Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000199.1 Hibiscus syriacus cultivar Beakdansim tig00000355_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: 66145
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.33
Found at i:2000 original size:19 final size:18
Alignment explanation
Indices: 1976--2011 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1966 TCAAGGAGTA
1976 AATTGAATCAAATGAATTT
1 AATTGAATCAAAT-AATTT
*
1995 AATTGACTCAAATAATT
1 AATTGAATCAAATAATT
2012 CTAACAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.36
Consensus pattern (18 bp):
AATTGAATCAAATAATTT
Found at i:5134 original size:45 final size:45
Alignment explanation
Indices: 5062--5148 Score: 138
Period size: 45 Copynumber: 1.9 Consensus size: 45
5052 ATTTATTTTC
*
5062 ATTTTTCGAATAAGCATGCGAACTAGATATCATGCGGTTAGGTTT
1 ATTTTTCGAATAAGCATGCGAACTAGATATCACGCGGTTAGGTTT
* * *
5107 ATTTTTCGAATAAGCATGTGAATTAGATATCACGTGGTTAGG
1 ATTTTTCGAATAAGCATGCGAACTAGATATCACGCGGTTAGG
5149 GTTTTTATGT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (45 bp):
ATTTTTCGAATAAGCATGCGAACTAGATATCACGCGGTTAGGTTT
Found at i:7157 original size:18 final size:18
Alignment explanation
Indices: 7134--7174 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
7124 GGGAGGTTGA
7134 GAGTCTGAAGAAACAAGT
1 GAGTCTGAAGAAACAAGT
*
7152 GAGTCTGAATAAACAAGT
1 GAGTCTGAAGAAACAAGT
7170 GAGTC
1 GAGTC
7175 AACTTGAGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.41, C:0.12, G:0.27, T:0.20
Consensus pattern (18 bp):
GAGTCTGAAGAAACAAGT
Found at i:11018 original size:21 final size:21
Alignment explanation
Indices: 10992--11035 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
10982 TTTTACAAAG
10992 TAATGCACTAGAAATTTCCCC
1 TAATGCACTAGAAATTTCCCC
11013 TAATGCACTAGAAATTTCCCC
1 TAATGCACTAGAAATTTCCCC
11034 TA
1 TA
11036 TTGTTCGTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.27, G:0.09, T:0.30
Consensus pattern (21 bp):
TAATGCACTAGAAATTTCCCC
Found at i:14715 original size:7 final size:7
Alignment explanation
Indices: 14703--14879 Score: 101
Period size: 7 Copynumber: 23.7 Consensus size: 7
14693 GAATAAGAAT
14703 GAAAAAA
1 GAAAAAA
14710 GAAAAAA
1 GAAAAAA
*
14717 GAAAAGA
1 GAAAAAA
14724 GAAAAAA
1 GAAAAAA
*
14731 TAAAAAAGA
1 -GAAAAA-A
14740 GAAAAAA
1 GAAAAAA
14747 TGAAAAAGA
1 -GAAAAA-A
*
14756 GAAAAAT
1 GAAAAAA
14763 GAAAAAGA
1 GAAAAA-A
*
14771 GAAAAAT
1 GAAAAAA
14778 GAAAAAGA
1 GAAAAA-A
*
14786 GAAAAAT
1 GAAAAAA
**
14793 GAAACAGGG
1 GAAA-A-AA
*
14802 GAAAAAT
1 GAAAAAA
*
14809 GAAAAAGG
1 GAAAAA-A
14817 GAAAACAA
1 GAAAA-AA
14825 -ATAAGAAA
1 GA-AA-AAA
14833 TGAAAAAA
1 -GAAAAAA
14841 TG-AAAAA
1 -GAAAAAA
14848 GAAAAGAA
1 GAAAA-AA
14856 -AAAAAA
1 GAAAAAA
*
14862 AAAAAAA
1 GAAAAAA
14869 G-AAAAA
1 GAAAAAA
14875 GAAAA
1 GAAAA
14880 TAAAAAGGAG
Statistics
Matches: 136, Mismatches: 16, Indels: 36
0.72 0.09 0.19
Matches are distributed among these distances:
6 9 0.07
7 64 0.47
8 52 0.38
9 10 0.07
10 1 0.01
ACGTcount: A:0.76, C:0.01, G:0.18, T:0.05
Consensus pattern (7 bp):
GAAAAAA
Found at i:14737 original size:16 final size:16
Alignment explanation
Indices: 14700--14876 Score: 166
Period size: 15 Copynumber: 11.7 Consensus size: 16
14690 CTTGAATAAG
14700 AATGAAAAA-AGAAAA
1 AATGAAAAAGAGAAAA
14715 AA-G-AAAAGAGAAAA
1 AATGAAAAAGAGAAAA
*
14729 AATAAAAAAGAGAAAA
1 AATGAAAAAGAGAAAA
14745 AATGAAAAAGAG-AAA
1 AATGAAAAAGAGAAAA
14760 AATGAAAAAGAG-AAA
1 AATGAAAAAGAGAAAA
14775 AATGAAAAAGAG-AAA
1 AATGAAAAAGAGAAAA
* * *
14790 AATGAAACAGGGGAAA
1 AATGAAAAAGAGAAAA
*
14806 AATGAAAAAGGGAAAACA
1 AATGAAAAAGAG-AAA-A
*
14824 AAT-AAGAAA-TGAAAA
1 AATGAA-AAAGAGAAAA
14839 AATGAAAAAGA-AAAGA
1 AATGAAAAAGAGAAA-A
14855 AA--AAAAA-A-AAAA
1 AATGAAAAAGAGAAAA
14867 AA-GAAAAAGA
1 AATGAAAAAGA
14877 AAATAAAAAG
Statistics
Matches: 142, Mismatches: 8, Indels: 25
0.81 0.05 0.14
Matches are distributed among these distances:
12 3 0.02
13 13 0.09
14 15 0.11
15 55 0.39
16 44 0.31
17 5 0.04
18 7 0.05
ACGTcount: A:0.75, C:0.01, G:0.18, T:0.06
Consensus pattern (16 bp):
AATGAAAAAGAGAAAA
Found at i:14865 original size:19 final size:19
Alignment explanation
Indices: 14827--14885 Score: 55
Period size: 21 Copynumber: 2.9 Consensus size: 19
14817 GAAAACAAAT
* **
14827 AAGAAATGAAAAAATGAAA
1 AAGAAAAGAAAAAAAAAAA
14846 AAGAAAAGAAAAAAAAAAAAA
1 AAGAAAAG--AAAAAAAAAAA
14867 AAGAAAAAGAAAATAAAAA
1 AAG-AAAAGAAAA-AAAAA
14886 GGAGGTATCA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
19 7 0.21
20 4 0.12
21 17 0.52
22 5 0.15
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (19 bp):
AAGAAAAGAAAAAAAAAAA
Found at i:16168 original size:37 final size:37
Alignment explanation
Indices: 16118--16226 Score: 159
Period size: 37 Copynumber: 2.9 Consensus size: 37
16108 TCGAAACAAG
* *
16118 TCAATCTTAAGCCTTCACGAAAGAGCAGTGAAGCAAT
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
16155 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
*
16192 TC-ATCTATAAGCCTTCAC-AGAAGAATAGTGAAGCA
1 TCAATCT-TAAGCCTTCACGA-AAGAGTAGTGAAGCA
16227 GACTAATTTT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
36 5 0.07
37 62 0.93
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.22
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGAAAGAGTAGTGAAGCAAA
Found at i:16319 original size:55 final size:54
Alignment explanation
Indices: 16257--16398 Score: 158
Period size: 55 Copynumber: 2.6 Consensus size: 54
16247 TTCAAATCTA
* *
16257 ATACTCCCTGAAAGAATAGGAAGTGAACCCGTTTGCTGAAAATTGTTCGACTCTT
1 ATACTCCCTGAAAGAATAGGGAG-GAACCCGTTTGCTGAAAATAGTTCGACTCTT
* * ** * * *
16312 ATACTCCCTGAACGAATAGGGAGCAGACATGTTTGCTGAAGATAGTTCGAGTTTT
1 ATACTCCCTGAAAGAATAGGGAGGA-ACCCGTTTGCTGAAAATAGTTCGACTCTT
* *
16367 ATACTCCCTGAAGGAAAAGGGAGCGAACCCGT
1 ATACTCCCTGAAAGAATAGGGAG-GAACCCGT
16399 CATTCGAAGA
Statistics
Matches: 71, Mismatches: 14, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
54 1 0.01
55 69 0.97
56 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.25
Consensus pattern (54 bp):
ATACTCCCTGAAAGAATAGGGAGGAACCCGTTTGCTGAAAATAGTTCGACTCTT
Found at i:18875 original size:23 final size:22
Alignment explanation
Indices: 18831--18875 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
18821 AATGTCATGG
*
18831 GGGAACCGATACCCCCAGAGGA
1 GGGAACCGATACCCCCAAAGGA
*
18853 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
18876 AAATTGAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.31, G:0.29, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:22832 original size:21 final size:21
Alignment explanation
Indices: 22806--22849 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
22796 ATTCTAGGCT
* *
22806 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
22827 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
22848 AG
1 AG
22850 CGAATAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.30, C:0.27, G:0.27, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:22919 original size:23 final size:22
Alignment explanation
Indices: 22875--22919 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
22865 AATGTCATGG
*
22875 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
*
22897 GGGAACCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
22920 AAATTGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.31, C:0.33, G:0.27, T:0.09
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:24468 original size:100 final size:102
Alignment explanation
Indices: 24287--24509 Score: 380
Period size: 100 Copynumber: 2.2 Consensus size: 102
24277 TTCGAGGGTC
* *
24287 TATGTAGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACA-GTGTGAAGTCTGGTGAGACACATAC
24352 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
24390 T-TGTGGTCCTTTGGGACATATATGTATTCTTTGGAACA-TGTGAAGTCTGGTGAGACATATACT
1 TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACT
24453 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
24490 TATGTGGTCCTTAT-GGACAT
1 TATGTGGTCCTT-TGGGACAT
24510 TATTATATGG
Statistics
Matches: 115, Mismatches: 3, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
100 62 0.54
101 16 0.14
102 36 0.31
103 1 0.01
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTTGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:24565 original size:46 final size:46
Alignment explanation
Indices: 24513--24623 Score: 204
Period size: 46 Copynumber: 2.4 Consensus size: 46
24503 TGGACATTAT
*
24513 TATATGGTACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
24559 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
*
24605 TATATGGCACTTCGGTGCA
1 TATATGGCACTACGGTGCA
24624 TTTATATGAG
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.23, C:0.26, G:0.24, T:0.26
Consensus pattern (46 bp):
TATATGGCACTACGGTGCAACTCTACGCGGCACTACGGTGCAATTC
Found at i:24613 original size:23 final size:23
Alignment explanation
Indices: 24513--24631 Score: 134
Period size: 23 Copynumber: 5.3 Consensus size: 23
24503 TGGACATTAT
* *
24513 TATATGGTACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
24536 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
24559 TATATGGCACTACGGTGCAACTC
1 TATATGGCACTACGGTGCAATTC
***
24582 TACGCGGCACTACGGTGCAATTC
1 TATATGGCACTACGGTGCAATTC
*
24605 TATATGGCACTTCGGTGC-ATT-
1 TATATGGCACTACGGTGCAATTC
24626 TATATG
1 TATATG
24632 AGCTGTGGTG
Statistics
Matches: 79, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
21 6 0.08
22 3 0.04
23 70 0.89
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.29
Consensus pattern (23 bp):
TATATGGCACTACGGTGCAATTC
Found at i:37758 original size:47 final size:48
Alignment explanation
Indices: 37667--37775 Score: 141
Period size: 47 Copynumber: 2.3 Consensus size: 48
37657 AAACATAATT
* *
37667 CAGGTCAAGTATCATATCAGAATCCAATTCATGTATCAGATCAGAATC
1 CAGGTCAGGTATCAGATCAGAATCCAATTCATGTATCAGATCAGAATC
* * * *
37715 CAGTTCATGTATCAGATCATAATCC-ATGTCA-GTATCATATCAGAATC
1 CAGGTCAGGTATCAGATCAGAATCCAAT-TCATGTATCAGATCAGAATC
37762 CAGGTCAGGTATCA
1 CAGGTCAGGTATCA
37776 TAAGAGAATT
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
47 29 0.55
48 24 0.45
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (48 bp):
CAGGTCAGGTATCAGATCAGAATCCAATTCATGTATCAGATCAGAATC
Found at i:37784 original size:24 final size:24
Alignment explanation
Indices: 37667--37777 Score: 134
Period size: 24 Copynumber: 4.7 Consensus size: 24
37657 AAACATAATT
*
37667 CAGGTCAAGTATCATATCAGAATC
1 CAGGTCATGTATCATATCAGAATC
** *
37691 CAATTCATGTATCAGATCAGAATC
1 CAGGTCATGTATCATATCAGAATC
* * *
37715 CAGTTCATGTATCAGATCATAATC
1 CAGGTCATGTATCATATCAGAATC
*
37739 CATGTCA-GTATCATATCAGAATC
1 CAGGTCATGTATCATATCAGAATC
*
37762 CAGGTCAGGTATCATA
1 CAGGTCATGTATCATA
37778 AGAGAATTCA
Statistics
Matches: 75, Mismatches: 11, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
23 20 0.27
24 55 0.73
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.29
Consensus pattern (24 bp):
CAGGTCATGTATCATATCAGAATC
Found at i:42053 original size:24 final size:24
Alignment explanation
Indices: 42026--42124 Score: 83
Period size: 24 Copynumber: 4.2 Consensus size: 24
42016 TATATCAAAA
* *
42026 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * *
42050 ATCATATCAGAATCCAGGTCATGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * *
42074 ATCAGATCAGAATCCATGTC-AGT
1 ATCAAAACAGAATCCAGGTCAAGT
* * * *
42097 AGCAAATCAGAATCTAGGTCAGGT
1 ATCAAAACAGAATCCAGGTCAAGT
42121 ATCA
1 ATCA
42125 TATGAGAATT
Statistics
Matches: 60, Mismatches: 14, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
23 18 0.30
24 42 0.70
ACGTcount: A:0.38, C:0.19, G:0.17, T:0.25
Consensus pattern (24 bp):
ATCAAAACAGAATCCAGGTCAAGT
Found at i:42133 original size:24 final size:23
Alignment explanation
Indices: 42040--42133 Score: 107
Period size: 24 Copynumber: 4.0 Consensus size: 23
42030 AAACATAATT
42040 CAGGTCAAGTATCATATCAGAATC
1 CAGGTC-AGTATCATATCAGAATC
*
42064 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCA-GTATCATATCAGAATC
* * *
42088 CATGTCAGTAGCAAATCAGAATC
1 CAGGTCAGTATCATATCAGAATC
* *
42111 TAGGTCAGGTATCATATGAGAAT
1 CAGGTCA-GTATCATATCAGAAT
42134 TCAAATCGGA
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
23 20 0.34
24 39 0.66
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (23 bp):
CAGGTCAGTATCATATCAGAATC
Found at i:46191 original size:2 final size:2
Alignment explanation
Indices: 46184--46238 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
46174 ATCCTTTAAA
46184 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
46226 AC AC AC AC AC AC A
1 AC AC AC AC AC AC A
46239 TATATATATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:46449 original size:24 final size:24
Alignment explanation
Indices: 46436--46553 Score: 157
Period size: 24 Copynumber: 5.0 Consensus size: 24
46426 AAACATAATT
46436 CAGGTCAAGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* *
46460 CAGGTCATGTAACAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
46484 CAGGTCATGTATCAGATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
*
46508 CAGGTC-AGTATCATATCAGAATC
1 CAGGTCAAGTATCAGATCAGAATC
* * * *
46531 CATGTCAGGTATCATAACAGAAT
1 CAGGTCAAGTATCAGATCAGAAT
46554 TCAAATTGGA
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
23 20 0.24
24 65 0.76
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.24
Consensus pattern (24 bp):
CAGGTCAAGTATCAGATCAGAATC
Found at i:48702 original size:25 final size:23
Alignment explanation
Indices: 48655--48711 Score: 87
Period size: 25 Copynumber: 2.4 Consensus size: 23
48645 GGTTAACGCT
48655 GGTCGGGTTGGTCAGTCGGACCG
1 GGTCGGGTTGGTCAGTCGGACCG
*
48678 GGTCGGTTTGGGTCGAGTCGGACCG
1 GGTCGGGTT-GGTC-AGTCGGACCG
48703 GGTCGGGTT
1 GGTCGGGTT
48712 AAACTAGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 8 0.27
24 4 0.13
25 18 0.60
ACGTcount: A:0.07, C:0.19, G:0.49, T:0.25
Consensus pattern (23 bp):
GGTCGGGTTGGTCAGTCGGACCG
Found at i:59171 original size:43 final size:43
Alignment explanation
Indices: 59098--59189 Score: 148
Period size: 43 Copynumber: 2.1 Consensus size: 43
59088 TAGACTCCTC
* * *
59098 AATTGAAAAAAATAGATGCTAGTTATGTGATCATTAATTATTAG
1 AATT-AAAAAAATAGATACTAGTGAAGTGATCATTAATTATTAG
59142 AATTAAAAAAATAGATACTAGTGAAGTGATCATTAATTATTAG
1 AATTAAAAAAATAGATACTAGTGAAGTGATCATTAATTATTAG
59185 AATTA
1 AATTA
59190 TCGGTCCTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
43 41 0.91
44 4 0.09
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (43 bp):
AATTAAAAAAATAGATACTAGTGAAGTGATCATTAATTATTAG
Found at i:60114 original size:16 final size:16
Alignment explanation
Indices: 60095--60133 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
60085 TTTAATAAGT
60095 AACGAGTTTAACGAGC
1 AACGAGTTTAACGAGC
*
60111 AACGAATTTAACGAGC
1 AACGAGTTTAACGAGC
60127 AACGAGT
1 AACGAGT
60134 CAAGTACTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (16 bp):
AACGAGTTTAACGAGC
Done.