Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009491.1 Hibiscus syriacus cultivar Beakdansim tig00114599_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: 35713
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Found at i:6315 original size:13 final size:14
Alignment explanation
Indices: 6294--6334 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
6284 AAAAAAACAA
6294 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
6309 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
6323 AAAAAAACAAAA
1 AAAAAAA-AAAA
6335 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:6326 original size:9 final size:9
Alignment explanation
Indices: 6275--6355 Score: 52
Period size: 8 Copynumber: 9.6 Consensus size: 9
6265 ATTTTTTTTT
6275 CAAAAAA-A
1 CAAAAAAGA
6283 CAAAAAA-A
1 CAAAAAAGA
*
6291 CAAAAAACA
1 CAAAAAAGA
*
6300 -AAAAAAGG
1 CAAAAAAGA
6308 C--AAAA-A
1 CAAAAAAGA
*
6314 -AAAAAAGG
1 CAAAAAAGA
6322 CAAAAAA-A
1 CAAAAAAGA
6330 CAAAAAAAGA
1 C-AAAAAAGA
6340 GCCAAAAAAGA
1 --CAAAAAAGA
6351 CAAAA
1 CAAAA
6356 TTTCAAAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 19
0.71 0.06 0.23
Matches are distributed among these distances:
7 8 0.14
8 22 0.38
9 18 0.31
10 1 0.02
11 8 0.14
12 1 0.02
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (9 bp):
CAAAAAAGA
Found at i:6334 original size:20 final size:21
Alignment explanation
Indices: 6311--6355 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 21
6301 AAAAAGGCAA
*
6311 AAAAAAAAAGGCAAAAAA-AC
1 AAAAAAAAAGCCAAAAAAGAC
*
6331 AAAAAAAGAGCCAAAAAAGAC
1 AAAAAAAAAGCCAAAAAAGAC
6352 AAAA
1 AAAA
6356 TTTCAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.78, C:0.11, G:0.11, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGCCAAAAAAGAC
Found at i:6355 original size:8 final size:8
Alignment explanation
Indices: 6275--6337 Score: 69
Period size: 8 Copynumber: 8.0 Consensus size: 8
6265 ATTTTTTTTT
6275 CAAAAAAA
1 CAAAAAAA
6283 CAAAAAAA
1 CAAAAAAA
6291 C-AAAAAA
1 CAAAAAAA
6298 CAAAAAAA
1 CAAAAAAA
6306 GGC-AAAAAA
1 --CAAAAAAA
**
6315 -AAAAAGG
1 CAAAAAAA
6322 CAAAAAAA
1 CAAAAAAA
6330 CAAAAAAA
1 CAAAAAAA
6338 GAGCCAAAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 10
0.77 0.07 0.17
Matches are distributed among these distances:
7 11 0.24
8 28 0.61
9 6 0.13
10 1 0.02
ACGTcount: A:0.83, C:0.11, G:0.06, T:0.00
Consensus pattern (8 bp):
CAAAAAAA
Found at i:10782 original size:36 final size:36
Alignment explanation
Indices: 10730--10842 Score: 174
Period size: 36 Copynumber: 3.2 Consensus size: 36
10720 GATACTATTT
*
10730 TCATCACCATAATCCATCTCCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
10766 TCATCACCATAGTCCATCACCATTATCACGCCTATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
* *
10802 TCATCACCATATTCCATCACCA-TATCACGCCAATA
1 TCATCACCATAATCCATCACCATTATCACGCCTATA
*
10837 ACATCA
1 TCATCA
10843 TCCTTCCATT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
35 17 0.24
36 55 0.76
ACGTcount: A:0.33, C:0.36, G:0.04, T:0.27
Consensus pattern (36 bp):
TCATCACCATAATCCATCACCATTATCACGCCTATA
Found at i:10785 original size:13 final size:11
Alignment explanation
Indices: 10730--10828 Score: 67
Period size: 13 Copynumber: 8.3 Consensus size: 11
10720 GATACTATTT
10730 TCATCACCATAA
1 TCATCACCAT-A
*
10742 TCCATCTCCATTA
1 T-CATCACCA-TA
*
10755 TCA-CGCCTATA
1 TCATCACC-ATA
10766 TCATCACCATA
1 TCATCACCATA
10777 GTCCATCACCATTA
1 -T-CATCACCA-TA
*
10791 TCA-CGCCTATA
1 TCATCACC-ATA
10802 TCATCACCATA
1 TCATCACCATA
10813 TTCCATCACCATA
1 -T-CATCACCATA
10826 TCA
1 TCA
10829 CGCCAATAAC
Statistics
Matches: 71, Mismatches: 5, Indels: 23
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.34
12 16 0.23
13 28 0.39
14 3 0.04
ACGTcount: A:0.31, C:0.36, G:0.03, T:0.29
Consensus pattern (11 bp):
TCATCACCATA
Found at i:10857 original size:33 final size:33
Alignment explanation
Indices: 10731--10857 Score: 112
Period size: 36 Copynumber: 3.6 Consensus size: 33
10721 ATACTATTTT
* * *
10731 CATCACCATAATCCATCTCCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
* *
10767 CATCACCATAGTCCATCACCATTATCACGCCTATAT
1 CATCACCAT--TCCATCACCA-TATCACGCCAATAA
10803 CATCACCATATTCCATCACCATATCACGCCAATAA
1 CATCACC--ATTCCATCACCATATCACGCCAATAA
*
10838 CATCATCC-TTCCATTACCAT
1 CATCA-CCATTCCATCACCAT
10858 TACATCACCA
Statistics
Matches: 83, Mismatches: 5, Indels: 9
0.86 0.05 0.09
Matches are distributed among these distances:
33 11 0.13
35 17 0.20
36 53 0.64
38 2 0.02
ACGTcount: A:0.31, C:0.37, G:0.03, T:0.28
Consensus pattern (33 bp):
CATCACCATTCCATCACCATATCACGCCAATAA
Found at i:12779 original size:22 final size:23
Alignment explanation
Indices: 12748--12798 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
12738 TTAGAAGTTT
*
12748 GTGATAATATAGGCGTGAT-ATG
1 GTGATGATATAGGCGTGATAATG
12770 GTGATGATATAGGCGTGATAATG
1 GTGATGATATAGGCGTGATAATG
12793 GTGATG
1 GTGATG
12799 GACAGATTGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 18 0.67
23 9 0.33
ACGTcount: A:0.29, C:0.04, G:0.35, T:0.31
Consensus pattern (23 bp):
GTGATGATATAGGCGTGATAATG
Found at i:21954 original size:26 final size:27
Alignment explanation
Indices: 21894--21954 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
21884 TTGGCTTGCT
21894 TTCTTTT-TGAATTTCTTTTTCTTTTC
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
* *
21920 TTCTATTCTG-ATTTTTTTTTCTTTT-
1 TTCTTTTCTGAATTTCTTTTTCTTTTC
21945 TGTCTTTTCT
1 T-TCTTTTCT
21955 TTCTTTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 1 0.03
26 27 0.90
27 2 0.07
ACGTcount: A:0.07, C:0.15, G:0.05, T:0.74
Consensus pattern (27 bp):
TTCTTTTCTGAATTTCTTTTTCTTTTC
Found at i:32067 original size:33 final size:33
Alignment explanation
Indices: 32025--32093 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
32015 GTTGATGAAT
*
32025 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
32058 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
32091 GAA
1 GAA
32094 TATGGTGATG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Found at i:32134 original size:36 final size:36
Alignment explanation
Indices: 32064--32176 Score: 165
Period size: 36 Copynumber: 3.2 Consensus size: 36
32054 AATGGAAGGA
* *
32064 TGATGTTATTGGCGTGAT-ATGGTGATGGAATATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
*
32099 TGATGATATAGGCGTGATAATGGTGATGGACTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
* * *
32135 TGATAATATAGGCGTGATAATGGAGATGGATTATGG
1 TGATGATATAGGCGTGATAATGGTGATGGAATATGG
32171 TGATGA
1 TGATGA
32177 AAATAGTATC
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
35 16 0.23
36 54 0.77
ACGTcount: A:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (36 bp):
TGATGATATAGGCGTGATAATGGTGATGGAATATGG
Found at i:32136 original size:13 final size:11
Alignment explanation
Indices: 32078--32176 Score: 58
Period size: 13 Copynumber: 8.3 Consensus size: 11
32068 GTTATTGGCG
32078 TGATATGGTGA
1 TGATATGGTGA
32089 TGGAATATGGTGA
1 T-G-ATATGGTGA
*
32102 TGATATAGGCG-
1 TGATAT-GGTGA
32113 TGATAATGGTGA
1 TGAT-ATGGTGA
32125 TGGACTATGGTGA
1 T-GA-TATGGTGA
* *
32138 TAATATAGGCG-
1 TGATAT-GGTGA
*
32149 TGATAATGGAGA
1 TGAT-ATGGTGA
32161 TGGATTATGGTGA
1 T-GA-TATGGTGA
32174 TGA
1 TGA
32177 AAATAGTATC
Statistics
Matches: 69, Mismatches: 7, Indels: 23
0.70 0.07 0.23
Matches are distributed among these distances:
11 21 0.30
12 17 0.25
13 29 0.42
14 2 0.03
ACGTcount: A:0.30, C:0.03, G:0.35, T:0.31
Consensus pattern (11 bp):
TGATATGGTGA
Done.