Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001969.1 Hibiscus syriacus cultivar Beakdansim tig00003978_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: 42764
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5136 original size:18 final size:17
Alignment explanation
Indices: 5113--5169 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 17
5103 ATTGTTAACA
5113 AACAATTAGTATCTTTTT
1 AACAATT-GTATCTTTTT
5131 AACAATTGATATCATTTTGTT
1 AACAATTG-TATC--TTT-TT
5152 AACAATTGGTATCTTTTT
1 AACAATT-GTATCTTTTT
5170 CATTAAACAT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 1 0.03
18 13 0.38
19 3 0.09
20 3 0.09
21 13 0.38
22 1 0.03
ACGTcount: A:0.32, C:0.11, G:0.09, T:0.49
Consensus pattern (17 bp):
AACAATTGTATCTTTTT
Found at i:5155 original size:21 final size:21
Alignment explanation
Indices: 5129--5169 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
5119 TAGTATCTTT
5129 TTAACAATTGATATCATTTTG
1 TTAACAATTGATATCATTTTG
* *
5150 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCATTTT
5170 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATCATTTTG
Found at i:9536 original size:24 final size:24
Alignment explanation
Indices: 9509--9557 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
9499 TGCATGACAT
9509 TGTACATAGATGTTTTATACATCA
1 TGTACATAGATGTTTTATACATCA
* *
9533 TGTACATATATGTTTTATTCATCA
1 TGTACATAGATGTTTTATACATCA
9557 T
1 T
9558 CAGGAAGACT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (24 bp):
TGTACATAGATGTTTTATACATCA
Found at i:13059 original size:24 final size:28
Alignment explanation
Indices: 13000--13062 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 28
12990 CTTCCGAGTA
13000 TTCCCTCGCTCGACGCGCCGTCGTGATCAC
1 TTCCCTC-CTCGACGCGCCGTCGTGAT-AC
*
13030 TCCCCTCCTCG-C-CGCCGTCG-GAT-C
1 TTCCCTCCTCGACGCGCCGTCGTGATAC
13054 TTCCCTCCT
1 TTCCCTCCT
13063 ACAACAATCG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
24 9 0.29
26 3 0.10
27 8 0.26
28 1 0.03
29 4 0.13
30 6 0.19
ACGTcount: A:0.06, C:0.49, G:0.19, T:0.25
Consensus pattern (28 bp):
TTCCCTCCTCGACGCGCCGTCGTGATAC
Found at i:13863 original size:6 final size:6
Alignment explanation
Indices: 13852--13905 Score: 72
Period size: 6 Copynumber: 8.7 Consensus size: 6
13842 TTTATTTATT
* *
13852 TATATA TATATA TATATG TATGTATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TA--TATG TATATG TATATG TATATG TATATG
13902 TATA
1 TATA
13906 AGCATTCAAA
Statistics
Matches: 45, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
6 39 0.87
8 6 0.13
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:17852 original size:45 final size:45
Alignment explanation
Indices: 17785--17879 Score: 163
Period size: 45 Copynumber: 2.1 Consensus size: 45
17775 GGAAGAACGA
* * *
17785 AGAATCTTCTTATCAGAGTTCAGATTCTCCTAATCCAACTGCACT
1 AGAATCTTCTTACCAGACTTCAGATTCCCCTAATCCAACTGCACT
17830 AGAATCTTCTTACCAGACTTCAGATTCCCCTAATCCAACTGCACT
1 AGAATCTTCTTACCAGACTTCAGATTCCCCTAATCCAACTGCACT
17875 AGAAT
1 AGAAT
17880 GCAGCGGGGG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 47 1.00
ACGTcount: A:0.31, C:0.28, G:0.11, T:0.31
Consensus pattern (45 bp):
AGAATCTTCTTACCAGACTTCAGATTCCCCTAATCCAACTGCACT
Found at i:19142 original size:20 final size:20
Alignment explanation
Indices: 19097--19148 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
19087 AAATAGCTAA
19097 CGAATTCGCAAC-TCAATTT
1 CGAATTCGCAACATCAATTT
19116 CGAATTCGCAACAT-AATTTT
1 CGAATTCGCAACATCAA-TTT
*
19136 TGAATTCGCAACA
1 CGAATTCGCAACA
19149 AGAATTTACA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.35, C:0.23, G:0.12, T:0.31
Consensus pattern (20 bp):
CGAATTCGCAACATCAATTT
Found at i:19225 original size:20 final size:21
Alignment explanation
Indices: 19202--19257 Score: 80
Period size: 20 Copynumber: 2.7 Consensus size: 21
19192 AGTTTTCAAA
*
19202 TTCGCAACTCGAATTCG-GAT
1 TTCGCAACTCGAATTCGCAAT
19222 TTCGCAACTCGAATTCGCCAAT
1 TTCGCAACTCGAATTCG-CAAT
19244 TTCGCAACTC-AATT
1 TTCGCAACTCGAATT
19258 TTTGAATTCG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
20 17 0.52
21 4 0.12
22 12 0.36
ACGTcount: A:0.27, C:0.29, G:0.14, T:0.30
Consensus pattern (21 bp):
TTCGCAACTCGAATTCGCAAT
Found at i:19266 original size:62 final size:61
Alignment explanation
Indices: 19101--19267 Score: 153
Period size: 62 Copynumber: 2.7 Consensus size: 61
19091 AGCTAACGAA
*
19101 TTCGCAACTC-AATTTCG--AATTCGCAACAT-AATTTTTGAATTCGCAACAAGAATTTACAT
1 TTCGCAACTCGAA-TTCGCCAATTCGCAAC-TCAATTTTTGAATTCGCAACAAGAATTCACAT
** * ** * ** ** **
19160 TTCGTTACACGAATTTACCAAATTCGCAACTCAGTTTTCAAATTCGCAACTCGAATTCGGAT
1 TTCGCAACTCGAATTCGCC-AATTCGCAACTCAATTTTTGAATTCGCAACAAGAATTCACAT
19222 TTCGCAACTCGAATTCGCCAATTTCGCAACTCAATTTTTGAATTCG
1 TTCGCAACTCGAATTCGCCAA-TTCGCAACTCAATTTTTGAATTCG
19268 AGTTGCGAAA
Statistics
Matches: 81, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
59 9 0.11
60 2 0.02
61 3 0.04
62 67 0.83
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.34
Consensus pattern (61 bp):
TTCGCAACTCGAATTCGCCAATTCGCAACTCAATTTTTGAATTCGCAACAAGAATTCACAT
Found at i:25918 original size:2 final size:2
Alignment explanation
Indices: 25911--25974 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
25901 TGGGAACTCC
25911 AT AT AT AT AT AT 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 AT AT AT AT AT AT
25953 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
25975 TAAATGTTTG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29827 original size:23 final size:23
Alignment explanation
Indices: 29797--29840 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
29787 TTACAATGTT
29797 AATTAATAAAGAGATAAATTTCA
1 AATTAATAAAGAGATAAATTTCA
* *
29820 AATTAATAGAGGGATAAATTT
1 AATTAATAAAGAGATAAATTT
29841 AATTTCTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.14, T:0.32
Consensus pattern (23 bp):
AATTAATAAAGAGATAAATTTCA
Done.