Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008553.1 Hibiscus syriacus cultivar Beakdansim tig00111448_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: 57067
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:28661 original size:3 final size:3
Alignment explanation
Indices: 28618--28647 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28608 ATTTGGCTTA
28618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
28648 TAAACCTTAA
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:31342 original size:31 final size:31
Alignment explanation
Indices: 31306--31364 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
31296 ATTAAATCTG
31306 ACATGATCTTTTATTACCACAAGCAGCAACT
1 ACATGATCTTTTATTACCACAAGCAGCAACT
31337 ACATGATCTTTTATTACCACAAGCAGCA
1 ACATGATCTTTTATTACCACAAGCAGCA
31365 TCGAAGTTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.36, C:0.25, G:0.10, T:0.29
Consensus pattern (31 bp):
ACATGATCTTTTATTACCACAAGCAGCAACT
Found at i:31523 original size:86 final size:86
Alignment explanation
Indices: 31314--31519 Score: 337
Period size: 85 Copynumber: 2.4 Consensus size: 86
31304 TGACATGATC
* *
31314 TTTTATTACCACAAGCAGCAACT-ACATGATCTTTTATTACCACAAGCAGCATCGAAGTTGTTTT
1 TTTTATTACCACAAGCAGCAACTGGCATGATCTTTTATTACCACAAGCAACATCGAAGTTGTTTT
*
31378 TCCCCTGCAATTCAAACAATT
66 CCCCCTGCAATTCAAACAATT
*
31399 TTTTATTACCACAAGCAGCAACTGAG-ATGATCTTTTATTACCACAAGCAACATTGAAGTTG-TT
1 TTTTATTACCACAAGCAGCAACTG-GCATGATCTTTTATTACCACAAGCAACATCGAAGTTGTTT
*
31462 TCCCCCTGCAATTCATACAATT
65 TCCCCCTGCAATTCAAACAATT
31484 TTTTATTACCACAAGCAGCAACTGGCATGATCTTTT
1 TTTTATTACCACAAGCAGCAACTGGCATGATCTTTT
31520 TATTGGCTTC
Statistics
Matches: 113, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
84 1 0.01
85 79 0.70
86 33 0.29
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (86 bp):
TTTTATTACCACAAGCAGCAACTGGCATGATCTTTTATTACCACAAGCAACATCGAAGTTGTTTT
CCCCCTGCAATTCAAACAATT
Found at i:31804 original size:21 final size:21
Alignment explanation
Indices: 31780--31823 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
31770 AAGATCACCA
31780 TGTGCTCCTAGAGACATATGG
1 TGTGCTCCTAGAGACATATGG
31801 TGTGCTCCTAGAGACATATGG
1 TGTGCTCCTAGAGACATATGG
31822 TG
1 TG
31824 GTCACTGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.30
Consensus pattern (21 bp):
TGTGCTCCTAGAGACATATGG
Found at i:32645 original size:3 final size:3
Alignment explanation
Indices: 32637--32668 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
32627 AATGTAAAGA
*
32637 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
32669 GATATCAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:34122 original size:2 final size:2
Alignment explanation
Indices: 34117--34142 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
34107 AAGATATATA
34117 TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG
34143 AAGTTTTAAG
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:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:40042 original size:2 final size:2
Alignment explanation
Indices: 40024--40105 Score: 66
Period size: 2 Copynumber: 43.5 Consensus size: 2
40014 TAACGATGGT
* * * *
40024 TA TA TG TA TA TA CA TA TA TA TA TA -A TA -A AA TA -A AA TA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
40062 AA TA TA CA TA -A AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
40103 TA T
1 TA T
40106 GAATAAAGGA
Statistics
Matches: 65, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
1 5 0.08
2 60 0.92
ACGTcount: A:0.56, C:0.02, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Found at i:40060 original size:10 final size:11
Alignment explanation
Indices: 40041--40078 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
40031 ATATACATAT
40041 ATATATAATAAA
1 ATATA-AATAAA
40053 ATA-AAATAAA
1 ATATAAATAAA
*
40063 ATATACATAAA
1 ATATAAATAAA
40074 ATATA
1 ATATA
40079 TATATATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 9 0.38
11 12 0.50
12 3 0.12
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (11 bp):
ATATAAATAAA
Found at i:40123 original size:63 final size:61
Alignment explanation
Indices: 40024--40149 Score: 159
Period size: 59 Copynumber: 2.0 Consensus size: 61
40014 TAACGATGGT
*
40024 TATATGTATATACATATATATATAATAAAATAAAATAAAAT-ATACAT-AAAATATA-TATA
1 TATATATATATACATATATATATAATAAAATAAAATAAAATAATA-ATGAAAATATAGTATA
* *
40083 TATATATATATATATATATATATGAATAAAGGAATAAAATATAATAATAATGAAAATATAGTATA
1 TATATATATATACATATATATAT-AAT-AA--AATAAAATAAAATAATAATGAAAATATAGTATA
40148 TA
1 TA
40150 ATAATAGTAG
Statistics
Matches: 57, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
59 21 0.37
60 3 0.05
61 2 0.04
63 14 0.25
64 11 0.19
65 6 0.11
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.36
Consensus pattern (61 bp):
TATATATATATACATATATATATAATAAAATAAAATAAAATAATAATGAAAATATAGTATA
Found at i:41130 original size:22 final size:23
Alignment explanation
Indices: 41089--41136 Score: 73
Period size: 22 Copynumber: 2.1 Consensus size: 23
41079 AAAAAAAATG
41089 TAAATATAATATAATTTATAATA
1 TAAATATAATATAATTTATAATA
41112 TAAATAT-ATAT-ATTATATAATA
1 TAAATATAATATAATT-TATAATA
41134 TAA
1 TAA
41137 GGACGAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
21 3 0.12
22 14 0.58
23 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATATAATATAATTTATAATA
Found at i:41765 original size:211 final size:211
Alignment explanation
Indices: 41369--41943 Score: 981
Period size: 211 Copynumber: 2.8 Consensus size: 211
41359 GAAATCAAAC
* * *
41369 TCGTGAAGTTGAACTTGCGTTATCCGGAGTCCAATATCCTTC--------GTTGAAATTGGCTCT
1 TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
41426 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGT----TT--A----CGTTGTC
66 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
41481 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
131 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
41546 ACCAGCGGTCCCTTCG
196 ACCAGCGGTCCCTTCG
41562 TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
1 TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
41627 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
66 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
41692 CGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
131 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
41757 ACCAGCGGTCCCTTCG
196 ACCAGCGGTCCCTTCG
41773 TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-
1 TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
41837 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
66 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
41902 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
131 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
41944 GGTAAAACCT
Statistics
Matches: 359, Mismatches: 5, Indels: 19
0.94 0.01 0.05
Matches are distributed among these distances:
193 39 0.11
201 60 0.17
205 2 0.01
207 1 0.00
210 106 0.30
211 151 0.42
ACGTcount: A:0.23, C:0.19, G:0.25, T:0.34
Consensus pattern (211 bp):
TCGTGAAGTTGAACTTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACA
ACCAGCGGTCCCTTCG
Found at i:41794 original size:105 final size:105
Alignment explanation
Indices: 41471--41943 Score: 910
Period size: 105 Copynumber: 4.5 Consensus size: 105
41461 CCTTCGTCGT
41471 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
41536 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
41576 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAAT
1 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAAAT
41641 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
65 GTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
* *
41682 TTGCGTTGTCCGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
41747 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
41787 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
1 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
41852 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
66 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
41892 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
41944 GGTAAAACCT
Statistics
Matches: 362, Mismatches: 5, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
105 259 0.72
106 103 0.28
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
TTACGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATG
TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
Found at i:52193 original size:19 final size:19
Alignment explanation
Indices: 52155--52194 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52145 ATGGTTAGTA
*
52155 AAATAAAAATAATGAAAAT
1 AAATAAAAATAATCAAAAT
52174 AAATAAAAATAA-CAAGAAT
1 AAATAAAAATAATCAA-AAT
52193 AA
1 AA
52195 TGGCAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 2 0.11
19 17 0.89
ACGTcount: A:0.75, C:0.03, G:0.05, T:0.17
Consensus pattern (19 bp):
AAATAAAAATAATCAAAAT
Found at i:53501 original size:17 final size:17
Alignment explanation
Indices: 53471--53516 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
53461 ATATAATATT
53471 AATAAATAAA-TAAAACTA
1 AATAAA-AAACTAAAA-TA
53489 AA-AAAAAACTAAAATA
1 AATAAAAAACTAAAATA
*
53505 AATAAATAACTA
1 AATAAAAAACTA
53517 TGATCAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.28
17 16 0.64
18 2 0.08
ACGTcount: A:0.74, C:0.07, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAAAACTAAAATA
Found at i:53772 original size:2 final size:2
Alignment explanation
Indices: 53754--53830 Score: 63
Period size: 2 Copynumber: 40.5 Consensus size: 2
53744 TAACGATGGT
* * * * *
53754 TA TA TG TA TA TA CA TA TA TA TA -A TA AA TA -A AA TA -A AA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
53793 TA CA TA -A AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
53831 GAATAAAGGA
Statistics
Matches: 60, Mismatches: 11, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
1 4 0.07
2 56 0.93
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (2 bp):
TA
Done.