Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008672.1 Hibiscus syriacus cultivar Beakdansim tig00111685_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: 46452
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:5610 original size:17 final size:17
Alignment explanation
Indices: 5579--5612 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5569 ACGTGTATTT
**
5579 TATTGTTAATGTGATAA
1 TATTGTTAACATGATAA
5596 TATTGTTAACATGATAA
1 TATTGTTAACATGATAA
5613 CTTACACGGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.03, G:0.15, T:0.44
Consensus pattern (17 bp):
TATTGTTAACATGATAA
Found at i:5821 original size:2 final size:2
Alignment explanation
Indices: 5814--5840 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5804 CTTATTATTA
5814 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
5841 ATGGTATTGT
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8105 original size:20 final size:21
Alignment explanation
Indices: 8080--8119 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
8070 TCTATTAGTT
*
8080 ATTAGATAGGATCA-TTTTTA
1 ATTAGATAGAATCAGTTTTTA
8100 ATTAGATAGAATCAGTTTTT
1 ATTAGATAGAATCAGTTTTT
8120 TATTCTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (21 bp):
ATTAGATAGAATCAGTTTTTA
Found at i:8142 original size:53 final size:52
Alignment explanation
Indices: 8027--8176 Score: 257
Period size: 53 Copynumber: 2.9 Consensus size: 52
8017 CTAAATTAAA
* * *
8027 TATTAGATAGGACCAGTTTTAATGAGATAGAATCAGTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
8079 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTTATTCTATTAGT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAG-TTTTTATTCTATTAGT
8132 TATTAGATAGGATCATTTTTAATTAGATAGAATCA-TTTTTATTCT
1 TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCT
8177 GTTGCTAATT
Statistics
Matches: 94, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.11
52 33 0.35
53 51 0.54
ACGTcount: A:0.33, C:0.07, G:0.14, T:0.47
Consensus pattern (52 bp):
TATTAGATAGGATCATTTTTAATTAGATAGAATCAGTTTTTATTCTATTAGT
Found at i:8158 original size:20 final size:20
Alignment explanation
Indices: 8133--8172 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
8123 TCTATTAGTT
*
8133 ATTAGATAGGATCATTTTTA
1 ATTAGATAGAATCATTTTTA
8153 ATTAGATAGAATCATTTTTA
1 ATTAGATAGAATCATTTTTA
8173 TTCTGTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (20 bp):
ATTAGATAGAATCATTTTTA
Found at i:13273 original size:21 final size:21
Alignment explanation
Indices: 13236--13279 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
13226 CATTCATTAA
*
13236 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
13256 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
13278 TT
1 TT
13280 TACTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 7 0.35
21 9 0.45
22 4 0.20
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:13608 original size:23 final size:24
Alignment explanation
Indices: 13582--13628 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
13572 CCATTTATAT
13582 TTTA-TTATATTTTC-TTCTTTTTC
1 TTTATTTATATTTTCGTT-TTTTTC
*
13605 TTTATTTGTATTTTCGTTTTTTTC
1 TTTATTTATATTTTCGTTTTTTTC
13629 CTTTGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 15 0.71
25 2 0.10
ACGTcount: A:0.11, C:0.11, G:0.04, T:0.74
Consensus pattern (24 bp):
TTTATTTATATTTTCGTTTTTTTC
Found at i:24115 original size:1 final size:1
Alignment explanation
Indices: 24109--24157 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
24099 TCCTAAGTTG
* * * *
24109 AAAAAAAAAGAAAAAAAAAGAAAAAAAAAAGAAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
24158 CGTTTGGGTG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (1 bp):
A
Found at i:24123 original size:10 final size:10
Alignment explanation
Indices: 24108--24157 Score: 75
Period size: 10 Copynumber: 4.9 Consensus size: 10
24098 GTCCTAAGTT
24108 GAAAAAAAAA
1 GAAAAAAAAA
24118 GAAAAAAAAA
1 GAAAAAAAAA
24128 GAAAAAAAAAA
1 G-AAAAAAAAA
24139 GAAAAAAAAA
1 GAAAAAAAAA
24149 -AAGAAAAAA
1 GAA-AAAAAA
24158 CGTTTGGGTG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
9 2 0.05
10 26 0.68
11 10 0.26
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:24126 original size:12 final size:11
Alignment explanation
Indices: 24109--24157 Score: 82
Period size: 11 Copynumber: 4.5 Consensus size: 11
24099 TCCTAAGTTG
24109 AAAAAAAAAG-
1 AAAAAAAAAGA
24119 AAAAAAAAAGA
1 AAAAAAAAAGA
24130 AAAAAAAAAGAA
1 AAAAAAAAAG-A
24142 AAAAAAAAAGA
1 AAAAAAAAAGA
24153 AAAAA
1 AAAAA
24158 CGTTTGGGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
10 10 0.27
11 16 0.43
12 11 0.30
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAGA
Found at i:25124 original size:105 final size:105
Alignment explanation
Indices: 24942--25575 Score: 1142
Period size: 105 Copynumber: 6.0 Consensus size: 105
24932 AGGTTTTACC
24942 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
25007 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
25047 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
25112 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
25152 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCATACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
25217 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
25257 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCAAG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
25322 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* * *
25362 CAGAGCTAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
25427 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
25467 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGGCAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
25532 ACGAAGGGACCGCTGGTTGTCAATAAACAATTACCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCAATTT
25573 CAG
1 CAG
25576 CTTCACAACG
Statistics
Matches: 514, Mismatches: 14, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
105 502 0.98
106 12 0.02
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:25658 original size:20 final size:20
Alignment explanation
Indices: 25633--25674 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
25623 CCAGAACTCT
25633 GAGTTCGATTTCAACTTCAC
1 GAGTTCGATTTCAACTTCAC
*
25653 GAGTTCGATTTCAATTTCAC
1 GAGTTCGATTTCAACTTCAC
25673 GA
1 GA
25675 CGAAGGATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (20 bp):
GAGTTCGATTTCAACTTCAC
Found at i:27360 original size:21 final size:21
Alignment explanation
Indices: 27323--27367 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
27313 CATTCATTAA
*
27323 TTATTTATTCCATTTTTA-TT
1 TTATTTATTCCACTTTTACTT
*
27343 TTATTTATTTCCCCTTTTACTT
1 TTATTTA-TTCCACTTTTACTT
27365 TTA
1 TTA
27368 CTATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 7 0.33
21 9 0.43
22 5 0.24
ACGTcount: A:0.18, C:0.16, G:0.00, T:0.67
Consensus pattern (21 bp):
TTATTTATTCCACTTTTACTT
Found at i:27618 original size:16 final size:17
Alignment explanation
Indices: 27586--27618 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
27576 ATTACGTATA
*
27586 TTTTTTTTTCCTCTTTC
1 TTTTTTTTTCATCTTTC
27603 TTTTTTTTTCAT-TTTC
1 TTTTTTTTTCATCTTTC
27619 ATTGCTTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTTTTTCATCTTTC
Found at i:27694 original size:23 final size:24
Alignment explanation
Indices: 27668--27714 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
27658 CCATTTATAT
27668 TTTA-TTATATTTTC-TTCTTTTTC
1 TTTATTTATATTTTCATT-TTTTTC
*
27691 TTTATTTGTATTTTCATTTTTTTC
1 TTTATTTATATTTTCATTTTTTTC
27715 CTTTGCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 15 0.71
25 2 0.10
ACGTcount: A:0.13, C:0.11, G:0.02, T:0.74
Consensus pattern (24 bp):
TTTATTTATATTTTCATTTTTTTC
Found at i:38978 original size:11 final size:13
Alignment explanation
Indices: 38947--38976 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38937 TATAAAAATT
38947 ATATATTATTTTA
1 ATATATTATTTTA
38960 ATATATTATTTTA
1 ATATATTATTTTA
38973 ATAT
1 ATAT
38977 TAATAATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
ATATATTATTTTA
Found at i:41832 original size:22 final size:21
Alignment explanation
Indices: 41780--41840 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
41770 GGCATGTGAA
* *
41780 ATCTATGTCCCGAAGGACGTC
1 ATCTATGTCCCGAATGACCTC
41801 ATCTATGTCCCGAATGACCT-
1 ATCTATGTCCCGAATGACCTC
*
41821 ATTCATATGTCCCCAATGAC
1 A-TC-TATGTCCCGAATGAC
41841 ATAGGTACTT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 1 0.03
21 20 0.57
22 14 0.40
ACGTcount: A:0.26, C:0.30, G:0.16, T:0.28
Consensus pattern (21 bp):
ATCTATGTCCCGAATGACCTC
Found at i:42156 original size:20 final size:18
Alignment explanation
Indices: 42117--42156 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 18
42107 TGCATACCTC
*
42117 ATGTTCATATAATCTCTT
1 ATGTTCATATAATATCTT
42135 ATGTTCATATCACATATCTT
1 ATGTTCATAT-A-ATATCTT
42155 AT
1 AT
42157 AACATATTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 10 0.53
19 1 0.05
20 8 0.42
ACGTcount: A:0.30, C:0.17, G:0.05, T:0.47
Consensus pattern (18 bp):
ATGTTCATATAATATCTT
Found at i:43211 original size:17 final size:18
Alignment explanation
Indices: 43189--43222 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
43179 CCATAACTTA
43189 TCATT-CTTTAAGTTTCT
1 TCATTCCTTTAAGTTTCT
43206 TCATTCCTTTAAGTTTC
1 TCATTCCTTTAAGTTTC
43223 AATAGTCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.18, C:0.21, G:0.06, T:0.56
Consensus pattern (18 bp):
TCATTCCTTTAAGTTTCT
Found at i:45271 original size:64 final size:63
Alignment explanation
Indices: 45203--45391 Score: 151
Period size: 64 Copynumber: 2.9 Consensus size: 63
45193 TACACTGATA
*
45203 GTGCATCGATGCATAAATATGC-TTCGATGTTTTGAA-AA-AGCCT-GAGTGCATCGATGCA-TG
1 GTGCATCG-TGCATAAA-AT-CATTCGATGTTTT-AATAATA-CATGGAGTGCATCGATGCATTG
*
45263 TCTT
61 T-AT
45267 GTGCATCTGTGCATAAAATCAATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATTGTAT
1 GTGCATC-GTGCATAAAATC-ATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATTGTAT
* * * * *
45332 GTGCATCGGTACACT-AAAGCTATTCGATG-TTCAATTAAAACA-AGAGTGCATCGATGCATT
1 GTGCATC-GTGCA-TAAAATC-ATTCGATGTTTTAA-TAATACATGGAGTGCATCGATGCATT
45392 AATTTATGCA
Statistics
Matches: 107, Mismatches: 9, Indels: 18
0.80 0.07 0.13
Matches are distributed among these distances:
62 1 0.01
63 4 0.04
64 51 0.48
65 47 0.44
66 4 0.04
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (63 bp):
GTGCATCGTGCATAAAATCATTCGATGTTTTAATAATACATGGAGTGCATCGATGCATTGTAT
Found at i:45337 original size:65 final size:65
Alignment explanation
Indices: 45246--45391 Score: 165
Period size: 65 Copynumber: 2.3 Consensus size: 65
45236 GAAAAAGCCT
* * * * * *
45246 GAGTGCATCGATGCA-TGTCTTGTGCATCTGTGCA-TAAAATCAATTCGATGTTTTAA-TAATAC
1 GAGTGCATCGATGCATTGTCATGTGCATCGGTACACT-AAAGCAATTCGATG-TTCAATTAAAAC
*
45308 ATG
64 A-A
*
45311 GAGTGCATCGATGCATTGT-ATGTGCATCGGTACACTAAAGCTATTCGATGTTCAATTAAAACAA
1 GAGTGCATCGATGCATTGTCATGTGCATCGGTACACTAAAGCAATTCGATGTTCAATTAAAACAA
45375 GAGTGCATCGATGCATT
1 GAGTGCATCGATGCATT
45392 AATTTATGCA
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
64 21 0.30
65 45 0.64
66 4 0.06
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (65 bp):
GAGTGCATCGATGCATTGTCATGTGCATCGGTACACTAAAGCAATTCGATGTTCAATTAAAACAA
Found at i:45733 original size:13 final size:12
Alignment explanation
Indices: 45711--45738 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
45701 ATTTTTAAGA
45711 AAATCATTTTTG
1 AAATCATTTTTG
45723 AAATCATTTTTG
1 AAATCATTTTTG
45735 AAAT
1 AAAT
45739 TGTTCCCCCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.46
Consensus pattern (12 bp):
AAATCATTTTTG
Done.