Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 88 of 198
Found at i:28377351 original size:34 final size:34
Alignment explanation
Indices: 28377308--28377379 Score: 144
Period size: 34 Copynumber: 2.1 Consensus size: 34
28377298 ACACACCTAT
28377308 AAGTAAATTTCTTTCTTGGTTACCCAACCATCCA
1 AAGTAAATTTCTTTCTTGGTTACCCAACCATCCA
28377342 AAGTAAATTTCTTTCTTGGTTACCCAACCATCCA
1 AAGTAAATTTCTTTCTTGGTTACCCAACCATCCA
28377376 AAGT
1 AAGT
28377380 TATAAAATGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.35
Consensus pattern (34 bp):
AAGTAAATTTCTTTCTTGGTTACCCAACCATCCA
Found at i:28383726 original size:24 final size:23
Alignment explanation
Indices: 28383663--28383726 Score: 67
Period size: 24 Copynumber: 2.7 Consensus size: 23
28383653 TAAAAATAAA
28383663 ATATTTAA-AATATTATTAAATT
1 ATATTTAATAATATTATTAAATT
** * *
28383685 ATATATTTTTATTTTTATTAAATT
1 ATAT-TTAATAATATTATTAAATT
28383709 ATATTTAATAATAATTAT
1 ATATTTAATAAT-ATTAT
28383727 ATTAGAATAT
Statistics
Matches: 31, Mismatches: 8, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
22 4 0.13
23 7 0.23
24 20 0.65
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (23 bp):
ATATTTAATAATATTATTAAATT
Found at i:28383994 original size:16 final size:16
Alignment explanation
Indices: 28383943--28383995 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
28383933 ATTCAACCAA
*
28383943 ACAGTTCTATTTCATT
1 ACAGCTCTATTTCATT
* *
28383959 ACAACTCTATTCCATT
1 ACAGCTCTATTTCATT
28383975 ACAGCTCTATTTCATT
1 ACAGCTCTATTTCATT
28383991 ACAGC
1 ACAGC
28383996 AAACCAAACA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.28, C:0.26, G:0.06, T:0.40
Consensus pattern (16 bp):
ACAGCTCTATTTCATT
Found at i:28385504 original size:45 final size:45
Alignment explanation
Indices: 28385381--28385553 Score: 177
Period size: 45 Copynumber: 3.8 Consensus size: 45
28385371 TATACACCTA
** * *
28385381 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCAGGAC-T
1 AAATGAGTAAGACCATAGCTAAAAGACACTATGGCATCATGACAT
* * *
28385425 AGAATGATTAAGACCATAGCTGAAAGACGCTATGGCATCATGACAT
1 A-AATGAGTAAGACCATAGCTAAAAGACACTATGGCATCATGACAT
* * ** *
28385471 AAATGAGTAAGACTATAGCTAAAAGACACTATGGAATCATGGTAA
1 AAATGAGTAAGACCATAGCTAAAAGACACTATGGCATCATGACAT
* * ***
28385516 AAAGGACTAAGACCATAGCTGGGAGACACTATGGCATC
1 AAATGAGTAAGACCATAGCTAAAAGACACTATGGCATC
28385554 CTTTGATGAT
Statistics
Matches: 107, Mismatches: 20, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
44 1 0.01
45 104 0.97
46 2 0.02
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (45 bp):
AAATGAGTAAGACCATAGCTAAAAGACACTATGGCATCATGACAT
Found at i:28385534 original size:90 final size:89
Alignment explanation
Indices: 28385381--28385553 Score: 215
Period size: 90 Copynumber: 1.9 Consensus size: 89
28385371 TATACACCTA
** * * *
28385381 AAATGAGTAAGACCATAGCTAAAAGATGCTATGACATCAGGACTAGAATGATTAAGACCATAGCT
1 AAATGAGTAAGACCATAGCTAAAAGACACTATGACATCAGGAC-AAAAGGACTAAGACCATAGCT
*
28385446 GAAAGACGCTATGGCATCATGACAT
65 GAAAGACACTATGGCATCATGACAT
*
28385471 AAATGAGTAAGACTATAGCTAAAAGACACTATGGA-ATCATGGTA-AAAAGGACTAAGACCATAG
1 AAATGAGTAAGACCATAGCTAAAAGACACTAT-GACATCA-GG-ACAAAAGGACTAAGACCATAG
**
28385534 CTGGGAGACACTATGGCATC
63 CTGAAAGACACTATGGCATC
28385554 CTTTGATGAT
Statistics
Matches: 71, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
90 66 0.93
91 4 0.06
92 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.22, T:0.20
Consensus pattern (89 bp):
AAATGAGTAAGACCATAGCTAAAAGACACTATGACATCAGGACAAAAGGACTAAGACCATAGCTG
AAAGACACTATGGCATCATGACAT
Found at i:28394450 original size:15 final size:15
Alignment explanation
Indices: 28394430--28394468 Score: 60
Period size: 15 Copynumber: 2.5 Consensus size: 15
28394420 TTTTAAATTT
28394430 TATTATTATAACATA
1 TATTATTATAACATA
*
28394445 TATTATTATAACTTA
1 TATTATTATAACATA
28394460 TATATATTA
1 TAT-TATTA
28394469 AGTTAATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TATTATTATAACATA
Found at i:28402494 original size:61 final size:63
Alignment explanation
Indices: 28402424--28402557 Score: 152
Period size: 64 Copynumber: 2.1 Consensus size: 63
28402414 TTAACTTAAG
* * *
28402424 TAAATGAACTAAAACAT-ATGCATCAAT-TATTTC-AGTAACTAG-TTAATTAAAGAAGCATA-A
1 TAAATGAACT-AAAC-TCATGCATCAATATAATCCTAGGAACTAGATTAATT-AAGAAGCATATA
28402484 T
63 T
*
28402485 TAAATGAACTTAACTCATGCATCAATAAATAATCCTAGGAACTAGATTAATTAAGAAGCATATAT
1 TAAATGAACTAAACTCATGCATCAAT--ATAATCCTAGGAACTAGATTAATTAAGAAGCATATAT
28402550 TAAATGAA
1 TAAATGAA
28402558 GTTCAATAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
59 1 0.02
60 13 0.21
61 10 0.16
63 4 0.06
64 18 0.29
65 16 0.26
ACGTcount: A:0.48, C:0.12, G:0.10, T:0.30
Consensus pattern (63 bp):
TAAATGAACTAAACTCATGCATCAATATAATCCTAGGAACTAGATTAATTAAGAAGCATATAT
Found at i:28414660 original size:10 final size:10
Alignment explanation
Indices: 28414641--28414675 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
28414631 TTTTTTTTTC
28414641 AATTTT-AAT
1 AATTTTAAAT
28414650 AATTTTAAAT
1 AATTTTAAAT
*
28414660 AATTTTAAAC
1 AATTTTAAAT
28414670 AATTTT
1 AATTTT
28414676 TTTATAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (10 bp):
AATTTTAAAT
Found at i:28414682 original size:21 final size:20
Alignment explanation
Indices: 28414616--28414684 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
28414606 GATGTTAAAA
28414616 TTATAATTTTAATAATTTTT
1 TTATAATTTTAATAATTTTT
*
28414636 TTTTCAATTTTAATAA-TTTT
1 TTAT-AATTTTAATAATTTTT
** *
28414656 AAATAATTTTAAACAATTTTT
1 TTATAATTTT-AATAATTTTT
28414677 TTATAATT
1 TTATAATT
28414685 CATTTTAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
19 6 0.15
20 12 0.31
21 21 0.54
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
TTATAATTTTAATAATTTTT
Found at i:28417194 original size:23 final size:24
Alignment explanation
Indices: 28417168--28417220 Score: 56
Period size: 23 Copynumber: 2.3 Consensus size: 24
28417158 GTTTGATAAA
28417168 AAAAATATCCTAT-AAAAAATTTG
1 AAAAATATCCTATCAAAAAATTTG
* * **
28417191 AAAAGT-TCCTGTCAAAATCTTTG
1 AAAAATATCCTATCAAAAAATTTG
28417214 AAAAATA
1 AAAAATA
28417221 ATTATTTTAT
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (24 bp):
AAAAATATCCTATCAAAAAATTTG
Found at i:28419317 original size:20 final size:19
Alignment explanation
Indices: 28419256--28419320 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
28419246 CGATTAAGTC
*
28419256 TTATAAATTTTATAATTTTTT
1 TTATAAAATTTAT-A-TTTTT
* *
28419277 TTAAAAAATTGTAT-TTATT
1 TTATAAAATT-TATATTTTT
28419296 TTATAAAATTTATATCTTTT
1 TTATAAAATTTATAT-TTTT
28419316 TTATA
1 TTATA
28419321 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
18 3 0.08
19 14 0.39
20 8 0.22
21 8 0.22
22 3 0.08
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (19 bp):
TTATAAAATTTATATTTTT
Found at i:28420081 original size:60 final size:63
Alignment explanation
Indices: 28419987--28420105 Score: 154
Period size: 60 Copynumber: 1.9 Consensus size: 63
28419977 ATTAAATTAT
* * *
28419987 ATTTTAAAATAATTATAATATTTAATTTAAAATTATTAGCT-AAAAAATTGTGATAATTGTTC
1 ATTTAAAAATAATTATAATATTTAAATTAAAATTATTAACTAAAAAAATTGTGATAATTGTTC
* * * *
28420049 ATTTAAAAATAATTA-GA-ATTTAAATTACAATTATTAATTAAAAAAATTGTGCTAATT
1 ATTTAAAAATAATTATAATATTTAAATTAAAATTATTAACTAAAAAAATTGTGATAATT
28420106 TTAAAATAGA
Statistics
Matches: 49, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
60 18 0.37
61 17 0.35
62 14 0.29
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (63 bp):
ATTTAAAAATAATTATAATATTTAAATTAAAATTATTAACTAAAAAAATTGTGATAATTGTTC
Found at i:28429919 original size:41 final size:41
Alignment explanation
Indices: 28429874--28429959 Score: 115
Period size: 41 Copynumber: 2.1 Consensus size: 41
28429864 TCATTTTCGA
*
28429874 CTTTTTCA-TTGATATCCTTTTCGGATAGCGA-CCTTTTCAAC
1 CTTTTTCATTTGATATCCTTTTCGAATA--GATCCTTTTCAAC
*
28429915 C-TTTTCATTTGATATCCTTTTCGAATATATCCTTTTCAAC
1 CTTTTTCATTTGATATCCTTTTCGAATAGATCCTTTTCAAC
28429955 CTTTT
1 CTTTT
28429960 CATGTGTTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
39 1 0.03
40 17 0.43
41 22 0.55
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (41 bp):
CTTTTTCATTTGATATCCTTTTCGAATAGATCCTTTTCAAC
Found at i:28429921 original size:40 final size:39
Alignment explanation
Indices: 28429867--28429971 Score: 122
Period size: 40 Copynumber: 2.6 Consensus size: 39
28429857 ATTGCTATCA
* * *
28429867 TTTTCGACTTTTTCATTGATATCCTTTTCGGATAGCGA-CC
1 TTTTCAACCTTTTCATTGATATCCTTTTCGAATA--GATCC
*
28429907 TTTTCAACCTTTTCATTTGATATCCTTTTCGAATATATCC
1 TTTTCAACCTTTTCA-TTGATATCCTTTTCGAATAGATCC
*
28429947 TTTTCAACCTTTTCATGTGTTATCC
1 TTTTCAACCTTTTCAT-TGATATCC
28429972 CGGGTAACTT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
39 2 0.04
40 37 0.65
41 18 0.32
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.49
Consensus pattern (39 bp):
TTTTCAACCTTTTCATTGATATCCTTTTCGAATAGATCC
Found at i:28435301 original size:17 final size:18
Alignment explanation
Indices: 28435271--28435306 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28435261 TATCATGTAC
*
28435271 ACTGTATTGCTTATTTGT
1 ACTGTATTGATTATTTGT
28435289 ACTG-ATTGATTATTTGT
1 ACTGTATTGATTATTTGT
28435306 A
1 A
28435307 TTCATTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (18 bp):
ACTGTATTGATTATTTGT
Found at i:28446242 original size:42 final size:42
Alignment explanation
Indices: 28446178--28446300 Score: 149
Period size: 42 Copynumber: 2.9 Consensus size: 42
28446168 CTTGAAAAGG
* *
28446178 GCGGCTCGAATCTTGATTAGAATGGGGCATGGGATGATTAGA
1 GCGGCTCGAATCTTGATCAGAATGGGGCATGGGATGATCAGA
* *
28446220 GCGGTTCGAATCTTAATCAGAATGGGGCATGAGG-TGATCAGA
1 GCGGCTCGAATCTTGATCAGAATGGGGCATG-GGATGATCAGA
** * * *
28446262 GCAACTCGAATTTTGATCAGATTGGGGCATGTGATGATC
1 GCGGCTCGAATCTTGATCAGAATGGGGCATGGGATGATC
28446301 TTGTTATACT
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.01
42 65 0.96
43 2 0.03
ACGTcount: A:0.27, C:0.14, G:0.33, T:0.27
Consensus pattern (42 bp):
GCGGCTCGAATCTTGATCAGAATGGGGCATGGGATGATCAGA
Found at i:28447566 original size:45 final size:44
Alignment explanation
Indices: 28447517--28447744 Score: 139
Period size: 45 Copynumber: 5.1 Consensus size: 44
28447507 AGAGCAGACT
28447517 GAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATC
1 GAAGATAACAGATCTT-TCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * * * *
28447562 GAAGACACCAG-CCTTGCCTCC-ATGAGTTTGCAACGGAGTAGA-C
1 GAAGATAACAGATCTTTCTTCCTAT-A-TTGGCAGCGAAGTAGATC
28447605 TGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATC
1 -GAAGATAACAGATCTT-TCTTCCTATATTGGCAGCGAAGTAGATC
* * * * * * *
28447651 -AATGACACCAG-CCTTGCCTCCT-TGAGTTTGCAGC-AGAGCAGA-C
1 GAA-GATAACAGATCTTTCTTCCTAT-A-TTGGCAGCGA-AGTAGATC
* * *
28447694 TAAAGATAATAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATC
1 -GAAGATAACAGATCTT-TCTTCCTATATTGGCAGCGAAGTAGATC
28447740 GAAGA
1 GAAGA
28447745 CACCAATCTT
Statistics
Matches: 133, Mismatches: 32, Indels: 36
0.66 0.16 0.18
Matches are distributed among these distances:
42 3 0.02
43 14 0.11
44 47 0.35
45 52 0.39
46 14 0.11
47 3 0.02
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (44 bp):
GAAGATAACAGATCTTTCTTCCTATATTGGCAGCGAAGTAGATC
Found at i:28447612 original size:89 final size:89
Alignment explanation
Indices: 28447500--28447865 Score: 500
Period size: 89 Copynumber: 4.1 Consensus size: 89
28447490 CTCCCTGAAG
*
28447500 TTGCAGTAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
1 TTGCAGCAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
*
28447565 GACACCAGCCTTGCCTCCATGAGT
66 GACACCAGCCTTGCCTCCTTGAGT
* * *
28447589 TTGCAACGGAGTAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATC-AA
1 TTGCAGCAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
28447653 TGACACCAGCCTTGCCTCCTTGAGT
66 -GACACCAGCCTTGCCTCCTTGAGT
* * * *
28447678 TTGCAGCAGAGCAGACTAAAGATAATAGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAA
1 TTGCAGCAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
** * *
28447743 GACACCAATCTTGCCTCCCTCAGT
66 GACACCAGCCTTGCCTCCTTGAGT
* * * * * * * * *
28447767 TTACAGTAGAGGAGACTGAAGATAACAGATCTCATCTTCCTGTACTGGCAGTGAAGCAGATCAAA
1 TTGCAGCAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
* *
28447832 AACACCAGTCTTGCCTCCTTGAGT
66 GACACCAGCCTTGCCTCCTTGAGT
28447856 TTGCAGCAGA
1 TTGCAGCAGA
28447866 TCTTGTCTTT
Statistics
Matches: 242, Mismatches: 33, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
88 2 0.01
89 238 0.98
90 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (89 bp):
TTGCAGCAGAGCAGACTGAAGATAACAGATCTTATCTTCCTATATTGGCAGCGAAGTAGATCGAA
GACACCAGCCTTGCCTCCTTGAGT
Found at i:28447996 original size:159 final size:159
Alignment explanation
Indices: 28447704--28448022 Score: 458
Period size: 159 Copynumber: 2.0 Consensus size: 159
28447694 TAAAGATAAT
* * *
28447704 AGATCTTGTCTTCCTGTATTGGCAGCGAAGTAGATCGAAGACACCAATCTTGCCTCCCTCAGTTT
1 AGATCTTGTCTTCATGTATTGGCAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTCAGTTT
* * **
28447769 ACAGTAGAGGAGACTGAAGATAACAGATCTCATCTTCCTGTACTGGCAGTGAAGCAGATCAAAAA
66 ACAGCAGAGCAGACTGAAGATAACAGATCTCATCTTCCTGTACTGGCAACGAAGCAGATCAAAAA
* *
28447834 CACCAGTCTTGCCTCCTTGAGTTTGCAGC
131 CACCAGCCTTGCCTCCCTGAGTTTGCAGC
* * *
28447863 AGATCTTGTCTTTATGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTTT
1 AGATCTTGTCTTCATGTATTGGCAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTCAGTTT
* ** * * * * *
28447928 GCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTTCTGTATTGGCAACGAAGTAGATCGAAGA
66 ACAGCAGAGCAGACTGAAGATAACAGATCTCATCTTCCTGTACTGGCAACGAAGCAGATCAAAAA
28447993 CACCAGCCTTGCCTCCCTGAGTTTGCAGC
131 CACCAGCCTTGCCTCCCTGAGTTTGCAGC
28448022 A
1 A
28448023 AAGCAGACTG
Statistics
Matches: 140, Mismatches: 20, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
159 140 1.00
ACGTcount: A:0.27, C:0.24, G:0.22, T:0.26
Consensus pattern (159 bp):
AGATCTTGTCTTCATGTATTGGCAGCAAAGTAGATCGAAGACACCAACCTTGCCTCCCTCAGTTT
ACAGCAGAGCAGACTGAAGATAACAGATCTCATCTTCCTGTACTGGCAACGAAGCAGATCAAAAA
CACCAGCCTTGCCTCCCTGAGTTTGCAGC
Found at i:28448013 original size:89 final size:89
Alignment explanation
Indices: 28447862--28448194 Score: 483
Period size: 89 Copynumber: 3.8 Consensus size: 89
28447852 GAGTTTGCAG
* *
28447862 CAGATCTTGTCTTTATGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
1 CAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
28447927 TGCAGCAGAGCAGACTGAAGATAA
66 TGCAGCAGAGCAGACTGAAGATAA
*
28447951 CAGATCTTGTCTTTCTGTATTGGCAACGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
1 CAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
*
28448016 TGCAGCAAAGCAGACTGAAGATAA
66 TGCAGCAGAGCAGACTGAAGATAA
* *
28448040 CAGATCTTGTC-TTCTTGTATTGGCAGC-ATAGTAGATCGAA-AAACCAACCTTGCCTCCCTGAG
1 CAGATCTTGTCTTTC-TGTATTGGCAGCGA-AGTAGATCGAAGACACCAGCCTTGCCTCCCTGAG
* *
28448102 TTTGCAGCGGAACAGACTGAAGATAA
64 TTTGCAGCAGAGCAGACTGAAGATAA
* * * * * * * *
28448128 CATATTTTGTCTTCCTATATTGGCAGTGAAGCAGATCGAAAACACCAGCCTTGCCTCTCTGAGTT
1 CAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
28448193 TG
66 TG
28448195 TAGTAGAGTA
Statistics
Matches: 220, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
88 76 0.35
89 144 0.65
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (89 bp):
CAGATCTTGTCTTTCTGTATTGGCAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
TGCAGCAGAGCAGACTGAAGATAA
Found at i:28448166 original size:177 final size:178
Alignment explanation
Indices: 28447862--28448194 Score: 517
Period size: 177 Copynumber: 1.9 Consensus size: 178
28447852 GAGTTTGCAG
* *
28447862 CAGATCTTGTCTTTATGTATTGGCAGCAAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGAGTT
1 CAGATCTTGTCTTTATGTATTGGCAGCAAAGTAGATCGAAGAAACCAACCTTGCCTCCCTGAGTT
* * * * *
28447927 TGCAGCAGAGCAGACTGAAGATAACAGATCTTGTCTTTCTGTATTGGCAACGAAGTAGATCGAAG
66 TGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAACGAAGCAGATCGAAA
28447992 ACACCAGCCTTGCCTCCCTGAGTTTGCAGCAAAGCAGACTGAAGATAA
131 ACACCAGCCTTGCCTCCCTGAGTTTGCAGCAAAGCAGACTGAAGATAA
*
28448040 CAGATCTTGTCTTCT-TGTATTGGCAGCATAGTAGATCGAA-AAACCAACCTTGCCTCCCTGAGT
1 CAGATCTTGTCTT-TATGTATTGGCAGCAAAGTAGATCGAAGAAACCAACCTTGCCTCCCTGAGT
* * * **
28448103 TTGCAGCGGAACAGACTGAAGATAACATATTTTGTCTTCCTATATTGGCAGTGAAGCAGATCGAA
65 TTGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAACGAAGCAGATCGAA
*
28448168 AACACCAGCCTTGCCTCTCTGAGTTTG
130 AACACCAGCCTTGCCTCCCTGAGTTTG
28448195 TAGTAGAGTA
Statistics
Matches: 140, Mismatches: 14, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
177 102 0.73
178 37 0.26
179 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.27
Consensus pattern (178 bp):
CAGATCTTGTCTTTATGTATTGGCAGCAAAGTAGATCGAAGAAACCAACCTTGCCTCCCTGAGTT
TGCAGCAGAACAGACTGAAGATAACAGATCTTGTCTTCCTATATTGGCAACGAAGCAGATCGAAA
ACACCAGCCTTGCCTCCCTGAGTTTGCAGCAAAGCAGACTGAAGATAA
Found at i:28448621 original size:44 final size:44
Alignment explanation
Indices: 28448525--28448645 Score: 127
Period size: 44 Copynumber: 2.7 Consensus size: 44
28448515 AAAAAACAAG
* * *
28448525 TCTTATCT-CCTTGAAAGTTGCAGTGGAGCAGATTGAAGTTATAAA
1 TCTTATCTCCCTT--AAGTTGCAGTGGAGCAGATTAAAATGATAAA
* **
28448570 TCCTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATGATGGA
1 TCTTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATGATAAA
* * * *
28448614 TCTTATCTCTCTGAAGTTGCAATAGAGCAGAT
1 TCTTATCTCCCTTAAGTTGCAGTGGAGCAGAT
28448646 CGCATCAGAC
Statistics
Matches: 64, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
44 53 0.83
45 7 0.11
46 4 0.06
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (44 bp):
TCTTATCTCCCTTAAGTTGCAGTGGAGCAGATTAAAATGATAAA
Found at i:28450971 original size:9 final size:9
Alignment explanation
Indices: 28450959--28451002 Score: 70
Period size: 9 Copynumber: 4.9 Consensus size: 9
28450949 ATCATCATCC
28450959 TCATCGTCG
1 TCATCGTCG
28450968 TCATCGTCG
1 TCATCGTCG
*
28450977 TCATTGTCG
1 TCATCGTCG
*
28450986 TCATCGTCC
1 TCATCGTCG
28450995 TCATCGTC
1 TCATCGTC
28451003 CTTTTTGCAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 32 1.00
ACGTcount: A:0.11, C:0.34, G:0.18, T:0.36
Consensus pattern (9 bp):
TCATCGTCG
Found at i:28450980 original size:18 final size:18
Alignment explanation
Indices: 28450950--28451002 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
28450940 CGAAGAAACA
*
28450950 TCATCATCCTCATCGTCG
1 TCATCGTCCTCATCGTCG
* *
28450968 TCATCGTCGTCATTGTCG
1 TCATCGTCCTCATCGTCG
28450986 TCATCGTCCTCATCGTC
1 TCATCGTCCTCATCGTC
28451003 CTTTTTGCAA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.13, C:0.36, G:0.15, T:0.36
Consensus pattern (18 bp):
TCATCGTCCTCATCGTCG
Found at i:28451003 original size:9 final size:9
Alignment explanation
Indices: 28450950--28451004 Score: 65
Period size: 9 Copynumber: 6.1 Consensus size: 9
28450940 CGAAGAAACA
*
28450950 TCATCATCC
1 TCATCGTCC
*
28450959 TCATCGTCG
1 TCATCGTCC
*
28450968 TCATCGTCG
1 TCATCGTCC
* *
28450977 TCATTGTCG
1 TCATCGTCC
28450986 TCATCGTCC
1 TCATCGTCC
28450995 TCATCGTCC
1 TCATCGTCC
28451004 T
1 T
28451005 TTTTGCAACT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 41 1.00
ACGTcount: A:0.13, C:0.36, G:0.15, T:0.36
Consensus pattern (9 bp):
TCATCGTCC
Found at i:28453391 original size:72 final size:72
Alignment explanation
Indices: 28453274--28453422 Score: 298
Period size: 72 Copynumber: 2.1 Consensus size: 72
28453264 TTTAAATTTC
28453274 ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
1 ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
28453339 TTTAAAT
66 TTTAAAT
28453346 ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
1 ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
28453411 TTTAAAT
66 TTTAAAT
28453418 ATTTT
1 ATTTT
28453423 TAATGTTTGA
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 77 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.44
Consensus pattern (72 bp):
ATTTTGGGCAATTAAAGACATAGTTTTCTAGTATTTTATTAAAAACGGTAAGTAATTATTTTAGA
TTTAAAT
Found at i:28453532 original size:13 final size:13
Alignment explanation
Indices: 28453514--28453611 Score: 115
Period size: 13 Copynumber: 7.2 Consensus size: 13
28453504 ATATTAAAAG
*
28453514 TTAAAACATTATA
1 TTAAAACAGTATA
28453527 TTAAAACAGTATA
1 TTAAAACAGTATA
28453540 TATATATAACAGTATA
1 T-TA-A-AACAGTATA
*
28453556 TTAAAACAATATA
1 TTAAAACAGTATA
*
28453569 TTAAAAAAGTATA
1 TTAAAACAGTATA
* *
28453582 TTTATAATAGTATA
1 -TTAAAACAGTATA
28453596 TTAAAACAGTATA
1 TTAAAACAGTATA
28453609 TTA
1 TTA
28453612 CATTAAAAAT
Statistics
Matches: 73, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
13 46 0.63
14 14 0.19
15 3 0.04
16 10 0.14
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (13 bp):
TTAAAACAGTATA
Found at i:28453594 original size:40 final size:42
Alignment explanation
Indices: 28453514--28453611 Score: 146
Period size: 40 Copynumber: 2.4 Consensus size: 42
28453504 ATATTAAAAG
* *
28453514 TTAAAACATTATATTAAAACAGTATATATATATAACAGTATA
1 TTAAAACAATATATTAAAAAAGTATATATATATAACAGTATA
*
28453556 TTAAAACAATATATTAAAAAAGTATAT-T-TATAATAGTATA
1 TTAAAACAATATATTAAAAAAGTATATATATATAACAGTATA
*
28453596 TTAAAACAGTATATTA
1 TTAAAACAATATATTA
28453612 CATTAAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 26 0.50
41 1 0.02
42 25 0.48
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (42 bp):
TTAAAACAATATATTAAAAAAGTATATATATATAACAGTATA
Found at i:28456253 original size:17 final size:18
Alignment explanation
Indices: 28456223--28456258 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
28456213 TATCATGTAC
*
28456223 ACTGTATTGCTTATTTGT
1 ACTGTATTGATTATTTGT
28456241 ACTG-ATTGATTATTTGT
1 ACTGTATTGATTATTTGT
28456258 A
1 A
28456259 TTCATTAGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.53
Consensus pattern (18 bp):
ACTGTATTGATTATTTGT
Found at i:28457416 original size:30 final size:30
Alignment explanation
Indices: 28457377--28457468 Score: 123
Period size: 30 Copynumber: 3.1 Consensus size: 30
28457367 AACCCTCAAA
* *
28457377 CCTTTTCACTTTTCCCCCAGAACTTTGACT
1 CCTTCTCACTTTTCCCCCAAAACTTTGACT
*
28457407 CCTTCTCAC-TTTCCCATCAAAACTTTGACT
1 CCTTCTCACTTTTCCC-CCAAAACTTTGACT
* *
28457437 CCTTCTCACTTTTTCCCCAAAACTTTTACT
1 CCTTCTCACTTTTCCCCCAAAACTTTGACT
28457467 CC
1 CC
28457469 CCTCCCATCC
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
29 6 0.11
30 43 0.80
31 5 0.09
ACGTcount: A:0.20, C:0.38, G:0.03, T:0.39
Consensus pattern (30 bp):
CCTTCTCACTTTTCCCCCAAAACTTTGACT
Found at i:28467371 original size:13 final size:13
Alignment explanation
Indices: 28467355--28467417 Score: 99
Period size: 13 Copynumber: 4.8 Consensus size: 13
28467345 TTTAAACCAA
28467355 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* * *
28467368 ACTTCTGAAAAAC
1 ACTTTTCAAAAGC
28467381 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28467394 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
28467407 ACTTTTCAAAA
1 ACTTTTCAAAA
28467418 ACAATGAAGA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 44 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:28469676 original size:28 final size:27
Alignment explanation
Indices: 28469630--28469691 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
28469620 ATCATAGTAG
*
28469630 TTTTTTCGTCTGCCGTTTTGGCACGCAAT
1 TTTTTTCGTCTGCCGTTTT-G-ACACAAT
* *
28469659 TTTTTTCGTTTGTC-TTTTGACACAAT
1 TTTTTTCGTCTGCCGTTTTGACACAAT
28469685 TTTTTTC
1 TTTTTTC
28469692 TAGGGCTCGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 13 0.43
27 1 0.03
28 4 0.13
29 12 0.40
ACGTcount: A:0.11, C:0.19, G:0.15, T:0.55
Consensus pattern (27 bp):
TTTTTTCGTCTGCCGTTTTGACACAAT
Found at i:28472586 original size:224 final size:224
Alignment explanation
Indices: 28472196--28472647 Score: 904
Period size: 224 Copynumber: 2.0 Consensus size: 224
28472186 TTTCTTGCTT
28472196 TTTTTTACAATAAAAATATTGGCATATTGTAGGCAATGATGCTATGAAATACTATCTTGCGGTTC
1 TTTTTTACAATAAAAATATTGGCATATTGTAGGCAATGATGCTATGAAATACTATCTTGCGGTTC
28472261 TTCGTGGGGAGGTTGCCATTGAGGAAATAAATAAGACTCATATTGTCTTGATCCCGAAGGTCAGT
66 TTCGTGGGGAGGTTGCCATTGAGGAAATAAATAAGACTCATATTGTCTTGATCCCGAAGGTCAGT
28472326 AGTCCCAGAAACATGACGTAATTTAGACCTATTAGCTTGTACAATGTTCTGTACAAAATCATTGC
131 AGTCCCAGAAACATGACGTAATTTAGACCTATTAGCTTGTACAATGTTCTGTACAAAATCATTGC
28472391 TAAAGTAATAGTGGGCAGAATGAGTGGAG
196 TAAAGTAATAGTGGGCAGAATGAGTGGAG
28472420 TTTTTTACAATAAAAATATTGGCATATTGTAGGCAATGATGCTATGAAATACTATCTTGCGGTTC
1 TTTTTTACAATAAAAATATTGGCATATTGTAGGCAATGATGCTATGAAATACTATCTTGCGGTTC
28472485 TTCGTGGGGAGGTTGCCATTGAGGAAATAAATAAGACTCATATTGTCTTGATCCCGAAGGTCAGT
66 TTCGTGGGGAGGTTGCCATTGAGGAAATAAATAAGACTCATATTGTCTTGATCCCGAAGGTCAGT
28472550 AGTCCCAGAAACATGACGTAATTTAGACCTATTAGCTTGTACAATGTTCTGTACAAAATCATTGC
131 AGTCCCAGAAACATGACGTAATTTAGACCTATTAGCTTGTACAATGTTCTGTACAAAATCATTGC
28472615 TAAAGTAATAGTGGGCAGAATGAGTGGAG
196 TAAAGTAATAGTGGGCAGAATGAGTGGAG
28472644 TTTT
1 TTTT
28472648 GAAAGGTTGT
Statistics
Matches: 228, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
224 228 1.00
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (224 bp):
TTTTTTACAATAAAAATATTGGCATATTGTAGGCAATGATGCTATGAAATACTATCTTGCGGTTC
TTCGTGGGGAGGTTGCCATTGAGGAAATAAATAAGACTCATATTGTCTTGATCCCGAAGGTCAGT
AGTCCCAGAAACATGACGTAATTTAGACCTATTAGCTTGTACAATGTTCTGTACAAAATCATTGC
TAAAGTAATAGTGGGCAGAATGAGTGGAG
Found at i:28477277 original size:20 final size:20
Alignment explanation
Indices: 28477254--28477294 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
28477244 AATTAAACCG
28477254 AGCTCAAACGAGCTAAATTA
1 AGCTCAAACGAGCTAAATTA
***
28477274 AGCTCATGTGAGCTAAATTA
1 AGCTCAAACGAGCTAAATTA
28477294 A
1 A
28477295 AATTAGCTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
AGCTCAAACGAGCTAAATTA
Found at i:28479041 original size:33 final size:33
Alignment explanation
Indices: 28479003--28479074 Score: 101
Period size: 33 Copynumber: 2.2 Consensus size: 33
28478993 GATTACTCTC
28479003 TTCACTCG-TTTCTTTTACAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTT-CAGACTCTCTTTCTTT
* *
28479036 TTCACTCGATTTCTTTTCAGGCTCTTTTTCTTT
1 TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
*
28479069 TCCACT
1 TTCACT
28479075 TTCGTTTTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 27 0.77
34 8 0.23
ACGTcount: A:0.11, C:0.28, G:0.07, T:0.54
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAGACTCTCTTTCTTT
Found at i:28480283 original size:9 final size:10
Alignment explanation
Indices: 28480263--28480315 Score: 72
Period size: 10 Copynumber: 5.4 Consensus size: 10
28480253 ATAAAAAAAA
*
28480263 TTTTGAATTT
1 TTTTCAATTT
*
28480273 TTTTCTA-TT
1 TTTTCAATTT
*
28480282 TTTTCTATTT
1 TTTTCAATTT
28480292 TTTTCAATTT
1 TTTTCAATTT
28480302 TTTTCAATTT
1 TTTTCAATTT
28480312 TTTT
1 TTTT
28480316 TACAATGACT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
9 9 0.23
10 30 0.77
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (10 bp):
TTTTCAATTT
Found at i:28480304 original size:12 final size:11
Alignment explanation
Indices: 28480280--28480321 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
28480270 TTTTTTTCTA
*
28480280 TTTTTTCTA-T
1 TTTTTTCAATT
28480290 TTTTTTCAA-T
1 TTTTTTCAATT
28480300 TTTTTTCAATT
1 TTTTTTCAATT
28480311 TTTTTTACAAT
1 TTTTTT-CAAT
28480322 GACTTACTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
10 18 0.62
11 7 0.24
12 4 0.14
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTTTCAATT
Found at i:28486947 original size:9 final size:9
Alignment explanation
Indices: 28486929--28487019 Score: 53
Period size: 9 Copynumber: 9.6 Consensus size: 9
28486919 GAATGATTTT
*
28486929 TTTTTGAAA
1 TTTTTAAAA
28486938 TTTTTAAAA
1 TTTTTAAAA
*
28486947 TTTATTTAATA
1 -TT-TTTAAAA
28486958 TTTTTATAAA
1 TTTTTA-AAA
28486968 -TTTTAATAA
1 TTTTTAA-AA
28486977 TGTTTTTAAAAA
1 --TTTTT-AAAA
*
28486989 TTTATAAAA
1 TTTTTAAAA
*
28486998 --TTTAAAT
1 TTTTTAAAA
28487005 TTTTTAAATA
1 TTTTTAAA-A
28487015 TTTTT
1 TTTTT
28487020 TAATTTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 21
0.70 0.08 0.23
Matches are distributed among these distances:
7 5 0.08
8 1 0.02
9 29 0.45
10 15 0.23
11 6 0.09
12 6 0.09
13 2 0.03
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (9 bp):
TTTTTAAAA
Found at i:28486968 original size:21 final size:21
Alignment explanation
Indices: 28486937--28486995 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
28486927 TTTTTTTGAA
*
28486937 ATTTTTAAAATTTAT-TTAAT
1 ATTTTTAAAATTTATAATAAT
28486957 ATTTTTATAAATTT-TAATAAT
1 ATTTTTA-AAATTTATAATAAT
*
28486978 GTTTTTAAAAATTTATAA
1 ATTTTT-AAAATTTATAA
28486996 AATTTAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 8 0.24
21 21 0.64
22 4 0.12
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTTTTAAAATTTATAATAAT
Found at i:28487118 original size:8 final size:8
Alignment explanation
Indices: 28487095--28487141 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
28487085 CTAGTAAAAG
28487095 TATTTCTTT
1 TATTT-TTT
*
28487104 TAATTTTT
1 TATTTTTT
28487112 TATTTTTT
1 TATTTTTT
28487120 TA-TTTTT
1 TATTTTTT
* *
28487127 GAATTTTT
1 TATTTTTT
28487135 TATTTTT
1 TATTTTT
28487142 GATGACATGG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
7 6 0.19
8 22 0.69
9 4 0.12
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (8 bp):
TATTTTTT
Found at i:28487119 original size:15 final size:15
Alignment explanation
Indices: 28487101--28487143 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
28487091 AAAGTATTTC
* * *
28487101 TTTTAATTTTTTATT
1 TTTTTATTTTTGAAT
28487116 TTTTTATTTTTGAAT
1 TTTTTATTTTTGAAT
28487131 TTTTTATTTTTGA
1 TTTTTATTTTTGA
28487144 TGACATGGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.77
Consensus pattern (15 bp):
TTTTTATTTTTGAAT
Found at i:28490693 original size:29 final size:29
Alignment explanation
Indices: 28490660--28490716 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
28490650 TCTATGACTT
28490660 GATCAAATTAATATTTCTACTATTAAATG
1 GATCAAATTAATATTTCTACTATTAAATG
* * * *
28490689 GATCAATTTAATCTTTGTACTGTTAAAT
1 GATCAAATTAATATTTCTACTATTAAAT
28490717 TAAATTAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (29 bp):
GATCAAATTAATATTTCTACTATTAAATG
Found at i:28496900 original size:49 final size:49
Alignment explanation
Indices: 28496726--28496907 Score: 170
Period size: 50 Copynumber: 3.7 Consensus size: 49
28496716 GTGAGGTCCT
* * * * **
28496726 ATGTAAGAACATGTCTGGGACATGGCGTTGGCACCGAGACGAGAGGTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAAGAGAACTCCC
*** * * *
28496776 CCATAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAACTCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACAAGAGAACTCCC
* *
28496826 ATGTAAGACCATATCTGGGATATGGCATTGGCA-GTACAAGA-AACATCCC
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCACG-ACAAGAGAAC-TCCC
* *
28496875 ATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 ATGTAAGACCATGTCTGGGACATGGCATTGGCA
28496908 TGTTATTATC
Statistics
Matches: 108, Mismatches: 22, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
48 4 0.04
49 37 0.34
50 67 0.62
ACGTcount: A:0.29, C:0.23, G:0.27, T:0.21
Consensus pattern (49 bp):
ATGTAAGACCATGTCTGGGACATGGCATTGGCACGACAAGAGAACTCCC
Found at i:28514888 original size:6 final size:6
Alignment explanation
Indices: 28514877--28514903 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
28514867 GACTCTCTGA
28514877 TATATG TATATG TATATG TATATG TAT
1 TATATG TATATG TATATG TATATG TAT
28514904 GTGTCAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.52
Consensus pattern (6 bp):
TATATG
Found at i:28515843 original size:19 final size:18
Alignment explanation
Indices: 28515800--28515844 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 18
28515790 AAAATTTGAA
28515800 AATAATT-ATAAAAATTT
1 AATAATTAATAAAAATTT
*
28515817 ATTAAATTAATAAAAATATT
1 AAT-AATTAATAAAAAT-TT
28515837 AATAATTA
1 AATAATTA
28515845 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 2 0.09
18 4 0.17
19 13 0.57
20 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AATAATTAATAAAAATTT
Found at i:28516704 original size:24 final size:24
Alignment explanation
Indices: 28516660--28516705 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
28516650 ACTTTTTTTA
* *
28516660 TTAATTTATAAAATTTTATATATT
1 TTAATTTATAAAATATAATATATT
28516684 TTAATTT-TAAAATAATAATATA
1 TTAATTTATAAAAT-ATAATATA
28516706 AATAACATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (24 bp):
TTAATTTATAAAATATAATATATT
Found at i:28516889 original size:8 final size:8
Alignment explanation
Indices: 28516878--28516913 Score: 72
Period size: 8 Copynumber: 4.5 Consensus size: 8
28516868 TATTTTAAAG
28516878 ATTTTTTA
1 ATTTTTTA
28516886 ATTTTTTA
1 ATTTTTTA
28516894 ATTTTTTA
1 ATTTTTTA
28516902 ATTTTTTA
1 ATTTTTTA
28516910 ATTT
1 ATTT
28516914 AAATTTGTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (8 bp):
ATTTTTTA
Found at i:28521375 original size:24 final size:24
Alignment explanation
Indices: 28521347--28521399 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
28521337 ACTCCACTAC
*
28521347 ACTCCACAGTAGGAGTT-CTCCAGA
1 ACTCCACAATAGGAGTTCCT-CAGA
28521371 ACTCCACAATAGGAGTTCCTCAGA
1 ACTCCACAATAGGAGTTCCTCAGA
28521395 ACTCC
1 ACTCC
28521400 TCTACCTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (24 bp):
ACTCCACAATAGGAGTTCCTCAGA
Found at i:28521755 original size:44 final size:45
Alignment explanation
Indices: 28521590--28521758 Score: 164
Period size: 45 Copynumber: 3.8 Consensus size: 45
28521580 AAGTTGCTAA
* * * ***
28521590 TAATAAGGTGTGGGTAAACCA-TAAATCGGTACAGATAAAAGCCAC
1 TAATACGGTGTGGATAAACCACTAAAT-GGTGCAGATAAAAGTTGC
* * * * *
28521635 TAAAATGATATGGATAAACCTCTAAATGGTGCAGATAAAAGTTGC
1 TAATACGGTGTGGATAAACCACTAAATGGTGCAGATAAAAGTTGC
* *
28521680 TAATACGGTGTGGATAAACCATTAAATGGTGCGGATAAAAGTTGC
1 TAATACGGTGTGGATAAACCACTAAATGGTGCAGATAAAAGTTGC
* *
28521725 TAATA-TGTGT-GAGTAAACCACTAAACGGTGCAGA
1 TAATACGGTGTGGA-TAAACCACTAAATGGTGCAGA
28521759 CAAGCTACTA
Statistics
Matches: 101, Mismatches: 21, Indels: 5
0.80 0.17 0.04
Matches are distributed among these distances:
43 2 0.02
44 22 0.22
45 72 0.71
46 5 0.05
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.24
Consensus pattern (45 bp):
TAATACGGTGTGGATAAACCACTAAATGGTGCAGATAAAAGTTGC
Found at i:28524676 original size:21 final size:21
Alignment explanation
Indices: 28524652--28524703 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
28524642 GTGGTAATGG
28524652 GAAACCACAAGTTGGGAAGAA
1 GAAACCACAAGTTGGGAAGAA
28524673 GAAACCACAAGTTGGGAAGAA
1 GAAACCACAAGTTGGGAAGAA
28524694 GAAACC-CAAG
1 GAAACCACAAG
28524704 AGGAAAAGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.48, C:0.17, G:0.27, T:0.08
Consensus pattern (21 bp):
GAAACCACAAGTTGGGAAGAA
Found at i:28527912 original size:18 final size:17
Alignment explanation
Indices: 28527889--28527928 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
28527879 TCTTGAATCA
28527889 AATTTTATAACTTTTAAT
1 AATTTTAT-ACTTTTAAT
**
28527907 AATTTTATTTTTTTAAT
1 AATTTTATACTTTTAAT
28527924 AATTT
1 AATTT
28527929 CTTTAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTTATACTTTTAAT
Found at i:28534468 original size:27 final size:27
Alignment explanation
Indices: 28534379--28534633 Score: 155
Period size: 27 Copynumber: 9.5 Consensus size: 27
28534369 TTAGCCCACT
* * * *
28534379 GGGACAATAAAAACGGGGTAGTCCGTC
1 GGGACAGTAAACACAGGGTAGTCCATC
* * * * *
28534406 GAGATAGCAAACACGGGGTAGTCCGTC
1 GGGACAGTAAACACAGGGTAGTCCATC
* *
28534433 AGGATAGTAAACACAGGGTAGTCCATC
1 GGGACAGTAAACACAGGGTAGTCCATC
* *
28534460 GGGACAGTAAACACAGAGTAATCCA-C
1 GGGACAGTAAACACAGGGTAGTCCATC
* *
28534486 TGGGACAGTAAAAAAAAGGGTAGT-C-TGC
1 -GGGACAGT-AAACACAGGGTAGTCCAT-C
* **
28534514 TGGGATAGTAAACAC--GGTAGTCCGCC
1 -GGGACAGTAAACACAGGGTAGTCCATC
** *
28534540 ATGACAGTAAACACAGGGTAGTCTATC
1 GGGACAGTAAACACAGGGTAGTCCATC
* *
28534567 GGGACAGTAAACA-TGAGGTAGTCC-GC
1 GGGACAGTAAACACAG-GGTAGTCCATC
** * *
28534593 TAAGACAATAAACACAGGGTAGTCCACC
1 -GGGACAGTAAACACAGGGTAGTCCATC
*
28534621 GGGACAATAAACA
1 GGGACAGTAAACA
28534634 TGTGAATTAT
Statistics
Matches: 176, Mismatches: 40, Indels: 24
0.73 0.17 0.10
Matches are distributed among these distances:
25 17 0.10
26 5 0.03
27 133 0.76
28 21 0.12
ACGTcount: A:0.36, C:0.20, G:0.28, T:0.16
Consensus pattern (27 bp):
GGGACAGTAAACACAGGGTAGTCCATC
Found at i:28534496 original size:54 final size:53
Alignment explanation
Indices: 28534394--28534633 Score: 200
Period size: 54 Copynumber: 4.5 Consensus size: 53
28534384 AATAAAAACG
* * * * * * *
28534394 GGGTAGTCCGTCGAGATAGCAAACACGGGGTAGTCCG-TCAGGATAGTAAACACA
1 GGGTAGTCCATCGGGACAGTAAACAC-GAGTAGTCCGCT-AAGACAGTAAACACA
* * ** * *
28534448 GGGTAGTCCATCGGGACAGTAAACACAGAGTAATCCACTGGGACAGTAAAAAAAA
1 GGGTAGTCCATCGGGACAGTAAACAC-GAGTAGTCCGCTAAGACAGT-AAACACA
* * *
28534503 GGGTAGT-C-TGCTGGGATAGTAAACACG-GTAGTCCGCCATGACAGTAAACACA
1 GGGTAGTCCAT-C-GGGACAGTAAACACGAGTAGTCCGCTAAGACAGTAAACACA
* * *
28534555 GGGTAGTCTATCGGGACAGTAAACATGAGGTAGTCCGCTAAGACAATAAACACA
1 GGGTAGTCCATCGGGACAGTAAACACGA-GTAGTCCGCTAAGACAGTAAACACA
* *
28534609 GGGTAGTCCACCGGGACAATAAACA
1 GGGTAGTCCATCGGGACAGTAAACA
28534634 TGTGAATTAT
Statistics
Matches: 149, Mismatches: 29, Indels: 16
0.77 0.15 0.08
Matches are distributed among these distances:
52 25 0.17
53 15 0.10
54 83 0.56
55 26 0.17
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (53 bp):
GGGTAGTCCATCGGGACAGTAAACACGAGTAGTCCGCTAAGACAGTAAACACA
Found at i:28534561 original size:107 final size:107
Alignment explanation
Indices: 28534374--28534579 Score: 281
Period size: 107 Copynumber: 1.9 Consensus size: 107
28534364 CCATTTTAGC
** * *
28534374 CCACTGGGACAATAAAAACGGGGTAGTCCGTCGAGATAGCAAACACGGGGTAGTCCGTCAGGATA
1 CCACTGGGACAATAAAAAAAGGGTAGTCCGTCGAGATAGCAAACAC-GGGTAGTCCGCCAGGACA
28534439 GTAAACACAGGGTAGTCCATCGGGACAGTAAACACAGAGTAAT
65 GTAAACACAGGGTAGTCCATCGGGACAGTAAACACAGAGTAAT
* * * * *
28534482 CCACTGGGACAGTAAAAAAAAGGGTAGTCTG-CTGGGATAGTAAACAC-GGTAGTCCGCCATGAC
1 CCACTGGGACAAT-AAAAAAAGGGTAGTCCGTC-GAGATAGCAAACACGGGTAGTCCGCCAGGAC
*
28534545 AGTAAACACAGGGTAGTCTATCGGGACAGTAAACA
64 AGTAAACACAGGGTAGTCCATCGGGACAGTAAACA
28534580 TGAGGTAGTC
Statistics
Matches: 86, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
107 47 0.55
108 13 0.15
109 26 0.30
ACGTcount: A:0.35, C:0.20, G:0.28, T:0.17
Consensus pattern (107 bp):
CCACTGGGACAATAAAAAAAGGGTAGTCCGTCGAGATAGCAAACACGGGTAGTCCGCCAGGACAG
TAAACACAGGGTAGTCCATCGGGACAGTAAACACAGAGTAAT
Found at i:28535412 original size:21 final size:20
Alignment explanation
Indices: 28535380--28535418 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
28535370 ACGCCTACGA
*
28535380 AAAGATCGCTTGGATTTAAG
1 AAAGATCACTTGGATTTAAG
28535400 AAAGAGTCACTTGGATTTA
1 AAAGA-TCACTTGGATTTA
28535419 TCCATGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.36, C:0.10, G:0.23, T:0.31
Consensus pattern (20 bp):
AAAGATCACTTGGATTTAAG
Found at i:28535572 original size:13 final size:13
Alignment explanation
Indices: 28535554--28535578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28535544 TTATTTATCA
28535554 TTTAAATATATAG
1 TTTAAATATATAG
28535567 TTTAAATATATA
1 TTTAAATATATA
28535579 TAAATTAAAA
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:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTAAATATATAG
Found at i:28535603 original size:11 final size:11
Alignment explanation
Indices: 28535582--28535629 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
28535572 ATATATATAA
28535582 ATTAA-AATAT
1 ATTAATAATAT
28535592 ATTAATAATAT
1 ATTAATAATAT
*
28535603 ATAAAT-A-AT
1 ATTAATAATAT
28535612 ATTAATAATAT
1 ATTAATAATAT
*
28535623 AATAATA
1 ATTAATA
28535630 TAGAAAGAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
9 7 0.22
10 7 0.22
11 18 0.56
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTAATAATAT
Found at i:28535611 original size:14 final size:14
Alignment explanation
Indices: 28535574--28535631 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
28535564 TAGTTTAAAT
28535574 ATATATAAATTAA-A
1 ATATATAAA-TAATA
28535588 ATATAT---TAATA
1 ATATATAAATAATA
28535599 ATATATAAATAATA
1 ATATATAAATAATA
*
28535613 TTA-ATAATATAATA
1 ATATATAA-ATAATA
28535627 ATATA
1 ATATA
28535632 GAAAGAAAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
10 3 0.08
11 7 0.19
13 4 0.11
14 21 0.58
15 1 0.03
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (14 bp):
ATATATAAATAATA
Found at i:28535629 original size:20 final size:20
Alignment explanation
Indices: 28535586--28535623 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28535576 ATATAAATTA
28535586 AAAT-ATATTAATAATATAT
1 AAATAATATTAATAATATAT
28535605 AAATAATATTAATAATATA
1 AAATAATATTAATAATATA
28535624 ATAATATAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAATATTAATAATATAT
Found at i:28544282 original size:29 final size:29
Alignment explanation
Indices: 28544222--28544297 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
28544212 AACCTGACCT
* ** *
28544222 ACAACTTGTGTGAG-GAGCCCAAAATGTC
1 ACAACTTGTGTGAGCAAATCCAAAATATC
28544250 ACAACTTGTGTGAGCAAATCCAAAATATC
1 ACAACTTGTGTGAGCAAATCCAAAATATC
28544279 ACAACTTGTGTGAGCAAAT
1 ACAACTTGTGTGAGCAAAT
28544298 TTGAGCATTA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
28 14 0.33
29 29 0.67
ACGTcount: A:0.37, C:0.20, G:0.20, T:0.24
Consensus pattern (29 bp):
ACAACTTGTGTGAGCAAATCCAAAATATC
Found at i:28546369 original size:23 final size:24
Alignment explanation
Indices: 28546330--28546401 Score: 78
Period size: 23 Copynumber: 3.0 Consensus size: 24
28546320 CCATATATAT
* *
28546330 ATATATATATATCATAAATATATTA
1 ATATAT-TATATAATAAATAAATTA
28546355 A-A-ATTATATTAATAAATAAATTA
1 ATATATTATA-TAATAAATAAATTA
*
28546378 ATATATTATATAAT-ATTAAATTA
1 ATATATTATATAATAAATAAATTA
28546401 A
1 A
28546402 AAATTATTAG
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
22 4 0.10
23 24 0.59
24 6 0.15
25 7 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATTATATAATAAATAAATTA
Found at i:28550319 original size:19 final size:20
Alignment explanation
Indices: 28550296--28550343 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 20
28550286 ATTATAAAAA
28550296 AATAAAAATTAATAAAAGTT
1 AATAAAAATTAATAAAAGTT
* *
28550316 -ATAAAAATTACTAAAATTT
1 AATAAAAATTAATAAAAGTT
28550335 AATAAAAAT
1 AATAAAAAT
28550344 ATAAAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (20 bp):
AATAAAAATTAATAAAAGTT
Found at i:28550368 original size:9 final size:9
Alignment explanation
Indices: 28550282--28550369 Score: 81
Period size: 9 Copynumber: 9.4 Consensus size: 9
28550272 ACATGTGGCA
28550282 AAAAATTAT
1 AAAAATTAT
*
28550291 AAAAA-AAT
1 AAAAATTAT
28550299 AAAAATTAAT
1 AAAAATT-AT
*
28550309 AAAAGTTAT
1 AAAAATTAT
28550318 AAAAATTACT
1 AAAAATTA-T
*
28550328 AAAATTTAAT
1 AAAAATT-AT
28550338 AAAAA-TAT
1 AAAAATTAT
*
28550346 AAAATATATTT
1 AAAA-AT-TAT
28550357 AAAAATTAT
1 AAAAATTAT
28550366 AAAA
1 AAAA
28550370 TGCATCAAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 14
0.74 0.09 0.16
Matches are distributed among these distances:
8 13 0.20
9 22 0.34
10 22 0.34
11 7 0.11
ACGTcount: A:0.67, C:0.01, G:0.01, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:28551499 original size:12 final size:12
Alignment explanation
Indices: 28551482--28551506 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
28551472 CAACTATGTG
28551482 TTAGGTCGTGTA
1 TTAGGTCGTGTA
28551494 TTAGGTCGTGTA
1 TTAGGTCGTGTA
28551506 T
1 T
28551507 ACCTGTAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.08, G:0.32, T:0.44
Consensus pattern (12 bp):
TTAGGTCGTGTA
Found at i:28554374 original size:28 final size:28
Alignment explanation
Indices: 28554305--28554375 Score: 106
Period size: 28 Copynumber: 2.5 Consensus size: 28
28554295 GAATATATAA
28554305 TAAATATAAATTTTTTATTTTTTTAATTT
1 TAAA-ATAAATTTTTTATTTTTTTAATTT
** *
28554334 TAAAATACTTTTTTTATTTTTTTATTTT
1 TAAAATAAATTTTTTATTTTTTTAATTT
28554362 TAAAATAAATTTTT
1 TAAAATAAATTTTT
28554376 GGTGTTTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 33 0.89
29 4 0.11
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (28 bp):
TAAAATAAATTTTTTATTTTTTTAATTT
Found at i:28555896 original size:3 final size:3
Alignment explanation
Indices: 28555888--28555956 Score: 138
Period size: 3 Copynumber: 23.0 Consensus size: 3
28555878 CACGATCAAG
28555888 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28555936 AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT
28555957 GAAAAGATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:28556299 original size:36 final size:36
Alignment explanation
Indices: 28556259--28556334 Score: 84
Period size: 36 Copynumber: 2.1 Consensus size: 36
28556249 TCAAACATAG
*
28556259 AAAATATATAAAAGTATGT-GTATATATATAT-TTATA
1 AAAAT-TA-AAAAATATGTAGTATATATATATATTATA
* *
28556295 AAAATTAAAAAATGTGTACGTATATGTATATATTATA
1 AAAATTAAAAAATATGTA-GTATATATATATATTATA
28556332 AAA
1 AAA
28556335 CGTATGTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
34 8 0.24
35 2 0.06
36 16 0.47
37 8 0.24
ACGTcount: A:0.51, C:0.01, G:0.09, T:0.38
Consensus pattern (36 bp):
AAAATTAAAAAATATGTAGTATATATATATATTATA
Found at i:28556650 original size:23 final size:23
Alignment explanation
Indices: 28556624--28556668 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
28556614 AAGAGATTTG
* *
28556624 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
28556647 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
28556669 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:28556913 original size:22 final size:23
Alignment explanation
Indices: 28556871--28556915 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
28556861 AAATTAAATA
28556871 TCTAAGATTACAAAATCATATCT
1 TCTAAGATTACAAAATCATATCT
* *
28556894 TCTAAGATTGC-ATATCATATCT
1 TCTAAGATTACAAAATCATATCT
28556916 AAGATTGTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.18, G:0.07, T:0.38
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATCT
Found at i:28557241 original size:20 final size:20
Alignment explanation
Indices: 28557195--28557243 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
28557185 ATAAAAATTA
28557195 TAAAAAAATCAAAATTAGTTT
1 TAAAAAAATCAAAATTA-TTT
28557216 TAAAAAAAT-AAAATT-TTT
1 TAAAAAAATCAAAATTATTT
*
28557234 GTATAAAAAT
1 -TAAAAAAAT
28557244 TCTAGAAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
18 3 0.12
19 8 0.31
20 6 0.23
21 9 0.35
ACGTcount: A:0.59, C:0.02, G:0.04, T:0.35
Consensus pattern (20 bp):
TAAAAAAATCAAAATTATTT
Found at i:28559285 original size:20 final size:18
Alignment explanation
Indices: 28559250--28559291 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 18
28559240 TTAAAAATTA
28559250 TTTTTATCATAATAATAAT
1 TTTTTATCATAATAAT-AT
28559269 TTTTTAT-AGTAACTAATAT
1 TTTTTATCA-TAA-TAATAT
28559288 TTTT
1 TTTT
28559292 AAAAAAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 1 0.05
19 16 0.76
20 4 0.19
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTATCATAATAATAT
Found at i:28560982 original size:22 final size:22
Alignment explanation
Indices: 28560909--28560972 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
28560899 AAATCATGTT
* * *
28560909 TAACGAACTAAACCCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
28560931 TAACGTACTAAGCTCTCATGGC
1 TAACGTACTAAGCTCTCATGGC
28560953 TAACGTACTAAGCTCTCATG
1 TAACGTACTAAGCTCTCATG
28560973 TTTCACGTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 39 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (22 bp):
TAACGTACTAAGCTCTCATGGC
Found at i:28564557 original size:21 final size:21
Alignment explanation
Indices: 28564533--28564594 Score: 52
Period size: 21 Copynumber: 3.0 Consensus size: 21
28564523 TTCAAAAGCC
28564533 TGAGGGTTGAACAGAAGCTCA
1 TGAGGGTTGAACAGAAGCTCA
* * * * * *
28564554 TGAGAGCTAAATAGAAACCCA
1 TGAGGGTTGAACAGAAGCTCA
* *
28564575 TAAGGGTTGAACGGAAGCTC
1 TGAGGGTTGAACAGAAGCTC
28564595 GTAAGAGCTG
Statistics
Matches: 27, Mismatches: 14, Indels: 0
0.66 0.34 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (21 bp):
TGAGGGTTGAACAGAAGCTCA
Found at i:28564594 original size:42 final size:41
Alignment explanation
Indices: 28564535--28564690 Score: 143
Period size: 42 Copynumber: 3.7 Consensus size: 41
28564525 CAAAAGCCTG
*
28564535 AGGGTTGAACAGAAGCTCATGAGAGCTAAATAGAAACCCATA
1 AGGGTTAAACAGAAGCTCATGAGAGCTAAA-AGAAACCCATA
* * * * **
28564577 AGGGTTGAACGGAAGCTCGTAAGAGCTGAACGGAAACCCATA
1 AGGGTTAAACAGAAGCTCATGAGAGCT-AAAAGAAACCCATA
* * * *
28564619 AAGGTTAAACAGAAGCTCAAT-AGAGCTGAACGAAAACTCATA
1 AGGGTTAAACAGAAGCTC-ATGAGAGCTAAAAG-AAACCCATA
* * *
28564661 TGAGTTAAACAGAAGCTCGTGAGAGCTAAA
1 AGGGTTAAACAGAAGCTCATGAGAGCTAAA
28564691 CGGAAAGTAA
Statistics
Matches: 92, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
41 3 0.03
42 86 0.93
43 3 0.03
ACGTcount: A:0.42, C:0.17, G:0.25, T:0.17
Consensus pattern (41 bp):
AGGGTTAAACAGAAGCTCATGAGAGCTAAAAGAAACCCATA
Found at i:28567530 original size:18 final size:17
Alignment explanation
Indices: 28567497--28567535 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
28567487 TTTTATAAAT
28567497 TGTGAATTATATTTGATA
1 TGTGAATTATATTTGA-A
28567515 TGTGAATTA-ATATTGAA
1 TGTGAATTATAT-TTGAA
28567532 TGTG
1 TGTG
28567536 GAAGAAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (17 bp):
TGTGAATTATATTTGAA
Found at i:28567667 original size:8 final size:8
Alignment explanation
Indices: 28567654--28567682 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
28567644 CACTAGAGAT
28567654 CAGTGTTA
1 CAGTGTTA
28567662 CAGTGTTA
1 CAGTGTTA
28567670 CAGTGTTA
1 CAGTGTTA
28567678 CAGTG
1 CAGTG
28567683 AGTCCTGGGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.14, G:0.28, T:0.34
Consensus pattern (8 bp):
CAGTGTTA
Found at i:28567795 original size:23 final size:23
Alignment explanation
Indices: 28567769--28567821 Score: 106
Period size: 23 Copynumber: 2.3 Consensus size: 23
28567759 AGTGTTATTG
28567769 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28567792 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
28567815 ATCAGTG
1 ATCAGTG
28567822 TGACACTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:28576321 original size:19 final size:19
Alignment explanation
Indices: 28576283--28576321 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28576273 GATATTTTTG
*
28576283 TAAAAAACTATTTAATATA
1 TAAAAAACTATTTAAAATA
28576302 TAAAAAA-TATTTATAAATA
1 TAAAAAACTATTTA-AAATA
28576321 T
1 T
28576322 TAAATGAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAAAACTATTTAAAATA
Found at i:28576615 original size:21 final size:19
Alignment explanation
Indices: 28576566--28576621 Score: 85
Period size: 19 Copynumber: 2.8 Consensus size: 19
28576556 AATTTTCGAG
28576566 GATATACAATCTTAGATAT
1 GATATACAATCTTAGATAT
*
28576585 GATATGCAATCTTAGATAT
1 GATATACAATCTTAGATAT
28576604 GATATATACAATCTTAGA
1 G--ATATACAATCTTAGA
28576622 AGATATGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 19 0.58
21 14 0.42
ACGTcount: A:0.41, C:0.11, G:0.12, T:0.36
Consensus pattern (19 bp):
GATATACAATCTTAGATAT
Found at i:28577650 original size:21 final size:24
Alignment explanation
Indices: 28577624--28577674 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
28577614 TATTTTTATG
28577624 TATATATGT-A-A-TTATTATATA
1 TATATATGTAAGATTTATTATATA
28577645 TATATATGTACAGATTTATTATATA
1 TATATATGTA-AGATTTATTATATA
28577670 TATAT
1 TATAT
28577675 GTATATGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
21 9 0.35
23 1 0.04
24 1 0.04
25 15 0.58
ACGTcount: A:0.41, C:0.02, G:0.06, T:0.51
Consensus pattern (24 bp):
TATATATGTAAGATTTATTATATA
Found at i:28591244 original size:35 final size:37
Alignment explanation
Indices: 28591184--28591256 Score: 114
Period size: 35 Copynumber: 2.0 Consensus size: 37
28591174 TTTTGAAACC
* *
28591184 ATTAACTTTTTTTCTTTTTGGTTACATGAGCCAATTA
1 ATTAACTCTTTTTCTTTTTGGTTACATGAACCAATTA
28591221 ATTAACTCTTTTT-TTTTT-GTTACATGAACCAATTA
1 ATTAACTCTTTTTCTTTTTGGTTACATGAACCAATTA
28591256 A
1 A
28591257 CTTTAATTCA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 17 0.50
36 5 0.15
37 12 0.35
ACGTcount: A:0.27, C:0.14, G:0.08, T:0.51
Consensus pattern (37 bp):
ATTAACTCTTTTTCTTTTTGGTTACATGAACCAATTA
Found at i:28591255 original size:31 final size:33
Alignment explanation
Indices: 28591180--28591258 Score: 83
Period size: 37 Copynumber: 2.4 Consensus size: 33
28591170 TGGATTTTGA
*
28591180 AACC-ATTAACTTTTTTTCTTTTTGGTTACATG
1 AACCAATTAACTCTTTTTCTTTTTGGTTACATG
*
28591212 AGCCAATTAATTAACTCTTTTT-TTTTT-GTTACATG
1 AACC----AATTAACTCTTTTTCTTTTTGGTTACATG
28591247 AACCAATTAACT
1 AACCAATTAACT
28591259 TTAATTCATT
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
31 8 0.21
32 3 0.08
35 11 0.28
36 5 0.13
37 12 0.31
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.48
Consensus pattern (33 bp):
AACCAATTAACTCTTTTTCTTTTTGGTTACATG
Found at i:28591384 original size:27 final size:27
Alignment explanation
Indices: 28591330--28591393 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
28591320 AAATATTCTT
28591330 TAAATTAAT-AAATATTAATGTATCGA
1 TAAATTAATAAAATATTAATGTATCGA
* * * *
28591356 TAAATTAATAAAATTTTCATTTATTGA
1 TAAATTAATAAAATATTAATGTATCGA
*
28591383 TAAACTAATAA
1 TAAATTAATAA
28591394 CCTCAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.41
Consensus pattern (27 bp):
TAAATTAATAAAATATTAATGTATCGA
Found at i:28596315 original size:17 final size:18
Alignment explanation
Indices: 28596283--28596316 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
28596273 CCATGTGGCC
28596283 TGCCCGTGTGGGCCCACA
1 TGCCCGTGTGGGCCCACA
28596301 TGCCCGTGT-GGCCCAC
1 TGCCCGTGTGGGCCCAC
28596317 TCAGCCGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.09, C:0.41, G:0.32, T:0.18
Consensus pattern (18 bp):
TGCCCGTGTGGGCCCACA
Found at i:28606872 original size:78 final size:78
Alignment explanation
Indices: 28606743--28606927 Score: 248
Period size: 78 Copynumber: 2.4 Consensus size: 78
28606733 AATTGTATTC
* * *
28606743 TGTTTCAAATAGAAATTCAATTGAACAATCCTGTTTTAGGAATTTATTCTTGTCGTTTAA-AAGG
1 TGTTTCAAATAGAAAATCAATTGAACAATCCAGTTTTAGGAATTTATTCTTGCCGTTTAACAA-G
*
28606807 ATTTGTTTGATTTT
65 ATTTGTTTAATTTT
* * *
28606821 TGTTTCAAATTGAAAATCAATTGAATAATCCAGTTTTAGGATTTTATTCTTGCCGTTTAACAAGA
1 TGTTTCAAATAGAAAATCAATTGAACAATCCAGTTTTAGGAATTTATTCTTGCCGTTTAACAAGA
*
28606886 TTTTTTTAATTTT
66 TTTGTTTAATTTT
* *
28606899 TGTTTTAAACAGAAAA-CTAATTGAACAAT
1 TGTTTCAAATAGAAAATC-AATTGAACAAT
28606928 TCTGTTCAGG
Statistics
Matches: 93, Mismatches: 12, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
77 1 0.01
78 90 0.97
79 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.13, T:0.44
Consensus pattern (78 bp):
TGTTTCAAATAGAAAATCAATTGAACAATCCAGTTTTAGGAATTTATTCTTGCCGTTTAACAAGA
TTTGTTTAATTTT
Found at i:28615465 original size:20 final size:20
Alignment explanation
Indices: 28615440--28615494 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
28615430 TTCTTTCAGT
28615440 GGTATCACGATATCCTTTTG
1 GGTATCACGATATCCTTTTG
28615460 GGTATCACGATATCCTTTTG
1 GGTATCACGATATCCTTTTG
*
28615480 GGTATCACAATATCC
1 GGTATCACGATATCC
28615495 ACCTCCCAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.24, C:0.22, G:0.18, T:0.36
Consensus pattern (20 bp):
GGTATCACGATATCCTTTTG
Found at i:28615772 original size:10 final size:10
Alignment explanation
Indices: 28615742--28615775 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
28615732 TTAGTTTAGG
28615742 TTTAGTTTTC
1 TTTAGTTTTC
*
28615752 TCTAGGTTTTC
1 TTTA-GTTTTC
28615763 TTTAGTTTTC
1 TTTAGTTTTC
28615773 TTT
1 TTT
28615776 CAACTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.09, C:0.12, G:0.12, T:0.68
Consensus pattern (10 bp):
TTTAGTTTTC
Found at i:28617606 original size:12 final size:13
Alignment explanation
Indices: 28617565--28617605 Score: 57
Period size: 12 Copynumber: 3.2 Consensus size: 13
28617555 GGTTTTCTCC
*
28617565 AAAATGAAAATGA
1 AAAATGAAAAAGA
28617578 AAAA-GAAAAAGA
1 AAAATGAAAAAGA
28617590 AAAATGAAAAATGA
1 AAAATGAAAAA-GA
28617604 AA
1 AA
28617606 TTTACCTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 11 0.44
13 10 0.40
14 4 0.16
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.10
Consensus pattern (13 bp):
AAAATGAAAAAGA
Found at i:28619659 original size:36 final size:36
Alignment explanation
Indices: 28619613--28619685 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
28619603 TAAATACTTA
28619613 TCTTAATAGTATTTTATTAATTTAATATTAATGTGG
1 TCTTAATAGTATTTTATTAATTTAATATTAATGTGG
28619649 TCTTAATAGTATTTTATTAATTTAATATTAATGTGG
1 TCTTAATAGTATTTTATTAATTTAATATTAATGTGG
28619685 T
1 T
28619686 TATCTTAATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (36 bp):
TCTTAATAGTATTTTATTAATTTAATATTAATGTGG
Found at i:28619673 original size:5 final size:6
Alignment explanation
Indices: 28619663--28619809 Score: 95
Period size: 6 Copynumber: 26.0 Consensus size: 6
28619653 AATAGTATTT
* * * *
28619663 TATTAA T-TTAA TATTAA TGTGGTTA TCTTAA TATTAA AATTAA T-TTAA
1 TATTAA TATTAA TATTAA TAT--TAA TATTAA TATTAA TATTAA TATTAA
* *
28619711 TATTTAA TATTAA -ATTTAA TA-TAA TATTTA TATTGA TA--AA TATT-A
1 TA-TTAA TATTAA TA-TTAA TATTAA TATTAA TATTAA TATTAA TATTAA
* *
28619756 TATTAA T-TTAA TA-TAA TATTTA TATTGA TA--AA TATT-A TATTAA
1 TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA TATTAA
28619799 T-TTAA TATTAA
1 TATTAA TATTAA
28619810 AATAATTAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 34
0.70 0.08 0.22
Matches are distributed among these distances:
4 6 0.05
5 41 0.37
6 53 0.48
7 7 0.06
8 4 0.04
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (6 bp):
TATTAA
Found at i:28619754 original size:16 final size:16
Alignment explanation
Indices: 28619733--28619796 Score: 67
Period size: 16 Copynumber: 3.8 Consensus size: 16
28619723 AATTTAATAT
28619733 AATATTTATATTGATA
1 AATATTTATATTGATA
*
28619749 AATATTATATTAATTTAATA
1 AATATT-TA-T-A-TTGATA
28619769 TAATATTTATATTGATA
1 -AATATTTATATTGATA
28619786 AATA-TTATATT
1 AATATTTATATT
28619797 AATTTAATAT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 7 0.17
16 10 0.24
17 7 0.17
18 2 0.05
19 2 0.05
20 7 0.17
21 6 0.15
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AATATTTATATTGATA
Found at i:28619758 original size:21 final size:21
Alignment explanation
Indices: 28619728--28619796 Score: 85
Period size: 21 Copynumber: 3.5 Consensus size: 21
28619718 TATTAAATTT
28619728 AATATAATATTTATATTGATA
1 AATATAATATTTATATTGATA
*
28619749 AATATTATA-TTA-ATT--T-
1 AATATAATATTTATATTGATA
28619765 AATATAATATTTATATTGATA
1 AATATAATATTTATATTGATA
*
28619786 AATATTATATT
1 AATATAATATT
28619797 AATTTAATAT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
16 8 0.20
17 4 0.10
18 3 0.08
19 3 0.08
20 4 0.10
21 18 0.45
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (21 bp):
AATATAATATTTATATTGATA
Found at i:28619766 original size:37 final size:37
Alignment explanation
Indices: 28619717--28619806 Score: 171
Period size: 37 Copynumber: 2.4 Consensus size: 37
28619707 TTAATATTTA
28619717 ATATTAAATTTAATATAATATTTATATTGATAAATATT
1 ATATT-AATTTAATATAATATTTATATTGATAAATATT
28619755 ATATTAATTTAATATAATATTTATATTGATAAATATT
1 ATATTAATTTAATATAATATTTATATTGATAAATATT
28619792 ATATTAATTTAATAT
1 ATATTAATTTAATAT
28619807 TAAAATAATT
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
37 47 0.90
38 5 0.10
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (37 bp):
ATATTAATTTAATATAATATTTATATTGATAAATATT
Found at i:28620872 original size:2 final size:2
Alignment explanation
Indices: 28620865--28620906 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
28620855 TTGTCAAGTT
28620865 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
28620907 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:28626303 original size:42 final size:42
Alignment explanation
Indices: 28626251--28626350 Score: 164
Period size: 42 Copynumber: 2.4 Consensus size: 42
28626241 GCTCTCGGTA
*
28626251 TCGCACACTTAGTGCCCGTTATTCAACATCATCATTTTAATT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
* *
28626293 TCGCACACTTAGTGCCCATTATTCAACATCGTCATTTTAGTT
1 TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
*
28626335 TCACACACTTAGTGCC
1 TCGCACACTTAGTGCC
28626351 GTTCATATAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.25, C:0.28, G:0.11, T:0.36
Consensus pattern (42 bp):
TCGCACACTTAGTGCCCATTATTCAACATCATCATTTTAATT
Found at i:28635902 original size:43 final size:43
Alignment explanation
Indices: 28635833--28635936 Score: 165
Period size: 43 Copynumber: 2.4 Consensus size: 43
28635823 AATTCATGTC
* *
28635833 CACACGGCCT-GAGACACGGGTGTGTGACTTAGCCGTGTGTGA
1 CACACGGCCTAGCGACACGGGTGTGTGAATTAGCCGTGTGTGA
*
28635875 CACACGGCCTAGCGACATGGGTGTGTGAATTAGCCGTGTGTGA
1 CACACGGCCTAGCGACACGGGTGTGTGAATTAGCCGTGTGTGA
*
28635918 CACACAGCCTAGCGACACG
1 CACACGGCCTAGCGACACG
28635937 ACTATGTGTC
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
42 10 0.18
43 46 0.82
ACGTcount: A:0.22, C:0.26, G:0.33, T:0.19
Consensus pattern (43 bp):
CACACGGCCTAGCGACACGGGTGTGTGAATTAGCCGTGTGTGA
Found at i:28637881 original size:13 final size:14
Alignment explanation
Indices: 28637861--28637899 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
28637851 ACAATGGCAT
28637861 CGAAATAATATAAA
1 CGAAATAATATAAA
28637875 C-AAATAA-ATAAA
1 CGAAATAATATAAA
28637887 CGAAATTAATATA
1 CGAAA-TAATATA
28637900 CAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
12 6 0.27
13 9 0.41
14 4 0.18
15 3 0.14
ACGTcount: A:0.64, C:0.08, G:0.05, T:0.23
Consensus pattern (14 bp):
CGAAATAATATAAA
Found at i:28637910 original size:27 final size:26
Alignment explanation
Indices: 28637861--28637912 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
28637851 ACAATGGCAT
*
28637861 CGAAATAATATAAACAAATAAATAAA
1 CGAAATAATATAAACAAAAAAATAAA
28637887 CGAAATTAATATACAA-AAAAAAATAA
1 CGAAA-TAATATA-AACAAAAAAATAA
28637913 TCCATGACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 5 0.22
27 16 0.70
28 2 0.09
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (26 bp):
CGAAATAATATAAACAAAAAAATAAA
Found at i:28638237 original size:16 final size:17
Alignment explanation
Indices: 28638216--28638262 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
28638206 ATATATGTAT
28638216 ATATATAAATATAAAAA
1 ATATATAAATATAAAAA
* * *
28638233 A-ATATTCATTAGAAAAA
1 ATATA-TAAATATAAAAA
28638250 ATATATAAATATA
1 ATATATAAATATA
28638263 TACATGTACA
Statistics
Matches: 22, Mismatches: 6, Indels: 4
0.69 0.19 0.12
Matches are distributed among these distances:
16 3 0.14
17 16 0.73
18 3 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (17 bp):
ATATATAAATATAAAAA
Found at i:28638277 original size:24 final size:24
Alignment explanation
Indices: 28638250--28638304 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
28638240 ATTAGAAAAA
* *
28638250 ATATATAAATAT-ATACATGTACAT
1 ATATATAAAAATAAT-CATCTACAT
* *
28638274 ATATAAAAAAATAATTATCTACAT
1 ATATATAAAAATAATCATCTACAT
28638298 ATATATA
1 ATATATA
28638305 GATTATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
24 23 0.92
25 2 0.08
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATAAAAATAATCATCTACAT
Found at i:28638316 original size:34 final size:33
Alignment explanation
Indices: 28638273--28638336 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
28638263 TACATGTACA
28638273 TATATAAAAAAATAATTATCTACATATATATAGAT
1 TATATAAAAAAATAATTA-C-ACATATATATAGAT
* *
28638308 TATA-AAAAAGATAATTACATATATATATA
1 TATATAAAAAAATAATTACACATATATATA
28638337 AAAACAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 10 0.37
33 1 0.04
34 12 0.44
35 4 0.15
ACGTcount: A:0.56, C:0.05, G:0.03, T:0.36
Consensus pattern (33 bp):
TATATAAAAAAATAATTACACATATATATAGAT
Found at i:28638523 original size:17 final size:17
Alignment explanation
Indices: 28638501--28638544 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
28638491 TAGGAAATAA
*
28638501 AAAATGTATATGTCTAT
1 AAAATGTATATGTATAT
*
28638518 AAAATGTAAATGTATAT
1 AAAATGTATATGTATAT
*
28638535 -ATATGTATAT
1 AAAATGTATAT
28638545 AAAAGTTATG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
16 8 0.35
17 15 0.65
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.41
Consensus pattern (17 bp):
AAAATGTATATGTATAT
Found at i:28638573 original size:2 final size:2
Alignment explanation
Indices: 28638566--28638598 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
28638556 AAATAGAATA
28638566 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
28638599 GTGCATGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:28638599 original size:60 final size:59
Alignment explanation
Indices: 28638468--28638600 Score: 135
Period size: 60 Copynumber: 2.2 Consensus size: 59
28638458 TATAAAAGTG
* * * * * *
28638468 TATATAT-ATATGCATATAAAAGTTAGGAAATAAAAAATGTATATGTCTATAAAATGTA
1 TATATATAATATGTATATAAAAGTTAGCAAATAAAAAATATATATATATATAAAATATA
* * * *
28638526 AATGTATATATATGTATATAAAAGTTATGCAAATAGAATAATATATATATATAT-ATATATA
1 TATATATA-ATATGTATATAAAAGTTA-GCAAATA-AAAAATATATATATATATAAAATATA
28638587 TATATATAATATGT
1 TATATATAATATGT
28638601 GCATGTTGTT
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
58 5 0.08
60 23 0.39
61 17 0.29
62 14 0.24
ACGTcount: A:0.50, C:0.02, G:0.10, T:0.38
Consensus pattern (59 bp):
TATATATAATATGTATATAAAAGTTAGCAAATAAAAAATATATATATATATAAAATATA
Found at i:28639067 original size:19 final size:19
Alignment explanation
Indices: 28639020--28639096 Score: 100
Period size: 19 Copynumber: 3.8 Consensus size: 19
28639010 AAATTAAATC
*
28639020 TCTAAGATTACAAAATCATATA
1 TCTAAGATTAC-ATATC--ATA
*
28639042 TTCTAAGATTGCATATCATA
1 -TCTAAGATTACATATCATA
28639062 TCTAAGATTACATATCATA
1 TCTAAGATTACATATCATA
28639081 TCTAAGATTACATATC
1 TCTAAGATTACATATC
28639097 CTTGAAGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 34 0.67
20 3 0.06
22 4 0.08
23 10 0.20
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:28639530 original size:15 final size:16
Alignment explanation
Indices: 28639510--28639584 Score: 74
Period size: 15 Copynumber: 4.9 Consensus size: 16
28639500 CATGTCTTCT
28639510 TGTTTATT-TTATTAC
1 TGTTTATTATTATTAC
28639525 TGTTTATTATTATTA-
1 TGTTTATTATTATTAC
28639540 T-TATTATTATTATTA-
1 TGT-TTATTATTATTAC
28639555 T-TATTATTATTATTA-
1 TGT-TTATTATTATTAC
28639570 T-TATTATTATTATTA
1 TGT-TTATTATTATTA
28639585 TTATTATAGG
Statistics
Matches: 58, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
14 1 0.02
15 51 0.88
16 6 0.10
ACGTcount: A:0.29, C:0.01, G:0.03, T:0.67
Consensus pattern (16 bp):
TGTTTATTATTATTAC
Found at i:28639536 original size:3 final size:3
Alignment explanation
Indices: 28639528--28639609 Score: 130
Period size: 3 Copynumber: 27.0 Consensus size: 3
28639518 TTATTACTGT
28639528 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
28639576 TTA TTA TTA TTA TTA -TA GGTTA TGA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA --TTA TTA TTA TTA TTA
28639610 GTAATTTCAT
Statistics
Matches: 74, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
2 2 0.03
3 70 0.95
5 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:28641191 original size:6 final size:6
Alignment explanation
Indices: 28641164--28641226 Score: 65
Period size: 6 Copynumber: 10.5 Consensus size: 6
28641154 AGTGACTTTA
* * * *
28641164 TTTAGT TTTATGT TTT-TA TTTATT TTTATT TTTAGT TTTAGT TTTATT
1 TTTATT TTTAT-T TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
*
28641212 TTTATT GTTATT TTT
1 TTTATT TTTATT TTT
28641227 TTCCGAATTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
5 3 0.06
6 41 0.85
7 4 0.08
ACGTcount: A:0.16, C:0.00, G:0.08, T:0.76
Consensus pattern (6 bp):
TTTATT
Found at i:28642015 original size:13 final size:13
Alignment explanation
Indices: 28641997--28642021 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28641987 AAACCCCGTT
28641997 GATATCGAGATTC
1 GATATCGAGATTC
28642010 GATATCGAGATT
1 GATATCGAGATT
28642022 AATGTTGTAA
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:0.32, C:0.12, G:0.24, T:0.32
Consensus pattern (13 bp):
GATATCGAGATTC
Found at i:28644004 original size:78 final size:78
Alignment explanation
Indices: 28643875--28644031 Score: 314
Period size: 78 Copynumber: 2.0 Consensus size: 78
28643865 TAACCTTGTC
28643875 GTGGTTTACTCCATGACACTCCTACGAAGGAAGGCAAAGGAATGATGCGTGAGGAGTGGGAGATT
1 GTGGTTTACTCCATGACACTCCTACGAAGGAAGGCAAAGGAATGATGCGTGAGGAGTGGGAGATT
28643940 GCAAGGTGGACAT
66 GCAAGGTGGACAT
28643953 GTGGTTTACTCCATGACACTCCTACGAAGGAAGGCAAAGGAATGATGCGTGAGGAGTGGGAGATT
1 GTGGTTTACTCCATGACACTCCTACGAAGGAAGGCAAAGGAATGATGCGTGAGGAGTGGGAGATT
28644018 GCAAGGTGGACAT
66 GCAAGGTGGACAT
28644031 G
1 G
28644032 GTTATTTTCA
Statistics
Matches: 79, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 79 1.00
ACGTcount: A:0.29, C:0.15, G:0.35, T:0.20
Consensus pattern (78 bp):
GTGGTTTACTCCATGACACTCCTACGAAGGAAGGCAAAGGAATGATGCGTGAGGAGTGGGAGATT
GCAAGGTGGACAT
Found at i:28653873 original size:101 final size:100
Alignment explanation
Indices: 28653729--28653976 Score: 336
Period size: 101 Copynumber: 2.5 Consensus size: 100
28653719 TTATTCAAAT
*
28653729 GTAAGACCATGGTTGGGACCATGGCAGTGTATATATGTAAGACCATAGCTAGGATATGGAATTCT
1 GTAAGACCATGGTT-GGACCATGGCAGTGT-TATATGTAAGACCATAGCTAGGATATGGAATTAT
*
28653794 GATGATAAAACCATAACTGGGTTATGGCACTATGGAC
64 GATGATAAAACCATAACTGGGTTATGGCACTATGAAC
* * * *
28653831 GTAAGACCATGGTTGGACCATGGCAGTGTTTATATGTAAGACCATAGTTGGGCTATGGCATTATG
1 GTAAGACCATGGTTGGACCATGGCAGTG-TTATATGTAAGACCATAGCTAGGATATGGAATTATG
* *
28653896 ATGATAAGACCATAATTGGGTTATGGCACTATGAAC
65 ATGATAAAACCATAACTGGGTTATGGCACTATGAAC
* * * * * *
28653932 GTAATACCATGGTAGGGCCATGACAATG-CATATGTAAGACCATAG
1 GTAAGACCATGGTTGGACCATGGCAGTGTTATATGTAAGACCATAG
28653977 TTGGATTATG
Statistics
Matches: 131, Mismatches: 14, Indels: 5
0.87 0.09 0.03
Matches are distributed among these distances:
99 16 0.12
101 100 0.76
102 15 0.11
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.27
Consensus pattern (100 bp):
GTAAGACCATGGTTGGACCATGGCAGTGTTATATGTAAGACCATAGCTAGGATATGGAATTATGA
TGATAAAACCATAACTGGGTTATGGCACTATGAAC
Found at i:28653909 original size:33 final size:32
Alignment explanation
Indices: 28653727--28653980 Score: 125
Period size: 33 Copynumber: 7.6 Consensus size: 32
28653717 AATTATTCAA
* * *
28653727 ATGTAAGACCATGGTTGGGACCATGGCAGTGTATAT
1 ATGTAAGACCATAGTTGGG-CTATGGCA-T-TAT-G
* * * * *
28653763 ATGTAAGACCATAGCTAGGATATGGAATTCTG
1 ATGTAAGACCATAGTTGGGCTATGGCATTATG
* ** * *
28653795 ATGATAAAACCATAACTGGGTTATGGCACTATGG
1 ATG-TAAGACCATAGTTGGGCTATGGCATTAT-G
* * * *
28653829 ACGTAAGACCATGGTTGGACCATGGCAGTGTTTAT-
1 ATGTAAGACCATAGTTGGGCTATGGCA----TTATG
28653864 ATGTAAGACCATAGTTGGGCTATGGCATTATG
1 ATGTAAGACCATAGTTGGGCTATGGCATTATG
* * *
28653896 ATGATAAGACCATAATTGGGTTATGGCACTATG
1 ATG-TAAGACCATAGTTGGGCTATGGCATTATG
* * * * * * *
28653929 AACGTAATACCATGGTAGGGCCATGACAATGCAT-
1 -ATGTAAGACCATAGTTGGGCTATGGC-AT-TATG
28653963 ATGTAAGACCATAGTTGG
1 ATGTAAGACCATAGTTGG
28653981 ATTATGAAAC
Statistics
Matches: 162, Mismatches: 45, Indels: 25
0.70 0.19 0.11
Matches are distributed among these distances:
31 4 0.02
32 6 0.04
33 96 0.59
34 7 0.04
35 30 0.19
36 16 0.10
37 3 0.02
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (32 bp):
ATGTAAGACCATAGTTGGGCTATGGCATTATG
Found at i:28658185 original size:4 final size:4
Alignment explanation
Indices: 28658176--28658218 Score: 79
Period size: 4 Copynumber: 11.0 Consensus size: 4
28658166 TTTTCGACCT
28658176 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA -TAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA TTAA
28658219 GAAAATCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 3 0.08
4 35 0.92
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (4 bp):
TTAA
Found at i:28659195 original size:16 final size:16
Alignment explanation
Indices: 28659174--28659204 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28659164 GGGGAAAATA
*
28659174 AAAAGTTTTAGGGAAT
1 AAAAGTTTGAGGGAAT
28659190 AAAAGTTTGAGGGAA
1 AAAAGTTTGAGGGAA
28659205 AGTAAATAGG
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:0.45, C:0.00, G:0.29, T:0.26
Consensus pattern (16 bp):
AAAAGTTTGAGGGAAT
Found at i:28659570 original size:9 final size:9
Alignment explanation
Indices: 28659556--28659592 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
28659546 TATAGTTTGA
28659556 TATTCGAAT
1 TATTCGAAT
28659565 TATTCGAAT
1 TATTCGAAT
*
28659574 TATTCGAGT
1 TATTCGAAT
28659583 TATTCGAAT
1 TATTCGAAT
28659592 T
1 T
28659593 CGAAAATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:28665668 original size:16 final size:16
Alignment explanation
Indices: 28665647--28665678 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
28665637 GTTTTGTTGC
*
28665647 TAATTTTACTTTTTCA
1 TAATTTCACTTTTTCA
28665663 TAATTTCACTTTTTCA
1 TAATTTCACTTTTTCA
28665679 CTTTCAATCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.25, C:0.16, G:0.00, T:0.59
Consensus pattern (16 bp):
TAATTTCACTTTTTCA
Found at i:28665969 original size:51 final size:51
Alignment explanation
Indices: 28665906--28666096 Score: 246
Period size: 51 Copynumber: 3.8 Consensus size: 51
28665896 CCGGTTCACA
* * *
28665906 TAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCTGATACATG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
* * * *
28665957 TAGTAGCTTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCG
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCTGGTACACG
* *
28666008 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCA-T-TCTGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCTGGTACACG
28666058 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACT
28666097 TTCACTTTCA
Statistics
Matches: 119, Mismatches: 15, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
49 4 0.03
50 43 0.36
51 69 0.58
52 2 0.02
53 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCTGGTACACG
Found at i:28669048 original size:13 final size:13
Alignment explanation
Indices: 28669030--28669054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28669020 CAATACGTGA
28669030 AGAATCAGTCCCG
1 AGAATCAGTCCCG
28669043 AGAATCAGTCCC
1 AGAATCAGTCCC
28669055 TGTTGGGACA
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:0.32, C:0.32, G:0.20, T:0.16
Consensus pattern (13 bp):
AGAATCAGTCCCG
Found at i:28677936 original size:38 final size:38
Alignment explanation
Indices: 28677885--28677964 Score: 119
Period size: 38 Copynumber: 2.1 Consensus size: 38
28677875 GACATCCTCG
*
28677885 AGTGTAATTGTACACTCG-CTGCAGGGGAGATATATCGT
1 AGTGTAATTGTACACTCGCCT-CAGGGGAGATAGATCGT
*
28677923 AGTGTAATTGTACATTCGCCTCAGGGGAGATAGATCGT
1 AGTGTAATTGTACACTCGCCTCAGGGGAGATAGATCGT
28677961 -GTGT
1 AGTGT
28677965 GTCTCCAGTC
Statistics
Matches: 39, Mismatches: 2, Indels: 3
0.89 0.05 0.07
Matches are distributed among these distances:
37 4 0.10
38 33 0.85
39 2 0.05
ACGTcount: A:0.25, C:0.15, G:0.30, T:0.30
Consensus pattern (38 bp):
AGTGTAATTGTACACTCGCCTCAGGGGAGATAGATCGT
Found at i:28679390 original size:22 final size:22
Alignment explanation
Indices: 28679365--28679412 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
28679355 TAAAGAACTT
**
28679365 AAACTTACCATTGTATTAAATG
1 AAACTTACCAACGTATTAAATG
*
28679387 AAACTTACCAACGTATTAAATT
1 AAACTTACCAACGTATTAAATG
28679409 AAAC
1 AAAC
28679413 AACCATGAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.31
Consensus pattern (22 bp):
AAACTTACCAACGTATTAAATG
Done.