Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000812.1 Hibiscus syriacus cultivar Beakdansim tig00001572_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: 70380
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:9374 original size:20 final size:20
Alignment explanation
Indices: 9336--9374 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
9326 TTTGTTAGTT
**
9336 ATTAGATAGGGTCAATTTTA
1 ATTAGATAGAATCAATTTTA
*
9356 ATTAGATAGAATCAGTTTT
1 ATTAGATAGAATCAATTTT
9375 TTTATTCTGT
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:0.36, C:0.05, G:0.18, T:0.41
Consensus pattern (20 bp):
ATTAGATAGAATCAATTTTA
Found at i:9386 original size:54 final size:54
Alignment explanation
Indices: 9320--9428 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
9310 TAACTAGATA
* *
9320 TTTTATTTTGTTAGTTATTAGATAGGGTCAATTTTAATTAGATAGAATCAGTTT
1 TTTTATTCTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTT
*
9374 TTTTATTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTT
1 TTTTATTCTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTT
9428 T
1 T
9429 ATTCTGTTGT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.50
Consensus pattern (54 bp):
TTTTATTCTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTT
Found at i:9415 original size:20 final size:20
Alignment explanation
Indices: 9390--9429 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
9380 TCTGTTAGTT
*
9390 ATTAGATAGGATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
9410 ATTAGATAGAATCAGTTTTA
1 ATTAGATAGAATCAGTTTTA
9430 TTCTGTTGTT
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:0.17, T:0.40
Consensus pattern (20 bp):
ATTAGATAGAATCAGTTTTA
Found at i:9440 original size:54 final size:53
Alignment explanation
Indices: 9326--9440 Score: 176
Period size: 54 Copynumber: 2.1 Consensus size: 53
9316 GATATTTTAT
* *
9326 TTTGTTAGTTATTAGATAGGGTCAATTTTAATTAGATAGAATCAGTTTTTTTA
1 TTTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTTTATTA
* *
9379 TTCTGTTAGTTATTAGATAGGATCAGTTTTAATTAGATAGAATCAGTTTTATTC
1 TT-TGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTTTATTA
9433 TGTTGTTA
1 T-TTGTTA
9441 ATTTTATGCA
Statistics
Matches: 56, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
53 2 0.04
54 53 0.95
55 1 0.02
ACGTcount: A:0.29, C:0.05, G:0.17, T:0.49
Consensus pattern (53 bp):
TTTGTTAGTTATTAGATAGGATCAATTTTAATTAGATAGAATCAGTTTTATTA
Found at i:15832 original size:23 final size:22
Alignment explanation
Indices: 15806--15850 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
15796 TTATTTATTG
15806 TATTTTAA-AATATTAAAATAATA
1 TATTTTAATAATA-TAAAA-AATA
15829 TATTTTAATAATATAAAAAATA
1 TATTTTAATAATATAAAAAATA
15851 AAAAACCCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 13 0.62
24 4 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TATTTTAATAATATAAAAAATA
Found at i:17511 original size:13 final size:13
Alignment explanation
Indices: 17493--17517 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17483 GCTATTTCAT
17493 CAAAATTCAATTC
1 CAAAATTCAATTC
17506 CAAAATTCAATT
1 CAAAATTCAATT
17518 GCACCGTGAC
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:0.48, C:0.20, G:0.00, T:0.32
Consensus pattern (13 bp):
CAAAATTCAATTC
Found at i:18319 original size:29 final size:29
Alignment explanation
Indices: 18275--18378 Score: 115
Period size: 29 Copynumber: 3.6 Consensus size: 29
18265 CTTTTTAAAA
* ***
18275 TAATTA-CAAAATAGCACCCATTTCGAAT
1 TAATTACCAGAATAGCACCCAAAACGAAT
18303 TAATTACCAGAATAGCA-CCAAAACCGAAT
1 TAATTACCAGAATAGCACCCAAAA-CGAAT
*
18332 TATTTACCAGAATAGCA-CCAAAACTGAAT
1 TAATTACCAGAATAGCACCCAAAAC-GAAT
*
18361 TATTTACCAGAATAGCAC
1 TAATTACCAGAATAGCAC
18379 AGATCAACGG
Statistics
Matches: 67, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
28 10 0.15
29 57 0.85
ACGTcount: A:0.44, C:0.22, G:0.10, T:0.24
Consensus pattern (29 bp):
TAATTACCAGAATAGCACCCAAAACGAAT
Found at i:18423 original size:17 final size:17
Alignment explanation
Indices: 18401--18434 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18391 AATCGAGTCG
18401 GGTCAACGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
*
18418 GGTCAATGGGTCGGGTC
1 GGTCAACGGGTCGGGTC
18435 ATGACCGGTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.21, G:0.47, T:0.21
Consensus pattern (17 bp):
GGTCAACGGGTCGGGTC
Found at i:22712 original size:27 final size:27
Alignment explanation
Indices: 22677--22735 Score: 75
Period size: 27 Copynumber: 2.1 Consensus size: 27
22667 TATATTATTC
22677 TATACAAAAACAATAAAT-TAATAATATAT
1 TATA-AAAAA-AATAAATCTAA-AATATAT
*
22706 TATAAAAAAAATAAATCTAAAATATTT
1 TATAAAAAAAATAAATCTAAAATATAT
22733 TAT
1 TAT
22736 TTTAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 16 0.57
28 8 0.29
29 4 0.14
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (27 bp):
TATAAAAAAAATAAATCTAAAATATAT
Found at i:24998 original size:26 final size:25
Alignment explanation
Indices: 24968--25031 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 25
24958 AGTAAAATAA
24968 TAATAATTATTTATTTATTAGAAAAT
1 TAATAATTATTTATTT-TTAGAAAAT
* *
24994 TAATAAATTATTCATTTTTAGTAAAT
1 TAAT-AATTATTTATTTTTAGAAAAT
*
25020 TAGTAATT-TTTA
1 TAATAATTATTTA
25032 ATGAAATGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
24 3 0.09
25 4 0.12
26 15 0.45
27 11 0.33
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (25 bp):
TAATAATTATTTATTTTTAGAAAAT
Found at i:25020 original size:18 final size:18
Alignment explanation
Indices: 24997--25031 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
24987 AGAAAATTAA
* *
24997 TAAATTATTCATTTTTAG
1 TAAATTAGTAATTTTTAG
25015 TAAATTAGTAATTTTTA
1 TAAATTAGTAATTTTTA
25032 ATGAAATGAG
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:0.37, C:0.03, G:0.06, T:0.54
Consensus pattern (18 bp):
TAAATTAGTAATTTTTAG
Found at i:35853 original size:90 final size:89
Alignment explanation
Indices: 35719--35884 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 89
35709 CTTTTATAGT
35719 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
1 CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
* *
35784 GGAATTTAATAATCCTCTTACATC
66 GAAATTAAATAATCCTCTTACATC
*
35808 CAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
1 CAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTTAATTAAT
35873 TGAAATTAAATA
65 TGAAATTAAATA
35885 TTTGGGATTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
89 23 0.32
90 50 0.68
ACGTcount: A:0.38, C:0.11, G:0.07, T:0.43
Consensus pattern (89 bp):
CAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTAATTAATT
GAAATTAAATAATCCTCTTACATC
Found at i:45925 original size:21 final size:21
Alignment explanation
Indices: 45901--45942 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
45891 ATAAATTTTT
*
45901 ATTTTGATTAAATTTACTATG
1 ATTTTGATTAAATTTAATATG
45922 ATTTTGATTAAATTTAATATG
1 ATTTTGATTAAATTTAATATG
45943 TTATTGTGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.02, G:0.10, T:0.52
Consensus pattern (21 bp):
ATTTTGATTAAATTTAATATG
Found at i:49270 original size:16 final size:16
Alignment explanation
Indices: 49234--49271 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
49224 CGTGAATATC
*
49234 ATTATTTTTTGTGACA
1 ATTATTTTTTGTAACA
*
49250 A-TATTTTTTGTAATA
1 ATTATTTTTTGTAACA
49265 ATTATTT
1 ATTATTT
49272 ATACCTATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.29, C:0.03, G:0.08, T:0.61
Consensus pattern (16 bp):
ATTATTTTTTGTAACA
Found at i:49648 original size:15 final size:16
Alignment explanation
Indices: 49621--49650 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49611 TTTTTAGTCA
49621 TAGTTACTAAAACTTT
1 TAGTTACTAAAACTTT
49637 TAGTTA-TAAAACTT
1 TAGTTACTAAAACTT
49651 GTCACTATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (16 bp):
TAGTTACTAAAACTTT
Found at i:49875 original size:15 final size:15
Alignment explanation
Indices: 49855--49889 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
49845 CAAAAAAACT
49855 ATTAATAGTGACAAA
1 ATTAATAGTGACAAA
**
49870 ATTAATTTTGACAAA
1 ATTAATAGTGACAAA
49885 ATTAA
1 ATTAA
49890 ATTTGACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (15 bp):
ATTAATAGTGACAAA
Found at i:49902 original size:14 final size:15
Alignment explanation
Indices: 49863--49907 Score: 74
Period size: 15 Copynumber: 3.1 Consensus size: 15
49853 CTATTAATAG
*
49863 TGACAAAATTAATTT
1 TGACAAAATTAAATT
49878 TGACAAAATTAAATT
1 TGACAAAATTAAATT
49893 TGAC-AAATTAAATT
1 TGACAAAATTAAATT
49907 T
1 T
49908 ATCACAATAG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
14 11 0.38
15 18 0.62
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
TGACAAAATTAAATT
Found at i:51331 original size:2 final size:2
Alignment explanation
Indices: 51324--51364 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
51314 CGAAGATTTC
51324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
51365 GTTCATTCTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:53970 original size:15 final size:15
Alignment explanation
Indices: 53923--53974 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
53913 CTTGTTTCAT
53923 ATAATATTATTTAAA
1 ATAATATTATTTAAA
*
53938 ATTAA-ATTATCTAAAAA
1 A-TAATATTAT-T-TAAA
53955 ATAATATTATTTAAA
1 ATAATATTATTTAAA
53970 ATAAT
1 ATAAT
53975 TAATCAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 14 0.45
16 8 0.26
17 9 0.29
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
ATAATATTATTTAAA
Found at i:54849 original size:15 final size:15
Alignment explanation
Indices: 54831--54872 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
54821 TAGTAATTTA
*
54831 ATTTTTATTTTTAAT
1 ATTTTTATATTTAAT
54846 ATTTTTATATTTAAT
1 ATTTTTATATTTAAT
54861 -TTTTCTATATTT
1 ATTTT-TATATTT
54873 GTATAGTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.71
Consensus pattern (15 bp):
ATTTTTATATTTAAT
Found at i:55901 original size:22 final size:22
Alignment explanation
Indices: 55869--55910 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
55859 TAATAATATA
55869 TTTTTAATTTTT-AGTAATTTTT
1 TTTTTAATTTTTGA-TAATTTTT
*
55891 TTTTTATTTTTTGATAATTT
1 TTTTTAATTTTTGATAATTT
55911 ACATTTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTTAATTTTTGATAATTTTT
Found at i:57072 original size:18 final size:18
Alignment explanation
Indices: 57049--57090 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
57039 CCTCAACAAT
57049 ATTTCTAAAATTCCCTAA
1 ATTTCTAAAATTCCCTAA
57067 ATTTCTAAAATTCCCTAA
1 ATTTCTAAAATTCCCTAA
57085 ATTTCT
1 ATTTCT
57091 TATTCTTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (18 bp):
ATTTCTAAAATTCCCTAA
Found at i:57152 original size:20 final size:20
Alignment explanation
Indices: 57109--57158 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
57099 GAACTGAGTT
* * *
57109 AGTATCGATATTTACTTATC
1 AGTATCGATATTGACTAAGC
*
57129 AGTATCGATATTGACTAAGG
1 AGTATCGATATTGACTAAGC
*
57149 AGTATTGATA
1 AGTATCGATA
57159 CCTCCATTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (20 bp):
AGTATCGATATTGACTAAGC
Found at i:59353 original size:2 final size:2
Alignment explanation
Indices: 59346--59388 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
59336 GACTATTCAA
59346 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
59388 A
1 A
59389 AAAGTTAAGA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:61156 original size:38 final size:38
Alignment explanation
Indices: 61073--61165 Score: 134
Period size: 38 Copynumber: 2.4 Consensus size: 38
61063 AATACAAATA
*
61073 CCTTTTGGTTTAAGTTTATATTACTCATTATAAGATTG
1 CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATTG
*
61111 CCCTTTGGTTTAAGTTTATATTACCCATTATAAGATTAG
1 CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATT-G
*
61150 -TTTTTGGGTTTAAGTT
1 CCTTTT-GGTTTAAGTT
61166 GATTCAGAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
38 38 0.78
39 11 0.22
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (38 bp):
CCTTTTGGTTTAAGTTTATATTACCCATTATAAGATTG
Found at i:65998 original size:19 final size:19
Alignment explanation
Indices: 65953--65991 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
65943 TACAATGTTC
*
65953 CTAATAATTTGCTTATTAAG
1 CTAAT-ATTTGCTTATCAAG
65973 CTAATATTTGCTTATCAAG
1 CTAATATTTGCTTATCAAG
65992 TTTATATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.33, C:0.13, G:0.10, T:0.44
Consensus pattern (19 bp):
CTAATATTTGCTTATCAAG
Done.