Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006041.1 Hibiscus syriacus cultivar Beakdansim tig00014263_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: 61564
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:1515 original size:18 final size:19
Alignment explanation
Indices: 1475--1524 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
1465 AGTTGACTTA
1475 GTGTATCGGTACATCCTAG
1 GTGTATCGGTACATCCTAG
1494 GTGTATCGGTACATCC-AG
1 GTGTATCGGTACATCCTAG
1512 GTGTATCGGTACA
1 GTGTATCGGTACA
1525 CTAATTACAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 15 0.48
19 16 0.52
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.30
Consensus pattern (19 bp):
GTGTATCGGTACATCCTAG
Found at i:3452 original size:21 final size:22
Alignment explanation
Indices: 3426--3484 Score: 75
Period size: 23 Copynumber: 2.7 Consensus size: 22
3416 ACCCTACGAC
* *
3426 TGTATCGGTACAC-TCGAGGAG
1 TGTATCGGTACACATCAAGGAA
*
3447 TGTATCGATACACATTCAAGGAA
1 TGTATCGGTACACA-TCAAGGAA
3470 TGTATCGGTACACAT
1 TGTATCGGTACACAT
3485 TAATAGTGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 12 0.38
22 1 0.03
23 19 0.59
ACGTcount: A:0.31, C:0.19, G:0.24, T:0.27
Consensus pattern (22 bp):
TGTATCGGTACACATCAAGGAA
Found at i:3496 original size:21 final size:23
Alignment explanation
Indices: 3426--3502 Score: 81
Period size: 21 Copynumber: 3.5 Consensus size: 23
3416 ACCCTACGAC
* *
3426 TGTATCGGTACAC--TCGAGGAG
1 TGTATCGATACACATTCAAGGAG
*
3447 TGTATCGATACACATTCAAGGAA
1 TGTATCGATACACATTCAAGGAG
* *
3470 TGTATCGGTACACATT-AA-TAG
1 TGTATCGATACACATTCAAGGAG
3491 TGTATCGATACA
1 TGTATCGATACA
3503 TAGCAACGGT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
21 24 0.51
22 2 0.04
23 21 0.45
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (23 bp):
TGTATCGATACACATTCAAGGAG
Found at i:8878 original size:23 final size:24
Alignment explanation
Indices: 8852--8897 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
8842 TTTATTTCTG
*
8852 TTTTTTA-TTTATTAC-TATTATT
1 TTTTTTATTTTAATACTTATTATT
8874 TTTTTTATTTTAATACTTATTATT
1 TTTTTTATTTTAATACTTATTATT
8898 ACTATTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 7 0.33
23 7 0.33
24 7 0.33
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (24 bp):
TTTTTTATTTTAATACTTATTATT
Found at i:9198 original size:20 final size:21
Alignment explanation
Indices: 9175--9213 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
9165 TTGCTTCATT
*
9175 CTTTTTCTT-GTTTATTTTTA
1 CTTTTACTTAGTTTATTTTTA
*
9195 CTTTTACTTATTTTATTTT
1 CTTTTACTTAGTTTATTTT
9214 CTTATTTTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (21 bp):
CTTTTACTTAGTTTATTTTTA
Found at i:9219 original size:13 final size:15
Alignment explanation
Indices: 9190--9221 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
9180 TCTTGTTTAT
9190 TTTTACTTTTACTTA
1 TTTTACTTTTACTTA
9205 TTTTA-TTTT-CTTA
1 TTTTACTTTTACTTA
9218 TTTT
1 TTTT
9222 TTATCTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 4 0.24
15 5 0.29
ACGTcount: A:0.16, C:0.09, G:0.00, T:0.75
Consensus pattern (15 bp):
TTTTACTTTTACTTA
Found at i:12771 original size:21 final size:21
Alignment explanation
Indices: 12745--12794 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
12735 TAGAGCACTG
12745 AAGAGTCCATCAAGAA-AAACC
1 AAGAGTCCATCAAGAACAAA-C
12766 AAGAGTCCATCAAGAACAAAC
1 AAGAGTCCATCAAGAACAAAC
*
12787 AGGAGTCC
1 AAGAGTCC
12795 TTGGTCGACC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 24 0.89
22 3 0.11
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.10
Consensus pattern (21 bp):
AAGAGTCCATCAAGAACAAAC
Found at i:15530 original size:32 final size:32
Alignment explanation
Indices: 15489--15553 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
15479 ATAAGGTGCC
15489 AAGAATGGAAGAGGGTTCGGGAAATTTCTGTA
1 AAGAATGGAAGAGGGTTCGGGAAATTTCTGTA
*
15521 AAGAATGGAAGAGGGTTCGGGAAATTTTTGTA
1 AAGAATGGAAGAGGGTTCGGGAAATTTCTGTA
15553 A
1 A
15554 GGAAGGATTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (32 bp):
AAGAATGGAAGAGGGTTCGGGAAATTTCTGTA
Found at i:22116 original size:22 final size:21
Alignment explanation
Indices: 22085--22126 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
22075 TTATTTCTGT
*
22085 TTTTTATTTATTACTATTATA
1 TTTTTATTTAATACTATTATA
22106 TTTTTATTTTAATACTATTAT
1 TTTTTA-TTTAATACTATTAT
22127 TTCTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTTATTTAATACTATTATA
Found at i:22161 original size:2 final size:2
Alignment explanation
Indices: 22154--22191 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
22144 CCTTGTTATT
22154 TA TA TA TA TA TA TA TA -A T- TA TA TA TA TA TA T- TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
22192 TCATATAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
1 3 0.09
2 30 0.91
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:22197 original size:13 final size:13
Alignment explanation
Indices: 22154--22191 Score: 62
Period size: 12 Copynumber: 3.1 Consensus size: 13
22144 CCTTGTTATT
22154 TATATA-TATATA
1 TATATATTATATA
22166 TATA-ATTATATA
1 TATATATTATATA
22178 TATATATTATATA
1 TATATATTATATA
22191 T
1 T
22192 TCATATAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.04
12 14 0.58
13 9 0.38
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TATATATTATATA
Found at i:22198 original size:31 final size:31
Alignment explanation
Indices: 22153--22216 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
22143 ACCTTGTTAT
22153 TTATATATATATATA-TAATTATATA-TATATA
1 TTATATATATATATAGT-ATTAT-TACTATATA
22184 TTATATAT-TCATATAGTATTATTACTATATA
1 TTATATATAT-ATATAGTATTATTACTATATA
22215 TT
1 TT
22217 TTGCTATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
30 3 0.10
31 26 0.87
32 1 0.03
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.53
Consensus pattern (31 bp):
TTATATATATATATAGTATTATTACTATATA
Found at i:22216 original size:13 final size:14
Alignment explanation
Indices: 22154--22216 Score: 55
Period size: 12 Copynumber: 4.6 Consensus size: 14
22144 CCTTGTTATT
22154 TATATA-TATATA-
1 TATATATTATATAC
22166 TATA-ATTATATA-
1 TATATATTATATAC
22178 TATATATTATATATTC
1 TATATATTATATA--C
22194 ATATAGTATTAT-TAC
1 -TATA-TATTATATAC
22209 TATATATT
1 TATATATT
22217 TTGCTATTAA
Statistics
Matches: 44, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
11 1 0.02
12 14 0.32
13 12 0.27
14 4 0.09
15 1 0.02
17 6 0.14
18 6 0.14
ACGTcount: A:0.43, C:0.03, G:0.02, T:0.52
Consensus pattern (14 bp):
TATATATTATATAC
Found at i:22311 original size:5 final size:5
Alignment explanation
Indices: 22294--22358 Score: 51
Period size: 5 Copynumber: 12.8 Consensus size: 5
22284 ACTTACATTT
* * * * *
22294 TTTTA TTTT- TTTTA TTTTA TGTGA TTTTA TTTTG TTTCA TTTATT TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT-TA TTTTA
*
22344 TTTTC TTTGTA TTTT
1 TTTTA TTT-TA TTTT
22359 TCCTCATTAT
Statistics
Matches: 45, Mismatches: 12, Indels: 6
0.71 0.19 0.10
Matches are distributed among these distances:
4 4 0.09
5 34 0.76
6 7 0.16
ACGTcount: A:0.14, C:0.03, G:0.06, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:40312 original size:15 final size:16
Alignment explanation
Indices: 40287--40336 Score: 63
Period size: 15 Copynumber: 3.4 Consensus size: 16
40277 AAGGTTGAGG
40287 TTTGTTCAATATTGCA
1 TTTGTTCAATATTGCA
40303 TTTG-TCAATATTGCA
1 TTTGTTCAATATTGCA
*
40318 TTT-TT-TA-ATTGCA
1 TTTGTTCAATATTGCA
40331 TTTGTT
1 TTTGTT
40337 AGCTTAGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 9 0.29
14 3 0.10
15 15 0.48
16 4 0.13
ACGTcount: A:0.22, C:0.10, G:0.12, T:0.56
Consensus pattern (16 bp):
TTTGTTCAATATTGCA
Found at i:47144 original size:24 final size:24
Alignment explanation
Indices: 47106--47161 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
47096 AACCACAGCT
* * * *
47106 CGTATAAATTGCACCGAAGTGCCG
1 CGTAGAAAATGCACCAAAGTGCCA
*
47130 TGTAGAAAATGCACCAAAGTGCCA
1 CGTAGAAAATGCACCAAAGTGCCA
47154 CGTAGAAA
1 CGTAGAAA
47162 TGTCCCGACG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (24 bp):
CGTAGAAAATGCACCAAAGTGCCA
Found at i:47197 original size:23 final size:23
Alignment explanation
Indices: 47143--47198 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
47133 AGAAAATGCA
*
47143 CCAAAGTG-CCACGTAGAAATGTC
1 CCAAAG-GACCACATAGAAATGTC
* * *
47166 CCGACGGACCACATAGATATGTC
1 CCAAAGGACCACATAGAAATGTC
47189 CCAAAGGACC
1 CCAAAGGACC
47199 GCGCAAAACC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.34, C:0.30, G:0.21, T:0.14
Consensus pattern (23 bp):
CCAAAGGACCACATAGAAATGTC
Done.