Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000472.1 Hibiscus syriacus cultivar Beakdansim tig00000879_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: 67540
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:2101 original size:27 final size:28
Alignment explanation
Indices: 2049--2102 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
2039 GTTTTGATAA
*
2049 TTTAAAATTTTTTATTTAATAAAACAAC
1 TTTAAAATATTTTATTTAATAAAACAAC
*
2077 TTTAAAATATTTT-TTTATTAAAACAA
1 TTTAAAATATTTTATTTAATAAAACAA
2103 AGCCCAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTAAAATATTTTATTTAATAAAACAAC
Found at i:4646 original size:39 final size:39
Alignment explanation
Indices: 4595--4698 Score: 140
Period size: 39 Copynumber: 2.7 Consensus size: 39
4585 TGCTCATCGA
* *
4595 CTTTGTGCTCAGGGTAAGTCCTTACC-TCAGACTCCTCGG
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAAG-CTCCTCAG
* *
4634 CTTTGTGATCAGGGTAAGTCCTTACCGTAAGCTCCTTAG
1 CTTTGTGCTCAGGGTAAGTCCTTACCGTAAGCTCCTCAG
*
4673 CTTTGTTCTCAGGGTAA-TCCTTACCG
1 CTTTGTGCTCAGGGTAAGTCCTTACCG
4699 CATGTCCTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
38 9 0.16
39 46 0.79
40 3 0.05
ACGTcount: A:0.17, C:0.27, G:0.22, T:0.34
Consensus pattern (39 bp):
CTTTGTGCTCAGGGTAAGTCCTTACCGTAAGCTCCTCAG
Found at i:10131 original size:21 final size:21
Alignment explanation
Indices: 10076--10197 Score: 79
Period size: 21 Copynumber: 5.7 Consensus size: 21
10066 GTTCTTCGGG
*
10076 ATATATGTGATC-TTTCGGAAC
1 ATATATGTGGTCATTT-GGAAC
* **
10097 ATATATGCT-ATCATTTTTAAC
1 ATATATG-TGGTCATTTGGAAC
* *
10118 ATATATTTGGTCATTTGGCAC
1 ATATATGTGGTCATTTGGAAC
*
10139 ATATATGTGGTCATACTGGATA-
1 ATATATGTGGTCAT-TTGGA-AC
* ** *
10161 ATTCTATGTGGTCATACGGGAC
1 A-TATATGTGGTCATTTGGAAC
10183 ATATATGTGGTCATT
1 ATATATGTGGTCATT
10198 CGGGACATTT
Statistics
Matches: 78, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
20 1 0.01
21 53 0.68
22 11 0.14
23 13 0.17
ACGTcount: A:0.28, C:0.13, G:0.19, T:0.40
Consensus pattern (21 bp):
ATATATGTGGTCATTTGGAAC
Found at i:10201 original size:21 final size:21
Alignment explanation
Indices: 10116--10205 Score: 90
Period size: 21 Copynumber: 4.2 Consensus size: 21
10106 ATCATTTTTA
* ** *
10116 ACATATATTTGGTCATTTGGC
1 ACATATATGTGGTCATACGGG
*
10137 ACATATATGTGGTCATACTGG
1 ACATATATGTGGTCATACGGG
* *
10158 ATAATTCTATGTGGTCATACGGG
1 A-CA-TATATGTGGTCATACGGG
*
10181 ACATATATGTGGTCATTCGGG
1 ACATATATGTGGTCATACGGG
10202 ACAT
1 ACAT
10206 TTTGTATGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
21 37 0.66
22 2 0.04
23 17 0.30
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (21 bp):
ACATATATGTGGTCATACGGG
Found at i:16266 original size:19 final size:19
Alignment explanation
Indices: 16242--16288 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
16232 CAGAAAAGGG
16242 TATCGATACTCAAGTACAA
1 TATCGATACTCAAGTACAA
16261 TATCGATACTCAAGTACAA
1 TATCGATACTCAAGTACAA
*
16280 TATCAATAC
1 TATCGATAC
16289 CATCGTAAAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.43, C:0.21, G:0.09, T:0.28
Consensus pattern (19 bp):
TATCGATACTCAAGTACAA
Found at i:16924 original size:21 final size:21
Alignment explanation
Indices: 16894--17037 Score: 103
Period size: 21 Copynumber: 6.8 Consensus size: 21
16884 AGGGTTCTAC
16894 GTGGTCCTTCGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
* *
16915 GTGATCCTTCGGAACATATAT
1 GTGGTCCTTCGGGACATATAT
*** **
16936 GCAATCCTTTTTGGACATATAT
1 GTGGTCC-TTCGGGACATATAT
* * *
16958 TTGGTCCTT-TGGA-AAATAT
1 GTGGTCCTTCGGGACATATAT
* * * *
16977 ATGGTCATACGGGACAATTCTAT
1 GTGGTCCTTCGGGAC-A-TATAT
*
17000 GTGGTCCTACGGGACATATAT
1 GTGGTCCTTCGGGACATATAT
*
17021 GTGGTCATTCGGGACAT
1 GTGGTCCTTCGGGACAT
17038 TTTTTATGGC
Statistics
Matches: 95, Mismatches: 23, Indels: 10
0.74 0.18 0.08
Matches are distributed among these distances:
19 11 0.12
20 7 0.07
21 45 0.47
22 16 0.17
23 16 0.17
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
GTGGTCCTTCGGGACATATAT
Found at i:20014 original size:18 final size:18
Alignment explanation
Indices: 19970--20033 Score: 67
Period size: 18 Copynumber: 3.6 Consensus size: 18
19960 CTGAACCGGT
*
19970 CAACCGTTGATCGTTAAT
1 CAACCGTTGATCGTTAAC
* * *
19988 CGACTGTTGACCGTTAAC
1 CAACCGTTGATCGTTAAC
*
20006 CAACCGTTGATCGTTGAC
1 CAACCGTTGATCGTTAAC
*
20024 CGA-CGTTGAT
1 CAACCGTTGAT
20034 TTTTTTCGAA
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
17 7 0.19
18 30 0.81
ACGTcount: A:0.23, C:0.25, G:0.22, T:0.30
Consensus pattern (18 bp):
CAACCGTTGATCGTTAAC
Found at i:24131 original size:34 final size:34
Alignment explanation
Indices: 24091--24310 Score: 247
Period size: 34 Copynumber: 6.6 Consensus size: 34
24081 GGATTTTGCA
*
24091 TCTCTTTTGCACTGTGTACTTATATGATTGTGTT
1 TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
** *
24125 TCTCTTTAACACTGTGTACTTATACGCTTGTGTT
1 TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
*
24159 TCTCTTTTGCACTGTGTACTTATATGATTGTGTT
1 TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
*
24193 TCTCTTTTGCACTGTGTACTTATACGCTTGTGTT
1 TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
* **
24227 TCTCTTTTGTAC--TGTA-TGTATACGA-T-TGCA
1 TCTCTTTTGCACTGTGTACT-TATACGATTGTGTT
* * ** **
24257 TCTCTCTTGCACTGTGTGCTTATACG--CCTGCA
1 TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
24289 TCTCTTTTGCACTGTGTACTTA
1 TCTCTTTTGCACTGTGTACTTA
24311 AACGGTTGCA
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
30 12 0.07
31 2 0.01
32 43 0.27
33 1 0.01
34 103 0.64
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (34 bp):
TCTCTTTTGCACTGTGTACTTATACGATTGTGTT
Found at i:24163 original size:68 final size:68
Alignment explanation
Indices: 24091--24241 Score: 275
Period size: 68 Copynumber: 2.2 Consensus size: 68
24081 GGATTTTGCA
24091 TCTCTTTTGCACTGTGTACTTATATGATTGTGTTTCTCTTTAACACTGTGTACTTATACGCTTGT
1 TCTCTTTTGCACTGTGTACTTATATGATTGTGTTTCTCTTTAACACTGTGTACTTATACGCTTGT
24156 GTT
66 GTT
**
24159 TCTCTTTTGCACTGTGTACTTATATGATTGTGTTTCTCTTTTGCACTGTGTACTTATACGCTTGT
1 TCTCTTTTGCACTGTGTACTTATATGATTGTGTTTCTCTTTAACACTGTGTACTTATACGCTTGT
24224 GTT
66 GTT
*
24227 TCTCTTTTGTACTGT
1 TCTCTTTTGCACTGT
24242 ATGTATACGA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
68 80 1.00
ACGTcount: A:0.14, C:0.18, G:0.17, T:0.52
Consensus pattern (68 bp):
TCTCTTTTGCACTGTGTACTTATATGATTGTGTTTCTCTTTAACACTGTGTACTTATACGCTTGT
GTT
Found at i:24271 original size:30 final size:31
Alignment explanation
Indices: 24227--24303 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
24217 CGCTTGTGTT
* *
24227 TCTCTTTTGTACTGTATG-TATACGATTGCA
1 TCTCTTTTGCACTGTATGCTATACGACTGCA
* * *
24257 TCTCTCTTGCACTGTGTGCTTATACGCCTGCA
1 TCTCTTTTGCACTGTATGC-TATACGACTGCA
24289 TCTCTTTTGCACTGT
1 TCTCTTTTGCACTGT
24304 GTACTTAAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
30 15 0.38
32 24 0.62
ACGTcount: A:0.14, C:0.25, G:0.17, T:0.44
Consensus pattern (31 bp):
TCTCTTTTGCACTGTATGCTATACGACTGCA
Found at i:30589 original size:2 final size:2
Alignment explanation
Indices: 30582--30616 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
30572 TGTTTTGGCT
30582 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30617 TAAGCAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:32413 original size:14 final size:14
Alignment explanation
Indices: 32394--32429 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
32384 TCTGATGACC
32394 ATTGCTTCACTTCA
1 ATTGCTTCACTTCA
32408 ATTGCTTCACTTCA
1 ATTGCTTCACTTCA
32422 ATTGCTTC
1 ATTGCTTC
32430 GTTGTTTACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.19, C:0.28, G:0.08, T:0.44
Consensus pattern (14 bp):
ATTGCTTCACTTCA
Found at i:41516 original size:22 final size:21
Alignment explanation
Indices: 41456--41519 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
41446 AGTCGAGGGT
41456 TTCATAGGTCCTTCGGGACAA
1 TTCATAGGTCCTTCGGGACAA
* *
41477 CTCATAGGTTCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACA-A
* *
41499 TTCACAGGTCCTTTGGGACAA
1 TTCATAGGTCCTTCGGGACAA
41520 AATTTCATAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.23, C:0.23, G:0.23, T:0.30
Consensus pattern (21 bp):
TTCATAGGTCCTTCGGGACAA
Found at i:42039 original size:11 final size:11
Alignment explanation
Indices: 42020--42054 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
42010 TTTTTACGGA
*
42020 AGTATTGTAGC
1 AGTACTGTAGC
42031 AGTACTGTAGC
1 AGTACTGTAGC
42042 AGTACTGTAGC
1 AGTACTGTAGC
42053 AG
1 AG
42055 GGGAATCGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.29
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:42071 original size:22 final size:22
Alignment explanation
Indices: 42046--42091 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
42036 TGTAGCAGTA
*
42046 CTGTAGCAGGGGAATCGGTTCC
1 CTGTAGCAGGGGAATCGATTCC
42068 CTGTAGCAGGGGAATCGATTCC
1 CTGTAGCAGGGGAATCGATTCC
42090 CT
1 CT
42092 ATTTGTAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.20, C:0.24, G:0.33, T:0.24
Consensus pattern (22 bp):
CTGTAGCAGGGGAATCGATTCC
Found at i:42509 original size:24 final size:24
Alignment explanation
Indices: 42475--42523 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
42465 CTGGTATGGT
42475 AATGAGTATGTTAATTTGCTAATAG
1 AATGAGTATGTTAATTT-CTAATAG
* *
42500 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATGTTAATTTCTAATAG
42523 A
1 A
42524 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 7 0.32
24 10 0.45
25 5 0.23
ACGTcount: A:0.37, C:0.02, G:0.16, T:0.45
Consensus pattern (24 bp):
AATGAGTATGTTAATTTCTAATAG
Found at i:47711 original size:22 final size:22
Alignment explanation
Indices: 47674--47733 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 22
47664 ACCCCTATGA
47674 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCTTT-AAG
*
47697 GGGAACCAATTCCCCCTTTAAG
1 GGGAACCGATTCCCCCTTTAAG
47719 GGGAA-CGATTCCCCC
1 GGGAACCGATTCCCCC
47734 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.26
22 8 0.23
23 18 0.51
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.20
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTTAAG
Found at i:49761 original size:17 final size:17
Alignment explanation
Indices: 49728--49761 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
49718 TTGAATATTT
* *
49728 TGGATTGTTTGATTTTG
1 TGGATTGTTAGACTTTG
49745 TGGATTGTTAGACTTTG
1 TGGATTGTTAGACTTTG
49762 GATTTGTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.03, G:0.29, T:0.53
Consensus pattern (17 bp):
TGGATTGTTAGACTTTG
Found at i:63851 original size:10 final size:10
Alignment explanation
Indices: 63830--63858 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
63820 TTATGACTCG
63830 TTTTAA-TTT
1 TTTTAATTTT
63839 TTTTAATTTT
1 TTTTAATTTT
63849 TTTTAATTTT
1 TTTTAATTTT
63859 AATTATTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTAATTTT
Found at i:63858 original size:16 final size:16
Alignment explanation
Indices: 63839--63873 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
63829 GTTTTAATTT
* *
63839 TTTTAATTTTTTTTAA
1 TTTTAATTATTTTAAA
63855 TTTTAATTATTTTAAA
1 TTTTAATTATTTTAAA
63871 TTT
1 TTT
63874 ATGACTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTAATTATTTTAAA
Done.