Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 171 of 206
Found at i:52082532 original size:41 final size:41
Alignment explanation
Indices: 52082468--52082607 Score: 185
Period size: 41 Copynumber: 3.4 Consensus size: 41
52082458 TCATTACTAA
* *
52082468 CCTTTTCGACCTTTTCA-TTGATAT-TTTCTTCAAATATCGT
1 CCTTTTCAACCTTTTCATTTGATATCTTT-TTCAGATATCGT
* * * * *
52082508 CATTTCCAACCTTTTTATTTGATATCCTTTTCGGATATCGT
1 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
*
52082549 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCAT
1 CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
52082590 CCTTTTCAACCTTTTCAT
1 CCTTTTCAACCTTTTCAT
52082608 AGATTCAGGA
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
40 13 0.15
41 70 0.82
42 2 0.02
ACGTcount: A:0.20, C:0.24, G:0.06, T:0.50
Consensus pattern (41 bp):
CCTTTTCAACCTTTTCATTTGATATCTTTTTCAGATATCGT
Found at i:52082807 original size:20 final size:20
Alignment explanation
Indices: 52082769--52082807 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
52082759 AGATATCAAT
*
52082769 TAATATTATAAATTCAAATG
1 TAATATTATAAAATCAAATG
* *
52082789 TAATATTTTAAAATGAAAT
1 TAATATTATAAAATCAAAT
52082808 ACGAACTTAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (20 bp):
TAATATTATAAAATCAAATG
Found at i:52086756 original size:17 final size:17
Alignment explanation
Indices: 52086715--52086757 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
52086705 AACAGAAGTT
52086715 TGCGAGCTCACCAAGAC
1 TGCGAGCTCACCAAGAC
* * *
52086732 TGCAAGCTCACCAATAG
1 TGCGAGCTCACCAAGAC
52086749 TGCGAGCTC
1 TGCGAGCTC
52086758 TTTACCTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.33, G:0.23, T:0.16
Consensus pattern (17 bp):
TGCGAGCTCACCAAGAC
Found at i:52092746 original size:11 final size:11
Alignment explanation
Indices: 52092730--52092760 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
52092720 TCATTCATTA
52092730 TTTTATTCAAT
1 TTTTATTCAAT
52092741 TTTTATTCAAT
1 TTTTATTCAAT
*
52092752 TTTCATTCA
1 TTTTATTCA
52092761 TTTAAGCCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTATTCAAT
Found at i:52093819 original size:30 final size:30
Alignment explanation
Indices: 52093781--52093850 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
52093771 TCCACCCTTA
* * *
52093781 AAATATTTACACTATTGATCCTTCAAATTTT
1 AAATATTTACACT-TTAACCCCTCAAATTTT
*
52093812 -CATATTTACACTTTAACCCCTCAAATTTT
1 AAATATTTACACTTTAACCCCTCAAATTTT
52093841 AAATATTTAC
1 AAATATTTAC
52093851 TCTTGGGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
29 14 0.42
30 19 0.58
ACGTcount: A:0.36, C:0.20, G:0.01, T:0.43
Consensus pattern (30 bp):
AAATATTTACACTTTAACCCCTCAAATTTT
Found at i:52119055 original size:23 final size:22
Alignment explanation
Indices: 52119012--52119055 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
52119002 ATATAAGTCG
52119012 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
52119035 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
52119056 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:52119257 original size:51 final size:50
Alignment explanation
Indices: 52119199--52119332 Score: 171
Period size: 50 Copynumber: 2.7 Consensus size: 50
52119189 TCGGTTCACA
* *
52119199 TAGTAGCCTGCACATAGTACTACACATGTGATCATTACCA-TCTGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGA-C-CTACCATTCCGATACACG
* * *
52119250 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCCGGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTACCATTCCGATACACG
* * *
52119300 TAGTAGCCTACACATAGTAGTACACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACATGTGACC
52119333 ATCACTTTCA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
49 4 0.05
50 39 0.53
51 30 0.41
ACGTcount: A:0.31, C:0.28, G:0.17, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCTACCATTCCGATACACG
Found at i:52125839 original size:29 final size:29
Alignment explanation
Indices: 52125806--52125865 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
52125796 CCACTACCTC
52125806 TATTGTTGCCT-TCAGATCTCCACACCCTT
1 TATTGTTGCCTCT-AGATCTCCACACCCTT
* *
52125835 TATTGTTGCCTCTGGATCTCCACACCTTT
1 TATTGTTGCCTCTAGATCTCCACACCCTT
52125864 TA
1 TA
52125866 GGGTTTCCTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.17, C:0.32, G:0.12, T:0.40
Consensus pattern (29 bp):
TATTGTTGCCTCTAGATCTCCACACCCTT
Found at i:52125875 original size:29 final size:29
Alignment explanation
Indices: 52125820--52125876 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
52125810 GTTGCCTTCA
**
52125820 GATCTCCACACCCTTTATTGTTGCCTCTG
1 GATCTCCACACCCTTTAGGGTTGCCTCTG
* *
52125849 GATCTCCACACCTTTTAGGGTTTCCTCT
1 GATCTCCACACCCTTTAGGGTTGCCTCT
52125877 TTTGGCTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.14, C:0.33, G:0.14, T:0.39
Consensus pattern (29 bp):
GATCTCCACACCCTTTAGGGTTGCCTCTG
Found at i:52126529 original size:23 final size:23
Alignment explanation
Indices: 52126503--52126548 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
52126493 GCGTAACTGC
52126503 TGTATAGTAATAGGGTGCCCGAA
1 TGTATAGTAATAGGGTGCCCGAA
* *
52126526 TGTATAGTTATAGGGTGCGCGAA
1 TGTATAGTAATAGGGTGCCCGAA
52126549 GCCCACCTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.11, G:0.33, T:0.28
Consensus pattern (23 bp):
TGTATAGTAATAGGGTGCCCGAA
Found at i:52128528 original size:20 final size:19
Alignment explanation
Indices: 52128503--52128672 Score: 85
Period size: 20 Copynumber: 8.5 Consensus size: 19
52128493 ACTTGTATGG
52128503 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTC-GTGCCTCT
*
52128523 GTTTGCACCTTCAATGCCTCT
1 GTTTGCA-CTTC-GTGCCTCT
* * *
52128544 ATTCT-CACTTTGGTGTCTCT
1 GTT-TGCAC-TTCGTGCCTCT
52128564 GTTTGCACTCTCGTGCCTCT
1 GTTTGCACT-TCGTGCCTCT
* * *
52128584 GATTGCA-TAATCTTGACTCT
1 GTTTGCACT--TCGTGCCTCT
* * *
52128604 GTTTGTACTCCAGTACCTCT
1 GTTTGCACTTC-GTGCCTCT
**
52128624 AATTGCA-TAATCGTGCCTCT
1 GTTTGCACT--TCGTGCCTCT
* *
52128644 ATTTGCACTACAGTGCCTCT
1 GTTTGCACTTC-GTGCCTCT
52128664 GTTTGCACT
1 GTTTGCACT
52128673 CCAGATCCCC
Statistics
Matches: 111, Mismatches: 27, Indels: 24
0.69 0.17 0.15
Matches are distributed among these distances:
19 6 0.05
20 84 0.76
21 20 0.18
22 1 0.01
ACGTcount: A:0.15, C:0.28, G:0.17, T:0.40
Consensus pattern (19 bp):
GTTTGCACTTCGTGCCTCT
Found at i:52128540 original size:21 final size:20
Alignment explanation
Indices: 52128503--52128543 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
52128493 ACTTGTATGG
**
52128503 GTTTGCACTTCGGTGCCTCT
1 GTTTGCACTTCAATGCCTCT
52128523 GTTTGCACCTTCAATGCCTCT
1 GTTTGCA-CTTCAATGCCTCT
52128544 ATTCTCACTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.10, C:0.32, G:0.20, T:0.39
Consensus pattern (20 bp):
GTTTGCACTTCAATGCCTCT
Found at i:52128604 original size:40 final size:39
Alignment explanation
Indices: 52128560--52128670 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 39
52128550 ACTTTGGTGT
*
52128560 CTCTGTTTGCACTCTCGTGCCTCTGATTGCATAATCTTGA
1 CTCTGTTTGCACTC-CGTGCCTCTGATTGCATAATCGTGA
* * * *
52128600 CTCTGTTTGTACTCCAGTACCTCTAATTGCATAATCGTGC
1 CTCTGTTTGCACTCC-GTGCCTCTGATTGCATAATCGTGA
* * *
52128640 CTCTATTTGCACTACAGTGCCTCTGTTTGCA
1 CTCTGTTTGCACT-CCGTGCCTCTGATTGCA
52128671 CTCCAGATCC
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
39 1 0.02
40 56 0.97
41 1 0.02
ACGTcount: A:0.17, C:0.28, G:0.16, T:0.39
Consensus pattern (39 bp):
CTCTGTTTGCACTCCGTGCCTCTGATTGCATAATCGTGA
Found at i:52136515 original size:16 final size:16
Alignment explanation
Indices: 52136494--52136525 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52136484 GTTTTGTTGC
*
52136494 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
52136510 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
52136526 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:52136816 original size:51 final size:52
Alignment explanation
Indices: 52136746--52136945 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 52
52136736 TTAATGATAT
* * * *
52136746 CGGTTCACATAGTAGCCTGCACATAGTACTACACATGTGATC-ATCACTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCGATCACTATC
* * *
52136797 CGATACACGTAGTATCCTGCACATAGTACTACACACGTGATCGA--AGCTATC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCGATCA-CTATC
* * * * * * *
52136848 CGGTACGCATAGTAGCCTACAGATAGTACTACACATGCGACCTATCA-T-TC
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCGATCACTATC
*
52136898 TGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACT
1 CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCGATCACT
52136946 TTCACTTTCA
Statistics
Matches: 122, Mismatches: 22, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
49 4 0.03
50 39 0.32
51 77 0.63
52 1 0.01
53 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.24
Consensus pattern (52 bp):
CGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGACCGATCACTATC
Found at i:52136929 original size:101 final size:102
Alignment explanation
Indices: 52136753--52136937 Score: 284
Period size: 101 Copynumber: 1.8 Consensus size: 102
52136743 TATCGGTTCA
* * * *
52136753 CATAGTAGCCTGCACATAGTACTACACATGTGATCATCACTATCCGATACACGTAGTATCCTGCA
1 CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
52136818 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * *
52136855 CATAGTAGCCTACAGATAGTACTACACATGCGACCTATCA-T-TCTGGTACACGTAGTAGCCTGC
1 CATAGTAGCCTACACATAGTACTACACATGCGACC-ATCACTATCCGATACACGTAGTAGCCTGC
52136918 ACATAGTACTACACACGTGA
65 ACATAGTACTACACACGTGA
52136938 CCATCACTTT
Statistics
Matches: 75, Mismatches: 7, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
101 39 0.52
102 32 0.43
103 4 0.05
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (102 bp):
CATAGTAGCCTACACATAGTACTACACATGCGACCATCACTATCCGATACACGTAGTAGCCTGCA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:52147317 original size:2 final size:2
Alignment explanation
Indices: 52147310--52147341 Score: 55
Period size: 2 Copynumber: 15.5 Consensus size: 2
52147300 ATACATGTAA
52147310 AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
52147342 AACCTTCTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52148262 original size:19 final size:20
Alignment explanation
Indices: 52148240--52148279 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
52148230 TTCTATCCAT
52148240 AAAATAT-TAAACCATAATC
1 AAAATATCTAAACCATAATC
52148259 AAAATATGCCTAAACCATAAT
1 AAAATAT--CTAAACCATAAT
52148280 TCACTCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
22 11 0.61
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (20 bp):
AAAATATCTAAACCATAATC
Found at i:52149020 original size:43 final size:43
Alignment explanation
Indices: 52148935--52149094 Score: 173
Period size: 43 Copynumber: 3.7 Consensus size: 43
52148925 TTCGTACAAC
* * * * *
52148935 GCCAACGTCCCAGACGTGATCTTACATGTAATCAC-AGATCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGAAAACACAAG-TCGAT
* * *
52148978 GCC-GCTATCTCGGACAG-GGTCTTACACGAAAACACAAGTCGAT
1 GCCAAC-ATCCCAGAC-GTGGTCTTACACGAAAACACAAGTCGAT
* *
52149021 GCCAACGTCCCAGACGTGGTCTTACAGGAAAACACAAGTCGAT
1 GCCAACATCCCAGACGTGGTCTTACACGAAAACACAAGTCGAT
*
52149064 GCCAACGTCCCAGACGTGGTCTTACACGAAA
1 GCCAACATCCCAGACGTGGTCTTACACGAAA
52149095 TCACTTATCA
Statistics
Matches: 98, Mismatches: 14, Indels: 10
0.80 0.11 0.08
Matches are distributed among these distances:
42 2 0.02
43 92 0.94
44 4 0.04
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (43 bp):
GCCAACATCCCAGACGTGGTCTTACACGAAAACACAAGTCGAT
Found at i:52149085 original size:86 final size:86
Alignment explanation
Indices: 52148935--52149094 Score: 200
Period size: 86 Copynumber: 1.9 Consensus size: 86
52148925 TTCGTACAAC
* * * * * *
52148935 GCCAACGTCCCAGACGTGATCTTACATGTAATCACAGATCGATGCCGCTATCTCGGACAGGGTCT
1 GCCAACGTCCCAGACGTGATCTTACAGGAAAACACAGATCGATGCCACTATCCCAGACAGGGTCT
52149000 TACACGAAAACACAAGTCGAT
66 TACACGAAAACACAAGTCGAT
* *
52149021 GCCAACGTCCCAGACGTGGTCTTACAGGAAAACACA-AGTCGATGCCAAC-GTCCCAGAC-GTGG
1 GCCAACGTCCCAGACGTGATCTTACAGGAAAACACAGA-TCGATGCC-ACTATCCCAGACAG-GG
52149083 TCTTACACGAAA
63 TCTTACACGAAA
52149095 TCACTTATCA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
85 2 0.03
86 60 0.95
87 1 0.02
ACGTcount: A:0.31, C:0.29, G:0.22, T:0.19
Consensus pattern (86 bp):
GCCAACGTCCCAGACGTGATCTTACAGGAAAACACAGATCGATGCCACTATCCCAGACAGGGTCT
TACACGAAAACACAAGTCGAT
Found at i:52155255 original size:26 final size:26
Alignment explanation
Indices: 52155166--52155257 Score: 121
Period size: 26 Copynumber: 3.5 Consensus size: 26
52155156 CATTAGGGCA
*
52155166 TAGCAGGCTTCGAGTTGGTGTATATT
1 TAGCAGGCTTCGAGCTGGTGTATATT
* * *
52155192 TAGCTGGCTTTGAGCTGGTGTATTTT
1 TAGCAGGCTTCGAGCTGGTGTATATT
* * *
52155218 TAGTAGGTTTCGTGCTGGTGTATATT
1 TAGCAGGCTTCGAGCTGGTGTATATT
52155244 TAGCAGGCTTCGAG
1 TAGCAGGCTTCGAG
52155258 TCGTTGTTTT
Statistics
Matches: 53, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (26 bp):
TAGCAGGCTTCGAGCTGGTGTATATT
Found at i:52160218 original size:37 final size:37
Alignment explanation
Indices: 52160176--52160282 Score: 104
Period size: 37 Copynumber: 3.1 Consensus size: 37
52160166 TAATATAATT
52160176 TTAATAGTTTAATATTAAATTTAATTTAATATTTATC
1 TTAATAGTTTAATATTAAATTTAATTTAATATTTATC
* * *
52160213 TTAATAGTATT-TTATT-AATTTAATATTAA-A-GTA-A
1 TTAATAGT-TTAATATTAAATTTAAT-TTAATATTTATC
*
52160247 TT-AT--TTTAATATTAAATTTAATTTAATGTTTATC
1 TTAATAGTTTAATATTAAATTTAATTTAATATTTATC
52160281 TT
1 TT
52160283 GTAGATAAAC
Statistics
Matches: 56, Mismatches: 7, Indels: 17
0.70 0.09 0.21
Matches are distributed among these distances:
30 2 0.04
31 9 0.16
32 8 0.14
33 4 0.07
34 4 0.07
35 2 0.04
36 9 0.16
37 16 0.29
38 2 0.04
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (37 bp):
TTAATAGTTTAATATTAAATTTAATTTAATATTTATC
Found at i:52162400 original size:94 final size:90
Alignment explanation
Indices: 52162285--52162456 Score: 238
Period size: 94 Copynumber: 1.9 Consensus size: 90
52162275 ACATATATTA
*** * *
52162285 AATTTGGTTAATTCGGTTAATTTTTTT-TATCTTTTTATACTTGTTTTAACCAAAAAACAAAAAA
1 AATTTGGTTAATTCAACTAATTTTTTTATAT-GTGTTATACTTGTTTTAACC--AAAA-AAAAAA
52162349 AAATATAAATTTTGGTTATTTCATTCGATT
62 AAATATAAA-TTTGGTTATTTCATTCGATT
*
52162379 AATTTGGTTAATTCAACTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAATAAAAAAT
1 AATTTGGTTAATTCAACTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAAAAAAAAAT
52162444 ATAAATTTGGTTA
66 ATAAATTTGGTTA
52162457 AATCGACCGA
Statistics
Matches: 71, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
90 8 0.11
91 14 0.20
92 4 0.06
94 42 0.59
95 3 0.04
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (90 bp):
AATTTGGTTAATTCAACTAATTTTTTTATATGTGTTATACTTGTTTTAACCAAAAAAAAAAAAAT
ATAAATTTGGTTATTTCATTCGATT
Found at i:52163199 original size:27 final size:27
Alignment explanation
Indices: 52163159--52163211 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
52163149 GCAATCAGTA
*
52163159 TAGTCCGCTGAGACAGTAAACATGAGG
1 TAGTCCGCTAAGACAGTAAACATGAGG
* *
52163186 TAGTCTGCTAAGACATTAAACATGAG
1 TAGTCCGCTAAGACAGTAAACATGAG
52163212 AATTTAGGTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.25, T:0.23
Consensus pattern (27 bp):
TAGTCCGCTAAGACAGTAAACATGAGG
Found at i:52168852 original size:13 final size:13
Alignment explanation
Indices: 52168836--52168877 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
52168826 AAAAATGATT
52168836 ATAAATATCATTA
1 ATAAATATCATTA
*
52168849 ATAACA-ATGATT-
1 ATAA-ATATCATTA
52168861 ATAAATATCATTA
1 ATAAATATCATTA
52168874 ATAA
1 ATAA
52168878 CATCACAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
11 1 0.04
12 9 0.38
13 13 0.54
14 1 0.04
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (13 bp):
ATAAATATCATTA
Found at i:52168858 original size:25 final size:25
Alignment explanation
Indices: 52168822--52168879 Score: 102
Period size: 25 Copynumber: 2.4 Consensus size: 25
52168812 ATAGAAATAA
52168822 ATTAA-AA-AATGATTATAAATATC
1 ATTAATAACAATGATTATAAATATC
52168845 ATTAATAACAATGATTATAAATATC
1 ATTAATAACAATGATTATAAATATC
52168870 ATTAATAACA
1 ATTAATAACA
52168880 TCACAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 5 0.15
24 2 0.06
25 26 0.79
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.34
Consensus pattern (25 bp):
ATTAATAACAATGATTATAAATATC
Found at i:52170413 original size:18 final size:17
Alignment explanation
Indices: 52170375--52170424 Score: 64
Period size: 18 Copynumber: 2.9 Consensus size: 17
52170365 TGTATTATAA
52170375 TATTAATTAATAAAAAT
1 TATTAATTAATAAAAAT
* *
52170392 TATTAGTTATTAAAATAT
1 TATTAATTAATAAAA-AT
*
52170410 TATTATTTAATAAAA
1 TATTAATTAATAAAA
52170425 GTTTAGGGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 13 0.46
18 15 0.54
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
TATTAATTAATAAAAAT
Found at i:52181567 original size:31 final size:31
Alignment explanation
Indices: 52181529--52181589 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52181519 GGCCCATTTT
52181529 TATTTTAAAAAT-TTTAAAAAATTAAAAAAAG
1 TATTTTAAAAATATTT-AAAAATTAAAAAAAG
*
52181560 TATTTTAAAAATATTTTAAAATTAAAAAAA
1 TATTTTAAAAATATTTAAAAATTAAAAAAA
52181590 TTAAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 25 0.89
32 3 0.11
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.38
Consensus pattern (31 bp):
TATTTTAAAAATATTTAAAAATTAAAAAAAG
Found at i:52181569 original size:11 final size:11
Alignment explanation
Indices: 52181529--52181689 Score: 59
Period size: 11 Copynumber: 15.8 Consensus size: 11
52181519 GGCCCATTTT
52181529 TATTTT-AAAA
1 TATTTTAAAAA
52181539 -ATTTTAAAAA
1 TATTTTAAAAA
**
52181549 -ATTAAAAAAA
1 TATTTTAAAAA
52181559 GTATTTTAAAAA
1 -TATTTTAAAAA
52181571 TATTTT--AAA
1 TATTTTAAAAA
52181580 -A--TTAAAAA
1 TATTTTAAAAA
* **
52181588 AATTAAAAAAAAA
1 TATT--TTAAAAA
52181601 TATTTTAAAAA
1 TATTTTAAAAA
52181612 TATTTT--AAA
1 TATTTTAAAAA
52181621 -A--TTAAAAA
1 TATTTTAAAAA
* *
52181629 AATTTAAAAAAA
1 TATTT-TAAAAA
52181641 TATTTT--AAA
1 TATTTTAAAAA
52181650 -A-TTTAAAAA
1 TATTTTAAAAA
* **
52181659 AATTAAAAAAA
1 TATTTTAAAAA
* *
52181670 TATGTAAAAAA
1 TATTTTAAAAA
52181681 TATTTTAAA
1 TATTTTAAA
52181690 TTTTAAAAAA
Statistics
Matches: 112, Mismatches: 19, Indels: 39
0.66 0.11 0.23
Matches are distributed among these distances:
6 4 0.04
7 3 0.03
8 9 0.08
9 19 0.17
10 13 0.12
11 39 0.35
12 17 0.15
13 8 0.07
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:52181589 original size:41 final size:40
Alignment explanation
Indices: 52181529--52181689 Score: 186
Period size: 40 Copynumber: 4.0 Consensus size: 40
52181519 GGCCCATTTT
**
52181529 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAAATTAAAAAAA-TATTTTAAAAA
52181571 TATTTTAAAATT-AAAAAAATTAAAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAAATT--AAAAAAATATTTTAAAAA
*
52181612 TATTTTAAAATTAAAAAAATTTAAAAAAATATTTT-AAAA
1 TATTTTAAAATTAAAAAAAATTAAAAAAATATTTTAAAAA
**
52181651 T-TTAAAAAAATTAAAAAAATATGT-AAAAAATATTTTAAA
1 TATT-TTAAAATTAAAAAAA-AT-TAAAAAAATATTTTAAA
52181690 TTTTAAAAAA
Statistics
Matches: 107, Mismatches: 5, Indels: 15
0.84 0.04 0.12
Matches are distributed among these distances:
38 2 0.02
39 18 0.17
40 34 0.32
41 32 0.30
42 21 0.20
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAAATTAAAAAAATATTTTAAAAA
Found at i:52181594 original size:40 final size:40
Alignment explanation
Indices: 52181529--52181689 Score: 200
Period size: 41 Copynumber: 4.0 Consensus size: 40
52181519 GGCCCATTTT
* *
52181529 TATTTTAAAAATTTTAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAA-TTAAAAAAATTAAAAAAAATATTTTAAAAA
52181571 TATTTTAAAATTAAAAAAATTAAAAAAAAATATTTTAAAAA
1 TATTTTAAAATTAAAAAAATT-AAAAAAAATATTTTAAAAA
*
52181612 TATTTTAAAATTAAAAAAATTTAAAAAAATATTTT-AAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAATATTTTAAAAA
** **
52181651 T-TTAAAAAAATTAAAAAAATATGTAAAAAATATTTTAAA
1 TATT-TTAAAATTAAAAAAAT-TAAAAAAAATATTTTAAA
52181690 TTTTAAAAAA
Statistics
Matches: 108, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.02
39 19 0.18
40 36 0.33
41 45 0.42
42 6 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAATATTTTAAAAA
Found at i:52181595 original size:8 final size:9
Alignment explanation
Indices: 52181577--52181670 Score: 52
Period size: 9 Copynumber: 10.6 Consensus size: 9
52181567 AAAATATTTT
52181577 AAAATTAAA
1 AAAATTAAA
52181586 AAAATT-AA
1 AAAATTAAA
52181594 AAAA--AAA
1 AAAATTAAA
* **
52181601 TATTTTAAA
1 AAAATTAAA
* **
52181610 AATATTTTA
1 AAAATTAAA
52181619 -AAATTAAA
1 AAAATTAAA
52181627 AAAATTTAAAA
1 AAAA-TT-AAA
**
52181638 AAATATTTTA
1 AAA-ATTAAA
*
52181648 AAATTTAAA
1 AAAATTAAA
52181657 AAAATTAAA
1 AAAATTAAA
52181666 AAAAT
1 AAAAT
52181671 ATGTAAAAAA
Statistics
Matches: 62, Mismatches: 16, Indels: 14
0.67 0.17 0.15
Matches are distributed among these distances:
7 3 0.05
8 11 0.18
9 33 0.53
10 6 0.10
11 8 0.13
12 1 0.02
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAATTAAA
Found at i:52181652 original size:20 final size:20
Alignment explanation
Indices: 52181627--52181702 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
52181617 TAAAATTAAA
52181627 AAAATTTAAAAAAATATTTT
1 AAAATTTAAAAAAATATTTT
***
52181647 AAAATTTAAAAAAAT-TAAA
1 AAAATTTAAAAAAATATTTT
52181666 AAAATATGT-AAAAAATATTTT
1 AAAAT-T-TAAAAAAATATTTT
*
52181687 AAATTTTAAAAAAATA
1 AAAATTTAAAAAAATA
52181703 AATATATTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 8
0.75 0.12 0.13
Matches are distributed among these distances:
19 7 0.16
20 32 0.71
21 6 0.13
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.34
Consensus pattern (20 bp):
AAAATTTAAAAAAATATTTT
Found at i:52181679 original size:29 final size:29
Alignment explanation
Indices: 52181607--52181672 Score: 116
Period size: 29 Copynumber: 2.3 Consensus size: 29
52181597 AAAATATTTT
52181607 AAAAATATTTTAAAATTAAAAAAATTTAA
1 AAAAATATTTTAAAATTAAAAAAATTTAA
52181636 AAAAATATTTTAAAATTTAAAAAAA-TTAA
1 AAAAATATTTTAAAA-TTAAAAAAATTTAA
52181665 AAAAATAT
1 AAAAATAT
52181673 GTAAAAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
29 27 0.75
30 9 0.25
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (29 bp):
AAAAATATTTTAAAATTAAAAAAATTTAA
Found at i:52203762 original size:79 final size:79
Alignment explanation
Indices: 52203631--52203789 Score: 318
Period size: 79 Copynumber: 2.0 Consensus size: 79
52203621 AGAAAGTGGC
52203631 TAGTGTCTAGAGTAGGAATTACAGTTACCTTACCCATTTAGGCTCTAATTAACCTGCTAGTGCAT
1 TAGTGTCTAGAGTAGGAATTACAGTTACCTTACCCATTTAGGCTCTAATTAACCTGCTAGTGCAT
52203696 CACTAATGAAGGTA
66 CACTAATGAAGGTA
52203710 TAGTGTCTAGAGTAGGAATTACAGTTACCTTACCCATTTAGGCTCTAATTAACCTGCTAGTGCAT
1 TAGTGTCTAGAGTAGGAATTACAGTTACCTTACCCATTTAGGCTCTAATTAACCTGCTAGTGCAT
52203775 CACTAATGAAGGTA
66 CACTAATGAAGGTA
52203789 T
1 T
52203790 CTCAACTTTG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
79 80 1.00
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (79 bp):
TAGTGTCTAGAGTAGGAATTACAGTTACCTTACCCATTTAGGCTCTAATTAACCTGCTAGTGCAT
CACTAATGAAGGTA
Found at i:52204510 original size:15 final size:15
Alignment explanation
Indices: 52204490--52204519 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52204480 TTTCATTTGG
52204490 CCCTCTAAGCAGTAA
1 CCCTCTAAGCAGTAA
52204505 CCCTCTAAGCAGTAA
1 CCCTCTAAGCAGTAA
52204520 ATAGTTAAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.33, G:0.13, T:0.20
Consensus pattern (15 bp):
CCCTCTAAGCAGTAA
Found at i:52206594 original size:21 final size:21
Alignment explanation
Indices: 52206570--52206610 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
52206560 TTAATTGGGG
52206570 AAAGGTATGAAATTTCCCTCC
1 AAAGGTATGAAATTTCCCTCC
52206591 AAAGGTATGAAATTTCCCTC
1 AAAGGTATGAAATTTCCCTC
52206611 TAAATAGAAA
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:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (21 bp):
AAAGGTATGAAATTTCCCTCC
Found at i:52206823 original size:2 final size:2
Alignment explanation
Indices: 52206816--52206846 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
52206806 TACATGTTTC
52206816 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
52206847 AAGCTTTAGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:52206976 original size:21 final size:21
Alignment explanation
Indices: 52206951--52206992 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
52206941 ACGAAAAGCT
*
52206951 CCTCTTGTGAAACTAAAGCAA
1 CCTCTTGCGAAACTAAAGCAA
52206972 CCTCTTGCGAAACTAAAGCAA
1 CCTCTTGCGAAACTAAAGCAA
52206993 TCATTTAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.38, C:0.26, G:0.14, T:0.21
Consensus pattern (21 bp):
CCTCTTGCGAAACTAAAGCAA
Found at i:52212018 original size:61 final size:61
Alignment explanation
Indices: 52211938--52212056 Score: 238
Period size: 61 Copynumber: 2.0 Consensus size: 61
52211928 ACTGATAGGG
52211938 TGCTTCGTCGATCTTCCAAGCCTTCTCTATACACAAATATCGACTGCAATGCACTATCAGT
1 TGCTTCGTCGATCTTCCAAGCCTTCTCTATACACAAATATCGACTGCAATGCACTATCAGT
52211999 TGCTTCGTCGATCTTCCAAGCCTTCTCTATACACAAATATCGACTGCAATGCACTATC
1 TGCTTCGTCGATCTTCCAAGCCTTCTCTATACACAAATATCGACTGCAATGCACTATC
52212057 TGCCGCTGTC
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 58 1.00
ACGTcount: A:0.26, C:0.30, G:0.13, T:0.31
Consensus pattern (61 bp):
TGCTTCGTCGATCTTCCAAGCCTTCTCTATACACAAATATCGACTGCAATGCACTATCAGT
Found at i:52215104 original size:19 final size:19
Alignment explanation
Indices: 52215082--52215134 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
52215072 ATACAAGGGG
*
52215082 ACTTTACCGATACAAGTCC
1 ACTTTACCCATACAAGTCC
* *
52215101 ACTTTTA-CTATACAGGTCC
1 AC-TTTACCCATACAAGTCC
52215120 ACTTCTACCCATACA
1 ACTT-TACCCATACA
52215135 TCTTGTGAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 2 0.07
19 16 0.57
20 10 0.36
ACGTcount: A:0.30, C:0.32, G:0.08, T:0.30
Consensus pattern (19 bp):
ACTTTACCCATACAAGTCC
Found at i:52215320 original size:9 final size:9
Alignment explanation
Indices: 52215306--52215336 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
52215296 AAGCCTTCAA
52215306 TTCTTTATT
1 TTCTTTATT
52215315 TTCTTTATT
1 TTCTTTATT
52215324 TTCTTTATT
1 TTCTTTATT
52215333 TTCT
1 TTCT
52215337 CTTGTATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (9 bp):
TTCTTTATT
Found at i:52215563 original size:28 final size:29
Alignment explanation
Indices: 52215520--52215574 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
52215510 GATTGTAAAA
*
52215520 GGTTTCTAGTTGAGCCACAAAAGCTAGAT
1 GGTTTCTAGTTGAGCCACAAAAACTAGAT
* *
52215549 GGTTT-TAGTTTAGCCATAAAAACTAG
1 GGTTTCTAGTTGAGCCACAAAAACTAG
52215575 GGGAGAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.31
Consensus pattern (29 bp):
GGTTTCTAGTTGAGCCACAAAAACTAGAT
Found at i:52226506 original size:17 final size:18
Alignment explanation
Indices: 52226480--52226521 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
52226470 ATCAAAACTA
*
52226480 TATAAGATATT-TGTTAT
1 TATAAAATATTATGTTAT
*
52226497 TATAAAATATTATTTTAT
1 TATAAAATATTATGTTAT
52226515 TATAAAA
1 TATAAAA
52226522 CAAATTTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.45
18 12 0.55
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TATAAAATATTATGTTAT
Found at i:52226530 original size:17 final size:18
Alignment explanation
Indices: 52226493--52226530 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
52226483 AAGATATTTG
* *
52226493 TTATTATAAAATATTATT
1 TTATTATAAAACATAATT
52226511 TTATTATAAAACA-AATT
1 TTATTATAAAACATAATT
52226528 TTA
1 TTA
52226531 GTTGTCAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (18 bp):
TTATTATAAAACATAATT
Found at i:52226672 original size:2 final size:2
Alignment explanation
Indices: 52226667--52226695 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
52226657 TCAACTTTTC
52226667 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
52226696 TAAGGGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:52227360 original size:87 final size:88
Alignment explanation
Indices: 52227242--52227413 Score: 224
Period size: 87 Copynumber: 2.0 Consensus size: 88
52227232 CTTGAAGACG
** *
52227242 TATCATATTTAGAAAAGGAACATATTATTAAA-TTTCTTCCATG-ATCTACCATTTCTATTCATT
1 TATCATATTTAGAAAAAAAACATATTATTAAATTTTC-TCAATGAAT-TACCATTTCTATTCATT
52227305 GTCTTTTCAATATCAATCAAAGTGA
64 GTCTTTTCAATATCAATCAAAGTGA
* ** * *
52227330 TATCATATTT-GAAAAAAAACATATTTTTAAATTTTCTCAATGAATTATTATTTTTATTCGTTGT
1 TATCATATTTAGAAAAAAAACATATTATTAAATTTTCTCAATGAATTACCATTTCTATTCATTGT
*
52227394 GTTTTCAATATCAATCAAAG
66 CTTTTCAATATCAATCAAAG
52227414 CGATCATTCC
Statistics
Matches: 73, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
87 57 0.78
88 16 0.22
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (88 bp):
TATCATATTTAGAAAAAAAACATATTATTAAATTTTCTCAATGAATTACCATTTCTATTCATTGT
CTTTTCAATATCAATCAAAGTGA
Found at i:52227942 original size:89 final size:87
Alignment explanation
Indices: 52227782--52227953 Score: 247
Period size: 89 Copynumber: 2.0 Consensus size: 87
52227772 GGAATTATTA
* * *
52227782 TTTGATGATATTGAAAAGACAATGAATAGAAATGGTAGATCATTGAGGAAATTAAAAAAATATAT
1 TTTGATGATATTGAAAAAACAATAAATAAAAATGGTAGATCATTGAGGAAATTAAAAAAATATAT
*
52227847 TCTTTTTCCAAATATGATATCAC
66 CCTTTTT-CAAATATGATATCAC
* * *
52227870 TTTGATTGATATTGAAAAAACAATAAATAAAAATGGTAGATCATTGAGGAAATT-TAAAACTATG
1 TTTGA-TGATATTGAAAAAACAATAAATAAAAATGGTAGATCATTGAGGAAATTAAAAAAATATA
52227934 TCCTTTTTTCAAATATGATA
65 TCC-TTTTTCAAATATGATA
52227954 CATCTTCAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 25 0.33
89 50 0.67
ACGTcount: A:0.44, C:0.08, G:0.14, T:0.34
Consensus pattern (87 bp):
TTTGATGATATTGAAAAAACAATAAATAAAAATGGTAGATCATTGAGGAAATTAAAAAAATATAT
CCTTTTTCAAATATGATATCAC
Found at i:52230390 original size:23 final size:23
Alignment explanation
Indices: 52230360--52230409 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
52230350 AAACTTACCG
52230360 AACA-TATTAAATTAAACAACCA
1 AACATTATTAAATTAAACAACCA
52230382 AACATTATTAAATTAAACAACCA
1 AACATTATTAAATTAAACAACCA
52230405 AACAT
1 AACAT
52230410 ACTTTCACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 4 0.15
23 23 0.85
ACGTcount: A:0.58, C:0.18, G:0.00, T:0.24
Consensus pattern (23 bp):
AACATTATTAAATTAAACAACCA
Found at i:52230566 original size:2 final size:2
Alignment explanation
Indices: 52230561--52230595 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
52230551 ACACACACAC
52230561 AT AT AT AT AT AT AT AT AT 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
52230596 CTACTACTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:52230827 original size:2 final size:2
Alignment explanation
Indices: 52230822--52230855 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
52230812 ACACACACAC
52230822 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52230856 CCATTACACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52231198 original size:41 final size:41
Alignment explanation
Indices: 52231141--52231357 Score: 265
Period size: 41 Copynumber: 5.3 Consensus size: 41
52231131 ATACAAATTA
* * * *
52231141 CCTGACACAATACACTGGTACAAAGCCTGCTAGGCTCAAGG
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
* ** *
52231182 CCTGATACAATACACTGATACGAAGCCTACTAGGCTCACA-G
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCA-AGG
*
52231223 CCTGATACAATACACCGGCATGAAGCCTGCTAGGCTCAAGG
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
* * * *
52231264 CCTGATATAATACACCGACACAAAGCCTGCTAGGCTCAAGT
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
* * *
52231305 CCTGATACAATAGACCAGCACGAAGCCTACTAGGCTCAAGG
1 CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
*
52231346 CCTGACACAATA
1 CCTGATACAATA
52231358 TCTCCGGTAT
Statistics
Matches: 152, Mismatches: 22, Indels: 4
0.85 0.12 0.02
Matches are distributed among these distances:
40 1 0.01
41 150 0.99
42 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (41 bp):
CCTGATACAATACACCGGCACGAAGCCTGCTAGGCTCAAGG
Found at i:52239251 original size:30 final size:29
Alignment explanation
Indices: 52239205--52239289 Score: 77
Period size: 30 Copynumber: 2.9 Consensus size: 29
52239195 GTTAGTATTT
*
52239205 AATTAATTTTTTAAAATTTTAAAAATTCAA
1 AATT-ATTTTTAAAAATTTTAAAAATTCAA
* *
52239235 AATATATTTTTAAAAA--TGAAAAATTATTAA
1 AAT-TATTTTTAAAAATTTTAAAAA-T-TCAA
*
52239265 AATTA-TTTTAAAATTTTTAAAAATT
1 AATTATTTTTAAAAATTTTAAAAATT
52239290 AATTAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
28 15 0.33
29 4 0.09
30 25 0.56
31 1 0.02
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (29 bp):
AATTATTTTTAAAAATTTTAAAAATTCAA
Found at i:52239262 original size:20 final size:21
Alignment explanation
Indices: 52239221--52239262 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
52239211 TTTTTTAAAA
**
52239221 TTTTAAAAATTCAAAATATAT
1 TTTTAAAAATGAAAAATATAT
52239242 TTTTAAAAATGAAAAAT-TAT
1 TTTTAAAAATGAAAAATATAT
52239262 T
1 T
52239263 AAAATTATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (21 bp):
TTTTAAAAATGAAAAATATAT
Found at i:52239290 original size:30 final size:29
Alignment explanation
Indices: 52239209--52239296 Score: 85
Period size: 28 Copynumber: 3.0 Consensus size: 29
52239199 GTATTTAATT
*
52239209 AATT-TTTTAAAATTTTAAAAA-T-TCAA
1 AATTATTTTAAAATTTTAAAAATTATTAA
* *
52239235 AATATATTTTTAAAA-ATGAAAAATTATTAA
1 AAT-TA-TTTTAAAATTTTAAAAATTATTAA
52239265 AATTATTTTAAAATTTTTAAAAATTAATTAA
1 AATTATTTTAAAA-TTTTAAAAATT-ATTAA
52239296 A
1 A
52239297 TAATAACATG
Statistics
Matches: 49, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
26 3 0.06
27 1 0.02
28 14 0.29
29 11 0.22
30 14 0.29
31 6 0.12
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (29 bp):
AATTATTTTAAAATTTTAAAAATTATTAA
Found at i:52239295 original size:20 final size:20
Alignment explanation
Indices: 52239254--52239296 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
52239244 TTAAAAATGA
*
52239254 AAAATTATTAAAATTATTTT
1 AAAATTATTAAAATTATATT
*
52239274 AAAATTTTTAAAAATTA-ATT
1 AAAATTATT-AAAATTATATT
52239294 AAA
1 AAA
52239297 TAATAACATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAATTATTAAAATTATATT
Found at i:52241987 original size:48 final size:49
Alignment explanation
Indices: 52241885--52242020 Score: 193
Period size: 48 Copynumber: 2.8 Consensus size: 49
52241875 AATCTATAAA
* * * *
52241885 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTAAAACCACTT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTT-C-GAAAAACCACAT
* *
52241936 CCTCCACCTGTTCCAATCTACAAACCTCCACCAGTT-GAAAAACCACAT
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCGAAAAACCACAT
52241984 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTC
1 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTC
52242021 CAGTATACAA
Statistics
Matches: 76, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
48 44 0.58
51 32 0.42
ACGTcount: A:0.28, C:0.40, G:0.07, T:0.24
Consensus pattern (49 bp):
CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCGAAAAACCACAT
Found at i:52242023 original size:24 final size:24
Alignment explanation
Indices: 52241864--52242024 Score: 112
Period size: 24 Copynumber: 6.6 Consensus size: 24
52241854 TCCCGTAAAC
* *
52241864 CCACCTGTTCCAATCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
52241888 CCACCAGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
* *
52241912 CCTCCAGTTCCAG--TAAAACCACTTCCT
1 CCACCAGTTCCAGTCTATAA--A---CCT
* * *
52241939 CCACCTGTTCCAATCTACAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
** ** * * *
52241963 CCACCAGTTGAAAAACCA-CATCCT
1 CCACCAGTT-CCAGTCTATAAACCT
*
52241987 CCACCTGTTCCAGTCTATAAACCT
1 CCACCAGTTCCAGTCTATAAACCT
52242011 CCACCAGTTCCAGT
1 CCACCAGTTCCAGT
52242025 ATACAAGAAA
Statistics
Matches: 104, Mismatches: 24, Indels: 18
0.71 0.16 0.12
Matches are distributed among these distances:
22 4 0.04
23 3 0.03
24 75 0.72
25 4 0.04
27 14 0.13
29 4 0.04
ACGTcount: A:0.29, C:0.39, G:0.07, T:0.25
Consensus pattern (24 bp):
CCACCAGTTCCAGTCTATAAACCT
Found at i:52242050 original size:33 final size:33
Alignment explanation
Indices: 52242008--52242180 Score: 157
Period size: 33 Copynumber: 5.5 Consensus size: 33
52241998 AGTCTATAAA
* **
52242008 CCTCCACCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * *
52242041 CCTCCACCAGTTCCAG--T-C--TATA--A-AT
1 CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* *
52242066 C-TCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* *
52242098 CCTCCTCCAGTTCCAGTCTATAAGAAACCACAT
1 CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* **
52242131 CCACCTCCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
*
52242164 CCTCCCCCAGTTCCAGT
1 CCTCCTCCAGTTCCAGT
52242181 CTATAAATCT
Statistics
Matches: 112, Mismatches: 19, Indels: 18
0.75 0.13 0.12
Matches are distributed among these distances:
24 12 0.11
25 2 0.02
26 2 0.02
27 1 0.01
28 2 0.02
29 2 0.02
30 1 0.01
31 1 0.01
32 3 0.03
33 86 0.77
ACGTcount: A:0.29, C:0.36, G:0.12, T:0.23
Consensus pattern (33 bp):
CCTCCTCCAGTTCCAGTATACAAGAAACCACAT
Found at i:52242063 original size:57 final size:57
Alignment explanation
Indices: 52241885--52242347 Score: 339
Period size: 57 Copynumber: 8.4 Consensus size: 57
52241875 AATCTATAAA
*
52241885 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAG--T---A-AAACCACTT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * * *
52241936 CCTCCACCTGTTCCAATCTACAAA---CCTCCA---CCAGT-T-GAA-AAACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * **
52241984 CCTCCACCTGTTCCAGTCTATAAACCTCCACCAGTTCCAGTATACAAGAAACCATGT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * *
52242041 CCTCCACCAGTTCCAGTCTATAAATCTCCTCCGGTTCCAGTATACAAGAAACCGCAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* **
52242098 CCTCCTCCAGTTCCAGTCTATAAGAAACCACATCCACCTCCAGTTCCAGTATACAAGAAACCATG
1 CCTCCACCAGTTCCAGTCTAT---AAA-C-C-T---CCTCCAGTTCCAGTATACAAGAAACCACA
52242163 T
57 T
* *
52242164 CCTCCCCCAGTTCCAGTCTATAAATCTCCTCCAGTTCC-G-------G-AACCACAT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * * * * *
52242212 CCTCCGCCAGTTCCAGTCCATAAGCCTCCTCCAGTTCCGGTATACAAGAAACGA-GT
1 CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * * * * * * *
52242268 CCCTCCTCCGGTTCCAATCTACAAGCCCCCTCCAGTTCCTGTATACAACAAACCAC-T
1 -CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
* * *
52242325 ACCTCCCCCGGTTCCAGTGTATA
1 -CCTCCACCAGTTCCAGTCTATA
52242348 CGAAGCCACT
Statistics
Matches: 333, Mismatches: 47, Indels: 58
0.76 0.11 0.13
Matches are distributed among these distances:
45 4 0.01
46 1 0.00
48 77 0.23
49 2 0.01
51 26 0.08
54 5 0.02
55 1 0.00
56 5 0.02
57 156 0.47
60 4 0.01
61 1 0.00
62 1 0.00
63 4 0.01
66 46 0.14
ACGTcount: A:0.27, C:0.38, G:0.11, T:0.24
Consensus pattern (57 bp):
CCTCCACCAGTTCCAGTCTATAAACCTCCTCCAGTTCCAGTATACAAGAAACCACAT
Found at i:52242216 original size:24 final size:24
Alignment explanation
Indices: 52242189--52242251 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
52242179 GTCTATAAAT
* *
52242189 CTCCTCCAGTTCCGGAACCA-CATC
1 CTCCTCCAGTTCCGG-ACCATAAGC
* * *
52242213 CTCCGCCAGTTCCAGTCCATAAGC
1 CTCCTCCAGTTCCGGACCATAAGC
52242237 CTCCTCCAGTTCCGG
1 CTCCTCCAGTTCCGG
52242252 TATACAAGAA
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 3 0.10
24 28 0.90
ACGTcount: A:0.17, C:0.44, G:0.16, T:0.22
Consensus pattern (24 bp):
CTCCTCCAGTTCCGGACCATAAGC
Found at i:52242440 original size:18 final size:18
Alignment explanation
Indices: 52242417--52242452 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52242407 TACAAGCCAC
52242417 TCCCTCCACTTCCC-AAGA
1 TCCCTCCA-TTCCCTAAGA
52242435 TCCCTCCATTCCCTAAGA
1 TCCCTCCATTCCCTAAGA
52242453 AGCCATGCCC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.22, C:0.47, G:0.06, T:0.25
Consensus pattern (18 bp):
TCCCTCCATTCCCTAAGA
Found at i:52242524 original size:60 final size:60
Alignment explanation
Indices: 52242460--52242579 Score: 215
Period size: 60 Copynumber: 2.0 Consensus size: 60
52242450 AGAAGCCATG
52242460 CCCTCCCCTTCCTAAGCTACCCCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCCCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
*
52242520 CCCTCCCCTTCCTAAGCTACCTCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
1 CCCTCCCCTTCCTAAGCTACCCCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
52242580 TCCCAAGTTC
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
59 4 0.07
60 54 0.93
ACGTcount: A:0.20, C:0.49, G:0.05, T:0.26
Consensus pattern (60 bp):
CCCTCCCCTTCCTAAGCTACCCCCTCTCCCTAAGATTCCTCCCAAGTATTTCCACCACCA
Found at i:52242604 original size:60 final size:60
Alignment explanation
Indices: 52242477--52242596 Score: 136
Period size: 60 Copynumber: 2.0 Consensus size: 60
52242467 CTTCCTAAGC
* ** * **
52242477 TACCCCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCCCCTTCCTAAGC
1 TACCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAA
* * *
52242537 TACCTCCTC-TCCCTAAGATTCCTCCCAAGTATTTCCACCACCATCC-CAAGTTCGGAAAA
1 TACCTCCTCTTCCC-AAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAA
52242596 T
1 T
52242597 GGCCTCCTTT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
59 11 0.22
60 39 0.78
ACGTcount: A:0.23, C:0.44, G:0.07, T:0.26
Consensus pattern (60 bp):
TACCTCCTCTTCCCAAGATTCCTCCCAAGTATTTCCACCACCACCCTCAACTTCCGAAAA
Found at i:52247204 original size:39 final size:40
Alignment explanation
Indices: 52247161--52247247 Score: 106
Period size: 40 Copynumber: 2.2 Consensus size: 40
52247151 GAATTATGGG
* * *
52247161 ATACTGGATATTGTTTTG-ATTACTG-AGTGAATTGTGAAA
1 ATACTGAATATTGTTATGTA-TAATGCAGTGAATTGTGAAA
*
52247200 ATACTGAATATTGTTATGTATAATGCATTGAATTGTGAAA
1 ATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAAA
*
52247240 TTACTGAA
1 ATACTGAA
52247248 GTAAAGAATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
39 20 0.49
40 21 0.51
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.40
Consensus pattern (40 bp):
ATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAAA
Found at i:52247474 original size:38 final size:39
Alignment explanation
Indices: 52247422--52247504 Score: 116
Period size: 39 Copynumber: 2.2 Consensus size: 39
52247412 ATTTGCCGGC
*
52247422 TTACTGATCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATCAGGCACTTTATGTGCCGAATACTGTTACTG
* *
52247460 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGA-TCAGGCACTTTATGTGCCGAATACTGTTACTG
52247499 TTACTG
1 TTACTG
52247505 TTACTGACTC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 12 0.30
39 28 0.70
ACGTcount: A:0.19, C:0.20, G:0.22, T:0.39
Consensus pattern (39 bp):
TTACTGATCAGGCACTTTATGTGCCGAATACTGTTACTG
Found at i:52247502 original size:39 final size:40
Alignment explanation
Indices: 52247422--52247594 Score: 149
Period size: 45 Copynumber: 4.2 Consensus size: 40
52247412 ATTTGCCGGC
* * *
52247422 TTACTGA-TCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATTCAGGCACTTTGTGTGTCGAATACTGTTACTG
52247460 TTACTGATTC-GGCACTTTGTGTGTCGAATACTGTTACTG
1 TTACTGATTCAGGCACTTTGTGTGTCGAATACTGTTACTG
* *
52247499 TTACTG-TTACTGACTCGACACTTTGTGTGTCGAATACTGTTACCG
1 TTACTGATT-C--A---GGCACTTTGTGTGTCGAATACTGTTACTG
*
52247544 TTACTG-TTACAGGTTCAACACTTTGTGTGTTGAATACTGTTACTG
1 TTACTGATT-CAGG-----CACTTTGTGTGTCGAATACTGTTACTG
52247589 TTACTG
1 TTACTG
52247595 TTATTGATTA
Statistics
Matches: 113, Mismatches: 8, Indels: 21
0.80 0.06 0.15
Matches are distributed among these distances:
38 14 0.12
39 29 0.26
40 1 0.01
43 1 0.01
45 68 0.60
ACGTcount: A:0.20, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TTACTGATTCAGGCACTTTGTGTGTCGAATACTGTTACTG
Found at i:52247521 original size:45 final size:45
Alignment explanation
Indices: 52247449--52247603 Score: 238
Period size: 45 Copynumber: 3.4 Consensus size: 45
52247439 ATGTGCCGAC
*
52247449 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
*
52247494 TACTGTTACTGTTACTGACTCGACACTTTGTGTGTCGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
* * * * *
52247539 TACCGTTACTGTTACAGGTTCAACACTTTGTGTGTTGAATACTGT
1 TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
*
52247584 TACTGTTACTGTTATTGATT
1 TACTGTTACTGTTACTGATT
52247604 ACTGTATACT
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 98 1.00
ACGTcount: A:0.20, C:0.17, G:0.20, T:0.43
Consensus pattern (45 bp):
TACTGTTACTGTTACTGATTCGACACTTTGTGTGTCGAATACTGT
Found at i:52249955 original size:27 final size:29
Alignment explanation
Indices: 52249901--52249969 Score: 108
Period size: 27 Copynumber: 2.5 Consensus size: 29
52249891 AATAAAAAAA
*
52249901 TTACCAAAATGT-TATACATTTTTATTAT
1 TTACCAAAATATATATACATTTTTATTAT
52249929 TTACCAAAATATATATA-ATTTTT-TTAT
1 TTACCAAAATATATATACATTTTTATTAT
52249956 TTACCAAAATATAT
1 TTACCAAAATATAT
52249970 CAAAAAAAAC
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 18 0.46
28 17 0.44
29 4 0.10
ACGTcount: A:0.41, C:0.10, G:0.01, T:0.48
Consensus pattern (29 bp):
TTACCAAAATATATATACATTTTTATTAT
Found at i:52250014 original size:18 final size:18
Alignment explanation
Indices: 52249970--52250013 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
52249960 CAAAATATAT
52249970 CAAAAAAAACCAAAAAAA
1 CAAAAAAAACCAAAAAAA
52249988 CAAAAAAAA-C-AAAAAA
1 CAAAAAAAACCAAAAAAA
52250004 CAGAAAAAAA
1 CA-AAAAAAA
52250014 AACCTGGACC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.32
17 8 0.32
18 9 0.36
ACGTcount: A:0.84, C:0.14, G:0.02, T:0.00
Consensus pattern (18 bp):
CAAAAAAAACCAAAAAAA
Found at i:52250084 original size:27 final size:27
Alignment explanation
Indices: 52250044--52250122 Score: 122
Period size: 27 Copynumber: 2.9 Consensus size: 27
52250034 TTCCCTGGGT
*
52250044 CAAGGGAACACTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
*
52250071 GAAGGGAACCCTGTTGGCGGCACCAAA
1 CAAGGGAACCCTGTTGGCGGCACCAAA
**
52250098 CAAGGGTTCCCTGTTGGCGGCACCA
1 CAAGGGAACCCTGTTGGCGGCACCA
52250123 CTCGTGTTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.27, C:0.28, G:0.32, T:0.14
Consensus pattern (27 bp):
CAAGGGAACCCTGTTGGCGGCACCAAA
Found at i:52254722 original size:28 final size:28
Alignment explanation
Indices: 52254690--52254758 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
52254680 TTTTTTTAAA
*
52254690 AATATTTTGGTAAATAATAAAAA-TTAT
1 AATATTTTGGTAAATAAAAAAAAGTTAT
*
52254717 ATATATTTTGGTCAATAAAAAAAAGTTAT
1 A-ATATTTTGGTAAATAAAAAAAAGTTAT
52254746 AATATTTTGGTAA
1 AATATTTTGGTAA
52254759 TTTTTTATTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.03
28 31 0.84
29 5 0.14
ACGTcount: A:0.48, C:0.01, G:0.10, T:0.41
Consensus pattern (28 bp):
AATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:52255715 original size:37 final size:34
Alignment explanation
Indices: 52255660--52255781 Score: 138
Period size: 37 Copynumber: 3.4 Consensus size: 34
52255650 NNNNNNNNNN
**
52255660 TTCTTTTT-TTTCCCTCCTCTCCTTTCCCTTTCC
1 TTCTTTTTCTTTCTTTCCTCTCCTTTCCCTTTCC
* *
52255693 TTCATTATTTTCTTTCTTTCCTCCCCTTTCCCTTTTCT
1 TTC--T-TTTTCTTTCTTTCCTCTCCTTTCCC-TTTCC
*
52255731 TTCCTCTTTTCTTTCTTTCCTCTCCTTTCCTTTTCC
1 TT-CT-TTTTCTTTCTTTCCTCTCCTTTCCCTTTCC
52255767 TTCTTTTTCTTTCTT
1 TTCTTTTTCTTTCTT
52255782 CCCTTCTTCT
Statistics
Matches: 75, Mismatches: 8, Indels: 11
0.80 0.09 0.12
Matches are distributed among these distances:
33 3 0.04
34 11 0.15
35 3 0.04
36 10 0.13
37 41 0.55
38 6 0.08
39 1 0.01
ACGTcount: A:0.02, C:0.36, G:0.00, T:0.62
Consensus pattern (34 bp):
TTCTTTTTCTTTCTTTCCTCTCCTTTCCCTTTCC
Found at i:52255799 original size:17 final size:17
Alignment explanation
Indices: 52255765--52255812 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
52255755 CTTTCCTTTT
*
52255765 CCTTCTTTTTCTTTCTTC
1 CCTTCTTCTTC-TTCTTC
52255783 CCTTCTTCTTCTTCTTC
1 CCTTCTTCTTCTTCTTC
* *
52255800 CCCTCTCCTTCTT
1 CCTTCTTCTTCTT
52255813 TCCCCCAACA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 17 0.63
18 10 0.37
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (17 bp):
CCTTCTTCTTCTTCTTC
Found at i:52255964 original size:21 final size:19
Alignment explanation
Indices: 52255927--52255967 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52255917 TCGGTCCAGA
*
52255927 TTTTTTTTTGTTTTTTTGG
1 TTTTTTTTTGTTATTTTGG
52255946 TTTTTTTTTGATATATTTTGG
1 TTTTTTTTTG-T-TATTTTGG
52255967 T
1 T
52255968 AAAAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 10 0.53
20 1 0.05
21 8 0.42
ACGTcount: A:0.07, C:0.00, G:0.15, T:0.78
Consensus pattern (19 bp):
TTTTTTTTTGTTATTTTGG
Found at i:52256215 original size:15 final size:15
Alignment explanation
Indices: 52256195--52256269 Score: 68
Period size: 15 Copynumber: 5.1 Consensus size: 15
52256185 TAATAGTGTG
52256195 TAATTACTTTAATTA
1 TAATTACTTTAATTA
52256210 TAATTACTTTAA-TA
1 TAATTACTTTAATTA
* * *
52256224 -AGTT--TTAATAGTGTG
1 TAATTACTT--TAAT-TA
52256239 TAATTACTTTAATTA
1 TAATTACTTTAATTA
52256254 TAATTACTTTAATTA
1 TAATTACTTTAATTA
52256269 T
1 T
52256270 GTTTTGAATT
Statistics
Matches: 47, Mismatches: 6, Indels: 14
0.70 0.09 0.21
Matches are distributed among these distances:
11 2 0.04
13 5 0.11
14 2 0.04
15 30 0.64
16 6 0.13
18 2 0.04
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.52
Consensus pattern (15 bp):
TAATTACTTTAATTA
Found at i:52256229 original size:44 final size:44
Alignment explanation
Indices: 52256179--52256266 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
52256169 ACGATATTAC
52256179 AAGTTTTAATAGTGTGTAATTACTTTAATTATAATTACTTTAAT
1 AAGTTTTAATAGTGTGTAATTACTTTAATTATAATTACTTTAAT
52256223 AAGTTTTAATAGTGTGTAATTACTTTAATTATAATTACTTTAAT
1 AAGTTTTAATAGTGTGTAATTACTTTAATTATAATTACTTTAAT
52256267 TATGTTTTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (44 bp):
AAGTTTTAATAGTGTGTAATTACTTTAATTATAATTACTTTAAT
Found at i:52256665 original size:6 final size:6
Alignment explanation
Indices: 52256656--52256694 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
52256646 ATTTTTTAAT
*
52256656 TTAGGG TTAGGG TTAGAG TTAGGG TTAGGG TTTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG -TTAGGG TT
52256695 TTTATTTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.18, C:0.00, G:0.44, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:52256833 original size:29 final size:28
Alignment explanation
Indices: 52256751--52256837 Score: 86
Period size: 29 Copynumber: 3.0 Consensus size: 28
52256741 GTTTAGAGGG
* *
52256751 TCTGAAAAATAA-TTTGTACAAGATGGAT
1 TCTGAAAAATAATTTTG-ACGAGATGGGT
* * * *
52256779 TCTAAAAAAATAGTTTTGAGGGGATGGGT
1 TCT-GAAAAATAATTTTGACGAGATGGGT
52256808 TCTGAAGAAATAATTTTGACGAGATGGGT
1 TCTGAA-AAATAATTTTGACGAGATGGGT
52256837 T
1 T
52256838 GAGTTTTGTA
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
28 5 0.11
29 37 0.80
30 4 0.09
ACGTcount: A:0.37, C:0.06, G:0.25, T:0.32
Consensus pattern (28 bp):
TCTGAAAAATAATTTTGACGAGATGGGT
Found at i:52260039 original size:41 final size:41
Alignment explanation
Indices: 52259980--52260137 Score: 185
Period size: 41 Copynumber: 3.9 Consensus size: 41
52259970 ATATGAGATT
* * * *
52259980 TTCAGGCTTAATGCCTAGCAGGCTTGATGCCGGTGAATTAT
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAA
*
52260021 TTTAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAA
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAA
*
52260062 TTCAGACTTTATGTCTAGCAGGCTTTG-TGCCGGTGAAATGAA
1 TTCAGACTTTATGTCTAGCAGGC-TTGATGCCGGTG-AATTAA
* * * * *
52260104 -TCGGGCTTTGTGCCTAGCAGGCTTTATGCCGGTG
1 TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTG
52260138 TTTTATACAA
Statistics
Matches: 102, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
40 2 0.02
41 92 0.90
42 8 0.08
ACGTcount: A:0.20, C:0.18, G:0.28, T:0.34
Consensus pattern (41 bp):
TTCAGACTTTATGTCTAGCAGGCTTGATGCCGGTGAATTAA
Found at i:52260834 original size:14 final size:15
Alignment explanation
Indices: 52260810--52260844 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
52260800 TACTTTAATC
52260810 ATGGATTAGTATTT-T
1 ATGG-TTAGTATTTAT
52260825 ATGGTTAGTATTTAT
1 ATGGTTAGTATTTAT
52260840 ATGGT
1 ATGGT
52260845 AATATATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (15 bp):
ATGGTTAGTATTTAT
Found at i:52263804 original size:6 final size:6
Alignment explanation
Indices: 52263793--52263817 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
52263783 CACGCTCCTA
52263793 TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT T
52263818 GGTTAAGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:52263907 original size:111 final size:110
Alignment explanation
Indices: 52263709--52263911 Score: 291
Period size: 111 Copynumber: 1.8 Consensus size: 110
52263699 TTTTTTTTTC
* * *
52263709 TTAAGAATATATTGGCCCTTTTGACGCGAAGTGAGATGACAACCCAAGCACCCCACCCCGATTAC
1 TTAAGAATATATTGGCCATTTTGACACGAAGTGAGATGACAACCCAAGCACCCCACCCAGATTAC
* *
52263774 TCAGCCTAACACGCTCCTATTTTATTTTTATTTTTATTTTTATTGG
66 TCAACCTAACACACTCCTATTTT-TTTTTATTTTTATTTTTATTGG
* * * *
52263820 TTAAGAATGTTTTGGCCATTTTGACACGAAGTGGGATGACAACCTAAGCACCCCACCCAG-TTAC
1 TTAAGAATATATTGGCCATTTTGACACGAAGTGAGATGACAACCCAAGCACCCCACCCAGATTAC
* *
52263884 TCAACCTAACACACTCTTAATTTTTTTT
66 TCAACCTAACACACTCCTATTTTTTTTT
52263912 GTTTAATTTC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
109 5 0.06
110 23 0.28
111 53 0.65
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (110 bp):
TTAAGAATATATTGGCCATTTTGACACGAAGTGAGATGACAACCCAAGCACCCCACCCAGATTAC
TCAACCTAACACACTCCTATTTTTTTTTATTTTTATTTTTATTGG
Found at i:52279129 original size:16 final size:18
Alignment explanation
Indices: 52279100--52279132 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
52279090 AGTTAAATTT
52279100 ATTATCATACTAATTAAA
1 ATTATCATACTAATTAAA
52279118 ATTAT-ATA-TAATTAA
1 ATTATCATACTAATTAA
52279133 TGAAAAGCCG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.47
17 3 0.20
18 5 0.33
ACGTcount: A:0.52, C:0.06, G:0.00, T:0.42
Consensus pattern (18 bp):
ATTATCATACTAATTAAA
Found at i:52281903 original size:19 final size:19
Alignment explanation
Indices: 52281871--52281923 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
52281861 ACCATTGTTC
*
52281871 TTTTTT-TCATTTTTGAGT
1 TTTTTTATCAATTTTGAGT
*
52281889 TTTTTTATCAATTTT-TGT
1 TTTTTTATCAATTTTGAGT
*
52281907 TTTTTTAATCTATTTTG
1 TTTTTT-ATCAATTTTG
52281924 TCTAATAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.15, C:0.06, G:0.08, T:0.72
Consensus pattern (19 bp):
TTTTTTATCAATTTTGAGT
Found at i:52281924 original size:18 final size:18
Alignment explanation
Indices: 52281865--52281913 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 18
52281855 CTATTAACCA
*
52281865 TTGTTCTTTTTTTC-ATTT
1 TTGTT-TTTTTATCAATTT
52281883 TTGAGTTTTTTTATCAATTT
1 TT--GTTTTTTTATCAATTT
52281903 TTGTTTTTTTA
1 TTGTTTTTTTA
52281914 ATCTATTTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 11 0.41
19 7 0.26
20 9 0.33
ACGTcount: A:0.12, C:0.06, G:0.08, T:0.73
Consensus pattern (18 bp):
TTGTTTTTTTATCAATTT
Found at i:52283499 original size:125 final size:126
Alignment explanation
Indices: 52283203--52283541 Score: 581
Period size: 125 Copynumber: 2.7 Consensus size: 126
52283193 CGTCTCTGGT
* * * *
52283203 CAAATAGTATAAAATCGCTTCTACCAAGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* * *
52283268 TGGACACGATTTTGCTATAGGAGGTCATGTAAGAAATAATTTTTTTTCTAATTTTTCTGAG
66 TGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
52283329 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
*
52283394 TGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTCTGATGTTTCTGAG
66 TGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
52283454 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
* *
52283519 TGGGCGCGATTTTGCTACAGTAG
66 TGGACACGATTTTGCTACAGTAG
52283542 CAAGTTTGGG
Statistics
Matches: 203, Mismatches: 10, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
125 105 0.52
126 98 0.48
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (126 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
TGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTCTAATGTTTCTGAG
Found at i:52284415 original size:26 final size:26
Alignment explanation
Indices: 52284382--52284438 Score: 114
Period size: 26 Copynumber: 2.2 Consensus size: 26
52284372 TAAAGTGTTC
52284382 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
52284408 AAAATATGTAAAATTATTAAGCCAAA
1 AAAATATGTAAAATTATTAAGCCAAA
52284434 AAAAT
1 AAAAT
52284439 TTAGGTTAGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.60, C:0.07, G:0.07, T:0.26
Consensus pattern (26 bp):
AAAATATGTAAAATTATTAAGCCAAA
Found at i:52284489 original size:29 final size:29
Alignment explanation
Indices: 52284436--52284740 Score: 485
Period size: 29 Copynumber: 10.7 Consensus size: 29
52284426 AAGCCAAAAA
*
52284436 AATTTAGGTTA-GTTTTGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
52284464 AATTTAGGTTAGGTTTAGAGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
52284493 AATTTAGGTTA-GATTAGGGTTTTAAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
52284521 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
52284550 AATTTAGGTTAGG-TTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
52284578 AATTTAGGTTAGG-TTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
52284606 AATTTAGGTTA-GATTAGGTTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
52284634 AATTTAGGTTAGGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA-GGTTTAGGGTTTTTAATT
52284664 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
52284693 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTTAGGGTTTTTAATT
*
52284722 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTAGGTTTAGG
52284741 TTAGGGTTTT
Statistics
Matches: 257, Mismatches: 15, Indels: 9
0.91 0.05 0.03
Matches are distributed among these distances:
27 1 0.00
28 113 0.44
29 118 0.46
30 25 0.10
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (29 bp):
AATTTAGGTTAGGTTTAGGGTTTTTAATT
Found at i:52284524 original size:57 final size:57
Alignment explanation
Indices: 52284436--52284733 Score: 490
Period size: 57 Copynumber: 5.2 Consensus size: 57
52284426 AAGCCAAAAA
* * *
52284436 AATTTAGGTTAGTTTTGGGTTTTTAATTAATTTAGGTTAGGTTTAGAGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
*
52284493 AATTTAGGTTAGATTAGGGTTTTAAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
52284550 AATTTAGGTTAGGTTAGGGTTTTTAATTAATTTAGGTTAGG-TTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
* *
52284606 AATTTAGGTTAGATTAGGTTTTTTAATTAATTTAGGTTAGGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTA-GGTTTAGGGTTTTTAATT
*
52284664 AATTTAGGTTAGGTTTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTA-GATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
52284722 AATTTAGGTTAG
1 AATTTAGGTTAG
52284734 GGTTAGGTTA
Statistics
Matches: 226, Mismatches: 12, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
56 51 0.23
57 95 0.42
58 54 0.24
59 26 0.12
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (57 bp):
AATTTAGGTTAGATTAGGGTTTTTAATTAATTTAGGTTAGGTTTAGGGTTTTTAATT
Found at i:52284766 original size:29 final size:28
Alignment explanation
Indices: 52284436--52284740 Score: 466
Period size: 28 Copynumber: 10.6 Consensus size: 28
52284426 AAGCCAAAAA
* *
52284436 AATTTAGGTTAGTTTTGGGTTTTTAATT
1 AATTTAGGTTAGGTTAGGGTTTTTAATT
*
52284464 AATTTAGGTTAGGTTTAGAGTTTTTAATT
1 AATTTAGGTTAGG-TTAGGGTTTTTAATT
* *
52284493 AATTTAGGTTAGATTAGGGTTTTAAATT
1 AATTTAGGTTAGGTTAGGGTTTTTAATT
52284521 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGG-TTAGGGTTTTTAATT
52284550 AATTTAGGTTAGGTTAGGGTTTTTAATT
1 AATTTAGGTTAGGTTAGGGTTTTTAATT
*
52284578 AATTTAGGTTAGGTTAGGGTTTTTAGTT
1 AATTTAGGTTAGGTTAGGGTTTTTAATT
* *
52284606 AATTTAGGTTAGATTAGGTTTTTTAATT
1 AATTTAGGTTAGGTTAGGGTTTTTAATT
*
52284634 AATTTAGGTTAGGGTTTAGGGTTTTTAGTT
1 AATTTAGGTTA-GG-TTAGGGTTTTTAATT
52284664 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGG-TTAGGGTTTTTAATT
52284693 AATTTAGGTTAGGTTTAGGGTTTTTAATT
1 AATTTAGGTTAGG-TTAGGGTTTTTAATT
52284722 AATTTAGGTTAGGGTTAGG
1 AATTTAGGTTA-GGTTAGG
52284741 TTAGGGTTTT
Statistics
Matches: 256, Mismatches: 16, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
28 115 0.45
29 115 0.45
30 26 0.10
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (28 bp):
AATTTAGGTTAGGTTAGGGTTTTTAATT
Found at i:52284842 original size:26 final size:25
Alignment explanation
Indices: 52284811--52284859 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
52284801 CTTAAAAAAT
52284811 TTCTATGCGTATTACATCAAATAAAC
1 TTCTAT-CGTATTACATCAAATAAAC
**
52284837 TTCTATTTTATTACATCAAATAA
1 TTCTATCGTATTACATCAAATAA
52284860 TAAAATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.71
26 6 0.29
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.41
Consensus pattern (25 bp):
TTCTATCGTATTACATCAAATAAAC
Found at i:52285000 original size:24 final size:24
Alignment explanation
Indices: 52284973--52285025 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
52284963 GGCGGTTGTT
*
52284973 CTTCCTCTGGTGGTGATTGTGGTC
1 CTTCCTCCGGTGGTGATTGTGGTC
* *
52284997 CTTCCTCCGGTGGTGGTTGTGGTT
1 CTTCCTCCGGTGGTGATTGTGGTC
52285021 CTTCC
1 CTTCC
52285026 GGTTCCGCAT
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:0.02, C:0.25, G:0.32, T:0.42
Consensus pattern (24 bp):
CTTCCTCCGGTGGTGATTGTGGTC
Found at i:52285980 original size:7 final size:7
Alignment explanation
Indices: 52285970--52285994 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52285960 TTATATACAT
52285970 AATACTA
1 AATACTA
52285977 AATACTA
1 AATACTA
52285984 AATACTA
1 AATACTA
52285991 AATA
1 AATA
52285995 TCAATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:52287093 original size:30 final size:29
Alignment explanation
Indices: 52287059--52287122 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
52287049 GCCATTGATG
52287059 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAA-TTAAAATTATTTTAA
*
52287089 AAAATATAAAAAAATTATAATTATTTTAA
1 AAAATATAAAAAAATTAAAATTATTTTAA
52287118 AAAAT
1 AAAAT
52287123 GGATTTGAGA
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
AAAATATAAAAAAATTAAAATTATTTTAA
Found at i:52288225 original size:11 final size:10
Alignment explanation
Indices: 52288197--52288236 Score: 53
Period size: 11 Copynumber: 3.7 Consensus size: 10
52288187 TAGTTTACCC
52288197 TTAAATAAAAT
1 TTAAA-AAAAT
52288208 TTAAAAAAAT
1 TTAAAAAAAT
52288218 TTATAAAAAAT
1 TTA-AAAAAAT
52288229 ATTAAAAA
1 -TTAAAAA
52288237 TAGATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 8 0.30
11 16 0.59
12 3 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAAAAAAAT
Found at i:52292469 original size:63 final size:63
Alignment explanation
Indices: 52292340--52292460 Score: 188
Period size: 63 Copynumber: 1.9 Consensus size: 63
52292330 CTATTATAGC
* ** *
52292340 TTTATTCCATTCCAGTGAACCAAACATACCATTAGAGAATGAATCCACGCATTCCATTACAGT
1 TTTATTCCATTCCAGTGAACCAAACATACCATTAGAGAATGAAGCCACGCACCCCATCACAGT
* *
52292403 TTTATTTCATTCCAGTGAACCAAACATGCCATTAGAGAATGAAGCCACGCACCCCATC
1 TTTATTCCATTCCAGTGAACCAAACATACCATTAGAGAATGAAGCCACGCACCCCATC
52292461 CCTTTTTTAC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.26
Consensus pattern (63 bp):
TTTATTCCATTCCAGTGAACCAAACATACCATTAGAGAATGAAGCCACGCACCCCATCACAGT
Found at i:52297134 original size:18 final size:18
Alignment explanation
Indices: 52297111--52297146 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
52297101 AATAAAATGC
52297111 GTATAATAAA-ATTAAAAT
1 GTATAA-AAATATTAAAAT
52297129 GTATAAAAATATTAAAAT
1 GTATAAAAATATTAAAAT
52297147 AAAATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.18
18 14 0.82
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.33
Consensus pattern (18 bp):
GTATAAAAATATTAAAAT
Found at i:52304003 original size:23 final size:22
Alignment explanation
Indices: 52303921--52304005 Score: 107
Period size: 23 Copynumber: 3.7 Consensus size: 22
52303911 TACACATTAG
* *
52303921 TCACTTTAATATTTAATCATAAA
1 TCACATTAAT-TTTAAGCATAAA
52303944 TCACATTAATATTTAAGCATAAA
1 TCACATTAAT-TTTAAGCATAAA
*
52303967 GCACATTAAATTTTAAGCATAAA
1 TCACATT-AATTTTAAGCATAAA
52303990 TCACATTAAGTTTTAA
1 TCACATTAA-TTTTAA
52304006 CACATTTAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.04
23 51 0.91
24 3 0.05
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.38
Consensus pattern (22 bp):
TCACATTAATTTTAAGCATAAA
Found at i:52310873 original size:20 final size:20
Alignment explanation
Indices: 52310848--52310886 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
52310838 TACTTTCTTC
52310848 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
52310868 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
52310887 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:52311217 original size:50 final size:50
Alignment explanation
Indices: 52311142--52311283 Score: 133
Period size: 50 Copynumber: 2.8 Consensus size: 50
52311132 CTGTACTACA
* * * * ** * *
52311142 AATGTCATATCCCAGATATGGTCTTAC-ATGAGAGTTCTCATATTGGTGCC
1 AATGCCATGTCCCAGACATAGTCTTACGA-GAGACCTCTCATATCGGTACC
* * * *
52311192 CATGCCATGTCCCAGGCATAGTCTTACGAGGGACCTCTCATCTCGGTACC
1 AATGCCATGTCCCAGACATAGTCTTACGAGAGACCTCTCATATCGGTACC
* * *
52311242 AATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 AATGCCATGTCCCAGACATAGTCTTACGAGAGACCTCTCATA
52311284 ACCTCAATAA
Statistics
Matches: 74, Mismatches: 17, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
50 73 0.99
51 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (50 bp):
AATGCCATGTCCCAGACATAGTCTTACGAGAGACCTCTCATATCGGTACC
Found at i:52311302 original size:56 final size:52
Alignment explanation
Indices: 52311188--52311324 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 52
52311178 CTCATATTGG
* * * **
52311188 TGCCCATGCCATGTCCCAGGCATAGTCTTACGAGGGACCTCTCATCTCGGTA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGAGGGACCTCTCATCTCAATA
*
52311240 --CCAATGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAACCTCAATAA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACGAGGGACCTCTCAT---CTCAAT-A
*
52311294 TGCCAATGCCATGTCCCAGACATGATCTTAC
1 TGCCAATGCCATGTCCCAGACATGGTCTTAC
52311325 ATAGGGTCTT
Statistics
Matches: 72, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
50 39 0.54
53 4 0.06
54 1 0.01
56 28 0.39
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (52 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACGAGGGACCTCTCATCTCAATA
Found at i:52312614 original size:15 final size:16
Alignment explanation
Indices: 52312594--52312625 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
52312584 GGATGTTGTA
52312594 TGTAATTCATCT-ATT
1 TGTAATTCATCTGATT
52312609 TGTAATTCATCTGATT
1 TGTAATTCATCTGATT
52312625 T
1 T
52312626 AGTAGATGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (16 bp):
TGTAATTCATCTGATT
Found at i:52317759 original size:19 final size:20
Alignment explanation
Indices: 52317721--52317759 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52317711 CTTTCTTTTA
*
52317721 TCTTTTATTTACTTAAATTT
1 TCTTTTATTTACTCAAATTT
52317741 TCTTTTATTTAC-CAAATTT
1 TCTTTTATTTACTCAAATTT
52317760 CTACTTTAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.62
Consensus pattern (20 bp):
TCTTTTATTTACTCAAATTT
Found at i:52327576 original size:19 final size:20
Alignment explanation
Indices: 52327539--52327576 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
52327529 CTTTCTTTTA
52327539 TCTTTTATTTACTTAAATTT
1 TCTTTTATTTACTTAAATTT
52327559 TCTTTTATTTAC-TAAATT
1 TCTTTTATTTACTTAAATT
52327577 ACTACTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.26, C:0.11, G:0.00, T:0.63
Consensus pattern (20 bp):
TCTTTTATTTACTTAAATTT
Found at i:52329090 original size:360 final size:360
Alignment explanation
Indices: 52328423--52329116 Score: 1343
Period size: 360 Copynumber: 1.9 Consensus size: 360
52328413 TATATGTTCA
*
52328423 GTTTTTAGAAATTCTCATACTTTTTGTTATATGTTCAGTTAAGTCCTTATTTGTTTCCGGATTGG
1 GTTTTCAGAAATTCTCATACTTTTTGTTATATGTTCAGTTAAGTCCTTATTTGTTTCCGGATTGG
52328488 TTTAAGAGCCTTCGTAAGATCGTTTGAGACTTGGATTTGATTATAAATCATGGTATACTTAAAAT
66 TTTAAGAGCCTTCGTAAGATCGTTTGAGACTTGGATTTGATTATAAATCATGGTATACTTAAAAT
52328553 ATGAAATGTTTAATGTTTGGGTTGATTGTTAATACCGATTTTGGATGTAATTGTTCTATTATATT
131 ATGAAATGTTTAATGTTTGGGTTGATTGTTAATACCGATTTTGGATGTAATTGTTCTATTATATT
*
52328618 AATTTTTCGAACTGGGTAAGGGGTGTTACACTAATATTCATTTTTCTATTTCCAAAATTAAACAT
196 AATTTTTCGAACTGGGTAAAGGGTGTTACACTAATATTCATTTTTCTATTTCCAAAATTAAACAT
52328683 CTTAATTAATTTTCCAATTAAATAATATTCTTCACACAATTCTAATTCTATTAAAATCATTCAAT
261 CTTAATTAATTTTCCAATTAAATAATATTCTTCACACAATTCTAATTCTATTAAAATCATTCAAT
52328748 AAGTTTACTCTAATTCTAATTCTAATTCTATTTCT
326 AAGTTTACTCTAATTCTAATTCTAATTCTATTTCT
52328783 GTTTTCAGAAATTCTCATACTTTTTGTTATATGTTCAGTTAAGTCCTTATTTGTTTCCGGATTGG
1 GTTTTCAGAAATTCTCATACTTTTTGTTATATGTTCAGTTAAGTCCTTATTTGTTTCCGGATTGG
52328848 TTTAAGAGCCTTCGTAAGATCGTTTGAGACTTGGATTTGATTATAAATCATGGTATACTTAAAAT
66 TTTAAGAGCCTTCGTAAGATCGTTTGAGACTTGGATTTGATTATAAATCATGGTATACTTAAAAT
* *
52328913 TTGAAATGTTTAATGTTTGGGTTGATTGTTAATACCGGTTTTGGATGTAATTGTTCTATTATATT
131 ATGAAATGTTTAATGTTTGGGTTGATTGTTAATACCGATTTTGGATGTAATTGTTCTATTATATT
*
52328978 AATTTTTCGAACTGGGTAAAGGGTGTTACACTAATATTCATTTTTCTATTTCCCAAATTAAACAT
196 AATTTTTCGAACTGGGTAAAGGGTGTTACACTAATATTCATTTTTCTATTTCCAAAATTAAACAT
52329043 CTTAATTAATTTTCCAATTAAATAATATTCTTCACACAATTCTAATTCTATTAAAATCATTCAAT
261 CTTAATTAATTTTCCAATTAAATAATATTCTTCACACAATTCTAATTCTATTAAAATCATTCAAT
52329108 AAGTTTACT
326 AAGTTTACT
52329117 ATCATTTAAT
Statistics
Matches: 329, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
360 329 1.00
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (360 bp):
GTTTTCAGAAATTCTCATACTTTTTGTTATATGTTCAGTTAAGTCCTTATTTGTTTCCGGATTGG
TTTAAGAGCCTTCGTAAGATCGTTTGAGACTTGGATTTGATTATAAATCATGGTATACTTAAAAT
ATGAAATGTTTAATGTTTGGGTTGATTGTTAATACCGATTTTGGATGTAATTGTTCTATTATATT
AATTTTTCGAACTGGGTAAAGGGTGTTACACTAATATTCATTTTTCTATTTCCAAAATTAAACAT
CTTAATTAATTTTCCAATTAAATAATATTCTTCACACAATTCTAATTCTATTAAAATCATTCAAT
AAGTTTACTCTAATTCTAATTCTAATTCTATTTCT
Found at i:52329252 original size:57 final size:56
Alignment explanation
Indices: 52329154--52329265 Score: 140
Period size: 57 Copynumber: 2.0 Consensus size: 56
52329144 ATTTCCAGGT
* * *
52329154 CATTTTCATTTTTCATTTTTATTTTTGAAAAATCCTCATTCATTTTCAAATGTTTC
1 CATTTTCATTTTTCATTTTCATTTTGGAAAAATCCTCATTCATTTCCAAATGTTTC
52329210 CATTTCTCTATTTTT-ATTTTCATTTTGGATAAAA-CCAT-ATTCATTTCCAAATGTTT
1 CATTT-TC-ATTTTTCATTTTCATTTTGGA-AAAATCC-TCATTCATTTCCAAATGTTT
52329266 TTCAATTCTC
Statistics
Matches: 49, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
56 5 0.10
57 33 0.67
58 11 0.22
ACGTcount: A:0.26, C:0.16, G:0.04, T:0.54
Consensus pattern (56 bp):
CATTTTCATTTTTCATTTTCATTTTGGAAAAATCCTCATTCATTTCCAAATGTTTC
Found at i:52335038 original size:25 final size:24
Alignment explanation
Indices: 52334979--52335043 Score: 85
Period size: 26 Copynumber: 2.6 Consensus size: 24
52334969 CTTATGAACG
52334979 TCCCGTATATAGCTCTTTGTGAGCT
1 TCCCGT-TATAGCTCTTTGTGAGCT
*
52335004 TCTCGATTATAGCCTCTTTGTGAGCT
1 TCCCG-TTATAG-CTCTTTGTGAGCT
*
52335030 TCCCGTTATTGCTC
1 TCCCGTTATAGCTC
52335044 GCTTGAACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
24 3 0.09
25 14 0.40
26 18 0.51
ACGTcount: A:0.14, C:0.26, G:0.18, T:0.42
Consensus pattern (24 bp):
TCCCGTTATAGCTCTTTGTGAGCT
Found at i:52335141 original size:24 final size:25
Alignment explanation
Indices: 52335114--52335161 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
52335104 CTCGTTAATT
52335114 GCTCTTCG-AAGCTACCTGTTATAG
1 GCTCTTCGTAAGCTACCTGTTATAG
* * *
52335138 GCTCTTTGTGAGCTTCCTGTTATA
1 GCTCTTCGTAAGCTACCTGTTATA
52335162 TTGGCCGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.17, C:0.23, G:0.21, T:0.40
Consensus pattern (25 bp):
GCTCTTCGTAAGCTACCTGTTATAG
Found at i:52335176 original size:25 final size:26
Alignment explanation
Indices: 52335148--52335214 Score: 84
Period size: 25 Copynumber: 2.7 Consensus size: 26
52335138 GCTCTTTGTG
52335148 AGCTTCCTGTTATATTGGCCGA-ATA
1 AGCTTCCTGTTATATTGGCCGACATA
* * * *
52335173 AGCTTCCCGTTACA-TGGCTGACATG
1 AGCTTCCTGTTATATTGGCCGACATA
52335198 AGCTTCCTGTTATATTG
1 AGCTTCCTGTTATATTG
52335215 CTTGAGAGTG
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
24 6 0.18
25 26 0.76
26 2 0.06
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (26 bp):
AGCTTCCTGTTATATTGGCCGACATA
Found at i:52337363 original size:28 final size:28
Alignment explanation
Indices: 52337310--52337363 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
52337300 CTTTTTCCTT
* *
52337310 TTGTCCTAGCGGACTTACATTGTGTTTA
1 TTGTCCCAGCGGACTTACATTCTGTTTA
52337338 TTGTCCCAGCGGACTT-CATCTCTGTT
1 TTGTCCCAGCGGACTTACAT-TCTGTT
52337364 CCGTTTTTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.15, C:0.24, G:0.20, T:0.41
Consensus pattern (28 bp):
TTGTCCCAGCGGACTTACATTCTGTTTA
Found at i:52345431 original size:51 final size:54
Alignment explanation
Indices: 52345376--52345505 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 54
52345366 GCTGCTATAG
52345376 CATCTTTCATCTATGGTCTTACA-CCGAT-TACCT-TAA-A-CATTGCTGCCATGA
1 CATCTTTCATCTATGGTCTTACAGCC-ATATACCTATAATACCA-TGCTGCCATGA
52345427 CATCTTTCATCTATGGTCTTA-AGCCATATACCTATAACTTGTACCATGCTGCCATGA
1 CATCTTTCATCTATGGTCTTACAGCCATATACCTATAA----TACCATGCTGCCATGA
*
52345484 CATCTTTCATCCATGGTCTTAC
1 CATCTTTCATCTATGGTCTTAC
52345506 GCTACGTACA
Statistics
Matches: 68, Mismatches: 1, Indels: 13
0.83 0.01 0.16
Matches are distributed among these distances:
50 3 0.04
51 28 0.41
52 3 0.04
57 32 0.47
58 2 0.03
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.36
Consensus pattern (54 bp):
CATCTTTCATCTATGGTCTTACAGCCATATACCTATAATACCATGCTGCCATGA
Found at i:52346146 original size:33 final size:33
Alignment explanation
Indices: 52346104--52346169 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
52346094 GAACCTTACC
52346104 CGCTTGCTGGTTTCCCCACTTTTCCAACTCCCT
1 CGCTTGCTGGTTTCCCCACTTTTCCAACTCCCT
52346137 CGCTTGCTGGTTTCCCCACTTTTCCAACTCCCT
1 CGCTTGCTGGTTTCCCCACTTTTCCAACTCCCT
52346170 ACTCCTGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.09, C:0.42, G:0.12, T:0.36
Consensus pattern (33 bp):
CGCTTGCTGGTTTCCCCACTTTTCCAACTCCCT
Found at i:52356046 original size:33 final size:34
Alignment explanation
Indices: 52356001--52356100 Score: 121
Period size: 34 Copynumber: 3.0 Consensus size: 34
52355991 AACGGACCTC
*
52356001 TCGTGTTTATTGTCCTGGCAGACTTA-CTTTATT
1 TCGTGTTTATTGTCCTGGCAGACTTATCTCTATT
* **
52356034 TCGTATTTATTGTCCTGGGGGACTTATCTCTATT
1 TCGTGTTTATTGTCCTGGCAGACTTATCTCTATT
* * * *
52356068 CCATGTTTACTGTCCTGACAGACTTATCTCTAT
1 TCGTGTTTATTGTCCTGGCAGACTTATCTCTAT
52356101 GGATGCCATG
Statistics
Matches: 55, Mismatches: 11, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
33 23 0.42
34 32 0.58
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.45
Consensus pattern (34 bp):
TCGTGTTTATTGTCCTGGCAGACTTATCTCTATT
Found at i:52359274 original size:101 final size:101
Alignment explanation
Indices: 52359077--52359299 Score: 266
Period size: 101 Copynumber: 2.2 Consensus size: 101
52359067 ACACATGCAT
* ** * * *
52359077 TGTCATGGCCCAACCATGGTCTTACGTTCGTACTGCCATAACCCAGTTATGGTCTTATCATTAGA
1 TGTCATGGTCCAACCATGGTCTTACGTTCAAACTGCCATAACCCAATTATGCTCTTATCATTAAA
* * * * *
52359142 ATGTCATAACCCAGCTATAGTCTTACTTATAAATAC
66 ATGCCATAACCCAACTATAGTATTACATATAAACAC
* * * *
52359178 TGTCATGGTCCAACCATTGTCTTACGTTCAAAGTGTCATAACCCAATTATGCTCTTTTCATTAAA
1 TGTCATGGTCCAACCATGGTCTTACGTTCAAACTGCCATAACCCAATTATGCTCTTATCATTAAA
* * *
52359243 ATGCCATATCCCAACTATGGTATTACATATAAACAT
66 ATGCCATAACCCAACTATAGTATTACATATAAACAC
* *
52359279 TGCCATGGTCCAAGCATGGTC
1 TGTCATGGTCCAACCATGGTC
52359300 ATATTAGTCA
Statistics
Matches: 101, Mismatches: 21, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (101 bp):
TGTCATGGTCCAACCATGGTCTTACGTTCAAACTGCCATAACCCAATTATGCTCTTATCATTAAA
ATGCCATAACCCAACTATAGTATTACATATAAACAC
Found at i:52370754 original size:2 final size:2
Alignment explanation
Indices: 52370747--52370771 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
52370737 TGATTGGTGA
52370747 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
52370772 GGTTGTTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:52371482 original size:78 final size:78
Alignment explanation
Indices: 52371365--52371509 Score: 281
Period size: 78 Copynumber: 1.9 Consensus size: 78
52371355 AAATACTTTT
52371365 TTTTTTAATTTTATAATTCTTTGTATGGGTTTTAATTATAGTTTCATAATTTTATTTATAACATA
1 TTTTTTAATTTTATAATTCTTTGTATGGGTTTTAATTATAGTTTCATAATTTTATTTATAACATA
52371430 TAATACAAAATAC
66 TAATACAAAATAC
*
52371443 TTTTTTAATTTTATAATTTTTTGTATGGGTTTTAATTATAGTTTCATAATTTTATTTATAACATA
1 TTTTTTAATTTTATAATTCTTTGTATGGGTTTTAATTATAGTTTCATAATTTTATTTATAACATA
52371508 TA
66 TA
52371510 TTATAATTCT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (78 bp):
TTTTTTAATTTTATAATTCTTTGTATGGGTTTTAATTATAGTTTCATAATTTTATTTATAACATA
TAATACAAAATAC
Found at i:52378801 original size:142 final size:142
Alignment explanation
Indices: 52378545--52378824 Score: 508
Period size: 142 Copynumber: 2.0 Consensus size: 142
52378535 TTTTGGGTGG
52378545 AAGATATCTGCAAGTTTATGAATGATTTTTATCTGGACAATTTTACGGAGCAATAAAAACTACAC
1 AAGATATCTGCAAGTTTATGAATGATTTTTATCTGGACAATTTTACGGAGCAATAAAAACTACAC
* * *
52378610 ATGAAGATTCAATTGGAGTTTTTTCAACTTGATGCTTATCAAAGCACAGAGTTGCAGAAAGCTAC
66 ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
52378675 TACAGTTGCAGA
131 TACAGTTGCAGA
*
52378687 AAGATATCTGCAAGTTTATGAATGATTTTTATAC-GGACAATTTTACGGAGCAATAAAAATTACA
1 AAGATATCTGCAAGTTTATGAATGATTTTTAT-CTGGACAATTTTACGGAGCAATAAAAACTACA
52378751 CATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTA
65 CATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTA
52378816 CTACAGTTG
130 CTACAGTTG
52378825 TTGAGTTGTG
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
142 132 0.99
143 1 0.01
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (142 bp):
AAGATATCTGCAAGTTTATGAATGATTTTTATCTGGACAATTTTACGGAGCAATAAAAACTACAC
ATGAAGATTCAATTGGAGTATTTTCAACTTGATGATCATCAAAGCACAGAGTTGCAGAAAGCTAC
TACAGTTGCAGA
Found at i:52379062 original size:40 final size:40
Alignment explanation
Indices: 52378988--52379166 Score: 234
Period size: 40 Copynumber: 4.5 Consensus size: 40
52378978 CAAAAAGTCA
* * *
52378988 AGCATTAGCGGCG-TTTCTGAAACAAACGTCGCTATAGGTCG
1 AGCATTAGCGGCGCTTTTTG-AA-AAACGCCGCTATAGATCG
* *
52379029 AGCATTAGCGGTGCTTTTTGAAAAACGCCGCTATAGATTG
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCG
* *
52379069 AGCATTAGCGGCGCTTTTTGAAAAACGTCGCTATAGATCA
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCG
* * * *
52379109 AGCATTAACGACGCTTCTCGAAAAACGCCGCTATAGATCG
1 AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCG
52379149 AGCATTAGCGGCGCTTTT
1 AGCATTAGCGGCGCTTTT
52379167 CAAAAAGCGC
Statistics
Matches: 119, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
40 100 0.84
41 14 0.12
42 5 0.04
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (40 bp):
AGCATTAGCGGCGCTTTTTGAAAAACGCCGCTATAGATCG
Found at i:52379293 original size:40 final size:40
Alignment explanation
Indices: 52379217--52379325 Score: 128
Period size: 40 Copynumber: 2.7 Consensus size: 40
52379207 AGCTTTAGTG
* * * *
52379217 GCATTAGCGACGCTTTTTTAAAACACGCCGCAATAGATCGA
1 GCATTAGCGGCGCTTTTTGAAAA-ACGCCACAATAGATCAA
* *
52379258 GCATTAGCGGCGCTATTTGAAAAACGCCACTATAGATCAA
1 GCATTAGCGGCGCTTTTTGAAAAACGCCACAATAGATCAA
* * *
52379298 GCATTAGAGGCACTTTTTGGAAAACGCC
1 GCATTAGCGGCGCTTTTTGAAAAACGCC
52379326 GCAAAAAAGT
Statistics
Matches: 58, Mismatches: 10, Indels: 1
0.84 0.14 0.01
Matches are distributed among these distances:
40 38 0.66
41 20 0.34
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (40 bp):
GCATTAGCGGCGCTTTTTGAAAAACGCCACAATAGATCAA
Done.