Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008718.1 Hibiscus syriacus cultivar Beakdansim tig00111773_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: 53468
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Found at i:3786 original size:13 final size:13
Alignment explanation
Indices: 3764--3793 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
3754 ACTAAACACC
3764 TTTC-ACATACCT
1 TTTCAACATACCT
3776 TTTCAACATACCT
1 TTTCAACATACCT
3789 TTTCA
1 TTTCA
3794 TCTTTGGCCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 4 0.24
13 13 0.76
ACGTcount: A:0.27, C:0.30, G:0.00, T:0.43
Consensus pattern (13 bp):
TTTCAACATACCT
Found at i:7800 original size:28 final size:28
Alignment explanation
Indices: 7769--7835 Score: 68
Period size: 27 Copynumber: 2.4 Consensus size: 28
7759 AAAAAAAATC
*
7769 AGAAAACAAAGT-GAAGCACTC-AAAAGAA
1 AGAAAACAAAGTCCAA-CACTCAAAAAG-A
*
7797 AGAAAA-AAAATCCAACACTCAAAAAGA
1 AGAAAACAAAGTCCAACACTCAAAAAGA
7824 AGAAAATCAAAG
1 AGAAAA-CAAAG
7836 AAAAGAATAG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
27 16 0.50
28 13 0.41
29 3 0.09
ACGTcount: A:0.64, C:0.15, G:0.13, T:0.07
Consensus pattern (28 bp):
AGAAAACAAAGTCCAACACTCAAAAAGA
Found at i:9349 original size:24 final size:25
Alignment explanation
Indices: 9321--9368 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
9311 ACCTATTTTT
* * *
9321 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
9345 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
9369 GATCATTGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Found at i:17458 original size:10 final size:10
Alignment explanation
Indices: 17443--17471 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
17433 GATGACAAAG
17443 GTAGCTGAAT
1 GTAGCTGAAT
17453 GTAGCTGAAT
1 GTAGCTGAAT
17463 GTAGCTGAA
1 GTAGCTGAA
17472 CGTACTGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.31, T:0.28
Consensus pattern (10 bp):
GTAGCTGAAT
Found at i:23215 original size:19 final size:20
Alignment explanation
Indices: 23191--23243 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 20
23181 CGGCCAAGAG
*
23191 CATGTATCTTCAAT-AAAAT
1 CATGTATTTTCAATAAAAAT
*
23210 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-ATAAAAAT
23231 CATGTATTTTCAA
1 CATGTATTTTCAA
23244 AGGGGTTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 11 0.38
20 1 0.03
21 17 0.59
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCAATAAAAAT
Found at i:26144 original size:22 final size:21
Alignment explanation
Indices: 26118--26159 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
26108 GGTTGCGGAA
*
26118 TTGATGGTCTTGATGGATGAAG
1 TTGATGATCTTGAT-GATGAAG
*
26140 TTGATGATGTTGATGATGAA
1 TTGATGATCTTGATGATGAA
26160 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.26, C:0.02, G:0.33, T:0.38
Consensus pattern (21 bp):
TTGATGATCTTGATGATGAAG
Found at i:26538 original size:21 final size:19
Alignment explanation
Indices: 26514--26563 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 19
26504 GAAACCCCTT
26514 TGAAAATACAGGATTTTTAAA
1 TGAAAATACAGGA-TTTT-AA
*
26535 TGAAAATACATGATTTTAA
1 TGAAAATACAGGATTTTAA
*
26554 TGAAGATACA
1 TGAAAATACA
26564 TGCTTTTGGC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 11 0.41
20 4 0.15
21 12 0.44
ACGTcount: A:0.48, C:0.06, G:0.14, T:0.32
Consensus pattern (19 bp):
TGAAAATACAGGATTTTAA
Found at i:26557 original size:19 final size:20
Alignment explanation
Indices: 26514--26570 Score: 71
Period size: 19 Copynumber: 2.9 Consensus size: 20
26504 GAAACCCCTT
*
26514 TGAAAATACAGGATTTTTAAA
1 TGAAAATACATGA-TTTTAAA
26535 TGAAAATACATGATTTT-AA
1 TGAAAATACATGATTTTAAA
* *
26554 TGAAGATACATGCTTTT
1 TGAAAATACATGATTTT
26571 GGCCGAATGG
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.52
20 4 0.12
21 12 0.36
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:27512 original size:30 final size:31
Alignment explanation
Indices: 27471--27530 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
27461 ACATGCTGCC
**
27471 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
*
27502 ATGA-ATCTAAAACATATGTAAACATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
27531 TAAAGCTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.53, C:0.10, G:0.08, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:38781 original size:14 final size:13
Alignment explanation
Indices: 38764--38813 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
38754 GTGCAAAAAG
38764 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
38778 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
38791 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
38802 AAAGAAAAAGAA
1 AAAGAAAAAGAA
38814 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:38810 original size:19 final size:18
Alignment explanation
Indices: 38758--38813 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
38748 ATTGGAGTGC
38758 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
38775 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
38794 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
38813 A
1 A
38814 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:38811 original size:11 final size:11
Alignment explanation
Indices: 38758--38813 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
38748 ATTGGAGTGC
38758 AAAAAG-AAAG
1 AAAAAGAAAAG
38768 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
38782 AAGAAGAAAAG
1 AAAAAGAAAAG
38793 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
38806 AAAAAGAA
1 AAAAAGAA
38814 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:43046 original size:14 final size:13
Alignment explanation
Indices: 43029--43078 Score: 52
Period size: 14 Copynumber: 3.9 Consensus size: 13
43019 GTGCAAAAAG
43029 AAAGAAAAAGACAA
1 AAAGAAAAAGA-AA
*
43043 AAAGAAGAAGAAA
1 AAAGAAAAAGAAA
43056 AGAAG-AAAAG--A
1 A-AAGAAAAAGAAA
43067 AAAGAAAAAGAA
1 AAAGAAAAAGAA
43079 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 3 0.10
11 7 0.23
13 7 0.23
14 13 0.43
ACGTcount: A:0.78, C:0.02, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAGAAAAAGAAA
Found at i:43075 original size:19 final size:18
Alignment explanation
Indices: 43023--43078 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
43013 ATTGGAGTGC
43023 AAAAAG-AAAGAAAAAGA
1 AAAAAGAAAAGAAAAAGA
43040 CAAAAAGAAGAAG-AAAAGA
1 -AAAAAGAA-AAGAAAAAGA
43059 AGAAAAGAAAAGAAAAAGA
1 A-AAAAGAAAAGAAAAAGA
43078 A
1 A
43079 TTCAAAAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 10 0.29
19 21 0.62
20 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAGAAAAAGA
Found at i:43076 original size:11 final size:11
Alignment explanation
Indices: 43023--43078 Score: 51
Period size: 11 Copynumber: 4.7 Consensus size: 11
43013 ATTGGAGTGC
43023 AAAAAG-AAAG
1 AAAAAGAAAAG
43033 AAAAAGACAAAAAG
1 AAAAAG---AAAAG
*
43047 AAGAAGAAAAG
1 AAAAAGAAAAG
43058 AAGAAAAGAAAAG
1 -A-AAAAGAAAAG
43071 AAAAAGAA
1 AAAAAGAA
43079 TTCAAAAAGA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 12 0.32
12 2 0.05
13 9 0.24
14 9 0.24
ACGTcount: A:0.79, C:0.02, G:0.20, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:49292 original size:11 final size:11
Alignment explanation
Indices: 49278--49333 Score: 51
Period size: 13 Copynumber: 4.7 Consensus size: 11
49268 TCTTTTTGAA
49278 TTCTTTTTCTT
1 TTCTTTTTCTT
49289 TTCTTTTCTTCTT
1 TTC-TTT-TTCTT
*
49302 TTCTTCTTCTTTT
1 TTCTT-TT-TCTT
49315 TGTCTTTTTC-T
1 T-TCTTTTTCTT
49326 TTCTTTTT
1 TTCTTTTT
49334 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 7 0.18
11 5 0.13
12 7 0.18
13 15 0.39
14 4 0.11
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (11 bp):
TTCTTTTTCTT
Found at i:49302 original size:19 final size:18
Alignment explanation
Indices: 49278--49333 Score: 71
Period size: 18 Copynumber: 3.1 Consensus size: 18
49268 TCTTTTTGAA
49278 TTCTTTTTCTTTTCTTTT
1 TTCTTTTTCTTTTCTTTT
49296 CTTC-TTTTCTTCTTCTTTT
1 -TTCTTTTTCTT-TTCTTTT
49315 TGTCTTTTTC-TTTCTTTT
1 T-TCTTTTTCTTTTCTTTT
49333 T
1 T
49334 GCACTCCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 16 0.47
19 13 0.38
20 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.79
Consensus pattern (18 bp):
TTCTTTTTCTTTTCTTTT
Done.