Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008881.1 Hibiscus syriacus cultivar Beakdansim tig00112127_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: 608427
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 3 of 3
Found at i:581279 original size:2 final size:2
Alignment explanation
Indices: 581272--581337 Score: 125
Period size: 2 Copynumber: 33.5 Consensus size: 2
581262 TTTTATTTTC
581272 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
581314 AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
581338 GTCATTACAT
Statistics
Matches: 63, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 62 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:586772 original size:37 final size:37
Alignment explanation
Indices: 586728--586802 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
586718 TTTATCAATC
* *
586728 TCCATTCTCCATGCTTGAAACGTCACCTTCTAATCTT
1 TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
* * *
586765 TCCATTCTCCATGCCTAAAAGGTTATCTTCTAATCTT
1 TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
586802 T
1 T
586803 GATTATGATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.23, C:0.29, G:0.08, T:0.40
Consensus pattern (37 bp):
TCCATTCTCCATGCCTAAAACGTCACCTTCTAATCTT
Found at i:586981 original size:45 final size:45
Alignment explanation
Indices: 586906--587003 Score: 135
Period size: 45 Copynumber: 2.2 Consensus size: 45
586896 TAACATAGCT
* * *
586906 AAATTTCATGAATGAAACTCCATTTTCATTTTCATTTCCATTTCC
1 AAATTTCATGAATGAAACTCCATTTCCATTTCCATTCCCATTTCC
*
586951 AAATTTCATGAATGAAAC-CCAATTTCCATTTCCATTCCCATTTGC
1 AAATTTCATGAATGAAACTCC-ATTTCCATTTCCATTCCCATTTCC
*
586996 AATTTTCA
1 AAATTTCA
587004 ATTTTCATGT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 2 0.04
45 45 0.96
ACGTcount: A:0.31, C:0.23, G:0.05, T:0.41
Consensus pattern (45 bp):
AAATTTCATGAATGAAACTCCATTTCCATTTCCATTCCCATTTCC
Found at i:592642 original size:20 final size:19
Alignment explanation
Indices: 592613--592665 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
592603 TTATTCAATG
* *
592613 GGTATTGATACTGTAGGTGA
1 GGTATCGATACTGCAGG-GA
*
592633 GGTATCGATACTCGCAGGGT
1 GGTATCGATACT-GCAGGGA
592653 GGTATCGATACTG
1 GGTATCGATACTG
592666 AGTTCACTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 1 0.03
20 24 0.83
21 4 0.14
ACGTcount: A:0.23, C:0.13, G:0.34, T:0.30
Consensus pattern (19 bp):
GGTATCGATACTGCAGGGA
Found at i:594463 original size:34 final size:34
Alignment explanation
Indices: 594420--594500 Score: 162
Period size: 34 Copynumber: 2.4 Consensus size: 34
594410 CTGAAGATAG
594420 AAAAAATATTGATGACGACCTTTAATAAGTGCTC
1 AAAAAATATTGATGACGACCTTTAATAAGTGCTC
594454 AAAAAATATTGATGACGACCTTTAATAAGTGCTC
1 AAAAAATATTGATGACGACCTTTAATAAGTGCTC
594488 AAAAAATATTGAT
1 AAAAAATATTGAT
594501 TAATGCTGCT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (34 bp):
AAAAAATATTGATGACGACCTTTAATAAGTGCTC
Found at i:598750 original size:54 final size:51
Alignment explanation
Indices: 598678--598783 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 51
598668 TATTCGCCTG
598678 TCCCACCCCCCCCCCATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
1 TCCCACCCCCCCCCCATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
598729 TCCCACCCCCACCCCCACATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
1 TCCCA-CCCC-CCCCC-CATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
598783 T
1 T
598784 AGTATGAAAT
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 5 0.10
52 4 0.08
53 5 0.10
54 38 0.73
ACGTcount: A:0.28, C:0.41, G:0.02, T:0.29
Consensus pattern (51 bp):
TCCCACCCCCCCCCCATTCAAATATTTTCTTATCCTCAAGCAAATCAACTT
Found at i:599946 original size:37 final size:37
Alignment explanation
Indices: 599880--599952 Score: 94
Period size: 37 Copynumber: 2.0 Consensus size: 37
599870 TAGTATTAAT
*
599880 CCGACCCAAAAATCAACCAACCTGGTATTGACCCGAC
1 CCGACCCAAAAATCAACCAACCTGATATTGACCCGAC
* * *
599917 CCGATCCAAAAATCAACCGATCC-GATATTGATCCGA
1 CCGACCCAAAAATCAACC-AACCTGATATTGACCCGA
599953 ACCGGAAAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
37 28 0.90
38 3 0.10
ACGTcount: A:0.36, C:0.34, G:0.14, T:0.16
Consensus pattern (37 bp):
CCGACCCAAAAATCAACCAACCTGATATTGACCCGAC
Found at i:601777 original size:27 final size:28
Alignment explanation
Indices: 601739--601794 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
601729 CGCTATGACT
601739 CTTATAAGGCGAC-ATTTTGGCAAACGC
1 CTTATAAGGCGACAATTTTGGCAAACGC
*
601766 CTTATAAGGCGACAATTTTGGTAAACGC
1 CTTATAAGGCGACAATTTTGGCAAACGC
601794 C
1 C
601795 ACTACCGACG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
27 13 0.48
28 14 0.52
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.27
Consensus pattern (28 bp):
CTTATAAGGCGACAATTTTGGCAAACGC
Found at i:602955 original size:25 final size:25
Alignment explanation
Indices: 602903--602955 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
602893 GGTTTTAAAA
* *
602903 ATATATACATTTGAAATTATACTTT
1 ATATATACATTTGAAATTATAATAT
**
602928 ATATATAGTTTTGAAATTATAATAT
1 ATATATACATTTGAAATTATAATAT
602953 ATA
1 ATA
602956 GTTTTAAAAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (25 bp):
ATATATACATTTGAAATTATAATAT
Found at i:602977 original size:24 final size:21
Alignment explanation
Indices: 602928--602984 Score: 69
Period size: 21 Copynumber: 2.6 Consensus size: 21
602918 ATTATACTTT
*
602928 ATATATAGTTTTGAAATTATA
1 ATATATAGTTTTAAAATTATA
602949 ATATATAGTTTTAAAACGTATATA
1 ATATATAGTTTTAAAA--T-TATA
*
602973 ATATATAATTTT
1 ATATATAGTTTT
602985 GATAAAAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 15 0.48
23 1 0.03
24 15 0.48
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.47
Consensus pattern (21 bp):
ATATATAGTTTTAAAATTATA
Found at i:603023 original size:20 final size:19
Alignment explanation
Indices: 602998--603045 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
602988 AAAAAATATA
602998 TATAATATATTTTTGGAAAT
1 TATAATATATTTTT-GAAAT
**
603018 TATAAT-GGTTTTTGAAAT
1 TATAATATATTTTTGAAAT
*
603036 TATAACATAT
1 TATAATATAT
603046 AGTTTTTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
18 10 0.45
19 6 0.27
20 6 0.27
ACGTcount: A:0.40, C:0.02, G:0.10, T:0.48
Consensus pattern (19 bp):
TATAATATATTTTTGAAAT
Found at i:603084 original size:20 final size:21
Alignment explanation
Indices: 603042--603087 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
603032 AAATTATAAC
*
603042 ATATAGTTTTTAAAACGCATAT
1 ATATAATTTTTAAAAC-CATAT
*
603064 ATATAATTTTTAAAA-CTTAT
1 ATATAATTTTTAAAACCATAT
603084 ATAT
1 ATAT
603088 TTTTGTCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 8 0.36
22 14 0.64
ACGTcount: A:0.43, C:0.07, G:0.04, T:0.46
Consensus pattern (21 bp):
ATATAATTTTTAAAACCATAT
Done.