Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005338.1 Hibiscus syriacus cultivar Beakdansim tig00012090_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: 58067
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:3260 original size:20 final size:21
Alignment explanation
Indices: 3231--3286 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
3221 TTTGTGCTTC
*
3231 ATGCACCGATGCAT-TT-AACA
1 ATGCATCGATGCATCTTGAA-A
*
3251 ATGCATCGATGCATCCTTGAAT
1 ATGCATCGATGCAT-CTTGAAA
3273 ATGCATCGATGCAT
1 ATGCATCGATGCAT
3287 AAGACCATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 13 0.42
22 16 0.52
23 2 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGCATCGATGCATCTTGAAA
Found at i:4857 original size:21 final size:21
Alignment explanation
Indices: 4815--4858 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4805 ACCCCGGGAG
*
4815 CTAGTTCTTCACGAGCTGCTC
1 CTAGTTCTTCACGAGCTCCTC
* *
4836 CTAGTTCTTCTCGTGCTCCTC
1 CTAGTTCTTCACGAGCTCCTC
4857 CT
1 CT
4859 CCTCCTCCAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.36, G:0.16, T:0.39
Consensus pattern (21 bp):
CTAGTTCTTCACGAGCTCCTC
Found at i:5911 original size:19 final size:19
Alignment explanation
Indices: 5887--5925 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
5877 TCGAATGCAT
*
5887 TCCATGCACCGATGCACTC
1 TCCATGCACCAATGCACTC
*
5906 TCCATGCATCAATGCACTC
1 TCCATGCACCAATGCACTC
5925 T
1 T
5926 GAATATTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.13, T:0.26
Consensus pattern (19 bp):
TCCATGCACCAATGCACTC
Found at i:6025 original size:64 final size:65
Alignment explanation
Indices: 5873--6033 Score: 209
Period size: 65 Copynumber: 2.5 Consensus size: 65
5863 GAATTAATTG
* * *** *
5873 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCAATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCAATGCACTCAGAATATTTTCAA
* * **
5938 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCA-TCAGGCTATTTTTC-
1 AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCAATGCACTCAGAATA-TTTTCA
6001 A
65 A
6002 AACATCGAATGCATTTCATGCATCGATGCACA
1 AACATCGAATGCATTTCATGCATCGATGCACA
6034 CTTGGTGCAC
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
64 37 0.44
65 47 0.56
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCATTTCATGCATCGATGCACAAGCCATGCATCAATGCACTCAGAATATTTTCAA
Found at i:6048 original size:64 final size:64
Alignment explanation
Indices: 5873--6053 Score: 211
Period size: 64 Copynumber: 2.8 Consensus size: 64
5863 GAATTAATTG
* * * * *
5873 AACATCGAATGCATTCCATGCACCGATGCACTCTCCATGCATCAATGCACTCTGAATATTTTCAA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCA-TCAGAATATTTTCAA
* ** **
5938 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCATCAGGCTATTTTTC-A
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATA-TTTTCAA
*** *
6002 AACATCGAATGCATTTCATGCATCGATGCACACTTGGTGCACCGATGCATCA
1 AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCA
6054 AGTGTTCCAA
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 51 0.52
65 47 0.48
ACGTcount: A:0.30, C:0.27, G:0.17, T:0.27
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACACTCCATGCATCGATGCATCAGAATATTTTCAA
Found at i:12656 original size:2 final size:2
Alignment explanation
Indices: 12651--12698 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
12641 AATTACCGAG
12651 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
12693 TA TA TA
1 TA TA TA
12699 AATAAGTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13739 original size:33 final size:34
Alignment explanation
Indices: 13672--13740 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
13662 CCTAATTTTT
*
13672 CAATTCGTTCGAGTGCCACTAAAATTTTCGGAAA
1 CAATTCGTTCAAGTGCCACTAAAATTTTCGGAAA
13706 CAATTCGTTCAAGTGCCACTAAAA-TTTCGGAAA
1 CAATTCGTTCAAGTGCCACTAAAATTTTCGGAAA
13739 CA
1 CA
13741 GGCCTGATGG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 11 0.32
34 23 0.68
ACGTcount: A:0.35, C:0.22, G:0.16, T:0.28
Consensus pattern (34 bp):
CAATTCGTTCAAGTGCCACTAAAATTTTCGGAAA
Found at i:16474 original size:2 final size:2
Alignment explanation
Indices: 16467--16493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16457 CCTTGAAAGA
16467 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16494 CTTGTCAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:24286 original size:17 final size:18
Alignment explanation
Indices: 24249--24289 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
24239 ATATTGTGTA
*
24249 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
24267 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
24284 TTTACT
1 TTTACT
24290 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:26631 original size:35 final size:34
Alignment explanation
Indices: 26591--26677 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 34
26581 GTATTTCAGT
26591 TAATTTTGTT-T-TTTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTTACCATTTAATA-C--TTATTG
*
26626 TAATTTGGTTATCATTTACCATTTAATACTTATTG
1 TAATTTTGTTAT-ATTTACCATTTAATACTTATTG
* *
26661 TAAGTTTGTTGTATTTA
1 TAATTTTGTTATATTTA
26678 AAATTATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 24 0.53
36 1 0.02
37 1 0.02
38 14 0.31
ACGTcount: A:0.26, C:0.08, G:0.10, T:0.55
Consensus pattern (34 bp):
TAATTTTGTTATATTTACCATTTAATACTTATTG
Found at i:27960 original size:6 final size:6
Alignment explanation
Indices: 27951--27976 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
27941 CTTCGACAAG
27951 AGCAAA AGCAAA AGCAAA AGCAAA AG
1 AGCAAA AGCAAA AGCAAA AGCAAA AG
27977 TAACTGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.65, C:0.15, G:0.19, T:0.00
Consensus pattern (6 bp):
AGCAAA
Found at i:30548 original size:3 final size:3
Alignment explanation
Indices: 30542--30587 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
30532 AAAAATATAA
*
30542 TAT TAT TAT TCT TAT TAT TA- TAT TAT TAT TAT TATT TAT T-T TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT
30586 TA
1 TA
30588 CAACTTTTGC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 4 0.11
3 31 0.82
4 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30567 original size:17 final size:16
Alignment explanation
Indices: 30544--30587 Score: 63
Period size: 17 Copynumber: 2.8 Consensus size: 16
30534 AAATATAATA
*
30544 TTATTATTCTTATTAT
1 TTATTATTATTATTAT
30560 TATATTATTATTATTAT
1 T-TATTATTATTATTAT
30577 TTATT-TTATTA
1 TTATTATTATTA
30588 CAACTTTTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
15 6 0.23
16 5 0.19
17 15 0.58
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTATTATTATTAT
Found at i:31363 original size:16 final size:16
Alignment explanation
Indices: 31342--31381 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
31332 TCTCTTATGC
*
31342 AAATGAATAAATGAGA
1 AAATGAAGAAATGAGA
31358 AAATGAAGAAATGAGA
1 AAATGAAGAAATGAGA
31374 AAATGAAG
1 AAATGAAG
31382 GAGAAATAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (16 bp):
AAATGAAGAAATGAGA
Found at i:31749 original size:39 final size:37
Alignment explanation
Indices: 31650--31749 Score: 96
Period size: 39 Copynumber: 2.6 Consensus size: 37
31640 TTTTCCTTTA
* *
31650 TTTATTTTATTTAATCTAATA-TATTTATATATTTTTT
1 TTTA-TTTATTTAATTTAATATTATTTATATATTATTT
** *
31687 TATTATTT-TTTCCTGTTATTATTATTATATATATGTATTT
1 T-TTATTTATTTAAT-TTAATATTATT-TATATAT-TATTT
31727 TTTATTTATTTAATTTAATATTA
1 TTTATTTATTTAATTTAATATTA
31750 ATATTTATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
36 4 0.08
37 8 0.16
38 7 0.14
39 21 0.43
40 9 0.18
ACGTcount: A:0.29, C:0.03, G:0.02, T:0.66
Consensus pattern (37 bp):
TTTATTTATTTAATTTAATATTATTTATATATTATTT
Found at i:31763 original size:43 final size:40
Alignment explanation
Indices: 31646--31773 Score: 104
Period size: 45 Copynumber: 3.1 Consensus size: 40
31636 CTTTTTTTCC
*
31646 TTTATTTATTTTATTTAATCTAATA--TATTTATATATTTT
1 TTTATTTA-TTTATTTAATTTAATATTTATTTATATATTTT
** *
31685 TTTA-TTATTT-TTTCCTGTTATTA-TTATTATATATATGTATTT
1 TTTATTTATTTATTTAAT-TTAATATTTATT-TATATA--T-TTT
*
31727 TTTATTTATTTAATTTAATATTAATATTTATTTATATATGTT
1 TTTATTTATTT-ATTTAAT-TTAATATTTATTTATATATTTT
31769 TTTAT
1 TTTAT
31774 GTTTATTTCT
Statistics
Matches: 70, Mismatches: 9, Indels: 17
0.73 0.09 0.18
Matches are distributed among these distances:
36 4 0.06
37 7 0.10
38 7 0.10
39 10 0.14
41 1 0.01
42 14 0.20
43 7 0.10
45 15 0.21
46 5 0.07
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (40 bp):
TTTATTTATTTATTTAATTTAATATTTATTTATATATTTT
Found at i:31924 original size:17 final size:17
Alignment explanation
Indices: 31891--31943 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
31881 TGGTTATGGC
*
31891 TCAACTTTTT-TCATTTT
1 TCAACTTTTTCT-TTTTT
31908 TCAACTTTTTCTTTTTT
1 TCAACTTTTTCTTTTTT
**
31925 TCAACCTTTGACTTTTTT
1 TCAA-CTTTTTCTTTTTT
31943 T
1 T
31944 TCTTTTGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.15, C:0.19, G:0.02, T:0.64
Consensus pattern (17 bp):
TCAACTTTTTCTTTTTT
Found at i:35096 original size:24 final size:24
Alignment explanation
Indices: 35069--35124 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
35059 TGAACATTCG
*
35069 GTTATGTTCGTTTATATGCGTTTA
1 GTTATGTTCGTTTATATGCGTTCA
*
35093 GTTATGTTCGTTTATGTGCGTTCA
1 GTTATGTTCGTTTATATGCGTTCA
*
35117 TTTATGTT
1 GTTATGTT
35125 TAACCTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.14, C:0.09, G:0.21, T:0.55
Consensus pattern (24 bp):
GTTATGTTCGTTTATATGCGTTCA
Found at i:35388 original size:33 final size:33
Alignment explanation
Indices: 35346--35435 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
35336 ATTTTCATTT
*
35346 CTGCAACGATTCGACGGGGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
*
35379 CTGCAACGATTTGACGGAGCTTCAAGTCTTCAA
1 CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
* *
35412 CTGCAACAATTCGACAGAGCTTCA
1 CTGCAACGATTCGACGGAGCTTCA
35436 TCTCTTTCCC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (33 bp):
CTGCAACGATTCGACGGAGCTTCAAGTCTTCAA
Found at i:36673 original size:10 final size:10
Alignment explanation
Indices: 36658--36732 Score: 52
Period size: 10 Copynumber: 7.7 Consensus size: 10
36648 GGGTCTCTAA
36658 CGTTTATGTT
1 CGTTTATGTT
36668 CGTTTATGTT
1 CGTTTATGTT
36678 CG----TGTT
1 CGTTTATGTT
*
36684 CATTTATGTT
1 CGTTTATGTT
*
36694 CGTGTT-CGTTT
1 CGT-TTATG-TT
* *
36705 ATGTTTGTGTT
1 -CGTTTATGTT
36716 CGTTTATGTT
1 CGTTTATGTT
36726 CGTTTAT
1 CGTTTAT
36733 TTATTAAATG
Statistics
Matches: 50, Mismatches: 7, Indels: 16
0.68 0.10 0.22
Matches are distributed among these distances:
6 5 0.10
10 34 0.68
11 8 0.16
12 3 0.06
ACGTcount: A:0.09, C:0.11, G:0.21, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:36689 original size:16 final size:16
Alignment explanation
Indices: 36664--36728 Score: 112
Period size: 16 Copynumber: 4.1 Consensus size: 16
36654 CTAACGTTTA
36664 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
36680 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
*
36696 TGTTCGTTTATGTTTG
1 TGTTCGTTTATGTTCG
36712 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
36728 T
1 T
36729 TTATTTATTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 45 1.00
ACGTcount: A:0.08, C:0.11, G:0.23, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:36824 original size:15 final size:16
Alignment explanation
Indices: 36797--36827 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
36787 AAAAAAAGTT
36797 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
36813 TGTTCG-TTATGTTCG
1 TGTTCGTTTATGTTCG
36828 CTTATTTATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:39961 original size:31 final size:31
Alignment explanation
Indices: 39915--40070 Score: 258
Period size: 31 Copynumber: 5.0 Consensus size: 31
39905 AGGGTCGAGG
* *
39915 GTTTACCTATGTTCTTTGGGACATATGGGCT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
39946 GTTTGCCTATATTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
39977 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
40008 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
40039 GTTTACCTATGTTCTTCGGGATATATAGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
40070 G
1 G
40071 GTCCTTCGGG
Statistics
Matches: 117, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 117 1.00
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:40533 original size:27 final size:27
Alignment explanation
Indices: 40495--40554 Score: 120
Period size: 27 Copynumber: 2.2 Consensus size: 27
40485 CAGATCAGAA
40495 AAGAAATGTATAGTATGTATTTGTAAT
1 AAGAAATGTATAGTATGTATTTGTAAT
40522 AAGAAATGTATAGTATGTATTTGTAAT
1 AAGAAATGTATAGTATGTATTTGTAAT
40549 AAGAAA
1 AAGAAA
40555 AGTGGTTGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.18, T:0.37
Consensus pattern (27 bp):
AAGAAATGTATAGTATGTATTTGTAAT
Found at i:45189 original size:3 final size:3
Alignment explanation
Indices: 45137--45220 Score: 64
Period size: 3 Copynumber: 27.3 Consensus size: 3
45127 CAAATGAAAA
* * * * *
45137 ATT AAT ATT ATTT ATT AAT ATT AAT ATT TTT AATT ATT A-T ATAG ATTT
1 ATT ATT ATT A-TT ATT ATT ATT ATT ATT ATT -ATT ATT ATT AT-T A-TT
*
45185 ATT ATT ATT ATT ATT ATT ATT ATT A-T ATT ATA ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
45221 AGTATCTAAG
Statistics
Matches: 63, Mismatches: 12, Indels: 12
0.72 0.14 0.14
Matches are distributed among these distances:
2 4 0.06
3 51 0.81
4 7 0.11
5 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:55889 original size:26 final size:27
Alignment explanation
Indices: 55855--55908 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
55845 TTTTACAAAA
*
55855 TAATAATACTCAAAAGTAC-ATTTTTT
1 TAATAATACTCAAAAGTACTATTATTT
55881 TAATAATACTCAAAAGTACTATTATTT
1 TAATAATACTCAAAAGTACTATTATTT
55908 T
1 T
55909 CGAATTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 19 0.73
27 7 0.27
ACGTcount: A:0.43, C:0.11, G:0.04, T:0.43
Consensus pattern (27 bp):
TAATAATACTCAAAAGTACTATTATTT
Done.