Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002406.1 Hibiscus syriacus cultivar Beakdansim tig00004924_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: 73911
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:2708 original size:2 final size:2
Alignment explanation
Indices: 2701--2727 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2691 TGAATTTTGC
2701 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2728 TATTTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3296 original size:20 final size:19
Alignment explanation
Indices: 3258--3297 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
3248 ATATAAAAAG
* *
3258 TTATTTAATTAAATTATTA
1 TTATTTAAATAAATCATTA
3277 TTATTATAAATAAATCATTA
1 TTATT-TAAATAAATCATTA
3297 T
1 T
3298 GCGATTAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTTAAATAAATCATTA
Found at i:7748 original size:15 final size:16
Alignment explanation
Indices: 7728--7767 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
7718 AAGGTAAACT
*
7728 GAACCGAAATTAA-CC
1 GAACCGAAATCAACCC
7743 GAACCGAAATCAACCC
1 GAACCGAAATCAACCC
*
7759 GAACTGAAA
1 GAACCGAAA
7768 GTAATATGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.55
16 10 0.45
ACGTcount: A:0.47, C:0.28, G:0.15, T:0.10
Consensus pattern (16 bp):
GAACCGAAATCAACCC
Found at i:17041 original size:29 final size:29
Alignment explanation
Indices: 17008--17082 Score: 123
Period size: 29 Copynumber: 2.6 Consensus size: 29
16998 AAAAATATTG
17008 AATACTTTAGGTACTTATTTTGACCAAAA
1 AATACTTTAGGTACTTATTTTGACCAAAA
* * *
17037 AATACTCTATGTACCTATTTTGACCAAAA
1 AATACTTTAGGTACTTATTTTGACCAAAA
17066 AATACTTTAGGTACTTA
1 AATACTTTAGGTACTTA
17083 GATTTAAAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.37, C:0.16, G:0.09, T:0.37
Consensus pattern (29 bp):
AATACTTTAGGTACTTATTTTGACCAAAA
Found at i:25309 original size:18 final size:19
Alignment explanation
Indices: 25268--25312 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 19
25258 TTATTCTCTT
25268 ATTTTT-TTTACTTTAATC
1 ATTTTTATTTACTTTAATC
*
25286 ACTTTTATTTA-TTTAATC
1 ATTTTTATTTACTTTAATC
*
25304 GTTTTTATT
1 ATTTTTATT
25313 ACTACTTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.22, C:0.09, G:0.02, T:0.67
Consensus pattern (19 bp):
ATTTTTATTTACTTTAATC
Found at i:30846 original size:5 final size:5
Alignment explanation
Indices: 30824--30876 Score: 53
Period size: 5 Copynumber: 11.6 Consensus size: 5
30814 ATTCTGTTAC
* *
30824 ATTTT A-TTT A-TTT A-TTT ATTTT ATTTT ATTTT -TTGT -TTTT GTTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
30869 ATTTT ATT
1 ATTTT ATT
30877 CAATCAAACA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
4 18 0.42
5 25 0.58
ACGTcount: A:0.17, C:0.00, G:0.04, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:30853 original size:18 final size:18
Alignment explanation
Indices: 30824--30873 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
30814 ATTCTGTTAC
30824 ATTTTA-TTTATTTATTT-
1 ATTTTATTTTATTT-TTTG
30841 ATTTTATTTTATTTTTTG
1 ATTTTATTTTATTTTTTG
* *
30859 TTTTTGTTTTATTTT
1 ATTTTATTTTATTTT
30874 ATTCAATCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (18 bp):
ATTTTATTTTATTTTTTG
Found at i:31794 original size:21 final size:22
Alignment explanation
Indices: 31769--31818 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
31759 CTCCATTGGG
*
31769 AAAAACAGCAATTC-AAAAA-A
1 AAAAAAAGCAATTCGAAAAAGA
**
31789 AAAAAAAGCTGTTCGAAAAAGA
1 AAAAAAAGCAATTCGAAAAAGA
31811 AAAAAAAG
1 AAAAAAAG
31819 AAAAAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 11 0.44
21 5 0.20
22 9 0.36
ACGTcount: A:0.68, C:0.10, G:0.12, T:0.10
Consensus pattern (22 bp):
AAAAAAAGCAATTCGAAAAAGA
Found at i:33085 original size:18 final size:18
Alignment explanation
Indices: 33062--33129 Score: 136
Period size: 18 Copynumber: 3.8 Consensus size: 18
33052 TGCTTATTCT
33062 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
33080 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
33098 TTTTCAAAATCAAAACAG
1 TTTTCAAAATCAAAACAG
33116 TTTTCAAAATCAAA
1 TTTTCAAAATCAAA
33130 GATTGACTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.50, C:0.16, G:0.04, T:0.29
Consensus pattern (18 bp):
TTTTCAAAATCAAAACAG
Found at i:35373 original size:15 final size:15
Alignment explanation
Indices: 35353--35382 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
35343 TATCACAATC
35353 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
35368 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
35383 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Done.