Multiple sequence alignment - TraesCS2A01G403800

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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 TraesCS2A01G403800 chr2A 100.000 3272 0 0 1 3272 659322650 659325921 0.000000e+00 6043
1 TraesCS2A01G403800 chr2A 76.271 236 45 6 200 435 429715163 429714939 7.420000e-22 115
2 TraesCS2A01G403800 chr2D 92.572 2854 134 23 185 3011 515629262 515632064 0.000000e+00 4024
3 TraesCS2A01G403800 chr2B 95.443 1909 63 15 631 2527 607106210 607108106 0.000000e+00 3022
4 TraesCS2A01G403800 chr2B 90.674 386 20 10 2565 2943 607108100 607108476 1.750000e-137 499
5 TraesCS2A01G403800 chr2B 80.186 323 48 9 2949 3263 607108522 607108836 9.130000e-56 228
6 TraesCS2A01G403800 chr6A 84.179 1182 167 14 993 2167 470212847 470214015 0.000000e+00 1129
7 TraesCS2A01G403800 chr6D 83.983 1180 165 17 997 2167 331255280 331256444 0.000000e+00 1110
8 TraesCS2A01G403800 chr6B 83.759 1176 175 14 997 2167 489715041 489713877 0.000000e+00 1099
9 TraesCS2A01G403800 chr1D 100.000 157 0 0 1 157 58700025 58700181 1.150000e-74 291
10 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 14268569 14268725 1.150000e-74 291
11 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 16956978 16957134 1.150000e-74 291
12 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 25327857 25328013 1.150000e-74 291
13 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 35704214 35704370 1.150000e-74 291
14 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 72848337 72848493 1.150000e-74 291
15 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 112149182 112149338 1.150000e-74 291
16 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 333683131 333682975 1.150000e-74 291
17 TraesCS2A01G403800 chr1A 100.000 157 0 0 1 157 356729307 356729463 1.150000e-74 291


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 TraesCS2A01G403800 chr2A 659322650 659325921 3271 False 6043.000000 6043 100.000000 1 3272 1 chr2A.!!$F1 3271
1 TraesCS2A01G403800 chr2D 515629262 515632064 2802 False 4024.000000 4024 92.572000 185 3011 1 chr2D.!!$F1 2826
2 TraesCS2A01G403800 chr2B 607106210 607108836 2626 False 1249.666667 3022 88.767667 631 3263 3 chr2B.!!$F1 2632
3 TraesCS2A01G403800 chr6A 470212847 470214015 1168 False 1129.000000 1129 84.179000 993 2167 1 chr6A.!!$F1 1174
4 TraesCS2A01G403800 chr6D 331255280 331256444 1164 False 1110.000000 1110 83.983000 997 2167 1 chr6D.!!$F1 1170
5 TraesCS2A01G403800 chr6B 489713877 489715041 1164 True 1099.000000 1099 83.759000 997 2167 1 chr6B.!!$R1 1170

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
119 120 0.174845 CGACCGCCACTCATAAGGAA 59.825 55.0 0.00 0.0 0.00 3.36 F
158 159 0.179100 ATGCTCCGACTTCATCACGG 60.179 55.0 0.00 0.0 46.71 4.94 F
419 420 0.179108 GGTGTCCGAGTCCTATGTGC 60.179 60.0 0.00 0.0 0.00 4.57 F
444 445 0.179169 GTCCGGACTCTAGCAACGTC 60.179 60.0 27.64 0.0 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1377 1405 1.446272 GTAGCCGACGCAGAAGCTT 60.446 57.895 0.00 0.00 39.10 3.74 R
1908 1936 1.817099 GAGGTTGATGCAGAGGCCG 60.817 63.158 0.00 0.00 40.13 6.13 R
2260 2288 1.449601 AGGATGCTTACGCGTTGGG 60.450 57.895 20.78 9.35 39.65 4.12 R
2361 2391 1.619827 CCATGCCCAACTCAACATTGT 59.380 47.619 0.00 0.00 0.00 2.71 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
38 39 8.970691 TGCAAAAATCTAGAAGTTATCAAAGC 57.029 30.769 0.00 0.00 0.00 3.51
39 40 8.575589 TGCAAAAATCTAGAAGTTATCAAAGCA 58.424 29.630 0.00 0.00 0.00 3.91
40 41 9.410556 GCAAAAATCTAGAAGTTATCAAAGCAA 57.589 29.630 0.00 0.00 0.00 3.91
50 51 8.175716 AGAAGTTATCAAAGCAAAGTATTACGC 58.824 33.333 0.00 0.00 0.00 4.42
51 52 6.475207 AGTTATCAAAGCAAAGTATTACGCG 58.525 36.000 3.53 3.53 32.44 6.01
52 53 3.111958 TCAAAGCAAAGTATTACGCGC 57.888 42.857 5.73 0.00 32.44 6.86
53 54 2.480802 TCAAAGCAAAGTATTACGCGCA 59.519 40.909 5.73 0.00 32.44 6.09
54 55 3.126171 TCAAAGCAAAGTATTACGCGCAT 59.874 39.130 5.73 0.18 32.44 4.73
55 56 2.737467 AGCAAAGTATTACGCGCATG 57.263 45.000 5.73 0.00 32.44 4.06
56 57 1.112459 GCAAAGTATTACGCGCATGC 58.888 50.000 5.73 7.91 37.91 4.06
57 58 1.268032 GCAAAGTATTACGCGCATGCT 60.268 47.619 17.13 4.63 39.65 3.79
58 59 2.629022 CAAAGTATTACGCGCATGCTC 58.371 47.619 17.13 6.91 39.65 4.26
59 60 1.217882 AAGTATTACGCGCATGCTCC 58.782 50.000 17.13 5.62 39.65 4.70
60 61 0.389391 AGTATTACGCGCATGCTCCT 59.611 50.000 17.13 0.00 39.65 3.69
61 62 1.611977 AGTATTACGCGCATGCTCCTA 59.388 47.619 17.13 0.00 39.65 2.94
62 63 1.986378 GTATTACGCGCATGCTCCTAG 59.014 52.381 17.13 0.00 39.65 3.02
63 64 0.319900 ATTACGCGCATGCTCCTAGG 60.320 55.000 17.13 0.82 39.65 3.02
64 65 2.363711 TTACGCGCATGCTCCTAGGG 62.364 60.000 17.13 10.41 39.65 3.53
65 66 4.976925 CGCGCATGCTCCTAGGGG 62.977 72.222 17.13 6.61 39.65 4.79
66 67 4.632974 GCGCATGCTCCTAGGGGG 62.633 72.222 17.13 4.51 38.39 5.40
67 68 2.844362 CGCATGCTCCTAGGGGGA 60.844 66.667 17.13 8.46 42.77 4.81
68 69 2.219875 CGCATGCTCCTAGGGGGAT 61.220 63.158 10.43 10.43 44.15 3.85
69 70 0.904865 CGCATGCTCCTAGGGGGATA 60.905 60.000 16.38 0.00 44.15 2.59
70 71 0.908198 GCATGCTCCTAGGGGGATAG 59.092 60.000 16.38 11.27 44.15 2.08
71 72 1.553417 GCATGCTCCTAGGGGGATAGA 60.553 57.143 16.38 0.00 44.15 1.98
72 73 2.896153 GCATGCTCCTAGGGGGATAGAT 60.896 54.545 16.38 0.00 44.15 1.98
73 74 3.458831 CATGCTCCTAGGGGGATAGATT 58.541 50.000 16.38 0.00 44.15 2.40
74 75 2.907892 TGCTCCTAGGGGGATAGATTG 58.092 52.381 11.65 0.00 44.15 2.67
75 76 2.192263 GCTCCTAGGGGGATAGATTGG 58.808 57.143 11.65 0.00 44.15 3.16
76 77 2.495572 GCTCCTAGGGGGATAGATTGGT 60.496 54.545 11.65 0.00 44.15 3.67
77 78 3.246021 GCTCCTAGGGGGATAGATTGGTA 60.246 52.174 11.65 0.00 44.15 3.25
78 79 4.615513 CTCCTAGGGGGATAGATTGGTAG 58.384 52.174 9.46 0.00 44.15 3.18
79 80 3.340049 TCCTAGGGGGATAGATTGGTAGG 59.660 52.174 9.46 0.00 39.58 3.18
80 81 3.340049 CCTAGGGGGATAGATTGGTAGGA 59.660 52.174 0.00 0.00 37.23 2.94
81 82 4.202901 CCTAGGGGGATAGATTGGTAGGAA 60.203 50.000 0.00 0.00 37.23 3.36
82 83 4.311208 AGGGGGATAGATTGGTAGGAAA 57.689 45.455 0.00 0.00 0.00 3.13
83 84 4.652628 AGGGGGATAGATTGGTAGGAAAA 58.347 43.478 0.00 0.00 0.00 2.29
84 85 4.665483 AGGGGGATAGATTGGTAGGAAAAG 59.335 45.833 0.00 0.00 0.00 2.27
85 86 4.663592 GGGGGATAGATTGGTAGGAAAAGA 59.336 45.833 0.00 0.00 0.00 2.52
86 87 5.456330 GGGGGATAGATTGGTAGGAAAAGAC 60.456 48.000 0.00 0.00 0.00 3.01
87 88 5.456330 GGGGATAGATTGGTAGGAAAAGACC 60.456 48.000 0.00 0.00 36.17 3.85
88 89 5.132144 GGGATAGATTGGTAGGAAAAGACCA 59.868 44.000 0.00 0.00 44.08 4.02
89 90 6.183361 GGGATAGATTGGTAGGAAAAGACCAT 60.183 42.308 0.00 0.00 45.09 3.55
90 91 6.937465 GGATAGATTGGTAGGAAAAGACCATC 59.063 42.308 0.00 0.00 45.09 3.51
91 92 4.770795 AGATTGGTAGGAAAAGACCATCG 58.229 43.478 0.00 0.00 45.09 3.84
92 93 2.396590 TGGTAGGAAAAGACCATCGC 57.603 50.000 0.00 0.00 40.87 4.58
93 94 1.906574 TGGTAGGAAAAGACCATCGCT 59.093 47.619 0.00 0.00 40.87 4.93
94 95 2.093658 TGGTAGGAAAAGACCATCGCTC 60.094 50.000 0.00 0.00 40.87 5.03
95 96 2.194271 GTAGGAAAAGACCATCGCTCG 58.806 52.381 0.00 0.00 0.00 5.03
96 97 0.608640 AGGAAAAGACCATCGCTCGT 59.391 50.000 0.00 0.00 0.00 4.18
97 98 1.000145 GGAAAAGACCATCGCTCGTC 59.000 55.000 0.00 0.00 0.00 4.20
98 99 1.000145 GAAAAGACCATCGCTCGTCC 59.000 55.000 0.00 0.00 0.00 4.79
99 100 0.391263 AAAAGACCATCGCTCGTCCC 60.391 55.000 0.00 0.00 0.00 4.46
100 101 2.240162 AAAGACCATCGCTCGTCCCC 62.240 60.000 0.00 0.00 0.00 4.81
101 102 4.570663 GACCATCGCTCGTCCCCG 62.571 72.222 0.00 0.00 0.00 5.73
103 104 4.570663 CCATCGCTCGTCCCCGAC 62.571 72.222 0.00 0.00 38.40 4.79
104 105 4.570663 CATCGCTCGTCCCCGACC 62.571 72.222 0.00 0.00 38.40 4.79
114 115 3.151710 CCCCGACCGCCACTCATA 61.152 66.667 0.00 0.00 0.00 2.15
115 116 2.727392 CCCCGACCGCCACTCATAA 61.727 63.158 0.00 0.00 0.00 1.90
116 117 1.227263 CCCGACCGCCACTCATAAG 60.227 63.158 0.00 0.00 0.00 1.73
117 118 1.227263 CCGACCGCCACTCATAAGG 60.227 63.158 0.00 0.00 0.00 2.69
118 119 1.672854 CCGACCGCCACTCATAAGGA 61.673 60.000 0.00 0.00 0.00 3.36
119 120 0.174845 CGACCGCCACTCATAAGGAA 59.825 55.000 0.00 0.00 0.00 3.36
120 121 1.802880 CGACCGCCACTCATAAGGAAG 60.803 57.143 0.00 0.00 0.00 3.46
121 122 1.480954 GACCGCCACTCATAAGGAAGA 59.519 52.381 0.00 0.00 0.00 2.87
122 123 1.207329 ACCGCCACTCATAAGGAAGAC 59.793 52.381 0.00 0.00 0.00 3.01
123 124 1.207089 CCGCCACTCATAAGGAAGACA 59.793 52.381 0.00 0.00 0.00 3.41
124 125 2.354704 CCGCCACTCATAAGGAAGACAA 60.355 50.000 0.00 0.00 0.00 3.18
125 126 3.535561 CGCCACTCATAAGGAAGACAAT 58.464 45.455 0.00 0.00 0.00 2.71
126 127 3.557595 CGCCACTCATAAGGAAGACAATC 59.442 47.826 0.00 0.00 0.00 2.67
127 128 4.517285 GCCACTCATAAGGAAGACAATCA 58.483 43.478 0.00 0.00 0.00 2.57
128 129 4.943705 GCCACTCATAAGGAAGACAATCAA 59.056 41.667 0.00 0.00 0.00 2.57
129 130 5.591877 GCCACTCATAAGGAAGACAATCAAT 59.408 40.000 0.00 0.00 0.00 2.57
130 131 6.767902 GCCACTCATAAGGAAGACAATCAATA 59.232 38.462 0.00 0.00 0.00 1.90
131 132 7.283127 GCCACTCATAAGGAAGACAATCAATAA 59.717 37.037 0.00 0.00 0.00 1.40
132 133 9.177608 CCACTCATAAGGAAGACAATCAATAAA 57.822 33.333 0.00 0.00 0.00 1.40
146 147 9.121517 GACAATCAATAAATAAATCATGCTCCG 57.878 33.333 0.00 0.00 0.00 4.63
147 148 8.849168 ACAATCAATAAATAAATCATGCTCCGA 58.151 29.630 0.00 0.00 0.00 4.55
148 149 9.121517 CAATCAATAAATAAATCATGCTCCGAC 57.878 33.333 0.00 0.00 0.00 4.79
149 150 8.627208 ATCAATAAATAAATCATGCTCCGACT 57.373 30.769 0.00 0.00 0.00 4.18
150 151 8.450578 TCAATAAATAAATCATGCTCCGACTT 57.549 30.769 0.00 0.00 0.00 3.01
151 152 8.559536 TCAATAAATAAATCATGCTCCGACTTC 58.440 33.333 0.00 0.00 0.00 3.01
152 153 8.344831 CAATAAATAAATCATGCTCCGACTTCA 58.655 33.333 0.00 0.00 0.00 3.02
153 154 6.949352 AAATAAATCATGCTCCGACTTCAT 57.051 33.333 0.00 0.00 0.00 2.57
154 155 6.551385 AATAAATCATGCTCCGACTTCATC 57.449 37.500 0.00 0.00 0.00 2.92
155 156 3.548745 AATCATGCTCCGACTTCATCA 57.451 42.857 0.00 0.00 0.00 3.07
156 157 2.299993 TCATGCTCCGACTTCATCAC 57.700 50.000 0.00 0.00 0.00 3.06
157 158 0.926155 CATGCTCCGACTTCATCACG 59.074 55.000 0.00 0.00 0.00 4.35
158 159 0.179100 ATGCTCCGACTTCATCACGG 60.179 55.000 0.00 0.00 46.71 4.94
159 160 2.167861 GCTCCGACTTCATCACGGC 61.168 63.158 0.00 0.00 45.25 5.68
160 161 1.519455 CTCCGACTTCATCACGGCC 60.519 63.158 0.00 0.00 45.25 6.13
161 162 2.225791 CTCCGACTTCATCACGGCCA 62.226 60.000 2.24 0.00 45.25 5.36
162 163 1.375396 CCGACTTCATCACGGCCAA 60.375 57.895 2.24 0.00 40.19 4.52
163 164 1.361668 CCGACTTCATCACGGCCAAG 61.362 60.000 2.24 0.00 40.19 3.61
164 165 1.361668 CGACTTCATCACGGCCAAGG 61.362 60.000 2.24 0.00 0.00 3.61
165 166 1.648467 GACTTCATCACGGCCAAGGC 61.648 60.000 2.24 1.52 41.06 4.35
196 197 3.312404 CCGATTGGGTATCTGGCTG 57.688 57.895 0.00 0.00 0.00 4.85
199 200 1.138859 CGATTGGGTATCTGGCTGTCA 59.861 52.381 0.00 0.00 0.00 3.58
270 271 2.125793 GGGGTGCGAACGTCCTAC 60.126 66.667 0.00 0.00 0.00 3.18
281 282 0.530744 ACGTCCTACGATGCATGTGT 59.469 50.000 2.46 5.02 46.05 3.72
287 288 0.323302 TACGATGCATGTGTGGTGGT 59.677 50.000 2.46 0.00 0.00 4.16
290 291 0.961019 GATGCATGTGTGGTGGTTGT 59.039 50.000 2.46 0.00 0.00 3.32
305 306 2.292016 TGGTTGTAAAGGTGCATTGACG 59.708 45.455 0.00 0.00 0.00 4.35
310 311 0.884704 AAAGGTGCATTGACGACGCT 60.885 50.000 0.00 0.00 0.00 5.07
312 313 2.027073 GGTGCATTGACGACGCTGA 61.027 57.895 0.00 0.00 0.00 4.26
327 328 2.599281 TGAACGAGGAGGGTGCGA 60.599 61.111 0.00 0.00 0.00 5.10
349 350 5.587043 CGAATGCAAAGTAACAGGGGTATAA 59.413 40.000 0.00 0.00 0.00 0.98
355 356 6.577638 GCAAAGTAACAGGGGTATAAAGGAGA 60.578 42.308 0.00 0.00 0.00 3.71
373 374 4.352298 AGGAGAAGTGGAAGAAAAGTGGAT 59.648 41.667 0.00 0.00 0.00 3.41
374 375 4.457257 GGAGAAGTGGAAGAAAAGTGGATG 59.543 45.833 0.00 0.00 0.00 3.51
388 389 4.533919 AGTGGATGAGAAGTGAGACTTG 57.466 45.455 0.00 0.00 38.80 3.16
397 398 2.088104 AGTGAGACTTGAGTGGGTCA 57.912 50.000 0.00 0.00 35.18 4.02
398 399 1.967066 AGTGAGACTTGAGTGGGTCAG 59.033 52.381 0.00 0.00 36.21 3.51
411 412 2.647158 GGTCAGGGGTGTCCGAGTC 61.647 68.421 0.00 0.00 41.52 3.36
419 420 0.179108 GGTGTCCGAGTCCTATGTGC 60.179 60.000 0.00 0.00 0.00 4.57
443 444 1.593296 GGTCCGGACTCTAGCAACGT 61.593 60.000 32.52 0.00 0.00 3.99
444 445 0.179169 GTCCGGACTCTAGCAACGTC 60.179 60.000 27.64 0.00 0.00 4.34
445 446 0.607217 TCCGGACTCTAGCAACGTCA 60.607 55.000 0.00 0.00 0.00 4.35
446 447 0.456312 CCGGACTCTAGCAACGTCAC 60.456 60.000 0.00 0.00 0.00 3.67
447 448 0.522180 CGGACTCTAGCAACGTCACT 59.478 55.000 0.00 0.00 0.00 3.41
487 488 3.945304 AAATGGACGTCCGGACCGC 62.945 63.158 28.52 19.52 39.43 5.68
532 533 9.620660 ATCATTGTTGTTAAAATAAGTTCGGAC 57.379 29.630 0.00 0.00 0.00 4.79
536 537 7.987649 TGTTGTTAAAATAAGTTCGGACAACT 58.012 30.769 14.57 0.00 43.45 3.16
537 538 8.124199 TGTTGTTAAAATAAGTTCGGACAACTC 58.876 33.333 14.57 0.00 43.45 3.01
556 557 2.189499 GGTCTGAATGGATGCGGGC 61.189 63.158 0.00 0.00 0.00 6.13
565 566 2.546494 GGATGCGGGCGATTTGAGG 61.546 63.158 0.00 0.00 0.00 3.86
566 567 1.523711 GATGCGGGCGATTTGAGGA 60.524 57.895 0.00 0.00 0.00 3.71
568 569 1.376609 ATGCGGGCGATTTGAGGAAC 61.377 55.000 0.00 0.00 0.00 3.62
578 579 3.681034 CGATTTGAGGAACAGGAGATGCT 60.681 47.826 0.00 0.00 0.00 3.79
579 580 3.340814 TTTGAGGAACAGGAGATGCTC 57.659 47.619 0.00 0.00 35.90 4.26
593 594 4.498345 GGAGATGCTCTAACGAACCTACAG 60.498 50.000 0.00 0.00 0.00 2.74
612 613 7.822822 ACCTACAGTTTGGTCATAACTCATAAC 59.177 37.037 0.00 0.00 33.73 1.89
624 625 2.453521 ACTCATAACCCACGAGCACTA 58.546 47.619 0.00 0.00 0.00 2.74
707 732 1.609555 GCCGGTGGTCTACATAGAGAG 59.390 57.143 1.90 0.00 32.01 3.20
760 785 2.433664 CCGCCCCACAAGACGTAC 60.434 66.667 0.00 0.00 0.00 3.67
775 800 1.817447 ACGTACAGAACTAGAGCACCC 59.183 52.381 0.00 0.00 0.00 4.61
776 801 1.816835 CGTACAGAACTAGAGCACCCA 59.183 52.381 0.00 0.00 0.00 4.51
777 802 2.427453 CGTACAGAACTAGAGCACCCAT 59.573 50.000 0.00 0.00 0.00 4.00
778 803 3.489398 CGTACAGAACTAGAGCACCCATC 60.489 52.174 0.00 0.00 0.00 3.51
779 804 1.478510 ACAGAACTAGAGCACCCATCG 59.521 52.381 0.00 0.00 0.00 3.84
780 805 1.478510 CAGAACTAGAGCACCCATCGT 59.521 52.381 0.00 0.00 0.00 3.73
781 806 2.688446 CAGAACTAGAGCACCCATCGTA 59.312 50.000 0.00 0.00 0.00 3.43
788 813 2.769663 AGAGCACCCATCGTACCATTTA 59.230 45.455 0.00 0.00 0.00 1.40
860 885 1.228124 CCCCTTCACAGAACGGCAA 60.228 57.895 0.00 0.00 0.00 4.52
924 949 1.202486 ACCCAACACGTCACTGTAGTG 60.202 52.381 5.67 5.67 46.91 2.74
966 991 5.275067 ACAAGAGATCTCACCAGCTAATC 57.725 43.478 24.39 0.00 0.00 1.75
1377 1405 4.383861 CTCGTGCTCAGCCAGGCA 62.384 66.667 15.80 0.00 36.01 4.75
1995 2023 2.105128 CTGCTCTACGGGAAGCGG 59.895 66.667 0.51 0.51 0.00 5.52
2112 2140 3.749064 GTCTGCGTCCTGCTCGGA 61.749 66.667 0.00 0.00 46.63 4.55
2148 2176 1.135199 GCATTCCACATGAAGGTGCTG 60.135 52.381 0.00 2.46 36.48 4.41
2194 2222 2.125952 TCGCTGATGTGGCTGTCG 60.126 61.111 0.00 0.00 0.00 4.35
2260 2288 1.154150 GCGCAGATGTTTGGTGCTC 60.154 57.895 0.30 0.00 34.92 4.26
2299 2328 1.398390 GCATCAACAAGGACACGGATC 59.602 52.381 0.00 0.00 0.00 3.36
2361 2391 0.251653 AGACCCGTCCAGTTCAGCTA 60.252 55.000 0.00 0.00 0.00 3.32
2363 2393 0.830444 ACCCGTCCAGTTCAGCTACA 60.830 55.000 0.00 0.00 0.00 2.74
2472 2507 5.277490 CGGCCAAATCTGTATTGTAGATGTG 60.277 44.000 2.24 0.00 38.88 3.21
2483 2518 3.548745 TGTAGATGTGGCAAGGATCAG 57.451 47.619 0.00 0.00 0.00 2.90
2602 2639 5.755409 TTGCCTAGTTCTGAAAGGATGTA 57.245 39.130 11.45 0.00 31.64 2.29
2627 2664 8.702163 AGATTGTGTAGGTTTTGTTTTTCTTG 57.298 30.769 0.00 0.00 0.00 3.02
2683 2720 2.344950 GCAGTGATCTGTGGAGTTCTG 58.655 52.381 0.00 0.00 43.05 3.02
2687 2724 2.037772 GTGATCTGTGGAGTTCTGGTGT 59.962 50.000 0.00 0.00 0.00 4.16
2840 2877 9.787532 CTGTTCAAGTTCTCTGTTTATTTTTCA 57.212 29.630 0.00 0.00 0.00 2.69
2875 2912 8.748412 TCATCCTGTTATTTTTCACCAAATAGG 58.252 33.333 0.00 0.00 45.67 2.57
2983 3066 9.212641 CAGATGGATTACAAAGAGTACATATGG 57.787 37.037 7.80 0.00 29.38 2.74
3007 3090 6.239176 GGGGTCATCACAAGAAACAAACATAA 60.239 38.462 0.00 0.00 0.00 1.90
3011 3094 8.702438 GTCATCACAAGAAACAAACATAAATGG 58.298 33.333 0.00 0.00 0.00 3.16
3014 3097 7.946207 TCACAAGAAACAAACATAAATGGCTA 58.054 30.769 0.00 0.00 0.00 3.93
3016 3099 6.868339 ACAAGAAACAAACATAAATGGCTAGC 59.132 34.615 6.04 6.04 0.00 3.42
3018 3101 6.389906 AGAAACAAACATAAATGGCTAGCAC 58.610 36.000 18.24 6.66 0.00 4.40
3037 3120 3.877559 CACTATTGCATGAAGGACTCCA 58.122 45.455 0.00 0.00 0.00 3.86
3038 3121 3.875727 CACTATTGCATGAAGGACTCCAG 59.124 47.826 0.00 0.00 0.00 3.86
3048 3131 5.730296 TGAAGGACTCCAGAAGAAGTAAG 57.270 43.478 0.00 0.00 0.00 2.34
3058 3141 9.095700 ACTCCAGAAGAAGTAAGACTAGAATTT 57.904 33.333 0.00 0.00 0.00 1.82
3069 3152 9.915629 AGTAAGACTAGAATTTCACTACAACAG 57.084 33.333 0.00 0.00 0.00 3.16
3074 3157 8.779354 ACTAGAATTTCACTACAACAGAATCC 57.221 34.615 0.00 0.00 0.00 3.01
3075 3158 8.598041 ACTAGAATTTCACTACAACAGAATCCT 58.402 33.333 0.00 0.00 0.00 3.24
3076 3159 7.678947 AGAATTTCACTACAACAGAATCCTG 57.321 36.000 0.00 0.00 45.76 3.86
3085 3168 3.186345 CAGAATCCTGTGCCATGCT 57.814 52.632 0.00 0.00 35.70 3.79
3086 3169 0.738975 CAGAATCCTGTGCCATGCTG 59.261 55.000 0.00 0.00 35.70 4.41
3087 3170 0.622136 AGAATCCTGTGCCATGCTGA 59.378 50.000 0.00 0.00 0.00 4.26
3088 3171 1.005097 AGAATCCTGTGCCATGCTGAA 59.995 47.619 0.00 0.00 0.00 3.02
3089 3172 1.820519 GAATCCTGTGCCATGCTGAAA 59.179 47.619 0.00 0.00 0.00 2.69
3096 3179 1.153509 GCCATGCTGAAATGTGCCC 60.154 57.895 0.00 0.00 0.00 5.36
3099 3182 1.304381 ATGCTGAAATGTGCCCCGT 60.304 52.632 0.00 0.00 0.00 5.28
3101 3184 1.080569 GCTGAAATGTGCCCCGTTG 60.081 57.895 0.00 0.00 0.00 4.10
3116 3199 2.158559 CCGTTGAAATGTCATCCACCA 58.841 47.619 0.00 0.00 32.48 4.17
3128 3211 0.689080 ATCCACCATCGTCCTCTGCT 60.689 55.000 0.00 0.00 0.00 4.24
3131 3224 2.202987 CCATCGTCCTCTGCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
3152 3245 1.593196 CCGAGGCAACACTGAAGAAA 58.407 50.000 0.00 0.00 41.41 2.52
3158 3251 2.487265 GGCAACACTGAAGAAAGAGGGA 60.487 50.000 0.00 0.00 0.00 4.20
3159 3252 3.416156 GCAACACTGAAGAAAGAGGGAT 58.584 45.455 0.00 0.00 0.00 3.85
3160 3253 3.438434 GCAACACTGAAGAAAGAGGGATC 59.562 47.826 0.00 0.00 0.00 3.36
3161 3254 4.805609 GCAACACTGAAGAAAGAGGGATCT 60.806 45.833 0.00 0.00 0.00 2.75
3162 3255 4.550076 ACACTGAAGAAAGAGGGATCTG 57.450 45.455 0.00 0.00 0.00 2.90
3163 3256 3.269178 CACTGAAGAAAGAGGGATCTGC 58.731 50.000 0.00 0.00 0.00 4.26
3165 3258 1.208052 TGAAGAAAGAGGGATCTGCCG 59.792 52.381 0.00 0.00 37.63 5.69
3166 3259 1.208293 GAAGAAAGAGGGATCTGCCGT 59.792 52.381 0.00 0.00 37.63 5.68
3181 3279 1.819229 CCGTCACAGATCTGGAGGG 59.181 63.158 26.08 25.60 33.21 4.30
3183 3281 0.972983 CGTCACAGATCTGGAGGGGT 60.973 60.000 26.08 1.31 34.19 4.95
3198 3296 4.200092 GGAGGGGTACTTTTGCATAGAAG 58.800 47.826 3.58 3.86 0.00 2.85
3214 3312 3.685139 AGAAGGATGCTTTTCGAGTCA 57.315 42.857 0.00 0.00 0.00 3.41
3220 3318 4.946157 AGGATGCTTTTCGAGTCAATGAAT 59.054 37.500 0.00 0.00 0.00 2.57
3239 3337 2.665185 GGACAACCGCAAGCGACT 60.665 61.111 16.97 0.00 42.83 4.18
3244 3342 0.388649 CAACCGCAAGCGACTAGACT 60.389 55.000 16.97 0.00 42.83 3.24
3248 3346 1.136872 CGCAAGCGACTAGACTGAGC 61.137 60.000 9.11 0.00 42.83 4.26
3265 3363 4.025401 CCTTTGTGGCACGTCGGC 62.025 66.667 13.77 4.92 41.67 5.54
3266 3364 2.972505 CTTTGTGGCACGTCGGCT 60.973 61.111 13.77 0.00 41.89 5.52
3267 3365 3.240606 CTTTGTGGCACGTCGGCTG 62.241 63.158 13.77 0.00 41.89 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 9.410556 GCTTTGATAACTTCTAGATTTTTGCAA 57.589 29.630 0.00 0.00 0.00 4.08
13 14 8.575589 TGCTTTGATAACTTCTAGATTTTTGCA 58.424 29.630 0.00 0.00 0.00 4.08
14 15 8.970691 TGCTTTGATAACTTCTAGATTTTTGC 57.029 30.769 0.00 0.00 0.00 3.68
24 25 8.175716 GCGTAATACTTTGCTTTGATAACTTCT 58.824 33.333 0.00 0.00 0.00 2.85
25 26 7.162062 CGCGTAATACTTTGCTTTGATAACTTC 59.838 37.037 0.00 0.00 0.00 3.01
26 27 6.959311 CGCGTAATACTTTGCTTTGATAACTT 59.041 34.615 0.00 0.00 0.00 2.66
27 28 6.475207 CGCGTAATACTTTGCTTTGATAACT 58.525 36.000 0.00 0.00 0.00 2.24
28 29 5.169032 GCGCGTAATACTTTGCTTTGATAAC 59.831 40.000 8.43 0.00 0.00 1.89
29 30 5.163844 TGCGCGTAATACTTTGCTTTGATAA 60.164 36.000 8.43 0.00 0.00 1.75
30 31 4.330347 TGCGCGTAATACTTTGCTTTGATA 59.670 37.500 8.43 0.00 0.00 2.15
31 32 3.126171 TGCGCGTAATACTTTGCTTTGAT 59.874 39.130 8.43 0.00 0.00 2.57
32 33 2.480802 TGCGCGTAATACTTTGCTTTGA 59.519 40.909 8.43 0.00 0.00 2.69
33 34 2.845486 TGCGCGTAATACTTTGCTTTG 58.155 42.857 8.43 0.00 0.00 2.77
34 35 3.425404 CATGCGCGTAATACTTTGCTTT 58.575 40.909 8.43 0.00 0.00 3.51
35 36 2.791158 GCATGCGCGTAATACTTTGCTT 60.791 45.455 8.43 0.00 0.00 3.91
36 37 1.268032 GCATGCGCGTAATACTTTGCT 60.268 47.619 8.43 0.00 0.00 3.91
37 38 1.112459 GCATGCGCGTAATACTTTGC 58.888 50.000 8.43 5.05 0.00 3.68
38 39 2.599848 GGAGCATGCGCGTAATACTTTG 60.600 50.000 15.49 0.00 45.49 2.77
39 40 1.597663 GGAGCATGCGCGTAATACTTT 59.402 47.619 15.49 0.00 45.49 2.66
40 41 1.202533 AGGAGCATGCGCGTAATACTT 60.203 47.619 15.13 0.00 45.49 2.24
41 42 0.389391 AGGAGCATGCGCGTAATACT 59.611 50.000 15.13 2.32 45.49 2.12
42 43 1.986378 CTAGGAGCATGCGCGTAATAC 59.014 52.381 21.38 5.32 45.49 1.89
43 44 1.067846 CCTAGGAGCATGCGCGTAATA 60.068 52.381 21.38 9.02 45.49 0.98
44 45 0.319900 CCTAGGAGCATGCGCGTAAT 60.320 55.000 21.38 8.40 45.49 1.89
45 46 1.067416 CCTAGGAGCATGCGCGTAA 59.933 57.895 21.38 6.99 45.49 3.18
46 47 2.728180 CCTAGGAGCATGCGCGTA 59.272 61.111 20.19 20.19 45.49 4.42
47 48 4.227134 CCCTAGGAGCATGCGCGT 62.227 66.667 20.11 20.11 45.49 6.01
48 49 4.976925 CCCCTAGGAGCATGCGCG 62.977 72.222 15.49 0.00 45.49 6.86
49 50 4.632974 CCCCCTAGGAGCATGCGC 62.633 72.222 13.62 13.62 38.24 6.09
50 51 2.844362 TCCCCCTAGGAGCATGCG 60.844 66.667 11.48 0.00 40.93 4.73
58 59 3.340049 TCCTACCAATCTATCCCCCTAGG 59.660 52.174 0.06 0.06 0.00 3.02
59 60 4.694280 TCCTACCAATCTATCCCCCTAG 57.306 50.000 0.00 0.00 0.00 3.02
60 61 5.443277 TTTCCTACCAATCTATCCCCCTA 57.557 43.478 0.00 0.00 0.00 3.53
61 62 4.311208 TTTCCTACCAATCTATCCCCCT 57.689 45.455 0.00 0.00 0.00 4.79
62 63 4.663592 TCTTTTCCTACCAATCTATCCCCC 59.336 45.833 0.00 0.00 0.00 5.40
63 64 5.456330 GGTCTTTTCCTACCAATCTATCCCC 60.456 48.000 0.00 0.00 35.73 4.81
64 65 5.132144 TGGTCTTTTCCTACCAATCTATCCC 59.868 44.000 0.00 0.00 42.74 3.85
65 66 6.248569 TGGTCTTTTCCTACCAATCTATCC 57.751 41.667 0.00 0.00 42.74 2.59
74 75 2.552031 GAGCGATGGTCTTTTCCTACC 58.448 52.381 0.00 0.00 36.24 3.18
75 76 2.194271 CGAGCGATGGTCTTTTCCTAC 58.806 52.381 0.00 0.00 0.00 3.18
76 77 1.822990 ACGAGCGATGGTCTTTTCCTA 59.177 47.619 0.00 0.00 0.00 2.94
77 78 0.608640 ACGAGCGATGGTCTTTTCCT 59.391 50.000 0.00 0.00 0.00 3.36
78 79 1.000145 GACGAGCGATGGTCTTTTCC 59.000 55.000 8.67 0.00 0.00 3.13
79 80 1.000145 GGACGAGCGATGGTCTTTTC 59.000 55.000 15.41 0.00 33.70 2.29
80 81 0.391263 GGGACGAGCGATGGTCTTTT 60.391 55.000 15.41 0.00 33.70 2.27
81 82 1.218316 GGGACGAGCGATGGTCTTT 59.782 57.895 15.41 0.00 33.70 2.52
82 83 2.722201 GGGGACGAGCGATGGTCTT 61.722 63.158 15.41 0.00 33.70 3.01
83 84 3.148279 GGGGACGAGCGATGGTCT 61.148 66.667 15.41 0.00 33.70 3.85
96 97 3.665515 TATGAGTGGCGGTCGGGGA 62.666 63.158 0.00 0.00 0.00 4.81
97 98 2.644555 CTTATGAGTGGCGGTCGGGG 62.645 65.000 0.00 0.00 0.00 5.73
98 99 1.227263 CTTATGAGTGGCGGTCGGG 60.227 63.158 0.00 0.00 0.00 5.14
99 100 1.227263 CCTTATGAGTGGCGGTCGG 60.227 63.158 0.00 0.00 0.00 4.79
100 101 0.174845 TTCCTTATGAGTGGCGGTCG 59.825 55.000 0.00 0.00 0.00 4.79
101 102 1.480954 TCTTCCTTATGAGTGGCGGTC 59.519 52.381 0.00 0.00 0.00 4.79
102 103 1.207329 GTCTTCCTTATGAGTGGCGGT 59.793 52.381 0.00 0.00 0.00 5.68
103 104 1.207089 TGTCTTCCTTATGAGTGGCGG 59.793 52.381 0.00 0.00 0.00 6.13
104 105 2.672961 TGTCTTCCTTATGAGTGGCG 57.327 50.000 0.00 0.00 0.00 5.69
105 106 4.517285 TGATTGTCTTCCTTATGAGTGGC 58.483 43.478 0.00 0.00 0.00 5.01
106 107 8.737168 TTATTGATTGTCTTCCTTATGAGTGG 57.263 34.615 0.00 0.00 0.00 4.00
120 121 9.121517 CGGAGCATGATTTATTTATTGATTGTC 57.878 33.333 0.00 0.00 0.00 3.18
121 122 8.849168 TCGGAGCATGATTTATTTATTGATTGT 58.151 29.630 0.00 0.00 0.00 2.71
122 123 9.121517 GTCGGAGCATGATTTATTTATTGATTG 57.878 33.333 0.00 0.00 0.00 2.67
123 124 9.071276 AGTCGGAGCATGATTTATTTATTGATT 57.929 29.630 0.00 0.00 0.00 2.57
124 125 8.627208 AGTCGGAGCATGATTTATTTATTGAT 57.373 30.769 0.00 0.00 0.00 2.57
125 126 8.450578 AAGTCGGAGCATGATTTATTTATTGA 57.549 30.769 0.00 0.00 0.00 2.57
126 127 8.344831 TGAAGTCGGAGCATGATTTATTTATTG 58.655 33.333 0.00 0.00 0.00 1.90
127 128 8.450578 TGAAGTCGGAGCATGATTTATTTATT 57.549 30.769 0.00 0.00 0.00 1.40
128 129 8.627208 ATGAAGTCGGAGCATGATTTATTTAT 57.373 30.769 0.00 0.00 0.00 1.40
129 130 7.714813 TGATGAAGTCGGAGCATGATTTATTTA 59.285 33.333 0.00 0.00 0.00 1.40
130 131 6.543465 TGATGAAGTCGGAGCATGATTTATTT 59.457 34.615 0.00 0.00 0.00 1.40
131 132 6.017605 GTGATGAAGTCGGAGCATGATTTATT 60.018 38.462 0.00 0.00 0.00 1.40
132 133 5.468072 GTGATGAAGTCGGAGCATGATTTAT 59.532 40.000 0.00 0.00 0.00 1.40
133 134 4.811024 GTGATGAAGTCGGAGCATGATTTA 59.189 41.667 0.00 0.00 0.00 1.40
134 135 3.624861 GTGATGAAGTCGGAGCATGATTT 59.375 43.478 0.00 0.00 0.00 2.17
135 136 3.201290 GTGATGAAGTCGGAGCATGATT 58.799 45.455 0.00 0.00 0.00 2.57
136 137 2.800985 CGTGATGAAGTCGGAGCATGAT 60.801 50.000 0.00 0.00 0.00 2.45
137 138 1.469767 CGTGATGAAGTCGGAGCATGA 60.470 52.381 0.00 0.00 0.00 3.07
138 139 0.926155 CGTGATGAAGTCGGAGCATG 59.074 55.000 0.00 0.00 0.00 4.06
139 140 0.179100 CCGTGATGAAGTCGGAGCAT 60.179 55.000 0.00 0.00 46.05 3.79
140 141 1.215382 CCGTGATGAAGTCGGAGCA 59.785 57.895 0.00 0.00 46.05 4.26
141 142 2.167861 GCCGTGATGAAGTCGGAGC 61.168 63.158 7.01 0.00 46.05 4.70
142 143 1.519455 GGCCGTGATGAAGTCGGAG 60.519 63.158 7.01 0.00 46.05 4.63
143 144 1.822114 TTGGCCGTGATGAAGTCGGA 61.822 55.000 7.01 0.00 46.05 4.55
144 145 1.361668 CTTGGCCGTGATGAAGTCGG 61.362 60.000 0.00 0.00 45.94 4.79
145 146 1.361668 CCTTGGCCGTGATGAAGTCG 61.362 60.000 0.00 0.00 0.00 4.18
146 147 1.648467 GCCTTGGCCGTGATGAAGTC 61.648 60.000 0.00 0.00 0.00 3.01
147 148 1.675641 GCCTTGGCCGTGATGAAGT 60.676 57.895 0.00 0.00 0.00 3.01
148 149 2.753966 CGCCTTGGCCGTGATGAAG 61.754 63.158 6.02 0.00 0.00 3.02
149 150 2.745884 CGCCTTGGCCGTGATGAA 60.746 61.111 6.02 0.00 0.00 2.57
178 179 0.469917 ACAGCCAGATACCCAATCGG 59.530 55.000 0.00 0.00 39.79 4.18
179 180 1.138859 TGACAGCCAGATACCCAATCG 59.861 52.381 0.00 0.00 39.79 3.34
180 181 3.209410 CTTGACAGCCAGATACCCAATC 58.791 50.000 0.00 0.00 34.52 2.67
181 182 2.092212 CCTTGACAGCCAGATACCCAAT 60.092 50.000 0.00 0.00 0.00 3.16
182 183 1.281867 CCTTGACAGCCAGATACCCAA 59.718 52.381 0.00 0.00 0.00 4.12
183 184 0.911769 CCTTGACAGCCAGATACCCA 59.088 55.000 0.00 0.00 0.00 4.51
196 197 0.914417 TCCACCCAGGATCCCTTGAC 60.914 60.000 8.55 0.00 43.07 3.18
253 254 2.125793 GTAGGACGTTCGCACCCC 60.126 66.667 0.00 0.00 0.00 4.95
256 257 1.740043 GCATCGTAGGACGTTCGCAC 61.740 60.000 0.00 0.00 43.14 5.34
263 264 0.923403 CACACATGCATCGTAGGACG 59.077 55.000 0.00 0.00 44.19 4.79
270 271 0.109643 CAACCACCACACATGCATCG 60.110 55.000 0.00 0.00 0.00 3.84
281 282 2.363680 CAATGCACCTTTACAACCACCA 59.636 45.455 0.00 0.00 0.00 4.17
287 288 2.222213 CGTCGTCAATGCACCTTTACAA 59.778 45.455 0.00 0.00 0.00 2.41
290 291 0.793861 GCGTCGTCAATGCACCTTTA 59.206 50.000 0.00 0.00 39.85 1.85
305 306 2.182030 CCCTCCTCGTTCAGCGTC 59.818 66.667 0.00 0.00 42.13 5.19
310 311 1.541310 ATTCGCACCCTCCTCGTTCA 61.541 55.000 0.00 0.00 0.00 3.18
312 313 1.079127 CATTCGCACCCTCCTCGTT 60.079 57.895 0.00 0.00 0.00 3.85
327 328 6.379988 CCTTTATACCCCTGTTACTTTGCATT 59.620 38.462 0.00 0.00 0.00 3.56
349 350 4.166144 TCCACTTTTCTTCCACTTCTCCTT 59.834 41.667 0.00 0.00 0.00 3.36
355 356 5.310409 TCTCATCCACTTTTCTTCCACTT 57.690 39.130 0.00 0.00 0.00 3.16
373 374 2.630098 CCCACTCAAGTCTCACTTCTCA 59.370 50.000 0.00 0.00 36.03 3.27
374 375 2.630580 ACCCACTCAAGTCTCACTTCTC 59.369 50.000 0.00 0.00 36.03 2.87
388 389 2.593956 GGACACCCCTGACCCACTC 61.594 68.421 0.00 0.00 0.00 3.51
397 398 0.397254 CATAGGACTCGGACACCCCT 60.397 60.000 0.00 0.00 0.00 4.79
398 399 0.686769 ACATAGGACTCGGACACCCC 60.687 60.000 0.00 0.00 0.00 4.95
411 412 2.189521 GGACCACCGGCACATAGG 59.810 66.667 0.00 0.00 0.00 2.57
463 464 1.133869 CGGACGTCCATTTTTCCGC 59.866 57.895 32.80 3.24 44.16 5.54
487 488 5.864628 TGATACTCTATCGATTCGTGGAG 57.135 43.478 1.71 11.85 38.02 3.86
488 489 6.206829 ACAATGATACTCTATCGATTCGTGGA 59.793 38.462 1.71 0.94 38.02 4.02
489 490 6.382608 ACAATGATACTCTATCGATTCGTGG 58.617 40.000 1.71 0.00 38.02 4.94
490 491 7.379797 ACAACAATGATACTCTATCGATTCGTG 59.620 37.037 1.71 0.00 38.02 4.35
491 492 7.426410 ACAACAATGATACTCTATCGATTCGT 58.574 34.615 1.71 1.06 38.02 3.85
492 493 7.859613 ACAACAATGATACTCTATCGATTCG 57.140 36.000 1.71 0.00 38.02 3.34
515 516 6.073602 ACCGAGTTGTCCGAACTTATTTTAAC 60.074 38.462 0.00 0.00 0.00 2.01
522 523 2.030540 CAGACCGAGTTGTCCGAACTTA 60.031 50.000 0.00 0.00 35.83 2.24
523 524 1.038280 AGACCGAGTTGTCCGAACTT 58.962 50.000 0.00 0.00 35.83 2.66
532 533 1.667724 GCATCCATTCAGACCGAGTTG 59.332 52.381 0.00 0.00 0.00 3.16
536 537 1.143838 CCGCATCCATTCAGACCGA 59.856 57.895 0.00 0.00 0.00 4.69
537 538 1.889105 CCCGCATCCATTCAGACCG 60.889 63.158 0.00 0.00 0.00 4.79
544 545 0.751277 TCAAATCGCCCGCATCCATT 60.751 50.000 0.00 0.00 0.00 3.16
556 557 2.611292 GCATCTCCTGTTCCTCAAATCG 59.389 50.000 0.00 0.00 0.00 3.34
578 579 4.341806 TGACCAAACTGTAGGTTCGTTAGA 59.658 41.667 6.34 0.00 38.50 2.10
579 580 4.624015 TGACCAAACTGTAGGTTCGTTAG 58.376 43.478 6.34 0.00 38.50 2.34
593 594 5.163794 CGTGGGTTATGAGTTATGACCAAAC 60.164 44.000 10.51 7.29 44.98 2.93
612 613 0.034896 ACTGGTTTAGTGCTCGTGGG 59.965 55.000 0.00 0.00 38.49 4.61
692 717 3.206964 CGTGAGCTCTCTATGTAGACCA 58.793 50.000 16.19 0.00 0.00 4.02
744 769 1.736645 CTGTACGTCTTGTGGGGCG 60.737 63.158 0.00 0.00 0.00 6.13
760 785 1.478510 ACGATGGGTGCTCTAGTTCTG 59.521 52.381 0.00 0.00 0.00 3.02
775 800 4.447290 TGGTCCATGTAAATGGTACGATG 58.553 43.478 11.89 0.00 42.28 3.84
776 801 4.764050 TGGTCCATGTAAATGGTACGAT 57.236 40.909 11.89 0.00 42.28 3.73
777 802 4.020039 ACTTGGTCCATGTAAATGGTACGA 60.020 41.667 11.89 5.32 42.28 3.43
778 803 4.258543 ACTTGGTCCATGTAAATGGTACG 58.741 43.478 11.89 1.16 42.28 3.67
779 804 5.813080 GACTTGGTCCATGTAAATGGTAC 57.187 43.478 11.89 8.54 42.28 3.34
924 949 4.317529 CTCGAGGCGATTGAGCTC 57.682 61.111 6.82 6.82 34.61 4.09
966 991 1.661821 GAATCGGACGCAGGATCGG 60.662 63.158 0.00 0.00 0.00 4.18
1350 1378 4.377708 AGCACGAGCATGGCGTCA 62.378 61.111 7.77 0.00 45.49 4.35
1377 1405 1.446272 GTAGCCGACGCAGAAGCTT 60.446 57.895 0.00 0.00 39.10 3.74
1908 1936 1.817099 GAGGTTGATGCAGAGGCCG 60.817 63.158 0.00 0.00 40.13 6.13
2176 2204 2.447887 CGACAGCCACATCAGCGAC 61.448 63.158 0.00 0.00 34.64 5.19
2260 2288 1.449601 AGGATGCTTACGCGTTGGG 60.450 57.895 20.78 9.35 39.65 4.12
2361 2391 1.619827 CCATGCCCAACTCAACATTGT 59.380 47.619 0.00 0.00 0.00 2.71
2363 2393 2.014010 ACCATGCCCAACTCAACATT 57.986 45.000 0.00 0.00 0.00 2.71
2425 2455 2.551270 GGATACCATGAGGGCCTATGA 58.449 52.381 5.73 0.00 42.05 2.15
2472 2507 2.514824 GGTCGCCTGATCCTTGCC 60.515 66.667 0.00 0.00 0.00 4.52
2483 2518 2.280592 AGGTTCGTTGTGGTCGCC 60.281 61.111 0.00 0.00 0.00 5.54
2602 2639 7.277760 GCAAGAAAAACAAAACCTACACAATCT 59.722 33.333 0.00 0.00 0.00 2.40
2627 2664 6.654793 AACGAAACAAGATCTTCTATCTGC 57.345 37.500 4.57 0.00 0.00 4.26
2660 2697 0.244994 ACTCCACAGATCACTGCGAC 59.755 55.000 0.00 0.00 46.95 5.19
2808 2845 1.981495 AGAGAACTTGAACAGAGGGGG 59.019 52.381 0.00 0.00 0.00 5.40
2809 2846 2.370189 ACAGAGAACTTGAACAGAGGGG 59.630 50.000 0.00 0.00 0.00 4.79
2810 2847 3.760580 ACAGAGAACTTGAACAGAGGG 57.239 47.619 0.00 0.00 0.00 4.30
2858 2895 7.379750 CCGGTTTTCCTATTTGGTGAAAAATA 58.620 34.615 0.00 0.00 39.06 1.40
2872 2909 3.358118 CCCAATTTAGCCGGTTTTCCTA 58.642 45.455 1.90 0.00 37.95 2.94
2875 2912 1.273886 TGCCCAATTTAGCCGGTTTTC 59.726 47.619 1.90 0.00 0.00 2.29
2937 2976 8.347771 CCATCTGTCTAATGAATTTACATGTGG 58.652 37.037 9.11 0.00 0.00 4.17
2983 3066 4.647424 TGTTTGTTTCTTGTGATGACCC 57.353 40.909 0.00 0.00 0.00 4.46
3016 3099 3.875727 CTGGAGTCCTTCATGCAATAGTG 59.124 47.826 11.33 0.00 0.00 2.74
3018 3101 4.412796 TCTGGAGTCCTTCATGCAATAG 57.587 45.455 11.33 0.00 0.00 1.73
3026 3109 5.244178 GTCTTACTTCTTCTGGAGTCCTTCA 59.756 44.000 11.33 0.00 0.00 3.02
3028 3111 5.399113 AGTCTTACTTCTTCTGGAGTCCTT 58.601 41.667 11.33 0.00 0.00 3.36
3030 3113 6.181908 TCTAGTCTTACTTCTTCTGGAGTCC 58.818 44.000 0.73 0.73 0.00 3.85
3048 3131 8.874816 GGATTCTGTTGTAGTGAAATTCTAGTC 58.125 37.037 0.00 0.00 0.00 2.59
3069 3152 1.466856 TTCAGCATGGCACAGGATTC 58.533 50.000 0.00 0.00 46.40 2.52
3076 3159 0.738412 GGCACATTTCAGCATGGCAC 60.738 55.000 0.00 0.00 37.56 5.01
3077 3160 1.592743 GGCACATTTCAGCATGGCA 59.407 52.632 0.00 0.00 37.56 4.92
3078 3161 1.153509 GGGCACATTTCAGCATGGC 60.154 57.895 0.00 0.00 36.16 4.40
3079 3162 1.518774 GGGGCACATTTCAGCATGG 59.481 57.895 0.00 0.00 36.16 3.66
3080 3163 1.140161 CGGGGCACATTTCAGCATG 59.860 57.895 0.00 0.00 37.54 4.06
3081 3164 0.899717 AACGGGGCACATTTCAGCAT 60.900 50.000 0.00 0.00 0.00 3.79
3082 3165 1.530419 AACGGGGCACATTTCAGCA 60.530 52.632 0.00 0.00 0.00 4.41
3083 3166 1.080569 CAACGGGGCACATTTCAGC 60.081 57.895 0.00 0.00 0.00 4.26
3084 3167 0.958091 TTCAACGGGGCACATTTCAG 59.042 50.000 0.00 0.00 0.00 3.02
3085 3168 1.403814 TTTCAACGGGGCACATTTCA 58.596 45.000 0.00 0.00 0.00 2.69
3086 3169 2.288763 ACATTTCAACGGGGCACATTTC 60.289 45.455 0.00 0.00 0.00 2.17
3087 3170 1.691434 ACATTTCAACGGGGCACATTT 59.309 42.857 0.00 0.00 0.00 2.32
3088 3171 1.272212 GACATTTCAACGGGGCACATT 59.728 47.619 0.00 0.00 0.00 2.71
3089 3172 0.887933 GACATTTCAACGGGGCACAT 59.112 50.000 0.00 0.00 0.00 3.21
3096 3179 2.158559 TGGTGGATGACATTTCAACGG 58.841 47.619 0.00 0.00 34.61 4.44
3099 3182 3.684908 ACGATGGTGGATGACATTTCAA 58.315 40.909 0.00 0.00 34.61 2.69
3101 3184 2.614057 GGACGATGGTGGATGACATTTC 59.386 50.000 0.00 0.00 0.00 2.17
3116 3199 4.521062 GCGGCAGCAGAGGACGAT 62.521 66.667 3.18 0.00 44.35 3.73
3131 3224 2.664851 TTCAGTGTTGCCTCGGCG 60.665 61.111 0.00 0.00 45.51 6.46
3136 3229 2.487986 CCCTCTTTCTTCAGTGTTGCCT 60.488 50.000 0.00 0.00 0.00 4.75
3141 3234 3.307339 GCAGATCCCTCTTTCTTCAGTGT 60.307 47.826 0.00 0.00 0.00 3.55
3152 3245 1.305297 TGTGACGGCAGATCCCTCT 60.305 57.895 0.00 0.00 0.00 3.69
3160 3253 0.179116 CTCCAGATCTGTGACGGCAG 60.179 60.000 21.11 3.65 37.81 4.85
3161 3254 1.607801 CCTCCAGATCTGTGACGGCA 61.608 60.000 21.11 0.00 0.00 5.69
3162 3255 1.142748 CCTCCAGATCTGTGACGGC 59.857 63.158 21.11 0.00 0.00 5.68
3163 3256 1.680522 CCCCTCCAGATCTGTGACGG 61.681 65.000 21.11 17.83 0.00 4.79
3165 3258 1.757699 GTACCCCTCCAGATCTGTGAC 59.242 57.143 21.11 4.87 0.00 3.67
3166 3259 1.646447 AGTACCCCTCCAGATCTGTGA 59.354 52.381 21.11 15.86 0.00 3.58
3198 3296 4.685169 TTCATTGACTCGAAAAGCATCC 57.315 40.909 0.00 0.00 0.00 3.51
3226 3324 0.388649 CAGTCTAGTCGCTTGCGGTT 60.389 55.000 15.10 6.32 0.00 4.44
3227 3325 1.213013 CAGTCTAGTCGCTTGCGGT 59.787 57.895 15.10 5.69 0.00 5.68
3248 3346 4.025401 GCCGACGTGCCACAAAGG 62.025 66.667 0.00 0.00 41.84 3.11


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

AutoCloner maintained by Alex Coulton.