Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000198.1 Hibiscus syriacus cultivar Beakdansim tig00000354_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: 58989
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:1235 original size:59 final size:60
Alignment explanation
Indices: 1142--1255 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 60
1132 AGGTGGCACA
*
1142 AAGGCGCATGCCCGGGGATGCGCTTTACATGGGTTTTAGCTAACT-GGATGCCACGAGTGT
1 AAGGCGCATGCCCGGGGACGCGCTTTACATGGGTTTT-GCTAACTCGGATGCCACGAGTGT
* * * *
1202 AAGGCGCAT-CCCTGGGACGCGCTTTACCTGGGTTTTGCTGAGTCGGATGCCACG
1 AAGGCGCATGCCCGGGGACGCGCTTTACATGGGTTTTGCTAACTCGGATGCCACG
1256 CTGGTATTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 5 0.10
59 34 0.71
60 9 0.19
ACGTcount: A:0.18, C:0.25, G:0.33, T:0.25
Consensus pattern (60 bp):
AAGGCGCATGCCCGGGGACGCGCTTTACATGGGTTTTGCTAACTCGGATGCCACGAGTGT
Found at i:1878 original size:21 final size:20
Alignment explanation
Indices: 1839--1879 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1829 ATTATTATAA
1839 TTTTAAAATTAATAATAATT
1 TTTTAAAATTAATAATAATT
* *
1859 TTTTATAATATAATATTAATT
1 TTTTAAAAT-TAATAATAATT
1880 ATTATATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTTAAAATTAATAATAATT
Found at i:5277 original size:135 final size:135
Alignment explanation
Indices: 5046--5649 Score: 821
Period size: 133 Copynumber: 4.5 Consensus size: 135
5036 GTGAGTTTTC
* * * *
5046 GGGCGTGCCTTCCATTATTTTGTCAGAGAATATGTTATCGTTGT-CTTATTATGTCACTTATGTC
1 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT-TCCCTATTATGTCACTCATGTC
*** * *
5110 CCCGAAAAACTATTCATGTCTGTACCTATTTTTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCG
65 CCCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCG
5175 TTTCCGG
130 -TTCCGG
* * * *
5182 GGG-GCGCCTTCCATTATTTTGTTAGAGAATATATTATCATTTCCCTATTATGTCAATCATATCT
1 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGTC-
* * * * *
5246 CCC-GGGAAC-ATTTATGTCA-TACTTATTTTTTTTAGGGGACTTGGCAAAGTGGTGAAAGCTCA
65 CCCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCG
*
5308 TTCCCG
130 TTCCGG
* * *
5314 GGGCGCGTCTTCCATTATTTTGTCAGAGAATATATTATCATTGT-CCTATTATGTCACCCATGTC
1 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATT-TCCCTATTATGTCACTCATGTC
*
5378 CCCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTTAAAGCGCG
65 CCCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCG
5443 TT-CGG
130 TTCCGG
* * *
5448 GGGCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTATTA--TCACTCATGTCC
1 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGTCC
*
5511 CTCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGTGCG
66 C-CGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCG
5576 TTCTCGG
130 TTC-CGG
* * *
5583 GGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCTCTATTATGTCACTCATGTCC
1 GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGTCC
5648 CC
66 CC
5650 TAGTGACGCA
Statistics
Matches: 414, Mismatches: 41, Indels: 26
0.86 0.09 0.05
Matches are distributed among these distances:
132 23 0.06
133 162 0.39
134 66 0.16
135 143 0.35
136 7 0.02
137 13 0.03
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (135 bp):
GGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTTCCCTATTATGTCACTCATGTCC
CCGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGT
TCCGG
Found at i:5548 original size:268 final size:268
Alignment explanation
Indices: 5054--5649 Score: 864
Period size: 268 Copynumber: 2.2 Consensus size: 268
5044 TCGGGCGTGC
* * *
5054 CTTCCATTATTTTGTCAGAGAATATGTTATCGTTGTCTTATTATGTCACTTATGTCCCCGAAAAA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGTCCCCGAAAAA
* *
5119 CTATTCATGTCTGTACCTATTTTTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCCGGGG
66 CTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCCGGGG
* * *
5184 GGCGCCTTCCATTATTTTGTTAGAGAATATATTATCATTTCCCTATTATGTCAATCATATCTCCC
131 GGCACCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTATTA-GTCAATCATATCTCCC
* * *
5249 GGGAACATTTATGTCATACTTATTTTTTTTAGGGGACTTGGCAAAGTGGTGAAAGCT-CATTC-C
195 GGGAACATTCATGTCATACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAG-TGCATTCTC
5312 CGGGGCGCGT
259 CGGGGCGCGT
* * ***
5322 CTTCCATTATTTTGTCAGAGAATATATTATCATTGTCCTATTATGTCACCCATGTCCCCGGGGAA
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGTCCCCGAAAAA
*
5387 CTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTTAAAGCGCG-TT-CGGGG
66 CTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCCGGGG
* * * *
5450 GCGCACCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCTTATTA-TCACTCATGTC-CCT
131 G-GCACCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTATTAGTCAATCATATCTCC-
*
5513 CGGGGAACTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGTGCGTT
194 C-GGGAAC-ATTCATGTCA-TACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGTGCATT
*
5578 CTCGGGGGCGCGT
256 CTCCGGGGCGCGT
5591 CTTCCATTATTTTGTCAGAGAATATGTTATCATTG-CTCTATTATGTCACTCATGTCCCC
1 CTTCCATTATTTTGTCAGAGAATATGTTATCATTGTC-CTATTATGTCACTCATGTCCCC
5650 TAGTGACGCA
Statistics
Matches: 295, Mismatches: 25, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
264 2 0.01
265 10 0.03
266 12 0.04
267 54 0.18
268 152 0.52
269 65 0.22
ACGTcount: A:0.22, C:0.20, G:0.21, T:0.37
Consensus pattern (268 bp):
CTTCCATTATTTTGTCAGAGAATATGTTATCATTGTCCTATTATGTCACTCATGTCCCCGAAAAA
CTATTCATGTCAGTACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGCGCGTTTCCGGGG
GGCACCTTCCATTATTTTGTCAGAGAATATATTATCATTGCCCTATTAGTCAATCATATCTCCCG
GGAACATTCATGTCATACCTATTATTTTTAGGGGACTTGGCAAAGTGGTGAAAGTGCATTCTCCG
GGGCGCGT
Found at i:5877 original size:62 final size:61
Alignment explanation
Indices: 5791--5914 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 61
5781 TATGTGAAGT
* *
5791 TTGAATAAATGGATAAATTATTATGGATAAATTGAATAAATGTGAAGTGATAAGTTGGTTG
1 TTGAATAAATGGATAAAATATTATGGATAAATTGAATAAATGTGAAGTGATAAGTTAGTTG
*
5852 TTGAATAAATTGGATAAAATGTTATGGATAAATTGAATAAATGTGAAGTGATAAGTTAGTTG
1 TTGAATAAA-TGGATAAAATATTATGGATAAATTGAATAAATGTGAAGTGATAAGTTAGTTG
5914 T
1 T
5915 GACATTGAAA
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
61 9 0.15
62 50 0.85
ACGTcount: A:0.41, C:0.00, G:0.23, T:0.36
Consensus pattern (61 bp):
TTGAATAAATGGATAAAATATTATGGATAAATTGAATAAATGTGAAGTGATAAGTTAGTTG
Found at i:5904 original size:23 final size:23
Alignment explanation
Indices: 5856--5905 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
5846 TGGTTGTTGA
* * *
5856 ATAAATTGGATAAAATGTTATGG
1 ATAAATTGAATAAAATGTGAAGG
5879 ATAAATTGAAT-AAATGTGAAGTG
1 ATAAATTGAATAAAATGTGAAG-G
5902 ATAA
1 ATAA
5906 GTTAGTTGTG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (23 bp):
ATAAATTGAATAAAATGTGAAGG
Found at i:6015 original size:14 final size:14
Alignment explanation
Indices: 5996--6026 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
5986 TTACACGTGG
5996 GTTTTAATGTATAT
1 GTTTTAATGTATAT
6010 GTTTTAATGTATAT
1 GTTTTAATGTATAT
6024 GTT
1 GTT
6027 AAGGATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTTTAATGTATAT
Found at i:6192 original size:34 final size:34
Alignment explanation
Indices: 6147--6219 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
6137 TTAAGTTGAA
*
6147 TTTAATGTTAAATTTCAAATACTGTAATTTGTAT
1 TTTAATGTTAAATTTCAAATACTATAATTTGTAT
* *
6181 TTTAATTTTAAATTTCGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTCAAATACTATAATTTGTAT
6215 TTTAA
1 TTTAA
6220 AAACATTTAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (34 bp):
TTTAATGTTAAATTTCAAATACTATAATTTGTAT
Found at i:6756 original size:21 final size:21
Alignment explanation
Indices: 6732--6783 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
6722 GGTGTCATAA
*
6732 AACCTTGCGGGCTAGGCATGT
1 AACCTTGCGGGCTAGGAATGT
*
6753 AACCTGGCGGGCTAGGAATGT
1 AACCTTGCGGGCTAGGAATGT
*
6774 AACCCTGCGG
1 AACCTTGCGG
6784 AGATGGCATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (21 bp):
AACCTTGCGGGCTAGGAATGT
Found at i:6807 original size:42 final size:42
Alignment explanation
Indices: 6756--6839 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
6746 GGCATGTAAC
* *
6756 CTGGCGGGCTAGGAATGTAACCCTGCGGAGATGGCATATGAA
1 CTGGCGGGCTAGGAATATAACCCTGAGGAGATGGCATATGAA
* * * * * *
6798 CTGGTGGGCTTGGCATATACCCCTGAGGAGATGTCATCTGAA
1 CTGGCGGGCTAGGAATATAACCCTGAGGAGATGGCATATGAA
6840 ATGGAGGTCT
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.23
Consensus pattern (42 bp):
CTGGCGGGCTAGGAATATAACCCTGAGGAGATGGCATATGAA
Found at i:6855 original size:42 final size:42
Alignment explanation
Indices: 6776--6864 Score: 106
Period size: 42 Copynumber: 2.1 Consensus size: 42
6766 AGGAATGTAA
* * * *
6776 CCCTGCGGAGATGGCATATGAACTGGTGGGCTTGGCATATAC
1 CCCTGAGGAGATGGCATATGAAATGGAGGGCTGGGCATATAC
* * * *
6818 CCCTGAGGAGATGTCATCTGAAATGGAGGTCTGGGCATGTAC
1 CCCTGAGGAGATGGCATATGAAATGGAGGGCTGGGCATATAC
6860 CCCTG
1 CCCTG
6865 TGGCATCATC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (42 bp):
CCCTGAGGAGATGGCATATGAAATGGAGGGCTGGGCATATAC
Found at i:10502 original size:14 final size:13
Alignment explanation
Indices: 10470--10503 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
10460 CCTTTTTTTT
10470 ATTTTTTATTAAA
1 ATTTTTTATTAAA
*
10483 GTTTTTTATTAAA
1 ATTTTTTATTAAA
10496 ATATTTTT
1 AT-TTTTT
10504 CATTTATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
ATTTTTTATTAAA
Found at i:13481 original size:14 final size:16
Alignment explanation
Indices: 13462--13498 Score: 60
Period size: 14 Copynumber: 2.4 Consensus size: 16
13452 CATTCATTCC
13462 CTCTCTCT-ATCTCT-
1 CTCTCTCTAATCTCTG
13476 CTCTCTCTAATCTCTG
1 CTCTCTCTAATCTCTG
13492 CTCTCTC
1 CTCTCTC
13499 GATTCAGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 6 0.29
16 7 0.33
ACGTcount: A:0.08, C:0.43, G:0.03, T:0.46
Consensus pattern (16 bp):
CTCTCTCTAATCTCTG
Found at i:17461 original size:30 final size:30
Alignment explanation
Indices: 17404--17462 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
17394 CCGAAATTTA
* * *
17404 TTCGGTTCGGTTAATACTTTAATAAAAAAG
1 TTCGGTTCGGTTAACACTTAAAGAAAAAAG
**
17434 TTCGGTTCGGTTAACGGTTAAAGAAAAAA
1 TTCGGTTCGGTTAACACTTAAAGAAAAAA
17463 AAAGTTTAGT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.32
Consensus pattern (30 bp):
TTCGGTTCGGTTAACACTTAAAGAAAAAAG
Found at i:27486 original size:21 final size:20
Alignment explanation
Indices: 27460--27498 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
27450 TAAGGAATTA
27460 AACATCATAAACAAAACAAAT
1 AACATCATAAA-AAAACAAAT
*
27481 AACATCATACAAAAACAA
1 AACATCATAAAAAAACAA
27499 CCATTCATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.21, G:0.00, T:0.13
Consensus pattern (20 bp):
AACATCATAAAAAAACAAAT
Found at i:30639 original size:24 final size:21
Alignment explanation
Indices: 30604--30646 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
30594 GGCTCATTCT
*
30604 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
30627 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
30647 ATCTTATGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:34222 original size:20 final size:20
Alignment explanation
Indices: 34193--34231 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
34183 TTTCCACCAC
*
34193 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATGATCCTAA
*
34213 ATGCATCTATATGATCCTA
1 ATGCAACTATATGATCCTA
34232 TATGAGCTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATGATCCTAA
Found at i:48188 original size:20 final size:20
Alignment explanation
Indices: 48151--48189 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
48141 TTTCCACCAC
**
48151 ATGCAACTATATGCTCCTAA
1 ATGCAACTATATAATCCTAA
*
48171 ATGCATCTATATAATCCTA
1 ATGCAACTATATAATCCTA
48190 TATGGGCTTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.36, C:0.23, G:0.08, T:0.33
Consensus pattern (20 bp):
ATGCAACTATATAATCCTAA
Found at i:56552 original size:22 final size:22
Alignment explanation
Indices: 56527--56570 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56517 AATAGTACTG
* *
56527 TGAACAGTAATGTATAATACCA
1 TGAACAGTAATGAACAATACCA
56549 TGAACAGTAATGAACAATACCA
1 TGAACAGTAATGAACAATACCA
56571 AATGCTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.23
Consensus pattern (22 bp):
TGAACAGTAATGAACAATACCA
Found at i:57484 original size:22 final size:22
Alignment explanation
Indices: 57459--57519 Score: 86
Period size: 22 Copynumber: 2.8 Consensus size: 22
57449 GGCATGTGAA
57459 ATTTATCCCGAAGGACCTATGT
1 ATTTATCCCGAAGGACCTATGT
*
57481 ATTTATCCCGAAGGACCTCTGT
1 ATTTATCCCGAAGGACCTATGT
* * *
57503 ATATGTCTCGAAGGACC
1 ATTTATCCCGAAGGACC
57520 GTGTAGACCC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.30
Consensus pattern (22 bp):
ATTTATCCCGAAGGACCTATGT
Done.