Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001491.1 Hibiscus syriacus cultivar Beakdansim tig00002898_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: 49584
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:3357 original size:3 final size:3
Alignment explanation
Indices: 3349--3395 Score: 60
Period size: 3 Copynumber: 16.0 Consensus size: 3
3339 ATTTTTTATT
** *
3349 TAA TAA TAA TAA TAA T-A TGC TAA TAT TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3396 AACGAAATGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:5658 original size:21 final size:21
Alignment explanation
Indices: 5615--5659 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
5605 TAAGATGTTG
* *
5615 TTTTAATAAAATTAAAATTGT
1 TTTTAATAAAATGAAAATCGT
* *
5636 TTTTATTAAAATGACAATCGT
1 TTTTAATAAAATGAAAATCGT
5657 TTT
1 TTT
5660 GGGTGCCGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.04, G:0.07, T:0.49
Consensus pattern (21 bp):
TTTTAATAAAATGAAAATCGT
Found at i:6889 original size:14 final size:13
Alignment explanation
Indices: 6870--6904 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
6860 CATCCAAACT
6870 AAATATATATATC
1 AAATATATATATC
6883 AAA-ATATATATC
1 AAATATATATATC
6895 AAA-ATATATA
1 AAATATATATA
6905 AACTAATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 19 0.86
13 3 0.14
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (13 bp):
AAATATATATATC
Found at i:6891 original size:12 final size:12
Alignment explanation
Indices: 6874--6904 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
6864 CAAACTAAAT
6874 ATATATATCAAA
1 ATATATATCAAA
6886 ATATATATCAAA
1 ATATATATCAAA
6898 ATATATA
1 ATATATA
6905 AACTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATATATCAAA
Found at i:7181 original size:60 final size:59
Alignment explanation
Indices: 7060--7185 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 59
7050 AATGACTATT
** * * * * * *
7060 ATTTTAAATTGGTTCTTAAACTTTAAATATTCTAATTTCATCACTAAACTATGATTTTC
1 ATTTTAAATAAGTCCTTAAACTTTAAATATTCTAATTTAATCACCAAACTATAACTCTC
* *
7119 ATTTTAAATAAGTCCTTAAACTTTTGAATATATC-AATTTAATCCCCAAACTATAACTCTC
1 ATTTTAAATAAGTCCTTAAAC-TTTAAATAT-TCTAATTTAATCACCAAACTATAACTCTC
7179 ATTTTAA
1 ATTTTAA
7186 TTTGCTCTCC
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
59 18 0.33
60 35 0.64
61 2 0.04
ACGTcount: A:0.37, C:0.16, G:0.04, T:0.44
Consensus pattern (59 bp):
ATTTTAAATAAGTCCTTAAACTTTAAATATTCTAATTTAATCACCAAACTATAACTCTC
Found at i:12246 original size:10 final size:10
Alignment explanation
Indices: 12231--12271 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
12221 TTCATCACAC
12231 CAAATTCTCT
1 CAAATTCTCT
12241 CAAATTCTCT
1 CAAATTCTCT
* *
12251 CAATTTATCT
1 CAAATTCTCT
*
12261 CAAATACTCT
1 CAAATTCTCT
12271 C
1 C
12272 TCTATTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.32, C:0.29, G:0.00, T:0.39
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:12348 original size:17 final size:18
Alignment explanation
Indices: 12313--12353 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
12303 ATATTATGTA
*
12313 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
12331 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
12348 TTTACT
1 TTTACT
12354 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:14054 original size:18 final size:18
Alignment explanation
Indices: 14031--14069 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
14021 ACAGCAGCCA
*
14031 CCGCAGCCATTTATGATG
1 CCGCAGCCATATATGATG
14049 CCGCAGCCATATATGATG
1 CCGCAGCCATATATGATG
14067 CCG
1 CCG
14070 TCATCGCCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.31, G:0.23, T:0.23
Consensus pattern (18 bp):
CCGCAGCCATATATGATG
Found at i:14690 original size:35 final size:33
Alignment explanation
Indices: 14651--14735 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
14641 ATATTTTAGT
*
14651 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTCAAT-TC--TTATTG
*
14686 TAATTTGGTTATCATTTACCATTCAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTCAATTCTTATTG
* *
14721 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
14736 TAAATACCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.26, C:0.09, G:0.11, T:0.54
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTCAATTCTTATTG
Found at i:19087 original size:60 final size:60
Alignment explanation
Indices: 18957--19087 Score: 160
Period size: 60 Copynumber: 2.2 Consensus size: 60
18947 ATAAACTTTT
* * *
18957 AATTTTATCCCTAAACTATGACTATCATTCTAAATTAGACCTCAAACTTTTAAATATTTC
1 AATTTTATCCCCAAACTATGACTATCATTCTAAATTAGACCTCAAACTTTTAAACATTCC
* *
19017 TATTTTATCCCCAAACTATGATCT-TCATTCTAAATTA-ATCC-CTAAACTTTTGAACATTCC
1 AATTTTATCCCCAAACTATGA-CTATCATTCTAAATTAGA-CCTC-AAACTTTTAAACATTCC
*
19077 AATTTCATCCC
1 AATTTTATCCC
19088 TTATTAGAAT
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
59 2 0.03
60 57 0.93
61 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.03, T:0.40
Consensus pattern (60 bp):
AATTTTATCCCCAAACTATGACTATCATTCTAAATTAGACCTCAAACTTTTAAACATTCC
Found at i:24943 original size:23 final size:23
Alignment explanation
Indices: 24917--24962 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
24907 TACTCTCTCT
*
24917 TATTTTATTTATTTTAATT-TTAA
1 TATTTT-TTTAATTTAATTATTAA
24940 TATTTTTTTAATTTAATTATTAA
1 TATTTTTTTAATTTAATTATTAA
24963 CTTTATACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TATTTTTTTAATTTAATTATTAA
Found at i:24960 original size:17 final size:19
Alignment explanation
Indices: 24921--24960 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
24911 CTCTCTTATT
24921 TTATTTATTTTAATTTTAA
1 TTATTTATTTTAATTTTAA
24940 -TATTT-TTTTAA-TTTAA
1 TTATTTATTTTAATTTTAA
24956 TTATT
1 TTATT
24961 AACTTTATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 10 0.50
18 5 0.25
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (19 bp):
TTATTTATTTTAATTTTAA
Found at i:41441 original size:3 final size:3
Alignment explanation
Indices: 41426--41455 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
41416 ACCTAGTTTA
*
41426 TCT TCT CCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
41456 GCATCACCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.37, G:0.00, T:0.63
Consensus pattern (3 bp):
TCT
Found at i:48203 original size:3 final size:3
Alignment explanation
Indices: 48195--48231 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
48185 TTGGACCTTT
48195 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
48232 CAATTTCACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.