Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005173.1 Hibiscus syriacus cultivar Beakdansim tig00011672_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: 46676
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1823 original size:17 final size:16
Alignment explanation
Indices: 1790--1824 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
1780 TACATGAAAT
*
1790 AAAATAAATATATATA
1 AAAATAAATACATATA
1806 AAAATAATATACATATA
1 AAAATAA-ATACATATA
1823 AA
1 AA
1825 TATTATGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (16 bp):
AAAATAAATACATATA
Found at i:1826 original size:27 final size:29
Alignment explanation
Indices: 1793--1860 Score: 76
Period size: 27 Copynumber: 2.5 Consensus size: 29
1783 ATGAAATAAA
1793 ATAAATATATAT-AAA-AATAA-TATACAT
1 ATAAATAT-TATGAAATAATAAGTATACAT
1820 ATAAATATTATGAAATAATAAGTAT--AT
1 ATAAATATTATGAAATAATAAGTATACAT
*
1847 ATAAAAATT-TGAAA
1 ATAAATATTATGAAA
1861 AGAAAGAATT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
26 8 0.22
27 21 0.57
28 5 0.14
29 3 0.08
ACGTcount: A:0.60, C:0.01, G:0.04, T:0.34
Consensus pattern (29 bp):
ATAAATATTATGAAATAATAAGTATACAT
Found at i:2333 original size:15 final size:15
Alignment explanation
Indices: 2286--2333 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
2276 TATTATTAAA
*
2286 AATTCAAATATATTT
1 AATTCAAATATTTTT
* **
2301 AATTTATAATCCTTTT
1 AATTCA-AATATTTTT
2317 AATTCAAATATTTTT
1 AATTCAAATATTTTT
2332 AA
1 AA
2334 AAATATATCA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
15 14 0.56
16 11 0.44
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (15 bp):
AATTCAAATATTTTT
Found at i:4035 original size:3 final size:3
Alignment explanation
Indices: 4027--4100 Score: 98
Period size: 3 Copynumber: 24.7 Consensus size: 3
4017 GGCCCGTTTG
**
4027 TAA TAA TAA TTT TAA TAA TAA TAAA TAA -AA TAA TAA TAA TATA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TA-A TAA
4073 -AA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
4101 GAAAATGGGA
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
2 4 0.06
3 53 0.84
4 6 0.10
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4901 original size:103 final size:103
Alignment explanation
Indices: 4722--4928 Score: 396
Period size: 103 Copynumber: 2.0 Consensus size: 103
4712 GGGGAGGGGG
* *
4722 AGGGACCTTATTGAAAATGAACTAAAAGTTCGATGGTTGTATTGCTAGTTTCAAAATTAGGTGAT
1 AGGGACCTTACTGAAAATGAACTAAAAGTTCGATGATTGTATTGCTAGTTTCAAAATTAGGTGAT
4787 CAAAATGCAAGCGTCCTATAAGTTCAAAGACTATTTAT
66 CAAAATGCAAGCGTCCTATAAGTTCAAAGACTATTTAT
4825 AGGGACCTTACTGAAAATGAACTAAAAGTTCGATGATTGTATTGCTAGTTTCAAAATTAGGTGAT
1 AGGGACCTTACTGAAAATGAACTAAAAGTTCGATGATTGTATTGCTAGTTTCAAAATTAGGTGAT
4890 CAAAATGCAAGCGTCCTATAAGTTCAAAGACTATTTAT
66 CAAAATGCAAGCGTCCTATAAGTTCAAAGACTATTTAT
4928 A
1 A
4929 TACTTTACCT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 102 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (103 bp):
AGGGACCTTACTGAAAATGAACTAAAAGTTCGATGATTGTATTGCTAGTTTCAAAATTAGGTGAT
CAAAATGCAAGCGTCCTATAAGTTCAAAGACTATTTAT
Found at i:6702 original size:2 final size:2
Alignment explanation
Indices: 6695--6719 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
6685 AAAATTTAGT
6695 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 T
6720 TTACATTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7036 original size:15 final size:16
Alignment explanation
Indices: 7009--7039 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
6999 GCTTTTAAAA
7009 TTAAAATATATATATT
1 TTAAAATATATATATT
7025 TTAAAA-ATATATATT
1 TTAAAATATATATATT
7040 ATATCTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTAAAATATATATATT
Found at i:9672 original size:3 final size:3
Alignment explanation
Indices: 9664--9692 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9654 TAATATCTTG
9664 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
9693 TTCATGTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:18346 original size:15 final size:16
Alignment explanation
Indices: 18318--18350 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
18308 AAAATCTTTC
18318 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
18334 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
18349 TT
1 TT
18351 GATCTACCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:19120 original size:16 final size:16
Alignment explanation
Indices: 19096--19129 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
19086 TATCGTCGAC
*
19096 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
19112 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
19128 CG
1 CG
19130 CGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:21037 original size:13 final size:14
Alignment explanation
Indices: 21019--21056 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
21009 TACCCTACGT
21019 TTAAATTA-AAACC
1 TTAAATTATAAACC
21032 TTAAATTATAAACC
1 TTAAATTATAAACC
* *
21046 CTAAATCATAA
1 TTAAATTATAA
21057 CCCCATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
TTAAATTATAAACC
Done.