Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004368.1 Hibiscus syriacus cultivar Beakdansim tig00009570_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: 56689
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1322 original size:34 final size:34
Alignment explanation
Indices: 1279--1345 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
1269 TATCTGTTCA
1279 AAATATAACTCTCACCATTTGACATTAAACGTTT
1 AAATATAACTCTCACCATTTGACATTAAACGTTT
*
1313 AAATATAACTCTCACCATTTGACATTGAACGTT
1 AAATATAACTCTCACCATTTGACATTAAACGTT
1346 CACGTCCCTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.37, C:0.21, G:0.07, T:0.34
Consensus pattern (34 bp):
AAATATAACTCTCACCATTTGACATTAAACGTTT
Found at i:1460 original size:62 final size:60
Alignment explanation
Indices: 1363--1483 Score: 206
Period size: 62 Copynumber: 2.0 Consensus size: 60
1353 CTGACATTCC
*
1363 CAATACTTGAACTCGAGACCTCTAAAATCGCTTGATTCGTAAAAAGGTGATTATTTACCACT
1 CAATACTTGAACTCGAGACCTCGAAAATCGCTTGATTCGT-AAAAGGTG-TTATTTACCACT
*
1425 CAATACTTGAACTCGAGACCTCGGAAATCGCTTGATTCGTAAAAGGTGTTATTTACCAC
1 CAATACTTGAACTCGAGACCTCGAAAATCGCTTGATTCGTAAAAGGTGTTATTTACCAC
1484 CGAGATCGCT
Statistics
Matches: 57, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
60 11 0.19
61 8 0.14
62 38 0.67
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.30
Consensus pattern (60 bp):
CAATACTTGAACTCGAGACCTCGAAAATCGCTTGATTCGTAAAAGGTGTTATTTACCACT
Found at i:1906 original size:22 final size:22
Alignment explanation
Indices: 1871--1915 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
1861 AAATAATGAC
* *
1871 AAATTATATGTATACATTTATT
1 AAATTATATATATACAATTATT
* *
1893 AAATTTTATATATATAATTATT
1 AAATTATATATATACAATTATT
1915 A
1 A
1916 TTATAATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
AAATTATATATATACAATTATT
Found at i:4040 original size:8 final size:8
Alignment explanation
Indices: 4027--4052 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4017 GACTAAAATG
4027 GAAACTTT
1 GAAACTTT
4035 GAAACTTT
1 GAAACTTT
4043 GAAACTTT
1 GAAACTTT
4051 GA
1 GA
4053 GGTATGATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (8 bp):
GAAACTTT
Found at i:5633 original size:23 final size:23
Alignment explanation
Indices: 5607--5668 Score: 83
Period size: 23 Copynumber: 2.7 Consensus size: 23
5597 TATGTAGTCC
5607 TTCGGGACAATTCTATGCGGTCA
1 TTCGGGACAATTCTATGCGGTCA
**
5630 TTCGGGACAATTCTATATGGTCA
1 TTCGGGACAATTCTATGCGGTCA
5653 TTC--GACAAATTCTATG
1 TTCGGGAC-AATTCTATG
5669 TACCCCTAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.09
22 8 0.23
23 24 0.69
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (23 bp):
TTCGGGACAATTCTATGCGGTCA
Found at i:9665 original size:21 final size:21
Alignment explanation
Indices: 9632--9680 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
9622 TTCTACGTGG
* *
9632 TCCTTCGGGACATATATGTAA
1 TCCTTTGGAACATATATGTAA
*
9653 TCCTTTGGAACATATATGTTA
1 TCCTTTGGAACATATATGTAA
*
9674 TACTTTG
1 TCCTTTG
9681 TTACACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (21 bp):
TCCTTTGGAACATATATGTAA
Found at i:9782 original size:23 final size:24
Alignment explanation
Indices: 9751--9801 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
9741 ATATGTGTTA
* *
9751 TATGTGGTCCATCGGGAC-AATTC
1 TATGCGGTCCATCAGGACAAATTC
* *
9774 TATGCGGTCCTTTAGGACAAATTC
1 TATGCGGTCCATCAGGACAAATTC
9798 TATG
1 TATG
9802 TGCCCCTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 14 0.61
24 9 0.39
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.33
Consensus pattern (24 bp):
TATGCGGTCCATCAGGACAAATTC
Found at i:11016 original size:30 final size:31
Alignment explanation
Indices: 10955--11032 Score: 131
Period size: 30 Copynumber: 2.5 Consensus size: 31
10945 GGTCAAATAT
*
10955 ATATTTTATCTAAAATTTAAGAATTAAATTA
1 ATATTTTATCTAAAATTTAAGAATAAAATTA
10986 ATATTTTATCTAAAATTTAA-AATAAAATTA
1 ATATTTTATCTAAAATTTAAGAATAAAATTA
*
11016 ATATTATATCTAAAATT
1 ATATTTTATCTAAAATT
11033 CAAGTATCAT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 25 0.56
31 20 0.44
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (31 bp):
ATATTTTATCTAAAATTTAAGAATAAAATTA
Found at i:11050 original size:19 final size:19
Alignment explanation
Indices: 11008--11052 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
10998 AAATTTAAAA
*
11008 TAAAATT-AATATTATATC
1 TAAAATTCAATATCATATC
11026 TAAAATTCAAGTATCATAT-
1 TAAAATTCAA-TATCATATC
11045 TAAAATTC
1 TAAAATTC
11053 TATCATTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 10 0.42
20 7 0.29
ACGTcount: A:0.49, C:0.09, G:0.02, T:0.40
Consensus pattern (19 bp):
TAAAATTCAATATCATATC
Found at i:15773 original size:17 final size:18
Alignment explanation
Indices: 15736--15776 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
15726 CTATTATGTA
*
15736 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
15754 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
15771 TTTACT
1 TTTACT
15777 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:15974 original size:110 final size:111
Alignment explanation
Indices: 15846--16058 Score: 401
Period size: 110 Copynumber: 1.9 Consensus size: 111
15836 ATATATCTTT
*
15846 ACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
*
15911 TGA-TTATTTAATGCATGATTATTAGATTAAGAATTAAATATCTCG
66 TGATTTATTTAATACATGATTATTAGATTAAGAATTAAATATCTCG
15956 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
1 ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
16021 TGATTTATTTAATACATGATTATTAGATTAAGAATTAA
66 TGATTTATTTAATACATGATTATTAGATTAAGAATTAA
16059 TTTTTGTAAT
Statistics
Matches: 100, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
110 67 0.67
111 33 0.33
ACGTcount: A:0.38, C:0.08, G:0.11, T:0.44
Consensus pattern (111 bp):
ACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAATAATTAGT
TGATTTATTTAATACATGATTATTAGATTAAGAATTAAATATCTCG
Found at i:17751 original size:9 final size:9
Alignment explanation
Indices: 17733--17771 Score: 60
Period size: 9 Copynumber: 4.3 Consensus size: 9
17723 TGCTCAGGAC
17733 GACGACGAT
1 GACGACGAT
*
17742 GACGATGAT
1 GACGACGAT
*
17751 GACGACGAC
1 GACGACGAT
17760 GACGACGAT
1 GACGACGAT
17769 GAC
1 GAC
17772 AGCGAGGAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.10
Consensus pattern (9 bp):
GACGACGAT
Found at i:24868 original size:10 final size:10
Alignment explanation
Indices: 24853--24893 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
24843 TTCATCAAAC
24853 CAAATTCTCT
1 CAAATTCTCT
*
24863 CAAATTTTCT
1 CAAATTCTCT
*
24873 CAATTTCTCT
1 CAAATTCTCT
*
24883 CAAATACTCT
1 CAAATTCTCT
24893 C
1 C
24894 TCTTTAAGGT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:24970 original size:17 final size:18
Alignment explanation
Indices: 24933--24973 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
24923 ATATTATGTA
*
24933 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
24951 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
24968 TTTACT
1 TTTACT
24974 AATATAATTT
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:27008 original size:15 final size:15
Alignment explanation
Indices: 26988--27022 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
26978 ATCTGCTTAG
26988 GATGACGACGATGAT
1 GATGACGACGATGAT
* *
27003 GATGACGATGGTGAT
1 GATGACGACGATGAT
27018 GATGA
1 GATGA
27023 TGACAGCGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.31, C:0.09, G:0.37, T:0.23
Consensus pattern (15 bp):
GATGACGACGATGAT
Found at i:27210 original size:26 final size:24
Alignment explanation
Indices: 27139--27210 Score: 62
Period size: 26 Copynumber: 3.0 Consensus size: 24
27129 TTATATTTGT
27139 ATTTACTTTATTTTGTTAAATTGTA
1 ATTTACTTTATTTTGTTAAATT-TA
*
27164 ATTT--TTTATTATT-TCT-CATTTA
1 ATTTACTTTATT-TTGT-TAAATTTA
27186 ATACTTACTTTATTTTGTTAAATTT
1 AT--TTACTTTATTTTGTTAAATTT
27211 GTTGGACTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 15
0.69 0.04 0.28
Matches are distributed among these distances:
22 4 0.11
23 10 0.27
24 5 0.14
25 7 0.19
26 11 0.30
ACGTcount: A:0.26, C:0.07, G:0.04, T:0.62
Consensus pattern (24 bp):
ATTTACTTTATTTTGTTAAATTTA
Found at i:31239 original size:21 final size:19
Alignment explanation
Indices: 31213--31253 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
31203 TCGAGTCATT
31213 TGATCATTAAAATTTATAAAA
1 TGATCATT-AAA-TTATAAAA
*
31234 TGATCATTTAATTATAAAA
1 TGATCATTAAATTATAAAA
31253 T
1 T
31254 ATTGTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 9 0.47
20 2 0.11
21 8 0.42
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (19 bp):
TGATCATTAAATTATAAAA
Found at i:47280 original size:46 final size:46
Alignment explanation
Indices: 47208--47308 Score: 159
Period size: 46 Copynumber: 2.2 Consensus size: 46
47198 TTAAAACCCT
*
47208 TATTTTGATATGTTTGAGTCTAGATTTATTTAAATGTCGGTCCGTA
1 TATTTTGATATGTTTGAGTCTAGATTTATTTAAATGTCGGTCCGAA
* *
47254 TATTTTGATATGTTTGAGTC-ATGATTTATTTAAATGTTGGTCTGAA
1 TATTTTGATATGTTTGAGTCTA-GATTTATTTAAATGTCGGTCCGAA
47300 TATTTTGAT
1 TATTTTGAT
47309 TTATTTTTGG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
45 1 0.02
46 50 0.98
ACGTcount: A:0.25, C:0.06, G:0.19, T:0.50
Consensus pattern (46 bp):
TATTTTGATATGTTTGAGTCTAGATTTATTTAAATGTCGGTCCGAA
Found at i:52306 original size:6 final size:6
Alignment explanation
Indices: 52297--52341 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
52287 GATAAAATGA
* *
52297 AAAAGT AAAAGT AAAAAT AAAAGT -AAAGT AAAAGT AAAAAT AAAA
1 AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAAGT AAAA
52342 AATAAAAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
5 5 0.14
6 30 0.86
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (6 bp):
AAAAGT
Found at i:52328 original size:23 final size:23
Alignment explanation
Indices: 52298--52341 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
52288 ATAAAATGAA
52298 AAAGTAAAAGTAAAAATAAAAGT
1 AAAGTAAAAGTAAAAATAAAAGT
52321 AAAGTAAAAGTAAAAATAAAA
1 AAAGTAAAAGTAAAAATAAAA
52342 AATAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.11, T:0.16
Consensus pattern (23 bp):
AAAGTAAAAGTAAAAATAAAAGT
Found at i:52330 original size:11 final size:11
Alignment explanation
Indices: 52298--52334 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
52288 ATAAAATGAA
52298 AAAGTAAAAGT
1 AAAGTAAAAGT
*
52309 AAAAATAAAAGT
1 -AAAGTAAAAGT
52321 AAAGTAAAAGT
1 AAAGTAAAAGT
52332 AAA
1 AAA
52335 AATAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (11 bp):
AAAGTAAAAGT
Found at i:52342 original size:6 final size:6
Alignment explanation
Indices: 52290--52350 Score: 52
Period size: 6 Copynumber: 9.8 Consensus size: 6
52280 AAGGAAAGAT
* * * *
52290 AAAATGA AAAAGTA AAAGTA AAAATA AAAGT- AAAGTA AAAGTA AAAATAA
1 AAAAT-A AAAA-TA AAAATA AAAATA AAAATA AAAATA AAAATA AAAAT-A
52340 AAAATA AAAAT
1 AAAATA AAAAT
52351 TAAGTGATTG
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
5 5 0.11
6 27 0.57
7 14 0.30
8 1 0.02
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:52853 original size:114 final size:114
Alignment explanation
Indices: 52651--52881 Score: 390
Period size: 114 Copynumber: 2.0 Consensus size: 114
52641 AGTTCAATTG
* *
52651 CTTAATTCCCAAAGGAGTTTTAAACAATTTTCTATATGCCCAAAGTTCTTCATCTAACTTTGGCG
1 CTTAATTCCCAAAGGAGTTTTAAACAATGTTCTATATGCCCAAAGTGCTTCATCTAACTTTGGCG
* *
52716 ACCAATATTTCCGCCTTGGGTTCACCATTTTTTCTAAAATATGCTTGAT
66 AACAATATTTCCGCCTTGGGTTCACCATTTTTTCTAAAACATGCTTGAT
52765 CTTAATTCCCAAAGGAGTTTTAAACAATGTTCTATATGCCCAAAGTGCTTCATCTAACTTTGGCG
1 CTTAATTCCCAAAGGAGTTTTAAACAATGTTCTATATGCCCAAAGTGCTTCATCTAACTTTGGCG
* * * *
52830 AACAGTATTTCTGCCTTGTGTTCACCATTTTTTCTAAAACCTGCTTGAT
66 AACAATATTTCCGCCTTGGGTTCACCATTTTTTCTAAAACATGCTTGAT
52879 CTT
1 CTT
52882 TCGATTATAT
Statistics
Matches: 109, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 109 1.00
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.39
Consensus pattern (114 bp):
CTTAATTCCCAAAGGAGTTTTAAACAATGTTCTATATGCCCAAAGTGCTTCATCTAACTTTGGCG
AACAATATTTCCGCCTTGGGTTCACCATTTTTTCTAAAACATGCTTGAT
Done.