Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007081.1 Hibiscus syriacus cultivar Beakdansim tig00018479_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: 60309
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9371 original size:21 final size:20
Alignment explanation
Indices: 9347--9385 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
9337 TATCAAGGCC
9347 TTTGTTGAAGCCATGAAATAT
1 TTTGTTGAAGCCAT-AAATAT
9368 TTTGTTGAAGCCATAAAT
1 TTTGTTGAAGCCATAAAT
9386 TCTTACAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.33, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTTGAAGCCATAAATAT
Found at i:10171 original size:42 final size:43
Alignment explanation
Indices: 10122--10202 Score: 110
Period size: 42 Copynumber: 1.9 Consensus size: 43
10112 AAGAAAAATA
*
10122 TGCAAGAGTAAACAAATAAAAATTGCTAAAGC-AAAAATTAAT
1 TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAATTAAT
** * *
10164 TGCAAGAGTAAGTAAATAAAAGTTGATAAGGCTAAAAAT
1 TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAAT
10203 GTTCGAGTTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
42 27 0.82
43 6 0.18
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.22
Consensus pattern (43 bp):
TGCAAGAGTAAACAAATAAAAATTGATAAAGCTAAAAATTAAT
Found at i:14043 original size:20 final size:19
Alignment explanation
Indices: 14011--14057 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
14001 TTGTTTCCAT
14011 ATTCAAGAA-AATAATATTAA
1 ATTCAA-AATAAT-ATATTAA
*
14031 ATTCAAAATAATATTTTAA
1 ATTCAAAATAATATATTAA
14050 A-TCAAAAT
1 ATTCAAAAT
14058 TTTACCCTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 7 0.28
19 9 0.36
20 9 0.36
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.34
Consensus pattern (19 bp):
ATTCAAAATAATATATTAA
Found at i:14051 original size:19 final size:16
Alignment explanation
Indices: 14018--14057 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 16
14008 CATATTCAAG
14018 AAAATAATATTAAATTC
1 AAAATAATATTAAA-TC
14035 AAAATAATATTTTAAATC
1 AAAATAATA--TTAAATC
14053 AAAAT
1 AAAAT
14058 TTTACCCTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 7 0.33
19 5 0.24
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (16 bp):
AAAATAATATTAAATC
Found at i:21202 original size:22 final size:21
Alignment explanation
Indices: 21141--21202 Score: 79
Period size: 22 Copynumber: 2.9 Consensus size: 21
21131 TTGGTGCAGA
*
21141 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATACCCCC-TGAAG
* *
21163 GGGAACCGATTCCCCCTGTAG
1 GGGAACCGATACCCCCTGAAG
21184 GGGAACCGATAACCCCCTG
1 GGGAACCGAT-ACCCCCTG
21203 GGGTTCTGGT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 14 0.40
22 21 0.60
ACGTcount: A:0.24, C:0.32, G:0.27, T:0.16
Consensus pattern (21 bp):
GGGAACCGATACCCCCTGAAG
Found at i:22713 original size:18 final size:18
Alignment explanation
Indices: 22679--22715 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
22669 GAACAGCACA
*
22679 AGGAACAAGCTCCACCAG
1 AGGAACAAGCACCACCAG
*
22697 AGGAACAAGCACGACCAG
1 AGGAACAAGCACCACCAG
22715 A
1 A
22716 AGATCAAATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.43, C:0.30, G:0.24, T:0.03
Consensus pattern (18 bp):
AGGAACAAGCACCACCAG
Found at i:23988 original size:10 final size:10
Alignment explanation
Indices: 23957--23991 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 10
23947 GAAGCCATTG
23957 ATCAACAACA
1 ATCAACAACA
**
23967 AGAAACAACA
1 ATCAACAACA
23977 ATCAACAACA
1 ATCAACAACA
23987 ATCAA
1 ATCAA
23992 GAGAGAATCA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.63, C:0.26, G:0.03, T:0.09
Consensus pattern (10 bp):
ATCAACAACA
Found at i:24516 original size:29 final size:28
Alignment explanation
Indices: 24483--24554 Score: 103
Period size: 29 Copynumber: 2.6 Consensus size: 28
24473 AACTAAATAA
24483 ACACCAACTTTCTTTTTTCTCCTTCAACT
1 ACACCAACTTTCTTTTTT-TCCTTCAACT
*
24512 ACACCAACTTTCTTTCTTTTCCTTGAACT
1 ACACCAACTTTCTTT-TTTTCCTTCAACT
24541 ACACCAA-TTT-TTTT
1 ACACCAACTTTCTTTT
24555 AACTTCACCG
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 1 0.02
27 3 0.07
28 3 0.07
29 31 0.76
30 3 0.07
ACGTcount: A:0.22, C:0.31, G:0.01, T:0.46
Consensus pattern (28 bp):
ACACCAACTTTCTTTTTTTCCTTCAACT
Found at i:25108 original size:19 final size:21
Alignment explanation
Indices: 25084--25129 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
25074 ATTATTAGGG
*
25084 TAAACTAAC-A-TTTAGTACT
1 TAAACTAACAATTTTAGTAAT
*
25103 TAAACTATCAATTTTAGTAAT
1 TAAACTAACAATTTTAGTAAT
25124 TAAACT
1 TAAACT
25130 TTTATTTTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 8 0.35
20 1 0.04
21 14 0.61
ACGTcount: A:0.43, C:0.13, G:0.04, T:0.39
Consensus pattern (21 bp):
TAAACTAACAATTTTAGTAAT
Found at i:28675 original size:83 final size:83
Alignment explanation
Indices: 28588--28808 Score: 275
Period size: 83 Copynumber: 2.7 Consensus size: 83
28578 CGTTTTTCTA
* * * * ** *
28588 AAAACGCCGCAATAGGGTGCTAAATTAGCGGCGTTTAT-ATCACAAACGCTTCAATAGATTATAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTT-TGACCACAAACGCCACAATAGAGTATAA
* *
28652 ATTTTGCGGCGATTTAGCC
65 AATTTGCGGCGATTGAGCC
* * *
28671 AAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTGACCACAAACGCCACAATAGAGTATAAA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGACCACAAACGCCACAATAGAGTATAAA
*
28736 ATTTGCGGCGATTGAGTC
66 ATTTGCGGCGATTGAGCC
* * *
28754 AAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTTGA-CAAAAACGCCGCAATA
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGACCACAAACGCCACAATA
28809 TATTACACAT
Statistics
Matches: 118, Mismatches: 19, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
82 15 0.13
83 103 0.87
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (83 bp):
AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGACCACAAACGCCACAATAGAGTATAAA
ATTTGCGGCGATTGAGCC
Found at i:28719 original size:42 final size:40
Alignment explanation
Indices: 28588--28808 Score: 153
Period size: 41 Copynumber: 5.3 Consensus size: 40
28578 CGTTTTTCTA
* * *
28588 AAAACGCCGCAATAGGGTGCTAAATTAGCGGCGTTTAT-ATC
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTT-TGA-C
** ** * * *
28629 ACAAACGCTTCAATAGA-TTATAAATTTTGCGGCGATTTAGCC
1 A-AAACGCCGCAATAGAGTGGTAAA-TTGGCGGCG-TTTTGAC
* * *
28671 AAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTGACC
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGA-C
* * * *
28712 ACAAACGCCACAATAGAGT-ATAAAATTTGCGGCG-ATTGAGTC
1 A-AAACGCCGCAATAGAGTGGT-AAATTGGCGGCGTTTTGA--C
*
28754 AAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTTGAC
1 AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGAC
28794 AAAAACGCCGCAATA
1 -AAAACGCCGCAATA
28809 TATTACACAT
Statistics
Matches: 137, Mismatches: 31, Indels: 24
0.71 0.16 0.12
Matches are distributed among these distances:
40 5 0.04
41 71 0.52
42 58 0.42
43 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.23, T:0.23
Consensus pattern (40 bp):
AAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTTGAC
Found at i:37616 original size:21 final size:21
Alignment explanation
Indices: 37598--37683 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
37588 ATGAAGCAAG
*
37598 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
37619 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
37640 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
37661 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
37682 GG
1 GG
37684 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:37684 original size:21 final size:21
Alignment explanation
Indices: 37606--37698 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
37596 AGGGAAACAG
* *
37606 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
37628 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
37648 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
37669 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
37690 AGAGAGAAG
1 AGAGAGAAG
37699 TAATATATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:38169 original size:43 final size:42
Alignment explanation
Indices: 38051--38176 Score: 110
Period size: 43 Copynumber: 2.9 Consensus size: 42
38041 GTTTTTGATA
* * *
38051 AAAACGCCGCAAAATCTCAATACATATTCTGCGGCGTTTGTAAG
1 AAAACGCCGCTAAATATCAATACAT-TT-TGCGGCATTTGTAAG
* * * * * *
38095 AAAACGCCGGTAAAAATAAAAATATTCTGCGGCATTT-TAATG
1 AAAACGCCGCTAAATATCAATACATTTTGCGGCATTTGTAA-G
* *
38137 ATAAACGCCGCTAAATATCAATACCTTTTGCGGCGTTTGT
1 A-AAACGCCGCTAAATATCAATACATTTTGCGGCATTTGT
38177 TGAACAATCA
Statistics
Matches: 62, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
41 3 0.05
42 11 0.18
43 29 0.47
44 19 0.31
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (42 bp):
AAAACGCCGCTAAATATCAATACATTTTGCGGCATTTGTAAG
Found at i:41553 original size:19 final size:19
Alignment explanation
Indices: 41529--41576 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
41519 TCATTGATCA
41529 ATGATGTATGTACATGTGT
1 ATGATGTATGTACATGTGT
*
41548 ATGATGAATGTACATGTGT
1 ATGATGTATGTACATGTGT
*
41567 ATGAAGTATG
1 ATGATGTATG
41577 AATACATTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.27, T:0.38
Consensus pattern (19 bp):
ATGATGTATGTACATGTGT
Found at i:41597 original size:2 final size:2
Alignment explanation
Indices: 41590--41623 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
41580 ACATTCATAA
41590 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
41624 GTATTAAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42125 original size:23 final size:24
Alignment explanation
Indices: 42080--42129 Score: 61
Period size: 23 Copynumber: 2.1 Consensus size: 24
42070 ATCTTTTATA
42080 TATAGTTTAAAATTTTAAGTTAAAT
1 TATAGTTTAAAATTTTAAGTT-AAT
42105 TATA-TTT-AAATTATTAA-TTAAT
1 TATAGTTTAAAATT-TTAAGTTAAT
42127 TAT
1 TAT
42130 TACATAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 6 0.25
23 7 0.29
24 7 0.29
25 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (24 bp):
TATAGTTTAAAATTTTAAGTTAAT
Found at i:47763 original size:13 final size:13
Alignment explanation
Indices: 47747--47771 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47737 AATGTAAACT
47747 GTCAAAGGTCAAA
1 GTCAAAGGTCAAA
47760 GTCAAAGGTCAA
1 GTCAAAGGTCAA
47772 CACGCAGGTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.16, G:0.24, T:0.16
Consensus pattern (13 bp):
GTCAAAGGTCAAA
Found at i:48382 original size:25 final size:25
Alignment explanation
Indices: 48354--48413 Score: 111
Period size: 25 Copynumber: 2.4 Consensus size: 25
48344 GGGGTGACTA
48354 GGGATTTTGGGATTTTGGAAAATTG
1 GGGATTTTGGGATTTTGGAAAATTG
*
48379 GGGATTTTAGGATTTTGGAAAATTG
1 GGGATTTTGGGATTTTGGAAAATTG
48404 GGGATTTTGG
1 GGGATTTTGG
48414 TGTTTTATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (25 bp):
GGGATTTTGGGATTTTGGAAAATTG
Found at i:50967 original size:20 final size:19
Alignment explanation
Indices: 50920--50973 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
50910 ACTTAGGCTG
**
50920 GTTCAAGTTGACTCAGTTT
1 GTTCAAGTTGACTCAGTCA
*
50939 GGTCTAAGTTGACTCAGATCA
1 GTTC-AAGTTGACTCAG-TCA
50960 GTTCAAGTTGACTC
1 GTTCAAGTTGACTC
50974 GAATTGGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.10
20 22 0.76
21 4 0.14
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (19 bp):
GTTCAAGTTGACTCAGTCA
Found at i:55459 original size:25 final size:27
Alignment explanation
Indices: 55425--55480 Score: 89
Period size: 25 Copynumber: 2.1 Consensus size: 27
55415 GGTCAATAGG
55425 CTTTCGGGTTTGAA-T-ACAAAATGGA
1 CTTTCGGGTTTGAATTGACAAAATGGA
55450 CTTTCGGGTTTGAATTTGACAAAATGGA
1 CTTTCGGGTTTGAA-TTGACAAAATGGA
55478 CTT
1 CTT
55481 CGAATTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 14 0.50
27 1 0.04
28 13 0.46
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (27 bp):
CTTTCGGGTTTGAATTGACAAAATGGA
Found at i:55687 original size:20 final size:20
Alignment explanation
Indices: 55664--55710 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
55654 TTGGTTTGAT
* *
55664 TTGACTCATATTGAATCAAG
1 TTGACTCAAATCGAATCAAG
* *
55684 TTGACTCAAATCGATTCGAG
1 TTGACTCAAATCGAATCAAG
55704 TTGACTC
1 TTGACTC
55711 GAACCAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (20 bp):
TTGACTCAAATCGAATCAAG
Found at i:55720 original size:20 final size:20
Alignment explanation
Indices: 55682--55720 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
55672 TATTGAATCA
* *
55682 AGTTGACTCAAATCGATTCG
1 AGTTGACTCAAACCAATTCG
*
55702 AGTTGACTCGAACCAATTC
1 AGTTGACTCAAACCAATTC
55721 TAAGTCGGGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.28
Consensus pattern (20 bp):
AGTTGACTCAAACCAATTCG
Done.