Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005909.1 Hibiscus syriacus cultivar Beakdansim tig00013879_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: 63722
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:7145 original size:30 final size:31
Alignment explanation
Indices: 7078--7163 Score: 113
Period size: 31 Copynumber: 2.8 Consensus size: 31
7068 TTTTGATTTG
* *
7078 TCCCT-ATTTTTATGGTTAATTATACCTTGC
1 TCCCTCATTTTTATGGTTAATTATACATTGA
*
7108 CCCCTCATTTTTATGGTTAATTATACATT-A
1 TCCCTCATTTTTATGGTTAATTATACATTGA
*
7138 TCCCTCATTTTTTATGATTAATTATA
1 TCCCTCA-TTTTTATGGTTAATTATA
7164 TTTTACCTCC
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
30 10 0.20
31 39 0.80
ACGTcount: A:0.24, C:0.19, G:0.07, T:0.50
Consensus pattern (31 bp):
TCCCTCATTTTTATGGTTAATTATACATTGA
Found at i:8837 original size:13 final size:12
Alignment explanation
Indices: 8815--8844 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
8805 GAACAATCTC
8815 TTTTTATTTTTA
1 TTTTTATTTTTA
8827 TTTTTATTTTTTA
1 TTTTTA-TTTTTA
8840 TTTTT
1 TTTTT
8845 TGTCATGATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:8845 original size:7 final size:6
Alignment explanation
Indices: 8815--8844 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
8805 GAACAATCTC
8815 TTTTTA TTTTTA TTTTTA TTTTTTA TTTTT
1 TTTTTA TTTTTA TTTTTA -TTTTTA TTTTT
8845 TGTCATGATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 17 0.74
7 6 0.26
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (6 bp):
TTTTTA
Found at i:9244 original size:16 final size:16
Alignment explanation
Indices: 9223--9257 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9213 GGCTTTCCCA
9223 TTTCTTCCTCATCTTC
1 TTTCTTCCTCATCTTC
* *
9239 TTTCTTTCTCTTCTTC
1 TTTCTTCCTCATCTTC
9255 TTT
1 TTT
9258 TCCTTTTCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (16 bp):
TTTCTTCCTCATCTTC
Found at i:10388 original size:23 final size:22
Alignment explanation
Indices: 10340--10388 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
10330 ACACTCATAT
* *
10340 AATTGCACCAAGTGCCACTTAT
1 AATTGCACCAAGTGCCACGTAG
* *
10362 AATTGCACCGGAGTGCCGCGTAG
1 AATTGCACC-AAGTGCCACGTAG
10385 AATT
1 AATT
10389 ATCGTAGTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (22 bp):
AATTGCACCAAGTGCCACGTAG
Found at i:10589 original size:100 final size:102
Alignment explanation
Indices: 10416--10630 Score: 362
Period size: 100 Copynumber: 2.1 Consensus size: 102
10406 TAATGTCCAT
* *
10416 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
10481 GACTTCACACATGTTCCAAAGAATAC-ATATGT-CCG
66 GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
*
10516 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
10581 TACTTCACATATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACA-ATATGTCCCG
10619 AAGGACCACATA
1 AAGGACCACATA
10631 GACCCTCGAC
Statistics
Matches: 107, Mismatches: 5, Indels: 3
0.93 0.04 0.03
Matches are distributed among these distances:
100 86 0.80
102 6 0.06
103 15 0.14
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACAATATGTCCCG
Found at i:13412 original size:20 final size:20
Alignment explanation
Indices: 13363--13401 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
13353 CTTAAGGGTA
*
13363 TATCGATACTCCAATACCAT
1 TATCAATACTCCAATACCAT
13383 TATCAATACTCC-ATACCAT
1 TATCAATACTCCAATACCAT
13402 AGTATCATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.36, C:0.31, G:0.03, T:0.31
Consensus pattern (20 bp):
TATCAATACTCCAATACCAT
Found at i:19892 original size:21 final size:20
Alignment explanation
Indices: 19868--19916 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
19858 AAGGGGATCA
19868 ATCCTTTGGTCGAAGGGAACG
1 ATCCTTTGG-CGAAGGGAACG
* * *
19889 ATCCTTTTGCTAAGGGATCG
1 ATCCTTTGGCGAAGGGAACG
19909 ATCCTTTG
1 ATCCTTTG
19917 AGCTAGATAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.33
Consensus pattern (20 bp):
ATCCTTTGGCGAAGGGAACG
Found at i:20218 original size:20 final size:20
Alignment explanation
Indices: 20193--20244 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
20183 AAACATACTA
*
20193 TGGTATTGATACTAACCTCT
1 TGGTATCGATACTAACCTCT
20213 TGGTATCGATACTAACCTCT
1 TGGTATCGATACTAACCTCT
*
20233 TGGTATCAATAC
1 TGGTATCGATAC
20245 CACCCATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (20 bp):
TGGTATCGATACTAACCTCT
Found at i:29213 original size:20 final size:20
Alignment explanation
Indices: 29188--29225 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
29178 TTTTGGTGCA
*
29188 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
*
29208 GAGGGAACCGATTCCCCC
1 GAGGGAACCGATACCCCC
29226 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.34, G:0.26, T:0.13
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Found at i:31972 original size:20 final size:20
Alignment explanation
Indices: 31947--31998 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
31937 CTCGGAGGGA
*
31947 ACCGATTCCCCTTGGGGGGT
1 ACCGATTCCCCTTCGGGGGT
31967 ACCGATTTCCCC-TCGGGGGT
1 ACCGA-TTCCCCTTCGGGGGT
31987 ACCGATTCCCCT
1 ACCGATTCCCCT
31999 CCCCCTTGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 6 0.21
20 17 0.59
21 6 0.21
ACGTcount: A:0.12, C:0.37, G:0.27, T:0.25
Consensus pattern (20 bp):
ACCGATTCCCCTTCGGGGGT
Found at i:37745 original size:32 final size:32
Alignment explanation
Indices: 37678--37758 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 32
37668 TTTGTCCCTA
* *
37678 TTTTTATGGTTAATTATACCTGGCCCCCTCAT
1 TTTTTATGGTTAATTATACATGGACCCCTCAT
* *
37710 TTTTTATGGTTAATTATACAT-TATCCCTCAT
1 TTTTTATGGTTAATTATACATGGACCCCTCAT
* *
37741 TTTTTATGATTAGTTATA
1 TTTTTATGGTTAATTATA
37759 TTTTACCTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
31 23 0.53
32 20 0.47
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (32 bp):
TTTTTATGGTTAATTATACATGGACCCCTCAT
Found at i:41230 original size:20 final size:20
Alignment explanation
Indices: 41202--41241 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
41192 TTAAGGGTAG
*
41202 TATCGATACTCCAATACCAT
1 TATCAATACTCCAATACCAT
*
41222 TATCAATACTCCCATACCAT
1 TATCAATACTCCAATACCAT
41242 AGTATCGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.33, G:0.03, T:0.30
Consensus pattern (20 bp):
TATCAATACTCCAATACCAT
Found at i:56081 original size:20 final size:20
Alignment explanation
Indices: 56054--56130 Score: 93
Period size: 20 Copynumber: 3.8 Consensus size: 20
56044 ATTGTTGTCC
*
56054 AAGGGATCGATCATTTTTC-
1 AAGGGATCGATCCTTTTTCG
*
56073 AAGGGGATCGATCCTTTGGTCG
1 AA-GGGATCGATCCTTT-TTCG
* *
56095 AAGGGATCGATCCTTTTGCT
1 AAGGGATCGATCCTTTTTCG
56115 AAGGGATCGATCCTTT
1 AAGGGATCGATCCTTT
56131 GAGCTAGATA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.60
21 16 0.32
22 2 0.04
ACGTcount: A:0.22, C:0.18, G:0.27, T:0.32
Consensus pattern (20 bp):
AAGGGATCGATCCTTTTTCG
Found at i:56121 original size:41 final size:41
Alignment explanation
Indices: 56054--56131 Score: 122
Period size: 41 Copynumber: 1.9 Consensus size: 41
56044 ATTGTTGTCC
*
56054 AAGGGATCGATCATTTTTCAAGGGGATCGATCCTTTGGTCG
1 AAGGGATCGATCATTTTGCAAGGGGATCGATCCTTTGGTCG
*
56095 AAGGGATCGATCCTTTTGCTAA-GGGATCGATCCTTTG
1 AAGGGATCGATCATTTTGC-AAGGGGATCGATCCTTTG
56132 AGCTAGATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
41 32 0.94
42 2 0.06
ACGTcount: A:0.22, C:0.18, G:0.28, T:0.32
Consensus pattern (41 bp):
AAGGGATCGATCATTTTGCAAGGGGATCGATCCTTTGGTCG
Done.