Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007395.1 Hibiscus syriacus cultivar Beakdansim tig00019944_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: 51414
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:335 original size:17 final size:18
Alignment explanation
Indices: 301--341 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
291 GGTCTAGGAG
*
301 TCTTTTCTTTTCTCTTTT
1 TCTTTTCTTCTCTCTTTT
*
319 TGTTTTCTTCT-TCTTTT
1 TCTTTTCTTCTCTCTTTT
336 TCTTTT
1 TCTTTT
342 GTTGTAGCAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (18 bp):
TCTTTTCTTCTCTCTTTT
Found at i:1257 original size:21 final size:21
Alignment explanation
Indices: 1232--1271 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
1222 TTTGGCCGAA
*
1232 TAGGAAGCATGCTTGAATGGT
1 TAGGAAACATGCTTGAATGGT
1253 TAGGAAACATGCTTGAATG
1 TAGGAAACATGCTTGAATG
1272 ATGCACATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.10, G:0.30, T:0.28
Consensus pattern (21 bp):
TAGGAAACATGCTTGAATGGT
Found at i:4808 original size:27 final size:27
Alignment explanation
Indices: 4770--4823 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
4760 TAATATGAGA
4770 TATGAATTATCGTATAGAAGGCATAGG
1 TATGAATTATCGTATAGAAGGCATAGG
4797 TATGAATTATCGTATAGAAGGCATAGG
1 TATGAATTATCGTATAGAAGGCATAGG
4824 ACATTCATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.37, C:0.07, G:0.26, T:0.30
Consensus pattern (27 bp):
TATGAATTATCGTATAGAAGGCATAGG
Found at i:15112 original size:28 final size:28
Alignment explanation
Indices: 15081--15145 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
15071 GTAAATTTTG
15081 TATCGATACTCTCAAAGAGTATCGATAA
1 TATCGATACTCTCAAAGAGTATCGATAA
*
15109 TATCGATGCTCTCAAAGAGTATCGATAA
1 TATCGATACTCTCAAAGAGTATCGATAA
15137 TATCGATAC
1 TATCGATAC
15146 CAAGGCAGAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 35 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (28 bp):
TATCGATACTCTCAAAGAGTATCGATAA
Found at i:17175 original size:35 final size:35
Alignment explanation
Indices: 17099--17215 Score: 135
Period size: 35 Copynumber: 3.3 Consensus size: 35
17089 TACTATTTGT
* * *
17099 TCATCACCATCCTCCATCGCCATTTTCATGCCTATA
1 TCATCACCATCTTCCATCACCA-TTTCACGCCTATA
* * *
17135 ACATCACCATCTTCCATCACCATTGCACACCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
** *
17170 TCATCAATATCTTCTATCACCATTTCACGCCTATA
1 TCATCACCATCTTCCATCACCATTTCACGCCTATA
*
17205 TAATCACCATC
1 TCATCACCATC
17216 ATACTACCAT
Statistics
Matches: 66, Mismatches: 15, Indels: 1
0.80 0.18 0.01
Matches are distributed among these distances:
35 47 0.71
36 19 0.29
ACGTcount: A:0.28, C:0.37, G:0.03, T:0.32
Consensus pattern (35 bp):
TCATCACCATCTTCCATCACCATTTCACGCCTATA
Found at i:21566 original size:13 final size:13
Alignment explanation
Indices: 21512--21570 Score: 52
Period size: 13 Copynumber: 4.8 Consensus size: 13
21502 ACTATATGTT
21512 CATCACCATTTTC
1 CATCACCATTTTC
* *
21525 CAACATCATTTT-
1 CATCACCATTTTC
* **
21537 CA-CACC-TATAA
1 CATCACCATTTTC
21548 CATCACCATTTTC
1 CATCACCATTTTC
21561 CATCACCATT
1 CATCACCATT
21571 GCACGCCAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
10 2 0.06
11 5 0.14
12 6 0.17
13 22 0.63
ACGTcount: A:0.31, C:0.36, G:0.00, T:0.34
Consensus pattern (13 bp):
CATCACCATTTTC
Found at i:21770 original size:15 final size:15
Alignment explanation
Indices: 21750--21788 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
21740 TACTTTGATA
21750 TCATTTCTT-TCCATT
1 TCATTTCTTAT-CATT
21765 TCATTTCTTATCATT
1 TCATTTCTTATCATT
*
21780 TCCTTTCTT
1 TCATTTCTT
21789 CTTCTATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 21 0.95
16 1 0.05
ACGTcount: A:0.13, C:0.26, G:0.00, T:0.62
Consensus pattern (15 bp):
TCATTTCTTATCATT
Found at i:34838 original size:13 final size:13
Alignment explanation
Indices: 34820--34852 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
34810 GTTTTGATAT
34820 TCGAATAATTATA
1 TCGAATAATTATA
34833 TCGAATAATTATA
1 TCGAATAATTATA
34846 TCGAATA
1 TCGAATA
34853 TACTTAGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.36
Consensus pattern (13 bp):
TCGAATAATTATA
Found at i:38998 original size:24 final size:24
Alignment explanation
Indices: 38953--38998 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
38943 TGTGTTACAA
* * **
38953 ACACCATATTTAATTGGCATTTCC
1 ACACAATATTTAACTGAAATTTCC
38977 ACACAATATTTAACTGAAATTT
1 ACACAATATTTAACTGAAATTT
38999 ATTATAACAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (24 bp):
ACACAATATTTAACTGAAATTTCC
Done.