATAATAATAATA
* *
50355441 ATAAT-GACGATTAATAATAATAATAATA
1 ATAATAG-CAATTAAGAATAATAATAATA
50355469 ATAATAGCAATTAA
1 ATAATAGCAATTAA
50355483 CAATTTAAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
28 32 0.91
29 3 0.09
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.31
Consensus pattern (28 bp):
ATAATAGCAATTAAGAATAATAATAATA
Found at i:50357225 original size:6 final size:6
Alignment explanation
Indices: 50357211--50357382 Score: 87
Period size: 6 Copynumber: 28.0 Consensus size: 6
50357201 ACCTGCCAAA
* * ** * *
50357211 CAAAGT CAAAAT CAAAAT CGAAAT --AACC CTAAAT CAAAAT CCAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
* * * * * * **
50357257 CGAAAT CAAAAT CAAAAT CTAAAT CTAAAT CGAGAT CGAAAT TGAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
* * ** *
50357305 CAAAAT CAGAAT CAATGAGTGTTT CAAAAT TGAAAT CAAAAT CGAAAT
1 CAAAAT CAAAAT CAA--A----AT CAAAAT CAAAAT CAAAAT CAAAAT
* *
50357353 CAAAAT CAAAAT CAGAAT CGAAAT CAAAAT
1 CAAAAT CAAAAT CAAAAT CAAAAT CAAAAT
50357383 TGAAATCGAA
Statistics
Matches: 127, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
4 2 0.02
6 119 0.94
8 1 0.01
10 1 0.01
12 4 0.03
ACGTcount: A:0.54, C:0.16, G:0.09, T:0.21
Consensus pattern (6 bp):
CAAAAT
Found at i:50357234 original size:12 final size:12
Alignment explanation
Indices: 50357219--50357394 Score: 119
Period size: 12 Copynumber: 14.8 Consensus size: 12
50357209 AACAAAGTCA
50357219 AAATCAAAATCG
1 AAATCAAAATCG
** *
50357231 AAAT--AACCCT
1 AAATCAAAATCG
*
50357241 AAATCAAAATCC
1 AAATCAAAATCG
* *
50357253 AAATCGAAATCA
1 AAATCAAAATCG
*
50357265 AAATCAAAATCT
1 AAATCAAAATCG
*
50357277 AAATCTAAATCG
1 AAATCAAAATCG
* * *
50357289 AGATCGAAATTG
1 AAATCAAAATCG
50357301 AAATCAAAATC-
1 AAATCAAAATCG
*
50357312 AGAATCAATGAGT-G
1 A-AATCAA--AATCG
** *
50357326 -TTTCAAAATTG
1 AAATCAAAATCG
50357337 AAATCAAAATCG
1 AAATCAAAATCG
*
50357349 AAATCAAAATCA
1 AAATCAAAATCG
*
50357361 AAATCAGAATCG
1 AAATCAAAATCG
*
50357373 AAATCAAAATTG
1 AAATCAAAATCG
*
50357385 AAATCGAAAT
1 AAATCAAAAT
50357395 AACCCTAAAT
Statistics
Matches: 125, Mismatches: 31, Indels: 16
0.73 0.18 0.09
Matches are distributed among these distances:
10 9 0.07
11 2 0.02
12 112 0.90
14 2 0.02
ACGTcount: A:0.54, C:0.15, G:0.09, T:0.22
Consensus pattern (12 bp):
AAATCAAAATCG
Found at i:50357388 original size:6 final size:6
Alignment explanation
Indices: 50357331--50357394 Score: 58
Period size: 6 Copynumber: 10.7 Consensus size: 6
50357321 GAGTGTTTCA
* * * * *
50357331 AAATTG AAATCA AAATCG AAATCA AAATCA AAATC- AGAATCG AAATCA
1 AAATCG AAATCG AAATCG AAATCG AAATCG AAATCG A-AATCG AAATCG
*
50357379 AAATTG AAATCG AAAT
1 AAATCG AAATCG AAAT
50357395 AACCCTAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
5 1 0.02
6 46 0.96
7 1 0.02
ACGTcount: A:0.58, C:0.12, G:0.09, T:0.20
Consensus pattern (6 bp):
AAATCG
Found at i:50359055 original size:21 final size:21
Alignment explanation
Indices: 50359025--50359069 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
50359015 TAAGAATTCT
*
50359025 TTTTAATAATAGACTTAACAA
1 TTTTAATAATAGACGTAACAA
* *
50359046 TTTTACTAATAGAGGTAACAA
1 TTTTAATAATAGACGTAACAA
50359067 TTT
1 TTT
50359070 GAAAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.09, G:0.09, T:0.40
Consensus pattern (21 bp):
TTTTAATAATAGACGTAACAA
Found at i:50364164 original size:30 final size:30
Alignment explanation
Indices: 50364128--50364190 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
50364118 ATTTATTTTA
50364128 TTGTTAATTTTGTTATTATTTTAAAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
*
50364158 TTGTTAATTTTGTTATTATTTTAGAGGCAT
1 TTGTTAATTTTGTTATTATTTTAAAGGCAT
50364188 TTG
1 TTG
50364191 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.24, C:0.03, G:0.16, T:0.57
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAAAGGCAT
Found at i:50364788 original size:15 final size:15
Alignment explanation
Indices: 50364768--50364797 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
50364758 TATTTTAGTT
*
50364768 ATATTAGGATAATTA
1 ATATTAAGATAATTA
50364783 ATATTAAGATAATTA
1 ATATTAAGATAATTA
50364798 TTAAGGATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (15 bp):
ATATTAAGATAATTA
Found at i:50368745 original size:4 final size:4
Alignment explanation
Indices: 50368736--50368800 Score: 71
Period size: 4 Copynumber: 15.5 Consensus size: 4
50368726 CAACCCAATT
50368736 TTTA TTTA TTTA TTTA TTTA TTTTA TTTA CTTTA TTTA -TTA CTTTA TTTTAA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA -TTTA TTTA TTTA -TTTA -TTT-A
50368788 TTTA -TTA TTTA TT
1 TTTA TTTA TTTA TT
50368801 ACTTATTTGG
Statistics
Matches: 54, Mismatches: 1, Indels: 12
0.81 0.01 0.18
Matches are distributed among these distances:
3 6 0.11
4 30 0.56
5 17 0.31
6 1 0.02
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:50368769 original size:22 final size:21
Alignment explanation
Indices: 50368735--50368800 Score: 82
Period size: 21 Copynumber: 3.1 Consensus size: 21
50368725 GCAACCCAAT
50368735 TTTTATTTATTTATTTATTTA
1 TTTTATTTATTTATTTATTTA
50368756 TTTTATTTACTTTATTTA-TTA
1 TTTTATTTA-TTTATTTATTTA
*
50368777 CTTTATTTTAATTTA-TTATTTA
1 TTTTA-TTT-ATTTATTTATTTA
50368799 TT
1 TT
50368801 ACTTATTTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
21 19 0.49
22 19 0.49
23 1 0.03
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTATTTATTTATTTATTTA
Found at i:50368808 original size:18 final size:19
Alignment explanation
Indices: 50368733--50368808 Score: 74
Period size: 18 Copynumber: 4.2 Consensus size: 19
50368723 AGGCAACCCA
*
50368733 ATTT-TTATTTATTTATTT
1 ATTTATTATTTATTTACTT
50368751 ATTTA-T-TTTATTTACTTT
1 ATTTATTATTTATTTAC-TT
*
50368769 ATTTATTACTTTATTT--TA
1 ATTTATTA-TTTATTTACTT
50368787 ATTTATTATTTA-TTACTT
1 ATTTATTATTTATTTACTT
50368805 ATTT
1 ATTT
50368809 GGATATTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
16 2 0.04
17 12 0.25
18 26 0.54
19 1 0.02
21 7 0.15
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (19 bp):
ATTTATTATTTATTTACTT
Found at i:50369846 original size:16 final size:16
Alignment explanation
Indices: 50369827--50369887 Score: 56
Period size: 16 Copynumber: 3.8 Consensus size: 16
50369817 TTCCTAAAGC
50369827 ATAAAAAATATAAATA
1 ATAAAAAATATAAATA
50369843 ATAAATAAATATAAATCA
1 ATAAA-AAATATAAAT-A
*
50369861 A-AATAAATA-AAA-A
1 ATAAAAAATATAAATA
*
50369874 AGAAAAATATATAA
1 ATAAAAA-ATATAA
50369888 TTTAGGGACT
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 2 0.05
14 4 0.11
15 6 0.16
16 12 0.32
17 12 0.32
18 2 0.05
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.23
Consensus pattern (16 bp):
ATAAAAAATATAAATA
Found at i:50369873 original size:10 final size:10
Alignment explanation
Indices: 50369827--50369873 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
50369817 TTCCTAAAGC
*
50369827 ATAAAAA-AT
1 ATAAAAATAA
50369836 ATAAATAATAA
1 ATAAA-AATAA
*
50369847 ATAAATATAA
1 ATAAAAATAA
*
50369857 ATCAAAATAA
1 ATAAAAATAA
50369867 ATAAAAA
1 ATAAAAA
50369874 AGAAAAATAT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
9 5 0.16
10 20 0.65
11 6 0.19
ACGTcount: A:0.74, C:0.02, G:0.00, T:0.23
Consensus pattern (10 bp):
ATAAAAATAA
Found at i:50370461 original size:15 final size:15
Alignment explanation
Indices: 50370436--50370470 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
50370426 GACTCTATTT
*
50370436 TAATT-ATATTAGGA
1 TAATTAATATTAAGA
50370450 TAATTAATATTAAGA
1 TAATTAATATTAAGA
50370465 TAATTA
1 TAATTA
50370471 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:50375277 original size:33 final size:35
Alignment explanation
Indices: 50375182--50375278 Score: 89
Period size: 33 Copynumber: 2.8 Consensus size: 35
50375172 TTAATATTTT
*
50375182 AATATATGAAATATAAATTTTAAATATTT--TTAAGC
1 AATATAT-AAAT-TATATTTTAAATATTTAATTAAGC
* *
50375217 AATAAATATTAATTAT-TTATAAA-ATTTAATT-AG-
1 AAT--ATATAAATTATATTTTAAATATTTAATTAAGC
50375250 AATATATAAATTATATTTTAAATATTTAA
1 AATATATAAATTATATTTTAAATATTTAA
50375279 ATATAACCAT
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
31 10 0.20
32 6 0.12
33 13 0.25
34 8 0.16
35 7 0.14
36 3 0.06
37 4 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (35 bp):
AATATATAAATTATATTTTAAATATTTAATTAAGC
Found at i:50376378 original size:27 final size:27
Alignment explanation
Indices: 50376340--50376393 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
50376330 ATTTACAAAA
50376340 AGTATATTTAGATGCATCAATATTAAT
1 AGTATATTTAGATGCATCAATATTAAT
50376367 AGTATATTTAGATGCATCAATATTAAT
1 AGTATATTTAGATGCATCAATATTAAT
50376394 TTGTCTTCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (27 bp):
AGTATATTTAGATGCATCAATATTAAT
Found at i:50378079 original size:25 final size:24
Alignment explanation
Indices: 50378051--50378143 Score: 71
Period size: 25 Copynumber: 3.8 Consensus size: 24
50378041 AGCTCCAAAG
50378051 AGCCATTAATCGGGAAGCTCCGGAT
1 AGCCA-TAATCGGGAAGCTCCGGAT
* ** *
50378076 AGCCATATATCGGGAAGTTCAAGCT
1 AGCCATA-ATCGGGAAGCTCCGGAT
* * *
50378101 AGCCAT-ATTGGGAAGCTCCGAAG
1 AGCCATAATCGGGAAGCTCCGGAT
* *
50378124 AGCTATTAATCAGGAAGCTC
1 AGCCA-TAATCGGGAAGCTC
50378144 ACGAAGAGCC
Statistics
Matches: 51, Mismatches: 14, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
23 14 0.27
24 3 0.06
25 34 0.67
ACGTcount: A:0.31, C:0.22, G:0.26, T:0.22
Consensus pattern (24 bp):
AGCCATAATCGGGAAGCTCCGGAT
Found at i:50378641 original size:21 final size:20
Alignment explanation
Indices: 50378603--50378651 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 20
50378593 GATCTATACG
*
50378603 AATA-AATTTAACTCAATTT
1 AATACAATTTAACTCAATTC
*
50378622 AATACAATTTATATTCAATTC
1 AATACAATTTA-ACTCAATTC
*
50378643 AATCCAATT
1 AATACAATT
50378652 CACATCTTAG
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 6 0.24
21 15 0.60
ACGTcount: A:0.45, C:0.14, G:0.00, T:0.41
Consensus pattern (20 bp):
AATACAATTTAACTCAATTC
Found at i:50380554 original size:21 final size:21
Alignment explanation
Indices: 50380526--50380567 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
50380516 GTGTGAGAAG
*
50380526 TTTAAAATT-TTTTATTTTTT
1 TTTAAAATTGATTTATTTTTT
50380546 TTTATAAATTGATTTATTTTTT
1 TTTA-AAATTGATTTATTTTTT
50380568 GTGGCGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 4 0.21
21 5 0.26
22 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (21 bp):
TTTAAAATTGATTTATTTTTT
Found at i:50380849 original size:76 final size:76
Alignment explanation
Indices: 50380643--50380873 Score: 336
Period size: 76 Copynumber: 3.0 Consensus size: 76
50380633 CCGCAAAATT
* * *
50380643 TTTTTCATTTTGAACAAAATGATGCCGTTTTGTTATGCTAAAAATTTTTTATTTTATTTTTTTAT
1 TTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTTAT
* *
50380708 ATATTGATTTGTTT
66 AAATTGA--T-TTA
* * * *
50380722 TTTGTTCATTTTCAGCAAAATGACGCCGTTTTGCTATGTTAAAAAAATTTTATTTTATTTTTTTA
1 TTT-TTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTTA
50380787 TAAATTGATTTA
65 TAAATTGATTTA
*
50380799 TTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTTATTTTGTTTTTTTAT
1 TTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTTAT
50380864 AAATTGATTT
66 AAATTGATTT
50380874 CTTATAAAAT
Statistics
Matches: 137, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
76 67 0.49
77 5 0.04
78 1 0.01
79 3 0.02
80 61 0.45
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (76 bp):
TTTTTCATTTTGAACAAAATGACGCCGTTTTGCTATGCTAAAAAATTTTTATTTTATTTTTTTAT
AAATTGATTTA
Found at i:50381474 original size:14 final size:14
Alignment explanation
Indices: 50381455--50381488 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
50381445 AACCTTAAAT
50381455 CCCTAAC-TCTTAAC
1 CCCTAACATC-TAAC
50381469 CCCTAACATCTAAC
1 CCCTAACATCTAAC
50381483 CCCTAA
1 CCCTAA
50381489 ACCCCTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 17 0.89
15 2 0.11
ACGTcount: A:0.32, C:0.44, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAACATCTAAC
Found at i:50381518 original size:21 final size:20
Alignment explanation
Indices: 50381488--50381528 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
50381478 CTAACCCCTA
*
50381488 AACCCCTAAACCTTAAATCCC
1 AACCCCTAAACCAT-AATCCC
*
50381509 AACCCTTAAACCATAATCCC
1 AACCCCTAAACCATAATCCC
50381529 TAATTCATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (20 bp):
AACCCCTAAACCATAATCCC
Found at i:50381537 original size:14 final size:14
Alignment explanation
Indices: 50381519--50381560 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
50381509 AACCCTTAAA
50381519 CCATAATCCCTAAT
1 CCATAATCCCTAAT
*
50381533 TCATAATCCCTAAAT
1 CCATAATCCCT-AAT
*
50381548 CCATACTCCCTAA
1 CCATAATCCCTAA
50381561 ACCTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 12 0.50
15 12 0.50
ACGTcount: A:0.36, C:0.36, G:0.00, T:0.29
Consensus pattern (14 bp):
CCATAATCCCTAAT
Found at i:50381557 original size:15 final size:15
Alignment explanation
Indices: 50381515--50381561 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
50381505 TCCCAACCCT
50381515 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
*
50381529 T-AATTCATAATCCC
1 TAAATCCATAATCCC
*
50381543 TAAATCCATACTCCC
1 TAAATCCATAATCCC
50381558 TAAA
1 TAAA
50381562 CCTTAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 2 0.07
14 11 0.39
15 15 0.54
ACGTcount: A:0.40, C:0.32, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:50381767 original size:15 final size:15
Alignment explanation
Indices: 50381747--50381816 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
50381737 CCTAGCACAT
*
50381747 CTAACCCCTAAACCC
1 CTAACCCCTAAATCC
50381762 CTAACCCTCT-AATCC
1 CTAACCC-CTAAATCC
* *
50381777 CTAAACCTTAAATCC
1 CTAACCCCTAAATCC
50381792 C-AACCCCT-AATCC
1 CTAACCCCTAAATCC
* *
50381805 ATAATCCCTAAA
1 CTAACCCCTAAA
50381817 CCCATACTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
13 5 0.11
14 12 0.27
15 25 0.57
16 2 0.05
ACGTcount: A:0.36, C:0.43, G:0.00, T:0.21
Consensus pattern (15 bp):
CTAACCCCTAAATCC
Found at i:50382530 original size:114 final size:113
Alignment explanation
Indices: 50382113--50382643 Score: 644
Period size: 114 Copynumber: 4.7 Consensus size: 113
50382103 AGCATTTTTG
*
50382113 GCCGCTAAATCCCTGAAAGCTTAGAAAACGGCGTCGTTGGGCTTAGAATTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAG-ATTTTTTGCGGCGCTTTC
* * *
50382178 TCAAAAACGCCACTAAAGCCCTCAACATTAGCGGCGCTTTCTTAAAAAC
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * *
50382227 GCCACTAAATCCCTGAAAGCTCAGAAAACGGCATCGTTGGGCTCAGGTTTTTTACGGCGCTTTCT
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGATTTTTTGCGGCGCTTTCT
50382292 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAA-
66 CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* * * * * * * *
50382339 --CGCTAAATCCCCGAAAGCTAACAAAACAGCGTCGTCGGGTTTAGGATTTCTTGCGGCG-TTTT
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTA-GATTTTTTGCGGCGCTTTC
* * * * * *
50382401 TGAGGAAGCGCCGCTAAATCCCTGAGCATTAGCGACGCTTTAC-CAAAAAC
65 TCA-AAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTT-CTTAAAAAC
* * *
50382451 GCCGCTAAATCCCTGAAAGCTCACAAAACGGCGTCGTTGGGCTTAAGTTTTTTTGCGGCACTTTC
1 GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTT-AGATTTTTTGCGGCGCTTTC
* *
50382516 TCAAAAACGTCGCTAAAACCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
65 TCAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
* ** * * *
50382565 GCCTCTAAA-CCCTCGAAAGCTTGGGAAACGGTGTCGTTGGGCTTAG-GTTTTTGCGGCGCTTTC
1 GCCGCTAAATCCCT-GAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGATTTTTTGCGGCGCTTTC
*
50382628 TCAAAAATGCCGCTAA
65 TCAAAAACGCCGCTAA
50382644 TGCTTATTTT
Statistics
Matches: 353, Mismatches: 54, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
110 39 0.11
111 49 0.14
112 30 0.08
113 68 0.19
114 161 0.46
115 6 0.02
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.25
Consensus pattern (113 bp):
GCCGCTAAATCCCTGAAAGCTCAGAAAACGGCGTCGTTGGGCTTAGATTTTTTGCGGCGCTTTCT
CAAAAACGCCGCTAAAGCCCTGAGCATTAGCGGCGCTTTCTTAAAAAC
Found at i:50383581 original size:20 final size:20
Alignment explanation
Indices: 50383548--50383587 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
50383538 TTAACAAACT
*
50383548 TTTAATTATAATATAATATA
1 TTTAAGTATAATATAATATA
*
50383568 TTTAAGTATCATATAATATA
1 TTTAAGTATAATATAATATA
50383588 AATTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (20 bp):
TTTAAGTATAATATAATATA
Found at i:50384334 original size:21 final size:23
Alignment explanation
Indices: 50384281--50384330 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
50384271 TGTATGTGTT
50384281 ATAA-ATTATATAATATATAAAA
1 ATAACATTATATAATATATAAAA
*
50384303 GTAACATTATATAATATATTAAAA
1 ATAACATTATATAATATA-TAAAA
50384327 ATAA
1 ATAA
50384331 TATAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 3 0.12
23 13 0.54
24 8 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAACATTATATAATATATAAAA
Found at i:50407445 original size:57 final size:56
Alignment explanation
Indices: 50407357--50407463 Score: 135
Period size: 57 Copynumber: 1.9 Consensus size: 56
50407347 TCTAATTATG
* *
50407357 ATTTTTTTTTCACCCAATTACAAAAAATTACAAAATAGTCA-TCAAACTATTAGTAA
1 ATTTTTTTGTCACCCAATTACAAAAAATTACAAAATAATCACTC-AACTATTAGTAA
* ** *
50407413 ATTTTTTTGGTCACCTAATTATGAAAAGTTACAAAATAATCACTCAACTAT
1 ATTTTTTT-GTCACCCAATTACAAAAAATTACAAAATAATCACTCAACTAT
50407464 ATTGAATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
56 8 0.19
57 33 0.77
58 2 0.05
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (56 bp):
ATTTTTTTGTCACCCAATTACAAAAAATTACAAAATAATCACTCAACTATTAGTAA
Found at i:50416779 original size:20 final size:21
Alignment explanation
Indices: 50416725--50416784 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
50416715 GGTCGATCCG
50416725 AATTTAATT-TAAATAATATAA
1 AATTTAATTATAAA-AATATAA
*
50416746 ATATTT-TTTA-AAAAAT-TAA
1 A-ATTTAATTATAAAAATATAA
50416765 AATTTAATTATAAAAATATA
1 AATTTAATTATAAAAATATA
50416785 TTTTTAATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 10
0.73 0.05 0.23
Matches are distributed among these distances:
18 4 0.12
19 7 0.22
20 9 0.28
21 8 0.25
22 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
AATTTAATTATAAAAATATAA
Found at i:50417621 original size:19 final size:19
Alignment explanation
Indices: 50417592--50417635 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
50417582 AATTATTCTC
50417592 AAAATATTAATT-AAATAATT
1 AAAA-ATTAATTAAAATAA-T
50417612 AAAAATTAATTAAAATAAT
1 AAAAATTAATTAAAATAAT
50417631 AAAAA
1 AAAAA
50417636 AATTCTCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
AAAAATTAATTAAAATAAT
Found at i:50417636 original size:20 final size:19
Alignment explanation
Indices: 50417592--50417636 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
50417582 AATTATTCTC
*
50417592 AAAATATTAATTAAATAAT
1 AAAAAATTAATTAAATAAT
*
50417611 TAAAAATTAATTAAAATAAT
1 AAAAAATTAATT-AAATAAT
50417631 AAAAAA
1 AAAAAA
50417637 ATTCTCAACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAAATTAATTAAATAAT
Found at i:50419142 original size:108 final size:108
Alignment explanation
Indices: 50418953--50419168 Score: 414
Period size: 108 Copynumber: 2.0 Consensus size: 108
50418943 TTGCTCACCC
*
50418953 CTATTAGGTACACATGGTCAGTTACTTACTCAGAATCGAGGTAAGTCACACCATGAGCGTTACAA
1 CTATTAGGTACACATGGTCAGTTACTTACTCAGAATCGAGGTAAGTCACACCATGAGCGCTACAA
50419018 GTGAATAAATCCATAAACAAATCCAATATAAATTCTACTATTG
66 GTGAATAAATCCATAAACAAATCCAATATAAATTCTACTATTG
*
50419061 CTATTAGGTACACATGGTCAGTTACTTACTCAGCATCGAGGTAAGTCACACCATGAGCGCTACAA
1 CTATTAGGTACACATGGTCAGTTACTTACTCAGAATCGAGGTAAGTCACACCATGAGCGCTACAA
50419126 GTGAATAAATCCATAAACAAATCCAATATAAATTCTACTATTG
66 GTGAATAAATCCATAAACAAATCCAATATAAATTCTACTATTG
50419169 GGTCCAGTCC
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
108 106 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (108 bp):
CTATTAGGTACACATGGTCAGTTACTTACTCAGAATCGAGGTAAGTCACACCATGAGCGCTACAA
GTGAATAAATCCATAAACAAATCCAATATAAATTCTACTATTG
Done.