Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003901.1 Hibiscus syriacus cultivar Beakdansim tig00008430_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: 70801
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.32
Found at i:3904 original size:31 final size:31
Alignment explanation
Indices: 3868--3981 Score: 124
Period size: 31 Copynumber: 3.7 Consensus size: 31
3858 ACTTAATGAG
*
3868 CACGAGTTGAGCAACAAGTTTTTTTAACGAA
1 CACGAGTCGAGCAACAAGTTTTTTTAACGAA
* *
3899 CACGAGTTGAGCAACAATTTTTTTTAAC-AA
1 CACGAGTCGAGCAACAAGTTTTTTTAACGAA
* * * * *
3929 GCACGAGTCGAGAAACAAATTGTTTTAATGAG
1 -CACGAGTCGAGCAACAAGTTTTTTTAACGAA
*
3961 CACAAGTCGAGCAA-AAGTTTT
1 CACGAGTCGAGCAACAAGTTTT
3982 AACGAGTAAC
Statistics
Matches: 70, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
30 7 0.10
31 62 0.89
32 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (31 bp):
CACGAGTCGAGCAACAAGTTTTTTTAACGAA
Found at i:19638 original size:11 final size:11
Alignment explanation
Indices: 19622--19646 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
19612 TCTTATTATA
19622 AACAATAATTG
1 AACAATAATTG
19633 AACAATAATTG
1 AACAATAATTG
19644 AAC
1 AAC
19647 CCTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.12, G:0.08, T:0.24
Consensus pattern (11 bp):
AACAATAATTG
Found at i:20638 original size:24 final size:24
Alignment explanation
Indices: 20606--20651 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
20596 CAATTGTTCC
20606 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
20630 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
20652 TCCAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:25764 original size:24 final size:24
Alignment explanation
Indices: 25732--25777 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
25722 CAATTGTTCC
25732 TGCTTCCTCGTCTCTCTTCTTCGA
1 TGCTTCCTCGTCTCTCTTCTTCGA
*
25756 TGCTTCCTCTTCTCTCTTCTTC
1 TGCTTCCTCGTCTCTCTTCTTC
25778 TCCAACCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.02, C:0.39, G:0.09, T:0.50
Consensus pattern (24 bp):
TGCTTCCTCGTCTCTCTTCTTCGA
Found at i:28930 original size:32 final size:33
Alignment explanation
Indices: 28855--28920 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
28845 CGAATTACAT
** *
28855 AGTCCAACATGTAAACATAATTAAAAAAATGTT
1 AGTCCAACATCCAAACATAATTAAAAAAATGTC
28888 AGTCCAACATCCAAACATAATT-AAAAAATGTC
1 AGTCCAACATCCAAACATAATTAAAAAAATGTC
28920 A
1 A
28921 TGTTAACATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 10 0.33
33 20 0.67
ACGTcount: A:0.52, C:0.17, G:0.08, T:0.24
Consensus pattern (33 bp):
AGTCCAACATCCAAACATAATTAAAAAAATGTC
Found at i:29014 original size:3 final size:3
Alignment explanation
Indices: 29006--29035 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28996 ATAATTTTGA
29006 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29036 CGAGTGATCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:29212 original size:68 final size:68
Alignment explanation
Indices: 29027--29301 Score: 362
Period size: 68 Copynumber: 4.1 Consensus size: 68
29017 TAATAATAAT
* *
29027 AATAATAATCGAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAAGTAGTTTACC
1 AATAATAATCAAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
29092 CTA
66 CTA
* ** ** * *
29095 AATAAAAAT-ATA-T-AT-ATGAGTTATATTAGATACTATATAAGTGACCAAATAGGTAGTTTAC
1 AATAATAATCA-AGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTAC
29156 CCTA
65 CCTA
* * *
29160 AATAATAATCAAGTGATCAAAACATAAATTAAATAATATATAAGTTATCAAATAGGTAGTTTACC
1 AATAATAATCAAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
29225 CTA
66 CTA
* * * *
29228 AATAATAATCGAGTGACCAAAATATAGATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
1 AATAATAATCAAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
29293 CTA
66 CTA
29296 AA-AATA
1 AATAATA
29302 TTCCTAACCA
Statistics
Matches: 176, Mismatches: 26, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
65 52 0.30
66 4 0.02
67 7 0.04
68 113 0.64
ACGTcount: A:0.48, C:0.11, G:0.12, T:0.30
Consensus pattern (68 bp):
AATAATAATCAAGTGATCAAAACATAAATTAGATAATATATAAGTGACCAAATAGGTAGTTTACC
CTA
Found at i:32854 original size:135 final size:134
Alignment explanation
Indices: 32494--32872 Score: 446
Period size: 130 Copynumber: 2.8 Consensus size: 134
32484 GCTCATCTGC
* * * * *
32494 GATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACATGGTTCC-ACTCTGCTGGGGACGG
1 GATGAAGAG-TTCTTGGCCATCTTTAGG-AAGGTGATAACATGGTTCCTACGC-GATGAGGACGG
* * * * * **
32558 CTGGTTATCTGAGGTTGACACGGCTCATACGTGATGAAGAGTTCTGGTCATGGGATGACATTACT
63 CTGGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCATAGGATGACACGACT
32623 CATACAT
128 CATACAT
* *
32630 GATGAAGAGTTCTTGGCCATC--TA--AAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTG
1 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGAGGACGGCTG
* * *
32691 GTTATCTAAGGGTGACACGGTTCCTACGTGATGAGGAAATCTGGTCGA-AGGATGACACGACTCA
66 GTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTC-ATAGGATGACACGACTCA
* *
32755 TGCGT
130 TACAT
* *
32760 GATGAAGAGTTCTTGGCCATCTTTAGGAAGGGTGATAACTTGGTTCCTACGCGATGAGGATGGCT
1 GATGAAGAGTTCTTGGCCATCTTTAGGAA-GGTGATAACATGGTTCCTACGCGATGAGGACGGCT
* ***
32825 GGTTATCTAATGTTGACGTTGCTCCTACGTGATGAGGAGATCTGGTCA
65 GGTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCA
32873 GCTGATGTTG
Statistics
Matches: 206, Mismatches: 30, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
130 105 0.51
131 3 0.01
132 2 0.01
133 2 0.01
134 3 0.01
135 82 0.40
136 9 0.04
ACGTcount: A:0.25, C:0.17, G:0.30, T:0.28
Consensus pattern (134 bp):
GATGAAGAGTTCTTGGCCATCTTTAGGAAGGTGATAACATGGTTCCTACGCGATGAGGACGGCTG
GTTATCTAAGGTTGACACGGCTCCTACGTGATGAGGAGATCTGGTCATAGGATGACACGACTCAT
ACAT
Found at i:54807 original size:171 final size:171
Alignment explanation
Indices: 54522--54864 Score: 650
Period size: 171 Copynumber: 2.0 Consensus size: 171
54512 GGAAAAATTG
54522 AAACATCAATGAGATTTTCGAGCCCGAGCTTAAAGGTGAGTGATATTTGAAGTAGTTTACCCTAA
1 AAACATCAATGAGATTTTCGAGCCCGAGCTTAAAGGTGAGTGATATTTGAAGTAGTTTACCCTAA
* *
54587 AATTTAATCATTGAATCTCAATGATTATCATATCTTAACCATAATGTTAGCATTCAACTCATAAT
66 AATTTAATCATAGAATCTCAATGATTATCATATCTCAACCATAATGTTAGCATTCAACTCATAAT
*
54652 ACCATCAAATTTTTAACAAAAAATGACGAGTTTGGAACATA
131 ACCATCAAAATTTTAACAAAAAATGACGAGTTTGGAACATA
54693 AAACATCAATGAGATTTTCGAGCCCGAGCTTAAAGGTGAGTGATATTTGAAGTAGTTTACCCTAA
1 AAACATCAATGAGATTTTCGAGCCCGAGCTTAAAGGTGAGTGATATTTGAAGTAGTTTACCCTAA
*
54758 AATTTAATCATAGAATCTCAATGATTATCATATCTCAACCATAATGTTAGCGTTCAACTCATAAT
66 AATTTAATCATAGAATCTCAATGATTATCATATCTCAACCATAATGTTAGCATTCAACTCATAAT
54823 ACCATCAAAATTTTAACAAAAAATGACGAGTTTGGAACATA
131 ACCATCAAAATTTTAACAAAAAATGACGAGTTTGGAACATA
54864 A
1 A
54865 TGAATAGTCG
Statistics
Matches: 168, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
171 168 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (171 bp):
AAACATCAATGAGATTTTCGAGCCCGAGCTTAAAGGTGAGTGATATTTGAAGTAGTTTACCCTAA
AATTTAATCATAGAATCTCAATGATTATCATATCTCAACCATAATGTTAGCATTCAACTCATAAT
ACCATCAAAATTTTAACAAAAAATGACGAGTTTGGAACATA
Found at i:55072 original size:2 final size:2
Alignment explanation
Indices: 55065--55090 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
55055 TAAAAGATAA
55065 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
55091 TTAGGTTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.