Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004377.1 Hibiscus syriacus cultivar Beakdansim tig00009596_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: 67132
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3053 original size:23 final size:24
Alignment explanation
Indices: 2980--3053 Score: 57
Period size: 23 Copynumber: 3.2 Consensus size: 24
2970 TTTACCTTTT
* *
2980 ATTTTAAATAA-TTA-ATTTTAAA
1 ATTTTAATTAATTTAGAATTTAAA
* *
3002 ATTTTAATTAATTTATAA-TTATA
1 ATTTTAATTAATTTAGAATTTAAA
**
3025 CGTTTAATT-ATTTAGAATTTAAA
1 ATTTTAATTAATTTAGAATTTAAA
*
3048 TTTTTA
1 ATTTTA
3054 TAAATTAAAT
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
22 17 0.43
23 22 0.55
24 1 0.03
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.54
Consensus pattern (24 bp):
ATTTTAATTAATTTAGAATTTAAA
Found at i:6368 original size:31 final size:31
Alignment explanation
Indices: 6333--6421 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
6323 AATAAAAATA
6333 AATTT-AAAGTTAGAATGATTAAATTAAGAGT
1 AATTTAAAAGTTA-AATGATTAAATTAAGAGT
* *
6364 AATTTAAAAGTTAAGTGATTAAATTAGGAGT
1 AATTTAAAAGTTAAATGATTAAATTAAGAGT
** *
6395 AATTTGGAAGTTAAATAATTAAATTAA
1 AATTTAAAAGTTAAATGATTAAATTAA
6422 AAAAAATCTA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 43 0.86
32 7 0.14
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (31 bp):
AATTTAAAAGTTAAATGATTAAATTAAGAGT
Found at i:32235 original size:24 final size:24
Alignment explanation
Indices: 32207--32269 Score: 92
Period size: 24 Copynumber: 2.7 Consensus size: 24
32197 CAGTCACCAC
*
32207 TGCCACACAGAATTTGCACCGAAG
1 TGCCACATAGAATTTGCACCGAAG
* *
32231 TGCCATATAGAATATGCACCGAAG
1 TGCCACATAGAATTTGCACCGAAG
32255 TGCCACATA-AATTTG
1 TGCCACATAGAATTTG
32270 TCCCGAAAGA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 5 0.15
24 29 0.85
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (24 bp):
TGCCACATAGAATTTGCACCGAAG
Found at i:32310 original size:22 final size:23
Alignment explanation
Indices: 32264--32312 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 23
32254 GTGCCACATA
32264 AATTTGTCCCGAAAGATCGCGTAG
1 AATTTGTCCCGAAAGA-CGCGTAG
*
32288 AATTTGTCCCGAAGGA-GCGTAG
1 AATTTGTCCCGAAAGACGCGTAG
32310 AAT
1 AAT
32313 CTTCGACTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 9 0.38
24 15 0.62
ACGTcount: A:0.31, C:0.18, G:0.27, T:0.24
Consensus pattern (23 bp):
AATTTGTCCCGAAAGACGCGTAG
Found at i:32448 original size:15 final size:15
Alignment explanation
Indices: 32430--32489 Score: 75
Period size: 15 Copynumber: 4.0 Consensus size: 15
32420 CATAATTTAC
*
32430 ATTCGCATAGAACAT
1 ATTCACATAGAACAT
* *
32445 ATTCACTTAGCACAT
1 ATTCACATAGAACAT
32460 ATTCACATAGAACAT
1 ATTCACATAGAACAT
* *
32475 CTTCACATATAACAT
1 ATTCACATAGAACAT
32490 GTAATCATAG
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.30
Consensus pattern (15 bp):
ATTCACATAGAACAT
Found at i:33139 original size:20 final size:20
Alignment explanation
Indices: 33116--33160 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
33106 TATTGGTCTC
33116 GATAC-CTCCACATCAGTATT
1 GATACACTCCA-ATCAGTATT
*
33136 GATACTACTTCAATCAGTATT
1 GATAC-ACTCCAATCAGTATT
33157 GATA
1 GATA
33161 TTGTTCATCC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (20 bp):
GATACACTCCAATCAGTATT
Found at i:34900 original size:24 final size:24
Alignment explanation
Indices: 34873--34982 Score: 102
Period size: 24 Copynumber: 4.6 Consensus size: 24
34863 GTAAACGGAG
*
34873 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
34897 ATATCAGATATCAGAACAGAATCC
1 ATATCAGAAATCAGAACAGAATTC
*
34921 AGATCAG-AATCAGAACAGAATTC
1 ATATCAGAAATCAGAACAGAATTC
* *
34944 AGGTAAC-G-TATCAGAACAGAATTC
1 A--TATCAGAAATCAGAACAGAATTC
*
34968 A-ATTCGGAAATCAGA
1 ATA-TCAGAAATCAGA
34983 TAAAATATTT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 16 0.23
24 50 0.71
25 2 0.03
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (24 bp):
ATATCAGAAATCAGAACAGAATTC
Found at i:34904 original size:12 final size:12
Alignment explanation
Indices: 34877--34968 Score: 66
Period size: 12 Copynumber: 7.8 Consensus size: 12
34867 ACGGAGATAT
* *
34877 CAGAAATCAAAA
1 CAGAATTCAGAA
* *
34889 CAGAATTCATAT
1 CAGAATTCAGAA
34901 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
34913 CAGAATCCAGAT
1 CAGAATTCAGAA
34925 CAGAA-TCAGAA
1 CAGAATTCAGAA
34936 CAGAATTCAGGTAA
1 CAGAATTCA-G-AA
*
34950 C-GTA-TCAGAA
1 CAGAATTCAGAA
34960 CAGAATTCA
1 CAGAATTCA
34969 ATTCGGAAAT
Statistics
Matches: 62, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
10 3 0.05
11 14 0.23
12 37 0.60
13 5 0.08
14 3 0.05
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:34956 original size:47 final size:48
Alignment explanation
Indices: 34875--34965 Score: 125
Period size: 47 Copynumber: 1.9 Consensus size: 48
34865 AAACGGAGAT
*
34875 ATCAGAAATCAAAACAGAATTCATATCAGATATCAGAACAGAATCCAG
1 ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
*
34923 ATCAG-AATCAGAACAGAATTCAGGTAAC-G-TATCAGAACAGAAT
1 ATCAGAAATCAAAACAGAATTCA--TAACAGATATCAGAACAGAAT
34966 TCAATTCGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
47 30 0.77
48 6 0.15
49 3 0.08
ACGTcount: A:0.48, C:0.18, G:0.15, T:0.19
Consensus pattern (48 bp):
ATCAGAAATCAAAACAGAATTCATAACAGATATCAGAACAGAATCCAG
Found at i:36082 original size:18 final size:18
Alignment explanation
Indices: 36061--36098 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
36051 TGTCATCTGG
*
36061 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
36079 TCTTATCATTTACTTCAA
1 TCTTATCATTTAATTCAA
36097 TC
1 TC
36099 CTTTTGAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.18, G:0.00, T:0.53
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:45325 original size:37 final size:37
Alignment explanation
Indices: 45284--45354 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
45274 TGAATATGCA
45284 AGTTGGATTGCAGCTCAGCTGGACATAAAGGTTCGTG
1 AGTTGGATTGCAGCTCAGCTGGACATAAAGGTTCGTG
*
45321 AGTTGGATTGCAGCTCAGTTGGACATAAAGGTTC
1 AGTTGGATTGCAGCTCAGCTGGACATAAAGGTTC
45355 CCAAAACGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.31, T:0.28
Consensus pattern (37 bp):
AGTTGGATTGCAGCTCAGCTGGACATAAAGGTTCGTG
Found at i:49937 original size:69 final size:74
Alignment explanation
Indices: 49856--49998 Score: 206
Period size: 69 Copynumber: 2.0 Consensus size: 74
49846 AAATTATCAA
*
49856 TAAATAAATTTTAAGATATAAAAATATTATTAAATTTAA-AATATT-A-A-TT-TTTATATTTTA
1 TAAATAAATTTTAAAATATAAAAATATTATTAAATTTAATAATATTAAGATTTATTTATATTTTA
49916 AAATATAAG
66 AAATATAAG
* * *
49925 TAAATAAATTTTAAAATTTTAAAATATTATTAAATTTAATAATCTTGAAGATTTATTTATATTTT
1 TAAATAAATTTTAAAATATAAAAATATTATTAAATTTAATAATATT-AAGATTTATTTATATTTT
49990 AAAATATAA
65 AAAATATAA
49999 AAAATTTAAT
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
69 36 0.56
70 5 0.08
72 1 0.02
73 1 0.02
74 2 0.03
75 19 0.30
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (74 bp):
TAAATAAATTTTAAAATATAAAAATATTATTAAATTTAATAATATTAAGATTTATTTATATTTTA
AAATATAAG
Found at i:53751 original size:31 final size:29
Alignment explanation
Indices: 53683--53751 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
53673 TAATTCAATA
* * *
53683 AACAAAATGTAACAATTGATTACATAAGG
1 AACAAAATGTAAAAATCGATAACATAAGG
*
53712 GACTAAAATGTAATAAATCGATAACATAAGTG
1 AAC-AAAATGTAA-AAATCGATAACATAAG-G
53744 AACAAAAT
1 AACAAAAT
53752 TCTAATTTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
29 2 0.06
30 9 0.28
31 18 0.56
32 3 0.09
ACGTcount: A:0.54, C:0.10, G:0.13, T:0.23
Consensus pattern (29 bp):
AACAAAATGTAAAAATCGATAACATAAGG
Found at i:61855 original size:19 final size:19
Alignment explanation
Indices: 61833--61871 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
61823 GTTTACCAGC
* *
61833 AATTGTAAAGTTTTTATTT
1 AATTATAAACTTTTTATTT
*
61852 AATTATGAACTTTTTATTT
1 AATTATAAACTTTTTATTT
61871 A
1 A
61872 TTTTGTTTGT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (19 bp):
AATTATAAACTTTTTATTT
Found at i:62790 original size:18 final size:18
Alignment explanation
Indices: 62748--62791 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
62738 TGATCGGTCA
62748 CGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
* *
62766 AGGCCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
62784 CGACCCGA
1 CGACCCGA
62792 TCATTGACCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.18, C:0.48, G:0.25, T:0.09
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:62903 original size:29 final size:29
Alignment explanation
Indices: 62810--62889 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
62800 CGTTGACCAC
62810 TGCTATTCTGGTAAATAATTCGGTTTTGG
1 TGCTATTCTGGTAAATAATTCGGTTTTGG
*
62839 TGCTATTCTGGTAAATAATTTGGTTTTGG
1 TGCTATTCTGGTAAATAATTCGGTTTTGG
*
62868 TGCTATTCTGGTAATTAATTCG
1 TGCTATTCTGGTAAATAATTCG
62890 AAATGGGTGC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.21, C:0.10, G:0.23, T:0.46
Consensus pattern (29 bp):
TGCTATTCTGGTAAATAATTCGGTTTTGG
Done.