Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000077.1 Hibiscus syriacus cultivar Beakdansim tig00000141_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: 58784
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17163 original size:21 final size:21
Alignment explanation
Indices: 17120--17165 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
17110 AAGAAATATT
* *
17120 AATATTAATATTAATAATAAA
1 AATACTAATAATAATAATAAA
* *
17141 AATACTAATAATAATATTTAA
1 AATACTAATAATAATAATAAA
17162 AATA
1 AATA
17166 TTTTTTTCGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (21 bp):
AATACTAATAATAATAATAAA
Found at i:17354 original size:84 final size:84
Alignment explanation
Indices: 17213--17381 Score: 268
Period size: 84 Copynumber: 2.0 Consensus size: 84
17203 CTCTCTTTAC
* * *
17213 ACATTCTTGTGTTAACAAGGATAAGACAAAGAAGAAAAAGACAACAAATTTTTGTCCGATAAATG
1 ACATTATTGTGTTAACAAAGATAAGACAAAGAAGAAAAAAACAACAAATTTTTGTCCGATAAATG
17278 AAACATGTGACATAAACAA
66 AAACATGTGACATAAACAA
* * *
17297 ACATTATTGTGTTAATAAAGATATGACAAAGACGAAAAAAACAA-ACAATTTTTGTCCGATAAAT
1 ACATTATTGTGTTAACAAAGATAAGACAAAGAAGAAAAAAACAACA-AATTTTTGTCCGATAAAT
17361 GAAACATGTGACATAAACAA
65 GAAACATGTGACATAAACAA
17381 A
1 A
17382 AATATATATA
Statistics
Matches: 78, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
83 1 0.01
84 77 0.99
ACGTcount: A:0.50, C:0.12, G:0.14, T:0.24
Consensus pattern (84 bp):
ACATTATTGTGTTAACAAAGATAAGACAAAGAAGAAAAAAACAACAAATTTTTGTCCGATAAATG
AAACATGTGACATAAACAA
Found at i:17805 original size:19 final size:19
Alignment explanation
Indices: 17783--17826 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17773 TTACAAATAT
*
17783 AAAAAGTCAGAAAAAATT-C
1 AAAAAATCAG-AAAAATTAC
*
17802 AAAAAATCCGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
17821 AAAAAA
1 AAAAAA
17827 ATTAATATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 15 0.68
ACGTcount: A:0.68, C:0.11, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:17865 original size:25 final size:25
Alignment explanation
Indices: 17837--17889 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 25
17827 ATTAATATGA
*
17837 TTATTTATC-TAATTTAAATATATTT
1 TTATCTATCTTAATTT-AATATATTT
17862 TTATCTATCTTATAATTTAATATATTT
1 TTATCTATC-T-TAATTTAATATATTT
17889 T
1 T
17890 AACTAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 8 0.33
27 10 0.42
28 6 0.25
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATCTATCTTAATTTAATATATTT
Found at i:17985 original size:20 final size:20
Alignment explanation
Indices: 17960--18001 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
17950 TAGCAAATCT
*
17960 GCACAGTGGCGATGGAACTG
1 GCACAGTGACGATGGAACTG
*
17980 GCACAGTGATGATGGAACTG
1 GCACAGTGACGATGGAACTG
18000 GC
1 GC
18002 GCAGGGCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.26, C:0.19, G:0.38, T:0.17
Consensus pattern (20 bp):
GCACAGTGACGATGGAACTG
Found at i:24149 original size:15 final size:15
Alignment explanation
Indices: 24129--24162 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
24119 CACCTCAAAC
*
24129 CTTCACCTTCTCCTT
1 CTTCACCGTCTCCTT
24144 CTTCACCGTCTCCTT
1 CTTCACCGTCTCCTT
24159 CTTC
1 CTTC
24163 GCCCTGTTCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.06, C:0.47, G:0.03, T:0.44
Consensus pattern (15 bp):
CTTCACCGTCTCCTT
Found at i:26056 original size:34 final size:34
Alignment explanation
Indices: 26013--26082 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
26003 ACCACTACTG
26013 CACATTGATTGAATCATTGACCTAATCTTTATCA
1 CACATTGATTGAATCATTGACCTAATCTTTATCA
26047 CACATTGATTGAATCATTGACCTAATCTTTATCA
1 CACATTGATTGAATCATTGACCTAATCTTTATCA
26081 CA
1 CA
26083 AAACGGAAAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (34 bp):
CACATTGATTGAATCATTGACCTAATCTTTATCA
Found at i:31223 original size:20 final size:20
Alignment explanation
Indices: 31168--31224 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
31158 GCGATCGATA
* *
31168 ATTCGCAATGCGA-TCTCCG
1 ATTCGCAATGCGATTTTCAG
*
31187 ATATCGCAAAT-CAATTTTCAG
1 AT-TCGC-AATGCGATTTTCAG
31208 ATTCGCAATGCGATTTT
1 ATTCGCAATGCGATTTT
31225 GGACTATCGC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
19 5 0.17
20 16 0.53
21 9 0.30
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (20 bp):
ATTCGCAATGCGATTTTCAG
Found at i:31235 original size:21 final size:21
Alignment explanation
Indices: 31210--31278 Score: 86
Period size: 21 Copynumber: 3.3 Consensus size: 21
31200 ATTTTCAGAT
*
31210 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAATTTGGACTA
* * *
31231 TCGCAATGCGAATATGTA-AA
1 TCGCAATGCGAATTTGGACTA
*
31251 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAATTTGGACTA
31272 TCGCAAT
1 TCGCAAT
31279 ACTATGTGGG
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.41
21 23 0.59
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGAATTTGGACTA
Found at i:33255 original size:21 final size:21
Alignment explanation
Indices: 33225--33449 Score: 132
Period size: 21 Copynumber: 10.8 Consensus size: 21
33215 GATTTACATA
*
33225 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
33246 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* * *
33267 TTCGCGTTGCGATTTATTCAAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
33290 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* * *
33311 TT--CGATGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
33332 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
33351 TTCGCTTTGCGATTTATTCCAAG
1 TTCGCGTTGCGA--TAGTCCAAG
* *
33374 TT--CGTTGTGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
33393 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
33416 TTCGC--TGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
33435 TT--CGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
33450 GAACGTGTCG
Statistics
Matches: 170, Mismatches: 22, Indels: 26
0.78 0.10 0.12
Matches are distributed among these distances:
17 1 0.01
19 37 0.22
21 103 0.61
23 29 0.17
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:33277 original size:42 final size:41
Alignment explanation
Indices: 33250--33445 Score: 220
Period size: 42 Copynumber: 4.7 Consensus size: 41
33240 TCCAAGTTCG
* *
33250 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
* * *
33292 CGTTGCGATTTATTCCAAATT--CGATGCGATTTATTCCAAATT
1 CGTTGCGA--TAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
33334 CGTTGCGATAGTCCAAGTTCGCTTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
33376 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTATTCCAAATT
*
33418 CGCTGCGATAGTCCAAGTT--CGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGAT
33446 AGTCGAACGT
Statistics
Matches: 133, Mismatches: 17, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
39 1 0.01
40 17 0.13
42 107 0.80
44 8 0.06
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:33352 original size:84 final size:83
Alignment explanation
Indices: 33250--33445 Score: 254
Period size: 84 Copynumber: 2.4 Consensus size: 83
33240 TCCAAGTTCG
* *
33250 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCAAAATTCGTTGCGATTTATTCCAAATT-C
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCAAAATTCGTTGCGA--TAGTCCAAATTCC
33314 GATGCGATTTATTCCAAATT
64 GATGCGATTTATTCCAAATT
* * * * * *
33334 CGTTGCGATAGTCCAAGTTCGCTTTGCGATTTATTCCAAGTTCGTTGTGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCAAAATTCGTTGCGATAGTCCAAATTC-CG
*
33399 TTGCGATTTATTCCAAATT
65 ATGCGATTTATTCCAAATT
*
33418 CGCTGCGATAGTCCAAGTT--CGTTGCGAT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGAT
33446 AGTCGAACGT
Statistics
Matches: 99, Mismatches: 11, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
82 16 0.16
84 83 0.84
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (83 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCAAAATTCGTTGCGATAGTCCAAATTCCGA
TGCGATTTATTCCAAATT
Found at i:33483 original size:6 final size:6
Alignment explanation
Indices: 33472--33496 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
33462 GACACGTATT
33472 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
33497 GACGTGACGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:33996 original size:6 final size:6
Alignment explanation
Indices: 33987--34023 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
33977 CCGTCTCGTC
33987 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
34024 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:34201 original size:21 final size:21
Alignment explanation
Indices: 34175--34228 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
34165 GCTTGGAAAC
*
34175 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* * *
34196 TCGCAATACGAACTTGGATTA
1 TCGCAATGCGAACTTCGACTA
34217 TCGCAATGCGAA
1 TCGCAATGCGAA
34229 TATGTAAATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:35180 original size:2 final size:2
Alignment explanation
Indices: 35173--35197 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35163 TATGAATACT
35173 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 T
35198 GTATGTATCG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:37291 original size:23 final size:23
Alignment explanation
Indices: 37265--37315 Score: 102
Period size: 23 Copynumber: 2.2 Consensus size: 23
37255 GGGAAGTGTT
37265 ACAGAGAATATCAGTTACAGTTA
1 ACAGAGAATATCAGTTACAGTTA
37288 ACAGAGAATATCAGTTACAGTTA
1 ACAGAGAATATCAGTTACAGTTA
37311 ACAGA
1 ACAGA
37316 AATGGGTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.24
Consensus pattern (23 bp):
ACAGAGAATATCAGTTACAGTTA
Found at i:44096 original size:23 final size:21
Alignment explanation
Indices: 44049--44128 Score: 81
Period size: 21 Copynumber: 3.8 Consensus size: 21
44039 AGAACCCCAG
* ***
44049 GGGGGTATCGATTCCCCTGTG
1 GGGGGAATCGATTCCCCTCAA
44070 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATTCCCC-TC-AA
*
44093 GGGGGAATCGGTT-CCCTCAA
1 GGGGGAATCGATTCCCCTCAA
*
44113 GGGGGGATCGATTCCC
1 GGGGGAATCGATTCCC
44129 TCTGCACCAA
Statistics
Matches: 49, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
20 13 0.27
21 20 0.41
22 4 0.08
23 12 0.24
ACGTcount: A:0.17, C:0.25, G:0.35, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGATTCCCCTCAA
Found at i:44116 original size:20 final size:21
Alignment explanation
Indices: 44070--44130 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
44060 TTCCCCTGTG
44070 GGGGGAATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TCAAA
*
44093 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGATTCCCTCAAA
*
44113 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
44131 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 18 0.51
21 2 0.06
22 3 0.09
23 12 0.34
ACGTcount: A:0.20, C:0.26, G:0.33, T:0.21
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTCAAA
Found at i:54223 original size:30 final size:30
Alignment explanation
Indices: 54151--54238 Score: 83
Period size: 30 Copynumber: 3.0 Consensus size: 30
54141 TTTGTAATTT
* * *
54151 TTTCCAAAATTATATTTTAATC-CCTAAAC
1 TTTCCAAATTTATAATTTGATCACCTAAAC
* *
54180 TTTTCAAAGTTTATACTTTGATCACC-AAAC
1 TTTCCAAA-TTTATAATTTGATCACCTAAAC
*
54210 TTTACCAAATTTATAATTTGGTCA-CTAAA
1 TTT-CCAAATTTATAATTTGATCACCTAAA
54239 TAAATCCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
29 8 0.17
30 34 0.71
31 6 0.12
ACGTcount: A:0.36, C:0.18, G:0.05, T:0.41
Consensus pattern (30 bp):
TTTCCAAATTTATAATTTGATCACCTAAAC
Found at i:56656 original size:20 final size:20
Alignment explanation
Indices: 56627--56681 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
56617 GAGGGTTCAT
* *
56627 AGGTCTTTCGGGATATACAG
1 AGGTCATTCGGGACATACAG
*
56647 AGGTCATTCGGGACATACAT
1 AGGTCATTCGGGACATACAG
* *
56667 AGGCCATTCAGGACA
1 AGGTCATTCGGGACA
56682 AATTTCATAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (20 bp):
AGGTCATTCGGGACATACAG
Done.