Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000355.1 Hibiscus syriacus cultivar Beakdansim tig00000651_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: 82865
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:16786 original size:13 final size:13
Alignment explanation
Indices: 16768--16804 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
16758 ATGCTATATA
16768 AAAAAGAGTGGCT
1 AAAAAGAGTGGCT
16781 AAAAAGAGTGGCT
1 AAAAAGAGTGGCT
16794 AAAAAGAGTGG
1 AAAAAGAGTGG
16805 AACTGAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.49, C:0.05, G:0.32, T:0.14
Consensus pattern (13 bp):
AAAAAGAGTGGCT
Found at i:20125 original size:236 final size:236
Alignment explanation
Indices: 19712--20184 Score: 829
Period size: 236 Copynumber: 2.0 Consensus size: 236
19702 ATTTGTTGTC
* * ** ** *
19712 CTGTTTTCTTATCTATTCTCGATTAATTTTTTTTATCTTTTCGTATACACATCAAAATCAGTAGT
1 CTGTTTTATGATCTATTCTCGATTAAAATTTAATATCTTTTCGTATACACATCAAAATCAATAGT
* *
19777 TGTCTATTGTAAATAAAACTAGACTGACATACGAATCCAACGATATAAAATCACCCTCTAATCAA
66 TGTCTATTGTAAATAAAACTAGACTGACATACAAATCCAACAATATAAAATCACCCTCTAATCAA
19842 TTCTTCATAATTTATAGTAAATTTCTAAACTCACTGTTCGAATCAAAATTTCTAGACAACTTTCT
131 TTCTTCATAATTTATAGTAAATTTCTAAACTCACTGTTCGAATCAAAATTTCTAGACAACTTTCT
19907 TTATTAGCATCCTTAACTAATTCCATAATTCTATAAGCTTA
196 TTATTAGCATCCTTAACTAATTCCATAATTCTATAAGCTTA
*
19948 CTGTTTTATGATCTATTCTCGATTAAAATTTAATATCTTTTCGTATACAGATCAAAATCAATAGT
1 CTGTTTTATGATCTATTCTCGATTAAAATTTAATATCTTTTCGTATACACATCAAAATCAATAGT
*
20013 TGTCTGTTGTAAATAAAACTAGACTGACATACAAATCCAACAATATAAAATCACCCTCTAATCAA
66 TGTCTATTGTAAATAAAACTAGACTGACATACAAATCCAACAATATAAAATCACCCTCTAATCAA
*
20078 TTCTTCATAATTTATAGTAAATTTCTAAACTCACTGTTCGAATCAAAATTTCTGGACAACTTTCT
131 TTCTTCATAATTTATAGTAAATTTCTAAACTCACTGTTCGAATCAAAATTTCTAGACAACTTTCT
*
20143 TTATTAGCATCCTTAACTCATTCCATAATTCTATAAGCTTA
196 TTATTAGCATCCTTAACTAATTCCATAATTCTATAAGCTTA
20184 C
1 C
20185 CAAATGAATA
Statistics
Matches: 224, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
236 224 1.00
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (236 bp):
CTGTTTTATGATCTATTCTCGATTAAAATTTAATATCTTTTCGTATACACATCAAAATCAATAGT
TGTCTATTGTAAATAAAACTAGACTGACATACAAATCCAACAATATAAAATCACCCTCTAATCAA
TTCTTCATAATTTATAGTAAATTTCTAAACTCACTGTTCGAATCAAAATTTCTAGACAACTTTCT
TTATTAGCATCCTTAACTAATTCCATAATTCTATAAGCTTA
Found at i:22249 original size:31 final size:30
Alignment explanation
Indices: 22209--22267 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
22199 CATAACCTTT
* * *
22209 CAAAATTATATTTTTGGTCCCTAAACTTTTA
1 CAAAATTATA-CTTTAGCCCCTAAACTTTTA
*
22240 CAAATTTATACTTTAGCCCCTAAACTTT
1 CAAAATTATACTTTAGCCCCTAAACTTT
22268 CAAAACAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
30 15 0.62
31 9 0.38
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.42
Consensus pattern (30 bp):
CAAAATTATACTTTAGCCCCTAAACTTTTA
Found at i:22520 original size:27 final size:27
Alignment explanation
Indices: 22489--22566 Score: 147
Period size: 27 Copynumber: 2.9 Consensus size: 27
22479 TCATACACTG
*
22489 TTTAAATCGTTGAAAATTATTTAAATA
1 TTTAAATTGTTGAAAATTATTTAAATA
22516 TTTAAATTGTTGAAAATTATTTAAATA
1 TTTAAATTGTTGAAAATTATTTAAATA
22543 TTTAAATTGTTGAAAATTATTTAA
1 TTTAAATTGTTGAAAATTATTTAA
22567 GTCCATATTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (27 bp):
TTTAAATTGTTGAAAATTATTTAAATA
Found at i:22565 original size:19 final size:18
Alignment explanation
Indices: 22489--22566 Score: 54
Period size: 19 Copynumber: 4.3 Consensus size: 18
22479 TCATACACTG
*
22489 TTTAAATCGTTGAAAATTA
1 TTTAAATTGTT-AAAATTA
*
22508 TTTAAATAT-TT-AAATTG
1 TTTAAAT-TGTTAAAATTA
* * *
22525 TTGAAAATTATTTAAA-TA
1 TT-TAAATTGTTAAAATTA
22543 TTTAAATTGTTGAAAATTA
1 TTTAAATTGTT-AAAATTA
22562 TTTAA
1 TTTAA
22567 GTCCATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
17 15 0.33
18 12 0.26
19 19 0.41
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (18 bp):
TTTAAATTGTTAAAATTA
Found at i:29053 original size:61 final size:60
Alignment explanation
Indices: 28951--29094 Score: 200
Period size: 61 Copynumber: 2.4 Consensus size: 60
28941 GACAATTCTA
* ** *
28951 TAACTTTTAATAGTCGAGAGACTCAACAAAACAACATTCTATAGTCAGAGGCTCATTTTC
1 TAACTTTTAATAGTCGAGAGACTCAACAAAACAACATTCTATAGGCAGAGGAACATTATC
* * *
29011 TAACTTTTAATAGTCGAGA-ATTTTCAACAAAACAACCTTCTATAGGCAGAGGAACATTATG
1 TAACTTTTAATAGTCGAGAGA--CTCAACAAAACAACATTCTATAGGCAGAGGAACATTATC
29072 TAACTTTTAATAGTCGAGAGACT
1 TAACTTTTAATAGTCGAGAGACT
29095 TAATAAAGTA
Statistics
Matches: 73, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.01
60 20 0.27
61 51 0.70
62 1 0.01
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.31
Consensus pattern (60 bp):
TAACTTTTAATAGTCGAGAGACTCAACAAAACAACATTCTATAGGCAGAGGAACATTATC
Found at i:34076 original size:23 final size:23
Alignment explanation
Indices: 34050--34096 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
34040 ACGTAAGGAG
34050 TTGTGCAATCTCAAGAGCTTTCT
1 TTGTGCAATCTCAAGAGCTTTCT
34073 TTGTGCAATCTCAAGAGCTTTCT
1 TTGTGCAATCTCAAGAGCTTTCT
34096 T
1 T
34097 GCTCAATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (23 bp):
TTGTGCAATCTCAAGAGCTTTCT
Found at i:35114 original size:22 final size:22
Alignment explanation
Indices: 35089--35139 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
35079 TTGTTTTAGA
35089 ACCTAAACTTTTAATTAACCAT
1 ACCTAAACTTTTAATTAACCAT
35111 ACCTAAACTTTTAATTAACCAT
1 ACCTAAACTTTTAATTAACCAT
35133 ACCTAAA
1 ACCTAAA
35140 GTTTAGCTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.43, C:0.24, G:0.00, T:0.33
Consensus pattern (22 bp):
ACCTAAACTTTTAATTAACCAT
Found at i:35173 original size:29 final size:29
Alignment explanation
Indices: 35140--35196 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
35130 CATACCTAAA
* *
35140 GTTTAGCTTTTGTTTTATTTTAGTACCAT
1 GTTTAGCTTTTGTTTCATTTTACTACCAT
*
35169 GTTTAGTTTTTGTTTCATTTTACTACCA
1 GTTTAGCTTTTGTTTCATTTTACTACCA
35197 CATTCAAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.18, C:0.12, G:0.12, T:0.58
Consensus pattern (29 bp):
GTTTAGCTTTTGTTTCATTTTACTACCAT
Found at i:38083 original size:13 final size:13
Alignment explanation
Indices: 38065--38089 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
38055 ACATATGTAC
38065 TTTCAATTCCTCT
1 TTTCAATTCCTCT
38078 TTTCAATTCCTC
1 TTTCAATTCCTC
38090 CTTCATTTTA
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:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTCAATTCCTCT
Found at i:38172 original size:45 final size:44
Alignment explanation
Indices: 38087--38178 Score: 130
Period size: 45 Copynumber: 2.1 Consensus size: 44
38077 TTTTCAATTC
38087 CTCCTTCATTTTAAGTATATATTTAACCAAATTTGAACTGCATG
1 CTCCTTCATTTTAAGTATATATTTAACCAAATTTGAACTGCATG
* * * * *
38131 CTCCTTTATTTTAAGTCTATTTTTTTACCAAATTTTAACTGCATG
1 CTCCTTCATTTTAAGTATA-TATTTAACCAAATTTGAACTGCATG
38176 CTC
1 CTC
38179 ATATACCACT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 17 0.40
45 25 0.60
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.46
Consensus pattern (44 bp):
CTCCTTCATTTTAAGTATATATTTAACCAAATTTGAACTGCATG
Found at i:41338 original size:2 final size:2
Alignment explanation
Indices: 41331--41358 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
41321 ACATACATTC
41331 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
41359 GAGGGAGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48068 original size:83 final size:83
Alignment explanation
Indices: 47913--48232 Score: 411
Period size: 83 Copynumber: 3.9 Consensus size: 83
47903 TTTCGAGAGA
* *
47913 GTTTTACTCCAACTAAAACTCTTTTAATATATAAA---AAA-AGATAATAATATCTTTTAAATTT
1 GTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAATTT
*
47974 AAAATATTAAATCTGAGG
66 ATAATATTAAATCTGAGG
* * * *
47992 GTTTTTCTCTAACCAAAACTCTTTTAATATCTAAATTTAAATAGGTTATAATATCTTTTAAATTT
1 GTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAATTT
* * *
48057 ATAATAATAAATATGAGA
66 ATAATATTAAATCTGAGG
* * * * *
48075 GTTTTACTCTAACGAAAACTCTTTTAATATCTAAATTTAAACAAATTATAATATCTTTTAAATTT
1 GTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAATTT
*
48140 ATGATATTAAATCT-AGG
66 ATAATATTAAATCTGAGG
* *
48157 AGTTTTACTCCAATCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATAGT-GTTTAAAT
1 -GTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATA-TCTTTTAAAT
48221 TTA-AATATTAAA
64 TTATAATATTAAA
48233 CATATATTTT
Statistics
Matches: 208, Mismatches: 27, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
79 31 0.15
82 13 0.06
83 163 0.78
84 1 0.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (83 bp):
GTTTTACTCCAACCAAAACTCTTTTAATATCTAAATTTAAATAGATAATAATATCTTTTAAATTT
ATAATATTAAATCTGAGG
Found at i:52766 original size:56 final size:56
Alignment explanation
Indices: 52699--52812 Score: 210
Period size: 56 Copynumber: 2.0 Consensus size: 56
52689 TCGGTTCTAT
52699 GCTTGACTTAGGTTGAACTTGTAAAACAGAGCTCCGGGTTTGCTTTATCAATTTGG
1 GCTTGACTTAGGTTGAACTTGTAAAACAGAGCTCCGGGTTTGCTTTATCAATTTGG
* *
52755 GCTTGACTTAGGTTGAACTTGTAAAACAGGGCTCTGGGTTTGCTTTATCAATTTGG
1 GCTTGACTTAGGTTGAACTTGTAAAACAGAGCTCCGGGTTTGCTTTATCAATTTGG
52811 GC
1 GC
52813 CTCCAAACAT
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 56 1.00
ACGTcount: A:0.22, C:0.16, G:0.26, T:0.36
Consensus pattern (56 bp):
GCTTGACTTAGGTTGAACTTGTAAAACAGAGCTCCGGGTTTGCTTTATCAATTTGG
Found at i:56148 original size:21 final size:21
Alignment explanation
Indices: 56106--56150 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
56096 ATCCGAAAAA
* *
56106 ATCGGATATTCGAAATTTCGG
1 ATCGGATATTCCAAATTCCGG
56127 ATCGGATA-TCCAAATATCCGG
1 ATCGGATATTCCAAAT-TCCGG
56148 ATC
1 ATC
56151 CGAATCCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (21 bp):
ATCGGATATTCCAAATTCCGG
Found at i:68262 original size:51 final size:46
Alignment explanation
Indices: 68194--68301 Score: 128
Period size: 46 Copynumber: 2.2 Consensus size: 46
68184 TAGCGTGTAT
* *
68194 CAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTATATAGCGCGGGG
1 CAGGTACCGCGCTATACCTTTA-----AACATAATTTTATATAGCGCGGAG
*
68245 CAGGTACCGCGAC-ATACCTTTAAACATAATTTTATATAGCGCGGAT
1 CAGGTACCGCG-CTATACCTTTAAACATAATTTTATATAGCGCGGAG
68291 CAGGTACCGCG
1 CAGGTACCGCG
68302 TTTTGTATAA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
46 32 0.60
51 20 0.38
52 1 0.02
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.27
Consensus pattern (46 bp):
CAGGTACCGCGCTATACCTTTAAACATAATTTTATATAGCGCGGAG
Found at i:72351 original size:18 final size:18
Alignment explanation
Indices: 72313--72351 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
72303 AAAGGCGATG
* *
72313 GCGGCATCATATATGGTT
1 GCGGCATCATATATAGCT
72331 GCGGCATCATATATAGCT
1 GCGGCATCATATATAGCT
72349 GCG
1 GCG
72352 ATGGCTGTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.21, G:0.28, T:0.28
Consensus pattern (18 bp):
GCGGCATCATATATAGCT
Found at i:74123 original size:20 final size:20
Alignment explanation
Indices: 74095--74133 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
74085 CCTTAAAAAG
* *
74095 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGAAAAATTT
74115 AGAGAATTTGAGAAAAATT
1 AGAGAATTTGAGAAAAATT
74134 GGTATGATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (20 bp):
AGAGAATTTGAGAAAAATTT
Found at i:74617 original size:60 final size:61
Alignment explanation
Indices: 74472--74658 Score: 177
Period size: 60 Copynumber: 3.1 Consensus size: 61
74462 TTACATCATA
* * * * * * * *
74472 CATCCTCAATCTATGACT-CTCATTTTAAATTGGTCCCTAAACTTTTAAACATTTTAATTT
1 CATCCTCAAACAATGACTATTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCATTTT
* *
74532 CATCCTTAAACAATGACTATT-ATTCTAAATTAGTCCTTAAACTTTTGAACATTTCATTTT
1 CATCCTCAAACAATGACTATTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCATTTT
*** * *
74592 CAT-CTACAAATTGTGA-TATTCATTCTAAACTAGTCCCTAAACTTTTTGAATATTTCAATTTT
1 CATCCT-CAAACAATGACTATTCATTCTAAATTAGTCCCTAAAC-TTTTGAACATTTC-ATTTT
74654 -ATCCT
1 CATCCT
74659 AAATTATGTG
Statistics
Matches: 104, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
59 6 0.06
60 76 0.73
61 15 0.14
62 7 0.07
ACGTcount: A:0.32, C:0.20, G:0.05, T:0.43
Consensus pattern (61 bp):
CATCCTCAAACAATGACTATTCATTCTAAATTAGTCCCTAAACTTTTGAACATTTCATTTT
Found at i:74912 original size:29 final size:29
Alignment explanation
Indices: 74810--74918 Score: 80
Period size: 29 Copynumber: 3.8 Consensus size: 29
74800 AAGATTTAAA
**
74810 AGTTTAGGGACCAATTTAGAATGATTCAT
1 AGTTTAGGGATAAATTTAGAATGATTCAT
* * * *
74839 AGTTTAGGGGTGAAA-TCAGAAT-ATTAAAA
1 AGTTTAGGGAT-AAATTTAGAATGATT-CAT
* * *
74868 ATTTTAAGGACT-AATTTAGAATGAGTCAT
1 AGTTTAGGGA-TAAATTTAGAATGATTCAT
*
74897 AGTTTAGGGATAAATTTGGAAT
1 AGTTTAGGGATAAATTTAGAAT
74919 ATCAATCAGC
Statistics
Matches: 58, Mismatches: 16, Indels: 12
0.67 0.19 0.14
Matches are distributed among these distances:
28 6 0.10
29 47 0.81
30 5 0.09
ACGTcount: A:0.39, C:0.06, G:0.22, T:0.34
Consensus pattern (29 bp):
AGTTTAGGGATAAATTTAGAATGATTCAT
Found at i:74920 original size:58 final size:58
Alignment explanation
Indices: 74798--74911 Score: 158
Period size: 58 Copynumber: 2.0 Consensus size: 58
74788 GGATAGAATT
* * * * *
74798 AGAAGATTTAAAAGTTTAGGGACCAATTTAGAATGATTCATAGTTTAGGGGTGAAATC
1 AGAATATTAAAAAGTTTAAGGACCAATTTAGAATGAGTCATAGTTTAGGGATGAAATC
* *
74856 AGAATATTAAAAATTTTAAGGACTAATTTAGAATGAGTCATAGTTTAGGGAT-AAAT
1 AGAATATTAAAAAGTTTAAGGACCAATTTAGAATGAGTCATAGTTTAGGGATGAAAT
74912 TTGGAATATC
Statistics
Matches: 49, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
57 4 0.08
58 45 0.92
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.32
Consensus pattern (58 bp):
AGAATATTAAAAAGTTTAAGGACCAATTTAGAATGAGTCATAGTTTAGGGATGAAATC
Done.