Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005748.1 Hibiscus syriacus cultivar Beakdansim tig00013445_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: 65007
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:4736 original size:13 final size:12
Alignment explanation
Indices: 4685--4768 Score: 56
Period size: 13 Copynumber: 7.2 Consensus size: 12
4675 AATGGAATTT
4685 GGTGATGATATA
1 GGTGATGATATA
*
4697 GGCG-TGATAT-
1 GGTGATGATATA
4707 GGTGATGGACTAT-
1 GGTGAT-GA-TATA
4720 GGTGATGATATA
1 GGTGATGATATA
4732 GG-G-TGATA-A
1 GGTGATGATATA
*
4741 TGGTGATGGA-AGA
1 -GGTGAT-GATATA
4754 TGGTGATGATATA
1 -GGTGATGATATA
4767 GG
1 GG
4769 GGTGATAATG
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
9 1 0.02
10 10 0.17
11 12 0.20
12 15 0.25
13 21 0.36
ACGTcount: A:0.29, C:0.02, G:0.39, T:0.30
Consensus pattern (12 bp):
GGTGATGATATA
Found at i:4779 original size:36 final size:36
Alignment explanation
Indices: 4684--4798 Score: 189
Period size: 35 Copynumber: 3.2 Consensus size: 36
4674 AAATGGAATT
* **
4684 TGGTGATGATATAGGCGTGAT-ATGGTGATGGACTA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
4719 TGGTGATGATATA-GGGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
4754 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
1 TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
4790 TGGTGATGA
1 TGGTGATGA
4799 ACAGATTGTA
Statistics
Matches: 75, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
34 6 0.08
35 38 0.51
36 31 0.41
ACGTcount: A:0.29, C:0.02, G:0.40, T:0.30
Consensus pattern (36 bp):
TGGTGATGATATAGGGGTGATAATGGTGATGGAAGA
Found at i:7172 original size:17 final size:17
Alignment explanation
Indices: 7097--7173 Score: 56
Period size: 17 Copynumber: 4.7 Consensus size: 17
7087 CCTTGGCTTA
* *
7097 CTTTCTTTTTGACATTT
1 CTTTCTTTTTGTCTTTT
7114 C-TTC-TTTT-TCTTTT
1 CTTTCTTTTTGTCTTTT
**
7128 CTTT-TTTTCTGAATTTT
1 CTTTCTTTT-TGTCTTTT
*
7145 -TTTATTTTTTGTCTTTT
1 CTTT-CTTTTTGTCTTTT
7162 CTTTCTTTTTGT
1 CTTTCTTTTTGT
7174 ACTTCAATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
14 5 0.11
15 9 0.20
16 7 0.15
17 18 0.39
18 7 0.15
ACGTcount: A:0.06, C:0.14, G:0.05, T:0.74
Consensus pattern (17 bp):
CTTTCTTTTTGTCTTTT
Found at i:17154 original size:24 final size:21
Alignment explanation
Indices: 17120--17162 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
17110 TGCACAAGAT
*
17120 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
17142 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
17163 AGAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:22357 original size:11 final size:12
Alignment explanation
Indices: 22338--22394 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
22328 TTTTTGACTT
22338 TTCTTCTTTTTC
1 TTCTTCTTTTTC
22350 TT-TTCTTTTT-
1 TTCTTCTTTTTC
*
22360 TTCTGAATTTTTTTC
1 TTCT---TCTTTTTC
22375 TTCTT-TTTTTC
1 TTCTTCTTTTTC
22386 TT-TTCTTTT
1 TTCTTCTTTT
22395 ATTTTTGTAC
Statistics
Matches: 38, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
10 4 0.11
11 21 0.55
12 3 0.08
14 6 0.16
15 4 0.11
ACGTcount: A:0.04, C:0.16, G:0.02, T:0.79
Consensus pattern (12 bp):
TTCTTCTTTTTC
Found at i:22360 original size:13 final size:13
Alignment explanation
Indices: 22324--22394 Score: 67
Period size: 13 Copynumber: 5.6 Consensus size: 13
22314 CTTGGCTTGC
**
22324 TTTCTTTTTGACT
1 TTTCTTTTTTTCT
22337 TTTCTTCTTTTTCT
1 TTTCTT-TTTTTCT
22351 TTTCTTTTTTTC-
1 TTTCTTTTTTTCT
***
22363 TGAATTTTTTTC-
1 TTTCTTTTTTTCT
22375 -TTCTTTTTTTCT
1 TTTCTTTTTTTCT
22387 TTTCTTTT
1 TTTCTTTT
22395 ATTTTTGTAC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
11 8 0.17
12 9 0.19
13 19 0.40
14 11 0.23
ACGTcount: A:0.04, C:0.15, G:0.03, T:0.77
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:22385 original size:31 final size:30
Alignment explanation
Indices: 22323--22394 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 30
22313 CCTTGGCTTG
*
22323 CTTTCTTTTTGACTTTTCTTCTTTTTCTTTT
1 CTTT-TTTTTGAATTTTCTTCTTTTTCTTTT
*
22354 CTTTTTTTCTGAATTTTTTTCTTCTTT-TTTT
1 CTTTTTTT-TGAATTTTCTTCTT-TTTCTTTT
22385 CTTTTCTTTT
1 CTTTT-TTTT
22395 ATTTTTGTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
30 4 0.11
31 26 0.72
32 6 0.17
ACGTcount: A:0.04, C:0.17, G:0.03, T:0.76
Consensus pattern (30 bp):
CTTTTTTTTGAATTTTCTTCTTTTTCTTTT
Found at i:22394 original size:23 final size:25
Alignment explanation
Indices: 22341--22394 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 25
22331 TTGACTTTTC
*
22341 TTCTTTTTCTTTTCTTTTTTTCTGA
1 TTCTTTTTCTCTTCTTTTTTTCTGA
* *
22366 AT-TTTTT-TCTTCTTTTTTTCT-T
1 TTCTTTTTCTCTTCTTTTTTTCTGA
22388 TTCTTTT
1 TTCTTTT
22395 ATTTTTGTAC
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
22 1 0.04
23 17 0.71
24 5 0.21
25 1 0.04
ACGTcount: A:0.04, C:0.15, G:0.02, T:0.80
Consensus pattern (25 bp):
TTCTTTTTCTCTTCTTTTTTTCTGA
Found at i:22400 original size:16 final size:16
Alignment explanation
Indices: 22325--22392 Score: 50
Period size: 16 Copynumber: 4.1 Consensus size: 16
22315 TTGGCTTGCT
**
22325 TTCTTTTTGACTTTTC
1 TTCTTTTTTTCTTTTC
22341 TTC--TTTTTCTTTTC
1 TTCTTTTTTTCTTTTC
* *
22355 TTTTTTTCTGAATTTTTTTC
1 TTCTTTT-T---TTCTTTTC
22375 TTCTTTTTTTCTTTTC
1 TTCTTTTTTTCTTTTC
22391 TT
1 TT
22393 TTATTTTTGT
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
14 11 0.28
16 14 0.35
17 1 0.03
19 1 0.03
20 13 0.32
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.76
Consensus pattern (16 bp):
TTCTTTTTTTCTTTTC
Found at i:34258 original size:16 final size:16
Alignment explanation
Indices: 34237--34279 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
34227 TTTTAACTTC
34237 TCTTTTTCTT-TTCTTT
1 TCTTTTT-TTCTTCTTT
34253 TCTTTTTTTCTTCTTT
1 TCTTTTTTTCTTCTTT
*
34269 TCTTCTTTTCT
1 TCTTTTTTTCT
34280 GATTTTTCTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (16 bp):
TCTTTTTTTCTTCTTT
Found at i:34274 original size:11 final size:11
Alignment explanation
Indices: 34237--34275 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
34227 TTTTAACTTC
*
34237 TCTTTTTCTTT
1 TCTTCTTCTTT
34248 TCTT-TTCTTT
1 TCTTCTTCTTT
*
34258 TTTTCTTCTTT
1 TCTTCTTCTTT
34269 TCTTCTT
1 TCTTCTT
34276 TTCTGATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TCTTCTTCTTT
Found at i:39186 original size:19 final size:18
Alignment explanation
Indices: 39162--39197 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
39152 CGGCCAAGAG
39162 CATGTATCTTCATTAAAAT
1 CATGTATCTTCA-TAAAAT
*
39181 CATGTATTTTCATAAAA
1 CATGTATCTTCATAAAA
39198 AAAGCATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.39, C:0.14, G:0.06, T:0.42
Consensus pattern (18 bp):
CATGTATCTTCATAAAAT
Found at i:39198 original size:19 final size:20
Alignment explanation
Indices: 39160--39213 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
39150 TTCGGCCAAG
* *
39160 AGCATGTATCTTCAT-TAAA
1 AGCATGTATTTTCATAAAAA
*
39179 ATCATGTATTTTCATAAAAAA
1 AGCATGTATTTTCAT-AAAAA
39200 AGCATGTATTTTCA
1 AGCATGTATTTTCA
39214 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
19 13 0.45
21 16 0.55
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (20 bp):
AGCATGTATTTTCATAAAAA
Found at i:41894 original size:16 final size:16
Alignment explanation
Indices: 41873--41904 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41863 TAGTTAGCTC
41873 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
41889 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
41905 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:46445 original size:19 final size:19
Alignment explanation
Indices: 46418--46467 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
46408 ACCATCTCTA
* *
46418 TCTTTTTATTTATTTTCAT
1 TCTTATTATTTATTTTAAT
46437 TCTTATTATTTATTTTAAT
1 TCTTATTATTTATTTTAAT
46456 TACTTATATATT
1 T-CTTAT-TATT
46468 ACCCTTTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 18 0.67
20 5 0.19
21 4 0.15
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.68
Consensus pattern (19 bp):
TCTTATTATTTATTTTAAT
Found at i:60716 original size:28 final size:28
Alignment explanation
Indices: 60653--60716 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 28
60643 CTTTTATTTT
* *
60653 CTTTGCTTTCTTCTTTTTGAGTGCTGGA
1 CTTTGTTTTCTTCTTTTTGAGTGCTGCA
* *
60681 -TTTTTTTTCTT-TCTTTTGAGTGCTTCA
1 CTTTGTTTTCTTCT-TTTTGAGTGCTGCA
60708 CTTTGTTTT
1 CTTTGTTTT
60717 ATGATTTTTC
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
26 1 0.03
27 21 0.72
28 7 0.24
ACGTcount: A:0.06, C:0.16, G:0.16, T:0.62
Consensus pattern (28 bp):
CTTTGTTTTCTTCTTTTTGAGTGCTGCA
Done.