Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01007460.1 Kokia drynarioides strain JFW-HI SEQ_122081, whole genome shotgun sequence
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: 612245
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Warning! 56 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:6625 original size:32 final size:32
Alignment explanation
Indices: 6589--6649 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
6579 GCTCTTCTGC
* *
6589 ATTTTTACTTTGTTTTAATTT-TGTCCTTTTTT
1 ATTTTTACTTTATTATAATTTCT-TCCTTTTTT
*
6621 ATTTTTAGTTTATTATAATTTCTTCCTTT
1 ATTTTTACTTTATTATAATTTCTTCCTTT
6650 AATTTTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
32 24 0.96
33 1 0.04
ACGTcount: A:0.16, C:0.10, G:0.05, T:0.69
Consensus pattern (32 bp):
ATTTTTACTTTATTATAATTTCTTCCTTTTTT
Found at i:7153 original size:4 final size:4
Alignment explanation
Indices: 7114--7177 Score: 56
Period size: 4 Copynumber: 15.2 Consensus size: 4
7104 TTATCACTAA
* * *
7114 TATT TTTT TATT TAAT TATGT TATT AATT GTATT TATT TATT TATCT TATT
1 TATT TATT TATT TATT TAT-T TATT TATT -TATT TATT TATT TAT-T TATT
* *
7165 CATG TATT TATT T
1 TATT TATT TATT T
7178 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
4 36 0.77
5 11 0.23
ACGTcount: A:0.25, C:0.03, G:0.05, T:0.67
Consensus pattern (4 bp):
TATT
Found at i:7153 original size:26 final size:25
Alignment explanation
Indices: 7120--7177 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 25
7110 CTAATATTTT
*
7120 TTTATTTAATTATGTTATTAATTGTA
1 TTTATTTAATTATCTTATTAA-TGTA
* *
7146 TTTATTTATTTATCTTATTCATGTA
1 TTTATTTAATTATCTTATTAATGTA
7171 TTTATTT
1 TTTATTT
7178 TTTTTATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 11 0.38
26 18 0.62
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.66
Consensus pattern (25 bp):
TTTATTTAATTATCTTATTAATGTA
Found at i:10297 original size:16 final size:17
Alignment explanation
Indices: 10278--10326 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 17
10268 AAATTTTCAC
10278 TAAAA-AAAAGAGAAAA
1 TAAAAGAAAAGAGAAAA
*
10294 TAAAAGAAAATA-AAAA
1 TAAAAGAAAAGAGAAAA
*
10310 TAAAAGAAAAAAGAAAA
1 TAAAAGAAAAGAGAAAA
10327 AAGAAAAAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 20 0.69
17 9 0.31
ACGTcount: A:0.82, C:0.00, G:0.10, T:0.08
Consensus pattern (17 bp):
TAAAAGAAAAGAGAAAA
Found at i:10323 original size:7 final size:7
Alignment explanation
Indices: 10295--10339 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
10285 AAGAGAAAAT
10295 AAAAGAA
1 AAAAGAA
*
10302 AATAAAAA
1 AA-AAGAA
10310 TAAAAGAA
1 -AAAAGAA
10318 AAAAGAA
1 AAAAGAA
10325 AAAAG-A
1 AAAAGAA
10331 AAAAGAA
1 AAAAGAA
10338 AA
1 AA
10340 GGAGAGGCTG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
6 6 0.18
7 17 0.52
8 8 0.24
9 2 0.06
ACGTcount: A:0.84, C:0.00, G:0.11, T:0.04
Consensus pattern (7 bp):
AAAAGAA
Found at i:11372 original size:50 final size:50
Alignment explanation
Indices: 11303--11541 Score: 245
Period size: 50 Copynumber: 4.8 Consensus size: 50
11293 AAAGTTGTAA
* *
11303 TGGAATAGAGTGAAGCCATAACCCTAAATCCTATATCCTTAAAGTTACAG
1 TGGAATAGAGTGAAACCATAACCCTAAATCCTATATCCTTGAAGTTACAG
*
11353 TGGAATAGAGTGAAACCATAACCCCAAAT-CTATATCCTTGAAGTTACAG
1 TGGAATAGAGTGAAACCATAACCCTAAATCCTATATCCTTGAAGTTACAG
* * * *
11402 TGGAATGGAGTGAAACCACAACCCCAAATCCTATATCCTTGAAGTTATAG
1 TGGAATAGAGTGAAACCATAACCCTAAATCCTATATCCTTGAAGTTACAG
* *** * * *
11452 TGG-ATCAGA-TTATAA-C-TAATAGTAGCATCTCTCAATCTCCCTGAAGTTACAG
1 TGGAAT-AGAGTGA-AACCATAACCCTA-AATC-CT--ATATCCTTGAAGTTACAG
* *
11504 TGGAATGGAGTGAAGCCATAACCCTAAATCCTATATCC
1 TGGAATAGAGTGAAACCATAACCCTAAATCCTATATCC
11542 CTACAATTGC
Statistics
Matches: 153, Mismatches: 25, Indels: 22
0.76 0.12 0.11
Matches are distributed among these distances:
48 3 0.02
49 54 0.35
50 60 0.39
52 23 0.15
53 8 0.05
54 5 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (50 bp):
TGGAATAGAGTGAAACCATAACCCTAAATCCTATATCCTTGAAGTTACAG
Found at i:11527 original size:102 final size:102
Alignment explanation
Indices: 11198--11950 Score: 533
Period size: 102 Copynumber: 7.5 Consensus size: 102
11188 CCTAAAATTA
** * * * *
11198 TAGTGGAATGGAGTGAAGCCACAAGACCAAATCCTGTATCCCCGAA-TTTCAAGTGGATCTGATT
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTAC-AGTGGATCAGATT
** * *
11262 AAAACTAACAGTAATAGATCTCAATCT-CTCTAAAGTTG
65 AAAACTAACAGTAGCAAATCTCAATCTCCT-TGAAGTTG
* * * * * *
11300 TAATGGAATAGAGTGAAGCCATAACCCTAAATCCTATATCCTTAAAGTTACAGTGGAAT-AGAGT
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTACAGTGG-ATCAGA-T
* * ** * *
11364 GAAACCATAAC---CCCAAATCT--ATATCCTTGAAGTTA
64 TAAAAC-TAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
* * * *
11399 CAGTGGAATGGAGTGAAACCACAACCCCAAATCCTATATCCTTGAAGTTATAGTGGATCAGATTA
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTA
* * ** * *
11464 TAACTAATAGTAGCATCTCTCAATCTCCCTGAAGTTA
66 AAACTAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
* * * * * * *
11501 CAGTGGAATGGAGTGAAGCCATAACCCTAAATCCTATATCCCT-ACAATTGCAGTAGATCAAATT
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGA-AGTTACAGTGGATCAGATT
* * *
11565 AAAACTAACAGTAGCAGATCTTAGTCTCCTTGAAGTTG
65 AAAACTAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
* * ** * *
11603 -AGTAGAAT---G-G-A-CCACAACACCAAATCCTATATCCCTGAAGTTGTAATGGATCATATTA
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTA
* *
11661 AAACTAACAGTAACAAATCTCAATCTCCTTTAAGTTG
66 AAACTAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
* * ** ** * * * *
11698 TAATGGAATGGAGTGACGTTACAAGACCAAA-CCTTATAT-CCTTAAGGTTGCAGTAGATCGGAT
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCC-TATATCCCTGAA-GTTACAGTGGATCAGAT
* * * * *
11761 TAAAGCTCACAGTAGCATATCTAAATCTTCTTGAAGTTG
64 TAAAACTAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
** * * *
11800 TAGTGGAATGGAGTGAAGTTACAAACCCAAATCCTATATCCCTGAAGTTACA-TGAATCATATTA
1 TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTA
* **
11864 AAGCT-ACAGTAGCAAATCTTTATCT-CTCTGAAGTTG
66 AAACTAACAGTAGCAAATCTCAATCTCCT-TGAAGTTG
* * * * * * * *
11900 CAGTAGAGT-AAGATGAAGCTACTACACCAAATCCTATACCCCTGAAGTTAC
1 TAGTGGAATGGAG-TGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTAC
11951 GGTGTGTCGA
Statistics
Matches: 514, Mismatches: 111, Indels: 54
0.76 0.16 0.08
Matches are distributed among these distances:
95 69 0.13
96 8 0.02
97 4 0.01
98 7 0.01
99 65 0.13
100 72 0.14
101 33 0.06
102 235 0.46
103 17 0.03
104 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (102 bp):
TAGTGGAATGGAGTGAAGCCACAACCCCAAATCCTATATCCCTGAAGTTACAGTGGATCAGATTA
AAACTAACAGTAGCAAATCTCAATCTCCTTGAAGTTG
Found at i:11738 original size:197 final size:198
Alignment explanation
Indices: 11416--11898 Score: 458
Period size: 197 Copynumber: 2.4 Consensus size: 198
11406 ATGGAGTGAA
* * * * * * **
11416 ACCACAACCCCAAATCCTATATCCTTGAAGTTATAGTGGATCAGATTATAACTAATAGTAGCATC
1 ACCACAACACCAAATCCTATATCCCTGAAGTTATAATGGATCAGATTAAAACTAACAGTAACAAA
* * *
11481 TCTCAATCTCCCTGAAGTTACAGTGGAATGGAGTGAAGCCATAACCCTAAATCCTATATCCCTAC
66 TCTCAATCTCCCTGAAGTTACAATGGAATGGAGTGAAGCCACAAACCTAAATCCTATATCCCTA-
* *
11546 A-ATTGCAGTAGATCAAATTAAAACTAACAGTAGCAGATCTTAGTCTCCTTGAAGTTG-AGTAGA
130 AGATTGCAGTAGATCAAATTAAAACTAACAGTAGCAGATCTAAATCTCCTTGAAGTTGTAGTAGA
11609 ATGG
195 ATGG
* *
11613 ACCACAACACCAAATCCTATATCCCTGAAGTTGTAATGGATCATATTAAAACTAACAGTAACAAA
1 ACCACAACACCAAATCCTATATCCCTGAAGTTATAATGGATCAGATTAAAACTAACAGTAACAAA
* * ** * ** *
11678 TCTCAATCTCCTTTAAGTTGTAATGGAATGGAGTGACGTTACAAGACC-AAA-CCTTATATCCTT
66 TCTCAATCTCCCTGAAGTTACAATGGAATGGAGTGAAGCCACAA-ACCTAAATCC-TATATCCCT
* ** * * * * *
11741 AAGGTTGCAGTAGATCGGATTAAAGCTCACAGTAGCATATCTAAATCTTCTTGAAGTTGTAGTGG
129 AAGATTGCAGTAGATCAAATTAAAACTAACAGTAGCAGATCTAAATCTCCTTGAAGTTGTAGTAG
11806 AATGG
194 AATGG
** * * * *
11811 AGTGA-AGTTACAAACCCAAATCCTATATCCCTGAAGTTA-CATGAATCATATTAAAGCT-ACAG
1 A-CCACA---AC--A-CCAAATCCTATATCCCTGAAGTTATAATGGATCAGATTAAAACTAACAG
* ** *
11873 TAGCAAATCTTTATCTCTCTGAAGTT
59 TAACAAATCTCAATCTCCCTGAAGTT
11899 GCAGTAGAGT
Statistics
Matches: 232, Mismatches: 43, Indels: 17
0.79 0.15 0.06
Matches are distributed among these distances:
196 3 0.01
197 149 0.64
198 13 0.06
199 1 0.00
201 2 0.01
202 24 0.10
203 17 0.07
204 23 0.10
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.29
Consensus pattern (198 bp):
ACCACAACACCAAATCCTATATCCCTGAAGTTATAATGGATCAGATTAAAACTAACAGTAACAAA
TCTCAATCTCCCTGAAGTTACAATGGAATGGAGTGAAGCCACAAACCTAAATCCTATATCCCTAA
GATTGCAGTAGATCAAATTAAAACTAACAGTAGCAGATCTAAATCTCCTTGAAGTTGTAGTAGAA
TGG
Found at i:13721 original size:4 final size:4
Alignment explanation
Indices: 13687--13777 Score: 70
Period size: 4 Copynumber: 23.8 Consensus size: 4
13677 TTTAGTCCGT
* *
13687 TTTA -TTA TTT- TTTA TCTGTA TTTA TTCA TTTA TTT- TAGTA TTTA TTT-
1 TTTA TTTA TTTA TTTA T-T-TA TTTA TTTA TTTA TTTA T-TTA TTTA TTTA
* *
13734 TTTA TTT- TTTA TTTC GTT- TTTA TTTA TTTA TTTA -TTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
13778 TTATGTCATT
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
3 18 0.26
4 46 0.66
5 3 0.04
6 3 0.04
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (4 bp):
TTTA
Found at i:13737 original size:7 final size:7
Alignment explanation
Indices: 13727--13779 Score: 54
Period size: 7 Copynumber: 7.3 Consensus size: 7
13717 TATTTTAGTA
13727 TTTATTT
1 TTTATTT
13734 TTTATTT
1 TTTATTT
13741 TTTATTT
1 TTTATTT
*
13748 CGTTT-TTA
1 --TTTATTT
13756 TTTATTT
1 TTTATTT
*
13763 ATTTATTA
1 -TTTATTT
13771 TTTATTT
1 TTTATTT
13778 TT
1 TT
13780 ATGTCATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
6 3 0.08
7 24 0.63
8 8 0.21
9 3 0.08
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (7 bp):
TTTATTT
Found at i:13740 original size:44 final size:44
Alignment explanation
Indices: 13686--13779 Score: 127
Period size: 44 Copynumber: 2.1 Consensus size: 44
13676 ATTTAGTCCG
13686 TTTTATTATTTTTTATCT-GTATTTATTCATTTATTTTAGTATTTA
1 TTTT-TTATTTTTTATCTCGTATTTATTCATTTA-TTTAGTATTTA
* * * *
13731 TTTTTTATTTTTTATTTCGTTTTTATTTATTTATTTATTATTTA
1 TTTTTTATTTTTTATCTCGTATTTATTCATTTATTTAGTATTTA
13775 TTTTT
1 TTTTT
13780 ATGTCATTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
44 27 0.61
45 17 0.39
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.74
Consensus pattern (44 bp):
TTTTTTATTTTTTATCTCGTATTTATTCATTTATTTAGTATTTA
Found at i:13756 original size:37 final size:37
Alignment explanation
Indices: 13715--13796 Score: 96
Period size: 37 Copynumber: 2.2 Consensus size: 37
13705 TATTTATTCA
* * *
13715 TTTATTTTA-GTATTTATTTTTTATTTTTTATTTCGTT
1 TTTATTTTATGTATTTATTATTTA-TTTTTATGTCATT
*
13752 TTTA-TTTATTTATTTATTATTTATTTTTATGTCATT
1 TTTATTTTATGTATTTATTATTTATTTTTATGTCATT
13788 TTATATTTT
1 TT-TATTTT
13797 TTTCTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
36 17 0.45
37 18 0.47
38 3 0.08
ACGTcount: A:0.20, C:0.02, G:0.04, T:0.74
Consensus pattern (37 bp):
TTTATTTTATGTATTTATTATTTATTTTTATGTCATT
Found at i:13761 original size:15 final size:15
Alignment explanation
Indices: 13687--13777 Score: 80
Period size: 15 Copynumber: 5.9 Consensus size: 15
13677 TTTAGTCCGT
13687 TTTATTATTT-TTTA
1 TTTATTATTTATTTA
*
13701 TCTGTATTTATTCATTTA
1 T-T-TA-TTATTTATTTA
*
13719 TTTTAGTATTTATTT-
1 -TTTATTATTTATTTA
* *
13734 TTTATTTTTTATTTCG
1 TTTATTATTTATTT-A
13750 TTT-TTATTTATTTA
1 TTTATTATTTATTTA
13764 TTTATTATTTATTT
1 TTTATTATTTATTT
13778 TTATGTCATT
Statistics
Matches: 62, Mismatches: 7, Indels: 15
0.74 0.08 0.18
Matches are distributed among these distances:
14 16 0.26
15 20 0.32
16 13 0.21
17 7 0.11
18 5 0.08
19 1 0.02
ACGTcount: A:0.20, C:0.03, G:0.03, T:0.74
Consensus pattern (15 bp):
TTTATTATTTATTTA
Found at i:13779 original size:26 final size:26
Alignment explanation
Indices: 13691--13829 Score: 81
Period size: 26 Copynumber: 5.3 Consensus size: 26
13681 GTCCGTTTTA
*
13691 TTATTTTTTATCTGTATTTATTCATTTATT
1 TTATTTTTTAT-T-TATTTATTTA-TTA-T
* * *
13721 TTAGTATTTATTT-TTTATTTTTTAT
1 TTATTTTTTATTTATTTATTTATTAT
**
13746 TTCGTTTTTATTTATTTATTTATTAT
1 TTATTTTTTATTTATTTATTTATTAT
* *
13772 TTA-TTTTTATGTCATTT-TATATT-T
1 TTATTTTTTAT-TTATTTATTTATTAT
* * *
13796 TTTTCTTTTTATTTAATTATATA-TATT
1 TTAT-TTTTTATTTATTTATTTATTA-T
13823 TTATTTT
1 TTATTTT
13830 GTCCTTGATT
Statistics
Matches: 88, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
24 3 0.03
25 29 0.33
26 35 0.40
27 10 0.11
28 1 0.01
29 1 0.01
30 9 0.10
ACGTcount: A:0.21, C:0.04, G:0.03, T:0.73
Consensus pattern (26 bp):
TTATTTTTTATTTATTTATTTATTAT
Found at i:13986 original size:12 final size:12
Alignment explanation
Indices: 13969--13998 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
13959 TATTTTTTAT
13969 TTAATTGTGATA
1 TTAATTGTGATA
*
13981 TTAATTGTGTTA
1 TTAATTGTGATA
13993 TTAATT
1 TTAATT
13999 ATATTTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (12 bp):
TTAATTGTGATA
Found at i:14016 original size:17 final size:16
Alignment explanation
Indices: 13990--14023 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
13980 ATTAATTGTG
13990 TTATTAATTATATTTAT
1 TTATTAATTAT-TTTAT
*
14007 TTATTTATTATTTTAT
1 TTATTAATTATTTTAT
14023 T
1 T
14024 CATGTATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTATTAATTATTTTAT
Found at i:16025 original size:24 final size:25
Alignment explanation
Indices: 15972--16025 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
15962 TGAAGTACTT
*
15972 AACAGAAGCGCAAAAGTGCTGGGGA
1 AACAGAAGCACAAAAGTGCTGGGGA
* *
15997 AACAGAAGCACATAAGTG-TTGGGA
1 AACAGAAGCACAAAAGTGCTGGGGA
16021 AACAG
1 AACAG
16026 TTGACACACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.43, C:0.15, G:0.31, T:0.11
Consensus pattern (25 bp):
AACAGAAGCACAAAAGTGCTGGGGA
Found at i:16056 original size:22 final size:22
Alignment explanation
Indices: 16030--16119 Score: 153
Period size: 22 Copynumber: 4.0 Consensus size: 22
16020 AAACAGTTGA
16030 CACACACAGTGCTGAACAGAAG
1 CACACACAGTGCTGAACAGAAG
*
16052 CACACACAGTGCTGAATAGAAG
1 CACACACAGTGCTGAACAGAAG
*
16074 CACACACAGTGCTAAACAGAAG
1 CACACACAGTGCTGAACAGAAG
16096 CACACACAGTGCTGAACAGTAAG
1 CACACACAGTGCTGAACAG-AAG
16119 C
1 C
16120 GCTCTAGCGT
Statistics
Matches: 63, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
22 59 0.94
23 4 0.06
ACGTcount: A:0.41, C:0.27, G:0.21, T:0.11
Consensus pattern (22 bp):
CACACACAGTGCTGAACAGAAG
Found at i:17937 original size:25 final size:24
Alignment explanation
Indices: 17909--17986 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 24
17899 TACTTTTCCG
17909 AATTCGATTCAATAGTCTAATTCTC
1 AATTCG-TTCAATAGTCTAATTCTC
* * * * * *
17934 AATTC-TACTATATTACT-GTTTTG
1 AATTCGTTCAATAGT-CTAATTCTC
17957 AATTCGGTTCAATAGTCTAATTCTC
1 AATTC-GTTCAATAGTCTAATTCTC
17982 AATTC
1 AATTC
17987 TACTCTATTA
Statistics
Matches: 37, Mismatches: 12, Indels: 8
0.65 0.21 0.14
Matches are distributed among these distances:
23 14 0.38
24 4 0.11
25 19 0.51
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (24 bp):
AATTCGTTCAATAGTCTAATTCTC
Found at i:18007 original size:48 final size:48
Alignment explanation
Indices: 17872--18016 Score: 245
Period size: 48 Copynumber: 3.0 Consensus size: 48
17862 TTTTAACTAC
* * *
17872 ATAGTCTAATTCTCAATTCTACTCTATTACTTTTCCGAATTCGATTCA
1 ATAGTCTAATTCTCAATTCTACTCTATTACTGTTCTGAATTCGGTTCA
* *
17920 ATAGTCTAATTCTCAATTCTACTATATTACTGTTTTGAATTCGGTTCA
1 ATAGTCTAATTCTCAATTCTACTCTATTACTGTTCTGAATTCGGTTCA
17968 ATAGTCTAATTCTCAATTCTACTCTATTACTGTTCTGAATTCGGTTCA
1 ATAGTCTAATTCTCAATTCTACTCTATTACTGTTCTGAATTCGGTTCA
18016 A
1 A
18017 GAACGCGGAT
Statistics
Matches: 90, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 90 1.00
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (48 bp):
ATAGTCTAATTCTCAATTCTACTCTATTACTGTTCTGAATTCGGTTCA
Found at i:24184 original size:16 final size:16
Alignment explanation
Indices: 24163--24193 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
24153 ATAATGTGAA
24163 AATAAAGATAAAATGT
1 AATAAAGATAAAATGT
*
24179 AATAAAGGTAAAATG
1 AATAAAGATAAAATG
24194 GGATCCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.16, T:0.23
Consensus pattern (16 bp):
AATAAAGATAAAATGT
Found at i:24986 original size:49 final size:49
Alignment explanation
Indices: 24894--24987 Score: 125
Period size: 49 Copynumber: 1.9 Consensus size: 49
24884 ATAATTTTGG
* * * * *
24894 GTGCAATTGAAGAATACTTATGCGGCGATAATTTTGGGCGCAATTCTGA
1 GTGCAATCGAAAAATACTTATGCAGCGATAATTCTGGACGCAATTCTGA
* *
24943 GTGCAATCGAAAAATACTTATGCAGCGATAGTTCTGGATGCAATT
1 GTGCAATCGAAAAATACTTATGCAGCGATAATTCTGGACGCAATT
24988 TGAAGAATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
49 38 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (49 bp):
GTGCAATCGAAAAATACTTATGCAGCGATAATTCTGGACGCAATTCTGA
Found at i:28947 original size:38 final size:38
Alignment explanation
Indices: 28905--28992 Score: 90
Period size: 38 Copynumber: 2.3 Consensus size: 38
28895 ATGTAGCAAC
*
28905 ATTCTTGGGTGCAA-TTGAAGAATACTTATGCAGCGATA
1 ATTCTTGGGTGCAATTTAAAGAATACTTATGCAGCGA-A
* * * * *
28943 ATTC-TAGATGCAATTTAAAGAATATTTATGCAGTGAC
1 ATTCTTGGGTGCAATTTAAAGAATACTTATGCAGCGAA
*
28980 AGTCTTGGGTGCA
1 ATTCTTGGGTGCA
28993 TTCCAAAAAA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
37 10 0.26
38 29 0.74
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (38 bp):
ATTCTTGGGTGCAATTTAAAGAATACTTATGCAGCGAA
Found at i:29355 original size:16 final size:17
Alignment explanation
Indices: 29322--29355 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
29312 ATGAGTTAGA
*
29322 ATAATGTTTAGATATTT
1 ATAATGGTTAGATATTT
29339 ATAATGGTTAG-TATTT
1 ATAATGGTTAGATATTT
29355 A
1 A
29356 GGGTTTCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (17 bp):
ATAATGGTTAGATATTT
Found at i:36483 original size:2 final size:2
Alignment explanation
Indices: 36478--36504 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
36468 TGAAATATTA
36478 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 A
36505 GTGTAAATAT
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:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36723 original size:47 final size:47
Alignment explanation
Indices: 36654--36810 Score: 215
Period size: 47 Copynumber: 3.3 Consensus size: 47
36644 AAGGAGGAAG
* *
36654 AAGTGGCAGTTTATCTGCAAAAGTGGTGACTTGTCCACAATATTATA
1 AAGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATA
* * *
36701 AAGTGACAGTTTATCTGCAAAAGTGGTGGTTTGTCCACAATTTTATT
1 AAGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATA
* ** *
36748 AAGTGACAGTTTATCTGCAAAAATGGTGGCTTGTTTACAATATTATC
1 AAGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATA
* *
36795 AAGCGGCAGTTTATCT
1 AAGTGACAGTTTATCT
36811 ACAATACTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 97 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (47 bp):
AAGTGACAGTTTATCTGCAAAAGTGGTGGCTTGTCCACAATATTATA
Found at i:40117 original size:18 final size:18
Alignment explanation
Indices: 40094--40136 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
40084 CAAACCAAGT
*
40094 TTGACCATTGACCGACCG
1 TTGACCATTGACCGACCA
* **
40112 TTGACCGTTGATTGACCA
1 TTGACCATTGACCGACCA
40130 TTGACCA
1 TTGACCA
40137 ACCGTCGACC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (18 bp):
TTGACCATTGACCGACCA
Found at i:40178 original size:14 final size:14
Alignment explanation
Indices: 40168--40208 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
40158 ATAGTTGATC
40168 GTTGACCGTTGACT
1 GTTGACCGTTGACT
40182 GTTGACC-TTGACT
1 GTTGACCGTTGACT
*
40195 -TTGATCTGTTGACT
1 GTTGA-CCGTTGACT
40209 TTTTTCGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
12 4 0.17
13 7 0.29
14 13 0.54
ACGTcount: A:0.15, C:0.20, G:0.24, T:0.41
Consensus pattern (14 bp):
GTTGACCGTTGACT
Found at i:47311 original size:18 final size:18
Alignment explanation
Indices: 47285--47333 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
47275 CATACCAAAT
*
47285 TTGATCGTTGACCAACCA
1 TTGACCGTTGACCAACCA
*
47303 TTGACCGTTGACCAACCG
1 TTGACCGTTGACCAACCA
* *
47321 TCGACCATTGACC
1 TTGACCGTTGACC
47334 GTTGATCGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.24, C:0.33, G:0.18, T:0.24
Consensus pattern (18 bp):
TTGACCGTTGACCAACCA
Found at i:57876 original size:88 final size:88
Alignment explanation
Indices: 57727--57906 Score: 315
Period size: 88 Copynumber: 2.0 Consensus size: 88
57717 ATCATTCTAA
57727 CTTATGTAAAGCTTCATGTGAAATTACTTAACTAGAAGATCTTGAGTGTATAACCATCAACTCAA
1 CTTATGTAAAGCTTCATGTGAAATTACTTAACTAGAAGATCTTGAGTGTATAACCATCAACTCAA
57792 CACATATCACATTATGTACCAAC
66 CACATATCACATTATGTACCAAC
* * * * *
57815 CTTATGTAGAGCTTCATGTGAAGTTAGTTTACTAGAAGATCTTGAGTGTATAACTATCAACTCAA
1 CTTATGTAAAGCTTCATGTGAAATTACTTAACTAGAAGATCTTGAGTGTATAACCATCAACTCAA
57880 CACATATCACATTATGTACCAAC
66 CACATATCACATTATGTACCAAC
57903 CTTA
1 CTTA
57907 CTAAGTGACA
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
88 87 1.00
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (88 bp):
CTTATGTAAAGCTTCATGTGAAATTACTTAACTAGAAGATCTTGAGTGTATAACCATCAACTCAA
CACATATCACATTATGTACCAAC
Found at i:58824 original size:244 final size:244
Alignment explanation
Indices: 58378--58858 Score: 757
Period size: 244 Copynumber: 2.0 Consensus size: 244
58368 GGTTCCATCG
** *
58378 AAAACATCAATTACATAATACTTATGTATGTTTTTTACTCACATGATTTATTGTAAAATAATAAA
1 AAAACATCAATTACATAATACTTATGTATGTTTTCGACTCACATGATTTATTCTAAAATAATAAA
* * * * *
58443 ATAAATAAATCCTACGAGTAGATGATAGTCCACGATCTAATTACATACCCAAGAATTAATGATAA
66 ATAAATAAATCCTACAAGAAGATGATAGCCCACGAACTAATTACATACCCAAGAATTAATGAAAA
*
58508 TTACAACCAAATTTCTAATAATCACAACTTTGGAAAAATTATTTTATAATAAATAAATAATAATA
131 TTACAACCAAATTTCTAATAATCACAACTTTGGAAAAATTACTTTATAATAAATAAATAATAATA
* *
58573 GCATACATTCATTTACATATATATCCCTAAACATGCTGATAACTACACT
196 ACATACATTCATTCACATATATATCCCTAAACATGCTGATAACTACACT
* * *
58622 AAAATATCAGTTACATAATACTTATGTCTGTTTTCGACTCACATGATTTATTCTAAAATAATAAA
1 AAAACATCAATTACATAATACTTATGTATGTTTTCGACTCACATGATTTATTCTAAAATAATAAA
* *
58687 ATAAATAAATCCTATAAGAAGATGATAGCCCACGAACTAATTACATAGCCAAGAATTAATGAAAA
66 ATAAATAAATCCTACAAGAAGATGATAGCCCACGAACTAATTACATACCCAAGAATTAATGAAAA
* * *
58752 TTACAATCAAATTTCTAATAATCACAA-TTTTGACAAAATTACTTTATCATAAATAAATAATAAT
131 TTACAACCAAATTTCTAATAATCACAACTTTGGA-AAAATTACTTTATAATAAATAAATAATAAT
* *
58816 AACATACATTCATTCACATATATATGCTTAAACATGCTGATAA
195 AACATACATTCATTCACATATATATCCCTAAACATGCTGATAA
58859 TTATAACAAT
Statistics
Matches: 215, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
243 5 0.02
244 210 0.98
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.33
Consensus pattern (244 bp):
AAAACATCAATTACATAATACTTATGTATGTTTTCGACTCACATGATTTATTCTAAAATAATAAA
ATAAATAAATCCTACAAGAAGATGATAGCCCACGAACTAATTACATACCCAAGAATTAATGAAAA
TTACAACCAAATTTCTAATAATCACAACTTTGGAAAAATTACTTTATAATAAATAAATAATAATA
ACATACATTCATTCACATATATATCCCTAAACATGCTGATAACTACACT
Found at i:59673 original size:16 final size:15
Alignment explanation
Indices: 59642--59682 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
59632 AGACCTTATA
59642 AATTAATTTT-AATT
1 AATTAATTTTCAATT
59656 AATTAATTTTCCAATT
1 AATTAATTTT-CAATT
*
59672 AAATAATTTTC
1 AATTAATTTTC
59683 TCAACTCGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 10 0.42
15 1 0.04
16 13 0.54
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTAATTTTCAATT
Found at i:62488 original size:16 final size:18
Alignment explanation
Indices: 62449--62482 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
62439 TAAATTTATA
62449 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
62466 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
62483 AATTTAGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:63228 original size:23 final size:24
Alignment explanation
Indices: 63198--63243 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
63188 GGTTTAGAAA
63198 AAAATTATAA-TTTAAAAAATAAT
1 AAAATTATAATTTTAAAAAATAAT
*
63221 AAAATTATAATTTTGAAAAATAA
1 AAAATTATAATTTTAAAAAATAA
63244 ATTAAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 10 0.48
24 11 0.52
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
AAAATTATAATTTTAAAAAATAAT
Found at i:66993 original size:41 final size:41
Alignment explanation
Indices: 66936--67017 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
66926 TCAATCCATG
66936 CAACAGTTCCAAACCCTCCAATGAAATATATATCACTGAAA
1 CAACAGTTCCAAACCCTCCAATGAAATATATATCACTGAAA
** **
66977 CAACAGTTTTAAACCCTCTGATGAAATATATATCACTGAAA
1 CAACAGTTCCAAACCCTCCAATGAAATATATATCACTGAAA
67018 TGAATTTTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.26
Consensus pattern (41 bp):
CAACAGTTCCAAACCCTCCAATGAAATATATATCACTGAAA
Found at i:68337 original size:23 final size:23
Alignment explanation
Indices: 68297--68340 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
68287 GGAATATTTC
*
68297 TTTACTTAGAGTTAATGTTTTAA
1 TTTACTTAGACTTAATGTTTTAA
68320 TTTACTTAG-CTTATATGTTTT
1 TTTACTTAGACTTA-ATGTTTT
68341 TCATTCAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.25, C:0.07, G:0.11, T:0.57
Consensus pattern (23 bp):
TTTACTTAGACTTAATGTTTTAA
Found at i:79277 original size:18 final size:18
Alignment explanation
Indices: 79243--79279 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
79233 ATTTTTAGCA
79243 CTTAGTTTAGTTTTCATG
1 CTTAGTTTAGTTTTCATG
79261 CTTAGTTTAGTTTTCATG
1 CTTAGTTTAGTTTTCATG
79279 C
1 C
79280 ATATCATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (18 bp):
CTTAGTTTAGTTTTCATG
Found at i:83566 original size:15 final size:15
Alignment explanation
Indices: 83541--83573 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
83531 AACTTCATAG
83541 TTATGGAGATAATGGT
1 TTATGGAGATAAT-GT
83557 TTAT-GAGATAATGT
1 TTATGGAGATAATGT
83571 TTA
1 TTA
83574 GAAACCCAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.33, C:0.00, G:0.24, T:0.42
Consensus pattern (15 bp):
TTATGGAGATAATGT
Found at i:84081 original size:40 final size:40
Alignment explanation
Indices: 84021--84207 Score: 198
Period size: 40 Copynumber: 4.7 Consensus size: 40
84011 GTAGTGTTTA
* * *
84021 AATACATTCAAGCTTTGGCTTAGTAGGCTATGAGCCGATG
1 AATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGATG
* * * *
84061 AATACATTCAATCTTCGGCTTAGCAAGCTACGAGCTGGTG
1 AATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGATG
* * * *
84101 AATACATTCAAGCTTCGACTTAACAGGCTATGAGAC-AGTG
1 AATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGA-TG
* * *
84141 AATACATTTAAGCTTCGGCTTAGCAGGCTACGAGTCGGTG
1 AATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGATG
* * *
84181 AATATATTCAAGCCT-AGCTTAGCAGGC
1 AATACATTCAAGCTTCGGCTTAGCAGGC
84208 GATATGTCGG
Statistics
Matches: 120, Mismatches: 25, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
39 11 0.09
40 109 0.91
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.27
Consensus pattern (40 bp):
AATACATTCAAGCTTCGGCTTAGCAGGCTACGAGCCGATG
Found at i:84157 original size:80 final size:80
Alignment explanation
Indices: 84021--84193 Score: 233
Period size: 80 Copynumber: 2.2 Consensus size: 80
84011 GTAGTGTTTA
* * ** * *
84021 AATACATTCAAGCTTTGGCTTAGTAGGCTATGAGCCGATGAATACATTCAATCTTCGGCTTAGCA
1 AATACATTCAAGCTTCGACTTAACAGGCTATGAGCAGATGAATACATTCAAGCTTCGGCTTAGCA
84086 AGCTACGAG-CTGGTG
66 AGCTACGAGTC-GGTG
*
84101 AATACATTCAAGCTTCGACTTAACAGGCTATGAGACAG-TGAATACATTTAAGCTTCGGCTTAGC
1 AATACATTCAAGCTTCGACTTAACAGGCTATGAG-CAGATGAATACATTCAAGCTTCGGCTTAGC
*
84165 AGGCTACGAGTCGGTG
65 AAGCTACGAGTCGGTG
*
84181 AATATATTCAAGC
1 AATACATTCAAGC
84194 CTAGCTTAGC
Statistics
Matches: 82, Mismatches: 9, Indels: 4
0.86 0.09 0.04
Matches are distributed among these distances:
80 79 0.96
81 3 0.04
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.28
Consensus pattern (80 bp):
AATACATTCAAGCTTCGACTTAACAGGCTATGAGCAGATGAATACATTCAAGCTTCGGCTTAGCA
AGCTACGAGTCGGTG
Found at i:93077 original size:20 final size:21
Alignment explanation
Indices: 93041--93079 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
93031 CATTTGTTTA
*
93041 TTTACTTTTATTTGTTTCACT
1 TTTACTTTTAGTTGTTTCACT
93062 TTTACTTTT-GTTGTTTCA
1 TTTACTTTTAGTTGTTTCA
93080 AATTCCTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.13, C:0.13, G:0.08, T:0.67
Consensus pattern (21 bp):
TTTACTTTTAGTTGTTTCACT
Found at i:94838 original size:17 final size:18
Alignment explanation
Indices: 94816--94855 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
94806 ATAAATTTCA
*
94816 TGCATTTT-TATTGTCAT
1 TGCATTTTATATTGTCAC
*
94833 TGCATTTTATTTTGTCAC
1 TGCATTTTATATTGTCAC
94851 TGCAT
1 TGCAT
94856 CTTTGTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.17, C:0.15, G:0.12, T:0.55
Consensus pattern (18 bp):
TGCATTTTATATTGTCAC
Found at i:101494 original size:24 final size:24
Alignment explanation
Indices: 101467--101523 Score: 105
Period size: 24 Copynumber: 2.4 Consensus size: 24
101457 CTCTGGTAAT
*
101467 AGTGGTCCACATTGGGCCACTTGA
1 AGTGATCCACATTGGGCCACTTGA
101491 AGTGATCCACATTGGGCCACTTGA
1 AGTGATCCACATTGGGCCACTTGA
101515 AGTGATCCA
1 AGTGATCCA
101524 TCTAACACGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.25, C:0.25, G:0.26, T:0.25
Consensus pattern (24 bp):
AGTGATCCACATTGGGCCACTTGA
Found at i:101853 original size:17 final size:17
Alignment explanation
Indices: 101782--101853 Score: 74
Period size: 17 Copynumber: 4.2 Consensus size: 17
101772 TGTTAATAAG
101782 CATTGTCATTGCA-TTC
1 CATTGTCATTGCATTTC
* *
101798 TCATTGTCATTACATTTT
1 -CATTGTCATTGCATTTC
* * * *
101816 AATTGTCATCGAATTTG
1 CATTGTCATTGCATTTC
101833 CATTGTCATTGCATTTC
1 CATTGTCATTGCATTTC
101850 CATT
1 CATT
101854 TGTCCTTATA
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
17 41 0.95
18 2 0.05
ACGTcount: A:0.22, C:0.19, G:0.11, T:0.47
Consensus pattern (17 bp):
CATTGTCATTGCATTTC
Found at i:102446 original size:2 final size:2
Alignment explanation
Indices: 102439--102476 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
102429 GAAGAAAAAG
102439 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
102477 TACTGTACAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:111886 original size:80 final size:79
Alignment explanation
Indices: 111742--111899 Score: 235
Period size: 80 Copynumber: 2.0 Consensus size: 79
111732 ATACAAGCAC
* *
111742 TAATTTCATTTTAACTCTTATAGGGAAGCCAATAAGTCATGTCTCTTCATTAGGATCTGTTGTAG
1 TAATTTCATTTTAACTCTTATAGGGAAGCCAATAAGTAATGTCTCTTCATTAGGATCTGATGTAG
* *
111807 TTGAAAAGGCATGG
66 CTAAAAAGGCATGG
* * * *
111821 TAATTTCGTTTTTAACTCTTGTAGGGAAGCCAATGAGTAATGTCTCTTCATTAGGATTTGATGTA
1 TAATTTC-ATTTTAACTCTTATAGGGAAGCCAATAAGTAATGTCTCTTCATTAGGATCTGATGTA
111886 GCTAAAAAGGCATG
65 GCTAAAAAGGCATG
111900 ACATTTCTCC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
79 7 0.10
80 63 0.90
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (79 bp):
TAATTTCATTTTAACTCTTATAGGGAAGCCAATAAGTAATGTCTCTTCATTAGGATCTGATGTAG
CTAAAAAGGCATGG
Found at i:112461 original size:48 final size:48
Alignment explanation
Indices: 112339--112461 Score: 201
Period size: 48 Copynumber: 2.6 Consensus size: 48
112329 TTAATGCAAG
* * *
112339 GCATTTAACAAACAAAACATTTAATAATGCAGATTACTAAACAAAGAT
1 GCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGAA
* *
112387 GCATTTAACAAACAAAACACTCAATGATGCAGATTATTAAACAAAGAA
1 GCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGAA
112435 GCATTTAACAAACAAAACACTTAATGA
1 GCATTTAACAAACAAAACACTTAATGA
112462 AGCATAAATA
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 69 1.00
ACGTcount: A:0.52, C:0.16, G:0.09, T:0.23
Consensus pattern (48 bp):
GCATTTAACAAACAAAACACTTAATGATGCAGATTACTAAACAAAGAA
Found at i:118452 original size:18 final size:18
Alignment explanation
Indices: 118425--118471 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
118415 CAAAGAAGAC
*
118425 GTCGACGCAACTACCTAA
1 GTCGATGCAACTACCTAA
*
118443 GTCGATGCAACTGCCTAA
1 GTCGATGCAACTACCTAA
118461 GTCGATGCAAC
1 GTCGATGCAAC
118472 CTGTTATTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.30, G:0.21, T:0.19
Consensus pattern (18 bp):
GTCGATGCAACTACCTAA
Found at i:124171 original size:12 final size:12
Alignment explanation
Indices: 124131--124176 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
124121 ATCTTGAGGA
124131 GAAGAAGGAAAAT
1 GAAGAA-GAAAAT
* * *
124144 GAGGAAGAGAAG
1 GAAGAAGAAAAT
124156 GAAGAAGAAAAT
1 GAAGAAGAAAAT
124168 GAAGAAGAA
1 GAAGAAGAA
124177 GAGAAGGATG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 22 0.81
13 5 0.19
ACGTcount: A:0.61, C:0.00, G:0.35, T:0.04
Consensus pattern (12 bp):
GAAGAAGAAAAT
Found at i:128304 original size:39 final size:39
Alignment explanation
Indices: 128254--128349 Score: 120
Period size: 42 Copynumber: 2.4 Consensus size: 39
128244 TCTCGATTAG
* *
128254 GGGTAAAAGATTGGATGGCTTTAATCTGCCCCATGGTCA
1 GGGTAAGAGATTGGATGGCTTTAATCTACCCCATGGTCA
* * *
128293 GGGTAAGAGATTGGATAATGTCTTTAATCTACCTCATGGTCG
1 GGGTAAGAGATTGG---ATGGCTTTAATCTACCCCATGGTCA
128335 GGGTAAGAGATTGGA
1 GGGTAAGAGATTGGA
128350 AGTCTTCTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
39 14 0.29
42 35 0.71
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.29
Consensus pattern (39 bp):
GGGTAAGAGATTGGATGGCTTTAATCTACCCCATGGTCA
Found at i:128318 original size:42 final size:42
Alignment explanation
Indices: 128276--128500 Score: 177
Period size: 42 Copynumber: 5.2 Consensus size: 42
128266 GGATGGCTTT
*
128276 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATAATGTCTTT
1 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATAATGTCTTC
* * * * *
128318 AATCTACCTCATGGTCGGGGTAAGAGATTGGA-AGTCTTCTTC
1 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATAAT-GTCTTC
* * * * **
128360 AATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGTCTTC
1 AATCTG-CCC-CATG--GTCA-GGGTAAGAGATTGGATAATGTCTTC
* * * *
128407 AATCTGTCCCGTGGTCGGGGTAAGAGATTGGATGATGTCTTC
1 AATCTGCCCCATGGTCAGGGTAAGAGATTGGATAATGTCTTC
* * * *
128449 GATCTGCCCCAT-GCCTAGGGTAAGAGATTAGAATACT-TCTTC
1 AATCTGCCCCATGGTC-AGGGTAAGAGATT-GGATAATGTCTTC
128491 AATCTGCCCC
1 AATCTGCCCC
128501 TCTTGATTTT
Statistics
Matches: 143, Mismatches: 31, Indels: 18
0.74 0.16 0.09
Matches are distributed among these distances:
41 4 0.03
42 96 0.67
43 7 0.05
44 3 0.02
45 3 0.02
46 3 0.02
47 25 0.17
48 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (42 bp):
AATCTGCCCCATGGTCAGGGTAAGAGATTGGATAATGTCTTC
Found at i:128448 original size:89 final size:89
Alignment explanation
Indices: 128293--128458 Score: 219
Period size: 89 Copynumber: 1.9 Consensus size: 89
128283 CCCATGGTCA
* * *
128293 GGGTAAGAGATTGGATAATGTCTTTAATCTACCTCATGGTCGGGGTAAGAGATTGGAAGTCTTCT
1 GGGTAAAAGATTGGATAATGTCTTCAATCTACCTCATGGTCGGGGTAAGAGATTGGAAGTCGTCT
128358 TCAATCTGCCCCTCTTGATTTTAG
66 TCAATCTGCCCCTCTTGATTTTAG
** * * *
128382 GGGTAAAAGATTGGATGGTGTCTTCAATCTGTCC-CGTGGTCGGGGTAAGAGATTGGATGAT-GT
1 GGGTAAAAGATTGGATAATGTCTTCAATCT-ACCTCATGGTCGGGGTAAGAGATTGGAAG-TCGT
*
128445 CTTCGATCTGCCCC
64 CTTCAATCTGCCCC
128459 ATGCCTAGGG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
89 63 0.95
90 3 0.05
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (89 bp):
GGGTAAAAGATTGGATAATGTCTTCAATCTACCTCATGGTCGGGGTAAGAGATTGGAAGTCGTCT
TCAATCTGCCCCTCTTGATTTTAG
Found at i:128470 original size:131 final size:131
Alignment explanation
Indices: 128231--128547 Score: 416
Period size: 131 Copynumber: 2.5 Consensus size: 131
128221 AGATAATAGT
* *
128231 TTCAATCTGCCCCTCTCGA--TTAGGGGTAAAAGATTGGAT-G-G-CTTTAATCTGCCCCATGGT
1 TTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGT
* * * * *
128291 CAGGGTAAGAGATTGGATAATGTCTTTAATCTACCTCATGGTCGGGGTAAGAGATTGGAAGT-CT
66 CAGGGTAAGAGATTGGATAATGTCTTCAATCTACCCCATGCTCAGGGTAAGAGATTAGAA-TACT
128355 TC
130 TC
* *
128357 TTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGTCTTCAATCTGTCCCGTGGT
1 TTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGT
* * * *
128422 CGGGGTAAGAGATTGGATGATGTCTTCGATCTGCCCCATGC-CTAGGGTAAGAGATTAGAATACT
66 CAGGGTAAGAGATTGGATAATGTCTTCAATCTACCCCATGCTC-AGGGTAAGAGATTAGAATACT
128486 TC
130 TC
* *
128488 TTCAATCTGCCCCTCTTGATTTTAGGGGTAAATGATTGGATGATGGT-TTCAATCTGCCCC
1 TTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGT-GTCTTCAATCTGCCCC
128548 TCTTAACTTA
Statistics
Matches: 167, Mismatches: 16, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
126 18 0.11
128 20 0.12
129 1 0.01
130 3 0.02
131 123 0.74
132 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.26, T:0.32
Consensus pattern (131 bp):
TTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGTCTTCAATCTGCCCCATGGT
CAGGGTAAGAGATTGGATAATGTCTTCAATCTACCCCATGCTCAGGGTAAGAGATTAGAATACTT
C
Found at i:128585 original size:46 final size:46
Alignment explanation
Indices: 128356--128766 Score: 288
Period size: 46 Copynumber: 9.0 Consensus size: 46
128346 TGGAAGTCTT
** *
128356 CTTCAATCTGCCCCTCTTGATTTTAGGGGTAAAAGATTGGATGGTGT
1 CTTCAATCTGCCCCTCTT-AACTTAGGGGTAAAAGATTGGATGGTGG
* ** * * *
128403 CTTCAATCTGTCCCGTGGT--C---GGGGTAAGAGATTGGATGATGT
1 CTTCAATCTG-CCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGG
* * * * * * ** *
128445 CTTCGATCTG-CCC-CAT-GCCTA-GGGTAAGAGATTAGAATACT-T
1 CTTCAATCTGCCCCTCTTAACTTAGGGGTAAAAGATT-GGATGGTGG
** * *
128487 CTTCAATCTGCCCCTCTTGATTTTAGGGGTAAATGATTGGATGATGG
1 CTTCAATCTGCCCCTCTT-AACTTAGGGGTAAAAGATTGGATGGTGG
* * * *
128534 TTTCAATCTGCCCCTCTTAACTTAAGGGTAAAATATTGGATGGTAG
1 CTTCAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGG
* *
128580 CTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGG
1 CTTCAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGG
* * * * *
128626 CTTCAATCAATCTACCCCTTTTGACTTTAGGGGTAAAAGATTAGATGATGG
1 C-T---TCAATCTGCCCCTCTTAAC-TTAGGGGTAAAAGATTGGATGGTGG
* * * *
128677 CTTGAATCTGCCCC-ATTGACTTAAGGGTAAAAGATTGGATGGTGG
1 CTTCAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGG
* * *
128722 CTTTAATTTGCCCCTCTTGAA-TTAGGGGTAAAAGAATGGATGGTG
1 CTTCAATCTGCCCCTCTT-AACTTAGGGGTAAAAGATTGGATGGTG
128767 ATGTAACTTC
Statistics
Matches: 290, Mismatches: 55, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
39 1 0.00
40 3 0.01
42 51 0.18
43 7 0.02
44 2 0.01
45 34 0.12
46 97 0.33
47 49 0.17
48 5 0.02
50 17 0.06
51 24 0.08
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (46 bp):
CTTCAATCTGCCCCTCTTAACTTAGGGGTAAAAGATTGGATGGTGG
Found at i:128705 original size:96 final size:93
Alignment explanation
Indices: 128487--128756 Score: 280
Period size: 96 Copynumber: 2.9 Consensus size: 93
128477 TAGAATACTT
* * * * * *
128487 CTTCAATCTGCCCCTCTTGATTTTAGGGGTAAATGATTGGATGATGG-TTTCAATCTGCCCCTCT
1 CTTCAATCTGTCCCTCTTGA-CTTAAGGGTAAAAGATTGGATGGTGGCTTTCAATCTACCCCTCT
* * *
128551 TAACTTAAGGGTAAAATATTGGATGGTAG
65 TAACTTAAGGGTAAAAGATTAGATGATAG
*
128580 CTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGGATGGTGGCTTCAATCAATCTACCCCT
1 CTTCAATCTGTCCCTCTTGACTTAAGGGTAAAAGATTGGATGGTGGCTT---TCAATCTACCCCT
* * * *
128645 TTTGACTTTAGGGGTAAAAGATTAGATGATGG
63 CTTAAC-TTAAGGGTAAAAGATTAGATGATAG
* * *
128677 CTTGAATCTG-CCC-CATTGACTTAAGGGTAAAAGATTGGATGGTGGCTTT-AATTTGCCCCTCT
1 CTTCAATCTGTCCCTC-TTGACTTAAGGGTAAAAGATTGGATGGTGGCTTTCAATCTACCCCTCT
*
128739 TGAA-TTAGGGGTAAAAGA
65 T-AACTTAAGGGTAAAAGA
128757 ATGGATGGTG
Statistics
Matches: 152, Mismatches: 18, Indels: 16
0.82 0.10 0.09
Matches are distributed among these distances:
91 14 0.09
92 34 0.22
93 23 0.15
95 1 0.01
96 51 0.34
97 29 0.19
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (93 bp):
CTTCAATCTGTCCCTCTTGACTTAAGGGTAAAAGATTGGATGGTGGCTTTCAATCTACCCCTCTT
AACTTAAGGGTAAAAGATTAGATGATAG
Found at i:128751 original size:142 final size:143
Alignment explanation
Indices: 128489--128766 Score: 405
Period size: 142 Copynumber: 2.0 Consensus size: 143
128479 GAATACTTCT
* * * * * *
128489 TCAATCTGCCCCTCTTGATTTTAGGGGTAAATGATTGGATGATGGTTTCAATCTGCCCCTCTTAA
1 TCAATCTACCCCTCTTGACTTTAGGGGTAAAAGATTAGATGATGGCTTCAATCTGCCCCTATTAA
* * * *
128554 CTTAAGGGTAAAATATTGGATGGTAGCTTCAATCTGTCCCTCTTGACTTAGGGGTAAAAGATTGG
66 CTTAAGGGTAAAAGATTGGATGGTAGCTTCAATCTGCCCCTCTTGAATTAGGGGTAAAAGAATGG
128619 ATGGTGGCTTCAA
131 ATGGTGGCTTCAA
* * *
128632 TCAATCTACCCCTTTTGACTTTAGGGGTAAAAGATTAGATGATGGCTTGAATCTGCCCC-ATTGA
1 TCAATCTACCCCTCTTGACTTTAGGGGTAAAAGATTAGATGATGGCTTCAATCTGCCCCTATTAA
* * *
128696 CTTAAGGGTAAAAGATTGGATGGTGGCTTTAATTTGCCCCTCTTGAATTAGGGGTAAAAGAATGG
66 CTTAAGGGTAAAAGATTGGATGGTAGCTTCAATCTGCCCCTCTTGAATTAGGGGTAAAAGAATGG
128761 ATGGTG
131 ATGGTG
128767 ATGTAACTTC
Statistics
Matches: 119, Mismatches: 16, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
142 67 0.56
143 52 0.44
ACGTcount: A:0.26, C:0.16, G:0.25, T:0.33
Consensus pattern (143 bp):
TCAATCTACCCCTCTTGACTTTAGGGGTAAAAGATTAGATGATGGCTTCAATCTGCCCCTATTAA
CTTAAGGGTAAAAGATTGGATGGTAGCTTCAATCTGCCCCTCTTGAATTAGGGGTAAAAGAATGG
ATGGTGGCTTCAA
Found at i:129345 original size:188 final size:190
Alignment explanation
Indices: 128827--129607 Score: 831
Period size: 189 Copynumber: 4.1 Consensus size: 190
128817 ACTCATTTGG
* * * * * * *
128827 ATCCGATCAACTGCAACTTTAAGGATATAGGA-TCTGCTGCTTCACTGCACTCCACTATAACCTC
1 ATCCGACCCACTGCAAC-TTAAGGGTATAAGATTTTGGTGCTTCACTCCACTCCACTATAACCTC
* * *
128891 AGGGACATTGAGATCTACTACCTATTTTGA-CCACTTCCCTATACCTCACCAGGAAGATGGGATT
65 AGGGACATTGAGATCTGCTACCTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATGAGATT
* * * * ** *
128955 TGAAGACTTACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTACTTTGA-TGTTTTA
130 TGAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTACTTCCATTATTTTA
* ** * * * * *
129015 ATCTGACCCACTATAACTCAAGGGTATAAGATTTTGGCGCTTCACCCCACTCCATTGTAACCTCA
1 ATCCGACCCACTGCAACTTAAGGGTATAAGATTTTGGTGCTTCACTCCACTCCACTATAACCTCA
* * * * * * * * *
129080 GGGACGTTGAGATTTGTTGCCTATTTTTATCCACTTCTCTGTACCTCATCAGGAAGATGTGATTT
66 GGGACATTGAGATCTGCTACCTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATGAGATTT
* * * * *
129145 AAAGTTTCACTCCACTCC-TTCGTAACCTTAGTGACGTTGAGCTCTAC-TCCATTATTTTC
131 GAAGTCTCACTCCACTCCACT-GTAACCTTAGGGACGTTGAGCTCTACTTCCATTATTTTA
* * * * *
129204 ATCCGATCCACTGCAACTTAGGGGTATAGGA-TTTGGTGCTTCACTCCACTCAACTAAAACCTCA
1 ATCCGACCCACTGCAACTTAAGGGTATAAGATTTTGGTGCTTCACTCCACTCCACTATAACCTCA
* * *
129268 AGGACATTGAGATCTGCTACCTATTCTGACCCACTTCTCTATACCTCACTAGGAAGATGAGATTT
66 GGGACATTGAGATCTGCTACCTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATGAGATTT
** * * * * *
129333 GAAGTCTCACTCCACTTTACTATAACCTTAGGGACATTGAGCTTTGCTTCC-TTATTTTG
131 GAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTACTTCCATTATTTTA
** * * * *
129392 ATCTAACCCACTGCAACTTAAAGGTATAAGATTTTGGTGCTTCACTCCACTCCACTGTAGCCTTA
1 ATCCGACCCACTGCAACTTAAGGGTATAAGATTTTGGTGCTTCACTCCACTCCACTATAACCTCA
* * * *
129457 GGGACATTGGGATCTGCTACCTATTTTGACCTACTTCTTTGTACCTCACCAGGAAGATGAGATTT
66 GGGACATTGAGATCTGCTACCTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATGAGATTT
* * * * *
129522 GAAATCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTGTGCTT-CGTTGTTTTA
131 GAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTACTTCCATTATTTTA
** * *
129581 ATCTAACCCATTGTAACTTAAGGGTAT
1 ATCCGACCCACTGCAACTTAAGGGTAT
129608 TAATATTTGC
Statistics
Matches: 483, Mismatches: 102, Indels: 15
0.81 0.17 0.03
Matches are distributed among these distances:
187 11 0.02
188 212 0.44
189 260 0.54
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.32
Consensus pattern (190 bp):
ATCCGACCCACTGCAACTTAAGGGTATAAGATTTTGGTGCTTCACTCCACTCCACTATAACCTCA
GGGACATTGAGATCTGCTACCTATTTTGACCCACTTCTCTATACCTCACCAGGAAGATGAGATTT
GAAGTCTCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTACTTCCATTATTTTA
Found at i:129482 original size:377 final size:377
Alignment explanation
Indices: 128827--129564 Score: 953
Period size: 377 Copynumber: 2.0 Consensus size: 377
128817 ACTCATTTGG
* * *
128827 ATCCGATCAACTGCAACTTTAAGGATATAGGATCTGCTGCTTCACTGCACTCCACTATAACCTCA
1 ATCCGATCAACTGCAACTTTAAGGATATAGGATCTGCTGCTTCACTCCACTCAACTAAAACCTCA
* * *
128892 GGGACATTGAGATCTACTACCTATTTTGACCACTTCCCTATACCTCACCAGGAAGATGGGATTTG
66 AGGACATTGAGATCTACTACCTATTCTGACCACTTCCCTATACCTCACCAGGAAGATGAGATTTG
* * * ** * *
128957 AAGACTTACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTACTTTGATGTTTTAATCTGAC
131 AAGACTCACTCCACTCCACTATAACCTCAAGGACATTGAGCTCTACTTCCATATTTTAATCTAAC
* * * *
129022 CCACTATAACTCAAGGGTATAAGATTTTGGCGCTTCACCCCACTCCATTGTAACCTCAGGGACGT
196 CCACTACAACTCAAAGGTATAAGATTTTGGCGCTTCACCCCACTCCACTGTAACCTCAGGGACAT
* * * * * *
129087 TGAGATTTGTTGCCTATTTTTATCC-ACTTCTCTGTACCTCATCAGGAAGATGTGATTT-AAAGT
261 TGAGATCTGCTACCTATTTTGA-CCTACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAA-T
* * *
129150 TTCACTCCACTCC-TTCGTAACCTTAGTGACGTTGAGCTCTACTCCATTATTTTC
324 CTCACTCCACTCCACT-GTAACCTTAGGGACGTTGAGCTCTACTCCATTATTTTC
* * * * *
129204 ATCCGATCCACTGCAAC-TTAGGGGTATAGGATTTGGTGCTTCACTCCACTCAACTAAAACCTCA
1 ATCCGATCAACTGCAACTTTAAGGATATAGGATCTGCTGCTTCACTCCACTCAACTAAAACCTCA
* * *
129268 AGGACATTGAGATCTGCTACCTATTCTGACCCACTTCTCTATACCTCACTAGGAAGATGAGATTT
66 AGGACATTGAGATCTACTACCTATTCTGA-CCACTTCCCTATACCTCACCAGGAAGATGAGATTT
* ** * * * * * *
129333 GAAGTCTCACTCCACTTTACTATAACCTTAGGGACATTGAGCTTTGCTTCCTTATTTTGATCTAA
130 GAAGACTCACTCCACTCCACTATAACCTCAAGGACATTGAGCTCTACTTCCATATTTTAATCTAA
* * * * * *
129398 CCCACTGCAACTTAAAGGTATAAGATTTTGGTGCTTCACTCCACTCCACTGTAGCCTTAGGGACA
195 CCCACTACAACTCAAAGGTATAAGATTTTGGCGCTTCACCCCACTCCACTGTAACCTCAGGGACA
* *
129463 TTGGGATCTGCTACCTATTTTGACCTACTTCTTTGTACCTCACCAGGAAGATGAGATTTGAAATC
260 TTGAGATCTGCTACCTATTTTGACCTACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAATC
129528 TCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCT
325 TCACTCCACTCCACTGTAACCTTAGGGACGTTGAGCT
129565 GTGCTTCGTT
Statistics
Matches: 306, Mismatches: 51, Indels: 8
0.84 0.14 0.02
Matches are distributed among these distances:
376 68 0.22
377 234 0.76
378 4 0.01
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (377 bp):
ATCCGATCAACTGCAACTTTAAGGATATAGGATCTGCTGCTTCACTCCACTCAACTAAAACCTCA
AGGACATTGAGATCTACTACCTATTCTGACCACTTCCCTATACCTCACCAGGAAGATGAGATTTG
AAGACTCACTCCACTCCACTATAACCTCAAGGACATTGAGCTCTACTTCCATATTTTAATCTAAC
CCACTACAACTCAAAGGTATAAGATTTTGGCGCTTCACCCCACTCCACTGTAACCTCAGGGACAT
TGAGATCTGCTACCTATTTTGACCTACTTCTCTGTACCTCACCAGGAAGATGAGATTTGAAATCT
CACTCCACTCCACTGTAACCTTAGGGACGTTGAGCTCTACTCCATTATTTTC
Found at i:129541 original size:95 final size:95
Alignment explanation
Indices: 128868--129562 Score: 311
Period size: 95 Copynumber: 7.4 Consensus size: 95
128858 ATCTGCTGCT
* * * * * *
128868 TCACTGCACTCCACTATAACCTCAGGGACATTGAGATCTACTACCTATTTTGACC-ACTTCCCTA
1 TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACCTATTTTGACCTACTTCTCTG
* * *
128932 TACCTCACCAGGAAGATGGGATTTGAAGAC
66 TACCTCACAAGGAAGATGAGATTTGAAGTC
* * * * * * *** * * * * *
128962 TTACTCCACTCCACTGTAACCTCAAGGACGTTGAGCTCTACTTTGATGTTTTAATCTGAC-CCAC
1 TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGC-TACCTATTTTGACCT-ACTTCTC
* * * **
129026 TATAACT--CAAGG--GTATAAGATTTTGGCG-C
64 TGTACCTCACAAGGAAG-ATGAGA-TTTGAAGTC
* * * * * * * *
129055 TTCACCCCACTCCATTGTAACCTCAGGGACGTTGAGATTTGTTGCCTATTTTTATCC-ACTTCTC
1 -TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACCTATTTTGA-CCTACTTCTC
* * *
129119 TGTACCTCATC-AGGAAGATGTGATTTAAAGTT
64 TGTACCTCA-CAAGGAAGATGAGATTTGAAGTC
* * * * * * * *
129151 TCACTCCACTCC-TTCGTAACCTTAGTGACGTTGAGCTCTACT-CCATTATTTTCATCCGA-TCC
1 TCACTCCACTCCACT-GTAACCTTAGGGACATTGAGATCTGCTACC--TATTTTGA-CCTACTTC
* * * * ** * *
129213 ACTGCAACTTA-GGGGTATA-G-GATTTG--GTGC
62 TCTGTACCTCACAAGGAAGATGAGATTTGAAGT-C
* ** * * * *
129243 TTCACTCCACTCAACTAAAACCTCAAGGACATTGAGATCTGCTACCTATTCTGACCCACTTCTCT
1 -TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACCTATTTTGACCTACTTCTCT
* *
129308 ATACCTCACTAGGAAGATGAGATTTGAAGTC
65 GTACCTCACAAGGAAGATGAGATTTGAAGTC
** * * * * * * *
129339 TCACTCCACTTTACTATAACCTTAGGGACATTGAGCTTTGCTTCCTTATTTTGATCTAAC-CCAC
1 TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACC-TATTTTGACCT-ACTTCTC
* * * * *
129403 TGCAACTTA-AAGG--TATAAGATTTTG--GTGC
64 TGTACCTCACAAGGAAGATGAGA-TTTGAAGT-C
* * *
129432 TTCACTCCACTCCACTGTAGCCTTAGGGACATTGGGATCTGCTACCTATTTTGACCTACTTCTTT
1 -TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACCTATTTTGACCTACTTCTCT
* *
129497 GTACCTCACCAGGAAGATGAGATTTGAAATC
65 GTACCTCACAAGGAAGATGAGATTTGAAGTC
*
129528 TCACTCCACTCCACTGTAACCTTAGGGACGTTGAG
1 TCACTCCACTCCACTGTAACCTTAGGGACATTGAG
129563 CTGTGCTTCG
Statistics
Matches: 434, Mismatches: 127, Indels: 79
0.68 0.20 0.12
Matches are distributed among these distances:
91 5 0.01
92 21 0.05
93 81 0.19
94 131 0.30
95 133 0.31
96 54 0.12
97 9 0.02
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (95 bp):
TCACTCCACTCCACTGTAACCTTAGGGACATTGAGATCTGCTACCTATTTTGACCTACTTCTCTG
TACCTCACAAGGAAGATGAGATTTGAAGTC
Found at i:129923 original size:49 final size:49
Alignment explanation
Indices: 129879--130327 Score: 365
Period size: 49 Copynumber: 9.2 Consensus size: 49
129869 TCATCTTCAG
* *
129879 GGTATAGGGTTCACCATTACGGCTTTAATCTTTCCCAT-CACATCTCTAA
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCC-TCCACATCTCTAA
*** * * * *
129928 GGTATAAGGTTTGTCGTTGCAGC-TTCATCCTTTCCCTCCACATCTCTAG
1 GGTATAAGGTTCACCATTGCGGCTTTAAT-CTTTCCCTCCACATCTCTAA
* * * * *
129977 GGTATAAGATTCGCCATTGCGGCTTCAATCTTTCTCAT-CACATCTTTAA
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTC-CCTCCACATCTCTAA
* * * *
130026 GGTATAAGGTTCATCATTGCGACTTTAACCTTTCCCTCCACATCTCAAA
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCCTCCACATCTCTAA
* * * * *
130075 GGTATAAGGTTCGCCATTGCGGCTTCAACCTTTTCCTCCAAATCTC-AA
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCCTCCACATCTCTAA
* * * * * *
130123 TGGTACAAGATTCGCCATTGTGGCTTCAATCTTTCCCAT-CACATCTTTAA
1 -GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCC-TCCACATCTCTAA
***** *** * *
130173 GGTATAAGGTTTGTTGTTATAGCTTCAACCTTTCCCTCCACATCTCT-A
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCCTCCACATCTCTAA
* * *
130221 GCGTATAAGATTCA-CAGTTGCGGCTTTAACCTTTCCCTCCACATCTCTAC
1 G-GTATAAGGTTCACCA-TTGCGGCTTTAATCTTTCCCTCCACATCTCTAA
* * *
130271 GGTATAAGATTCACCATTACGACTTTAATCTTTCCCTCCACATCTCTACA
1 GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCCTCCACATCTCTA-A
130321 -GTATAAG
1 GGTATAAG
130328 ATTTGACGTT
Statistics
Matches: 321, Mismatches: 65, Indels: 28
0.78 0.16 0.07
Matches are distributed among these distances:
48 12 0.04
49 298 0.93
50 11 0.03
ACGTcount: A:0.24, C:0.27, G:0.14, T:0.35
Consensus pattern (49 bp):
GGTATAAGGTTCACCATTGCGGCTTTAATCTTTCCCTCCACATCTCTAA
Found at i:129932 original size:98 final size:96
Alignment explanation
Indices: 129800--130099 Score: 252
Period size: 98 Copynumber: 3.1 Consensus size: 96
129790 TTTGCCTTTG
* * *
129800 CGGCTTTAATC-TTCCTCTTCACATATTCAGGGTATAAGGTTTATCGTTAC-GTCTTCAAT-CTA
1 CGGCTTTAATCTTTCC-CATCACATCTT-AAGGTATAAGGTTTATCGTTACAG-CTTC-ATCCT-
* * *
129862 CTT-CTCCTCATCT-TCAGGGTATAGGGTTCACCATTA
61 -TTCCTCCACATCTCT-AGGGTATAAGATTCACCATTA
* *
129898 CGGCTTTAATCTTTCCCATCACATCTCTAAGGTATAAGGTTTGTCGTTGCAGCTTCATCCTTTCC
1 CGGCTTTAATCTTTCCCATCACATCT-TAAGGTATAAGGTTTATCGTTACAGCTTCATCCTTT-C
* *
129963 CTCCACATCTCTAGGGTATAAGATTCGCCATTG
64 CTCCACATCTCTAGGGTATAAGATTCACCATTA
* * * * * * *
129996 CGGCTTCAATCTTTCTCATCACATCTTTAAGGTATAAGGTTCATCATTGC-GACTTTAACCTTTC
1 CGGCTTTAATCTTTCCCATCACATC-TTAAGGTATAAGGTTTATCGTTACAG-CTTCATCCTTT-
* * * * *
130060 CCTCCACATCTCAAAGGTATAAGGTTCGCCATTG
63 CCTCCACATCTCTAGGGTATAAGATTCACCATTA
130094 CGGCTT
1 CGGCTT
130100 CAACCTTTTC
Statistics
Matches: 173, Mismatches: 20, Indels: 18
0.82 0.09 0.09
Matches are distributed among these distances:
96 2 0.01
97 3 0.02
98 160 0.92
99 8 0.05
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.36
Consensus pattern (96 bp):
CGGCTTTAATCTTTCCCATCACATCTTAAGGTATAAGGTTTATCGTTACAGCTTCATCCTTTCCT
CCACATCTCTAGGGTATAAGATTCACCATTA
Found at i:130100 original size:147 final size:145
Alignment explanation
Indices: 129870--130315 Score: 484
Period size: 147 Copynumber: 3.0 Consensus size: 145
129860 TACTTCTCCT
* * * * * *
129870 CATCTTCAGGGTATAGGGTTCACCATTACGGCTTTAATCTTTCCCAT-CACATCTCTAAGGTATA
1 CATCTTTAAGGTATAAGGTTCATCATT-CGACTTTAACCTTTCCC-TCCACATCTC-AAGGTATA
* * * * * *
129934 AGGTTTGTCGTTGCAGCTTCATCCTTTCCCTCCACATCTCTAGGGTATAAGATTCGCCATTGCGG
63 AGGTTCGACATTGCGGCTTCAACCTTTCCCTCCACATCTCTACGGTATAAGATTCGCCATTGCGG
*
129999 CTTCAATCTTTCTCATCA
128 CTTCAATCTTTCCCATCA
130017 CATCTTTAAGGTATAAGGTTCATCATTGCGACTTTAACCTTTCCCTCCACATCTCAAAGGTATAA
1 CATCTTTAAGGTATAAGGTTCATCATT-CGACTTTAACCTTTCCCTCCACATCTC-AAGGTATAA
* * * * * * *
130082 GGTTCGCCATTGCGGCTTCAACCTTTTCCTCCAAATCTCAATGGTACAAGATTCGCCATTGTGGC
64 GGTTCGACATTGCGGCTTCAACCTTTCCCTCCACATCTCTACGGTATAAGATTCGCCATTGCGGC
130147 TTCAATCTTTCCCATCA
129 TTCAATCTTTCCCATCA
** ** ** * *
130164 CATCTTTAAGGTATAAGGTTTGTTGTTATAGCTTCAACCTTTCCCTCCACATCTCTAGCGTATAA
1 CATCTTTAAGGTATAAGGTTCATCATTCGA-CTTTAACCTTTCCCTCCACATCTCAAG-GTATAA
* * * * *
130229 GATTC-ACAGTTGCGGCTTTAACCTTTCCCTCCACATCTCTACGGTATAAGATTCACCATTACGA
64 GGTTCGACA-TTGCGGCTTCAACCTTTCCCTCCACATCTCTACGGTATAAGATTCGCCATTGCGG
*
130293 CTTTAATCTTTCCC-TCCA
128 CTTCAATCTTTCCCAT-CA
130311 CATCT
1 CATCT
130316 CTACAGTATA
Statistics
Matches: 253, Mismatches: 41, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
146 7 0.03
147 246 0.97
ACGTcount: A:0.23, C:0.28, G:0.14, T:0.35
Consensus pattern (145 bp):
CATCTTTAAGGTATAAGGTTCATCATTCGACTTTAACCTTTCCCTCCACATCTCAAGGTATAAGG
TTCGACATTGCGGCTTCAACCTTTCCCTCCACATCTCTACGGTATAAGATTCGCCATTGCGGCTT
CAATCTTTCCCATCA
Found at i:139783 original size:21 final size:21
Alignment explanation
Indices: 139757--139803 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
139747 GGTTGGTACG
* *
139757 AAGGACAAAAAGAGGAAGCAC
1 AAGGACAAAAAGAAGAAACAC
*
139778 AAGGACAAGAAGAAGAAACAC
1 AAGGACAAAAAGAAGAAACAC
139799 AAGGA
1 AAGGA
139804 GGAAGAAGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.60, C:0.13, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGGACAAAAAGAAGAAACAC
Found at i:146363 original size:17 final size:17
Alignment explanation
Indices: 146349--146406 Score: 62
Period size: 17 Copynumber: 3.4 Consensus size: 17
146339 TAATTGTCCT
146349 TGCATTTATATTGTCAC
1 TGCATTTATATTGTCAC
* * *
146366 TACATTTTTATTGTCGC
1 TGCATTTATATTGTCAC
* * *
146383 TGCATCTACATTGTCAT
1 TGCATTTATATTGTCAC
146400 TGCATTT
1 TGCATTT
146407 CCATATATAT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.21, C:0.19, G:0.12, T:0.48
Consensus pattern (17 bp):
TGCATTTATATTGTCAC
Found at i:152862 original size:14 final size:15
Alignment explanation
Indices: 152837--152869 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
152827 AGAAAATTGA
152837 AAAACAATTTTAATT
1 AAAACAATTTTAATT
152852 AAAAC-ATTTTAATT
1 AAAACAATTTTAATT
152866 AAAA
1 AAAA
152870 ATGAGCACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAACAATTTTAATT
Found at i:152870 original size:15 final size:16
Alignment explanation
Indices: 152831--152870 Score: 57
Period size: 14 Copynumber: 2.6 Consensus size: 16
152821 TTTTGAAGAA
152831 AATTGAAAAACAATTTT
1 AATT-AAAAACAATTTT
152848 AATT-AAAAC-ATTTT
1 AATTAAAAACAATTTT
152862 AATTAAAAA
1 AATTAAAAA
152871 TGAGCACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.41
15 9 0.41
17 4 0.18
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (16 bp):
AATTAAAAACAATTTT
Found at i:162153 original size:26 final size:25
Alignment explanation
Indices: 162123--162212 Score: 99
Period size: 26 Copynumber: 3.5 Consensus size: 25
162113 TCATACGAGC
*
162123 CCAGTTCAGTATATCGCTCTTTCGAA
1 CCAGTACAGTATATCGCTCTTTCG-A
* *
162149 CCAGTACAGTATAACGCTCTTTTGA
1 CCAGTACAGTATATCGCTCTTTCGA
* *
162174 CCTAGTACAATATATCGCTCTTACGA
1 CC-AGTACAGTATATCGCTCTTTCGA
*
162200 GGCAGTACAGTAT
1 -CCAGTACAGTAT
162213 CTTCGAGTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
25 3 0.06
26 49 0.92
27 1 0.02
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (25 bp):
CCAGTACAGTATATCGCTCTTTCGA
Found at i:173404 original size:17 final size:18
Alignment explanation
Indices: 173382--173422 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
173372 TTAGTTTTCA
173382 TGCATTCTT-ATTGTGC-C
1 TGCATTCTTAATTGT-CAC
173399 TGCATT-TTAATTGTCAC
1 TGCATTCTTAATTGTCAC
173416 TGCATTC
1 TGCATTC
173423 CTTTTAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 18 0.86
ACGTcount: A:0.17, C:0.22, G:0.15, T:0.46
Consensus pattern (18 bp):
TGCATTCTTAATTGTCAC
Found at i:186124 original size:28 final size:29
Alignment explanation
Indices: 186085--186141 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 29
186075 ATTCTTTGTA
*
186085 AAAATTGGTTGTTAATTT-TATAAATATT
1 AAAATTAGTTGTTAATTTATATAAATATT
* *
186113 AAAATTAGTTGTTTATTTATGTAAATATT
1 AAAATTAGTTGTTAATTTATATAAATATT
186142 TTTAAAACAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 16 0.64
29 9 0.36
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.51
Consensus pattern (29 bp):
AAAATTAGTTGTTAATTTATATAAATATT
Found at i:186196 original size:11 final size:11
Alignment explanation
Indices: 186180--186204 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
186170 ATTTAAATTA
186180 TTTTTTTTATT
1 TTTTTTTTATT
186191 TTTTTTTTATT
1 TTTTTTTTATT
186202 TTT
1 TTT
186205 CAAAATGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:187680 original size:18 final size:18
Alignment explanation
Indices: 187640--187681 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
187630 TTGAAGAAGA
187640 AGAAGAAAAAGAAGACCC
1 AGAAGAAAAAGAAGACCC
* * *
187658 TGAAGAAGAAGAAGATCC
1 AGAAGAAAAAGAAGACCC
187676 AGAAGA
1 AGAAGA
187682 GGCTCTTGAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.57, C:0.12, G:0.26, T:0.05
Consensus pattern (18 bp):
AGAAGAAAAAGAAGACCC
Found at i:194952 original size:26 final size:26
Alignment explanation
Indices: 194930--195055 Score: 137
Period size: 26 Copynumber: 4.8 Consensus size: 26
194920 CAATATATCA
*
194930 CTCTTTCGAGTCAATACAGTATAACG
1 CTCTTTCGAGCCAATACAGTATAACG
* *
194956 CTCTTGT-GAGCCAGTACAGTATAAAG
1 CTCTT-TCGAGCCAATACAGTATAACG
* *
194982 CTTTTTTGAGCCAATACAGTATAACG
1 CTCTTTCGAGCCAATACAGTATAACG
* * *
195008 CTCTTTCGAGCCAGTACATTATATCG
1 CTCTTTCGAGCCAATACAGTATAACG
* * *
195034 CTCTTACGAGCCAGTATAGTAT
1 CTCTTTCGAGCCAATACAGTAT
195056 CTTTGAGTCT
Statistics
Matches: 84, Mismatches: 14, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
25 1 0.01
26 82 0.98
27 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.32
Consensus pattern (26 bp):
CTCTTTCGAGCCAATACAGTATAACG
Found at i:195045 original size:52 final size:53
Alignment explanation
Indices: 194909--195055 Score: 163
Period size: 52 Copynumber: 2.8 Consensus size: 53
194899 TTAGCTCATA
* * *
194909 CGAGCCCAGTTCAATATATCACTCTTTCGAGTCAATACAGTATAACGCTCTTGT
1 CGAG-CCAGTACAATATATCGCTCTTTCGAGCCAATACAGTATAACGCTCTTGT
* ** * *
194963 -GAGCCAGTACAGTATAAAGCTTTTTTGAGCCAATACAGTATAACGCTCTT-T
1 CGAGCCAGTACAATATATCGCTCTTTCGAGCCAATACAGTATAACGCTCTTGT
* * * *
195014 CGAGCCAGTACATTATATCGCTCTTACGAGCCAGTATAGTAT
1 CGAGCCAGTACAATATATCGCTCTTTCGAGCCAATACAGTAT
195056 CTTTGAGTCT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
51 1 0.01
52 72 0.95
53 3 0.04
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (53 bp):
CGAGCCAGTACAATATATCGCTCTTTCGAGCCAATACAGTATAACGCTCTTGT
Found at i:196757 original size:627 final size:632
Alignment explanation
Indices: 195546--196812 Score: 2145
Period size: 627 Copynumber: 2.0 Consensus size: 632
195536 GCAACCAATT
*
195546 ATTTCACAACAAATACATGTAATTTCATCCTTTTAGGATTTTAGTCCTTATACTCTAAAATCATC
1 ATTTCACAACAAATACATGTAATTTCATCCTTTTAGCATTTTAGTCCTTATACTCTAAAATCATC
195611 AAAAATCACTTTACAAAATCAACCAATCTATCAACCAAGCTTCCAAAACTTTCATAAAATTTTAA
66 AAAAATCACTTT----AATCAA-CAA--TATCAACCAAGCTTCCAAAACTTTCATAAAATTTTAA
* * *
195676 GAATAAGCTTATTCATCAATGGAAAAATTTATAACATTTGACAGATTTACAAATTAGTCCTTGGG
124 AAATAAGCTTATTCATCAATGAAAAAATTTATAACATTTGACAAATTTACAAATTAGTCCTTGGG
*
195741 TTAGCTAGAGTAAGCTAATACTGACTCAATAACATAAAAATCACAAAAAACAGACAAAATTTACT
189 TTAGCTAGAGTAAGCTAATACTGACTCAATAAAATAAAAATCACAAAAAACAGACAAAATTTACT
* * *
195806 CACCAAATCAAAGGACCAAAACTCAAATGAAGCTCCCTTTTAATGGTTTTAGGGTTTCAGTTTGA
254 CACCAAATCAAAAGACCAAAACTCAAATGAAGCTCCCCTTTAATGGTTTTAGGGTTTCAGTTGGA
195871 AGAAGAAGAAGAAGCTAAGAAATTAGCTTATTTTACTTAAGTTTTATGATTAGCATTCAAGCTTT
319 AGAAGAAGAAGAAGCTAAGAAATTAGCTTATTTTACTTAAGTTTTATGATTAGCATTCAAGCTTT
* *
195936 GTTAATTTACAACTTTACCCTTATTAGCTAATAGATTTTCTTAATATAGTGAACCAAATACTAAG
384 GTTAATTTAAAACTTTACCCTTATTAGCTAATAGATTTTCTCAATATAGTGAACCAAATACTAAG
* * *
196001 CCTGACAAGCCTAAAAAGTCATCTGGGTGGGAATGAACCCAAAATTGGTATTGCCCATTCGTGAA
449 CCTGACAAGCCTAAAAAGTCATCTAGGTAGGAAAGAACCCAAAATTGGTATTGCCCATTCGTGAA
196066 CATCTTTTCCCCAAACCATTTTAGACTATGACATCTAGCTATAAGTAGTCTTTATTGACTCATTA
514 CATCTTTTCCCCAAACCATTTTAGACTATGACATCTAGCTATAAGTAGTCTTTATTGACTCATTA
* *
196131 TGTTGGTGGAATATCAGAAGATCCTACTAGGGTTGCGACTATTTAATTGAAGCA
579 TGTTGGTGGAAGATCAGAAGATCCTACTAGGGTTACGACTATTTAATTGAAGCA
*
196185 ATTTCGCAACAAATACATGTAATTTCATCCTTTTAGCATTTTAGTCCTTATACTCTAAAATCATC
1 ATTTCACAACAAATACATGTAATTTCATCCTTTTAGCATTTTAGTCCTTATACTCTAAAATCATC
* * *
196250 AAAATTCACTTT-A-C-A-AA-ATCAACCAAGCTTCCAAACCTTTCATAAACTTTTAAAAATAAG
66 AAAAATCACTTTAATCAACAATATCAACCAAGCTTCCAAAACTTTCATAAAATTTTAAAAATAAG
*
196310 CTTATTCATCAATGAAAAAATTTATAACATTTGACAAATTTACAAGTTAGTCCTTGGGTTAGCTA
131 CTTATTCATCAATGAAAAAATTTATAACATTTGACAAATTTACAAATTAGTCCTTGGGTTAGCTA
*
196375 GAGTAAGCTAATACTGACTCAATAAAATAAAAATCACAAAAAAC-GA-ATGAATTTTACTCACCA
196 GAGTAAGCTAATACTGACTCAATAAAATAAAAATCACAAAAAACAGACA--AAATTTACTCACCA
*
196438 AATCAAAAGACCAAAACTCAAATGAAGCTCCCCTTTAATGGTTTTAGGGTTTTTAGTTGGAAGAA
259 AATCAAAAGACCAAAACTCAAATGAAGCTCCCCTTTAATGGTTTTAGGG-TTTCAGTTGGAAGAA
*
196503 GAAGAAGAAGCTAAGAAATTAGCTTATTTTACTTATGTTTTATGATTAGCATTCAAGCTTTGTTA
323 GAAGAAGAAGCTAAGAAATTAGCTTATTTTACTTAAGTTTTATGATTAGCATTCAAGCTTTGTTA
* *
196568 ATTTAAAACTTTACCCTTATTAGCTAATAGATTTTCTCAATATAGTGAACCAAATACTAGGCTTG
388 ATTTAAAACTTTACCCTTATTAGCTAATAGATTTTCTCAATATAGTGAACCAAATACTAAGCCTG
196633 ACAAGCCTAAAAAGTCATCTAGGTAGGAAAGAACCCAAAATTGGTATTGCCCATTCGTGAACATC
453 ACAAGCCTAAAAAGTCATCTAGGTAGGAAAGAACCCAAAATTGGTATTGCCCATTCGTGAACATC
*
196698 TTTT-CCCAAACCATTTTAGACTATGAGATCTAGCTATAAGTAGTCTTTATTGACTCATTATGTT
518 TTTTCCCCAAACCATTTTAGACTATGACATCTAGCTATAAGTAGTCTTTATTGACTCATTATGTT
*
196762 GGTGGAAGATCAGAAGATCCTACTAGGGTTACGACTATTTGATTGAAGCA
583 GGTGGAAGATCAGAAGATCCTACTAGGGTTACGACTATTTAATTGAAGCA
196812 A
1 A
196813 AGTCCCCAAA
Statistics
Matches: 598, Mismatches: 27, Indels: 18
0.93 0.04 0.03
Matches are distributed among these distances:
625 1 0.00
626 2 0.00
627 312 0.52
628 204 0.34
630 2 0.00
632 1 0.00
633 1 0.00
634 1 0.00
639 74 0.12
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.32
Consensus pattern (632 bp):
ATTTCACAACAAATACATGTAATTTCATCCTTTTAGCATTTTAGTCCTTATACTCTAAAATCATC
AAAAATCACTTTAATCAACAATATCAACCAAGCTTCCAAAACTTTCATAAAATTTTAAAAATAAG
CTTATTCATCAATGAAAAAATTTATAACATTTGACAAATTTACAAATTAGTCCTTGGGTTAGCTA
GAGTAAGCTAATACTGACTCAATAAAATAAAAATCACAAAAAACAGACAAAATTTACTCACCAAA
TCAAAAGACCAAAACTCAAATGAAGCTCCCCTTTAATGGTTTTAGGGTTTCAGTTGGAAGAAGAA
GAAGAAGCTAAGAAATTAGCTTATTTTACTTAAGTTTTATGATTAGCATTCAAGCTTTGTTAATT
TAAAACTTTACCCTTATTAGCTAATAGATTTTCTCAATATAGTGAACCAAATACTAAGCCTGACA
AGCCTAAAAAGTCATCTAGGTAGGAAAGAACCCAAAATTGGTATTGCCCATTCGTGAACATCTTT
TCCCCAAACCATTTTAGACTATGACATCTAGCTATAAGTAGTCTTTATTGACTCATTATGTTGGT
GGAAGATCAGAAGATCCTACTAGGGTTACGACTATTTAATTGAAGCA
Found at i:202137 original size:30 final size:29
Alignment explanation
Indices: 202081--202137 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 29
202071 ATGCATGAAA
*
202081 TTAATTGTTTAATACTATTTAATTGAAGC
1 TTAATTGTTTAATACTATTCAATTGAAGC
202110 TTAATTGGTGTTAATA-TATTCAATTGAA
1 TTAATT-GT-TTAATACTATTCAATTGAA
202138 AGTGTATGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 6 0.24
30 13 0.52
31 6 0.24
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.47
Consensus pattern (29 bp):
TTAATTGTTTAATACTATTCAATTGAAGC
Found at i:206624 original size:15 final size:15
Alignment explanation
Indices: 206604--206642 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
206594 ACCAACGTGA
206604 GTGCAATTTACCCGG
1 GTGCAATTTACCCGG
206619 GTGCAATTTACCCGG
1 GTGCAATTTACCCGG
206634 GTGCAATTT
1 GTGCAATTT
206643 TAGTCTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.26, T:0.31
Consensus pattern (15 bp):
GTGCAATTTACCCGG
Found at i:243520 original size:28 final size:28
Alignment explanation
Indices: 243475--243538 Score: 112
Period size: 28 Copynumber: 2.3 Consensus size: 28
243465 TTCTACCGAA
243475 ACAAGTA-TGCAGAATTCAAGTAATCAT
1 ACAAGTATTGCAGAATTCAAGTAATCAT
*
243502 ACAAGTATTGCAGATTTCAAGTAATCAT
1 ACAAGTATTGCAGAATTCAAGTAATCAT
243530 ACAAGTATT
1 ACAAGTATT
243539 CAAAGTTACC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 7 0.20
28 28 0.80
ACGTcount: A:0.42, C:0.14, G:0.14, T:0.30
Consensus pattern (28 bp):
ACAAGTATTGCAGAATTCAAGTAATCAT
Found at i:253658 original size:15 final size:15
Alignment explanation
Indices: 253644--253672 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
253634 AGGCACAAGA
253644 AGGAGG-AGAAGAAG
1 AGGAGGAAGAAGAAG
253658 AGGAGGAAGAAGAAG
1 AGGAGGAAGAAGAAG
253673 CACCATGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (15 bp):
AGGAGGAAGAAGAAG
Found at i:268610 original size:22 final size:23
Alignment explanation
Indices: 268567--268610 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
268557 AAAAATTATT
*
268567 AAAATTAAAAAATAATATTATAA
1 AAAATTAAAAAATAATAGTATAA
* *
268590 AAAATTAATAAAT-TTAGTATA
1 AAAATTAAAAAATAATAGTATA
268611 CATAACCAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
AAAATTAAAAAATAATAGTATAA
Found at i:268789 original size:26 final size:24
Alignment explanation
Indices: 268759--268816 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
268749 ATTTAACTTT
268759 ATTTATAATATCAATTATAAAATTAA
1 ATTTATAATATCAATTATAAAA-T-A
*
268785 ATTTAT-ATA-GAATTATAAAATA
1 ATTTATAATATCAATTATAAAATA
268807 ATTT-TAATAT
1 ATTTATAATAT
268817 GTTTTAATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
21 1 0.03
22 8 0.28
23 1 0.03
24 10 0.34
25 3 0.10
26 6 0.21
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (24 bp):
ATTTATAATATCAATTATAAAATA
Found at i:270171 original size:9 final size:9
Alignment explanation
Indices: 270154--270189 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
270144 CCGATCGATT
270154 AATCGAATTA
1 AATC-AATTA
270164 AATCAATTA
1 AATCAATTA
270173 AATCAATTA
1 AATCAATTA
*
270182 ATTCAATT
1 AATCAATT
270190 TTAACTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 21 0.84
10 4 0.16
ACGTcount: A:0.50, C:0.11, G:0.03, T:0.36
Consensus pattern (9 bp):
AATCAATTA
Found at i:270441 original size:5 final size:5
Alignment explanation
Indices: 270431--270472 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
270421 TCTTGTTTTC
* *
270431 TCTTT TCTTT TCCTTT CCTTT TCTTT TCCTT TCTTT TCTTT T
1 TCTTT TCTTT T-CTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
270473 TCTACCTAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
5 28 0.88
6 4 0.12
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (5 bp):
TCTTT
Found at i:270453 original size:16 final size:16
Alignment explanation
Indices: 270427--270472 Score: 76
Period size: 16 Copynumber: 2.9 Consensus size: 16
270417 TATCTCTTGT
270427 TTTCTCTTTTCTTTTCC
1 TTTC-CTTTTCTTTTCC
270444 TTTCCTTTTCTTTTCC
1 TTTCCTTTTCTTTTCC
270460 TTT-CTTTTCTTTT
1 TTTCCTTTTCTTTT
270473 TCTACCTAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.34
16 15 0.52
17 4 0.14
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCCTTTTCTTTTCC
Found at i:275051 original size:23 final size:22
Alignment explanation
Indices: 274976--275054 Score: 59
Period size: 23 Copynumber: 3.5 Consensus size: 22
274966 AATCGACCTG
* *
274976 ACCCGTTGACTTTGACCAACCTA
1 ACCCGTTAACTTTGATCAACC-A
* * * *
274999 ACCCGTTGACTTTAATCGACTCG
1 ACCCGTTAACTTTGATCAAC-CA
**
275022 AGTCGTTAACTTTGATCAACCAA
1 ACCCGTTAACTTTGATCAACC-A
275045 ACCCGTTAAC
1 ACCCGTTAAC
275055 CATTGACTTT
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.28, C:0.30, G:0.14, T:0.28
Consensus pattern (22 bp):
ACCCGTTAACTTTGATCAACCA
Found at i:276472 original size:62 final size:62
Alignment explanation
Indices: 276373--276490 Score: 211
Period size: 62 Copynumber: 1.9 Consensus size: 62
276363 TGCGATAGTG
*
276373 ACCCTTTGGATTCAGTCGTATCTTCTAGGCCGGGTAAAAGGGGTTACATTATTTATACTTAT
1 ACCCTTTGGATTCAGTCGTATCTTCTAGGCCGAGTAAAAGGGGTTACATTATTTATACTTAT
276435 ACCCTTTGGATTC-GATCGTATCTTCTAGGCCGAGTAAAAGGGGTTACATTATTTAT
1 ACCCTTTGGATTCAG-TCGTATCTTCTAGGCCGAGTAAAAGGGGTTACATTATTTAT
276491 GGATGATTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
61 1 0.02
62 53 0.98
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (62 bp):
ACCCTTTGGATTCAGTCGTATCTTCTAGGCCGAGTAAAAGGGGTTACATTATTTATACTTAT
Found at i:278078 original size:41 final size:40
Alignment explanation
Indices: 277993--278085 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 40
277983 TTCAACGAAA
* *
277993 AAAGTCAACAGGTCGAGTCAATAGGTCAGGTCAACGGTTT
1 AAAGTCAACAGGTCAAGTCAATAGGTCAGGTCAACGGTTC
* * * *
278033 AAAGTCAACGGGTCAAAGTTAATAGGTTAGGTCAATTGG-TC
1 AAAGTCAACAGGTC-AAGTCAATAGGTCAGGTCAA-CGGTTC
278074 AAAGTC-ACAGGT
1 AAAGTCAACAGGT
278086 TTGGGTCAAT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
40 18 0.41
41 24 0.55
42 2 0.05
ACGTcount: A:0.34, C:0.15, G:0.27, T:0.24
Consensus pattern (40 bp):
AAAGTCAACAGGTCAAGTCAATAGGTCAGGTCAACGGTTC
Found at i:279440 original size:12 final size:12
Alignment explanation
Indices: 279420--279453 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
279410 AAGAGGATAA
*
279420 AAAATAAAAGAG
1 AAAAGAAAAGAG
*
279432 AAAAGAAAATAG
1 AAAAGAAAAGAG
279444 AAAAGAAAAG
1 AAAAGAAAAG
279454 CAAGAGTTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAAGAAAAGAG
Found at i:279440 original size:17 final size:17
Alignment explanation
Indices: 279420--279453 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
279410 AAGAGGATAA
279420 AAAATA-AAAGAGAAAAG
1 AAAATAGAAA-AGAAAAG
279437 AAAATAGAAAAGAAAAG
1 AAAATAGAAAAGAAAAG
279454 CAAGAGTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.76, C:0.00, G:0.18, T:0.06
Consensus pattern (17 bp):
AAAATAGAAAAGAAAAG
Found at i:287219 original size:42 final size:42
Alignment explanation
Indices: 287136--287310 Score: 201
Period size: 42 Copynumber: 4.1 Consensus size: 42
287126 CAAACACTTG
* *
287136 ATGTATAAATGGAAGACTCATGTCTCGGAATGAGCATGAGAAT
1 ATGTTTAAA-GGAAGACTCATGTCTCAGAATGAGCATGAGAAT
** * * *
287179 ATGTTTAAAGGAAGACTTGTGACTCAGAATAAGCACGAGAAT
1 ATGTTTAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
* * * *
287221 ATGTTTAAAAAGGAAGACTTATGTCTAAGGATGAG--TGAGATT
1 ATGTTT--AAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
*
287263 ATGTTTAAAGGAAGACTCATGTCTCAGAATGAGCATGAGATT
1 ATGTTTAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
287305 ATGTTT
1 ATGTTT
287311 GAAAACAAAG
Statistics
Matches: 111, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
40 24 0.22
42 57 0.51
43 8 0.07
44 22 0.20
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (42 bp):
ATGTTTAAAGGAAGACTCATGTCTCAGAATGAGCATGAGAAT
Found at i:287289 original size:84 final size:85
Alignment explanation
Indices: 287146--287327 Score: 224
Period size: 84 Copynumber: 2.1 Consensus size: 85
287136 ATGTATAAAT
* * **
287146 GGAAGACTCATGTCTCGGAATGAGCATGAGAATATGTTTAAAGGAAGACTTGTGACTCAGAATAA
1 GGAAGACTTATGTCTAGGAATGAG-ATGAGAATATGTTTAAAGGAAGACTCATGACTCAGAATAA
287211 GCACGAGAATATGTTTAAAAA
65 GCACGAGAATATGTTTAAAAA
* * *
287232 GGAAGACTTATGTCTAAGG-ATGAG-TGAGATTATGTTTAAAGGAAGACTCATGTCTCAGAATGA
1 GGAAGACTTATGTCT-AGGAATGAGATGAGAATATGTTTAAAGGAAGACTCATGACTCAGAATAA
* * *
287295 GCATGAGATTATGTTTGAAAA
65 GCACGAGAATATGTTTAAAAA
**
287316 CAAAGACTTATG
1 GGAAGACTTATG
287328 CCTCGGTAGA
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
84 62 0.75
86 19 0.23
87 2 0.02
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (85 bp):
GGAAGACTTATGTCTAGGAATGAGATGAGAATATGTTTAAAGGAAGACTCATGACTCAGAATAAG
CACGAGAATATGTTTAAAAA
Found at i:289219 original size:16 final size:16
Alignment explanation
Indices: 289198--289237 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
289188 CGTCTTATTG
289198 GTGACTTTATAATTTT
1 GTGACTTTATAATTTT
289214 GTGACTTTATAATTTT
1 GTGACTTTATAATTTT
*
289230 GTCACTTT
1 GTGACTTT
289238 TCACATGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.23, C:0.10, G:0.12, T:0.55
Consensus pattern (16 bp):
GTGACTTTATAATTTT
Found at i:295908 original size:5 final size:5
Alignment explanation
Indices: 295898--295945 Score: 51
Period size: 5 Copynumber: 9.2 Consensus size: 5
295888 TGAAGGAACA
* * *
295898 TTTAT TTTAT TATAT TTTATT TTTATT TTTAT TTCAT TTTCT TTTAT T
1 TTTAT TTTAT TTTAT TTTA-T TTTA-T TTTAT TTTAT TTTAT TTTAT T
295946 ATTCAGTATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
5 25 0.69
6 11 0.31
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:312667 original size:13 final size:13
Alignment explanation
Indices: 312651--312675 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312641 AAAAAAATGA
312651 GAAAAAGAAGAAT
1 GAAAAAGAAGAAT
312664 GAAAAAGAAGAA
1 GAAAAAGAAGAA
312676 AGAATAAATT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (13 bp):
GAAAAAGAAGAAT
Found at i:314815 original size:9 final size:9
Alignment explanation
Indices: 314801--314857 Score: 61
Period size: 9 Copynumber: 6.9 Consensus size: 9
314791 GCAAATGATT
314801 TTAAAATTA
1 TTAAAATTA
314810 TTAAAATTA
1 TTAAAATTA
314819 TTAAAATTA
1 TTAAAATTA
314828 TT---ATT-
1 TTAAAATTA
*
314833 TTGAAA-TA
1 TTAAAATTA
*
314841 ATAAAATTA
1 TTAAAATTA
314850 TTAAAATT
1 TTAAAATT
314858 TCCAATTTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
7 1 0.03
8 5 0.12
9 29 0.73
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (9 bp):
TTAAAATTA
Found at i:325547 original size:27 final size:29
Alignment explanation
Indices: 325517--325576 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 29
325507 GGAAAATGTC
325517 TTCTTCTTCT-TTTTC-CTTCTCCTCTTT
1 TTCTTCTTCTATTTTCTCTTCTCCTCTTT
*
325544 TTC-T-TTCTATTTTCTCTTCTCTTCTTT
1 TTCTTCTTCTATTTTCTCTTCTCCTCTTT
*
325571 TGCTTC
1 TTCTTC
325577 AATACCCCAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
25 4 0.15
26 6 0.22
27 16 0.59
28 1 0.04
ACGTcount: A:0.02, C:0.30, G:0.02, T:0.67
Consensus pattern (29 bp):
TTCTTCTTCTATTTTCTCTTCTCCTCTTT
Found at i:340820 original size:81 final size:81
Alignment explanation
Indices: 340678--340832 Score: 229
Period size: 81 Copynumber: 1.9 Consensus size: 81
340668 CCTAGTGCTA
* ** * *
340678 AAGGTCTTATTTATAGCTTTACATAGTCGTTTTTCCTCAACTGTAAGTCAATTACCGTCCTTTGT
1 AAGGTCTTATTTATAGCTTTACATAGTCATTTTTCCTCAACCCTAAGTCAATTACCATCCTTCGT
340743 GTTTAAATTGTATTGT
66 GTTTAAATTGTATTGT
* * * *
340759 AAGGTCTTATTTATAGCTTTACATGGTCATTTTTCCTCAACCCTAAGTTAGTTATCATCCTTCGT
1 AAGGTCTTATTTATAGCTTTACATAGTCATTTTTCCTCAACCCTAAGTCAATTACCATCCTTCGT
340824 GTTTAAATT
66 GTTTAAATT
340833 ATTTTGTGAA
Statistics
Matches: 65, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.24, C:0.17, G:0.14, T:0.45
Consensus pattern (81 bp):
AAGGTCTTATTTATAGCTTTACATAGTCATTTTTCCTCAACCCTAAGTCAATTACCATCCTTCGT
GTTTAAATTGTATTGT
Found at i:345093 original size:18 final size:18
Alignment explanation
Indices: 345067--345112 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
345057 GCGCAACCTG
345067 ATCAGATGCAGTCACATA
1 ATCAGATGCAGTCACATA
* * *
345085 CTTAGATGCAGTCATATA
1 ATCAGATGCAGTCACATA
345103 ATCAGATGCA
1 ATCAGATGCA
345113 ACCACATGCT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.26
Consensus pattern (18 bp):
ATCAGATGCAGTCACATA
Found at i:351037 original size:23 final size:23
Alignment explanation
Indices: 351008--351052 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
350998 GTATTGAAGC
*
351008 AGAAGAA-GAGAAGAGAAAAGAAA
1 AGAAGAAGGA-AAAAGAAAAGAAA
351031 AGAAGAAGGAAAAAGAAAAGAA
1 AGAAGAAGGAAAAAGAAAAGAA
351053 GTTGAAAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (23 bp):
AGAAGAAGGAAAAAGAAAAGAAA
Found at i:357350 original size:17 final size:18
Alignment explanation
Indices: 357328--357365 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
357318 AGAAAAATAT
357328 TTCAATTT-GT-CATTTCA
1 TTCAATTTAGTCCA-TTCA
357345 TTCAATTTAGTCCATTCA
1 TTCAATTTAGTCCATTCA
357363 TTC
1 TTC
357366 TAGTCTAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 9 0.47
19 2 0.11
ACGTcount: A:0.24, C:0.21, G:0.05, T:0.50
Consensus pattern (18 bp):
TTCAATTTAGTCCATTCA
Found at i:358372 original size:11 final size:11
Alignment explanation
Indices: 358356--358390 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
358346 TGTTTTAATA
*
358356 TATTTTAACTT
1 TATTTTAACAT
358367 TATTTTAACAT
1 TATTTTAACAT
*
358378 TAATTTAACAT
1 TATTTTAACAT
358389 TA
1 TA
358391 AAATAACATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.54
Consensus pattern (11 bp):
TATTTTAACAT
Found at i:360553 original size:20 final size:20
Alignment explanation
Indices: 360507--360558 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
360497 TTTTTAAGTG
* * *
360507 TTAAAATGATTTTGACTTAT
1 TTAAAATCATTTCGACATAT
* * *
360527 TTCAAATTATTTCGACATGT
1 TTAAAATCATTTCGACATAT
360547 TTAAAATCATTT
1 TTAAAATCATTT
360559 TAACTTGATT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (20 bp):
TTAAAATCATTTCGACATAT
Found at i:371292 original size:24 final size:24
Alignment explanation
Indices: 371242--371299 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 24
371232 CCTTGGACAA
371242 TTATTTCTTTCTTAGATTTAGGCTTAG
1 TTATTTCTTTCTTAGATTT--G-TTAG
371269 TTTATTTCTTTCTTAGATTT-TTAG
1 -TTATTTCTTTCTTAGATTTGTTAG
371293 TTATTTC
1 TTATTTC
371300 ATTTTCGTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 7 0.23
24 4 0.13
28 19 0.63
ACGTcount: A:0.17, C:0.10, G:0.10, T:0.62
Consensus pattern (24 bp):
TTATTTCTTTCTTAGATTTGTTAG
Found at i:383351 original size:12 final size:11
Alignment explanation
Indices: 383329--383362 Score: 50
Period size: 12 Copynumber: 3.0 Consensus size: 11
383319 AAACTGAAAT
*
383329 TAAACAAATAA
1 TAAAAAAATAA
383340 TAAAAGAAATAA
1 TAAAA-AAATAA
383352 TAAAAAAATAA
1 TAAAAAAATAA
383363 GATAAAAGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.76, C:0.03, G:0.03, T:0.18
Consensus pattern (11 bp):
TAAAAAAATAA
Found at i:384179 original size:25 final size:26
Alignment explanation
Indices: 384145--384195 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
384135 TAAAGACAAC
* *
384145 AATGTAAATGAACATAAAATTGAATT
1 AATGTAAATGAAAAGAAAATTGAATT
*
384171 AATG-AAATGAAAAGAAACTTGAATT
1 AATGTAAATGAAAAGAAAATTGAATT
384196 GTATAGCAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.55, C:0.04, G:0.14, T:0.27
Consensus pattern (26 bp):
AATGTAAATGAAAAGAAAATTGAATT
Found at i:391686 original size:31 final size:31
Alignment explanation
Indices: 391648--391709 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
391638 GACTATTGCT
391648 TTACAATAAAACTGAAATTTTAAAATTAAAA
1 TTACAATAAAACTGAAATTTTAAAATTAAAA
391679 TTACAATAAAACTGAAATTTTAAAATTAAAA
1 TTACAATAAAACTGAAATTTTAAAATTAAAA
391710 AATATAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.58, C:0.06, G:0.03, T:0.32
Consensus pattern (31 bp):
TTACAATAAAACTGAAATTTTAAAATTAAAA
Found at i:391696 original size:17 final size:17
Alignment explanation
Indices: 391648--391697 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
391638 GACTATTGCT
391648 TTACAATAAAACTGAAA
1 TTACAATAAAACTGAAA
* * *
391665 TT---TTAAAATTAAAA
1 TTACAATAAAACTGAAA
391679 TTACAATAAAACTGAAA
1 TTACAATAAAACTGAAA
391696 TT
1 TT
391698 TTAAAATTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 6
0.67 0.17 0.17
Matches are distributed among these distances:
14 11 0.46
17 13 0.54
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (17 bp):
TTACAATAAAACTGAAA
Found at i:391928 original size:33 final size:33
Alignment explanation
Indices: 391890--391958 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
391880 TTAAATTAAA
*
391890 ATACATATAATAATTCTACAACTTAAACAAAAT
1 ATACATATAATAAATCTACAACTTAAACAAAAT
391923 ATACATATAATAAATCTACAACTTAAACAAAAT
1 ATACATATAATAAATCTACAACTTAAACAAAAT
391956 ATA
1 ATA
391959 AGGTGTAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (33 bp):
ATACATATAATAAATCTACAACTTAAACAAAAT
Found at i:395128 original size:30 final size:30
Alignment explanation
Indices: 395108--395208 Score: 134
Period size: 30 Copynumber: 3.4 Consensus size: 30
395098 GTTCCCTTAT
395108 CTTTCTAAAAATTTCATTTTGACCCTCAAA
1 CTTTCTAAAAATTTCATTTTGACCCTCAAA
*
395138 CTTTCTAAAAATATCATTTTGA-CCT-AAA
1 CTTTCTAAAAATTTCATTTTGACCCTCAAA
* * *
395166 CTTTTTAAGAATTGCATTTTGACCCTCAAA
1 CTTTCTAAAAATTTCATTTTGACCCTCAAA
* *
395196 CTTTTTGAAAATT
1 CTTTCTAAAAATT
395209 ACAATTTAAC
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
28 21 0.34
29 6 0.10
30 35 0.56
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.42
Consensus pattern (30 bp):
CTTTCTAAAAATTTCATTTTGACCCTCAAA
Found at i:395354 original size:17 final size:16
Alignment explanation
Indices: 395325--395375 Score: 52
Period size: 18 Copynumber: 3.1 Consensus size: 16
395315 TTTTTTTCTT
395325 TTAAAA-TT-TTTTTA
1 TTAAAATTTCTTTTTA
395339 TATAAAATTTCATTTTTA
1 T-TAAAATTTC-TTTTTA
395357 TTAAAAATTTCGTTTTTA
1 TT-AAAATTTC-TTTTTA
395375 T
1 T
395376 CCTCTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
14 1 0.03
15 5 0.16
16 2 0.06
17 1 0.03
18 22 0.71
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (16 bp):
TTAAAATTTCTTTTTA
Found at i:395354 original size:18 final size:18
Alignment explanation
Indices: 395333--395375 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
395323 TTTTAAAATT
395333 TTTTTA-TATAAAATTTCA
1 TTTTTATTA-AAAATTTCA
*
395351 TTTTTATTAAAAATTTCG
1 TTTTTATTAAAAATTTCA
395369 TTTTTAT
1 TTTTTAT
395376 CCTCTTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 21 0.91
19 2 0.09
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (18 bp):
TTTTTATTAAAAATTTCA
Found at i:399936 original size:81 final size:81
Alignment explanation
Indices: 399829--399999 Score: 256
Period size: 81 Copynumber: 2.1 Consensus size: 81
399819 ATGGAGGCAG
*
399829 TTAA-CAAGAATATCAAGAAGATCGAGACCTACAAATATTGGCATGAGAAGTTATCATTTGCTCT
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATGAGAAGTTATCATTTGCTCT
*
399893 CTACGCTTATTGAA-CA
66 CTACGCCTATT-AAGCA
* * *
399909 TTAATCAAGAATATCGAGAAGATCGAGACTTGCAAAGATTGGCATGAGAAGTTATCATTTGCTCT
1 TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATGAGAAGTTATCATTTGCTCT
*
399974 TTACGCCTATTAAGCA
66 CTACGCCTATTAAGCA
*
399990 TCAATCAAGA
1 TTAATCAAGA
400000 TTTTATTGAG
Statistics
Matches: 82, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
80 6 0.07
81 76 0.93
ACGTcount: A:0.37, C:0.17, G:0.18, T:0.29
Consensus pattern (81 bp):
TTAATCAAGAATATCAAGAAGATCGAGACCTACAAAGATTGGCATGAGAAGTTATCATTTGCTCT
CTACGCCTATTAAGCA
Found at i:400460 original size:19 final size:17
Alignment explanation
Indices: 400438--400494 Score: 53
Period size: 19 Copynumber: 3.2 Consensus size: 17
400428 AAATAAAAAT
*
400438 AAAAAAAAGAGGAAAGA
1 AAAAAAAAAAGGAAAGA
*
400455 GAAAAAGAAAAAAGAAAGAA
1 -AAAAA-AAAAAGGAAAG-A
400475 AAAAAGAAAAAGGAAA-A
1 AAAAA-AAAAAGGAAAGA
400492 AAA
1 AAA
400495 GAAGGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
17 4 0.12
18 5 0.15
19 24 0.71
20 1 0.03
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAGGAAAGA
Found at i:400466 original size:7 final size:7
Alignment explanation
Indices: 400425--400493 Score: 52
Period size: 7 Copynumber: 9.9 Consensus size: 7
400415 TTTCACCCAA
*
400425 AAAAAAT
1 AAAAAAG
*
400432 AAAAATAA
1 AAAAA-AG
400440 AAAAAAG
1 AAAAAAG
**
400447 AGGAAAG
1 AAAAAAG
400454 AGAAAAAG
1 A-AAAAAG
400462 AAAAAAG
1 AAAAAAG
*
400469 -AAAGA-
1 AAAAAAG
400474 AAAAAAG
1 AAAAAAG
*
400481 AAAAAGG
1 AAAAAAG
400488 AAAAAA
1 AAAAAA
400494 AGAAGGAAAA
Statistics
Matches: 48, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
6 8 0.17
7 29 0.60
8 11 0.23
ACGTcount: A:0.81, C:0.00, G:0.16, T:0.03
Consensus pattern (7 bp):
AAAAAAG
Found at i:400468 original size:15 final size:14
Alignment explanation
Indices: 400426--400497 Score: 60
Period size: 15 Copynumber: 5.1 Consensus size: 14
400416 TTCACCCAAA
* *
400426 AAAAATAAAAATAAA
1 AAAAAGAAAAA-AAG
* *
400441 AAAAAGAGGAAAGAG
1 AAAAAGA-AAAAAAG
400456 AAAAAG-AAAAAAG
1 AAAAAGAAAAAAAG
400469 --AAAGAAAAAAAG
1 AAAAAGAAAAAAAG
400481 AAAAAGGAAAAAAAG
1 AAAAA-GAAAAAAAG
400496 AA
1 AA
400498 GGAAAAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
11 4 0.09
12 7 0.15
13 5 0.11
14 3 0.07
15 24 0.52
16 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.03
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:400477 original size:12 final size:12
Alignment explanation
Indices: 400458--400506 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
400448 GGAAAGAGAA
400458 AAAG-AAAAAAG
1 AAAGAAAAAAAG
400469 AAAGAAAAAAAG
1 AAAGAAAAAAAG
400481 AAAAAGGAAAAAAAG
1 --AAA-GAAAAAAAG
*
400496 AAGGAAAAAAA
1 AAAGAAAAAAA
400507 AGGGAGAGGT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
11 4 0.12
12 15 0.45
13 2 0.06
14 3 0.09
15 9 0.27
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:400492 original size:27 final size:25
Alignment explanation
Indices: 400424--400506 Score: 80
Period size: 27 Copynumber: 3.3 Consensus size: 25
400414 ATTTCACCCA
* *
400424 AAAAAAATAAAAA-TAAAAA-AAAG
1 AAAAAAAGAAAAAGAAAAAAGAAAG
* *
400447 AGGAAAGAGAAAAAGAAAAAAGAAAG
1 A-AAAAAAGAAAAAGAAAAAAGAAAG
*
400473 AAAAAAAGAAAAAGGAAAAAAAGAAGG
1 AAAAAAAGAAAAA-G-AAAAAAGAAAG
400500 AAAAAAA
1 AAAAAAA
400507 AGGGAGAGGT
Statistics
Matches: 48, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
23 1 0.02
24 9 0.19
25 15 0.31
26 6 0.12
27 17 0.35
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (25 bp):
AAAAAAAGAAAAAGAAAAAAGAAAG
Found at i:400502 original size:19 final size:19
Alignment explanation
Indices: 400449--400505 Score: 71
Period size: 19 Copynumber: 3.0 Consensus size: 19
400439 AAAAAAAGAG
*
400449 GAAAGAGAAAAAGAAAAAA
1 GAAAGAAAAAAAGAAAAAA
*
400468 GAAAGAAAAAAAGAAAAAG
1 GAAAGAAAAAAAGAAAAAA
*
400487 GAAA-AAAAGAAGGAAAAAA
1 GAAAGAAAA-AAAGAAAAAA
400506 AAGGGAGAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
18 4 0.12
19 29 0.88
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
GAAAGAAAAAAAGAAAAAA
Found at i:401032 original size:112 final size:113
Alignment explanation
Indices: 400819--401128 Score: 491
Period size: 113 Copynumber: 2.8 Consensus size: 113
400809 CAATATTTGT
* *
400819 ATTCATGTGAGCTTTGCCTCTAATAAAATTCAATTTT-TCCACCTCACAACCATGTTCAAACATT
1 ATTCATGCGAGCTTTGCCTCTAATAAAATTCAATTTTATCCACCTCACAACCATGTTCAAGCATT
*
400883 TTTGCATTGACATAACA-TTAGTGGACTAATGATTTTTTAACCATTTA
66 TTTGCATTGAAATAACAGTTAGTGGACTAATGATTTTTTAACCATTTA
* *
400930 ATTCATGCGAGCTTTGCCTCCAATAAAATTCAATTTTATCCACCTCATAACCATGTTCAAGCATT
1 ATTCATGCGAGCTTTGCCTCTAATAAAATTCAATTTTATCCACCTCACAACCATGTTCAAGCATT
* *
400995 TTTGCATTGAAATAACAGTTAGTGGACTAATGATTTTTTAATCTTTTA
66 TTTGCATTGAAATAACAGTTAGTGGACTAATGATTTTTTAACCATTTA
* * * *
401043 ATTTACGCGAGCTTTGCCTCTAAT-AAATATCAATTTTATCCACCTTACAACCCTGTTCAAGCAT
1 ATTCATGCGAGCTTTGCCTCTAATAAAAT-TCAATTTTATCCACCTCACAACCATGTTCAAGCAT
401107 TTTTGCATTGAAATAACAGTTA
65 TTTTGCATTGAAATAACAGTTA
401129 ATGGTCAAAC
Statistics
Matches: 183, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
111 35 0.19
112 45 0.25
113 103 0.56
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (113 bp):
ATTCATGCGAGCTTTGCCTCTAATAAAATTCAATTTTATCCACCTCACAACCATGTTCAAGCATT
TTTGCATTGAAATAACAGTTAGTGGACTAATGATTTTTTAACCATTTA
Found at i:401627 original size:50 final size:50
Alignment explanation
Indices: 401563--401875 Score: 210
Period size: 50 Copynumber: 6.3 Consensus size: 50
401553 AGGGAACATG
* * * *
401563 AAGATATGAAGGGAAATGTTGAGGCTGCAACGATGAACCCGA-TACCTTAA
1 AAGATGTGATGGGAAA-GTTGAGGCCGCAACGATGAATCCGAGTACCTTAA
* * ** * *
401613 AAGATGTGATGGGAAGGATTGAGGCCGTAACGACAAATCC-AGTACCAT-G
1 AAGATGTGATGGGAAAG-TTGAGGCCGCAACGATGAATCCGAGTACCTTAA
* * * * * *
401662 AAGATATGAAGGGAAAGGTGAAGGCTGCAATGATGAATCC-AGTACCTTAG
1 AAGATGTGATGGGAAAGTTG-AGGCCGCAACGATGAATCCGAGTACCTTAA
* * * * * *
401712 AAGATGTGATAGGAAAGATTGATGCCGCAACGACGAATCTGA-TACCAT-G
1 AAGATGTGATGGGAAAG-TTGAGGCCGCAACGATGAATCCGAGTACCTTAA
* * * * * *
401761 AAGATATGAAGGGAAATGTTGAGGCTGCAACGGTGAACCCGA-TACCCTAA
1 AAGATGTGATGGGAAA-GTTGAGGCCGCAACGATGAATCCGAGTACCTTAA
** * * *
401811 AAGATGTGATGGGAAAGGTTGAGGCCATAATGGTGAA-CCTAGTACCTTAA
1 AAGATGTGATGGGAAA-GTTGAGGCCGCAACGATGAATCCGAGTACCTTAA
*
401861 AAGATGTGATAGGAA
1 AAGATGTGATGGGAA
401876 GAATTTTGGT
Statistics
Matches: 203, Mismatches: 51, Indels: 18
0.75 0.19 0.07
Matches are distributed among these distances:
48 2 0.01
49 77 0.38
50 121 0.60
51 3 0.01
ACGTcount: A:0.37, C:0.14, G:0.29, T:0.20
Consensus pattern (50 bp):
AAGATGTGATGGGAAAGTTGAGGCCGCAACGATGAATCCGAGTACCTTAA
Found at i:401732 original size:99 final size:99
Alignment explanation
Indices: 401559--401836 Score: 391
Period size: 99 Copynumber: 2.8 Consensus size: 99
401549 ATCAAGGGAA
401559 CATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGATGAACCCGATACCTTAAAAGATGTGATG
1 CATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGATGAACCCGATACCTTAAAAGATGTGATG
* *
401624 GGAAGGATTGAGGCCGTAACGACAAATCCAG-TAC
66 GGAAAGATTGAGGCCGCAACGACAAAT-CAGATAC
* * * *
401658 CATGAAGATATGAAGGGAAA-GGTGAAGGCTGCAATGATGAATCC-AGTACCTTAGAAGATGTGA
1 CATGAAGATATGAAGGGAAATGTTG-AGGCTGCAACGATGAACCCGA-TACCTTAAAAGATGTGA
* * * *
401721 TAGGAAAGATTGATGCCGCAACGACGAATCTGATAC
64 TGGGAAAGATTGAGGCCGCAACGACAAATCAGATAC
* *
401757 CATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGGTGAACCCGATACCCTAAAAGATGTGATG
1 CATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGATGAACCCGATACCTTAAAAGATGTGATG
*
401822 GGAAAGGTTGAGGCC
66 GGAAAGATTGAGGCC
401837 ATAATGGTGA
Statistics
Matches: 155, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
98 6 0.04
99 145 0.94
100 4 0.03
ACGTcount: A:0.36, C:0.15, G:0.29, T:0.19
Consensus pattern (99 bp):
CATGAAGATATGAAGGGAAATGTTGAGGCTGCAACGATGAACCCGATACCTTAAAAGATGTGATG
GGAAAGATTGAGGCCGCAACGACAAATCAGATAC
Done.