Multiple sequence alignment - TraesCS1A01G366100

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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 TraesCS1A01G366100 chr1A 100.000 3029 0 0 1 3029 544999185 545002213 0.000000e+00 5594
1 TraesCS1A01G366100 chr1A 80.769 1170 119 55 133 1272 544747477 544748570 0.000000e+00 817
2 TraesCS1A01G366100 chr1A 87.253 659 66 10 1397 2043 545009127 545008475 0.000000e+00 736
3 TraesCS1A01G366100 chr1A 91.124 507 42 1 1397 1900 544928174 544928680 0.000000e+00 684
4 TraesCS1A01G366100 chr1A 83.595 701 66 24 1417 2086 545299256 545298574 2.000000e-171 612
5 TraesCS1A01G366100 chr1A 80.998 421 43 26 688 1076 544927550 544927965 1.770000e-77 300
6 TraesCS1A01G366100 chr1D 87.472 2195 159 58 696 2835 449846521 449848654 0.000000e+00 2423
7 TraesCS1A01G366100 chr1D 85.737 1234 96 42 704 1900 449660074 449661264 0.000000e+00 1230
8 TraesCS1A01G366100 chr1D 82.672 1512 134 71 447 1900 449674076 449675517 0.000000e+00 1223
9 TraesCS1A01G366100 chr1D 88.152 633 57 9 1417 2043 449923208 449922588 0.000000e+00 737
10 TraesCS1A01G366100 chr1D 83.938 772 72 28 1352 2086 450044902 450044146 0.000000e+00 691
11 TraesCS1A01G366100 chr1D 84.270 623 49 29 694 1275 449923928 449923314 2.040000e-156 562
12 TraesCS1A01G366100 chr1D 81.069 655 79 28 697 1319 449983754 449983113 5.870000e-132 481
13 TraesCS1A01G366100 chr1D 86.434 258 32 3 133 390 449749928 449750182 2.300000e-71 279
14 TraesCS1A01G366100 chr1D 84.758 269 25 8 363 616 449659547 449659814 3.880000e-64 255
15 TraesCS1A01G366100 chr1D 92.216 167 12 1 133 299 449673867 449674032 5.050000e-58 235
16 TraesCS1A01G366100 chr1B 89.742 1472 106 21 1396 2835 615732508 615733966 0.000000e+00 1840
17 TraesCS1A01G366100 chr1B 80.879 1229 129 48 133 1271 615624684 615625896 0.000000e+00 870
18 TraesCS1A01G366100 chr1B 88.254 630 50 7 1417 2043 615744798 615744190 0.000000e+00 732
19 TraesCS1A01G366100 chr1B 87.619 630 48 18 724 1333 615731879 615732498 0.000000e+00 704
20 TraesCS1A01G366100 chr1B 91.786 487 37 1 1417 1900 615582130 615582616 0.000000e+00 675
21 TraesCS1A01G366100 chr1B 95.941 271 11 0 1001 1271 615581739 615582009 9.970000e-120 440
22 TraesCS1A01G366100 chr1B 85.551 263 28 8 133 394 615731268 615731521 1.790000e-67 267
23 TraesCS1A01G366100 chr1B 86.000 150 12 7 2833 2976 615734027 615734173 5.230000e-33 152
24 TraesCS1A01G366100 chr6D 83.090 343 38 7 1091 1422 83226436 83226103 8.210000e-76 294
25 TraesCS1A01G366100 chr6D 92.537 134 10 0 1 134 420353476 420353609 3.080000e-45 193
26 TraesCS1A01G366100 chr5A 93.333 135 8 1 1 135 297737465 297737598 6.620000e-47 198
27 TraesCS1A01G366100 chr4D 92.593 135 9 1 1 135 404921118 404921251 3.080000e-45 193
28 TraesCS1A01G366100 chr4D 91.852 135 10 1 1 135 7763739 7763872 1.430000e-43 187
29 TraesCS1A01G366100 chr2D 92.593 135 9 1 1 135 580129432 580129565 3.080000e-45 193
30 TraesCS1A01G366100 chr2D 90.845 142 12 1 1 142 642827206 642827066 3.990000e-44 189
31 TraesCS1A01G366100 chr7A 92.537 134 9 1 1 134 16025698 16025566 1.110000e-44 191
32 TraesCS1A01G366100 chr3D 91.912 136 10 1 1 136 496111372 496111238 3.990000e-44 189
33 TraesCS1A01G366100 chr5D 91.852 135 10 1 1 135 65758438 65758571 1.430000e-43 187


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 TraesCS1A01G366100 chr1A 544999185 545002213 3028 False 5594.00 5594 100.0000 1 3029 1 chr1A.!!$F2 3028
1 TraesCS1A01G366100 chr1A 544747477 544748570 1093 False 817.00 817 80.7690 133 1272 1 chr1A.!!$F1 1139
2 TraesCS1A01G366100 chr1A 545008475 545009127 652 True 736.00 736 87.2530 1397 2043 1 chr1A.!!$R1 646
3 TraesCS1A01G366100 chr1A 545298574 545299256 682 True 612.00 612 83.5950 1417 2086 1 chr1A.!!$R2 669
4 TraesCS1A01G366100 chr1A 544927550 544928680 1130 False 492.00 684 86.0610 688 1900 2 chr1A.!!$F3 1212
5 TraesCS1A01G366100 chr1D 449846521 449848654 2133 False 2423.00 2423 87.4720 696 2835 1 chr1D.!!$F2 2139
6 TraesCS1A01G366100 chr1D 449659547 449661264 1717 False 742.50 1230 85.2475 363 1900 2 chr1D.!!$F3 1537
7 TraesCS1A01G366100 chr1D 449673867 449675517 1650 False 729.00 1223 87.4440 133 1900 2 chr1D.!!$F4 1767
8 TraesCS1A01G366100 chr1D 450044146 450044902 756 True 691.00 691 83.9380 1352 2086 1 chr1D.!!$R2 734
9 TraesCS1A01G366100 chr1D 449922588 449923928 1340 True 649.50 737 86.2110 694 2043 2 chr1D.!!$R3 1349
10 TraesCS1A01G366100 chr1D 449983113 449983754 641 True 481.00 481 81.0690 697 1319 1 chr1D.!!$R1 622
11 TraesCS1A01G366100 chr1B 615624684 615625896 1212 False 870.00 870 80.8790 133 1271 1 chr1B.!!$F1 1138
12 TraesCS1A01G366100 chr1B 615731268 615734173 2905 False 740.75 1840 87.2280 133 2976 4 chr1B.!!$F3 2843
13 TraesCS1A01G366100 chr1B 615744190 615744798 608 True 732.00 732 88.2540 1417 2043 1 chr1B.!!$R1 626
14 TraesCS1A01G366100 chr1B 615581739 615582616 877 False 557.50 675 93.8635 1001 1900 2 chr1B.!!$F2 899

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
175 176 0.032130 TGATTAGGTCCGAGCGATGC 59.968 55.0 0.00 0.00 0.00 3.91 F
952 1376 0.109226 AGACGTTGCTTAGCTCGTCC 60.109 55.0 31.97 21.96 46.97 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1350 1792 0.238553 CACTCACTCTGCTCGAACGA 59.761 55.0 0.00 0.0 0.0 3.85 R
2752 3323 0.106335 CTAGGCGACGACCTCTCCTA 59.894 60.0 13.05 5.5 41.5 2.94 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
56 57 1.361793 TTTTTCTCCCGCCGTAATCG 58.638 50.000 0.00 0.00 0.00 3.34
71 72 5.499268 CGTAATCGGTCTTGTTCGTTAAA 57.501 39.130 0.00 0.00 0.00 1.52
72 73 6.086319 CGTAATCGGTCTTGTTCGTTAAAT 57.914 37.500 0.00 0.00 0.00 1.40
73 74 6.527957 CGTAATCGGTCTTGTTCGTTAAATT 58.472 36.000 0.00 0.00 0.00 1.82
74 75 7.011189 CGTAATCGGTCTTGTTCGTTAAATTT 58.989 34.615 0.00 0.00 0.00 1.82
75 76 8.161610 CGTAATCGGTCTTGTTCGTTAAATTTA 58.838 33.333 0.00 0.00 0.00 1.40
76 77 9.977762 GTAATCGGTCTTGTTCGTTAAATTTAT 57.022 29.630 0.00 0.00 0.00 1.40
77 78 8.889849 AATCGGTCTTGTTCGTTAAATTTATG 57.110 30.769 0.00 0.00 0.00 1.90
78 79 6.833839 TCGGTCTTGTTCGTTAAATTTATGG 58.166 36.000 0.00 0.00 0.00 2.74
79 80 6.427547 TCGGTCTTGTTCGTTAAATTTATGGT 59.572 34.615 0.00 0.00 0.00 3.55
80 81 6.739550 CGGTCTTGTTCGTTAAATTTATGGTC 59.260 38.462 0.00 0.00 0.00 4.02
81 82 7.571613 CGGTCTTGTTCGTTAAATTTATGGTCA 60.572 37.037 0.00 0.00 0.00 4.02
82 83 8.077386 GGTCTTGTTCGTTAAATTTATGGTCAA 58.923 33.333 0.00 2.09 0.00 3.18
83 84 9.453325 GTCTTGTTCGTTAAATTTATGGTCAAA 57.547 29.630 0.00 0.00 0.00 2.69
88 89 9.931710 GTTCGTTAAATTTATGGTCAAAATTCG 57.068 29.630 0.00 0.00 35.91 3.34
89 90 9.894783 TTCGTTAAATTTATGGTCAAAATTCGA 57.105 25.926 0.00 0.00 35.91 3.71
90 91 9.332301 TCGTTAAATTTATGGTCAAAATTCGAC 57.668 29.630 0.00 0.37 35.91 4.20
101 102 6.496524 GTCAAAATTCGACCTCAAAAAGTG 57.503 37.500 0.00 0.00 0.00 3.16
102 103 5.040635 TCAAAATTCGACCTCAAAAAGTGC 58.959 37.500 0.00 0.00 0.00 4.40
103 104 2.969443 ATTCGACCTCAAAAAGTGCG 57.031 45.000 0.00 0.00 0.00 5.34
104 105 0.941542 TTCGACCTCAAAAAGTGCGG 59.058 50.000 0.00 0.00 38.16 5.69
105 106 0.882927 TCGACCTCAAAAAGTGCGGG 60.883 55.000 0.00 0.00 36.31 6.13
106 107 1.285950 GACCTCAAAAAGTGCGGGC 59.714 57.895 0.00 0.00 36.31 6.13
107 108 2.255252 CCTCAAAAAGTGCGGGCG 59.745 61.111 0.00 0.00 0.00 6.13
108 109 2.255252 CTCAAAAAGTGCGGGCGG 59.745 61.111 0.00 0.00 0.00 6.13
109 110 2.203224 TCAAAAAGTGCGGGCGGA 60.203 55.556 0.00 0.00 0.00 5.54
110 111 2.050442 CAAAAAGTGCGGGCGGAC 60.050 61.111 0.00 0.00 36.69 4.79
112 113 1.071814 AAAAAGTGCGGGCGGACTA 59.928 52.632 0.00 0.00 45.93 2.59
113 114 0.322187 AAAAAGTGCGGGCGGACTAT 60.322 50.000 0.00 0.00 45.93 2.12
114 115 0.538118 AAAAGTGCGGGCGGACTATA 59.462 50.000 0.00 0.00 45.93 1.31
115 116 0.756903 AAAGTGCGGGCGGACTATAT 59.243 50.000 0.00 0.00 45.93 0.86
116 117 0.756903 AAGTGCGGGCGGACTATATT 59.243 50.000 0.00 0.00 45.93 1.28
117 118 0.756903 AGTGCGGGCGGACTATATTT 59.243 50.000 0.00 0.00 44.84 1.40
118 119 1.140252 AGTGCGGGCGGACTATATTTT 59.860 47.619 0.00 0.00 44.84 1.82
119 120 1.263217 GTGCGGGCGGACTATATTTTG 59.737 52.381 0.00 0.00 33.56 2.44
120 121 1.139256 TGCGGGCGGACTATATTTTGA 59.861 47.619 0.00 0.00 0.00 2.69
121 122 2.215196 GCGGGCGGACTATATTTTGAA 58.785 47.619 0.00 0.00 0.00 2.69
122 123 2.614983 GCGGGCGGACTATATTTTGAAA 59.385 45.455 0.00 0.00 0.00 2.69
123 124 3.252458 GCGGGCGGACTATATTTTGAAAT 59.748 43.478 0.00 0.00 0.00 2.17
124 125 4.783242 CGGGCGGACTATATTTTGAAATG 58.217 43.478 0.00 0.00 0.00 2.32
125 126 4.320202 CGGGCGGACTATATTTTGAAATGG 60.320 45.833 0.00 0.00 0.00 3.16
126 127 4.825085 GGGCGGACTATATTTTGAAATGGA 59.175 41.667 0.00 0.00 0.00 3.41
127 128 5.048713 GGGCGGACTATATTTTGAAATGGAG 60.049 44.000 0.00 0.06 0.00 3.86
128 129 5.048713 GGCGGACTATATTTTGAAATGGAGG 60.049 44.000 0.00 0.00 0.00 4.30
129 130 5.048713 GCGGACTATATTTTGAAATGGAGGG 60.049 44.000 0.00 0.00 0.00 4.30
130 131 6.296026 CGGACTATATTTTGAAATGGAGGGA 58.704 40.000 0.00 0.00 0.00 4.20
131 132 6.428159 CGGACTATATTTTGAAATGGAGGGAG 59.572 42.308 0.00 0.00 0.00 4.30
175 176 0.032130 TGATTAGGTCCGAGCGATGC 59.968 55.000 0.00 0.00 0.00 3.91
205 206 0.109551 CCGAGTCCATCCATCGATCG 60.110 60.000 9.36 9.36 38.72 3.69
207 208 1.135831 CGAGTCCATCCATCGATCGAG 60.136 57.143 23.84 14.59 38.72 4.04
275 280 0.752658 CCCCATGCACTCGTATCAGA 59.247 55.000 0.00 0.00 0.00 3.27
291 296 4.819105 ATCAGAATGGAACGTGAAGGTA 57.181 40.909 0.00 0.00 36.16 3.08
299 304 1.125711 AACGTGAAGGTAGGCAGGGT 61.126 55.000 0.00 0.00 0.00 4.34
301 306 1.258445 CGTGAAGGTAGGCAGGGTCT 61.258 60.000 0.00 0.00 0.00 3.85
302 307 0.984995 GTGAAGGTAGGCAGGGTCTT 59.015 55.000 0.00 0.00 0.00 3.01
303 308 1.351350 GTGAAGGTAGGCAGGGTCTTT 59.649 52.381 0.00 0.00 0.00 2.52
304 309 2.570302 GTGAAGGTAGGCAGGGTCTTTA 59.430 50.000 0.00 0.00 0.00 1.85
307 312 1.188863 GGTAGGCAGGGTCTTTACGA 58.811 55.000 0.00 0.00 0.00 3.43
308 313 1.551883 GGTAGGCAGGGTCTTTACGAA 59.448 52.381 0.00 0.00 0.00 3.85
309 314 2.027837 GGTAGGCAGGGTCTTTACGAAA 60.028 50.000 0.00 0.00 0.00 3.46
310 315 2.943036 AGGCAGGGTCTTTACGAAAA 57.057 45.000 0.00 0.00 0.00 2.29
311 316 2.501261 AGGCAGGGTCTTTACGAAAAC 58.499 47.619 0.00 0.00 0.00 2.43
313 318 2.501261 GCAGGGTCTTTACGAAAACCT 58.499 47.619 0.00 0.00 32.22 3.50
323 340 2.814280 ACGAAAACCTGACGTGATCT 57.186 45.000 0.00 0.00 38.79 2.75
349 366 2.243602 TTAATCGGCCGGTGATTACC 57.756 50.000 27.83 7.05 43.89 2.85
361 381 2.426024 GGTGATTACCTGACGCTCAGTA 59.574 50.000 0.00 4.69 42.80 2.74
405 459 4.119136 GCAGTAATCTCTCTTTCTCAGCC 58.881 47.826 0.00 0.00 0.00 4.85
414 468 3.679980 TCTCTTTCTCAGCCGAAAAATCG 59.320 43.478 0.00 0.00 32.95 3.34
476 531 1.332028 GCCGTGACGCGATTCTTAATG 60.332 52.381 15.93 0.00 44.77 1.90
529 607 1.404035 GGCTACCGTTGGGCTTAATTG 59.596 52.381 0.00 0.00 36.48 2.32
558 644 2.805671 CGCACTTAATCAACAGTGTGGA 59.194 45.455 1.96 1.96 44.44 4.02
597 698 1.157585 GAAAGACGGGCTTCCTTGTC 58.842 55.000 0.00 0.00 35.24 3.18
622 723 1.423921 AGGAAAATCACGTCCCCAACT 59.576 47.619 0.00 0.00 34.13 3.16
646 807 1.548269 CCCACACACCTTCTCTCTCTC 59.452 57.143 0.00 0.00 0.00 3.20
647 808 2.524306 CCACACACCTTCTCTCTCTCT 58.476 52.381 0.00 0.00 0.00 3.10
764 1087 0.465097 AGCTCCAATCCATTGCCTCG 60.465 55.000 0.00 0.00 36.48 4.63
808 1151 2.644212 CGCTGCCTCACCTCACTCT 61.644 63.158 0.00 0.00 0.00 3.24
872 1244 1.519498 GCCTCCCCCATATATACCCC 58.481 60.000 0.00 0.00 0.00 4.95
875 1247 2.226039 CCTCCCCCATATATACCCCACA 60.226 54.545 0.00 0.00 0.00 4.17
892 1270 3.587061 CCCACAATATATACCCAGCAGGA 59.413 47.826 0.00 0.00 39.89 3.86
904 1282 1.407299 CCAGCAGGAAACCATCGATCA 60.407 52.381 0.00 0.00 36.89 2.92
932 1336 1.800586 CGCCATTACCTCAATCCATCG 59.199 52.381 0.00 0.00 0.00 3.84
933 1337 2.547855 CGCCATTACCTCAATCCATCGA 60.548 50.000 0.00 0.00 0.00 3.59
942 1346 1.204704 TCAATCCATCGAGACGTTGCT 59.795 47.619 0.00 0.00 0.00 3.91
952 1376 0.109226 AGACGTTGCTTAGCTCGTCC 60.109 55.000 31.97 21.96 46.97 4.79
975 1400 0.183014 TAGCTAGCTACGAGGCCAGT 59.817 55.000 20.67 7.41 0.00 4.00
999 1437 4.821589 GCCGCCGGAGAGGAACTG 62.822 72.222 7.68 0.00 41.55 3.16
1089 1527 3.093057 AGACGAGAAGCTCTACAACCAT 58.907 45.455 0.00 0.00 0.00 3.55
1188 1626 0.824109 TCCGCTGGATCAACTACCTG 59.176 55.000 0.00 0.00 0.00 4.00
1191 1629 0.811616 GCTGGATCAACTACCTGCGG 60.812 60.000 0.00 0.00 40.18 5.69
1291 1730 1.577134 CCGTGCAATTGCGAATTTACG 59.423 47.619 24.58 24.20 45.83 3.18
1294 1733 2.592459 GTGCAATTGCGAATTTACGGTC 59.408 45.455 24.58 0.00 45.83 4.79
1299 1738 4.712122 ATTGCGAATTTACGGTCCAATT 57.288 36.364 0.00 0.00 0.00 2.32
1319 1761 6.199908 CCAATTCGTTCAGTTACAATTGCAAA 59.800 34.615 1.71 0.00 34.47 3.68
1346 1788 2.181372 TACAGTGTTGCAATGCGCGG 62.181 55.000 8.83 0.47 46.97 6.46
1347 1789 2.977456 AGTGTTGCAATGCGCGGA 60.977 55.556 8.83 5.00 46.97 5.54
1348 1790 2.502510 GTGTTGCAATGCGCGGAG 60.503 61.111 8.83 0.00 46.97 4.63
1349 1791 2.667874 TGTTGCAATGCGCGGAGA 60.668 55.556 8.83 0.00 46.97 3.71
1350 1792 2.039974 TGTTGCAATGCGCGGAGAT 61.040 52.632 8.83 0.00 46.97 2.75
1382 1824 6.209589 AGCAGAGTGAGTGAACTGAAGTATTA 59.790 38.462 0.00 0.00 32.90 0.98
1408 1857 2.153817 CGACATGTATACTGATGCGTGC 59.846 50.000 0.00 0.00 38.01 5.34
1955 2458 2.031163 ACCGCTGGAGCACAAGTC 59.969 61.111 0.00 0.00 42.21 3.01
1959 2462 1.676384 GCTGGAGCACAAGTCCTCT 59.324 57.895 0.00 0.00 41.59 3.69
2011 2514 4.489679 AGTTTCGATTTCAACTTGGAGC 57.510 40.909 0.00 0.00 28.27 4.70
2090 2594 0.541863 ATCTCGATTCCCACCCACAC 59.458 55.000 0.00 0.00 0.00 3.82
2091 2595 0.834261 TCTCGATTCCCACCCACACA 60.834 55.000 0.00 0.00 0.00 3.72
2092 2596 0.673644 CTCGATTCCCACCCACACAC 60.674 60.000 0.00 0.00 0.00 3.82
2093 2597 1.125093 TCGATTCCCACCCACACACT 61.125 55.000 0.00 0.00 0.00 3.55
2094 2598 0.673644 CGATTCCCACCCACACACTC 60.674 60.000 0.00 0.00 0.00 3.51
2134 2641 1.680338 ACAGGACAGCAAAGAACCAC 58.320 50.000 0.00 0.00 0.00 4.16
2135 2642 0.954452 CAGGACAGCAAAGAACCACC 59.046 55.000 0.00 0.00 0.00 4.61
2136 2643 0.550914 AGGACAGCAAAGAACCACCA 59.449 50.000 0.00 0.00 0.00 4.17
2143 2650 0.961753 CAAAGAACCACCAGAAGGCC 59.038 55.000 0.00 0.00 39.06 5.19
2145 2652 0.555769 AAGAACCACCAGAAGGCCAA 59.444 50.000 5.01 0.00 39.06 4.52
2206 2713 2.951457 TTCACAGAGACGACACACAA 57.049 45.000 0.00 0.00 0.00 3.33
2212 2719 2.663602 CAGAGACGACACACAATACAGC 59.336 50.000 0.00 0.00 0.00 4.40
2214 2721 1.343142 AGACGACACACAATACAGCCA 59.657 47.619 0.00 0.00 0.00 4.75
2245 2753 5.918576 TCGTACAGAGAACATTGTTGTGTAG 59.081 40.000 6.80 6.60 35.83 2.74
2248 2758 7.060748 CGTACAGAGAACATTGTTGTGTAGTAG 59.939 40.741 6.80 3.85 35.83 2.57
2263 2773 8.919661 GTTGTGTAGTAGTAGTAATCAAACACC 58.080 37.037 6.96 0.00 35.10 4.16
2299 2809 5.757886 ACATTTGTCGAAATATAATGCCGG 58.242 37.500 0.00 0.00 30.20 6.13
2300 2810 4.822036 TTTGTCGAAATATAATGCCGGG 57.178 40.909 2.18 0.00 0.00 5.73
2305 2836 2.159627 CGAAATATAATGCCGGGCTCAC 59.840 50.000 21.46 1.02 0.00 3.51
2323 2854 0.895530 ACTGATGTGTCCGGGTGTAG 59.104 55.000 0.00 0.00 0.00 2.74
2325 2856 2.097036 CTGATGTGTCCGGGTGTAGTA 58.903 52.381 0.00 0.00 0.00 1.82
2330 2861 2.699846 TGTGTCCGGGTGTAGTACTTTT 59.300 45.455 0.00 0.00 0.00 2.27
2355 2886 6.618287 TCTCAACAATAATTTAGCGATGGG 57.382 37.500 0.00 0.00 0.00 4.00
2393 2924 1.278985 CATGCAGGTTACTGTCTCCCA 59.721 52.381 0.00 0.00 46.62 4.37
2507 3038 1.376609 CCAGCGAGGCCACATTAACC 61.377 60.000 5.01 0.00 0.00 2.85
2515 3050 4.714632 GAGGCCACATTAACCTTGCTATA 58.285 43.478 5.01 0.00 32.67 1.31
2531 3066 2.709125 TATACGTCCATGCTGGCCGC 62.709 60.000 11.92 11.92 43.57 6.53
2540 3075 3.199551 GCTGGCCGCAATCAATCA 58.800 55.556 13.61 0.00 38.92 2.57
2541 3076 1.065273 GCTGGCCGCAATCAATCAG 59.935 57.895 13.61 0.00 38.92 2.90
2542 3077 1.660560 GCTGGCCGCAATCAATCAGT 61.661 55.000 13.61 0.00 38.92 3.41
2555 3090 9.855361 CGCAATCAATCAGTAGTAGAAAATTAG 57.145 33.333 0.00 0.00 0.00 1.73
2557 3092 9.855361 CAATCAATCAGTAGTAGAAAATTAGCG 57.145 33.333 0.00 0.00 0.00 4.26
2575 3110 1.588597 GCCAGGAAGAAAAGCCAGC 59.411 57.895 0.00 0.00 0.00 4.85
2576 3111 1.181098 GCCAGGAAGAAAAGCCAGCA 61.181 55.000 0.00 0.00 0.00 4.41
2578 3113 0.600057 CAGGAAGAAAAGCCAGCACC 59.400 55.000 0.00 0.00 0.00 5.01
2606 3141 2.825264 GGAGATCCTCCCGGCAAG 59.175 66.667 0.00 0.00 44.36 4.01
2608 3143 2.041265 AGATCCTCCCGGCAAGGT 59.959 61.111 17.85 8.02 38.74 3.50
2610 3145 2.041265 ATCCTCCCGGCAAGGTCT 59.959 61.111 17.85 6.96 38.74 3.85
2613 3148 3.382832 CTCCCGGCAAGGTCTCGT 61.383 66.667 0.00 0.00 38.74 4.18
2614 3149 2.920912 TCCCGGCAAGGTCTCGTT 60.921 61.111 0.00 0.00 38.74 3.85
2615 3150 2.434359 CCCGGCAAGGTCTCGTTC 60.434 66.667 0.00 0.00 38.74 3.95
2616 3151 2.809601 CCGGCAAGGTCTCGTTCG 60.810 66.667 0.00 0.00 34.51 3.95
2617 3152 2.809601 CGGCAAGGTCTCGTTCGG 60.810 66.667 0.00 0.00 0.00 4.30
2618 3153 3.119096 GGCAAGGTCTCGTTCGGC 61.119 66.667 0.00 0.00 0.00 5.54
2619 3154 3.119096 GCAAGGTCTCGTTCGGCC 61.119 66.667 0.00 0.00 0.00 6.13
2620 3155 2.809601 CAAGGTCTCGTTCGGCCG 60.810 66.667 22.12 22.12 0.00 6.13
2621 3156 4.065281 AAGGTCTCGTTCGGCCGG 62.065 66.667 27.83 9.82 0.00 6.13
2697 3268 1.616628 AGGGCGGAGAGGGACAAAT 60.617 57.895 0.00 0.00 0.00 2.32
2711 3282 2.289945 GGACAAATGACTCCACTGCTCT 60.290 50.000 0.00 0.00 0.00 4.09
2749 3320 4.680237 CGGCGAACTGCTGGGTGA 62.680 66.667 0.00 0.00 46.76 4.02
2752 3323 1.078848 GCGAACTGCTGGGTGAGAT 60.079 57.895 0.00 0.00 41.73 2.75
2755 3326 1.202463 CGAACTGCTGGGTGAGATAGG 60.202 57.143 0.00 0.00 0.00 2.57
2760 3331 1.337118 GCTGGGTGAGATAGGAGAGG 58.663 60.000 0.00 0.00 0.00 3.69
2796 3367 1.001048 CGCTAACATGGCATGATTGGG 60.001 52.381 32.74 24.20 0.00 4.12
2797 3368 1.269936 GCTAACATGGCATGATTGGGC 60.270 52.381 32.74 22.03 0.00 5.36
2976 3613 2.113139 CCAGACCACCCAGCGTTT 59.887 61.111 0.00 0.00 0.00 3.60
2977 3614 1.528309 CCAGACCACCCAGCGTTTT 60.528 57.895 0.00 0.00 0.00 2.43
2978 3615 1.515521 CCAGACCACCCAGCGTTTTC 61.516 60.000 0.00 0.00 0.00 2.29
2980 3617 2.593436 ACCACCCAGCGTTTTCGG 60.593 61.111 0.00 0.00 44.29 4.30
2981 3618 3.361977 CCACCCAGCGTTTTCGGG 61.362 66.667 0.00 0.00 44.29 5.14
2982 3619 2.281208 CACCCAGCGTTTTCGGGA 60.281 61.111 0.00 0.00 44.29 5.14
2983 3620 2.032071 ACCCAGCGTTTTCGGGAG 59.968 61.111 0.00 0.00 44.29 4.30
2984 3621 2.032071 CCCAGCGTTTTCGGGAGT 59.968 61.111 0.00 0.00 44.29 3.85
2985 3622 2.325082 CCCAGCGTTTTCGGGAGTG 61.325 63.158 0.00 0.00 44.29 3.51
2986 3623 2.325082 CCAGCGTTTTCGGGAGTGG 61.325 63.158 0.00 0.00 44.29 4.00
2987 3624 2.668550 AGCGTTTTCGGGAGTGGC 60.669 61.111 0.00 0.00 44.29 5.01
2988 3625 2.668550 GCGTTTTCGGGAGTGGCT 60.669 61.111 0.00 0.00 44.29 4.75
2989 3626 2.966309 GCGTTTTCGGGAGTGGCTG 61.966 63.158 0.00 0.00 44.29 4.85
2990 3627 1.301401 CGTTTTCGGGAGTGGCTGA 60.301 57.895 0.00 0.00 39.94 4.26
2991 3628 0.673644 CGTTTTCGGGAGTGGCTGAT 60.674 55.000 0.00 0.00 39.94 2.90
2992 3629 0.804989 GTTTTCGGGAGTGGCTGATG 59.195 55.000 0.00 0.00 0.00 3.07
2993 3630 0.960364 TTTTCGGGAGTGGCTGATGC 60.960 55.000 0.00 0.00 38.76 3.91
2994 3631 1.841302 TTTCGGGAGTGGCTGATGCT 61.841 55.000 0.00 0.00 39.59 3.79
2995 3632 2.513204 CGGGAGTGGCTGATGCTG 60.513 66.667 0.00 0.00 39.59 4.41
2996 3633 2.827642 GGGAGTGGCTGATGCTGC 60.828 66.667 0.00 0.00 39.59 5.25
2997 3634 2.827642 GGAGTGGCTGATGCTGCC 60.828 66.667 8.21 8.21 46.46 4.85
3017 3654 3.033114 TGCATGTGCGCAATTAAGC 57.967 47.368 14.00 13.14 45.83 3.09
3018 3655 0.243095 TGCATGTGCGCAATTAAGCA 59.757 45.000 14.00 15.80 45.83 3.91
3023 3660 2.939781 TGCGCAATTAAGCACCTCA 58.060 47.368 8.16 0.00 38.59 3.86
3024 3661 1.462616 TGCGCAATTAAGCACCTCAT 58.537 45.000 8.16 0.00 38.59 2.90
3025 3662 1.818060 TGCGCAATTAAGCACCTCATT 59.182 42.857 8.16 0.00 38.59 2.57
3026 3663 2.187707 GCGCAATTAAGCACCTCATTG 58.812 47.619 0.30 0.00 0.00 2.82
3027 3664 2.801063 CGCAATTAAGCACCTCATTGG 58.199 47.619 0.00 0.00 42.93 3.16
3028 3665 2.480073 CGCAATTAAGCACCTCATTGGG 60.480 50.000 0.00 0.00 41.11 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 1.361793 CGATTACGGCGGGAGAAAAA 58.638 50.000 13.24 0.00 35.72 1.94
38 39 3.053662 CGATTACGGCGGGAGAAAA 57.946 52.632 13.24 0.00 35.72 2.29
39 40 4.819082 CGATTACGGCGGGAGAAA 57.181 55.556 13.24 0.00 35.72 2.52
49 50 5.499268 TTTAACGAACAAGACCGATTACG 57.501 39.130 0.00 0.00 39.43 3.18
50 51 9.977762 ATAAATTTAACGAACAAGACCGATTAC 57.022 29.630 1.21 0.00 0.00 1.89
51 52 9.976255 CATAAATTTAACGAACAAGACCGATTA 57.024 29.630 1.21 0.00 0.00 1.75
52 53 7.966204 CCATAAATTTAACGAACAAGACCGATT 59.034 33.333 1.21 0.00 0.00 3.34
53 54 7.120138 ACCATAAATTTAACGAACAAGACCGAT 59.880 33.333 1.21 0.00 0.00 4.18
54 55 6.427547 ACCATAAATTTAACGAACAAGACCGA 59.572 34.615 1.21 0.00 0.00 4.69
55 56 6.604930 ACCATAAATTTAACGAACAAGACCG 58.395 36.000 1.21 0.00 0.00 4.79
56 57 7.586747 TGACCATAAATTTAACGAACAAGACC 58.413 34.615 1.21 0.00 0.00 3.85
57 58 9.453325 TTTGACCATAAATTTAACGAACAAGAC 57.547 29.630 1.21 0.00 0.00 3.01
62 63 9.931710 CGAATTTTGACCATAAATTTAACGAAC 57.068 29.630 1.21 0.00 35.83 3.95
63 64 9.894783 TCGAATTTTGACCATAAATTTAACGAA 57.105 25.926 1.21 0.00 35.83 3.85
64 65 9.332301 GTCGAATTTTGACCATAAATTTAACGA 57.668 29.630 1.21 0.00 35.83 3.85
78 79 5.051708 GCACTTTTTGAGGTCGAATTTTGAC 60.052 40.000 8.09 8.09 35.60 3.18
79 80 5.040635 GCACTTTTTGAGGTCGAATTTTGA 58.959 37.500 0.00 0.00 0.00 2.69
80 81 4.085619 CGCACTTTTTGAGGTCGAATTTTG 60.086 41.667 0.00 0.00 0.00 2.44
81 82 4.041723 CGCACTTTTTGAGGTCGAATTTT 58.958 39.130 0.00 0.00 0.00 1.82
82 83 3.550030 CCGCACTTTTTGAGGTCGAATTT 60.550 43.478 0.00 0.00 40.25 1.82
83 84 2.031157 CCGCACTTTTTGAGGTCGAATT 60.031 45.455 0.00 0.00 40.25 2.17
84 85 1.535462 CCGCACTTTTTGAGGTCGAAT 59.465 47.619 0.00 0.00 40.25 3.34
85 86 0.941542 CCGCACTTTTTGAGGTCGAA 59.058 50.000 0.00 0.00 40.25 3.71
86 87 0.882927 CCCGCACTTTTTGAGGTCGA 60.883 55.000 0.00 0.00 43.56 4.20
87 88 1.574428 CCCGCACTTTTTGAGGTCG 59.426 57.895 0.00 0.00 43.56 4.79
88 89 1.285950 GCCCGCACTTTTTGAGGTC 59.714 57.895 0.00 0.00 43.56 3.85
89 90 2.551912 CGCCCGCACTTTTTGAGGT 61.552 57.895 0.00 0.00 43.56 3.85
90 91 2.255252 CGCCCGCACTTTTTGAGG 59.745 61.111 0.00 0.00 44.65 3.86
91 92 2.255252 CCGCCCGCACTTTTTGAG 59.745 61.111 0.00 0.00 0.00 3.02
92 93 2.203224 TCCGCCCGCACTTTTTGA 60.203 55.556 0.00 0.00 0.00 2.69
93 94 1.231958 TAGTCCGCCCGCACTTTTTG 61.232 55.000 0.00 0.00 0.00 2.44
94 95 0.322187 ATAGTCCGCCCGCACTTTTT 60.322 50.000 0.00 0.00 0.00 1.94
95 96 0.538118 TATAGTCCGCCCGCACTTTT 59.462 50.000 0.00 0.00 0.00 2.27
96 97 0.756903 ATATAGTCCGCCCGCACTTT 59.243 50.000 0.00 0.00 0.00 2.66
97 98 0.756903 AATATAGTCCGCCCGCACTT 59.243 50.000 0.00 0.00 0.00 3.16
98 99 0.756903 AAATATAGTCCGCCCGCACT 59.243 50.000 0.00 0.00 0.00 4.40
99 100 1.263217 CAAAATATAGTCCGCCCGCAC 59.737 52.381 0.00 0.00 0.00 5.34
100 101 1.139256 TCAAAATATAGTCCGCCCGCA 59.861 47.619 0.00 0.00 0.00 5.69
101 102 1.873698 TCAAAATATAGTCCGCCCGC 58.126 50.000 0.00 0.00 0.00 6.13
102 103 4.320202 CCATTTCAAAATATAGTCCGCCCG 60.320 45.833 0.00 0.00 0.00 6.13
103 104 4.825085 TCCATTTCAAAATATAGTCCGCCC 59.175 41.667 0.00 0.00 0.00 6.13
104 105 5.048713 CCTCCATTTCAAAATATAGTCCGCC 60.049 44.000 0.00 0.00 0.00 6.13
105 106 5.048713 CCCTCCATTTCAAAATATAGTCCGC 60.049 44.000 0.00 0.00 0.00 5.54
106 107 6.296026 TCCCTCCATTTCAAAATATAGTCCG 58.704 40.000 0.00 0.00 0.00 4.79
107 108 7.290813 ACTCCCTCCATTTCAAAATATAGTCC 58.709 38.462 0.00 0.00 0.00 3.85
108 109 9.274206 GTACTCCCTCCATTTCAAAATATAGTC 57.726 37.037 0.00 0.00 0.00 2.59
109 110 8.218488 GGTACTCCCTCCATTTCAAAATATAGT 58.782 37.037 0.00 0.00 0.00 2.12
110 111 8.217799 TGGTACTCCCTCCATTTCAAAATATAG 58.782 37.037 0.00 0.00 0.00 1.31
111 112 7.996644 GTGGTACTCCCTCCATTTCAAAATATA 59.003 37.037 0.00 0.00 36.09 0.86
112 113 6.833933 GTGGTACTCCCTCCATTTCAAAATAT 59.166 38.462 0.00 0.00 36.09 1.28
113 114 6.184789 GTGGTACTCCCTCCATTTCAAAATA 58.815 40.000 0.00 0.00 36.09 1.40
114 115 5.016831 GTGGTACTCCCTCCATTTCAAAAT 58.983 41.667 0.00 0.00 36.09 1.82
115 116 4.141135 TGTGGTACTCCCTCCATTTCAAAA 60.141 41.667 0.00 0.00 36.09 2.44
116 117 3.396276 TGTGGTACTCCCTCCATTTCAAA 59.604 43.478 0.00 0.00 36.09 2.69
117 118 2.983192 TGTGGTACTCCCTCCATTTCAA 59.017 45.455 0.00 0.00 36.09 2.69
118 119 2.626785 TGTGGTACTCCCTCCATTTCA 58.373 47.619 0.00 0.00 36.09 2.69
119 120 3.933861 ATGTGGTACTCCCTCCATTTC 57.066 47.619 0.00 0.00 36.09 2.17
120 121 4.344104 CAAATGTGGTACTCCCTCCATTT 58.656 43.478 0.00 0.00 41.80 2.32
121 122 3.877735 GCAAATGTGGTACTCCCTCCATT 60.878 47.826 0.00 0.00 37.19 3.16
122 123 2.357154 GCAAATGTGGTACTCCCTCCAT 60.357 50.000 0.00 0.00 36.09 3.41
123 124 1.004277 GCAAATGTGGTACTCCCTCCA 59.996 52.381 0.00 0.00 0.00 3.86
124 125 1.004277 TGCAAATGTGGTACTCCCTCC 59.996 52.381 0.00 0.00 0.00 4.30
125 126 2.489938 TGCAAATGTGGTACTCCCTC 57.510 50.000 0.00 0.00 0.00 4.30
126 127 2.680805 CGATGCAAATGTGGTACTCCCT 60.681 50.000 0.00 0.00 0.00 4.20
127 128 1.670811 CGATGCAAATGTGGTACTCCC 59.329 52.381 0.00 0.00 0.00 4.30
128 129 1.064060 GCGATGCAAATGTGGTACTCC 59.936 52.381 0.00 0.00 0.00 3.85
129 130 2.009774 AGCGATGCAAATGTGGTACTC 58.990 47.619 0.00 0.00 0.00 2.59
130 131 2.113860 AGCGATGCAAATGTGGTACT 57.886 45.000 0.00 0.00 0.00 2.73
131 132 2.785679 GAAGCGATGCAAATGTGGTAC 58.214 47.619 0.00 0.00 0.00 3.34
205 206 0.317436 CGCGTCCAGATACAGAGCTC 60.317 60.000 5.27 5.27 0.00 4.09
207 208 1.946650 GCGCGTCCAGATACAGAGC 60.947 63.158 8.43 0.00 0.00 4.09
275 280 1.349688 TGCCTACCTTCACGTTCCATT 59.650 47.619 0.00 0.00 0.00 3.16
291 296 2.501261 GTTTTCGTAAAGACCCTGCCT 58.499 47.619 0.00 0.00 0.00 4.75
299 304 4.044336 TCACGTCAGGTTTTCGTAAAGA 57.956 40.909 0.00 0.00 36.05 2.52
301 306 4.624015 AGATCACGTCAGGTTTTCGTAAA 58.376 39.130 0.00 0.00 36.05 2.01
302 307 4.247267 AGATCACGTCAGGTTTTCGTAA 57.753 40.909 0.00 0.00 36.05 3.18
303 308 3.928727 AGATCACGTCAGGTTTTCGTA 57.071 42.857 0.00 0.00 36.05 3.43
304 309 2.814280 AGATCACGTCAGGTTTTCGT 57.186 45.000 0.00 0.00 38.34 3.85
307 312 4.703897 TCTCAAAGATCACGTCAGGTTTT 58.296 39.130 0.00 0.00 0.00 2.43
308 313 4.336889 TCTCAAAGATCACGTCAGGTTT 57.663 40.909 0.00 0.00 0.00 3.27
309 314 4.543590 ATCTCAAAGATCACGTCAGGTT 57.456 40.909 0.00 0.00 25.75 3.50
310 315 4.543590 AATCTCAAAGATCACGTCAGGT 57.456 40.909 0.00 0.00 32.89 4.00
311 316 6.074623 CGATTAATCTCAAAGATCACGTCAGG 60.075 42.308 13.45 0.00 32.89 3.86
313 318 5.748630 CCGATTAATCTCAAAGATCACGTCA 59.251 40.000 13.45 0.00 32.89 4.35
323 340 2.093394 TCACCGGCCGATTAATCTCAAA 60.093 45.455 30.73 0.00 0.00 2.69
361 381 0.034380 ATCAGGTCATGCTGCAGCTT 60.034 50.000 36.61 28.85 42.66 3.74
367 387 1.300481 CTGCTCATCAGGTCATGCTG 58.700 55.000 0.00 0.00 39.15 4.41
414 468 3.430895 TCGATTACAGAAAAACTCGGCAC 59.569 43.478 0.00 0.00 0.00 5.01
428 483 6.422400 TGCACTAATAATGCGATTCGATTACA 59.578 34.615 10.88 0.00 46.49 2.41
500 575 1.408127 CCAACGGTAGCCCATCAATGA 60.408 52.381 0.00 0.00 0.00 2.57
529 607 1.438651 TGATTAAGTGCGACACTGCC 58.561 50.000 12.22 4.57 44.62 4.85
558 644 0.679640 CTCTCCGAGAGCTCCACAGT 60.680 60.000 12.50 0.00 35.30 3.55
584 685 2.742372 CCACGACAAGGAAGCCCG 60.742 66.667 0.00 0.00 37.58 6.13
608 709 0.616891 GGGTTAGTTGGGGACGTGAT 59.383 55.000 0.00 0.00 0.00 3.06
622 723 1.975680 GAGAGAAGGTGTGTGGGGTTA 59.024 52.381 0.00 0.00 0.00 2.85
646 807 2.047844 CGGGGCACTGTGTCAGAG 60.048 66.667 15.06 0.74 35.18 3.35
647 808 3.625897 CCGGGGCACTGTGTCAGA 61.626 66.667 15.06 0.00 35.18 3.27
764 1087 0.389426 TAGGTTCGAAGCAAGGCGAC 60.389 55.000 27.46 0.00 36.11 5.19
808 1151 2.190843 CGGCGAGAGAGAGGGAGA 59.809 66.667 0.00 0.00 0.00 3.71
872 1244 5.473504 GGTTTCCTGCTGGGTATATATTGTG 59.526 44.000 10.07 0.00 36.25 3.33
875 1247 5.922960 TGGTTTCCTGCTGGGTATATATT 57.077 39.130 10.07 0.00 36.25 1.28
887 1265 2.808543 GGTATGATCGATGGTTTCCTGC 59.191 50.000 0.54 0.00 0.00 4.85
904 1282 2.244695 TGAGGTAATGGCGATCGGTAT 58.755 47.619 18.30 0.00 0.00 2.73
932 1336 1.261097 GACGAGCTAAGCAACGTCTC 58.739 55.000 20.13 0.00 46.90 3.36
933 1337 3.403276 GACGAGCTAAGCAACGTCT 57.597 52.632 20.13 0.00 46.90 4.18
942 1346 2.481854 CTAGCTACTCGGACGAGCTAA 58.518 52.381 20.46 6.72 45.61 3.09
952 1376 0.513820 GCCTCGTAGCTAGCTACTCG 59.486 60.000 38.62 30.65 44.80 4.18
984 1409 1.227089 CATCAGTTCCTCTCCGGCG 60.227 63.158 0.00 0.00 0.00 6.46
997 1422 2.102357 CGACGGACGTCCCATCAG 59.898 66.667 28.52 16.36 41.76 2.90
1062 1500 1.470051 AGAGCTTCTCGTCTTCCTCC 58.530 55.000 0.00 0.00 35.36 4.30
1291 1730 5.622770 ATTGTAACTGAACGAATTGGACC 57.377 39.130 0.00 0.00 0.00 4.46
1294 1733 5.218885 TGCAATTGTAACTGAACGAATTGG 58.781 37.500 7.40 0.00 35.48 3.16
1299 1738 7.489435 TGAAAATTTGCAATTGTAACTGAACGA 59.511 29.630 8.60 0.00 0.00 3.85
1319 1761 4.984161 GCATTGCAACACTGTACTGAAAAT 59.016 37.500 0.00 0.00 0.00 1.82
1346 1788 1.398739 TCACTCTGCTCGAACGATCTC 59.601 52.381 0.00 0.00 0.00 2.75
1347 1789 1.400142 CTCACTCTGCTCGAACGATCT 59.600 52.381 0.00 0.00 0.00 2.75
1348 1790 1.131504 ACTCACTCTGCTCGAACGATC 59.868 52.381 0.00 0.00 0.00 3.69
1349 1791 1.135546 CACTCACTCTGCTCGAACGAT 60.136 52.381 0.00 0.00 0.00 3.73
1350 1792 0.238553 CACTCACTCTGCTCGAACGA 59.761 55.000 0.00 0.00 0.00 3.85
1382 1824 3.005897 GCATCAGTATACATGTCGTCCCT 59.994 47.826 0.00 0.00 0.00 4.20
1414 1869 1.016130 GCGATCTGTGACCACCTGTG 61.016 60.000 0.00 0.00 0.00 3.66
1415 1870 1.293498 GCGATCTGTGACCACCTGT 59.707 57.895 0.00 0.00 0.00 4.00
1911 2389 1.227497 CTGCTCCATCTCCGCCTTC 60.227 63.158 0.00 0.00 0.00 3.46
1955 2458 1.845627 TTCTTGGCAGGGCAGAGAGG 61.846 60.000 0.00 0.00 0.00 3.69
1959 2462 1.073722 CTGTTCTTGGCAGGGCAGA 59.926 57.895 13.68 0.00 0.00 4.26
2010 2513 3.944087 AGTTCAGAAGTATGGTTCCAGC 58.056 45.455 0.00 0.00 0.00 4.85
2011 2514 6.712547 AGAAAAGTTCAGAAGTATGGTTCCAG 59.287 38.462 0.00 0.00 0.00 3.86
2090 2594 6.266323 ACTGACGTGCAAATATAGTAGAGTG 58.734 40.000 0.00 0.00 0.00 3.51
2091 2595 6.452494 ACTGACGTGCAAATATAGTAGAGT 57.548 37.500 0.00 0.00 0.00 3.24
2092 2596 7.415229 TGTACTGACGTGCAAATATAGTAGAG 58.585 38.462 0.00 0.00 32.64 2.43
2093 2597 7.324354 TGTACTGACGTGCAAATATAGTAGA 57.676 36.000 0.00 0.00 32.64 2.59
2094 2598 6.637254 CCTGTACTGACGTGCAAATATAGTAG 59.363 42.308 0.00 0.00 35.30 2.57
2134 2641 2.961062 CAATCCCTAATTGGCCTTCTGG 59.039 50.000 3.32 0.00 40.99 3.86
2143 2650 7.587757 GTACTACGTACGTACAATCCCTAATTG 59.412 40.741 23.60 11.66 38.84 2.32
2145 2652 6.204882 GGTACTACGTACGTACAATCCCTAAT 59.795 42.308 23.60 0.00 39.64 1.73
2169 2676 8.642908 TCTGTGAAAATCAACGTATGTATAGG 57.357 34.615 0.00 0.00 0.00 2.57
2179 2686 3.489416 TGTCGTCTCTGTGAAAATCAACG 59.511 43.478 0.00 0.00 29.73 4.10
2206 2713 3.487372 TGTACGAGCTCTATGGCTGTAT 58.513 45.455 12.85 0.00 43.20 2.29
2212 2719 3.628032 TGTTCTCTGTACGAGCTCTATGG 59.372 47.826 12.85 0.00 39.70 2.74
2214 2721 5.358442 ACAATGTTCTCTGTACGAGCTCTAT 59.642 40.000 12.85 2.11 39.70 1.98
2282 2792 2.415512 GAGCCCGGCATTATATTTCGAC 59.584 50.000 13.15 0.00 0.00 4.20
2292 2802 1.452651 CATCAGTGAGCCCGGCATT 60.453 57.895 13.15 0.00 0.00 3.56
2293 2803 2.191375 CATCAGTGAGCCCGGCAT 59.809 61.111 13.15 0.00 0.00 4.40
2305 2836 0.895530 ACTACACCCGGACACATCAG 59.104 55.000 0.73 0.00 0.00 2.90
2330 2861 7.416213 CCCCATCGCTAAATTATTGTTGAGAAA 60.416 37.037 0.00 0.00 0.00 2.52
2355 2886 3.694889 GTGTAATTCACGCAAGCCC 57.305 52.632 0.00 0.00 45.62 5.19
2393 2924 2.152016 GGAAAAGGCTAAAGCGTGACT 58.848 47.619 0.00 0.00 43.26 3.41
2478 3009 1.156645 GCCTCGCTGGAGCACTAATG 61.157 60.000 0.00 0.00 42.21 1.90
2531 3066 9.855361 CGCTAATTTTCTACTACTGATTGATTG 57.145 33.333 0.00 0.00 0.00 2.67
2540 3075 4.404715 TCCTGGCGCTAATTTTCTACTACT 59.595 41.667 7.64 0.00 0.00 2.57
2541 3076 4.690122 TCCTGGCGCTAATTTTCTACTAC 58.310 43.478 7.64 0.00 0.00 2.73
2542 3077 5.128171 TCTTCCTGGCGCTAATTTTCTACTA 59.872 40.000 7.64 0.00 0.00 1.82
2555 3090 2.205243 CTGGCTTTTCTTCCTGGCGC 62.205 60.000 0.00 0.00 0.00 6.53
2557 3092 1.181098 TGCTGGCTTTTCTTCCTGGC 61.181 55.000 0.00 0.00 0.00 4.85
2578 3113 2.611518 GAGGATCTCCACGTTGAAGTG 58.388 52.381 0.00 0.00 41.53 3.16
2603 3138 2.809601 CGGCCGAACGAGACCTTG 60.810 66.667 24.07 0.00 35.47 3.61
2604 3139 4.065281 CCGGCCGAACGAGACCTT 62.065 66.667 30.73 0.00 35.47 3.50
2628 3163 4.157120 AGGGCCATGGACGTACGC 62.157 66.667 18.40 8.19 0.00 4.42
2629 3164 2.202878 CAGGGCCATGGACGTACG 60.203 66.667 18.40 15.01 0.00 3.67
2630 3165 2.513897 GCAGGGCCATGGACGTAC 60.514 66.667 20.75 5.03 0.00 3.67
2631 3166 3.006133 TGCAGGGCCATGGACGTA 61.006 61.111 20.75 0.00 0.00 3.57
2632 3167 4.415150 CTGCAGGGCCATGGACGT 62.415 66.667 20.75 12.76 0.00 4.34
2633 3168 3.411114 ATCTGCAGGGCCATGGACG 62.411 63.158 20.75 10.56 0.00 4.79
2634 3169 1.527844 GATCTGCAGGGCCATGGAC 60.528 63.158 20.75 14.40 0.00 4.02
2635 3170 2.921435 GATCTGCAGGGCCATGGA 59.079 61.111 20.75 16.60 0.00 3.41
2636 3171 2.593725 CGATCTGCAGGGCCATGG 60.594 66.667 20.75 7.63 0.00 3.66
2637 3172 2.593725 CCGATCTGCAGGGCCATG 60.594 66.667 14.45 14.45 0.00 3.66
2638 3173 3.092511 ACCGATCTGCAGGGCCAT 61.093 61.111 15.13 0.00 0.00 4.40
2639 3174 3.785859 GACCGATCTGCAGGGCCA 61.786 66.667 15.13 0.00 0.00 5.36
2711 3282 1.229428 GCTGCTCAACAACAGTGCTA 58.771 50.000 0.00 0.00 36.26 3.49
2747 3318 1.810794 GCGACGACCTCTCCTATCTCA 60.811 57.143 0.00 0.00 0.00 3.27
2749 3320 0.535553 GGCGACGACCTCTCCTATCT 60.536 60.000 0.00 0.00 0.00 1.98
2752 3323 0.106335 CTAGGCGACGACCTCTCCTA 59.894 60.000 13.05 5.50 41.50 2.94
2755 3326 2.716864 GCTAGGCGACGACCTCTC 59.283 66.667 13.05 4.65 41.50 3.20
2786 3357 2.800736 GACGTGGCCCAATCATGC 59.199 61.111 0.00 0.00 0.00 4.06
2959 3596 1.515521 GAAAACGCTGGGTGGTCTGG 61.516 60.000 0.00 0.00 0.00 3.86
2976 3613 2.268920 GCATCAGCCACTCCCGAA 59.731 61.111 0.00 0.00 33.58 4.30
2977 3614 2.685017 AGCATCAGCCACTCCCGA 60.685 61.111 0.00 0.00 43.56 5.14
2978 3615 2.513204 CAGCATCAGCCACTCCCG 60.513 66.667 0.00 0.00 43.56 5.14
2979 3616 2.827642 GCAGCATCAGCCACTCCC 60.828 66.667 0.00 0.00 43.56 4.30
2995 3632 2.864007 TAATTGCGCACATGCACGGC 62.864 55.000 11.12 0.00 46.25 5.68
2996 3633 0.455802 TTAATTGCGCACATGCACGG 60.456 50.000 11.12 0.00 46.25 4.94
2997 3634 0.909174 CTTAATTGCGCACATGCACG 59.091 50.000 11.12 3.72 46.25 5.34
2998 3635 0.641783 GCTTAATTGCGCACATGCAC 59.358 50.000 11.12 0.00 46.25 4.57
2999 3636 0.243095 TGCTTAATTGCGCACATGCA 59.757 45.000 11.12 15.36 44.61 3.96
3000 3637 3.033114 TGCTTAATTGCGCACATGC 57.967 47.368 11.12 12.83 35.36 4.06
3005 3642 1.462616 ATGAGGTGCTTAATTGCGCA 58.537 45.000 5.66 5.66 44.39 6.09
3006 3643 2.187707 CAATGAGGTGCTTAATTGCGC 58.812 47.619 0.00 0.00 42.15 6.09
3007 3644 2.480073 CCCAATGAGGTGCTTAATTGCG 60.480 50.000 0.00 0.00 34.66 4.85
3008 3645 3.169355 CCCAATGAGGTGCTTAATTGC 57.831 47.619 0.00 0.00 34.66 3.56


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

AutoCloner maintained by Alex Coulton.