Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008542.1 Hibiscus syriacus cultivar Beakdansim tig00111431_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: 35884
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:5276 original size:42 final size:43
Alignment explanation
Indices: 5219--5324 Score: 124
Period size: 43 Copynumber: 2.5 Consensus size: 43
5209 TTTAACGCCA
* *
5219 CAAAATGCTACGTCTTTTAG-CGCATTTTAGTAACAAACGCTG
1 CAAAATGTTAGGTCTTTTAGTCGCATTTTAGTAACAAACGCTG
* ** * * *
5261 CAAAATGTTAGGTCTTTTAGTTGTGTTTTTGTAACAAATGTTG
1 CAAAATGTTAGGTCTTTTAGTCGCATTTTAGTAACAAACGCTG
*
5304 CAAAATGTTAGGTCATTTAGT
1 CAAAATGTTAGGTCTTTTAGT
5325 GGTGTTTTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
42 18 0.33
43 36 0.67
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (43 bp):
CAAAATGTTAGGTCTTTTAGTCGCATTTTAGTAACAAACGCTG
Found at i:5309 original size:43 final size:43
Alignment explanation
Indices: 5243--5333 Score: 137
Period size: 43 Copynumber: 2.1 Consensus size: 43
5233 TTTTAGCGCA
* * *
5243 TTTTAGTAACAAACGCTGCAAAATGTTAGGTCTTTTAGTTGTG
1 TTTTTGTAACAAACGCTGCAAAATGTTAGGTCATTTAGTGGTG
* *
5286 TTTTTGTAACAAATGTTGCAAAATGTTAGGTCATTTAGTGGTG
1 TTTTTGTAACAAACGCTGCAAAATGTTAGGTCATTTAGTGGTG
5329 TTTTT
1 TTTTT
5334 TTAGAACAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.44
Consensus pattern (43 bp):
TTTTTGTAACAAACGCTGCAAAATGTTAGGTCATTTAGTGGTG
Found at i:14673 original size:18 final size:17
Alignment explanation
Indices: 14640--14673 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
14630 TTTTGGGCTT
*
14640 ATTTTCAAATCAAAAGG
1 ATTTTCAAAACAAAAGG
14657 ATTTTCAAAAACAAAAG
1 ATTTTC-AAAACAAAAG
14674 CCAGCGTTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.12, G:0.09, T:0.26
Consensus pattern (17 bp):
ATTTTCAAAACAAAAGG
Found at i:15189 original size:12 final size:12
Alignment explanation
Indices: 15172--15196 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15162 ATCTTATAAA
15172 TATTTTATTATT
1 TATTTTATTATT
15184 TATTTTATTATT
1 TATTTTATTATT
15196 T
1 T
15197 TATCCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:19681 original size:16 final size:17
Alignment explanation
Indices: 19648--19683 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
19638 GGGCACTCAA
19648 AATAAATTTATCATTTT
1 AATAAATTTATCATTTT
*
19665 AATAAATTT-TGATTTT
1 AATAAATTTATCATTTT
19681 AAT
1 AAT
19684 TATGTTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (17 bp):
AATAAATTTATCATTTT
Found at i:24167 original size:66 final size:64
Alignment explanation
Indices: 23962--24186 Score: 310
Period size: 64 Copynumber: 3.5 Consensus size: 64
23952 TGCACTAAGA
* * * *
23962 GTGCATCGATGCATGAAGTGCATTCGATGTTTTAAAATAGCCTGAGTGGATTGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGTCTT
* * *
24026 GTGCATCGATGCATGAAGTGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGCATGTCTT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGTCTT
*
24090 GTGCATCGATGCATAAAATGCATTCGATGTTTTTTATAAA-AACCTGAGTGCATCGATGCATGGT
1 GTGCATCGATGCATAAAATGCATTCGATG--TTTTA-AAATAGCCTGAGTGCATCGATGCAT-GT
*
24154 -AT
62 CTT
*
24156 GTGCATCGATGCATAAAATGCATTCAATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
24187 CAATTTTTTC
Statistics
Matches: 148, Mismatches: 9, Indels: 8
0.90 0.05 0.05
Matches are distributed among these distances:
64 90 0.61
66 53 0.36
67 5 0.03
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGTCTT
Found at i:29093 original size:20 final size:22
Alignment explanation
Indices: 29068--29111 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
29058 GGTGCAATAT
*
29068 AAAATATTTAAAA-ATA-AAAA
1 AAAATATTAAAAACATATAAAA
29088 AAAATATTAAAAACATATAAAA
1 AAAATATTAAAAACATATAAAA
29110 AA
1 AA
29112 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.57
21 3 0.14
22 6 0.29
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAATATTAAAAACATATAAAA
Found at i:29112 original size:20 final size:19
Alignment explanation
Indices: 29064--29113 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
29054 TTATGGTGCA
* *
29064 ATATAAAATATTTAAAAAT
1 ATATAAAAAATTTAAAAAC
*
29083 A-AAAAAAAATATTAAAAAC
1 ATATAAAAAAT-TTAAAAAC
29102 ATATAAAAAATT
1 ATATAAAAAATT
29114 AATTAAATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.28
19 10 0.40
20 8 0.32
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
ATATAAAAAATTTAAAAAC
Found at i:29956 original size:23 final size:24
Alignment explanation
Indices: 29907--29958 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
29897 CAGTTTTGAC
*
29907 TGCCACGTAGAATTTGCACCGAAG
1 TGCCACGTAGAATATGCACCGAAG
29931 TGCCACGTAGAATATGCA-CGAAG
1 TGCCACGTAGAATATGCACCGAAG
29954 TGCCA
1 TGCCA
29959 TATAGATTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.31, C:0.25, G:0.25, T:0.19
Consensus pattern (24 bp):
TGCCACGTAGAATATGCACCGAAG
Found at i:29964 original size:23 final size:24
Alignment explanation
Indices: 29907--29964 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
29897 CAGTTTTGAC
* *
29907 TGCCACGTAGAATTTGCACCGAAG
1 TGCCACATAGAATATGCACCGAAG
*
29931 TGCCACGTAGAATATGCA-CGAAG
1 TGCCACATAGAATATGCACCGAAG
*
29954 TGCCATATAGA
1 TGCCACATAGA
29965 TTTGTCCCAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 14 0.45
24 17 0.55
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (24 bp):
TGCCACATAGAATATGCACCGAAG
Found at i:29995 original size:23 final size:23
Alignment explanation
Indices: 29960--30018 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
29950 GAAGTGCCAT
* * *
29960 ATAGATTTGTCCCAAAGGACCAC
1 ATAGAATTATCCCAAAAGACCAC
*
29983 GTAGAATTATCCCAAAAGACCAC
1 ATAGAATTATCCCAAAAGACCAC
*
30006 ATAGAATTTTCCC
1 ATAGAATTATCCC
30019 GAAGTACCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.37, C:0.25, G:0.14, T:0.24
Consensus pattern (23 bp):
ATAGAATTATCCCAAAAGACCAC
Done.