Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002214.1 Hibiscus syriacus cultivar Beakdansim tig00004508_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: 77383
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Found at i:6762 original size:60 final size:60
Alignment explanation
Indices: 6664--6785 Score: 190
Period size: 60 Copynumber: 2.0 Consensus size: 60
6654 AAACAGCTGC
*
6664 ACCAAAACGACATCTACATCAATAATCGTTTGCGTCATCATGCGATTACCGATTTAATGT
1 ACCAAAACGACATCCACATCAATAATCGTTTGCGTCATCATGCGATTACCGATTTAATGT
* * * * *
6724 ACCAAAACGACATCCGCATCAATAATTGTTTGCTTCATCGTGTGATTACCGATTTAATGT
1 ACCAAAACGACATCCACATCAATAATCGTTTGCGTCATCATGCGATTACCGATTTAATGT
6784 AC
1 AC
6786 GATATGTGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 56 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.31
Consensus pattern (60 bp):
ACCAAAACGACATCCACATCAATAATCGTTTGCGTCATCATGCGATTACCGATTTAATGT
Found at i:7457 original size:27 final size:27
Alignment explanation
Indices: 7427--7491 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
7417 AAACTGAATT
* *
7427 TTAATATAAACAATGACTTTTAAGTTA
1 TTAAAATAAACAATGAATTTTAAGTTA
* * *
7454 TTAAAATTAACTATTAATTTTAAGTTA
1 TTAAAATAAACAATGAATTTTAAGTTA
7481 TTAAAATAAAC
1 TTAAAATAAAC
7492 TATTATGTAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.42
Consensus pattern (27 bp):
TTAAAATAAACAATGAATTTTAAGTTA
Found at i:7492 original size:27 final size:27
Alignment explanation
Indices: 7444--7496 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
7434 AAACAATGAC
*
7444 TTTTAAGTTATTAAAATTAACTATTAA
1 TTTTAAGTTATTAAAATAAACTATTAA
7471 TTTTAAGTTATTAAAATAAACTATTA
1 TTTTAAGTTATTAAAATAAACTATTA
7497 TGTAGTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (27 bp):
TTTTAAGTTATTAAAATAAACTATTAA
Found at i:17356 original size:35 final size:35
Alignment explanation
Indices: 17315--17387 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
17305 ATTGAGAAAC
* *
17315 TATATAAAATTTTAGTTTTTATTTCATTTAAAAGT
1 TATATAAAATTTTAATTTTTATTTCATTTAAAAAT
17350 TATATAAAATTTTAATTTTTATTTCATTTAAAAAT
1 TATATAAAATTTTAATTTTTATTTCATTTAAAAAT
17385 TAT
1 TAT
17388 CCAATCATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (35 bp):
TATATAAAATTTTAATTTTTATTTCATTTAAAAAT
Found at i:24482 original size:13 final size:13
Alignment explanation
Indices: 24464--24489 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
24454 ACAAAAGCAG
24464 AAATCACATAATT
1 AAATCACATAATT
24477 AAATCACATAATT
1 AAATCACATAATT
24490 GGCTGCAAGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAATCACATAATT
Found at i:26547 original size:2 final size:2
Alignment explanation
Indices: 26540--26567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
26530 TACGTCTGTA
26540 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26568 TATCAATCGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:49700 original size:6 final size:6
Alignment explanation
Indices: 49691--50077 Score: 414
Period size: 6 Copynumber: 64.5 Consensus size: 6
49681 TATATATATG
* *
49691 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGCGTA TGCGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* * * * * *
49739 TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGCGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
49787 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
49835 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* * * * * * * *
49883 TGTGTA TGTGTA TGTGTA TGTGCA TATGCA TATGCA TATGCA TATGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* * * * * * * *
49931 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* * * * * * * *
49979 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
* * * * * * * *
50027 TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA TGTATA
1 TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA TGTGTA
50075 TGT
1 TGT
50078 TCAGGGCCGT
Statistics
Matches: 374, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 374 1.00
ACGTcount: A:0.24, C:0.03, G:0.26, T:0.47
Consensus pattern (6 bp):
TGTGTA
Found at i:64020 original size:19 final size:20
Alignment explanation
Indices: 63963--64009 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
63953 ATCCTATGAG
63963 TACT-TGAACATAAAGAAAA
1 TACTATGAACATAAAGAAAA
63982 TACTATGAACATAAAGAAAA
1 TACTATGAACATAAAGAAAA
64002 TACTATGA
1 TACTATGA
64010 CCAACAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 4 0.15
20 23 0.85
ACGTcount: A:0.55, C:0.11, G:0.11, T:0.23
Consensus pattern (20 bp):
TACTATGAACATAAAGAAAA
Found at i:69294 original size:41 final size:41
Alignment explanation
Indices: 69249--69375 Score: 134
Period size: 41 Copynumber: 3.1 Consensus size: 41
69239 AGAATTAATT
*
69249 TAGCGGCGTTTATCAAACAAACGCCGCAATAGGTTTGTTTA
1 TAGCGGCGTTTGTCAAACAAACGCCGCAATAGGTTTGTTTA
* * **
69290 TAGCGGCGTTTGTGCAAA-AAACACCGCAATAGATTAATAATT-
1 TAGCGGCGTTTGT-CAAACAAACGCCGCAATAGGTT--TGTTTA
* *
69332 TAGCGGCGTTTGT-ATAACAAACGCCGCCATATGTTTGTTTA
1 TAGCGGCGTTTGTCA-AACAAACGCCGCAATAGGTTTGTTTA
69373 TAG
1 TAG
69376 TGGCATTTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
40 4 0.06
41 32 0.46
42 30 0.43
43 3 0.04
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (41 bp):
TAGCGGCGTTTGTCAAACAAACGCCGCAATAGGTTTGTTTA
Found at i:69322 original size:83 final size:81
Alignment explanation
Indices: 69102--69379 Score: 276
Period size: 83 Copynumber: 3.4 Consensus size: 81
69092 TTTATATCTA
** * * * * *
69102 AAACGCCATAATAGATTTGTTTACAGTGGTGTTTTTTCAATAAACACCGCAATAGAATAGTAATT
1 AAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTGTCCAATAAACACCGCAATAGAA-A-TAATT
*
69167 TAGCGGTGTTTGTATAA-
64 TAGCGGCGTTTGTATAAC
* * * * *
69184 AAATGCCGCAACAAGG-TTGTTTATAGTGGCATGTGTCCAATAAACGA-CGCTATAGAGAATTAA
1 AAACGCCGCAA-TAGGTTTGTTTATAGTGGCGTTTGTCCAATAAAC-ACCGCAATAGA-AA-TAA
*
69247 TTTAGCGGCGTTTATCA-AAC
62 TTTAGCGGCGTTTGT-ATAAC
* * *
69267 AAACGCCGCAATAGGTTTGTTTATAGCGGCGTTTGTGCAAAAAACACCGCAATAGATTAATAATT
1 AAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTGTCCAATAAACACCGCAATAGA--AATAATT
69332 TAGCGGCGTTTGTATAAC
64 TAGCGGCGTTTGTATAAC
* *
69350 AAACGCCGCCATATGTTTGTTTATAGTGGC
1 AAACGCCGCAATAGGTTTGTTTATAGTGGC
69380 ATTTTTAAAA
Statistics
Matches: 159, Mismatches: 28, Indels: 17
0.78 0.14 0.08
Matches are distributed among these distances:
82 63 0.40
83 94 0.59
84 2 0.01
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (81 bp):
AAACGCCGCAATAGGTTTGTTTATAGTGGCGTTTGTCCAATAAACACCGCAATAGAAATAATTTA
GCGGCGTTTGTATAAC
Found at i:69833 original size:22 final size:22
Alignment explanation
Indices: 69803--69851 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
69793 TGTTTTTCTA
*
69803 CTTTCGAATACAAAAATAATAG
1 CTTTTGAATACAAAAATAATAG
** *
69825 CTTTTGAATATGATAATAATAG
1 CTTTTGAATACAAAAATAATAG
69847 CTTTT
1 CTTTT
69852 CAAAACTTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (22 bp):
CTTTTGAATACAAAAATAATAG
Found at i:73423 original size:18 final size:18
Alignment explanation
Indices: 73387--73423 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
73377 AATATTTATT
*
73387 TGATTAATTTAGTATCGA
1 TGATTAATTTAGTAGCGA
*
73405 TGATTAATTTAGTCGCGA
1 TGATTAATTTAGTAGCGA
73423 T
1 T
73424 AATTCTCAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.08, G:0.19, T:0.43
Consensus pattern (18 bp):
TGATTAATTTAGTAGCGA
Found at i:74783 original size:13 final size:14
Alignment explanation
Indices: 74765--74795 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
74755 GTATCATATT
74765 TCACATA-TTCATA
1 TCACATAGTTCATA
74778 TCACATAGTTCATA
1 TCACATAGTTCATA
74792 TCAC
1 TCAC
74796 TTGTATGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.35, C:0.26, G:0.03, T:0.35
Consensus pattern (14 bp):
TCACATAGTTCATA
Found at i:75337 original size:24 final size:24
Alignment explanation
Indices: 75281--75354 Score: 102
Period size: 24 Copynumber: 3.2 Consensus size: 24
75271 TTCCCTTGAA
*
75281 GTGCATCGATGCAT-TC-T-ACA-
1 GTGCATCGATGCATCCCTTAACAT
*
75301 GTGTATCGATGCATCCCTTAACAT
1 GTGCATCGATGCATCCCTTAACAT
75325 GTGCATCGATGCATCCCTTAACAT
1 GTGCATCGATGCATCCCTTAACAT
75349 GTGCAT
1 GTGCAT
75355 AGATACACTC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
22 1 0.02
23 3 0.06
24 29 0.62
ACGTcount: A:0.24, C:0.26, G:0.19, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTAACAT
Done.