Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001344.1 Hibiscus syriacus cultivar Beakdansim tig00002622_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: 107180
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4264 original size:2 final size:2
Alignment explanation
Indices: 4257--4287 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
4247 TATTTTTCTG
4257 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
4288 TTGTTTTAGA
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:4797 original size:2 final size:2
Alignment explanation
Indices: 4786--4849 Score: 121
Period size: 2 Copynumber: 32.5 Consensus size: 2
4776 TTATTAGTCT
4786 TA TA TA -A 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 TA TA TA TA
4827 TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA T
4850 TATTTCTACT
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 60 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9254 original size:2 final size:2
Alignment explanation
Indices: 9249--9281 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
9239 TATTATTAGT
9249 TA 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 TA T
9282 GTGTGTGTGT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10087 original size:15 final size:18
Alignment explanation
Indices: 10042--10088 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
10032 ATTATATTTT
10042 ATATTAATATTTATGTAA
1 ATATTAATATTTATGTAA
* *
10060 ATATTATTTTTTAT-TAA
1 ATATTAATATTTATGTAA
10077 A-A-TAATATTTAT
1 ATATTAATATTTAT
10089 AATTATTATT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
15 8 0.32
16 1 0.04
17 4 0.16
18 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (18 bp):
ATATTAATATTTATGTAA
Found at i:10109 original size:17 final size:18
Alignment explanation
Indices: 10084--10118 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
10074 TAAAATAATA
*
10084 TTTATAATTATT-ATTTT
1 TTTAGAATTATTAATTTT
10101 TTTAGAATTATTAATTTT
1 TTTAGAATTATTAATTTT
10119 GTGTGCTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (18 bp):
TTTAGAATTATTAATTTT
Found at i:11854 original size:21 final size:21
Alignment explanation
Indices: 11824--11871 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
11814 GCAGGGGTAC
* * *
11824 ATGCCCAGCCCTCCACTTCGT
1 ATGCCAAGCCCACCACTTCAT
*
11845 ATGCCAAGCCCACCAGTTCAT
1 ATGCCAAGCCCACCACTTCAT
11866 ATGCCA
1 ATGCCA
11872 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.21
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:11901 original size:21 final size:21
Alignment explanation
Indices: 11875--11989 Score: 164
Period size: 21 Copynumber: 5.5 Consensus size: 21
11865 TATGCCATCT
*
11875 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
11896 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
*
11917 CCGCCA-GGTTACATTCCGAGC
1 CCG-CAGGGTTACATTCCTAGC
11938 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
11959 CCGCCA-GGTTACATGT-CTAGC
1 CCG-CAGGGTTACAT-TCCTAGC
11980 CCGCAGGGTT
1 CCGCAGGGTT
11990 TTATACCATA
Statistics
Matches: 86, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.05
21 77 0.90
22 5 0.06
ACGTcount: A:0.18, C:0.34, G:0.26, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:11928 original size:42 final size:42
Alignment explanation
Indices: 11881--11989 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
11871 ATCTCCGCAG
11881 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
11923 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
1 GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
*
11965 GGTTACATGT-CTAGCCCGCAGGGTT
1 GGTTACAT-TCCGAGCCCGCAGGGTT
11990 TTATACCATA
Statistics
Matches: 65, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
42 64 0.98
43 1 0.02
ACGTcount: A:0.18, C:0.33, G:0.26, T:0.23
Consensus pattern (42 bp):
GGTTACATTCCGAGCCCGCAGGGTTACATTCCTAGCCCGCCA
Found at i:12563 original size:34 final size:34
Alignment explanation
Indices: 12513--12610 Score: 124
Period size: 34 Copynumber: 2.9 Consensus size: 34
12503 AAATGTTTTT
*
12513 AAAATACAAATTATATTATTCAAAATTTAAAATA
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* ** * *
12547 AAAATAAAAATAATATTATTTGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCAAAATTTAAAATA
* *
12581 AAAATATAAATTATAGTATTCAAAATTTAA
1 AAAATAAAAATTATATTATTCAAAATTTAA
12611 CATTAAATTT
Statistics
Matches: 53, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 53 1.00
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCAAAATTTAAAATA
Found at i:13286 original size:128 final size:127
Alignment explanation
Indices: 13015--13338 Score: 576
Period size: 128 Copynumber: 2.5 Consensus size: 127
13005 ACAATCCATC
* *
13015 TAGTGTCCCCGAGGGACATGAGTGACATAATAAGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
* * * *
13080 GGAATGGCGCCCTCGGGAACGCGCCTTCAAGTCCCCTGAGAAATAATAGATACTAATATGAA
66 TGAATGGCCCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGATACTAATATGAA
*
13142 TAATATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
13207 TGAATGCGCCCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGATACTAATATGAA
66 TGAATG-GCCCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGATACTAATATGAA
13270 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
1 TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
13335 TGAA
66 TGAA
13339 GGATATGTTA
Statistics
Matches: 188, Mismatches: 8, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
127 67 0.36
128 121 0.64
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (127 bp):
TAGTATCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGACAAAATAAT
TGAATGGCCCCCCCGGGAACGCGCCTTCAAGTCCCATGAGAAATAATAGATACTAATATGAA
Found at i:15759 original size:6 final size:6
Alignment explanation
Indices: 15748--15780 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
15738 AGAAAACCCG
15748 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAA
15781 AACCCACCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:21548 original size:49 final size:49
Alignment explanation
Indices: 21473--21567 Score: 154
Period size: 49 Copynumber: 1.9 Consensus size: 49
21463 AAGTGACGGA
*
21473 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAGGCAACCCCTCATC
1 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATC
* * *
21522 CAGGGGTGGACCTCCATGGTGTCCGGGGTATCCCAAGCAACCCCTC
1 CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTC
21568 CACAAGTGTC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 42 1.00
ACGTcount: A:0.18, C:0.37, G:0.31, T:0.15
Consensus pattern (49 bp):
CAGGGGCGGACCTCCATGGAGCCCGGGGTATCCCAAGCAACCCCTCATC
Found at i:26280 original size:6 final size:6
Alignment explanation
Indices: 26264--26312 Score: 91
Period size: 6 Copynumber: 8.3 Consensus size: 6
26254 ATAGATAAAT
26264 AAATT- AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
1 AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA AAATTA
26311 AA
1 AA
26313 GGGTAGATAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.12
6 38 0.88
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (6 bp):
AAATTA
Found at i:28020 original size:17 final size:19
Alignment explanation
Indices: 27994--28034 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
27984 GCATATAAAA
*
27994 TTATTGTTTTAAT-AAGTT
1 TTATTGTTTTAATGAAATT
28012 TTATT-TTTTAATGAAATT
1 TTATTGTTTTAATGAAATT
28030 TTATT
1 TTATT
28035 AAAATAACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.63
Consensus pattern (19 bp):
TTATTGTTTTAATGAAATT
Found at i:31842 original size:2 final size:2
Alignment explanation
Indices: 31835--31869 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
31825 CTAGATTTGA
*
31835 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC CC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
31870 AGCTGGAATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:36190 original size:2 final size:2
Alignment explanation
Indices: 36183--36229 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
36173 ATCGCAATCT
* * *
36183 TA TA TA TA TA CA TA TA TA TA TA TA TA TT TA TA TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
36225 TA TA T
1 TA TA T
36230 TATTGTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:37796 original size:23 final size:23
Alignment explanation
Indices: 37768--37821 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
37758 GACCCGAAGT
*
37768 AATAAAAAAAATTATTTTTATTC
1 AATAAAAAAAATTATTTTTATTA
37791 AATAAAAAAAATTATTTTTATTA
1 AATAAAAAAAATTATTTTTATTA
37814 AATAAAAA
1 AATAAAAA
37822 CAGTGACTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (23 bp):
AATAAAAAAAATTATTTTTATTA
Found at i:38711 original size:12 final size:13
Alignment explanation
Indices: 38675--38718 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
38665 GCCCCGATTA
38675 CCCGATTACCCGC
1 CCCGATTACCCGC
38688 CCCGATTACCCGC
1 CCCGATTACCCGC
*
38701 CCCGA-TACCCGA
1 CCCGATTACCCGC
38713 CCCGAT
1 CCCGAT
38719 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:38745 original size:2 final size:2
Alignment explanation
Indices: 38738--38835 Score: 78
Period size: 2 Copynumber: 51.0 Consensus size: 2
38728 AATAATTATT
* * * * *
38738 TA TA TA TA TA TA TA TA T- TA -A TA AA TT TA -A TT TA AA TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * *
38777 AA TA TA TA TT TA TA TA TT TA -A TT TA AA 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 TA TA TA TA
38818 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
38836 CTCGGCCCGA
Statistics
Matches: 74, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
1 4 0.05
2 70 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:38822 original size:31 final size:30
Alignment explanation
Indices: 38735--38824 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 30
38725 TAAAATAATT
* *
38735 ATTTATATATATATATATATTAATAAATTTA
1 ATTTAAATATATATATATATT-ATATATTTA
* *
38766 ATTTAAATAAAAATATATATTTATATATTTA
1 ATTTAAATATATATATATA-TTATATATTTA
38797 ATTTAAATATATATATATATATATATAT
1 ATTTAAATATATATATATAT-TATATAT
38825 ATATATATAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
30 1 0.02
31 48 0.94
32 2 0.04
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (30 bp):
ATTTAAATATATATATATATTATATATTTA
Found at i:38868 original size:12 final size:12
Alignment explanation
Indices: 38853--38887 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
38843 CGATTCTAGG
38853 CCCAATACCCGA
1 CCCAATACCCGA
*
38865 CCCAATACCCGG
1 CCCAATACCCGA
38877 CCCAATACCCG
1 CCCAATACCCG
38888 TTTAAATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.51, G:0.11, T:0.09
Consensus pattern (12 bp):
CCCAATACCCGA
Found at i:54614 original size:2 final size:2
Alignment explanation
Indices: 54607--54631 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
54597 TTATGAAATG
54607 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 T
54632 GTGTGAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:65912 original size:19 final size:19
Alignment explanation
Indices: 65886--65974 Score: 60
Period size: 18 Copynumber: 4.8 Consensus size: 19
65876 TGAAAATAAT
65886 TAAT-TTATAATAATTTAA
1 TAATATTATAATAATTTAA
* *
65904 TAATATTATTATAA-TTAT
1 TAATATTATAATAATTTAA
* * **
65922 TAAAATAATAATAA-AAAA
1 TAATATTATAATAATTTAA
* *
65940 TCATTTTA-ATATAATTTAA
1 TAATATTATA-ATAATTTAA
*
65959 TAATATTATTATAATT
1 TAATATTATAATAATT
65975 ATTAAAATAA
Statistics
Matches: 50, Mismatches: 17, Indels: 7
0.68 0.23 0.09
Matches are distributed among these distances:
17 1 0.02
18 27 0.54
19 22 0.44
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (19 bp):
TAATATTATAATAATTTAA
Found at i:66852 original size:21 final size:22
Alignment explanation
Indices: 66814--66855 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
66804 ATGCACAAAG
66814 TCGGATAATAAATCGATCCGGA
1 TCGGATAATAAATCGATCCGGA
*
66836 TCGGATAA-AAATTGATCCGG
1 TCGGATAATAAATCGATCCGG
66856 TTTTTTCACC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.58
22 8 0.42
ACGTcount: A:0.36, C:0.17, G:0.24, T:0.24
Consensus pattern (22 bp):
TCGGATAATAAATCGATCCGGA
Found at i:70501 original size:24 final size:24
Alignment explanation
Indices: 70452--70501 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
70442 CCTCTCTCAA
* *
70452 CAAGAACAATCTGTCTCTGCTGAG
1 CAAGAACAATCTGTCTCTACTAAG
* *
70476 CAAGATCATTCTGTCTCTACTAAG
1 CAAGAACAATCTGTCTCTACTAAG
70500 CA
1 CA
70502 TGTTCAACGC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.28
Consensus pattern (24 bp):
CAAGAACAATCTGTCTCTACTAAG
Found at i:78796 original size:15 final size:15
Alignment explanation
Indices: 78778--78833 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
78768 TAACCGGTTT
78778 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
78793 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
78810 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
78825 CGATTTTAA
1 CGGTTTTAA
78834 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:78806 original size:17 final size:17
Alignment explanation
Indices: 78781--78831 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
78771 CCGGTTTCGG
78781 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
78798 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
78813 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
78830 TT
1 TT
78832 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Found at i:79252 original size:13 final size:13
Alignment explanation
Indices: 79231--79285 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
79221 AAGTTCGATA
*
79231 AATTCAAATACTT
1 AATTGAAATACTT
79244 AATTGAAATACTT
1 AATTGAAATACTT
* *
79257 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
79271 AATTGAAATACTT
1 AATTGAAATACTT
79284 AA
1 AA
79286 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:79367 original size:32 final size:33
Alignment explanation
Indices: 79271--79369 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
79261 AACTCAACAT
* * *
79271 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
79304 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
79337 AATTCAAATACTTAAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAAACTTCCAAGTTCGATA
79369 A
1 A
79370 TTGAAACAAA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 12 0.19
33 51 0.81
ACGTcount: A:0.45, C:0.15, G:0.07, T:0.32
Consensus pattern (33 bp):
AATTCAAATACTTAAAAACTTCCAAGTTCGATA
Found at i:79388 original size:21 final size:21
Alignment explanation
Indices: 79364--79403 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
79354 ACTTCAAGTT
79364 CGATAATTGAAACAAAGTTTA
1 CGATAATTGAAACAAAGTTTA
*
79385 CGATAATTGAAATAAAGTT
1 CGATAATTGAAACAAAGTT
79404 ATAAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.15, T:0.30
Consensus pattern (21 bp):
CGATAATTGAAACAAAGTTTA
Found at i:87993 original size:25 final size:26
Alignment explanation
Indices: 87935--87993 Score: 61
Period size: 25 Copynumber: 2.3 Consensus size: 26
87925 CATGCAAATA
** *
87935 AATAATTTTTAAAAAAGGATTATTGT
1 AATAATTTTTAAAAAAAAATCATTGT
87961 --TAATTTTTTAAAAAAAAATCATT-T
1 AATAA-TTTTTAAAAAAAAATCATTGT
87985 AATAATTTT
1 AATAATTTT
87994 GTTTATATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 7
0.73 0.08 0.19
Matches are distributed among these distances:
24 4 0.15
25 20 0.74
26 3 0.11
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (26 bp):
AATAATTTTTAAAAAAAAATCATTGT
Found at i:89452 original size:42 final size:42
Alignment explanation
Indices: 89338--89452 Score: 149
Period size: 43 Copynumber: 2.7 Consensus size: 42
89328 CGAATTTTCG
* * *
89338 TGTTTGTTTCACGTAATTAGTTTTTCGAAAAATGTTTTCCCG
1 TGTTTGTTTCACGTAATTAGTTTTTCGGAAAATATTTTCCCA
* * *
89380 TATTTGTTTTCACGTAATTCGTTTTTCGGAAAATATTTTCTCA
1 TGTTTG-TTTCACGTAATTAGTTTTTCGGAAAATATTTTCCCA
* *
89423 TGTTTGTTTCACGTAATTGGTTTTCCGGAA
1 TGTTTGTTTCACGTAATTAGTTTTTCGGAA
89453 TGTAATTCAT
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 27 0.43
43 36 0.57
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.49
Consensus pattern (42 bp):
TGTTTGTTTCACGTAATTAGTTTTTCGGAAAATATTTTCCCA
Found at i:89759 original size:52 final size:52
Alignment explanation
Indices: 89652--89760 Score: 118
Period size: 52 Copynumber: 2.1 Consensus size: 52
89642 TTATTAATAT
* * *
89652 TTATAATAATATAATATTATATTTTAAATATTATATAAAATAATCAATTATA
1 TTATAATAATATAATATTATATTTTAAATATTAAATAAAATAATCAATAAAA
*
89704 TTATAATAATATAAGATATTATATTTT-TAT-TTAAATAATATATAAT-AA-AAAA
1 TTATAATAATAT-A-ATATTATATTTTAAATATTAAATAA-A-ATAATCAATAAAA
89756 TTATA
1 TTATA
89761 TATTTAATAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
52 26 0.53
53 6 0.12
54 17 0.35
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (52 bp):
TTATAATAATATAATATTATATTTTAAATATTAAATAAAATAATCAATAAAA
Found at i:89768 original size:26 final size:28
Alignment explanation
Indices: 89731--89795 Score: 69
Period size: 28 Copynumber: 2.2 Consensus size: 28
89721 ATTATATTTT
*
89731 TATTTAAATAAT-ATATAATAAAAAATTATA
1 TATTT-AATAATGA-ATAAT-ATAAATTATA
* *
89761 TATTTAATAATGAATAATATTATTTATA
1 TATTTAATAATGAATAATATAAATTATA
89789 TATTTAA
1 TATTTAA
89796 ACAATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 14 0.45
29 11 0.35
30 6 0.19
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TATTTAATAATGAATAATATAAATTATA
Found at i:89780 original size:19 final size:19
Alignment explanation
Indices: 89736--89786 Score: 52
Period size: 19 Copynumber: 2.7 Consensus size: 19
89726 ATTTTTATTT
89736 AAATAATATA--TAATAAA
1 AAATAATATATTTAATAAA
* *
89753 AAATTATATATTTAATAAT
1 AAATAATATATTTAATAAA
*
89772 GAATAATATTATTTA
1 AAATAATA-TATTTA
89787 TATATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 9 0.33
19 12 0.44
20 6 0.22
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (19 bp):
AAATAATATATTTAATAAA
Found at i:89831 original size:23 final size:23
Alignment explanation
Indices: 89805--89849 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
89795 AACAATATTT
89805 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
89828 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
89850 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:90183 original size:14 final size:14
Alignment explanation
Indices: 90149--90183 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
90139 AAATATAATT
*
90149 CATTTTACGGAAAA
1 CATTTTCCGGAAAA
90163 CATTTTCCGGAAAA
1 CATTTTCCGGAAAA
*
90177 CGTTTTC
1 CATTTTC
90184 AATAAATATA
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:0.31, C:0.20, G:0.14, T:0.34
Consensus pattern (14 bp):
CATTTTCCGGAAAA
Found at i:91670 original size:24 final size:25
Alignment explanation
Indices: 91643--91697 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
91633 GTATTCGAAA
91643 TTTGATCTTGG-TCAATACCCGGAC
1 TTTGATCTTGGTTCAATACCCGGAC
* * *
91667 TTTGATCTTGGTTCAATGCTCGGAT
1 TTTGATCTTGGTTCAATACCCGGAC
91692 TTTGAT
1 TTTGAT
91698 GATGTTTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 11 0.41
25 16 0.59
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (25 bp):
TTTGATCTTGGTTCAATACCCGGAC
Found at i:94230 original size:20 final size:21
Alignment explanation
Indices: 94174--94231 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
94164 CCCAAAGCTT
* *
94174 ATTTCGCGTTACGAATTTGAC
1 ATTTCGCGTTGCGAATTTAAC
*
94195 ATTT-GCGTTGCAAATTTAAC
1 ATTTCGCGTTGCGAATTTAAC
*
94215 -TTTCGCGTCGCGAATTT
1 ATTTCGCGTTGCGAATTT
94232 GTACCTTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
19 3 0.10
20 24 0.77
21 4 0.13
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (21 bp):
ATTTCGCGTTGCGAATTTAAC
Found at i:94369 original size:66 final size:65
Alignment explanation
Indices: 94286--94461 Score: 232
Period size: 66 Copynumber: 2.6 Consensus size: 65
94276 AATTTAAAAC
*
94286 AACAAATTAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTACAT-ATCAAAT
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTT-CATCATC-AAT
94350 TA
64 TA
* *
94352 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTCCTCATCAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTCATCATCAATTA
94416 AACAAATCAACTTTCAATGTA-AAATTCAATTAAACAAACAAAAAAA
1 AACAAATCAAC-TT---T-TACAAA-TCAATTAAACAAACAAAAAAA
94462 GTGTACCCCA
Statistics
Matches: 98, Mismatches: 4, Indels: 12
0.86 0.04 0.11
Matches are distributed among these distances:
64 18 0.18
65 23 0.23
66 32 0.33
68 4 0.04
69 15 0.15
70 6 0.06
ACGTcount: A:0.54, C:0.16, G:0.01, T:0.29
Consensus pattern (65 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAACAAAAAAATAATTCTTATTTCATCATCAATTA
Found at i:95957 original size:60 final size:60
Alignment explanation
Indices: 95887--96142 Score: 295
Period size: 60 Copynumber: 4.2 Consensus size: 60
95877 TAAACGCGCT
* * *
95887 TTGCGAATTTGACTTTCGCATTGCAAATTTGACTATC-GCGTTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACT-TCAGTGTTGCGAATTTGACTTTTGTG
** * *
95947 TTGCGAATTTGAAATTCTGTGTTGCGAATTTGACTT-ATGTGTTGCGAACTTGACTTTTGTG
1 TTGCGAATTTGACTTTC-GCGTTGCGAATTTGACTTCA-GTGTTGCGAATTTGACTTTTGTG
* * * **
96008 TTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGACTTCAGTGTTGTGAATTTGACTATTGCA
1 TTGCGAATTTGAC--TTTCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTTTGTG
* * *
96068 TTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGTGTTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTTTGTG
*
96128 TAGCGAATTTGACTT
1 TTGCGAATTTGACTT
96143 ATGTGTTGCG
Statistics
Matches: 164, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
59 1 0.01
60 112 0.68
61 49 0.30
62 2 0.01
ACGTcount: A:0.20, C:0.14, G:0.23, T:0.42
Consensus pattern (60 bp):
TTGCGAATTTGACTTTCGCGTTGCGAATTTGACTTCAGTGTTGCGAATTTGACTTTTGTG
Found at i:96127 original size:20 final size:20
Alignment explanation
Indices: 95887--96153 Score: 253
Period size: 20 Copynumber: 13.3 Consensus size: 20
95877 TAAACGCGCT
**
95887 TTGCGAATTTGACTT-TCGCA
1 TTGCGAATTTGACTTAT-GTG
* *
95907 TTGCAAATTTGAC-TATCGCG
1 TTGCGAATTTGACTTAT-GTG
*
95927 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
* *
95947 TTGCGAATTTGAAATTCTGTG
1 TTGCGAATTTG-ACTTATGTG
95968 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
* *
95988 TTGCGAACTTGACTTTTGTG
1 TTGCGAATTTGACTTATGTG
** *
96008 TTGCG-ATTT-ACAGATTCGCG
1 TTGCGAATTTGACTTA-T-GTG
96028 TTGCGAATTTGACTTCA-GTG
1 TTGCGAATTTGACTT-ATGTG
*
96048 TTGTGAATTTGAC-TAT-TG
1 TTGCGAATTTGACTTATGTG
*
96066 CATTGCGAATTTGAC-TATCGCG
1 --TTGCGAATTTGACTTAT-GTG
*
96088 TTGCGAATTTGACTTCTGTG
1 TTGCGAATTTGACTTATGTG
96108 TTGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
*
96128 TAGCGAATTTGACTTATGTG
1 TTGCGAATTTGACTTATGTG
96148 TTGCGA
1 TTGCGA
96154 TTTACATATT
Statistics
Matches: 206, Mismatches: 27, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
18 5 0.02
19 6 0.03
20 165 0.80
21 26 0.13
22 3 0.01
23 1 0.00
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTTATGTG
Found at i:96616 original size:20 final size:19
Alignment explanation
Indices: 96589--96627 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
96579 AAATTGGTTC
96589 ATGAAATATAAAATTATTT
1 ATGAAATATAAAATTATTT
* *
96608 ATGATAATATTATATTATTT
1 ATGA-AATATAAAATTATTT
96628 TATCTGGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (19 bp):
ATGAAATATAAAATTATTT
Found at i:96827 original size:2 final size:2
Alignment explanation
Indices: 96820--96849 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
96810 AACTTATAGA
96820 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
96850 TCTCTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:99140 original size:20 final size:21
Alignment explanation
Indices: 99115--99166 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
99105 TTTTCCCAAT
*
99115 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
99135 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
99156 TCGCAATGCGA
1 TCGCAATGCGA
99167 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:99180 original size:20 final size:20
Alignment explanation
Indices: 99155--99208 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
99145 AATTGGGAAA
99155 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
99175 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
99195 ATCGCAATGCGATA
1 ATCGCAATGCGATA
99209 ATACAAAATC
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:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:99868 original size:19 final size:19
Alignment explanation
Indices: 99821--99862 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
99811 ACGAGAGAAT
*
99821 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
99840 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
99859 CGCA
1 CGCA
99863 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:99880 original size:19 final size:19
Alignment explanation
Indices: 99858--99928 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
99848 GAAACAAAAA
99858 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
99877 TCGCGTTGCGATTTTTATT
1 TCGCATTGCGATTTTCATT
99896 TCGCAGTTGCGATTTTCATT
1 TCGCA-TTGCGATTTTCATT
*
99916 TCGCGTTGCGATT
1 TCGCATTGCGATT
99929 GTCTGGTCGC
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 29 0.63
20 17 0.37
ACGTcount: A:0.13, C:0.20, G:0.21, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:99904 original size:20 final size:19
Alignment explanation
Indices: 99858--100023 Score: 136
Period size: 20 Copynumber: 9.1 Consensus size: 19
99848 GAAACAAAAA
*
99858 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
99877 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
99896 TCGCAGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
99916 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
99932 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
99949 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
99963 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
99982 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
100002 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
100022 TC
1 TC
100024 AACCAAAAGA
Statistics
Matches: 119, Mismatches: 15, Indels: 26
0.74 0.09 0.16
Matches are distributed among these distances:
14 20 0.17
15 1 0.01
16 3 0.03
17 3 0.03
18 1 0.01
19 41 0.34
20 49 0.41
21 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:99948 original size:33 final size:33
Alignment explanation
Indices: 99911--99998 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
99901 GTTGCGATTT
* *
99911 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
99944 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
99977 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
99999 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:102094 original size:41 final size:41
Alignment explanation
Indices: 102017--102134 Score: 105
Period size: 42 Copynumber: 2.8 Consensus size: 41
102007 GACTCGCCTG
* * * * * *
102017 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCACTA
*
102059 TCATTCCTTG-AGAGTCCTCTCCCA-CGTTCAAGAGGCCACTG
1 TCA-TCCTTGAAGAGTCC-CTCCCACCGTTCAAGAGGCCACTA
* *
102100 TCATCGTTGAAGAGGTCCCTCCCACCATTCAAGAG
1 TCATCCTTGAAGA-GTCCCTCCCACCGTTCAAGAG
102135 CCCGATTCAC
Statistics
Matches: 63, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
40 5 0.08
41 26 0.41
42 28 0.44
43 4 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.25
Consensus pattern (41 bp):
TCATCCTTGAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:103495 original size:14 final size:14
Alignment explanation
Indices: 103476--103511 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
103466 ATTGTTTAAT
103476 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
103490 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
103504 TGATTTGT
1 TGATTTGT
103512 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:103694 original size:19 final size:20
Alignment explanation
Indices: 103650--103689 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
103640 GCAACGAGAG
103650 AATCGCAACGCGAAAATAAA
1 AATCGCAACGCGAAAATAAA
*
103670 AATCGCAACGCGAAATTAAA
1 AATCGCAACGCGAAAATAAA
103690 TTCGCGTTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.53, C:0.20, G:0.15, T:0.12
Consensus pattern (20 bp):
AATCGCAACGCGAAAATAAA
Found at i:103712 original size:19 final size:19
Alignment explanation
Indices: 103690--103840 Score: 62
Period size: 19 Copynumber: 8.7 Consensus size: 19
103680 CGAAATTAAA
103690 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
103709 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
103724 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
103742 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
103756 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
103775 TTTGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
103790 -TCTCGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
103808 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
103827 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
103841 AGACATTAGA
Statistics
Matches: 92, Mismatches: 24, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 26 0.28
16 6 0.07
17 6 0.07
19 44 0.48
20 10 0.11
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:103736 original size:33 final size:32
Alignment explanation
Indices: 103694--103820 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
103684 ATTAAATTCG
103694 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
103727 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
*
103760 CGTTGCGATTTTCATTTTGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
103793 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
103821 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:103783 original size:66 final size:66
Alignment explanation
Indices: 103687--103819 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
103677 ACGCGAAATT
*
103687 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
103752 G
66 G
* * *
103753 AAATTAGCGTTGCGATTTTCATTTTGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
103818 G
66 G
103819 A
1 A
103820 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.21, G:0.20, T:0.43
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:106343 original size:23 final size:24
Alignment explanation
Indices: 106293--106345 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
106283 CTGAAACATC
* *
106293 ATCAAAATCCGTGTATTGGCCAAT
1 ATCAAAATCCGGGTATTGGCCAAG
*
106317 ATCAAAGTCCGGGTA-TGGCCAAG
1 ATCAAAATCCGGGTATTGGCCAAG
106340 ATCAAA
1 ATCAAA
106346 TTTGAATACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 13 0.50
24 13 0.50
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGGCCAAG
Done.