Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007077.1 Hibiscus syriacus cultivar Beakdansim tig00018469_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: 62047
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Found at i:8975 original size:17 final size:16
Alignment explanation
Indices: 8953--8986 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
8943 TAAAAACTGT
8953 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
8970 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
8986 A
1 A
8987 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:15939 original size:18 final size:19
Alignment explanation
Indices: 15913--15970 Score: 73
Period size: 18 Copynumber: 3.1 Consensus size: 19
15903 CCGAGGGATT
15913 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
* * *
15932 AT-AGTGGTTCTTCGGAATA
1 ATCAGTGGTCCTTCGGGA-C
15951 ATCAGTGGTCCTTCGGGAC
1 ATCAGTGGTCCTTCGGGAC
15970 A
1 A
15971 AATATTCAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 13 0.42
19 5 0.16
20 13 0.42
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (19 bp):
ATCAGTGGTCCTTCGGGAC
Found at i:17109 original size:23 final size:23
Alignment explanation
Indices: 17083--17151 Score: 111
Period size: 23 Copynumber: 3.0 Consensus size: 23
17073 CACCACAGCT
*
17083 CGTAGAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
* *
17106 CGTAGAATTGCACCGTAGTGTCG
1 CGTAGAATTGCACCGTAGTGCCA
17129 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGTAGTGCCA
17152 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGTAGTGCCA
Found at i:18161 original size:21 final size:21
Alignment explanation
Indices: 18129--18171 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 21
18119 TGTTTGTTTA
18129 ATTGAGAGTGCATCGATGCAC
1 ATTGAGAGTGCATCGATGCAC
18150 ATTGA-AGATGCATCGATGCAC
1 ATTGAGAG-TGCATCGATGCAC
18171 A
1 A
18172 CAACCCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (21 bp):
ATTGAGAGTGCATCGATGCAC
Found at i:19269 original size:14 final size:14
Alignment explanation
Indices: 19247--19340 Score: 53
Period size: 14 Copynumber: 6.4 Consensus size: 14
19237 GGTTAGGGTG
19247 TTACATAAAATGAA
1 TTACATAAAATGAA
* **
19261 TTACCTAAAAACTGTT
1 TTACAT-AAAA-TGAA
19277 TTACATAAAATGAA
1 TTACATAAAATGAA
* * **
19291 ATATATGAAAATTGTT
1 TTACAT-AAAA-TGAA
*
19307 TTACGTAAAATGAA
1 TTACATAAAATGAA
* * *
19321 TTGCCTAAAATAAA
1 TTACATAAAATGAA
19335 TTACAT
1 TTACAT
19341 TTTGTAAAAA
Statistics
Matches: 56, Mismatches: 20, Indels: 8
0.67 0.24 0.10
Matches are distributed among these distances:
14 28 0.50
15 16 0.29
16 12 0.21
ACGTcount: A:0.48, C:0.10, G:0.09, T:0.34
Consensus pattern (14 bp):
TTACATAAAATGAA
Found at i:19281 original size:30 final size:30
Alignment explanation
Indices: 19247--19330 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
19237 GGTTAGGGTG
19247 TTACATAAAATGAATTACCTAAAAACTGTT
1 TTACATAAAATGAATTACCTAAAAACTGTT
* ** * *
19277 TTACATAAAATGAAATATATGAAAATTGTT
1 TTACATAAAATGAATTACCTAAAAACTGTT
* *
19307 TTACGTAAAATGAATTGCCTAAAA
1 TTACATAAAATGAATTACCTAAAA
19331 TAAATTACAT
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (30 bp):
TTACATAAAATGAATTACCTAAAAACTGTT
Found at i:20609 original size:26 final size:26
Alignment explanation
Indices: 20519--20617 Score: 76
Period size: 26 Copynumber: 3.6 Consensus size: 26
20509 TTCATTATTA
*
20519 ATAATATAATAATATTATATTTAAAAA-
1 ATAATATAAT-ATATTA-AATTAAAAAT
* *
20546 ATAATAGATAATATTAATTATATTAATAAT
1 ATAAT--ATAATA-T-ATTAAATTAAAAAT
* *
20576 TTATTATACAT-TATTAAATTAAAAAT
1 ATAATATA-ATATATTAAATTAAAAAT
20602 ATAATATAATATATTA
1 ATAATATAATATATTA
20618 TTATAATATA
Statistics
Matches: 56, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
25 2 0.04
26 23 0.41
27 6 0.11
28 4 0.07
29 14 0.25
30 7 0.12
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
ATAATATAATATATTAAATTAAAAAT
Found at i:23253 original size:31 final size:31
Alignment explanation
Indices: 23206--23268 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
23196 TTGGATTCAC
* *
23206 GAGTCAAATTAATATTTTATCTAAAGTTTAA
1 GAGTAAAATTAATATTTTATCTAAAATTTAA
*
23237 GAGTAAAATTAGTATTTTATCTAAAATTTAA
1 GAGTAAAATTAATATTTTATCTAAAATTTAA
23268 G
1 G
23269 TTTAAACAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.43, C:0.05, G:0.11, T:0.41
Consensus pattern (31 bp):
GAGTAAAATTAATATTTTATCTAAAATTTAA
Found at i:25999 original size:22 final size:21
Alignment explanation
Indices: 25974--26023 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 21
25964 ATCAATAAAA
* *
25974 ATATAGTTTTATACTAATATTT
1 ATATAATTTTATAATAA-ATTT
25996 ATATAATTTTATAATAAATTT
1 ATATAATTTTATAATAAATTT
*
26017 AAATAAT
1 ATATAAT
26024 AATTTTTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 10 0.40
22 15 0.60
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (21 bp):
ATATAATTTTATAATAAATTT
Found at i:26022 original size:21 final size:22
Alignment explanation
Indices: 25980--26023 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
25970 AAAAATATAG
* *
25980 TTTTATACTAATATTTATATAA
1 TTTTATAATAATATTTAAATAA
26002 TTTTATAATAA-ATTTAAATAA
1 TTTTATAATAATATTTAAATAA
26023 T
1 T
26024 AATTTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 10 0.50
22 10 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTATAATAATATTTAAATAA
Found at i:34063 original size:68 final size:69
Alignment explanation
Indices: 33911--34078 Score: 243
Period size: 68 Copynumber: 2.4 Consensus size: 69
33901 TTGTTGCTGG
* * **
33911 ATTTGCTTGAATTAGTTGGCTTT-TAGGGATGAAATTGAGTGTTGTTGTAGTACTTTTGGGGTTT
1 ATTTGTTTGAATTTGTTGG-TTTGTAGGGATGAAATTGAG-GTTGTTGTAACACTTTTGGGGTTT
33975 GATAGC
64 GATAGC
33981 ATTTGTTTGAATTTGTTGGTTTGTAGGGATGAAATTGA-G-TGTTGTAACACTTTTGGGGGTTTG
1 ATTTGTTTGAATTTGTTGGTTTGTAGGGATGAAATTGAGGTTGTTGTAACACTTTT-GGGGTTTG
34044 ATAGC
65 ATAGC
*
34049 ATTTGTTTGAATTTGTTGGTTTGTTGGGAT
1 ATTTGTTTGAATTTGTTGGTTTGTAGGGAT
34079 TTTAAGTCGA
Statistics
Matches: 91, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
67 13 0.14
68 43 0.47
69 3 0.03
70 32 0.35
ACGTcount: A:0.19, C:0.04, G:0.30, T:0.46
Consensus pattern (69 bp):
ATTTGTTTGAATTTGTTGGTTTGTAGGGATGAAATTGAGGTTGTTGTAACACTTTTGGGGTTTGA
TAGC
Found at i:39753 original size:27 final size:27
Alignment explanation
Indices: 39689--39754 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 27
39679 GTGTTCCTAA
**
39689 TGGTGGAAATGGCAACCCTAATGCTGC
1 TGGTGGAGGTGGCAACCCTAATGCTGC
* * *
39716 TGGTGGTGGTGGCAACCCTAATGTTGG
1 TGGTGGAGGTGGCAACCCTAATGCTGC
39743 TGGTGGAGGTGG
1 TGGTGGAGGTGG
39755 AGACGGTGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.18, C:0.15, G:0.41, T:0.26
Consensus pattern (27 bp):
TGGTGGAGGTGGCAACCCTAATGCTGC
Found at i:39827 original size:72 final size:72
Alignment explanation
Indices: 39750--39898 Score: 208
Period size: 72 Copynumber: 2.1 Consensus size: 72
39740 TGGTGGTGGA
* ** **
39750 GGTGGAGACGGTGGTGCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGGGGCTAAAGC
1 GGTGGAGACGGAGACGCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGC
*
39815 TGCTGGT
66 TGCCGGT
** * *
39822 GGTGGAGGTGGAGACGCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGCAGCTGAAGCTAAAGT
1 GGTGGAGACGGAGACGCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGC
39887 TGCCGGT
66 TGCCGGT
39894 GGTGG
1 GGTGG
39899 TGGTGGCGGC
Statistics
Matches: 67, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
72 67 1.00
ACGTcount: A:0.17, C:0.19, G:0.40, T:0.23
Consensus pattern (72 bp):
GGTGGAGACGGAGACGCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGC
TGCCGGT
Found at i:39904 original size:72 final size:72
Alignment explanation
Indices: 39765--39904 Score: 226
Period size: 72 Copynumber: 1.9 Consensus size: 72
39755 AGACGGTGGT
** *
39765 GCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGGGGCTAAAGCTGCTGGTGGTGGAGG
1 GCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGCTGCCGGTGGTGGAGG
39830 TGGAGAC
66 TGGAGAC
* * *
39837 GCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGCAGCTGAAGCTAAAGTTGCCGGTGGTGGTGG
1 GCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGCTGCCGGTGGTGGAGG
39902 TGG
66 TGG
39905 CGGCGGCGGA
Statistics
Matches: 62, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.17, C:0.20, G:0.39, T:0.24
Consensus pattern (72 bp):
GCTTCTGCTCAGGCTCGTGCTAAGGCTGAAGCTGAAGCTGAAGCTAAAGCTGCCGGTGGTGGAGG
TGGAGAC
Found at i:42621 original size:48 final size:48
Alignment explanation
Indices: 42456--42710 Score: 187
Period size: 48 Copynumber: 5.3 Consensus size: 48
42446 TGCTGCTCAG
* * * * * *
42456 GCTAATGTTGGTAGA-AGAGGTGGAGCTAGTGATTCTGGTAGTGGCCAA
1 GCTAATGTTGGTGGACA-TGGTGGTGCCAGTGCTTCTGGTAGTGGTCAA
* * * **
42504 GCTATTGTTGGTGGATATAGTGGTATC-GTTGCTTCTGGTAGTGG-CAAA
1 GCTAATGTTGGTGGACATGGTGGTGCCAG-TGCTTCTGGTAGTGGTC-AA
* *
42552 GCTAATATTGGTGGACATGGTGGTGCCAGTGCTTCTGGCAGTGGTCAA
1 GCTAATGTTGGTGGACATGGTGGTGCCAGTGCTTCTGGTAGTGGTCAA
* * * * *
42600 GCTAATGCTGGTGGA-AGTGGTGGTGCAAATGCTTC-AGTAAATGGTCAA
1 GCTAATGTTGGTGGACA-TGGTGGTGCCAGTGCTTCTGGT-AGTGGTCAA
* * * * * * * * *
42648 ACTAATATTAGTGGACATGGTGGCGCTAGTGTTTCTGGGAGTGATTAA
1 GCTAATGTTGGTGGACATGGTGGTGCCAGTGCTTCTGGTAGTGGTCAA
42696 GCTAATGTTGGTGGA
1 GCTAATGTTGGTGGA
42711 AGTGGCGACG
Statistics
Matches: 159, Mismatches: 39, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
47 4 0.03
48 150 0.94
49 5 0.03
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.31
Consensus pattern (48 bp):
GCTAATGTTGGTGGACATGGTGGTGCCAGTGCTTCTGGTAGTGGTCAA
Found at i:42623 original size:96 final size:96
Alignment explanation
Indices: 42474--42715 Score: 249
Period size: 96 Copynumber: 2.5 Consensus size: 96
42464 TGGTAGAAGA
* * * * * **
42474 GGTGGAGCTAGTGATTCTGGTAGTGGCCAAGCTATTGTTGGTGGATA-TAGTGGTATC-GTTGCT
1 GGTGGAGCTAGTGATTCTGGCAGTGGTCAAGCTAATGTTGGTGGA-AGTGGTGGT-GCAAATGCT
* * *
42537 TCTGGT-AGTGG-CAAAGCTAATATTGGTGGACAT
64 TC-AGTAAATGGTCAAA-CTAATATTAGTGGACAT
* * * *
42570 GGTGGTGCCAGTGCTTCTGGCAGTGGTCAAGCTAATGCTGGTGGAAGTGGTGGTGCAAATGCTTC
1 GGTGGAGCTAGTGATTCTGGCAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGTGCAAATGCTTC
42635 AGTAAATGGTCAAACTAATATTAGTGGACAT
66 AGTAAATGGTCAAACTAATATTAGTGGACAT
* * * * *
42666 GGTGGCGCTAGTGTTTCTGGGAGTGATTAAGCTAATGTTGGTGGAAGTGG
1 GGTGGAGCTAGTGATTCTGGCAGTGGTCAAGCTAATGTTGGTGGAAGTGG
42716 CGACGCTAGT
Statistics
Matches: 121, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
95 4 0.03
96 113 0.93
97 4 0.03
ACGTcount: A:0.22, C:0.12, G:0.35, T:0.31
Consensus pattern (96 bp):
GGTGGAGCTAGTGATTCTGGCAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGTGCAAATGCTTC
AGTAAATGGTCAAACTAATATTAGTGGACAT
Found at i:42940 original size:96 final size:96
Alignment explanation
Indices: 42840--43067 Score: 285
Period size: 96 Copynumber: 2.4 Consensus size: 96
42830 AAGTGGTACT
* * * *** * *
42840 GCTAGTGCTTCTGGTAGTGGTCAAGCTAACGTTGGTTGAAGTGGTGTCGCTATTGCTTCTAGGAA
1 GCTAGTGCTTCCGGTAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAACTAGTGCTTCCAGGAA
*
42905 AAGTGAAGCTAAAAGTGGAGGAAGTAGTGGC
66 AAGTGAAGCTAAAAGTGGAGAAAGTAGTGGC
* * * *
42936 GCTAGTACTTCCGGAAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAATTAGTGCTTCCGGGAA
1 GCTAGTGCTTCCGGTAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAACTAGTGCTTCCAGGAA
** *
43001 GGGTGAAGCTAAAAGTGGAGAAAGTAGTGGG
66 AAGTGAAGCTAAAAGTGGAGAAAGTAGTGGC
* * *
43032 GCCAGTGCTTCCAGTAGTGGTCAAGATAATGTTGGT
1 GCTAGTGCTTCCGGTAGTGGTCAAGCTAATGTTGGT
43068 AGAAATGGAG
Statistics
Matches: 111, Mismatches: 21, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
96 111 1.00
ACGTcount: A:0.25, C:0.12, G:0.36, T:0.27
Consensus pattern (96 bp):
GCTAGTGCTTCCGGTAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAACTAGTGCTTCCAGGAA
AAGTGAAGCTAAAAGTGGAGAAAGTAGTGGC
Found at i:42995 original size:48 final size:48
Alignment explanation
Indices: 42807--43067 Score: 170
Period size: 48 Copynumber: 5.4 Consensus size: 48
42797 TTTTTCTGGC
* *** * *
42807 AGTGGTCAAGCTAAGGTTGGTGGAAGTGGTACTGCTAGTGCTTCTGGT
1 AGTGGTCAAGCTAAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTCCGGA
* * ** * *
42855 AGTGGTCAAGCTAACGTTGGTTGAAGTGGTGTCGCTATTGCTTCTAGGA
1 AGTGGTCAAGCTAAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTC-CGGA
** * * * * *
42904 A-AAGTGAAGCTAAAAG-TGGAGGAAGTAGTGGCGCTAGTACTTCCGGA
1 AGTGGTCAAGCT-AAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTCCGGA
* **
42951 AGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAATTAGTGCTTCCGGGA
1 AGTGGTCAAGCTAAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTCC-GGA
* * * * * * * *
43000 AG-GGTGAAGCTAAAAG-TGGAGAAAGTAGTGGGGCCAGTGCTTCCAGT
1 AGTGGTCAAGCT-AAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTCCGGA
* *
43047 AGTGGTCAAGATAATGTTGGT
1 AGTGGTCAAGCTAAAGTTGGT
43068 AGAAATGGAG
Statistics
Matches: 161, Mismatches: 44, Indels: 16
0.73 0.20 0.07
Matches are distributed among these distances:
47 13 0.08
48 134 0.83
49 14 0.09
ACGTcount: A:0.25, C:0.12, G:0.36, T:0.27
Consensus pattern (48 bp):
AGTGGTCAAGCTAAAGTTGGTGGAAGTGGTGGAGCTAGTGCTTCCGGA
Found at i:43099 original size:96 final size:96
Alignment explanation
Indices: 42907--43106 Score: 233
Period size: 96 Copynumber: 2.1 Consensus size: 96
42897 TCTAGGAAAA
* * * *
42907 GTGAAGCTAAAAGTGGAGGAAGTAGTGGCGCTAGTACTTCCGGAAGTGGTCAAGCTAATGTTGGT
1 GTGAAGCTAAAAGTGGAGAAAGTAGTGGCGCCAGTACTTCCAGAAGTGGTCAAGATAATGTTGGT
* * * * ***
42972 GGAAGTGGTGGAATTAGTGCTTCCGGGAAGG
66 AGAAATGGTAGAACTAGTGCTTCCAAAAAGG
* * *
43003 GTGAAGCTAAAAGTGGAGAAAGTAGTGGGGCCAGTGCTTCCAGTAGTGGTCAAGATAATGTTGGT
1 GTGAAGCTAAAAGTGGAGAAAGTAGTGGCGCCAGTACTTCCAGAAGTGGTCAAGATAATGTTGGT
*
43068 AGAAATGG-AGACGCTAGTGCATT-CAAAAAGG
66 AGAAATGGTAGA-ACTAGTGC-TTCCAAAAAGG
43099 GTGAAGCT
1 GTGAAGCT
43107 TGTAATATCC
Statistics
Matches: 87, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
95 2 0.02
96 83 0.95
97 2 0.02
ACGTcount: A:0.29, C:0.12, G:0.36, T:0.23
Consensus pattern (96 bp):
GTGAAGCTAAAAGTGGAGAAAGTAGTGGCGCCAGTACTTCCAGAAGTGGTCAAGATAATGTTGGT
AGAAATGGTAGAACTAGTGCTTCCAAAAAGG
Found at i:44829 original size:22 final size:22
Alignment explanation
Indices: 44804--44849 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
44794 GTCGAGGGAT
*
44804 TATACAGTGGTCCTTCGGGACA
1 TATACAATGGTCCTTCGGGACA
*
44826 TATACAATGGTTCTTCGGGACA
1 TATACAATGGTCCTTCGGGACA
44848 TA
1 TA
44850 GTGGTCCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (22 bp):
TATACAATGGTCCTTCGGGACA
Found at i:45741 original size:48 final size:47
Alignment explanation
Indices: 45594--46911 Score: 530
Period size: 48 Copynumber: 27.8 Consensus size: 47
45584 TAGTGGGGCC
* * * * ** **
45594 AGTGCTTCTAGTAGTGGTCAAGCTAATGTTGGTAGAAGTGACGACGCT
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * ** *
45642 AGTGCATTC-GGAAAAGGGTGAAGCTAATATTGGTGGAATTGG-CATCACT
1 AGTGC-TTCTGG--AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGT-GCT
* * *
45691 AGTGCTTCTGGAAAGGGGGAATCTAATGTTTGTGGAAGTGGTGGTGCT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * *
45739 AGTACTTCCGGCAAGGGTGAAACTAATGTAT-GTGGAAGTGGTGATGCT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGT-TGGTGGAAGTGGTGGTGCT
* * * ***** *
45787 AGTGATTCTAGAAGTGGTTAAGCTAATGTTGGTGGAAGTGACAAAGCA
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * *
45835 AGTGCTTCTGGCAAGGGTGAAGGTAAAAG-TGGTGGAACTAGTGGTGCC
1 AGTGCTTCTGG-AAGGGTGAAGCT-AATGTTGGTGGAAGTGGTGGTGCT
* * * * ** *
45883 AGTGCTTCCGAAAATGGTCAAGCTAATGTTGGTGTTAGTGGCGGTGCT
1 AGTGCTTCTG-GAAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
** * * * **** *
45931 AGTGCTTCTGGAAGTGGCCATGCTATTGTTGCTGGAAGTGGCAACGCA
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * *
45979 AGTGCTTCTGGCAA-GGTGAAGGTAAAAG-TGGTGGAAGTGGTGGTACC
1 AGTGCTTCTGG-AAGGGTGAAGCT-AATGTTGGTGGAAGTGGTGGTGCT
* * * * * ** *
46026 AGTGCTTCCGGAAGTGGTCAAACTAGTATTGGTGGAAGTGACGGTACT
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * **
46074 AGTGCTTATAGCAAGGGTGAAGCTAAAAG-TGGTGGAAGTGGCAGTGCT
1 AGTGCTTCT-GGAAGGGTGAAGCT-AATGTTGGTGGAAGTGGTGGTGCT
* * * * * * *
46122 AGTTCTTCAGGCAGTGGTCAAGCTAATGTTGGTTGAAGTGGTGATGCC
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * *
46170 AATGCTTCTGGAAATGGTCAAGTTAATGTTGGTGGAAGTGGTGGCGCT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* *
46218 AGTGCTTCTGGAAAAGGG-GAAACTAA---------AAGTGGTGGCT-CC
1 AGTGCTTCTGG--AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGG-TGCT
* * * *
46257 AGTGCTTCCAGTAAGGGTCAAGCTAATATTGGTGGAAGTGGT-GT-CATT
1 AGTGCTT-CTGGAAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGC--T
* * * *
46305 AGTGCTTATGGAAGTGATCAAGCTAATGTTGGTAGAAGTAGG-GGTGCT
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGT-GGTGGTGCT
* * * * ** *
46353 GGTGGTTCTGGAAGTGGTCAAGCTAATGTTGGTGGAAGTAGCAGTGCA
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * **
46401 AGTGCTTCTGGCAAGGGTGAAGCTAATGTTGGTGGCAGTGGCGGCACT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * **
46449 AGTGTTTCCAGAAAGGGTGAAGCTAATGTAGGTGGAAGTGGCAGTGCT
1 AGTGCTT-CTGGAAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * *
46497 AGTGCTATC-GGTA--GTG--G-TCAA-GAT--AGGAAGTGGTGGTGCT
1 AGTGCT-TCTGGAAGGGTGAAGCT-AATGTTGGTGGAAGTGGTGGTGCT
* * * * *
46537 AGTGCTTCTGGGAGTGGTCAAGTTAATGTTTGTGGAAGTGGAGGTGCT
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * ** * * *
46585 AATGCTTC-GAAAGTGGCT-AAACTAATGTCAGTGGAAATGGCT-ATTCT
1 AGTGCTTCTGGAAG-GG-TGAAGCTAATGTTGGTGGAAGTGG-TGGTGCT
* * * * *
46632 AGTGCTTATGGCAGTGGTCAAGCCAATGTAGGTGGAAGTGGTGGTGCT
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * ** *
46680 AGTGCTTCCGGAAATGGAGAAACTAATGTAAGTGGAAGTGGTGATGCT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * *
46728 AGTACTTTTGGAAAGGGAGAAGCTAATATTGGTGGAATTGGTGGTGCT
1 AGTGCTTCTGG-AAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * * **** * * *
46776 AGTGCTACAGATAAGGGTGAAGCCAAAACAGGTGGAAATGGCGGTGTT
1 AGTGCTTCTG-GAAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
* * * **
46824 AGTGCTGT-TGGTAA-TG-GAACTGCTAATGTTAGTGGAGGTGGTGGTATT
1 AGTGCT-TCTGG-AAGGGTGAA--GCTAATGTTGGTGGAAGTGGTGGTGCT
* * * *
46872 AGTGCTTTTGGCAGTGGTAAAGCTAATGTCGGTGGAAGTG
1 AGTGCTTCTGGAAG-GGTGAAGCTAATGTTGGTGGAAGTG
46912 ACGAAACTAG
Statistics
Matches: 937, Mismatches: 260, Indels: 146
0.70 0.19 0.11
Matches are distributed among these distances:
38 5 0.01
39 25 0.03
40 24 0.03
42 2 0.00
43 5 0.01
45 6 0.01
46 10 0.01
47 88 0.09
48 701 0.75
49 66 0.07
50 5 0.01
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (47 bp):
AGTGCTTCTGGAAGGGTGAAGCTAATGTTGGTGGAAGTGGTGGTGCT
Found at i:45946 original size:24 final size:24
Alignment explanation
Indices: 45927--45972 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
45917 TTAGTGGCGG
45927 TGCTAGTGCTT-CTGGAAGTGGCCA
1 TGCTAGTG-TTGCTGGAAGTGGCCA
*
45951 TGCTATTGTTGCTGGAAGTGGC
1 TGCTAGTGTTGCTGGAAGTGGC
45973 AACGCAAGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.15, C:0.17, G:0.35, T:0.33
Consensus pattern (24 bp):
TGCTAGTGTTGCTGGAAGTGGCCA
Found at i:45989 original size:24 final size:24
Alignment explanation
Indices: 45931--45989 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
45921 TGGCGGTGCT
* * *
45931 AGTGCTTCTGGAAGTGGCCATGCT
1 AGTGCTTCTGGAAGTGGCAACGCA
*
45955 ATTG-TTGCTGGAAGTGGCAACGCA
1 AGTGCTT-CTGGAAGTGGCAACGCA
45979 AGTGCTTCTGG
1 AGTGCTTCTGG
45990 CAAGGTGAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
23 2 0.07
24 24 0.86
25 2 0.07
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.29
Consensus pattern (24 bp):
AGTGCTTCTGGAAGTGGCAACGCA
Found at i:46039 original size:95 final size:96
Alignment explanation
Indices: 45931--46114 Score: 217
Period size: 95 Copynumber: 1.9 Consensus size: 96
45921 TGGCGGTGCT
* ** * * * * * *
45931 AGTGCTTCTGGAAGTGGCCATGCTATTGTTGCTGGAAGTGGCAACGCAAGTGCTTCTGGCAA-GG
1 AGTGCTTCCGGAAGTGGCCAAACTAGTATTGCTGGAAGTGACAACACAAGTGCTTATAGCAAGGG
*
45995 TGAAGGTAAAAGTGGTGGAAGTGGTGGTACC
66 TGAAGCTAAAAGTGGTGGAAGTGGTGGTACC
* * *** *
46026 AGTGCTTCCGGAAGTGGTCAAACTAGTATTGGTGGAAGTGACGGTACTAGTGCTTATAGCAAGGG
1 AGTGCTTCCGGAAGTGGCCAAACTAGTATTGCTGGAAGTGACAACACAAGTGCTTATAGCAAGGG
46091 TGAAGCTAAAAGTGGTGGAAGTGG
66 TGAAGCTAAAAGTGGTGGAAGTGG
46115 CAGTGCTAGT
Statistics
Matches: 72, Mismatches: 16, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
95 47 0.65
96 25 0.35
ACGTcount: A:0.26, C:0.13, G:0.36, T:0.25
Consensus pattern (96 bp):
AGTGCTTCCGGAAGTGGCCAAACTAGTATTGCTGGAAGTGACAACACAAGTGCTTATAGCAAGGG
TGAAGCTAAAAGTGGTGGAAGTGGTGGTACC
Found at i:46161 original size:24 final size:24
Alignment explanation
Indices: 46134--46211 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
46124 TTCTTCAGGC
*
46134 AGTGGTCAAGCTAATGTTGGTTGA
1 AGTGGTCAAGCTAATGTTGGTGGA
* * * *
46158 AGTGGTGATGCCAATGCTT-CTGGA
1 AGTGGTCAAGCTAATG-TTGGTGGA
* *
46182 AATGGTCAAGTTAATGTTGGTGGA
1 AGTGGTCAAGCTAATGTTGGTGGA
46206 AGTGGT
1 AGTGGT
46212 GGCGCTAGTG
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
23 2 0.05
24 36 0.90
25 2 0.05
ACGTcount: A:0.24, C:0.09, G:0.35, T:0.32
Consensus pattern (24 bp):
AGTGGTCAAGCTAATGTTGGTGGA
Found at i:46537 original size:40 final size:40
Alignment explanation
Indices: 46482--46558 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 40
46472 TAATGTAGGT
*
46482 GGAAGTGGCAGTGCTAGTGCTATC-GGTAGTGGTCAAGATA
1 GGAAGTGGCAGTGCTAGTGCT-TCTGGGAGTGGTCAAGATA
**
46522 GGAAGTGGTGGTGCTAGTGCTTCTGGGAGTGGTCAAG
1 GGAAGTGGCAGTGCTAGTGCTTCTGGGAGTGGTCAAG
46559 TTAATGTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
39 2 0.06
40 31 0.94
ACGTcount: A:0.21, C:0.12, G:0.42, T:0.26
Consensus pattern (40 bp):
GGAAGTGGCAGTGCTAGTGCTTCTGGGAGTGGTCAAGATA
Found at i:46653 original size:95 final size:96
Alignment explanation
Indices: 46535--46716 Score: 242
Period size: 95 Copynumber: 1.9 Consensus size: 96
46525 AGTGGTGGTG
* * ** **
46535 CTAGTGCTTCTGGGAGTGGTCAAGTTAATGTTTGTGGAAGTGGAGGTGCTAATGCTT-C-GAAAG
1 CTAGTGCTTATGGCAGTGGTCAAGCCAATGTAGGTGGAAGTGGAGGTGCTAATGCTTCCGGAAA-
** *
46598 TGGCTAAACTAATGTCAGTGGAAATGGCTATT
65 TGGAGAAACTAATGTAAGTGGAAATGGCTATT
* *
46630 CTAGTGCTTATGGCAGTGGTCAAGCCAATGTAGGTGGAAGTGGTGGTGCTAGTGCTTCCGGAAAT
1 CTAGTGCTTATGGCAGTGGTCAAGCCAATGTAGGTGGAAGTGGAGGTGCTAATGCTTCCGGAAAT
46695 GGAGAAACTAATGTAAGTGGAA
66 GGAGAAACTAATGTAAGTGGAA
46717 GTGGTGATGC
Statistics
Matches: 74, Mismatches: 11, Indels: 3
0.84 0.12 0.03
Matches are distributed among these distances:
95 49 0.66
96 21 0.28
97 4 0.05
ACGTcount: A:0.26, C:0.12, G:0.33, T:0.29
Consensus pattern (96 bp):
CTAGTGCTTATGGCAGTGGTCAAGCCAATGTAGGTGGAAGTGGAGGTGCTAATGCTTCCGGAAAT
GGAGAAACTAATGTAAGTGGAAATGGCTATT
Found at i:46923 original size:48 final size:48
Alignment explanation
Indices: 46871--46974 Score: 145
Period size: 48 Copynumber: 2.2 Consensus size: 48
46861 GTGGTGGTAT
* * *
46871 TAGTGCTTTTGGCAGTGGTAAAGCTAATGTCGGTGGAAGTGACGAAAC
1 TAGTGCTTTTGACAGTGGTAAAGCTAATATCGGTGAAAGTGACGAAAC
* * **
46919 TAGTGTTTTTGACAGTGGTAAAGCTAATATCGGTGAAAGTGGCGACGC
1 TAGTGCTTTTGACAGTGGTAAAGCTAATATCGGTGAAAGTGACGAAAC
46967 TAGTGCTT
1 TAGTGCTT
46975 CAGGATTCGG
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 48 1.00
ACGTcount: A:0.26, C:0.12, G:0.32, T:0.30
Consensus pattern (48 bp):
TAGTGCTTTTGACAGTGGTAAAGCTAATATCGGTGAAAGTGACGAAAC
Found at i:47694 original size:30 final size:31
Alignment explanation
Indices: 47655--47713 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
47645 TTCATCAATG
*
47655 ACTTTTTAAATG-TTA-AATAATAATCATTAA
1 ACTTCTTAAATGATTACAA-AATAATCATTAA
*
47685 ACTTCTTAAATGATTACAAAATTATCATT
1 ACTTCTTAAATGATTACAAAATAATCATT
47714 GGAATTTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 11 0.44
31 12 0.48
32 2 0.08
ACGTcount: A:0.44, C:0.10, G:0.03, T:0.42
Consensus pattern (31 bp):
ACTTCTTAAATGATTACAAAATAATCATTAA
Found at i:50568 original size:24 final size:24
Alignment explanation
Indices: 50511--50592 Score: 87
Period size: 24 Copynumber: 3.4 Consensus size: 24
50501 TACTGGAAAA
*
50511 GGTGAAGCCAATGTTGGTGGACA-T
1 GGTGAAGCTAATGTTGGTGGA-AGT
* ** *
50535 AGTGGCGCTAATGCTT-TTGGAAGT
1 GGTGAAGCTAATG-TTGGTGGAAGT
50559 GGTGAAGCTAATGTTGGTGGAAGT
1 GGTGAAGCTAATGTTGGTGGAAGT
50583 GGTGAAGCTA
1 GGTGAAGCTA
50593 GTGCCTATGG
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
23 3 0.07
24 41 0.89
25 2 0.04
ACGTcount: A:0.24, C:0.10, G:0.38, T:0.28
Consensus pattern (24 bp):
GGTGAAGCTAATGTTGGTGGAAGT
Found at i:50575 original size:48 final size:48
Alignment explanation
Indices: 50497--52045 Score: 1081
Period size: 48 Copynumber: 32.1 Consensus size: 48
50487 AGAAGAGGTG
* ** * *
50497 GTGCTACTGGAAAAGGTGAAGCCAATGTTGGTGGACA-TAGTGGCGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGA-AGTGGTGGCGCTA
* * **
50545 ATGCTTTTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGAAGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * * * * *
50593 GTGCCTATGGCATTGGTCAAGCCAATGTTGTTGGACA-TGGTGGCGCAA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGA-AGTGGTGGCGCTA
* * *** * * * ** *
50641 GTGCTTTTGGTAGTGACCATGCCAATGTAGGTGGACA-TGGAAGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGA-AGTGGTGGCGCTA
* * * * * * *
50689 GGGCTTTCAGTAA-AGGTGAAACTAAAAG-TGGTGGAAGTGGCGGCGCTA
1 GTGC-TTCTGGAAGTGGTGAAGCT-AATGTTGGTGGAAGTGGTGGCGCTA
* * * * * *
50737 GTGCTTCCGGCAGCGGTCAAGCTAATGTTGGAGGAAGTGGTGGAGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * * **
50785 GTGCTTCTGGGAGTGGTCAAGCTAATGTTGGTGAAAGT-ATAAGTACTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGT-GGCGCTA
* * *
50833 GTGCTTCCGGTAAG-GGTGAAGCTAAAAG-TGGTGGAAGTGGCGGCGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCT-AATGTTGGTGGAAGTGGTGGCGCTA
* * * **
50881 GTGCTTCCGGCAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGAACTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* ** *
50929 GTGCTTCTGGAAGTGGTCAAGCTAATGTTGGTGGAAGTGGAAGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* ** * * * * *
50977 GTGCTTATGGAAAAGGTGAAGCTAAAAG-TGATGGAAATGGTGGCTCCA
1 GTGCTTCTGGAAGTGGTGAAGCT-AATGTTGGTGGAAGTGGTGGCGCTA
* * * * *
51025 ATGCTTCTGGCAGTGGTCAAGCTAATGTTGGTGGAAGTGGCGGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * *
51073 GTGCTTCCGGTAGTGGTCAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
** * *
51121 GTGC-TCTCGGAAAAGGTGAAGCTAATATTGGTGGAAGTGGCGGCGCTA
1 GTGCTTCT-GGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * **
51169 GCGTTTCCGGTAAG-GGTGAAGCTAATGTTGGTGGAAGTGGCAGCGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * *
51217 GTGTTTCCGGCAAG-GGTGAAGCTAATGTTGGTGGAAGTGGCGGCGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* ** * *
51265 GTGCTTCAGGCAAG-GGTGAAGCTAATGTAAGTGGTAGTGGTGGCACTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* *
51313 GTGCTTCTGGAAAG-GGTGAAGCTAATGTAGGTGGAAGTAGG-GGTGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGT-GGTGGCGCTA
* * *
51361 GTGCTTCTGGAAAG-GGAGAAGCTAATATTGGTGGAAGTGGTGGCGTTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * *** *
51409 GTGCTTCTGGAAGTGGTCAAGCTAATTTTGTTGGAAGTGGCACCGCTG
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* ** * * * * *
51457 GTGCTTCAGGAAAAGGTGAAGCTAAAAG-TGATGGAAATGGTGGTGCCA
1 GTGCTTCTGGAAGTGGTGAAGCT-AATGTTGGTGGAAGTGGTGGCGCTA
* * * * *
51505 GTGCTTCTAGTAGTGGTGAAGCTAATATTGGTCGAAGTGGCGGCGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * *
51553 GTTCTTCCGGTAAG-GGTGAAGCTAATGTTGGTAGAGGTGGAGGTGCTAGTGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGT---GGTG---GCGCTA
* * * * *
51607 GTGCTTCCGGCAAG-GGTGAAGTTAATGTTGGTGGAAATGGCGGTGCTA
1 GTGCTTCTGG-AAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * *
51655 GTGCTTCTGGAAATGGTCAAGCTAATGCTGGTGGAAGTGGTGGCGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * ** * * *
51703 GTGCTTCTGGAAGTGGTCATGCTAATGTTGGTCAAAGTGGCGGTGCCA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * * * *
51751 GTGCTTCCGGTAA-AGGTGAAGCTAAAAG-TGGTGGAAGCGGCGGAGCCA
1 GTGCTTCTGG-AAGTGGTGAAGCT-AATGTTGGTGGAAGTGGTGGCGCTA
* ** * * * * *
51799 ATGCTTCTGGAAGTGGCCAAACTAATGTTGCTGGAAGCGGCGGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * * *
51847 GTGCGTCTGGAAGTGGTCATGCTAATGTTGGTGGAGGTGGCGGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* ** * * * *
51895 GTGCTTCTGGAAGTAGCCATGCTCATGCTGGTGGAGGTGGTGGCGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * * * *
51943 GTGCCTCTGGAAGTGGTCATGCTCATGTTGGTGGAGGTGGTAGTGCTA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
* * * * *
51991 GTGCTTCTGGTAGTGGTCATGCTAGTGTTGGTGGACA-TGGTGGCGCCA
1 GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGA-AGTGGTGGCGCTA
*
52039 TTGCTTC
1 GTGCTTC
52046 AGGCTCCGGT
Statistics
Matches: 1192, Mismatches: 273, Indels: 72
0.78 0.18 0.05
Matches are distributed among these distances:
47 35 0.03
48 1083 0.91
49 31 0.03
51 6 0.01
54 37 0.03
ACGTcount: A:0.22, C:0.14, G:0.38, T:0.27
Consensus pattern (48 bp):
GTGCTTCTGGAAGTGGTGAAGCTAATGTTGGTGGAAGTGGTGGCGCTA
Found at i:50904 original size:24 final size:24
Alignment explanation
Indices: 50877--50952 Score: 75
Period size: 24 Copynumber: 3.2 Consensus size: 24
50867 AAGTGGCGGC
* *
50877 GCTAGTGCTTCCGGCAGTGGTCAA
1 GCTAGTGCTTCTGGAAGTGGTCAA
* * *
50901 GCTAATG-TTGGTGGAAGTGGTGGAA
1 GCTAGTGCTT-CTGGAAGTGGT-CAA
50926 -CTAGTGCTTCTGGAAGTGGTCAA
1 GCTAGTGCTTCTGGAAGTGGTCAA
50949 GCTA
1 GCTA
50953 ATGTTGGTGG
Statistics
Matches: 40, Mismatches: 8, Indels: 8
0.71 0.14 0.14
Matches are distributed among these distances:
23 4 0.10
24 32 0.80
25 4 0.10
ACGTcount: A:0.21, C:0.16, G:0.36, T:0.28
Consensus pattern (24 bp):
GCTAGTGCTTCTGGAAGTGGTCAA
Found at i:50963 original size:24 final size:24
Alignment explanation
Indices: 50892--50968 Score: 95
Period size: 24 Copynumber: 3.2 Consensus size: 24
50882 TGCTTCCGGC
50892 AGTGGTCAAGCTAATGTTGGTGGA
1 AGTGGTCAAGCTAATGTTGGTGGA
* * *
50916 AGTGGTGGAA-CTAGTGCTT-CTGGA
1 AGTGGT-CAAGCTAATG-TTGGTGGA
50940 AGTGGTCAAGCTAATGTTGGTGGA
1 AGTGGTCAAGCTAATGTTGGTGGA
50964 AGTGG
1 AGTGG
50969 AAGTGCTAGT
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
23 4 0.09
24 35 0.81
25 4 0.09
ACGTcount: A:0.23, C:0.09, G:0.39, T:0.29
Consensus pattern (24 bp):
AGTGGTCAAGCTAATGTTGGTGGA
Found at i:51051 original size:24 final size:24
Alignment explanation
Indices: 51024--51113 Score: 60
Period size: 24 Copynumber: 3.8 Consensus size: 24
51014 TGGTGGCTCC
*
51024 AATGCTTCTGGCAGTGGTCAAGCT
1 AATGCTTCTGGAAGTGGTCAAGCT
* **
51048 AATG-TTGGTGGAAGTGG-CGGTGCT
1 AATGCTT-CTGGAAGTGGTC-AAGCT
* * *
51072 AGTGCTTCCGGTAGTGGTCAAGCT
1 AATGCTTCTGGAAGTGGTCAAGCT
*
51096 AATG-TTGGTGGAAGTGGT
1 AATGCTT-CTGGAAGTGGT
51114 GGCGCTAGTG
Statistics
Matches: 47, Mismatches: 14, Indels: 10
0.66 0.20 0.14
Matches are distributed among these distances:
23 5 0.11
24 39 0.83
25 3 0.06
ACGTcount: A:0.19, C:0.13, G:0.38, T:0.30
Consensus pattern (24 bp):
AATGCTTCTGGAAGTGGTCAAGCT
Found at i:51120 original size:24 final size:24
Alignment explanation
Indices: 51093--51264 Score: 71
Period size: 24 Copynumber: 7.2 Consensus size: 24
51083 TAGTGGTCAA
51093 GCTAATGTTGGTGGAAGTGGTGGC
1 GCTAATGTTGGTGGAAGTGGTGGC
* * * ** **
51117 GCTAGTGCT-CTCGGAAAAGGTGAA
1 GCTAATGTTGGT-GGAAGTGGTGGC
* *
51141 GCTAATATTGGTGGAAGTGGCGGC
1 GCTAATGTTGGTGGAAGTGGTGGC
** *** **
51165 GCTAGCGTTTCCGGTAAG-GGTGAA
1 GCTAATGTTGGTGG-AAGTGGTGGC
**
51189 GCTAATGTTGGTGGAAGTGGCAGC
1 GCTAATGTTGGTGGAAGTGGTGGC
* *** **
51213 GCTAGTGTTTCCGGCAAG-GGTGAA
1 GCTAATGTTGGTGG-AAGTGGTGGC
*
51237 GCTAATGTTGGTGGAAGTGGCGGC
1 GCTAATGTTGGTGGAAGTGGTGGC
51261 GCTA
1 GCTA
51265 GTGCTTCAGG
Statistics
Matches: 93, Mismatches: 49, Indels: 12
0.60 0.32 0.08
Matches are distributed among these distances:
23 7 0.08
24 79 0.85
25 7 0.08
ACGTcount: A:0.21, C:0.14, G:0.40, T:0.25
Consensus pattern (24 bp):
GCTAATGTTGGTGGAAGTGGTGGC
Found at i:51384 original size:24 final size:23
Alignment explanation
Indices: 51310--51384 Score: 55
Period size: 24 Copynumber: 3.1 Consensus size: 23
51300 AGTGGTGGCA
51310 CTAGTGCTTCTGGAAAGGGTGAAG
1 CTAGTGCTTCTGGAAAGGG-GAAG
* ** *
51334 CTAATG-TAGGTGGAAGTAGGGG-TG
1 CTAGTGCT-TCTGGAA--AGGGGAAG
51358 CTAGTGCTTCTGGAAAGGGAGAAG
1 CTAGTGCTTCTGGAAAGGG-GAAG
51382 CTA
1 CTA
51385 ATATTGGTGG
Statistics
Matches: 37, Mismatches: 8, Indels: 12
0.65 0.14 0.21
Matches are distributed among these distances:
22 4 0.11
23 2 0.05
24 25 0.68
25 2 0.05
26 4 0.11
ACGTcount: A:0.27, C:0.11, G:0.39, T:0.24
Consensus pattern (23 bp):
CTAGTGCTTCTGGAAAGGGGAAG
Found at i:51633 original size:54 final size:54
Alignment explanation
Indices: 51549--51659 Score: 159
Period size: 54 Copynumber: 2.1 Consensus size: 54
51539 AAGTGGCGGC
* * **
51549 GCTAGTTCTTCCGGTAAGGGTGAAGCTAATGTTGGTAGAGGTGGAGGTGCTAGT
1 GCTAGTGCTTCCGGCAAGGGTGAAGCTAATGTTGGTAGAAATGGAGGTGCTAGT
* * *
51603 GCTAGTGCTTCCGGCAAGGGTGAAGTTAATGTTGGTGGAAATGGCGGTGCTAGT
1 GCTAGTGCTTCCGGCAAGGGTGAAGCTAATGTTGGTAGAAATGGAGGTGCTAGT
51657 GCT
1 GCT
51660 TCTGGAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 50 1.00
ACGTcount: A:0.20, C:0.13, G:0.39, T:0.29
Consensus pattern (54 bp):
GCTAGTGCTTCCGGCAAGGGTGAAGCTAATGTTGGTAGAAATGGAGGTGCTAGT
Found at i:51665 original size:24 final size:24
Alignment explanation
Indices: 51638--51714 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
51628 TTAATGTTGG
*
51638 TGGAAATGGCGGTGCTAGTGCTTC
1 TGGAAATGGCGGAGCTAGTGCTTC
* * **
51662 TGGAAATGGTC-AAGCTAATGCTGG
1 TGGAAATGG-CGGAGCTAGTGCTTC
* * *
51686 TGGAAGTGGTGGCGCTAGTGCTTC
1 TGGAAATGGCGGAGCTAGTGCTTC
51710 TGGAA
1 TGGAA
51715 GTGGTCATGC
Statistics
Matches: 39, Mismatches: 12, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
24 38 0.97
25 1 0.03
ACGTcount: A:0.21, C:0.14, G:0.38, T:0.27
Consensus pattern (24 bp):
TGGAAATGGCGGAGCTAGTGCTTC
Found at i:51715 original size:24 final size:24
Alignment explanation
Indices: 51651--51726 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 24
51641 AAATGGCGGT
*
51651 GCTAGTGCTTCTGGAAATGGTCAA
1 GCTAGTGCTTCTGGAAGTGGTCAA
* ** ***
51675 GCTAATGCTGGTGGAAGTGGTGGC
1 GCTAGTGCTTCTGGAAGTGGTCAA
*
51699 GCTAGTGCTTCTGGAAGTGGTCAT
1 GCTAGTGCTTCTGGAAGTGGTCAA
51723 GCTA
1 GCTA
51727 ATGTTGGTCA
Statistics
Matches: 39, Mismatches: 13, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.20, C:0.16, G:0.36, T:0.29
Consensus pattern (24 bp):
GCTAGTGCTTCTGGAAGTGGTCAA
Found at i:51869 original size:24 final size:24
Alignment explanation
Indices: 51842--52017 Score: 103
Period size: 24 Copynumber: 7.3 Consensus size: 24
51832 GAAGCGGCGG
*
51842 TGCTAGTGCGTCTGGAAGTGGTCA
1 TGCTAGTGCTTCTGGAAGTGGTCA
* * * *
51866 TGCTAATG-TTGGTGGAGGTGG-CGG
1 TGCTAGTGCTT-CTGGAAGTGGTC-A
* *
51890 TGCTAGTGCTTCTGGAAGTAGCCA
1 TGCTAGTGCTTCTGGAAGTGGTCA
** * **
51914 TGCTCA-TGCTGGTGGAGGTGGTGG
1 TGCT-AGTGCTTCTGGAAGTGGTCA
* *
51938 CGCTAGTGCCTCTGGAAGTGGTCA
1 TGCTAGTGCTTCTGGAAGTGGTCA
* *
51962 TGCTCA-TG-TTGGTGGAGGTGGT-A
1 TGCT-AGTGCTT-CTGGAAGTGGTCA
*
51985 GTGCTAGTGCTTCTGGTAGTGGTCA
1 -TGCTAGTGCTTCTGGAAGTGGTCA
52010 TGCTAGTG
1 TGCTAGTG
52018 TTGGTGGACA
Statistics
Matches: 109, Mismatches: 31, Indels: 24
0.66 0.19 0.15
Matches are distributed among these distances:
23 6 0.06
24 95 0.87
25 8 0.07
ACGTcount: A:0.14, C:0.15, G:0.40, T:0.31
Consensus pattern (24 bp):
TGCTAGTGCTTCTGGAAGTGGTCA
Done.