Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001517.1 Hibiscus syriacus cultivar Beakdansim tig00002964_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: 36913
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Found at i:1297 original size:34 final size:34
Alignment explanation
Indices: 1259--1327 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
1249 ATCAAAGTAG
1259 GGTTATTTTTATAAACATTTATTGGATAATTTGT
1 GGTTATTTTTATAAACATTTATTGGATAATTTGT
1293 GGTTATTTTTATAAACATTTATTGGATAATTTGT
1 GGTTATTTTTATAAACATTTATTGGATAATTTGT
1327 G
1 G
1328 TTGAGATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.16, T:0.52
Consensus pattern (34 bp):
GGTTATTTTTATAAACATTTATTGGATAATTTGT
Found at i:1338 original size:34 final size:34
Alignment explanation
Indices: 1266--1338 Score: 112
Period size: 34 Copynumber: 2.1 Consensus size: 34
1256 TAGGGTTATT
**
1266 TTTATAAACATTTATTGGATAATTTGTGGTTATT
1 TTTATAAACATTTATTGGATAATTTGTGGTTAGA
1300 TTTATAAACATTTATTGGATAATTTGT-GTTGAGA
1 TTTATAAACATTTATTGGATAATTTGTGGTT-AGA
1334 TTTAT
1 TTTAT
1339 CGGATAATCC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
33 3 0.08
34 33 0.92
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.52
Consensus pattern (34 bp):
TTTATAAACATTTATTGGATAATTTGTGGTTAGA
Found at i:1611 original size:17 final size:17
Alignment explanation
Indices: 1576--1613 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1566 AAAATATTTC
*
1576 TTTAATTAAATAATATT
1 TTTAATTAAAGAATATT
*
1593 TTTAATTAAAG-ATTTT
1 TTTAATTAAAGAATATT
1609 TTTAA
1 TTTAA
1614 AAAAATATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
TTTAATTAAAGAATATT
Found at i:1612 original size:16 final size:17
Alignment explanation
Indices: 1567--1613 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 17
1557 TTTTAGAAAA
*
1567 AAAT-ATTTCTTTAATT
1 AAATAATTTTTTTAATT
*
1583 AAATAATATTTTTAATT
1 AAATAATTTTTTTAATT
*
1600 AAA-GATTTTTTTAA
1 AAATAATTTTTTTAA
1614 AAAAATATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
16 13 0.50
17 13 0.50
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
AAATAATTTTTTTAATT
Found at i:4051 original size:23 final size:21
Alignment explanation
Indices: 4023--4070 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
4013 ATATTTATTA
4023 AAAATAATATAATTATAAATTTT
1 AAAATAA-ATAA-TATAAATTTT
* *
4046 AAAATAAATTATATATATTTT
1 AAAATAAATAATATAAATTTT
4067 AAAA
1 AAAA
4071 ATACTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 13 0.57
22 3 0.13
23 7 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAAATAAATAATATAAATTTT
Found at i:4057 original size:19 final size:22
Alignment explanation
Indices: 4028--4070 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
4018 TATTAAAAAT
4028 AATATAATTATA-A-ATTTTAA
1 AATATAATTATATATATTTTAA
4048 AATA-AATTATATATATTTTAA
1 AATATAATTATATATATTTTAA
4069 AA
1 AA
4071 ATACTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 7 0.33
20 5 0.24
21 9 0.43
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AATATAATTATATATATTTTAA
Found at i:20747 original size:20 final size:21
Alignment explanation
Indices: 20724--20767 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
20714 TATTATATGT
**
20724 ATATTTATGAATAT-ATAAAA
1 ATATTTAACAATATAATAAAA
20744 ATATTTAACAATATAATAAAA
1 ATATTTAACAATATAATAAAA
20765 ATA
1 ATA
20768 AAAATATCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 12 0.57
21 9 0.43
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
ATATTTAACAATATAATAAAA
Found at i:22172 original size:3 final size:3
Alignment explanation
Indices: 22166--22257 Score: 130
Period size: 3 Copynumber: 30.7 Consensus size: 3
22156 TTAATATATT
* *
22166 TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* ** *
22214 TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
22258 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 77 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:22264 original size:27 final size:27
Alignment explanation
Indices: 22166--22256 Score: 164
Period size: 27 Copynumber: 3.4 Consensus size: 27
22156 TTAATATATT
*
22166 TAATAATAATGATAATAATAATAATAA
1 TAATAATAATGATAATAATAATATTAA
22193 TAATAATAATGATAATAATAATATTAA
1 TAATAATAATGATAATAATAATATTAA
*
22220 TAATAATAAGGATAATAATAATATTAA
1 TAATAATAATGATAATAATAATATTAA
22247 TAATAATAAT
1 TAATAATAAT
22257 ATGGATAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (27 bp):
TAATAATAATGATAATAATAATATTAA
Found at i:22708 original size:113 final size:114
Alignment explanation
Indices: 22510--23275 Score: 1215
Period size: 113 Copynumber: 6.8 Consensus size: 114
22500 TCTTGATGAG
*
22510 TTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
22574 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
22623 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
* * *
22687 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
66 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
22736 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTAC-C
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTT-CTC
* * *
22799 TGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 TGGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
22849 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
* * * *
22913 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
22962 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
* * * * *
23026 GGAAAAGCTGTTCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
23075 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA-CTTTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
* * * *
23139 GGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
23188 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACC-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
** * * *
23252 TCAAAAAATAATCCATCAATTGAT
66 GGAAAAGATGATCCATCAAATGAT
23276 AGATTTGAAT
Statistics
Matches: 619, Mismatches: 28, Indels: 12
0.94 0.04 0.02
Matches are distributed among these distances:
112 5 0.01
113 608 0.98
114 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTTCTCT
GGAAAAGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:24223 original size:81 final size:82
Alignment explanation
Indices: 23899--24403 Score: 874
Period size: 82 Copynumber: 6.2 Consensus size: 82
23889 TACTATGAGC
* *
23899 AAATTCATCTTCCAAATTCAATGATTGTTCTG-TCCAACCAGATCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCT-AAACCAGGTCAGATAACTCAAAGAACACTT
*
23963 CCAGAAGATGCTATTGGC
65 CCAGAAGATGCTATTGGT
*
23981 AAATTCATCTTCTAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
24046 CAGAAGATGCTATTGGT
66 CAGAAGATGCTATTGGT
*
24063 AAATTCATCTTCCAAATTCAATGACTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
24128 CAGAAGATGCTATTGGT
66 CAGAAGATGCTATTGGT
24145 AAATTCATCTTCCAAATTCAATGA-TGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
1 AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
24209 CAGAAGATGCTATTGGT
66 CAGAAGATGCTATTGGT
*
24226 AAATTCATCTTCCAAATTCAATGATTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATT-GTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTT
24291 CCAGAAGATGCTATTGGT
65 CCAGAAGATGCTATTGGT
* * *
24309 AAATTCATCTTCC--ATTTAATGTTTGGTTCTGTTAAACCAGGTCAGATAACTCAAAGAACACTT
1 AAATTCATCTTCCAAATTCAATGATT-GTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTT
24372 CCAGAAGATGCTATTGGT
65 CCAGAAGATGCTATTGGT
24390 AAATTCATCTTCCA
1 AAATTCATCTTCCA
24404 TTTAATGTTT
Statistics
Matches: 410, Mismatches: 9, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
81 160 0.39
82 181 0.44
83 69 0.17
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (82 bp):
AAATTCATCTTCCAAATTCAATGATTGTTCTGCTAAACCAGGTCAGATAACTCAAAGAACACTTC
CAGAAGATGCTATTGGT
Found at i:25547 original size:9 final size:8
Alignment explanation
Indices: 25529--25605 Score: 66
Period size: 8 Copynumber: 9.0 Consensus size: 8
25519 CTTGACCCCC
25529 TTTTTCTT
1 TTTTTCTT
*
25537 TTTTCCTT
1 TTTTTCTT
25545 TTTTTCTT
1 TTTTTCTT
*
25553 TTTTTTTT
1 TTTTTCTT
25561 CTTTTTCATT
1 -TTTTTC-TT
*
25571 TTCTAT-TT
1 TT-TTTCTT
25579 TTTTTCTTT
1 TTTTTC-TT
25588 TTTCTTCTT
1 TTT-TTCTT
25597 TTTTCTCTT
1 TTTT-TCTT
25606 CAAGCATAAT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
7 2 0.04
8 26 0.46
9 21 0.38
10 7 0.12
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.82
Consensus pattern (8 bp):
TTTTTCTT
Found at i:25557 original size:11 final size:11
Alignment explanation
Indices: 25543--25600 Score: 73
Period size: 11 Copynumber: 5.3 Consensus size: 11
25533 TCTTTTTTCC
25543 TTTTTTTCTTT
1 TTTTTTTCTTT
25554 TTTTTTTCTTT
1 TTTTTTTCTTT
* *
25565 TTCATTTTCTAT
1 TT-TTTTTCTTT
25577 TTTTTTTC-TT
1 TTTTTTTCTTT
*
25587 TTTTCTTCTTT
1 TTTTTTTCTTT
25598 TTT
1 TTT
25601 CTCTTCAAGC
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
10 8 0.20
11 23 0.57
12 9 0.22
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:25565 original size:33 final size:33
Alignment explanation
Indices: 25528--25599 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
25518 CCTTGACCCC
* * *
25528 CTTTTTC-TTTTTTCCTTTTTTTCTTTTTTTTTT
1 CTTTTTCATTTTCTACTTTTTTTC-TTTTTTCTT
*
25561 CTTTTTCATTTTCTATTTTTTTTCTTTTTTCTT
1 CTTTTTCATTTTCTACTTTTTTTCTTTTTTCTT
25594 CTTTTT
1 CTTTTT
25600 TCTCTTCAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 21 0.62
34 13 0.38
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (33 bp):
CTTTTTCATTTTCTACTTTTTTTCTTTTTTCTT
Found at i:25602 original size:7 final size:7
Alignment explanation
Indices: 25529--25598 Score: 56
Period size: 6 Copynumber: 9.7 Consensus size: 7
25519 CTTGACCCCC
25529 TTTTTCT
1 TTTTTCT
25536 TTTTTCCT
1 TTTTT-CT
25544 TTTTT-T
1 TTTTTCT
*
25550 CTTTT-T
1 TTTTTCT
25556 TTTTTC-
1 TTTTTCT
25562 TTTTTCAT
1 TTTTTC-T
*
25570 TTTCTATTT
1 TTT-T-TCT
25579 TTTTTCT
1 TTTTTCT
25586 TTTTTCT
1 TTTTTCT
25593 TCTTTT
1 T-TTTT
25599 TTCTCTTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 13
0.75 0.06 0.19
Matches are distributed among these distances:
6 16 0.31
7 15 0.29
8 15 0.29
9 5 0.10
10 1 0.02
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (7 bp):
TTTTTCT
Done.