Multiple sequence alignment - TraesCS2A01G310700

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G310700 chr2A 100.000 2534 0 0 1 2534 534319660 534317127 0.000000e+00 4680.0
1 TraesCS2A01G310700 chr2D 92.007 2402 121 31 163 2534 396426332 396423972 0.000000e+00 3306.0
2 TraesCS2A01G310700 chr2B 91.443 2197 104 11 371 2534 469614517 469612372 0.000000e+00 2939.0
3 TraesCS2A01G310700 chr2B 94.828 58 3 0 2477 2534 9480943 9480886 9.650000e-15 91.6
4 TraesCS2A01G310700 chr5B 85.561 187 26 1 2348 2534 347532171 347532356 7.150000e-46 195.0
5 TraesCS2A01G310700 chr5B 79.197 274 33 13 39 306 13092645 13092900 4.340000e-38 169.0
6 TraesCS2A01G310700 chr3A 77.966 295 53 9 39 321 681330934 681330640 9.320000e-40 174.0
7 TraesCS2A01G310700 chr5A 86.709 158 17 3 2377 2534 395244967 395244814 3.350000e-39 172.0
8 TraesCS2A01G310700 chr5D 78.136 279 41 14 2269 2534 302846722 302846993 2.610000e-35 159.0
9 TraesCS2A01G310700 chr7D 85.256 156 16 2 12 160 6689852 6690007 1.210000e-33 154.0
10 TraesCS2A01G310700 chr7D 96.552 58 2 0 2477 2534 636666593 636666650 2.070000e-16 97.1
11 TraesCS2A01G310700 chr7D 82.828 99 11 6 2068 2164 611314353 611314447 1.620000e-12 84.2
12 TraesCS2A01G310700 chr7D 83.951 81 10 3 2068 2146 549871174 549871253 9.720000e-10 75.0
13 TraesCS2A01G310700 chr1D 78.327 263 40 12 39 287 465412990 465412731 1.210000e-33 154.0
14 TraesCS2A01G310700 chr1D 83.851 161 18 4 8 161 376772614 376772773 2.030000e-31 147.0
15 TraesCS2A01G310700 chr4B 88.618 123 12 2 39 160 545151449 545151328 5.650000e-32 148.0
16 TraesCS2A01G310700 chr4B 80.000 160 24 5 7 158 663886624 663886783 7.410000e-21 111.0
17 TraesCS2A01G310700 chr4B 94.828 58 3 0 2477 2534 439317280 439317223 9.650000e-15 91.6
18 TraesCS2A01G310700 chr4B 87.500 64 8 0 2083 2146 672103036 672102973 9.720000e-10 75.0
19 TraesCS2A01G310700 chr3B 80.000 205 34 6 1912 2113 157245709 157245909 7.310000e-31 145.0
20 TraesCS2A01G310700 chr3B 76.667 210 37 6 1940 2141 394944270 394944065 3.450000e-19 106.0
21 TraesCS2A01G310700 chr3B 89.041 73 8 0 2462 2534 382709223 382709151 9.650000e-15 91.6
22 TraesCS2A01G310700 chr1A 83.648 159 19 3 10 161 72501394 72501552 2.630000e-30 143.0
23 TraesCS2A01G310700 chr1A 76.042 288 46 15 43 312 416547546 416547264 7.360000e-26 128.0
24 TraesCS2A01G310700 chr3D 81.818 165 21 4 5 161 543004160 543003997 2.050000e-26 130.0
25 TraesCS2A01G310700 chr6D 85.124 121 14 1 43 159 152274126 152274246 1.230000e-23 121.0
26 TraesCS2A01G310700 chr6D 84.483 116 18 0 43 158 316104582 316104467 5.730000e-22 115.0
27 TraesCS2A01G310700 chr6D 78.947 114 22 2 1053 1165 428650033 428649921 2.700000e-10 76.8
28 TraesCS2A01G310700 chr7B 80.420 143 20 4 165 306 54476372 54476507 4.460000e-18 102.0
29 TraesCS2A01G310700 chr7B 80.952 126 24 0 181 306 611746342 611746217 1.600000e-17 100.0
30 TraesCS2A01G310700 chr6B 87.671 73 9 0 2462 2534 102074688 102074616 4.490000e-13 86.1
31 TraesCS2A01G310700 chr6B 78.947 114 22 2 1053 1165 645359829 645359717 2.700000e-10 76.8
32 TraesCS2A01G310700 chr7A 84.884 86 7 2 2071 2156 701367758 701367837 5.810000e-12 82.4
33 TraesCS2A01G310700 chr1B 78.014 141 20 10 2401 2534 370165249 370165113 7.520000e-11 78.7
34 TraesCS2A01G310700 chr1B 82.278 79 14 0 2068 2146 47769140 47769218 4.520000e-08 69.4
35 TraesCS2A01G310700 chr6A 78.947 114 22 2 1053 1165 573414239 573414127 2.700000e-10 76.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G310700 chr2A 534317127 534319660 2533 True 4680 4680 100.000 1 2534 1 chr2A.!!$R1 2533
1 TraesCS2A01G310700 chr2D 396423972 396426332 2360 True 3306 3306 92.007 163 2534 1 chr2D.!!$R1 2371
2 TraesCS2A01G310700 chr2B 469612372 469614517 2145 True 2939 2939 91.443 371 2534 1 chr2B.!!$R2 2163

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
976 988 0.029433 CTTCGATCATCTCCGTCGCA 59.971 55.0 0.0 0.0 35.48 5.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1876 1912 1.367346 TTACTGTTCATGGCAGGGGA 58.633 50.0 17.95 0.0 38.22 4.81 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 5.438117 CATTCAAGAACGGATTCATCATCG 58.562 41.667 0.00 0.00 37.29 3.84
24 25 4.385358 TCAAGAACGGATTCATCATCGA 57.615 40.909 0.00 0.00 37.29 3.59
25 26 4.948847 TCAAGAACGGATTCATCATCGAT 58.051 39.130 0.00 0.00 37.29 3.59
26 27 4.984785 TCAAGAACGGATTCATCATCGATC 59.015 41.667 0.00 0.00 37.29 3.69
27 28 4.862902 AGAACGGATTCATCATCGATCT 57.137 40.909 0.00 0.00 37.29 2.75
28 29 4.554292 AGAACGGATTCATCATCGATCTG 58.446 43.478 0.00 0.00 37.29 2.90
29 30 4.279420 AGAACGGATTCATCATCGATCTGA 59.721 41.667 0.00 0.00 37.29 3.27
30 31 3.906998 ACGGATTCATCATCGATCTGAC 58.093 45.455 0.00 0.00 31.73 3.51
31 32 2.913590 CGGATTCATCATCGATCTGACG 59.086 50.000 0.00 0.00 31.73 4.35
32 33 3.610349 CGGATTCATCATCGATCTGACGT 60.610 47.826 0.00 0.00 31.73 4.34
33 34 4.302455 GGATTCATCATCGATCTGACGTT 58.698 43.478 0.00 0.00 31.73 3.99
34 35 4.384247 GGATTCATCATCGATCTGACGTTC 59.616 45.833 0.00 0.00 31.73 3.95
35 36 4.370364 TTCATCATCGATCTGACGTTCA 57.630 40.909 0.00 0.00 34.70 3.18
36 37 3.695816 TCATCATCGATCTGACGTTCAC 58.304 45.455 0.00 0.00 34.70 3.18
37 38 3.128589 TCATCATCGATCTGACGTTCACA 59.871 43.478 0.00 0.00 34.70 3.58
38 39 3.569250 TCATCGATCTGACGTTCACAA 57.431 42.857 0.00 0.00 34.70 3.33
39 40 3.908213 TCATCGATCTGACGTTCACAAA 58.092 40.909 0.00 0.00 34.70 2.83
40 41 3.673338 TCATCGATCTGACGTTCACAAAC 59.327 43.478 0.00 0.00 34.70 2.93
41 42 3.086818 TCGATCTGACGTTCACAAACA 57.913 42.857 0.00 0.00 34.93 2.83
42 43 3.049912 TCGATCTGACGTTCACAAACAG 58.950 45.455 0.00 0.00 34.93 3.16
43 44 2.155732 CGATCTGACGTTCACAAACAGG 59.844 50.000 0.00 0.00 34.93 4.00
44 45 2.684001 TCTGACGTTCACAAACAGGT 57.316 45.000 0.00 0.00 34.93 4.00
45 46 2.980568 TCTGACGTTCACAAACAGGTT 58.019 42.857 0.00 0.00 34.93 3.50
46 47 2.933906 TCTGACGTTCACAAACAGGTTC 59.066 45.455 0.00 0.00 34.93 3.62
47 48 2.011222 TGACGTTCACAAACAGGTTCC 58.989 47.619 0.00 0.00 34.93 3.62
48 49 1.004292 GACGTTCACAAACAGGTTCCG 60.004 52.381 0.00 0.00 34.93 4.30
49 50 0.306533 CGTTCACAAACAGGTTCCGG 59.693 55.000 0.00 0.00 34.93 5.14
50 51 0.666374 GTTCACAAACAGGTTCCGGG 59.334 55.000 0.00 0.00 35.36 5.73
51 52 1.104577 TTCACAAACAGGTTCCGGGC 61.105 55.000 0.00 0.00 0.00 6.13
52 53 1.528309 CACAAACAGGTTCCGGGCT 60.528 57.895 0.00 0.00 0.00 5.19
53 54 1.228154 ACAAACAGGTTCCGGGCTC 60.228 57.895 0.00 0.00 0.00 4.70
54 55 1.073199 CAAACAGGTTCCGGGCTCT 59.927 57.895 0.00 0.00 0.00 4.09
55 56 1.073199 AAACAGGTTCCGGGCTCTG 59.927 57.895 0.00 9.39 0.00 3.35
56 57 1.415672 AAACAGGTTCCGGGCTCTGA 61.416 55.000 20.12 0.00 0.00 3.27
57 58 2.113243 AACAGGTTCCGGGCTCTGAC 62.113 60.000 20.12 3.92 0.00 3.51
58 59 3.382832 AGGTTCCGGGCTCTGACG 61.383 66.667 0.00 0.00 0.00 4.35
59 60 3.379445 GGTTCCGGGCTCTGACGA 61.379 66.667 0.00 0.00 0.00 4.20
60 61 2.182030 GTTCCGGGCTCTGACGAG 59.818 66.667 0.00 0.00 40.35 4.18
61 62 3.068691 TTCCGGGCTCTGACGAGG 61.069 66.667 0.00 0.00 37.75 4.63
62 63 3.578968 TTCCGGGCTCTGACGAGGA 62.579 63.158 0.00 0.00 37.75 3.71
63 64 3.068691 CCGGGCTCTGACGAGGAA 61.069 66.667 0.00 0.00 37.75 3.36
64 65 2.492090 CGGGCTCTGACGAGGAAG 59.508 66.667 0.00 0.00 37.75 3.46
65 66 2.046864 CGGGCTCTGACGAGGAAGA 61.047 63.158 0.00 0.00 37.75 2.87
66 67 1.813192 GGGCTCTGACGAGGAAGAG 59.187 63.158 0.00 0.00 42.40 2.85
67 68 0.968393 GGGCTCTGACGAGGAAGAGT 60.968 60.000 0.00 0.00 41.69 3.24
68 69 1.682394 GGGCTCTGACGAGGAAGAGTA 60.682 57.143 0.00 0.00 41.69 2.59
69 70 1.673920 GGCTCTGACGAGGAAGAGTAG 59.326 57.143 0.00 0.00 41.69 2.57
70 71 2.361789 GCTCTGACGAGGAAGAGTAGT 58.638 52.381 0.00 0.00 41.69 2.73
71 72 2.096819 GCTCTGACGAGGAAGAGTAGTG 59.903 54.545 0.00 0.00 41.69 2.74
72 73 2.085320 TCTGACGAGGAAGAGTAGTGC 58.915 52.381 0.00 0.00 0.00 4.40
73 74 1.813178 CTGACGAGGAAGAGTAGTGCA 59.187 52.381 0.00 0.00 0.00 4.57
74 75 2.425312 CTGACGAGGAAGAGTAGTGCAT 59.575 50.000 0.00 0.00 0.00 3.96
75 76 2.164422 TGACGAGGAAGAGTAGTGCATG 59.836 50.000 0.00 0.00 0.00 4.06
76 77 1.478510 ACGAGGAAGAGTAGTGCATGG 59.521 52.381 0.00 0.00 0.00 3.66
77 78 1.202463 CGAGGAAGAGTAGTGCATGGG 60.202 57.143 0.00 0.00 0.00 4.00
78 79 2.111384 GAGGAAGAGTAGTGCATGGGA 58.889 52.381 0.00 0.00 0.00 4.37
79 80 2.102252 GAGGAAGAGTAGTGCATGGGAG 59.898 54.545 0.00 0.00 0.00 4.30
80 81 2.111384 GGAAGAGTAGTGCATGGGAGA 58.889 52.381 0.00 0.00 0.00 3.71
81 82 2.159028 GGAAGAGTAGTGCATGGGAGAC 60.159 54.545 0.00 0.00 0.00 3.36
82 83 1.107114 AGAGTAGTGCATGGGAGACG 58.893 55.000 0.00 0.00 0.00 4.18
83 84 0.103208 GAGTAGTGCATGGGAGACGG 59.897 60.000 0.00 0.00 0.00 4.79
84 85 1.521681 GTAGTGCATGGGAGACGGC 60.522 63.158 0.00 0.00 0.00 5.68
85 86 3.076258 TAGTGCATGGGAGACGGCG 62.076 63.158 4.80 4.80 0.00 6.46
101 102 3.771160 CGGCGCCTGGAGTACCTT 61.771 66.667 26.68 0.00 37.04 3.50
102 103 2.125106 GGCGCCTGGAGTACCTTG 60.125 66.667 22.15 0.00 37.04 3.61
103 104 2.656069 GGCGCCTGGAGTACCTTGA 61.656 63.158 22.15 0.00 37.04 3.02
104 105 1.153549 GCGCCTGGAGTACCTTGAG 60.154 63.158 0.00 0.00 37.04 3.02
105 106 1.153549 CGCCTGGAGTACCTTGAGC 60.154 63.158 0.00 0.00 37.04 4.26
106 107 1.608717 CGCCTGGAGTACCTTGAGCT 61.609 60.000 0.00 0.00 37.04 4.09
107 108 0.107945 GCCTGGAGTACCTTGAGCTG 60.108 60.000 0.00 0.00 37.04 4.24
108 109 0.539051 CCTGGAGTACCTTGAGCTGG 59.461 60.000 0.00 0.00 37.04 4.85
109 110 0.107945 CTGGAGTACCTTGAGCTGGC 60.108 60.000 0.00 0.00 37.04 4.85
110 111 0.545309 TGGAGTACCTTGAGCTGGCT 60.545 55.000 0.00 0.00 37.04 4.75
111 112 0.176910 GGAGTACCTTGAGCTGGCTC 59.823 60.000 14.86 14.86 43.01 4.70
112 113 0.179124 GAGTACCTTGAGCTGGCTCG 60.179 60.000 16.33 6.32 45.48 5.03
113 114 0.900647 AGTACCTTGAGCTGGCTCGT 60.901 55.000 16.33 11.20 45.48 4.18
114 115 0.737715 GTACCTTGAGCTGGCTCGTG 60.738 60.000 16.33 11.45 45.48 4.35
115 116 1.185618 TACCTTGAGCTGGCTCGTGT 61.186 55.000 16.33 14.50 45.48 4.49
116 117 1.739562 CCTTGAGCTGGCTCGTGTC 60.740 63.158 16.33 0.00 45.48 3.67
117 118 1.739562 CTTGAGCTGGCTCGTGTCC 60.740 63.158 16.33 0.00 45.48 4.02
118 119 2.440385 CTTGAGCTGGCTCGTGTCCA 62.440 60.000 16.33 0.00 45.48 4.02
119 120 2.038814 TTGAGCTGGCTCGTGTCCAA 62.039 55.000 16.33 3.59 45.48 3.53
120 121 1.078848 GAGCTGGCTCGTGTCCAAT 60.079 57.895 6.84 0.00 33.06 3.16
121 122 1.364626 GAGCTGGCTCGTGTCCAATG 61.365 60.000 6.84 0.00 33.06 2.82
122 123 3.044059 GCTGGCTCGTGTCCAATGC 62.044 63.158 3.03 1.16 32.41 3.56
123 124 2.359850 TGGCTCGTGTCCAATGCC 60.360 61.111 0.00 0.00 43.49 4.40
124 125 3.134127 GGCTCGTGTCCAATGCCC 61.134 66.667 0.00 0.00 37.81 5.36
125 126 2.045926 GCTCGTGTCCAATGCCCT 60.046 61.111 0.00 0.00 0.00 5.19
126 127 1.220749 GCTCGTGTCCAATGCCCTA 59.779 57.895 0.00 0.00 0.00 3.53
127 128 1.090052 GCTCGTGTCCAATGCCCTAC 61.090 60.000 0.00 0.00 0.00 3.18
128 129 0.537188 CTCGTGTCCAATGCCCTACT 59.463 55.000 0.00 0.00 0.00 2.57
129 130 0.535335 TCGTGTCCAATGCCCTACTC 59.465 55.000 0.00 0.00 0.00 2.59
130 131 0.537188 CGTGTCCAATGCCCTACTCT 59.463 55.000 0.00 0.00 0.00 3.24
131 132 1.754803 CGTGTCCAATGCCCTACTCTA 59.245 52.381 0.00 0.00 0.00 2.43
132 133 2.223829 CGTGTCCAATGCCCTACTCTAG 60.224 54.545 0.00 0.00 0.00 2.43
133 134 1.762957 TGTCCAATGCCCTACTCTAGC 59.237 52.381 0.00 0.00 0.00 3.42
134 135 2.043227 GTCCAATGCCCTACTCTAGCT 58.957 52.381 0.00 0.00 0.00 3.32
135 136 2.436173 GTCCAATGCCCTACTCTAGCTT 59.564 50.000 0.00 0.00 0.00 3.74
136 137 2.435805 TCCAATGCCCTACTCTAGCTTG 59.564 50.000 0.00 0.00 0.00 4.01
137 138 2.216898 CAATGCCCTACTCTAGCTTGC 58.783 52.381 0.00 0.00 0.00 4.01
138 139 0.761802 ATGCCCTACTCTAGCTTGCC 59.238 55.000 0.00 0.00 0.00 4.52
139 140 1.068250 GCCCTACTCTAGCTTGCCG 59.932 63.158 0.00 0.00 0.00 5.69
140 141 1.742768 CCCTACTCTAGCTTGCCGG 59.257 63.158 0.00 0.00 0.00 6.13
141 142 1.068250 CCTACTCTAGCTTGCCGGC 59.932 63.158 22.73 22.73 0.00 6.13
142 143 1.299468 CTACTCTAGCTTGCCGGCG 60.299 63.158 23.90 9.82 37.29 6.46
143 144 1.725557 CTACTCTAGCTTGCCGGCGA 61.726 60.000 23.90 20.69 37.29 5.54
144 145 2.001361 TACTCTAGCTTGCCGGCGAC 62.001 60.000 23.90 13.81 37.29 5.19
145 146 4.143333 TCTAGCTTGCCGGCGACC 62.143 66.667 23.90 12.04 37.29 4.79
156 157 2.280592 GGCGACCGAACCAACACT 60.281 61.111 0.00 0.00 0.00 3.55
157 158 2.315386 GGCGACCGAACCAACACTC 61.315 63.158 0.00 0.00 0.00 3.51
158 159 1.300697 GCGACCGAACCAACACTCT 60.301 57.895 0.00 0.00 0.00 3.24
159 160 1.557443 GCGACCGAACCAACACTCTG 61.557 60.000 0.00 0.00 0.00 3.35
160 161 0.031585 CGACCGAACCAACACTCTGA 59.968 55.000 0.00 0.00 0.00 3.27
161 162 1.537348 CGACCGAACCAACACTCTGAA 60.537 52.381 0.00 0.00 0.00 3.02
172 173 0.600557 CACTCTGAACAGGACGAGCT 59.399 55.000 1.93 0.00 0.00 4.09
178 179 1.534235 AACAGGACGAGCTGGGAGT 60.534 57.895 0.00 0.00 0.00 3.85
179 180 0.251653 AACAGGACGAGCTGGGAGTA 60.252 55.000 0.00 0.00 0.00 2.59
180 181 0.681564 ACAGGACGAGCTGGGAGTAG 60.682 60.000 0.00 0.00 0.00 2.57
184 185 1.465794 GACGAGCTGGGAGTAGAACT 58.534 55.000 0.00 0.00 0.00 3.01
186 187 1.271982 ACGAGCTGGGAGTAGAACTGA 60.272 52.381 0.00 0.00 0.00 3.41
189 190 2.563179 GAGCTGGGAGTAGAACTGAACA 59.437 50.000 0.00 0.00 0.00 3.18
216 217 2.447250 CGCTCAAAGATCGCTACGTTA 58.553 47.619 0.00 0.00 0.00 3.18
231 232 9.850628 ATCGCTACGTTACATGTAATAATATGT 57.149 29.630 20.72 12.08 40.23 2.29
232 233 9.120422 TCGCTACGTTACATGTAATAATATGTG 57.880 33.333 20.72 14.47 37.89 3.21
263 264 7.291651 AGGTTTCTAATTCAAGGTATCCGGATA 59.708 37.037 20.49 20.49 0.00 2.59
266 267 7.182817 TCTAATTCAAGGTATCCGGATATGG 57.817 40.000 26.46 15.71 0.00 2.74
271 272 3.914426 AGGTATCCGGATATGGAATGC 57.086 47.619 26.46 11.87 42.46 3.56
302 303 2.363276 TGGCCGGTGACTATCCGT 60.363 61.111 1.90 0.00 45.63 4.69
306 307 1.745320 GCCGGTGACTATCCGTGGAT 61.745 60.000 1.90 6.63 45.63 3.41
307 308 0.032130 CCGGTGACTATCCGTGGATG 59.968 60.000 11.68 4.53 45.63 3.51
308 309 0.597637 CGGTGACTATCCGTGGATGC 60.598 60.000 11.68 2.07 42.62 3.91
309 310 0.464036 GGTGACTATCCGTGGATGCA 59.536 55.000 11.68 4.54 36.17 3.96
310 311 1.571919 GTGACTATCCGTGGATGCAC 58.428 55.000 11.68 7.39 36.17 4.57
311 312 1.137086 GTGACTATCCGTGGATGCACT 59.863 52.381 15.82 0.00 36.17 4.40
312 313 1.409064 TGACTATCCGTGGATGCACTC 59.591 52.381 15.82 5.50 36.17 3.51
313 314 0.385751 ACTATCCGTGGATGCACTCG 59.614 55.000 15.82 5.43 36.17 4.18
314 315 0.319040 CTATCCGTGGATGCACTCGG 60.319 60.000 15.82 12.56 43.65 4.63
316 317 2.264480 CCGTGGATGCACTCGGAA 59.736 61.111 15.82 0.00 44.86 4.30
317 318 1.811266 CCGTGGATGCACTCGGAAG 60.811 63.158 15.82 0.00 44.86 3.46
318 319 2.456119 CGTGGATGCACTCGGAAGC 61.456 63.158 15.82 0.00 0.00 3.86
319 320 2.125552 TGGATGCACTCGGAAGCG 60.126 61.111 0.00 0.00 0.00 4.68
320 321 2.125512 GGATGCACTCGGAAGCGT 60.126 61.111 0.00 0.00 0.00 5.07
321 322 2.167861 GGATGCACTCGGAAGCGTC 61.168 63.158 13.13 13.13 44.09 5.19
322 323 1.153745 GATGCACTCGGAAGCGTCT 60.154 57.895 13.88 0.00 42.13 4.18
323 324 0.100682 GATGCACTCGGAAGCGTCTA 59.899 55.000 13.88 0.00 42.13 2.59
324 325 0.179134 ATGCACTCGGAAGCGTCTAC 60.179 55.000 0.00 0.00 0.00 2.59
325 326 1.211969 GCACTCGGAAGCGTCTACA 59.788 57.895 0.00 0.00 0.00 2.74
326 327 0.179134 GCACTCGGAAGCGTCTACAT 60.179 55.000 0.00 0.00 0.00 2.29
327 328 1.065102 GCACTCGGAAGCGTCTACATA 59.935 52.381 0.00 0.00 0.00 2.29
328 329 2.287668 GCACTCGGAAGCGTCTACATAT 60.288 50.000 0.00 0.00 0.00 1.78
336 337 5.062934 CGGAAGCGTCTACATATGTTTGAAA 59.937 40.000 14.77 0.00 0.00 2.69
337 338 6.401688 CGGAAGCGTCTACATATGTTTGAAAA 60.402 38.462 14.77 0.00 0.00 2.29
358 359 7.435784 TGAAAAGTTAAATTTGTTAAGTCCGGC 59.564 33.333 1.03 0.00 0.00 6.13
360 361 6.250344 AGTTAAATTTGTTAAGTCCGGCTC 57.750 37.500 0.00 0.00 0.00 4.70
365 366 3.863142 TTGTTAAGTCCGGCTCTAGAC 57.137 47.619 0.00 1.38 0.00 2.59
408 409 1.664151 GGGTAGCATCACGCAGTTAAC 59.336 52.381 0.00 0.00 41.61 2.01
476 477 1.448540 CACGGATCGCTTTGAGGCT 60.449 57.895 0.00 0.00 0.00 4.58
512 513 8.437742 TCTTTAAACGACAACGATATTTCTTCC 58.562 33.333 0.00 0.00 42.66 3.46
601 602 0.100325 TTGCCTGTTTTCAGTGCACG 59.900 50.000 12.01 6.78 45.92 5.34
717 726 1.205893 TGCATGCATGTACACTCGGTA 59.794 47.619 26.79 0.00 0.00 4.02
748 757 0.394565 GGAGTGGTCAGACTGCAACT 59.605 55.000 0.00 6.63 34.59 3.16
870 882 2.523015 GTACGTATGAAGTGACACCGG 58.477 52.381 0.00 0.00 0.00 5.28
975 987 0.308068 TCTTCGATCATCTCCGTCGC 59.692 55.000 0.00 0.00 35.48 5.19
976 988 0.029433 CTTCGATCATCTCCGTCGCA 59.971 55.000 0.00 0.00 35.48 5.10
1005 1021 1.290203 GCAAGAAGCGATCGATGGAA 58.710 50.000 21.57 0.00 0.00 3.53
1128 1144 2.676471 GGCACCAAGACCCGCATT 60.676 61.111 0.00 0.00 0.00 3.56
1544 1560 2.125961 CCTACTAAGCTCGGCCCGT 61.126 63.158 1.63 0.00 0.00 5.28
1582 1598 3.068165 GCCGTTAATTAGGGGTACGTACT 59.932 47.826 24.07 8.34 32.24 2.73
1583 1599 4.277423 GCCGTTAATTAGGGGTACGTACTA 59.723 45.833 24.07 7.33 32.24 1.82
1635 1652 2.023888 TCCTTTCTCTGGAGAGGGGTAG 60.024 54.545 15.83 0.00 42.25 3.18
1653 1670 1.519455 GATGGAGTCGACGCCCAAG 60.519 63.158 31.74 0.00 34.71 3.61
1691 1708 3.305720 TCACGGGGCTACTCAGAATTAT 58.694 45.455 0.00 0.00 0.00 1.28
1696 1713 3.904339 GGGGCTACTCAGAATTATCCTCA 59.096 47.826 0.00 0.00 0.00 3.86
1704 1740 4.507710 TCAGAATTATCCTCAGTGTGTGC 58.492 43.478 0.00 0.00 0.00 4.57
1764 1800 2.196749 CATCATATCGGCCTGTATCGC 58.803 52.381 0.00 0.00 0.00 4.58
1824 1860 4.803098 TTCTAAGTTGCTCAGGGTAGTC 57.197 45.455 0.00 0.00 0.00 2.59
1833 1869 2.420687 GCTCAGGGTAGTCATCCTTTGG 60.421 54.545 0.00 0.00 0.00 3.28
1858 1894 7.922811 GGGCTTATTTATGGAAAAGTCATCTTG 59.077 37.037 0.00 0.00 33.79 3.02
1899 1935 3.119029 CCCCTGCCATGAACAGTAAATTG 60.119 47.826 12.83 0.00 33.09 2.32
1904 1940 6.146021 CCTGCCATGAACAGTAAATTGAAAAC 59.854 38.462 12.83 0.00 33.09 2.43
1905 1941 6.577103 TGCCATGAACAGTAAATTGAAAACA 58.423 32.000 0.00 0.00 0.00 2.83
1907 1943 7.010923 TGCCATGAACAGTAAATTGAAAACAAC 59.989 33.333 0.00 0.00 0.00 3.32
1908 1944 7.224557 GCCATGAACAGTAAATTGAAAACAACT 59.775 33.333 0.00 0.00 0.00 3.16
1909 1945 8.542132 CCATGAACAGTAAATTGAAAACAACTG 58.458 33.333 0.00 0.00 38.43 3.16
1980 2019 5.844301 AGTTTTGAGTGTTTGCAAAGTTG 57.156 34.783 13.26 0.00 35.64 3.16
2012 2052 5.705609 ATGACATTTGTGGAAGTTGTACC 57.294 39.130 0.00 0.00 0.00 3.34
2126 2168 7.487829 TGATGAAACTTTGCAAGTACTCAAAAC 59.512 33.333 10.08 4.73 41.91 2.43
2148 2190 4.308265 CATTCATCAATGTTTGCCACACA 58.692 39.130 0.00 0.00 38.61 3.72
2149 2191 3.367992 TCATCAATGTTTGCCACACAC 57.632 42.857 0.00 0.00 38.61 3.82
2150 2192 2.692041 TCATCAATGTTTGCCACACACA 59.308 40.909 0.00 0.00 38.61 3.72
2315 2357 2.504367 GCTTATATGCACCCGGTGAAT 58.496 47.619 22.37 18.94 35.71 2.57
2375 2419 4.560743 TTGAGTGCGGCAGGTGCA 62.561 61.111 1.18 0.00 44.36 4.57
2398 2442 6.237996 GCATGCACAATTTCATGACTAAATGG 60.238 38.462 14.21 0.00 41.82 3.16
2399 2443 6.343716 TGCACAATTTCATGACTAAATGGT 57.656 33.333 0.00 0.00 31.93 3.55
2405 2449 8.405531 ACAATTTCATGACTAAATGGTATTCGG 58.594 33.333 0.00 0.00 30.37 4.30
2482 2527 8.463930 AATGTTTCTCACAGGTCTGAAATTTA 57.536 30.769 4.84 0.00 39.40 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.234972 TCGATGATGAATCCGTTCTTGAATG 59.765 40.000 0.00 0.00 35.33 2.67
1 2 5.359756 TCGATGATGAATCCGTTCTTGAAT 58.640 37.500 0.00 0.00 35.33 2.57
2 3 4.754322 TCGATGATGAATCCGTTCTTGAA 58.246 39.130 0.00 0.00 35.33 2.69
3 4 4.385358 TCGATGATGAATCCGTTCTTGA 57.615 40.909 0.00 0.00 35.33 3.02
4 5 4.987285 AGATCGATGATGAATCCGTTCTTG 59.013 41.667 0.54 0.00 35.33 3.02
5 6 4.987285 CAGATCGATGATGAATCCGTTCTT 59.013 41.667 0.54 0.00 35.33 2.52
6 7 4.279420 TCAGATCGATGATGAATCCGTTCT 59.721 41.667 0.54 0.00 35.33 3.01
7 8 4.384247 GTCAGATCGATGATGAATCCGTTC 59.616 45.833 0.54 0.00 34.85 3.95
8 9 4.302455 GTCAGATCGATGATGAATCCGTT 58.698 43.478 0.54 0.00 30.80 4.44
9 10 3.610349 CGTCAGATCGATGATGAATCCGT 60.610 47.826 0.54 0.00 38.28 4.69
10 11 2.913590 CGTCAGATCGATGATGAATCCG 59.086 50.000 0.54 3.70 38.28 4.18
11 12 3.906998 ACGTCAGATCGATGATGAATCC 58.093 45.455 13.79 2.04 38.28 3.01
12 13 4.978580 TGAACGTCAGATCGATGATGAATC 59.021 41.667 13.79 11.40 38.28 2.52
13 14 4.742167 GTGAACGTCAGATCGATGATGAAT 59.258 41.667 13.79 3.86 38.28 2.57
14 15 4.105486 GTGAACGTCAGATCGATGATGAA 58.895 43.478 13.79 0.00 38.28 2.57
15 16 3.128589 TGTGAACGTCAGATCGATGATGA 59.871 43.478 13.79 9.90 38.28 2.92
16 17 3.438360 TGTGAACGTCAGATCGATGATG 58.562 45.455 0.54 4.48 41.18 3.07
17 18 3.782889 TGTGAACGTCAGATCGATGAT 57.217 42.857 0.54 0.00 34.46 2.45
18 19 3.569250 TTGTGAACGTCAGATCGATGA 57.431 42.857 0.54 0.00 34.46 2.92
19 20 3.428534 TGTTTGTGAACGTCAGATCGATG 59.571 43.478 0.54 0.00 38.65 3.84
20 21 3.649073 TGTTTGTGAACGTCAGATCGAT 58.351 40.909 0.00 0.00 38.65 3.59
21 22 3.049912 CTGTTTGTGAACGTCAGATCGA 58.950 45.455 0.00 0.00 38.65 3.59
22 23 2.155732 CCTGTTTGTGAACGTCAGATCG 59.844 50.000 0.00 0.00 38.65 3.69
23 24 3.131396 ACCTGTTTGTGAACGTCAGATC 58.869 45.455 0.00 0.00 38.65 2.75
24 25 3.194005 ACCTGTTTGTGAACGTCAGAT 57.806 42.857 0.00 0.00 38.65 2.90
25 26 2.684001 ACCTGTTTGTGAACGTCAGA 57.316 45.000 0.00 0.00 38.65 3.27
26 27 2.031683 GGAACCTGTTTGTGAACGTCAG 59.968 50.000 0.00 0.00 38.65 3.51
27 28 2.011222 GGAACCTGTTTGTGAACGTCA 58.989 47.619 0.00 0.00 38.65 4.35
28 29 1.004292 CGGAACCTGTTTGTGAACGTC 60.004 52.381 0.00 0.00 38.65 4.34
29 30 1.011333 CGGAACCTGTTTGTGAACGT 58.989 50.000 0.00 0.00 38.65 3.99
30 31 0.306533 CCGGAACCTGTTTGTGAACG 59.693 55.000 0.00 0.00 38.65 3.95
31 32 0.666374 CCCGGAACCTGTTTGTGAAC 59.334 55.000 0.73 0.00 36.29 3.18
32 33 1.104577 GCCCGGAACCTGTTTGTGAA 61.105 55.000 0.73 0.00 0.00 3.18
33 34 1.527380 GCCCGGAACCTGTTTGTGA 60.527 57.895 0.73 0.00 0.00 3.58
34 35 1.515521 GAGCCCGGAACCTGTTTGTG 61.516 60.000 0.73 0.00 0.00 3.33
35 36 1.228154 GAGCCCGGAACCTGTTTGT 60.228 57.895 0.73 0.00 0.00 2.83
36 37 1.073199 AGAGCCCGGAACCTGTTTG 59.927 57.895 0.73 0.00 0.00 2.93
37 38 1.073199 CAGAGCCCGGAACCTGTTT 59.927 57.895 0.73 0.00 0.00 2.83
38 39 1.841556 TCAGAGCCCGGAACCTGTT 60.842 57.895 0.73 0.00 0.00 3.16
39 40 2.203788 TCAGAGCCCGGAACCTGT 60.204 61.111 0.73 0.00 0.00 4.00
40 41 2.266055 GTCAGAGCCCGGAACCTG 59.734 66.667 0.73 6.82 0.00 4.00
41 42 3.382832 CGTCAGAGCCCGGAACCT 61.383 66.667 0.73 0.00 0.00 3.50
42 43 3.358076 CTCGTCAGAGCCCGGAACC 62.358 68.421 0.73 0.00 37.73 3.62
43 44 2.182030 CTCGTCAGAGCCCGGAAC 59.818 66.667 0.73 0.00 37.73 3.62
44 45 3.068691 CCTCGTCAGAGCCCGGAA 61.069 66.667 0.73 0.00 43.05 4.30
45 46 3.578968 TTCCTCGTCAGAGCCCGGA 62.579 63.158 0.73 0.00 43.05 5.14
46 47 3.068691 TTCCTCGTCAGAGCCCGG 61.069 66.667 0.00 0.00 43.05 5.73
47 48 1.999071 CTCTTCCTCGTCAGAGCCCG 61.999 65.000 0.00 0.00 43.05 6.13
48 49 0.968393 ACTCTTCCTCGTCAGAGCCC 60.968 60.000 0.00 0.00 43.05 5.19
49 50 1.673920 CTACTCTTCCTCGTCAGAGCC 59.326 57.143 0.00 0.00 43.05 4.70
50 51 2.096819 CACTACTCTTCCTCGTCAGAGC 59.903 54.545 0.00 0.00 43.05 4.09
51 52 2.096819 GCACTACTCTTCCTCGTCAGAG 59.903 54.545 0.00 0.00 43.98 3.35
52 53 2.085320 GCACTACTCTTCCTCGTCAGA 58.915 52.381 0.00 0.00 0.00 3.27
53 54 1.813178 TGCACTACTCTTCCTCGTCAG 59.187 52.381 0.00 0.00 0.00 3.51
54 55 1.905637 TGCACTACTCTTCCTCGTCA 58.094 50.000 0.00 0.00 0.00 4.35
55 56 2.480416 CCATGCACTACTCTTCCTCGTC 60.480 54.545 0.00 0.00 0.00 4.20
56 57 1.478510 CCATGCACTACTCTTCCTCGT 59.521 52.381 0.00 0.00 0.00 4.18
57 58 1.202463 CCCATGCACTACTCTTCCTCG 60.202 57.143 0.00 0.00 0.00 4.63
58 59 2.102252 CTCCCATGCACTACTCTTCCTC 59.898 54.545 0.00 0.00 0.00 3.71
59 60 2.114616 CTCCCATGCACTACTCTTCCT 58.885 52.381 0.00 0.00 0.00 3.36
60 61 2.111384 TCTCCCATGCACTACTCTTCC 58.889 52.381 0.00 0.00 0.00 3.46
61 62 2.480416 CGTCTCCCATGCACTACTCTTC 60.480 54.545 0.00 0.00 0.00 2.87
62 63 1.478510 CGTCTCCCATGCACTACTCTT 59.521 52.381 0.00 0.00 0.00 2.85
63 64 1.107114 CGTCTCCCATGCACTACTCT 58.893 55.000 0.00 0.00 0.00 3.24
64 65 0.103208 CCGTCTCCCATGCACTACTC 59.897 60.000 0.00 0.00 0.00 2.59
65 66 1.961180 GCCGTCTCCCATGCACTACT 61.961 60.000 0.00 0.00 0.00 2.57
66 67 1.521681 GCCGTCTCCCATGCACTAC 60.522 63.158 0.00 0.00 0.00 2.73
67 68 2.900273 GCCGTCTCCCATGCACTA 59.100 61.111 0.00 0.00 0.00 2.74
68 69 4.457496 CGCCGTCTCCCATGCACT 62.457 66.667 0.00 0.00 0.00 4.40
84 85 3.771160 AAGGTACTCCAGGCGCCG 61.771 66.667 23.20 16.10 38.49 6.46
85 86 2.125106 CAAGGTACTCCAGGCGCC 60.125 66.667 21.89 21.89 38.49 6.53
86 87 1.153549 CTCAAGGTACTCCAGGCGC 60.154 63.158 0.00 0.00 38.49 6.53
87 88 1.153549 GCTCAAGGTACTCCAGGCG 60.154 63.158 0.00 0.00 38.49 5.52
88 89 0.107945 CAGCTCAAGGTACTCCAGGC 60.108 60.000 0.00 0.00 38.49 4.85
89 90 0.539051 CCAGCTCAAGGTACTCCAGG 59.461 60.000 0.00 0.00 38.49 4.45
90 91 0.107945 GCCAGCTCAAGGTACTCCAG 60.108 60.000 0.00 0.00 38.49 3.86
91 92 0.545309 AGCCAGCTCAAGGTACTCCA 60.545 55.000 0.00 0.00 38.49 3.86
92 93 0.176910 GAGCCAGCTCAAGGTACTCC 59.823 60.000 14.70 0.00 42.31 3.85
93 94 0.179124 CGAGCCAGCTCAAGGTACTC 60.179 60.000 19.08 2.81 42.86 2.59
94 95 0.900647 ACGAGCCAGCTCAAGGTACT 60.901 55.000 19.08 0.00 42.86 2.73
95 96 0.737715 CACGAGCCAGCTCAAGGTAC 60.738 60.000 19.08 0.00 42.86 3.34
96 97 1.185618 ACACGAGCCAGCTCAAGGTA 61.186 55.000 19.08 0.00 42.86 3.08
97 98 2.345244 CACGAGCCAGCTCAAGGT 59.655 61.111 19.08 6.65 42.86 3.50
98 99 1.739562 GACACGAGCCAGCTCAAGG 60.740 63.158 19.08 9.92 42.86 3.61
99 100 1.739562 GGACACGAGCCAGCTCAAG 60.740 63.158 19.08 12.53 42.86 3.02
100 101 2.038814 TTGGACACGAGCCAGCTCAA 62.039 55.000 19.08 3.07 42.86 3.02
101 102 1.830587 ATTGGACACGAGCCAGCTCA 61.831 55.000 19.08 0.00 42.86 4.26
102 103 1.078848 ATTGGACACGAGCCAGCTC 60.079 57.895 9.67 9.67 36.64 4.09
103 104 1.376424 CATTGGACACGAGCCAGCT 60.376 57.895 0.00 0.00 36.64 4.24
104 105 3.044059 GCATTGGACACGAGCCAGC 62.044 63.158 0.00 0.00 36.64 4.85
105 106 2.401766 GGCATTGGACACGAGCCAG 61.402 63.158 0.00 0.00 44.59 4.85
106 107 2.359850 GGCATTGGACACGAGCCA 60.360 61.111 0.00 0.00 44.59 4.75
107 108 2.252072 TAGGGCATTGGACACGAGCC 62.252 60.000 0.00 0.00 44.48 4.70
108 109 1.090052 GTAGGGCATTGGACACGAGC 61.090 60.000 0.00 0.00 0.00 5.03
109 110 0.537188 AGTAGGGCATTGGACACGAG 59.463 55.000 0.00 0.00 0.00 4.18
110 111 0.535335 GAGTAGGGCATTGGACACGA 59.465 55.000 0.00 0.00 0.00 4.35
111 112 0.537188 AGAGTAGGGCATTGGACACG 59.463 55.000 0.00 0.00 0.00 4.49
112 113 2.483889 GCTAGAGTAGGGCATTGGACAC 60.484 54.545 0.00 0.00 0.00 3.67
113 114 1.762957 GCTAGAGTAGGGCATTGGACA 59.237 52.381 0.00 0.00 0.00 4.02
114 115 2.043227 AGCTAGAGTAGGGCATTGGAC 58.957 52.381 0.00 0.00 0.00 4.02
115 116 2.435805 CAAGCTAGAGTAGGGCATTGGA 59.564 50.000 0.00 0.00 0.00 3.53
116 117 2.843701 CAAGCTAGAGTAGGGCATTGG 58.156 52.381 0.00 0.00 0.00 3.16
117 118 2.216898 GCAAGCTAGAGTAGGGCATTG 58.783 52.381 0.00 0.00 0.00 2.82
118 119 1.141858 GGCAAGCTAGAGTAGGGCATT 59.858 52.381 0.00 0.00 0.00 3.56
119 120 0.761802 GGCAAGCTAGAGTAGGGCAT 59.238 55.000 0.00 0.00 0.00 4.40
120 121 1.676678 CGGCAAGCTAGAGTAGGGCA 61.677 60.000 0.00 0.00 0.00 5.36
121 122 1.068250 CGGCAAGCTAGAGTAGGGC 59.932 63.158 0.00 0.00 0.00 5.19
122 123 1.742768 CCGGCAAGCTAGAGTAGGG 59.257 63.158 0.00 0.00 0.00 3.53
123 124 1.068250 GCCGGCAAGCTAGAGTAGG 59.932 63.158 24.80 0.00 0.00 3.18
124 125 1.299468 CGCCGGCAAGCTAGAGTAG 60.299 63.158 28.98 0.37 0.00 2.57
125 126 1.751544 TCGCCGGCAAGCTAGAGTA 60.752 57.895 28.98 0.00 0.00 2.59
126 127 3.068691 TCGCCGGCAAGCTAGAGT 61.069 61.111 28.98 0.00 0.00 3.24
127 128 2.583593 GTCGCCGGCAAGCTAGAG 60.584 66.667 28.98 7.38 0.00 2.43
128 129 4.143333 GGTCGCCGGCAAGCTAGA 62.143 66.667 28.98 11.71 0.00 2.43
139 140 2.280592 AGTGTTGGTTCGGTCGCC 60.281 61.111 0.00 0.00 0.00 5.54
140 141 1.300697 AGAGTGTTGGTTCGGTCGC 60.301 57.895 0.00 0.00 0.00 5.19
141 142 0.031585 TCAGAGTGTTGGTTCGGTCG 59.968 55.000 0.00 0.00 0.00 4.79
142 143 1.865340 GTTCAGAGTGTTGGTTCGGTC 59.135 52.381 0.00 0.00 0.00 4.79
143 144 1.208535 TGTTCAGAGTGTTGGTTCGGT 59.791 47.619 0.00 0.00 0.00 4.69
144 145 1.867233 CTGTTCAGAGTGTTGGTTCGG 59.133 52.381 0.00 0.00 0.00 4.30
145 146 1.867233 CCTGTTCAGAGTGTTGGTTCG 59.133 52.381 1.00 0.00 0.00 3.95
146 147 2.872858 GTCCTGTTCAGAGTGTTGGTTC 59.127 50.000 1.00 0.00 0.00 3.62
147 148 2.741878 CGTCCTGTTCAGAGTGTTGGTT 60.742 50.000 1.00 0.00 0.00 3.67
148 149 1.202533 CGTCCTGTTCAGAGTGTTGGT 60.203 52.381 1.00 0.00 0.00 3.67
149 150 1.068588 TCGTCCTGTTCAGAGTGTTGG 59.931 52.381 1.00 0.00 0.00 3.77
150 151 2.398498 CTCGTCCTGTTCAGAGTGTTG 58.602 52.381 1.00 0.00 0.00 3.33
151 152 1.269831 GCTCGTCCTGTTCAGAGTGTT 60.270 52.381 1.00 0.00 33.57 3.32
152 153 0.315568 GCTCGTCCTGTTCAGAGTGT 59.684 55.000 1.00 0.00 33.57 3.55
153 154 0.600557 AGCTCGTCCTGTTCAGAGTG 59.399 55.000 1.00 0.00 33.57 3.51
154 155 0.600557 CAGCTCGTCCTGTTCAGAGT 59.399 55.000 1.00 0.00 33.57 3.24
155 156 0.108898 CCAGCTCGTCCTGTTCAGAG 60.109 60.000 1.00 0.00 0.00 3.35
156 157 1.536073 CCCAGCTCGTCCTGTTCAGA 61.536 60.000 1.00 0.00 0.00 3.27
157 158 1.079543 CCCAGCTCGTCCTGTTCAG 60.080 63.158 0.00 0.00 0.00 3.02
158 159 1.533033 TCCCAGCTCGTCCTGTTCA 60.533 57.895 0.00 0.00 0.00 3.18
159 160 1.216710 CTCCCAGCTCGTCCTGTTC 59.783 63.158 0.00 0.00 0.00 3.18
160 161 0.251653 TACTCCCAGCTCGTCCTGTT 60.252 55.000 0.00 0.00 0.00 3.16
161 162 0.681564 CTACTCCCAGCTCGTCCTGT 60.682 60.000 0.00 0.00 0.00 4.00
172 173 5.365619 GAGTTTTGTTCAGTTCTACTCCCA 58.634 41.667 0.00 0.00 0.00 4.37
178 179 4.056050 GAGCGGAGTTTTGTTCAGTTCTA 58.944 43.478 0.00 0.00 0.00 2.10
179 180 2.872858 GAGCGGAGTTTTGTTCAGTTCT 59.127 45.455 0.00 0.00 0.00 3.01
180 181 2.612212 TGAGCGGAGTTTTGTTCAGTTC 59.388 45.455 0.00 0.00 0.00 3.01
184 185 3.275143 TCTTTGAGCGGAGTTTTGTTCA 58.725 40.909 0.00 0.00 0.00 3.18
186 187 3.058914 CGATCTTTGAGCGGAGTTTTGTT 60.059 43.478 0.00 0.00 37.82 2.83
189 190 1.464997 GCGATCTTTGAGCGGAGTTTT 59.535 47.619 7.31 0.00 41.94 2.43
231 232 9.832445 GATACCTTGAATTAGAAACCTCATACA 57.168 33.333 0.00 0.00 0.00 2.29
232 233 9.274206 GGATACCTTGAATTAGAAACCTCATAC 57.726 37.037 0.00 0.00 0.00 2.39
234 235 6.992715 CGGATACCTTGAATTAGAAACCTCAT 59.007 38.462 0.00 0.00 0.00 2.90
235 236 6.346096 CGGATACCTTGAATTAGAAACCTCA 58.654 40.000 0.00 0.00 0.00 3.86
236 237 5.758784 CCGGATACCTTGAATTAGAAACCTC 59.241 44.000 0.00 0.00 0.00 3.85
243 244 7.182817 TCCATATCCGGATACCTTGAATTAG 57.817 40.000 26.28 8.08 0.00 1.73
249 250 3.941483 GCATTCCATATCCGGATACCTTG 59.059 47.826 26.28 19.46 34.19 3.61
283 284 2.717044 CGGATAGTCACCGGCCACA 61.717 63.158 0.00 0.00 45.65 4.17
293 294 1.600663 CGAGTGCATCCACGGATAGTC 60.601 57.143 0.00 0.00 46.62 2.59
302 303 2.125552 CGCTTCCGAGTGCATCCA 60.126 61.111 0.00 0.00 36.29 3.41
306 307 1.211969 GTAGACGCTTCCGAGTGCA 59.788 57.895 0.00 0.00 36.87 4.57
307 308 0.179134 ATGTAGACGCTTCCGAGTGC 60.179 55.000 0.00 0.00 36.87 4.40
308 309 3.243101 ACATATGTAGACGCTTCCGAGTG 60.243 47.826 6.56 0.00 39.33 3.51
309 310 2.950309 ACATATGTAGACGCTTCCGAGT 59.050 45.455 6.56 0.00 38.29 4.18
310 311 3.627732 ACATATGTAGACGCTTCCGAG 57.372 47.619 6.56 0.00 38.29 4.63
311 312 4.109766 CAAACATATGTAGACGCTTCCGA 58.890 43.478 9.21 0.00 38.29 4.55
312 313 4.109766 TCAAACATATGTAGACGCTTCCG 58.890 43.478 9.21 0.00 41.14 4.30
313 314 6.417191 TTTCAAACATATGTAGACGCTTCC 57.583 37.500 9.21 0.00 0.00 3.46
314 315 7.519002 ACTTTTCAAACATATGTAGACGCTTC 58.481 34.615 9.21 0.00 0.00 3.86
315 316 7.435068 ACTTTTCAAACATATGTAGACGCTT 57.565 32.000 9.21 0.00 0.00 4.68
316 317 7.435068 AACTTTTCAAACATATGTAGACGCT 57.565 32.000 9.21 0.00 0.00 5.07
317 318 9.601971 TTTAACTTTTCAAACATATGTAGACGC 57.398 29.630 9.21 0.00 0.00 5.19
336 337 6.489022 AGAGCCGGACTTAACAAATTTAACTT 59.511 34.615 5.05 0.00 0.00 2.66
337 338 6.002082 AGAGCCGGACTTAACAAATTTAACT 58.998 36.000 5.05 0.00 0.00 2.24
349 350 0.107312 AGCGTCTAGAGCCGGACTTA 60.107 55.000 5.05 0.00 34.64 2.24
358 359 4.987419 GCGTGAGAGCGTCTAGAG 57.013 61.111 0.00 0.00 0.00 2.43
476 477 6.908284 CGTTGTCGTTTAAAGAAGGAATTCAA 59.092 34.615 7.93 0.00 0.00 2.69
552 553 2.604046 AACAGACCATAGGCATCGAC 57.396 50.000 0.00 0.00 0.00 4.20
553 554 2.481276 CGAAACAGACCATAGGCATCGA 60.481 50.000 0.00 0.00 0.00 3.59
554 555 1.860950 CGAAACAGACCATAGGCATCG 59.139 52.381 0.00 0.00 0.00 3.84
555 556 1.599542 GCGAAACAGACCATAGGCATC 59.400 52.381 0.00 0.00 0.00 3.91
556 557 1.065491 TGCGAAACAGACCATAGGCAT 60.065 47.619 0.00 0.00 0.00 4.40
557 558 0.323302 TGCGAAACAGACCATAGGCA 59.677 50.000 0.00 0.00 0.00 4.75
558 559 1.398390 CTTGCGAAACAGACCATAGGC 59.602 52.381 0.00 0.00 0.00 3.93
559 560 2.699954 ACTTGCGAAACAGACCATAGG 58.300 47.619 0.00 0.00 0.00 2.57
601 602 4.093556 GTCACTAGCAGTAATGGAGCAAAC 59.906 45.833 0.00 0.00 0.00 2.93
721 730 2.301296 AGTCTGACCACTCCACATCTTG 59.699 50.000 3.76 0.00 0.00 3.02
975 987 0.594796 GCTTCTTGCCCAACGTGTTG 60.595 55.000 5.76 5.76 40.13 3.33
976 988 1.733526 GCTTCTTGCCCAACGTGTT 59.266 52.632 0.00 0.00 35.15 3.32
1005 1021 2.604686 TGCTCCTTGCCCGACTCT 60.605 61.111 0.00 0.00 42.00 3.24
1544 1560 2.191908 GCCATACACATCGGCCCA 59.808 61.111 0.00 0.00 40.07 5.36
1582 1598 2.172679 TGAGGTCAATGGCACGTACTA 58.827 47.619 0.00 0.00 0.00 1.82
1583 1599 0.973632 TGAGGTCAATGGCACGTACT 59.026 50.000 0.00 0.00 0.00 2.73
1635 1652 1.519455 CTTGGGCGTCGACTCCATC 60.519 63.158 25.02 10.09 0.00 3.51
1691 1708 1.134521 AGAAAACGCACACACTGAGGA 60.135 47.619 0.00 0.00 0.00 3.71
1696 1713 2.160813 ACGAAAAGAAAACGCACACACT 59.839 40.909 0.00 0.00 0.00 3.55
1704 1740 3.538638 CCAAACGCAACGAAAAGAAAACG 60.539 43.478 0.00 0.00 0.00 3.60
1764 1800 4.092968 GGGTAATGAGCTGACTAACAAACG 59.907 45.833 0.00 0.00 0.00 3.60
1824 1860 6.729690 TTCCATAAATAAGCCCAAAGGATG 57.270 37.500 0.00 0.00 33.47 3.51
1833 1869 8.470002 ACAAGATGACTTTTCCATAAATAAGCC 58.530 33.333 0.00 0.00 33.70 4.35
1876 1912 1.367346 TTACTGTTCATGGCAGGGGA 58.633 50.000 17.95 0.00 38.22 4.81
1944 1983 8.188531 ACACTCAAAACTTTCATCAATGTTTG 57.811 30.769 0.00 0.00 38.95 2.93
1980 2019 5.472148 TCCACAAATGTCATTTCAGAATGC 58.528 37.500 7.87 0.00 41.94 3.56
2126 2168 4.150980 GTGTGTGGCAAACATTGATGAATG 59.849 41.667 14.67 3.09 41.97 2.67
2223 2265 4.095946 AGCCAAAAATAAGGGATGCAGAA 58.904 39.130 0.00 0.00 0.00 3.02
2226 2268 7.009550 TCATATAGCCAAAAATAAGGGATGCA 58.990 34.615 0.00 0.00 0.00 3.96
2265 2307 5.753438 CACCGAATTGAAGATCCGATTCTTA 59.247 40.000 9.14 0.00 36.10 2.10
2298 2340 6.422344 TTTACTATTCACCGGGTGCATATA 57.578 37.500 22.42 16.39 32.98 0.86
2375 2419 6.938507 ACCATTTAGTCATGAAATTGTGCAT 58.061 32.000 0.00 0.00 0.00 3.96
2380 2424 8.620416 TCCGAATACCATTTAGTCATGAAATTG 58.380 33.333 0.00 0.00 0.00 2.32
2398 2442 1.370657 CCGCGAGCTCTCCGAATAC 60.371 63.158 20.73 0.00 0.00 1.89
2399 2443 3.031495 CCGCGAGCTCTCCGAATA 58.969 61.111 20.73 0.00 0.00 1.75
2405 2449 3.253955 TTTTTGCCGCGAGCTCTC 58.746 55.556 8.23 2.14 44.23 3.20
2482 2527 4.465660 TCAGTAGCTCTCAGCAAAGAAGAT 59.534 41.667 0.00 0.00 45.56 2.40


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.