Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005530.1 Hibiscus syriacus cultivar Beakdansim tig00012787_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: 255786
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
File 2 of 2
Found at i:219767 original size:24 final size:24
Alignment explanation
Indices: 219717--219767 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
219707 AGGTTAACGG
* *
219717 GTTAACTCGGTCAACCCGATCTGA
1 GTTAACTCGATCAACCCGATCTAA
* * *
219741 GTTAACTCGATCAGCTCGGTCTAA
1 GTTAACTCGATCAACCCGATCTAA
219765 GTT
1 GTT
219768 GACTTTGCTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.24, C:0.25, G:0.22, T:0.29
Consensus pattern (24 bp):
GTTAACTCGATCAACCCGATCTAA
Found at i:224368 original size:30 final size:30
Alignment explanation
Indices: 224334--224415 Score: 105
Period size: 30 Copynumber: 2.7 Consensus size: 30
224324 AATCGAAAAT
*
224334 TTAAA-TTTTGAAAATTTACACTTTTAGTTC
1 TTAAACTTTT-AAAATTTACACTTTTAGTCC
*
224364 TTAAACTTTTACAATTTTACAC-TTTAGTCC
1 TTAAACTTTTA-AAATTTACACTTTTAGTCC
*
224394 GTAAACTTTTAAAATTTACACT
1 TTAAACTTTTAAAATTTACACT
224416 CCAGTCACCA
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
29 9 0.20
30 23 0.51
31 13 0.29
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (30 bp):
TTAAACTTTTAAAATTTACACTTTTAGTCC
Found at i:224421 original size:29 final size:30
Alignment explanation
Indices: 224365--224421 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
224355 TTTTAGTTCT
* **
224365 TAAACTTTTACAATTTTACACTTTAGTCCG
1 TAAACTTTTACAAATTTACACTCCAGTCCG
224395 TAAACTTTTA-AAATTTACACTCCAGTC
1 TAAACTTTTACAAATTTACACTCCAGTC
224422 ACCAGTTCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 14 0.58
30 10 0.42
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (30 bp):
TAAACTTTTACAAATTTACACTCCAGTCCG
Found at i:225840 original size:23 final size:23
Alignment explanation
Indices: 225809--225869 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 23
225799 CACCACAGCT
* *
225809 CGTATAATTGCATCGAAGTACCA
1 CGTAGAATTGCACCGAAGTACCA
* * *
225832 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTACCA
*
225855 CGTAGAATTACACCG
1 CGTAGAATTGCACCG
225870 TAGTGCCATA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTACCA
Found at i:225874 original size:23 final size:23
Alignment explanation
Indices: 225832--225876 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
225822 CGAAGTACCA
*
225832 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTACACCGGAGTGCCG
*
225855 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGGAGTGCC
225877 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.29, T:0.20
Consensus pattern (23 bp):
CGTAGAATTACACCGGAGTGCCG
Found at i:226056 original size:103 final size:103
Alignment explanation
Indices: 225893--226105 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
225883 TAATGTCCAT
* *
225893 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
* *
225958 GACTTCACACATGTTCTAAAGAATATATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
225996 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
226061 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
226099 AAGGACC
1 AAGGACC
226106 GCGTAGACCC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:231037 original size:23 final size:23
Alignment explanation
Indices: 231011--231079 Score: 77
Period size: 23 Copynumber: 3.0 Consensus size: 23
231001 CACCACAGCT
* *
231011 CGTATAATTACACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
231034 CGTAGAATTGTACC-AGAGTGCCG
1 CGTAGAATTGCACCGA-AGTGCCA
*
231057 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
231080 TATAATAATG
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
22 1 0.03
23 36 0.97
ACGTcount: A:0.29, C:0.25, G:0.25, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:231266 original size:103 final size:103
Alignment explanation
Indices: 231095--231307 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
231085 TAATGTCCAT
* * * *
231095 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCAGCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGCCTCACCA
231160 GACTTCACACATGTTCCAAAGAACACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAACACATATATGTCCCG
*
231198 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGCCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGCCTCACCA
*
231263 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAACACATATATGTCCCG
231301 AAGGACC
1 AAGGACC
231308 GCGTAGACCC
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.25
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGCCTCACCA
GACTTCACACATGTTCCAAAGAACACATATATGTCCCG
Found at i:232662 original size:22 final size:21
Alignment explanation
Indices: 232637--232696 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
232627 CGTTTGAGGG
*
232637 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
232659 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
232679 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
232697 CCCATAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:239852 original size:41 final size:41
Alignment explanation
Indices: 239795--239881 Score: 147
Period size: 41 Copynumber: 2.1 Consensus size: 41
239785 GTAATAATAT
* * *
239795 TAATTATGAATAAAGATTCTTCAATGATTGAGAACTGAAAA
1 TAATTATGAATAAAGATTCTTCAACGATTGACAACTAAAAA
239836 TAATTATGAATAAAGATTCTTCAACGATTGACAACTAAAAA
1 TAATTATGAATAAAGATTCTTCAACGATTGACAACTAAAAA
239877 TAATT
1 TAATT
239882 TAAATCTTGA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (41 bp):
TAATTATGAATAAAGATTCTTCAACGATTGACAACTAAAAA
Found at i:250234 original size:29 final size:29
Alignment explanation
Indices: 250192--250249 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
250182 AACTGACCTG
250192 ACTCATGGTCATCTTTACACTATACCATA
1 ACTCATGGTCATCTTTACACTATACCATA
250221 ACTCATGGTCATCTTTACACTATACCATA
1 ACTCATGGTCATCTTTACACTATACCATA
250250 TAAGTATTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.31, C:0.28, G:0.07, T:0.34
Consensus pattern (29 bp):
ACTCATGGTCATCTTTACACTATACCATA
Found at i:254201 original size:76 final size:75
Alignment explanation
Indices: 254074--254219 Score: 256
Period size: 76 Copynumber: 1.9 Consensus size: 75
254064 AGTTATATAT
* *
254074 GTTGTTGCCCGTCGTGATTCTAATAAGAAACTCCGCAGTGCTTGAAGTGATTCTGAAAGTGCAAA
1 GTTGTTGCCCGTCGTGATTCTAATAAGAAACTCCGCACTGCTTGAAATGATTCTGAAAGTGCAAA
254139 ATTAATGTAC
66 ATTAATGTAC
*
254149 GTTGTTGCCCGATCGTGATTCTAGTAAGAAACTCCGCACTGCTTGAAATGATTCTGAAAGTGCAA
1 GTTGTTGCCCG-TCGTGATTCTAATAAGAAACTCCGCACTGCTTGAAATGATTCTGAAAGTGCAA
254214 AATTAA
65 AATTAA
254220 CGTTGTGAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
75 11 0.16
76 56 0.84
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (75 bp):
GTTGTTGCCCGTCGTGATTCTAATAAGAAACTCCGCACTGCTTGAAATGATTCTGAAAGTGCAAA
ATTAATGTAC
Found at i:254656 original size:17 final size:17
Alignment explanation
Indices: 254634--254677 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
254624 TATGTTGATG
254634 AATGAACTAGTTTAATT
1 AATGAACTAGTTTAATT
* * *
254651 AATGAATTAATTTTATT
1 AATGAACTAGTTTAATT
*
254668 CATGAACTAG
1 AATGAACTAG
254678 ATGTATGAAT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (17 bp):
AATGAACTAGTTTAATT
Done.