Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008664.1 Hibiscus syriacus cultivar Beakdansim tig00111667_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: 53360
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6880 original size:10 final size:9
Alignment explanation
Indices: 6845--6943 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
6835 GCTGCTGGAA
*
6845 ACCGGTTTA
1 ACCGGTTTG
*
6854 ACCGGTTTTCA
1 ACCGG-TTT-G
6865 ACCGGTTCTG
1 ACCGGTT-TG
6875 ACCGGTTTG
1 ACCGGTTTG
*
6884 ACCGGTTTCA
1 ACCGGTTT-G
*
6894 ACCGGTTCG
1 ACCGGTTTG
6903 AACCGGTTTG
1 -ACCGGTTTG
*
6913 ACCGGTCTG
1 ACCGGTTTG
6922 ACTCGGTTTG
1 AC-CGGTTTG
*
6932 ACCGGTCTG
1 ACCGGTTTG
6941 ACC
1 ACC
6944 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:6889 original size:19 final size:19
Alignment explanation
Indices: 6846--6943 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
6836 CTGCTGGAAA
* * *
6846 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
6866 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
6885 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
6905 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
6923 CTCGGTTTGACCGG-TCTGA
1 C-CGGTTTGACCGGTTCTGA
6942 CC
1 CC
6944 CGACCCGACC
Statistics
Matches: 68, Mismatches: 4, Indels: 14
0.79 0.05 0.16
Matches are distributed among these distances:
18 6 0.09
19 39 0.57
20 15 0.22
21 8 0.12
ACGTcount: A:0.14, C:0.29, G:0.28, T:0.30
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:6907 original size:29 final size:30
Alignment explanation
Indices: 6844--6918 Score: 118
Period size: 29 Copynumber: 2.5 Consensus size: 30
6834 GGCTGCTGGA
*
6844 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
6875 -ACCGGTTTGACCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
6903 AACCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
6919 CTGACTCGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:6928 original size:29 final size:28
Alignment explanation
Indices: 6845--6943 Score: 101
Period size: 29 Copynumber: 3.4 Consensus size: 28
6835 GCTGCTGGAA
* *
6845 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TCTCAACCGGTTC-G
*
6875 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTCTCAACCGGTTCG
* *
6903 AACCGGTTTGACCGGTCT-GACTCGGTTTG
1 -ACCGGTTTGACCGGTCTCAAC-CGGTTCG
*
6932 ACCGGTCTGACC
1 ACCGGTTTGACC
6944 CGACCCGACC
Statistics
Matches: 62, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
28 14 0.23
29 35 0.56
30 13 0.21
ACGTcount: A:0.15, C:0.28, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTCTCAACCGGTTCG
Found at i:6950 original size:5 final size:5
Alignment explanation
Indices: 6940--6997 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
6930 TGACCGGTCT
* *
6940 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
6989 GACCC GACC
1 GACCC GACC
6998 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:6966 original size:22 final size:22
Alignment explanation
Indices: 6940--7004 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
6930 TGACCGGTCT
6940 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
6962 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
6984 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
7005 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:7006 original size:7 final size:7
Alignment explanation
Indices: 6994--7031 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
6984 GACCCGACCC
6994 GACCGTT
1 GACCGTT
7001 GACCGTT
1 GACCGTT
7008 GACCGTT
1 GACCGTT
7015 GACCGTT
1 GACCGTT
7022 GACCGTT
1 GACCGTT
7029 GAC
1 GAC
7032 TTTCTTTGAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:11445 original size:51 final size:51
Alignment explanation
Indices: 11374--11478 Score: 210
Period size: 51 Copynumber: 2.1 Consensus size: 51
11364 CATTCTTCTT
11374 TTGTTCACACTTTAGGTCATTTATTATTTCAAGAAAAACCTAGGTATTTTG
1 TTGTTCACACTTTAGGTCATTTATTATTTCAAGAAAAACCTAGGTATTTTG
11425 TTGTTCACACTTTAGGTCATTTATTATTTCAAGAAAAACCTAGGTATTTTG
1 TTGTTCACACTTTAGGTCATTTATTATTTCAAGAAAAACCTAGGTATTTTG
11476 TTG
1 TTG
11479 ACAATCTTCC
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.44
Consensus pattern (51 bp):
TTGTTCACACTTTAGGTCATTTATTATTTCAAGAAAAACCTAGGTATTTTG
Found at i:11652 original size:18 final size:18
Alignment explanation
Indices: 11629--11664 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
11619 GGGTGTGAAT
11629 TGTCTATGAAATGTAATG
1 TGTCTATGAAATGTAATG
11647 TGTCTATGAAATGTAATG
1 TGTCTATGAAATGTAATG
11665 GGTCGGGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.22, T:0.39
Consensus pattern (18 bp):
TGTCTATGAAATGTAATG
Found at i:17702 original size:20 final size:20
Alignment explanation
Indices: 17662--17704 Score: 61
Period size: 22 Copynumber: 2.1 Consensus size: 20
17652 TAATTTATTG
17662 AAATTTTAAAATATTTTAATT
1 AAATTTTAAAATA-TTTAATT
17683 AAATCTTTAAAATA-TTAATT
1 AAAT-TTTAAAATATTTAATT
17703 AA
1 AA
17705 TATTATGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.38
21 4 0.19
22 9 0.43
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTTAAAATATTTAATT
Found at i:21584 original size:29 final size:29
Alignment explanation
Indices: 21541--21623 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
21531 CTCACCTAAC
21541 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
21571 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
21600 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
21624 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:26352 original size:29 final size:29
Alignment explanation
Indices: 26309--26391 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
26299 CTCACCTAAC
26309 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
26339 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
26368 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
26392 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:33014 original size:12 final size:12
Alignment explanation
Indices: 32997--33021 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32987 GATTTTAAAA
32997 AATCAATCAACC
1 AATCAATCAACC
33009 AATCAATCAACC
1 AATCAATCAACC
33021 A
1 A
33022 GTACATGGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (12 bp):
AATCAATCAACC
Found at i:46207 original size:13 final size:13
Alignment explanation
Indices: 46189--46236 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
46179 AAATTAGTCC
46189 TGAATAATTTTTT
1 TGAATAATTTTTT
* **
46202 TGAATAAATTAGTCC
1 TGAAT-AATT-TTTT
46217 TGAATAATTTTTT
1 TGAATAATTTTTT
46230 TGAATAA
1 TGAATAA
46237 ATTAGTCCTT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
13 13 0.48
14 8 0.30
15 6 0.22
ACGTcount: A:0.38, C:0.04, G:0.10, T:0.48
Consensus pattern (13 bp):
TGAATAATTTTTT
Found at i:46209 original size:28 final size:28
Alignment explanation
Indices: 46173--46245 Score: 137
Period size: 28 Copynumber: 2.6 Consensus size: 28
46163 TAACAGGAAC
*
46173 TTGATTAAATTAGTCCTGAATAATTTTT
1 TTGAATAAATTAGTCCTGAATAATTTTT
46201 TTGAATAAATTAGTCCTGAATAATTTTT
1 TTGAATAAATTAGTCCTGAATAATTTTT
46229 TTGAATAAATTAGTCCT
1 TTGAATAAATTAGTCCT
46246 TAATTATTAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (28 bp):
TTGAATAAATTAGTCCTGAATAATTTTT
Found at i:49623 original size:227 final size:226
Alignment explanation
Indices: 49216--49661 Score: 777
Period size: 227 Copynumber: 2.0 Consensus size: 226
49206 TGTAAATATC
* * *
49216 TATCCTTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
* *
49281 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAACAATCAAATAATTTTTT
66 TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAACAATCAAATAATATTTT
*
49346 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAATTGA
131 GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
49411 AACATAAATTACATAACTTTCAAAAAAGTATA
196 AACATAAATTACATAACTTT-AAAAAAGTATA
*
49443 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
49508 TTAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAACAATCAAATAA-ATTT
65 TTAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAACAATCAAATAATATTT
* *
49572 TGTGTAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAATAAATTG
130 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTG
49637 AAACATAAATTACATAACTTTAAAA
195 AAACATAAATTACATAACTTTAAAA
49662 GCAGTTTTAA
Statistics
Matches: 208, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
226 4 0.02
227 122 0.59
228 82 0.39
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (226 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTATTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAACAATCAAATAATATTTT
GTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATAAAACACTATTAAAAAAATTGA
AACATAAATTACATAACTTTAAAAAAGTATA
Found at i:49757 original size:19 final size:20
Alignment explanation
Indices: 49726--49771 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
49716 CGATATACCA
49726 GGTAAAAATATGA-AAAACC
1 GGTAAAAATATGATAAAACC
49745 GGTAACAAA-ATGATAAAACC
1 GGTAA-AAATATGATAAAACC
49765 GGTAAAA
1 GGTAAAA
49772 TTAAAAGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.57, C:0.11, G:0.17, T:0.15
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Done.