Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006365.1 Hibiscus syriacus cultivar Beakdansim tig00015288_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: 53918
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Found at i:1840 original size:11 final size:12
Alignment explanation
Indices: 1805--1856 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
1795 AGAAAGCAAA
* *
1805 AGCTCAGAATTG
1 AGCTTAGAATCG
* *
1817 AGCTCAAAATCG
1 AGCTTAGAATCG
1829 AGCTT-GAATCG
1 AGCTTAGAATCG
*
1840 AGTTTAGAATCG
1 AGCTTAGAATCG
1852 AGCTT
1 AGCTT
1857 CAATTGAGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
11 9 0.27
12 24 0.73
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (12 bp):
AGCTTAGAATCG
Found at i:5408 original size:24 final size:24
Alignment explanation
Indices: 5376--5426 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
5366 TTTGCAGTTG
5376 ATGAACAAATCCCATATCATGACT
1 ATGAACAAATCCCATATCATGACT
5400 ATGAACAAATCCCATATCATGACT
1 ATGAACAAATCCCATATCATGACT
5424 ATG
1 ATG
5427 GATGTCAATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.25
Consensus pattern (24 bp):
ATGAACAAATCCCATATCATGACT
Found at i:6841 original size:14 final size:14
Alignment explanation
Indices: 6822--6873 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
6812 TAGACTGAAT
6822 ATAAACAAACAAAC
1 ATAAACAAACAAAC
* *
6836 ATAAACGAACATAC
1 ATAAACAAACAAAC
*
6850 ATAAATAAACAAAC
1 ATAAACAAACAAAC
6864 ATAAACAAAC
1 ATAAACAAAC
6874 GGATTATAGA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 32 1.00
ACGTcount: A:0.67, C:0.19, G:0.02, T:0.12
Consensus pattern (14 bp):
ATAAACAAACAAAC
Found at i:6846 original size:10 final size:10
Alignment explanation
Indices: 6828--6873 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
6818 GAATATAAAC
6828 AAACAAACAT
1 AAACAAACAT
*
6838 AAACGAACAT
1 AAACAAACAT
6848 --ACATAA-AT
1 AAACA-AACAT
6856 AAACAAACAT
1 AAACAAACAT
6866 AAACAAAC
1 AAACAAAC
6874 GGATTATAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
8 4 0.13
9 4 0.13
10 22 0.73
ACGTcount: A:0.67, C:0.20, G:0.02, T:0.11
Consensus pattern (10 bp):
AAACAAACAT
Found at i:7179 original size:13 final size:13
Alignment explanation
Indices: 7157--7198 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
7147 AAAATTAATA
7157 ATAATATTTAATTT
1 ATAAT-TTTAATTT
7171 ATAATTTTAATTT
1 ATAATTTTAATTT
*
7184 A-AATGTTAATATT
1 ATAATTTTAAT-TT
7197 AT
1 AT
7199 TAGAATTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
12 8 0.32
13 12 0.48
14 5 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (13 bp):
ATAATTTTAATTT
Found at i:11717 original size:2 final size:2
Alignment explanation
Indices: 11671--11705 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
11661 ATATGATTAA
11671 AT AT GAT 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 AT AT AT
11706 TAAAATTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17002 original size:21 final size:21
Alignment explanation
Indices: 16978--17017 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
16968 TTCTACGTGG
16978 TCCTTC-GAGACATATATGTAA
1 TCCTTCGGA-ACATATATGTAA
*
16999 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
17018 GGTACTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:17025 original size:21 final size:21
Alignment explanation
Indices: 16987--17027 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16977 GTCCTTCGAG
*
16987 ACATATATGTAATCCTTTGGA
1 ACATATATGTAATACTTTGGA
**
17008 ACATATATGTGGTACTTTGG
1 ACATATATGTAATACTTTGG
17028 TACACTTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (21 bp):
ACATATATGTAATACTTTGGA
Found at i:17121 original size:18 final size:18
Alignment explanation
Indices: 17098--17147 Score: 82
Period size: 18 Copynumber: 2.8 Consensus size: 18
17088 TATGTGATAT
*
17098 GTGGTCCTTCGGGACACA
1 GTGGTCATTCGGGACACA
17116 GTGGTCATTCGGGACACA
1 GTGGTCATTCGGGACACA
*
17134 GTGGTCATTTGGGA
1 GTGGTCATTCGGGA
17148 TAAATCCTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.18, C:0.20, G:0.36, T:0.26
Consensus pattern (18 bp):
GTGGTCATTCGGGACACA
Found at i:18230 original size:64 final size:64
Alignment explanation
Indices: 18162--18340 Score: 243
Period size: 64 Copynumber: 2.8 Consensus size: 64
18152 TTTAAAGAAG
* * * *
18162 AAACATTGAATGTCTTGAGTGTATCGATGCACAGTTAGTCCATCGATGCACCCATTTAAAATGA
1 AAACATCGAATGTCTTGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* * * * *
18226 AAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCCCTTAAGATTA
1 AAACATCGAATGTCTTGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* *
18290 AAACATCGAATGTAATT-TGTGTACCGATGCACAGTTAGTGCATCGATGCAC
1 AAACATCGAATGT-CTTGAGTGTACCGATGCACAGTTAGTGCATCGATGCAC
18341 AGTTAGTGCA
Statistics
Matches: 101, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
64 100 0.99
65 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (64 bp):
AAACATCGAATGTCTTGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
Found at i:18338 original size:19 final size:19
Alignment explanation
Indices: 18314--18360 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
18304 ATTTGTGTAC
18314 CGATGCACAGTTAGTGCAT
1 CGATGCACAGTTAGTGCAT
18333 CGATGCACAGTTAGTGCAT
1 CGATGCACAGTTAGTGCAT
18352 CGATGCACA
1 CGATGCACA
18361 CATTAAGGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (19 bp):
CGATGCACAGTTAGTGCAT
Found at i:18950 original size:18 final size:18
Alignment explanation
Indices: 18927--18981 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
18917 TCGAGGGATT
*
18927 ATAGTGGTCCTTTGGGAC
1 ATAGTGGTCCTTCGGGAC
*
18945 ATAGTGGTCATTCGGGAC
1 ATAGTGGTCCTTCGGGAC
*
18963 AGAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
18981 A
1 A
18982 AATATTTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.35, T:0.27
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Found at i:26721 original size:64 final size:64
Alignment explanation
Indices: 26590--26768 Score: 216
Period size: 64 Copynumber: 2.8 Consensus size: 64
26580 TTTAAAGAAG
* * *
26590 AAACATCGAATGCCTTGAGTGTACCGATGCATAGTTAGTGCATCGATGCACCCATTTAAAATGA
1 AAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* * *
26654 AAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCCCTTAAGATTA
1 AAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* * ** ** * *
26718 AAACAGCTAATGTAATTTGTGTACCGATGCACAAG-TAGTACATCAATGCAC
1 AAACATCGAATGCCATGAGTGTACCGATGCAC-AGTTAGTGCATCGATGCAC
26769 ACATTAAGGA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
64 98 0.98
65 2 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.25
Consensus pattern (64 bp):
AAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
Found at i:27358 original size:17 final size:17
Alignment explanation
Indices: 27336--27385 Score: 82
Period size: 18 Copynumber: 2.9 Consensus size: 17
27326 TCGAGGGATT
27336 ATAGTGGTCCTTTGGAC
1 ATAGTGGTCCTTTGGAC
*
27353 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTT-TGGAC
27371 ATAGTGGTCCTTTGG
1 ATAGTGGTCCTTTGG
27386 GACAAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.16, C:0.18, G:0.32, T:0.34
Consensus pattern (17 bp):
ATAGTGGTCCTTTGGAC
Found at i:31252 original size:2 final size:2
Alignment explanation
Indices: 31245--31306 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
31235 TAATTAAAGA
31245 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
31287 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
31307 TAGCTACACG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31973 original size:64 final size:64
Alignment explanation
Indices: 31880--32057 Score: 239
Period size: 64 Copynumber: 2.8 Consensus size: 64
31870 CTTAAAGAAG
* * * * *
31880 AAACATCGAATGCCTTGAGTGTACTGATGCACAGTTAGTGCATCGATGCACGCATTTAAAATGA
1 AAACATCGAATGTCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* * *
31944 AAACATCGAATGTCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCCCTTAAGATTA
1 AAACATCGAATGTCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
* ** * *
32008 AAACATCGAATGTAATTTGTGTACCGATTCACAGGTAGTGCATCGATGCA
1 AAACATCGAATGTCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCA
32058 TACATTAAGG
Statistics
Matches: 101, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
64 101 1.00
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.26
Consensus pattern (64 bp):
AAACATCGAATGTCATGAGTGTACCGATGCACAGTTAGTGCATCGATGCACCCACTTAAAATGA
Found at i:32646 original size:18 final size:18
Alignment explanation
Indices: 32623--32677 Score: 92
Period size: 18 Copynumber: 3.1 Consensus size: 18
32613 TCGAGGGATT
32623 ATAGTGGTCCTTTGGGAC
1 ATAGTGGTCCTTTGGGAC
**
32641 ATAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTTGGGAC
32659 ATAGTGGTCCTTTGGGAC
1 ATAGTGGTCCTTTGGGAC
32677 A
1 A
32678 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.20, C:0.18, G:0.31, T:0.31
Consensus pattern (18 bp):
ATAGTGGTCCTTTGGGAC
Found at i:38741 original size:44 final size:45
Alignment explanation
Indices: 38691--38794 Score: 149
Period size: 45 Copynumber: 2.3 Consensus size: 45
38681 ACGCATTCAA
* * *
38691 AGTGTACTGATGCACTC-TTTAAAGAAG-AAACATCGAATGCCTTG
1 AGTGTACCGATGCACCCATTTAAA-AAGAAAACATCGAATGCCATG
*
38735 AGTGTACCGATGCACCCATTTAAAATGAAAACATCGAATGCCATG
1 AGTGTACCGATGCACCCATTTAAAAAGAAAACATCGAATGCCATG
38780 AGTGTACCGATGCAC
1 AGTGTACCGATGCAC
38795 AGTTAGTGCA
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
44 17 0.31
45 37 0.69
ACGTcount: A:0.35, C:0.21, G:0.20, T:0.24
Consensus pattern (45 bp):
AGTGTACCGATGCACCCATTTAAAAAGAAAACATCGAATGCCATG
Found at i:38849 original size:64 final size:64
Alignment explanation
Indices: 38742--38877 Score: 191
Period size: 64 Copynumber: 2.1 Consensus size: 64
38732 TTGAGTGTAC
* *
38742 CGATGCACCCATTTAAAATGAAAACATCGAATGCCATGAGTGTACCGATGCACAGTTAGTGCAT
1 CGATGCACCCATTTAAAATGAAAACATCGAATGCAATGAGTGTACCGATGCACAGGTAGTGCAT
* * * * * **
38806 CGATGCACCCCTTTAAGATTAAAACATTGAATGTAATTTGTGTACCGATGCACAGGTAGTGCAT
1 CGATGCACCCATTTAAAATGAAAACATCGAATGCAATGAGTGTACCGATGCACAGGTAGTGCAT
38870 CGATGCAC
1 CGATGCAC
38878 ACATAAGGAA
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (64 bp):
CGATGCACCCATTTAAAATGAAAACATCGAATGCAATGAGTGTACCGATGCACAGGTAGTGCAT
Found at i:39463 original size:18 final size:18
Alignment explanation
Indices: 39440--39488 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
39430 TTGAGGAATT
*
39440 ATAGTGGTCCTTTGAGAC
1 ATAGTGGTCCTTCGAGAC
*
39458 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCGAGAC
39476 ATAGTGGTCCTTC
1 ATAGTGGTCCTTC
39489 AGGACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.18, C:0.20, G:0.29, T:0.33
Consensus pattern (18 bp):
ATAGTGGTCCTTCGAGAC
Found at i:39493 original size:18 final size:18
Alignment explanation
Indices: 39440--39494 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
39430 TTGAGGAATT
*
39440 ATAGTGGTCCTT-TGAGAC
1 ATAGTGGTCCTTCAG-GAC
*
39458 ATAGTGGTCCTTCGGGAC
1 ATAGTGGTCCTTCAGGAC
39476 ATAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTCAGGAC
39494 A
1 A
39495 AATATTCAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
18 33 0.97
19 1 0.03
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCAGGAC
Found at i:49524 original size:20 final size:20
Alignment explanation
Indices: 49487--49529 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
49477 ATTCCACCAC
49487 ATGCAACTAAATGCTCCTAA
1 ATGCAACTAAATGCTCCTAA
* * *
49507 ATGCATCTACATGGTCCTAA
1 ATGCAACTAAATGCTCCTAA
49527 ATG
1 ATG
49530 AGCTATTAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (20 bp):
ATGCAACTAAATGCTCCTAA
Found at i:50184 original size:18 final size:18
Alignment explanation
Indices: 50161--50215 Score: 83
Period size: 18 Copynumber: 3.1 Consensus size: 18
50151 TTGAAGGATT
*
50161 ATAGTGGTCTTTCGGGAC
1 ATAGTGGTCCTTCGGGAC
*
50179 ATAGTGGTCCTTCAGGAC
1 ATAGTGGTCCTTCGGGAC
*
50197 ATAGTGGTCCTTCGAGAC
1 ATAGTGGTCCTTCGGGAC
50215 A
1 A
50216 AATATTCAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (18 bp):
ATAGTGGTCCTTCGGGAC
Done.