Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000192.1 Hibiscus syriacus cultivar Beakdansim tig00000342_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: 57124
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:18079 original size:3 final size:3
Alignment explanation
Indices: 18071--18103 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
18061 AGCAACATTT
18071 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
18104 GATTGGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:18606 original size:136 final size:136
Alignment explanation
Indices: 18355--18680 Score: 481
Period size: 136 Copynumber: 2.4 Consensus size: 136
18345 GATGGATTTG
* * * *
18355 AACTATCTCGAGCGATATGATGTTGATCCAACTCCTCATATGATGGAATCGAGTCAAAATGTGAT
1 AACTATCTCGAGCGAGATGATGTTGATCCAACTCCTTATATGATGGAATCGAGCCAAAAGGTGAT
18420 ATTGATCCAACTCCTTATATAATGGATTTAAACCTCAAGTAAAATGATATTGAAGTTTAAGCTTC
66 ATTGATCCAACTCCTTATATAATGGATTTAAACCTCAAGTAAAATGATATTGAAGTTTAAGCTTC
**
18485 AAGGGA
131 AAGAAA
* * **
18491 AACTATCTCGAGCGAGATGATGTTGATCCAACTTCTTACATGATGGAATTTAGCCAAAAGGTGAT
1 AACTATCTCGAGCGAGATGATGTTGATCCAACTCCTTATATGATGGAATCGAGCCAAAAGGTGAT
* * * * * *
18556 ATTGATCCAACTCCTTATGTGATGGATTTAAACCTCAAGTGAAATTATATTGAAGTTTGAGTTTC
66 ATTGATCCAACTCCTTATATAATGGATTTAAACCTCAAGTAAAATGATATTGAAGTTTAAGCTTC
18621 AAGAAA
131 AAGAAA
* * *
18627 AACTATCCCGAGCGAGATGATGTTGATCTAACTCCTTATGTGATGGAATCGAGC
1 AACTATCTCGAGCGAGATGATGTTGATCCAACTCCTTATATGATGGAATCGAGC
18681 AATGGTTTAA
Statistics
Matches: 167, Mismatches: 23, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
136 167 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.31
Consensus pattern (136 bp):
AACTATCTCGAGCGAGATGATGTTGATCCAACTCCTTATATGATGGAATCGAGCCAAAAGGTGAT
ATTGATCCAACTCCTTATATAATGGATTTAAACCTCAAGTAAAATGATATTGAAGTTTAAGCTTC
AAGAAA
Found at i:21233 original size:21 final size:22
Alignment explanation
Indices: 21204--21244 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
21194 ATCGCATGTT
21204 TCTTGAATATATCT-TCTATCA
1 TCTTGAATATATCTATCTATCA
*
21225 TCTTTAATATATCTATCTAT
1 TCTTGAATATATCTATCTAT
21245 GAGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.29, C:0.17, G:0.02, T:0.51
Consensus pattern (22 bp):
TCTTGAATATATCTATCTATCA
Found at i:24041 original size:20 final size:20
Alignment explanation
Indices: 24016--24056 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
24006 TAATTCCACC
24016 AAATGCAACTACATGATCCT
1 AAATGCAACTACATGATCCT
* * *
24036 AAATGCATCTATATGGTCCT
1 AAATGCAACTACATGATCCT
24056 A
1 A
24057 CATGTTCCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (20 bp):
AAATGCAACTACATGATCCT
Found at i:26720 original size:9 final size:9
Alignment explanation
Indices: 26698--26740 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
26688 AATCCTAAAA
26698 GAAAA-AAT
1 GAAAATAAT
26706 GAAAAATAAT
1 G-AAAATAAT
26716 GAAAATAACT
1 GAAAATAA-T
26726 GAAAATAAT
1 GAAAATAAT
*
26735 AAAAAT
1 GAAAAT
26741 TTGCGTGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
8 1 0.03
9 17 0.55
10 13 0.42
ACGTcount: A:0.70, C:0.02, G:0.09, T:0.19
Consensus pattern (9 bp):
GAAAATAAT
Found at i:39020 original size:20 final size:20
Alignment explanation
Indices: 38995--39034 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
38985 GGTTATGCCA
38995 CTGTTAGATTTTTAAATTAG
1 CTGTTAGATTTTTAAATTAG
39015 CTGTTAGATTTTTAAATTAG
1 CTGTTAGATTTTTAAATTAG
39035 TAAATTGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
CTGTTAGATTTTTAAATTAG
Found at i:40740 original size:36 final size:36
Alignment explanation
Indices: 40700--40769 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
40690 AAGTCTCTGC
* * * *
40700 AGGTTCAGCTCCGATCAAGCTGGTAATTCCTTATGT
1 AGGTTCAACACCGATCAAACTAGTAATTCCTTATGT
*
40736 AGGTTCAACACTGATCAAACTAGTAATTCCTTAT
1 AGGTTCAACACCGATCAAACTAGTAATTCCTTAT
40770 AGACATAAGG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (36 bp):
AGGTTCAACACCGATCAAACTAGTAATTCCTTATGT
Found at i:44795 original size:2 final size:2
Alignment explanation
Indices: 44788--44855 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
44778 CATGCCAACC
44788 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
44830 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
44856 TGTTTTTTAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45266 original size:2 final size:2
Alignment explanation
Indices: 45254--45295 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
45244 AAAAATTCTC
45254 AT AT A- 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
45295 A
1 A
45296 ATAAAATTAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48406 original size:30 final size:30
Alignment explanation
Indices: 48355--48462 Score: 105
Period size: 30 Copynumber: 3.6 Consensus size: 30
48345 CCCATGAAAG
* *
48355 CAAACCAAAGAAAGA-AGAAACCCACCACAA
1 CAAACCAAAGAAA-ACAAAAACCCATCACAA
*
48385 CAAACCAAAGAAAACAAAAACCC-TCACAG
1 CAAACCAAAGAAAACAAAAACCCATCACAA
* * *
48414 CAGAAGCAAAGGAAACAAAAGCCCATCACAA
1 CA-AACCAAAGAAAACAAAAACCCATCACAA
*
48445 CAAAAACAAAG-AAACAAA
1 C-AAACCAAAGAAAACAAA
48463 TATAGGGGTA
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
29 7 0.11
30 45 0.68
31 13 0.20
32 1 0.02
ACGTcount: A:0.61, C:0.27, G:0.10, T:0.02
Consensus pattern (30 bp):
CAAACCAAAGAAAACAAAAACCCATCACAA
Found at i:48766 original size:22 final size:22
Alignment explanation
Indices: 48741--48809 Score: 138
Period size: 22 Copynumber: 3.1 Consensus size: 22
48731 ATTGGTTTAA
48741 TTATAAATTTAGTCCTTCAACT
1 TTATAAATTTAGTCCTTCAACT
48763 TTATAAATTTAGTCCTTCAACT
1 TTATAAATTTAGTCCTTCAACT
48785 TTATAAATTTAGTCCTTCAACT
1 TTATAAATTTAGTCCTTCAACT
48807 TTA
1 TTA
48810 AGTATTGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.32, C:0.17, G:0.04, T:0.46
Consensus pattern (22 bp):
TTATAAATTTAGTCCTTCAACT
Found at i:49475 original size:17 final size:18
Alignment explanation
Indices: 49455--49489 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
49445 ATTATTTAAT
49455 AAATTTA-AATTAAAAAA
1 AAATTTATAATTAAAAAA
*
49472 AAATTTATATTTAAAAAA
1 AAATTTATAATTAAAAAA
49490 TTAAATAAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTTATAATTAAAAAA
Found at i:50576 original size:2 final size:2
Alignment explanation
Indices: 50503--50563 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
50493 GTTTTATTTT
50503 TA 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 TA
50545 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
50564 GATTCCTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:50619 original size:64 final size:64
Alignment explanation
Indices: 50544--50663 Score: 213
Period size: 64 Copynumber: 1.9 Consensus size: 64
50534 ATATATATAT
* *
50544 ATATATATATATATATATATGATTCCTATATATTAGATTTAGCTCATTGATTAAGGCTTTCTTG
1 ATATATATATATATATATATGATTCCTAAATATTAGATTTAGCTCATGGATTAAGGCTTTCTTG
*
50608 ATATATATATATATATATATGATTCCTAAATATTAGATTTAGTTCATGGATTAAGG
1 ATATATATATATATATATATGATTCCTAAATATTAGATTTAGCTCATGGATTAAGG
50664 GTTGCTTGGT
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 53 1.00
ACGTcount: A:0.36, C:0.07, G:0.12, T:0.45
Consensus pattern (64 bp):
ATATATATATATATATATATGATTCCTAAATATTAGATTTAGCTCATGGATTAAGGCTTTCTTG
Found at i:56765 original size:15 final size:15
Alignment explanation
Indices: 56747--56802 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
56737 TAACTGGTTT
56747 CGGTTTTAAAAAAAC
1 CGGTTTTAAAAAAAC
*
56762 CGGTTTTTTTAAAAAAC
1 CGG--TTTTAAAAAAAC
*
56779 CGGTTATAAAAAAAC
1 CGGTTTTAAAAAAAC
*
56794 CGATTTTAA
1 CGGTTTTAA
56803 TATTCCAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 20 0.59
17 14 0.41
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.32
Consensus pattern (15 bp):
CGGTTTTAAAAAAAC
Found at i:56775 original size:17 final size:17
Alignment explanation
Indices: 56750--56800 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
56740 CTGGTTTCGG
56750 TTTTAAAAAAACCGGTT
1 TTTTAAAAAAACCGGTT
*
56767 TTTTTAAAAAACCGG--
1 TTTTAAAAAAACCGGTT
* *
56782 TTATAAAAAAACCGATT
1 TTTTAAAAAAACCGGTT
56799 TT
1 TT
56801 AATATTCCAG
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 12 0.43
17 16 0.57
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (17 bp):
TTTTAAAAAAACCGGTT
Done.