Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002973.1 Hibiscus syriacus cultivar Beakdansim tig00006149_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: 57451
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:5999 original size:20 final size:20
Alignment explanation
Indices: 5963--6000 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
5953 ATCTTATTAC
**
5963 CTGATAATCTTTTATTCCCA
1 CTGATAATCTTACATTCCCA
5983 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
6001 GTTAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCCA
Found at i:6404 original size:28 final size:28
Alignment explanation
Indices: 6364--6419 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
6354 TTCTAATGAA
6364 ATATTTTATTAAAACTCATCAAATCGAC
1 ATATTTTATTAAAACTCATCAAATCGAC
*
6392 ATATTTTATTAAAACTCATCAAGTCGAC
1 ATATTTTATTAAAACTCATCAAATCGAC
6420 GTGATAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.05, T:0.36
Consensus pattern (28 bp):
ATATTTTATTAAAACTCATCAAATCGAC
Found at i:6900 original size:15 final size:15
Alignment explanation
Indices: 6880--6909 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
6870 CACTTTTATT
6880 TCATTTTGGTCACCC
1 TCATTTTGGTCACCC
6895 TCATTTTGGTCACCC
1 TCATTTTGGTCACCC
6910 AGCTATTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.33, G:0.13, T:0.40
Consensus pattern (15 bp):
TCATTTTGGTCACCC
Found at i:12662 original size:16 final size:16
Alignment explanation
Indices: 12643--12696 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
12633 AAAAAAAATT
12643 ATTAAAATAAATTAAA
1 ATTAAAATAAATTAAA
*
12659 ATTAAAATAATTTAAA
1 ATTAAAATAAATTAAA
* *
12675 A-TAAAAAAAATATTAA
1 ATTAAAATAAAT-TAAA
12691 ATTAAA
1 ATTAAA
12697 GGGTAAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
15 8 0.25
16 20 0.62
17 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
ATTAAAATAAATTAAA
Found at i:13701 original size:14 final size:14
Alignment explanation
Indices: 13682--13723 Score: 68
Period size: 14 Copynumber: 3.0 Consensus size: 14
13672 ATAAAATATG
13682 GTATGAACAGTA-C
1 GTATGAACAGTATC
13695 TGTATGAACAGTATC
1 -GTATGAACAGTATC
13710 GTATGAACAGTATC
1 GTATGAACAGTATC
13724 CCAAATGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 26 0.96
15 1 0.04
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (14 bp):
GTATGAACAGTATC
Found at i:15416 original size:2 final size:2
Alignment explanation
Indices: 15409--15460 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
15399 ACCAATTCTG
15409 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
15451 AT AT AT AT AT
1 AT AT AT AT AT
15461 CTTACTCATG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23411 original size:40 final size:40
Alignment explanation
Indices: 23367--23469 Score: 134
Period size: 40 Copynumber: 2.6 Consensus size: 40
23357 CCGTTTATTT
* *
23367 ATTAAATGAATGAATATGAATAAGATTTTATGTCCGTTTA
1 ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
* * * * *
23407 ATTAAATAAAAGAACATGAACATGATTTTGTGTTCGTTTA
1 ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
*
23447 ATTAAATGAATGAACACGAACAA
1 ATTAAATGAATGAACATGAACAA
23470 ATGATTTACT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 52 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.34
Consensus pattern (40 bp):
ATTAAATGAATGAACATGAACAAGATTTTATGTCCGTTTA
Found at i:28746 original size:200 final size:201
Alignment explanation
Indices: 28391--28767 Score: 569
Period size: 200 Copynumber: 1.9 Consensus size: 201
28381 AGAAATAGTT
* **
28391 TTTCCCAACCTAAATCCTTAAATTACAAAACTTTCACCGTTTTATTTTCGCATACCATCGAATTA
1 TTTCCCAACCTAAATCCCTAAATTACAAAACCATCACCGTTTTATTTTCGCATACCATCG----A
** * *
28456 ATCTCCAGTCGTCATGTTGTGCACCGCCACTGTTAGTGTGCTCGTTGTCACCTCGCAACCAAAGC
62 ATCTCCAGTCGTCATGTCATGCACCGCCACCGTTAGTGTGCTCGTCGTCACCTCGCAACCAAAGC
* *
28521 CCGACCATCCCCTTGTCGAGATCCACGGCCAAATGTCGTAAATCGCCAAAACAAATCCCCAATCA
127 CCGACCATCCCCTTGTCGAGATCCACCGCCAAATGCCGTAAATCGCCAAAACAAATCCCCAATCA
28586 AAATCGAGCC
192 AAATCGAGCC
*
28596 TTTCCCAACCTAAATCCCTAAATTACAAAACCATCACCGTTTTATTTTCGCCTACCATCG-ATCT
1 TTTCCCAACCTAAATCCCTAAATTACAAAACCATCACCGTTTTATTTTCGCATACCATCGAATCT
* *
28660 CCAGTCGTCATGTCATGCACCGCCACCGTTGGTGTGCTTGTCGTCACCTCGCAACCAAAGCCCGA
66 CCAGTCGTCATGTCATGCACCGCCACCGTTAGTGTGCTCGTCGTCACCTCGCAACCAAAGCCCGA
* *
28725 CTATCCCCTTGTC-ATGATCCACCGCCAAATGCCGTAAGTCGCC
131 CCATCCCCTTGTCGA-GATCCACCGCCAAATGCCGTAAATCGCC
28768 CTCGATCGTC
Statistics
Matches: 157, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
199 1 0.01
200 100 0.64
205 56 0.36
ACGTcount: A:0.26, C:0.34, G:0.14, T:0.26
Consensus pattern (201 bp):
TTTCCCAACCTAAATCCCTAAATTACAAAACCATCACCGTTTTATTTTCGCATACCATCGAATCT
CCAGTCGTCATGTCATGCACCGCCACCGTTAGTGTGCTCGTCGTCACCTCGCAACCAAAGCCCGA
CCATCCCCTTGTCGAGATCCACCGCCAAATGCCGTAAATCGCCAAAACAAATCCCCAATCAAAAT
CGAGCC
Found at i:35151 original size:21 final size:21
Alignment explanation
Indices: 35107--35151 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
35097 GCTTAACGCA
* *
35107 TTTAGTATTTAAACTATCAGT
1 TTTAGTAATTAAACTATCAAT
* *
35128 TTTAGTAATTAAACTTTTAAT
1 TTTAGTAATTAAACTATCAAT
35149 TTT
1 TTT
35152 TTCAAAACTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAGTAATTAAACTATCAAT
Found at i:40512 original size:21 final size:20
Alignment explanation
Indices: 40473--40519 Score: 67
Period size: 21 Copynumber: 2.3 Consensus size: 20
40463 TAAGTATAAA
*
40473 TATAATTTAAATATTATATT
1 TATAATTTAAATATAATATT
*
40493 TTTAATTTATAATATAATATT
1 TATAATTTA-AATATAATATT
40514 TATAAT
1 TATAAT
40520 AGATATTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATAATTTAAATATAATATT
Found at i:46789 original size:25 final size:25
Alignment explanation
Indices: 46755--46803 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
46745 TAGTTAATTA
* *
46755 TATTCAATTAATTTAAATTTATATG
1 TATTCAATTAATTCAAAATTATATG
*
46780 TATTTAATTAATTCAAAATTATAT
1 TATTCAATTAATTCAAAATTATAT
46804 ACATAGTTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (25 bp):
TATTCAATTAATTCAAAATTATATG
Found at i:48824 original size:27 final size:28
Alignment explanation
Indices: 48763--48826 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 28
48753 TATTGTATGA
48763 TATTTA-TATTTTATCTTACATTTAAAT
1 TATTTATTATTTTATCTTACATTTAAAT
*
48790 TATTTATTATTTTATCTTATA-TTAAAT
1 TATTTATTATTTTATCTTACATTTAAAT
48817 TATTTATTAT
1 TATTTATTAT
48827 AATGATCAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
27 22 0.63
28 13 0.37
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (28 bp):
TATTTATTATTTTATCTTACATTTAAAT
Found at i:55623 original size:23 final size:23
Alignment explanation
Indices: 55597--55640 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
55587 GATTCAAGTC
* *
55597 CATCTACTGTTTGTTGACTGGAT
1 CATCTACCGTTTATTGACTGGAT
55620 CATCTACCGTTTATTGACTGG
1 CATCTACCGTTTATTGACTGG
55641 TTCAGCTGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (23 bp):
CATCTACCGTTTATTGACTGGAT
Done.