Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008378.1 Hibiscus syriacus cultivar Beakdansim tig00111138_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: 241419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:234938 original size:46 final size:43
Alignment explanation
Indices: 234849--234976 Score: 126
Period size: 44 Copynumber: 3.0 Consensus size: 43
234839 CAAAATGCTT
* *
234849 TATATATTATATATTTTCAAAATCTTTTAAAAACTATAATATA
1 TATATATTATATATATTCAAAATATTTTAAAAACTATAATATA
*
234892 TATATATATATATATATTGAAAA-ATGTTTAAAAACTAT-ATAT-
1 TATATAT-TATATATATTCAAAATAT-TTTAAAAACTATAATATA
* *
234934 TATAT-TTAT-T-T-TTAAAAATGTTTTAAAAACTGTATAATATA
1 TATATATTATATATATTCAAAATATTTTAAAAAC--TATAATATA
234975 TA
1 TA
234977 AATGTTTTCA
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
37 15 0.21
38 2 0.03
39 4 0.05
40 7 0.10
41 3 0.04
42 5 0.07
43 12 0.16
44 25 0.34
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (43 bp):
TATATATTATATATATTCAAAATATTTTAAAAACTATAATATA
Found at i:234959 original size:37 final size:37
Alignment explanation
Indices: 234890--235130 Score: 211
Period size: 37 Copynumber: 6.4 Consensus size: 37
234880 AACTATAATA
* *
234890 TATATATATATATATATATTGAAAAATG-TTTAAAAAC
1 TATATAT-TATATATATTTTTAAAAATGTTTTAAAAAC
*
234927 TATATATTATATTTATTTTTAAAAATGTTTTAAAAAC
1 TATATATTATATATATTTTTAAAAATGTTTTAAAAAC
* * * * **
234964 TGTATAATATATAAATGTTTTCAAAATGTTTTCGAAAC
1 TATATATTATATATAT-TTTTAAAAATGTTTTAAAAAC
235002 TATATATTATATATA-TTTTAAAAATGTTTTCAAAAAC
1 TATATATTATATATATTTTTAAAAATGTTTT-AAAAAC
* * * ** * *
235039 TATATAATATATAAATTTTCGAAAACCGTTTTCTGAAAAT
1 TATATATTATATATATTTT-TAAAAATG-TTT-TAAAAAC
* *
235079 TATATATTATAT-T-TTGTTAAAAACGTTTTCAAAAAC
1 TATATATTATATATATTTTTAAAAATGTTTT-AAAAAC
*
235115 TATATTACTATATATA
1 TATA-TATTATATATA
235131 CATATATAAA
Statistics
Matches: 162, Mismatches: 31, Indels: 20
0.76 0.15 0.09
Matches are distributed among these distances:
35 1 0.01
36 42 0.26
37 58 0.36
38 37 0.23
39 5 0.03
40 18 0.11
41 1 0.01
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (37 bp):
TATATATTATATATATTTTTAAAAATGTTTTAAAAAC
Found at i:235013 original size:75 final size:78
Alignment explanation
Indices: 234922--235128 Score: 268
Period size: 75 Copynumber: 2.7 Consensus size: 78
234912 AAAATGTTTA
*
234922 AAAACTATATATTATATTTATTTTTAAAAATGTTTT-AAAAACTGTATAATATATAAATGTTTTC
1 AAAACTATATATTATATTTATTTTTAAAAATGTTTTCAAAAACTATATAATATATAAA--TTTTC
*
234986 -AAAA-TGTTTTC-G
64 GAAAACCGTTTTCTG
*
234998 -AAACTATATATTATATATA-TTTTAAAAATGTTTTCAAAAACTATATAATATATAAATTTTCGA
1 AAAACTATATATTATATTTATTTTTAAAAATGTTTTCAAAAACTATATAATATATAAATTTTCGA
235061 AAACCGTTTTCTG
66 AAACCGTTTTCTG
* * * *
235074 AAAATTATATATTATA-TT-TTGTTAAAAACGTTTTCAAAAACTATATTACTATATA
1 AAAACTATATATTATATTTATTTTTAAAAATGTTTTCAAAAACTATA-TAATATATA
235129 TACATATATA
Statistics
Matches: 116, Mismatches: 8, Indels: 13
0.85 0.06 0.09
Matches are distributed among these distances:
73 5 0.04
74 19 0.16
75 44 0.38
76 26 0.22
77 22 0.19
ACGTcount: A:0.43, C:0.07, G:0.05, T:0.44
Consensus pattern (78 bp):
AAAACTATATATTATATTTATTTTTAAAAATGTTTTCAAAAACTATATAATATATAAATTTTCGA
AAACCGTTTTCTG
Found at i:235150 original size:15 final size:15
Alignment explanation
Indices: 235126--235156 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
235116 ATATTACTAT
235126 ATATACATATATAAA
1 ATATACATATATAAA
*
235141 ATATATATATATAAA
1 ATATACATATATAAA
235156 A
1 A
235157 CAAAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATACATATATAAA
Found at i:236192 original size:65 final size:65
Alignment explanation
Indices: 236058--236212 Score: 197
Period size: 65 Copynumber: 2.4 Consensus size: 65
236048 ATAAATTTCT
* * *
236058 TGTTTCAAGGGAAAATTGTCTCAAGCGAGACGAAATTTGTTTCATGGGAAACAATCTCAAAGGTT
1 TGTTTCAAGGG-AAATTGTCTCAAGAGAGACGAAA-TTGTTTCAAGGGAAACAATCTCAAAGGTG
236123 GG
64 GG
* * *
236125 TGTTTTCAAGAGAAATTGTCTCAAGAGAGAC-AACA-TGTTTTAAGGGAAACAATCTCAAATGTG
1 TG-TTTCAAGGGAAATTGTCTCAAGAGAGACGAA-ATTGTTTCAAGGGAAACAATCTCAAAGGTG
236188 GG
64 GG
*
236190 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAGGGAAATTGTCTCAA
236213 AACTCGTTTC
Statistics
Matches: 78, Mismatches: 8, Indels: 7
0.84 0.09 0.08
Matches are distributed among these distances:
64 19 0.24
65 28 0.36
66 2 0.03
67 21 0.27
68 8 0.10
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (65 bp):
TGTTTCAAGGGAAATTGTCTCAAGAGAGACGAAATTGTTTCAAGGGAAACAATCTCAAAGGTGGG
Found at i:236380 original size:96 final size:94
Alignment explanation
Indices: 236218--236506 Score: 373
Period size: 96 Copynumber: 3.0 Consensus size: 94
236208 CTCAAAACTC
* * *
236218 GTTTCAAGGGGAACTGATTCAAATATTTTATTTTCAATGGAAATGTTTTCAAAGTTTATATTTCA
1 GTTTCAAGGGAAACTGATTCAAATATTTT-TTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCA
*
236283 AGAGAAATTGTCTCAAGGGAGACAAAATTT
65 AGAGAAACTGTCTCAAGGGAGACAAAATTT
*
236313 GTTTCAAGGGAAACTGATTCAAATATTTTGTGTTTCAAGGGAAACGTTTTCAAAGTTTATGTTTC
1 GTTTCAAGGGAAACTGATTCAAATATTTT-T-TTTCAAGGGAAATGTTTTCAAAGTTTATGTTTC
236378 AAGAGAAACTGTCTCAAGGGAGACAAAATTT
64 AAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * ** *
236409 GTTTCAAGGGAAACT-ATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 GTTTCAAGGGAAACTGAT-TC-----A-A-ATATTTTTTTTCAAGGGAAATGTTTTCAAAGTTTA
*
236473 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA
58 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA
236507 AAAATTTTCA
Statistics
Matches: 172, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
95 31 0.18
96 77 0.45
101 59 0.34
102 1 0.01
103 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.33
Consensus pattern (94 bp):
GTTTCAAGGGAAACTGATTCAAATATTTTTTTTCAAGGGAAATGTTTTCAAAGTTTATGTTTCAA
GAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:236394 original size:29 final size:30
Alignment explanation
Indices: 236312--236388 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
236302 AGACAAAATT
* *
236312 TGTTTCAAGGGAAACTGATTCAAATATTTTG
1 TGTTTCAAGGGAAACTGATTC-AATAGTTTA
*
236343 TGTTTCAAGGGAAAC-GTTTTCAA-AGTTTA
1 TGTTTCAAGGGAAACTG-ATTCAATAGTTTA
*
236372 TGTTTCAAGAGAAACTG
1 TGTTTCAAGGGAAACTG
236389 TCTCAAGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 18 0.45
30 4 0.10
31 18 0.45
ACGTcount: A:0.32, C:0.10, G:0.21, T:0.36
Consensus pattern (30 bp):
TGTTTCAAGGGAAACTGATTCAATAGTTTA
Found at i:236422 original size:36 final size:36
Alignment explanation
Indices: 236372--236457 Score: 127
Period size: 36 Copynumber: 2.4 Consensus size: 36
236362 TCAAAGTTTA
* * *
236372 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
236408 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
**
236444 CATTTCAAGGGAAA
1 TGTTTCAAGGGAAA
236458 TGTTTTCAAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
Found at i:236570 original size:76 final size:75
Alignment explanation
Indices: 236490--236656 Score: 178
Period size: 76 Copynumber: 2.2 Consensus size: 75
236480 AGAGAAACTG
* * * * *
236490 TCTCAAGGGAGATAAAAAAAAT-T-TTCAAGGGAAACTGTCTCTAGCGAGATAAAATATTTTGTT
1 TCTCAAGCGAGATAAAAAAAATCTGTTCAA-GGAAACTATCTCAAGCGAGATAAAAT-CTTTATT
*
236553 TCGAGGGAAACCA
64 TCGAGAG-AACCA
* *** *
236566 TCTCAAGCGAGA-CAAAATCTTCTGTTCGAGGAAACTATCTCAAGCGAGATAAAATCTTTATTTC
1 TCTCAAGCGAGATAAAAAAAATCTGTTCAAGGAAACTATCTCAAGCGAGATAAAATCTTTATTTC
*
236630 GAGAGAACTA
66 GAGAGAACCA
236640 TCTCAAGCGAGATAAAA
1 TCTCAAGCGAGATAAAA
236657 TATTCTTTTA
Statistics
Matches: 75, Mismatches: 13, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
74 16 0.21
75 19 0.25
76 36 0.48
77 4 0.05
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (75 bp):
TCTCAAGCGAGATAAAAAAAATCTGTTCAAGGAAACTATCTCAAGCGAGATAAAATCTTTATTTC
GAGAGAACCA
Found at i:236575 original size:39 final size:39
Alignment explanation
Indices: 236473--236660 Score: 181
Period size: 37 Copynumber: 5.0 Consensus size: 39
236463 TCAATGTTTA
* * * * ***
236473 TGTTTCAAGAGAAACTGTCTCAAGGGAGATAAAA-AAAA
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
* * *
236511 T-TTTCAAGGGAAACTGTCTCTAGCGAGATAAAATATTT
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
* * * *
236549 TGTTTCGAGGGAAACCATCTCAAGCGAGACAAAATCTTC
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
*
236588 TG-TTCGA-GGAAACTATCTCAAGCGAGATAAAAT-CTT
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
* *
236624 TATTTCGAGAG-AACTATCTCAAGCGAGATAAAATATT
1 TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATT
236661 CTTTTAAAAC
Statistics
Matches: 125, Mismatches: 20, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
36 2 0.02
37 81 0.65
38 10 0.08
39 32 0.26
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (39 bp):
TGTTTCGAGGGAAACTATCTCAAGCGAGATAAAATATTT
Found at i:236836 original size:72 final size:73
Alignment explanation
Indices: 236693--236838 Score: 199
Period size: 72 Copynumber: 2.0 Consensus size: 73
236683 AATGAAATGC
* * *
236693 CTTCTTTCGAGTGAAAACGGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATATTGAATG
1 CTTCTTTCGAGTGAAAACAGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATACTCAATG
236758 AAATAAAT
66 AAATAAAT
* *
236766 CTTCTTTCGAGT-AAAACAGTCTCAAGTGAGACAAAGTC-TGTTTTAAGAAAAGCAAT-CTCAAG
1 CTTCTTTCGAGTGAAAACAGTCTCAAGCGAGACAAA-TCTTGTTTTAAGAAAAACAATACTCAA-
*
236828 TGAGATAAAT
64 TGAAATAAAT
236838 C
1 C
236839 ATCTGCATTA
Statistics
Matches: 65, Mismatches: 6, Indels: 5
0.86 0.08 0.07
Matches are distributed among these distances:
71 3 0.05
72 48 0.74
73 14 0.22
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (73 bp):
CTTCTTTCGAGTGAAAACAGTCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAATACTCAATG
AAATAAAT
Found at i:238043 original size:94 final size:95
Alignment explanation
Indices: 237912--238109 Score: 283
Period size: 95 Copynumber: 2.1 Consensus size: 95
237902 AATATCATTG
*
237912 TATTATAATCACCTTTATCAGGCTAGCTAAATATTATCCATAAAG-CAGG-GCGTTTAACCAATT
1 TATTATAAACACCTTTATCAGGCTAGCTAAATATTATCCATAAAGTC-GGAGCGTTTAACCAATT
* *
237975 TCTCTAGAGGGACAACTCAAGCTTTATTGCA
65 GCTCTAGAGGAACAACTCAAGCTTTATTGCA
* * * * *
238006 TATTATAAACGCCTTTATTAGGCTAGCTGAATCTTATCCATAAAGTCGGAGCGTTTAGCCAATTG
1 TATTATAAACACCTTTATCAGGCTAGCTAAATATTATCCATAAAGTCGGAGCGTTTAACCAATTG
*
238071 CTCTAGAGGAACAACTCAAGCTTTATTGTA
66 CTCTAGAGGAACAACTCAAGCTTTATTGCA
238101 TATATATAA
1 TAT-TATAA
238110 TATTATAATC
Statistics
Matches: 92, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
94 42 0.46
95 45 0.49
96 5 0.05
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.33
Consensus pattern (95 bp):
TATTATAAACACCTTTATCAGGCTAGCTAAATATTATCCATAAAGTCGGAGCGTTTAACCAATTG
CTCTAGAGGAACAACTCAAGCTTTATTGCA
Done.