Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008157.1 Hibiscus syriacus cultivar Beakdansim tig00110724_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: 217995
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:179846 original size:13 final size:13
Alignment explanation
Indices: 179828--179876 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
179818 AATAAAAATA
179828 ATTAAATACAAAC
1 ATTAAATACAAAC
179841 ATTAAATACAAAC
1 ATTAAATACAAAC
* *
179854 ATTATAATTCAAATA
1 ATTA-AATACAAA-C
179869 ATTAAATA
1 ATTAAATA
179877 ATAAAAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 17 0.55
14 10 0.32
15 4 0.13
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:179901 original size:21 final size:21
Alignment explanation
Indices: 179876--179942 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 21
179866 ATAATTAAAT
179876 AATAAAAACATTAAAAAACAA
1 AATAAAAACATTAAAAAACAA
* ** * **
179897 AATAAATA-A-TCCATAATTA
1 AATAAAAACATTAAAAAACAA
*
179916 AATAAAAACATTAAGAAACAA
1 AATAAAAACATTAAAAAACAA
179937 AATAAA
1 AATAAA
179943 GAAAAATAAG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
19 12 0.39
20 2 0.06
21 17 0.55
ACGTcount: A:0.70, C:0.09, G:0.01, T:0.19
Consensus pattern (21 bp):
AATAAAAACATTAAAAAACAA
Found at i:182281 original size:6 final size:6
Alignment explanation
Indices: 182270--182320 Score: 77
Period size: 6 Copynumber: 8.5 Consensus size: 6
182260 AGATGTTTAT
*
182270 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGG- AGGGGG AGGCGGA
1 AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGGGGA AGG-GGA
182318 AGG
1 AGG
182321 ATGGTTGGAT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
5 5 0.12
6 32 0.76
7 5 0.12
ACGTcount: A:0.29, C:0.02, G:0.69, T:0.00
Consensus pattern (6 bp):
AGGGGA
Found at i:183634 original size:2 final size:2
Alignment explanation
Indices: 183627--183665 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
183617 ATTTAATTTG
*
183627 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
183666 ATGGTATTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:183965 original size:19 final size:18
Alignment explanation
Indices: 183941--183993 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
183931 TAAAAAAAGA
183941 TAAAAATATTGACACCACT
1 TAAAAATATTGACA-CACT
*
183960 TAAAAAATATTGACACTCT
1 T-AAAAATATTGACACACT
*
183979 TAAAGAAAATTGACA
1 TAAA-AATATTGACA
183994 TCGATGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 3 0.10
19 14 0.47
20 13 0.43
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (18 bp):
TAAAAATATTGACACACT
Found at i:183967 original size:20 final size:19
Alignment explanation
Indices: 183942--183993 Score: 70
Period size: 20 Copynumber: 2.7 Consensus size: 19
183932 AAAAAAAGAT
183942 AAAAATATTGACACCACTTA
1 AAAAATATTGACA-CACTTA
*
183962 AAAAATATTGACACTCTTA
1 AAAAATATTGACACACTTA
183981 AAGAAA-ATTGACA
1 AA-AAATATTGACA
183994 TCGATGTTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.52, C:0.15, G:0.08, T:0.25
Consensus pattern (19 bp):
AAAAATATTGACACACTTA
Found at i:184185 original size:21 final size:21
Alignment explanation
Indices: 184144--184185 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
184134 ATAATAAACT
*
184144 TTTATTATAAGTACTACTTTA
1 TTTATTATAAGTACCACTTTA
* *
184165 TTTATTATAGGTACCATTTTA
1 TTTATTATAAGTACCACTTTA
184186 AAAGTAATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.10, G:0.07, T:0.52
Consensus pattern (21 bp):
TTTATTATAAGTACCACTTTA
Found at i:184244 original size:16 final size:18
Alignment explanation
Indices: 184223--184259 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
184213 ATTGATAAAA
184223 AAAAAT-ATACTAA-TTT
1 AAAAATAATACTAAGTTT
184239 AAAAATAAATACTAAGTTT
1 AAAAAT-AATACTAAGTTT
184258 AA
1 AA
184260 GAATCAAATC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.33
18 7 0.39
19 5 0.28
ACGTcount: A:0.59, C:0.05, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAAATAATACTAAGTTT
Found at i:185627 original size:90 final size:90
Alignment explanation
Indices: 185511--185688 Score: 320
Period size: 90 Copynumber: 2.0 Consensus size: 90
185501 TAATCTCGAA
* *
185511 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
185576 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTCGGATATAAAAGGAT
185601 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
*
185666 TAGGGTAACTCGGCTATAAAAGG
66 TAGGGTAACTCGGATATAAAAGG
185689 GTGTGTTAGG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
90 84 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTCGGATATAAAAGGAT
Found at i:187646 original size:19 final size:19
Alignment explanation
Indices: 187619--187656 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
187609 GGTTCGCCGC
* *
187619 CGATGAGCGGTGGCCGGCG
1 CGATCAGCGGCGGCCGGCG
187638 CGATCAGCGGCGGCCGGCG
1 CGATCAGCGGCGGCCGGCG
187657 TGGTGGCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.11, C:0.32, G:0.50, T:0.08
Consensus pattern (19 bp):
CGATCAGCGGCGGCCGGCG
Found at i:189410 original size:10 final size:10
Alignment explanation
Indices: 189397--189428 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
189387 TTATTTCTTG
189397 TTATTTTTAT
1 TTATTTTTAT
*
189407 TTATTTTCAT
1 TTATTTTTAT
189417 TTATTTTTAT
1 TTATTTTTAT
189427 TT
1 TT
189429 TACTAACCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (10 bp):
TTATTTTTAT
Found at i:198847 original size:1 final size:1
Alignment explanation
Indices: 198841--198866 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
198831 TCCTAAGTTG
198841 AAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAA
198867 CGTTTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:199850 original size:105 final size:103
Alignment explanation
Indices: 199668--200336 Score: 944
Period size: 105 Copynumber: 6.5 Consensus size: 103
199658 AGGTTTTACC
* *
199668 CAGAGCCAATTTCAAATTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
199733 ACGAAGGGACCGCTGGTTGTCAACAAATATTTCTCAATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-ATTTC-CAATTT
199773 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
199838 ACGAAAGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-ATTTC-CAATTT
199878 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
199943 ACGAAGGGACCGCTGGTTGTCAA-TAAA----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
* *
199976 CAGGGCCAATTTCAACTTCATAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
200041 ACGAAGGGACCGCTGGTTGTCAA-TAAA----CAATTC
66 ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
*
200074 CAGAGCCAATTTCAACTTCACAACAAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
200139 ACGAAGGGACTGCTGGTTGTCAATAAACAACTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAA-CAA-AA-TTTCCAATTT
* * * * *
200180 CAGAGCCAATTTCAACTTCACAACGAAGGAGATTGGGCCCCAGACAACACAAGTTCAACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
200245 ACGAAGGGACCGCTGGTTGTCAACAAGTAATTTCCCGGTTT
66 ACGAAGGGACCGCTGGTTGTCAACAA--AATTT-CCAATTT
* * * * * *
200286 TAGAGCCAATTTCAACTTCACATCAAAGGATATTGGCCTCGAAACAACGCA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCA
200337 TCTTGCATTG
Statistics
Matches: 517, Mismatches: 37, Indels: 19
0.90 0.06 0.03
Matches are distributed among these distances:
98 185 0.36
100 1 0.00
101 2 0.00
103 1 0.00
104 2 0.00
105 191 0.37
106 135 0.26
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (103 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAAATTTCCAATTT
Found at i:201486 original size:20 final size:20
Alignment explanation
Indices: 201461--201502 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
201451 CAAGGTTCGC
* *
201461 CGCCGATGAGCGGTGGCCGG
1 CGCCGATCAGCGGCGGCCGG
201481 CGCCGATCAGCGGCGGCCGG
1 CGCCGATCAGCGGCGGCCGG
201501 CG
1 CG
201503 TGGTGGCCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.36, G:0.48, T:0.07
Consensus pattern (20 bp):
CGCCGATCAGCGGCGGCCGG
Found at i:202865 original size:30 final size:31
Alignment explanation
Indices: 202795--202868 Score: 80
Period size: 30 Copynumber: 2.4 Consensus size: 31
202785 AACGTCAAAG
* ** *
202795 TGACCAAAACTTAATAAAACAATAATGTAAG
1 TGACTAAAACTTAATAAAACAATAACATAAA
*
202826 TGA-TCAAAACTTAAT-AAATAATAACATAAA
1 TGACT-AAAACTTAATAAAACAATAACATAAA
202856 TGACTAAAACTTA
1 TGACTAAAACTTA
202869 TGTTTTTCTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
30 22 0.61
31 14 0.39
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.26
Consensus pattern (31 bp):
TGACTAAAACTTAATAAAACAATAACATAAA
Done.