Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003273.1 Hibiscus syriacus cultivar Beakdansim tig00006879_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: 64253
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:10119 original size:11 final size:11
Alignment explanation
Indices: 10103--10133 Score: 55
Period size: 10 Copynumber: 2.9 Consensus size: 11
10093 CGGGATCTTA
10103 TTTTCAATTTT
1 TTTTCAATTTT
10114 TTTTCAA-TTT
1 TTTTCAATTTT
10124 TTTTCAATTT
1 TTTTCAATTT
10134 AGCTTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
10 10 0.53
11 9 0.47
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTCAATTTT
Found at i:13516 original size:347 final size:348
Alignment explanation
Indices: 12879--13516 Score: 865
Period size: 347 Copynumber: 1.8 Consensus size: 348
12869 CTCGAGCCAC
12879 ACTTATGAGAATTCATGGACTACTGTCATGAACCACATGACATGGTTTTTAAACACCCCTTCTCG
1 ACTTATGAGAATTCATGGACTACTGTCATGAACCACATGACATGGTTTTTAAACACCCCTTCTCG
* * * * * * * *
12944 CTACACACTAGTGAAACTATGGATAAAACATATATATATCAATCACAGACAAATACAATAGTGGT
66 CCACACACAAGTGAAACCATGGAGAAAACA-ATATAGACCAATCACAGACAAAGACAATAGTGGC
** * * *
13009 TGATGTCATGTTGATTTTTAACCAAAACACTAAATTTCAAGAATCATGTTCAAATGAGGATTTCA
130 CAATGCCATGTTGATTTTTAACCAAAACACTAAATTTCAAGAATCATATTCAAATGAGGATATCA
*
13074 ATACAACAAGAATTTGATTCCAACAAGGAATAAACAACTACTAAAGAACATCAAGACACATCATA
195 AGACAACAAGAATTTGATTCCAACAAGGAATAAACAACTACTAAAGAACATCAAGACACATCATA
*
13139 TTGACCCAAATAAGTTTTTTTCAAGTTTTCCACTTGAAAAGTTGAAAAACACATCATATTGATCC
260 TTGACCCAAATAAGTATTTTTCAAGTTTTCCACTTGAAAAGTTGAAAAACACATCATATTGATCC
13204 AATTAAGTGTTTAAACTTTTCCAT
325 AATTAAGTGTTTAAACTTTTCCAT
* * * *
13228 ACTTATGAGACTTCATGGACTGCTGTCATGAGCCAC-TAGACATGGTTTTTAAACACTCCTTCTC
1 ACTTATGAGAATTCATGGACTACTGTCATGAACCACAT-GACATGGTTTTTAAACACCCCTTCTC
* * * * *
13292 GCCACAGACAAGTGAAACCATGGAGAAAAC-ATATGGACCAGTCACATAGAAAGAC-ATCAGTGG
65 GCCACACACAAGTGAAACCATGGAGAAAACAATATAGACCAATCACAGACAAAGACAAT-AGTGG
* *
13355 CCAATGCCATGTTGATTTTTAACCAAAACA-TCGAATTTCAAGAATTATATTCAAAAT-AGGATA
129 CCAATGCCATGTTGATTTTTAACCAAAACACT-AAATTTCAAGAATCATATTC-AAATGAGGATA
* * *
13418 TCAAGACAACAAGAATTTGATTCCAACAAGGAATAAACAACTACTAAAGCACAT-AGAGACTCGT
192 TCAAGACAACAAGAATTTGATTCCAACAAGGAATAAACAACTACTAAAGAACATCA-AGACACAT
* * ** * *
13482 CATATTGATCTAGTTACGTATTTTTCATGTTTTCC
256 CATATTGACCCAAATAAGTATTTTTCAAGTTTTCC
13517 TCTCCATACA
Statistics
Matches: 249, Mismatches: 35, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
346 4 0.02
347 157 0.63
348 5 0.02
349 83 0.33
ACGTcount: A:0.38, C:0.19, G:0.14, T:0.29
Consensus pattern (348 bp):
ACTTATGAGAATTCATGGACTACTGTCATGAACCACATGACATGGTTTTTAAACACCCCTTCTCG
CCACACACAAGTGAAACCATGGAGAAAACAATATAGACCAATCACAGACAAAGACAATAGTGGCC
AATGCCATGTTGATTTTTAACCAAAACACTAAATTTCAAGAATCATATTCAAATGAGGATATCAA
GACAACAAGAATTTGATTCCAACAAGGAATAAACAACTACTAAAGAACATCAAGACACATCATAT
TGACCCAAATAAGTATTTTTCAAGTTTTCCACTTGAAAAGTTGAAAAACACATCATATTGATCCA
ATTAAGTGTTTAAACTTTTCCAT
Found at i:26331 original size:23 final size:25
Alignment explanation
Indices: 26290--26337 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
26280 TTCTTTTAAT
*
26290 TATATGATTTAATAATATAATATAA
1 TATATGATTTAATAATATAACATAA
*
26315 TATAT-ATTT-ATATTATAACATAA
1 TATATGATTTAATAATATAACATAA
26338 ATCAAACTCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 12 0.57
24 4 0.19
25 5 0.24
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (25 bp):
TATATGATTTAATAATATAACATAA
Found at i:33733 original size:24 final size:24
Alignment explanation
Indices: 33706--33751 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
33696 AATCATATTA
*
33706 TGAAATATTTTCATA-ATGATTTTC
1 TGAAATAGTTT-ATAGATGATTTTC
33730 TGAAATAGTTTATAGATGATTT
1 TGAAATAGTTTATAGATGATTT
33752 CAGGTATTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.48
Consensus pattern (24 bp):
TGAAATAGTTTATAGATGATTTTC
Found at i:43893 original size:46 final size:46
Alignment explanation
Indices: 43613--43882 Score: 387
Period size: 46 Copynumber: 5.9 Consensus size: 46
43603 TCATGAACCT
* * * * *
43613 TTATGCATTTTCATTTGTGGCATCATTTCATGCCAATAATGCATCA
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
43659 TTATGCATTTTCATTTATAGAATCCTTTCATGCCAATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
43705 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * * *
43751 TTATGCATTTTTATTTATGGAATCATGTCATGCCGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
**
43797 TTATGCATTTTCATTTATGGCATCCTTTCATGGTGATAATGCACCG
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
* * *
43843 TTATGGATTTTCATTGATGGCATCCTTTCATGCTGATAAT
1 TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAAT
43883 ACATCATTAT
Statistics
Matches: 202, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 202 1.00
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (46 bp):
TTATGCATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCG
Found at i:54597 original size:22 final size:22
Alignment explanation
Indices: 54567--54608 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
54557 AGCAGTTAAA
* *
54567 AAACTATGAAACCCTAATAATG
1 AAACCATGAAACCATAATAATG
54589 AAACCATGAAACCATAATAA
1 AAACCATGAAACCATAATAA
54609 AACCAAACCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.55, C:0.19, G:0.07, T:0.19
Consensus pattern (22 bp):
AAACCATGAAACCATAATAATG
Found at i:57631 original size:13 final size:12
Alignment explanation
Indices: 57593--57646 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
57583 CCATTTCATG
57593 TTATTATTATATA
1 TTATT-TTATATA
**
57606 TTATCATATTATA
1 TTATTTTA-TATA
57619 TTATTGTTATATA
1 TTATT-TTATATA
57632 TTATTTT-TATA
1 TTATTTTATATA
57643 TTAT
1 TTAT
57647 GTGGTGTAGT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
11 8 0.23
12 4 0.11
13 21 0.60
14 2 0.06
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (12 bp):
TTATTTTATATA
Found at i:57679 original size:18 final size:18
Alignment explanation
Indices: 57656--57693 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
57646 TGTGGTGTAG
*
57656 TATTTATAATATATTA-AT
1 TATTTAGAAT-TATTATAT
57674 TATTTAGAATTATTATAT
1 TATTTAGAATTATTATAT
57692 TA
1 TA
57694 AATAAATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 5 0.28
18 13 0.72
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (18 bp):
TATTTAGAATTATTATAT
Done.