Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006632.1 Hibiscus syriacus cultivar Beakdansim tig00016299_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: 50331
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:3808 original size:13 final size:14
Alignment explanation
Indices: 3790--3818 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3780 AATAGCTTTG
3790 TTTTTGT-TTTTAT
1 TTTTTGTGTTTTAT
3803 TTTTTGTGTTTTAT
1 TTTTTGTGTTTTAT
3817 TT
1 TT
3819 GACTGCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.07, C:0.00, G:0.10, T:0.83
Consensus pattern (14 bp):
TTTTTGTGTTTTAT
Found at i:8869 original size:25 final size:27
Alignment explanation
Indices: 8804--8884 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 27
8794 AAAAGGGAAT
8804 GGAAAAAATAGAAAAACATAAAAAAAGA
1 GGAAAAAATA-AAAAACATAAAAAAAGA
*
8832 AGAAAAACA-AAAACAA-A-AAAAAAAG-
1 GGAAAAA-ATAAAA-AACATAAAAAAAGA
8857 GGAAAAAATAAAAAA-ATAATAAATAAGA
1 GGAAAAAATAAAAAACATAA-AAA-AAGA
8885 AATAAGAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 14
0.73 0.03 0.23
Matches are distributed among these distances:
24 4 0.09
25 12 0.27
26 11 0.25
27 7 0.16
28 9 0.20
29 1 0.02
ACGTcount: A:0.78, C:0.04, G:0.11, T:0.07
Consensus pattern (27 bp):
GGAAAAAATAAAAAACATAAAAAAAGA
Found at i:11171 original size:42 final size:42
Alignment explanation
Indices: 11112--11214 Score: 111
Period size: 42 Copynumber: 2.5 Consensus size: 42
11102 TCAAGGGTTT
* * *
11112 CATGATGAGTAAGTCCTTTGATCCA-TCAGTAAGTCTTTATAG
1 CATGATGAGTAAGTCCTTCGAGCCATTCA-TAAGTCTTTAGAG
* *
11154 CATGATGCGTAAGTCCTTCGAGCCATTTATAAGTCTTTAGAG
1 CATGATGAGTAAGTCCTTCGAGCCATTCATAAGTCTTTAGAG
* * *
11196 CAAGATCA-TAAGACCTTCG
1 CATGATGAGTAAGTCCTTCG
11215 GAACATCCAT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 10 0.20
42 39 0.76
43 2 0.04
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.32
Consensus pattern (42 bp):
CATGATGAGTAAGTCCTTCGAGCCATTCATAAGTCTTTAGAG
Found at i:12802 original size:16 final size:16
Alignment explanation
Indices: 12781--12812 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12771 TAATTGCAGC
12781 TTTTGTATTTACTGTT
1 TTTTGTATTTACTGTT
*
12797 TTTTGTATTTATTGTT
1 TTTTGTATTTACTGTT
12813 CTAGCCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.12, C:0.03, G:0.12, T:0.72
Consensus pattern (16 bp):
TTTTGTATTTACTGTT
Found at i:13284 original size:42 final size:42
Alignment explanation
Indices: 13227--13322 Score: 165
Period size: 42 Copynumber: 2.3 Consensus size: 42
13217 TAACTTTTTA
*
13227 TTATTTTATTATCATTAAATGTTGTGATATGTTTTTACTATAT
1 TTATATTA-TATCATTAAATGTTGTGATATGTTTTTACTATAT
13270 TTATATTATATCATTAAATGTTGTGATATGTTTTTACTATAT
1 TTATATTATATCATTAAATGTTGTGATATGTTTTTACTATAT
*
13312 TTACATTATAT
1 TTATATTATAT
13323 TTTACATTTA
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
42 44 0.86
43 7 0.14
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.56
Consensus pattern (42 bp):
TTATATTATATCATTAAATGTTGTGATATGTTTTTACTATAT
Found at i:18954 original size:22 final size:22
Alignment explanation
Indices: 18926--19000 Score: 98
Period size: 22 Copynumber: 3.4 Consensus size: 22
18916 GCGGTCCTTT
*
18926 GGGACAAATACATAGGTTTTTC
1 GGGACAAATACATAGGTTATTC
*
18948 GGGACAAATTCATA-GTTCATTC
1 GGGACAAATACATAGGTT-ATTC
* *
18970 GGGATAAATACATAGGTCATTC
1 GGGACAAATACATAGGTTATTC
18992 GGGACAAAT
1 GGGACAAAT
19001 TTCATATGGC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
21 3 0.07
22 40 0.89
23 2 0.04
ACGTcount: A:0.35, C:0.15, G:0.23, T:0.28
Consensus pattern (22 bp):
GGGACAAATACATAGGTTATTC
Found at i:33613 original size:122 final size:122
Alignment explanation
Indices: 33392--33637 Score: 447
Period size: 122 Copynumber: 2.0 Consensus size: 122
33382 ATGCTCAAGG
*
33392 TTGTGGAAAGGATTGACTTGTATGTGGTATGATAACTGGACTGATGGCACTAAACCATTTGTAGC
1 TTGTGGAAAGGATTGACTTGTATGTGGTATGATAACTGGACTGAAGGCACTAAACCATTTGTAGC
*
33457 ATTTTATCAAAATGGTGACCCTCTTCTACAGACACCAGTAAATGTGATGGTTATGCC
66 ATTTTATCAAAATGGTGACCCTCTTCCACAGACACCAGTAAATGTGATGGTTATGCC
* *
33514 TTGTGGAAAGGATTGACTTGTATGTGGTATGATAACTGGATTGAAGGCACTAAACCATTTTTAGC
1 TTGTGGAAAGGATTGACTTGTATGTGGTATGATAACTGGACTGAAGGCACTAAACCATTTGTAGC
*
33579 ATTTTATCAAAATGGTGACCCTCTTCCACCGACACCAGTAAATGTGATGGTTATGCC
66 ATTTTATCAAAATGGTGACCCTCTTCCACAGACACCAGTAAATGTGATGGTTATGCC
33636 TT
1 TT
33638 TCGGTCAATG
Statistics
Matches: 119, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
122 119 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (122 bp):
TTGTGGAAAGGATTGACTTGTATGTGGTATGATAACTGGACTGAAGGCACTAAACCATTTGTAGC
ATTTTATCAAAATGGTGACCCTCTTCCACAGACACCAGTAAATGTGATGGTTATGCC
Found at i:39944 original size:15 final size:15
Alignment explanation
Indices: 39926--39962 Score: 53
Period size: 12 Copynumber: 2.7 Consensus size: 15
39916 GGGTCTGAAC
39926 CTCTTCTTCTTCTGA
1 CTCTTCTTCTTCTGA
39941 --C-TCTTCTTCTGA
1 CTCTTCTTCTTCTGA
39953 CTCTTCTTCT
1 CTCTTCTTCT
39963 ACCATAGGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 6
0.76 0.00 0.24
Matches are distributed among these distances:
12 11 0.58
13 1 0.05
14 1 0.05
15 6 0.32
ACGTcount: A:0.05, C:0.35, G:0.05, T:0.54
Consensus pattern (15 bp):
CTCTTCTTCTTCTGA
Found at i:39947 original size:12 final size:12
Alignment explanation
Indices: 39930--39962 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
39920 CTGAACCTCT
39930 TCTTCTTCTGAC
1 TCTTCTTCTGAC
39942 TCTTCTTCTGAC
1 TCTTCTTCTGAC
39954 TCTTCTTCT
1 TCTTCTTCT
39963 ACCATAGGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.06, C:0.33, G:0.06, T:0.55
Consensus pattern (12 bp):
TCTTCTTCTGAC
Found at i:42722 original size:18 final size:17
Alignment explanation
Indices: 42699--42732 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42689 TTTCACTAAT
*
42699 AGAGA-AAATATTACAA
1 AGAGAGAAATAATACAA
42715 AGAGAGAAATAATACAA
1 AGAGAGAAATAATACAA
42732 A
1 A
42733 TAGCCTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.65, C:0.06, G:0.15, T:0.15
Consensus pattern (17 bp):
AGAGAGAAATAATACAA
Found at i:44938 original size:15 final size:16
Alignment explanation
Indices: 44902--44940 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
44892 AAAGCCTCTG
*
44902 AATCATTCAGCATTTA
1 AATCATTCAGCACTTA
*
44918 AATCATTCAGCGCTT-
1 AATCATTCAGCACTTA
44933 AATCATTC
1 AATCATTC
44941 TAAGTAAACA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 8 0.38
16 13 0.62
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (16 bp):
AATCATTCAGCACTTA
Found at i:48043 original size:26 final size:28
Alignment explanation
Indices: 47996--48052 Score: 64
Period size: 26 Copynumber: 2.1 Consensus size: 28
47986 TGTAAACATA
* *
47996 AAATATATAAAAATTCATATAAATTA-T
1 AAATAAATAAAAATTCAAATAAATTACT
* *
48023 AAATAAAT-AAAATTTAAATAATTTACT
1 AAATAAATAAAAATTCAAATAAATTACT
48050 AAA
1 AAA
48053 ATAATATTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (28 bp):
AAATAAATAAAAATTCAAATAAATTACT
Found at i:49524 original size:15 final size:15
Alignment explanation
Indices: 49504--49533 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
49494 ATTTTACGAA
49504 TGATTTTATAAGTAT
1 TGATTTTATAAGTAT
*
49519 TGATTTTCTAAGTAT
1 TGATTTTATAAGTAT
49534 ATTCGATACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.03, G:0.13, T:0.53
Consensus pattern (15 bp):
TGATTTTATAAGTAT
Found at i:50028 original size:10 final size:11
Alignment explanation
Indices: 49995--50030 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
49985 TAAAAAAACA
49995 AGAATCAAAAG
1 AGAATCAAAAG
50006 AGAATCAAAAG
1 AGAATCAAAAG
50017 AGAATC-AAAG
1 AGAATCAAAAG
50027 AGAA
1 AGAA
50031 AGCATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 8 0.32
11 17 0.68
ACGTcount: A:0.64, C:0.08, G:0.19, T:0.08
Consensus pattern (11 bp):
AGAATCAAAAG
Done.