Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold8
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: 6381039
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 22487 characters in sequence are not A, C, G, or T
File 18 of 33
Found at i:2606828 original size:25 final size:25
Alignment explanation
Indices: 2606799--2606870 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 25
2606789 ATTATATCAT
2606799 ATTTAAATATATTTATATATTT-TAA
1 ATTT-AATATATTTATATATTTATAA
*
2606824 ATTTAATATA-ATATAT-TTATATAA
1 ATTTAATATATTTATATATT-TATAA
*
2606848 ATTTTAATATATTAATA-ATTTAT
1 A-TTTAATATATTTATATATTTAT
2606871 TGTTTTATAA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 2 0.05
23 6 0.15
24 10 0.26
25 16 0.41
26 5 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (25 bp):
ATTTAATATATTTATATATTTATAA
Found at i:2606836 original size:29 final size:32
Alignment explanation
Indices: 2606804--2606864 Score: 92
Period size: 29 Copynumber: 2.0 Consensus size: 32
2606794 ATCATATTTA
2606804 AATATATTTATAT-ATTTTAA-AT-TTAATAT
1 AATATATTTATATAATTTTAATATATTAATAT
2606833 AATATATTTATATAAATTTTAATATATTAATA
1 AATATATTTATAT-AATTTTAATATATTAATA
2606865 ATTTATTGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
29 13 0.46
31 7 0.25
32 2 0.07
33 6 0.21
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (32 bp):
AATATATTTATATAATTTTAATATATTAATAT
Found at i:2606860 original size:49 final size:48
Alignment explanation
Indices: 2606776--2606868 Score: 116
Period size: 49 Copynumber: 1.9 Consensus size: 48
2606766 TTGACGAAAT
* * *
2606776 TTTAATTATTATAATTATATCATATTTAAATATATTTATATATTTTAAA
1 TTTAATTAATATAATTATATCAAATTTAAATATATTAATA-ATTTTAAA
* *
2606825 TTTAATATAATATATTTATAT-AAATTTTAATATATTAATAATTT
1 TTTAAT-TAATATAATTATATCAAATTTAAATATATTAATAATTT
2606869 ATTGTTTTAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
48 4 0.11
49 22 0.58
50 12 0.32
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (48 bp):
TTTAATTAATATAATTATATCAAATTTAAATATATTAATAATTTTAAA
Found at i:2606899 original size:41 final size:46
Alignment explanation
Indices: 2606830--2606912 Score: 113
Period size: 41 Copynumber: 1.9 Consensus size: 46
2606820 TTAAATTTAA
2606830 TATAATATATTTATATAAATTTTAATATATTAATAATTTATTGTTT
1 TATAATATATTTATATAAATTTTAATATATTAATAATTTATTGTTT
* *
2606876 TATAA-AT-TTTA-ATAAA-TTT-ATATATTTATATTTTATT
1 TATAATATATTTATATAAATTTTAATATATTAATAATTTATT
2606913 TATATTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 16 0.46
42 3 0.09
43 5 0.14
44 4 0.11
45 2 0.06
46 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (46 bp):
TATAATATATTTATATAAATTTTAATATATTAATAATTTATTGTTT
Found at i:2606910 original size:33 final size:33
Alignment explanation
Indices: 2606821--2606911 Score: 105
Period size: 33 Copynumber: 2.7 Consensus size: 33
2606811 TTATATATTT
*
2606821 TAAATTTA-ATATAATATATTTATATAAATTTTAA
1 TAAATTTATATAT-TTATATTT-TATAAATTTTAA
* * *
2606855 TATATTAATA-ATTTATTGTTTTATAAATTTTAA
1 TAAATTTATATATTTA-TATTTTATAAATTTTAA
2606888 TAAATTTATATATTTATATTTTAT
1 TAAATTTATATATTTATATTTTAT
2606912 TTATATTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
33 29 0.62
34 17 0.36
35 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (33 bp):
TAAATTTATATATTTATATTTTATAAATTTTAA
Found at i:2606914 original size:11 final size:11
Alignment explanation
Indices: 2606898--2606963 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 11
2606888 TAAATTTATA
2606898 TATTTATATTT
1 TATTTATATTT
2606909 TATTTATATTT
1 TATTTATATTT
*
2606920 T-TTTATTATAT
1 TATTTA-TATTT
* *
2606931 TATATAAATTAT
1 TATTTATATT-T
*
2606943 TA-TTATATTA
1 TATTTATATTT
*
2606953 TATTTAAATTT
1 TATTTATATTT
2606964 GTTTGACGTG
Statistics
Matches: 42, Mismatches: 9, Indels: 8
0.71 0.15 0.14
Matches are distributed among these distances:
10 6 0.14
11 30 0.71
12 6 0.14
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (11 bp):
TATTTATATTT
Found at i:2606915 original size:19 final size:19
Alignment explanation
Indices: 2606785--2606955 Score: 69
Period size: 19 Copynumber: 9.2 Consensus size: 19
2606775 TTTTAATTAT
* *
2606785 TATAATTATATCATATTTAAA
1 TATATTTATATTATATTT--A
2606806 TATATTTATA-TAT-TTTA
1 TATATTTATATTATATTTA
2606823 -A-ATTTAATATAATATATTTA
1 TATATTT-ATAT--TATATTTA
*
2606843 TATAAATTT-TAATATA-TTA
1 TAT--ATTTATATTATATTTA
* *
2606862 -ATAATT-TATTGT-TTTA
1 TATATTTATATTATATTTA
* * *
2606878 TAAATTT-TAATAAATTTA
1 TATATTTATATTATATTTA
*
2606896 TATATTTATATTTTATTTA
1 TATATTTATATTATATTTA
* *
2606915 TATTTTTTTATTATA-TTA
1 TATATTTATATTATATTTA
*
2606933 TATAAATTATTATTATA-TTA
1 TAT-ATTTA-TATTATATTTA
2606953 TAT
1 TAT
2606956 TTAAATTTGT
Statistics
Matches: 114, Mismatches: 21, Indels: 31
0.69 0.13 0.19
Matches are distributed among these distances:
15 4 0.04
16 14 0.12
17 8 0.07
18 18 0.16
19 31 0.27
20 23 0.20
21 10 0.09
22 2 0.02
24 4 0.04
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
TATATTTATATTATATTTA
Found at i:2606924 original size:47 final size:44
Alignment explanation
Indices: 2606840--2606963 Score: 119
Period size: 47 Copynumber: 2.8 Consensus size: 44
2606830 TATAATATAT
* * *
2606840 TTATATAAATT-TTAATATATTAATAATT-TATTGTTTTATAA-A
1 TTATATAAATTATTATTATATT-ATATTTATATTTTTTTATAATA
* * *
2606882 TTTTAATAAATTTATATATTTATATTTTATTTATATTTTTTTATTATA
1 TTAT-ATAAA-TTAT-TA-TTATATTATATTTATATTTTTTTATAATA
*
2606930 TTATATAAATTATTATTATATTATATTTAAATTT
1 TTATATAAATTATTATTATATTATATTTATATTT
2606964 GTTTGACGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
42 3 0.05
43 5 0.08
44 19 0.29
45 3 0.05
46 10 0.15
47 22 0.33
48 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (44 bp):
TTATATAAATTATTATTATATTATATTTATATTTTTTTATAATA
Found at i:2615503 original size:2 final size:2
Alignment explanation
Indices: 2615496--2615521 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2615486 GAGAAGCTCT
2615496 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
2615522 AAAGAAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2616082 original size:9 final size:9
Alignment explanation
Indices: 2616065--2616132 Score: 50
Period size: 9 Copynumber: 7.6 Consensus size: 9
2616055 ATAATTAATA
*
2616065 ATTAAATTT
1 ATTATATTT
2616074 ATTATATTT
1 ATTATATTT
*
2616083 AATATATTT
1 ATTATATTT
*
2616092 -TTATTTTTT
1 ATTA-TATTT
2616101 ATTATATTT
1 ATTATATTT
* *
2616110 AATAGTTTTT
1 ATTA-TATTT
*
2616120 ATTGTATTT
1 ATTATATTT
2616129 -TTAT
1 ATTAT
2616133 TTTTTCGTAA
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
8 5 0.11
9 31 0.69
10 9 0.20
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
ATTATATTT
Found at i:2616101 original size:18 final size:18
Alignment explanation
Indices: 2616080--2616137 Score: 71
Period size: 18 Copynumber: 3.2 Consensus size: 18
2616070 ATTTATTATA
*
2616080 TTTAATATATTTTTATTT
1 TTTATTATATTTTTATTT
* *
2616098 TTTATTATATTTAATAGTT
1 TTTATTATATTT-TTATTT
*
2616117 TTTATTGTATTTTTATTT
1 TTTATTATATTTTTATTT
2616135 TTT
1 TTT
2616138 CGTAAAATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 18 0.55
19 15 0.45
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (18 bp):
TTTATTATATTTTTATTT
Found at i:2616132 original size:27 final size:28
Alignment explanation
Indices: 2616070--2616132 Score: 87
Period size: 27 Copynumber: 2.3 Consensus size: 28
2616060 TAATAATTAA
2616070 ATTTATTATATTTAATATATTTTTATTT
1 ATTTATTATATTTAATATATTTTTATTT
*
2616098 -TTTATTATATTTAATA-GTTTTTATTGT
1 ATTTATTATATTTAATATATTTTTATT-T
2616125 ATTT-TTAT
1 ATTTATTAT
2616133 TTTTTCGTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
26 8 0.25
27 21 0.66
28 3 0.09
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (28 bp):
ATTTATTATATTTAATATATTTTTATTT
Found at i:2616137 original size:19 final size:19
Alignment explanation
Indices: 2616080--2616137 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
2616070 ATTTATTATA
*
2616080 TTTAATATATTTTTA-TTT
1 TTTATTATATTTTTATTTT
* *
2616098 TTTATTATA-TTTAATAGTT
1 TTTATTATATTTTTAT-TTT
*
2616117 TTTATTGTATTTTTATTTT
1 TTTATTATATTTTTATTTT
2616136 TT
1 TT
2616138 CGTAAAATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
17 4 0.13
18 8 0.26
19 14 0.45
20 5 0.16
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.72
Consensus pattern (19 bp):
TTTATTATATTTTTATTTT
Found at i:2623010 original size:4 final size:4
Alignment explanation
Indices: 2623001--2623060 Score: 66
Period size: 4 Copynumber: 15.0 Consensus size: 4
2622991 AAGTATGTTA
* * * * * *
2623001 TCTC TCTC TCCC TCCC TCCC TCCC TCCC TCCC TCTC TCTC TCTC TCTC
1 TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC TCTC
2623049 TCTC TCTC TCTC
1 TCTC TCTC TCTC
2623061 ATACAAACAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 54 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (4 bp):
TCTC
Found at i:2628536 original size:123 final size:123
Alignment explanation
Indices: 2628317--2628541 Score: 450
Period size: 123 Copynumber: 1.8 Consensus size: 123
2628307 TTAAGGTTGG
2628317 TCTGCTTGATGAAGAGAAAACTCTTCCCTTGGGAACGGAAATCAGTGCTGTTGGCATTTGCGGTT
1 TCTGCTTGATGAAGAGAAAACTCTTCCCTTGGGAACGGAAATCAGTGCTGTTGGCATTTGCGGTT
2628382 TAAATAATGGAGTGCCTGAAATTAGGGCATGCAAGGAAATCAGTGCCTGAAACTTTTC
66 TAAATAATGGAGTGCCTGAAATTAGGGCATGCAAGGAAATCAGTGCCTGAAACTTTTC
2628440 TCTGCTTGATGAAGAGAAAACTCTTCCCTTGGGAACGGAAATCAGTGCTGTTGGCATTTGCGGTT
1 TCTGCTTGATGAAGAGAAAACTCTTCCCTTGGGAACGGAAATCAGTGCTGTTGGCATTTGCGGTT
2628505 TAAATAATGGAGTGCCTGAAATTAGGGCATGCAAGGA
66 TAAATAATGGAGTGCCTGAAATTAGGGCATGCAAGGA
2628542 GCTTCCTTTT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
123 102 1.00
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.28
Consensus pattern (123 bp):
TCTGCTTGATGAAGAGAAAACTCTTCCCTTGGGAACGGAAATCAGTGCTGTTGGCATTTGCGGTT
TAAATAATGGAGTGCCTGAAATTAGGGCATGCAAGGAAATCAGTGCCTGAAACTTTTC
Found at i:2632042 original size:9 final size:9
Alignment explanation
Indices: 2632028--2632053 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
2632018 ATTATTCGCA
2632028 GCAGCAGCG
1 GCAGCAGCG
2632037 GCAGCAGCG
1 GCAGCAGCG
2632046 GCAGCAGC
1 GCAGCAGC
2632054 AGCAATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.23, C:0.35, G:0.42, T:0.00
Consensus pattern (9 bp):
GCAGCAGCG
Found at i:2633604 original size:2 final size:2
Alignment explanation
Indices: 2633597--2633622 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2633587 TAATTACAAC
2633597 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
2633623 ACGATTGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2637720 original size:18 final size:18
Alignment explanation
Indices: 2637697--2637732 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2637687 ACTTTTCAAC
2637697 GTGAGATCCAAATCTCAT
1 GTGAGATCCAAATCTCAT
2637715 GTGAGATCCAAATCTCAT
1 GTGAGATCCAAATCTCAT
2637733 ACCTTGCGCC
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:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (18 bp):
GTGAGATCCAAATCTCAT
Found at i:2639267 original size:20 final size:20
Alignment explanation
Indices: 2639242--2639334 Score: 67
Period size: 20 Copynumber: 4.8 Consensus size: 20
2639232 TTAAATTTTT
2639242 TATTATAATTATATTTTAAA
1 TATTATAATTATATTTTAAA
*
2639262 TATTATATATT-TA-TATAAA
1 TATTATA-ATTATATTTTAAA
2639281 T-TT-TAA-TATATTAATTAAA
1 TATTATAATTATATT--TTAAA
2639300 -ATTAT-ATTATATTTGT-AA
1 TATTATAATTATATTT-TAAA
*
2639318 TATTTTTAATTATATTT
1 TA-TTATAATTATATTT
2639335 ACTTTTTATC
Statistics
Matches: 58, Mismatches: 3, Indels: 23
0.69 0.04 0.27
Matches are distributed among these distances:
15 1 0.02
16 3 0.05
17 3 0.05
18 5 0.09
19 15 0.26
20 19 0.33
21 12 0.21
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (20 bp):
TATTATAATTATATTTTAAA
Found at i:2639299 original size:19 final size:18
Alignment explanation
Indices: 2639257--2639306 Score: 57
Period size: 19 Copynumber: 2.7 Consensus size: 18
2639247 TAATTATATT
*
2639257 TTAAATATTATATATTTA
1 TTAAATATTATATATTAA
*
2639275 TATAAATTTTAATATATTAA
1 T-TAAATATT-ATATATTAA
2639295 TTAAA-ATTATAT
1 TTAAATATTATAT
2639307 TATATTTGTA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
17 4 0.15
18 3 0.11
19 11 0.41
20 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (18 bp):
TTAAATATTATATATTAA
Found at i:2639993 original size:2 final size:2
Alignment explanation
Indices: 2639986--2640017 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2639976 GATGAATGCT
2639986 TA TA 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
2640018 ATTAATAGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2642912 original size:15 final size:15
Alignment explanation
Indices: 2642884--2642927 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
2642874 TTGTTGAGAA
* *
2642884 TGTTGCTGTAGCTGC
1 TGTTGATGTTGCTGC
*
2642899 TGTTGTTGTTGCTGC
1 TGTTGATGTTGCTGC
*
2642914 TGCTGATGTTGCTG
1 TGTTGATGTTGCTG
2642928 TGGCTGCTGC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.05, C:0.16, G:0.34, T:0.45
Consensus pattern (15 bp):
TGTTGATGTTGCTGC
Found at i:2642918 original size:21 final size:21
Alignment explanation
Indices: 2642884--2642937 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2642874 TTGTTGAGAA
* *
2642884 TGTTGCTG-TAGCTGCTGTTGT
1 TGTTGCTGCT-GCTGATGTTGC
2642905 TGTTGCTGCTGCTGATGTTGC
1 TGTTGCTGCTGCTGATGTTGC
*
2642926 TGTGGCTGCTGC
1 TGTTGCTGCTGC
2642938 ATTTGAGGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.04, C:0.19, G:0.35, T:0.43
Consensus pattern (21 bp):
TGTTGCTGCTGCTGATGTTGC
Found at i:2644189 original size:3 final size:3
Alignment explanation
Indices: 2644181--2644234 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
2644171 ATAAGAATAC
2644181 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
2644229 ATT ATT
1 ATT ATT
2644235 CAAGCTGAGC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2645797 original size:3 final size:3
Alignment explanation
Indices: 2645789--2645813 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2645779 AACTAAACTG
2645789 AGC AGC AGC AGC AGC AGC AGC AGC A
1 AGC AGC AGC AGC AGC AGC AGC AGC A
2645814 CCACTGAGCA
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:0.36, C:0.32, G:0.32, T:0.00
Consensus pattern (3 bp):
AGC
Found at i:2646117 original size:3 final size:3
Alignment explanation
Indices: 2646111--2646145 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2646101 CTGCTGCTGC
2646111 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT TG
2646146 GGGAATAGCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.00, G:0.34, T:0.66
Consensus pattern (3 bp):
TGT
Found at i:2649745 original size:2 final size:2
Alignment explanation
Indices: 2649733--2649769 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
2649723 TTGAATCTAA
*
2649733 TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
2649770 TTTATCGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 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):
TC
Found at i:2652539 original size:39 final size:44
Alignment explanation
Indices: 2652496--2652585 Score: 102
Period size: 39 Copynumber: 2.2 Consensus size: 44
2652486 AAAAATACTG
*
2652496 TTAAA-ACAACATAAATA-AT-TAAATATA-TAT-ATCAAAATT-
1 TTAAATACAA-ATAAATATATAAAAATATATTATAATCAAAATTA
* *
2652535 TTAAATATAAATAAATATATAAAAATATATTATAATCATAATTA
1 TTAAATACAAATAAATATATAAAAATATATTATAATCAAAATTA
2652579 TTAAATA
1 TTAAATA
2652586 ATTATATATT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
39 12 0.29
40 5 0.12
41 7 0.17
42 3 0.07
43 8 0.19
44 7 0.17
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (44 bp):
TTAAATACAAATAAATATATAAAAATATATTATAATCAAAATTA
Found at i:2652604 original size:13 final size:13
Alignment explanation
Indices: 2652585--2652628 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
2652575 ATTATTAAAT
2652585 AATTATATATTTA
1 AATTATATATTTA
* *
2652598 TATTATATTTTTA
1 AATTATATATTTA
*
2652611 AATTATAT-TTAA
1 AATTATATATTTA
2652623 AATTAT
1 AATTAT
2652629 TAAATTTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
12 9 0.33
13 18 0.67
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
AATTATATATTTA
Found at i:2659416 original size:10 final size:9
Alignment explanation
Indices: 2659399--2659426 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2659389 ATTACCTATC
2659399 TCTTTTTTT
1 TCTTTTTTT
2659408 TCTTTTTTT
1 TCTTTTTTT
2659417 TCTTTTTTT
1 TCTTTTTTT
2659426 T
1 T
2659427 GAAAAAGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:2663506 original size:3 final size:3
Alignment explanation
Indices: 2663492--2663531 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
2663482 TTCTACTTGA
* *
2663492 TCT TCT TTT TCT TCT TCT TCT TCT TCT TCC TCTT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT
2663532 CCAGAGATCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 30 0.94
4 2 0.06
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:2665421 original size:37 final size:37
Alignment explanation
Indices: 2665371--2665447 Score: 154
Period size: 37 Copynumber: 2.1 Consensus size: 37
2665361 GATACTAAGA
2665371 TTCAACTGCTTGATCTTCCTGGAATTATTGAAGGTGC
1 TTCAACTGCTTGATCTTCCTGGAATTATTGAAGGTGC
2665408 TTCAACTGCTTGATCTTCCTGGAATTATTGAAGGTGC
1 TTCAACTGCTTGATCTTCCTGGAATTATTGAAGGTGC
2665445 TTC
1 TTC
2665448 TGAAGGCAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 40 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (37 bp):
TTCAACTGCTTGATCTTCCTGGAATTATTGAAGGTGC
Found at i:2668761 original size:2 final size:2
Alignment explanation
Indices: 2668754--2668784 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2668744 AAACACATAA
2668754 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2668785 AGAAGTAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2669038 original size:19 final size:19
Alignment explanation
Indices: 2669014--2669053 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2669004 AGTAGGTTCT
*
2669014 TTAAGCTTCAAATTAACTA
1 TTAAGCTTCAAATTAAATA
*
2669033 TTAAGCTTCGAATTAAATA
1 TTAAGCTTCAAATTAAATA
2669052 TT
1 TT
2669054 TAGATGAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
TTAAGCTTCAAATTAAATA
Found at i:2669903 original size:6 final size:6
Alignment explanation
Indices: 2669892--2669919 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
2669882 TTAGCACGAT
2669892 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTT
2669920 GTCGTTTATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTA
Found at i:2671347 original size:20 final size:19
Alignment explanation
Indices: 2671270--2671358 Score: 71
Period size: 16 Copynumber: 4.8 Consensus size: 19
2671260 TTCTTGATAA
2671270 ATATCATATATATAAAT-AT
1 ATAT-ATATATATAAATGAT
2671289 ATAT-TA-ATATAAAT-AT
1 ATATATATATATAAATGAT
* * *
2671305 ATATATAT-TTTAAAAGTT
1 ATATATATATATAAATGAT
* *
2671323 TTATATATATTTAAATGAT
1 ATATATATATATAAATGAT
*
2671342 AATATATAAATATAAAT
1 -ATATATATATATAAAT
2671359 ATTAAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
16 14 0.25
17 9 0.16
18 8 0.14
19 12 0.21
20 13 0.23
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.45
Consensus pattern (19 bp):
ATATATATATATAAATGAT
Found at i:2671351 original size:14 final size:13
Alignment explanation
Indices: 2671324--2671370 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
2671314 TTAAAAGTTT
*
2671324 TATATATATTTAAA
1 TATA-ATATATAAA
2671338 TGATAATATATAAA
1 T-ATAATATATAAA
2671352 TATAA-ATATTAAA
1 TATAATATA-TAAA
2671365 TATAAT
1 TATAAT
2671371 TTTTTTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
12 3 0.10
13 13 0.45
14 10 0.34
15 3 0.10
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (13 bp):
TATAATATATAAA
Found at i:2673068 original size:31 final size:29
Alignment explanation
Indices: 2673029--2673095 Score: 75
Period size: 28 Copynumber: 2.3 Consensus size: 29
2673019 TAAAAATTAA
2673029 ATTA-TATAAAACTTTATATATTAATATTTTT
1 ATTATTAT-AAACTTTA-ATA-TAATATTTTT
* *
2673060 ATT-TTATAAATTTTAATATAATTTTTTT
1 ATTATTATAAACTTTAATATAATATTTTT
2673088 ATTATTAT
1 ATTATTAT
2673096 TTTAATTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 12 0.38
29 7 0.22
30 7 0.22
31 6 0.19
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (29 bp):
ATTATTATAAACTTTAATATAATATTTTT
Found at i:2673101 original size:20 final size:20
Alignment explanation
Indices: 2673078--2673115 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
2673068 AATTTTAATA
2673078 TAATT-TTTTTATTATTATTT
1 TAATTATTTTTA-TATTATTT
2673098 TAATTATTTTTATATTAT
1 TAATTATTTTTATATTAT
2673116 ATATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (20 bp):
TAATTATTTTTATATTATTT
Found at i:2673122 original size:26 final size:25
Alignment explanation
Indices: 2673043--2673123 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 25
2673033 TATAAAACTT
*
2673043 TATATATTAA-TATTTTTATTT-TA
1 TATATTTTAATTATTTTTATTTATA
* *
2673066 TAAATTTTAATATAATTTT-TTTAT-
1 TATATTTTAAT-TATTTTTATTTATA
2673090 TATTATTTTAATTATTTTTATATTATA
1 TA-TATTTTAATTATTTTTAT-TTATA
2673117 TATATTT
1 TATATTT
2673124 ATACTTTACG
Statistics
Matches: 46, Mismatches: 5, Indels: 11
0.74 0.08 0.18
Matches are distributed among these distances:
23 8 0.17
24 11 0.24
25 16 0.35
26 9 0.20
27 2 0.04
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (25 bp):
TATATTTTAATTATTTTTATTTATA
Found at i:2674255 original size:2 final size:2
Alignment explanation
Indices: 2674248--2674277 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
2674238 TAAAAAGAAC
2674248 AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2674278 AGAATGGCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2674281 original size:10 final size:11
Alignment explanation
Indices: 2674248--2674281 Score: 52
Period size: 12 Copynumber: 3.1 Consensus size: 11
2674238 TAAAAAGAAC
2674248 AGAGAGAGAGA
1 AGAGAGAGAGA
2674259 GAGAGAGAGAGA
1 -AGAGAGAGAGA
2674271 AGAGAGA-AGA
1 AGAGAGAGAGA
2674281 A
1 A
2674282 TGGCATAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 4 0.18
11 7 0.32
12 11 0.50
ACGTcount: A:0.56, C:0.00, G:0.44, T:0.00
Consensus pattern (11 bp):
AGAGAGAGAGA
Found at i:2674893 original size:61 final size:62
Alignment explanation
Indices: 2674775--2674895 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 62
2674765 AACCAGTAAC
* * * * **
2674775 AAAATCATATATAATTTATTAATAGAGTTTGTTTTTAGATATTGACATTAATTTTTTTTAAT
1 AAAATCATAGATAATTTAATAATAGAGTTTGTTTTTAGATACTGACATCAAAATTTTTTAAT
*
2674837 AAAATCTTAGATAA-TTAATAATAGAGTTTGTTTTTAGATACTGACATCAAAATTTTTTA
1 AAAATCATAGATAATTTAATAATAGAGTTTGTTTTTAGATACTGACATCAAAATTTTTTA
2674896 CTTTTATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
61 40 0.77
62 12 0.23
ACGTcount: A:0.39, C:0.05, G:0.09, T:0.47
Consensus pattern (62 bp):
AAAATCATAGATAATTTAATAATAGAGTTTGTTTTTAGATACTGACATCAAAATTTTTTAAT
Found at i:2674912 original size:20 final size:19
Alignment explanation
Indices: 2674890--2674927 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
2674880 ACATCAAAAT
*
2674890 TTTTTACTTTTATAAATAA
1 TTTTTAATTTTATAAATAA
*
2674909 TTTTTAATTTTATTAATAA
1 TTTTTAATTTTATAAATAA
2674928 AATTAAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.61
Consensus pattern (19 bp):
TTTTTAATTTTATAAATAA
Found at i:2675235 original size:13 final size:14
Alignment explanation
Indices: 2675209--2675240 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
2675199 TAATTTAAAT
2675209 TTTATTTATTGATA
1 TTTATTTATTGATA
2675223 TTTATTT-TTGATA
1 TTTATTTATTGATA
2675236 TTTAT
1 TTTAT
2675241 CATAATTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (14 bp):
TTTATTTATTGATA
Found at i:2681696 original size:5 final size:5
Alignment explanation
Indices: 2681680--2681850 Score: 52
Period size: 5 Copynumber: 36.0 Consensus size: 5
2681670 ATGTGTAAAA
* *
2681680 ATAAT ATAAAT ATAAT ATTAAA AAAAT A-ATAT ATAAT ATAAAAT ATAAT
1 ATAAT AT-AAT ATAAT A-TAAT ATAAT ATA-AT ATAAT AT--AAT ATAAT
* * * * *
2681729 A-AA- ATAA- AAAAT ATTAT ATAA- AT-AT ATTAAT ATATT AAAAT -TTAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A-TAAT ATAAT ATAAT ATAAT
* * * *
2681774 ATAAT ATAA- ATTAT -TAAT ATATT A-AAT TTTAT ATAA- AT-AT ATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2681819 ACGTAA- A-AAT AT-A- ATAAT ATAAT ATAA- ATAAT
1 A--TAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT
2681851 CCGTATTCTT
Statistics
Matches: 121, Mismatches: 21, Indels: 48
0.64 0.11 0.25
Matches are distributed among these distances:
3 7 0.06
4 32 0.26
5 60 0.50
6 14 0.12
7 8 0.07
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:2681712 original size:19 final size:20
Alignment explanation
Indices: 2681688--2681735 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
2681678 AAATAATATA
*
2681688 AATATAATATTA-AAAAAAT
1 AATATAATAATATAAAAAAT
*
2681707 AATAT-ATAATATAAAATAT
1 AATATAATAATATAAAAAAT
*
2681726 AATAAAATAA
1 AATATAATAA
2681736 AAAATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (20 bp):
AATATAATAATATAAAAAAT
Found at i:2681715 original size:21 final size:22
Alignment explanation
Indices: 2681675--2681734 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
2681665 TTTACATGTG
2681675 TAAAAATAATATAAATATAATA
1 TAAAAATAATATAAATATAATA
*
2681697 TTAAAAA-AATA-ATATATAATA
1 -TAAAAATAATATAAATATAATA
2681718 TAAAATATAATA-AAATA
1 TAAAA-ATAATATAAATA
2681735 AAAAATATTA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 5 0.15
21 10 0.30
22 12 0.36
23 6 0.18
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (22 bp):
TAAAAATAATATAAATATAATA
Found at i:2681748 original size:36 final size:35
Alignment explanation
Indices: 2681680--2681769 Score: 98
Period size: 34 Copynumber: 2.6 Consensus size: 35
2681670 ATGTGTAAAA
*
2681680 ATAATAT-AAATATAAT--ATTAAAAAAATAATAT
1 ATAATATAAAATATAATAAAATAAAAAAATAATAT
*
2681712 ATAATATAAAATATAATAAAAT-AAAAAATATTAT
1 ATAATATAAAATATAATAAAATAAAAAAATAATAT
* *
2681746 ATAAATATATTAATATATTAAAAT
1 AT-AATATA-AAATATAATAAAAT
2681770 TTATATAATA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
32 7 0.14
33 9 0.18
34 13 0.27
35 8 0.16
36 12 0.24
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (35 bp):
ATAATATAAAATATAATAAAATAAAAAAATAATAT
Found at i:2681799 original size:16 final size:16
Alignment explanation
Indices: 2681743--2681801 Score: 61
Period size: 16 Copynumber: 3.7 Consensus size: 16
2681733 TAAAAAATAT
2681743 TATA-TAAATATATTAA
1 TATATTAAAT-TATTAA
*
2681759 TATATTAAA--ATTTA
1 TATATTAAATTATTAA
2681773 TATAATATAAATTATTAA
1 TAT-AT-TAAATTATTAA
2681791 TATATTAAATT
1 TATATTAAATT
2681802 TTATATAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 7 0.19
15 2 0.06
16 14 0.39
17 6 0.17
18 7 0.19
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TATATTAAATTATTAA
Found at i:2681812 original size:20 final size:18
Alignment explanation
Indices: 2681743--2681815 Score: 61
Period size: 18 Copynumber: 4.3 Consensus size: 18
2681733 TAAAAAATAT
*
2681743 TATA-TAAATATAT-TAA
1 TATATTAAATTTATATAA
2681759 TATATTAAAATTTATAT-A
1 TATATT-AAATTTATATAA
2681777 -ATA-TAAA-TTAT-TAA
1 TATATTAAATTTATATAA
2681791 TATATTAAATTTTATATAAA
1 TATATTAAA-TTTATAT-AA
2681811 TATAT
1 TATAT
2681816 AATACGTAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 16
0.73 0.02 0.25
Matches are distributed among these distances:
13 1 0.02
14 5 0.11
15 6 0.13
16 9 0.20
17 4 0.09
18 12 0.26
19 2 0.04
20 7 0.15
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (18 bp):
TATATTAAATTTATATAA
Found at i:2683070 original size:12 final size:12
Alignment explanation
Indices: 2683035--2683076 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
2683025 CATAGATGGC
*
2683035 ATCTATCCATCC
1 ATCTATCCATCT
*
2683047 ATCCATCCATCT
1 ATCTATCCATCT
*
2683059 ATCTATCTATCT
1 ATCTATCCATCT
2683071 ATCTAT
1 ATCTAT
2683077 ATGTAATTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.26, C:0.33, G:0.00, T:0.40
Consensus pattern (12 bp):
ATCTATCCATCT
Found at i:2683642 original size:24 final size:25
Alignment explanation
Indices: 2683606--2683663 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 25
2683596 TGTTTTATCT
* * * *
2683606 AACAATATTAAATATAATT-ATTCA
1 AACATTATAAAATAAAATTAATTAA
*
2683630 AATATTATAAAATAAAATTAATTAA
1 AACATTATAAAATAAAATTAATTAA
2683655 AACATTATA
1 AACATTATA
2683664 TAATCTGAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (25 bp):
AACATTATAAAATAAAATTAATTAA
Found at i:2683715 original size:18 final size:18
Alignment explanation
Indices: 2683692--2683736 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
2683682 TTAAATTTAT
2683692 ATAATATAAA-TTATAAAA
1 ATAATA-AAATTTATAAAA
*
2683710 ATAATAAAATTTATATAA
1 ATAATAAAATTTATAAAA
2683728 AT-ATAAAAT
1 ATAATAAAAT
2683737 ATTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
ATAATAAAATTTATAAAA
Found at i:2686300 original size:33 final size:31
Alignment explanation
Indices: 2686258--2686318 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 31
2686248 AAATAAAAAA
2686258 TAATATAAATATATAAATATATTATAATTTATG
1 TAATATAAAT-TATAAATATATTA-AATTTATG
* *
2686291 TAATATAAATTATTAATTTATTAAATTT
1 TAATATAAATTATAAATATATTAAATTT
2686319 TAAATTATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 5 0.19
32 11 0.42
33 10 0.38
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (31 bp):
TAATATAAATTATAAATATATTAAATTTATG
Found at i:2686341 original size:23 final size:24
Alignment explanation
Indices: 2686294--2686346 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
2686284 ATTTATGTAA
*
2686294 TATAAATTATTAATTTATTAAATT
1 TATAAATTATGAATTTATTAAATT
* * *
2686318 T-TAAATTATGATTTTTTTATATT
1 TATAAATTATGAATTTATTAAATT
2686341 TATAAA
1 TATAAA
2686347 AAAATGGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (24 bp):
TATAAATTATGAATTTATTAAATT
Found at i:2686524 original size:12 final size:12
Alignment explanation
Indices: 2686503--2686533 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
2686493 GGCATGCATA
*
2686503 TATTTAACCTTT
1 TATTTTACCTTT
2686515 TATTTTACCTTT
1 TATTTTACCTTT
2686527 TATTTTA
1 TATTTTA
2686534 TGATTATATA
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:0.23, C:0.13, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTTACCTTT
Found at i:2686698 original size:2 final size:2
Alignment explanation
Indices: 2686691--2686727 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2686681 ATGGAATGTG
2686691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2686728 TATGTGCTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2693878 original size:3 final size:3
Alignment explanation
Indices: 2693864--2693896 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
2693854 ATTTTAAAAG
*
2693864 ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2693897 CCAAAACTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:2698243 original size:11 final size:11
Alignment explanation
Indices: 2698229--2698264 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2698219 TAAAATTTAA
2698229 TAAAAATATAT
1 TAAAAATATAT
2698240 TAAAAATATAT
1 TAAAAATATAT
*
2698251 AAATAAATATAT
1 TAA-AAATATAT
2698263 TA
1 TA
2698265 TGATTAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.59
12 9 0.41
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAAAAATATAT
Found at i:2698575 original size:24 final size:24
Alignment explanation
Indices: 2698548--2698593 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
2698538 AAATTTGATC
*
2698548 AAATTTT-AATTAAATTTTAAATAA
1 AAATTTTAAATT-AATTTAAAATAA
2698572 AAATTTTAAATTAATTTAAAAT
1 AAATTTTAAATTAATTTAAAAT
2698594 TTTAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AAATTTTAAATTAATTTAAAATAA
Found at i:2698585 original size:18 final size:18
Alignment explanation
Indices: 2698564--2698621 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
2698554 TAATTAAATT
2698564 TTAAATAAAAATTTTAAA
1 TTAAATAAAAATTTTAAA
* *
2698582 TTAATTTAAAATTTT-AA
1 TTAAATAAAAATTTTAAA
*
2698599 --AAATAAAAATCATTAAA
1 TTAAATAAAAAT-TTTAAA
2698616 TTAAAT
1 TTAAAT
2698622 TTTAAATCAC
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
15 8 0.26
16 2 0.06
17 4 0.13
18 13 0.42
19 4 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
TTAAATAAAAATTTTAAA
Found at i:2698590 original size:34 final size:33
Alignment explanation
Indices: 2698559--2698628 Score: 90
Period size: 33 Copynumber: 2.1 Consensus size: 33
2698549 AATTTTAATT
*
2698559 AAATTTT-AAATAAAAAT-TTTAAATTAATTTA
1 AAATTTTAAAATAAAAATCATTAAATTAATTTA
*
2698590 AAATTTTAAAAATAAAAATCATTAAATTAAATTTT
1 AAATTTT-AAAATAAAAATCATTAAATT-AATTTA
2698625 AAAT
1 AAAT
2698629 CACAAAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 7 0.21
33 10 0.30
34 7 0.21
35 9 0.27
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.41
Consensus pattern (33 bp):
AAATTTTAAAATAAAAATCATTAAATTAATTTA
Found at i:2698598 original size:13 final size:13
Alignment explanation
Indices: 2698548--2698585 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
2698538 AAATTTGATC
2698548 AAATTTT-AATT-
1 AAATTTTAAATTA
*
2698559 AAATTTTAAATAA
1 AAATTTTAAATTA
2698572 AAATTTTAAATTA
1 AAATTTTAAATTA
2698585 A
1 A
2698586 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 7 0.30
12 3 0.13
13 13 0.57
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
AAATTTTAAATTA
Found at i:2698635 original size:29 final size:29
Alignment explanation
Indices: 2698581--2698637 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2698571 AAAATTTTAA
* *
2698581 ATTAATTTAAAATTTTAAAAATAAAAATC
1 ATTAAATTAAAATTTTAAAAACAAAAATC
*
2698610 ATTAAATT-AAATTTTAAATCACAAAAAT
1 ATTAAATTAAAATTTTAAA-AACAAAAAT
2698638 TTCTGACGCT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 10 0.42
29 14 0.58
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (29 bp):
ATTAAATTAAAATTTTAAAAACAAAAATC
Found at i:2707679 original size:1 final size:1
Alignment explanation
Indices: 2707673--2707700 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
2707663 CCCAAAGAAG
2707673 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
2707701 CAAAGCCTAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2710912 original size:21 final size:21
Alignment explanation
Indices: 2710888--2710931 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
2710878 CCTCTTGACA
2710888 TTTTCAAAGATCCTTTTGGGC
1 TTTTCAAAGATCCTTTTGGGC
2710909 TTTTCAAAGATCCTTTTGGGC
1 TTTTCAAAGATCCTTTTGGGC
2710930 TT
1 TT
2710932 CCTCATAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.45
Consensus pattern (21 bp):
TTTTCAAAGATCCTTTTGGGC
Found at i:2713668 original size:2 final size:2
Alignment explanation
Indices: 2713661--2713690 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2713651 GTTTTAATAC
2713661 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2713691 TATCTAGTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2713922 original size:12 final size:12
Alignment explanation
Indices: 2713905--2713930 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
2713895 AGAGGAGTAT
2713905 GTATTAATATAA
1 GTATTAATATAA
2713917 GTATTAATATAA
1 GTATTAATATAA
2713929 GT
1 GT
2713931 GTATTTAAAT
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:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (12 bp):
GTATTAATATAA
Found at i:2714105 original size:24 final size:23
Alignment explanation
Indices: 2714066--2714140 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 23
2714056 AATAAAATAT
2714066 TATAATATTAAAAAATAATATAAA
1 TATAATATTAAAAAAT-ATATAAA
2714090 TATAATA-TAAATAAATATATAAA
1 TATAATATTAAA-AAATATATAAA
**
2714113 T-T--TATTAAAATTTATA-AAA
1 TATAATATTAAAAAATATATAAA
2714132 TATAA-ATTA
1 TATAATATTA
2714141 TTAATTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
19 4 0.09
20 8 0.18
21 8 0.18
22 1 0.02
23 12 0.27
24 11 0.25
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
TATAATATTAAAAAATATATAAA
Found at i:2714109 original size:23 final size:24
Alignment explanation
Indices: 2714066--2714113 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
2714056 AATAAAATAT
2714066 TATAATATTAAAAAATAATATAAA
1 TATAATATTAAAAAATAATATAAA
2714090 TATAATA-TAAATAAAT-ATATAAA
1 TATAATATTAAA-AAATAATATAAA
2714113 T
1 T
2714114 TTATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (24 bp):
TATAATATTAAAAAATAATATAAA
Found at i:2714155 original size:24 final size:24
Alignment explanation
Indices: 2714100--2714161 Score: 74
Period size: 24 Copynumber: 2.5 Consensus size: 24
2714090 TATAATATAA
2714100 ATAAATATATAAATTTATTAAAATTT
1 ATAAA-ATATAAATTTATT-AAATTT
2714126 ATAAAATATAAA-TTATT-AATTT
1 ATAAAATATAAATTTATTAAATTT
2714148 ATCAAAAATATAAA
1 AT--AAAATATAAA
2714162 ATAAATTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
22 7 0.21
24 15 0.44
25 7 0.21
26 5 0.15
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (24 bp):
ATAAAATATAAATTTATTAAATTT
Found at i:2714169 original size:22 final size:21
Alignment explanation
Indices: 2714082--2714169 Score: 61
Period size: 22 Copynumber: 3.8 Consensus size: 21
2714072 ATTAAAAAAT
**
2714082 AATATAAATATAATATAAATAA
1 AATATAAATATAA-ATTTATAA
2714104 ATATATAAATTTATTAAAATTTATAA
1 A-ATATAAA--TA-T-AAATTTATAA
*
2714130 AATATAAATTATTAATTTATCAAA
1 AATATAAA-TATAAATTTAT--AA
2714154 AATATAAA-ATAAATTT
1 AATATAAATATAAATTT
2714170 TCGTTTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
22 15 0.27
23 8 0.15
24 13 0.24
25 9 0.16
26 8 0.15
27 2 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (21 bp):
AATATAAATATAAATTTATAA
Found at i:2715019 original size:2 final size:2
Alignment explanation
Indices: 2715012--2715045 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2715002 TTACTTGTTT
2715012 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2715046 TTGTTAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:2719019 original size:2 final size:2
Alignment explanation
Indices: 2719012--2719060 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2719002 ATGATTCATC
2719012 TA TA TA TA TA TA TA 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 TA TA TA TA
2719054 TA TA TA T
1 TA TA TA T
2719061 TTGGTCCAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2732324 original size:5 final size:5
Alignment explanation
Indices: 2732314--2732421 Score: 80
Period size: 5 Copynumber: 21.2 Consensus size: 5
2732304 AATTAATTTT
* * *
2732314 TTATA TTATA TTATA TAATA TTAATA TTTTA TTTATA TTATTT TTATA
1 TTATA TTATA TTATA TTATA TT-ATA TTATA -TTATA TTA-TA TTATA
* *
2732362 TTATA TTATAA TTTTAA TTA-A TTAT- TTATA TAATA CTTATA TTATA
1 TTATA TTAT-A TTAT-A TTATA TTATA TTATA TTATA -TTATA TTATA
*
2732408 TT-T- TTACA TTATA T
1 TTATA TTATA TTATA T
2732422 ATGAATTTAT
Statistics
Matches: 82, Mismatches: 12, Indels: 18
0.73 0.11 0.16
Matches are distributed among these distances:
3 2 0.02
4 9 0.11
5 46 0.56
6 25 0.30
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:2732324 original size:33 final size:33
Alignment explanation
Indices: 2732286--2732403 Score: 110
Period size: 38 Copynumber: 3.3 Consensus size: 33
2732276 TTATAATAAT
2732286 TTATATTATATAAATTTTAATTAATTTTTTATA
1 TTATATTATATAAATTTTAATTAATTTTTTATA
* * * *
2732319 TTATATTATATAATATTAATATTTTATTTATATTATTT
1 TTATATTATATAA-ATT-TTAATTAATTT-T-TTA-TA
*
2732357 TTATATTATATTATAATTTTAATTAATTATTTATA
1 TTATATTATA-TA-AATTTTAATTAATTTTTTATA
*
2732392 TAATACTTATAT
1 TTATA-TTATAT
2732404 TATATTTTTA
Statistics
Matches: 67, Mismatches: 10, Indels: 14
0.74 0.11 0.15
Matches are distributed among these distances:
33 13 0.19
34 3 0.04
35 14 0.21
36 9 0.13
37 4 0.06
38 18 0.27
39 5 0.07
40 1 0.01
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (33 bp):
TTATATTATATAAATTTTAATTAATTTTTTATA
Found at i:2732335 original size:43 final size:43
Alignment explanation
Indices: 2732286--2732371 Score: 119
Period size: 43 Copynumber: 2.1 Consensus size: 43
2732276 TTATAATAAT
*
2732286 TTATATTATA-TAA-ATTTTAATTA-A-T-TTTTTATATTATA
1 TTATATAATATTAATATTTTAATTATATTATTTTTATATTATA
*
2732324 TTATATAATATTAATATTTTATTTATATTATTTTTATATTATA
1 TTATATAATATTAATATTTTAATTATATTATTTTTATATTATA
2732367 TTATA
1 TTATA
2732372 ATTTTAATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
38 9 0.22
39 3 0.07
40 9 0.22
41 1 0.02
42 1 0.02
43 18 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
TTATATAATATTAATATTTTAATTATATTATTTTTATATTATA
Found at i:2732387 original size:41 final size:41
Alignment explanation
Indices: 2732311--2732409 Score: 119
Period size: 41 Copynumber: 2.4 Consensus size: 41
2732301 TTTAATTAAT
* *
2732311 TTTTTATATTATATTATATAATATTAATATTTTATTTATATTA
1 TTTTTATATTATA-T-TATAATATTAATATATTATTTATATAA
*
2732354 TTTTTATATTATATTATAATTTTAAT-TAATTATTTATATAA
1 TTTTTATATTATATTATAATATTAATAT-ATTATTTATATAA
**
2732395 TACTTATATTATATT
1 TTTTTATATTATATT
2732410 TTTACATTAT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
40 1 0.02
41 35 0.70
42 1 0.02
43 13 0.26
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (41 bp):
TTTTTATATTATATTATAATATTAATATATTATTTATATAA
Found at i:2732677 original size:39 final size:39
Alignment explanation
Indices: 2732608--2732689 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
2732598 CCTCTAACAA
* * *
2732608 GCAAAAAACGTCCCACCAATGTCGAGTTCGATGTAACTT
1 GCAAAAAAAGTCACACCAACGTCGAGTTCGATGTAACTT
*
2732647 GCAAAAAAAGTCACACCGACGTCG-GATTCGATGTAACTT
1 GCAAAAAAAGTCACACCAACGTCGAG-TTCGATGTAACTT
2732686 GCAA
1 GCAA
2732690 CTCATTAAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
38 1 0.03
39 37 0.97
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.21
Consensus pattern (39 bp):
GCAAAAAAAGTCACACCAACGTCGAGTTCGATGTAACTT
Found at i:2732815 original size:2 final size:2
Alignment explanation
Indices: 2732808--2732844 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2732798 GTATGCATAA
2732808 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2732845 CACATTTGTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2741074 original size:24 final size:24
Alignment explanation
Indices: 2741042--2741093 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
2741032 CCACCTATCA
2741042 ATATATAAACATAAGCATTTTGCC
1 ATATATAAACATAAGCATTTTGCC
*
2741066 ATATATAAACATAAGCATTTTGCT
1 ATATATAAACATAAGCATTTTGCC
2741090 ATAT
1 ATAT
2741094 CATCATTGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (24 bp):
ATATATAAACATAAGCATTTTGCC
Found at i:2744759 original size:30 final size:31
Alignment explanation
Indices: 2744687--2744759 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
2744677 TAGTGACTTC
**
2744687 AATATTTAAATTTTCTTTTTATTTTATGAAT
1 AATATTTAAATTTTCTTTTTATTAAATGAAT
2744718 AATATTTAAATTTTCTTTTT-TTAAAT-AAT
1 AATATTTAAATTTTCTTTTTATTAAATGAAT
*
2744747 TATATATTAAATT
1 AATAT-TTAAATT
2744760 AGATCTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
29 7 0.18
30 11 0.29
31 20 0.53
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (31 bp):
AATATTTAAATTTTCTTTTTATTAAATGAAT
Found at i:2747737 original size:3 final size:3
Alignment explanation
Indices: 2747729--2747760 Score: 55
Period size: 3 Copynumber: 10.3 Consensus size: 3
2747719 ACTTACTATC
2747729 TTA TTA TTA TTA TTA TTA TTA TTA TTAA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA T
2747761 ATTTTATGAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:2748622 original size:22 final size:22
Alignment explanation
Indices: 2748595--2748645 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
2748585 ATATAATTAT
*
2748595 ATAAATAATTTAATTTTTTTCAA
1 ATAAATAATTTAATTTATTT-AA
*
2748618 A-AAATAATTTTATTTATTTAA
1 ATAAATAATTTAATTTATTTAA
2748639 ATAAATA
1 ATAAATA
2748646 CTACATTCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 21 0.84
23 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATAAATAATTTAATTTATTTAA
Found at i:2752999 original size:32 final size:32
Alignment explanation
Indices: 2752940--2753039 Score: 91
Period size: 32 Copynumber: 3.1 Consensus size: 32
2752930 TTAATATTAT
* *
2752940 ATTTAAAATATT-ATGTA-TTATTTATATAAA
1 ATTTAACATATTAATATATTTATTTATATAAA
*
2752970 ATTTAA-TTCATTAATA-ATTTATGTTATATAAA
1 ATTTAACAT-ATTAATATATTTAT-TTATATAAA
* *
2753002 CTTTAACATATTCATATATTTATATTATATTAAA
1 ATTTAACATATTAATATATTTAT-TTATA-TAAA
2753036 ATTT
1 ATTT
2753040 TTATTATATT
Statistics
Matches: 56, Mismatches: 7, Indels: 10
0.77 0.10 0.14
Matches are distributed among these distances:
29 1 0.02
30 10 0.18
31 6 0.11
32 20 0.36
33 12 0.21
34 7 0.12
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (32 bp):
ATTTAACATATTAATATATTTATTTATATAAA
Found at i:2753055 original size:17 final size:17
Alignment explanation
Indices: 2752957--2753049 Score: 56
Period size: 17 Copynumber: 5.7 Consensus size: 17
2752947 ATATTATGTA
2752957 TTAT-TTATA-TAAAAT
1 TTATATTATATTAAAAT
*
2752972 TTA-ATT-CATTAATAAT
1 TTATATTATATTAA-AAT
* *
2752988 TTATGTTATA-TAAACT
1 TTATATTATATTAAAAT
* *
2753004 TTA-A-CATATTCATATAT
1 TTATATTATATT-A-AAAT
2753021 TTATATTATATTAAAAT
1 TTATATTATATTAAAAT
*
2753038 TTTTATTATATT
1 TTATATTATATT
2753050 TTAATTATTT
Statistics
Matches: 57, Mismatches: 11, Indels: 18
0.66 0.13 0.21
Matches are distributed among these distances:
14 4 0.07
15 9 0.16
16 12 0.21
17 24 0.42
18 3 0.05
19 5 0.09
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (17 bp):
TTATATTATATTAAAAT
Found at i:2754710 original size:14 final size:14
Alignment explanation
Indices: 2754693--2754754 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
2754683 AATAATTAAA
2754693 ATATAATAAATATT
1 ATATAATAAATATT
*
2754707 ATATAAATAAATA-A
1 ATAT-AATAAATATT
* *
2754721 ATATATTAAAAATT
1 ATATAATAAATATT
2754735 ATATAATATAA-ATT
1 ATATAATA-AATATT
2754749 AT-TAAT
1 ATATAAT
2754755 TTATTAAAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
13 10 0.25
14 20 0.50
15 10 0.25
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATAATAAATATT
Found at i:2754719 original size:33 final size:33
Alignment explanation
Indices: 2754657--2754816 Score: 91
Period size: 34 Copynumber: 4.8 Consensus size: 33
2754647 GCAGCATGTG
*
2754657 TATATATATATATATATATACAATAAAATAATTAAAA
1 TATA-ATAAATAT-TATATA-AAT-AAATAATTAAAA
2754694 TATAATAAATATTATATAAAT--A-AA-T-AAA
1 TATAATAAATATTATATAAATAAATAATTAAAA
* * * **
2754722 TATATTAAAAATTATATAATATAAATTATTAATT
1 TATAATAAATATTATATAA-ATAAATAATTAAAA
* * *
2754756 TATTAAAAAATA-TATA-AATATATAATATTTTAAA
1 TA-TAATAAATATTATATAA-ATA-AATAATTAAAA
* * *
2754790 TATAATAATTATTACATAAAAAAATAA
1 TATAATAAATATTATATAAATAAATAA
2754817 AGATTAGGGA
Statistics
Matches: 94, Mismatches: 19, Indels: 24
0.69 0.14 0.18
Matches are distributed among these distances:
28 20 0.21
29 3 0.03
30 2 0.02
31 2 0.02
32 1 0.01
33 18 0.19
34 23 0.24
35 14 0.15
36 7 0.07
37 4 0.04
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (33 bp):
TATAATAAATATTATATAAATAAATAATTAAAA
Found at i:2754733 original size:19 final size:20
Alignment explanation
Indices: 2754682--2754733 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2754672 ATATACAATA
2754682 AAATA-ATT-AAAATATAAT
1 AAATATATTAAAAATATAAT
*
2754700 AAATAT-TATATAAATA-AAT
1 AAATATAT-TAAAAATATAAT
2754719 AAATATATTAAAAAT
1 AAATATATTAAAAAT
2754734 TATATAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.21
19 16 0.57
20 6 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATATTAAAAATATAAT
Found at i:2754764 original size:32 final size:29
Alignment explanation
Indices: 2754691--2754789 Score: 96
Period size: 28 Copynumber: 3.4 Consensus size: 29
2754681 AAAATAATTA
* *
2754691 AAATATAATAAATATTATATAA-ATAAAT
1 AAATATATTAAAAATTATATAATATAAAT
2754719 AAATATATTAAAAATTATATAATATAAATT
1 AAATATATTAAAAATTATATAATATAAA-T
* * *
2754749 ATTAATTTATTAAAAAATATATAA-ATATAT
1 A--AATATATTAAAAATTATATAATATAAAT
*
2754779 -AATATTTTAAA
1 AAATATATTAAA
2754790 TATAATAATT
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
27 9 0.15
28 20 0.33
29 5 0.08
30 3 0.05
31 4 0.07
32 19 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (29 bp):
AAATATATTAAAAATTATATAATATAAAT
Found at i:2755596 original size:20 final size:21
Alignment explanation
Indices: 2755555--2755596 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
2755545 CCCATTGACT
*
2755555 GGCAATATAGAGTACTTAACAA
1 GGCAATAAAGAGTAC-TAACAA
2755577 GGCAATAAAGAGTA-TAACAA
1 GGCAATAAAGAGTACTAACAA
2755597 AGCTACAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
22 13 0.68
ACGTcount: A:0.50, C:0.12, G:0.19, T:0.19
Consensus pattern (21 bp):
GGCAATAAAGAGTACTAACAA
Found at i:2759361 original size:4 final size:4
Alignment explanation
Indices: 2759352--2759381 Score: 51
Period size: 4 Copynumber: 7.5 Consensus size: 4
2759342 ACTTCGGGCA
*
2759352 TAAT TAAT TAAT TAAT TAAT TACT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TA
2759382 TTATTACGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:2760091 original size:14 final size:15
Alignment explanation
Indices: 2760065--2760093 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2760055 TAATTAAATT
2760065 TAAATTAATATTTAA
1 TAAATTAATATTTAA
2760080 TAAATT-ATATTTAA
1 TAAATTAATATTTAA
2760094 CTTTAAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
TAAATTAATATTTAA
Found at i:2760120 original size:17 final size:17
Alignment explanation
Indices: 2760100--2760176 Score: 54
Period size: 17 Copynumber: 4.6 Consensus size: 17
2760090 TTAACTTTAA
2760100 ATAAATAGAATTTAAAT
1 ATAAATAGAATTTAAAT
* **
2760117 ATAAATTTAAAATTT-TTT
1 ATAAA--TAGAATTTAAAT
* * *
2760135 ATAAATATAAATAAAAT
1 ATAAATAGAATTTAAAT
2760152 ATAAATA-AATTTAAA-
1 ATAAATAGAATTTAAAT
2760167 ATAAAT-GAAT
1 ATAAATAGAAT
2760177 AAACATCAGA
Statistics
Matches: 46, Mismatches: 10, Indels: 10
0.70 0.15 0.15
Matches are distributed among these distances:
15 9 0.20
16 11 0.24
17 13 0.28
18 6 0.13
19 7 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATAAATAGAATTTAAAT
Found at i:2760719 original size:2 final size:2
Alignment explanation
Indices: 2760712--2760750 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
2760702 GGTCCAACTC
2760712 TA TA TA TA T- TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2760751 GGACATAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 33 0.94
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:2761510 original size:12 final size:12
Alignment explanation
Indices: 2761493--2761525 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2761483 AACCAATGAC
2761493 ATTATTATTATA
1 ATTATTATTATA
*
2761505 ATTATTATTATG
1 ATTATTATTATA
2761517 ATTATTATT
1 ATTATTATT
2761526 TTCTCTAGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (12 bp):
ATTATTATTATA
Found at i:2762023 original size:3 final size:3
Alignment explanation
Indices: 2762015--2762039 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2762005 TATTTTCCAT
2762015 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2762040 ATTAAATTAA
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2769465 original size:3 final size:3
Alignment explanation
Indices: 2769457--2769481 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2769447 TCTCAACTTT
2769457 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
2769482 CAAATTTGGT
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:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2773403 original size:30 final size:30
Alignment explanation
Indices: 2773316--2773404 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
2773306 TTATGTTACG
*
2773316 ATATATTATTAATAAATAAATAA-ATAATTTTA
1 ATATTTTA-TAATAAATAAATAATATAA--TTA
*
2773348 AAATTTT-TAA-AAATAAAT-ATAATAATT-
1 ATATTTTATAATAAATAAATAAT-ATAATTA
2773375 ATATTTTATAATAAATAATATAATATAATT
1 ATATTTTATAATAAATAA-ATAATATAATT
2773405 CATTAATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
27 6 0.12
28 6 0.12
29 14 0.29
30 15 0.31
31 2 0.04
32 5 0.10
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
ATATTTTATAATAAATAAATAATATAATTA
Found at i:2775016 original size:19 final size:19
Alignment explanation
Indices: 2774992--2775052 Score: 59
Period size: 19 Copynumber: 3.2 Consensus size: 19
2774982 GTAATTACTT
2774992 ATTTTTTAATATATTTTTA
1 ATTTTTTAATATATTTTTA
* ** *
2775011 ATTTTTTATTATAAATTAA
1 ATTTTTTAATATATTTTTA
* *
2775030 ATTTTTTTATAAATTTATTA
1 ATTTTTTAATATATTT-TTA
2775050 ATT
1 ATT
2775053 AAATTATATA
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 26 0.84
20 5 0.16
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
ATTTTTTAATATATTTTTA
Found at i:2775029 original size:18 final size:17
Alignment explanation
Indices: 2775008--2775044 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
2774998 TAATATATTT
*
2775008 TTAATTTTTTATTATAAA
1 TTAAATTTTT-TTATAAA
2775026 TTAAATTTTTTTATAAA
1 TTAAATTTTTTTATAAA
2775043 TT
1 TT
2775045 TATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAAATTTTTTTATAAA
Found at i:2775809 original size:2 final size:2
Alignment explanation
Indices: 2775802--2775827 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2775792 GTAAAATGAA
2775802 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
2775828 GAAAGGGTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2783566 original size:49 final size:49
Alignment explanation
Indices: 2783513--2783611 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
2783503 AACATTTAAA
2783513 ATATAACCTAATTGAAACAAGAATGGAAAGAGAACAAACATTTCTATGT
1 ATATAACCTAATTGAAACAAGAATGGAAAGAGAACAAACATTTCTATGT
2783562 ATATAACCTAATTGAAACAAGAATGGAAAGAGAACAAACATTTCTATGT
1 ATATAACCTAATTGAAACAAGAATGGAAAGAGAACAAACATTTCTATGT
2783611 A
1 A
2783612 CTTATATTAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.49, C:0.12, G:0.14, T:0.24
Consensus pattern (49 bp):
ATATAACCTAATTGAAACAAGAATGGAAAGAGAACAAACATTTCTATGT
Found at i:2790022 original size:23 final size:22
Alignment explanation
Indices: 2789984--2790029 Score: 58
Period size: 21 Copynumber: 2.0 Consensus size: 22
2789974 TATAAATTAC
2789984 ATAATATACATAAAAA-TAAAA
1 ATAATATACATAAAAATTAAAA
*
2790005 ATAATATATATTACAAAATTAAAA
1 ATAATATACA-TA-AAAATTAAAA
2790029 A
1 A
2790030 CAAATTGAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 2 0.10
23 4 0.19
24 6 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (22 bp):
ATAATATACATAAAAATTAAAA
Found at i:2799780 original size:22 final size:23
Alignment explanation
Indices: 2799753--2799811 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 23
2799743 TTTTTTTTGA
2799753 ATTAAATAATAATATTTTTATTT
1 ATTAAATAATAATATTTTTATTT
2799776 A-TAAAT-AT--TA-TTTTATTT
1 ATTAAATAATAATATTTTTATTT
*
2799794 ATTAGAATAAAAATATTT
1 ATTA-AATAATAATATTT
2799812 AAAAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 11
0.71 0.02 0.27
Matches are distributed among these distances:
18 9 0.31
19 4 0.14
20 3 0.10
21 3 0.10
22 5 0.17
23 3 0.10
24 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTAAATAATAATATTTTTATTT
Found at i:2800664 original size:19 final size:19
Alignment explanation
Indices: 2800635--2800679 Score: 65
Period size: 18 Copynumber: 2.4 Consensus size: 19
2800625 GTTAAATTTT
* *
2800635 TTAAATTTTTAATTAATA-
1 TTAAATTTTTTATTAAAAC
2800653 TTAAATTTTTTATTAAAAC
1 TTAAATTTTTTATTAAAAC
2800672 TTAAATTT
1 TTAAATTT
2800680 AAATATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (19 bp):
TTAAATTTTTTATTAAAAC
Found at i:2800707 original size:19 final size:19
Alignment explanation
Indices: 2800673--2800724 Score: 63
Period size: 19 Copynumber: 2.7 Consensus size: 19
2800663 TATTAAAACT
2800673 TAAATTT-AAATATAAATAA
1 TAAATTTAAAATATAAAT-A
2800692 TAAATTTAAAAT-TAAATA
1 TAAATTTAAAATATAAATA
*
2800710 TGAAAATTAAAATAT
1 T-AAATTTAAAATAT
2800725 TTTTTATCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 2 0.07
19 22 0.76
20 5 0.17
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATTTAAAATATAAATA
Found at i:2800715 original size:13 final size:12
Alignment explanation
Indices: 2800673--2800720 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
2800663 TATTAAAACT
*
2800673 TAAATTTAAATA
1 TAAAATTAAATA
* *
2800685 TAAATAATAAATT
1 TAAA-ATTAAATA
2800698 TAAAATTAAATA
1 TAAAATTAAATA
2800710 TGAAAATTAAA
1 T-AAAATTAAA
2800721 ATATTTTTTA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:2802249 original size:29 final size:27
Alignment explanation
Indices: 2802210--2802273 Score: 74
Period size: 29 Copynumber: 2.3 Consensus size: 27
2802200 TTTATACATT
* *
2802210 AATTATAAAATAACAAATTTTATAAATAA
1 AATTATTAAATAACAAATATT-T-AATAA
*
2802239 AATTATTAAATAATAAATATTTAATAA
1 AATTATTAAATAACAAATATTTAATAA
2802266 AATATATT
1 AAT-TATT
2802274 TAAAAATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 8 0.26
28 5 0.16
29 18 0.58
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (27 bp):
AATTATTAAATAACAAATATTTAATAA
Found at i:2802259 original size:14 final size:14
Alignment explanation
Indices: 2802232--2802297 Score: 50
Period size: 14 Copynumber: 4.8 Consensus size: 14
2802222 ACAAATTTTA
*
2802232 TAAATAA-AATTAT
1 TAAATAATAAATAT
2802245 TAAATAATAAATAT
1 TAAATAATAAATAT
*
2802259 TTAATAA-AATATATT
1 TAAATAATAA-ATA-T
*
2802274 TAAA-AAT-AATAA
1 TAAATAATAAATAT
2802286 TAAATAAATAAA
1 TAAAT-AATAAA
2802298 ATAAAATACA
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
12 4 0.10
13 12 0.29
14 20 0.48
15 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAATAATAAATAT
Found at i:2802284 original size:27 final size:27
Alignment explanation
Indices: 2802231--2802293 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
2802221 AACAAATTTT
2802231 ATAAATAAAATTATTAAATAATAAATA
1 ATAAATAAAATTATTAAATAATAAATA
* *
2802258 TTTAATAAAATATATTTAAA-AAT-AATA
1 ATAAATAAAAT-TA-TTAAATAATAAATA
2802285 ATAAATAAA
1 ATAAATAAA
2802294 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 20 0.67
28 5 0.17
29 5 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
ATAAATAAAATTATTAAATAATAAATA
Found at i:2802684 original size:31 final size:31
Alignment explanation
Indices: 2802649--2802736 Score: 94
Period size: 31 Copynumber: 2.8 Consensus size: 31
2802639 CAATTTAAGT
2802649 TAAAAGATTTATTTATATTAAAAAA-A-TTAAA
1 TAAAA-ATTTATTTA-ATTAAAAAATATTTAAA
*
2802680 TAAAAA--TATTAAATTTAAAAATATATTTAAA
1 TAAAAATTTATTTAA-TTAAAAA-ATATTTAAA
2802711 TAAAAATTATATTTAATTAAAAAATA
1 TAAAAATT-TATTTAATTAAAAAATA
2802737 ATTGAGTTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
27 1 0.02
28 12 0.25
29 1 0.02
30 2 0.04
31 16 0.33
32 3 0.06
33 7 0.15
34 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (31 bp):
TAAAAATTTATTTAATTAAAAAATATTTAAA
Found at i:2802700 original size:15 final size:14
Alignment explanation
Indices: 2802665--2802703 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
2802655 ATTTATTTAT
*
2802665 ATTAAAAAAATTAA
1 ATTAAAAATATTAA
2802679 A-TAAAAATATTAA
1 ATTAAAAATATTAA
2802692 ATTTAAAAATAT
1 A-TTAAAAATAT
2802704 ATTTAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
13 12 0.55
14 1 0.05
15 9 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (14 bp):
ATTAAAAATATTAA
Found at i:2802709 original size:18 final size:18
Alignment explanation
Indices: 2802688--2802736 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
2802678 AATAAAAATA
2802688 TTAAATTTAAAAATATAT
1 TTAAATTTAAAAATATAT
2802706 TTAAA--TAAAAATTATAT
1 TTAAATTTAAAAA-TATAT
*
2802723 TT-AATTAAAAAATA
1 TTAAATTTAAAAATA
2802737 ATTGAGTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
16 8 0.30
17 9 0.33
18 10 0.37
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TTAAATTTAAAAATATAT
Found at i:2802716 original size:17 final size:17
Alignment explanation
Indices: 2802696--2802736 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
2802686 TATTAAATTT
2802696 AAAAATATATTTAAATA
1 AAAAATATATTTAAATA
* *
2802713 AAAATTATATTTAATTA
1 AAAAATATATTTAAATA
2802730 AAAAATA
1 AAAAATA
2802737 ATTGAGTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
AAAAATATATTTAAATA
Found at i:2802984 original size:15 final size:15
Alignment explanation
Indices: 2802919--2802986 Score: 52
Period size: 15 Copynumber: 4.6 Consensus size: 15
2802909 ATTTTAAACT
2802919 TAAAAATATTAAATTAA
1 TAAAAATA-TAAATT-A
* *
2802936 TAAAAA-CTAAATTT
1 TAAAAATATAAATTA
*
2802950 TAAAAATAT--ATTT
1 TAAAAATATAAATTA
**
2802963 TCTAAATATAAATTA
1 TAAAAATATAAATTA
2802978 TAAAAATAT
1 TAAAAATAT
2802987 GATATAAATA
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
13 11 0.28
14 6 0.15
15 17 0.43
17 6 0.15
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (15 bp):
TAAAAATATAAATTA
Found at i:2803755 original size:18 final size:17
Alignment explanation
Indices: 2803705--2803792 Score: 81
Period size: 18 Copynumber: 4.9 Consensus size: 17
2803695 AATAATTTTA
2803705 TTTAAATTTAATTATAAT
1 TTTAAATTTAA-TATAAT
2803723 ATATTAATATTTAATATAAT
1 -T-TTAA-ATTTAATATAAT
*
2803743 TTTAAATTATAATATATTT
1 TTTAAATT-TAATATA-AT
* *
2803762 TTTAAAATTAAT-TTAT
1 TTTAAATTTAATATAAT
2803778 TTTAAATTTAA-ATAA
1 TTTAAATTTAATATAA
2803793 AAATAAAAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
16 13 0.22
17 4 0.07
18 15 0.26
19 10 0.17
20 10 0.17
21 6 0.10
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTAAATTTAATATAAT
Found at i:2804962 original size:15 final size:15
Alignment explanation
Indices: 2804944--2805035 Score: 54
Period size: 15 Copynumber: 6.3 Consensus size: 15
2804934 TAATTGGGAT
2804944 AAATTTAAATTTAAA
1 AAATTTAAATTTAAA
*
2804959 AAATATT-TATTT-AA
1 AAAT-TTAAATTTAAA
*
2804973 AAA-TT-AATTTATAC
1 AAATTTAAATTTA-AA
2804987 AAA-TTAAA--TAAA
1 AAATTTAAATTTAAA
* *
2804999 TAATTTAATATTTAGAT
1 AAATTTAA-ATTTA-AA
*
2805016 AAATTTAATTTTAAA
1 AAATTTAAATTTAAA
2805031 AAATT
1 AAATT
2805036 AGGATATTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 18
0.69 0.10 0.21
Matches are distributed among these distances:
12 9 0.15
13 6 0.10
14 12 0.20
15 16 0.27
16 8 0.14
17 8 0.14
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (15 bp):
AAATTTAAATTTAAA
Found at i:2805389 original size:29 final size:29
Alignment explanation
Indices: 2805354--2805455 Score: 91
Period size: 29 Copynumber: 3.3 Consensus size: 29
2805344 TAAAATAAAA
2805354 TAAATAAAAAATTAAATTTTTATTATTTT
1 TAAATAAAAAATTAAATTTTTATTATTTT
*
2805383 TAAATAATAAAATTTAAA-TTTT-TTAATTT
1 TAAATAA-AAAA-TTAAATTTTTATTATTTT
* * *
2805412 TATATTAAAAATTTAAAATATTTATTATTTAAT
1 TA-AATAAAAAATT-AAATTTTTATTATTT--T
2805445 TAATATAAAAA
1 TAA-ATAAAAA
2805456 TTCTTTATTA
Statistics
Matches: 58, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
28 2 0.03
29 21 0.36
30 15 0.26
31 10 0.17
32 1 0.02
33 9 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TAAATAAAAAATTAAATTTTTATTATTTT
Done.