Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005780.1 Hibiscus syriacus cultivar Beakdansim tig00013534_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: 57489
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:4537 original size:22 final size:23
Alignment explanation
Indices: 4507--4561 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
4497 ATGCTAATGG
* * *
4507 AATGATGATGTTATTGGCGTGAT
1 AATGGTGATGATATAGGCGTGAT
4530 -ATGGTGATGATATAGGCGTGAT
1 AATGGTGATGATATAGGCGTGAT
4552 AATGGTGATG
1 AATGGTGATG
4562 GACTATGGTG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.35
Consensus pattern (23 bp):
AATGGTGATGATATAGGCGTGAT
Found at i:4576 original size:36 final size:36
Alignment explanation
Indices: 4529--4611 Score: 148
Period size: 36 Copynumber: 2.3 Consensus size: 36
4519 ATTGGCGTGA
*
4529 TATGGTGATGATATAGGCGTGATAATGGTGATGGAC
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
*
4565 TATGGTGATGATATAGGCGTGATAATGGAGATGGAT
1 TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
4601 TATGGTGATGA
1 TATGGTGATGA
4612 AAATAGTATC
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 45 1.00
ACGTcount: A:0.29, C:0.04, G:0.36, T:0.31
Consensus pattern (36 bp):
TATGGTGATGATATAGGCGTGATAATGGAGATGGAC
Found at i:4982 original size:18 final size:18
Alignment explanation
Indices: 4959--4998 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
4949 GGAAACAAAT
*
4959 GATGCTTGGATTAGGGGA
1 GATGCTTGGATGAGGGGA
4977 GATGCTTGGATGAGGGGA
1 GATGCTTGGATGAGGGGA
4995 GATG
1 GATG
4999 TCTTTGGCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.23, C:0.05, G:0.47, T:0.25
Consensus pattern (18 bp):
GATGCTTGGATGAGGGGA
Found at i:6774 original size:23 final size:24
Alignment explanation
Indices: 6746--6804 Score: 86
Period size: 23 Copynumber: 2.5 Consensus size: 24
6736 AAAATCAGCA
6746 AAGAAAATAAAAGCACTC-AAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
* *
6769 AAGAAATTGAAAGCACTCGAAAAG
1 AAGAAAATAAAAGCACTCGAAAAG
6793 AAGAAAA-AAAAG
1 AAGAAAATAAAAG
6805 AAAGAAAAGT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.65
24 11 0.35
ACGTcount: A:0.64, C:0.10, G:0.17, T:0.08
Consensus pattern (24 bp):
AAGAAAATAAAAGCACTCGAAAAG
Found at i:11843 original size:36 final size:36
Alignment explanation
Indices: 11795--11899 Score: 176
Period size: 36 Copynumber: 2.9 Consensus size: 36
11785 GATACAATCT
*
11795 GTCCATCACCATTATCACGTCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
11831 TTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
*
11867 GTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
11900 ACTTCTAAAT
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
35 21 0.32
36 44 0.68
ACGTcount: A:0.30, C:0.35, G:0.05, T:0.30
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:12536 original size:16 final size:15
Alignment explanation
Indices: 12503--12554 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
12493 GTAAGTTATC
12503 TTCATTTTTTATCAT
1 TTCATTTTTTATCAT
12518 TTCATTTCTTTATTC-T
1 TTCATTT-TTTA-TCAT
* * *
12534 TTCATCTTTTCTTAT
1 TTCATTTTTTATCAT
12549 TTCATT
1 TTCATT
12555 ACCATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
14 1 0.03
15 16 0.53
16 11 0.37
17 2 0.07
ACGTcount: A:0.15, C:0.17, G:0.00, T:0.67
Consensus pattern (15 bp):
TTCATTTTTTATCAT
Found at i:19611 original size:22 final size:22
Alignment explanation
Indices: 19583--19626 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
19573 CATCTTCCAT
19583 TATCACGCCTATATCATCACCA
1 TATCACGCCTATATCATCACCA
19605 TATCACGCCTATATCATCACCA
1 TATCACGCCTATATCATCACCA
19627 AATTCTCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.36, G:0.05, T:0.27
Consensus pattern (22 bp):
TATCACGCCTATATCATCACCA
Found at i:20705 original size:33 final size:33
Alignment explanation
Indices: 20663--20731 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
20653 GTTGATGAAT
*
20663 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
20696 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
20729 GAA
1 GAA
20732 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:20736 original size:13 final size:12
Alignment explanation
Indices: 20717--20781 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
20707 TTATTGGCGT
20717 GATATGGTGATG
1 GATATGGTGATG
20729 GAATATGGTGAT-
1 G-ATATGGTGATG
*
20741 GATATAGGCG-T-
1 GATAT-GGTGATG
20752 GATAATGGTGATG
1 GAT-ATGGTGATG
20765 GACTATGGTGAT-
1 GA-TATGGTGATG
20777 GATAT
1 GATAT
20782 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:20772 original size:36 final size:36
Alignment explanation
Indices: 20702--20812 Score: 161
Period size: 36 Copynumber: 3.1 Consensus size: 36
20692 AATGGAAGGA
* *
20702 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
20737 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
20773 TGATGATATAGGCGTGATAATGGAGATGGATTATTG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
20809 TGAT
1 TGAT
20813 AAAAATAGTA
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 16 0.23
36 53 0.77
ACGTcount: A:0.27, C:0.04, G:0.35, T:0.34
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:26440 original size:33 final size:33
Alignment explanation
Indices: 26398--26467 Score: 88
Period size: 33 Copynumber: 2.1 Consensus size: 33
26388 GTTGATGAAT
*
26398 GAATGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAATGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
26431 GAATGATGATGTTATTGGCGTGATATGGTGATG
1 GAATGATGATGTTAATGGCGTGAAATGGTAATG
26464 GAAT
1 GAAT
26468 ATGGTGATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.31, C:0.01, G:0.33, T:0.34
Consensus pattern (33 bp):
GAATGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:26471 original size:13 final size:12
Alignment explanation
Indices: 26452--26516 Score: 57
Period size: 13 Copynumber: 5.4 Consensus size: 12
26442 TTATTGGCGT
26452 GATATGGTGATG
1 GATATGGTGATG
26464 GAATATGGTGAT-
1 G-ATATGGTGATG
*
26476 GATATAGGCG-T-
1 GATAT-GGTGATG
26487 GATAATGGTGATG
1 GAT-ATGGTGATG
26500 GACTATGGTGAT-
1 GA-TATGGTGATG
26512 GATAT
1 GATAT
26517 AGGCGTGATA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
11 14 0.31
12 10 0.22
13 20 0.44
14 1 0.02
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.32
Consensus pattern (12 bp):
GATATGGTGATG
Found at i:26507 original size:36 final size:35
Alignment explanation
Indices: 26421--26549 Score: 163
Period size: 36 Copynumber: 3.7 Consensus size: 35
26411 ATGGTGATGA
* * * *
26421 AATGGTAATGGA-ATGATGATGTTATTGGCGTGAT
1 AATGGTGATGGATATGGTGATGATATAGGCGTGAT
26455 -ATGGTGATGGAATATGGTGATGATATAGGCGTGAT
1 AATGGTGATGG-ATATGGTGATGATATAGGCGTGAT
26490 AATGGTGATGGACTATGGTGATGATATAGGCGTGAT
1 AATGGTGATGGA-TATGGTGATGATATAGGCGTGAT
* *
26526 AATAGAGATGGATTATGGTGATGA
1 AATGGTGATGGA-TATGGTGATGA
26550 AAATAGTATC
Statistics
Matches: 84, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
33 9 0.11
34 1 0.01
35 20 0.24
36 54 0.64
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.32
Consensus pattern (35 bp):
AATGGTGATGGATATGGTGATGATATAGGCGTGAT
Found at i:32538 original size:28 final size:25
Alignment explanation
Indices: 32483--32538 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
32473 TTCTTTGCTT
**
32483 TTTCTTCTTTTGAGTGCTGGATTTC
1 TTTCTTCTTTTGAGTGCTCAATTTC
32508 TTTCTTTCTTTTGGAGTGCTTCAATTTC
1 TTTC-TTCTTTT-GAGTGC-TCAATTTC
32536 TTT
1 TTT
32539 TCTGATTTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 4 0.15
26 7 0.27
27 6 0.23
28 9 0.35
ACGTcount: A:0.09, C:0.16, G:0.16, T:0.59
Consensus pattern (25 bp):
TTTCTTCTTTTGAGTGCTCAATTTC
Found at i:46117 original size:16 final size:16
Alignment explanation
Indices: 46096--46127 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46086 TAGTTAGCTC
46096 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
46112 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
46128 TGGTGGAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:47266 original size:19 final size:20
Alignment explanation
Indices: 47242--47281 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
47232 ATCTTTTTAT
47242 TTATTTAATTTCATT-CTTA
1 TTATTTAATTTCATTACTTA
*
47261 TTATTTATTTTCATTACTTA
1 TTATTTAATTTCATTACTTA
47281 T
1 T
47282 ATTATTACCC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.25, C:0.10, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTAATTTCATTACTTA
Found at i:50153 original size:19 final size:20
Alignment explanation
Indices: 50137--50181 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
50127 ATTTATTTCA
50137 TTTCATT-CTTATTATTTAT
1 TTTCATTACTTATTATTTAT
50156 TTTCATTACTTA-TA-TTAT
1 TTTCATTACTTATTATTTAT
50174 TATTCATT
1 T-TTCATT
50182 TTTTAAACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.21
19 15 0.62
20 4 0.17
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (20 bp):
TTTCATTACTTATTATTTAT
Done.