Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004384.1 Hibiscus syriacus cultivar Beakdansim tig00009612_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: 72570
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:152 original size:16 final size:16
Alignment explanation
Indices: 131--163 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
121 TTCATAATTA
131 GTTGTTGCCCATTGAT
1 GTTGTTGCCCATTGAT
147 GTTGTTGCCCATTGAT
1 GTTGTTGCCCATTGAT
163 G
1 G
164 CCATGTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.18, G:0.27, T:0.42
Consensus pattern (16 bp):
GTTGTTGCCCATTGAT
Found at i:2279 original size:16 final size:16
Alignment explanation
Indices: 2258--2290 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2248 CAACGTCATT
2258 ATTCCAACCGATCCTA
1 ATTCCAACCGATCCTA
2274 ATTCCAACCGATCCTA
1 ATTCCAACCGATCCTA
2290 A
1 A
2291 AGAAGTCTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.36, G:0.06, T:0.24
Consensus pattern (16 bp):
ATTCCAACCGATCCTA
Found at i:6302 original size:18 final size:17
Alignment explanation
Indices: 6279--6339 Score: 61
Period size: 18 Copynumber: 3.5 Consensus size: 17
6269 ATTGGAGTAC
6279 AAAAAGAAAGAAAAGATA
1 AAAAAG-AAGAAAAGATA
**
6297 AAAAAGAAGAAAATTTCA
1 AAAAAGAAGAAAAGAT-A
*
6315 TAAAAGAAGAAAAGA-A
1 AAAAAGAAGAAAAGATA
6331 AAAGAAGAA
1 AAA-AAGAA
6340 TTTCAAAAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
16 3 0.09
17 13 0.37
18 19 0.54
ACGTcount: A:0.74, C:0.02, G:0.16, T:0.08
Consensus pattern (17 bp):
AAAAAGAAGAAAAGATA
Found at i:8481 original size:21 final size:21
Alignment explanation
Indices: 8455--8500 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
8445 CACCTCCCTT
8455 CATTAAAACA-ACATGTATTTC
1 CATTAAAA-AGACATGTATTTC
*
8476 CATTAAAAAGATATGTATTTC
1 CATTAAAAAGACATGTATTTC
8497 CATT
1 CATT
8501 TGGCCACTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.04
21 22 0.96
ACGTcount: A:0.41, C:0.15, G:0.07, T:0.37
Consensus pattern (21 bp):
CATTAAAAAGACATGTATTTC
Found at i:10619 original size:14 final size:14
Alignment explanation
Indices: 10599--10635 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
10589 ATGATAGAGA
*
10599 ATGGTGATGGAAAG
1 ATGGTGATGAAAAG
*
10613 TTGGTGATGAAAAG
1 ATGGTGATGAAAAG
10627 ATGGTGATG
1 ATGGTGATG
10636 TTATAGGTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.32, C:0.00, G:0.41, T:0.27
Consensus pattern (14 bp):
ATGGTGATGAAAAG
Found at i:14471 original size:90 final size:89
Alignment explanation
Indices: 14360--14522 Score: 281
Period size: 90 Copynumber: 1.8 Consensus size: 89
14350 TAATTTCAAT
*
14360 TAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCCAATATGATTAGGGTAACT
1 TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAA-CCCCAATATGATTAGGGTAACT
14425 TGGATATAAGAGGATTATTAAATTC
65 TGGATATAAGAGGATTATTAAATTC
* *
14450 TAATTAATTAAATATATATTTAATTAATTGGAAATAATAAAACCCTAATATGATTAGGGTAACTT
1 TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAACCCCAATATGATTAGGGTAACTT
*
14515 GGCTATAA
66 GGATATAA
14523 AAGGGTGTGT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
89 29 0.42
90 40 0.58
ACGTcount: A:0.45, C:0.07, G:0.12, T:0.37
Consensus pattern (89 bp):
TAATTAATTAAATATAGATTTAATTAATTGGAAATAATAAAACCCCAATATGATTAGGGTAACTT
GGATATAAGAGGATTATTAAATTC
Found at i:16581 original size:15 final size:15
Alignment explanation
Indices: 16561--16606 Score: 58
Period size: 15 Copynumber: 2.9 Consensus size: 15
16551 TTTGATATCA
16561 TTTCTTTCCATTTCC
1 TTTCTTTCCATTTCC
16576 TTTCTTAT-CATTTCC
1 TTTCTT-TCCATTTCC
16591 TTTCTTCTTCCATTTC
1 TTTC-T-TTCCATTTC
16607 TTATTTCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 17 0.63
16 3 0.11
17 7 0.26
ACGTcount: A:0.09, C:0.30, G:0.00, T:0.61
Consensus pattern (15 bp):
TTTCTTTCCATTTCC
Found at i:25620 original size:20 final size:21
Alignment explanation
Indices: 25597--25676 Score: 74
Period size: 20 Copynumber: 3.8 Consensus size: 21
25587 TTGGTGCAGA
*
25597 GGGAATCGATCCCCCCATGA-
1 GGGAACCGATCCCCCCATGAG
**
25617 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCCCATG-AG
*
25640 GGGAACCGATCCCCCCA-CAG
1 GGGAACCGATCCCCCCATGAG
*
25660 GGGAATCGATACCCCCC
1 GGGAACCGAT-CCCCCC
25677 TGGGGTTCTG
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
20 19 0.39
21 14 0.29
22 7 0.14
23 9 0.18
ACGTcount: A:0.24, C:0.38, G:0.25, T:0.14
Consensus pattern (21 bp):
GGGAACCGATCCCCCCATGAG
Found at i:27950 original size:19 final size:20
Alignment explanation
Indices: 27921--27960 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
27911 TGTGTTTTAA
27921 GTGTGTTTAAAATGATAAAT
1 GTGTGTTTAAAATGATAAAT
27941 GTGT-TTTAAAATGATAAAT
1 GTGTGTTTAAAATGATAAAT
27960 G
1 G
27961 GGAGAAGTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.40, C:0.00, G:0.20, T:0.40
Consensus pattern (20 bp):
GTGTGTTTAAAATGATAAAT
Found at i:29990 original size:19 final size:18
Alignment explanation
Indices: 29958--29993 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
29948 ACATGATTTG
29958 TTTTATGAAAATACATGA
1 TTTTATGAAAATACATGA
*
29976 TTTTAATGAAGATACATG
1 TTTT-ATGAAAATACATG
29994 CTCTTGGCTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.42, C:0.06, G:0.14, T:0.39
Consensus pattern (18 bp):
TTTTATGAAAATACATGA
Found at i:33678 original size:15 final size:15
Alignment explanation
Indices: 33643--33671 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33633 GTGCTTCAAC
33643 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
33657 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
33672 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:37962 original size:15 final size:15
Alignment explanation
Indices: 37927--37955 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
37917 GTGCTTCAAC
37927 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
37941 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
37956 CTTTTTGAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (15 bp):
TTCTTTGCTTTTCTT
Found at i:44314 original size:17 final size:17
Alignment explanation
Indices: 44292--44324 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
44282 TGGCATAAAA
44292 GAAATGGATATGGTAAT
1 GAAATGGATATGGTAAT
44309 GAAATGGATATGGTAA
1 GAAATGGATATGGTAA
44325 AGGTAAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.27
Consensus pattern (17 bp):
GAAATGGATATGGTAAT
Found at i:46074 original size:19 final size:20
Alignment explanation
Indices: 46050--46089 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
46040 TATCCTTTTT
46050 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
46069 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
46089 T
1 T
46090 ATTATTATTC
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:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:46383 original size:19 final size:18
Alignment explanation
Indices: 46352--46416 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 18
46342 AATTGGAGTG
*
46352 CAAAAATAA-AGAAAAAGA
1 CAAAAAGAAGAGAAAAA-A
*
46370 CAAAAAGAAGAGAAAAAT
1 CAAAAAGAAGAGAAAAAA
*
46388 CAGAAAAGAAGAAAAGAAAA
1 CA-AAAAGAAGAGAA-AAAA
*
46408 GAAAAAGAA
1 CAAAAAGAA
46417 TTCAAAAAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 10 0.26
19 25 0.64
20 4 0.10
ACGTcount: A:0.75, C:0.05, G:0.17, T:0.03
Consensus pattern (18 bp):
CAAAAAGAAGAGAAAAAA
Found at i:52031 original size:5 final size:5
Alignment explanation
Indices: 52021--52046 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
52011 TGACTTAGAA
52021 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
52047 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:54892 original size:16 final size:16
Alignment explanation
Indices: 54858--54891 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54848 TTCAACTTTC
*
54858 TTTCTTTTTCTTTTCT
1 TTTCTTTTTCTTCTCT
54874 TTTCTTTTTCTTC-CT
1 TTTCTTTTTCTTCTCT
54889 TTT
1 TTT
54892 TGAGTGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTTTTTCTTCTCT
Found at i:54919 original size:23 final size:25
Alignment explanation
Indices: 54880--54933 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 25
54870 TTCTTTTCTT
54880 TTTCTTCCTTTTTGAGTGCTTTCAA
1 TTTCTTCCTTTTTGAGTGCTTTCAA
* *
54905 TTTCTT-C-TTTTGAGTGCTTTGAT
1 TTTCTTCCTTTTTGAGTGCTTTCAA
54928 TTTCTT
1 TTTCTT
54934 TGCTGGATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
23 20 0.74
24 1 0.04
25 6 0.22
ACGTcount: A:0.09, C:0.17, G:0.13, T:0.61
Consensus pattern (25 bp):
TTTCTTCCTTTTTGAGTGCTTTCAA
Found at i:60907 original size:35 final size:37
Alignment explanation
Indices: 60861--60940 Score: 128
Period size: 35 Copynumber: 2.2 Consensus size: 37
60851 TTTGAGAATT
*
60861 TGGTGATGATATAGGCGTGAT-ATGG-TGATGGACTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
*
60896 TGGTGATGATATAGGCGTGATAATGGAAGATGGATTA
1 TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
60933 TGGTGATG
1 TGGTGATG
60941 GAAATAGTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
35 21 0.51
36 4 0.10
37 16 0.39
ACGTcount: A:0.28, C:0.04, G:0.38, T:0.31
Consensus pattern (37 bp):
TGGTGATGATATAGGCGTGATAATGGAAGATGGACTA
Found at i:67335 original size:16 final size:15
Alignment explanation
Indices: 67316--67358 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
67306 CTTTATTATC
*
67316 TTATTTCATCTTCTGT
1 TTATTT-ATATTCTGT
*
67332 TTATTTATATTTTGT
1 TTATTTATATTCTGT
67347 TTATTT-TATTCT
1 TTATTTATATTCT
67359 AATCTTATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
14 5 0.21
15 13 0.54
16 6 0.25
ACGTcount: A:0.16, C:0.09, G:0.05, T:0.70
Consensus pattern (15 bp):
TTATTTATATTCTGT
Found at i:67981 original size:19 final size:18
Alignment explanation
Indices: 67925--67981 Score: 53
Period size: 19 Copynumber: 3.1 Consensus size: 18
67915 ATTAGAGTGC
67925 AAAAAGAAAGAAAAGAAA-A
1 AAAAAGAAA-AAAA-AAAGA
* **
67944 AAAAAGAGAAAAATCAGA
1 AAAAAGAAAAAAAAAAGA
67962 AAAGAAGAAAAAAAAAAGA
1 AAA-AAGAAAAAAAAAAGA
67981 A
1 A
67982 TTCAAAAAGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
17 1 0.03
18 8 0.27
19 21 0.70
ACGTcount: A:0.81, C:0.02, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAAAAAAAAGA
Found at i:67993 original size:30 final size:30
Alignment explanation
Indices: 67924--67999 Score: 77
Period size: 29 Copynumber: 2.5 Consensus size: 30
67914 AATTAGAGTG
67924 CAAAAAGAAAGAAAAGAAAAAAAAAGAGAA
1 CAAAAAGAAAGAAAAGAAAAAAAAAGAGAA
* *
67954 -AAATCAGAAA-AGAAGAAAAAAAAA-AGAA
1 CAAA-AAGAAAGAAAAGAAAAAAAAAGAGAA
*
67982 TTCAAAAAGAAAGCAAAG
1 --CAAAAAGAAAGAAAAG
68000 CCAAGGAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
28 4 0.11
29 16 0.44
30 10 0.28
31 6 0.17
ACGTcount: A:0.75, C:0.05, G:0.16, T:0.04
Consensus pattern (30 bp):
CAAAAAGAAAGAAAAGAAAAAAAAAGAGAA
Done.