Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001461.1 Hibiscus syriacus cultivar Beakdansim tig00002823_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: 73881
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:6396 original size:19 final size:20
Alignment explanation
Indices: 6354--6391 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6344 CCCCCTTTGA
*
6354 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
6374 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
6392 TAGGGTTCTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:10751 original size:88 final size:89
Alignment explanation
Indices: 10623--10874 Score: 276
Period size: 88 Copynumber: 2.8 Consensus size: 89
10613 TTATTTGTGT
* * * *
10623 TTTAGTCCCTTAAGTTTTTG-TTTTGCTATTTTAGTCCCTTAAGTTTATGTTTTTGCTATTTTAG
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCTATTTTAGTCCCTTAAATGTATATTTTTACTATTTTAG
* *
10687 TCCTTTAAA-TGTATTTTTACTAA
66 TCCTTTAAATTCTATTTATACTAA
*
10710 TTTAGTCCCTTAAGTTTTTGTTTTTG-TGATTTTAGTCCCTTAAATGTCTATTTTTACTATTTTA
1 TTTAGTCCCTTAAGTTTTTGTTTTTGCT-ATTTTAGTCCCTTAAATGTATATTTTTACTATTTTA
* *
10774 GTCCTTTAAATTTCTATTTATGCTAT
65 GTCCTTTAAA-TTCTATTTATACTAA
* * * * * * * *
10800 TTTAATCCCTTAAGTTTTGTTTTTCTTTCTATTTTAGTCCTTTTAATTTTTATTTTTGCTATTTT
1 TTTAGTCCCTTAAGTTTT-TGTTT-TTGCTATTTTAGTCCCTTAAATGTATATTTTTACTATTTT
* *
10865 AATCCCTTAA
64 AGTCCTTTAA
10875 GTTTTGATTT
Statistics
Matches: 139, Mismatches: 19, Indels: 9
0.83 0.11 0.05
Matches are distributed among these distances:
87 21 0.15
88 46 0.33
90 27 0.19
91 4 0.03
92 40 0.29
93 1 0.01
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.58
Consensus pattern (89 bp):
TTTAGTCCCTTAAGTTTTTGTTTTTGCTATTTTAGTCCCTTAAATGTATATTTTTACTATTTTAG
TCCTTTAAATTCTATTTATACTAA
Found at i:10901 original size:29 final size:29
Alignment explanation
Indices: 10622--10924 Score: 272
Period size: 30 Copynumber: 10.1 Consensus size: 29
10612 TTTATTTGTG
10622 TTTTAGTCCCTTAAGTTTT-TGTTTTGCTA
1 TTTTAGTCCCTTAAGTTTTAT-TTTTGCTA
*
10651 TTTTAGTCCCTTAAGTTTATGTTTTTGCTA
1 TTTTAGTCCCTTAAGTTT-TATTTTTGCTA
* * * *
10681 TTTTAGTCCTTTAA-ATGTATTTTTACTA
1 TTTTAGTCCCTTAAGTTTTATTTTTGCTA
* *
10709 ATTTAGTCCCTTAAGTTTTTGTTTTTG-TGA
1 TTTTAGTCCCTTAAG-TTTTATTTTTGCT-A
* * *
10739 TTTTAGTCCCTTAAATGTCTATTTTTACTA
1 TTTTAGTCCCTTAAGT-TTTATTTTTGCTA
* * *
10769 TTTTAGTCCTTTAAATTTCTATTTATGCTA
1 TTTTAGTCCCTTAAGTTT-TATTTTTGCTA
* * *
10799 TTTTAATCCCTTAAGTTTTGTTTTTCTTTCTA
1 TTTTAGTCCCTTAAG-TTT-TATTT-TTGCTA
* *
10831 TTTTAGTCCTTTTAATTTTTATTTTTGCTA
1 TTTTAGTCC-CTTAAGTTTTATTTTTGCTA
*
10861 TTTTAATCCCTTAAGTTTTGATTTTTGCTA
1 TTTTAGTCCCTTAAGTTTT-ATTTTTGCTA
* *
10891 TTTTAGTCCTTTTAA-TTCCTATTTTTGCTA
1 TTTTAGTCC-CTTAAGTT-TTATTTTTGCTA
10921 TTTT
1 TTTT
10925 TTCTATTTTA
Statistics
Matches: 222, Mismatches: 38, Indels: 27
0.77 0.13 0.09
Matches are distributed among these distances:
28 21 0.09
29 30 0.14
30 134 0.60
31 18 0.08
32 15 0.07
33 4 0.02
ACGTcount: A:0.18, C:0.13, G:0.09, T:0.59
Consensus pattern (29 bp):
TTTTAGTCCCTTAAGTTTTATTTTTGCTA
Found at i:10904 original size:39 final size:38
Alignment explanation
Indices: 10861--10938 Score: 95
Period size: 39 Copynumber: 2.0 Consensus size: 38
10851 ATTTTTGCTA
10861 TTTTAATCCCTTAAGTTTTG-ATTTTTGCTATTTTAGTCC
1 TTTTAATCCC-T-AGTTTTGCATTTTTGCTATTTTAGTCC
* * *
10900 TTTTAATTCCTATTTTTGCTATTTTTTCTATTTTAGTCC
1 TTTTAATCCCTAGTTTTGC-ATTTTTGCTATTTTAGTCC
10939 CTTAAGTTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
37 6 0.18
38 1 0.03
39 27 0.79
ACGTcount: A:0.17, C:0.15, G:0.08, T:0.60
Consensus pattern (38 bp):
TTTTAATCCCTAGTTTTGCATTTTTGCTATTTTAGTCC
Found at i:10955 original size:39 final size:38
Alignment explanation
Indices: 10881--10962 Score: 103
Period size: 39 Copynumber: 2.1 Consensus size: 38
10871 TTAAGTTTTG
*
10881 ATTTTTGCTATTTTAGTCCTTTTAATTCCTATTTTTGCT
1 ATTTTTGCTATTTTAGTCCTCTTAATTCCTATTTTT-CT
* * *
10920 ATTTTTTCTATTTTAGTCC-CTTAAGTTTCTTTTTTTCT
1 ATTTTTGCTATTTTAGTCCTCTTAA-TTCCTATTTTTCT
10958 ATTTT
1 ATTTT
10963 GATCTTTTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
38 11 0.29
39 27 0.71
ACGTcount: A:0.15, C:0.15, G:0.06, T:0.65
Consensus pattern (38 bp):
ATTTTTGCTATTTTAGTCCTCTTAATTCCTATTTTTCT
Found at i:18092 original size:19 final size:18
Alignment explanation
Indices: 18063--18099 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
18053 TGGTTAAAGT
*
18063 TAATTTTTTAAAATTTAA
1 TAATTTTTTAAAAATTAA
18081 TAATTATTTTAAAAATTAA
1 TAATT-TTTTAAAAATTAA
18100 AAATGGTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TAATTTTTTAAAAATTAA
Found at i:19274 original size:21 final size:21
Alignment explanation
Indices: 19191--19284 Score: 75
Period size: 21 Copynumber: 4.5 Consensus size: 21
19181 AGTGACTTTG
**
19191 GGATCGATCCCTTTACA-AAAA
1 GGATCGATCCCTCGA-AGAAAA
* * * *
19212 TGATCGATCCATAGAGGAAAA
1 GGATCGATCCCTCGAAGAAAA
* *
19233 AGATCGATCCCTTC-AACAAAA
1 GGATCGATCCC-TCGAAGAAAA
*
19254 GGATCGATCCCTCGATGAAAA
1 GGATCGATCCCTCGAAGAAAA
19275 GGATCGATCC
1 GGATCGATCC
19285 TTTCCCCTAA
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.04
21 54 0.95
22 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (21 bp):
GGATCGATCCCTCGAAGAAAA
Found at i:19297 original size:42 final size:42
Alignment explanation
Indices: 19192--19307 Score: 117
Period size: 42 Copynumber: 2.8 Consensus size: 42
19182 GTGACTTTGG
* * *
19192 GATCGATCCCTT-TACAAAAATGATCGATCCATAGAGGAAAAA
1 GATCGATCCCTTCAAC-AAAAGGATCGATCCCTAGAGGAAAAA
* * *
19234 GATCGATCCCTTCAACAAAAGGATCGATCCCTCGATGAAAAG
1 GATCGATCCCTTCAACAAAAGGATCGATCCCTAGAGGAAAAA
* ** * *
19276 GATCGATCCTTTCCCCTAAAGGATTGATCCCT
1 GATCGATCCCTTCAACAAAAGGATCGATCCCT
19308 TTGTTACAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
42 60 0.97
43 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (42 bp):
GATCGATCCCTTCAACAAAAGGATCGATCCCTAGAGGAAAAA
Found at i:19749 original size:49 final size:49
Alignment explanation
Indices: 19689--19786 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
19679 CTCTTTGGGA
19689 GAGAGTGTATTCAAGGTTTTAGGGTATAAACCTTGAAGTGTTTGTAAGG
1 GAGAGTGTATTCAAGGTTTTAGGGTATAAACCTTGAAGTGTTTGTAAGG
*
19738 GAGAGTGTATTCAAGGTTTTGGGGTATAAACCTTGAAGTGTTTGTAAGG
1 GAGAGTGTATTCAAGGTTTTAGGGTATAAACCTTGAAGTGTTTGTAAGG
19787 TTACACCTTA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.28, C:0.06, G:0.32, T:0.35
Consensus pattern (49 bp):
GAGAGTGTATTCAAGGTTTTAGGGTATAAACCTTGAAGTGTTTGTAAGG
Found at i:20717 original size:15 final size:16
Alignment explanation
Indices: 20690--20724 Score: 63
Period size: 15 Copynumber: 2.2 Consensus size: 16
20680 GCTTTCAAAA
20690 TTGAAAAATGAAAATT
1 TTGAAAAATGAAAATT
20706 TTGAAAAA-GAAAATT
1 TTGAAAAATGAAAATT
20721 TTGA
1 TTGA
20725 TTTGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.58
16 8 0.42
ACGTcount: A:0.54, C:0.00, G:0.14, T:0.31
Consensus pattern (16 bp):
TTGAAAAATGAAAATT
Found at i:21647 original size:21 final size:21
Alignment explanation
Indices: 21622--21679 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
21612 ATATTCCTAA
*
21622 AAAGGATTGATCCCTTTTCAT-
1 AAAGGATCGATCCCTTTT-ATC
* *
21643 AAAGGATCGATCTCTTTTTTC
1 AAAGGATCGATCCCTTTTATC
21664 AAAGGATCGATCCCTT
1 AAAGGATCGATCCCTT
21680 CTTGTCGATA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (21 bp):
AAAGGATCGATCCCTTTTATC
Found at i:38966 original size:20 final size:20
Alignment explanation
Indices: 38937--38992 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
38927 TACTGAGGAG
*
38937 GGTGAGTATCAATACTTCCA
1 GGTGATTATCAATACTTCCA
38957 GGTGATTATCAATACTTCCA
1 GGTGATTATCAATACTTCCA
38977 GGTGATTATCAATACT
1 GGTGATTATCAATACT
38993 GAGATTAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (20 bp):
GGTGATTATCAATACTTCCA
Found at i:39096 original size:20 final size:22
Alignment explanation
Indices: 39041--39098 Score: 66
Period size: 20 Copynumber: 2.7 Consensus size: 22
39031 GATACCCAAT
*
39041 GGAGTATCGATACCACTAGAAGG
1 GGAGTATCGATACCACAAGAA-G
* *
39064 GGAGTACCAATACC-CAAGAA-
1 GGAGTATCGATACCACAAGAAG
39084 GGAGTATCGATACCA
1 GGAGTATCGATACCA
39099 GTATGATATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
20 12 0.41
22 5 0.17
23 12 0.41
ACGTcount: A:0.38, C:0.21, G:0.26, T:0.16
Consensus pattern (22 bp):
GGAGTATCGATACCACAAGAAG
Found at i:48227 original size:113 final size:113
Alignment explanation
Indices: 48029--48256 Score: 447
Period size: 113 Copynumber: 2.0 Consensus size: 113
48019 AATATTCCAC
48029 GTCCTACACAATACTATAATCTCCTCCTCTACAAATAACCAGTTGGTCTAGTGGGATGAGGAATT
1 GTCCTACACAATACTATAATCTCCTCCTCTACAAATAACCAGTTGGTCTAGTGGGATGAGGAATT
*
48094 AGATATCTTAAGCAATGTTAGTTTCGAATCCTTACGATTGTGAATGGA
66 AGATATCTTAAGCAATGTTAGTTTCGAATCCTTACGATTGTAAATGGA
48142 GTCCTACACAATACTATAATCTCCTCCTCTACAAATAACCAGTTGGTCTAGTGGGATGAGGAATT
1 GTCCTACACAATACTATAATCTCCTCCTCTACAAATAACCAGTTGGTCTAGTGGGATGAGGAATT
48207 AGATATCTTAAGCAATGTTAGTTTCGAATCCTTACGATTGTAAATGGA
66 AGATATCTTAAGCAATGTTAGTTTCGAATCCTTACGATTGTAAATGGA
48255 GT
1 GT
48257 AAATTAGGTT
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
113 114 1.00
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (113 bp):
GTCCTACACAATACTATAATCTCCTCCTCTACAAATAACCAGTTGGTCTAGTGGGATGAGGAATT
AGATATCTTAAGCAATGTTAGTTTCGAATCCTTACGATTGTAAATGGA
Found at i:51518 original size:16 final size:16
Alignment explanation
Indices: 51497--51540 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
51487 TTATGACATC
*
51497 CTAGCTATTTA-TGTTT
1 CTAGCTA-TTACTGATT
51513 CTAGCTATTACTGATT
1 CTAGCTATTACTGATT
*
51529 CTAGCTGTTACT
1 CTAGCTATTACT
51541 ATTTTTTAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (16 bp):
CTAGCTATTACTGATT
Found at i:56943 original size:16 final size:16
Alignment explanation
Indices: 56922--56976 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
56912 ACATCATAGC
*
56922 TGTTACTTTTTCTAGT
1 TGTTACTTATTCTAGT
* *
56938 TGTTACTGATTCTAGC
1 TGTTACTTATTCTAGT
56954 TGTTA-TTGATTCTAGT
1 TGTTACTT-ATTCTAGT
56970 TGTTACT
1 TGTTACT
56977 ATTTTTAGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
15 1 0.03
16 30 0.94
17 1 0.03
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (16 bp):
TGTTACTTATTCTAGT
Found at i:62833 original size:22 final size:22
Alignment explanation
Indices: 62808--62850 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
62798 TCGGAAACAC
*
62808 TTGATCTTATTTCTAGAATCAT
1 TTGATCTTATTTCTAAAATCAT
62830 TTGATCTTATTTCTAAAATCA
1 TTGATCTTATTTCTAAAATCA
62851 AGTTCCACCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.07, T:0.49
Consensus pattern (22 bp):
TTGATCTTATTTCTAAAATCAT
Found at i:71968 original size:21 final size:21
Alignment explanation
Indices: 71943--71985 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
71933 TGAGACATTA
71943 GTGCATGAGTTTGCCAAAGAG
1 GTGCATGAGTTTGCCAAAGAG
71964 GTGCATGAGTTTGCCAAAGAG
1 GTGCATGAGTTTGCCAAAGAG
71985 G
1 G
71986 GTGGATTTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.28, C:0.14, G:0.35, T:0.23
Consensus pattern (21 bp):
GTGCATGAGTTTGCCAAAGAG
Found at i:73272 original size:30 final size:29
Alignment explanation
Indices: 73238--73326 Score: 99
Period size: 30 Copynumber: 3.0 Consensus size: 29
73228 CACCATCGAT
73238 GCCTCATCCTTTACCAATTCCACCACCAAG
1 GCCTCATCCTTT-CCAATTCCACCACCAAG
* * *
73268 GCCTCCTCCTTTCCCAATGCCACCATCAAG
1 GCCTCATCCTTT-CCAATTCCACCACCAAG
*
73298 CCCTCCA-CGCTTTCCAATTCCACCACCAA
1 GCCT-CATC-CTTTCCAATTCCACCACCAA
73327 AACCAATGTC
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
30 44 0.90
31 5 0.10
ACGTcount: A:0.24, C:0.47, G:0.07, T:0.22
Consensus pattern (29 bp):
GCCTCATCCTTTCCAATTCCACCACCAAG
Found at i:73493 original size:72 final size:74
Alignment explanation
Indices: 73410--73547 Score: 192
Period size: 72 Copynumber: 1.9 Consensus size: 74
73400 CCTTTCCAAA
** *
73410 GCCACCACCAAAGCCTTTTCCTTTCCCAAACCCACCTCC-AGT-CCCC-CTCTTTACAATGCCAC
1 GCCACCACCAAAGCCTCCTCCTTTCCCAAACCCA-CTCCAAGTCCCCCACCCTTTACAATGCCAC
73472 CATCAATCCC
65 CATCAATCCC
* * *
73482 GCCACCACCAAAGTCTCCTCCTTTCCCAAACCTACTCCAAGTCCCCCACCCTTTCCAATGCCACC
1 GCCACCACCAAAGCCTCCTCCTTTCCCAAACCCACTCCAAGTCCCCCACCCTTTACAATGCCACC
73547 A
66 A
73548 CCAAGCCTCC
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
71 4 0.07
72 33 0.58
73 4 0.07
74 16 0.28
ACGTcount: A:0.24, C:0.49, G:0.06, T:0.21
Consensus pattern (74 bp):
GCCACCACCAAAGCCTCCTCCTTTCCCAAACCCACTCCAAGTCCCCCACCCTTTACAATGCCACC
ATCAATCCC
Found at i:73617 original size:18 final size:18
Alignment explanation
Indices: 73594--73630 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
73584 CACCTCCAAG
**
73594 CCTCCTCCACCACCACCA
1 CCTCCTCCAAAACCACCA
73612 CCTCCTCCAAAACCACCA
1 CCTCCTCCAAAACCACCA
73630 C
1 C
73631 ACCCTTTGTC
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:0.27, C:0.62, G:0.00, T:0.11
Consensus pattern (18 bp):
CCTCCTCCAAAACCACCA
Done.