Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004808.1 Hibiscus syriacus cultivar Beakdansim tig00010829_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: 45151
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:5034 original size:2 final size:2
Alignment explanation
Indices: 5027--5056 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5017 TCGCCATCGG
5027 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5057 TTGTGAACAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10247 original size:59 final size:59
Alignment explanation
Indices: 10130--10249 Score: 156
Period size: 59 Copynumber: 2.0 Consensus size: 59
10120 GTTCCTTGAT
* * *
10130 TATACGATGTTATTTGTTGGATCTTTCGACTATTAAAAGTTACAAAATGGTTTCTCGAC
1 TATACGATGATATTTGTTGGATCTTTCGACTATTAAAAATTACAAAATGATTTCTCGAC
*
10189 TATA-GATGATATTCTGTTGGGAT-TTTCGACTATTAAAAATTATAAAATGATTAT-TCGAC
1 TATACGATGATATT-TGTT-GGATCTTTCGACTATTAAAAATTACAAAATGATT-TCTCGAC
10248 TA
1 TA
10250 CTTATATGTT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
58 8 0.15
59 41 0.76
60 5 0.09
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.41
Consensus pattern (59 bp):
TATACGATGATATTTGTTGGATCTTTCGACTATTAAAAATTACAAAATGATTTCTCGAC
Found at i:10909 original size:17 final size:17
Alignment explanation
Indices: 10882--10927 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
10872 ATATAAATAT
10882 AAAAT-TTTAAATATAA
1 AAAATATTTAAATATAA
*
10898 AAAATATTTAAA-ATAT
1 AAAATATTTAAATATAA
*
10914 ATAATAATTTAAAT
1 AAAAT-ATTTAAAT
10928 TTTCTAAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAAATATTTAAATATAA
Found at i:10919 original size:16 final size:16
Alignment explanation
Indices: 10876--10926 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
10866 TAAGAGATAT
10876 AAATATAAAAT-TTTA
1 AAATATAAAATATTTA
*
10891 AATATAAAAAATATTTA
1 AA-ATATAAAATATTTA
*
10908 AAATATATAATAATTTA
1 AAATATAAAAT-ATTTA
10925 AA
1 AA
10927 TTTTCTAAAG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
15 2 0.07
16 15 0.50
17 13 0.43
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAATATAAAATATTTA
Found at i:12147 original size:41 final size:44
Alignment explanation
Indices: 12085--12167 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 44
12075 ACATCACTAG
*
12085 TCATCAAACTATTATCAC-TTTTATAGTTTCGTCACTAATTGTCC
1 TCATCAAACTATTATCACTTTTTA-AGTTTAGTCACTAATTGTCC
*
12129 TCAT-AAA-TATTAT-ACTTTTTAATTTTAGTCACTAATTGT
1 TCATCAAACTATTATCACTTTTTAAGTTTAGTCACTAATTGT
12168 TATAAAATTA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
41 18 0.50
42 11 0.31
43 3 0.08
44 4 0.11
ACGTcount: A:0.30, C:0.17, G:0.06, T:0.47
Consensus pattern (44 bp):
TCATCAAACTATTATCACTTTTTAAGTTTAGTCACTAATTGTCC
Found at i:32889 original size:19 final size:19
Alignment explanation
Indices: 32865--32903 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
32855 TTATGAGTGA
*
32865 GGATTAAACTTACCATTAT
1 GGATTAAACTTACAATTAT
32884 GGATTAAACTTACAATTAT
1 GGATTAAACTTACAATTAT
32903 G
1 G
32904 ATAAGGGATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (19 bp):
GGATTAAACTTACAATTAT
Found at i:33585 original size:31 final size:31
Alignment explanation
Indices: 33550--33645 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 31
33540 AAATTTTAAC
* * *
33550 TTGACCCCTGAATTTTAGACAAAATACTATT
1 TTGACCCATGAATTTTAGATAAAATACTAAT
* * *
33581 TTGA-CCTTAAATTTTAGATAGAATACTAAT
1 TTGACCCATGAATTTTAGATAAAATACTAAT
* * *
33611 TTAACTCATGAACTTTAGATAAAATA-TCAAT
1 TTGACCCATGAATTTTAGATAAAATACT-AAT
33642 TTGA
1 TTGA
33646 TCTCTGAATC
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 25 0.49
31 26 0.51
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.38
Consensus pattern (31 bp):
TTGACCCATGAATTTTAGATAAAATACTAAT
Found at i:35623 original size:8 final size:7
Alignment explanation
Indices: 35607--35641 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
35597 TTTAATTTTT
35607 AATTTAA
1 AATTTAA
*
35614 ATTTTAA
1 AATTTAA
35621 AATTTAA
1 AATTTAA
35628 AATTTAA
1 AATTTAA
35635 AATTTAA
1 AATTTAA
35642 TCCATAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
AATTTAA
Found at i:38441 original size:264 final size:265
Alignment explanation
Indices: 37971--38499 Score: 1024
Period size: 264 Copynumber: 2.0 Consensus size: 265
37961 ACAAGGGGAA
37971 TGTTAGTGTATGTGAATGCAACACGTGCAACTGATGTGCATGATGGTTGTGCAGCTAAGGATTGG
1 TGTTAGTGTATGTGAATGCAACACGTGCAACTGATGTGCATGATGGTTGTGCAGCTAAGGATTGG
38036 TTCACTGCAGCTGATCAGTTGAAGCAGTTAGTTTGTTGTGAAATTAGTTACATCAGTTTCAGCTA
66 TTCACTGCAGCTGATCAGTTGAAGCAGTTAGTTTGTTGTGAAATTAGTTACATCAGTTTCAGCTA
*
38101 TAGTACTAGCTATAAATACTCTCCTTGAGAATTGTTATAAACACTCTTAAAGATAATGAATTTCA
131 TAGTACTAGCTATAAATACTCTCCTTGAGAATTATTATAAACACTCTTAAAGATAATGAATTTCA
38166 GAAGTTCTCTTTCGTTTATTCTCTTTGTTCTTACTTTCATAGCTTAGACATTTGTTCAT-ATCTT
196 GAAGTTCTCTTTCGTTTATTCTCTTTGTTCTTACTTTCATAGCTTAGACATTTGTTCATAATCTT
38230 TACAT
261 TACAT
* *
38235 TGTTAGTGTATGTGAATGCAACACGTGCAACTGCTGTGCATGATGGTTGTGCAGTTAAGGATTGG
1 TGTTAGTGTATGTGAATGCAACACGTGCAACTGATGTGCATGATGGTTGTGCAGCTAAGGATTGG
38300 TTCACTGCAGCTGATCAGTTGAAGCAGTTAGTTTGTTGTGAAATTAGTTACATCAGTTTCAGCTA
66 TTCACTGCAGCTGATCAGTTGAAGCAGTTAGTTTGTTGTGAAATTAGTTACATCAGTTTCAGCTA
38365 TAGTACTAGCTATAAATACTCTCCTTGAGAATTATTATAAACACTCTTAAAGATAATGAATTTCA
131 TAGTACTAGCTATAAATACTCTCCTTGAGAATTATTATAAACACTCTTAAAGATAATGAATTTCA
38430 GAAGTTCTCTTTCGTTTATTCTCTTTGTTCTTACTTTCATAGCTTAGACATTTGTTCATAATCTT
196 GAAGTTCTCTTTCGTTTATTCTCTTTGTTCTTACTTTCATAGCTTAGACATTTGTTCATAATCTT
38495 TACAT
261 TACAT
38500 GGTATCAGAG
Statistics
Matches: 261, Mismatches: 3, Indels: 1
0.98 0.01 0.00
Matches are distributed among these distances:
264 251 0.96
265 10 0.04
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (265 bp):
TGTTAGTGTATGTGAATGCAACACGTGCAACTGATGTGCATGATGGTTGTGCAGCTAAGGATTGG
TTCACTGCAGCTGATCAGTTGAAGCAGTTAGTTTGTTGTGAAATTAGTTACATCAGTTTCAGCTA
TAGTACTAGCTATAAATACTCTCCTTGAGAATTATTATAAACACTCTTAAAGATAATGAATTTCA
GAAGTTCTCTTTCGTTTATTCTCTTTGTTCTTACTTTCATAGCTTAGACATTTGTTCATAATCTT
TACAT
Found at i:39192 original size:11 final size:10
Alignment explanation
Indices: 39161--39196 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
39151 CACCATCTTC
*
39161 AAGAACCTCC
1 AAGAACCTCA
39171 AAGAACCTCA
1 AAGAACCTCA
39181 AAGAATCCTCA
1 AAGAA-CCTCA
39192 AAGAA
1 AAGAA
39197 AAGAGGCAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.50, C:0.28, G:0.11, T:0.11
Consensus pattern (10 bp):
AAGAACCTCA
Done.