Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002296.1 Hibiscus syriacus cultivar Beakdansim tig00004669_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: 48912
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Found at i:17031 original size:21 final size:21
Alignment explanation
Indices: 16993--17045 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 21
16983 TACTTTGATA
*
16993 TCATTTCTTTCCATTTC-ATT
1 TCATTTCTTTCAATTTCAATT
17013 TCATTTCTTATCAATTTCAATT
1 TCATTTCTT-TCAATTTCAATT
17035 TC-TTTCATTTC
1 TCATTTC-TTTC
17046 TTATTTCCAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.31
21 13 0.45
22 7 0.24
ACGTcount: A:0.19, C:0.23, G:0.00, T:0.58
Consensus pattern (21 bp):
TCATTTCTTTCAATTTCAATT
Found at i:20631 original size:10 final size:11
Alignment explanation
Indices: 20616--20665 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
20606 TTTTTTTTTC
20616 AAAAAAA-CCAA
1 AAAAAAAGCC-A
20627 AAAAAAAGGCACA
1 AAAAAAA-GC-CA
*
20640 AAAAAAAGGC-
1 AAAAAAAGCCA
20650 AAAAAAAGCCA
1 AAAAAAAGCCA
20661 AAAAA
1 AAAAA
20666 GCCAAAATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
10 9 0.27
11 13 0.39
12 1 0.03
13 9 0.27
14 1 0.03
ACGTcount: A:0.76, C:0.14, G:0.10, T:0.00
Consensus pattern (11 bp):
AAAAAAAGCCA
Found at i:20642 original size:13 final size:12
Alignment explanation
Indices: 20624--20656 Score: 57
Period size: 13 Copynumber: 2.7 Consensus size: 12
20614 TCAAAAAAAC
20624 CAAAAAAAAAGG
1 CAAAAAAAAAGG
20636 CACAAAAAAAAGG
1 CA-AAAAAAAAGG
20649 CAAAAAAA
1 CAAAAAAA
20657 GCCAAAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.76, C:0.12, G:0.12, T:0.00
Consensus pattern (12 bp):
CAAAAAAAAAGG
Found at i:26209 original size:19 final size:20
Alignment explanation
Indices: 26187--26226 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
26177 TAATTTAACA
26187 TAGGAT-GATTAATTATTTT
1 TAGGATAGATTAATTATTTT
*
26206 TAGGATCAGATTTATTATTTT
1 TAGGAT-AGATTAATTATTTT
26227 ATTAGGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 6 0.33
21 12 0.67
ACGTcount: A:0.30, C:0.03, G:0.15, T:0.53
Consensus pattern (20 bp):
TAGGATAGATTAATTATTTT
Found at i:26315 original size:42 final size:47
Alignment explanation
Indices: 26216--26315 Score: 117
Period size: 42 Copynumber: 2.3 Consensus size: 47
26206 TAGGATCAGA
*
26216 TTTATT-AT-TTTATTAGGAATTAAGGTTGGTTAAAACAATATTTTAG
1 TTTATTAATATTTATTAGGAATTAAGG-TGGTTAAAACAATAGTTTAG
*
26262 -TTATTATTATTTATTAGGAATT-A-G-GGTTAAAAC-AT-GTTTAG
1 TTTATTAATATTTATTAGGAATTAAGGTGGTTAAAACAATAGTTTAG
26303 TTTATTAATATTT
1 TTTATTAATATTT
26316 TATTCTTTAG
Statistics
Matches: 48, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
41 5 0.10
42 13 0.27
43 9 0.19
45 6 0.12
46 2 0.04
47 13 0.27
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (47 bp):
TTTATTAATATTTATTAGGAATTAAGGTGGTTAAAACAATAGTTTAG
Found at i:26318 original size:43 final size:47
Alignment explanation
Indices: 26221--26319 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 47
26211 TCAGATTTAT
* *
26221 TATTTTATTAGGAATTAAGGTTGGTTAAAACAATATTTTAGTTATTAT
1 TATTTTATTAGGAATTAAGG-TGGTTAAAACAATAGTTTAGTTATTAA
26269 TA-TTTATTAGGAATT-A-G-GGTTAAAAC-AT-GTTTAGTTTATTAA
1 TATTTTATTAGGAATTAAGGTGGTTAAAACAATAGTTTAG-TTATTAA
26311 TATTTTATT
1 TATTTTATT
26320 CTTTAGTTAT
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
41 5 0.11
42 10 0.21
43 15 0.32
45 1 0.02
46 1 0.02
47 13 0.28
48 2 0.04
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.49
Consensus pattern (47 bp):
TATTTTATTAGGAATTAAGGTGGTTAAAACAATAGTTTAGTTATTAA
Found at i:31603 original size:12 final size:14
Alignment explanation
Indices: 31576--31607 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
31566 ACGTAAAATC
31576 AAAATATAATATTT
1 AAAATATAATATTT
31590 AAAATAT-A-ATTT
1 AAAATATAATATTT
31602 AAAATA
1 AAAATA
31608 GAACCGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 10 0.56
13 1 0.06
14 7 0.39
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
AAAATATAATATTT
Found at i:33785 original size:20 final size:19
Alignment explanation
Indices: 33762--33830 Score: 120
Period size: 20 Copynumber: 3.5 Consensus size: 19
33752 CAGATCGAAA
33762 TGAGTCAACTCGATCTGATC
1 TGAGTCAAC-CGATCTGATC
33782 TGAGTCAACCTGATCTGATC
1 TGAGTCAACC-GATCTGATC
33802 TGAGTCAACCGATCTGATC
1 TGAGTCAACCGATCTGATC
33821 TGAGTCAACC
1 TGAGTCAACC
33831 TGAACCGGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 3
0.94 0.00 0.06
Matches are distributed among these distances:
19 20 0.42
20 28 0.58
ACGTcount: A:0.26, C:0.26, G:0.20, T:0.28
Consensus pattern (19 bp):
TGAGTCAACCGATCTGATC
Found at i:33843 original size:39 final size:40
Alignment explanation
Indices: 33762--33843 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 40
33752 CAGATCGAAA
* *
33762 TGAGTCAACTCGATCTGATCTGAGTCAACCTGATCTGATC
1 TGAGTCAACTCGATCTGATCTGAGTCAACCTGAACCGATC
*
33802 TGAGTCAAC-CGATCTGATCTGAGTCAACCTGAACCGGTC
1 TGAGTCAACTCGATCTGATCTGAGTCAACCTGAACCGATC
33841 TGA
1 TGA
33844 CCCGTTAACT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
39 30 0.77
40 9 0.23
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.27
Consensus pattern (40 bp):
TGAGTCAACTCGATCTGATCTGAGTCAACCTGAACCGATC
Found at i:40366 original size:18 final size:18
Alignment explanation
Indices: 40342--40438 Score: 119
Period size: 18 Copynumber: 5.5 Consensus size: 18
40332 CAACATTTCA
40342 CAGTTATCAGATGATTTT
1 CAGTTATCAGATGATTTT
* *
40360 TAGTTATCAGAT-ATTTA
1 CAGTTATCAGATGATTTT
40377 CAGTTATCAGATGATTTT
1 CAGTTATCAGATGATTTT
* *
40395 CAGTCATCAGATG-TTTA
1 CAGTTATCAGATGATTTT
40412 CAGTTATCAGATG-TTTT
1 CAGTTATCAGATGATTTT
*
40429 ACAATTATCA
1 -CAGTTATCA
40439 AACGTAGATT
Statistics
Matches: 68, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
17 33 0.49
18 35 0.51
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.42
Consensus pattern (18 bp):
CAGTTATCAGATGATTTT
Found at i:40380 original size:35 final size:35
Alignment explanation
Indices: 40325--40438 Score: 151
Period size: 35 Copynumber: 3.3 Consensus size: 35
40315 TAAATGTTTA
*
40325 CAGTTATCA-ACATTTCACAGTTATCAGATGATTTT
1 CAGTTATCAGATATTT-ACAGTTATCAGATGATTTT
*
40360 TAGTTATCAGATATTTACAGTTATCAGATGATTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
* *
40395 CAGTCATCAGATGTTTACAGTTATCAGATG-TTTT
1 CAGTTATCAGATATTTACAGTTATCAGATGATTTT
*
40429 ACAATTATCA
1 -CAGTTATCA
40439 AACGTAGATT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
34 4 0.06
35 61 0.87
36 5 0.07
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.41
Consensus pattern (35 bp):
CAGTTATCAGATATTTACAGTTATCAGATGATTTT
Found at i:40381 original size:17 final size:18
Alignment explanation
Indices: 40321--40438 Score: 136
Period size: 17 Copynumber: 6.7 Consensus size: 18
40311 ATTCTAAATG
*
40321 TTTACAGTTATCA-A-CA
1 TTTACAGTTATCAGATGA
40337 TTTCACAGTTATCAGATGA
1 TTT-ACAGTTATCAGATGA
**
40356 TTTTTAGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
40373 TTTACAGTTATCAGATGA
1 TTTACAGTTATCAGATGA
* *
40391 TTTTCAGTCATCAGATG-
1 TTTACAGTTATCAGATGA
*
40408 TTTACAGTTATCAGATGT
1 TTTACAGTTATCAGATGA
*
40426 TTTACAATTATCA
1 TTTACAGTTATCA
40439 AACGTAGATT
Statistics
Matches: 87, Mismatches: 10, Indels: 8
0.83 0.10 0.08
Matches are distributed among these distances:
16 3 0.03
17 40 0.46
18 40 0.46
19 4 0.05
ACGTcount: A:0.31, C:0.14, G:0.13, T:0.42
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:40961 original size:20 final size:20
Alignment explanation
Indices: 40933--40975 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
40923 ATTGTTTTTA
40933 TTTACATTTT-CATTTTATTG
1 TTTACATTTTGCATTTTA-TG
* *
40953 TTTATATTTTGTATTTTATG
1 TTTACATTTTGCATTTTATG
40973 TTT
1 TTT
40976 TAGCTATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.70
Consensus pattern (20 bp):
TTTACATTTTGCATTTTATG
Found at i:43155 original size:21 final size:20
Alignment explanation
Indices: 43125--43166 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 20
43115 AAACTTATAG
43125 AAATAATATCATGTAATTTTTA
1 AAATAATATCA--TAATTTTTA
43147 AAAT-ATATCATAATTTTTA
1 AAATAATATCATAATTTTTA
43166 A
1 A
43167 TCTATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 10 0.50
21 6 0.30
22 4 0.20
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (20 bp):
AAATAATATCATAATTTTTA
Done.