Multiple sequence alignment - TraesCS2A01G390800

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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 TraesCS2A01G390800 chr2A 100.000 5140 0 0 1 5140 640268732 640273871 0.000000e+00 9492.0
1 TraesCS2A01G390800 chr2A 89.481 713 52 9 2194 2891 302436618 302437322 0.000000e+00 880.0
2 TraesCS2A01G390800 chr2A 89.422 709 46 12 2198 2891 424538239 424537545 0.000000e+00 867.0
3 TraesCS2A01G390800 chr2A 78.531 354 38 14 1002 1345 348629164 348628839 1.130000e-46 198.0
4 TraesCS2A01G390800 chr2A 79.801 302 33 14 1040 1341 259175862 259175589 1.460000e-45 195.0
5 TraesCS2A01G390800 chr2A 88.199 161 14 4 1838 1998 424538504 424538349 2.440000e-43 187.0
6 TraesCS2A01G390800 chr2D 91.172 3908 178 76 744 4539 493177597 493173745 0.000000e+00 5151.0
7 TraesCS2A01G390800 chr2D 90.463 713 45 7 2194 2891 245572830 245572126 0.000000e+00 918.0
8 TraesCS2A01G390800 chr2D 85.343 539 35 16 191 704 493178191 493177672 7.630000e-143 518.0
9 TraesCS2A01G390800 chr2B 88.938 3878 192 100 758 4539 581471536 581467800 0.000000e+00 4566.0
10 TraesCS2A01G390800 chr2B 85.933 654 46 24 1967 2595 42565044 42565676 0.000000e+00 656.0
11 TraesCS2A01G390800 chr2B 88.676 521 27 18 191 698 581472148 581471647 1.580000e-169 606.0
12 TraesCS2A01G390800 chr2B 83.333 114 10 6 3 115 581472296 581472191 4.240000e-16 97.1
13 TraesCS2A01G390800 chr1D 95.702 605 24 2 4537 5140 474732095 474732698 0.000000e+00 972.0
14 TraesCS2A01G390800 chr5B 88.128 716 49 11 2190 2891 291605669 291604976 0.000000e+00 819.0
15 TraesCS2A01G390800 chr5B 81.196 920 105 35 1369 2255 496648921 496648037 0.000000e+00 678.0
16 TraesCS2A01G390800 chr5B 89.308 159 12 4 1838 1996 291605927 291605774 1.460000e-45 195.0
17 TraesCS2A01G390800 chr5A 87.938 713 60 10 2194 2891 222769863 222769162 0.000000e+00 817.0
18 TraesCS2A01G390800 chr5A 78.671 286 53 8 1182 1462 689897000 689897282 3.160000e-42 183.0
19 TraesCS2A01G390800 chr5A 87.421 159 15 4 1838 1996 222770121 222769968 1.470000e-40 178.0
20 TraesCS2A01G390800 chr4A 87.921 712 58 10 2194 2891 535941721 535942418 0.000000e+00 813.0
21 TraesCS2A01G390800 chr4A 83.626 684 66 21 1967 2627 375968765 375968105 7.360000e-168 601.0
22 TraesCS2A01G390800 chr4A 84.080 603 72 15 4539 5136 682993214 682992631 1.250000e-155 560.0
23 TraesCS2A01G390800 chr7B 87.133 715 55 10 2194 2891 428783910 428784604 0.000000e+00 776.0
24 TraesCS2A01G390800 chr7B 82.210 371 53 11 4778 5140 608864602 608864237 1.800000e-79 307.0
25 TraesCS2A01G390800 chr7B 88.050 159 14 3 1838 1996 428783649 428783802 3.160000e-42 183.0
26 TraesCS2A01G390800 chr7A 83.313 827 81 30 1365 2182 369895114 369894336 0.000000e+00 710.0
27 TraesCS2A01G390800 chr7A 83.333 684 67 22 1967 2627 320367651 320366992 5.730000e-164 588.0
28 TraesCS2A01G390800 chr7A 86.119 353 35 9 1002 1341 369895451 369895100 8.130000e-98 368.0
29 TraesCS2A01G390800 chr7A 86.333 300 28 11 1042 1341 705117580 705117294 1.070000e-81 315.0
30 TraesCS2A01G390800 chr7A 85.667 300 30 12 1042 1341 408599505 408599791 2.330000e-78 303.0
31 TraesCS2A01G390800 chr7A 82.703 185 28 4 1637 1821 611728484 611728664 1.480000e-35 161.0
32 TraesCS2A01G390800 chr1A 82.439 820 86 28 1370 2180 382777870 382777100 0.000000e+00 664.0
33 TraesCS2A01G390800 chr1A 83.697 687 62 30 1967 2627 158971993 158972655 2.050000e-168 603.0
34 TraesCS2A01G390800 chr1A 84.158 606 68 14 4535 5136 441837910 441837329 3.470000e-156 562.0
35 TraesCS2A01G390800 chr1A 86.218 312 37 5 1034 1341 382778169 382777860 2.970000e-87 333.0
36 TraesCS2A01G390800 chr6B 84.358 716 62 27 1967 2659 518610139 518610827 0.000000e+00 656.0
37 TraesCS2A01G390800 chr6B 86.322 329 39 6 1147 1471 512234442 512234768 2.280000e-93 353.0
38 TraesCS2A01G390800 chr6B 85.220 318 33 10 1882 2188 637179454 637179768 1.070000e-81 315.0
39 TraesCS2A01G390800 chr7D 85.050 602 69 10 4538 5136 599195828 599196411 1.230000e-165 593.0
40 TraesCS2A01G390800 chr7D 82.703 185 28 4 1637 1821 531439814 531439994 1.480000e-35 161.0
41 TraesCS2A01G390800 chr1B 81.011 811 98 33 1379 2182 82619649 82618888 1.230000e-165 593.0
42 TraesCS2A01G390800 chr1B 85.987 157 13 6 1002 1149 468219628 468219472 5.330000e-35 159.0
43 TraesCS2A01G390800 chr6A 84.080 603 72 15 4539 5136 553764598 553765181 1.250000e-155 560.0
44 TraesCS2A01G390800 chr6A 86.875 320 37 5 1156 1471 452099978 452099660 2.280000e-93 353.0
45 TraesCS2A01G390800 chr6A 85.632 174 15 3 2856 3029 409745543 409745380 1.900000e-39 174.0
46 TraesCS2A01G390800 chr6A 78.369 282 50 11 1195 1471 410583959 410583684 6.840000e-39 172.0
47 TraesCS2A01G390800 chr3A 83.887 602 65 15 4538 5136 437989882 437990454 3.500000e-151 545.0
48 TraesCS2A01G390800 chr3A 83.476 351 46 8 4795 5140 545289384 545289727 2.990000e-82 316.0
49 TraesCS2A01G390800 chr5D 81.781 494 64 17 4666 5136 370956422 370956912 1.740000e-104 390.0
50 TraesCS2A01G390800 chr5D 95.556 45 2 0 4686 4730 370956494 370956538 7.140000e-09 73.1
51 TraesCS2A01G390800 chr6D 86.562 320 38 5 1156 1471 315178643 315178325 1.060000e-91 348.0
52 TraesCS2A01G390800 chr6D 78.873 284 45 13 1195 1471 304735660 304735935 1.470000e-40 178.0
53 TraesCS2A01G390800 chr3B 83.143 350 35 14 1002 1341 397265564 397265229 1.080000e-76 298.0
54 TraesCS2A01G390800 chr3B 85.632 174 15 3 2856 3029 245468780 245468943 1.900000e-39 174.0
55 TraesCS2A01G390800 chr3B 91.589 107 9 0 2923 3029 397264562 397264456 1.150000e-31 148.0
56 TraesCS2A01G390800 chr4B 86.207 174 14 3 2856 3029 360899011 360898848 4.090000e-41 180.0
57 TraesCS2A01G390800 chr4B 94.393 107 6 0 2923 3029 205679051 205679157 1.140000e-36 165.0


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 TraesCS2A01G390800 chr2A 640268732 640273871 5139 False 9492.000000 9492 100.000000 1 5140 1 chr2A.!!$F2 5139
1 TraesCS2A01G390800 chr2A 302436618 302437322 704 False 880.000000 880 89.481000 2194 2891 1 chr2A.!!$F1 697
2 TraesCS2A01G390800 chr2A 424537545 424538504 959 True 527.000000 867 88.810500 1838 2891 2 chr2A.!!$R3 1053
3 TraesCS2A01G390800 chr2D 493173745 493178191 4446 True 2834.500000 5151 88.257500 191 4539 2 chr2D.!!$R2 4348
4 TraesCS2A01G390800 chr2D 245572126 245572830 704 True 918.000000 918 90.463000 2194 2891 1 chr2D.!!$R1 697
5 TraesCS2A01G390800 chr2B 581467800 581472296 4496 True 1756.366667 4566 86.982333 3 4539 3 chr2B.!!$R1 4536
6 TraesCS2A01G390800 chr2B 42565044 42565676 632 False 656.000000 656 85.933000 1967 2595 1 chr2B.!!$F1 628
7 TraesCS2A01G390800 chr1D 474732095 474732698 603 False 972.000000 972 95.702000 4537 5140 1 chr1D.!!$F1 603
8 TraesCS2A01G390800 chr5B 496648037 496648921 884 True 678.000000 678 81.196000 1369 2255 1 chr5B.!!$R1 886
9 TraesCS2A01G390800 chr5B 291604976 291605927 951 True 507.000000 819 88.718000 1838 2891 2 chr5B.!!$R2 1053
10 TraesCS2A01G390800 chr5A 222769162 222770121 959 True 497.500000 817 87.679500 1838 2891 2 chr5A.!!$R1 1053
11 TraesCS2A01G390800 chr4A 535941721 535942418 697 False 813.000000 813 87.921000 2194 2891 1 chr4A.!!$F1 697
12 TraesCS2A01G390800 chr4A 375968105 375968765 660 True 601.000000 601 83.626000 1967 2627 1 chr4A.!!$R1 660
13 TraesCS2A01G390800 chr4A 682992631 682993214 583 True 560.000000 560 84.080000 4539 5136 1 chr4A.!!$R2 597
14 TraesCS2A01G390800 chr7B 428783649 428784604 955 False 479.500000 776 87.591500 1838 2891 2 chr7B.!!$F1 1053
15 TraesCS2A01G390800 chr7A 320366992 320367651 659 True 588.000000 588 83.333000 1967 2627 1 chr7A.!!$R1 660
16 TraesCS2A01G390800 chr7A 369894336 369895451 1115 True 539.000000 710 84.716000 1002 2182 2 chr7A.!!$R3 1180
17 TraesCS2A01G390800 chr1A 158971993 158972655 662 False 603.000000 603 83.697000 1967 2627 1 chr1A.!!$F1 660
18 TraesCS2A01G390800 chr1A 441837329 441837910 581 True 562.000000 562 84.158000 4535 5136 1 chr1A.!!$R1 601
19 TraesCS2A01G390800 chr1A 382777100 382778169 1069 True 498.500000 664 84.328500 1034 2180 2 chr1A.!!$R2 1146
20 TraesCS2A01G390800 chr6B 518610139 518610827 688 False 656.000000 656 84.358000 1967 2659 1 chr6B.!!$F2 692
21 TraesCS2A01G390800 chr7D 599195828 599196411 583 False 593.000000 593 85.050000 4538 5136 1 chr7D.!!$F2 598
22 TraesCS2A01G390800 chr1B 82618888 82619649 761 True 593.000000 593 81.011000 1379 2182 1 chr1B.!!$R1 803
23 TraesCS2A01G390800 chr6A 553764598 553765181 583 False 560.000000 560 84.080000 4539 5136 1 chr6A.!!$F1 597
24 TraesCS2A01G390800 chr3A 437989882 437990454 572 False 545.000000 545 83.887000 4538 5136 1 chr3A.!!$F1 598
25 TraesCS2A01G390800 chr3B 397264456 397265564 1108 True 223.000000 298 87.366000 1002 3029 2 chr3B.!!$R1 2027


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
94 95 0.034756 AAGGCATATCGCATACGGCA 59.965 50.0 0.00 0.00 45.17 5.69 F
183 184 0.168348 CTGCTGCTGCTGCTGTTTAG 59.832 55.0 27.67 15.15 39.81 1.85 F
209 217 0.179000 ACAGCCGATCCAGTGAATCC 59.821 55.0 0.00 0.00 0.00 3.01 F
753 826 0.179100 ACGTCTCCATTCCTGATGCG 60.179 55.0 0.00 0.00 34.25 4.73 F
2090 2308 0.033781 CGACGACCAACCCCTAACAA 59.966 55.0 0.00 0.00 0.00 2.83 F
2599 2931 0.165295 GGAAGCAAACGTAACGCCTC 59.835 55.0 0.00 0.00 0.00 4.70 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1862 2045 0.329931 ACGGAGAGAGCAGAGAAGGA 59.670 55.000 0.00 0.0 0.00 3.36 R
1914 2097 0.599204 ACAGTAACAGCAACGACCCG 60.599 55.000 0.00 0.0 0.00 5.28 R
2037 2253 2.546373 CGGTTAACAAGTGAGAACGGGA 60.546 50.000 8.10 0.0 0.00 5.14 R
2717 3118 2.333014 GTCAGGCTGAAGTCGAAGAAG 58.667 52.381 20.62 0.0 39.69 2.85 R
2970 3378 0.173708 CGGAGGTGACAGTCTAAGCC 59.826 60.000 1.31 0.0 0.00 4.35 R
4427 4859 0.323725 AGTCGGCGGTTTACCCTCTA 60.324 55.000 7.21 0.0 0.00 2.43 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
37 38 2.107366 TGATCCCAATCACGCTAGACA 58.893 47.619 0.00 0.00 36.98 3.41
42 43 1.672737 CCAATCACGCTAGACAGTGCA 60.673 52.381 0.00 0.00 38.19 4.57
81 82 0.108329 CGACTAACGGACCAAGGCAT 60.108 55.000 0.00 0.00 38.46 4.40
82 83 1.135527 CGACTAACGGACCAAGGCATA 59.864 52.381 0.00 0.00 38.46 3.14
83 84 2.223971 CGACTAACGGACCAAGGCATAT 60.224 50.000 0.00 0.00 38.46 1.78
84 85 3.391049 GACTAACGGACCAAGGCATATC 58.609 50.000 0.00 0.00 0.00 1.63
85 86 2.223971 ACTAACGGACCAAGGCATATCG 60.224 50.000 0.00 0.00 0.00 2.92
86 87 0.814010 AACGGACCAAGGCATATCGC 60.814 55.000 0.00 0.00 41.28 4.58
92 93 1.078709 CCAAGGCATATCGCATACGG 58.921 55.000 0.00 0.00 45.17 4.02
93 94 0.443869 CAAGGCATATCGCATACGGC 59.556 55.000 0.00 0.00 45.17 5.68
94 95 0.034756 AAGGCATATCGCATACGGCA 59.965 50.000 0.00 0.00 45.17 5.69
96 97 0.670546 GGCATATCGCATACGGCAGT 60.671 55.000 0.00 0.00 45.17 4.40
101 102 1.762222 ATCGCATACGGCAGTTTCGC 61.762 55.000 0.00 0.00 45.17 4.70
115 116 0.317160 TTTCGCCGAAGCTTCAGAGA 59.683 50.000 25.47 18.51 36.60 3.10
116 117 0.317160 TTCGCCGAAGCTTCAGAGAA 59.683 50.000 25.47 22.89 36.60 2.87
117 118 0.317160 TCGCCGAAGCTTCAGAGAAA 59.683 50.000 25.47 3.46 36.60 2.52
118 119 1.148310 CGCCGAAGCTTCAGAGAAAA 58.852 50.000 25.47 0.00 36.60 2.29
119 120 1.127582 CGCCGAAGCTTCAGAGAAAAG 59.872 52.381 25.47 6.97 36.60 2.27
120 121 2.147150 GCCGAAGCTTCAGAGAAAAGT 58.853 47.619 25.47 0.00 35.50 2.66
121 122 2.550180 GCCGAAGCTTCAGAGAAAAGTT 59.450 45.455 25.47 0.00 35.50 2.66
122 123 3.746492 GCCGAAGCTTCAGAGAAAAGTTA 59.254 43.478 25.47 0.00 35.50 2.24
123 124 4.393371 GCCGAAGCTTCAGAGAAAAGTTAT 59.607 41.667 25.47 0.00 35.50 1.89
124 125 5.106515 GCCGAAGCTTCAGAGAAAAGTTATT 60.107 40.000 25.47 0.00 35.50 1.40
125 126 6.568653 GCCGAAGCTTCAGAGAAAAGTTATTT 60.569 38.462 25.47 0.00 35.50 1.40
126 127 7.363431 CCGAAGCTTCAGAGAAAAGTTATTTT 58.637 34.615 25.47 0.00 41.34 1.82
127 128 7.862873 CCGAAGCTTCAGAGAAAAGTTATTTTT 59.137 33.333 25.47 0.00 41.59 1.94
153 154 8.973835 TTTAAATGTTCAGACAAAAGTTTCGT 57.026 26.923 0.00 0.00 39.66 3.85
155 156 9.710979 TTAAATGTTCAGACAAAAGTTTCGTAG 57.289 29.630 0.00 0.00 39.66 3.51
159 160 6.477688 TGTTCAGACAAAAGTTTCGTAGTAGG 59.522 38.462 0.00 0.00 31.49 3.18
167 168 4.961435 AGTTTCGTAGTAGGACTACTGC 57.039 45.455 19.48 17.17 46.68 4.40
168 169 4.587891 AGTTTCGTAGTAGGACTACTGCT 58.412 43.478 19.48 0.00 46.68 4.24
169 170 4.395542 AGTTTCGTAGTAGGACTACTGCTG 59.604 45.833 19.48 14.37 46.68 4.41
173 174 0.820871 AGTAGGACTACTGCTGCTGC 59.179 55.000 11.00 8.89 44.11 5.25
175 176 0.820226 TAGGACTACTGCTGCTGCTG 59.180 55.000 18.66 18.66 42.70 4.41
176 177 2.105466 GGACTACTGCTGCTGCTGC 61.105 63.158 22.51 22.51 41.07 5.25
178 179 1.360194 GACTACTGCTGCTGCTGCTG 61.360 60.000 27.75 27.75 41.07 4.41
182 183 0.535780 ACTGCTGCTGCTGCTGTTTA 60.536 50.000 28.83 11.88 41.07 2.01
183 184 0.168348 CTGCTGCTGCTGCTGTTTAG 59.832 55.000 27.67 15.15 39.81 1.85
186 187 1.000938 GCTGCTGCTGCTGTTTAGTTT 60.001 47.619 22.10 0.00 39.81 2.66
187 188 2.226437 GCTGCTGCTGCTGTTTAGTTTA 59.774 45.455 22.10 0.00 39.81 2.01
189 190 2.226437 TGCTGCTGCTGTTTAGTTTAGC 59.774 45.455 17.00 1.69 40.48 3.09
190 191 2.226437 GCTGCTGCTGTTTAGTTTAGCA 59.774 45.455 8.53 0.00 44.45 3.49
191 192 3.814945 CTGCTGCTGTTTAGTTTAGCAC 58.185 45.455 0.00 0.00 42.05 4.40
192 193 3.210227 TGCTGCTGTTTAGTTTAGCACA 58.790 40.909 0.00 0.00 42.05 4.57
196 197 3.455619 CTGTTTAGTTTAGCACAGCCG 57.544 47.619 0.00 0.00 30.79 5.52
197 198 3.064207 CTGTTTAGTTTAGCACAGCCGA 58.936 45.455 0.00 0.00 30.79 5.54
198 199 3.670625 TGTTTAGTTTAGCACAGCCGAT 58.329 40.909 0.00 0.00 0.00 4.18
206 214 1.375908 GCACAGCCGATCCAGTGAA 60.376 57.895 0.00 0.00 33.99 3.18
209 217 0.179000 ACAGCCGATCCAGTGAATCC 59.821 55.000 0.00 0.00 0.00 3.01
225 233 2.698855 ATCCAATCCAGTCCAACGAG 57.301 50.000 0.00 0.00 0.00 4.18
229 237 0.400213 AATCCAGTCCAACGAGCCAA 59.600 50.000 0.00 0.00 0.00 4.52
230 238 0.321653 ATCCAGTCCAACGAGCCAAC 60.322 55.000 0.00 0.00 0.00 3.77
231 239 1.966451 CCAGTCCAACGAGCCAACC 60.966 63.158 0.00 0.00 0.00 3.77
232 240 1.227823 CAGTCCAACGAGCCAACCA 60.228 57.895 0.00 0.00 0.00 3.67
240 248 2.604174 CGAGCCAACCACGTGGAAC 61.604 63.158 40.21 23.90 41.65 3.62
282 290 6.830114 AAACAAAGATATACTACTGCTCGC 57.170 37.500 0.00 0.00 0.00 5.03
283 291 5.515797 ACAAAGATATACTACTGCTCGCA 57.484 39.130 0.00 0.00 0.00 5.10
339 363 2.429930 CCGCACCCAACCAGAGAA 59.570 61.111 0.00 0.00 0.00 2.87
340 364 1.672356 CCGCACCCAACCAGAGAAG 60.672 63.158 0.00 0.00 0.00 2.85
341 365 1.371183 CGCACCCAACCAGAGAAGA 59.629 57.895 0.00 0.00 0.00 2.87
342 366 0.671781 CGCACCCAACCAGAGAAGAG 60.672 60.000 0.00 0.00 0.00 2.85
343 367 0.687354 GCACCCAACCAGAGAAGAGA 59.313 55.000 0.00 0.00 0.00 3.10
357 381 4.023291 GAGAAGAGAGGTCAAGTGGATCT 58.977 47.826 0.00 0.00 40.60 2.75
469 497 1.741770 CTCCCGTTGTACTGCAGCC 60.742 63.158 15.27 5.21 0.00 4.85
587 624 4.295119 GTGCGTCCGTGGGAGTGT 62.295 66.667 0.00 0.00 29.39 3.55
588 625 4.293648 TGCGTCCGTGGGAGTGTG 62.294 66.667 0.00 0.00 29.39 3.82
667 716 3.611674 GGGTGGTGGGTTTTGGCG 61.612 66.667 0.00 0.00 0.00 5.69
671 720 3.666253 GGTGGGTTTTGGCGACCG 61.666 66.667 0.00 0.00 38.08 4.79
716 789 1.502163 CGCGGCCTTCATCATCTTCC 61.502 60.000 0.00 0.00 0.00 3.46
717 790 1.169034 GCGGCCTTCATCATCTTCCC 61.169 60.000 0.00 0.00 0.00 3.97
720 793 1.169034 GCCTTCATCATCTTCCCGCC 61.169 60.000 0.00 0.00 0.00 6.13
724 797 2.768344 ATCATCTTCCCGCCCGGT 60.768 61.111 0.00 0.00 0.00 5.28
748 821 0.456221 ACGCTACGTCTCCATTCCTG 59.544 55.000 0.00 0.00 33.69 3.86
749 822 0.738975 CGCTACGTCTCCATTCCTGA 59.261 55.000 0.00 0.00 0.00 3.86
750 823 1.338337 CGCTACGTCTCCATTCCTGAT 59.662 52.381 0.00 0.00 0.00 2.90
751 824 2.748605 GCTACGTCTCCATTCCTGATG 58.251 52.381 0.00 0.00 35.42 3.07
753 826 0.179100 ACGTCTCCATTCCTGATGCG 60.179 55.000 0.00 0.00 34.25 4.73
781 901 2.414481 CTCTCACTCGTTTCTTGCCATG 59.586 50.000 0.00 0.00 0.00 3.66
829 953 9.959775 CTAGCGTTTCTTTCTGTTTTCTATTAG 57.040 33.333 0.00 0.00 0.00 1.73
889 1014 8.738645 AAAAGGCAATTGTTTGTTTAATACCA 57.261 26.923 7.40 0.00 35.17 3.25
890 1015 7.961325 AAGGCAATTGTTTGTTTAATACCAG 57.039 32.000 7.40 0.00 35.17 4.00
891 1016 5.931724 AGGCAATTGTTTGTTTAATACCAGC 59.068 36.000 7.40 0.00 35.17 4.85
892 1017 5.698545 GGCAATTGTTTGTTTAATACCAGCA 59.301 36.000 7.40 0.00 35.17 4.41
893 1018 6.128580 GGCAATTGTTTGTTTAATACCAGCAG 60.129 38.462 7.40 0.00 35.17 4.24
894 1019 6.423604 GCAATTGTTTGTTTAATACCAGCAGT 59.576 34.615 7.40 0.00 35.17 4.40
895 1020 7.042119 GCAATTGTTTGTTTAATACCAGCAGTT 60.042 33.333 7.40 0.00 35.17 3.16
898 1023 7.283625 TGTTTGTTTAATACCAGCAGTTCAT 57.716 32.000 0.00 0.00 0.00 2.57
899 1024 7.367285 TGTTTGTTTAATACCAGCAGTTCATC 58.633 34.615 0.00 0.00 0.00 2.92
900 1025 5.794687 TGTTTAATACCAGCAGTTCATCG 57.205 39.130 0.00 0.00 0.00 3.84
901 1026 4.094294 TGTTTAATACCAGCAGTTCATCGC 59.906 41.667 0.00 0.00 0.00 4.58
902 1027 2.698855 AATACCAGCAGTTCATCGCT 57.301 45.000 0.00 0.00 39.66 4.93
932 1072 1.232119 CAACCCTTCACGTTACCACC 58.768 55.000 0.00 0.00 0.00 4.61
962 1116 1.492873 CACGCACATGGACGTCTTG 59.507 57.895 16.46 15.42 41.32 3.02
968 1122 0.603707 ACATGGACGTCTTGTGCCTG 60.604 55.000 16.46 4.15 39.77 4.85
1016 1170 3.499737 CATGGGCTCACGGCGTTC 61.500 66.667 11.19 1.97 42.94 3.95
1263 1436 2.887568 CTGCTCATCGGCGTGGTC 60.888 66.667 6.85 1.56 34.52 4.02
1481 1654 0.461339 TTCGGCGGTAATCAAGCTCC 60.461 55.000 7.21 0.00 0.00 4.70
1482 1655 1.887707 CGGCGGTAATCAAGCTCCC 60.888 63.158 0.00 0.00 0.00 4.30
1483 1656 1.526225 GGCGGTAATCAAGCTCCCC 60.526 63.158 0.00 0.00 0.00 4.81
1484 1657 1.526225 GCGGTAATCAAGCTCCCCC 60.526 63.158 0.00 0.00 0.00 5.40
1485 1658 1.227556 CGGTAATCAAGCTCCCCCG 60.228 63.158 0.00 0.00 0.00 5.73
1603 1777 8.887717 CAAATCTTGATTACTAGCTTGCTAACT 58.112 33.333 0.00 0.00 0.00 2.24
1607 1781 8.191446 TCTTGATTACTAGCTTGCTAACTACTG 58.809 37.037 0.00 0.00 0.00 2.74
1625 1803 2.806856 GATTCGTGCTCTGCGCTGG 61.807 63.158 14.70 6.44 40.11 4.85
1637 1815 2.593725 CGCTGGATCCTGGGCATG 60.594 66.667 20.32 4.62 0.00 4.06
1638 1816 2.910994 GCTGGATCCTGGGCATGC 60.911 66.667 19.23 9.90 0.00 4.06
1825 2003 3.835395 CTCCCTCTCAGAAAGGTACAGTT 59.165 47.826 0.00 0.00 31.51 3.16
1829 2007 4.282195 CCTCTCAGAAAGGTACAGTTCAGT 59.718 45.833 9.63 0.00 0.00 3.41
1862 2045 0.694771 TTTCCATGCTCCTGTGCTCT 59.305 50.000 0.00 0.00 0.00 4.09
1890 2073 1.142748 CTCTCTCCGTGTCCATGGC 59.857 63.158 6.96 2.72 37.40 4.40
1914 2097 1.202348 CCGCACTTCCTGATTTTTCCC 59.798 52.381 0.00 0.00 0.00 3.97
2085 2301 1.477685 AACATCGACGACCAACCCCT 61.478 55.000 0.00 0.00 0.00 4.79
2088 2306 0.533951 ATCGACGACCAACCCCTAAC 59.466 55.000 0.00 0.00 0.00 2.34
2089 2307 0.827089 TCGACGACCAACCCCTAACA 60.827 55.000 0.00 0.00 0.00 2.41
2090 2308 0.033781 CGACGACCAACCCCTAACAA 59.966 55.000 0.00 0.00 0.00 2.83
2091 2309 1.804601 GACGACCAACCCCTAACAAG 58.195 55.000 0.00 0.00 0.00 3.16
2092 2310 1.071228 GACGACCAACCCCTAACAAGT 59.929 52.381 0.00 0.00 0.00 3.16
2093 2311 1.071228 ACGACCAACCCCTAACAAGTC 59.929 52.381 0.00 0.00 0.00 3.01
2094 2312 1.071071 CGACCAACCCCTAACAAGTCA 59.929 52.381 0.00 0.00 0.00 3.41
2095 2313 2.290071 CGACCAACCCCTAACAAGTCAT 60.290 50.000 0.00 0.00 0.00 3.06
2103 2321 7.124147 CCAACCCCTAACAAGTCATATCATTTT 59.876 37.037 0.00 0.00 0.00 1.82
2105 2323 6.833933 ACCCCTAACAAGTCATATCATTTTCC 59.166 38.462 0.00 0.00 0.00 3.13
2120 2338 1.522668 TTTCCACAATGCTGACGGAG 58.477 50.000 0.00 0.00 31.95 4.63
2310 2564 5.045651 TCAAGGAGATAAGAATGCAAGGTCA 60.046 40.000 0.00 0.00 0.00 4.02
2385 2655 4.657055 TCAAATCGTGTTTCAACTGTGTG 58.343 39.130 0.00 0.00 0.00 3.82
2599 2931 0.165295 GGAAGCAAACGTAACGCCTC 59.835 55.000 0.00 0.00 0.00 4.70
2603 2935 3.788333 AGCAAACGTAACGCCTCTATA 57.212 42.857 0.00 0.00 0.00 1.31
2604 2936 4.317671 AGCAAACGTAACGCCTCTATAT 57.682 40.909 0.00 0.00 0.00 0.86
2606 2938 4.046462 GCAAACGTAACGCCTCTATATGA 58.954 43.478 0.00 0.00 0.00 2.15
2612 2944 5.298777 ACGTAACGCCTCTATATGACTTCTT 59.701 40.000 0.00 0.00 0.00 2.52
2654 3055 8.558973 AACAATTTTCAAGTTTCAATGGTTGA 57.441 26.923 0.00 0.00 38.04 3.18
2717 3118 1.876156 GATGATTCCGTGGCCAGATTC 59.124 52.381 5.11 7.82 0.00 2.52
2858 3260 0.324460 AGGAGGGGAAGTGGTACTCG 60.324 60.000 0.00 0.00 0.00 4.18
2921 3323 0.744414 AGGTGTGTGTCAGTGTGTGC 60.744 55.000 0.00 0.00 0.00 4.57
2936 3340 3.723764 GTGTGTGCGTGTTACTGAATTTG 59.276 43.478 0.00 0.00 0.00 2.32
2969 3373 3.327757 TCAAGGACTAGTTCAGGCACAAT 59.672 43.478 3.42 0.00 31.57 2.71
2970 3378 3.340814 AGGACTAGTTCAGGCACAATG 57.659 47.619 3.42 0.00 31.57 2.82
2983 3391 2.426522 GCACAATGGCTTAGACTGTCA 58.573 47.619 10.88 0.00 0.00 3.58
3006 3414 1.353022 TCCGTTTATGTCCAGGCCTTT 59.647 47.619 0.00 0.00 0.00 3.11
3084 3492 2.159043 CGTCACCCTCAAGAGCATACAT 60.159 50.000 0.00 0.00 0.00 2.29
3120 3528 0.389166 GCCGTCTCAACAGAGGTGAG 60.389 60.000 5.72 5.72 33.34 3.51
3127 3535 3.055819 TCTCAACAGAGGTGAGTTATGGC 60.056 47.826 11.44 0.00 0.00 4.40
3166 3574 4.607235 CGCGTTTCTTTGATCTGTTGTTAC 59.393 41.667 0.00 0.00 0.00 2.50
3167 3575 4.607235 GCGTTTCTTTGATCTGTTGTTACG 59.393 41.667 0.00 0.00 0.00 3.18
3452 3874 0.035534 TCACCGACATGAACATGGGG 60.036 55.000 17.25 17.98 42.91 4.96
4126 4548 1.402968 GCCGATGTGCATGAAGTTCAT 59.597 47.619 12.75 12.75 37.65 2.57
4174 4596 3.555956 CACAACGTCAGATTACATAGGCC 59.444 47.826 0.00 0.00 0.00 5.19
4220 4652 1.155859 AGAGCATTTTGGGGTGGCA 59.844 52.632 0.00 0.00 0.00 4.92
4240 4672 5.808540 TGGCAATTACGTTACATAGAGTGAC 59.191 40.000 0.00 0.00 33.66 3.67
4369 4801 2.228103 TGTTGTCGCCTACAGACTACAG 59.772 50.000 8.92 0.00 44.66 2.74
4386 4818 8.132362 CAGACTACAGAGAATATGGTGTCTTAC 58.868 40.741 0.00 0.00 34.45 2.34
4420 4852 4.571372 GAGAATCTCGAACTAATCCCGT 57.429 45.455 0.00 0.00 0.00 5.28
4422 4854 5.340439 AGAATCTCGAACTAATCCCGTTT 57.660 39.130 0.00 0.00 0.00 3.60
4424 4856 6.505272 AGAATCTCGAACTAATCCCGTTTAG 58.495 40.000 0.00 0.00 35.68 1.85
4427 4859 6.029346 TCTCGAACTAATCCCGTTTAGTTT 57.971 37.500 13.38 2.76 46.96 2.66
4428 4860 7.156876 TCTCGAACTAATCCCGTTTAGTTTA 57.843 36.000 13.38 7.32 46.96 2.01
4429 4861 7.253422 TCTCGAACTAATCCCGTTTAGTTTAG 58.747 38.462 13.38 13.29 46.96 1.85
4430 4862 7.121168 TCTCGAACTAATCCCGTTTAGTTTAGA 59.879 37.037 13.38 14.60 46.96 2.10
4432 4864 6.474751 CGAACTAATCCCGTTTAGTTTAGAGG 59.525 42.308 13.38 0.00 46.96 3.69
4438 4870 5.793817 TCCCGTTTAGTTTAGAGGGTAAAC 58.206 41.667 0.00 0.29 39.78 2.01
4441 4873 4.091945 CGTTTAGTTTAGAGGGTAAACCGC 59.908 45.833 4.43 0.00 46.96 5.68
4445 4877 0.532115 TTAGAGGGTAAACCGCCGAC 59.468 55.000 0.00 0.00 46.96 4.79
4449 4881 0.462789 AGGGTAAACCGCCGACTATG 59.537 55.000 0.00 0.00 46.96 2.23
4461 4894 3.243177 CGCCGACTATGTTTTAGAAGAGC 59.757 47.826 0.00 0.00 0.00 4.09
4466 4899 6.019479 CCGACTATGTTTTAGAAGAGCACATC 60.019 42.308 0.00 0.00 30.70 3.06
4502 4941 7.997107 AAAAAGTGTCTTTTTAACCGATTCC 57.003 32.000 15.52 0.00 30.64 3.01
4506 4945 4.758165 GTGTCTTTTTAACCGATTCCCTGA 59.242 41.667 0.00 0.00 0.00 3.86
4514 4953 4.360951 AACCGATTCCCTGAACTTAACA 57.639 40.909 0.00 0.00 0.00 2.41
4520 4959 6.395629 CGATTCCCTGAACTTAACAGAGTAA 58.604 40.000 0.00 0.00 37.54 2.24
4523 4962 8.990163 ATTCCCTGAACTTAACAGAGTAAAAA 57.010 30.769 0.00 0.00 37.54 1.94
4524 4963 8.446599 TTCCCTGAACTTAACAGAGTAAAAAG 57.553 34.615 0.00 0.00 37.54 2.27
4525 4964 7.798071 TCCCTGAACTTAACAGAGTAAAAAGA 58.202 34.615 0.00 0.00 37.54 2.52
4527 4966 7.931948 CCCTGAACTTAACAGAGTAAAAAGAGA 59.068 37.037 0.00 0.00 37.54 3.10
4528 4967 9.495572 CCTGAACTTAACAGAGTAAAAAGAGAT 57.504 33.333 0.00 0.00 37.54 2.75
4605 5044 7.201857 GCTAAGCCATCCATTTGTTAGAGATTT 60.202 37.037 0.00 0.00 0.00 2.17
4617 5056 5.255687 TGTTAGAGATTTGGACACATGCAT 58.744 37.500 0.00 0.00 0.00 3.96
4729 5172 9.453572 TCAATCATTTATTACTATGCTCCATCC 57.546 33.333 0.00 0.00 0.00 3.51
4730 5173 8.680903 CAATCATTTATTACTATGCTCCATCCC 58.319 37.037 0.00 0.00 0.00 3.85
4731 5174 7.328404 TCATTTATTACTATGCTCCATCCCA 57.672 36.000 0.00 0.00 0.00 4.37
4732 5175 7.754624 TCATTTATTACTATGCTCCATCCCAA 58.245 34.615 0.00 0.00 0.00 4.12
4733 5176 7.665559 TCATTTATTACTATGCTCCATCCCAAC 59.334 37.037 0.00 0.00 0.00 3.77
4734 5177 6.508030 TTATTACTATGCTCCATCCCAACA 57.492 37.500 0.00 0.00 0.00 3.33
4735 5178 2.717639 ACTATGCTCCATCCCAACAC 57.282 50.000 0.00 0.00 0.00 3.32
4736 5179 1.134401 ACTATGCTCCATCCCAACACG 60.134 52.381 0.00 0.00 0.00 4.49
4737 5180 0.908910 TATGCTCCATCCCAACACGT 59.091 50.000 0.00 0.00 0.00 4.49
4738 5181 0.038166 ATGCTCCATCCCAACACGTT 59.962 50.000 0.00 0.00 0.00 3.99
4739 5182 0.605319 TGCTCCATCCCAACACGTTC 60.605 55.000 0.00 0.00 0.00 3.95
4740 5183 0.605319 GCTCCATCCCAACACGTTCA 60.605 55.000 0.00 0.00 0.00 3.18
4744 5187 0.874390 CATCCCAACACGTTCACCAG 59.126 55.000 0.00 0.00 0.00 4.00
4896 5353 2.984562 TCCGCATATTTGTGCTTCTCA 58.015 42.857 0.00 0.00 42.88 3.27
5050 5509 4.685924 TCTTGTTTAAAAGGTCTCGTCGT 58.314 39.130 0.00 0.00 0.00 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.530744 TGGGATCACACTCACTACGC 59.469 55.000 0.00 0.00 0.00 4.42
37 38 4.142902 GCGTAATATTGTTGTGTCTGCACT 60.143 41.667 0.00 0.00 45.44 4.40
42 43 4.090930 GTCGTGCGTAATATTGTTGTGTCT 59.909 41.667 0.00 0.00 0.00 3.41
51 52 4.037690 GTCCGTTAGTCGTGCGTAATATT 58.962 43.478 0.00 0.00 37.94 1.28
53 54 2.223249 GGTCCGTTAGTCGTGCGTAATA 60.223 50.000 0.00 0.00 37.94 0.98
55 56 0.109781 GGTCCGTTAGTCGTGCGTAA 60.110 55.000 0.00 0.00 37.94 3.18
56 57 1.233950 TGGTCCGTTAGTCGTGCGTA 61.234 55.000 0.00 0.00 37.94 4.42
70 71 2.076863 GTATGCGATATGCCTTGGTCC 58.923 52.381 0.00 0.00 45.60 4.46
73 74 1.078709 CCGTATGCGATATGCCTTGG 58.921 55.000 4.21 0.00 45.60 3.61
81 82 1.483316 CGAAACTGCCGTATGCGATA 58.517 50.000 4.21 0.00 45.60 2.92
82 83 1.762222 GCGAAACTGCCGTATGCGAT 61.762 55.000 4.21 0.00 45.60 4.58
83 84 2.449525 GCGAAACTGCCGTATGCGA 61.450 57.895 4.21 0.00 45.60 5.10
84 85 2.021380 GCGAAACTGCCGTATGCG 59.979 61.111 0.00 0.00 45.60 4.73
85 86 2.403586 GGCGAAACTGCCGTATGC 59.596 61.111 0.00 0.00 46.75 3.14
96 97 2.805295 TTTCTCTGAAGCTTCGGCGAAA 60.805 45.455 33.98 33.98 42.01 3.46
101 102 6.487689 AATAACTTTTCTCTGAAGCTTCGG 57.512 37.500 26.56 26.56 34.85 4.30
127 128 9.413048 ACGAAACTTTTGTCTGAACATTTAAAA 57.587 25.926 0.00 0.00 34.73 1.52
128 129 8.973835 ACGAAACTTTTGTCTGAACATTTAAA 57.026 26.923 0.00 0.00 34.73 1.52
129 130 9.710979 CTACGAAACTTTTGTCTGAACATTTAA 57.289 29.630 0.00 0.00 34.73 1.52
130 131 8.885722 ACTACGAAACTTTTGTCTGAACATTTA 58.114 29.630 0.00 0.00 34.73 1.40
131 132 7.758495 ACTACGAAACTTTTGTCTGAACATTT 58.242 30.769 0.00 0.00 34.73 2.32
132 133 7.316544 ACTACGAAACTTTTGTCTGAACATT 57.683 32.000 0.00 0.00 34.73 2.71
133 134 6.920569 ACTACGAAACTTTTGTCTGAACAT 57.079 33.333 0.00 0.00 34.73 2.71
134 135 6.477688 CCTACTACGAAACTTTTGTCTGAACA 59.522 38.462 0.00 0.00 0.00 3.18
135 136 6.698766 TCCTACTACGAAACTTTTGTCTGAAC 59.301 38.462 0.00 0.00 0.00 3.18
136 137 6.698766 GTCCTACTACGAAACTTTTGTCTGAA 59.301 38.462 0.00 0.00 0.00 3.02
137 138 6.040166 AGTCCTACTACGAAACTTTTGTCTGA 59.960 38.462 0.00 0.00 0.00 3.27
138 139 6.214399 AGTCCTACTACGAAACTTTTGTCTG 58.786 40.000 0.00 0.00 0.00 3.51
139 140 6.402456 AGTCCTACTACGAAACTTTTGTCT 57.598 37.500 0.00 0.00 0.00 3.41
140 141 7.559835 GTAGTCCTACTACGAAACTTTTGTC 57.440 40.000 1.73 0.00 41.27 3.18
152 153 4.493801 AGCAGCAGCAGTAGTCCTACTAC 61.494 52.174 3.17 8.81 43.98 2.73
153 154 2.025155 GCAGCAGCAGTAGTCCTACTA 58.975 52.381 6.66 0.00 43.98 1.82
154 155 0.820871 GCAGCAGCAGTAGTCCTACT 59.179 55.000 1.08 1.08 46.52 2.57
155 156 0.820871 AGCAGCAGCAGTAGTCCTAC 59.179 55.000 3.17 0.00 45.49 3.18
159 160 1.079266 AGCAGCAGCAGCAGTAGTC 60.079 57.895 12.92 0.00 45.49 2.59
167 168 3.669023 GCTAAACTAAACAGCAGCAGCAG 60.669 47.826 3.17 0.00 45.49 4.24
168 169 2.226437 GCTAAACTAAACAGCAGCAGCA 59.774 45.455 3.17 0.00 45.49 4.41
169 170 2.226437 TGCTAAACTAAACAGCAGCAGC 59.774 45.455 0.00 0.00 40.26 5.25
176 177 3.064207 TCGGCTGTGCTAAACTAAACAG 58.936 45.455 0.00 0.00 42.35 3.16
178 179 3.063588 GGATCGGCTGTGCTAAACTAAAC 59.936 47.826 0.00 0.00 0.00 2.01
182 183 0.613260 TGGATCGGCTGTGCTAAACT 59.387 50.000 0.00 0.00 0.00 2.66
183 184 1.009829 CTGGATCGGCTGTGCTAAAC 58.990 55.000 0.00 0.00 0.00 2.01
186 187 0.970427 TCACTGGATCGGCTGTGCTA 60.970 55.000 0.00 0.00 0.00 3.49
187 188 1.830587 TTCACTGGATCGGCTGTGCT 61.831 55.000 0.00 0.00 0.00 4.40
189 190 1.293924 GATTCACTGGATCGGCTGTG 58.706 55.000 0.00 3.58 0.00 3.66
190 191 0.179000 GGATTCACTGGATCGGCTGT 59.821 55.000 0.00 0.00 0.00 4.40
191 192 0.178767 TGGATTCACTGGATCGGCTG 59.821 55.000 0.00 0.00 0.00 4.85
192 193 0.911769 TTGGATTCACTGGATCGGCT 59.088 50.000 0.00 0.00 0.00 5.52
194 195 2.158769 TGGATTGGATTCACTGGATCGG 60.159 50.000 0.00 0.00 0.00 4.18
195 196 3.136763 CTGGATTGGATTCACTGGATCG 58.863 50.000 0.00 0.00 0.00 3.69
196 197 4.133078 GACTGGATTGGATTCACTGGATC 58.867 47.826 0.00 0.00 0.00 3.36
197 198 3.117738 GGACTGGATTGGATTCACTGGAT 60.118 47.826 0.00 0.00 0.00 3.41
198 199 2.239654 GGACTGGATTGGATTCACTGGA 59.760 50.000 0.00 0.00 0.00 3.86
206 214 1.407437 GCTCGTTGGACTGGATTGGAT 60.407 52.381 0.00 0.00 0.00 3.41
209 217 0.321564 TGGCTCGTTGGACTGGATTG 60.322 55.000 0.00 0.00 0.00 2.67
225 233 2.551912 CCAGTTCCACGTGGTTGGC 61.552 63.158 32.74 20.20 36.48 4.52
231 239 3.240606 CTTGCGCCAGTTCCACGTG 62.241 63.158 9.08 9.08 0.00 4.49
232 240 2.972505 CTTGCGCCAGTTCCACGT 60.973 61.111 4.18 0.00 0.00 4.49
240 248 2.420628 TTTTGATCAACTTGCGCCAG 57.579 45.000 7.89 5.76 0.00 4.85
265 273 2.490115 GGCTGCGAGCAGTAGTATATCT 59.510 50.000 23.79 0.00 44.75 1.98
339 363 3.464720 TGAGATCCACTTGACCTCTCT 57.535 47.619 0.00 0.00 34.73 3.10
340 364 3.118811 CCTTGAGATCCACTTGACCTCTC 60.119 52.174 0.00 0.00 34.33 3.20
341 365 2.836981 CCTTGAGATCCACTTGACCTCT 59.163 50.000 0.00 0.00 0.00 3.69
342 366 2.834549 TCCTTGAGATCCACTTGACCTC 59.165 50.000 0.00 0.00 0.00 3.85
343 367 2.907892 TCCTTGAGATCCACTTGACCT 58.092 47.619 0.00 0.00 0.00 3.85
357 381 0.108585 AGCGCTTGTTCCTTCCTTGA 59.891 50.000 2.64 0.00 0.00 3.02
469 497 0.178973 AAACGGGGAGAAGTTTGGGG 60.179 55.000 0.00 0.00 38.90 4.96
667 716 1.611491 TGGTTTTCTTGCAATCCGGTC 59.389 47.619 0.00 0.00 0.00 4.79
671 720 2.627699 TCACCTGGTTTTCTTGCAATCC 59.372 45.455 0.00 0.00 0.00 3.01
704 753 1.146041 CGGGCGGGAAGATGATGAA 59.854 57.895 0.00 0.00 0.00 2.57
706 755 2.281070 CCGGGCGGGAAGATGATG 60.281 66.667 4.88 0.00 38.47 3.07
707 756 2.325393 GAACCGGGCGGGAAGATGAT 62.325 60.000 18.95 0.00 39.97 2.45
738 811 2.028420 TCAACGCATCAGGAATGGAG 57.972 50.000 0.00 0.00 35.77 3.86
745 818 1.137675 TGAGAGGATCAACGCATCAGG 59.862 52.381 0.00 0.00 37.82 3.86
746 819 2.159128 AGTGAGAGGATCAACGCATCAG 60.159 50.000 0.00 0.00 40.43 2.90
748 821 2.468831 GAGTGAGAGGATCAACGCATC 58.531 52.381 0.00 0.00 40.43 3.91
749 822 1.202348 CGAGTGAGAGGATCAACGCAT 60.202 52.381 0.00 0.00 40.43 4.73
750 823 0.171231 CGAGTGAGAGGATCAACGCA 59.829 55.000 0.00 0.00 40.43 5.24
751 824 0.171455 ACGAGTGAGAGGATCAACGC 59.829 55.000 0.00 0.00 40.43 4.84
753 826 4.181309 AGAAACGAGTGAGAGGATCAAC 57.819 45.455 0.00 0.00 40.43 3.18
781 901 1.227205 CATCCGCTCTGCTCCAGAC 60.227 63.158 0.00 0.00 35.39 3.51
801 925 3.898517 AAACAGAAAGAAACGCTAGGC 57.101 42.857 0.00 0.00 0.00 3.93
804 928 9.485206 ACTAATAGAAAACAGAAAGAAACGCTA 57.515 29.630 0.00 0.00 0.00 4.26
889 1014 1.276421 ACTAACCAGCGATGAACTGCT 59.724 47.619 0.06 0.00 43.58 4.24
890 1015 1.661112 GACTAACCAGCGATGAACTGC 59.339 52.381 0.06 0.00 33.65 4.40
891 1016 2.959516 TGACTAACCAGCGATGAACTG 58.040 47.619 0.06 0.00 34.82 3.16
892 1017 3.244078 TGTTGACTAACCAGCGATGAACT 60.244 43.478 0.06 0.00 35.92 3.01
893 1018 3.064207 TGTTGACTAACCAGCGATGAAC 58.936 45.455 0.06 0.00 35.92 3.18
894 1019 3.394674 TGTTGACTAACCAGCGATGAA 57.605 42.857 0.06 0.00 35.92 2.57
895 1020 3.064207 GTTGTTGACTAACCAGCGATGA 58.936 45.455 0.06 0.00 35.92 2.92
898 1023 1.873698 GGTTGTTGACTAACCAGCGA 58.126 50.000 0.00 0.00 45.43 4.93
942 1082 4.134187 GACGTCCATGTGCGTGCG 62.134 66.667 14.96 2.27 41.70 5.34
952 1092 1.116536 TACCAGGCACAAGACGTCCA 61.117 55.000 13.01 0.00 0.00 4.02
954 1094 0.317479 ACTACCAGGCACAAGACGTC 59.683 55.000 7.70 7.70 0.00 4.34
958 1112 6.308015 ACAAATATACTACCAGGCACAAGA 57.692 37.500 0.00 0.00 0.00 3.02
962 1116 6.530181 GCAAAAACAAATATACTACCAGGCAC 59.470 38.462 0.00 0.00 0.00 5.01
965 1119 5.741982 GCGCAAAAACAAATATACTACCAGG 59.258 40.000 0.30 0.00 0.00 4.45
968 1122 4.203563 GCGCGCAAAAACAAATATACTACC 59.796 41.667 29.10 0.00 0.00 3.18
1263 1436 2.844122 TCATGACGATCACGGTGTAG 57.156 50.000 8.17 3.65 44.46 2.74
1481 1654 3.237741 GAGAGGGATGGAGCGGGG 61.238 72.222 0.00 0.00 0.00 5.73
1482 1655 3.237741 GGAGAGGGATGGAGCGGG 61.238 72.222 0.00 0.00 0.00 6.13
1483 1656 3.237741 GGGAGAGGGATGGAGCGG 61.238 72.222 0.00 0.00 0.00 5.52
1484 1657 2.123077 AGGGAGAGGGATGGAGCG 60.123 66.667 0.00 0.00 0.00 5.03
1485 1658 2.206536 CGAGGGAGAGGGATGGAGC 61.207 68.421 0.00 0.00 0.00 4.70
1520 1693 4.406326 TGAATTGGGGGTGATTGATTGATG 59.594 41.667 0.00 0.00 0.00 3.07
1603 1777 3.329114 CGCAGAGCACGAATCAGTA 57.671 52.632 0.00 0.00 0.00 2.74
1635 1813 3.142838 GAACCCGCCTGCATGCAT 61.143 61.111 22.97 3.67 0.00 3.96
1646 1824 1.375523 CAAGAAGGACCCGAACCCG 60.376 63.158 0.00 0.00 0.00 5.28
1825 2003 5.309638 TGGAAATGGAATCGTTTGTACTGA 58.690 37.500 0.00 0.00 32.71 3.41
1829 2007 4.704540 AGCATGGAAATGGAATCGTTTGTA 59.295 37.500 0.00 0.00 32.71 2.41
1862 2045 0.329931 ACGGAGAGAGCAGAGAAGGA 59.670 55.000 0.00 0.00 0.00 3.36
1890 2073 1.021390 AAATCAGGAAGTGCGGCTCG 61.021 55.000 0.00 0.00 0.00 5.03
1914 2097 0.599204 ACAGTAACAGCAACGACCCG 60.599 55.000 0.00 0.00 0.00 5.28
2037 2253 2.546373 CGGTTAACAAGTGAGAACGGGA 60.546 50.000 8.10 0.00 0.00 5.14
2040 2256 2.746269 TCCGGTTAACAAGTGAGAACG 58.254 47.619 8.10 0.00 0.00 3.95
2088 2306 7.222031 CAGCATTGTGGAAAATGATATGACTTG 59.778 37.037 1.22 0.00 39.46 3.16
2089 2307 7.123098 TCAGCATTGTGGAAAATGATATGACTT 59.877 33.333 1.22 0.00 39.46 3.01
2090 2308 6.604396 TCAGCATTGTGGAAAATGATATGACT 59.396 34.615 1.22 0.00 39.46 3.41
2091 2309 6.694411 GTCAGCATTGTGGAAAATGATATGAC 59.306 38.462 1.22 7.51 39.46 3.06
2092 2310 6.458615 CGTCAGCATTGTGGAAAATGATATGA 60.459 38.462 1.22 0.06 39.46 2.15
2093 2311 5.684184 CGTCAGCATTGTGGAAAATGATATG 59.316 40.000 1.22 0.00 39.46 1.78
2094 2312 5.221106 CCGTCAGCATTGTGGAAAATGATAT 60.221 40.000 1.22 0.00 39.46 1.63
2095 2313 4.096231 CCGTCAGCATTGTGGAAAATGATA 59.904 41.667 1.22 0.00 39.46 2.15
2120 2338 5.547181 AGAAAATAAAACGCAGACTAGGC 57.453 39.130 0.00 0.00 0.00 3.93
2182 2410 7.653647 TGAAAGTGTTTGGTTATTAGCGATTT 58.346 30.769 0.00 0.00 0.00 2.17
2191 2419 5.768164 CCAGTACCTGAAAGTGTTTGGTTAT 59.232 40.000 0.00 0.00 32.44 1.89
2310 2564 2.341846 TCACGCAAAAGAAAGGGTCT 57.658 45.000 0.00 0.00 38.69 3.85
2376 2645 5.328691 TCTAAAGCGTTTTTCACACAGTTG 58.671 37.500 1.60 0.00 0.00 3.16
2385 2655 4.615541 CCATCCGTTTCTAAAGCGTTTTTC 59.384 41.667 1.60 0.00 0.00 2.29
2676 3077 9.252326 ATCATCGAGGATTTAAAACGGTGAACG 62.252 40.741 19.01 0.00 44.76 3.95
2717 3118 2.333014 GTCAGGCTGAAGTCGAAGAAG 58.667 52.381 20.62 0.00 39.69 2.85
2858 3260 4.821589 CTCGAGGACGCCTTGGCC 62.822 72.222 3.91 0.00 35.77 5.36
2870 3272 2.172372 GCCTGACATGCTGCTCGAG 61.172 63.158 8.45 8.45 0.00 4.04
2871 3273 2.125391 GCCTGACATGCTGCTCGA 60.125 61.111 0.00 0.00 0.00 4.04
2921 3323 3.896648 ACAGCCAAATTCAGTAACACG 57.103 42.857 0.00 0.00 0.00 4.49
2936 3340 2.262423 AGTCCTTGACAAGAACAGCC 57.738 50.000 16.99 0.00 34.60 4.85
2969 3373 1.267121 GGAGGTGACAGTCTAAGCCA 58.733 55.000 1.31 0.00 0.00 4.75
2970 3378 0.173708 CGGAGGTGACAGTCTAAGCC 59.826 60.000 1.31 0.00 0.00 4.35
2983 3391 0.252197 GCCTGGACATAAACGGAGGT 59.748 55.000 0.00 0.00 0.00 3.85
3120 3528 6.021596 CGAACAAATCTTGTACTGCCATAAC 58.978 40.000 0.00 0.00 44.59 1.89
3127 3535 3.788434 ACGCGAACAAATCTTGTACTG 57.212 42.857 15.93 0.00 44.59 2.74
3166 3574 3.377439 CATGCATGGTTCATTTCATCCG 58.623 45.455 19.40 0.00 0.00 4.18
3167 3575 3.128349 GCATGCATGGTTCATTTCATCC 58.872 45.455 27.34 2.70 0.00 3.51
3452 3874 1.435577 CCACCTTGCCGTAGTTGTAC 58.564 55.000 0.00 0.00 0.00 2.90
3824 4246 3.854459 GCGAAGGCGAAGAAGGCG 61.854 66.667 0.00 0.00 41.99 5.52
4126 4548 0.753479 CTCTCTCTAGCTTCCGGGCA 60.753 60.000 0.00 0.00 34.17 5.36
4174 4596 5.973651 TTTGCTTCTTCTATATGCAGACG 57.026 39.130 0.00 0.00 35.02 4.18
4220 4652 5.039333 GGCGTCACTCTATGTAACGTAATT 58.961 41.667 0.00 0.00 32.54 1.40
4386 4818 5.881447 TCGAGATTCTCTAAGAAACGAAGG 58.119 41.667 11.75 0.00 37.82 3.46
4419 4851 4.393062 GGCGGTTTACCCTCTAAACTAAAC 59.607 45.833 3.64 0.00 37.51 2.01
4420 4852 4.578871 GGCGGTTTACCCTCTAAACTAAA 58.421 43.478 3.64 0.00 37.51 1.85
4422 4854 2.166254 CGGCGGTTTACCCTCTAAACTA 59.834 50.000 0.00 0.00 37.51 2.24
4424 4856 1.066929 TCGGCGGTTTACCCTCTAAAC 60.067 52.381 7.21 0.00 36.86 2.01
4427 4859 0.323725 AGTCGGCGGTTTACCCTCTA 60.324 55.000 7.21 0.00 0.00 2.43
4428 4860 0.323725 TAGTCGGCGGTTTACCCTCT 60.324 55.000 7.21 0.00 0.00 3.69
4429 4861 0.749049 ATAGTCGGCGGTTTACCCTC 59.251 55.000 7.21 0.00 0.00 4.30
4430 4862 0.462789 CATAGTCGGCGGTTTACCCT 59.537 55.000 7.21 0.00 0.00 4.34
4432 4864 2.014335 AACATAGTCGGCGGTTTACC 57.986 50.000 7.21 0.00 0.00 2.85
4438 4870 3.777478 TCTTCTAAAACATAGTCGGCGG 58.223 45.455 7.21 0.00 0.00 6.13
4441 4873 5.168569 TGTGCTCTTCTAAAACATAGTCGG 58.831 41.667 0.00 0.00 0.00 4.79
4482 4921 4.760204 CAGGGAATCGGTTAAAAAGACACT 59.240 41.667 0.00 0.00 0.00 3.55
4483 4922 4.758165 TCAGGGAATCGGTTAAAAAGACAC 59.242 41.667 0.00 0.00 0.00 3.67
4484 4923 4.975631 TCAGGGAATCGGTTAAAAAGACA 58.024 39.130 0.00 0.00 0.00 3.41
4485 4924 5.472478 AGTTCAGGGAATCGGTTAAAAAGAC 59.528 40.000 0.00 0.00 0.00 3.01
4486 4925 5.627135 AGTTCAGGGAATCGGTTAAAAAGA 58.373 37.500 0.00 0.00 0.00 2.52
4487 4926 5.959618 AGTTCAGGGAATCGGTTAAAAAG 57.040 39.130 0.00 0.00 0.00 2.27
4498 4937 8.990163 TTTTTACTCTGTTAAGTTCAGGGAAT 57.010 30.769 0.00 0.00 36.93 3.01
4502 4941 8.888579 TCTCTTTTTACTCTGTTAAGTTCAGG 57.111 34.615 0.00 0.00 34.15 3.86
4514 4953 9.796120 CTCGAGTCAAATATCTCTTTTTACTCT 57.204 33.333 3.62 0.00 31.97 3.24
4520 4959 9.658799 TCATTTCTCGAGTCAAATATCTCTTTT 57.341 29.630 13.13 0.00 0.00 2.27
4523 4962 8.420222 ACATCATTTCTCGAGTCAAATATCTCT 58.580 33.333 13.13 0.00 0.00 3.10
4524 4963 8.586570 ACATCATTTCTCGAGTCAAATATCTC 57.413 34.615 13.13 0.00 0.00 2.75
4525 4964 8.954950 AACATCATTTCTCGAGTCAAATATCT 57.045 30.769 13.13 0.00 0.00 1.98
4527 4966 8.954950 AGAACATCATTTCTCGAGTCAAATAT 57.045 30.769 13.13 4.59 29.24 1.28
4528 4967 9.302345 GTAGAACATCATTTCTCGAGTCAAATA 57.698 33.333 13.13 2.64 37.09 1.40
4529 4968 7.278868 GGTAGAACATCATTTCTCGAGTCAAAT 59.721 37.037 13.13 9.19 37.09 2.32
4532 4971 5.185056 TGGTAGAACATCATTTCTCGAGTCA 59.815 40.000 13.13 0.05 37.09 3.41
4533 4972 5.651530 TGGTAGAACATCATTTCTCGAGTC 58.348 41.667 13.13 0.00 37.09 3.36
4534 4973 5.661056 TGGTAGAACATCATTTCTCGAGT 57.339 39.130 13.13 0.00 37.09 4.18
4535 4974 5.050499 GCATGGTAGAACATCATTTCTCGAG 60.050 44.000 5.93 5.93 37.09 4.04
4575 5014 3.555966 ACAAATGGATGGCTTAGCTACC 58.444 45.455 3.59 6.09 0.00 3.18
4578 5017 5.104360 TCTCTAACAAATGGATGGCTTAGCT 60.104 40.000 3.59 0.00 0.00 3.32
4605 5044 4.694760 AGCTAGAATATGCATGTGTCCA 57.305 40.909 10.16 0.00 0.00 4.02
4617 5056 5.753438 CCGTGAAATACAGCAAGCTAGAATA 59.247 40.000 0.00 0.00 0.00 1.75
4724 5167 0.536233 TGGTGAACGTGTTGGGATGG 60.536 55.000 0.00 0.00 0.00 3.51
4728 5171 0.105964 TCTCTGGTGAACGTGTTGGG 59.894 55.000 0.00 0.00 0.00 4.12
4729 5172 1.948104 TTCTCTGGTGAACGTGTTGG 58.052 50.000 0.00 0.00 0.00 3.77
4730 5173 2.349817 GCATTCTCTGGTGAACGTGTTG 60.350 50.000 0.00 0.00 0.00 3.33
4731 5174 1.873591 GCATTCTCTGGTGAACGTGTT 59.126 47.619 0.00 0.00 0.00 3.32
4732 5175 1.202639 TGCATTCTCTGGTGAACGTGT 60.203 47.619 0.00 0.00 0.00 4.49
4733 5176 1.195448 GTGCATTCTCTGGTGAACGTG 59.805 52.381 0.00 0.00 0.00 4.49
4734 5177 1.202639 TGTGCATTCTCTGGTGAACGT 60.203 47.619 0.00 0.00 0.00 3.99
4735 5178 1.511850 TGTGCATTCTCTGGTGAACG 58.488 50.000 0.00 0.00 0.00 3.95
4736 5179 3.988379 TTTGTGCATTCTCTGGTGAAC 57.012 42.857 0.00 0.00 0.00 3.18
4737 5180 3.243501 GCTTTTGTGCATTCTCTGGTGAA 60.244 43.478 0.00 0.00 0.00 3.18
4738 5181 2.294233 GCTTTTGTGCATTCTCTGGTGA 59.706 45.455 0.00 0.00 0.00 4.02
4739 5182 2.295349 AGCTTTTGTGCATTCTCTGGTG 59.705 45.455 0.00 0.00 34.99 4.17
4740 5183 2.590821 AGCTTTTGTGCATTCTCTGGT 58.409 42.857 0.00 0.00 34.99 4.00
4744 5187 4.367386 AGCATAGCTTTTGTGCATTCTC 57.633 40.909 13.23 0.00 45.46 2.87
4854 5311 7.205297 CGGATGCATCTTCTATTGGAATTTTT 58.795 34.615 25.28 0.00 33.01 1.94
4896 5353 6.547141 TGATCTTGTTTGAAAGACCTTGTCAT 59.453 34.615 0.00 0.00 38.95 3.06
4949 5406 7.743520 TTACCGTGTTTCAAACTTTGATTTC 57.256 32.000 5.03 0.92 39.84 2.17
5016 5473 7.775561 ACCTTTTAAACAAGATCAGACAAGAGT 59.224 33.333 0.00 0.00 0.00 3.24
5017 5474 8.159344 ACCTTTTAAACAAGATCAGACAAGAG 57.841 34.615 0.00 0.00 0.00 2.85
5050 5509 0.323269 TTGCATCTTTGGGATCCGCA 60.323 50.000 5.45 4.82 33.42 5.69



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

AutoCloner maintained by Alex Coulton.