Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000929.1 Hibiscus syriacus cultivar Beakdansim tig00001854_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: 83582
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:7192 original size:3 final size:3
Alignment explanation
Indices: 7184--7212 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
7174 TTTAATTTAC
7184 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
7213 ATAAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:11196 original size:32 final size:31
Alignment explanation
Indices: 11150--11210 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 31
11140 TGGATATTAT
11150 TGAATTTTATTTTTAATATATAAATGATTTTC
1 TGAATTTTATTTTT-ATATATAAATGATTTTC
* *
11182 TGAATTTGTA-TTTTATCTATAAATTATTT
1 TGAATTT-TATTTTTATATATAAATGATTT
11211 CAGAGTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 13 0.50
32 11 0.42
33 2 0.08
ACGTcount: A:0.33, C:0.03, G:0.07, T:0.57
Consensus pattern (31 bp):
TGAATTTTATTTTTATATATAAATGATTTTC
Found at i:16289 original size:33 final size:33
Alignment explanation
Indices: 16247--16310 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
16237 TTTTTACTGA
*
16247 AAATGTTAATATTAGATTCTATCGGAAATTAGG
1 AAATGTTAATATTAGATTATATCGGAAATTAGG
*
16280 AAATGTTAATATTGGATTATATCGGAAATTA
1 AAATGTTAATATTAGATTATATCGGAAATTA
16311 ATTAATAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.38
Consensus pattern (33 bp):
AAATGTTAATATTAGATTATATCGGAAATTAGG
Found at i:16453 original size:16 final size:16
Alignment explanation
Indices: 16432--16465 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
16422 ATTTTCGTAC
16432 TCAAAATTACCACAAA
1 TCAAAATTACCACAAA
16448 TCAAAATTACCACAAA
1 TCAAAATTACCACAAA
16464 TC
1 TC
16466 GAAGAAAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.26, G:0.00, T:0.21
Consensus pattern (16 bp):
TCAAAATTACCACAAA
Found at i:17310 original size:12 final size:11
Alignment explanation
Indices: 17283--17307 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
17273 TTCATTAGAA
17283 TTTAATATTTT
1 TTTAATATTTT
17294 TTTAATATTTT
1 TTTAATATTTT
17305 TTT
1 TTT
17308 TAAAATTAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTAATATTTT
Found at i:18085 original size:17 final size:17
Alignment explanation
Indices: 18022--18085 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
18012 AGTTGGTATG
*
18022 AATATTTATGAAATCTAA
1 AATATTTAT-AAATTTAA
*
18040 AATA-TTATAAA-TCAA
1 AATATTTATAAATTTAA
*
18055 TAATATATT-CAAATTTAA
1 -AATAT-TTATAAATTTAA
18073 AATATTTATAAAT
1 AATATTTATAAAT
18086 AAAAATACCA
Statistics
Matches: 36, Mismatches: 5, Indels: 11
0.69 0.10 0.21
Matches are distributed among these distances:
15 2 0.06
16 9 0.25
17 16 0.44
18 9 0.25
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
AATATTTATAAATTTAA
Found at i:18092 original size:16 final size:17
Alignment explanation
Indices: 18022--18092 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
18012 AGTTGGTATG
*
18022 AATATTTATGAAATCTAA
1 AATATTTAT-AAATCAAA
*
18040 AATA-TTATAAATCAAT
1 AATATTTATAAATCAAA
* **
18056 AATATATT-CAAATTTAA
1 AATAT-TTATAAATCAAA
18073 AATATTTATAAAT-AAA
1 AATATTTATAAATCAAA
18089 AATA
1 AATA
18093 CCAATACAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
16 18 0.43
17 18 0.43
18 6 0.14
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (17 bp):
AATATTTATAAATCAAA
Found at i:22542 original size:2 final size:2
Alignment explanation
Indices: 22535--22575 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
22525 CTAATATAAT
22535 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA TA T
22576 TTAAATTTTG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:30513 original size:15 final size:15
Alignment explanation
Indices: 30493--30522 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30483 GATTAATAGG
30493 ATTAATAAAACAAAA
1 ATTAATAAAACAAAA
*
30508 ATTAATAAAATAAAA
1 ATTAATAAAACAAAA
30523 TAAATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
ATTAATAAAACAAAA
Found at i:30897 original size:16 final size:16
Alignment explanation
Indices: 30868--30902 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
30858 AAATTTTTAA
*
30868 TTTTATATAATTTATT
1 TTTTAAATAATTTATT
*
30884 TTTTAAATATTTTATT
1 TTTTAAATAATTTATT
30900 TTT
1 TTT
30903 AGTCTTTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAAATAATTTATT
Found at i:35555 original size:38 final size:38
Alignment explanation
Indices: 35513--35593 Score: 99
Period size: 38 Copynumber: 2.1 Consensus size: 38
35503 ACATAGTATG
* * *
35513 GACTCATTCGTTTATGTTCACGAACAATGTTATTTATT
1 GACTCAGTCATTTATGTTCACGAACAATGTCATTTATT
* * * *
35551 GACTCGGTCATTTATGTTCATGAACATTGTCGTTTATT
1 GACTCAGTCATTTATGTTCACGAACAATGTCATTTATT
35589 GACTC
1 GACTC
35594 GTTTATAAGC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.23, C:0.17, G:0.16, T:0.43
Consensus pattern (38 bp):
GACTCAGTCATTTATGTTCACGAACAATGTCATTTATT
Found at i:38688 original size:29 final size:29
Alignment explanation
Indices: 38646--38704 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
38636 ATTTTCACCT
38646 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
38675 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
38704 A
1 A
38705 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:43381 original size:29 final size:29
Alignment explanation
Indices: 43339--43397 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
43329 ATTTTCACCT
43339 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
43368 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
43397 A
1 A
43398 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:43652 original size:24 final size:23
Alignment explanation
Indices: 43625--43677 Score: 61
Period size: 24 Copynumber: 2.3 Consensus size: 23
43615 ATTAAAAATG
* * *
43625 ATAAAATTTTAGAATTTTAGGAAA
1 ATAAAATTATAAAATTTCA-GAAA
*
43649 ATAAACTTATAAAATTTCAGAAA
1 ATAAAATTATAAAATTTCAGAAA
43672 ATAAAA
1 ATAAAA
43678 ATAAATTTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.32
Consensus pattern (23 bp):
ATAAAATTATAAAATTTCAGAAA
Found at i:55207 original size:27 final size:28
Alignment explanation
Indices: 55150--55208 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
55140 TAATATGATG
* *
55150 GAGGATGAAGAAAAAAATAGAAGGAGAT
1 GAGGAGGAAGAAAAAAATAGAAGAAGAT
* * *
55178 GAGGAGGAAGATAAAGA-AGAAGAAGCT
1 GAGGAGGAAGAAAAAAATAGAAGAAGAT
55205 GAGG
1 GAGG
55209 GTAAAGAACA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.53, C:0.02, G:0.37, T:0.08
Consensus pattern (28 bp):
GAGGAGGAAGAAAAAAATAGAAGAAGAT
Found at i:60340 original size:264 final size:254
Alignment explanation
Indices: 59831--60441 Score: 853
Period size: 264 Copynumber: 2.4 Consensus size: 254
59821 CTTATTCATA
*
59831 TATTGAATAAAAAT-ATTTTTTTATTATTTTGGGTC-AGGTCGGGTTTCTAATTTATATATTCGG
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGA-GTC-GGTTTCTAATTTATATATTCGG
* *
59894 GTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTCGGTTTTTTTTAAGTGTGATATTCGGG
64 GTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTC--G-AGG-TTTTTTTAAGTGTGATATTCGAG
* *
59959 TCGGGTCGAGTTCGGGTTTAGGGTAAAAATACCCGACCCGAAAATATATATAATTTTACCTTATA
125 TCGGGACGAGTTCGGGTTTAGGGTAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATA
*
60024 TATTTAGGAATAATTACAATAATACCCATCTATATATAATTTTTTTTCAATTAAATCACTGTTTT
190 TATTTAGGAATAATTACAATAATACCCATCTATATATAATTTTTTTTCAATTAAATCAATGTTTT
60089 TATTGAATAAAAATAATTTTTTATTATTATTTCGGGTCGGGTTGAGTCGGATTTCTAATTTATAT
1 TATTGAATAAAAATAA-TTTTT-TTATTATTTCGGGTC-----GAGTCGG-TTTCTAATTTATAT
*
60154 ATTCGGGTCGGGTCGGGTGAAGCTTTATTTTGGTCGGGTC-AGG-TTTTTTAAGTGTGATATTCG
58 ATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGAGGTTTTTTTAAGTGTGATATTCG
* * * * *
60217 AGTCTGGACGGGTTCGGGTTTATGGTGAAAATACCCGACCCGACTCAAAAAATATATAATTTTAT
123 AGTCGGGACGAGTTCGGGTTTAGGGTAAAAATACCCGACCCG----AAAAAATATATAATTTTAC
* * *
60282 CTTATATATTTAGGAATAATTACAATAATACCCCTCTATATATATTTTTTTTTCAATTAAGTCAA
184 CTTATATATTTAGGAATAATTACAATAATACCCATCTATATATAATTTTTTTTCAATTAAATCAA
60347 TGTTTT
249 TGTTTT
*
60353 TATTGAATAAAAATAA-TTTTTTATTATTTCGGGTCGA----GTTTCTAATTCATATATTCGGGT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGAGTCGGTTTCTAATTTATATATTCGGGT
60413 CGGGTCGGGTGAAACTTTATTTTGGTCGG
66 CGGGTCGGGTGAAACTTTATTTTGGTCGG
60442 ATAGGGTCTC
Statistics
Matches: 322, Mismatches: 17, Indels: 35
0.86 0.05 0.09
Matches are distributed among these distances:
251 49 0.15
252 1 0.00
256 2 0.01
258 14 0.04
259 1 0.00
260 61 0.19
261 29 0.09
262 6 0.02
264 100 0.31
265 2 0.01
266 56 0.17
267 1 0.00
ACGTcount: A:0.27, C:0.11, G:0.20, T:0.42
Consensus pattern (254 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCGAGTCGGTTTCTAATTTATATATTCGGGT
CGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGAGGTTTTTTTAAGTGTGATATTCGAGTCGGGA
CGAGTTCGGGTTTAGGGTAAAAATACCCGACCCGAAAAAATATATAATTTTACCTTATATATTTA
GGAATAATTACAATAATACCCATCTATATATAATTTTTTTTCAATTAAATCAATGTTTT
Found at i:61244 original size:3 final size:3
Alignment explanation
Indices: 61236--61277 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
61226 TTCTCTCACA
61236 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
61278 ATGTTCTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:77100 original size:2 final size:2
Alignment explanation
Indices: 77089--77125 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
77079 AATTAAAATT
77089 TA TA -A 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
77126 ATCATTCAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.