Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002255.1 Hibiscus syriacus cultivar Beakdansim tig00004585_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: 57567
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:4104 original size:2 final size:2
Alignment explanation
Indices: 4097--4140 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
4087 GTCCGAGTGT
4097 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA T- TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4136 TA TA T
1 TA TA T
4141 TTTTATATTT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
1 3 0.08
2 36 0.92
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6511 original size:44 final size:47
Alignment explanation
Indices: 6437--6525 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 47
6427 TTAGTATTAT
* * * *
6437 TTTATTTTCTGAATAAATGCATGCGAACTAGAAATCATGCGGTTAAG
1 TTTATTTCCAGAATAAATGCATGCGAACTAGAAAACATGAGGTTAAG
6484 TTTATTTCCAGAA-AAA-GCATG-GAACTAGAAAACATGAGGTTA
1 TTTATTTCCAGAATAAATGCATGCGAACTAGAAAACATGAGGTTA
6526 GGATGTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 19 0.50
45 5 0.13
46 3 0.08
47 11 0.29
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (47 bp):
TTTATTTCCAGAATAAATGCATGCGAACTAGAAAACATGAGGTTAAG
Found at i:10457 original size:28 final size:29
Alignment explanation
Indices: 10399--10560 Score: 188
Period size: 29 Copynumber: 5.7 Consensus size: 29
10389 GCACCCTAAT
* *
10399 TAATTACGAAACTAACACCCTTTTAAAAA
1 TAATTACAAAACTAGCACCCTTTTAAAAA
* *
10428 TATTTACAAAACTAACA-CCTTTTAAAAA
1 TAATTACAAAACTAGCACCCTTTTAAAAA
* * *
10456 TAATTATGAAAA-TATCACCC-TTTCAAAA
1 TAATTA-CAAAACTAGCACCCTTTTAAAAA
*
10484 TAATTTCAAAACTAGCACCCTTTTAAAAA
1 TAATTACAAAACTAGCACCCTTTTAAAAA
*
10513 TAATTATGAAAA-TAGCACCCTTTTAAAAA
1 TAATTA-CAAAACTAGCACCCTTTTAAAAA
*
10542 TAATTACAAAAATAGCACC
1 TAATTACAAAACTAGCACC
10561 TGTCGGGTCG
Statistics
Matches: 114, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
27 4 0.04
28 43 0.38
29 63 0.55
30 4 0.04
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.30
Consensus pattern (29 bp):
TAATTACAAAACTAGCACCCTTTTAAAAA
Found at i:10475 original size:57 final size:57
Alignment explanation
Indices: 10399--10561 Score: 222
Period size: 57 Copynumber: 2.9 Consensus size: 57
10389 GCACCCTAAT
* * *
10399 TAATTACGAAACTAACACCCTTTTAAAAATATTTACAAAACTAACACCTTTTAAAAA
1 TAATTATGAAAATAACACCCTTTTAAAAATATTTACAAAACTAGCACCTTTTAAAAA
* *
10456 TAATTATGAAAATATCACCC-TTTCAAAATAATTT-CAAAACTAGCACCCTTTTAAAAA
1 TAATTATGAAAATAACACCCTTTTAAAAAT-ATTTACAAAACTAGCA-CCTTTTAAAAA
* * *
10513 TAATTATGAAAATAGCACCCTTTTAAAAATAATTACAAAAATAGCACCT
1 TAATTATGAAAATAACACCCTTTTAAAAATATTTACAAAACTAGCACCT
10562 GTCGGGTCGG
Statistics
Matches: 93, Mismatches: 9, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
56 18 0.19
57 57 0.61
58 18 0.19
ACGTcount: A:0.48, C:0.18, G:0.04, T:0.30
Consensus pattern (57 bp):
TAATTATGAAAATAACACCCTTTTAAAAATATTTACAAAACTAGCACCTTTTAAAAA
Found at i:15097 original size:39 final size:40
Alignment explanation
Indices: 15036--15115 Score: 117
Period size: 39 Copynumber: 2.0 Consensus size: 40
15026 TCTAGAAAAT
*
15036 TAAAGCCTCCGGGTCATTTGTAAAACCTTCAGGTAATTTG
1 TAAAGCCTCCGGGTAATTTGTAAAACCTTCAGGTAATTTG
* * *
15076 TAAAGCCTTC-GGTAATTTGTAAAGCCTTCGGGTAATTTG
1 TAAAGCCTCCGGGTAATTTGTAAAACCTTCAGGTAATTTG
15115 T
1 T
15116 GAATCCTTTG
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 27 0.75
40 9 0.25
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.35
Consensus pattern (40 bp):
TAAAGCCTCCGGGTAATTTGTAAAACCTTCAGGTAATTTG
Found at i:15123 original size:20 final size:20
Alignment explanation
Indices: 15036--15135 Score: 121
Period size: 20 Copynumber: 5.0 Consensus size: 20
15026 TCTAGAAAAT
* *
15036 TAAAGCCTCCGGGTCATTTG
1 TAAAGCCTTCGGGTAATTTG
* *
15056 TAAAACCTTCAGGTAATTTG
1 TAAAGCCTTCGGGTAATTTG
15076 TAAAGCCTTC-GGTAATTTG
1 TAAAGCCTTCGGGTAATTTG
15095 TAAAGCCTTCGGGTAATTTG
1 TAAAGCCTTCGGGTAATTTG
* * * *
15115 TGAATCCTTTGGGTCATTTG
1 TAAAGCCTTCGGGTAATTTG
15135 T
1 T
15136 CAGTCTTTCA
Statistics
Matches: 70, Mismatches: 9, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
19 19 0.27
20 51 0.73
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (20 bp):
TAAAGCCTTCGGGTAATTTG
Found at i:15705 original size:23 final size:25
Alignment explanation
Indices: 15653--15705 Score: 65
Period size: 23 Copynumber: 2.2 Consensus size: 25
15643 TTATATTAAT
*
15653 ATATATATATATATATTATGTATTA
1 ATATATATATATATATTATGTATGA
*
15678 ATATAT-TAT-TATATTATTTATGA
1 ATATATATATATATATTATGTATGA
*
15701 TTATA
1 ATATA
15706 AATGGAGGCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.64
24 3 0.12
25 6 0.24
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (25 bp):
ATATATATATATATATTATGTATGA
Found at i:16708 original size:2 final size:2
Alignment explanation
Indices: 16701--16727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16691 TAGTTACTGT
16701 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
16728 TTAAGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28757 original size:30 final size:30
Alignment explanation
Indices: 28678--28757 Score: 92
Period size: 30 Copynumber: 2.7 Consensus size: 30
28668 AAGTATGCAT
*
28678 CTAATAACAAATATTGAAAAAATTAGGCTC
1 CTAATAATAAATATTGAAAAAATTAGGCTC
* *
28708 CTGATAATAAGTATTGAAAAAATT-GGC-C
1 CTAATAATAAATATTGAAAAAATTAGGCTC
*
28736 CTTAATAATAAATGTTAGAAAA
1 C-TAATAATAAATATT-GAAAA
28758 TGATATTGGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
28 2 0.05
29 14 0.33
30 26 0.62
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (30 bp):
CTAATAATAAATATTGAAAAAATTAGGCTC
Found at i:28893 original size:31 final size:30
Alignment explanation
Indices: 28828--28897 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 30
28818 TGCCCTTAAT
*
28828 AATAAATATTAAAAAAATTAAGCCTATAAT
1 AATAAATATTAAAAAAATTAAGCCTATAAC
* *
28858 AATAAATATTAGAAAAAATTATGTCC-ATTAC
1 AATAAATATTA-AAAAAATTAAG-CCTATAAC
28889 AATAAATAT
1 AATAAATAT
28898 CGGAGAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
30 11 0.31
31 22 0.63
32 2 0.06
ACGTcount: A:0.57, C:0.07, G:0.04, T:0.31
Consensus pattern (30 bp):
AATAAATATTAAAAAAATTAAGCCTATAAC
Found at i:36503 original size:61 final size:61
Alignment explanation
Indices: 36438--36561 Score: 187
Period size: 61 Copynumber: 2.0 Consensus size: 61
36428 ATTTTGATAA
* * * *
36438 ATATTAGGGTTACTTTTGA-CACTATACCTATAAATATATTAGCAAATGCATAATGTAAACT
1 ATATTAGGGGTAATTTT-ATCACTAGACCTATAAATATATTAGCAAATGCATAAGGTAAACT
*
36499 ATATTAGGGGTAATTTTATCATTAGACCTATAAATATATTAGCAAATGCATAAGGTAAACT
1 ATATTAGGGGTAATTTTATCACTAGACCTATAAATATATTAGCAAATGCATAAGGTAAACT
36560 AT
1 AT
36562 GTATTTTTGT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 1 0.02
61 56 0.98
ACGTcount: A:0.40, C:0.11, G:0.13, T:0.35
Consensus pattern (61 bp):
ATATTAGGGGTAATTTTATCACTAGACCTATAAATATATTAGCAAATGCATAAGGTAAACT
Found at i:37492 original size:2 final size:2
Alignment explanation
Indices: 37480--37520 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
37470 GCGTACACAA
*
37480 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
37521 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:37525 original size:2 final size:2
Alignment explanation
Indices: 37520--37555 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
37510 TCTCTCTCTC
37520 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37556 GAGAGAGAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45144 original size:61 final size:60
Alignment explanation
Indices: 45097--45217 Score: 172
Period size: 61 Copynumber: 2.0 Consensus size: 60
45087 ATTTTGATAA
* * *
45097 ATATTAGGGTTACTTTTGA-CACTATACCTATAAATATATTAGCAAATGCATAATGTAAAC
1 ATATTAGGGGTAATTTT-ATCACTAGACCTATAAATATATTAGCAAATGCATAATGTAAAC
* *
45157 TATATTAGGGGTAATTTTATCATTAGACCTATAAATATATTAGCAAATGCATAAGGTAAAC
1 -ATATTAGGGGTAATTTTATCACTAGACCTATAAATATATTAGCAAATGCATAATGTAAAC
45218 TATGTATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
60 1 0.02
61 53 0.98
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (60 bp):
ATATTAGGGGTAATTTTATCACTAGACCTATAAATATATTAGCAAATGCATAATGTAAAC
Found at i:46150 original size:2 final size:2
Alignment explanation
Indices: 46138--46178 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
46128 GCGTACACAA
*
46138 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
46179 ATATATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:46183 original size:2 final size:2
Alignment explanation
Indices: 46178--46217 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
46168 TCTCTCTCTC
46178 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46218 GAGAGAGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.