Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000487.1 Hibiscus syriacus cultivar Beakdansim tig00000929_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: 68108
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:16433 original size:60 final size:59
Alignment explanation
Indices: 16323--16488 Score: 144
Period size: 60 Copynumber: 2.8 Consensus size: 59
16313 TTATCATTTC
* * * * *
16323 AAATTAGTCACAAAACTTATAATTATTAT-AATTTCATACCT-AAACCATGAC-TATCGTAAT
1 AAATTAGTCCCCAAACTT-TAAATATT-TCAATTTCAT-CCTCAAACTATGACAT-TCATAAT
* * **
16383 AAATTAGTCCTCAAAGCTTTAAA-ATTTTCATTTTCATCCTCAAACTATGACATTCATTCT
1 AAATTAGTCCCCAAA-CTTTAAATA-TTTCAATTTCATCCTCAAACTATGACATTCATAAT
* *
16443 AAGTTGGTCCCCAAACTTTAAATATTTCAATTTCAT-CTCAAACTAT
1 AAATTAGTCCCCAAACTTTAAATATTTCAATTTCATCCTCAAACTAT
16489 ACCTATATAC
Statistics
Matches: 87, Mismatches: 13, Indels: 14
0.76 0.11 0.12
Matches are distributed among these distances:
58 10 0.11
59 23 0.26
60 50 0.57
61 4 0.05
ACGTcount: A:0.37, C:0.20, G:0.05, T:0.37
Consensus pattern (59 bp):
AAATTAGTCCCCAAACTTTAAATATTTCAATTTCATCCTCAAACTATGACATTCATAAT
Found at i:21990 original size:3 final size:3
Alignment explanation
Indices: 21984--22013 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
21974 GTTTAAGCCG
21984 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
22014 TCGTATTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:25482 original size:2 final size:2
Alignment explanation
Indices: 25475--25502 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
25465 GCTGCAACAA
25475 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
25503 CTTAACTGTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31125 original size:21 final size:21
Alignment explanation
Indices: 31110--31154 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
31100 GTGGTTTCAT
31110 GATGCATGTGAGTGGTCGTAA
1 GATGCATGTGAGTGGTCGTAA
31131 GATGCATGTGAGTGGTCGTAA
1 GATGCATGTGAGTGGTCGTAA
31152 GAT
1 GAT
31155 TCATAGAAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.38, T:0.29
Consensus pattern (21 bp):
GATGCATGTGAGTGGTCGTAA
Found at i:44644 original size:43 final size:41
Alignment explanation
Indices: 44597--44679 Score: 96
Period size: 41 Copynumber: 2.0 Consensus size: 41
44587 ATAAAAAGCG
* *
44597 AGATTGAATAATATT-AGTACCTCAATTATAAATATAAAAAAAA
1 AGATTGAA-AA-ATTAAGGACCT-AATTATAAAAATAAAAAAAA
* *
44640 AGATTTAAAAATTAAGGATCTAATTATAAAAATAAAAAAA
1 AGATTGAAAAATTAAGGACCTAATTATAAAAATAAAAAAA
44680 TGAAATCTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
41 21 0.60
42 7 0.20
43 7 0.20
ACGTcount: A:0.59, C:0.05, G:0.07, T:0.29
Consensus pattern (41 bp):
AGATTGAAAAATTAAGGACCTAATTATAAAAATAAAAAAAA
Found at i:62710 original size:3 final size:3
Alignment explanation
Indices: 62698--62795 Score: 56
Period size: 3 Copynumber: 31.7 Consensus size: 3
62688 TAATACTACG
* **
62698 TAA TAG TAA TAA TAA TAA TAA TAA TAA TGT TAAA TAA TAAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T-AA TAA TAA
* ** * * *
62745 GAAA TGT TAA T-A TAA TAA TAT TAA T-A TAC TAA TAC TATA TAA TATA
1 -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TA-A
62791 TAA TA
1 TAA TA
62796 TAAATATTAT
Statistics
Matches: 70, Mismatches: 18, Indels: 14
0.69 0.18 0.14
Matches are distributed among these distances:
2 4 0.06
3 55 0.79
4 11 0.16
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:64548 original size:5 final size:5
Alignment explanation
Indices: 64535--64577 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
64525 CCTTTTCCGT
* * *
64535 TTGAA TTGAG TTGAG TTGAG TTGAG TTGAG CTGAG CTGAG TTG
1 TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTGAG TTG
64578 TGGTCCAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 35 1.00
ACGTcount: A:0.21, C:0.05, G:0.37, T:0.37
Consensus pattern (5 bp):
TTGAG
Found at i:65127 original size:33 final size:33
Alignment explanation
Indices: 65090--65158 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
65080 TTGGTTGGAT
65090 TTATCATCACGTCGTTGACATAAGTTTTCAAGC
1 TTATCATCACGTCGTTGACATAAGTTTTCAAGC
65123 TTATCATCACGTCGTTGACATAAGTTTTCAAGC
1 TTATCATCACGTCGTTGACATAAGTTTTCAAGC
65156 TTA
1 TTA
65159 CTTTCTTGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (33 bp):
TTATCATCACGTCGTTGACATAAGTTTTCAAGC
Done.