Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002916.1 Hibiscus syriacus cultivar Beakdansim tig00006029_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: 58262
ACGTcount: A:0.35, C:0.19, G:0.16, T:0.31
Found at i:4740 original size:2 final size:2
Alignment explanation
Indices: 4733--4760 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4723 AATCACTCCA
4733 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
4761 GGTATTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9644 original size:16 final size:17
Alignment explanation
Indices: 9612--9647 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
9602 CCAATGACTA
9612 GAAATGATTGAAAGAAT
1 GAAATGATTGAAAGAAT
9629 GAAATGATTG-AAGAAT
1 GAAATGATTGAAAGAAT
9645 GAA
1 GAA
9648 TTCTTGAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.22
Consensus pattern (17 bp):
GAAATGATTGAAAGAAT
Found at i:12321 original size:96 final size:97
Alignment explanation
Indices: 12155--12352 Score: 335
Period size: 96 Copynumber: 2.0 Consensus size: 97
12145 TTAAGAGTAG
* *
12155 GTTATACACTTCTTACAAAAAAAAAGTAGTCAATAAACTACTAGTTTTTAACAGCAAAAAACTAT
1 GTTATACAATTCTTAC-AAAAAAAAGGAGTCAATAAACTACTAGTTTTTAACAGCAAAAAACTAT
12220 GGTGACTAACAGTCGTAGCAGTAATCTTTTTAT
65 GGTGACTAACAGTCGTAGCAGTAATCTTTTTAT
* **
12253 GTTATACAATTCTTAC-AAAAAAAGGAGTCGATAAACTACTAGTTTTTAATGGCAAAAAACTATG
1 GTTATACAATTCTTACAAAAAAAAGGAGTCAATAAACTACTAGTTTTTAACAGCAAAAAACTATG
12317 GTGACTAACAGTCGTAGCAGTAATCTTTTTAT
66 GTGACTAACAGTCGTAGCAGTAATCTTTTTAT
12349 GTTA
1 GTTA
12353 AAAGGACAAT
Statistics
Matches: 95, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 80 0.84
98 15 0.16
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (97 bp):
GTTATACAATTCTTACAAAAAAAAGGAGTCAATAAACTACTAGTTTTTAACAGCAAAAAACTATG
GTGACTAACAGTCGTAGCAGTAATCTTTTTAT
Found at i:18252 original size:21 final size:21
Alignment explanation
Indices: 18227--18266 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
18217 AAAGGCATTG
18227 GAAAATATATCATAAAATATA
1 GAAAATATATCATAAAATATA
* *
18248 GAAAATGTGTCATAAAATA
1 GAAAATATATCATAAAATA
18267 GAATTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.10, T:0.28
Consensus pattern (21 bp):
GAAAATATATCATAAAATATA
Found at i:19928 original size:2 final size:2
Alignment explanation
Indices: 19921--19951 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
19911 CATATTATTA
19921 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 A
19952 ATTTTGATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:22827 original size:31 final size:31
Alignment explanation
Indices: 22787--22852 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
22777 TTCAATACAA
* *
22787 TCCCAAAACATTTAGTCGGTTTGCAATATGG
1 TCCCAAAACAGTTAGTCCGTTTGCAATATGG
*
22818 TCCCTAAACAGTTAGTCCGTTTGCAATATGG
1 TCCCAAAACAGTTAGTCCGTTTGCAATATGG
22849 TCCC
1 TCCC
22853 CGACGTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.32
Consensus pattern (31 bp):
TCCCAAAACAGTTAGTCCGTTTGCAATATGG
Found at i:24854 original size:31 final size:31
Alignment explanation
Indices: 24812--24872 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
24802 TACAAAATAA
24812 TCCCCCAACATTTAGTCCGTTTGCAATATGG
1 TCCCCCAACATTTAGTCCGTTTGCAATATGG
* * *
24843 TCCCTCAACATTTAGTCTGTTTTCAATATG
1 TCCCCCAACATTTAGTCCGTTTGCAATATG
24873 TTCACCGACG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCGTTTGCAATATGG
Found at i:27747 original size:2 final size:2
Alignment explanation
Indices: 27742--27770 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
27732 ACCCCCCCTT
27742 TC TC TC TC TC TC TC TC TC TC TC T- TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
27771 CCTAGAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:34315 original size:2 final size:2
Alignment explanation
Indices: 34308--34346 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
34298 GTCCATATGC
34308 AT AT AT 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 AT AT AT A
34347 GAGAGAGAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34351 original size:2 final size:2
Alignment explanation
Indices: 34346--34392 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
34336 ATATATATAT
*
34346 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AA AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
34388 AG AG A
1 AG AG A
34393 AACTTTCATA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:37448 original size:60 final size:60
Alignment explanation
Indices: 37340--37462 Score: 147
Period size: 60 Copynumber: 2.0 Consensus size: 60
37330 GATTACTGTT
* * * * * * * *
37340 ATTTTAAATTAATCCCTAAACTTTTTAACATTCTAATTTTATCTCCAAACTATGACTCTC
1 ATTTTAAATTAATCCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTC
* * *
37400 ATTTTATATTGATCTCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTC
1 ATTTTAAATTAATCCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTC
37460 ATT
1 ATT
37463 CTCAATTGGC
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 52 1.00
ACGTcount: A:0.35, C:0.24, G:0.02, T:0.40
Consensus pattern (60 bp):
ATTTTAAATTAATCCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTC
Found at i:37479 original size:60 final size:60
Alignment explanation
Indices: 37353--37484 Score: 140
Period size: 60 Copynumber: 2.2 Consensus size: 60
37343 TTAAATTAAT
* * * * * * * * * *
37353 CCCTAAACTTTTTAACATTCTAATTTTATCTCCAAACTATGACTCTCATTTTATATTGAT
1 CCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTCATTTCATATTGAC
* *
37413 CTCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTCATTCTCA-ATTGGC
1 CCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTCATT-TCATATTGAC
37473 CCCTAAACTTTT
1 CCCTAAACTTTT
37485 GAGCATTCCA
Statistics
Matches: 58, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
60 56 0.97
61 2 0.03
ACGTcount: A:0.32, C:0.27, G:0.03, T:0.38
Consensus pattern (60 bp):
CCCTAAACTTTTAAACATTCAAAATTCACCCCCAAACTATAACCCTCATTTCATATTGAC
Found at i:38671 original size:32 final size:31
Alignment explanation
Indices: 38635--38711 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
38625 CGGGGCCGTG
*
38635 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
38667 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
38698 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
38712 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:38694 original size:63 final size:63
Alignment explanation
Indices: 38588--38711 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
38578 CCCTAAGGGA
* * ** *
38588 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
38651 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
38712 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:39593 original size:7 final size:7
Alignment explanation
Indices: 39581--39618 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
39571 GTCAAAGAAA
39581 GTCAACG
1 GTCAACG
39588 GTCAACG
1 GTCAACG
*
39595 GTC-ACA
1 GTCAACG
39601 GTCAACG
1 GTCAACG
39608 GTCAACG
1 GTCAACG
39615 GTCA
1 GTCA
39619 GGTCAGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:39605 original size:20 final size:20
Alignment explanation
Indices: 39580--39618 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
39570 GGTCAAAGAA
39580 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
39600 AGTCAACGGTCAACGGTCA
1 AGTCAACGGTCAACGGTCA
39619 GGTCAGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:39629 original size:17 final size:17
Alignment explanation
Indices: 39607--39663 Score: 60
Period size: 17 Copynumber: 3.4 Consensus size: 17
39597 CACAGTCAAC
*
39607 GGTCAACGGTCAGGTCA
1 GGTCAACAGTCAGGTCA
* * *
39624 GGTCAACATTCGGGTCG
1 GGTCAACAGTCAGGTCA
* *
39641 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCAGGTCA
39658 GGTCAA
1 GGTCAA
39664 TCCGATTCAG
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 35 1.00
ACGTcount: A:0.21, C:0.23, G:0.37, T:0.19
Consensus pattern (17 bp):
GGTCAACAGTCAGGTCA
Found at i:39682 original size:19 final size:19
Alignment explanation
Indices: 39658--39725 Score: 64
Period size: 19 Copynumber: 3.5 Consensus size: 19
39648 AGTCGGGTCG
* *
39658 GGTCAATCCGATTCAGACC
1 GGTCAAACCGATTAAGACC
* *
39677 GGTCAAACCGGTTAAGATC
1 GGTCAAACCGATTAAGACC
* * *
39696 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGATT-AAGACC
39716 GGTCAAACCG
1 GGTCAAACCG
39726 GTTTTCCATC
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 28 0.68
20 13 0.32
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGATTAAGACC
Found at i:39688 original size:9 final size:9
Alignment explanation
Indices: 39674--39727 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
39664 TCCGATTCAG
39674 ACCGGTCAA
1 ACCGGTCAA
*
39683 ACCGGTTAA
1 ACCGGTCAA
*
39692 GATCGGTCAA
1 -ACCGGTCAA
39702 ACCGGTTCAAA
1 ACCGG-TC-AA
*
39713 ACTGGTCAA
1 ACCGGTCAA
39722 ACCGGT
1 ACCGGT
39728 TTTCCATCAG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
9 19 0.53
10 11 0.31
11 6 0.17
ACGTcount: A:0.31, C:0.26, G:0.24, T:0.19
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:39721 original size:20 final size:19
Alignment explanation
Indices: 39676--39728 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
39666 CGATTCAGAC
*
39676 CGGTCAAACCGGTTAAGAT
1 CGGTCAAACCGGTTAAAAT
39695 CGGTCAAACCGGTTCAAAA-
1 CGGTCAAACCGGTT-AAAAT
39714 CTGGTCAAACCGGTT
1 C-GGTCAAACCGGTT
39729 TTCCATCAGC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
19 15 0.48
20 16 0.52
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (19 bp):
CGGTCAAACCGGTTAAAAT
Found at i:46036 original size:63 final size:63
Alignment explanation
Indices: 45920--46043 Score: 144
Period size: 63 Copynumber: 2.0 Consensus size: 63
45910 CCCTAAGGGA
* * ** * *
45920 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTATCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
45983 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
46044 GTCACATTAG
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:46925 original size:7 final size:7
Alignment explanation
Indices: 46913--46950 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
46903 GTCAAAGAAA
46913 GTCAACG
1 GTCAACG
46920 GTCAACG
1 GTCAACG
*
46927 GTC-ACA
1 GTCAACG
46933 GTCAACG
1 GTCAACG
46940 GTCAACG
1 GTCAACG
46947 GTCA
1 GTCA
46951 GGTCGGGTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 5 0.18
7 23 0.82
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:46937 original size:20 final size:20
Alignment explanation
Indices: 46912--46950 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
46902 GGTCAAAGAA
46912 AGTCAACGGTCAACGGTCAC
1 AGTCAACGGTCAACGGTCAC
46932 AGTCAACGGTCAACGGTCA
1 AGTCAACGGTCAACGGTCA
46951 GGTCGGGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.31, C:0.28, G:0.26, T:0.15
Consensus pattern (20 bp):
AGTCAACGGTCAACGGTCAC
Found at i:46961 original size:17 final size:17
Alignment explanation
Indices: 46939--46979 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
46929 CACAGTCAAC
*
46939 GGTCAACGGTCAGGTCG
1 GGTCAACAGTCAGGTCG
* *
46956 GGTCAACATTCGGGTCG
1 GGTCAACAGTCAGGTCG
46973 GGTCAAC
1 GGTCAAC
46980 CCGGTTCAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.20, C:0.24, G:0.37, T:0.20
Consensus pattern (17 bp):
GGTCAACAGTCAGGTCG
Found at i:46997 original size:19 final size:18
Alignment explanation
Indices: 46973--47012 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
46963 ATTCGGGTCG
* *
46973 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGG-TCAAACC
46992 GGTCAAACCGGTCAAACC
1 GGTCAAACCGGTCAAACC
47010 GGT
1 GGT
47013 TTTCCAGCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (18 bp):
GGTCAAACCGGTCAAACC
Found at i:47003 original size:9 final size:9
Alignment explanation
Indices: 46973--47012 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
46963 ATTCGGGTCG
*
46973 GGTCAACCC
1 GGTCAAACC
*
46982 GGTTCAGACC
1 GG-TCAAACC
46992 GGTCAAACC
1 GGTCAAACC
47001 GGTCAAACC
1 GGTCAAACC
47010 GGT
1 GGT
47013 TTTCCAGCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 20 0.74
10 7 0.26
ACGTcount: A:0.25, C:0.33, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:53643 original size:23 final size:23
Alignment explanation
Indices: 53617--53741 Score: 108
Period size: 23 Copynumber: 5.3 Consensus size: 23
53607 CACCACAACT
53617 CATATAATTGCACCGAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
53640 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
53663 CGTAGAATTGCACC-ATAGTGCCA
1 CATATAATTGCACCGA-AGTGCCA
* * *
53686 TATAATAATTGCACCGGAGTGCCG
1 CAT-ATAATTGCACCGAAGTGCCA
* * * *
53710 CGTAGAATTACACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
53733 TATAATAAT
1 CAT-ATAAT
53742 GTCCATGAGG
Statistics
Matches: 78, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
23 57 0.73
24 21 0.27
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:53705 original size:47 final size:47
Alignment explanation
Indices: 53622--53741 Score: 190
Period size: 47 Copynumber: 2.6 Consensus size: 47
53612 CAACTCATAT
*
53622 AATTGCACCGA-AGTGCCACAT-ATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-ATAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
53668 AATTGCACCATAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
1 AATTGCACCATAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
* *
53715 AATTACACCGTAGTGCCATATAATAAT
1 AATTGCACCATAGTGCCATATAATAAT
53742 GTCCATGAGG
Statistics
Matches: 69, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
45 1 0.01
46 18 0.26
47 50 0.72
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (47 bp):
AATTGCACCATAGTGCCATATAATAATTGCACCGGAGTGCCGCGTAG
Found at i:53919 original size:103 final size:103
Alignment explanation
Indices: 53749--53965 Score: 407
Period size: 103 Copynumber: 2.1 Consensus size: 103
53739 AATGTCCATG
* *
53749 AGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAG
1 AGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
53814 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
*
53852 AGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAG
1 AGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
53917 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
53955 AGGACCACATA
1 AGGACCACATA
53966 GACCCTCGAC
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 111 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCGA
Done.