Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002647.1 Hibiscus syriacus cultivar Beakdansim tig00005406_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: 7027529
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 26 of 26
Found at i:7010948 original size:16 final size:16
Alignment explanation
Indices: 7010922--7011117 Score: 94
Period size: 16 Copynumber: 11.6 Consensus size: 16
7010912 ATATATGAGA
* *
7010922 GAGAGAAGGAGAGAGG
1 GAGAGAGGGAGAGGGG
*
7010938 GAGAGGGGGAGAGGGG
1 GAGAGAGGGAGAGGGG
* *
7010954 GAGAGGGGGAGAGGGA
1 GAGAGAGGGAGAGGGG
*
7010970 AAGAGA-GGA-AGGGACG
1 GAGAGAGGGAGAGGG--G
**
7010986 GAGTGAGAGACAGAGGTGGG
1 GA--GAGAGGGAGA-G-GGG
* *
7011006 GAAAGGGGGAGAGAGAGGG
1 GAGA-GAGG-GAGAG-GGG
* *
7011025 GAAATAGGGAGAGGGG
1 GAGAGAGGGAGAGGGG
7011041 GAGAGAGGGAGAGAGGG
1 GAGAGAGGGAGAG-GGG
*
7011058 AGAGCGAGGGAGAGAGGG
1 -GAGAGAGGGAGAG-GGG
*
7011076 AGAGCGAGGGAGAGCGGG
1 -GAGAGAGGGAGAG-GGG
*
7011094 G-GAGAGGGAG-GGAGA
1 GAGAGAGGGAGAGG-GG
7011109 GAGAGAGGG
1 GAGAGAGGG
7011118 GTATGGGAGA
Statistics
Matches: 143, Mismatches: 23, Indels: 28
0.74 0.12 0.14
Matches are distributed among these distances:
14 5 0.03
15 6 0.04
16 62 0.43
17 9 0.06
18 40 0.28
19 11 0.08
20 7 0.05
21 1 0.01
22 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.62, T:0.02
Consensus pattern (16 bp):
GAGAGAGGGAGAGGGG
Found at i:7010949 original size:14 final size:14
Alignment explanation
Indices: 7010918--7010969 Score: 59
Period size: 14 Copynumber: 3.6 Consensus size: 14
7010908 ATATATATAT
* * *
7010918 GAGAGAGAGAAGGA
1 GAGAGGGAGAGGGG
7010932 GAGAGGGAGAGGGG
1 GAGAGGGAGAGGGG
7010946 GAGAGGGGGAGAGGGG
1 GAGA--GGGAGAGGGG
7010962 GAGAGGGA
1 GAGAGGGA
7010970 AAGAGAGGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
14 19 0.58
16 14 0.42
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (14 bp):
GAGAGGGAGAGGGG
Found at i:7010956 original size:24 final size:24
Alignment explanation
Indices: 7010929--7011118 Score: 93
Period size: 24 Copynumber: 7.7 Consensus size: 24
7010919 AGAGAGAGAA
7010929 GGAGAGAGGGAGAGGGGGAGAGGG
1 GGAGAGAGGGAGAGGGGGAGAGGG
* ** *
7010953 GGAGAGGGGGAGAGGGAAAGAGAG
1 GGAGAGAGGGAGAGGGGGAGAGGG
* * * * **
7010977 GAAGGGACGGAGTGAGAGACAGAGGTG
1 GGAGAGA-GG-GAGAGGGGGAGAGG-G
* * *
7011004 GG-GAAAGGG-G-GAGAGAGA-GG
1 GGAGAGAGGGAGAGGGGGAGAGGG
* * *
7011024 GGAAATAGGGAGAGGGGGAGAGAG
1 GGAGAGAGGGAGAGGGGGAGAGGG
7011048 GGAGAGAGGGAGAGCGAGGGAGAGAGG
1 GGAGAGAGGGAGAG-G-GGGAGAG-GG
*
7011075 GAGAGCGAGGGAGAGCGGGGGAGAGGG
1 G-GAGAGAGGGAGA--GGGGGAGAGGG
*
7011102 AGG-GAGAGAGAGAGGGG
1 -GGAGAGAGGGAGAGGGG
7011119 TATGGGAGAG
Statistics
Matches: 126, Mismatches: 26, Indels: 28
0.70 0.14 0.16
Matches are distributed among these distances:
20 3 0.02
21 6 0.05
22 8 0.06
23 7 0.06
24 42 0.33
25 5 0.04
26 27 0.21
27 7 0.06
28 19 0.15
29 1 0.01
30 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.63, T:0.02
Consensus pattern (24 bp):
GGAGAGAGGGAGAGGGGGAGAGGG
Found at i:7011048 original size:10 final size:9
Alignment explanation
Indices: 7011016--7011118 Score: 69
Period size: 8 Copynumber: 12.1 Consensus size: 9
7011006 GAAAGGGGGA
7011016 GAGAGAGGG
1 GAGAGAGGG
* *
7011025 GAAATA-GG
1 GAGAGAGGG
7011033 GAGAG-GGG
1 GAGAGAGGG
7011041 GAGAGA-GG
1 GAGAGAGGG
7011049 GAGAGA-GG
1 GAGAGAGGG
*
7011057 GAGAGCGAGG
1 GAGAGAG-GG
7011067 GAGAGA-GG
1 GAGAGAGGG
*
7011075 GAGAGCGAGG
1 GAGAGAG-GG
*
7011085 GAGAGCGGG
1 GAGAGAGGG
7011094 G-GAGA-GG
1 GAGAGAGGG
* *
7011101 GAGGGA-GA
1 GAGAGAGGG
7011109 GAGAGAGGG
1 GAGAGAGGG
7011118 G
1 G
7011119 TATGGGAGAG
Statistics
Matches: 74, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
7 3 0.04
8 46 0.62
9 9 0.12
10 16 0.22
ACGTcount: A:0.33, C:0.03, G:0.63, T:0.01
Consensus pattern (9 bp):
GAGAGAGGG
Found at i:7011052 original size:6 final size:6
Alignment explanation
Indices: 7011030--7011176 Score: 74
Period size: 6 Copynumber: 24.2 Consensus size: 6
7011020 GAGGGGAAAT
* * *
7011030 AGGGAG AGGGGG AGAGAG -GGAGAG AGGGAG AGCGAG -GGAGAG AGGGAG
1 AGGGAG AGGGAG AGGGAG AGG-GAG AGGGAG AGGGAG AGG-GAG AGGGAG
* * * *
7011078 AGCGAG -GGAGAG CGGGGG AGAGG-G AGGGAG AGAGAG AGGG-G TATGGGAG
1 AGGGAG AGG-GAG AGGGAG AG-GGAG AGGGAG AGGGAG AGGGAG -A-GGGAG
* * *
7011127 AGGGAG -GGG-G ATGGGAG AGGGAAAG AGAGAG AGGGGG AGGGAG AGAGAG
1 AGGGAG AGGGAG A-GGGAG AGGG--AG AGGGAG AGGGAG AGGGAG AGGGAG
7011176 A
1 A
7011177 TGCCGCAAAG
Statistics
Matches: 108, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
4 1 0.01
5 9 0.08
6 78 0.72
7 14 0.13
8 6 0.06
ACGTcount: A:0.33, C:0.02, G:0.63, T:0.02
Consensus pattern (6 bp):
AGGGAG
Found at i:7011056 original size:18 final size:18
Alignment explanation
Indices: 7010922--7011111 Score: 110
Period size: 18 Copynumber: 10.8 Consensus size: 18
7010912 ATATATGAGA
*
7010922 GAGAGAAGGAGAGA--GG
1 GAGAGAGGGAGAGAGGGG
7010938 GAGAG-GGG-GAGAGGGG
1 GAGAGAGGGAGAGAGGGG
*
7010954 GAGAG-GGG-GAGAGGGA
1 GAGAGAGGGAGAGAGGGG
* * * * *
7010970 AAGAGAGGAAGGGACGGA
1 GAGAGAGGGAGAGAGGGG
* **
7010988 GTGAGAGACAGAG-GTGGG
1 GAGAGAGGGAGAGAG-GGG
* *
7011006 GAAAGGGGGAGAGAGAGGG
1 GAGAGAGGGAGAGAG-GGG
* *
7011025 GAAATA-GG-GAGAGGGG
1 GAGAGAGGGAGAGAGGGG
*
7011041 GAGAGAGGGAGAGAGGGA
1 GAGAGAGGGAGAGAGGGG
* *
7011059 GAGCGAGGGAGAGAGGGA
1 GAGAGAGGGAGAGAGGGG
* *
7011077 GAGCGAGGGAGAGCGGGG
1 GAGAGAGGGAGAGAGGGG
7011095 GAGAGGGAGGGAGAGAG
1 GAGA--GAGGGAGAGAG
7011112 AGAGGGGTAT
Statistics
Matches: 135, Mismatches: 29, Indels: 16
0.75 0.16 0.09
Matches are distributed among these distances:
14 4 0.03
15 2 0.01
16 33 0.24
17 9 0.07
18 69 0.51
19 8 0.06
20 10 0.07
ACGTcount: A:0.34, C:0.03, G:0.62, T:0.02
Consensus pattern (18 bp):
GAGAGAGGGAGAGAGGGG
Found at i:7011133 original size:17 final size:17
Alignment explanation
Indices: 7011093--7011148 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
7011083 GGGAGAGCGG
*
7011093 GGGAGAGGGA-GGGAGA
1 GGGAGGGGGATGGGAGA
*
7011109 GAGAGAGGGGTATGGGAGA
1 G-G-GAGGGGGATGGGAGA
7011128 GGGAGGGGGATGGGAGA
1 GGGAGGGGGATGGGAGA
7011145 GGGA
1 GGGA
7011149 AAGAGAGAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.03
17 19 0.56
18 7 0.21
19 7 0.21
ACGTcount: A:0.29, C:0.00, G:0.66, T:0.05
Consensus pattern (17 bp):
GGGAGGGGGATGGGAGA
Found at i:7011176 original size:18 final size:18
Alignment explanation
Indices: 7011030--7011145 Score: 105
Period size: 18 Copynumber: 6.4 Consensus size: 18
7011020 GAGGGGAAAT
*
7011030 AGGGAGAG-GGG-GAGAG
1 AGGGAGAGAGGGAGAGGG
*
7011046 AGGGAGAGAGGGAGAGCG
1 AGGGAGAGAGGGAGAGGG
*
7011064 AGGGAGAGAGGGAGAGCG
1 AGGGAGAGAGGGAGAGGG
*
7011082 AGGGAGAGCGGGGGAGAGGG
1 AGGGAGA--GAGGGAGAGGG
*
7011102 AGGGAGAGAGAGAG-GGG
1 AGGGAGAGAGGGAGAGGG
* *
7011119 TATGG-GAGAGGGAGGGGG
1 -AGGGAGAGAGGGAGAGGG
7011137 ATGGGAGAG
1 A-GGGAGAG
7011146 GGAAAGAGAG
Statistics
Matches: 84, Mismatches: 8, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.10
17 15 0.18
18 42 0.50
19 3 0.04
20 16 0.19
ACGTcount: A:0.30, C:0.03, G:0.65, T:0.03
Consensus pattern (18 bp):
AGGGAGAGAGGGAGAGGG
Found at i:7018141 original size:42 final size:42
Alignment explanation
Indices: 7018014--7018148 Score: 100
Period size: 42 Copynumber: 3.2 Consensus size: 42
7018004 TATTGTGGCA
* * *
7018014 TTTTTCATAAAAACGCCGA-AATAGAGTAGTACTTTAGCGGCG-
1 TTTTTCA-AAAAACACC-ACAAAAGAGTAGTACTTTAGCGTCGT
* * * * * *
7018056 CTTTT-AACAAACACCACAAAAGGATTAAT-CTATAGTAGT-GT
1 TTTTTCAAAAAACACCACAAAA-GAGTAGTACTTTAG-CGTCGT
*
7018097 TTTTTCAAAAAACACCACAACAGAGTAGTACTTTAGCGTCGT
1 TTTTTCAAAAAACACCACAAAAGAGTAGTACTTTAGCGTCGT
7018139 TTTTTACAAA
1 TTTTT-CAAA
7018149 CGCCGCAAAT
Statistics
Matches: 69, Mismatches: 16, Indels: 15
0.69 0.16 0.15
Matches are distributed among these distances:
39 1 0.01
40 16 0.23
41 18 0.26
42 30 0.43
43 4 0.06
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (42 bp):
TTTTTCAAAAAACACCACAAAAGAGTAGTACTTTAGCGTCGT
Found at i:7025625 original size:45 final size:43
Alignment explanation
Indices: 7025558--7025667 Score: 107
Period size: 45 Copynumber: 2.5 Consensus size: 43
7025548 ACAATATTAA
* * * *
7025558 CATTATATAATTTTGACCTTTTGCGGCGTTTGTATCCAAAAAATGC
1 CATTATAT-ATCTAGACCTTTTGCAGCGTATGT-TCC-AAAAATGC
* *
7025604 CATTATATATCTAGACCTTTTGCAGTGTATGTTTCAAAAATGC
1 CATTATATATCTAGACCTTTTGCAGCGTATGTTCCAAAAATGC
7025647 CGATATATATATC-A-ACCTTTT
1 C-AT-TATATATCTAGACCTTTT
7025668 TCGAATTTTG
Statistics
Matches: 56, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
43 16 0.29
44 5 0.09
45 27 0.48
46 8 0.14
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (43 bp):
CATTATATATCTAGACCTTTTGCAGCGTATGTTCCAAAAATGC
Found at i:7025685 original size:43 final size:43
Alignment explanation
Indices: 7025558--7025685 Score: 100
Period size: 43 Copynumber: 2.9 Consensus size: 43
7025548 ACAATATTAA
* * ***
7025558 CATTATATAATTTTGACCTTTTGCGGCGTTTGTATCCAAAAAATGC
1 CATTATAT-ATCTAGACCTTTTGCAATGTTTGT-TCC-AAAAATGC
* * *
7025604 CATTATATATCTAGACCTTTTGCAGTGTATGTTTCAAAAATGC
1 CATTATATATCTAGACCTTTTGCAATGTTTGTTCCAAAAATGC
*
7025647 CGATATATATATC-A-ACCTTTTTCGAAT-TTTGTTCCAAAA
1 C-AT-TATATATCTAGACCTTTTGC-AATGTTTGTTCCAAAA
7025686 CGCTGCTATA
Statistics
Matches: 69, Mismatches: 10, Indels: 9
0.78 0.11 0.10
Matches are distributed among these distances:
43 27 0.39
44 7 0.10
45 27 0.39
46 8 0.12
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.40
Consensus pattern (43 bp):
CATTATATATCTAGACCTTTTGCAATGTTTGTTCCAAAAATGC
Done.