Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001309.1 Hibiscus syriacus cultivar Beakdansim tig00002551_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: 73905
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:7647 original size:14 final size:15
Alignment explanation
Indices: 7620--7649 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
7610 TCTTGTCTCC
7620 TCAAAACGTTCTTTT
1 TCAAAACGTTCTTTT
7635 TCAAAAC-TTCTTTT
1 TCAAAACGTTCTTTT
7649 T
1 T
7650 ATGACCTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.27, C:0.20, G:0.03, T:0.50
Consensus pattern (15 bp):
TCAAAACGTTCTTTT
Found at i:7963 original size:19 final size:21
Alignment explanation
Indices: 7920--7964 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
7910 TCATATATCA
7920 TTCACTGCATACTATATGATT
1 TTCACTGCATACTATATGATT
7941 TTCA-TGCATAAC-ATATG-TT
1 TTCACTGCAT-ACTATATGATT
7960 TTCAC
1 TTCAC
7965 ATCTTTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.29, C:0.20, G:0.09, T:0.42
Consensus pattern (21 bp):
TTCACTGCATACTATATGATT
Found at i:16870 original size:16 final size:16
Alignment explanation
Indices: 16849--16897 Score: 98
Period size: 16 Copynumber: 3.1 Consensus size: 16
16839 TAGTTAGCTC
16849 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
16865 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
16881 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
16897 A
1 A
16898 GGTGGCATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.43
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:22572 original size:15 final size:15
Alignment explanation
Indices: 22537--22565 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22527 GTGCTTCAAC
22537 TTCTTT-CTTTTCTT
1 TTCTTTGCTTTTCTT
22551 TTCTTTGCTTTTCTT
1 TTCTTTGCTTTTCTT
22566 CTTTTTGAAT
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:22588 original size:27 final size:28
Alignment explanation
Indices: 22558--22619 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
22548 CTTTTCTTTG
* *
22558 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
22585 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
22613 CTTTTCT
1 CTTTTCT
22620 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:25219 original size:27 final size:28
Alignment explanation
Indices: 25189--25250 Score: 74
Period size: 27 Copynumber: 2.2 Consensus size: 28
25179 CTTTTCTTTG
* *
25189 CTTTTCTTCTTTTTGAATGC-TGAATTT
1 CTTTTCTTCTTTTGGAATGCTTCAATTT
*
25216 C-TTTCTTTCTTTTGGAGTGCTTCAATTT
1 CTTTTC-TTCTTTTGGAATGCTTCAATTT
25244 CTTTTCT
1 CTTTTCT
25251 GATTTTCTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.14
27 13 0.45
28 8 0.28
29 4 0.14
ACGTcount: A:0.11, C:0.18, G:0.11, T:0.60
Consensus pattern (28 bp):
CTTTTCTTCTTTTGGAATGCTTCAATTT
Found at i:31713 original size:23 final size:23
Alignment explanation
Indices: 31687--31733 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
31677 CTATCTTATA
*
31687 CTATTATATCATAAGCATGCATT
1 CTATTATATCATAAGCATACATT
* *
31710 CTATTCTATTATAAGCATACATT
1 CTATTATATCATAAGCATACATT
31733 C
1 C
31734 ACATGTTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.19, G:0.06, T:0.40
Consensus pattern (23 bp):
CTATTATATCATAAGCATACATT
Found at i:48096 original size:47 final size:44
Alignment explanation
Indices: 48025--48150 Score: 144
Period size: 47 Copynumber: 2.8 Consensus size: 44
48015 TATAAAATCT
* *
48025 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCATTAAT-ACATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
48070 CTTACCATTTAAATTACATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCA-TT-AA-TACATAAGCTCGTAAGCTTATTTTACCAAAATA
* * * *
48117 CTTGCCATTAATCCGTAAGCTCATAAGCTTATTT
1 CTTACCATTAATACATAAGCTCGTAAGCTTATTT
48151 GCATGGTTAC
Statistics
Matches: 70, Mismatches: 8, Indels: 7
0.82 0.09 0.08
Matches are distributed among these distances:
44 20 0.29
45 9 0.13
46 4 0.06
47 36 0.51
48 1 0.01
ACGTcount: A:0.32, C:0.22, G:0.08, T:0.38
Consensus pattern (44 bp):
CTTACCATTAATACATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:48309 original size:40 final size:40
Alignment explanation
Indices: 48254--48375 Score: 226
Period size: 40 Copynumber: 3.0 Consensus size: 40
48244 ACCGTAGTGC
*
48254 TACACATAAGGTCGTGCCCACCATATACACCTAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
48294 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
48334 TACACATAAGGTCGTGCCCACCATATACACCGAAATGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
48374 TA
1 TA
48376 TAAACCTGCA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 80 1.00
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:52174 original size:16 final size:17
Alignment explanation
Indices: 52153--52184 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
52143 AGCAACAAGA
52153 AAAAAGAAAA-AAAAAT
1 AAAAAGAAAAGAAAAAT
52169 AAAAAGAAAAGAAAAA
1 AAAAAGAAAAGAAAAA
52185 GACTCCTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.88, C:0.00, G:0.09, T:0.03
Consensus pattern (17 bp):
AAAAAGAAAAGAAAAAT
Found at i:56425 original size:14 final size:14
Alignment explanation
Indices: 56406--56432 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
56396 GACTTTGCAC
56406 TTTTTCTTTTTGTA
1 TTTTTCTTTTTGTA
56420 TTTTTCTTTTTGT
1 TTTTTCTTTTTGT
56433 TGCACGTTGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.04, C:0.07, G:0.07, T:0.81
Consensus pattern (14 bp):
TTTTTCTTTTTGTA
Found at i:58753 original size:20 final size:19
Alignment explanation
Indices: 58710--58760 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 19
58700 CGGCCAAGAG
* *
58710 CATGTATCTTCATTTAAAT
1 CATGTATTTTCATTAAAAT
*
58729 AATGTATTTTCATTAAAAAT
1 CATGTATTTTCATT-AAAAT
58749 CATGTATTTTCA
1 CATGTATTTTCA
58761 AAGGGGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 12 0.44
20 15 0.56
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:59568 original size:16 final size:16
Alignment explanation
Indices: 59547--59580 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
59537 AAAAAGCAAC
59547 AAGAAAGAAGAAAA-AA
1 AAGAAA-AAGAAAAGAA
59563 AAGAAAAAGAAAAGAA
1 AAGAAAAAGAAAAGAA
59579 AA
1 AA
59581 AGACTCCTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (16 bp):
AAGAAAAAGAAAAGAA
Found at i:59577 original size:11 final size:11
Alignment explanation
Indices: 59550--59583 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
59540 AAGCAACAAG
*
59550 AAAGAAGAAAAA
1 AAAGAA-AAAGA
59562 AAAGAAAAAGA
1 AAAGAAAAAGA
59573 AAAGAAAAAGA
1 AAAGAAAAAGA
59584 CTCCTACATC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 15 0.71
12 6 0.29
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAGA
Found at i:59636 original size:18 final size:18
Alignment explanation
Indices: 59609--59650 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
59599 TGGAGTGCAA
59609 AAGAAAGAAAAGAA-AAAG
1 AAGAAAGAAAA-AACAAAG
*
59627 AAGAATGAAAAAACAAAG
1 AAGAAAGAAAAAACAAAG
59645 AA-AAAG
1 AAGAAAG
59651 TGAAGCAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.02
Consensus pattern (18 bp):
AAGAAAGAAAAAACAAAG
Found at i:65549 original size:14 final size:14
Alignment explanation
Indices: 65530--65564 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
65520 AAAATAATGG
65530 TTGAAAAGCTTGGC
1 TTGAAAAGCTTGGC
65544 TTGAAAAGCTTGGC
1 TTGAAAAGCTTGGC
65558 TTGAAAA
1 TTGAAAA
65565 CGATGAAGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.29
Consensus pattern (14 bp):
TTGAAAAGCTTGGC
Found at i:69930 original size:19 final size:20
Alignment explanation
Indices: 69906--69951 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
69896 CGACCAAGAG
**
69906 CATGTATCTTCAT-TTAAAT
1 CATGTATCTTCATCAAAAAT
*
69925 CATGTATTTTCATCAAAAAT
1 CATGTATCTTCATCAAAAAT
69945 CATGTAT
1 CATGTAT
69952 TTTGAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.35, C:0.15, G:0.07, T:0.43
Consensus pattern (20 bp):
CATGTATCTTCATCAAAAAT
Found at i:70373 original size:35 final size:35
Alignment explanation
Indices: 70297--70412 Score: 178
Period size: 35 Copynumber: 3.3 Consensus size: 35
70287 TTCTATATGT
* *
70297 TCATCACCATCTTCAATCACCATTTTCACACCTATA
1 TCATCACCATCTTCTATCACCA-TTTCACGCCTATA
*
70333 TCATCACCATCTTCTATCACCATTGCACGCCTATA
1 TCATCACCATCTTCTATCACCATTTCACGCCTATA
* *
70368 TCATCACCATATTCTATCACCATTTCACGTCTATA
1 TCATCACCATCTTCTATCACCATTTCACGCCTATA
70403 TCATCACCAT
1 TCATCACCAT
70413 TCCCTTACCA
Statistics
Matches: 74, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
35 53 0.72
36 21 0.28
ACGTcount: A:0.28, C:0.35, G:0.03, T:0.34
Consensus pattern (35 bp):
TCATCACCATCTTCTATCACCATTTCACGCCTATA
Found at i:70388 original size:13 final size:12
Alignment explanation
Indices: 70296--70394 Score: 66
Period size: 13 Copynumber: 8.3 Consensus size: 12
70286 ATTCTATATG
*
70296 TTCATCACCATC
1 TTCATCACCATA
*
70308 TTCAATCACCATT
1 TTC-ATCACCATA
70321 TTCA-CACC-TA
1 TTCATCACCATA
*
70331 TATCATCACCATC
1 T-TCATCACCATA
70344 TTCTATCACCAT-
1 TTC-ATCACCATA
* *
70356 TGCA-CGCC-TA
1 TTCATCACCATA
70366 TATCATCACCATA
1 T-TCATCACCATA
70379 TTCTATCACCAT-
1 TTC-ATCACCATA
70391 TTCA
1 TTCA
70395 CGTCTATATC
Statistics
Matches: 70, Mismatches: 7, Indels: 21
0.71 0.07 0.21
Matches are distributed among these distances:
9 1 0.01
10 6 0.09
11 11 0.16
12 20 0.29
13 32 0.46
ACGTcount: A:0.28, C:0.35, G:0.02, T:0.34
Consensus pattern (12 bp):
TTCATCACCATA
Done.