Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009205.1 Hibiscus syriacus cultivar Beakdansim tig00112791_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: 274913
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 2
Found at i:269751 original size:3 final size:3
Alignment explanation
Indices: 269743--269835 Score: 168
Period size: 3 Copynumber: 31.0 Consensus size: 3
269733 TTAATATATT
*
269743 TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
269791 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA AAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
269836 ATCAATATGG
Statistics
Matches: 86, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:270425 original size:113 final size:113
Alignment explanation
Indices: 270091--270748 Score: 1072
Period size: 113 Copynumber: 5.8 Consensus size: 113
270081 TCTTGATGAG
****
270091 TTCTTCTCATTATGAACTTCTTCATCCTTCTTTC-GATGAGTTCTTCTCATTATGAACTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTC-TTCAGATGAGTTCTTCTCATTATGAACTCGAACT
* * * * *
270155 AGAAAAGTTGATCCATCAAGTGATGGATTTGAGCAAAA-ATCTGAACAAA
65 GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGT-TGAACAAA
270204 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCT-ATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* **
270268 GAAAAGCTAATTTATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
270316 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
270381 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
270429 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
270494 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
66 GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
**
270542 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTC-CTCT
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TCGAACT
*** * *
270606 GGAAAAGCGGATCTATCAAGTGATGGATTTGAGCAAAAGGTTGAACAAA
65 GGAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
270655 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
1 TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
* *
270720 GAAAAGATAATCCATCAAGTAATGGATTT
66 GAAAAGATAATCCATCAAGTGATAGATTT
270749 AAATCTTTGC
Statistics
Matches: 512, Mismatches: 28, Indels: 10
0.93 0.05 0.02
Matches are distributed among these distances:
112 104 0.20
113 406 0.79
114 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCATCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCGAACTG
GAAAAGATAATCCATCAAGTGATAGATTTGAGCAAAAGGTTGAACAAA
Found at i:271681 original size:85 final size:85
Alignment explanation
Indices: 271539--271965 Score: 682
Period size: 85 Copynumber: 5.1 Consensus size: 85
271529 CTATGAGCAA
* * * * * *
271539 ATTCATCTTT-CAATTTCAATAACTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTC
1 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
271603 CAGAAGATGCTATTGGGCAC
66 CAGAAGATGCTATTGGGCAC
* * *
271623 ATTCATCTTTCCAAATTCAATGATTGGTTTTACCAAACCAGATCAGATAACTCAAAGAACACTTC
1 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
271688 CAGAAGATGCTATTGGGCAC
66 CAGAAGATGCTATTGGGCAC
* * *
271708 TTTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAAATAACTCAAAGAACAGTTC
1 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
271773 CAGAAGATGCTATTGGGCAC
66 CAGAAGATGCTATTGGGCAC
271793 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
1 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
*
271858 CAGAAGATGCTA-TGAGCAC
66 CAGAAGATGCTATTGGGCAC
* *
271877 ATTCCTCTTT-CAAATTCAACGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
1 ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
*
271941 CAGAAGATGCTA-TGAGCAC
66 CAGAAGATGCTATTGGGCAC
271960 ATTCAT
1 ATTCAT
271966 TTGTTTCAGT
Statistics
Matches: 326, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
83 77 0.24
84 25 0.08
85 224 0.69
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (85 bp):
ATTCATCTTTCCAAATTCAATGATTGATTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGGCAC
Found at i:272779 original size:16 final size:16
Alignment explanation
Indices: 272728--272780 Score: 61
Period size: 16 Copynumber: 3.1 Consensus size: 16
272718 AATACAAGAG
272728 TAAATTGAATCTTCGAAAA
1 TAAATTGAA-CTT-G-AAA
* *
272747 TAAATTGAATTTTAAA
1 TAAATTGAACTTGAAA
272763 TAAATTGAACTTGAAA
1 TAAATTGAACTTGAAA
272779 TA
1 TA
272781 GATAGAATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 19 0.63
18 2 0.07
19 9 0.30
ACGTcount: A:0.49, C:0.06, G:0.09, T:0.36
Consensus pattern (16 bp):
TAAATTGAACTTGAAA
Found at i:273115 original size:1 final size:1
Alignment explanation
Indices: 273111--273174 Score: 56
Period size: 1 Copynumber: 64.0 Consensus size: 1
273101 ATTTTTTTCC
* * * * * * * *
273111 TTTTTTTTTCTTTTTTCTTTTTTCTCTTTTTTCTTTTTCTTTTTTCTTTTTTTTTCTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
273175 CTATCTTCAA
Statistics
Matches: 47, Mismatches: 16, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
1 47 1.00
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (1 bp):
T
Found at i:273124 original size:7 final size:7
Alignment explanation
Indices: 273114--273176 Score: 78
Period size: 7 Copynumber: 9.1 Consensus size: 7
273104 TTTTTCCTTT
273114 TTTTTTC
1 TTTTTTC
273121 TTTTTTC
1 TTTTTTC
273128 TTTTTTC
1 TTTTTTC
273135 TCTTTTT-
1 T-TTTTTC
273142 TCTTTTTC
1 T-TTTTTC
273150 TTTTTTC
1 TTTTTTC
273157 TTTTTT-
1 TTTTTTC
*
273163 TTTCTT-
1 TTTTTTC
273169 TTTTTTC
1 TTTTTTC
273176 T
1 T
273177 ATCTTCAAGC
Statistics
Matches: 51, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
6 10 0.20
7 35 0.69
8 6 0.12
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (7 bp):
TTTTTTC
Found at i:273140 original size:23 final size:24
Alignment explanation
Indices: 273103--273172 Score: 99
Period size: 23 Copynumber: 3.0 Consensus size: 24
273093 GACCCCTCAT
*
273103 TTTTTTCCTTTTTTTTTCTTTTTTC
1 TTTTTT-CTTCTTTTTTCTTTTTTC
273128 TTTTTTC-TCTTTTTTC-TTTTTC
1 TTTTTTCTTCTTTTTTCTTTTTTC
*
273150 TTTTTTCTTTTTTTTTCTTTTTT
1 TTTTTTCTTCTTTTTTCTTTTTT
273173 TTCTATCTTC
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
22 13 0.32
23 16 0.39
24 6 0.15
25 6 0.15
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (24 bp):
TTTTTTCTTCTTTTTTCTTTTTTC
Found at i:273157 original size:29 final size:29
Alignment explanation
Indices: 273111--273174 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
273101 ATTTTTTTCC
273111 TTTTTTTTTCTTTTTTC-TTTTTTCTCTT
1 TTTTTTTTTCTTTTTTCTTTTTTTCTCTT
*
273139 TTTTCTTTTTCTTTTTTCTTTTTTTTTCTT
1 TTTT-TTTTTCTTTTTTCTTTTTTTCTCTT
273169 TTTTTT
1 TTTTTT
273175 CTATCTTCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 15 0.45
30 14 0.42
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (29 bp):
TTTTTTTTTCTTTTTTCTTTTTTTCTCTT
Found at i:273174 original size:9 final size:9
Alignment explanation
Indices: 273102--273176 Score: 80
Period size: 9 Copynumber: 8.1 Consensus size: 9
273092 TGACCCCTCA
*
273102 TTTTTTTCC
1 TTTTTTTTC
273111 TTTTTTTT-
1 TTTTTTTTC
*
273119 TCTTTTTTC
1 TTTTTTTTC
*
273128 TTTTTTCTC
1 TTTTTTTTC
*
273137 TTTTTTCTTT
1 TTTTTT-TTC
273147 TTCTTTTTTC
1 TT-TTTTTTC
273157 TTTTTTTTTC
1 -TTTTTTTTC
273167 TTTTTTTTC
1 TTTTTTTTC
273176 T
1 T
273177 ATCTTCAAGC
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
8 7 0.13
9 30 0.55
10 12 0.22
11 6 0.11
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:273181 original size:13 final size:11
Alignment explanation
Indices: 273102--273174 Score: 78
Period size: 11 Copynumber: 6.5 Consensus size: 11
273092 TGACCCCTCA
*
273102 TTTTTTTCCTT
1 TTTTTTTCTTT
273113 TTTTTTTCTTT
1 TTTTTTTCTTT
273124 TTTCTTTT-TTCT
1 TTT-TTTTCTT-T
*
273136 CTTTTTTCTTT
1 TTTTTTTCTTT
273147 TTCTTTTT-TCTT
1 TT-TTTTTCT-TT
273159 TTTTTTTCTTT
1 TTTTTTTCTTT
273170 TTTTT
1 TTTTT
273175 CTATCTTCAA
Statistics
Matches: 53, Mismatches: 3, Indels: 12
0.78 0.04 0.18
Matches are distributed among these distances:
11 34 0.64
12 19 0.36
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTTCTTT
Done.