Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007362.1 Hibiscus syriacus cultivar Beakdansim tig00019755_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: 55827
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:925 original size:22 final size:23
Alignment explanation
Indices: 900--945 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 23
890 ATATCAATTT
900 ATATGAGAAAAAT-TAATAT-AAA
1 ATATGA-AAAAATATAATATGAAA
*
922 ATATTAAAAAATATAATATGAAA
1 ATATGAAAAAATATAATATGAAA
945 A
1 A
946 CCTTTTATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 11 0.52
23 4 0.19
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (23 bp):
ATATGAAAAAATATAATATGAAA
Found at i:7129 original size:33 final size:33
Alignment explanation
Indices: 7087--7189 Score: 134
Period size: 33 Copynumber: 3.1 Consensus size: 33
7077 GGTGGTGACA
* * * *
7087 GCGACAATGACAACAATAGCGGCAATAATGATG
1 GCGACAATGACAACAGTAGCAGCAACAACGATG
* *
7120 GCGACAATGACAACAGTATCATCAACAACGATG
1 GCGACAATGACAACAGTAGCAGCAACAACGATG
* *
7153 GCGACAATGGCAACAGTAGCATCAACAACGATG
1 GCGACAATGACAACAGTAGCAGCAACAACGATG
7186 GCGA
1 GCGA
7190 TGGTAGTAAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (33 bp):
GCGACAATGACAACAGTAGCAGCAACAACGATG
Found at i:7240 original size:40 final size:40
Alignment explanation
Indices: 7161--7240 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
7151 TGGCGACAAT
* * *
7161 GGCAACAGTAGCATCAACAACGATGGCGATGGTAGTAACA
1 GGCAACAATAGCATCAACAACGATGGCGATGGCAATAACA
*
7201 GGCAACAATAGCGA-CAATAACGATGGCGATGGCAATAACA
1 GGCAACAATAGC-ATCAACAACGATGGCGATGGCAATAACA
7241 TCTACTGTAG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 34 0.97
41 1 0.03
ACGTcount: A:0.40, C:0.20, G:0.26, T:0.14
Consensus pattern (40 bp):
GGCAACAATAGCATCAACAACGATGGCGATGGCAATAACA
Found at i:30174 original size:26 final size:26
Alignment explanation
Indices: 30145--30199 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
30135 ACCACTTTCT
30145 CAAAACTATTGGGCCTTACTTAAGCC
1 CAAAACTATTGGGCCTTACTTAAGCC
*
30171 CAAAACTATTGGGCCTTACTTAAGTC
1 CAAAACTATTGGGCCTTACTTAAGCC
30197 CAA
1 CAA
30200 TACCTTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.33, C:0.25, G:0.15, T:0.27
Consensus pattern (26 bp):
CAAAACTATTGGGCCTTACTTAAGCC
Found at i:37017 original size:37 final size:37
Alignment explanation
Indices: 36967--37040 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
36957 TACCCCACAC
*
36967 GAGGTACTTCTTAGAGGAAAAGGGTTATGTTCTGGAT
1 GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
*
37004 GAGGTACTTCTTAGAGGAGAAGGGTTATGCTCTGGAT
1 GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
37041 TCGTACTCGT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.26, C:0.09, G:0.34, T:0.31
Consensus pattern (37 bp):
GAGGTACTTCTTAGAGGAAAAGGGTTATGCTCTGGAT
Found at i:43418 original size:12 final size:12
Alignment explanation
Indices: 43401--43436 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
43391 AGTTAATGCC
43401 TGATGTGGCAGT
1 TGATGTGGCAGT
*
43413 TGATGTGGC-GA
1 TGATGTGGCAGT
43424 TGATGTGGCAGT
1 TGATGTGGCAGT
43436 T
1 T
43437 AACGTGGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.17, C:0.08, G:0.42, T:0.33
Consensus pattern (12 bp):
TGATGTGGCAGT
Found at i:43427 original size:23 final size:23
Alignment explanation
Indices: 43401--43454 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
43391 AGTTAATGCC
* *
43401 TGATGTGGCAGTTGATGTGGCGA
1 TGATGTGGCAGTTAACGTGGCGA
*
43424 TGATGTGGCAGTTAACGTGGTGA
1 TGATGTGGCAGTTAACGTGGCGA
*
43447 TGAAGTGG
1 TGATGTGG
43455 TAGCTGACGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.20, C:0.07, G:0.43, T:0.30
Consensus pattern (23 bp):
TGATGTGGCAGTTAACGTGGCGA
Found at i:43429 original size:11 final size:12
Alignment explanation
Indices: 43401--43434 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
43391 AGTTAATGCC
*
43401 TGATGTGGCAGT
1 TGATGTGGCAGA
43413 TGATGTGGC-GA
1 TGATGTGGCAGA
43424 TGATGTGGCAG
1 TGATGTGGCAG
43435 TTAACGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.18, C:0.09, G:0.44, T:0.29
Consensus pattern (12 bp):
TGATGTGGCAGA
Found at i:43507 original size:23 final size:23
Alignment explanation
Indices: 43481--43536 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
43471 CAATTAACAT
43481 CTTCTAGAAGGCCCAATCATCAA
1 CTTCTAGAAGGCCCAATCATCAA
*
43504 CTTCTAGAAGGTCCAATCATCAA
1 CTTCTAGAAGGCCCAATCATCAA
43527 CTTCTAGAAG
1 CTTCTAGAAG
43537 ATTCAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.34, C:0.27, G:0.14, T:0.25
Consensus pattern (23 bp):
CTTCTAGAAGGCCCAATCATCAA
Found at i:43543 original size:23 final size:23
Alignment explanation
Indices: 43481--43545 Score: 94
Period size: 23 Copynumber: 2.8 Consensus size: 23
43471 CAATTAACAT
**
43481 CTTCTAGAAGGCCCAATCATCAA
1 CTTCTAGAAGATCCAATCATCAA
*
43504 CTTCTAGAAGGTCCAATCATCAA
1 CTTCTAGAAGATCCAATCATCAA
*
43527 CTTCTAGAAGATTCAATCA
1 CTTCTAGAAGATCCAATCA
43546 ACAGTGGCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.26
Consensus pattern (23 bp):
CTTCTAGAAGATCCAATCATCAA
Found at i:49960 original size:34 final size:34
Alignment explanation
Indices: 49899--49965 Score: 93
Period size: 34 Copynumber: 1.9 Consensus size: 34
49889 TTCTTGAGAG
49899 TTGTTTTCTCCTTTTTATCAAGAGAGAA-TTGTTA
1 TTGTTTTCTCCTTTTTATC-AGAGAGAAGTTGTTA
49933 TTGTTTTCTCCTTGTTATATC-GAGAGAAGTTGT
1 TTGTTTTCTCCTT-TT-TATCAGAGAGAAGTTGT
49966 AATTCCTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
34 20 0.67
35 6 0.20
36 4 0.13
ACGTcount: A:0.21, C:0.12, G:0.18, T:0.49
Consensus pattern (34 bp):
TTGTTTTCTCCTTTTTATCAGAGAGAAGTTGTTA
Done.