Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003162.1 Hibiscus syriacus cultivar Beakdansim tig00006655_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: 162325
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
File 2 of 2
Found at i:152102 original size:20 final size:20
Alignment explanation
Indices: 152032--152134 Score: 68
Period size: 20 Copynumber: 5.0 Consensus size: 20
152022 TCATCATGCT
*
152032 CGAAAGACTTACTGATGGTC
1 CGAAAGACTTACTGATGGCC
* *
152052 CG-AAGAACTTCATCATCAT-GCT
1 CGAAAG-ACTT-A-C-TGATGGCC
152074 CGAAAGACTTACTGATGGCC
1 CGAAAGACTTACTGATGGCC
* * *
152094 CGAAGGACTTCATCATCAT-GCT
1 CGAAAGACTT-A-C-TGATGGCC
152116 CGAAAGACTTACTGATGGC
1 CGAAAGACTTACTGATGGC
152135 ACTTACTGAT
Statistics
Matches: 63, Mismatches: 10, Indels: 20
0.68 0.11 0.22
Matches are distributed among these distances:
19 9 0.14
20 21 0.33
21 4 0.06
22 20 0.32
23 9 0.14
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (20 bp):
CGAAAGACTTACTGATGGCC
Found at i:152128 original size:42 final size:42
Alignment explanation
Indices: 151883--152280 Score: 224
Period size: 42 Copynumber: 9.4 Consensus size: 42
151873 AATGCTTAAA
* * **
151883 ATGGCCCGAAGGACTT-ATCATCTTGCTTGAAAGACTTACAA
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* * *
151924 ATGACCCGAAGGATTTCATCATCATGCTCGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
** * * * **
151966 AT-G---GATTTG-CTTCA-CTACTCTTCGGT-G-AAGGCTTACAA
1 ATGGCCCGA-AGGACTTCATC-A-TCAT-GCTCGAAAGACTTACTG
** * * *
152004 ATTACCCAAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* *
152046 ATGGTCCGAAGAACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
152088 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* ** ** * * * **
152130 ATGGCACTTACTGATGGGTTTGTTTCACTACTCTTCTGTGAAAG-CTTACAA
1 ATGGC-C---C-GAAGGACTT-CATCA-T-C-ATGCT-CGAAAGACTTACTG
* * * *
152181 ATTAG-CCTAAGGATTTAATCATCATGCTCGAAAGACTTACTG
1 A-TGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
* * * * *
152223 ATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTG
1 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
152265 ATGGCCCGAAGGACTT
1 ATGGCCCGAAGGACTT
152281 ACTAAGTGCA
Statistics
Matches: 268, Mismatches: 63, Indels: 51
0.70 0.16 0.13
Matches are distributed among these distances:
37 1 0.00
38 16 0.06
39 5 0.02
40 4 0.01
41 26 0.10
42 173 0.65
43 3 0.01
44 1 0.00
45 3 0.01
46 7 0.03
47 7 0.03
48 3 0.01
49 1 0.00
50 2 0.01
51 9 0.03
52 7 0.03
ACGTcount: A:0.30, C:0.22, G:0.20, T:0.29
Consensus pattern (42 bp):
ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTG
Found at i:152140 original size:13 final size:13
Alignment explanation
Indices: 152122--152146 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
152112 TGCTCGAAAG
152122 ACTTACTGATGGC
1 ACTTACTGATGGC
152135 ACTTACTGATGG
1 ACTTACTGATGG
152147 GTTTGTTTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (13 bp):
ACTTACTGATGGC
Found at i:152272 original size:177 final size:177
Alignment explanation
Indices: 151958--152280 Score: 520
Period size: 177 Copynumber: 1.8 Consensus size: 177
151948 TGCTCGAAAG
* *
151958 ACTTATTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTACAAATTACCCAAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAAGCTTACAAATTACCCAAAGGATTTAAT
* * *
152023 CATCATGCTCGAAAGACTTACTGATGGTCCGAAGAACTTCATCATCATGCTCGAAAGACTTACTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGAACTTAAGCATCATGCTCGAAAGACTTACTG
152088 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
131 ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
* * * * *
152135 ACTTACTGATGGGTTTGTTTCACTACTCTTCTGTGAAAGCTTACAAATTAGCCTAAGGATTTAAT
1 ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAAGCTTACAAATTACCCAAAGGATTTAAT
* * * *
152200 CATCATGCTCGAAAGACTTACTGATGGCCCTAAGGATTTAAGCATCATGCTCGAAAGACTTATTG
66 CATCATGCTCGAAAGACTTACTGATGGCCCGAAGAACTTAAGCATCATGCTCGAAAGACTTACTG
152265 ATGGCCCGAAGGACTT
131 ATGGCCCGAAGGACTT
152281 ACTAAGTGCA
Statistics
Matches: 132, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
177 132 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.30
Consensus pattern (177 bp):
ACTTACTGATGGATTTGCTTCACTACTCTTCGGTGAAAGCTTACAAATTACCCAAAGGATTTAAT
CATCATGCTCGAAAGACTTACTGATGGCCCGAAGAACTTAAGCATCATGCTCGAAAGACTTACTG
ATGGCCCGAAGGACTTCATCATCATGCTCGAAAGACTTACTGATGGC
Found at i:158053 original size:6 final size:6
Alignment explanation
Indices: 158042--158080 Score: 60
Period size: 6 Copynumber: 6.3 Consensus size: 6
158032 AAATACATGT
*
158042 AATGCA AATGCA AATGCA AATGCCA AATGCA AATACA AA
1 AATGCA AATGCA AATGCA AATG-CA AATGCA AATGCA AA
158081 AGGTGTCATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
6 25 0.81
7 6 0.19
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (6 bp):
AATGCA
Found at i:158068 original size:19 final size:18
Alignment explanation
Indices: 158042--158080 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
158032 AAATACATGT
*
158042 AATGCAAATGCAAATGCA
1 AATGCAAATGCAAATACA
158060 AATGCCAAATGCAAATACA
1 AATG-CAAATGCAAATACA
158079 AA
1 AA
158081 AGGTGTCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.54, C:0.18, G:0.13, T:0.15
Consensus pattern (18 bp):
AATGCAAATGCAAATACA
Done.