Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002409.1 Hibiscus syriacus cultivar Beakdansim tig00004927_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: 41442
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:6249 original size:23 final size:25
Alignment explanation
Indices: 6223--6282 Score: 83
Period size: 23 Copynumber: 2.6 Consensus size: 25
6213 GATTGGGTTA
*
6223 AACATAAAT-GAATGAACATAAA-G
1 AACATAAATCGAACGAACATAAACG
6246 AACAT-AATCGAACGAACATAAACG
1 AACATAAATCGAACGAACATAAACG
6270 AACAT-AATCGAAC
1 AACATAAATCGAAC
6283 ATAACCGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 3 0.09
23 17 0.50
24 14 0.41
ACGTcount: A:0.57, C:0.17, G:0.12, T:0.15
Consensus pattern (25 bp):
AACATAAATCGAACGAACATAAACG
Found at i:6269 original size:10 final size:10
Alignment explanation
Indices: 6256--6292 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
6246 AACATAATCG
6256 AACGAACATA
1 AACGAACATA
6266 AACGAACATA
1 AACGAACATA
*
6276 ATCGAACATA
1 AACGAACATA
*
6286 ACCGAAC
1 AACGAAC
6293 GAATATAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.54, C:0.24, G:0.11, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:6300 original size:14 final size:14
Alignment explanation
Indices: 6278--6307 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
6268 CGAACATAAT
6278 CGAACATAACCGAA
1 CGAACATAACCGAA
*
6292 CGAATATAACCGAA
1 CGAACATAACCGAA
6306 CG
1 CG
6308 TTCACGAACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.27, G:0.17, T:0.10
Consensus pattern (14 bp):
CGAACATAACCGAA
Found at i:6316 original size:34 final size:34
Alignment explanation
Indices: 6236--6306 Score: 99
Period size: 34 Copynumber: 2.1 Consensus size: 34
6226 ATAAATGAAT
* *
6236 GAACATAA-AGAACATAATCGAACGAACATAAAC
1 GAACATAATCGAACATAACCGAACGAACATAAAC
* *
6269 GAACATAATCGAACATAACCGAACGAATATAACC
1 GAACATAATCGAACATAACCGAACGAACATAAAC
6303 GAAC
1 GAAC
6307 GTTCACGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 8 0.24
34 25 0.76
ACGTcount: A:0.54, C:0.21, G:0.13, T:0.13
Consensus pattern (34 bp):
GAACATAATCGAACATAACCGAACGAACATAAAC
Found at i:18851 original size:2 final size:2
Alignment explanation
Indices: 18844--18888 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
18834 CTAGGGACAT
18844 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
18886 TA T
1 TA T
18889 GTTGGCAGCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20020 original size:3 final size:3
Alignment explanation
Indices: 20012--20043 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
20002 ATGACATGTC
20012 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20044 AATAAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:22971 original size:13 final size:14
Alignment explanation
Indices: 22953--22987 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
22943 AAATTGAATT
*
22953 ATATTTTTTG-AAA
1 ATATTTTATGAAAA
22966 ATATTTTATGAAAA
1 ATATTTTATGAAAA
22980 ATATTTTA
1 ATATTTTA
22988 CTATGTTTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 9 0.45
14 11 0.55
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (14 bp):
ATATTTTATGAAAA
Found at i:23300 original size:23 final size:22
Alignment explanation
Indices: 23256--23309 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
23246 ATTGTTATAT
23256 TATATTTTAAAAATATTAATTA
1 TATATTTTAAAAATATTAATTA
* * *
23278 GTATATTTTAAATATCTTTATTA
1 -TATATTTTAAAAATATTAATTA
23301 TAATATTTT
1 T-ATATTTT
23310 TAGATTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 1 0.04
23 26 0.96
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (22 bp):
TATATTTTAAAAATATTAATTA
Found at i:23443 original size:29 final size:29
Alignment explanation
Indices: 23422--23520 Score: 86
Period size: 27 Copynumber: 3.6 Consensus size: 29
23412 ATAATTTATT
23422 TTATATTATTAAAATAAAAATATAATATC
1 TTATATTATTAAAATAAAAATATAATATC
* * *
23451 TTATATTATTATAAT-ATAAT-TGATTAT-
1 TTATATTATTAAAATAAAAATAT-AATATC
*
23478 TT-TATTA-TAATATTAAAAATATAATA--
1 TTATATTATTAA-AATAAAAATATAATATC
23504 TTATATTATTAGAAATA
1 TTATATTATTA-AAATA
23521 TTAATAAATA
Statistics
Matches: 55, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
25 2 0.04
26 9 0.16
27 15 0.27
28 14 0.25
29 15 0.27
ACGTcount: A:0.49, C:0.01, G:0.02, T:0.47
Consensus pattern (29 bp):
TTATATTATTAAAATAAAAATATAATATC
Found at i:23508 original size:22 final size:23
Alignment explanation
Indices: 23480--23526 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
23470 TTGATTATTT
23480 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
23502 TATTATATTATTAGAAATATTAA
1 TATTATAATATTAAAAATATTAA
23525 TA
1 TA
23527 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:23531 original size:22 final size:22
Alignment explanation
Indices: 23488--23531 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
23478 TTTATTATAA
*
23488 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
23510 TATTAGAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
23532 ATTTTAATAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:26341 original size:21 final size:22
Alignment explanation
Indices: 26316--26366 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
26306 ATTTTAATGA
**
26316 TTTAATTATATT-TGATTATAT
1 TTTAATTATATTAAAATTATAT
*
26337 TTTAATCATATTAAAAATTATAT
1 TTTAATTATATT-AAAATTATAT
26360 TTTAATT
1 TTTAATT
26367 TAATCATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 11 0.46
23 13 0.54
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TTTAATTATATTAAAATTATAT
Found at i:35193 original size:19 final size:19
Alignment explanation
Indices: 35169--35205 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35159 GTTGCAATTT
*
35169 GACAAAACCGGTTGAAATA
1 GACAAAACCGGTAGAAATA
*
35188 GACAAAACTGGTAGAAAT
1 GACAAAACCGGTAGAAAT
35206 TTGACAATAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.14, G:0.22, T:0.16
Consensus pattern (19 bp):
GACAAAACCGGTAGAAATA
Found at i:35222 original size:39 final size:40
Alignment explanation
Indices: 35164--35240 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
35154 AACACGTTGC
* *
35164 AATTTGACAAAACCGGTTGAAA-TAGACAAAACTGGTAGA
1 AATTTGACAAAACCAGTTGAAATTAGACAAAACAGGTAGA
* * *
35203 AATTTGACAATACTAGTTGAAATTGGACAAAACAGGTA
1 AATTTGACAAAACCAGTTGAAATTAGACAAAACAGGTA
35241 TAGCGCGACC
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
39 19 0.59
40 13 0.41
ACGTcount: A:0.45, C:0.12, G:0.19, T:0.23
Consensus pattern (40 bp):
AATTTGACAAAACCAGTTGAAATTAGACAAAACAGGTAGA
Found at i:35224 original size:20 final size:20
Alignment explanation
Indices: 35159--35235 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
35149 AGTATAACAC
* *
35159 GTTGCAATTTGACAAAACCG
1 GTTGAAATTTGACAAAACTG
*
35179 GTTGAAA-TAGACAAAACTG
1 GTTGAAATTTGACAAAACTG
* * *
35198 GTAGAAATTTGACAATACTA
1 GTTGAAATTTGACAAAACTG
*
35218 GTTGAAATTGGACAAAAC
1 GTTGAAATTTGACAAAAC
35236 AGGTATAGCG
Statistics
Matches: 46, Mismatches: 10, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
19 16 0.35
20 30 0.65
ACGTcount: A:0.43, C:0.13, G:0.19, T:0.25
Consensus pattern (20 bp):
GTTGAAATTTGACAAAACTG
Found at i:35283 original size:20 final size:20
Alignment explanation
Indices: 35248--35311 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
35238 GTATAGCGCG
35248 ACCGATTGGAAA-TTGACAAA
1 ACCGATT-GAAATTTGACAAA
* *
35268 ACCGATTGAAATTTGATAAT
1 ACCGATTGAAATTTGACAAA
* * **
35288 ACTGGTTTTAATTTGACAAA
1 ACCGATTGAAATTTGACAAA
35308 ACCG
1 ACCG
35312 GTAAAGCACT
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
19 4 0.12
20 30 0.88
ACGTcount: A:0.39, C:0.14, G:0.17, T:0.30
Consensus pattern (20 bp):
ACCGATTGAAATTTGACAAA
Done.