Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004966.1 Hibiscus syriacus cultivar Beakdansim tig00011158_pilon, 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: 87575
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Found at i:198 original size:19 final size:19
Alignment explanation
Indices: 160--206 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
150 CGAGTATCGA
*
160 TATCGAT-CTTAAGGTGAG
1 TATCGATACTCAAGGTGAG
*
178 TATCGATACTCAAGTTGAG
1 TATCGATACTCAAGGTGAG
197 TATCGATACT
1 TATCGATACT
207 TCTTCCTTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 7 0.27
19 19 0.73
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (19 bp):
TATCGATACTCAAGGTGAG
Found at i:4940 original size:105 final size:104
Alignment explanation
Indices: 4800--5072 Score: 422
Period size: 105 Copynumber: 2.6 Consensus size: 104
4790 CCTTTTGTCG
4800 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGTGTGAATTTG
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGG-GTGAATTTG
* *
4865 AAAGGAATGA-GCTCTTCTCATTACGAACATTCTCCTTTAA
65 AAAAGAA-CATGCTCTTCTCATTACGAACATTCTCCTTTAA
* * *
4905 GATGAGTTCTTCTCATTATGAACTCTTCTGAAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTG
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTG-GGTGAATTTG
* *
4970 AAAAGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAG
65 AAAAGAACATGCTCTTCTCATTACGAACATTCTCCTTTAA
* *
5010 GACGAGTTCTTCTCATTATGAACTATTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATT
1 GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCT-GGGTGAATT
5073 ATAGTTGTTG
Statistics
Matches: 153, Mismatches: 12, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
104 1 0.01
105 150 0.98
106 2 0.01
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.38
Consensus pattern (104 bp):
GATGAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGTGAATTTGA
AAAGAACATGCTCTTCTCATTACGAACATTCTCCTTTAA
Found at i:6022 original size:17 final size:16
Alignment explanation
Indices: 6013--6043 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6003 TTTCATTTTT
6013 TTCATTTTTTCATTCA
1 TTCATTTTTTCATTCA
6029 TTCATTTTTTC-TTCA
1 TTCATTTTTTCATTCA
6044 AGCATAGTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.16, C:0.19, G:0.00, T:0.65
Consensus pattern (16 bp):
TTCATTTTTTCATTCA
Found at i:12433 original size:21 final size:20
Alignment explanation
Indices: 12404--12453 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
12394 ATATTAAATA
* *
12404 TTTTCTATATTATTAAATGCC
1 TTTTATATATT-TTAAATGAC
* *
12425 TTTTATATATTTTTATTGAC
1 TTTTATATATTTTAAATGAC
12445 TTTTATATA
1 TTTTATATA
12454 CATTTTAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.28, C:0.08, G:0.04, T:0.60
Consensus pattern (20 bp):
TTTTATATATTTTAAATGAC
Found at i:12698 original size:2 final size:2
Alignment explanation
Indices: 12691--12724 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12681 ACTCTACTGT
12691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12725 ATTTACCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:23067 original size:23 final size:23
Alignment explanation
Indices: 23032--23079 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
23022 ATCAAGTACA
* *
23032 ATAATATATTAGGTAACGTTTAT
1 ATAATATAATAGGTAACGCTTAT
* *
23055 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAACGCTTAT
23078 AT
1 AT
23080 TGATCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.40
Consensus pattern (23 bp):
ATAATATAATAGGTAACGCTTAT
Found at i:24011 original size:182 final size:182
Alignment explanation
Indices: 23699--24152 Score: 673
Period size: 182 Copynumber: 2.5 Consensus size: 182
23689 ATTTTTATAC
* *
23699 TACCGATTTTGTCATTTCGAGATCGATTTTGT-TATATTTTTACTTGTTATATTGTTATGGATCG
1 TACCGATTTTGTCATTTCGAGATCGATTTTATCT-TATTTTTACATGTTATATTGTTATGGATCG
* *
23763 ATATATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAA
65 ATACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAA
* *
23828 GTGTAGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTT
130 GTGTAGATACTTATAATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTT
* * * *
23881 TACCGATTTTTTTATTTCGAGACCGGTTTTATCTTATTTTTACATGTTATATTGTTATGGATCGA
1 TACCGATTTTGTCATTTCGAGATCGATTTTATCTTATTTTTACATGTTATATTGTTATGGATCGA
* *
23946 TACATTTTTATAAAGTTTCGACACTTTATTAGCGCTATAACTT-TTTCTCTTTTAAATTTCAAAA
66 TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTT-TCTTTTAAATTCCAAAA
* *
24010 GTGTCGATACTTATAATAAAGTATCGACACTATCAAAATATCTGGTAGCGCTT
130 GTGTAGATACTTATAATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTT
** * * *
24063 TACCTG-TTTTGTCATTTATAGATCGATTTTATCAGT-TTTTTACCTGTTTTATTGTTATGGATC
1 TACC-GATTTTGTCATTTCGAGATCGATTTTATC-TTATTTTTACATGTTATATTGTTATGGATC
24126 GATACATTTTTATAAAGTATCGACACT
64 GATACATTTTTATAAAGTATCGACACT
24153 ATCAACATAT
Statistics
Matches: 244, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
181 3 0.01
182 238 0.98
183 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
TACCGATTTTGTCATTTCGAGATCGATTTTATCTTATTTTTACATGTTATATTGTTATGGATCGA
TACATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAG
TGTAGATACTTATAATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTT
Found at i:24378 original size:113 final size:112
Alignment explanation
Indices: 24025--24486 Score: 723
Period size: 111 Copynumber: 4.1 Consensus size: 112
24015 GATACTTATA
* * *
24025 ATAAAGTATCGACACTATCAAAATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGAT
1 ATAAAGTATCGACACTATCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * *
24090 TTTATCAGTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
24137 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
24202 TTTGTCA-TTTTTTATCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
24248 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
24313 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
24361 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACC-AG
1 ATAAAGTATCGACACTATCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGA-
* * *
24425 TTTTGT-ATTTTTTTACTTGTTATATTGTTATGGATCAATATATTTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
24472 ATAAAGTATGGACAC
1 ATAAAGTATCGACAC
24487 AAACCGACAA
Statistics
Matches: 328, Mismatches: 19, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
111 156 0.48
112 69 0.21
113 103 0.31
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:24416 original size:224 final size:223
Alignment explanation
Indices: 24025--24486 Score: 723
Period size: 224 Copynumber: 2.1 Consensus size: 223
24015 GATACTTATA
* *
24025 ATAAAGTATCGACACTATCAAAATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGAT
1 ATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
*
24090 TTTATCAGTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
66 TTTATCAGTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
*
24155 CAACATATCCGGTAGCGCTTTACCTGTTTTTTCATTTATAGACC-GATTTTGTCA-TTTTTTA-T
131 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAG-TTTTGT-ATTTTTTTACT
*
24217 CTGTTATATTGTTATGGATCGATACATTTTT
194 -TGTTATATTGTTATGGATCAATACATTTTT
* *
24248 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
* * * *
24313 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTT
66 TTTATCA-GTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
* * *
24378 TCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTACTT
130 TCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTACTT
*
24443 GTTATATTGTTATGGATCAATATATTTTT
195 GTTATATTGTTATGGATCAATACATTTTT
*
24472 ATAAAGTATGGACAC
1 ATAAAGTATCGACAC
24487 AAACCGACAA
Statistics
Matches: 219, Mismatches: 16, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
223 68 0.31
224 149 0.68
225 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (223 bp):
ATAAAGTATCGACACTATCAAAATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
TTTATCAGTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTACTTG
TTATATTGTTATGGATCAATACATTTTT
Found at i:26150 original size:14 final size:14
Alignment explanation
Indices: 26131--26159 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
26121 GCATTATAAG
26131 ACTATGCCATCATA
1 ACTATGCCATCATA
26145 ACTATGCCATCATA
1 ACTATGCCATCATA
26159 A
1 A
26160 TTCATGTAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.28, G:0.07, T:0.28
Consensus pattern (14 bp):
ACTATGCCATCATA
Found at i:27877 original size:32 final size:32
Alignment explanation
Indices: 27836--27899 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
27826 CAATACTTCC
27836 CTGTTCCTCCAGCTCGACATAATCCACCACCT
1 CTGTTCCTCCAGCTCGACATAATCCACCACCT
*
27868 CTGTTCCTCCAGCTCGACATATTCCACCACCT
1 CTGTTCCTCCAGCTCGACATAATCCACCACCT
27900 TCAATAAGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.20, C:0.44, G:0.09, T:0.27
Consensus pattern (32 bp):
CTGTTCCTCCAGCTCGACATAATCCACCACCT
Found at i:30768 original size:20 final size:21
Alignment explanation
Indices: 30743--30794 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
30733 TTTTCCCAAT
*
30743 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30763 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
30784 TCGCAATGCGA
1 TCGCAATGCGA
30795 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:30825 original size:41 final size:41
Alignment explanation
Indices: 30780--30857 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
30770 GCGAATTGGG
* * *
30780 AAAATCGCAATGCGATACTGACTATCACAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATAATAC
* * *
30821 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCACAACGCGATA
30858 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCACAACGCGATAATAC
Found at i:30850 original size:20 final size:20
Alignment explanation
Indices: 30825--30877 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
30815 TAATACAAAA
* *
30825 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
30845 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
30865 TCGCAACGCGATA
1 TCGCAACGCGATA
30878 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:31141 original size:26 final size:22
Alignment explanation
Indices: 31065--31130 Score: 114
Period size: 22 Copynumber: 3.0 Consensus size: 22
31055 ACTCTCTCAC
**
31065 CCATCTCCGATGAAATCCGTCT
1 CCATCTCCGGCGAAATCCGTCT
31087 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGGCGAAATCCGTCT
31109 CCATCTCCGGCGAAATCCGTCT
1 CCATCTCCGGCGAAATCCGTCT
31131 ATCTCCATCT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.20, C:0.39, G:0.17, T:0.24
Consensus pattern (22 bp):
CCATCTCCGGCGAAATCCGTCT
Found at i:31449 original size:20 final size:20
Alignment explanation
Indices: 31392--31440 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
31382 GCGATTCTCT
**
31392 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
31412 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
*
31432 TGTTGCGAT
1 CGTTGCGAT
31441 TTTCATTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:32790 original size:18 final size:18
Alignment explanation
Indices: 32769--32906 Score: 190
Period size: 18 Copynumber: 7.6 Consensus size: 18
32759 TCCACTTCAG
*
32769 GAGCCATCACATCGCCCA
1 GAGCTATCACATCGCCCA
* *
32787 GAGCTATCACCTCACCCA
1 GAGCTATCACATCGCCCA
*
32805 GAGCCATCATCTGATCGACCC-
1 GAGCTATCA-C--ATCG-CCCA
32826 G-GCTATCACATCGCCCA
1 GAGCTATCACATCGCCCA
32843 GAGCTATCACATCGCCCA
1 GAGCTATCACATCGCCCA
32861 GAGCTATCACATCGCCCA
1 GAGCTATCACATCGCCCA
32879 GAGCTATCACATCGCCCA
1 GAGCTATCACATCGCCCA
32897 GAGCTATCAC
1 GAGCTATCAC
32907 CTCTTCTCCA
Statistics
Matches: 107, Mismatches: 7, Indels: 12
0.85 0.06 0.10
Matches are distributed among these distances:
16 3 0.03
17 5 0.05
18 85 0.79
19 2 0.02
20 6 0.06
21 3 0.03
22 3 0.03
ACGTcount: A:0.27, C:0.40, G:0.17, T:0.17
Consensus pattern (18 bp):
GAGCTATCACATCGCCCA
Found at i:33377 original size:19 final size:20
Alignment explanation
Indices: 33323--33368 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
33313 TAGTTTACTT
* *
33323 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
33343 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
33363 TCGCAA
1 TCGCAA
33369 TGTGAAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.26, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:33422 original size:32 final size:33
Alignment explanation
Indices: 33362--33452 Score: 130
Period size: 32 Copynumber: 2.8 Consensus size: 33
33352 GGAAATGGCT
* * *
33362 ATCGCAATGTGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
33395 ATCGCAATACGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
33427 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
33453 TGCGATTTGT
Statistics
Matches: 51, Mismatches: 6, Indels: 2
0.86 0.10 0.03
Matches are distributed among these distances:
32 28 0.55
33 23 0.45
ACGTcount: A:0.49, C:0.19, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:33430 original size:14 final size:14
Alignment explanation
Indices: 33378--33435 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
33368 ATGTGAAATG
* *
33378 AAAATCGTAACGAC
1 AAAATCGCAACGAA
33392 AAAATCGCAATACGAA
1 AAAATCGC-A-ACGAA
33408 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
33424 AAAATCGCAACG
1 AAAATCGCAACG
33436 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 18 0.47
15 1 0.03
16 11 0.29
17 1 0.03
18 7 0.18
ACGTcount: A:0.52, C:0.21, G:0.16, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:33446 original size:19 final size:19
Alignment explanation
Indices: 33392--33457 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
33382 TCGTAACGAC
*
33392 AAAATCGCAATACGAAATG
1 AAAATCGCAATGCGAAATG
33411 -AAATCGCAA--CG-AA--
1 AAAATCGCAATGCGAAATG
*
33424 AAAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATG
33443 AAAATCGCAATGCGA
1 AAAATCGCAATGCGA
33458 TTTGTGTTTC
Statistics
Matches: 40, Mismatches: 1, Indels: 12
0.75 0.02 0.23
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
16 4 0.10
17 2 0.05
18 9 0.22
19 14 0.35
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.12
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:33500 original size:32 final size:33
Alignment explanation
Indices: 33464--33542 Score: 124
Period size: 32 Copynumber: 2.4 Consensus size: 33
33454 GCGATTTGTG
* *
33464 TTTCGCATTGTGATTTTGTCGTTTAGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGAGATTTTCA
*
33496 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGAGATTTTCA
33529 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
33543 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 24 0.56
33 19 0.44
ACGTcount: A:0.14, C:0.16, G:0.20, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGAGATTTTCA
Found at i:33561 original size:20 final size:19
Alignment explanation
Indices: 33527--33582 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
33517 TTGCGATTTT
*
33527 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
33546 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
33566 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
33583 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:35614 original size:14 final size:14
Alignment explanation
Indices: 35595--35648 Score: 63
Period size: 14 Copynumber: 3.5 Consensus size: 14
35585 CGAAATGGCT
35595 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
35609 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
35628 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
35642 ATCGCAA
1 ATCGCAA
35649 TGCGATTTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
14 18 0.51
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.31
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:35666 original size:33 final size:33
Alignment explanation
Indices: 35576--35653 Score: 120
Period size: 33 Copynumber: 2.4 Consensus size: 33
35566 AAAACAGACT
* ***
35576 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
35609 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
35642 ATCGCAATGCGA
1 ATCGCAATGCGA
35654 TTTTCATTTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 41 1.00
ACGTcount: A:0.42, C:0.22, G:0.23, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:35697 original size:20 final size:20
Alignment explanation
Indices: 35672--35729 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
35662 TCGCATTGCG
*
35672 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
35692 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
35712 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
35730 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:36009 original size:19 final size:18
Alignment explanation
Indices: 35957--36013 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
35947 AGTGAGATCA
35957 CAATGCGAAAAGAAAATCG
1 CAATGCG-AAAGAAAATCG
*
35976 CAA--C--AAGATAATCG
1 CAATGCGAAAGAAAATCG
35990 CAATGCGAAATGAAAATCG
1 CAATGCGAAA-GAAAATCG
36009 CAATG
1 CAATG
36014 ACAAAATCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
14 12 0.39
16 1 0.03
17 1 0.03
18 2 0.06
19 15 0.48
ACGTcount: A:0.49, C:0.18, G:0.19, T:0.14
Consensus pattern (18 bp):
CAATGCGAAAGAAAATCG
Found at i:36022 original size:33 final size:33
Alignment explanation
Indices: 35957--36025 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
35947 AGTGAGATCA
* *
35957 CAATGCGAAAAGAAAATCGCAACAAGATAATCG
1 CAATGCGAAAAGAAAATCGCAACAACAAAATCG
* **
35990 CAATGCGAAATGAAAATCGCAATGACAAAATCG
1 CAATGCGAAAAGAAAATCGCAACAACAAAATCG
36023 CAA
1 CAA
36026 CGATTTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.51, C:0.19, G:0.17, T:0.13
Consensus pattern (33 bp):
CAATGCGAAAAGAAAATCGCAACAACAAAATCG
Found at i:36080 original size:33 final size:33
Alignment explanation
Indices: 36025--36148 Score: 142
Period size: 33 Copynumber: 3.7 Consensus size: 33
36015 CAAAATCGCA
* * *
36025 ACGATTTTAATTTTCGCTTTGCGATTCCCTCGTT
1 ACGATTTTCA-TTTCGCATTGCGATTCTCTCGTT
36059 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
* * *
36092 -GGCTTTTTCATTTCGCATTGCGATTCTATCGTT
1 ACG-ATTTTCATTTCGCATTGCGATTCTCTCGTT
* * *
36125 GCGATTTGCATTTCGTATTGCGAT
1 ACGATTTTCATTTCGCATTGCGAT
36149 GGTCAAATGA
Statistics
Matches: 78, Mismatches: 10, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 1 0.01
33 67 0.86
34 10 0.13
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ACGATTTTCATTTCGCATTGCGATTCTCTCGTT
Found at i:36928 original size:24 final size:24
Alignment explanation
Indices: 36901--36954 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
36891 GTATTCGAAA
* *
36901 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
36925 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
36949 TTTGAT
1 TTTGAT
36955 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:38680 original size:2 final size:2
Alignment explanation
Indices: 38633--38663 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
38623 ACAAAACATG
38633 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38664 GAAATAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:40825 original size:105 final size:105
Alignment explanation
Indices: 40626--41153 Score: 903
Period size: 105 Copynumber: 5.0 Consensus size: 105
40616 GTTGTGAAGT
* * * *
40626 TGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCGTGAAGTTGAACTTGTGTTGT
1 TGAAATTGAGAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGT
*
40691 CTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTC
65 CTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
40732 TGAAATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
* *
40797 TGGAGTCCAATATCCTTCGTTCTAAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
40837 TGAATTTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGTT
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
40902 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
40942 TGGAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
41007 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* * *
41047 TGAAATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
41112 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
41152 TG
1 TG
41154 GGTAAAACCT
Statistics
Matches: 400, Mismatches: 22, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
105 389 0.97
106 11 0.03
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:41109 original size:315 final size:305
Alignment explanation
Indices: 40541--41153 Score: 951
Period size: 315 Copynumber: 2.0 Consensus size: 305
40531 CTGGGACTGG
* * *
40541 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTACTGTCTTGAGTTC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCACTGTCTTGAGTCC
*
40606 AATATCCTTCGTTGTGAAGTTGAAATTGGGAAATTGTTTATTGACAACCAGCGGTACCTTCGTCG
66 AATATCCTTCGTTGTGAAGTTGAAATTGGGAAAATGTTTATTGACAACCAGCGGTACCTTCGTCG
* *
40671 TGAAGTTGAACTTGTGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAA
131 TGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAA
* * * *
40736 ATTGAGAGATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGA
196 ATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGA
40801 GTCCAATATCCTTCGTTCTAAAGTTGAAATTGGCTCTGAATTTGA
261 GTCCAATATCCTTCGTTCTAAAGTTGAAATTGGCTCTGAATTTGA
**
40846 GAAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCGTTGT-TTGGAGTC
1 GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCACTGTCTT-GAGTC
*
40909 CAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGAATTGAGAAATGTTTGTTGACAACCAGCG
65 CAATATCCTTCGTTGTGAAGTTGAAA-----T-TGG----GA-AAATGTTTATTGACAACCAGCG
* *
40974 GTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAA
119 GTACCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAA
41039 ATTGGCTCTGAAATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACAT
184 ATTGGCTCTGAAATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACAT
* *
41104 GCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
249 GCGTTGTCTGGAGTCCAATATCCTTCGTTCTAAAGTTGAAATTGGCTCTG
41154 GGTAAAACCT
Statistics
Matches: 279, Mismatches: 17, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
303 2 0.01
304 77 0.28
305 4 0.01
309 1 0.00
310 3 0.01
314 2 0.01
315 190 0.68
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (305 bp):
GAAATTGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAATTGAACTTGCACTGTCTTGAGTCC
AATATCCTTCGTTGTGAAGTTGAAATTGGGAAAATGTTTATTGACAACCAGCGGTACCTTCGTCG
TGAAGTTGAACATGCGTTGTCTGGAGTCCAATATCCTTCATTGTGAAGTTGAAATTGGCTCTGAA
ATTAAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGGA
GTCCAATATCCTTCGTTCTAAAGTTGAAATTGGCTCTGAATTTGA
Found at i:42011 original size:12 final size:10
Alignment explanation
Indices: 41990--42026 Score: 56
Period size: 10 Copynumber: 3.5 Consensus size: 10
41980 CGTTCTTCTC
41990 TTTTTGTTTT
1 TTTTTGTTTT
42000 TGTTTATGTTTT
1 T-TTT-TGTTTT
42012 TTTTTGTTTT
1 TTTTTGTTTT
42022 TTTTT
1 TTTTT
42027 TCAACTTAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 12 0.48
11 6 0.24
12 7 0.28
ACGTcount: A:0.03, C:0.00, G:0.11, T:0.86
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:49721 original size:84 final size:84
Alignment explanation
Indices: 49580--49749 Score: 313
Period size: 84 Copynumber: 2.0 Consensus size: 84
49570 TATCTGAAGC
*
49580 TCGTTTGCTTGCCTCTTGAACCCATCTACAATACCTTCTAGCTCAGCTATTGTCTTGCCATCTTT
1 TCGTTTGCTTGCCTCTTGAACCCATCTACAATACCTTCTAACTCAGCTATTGTCTTGCCATCTTT
49645 CTCATGTTGTTTTTCTAAG
66 CTCATGTTGTTTTTCTAAG
*
49664 TCGTTTGCTTGCCTCTTGAACCCATCTACAATAGCTTCTAACTCAGCTATTGTCTTGCCATCTTT
1 TCGTTTGCTTGCCTCTTGAACCCATCTACAATACCTTCTAACTCAGCTATTGTCTTGCCATCTTT
*
49729 CTCATGTTTTTTTTCTAAG
66 CTCATGTTGTTTTTCTAAG
49748 TC
1 TC
49750 AGCTATCCGA
Statistics
Matches: 83, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.17, C:0.27, G:0.12, T:0.44
Consensus pattern (84 bp):
TCGTTTGCTTGCCTCTTGAACCCATCTACAATACCTTCTAACTCAGCTATTGTCTTGCCATCTTT
CTCATGTTGTTTTTCTAAG
Found at i:51560 original size:10 final size:10
Alignment explanation
Indices: 51547--51575 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
51537 TAAAATAGAG
51547 ATAAATAAAA
1 ATAAATAAAA
51557 ATAAATAAAA
1 ATAAATAAAA
51567 ATAAATAAA
1 ATAAATAAA
51576 TGGTAAAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:53005 original size:2 final size:2
Alignment explanation
Indices: 52998--53030 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
52988 AAATAATAAA
52998 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
53031 AATTAAATAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:55674 original size:19 final size:19
Alignment explanation
Indices: 55652--55782 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
55642 GGAAATTACT
55652 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
55671 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
55685 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
55704 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
55718 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
55737 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
55751 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
55770 ATTGCAACGCGAA
1 ATCGCAATGCGAA
55783 TTTAATTTCG
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 27 0.33
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:55694 original size:33 final size:33
Alignment explanation
Indices: 55652--55778 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
55642 GGAAATTACT
55652 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
55685 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
55717 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
55751 ATCGCAATGCGAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
55779 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:55759 original size:66 final size:66
Alignment explanation
Indices: 55653--55785 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
55643 GAAATTACTA
*
55653 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
55718 T
66 T
* *
55719 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATTGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
55784 T
66 T
55785 T
1 T
55786 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.41, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:55810 original size:14 final size:14
Alignment explanation
Indices: 55793--55849 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
55783 TTTAATTTCG
55793 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
55807 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
55826 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
55840 CGTTGCGATT
1 CGTTGCGATT
55850 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:55829 original size:33 final size:33
Alignment explanation
Indices: 55778--55867 Score: 153
Period size: 33 Copynumber: 2.7 Consensus size: 33
55768 AAATTGCAAC
* *
55778 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
55811 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
55844 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
55868 AGTACTTTTT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.13, C:0.22, G:0.21, T:0.43
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:55831 original size:19 final size:19
Alignment explanation
Indices: 55807--55867 Score: 69
Period size: 19 Copynumber: 3.5 Consensus size: 19
55797 GCGATTCTCT
55807 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
55826 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
55840 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
55859 CATTGCGAT
1 CGTTGCGAT
55868 AGTACTTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
14 10 0.29
16 3 0.09
17 3 0.09
19 18 0.53
ACGTcount: A:0.11, C:0.23, G:0.21, T:0.44
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:55995 original size:14 final size:14
Alignment explanation
Indices: 55976--56010 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
55966 TCAATTAAAT
55976 AAATCAACTTTTAC
1 AAATCAACTTTTAC
*
55990 AAATCACCTTTTAC
1 AAATCAACTTTTAC
56004 AAATCAA
1 AAATCAA
56011 TTAACCAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (14 bp):
AAATCAACTTTTAC
Found at i:57931 original size:94 final size:94
Alignment explanation
Indices: 57770--57984 Score: 369
Period size: 94 Copynumber: 2.3 Consensus size: 94
57760 GAATAATTTC
*
57770 AATTGGCAGCAAACGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
* *
57835 ACAGTGTTAAAGAATACACAGTTTAGCAG
66 ACAGTGATAAAGAACACACAGTTTAGCAG
*
57864 AATTGGCAGGAACCGAACAAATTTACTTTCAACCAAAAGACAAATA-AAAGACAAATACTAACTT
1 AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAA-ACAAAGACAAATACTAACTT
57928 CACAGTGATAAAGAACACACAGTTTAGCAG
65 CACAGTGATAAAGAACACACAGTTTAGCAG
*
57958 AATTGGCAGCAACCGAATAAATTTACT
1 AATTGGCAGCAACCGAACAAATTTACT
57985 AAGCAATCTA
Statistics
Matches: 114, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
94 113 0.99
95 1 0.01
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.20
Consensus pattern (94 bp):
AATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTC
ACAGTGATAAAGAACACACAGTTTAGCAG
Found at i:59751 original size:33 final size:33
Alignment explanation
Indices: 59694--59792 Score: 153
Period size: 33 Copynumber: 3.0 Consensus size: 33
59684 ACGAGATAAT
*
59694 GAGAATCGTAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
59728 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
59761 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
59793 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
33 47 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.22, G:0.26, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:59786 original size:19 final size:19
Alignment explanation
Indices: 59669--59814 Score: 96
Period size: 19 Copynumber: 8.1 Consensus size: 19
59659 TCTTTTGGTT
*
59669 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
* *
59688 GATAATGAGAATCGTAACGC
1 GA-AATGAAAATCGCAACGC
**
59708 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
59726 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
59742 GAAATGACTATCGCGA--C
1 GAAATGAAAATCGCAACGC
*
59759 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
59775 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* *
59794 GAAATGAAAATTGCAATGC
1 GAAATGAAAATCGCAACGC
59813 GA
1 GA
59815 TTTTGGTTTC
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 17 0.17
15 2 0.02
16 4 0.04
17 3 0.03
18 3 0.03
19 42 0.43
20 25 0.26
21 2 0.02
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:59832 original size:19 final size:18
Alignment explanation
Indices: 59810--59877 Score: 55
Period size: 20 Copynumber: 3.5 Consensus size: 18
59800 AAAATTGCAA
*
59810 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
* *
59829 TGCGTTTTTTTATTTCGTGT
1 TGCG--ATTTTATTTCGCGT
*
59849 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTT-CGCGT
59869 TGCGATTTT
1 TGCGATTTT
59878 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.03
19 12 0.32
20 21 0.55
21 4 0.11
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:60423 original size:20 final size:20
Alignment explanation
Indices: 60398--60446 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
60388 TATGTAAATT
60398 GCGTTGCGAAAGTCAGAATC
1 GCGTTGCGAAAGTCAGAATC
*
60418 GCGTTGCGAAAGTCAGTATC
1 GCGTTGCGAAAGTCAGAATC
*
60438 TCGTTGCGA
1 GCGTTGCGA
60447 TTTTGTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.24
Consensus pattern (20 bp):
GCGTTGCGAAAGTCAGAATC
Found at i:60480 original size:20 final size:20
Alignment explanation
Indices: 60455--60508 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
60445 GATTTTGTAT
60455 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
60475 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
60495 TATCGCATTGCGAT
1 TATCGCATTGCGAT
60509 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:60529 original size:61 final size:61
Alignment explanation
Indices: 60415--60529 Score: 133
Period size: 61 Copynumber: 1.9 Consensus size: 61
60405 GAAAGTCAGA
* * * ** * *
60415 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATGGCGATAGTAAGT
* *
60476 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT-TCGCGTGGCGAT
1 ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAATATCGCATGGCGAT
60530 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
61 42 0.95
62 2 0.05
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAATATCGCATGGCGATAGTAAGT
Found at i:60548 original size:20 final size:21
Alignment explanation
Indices: 60497--60548 Score: 52
Period size: 20 Copynumber: 2.5 Consensus size: 21
60487 ATAGTCAGTA
*
60497 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* * **
60518 TCGCGTGGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
60538 TCGCATTGCGA
1 TCGCATTGCGA
60549 ATTGGGAAAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.17, C:0.25, G:0.21, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:61832 original size:18 final size:18
Alignment explanation
Indices: 61809--61873 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
61799 ATGATAAACA
61809 ATATCATACATAATAGTC
1 ATATCATACATAATAGTC
* * **
61827 ATATCAAAGGCATGATAAAC
1 ATATCATA--CATAATAGTC
*
61847 AATATCATGCATAATAGTC
1 -ATATCATACATAATAGTC
61866 ATATCATA
1 ATATCATA
61874 TTCTTTTTCA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
18 14 0.41
19 7 0.21
20 7 0.21
21 6 0.18
ACGTcount: A:0.46, C:0.15, G:0.09, T:0.29
Consensus pattern (18 bp):
ATATCATACATAATAGTC
Found at i:61832 original size:39 final size:39
Alignment explanation
Indices: 61789--61871 Score: 132
Period size: 39 Copynumber: 2.1 Consensus size: 39
61779 CTCATGATTT
61789 TATCAAA-ACAATGATAAACAATATCATACATAATAGTCA
1 TATCAAAGAC-ATGATAAACAATATCATACATAATAGTCA
* *
61828 TATCAAAGGCATGATAAACAATATCATGCATAATAGTCA
1 TATCAAAGACATGATAAACAATATCATACATAATAGTCA
61867 TATCA
1 TATCA
61872 TATTCTTTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 40 0.98
40 1 0.02
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (39 bp):
TATCAAAGACATGATAAACAATATCATACATAATAGTCA
Found at i:61921 original size:13 final size:13
Alignment explanation
Indices: 61901--61960 Score: 68
Period size: 13 Copynumber: 4.7 Consensus size: 13
61891 ACAATACAAA
*
61901 ACTTTCATATCTC
1 ACTTTCATATTTC
* *
61914 ATTTTCATCTTTC
1 ACTTTCATATTTC
61927 ACTTTCATA-TTC
1 ACTTTCATATTTC
*
61939 ACTTTCACATTTC
1 ACTTTCATATTTC
*
61952 ATTTTCATA
1 ACTTTCATA
61961 ATATATACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
12 11 0.29
13 27 0.71
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (13 bp):
ACTTTCATATTTC
Found at i:62370 original size:12 final size:12
Alignment explanation
Indices: 62353--62388 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
62343 TAAATAGTAA
62353 TGAACAATACCG
1 TGAACAATACCG
*
62365 TGAACAATACCA
1 TGAACAATACCG
*
62377 TGAACAGTACCG
1 TGAACAATACCG
62389 ATTCTAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.17
Consensus pattern (12 bp):
TGAACAATACCG
Found at i:63055 original size:32 final size:32
Alignment explanation
Indices: 62978--63107 Score: 203
Period size: 32 Copynumber: 4.1 Consensus size: 32
62968 GCTCGTATAA
*
62978 TAAT-CTGTCCATATGTCCC-GAAGAACATAGG
1 TAATACTGTCCATATGTCCCAAAAG-ACATAGG
* *
63009 TAA-ATTGTCCATATGTCCCGAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
63040 TAATACTGTCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
63072 TAATACTGTCCATATGTCCCAAAAGACATAGG
1 TAATACTGTCCATATGTCCCAAAAGACATAGG
63104 TAAT
1 TAAT
63108 CCCTCGACTC
Statistics
Matches: 92, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
31 27 0.29
32 65 0.71
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (32 bp):
TAATACTGTCCATATGTCCCAAAAGACATAGG
Found at i:66354 original size:20 final size:21
Alignment explanation
Indices: 66329--66376 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
66319 AAAAATAGTC
*
66329 AAATTCCA-CATTCTAACACT
1 AAATTCCATCACTCTAACACT
*
66349 AAATT-CATCACTCTAACATT
1 AAATTCCATCACTCTAACACT
*
66369 AATTTCCA
1 AAATTCCA
66377 GCATATTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 19 0.83
21 2 0.09
ACGTcount: A:0.40, C:0.27, G:0.00, T:0.33
Consensus pattern (21 bp):
AAATTCCATCACTCTAACACT
Found at i:75034 original size:13 final size:13
Alignment explanation
Indices: 75016--75041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
75006 GTTGTTATAT
75016 TTTTTTATAAATA
1 TTTTTTATAAATA
75029 TTTTTTATAAATA
1 TTTTTTATAAATA
75042 ATATTATTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TTTTTTATAAATA
Found at i:75051 original size:17 final size:17
Alignment explanation
Indices: 75025--75096 Score: 55
Period size: 17 Copynumber: 4.4 Consensus size: 17
75015 TTTTTTTATA
75025 AATATT-TTTTATAAAT
1 AATATTATTTTATAAAT
*
75041 AATATTATTTTTTATAA-
1 AATATTATTTTATA-AAT
* *
75058 AATAATATTTATATAATT
1 AATATTATTT-TATAAAT
*
75076 ATTATT-TTTT-TAAAT
1 AATATTATTTTATAAAT
75091 -ATATTA
1 AATATTA
75097 ATTATTTATT
Statistics
Matches: 43, Mismatches: 8, Indels: 11
0.69 0.13 0.18
Matches are distributed among these distances:
14 4 0.09
15 4 0.09
16 7 0.16
17 19 0.44
18 9 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
AATATTATTTTATAAAT
Found at i:75051 original size:19 final size:20
Alignment explanation
Indices: 75027--75066 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
75017 TTTTTATAAA
75027 TATTTTTTAT-AAATAATAT
1 TATTTTTTATAAAATAATAT
75046 TATTTTTTATAAAATAATAT
1 TATTTTTTATAAAATAATAT
75066 T
1 T
75067 TATATAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTTTTTATAAAATAATAT
Found at i:75057 original size:32 final size:31
Alignment explanation
Indices: 75016--75110 Score: 99
Period size: 32 Copynumber: 3.1 Consensus size: 31
75006 GTTGTTATAT
*
75016 TTTTTTATAAATATTTTTTATA-AATAATATTA
1 TTTTTTATAAATATTATTTATATAAT--TATTA
*
75048 TTTTTTATAAAATAATATTTATATAATTATTA
1 TTTTTTAT-AAATATTATTTATATAATTATTA
* *
75080 TTTTTT-TAAATA-TATTAAT-TATTTATTA
1 TTTTTTATAAATATTATTTATATAATTATTA
75108 TTT
1 TTT
75111 GTGCTAATTA
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
28 11 0.19
29 6 0.11
30 5 0.09
31 1 0.02
32 19 0.33
33 12 0.21
34 3 0.05
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (31 bp):
TTTTTTATAAATATTATTTATATAATTATTA
Found at i:75225 original size:28 final size:27
Alignment explanation
Indices: 75194--75252 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
75184 CTCAAGACAT
75194 TTTAGTGAT-ATGGTAATATTTTTTTTAA
1 TTTA-TGATAATGGTAATA-TTTTTTTAA
* * *
75222 TTTATGTTAATGTTTATATTTTTTTAA
1 TTTATGATAATGGTAATATTTTTTTAA
75249 TTTA
1 TTTA
75253 AATTTATCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 16 0.59
28 11 0.41
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (27 bp):
TTTATGATAATGGTAATATTTTTTTAA
Found at i:76526 original size:24 final size:24
Alignment explanation
Indices: 76481--76530 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
76471 ATAAAGAACC
*
76481 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
76505 AAAATAAAGTTTAAACAT-CCATTA
1 AAAATAAA-CTTAAACATACCATTA
76529 AA
1 AA
76531 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 16 0.70
25 7 0.30
ACGTcount: A:0.58, C:0.12, G:0.02, T:0.28
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:79821 original size:26 final size:25
Alignment explanation
Indices: 79785--79860 Score: 86
Period size: 26 Copynumber: 3.0 Consensus size: 25
79775 ATGAATGAAG
79785 GAAAGAGAAAAAGTAAAAGTAAAAAT
1 GAAAGAGAAAAAG-AAAAGTAAAAAT
*
79811 GAAAGAGAAAAA-AAAATTAATAAA-
1 GAAAGAGAAAAAGAAAAGTAA-AAAT
79835 GAAAGAG-AAAAGAAAAAGTTAAAAAT
1 GAAAGAGAAAAAG-AAAAG-TAAAAAT
79861 TTAAGAGGGA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
23 4 0.09
24 14 0.33
25 10 0.23
26 15 0.35
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (25 bp):
GAAAGAGAAAAAGAAAAGTAAAAAT
Found at i:79826 original size:30 final size:28
Alignment explanation
Indices: 79754--79826 Score: 67
Period size: 29 Copynumber: 2.5 Consensus size: 28
79744 GGCTATGGAG
**
79754 AGAGAATAAAAAAAGAAAAAGATGAATGA
1 AGAGAA-AAAAAAAGAAAAAGAAAAATGA
*
79783 AG-GAAAGAGAAAAAGTAAAAGTAAAAATGAA
1 AGAGAAA-A-AAAAAGAAAAAG-AAAAATG-A
79814 AGAGAAAAAAAAA
1 AGAGAAAAAAAAA
79827 TTAATAAAGA
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
27 1 0.03
28 4 0.11
29 13 0.36
30 10 0.28
31 4 0.11
32 4 0.11
ACGTcount: A:0.71, C:0.00, G:0.21, T:0.08
Consensus pattern (28 bp):
AGAGAAAAAAAAAGAAAAAGAAAAATGA
Found at i:79867 original size:26 final size:26
Alignment explanation
Indices: 79785--79860 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 26
79775 ATGAATGAAG
*
79785 GAAAGAGAAAAAGTAAAAG-TAAAAAT
1 GAAAGAG-AAAAGAAAAAGTTAAAAAT
79811 GAAAGAGAAAA-AAAAA-TTAATAAA-
1 GAAAGAGAAAAGAAAAAGTTAA-AAAT
79835 GAAAGAGAAAAGAAAAAGTTAAAAAT
1 GAAAGAGAAAAGAAAAAGTTAAAAAT
79861 TTAAGAGGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 10
0.80 0.02 0.18
Matches are distributed among these distances:
24 18 0.41
25 15 0.34
26 11 0.25
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.12
Consensus pattern (26 bp):
GAAAGAGAAAAGAAAAAGTTAAAAAT
Found at i:81931 original size:23 final size:23
Alignment explanation
Indices: 81905--81949 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
81895 CACCACAGCT
*
81905 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
81928 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
81950 ATATAATGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:82187 original size:149 final size:149
Alignment explanation
Indices: 81917--82231 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
81907 TATAATTGCA
*
81917 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAA
* * *
81981 TTCCTTAAGAATCATATATATATGCTAGGGATCATATATGTGTCTTTCCAGACTTCACACTTGTT
65 TTCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTT
82046 CCAAAGAATATACATATGTC
130 CCAAAGAATATACATATGTC
82066 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
82131 TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
82196 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
82215 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
82232 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATGATGTCCATAAGGACCACATAGAAT
TCCTTAAGAATCATATACATATGCTAGGGATAATATATGTGTCTTTCCAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:83138 original size:18 final size:18
Alignment explanation
Indices: 83117--83151 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
83107 TCCCATCTAG
83117 CTTATC-TTATATGTTCAT
1 CTTATCATT-TATGTTCAT
83135 CTTATCATTTATGTTCA
1 CTTATCATTTATGTTCA
83152 AATCTCCTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.23, C:0.17, G:0.06, T:0.54
Consensus pattern (18 bp):
CTTATCATTTATGTTCAT
Found at i:83755 original size:21 final size:21
Alignment explanation
Indices: 83731--83775 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
83721 TGTTGTTCGT
* *
83731 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
83752 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
83773 TTG
1 TTG
83776 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:87226 original size:144 final size:140
Alignment explanation
Indices: 86994--87294 Score: 484
Period size: 144 Copynumber: 2.1 Consensus size: 140
86984 GATAGTTGCA
86994 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCACATAGAAT
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCACATAGAAT
*
87058 TCCTTAAGAATCATATACATATGCTAGGGATCATATGTGTCTTTCCAGACTTCACACATGTTCCA
65 TCCTTAAGAATCATATACATATGCTAGGGAT-A-ATATGTCTTTCCAGACTT--CACATGTTCCA
87123 AAGAATATACATATGT
126 AAGAATATACATA-GT
*
87139 CCCGAAGGACCGCGTAGAATTGCA-TGTAGTGCCATATAATGATGTCCATAA-GA-CACATAGAA
1 -CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATAT-ATGATGTCCATAAGGACCACATAGAA
87201 TTCCTTAAGAATCATATACATATGCTAGGGATAATATGTCTTTCCAGACTTCACATGTTCCAAAG
64 TTCCTTAAGAATCATATACATATGCTAGGGATAATATGTCTTTCCAGACTTCACATGTTCCAAAG
87266 AATATACATAGT
129 AATATACATAGT
87278 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
87295 CCCTCGACTC
Statistics
Matches: 151, Mismatches: 2, Indels: 12
0.92 0.01 0.07
Matches are distributed among these distances:
138 17 0.11
139 2 0.01
140 24 0.16
142 17 0.11
143 1 0.01
144 41 0.27
145 15 0.10
146 34 0.23
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.27
Consensus pattern (140 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATATGATGTCCATAAGGACCACATAGAATT
CCTTAAGAATCATATACATATGCTAGGGATAATATGTCTTTCCAGACTTCACATGTTCCAAAGAA
TATACATAGT
Done.