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 154 of 206
Found at i:46670994 original size:27 final size:26
Alignment explanation
Indices: 46670782--46670995 Score: 207
Period size: 27 Copynumber: 7.9 Consensus size: 26
46670772 GGGTATAACA
* * *
46670782 GTCATTTTACCCTATAGGCGTAATTCGG
1 GTCATTTTACCCT-TTGGGGTATTTC-G
* * *
46670810 GT-ATTTTACCCTTCGTGGCTATTTCT
1 GTCATTTTACCCTTTG-GGGTATTTCG
*
46670836 GTCATTTTACCCTTTAGGGGTACTTCG
1 GTCATTTTACCCTTT-GGGGTATTTCG
* *
46670863 GCCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTTG-GGGTATTTCG
* *
46670890 ATCATTTTACCCTTCGAGGGTATTTCG
1 GTCATTTTACCCTTTG-GGGTATTTCG
* *
46670917 ATCATTTTACCCTTTGGGGGTATTTCA
1 GTCATTTTACCCTTT-GGGGTATTTCG
46670944 GTCATTTTA-CCTTTCGTGGGTATTTCG
1 GTCATTTTACCCTTT-G-GGGTATTTCG
46670971 GTCATTTTACCCTTTGGGGATATTT
1 GTCATTTTACCCTTTGGGG-TATTT
46670996 TGGGCTTACC
Statistics
Matches: 159, Mismatches: 19, Indels: 17
0.82 0.10 0.09
Matches are distributed among these distances:
26 14 0.09
27 136 0.86
28 9 0.06
ACGTcount: A:0.16, C:0.21, G:0.20, T:0.43
Consensus pattern (26 bp):
GTCATTTTACCCTTTGGGGTATTTCG
Found at i:46674764 original size:17 final size:18
Alignment explanation
Indices: 46674742--46674782 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 18
46674732 ATGTATAAGT
46674742 ATGTATAT-TAATTA-AAA
1 ATGTATATGT-ATTATAAA
*
46674759 ATGTATGTGTATTATAAA
1 ATGTATATGTATTATAAA
46674777 ATGTAT
1 ATGTAT
46674783 GCATGTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 11 0.52
18 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.12, T:0.44
Consensus pattern (18 bp):
ATGTATATGTATTATAAA
Found at i:46674764 original size:21 final size:18
Alignment explanation
Indices: 46674740--46674783 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
46674730 ACATGTATAA
46674740 GTATGTATATTAATTAAAAAT
1 GTATGTATATT-A-T-AAAAT
*
46674761 GTATGTGTATTATAAAAT
1 GTATGTATATTATAAAAT
46674779 GTATG
1 GTATG
46674784 CATGTATATG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 10 0.45
19 1 0.05
20 1 0.05
21 10 0.45
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.43
Consensus pattern (18 bp):
GTATGTATATTATAAAAT
Found at i:46676375 original size:15 final size:15
Alignment explanation
Indices: 46676352--46676386 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46676342 TTTTGCAATT
*
46676352 TTTTTATTTTTTTAA
1 TTTTAATTTTTTTAA
*
46676367 TTTTAATTTTTTTAT
1 TTTTAATTTTTTTAA
46676382 TTTTA
1 TTTTA
46676387 GTGATTCTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTAATTTTTTTAA
Found at i:46678703 original size:24 final size:22
Alignment explanation
Indices: 46678673--46678751 Score: 68
Period size: 24 Copynumber: 3.3 Consensus size: 22
46678663 CAAGTTGCAA
46678673 GTTGTGGATAAGTCACTCAATAAC
1 GTTGTGG-TAAG-CACTCAATAAC
* * *
46678697 GTGGTGGCCAAGCTACTCAATAGC
1 GTTGTGG-TAAGC-ACTCAATAAC
*
46678721 ATTGTGGTCAAGCCACTCAATAAC
1 GTTGTGGT-AAG-CACTCAATAAC
46678745 GTTGTGG
1 GTTGTGG
46678752 CCTAGCCATT
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
23 1 0.02
24 41 0.95
25 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.27
Consensus pattern (22 bp):
GTTGTGGTAAGCACTCAATAAC
Found at i:46678745 original size:48 final size:48
Alignment explanation
Indices: 46678686--46678790 Score: 156
Period size: 48 Copynumber: 2.2 Consensus size: 48
46678676 GTGGATAAGT
* * *
46678686 CACTCAATAACGTGGTGGCCAAGCTACTCAATAGCATTGTGGTCAAGC
1 CACTCAATAACGTGGTGGCCAAGCCACTCAATAACAATGTGGTCAAGC
* * *
46678734 CACTCAATAACGTTGTGGCCTAGCCATTCAATAACAATGTGGTCAAGC
1 CACTCAATAACGTGGTGGCCAAGCCACTCAATAACAATGTGGTCAAGC
46678782 CACTCAATA
1 CACTCAATA
46678791 TTGTAGTAAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 51 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (48 bp):
CACTCAATAACGTGGTGGCCAAGCCACTCAATAACAATGTGGTCAAGC
Found at i:46678758 original size:24 final size:24
Alignment explanation
Indices: 46678686--46678790 Score: 120
Period size: 24 Copynumber: 4.4 Consensus size: 24
46678676 GTGGATAAGT
* *
46678686 CACTCAATAACGTGGTGGCCAAGC
1 CACTCAATAACATTGTGGCCAAGC
* * *
46678710 TACTCAATAGCATTGTGGTCAAGC
1 CACTCAATAACATTGTGGCCAAGC
* *
46678734 CACTCAATAACGTTGTGGCCTAGC
1 CACTCAATAACATTGTGGCCAAGC
* * *
46678758 CATTCAATAACAATGTGGTCAAGC
1 CACTCAATAACATTGTGGCCAAGC
46678782 CACTCAATA
1 CACTCAATA
46678791 TTGTAGTAAA
Statistics
Matches: 65, Mismatches: 16, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (24 bp):
CACTCAATAACATTGTGGCCAAGC
Found at i:46678947 original size:42 final size:42
Alignment explanation
Indices: 46678879--46678987 Score: 157
Period size: 42 Copynumber: 2.6 Consensus size: 42
46678869 TTTTCAGTAA
* * * *
46678879 ACATGCTTAAGATGCGATTCAGATTTATAATCTAA-ATAGTCG
1 ACATGCTTAACATGCAAATCATATTTATAATC-AACATAGTCG
46678921 ACATGCTTAACATGCAAATCATATTTATAATCAACATAGTCG
1 ACATGCTTAACATGCAAATCATATTTATAATCAACATAGTCG
*
46678963 GCATGCTTAACATGCAAATCATATT
1 ACATGCTTAACATGCAAATCATATT
46678988 CCAATATCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
41 2 0.03
42 59 0.97
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.32
Consensus pattern (42 bp):
ACATGCTTAACATGCAAATCATATTTATAATCAACATAGTCG
Found at i:46679008 original size:42 final size:42
Alignment explanation
Indices: 46678880--46679009 Score: 129
Period size: 42 Copynumber: 3.1 Consensus size: 42
46678870 TTTCAGTAAA
* * * * * * * *
46678880 CATGCTTAAGATGCGATTCAGATTTATAATCTAAATAGTCGA
1 CATGCTTAACATGCAAATCATATTAATAATCAAAATAGTAGG
* * *
46678922 CATGCTTAACATGCAAATCATATTTATAATCAACATAGTCGG
1 CATGCTTAACATGCAAATCATATTAATAATCAAAATAGTAGG
46678964 CATGCTTAACATGCAAATCATATTCCAAT-ATCAAAATAG-AGG
1 CATGCTTAACATGCAAATCATATT--AATAATCAAAATAGTAGG
46679006 CATG
1 CATG
46679010 ATTTATTTAT
Statistics
Matches: 76, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
42 65 0.86
43 9 0.12
44 2 0.03
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (42 bp):
CATGCTTAACATGCAAATCATATTAATAATCAAAATAGTAGG
Found at i:46686144 original size:29 final size:29
Alignment explanation
Indices: 46686110--46686169 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
46686100 TTTTTAAAAA
* *
46686110 AATTATATTTTAGCCTCTAAA-TTTTTCAT
1 AATTATATTTGAGCCCCTAAACTTTTT-AT
46686139 AATTATATTTGAGCCCCTAAACTTTTTAT
1 AATTATATTTGAGCCCCTAAACTTTTTAT
46686168 AA
1 AA
46686170 ATTGCATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 23 0.82
30 5 0.18
ACGTcount: A:0.33, C:0.15, G:0.05, T:0.47
Consensus pattern (29 bp):
AATTATATTTGAGCCCCTAAACTTTTTAT
Found at i:46686779 original size:19 final size:19
Alignment explanation
Indices: 46686729--46686782 Score: 69
Period size: 18 Copynumber: 2.9 Consensus size: 19
46686719 GAAAAAAAAG
*
46686729 AAAAAAGGAA-ACGAGAGA
1 AAAAAAGGAAGAGGAGAGA
46686747 AAGAAAA-G-AGAGGAGAGA
1 AA-AAAAGGAAGAGGAGAGA
46686765 AAAAAAGGAAGAGGAGAG
1 AAAAAAGGAAGAGGAGAG
46686783 GAAGAGAGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
17 5 0.16
18 13 0.42
19 13 0.42
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (19 bp):
AAAAAAGGAAGAGGAGAGA
Found at i:46686899 original size:11 final size:10
Alignment explanation
Indices: 46686883--46686990 Score: 52
Period size: 11 Copynumber: 11.0 Consensus size: 10
46686873 AGGGCTAAAG
46686883 GAAGAAGAAGA
1 GAAGAAGAA-A
46686894 GAAGAAAGAAA
1 GAAG-AAGAAA
46686905 GAAGAA-AAA
1 GAAGAAGAAA
*
46686914 GGA-AAGAAA
1 GAAGAAGAAA
*
46686923 AAAG-AGAAA
1 GAAGAAGAAA
46686932 -AAG-AGAAA
1 GAAGAAGAAA
*
46686940 AAAGAAAGAAA
1 GAAG-AAGAAA
*
46686951 AAAGGAA-AAA
1 GAA-GAAGAAA
46686961 GGAA-AA-AAA
1 -GAAGAAGAAA
*
46686970 GAAAAAGGAAA
1 GAAGAA-GAAA
*
46686981 GAAAAAGAAA
1 GAAGAAGAAA
46686991 AATAGAAAAA
Statistics
Matches: 82, Mismatches: 4, Indels: 23
0.75 0.04 0.21
Matches are distributed among these distances:
8 13 0.16
9 24 0.29
10 9 0.11
11 30 0.37
12 6 0.07
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (10 bp):
GAAGAAGAAA
Found at i:46686909 original size:7 final size:7
Alignment explanation
Indices: 46686883--46686989 Score: 59
Period size: 7 Copynumber: 15.4 Consensus size: 7
46686873 AGGGCTAAAG
46686883 GAAG-AA
1 GAAGAAA
46686889 GAAGAGAA
1 GAAGA-AA
46686897 GAAAGAAA
1 G-AAGAAA
46686905 GAAGAAA
1 GAAGAAA
46686912 -AAGGAAA
1 GAA-GAAA
*
46686919 GAAAAAA
1 GAAGAAA
46686926 G-AGAAA
1 GAAGAAA
*
46686932 AAGAGAAA
1 GA-AGAAA
*
46686940 AAAGAAA
1 GAAGAAA
*
46686947 GAAAAAA
1 GAAGAAA
46686954 GGAA-AAA
1 -GAAGAAA
46686961 GGAA-AAA
1 -GAAGAAA
46686968 -AAGAAA
1 GAAGAAA
46686974 -AAGGAAA
1 GAA-GAAA
46686981 GAA-AAA
1 GAAGAAA
46686987 GAA
1 GAA
46686990 AAATAGAAAA
Statistics
Matches: 85, Mismatches: 5, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
5 2 0.02
6 21 0.25
7 38 0.45
8 20 0.24
9 4 0.05
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (7 bp):
GAAGAAA
Found at i:46686930 original size:34 final size:30
Alignment explanation
Indices: 46686920--46687023 Score: 83
Period size: 31 Copynumber: 3.4 Consensus size: 30
46686910 AAAAGGAAAG
46686920 AAAAA-AGAGAAAA-AGAGAAAAAA-GAAAGA
1 AAAAAGAGA-AAAAGAGA-AAAAAAGGAAAGA
*
46686949 AAAAAG-GAAAAAG-GAAAAAAAGAAAAAGGA
1 AAAAAGAGAAAAAGAGAAAAAAAG-GAAA-GA
* *
46686979 AAGAAAAAGAAAAATAGAAAAAAAAGGAAAGA
1 AA-AAAGAGAAAAAGAG-AAAAAAAGGAAAGA
*
46687011 GAAAAGAGAAAAA
1 AAAAAGAGAAAAA
46687024 ATAGAAACAA
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
27 6 0.10
28 6 0.10
29 10 0.17
30 4 0.07
31 13 0.22
32 9 0.15
33 4 0.07
34 8 0.13
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (30 bp):
AAAAAGAGAAAAAGAGAAAAAAAGGAAAGA
Found at i:46686949 original size:42 final size:42
Alignment explanation
Indices: 46686885--46687054 Score: 136
Period size: 42 Copynumber: 4.0 Consensus size: 42
46686875 GGCTAAAGGA
* *
46686885 AGAAGAAGAGAAGAAAGAAAGAAGAAAAAGGAAAGAAAAAAG
1 AGAAAAAGAGAAAAAAGAAAGAAGAAAAAGGAAAGAAAAAAG
46686927 AGAAAAAGAGAAAAAAGAAAG-A-AAAAAGGAAAAAGGAAAAAA-
1 AGAAAAAGAGAAAAAAGAAAGAAGAAAAAGG--AAA-GAAAAAAG
* * *
46686969 AGAAAAAGGAAAGAAAAAGAAAAATAGAAAAAAAAGGAAAGAGAAAAG
1 AGAAAAA-G--AG-AAAA-AAGAA-AGAAGAAAAAGGAAAGAAAAAAG
* * *
46687017 AGAAAAAATAGAAACAA-ATAGAAGAAAAA-GAAA-AAAAA
1 AG-AAAAAGAGAAAAAAGAAAGAAGAAAAAGGAAAGAAAAA
46687055 CAGCAGCAAG
Statistics
Matches: 106, Mismatches: 9, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
40 11 0.10
41 5 0.05
42 38 0.36
43 9 0.08
44 2 0.02
45 5 0.05
46 6 0.06
47 10 0.09
48 7 0.07
49 6 0.06
50 7 0.07
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.02
Consensus pattern (42 bp):
AGAAAAAGAGAAAAAAGAAAGAAGAAAAAGGAAAGAAAAAAG
Found at i:46686976 original size:62 final size:63
Alignment explanation
Indices: 46686890--46687023 Score: 179
Period size: 62 Copynumber: 2.2 Consensus size: 63
46686880 AAGGAAGAAG
* *
46686890 AAGAGAAGAAA-G-AAAGAAGAAAAAGGAAAGAAAAAAGAGAAAA-AGAGAAAAAA-GAAAGAAA
1 AAGAGAA-AAAGGAAAAAAAGAAAAAGGAAAG-AAAAAGA-AAAATAGAAAAAAAAGGAAAGAAA
46686951 A
63 A
*
46686952 AAG-GAAAAAGGAAAAAAAGAAAAAGGAAAGAAAAAGAAAAATAGAAAAAAAAGGAAAGAGAA
1 AAGAGAAAAAGGAAAAAAAGAAAAAGGAAAGAAAAAGAAAAATAGAAAAAAAAGGAAAGAAAA
46687014 AAGAGAAAAA
1 AAGAGAAAAA
46687024 ATAGAAACAA
Statistics
Matches: 64, Mismatches: 3, Indels: 9
0.84 0.04 0.12
Matches are distributed among these distances:
60 7 0.11
61 20 0.31
62 31 0.48
63 6 0.09
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (63 bp):
AAGAGAAAAAGGAAAAAAAGAAAAAGGAAAGAAAAAGAAAAATAGAAAAAAAAGGAAAGAAAA
Found at i:46686992 original size:7 final size:7
Alignment explanation
Indices: 46686916--46687024 Score: 69
Period size: 8 Copynumber: 14.4 Consensus size: 7
46686906 AAGAAAAAGG
46686916 AAAGAAA
1 AAAGAAA
46686923 AAAGAGAA
1 AAAGA-AA
*
46686931 AAAGAGA
1 AAAGAAA
*
46686938 AAA-AAG
1 AAAGAAA
46686944 AAAGAAA
1 AAAGAAA
46686951 AAAGGAAA
1 AAA-GAAA
*
46686959 AAGGAAAA
1 AAAG-AAA
46686967 AAAGAAA
1 AAAGAAA
*
46686974 AAGGAAAGAA
1 AA--AGA-AA
46686984 AAAGAAA
1 AAAGAAA
46686991 AATAGAAA
1 AA-AGAAA
46686999 AAA-AAGGA
1 AAAGAA--A
46687007 AAGAGAAA
1 AA-AGAAA
*
46687015 AGAGAAA
1 AAAGAAA
46687022 AAA
1 AAA
46687025 TAGAAACAAA
Statistics
Matches: 80, Mismatches: 10, Indels: 24
0.70 0.09 0.21
Matches are distributed among these distances:
6 6 0.08
7 32 0.40
8 33 0.41
9 3 0.04
10 6 0.08
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (7 bp):
AAAGAAA
Found at i:46687013 original size:16 final size:16
Alignment explanation
Indices: 46686879--46687054 Score: 90
Period size: 18 Copynumber: 10.2 Consensus size: 16
46686869 GGCTAGGGCT
*
46686879 AAAGGAAGAAGAAGAGAA
1 AAAGGAAAAAGAA-A-AA
46686897 GAAA-GAAAGAAGAAAAA
1 -AAAGGAAA-AAGAAAAA
*
46686914 GGAAAGAAAAAAGAGAAAA
1 --AAAGGAAAAAGA-AAAA
* *
46686933 AGAGAAAAAAGAAAGAAA
1 AAAGGAAAAAG-AA-AAA
*
46686951 AAAGGAAAAAGGAAAA
1 AAAGGAAAAAGAAAAA
46686967 AAA-GAAAAAGGAAAGAA
1 AAAGGAAAAA-GAAA-AA
*
46686984 AAAGAAAAATAGAAAAA
1 AAAGGAAAA-AGAAAAA
*
46687001 AAAGGAAAGAGAAAAGA
1 AAAGGAAAAAGAAAA-A
*
46687018 GAAA--AAATAGAAACAA
1 -AAAGGAAAAAGAAA-AA
*
46687034 ATAGAAGAAAAAGAAAAA
1 A-A-AGGAAAAAGAAAAA
46687052 AAA
1 AAA
46687055 CAGCAGCAAG
Statistics
Matches: 128, Mismatches: 12, Indels: 37
0.72 0.07 0.21
Matches are distributed among these distances:
15 7 0.05
16 26 0.20
17 32 0.25
18 39 0.30
19 24 0.19
ACGTcount: A:0.76, C:0.01, G:0.22, T:0.02
Consensus pattern (16 bp):
AAAGGAAAAAGAAAAA
Found at i:46687030 original size:22 final size:22
Alignment explanation
Indices: 46686895--46687024 Score: 83
Period size: 25 Copynumber: 5.8 Consensus size: 22
46686885 AGAAGAAGAG
*
46686895 AAGAAAGAA-AGAAGAAAAAGGA
1 AAGAAA-AAGAGAAAAAAAAGGA
*
46686917 AAGAAAAA-AG-AGAAAAA-GA
1 AAGAAAAAGAGAAAAAAAAGGA
*
46686936 GA-AAAAAGA-AAGAAAAAAGGAAA
1 AAGAAAAAGAGAA-AAAAAAGG--A
* *
46686959 AAGGAAAAAAAGAAAAAGGAAAGAAA
1 AA-GAAAAAGAGAAAAA--AAAG-GA
*
46686985 AAGAAAAATAGAAAAAAAAGGA
1 AAGAAAAAGAGAAAAAAAAGGA
46687007 AAGAGAAAAGAGAAAAAA
1 AAGA-AAAAGAGAAAAAA
46687025 TAGAAACAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 25
0.73 0.07 0.21
Matches are distributed among these distances:
18 5 0.06
19 5 0.06
20 12 0.14
21 5 0.06
22 11 0.13
23 18 0.21
25 22 0.25
26 5 0.06
27 4 0.05
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (22 bp):
AAGAAAAAGAGAAAAAAAAGGA
Found at i:46688036 original size:3 final size:3
Alignment explanation
Indices: 46688022--46688075 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
46688012 TGCTATGATT
* *
46688022 TTA TTT TTA TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46688070 TTA TTA
1 TTA TTA
46688076 CTATACATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:46689415 original size:17 final size:17
Alignment explanation
Indices: 46689393--46689445 Score: 70
Period size: 17 Copynumber: 3.1 Consensus size: 17
46689383 GTAATTTATC
46689393 AAAATTTTCGTGTTTCA
1 AAAATTTTCGTGTTTCA
*
46689410 AAAATTTTCGAGTTTTCA
1 AAAATTTTCGTG-TTTCA
* *
46689428 ATAATTCTCGTGTTTCA
1 AAAATTTTCGTGTTTCA
46689445 A
1 A
46689446 TCAGATCCTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
17 17 0.55
18 14 0.45
ACGTcount: A:0.30, C:0.13, G:0.11, T:0.45
Consensus pattern (17 bp):
AAAATTTTCGTGTTTCA
Found at i:46701299 original size:76 final size:75
Alignment explanation
Indices: 46701146--46701583 Score: 481
Period size: 76 Copynumber: 5.8 Consensus size: 75
46701136 TTTCAAAAAT
* * * *
46701146 TATTTTTCAATTTTTGTTTTTCACAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGG-C
**
46701211 ACACGCCGAGG
65 ACACGCTAAGG
* *
46701222 TATTTTTCAATTTCTATTTTTGAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGC
1 TATTTTTCAATTTCTATTTTT-CAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGC
46701287 ACACGCTAAGG
65 ACACGCTAAGG
* ** *
46701298 TATTTTTTAATTTCTATTTTTTTTTGAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAG
1 TATTTTTCAATTTCTA---TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAG
46701363 GCACACGCTAAGG
63 GCACACGCTAAGG
* ** * *
46701376 TATTTTTTAATTTCTATTTTTTTGAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGAGT
1 TATTTTTCAATTTCTA-TTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTC-AGG
** *
46701441 CGTACACTAAGG
64 CACACGCTAAGG
* * * *
46701453 TATTTTT-AATTTATGTTTTTCAAAAATCAACTCATAAT-CTGAGAGGTGAGTTGAGCATCGGGT
1 TATTTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGCCTCAGG-
* *
46701516 CACATGCTGAGG
64 CACACGCTAAGG
* * *
46701528 TA-TTTTCAATTACTATTTCTT-AAAGATCAACTCATAAT-CTGAGAGGTGAATTGAGC
1 TATTTTTCAATTTCTATTT-TTCAAAAATCAACTCATAATGC-GAGAGGTGAGTTGAGC
46701584 TTTAAATCAC
Statistics
Matches: 320, Mismatches: 33, Indels: 19
0.86 0.09 0.05
Matches are distributed among these distances:
74 6 0.02
75 88 0.28
76 97 0.30
77 56 0.17
78 68 0.21
79 5 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (75 bp):
TATTTTTCAATTTCTATTTTTCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCAGGCA
CACGCTAAGG
Found at i:46701348 original size:78 final size:76
Alignment explanation
Indices: 46701170--46701583 Score: 482
Period size: 75 Copynumber: 5.4 Consensus size: 76
46701160 TGTTTTTCAC
* * ** *
46701170 AAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCCGAGGTATTTTTCAATTT
1 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGG-CACACGCTAAGGTATTTTTTAATTT
**
46701235 CTATTTTTGAAA
65 CTATTTTTTTAA
46701247 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGCACACGCTAAGGTATTTTTTAATTTC
1 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGCACACGCTAAGGTATTTTTTAATTTC
*
46701312 TATTTTTTTTTGA
66 TA--TTTTTTTAA
46701325 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGCACACGCTAAGGTATTTTTTAATTTC
1 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGCACACGCTAAGGTATTTTTTAATTTC
*
46701390 TATTTTTTTGA
66 TATTTTTTTAA
* ** *
46701401 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGAGTCGTACACTAAGGTA-TTTTTAA-TT
1 AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTC-AGGCACACGCTAAGGTATTTTTTAATTT
*
46701464 -TATGTTTTTCAA
65 CTAT-TTTTTTAA
* * * * * *
46701476 AAATCAACTCATAAT-CTGAGAGGTGAGTTGAGCATCGGGTCACATGCTGAGGTA-TTTTCAATT
1 AAATCAACTCATAATGC-GATAGGTGAGTTGAGCCTCAGG-CACACGCTAAGGTATTTTTTAATT
* *
46701539 ACTA-TTTCTTAA
64 TCTATTTTTTTAA
* * *
46701551 AGATCAACTCATAAT-CTGAGAGGTGAATTGAGC
1 AAATCAACTCATAATGC-GATAGGTGAGTTGAGC
46701584 TTTAAATCAC
Statistics
Matches: 300, Mismatches: 29, Indels: 18
0.86 0.08 0.05
Matches are distributed among these distances:
74 5 0.02
75 92 0.31
76 78 0.26
77 52 0.17
78 73 0.24
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (76 bp):
AAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCAGGCACACGCTAAGGTATTTTTTAATTTC
TATTTTTTTAA
Found at i:46701787 original size:5 final size:5
Alignment explanation
Indices: 46701770--46701800 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
46701760 TAGCCTCTTA
46701770 TTGTT TT-TT TTGTT TTGTT TTGTT TTGTT TT
1 TTGTT TTGTT TTGTT TTGTT TTGTT TTGTT TT
46701801 TATGCTTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTGTT
Found at i:46702663 original size:22 final size:21
Alignment explanation
Indices: 46702635--46702741 Score: 96
Period size: 22 Copynumber: 5.0 Consensus size: 21
46702625 AGGGTTAAAG
46702635 GAAGAAAAAGAGAAGAAAGAAA
1 GAAGAAAAAGAGAAGAAA-AAA
46702657 GAAGAAAAATGA-AAGAAAAAA
1 GAAGAAAAA-GAGAAGAAAAAA
*
46702678 AAGAGAAAAAGAGAA-AAAAAA
1 GA-AGAAAAAGAGAAGAAAAAA
*
46702699 GAAAGAAAAAGAAAAGAGGAAAAA
1 G-AAGAAAAAGAGAAGA--AAAAA
*
46702723 -AATAAAAAG-GAAAGAAAAA
1 GAAGAAAAAGAG-AAGAAAAA
46702742 TAAAAATAGA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
20 4 0.06
21 23 0.32
22 38 0.53
23 2 0.03
24 5 0.07
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (21 bp):
GAAGAAAAAGAGAAGAAAAAA
Found at i:46702676 original size:33 final size:32
Alignment explanation
Indices: 46702631--46702741 Score: 111
Period size: 33 Copynumber: 3.4 Consensus size: 32
46702621 GACTAGGGTT
* *
46702631 AAAGGAAGAAAAAGAGAAGA-AAGAAAGAAGAAA
1 AAAGAAAGAAAAAGA-AAGAGAA-AAAGAAAAAA
*
46702664 AATGAAAGAAAAA-AAAGAGAAAAAGAGAAAAA
1 AAAGAAAGAAAAAGAAAGAGAAAAAGA-AAAAA
*
46702696 AAAGAAAGAAAAAGAAAAGAGGAAAAA-AATAAA
1 AAAGAAAGAAAAAG-AAAGA-GAAAAAGAAAAAA
*
46702729 AAGGAAAGAAAAA
1 AAAGAAAGAAAAA
46702742 TAAAAATAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
31 9 0.13
32 19 0.28
33 27 0.40
34 6 0.09
35 6 0.09
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (32 bp):
AAAGAAAGAAAAAGAAAGAGAAAAAGAAAAAA
Found at i:46702680 original size:27 final size:26
Alignment explanation
Indices: 46702639--46702798 Score: 91
Period size: 28 Copynumber: 6.2 Consensus size: 26
46702629 TTAAAGGAAG
* *
46702639 AAAAAGAGAAGAAAGAAAGAAGAAAA
1 AAAAAGAAAAAAAAGAAAGAAGAAAA
* *
46702665 ATGAAAGAAAAAAAAGAGAAAAAGAGAAA
1 A-AAAAGAAAAAAAAGA-AAGAAGA-AAA
**
46702694 AAAAAGAAAGAAAAAG-AA-AAGAGGA
1 AAAAAGAAA-AAAAAGAAAGAAGAAAA
* *
46702719 AAAAA-ATAAAAAGGAAAGAA-AAATA
1 AAAAAGAAAAAAAAGAAAGAAGAAA-A
*
46702744 AAAATAGAATAAAAAGGAAAGAA-AAAA
1 AAAA-AGAA-AAAAAAGAAAGAAGAAAA
* * * *
46702771 CAAAA-AAATAGAAG-AACAAGAAAA
1 AAAAAGAAAAAAAAGAAAGAAGAAAA
46702795 AAAA
1 AAAA
46702799 TAGCAGCAGA
Statistics
Matches: 105, Mismatches: 18, Indels: 24
0.71 0.12 0.16
Matches are distributed among these distances:
23 9 0.09
24 16 0.15
25 15 0.14
26 7 0.07
27 19 0.18
28 29 0.28
29 10 0.10
ACGTcount: A:0.78, C:0.01, G:0.17, T:0.04
Consensus pattern (26 bp):
AAAAAGAAAAAAAAGAAAGAAGAAAA
Found at i:46702686 original size:10 final size:9
Alignment explanation
Indices: 46702636--46702798 Score: 85
Period size: 11 Copynumber: 16.2 Consensus size: 9
46702626 GGGTTAAAGG
46702636 AAGAAAAAGA
1 AAGAAAAA-A
46702646 GAAGAAAGAAA
1 -AAGAAA-AAA
46702657 GAAGAAAAATGA
1 -AAGAAAAA--A
46702669 AAGAAAAAA
1 AAGAAAAAA
46702678 AAGAGAAAAA
1 AAGA-AAAAA
*
46702688 GAGAAAAAA
1 AAGAAAAAA
46702697 AAGAAAGAAA
1 AAGAAA-AAA
46702707 AAGAAAAGAGGA
1 AAGAAAA-A--A
*
46702719 AAAAAATAAA
1 AAGAAA-AAA
46702729 AAGGAAAGAAA
1 AA-GAAA-AAA
*
46702740 AATAAAAATA
1 AAGAAAAA-A
*
46702750 GAATAAAAAGGA
1 -AAGAAAAA--A
46702762 AAGAAAAAA
1 AAGAAAAAA
*
46702771 CA-AAAAAA
1 AAGAAAAAA
* * *
46702779 TAGAAGAAC
1 AAGAAAAAA
46702788 AAGAAAAAA
1 AAGAAAAAA
46702797 AA
1 AA
46702799 TAGCAGCAGA
Statistics
Matches: 123, Mismatches: 15, Indels: 30
0.73 0.09 0.18
Matches are distributed among these distances:
8 7 0.06
9 32 0.26
10 27 0.22
11 45 0.37
12 11 0.09
13 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.18, T:0.04
Consensus pattern (9 bp):
AAGAAAAAA
Found at i:46702694 original size:17 final size:17
Alignment explanation
Indices: 46702668--46702798 Score: 65
Period size: 17 Copynumber: 7.7 Consensus size: 17
46702658 AAGAAAAATG
*
46702668 AAAGAAAAAAAAGAGAA
1 AAAGAAAAAAAAAAGAA
*
46702685 AAAGAGAAAAAAAAG--
1 AAAGAAAAAAAAAAGAA
* *
46702700 AAAGAAAAAGAAAAGAGG
1 AAAGAAAAAAAAAAGA-A
* *
46702718 AAA-AAAATAAAAAG-G
1 AAAGAAAAAAAAAAGAA
*
46702733 AAAGAAAAATAAAAA-TA
1 AAAGAAAAA-AAAAAGAA
* * **
46702750 GAATAAAAAGGAAAGAAA
1 AAAGAAAAAAAAAAG-AA
*
46702768 AAACAAAAAAATAGAAGAA
1 AAAGAAAAAAA-A-AAGAA
*
46702787 CAAGAAAAAAAA
1 AAAGAAAAAAAA
46702799 TAGCAGCAGA
Statistics
Matches: 85, Mismatches: 19, Indels: 19
0.69 0.15 0.15
Matches are distributed among these distances:
15 17 0.20
16 7 0.08
17 34 0.40
18 12 0.14
19 12 0.14
20 3 0.04
ACGTcount: A:0.79, C:0.02, G:0.16, T:0.04
Consensus pattern (17 bp):
AAAGAAAAAAAAAAGAA
Found at i:46702721 original size:46 final size:44
Alignment explanation
Indices: 46702636--46702730 Score: 97
Period size: 43 Copynumber: 2.2 Consensus size: 44
46702626 GGGTTAAAGG
*
46702636 AAGAAAAAGAGAAGAAAGAAAGAAGAAAAATGAAAGAAAAAAAA
1 AAGAAAAAAAGAAGAAAGAAAGAAGAAAAATGAAAGAAAAAAAA
* * **
46702680 GAGAAAAAGAGAA-AAA-AAAGAAAGAAAAA-GAAAAGAGGAAAAA
1 AAGAAAAAAAGAAGAAAGAAAG-AAGAAAAATG-AAAGAAAAAAAA
*
46702723 AATAAAAA
1 AAGAAAAA
46702731 GGAAAGAAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
42 5 0.11
43 27 0.61
44 12 0.27
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (44 bp):
AAGAAAAAAAGAAGAAAGAAAGAAGAAAAATGAAAGAAAAAAAA
Found at i:46702733 original size:15 final size:14
Alignment explanation
Indices: 46702683--46702746 Score: 58
Period size: 15 Copynumber: 4.4 Consensus size: 14
46702673 AAAAAAAGAG
46702683 AAAAAGAGAAAAAAA
1 AAAAAG-GAAAAAAA
* *
46702698 AGAAA-GAAAAAGA
1 AAAAAGGAAAAAAA
*
46702711 AAAGAGGAAAAAAA
1 AAAAAGGAAAAAAA
46702725 TAAAAAGGAAAGAAAA
1 -AAAAAGGAAA-AAAA
46702741 ATAAAA
1 A-AAAA
46702747 ATAGAATAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
13 10 0.26
14 7 0.18
15 14 0.36
16 8 0.21
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAAAGGAAAAAAA
Found at i:46702741 original size:28 final size:27
Alignment explanation
Indices: 46702681--46702780 Score: 100
Period size: 28 Copynumber: 3.7 Consensus size: 27
46702671 GAAAAAAAAG
*
46702681 AGAAAAAGAGAAAAAAA-AGAAA-GAA
1 AGAAAAAGAGAAAAAAATAAAAAGGAA
*
46702706 AAAGAAAAGAGGAAAAAAATAAAAAGGAA
1 AGA-AAAAGA-GAAAAAAATAAAAAGGAA
*
46702735 AGAAAAATA-AAAATAGAATAAAAAGGAA
1 AGAAAAAGAGAAAA-A-AATAAAAAGGAA
*
46702763 AGAAAAA-ACAAAAAAATA
1 AGAAAAAGAGAAAAAAATA
46702781 GAAGAACAAG
Statistics
Matches: 64, Mismatches: 4, Indels: 13
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.03
26 14 0.22
27 11 0.17
28 32 0.50
29 5 0.08
ACGTcount: A:0.78, C:0.01, G:0.16, T:0.05
Consensus pattern (27 bp):
AGAAAAAGAGAAAAAAATAAAAAGGAA
Found at i:46702785 original size:20 final size:20
Alignment explanation
Indices: 46702762--46702801 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
46702752 ATAAAAAGGA
46702762 AAGAA-AAAACAAAAAAATAG
1 AAGAACAAAA-AAAAAAATAG
*
46702782 AAGAACAAGAAAAAAAATAG
1 AAGAACAAAAAAAAAAATAG
46702802 CAGCAGACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.78, C:0.05, G:0.12, T:0.05
Consensus pattern (20 bp):
AAGAACAAAAAAAAAAATAG
Found at i:46720782 original size:3 final size:3
Alignment explanation
Indices: 46720776--46720816 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
46720766 CTACTACTAC
46720776 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46720817 AACTCCTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:46721157 original size:3 final size:3
Alignment explanation
Indices: 46721149--46721195 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
46721139 TTTCTACACA
46721149 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
46721196 AAGTATTGAG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:46721630 original size:31 final size:31
Alignment explanation
Indices: 46721559--46721642 Score: 127
Period size: 31 Copynumber: 2.7 Consensus size: 31
46721549 TGAGAGTTGG
* *
46721559 ATTAAATCAAAATTTCATGTATAAAATTGCAC
1 ATTAAATCAAAA-TTCATGTATAAAACTACAC
46721591 A--AAATCAAAATTCATGTATAAAACTACAC
1 ATTAAATCAAAATTCATGTATAAAACTACAC
46721620 ATTAAATCAAAATTCATGTATAA
1 ATTAAATCAAAATTCATGTATAA
46721643 TTTTGAGATT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 18 0.38
30 9 0.19
31 20 0.42
32 1 0.02
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (31 bp):
ATTAAATCAAAATTCATGTATAAAACTACAC
Found at i:46723212 original size:31 final size:31
Alignment explanation
Indices: 46723150--46723222 Score: 76
Period size: 31 Copynumber: 2.4 Consensus size: 31
46723140 ACGCCCATGC
* *
46723150 GGCCCACACGCCCTACCTGGCTCAATCGTGT
1 GGCCCACACGCCCTACCTGACTCAACCGTGT
* *
46723181 GGCCTACACGCTCTACCTGAC-CAACCTGTGT
1 GGCCCACACGCCCTACCTGACTCAACC-GTGT
* *
46723212 GACTCACACGC
1 GGCCCACACGC
46723223 TCGTGTGGCT
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
30 4 0.12
31 30 0.88
ACGTcount: A:0.19, C:0.41, G:0.21, T:0.19
Consensus pattern (31 bp):
GGCCCACACGCCCTACCTGACTCAACCGTGT
Found at i:46725192 original size:27 final size:27
Alignment explanation
Indices: 46725157--46725254 Score: 144
Period size: 27 Copynumber: 3.6 Consensus size: 27
46725147 ACAACTAAGA
*
46725157 AATAACCTTTGTGGCATACTCTAAAAG
1 AATAGCCTTTGTGGCATACTCTAAAAG
46725184 AATAGCCTTTGTGGCATACTCTAAAAG
1 AATAGCCTTTGTGGCATACTCTAAAAG
* *
46725211 AATAGCATTTGTGGCGA-ACTCGAAAAG
1 AATAGCCTTTGTGGC-ATACTCTAAAAG
*
46725238 AATAGCCTTTGTTGCAT
1 AATAGCCTTTGTGGCAT
46725255 GTTCTGATTG
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
26 1 0.02
27 62 0.97
28 1 0.02
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (27 bp):
AATAGCCTTTGTGGCATACTCTAAAAG
Found at i:46731952 original size:41 final size:41
Alignment explanation
Indices: 46731907--46732003 Score: 110
Period size: 39 Copynumber: 2.4 Consensus size: 41
46731897 AACATGTTTT
* * *
46731907 TGAGTATTGCGATATATATGCCTGAATATTATGTGAA-TATA
1 TGAGTATTGTGATATATATGCCTGAACATTAAGT-AATTATA
* *
46731948 TGAGTGTTGTG--ATATATGCTTGAACATTAAGTAATTATA
1 TGAGTATTGTGATATATATGCCTGAACATTAAGTAATTATA
*
46731987 TGAATATTGTGATATAT
1 TGAGTATTGTGATATAT
46732004 GCTTAAATGT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.04
39 31 0.67
41 13 0.28
ACGTcount: A:0.34, C:0.05, G:0.20, T:0.41
Consensus pattern (41 bp):
TGAGTATTGTGATATATATGCCTGAACATTAAGTAATTATA
Found at i:46731987 original size:39 final size:39
Alignment explanation
Indices: 46731920--46732046 Score: 123
Period size: 39 Copynumber: 3.3 Consensus size: 39
46731910 GTATTGCGAT
* * * * *
46731920 ATATATGCCTGAATATTATGTGAATATATGAGTGTTGTG
1 ATATATGCTTGAACATTAAGTGAATATATGAATATTGTG
46731959 ATATATGCTTGAACATTAAGT-AATTATATGAATATTGTG
1 ATATATGCTTGAACATTAAGTGAA-TATATGAATATTGTG
* ** * * *
46731998 ATATATGCTTAAATGTTATA-TGATTATATGATTAATGTG
1 ATATATGCTTGAACATTA-AGTGAATATATGAATATTGTG
46732037 ATATATGCTT
1 ATATATGCTT
46732047 AAAAGTGAAT
Statistics
Matches: 74, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
38 2 0.03
39 70 0.95
40 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (39 bp):
ATATATGCTTGAACATTAAGTGAATATATGAATATTGTG
Found at i:46741390 original size:16 final size:17
Alignment explanation
Indices: 46741353--46741401 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 17
46741343 TTGCTTTATG
*
46741353 TAATTAATGCAAAATAA
1 TAATTAATTCAAAATAA
*
46741370 -CATT-ATTCAAAATAA
1 TAATTAATTCAAAATAA
46741385 TAATTAATT-AAAATAA
1 TAATTAATTCAAAATAA
46741401 T
1 T
46741402 GAACTCCAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
15 10 0.37
16 14 0.52
17 3 0.11
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (17 bp):
TAATTAATTCAAAATAA
Found at i:46741551 original size:18 final size:17
Alignment explanation
Indices: 46741505--46741554 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
46741495 TAATTACAAT
* *
46741505 TTAAATTCTAATTATTT
1 TTAAATTATAATTATTC
*
46741522 TTAAGTTATAATTATTC
1 TTAAATTATAATTATTC
46741539 TTAAATGTATAATTAT
1 TTAAAT-TATAATTAT
46741555 CACAAATTCT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
17 19 0.68
18 9 0.32
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (17 bp):
TTAAATTATAATTATTC
Found at i:46742453 original size:8 final size:8
Alignment explanation
Indices: 46742440--46742480 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
46742430 TTTAACTCCC
46742440 TAAAATTA
1 TAAAATTA
46742448 TAAAATTA
1 TAAAATTA
46742456 TAAAGA-TA
1 TAAA-ATTA
46742464 T-AAATTA
1 TAAAATTA
46742471 TAAAATTA
1 TAAAATTA
46742479 TA
1 TA
46742481 TTTTTACTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 1 0.03
7 5 0.17
8 23 0.77
9 1 0.03
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (8 bp):
TAAAATTA
Found at i:46742480 original size:15 final size:15
Alignment explanation
Indices: 46742440--46742480 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
46742430 TTTAACTCCC
46742440 TAAAATTATAAAATTA
1 TAAAATTAT-AAATTA
46742456 TAAAGA-TATAAATTA
1 TAAA-ATTATAAATTA
46742471 TAAAATTATA
1 TAAAATTATA
46742481 TTTTTACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 7 0.30
17 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (15 bp):
TAAAATTATAAATTA
Found at i:46747586 original size:30 final size:30
Alignment explanation
Indices: 46747549--46747618 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
46747539 AATTAAATTC
* *
46747549 TAAAATTAAATTTAAGTATCAAATAAAA-A
1 TAAAATTAAATTCAAATATCAAATAAAATA
* *
46747578 TAAAAATTAAATTCAAATATTAAATTAAATA
1 T-AAAATTAAATTCAAATATCAAATAAAATA
46747609 TAAAATTAAA
1 TAAAATTAAA
46747619 CACAATTACT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 1 0.03
30 32 0.91
31 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (30 bp):
TAAAATTAAATTCAAATATCAAATAAAATA
Found at i:46747609 original size:12 final size:12
Alignment explanation
Indices: 46747531--46747618 Score: 58
Period size: 13 Copynumber: 7.2 Consensus size: 12
46747521 GTTTAATTTA
*
46747531 AAATACTAAATT
1 AAATATTAAATT
46747543 AAAT-TCTAAAATT
1 AAATAT-T-AAATT
*
46747556 AAAT-TTAAGTATC
1 AAATATTAA--ATT
*
46747569 AAATA--AAAAT
1 AAATATTAAATT
*
46747579 AAAAATTAAATT
1 AAATATTAAATT
46747591 CAAATATTAAATT
1 -AAATATTAAATT
*
46747604 AAATATAAAATT
1 AAATATTAAATT
46747616 AAA
1 AAA
46747619 CACAATTACT
Statistics
Matches: 60, Mismatches: 8, Indels: 16
0.71 0.10 0.19
Matches are distributed among these distances:
10 5 0.08
11 2 0.03
12 26 0.43
13 27 0.45
ACGTcount: A:0.61, C:0.05, G:0.01, T:0.33
Consensus pattern (12 bp):
AAATATTAAATT
Found at i:46747632 original size:30 final size:29
Alignment explanation
Indices: 46747575--46747632 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 29
46747565 TATCAAATAA
** *
46747575 AAATAAAAATTAAATTCAAATATTAAATT
1 AAATAAAAATTAAACACAAATACTAAATT
*
46747604 AAATATAAAATTAAACACAATTACTAAAT
1 AAATA-AAAATTAAACACAAATACTAAAT
46747633 GATAAATTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (29 bp):
AAATAAAAATTAAACACAAATACTAAATT
Found at i:46748414 original size:26 final size:27
Alignment explanation
Indices: 46748353--46748406 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
46748343 CATTGCAATT
46748353 AATAAAATAAAGTTATTTGTTTTTATC
1 AATAAAATAAAGTTATTTGTTTTTATC
46748380 AATAAAATAAAGTTATTTGTTTTTATC
1 AATAAAATAAAGTTATTTGTTTTTATC
46748407 TTTAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.41, C:0.04, G:0.07, T:0.48
Consensus pattern (27 bp):
AATAAAATAAAGTTATTTGTTTTTATC
Found at i:46750997 original size:12 final size:13
Alignment explanation
Indices: 46750975--46751019 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
46750965 AGGTTGAGGG
46750975 AGAAG-AAGATGA
1 AGAAGAAAGATGA
46750987 AG-AGAAAGATG-
1 AGAAGAAAGATGA
*
46750998 AGAAGAAAAAT-A
1 AGAAGAAAGATGA
46751010 AGAAGAAAGA
1 AGAAGAAAGA
46751020 CAAGGAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 4 0.14
12 24 0.86
ACGTcount: A:0.64, C:0.00, G:0.29, T:0.07
Consensus pattern (13 bp):
AGAAGAAAGATGA
Found at i:46751267 original size:30 final size:31
Alignment explanation
Indices: 46751201--46751268 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
46751191 ATGTTAATGG
46751201 GTGACTGATTTGTCACTTTTCGATAACGTTA
1 GTGACTGATTTGTCACTTTTCGATAACGTTA
* *
46751232 GTGACTGATTTGTTACTTTTTGA-AA-GTTGA
1 GTGACTGATTTGTCACTTTTCGATAACGTT-A
46751262 GTGACTG
1 GTGACTG
46751269 GATTGAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
29 3 0.09
30 10 0.29
31 21 0.62
ACGTcount: A:0.22, C:0.12, G:0.24, T:0.43
Consensus pattern (31 bp):
GTGACTGATTTGTCACTTTTCGATAACGTTA
Found at i:46751276 original size:20 final size:20
Alignment explanation
Indices: 46751251--46751288 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
46751241 TTGTTACTTT
46751251 TTGAAAGTT-GAGTGACTGGA
1 TTGAAA-TTAGAGTGACTGGA
46751271 TTGAAATTAGAGTGACTG
1 TTGAAATTAGAGTGACTG
46751289 TTTTGTCGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.32, C:0.05, G:0.32, T:0.32
Consensus pattern (20 bp):
TTGAAATTAGAGTGACTGGA
Found at i:46751954 original size:18 final size:18
Alignment explanation
Indices: 46751906--46751960 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
46751896 AATTTTTGAA
*
46751906 AAATATAAAAAAATTAAT
1 AAATATATAAAAATTAAT
*
46751924 GGAAAT-CAT-AAAATTAAT
1 --AAATATATAAAAATTAAT
*
46751942 AAATATATAAAAATAAAT
1 AAATATATAAAAATTAAT
46751960 A
1 A
46751961 TATTTTTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
16 4 0.14
17 2 0.07
18 18 0.62
19 1 0.03
20 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.27
Consensus pattern (18 bp):
AAATATATAAAAATTAAT
Found at i:46752151 original size:9 final size:9
Alignment explanation
Indices: 46752075--46752152 Score: 59
Period size: 9 Copynumber: 8.4 Consensus size: 9
46752065 ACAAAAAAAT
*
46752075 AAATAATAA
1 AAATTATAA
* *
46752084 ATATTGTAA
1 AAATTATAA
46752093 ATAATTAT-A
1 A-AATTATAA
46752102 AAATTATAA
1 AAATTATAA
* *
46752111 ACATTTTGGAA
1 AAATTAT--AA
*
46752122 AAATTATGA
1 AAATTATAA
*
46752131 AAATTAAAA
1 AAATTATAA
46752140 AAATTATAA
1 AAATTATAA
46752149 AAAT
1 AAAT
46752153 ATTCTTTTTC
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
8 6 0.12
9 35 0.67
10 4 0.08
11 7 0.13
ACGTcount: A:0.60, C:0.01, G:0.05, T:0.33
Consensus pattern (9 bp):
AAATTATAA
Found at i:46756272 original size:3 final size:3
Alignment explanation
Indices: 46756255--46756308 Score: 90
Period size: 3 Copynumber: 18.0 Consensus size: 3
46756245 TTCATTTCAT
* *
46756255 TTA TTA TCA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
46756303 TTA TTA
1 TTA TTA
46756309 ACACTTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:46757587 original size:15 final size:15
Alignment explanation
Indices: 46757567--46757601 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
46757557 TTTATTAAAT
*
46757567 AATAATATTTTATTA
1 AATAATATTATATTA
46757582 AATAATATTATATTA
1 AATAATATTATATTA
*
46757597 CATAA
1 AATAA
46757602 AAAAAGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (15 bp):
AATAATATTATATTA
Found at i:46758008 original size:45 final size:45
Alignment explanation
Indices: 46757957--46758045 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
46757947 GGAAAGTCTA
* *
46757957 CTTAGTACATTTGTCTATGGTGAAAGGGAAGTAGAGAACCTTGGC
1 CTTAGTACATTTGTCCATGGTGAAAGGGAAGTACAGAACCTTGGC
46758002 CTTAGTACATTTGTCCATGGTGAAAGGGAAGTACAGAACCTTGG
1 CTTAGTACATTTGTCCATGGTGAAAGGGAAGTACAGAACCTTGG
46758046 TCACTTTGTG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.29, C:0.15, G:0.28, T:0.28
Consensus pattern (45 bp):
CTTAGTACATTTGTCCATGGTGAAAGGGAAGTACAGAACCTTGGC
Found at i:46761113 original size:2 final size:2
Alignment explanation
Indices: 46761102--46761134 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
46761092 ATCTATAACT
46761102 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46761135 AACATAAGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:46761337 original size:19 final size:19
Alignment explanation
Indices: 46761287--46761338 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
46761277 ACATATCAAG
*
46761287 AATAAGTAATATTAATTATT
1 AATAAGTAATA-AAATTATT
46761307 AATAA-TAGATAAAATTATT
1 AATAAGTA-ATAAAATTATT
46761326 AATAAGTAATAAA
1 AATAAGTAATAAA
46761339 TTTTTATTAG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 19 0.66
20 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.37
Consensus pattern (19 bp):
AATAAGTAATAAAATTATT
Found at i:46761501 original size:2 final size:2
Alignment explanation
Indices: 46761494--46761531 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
46761484 TTTAATGACA
*
46761494 AT AT AT AT AT AT AT AT AT AT AT AG 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 AT AT
46761532 CAACTAGGCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:46761839 original size:20 final size:23
Alignment explanation
Indices: 46761814--46761858 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 23
46761804 AAATTGAAAA
46761814 ATTC-AATAATTTTA-A-TATAT
1 ATTCAAATAATTTTATATTATAT
*
46761834 ATTCAAATATTTTTATATTATAT
1 ATTCAAATAATTTTATATTATAT
46761857 AT
1 AT
46761859 AAAAATTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 4 0.19
21 9 0.43
22 1 0.05
23 7 0.33
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTCAAATAATTTTATATTATAT
Found at i:46761961 original size:28 final size:29
Alignment explanation
Indices: 46761904--46761963 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
46761894 AAAAATTATA
* *
46761904 TTTGAATTTCAAATTTCCAATTTGACTTT
1 TTTGAAATTCAAATTTCCAATTTGAATTT
*
46761933 TTTGAAATTCAAA-TTGCAATTTGAATTT
1 TTTGAAATTCAAATTTCCAATTTGAATTT
46761961 TTT
1 TTT
46761964 ATATTTGAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 16 0.57
29 12 0.43
ACGTcount: A:0.30, C:0.10, G:0.08, T:0.52
Consensus pattern (29 bp):
TTTGAAATTCAAATTTCCAATTTGAATTT
Found at i:46772940 original size:28 final size:28
Alignment explanation
Indices: 46772903--46772958 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
46772893 ACTATACTGG
*
46772903 TTTTTTC-AAATTAGTACTTAAAATATT
1 TTTTTTCAAAATTAGTACCTAAAATATT
* *
46772930 TTTTTGTCAAAATTGGTACCTAAACTATT
1 TTTTT-TCAAAATTAGTACCTAAAATATT
46772959 AAATCGTTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 2 0.08
29 17 0.71
ACGTcount: A:0.34, C:0.11, G:0.07, T:0.48
Consensus pattern (28 bp):
TTTTTTCAAAATTAGTACCTAAAATATT
Found at i:46773709 original size:26 final size:25
Alignment explanation
Indices: 46773670--46773718 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
46773660 TGAAGAAAGA
46773670 AGAAGAGTGGAAGCTTAAAGATGGT
1 AGAAGAGTGGAAGCTTAAAGATGGT
*
46773695 AGAAGCAGTGGAAGCTTGAAGATG
1 AGAAG-AGTGGAAGCTTAAAGATG
46773719 ATAAAATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 5 0.23
26 17 0.77
ACGTcount: A:0.39, C:0.06, G:0.37, T:0.18
Consensus pattern (25 bp):
AGAAGAGTGGAAGCTTAAAGATGGT
Found at i:46775637 original size:15 final size:14
Alignment explanation
Indices: 46775607--46775634 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
46775597 AAAAATATTT
46775607 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
46775621 TAAAAATAAAAAAA
1 TAAAAATAAAAAAA
46775635 ATATTTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
TAAAAATAAAAAAA
Found at i:46775672 original size:44 final size:46
Alignment explanation
Indices: 46775602--46775688 Score: 133
Period size: 44 Copynumber: 1.9 Consensus size: 46
46775592 CACAAAAAAA
*
46775602 TATTTTAAAAATAAAAAAATAAAAATAAAAAAA-ATATTTTTAAAG
1 TATTTTAAAAATAAAAAAATAAAAATAAAAAAATATATATTTAAAG
* *
46775647 TATTTT-AAAATTAAAAGATAAAAATAAAAAAATATATATTTA
1 TATTTTAAAAATAAAAAAATAAAAATAAAAAAATATATATTTA
46775689 TTATATTCGG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 24 0.63
45 14 0.37
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (46 bp):
TATTTTAAAAATAAAAAAATAAAAATAAAAAAATATATATTTAAAG
Found at i:46776600 original size:3 final size:3
Alignment explanation
Indices: 46776592--46776625 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
46776582 CCACCTGTAC
46776592 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
46776626 ACCAAATTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:46792086 original size:50 final size:50
Alignment explanation
Indices: 46791976--46792265 Score: 305
Period size: 50 Copynumber: 5.7 Consensus size: 50
46791966 AAATGCGAAA
* ** * * *
46791976 GCCATGTCCCAGACATGGTCTTACATAGGATGTTTCTTGTAC--TGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAT-CGGTGCCAAT
* * ** *
46792025 GCCATATCCCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCTAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
** * * *
46792075 GCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
* * * *
46792125 GCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
* *
46792175 GCCATGTCCTAGACATGGTCTTACATGAGACCTCTCATAATCTCGACGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TCG--G-TGCCAAT
46792231 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
46792266 TTATCCAAAT
Statistics
Matches: 203, Mismatches: 30, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 32 0.16
50 128 0.63
53 2 0.01
55 1 0.00
56 39 0.19
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAAT
Found at i:46814273 original size:12 final size:13
Alignment explanation
Indices: 46814248--46814277 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
46814238 TGGGCTATAA
46814248 TTATTGCATTTAT
1 TTATTGCATTTAT
46814261 TTATTGC-TTTAT
1 TTATTGCATTTAT
46814273 TTATT
1 TTATT
46814278 CATGTATGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.59
13 7 0.41
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.67
Consensus pattern (13 bp):
TTATTGCATTTAT
Found at i:46816663 original size:16 final size:15
Alignment explanation
Indices: 46816638--46816667 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
46816628 GGTTTACACC
46816638 AGATACAATTTTAAA
1 AGATACAATTTTAAA
46816653 AGATAACAATTTTAA
1 AGAT-ACAATTTTAA
46816668 GGCAGTGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (15 bp):
AGATACAATTTTAAA
Found at i:46823230 original size:27 final size:28
Alignment explanation
Indices: 46823171--46823224 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 28
46823161 AAAATAATTA
*
46823171 AAATTAAATATGTTAATAATTTAAGTGC
1 AAATTAAATATGTTAATAATTAAAGTGC
* *
46823199 AAATTAATTAT-TTTATAATTAAAGTG
1 AAATTAAATATGTTAATAATTAAAGTG
46823225 TGAATTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 13 0.57
28 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.09, T:0.43
Consensus pattern (28 bp):
AAATTAAATATGTTAATAATTAAAGTGC
Found at i:46831927 original size:20 final size:19
Alignment explanation
Indices: 46831902--46831948 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
46831892 TTCTCACTGC
46831902 TGTGCCTCTGCTTGCACATT
1 TGTGCCTCTGCTTGCAC-TT
*
46831922 TGTGCCTCTGTTTGCACTT
1 TGTGCCTCTGCTTGCACTT
46831941 TGGTGCCT
1 T-GTGCCT
46831949 TTTTATTGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 3 0.12
20 22 0.88
ACGTcount: A:0.06, C:0.28, G:0.23, T:0.43
Consensus pattern (19 bp):
TGTGCCTCTGCTTGCACTT
Found at i:46833891 original size:81 final size:80
Alignment explanation
Indices: 46833742--46833990 Score: 214
Period size: 81 Copynumber: 3.1 Consensus size: 80
46833732 ACTACAACAT
* * * * *
46833742 TGAAACACTAGCAAACTCTTTACTGATACTCTTTGGTGAACTCCCCAGTTCTTTGAAGTATTGAC
1 TGAAACACTAGCAAACTCATTACTAATACTCTTTGGTGAACTCCCCAGTTCGTCGAAGTAATGAC
46833807 GAACCCCTAGTTCGC
66 GAACCCCTAGTTCGC
* *
46833822 TGAAACACT-GACAAACTCATTACTAATACTCTATTGGTTAACTCCCTAGTTCGTCGAAGTACAT
1 TGAAACACTAG-CAAACTCATTACTAATACTCT-TTGGTGAACTCCCCAGTTCGTCGAAGTA-AT
**
46833886 G-CGAACCCCTAGTTTAC
63 GACGAACCCCTAGTTCGC
* * * * * * * * * * * * ** *
46833903 CGAAACACTGGCGAATTCCTTACTGATACTCTTTTGGAGAATTCCCCCGTTTGCCAAAGTTTTGT
1 TGAAACACTAGCAAACTCATTACTAATACTC-TTTGGTGAACTCCCCAGTTCGTCGAAGTAATGA
* *
46833968 GGAACCCCTAGTTCAC
65 CGAACCCCTAGTTCGC
46833984 TGAAACA
1 TGAAACA
46833991 TTGGCGAACC
Statistics
Matches: 136, Mismatches: 27, Indels: 11
0.78 0.16 0.06
Matches are distributed among these distances:
79 1 0.01
80 30 0.22
81 101 0.74
82 4 0.03
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (80 bp):
TGAAACACTAGCAAACTCATTACTAATACTCTTTGGTGAACTCCCCAGTTCGTCGAAGTAATGAC
GAACCCCTAGTTCGC
Found at i:46837842 original size:34 final size:34
Alignment explanation
Indices: 46837798--46837865 Score: 118
Period size: 34 Copynumber: 2.0 Consensus size: 34
46837788 CAGATGAGCC
* *
46837798 AATTGGTGAGTATGATGGGAGATATTAAAAGGAA
1 AATTGATGAGTATGATGGAAGATATTAAAAGGAA
46837832 AATTGATGAGTATGATGGAAGATATTAAAAGGAA
1 AATTGATGAGTATGATGGAAGATATTAAAAGGAA
46837866 GGGAAGGAGT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.00, G:0.29, T:0.26
Consensus pattern (34 bp):
AATTGATGAGTATGATGGAAGATATTAAAAGGAA
Found at i:46846308 original size:18 final size:19
Alignment explanation
Indices: 46846280--46846316 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
46846270 GCATTCACAT
46846280 CTTTCCTCTCTTCTCTCCA
1 CTTTCCTCTCTTCTCTCCA
*
46846299 CTTT-CTCTCTTCTTTCCA
1 CTTTCCTCTCTTCTCTCCA
46846317 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.05, C:0.43, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTCCTCTCTTCTCTCCA
Found at i:46853344 original size:27 final size:27
Alignment explanation
Indices: 46853292--46853345 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
46853282 ATTTAAACAT
* * * *
46853292 CTCTTAACTCCTTTAATCTCTCAAAAC
1 CTCTTAAATCCTTTAAACCCTAAAAAC
46853319 CTCTTAAATCCTTTAAACCCTAAAAAC
1 CTCTTAAATCCTTTAAACCCTAAAAAC
46853346 TCACTTTTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.35, C:0.31, G:0.00, T:0.33
Consensus pattern (27 bp):
CTCTTAAATCCTTTAAACCCTAAAAAC
Found at i:46854683 original size:21 final size:21
Alignment explanation
Indices: 46854654--46854693 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
46854644 CATGAAAGCG
*
46854654 AAGAGGAAGGAGAGGATGATA
1 AAGAAGAAGGAGAGGATGATA
*
46854675 AAGAAGAAGGAGATGATGA
1 AAGAAGAAGGAGAGGATGA
46854694 AATGGATTTT
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:0.50, C:0.00, G:0.40, T:0.10
Consensus pattern (21 bp):
AAGAAGAAGGAGAGGATGATA
Found at i:46858221 original size:17 final size:18
Alignment explanation
Indices: 46858188--46858221 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
46858178 ATGATATGTC
46858188 AAACTATGTTCGTGCTTG
1 AAACTATGTTCGTGCTTG
*
46858206 AAACTAT-TTGGTGCTT
1 AAACTATGTTCGTGCTT
46858222 ACTATTCTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.15, G:0.21, T:0.41
Consensus pattern (18 bp):
AAACTATGTTCGTGCTTG
Found at i:46862621 original size:23 final size:23
Alignment explanation
Indices: 46862595--46862642 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
46862585 CTTTCTTACT
* *
46862595 GTAATTTTCGGGGTATTACAGTA
1 GTAATTTTCGGGATATTACACTA
46862618 GTAATTTTCGGGATATTACACTA
1 GTAATTTTCGGGATATTACACTA
46862641 GT
1 GT
46862643 GTTTGATATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.27, C:0.10, G:0.23, T:0.40
Consensus pattern (23 bp):
GTAATTTTCGGGATATTACACTA
Found at i:46865480 original size:15 final size:16
Alignment explanation
Indices: 46865453--46865482 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
46865443 AAAAATAATT
46865453 AATATATATTATATAA
1 AATATATATTATATAA
46865469 AATATA-ATTATATA
1 AATATATATTATATA
46865483 TTAGTTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
AATATATATTATATAA
Found at i:46873304 original size:20 final size:19
Alignment explanation
Indices: 46873267--46873377 Score: 80
Period size: 20 Copynumber: 5.6 Consensus size: 19
46873257 TAGGACACCA
* *
46873267 AAGTGCAATCAAGAGCACG
1 AAGTGCAATCAGGGGCACG
*
46873286 AATGTGCAATCAGGGGCACCA
1 AA-GTGCAATCAGGGGCA-CG
*
46873307 AAGTGCAAAT-AGGGGCGCG
1 AAGTGC-AATCAGGGGCACG
* *
46873326 TAAGTGCAATCAAGGGTACCG
1 -AAGTGCAATCAGGGGCA-CG
* * *
46873347 AAGTACAAACAGGGGCATG
1 AAGTGCAATCAGGGGCACG
46873366 TAAGTGCAATCA
1 -AAGTGCAATCA
46873378 TTGAATAATT
Statistics
Matches: 70, Mismatches: 15, Indels: 13
0.71 0.15 0.13
Matches are distributed among these distances:
19 7 0.10
20 55 0.79
21 8 0.11
ACGTcount: A:0.37, C:0.19, G:0.30, T:0.14
Consensus pattern (19 bp):
AAGTGCAATCAGGGGCACG
Found at i:46873333 original size:40 final size:40
Alignment explanation
Indices: 46873262--46873377 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 40
46873252 CATAATAGGA
* * * * *
46873262 CACCAAAGTGCAATCAAGAGCACG-AATGTGCAATCAGGGG
1 CACCAAAGTACAAACAGGGGCACGTAA-GTGCAATCAAGGG
* * *
46873302 CACCAAAGTGCAAATAGGGGCGCGTAAGTGCAATCAAGGG
1 CACCAAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGG
* * *
46873342 TACCGAAGTACAAACAGGGGCATGTAAGTGCAATCA
1 CACCAAAGTACAAACAGGGGCACGTAAGTGCAATCA
46873378 TTGAATAATT
Statistics
Matches: 63, Mismatches: 12, Indels: 2
0.82 0.16 0.03
Matches are distributed among these distances:
40 61 0.97
41 2 0.03
ACGTcount: A:0.37, C:0.21, G:0.28, T:0.14
Consensus pattern (40 bp):
CACCAAAGTACAAACAGGGGCACGTAAGTGCAATCAAGGG
Found at i:46876894 original size:17 final size:15
Alignment explanation
Indices: 46876852--46876896 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
46876842 GGAGAAAGAG
46876852 AAAAAA-ATGTGTGA
1 AAAAAAGATGTGTGA
46876866 AAAAAAGATGTGTGA
1 AAAAAAGATGTGTGA
*
46876881 AAGAAAGATGTGTGA
1 AAAAAAGATGTGTGA
46876896 A
1 A
46876897 GTGAGGGATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 6 0.21
15 23 0.79
ACGTcount: A:0.53, C:0.00, G:0.27, T:0.20
Consensus pattern (15 bp):
AAAAAAGATGTGTGA
Found at i:46878991 original size:32 final size:32
Alignment explanation
Indices: 46878954--46879139 Score: 237
Period size: 32 Copynumber: 5.8 Consensus size: 32
46878944 CATAAGTACA
** * *
46878954 GTAATATGATTAGCACAAAGCCATCAGTAGTA
1 GTAATATGATCGGCACAAAGCCATCAGTAATG
* *
46878986 GTAATATGATCGGCACATAGCCATCGGTAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAATG
**
46879018 GTAATATGATCGGCACGCAGCCATCAGTAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAATG
* * *
46879050 GTAATATGATCAGTACACAGCCATCAGTAATG
1 GTAATATGATCGGCACAAAGCCATCAGTAATG
* * *
46879082 GTAATATGATCGGCACACAGCCATCAGTAGTC
1 GTAATATGATCGGCACAAAGCCATCAGTAATG
*
46879114 GTAATATGATCGACACAAAGCCATCA
1 GTAATATGATCGGCACAAAGCCATCA
46879140 ATAGCATTGC
Statistics
Matches: 136, Mismatches: 18, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 136 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (32 bp):
GTAATATGATCGGCACAAAGCCATCAGTAATG
Found at i:46879118 original size:96 final size:96
Alignment explanation
Indices: 46878954--46879139 Score: 264
Period size: 96 Copynumber: 1.9 Consensus size: 96
46878944 CATAAGTACA
* * * * *
46878954 GTAATATGATTAGCACAAAGCCATCAGTAGTAGTAATATGATCGGCACATAGCCATCGGTAATGG
1 GTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAGCCATCAGTAATCG
* **
46879019 TAATATGATCGGCACGCAGCCATCAGTAATG
66 TAATATGATCGACACAAAGCCATCAGTAATG
* * * *
46879050 GTAATATGATCAGTACACAGCCATCAGTAATGGTAATATGATCGGCACACAGCCATCAGTAGTCG
1 GTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAGCCATCAGTAATCG
46879115 TAATATGATCGACACAAAGCCATCA
66 TAATATGATCGACACAAAGCCATCA
46879140 ATAGCATTGC
Statistics
Matches: 78, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 78 1.00
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.23
Consensus pattern (96 bp):
GTAATATGATCAGCACAAAGCCATCAGTAATAGTAATATGATCGGCACACAGCCATCAGTAATCG
TAATATGATCGACACAAAGCCATCAGTAATG
Found at i:46879460 original size:27 final size:27
Alignment explanation
Indices: 46879431--46879765 Score: 386
Period size: 27 Copynumber: 12.4 Consensus size: 27
46879421 AGCAAAATAG
* *
46879431 TCATTTTACCCTACAGGGGCATCACGG
1 TCATTTTACCCTACAGGGGCATTACGA
*
46879458 TCATTTTACCCTACAGGGGCATTATGA
1 TCATTTTACCCTACAGGGGCATTACGA
* ** *
46879485 TCATTTTACCCTATAGGGGTGTTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* *
46879512 TCATTTTACCCTACAGGGCCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* **
46879539 TAATTTTACCCTACAAAGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
46879566 TCATTTTACCCTACAGGGGCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* *
46879593 TCATTTTACCCTACAAGGTCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* * * *
46879620 TTATTTTATCCTACAAGGTCATTACGA
1 TCATTTTACCCTACAGGGGCATTACGA
* *
46879647 TTATTTTATCCTACAGGGGCATTAC-A
1 TCATTTTACCCTACAGGGGCATTACGA
* * *
46879673 GTCATTTTATCCTACAAGGGCATTACAA
1 -TCATTTTACCCTACAGGGGCATTACGA
*
46879701 TCATTTTACCCTACAGGGGCATTACGG
1 TCATTTTACCCTACAGGGGCATTACGA
* ** * *
46879728 TAATTTTACCCT-TTGGGGTATTTCGA
1 TCATTTTACCCTACAGGGGCATTACGA
46879754 TCATTTTACCCT
1 TCATTTTACCCT
46879766 TTGAGGGTAT
Statistics
Matches: 267, Mismatches: 39, Indels: 5
0.86 0.13 0.02
Matches are distributed among these distances:
26 21 0.08
27 245 0.92
28 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.17, T:0.34
Consensus pattern (27 bp):
TCATTTTACCCTACAGGGGCATTACGA
Found at i:46879517 original size:81 final size:81
Alignment explanation
Indices: 46879430--46879819 Score: 390
Period size: 81 Copynumber: 4.8 Consensus size: 81
46879420 GAGCAAAATA
* * * * *
46879430 GTCATTTTACCCTACAGGGGCATCACGGTCATTTTACCCTACAGGGGCATTATGATCATTTTACC
1 GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCATTACGATCATTTTACC
* **
46879495 CTATAGGGGTGTTACG
66 CTACAGGGGCATTACG
* * *
46879511 GTCATTTTACCCTAC-AGGGCCATTACGGTAATTTTACCCTACAAAGGCATTACGATCATTTTAC
1 GTCATTTTACCCTACAAGGG-CATTACGATCATTTTACCCTACAAGGGCATTACGATCATTTTAC
46879575 CCTACAGGGGCATTACG
65 CCTACAGGGGCATTACG
* * * * * * *
46879592 ATCATTTTACCCTACAAGGTCATTACGATTATTTTATCCTACAAGGTCATTACGATTATTTTATC
1 GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCATTACGATCATTTTACC
*
46879657 CTACAGGGGCATTACA
66 CTACAGGGGCATTACG
* * * * *
46879673 GTCATTTTATCCTACAAGGGCATTACAATCATTTTACCCTACAGGGGCATTACGGTAATTTTACC
1 GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCATTACGATCATTTTACC
** * *
46879738 CT-TTGGGGTATTTCG
66 CTACAGGGGCATTACG
* *** * * * * * * *
46879753 ATCATTTTACCCTTTGAGGGTATT-CCAGTAATTTTACCCTTCAAGGGTATTTCGATAATTTTAC
1 GTCATTTTACCCTACAAGGGCATTACGA-TCATTTTACCCTACAAGGGCATTACGATCATTTTAC
46879817 CCT
65 CCT
46879820 TCGGGGGTAT
Statistics
Matches: 258, Mismatches: 48, Indels: 7
0.82 0.15 0.02
Matches are distributed among these distances:
79 2 0.01
80 62 0.24
81 191 0.74
82 3 0.01
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.35
Consensus pattern (81 bp):
GTCATTTTACCCTACAAGGGCATTACGATCATTTTACCCTACAAGGGCATTACGATCATTTTACC
CTACAGGGGCATTACG
Found at i:46879786 original size:27 final size:27
Alignment explanation
Indices: 46879727--46879866 Score: 153
Period size: 27 Copynumber: 5.2 Consensus size: 27
46879717 GGGCATTACG
46879727 GTAATTTTACCCTTTG-GGGTATTTC-
1 GTAATTTTACCCTTTGAGGGTATTTCA
* *
46879752 GATCATTTTACCCTTTGAGGGTATTCCA
1 G-TAATTTTACCCTTTGAGGGTATTTCA
**
46879780 GTAATTTTACCCTTCAAGGGTATTTC-
1 GTAATTTTACCCTTTGAGGGTATTTCA
* *
46879806 GATAATTTTACCCTTCGGGGGTATTTCA
1 G-TAATTTTACCCTTTGAGGGTATTTCA
* *
46879834 ATAATTTTA-CCTTTCGAGGGTATTTTA
1 GTAATTTTACCCTTT-GAGGGTATTTCA
46879861 GTAATT
1 GTAATT
46879867 ACAACCTTTC
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
25 1 0.01
26 19 0.20
27 75 0.78
28 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (27 bp):
GTAATTTTACCCTTTGAGGGTATTTCA
Found at i:46879818 original size:54 final size:54
Alignment explanation
Indices: 46879727--46879858 Score: 176
Period size: 54 Copynumber: 2.5 Consensus size: 54
46879717 GGGCATTACG
** * *
46879727 GTAATTTTACCCTT-TGGGGTATTTCGATCATTTTACCCTTTGAGGGTATTCCA
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCCA
* *
46879780 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTCA
1 GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCCA
* * *
46879834 ATAATTTTACCTTTCGAGGGTATTT
1 GTAATTTTACCCTTCAAGGGTATTT
46879859 TAGTAATTAC
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
53 14 0.20
54 55 0.80
ACGTcount: A:0.21, C:0.17, G:0.18, T:0.43
Consensus pattern (54 bp):
GTAATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGAGGGTATTCCA
Found at i:46879864 original size:81 final size:80
Alignment explanation
Indices: 46879460--46879866 Score: 219
Period size: 81 Copynumber: 5.0 Consensus size: 80
46879450 CATCACGGTC
* * * * * * ** *
46879460 ATTTTACCCTACAGGGGCATTATGATCATTTTACCCTATAGGGGTGTTACGGTCATTTTACCC-T
1 ATTTTACCCTACAAGGGCATTACGATAATTTTACCCT-TGGGGGTATTTCAATAATTTTACCCTT
** * * *
46879524 ACAGGGCCATTACGGTA
65 TGAGGG-TATTCCAGTA
* * ** * * * *
46879541 ATTTTACCCTACAAAGGCATTACGATCATTTTACCCTACAGGGGCATTACGATCATTTTACCC-T
1 ATTTTACCCTACAAGGGCATTACGATAATTTTACCCT-TGGGGGTATTTCAATAATTTTACCCTT
** * * *
46879605 ACAAGGTCATTAC-GATT
65 TGAGGGT-ATTCCAG-TA
* * * * ** * * * * * *
46879622 ATTTTATCCTACAAGGTCATTACGATTATTTTATCCTACAGGGGCATTACAGTCATTTTATCCTA
1 ATTTTACCCTACAAGGGCATTACGATAATTTTACCCT-TGGGGGTATTTCAATAATTTTACCCTT
** * * * *
46879687 CAAGGGCATTACAATC
65 TGAGGGTATTCCAGTA
* * * * *
46879703 ATTTTACCCTACAGGGGCATTACGGTAATTTTACCCTTTGGGGTATTTCGATCATTTTACCCTTT
1 ATTTTACCCTACAAGGGCATTACGATAATTTTACCCTTGGGGGTATTTCAATAATTTTACCCTTT
46879768 GAGGGTATTCCAGTA
66 GAGGGTATTCCAGTA
* * *
46879783 ATTTTACCCTTCAAGGGTATTTCGATAATTTTACCCTTCGGGGGTATTTCAATAATTTTA-CCTT
1 ATTTTACCCTACAAGGGCATTACGATAATTTTACCCTT-GGGGGTATTTCAATAATTTTACCCTT
**
46879847 TCGAGGGTATTTTAGTA
65 T-GAGGGTATTCCAGTA
46879864 ATT
1 ATT
46879867 ACAACCTTTC
Statistics
Matches: 265, Mismatches: 55, Indels: 12
0.80 0.17 0.04
Matches are distributed among these distances:
80 68 0.26
81 194 0.73
82 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.37
Consensus pattern (80 bp):
ATTTTACCCTACAAGGGCATTACGATAATTTTACCCTTGGGGGTATTTCAATAATTTTACCCTTT
GAGGGTATTCCAGTA
Found at i:46882993 original size:51 final size:50
Alignment explanation
Indices: 46882862--46883098 Score: 192
Period size: 51 Copynumber: 4.7 Consensus size: 50
46882852 GTGAAAGTGA
* ** **
46882862 TGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGA-ATGAA
1 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACACGTACCGGATA-GTT
* * * *
46882912 AGGT-AGCATGTGGAGTACTATGTGCAGGCTACTATACGTACCGGATAGCTT
1 TGGTCA-CGTGTGTAGTACTATGTGCAGGCTACTACACGTACCGGATAG-TT
* * ** * *
46882963 CGGTCACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCAGATA-TT
1 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACACGTACCGGATAGTT
* ** * *
46883012 AATGGTCACGTGTGTAGTACTATATGCAGGCTACTACGTGAACCGGAAAGTT
1 --TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACACGTACCGGATAGTT
* * * *
46883064 TGATAATGTGTGTAGTACTATGTGAAGGCTACTAC
1 TGGTCACGTGTGTAGTACTATGTGCAGGCTACTAC
46883099 GTGTATCGAA
Statistics
Matches: 150, Mismatches: 30, Indels: 14
0.77 0.15 0.07
Matches are distributed among these distances:
49 3 0.02
50 67 0.45
51 77 0.51
52 3 0.02
ACGTcount: A:0.26, C:0.16, G:0.28, T:0.30
Consensus pattern (50 bp):
TGGTCACGTGTGTAGTACTATGTGCAGGCTACTACACGTACCGGATAGTT
Found at i:46883130 original size:101 final size:100
Alignment explanation
Indices: 46882867--46883140 Score: 308
Period size: 101 Copynumber: 2.7 Consensus size: 100
46882857 AGTGATGGTC
* *
46882867 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTACCGGAATGA-AAGG-TAGCATGTGGAGTAC
1 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATC-GAATGATAAGGTTA-CATGTGTAGTAC
* * *
46882930 TATGTGCAGGCTACTATACGTACCGGATAGCTTCGGTC
64 TATGTGCAGGCTAC-ATACGTACCGGAAAGCTTCGATA
* *
46882968 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATC-AGAT-ATTAATGGTCACGTGTGTAGTA
1 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGA-ATGA-TAA-GGTTACATGTGTAGTA
* *
46883031 CTATATGCAGGCTAC-TACGTGAACCGGAAAG-TTTGATA
63 CTATGTGCAGGCTACATACGT--ACCGGAAAGCTTCGATA
* * * *
46883069 ATGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGAATGATAAGAGTTAAATGAGTAGTACT
1 ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGAATGATAAG-GTTACATGTGTAGTACT
46883134 ATGTGCA
65 ATGTGCA
46883141 AACGACCGAA
Statistics
Matches: 147, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
99 2 0.01
100 8 0.05
101 101 0.69
102 35 0.24
103 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (100 bp):
ACGTGTGTAGTACTATGTGTAGGCTACTACGTGTATCGAATGATAAGGTTACATGTGTAGTACTA
TGTGCAGGCTACATACGTACCGGAAAGCTTCGATA
Found at i:46889073 original size:41 final size:41
Alignment explanation
Indices: 46889019--46889153 Score: 207
Period size: 41 Copynumber: 3.3 Consensus size: 41
46889009 AATATTGTTG
* * *
46889019 AATTACACATACGTGCCCCTGTTTGTACTTCGGTACCCTTG
1 AATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTA
* *
46889060 AATTGCACATACGTGCCCCTATTTGTACTTTGGTACTCTTA
1 AATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTA
* *
46889101 AATTGCGCATACGTGCCCCTATTTGTACTTCGGTACCCATA
1 AATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTA
46889142 AATTGCACATAC
1 AATTGCACATAC
46889154 TACCTTATGT
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 84 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (41 bp):
AATTGCACATACGTGCCCCTATTTGTACTTCGGTACCCTTA
Found at i:46889700 original size:30 final size:30
Alignment explanation
Indices: 46889664--46889732 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
46889654 CCTGATACAT
46889664 GGACGTGTGTCTCAGCCGTGTAAGGCACAC
1 GGACGTGTGTCTCAGCCGTGTAAGGCACAC
*
46889694 GGACGTGTGTCTCAGCCGTGTGAGGCACAC
1 GGACGTGTGTCTCAGCCGTGTAAGGCACAC
*
46889724 GGCCGTGTG
1 GGACGTGTG
46889733 ACCCCTCCAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.16, C:0.26, G:0.38, T:0.20
Consensus pattern (30 bp):
GGACGTGTGTCTCAGCCGTGTAAGGCACAC
Found at i:46892382 original size:139 final size:138
Alignment explanation
Indices: 46892185--46892744 Score: 801
Period size: 138 Copynumber: 4.1 Consensus size: 138
46892175 TAGAAAAAGG
** * *
46892185 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATGTTTTAACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTAA
*
46892250 TATAACTATTTATATTAATAAATTCAGTAAAATATATACAATTAATA-TTT-T-TGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
46892312 CAAATATATATT
131 C----ATATATT
* *
46892324 AATTATATTC-TTCCTAAAAGAATATTAATTTTCATGTCTTTTATAATTTGACCAAAATTAATTA
1 AATTATATTCTTTCC-AAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTA
* * * *
46892388 ATATAATTGTTTATATTACT-AAGTAAGGTAAAATATATACAATTAATATTTTGTATGAATCAAA
65 ATATAACTGTTTATATTAATAAATTCA-GTAAAATATATACAATTAATATTTTGTATGAATCAAA
46892452 TTCATATATT
129 TTCATATATT
* *
46892462 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATATTTTGACTGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTAA
*
46892527 TATAACTGTTTATATTAATAAATTCGGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
66 TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
46892592 CATATATT
131 CATATATT
* * * *
46892600 AATTATATTCTTTCCAAAATAATATTAATTTCCATGTGTTTTAT-ACTTGATCGAAATTAATTAA
1 AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTAA
* * * * *
46892664 TATAATTGTTTATATTAATAAATTC-GATAAAATATGTGCAATTAATATTTTTTATGAATCGAAT
66 TATAACTGTTTATATTAATAAATTCAG-TAAAATATATACAATTAATATTTTGTATGAATCAAAT
46892728 TCATATATT
130 TCATATATT
46892737 AATTATAT
1 AATTATAT
46892745 ATATGTTCTC
Statistics
Matches: 382, Mismatches: 31, Indels: 18
0.89 0.07 0.04
Matches are distributed among these distances:
136 1 0.00
137 90 0.24
138 177 0.46
139 98 0.26
140 3 0.01
141 1 0.00
142 12 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (138 bp):
AATTATATTCTTTCCAAAAGAATATTAATTTCCATGTCTTTTATAATTTGACCGAAATTAATTAA
TATAACTGTTTATATTAATAAATTCAGTAAAATATATACAATTAATATTTTGTATGAATCAAATT
CATATATT
Found at i:46892508 original size:71 final size:70
Alignment explanation
Indices: 46892433--46892644 Score: 158
Period size: 71 Copynumber: 3.0 Consensus size: 70
46892423 TATACAATTA
46892433 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAGAATATTAATTTCCATG
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAA-AATATTAATTTCCATG
46892498 TCTTTT
65 TCTTTT
* * * * * **
46892504 ATATTTTG-ACTGAAAT-TAATT-A-ATA-TAACTGT-TTATATT--AATAAAT-TCGGTAAAAT
1 ATATTTTGTA-TG-AATCAAATTCATATATTAATTATATTCT-TTCCAAAAAATAT---TAATTT
* * *
46892560 --ATATACAATTA
60 CCATGT-C-TTTT
46892571 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAATAATATTAATTTCCATG
1 ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAA-AATATTAATTTCCATG
*
46892636 TGTTTT
65 TCTTTT
46892642 ATA
1 ATA
46892645 CTTGATCGAA
Statistics
Matches: 100, Mismatches: 21, Indels: 40
0.62 0.13 0.25
Matches are distributed among these distances:
64 1 0.01
65 6 0.06
66 7 0.07
67 23 0.23
68 9 0.09
69 6 0.06
70 9 0.09
71 26 0.26
72 6 0.06
73 6 0.06
74 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.46
Consensus pattern (70 bp):
ATATTTTGTATGAATCAAATTCATATATTAATTATATTCTTTCCAAAAAATATTAATTTCCATGT
CTTTT
Found at i:46898440 original size:21 final size:21
Alignment explanation
Indices: 46898416--46898455 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
46898406 AAATCCATTT
* *
46898416 CATCATCTGCTTCTTCTTCGC
1 CATCATCTCCTTCCTCTTCGC
*
46898437 CATCCTCTCCTTCCTCTTC
1 CATCATCTCCTTCCTCTTC
46898456 ACTTTCACGC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.07, C:0.45, G:0.05, T:0.42
Consensus pattern (21 bp):
CATCATCTCCTTCCTCTTCGC
Found at i:46901871 original size:3 final size:3
Alignment explanation
Indices: 46901863--46901906 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
46901853 ACTAGAATGC
46901863 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
46901907 TACCTTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:46902033 original size:3 final size:3
Alignment explanation
Indices: 46902027--46902097 Score: 142
Period size: 3 Copynumber: 23.7 Consensus size: 3
46902017 TAATAATATT
46902027 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
1 TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG TAG
46902075 TAG TAG TAG TAG TAG TAG TAG TA
1 TAG TAG TAG TAG TAG TAG TAG TA
46902098 ATGATAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 68 1.00
ACGTcount: A:0.34, C:0.00, G:0.32, T:0.34
Consensus pattern (3 bp):
TAG
Found at i:46902662 original size:42 final size:42
Alignment explanation
Indices: 46902553--46903062 Score: 585
Period size: 42 Copynumber: 12.2 Consensus size: 42
46902543 ATATACAATA
* * * *
46902553 CAATGAAAAGTAAATAGACTTTCACACCTGTGCCT-TAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
46902594 GAATGAAAAGTAAATGGACTTTCACACCTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * * * *
46902636 CATTGAAAATTCAACGGACCTCCACACTTGGGCATCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * * * *
46902678 CAATGAAAATTCAATGGACCTCCGCTCCGGGGTCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
46902720 CAATGAAAAGAAAATGGACCTCCGCACCTGGGTCTCTAAATA
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* *
46902762 CAATGAAAAGTAAATGGACCTCCACACTTGAGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* *
46902804 CAAT-AAAAATCAAATGGACCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGT-AAATGGACCTCCACACCTGGGCCTCTAAATG
* * *
46902846 CAATAAAAAGTAAATGGAACTCCACACCTGGGCCTTTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
46902888 CAGTAAAAAGTAAATGGACCTCCATACATGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* *
46902930 CAATGGAAAGTAAATGGACCTCCACACTTGGGCCTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * * *
46902972 CAAT-AAAATGTAAATGGGCCTCTACGCCTGGGCATCTAAATG
1 CAATGAAAA-GTAAATGGACCTCCACACCTGGGCCTCTAAATG
* * **
46903014 CAATGAAAAGTAAATGGACCTCCACTCCTAGGTTTCTAAATG
1 CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
46903056 CAATGAA
1 CAATGAA
46903063 TGTTTTCCTT
Statistics
Matches: 404, Mismatches: 60, Indels: 9
0.85 0.13 0.02
Matches are distributed among these distances:
41 40 0.10
42 355 0.88
43 9 0.02
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (42 bp):
CAATGAAAAGTAAATGGACCTCCACACCTGGGCCTCTAAATG
Found at i:46921007 original size:42 final size:42
Alignment explanation
Indices: 46920959--46921125 Score: 156
Period size: 42 Copynumber: 4.0 Consensus size: 42
46920949 AAGGAGCACA
* *
46920959 ATCACTTAAGCTCGCATAAGAAGCTTTGTTGATACACAGTTT
1 ATCACTTAAGCTCGCATAAGAAGCTTTGCTGATACACAGCTT
* * *
46921001 GTCACTTAAGCTCGCATGAGGAGCTTTGCTGATACACAGCTT
1 ATCACTTAAGCTCGCATAAGAAGCTTTGCTGATACACAGCTT
*** * * ** *
46921043 ATCACTTAAGCTCATGTAGGGAGCTTCACTGATACACAACTT
1 ATCACTTAAGCTCGCATAAGAAGCTTTGCTGATACACAGCTT
* * ** * *
46921085 GTCACTTAAGCTCAC-TGGGGAGCTTCGCTGATACACAGCTT
1 ATCACTTAAGCTCGCATAAGAAGCTTTGCTGATACACAGCTT
46921126 GTAAAAACCG
Statistics
Matches: 106, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
41 23 0.22
42 83 0.78
ACGTcount: A:0.27, C:0.23, G:0.20, T:0.29
Consensus pattern (42 bp):
ATCACTTAAGCTCGCATAAGAAGCTTTGCTGATACACAGCTT
Found at i:46921118 original size:41 final size:41
Alignment explanation
Indices: 46920988--46921127 Score: 183
Period size: 42 Copynumber: 3.4 Consensus size: 41
46920978 GAAGCTTTGT
* * * *
46920988 TGATACACAGTTTGTCACTTAAGCTCGCATGAGGAGCTTTGC
1 TGATACACAGCTTGTCACTTAAGCTCAC-TGGGGAGCTTCGC
* *
46921030 TGATACACAGCTTATCACTTAAGCTCA-TGTAGGGAGCTTCAC
1 TGATACACAGCTTGTCACTTAAGCTCACTG--GGGAGCTTCGC
*
46921072 TGATACACAACTTGTCACTTAAGCTCACTGGGGAGCTTCGC
1 TGATACACAGCTTGTCACTTAAGCTCACTGGGGAGCTTCGC
46921113 TGATACACAGCTTGT
1 TGATACACAGCTTGT
46921128 AAAAACCGTT
Statistics
Matches: 85, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
40 2 0.02
41 24 0.28
42 57 0.67
43 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (41 bp):
TGATACACAGCTTGTCACTTAAGCTCACTGGGGAGCTTCGC
Found at i:46924251 original size:28 final size:28
Alignment explanation
Indices: 46924219--46924294 Score: 125
Period size: 28 Copynumber: 2.7 Consensus size: 28
46924209 CAACAGTGTA
*
46924219 GGCCTTAGCCCAATATAGTAACAATGGG
1 GGCCTTAGCCCAATACAGTAACAATGGG
* *
46924247 GGCCTTAGCCCAATACAGTAACATTGTG
1 GGCCTTAGCCCAATACAGTAACAATGGG
46924275 GGCCTTAGCCCAATACAGTA
1 GGCCTTAGCCCAATACAGTA
46924295 TCGATACAGT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 45 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.22
Consensus pattern (28 bp):
GGCCTTAGCCCAATACAGTAACAATGGG
Found at i:46924563 original size:32 final size:31
Alignment explanation
Indices: 46924540--46924680 Score: 120
Period size: 32 Copynumber: 4.4 Consensus size: 31
46924530 TGATTGGCAT
* **
46924540 AACGCCATCAGTAGCAGTGATATGATTGGCA
1 AACGCCATCAGTAACAGTGATATGATCAGCA
* * * * *
46924571 CACAACTATCAGTAACGGTGATATGATCAACA
1 AAC-GCCATCAGTAACAGTGATATGATCAGCA
*
46924603 CAAAGCCATCAGTAACAGTGATATGATCAGCA
1 -AACGCCATCAGTAACAGTGATATGATCAGCA
* * * *
46924635 CACAGCCATCAGTAACGGTAATATGACCAGCA
1 AAC-GCCATCAGTAACAGTGATATGATCAGCA
*
46924667 TAAAGCCATCAGTA
1 -AACGCCATCAGTA
46924681 GCATCGCAGC
Statistics
Matches: 85, Mismatches: 21, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
31 3 0.04
32 80 0.94
33 2 0.02
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
AACGCCATCAGTAACAGTGATATGATCAGCA
Found at i:46924628 original size:64 final size:64
Alignment explanation
Indices: 46924543--46924680 Score: 195
Period size: 64 Copynumber: 2.2 Consensus size: 64
46924533 TTGGCATAAC
* ** * * *
46924543 GCCATCAGTAGCAGTGATATGATTGGCACACAACTATCAGTAACGGTGATATGATCAACACAAA
1 GCCATCAGTAACAGTGATATGATCAGCACACAACCATCAGTAACGGTAATATGACCAACACAAA
* * *
46924607 GCCATCAGTAACAGTGATATGATCAGCACACAGCCATCAGTAACGGTAATATGACCAGCATAAA
1 GCCATCAGTAACAGTGATATGATCAGCACACAACCATCAGTAACGGTAATATGACCAACACAAA
46924671 GCCATCAGTA
1 GCCATCAGTA
46924681 GCATCGCAGC
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 65 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (64 bp):
GCCATCAGTAACAGTGATATGATCAGCACACAACCATCAGTAACGGTAATATGACCAACACAAA
Found at i:46924887 original size:24 final size:25
Alignment explanation
Indices: 46924851--46924911 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
46924841 ATGCCATGCG
*
46924851 CAAAATCAGTCATACAATTCACAGA
1 CAAAATCAGTCATACAAATCACAGA
**
46924876 CAAAAT-AGTCATTTAAATCACAGA
1 CAAAATCAGTCATACAAATCACAGA
*
46924900 C-AAATCATTCAT
1 CAAAATCAGTCAT
46924912 TTTCATCACG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 4 0.13
24 21 0.68
25 6 0.19
ACGTcount: A:0.48, C:0.21, G:0.07, T:0.25
Consensus pattern (25 bp):
CAAAATCAGTCATACAAATCACAGA
Found at i:46924912 original size:24 final size:24
Alignment explanation
Indices: 46924869--46924938 Score: 79
Period size: 24 Copynumber: 2.9 Consensus size: 24
46924859 GTCATACAAT
*
46924869 TCACAGACAAAAT-AGTCATTTAAA
1 TCACAGAC-AAATCAATCATTTAAA
* **
46924893 TCACAGACAAATCATTCATTTTCA
1 TCACAGACAAATCAATCATTTAAA
*
46924917 TCACGGACAAATCAATCATTTA
1 TCACAGACAAATCAATCATTTA
46924939 CCCTCGAGGG
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.10
24 35 0.90
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (24 bp):
TCACAGACAAATCAATCATTTAAA
Found at i:46924991 original size:27 final size:25
Alignment explanation
Indices: 46924961--46925074 Score: 77
Period size: 27 Copynumber: 4.2 Consensus size: 25
46924951 AAAATAGTCA
*
46924961 TTTACCTTCCAAGGGCATTACGATCAT
1 TTTACCTT-CAAGGGTATT-CGATCAT
* * *
46924988 TTTACCTTACAGGGGTATTTTGGTCAT
1 TTTACCTT-CAAGGGTA-TTCGATCAT
*
46925015 TTTACCTTAAGAGGGTATCTCGATCAT
1 TTTACCTTCA-AGGGTAT-TCGATCAT
* *
46925042 TTTACCCTTTAGGGGTAATTC-AGTCAT
1 TTTA-CCTTCAAGGGT-ATTCGA-TCAT
46925069 TTTACC
1 TTTACC
46925075 CATTGAGGGT
Statistics
Matches: 70, Mismatches: 11, Indels: 13
0.74 0.12 0.14
Matches are distributed among these distances:
26 5 0.07
27 56 0.80
28 9 0.13
ACGTcount: A:0.23, C:0.20, G:0.18, T:0.39
Consensus pattern (25 bp):
TTTACCTTCAAGGGTATTCGATCAT
Found at i:46925075 original size:27 final size:27
Alignment explanation
Indices: 46925040--46925234 Score: 195
Period size: 27 Copynumber: 7.2 Consensus size: 27
46925030 TATCTCGATC
* * *
46925040 ATTTTACCC-TTTAGGGGTAATTCAGTC
1 ATTTTACCCATTGA-GGGTATTTCAGTA
46925067 ATTTTACCCATTGAGGGTATTTCAGTA
1 ATTTTACCCATTGAGGGTATTTCAGTA
*
46925094 ATTTTACCCATTGAGGGTATTTCGGTA
1 ATTTTACCCATTGAGGGTATTTCAGTA
* *
46925121 ATTTTACCCATCGAGAGTATTTC-GATA
1 ATTTTACCCATTGAGGGTATTTCAG-TA
**
46925148 ATTTTACCCATTTG-GGGTATTTCTCTA
1 ATTTTACCCA-TTGAGGGTATTTCAGTA
**
46925175 ATTTTACCC-TTCGAATGTATTTC-GATA
1 ATTTTACCCATT-GAGGGTATTTCAG-TA
*
46925202 ATTTTA-CCTTTCGAGGGTATTTCAGTA
1 ATTTTACCCATT-GAGGGTATTTCAGTA
46925229 ATTTTA
1 ATTTTA
46925235 GAGGCCCATT
Statistics
Matches: 145, Mismatches: 14, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
25 2 0.01
26 4 0.03
27 133 0.92
28 6 0.04
ACGTcount: A:0.24, C:0.16, G:0.16, T:0.43
Consensus pattern (27 bp):
ATTTTACCCATTGAGGGTATTTCAGTA
Found at i:46925083 original size:54 final size:53
Alignment explanation
Indices: 46924999--46925234 Score: 219
Period size: 54 Copynumber: 4.4 Consensus size: 53
46924989 TTACCTTACA
** * * *
46924999 GGGGTATTTTGGTCATTTTA-CCTTAAGAGGGTATCTCGATCATTTTACCCTTT
1 GGGGTATTTCAGTAATTTTACCCTT-AGAGGGTATTTCGATAATTTTACCCTTT
* * *
46925052 AGGGGTAATTCAGTCATTTTACCCATT-GAGGGTATTTC-AGTAATTTTACCCATT
1 -GGGGTATTTCAGTAATTTTACCC-TTAGAGGGTATTTCGA-TAATTTTACCCTTT
* * * *
46925106 GAGGGTATTTCGGTAATTTTACCCATCGAGAGTATTTCGATAATTTTACCCATTT
1 G-GGGTATTTCAGTAATTTTACCCTTAGAGGGTATTTCGATAATTTTACCC-TTT
** * **
46925161 GGGGTATTTCTCTAATTTTACCCTTCGAATGTATTTCGATAATTTTA-CCTTT
1 GGGGTATTTCAGTAATTTTACCCTTAGAGGGTATTTCGATAATTTTACCCTTT
46925213 CGAGGGTATTTCAGTAATTTTA
1 -G-GGGTATTTCAGTAATTTTA
46925235 GAGGCCCATT
Statistics
Matches: 154, Mismatches: 19, Indels: 18
0.81 0.10 0.09
Matches are distributed among these distances:
52 3 0.02
53 6 0.04
54 137 0.89
55 6 0.04
56 2 0.01
ACGTcount: A:0.23, C:0.16, G:0.18, T:0.42
Consensus pattern (53 bp):
GGGGTATTTCAGTAATTTTACCCTTAGAGGGTATTTCGATAATTTTACCCTTT
Found at i:46925110 original size:81 final size:82
Alignment explanation
Indices: 46925025--46925234 Score: 243
Period size: 81 Copynumber: 2.6 Consensus size: 82
46925015 TTTACCTTAA
* * * * *
46925025 GAGGGTATCTCGATCATTTTACCCTTTAG-GGGTAATTCAGTCATTTTACCCA-TTGAGGGTATT
1 GAGGGTATTTCGATAATTTTACCCTTTCGAGGGTATTTCAGTAATTTTACCCATTTG-GGGTATT
*
46925088 TCAGTAATTTTACCCATT-
65 TCACTAATTTTACCC-TTC
* * *
46925106 GAGGGTATTTCGGTAATTTTACCC-ATCGAGAGTATTTC-GATAATTTTACCCATTTGGGGTATT
1 GAGGGTATTTCGATAATTTTACCCTTTCGAGGGTATTTCAG-TAATTTTACCCATTTGGGGTATT
*
46925169 TCTCTAATTTTACCCTTC
65 TCACTAATTTTACCCTTC
**
46925187 GAATGTATTTCGATAATTTTA-CCTTTCGAGGGTATTTCAGTAATTTTA
1 GAGGGTATTTCGATAATTTTACCCTTTCGAGGGTATTTCAGTAATTTTA
46925235 GAGGCCCATT
Statistics
Matches: 108, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
80 7 0.06
81 97 0.90
82 4 0.04
ACGTcount: A:0.24, C:0.17, G:0.18, T:0.42
Consensus pattern (82 bp):
GAGGGTATTTCGATAATTTTACCCTTTCGAGGGTATTTCAGTAATTTTACCCATTTGGGGTATTT
CACTAATTTTACCCTTC
Found at i:46937067 original size:25 final size:24
Alignment explanation
Indices: 46937023--46937073 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
46937013 AAAAATTGAA
*
46937023 TAAAATATTAATTAATTATAATAAT
1 TAAAATATTAATCAATTATAA-AAT
46937048 TAAAATATTAATC-ATATATAAAAT
1 TAAAATATTAATCAAT-TATAAAAT
46937072 TA
1 TA
46937074 TAAAAAGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAAATATTAATCAATTATAAAAT
Found at i:46937240 original size:3 final size:3
Alignment explanation
Indices: 46937232--46937282 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
46937222 TCATAGTCCC
46937232 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
46937280 CAT
1 CAT
46937283 TATTTATAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:46938163 original size:3 final size:3
Alignment explanation
Indices: 46938155--46938198 Score: 52
Period size: 3 Copynumber: 13.3 Consensus size: 3
46938145 AAAAGAACCC
46938155 CAT CAT CAT CAT CCAT CAT CCAT CAT CCAT CAT CCAT CAT CAT C
1 CAT CAT CAT CAT -CAT CAT -CAT CAT -CAT CAT -CAT CAT CAT C
46938199 GACGTACTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 25 0.68
4 12 0.32
ACGTcount: A:0.30, C:0.41, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:46938173 original size:7 final size:7
Alignment explanation
Indices: 46938154--46938195 Score: 77
Period size: 7 Copynumber: 6.1 Consensus size: 7
46938144 AAAAAGAACC
46938154 CCATCAT
1 CCATCAT
46938161 -CATCAT
1 CCATCAT
46938167 CCATCAT
1 CCATCAT
46938174 CCATCAT
1 CCATCAT
46938181 CCATCAT
1 CCATCAT
46938188 CCATCAT
1 CCATCAT
46938195 C
1 C
46938196 ATCGACGTAC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.18
7 28 0.82
ACGTcount: A:0.29, C:0.43, G:0.00, T:0.29
Consensus pattern (7 bp):
CCATCAT
Found at i:46941490 original size:30 final size:29
Alignment explanation
Indices: 46941424--46941492 Score: 86
Period size: 30 Copynumber: 2.3 Consensus size: 29
46941414 TCATAAATTT
* *
46941424 AGAATTTAGTCAATTTACTTTTATTTTTA
1 AGAATTTAGTCAATATACTTTTATTTTCA
46941453 AGGAATTTAGTCAATATACTTTTCATATTTCA
1 A-GAATTTAGTCAATATACTTTT-AT-TTTCA
46941485 A-AATTTAG
1 AGAATTTAG
46941493 ATCCAACTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
29 1 0.03
30 27 0.77
31 2 0.06
32 5 0.14
ACGTcount: A:0.35, C:0.09, G:0.09, T:0.48
Consensus pattern (29 bp):
AGAATTTAGTCAATATACTTTTATTTTCA
Found at i:46941741 original size:4 final size:4
Alignment explanation
Indices: 46941734--46941848 Score: 58
Period size: 4 Copynumber: 29.2 Consensus size: 4
46941724 TAAAAAAAAT
* * * * * *
46941734 AGAG AGAG AGAG AG-G GGGG AGAG GGAG AGAG GGAG GGAG GGACG -GAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGA-G AGAG
* * * * * * * *
46941781 GGAG AG-G GGGG AGAG GGAG AGAG GGAG GGAG GGACG -GAG GGAG AGAG
1 AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGAG AGA-G AGAG AGAG AGAG
46941828 AGAG AGAG AGAG AGAG AGAG A
1 AGAG AGAG AGAG AGAG AGAG A
46941849 TTTTTTAAAT
Statistics
Matches: 91, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
3 6 0.07
4 83 0.91
5 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.63, T:0.00
Consensus pattern (4 bp):
AGAG
Found at i:46941747 original size:8 final size:8
Alignment explanation
Indices: 46941734--46941848 Score: 110
Period size: 8 Copynumber: 14.4 Consensus size: 8
46941724 TAAAAAAAAT
*
46941734 AGAGAGAG
1 AGAGAGGG
46941742 AGAGAGGGG
1 AGAGA-GGG
*
46941751 GGAGAGGG
1 AGAGAGGG
46941759 AGAGAGGG
1 AGAGAGGG
*
46941767 AGGGAGGG
1 AGAGAGGG
46941775 ACG-GAGGG
1 A-GAGAGGG
46941783 AGAG-GGG
1 AGAGAGGG
*
46941790 GGAGAGGG
1 AGAGAGGG
46941798 AGAGAGGG
1 AGAGAGGG
*
46941806 AGGGAGGG
1 AGAGAGGG
46941814 ACG-GAGGG
1 A-GAGAGGG
*
46941822 AGAGAGAG
1 AGAGAGGG
*
46941830 AGAGAGAG
1 AGAGAGGG
*
46941838 AGAGAGAG
1 AGAGAGGG
46941846 AGA
1 AGA
46941849 TTTTTTAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
7 8 0.09
8 77 0.83
9 8 0.09
ACGTcount: A:0.36, C:0.02, G:0.63, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:46941797 original size:39 final size:39
Alignment explanation
Indices: 46941743--46941843 Score: 166
Period size: 39 Copynumber: 2.6 Consensus size: 39
46941733 TAGAGAGAGA
46941743 GAGAGGGGGGAGAGGGAGAGAGGGAGGGAGGGACGGAGG
1 GAGAGGGGGGAGAGGGAGAGAGGGAGGGAGGGACGGAGG
46941782 GAGAGGGGGGAGAGGGAGAGAGGGAGGGAGGGACGGAGG
1 GAGAGGGGGGAGAGGGAGAGAGGGAGGGAGGGACGGAGG
* * *
46941821 GAGAGAGAGAGAGAGAGAGAGAG
1 GAGAG-GGGGGAGAGGGAGAGAG
46941844 AGAGATTTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
39 44 0.76
40 14 0.24
ACGTcount: A:0.33, C:0.02, G:0.65, T:0.00
Consensus pattern (39 bp):
GAGAGGGGGGAGAGGGAGAGAGGGAGGGAGGGACGGAGG
Found at i:46944035 original size:5 final size:5
Alignment explanation
Indices: 46944025--46944086 Score: 63
Period size: 5 Copynumber: 12.2 Consensus size: 5
46944015 GAACAAATAT
* * * *
46944025 ATTCG ATTCG ATTCG ATTCG ATTCT ATTTG ATTCG AATTCC ATCTC- ACTCG
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG -ATTCG AT-TCG ATTCG
46944076 ATTCG ATTCG A
1 ATTCG ATTCG A
46944087 GAAAACTTCA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
4 2 0.04
5 39 0.83
6 6 0.13
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.40
Consensus pattern (5 bp):
ATTCG
Found at i:46945117 original size:13 final size:13
Alignment explanation
Indices: 46945101--46945128 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46945091 AATAAATAAA
46945101 TATTTTTTAATTT
1 TATTTTTTAATTT
46945114 TATTTTTTAATTT
1 TATTTTTTAATTT
46945127 TA
1 TA
46945129 AAATACTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (13 bp):
TATTTTTTAATTT
Done.