Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001528.1 Hibiscus syriacus cultivar Beakdansim tig00002994_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: 71968
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:7973 original size:21 final size:21
Alignment explanation
Indices: 7940--8003 Score: 112
Period size: 21 Copynumber: 3.1 Consensus size: 21
7930 AACACATTGA
*
7940 ATAT-TAAAAAATATTTAAAT
1 ATATGTAAACAATATTTAAAT
7960 ATATGTAAACAATATTTAAAT
1 ATATGTAAACAATATTTAAAT
7981 ATATGTAAACAATATTTAAAT
1 ATATGTAAACAATATTTAAAT
8002 AT
1 AT
8004 TAAAGTAATA
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
20 4 0.10
21 38 0.90
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.39
Consensus pattern (21 bp):
ATATGTAAACAATATTTAAAT
Found at i:8039 original size:9 final size:10
Alignment explanation
Indices: 7939--8039 Score: 66
Period size: 10 Copynumber: 9.8 Consensus size: 10
7929 AAACACATTG
*
7939 AATATTAAAA
1 AATATTTAAA
7949 AATATTTAAA
1 AATATTTAAA
* *
7959 TATATGTAAA
1 AATATTTAAA
7969 CAATATTTAAA
1 -AATATTTAAA
* *
7980 TATATGTAAA
1 AATATTTAAA
7990 CAATATTT--A
1 -AATATTTAAA
7999 AATA-TTAAA
1 AATATTTAAA
8008 GTAATATTAAATAAA
1 --AATATT---TAAA
8023 AATATTTAAA
1 AATATTTAAA
8033 AAT-TTTA
1 AATATTTA
8040 CAACCCGTAT
Statistics
Matches: 72, Mismatches: 9, Indels: 21
0.71 0.09 0.21
Matches are distributed among these distances:
7 2 0.03
8 4 0.06
9 6 0.08
10 32 0.44
11 17 0.24
12 1 0.01
13 6 0.08
15 4 0.06
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (10 bp):
AATATTTAAA
Found at i:8178 original size:60 final size:60
Alignment explanation
Indices: 8097--8223 Score: 145
Period size: 60 Copynumber: 2.1 Consensus size: 60
8087 AATAGTCCAT
**
8097 TGACTATAGGAGATTGTTTTGTTAAGTCTTCC-GACTATTAAAAGTTACAAAATGATC-CTC
1 TGACTATAGGAGATTACTTTGTTAAGTC--CCTGACTATTAAAAGTTACAAAATGATCACTC
* * *
8157 TGACTATA-GAGAGTTACTTTGTTGAGTCCCTTGACTATTAAAATTTACAAAATGGTCACTC
1 TGACTATAGGAGA-TTACTTTGTTAAGTCCC-TGACTATTAAAAGTTACAAAATGATCACTC
8218 TG-CTAT
1 TGACTAT
8224 TCATTATGTT
Statistics
Matches: 58, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
58 2 0.03
59 4 0.07
60 47 0.81
61 5 0.09
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.37
Consensus pattern (60 bp):
TGACTATAGGAGATTACTTTGTTAAGTCCCTGACTATTAAAAGTTACAAAATGATCACTC
Found at i:27680 original size:36 final size:36
Alignment explanation
Indices: 27631--27699 Score: 102
Period size: 36 Copynumber: 1.9 Consensus size: 36
27621 TGGTTTTAAG
* *
27631 AAGAAAAAAAATCTCAAGTGAGATGAAATTTTCTTT
1 AAGAAAAAAAATCTCAAGTGAGATAAAAATTTCTTT
* *
27667 AAGAAAAACAATCTCAATTGAGATAAAAATTTC
1 AAGAAAAAAAATCTCAAGTGAGATAAAAATTTC
27700 AAGTGAAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.51, C:0.10, G:0.12, T:0.28
Consensus pattern (36 bp):
AAGAAAAAAAATCTCAAGTGAGATAAAAATTTCTTT
Found at i:29567 original size:23 final size:23
Alignment explanation
Indices: 29540--29588 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
29530 TGGTGGTTGA
*
29540 TTTAATGG-ATGTTTAGACTTTAT
1 TTTAATGGTATATTTA-ACTTTAT
*
29563 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
29586 TTT
1 TTT
29589 GTTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.27, C:0.02, G:0.14, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:41632 original size:21 final size:20
Alignment explanation
Indices: 41608--41666 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 20
41598 TTTCAGTTTT
41608 TCTTTTATTTCTTTTTATCTA
1 TCTTTT-TTTCTTTTTATCTA
* * *
41629 TCTTTTCTTTTTTTTTTTCTT
1 TCTTTT-TTTCTTTTTATCTA
41650 TCTTCTTTCTTCTTTTT
1 TCTT-TTT-TTCTTTTT
41667 TCCTTTTCTT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
21 22 0.71
22 9 0.29
ACGTcount: A:0.05, C:0.17, G:0.00, T:0.78
Consensus pattern (20 bp):
TCTTTTTTTCTTTTTATCTA
Found at i:41655 original size:7 final size:7
Alignment explanation
Indices: 41633--41695 Score: 60
Period size: 7 Copynumber: 9.3 Consensus size: 7
41623 TATCTATCTT
41633 TTCTTT-
1 TTCTTTC
*
41639 TT-TTTT
1 TTCTTTC
41645 TTCTTTC
1 TTCTTTC
41652 TTCTTTC
1 TTCTTTC
*
41659 TTCTTTT
1 TTCTTTC
*
41666 TTCCTT-
1 TTCTTTC
41672 TTCTTTC
1 TTCTTTC
*
41679 GTCTTTC
1 TTCTTTC
41686 TTCTCTTC
1 TTCT-TTC
41694 TT
1 TT
41696 TATTTTTATT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
5 3 0.06
6 9 0.19
7 30 0.64
8 5 0.11
ACGTcount: A:0.00, C:0.24, G:0.02, T:0.75
Consensus pattern (7 bp):
TTCTTTC
Found at i:41673 original size:34 final size:34
Alignment explanation
Indices: 41631--41695 Score: 87
Period size: 34 Copynumber: 1.9 Consensus size: 34
41621 TTTATCTATC
* **
41631 TTTTCTTTTTTTTTTTCTTTCTTCT-TTCTTCTT
1 TTTTCTTTTCTTTCGTCTTTCTTCTCTTCTTCTT
41664 TTTTCCTTTTCTTTCGTCTTTCTTCTCTTCTT
1 TTTT-CTTTTCTTTCGTCTTTCTTCTCTTCTT
41696 TATTTTTATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 4 0.15
34 18 0.67
35 5 0.19
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (34 bp):
TTTTCTTTTCTTTCGTCTTTCTTCTCTTCTTCTT
Found at i:41674 original size:27 final size:26
Alignment explanation
Indices: 41633--41689 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
41623 TATCTATCTT
* *
41633 TTCTTTTTTTTTTTCTTTCTTCTTTC
1 TTCTTTTTTCTTTTCTTTCGTCTTTC
41659 TTCTTTTTTCCTTTTCTTTCGTCTTTC
1 TTCTTTTTT-CTTTTCTTTCGTCTTTC
41686 TTCT
1 TTCT
41690 CTTCTTTATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.00, C:0.23, G:0.02, T:0.75
Consensus pattern (26 bp):
TTCTTTTTTCTTTTCTTTCGTCTTTC
Found at i:41724 original size:16 final size:15
Alignment explanation
Indices: 41686--41767 Score: 53
Period size: 16 Copynumber: 5.2 Consensus size: 15
41676 TTCGTCTTTC
41686 TTCTCTTCTTTATTTT
1 TTCTCTT-TTTATTTT
41702 TAT-TCTTTTATATTTT
1 T-TCTCTTTT-TATTTT
41718 TTCTCTTTTT-TGTCTT
1 TTCTCTTTTTAT-T-TT
* *
41734 GATTTTCTTTTTCTTTT
1 --TTCTCTTTTTATTTT
*
41751 CTCT-TTTTTATTTT
1 TTCTCTTTTTATTTT
41765 TTC
1 TTC
41768 AAGTGTAGTA
Statistics
Matches: 53, Mismatches: 5, Indels: 18
0.70 0.07 0.24
Matches are distributed among these distances:
14 12 0.23
15 7 0.13
16 20 0.38
17 3 0.06
18 10 0.19
19 1 0.02
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.76
Consensus pattern (15 bp):
TTCTCTTTTTATTTT
Found at i:41757 original size:7 final size:6
Alignment explanation
Indices: 41631--41758 Score: 55
Period size: 6 Copynumber: 19.7 Consensus size: 6
41621 TTTATCTATC
* * *
41631 TTTTCT TTTTTT TTTTCT TTCTTCT TTCTTCTT TTTTCC TTTTCT TTCGTCT
1 TTTTCT TTTTCT TTTTCT TT-TTCT TT-TTC-T TTTTCT TTTTCT TT-TTCT
* *
41683 TTCTTC- TCTTCT TTATT-T TTATTCT TTTATATT TTTTCT CTTTT-T
1 TT-TTCT TTTTCT TT-TTCT TT-TTCT TTT-T-CT TTTTCT -TTTTCT
**
41728 TGTCTTGA TTTTCT TTTTCT TTTCTCT TTTT
1 T-T-TTCT TTTTCT TTTTCT TTT-TCT TTTT
41759 TATTTTTTCA
Statistics
Matches: 96, Mismatches: 13, Indels: 26
0.71 0.10 0.19
Matches are distributed among these distances:
5 4 0.04
6 43 0.45
7 41 0.43
8 8 0.08
ACGTcount: A:0.04, C:0.18, G:0.02, T:0.76
Consensus pattern (6 bp):
TTTTCT
Found at i:42482 original size:14 final size:14
Alignment explanation
Indices: 42463--42491 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
42453 AAAAATAAAG
42463 CTACTAGGATTTTT
1 CTACTAGGATTTTT
42477 CTACTAGGATTTTT
1 CTACTAGGATTTTT
42491 C
1 C
42492 ATCCTTATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.21, C:0.17, G:0.14, T:0.48
Consensus pattern (14 bp):
CTACTAGGATTTTT
Found at i:46190 original size:21 final size:21
Alignment explanation
Indices: 46162--46215 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
46152 CAGTGGCATA
46162 TGAAATGGTTGTGGTGCCATC
1 TGAAATGGTTGTGGTGCCATC
* * * *
46183 TGATATGGCTGCGGTGCCATT
1 TGAAATGGTTGTGGTGCCATC
46204 TGAAATGGTTGT
1 TGAAATGGTTGT
46216 TGAATATACA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.13, G:0.33, T:0.35
Consensus pattern (21 bp):
TGAAATGGTTGTGGTGCCATC
Found at i:46770 original size:2 final size:2
Alignment explanation
Indices: 46763--46816 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
46753 CCATTGAAAC
46763 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
46805 TA TA TA TA TA TA
1 TA TA TA TA TA TA
46817 ATTCTTATCA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49344 original size:3 final size:3
Alignment explanation
Indices: 49336--49364 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
49326 CGTCCGGACC
49336 ATT ATT ATT ATT ATT ATT ATT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
49365 TCTTACACGC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 23 0.92
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
ATT
Found at i:55169 original size:4 final size:4
Alignment explanation
Indices: 55160--55189 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
55150 CAATAAAAAC
55160 AATA AATA AATA AATA AAT- AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AATA AAT
55190 GATAAGTAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (4 bp):
AATA
Found at i:55184 original size:11 final size:11
Alignment explanation
Indices: 55160--55194 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
55150 CAATAAAAAC
55160 AATAAATAAATA
1 AATAAAT-AATA
55172 AATAAATAATA
1 AATAAATAATA
*
55183 AATAAATGATA
1 AATAAATAATA
55194 A
1 A
55195 GTAGATAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAATAATA
Found at i:55736 original size:85 final size:85
Alignment explanation
Indices: 55639--55844 Score: 265
Period size: 85 Copynumber: 2.4 Consensus size: 85
55629 ATGTGCATTA
* *
55639 ATGACGTT-CATTGAGTGTCATTGATGCCCCCGTCATAAAT-TAAG-ATGACACACATTTGTGCG
1 ATGAC-TTACATTGAGTGTCATTGAAGCCCCCATCATAAATCT--GCATGACACACATTTGTGCG
55701 TCATAAATTTATGACACGCATGT
63 TCATAAATTTATGACACGCATGT
* * * * *
55724 ATGACTTACATTGTGCGTCATTGAAGCCCCCATCATAAATCTGCTTGACATACATTTGTGTGTCA
1 ATGACTTACATTGAGTGTCATTGAAGCCCCCATCATAAATCTGCATGACACACATTTGTGCGTCA
*
55789 TAAATTTATGACACTCATGT
66 TAAATTTATGACACGCATGT
* * *
55809 ATGACTTACATTGCGTGTCATTGAAGCACACATCAT
1 ATGACTTACATTGAGTGTCATTGAAGCCCCCATCAT
55845 TAAAAAAGAT
Statistics
Matches: 106, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
84 3 0.03
85 102 0.96
86 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (85 bp):
ATGACTTACATTGAGTGTCATTGAAGCCCCCATCATAAATCTGCATGACACACATTTGTGCGTCA
TAAATTTATGACACGCATGT
Found at i:55864 original size:85 final size:84
Alignment explanation
Indices: 55671--55864 Score: 235
Period size: 85 Copynumber: 2.3 Consensus size: 84
55661 GATGCCCCCG
* *
55671 TCATAAATTAAGATGACACACATTTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATT
1 TCATAAA-AAAGATGACAAACATTTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATT
* * *
55736 GTGCGTCATTGAAGCCCCCA
65 GCGCGTCATTGAAGCACACA
*** * * * *
55756 TCATAAATCTGCTTGACATACATTTGTGTGTCATAAATTTATGACACTCATGTATGACTTACATT
1 TCATAAAAAAG-ATGACAAACATTTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATT
*
55821 GCGTGTCATTGAAGCACACA
65 GCGCGTCATTGAAGCACACA
*
55841 TCATTAAAAAAGATGAAAAACATT
1 TCA-TAAAAAAGATGACAAACATT
55865 GGTTTTTCGT
Statistics
Matches: 91, Mismatches: 16, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
84 2 0.02
85 84 0.92
86 5 0.05
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (84 bp):
TCATAAAAAAGATGACAAACATTTGTGCGTCATAAATTTATGACACGCATGTATGACTTACATTG
CGCGTCATTGAAGCACACA
Found at i:58348 original size:39 final size:40
Alignment explanation
Indices: 58266--58353 Score: 101
Period size: 39 Copynumber: 2.2 Consensus size: 40
58256 CTTTTTTTTT
* * * *
58266 TCTT-TTTTTTCCCTTTTCGGTGTTCCTTCTCCTTTCTCT
1 TCTTCTTTTTTCCCTTTGCAGTGTCCCTTCTCCTTTCTCC
58305 TCTTCTTTTTT-CCTTTGCAGTGTCCCTTCTCCTTTAC-CC
1 TCTTCTTTTTTCCCTTTGCAGTGTCCCTTCTCCTTT-CTCC
*
58344 TCTTCCTTTT
1 TCTTCTTTTT
58354 CTTTCTTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
39 35 0.83
40 7 0.17
ACGTcount: A:0.02, C:0.33, G:0.07, T:0.58
Consensus pattern (40 bp):
TCTTCTTTTTTCCCTTTGCAGTGTCCCTTCTCCTTTCTCC
Found at i:58348 original size:42 final size:39
Alignment explanation
Indices: 58265--58339 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
58255 CCTTTTTTTT
* * *
58265 TTCTTTTTTTTCCCTTTTCGGTGTTCCTTCTCCTTTCTC
1 TTCTTTTTTTTCCCTTTGCAGTGTCCCTTCTCCTTTCTC
58304 TTCTTCTTTTTT-CCTTTGCAGTGTCCCTTCTCCTTT
1 TTCTT-TTTTTTCCCTTTGCAGTGTCCCTTCTCCTTT
58340 ACCCTCTTCC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
39 26 0.81
40 6 0.19
ACGTcount: A:0.01, C:0.31, G:0.08, T:0.60
Consensus pattern (39 bp):
TTCTTTTTTTTCCCTTTGCAGTGTCCCTTCTCCTTTCTC
Found at i:58384 original size:51 final size:50
Alignment explanation
Indices: 58310--58405 Score: 151
Period size: 51 Copynumber: 1.9 Consensus size: 50
58300 TCTCTTCTTC
58310 TTTTTTCCTTTGCAGTGTCCCTTCTCCTTTAC-CCTCTTCCTTTTCTTTCT
1 TTTTTTCCTTTGCAGTGTCCCTTCTCCTTT-CTCCTCTTCCTTTTCTTTCT
58360 TTTTTTCCGTCTT-CAGTGTCCCTTCTCCTTTCTCCTCTTCCTTTTC
1 TTTTTTCC-T-TTGCAGTGTCCCTTCTCCTTTCTCCTCTTCCTTTTC
58406 AACAAGTTCT
Statistics
Matches: 43, Mismatches: 0, Indels: 5
0.90 0.00 0.10
Matches are distributed among these distances:
50 9 0.21
51 32 0.74
52 2 0.05
ACGTcount: A:0.03, C:0.35, G:0.06, T:0.55
Consensus pattern (50 bp):
TTTTTTCCTTTGCAGTGTCCCTTCTCCTTTCTCCTCTTCCTTTTCTTTCT
Found at i:67289 original size:27 final size:26
Alignment explanation
Indices: 67244--67302 Score: 93
Period size: 27 Copynumber: 2.3 Consensus size: 26
67234 ATGAAGAAAT
67244 AAGAG-AAAAAAAAAGTTAAAAATGA
1 AAGAGAAAAAAAAAAGTTAAAAATGA
67269 AAGAGAAAAAGAAAAAGTTAAAAATGA
1 AAGAGAAAAA-AAAAAGTTAAAAATGA
*
67296 GAGAGAA
1 AAGAGAA
67303 TGGGTGATAT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
25 5 0.16
26 4 0.13
27 22 0.71
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.10
Consensus pattern (26 bp):
AAGAGAAAAAAAAAAGTTAAAAATGA
Done.