Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005790.1 Hibiscus syriacus cultivar Beakdansim tig00013569_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: 74205
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:383 original size:21 final size:18
Alignment explanation
Indices: 340--374 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
330 CAGCCAAGAG
*
340 CATGTATATTCATTAAAT
1 CATGTATTTTCATTAAAT
358 CATGTATTTTCATTAAA
1 CATGTATTTTCATTAAA
375 ACATCATGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
CATGTATTTTCATTAAAT
Found at i:4967 original size:18 final size:19
Alignment explanation
Indices: 4940--4982 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
4930 ATACTGCAAC
*
4940 AAAAAGTAAAAGAA-AGAAG
1 AAAAAGTAAAA-AAGAAAAG
4959 AAAAA-TAAAAAAGAAAAG
1 AAAAAGTAAAAAAGAAAAG
4977 AAAAAG
1 AAAAAG
4983 ACTCCTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 2 0.10
18 14 0.67
19 5 0.24
ACGTcount: A:0.79, C:0.00, G:0.16, T:0.05
Consensus pattern (19 bp):
AAAAAGTAAAAAAGAAAAG
Found at i:4972 original size:13 final size:13
Alignment explanation
Indices: 4940--4981 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
4930 ATACTGCAAC
*
4940 AAAAAGTAAAAGA
1 AAAAAGAAAAAGA
* *
4953 AAGAAGAAAAATA
1 AAAAAGAAAAAGA
4966 AAAAAG-AAAAGA
1 AAAAAGAAAAAGA
4978 AAAA
1 AAAA
4982 GACTCCTACA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:11249 original size:24 final size:23
Alignment explanation
Indices: 11218--11268 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 23
11208 CATATATAGC
*
11218 TATAATGATG-ATAACTTATTCAT
1 TATAATGAAGCATAACTTATT-AT
*
11241 TATATATGAAGCATAAGTTATTAT
1 TATA-ATGAAGCATAACTTATTAT
11265 TATA
1 TATA
11269 CACTATAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 4 0.17
24 11 0.46
25 9 0.38
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (23 bp):
TATAATGAAGCATAACTTATTAT
Found at i:14645 original size:35 final size:36
Alignment explanation
Indices: 14534--14645 Score: 172
Period size: 36 Copynumber: 3.1 Consensus size: 36
14524 ATACAATCTG
* *
14534 TCCATCACCATTATCATGCCTATATCATCACCATCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
14570 TCCATCACCATTATCACGCCTATATCATTACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
14606 TCCATCACCA-TATCACGCCTATATCATCACCAAAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
14641 TCCAT
1 TCCAT
14646 TTTTTCATTT
Statistics
Matches: 69, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 27 0.39
36 42 0.61
ACGTcount: A:0.30, C:0.36, G:0.04, T:0.30
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:14821 original size:20 final size:20
Alignment explanation
Indices: 14796--14835 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
14786 ATCCATTTCA
14796 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
14816 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
14836 CATTTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTCTTTCCTTTTTCCATTT
Found at i:15141 original size:14 final size:15
Alignment explanation
Indices: 15107--15153 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
15097 AATTTGGAGT
15107 GCAAAAGAAAGAAAA
1 GCAAAAGAAAGAAAA
*
15122 GAAAAAG-AAGAAAA
1 GCAAAAGAAAGAAAA
*
15136 TCAAAAGCAAAAGAAAA
1 GCAAAAG--AAAGAAAA
15153 G
1 G
15154 TGAAGCAAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 12 0.48
15 6 0.24
17 7 0.28
ACGTcount: A:0.72, C:0.06, G:0.19, T:0.02
Consensus pattern (15 bp):
GCAAAAGAAAGAAAA
Found at i:19180 original size:35 final size:36
Alignment explanation
Indices: 19069--19180 Score: 181
Period size: 36 Copynumber: 3.1 Consensus size: 36
19059 ATACAATCTG
*
19069 TCCATCACCATTATCACGCCTATATCATCACCATCT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
*
19105 TCCATCACCATTATCACGCCTATATCATCACCATAG
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
* *
19141 TCCATCACCA-TATCACGCCTATATTATCACCAAAT
1 TCCATCACCATTATCACGCCTATATCATCACCATAT
19176 TCCAT
1 TCCAT
19181 TTTTTCATTT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 27 0.38
36 44 0.62
ACGTcount: A:0.30, C:0.37, G:0.04, T:0.29
Consensus pattern (36 bp):
TCCATCACCATTATCACGCCTATATCATCACCATAT
Found at i:19354 original size:20 final size:20
Alignment explanation
Indices: 19331--19370 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
19321 ATCCATTTCA
19331 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
19351 ATTCTTTCCTTTTTCCATTT
1 ATTCTTTCCTTTTTCCATTT
19371 CAATTTCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.25, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTCTTTCCTTTTTCCATTT
Found at i:25606 original size:19 final size:20
Alignment explanation
Indices: 25565--25614 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
25555 GAAACCCCTT
*
25565 TGAAAATACA-TGATTTTTGA
1 TGAAAATACATTGA-TTTTAA
25585 TGAAAATACATTG-TTTTAA
1 TGAAAATACATTGATTTTAA
*
25604 TGAAGATACAT
1 TGAAAATACAT
25615 GCTCTTGGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 15 0.56
20 10 0.37
21 2 0.07
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.38
Consensus pattern (20 bp):
TGAAAATACATTGATTTTAA
Found at i:29533 original size:19 final size:20
Alignment explanation
Indices: 29496--29545 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
29486 AAACCATTTA
29496 GAAAATACATGATTTTTAAT
1 GAAAATACATGATTTTTAAT
29516 GAAAATACATGA-TTTTAAT
1 GAAAATACATGATTTTTAAT
*
29535 GAAGATACATG
1 GAAAATACATG
29546 CTCTTGGCTG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.46, C:0.06, G:0.14, T:0.34
Consensus pattern (20 bp):
GAAAATACATGATTTTTAAT
Found at i:33525 original size:16 final size:17
Alignment explanation
Indices: 33504--33540 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
33494 AACGGTCAAC
33504 GGTCAACGGTC-GGTCG
1 GGTCAACGGTCGGGTCG
33520 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
33537 GGTC
1 GGTC
33541 GGGTCAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.11, C:0.24, G:0.46, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:33531 original size:12 final size:12
Alignment explanation
Indices: 33514--33557 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
33504 GGTCAACGGT
33514 CGGTCGGGTCAA
1 CGGTCGGGTCAA
33526 CGGTCGGGTC--
1 CGGTCGGGTCAA
*
33536 GGGTCGGGTCAA
1 CGGTCGGGTCAA
*
33548 CGATCGGGTC
1 CGGTCGGGTC
33558 GGGTCAGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.33
12 18 0.67
ACGTcount: A:0.11, C:0.25, G:0.45, T:0.18
Consensus pattern (12 bp):
CGGTCGGGTCAA
Found at i:33543 original size:22 final size:22
Alignment explanation
Indices: 33497--33562 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
33487 GAAAGTCAAC
*
33497 GGTCAACGGTCAACGGTC-GGTCG
1 GGTCAACGGTC--GGGTCGGGTCG
33520 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
33542 GGTCAACGATCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
33563 AGACCGATCA
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
21 4 0.10
22 25 0.62
23 11 0.28
ACGTcount: A:0.14, C:0.24, G:0.44, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:33596 original size:9 final size:9
Alignment explanation
Indices: 33559--33628 Score: 59
Period size: 9 Copynumber: 7.3 Consensus size: 9
33549 GATCGGGTCG
*
33559 GGTCAGACC
1 GGTCAAACC
*
33568 GATCAAACC
1 GGTCAAACC
*
33577 GGCTCAGACC
1 GG-TCAAACC
33587 GGTCAAACC
1 GGTCAAACC
33596 GGTCAGAACC
1 GGTCA-AACC
*
33606 GGTTGAAAACC
1 GG-T-CAAACC
*
33617 GGTTAAACC
1 GGTCAAACC
33626 GGT
1 GGT
33629 TTCCAGCAGC
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.54
10 15 0.30
11 7 0.14
12 1 0.02
ACGTcount: A:0.30, C:0.29, G:0.27, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:33606 original size:19 final size:18
Alignment explanation
Indices: 33559--33608 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
33549 GATCGGGTCG
*
33559 GGTCAGACCGATCAAACC
1 GGTCAGACCGGTCAAACC
33577 GGCTCAGACCGGTCAAACC
1 GG-TCAGACCGGTCAAACC
33596 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
33609 TGAAAACCGG
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 6 0.21
19 23 0.79
ACGTcount: A:0.28, C:0.32, G:0.28, T:0.12
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:33627 original size:20 final size:21
Alignment explanation
Indices: 33591--33629 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33581 CAGACCGGTC
33591 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
33612 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
33630 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:40830 original size:16 final size:17
Alignment explanation
Indices: 40809--40846 Score: 69
Period size: 16 Copynumber: 2.3 Consensus size: 17
40799 AACGGTCAAC
40809 GGTCAACGGTC-GGTCG
1 GGTCAACGGTCGGGTCG
40825 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
40842 GGTCA
1 GGTCA
40847 GACCGGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:40835 original size:7 final size:7
Alignment explanation
Indices: 40789--40819 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
40779 GTCAAAGAAA
40789 GTCAACG
1 GTCAACG
40796 GTCAACG
1 GTCAACG
40803 GTCAACG
1 GTCAACG
40810 GTCAACG
1 GTCAACG
40817 GTC
1 GTC
40820 GGTCGGGTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:40860 original size:9 final size:9
Alignment explanation
Indices: 40842--40920 Score: 77
Period size: 10 Copynumber: 8.3 Consensus size: 9
40832 GGTCGGGTCG
*
40842 GGTCAGACC
1 GGTCAAACC
40851 GGTCAAACC
1 GGTCAAACC
* *
40860 GACTCAGACC
1 G-GTCAAACC
40870 GGTCAAACC
1 GGTCAAACC
40879 GGTCAAACC
1 GGTCAAACC
*
40888 GGTTCGAACC
1 GG-TCAAACC
*
40898 GGTTGAAACC
1 GG-TCAAACC
40908 GGTCAGAACC
1 GGTCA-AACC
40918 GGT
1 GGT
40921 TGAAAACCGG
Statistics
Matches: 58, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
9 28 0.48
10 30 0.52
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.14
Consensus pattern (9 bp):
GGTCAAACC
Found at i:40908 original size:20 final size:22
Alignment explanation
Indices: 40883--40932 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
40873 CAAACCGGTC
40883 AAACCGGTTC-GAACCGGTTG-
1 AAACCGGTTCAGAACCGGTTGA
40903 AAACCGG-TCAGAACCGGTTGA
1 AAACCGGTTCAGAACCGGTTGA
40924 AAACCGGTT
1 AAACCGGTT
40933 AAACCGTCAC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 2 0.07
20 17 0.63
21 7 0.26
22 1 0.04
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (22 bp):
AAACCGGTTCAGAACCGGTTGA
Found at i:40937 original size:20 final size:19
Alignment explanation
Indices: 40867--40938 Score: 74
Period size: 20 Copynumber: 3.7 Consensus size: 19
40857 ACCGACTCAG
* *
40867 ACCGGTCAAACCGG-TCAA
1 ACCGGTTAAACCGGTTGAA
*
40885 ACCGGTTCGAACCGGTTGAA
1 ACCGGTT-AAACCGGTTGAA
*
40905 ACCGGTCAGAACCGGTTGAAA
1 ACCGGTTA-AACCGGTTG-AA
40926 ACCGGTTAAACCG
1 ACCGGTTAAACCG
40939 TCACTACTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
18 6 0.14
19 6 0.14
20 23 0.52
21 9 0.20
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (19 bp):
ACCGGTTAAACCGGTTGAA
Found at i:40938 original size:9 final size:9
Alignment explanation
Indices: 40867--40938 Score: 63
Period size: 9 Copynumber: 7.4 Consensus size: 9
40857 ACCGACTCAG
*
40867 ACCGGTCAA
1 ACCGGTTAA
*
40876 ACCGGTCAA
1 ACCGGTTAA
*
40885 ACCGGTTCGA
1 ACCGGTT-AA
40895 ACCGGTTGAA
1 ACCGGTT-AA
*
40905 ACCGGTCAGA
1 ACCGGTTA-A
40915 ACCGGTTGAAA
1 ACCGGTT--AA
40926 ACCGGTTAA
1 ACCGGTTAA
40935 ACCG
1 ACCG
40939 TCACTACTTT
Statistics
Matches: 53, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
9 22 0.42
10 22 0.42
11 8 0.15
12 1 0.02
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:47268 original size:177 final size:177
Alignment explanation
Indices: 46972--47332 Score: 587
Period size: 177 Copynumber: 2.0 Consensus size: 177
46962 ACTGCCATGG
*
46972 TCTACCAAGTAGAATGTGGCTAGAATGCATAGGGACGATGTCACAAAGTACCTTATACTTGTACC
1 TCTACCAAGTAGAATGTGGCTAGAATGCATAGGGACGATGTCACAAAGTACCTTATACTTGCACC
* *
47037 TACCAACTGAAAAAGGTATTAGAACCTGTTTAGTAACGTTTAATTTACCTCCTTTATTGAGCCAT
66 TACCAACTGAAAAAGGAATTAGAACCTGTTTAGTAACGTTTAACTTACCTCCTTTATTGAGCCAT
* *
47102 TGGAGTTTATATTGAGTGGGATGCTTTCATGGTTGCAAACCAAGTTT
131 TGGAGTTTATATGGAGTGGGATGCTTTCATGGGTGCAAACCAAGTTT
* * * * *
47149 TCTACCAAGTAGAATGTGGCTAGCATGCATAGGGATGATGTCATAAAGTACCTTATCCTTGCATC
1 TCTACCAAGTAGAATGTGGCTAGAATGCATAGGGACGATGTCACAAAGTACCTTATACTTGCACC
* * *
47214 TACCAACTGAAAAAGGAATTAGAAGCTGTTTAGTAATGTTTAACTTACCTCCTTTATTGATCCAT
66 TACCAACTGAAAAAGGAATTAGAACCTGTTTAGTAACGTTTAACTTACCTCCTTTATTGAGCCAT
*
47279 TGGAGTTTATATGGAGTGGGATGCTTTGATGGGTGCAAACCAAGTTT
131 TGGAGTTTATATGGAGTGGGATGCTTTCATGGGTGCAAACCAAGTTT
*
47326 TCAACCA
1 TCTACCA
47333 TAAGAGTGTT
Statistics
Matches: 169, Mismatches: 15, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
177 169 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (177 bp):
TCTACCAAGTAGAATGTGGCTAGAATGCATAGGGACGATGTCACAAAGTACCTTATACTTGCACC
TACCAACTGAAAAAGGAATTAGAACCTGTTTAGTAACGTTTAACTTACCTCCTTTATTGAGCCAT
TGGAGTTTATATGGAGTGGGATGCTTTCATGGGTGCAAACCAAGTTT
Found at i:48924 original size:21 final size:21
Alignment explanation
Indices: 48900--48941 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
48890 AAAGTCACAA
48900 GGACTTAAGAAAGAGAATAAT
1 GGACTTAAGAAAGAGAATAAT
48921 GGACTTAAGAAAGAGAATAAT
1 GGACTTAAGAAAGAGAATAAT
48942 CTCACTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.52, C:0.05, G:0.24, T:0.19
Consensus pattern (21 bp):
GGACTTAAGAAAGAGAATAAT
Found at i:50110 original size:18 final size:18
Alignment explanation
Indices: 50087--50135 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
50077 AAAGGAAATC
50087 TTTGATTTTGAAAAACAT
1 TTTGATTTTGAAAAACAT
* *
50105 TTTGATTTTGAAAATCGT
1 TTTGATTTTGAAAAACAT
50123 TTTGATTTTGAAA
1 TTTGATTTTGAAA
50136 CATAAGAGCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.33, C:0.04, G:0.14, T:0.49
Consensus pattern (18 bp):
TTTGATTTTGAAAAACAT
Found at i:54459 original size:14 final size:13
Alignment explanation
Indices: 54427--54469 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
54417 TTGACGAAAC
*
54427 AAAAACAAAATCA
1 AAAAATAAAATCA
*
54440 AAAAATAAAATTA
1 AAAAATAAAATCA
54453 AATAAATAAAAT-A
1 AA-AAATAAAATCA
54466 AAAA
1 AAAA
54470 TATAGCGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
12 2 0.07
13 16 0.59
14 9 0.33
ACGTcount: A:0.79, C:0.05, G:0.00, T:0.16
Consensus pattern (13 bp):
AAAAATAAAATCA
Found at i:64999 original size:35 final size:35
Alignment explanation
Indices: 64915--65030 Score: 126
Period size: 35 Copynumber: 3.3 Consensus size: 35
64905 TGGTTAAGTA
* * * * *
64915 ATGGTGATGATATAAGCATAAAATAGTGTTAGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
* *
64950 ATGGTGATGTTATAGGCATGCAATGGTGATGGAAG
1 ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
* *
64985 ATGGTGATGATATAGGCGTGAAAATGGTTATGCG-AG
1 ATGGTGATGATATAGGCATG-AAATGGTGATG-GAAG
65021 ATGGTGATGA
1 ATGGTGATGA
65031 ACAGATAGTA
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
35 46 0.68
36 21 0.31
37 1 0.01
ACGTcount: A:0.34, C:0.04, G:0.34, T:0.28
Consensus pattern (35 bp):
ATGGTGATGATATAGGCATGAAATGGTGATGGAAG
Done.