Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004785.1 Hibiscus syriacus cultivar Beakdansim tig00010789_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: 53824
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:517 original size:18 final size:18
Alignment explanation
Indices: 494--566 Score: 101
Period size: 18 Copynumber: 3.9 Consensus size: 18
484 AGGGATAATC
494 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
512 AGTGGTTCTTCGGAACAAT
1 AGTGGTCCTTCGGGAC-AT
531 CAGTGGTCCTTCGGGACAT
1 -AGTGGTCCTTCGGGACAT
*
550 AGTGGTCTTTCGGGACA
1 AGTGGTCCTTCGGGACA
567 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
18 30 0.62
19 4 0.08
20 14 0.29
ACGTcount: A:0.19, C:0.21, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:4857 original size:95 final size:91
Alignment explanation
Indices: 4698--4885 Score: 306
Period size: 95 Copynumber: 2.0 Consensus size: 91
4688 AACCAAAAAA
4698 ACTCAATGTATAAAGTTGAATGATTAAATTAAAAAAACTAAAAGTATAATGAGTAAAATAAGAGA
1 ACTCAATGTATAAAGTTGAATGATTAAATTAAAAAAACTAAAAGTATAATGAGTAAAATAAGAGA
4763 TAGAGA-AAAATTCAGTGAATAAGTTT
66 TAGA-ATAAAATTCAGTGAATAAGTTT
*
4789 ACTCAATGTATAAAGTTGAGTGATTAAATTTAAAAAAAAAACTAAAAGTATAATGAGTAAAATAA
1 ACTCAATGTATAAAGTTGAATGATTAAA-TT---AAAAAAACTAAAAGTATAATGAGTAAAATAA
*
4854 GAGATATAATAAAATTCAGTGAATAAGTTT
62 GAGATAGAATAAAATTCAGTGAATAAGTTT
4884 AC
1 AC
4886 AATTTACGCA
Statistics
Matches: 90, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 27 0.30
92 2 0.02
94 1 0.01
95 60 0.67
ACGTcount: A:0.53, C:0.05, G:0.14, T:0.28
Consensus pattern (91 bp):
ACTCAATGTATAAAGTTGAATGATTAAATTAAAAAAACTAAAAGTATAATGAGTAAAATAAGAGA
TAGAATAAAATTCAGTGAATAAGTTT
Found at i:6998 original size:192 final size:192
Alignment explanation
Indices: 6666--7057 Score: 775
Period size: 192 Copynumber: 2.0 Consensus size: 192
6656 TTTGGGAAGC
*
6666 AACTTCAACCAAATGGACCTGGATGTTTCACGGGAAAGTTGTAACACGAAGATGAAAGGAAATCA
1 AACTGCAACCAAATGGACCTGGATGTTTCACGGGAAAGTTGTAACACGAAGATGAAAGGAAATCA
6731 CCATAAAATAAAGAAGGTTTTGCTCCATCATCATCAAATAAAGTAAAAAAAAGATGCCTATAAGG
66 CCATAAAATAAAGAAGGTTTTGCTCCATCATCATCAAATAAAGTAAAAAAAAGATGCCTATAAGG
6796 AAGGAAGATGATGAGCCGAGACCCTTCAATAGGAATACTTGCTTAGGAAGAAATTCACCAGG
131 AAGGAAGATGATGAGCCGAGACCCTTCAATAGGAATACTTGCTTAGGAAGAAATTCACCAGG
6858 AACTGCAACCAAATGGACCTGGATGTTTCACGGGAAAGTTGTAACACGAAGATGAAAGGAAATCA
1 AACTGCAACCAAATGGACCTGGATGTTTCACGGGAAAGTTGTAACACGAAGATGAAAGGAAATCA
6923 CCATAAAATAAAGAAGGTTTTGCTCCATCATCATCAAATAAAGTAAAAAAAAGATGCCTATAAGG
66 CCATAAAATAAAGAAGGTTTTGCTCCATCATCATCAAATAAAGTAAAAAAAAGATGCCTATAAGG
6988 AAGGAAGATGATGAGCCGAGACCCTTCAATAGGAATACTTGCTTAGGAAGAAATTCACCAGG
131 AAGGAAGATGATGAGCCGAGACCCTTCAATAGGAATACTTGCTTAGGAAGAAATTCACCAGG
7050 AACTGCAA
1 AACTGCAA
7058 TTGTAAATTT
Statistics
Matches: 199, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
192 199 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.20
Consensus pattern (192 bp):
AACTGCAACCAAATGGACCTGGATGTTTCACGGGAAAGTTGTAACACGAAGATGAAAGGAAATCA
CCATAAAATAAAGAAGGTTTTGCTCCATCATCATCAAATAAAGTAAAAAAAAGATGCCTATAAGG
AAGGAAGATGATGAGCCGAGACCCTTCAATAGGAATACTTGCTTAGGAAGAAATTCACCAGG
Found at i:18119 original size:12 final size:13
Alignment explanation
Indices: 18100--18145 Score: 67
Period size: 13 Copynumber: 3.6 Consensus size: 13
18090 TATATAAAAA
*
18100 TAATCGGGTCGGG
1 TAATCGGGCCGGG
18113 T-ATCGGGCCGGG
1 TAATCGGGCCGGG
*
18125 TAATCGAGCCGGG
1 TAATCGGGCCGGG
18138 TAATCGGG
1 TAATCGGG
18146 TAATAGGGGC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.17, C:0.20, G:0.43, T:0.20
Consensus pattern (13 bp):
TAATCGGGCCGGG
Found at i:20823 original size:12 final size:12
Alignment explanation
Indices: 20806--20860 Score: 96
Period size: 12 Copynumber: 4.8 Consensus size: 12
20796 ATATTGCAAA
20806 TGAACATGTTCG
1 TGAACATGTTCG
20818 TGAACATGTTCG
1 TGAACATGTTCG
20830 TGAACATG-T-G
1 TGAACATGTTCG
20840 TGAACATGTTCG
1 TGAACATGTTCG
20852 TGAACATGT
1 TGAACATGT
20861 AAAACAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
10 9 0.22
11 2 0.05
12 30 0.73
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (12 bp):
TGAACATGTTCG
Found at i:20845 original size:22 final size:23
Alignment explanation
Indices: 20806--20860 Score: 94
Period size: 22 Copynumber: 2.4 Consensus size: 23
20796 ATATTGCAAA
20806 TGAACATGTTCGTGAACATGTTCG
1 TGAACATG-TCGTGAACATGTTCG
20830 TGAACATGT-GTGAACATGTTCG
1 TGAACATGTCGTGAACATGTTCG
20852 TGAACATGT
1 TGAACATGT
20861 AAAACAAACA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 22 0.71
23 1 0.03
24 8 0.26
ACGTcount: A:0.27, C:0.15, G:0.25, T:0.33
Consensus pattern (23 bp):
TGAACATGTCGTGAACATGTTCG
Found at i:27756 original size:20 final size:20
Alignment explanation
Indices: 27733--27776 Score: 72
Period size: 19 Copynumber: 2.2 Consensus size: 20
27723 CTAAAACATT
27733 TAATAAGTTAAAATTTTCAA
1 TAATAAGTTAAAATTTTCAA
*
27753 TAAT-ATTTAAAATTTTCAA
1 TAATAAGTTAAAATTTTCAA
27772 TAATA
1 TAATA
27777 TTATTAAAGC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 18 0.82
20 4 0.18
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (20 bp):
TAATAAGTTAAAATTTTCAA
Found at i:27764 original size:19 final size:19
Alignment explanation
Indices: 27740--27778 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
27730 ATTTAATAAG
27740 TTAAAATTTTCAATAATAT
1 TTAAAATTTTCAATAATAT
27759 TTAAAATTTTCAATAATAT
1 TTAAAATTTTCAATAATAT
27778 T
1 T
27779 ATTAAAGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (19 bp):
TTAAAATTTTCAATAATAT
Found at i:41114 original size:82 final size:82
Alignment explanation
Indices: 40977--41138 Score: 306
Period size: 82 Copynumber: 2.0 Consensus size: 82
40967 CCCCCCTAAG
*
40977 ATTATTTTGAGAATTTGAAATTATTTCTGATACTCTCTTCACCATTATTATTATTTTTCTGTGAC
1 ATTATTTTGAGAAATTGAAATTATTTCTGATACTCTCTTCACCATTATTATTATTTTTCTGTGAC
41042 TGAAATTATGATTACAA
66 TGAAATTATGATTACAA
*
41059 ATTATTTTGAGAAATTGAAATTATTTCTGATGCTCTCTTCACCATTATTATTATTTTTCTGTGAC
1 ATTATTTTGAGAAATTGAAATTATTTCTGATACTCTCTTCACCATTATTATTATTTTTCTGTGAC
41124 TGAAATTATGATTAC
66 TGAAATTATGATTAC
41139 GTAACGAAAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
82 78 1.00
ACGTcount: A:0.30, C:0.12, G:0.10, T:0.48
Consensus pattern (82 bp):
ATTATTTTGAGAAATTGAAATTATTTCTGATACTCTCTTCACCATTATTATTATTTTTCTGTGAC
TGAAATTATGATTACAA
Found at i:44885 original size:16 final size:16
Alignment explanation
Indices: 44864--44895 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
44854 CGTTTAATAA
44864 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
*
44880 ATAAACGAACATAAAC
1 ATAAACGAACACAAAC
44896 GCTGGAGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.62, C:0.22, G:0.06, T:0.09
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:52321 original size:3 final size:3
Alignment explanation
Indices: 52313--52365 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
52303 GCCTGTAAAT
* * * * *
52313 ATA ATA ATA TTA ATAA ATT ATA ATA ATA ATT ATA ATA ATA AAA AAA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
52359 ATA ATA A
1 ATA ATA A
52366 AACGGGATAA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 38 0.93
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Done.