Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000246.1 Hibiscus syriacus cultivar Beakdansim tig00000433_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: 74513
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Found at i:217 original size:76 final size:79
Alignment explanation
Indices: 1--221 Score: 333
Period size: 80 Copynumber: 2.8 Consensus size: 79
1 TCCTTAGGTCCGTAGGG-TACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGG
1 TCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGG
65 GGCCTACCCAAGATA
66 GGCC-ACCCAAGATA
* * *
80 TACTTAGGTCCGTAGGGTTACCTTATGCACACAGCAAAAGAAACCAACCTAAGGATATGCCTTGG
1 TCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGG
* *
145 GGCC-GCCTAGATA
66 GGCCACCCAAGATA
* * *
158 TCCTTAGGTCTGTAGGGTTA-C-TATGCACACAATAAAGGAAACCAACCTAAGGATGTGCCTTGG
1 TCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGG
221 G
66 G
222 CTATCCAAGT
Statistics
Matches: 130, Mismatches: 11, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
76 39 0.30
77 1 0.01
78 25 0.19
79 16 0.12
80 49 0.38
ACGTcount: A:0.31, C:0.24, G:0.23, T:0.22
Consensus pattern (79 bp):
TCCTTAGGTCCGTAGGGTTACCTTATGCACACAACAAAGGAAACCAACCTAAGGATATGCCTTGG
GGCCACCCAAGATA
Found at i:5525 original size:79 final size:80
Alignment explanation
Indices: 5205--5657 Score: 664
Period size: 80 Copynumber: 5.7 Consensus size: 80
5195 CAACAAAAAG
* * * * * *
5205 GGAATCCAGCCTAAGGATATACCTTGAGTCC-ACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACC
** *
5269 TTAAACACACAGCTAA
65 TTATGCACACAGCAAA
*
5285 GGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
5350 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * *
5365 GGAAACCATCCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGAGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
5430 TATGCACACAGCAAA
66 TATGCACACAGCAAA
*
5445 GGAAACCAACCTAAGGATATGCCTTGGGG-CTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
5509 TATGCACACAGCAAA
66 TATGCACACAGCAAA
* * * *
5524 GGAAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCCTAGGT-TGTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
5588 TATGCACACAGC-AA
66 TATGCACACAGCAAA
* * *
5602 GAAAAACCAACCTAAGGATGTGCCTT-GGGCCTACCCAAGATATCCTTAGGTCCGTA
1 G-GAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
5658 AGGACTTACA
Statistics
Matches: 343, Mismatches: 26, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
78 27 0.08
79 124 0.36
80 186 0.54
81 6 0.02
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (80 bp):
GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCT
TATGCACACAGCAAA
Found at i:5549 original size:159 final size:158
Alignment explanation
Indices: 5205--5657 Score: 676
Period size: 159 Copynumber: 2.8 Consensus size: 158
5195 CAACAAAAAG
* * * * * * *
5205 GGAATCCAGCCTAAGGATATACCTTGAGTCC-ACCCAAGGACATCCTTAGATCCGTAGGGTTACC
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAA-GATATCCTTAGGTTCGTAGGGTTACC
** * *
5269 TTAAACACACAGCTAAGGGAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAG
65 TTATGCACACAGC-AAGGAAACCAACCTAAGGATATGCCTTGGGG-CTACCCAAGATATCCTTAG
5334 GTCCGTAGGGTTACCTTATGCACACAGCAAA
128 GTCCGTAGGGTTACCTTATGCACACAGCAAA
* *
5365 GGAAACCATCCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGAGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
5430 TATGCACACAGCAAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
66 TATGCACACAGC-AAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
5495 CCGTAGGGTTACCTTATGCACACAGCAAA
130 CCGTAGGGTTACCTTATGCACACAGCAAA
* * *
5524 GGAAACTAACCTAAGGATATGCCTTGGGGCCTACCCAAGATATCCCTAGGTT-GTAGGGTTACCT
1 GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
* * *
5588 TATGCACACAGCAAGAAAAACCAACCTAAGGATGTGCCTTGGGCCTACCCAAGATATCCTTAGGT
66 TATGCACACAGCAAG-GAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGT
5653 CCGTA
130 CCGTA
5658 AGGACTTACA
Statistics
Matches: 270, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
157 3 0.01
158 74 0.27
159 98 0.36
160 89 0.33
161 6 0.02
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (158 bp):
GGAAACCAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTTCGTAGGGTTACCT
TATGCACACAGCAAGGAAACCAACCTAAGGATATGCCTTGGGGCTACCCAAGATATCCTTAGGTC
CGTAGGGTTACCTTATGCACACAGCAAA
Found at i:8068 original size:28 final size:28
Alignment explanation
Indices: 8037--8090 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
8027 ATATGCAGTT
*
8037 GAAAGTGCCTCATAGATAATTTGCACTC
1 GAAAGTACCTCATAGATAATTTGCACTC
8065 GAAAGTACCTCATAGATAATTTGCAC
1 GAAAGTACCTCATAGATAATTTGCAC
8091 CATAGGTTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (28 bp):
GAAAGTACCTCATAGATAATTTGCACTC
Found at i:43685 original size:2 final size:2
Alignment explanation
Indices: 43678--43745 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
43668 ATCTGTTTAC
43678 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
43720 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
43746 GAACCTCTTT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44887 original size:23 final size:22
Alignment explanation
Indices: 44861--44903 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
44851 TATAAAAAAT
44861 TATTTTTTATTAAATATTTTTGA
1 TATTTTTTATTAAAT-TTTTTGA
*
44884 TATTTTTTATTTAATTTTTT
1 TATTTTTTATTAAATTTTTT
44904 AAATAATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (22 bp):
TATTTTTTATTAAATTTTTTGA
Found at i:45497 original size:2 final size:2
Alignment explanation
Indices: 45490--45541 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
45480 ATATACATTG
45490 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
45532 AT AT AT AT AT
1 AT AT AT AT AT
45542 GTATTTAATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46288 original size:13 final size:13
Alignment explanation
Indices: 46270--46296 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46260 CATAGTTGAA
46270 CAGTCTTCATATG
1 CAGTCTTCATATG
46283 CAGTCTTCATATG
1 CAGTCTTCATATG
46296 C
1 C
46297 GCGTATGTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (13 bp):
CAGTCTTCATATG
Found at i:52175 original size:13 final size:13
Alignment explanation
Indices: 52157--52190 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
52147 AATGGGCAAT
52157 TTTGAAAACTAAG-
1 TTTGAAAAC-AAGA
52170 TTTGAAAACAAGA
1 TTTGAAAACAAGA
52183 TTTGAAAA
1 TTTGAAAA
52191 TCAATATACG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.50, C:0.06, G:0.15, T:0.29
Consensus pattern (13 bp):
TTTGAAAACAAGA
Found at i:52693 original size:23 final size:23
Alignment explanation
Indices: 52641--52694 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
52631 TCGATTCCCT
* *
52641 AAAGGGGGAATTGGTTCTCATTC
1 AAAGGGGGAATTGGTTCCCATGC
*
52664 AAAGGGGGAATTGGTTCCCCTGC
1 AAAGGGGGAATTGGTTCCCATGC
*
52687 AAGGGGGG
1 AAAGGGGG
52695 TATCGATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.15, G:0.39, T:0.22
Consensus pattern (23 bp):
AAAGGGGGAATTGGTTCCCATGC
Found at i:58407 original size:18 final size:19
Alignment explanation
Indices: 58384--58422 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
58374 AATTTAATCG
*
58384 AATATATAA-TTAAAATTC
1 AATATAAAACTTAAAATTC
58402 AATATAAAATCTTAAAATTC
1 AATATAAAA-CTTAAAATTC
58422 A
1 A
58423 TTAACACTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
20 10 0.56
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (19 bp):
AATATAAAACTTAAAATTC
Found at i:59514 original size:3 final size:3
Alignment explanation
Indices: 59501--59556 Score: 105
Period size: 3 Copynumber: 19.0 Consensus size: 3
59491 GAAATCAAAC
59501 ATA AT- ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
59548 ATA ATA ATA
1 ATA ATA ATA
59557 GTGATAGTAA
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 50 0.96
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:63227 original size:20 final size:20
Alignment explanation
Indices: 63202--63239 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63192 TTTCATCTCA
*
63202 GTTCATCTAGTATCGATATT
1 GTTCATCCAGTATCGATATT
63222 GTTCATCCAGTATCGATA
1 GTTCATCCAGTATCGATA
63240 CTGAGAGGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.39
Consensus pattern (20 bp):
GTTCATCCAGTATCGATATT
Found at i:63442 original size:20 final size:20
Alignment explanation
Indices: 63417--63454 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
63407 TTTTGTCCTA
*
63417 GTTCATCTAGTATTGATATT
1 GTTCATCTAGTATCGATATT
63437 GTTCATCTAGTATCGATA
1 GTTCATCTAGTATCGATA
63455 CTTAAACTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.13, G:0.16, T:0.45
Consensus pattern (20 bp):
GTTCATCTAGTATCGATATT
Found at i:64017 original size:2 final size:2
Alignment explanation
Indices: 63997--64038 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
63987 GTTACATGTT
*
63997 TA TA T- TA TG TA TA -A 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
64037 TA
1 TA
64039 ATCTATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:64088 original size:21 final size:22
Alignment explanation
Indices: 64062--64146 Score: 74
Period size: 20 Copynumber: 4.0 Consensus size: 22
64052 TATCTTGTGA
*
64062 TATTTTTTA-ATTTTAAAATAT
1 TATTTTTTAGATTTTTAAATAT
*
64083 TA-TTTTTAG-TATTTT-AATTT
1 TATTTTTTAGAT-TTTTAAATAT
*
64103 TATTTTTTAGTATTTTTATATA-
1 TATTTTTTAG-ATTTTTAAATAT
*
64125 TA-TTTTTAAATTTTTAAATAT
1 TATTTTTTAGATTTTTAAATAT
64146 T
1 T
64147 TTATATTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 14
0.72 0.08 0.20
Matches are distributed among these distances:
20 23 0.45
21 19 0.37
22 6 0.12
23 3 0.06
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (22 bp):
TATTTTTTAGATTTTTAAATAT
Found at i:64096 original size:22 final size:22
Alignment explanation
Indices: 64071--64146 Score: 79
Period size: 21 Copynumber: 3.6 Consensus size: 22
64061 ATATTTTTTA
*
64071 ATTTTAAAATATTATTTTTAGT
1 ATTTTTAAATATTATTTTTAGT
*
64093 A-TTTT-AATTTTATTTTTTAGT
1 ATTTTTAAATATTA-TTTTTAGT
* *
64114 ATTTTTATATA-TATTTTTA-A
1 ATTTTTAAATATTATTTTTAGT
64134 ATTTTTAAATATT
1 ATTTTTAAATATT
64147 TTATATTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 16 0.36
21 19 0.43
22 7 0.16
23 2 0.05
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (22 bp):
ATTTTTAAATATTATTTTTAGT
Found at i:64727 original size:25 final size:25
Alignment explanation
Indices: 64694--64744 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
64684 TTTTATTAAG
64694 AAAAATATATTATCAATACTTTTTA
1 AAAAATATATTATCAATACTTTTTA
64719 AAAAATATATTATCAATACTTTTTA
1 AAAAATATATTATCAATACTTTTTA
64744 A
1 A
64745 CATGTGGACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (25 bp):
AAAAATATATTATCAATACTTTTTA
Found at i:65522 original size:30 final size:29
Alignment explanation
Indices: 65488--65561 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 29
65478 ATGAAAAGTC
* *
65488 ATAAATCGATCACTCACGTTATCATTTGTT
1 ATAAAT-GATCACTAACATTATCATTTGTT
* *
65518 ATAAAATGGTCACTAACATTATCGTTTGTT
1 AT-AAATGATCACTAACATTATCATTTGTT
*
65548 ATAAAATGGTCACT
1 AT-AAATGATCACT
65562 TTACATTAAC
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
30 35 0.90
31 4 0.10
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (29 bp):
ATAAATGATCACTAACATTATCATTTGTT
Found at i:67056 original size:73 final size:73
Alignment explanation
Indices: 66933--67078 Score: 247
Period size: 73 Copynumber: 2.0 Consensus size: 73
66923 ATTAAATAAT
* **
66933 TAATTTATAATTCAAATTGAATTGGTAAAGTAAAATTATACAACTAGTGTAACTAAATGAACCAT
1 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
66998 TTCCTTAA
66 TTCCTTAA
* *
67006 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTTGTGTAACTAAATGAATCAT
1 TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
67071 TTCCTTAA
66 TTCCTTAA
67079 ATAAAAATGA
Statistics
Matches: 68, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
73 68 1.00
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.36
Consensus pattern (73 bp):
TAATTTATAATTCAAATTGAATTGGTAAAATAAAAGCATACAACTAGTGTAACTAAATGAACCAT
TTCCTTAA
Found at i:71254 original size:19 final size:18
Alignment explanation
Indices: 71232--71272 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
71222 CCACCAACAT
*
71232 AAATTAAACATAACAAATA
1 AAATTAAA-ATAAAAAATA
*
71251 AAATTAAAATAAAAAATT
1 AAATTAAAATAAAAAATA
71269 AAAT
1 AAAT
71273 ACGACATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (18 bp):
AAATTAAAATAAAAAATA
Found at i:71719 original size:22 final size:20
Alignment explanation
Indices: 71694--71733 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
71684 CGCTGAATGT
71694 TGAACGGTTCAACATTCAGCGC
1 TGAACGGTTC--CATTCAGCGC
*
71716 TGAATGGTTCCATTCAGC
1 TGAACGGTTCCATTCAGC
71734 AGTAAACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
22 9 0.53
ACGTcount: A:0.25, C:0.25, G:0.23, T:0.28
Consensus pattern (20 bp):
TGAACGGTTCCATTCAGCGC
Done.