Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009360.1 Hibiscus syriacus cultivar Beakdansim tig00113183_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: 81616
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3039 original size:16 final size:16
Alignment explanation
Indices: 3018--3051 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3008 TGTAGGAGTC
3018 TTTTCTTTCTCTTTTG
1 TTTTCTTTCTCTTTTG
* *
3034 TTTTCTTTTTTTTTTG
1 TTTTCTTTCTCTTTTG
3050 TT
1 TT
3052 GCTTTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTTCTTTCTCTTTTG
Found at i:3461 original size:33 final size:33
Alignment explanation
Indices: 3397--3497 Score: 82
Period size: 33 Copynumber: 3.0 Consensus size: 33
3387 CTTGTTGATG
* * *
3397 AATG-AAGGATGAT-TTAATGGTGATGAAATGGT
1 AATGAAAGGATGATGTTATTGGCG-TGATATGGT
3429 AATGAAAGGATGATGTTATTGGCGTGATATGGT
1 AATGAAAGGATGATGTTATTGGCGTGATATGGT
* * *
3462 GATGGAATATGG-TGATGATATAGGCGTGATAATGGT
1 AAT-GAA-A-GGATGATGTTATTGGCGTGAT-ATGGT
3498 GATGGACAGA
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
32 4 0.07
33 19 0.33
34 10 0.18
35 17 0.30
36 7 0.12
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (33 bp):
AATGAAAGGATGATGTTATTGGCGTGATATGGT
Found at i:27465 original size:17 final size:18
Alignment explanation
Indices: 27437--27470 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
27427 GGTTAGGGTA
27437 GAAAGAATAGAAGAAATT
1 GAAAGAATAGAAGAAATT
27455 GAAAG-ATAGAAGAAAT
1 GAAAGAATAGAAGAAAT
27471 GATTTAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.62, C:0.00, G:0.24, T:0.15
Consensus pattern (18 bp):
GAAAGAATAGAAGAAATT
Found at i:30033 original size:26 final size:28
Alignment explanation
Indices: 30004--30075 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 28
29994 TTCATTGTTT
30004 CATAACTCATACCATTTC-CATAACA-A
1 CATAACTCATACCATTTCTCATAACATA
*
30030 CAT-ACTTCCACATCCATTTCTCATAACATA
1 CATAAC-T-CATA-CCATTTCTCATAACATA
*
30060 AATAAC-C-TACCATTTC
1 CATAACTCATACCATTTC
30076 ACCTTTACAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
25 2 0.05
26 11 0.30
27 4 0.11
28 8 0.22
29 7 0.19
30 3 0.08
31 2 0.05
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.31
Consensus pattern (28 bp):
CATAACTCATACCATTTCTCATAACATA
Found at i:48126 original size:19 final size:21
Alignment explanation
Indices: 48101--48152 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
48091 CGGCCAAGAG
*
48101 CATGTATCTTCA-TTAAAACT
1 CATGTATTTTCATTTAAAACT
*
48121 -ATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAACT
48141 CATGTATTTTCA
1 CATGTATTTTCA
48153 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
19 10 0.36
20 7 0.25
21 11 0.39
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAACT
Found at i:50381 original size:19 final size:20
Alignment explanation
Indices: 50357--50396 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
50347 TATCCCATCC
50357 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
50376 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
50396 T
1 T
50397 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:50701 original size:34 final size:31
Alignment explanation
Indices: 50660--50731 Score: 92
Period size: 34 Copynumber: 2.2 Consensus size: 31
50650 GTACAAAAAG
*
50660 AAAGAAAAGACA-AAAAGAAGAAGAAAATTCAGA
1 AAAGAAAAGA-AGAAAAGAAAAAG-AAATTCA-A
50693 AAATGAAAAGAAGAAAAGAAAAAGAAATTCAA
1 AAA-GAAAAGAAGAAAAGAAAAAGAAATTCAA
50725 AAAGAAA
1 AAAGAAA
50732 GCAAGCTAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
31 4 0.11
32 4 0.11
33 11 0.31
34 17 0.47
ACGTcount: A:0.72, C:0.04, G:0.17, T:0.07
Consensus pattern (31 bp):
AAAGAAAAGAAGAAAAGAAAAAGAAATTCAA
Found at i:53515 original size:19 final size:21
Alignment explanation
Indices: 53491--53542 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
53481 CGGCCAAGAG
*
53491 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
53510 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
53531 CATGTATTTTCA
1 CATGTATTTTCA
53543 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:53979 original size:19 final size:20
Alignment explanation
Indices: 53955--53994 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
53945 TATCCCATCC
53955 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
53974 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
53994 T
1 T
53995 ATTATTATCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:58764 original size:24 final size:25
Alignment explanation
Indices: 58737--58789 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 25
58727 ATGGACAAAA
*
58737 CTTTTGGCACTTCAAACGACATT-T
1 CTTTTGGAACTTCAAACGACATTAT
* *
58761 CTTTTGTAACTTCAAACGGCATTAT
1 CTTTTGGAACTTCAAACGACATTAT
58786 CTTT
1 CTTT
58790 GAAACATCAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
24 20 0.80
25 5 0.20
ACGTcount: A:0.25, C:0.23, G:0.11, T:0.42
Consensus pattern (25 bp):
CTTTTGGAACTTCAAACGACATTAT
Found at i:58790 original size:24 final size:24
Alignment explanation
Indices: 58745--58799 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
58735 AACTTTTGGC
*
58745 ACTTCAAACGACATTTCTTTTGTA
1 ACTTCAAACGACATTTCTTTTGAA
*
58769 ACTTCAAACGGCATTATC-TTTGAA
1 ACTTCAAACGACATT-TCTTTTGAA
*
58793 ACATCAA
1 ACTTCAA
58800 GAGACATATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.35
Consensus pattern (24 bp):
ACTTCAAACGACATTTCTTTTGAA
Found at i:61467 original size:26 final size:27
Alignment explanation
Indices: 61409--61467 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
61399 AGAAAATCAT
* *
61409 AAAAGAAATTGAAGCACTCCAAAAGAA
1 AAAAGAAATTCAAGCACTCAAAAAGAA
61436 AGAAAGAAA-TCAA-CACTCAAAAAGAA
1 A-AAAGAAATTCAAGCACTCAAAAAGAA
61462 GAAAAG
1 -AAAAG
61468 CAAAGAAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 16 0.57
27 5 0.18
28 7 0.25
ACGTcount: A:0.63, C:0.14, G:0.15, T:0.08
Consensus pattern (27 bp):
AAAAGAAATTCAAGCACTCAAAAAGAA
Found at i:67451 original size:11 final size:13
Alignment explanation
Indices: 67419--67448 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
67409 TGGCCAAAGA
67419 TGAAAAGGTATGT
1 TGAAAAGGTATGT
67432 TGAAAAGGTATG-
1 TGAAAAGGTATGT
67444 TGAAA
1 TGAAA
67449 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Done.