Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005789.1 Hibiscus syriacus cultivar Beakdansim tig00013566_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: 62314
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:1781 original size:47 final size:49
Alignment explanation
Indices: 1720--1841 Score: 151
Period size: 49 Copynumber: 2.5 Consensus size: 49
1710 ATATTAAGTG
* *
1720 CTACACTTTTTTATTTGTTTACTTACA-TT-GT-AAGTATGTGTTAAATA
1 CTACACTTTTTTATTTATTCACTTA-AGTTGGTGAAGTATGTGTTAAATA
* * *
1767 CTACATTTTTTTATTTATTCACTTAAGTTGGTGTAGTATGTGTTAAGTA
1 CTACACTTTTTTATTTATTCACTTAAGTTGGTGAAGTATGTGTTAAATA
*
1816 CTACACTTTTTTGTTTTATTCACTTA
1 CTACACTTTTTT-ATTTATTCACTTA
1842 CACGGTGTAA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
46 1 0.02
47 24 0.38
48 2 0.03
49 25 0.39
50 12 0.19
ACGTcount: A:0.25, C:0.11, G:0.11, T:0.52
Consensus pattern (49 bp):
CTACACTTTTTTATTTATTCACTTAAGTTGGTGAAGTATGTGTTAAATA
Found at i:1863 original size:50 final size:50
Alignment explanation
Indices: 1692--1928 Score: 215
Period size: 50 Copynumber: 4.8 Consensus size: 50
1682 AGATGTACAT
* *
1692 ACTTACATCGGTGTAAGTA--TATTAAGTGCTACACTTTTTTATTTGT-TT-
1 ACTTACA-CGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTT-TATTC
* * *
1740 ACTTACA--TTGTAAGTATGTGTTAAATACTACATTTTTTTA-TTTATTC
1 ACTTACACGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* *
1787 ACTTA-AGTTGGTGT-AGTATGTGTTAAGTACTACACTTTTTTGTTTTATTC
1 ACTTACA--CGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * *
1837 ACTTACACGGTGTAAGTTTGTATTAAGTGA-TACACTTGTTTATTTTATTC
1 ACTTACACGGTGTAAGTATGTGTTAAGT-ACTACACTTTTTTATTTTATTC
* * * * *
1887 ACTTACCCCGATGTAAATATGTGTTAAGTACTATATTTTTTT
1 ACTTA-CACGGTGTAAGTATGTGTTAAGTACTACACTTTTTT
1929 GTAATAATAG
Statistics
Matches: 153, Mismatches: 22, Indels: 25
0.76 0.11 0.12
Matches are distributed among these distances:
45 9 0.06
46 5 0.03
47 23 0.15
48 7 0.05
49 30 0.20
50 51 0.33
51 28 0.18
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (50 bp):
ACTTACACGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
Found at i:28744 original size:2 final size:2
Alignment explanation
Indices: 28733--28772 Score: 64
Period size: 2 Copynumber: 20.5 Consensus size: 2
28723 ATCCAAAGAG
*
28733 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
28773 TGATAAGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:33487 original size:31 final size:31
Alignment explanation
Indices: 33449--33519 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
33439 TGTTTAGTAT
*
33449 CTAAATTATCAATTTTGGTCTATTTGAATAC
1 CTAAATTATCAATTTTGGTCCATTTGAATAC
33480 CTAAATTATCAATTTTGGTCCATTTGAATAC
1 CTAAATTATCAATTTTGGTCCATTTGAATAC
33511 CTAAATTAT
1 CTAAATTAT
33520 AAATATTCGT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.34, C:0.14, G:0.08, T:0.44
Consensus pattern (31 bp):
CTAAATTATCAATTTTGGTCCATTTGAATAC
Found at i:34472 original size:2 final size:2
Alignment explanation
Indices: 34465--34498 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
34455 CTTTTAATTC
34465 CT CT CT CT CT CT CT CT CT CT CT CT C- CT -T CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
34499 TCCTTGGTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:35945 original size:2 final size:2
Alignment explanation
Indices: 35938--35970 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
35928 TGACATAATA
35938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35971 ATTGTCCAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36887 original size:23 final size:23
Alignment explanation
Indices: 36860--36915 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
36850 AAAAGCGTAC
* * *
36860 CACAAAGATAGAGATAAATGTGT
1 CACAAAGACAAAGATAAATATGT
*
36883 CACAAAAACAAAGATAAATATGT
1 CACAAAGACAAAGATAAATATGT
36906 CACAAAGACA
1 CACAAAGACA
36916 TAATTATTCT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.55, C:0.14, G:0.14, T:0.16
Consensus pattern (23 bp):
CACAAAGACAAAGATAAATATGT
Found at i:46459 original size:18 final size:18
Alignment explanation
Indices: 46436--46504 Score: 63
Period size: 18 Copynumber: 3.7 Consensus size: 18
46426 CTTTTGGAAA
46436 TTTAAAATTATT-ATATAT
1 TTTAAAATT-TTAATATAT
46454 TTTAAAATTTTAATATATT
1 TTTAAAATTTTAATATA-T
46473 TTTATTAAATCTTTAA-A-AT
1 TTTA--AAAT-TTTAATATAT
*
46492 TTTAAAAGTTTAA
1 TTTAAAATTTTAA
46505 GCGTGTACTT
Statistics
Matches: 45, Mismatches: 1, Indels: 12
0.78 0.02 0.21
Matches are distributed among these distances:
16 5 0.11
17 5 0.11
18 14 0.31
19 10 0.22
20 1 0.02
21 5 0.11
22 5 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (18 bp):
TTTAAAATTTTAATATAT
Found at i:48057 original size:60 final size:60
Alignment explanation
Indices: 47940--48076 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 60
47930 AACCTAGGAT
* * * *
47940 AAAG-TACACAAATGGTCCCTTGACTATAGGGTGTTGCTTTATTGAATCCTTTAACTATTA
1 AAAGTTACA-AAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCCTTCAACTATTA
** * * *
48000 AATTTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTCTTGAGT-CTCTCGACTATTA
1 AAAGTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCCT-TCAACTATTA
48060 AAAGTTACAAAATGGTC
1 AAAGTTACAAAATGGTC
48077 ATTCAAATAT
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
59 2 0.03
60 58 0.91
61 4 0.06
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (60 bp):
AAAGTTACAAAATGGTCCCCTAACTATAGGATGTTGCTTTATTGAATCCTTCAACTATTA
Found at i:50156 original size:2 final size:2
Alignment explanation
Indices: 50149--50187 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
50139 ATGAGAAAGG
50149 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
50188 CATACATACA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:51121 original size:21 final size:21
Alignment explanation
Indices: 51086--51126 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
51076 TAGCGTGTCA
* * *
51086 GTTCACGGTGTTGACGTGACG
1 GTTCACGATGCTGACATGACG
51107 GTTCACGATGCTGACATGAC
1 GTTCACGATGCTGACATGAC
51127 ATACAATCTG
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:0.20, C:0.22, G:0.32, T:0.27
Consensus pattern (21 bp):
GTTCACGATGCTGACATGACG
Found at i:57509 original size:60 final size:60
Alignment explanation
Indices: 57415--57530 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
57405 TAGTCCCCTG
* * * * *
57415 ACTACAGTGTATTGCTTTATTAAGTCCTTTGACTATGAAAAGTTACAGAATGATCATCTA
1 ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCATCTA
* * *
57475 ACTACAGAGTGTTGCTTCGTTAAGTCCATCGACTATTAAAAGTTACAAAATGATCA
1 ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCA
57531 CTCCACTATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
60 48 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
ACTACAGAGTATTGCTTCATTAAGTCCATCGACTATGAAAAGTTACAAAATGATCATCTA
Found at i:58075 original size:33 final size:34
Alignment explanation
Indices: 58027--58095 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 34
58017 TGGATTGAGT
*
58027 AACACGTCTCAACTATTTATTAAAGTTTTAATAA
1 AACACGTCGCAACTATTTATTAAAGTTTTAATAA
* *
58061 AACACGT-GCAACTATTTATTAAATTTTTATTAA
1 AACACGTCGCAACTATTTATTAAAGTTTTAATAA
58094 AA
1 AA
58096 GCTTTTAGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
33 25 0.78
34 7 0.22
ACGTcount: A:0.42, C:0.13, G:0.06, T:0.39
Consensus pattern (34 bp):
AACACGTCGCAACTATTTATTAAAGTTTTAATAA
Found at i:58510 original size:7 final size:8
Alignment explanation
Indices: 58484--58523 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
58474 TTTTTAAATT
*
58484 TAATATTA
1 TAATATAA
58492 TAATATAA
1 TAATATAA
58500 TAATA-AA
1 TAATATAA
*
58507 TAATATTA
1 TAATATAA
58515 TAATATAA
1 TAATATAA
58523 T
1 T
58524 TAACAAATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
TAATATAA
Done.