Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007067.1 Hibiscus syriacus cultivar Beakdansim tig00018362_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: 62695
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:1928 original size:32 final size:32
Alignment explanation
Indices: 1869--1929 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
1859 TTAATCTCAC
* *
1869 AAATATCGAGGGTCCCCACGGTTATTTTTGTA
1 AAATATCGAGGGTCCCCACGATCATTTTTGTA
*
1901 AAATATCG-GGGATCCCTACGATCATTTTT
1 AAATATCGAGGG-TCCCCACGATCATTTTT
1930 CGAGGATCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 3 0.12
32 22 0.88
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (32 bp):
AAATATCGAGGGTCCCCACGATCATTTTTGTA
Found at i:11954 original size:25 final size:27
Alignment explanation
Indices: 11926--11976 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
11916 ATATATGTTG
11926 AAATTGTAG-TT-TTATTAA-ATTGATT
1 AAATTGTAGATTCTT-TTAATATTGATT
11951 AAATTGTAGATTCTTTTAATATTGAT
1 AAATTGTAGATTCTTTTAATATTGAT
11977 ATGTATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 9 0.39
26 6 0.26
27 8 0.35
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (27 bp):
AAATTGTAGATTCTTTTAATATTGATT
Found at i:12179 original size:16 final size:16
Alignment explanation
Indices: 12152--12184 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
12142 AGTTATACAA
12152 TTTTAAATTTAAATATT
1 TTTTAAATTTAAA-ATT
12169 TTTTAAA-TTAAAATT
1 TTTTAAATTTAAAATT
12184 T
1 T
12185 AATTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 5 0.31
17 7 0.44
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TTTTAAATTTAAAATT
Found at i:12204 original size:22 final size:23
Alignment explanation
Indices: 12150--12208 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
12140 ATAGTTATAC
*
12150 AATTTTAAATTTAAATATTTTTTA
1 AATTTTAAATTT-AATATTTTTAA
*
12174 AA-TTAAAATTTAAT-TTTTTAA
1 AATTTTAAATTTAATATTTTTAA
12195 AATTTTAAATTTAA
1 AATTTTAAATTTAA
12209 GTGTCTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 8 0.26
22 13 0.42
23 8 0.26
24 2 0.06
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATTTTAAATTTAATATTTTTAA
Found at i:15258 original size:18 final size:18
Alignment explanation
Indices: 15232--15266 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
15222 TCGAAATGAC
*
15232 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
15250 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
15267 CCGGATGACA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:16441 original size:24 final size:24
Alignment explanation
Indices: 16414--16527 Score: 160
Period size: 24 Copynumber: 4.8 Consensus size: 24
16404 TTCGATTTGA
16414 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
16438 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
16462 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* *
16486 ATTCTGATCTGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
16509 ATTTCTGATATGATACTTG
1 A-TTCTGATCTGATACTTG
16528 GCCTGATTTA
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
23 3 0.04
24 78 0.95
25 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:16546 original size:24 final size:24
Alignment explanation
Indices: 16466--16539 Score: 69
Period size: 24 Copynumber: 3.1 Consensus size: 24
16456 ACATGGATTC
* * *
16466 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* * *
16490 TGATCTGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
*
16514 TGATATGATACTTGGCCTGATTTA
1 TGATATGATACTTGACCTGATTTA
16538 TG
1 TG
16540 TTTTGATTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
23 2 0.05
24 41 0.95
ACGTcount: A:0.20, C:0.16, G:0.20, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:34620 original size:121 final size:122
Alignment explanation
Indices: 34401--34644 Score: 400
Period size: 121 Copynumber: 2.0 Consensus size: 122
34391 AAATTCTAAA
*
34401 TGATAATCATACTGTATATTCTCCTCAAACTATACTTCTCCTAACCCATTATATTCATTATGAAG
1 TGATAATCATACTGTATATTCTCCTCAAACTATACTGCTCCTAACCCA-TATATTCATTATGAAG
* * * *
34466 CTTTGACCAAGCTAAATAATCTAGAAAAGGAATAATTTGGTTGCCAAGATCTGAGGCC
65 CTTTGACCAACCTAAATAATCTAGAAAAAGAATAATTTGATTCCCAAGATCTGAGGCC
*
34524 TGATAATCATACTGTATATTCTCGTCAAACTATACTGCTCCTAACCCA-ATATTCATTATGAAGC
1 TGATAATCATACTGTATATTCTCCTCAAACTATACTGCTCCTAACCCATATATTCATTATGAAGC
* *
34588 TTTGACCAACCTAAATAATCTAGAAAAAGAATAATTTGATTCCCCAGTTCTGAGGCC
66 TTTGACCAACCTAAATAATCTAGAAAAAGAATAATTTGATTCCCAAGATCTGAGGCC
34645 AGTATAAACC
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
121 67 0.59
123 46 0.41
ACGTcount: A:0.34, C:0.21, G:0.12, T:0.32
Consensus pattern (122 bp):
TGATAATCATACTGTATATTCTCCTCAAACTATACTGCTCCTAACCCATATATTCATTATGAAGC
TTTGACCAACCTAAATAATCTAGAAAAAGAATAATTTGATTCCCAAGATCTGAGGCC
Found at i:35742 original size:20 final size:21
Alignment explanation
Indices: 35709--35750 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
35699 GGAGACTGCA
35709 CAGGCTGATAAAATTGAGGTG
1 CAGGCTGATAAAATTGAGGTG
* *
35730 CAGG-TGATGAAATTGATGTG
1 CAGGCTGATAAAATTGAGGTG
35750 C
1 C
35751 CAGCTGGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (21 bp):
CAGGCTGATAAAATTGAGGTG
Found at i:43068 original size:16 final size:16
Alignment explanation
Indices: 43030--43073 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
43020 ACTGATCGAA
* *
43030 ATATATTTTTACATAC
1 ATATATTTTTAAAAAC
* *
43046 ATTTATTTTTAAAAAT
1 ATATATTTTTAAAAAC
43062 ATATATTTTTAA
1 ATATATTTTTAA
43074 TTTTTTTTGA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (16 bp):
ATATATTTTTAAAAAC
Found at i:46373 original size:3 final size:3
Alignment explanation
Indices: 46365--46392 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
46355 AAGCTTTCTC
46365 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
46393 GTCGAGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:47959 original size:25 final size:24
Alignment explanation
Indices: 47931--47985 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 24
47921 TTAAATGAAA
47931 AATAAATCAT-TTAAATTAAGTTAAT
1 AATAAAT-ATATTAAA-TAAGTTAAT
*
47956 AATAAAATATATTTAATAAGTTAAT
1 AAT-AAATATATTAAATAAGTTAAT
47981 -ATAAA
1 AATAAA
47986 AAGATATATT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
23 3 0.11
24 2 0.07
25 14 0.52
26 8 0.30
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (24 bp):
AATAAATATATTAAATAAGTTAAT
Found at i:47984 original size:27 final size:25
Alignment explanation
Indices: 47947--47996 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 25
47937 TCATTTAAAT
47947 TAAGTTAATAATAAA-ATATATTTAA
1 TAAGTTAATAA-AAAGATATATTTAA
47972 TAAGTTAATATAAAAAGATATATTT
1 TAAGTT-A-ATAAAAAGATATATTT
47997 TTTAAAGTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
25 6 0.27
26 4 0.18
27 12 0.55
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (25 bp):
TAAGTTAATAAAAAGATATATTTAA
Found at i:59608 original size:28 final size:28
Alignment explanation
Indices: 59577--59669 Score: 71
Period size: 29 Copynumber: 3.2 Consensus size: 28
59567 AGAAGAATTC
59577 TTTTTTCCAAATAATTTTAGGATTTGTA
1 TTTTTTCCAAATAATTTTAGGATTTGTA
** * * * * *
59605 TTTTTTTTTAATTGAGTTTA-TATTTGAAGAA
1 -TTTTTTCCAAATAATTTTAGGATTT---GTA
*
59636 TCTTTTCCAAATAATTTTAGGATTTGTA
1 TTTTTTCCAAATAATTTTAGGATTTGTA
59664 TTTTTT
1 TTTTTT
59670 TAATTTATTG
Statistics
Matches: 44, Mismatches: 16, Indels: 9
0.64 0.23 0.13
Matches are distributed among these distances:
28 11 0.25
29 14 0.32
30 13 0.30
31 6 0.14
ACGTcount: A:0.27, C:0.05, G:0.11, T:0.57
Consensus pattern (28 bp):
TTTTTTCCAAATAATTTTAGGATTTGTA
Found at i:59657 original size:59 final size:63
Alignment explanation
Indices: 59547--59686 Score: 216
Period size: 59 Copynumber: 2.2 Consensus size: 63
59537 AAAAACATGA
59547 ATTAATTGAGTTTATATTTGAGAAGAATTCTTTTTTCCAAATAATTTTAGGATTTGTATTTTTTT
1 ATTAATTGAGTTTATATTT-AGAAGAATTC-TTTTTCCAAATAATTTTAGGATTTGTATTTTTTT
59612 -TTAATTGAGTTTATATTT-GAAGAA-TC-TTTTCCAAATAATTTTAGGATTTGTATTTTTTT
1 ATTAATTGAGTTTATATTTAGAAGAATTCTTTTTCCAAATAATTTTAGGATTTGTATTTTTTT
*
59671 AATTTATTGAGTTTAT
1 -ATTAATTGAGTTTAT
59687 TGAGTTTAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 8
0.89 0.01 0.10
Matches are distributed among these distances:
59 33 0.46
61 15 0.21
62 6 0.08
64 18 0.25
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.54
Consensus pattern (63 bp):
ATTAATTGAGTTTATATTTAGAAGAATTCTTTTTCCAAATAATTTTAGGATTTGTATTTTTTT
Done.