Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004569.1 Hibiscus syriacus cultivar Beakdansim tig00010155_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: 84338
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:517 original size:128 final size:128
Alignment explanation
Indices: 283--614 Score: 422
Period size: 128 Copynumber: 2.6 Consensus size: 128
273 AGAGAGAATG
*
283 ATAATA-CTAATTATTTCC-ATCGAGAATAAA-TACCTCTCATGCCTTAAAGCAGTTATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATTA-CTCTCATGCCTTAAAGCAGTCATTTATTA
* * ** * * *
345 CTCCAATCGAAATGAGAGATATCACTATTTCTTCTTAAATTCAATATTGATTCAAGAGAAAAAA
65 CTCCAATCGAAATAAGAGACATCACTATTTCAACCTAAAATCAATATTGATCCAAGAGAAAAAA
* * *
409 ATAATATC-AATTATTTCCAATCGAGAATAAATTATCTCTTATGCCTTAAACCAGTCATTTAATA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATTA-CTCTCATGCCTTAAAGCAGTCATTTATTA
* * **
473 CTCCAATCGAAATAAGAGACATCGCTACTTT-AACCTAAAATCAATATTGATCCGAGAGAAAACG
65 CTCCAATCGAAATAAGAGACATCACTA-TTTCAACCTAAAATCAATATTGATCCAAGAGAAAAAA
* *
537 ATAATATCTAATTATTTCCAATCGAGAATAAATGACATCTCATGCCTTAAAGAAGTCATTTATTA
1 ATAATATCTAATTATTTCCAATCGAGAATAAATTAC-TCTCATGCCTTAAAGCAGTCATTTATTA
* *
602 CTCCTACCGAAAT
65 CTCCAATCGAAAT
615 GAAAAGATAT
Statistics
Matches: 177, Mismatches: 23, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
126 16 0.09
127 13 0.07
128 85 0.48
129 63 0.36
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.32
Consensus pattern (128 bp):
ATAATATCTAATTATTTCCAATCGAGAATAAATTACTCTCATGCCTTAAAGCAGTCATTTATTAC
TCCAATCGAAATAAGAGACATCACTATTTCAACCTAAAATCAATATTGATCCAAGAGAAAAAA
Found at i:1567 original size:106 final size:108
Alignment explanation
Indices: 1428--1621 Score: 261
Period size: 107 Copynumber: 1.8 Consensus size: 108
1418 TAAGAGGGTC
* *
1428 TAAACAACAAATAACCCTAAAATACATAGCATGCATAAGAAA-TGAGTAAATAA-AAATTTAGT-
1 TAAACAACAAATAACCCAAAAATACATAGCATGCATAA-AAACT-AGTAAATAACAAATTCAGTC
* *
1490 CCTATAGGTGACTTACATGCGAAAATACGCTAAACTATGGAAGAG
64 CCTATAGGTGACTAACATGCAAAAATACGCTAAACTATGGAAGAG
* * * *
1535 TAAACAACAAAT-ATCCAAAAATATATATCATGCATAAAAACTAGTAAATAACAAGTTCAGTCCC
1 TAAACAACAAATAACCCAAAAATACATAGCATGCATAAAAACTAGTAAATAACAAATTCAGTCCC
*
1599 TATATGTGACTAACATGCAAAAA
66 TATAGGTGACTAACATGCAAAAA
1622 CATGCGAGAG
Statistics
Matches: 75, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
105 12 0.16
106 29 0.39
107 34 0.45
ACGTcount: A:0.49, C:0.16, G:0.12, T:0.23
Consensus pattern (108 bp):
TAAACAACAAATAACCCAAAAATACATAGCATGCATAAAAACTAGTAAATAACAAATTCAGTCCC
TATAGGTGACTAACATGCAAAAATACGCTAAACTATGGAAGAG
Found at i:2601 original size:3 final size:3
Alignment explanation
Indices: 2593--2633 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
2583 CTTGGCTTGC
*
2593 ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2634 GTCAGGATGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:3068 original size:133 final size:132
Alignment explanation
Indices: 2931--3184 Score: 312
Period size: 133 Copynumber: 1.9 Consensus size: 132
2921 CTACTTAGAA
* * * * * ** *
2931 AAGATCAAATATGGAAAGAGGGGATCTA-TTCCGTTGCTTATTCAGGGGAAATCTGATATGGAGA
1 AAGATCAAATATAGAAAGAGAGAAT-AAGTTCCGCTGCTTATTCAGGAAAAATCAGATATGGAGA
* * *
2995 CATTGATTCATTCCACTATTCTTTAGGGAAGATTGAGTCGAGGCAGACTCGTTCCACTGCTGATC
65 CATCGATTCATCCCA-TATTCTTTAGGGAAGATTGAATCGAGGCAGACTCGTTCCACTGCTGATC
3060 AGGG
129 AGGG
* * * * *
3064 AAGATCAAATCTAGAAAGAGAGAATAAGTTCCGCTGCTTCTTCATGAAAAATCAGATTTGGAGAT
1 AAGATCAAATATAGAAAGAGAGAATAAGTTCCGCTGCTTATTCAGGAAAAATCAGATATGGAGAC
* * *
3129 GTCGATTCATCCCATGTTCTTTAGGGAAGATTGAATCGAGGCAGACTTGTTCCACT
66 ATCGATTCATCCCATATTCTTTAGGGAAGATTGAATCGAGGCAGACTCGTTCCACT
3185 TATCTTCAAG
Statistics
Matches: 101, Mismatches: 19, Indels: 3
0.82 0.15 0.02
Matches are distributed among these distances:
132 40 0.40
133 61 0.60
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (132 bp):
AAGATCAAATATAGAAAGAGAGAATAAGTTCCGCTGCTTATTCAGGAAAAATCAGATATGGAGAC
ATCGATTCATCCCATATTCTTTAGGGAAGATTGAATCGAGGCAGACTCGTTCCACTGCTGATCAG
GG
Found at i:31405 original size:22 final size:22
Alignment explanation
Indices: 31380--31440 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 22
31370 AATATTATGA
31380 AATTATTTAAAAATATTTATTT
1 AATTATTTAAAAATATTTATTT
*
31402 AA-T-TTT-AAAATCATATATTT
1 AATTATTTAAAAAT-ATTTATTT
*
31422 ACTTATTTGAAATAATATT
1 AATTATTT-AAA-AATATT
31441 AATTCTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 10
0.70 0.07 0.23
Matches are distributed among these distances:
19 5 0.17
20 11 0.37
21 2 0.07
22 5 0.17
24 4 0.13
25 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (22 bp):
AATTATTTAAAAATATTTATTT
Found at i:31411 original size:19 final size:20
Alignment explanation
Indices: 31384--31422 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
31374 TTATGAAATT
*
31384 ATTTAAAAAT-ATTTATTTA
1 ATTTAAAAATCATATATTTA
*
31403 ATTTTAAAATCATATATTTA
1 ATTTAAAAATCATATATTTA
31423 CTTATTTGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTTAAAAATCATATATTTA
Found at i:31815 original size:20 final size:20
Alignment explanation
Indices: 31790--31860 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
31780 ATACTAATAT
31790 AAAATTATTAATTAGGTTAA
1 AAAATTATTAATTAGGTTAA
* * **
31810 AAAATTAATTCAATCA-ATTTT
1 AAAATT-ATT-AATTAGGTTAA
31831 AAAATTATTAATTAGGTTAA
1 AAAATTATTAATTAGGTTAA
*
31851 AAATTTATTA
1 AAAATTATTA
31861 TTATTATTAT
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 4 0.10
20 20 0.51
21 11 0.28
22 4 0.10
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.42
Consensus pattern (20 bp):
AAAATTATTAATTAGGTTAA
Found at i:31863 original size:3 final size:3
Alignment explanation
Indices: 31855--31889 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
31845 GGTTAAAAAT
*
31855 TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
31890 TCTTTTAACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35985 original size:3 final size:3
Alignment explanation
Indices: 35977--36040 Score: 110
Period size: 3 Copynumber: 21.3 Consensus size: 3
35967 TAATTGTTTA
35977 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
36025 ATT AAT ATT AAT AAT A
1 AAT AAT AAT AAT AAT A
36041 CAGTTTTGTA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:36185 original size:2 final size:2
Alignment explanation
Indices: 36178--36225 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
36168 TATTTATAAC
36178 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
36220 TA TA TA
1 TA TA TA
36226 ATTGAAAGAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:39296 original size:17 final size:17
Alignment explanation
Indices: 39274--39314 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
39264 CCCGGATTAG
*
39274 TAAAAAAATAAAAAAAA
1 TAAAAAAACAAAAAAAA
*
39291 TAAAAAAACAAAAGAAA
1 TAAAAAAACAAAAAAAA
*
39308 GAAAAAA
1 TAAAAAA
39315 GTTTAAAGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.85, C:0.02, G:0.05, T:0.07
Consensus pattern (17 bp):
TAAAAAAACAAAAAAAA
Found at i:44042 original size:64 final size:64
Alignment explanation
Indices: 43939--44095 Score: 165
Period size: 64 Copynumber: 2.5 Consensus size: 64
43929 TTCAGTGTGT
* ** * * * *
43939 ATCGATGCACAGAAAGTACATCGATGCACCCATTAAAAATGGAAATATCGAATGCAATTAGTGC
1 ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAAATGAAAAAATCGAAGGCAATTAGTGC
* ** *
44003 ATCGATGCATAAGG-AGTGCATCGATGCACCC-TCTTAAAATGAAAAAATCGAAGGTGATTTGTG
1 ATCGATGCAT-AGGTAGTGCATCGATGCACCCAT-TAAAAATGAAAAAATCGAAGGCAATTAGTG
*
44066 T
64 C
*
44067 ATCGATGCATTGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGTAGTGCATCGATGCAC
44096 TTCAAGGAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
63 3 0.04
64 73 0.94
65 2 0.03
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (64 bp):
ATCGATGCATAGGTAGTGCATCGATGCACCCATTAAAAATGAAAAAATCGAAGGCAATTAGTGC
Found at i:45219 original size:2 final size:2
Alignment explanation
Indices: 45212--45250 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
45202 TAGGAAAAAT
* * *
45212 TA TA TA TA TA AA TA TA TA TC TA TT 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 T
45251 GAAGATGAAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45319 original size:2 final size:2
Alignment explanation
Indices: 45312--45373 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
45302 GAACATGGGA
45312 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
45354 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
45374 GATAAGACAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50457 original size:2 final size:2
Alignment explanation
Indices: 50450--50483 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
50440 TAGTAAAAAT
*
50450 TA TA TA TA TA AA 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
50484 GGATTATGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:50947 original size:23 final size:23
Alignment explanation
Indices: 50896--50954 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
50886 ACAACCTTAT
50896 ATGGCACTTCGGTGAATTTCTAC
1 ATGGCACTTCGGTGAATTTCTAC
**
50919 GCGGCACTAT-GGTGCAA-TTCTAC
1 ATGGCACT-TCGGTG-AATTTCTAC
*
50942 ATGGCAGTTCGGT
1 ATGGCACTTCGGT
50955 ACATTTATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 6
0.72 0.13 0.15
Matches are distributed among these distances:
22 1 0.04
23 24 0.86
24 3 0.11
ACGTcount: A:0.20, C:0.22, G:0.27, T:0.31
Consensus pattern (23 bp):
ATGGCACTTCGGTGAATTTCTAC
Found at i:52431 original size:273 final size:277
Alignment explanation
Indices: 52068--52621 Score: 909
Period size: 282 Copynumber: 2.0 Consensus size: 277
52058 GCTACTATTT
* **
52068 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTGATGTGGTGAATCGAGTACTTTCCATGTT
1 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTAAAATGGTGAATCGAGTACTTTCCATGTT
*
52133 ACTTCGATCTATCATTCGGAAGAATTT-G-A-A-AAAATGGGAGGAGAGTTTACCACATGTGGAG
66 ACTTCGATCTATCATTCGAAAGAATTTAGAATAGAAAATGGGAGGAGAGTTTACCACATGTGGAG
*
52194 TTTGCATACAACCGTTCAATCCATACTACTACAGGGCGTACACCTTTCGAAGTGGTGTATGGGTT
131 TTTGCATACAACCGTTCAATCCATACTACTACAGGGCGTACACCTTTCAAAGTGGTGTATGGGTT
* *
52259 CAATCCATTAACACCAATAGACTTGTTACCATTACCTGCTGATCAAATTATGAATAAAGATGGAC
196 CAATCCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAAATGGAC
52324 TTAACAAAGCTGAGTTC
261 TTAACAAAGCTGAGTTC
* * *
52341 TCCACCATTTGCCACCCTCAAACGGATGGTCAAACTAAAATGGTGAATCGAGTATTTTCCATGTT
1 TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTAAAATGGTGAATCGAGTACTTTCCATGTT
52406 ACTTCGATCTATCATTCGAAAGAATTTGAGAAAATTGAGAAAATGGGAGGAGAGTTTACCACATG
66 ACTTCGATCTATCATTCGAAAGAATTT-AG--AA-T-AGAAAATGGGAGGAGAGTTTACCACATG
* * *
52471 TGGAGTTTGCATACAACCGTTCAATCTATACTACTACGGGGCGTACGCCTTTCAAAGTGGTGTAT
126 TGGAGTTTGCATACAACCGTTCAATCCATACTACTACAGGGCGTACACCTTTCAAAGTGGTGTAT
*
52536 GGGTTCAATCCATTAACACCGATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAAA
191 GGGTTCAATCCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAAA
52601 TGGACTTAACAAAGCTGAGTT
256 TGGACTTAACAAAGCTGAGTT
52622 TGTTAAGAAG
Statistics
Matches: 258, Mismatches: 14, Indels: 9
0.92 0.05 0.03
Matches are distributed among these distances:
273 85 0.33
275 1 0.00
278 1 0.00
281 1 0.00
282 170 0.66
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (277 bp):
TCCACCACTTGCCACCCTCAAACGAATGGTCAAACTAAAATGGTGAATCGAGTACTTTCCATGTT
ACTTCGATCTATCATTCGAAAGAATTTAGAATAGAAAATGGGAGGAGAGTTTACCACATGTGGAG
TTTGCATACAACCGTTCAATCCATACTACTACAGGGCGTACACCTTTCAAAGTGGTGTATGGGTT
CAATCCATTAACACCAATAGACTTGTTACCATTACCTGCTAATCAAATTATGAATAAAAATGGAC
TTAACAAAGCTGAGTTC
Found at i:54259 original size:18 final size:18
Alignment explanation
Indices: 54236--54287 Score: 95
Period size: 18 Copynumber: 2.9 Consensus size: 18
54226 ACAACACTTA
*
54236 CCACGACAACACCATTTG
1 CCACGACAACGCCATTTG
54254 CCACGACAACGCCATTTG
1 CCACGACAACGCCATTTG
54272 CCACGACAACGCCATT
1 CCACGACAACGCCATT
54288 CATATTTCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.31, C:0.40, G:0.13, T:0.15
Consensus pattern (18 bp):
CCACGACAACGCCATTTG
Found at i:71751 original size:48 final size:48
Alignment explanation
Indices: 71691--71783 Score: 177
Period size: 48 Copynumber: 1.9 Consensus size: 48
71681 ATCAACAAGC
71691 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
1 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
*
71739 TTTTCAATATATGATAAATTATAGAATTACTAGAGATATTTGAGA
1 TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGA
71784 AAGAGATGGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.42, C:0.05, G:0.15, T:0.38
Consensus pattern (48 bp):
TTTTCAACATATGATAAATTATAGAATTACTAGAGATATTTGAGAGAG
Found at i:79500 original size:2 final size:2
Alignment explanation
Indices: 79493--79523 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
79483 CTCAAGAATA
79493 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
79524 CTCATATGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84145 original size:14 final size:14
Alignment explanation
Indices: 84126--84155 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
84116 TGCTTTCTTT
84126 CTTTTCAATTTTCA
1 CTTTTCAATTTTCA
*
84140 CTTTTCAGTTTTCA
1 CTTTTCAATTTTCA
84154 CT
1 CT
84156 ATATTTGTGG
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:0.17, C:0.23, G:0.03, T:0.57
Consensus pattern (14 bp):
CTTTTCAATTTTCA
Done.