Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A09
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: 81831061
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 3560000 characters in sequence are not A, C, G, or T
File 241 of 259
Found at i:75553131 original size:15 final size:15
Alignment explanation
Indices: 75553108--75553144 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
75553098 GATACAAATC
75553108 AAAA-AAAAAAGAAAG
1 AAAAGAAAAAA-AAAG
75553123 AAAAGAAAAAAAAAG
1 AAAAGAAAAAAAAAG
75553138 AAAAGAA
1 AAAAGAA
75553145 CATATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 15 0.71
16 6 0.29
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAAAAAAG
Found at i:75561087 original size:17 final size:18
Alignment explanation
Indices: 75561065--75561100 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
75561055 TAAATGAGTT
75561065 AATTAGGAT-TAAATTGG
1 AATTAGGATATAAATTGG
75561082 AATTAGGATATAAATTGG
1 AATTAGGATATAAATTGG
75561100 A
1 A
75561101 TAGAAATTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (18 bp):
AATTAGGATATAAATTGG
Found at i:75561821 original size:38 final size:38
Alignment explanation
Indices: 75561719--75561855 Score: 107
Period size: 38 Copynumber: 3.6 Consensus size: 38
75561709 GACCTCAAGT
* * *
75561719 CGATGAGACACTGGGTGTCACTATTTTACTTCGGATAGATT
1 CGATGAGACACTGGGTGTCA--ACTTTACTTCGGCTAG-TC
** * * * *
75561760 CGATGAGGTACTAGGT-ACCACTTTACTTCGGCTAGGC
1 CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTC
* *
75561797 CGATGAGACACTGGGTGTCAACTTTGCTTCGAACTA-TC
1 CGATGAGACACTGGGTGTCAACTTTACTTCG-GCTAGTC
* *
75561835 CGATGAGGCACTGGATGTCAA
1 CGATGAGACACTGGGTGTCAA
75561856 ACTGGTGTGT
Statistics
Matches: 75, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 13 0.17
38 45 0.60
39 3 0.04
40 1 0.01
41 13 0.17
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.28
Consensus pattern (38 bp):
CGATGAGACACTGGGTGTCAACTTTACTTCGGCTAGTC
Found at i:75563081 original size:18 final size:18
Alignment explanation
Indices: 75563058--75563093 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
75563048 CTTTTGAGAA
75563058 AAAAAAAAGATGATGGTT
1 AAAAAAAAGATGATGGTT
75563076 AAAAAAAAGATGATGGTT
1 AAAAAAAAGATGATGGTT
75563094 GTGATATCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.22, T:0.22
Consensus pattern (18 bp):
AAAAAAAAGATGATGGTT
Found at i:75567016 original size:31 final size:31
Alignment explanation
Indices: 75566981--75567039 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
75566971 GAAAAGTGGC
*
75566981 ATGGGATAATTT-TTTTTTGGTCCTTGAAATA
1 ATGGGAT-ATTTATTGTTTGGTCCTTGAAATA
*
75567012 ATGGGCTATTTATTGTTTGGTCCTTGAA
1 ATGGGATATTTATTGTTTGGTCCTTGAA
75567040 CCTCAACTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.22, C:0.08, G:0.22, T:0.47
Consensus pattern (31 bp):
ATGGGATATTTATTGTTTGGTCCTTGAAATA
Found at i:75569757 original size:21 final size:21
Alignment explanation
Indices: 75569731--75569771 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
75569721 AGACGAGCAA
* *
75569731 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
75569752 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
75569772 TTGAGCAGAT
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:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:75573801 original size:22 final size:21
Alignment explanation
Indices: 75573776--75573821 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
75573766 CTCATATTTA
* *
75573776 ATTTTAATTTTAATTATAACTT
1 ATTTAAATTATAATTATAA-TT
75573798 ATTTAAATTATAATTATAATT
1 ATTTAAATTATAATTATAATT
75573819 ATT
1 ATT
75573822 AAGATATGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTAAATTATAATTATAATT
Found at i:75575959 original size:18 final size:18
Alignment explanation
Indices: 75575932--75575988 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
75575922 TACGACCGTT
75575932 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
75575950 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
75575968 TACGGTACTGTTCCCGTA
1 TACGGTACTATTCACGTA
75575986 TAC
1 TAC
75575989 AGTAGTTGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:75587851 original size:3 final size:3
Alignment explanation
Indices: 75587845--75587900 Score: 96
Period size: 3 Copynumber: 18.7 Consensus size: 3
75587835 AGGAGGAGAG
75587845 GAA GAA GAA GGAA -AA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA -GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
75587890 GAA GAA GAA GA
1 GAA GAA GAA GA
75587901 CAGAGAGAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:75592357 original size:21 final size:21
Alignment explanation
Indices: 75592328--75592368 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
75592318 ATCTGCTCAA
* *
75592328 ACTCAACCTGTTTTGGAGTAC
1 ACTCAACCTGCTGTGGAGTAC
*
75592349 ACTCCACCTGCTGTGGAGTA
1 ACTCAACCTGCTGTGGAGTA
75592369 TTGCTCGTCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCAACCTGCTGTGGAGTAC
Found at i:75601947 original size:88 final size:87
Alignment explanation
Indices: 75601790--75602008 Score: 278
Period size: 88 Copynumber: 2.5 Consensus size: 87
75601780 ATAAGACTTT
* * * * *
75601790 TTTTCATTATTAAT-AGCACTACTAAAAAGAGGTAAAGTAAAGTAGTTTTATTTAATACCTAAAA
1 TTTT-ATTATTAATGA-CACTACTAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAA
* *
75601854 GGTTTTTTTATGTTTGGAAACGTA
64 AGTTTTGTTATGTTTGGAAACGTA
75601878 TTTTATTATTAATGACACTACTAAAAAAATAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAA
1 TTTTATTATTAATGACACTACTAAAAAAA-AGTGAAGTAACGTAGTTTTATTTAATAACTAAAAA
*
75601943 GTTTTGTTATGTTTGGAAATGTA
65 GTTTTGTTATGTTTGGAAACGTA
* * *
75601966 TTTCATTATTAATGATACTATTTAAAAAAAAAAGTGAAGTAAC
1 TTTTATTATTAATGACACTA-CT--AAAAAAAAGTGAAGTAAC
75602009 ATAAAAAGTT
Statistics
Matches: 115, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
87 22 0.19
88 74 0.64
89 1 0.01
90 11 0.10
91 7 0.06
ACGTcount: A:0.41, C:0.07, G:0.13, T:0.39
Consensus pattern (87 bp):
TTTTATTATTAATGACACTACTAAAAAAAAGTGAAGTAACGTAGTTTTATTTAATAACTAAAAAG
TTTTGTTATGTTTGGAAACGTA
Found at i:75602069 original size:74 final size:72
Alignment explanation
Indices: 75601933--75602082 Score: 205
Period size: 74 Copynumber: 2.1 Consensus size: 72
75601923 TTTTATTTAA
* *
75601933 TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATGATACTATTTAAAAAAAAA
1 TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATGACACTAGTTAAAAAAAAA
75601998 AGTGAAG
66 AGTGAAG
*
75602005 TAACATAAAAAGTTTTTTTTATGTTTGGAAATGTA-TTCTATTATTAATGACACT-GTTAAGAAA
1 TAAC-TAAAAAG-TTTTGTTATGTTTGGAAATGTATTTC-ATTATTAATGACACTAGTTAA-AAA
* *
75602068 AAAAGGTTAAG
62 AAAAAGTGAAG
75602079 TAAC
1 TAAC
75602083 GTAATTTTAT
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
72 4 0.06
73 14 0.20
74 51 0.74
ACGTcount: A:0.42, C:0.05, G:0.14, T:0.39
Consensus pattern (72 bp):
TAACTAAAAAGTTTTGTTATGTTTGGAAATGTATTTCATTATTAATGACACTAGTTAAAAAAAAA
AGTGAAG
Found at i:75602113 original size:91 final size:89
Alignment explanation
Indices: 75602010--75602403 Score: 445
Period size: 91 Copynumber: 4.5 Consensus size: 89
75602000 TGAAGTAACA
*
75602010 TAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAGGT
1 TAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATT-A-AAAAAAAGGT
*
75602075 TAAGTAACGTAATTTTATTTAATACC
64 GAAGTAACGTAATTTTATTTAATACC
* * * *
75602101 TAAAAAGTTTTTTTTTTTATGTTTTGAAATGTATTCTATTATTAATCACACTAAT-AAAAAATGG
1 TAAAAAG---TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAAGG
*
75602165 TGGAGTAACGTAATTTTATTTAATACC
63 TGAAGTAACGTAATTTTATTTAATACC
* * * * * *
75602192 TAAAATGTTTTTTTTTATGTTTGGAAATGTATTTTTTTATTAATGAGACTATT--AAAAAATGTA
1 TAAAAAG-TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAAGGTG
* *
75602255 AAGTAACGTAGTTTTTTATTTAATAAC
65 AAGTAACGTA--ATTTTATTTAATACC
75602282 T------TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAA-GTGA
1 TAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAAGGTGA
*
75602340 AGTAACGTAGTTTTATTTAATACC
66 AGTAACGTAATTTTATTTAATACC
* * *
75602364 T---AATTTTTTTTTAATCTTTGGAAATGTATTCCATTATTAA
1 TAAAAAGTTTTTTTT-ATGTTTGGAAATGTATTCTATTATTAA
75602404 AAAAGTGAAG
Statistics
Matches: 264, Mismatches: 28, Indels: 27
0.83 0.09 0.08
Matches are distributed among these distances:
82 14 0.05
83 42 0.16
84 12 0.05
85 14 0.05
86 25 0.09
88 16 0.06
89 40 0.15
90 14 0.05
91 46 0.17
94 41 0.16
ACGTcount: A:0.36, C:0.06, G:0.12, T:0.46
Consensus pattern (89 bp):
TAAAAAGTTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAAGGTGA
AGTAACGTAATTTTATTTAATACC
Found at i:75602232 original size:89 final size:88
Alignment explanation
Indices: 75602017--75602403 Score: 457
Period size: 83 Copynumber: 4.4 Consensus size: 88
75602007 ACATAAAAAG
* *
75602017 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTGTTAAGAAAAAAAGGTTAAGTAA
1 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACAC---TAATAAAAAAAGGTGAAGTAA
75602082 CGTAATTTTATTTAATACCTAAAAAGTTT
63 CGTAATTTTATTTAATACCT-AAAA--TT
* * * *
75602111 TTTTTTTTATGTTTTGAAATGTATTCTATTATTAATCACACTAATAAAAAATGGTGGAGTAACGT
1 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAAAGGTGAAGTAACGT
75602176 AATTTTATTTAATACCTAAAATGT
66 AATTTTATTTAATACCTAAAAT-T
* * * * * *
75602200 TTTTTTTTATGTTTGGAAATGTATTTTTTTATTAATGAGACT-ATTAAAAAATGTAAAGTAACGT
1 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAAAGGTGAAGTAACGT
* * *
75602264 -AGTTT-TTT-AT--TTAATAACT
66 AATTTTATTTAATACCTAA-AATT
* *
75602283 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTATTAAAAAAAAGTGAAGTAACGT
1 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAAAGGTGAAGTAACGT
*
75602348 AGTTTTATTTAATACCT--AATT
66 AATTTTATTTAATACCTAAAATT
* * *
75602369 TTTTTTTAATCTTTGGAAATGTATTCCATTATTAA
1 TTTTTTTTATGTTTGGAAATGTATTCTATTATTAA
75602404 AAAAGTGAAG
Statistics
Matches: 252, Mismatches: 33, Indels: 24
0.82 0.11 0.08
Matches are distributed among these distances:
83 43 0.17
84 20 0.08
85 5 0.02
86 41 0.16
87 6 0.02
88 18 0.07
89 39 0.15
90 4 0.02
91 37 0.15
94 39 0.15
ACGTcount: A:0.35, C:0.06, G:0.12, T:0.47
Consensus pattern (88 bp):
TTTTTTTTATGTTTGGAAATGTATTCTATTATTAATGACACTAATAAAAAAAGGTGAAGTAACGT
AATTTTATTTAATACCTAAAATT
Found at i:75604329 original size:3 final size:3
Alignment explanation
Indices: 75604321--75604374 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
75604311 AACCTTCACA
* * *
75604321 TAT TAT TAT TAT TAT TGT TAT TAT TAT TAT TTT TAC TAT CTAAT GTAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -T-AT -TAT
75604369 TAT TAT
1 TAT TAT
75604375 ACTTATTTTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
3 36 0.86
4 3 0.07
5 3 0.07
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:75604479 original size:18 final size:17
Alignment explanation
Indices: 75604432--75604485 Score: 56
Period size: 18 Copynumber: 3.1 Consensus size: 17
75604422 TTATTGTACG
*
75604432 TATATA-TATACTTTTA
1 TATATAGTATATTTTTA
75604448 TATATAGTATTATTTTTA
1 TATATAGTA-TATTTTTA
*
75604466 TATATCATTATATTTATTA
1 TATAT-AGTATATTT-TTA
75604485 T
1 T
75604486 TATGCTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
16 6 0.19
17 2 0.06
18 17 0.53
19 7 0.22
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (17 bp):
TATATAGTATATTTTTA
Found at i:75605100 original size:17 final size:17
Alignment explanation
Indices: 75605080--75605132 Score: 72
Period size: 17 Copynumber: 3.1 Consensus size: 17
75605070 TCGGATCCCA
75605080 AAAATTTTCGTGTTTTC
1 AAAATTTTCGTGTTTTC
*
75605097 AAAATTTTCGTGTTTTAA
1 AAAATTTTCGTGTTTT-C
*
75605115 AAAATTCTCGT-TTTTC
1 AAAATTTTCGTGTTTTC
75605131 AA
1 AA
75605133 TCGGATCACG
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
16 2 0.06
17 20 0.62
18 10 0.31
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.49
Consensus pattern (17 bp):
AAAATTTTCGTGTTTTC
Found at i:75607691 original size:17 final size:17
Alignment explanation
Indices: 75607659--75607691 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
75607649 TTAATCAATT
75607659 TTATTTTTTTATAAATG
1 TTATTTTTTTATAAATG
75607676 TTATATTTTTTA-AAAT
1 TTAT-TTTTTTATAAAT
75607692 ATTTGCAACT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TTATTTTTTTATAAATG
Found at i:75608945 original size:18 final size:18
Alignment explanation
Indices: 75608918--75608952 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
75608908 ATAAAGTGAC
75608918 ATTTACTTCCTAATTATA
1 ATTTACTTCCTAATTATA
*
75608936 ATTTATTTCCTAATTAT
1 ATTTACTTCCTAATTAT
75608953 CTATACGAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.14, G:0.00, T:0.54
Consensus pattern (18 bp):
ATTTACTTCCTAATTATA
Found at i:75609746 original size:78 final size:78
Alignment explanation
Indices: 75609617--75609768 Score: 277
Period size: 78 Copynumber: 1.9 Consensus size: 78
75609607 CAGAATCTGA
75609617 ATATATCGGACCGTGTATGTTTAAACCACATAAGGGAGAAAACACCAACAGTGACCTATATTTGA
1 ATATATCGGACCGTGTATGTTTAAACCACATAAGGGAGAAAACACCAACAGTGACCTATATTTGA
75609682 CAAAGACAAATTT
66 CAAAGACAAATTT
* * *
75609695 ATATATCGGACCGTGTTTGTTTAAACCGCATAAGGGCGAAAACACCAACAGTGACCTATATTTGA
1 ATATATCGGACCGTGTATGTTTAAACCACATAAGGGAGAAAACACCAACAGTGACCTATATTTGA
75609760 CAAAGACAA
66 CAAAGACAA
75609769 TTAATCACGC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
78 71 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (78 bp):
ATATATCGGACCGTGTATGTTTAAACCACATAAGGGAGAAAACACCAACAGTGACCTATATTTGA
CAAAGACAAATTT
Found at i:75612281 original size:10 final size:10
Alignment explanation
Indices: 75612268--75612292 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
75612258 TCCTTTTCCT
75612268 TTTTTTTTTG
1 TTTTTTTTTG
75612278 TTTTTTTTTG
1 TTTTTTTTTG
75612288 TTTTT
1 TTTTT
75612293 CCTTTTCTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:75616866 original size:20 final size:20
Alignment explanation
Indices: 75616838--75616895 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
75616828 TGCATATGGG
*
75616838 CAGGCCACACGGGCATGTTC
1 CAGGCCACACGGGCATGTCC
* *
75616858 CAGGTCACACGGGCGTGTCC
1 CAGGCCACACGGGCATGTCC
**
75616878 CAAACCACACGGGCATGT
1 CAGGCCACACGGGCATGT
75616896 GCCCCTATCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.22, C:0.34, G:0.29, T:0.14
Consensus pattern (20 bp):
CAGGCCACACGGGCATGTCC
Found at i:75618420 original size:28 final size:30
Alignment explanation
Indices: 75618360--75618420 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
75618350 TATTCCAAGC
** * *
75618360 TCAATTTCAGTCAATATTTTTCAGTATCGA
1 TCAATTTCAGTCAATATCATTCAGTAACAA
75618390 TCAATTT-A-TCAATATCATTCAGTAACAA
1 TCAATTTCAGTCAATATCATTCAGTAACAA
75618418 TCA
1 TCA
75618421 GTCATTCAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 19 0.70
29 1 0.04
30 7 0.26
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.39
Consensus pattern (30 bp):
TCAATTTCAGTCAATATCATTCAGTAACAA
Found at i:75619183 original size:20 final size:20
Alignment explanation
Indices: 75619146--75619183 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75619136 TTATCATACA
*
75619146 TATTAAATAATAATTTCAAC
1 TATTAAATAATAAGTTCAAC
*
75619166 TATTAAATATTAAGTTCA
1 TATTAAATAATAAGTTCA
75619184 GATTATAGAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (20 bp):
TATTAAATAATAAGTTCAAC
Found at i:75619224 original size:21 final size:21
Alignment explanation
Indices: 75619200--75619241 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
75619190 AGAAATACAA
*
75619200 ACCGTAATTTCTGAGCTAACC
1 ACCGTAATTTCCGAGCTAACC
75619221 ACCGTAATTTCCGAGCTAACC
1 ACCGTAATTTCCGAGCTAACC
75619242 CTCGTTGACT
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:0.29, C:0.31, G:0.14, T:0.26
Consensus pattern (21 bp):
ACCGTAATTTCCGAGCTAACC
Found at i:75620170 original size:17 final size:18
Alignment explanation
Indices: 75620142--75620176 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
75620132 AATTTAATTA
75620142 TTTTATCTAAAAAATATC
1 TTTTATCTAAAAAATATC
75620160 TTTTA-CTAAAAAATATC
1 TTTTATCTAAAAAATATC
75620177 ACAAATGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTTATCTAAAAAATATC
Found at i:75621979 original size:27 final size:26
Alignment explanation
Indices: 75621941--75622013 Score: 83
Period size: 26 Copynumber: 2.8 Consensus size: 26
75621931 GGGTGTGGTG
* *
75621941 CCTATCTAATAGGCGGCACCAGTGATC
1 CCTATCTGATAGGCGGCA-CAGTGATA
* * *
75621968 CCTATCTGATAGGCAGCACTGTGGTA
1 CCTATCTGATAGGCGGCACAGTGATA
*
75621994 CCTATCTGATAGGCGACACA
1 CCTATCTGATAGGCGGCACA
75622014 TCTAGTATTT
Statistics
Matches: 38, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 22 0.58
27 16 0.42
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (26 bp):
CCTATCTGATAGGCGGCACAGTGATA
Found at i:75622003 original size:26 final size:27
Alignment explanation
Indices: 75621934--75622007 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 27
75621924 GATATAGGGG
* * *
75621934 TGTGGTGCCTATCTAATAGGCGGCACC
1 TGTGGTACCTATCTGATAGGCAGCACC
* * *
75621961 AGTGATCCCTATCTGATAGGCAGCA-C
1 TGTGGTACCTATCTGATAGGCAGCACC
75621987 TGTGGTACCTATCTGATAGGC
1 TGTGGTACCTATCTGATAGGC
75622008 GACACATCTA
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
26 19 0.49
27 20 0.51
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (27 bp):
TGTGGTACCTATCTGATAGGCAGCACC
Found at i:75623451 original size:22 final size:22
Alignment explanation
Indices: 75623426--75623468 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
75623416 TATCCAAACA
75623426 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
75623448 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
75623469 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:75623472 original size:11 final size:11
Alignment explanation
Indices: 75623433--75623473 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
75623423 ACAATAACAA
75623433 CAAAATAGTAG
1 CAAAATAGTAG
* *
75623444 CAACATAATAG
1 CAAAATAGTAG
*
75623455 TAAAATAGTAG
1 CAAAATAGTAG
75623466 CAAAATAG
1 CAAAATAG
75623474 GGAGAAAACA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:75624244 original size:21 final size:22
Alignment explanation
Indices: 75624220--75624263 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
75624210 TTTCTGAATT
75624220 TTAAATATAATTTTTAA-AATA
1 TTAAATATAATTTTTAATAATA
*
75624241 TTAAATATATTTTTTAATAATA
1 TTAAATATAATTTTTAATAATA
75624263 T
1 T
75624264 AAAAATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TTAAATATAATTTTTAATAATA
Found at i:75624345 original size:20 final size:21
Alignment explanation
Indices: 75624320--75624363 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
75624310 GTTTTATAAT
*
75624320 ATTTTAAATGT-ATATTTTAA
1 ATTTTAAATATAATATTTTAA
75624340 ATTTTAAATATAATATTTTAA
1 ATTTTAAATATAATATTTTAA
75624361 ATT
1 ATT
75624364 ATTTTTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 10 0.45
21 12 0.55
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (21 bp):
ATTTTAAATATAATATTTTAA
Found at i:75624430 original size:19 final size:20
Alignment explanation
Indices: 75624408--75624450 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
75624398 TAATTAAAAG
* *
75624408 TTAAAAAAG-AATATTTTAT
1 TTAAAAAAGTAAAATTTGAT
75624427 TTAAAAAAGTAAAATTTGAT
1 TTAAAAAAGTAAAATTTGAT
75624447 TTAA
1 TTAA
75624451 TTAGAAAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.53, C:0.00, G:0.07, T:0.40
Consensus pattern (20 bp):
TTAAAAAAGTAAAATTTGAT
Found at i:75624708 original size:31 final size:31
Alignment explanation
Indices: 75624670--75624763 Score: 127
Period size: 30 Copynumber: 2.9 Consensus size: 31
75624660 TTTTATATTA
*
75624670 TTAAAAAAATATTTATAATTTAAAAAATAAT
1 TTAAAAAAATATTTAAAATTTAAAAAATAAT
75624701 TT-AAAAAATATTTAAAATTTAGAAAAATAAT
1 TTAAAAAAATATTTAAAATTTA-AAAAATAAT
*
75624732 TTCAAATATATATATTTAAAATTTAAAAAATA
1 TT-AAA-A-AAATATTTAAAATTTAAAAAATA
75624764 TATATTATAA
Statistics
Matches: 56, Mismatches: 2, Indels: 7
0.86 0.03 0.11
Matches are distributed among these distances:
30 18 0.32
31 13 0.23
33 2 0.04
34 8 0.14
35 15 0.27
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (31 bp):
TTAAAAAAATATTTAAAATTTAAAAAATAAT
Found at i:75624713 original size:11 final size:12
Alignment explanation
Indices: 75624684--75624717 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
75624674 AAAAATATTT
75624684 ATAATTTAAAAA
1 ATAATTTAAAAA
75624696 ATAATTTAAAAA
1 ATAATTTAAAAA
75624708 AT-ATTTAAAA
1 ATAATTTAAAA
75624718 TTTAGAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 8 0.36
12 14 0.64
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (12 bp):
ATAATTTAAAAA
Found at i:75624733 original size:20 final size:18
Alignment explanation
Indices: 75624698--75624764 Score: 68
Period size: 18 Copynumber: 3.8 Consensus size: 18
75624688 TTTAAAAAAT
75624698 AATTTAAAAAATATTTAA
1 AATTTAAAAAATATTTAA
*
75624716 AATTTAGAAAAATAATTTCA
1 AATTTA-AAAAAT-ATTTAA
* *
75624736 AA--T-ATATATATTTAA
1 AATTTAAAAAATATTTAA
75624751 AATTTAAAAAATAT
1 AATTTAAAAAATAT
75624765 ATATTATAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
15 7 0.18
16 4 0.11
17 1 0.03
18 13 0.34
19 6 0.16
20 7 0.18
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (18 bp):
AATTTAAAAAATATTTAA
Found at i:75624755 original size:22 final size:24
Alignment explanation
Indices: 75624729--75624791 Score: 85
Period size: 22 Copynumber: 2.7 Consensus size: 24
75624719 TTAGAAAAAT
75624729 AATTTCAAATATATATATT-T-AA
1 AATTTCAAATATATATATTATAAA
* *
75624751 AATTTAAAAAATATATATTATAAA
1 AATTTCAAATATATATATTATAAA
75624775 ACATTTCAAATATATAT
1 A-ATTTCAAATATATAT
75624792 TTCAAATTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 17 0.50
23 1 0.03
24 3 0.09
25 13 0.38
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (24 bp):
AATTTCAAATATATATATTATAAA
Found at i:75624766 original size:20 final size:19
Alignment explanation
Indices: 75624698--75624766 Score: 51
Period size: 20 Copynumber: 3.8 Consensus size: 19
75624688 TTTAAAAAAT
75624698 AATTTAAAAA-ATATTTAA
1 AATTTAAAAATATATTTAA
*
75624716 AATTTAGAAAA-ATAATTTCA
1 AATTTA-AAAATAT-ATTTAA
*
75624736 AA--T--ATATATATTTAA
1 AATTTAAAAATATATTTAA
75624751 AATTTAAAAAATATAT
1 AATTT-AAAAATATAT
75624767 ATTATAAAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
15 9 0.23
16 2 0.05
17 1 0.03
18 7 0.18
19 6 0.15
20 14 0.36
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.39
Consensus pattern (19 bp):
AATTTAAAAATATATTTAA
Found at i:75624808 original size:23 final size:22
Alignment explanation
Indices: 75624739--75624808 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 22
75624729 AATTTCAAAT
**
75624739 ATATATATTTAAAATTTAAAAA
1 ATATATATTTAAAATTTTTAAA
** *
75624761 ATATATATTATAAAACATTTCAA
1 ATATATATT-TAAAATTTTTAAA
*
75624784 ATATATATTTCAAATTTTTTAAA
1 ATATATATTT-AAAATTTTTAAA
75624807 AT
1 AT
75624809 TAATAATAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
22 10 0.27
23 27 0.73
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATATATTTAAAATTTTTAAA
Found at i:75624832 original size:14 final size:14
Alignment explanation
Indices: 75624813--75624842 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
75624803 TAAAATTAAT
75624813 AATAAATAAAAATA
1 AATAAATAAAAATA
*
75624827 AATAAATAAAGATA
1 AATAAATAAAAATA
75624841 AA
1 AA
75624843 GACAAAACTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (14 bp):
AATAAATAAAAATA
Found at i:75624894 original size:9 final size:9
Alignment explanation
Indices: 75624880--75624921 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
75624870 ACAATATGAC
75624880 AAAAGTAAA
1 AAAAGTAAA
75624889 AAAAGTAAA
1 AAAAGTAAA
**
75624898 AAAAAAAAA
1 AAAAGTAAA
75624907 ACAAAGTAAA
1 A-AAAGTAAA
75624917 AAAAG
1 AAAAG
75624922 AAACAGGGTG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 21 0.75
10 7 0.25
ACGTcount: A:0.81, C:0.02, G:0.10, T:0.07
Consensus pattern (9 bp):
AAAAGTAAA
Found at i:75626452 original size:17 final size:17
Alignment explanation
Indices: 75626426--75626464 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
75626416 GATTGTTATT
75626426 AAAA-ATAATTTAATAA
1 AAAATATAATTTAATAA
*
75626442 AAAATATAATTTAATAT
1 AAAATATAATTTAATAA
75626459 AAAATA
1 AAAATA
75626465 ATATATAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATATAATTTAATAA
Found at i:75627010 original size:22 final size:21
Alignment explanation
Indices: 75626977--75627030 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
75626967 GCAAAAGTAT
75626977 TTTCT-TTTTTTTTAATATTA
1 TTTCTCTTTTTTTTAATATTA
* *
75626997 TATTCTCTTTTTTTTCATCTTA
1 T-TTCTCTTTTTTTTAATATTA
*
75627019 TTTCCCTTTTTT
1 TTTCTCTTTTTT
75627031 AGCAAACTGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 1 0.03
21 14 0.48
22 14 0.48
ACGTcount: A:0.13, C:0.15, G:0.00, T:0.72
Consensus pattern (21 bp):
TTTCTCTTTTTTTTAATATTA
Found at i:75627027 original size:21 final size:22
Alignment explanation
Indices: 75626982--75627030 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
75626972 AGTATTTTCT
*
75626982 TTTTTTTTAATATTATATTCTC
1 TTTTTTTTAATATTATATTCCC
* *
75627004 TTTTTTTTCATCTTAT-TTCCC
1 TTTTTTTTAATATTATATTCCC
75627025 TTTTTT
1 TTTTTT
75627031 AGCAAACTGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 10 0.42
22 14 0.58
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (22 bp):
TTTTTTTTAATATTATATTCCC
Found at i:75627556 original size:14 final size:14
Alignment explanation
Indices: 75627537--75627571 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
75627527 TATTTATTCA
*
75627537 ATTATTTACTATTT
1 ATTATTTAATATTT
75627551 ATTATTTAATATTT
1 ATTATTTAATATTT
*
75627565 AATATTT
1 ATTATTT
75627572 GGTCGTTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (14 bp):
ATTATTTAATATTT
Found at i:75627565 original size:21 final size:22
Alignment explanation
Indices: 75627530--75627571 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
75627520 TAGTGCATAT
*
75627530 TTATTCAATTATTTACTATTTA
1 TTATTCAATTATTTAATATTTA
*
75627552 TTATTTAA-TATTTAATATTT
1 TTATTCAATTATTTAATATTT
75627572 GGTCGTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATTCAATTATTTAATATTTA
Found at i:75628235 original size:31 final size:31
Alignment explanation
Indices: 75628197--75628272 Score: 127
Period size: 31 Copynumber: 2.5 Consensus size: 31
75628187 TAATATATAA
75628197 CATGGACACATAAATAAGTTATGTTCATACT
1 CATGGACACATAAATAAGTTATGTTCATACT
75628228 CATGGACACATAAATAAGTTATGTTCATACT
1 CATGGACACATAAATAAGTTATGTTCATACT
* *
75628259 TATTGAC-CATAAAT
1 CATGGACACATAAAT
75628273 TTTTTATAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
30 7 0.16
31 36 0.84
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (31 bp):
CATGGACACATAAATAAGTTATGTTCATACT
Found at i:75636193 original size:20 final size:19
Alignment explanation
Indices: 75636168--75636219 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
75636158 TTCTAAAAAG
75636168 TAAAAATATTTTTATATTTT
1 TAAAAATATTTTTA-ATTTT
* *
75636188 TTAAAATAATTTTAATTTT
1 TAAAAATATTTTTAATTTT
75636207 TAAAAATAGTTTT
1 TAAAAATA-TTTT
75636220 CATAATTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TAAAAATATTTTTAATTTT
Found at i:75636207 original size:19 final size:20
Alignment explanation
Indices: 75636168--75636219 Score: 70
Period size: 19 Copynumber: 2.6 Consensus size: 20
75636158 TTCTAAAAAG
*
75636168 TAAAAATATTTTTATATTTT
1 TAAAAATAATTTTATATTTT
*
75636188 TTAAAATAATTTTA-ATTTT
1 TAAAAATAATTTTATATTTT
*
75636207 TAAAAATAGTTTT
1 TAAAAATAATTTT
75636220 CATAATTATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
TAAAAATAATTTTATATTTT
Found at i:75636372 original size:7 final size:8
Alignment explanation
Indices: 75636354--75636388 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
75636344 AATAAATAAC
75636354 AAAAATTA
1 AAAAATTA
75636362 AAAAATTA
1 AAAAATTA
*
75636370 AAAAAGATA
1 AAAAA-TTA
75636379 AAAAATTA
1 AAAAATTA
75636387 AA
1 AA
75636389 TCAATAATTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 17 0.71
9 7 0.29
ACGTcount: A:0.77, C:0.00, G:0.03, T:0.20
Consensus pattern (8 bp):
AAAAATTA
Found at i:75651855 original size:24 final size:24
Alignment explanation
Indices: 75651828--75651874 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
75651818 TTAGTATCAT
*
75651828 AATT-TAAATTAATACGAAGTAAAA
1 AATTATAAATT-ATACAAAGTAAAA
*
75651852 AATTATATATTATACAAAGTAAA
1 AATTATAAATTATACAAAGTAAA
75651875 GGAAAAAGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (24 bp):
AATTATAAATTATACAAAGTAAAA
Found at i:75659433 original size:12 final size:12
Alignment explanation
Indices: 75659416--75659446 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
75659406 GAAGCAGGGG
75659416 AGAAAAAGAGAA
1 AGAAAAAGAGAA
*
75659428 AGAAAAAGGGAA
1 AGAAAAAGAGAA
75659440 AGAAAAA
1 AGAAAAA
75659447 TAAAAGAGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AGAAAAAGAGAA
Found at i:75660392 original size:41 final size:42
Alignment explanation
Indices: 75660347--75660446 Score: 102
Period size: 38 Copynumber: 2.5 Consensus size: 42
75660337 CGACCTCAAG
* *
75660347 TCGATGAGACACTGGGTGTCACTAAATTT-CTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
** * * *
75660388 TCGATGAGGTACT-GG-GT-ACCAACTTTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
75660427 T-GATGAGACACTGGGTGTCA
1 TCGATGAGACACTGGGTGTCA
75660447 ACTATTACTT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
38 16 0.35
39 14 0.30
40 4 0.09
41 12 0.26
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TCGATGAGACACTGGGTGTCACCAAATTTACTTCGGATAGAC
Found at i:75660455 original size:39 final size:40
Alignment explanation
Indices: 75660347--75660458 Score: 113
Period size: 39 Copynumber: 2.8 Consensus size: 40
75660337 CGACCTCAAG
* *
75660347 TCGATGAGACACTGGGTGTC-ACTAAATTTCTTCGGATAGAT
1 TCGATGAGACACTGGGTGTCAACT--ATTACTTCGGATAGAC
** ** * *
75660388 TCGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAGGC
1 TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
75660427 T-GATGAGACACTGGGTGTCAACTATTACTTCG
1 TCGATGAGACACTGGGTGTCAACTATTACTTCG
75660459 AACTATCCGA
Statistics
Matches: 57, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
38 18 0.32
39 20 0.35
41 16 0.28
42 3 0.05
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (40 bp):
TCGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAC
Found at i:75660607 original size:18 final size:18
Alignment explanation
Indices: 75660584--75660624 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
75660574 GAAAAAAAAA
75660584 AGAAATT-GAATTATGAAT
1 AGAAATTGGAATTATG-AT
*
75660602 AGAAATTGGAATTGTGAT
1 AGAAATTGGAATTATGAT
75660620 AGAAA
1 AGAAA
75660625 GAGAAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29
Consensus pattern (18 bp):
AGAAATTGGAATTATGAT
Found at i:75661134 original size:20 final size:20
Alignment explanation
Indices: 75661111--75661148 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
75661101 GTTATTAAGT
75661111 TAAAAATTATGTTA-ATGATA
1 TAAAAATTA-GTTATATGATA
*
75661131 TAAATATTAGTTATATGA
1 TAAAAATTAGTTATATGA
75661149 ATGTGAAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.25
20 12 0.75
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (20 bp):
TAAAAATTAGTTATATGATA
Found at i:75671390 original size:15 final size:13
Alignment explanation
Indices: 75671371--75671431 Score: 61
Period size: 14 Copynumber: 4.5 Consensus size: 13
75671361 AATAATAATT
75671371 AAAATAATAAGAAA
1 AAAATAATAA-AAA
*
75671385 ATAAATAA-AAACA
1 A-AAATAATAAAAA
75671398 AAAATAATAAAAA
1 AAAATAATAAAAA
* *
75671411 AAACAAAATAAAAT
1 AAA-ATAATAAAAA
75671425 AAAATAA
1 AAAATAA
75671432 AATGAAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
12 6 0.15
13 13 0.33
14 14 0.36
15 6 0.15
ACGTcount: A:0.80, C:0.03, G:0.02, T:0.15
Consensus pattern (13 bp):
AAAATAATAAAAA
Found at i:75671408 original size:19 final size:20
Alignment explanation
Indices: 75671382--75671433 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 20
75671372 AAATAATAAG
75671382 AAAATAAATAAAAACAAAA-
1 AAAATAAATAAAAACAAAAT
*
75671401 ATAATAAA-AAAAACAAAAT
1 AAAATAAATAAAAACAAAAT
75671420 AAAATAAAATAAAA
1 AAAAT-AAATAAAA
75671434 TGAAAGAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 10 0.36
19 11 0.39
20 3 0.11
21 4 0.14
ACGTcount: A:0.83, C:0.04, G:0.00, T:0.13
Consensus pattern (20 bp):
AAAATAAATAAAAACAAAAT
Found at i:75671418 original size:5 final size:5
Alignment explanation
Indices: 75671370--75671434 Score: 57
Period size: 5 Copynumber: 13.2 Consensus size: 5
75671360 TAATAATAAT
*
75671370 TAAAA TAATAA GAAAA T-AAA TAAAA -ACAAA -AATAA TAAAA -AAAA
1 TAAAA TAA-AA TAAAA TAAAA TAAAA TA-AAA TAA-AA TAAAA TAAAA
*
75671414 CAAAA TAAAA TAAAA TAAAA T
1 TAAAA TAAAA TAAAA TAAAA T
75671435 GAAAGAATAG
Statistics
Matches: 51, Mismatches: 3, Indels: 12
0.77 0.05 0.18
Matches are distributed among these distances:
4 10 0.20
5 35 0.69
6 6 0.12
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (5 bp):
TAAAA
Found at i:75673197 original size:46 final size:46
Alignment explanation
Indices: 75673137--75673410 Score: 424
Period size: 46 Copynumber: 6.0 Consensus size: 46
75673127 TTTGACATGA
* * * * * *
75673137 TGCCATAGTGTCTTTCAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
75673183 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
75673229 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
75673275 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
75673321 TGCCATGGTTTCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
75673367 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
75673411 AGAGCACACT
Statistics
Matches: 212, Mismatches: 15, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
45 4 0.02
46 208 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:75677514 original size:16 final size:17
Alignment explanation
Indices: 75677480--75677516 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
75677470 GTAGATTAAA
*
75677480 AAAGAATACTACGATAT
1 AAAGAATAATACGATAT
75677497 AAAGAATAATAC-ATAT
1 AAAGAATAATACGATAT
75677513 AAAG
1 AAAG
75677517 CAAAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.59, C:0.08, G:0.11, T:0.22
Consensus pattern (17 bp):
AAAGAATAATACGATAT
Found at i:75678173 original size:22 final size:21
Alignment explanation
Indices: 75678148--75678203 Score: 55
Period size: 22 Copynumber: 2.7 Consensus size: 21
75678138 TAAGAAAAAA
75678148 AATAGATATAATATGAAGTAA-C
1 AATA-ATATAATAT-AAGTAATC
*
75678170 AAT-ATAT-ATATAAGTAATT
1 AATAATATAATATAAGTAATC
75678189 AATAAATATAATATA
1 AAT-AATATAATATA
75678204 TGAAAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
18 6 0.21
19 7 0.24
20 4 0.14
21 4 0.14
22 8 0.28
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.34
Consensus pattern (21 bp):
AATAATATAATATAAGTAATC
Found at i:75678226 original size:27 final size:26
Alignment explanation
Indices: 75678188--75678244 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
75678178 TATAAGTAAT
* *
75678188 TAATAAATATAATATATGAAAATATAA
1 TAATAAATATAAGAGATGAAAA-ATAA
* *
75678215 TAATATATATAAGAGATGTAAAATAA
1 TAATAAATATAAGAGATGAAAAATAA
75678241 TAAT
1 TAAT
75678245 TTAAGAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 8 0.31
27 18 0.69
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (26 bp):
TAATAAATATAAGAGATGAAAAATAA
Found at i:75678259 original size:3 final size:3
Alignment explanation
Indices: 75678253--75678312 Score: 50
Period size: 3 Copynumber: 19.0 Consensus size: 3
75678243 ATTTAAGAAA
* * *
75678253 AAT AAT ATAT AAT AAGT AAT AAT AAT ATAT AATT AAA AAT AAT ACT TAT
1 AAT AAT A-AT AAT AA-T AAT AAT AAT A-AT AA-T AAT AAT AAT AAT AAT
75678302 AAT AA- AAT AAT
1 AAT AAT AAT AAT
75678313 TTTATAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
2 2 0.04
3 32 0.70
4 12 0.26
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:75678284 original size:17 final size:16
Alignment explanation
Indices: 75678170--75678328 Score: 60
Period size: 17 Copynumber: 9.2 Consensus size: 16
75678160 ATGAAGTAAC
75678170 AATATATATATAAGTAATT
1 AATA-ATATATAA-TAA-T
75678189 AATAA-ATATAATATAT
1 AATAATATATAATA-AT
75678205 GAA-AATATAATAAT-AT
1 -AATAATAT-ATAATAAT
* *
75678221 ATATAAGAGATGTAA-AAT
1 A-AT-A-ATATATAATAAT
* * *
75678239 AATAATTTAAGAAAAAT
1 AATAATAT-ATAATAAT
75678256 AAT-ATATAATAAGTAAT
1 AATAATAT-ATAA-TAAT
*
75678273 AATAATATATAATTAAA
1 AATAATATATAA-TAAT
75678290 AATAATACTTATAATAA-
1 AATAATA--TATAATAAT
*
75678307 AATAATTTTATAATATAT
1 AATAA-TATATAATA-AT
75678325 AATA
1 AATA
75678329 TAAAAGTAAA
Statistics
Matches: 110, Mismatches: 12, Indels: 37
0.69 0.08 0.23
Matches are distributed among these distances:
15 3 0.03
16 25 0.23
17 45 0.41
18 25 0.23
19 12 0.11
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (16 bp):
AATAATATATAATAAT
Found at i:75678285 original size:44 final size:42
Alignment explanation
Indices: 75678170--75678285 Score: 123
Period size: 44 Copynumber: 2.7 Consensus size: 42
75678160 ATGAAGTAAC
*
75678170 AATATATATATAAGTAATTAATAAATATAATATATGAAAATAT
1 AATATATATATAAGTAA-TAATAAATATAATATAAGAAAATAT
* *
75678213 AATAATATATATAAG-AGAT-GTAAAATAATAATTTAAGAAAA-AT
1 AAT-ATATATATAAGTA-ATAAT-AAAT-ATAATATAAGAAAATAT
75678256 AATATATA-ATAAGTAATAATAATATATAAT
1 AATATATATATAAGTAATAATAA-ATATAAT
75678286 TAAAAATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 16
0.76 0.05 0.20
Matches are distributed among these distances:
41 14 0.23
42 10 0.16
43 14 0.23
44 24 0.39
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (42 bp):
AATATATATATAAGTAATAATAAATATAATATAAGAAAATAT
Found at i:75678291 original size:37 final size:41
Alignment explanation
Indices: 75678250--75678333 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 41
75678240 ATAATTTAAG
*
75678250 AAAAATAATA-TATAAT-AAGTAA-TAATAATATATAAT-T
1 AAAAATAATACTATAATAAAATAATTAATAATATATAATAT
*
75678287 AAAAATAATACTTATAATAAAATAATTTTATAATATATAATAT
1 AAAAATAATAC-TATAATAAAATAA-TTAATAATATATAATAT
75678330 AAAA
1 AAAA
75678334 GTAAAATTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 10 0.26
39 6 0.15
40 5 0.13
42 13 0.33
43 5 0.13
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.36
Consensus pattern (41 bp):
AAAAATAATACTATAATAAAATAATTAATAATATATAATAT
Found at i:75678309 original size:54 final size:52
Alignment explanation
Indices: 75678234--75678391 Score: 135
Period size: 54 Copynumber: 2.9 Consensus size: 52
75678224 TAAGAGATGT
* *
75678234 AAAATAATAATT-TAAGAAAAATAATATATAATAAGTAATAATAATATATAATTA
1 AAAATAATACTTATAA-TAAAATAATATATAATAA-TAATAATAA-ATATAATTA
* *
75678288 AAAATAATACTTATAATAAAATAATTTTATAATATATAAT-ATAAAAGTAAAATTA
1 AAAATAATACTTATAATAAAATAA-TATATAATA-ATAATAAT-AAA-TATAATTA
* **
75678343 GAAATAA-ACGAATAATAAAATATATATATGGAATAAT-ATAATAAATATA
1 AAAATAATACTTATAATAAAATA-ATATAT--AATAATAATAATAAATATA
75678392 GGACTAAATT
Statistics
Matches: 86, Mismatches: 9, Indels: 19
0.75 0.08 0.17
Matches are distributed among these distances:
53 3 0.03
54 43 0.50
55 35 0.41
56 5 0.06
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.33
Consensus pattern (52 bp):
AAAATAATACTTATAATAAAATAATATATAATAATAATAATAAATATAATTA
Found at i:75678378 original size:21 final size:21
Alignment explanation
Indices: 75678352--75678391 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
75678342 AGAAATAAAC
*
75678352 GAATAATAAAATATATATATG
1 GAATAATAAAATAAATATATG
*
75678373 GAATAATATAATAAATATA
1 GAATAATAAAATAAATATA
75678392 GGACTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.07, T:0.33
Consensus pattern (21 bp):
GAATAATAAAATAAATATATG
Found at i:75678618 original size:21 final size:21
Alignment explanation
Indices: 75678594--75678634 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
75678584 TATTAATACC
75678594 AAATTAAAAAAATAAAAAATG
1 AAATTAAAAAAATAAAAAATG
* **
75678615 AAATTAGAAGTATAAAAAAT
1 AAATTAAAAAAATAAAAAAT
75678635 TGCGAGAGGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
AAATTAAAAAAATAAAAAATG
Found at i:75691078 original size:20 final size:20
Alignment explanation
Indices: 75691029--75691078 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
75691019 ATAAAAATAA
*
75691029 TTATATTAATTATATATGTT
1 TTATATTTATTATATATGTT
** * *
75691049 AAATAATTATTATATATTTT
1 TTATATTTATTATATATGTT
75691069 TTATATTTAT
1 TTATATTTAT
75691079 ATTAAATTAC
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
TTATATTTATTATATATGTT
Found at i:75708526 original size:20 final size:21
Alignment explanation
Indices: 75708501--75708540 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
75708491 ATTATAAGCA
75708501 TTTAACAAT-TCATCCTGTAC
1 TTTAACAATCTCATCCTGTAC
*
75708521 TTTAACAATCTCATCGTGTA
1 TTTAACAATCTCATCCTGTA
75708541 TAAATTGTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (21 bp):
TTTAACAATCTCATCCTGTAC
Found at i:75716133 original size:43 final size:45
Alignment explanation
Indices: 75716080--75716163 Score: 109
Period size: 44 Copynumber: 1.9 Consensus size: 45
75716070 TTTTCAATGT
* * *
75716080 TTCAAATTTAATT-TTTATACTTTTATTTTTAATA-ATTTTAAAA
1 TTCAAATTTAATTATTAATAATATTATTTTTAATATATTTTAAAA
* *
75716123 TTCAAGTTTAATTATTAATAATATTATTTTTATTATATTTT
1 TTCAAATTTAATTATTAATAATATTATTTTTAATATATTTT
75716164 TATTAAATGA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
43 12 0.35
44 17 0.50
45 5 0.15
ACGTcount: A:0.36, C:0.04, G:0.01, T:0.60
Consensus pattern (45 bp):
TTCAAATTTAATTATTAATAATATTATTTTTAATATATTTTAAAA
Found at i:75724655 original size:11 final size:11
Alignment explanation
Indices: 75724641--75724678 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
75724631 TTTTCTCTCC
75724641 ATTTTACTACT
1 ATTTTACTACT
*
75724652 ATTTTACTATT
1 ATTTTACTACT
*
75724663 ATATTACTACT
1 ATTTTACTACT
75724674 ATTTT
1 ATTTT
75724679 GTTGTTATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (11 bp):
ATTTTACTACT
Found at i:75724860 original size:21 final size:21
Alignment explanation
Indices: 75724836--75724885 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
75724826 TTTGTTGAAA
*
75724836 AATATTTATTTTGATAT-TTTT
1 AATATTTATTTT-ATATATTAT
75724857 AATATTT-TTTTATATATTAT
1 AATATTTATTTTATATATTAT
75724877 ACATATTTA
1 A-ATATTTA
75724886 AAAAACATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 4 0.16
20 8 0.32
21 13 0.52
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (21 bp):
AATATTTATTTTATATATTAT
Found at i:75727706 original size:16 final size:16
Alignment explanation
Indices: 75727682--75727714 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
75727672 TCTTGAAAAG
75727682 AAAAAAGAAT-TCTTT
1 AAAAAAGAATGTCTTT
75727697 AAAAATAGAATGTCTTT
1 AAAAA-AGAATGTCTTT
75727714 A
1 A
75727715 CAGTTTATAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 5 0.31
17 6 0.38
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (16 bp):
AAAAAAGAATGTCTTT
Found at i:75739850 original size:19 final size:21
Alignment explanation
Indices: 75739809--75739857 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
75739799 CTCAATGAAT
75739809 ATAAACAATTTATTATTTCAA
1 ATAAACAATTTATTATTTCAA
75739830 ATAAACTAATTTA-TA-TT-AA
1 ATAAAC-AATTTATTATTTCAA
75739849 ATAAA-AATT
1 ATAAACAATT
75739858 AAGGACTAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 4 0.15
19 7 0.26
20 2 0.07
21 8 0.30
22 6 0.22
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAAACAATTTATTATTTCAA
Found at i:75740283 original size:6 final size:6
Alignment explanation
Indices: 75740272--75740298 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
75740262 TTCAAAGCAG
75740272 AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAA
75740299 TGCAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:75746620 original size:18 final size:20
Alignment explanation
Indices: 75746574--75746622 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
75746564 AAATGGAAAT
* *
75746574 TTTTATTTGAAATATATAGA
1 TTTTATTTAAAAAATATAGA
*
75746594 TTTTGTTTAAAAAATA-AG-
1 TTTTATTTAAAAAATATAGA
75746612 TTTTATTTAAA
1 TTTTATTTAAA
75746623 TACATTATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 10 0.40
19 2 0.08
20 13 0.52
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (20 bp):
TTTTATTTAAAAAATATAGA
Found at i:75752372 original size:22 final size:22
Alignment explanation
Indices: 75752345--75752458 Score: 128
Period size: 22 Copynumber: 5.3 Consensus size: 22
75752335 TATTTATTAG
75752345 GTAGATAAAATAATTTAATTGT
1 GTAGATAAAATAATTTAATTGT
* * *
75752367 GTAGATTAACTTATTT-ATTAG-
1 GTAGATAAAATAATTTAATT-GT
75752388 GTAGATAAAATAATTTAATTGT
1 GTAGATAAAATAATTTAATTGT
* * *
75752410 GTAGATTAACTTATTT-ATTAG-
1 GTAGATAAAATAATTTAATT-GT
75752431 GTAGATAAAATAATTTAATTGT
1 GTAGATAAAATAATTTAATTGT
75752453 GTAGAT
1 GTAGAT
75752459 TAACTAAACT
Statistics
Matches: 74, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
21 34 0.46
22 40 0.54
ACGTcount: A:0.40, C:0.02, G:0.15, T:0.43
Consensus pattern (22 bp):
GTAGATAAAATAATTTAATTGT
Found at i:75752378 original size:43 final size:43
Alignment explanation
Indices: 75752330--75752463 Score: 268
Period size: 43 Copynumber: 3.1 Consensus size: 43
75752320 TGCGAGAAGA
75752330 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
1 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
75752373 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
1 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
75752416 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
1 TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
75752459 TAACT
1 TAACT
75752464 AAACTTATAT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 91 1.00
ACGTcount: A:0.40, C:0.03, G:0.13, T:0.44
Consensus pattern (43 bp):
TAACTTATTTATTAGGTAGATAAAATAATTTAATTGTGTAGAT
Found at i:75763015 original size:17 final size:15
Alignment explanation
Indices: 75762993--75763042 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 15
75762983 ATATTTTACT
75762993 ATAAAAATAATTAAAAA
1 ATAAAAA-AA-TAAAAA
75763010 ATAAAAAAAATAGAAAA
1 AT-AAAAAAATA-AAAA
75763027 ATAGAAAAAATAAAAA
1 ATA-AAAAAATAAAAA
75763043 TATTAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
16 7 0.23
17 18 0.60
18 5 0.17
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (15 bp):
ATAAAAAAATAAAAA
Found at i:75763018 original size:8 final size:8
Alignment explanation
Indices: 75762993--75763042 Score: 55
Period size: 9 Copynumber: 5.9 Consensus size: 8
75762983 ATATTTTACT
75762993 ATAAAAATA
1 ATAAAAA-A
*
75763002 ATTAAAAA
1 ATAAAAAA
75763010 ATAAAAAAA
1 AT-AAAAAA
*
75763019 ATAGAAAA
1 ATAAAAAA
75763027 ATAGAAAAA
1 ATA-AAAAA
75763036 ATAAAAA
1 ATAAAAA
75763043 TATTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
8 15 0.43
9 20 0.57
ACGTcount: A:0.80, C:0.00, G:0.04, T:0.16
Consensus pattern (8 bp):
ATAAAAAA
Found at i:75763076 original size:9 final size:9
Alignment explanation
Indices: 75763059--75763136 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
75763049 ATATTAAATT
*
75763059 TTATTAAAA
1 TTATAAAAA
75763068 TTATAAAAA
1 TTATAAAAA
* * *
75763077 CTTGTCAATA
1 -TTATAAAAA
75763087 TTATAAAAA
1 TTATAAAAA
*
75763096 -TAGAAAAA
1 TTATAAAAA
*
75763104 TTCTAATAAA
1 TTATAA-AAA
75763114 TTATAAAAA
1 TTATAAAAA
*
75763123 TTTATAAAAC
1 -TTATAAAAA
75763133 TTAT
1 TTAT
75763137 TTAAAATATT
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
8 7 0.13
9 24 0.45
10 22 0.42
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (9 bp):
TTATAAAAA
Found at i:75763160 original size:36 final size:36
Alignment explanation
Indices: 75763117--75763185 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
75763107 TAATAAATTA
75763117 TAAAAA-TTTATAAAACTTATTTAAAATATTTTAGAT
1 TAAAAATTTTATAAAA-TTATTTAAAATATTTTAGAT
* * *
75763153 TAAAAATTTTTTAGAATTATTTAAAATTTTTTA
1 TAAAAATTTTATAAAATTATTTAAAATATTTTA
75763186 AAAATTGTAC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
36 22 0.76
37 7 0.24
ACGTcount: A:0.46, C:0.01, G:0.03, T:0.49
Consensus pattern (36 bp):
TAAAAATTTTATAAAATTATTTAAAATATTTTAGAT
Found at i:75763175 original size:10 final size:10
Alignment explanation
Indices: 75763155--75763188 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
75763145 TTTTAGATTA
75763155 AAAATTTTTT
1 AAAATTTTTT
* *
75763165 AGAATTATTT
1 AAAATTTTTT
75763175 AAAATTTTTT
1 AAAATTTTTT
75763185 AAAA
1 AAAA
75763189 ATTGTACAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (10 bp):
AAAATTTTTT
Found at i:75763658 original size:19 final size:19
Alignment explanation
Indices: 75763634--75763691 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
75763624 CATTCCAATT
*
75763634 TAAGTTTTTATTATTTTTA
1 TAAGTTTTTATAATTTTTA
*
75763653 TAAGTTTATATCAA-TTTTA
1 TAAGTTTTTAT-AATTTTTA
* *
75763672 -ATGCTTTTATAATTTTTA
1 TAAGTTTTTATAATTTTTA
75763690 TA
1 TA
75763692 GAATTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
17 2 0.06
18 12 0.39
19 16 0.52
20 1 0.03
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.60
Consensus pattern (19 bp):
TAAGTTTTTATAATTTTTA
Found at i:75763679 original size:28 final size:28
Alignment explanation
Indices: 75763648--75763701 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
75763638 TTTTTATTAT
75763648 TTTTATAAGTTTATAT-CAATTTTAATGC
1 TTTTATAA-TTTATATACAATTTTAATGC
* *
75763676 TTTTATAATTTTTATAGAATTTTAAT
1 TTTTATAATTTATATACAATTTTAAT
75763702 ACGTTTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 6 0.26
28 17 0.74
ACGTcount: A:0.33, C:0.04, G:0.06, T:0.57
Consensus pattern (28 bp):
TTTTATAATTTATATACAATTTTAATGC
Found at i:75765044 original size:11 final size:11
Alignment explanation
Indices: 75765030--75765055 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
75765020 AATTTTAAGT
75765030 TTTTTTTTTTG
1 TTTTTTTTTTG
75765041 TTTTTTTTTTG
1 TTTTTTTTTTG
75765052 TTTT
1 TTTT
75765056 CAGGGGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:75770431 original size:131 final size:131
Alignment explanation
Indices: 75770256--75770511 Score: 404
Period size: 131 Copynumber: 2.0 Consensus size: 131
75770246 AGAGAACATT
* * * * * *
75770256 AGTGAAATTCTAGAGGGATATTCGATTATTTTGAATAAACGGGAAATTGCAACCCAGCACGATAG
1 AGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATCGCAACCCAACACGATAG
75770321 GGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTGAAGAATTTTTAAAGACGT
66 GGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTGAAGAATTTTTAAAGACGT
75770386 G
131 G
* * *
75770387 AGTGAAATTCCAAAGGAATATTCGATTGTTTTGAAAAAAGGGGAAATCGCAACCCAACACGATGG
1 AGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATCGCAACCCAACACGATAG
* * *
75770452 GGCACGATTCCCCGAATTGCCAAACATCGAACATTGCCTTTGTTTTTAAGAATTTTTAAA
66 GGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTGAAGAATTTTTAAA
75770512 TGAATAATTA
Statistics
Matches: 113, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
131 113 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (131 bp):
AGTGAAATTCCAAAGGAATATTCGATTATTTTGAAAAAACGGGAAATCGCAACCCAACACGATAG
GGCACGATTCCCCGAATTGCCAAACATCGAACATTACCTTCGTTTTGAAGAATTTTTAAAGACGT
G
Found at i:75774595 original size:21 final size:21
Alignment explanation
Indices: 75774569--75774619 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
75774559 CTGTTTCTAC
*
75774569 TCTCACCGCTACAGTATCCAA
1 TCTCACCGCTACAGTAACCAA
* *
75774590 TCTCACCGCTATAGTAACTAA
1 TCTCACCGCTACAGTAACCAA
75774611 TCTCACCGC
1 TCTCACCGC
75774620 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.37, G:0.10, T:0.25
Consensus pattern (21 bp):
TCTCACCGCTACAGTAACCAA
Found at i:75794737 original size:3 final size:3
Alignment explanation
Indices: 75794731--75794756 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
75794721 TAGTTTTATT
75794731 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
75794757 TCTGTCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:75795770 original size:19 final size:19
Alignment explanation
Indices: 75795748--75795786 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
75795738 ACTTTTGAAG
*
75795748 TAAATATTTAATGATTTTT
1 TAAAAATTTAATGATTTTT
75795767 TAAAAATTTAATGATTTTT
1 TAAAAATTTAATGATTTTT
75795786 T
1 T
75795787 TAGTTCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (19 bp):
TAAAAATTTAATGATTTTT
Found at i:75799219 original size:39 final size:38
Alignment explanation
Indices: 75799171--75799308 Score: 181
Period size: 39 Copynumber: 3.6 Consensus size: 38
75799161 ATAAAGTATG
*
75799171 GTTTTAATTAATAATAAAACAAAATAGTATGTGGAAGTA
1 GTTTTAATTAACAATAAAACAAAATAGTATG-GGAAGTA
*
75799210 GTTTTAATTAACAATAAAACAAAATAGTATGGGGAAATA
1 GTTTTAATTAACAATAAAACAAAATAGTAT-GGGAAGTA
* *
75799249 GTTTTAATTAACAATAAAACAAAATAGCATGGGGAGT-
1 GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
* *
75799286 GTTTTTGATT-ATAATAAAACAAA
1 G-TTTTAATTAACAATAAAACAAA
75799309 GTAACATGGG
Statistics
Matches: 90, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
37 13 0.14
38 12 0.13
39 64 0.71
40 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.15, T:0.31
Consensus pattern (38 bp):
GTTTTAATTAACAATAAAACAAAATAGTATGGGAAGTA
Found at i:75800133 original size:17 final size:17
Alignment explanation
Indices: 75800111--75800143 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
75800101 ATATTTCTAA
*
75800111 TACTATTATGTTATTAC
1 TACTATTATATTATTAC
75800128 TACTATTATATTATTA
1 TACTATTATATTATTA
75800144 TTATATTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.09, G:0.03, T:0.55
Consensus pattern (17 bp):
TACTATTATATTATTAC
Found at i:75802468 original size:27 final size:27
Alignment explanation
Indices: 75802414--75802464 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
75802404 TGTCTTTCTT
*
75802414 CTCCTCTTCCTATCCCACGCTTTCACC
1 CTCCTCCTCCTATCCCACGCTTTCACC
* *
75802441 CTCCTCCTCCT-TCCCTCTCTTTCA
1 CTCCTCCTCCTATCCCACGCTTTCA
75802465 ACCCCACTCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 11 0.52
27 10 0.48
ACGTcount: A:0.08, C:0.53, G:0.02, T:0.37
Consensus pattern (27 bp):
CTCCTCCTCCTATCCCACGCTTTCACC
Found at i:75815393 original size:29 final size:31
Alignment explanation
Indices: 75815351--75815415 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 31
75815341 TAATAAATAT
*
75815351 AAAATTACACTTTAA-CACTTAAAAATGAAA
1 AAAATTACAATTTAATCACTTAAAAATGAAA
* * *
75815381 AAAATT-CAATTTAATCATTTAAAAATTATA
1 AAAATTACAATTTAATCACTTAAAAATGAAA
75815411 AAAAT
1 AAAAT
75815416 ATAAACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.23
30 23 0.77
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.32
Consensus pattern (31 bp):
AAAATTACAATTTAATCACTTAAAAATGAAA
Found at i:75832262 original size:11 final size:11
Alignment explanation
Indices: 75832228--75832262 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
75832218 AACCAGAAAC
*
75832228 AAAAAAAACAA
1 AAAAAAAAGAA
75832239 AAAAAAAAG-A
1 AAAAAAAAGAA
75832249 AAAAAAAAGAA
1 AAAAAAAAGAA
75832260 AAA
1 AAA
75832263 GGAAAAAGAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.45
11 12 0.55
ACGTcount: A:0.91, C:0.03, G:0.06, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:75832269 original size:16 final size:15
Alignment explanation
Indices: 75832228--75832269 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
75832218 AACCAGAAAC
*
75832228 AAAAA-AAACAAAAA
1 AAAAAGAAAAAAAAA
75832242 AAAAAGAAAAAAAAA
1 AAAAAGAAAAAAAAA
75832257 GAAAAAGGAAAAA
1 -AAAAA-GAAAAA
75832270 GACGATGATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 5 0.21
15 8 0.33
16 5 0.21
17 6 0.25
ACGTcount: A:0.88, C:0.02, G:0.10, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAAA
Found at i:75834493 original size:7 final size:7
Alignment explanation
Indices: 75834481--75834513 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
75834471 ATTTTAATAA
75834481 TATTTAC
1 TATTTAC
75834488 TATTTAC
1 TATTTAC
75834495 TATTTAC
1 TATTTAC
75834502 TATTTAC
1 TATTTAC
75834509 TATTT
1 TATTT
75834514 CAATCCTCGT
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:0.12, G:0.00, T:0.61
Consensus pattern (7 bp):
TATTTAC
Found at i:75838815 original size:29 final size:28
Alignment explanation
Indices: 75838783--75838840 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
75838773 TGGTCACTAA
75838783 TTTTATATTTTTAAAAATTAATTTTAATT
1 TTTTATATTTTTAAAAATTAA-TTTAATT
* *
75838812 TTTTCTTTTTTTAAAAATTAATTTAATT
1 TTTTATATTTTTAAAAATTAATTTAATT
75838840 T
1 T
75838841 CTCCAATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 8 0.30
29 19 0.70
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTATATTTTTAAAAATTAATTTAATT
Found at i:75839245 original size:15 final size:17
Alignment explanation
Indices: 75839221--75839253 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
75839211 TTTTTAAAAT
75839221 AATAATAAA-TTATTAA
1 AATAATAAATTTATTAA
75839237 AATAA-AAATTTATTAA
1 AATAATAAATTTATTAA
75839253 A
1 A
75839254 TCAGATTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 3 0.19
16 13 0.81
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (17 bp):
AATAATAAATTTATTAA
Found at i:75839251 original size:19 final size:19
Alignment explanation
Indices: 75839204--75839251 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
75839194 CCCCTTTATT
* *
75839204 AATTTAATTTTTAAAATAAT
1 AATTT-ATTATTAAAATAAA
**
75839224 AATAAATTATTAAAATAAA
1 AATTTATTATTAAAATAAA
75839243 AATTTATTA
1 AATTTATTA
75839252 AATCAGATTT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTTATTATTAAAATAAA
Found at i:75846394 original size:12 final size:12
Alignment explanation
Indices: 75846377--75846402 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
75846367 TTATCTATGA
75846377 TACTCAATATAT
1 TACTCAATATAT
75846389 TACTCAATATAT
1 TACTCAATATAT
75846401 TA
1 TA
75846403 ATGTATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (12 bp):
TACTCAATATAT
Found at i:75847020 original size:34 final size:31
Alignment explanation
Indices: 75846982--75847056 Score: 89
Period size: 30 Copynumber: 2.4 Consensus size: 31
75846972 TATATGCAAT
75846982 TTAACAAGTAAATGCCTCTAAAATAATAACAAAA
1 TTAACAAG-AAAT--CTCTAAAATAATAACAAAA
* *
75847016 TTAACAA-ATATCTTTAAAATAATAACAAAA
1 TTAACAAGAAATCTCTAAAATAATAACAAAA
*
75847046 TTAATAAGAAA
1 TTAACAAGAAA
75847057 ATAAGTTTTA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
30 24 0.67
31 2 0.06
32 3 0.08
34 7 0.19
ACGTcount: A:0.59, C:0.11, G:0.04, T:0.27
Consensus pattern (31 bp):
TTAACAAGAAATCTCTAAAATAATAACAAAA
Found at i:75847107 original size:22 final size:22
Alignment explanation
Indices: 75847082--75847124 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
75847072 TATCCAAACA
75847082 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* **
75847104 ATAATAGTAAAATAGTAGCAA
1 ATAACAACAAAATAGTAGCAA
75847125 AATAGGGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:75847128 original size:11 final size:11
Alignment explanation
Indices: 75847089--75847129 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
75847079 ACAATAACAA
75847089 CAAAATAGTAG
1 CAAAATAGTAG
* *
75847100 CAACATAATAG
1 CAAAATAGTAG
*
75847111 TAAAATAGTAG
1 CAAAATAGTAG
75847122 CAAAATAG
1 CAAAATAG
75847130 GGAGAAAATA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.56, C:0.10, G:0.15, T:0.20
Consensus pattern (11 bp):
CAAAATAGTAG
Found at i:75847431 original size:39 final size:39
Alignment explanation
Indices: 75847377--75847455 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
75847367 TAGGTGTAAC
75847377 TAGGGGTTAGTAGGACCTGCCTTCTAAAATGATTTTTTT
1 TAGGGGTTAGTAGGACCTGCCTTCTAAAATGATTTTTTT
75847416 TAGGGGTTAGTAGGACCTGCCTTCTAAAATGATTTTTTT
1 TAGGGGTTAGTAGGACCTGCCTTCTAAAATGATTTTTTT
75847455 T
1 T
75847456 TATTTAGGCA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.42
Consensus pattern (39 bp):
TAGGGGTTAGTAGGACCTGCCTTCTAAAATGATTTTTTT
Found at i:75847621 original size:15 final size:15
Alignment explanation
Indices: 75847598--75847634 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
75847588 AATTATATTT
*
75847598 TTACCATCACATAAA
1 TTACAATCACATAAA
75847613 TTACAATCACATAAA
1 TTACAATCACATAAA
75847628 TTACAAT
1 TTACAAT
75847635 TTAATTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (15 bp):
TTACAATCACATAAA
Found at i:75859848 original size:2 final size:2
Alignment explanation
Indices: 75859841--75859875 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
75859831 TGAATCACTC
75859841 CT CT 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 CT CT C
75859876 ACACACACAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:75862320 original size:6 final size:7
Alignment explanation
Indices: 75862305--75862329 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
75862295 GACATCAAGT
75862305 AAAATAA
1 AAAATAA
75862312 AAAATAA
1 AAAATAA
75862319 AAAATAA
1 AAAATAA
75862326 AAAA
1 AAAA
75862330 GCTAGCTTTA
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAATAA
Found at i:75869002 original size:16 final size:18
Alignment explanation
Indices: 75868971--75869003 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
75868961 TAATACTACT
75868971 ACTTTATTATTATTTATA
1 ACTTTATTATTATTTATA
75868989 ACTTT-TTA-TATTTAT
1 ACTTTATTATTATTTAT
75869004 TTTTCACTAA
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:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (18 bp):
ACTTTATTATTATTTATA
Found at i:75871601 original size:16 final size:18
Alignment explanation
Indices: 75871582--75871621 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
75871572 TATGTTTGTT
75871582 TACTGAG-AAG-TTTTTC
1 TACTGAGTAAGTTTTTTC
*
75871598 TACTGAGTTAGTTTTTTC
1 TACTGAGTAAGTTTTTTC
75871616 TACTGA
1 TACTGA
75871622 TTTTAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 7 0.33
17 2 0.10
18 12 0.57
ACGTcount: A:0.23, C:0.12, G:0.17, T:0.47
Consensus pattern (18 bp):
TACTGAGTAAGTTTTTTC
Found at i:75872829 original size:25 final size:24
Alignment explanation
Indices: 75872801--75872880 Score: 72
Period size: 23 Copynumber: 3.3 Consensus size: 24
75872791 AAAATTAATT
*
75872801 TAAATTTTTAAAAATTATAAAAATA
1 TAAATTTTT-AAAATAATAAAAATA
* *
75872826 TAAATTATTAAAATAAT-AAAATT
1 TAAATTTTTAAAATAATAAAAATA
* ** *
75872849 TATATTTTTACTATCATAAAAATA
1 TAAATTTTTAAAATAATAAAAATA
75872873 TATAATTT
1 TA-AATTT
75872881 AATTATTACT
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 17 0.40
24 14 0.33
25 12 0.28
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (24 bp):
TAAATTTTTAAAATAATAAAAATA
Found at i:75872832 original size:15 final size:16
Alignment explanation
Indices: 75872812--75872845 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
75872802 AAATTTTTAA
75872812 AAATTATAAAAAT-AT
1 AAATTATAAAAATAAT
*
75872827 AAATTATTAAAATAAT
1 AAATTATAAAAATAAT
75872843 AAA
1 AAA
75872846 ATTTATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATTATAAAAATAAT
Found at i:75872900 original size:30 final size:32
Alignment explanation
Indices: 75872835--75872901 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 32
75872825 ATAAATTATT
* *
75872835 AAAATAATAAAATTTATATTTTTACTATCATA
1 AAAATAATAAAATTTATATTATTACTATCAAA
* *
75872867 AAAAT-ATATAATTTA-ATTATTACTCTCAAA
1 AAAATAATAAAATTTATATTATTACTATCAAA
75872897 AAAAT
1 AAAAT
75872902 TTTCTACCGC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 17 0.55
31 9 0.29
32 5 0.16
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.40
Consensus pattern (32 bp):
AAAATAATAAAATTTATATTATTACTATCAAA
Found at i:75887824 original size:13 final size:14
Alignment explanation
Indices: 75887797--75887826 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
75887787 GGGTTTTCTG
75887797 TTTATTTTTCACTT
1 TTTATTTTTCACTT
75887811 TTTATTTTTC-CTT
1 TTTATTTTTCACTT
75887824 TTT
1 TTT
75887827 CAGAATTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTTCACTT
Found at i:75890965 original size:3 final size:3
Alignment explanation
Indices: 75890957--75890981 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
75890947 AATCCGACCC
75890957 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
75890982 CAAGAGTTAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:75901345 original size:14 final size:14
Alignment explanation
Indices: 75901309--75901351 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
75901299 GAGAGAGAAT
*
75901309 ATAAAGAAAAATGA
1 ATAAAGAAAAAAGA
* *
75901323 ATCATGAAAAAAGA
1 ATAAAGAAAAAAGA
*
75901337 ATAAGGAAAAAAGA
1 ATAAAGAAAAAAGA
75901351 A
1 A
75901352 GGGAGGGGGA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.70, C:0.02, G:0.16, T:0.12
Consensus pattern (14 bp):
ATAAAGAAAAAAGA
Found at i:75906604 original size:31 final size:30
Alignment explanation
Indices: 75906566--75906637 Score: 83
Period size: 31 Copynumber: 2.4 Consensus size: 30
75906556 AATTATACAT
75906566 AAATTTTAATTTAATGTATAATTATATATAT-
1 AAATTTTAATTTAATG-A-AATTATATATATA
* * * *
75906597 GAATTTTAACTTAGTGAAATTATATATGTA
1 AAATTTTAATTTAATGAAATTATATATATA
75906627 AAATTTTAATT
1 AAATTTTAATT
75906638 GCAGTTCAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
29 11 0.32
30 10 0.29
31 13 0.38
ACGTcount: A:0.43, C:0.01, G:0.07, T:0.49
Consensus pattern (30 bp):
AAATTTTAATTTAATGAAATTATATATATA
Done.