Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001052.1 Hibiscus syriacus cultivar Beakdansim tig00002082_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: 58356
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:3555 original size:23 final size:23
Alignment explanation
Indices: 3529--3588 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
3519 CATTAAAATA
3529 TTTAAAATATATTTGTT-AATATT
1 TTTAAAATATATTTGTTAAAT-TT
* *
3552 TTTAATAATATA-ATATTAAATTT
1 TTTAA-AATATATTTGTTAAATTT
3575 TTTAAAAT-TATTTG
1 TTTAAAATATATTTG
3589 ATATATAAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
21 2 0.07
22 4 0.13
23 15 0.50
24 9 0.30
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (23 bp):
TTTAAAATATATTTGTTAAATTT
Found at i:3748 original size:24 final size:24
Alignment explanation
Indices: 3706--3776 Score: 74
Period size: 24 Copynumber: 3.0 Consensus size: 24
3696 GTATTTAATA
* *
3706 TTAAT-AAAATAGTCTAAATTAT-T
1 TTAATAAAAATA-TTTAAAATATAT
3729 TTAATAAAAATATTTAAAATATAT
1 TTAATAAAAATATTTAAAATATAT
* *
3753 TTATTAATAATATTTAAAAATATA
1 TTAATAAAAATATTT-AAAATATA
3777 ATACAATATT
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
23 13 0.32
24 20 0.49
25 8 0.20
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (24 bp):
TTAATAAAAATATTTAAAATATAT
Found at i:3774 original size:10 final size:10
Alignment explanation
Indices: 3733--3775 Score: 50
Period size: 10 Copynumber: 3.9 Consensus size: 10
3723 ATTATTTTAA
3733 TAAAAATATT
1 TAAAAATATT
3743 TAAAATATATT
1 TAAAA-ATATT
3754 TATTAATAATATT
1 TA--AA-AATATT
3767 TAAAAATAT
1 TAAAAATAT
3776 AATACAATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
10 10 0.34
11 9 0.31
13 9 0.31
14 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
TAAAAATATT
Found at i:3896 original size:14 final size:14
Alignment explanation
Indices: 3864--3899 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3854 ATTTTTTTTT
*
3864 ATAAAATTTTAAAA
1 ATAATATTTTAAAA
*
3878 ATAATATTTTAACA
1 ATAATATTTTAAAA
3892 ATAATATT
1 ATAATATT
3900 AATTTTAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.42
Consensus pattern (14 bp):
ATAATATTTTAAAA
Found at i:4065 original size:14 final size:14
Alignment explanation
Indices: 4046--4072 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4036 CAAACACCGT
4046 AAAATATTTTTCAG
1 AAAATATTTTTCAG
4060 AAAATATTTTTCA
1 AAAATATTTTTCA
4073 AAAGATGTAA
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:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
AAAATATTTTTCAG
Found at i:13523 original size:16 final size:18
Alignment explanation
Indices: 13486--13530 Score: 67
Period size: 16 Copynumber: 2.6 Consensus size: 18
13476 AATATTTTTA
*
13486 TATTTTAAATACTTATAT
1 TATTTTAAAAACTTATAT
13504 TATTTTAAAAAC-TA-AT
1 TATTTTAAAAACTTATAT
13520 TATTTTAAAAA
1 TATTTTAAAAA
13531 AAATTAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
16 13 0.50
17 2 0.08
18 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTTTAAAAACTTATAT
Found at i:13532 original size:19 final size:20
Alignment explanation
Indices: 13510--13547 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13500 ATATTATTTT
13510 AAAAACTAATT-ATTTTAAA
1 AAAAACTAATTAATTTTAAA
*
13529 AAAAATTAATTAATTTTAA
1 AAAAACTAATTAATTTTAA
13548 TTATCTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (20 bp):
AAAAACTAATTAATTTTAAA
Found at i:13535 original size:15 final size:16
Alignment explanation
Indices: 13502--13536 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
13492 AAATACTTAT
*
13502 ATTATTTTAAAAACTA
1 ATTATTTTAAAAACAA
13518 ATTATTTTAAAAA-AA
1 ATTATTTTAAAAACAA
13533 ATTA
1 ATTA
13537 ATTAATTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 5 0.28
16 13 0.72
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATTATTTTAAAAACAA
Found at i:20711 original size:21 final size:22
Alignment explanation
Indices: 20662--20723 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
20652 ATACCCCCAT
20662 AAGGGAACCGATTCCCCCTTTG
1 AAGGGAACCGATTCCCCCTTTG
20684 AATGGGAACCGATTCCCTCC-TTG
1 AA-GGGAACCGATTCCC-CCTTTG
* *
20707 -AGGGAATCGATACCCCC
1 AAGGGAACCGATTCCCCC
20724 CACTGGTTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
20 2 0.06
21 12 0.33
22 3 0.08
23 17 0.47
24 2 0.06
ACGTcount: A:0.24, C:0.32, G:0.23, T:0.21
Consensus pattern (22 bp):
AAGGGAACCGATTCCCCCTTTG
Found at i:28735 original size:2 final size:2
Alignment explanation
Indices: 28728--28772 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
28718 TTCTACACAT
28728 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
28770 TA T
1 TA T
28773 TGGAACTTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35942 original size:28 final size:27
Alignment explanation
Indices: 35881--35955 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 27
35871 TAAAAATTTG
**
35881 TTTTTTTTAATAAATAAATACATTTTTTTTA
1 TTTTTTTTAA-AAAT-AAT--ATTTTTTAAA
35912 TTTTTTATTAAAAATAATATTTTTTAAA
1 TTTTTT-TTAAAAATAATATTTTTTAAA
35940 TTTTTTTTAAAAATAA
1 TTTTTTTTAAAAATAA
35956 ACGATAGACA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
27 10 0.24
28 14 0.34
30 3 0.07
31 10 0.24
32 4 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (27 bp):
TTTTTTTTAAAAATAATATTTTTTAAA
Found at i:48246 original size:19 final size:20
Alignment explanation
Indices: 48208--48246 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
48198 ATCCCCACTC
48208 AATAGTTTGACTCAAAAAAA
1 AATAGTTTGACTCAAAAAAA
48228 AATAGTTTGACTCAAAAAA
1 AATAGTTTGACTCAAAAAA
48247 TAATCAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.26
Consensus pattern (20 bp):
AATAGTTTGACTCAAAAAAA
Done.