Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004047.1 Hibiscus syriacus cultivar Beakdansim tig00008842_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: 53746
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17801 original size:6 final size:6
Alignment explanation
Indices: 17790--17817 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
17780 TCGTTCTTTT
17790 AAATAA AAATAA AAATAA AAATAA AAAT
1 AAATAA AAATAA AAATAA AAATAA AAAT
17818 GTTAATTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (6 bp):
AAATAA
Found at i:22402 original size:16 final size:16
Alignment explanation
Indices: 22381--22467 Score: 99
Period size: 16 Copynumber: 5.6 Consensus size: 16
22371 CTTCAAATTC
22381 ATTTAAATTTAAAATA
1 ATTTAAATTTAAAATA
*
22397 ATTTAAA-TTCAAATA
1 ATTTAAATTTAAAATA
*
22412 ATTTAAATTTAAAATG
1 ATTTAAATTTAAAATA
*
22428 ATGTT-AATATAAAATA
1 AT-TTAAATTTAAAATA
*
22444 ATTTAAATCT-AAATA
1 ATTTAAATTTAAAATA
*
22459 AATTAAATT
1 ATTTAAATT
22468 AATAAATTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
15 28 0.47
16 30 0.50
17 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (16 bp):
ATTTAAATTTAAAATA
Found at i:22412 original size:15 final size:15
Alignment explanation
Indices: 22381--22488 Score: 96
Period size: 15 Copynumber: 7.1 Consensus size: 15
22371 CTTCAAATTC
22381 ATTTAAATTTAAAATA
1 ATTTAAA-TTAAAATA
*
22397 ATTTAAATTCAAATA
1 ATTTAAATTAAAATA
*
22412 ATTTAAATTTAAAATG
1 ATTTAAA-TTAAAATA
22428 ATGTT-AATATAAAATA
1 AT-TTAAAT-TAAAATA
22444 ATTTAAATCT-AAATA
1 ATTTAAAT-TAAAATA
* *
22459 AATTAAATTAATA-A
1 ATTTAAATTAAAATA
* *
22473 ATTCAAATTAATATA
1 ATTTAAATTAAAATA
22488 A
1 A
22489 ATAAAAAATA
Statistics
Matches: 77, Mismatches: 9, Indels: 13
0.78 0.09 0.13
Matches are distributed among these distances:
14 13 0.17
15 33 0.43
16 29 0.38
17 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.40
Consensus pattern (15 bp):
ATTTAAATTAAAATA
Found at i:22448 original size:32 final size:31
Alignment explanation
Indices: 22381--22469 Score: 110
Period size: 31 Copynumber: 2.9 Consensus size: 31
22371 CTTCAAATTC
*
22381 ATTTAAATTTAAAATAATTTAAATTCAAATA
1 ATTTAAATTTAAAATAATTTAAATTAAAATA
*
22412 ATTTAAATTTAAAATGATGTT-AATATAAAATA
1 ATTTAAATTTAAAATAAT-TTAAAT-TAAAATA
* *
22444 ATTTAAATCT-AAATAAATTAAATTAA
1 ATTTAAATTTAAAATAATTTAAATTAA
22470 TAAATTCAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
30 5 0.10
31 28 0.56
32 17 0.34
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (31 bp):
ATTTAAATTTAAAATAATTTAAATTAAAATA
Found at i:22497 original size:23 final size:23
Alignment explanation
Indices: 22454--22497 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
22444 ATTTAAATCT
*
22454 AAATAAATTAAATTAATAAATTC
1 AAATAAATTAAATTAAAAAATTC
*
22477 AAATTAATATAAA-TAAAAAAT
1 AAATAAAT-TAAATTAAAAAAT
22498 AATCTGAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 14 0.78
24 4 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (23 bp):
AAATAAATTAAATTAAAAAATTC
Found at i:26582 original size:16 final size:17
Alignment explanation
Indices: 26563--26595 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
26553 ATATGATCCT
26563 AATAATTCAT-ATTCTG
1 AATAATTCATGATTCTG
*
26579 AATAATTGATGATTCTG
1 AATAATTCATGATTCTG
26596 TCAGTTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (17 bp):
AATAATTCATGATTCTG
Found at i:26778 original size:24 final size:24
Alignment explanation
Indices: 26751--26860 Score: 103
Period size: 24 Copynumber: 4.5 Consensus size: 24
26741 TTTTATCTGG
26751 TTTCTGATTTGAAATATGTTATGA
1 TTTCTGATTTGAAATATGTTATGA
* * *
26775 TTTCTGATTTGAATTCTGTTCTGA
1 TTTCTGATTTGAAATATGTTATGA
* *
26799 TTTCTGATCTGAATTATGTTATGA
1 TTTCTGATTTGAAATATGTTATGA
* * * *
26823 TATATGATATCTGATATATGATATGA
1 TTTCTGAT-T-TGAAATATGTTATGA
* *
26849 ATTCTGTTTTGA
1 TTTCTGATTTGA
26861 TTTTTGATAT
Statistics
Matches: 68, Mismatches: 16, Indels: 4
0.77 0.18 0.05
Matches are distributed among these distances:
24 51 0.75
25 1 0.01
26 16 0.24
ACGTcount: A:0.26, C:0.07, G:0.16, T:0.50
Consensus pattern (24 bp):
TTTCTGATTTGAAATATGTTATGA
Found at i:26839 original size:14 final size:14
Alignment explanation
Indices: 26820--26846 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
26810 AATTATGTTA
26820 TGATATATGATATC
1 TGATATATGATATC
26834 TGATATATGATAT
1 TGATATATGATAT
26847 GAATTCTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.15, T:0.44
Consensus pattern (14 bp):
TGATATATGATATC
Found at i:26850 original size:38 final size:38
Alignment explanation
Indices: 26794--26872 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
26784 TGAATTCTGT
* * *
26794 TCTGATTTCTGATCTGAATTATGTTATGATATATGATA
1 TCTGATATATGATATGAATTATGTTATGATATATGATA
* * * *
26832 TCTGATATATGATATGAATTCTGTTTTGATTTTTGATA
1 TCTGATATATGATATGAATTATGTTATGATATATGATA
26870 TCT
1 TCT
26873 CCGTTTATTG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.27, C:0.08, G:0.15, T:0.51
Consensus pattern (38 bp):
TCTGATATATGATATGAATTATGTTATGATATATGATA
Found at i:30355 original size:17 final size:17
Alignment explanation
Indices: 30335--30387 Score: 72
Period size: 17 Copynumber: 3.2 Consensus size: 17
30325 GTATTTTTAC
*
30335 ATTTAATTTTTTAAATA
1 ATTTAATTTTTAAAATA
*
30352 ATTTAA-ATTTAAAATA
1 ATTTAATTTTTAAAATA
*
30368 ATTTTATTTTTAAAATA
1 ATTTAATTTTTAAAATA
30385 ATT
1 ATT
30388 AAGTAAACCT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
16 13 0.42
17 18 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTAATTTTTAAAATA
Found at i:31240 original size:18 final size:18
Alignment explanation
Indices: 31217--31254 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
31207 AAAATATATA
31217 AATATTTTCCAACTTGTT
1 AATATTTTCCAACTTGTT
*
31235 AATATTTTCTAACTTGTT
1 AATATTTTCCAACTTGTT
31253 AA
1 AA
31255 AAAACAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.13, G:0.05, T:0.50
Consensus pattern (18 bp):
AATATTTTCCAACTTGTT
Found at i:37529 original size:21 final size:23
Alignment explanation
Indices: 37504--37556 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 23
37494 ACCAAATTCT
*
37504 ATTTTAATC-ATTA-ATCTTTTA
1 ATTTTAATCAATTAGATCATTTA
37525 ATTTT-ATCAATTAGATCATTTA
1 ATTTTAATCAATTAGATCATTTA
37547 ACTATTTAAT
1 A-T-TTTAAT
37557 TATTGTCAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
20 3 0.12
21 9 0.35
22 8 0.31
23 1 0.04
24 3 0.12
25 2 0.08
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (23 bp):
ATTTTAATCAATTAGATCATTTA
Found at i:42526 original size:3 final size:3
Alignment explanation
Indices: 42518--42544 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
42508 CAACACAAAG
42518 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
42545 GGCTTCATCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:50471 original size:14 final size:15
Alignment explanation
Indices: 50452--50480 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
50442 CAATGGACAA
50452 CAACGGTCA-CATGG
1 CAACGGTCACCATGG
50466 CAACGGTCACCATGG
1 CAACGGTCACCATGG
50481 AACCTCTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.28, C:0.31, G:0.28, T:0.14
Consensus pattern (15 bp):
CAACGGTCACCATGG
Found at i:52754 original size:2 final size:2
Alignment explanation
Indices: 52747--52776 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
52737 AAAATCTTAA
52747 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
52777 TCACGTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.