Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006754.1 Hibiscus syriacus cultivar Beakdansim tig00017023_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: 43271
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1988 original size:17 final size:16
Alignment explanation
Indices: 1968--2004 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
1958 TTTTTTCAAA
1968 ATTTTTATATTTTTGCT
1 ATTTTTATATTTTT-CT
*
1985 ATTTTTCTATTTTTCT
1 ATTTTTATATTTTTCT
2001 ATTT
1 ATTT
2005 GGTTTTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (16 bp):
ATTTTTATATTTTTCT
Found at i:1997 original size:7 final size:8
Alignment explanation
Indices: 1968--2004 Score: 56
Period size: 8 Copynumber: 4.5 Consensus size: 8
1958 TTTTTTCAAA
*
1968 ATTTTTAT
1 ATTTTTCT
1976 ATTTTTGCT
1 ATTTTT-CT
1985 ATTTTTCT
1 ATTTTTCT
1993 ATTTTTCT
1 ATTTTTCT
2001 ATTT
1 ATTT
2005 GGTTTTTTCT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
8 20 0.74
9 7 0.26
ACGTcount: A:0.16, C:0.08, G:0.03, T:0.73
Consensus pattern (8 bp):
ATTTTTCT
Found at i:4083 original size:224 final size:224
Alignment explanation
Indices: 3777--4314 Score: 726
Period size: 225 Copynumber: 2.4 Consensus size: 224
3767 TGGGGCTTTG
* * * * * ** * *
3777 AAAATCCGACAATAATATAATCGATTAATTTCTAAAAATATTATCAAGCATAATAACATATTATG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
**
3842 TAGCGCTTAAATAACGTAATAGGTAGT-GTCTTTTT-AAGCTGATAT-GACTTTGGAAATCCGAC
66 TAGCGCTTATGTAACGTAATAGGTA-TCGTCTTTTTAAAGC-G-TATGGACTTTGGAAATCCGAC
* *
3904 GATAACATAAT-CGTTAATTACTT-ATATTGTTATTAATATTATCAACATATTATGTAACGCTTA
128 GATAACA-AATACGTTAATTACTTAAT-TTGTTATTAATATTATCAACATATTAGGTAACGCCTA
3967 AAATGTTACCAAAGTTTAAGCTGATAGAGCCCTA
191 AAATGTTACCAAAGTTTAAGCTGATAGAGCCCTA
* * *
4001 GAAATGCAACGATAACATAAACTATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
* * *
4066 TAGCGCTTATGTAACGTAATAGGCATCGTCTTTTTAAAGCGTTTGGGACTTTGGAAATCTGACGA
66 TAGCGCTTATGTAACGTAATAGGTATCGTCTTTTTAAAGCGTAT-GGACTTTGGAAATCCGACGA
* **
4131 TAACAAATAGGTTAATTACTTAATTTGTTATTTGTATTATCAACATATTAGGTAACGCCTAAAAT
130 TAACAAATACGTTAATTACTTAATTTGTTATTAATATTATCAACATATTAGGTAACGCCTAAAAT
* *
4196 GTTACCACAGTTTAAGCTGATAGAGCCTTA
195 GTTACCAAAGTTTAAGCTGATAGAGCCCTA
* * * *
4226 AAAATCCGACGATAACATAATCGGTTAATTACTGGAAACATTACCAAGCATAATAACATATTAGG
1 AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
*
4291 TAGAGCTTATGTAACGTAATAGGT
66 TAGCGCTTATGTAACGTAATAGGT
4315 TGGCATTATT
Statistics
Matches: 275, Mismatches: 33, Indels: 11
0.86 0.10 0.03
Matches are distributed among these distances:
223 3 0.01
224 87 0.32
225 183 0.67
226 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.33
Consensus pattern (224 bp):
AAAATCCAACGATAACATAAACGATTAATTACTGGAAACATTATCAAGCATAATAACATATTAGG
TAGCGCTTATGTAACGTAATAGGTATCGTCTTTTTAAAGCGTATGGACTTTGGAAATCCGACGAT
AACAAATACGTTAATTACTTAATTTGTTATTAATATTATCAACATATTAGGTAACGCCTAAAATG
TTACCAAAGTTTAAGCTGATAGAGCCCTA
Found at i:7922 original size:54 final size:54
Alignment explanation
Indices: 7840--7943 Score: 190
Period size: 54 Copynumber: 1.9 Consensus size: 54
7830 TATTGCATCA
7840 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
1 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
* *
7894 GACAATGTTAAGCCAACTGAGGAATGCAATGAAGTACATATTGTTGATGA
1 GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGA
7944 TTCTAATAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.26
Consensus pattern (54 bp):
GACAATGTTAAACCAACCGAGGAATGCAATGAAGTACATATTGTTGATGAATCT
Found at i:11564 original size:66 final size:66
Alignment explanation
Indices: 11494--11618 Score: 178
Period size: 66 Copynumber: 1.9 Consensus size: 66
11484 CCATTATCCC
* *
11494 CTTAAGTTCACCCCTCAATTCCACAACTTTTTTCATCACCCCATCAAATTTTCCACCCATCACCA
1 CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCACCA
11559 T
66 T
* * * * * *
11560 CTTAAGTTCACCTCTCAATTCCTCTACTTCTTTCACCACTCCATCTATTTTTCCACCCA
1 CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCA
11619 CTTCCCCCTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.24, C:0.39, G:0.02, T:0.35
Consensus pattern (66 bp):
CTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCACCA
T
Found at i:11630 original size:66 final size:65
Alignment explanation
Indices: 11491--11631 Score: 167
Period size: 66 Copynumber: 2.1 Consensus size: 65
11481 CTCCCATTAT
* *
11491 CCCCTTAAGTTCACCCCTCAATTCCACAACTTTTTTCATCACCCCATCAAATTTTCCACCCATCA
1 CCCCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCA
* * * * * * *
11556 CCATCTTAAGTTCACCTCTCAATTCCTCTACTTCTTTCACCACTCCATCTATTTTTCCACCCACT
1 CC-CCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCA--
11621 TC-
63 TCA
11623 CCCCTTAAG
1 CCCCTTAAG
11632 CCTCTGAATT
Statistics
Matches: 63, Mismatches: 10, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
65 2 0.03
66 57 0.90
67 2 0.03
68 2 0.03
ACGTcount: A:0.23, C:0.41, G:0.02, T:0.34
Consensus pattern (65 bp):
CCCCTTAAGTTCACCCCTCAATTCCACAACTTCTTTCACCACCCCATCAAATTTTCCACCCATCA
Found at i:13209 original size:162 final size:163
Alignment explanation
Indices: 12886--13222 Score: 536
Period size: 162 Copynumber: 2.1 Consensus size: 163
12876 ATGAAACTAG
**
12886 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAATTATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
* * * *
12951 TATAGGTGCTAGTATTGCTTTTCTTTTTAATTCCAAAAGTATTGATACTTATTTGAATTGTATGG
66 TATAGGTGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCG
13016 ATACCTTCAACATATCCGGTAGCTATTTACCGA
131 ATACCTTCAACATATCCGGTAGCTATTTACCGA
* *
13049 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATTGATACATGTTTATAAAGCATCGATACTT
1 TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
* * *
13114 T-TAGGCT-CTATTATTTCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTTAATGGTATC
66 TATAGG-TGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATC
13177 GATACCTTCAACATATCCGGTAGC-ACTTTACCGA
130 GATACCTTCAACATATCCGGTAGCTA-TTTACCGA
13211 TTTTGTCATATT
1 TTTTGTCATATT
13223 AAACCCGGTT
Statistics
Matches: 161, Mismatches: 11, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
161 1 0.01
162 97 0.60
163 63 0.39
ACGTcount: A:0.27, C:0.15, G:0.12, T:0.46
Consensus pattern (163 bp):
TTTTGTCATATTTTTACCTGTTATATTGTTATGTATCGATACATATTTATAAAGCATCGATACTT
TATAGGTGCTAGTATTGCTTTTCTTTTAAATTCCAAAAGTATCGATACTTATTTGAATGGTATCG
ATACCTTCAACATATCCGGTAGCTATTTACCGA
Found at i:17402 original size:14 final size:15
Alignment explanation
Indices: 17385--17413 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17375 AATAAAAAGG
17385 AAATTAAGA-AAAAT
1 AAATTAAGATAAAAT
17399 AAATTAAGATAAAAT
1 AAATTAAGATAAAAT
17414 TTTTAATTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
AAATTAAGATAAAAT
Found at i:18261 original size:22 final size:23
Alignment explanation
Indices: 18230--18272 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
18220 CCGTTCGTCT
*
18230 TTCTAGAAGC-GTTGACTAGACC
1 TTCTAGAAGCTGCTGACTAGACC
*
18252 TTCTATAAGCTGCTGACTAGA
1 TTCTAGAAGCTGCTGACTAGA
18273 TTTCACGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (23 bp):
TTCTAGAAGCTGCTGACTAGACC
Found at i:23828 original size:2 final size:2
Alignment explanation
Indices: 23821--23859 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23811 ACGATTTTCT
23821 TA TA 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 TA TA T
23860 CGTATGAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:25301 original size:42 final size:42
Alignment explanation
Indices: 25170--25348 Score: 180
Period size: 42 Copynumber: 4.1 Consensus size: 42
25160 ATAGTGTTCA
* * *
25170 TATTTACATCAAAACAATATTCATATTTATACTT-GAATAAT
1 TATTTACATCAAAACAGTATTTATATTTACACTTAGAATAAT
*
25211 TATTTACATCAAAACAATGCCCATATTTAATTATTTACGCTTAGAATAAT
1 TATTTACATCAAAAC-A-G----TATTT-A-TATTTACACTTAGAATAAT
* *
25261 TATTTGCATCAAAACAGTGTTTATATTTACACTTAGAATAAT
1 TATTTACATCAAAACAGTATTTATATTTACACTTAGAATAAT
* * * * *
25303 TATTTGCATTAAAATAGTGTTTATATTTAAACTTAGAATAAT
1 TATTTACATCAAAACAGTATTTATATTTACACTTAGAATAAT
25345 TATT
1 TATT
25349 CTTCCATGGT
Statistics
Matches: 119, Mismatches: 10, Indels: 17
0.82 0.07 0.12
Matches are distributed among these distances:
41 15 0.13
42 62 0.52
43 1 0.01
44 4 0.03
47 4 0.03
48 2 0.02
49 10 0.08
50 21 0.18
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.42
Consensus pattern (42 bp):
TATTTACATCAAAACAGTATTTATATTTACACTTAGAATAAT
Found at i:28198 original size:22 final size:22
Alignment explanation
Indices: 28168--28212 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
28158 ATTGACTTTT
*
28168 TGGTTAAAGCCAAAGTCAACTC
1 TGGTCAAAGCCAAAGTCAACTC
28190 TGGTCAAAGCCAAAGTCAACTC
1 TGGTCAAAGCCAAAGTCAACTC
28212 T
1 T
28213 AGTTAATGGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (22 bp):
TGGTCAAAGCCAAAGTCAACTC
Found at i:41224 original size:109 final size:109
Alignment explanation
Indices: 41020--41231 Score: 257
Period size: 109 Copynumber: 1.9 Consensus size: 109
41010 GAATTGAAGT
* * * * *
41020 TGAATGTGTGTTACTTTTTTCAAGAATTATTAGAAATGCATTTTTTTGTTTATAAAAATGCAATA
1 TGAATATGTGTTACTGTTTTCAAGAATTATAAGAAATGCATTTTTTTGTTTATAAAAATCCAACA
* **
41085 GCTTGACTATAGACATTATAGGTATGTTCTCATTCAATTTATAA
66 GCCTGACTATAGACATTATAGGTACATTCTCATTCAATTTATAA
** *
41129 TGAATATGTGTT-CTGTTTTCAAGGGTTATAAGAAATGCATGATTTTTTGTTTAT-AAAATCCAG
1 TGAATATGTGTTACTGTTTTCAAGAATTATAAGAAATGCAT--TTTTTTGTTTATAAAAATCCAA
* * * *
41192 CAGCCTGATTATAGACTTTATAGTTCCATTCTCATTCAAT
64 CAGCCTGACTATAGACATTATAGGTACATTCTCATTCAAT
41232 GCAGTATGCA
Statistics
Matches: 86, Mismatches: 15, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
108 24 0.28
109 50 0.58
110 12 0.14
ACGTcount: A:0.31, C:0.11, G:0.15, T:0.43
Consensus pattern (109 bp):
TGAATATGTGTTACTGTTTTCAAGAATTATAAGAAATGCATTTTTTTGTTTATAAAAATCCAACA
GCCTGACTATAGACATTATAGGTACATTCTCATTCAATTTATAA
Found at i:41272 original size:14 final size:14
Alignment explanation
Indices: 41250--41283 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
41240 CACAAATTAG
*
41250 TTTATTGCTCTTAT
1 TTTAATGCTCTTAT
*
41264 TTTAATGCTTTTAT
1 TTTAATGCTCTTAT
41278 TTTAAT
1 TTTAAT
41284 TTTCAGTATG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTAATGCTCTTAT
Done.