Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 9 of 153
Found at i:2712863 original size:27 final size:27
Alignment explanation
Indices: 2712796--2712863 Score: 106
Period size: 25 Copynumber: 2.6 Consensus size: 27
2712786 AAAAATAAAA
2712796 ATTTACCAAAATAT-TATAACTTTTTTT
1 ATTTACCAAAATATATATAAC-TTTTTT
2712823 ATTTACCAAAATATATAT-A-TTTTTT
1 ATTTACCAAAATATATATAACTTTTTT
2712848 ATTTACCAAAATATAT
1 ATTTACCAAAATATAT
2712864 CAAAAAAAAC
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
25 22 0.55
27 15 0.38
28 3 0.08
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATATATAACTTTTTT
Found at i:2712966 original size:27 final size:27
Alignment explanation
Indices: 2712936--2713002 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
2712926 CGCCAATGGG
2712936 ATTGGCGGCACCAAAGGTGCCAAAACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
* *
2712963 ATTGGCGGCACCAATGGTGCCAATACC
1 ATTGGCGGCACCAAAGGTGCCAAAACC
2712990 ATTGGCGGCACCA
1 ATTGGCGGCACCA
2713003 GTGTATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGTGCCAAAACC
Found at i:2713056 original size:4 final size:4
Alignment explanation
Indices: 2713047--2713164 Score: 86
Period size: 4 Copynumber: 29.0 Consensus size: 4
2713037 GAAGGAGAGG
* *
2713047 GAAA GAAA GAAA GAAA G-AA -AAA GAAG GAAA GAAAA GGAAA G-GA GAAGA
1 GAAA GAAA GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA GAAA GAA-A
*
2713095 GAAGA GAAA AAAA GAAA GAAA G-AA G-AA GAAAA TGAAA GGAGAA GAAA
1 GAA-A GAAA GAAA GAAA GAAA GAAA GAAA G-AAA -GAAA -GA-AA GAAA
*
2713142 -AAA GAAA GAAA GAAG GAAA GAAA
1 GAAA GAAA GAAA GAAA GAAA GAAA
2713165 AGGAAAGGAA
Statistics
Matches: 94, Mismatches: 9, Indels: 22
0.75 0.07 0.18
Matches are distributed among these distances:
3 15 0.16
4 51 0.54
5 24 0.26
6 4 0.04
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (4 bp):
GAAA
Found at i:2713069 original size:18 final size:18
Alignment explanation
Indices: 2713048--2713184 Score: 98
Period size: 18 Copynumber: 7.2 Consensus size: 18
2713038 AAGGAGAGGG
2713048 AAAGAAAGAAAGAAAGAA
1 AAAGAAAGAAAGAAAGAA
* *
2713066 AAAGAAGGAAAGAAAAGGA
1 AAAGAAAGAAAG-AAAGAA
*
2713085 AAGGAGAAGAGAAGAGAA-AA
1 AAAGA-AAGA-AAGA-AAGAA
2713105 AAAGAAAGAAAGAAGAAGAA
1 AAAGAAAGAAAG-A-AAGAA
* *
2713125 AATGAAAGGAGAAGAAAAAA
1 AAAGAAA-GA-AAGAAAGAA
*
2713145 GAAAGAAAGAAGGAAAGAA
1 -AAAGAAAGAAAGAAAGAA
* *
2713164 AAGGAAAGGAAA-AATGAA
1 AAAGAAA-GAAAGAAAGAA
2713182 AAA
1 AAA
2713185 AAAAAGAAGA
Statistics
Matches: 94, Mismatches: 15, Indels: 20
0.73 0.12 0.16
Matches are distributed among these distances:
18 27 0.29
19 27 0.29
20 23 0.24
21 14 0.15
22 3 0.03
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (18 bp):
AAAGAAAGAAAGAAAGAA
Found at i:2713075 original size:26 final size:27
Alignment explanation
Indices: 2713046--2713164 Score: 104
Period size: 29 Copynumber: 4.3 Consensus size: 27
2713036 AGAAGGAGAG
2713046 GGAAAGAAAGAAAGA-AAGAAAAAGAA
1 GGAAAGAAAGAAAGAGAAGAAAAAGAA
*
2713072 GGAAAGAAAAGGAAAGGAGAAGAGAAGAGAA
1 GGAAAG-AAA-GAAA-GAGAAGA-AAAAGAA
** *
2713103 AAAAAGAAAGAAAGAAGAAGAAAATGAAA
1 GGAAAGAAAGAAAG-AGAAGAAAAAG-AA
2713132 GGAGAAGAAA-AAAGA-AAG--AAAGAA
1 GGA-AAGAAAGAAAGAGAAGAAAAAGAA
2713156 GGAAAGAAA
1 GGAAAGAAA
2713165 AGGAAAGGAA
Statistics
Matches: 77, Mismatches: 8, Indels: 19
0.74 0.08 0.18
Matches are distributed among these distances:
23 6 0.08
24 5 0.06
25 3 0.04
26 6 0.08
27 6 0.08
28 9 0.12
29 19 0.25
30 13 0.17
31 10 0.13
ACGTcount: A:0.70, C:0.00, G:0.29, T:0.01
Consensus pattern (27 bp):
GGAAAGAAAGAAAGAGAAGAAAAAGAA
Found at i:2713109 original size:45 final size:42
Alignment explanation
Indices: 2713038--2713199 Score: 165
Period size: 45 Copynumber: 3.8 Consensus size: 42
2713028 GGGGGACCAG
* *
2713038 AAGGAGAGG-GAAAGAAAGAAAGAAAGAAAAAGAAGGAAAGAA
1 AAGGAAAGGAGAAAGAAA-AAAAAAAGAAAAAGAAGGAAAGAA
2713080 AAGGAAAGGAGAAGAGAAGAGAAAAAAAGAAAGAAAGAA-G-AAGAA
1 AAGGAAAGGAGAA-AGAA-A-AAAAAAAG-AA-AAAGAAGGAAAGAA
* *
2713125 AATGAAAGGAG-AAGAAAAAAGAAAG--AAAGAAGGAAAGAA
1 AAGGAAAGGAGAAAGAAAAAAAAAAGAAAAAGAAGGAAAGAA
* *
2713164 AAGGAAAGGAAAAATGAAAAAAAAAAGAAGAAGAAG
1 AAGGAAAGGAGAAA-GAAAAAAAAAAGAAAAAGAAG
2713200 AGGGAAGGAA
Statistics
Matches: 101, Mismatches: 8, Indels: 21
0.78 0.06 0.16
Matches are distributed among these distances:
37 6 0.06
38 1 0.01
39 14 0.14
40 2 0.02
41 18 0.18
42 9 0.09
43 13 0.13
44 5 0.05
45 24 0.24
46 3 0.03
47 6 0.06
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (42 bp):
AAGGAAAGGAGAAAGAAAAAAAAAAGAAAAAGAAGGAAAGAA
Found at i:2713151 original size:33 final size:34
Alignment explanation
Indices: 2713102--2713209 Score: 101
Period size: 34 Copynumber: 3.1 Consensus size: 34
2713092 AGAGAAGAGA
*
2713102 AAAAAAGAAAGAAAGAAGAAGAAAATGAAAGGAGAA-G
1 AAAAAAGAAAGAAAGAAGAA-AAGA--AAAGGA-AAGG
*
2713139 AAAAAAGAAAGAAAGAAGGAAAGAAAAGGAAAGG
1 AAAAAAGAAAGAAAGAAGAAAAGAAAAGGAAAGG
* * * * *
2713173 AAAAATGAAAAAAAAAAGAAGAAGAAGAGGGAAGG
1 AAAAAAGAAAGAAAGAAGAA-AAGAAAAGGAAAGG
2713208 AA
1 AA
2713210 GGGAAAAAAA
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
33 2 0.03
34 23 0.38
35 14 0.23
36 3 0.05
37 19 0.31
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (34 bp):
AAAAAAGAAAGAAAGAAGAAAAGAAAAGGAAAGG
Found at i:2713177 original size:12 final size:11
Alignment explanation
Indices: 2713051--2713187 Score: 68
Period size: 12 Copynumber: 11.9 Consensus size: 11
2713041 GAGAGGGAAA
*
2713051 GAAAGAAAGAAA
1 GAAAGAAA-AAG
*
2713063 GAAA-AAGAAG
1 GAAAGAAAAAG
2713073 GAAAG-AAAAG
1 GAAAGAAAAAG
* *
2713083 GAAAGGAGAAG
1 GAAAGAAAAAG
*
2713094 AGAAGAGAAAAAAA
1 -GAA-AG-AAAAAG
2713108 GAAAGAAAGAAG
1 GAAAGAAA-AAG
*
2713120 AAGAAA-ATGAAAG
1 --GAAAGA-AAAAG
*
2713133 GAGAAGAAAAAA
1 GA-AAGAAAAAG
2713145 GAAAGAAAGAAG
1 GAAAGAAA-AAG
2713157 GAAAG-AAAAG
1 GAAAGAAAAAG
*
2713167 GAAAGGAAAAAT
1 GAAA-GAAAAAG
2713179 GAAA-AAAAA
1 GAAAGAAAAA
2713188 AAGAAGAAGA
Statistics
Matches: 98, Mismatches: 13, Indels: 30
0.70 0.09 0.21
Matches are distributed among these distances:
10 27 0.28
11 20 0.20
12 33 0.34
13 10 0.10
14 8 0.08
ACGTcount: A:0.71, C:0.00, G:0.28, T:0.01
Consensus pattern (11 bp):
GAAAGAAAAAG
Found at i:2713906 original size:24 final size:24
Alignment explanation
Indices: 2713878--2713926 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2713868 TGTTATAAGT
2713878 TTTTTTTATTTACCAAAAAATATA
1 TTTTTTTATTTACCAAAAAATATA
*
2713902 TTTTTTTATTTACCAAAATATATA
1 TTTTTTTATTTACCAAAAAATATA
2713926 T
1 T
2713927 AAAAAAACCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTTTTATTTACCAAAAAATATA
Found at i:2713906 original size:73 final size:73
Alignment explanation
Indices: 2713756--2713906 Score: 166
Period size: 72 Copynumber: 2.1 Consensus size: 73
2713746 TATTTCGGGT
* *
2713756 TTTTTAACAAAATATTACAAAAAATAAAAAAATACTAAAATATTATAATTTTTTTATTTACTAGA
1 TTTTTAACAAAATATTACAAAAAATAAAAAAATACCAAAATATTATAATTTTTTTATTTACCAGA
* * *
2713821 ATAATGGG
66 AAAATAGA
* *
2713829 TTTTT-ACAAATATATTA-AAAAAAT-TAAAAATAACCAAAATGTTATAAGTTTTTTTTATTTAC
1 TTTTTAACAAA-ATATTACAAAAAATAAAAAAAT-ACCAAAATATTATAA--TTTTTTTATTTAC
*
2713891 CA-AAAAATATA
62 CAGAAAAATAGA
2713902 TTTTT
1 TTTTT
2713907 TTATTTACCA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
71 6 0.09
72 25 0.38
73 21 0.32
74 14 0.21
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (73 bp):
TTTTTAACAAAATATTACAAAAAATAAAAAAATACCAAAATATTATAATTTTTTTATTTACCAGA
AAAATAGA
Found at i:2719266 original size:4 final size:4
Alignment explanation
Indices: 2719257--2719282 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2719247 CTAAAAACAA
2719257 TAAC TAAC TAAC TAAC TAAC TAAC TA
1 TAAC TAAC TAAC TAAC TAAC TAAC TA
2719283 TAATAATAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (4 bp):
TAAC
Found at i:2719431 original size:3 final size:3
Alignment explanation
Indices: 2719423--2719454 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2719413 TCTTAATACT
*
2719423 AAC AAC AAC AAC AAC AAC AAC AAC AAC GAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
2719455 TAATAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.66, C:0.31, G:0.03, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:2719538 original size:19 final size:21
Alignment explanation
Indices: 2719514--2719552 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
2719504 ACTAAAACAA
*
2719514 AAAATATTA-CAA-AATATAC
1 AAAATAATAGCAACAATATAC
2719533 AAAATAATAGCAACAATATA
1 AAAATAATAGCAACAATATA
2719553 ATCAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.64, C:0.10, G:0.03, T:0.23
Consensus pattern (21 bp):
AAAATAATAGCAACAATATAC
Found at i:2719721 original size:27 final size:26
Alignment explanation
Indices: 2719676--2719740 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 26
2719666 AATACTAGTA
2719676 GTGCCGCCAATTAGTTTGGCACCATTG
1 GTGCCGCCAA-TAGTTTGGCACCATTG
*
2719703 GTGCCGCCAATATTATTGGCACCATTG
1 GTGCCGCCAATAGT-TTGGCACCATTG
2719730 GTGCCGCCAAT
1 GTGCCGCCAAT
2719741 CCCATTGGCG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
26 3 0.08
27 33 0.92
ACGTcount: A:0.20, C:0.28, G:0.25, T:0.28
Consensus pattern (26 bp):
GTGCCGCCAATAGTTTGGCACCATTG
Found at i:2719747 original size:27 final size:27
Alignment explanation
Indices: 2719691--2719749 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
2719681 GCCAATTAGT
**
2719691 TTGGCACCATTGGTGCCGCCAATATTA
1 TTGGCACCATTGGTGCCGCCAATACCA
*
2719718 TTGGCACCATTGGTGCCGCCAATCCCA
1 TTGGCACCATTGGTGCCGCCAATACCA
2719745 TTGGC
1 TTGGC
2719750 GTGACCAGTA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.31, G:0.24, T:0.27
Consensus pattern (27 bp):
TTGGCACCATTGGTGCCGCCAATACCA
Found at i:2719840 original size:24 final size:26
Alignment explanation
Indices: 2719813--2719879 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 26
2719803 GTTTTTTTTG
*
2719813 ATATATTTTGGTAAAT-AAAAAAA-T
1 ATATATTTTGATAAATAAAAAAAATT
* *
2719837 ATATACTTTAATAAATAAAAAAAATT
1 ATATATTTTGATAAATAAAAAAAATT
2719863 ATAATATTTTGATAAAT
1 AT-ATATTTTGATAAAT
2719880 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 13 0.37
25 7 0.20
26 3 0.09
27 12 0.34
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (26 bp):
ATATATTTTGATAAATAAAAAAAATT
Found at i:2719865 original size:26 final size:25
Alignment explanation
Indices: 2719824--2719879 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
2719814 TATATTTTGG
2719824 TAAATAAAAAAATAT-ATACTTTAA
1 TAAATAAAAAAATATAATACTTTAA
* *
2719848 TAAATAAAAAAAATTATAATATTTTGA
1 TAAAT-AAAAAAA-TATAATACTTTAA
2719875 TAAAT
1 TAAAT
2719880 TTTTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 5 0.19
25 7 0.26
26 3 0.11
27 12 0.44
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (25 bp):
TAAATAAAAAAATATAATACTTTAA
Found at i:2721148 original size:18 final size:19
Alignment explanation
Indices: 2721103--2721153 Score: 54
Period size: 18 Copynumber: 2.7 Consensus size: 19
2721093 TCCAAGTTAG
2721103 ATAAA-AAAATTAAAATAA
1 ATAAATAAAATTAAAATAA
*
2721121 ATAACTAAAA-TAAAAT-A
1 ATAAATAAAATTAAAATAA
2721138 ATAAATCAAAAATTAA
1 ATAAAT--AAAATTAA
2721154 GGAAGCGAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 6 0.22
18 10 0.37
19 8 0.30
20 3 0.11
ACGTcount: A:0.73, C:0.04, G:0.00, T:0.24
Consensus pattern (19 bp):
ATAAATAAAATTAAAATAA
Found at i:2727043 original size:80 final size:80
Alignment explanation
Indices: 2726910--2727072 Score: 317
Period size: 80 Copynumber: 2.0 Consensus size: 80
2726900 CCACATAGGT
2726910 TTGTCATCATAGATTGAGAGTTTAGGCCCACGAATATAATTAGTCTCTTCTAATTCATCATTACT
1 TTGTCATCATAGATTGAGAGTTTAGGCCCACGAATATAATTAGTCTCTTCTAATTCATCATTACT
2726975 CCATAATTCATCGTC
66 CCATAATTCATCGTC
2726990 TTGTCATCATAGATTGAGAGTTTAGGCCCACGAATATAATTAGTCTCTTCTAATTCATCATTACT
1 TTGTCATCATAGATTGAGAGTTTAGGCCCACGAATATAATTAGTCTCTTCTAATTCATCATTACT
*
2727055 CTATAATTCATCGTC
66 CCATAATTCATCGTC
2727070 TTG
1 TTG
2727073 AAACTTCAAC
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
80 82 1.00
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.39
Consensus pattern (80 bp):
TTGTCATCATAGATTGAGAGTTTAGGCCCACGAATATAATTAGTCTCTTCTAATTCATCATTACT
CCATAATTCATCGTC
Found at i:2733554 original size:13 final size:14
Alignment explanation
Indices: 2733538--2733566 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
2733528 TTTGACTTAA
2733538 TTTTAATTA-TATT
1 TTTTAATTATTATT
2733551 TTTTAATTATTATT
1 TTTTAATTATTATT
2733565 TT
1 TT
2733567 ATTTAGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.60
14 6 0.40
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTAATTATTATT
Found at i:2734186 original size:18 final size:18
Alignment explanation
Indices: 2734163--2734203 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
2734153 TTTTACATAG
*
2734163 AAGAAACCGTGTAAGCGA
1 AAGAAACCGTGTAAGCAA
*
2734181 AAGAAACGGTGTAAGCAA
1 AAGAAACCGTGTAAGCAA
2734199 AAGAA
1 AAGAA
2734204 TTTCATATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.12, G:0.27, T:0.10
Consensus pattern (18 bp):
AAGAAACCGTGTAAGCAA
Found at i:2735697 original size:42 final size:42
Alignment explanation
Indices: 2735649--2735753 Score: 147
Period size: 42 Copynumber: 2.5 Consensus size: 42
2735639 ATGAGTTTTG
* ** *
2735649 GTTTAACCCTTATGGGTTTCTGTTCAGCTCTTTTGAGCTTCA
1 GTTTAACCCTTATGGGTTTCTGTTCAACTCTTACGAACTTCA
* *
2735691 GTTTAACCCTTATGGGTTTCCGTTCAACTCTTACGAACTTCC
1 GTTTAACCCTTATGGGTTTCTGTTCAACTCTTACGAACTTCA
*
2735733 GTTCAACCCTTATGGGTTTCT
1 GTTTAACCCTTATGGGTTTCT
2735754 ATTTAGCACT
Statistics
Matches: 55, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 55 1.00
ACGTcount: A:0.16, C:0.25, G:0.17, T:0.42
Consensus pattern (42 bp):
GTTTAACCCTTATGGGTTTCTGTTCAACTCTTACGAACTTCA
Found at i:2738195 original size:9 final size:9
Alignment explanation
Indices: 2738181--2738211 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2738171 GTTAAACGAA
2738181 TCGAGTTAT
1 TCGAGTTAT
*
2738190 TCGAGTTAA
1 TCGAGTTAT
2738199 TCGAGTTAT
1 TCGAGTTAT
2738208 TCGA
1 TCGA
2738212 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:2738368 original size:21 final size:21
Alignment explanation
Indices: 2738329--2738369 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2738319 CCCAAACTCC
*
2738329 CAAAACTTTTTACTTTTCCCT
1 CAAAACTTTTTACTCTTCCCT
2738350 CAAAAC-TTTTACTCCTTCCC
1 CAAAACTTTTTACT-CTTCCC
2738370 ACTTTCCCCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.24, C:0.34, G:0.00, T:0.41
Consensus pattern (21 bp):
CAAAACTTTTTACTCTTCCCT
Found at i:2747133 original size:18 final size:18
Alignment explanation
Indices: 2747106--2747198 Score: 141
Period size: 18 Copynumber: 5.2 Consensus size: 18
2747096 TACGACCGTT
2747106 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2747124 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
2747142 TACAGTACTATTTACGTA
1 TACGGTACTATTCACGTA
*
2747160 TACGGCACTATTCACGTA
1 TACGGTACTATTCACGTA
*
2747178 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
2747196 TAC
1 TAC
2747199 AGTAGTTGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 66 1.00
ACGTcount: A:0.28, C:0.24, G:0.16, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:2768813 original size:18 final size:18
Alignment explanation
Indices: 2768790--2768882 Score: 150
Period size: 18 Copynumber: 5.2 Consensus size: 18
2768780 CCCAACTACT
*
2768790 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
*
2768808 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
*
2768826 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
*
2768844 GTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACC
2768862 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
2768880 GTA
1 GTA
2768883 AACGGTCGTA
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 68 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2768842 original size:36 final size:36
Alignment explanation
Indices: 2768790--2768882 Score: 168
Period size: 36 Copynumber: 2.6 Consensus size: 36
2768780 CCCAACTACT
*
2768790 GTATACGTGAACAGTACCGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
*
2768826 GTATACGTGAATAGTACTGTATACGTGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
2768862 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
2768883 AACGGTCGTA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 54 1.00
ACGTcount: A:0.31, C:0.16, G:0.25, T:0.28
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTGAATAGTGCC
Found at i:2774776 original size:16 final size:16
Alignment explanation
Indices: 2774742--2774777 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
2774732 GTATCACGAG
*
2774742 TTAATTAGATATTAAT
1 TTAATTAGATAGTAAT
*
2774758 TTAATTAGATAGTAGT
1 TTAATTAGATAGTAAT
2774774 TTAA
1 TTAA
2774778 ATATTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (16 bp):
TTAATTAGATAGTAAT
Found at i:2775379 original size:28 final size:28
Alignment explanation
Indices: 2775325--2775387 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
2775315 GTTAAATAAG
*
2775325 TTTTATAAAATTTTAAAATATTTTTTAA
1 TTTTATAAAATTTTAAAATATTATTTAA
*
2775353 TTTTATAAAATTTT-AATTCATTATTTAA
1 TTTTATAAAATTTTAAAAT-ATTATTTAA
2775381 TTATTAT
1 TT-TTAT
2775388 TAGACCGATG
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
27 3 0.10
28 24 0.77
29 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (28 bp):
TTTTATAAAATTTTAAAATATTATTTAA
Found at i:2778551 original size:103 final size:103
Alignment explanation
Indices: 2778422--2778634 Score: 318
Period size: 103 Copynumber: 2.1 Consensus size: 103
2778412 CACTAACTTT
* * * * *
2778422 TTATCTTATTGATTTGTTAGATTTTTATTTACGATATTTCTTTCAATAGTTTTAGTTTTAATTTA
1 TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
* * *
2778487 ATTTTTTAATTTTCAAATCCCTTTTATTTTTATTTTAC
66 ACTTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
* * *
2778525 TTATTTTATTGATTTTTTAAAATTTTATATATGGTATTTATTTCAATAGTTTTAGTTTTAATTTA
1 TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
2778590 ACTTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
66 ACTTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
*
2778628 TGATTTT
1 TTATTTT
2778635 TTACTAATCA
Statistics
Matches: 98, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.26, C:0.07, G:0.06, T:0.61
Consensus pattern (103 bp):
TTATTTTATTGATTTGTTAAAATTTTATATACGATATTTATTTCAATAGTTTTAGTTTTAATTTA
ACTTTTAAATTTTAAAATCCCTTTTATTTTTATTTTAC
Found at i:2779675 original size:13 final size:13
Alignment explanation
Indices: 2779657--2779694 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
2779647 AGTTCTTCAT
2779657 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
2779670 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
2779683 TGCTTTTGAGAA
1 TGCTTTTGAGAA
2779695 ATTTGAGTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.11, G:0.26, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:2785281 original size:4 final size:4
Alignment explanation
Indices: 2785234--2785290 Score: 53
Period size: 4 Copynumber: 14.0 Consensus size: 4
2785224 ATACAAATTT
* * * *
2785234 TAAA TACAA TAAA GTAAA GAAA T-AA TAAA TGAA TGAA TATA TAAA TAAA
1 TAAA TA-AA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
2785283 TAAA TAAA
1 TAAA TAAA
2785291 ACAATACATA
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
3 3 0.07
4 33 0.75
5 8 0.18
ACGTcount: A:0.67, C:0.02, G:0.07, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:2786562 original size:18 final size:18
Alignment explanation
Indices: 2786539--2786573 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2786529 GTAATTAGAC
*
2786539 TTTATTATTTGGTCTTGT
1 TTTATTATTGGGTCTTGT
2786557 TTTATTATTGGGTCTTG
1 TTTATTATTGGGTCTTG
2786574 GGCCGGACGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.06, G:0.20, T:0.63
Consensus pattern (18 bp):
TTTATTATTGGGTCTTGT
Found at i:2787329 original size:25 final size:26
Alignment explanation
Indices: 2787276--2787344 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
2787266 CTTCTAAAAG
*
2787276 AAACTCAAGAGAAATTCTTGAAAGAA
1 AAACTCAAGAGAATTTCTTGAAAGAA
* *
2787302 AAACTCAATAGAATTTTTTGAAAGAA
1 AAACTCAAGAGAATTTCTTGAAAGAA
2787328 AAACTCAAAGAGAATTT
1 AAACTC-AAGAGAATTT
2787345 AATAACTCAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
26 29 0.76
27 9 0.24
ACGTcount: A:0.52, C:0.10, G:0.13, T:0.25
Consensus pattern (26 bp):
AAACTCAAGAGAATTTCTTGAAAGAA
Found at i:2796797 original size:17 final size:17
Alignment explanation
Indices: 2796775--2796807 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
2796765 TACTAAAAAT
2796775 ATAATTT-TATTATTTAA
1 ATAATTTATATT-TTTAA
2796792 ATAATTTATATTTTTA
1 ATAATTTATATTTTTA
2796808 TAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
ATAATTTATATTTTTAA
Found at i:2804079 original size:14 final size:14
Alignment explanation
Indices: 2804060--2804090 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2804050 ATCACACAAT
2804060 ACTCAATTTTCATC
1 ACTCAATTTTCATC
2804074 ACTCAATTTTCATC
1 ACTCAATTTTCATC
2804088 ACT
1 ACT
2804091 TGCTATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.42
Consensus pattern (14 bp):
ACTCAATTTTCATC
Found at i:2804394 original size:25 final size:25
Alignment explanation
Indices: 2804366--2804473 Score: 117
Period size: 25 Copynumber: 4.3 Consensus size: 25
2804356 GTACTAAACG
**
2804366 GAGAGCACCATTGTGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
2804391 GAGAGCACCAACGTGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
**** *
2804416 GAGAGCATTGGCGTACTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
** *
2804441 GAGAGCACTGACATGCTAATAATCA
1 GAGAGCACCAACGTGCTAATAATCA
*
2804466 GAAAGCAC
1 GAGAGCAC
2804474 GCTAAAGTTT
Statistics
Matches: 71, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 71 1.00
ACGTcount: A:0.39, C:0.20, G:0.21, T:0.19
Consensus pattern (25 bp):
GAGAGCACCAACGTGCTAATAATCA
Found at i:2805357 original size:26 final size:26
Alignment explanation
Indices: 2805328--2805385 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
2805318 GAAATCCCAA
2805328 GTTTTCTTT-CTTTCCTTCCCC-TTTTC
1 GTTTTCTTTCCTTT-C-TCCCCGTTTTC
2805354 GTTTTCTTTCCTTTCTCCCCTGTTTTC
1 GTTTTCTTTCCTTTCTCCCC-GTTTTC
2805381 GTTTT
1 GTTTT
2805386 GCTTCTCTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
25 5 0.17
26 10 0.34
27 14 0.48
ACGTcount: A:0.00, C:0.31, G:0.07, T:0.62
Consensus pattern (26 bp):
GTTTTCTTTCCTTTCTCCCCGTTTTC
Found at i:2807810 original size:20 final size:20
Alignment explanation
Indices: 2807786--2807836 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
2807776 AATTTTTTTT
2807786 TATAATTTTTTATTTTAAAAA
1 TATAATTTTTTA-TTTAAAAA
*
2807807 -ATAAGATTTTTATTTAAAAA
1 TATAA-TTTTTTATTTAAAAA
2807827 TATAATTTTT
1 TATAATTTTT
2807837 ATGTTTTATG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATAATTTTTTATTTAAAAA
Found at i:2807827 original size:19 final size:20
Alignment explanation
Indices: 2807786--2807838 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
2807776 AATTTTTTTT
2807786 TATAATTTTTTATTTTAAAAAA
1 TATAA-TTTTTA-TTTAAAAAA
2807808 TA-AGATTTTTATTT-AAAAA
1 TATA-ATTTTTATTTAAAAAA
2807827 TATAATTTTTAT
1 TATAATTTTTAT
2807839 GTTTTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 15 0.52
20 4 0.14
21 7 0.24
22 3 0.10
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (20 bp):
TATAATTTTTATTTAAAAAA
Found at i:2808058 original size:15 final size:15
Alignment explanation
Indices: 2808038--2808145 Score: 78
Period size: 15 Copynumber: 7.2 Consensus size: 15
2808028 TTTATGGAAA
*
2808038 ATCAAAGATATGGGT
1 ATCAAATATATGGGT
* **
2808053 ATCAAATA-ATAGAA
1 ATCAAATATATGGGT
*
2808067 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
2808083 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
*
2808097 AGTCAAAGATATGGGT
1 A-TCAAATATATGGGT
**
2808113 ATCAAATAT-TGGAA
1 ATCAAATATATGGGT
2808127 AGTCAAATATATGGGT
1 A-TCAAATATATGGGT
2808143 ATC
1 ATC
2808146 GAGATATTGG
Statistics
Matches: 68, Mismatches: 19, Indels: 12
0.69 0.19 0.12
Matches are distributed among these distances:
14 12 0.18
15 44 0.65
16 12 0.18
ACGTcount: A:0.44, C:0.07, G:0.21, T:0.27
Consensus pattern (15 bp):
ATCAAATATATGGGT
Found at i:2808075 original size:30 final size:30
Alignment explanation
Indices: 2808032--2808155 Score: 194
Period size: 30 Copynumber: 4.1 Consensus size: 30
2808022 TCCATATTTA
* *
2808032 TGGAAAATCAAAGATATGGGTATCAAATAA
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
*
2808062 TAGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
2808092 TGGAAAGTCAAAGATATGGGTATCAAATAT
1 TGGAAAGTCAAAGATATGGGTATCAAATAT
* *
2808122 TGGAAAGTCAAATATATGGGTATCGAGATAT
1 TGGAAAGTCAAAGATATGGGTATC-AAATAT
2808153 TGG
1 TGG
2808156 CATAATAAAA
Statistics
Matches: 87, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
30 79 0.91
31 8 0.09
ACGTcount: A:0.44, C:0.06, G:0.23, T:0.27
Consensus pattern (30 bp):
TGGAAAGTCAAAGATATGGGTATCAAATAT
Found at i:2812076 original size:15 final size:15
Alignment explanation
Indices: 2812056--2812133 Score: 61
Period size: 15 Copynumber: 5.2 Consensus size: 15
2812046 TTTATGGAAA
2812056 ATCAAAGATATGGGT
1 ATCAAAGATATGGGT
* * **
2812071 ATCAAATA-ATAGAA
1 ATCAAAGATATGGGT
2812085 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
* **
2812101 ATCAAATAT-TGGAA
1 ATCAAAGATATGGGT
2812115 AGTCAAAGATATGGGT
1 A-TCAAAGATATGGGT
2812131 ATC
1 ATC
2812134 GAGATATTGG
Statistics
Matches: 45, Mismatches: 14, Indels: 8
0.67 0.21 0.12
Matches are distributed among these distances:
14 8 0.18
15 29 0.64
16 8 0.18
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (15 bp):
ATCAAAGATATGGGT
Found at i:2812093 original size:30 final size:30
Alignment explanation
Indices: 2812052--2812133 Score: 137
Period size: 30 Copynumber: 2.7 Consensus size: 30
2812042 CATATTTATG
*
2812052 GAAAATCAAAGATATGGGTATCAAATAATA
1 GAAAGTCAAAGATATGGGTATCAAATAATA
* *
2812082 GAAAGTCAAAGATATGGGTATCAAATATTG
1 GAAAGTCAAAGATATGGGTATCAAATAATA
2812112 GAAAGTCAAAGATATGGGTATC
1 GAAAGTCAAAGATATGGGTATC
2812134 GAGATATTGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 49 1.00
ACGTcount: A:0.46, C:0.07, G:0.22, T:0.24
Consensus pattern (30 bp):
GAAAGTCAAAGATATGGGTATCAAATAATA
Found at i:2813119 original size:20 final size:20
Alignment explanation
Indices: 2813083--2813120 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2813073 AAATTATAAC
*
2813083 AATATTTATATTAATTTATT
1 AATATTTATAATAATTTATT
2813103 AATATTTTATAAT-ATTTA
1 AATA-TTTATAATAATTTA
2813121 AAATTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 9 0.56
21 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AATATTTATAATAATTTATT
Found at i:2817753 original size:6 final size:6
Alignment explanation
Indices: 2817742--2817766 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2817732 TGGTGAATGA
2817742 GAGAGG GAGAGG GAGAGG GAGAGG G
1 GAGAGG GAGAGG GAGAGG GAGAGG G
2817767 GCTTATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GAGAGG
Found at i:2820231 original size:7 final size:7
Alignment explanation
Indices: 2820219--2820246 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
2820209 ATCTTGGCAC
2820219 TCCTAAG
1 TCCTAAG
2820226 TCCTAAG
1 TCCTAAG
2820233 TCCTAAG
1 TCCTAAG
2820240 TCCTAAG
1 TCCTAAG
2820247 GAAATAATGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
TCCTAAG
Found at i:2831644 original size:6 final size:6
Alignment explanation
Indices: 2831571--2831624 Score: 81
Period size: 6 Copynumber: 8.8 Consensus size: 6
2831561 ATAAGAAAAA
* *
2831571 AAAAGT GAAAGT AAAAGT AAAAGT GAAAGT AAAAAGT AAAAGT AAAAGT
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT -AAAAGT AAAAGT AAAAGT
2831620 AAAAG
1 AAAAG
2831625 AAGAAAAAAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
6 38 0.88
7 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.20, T:0.15
Consensus pattern (6 bp):
AAAAGT
Found at i:2831650 original size:12 final size:12
Alignment explanation
Indices: 2831566--2831650 Score: 55
Period size: 12 Copynumber: 6.8 Consensus size: 12
2831556 AACAAATAAG
*
2831566 AAAAAAAAAGTG
1 AAAAAAAAAGTA
**
2831578 AAAGTAAAAGTA
1 AAAAAAAAAGTA
***
2831590 AAAGTGAAAGTA
1 AAAAAAAAAGTA
*
2831602 AAAAGTAAAAGTA
1 AAAA-AAAAAGTA
2831615 AAAGTAAAAGAAG-A
1 AAA--AAAA-AAGTA
2831629 AAAAACAAAAGTA
1 AAAAA-AAAAGTA
2831642 AAAAAAAAA
1 AAAAAAAAA
2831651 TTGATGCAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
12 32 0.53
13 18 0.30
14 6 0.10
15 4 0.07
ACGTcount: A:0.73, C:0.01, G:0.15, T:0.11
Consensus pattern (12 bp):
AAAAAAAAAGTA
Found at i:2832199 original size:27 final size:27
Alignment explanation
Indices: 2832147--2832197 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
2832137 GGAGATGGGT
2832147 AAAAACAAAGAATAAAATAAAGAAATA
1 AAAAACAAAGAATAAAATAAAGAAATA
*
2832174 AAAAATAAAGAA-AAAGA-AAAGAAA
1 AAAAACAAAGAATAAA-ATAAAGAAA
2832198 ATGATATGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.80, C:0.02, G:0.10, T:0.08
Consensus pattern (27 bp):
AAAAACAAAGAATAAAATAAAGAAATA
Found at i:2848676 original size:21 final size:21
Alignment explanation
Indices: 2848650--2848690 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2848640 ATCTGCTCAA
* *
2848650 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
2848671 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
2848691 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:2851768 original size:13 final size:13
Alignment explanation
Indices: 2851746--2851779 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
2851736 TCTTCATACT
*
2851746 TTTTAAATATGTA
1 TTTTATATATGTA
2851759 TTTTATATATGTA
1 TTTTATATATGTA
2851772 TTTTATAT
1 TTTTATAT
2851780 GTATATGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (13 bp):
TTTTATATATGTA
Found at i:2866490 original size:28 final size:29
Alignment explanation
Indices: 2866430--2866509 Score: 101
Period size: 28 Copynumber: 2.8 Consensus size: 29
2866420 CTACACCATA
*
2866430 GGTCACTCAACTATTGATTTTTTTAATTT
1 GGTCACCCAACTATTGATTTTTTTAATTT
*
2866459 GGTCACCCAACTATTGGTCTTTTTT-A-TT
1 GGTCACCCAACTATTGAT-TTTTTTAATTT
**
2866487 GGTCACCCAACTATCAATTTTTT
1 GGTCACCCAACTATTGATTTTTT
2866510 AGTTTGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
27 5 0.11
28 17 0.38
29 17 0.38
30 6 0.13
ACGTcount: A:0.23, C:0.20, G:0.11, T:0.46
Consensus pattern (29 bp):
GGTCACCCAACTATTGATTTTTTTAATTT
Found at i:2870429 original size:24 final size:24
Alignment explanation
Indices: 2870402--2870453 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2870392 TTAGTAAGTC
*
2870402 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2870426 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2870450 AAAT
1 AAAT
2870454 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2871825 original size:24 final size:24
Alignment explanation
Indices: 2871798--2871849 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
2871788 TTAGTAAGTC
*
2871798 AAATAAACTATACTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2871822 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2871846 AAAT
1 AAAT
2871850 CTTCTAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.56, C:0.10, G:0.02, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:2872208 original size:3 final size:3
Alignment explanation
Indices: 2872200--2872266 Score: 134
Period size: 3 Copynumber: 22.3 Consensus size: 3
2872190 GCAATGCCTC
2872200 TTA TTA TTA TTA 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
2872248 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
2872267 CATCATCATC
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2883567 original size:13 final size:13
Alignment explanation
Indices: 2883549--2883575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2883539 GCAATCAAGA
2883549 ACTGGCCCTTAAT
1 ACTGGCCCTTAAT
2883562 ACTGGCCCTTAAT
1 ACTGGCCCTTAAT
2883575 A
1 A
2883576 TTCTTTCTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.30, G:0.15, T:0.30
Consensus pattern (13 bp):
ACTGGCCCTTAAT
Found at i:2884325 original size:14 final size:14
Alignment explanation
Indices: 2884306--2884335 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2884296 TGGTACATGC
2884306 AATGCAAACAGAGA
1 AATGCAAACAGAGA
2884320 AATGCAAACAGAGA
1 AATGCAAACAGAGA
2884334 AA
1 AA
2884336 GTCATATAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.60, C:0.13, G:0.20, T:0.07
Consensus pattern (14 bp):
AATGCAAACAGAGA
Found at i:2885057 original size:25 final size:26
Alignment explanation
Indices: 2885014--2885062 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
2885004 AACTCTTTTT
* * *
2885014 AAAAGAATAATTTAGATTA-AAAAGA
1 AAAAGAAAAATTAAAATTATAAAAGA
2885039 AAAAGAAAAATTAAAATTATAAAA
1 AAAAGAAAAATTAAAATTATAAAA
2885063 ATTGTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (26 bp):
AAAAGAAAAATTAAAATTATAAAAGA
Found at i:2889674 original size:98 final size:98
Alignment explanation
Indices: 2889555--2889812 Score: 471
Period size: 98 Copynumber: 2.6 Consensus size: 98
2889545 TTTGAGTACT
*
2889555 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2889620 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
*
2889653 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
2889718 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* * *
2889751 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAA
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAA
2889813 AGTGATAAGT
Statistics
Matches: 154, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
98 154 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGTGACAAGTG
GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:2889684 original size:46 final size:46
Alignment explanation
Indices: 2889621--2889860 Score: 264
Period size: 46 Copynumber: 5.3 Consensus size: 46
2889611 TGACAAGTGG
* * * *
2889621 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
* *
2889667 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTAATCAAGTGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
* * *
2889713 AAGTGGAAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGAGAC
1 ------AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
*
2889765 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
*
2889811 AAAGTGATAA--G-T-G-----GCTACACTTATCTGATCAAGAAAC
1 AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
2889848 AAAGTGATAAGTG
1 AAAGTGATAAGTG
2889861 GCTACACTTA
Statistics
Matches: 172, Mismatches: 14, Indels: 23
0.82 0.07 0.11
Matches are distributed among these distances:
37 33 0.19
39 1 0.01
42 1 0.01
43 1 0.01
44 1 0.01
46 94 0.55
52 41 0.24
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (46 bp):
AAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGAC
Found at i:2889831 original size:37 final size:37
Alignment explanation
Indices: 2889787--2889895 Score: 186
Period size: 37 Copynumber: 3.0 Consensus size: 37
2889777 GATAGCTTTA
2889787 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
2889824 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
*
2889861 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
2889896 ATCATACGTA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
35 12 0.17
36 4 0.06
37 53 0.77
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
Found at i:2895724 original size:29 final size:30
Alignment explanation
Indices: 2895678--2895766 Score: 76
Period size: 29 Copynumber: 2.9 Consensus size: 30
2895668 AAATATATAT
*
2895678 TTTTTATACTTTT-TAAATAATTTTAATG-A
1 TTTTTA-ACTTTTAAAAATAATTTTAATGAA
*
2895707 TTTTTAACTTTTAAAAATAACTTTT-TTGAA
1 TTTTTAACTTTTAAAAATAA-TTTTAATGAA
* * *
2895737 TTTTTAAAATTTGTAAAAATCATTTAAATG
1 TTTTT-AACTTT-TAAAAATAATTTTAATG
2895767 CTGATGTGTC
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
28 6 0.12
29 14 0.29
30 10 0.21
31 8 0.17
32 10 0.21
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTTAACTTTTAAAAATAATTTTAATGAA
Found at i:2899525 original size:27 final size:29
Alignment explanation
Indices: 2899447--2899525 Score: 74
Period size: 33 Copynumber: 2.6 Consensus size: 29
2899437 CTGCAACGAT
*
2899447 ACCACTACCATCATCATCTGCACCAGTACCA
1 ACCA-TACCATCATCATCAGCACCA-TACCA
2899478 ACACAATCACCATCA-CGATCAGCACC-TA-CA
1 AC-C-AT-ACCATCATC-ATCAGCACCATACCA
2899508 ACCATACCATCATCATCA
1 ACCATACCATCATCATCA
2899526 TCATCTGCAA
Statistics
Matches: 42, Mismatches: 1, Indels: 14
0.74 0.02 0.25
Matches are distributed among these distances:
27 11 0.26
28 3 0.07
29 1 0.02
30 4 0.10
31 4 0.10
32 3 0.07
33 16 0.38
ACGTcount: A:0.37, C:0.41, G:0.05, T:0.18
Consensus pattern (29 bp):
ACCATACCATCATCATCAGCACCATACCA
Found at i:2899594 original size:36 final size:36
Alignment explanation
Indices: 2899522--2899597 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
2899512 TACCATCATC
* * *
2899522 ATCATCATCTGCAACAACAACATCAACATCATCACA
1 ATCATCATCTACAACAACAACACCAACATCAACACA
* *
2899558 ATCATCATCTACAACAGCAACACCATC-TCCAACACA
1 ATCATCATCTACAACAACAACACCAACAT-CAACACA
2899594 ATCA
1 ATCA
2899598 GCGGCTACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 33 0.97
ACGTcount: A:0.43, C:0.36, G:0.03, T:0.18
Consensus pattern (36 bp):
ATCATCATCTACAACAACAACACCAACATCAACACA
Found at i:2900104 original size:93 final size:93
Alignment explanation
Indices: 2899714--2900093 Score: 742
Period size: 93 Copynumber: 4.1 Consensus size: 93
2899704 CACCACCAGA
*
2899714 ACCAACACAATCAGCAACAACAGTAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
2899779 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
2899807 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
2899872 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
2899900 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
2899965 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
2899993 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
2900058 CACCATCATCGTCATCGTCGGTAGCAAC
66 CACCATCATCGTCATCGTCGGTAGCAAC
*
2900086 ACCGACAC
1 ACCAACAC
2900094 CGACACCAAC
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 285 1.00
ACGTcount: A:0.38, C:0.32, G:0.14, T:0.16
Consensus pattern (93 bp):
ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
CACCATCATCGTCATCGTCGGTAGCAAC
Found at i:2900163 original size:186 final size:182
Alignment explanation
Indices: 2899714--2900139 Score: 590
Period size: 186 Copynumber: 2.3 Consensus size: 182
2899704 CACCACCAGA
* * * * * * *
2899714 ACCAACACAATCAGCAACAACAGTAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACAC-A-CAGCAACAACA-CA-AGCCAACACAATCATCATCACAAATAACAACTACGACAC
2899779 CACCATCATCGTCATCGTCGGTAGCAACACCAACACAATCAGCAACAACAGAAGTGCCAGCACAA
62 CACCATCATCGTCATCGTCGGTAGCAACACCAACACAATCAGCAACAACAGAAGTGCCAGCACAA
2899844 TCATCATCACAAATAGCATCTACGATAGCACCATCATCGTCATCGTCGGTAGCAAC
127 TCATCATCACAAATAGCATCTACGATAGCACCATCATCGTCATCGTCGGTAGCAAC
* * * * * *
2899900 ACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCATCATCACAAATAGCATCTACGATAG
1 ACCAACAC-A-CAGCAACAACACAA--GCCAACACAATCATCATCACAAATAACAACTACGACAC
2899965 CACCATCATCGTCATCGTCGGTAGCAACACCAACACAATCAGCAACAACAGAAGTGCCAGCACAA
62 CACCATCATCGTCATCGTCGGTAGCAACACCAACACAATCAGCAACAACAGAAGTGCCAGCACAA
2900030 TCATCATCACAAATAGCATCTACGATAGCACCATCATCGTCATCGTCGGTAGCAAC
127 TCATCATCACAAATAGCATCTACGATAGCACCATCATCGTCATCGTCGGTAGCAAC
* * *
2900086 ACCGACAC-C-GACACCAACACCA-CCAACACAATCATCATCAC-AATCAACAACTAC
1 ACCAACACACAG-CAACAACACAAGCCAACACAATCATCATCACAAAT-AACAACTAC
2900140 AGCGACACCA
Statistics
Matches: 227, Mismatches: 9, Indels: 14
0.91 0.04 0.06
Matches are distributed among these distances:
179 3 0.01
180 25 0.11
182 1 0.00
183 9 0.04
185 1 0.00
186 188 0.83
ACGTcount: A:0.39, C:0.33, G:0.13, T:0.15
Consensus pattern (182 bp):
ACCAACACACAGCAACAACACAAGCCAACACAATCATCATCACAAATAACAACTACGACACCACC
ATCATCGTCATCGTCGGTAGCAACACCAACACAATCAGCAACAACAGAAGTGCCAGCACAATCAT
CATCACAAATAGCATCTACGATAGCACCATCATCGTCATCGTCGGTAGCAAC
Found at i:2903277 original size:60 final size:59
Alignment explanation
Indices: 2903164--2903293 Score: 154
Period size: 60 Copynumber: 2.2 Consensus size: 59
2903154 TTAATATAAC
* * * * * *
2903164 ATTTGGTACTTGAATTTGACACTTTTTTTTTTAATTTGGTACCTAAATTTTTTTTTATCTAA
1 ATTTGATACTTGAACTTGACAC-TATTTTTCTAATCTAGTACCTAAATTTTTTTTT-TC-AA
* *
2903226 TTTTGATACTTGAACTTGACAC-ATTTTTCTAATCTAGTACCTAAGTTTTTTTTTTCAA
1 ATTTGATACTTGAACTTGACACTATTTTTCTAATCTAGTACCTAAATTTTTTTTTTCAA
2903284 ATTTGATACT
1 ATTTGATACT
2903294 AAACTTGTCA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
58 11 0.19
59 2 0.03
60 27 0.46
62 19 0.32
ACGTcount: A:0.25, C:0.12, G:0.09, T:0.53
Consensus pattern (59 bp):
ATTTGATACTTGAACTTGACACTATTTTTCTAATCTAGTACCTAAATTTTTTTTTTCAA
Found at i:2903921 original size:32 final size:32
Alignment explanation
Indices: 2903871--2903939 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 32
2903861 TTGGACTAAA
** * *
2903871 TAAGTTTAGATATTAAATT-AAGAAAAAATTGT
1 TAAGTTTAGATACCAAATTGAAAAAAAAAAT-T
2903903 TAAGTTTAGATACCAAATTGAAAAAAAAAATT
1 TAAGTTTAGATACCAAATTGAAAAAAAAAATT
2903935 TAAGT
1 TAAGT
2903940 ACCAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 23 0.72
33 9 0.28
ACGTcount: A:0.52, C:0.03, G:0.12, T:0.33
Consensus pattern (32 bp):
TAAGTTTAGATACCAAATTGAAAAAAAAAATT
Found at i:2908754 original size:18 final size:19
Alignment explanation
Indices: 2908728--2908763 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
2908718 TTGTTTCATA
2908728 CAAAATTACA-TTAAAAAT
1 CAAAATTACACTTAAAAAT
*
2908746 CAAATTTACACTTAAAAA
1 CAAAATTACACTTAAAAA
2908764 AAACTTTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.28
Consensus pattern (19 bp):
CAAAATTACACTTAAAAAT
Found at i:2909153 original size:6 final size:6
Alignment explanation
Indices: 2909142--2909173 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
2909132 CATTTTATAT
2909142 CAATCA CAATCA CAATCA CAATCA CAATCA CA
1 CAATCA CAATCA CAATCA CAATCA CAATCA CA
2909174 TTTTTTATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.50, C:0.34, G:0.00, T:0.16
Consensus pattern (6 bp):
CAATCA
Found at i:2911286 original size:15 final size:15
Alignment explanation
Indices: 2911268--2911300 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
2911258 TAATCTTTAA
2911268 AAATTA-TAAAAATAT
1 AAATTATTAAAAAT-T
2911283 AAATTATTAAAAATT
1 AAATTATTAAAAATT
2911298 AAA
1 AAA
2911301 ATTTCATTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATTATTAAAAATT
Found at i:2917896 original size:6 final size:6
Alignment explanation
Indices: 2917887--2917916 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
2917877 ACAAAACAAT
2917887 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
1 GAGAAA GAGAAA GAGAAA GAGAAA GAGAAA
2917917 CGTGAAGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (6 bp):
GAGAAA
Found at i:2918407 original size:23 final size:20
Alignment explanation
Indices: 2918369--2918411 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
2918359 TAAGTCGATA
2918369 ATAAAAATTTATATTAATTTT
1 ATAAAAATTTATATT-ATTTT
2918390 ATAAAATATATTATATTATTTT
1 ATAAAA-AT-TTATATTATTTT
2918412 GATCATATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATAAAAATTTATATTATTTT
Found at i:2918425 original size:22 final size:20
Alignment explanation
Indices: 2918400--2918446 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 20
2918390 ATAAAATATA
2918400 TTATAT-TATTTTGATCATATTT
1 TTATATGTATTTTG-T-AT-TTT
2918422 TTAT-TGTATTTTGTATTTT
1 TTATATGTATTTTGTATTTT
2918441 TTATAT
1 TTATAT
2918447 AAAAAGTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
19 7 0.30
20 3 0.13
21 2 0.09
22 11 0.48
ACGTcount: A:0.23, C:0.02, G:0.06, T:0.68
Consensus pattern (20 bp):
TTATATGTATTTTGTATTTT
Found at i:2919053 original size:22 final size:22
Alignment explanation
Indices: 2919023--2919065 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2919013 TTATAGAAAA
*
2919023 TTATATTTTACAAATATTTTTT
1 TTATATTTTAAAAATATTTTTT
*
2919045 TTATTTTTTAAAAATATTTTT
1 TTATATTTTAAAAATATTTTT
2919066 ATATAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (22 bp):
TTATATTTTAAAAATATTTTTT
Found at i:2921136 original size:9 final size:9
Alignment explanation
Indices: 2921122--2921153 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
2921112 ATTATTTATT
2921122 AAAATAATA
1 AAAATAATA
2921131 AAAATAATA
1 AAAATAATA
2921140 AAAATAATA
1 AAAATAATA
2921149 AAAAT
1 AAAAT
2921154 TTAGACTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
AAAATAATA
Found at i:2922552 original size:18 final size:18
Alignment explanation
Indices: 2922525--2922561 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
2922515 ATATTCTATT
*
2922525 AATTTAAACTTAAATTTA
1 AATTTAAACTCAAATTTA
*
2922543 AATTTCAACTCAAATTTA
1 AATTTAAACTCAAATTTA
2922561 A
1 A
2922562 TGTTAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.41
Consensus pattern (18 bp):
AATTTAAACTCAAATTTA
Found at i:2947261 original size:2 final size:2
Alignment explanation
Indices: 2947256--2947288 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2947246 TTTTTTTTTT
*
2947256 TG TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2947289 TGGGTTCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2954129 original size:18 final size:17
Alignment explanation
Indices: 2954075--2954130 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
2954065 GGAGAAGCAG
2954075 AAGAGAATGGAAAATAA
1 AAGAGAATGGAAAATAA
* * *
2954092 AGAAAAAAAGGAAAAT-A
1 A-AGAGAATGGAAAATAA
2954109 AAGAGAATGGAAAATTAA
1 AAGAGAATGGAAAA-TAA
2954127 AAGA
1 AAGA
2954131 ACATAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
16 10 0.33
17 4 0.13
18 16 0.53
ACGTcount: A:0.68, C:0.00, G:0.21, T:0.11
Consensus pattern (17 bp):
AAGAGAATGGAAAATAA
Found at i:2955669 original size:27 final size:27
Alignment explanation
Indices: 2955639--2955690 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
2955629 GGCCAATCAC
2955639 ATTGGCGGCACCAAAGGCGCCAAAGAG
1 ATTGGCGGCACCAAAGGCGCCAAAGAG
* *
2955666 ATTGGCGGCACCAATGGTGCCAAAG
1 ATTGGCGGCACCAAAGGCGCCAAAG
2955691 GACTAAAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.33, T:0.12
Consensus pattern (27 bp):
ATTGGCGGCACCAAAGGCGCCAAAGAG
Found at i:2956251 original size:19 final size:19
Alignment explanation
Indices: 2956227--2956285 Score: 84
Period size: 19 Copynumber: 3.2 Consensus size: 19
2956217 TCTAATTAAG
2956227 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
* * *
2956246 TAATAA-ACTATTCTCATT
1 TAATAACTCTATTTTAATT
2956264 TAATAACTCTATTTTAATT
1 TAATAACTCTATTTTAATT
2956283 TAA
1 TAA
2956286 ATATTGGCTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (19 bp):
TAATAACTCTATTTTAATT
Found at i:2963977 original size:11 final size:11
Alignment explanation
Indices: 2963961--2963986 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2963951 CTCTTATAGT
2963961 AAAATATTTTA
1 AAAATATTTTA
2963972 AAAATATTTTA
1 AAAATATTTTA
2963983 AAAA
1 AAAA
2963987 AACACATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAATATTTTA
Found at i:2967397 original size:37 final size:37
Alignment explanation
Indices: 2967347--2967421 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
2967337 AAAAAATGAA
2967347 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
1 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
2967384 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
1 TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
2967421 T
1 T
2967422 ACATGAAGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.11, G:0.24, T:0.33
Consensus pattern (37 bp):
TGAAAAATTGACCTGATAAGTGGTGTCGAATTTATCG
Found at i:2972113 original size:22 final size:22
Alignment explanation
Indices: 2972079--2972127 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
2972069 TCTAAGCAAT
*
2972079 AATAATAAGAAAA-TAAAAACAA
1 AATAATAAAAAAAGTAAAAA-AA
*
2972101 AATATTAAAAAAAGTAAAAAAA
1 AATAATAAAAAAAGTAAAAAAA
2972123 AATAA
1 AATAA
2972128 ATACATTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (22 bp):
AATAATAAAAAAAGTAAAAAAA
Found at i:2972747 original size:36 final size:38
Alignment explanation
Indices: 2972707--2972797 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 38
2972697 TTAATTAATT
2972707 TTTAAAAATT-TT-AAATATATAAAAAT-TATTTTA-AAA
1 TTTAAAAATTATTAAAAT-TATAAAAATAT-TTTTATAAA
*
2972743 TTT-AAAATTATTAAAATTATAAAAATATTTTTATAAT
1 TTTAAAAATTATTAAAATTATAAAAATATTTTTATAAA
2972780 TTTAAAAAGTTAATTAAA
1 TTTAAAAA-TT-ATTAAA
2972798 TTCTGAATGT
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
35 6 0.13
36 19 0.40
37 10 0.21
38 4 0.09
39 2 0.04
40 6 0.13
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (38 bp):
TTTAAAAATTATTAAAATTATAAAAATATTTTTATAAA
Found at i:2972750 original size:28 final size:28
Alignment explanation
Indices: 2972706--2972762 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
2972696 TTTAATTAAT
*
2972706 TTTTAAAAATTTTAAATATATAAAAATTA
1 TTTTAAAAATTTAAAAT-TATAAAAATTA
*
2972735 TTTT-AAAATTTAAAATTATTAAAATTA
1 TTTTAAAAATTTAAAATTATAAAAATTA
2972762 T
1 T
2972763 AAAAATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
27 11 0.42
28 11 0.42
29 4 0.15
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (28 bp):
TTTTAAAAATTTAAAATTATAAAAATTA
Found at i:2972755 original size:21 final size:20
Alignment explanation
Indices: 2972714--2972773 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 20
2972704 ATTTTTAAAA
2972714 ATTTTAAATATATAAAAATT
1 ATTTTAAATATATAAAAATT
*
2972734 ATTTTAAA-AT-TTAAAATT
1 ATTTTAAATATATAAAAATT
*
2972752 A-TTAAAAT-TATAAAAA-T
1 ATTTTAAATATATAAAAATT
2972769 ATTTT
1 ATTTT
2972774 TATAATTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
17 8 0.24
18 15 0.45
19 2 0.06
20 8 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
ATTTTAAATATATAAAAATT
Found at i:2972758 original size:16 final size:17
Alignment explanation
Indices: 2972709--2972771 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
2972699 AATTAATTTT
*
2972709 TAAAAAT-TTTAAATATA
1 TAAAAATATTAAAAT-TA
2972726 TAAAAATTATTTTAAAATT-
1 TAAAAA-TA--TTAAAATTA
*
2972745 TAAAATTATTAAAATTA
1 TAAAAATATTAAAATTA
2972762 TAAAAATATT
1 TAAAAATATT
2972772 TTTATAATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
16 8 0.21
17 15 0.39
18 3 0.08
19 5 0.13
20 1 0.03
21 6 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAAAATATTAAAATTA
Found at i:2972772 original size:27 final size:28
Alignment explanation
Indices: 2972703--2972772 Score: 67
Period size: 27 Copynumber: 2.6 Consensus size: 28
2972693 GTATTTAATT
*
2972703 AATTTTTAAAAAT-TTTAAATATATAAA
1 AATTATTAAAAATATTTAAATATATAAA
** *
2972730 AATTATTTTAAA-ATTTAAA-ATTATTAA
1 AATTATTAAAAATATTTAAATA-TATAAA
2972757 AATTA-TAAAAATATTT
1 AATTATTAAAAATATTT
2972773 TTATAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
26 5 0.15
27 29 0.85
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (28 bp):
AATTATTAAAAATATTTAAATATATAAA
Found at i:2975522 original size:472 final size:472
Alignment explanation
Indices: 2974638--2975572 Score: 1843
Period size: 472 Copynumber: 2.0 Consensus size: 472
2974628 TGAAGCTTAT
2974638 GGGGAAGATCTTCTCAAGTGTTTGGAGAAGGAACTTACAAGTGATTTCGAGGTCAAATTTCGACA
1 GGGGAAGATCTTCTCAAGTGTTTGGAGAAGGAACTTACAAGTGATTTCGAGGTCAAATTTCGACA
2974703 TACATTTTGATGTCTGGCATTGGACATTTTTTTTTTGTAATAGTTTCGAATATTACGTTTTCTTT
66 TACATTTTGATGTCTGGCATTGGACATTTTTTTTTTGTAATAGTTTCGAATATTACGTTTTCTTT
2974768 AACTTACTGAGATTTTTGTTCTGCTTTGACATTCTACAGCGGGCTGTGCTGCTTTTTACGTTGGA
131 AACTTACTGAGATTTTTGTTCTGCTTTGACATTCTACAGCGGGCTGTGCTGCTTTTTACGTTGGA
2974833 CCCTGCAGAGCGAGATGCTCATCTGGCTAATGAAGCTACAAAGAAGTTCACATCAAGCAATTGGA
196 CCCTGCAGAGCGAGATGCTCATCTGGCTAATGAAGCTACAAAGAAGTTCACATCAAGCAATTGGA
2974898 TTCTCATGGAGATAGCTTGCAGTAGGTCTTCGCATGAACTACTCAATGTGAAAAAGGCGTATCAT
261 TTCTCATGGAGATAGCTTGCAGTAGGTCTTCGCATGAACTACTCAATGTGAAAAAGGCGTATCAT
*
2974963 GCTCGTTATAAGAAATCCCTTGAAGAAGATGTTGCTCACCACACTACCGGAGAGTACCGCAAGGT
326 GCTCGTTATAAGAAATCCCTTGAAGAAGATGTCGCTCACCACACTACCGGAGAGTACCGCAAGGT
2975028 TCCGGCTTGACTTTCTTTGCCATGCTTTTATCGTTCTCGAGTTGAATGCCTACATAAGATTTATA
391 TCCGGCTTGACTTTCTTTGCCATGCTTTTATCGTTCTCGAGTTGAATGCCTACATAAGATTTATA
2975093 AAGTGTTTTATTTCACC
456 AAGTGTTTTATTTCACC
2975110 GGGGAAGATCTTCTCAAGTGTTTGGAGAAGGAACTTACAAGTGATTTCGAGGTCAAATTTCGACA
1 GGGGAAGATCTTCTCAAGTGTTTGGAGAAGGAACTTACAAGTGATTTCGAGGTCAAATTTCGACA
2975175 TACATTTTGATGTCTGGCATTGGACATTTTTTTTTTGTAATAGTTTCGAATATTACGTTTTCTTT
66 TACATTTTGATGTCTGGCATTGGACATTTTTTTTTTGTAATAGTTTCGAATATTACGTTTTCTTT
2975240 AACTTACTGAGATTTTTGTTCTGCTTTGACATTCTACAGCGGGCTGTGCTGCTTTTTACGTTGGA
131 AACTTACTGAGATTTTTGTTCTGCTTTGACATTCTACAGCGGGCTGTGCTGCTTTTTACGTTGGA
2975305 CCCTGCAGAGCGAGATGCTCATCTGGCTAATGAAGCTACAAAGAAGTTCACATCAAGCAATTGGA
196 CCCTGCAGAGCGAGATGCTCATCTGGCTAATGAAGCTACAAAGAAGTTCACATCAAGCAATTGGA
2975370 TTCTCATGGAGATAGCTTGCAGTAGGTCTTCGCATGAACTACTCAATGTGAAAAAGGCGTATCAT
261 TTCTCATGGAGATAGCTTGCAGTAGGTCTTCGCATGAACTACTCAATGTGAAAAAGGCGTATCAT
*
2975435 GCTCGTTATAAGAAATCCCTTGAAGAAGATGTCGCTCACCACACTACCGGAGAGTACTGCAAGGT
326 GCTCGTTATAAGAAATCCCTTGAAGAAGATGTCGCTCACCACACTACCGGAGAGTACCGCAAGGT
*
2975500 TCCGGCTTGACTTTCTTTGCCATGCTTTTATCGTTCTTGAGTTGAATGCCTACATAAGATTTATA
391 TCCGGCTTGACTTTCTTTGCCATGCTTTTATCGTTCTCGAGTTGAATGCCTACATAAGATTTATA
2975565 AAGTGTTT
456 AAGTGTTT
2975573 GCTTATTTCA
Statistics
Matches: 460, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
472 460 1.00
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.34
Consensus pattern (472 bp):
GGGGAAGATCTTCTCAAGTGTTTGGAGAAGGAACTTACAAGTGATTTCGAGGTCAAATTTCGACA
TACATTTTGATGTCTGGCATTGGACATTTTTTTTTTGTAATAGTTTCGAATATTACGTTTTCTTT
AACTTACTGAGATTTTTGTTCTGCTTTGACATTCTACAGCGGGCTGTGCTGCTTTTTACGTTGGA
CCCTGCAGAGCGAGATGCTCATCTGGCTAATGAAGCTACAAAGAAGTTCACATCAAGCAATTGGA
TTCTCATGGAGATAGCTTGCAGTAGGTCTTCGCATGAACTACTCAATGTGAAAAAGGCGTATCAT
GCTCGTTATAAGAAATCCCTTGAAGAAGATGTCGCTCACCACACTACCGGAGAGTACCGCAAGGT
TCCGGCTTGACTTTCTTTGCCATGCTTTTATCGTTCTCGAGTTGAATGCCTACATAAGATTTATA
AAGTGTTTTATTTCACC
Found at i:2976885 original size:70 final size:70
Alignment explanation
Indices: 2976772--2976911 Score: 280
Period size: 70 Copynumber: 2.0 Consensus size: 70
2976762 AATGTTATTT
2976772 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
1 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
2976837 GAGGA
66 GAGGA
2976842 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
1 GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
2976907 GAGGA
66 GAGGA
2976912 TGAATAGTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
70 70 1.00
ACGTcount: A:0.44, C:0.07, G:0.19, T:0.30
Consensus pattern (70 bp):
GACGGGTTTTTTTACACTAATAAAAGAAATAATTATTAAAATAGAGTGGAAAGCAAATTATTTAC
GAGGA
Found at i:2977194 original size:25 final size:26
Alignment explanation
Indices: 2977164--2977221 Score: 70
Period size: 25 Copynumber: 2.3 Consensus size: 26
2977154 AGCTGTTTTA
*
2977164 ATTTTATAAATT-T-AATTTTTTAAAT
1 ATTTTATAAATTATAAATTCTTT-AAT
2977189 ATTTTAT-AATTATAAATTCTTTAAT
1 ATTTTATAAATTATAAATTCTTTAAT
2977214 A-TTTATAA
1 ATTTTATAA
2977222 TAATGATCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
24 9 0.31
25 13 0.45
26 7 0.24
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
ATTTTATAAATTATAAATTCTTTAAT
Found at i:2977971 original size:76 final size:76
Alignment explanation
Indices: 2977880--2978035 Score: 312
Period size: 76 Copynumber: 2.1 Consensus size: 76
2977870 TTTTCCACCG
2977880 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
1 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
2977945 GATCTAAAATA
66 GATCTAAAATA
2977956 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
1 TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
2978021 GATCTAAAATA
66 GATCTAAAATA
2978032 TATT
1 TATT
2978036 CATGGGGAGG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 80 1.00
ACGTcount: A:0.37, C:0.12, G:0.10, T:0.42
Consensus pattern (76 bp):
TATTTTTATAATTATTTATTTGTATTATTAACGTAAAAGACCCTTATTTGACACATCGGAGCATA
GATCTAAAATA
Found at i:2982364 original size:3 final size:3
Alignment explanation
Indices: 2982356--2982396 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
2982346 AGCATATACG
2982356 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2982397 CAGAAAACGA
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:2988852 original size:25 final size:25
Alignment explanation
Indices: 2988824--2988871 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
2988814 TAAAGTAAGA
*
2988824 TTAATTATAAAAATATTTTTTAAAT
1 TTAATTATAAAAATATATTTTAAAT
2988849 TTAATTATAAAAATATATTTTAA
1 TTAATTATAAAAATATATTTTAA
2988872 TAAAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTAATTATAAAAATATATTTTAAAT
Found at i:3001131 original size:16 final size:17
Alignment explanation
Indices: 3001112--3001150 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
3001102 TATTTTTATT
3001112 AAATTATTA--TATAATA
1 AAATTATTAGTTAT-ATA
3001128 AAATTATTAGTTATATA
1 AAATTATTAGTTATATA
3001145 AAATTA
1 AAATTA
3001151 AATTTATCGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.43
17 9 0.43
18 3 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (17 bp):
AAATTATTAGTTATATA
Found at i:3005785 original size:51 final size:51
Alignment explanation
Indices: 3005721--3005823 Score: 154
Period size: 51 Copynumber: 2.0 Consensus size: 51
3005711 GAAACTCTTT
* * *
3005721 CGGATCCGGTTTCTCGTCAAACGTATGATTATGAATTGG-GCTTGGTTAATC
1 CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAG-TTGGTTAATC
*
3005772 CGGATCCGATTTCTCATCAAATGTATGATTATGAAATGGAGTTGGTTAATC
1 CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAGTTGGTTAATC
3005823 C
1 C
3005824 AATGGGGTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
51 46 0.98
52 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (51 bp):
CGGATCCGATTTCTCATCAAACGTATGATTATGAAATGGAGTTGGTTAATC
Found at i:3037462 original size:44 final size:44
Alignment explanation
Indices: 3037411--3037532 Score: 244
Period size: 44 Copynumber: 2.8 Consensus size: 44
3037401 TACATTGGAT
3037411 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
3037455 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
3037499 GATATTGTCTAATTGTTAATTAGAGTAAATATAC
1 GATATTGTCTAATTGTTAATTAGAGTAAATATAC
3037533 CCACTATTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 78 1.00
ACGTcount: A:0.35, C:0.10, G:0.17, T:0.38
Consensus pattern (44 bp):
GATATTGTCTAATTGTTAATTAGAGTAAATATACTACACTGGGC
Found at i:3049334 original size:24 final size:24
Alignment explanation
Indices: 3049306--3049352 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
3049296 TGTTTCTTAT
3049306 ACAAAGAAAACA-AAAAGAAAATTA
1 ACAAA-AAAACACAAAAGAAAATTA
* *
3049330 ACAAAAAAGCACAAAAGATAATT
1 ACAAAAAAACACAAAAGAAAATT
3049353 TAATGTATCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 15 0.75
ACGTcount: A:0.70, C:0.11, G:0.09, T:0.11
Consensus pattern (24 bp):
ACAAAAAAACACAAAAGAAAATTA
Found at i:3051118 original size:13 final size:13
Alignment explanation
Indices: 3051100--3051126 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3051090 CTCCGAAACA
3051100 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
3051113 TTTTTTTTTCTGT
1 TTTTTTTTTCTGT
3051126 T
1 T
3051127 ACAACCGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (13 bp):
TTTTTTTTTCTGT
Found at i:3058347 original size:66 final size:65
Alignment explanation
Indices: 3058257--3058386 Score: 215
Period size: 66 Copynumber: 2.0 Consensus size: 65
3058247 CTAAAGTTTC
* *
3058257 ACAAAATTACGATTTTGCCTCTAGGCTCAGAAATTAAACTTTATTCCTTTTTTCTTATGTTTTAT
1 ACAAAATTACGATTTTGCCCCTAGGCTCAGAAATTAAACTTTA-TCCCTTTTTCTTATGTTTTAT
3058322 A
65 A
* *
3058323 ACAAAATTATGATTTTTCCCCTAGGCTCAGAAATTAAACTTTATCCCTTTTTCTTATGTTTTAT
1 ACAAAATTACGATTTTGCCCCTAGGCTCAGAAATTAAACTTTATCCCTTTTTCTTATGTTTTAT
3058387 GACATGCTGA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
65 20 0.33
66 40 0.67
ACGTcount: A:0.28, C:0.18, G:0.08, T:0.45
Consensus pattern (65 bp):
ACAAAATTACGATTTTGCCCCTAGGCTCAGAAATTAAACTTTATCCCTTTTTCTTATGTTTTATA
Found at i:3069222 original size:2 final size:2
Alignment explanation
Indices: 3069215--3069241 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3069205 GCATACTAAA
3069215 AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
3069242 ATACATAGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3080129 original size:20 final size:20
Alignment explanation
Indices: 3080106--3080143 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3080096 TTCTTTCTTT
3080106 CTTTTCTTTTTT-TTTTTCCC
1 CTTTT-TTTTTTGTTTTTCCC
3080126 CTTTTTTTTTTGTTTTTC
1 CTTTTTTTTTTGTTTTTC
3080144 AGTTTTTGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (20 bp):
CTTTTTTTTTTGTTTTTCCC
Found at i:3102307 original size:6 final size:6
Alignment explanation
Indices: 3102296--3102336 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
3102286 GAAAATTGGA
3102296 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
1 AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAGG AAAAG
3102337 AAGTTGTGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (6 bp):
AAAAGG
Found at i:3102844 original size:2 final size:2
Alignment explanation
Indices: 3102837--3102876 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
3102827 CTATTATCTT
3102837 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
3102877 CCTCCCCTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3111150 original size:18 final size:17
Alignment explanation
Indices: 3111114--3111166 Score: 67
Period size: 18 Copynumber: 3.2 Consensus size: 17
3111104 TATTTGATAT
3111114 ATTATTT-A-AAATT-A
1 ATTATTTGATAAATTAA
3111128 ATTATTTGATATAATTAA
1 ATTATTTGATA-AATTAA
3111146 ATTATTTGATAAATATAA
1 ATTATTTGATAAAT-TAA
3111164 ATT
1 ATT
3111167 TTAAATTCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.21
15 1 0.03
16 1 0.03
17 7 0.21
18 18 0.53
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
ATTATTTGATAAATTAA
Found at i:3120733 original size:20 final size:20
Alignment explanation
Indices: 3120672--3120745 Score: 66
Period size: 20 Copynumber: 3.7 Consensus size: 20
3120662 GTCACCATTT
3120672 AATTCATTTTAAAA-A-AAAA
1 AATT-ATTTTAAAATACAAAA
* *
3120691 AATATTTTTTAAAAT-CATTAA
1 AAT-TATTTTAAAATACA-AAA
3120712 AATTATTTTAAAATACAAAA
1 AATTATTTTAAAATACAAAA
3120732 AA-TATTTATAAAAT
1 AATTATTT-TAAAAT
3120746 TTTAAAAAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
19 16 0.36
20 22 0.49
21 7 0.16
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTATTTTAAAATACAAAA
Found at i:3120737 original size:19 final size:19
Alignment explanation
Indices: 3120677--3120745 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 19
3120667 CATTTAATTC
3120677 ATTTTAAAA-A-AAAAAAT
1 ATTTTAAAATACAAAAAAT
*
3120694 ATTTTTTAAAAT-CATTAAAATT
1 A--TTTTAAAATACA--AAAAAT
3120716 ATTTTAAAATACAAAAAAT
1 ATTTTAAAATACAAAAAAT
3120735 ATTTATAAAAT
1 ATTT-TAAAAT
3120746 TTTAAAAAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 13
0.74 0.04 0.23
Matches are distributed among these distances:
17 1 0.02
19 17 0.40
20 16 0.38
21 2 0.05
22 6 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (19 bp):
ATTTTAAAATACAAAAAAT
Found at i:3120752 original size:20 final size:19
Alignment explanation
Indices: 3120697--3120753 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
3120687 AAAAAATATT
*
3120697 TTTTAAAATCATTAAAATTA
1 TTTTAAAAT-ATTAAAAATA
**
3120717 TTTTAAAATACAAAAAATA
1 TTTTAAAATATTAAAAATA
*
3120736 TTTATAAAATTTTAAAAA
1 TTT-TAAAATATTAAAAA
3120754 ATTAATTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTAAAATATTAAAAATA
Found at i:3122541 original size:29 final size:30
Alignment explanation
Indices: 3122506--3122575 Score: 88
Period size: 29 Copynumber: 2.3 Consensus size: 30
3122496 AACGATAACG
*
3122506 TAAGTGACTAAAACGTAACAT-TTCAAACA
1 TAAGTGACTAAAACGTAACATGGTCAAACA
* *
3122535 TAAGTGACTAAAATGTAATATGGGTCAAACA
1 TAAGTGACTAAAACGTAACAT-GGTCAAACA
*
3122566 AAAGTGACTA
1 TAAGTGACTA
3122576 TTTTTTTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 19 0.54
31 16 0.46
ACGTcount: A:0.47, C:0.13, G:0.16, T:0.24
Consensus pattern (30 bp):
TAAGTGACTAAAACGTAACATGGTCAAACA
Found at i:3122879 original size:8 final size:10
Alignment explanation
Indices: 3122857--3122889 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3122847 AACAAATATA
*
3122857 AAAAAATTAT
1 AAAAATTTAT
3122867 AAAAATTT-T
1 AAAAATTTAT
3122876 AAAAATTTAT
1 AAAAATTTAT
3122886 AAAA
1 AAAA
3122890 GAAGTATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (10 bp):
AAAAATTTAT
Found at i:3124441 original size:2 final size:2
Alignment explanation
Indices: 3124434--3124464 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3124424 GCTTCTAAAT
3124434 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 T
3124465 TATAAATAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:3131493 original size:23 final size:24
Alignment explanation
Indices: 3131448--3131493 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
3131438 AGATGTATAC
**
3131448 AAAATAAATAAAAAATATTTTTAT
1 AAAATAAATAAAAAATAACTTTAT
*
3131472 AAAATAAAT-ATAAATAACTTTA
1 AAAATAAATAAAAAATAACTTTA
3131494 AATTTAACTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (24 bp):
AAAATAAATAAAAAATAACTTTAT
Found at i:3132100 original size:28 final size:31
Alignment explanation
Indices: 3132041--3132115 Score: 93
Period size: 28 Copynumber: 2.5 Consensus size: 31
3132031 CCGATTAGTG
*
3132041 ATTTAATATAAATATAAATATATATAATTATT
1 ATTTAACAT-AATATAAATATATATAATTATT
*
3132073 ATTTAACAT-ATATAATTA-ATATAA-TATT
1 ATTTAACATAATATAAATATATATAATTATT
*
3132101 TTTTAACATAATATA
1 ATTTAACATAATATA
3132116 TTTAGGTCGG
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
28 12 0.31
29 11 0.28
30 8 0.21
32 8 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (31 bp):
ATTTAACATAATATAAATATATATAATTATT
Found at i:3135458 original size:36 final size:36
Alignment explanation
Indices: 3135417--3135508 Score: 184
Period size: 36 Copynumber: 2.6 Consensus size: 36
3135407 ATATATATAT
3135417 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
3135453 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
1 ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
3135489 ATTGAAAATAAAAATAAAAA
1 ATTGAAAATAAAAATAAAAA
3135509 AGAATATGTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 56 1.00
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.22
Consensus pattern (36 bp):
ATTGAAAATAAAAATAAAAATAAAAAGAATATGTAA
Found at i:3135463 original size:30 final size:30
Alignment explanation
Indices: 3135427--3135539 Score: 127
Period size: 36 Copynumber: 3.4 Consensus size: 30
3135417 ATTGAAAATA
3135427 AAAATAAAAATAAAAAGAATATGTAAATTG
1 AAAATAAAAATAAAAAGAATATGTAAATTG
3135457 AAAATAAAAATAAAAATAAAAAGAATATGTAAATTG
1 ------AAAATAAAAATAAAAAGAATATGTAAATTG
3135493 AAAATAAAAATAAAAAAGAATATGTAAAAAATTG
1 AAAATAAAAAT-AAAAAGAATATGT---AAATTG
*
3135527 AATATAAAAATAA
1 AAAATAAAAATAA
3135540 CAAATTTAGT
Statistics
Matches: 72, Mismatches: 1, Indels: 11
0.86 0.01 0.13
Matches are distributed among these distances:
30 11 0.15
31 13 0.18
33 2 0.03
34 16 0.22
36 30 0.42
ACGTcount: A:0.70, C:0.00, G:0.08, T:0.22
Consensus pattern (30 bp):
AAAATAAAAATAAAAAGAATATGTAAATTG
Found at i:3135509 original size:7 final size:6
Alignment explanation
Indices: 3135421--3135478 Score: 55
Period size: 6 Copynumber: 9.7 Consensus size: 6
3135411 ATATATATTG
* * * * *
3135421 AAAATA AAAATA AAAATA AAAA-G AATATGT AAATTG AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAAT-A AAAATA AAAATA AAAATA
3135469 AAAATA AAAA
1 AAAATA AAAA
3135479 GAATATGTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
5 3 0.07
6 36 0.86
7 3 0.07
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:3135599 original size:20 final size:21
Alignment explanation
Indices: 3135555--3135600 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
3135545 TTAGTTAAAT
*
3135555 TTAAAAAAAAACTAAATATGT
1 TTAAAAAAAAACTAAATATGG
* *
3135576 TTAAAAATAAA-TAAATTTGG
1 TTAAAAAAAAACTAAATATGG
3135596 TTAAA
1 TTAAA
3135601 TTTTTACAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
TTAAAAAAAAACTAAATATGG
Found at i:3135644 original size:16 final size:17
Alignment explanation
Indices: 3135608--3135655 Score: 62
Period size: 18 Copynumber: 2.8 Consensus size: 17
3135598 AAATTTTTAC
3135608 AAAATTACAAGAAATTGT
1 AAAATTA-AAGAAATTGT
*
3135626 AAAATTAAA-AAATTTT
1 AAAATTAAAGAAATTGT
3135642 AAACATTAAAGAAA
1 AAA-ATTAAAGAAA
3135656 CAAAAATTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 9 0.33
17 8 0.30
18 10 0.37
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAATTAAAGAAATTGT
Done.