Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003616.1 Hibiscus syriacus cultivar Beakdansim tig00007646_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: 58688
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:764 original size:21 final size:20
Alignment explanation
Indices: 738--879 Score: 67
Period size: 21 Copynumber: 6.5 Consensus size: 20
728 ATTATTTTAA
738 ATTTTATTTATTTATTTATTT
1 ATTTTA-TTATTTATTTATTT
* *
759 ATTTTAGTATTTA-ATATATT
1 ATTTTATTATTTATTTAT-TT
779 ATGTTTATTATTTATTGTA-TT
1 AT-TTTATTATTTATT-TATTT
*
800 ATTTATGGTATATTATATATATATTCT
1 ATTT-T-AT-TATT-TAT-T-TATT-T
*
827 ATTCTTATTA-TTATTGATTT
1 ATT-TTATTATTTATTTATTT
* *
847 TTTTTCATT-TTTCTTTATATT
1 ATTTT-ATTATTTATTTAT-TT
868 ATTATTATTATT
1 ATT-TTATTATT
880 ACTTTTAGTA
Statistics
Matches: 92, Mismatches: 12, Indels: 33
0.67 0.09 0.24
Matches are distributed among these distances:
19 5 0.05
20 24 0.26
21 31 0.34
22 6 0.07
23 9 0.10
24 4 0.04
25 5 0.05
26 2 0.02
27 5 0.05
28 1 0.01
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.66
Consensus pattern (20 bp):
ATTTTATTATTTATTTATTT
Found at i:1169 original size:3 final size:3
Alignment explanation
Indices: 1161--1212 Score: 81
Period size: 3 Copynumber: 18.0 Consensus size: 3
1151 TACTTCCTTG
*
1161 TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT TAT TAC TAT TA- TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1207 TAT TAT
1 TAT TAT
1213 ATCTTTAACA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:1189 original size:17 final size:17
Alignment explanation
Indices: 1161--1212 Score: 86
Period size: 17 Copynumber: 3.0 Consensus size: 17
1151 TACTTCCTTG
1161 TATTATTATTATTATTAT
1 TATTA-TATTATTATTAT
*
1179 TATTATATTATTATTAC
1 TATTATATTATTATTAT
1196 TATTATATTATTATTAT
1 TATTATATTATTATTAT
1213 ATCTTTAACA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 27 0.84
18 5 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (17 bp):
TATTATATTATTATTAT
Found at i:2238 original size:21 final size:22
Alignment explanation
Indices: 2193--2238 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
2183 ATCAATCCTT
*
2193 AACTTAAATAAAAATACATTCA
1 AACTGAAATAAAAATACATTCA
*
2215 AACTGAAATAAAAATA-ATTGA
1 AACTGAAATAAAAATACATTCA
2236 AAC
1 AAC
2239 AATTCTTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (22 bp):
AACTGAAATAAAAATACATTCA
Found at i:2441 original size:31 final size:32
Alignment explanation
Indices: 2403--2462 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
2393 GAATTTTATA
2403 AGATAACAGTGTTGTGTCTATTTT-TAATGAT
1 AGATAACAGTGTTGTGTCTATTTTGTAATGAT
2434 AGATAACAGTGTTGTGTCTATTTTGTAAT
1 AGATAACAGTGTTGTGTCTATTTTGTAAT
2463 AAAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (32 bp):
AGATAACAGTGTTGTGTCTATTTTGTAATGAT
Found at i:4168 original size:4 final size:4
Alignment explanation
Indices: 4159--4183 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
4149 TAAGTCAATC
4159 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
4184 GCTGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:4715 original size:11 final size:11
Alignment explanation
Indices: 4699--4724 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4689 ACCTGAACGG
4699 CTATAACTTAA
1 CTATAACTTAA
4710 CTATAACTTAA
1 CTATAACTTAA
4721 CTAT
1 CTAT
4725 CCACTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
CTATAACTTAA
Found at i:37122 original size:2 final size:2
Alignment explanation
Indices: 37117--37180 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
37107 TATGCATTGT
37117 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37159 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
37181 GGGAGAAATC
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40680 original size:4 final size:4
Alignment explanation
Indices: 40671--40698 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
40661 ATTATTTTAA
40671 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
40699 TAGTATTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:40738 original size:12 final size:11
Alignment explanation
Indices: 40671--40823 Score: 65
Period size: 12 Copynumber: 13.9 Consensus size: 11
40661 ATTATTTTAA
40671 ATTTATTTATTT
1 ATTTA-TTATTT
40683 ATTTATTTATTT
1 ATTTA-TTATTT
*
40695 ATTTTAGTATTT
1 A-TTTATTATTT
* *
40707 AATATATTATGT
1 -ATTTATTATTT
40719 -TTTATTATTT
1 ATTTATTATTT
40729 ATTGTATTATTTT
1 ATT-TATTA-TTT
*
40742 ATGGTA-TA-TT
1 AT-TTATTATTT
* *
40752 ATATA-TATAT
1 ATTTATTATTT
*
40762 ATTCTATT-CTT
1 ATT-TATTATTT
*
40773 A-TTATTATTG
1 ATTTATTATTT
*
40783 ATTT-TTTTTT
1 ATTTATTATTT
40793 CATTT-TTCATTT
1 -ATTTATT-ATTT
40805 ATTTATTA-TT
1 ATTTATTATTT
40815 A-TTATTATT
1 ATTTATTATT
40824 ACCTTTTAGT
Statistics
Matches: 109, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
9 14 0.13
10 26 0.24
11 19 0.17
12 38 0.35
13 12 0.11
ACGTcount: A:0.27, C:0.03, G:0.04, T:0.67
Consensus pattern (11 bp):
ATTTATTATTT
Found at i:41122 original size:3 final size:3
Alignment explanation
Indices: 41114--41167 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
41104 TACTTCCTTG
*
41114 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41162 TAT TAT
1 TAT TAT
41168 CTTTTAACAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42194 original size:21 final size:22
Alignment explanation
Indices: 42149--42194 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
42139 ATCAATCCTT
*
42149 AACTTAAATAAAAATACATTCA
1 AACTGAAATAAAAATACATTCA
*
42171 AACTGAAATAAAAATA-ATTGA
1 AACTGAAATAAAAATACATTCA
42192 AAC
1 AAC
42195 AATTCTAACT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.61, C:0.11, G:0.04, T:0.24
Consensus pattern (22 bp):
AACTGAAATAAAAATACATTCA
Found at i:42371 original size:31 final size:32
Alignment explanation
Indices: 42333--42392 Score: 113
Period size: 31 Copynumber: 1.9 Consensus size: 32
42323 GAATTTTATA
42333 AGATAACAGTGTTGTGTCTATTTT-TAATGAT
1 AGATAACAGTGTTGTGTCTATTTTGTAATGAT
42364 AGATAACAGTGTTGTGTCTATTTTGTAAT
1 AGATAACAGTGTTGTGTCTATTTTGTAAT
42393 AAAATCTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 24 0.86
32 4 0.14
ACGTcount: A:0.28, C:0.07, G:0.20, T:0.45
Consensus pattern (32 bp):
AGATAACAGTGTTGTGTCTATTTTGTAATGAT
Found at i:44107 original size:4 final size:4
Alignment explanation
Indices: 44098--44122 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
44088 TAAGTCAATC
44098 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
44123 GCTGAAAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:44656 original size:11 final size:11
Alignment explanation
Indices: 44640--44665 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
44630 ACCTGAACGG
44640 CTATAACTTAA
1 CTATAACTTAA
44651 CTATAACTTAA
1 CTATAACTTAA
44662 CTAT
1 CTAT
44666 CCACTTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.42, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
CTATAACTTAA
Found at i:55145 original size:37 final size:37
Alignment explanation
Indices: 55095--55169 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
55085 GGGTAGGAAC
55095 CGGCATGGGCCCTTGGAGCTTTCTCCGCAGCTGATCG
1 CGGCATGGGCCCTTGGAGCTTTCTCCGCAGCTGATCG
55132 CGGCATGGGCCCTTGGAGCTTTCTCCGCAGCTGATCG
1 CGGCATGGGCCCTTGGAGCTTTCTCCGCAGCTGATCG
55169 C
1 C
55170 TGGAAATGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.11, C:0.33, G:0.32, T:0.24
Consensus pattern (37 bp):
CGGCATGGGCCCTTGGAGCTTTCTCCGCAGCTGATCG
Done.