Multiple sequence alignment - TraesCS2D01G397200

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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 TraesCS2D01G397200 chr2D 100.000 3578 0 0 1 3578 508244010 508240433 0.000000e+00 6608.0
1 TraesCS2D01G397200 chr2D 100.000 2597 0 0 3823 6419 508240188 508237592 0.000000e+00 4796.0
2 TraesCS2D01G397200 chr2D 80.966 352 49 11 2424 2771 168621490 168621827 4.940000e-66 263.0
3 TraesCS2D01G397200 chr2D 79.661 354 58 12 2420 2766 72617939 72618285 6.430000e-60 243.0
4 TraesCS2D01G397200 chr2A 93.182 2024 111 20 3823 5835 652773545 652771538 0.000000e+00 2948.0
5 TraesCS2D01G397200 chr2A 94.775 1665 72 5 1273 2931 652776103 652774448 0.000000e+00 2579.0
6 TraesCS2D01G397200 chr2A 96.235 664 24 1 2916 3578 652774229 652773566 0.000000e+00 1086.0
7 TraesCS2D01G397200 chr2A 91.656 755 28 12 499 1244 652776828 652776100 0.000000e+00 1013.0
8 TraesCS2D01G397200 chr2B 94.540 1868 77 12 1719 3576 597550117 597548265 0.000000e+00 2861.0
9 TraesCS2D01G397200 chr2B 94.318 968 50 4 4871 5835 597546189 597545224 0.000000e+00 1478.0
10 TraesCS2D01G397200 chr2B 93.649 866 45 7 3823 4685 597548239 597547381 0.000000e+00 1286.0
11 TraesCS2D01G397200 chr2B 94.935 691 26 4 566 1256 597551382 597550701 0.000000e+00 1074.0
12 TraesCS2D01G397200 chr2B 88.912 478 50 2 1 476 597553512 597553036 2.580000e-163 586.0
13 TraesCS2D01G397200 chr2B 92.250 400 19 4 1281 1679 597550701 597550313 2.020000e-154 556.0
14 TraesCS2D01G397200 chr2B 80.793 328 52 8 2424 2744 229536530 229536207 4.970000e-61 246.0
15 TraesCS2D01G397200 chr2B 93.373 166 9 2 4683 4847 597546344 597546180 1.790000e-60 244.0
16 TraesCS2D01G397200 chr2B 76.015 271 64 1 183 453 518738674 518738943 8.680000e-29 139.0
17 TraesCS2D01G397200 chr2B 80.337 178 28 7 4729 4903 131580975 131581148 1.880000e-25 128.0
18 TraesCS2D01G397200 chr2B 100.000 44 0 0 1678 1721 597550242 597550199 1.480000e-11 82.4
19 TraesCS2D01G397200 chr6B 91.729 532 35 5 5895 6417 195523595 195523064 0.000000e+00 730.0
20 TraesCS2D01G397200 chr1B 90.784 510 43 4 5907 6415 529930040 529930546 0.000000e+00 678.0
21 TraesCS2D01G397200 chr1B 80.571 175 31 3 4732 4905 73033186 73033014 1.450000e-26 132.0
22 TraesCS2D01G397200 chr5B 89.823 452 36 5 5935 6385 508805419 508804977 7.220000e-159 571.0
23 TraesCS2D01G397200 chr5B 78.472 288 62 0 166 453 20128827 20128540 8.500000e-44 189.0
24 TraesCS2D01G397200 chr5A 92.288 389 20 7 6039 6417 387223586 387223974 1.570000e-150 544.0
25 TraesCS2D01G397200 chr5A 80.277 289 54 3 166 453 464505985 464505699 1.400000e-51 215.0
26 TraesCS2D01G397200 chr5A 89.844 128 12 1 5895 6021 387223474 387223601 5.150000e-36 163.0
27 TraesCS2D01G397200 chr6A 91.495 388 13 10 6039 6417 30097258 30097634 3.430000e-142 516.0
28 TraesCS2D01G397200 chr6A 89.844 128 12 1 5895 6021 30097146 30097273 5.150000e-36 163.0
29 TraesCS2D01G397200 chr6A 76.087 322 69 8 86 402 84974658 84974976 1.850000e-35 161.0
30 TraesCS2D01G397200 chr4D 86.686 353 39 4 2425 2769 336228616 336228968 1.010000e-102 385.0
31 TraesCS2D01G397200 chr4D 75.806 434 87 11 30 457 464305529 464305108 3.030000e-48 204.0
32 TraesCS2D01G397200 chr3D 84.503 342 37 11 2430 2768 343451690 343451362 2.230000e-84 324.0
33 TraesCS2D01G397200 chr3A 84.393 346 37 11 2421 2762 459050487 459050819 2.230000e-84 324.0
34 TraesCS2D01G397200 chr6D 76.712 438 94 6 18 452 103206038 103206470 2.990000e-58 237.0
35 TraesCS2D01G397200 chr1D 82.657 271 44 3 2502 2772 458426826 458427093 2.990000e-58 237.0
36 TraesCS2D01G397200 chrUn 78.917 351 66 5 94 441 194667545 194667890 1.390000e-56 231.0
37 TraesCS2D01G397200 chr4A 77.364 349 75 3 77 422 91309403 91309750 3.030000e-48 204.0
38 TraesCS2D01G397200 chr4A 89.375 160 16 1 4738 4897 715440883 715440725 3.920000e-47 200.0
39 TraesCS2D01G397200 chr4A 79.070 258 44 8 169 424 67967640 67967889 1.110000e-37 169.0
40 TraesCS2D01G397200 chr7B 82.500 160 26 2 4737 4896 722089967 722090124 8.680000e-29 139.0
41 TraesCS2D01G397200 chr7A 83.444 151 23 2 4738 4888 677612162 677612014 8.680000e-29 139.0
42 TraesCS2D01G397200 chr7A 100.000 28 0 0 449 476 695183306 695183279 1.200000e-02 52.8
43 TraesCS2D01G397200 chr1A 77.215 237 54 0 166 402 65648910 65649146 8.680000e-29 139.0
44 TraesCS2D01G397200 chr1A 80.460 174 31 3 4732 4905 584507797 584507967 5.220000e-26 130.0
45 TraesCS2D01G397200 chr7D 82.468 154 25 2 4743 4896 586023537 586023386 4.040000e-27 134.0


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 TraesCS2D01G397200 chr2D 508237592 508244010 6418 True 5702.000 6608 100.000000 1 6419 2 chr2D.!!$R1 6418
1 TraesCS2D01G397200 chr2A 652771538 652776828 5290 True 1906.500 2948 93.962000 499 5835 4 chr2A.!!$R1 5336
2 TraesCS2D01G397200 chr2B 597545224 597553512 8288 True 1020.925 2861 93.997125 1 5835 8 chr2B.!!$R2 5834
3 TraesCS2D01G397200 chr6B 195523064 195523595 531 True 730.000 730 91.729000 5895 6417 1 chr6B.!!$R1 522
4 TraesCS2D01G397200 chr1B 529930040 529930546 506 False 678.000 678 90.784000 5907 6415 1 chr1B.!!$F1 508
5 TraesCS2D01G397200 chr5A 387223474 387223974 500 False 353.500 544 91.066000 5895 6417 2 chr5A.!!$F1 522

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
155 158 0.034337 GTTGGTGCCTGTCTTCGGTA 59.966 55.0 0.00 0.00 0.00 4.02 F
927 2494 0.174845 TGTTCGAGCGGTAGGGATTG 59.825 55.0 0.00 0.00 0.00 2.67 F
1263 2839 0.039888 CCACGCCGTTTACAAAAGGG 60.040 55.0 8.45 6.73 37.90 3.95 F
1390 2973 0.107643 TTGTTCGTGGCCACATGAGA 59.892 50.0 34.16 20.69 43.12 3.27 F
3071 5064 0.305922 GGCGATGTAGTCAATGCAGC 59.694 55.0 0.00 0.00 32.09 5.25 F
4428 6424 0.320334 CCTATGCACACACACGTCCA 60.320 55.0 0.00 0.00 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1244 2820 0.039888 CCCTTTTGTAAACGGCGTGG 60.040 55.000 15.70 7.64 0.00 4.94 R
1740 3480 1.406898 CTAGAGCTCATCGCCTGTCAA 59.593 52.381 17.77 0.00 40.39 3.18 R
2244 3996 1.616159 TTAGTGCTCCCACCTTTTGC 58.384 50.000 0.00 0.00 43.09 3.68 R
3291 5284 0.322816 TGGCCAGACATTTCAGAGGC 60.323 55.000 0.00 0.00 41.29 4.70 R
4487 6484 1.000896 CCAGCCGGGTTCAATCCTT 60.001 57.895 1.64 0.00 0.00 3.36 R
5849 8892 0.107848 GAACCGTTCGGATCATGGGT 60.108 55.000 18.28 0.00 0.00 4.51 R

All possible primers

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

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 3.584868 AAAAGCGAGGTAGCGGCGT 62.585 57.895 9.37 0.00 43.00 5.68
30 31 4.549516 GGTAGCGGCGTCGACTCC 62.550 72.222 16.53 14.74 39.00 3.85
46 47 6.238676 CGTCGACTCCCTGAAGATAGAATAAA 60.239 42.308 14.70 0.00 0.00 1.40
56 57 7.147479 CCTGAAGATAGAATAAAGTTCTCCCCA 60.147 40.741 0.00 0.00 0.00 4.96
65 66 2.042261 TTCTCCCCACTAGCCCCC 59.958 66.667 0.00 0.00 0.00 5.40
112 113 3.591254 GAGGGCGTGTGGAGGTGTC 62.591 68.421 0.00 0.00 0.00 3.67
116 117 1.373497 GCGTGTGGAGGTGTCTCTG 60.373 63.158 0.00 0.00 39.86 3.35
117 118 1.806461 GCGTGTGGAGGTGTCTCTGA 61.806 60.000 0.00 0.00 39.86 3.27
118 119 0.039074 CGTGTGGAGGTGTCTCTGAC 60.039 60.000 0.00 0.00 39.86 3.51
138 141 4.117685 GACGTATCTTGCGGGATTTAGTT 58.882 43.478 0.00 0.00 0.00 2.24
144 147 0.963355 TGCGGGATTTAGTTGGTGCC 60.963 55.000 0.00 0.00 0.00 5.01
155 158 0.034337 GTTGGTGCCTGTCTTCGGTA 59.966 55.000 0.00 0.00 0.00 4.02
161 164 3.118884 GGTGCCTGTCTTCGGTAAATCTA 60.119 47.826 0.00 0.00 0.00 1.98
162 165 4.443034 GGTGCCTGTCTTCGGTAAATCTAT 60.443 45.833 0.00 0.00 0.00 1.98
163 166 4.508124 GTGCCTGTCTTCGGTAAATCTATG 59.492 45.833 0.00 0.00 0.00 2.23
174 177 4.502604 CGGTAAATCTATGTGGATCCGGTT 60.503 45.833 7.39 0.00 31.37 4.44
180 183 1.734163 ATGTGGATCCGGTTTTCGTC 58.266 50.000 7.39 0.00 37.11 4.20
181 184 0.682852 TGTGGATCCGGTTTTCGTCT 59.317 50.000 7.39 0.00 37.11 4.18
237 240 2.349580 CGATTTGCGCTTCTCTTCATCA 59.650 45.455 9.73 0.00 0.00 3.07
248 251 2.762887 TCTCTTCATCAGCGGAGATTGT 59.237 45.455 0.00 0.00 31.02 2.71
251 254 4.433615 TCTTCATCAGCGGAGATTGTTAC 58.566 43.478 0.00 0.00 0.00 2.50
275 278 0.534203 GTGCGTTGGTCCTTTGGAGA 60.534 55.000 0.00 0.00 29.39 3.71
280 283 3.326747 CGTTGGTCCTTTGGAGACTTAG 58.673 50.000 0.00 0.00 34.56 2.18
283 286 2.038557 TGGTCCTTTGGAGACTTAGCAC 59.961 50.000 0.00 0.00 34.56 4.40
289 292 1.460504 TGGAGACTTAGCACGACGAT 58.539 50.000 0.00 0.00 0.00 3.73
304 307 4.070716 ACGACGATTTCCCGACTATCTAT 58.929 43.478 0.00 0.00 0.00 1.98
324 327 4.976224 ATTACAATAAGGTTTGTCCGGC 57.024 40.909 0.00 0.00 40.25 6.13
327 330 2.039879 ACAATAAGGTTTGTCCGGCTCT 59.960 45.455 0.00 0.00 41.99 4.09
341 344 2.730524 GCTCTGGTGAGGGAGAGGC 61.731 68.421 0.00 0.00 40.53 4.70
347 350 1.439644 GTGAGGGAGAGGCGATGAC 59.560 63.158 0.00 0.00 0.00 3.06
350 353 3.148279 GGGAGAGGCGATGACGGT 61.148 66.667 0.00 0.00 40.15 4.83
373 376 2.202676 GTCTTCGGCTCGCTCCAG 60.203 66.667 0.00 0.00 0.00 3.86
375 378 1.378119 TCTTCGGCTCGCTCCAGTA 60.378 57.895 0.00 0.00 0.00 2.74
386 389 2.751259 TCGCTCCAGTAATTGTAGTCGT 59.249 45.455 0.00 0.00 0.00 4.34
387 390 3.106672 CGCTCCAGTAATTGTAGTCGTC 58.893 50.000 0.00 0.00 0.00 4.20
392 395 4.577693 TCCAGTAATTGTAGTCGTCGCTAT 59.422 41.667 0.00 0.00 0.00 2.97
399 402 1.669779 GTAGTCGTCGCTATGTGGTCT 59.330 52.381 0.00 0.00 0.00 3.85
417 420 9.679661 ATGTGGTCTACAAACATGAATGTAATA 57.320 29.630 0.00 0.00 43.77 0.98
456 459 7.936847 TGTGTTCTTTTCACTACCATGATACTT 59.063 33.333 0.00 0.00 36.83 2.24
462 465 3.889538 TCACTACCATGATACTTCCTCCG 59.110 47.826 0.00 0.00 0.00 4.63
467 470 5.888982 ACCATGATACTTCCTCCGTAAAT 57.111 39.130 0.00 0.00 0.00 1.40
509 557 4.886247 TGTACACGGGAAGTTTTTCTTG 57.114 40.909 0.00 0.00 36.40 3.02
669 2236 3.717294 CCCACCCGACCTTCCCAG 61.717 72.222 0.00 0.00 0.00 4.45
670 2237 2.928396 CCACCCGACCTTCCCAGT 60.928 66.667 0.00 0.00 0.00 4.00
671 2238 2.526046 CCACCCGACCTTCCCAGTT 61.526 63.158 0.00 0.00 0.00 3.16
672 2239 1.003718 CACCCGACCTTCCCAGTTC 60.004 63.158 0.00 0.00 0.00 3.01
673 2240 2.222013 ACCCGACCTTCCCAGTTCC 61.222 63.158 0.00 0.00 0.00 3.62
674 2241 2.669240 CCGACCTTCCCAGTTCCC 59.331 66.667 0.00 0.00 0.00 3.97
749 2316 3.431725 GCAGTTGCACCGTAGCCC 61.432 66.667 0.00 0.00 41.59 5.19
927 2494 0.174845 TGTTCGAGCGGTAGGGATTG 59.825 55.000 0.00 0.00 0.00 2.67
1194 2766 1.898154 GGTGCGTGTCATACCCTCT 59.102 57.895 0.00 0.00 0.00 3.69
1195 2767 1.108776 GGTGCGTGTCATACCCTCTA 58.891 55.000 0.00 0.00 0.00 2.43
1240 2816 1.482182 ACCGATATTCTGCTGCTGTGA 59.518 47.619 0.00 0.00 0.00 3.58
1241 2817 2.093500 ACCGATATTCTGCTGCTGTGAA 60.093 45.455 0.00 3.63 0.00 3.18
1242 2818 2.286294 CCGATATTCTGCTGCTGTGAAC 59.714 50.000 0.00 0.00 0.00 3.18
1243 2819 3.193263 CGATATTCTGCTGCTGTGAACT 58.807 45.455 0.00 0.00 0.00 3.01
1244 2820 3.244814 CGATATTCTGCTGCTGTGAACTC 59.755 47.826 0.00 3.86 0.00 3.01
1245 2821 1.818642 ATTCTGCTGCTGTGAACTCC 58.181 50.000 0.00 0.00 0.00 3.85
1246 2822 0.469494 TTCTGCTGCTGTGAACTCCA 59.531 50.000 0.00 0.00 0.00 3.86
1247 2823 0.250038 TCTGCTGCTGTGAACTCCAC 60.250 55.000 0.00 0.00 45.88 4.02
1254 2830 3.727146 GTGAACTCCACGCCGTTT 58.273 55.556 0.00 0.00 35.86 3.60
1255 2831 2.903284 GTGAACTCCACGCCGTTTA 58.097 52.632 0.00 0.00 35.86 2.01
1256 2832 0.509929 GTGAACTCCACGCCGTTTAC 59.490 55.000 0.00 0.00 35.86 2.01
1257 2833 0.104487 TGAACTCCACGCCGTTTACA 59.896 50.000 0.00 0.00 0.00 2.41
1258 2834 1.219646 GAACTCCACGCCGTTTACAA 58.780 50.000 0.00 0.00 0.00 2.41
1259 2835 1.598601 GAACTCCACGCCGTTTACAAA 59.401 47.619 0.00 0.00 0.00 2.83
1260 2836 1.666054 ACTCCACGCCGTTTACAAAA 58.334 45.000 0.00 0.00 0.00 2.44
1261 2837 1.600485 ACTCCACGCCGTTTACAAAAG 59.400 47.619 0.00 0.00 0.00 2.27
1262 2838 0.945813 TCCACGCCGTTTACAAAAGG 59.054 50.000 2.68 2.68 40.02 3.11
1263 2839 0.039888 CCACGCCGTTTACAAAAGGG 60.040 55.000 8.45 6.73 37.90 3.95
1267 2843 2.427232 GCCGTTTACAAAAGGGGAAC 57.573 50.000 11.78 0.00 37.90 3.62
1268 2844 1.682323 GCCGTTTACAAAAGGGGAACA 59.318 47.619 11.78 0.00 37.90 3.18
1269 2845 2.544277 GCCGTTTACAAAAGGGGAACAC 60.544 50.000 11.78 0.00 37.90 3.32
1270 2846 2.688958 CCGTTTACAAAAGGGGAACACA 59.311 45.455 3.71 0.00 34.46 3.72
1271 2847 3.319689 CCGTTTACAAAAGGGGAACACAT 59.680 43.478 3.71 0.00 34.46 3.21
1279 2862 2.685850 AGGGGAACACATAACTACGC 57.314 50.000 0.00 0.00 0.00 4.42
1381 2964 3.964909 ACTCAATTTCTTTGTTCGTGGC 58.035 40.909 0.00 0.00 36.65 5.01
1390 2973 0.107643 TTGTTCGTGGCCACATGAGA 59.892 50.000 34.16 20.69 43.12 3.27
1604 3188 5.453339 GGCTATTGCACTCATACCAAGTCTA 60.453 44.000 0.66 0.00 41.91 2.59
1740 3480 5.772672 TGGTATTTGTGTGCCTCTGTTTTAT 59.227 36.000 0.00 0.00 0.00 1.40
1744 3484 4.829064 TGTGTGCCTCTGTTTTATTGAC 57.171 40.909 0.00 0.00 0.00 3.18
1770 3510 5.390613 GCGATGAGCTCTAGTTAGATTCTC 58.609 45.833 16.19 9.69 44.04 2.87
1799 3539 5.982890 ACACTTTCCCCAATAATTGTCTG 57.017 39.130 0.00 0.00 0.00 3.51
1935 3675 7.792032 TGATCCTTAGTCCCTACACATTTAAG 58.208 38.462 0.00 0.00 0.00 1.85
1940 3680 5.437191 AGTCCCTACACATTTAAGGAAGG 57.563 43.478 0.00 0.00 31.64 3.46
1951 3691 8.585018 ACACATTTAAGGAAGGAAATAGGTTTG 58.415 33.333 0.00 0.00 0.00 2.93
1969 3709 4.184629 GTTTGAATGACTAGGCGATGAGT 58.815 43.478 0.00 0.00 0.00 3.41
1985 3725 6.584563 GGCGATGAGTTCTAGTTAGATTCATC 59.415 42.308 20.63 20.63 42.64 2.92
2068 3816 5.853936 TGCTTCAAGTTAGTCTGTGTATGT 58.146 37.500 0.00 0.00 0.00 2.29
2069 3817 5.696270 TGCTTCAAGTTAGTCTGTGTATGTG 59.304 40.000 0.00 0.00 0.00 3.21
2070 3818 5.696724 GCTTCAAGTTAGTCTGTGTATGTGT 59.303 40.000 0.00 0.00 0.00 3.72
2071 3819 6.346919 GCTTCAAGTTAGTCTGTGTATGTGTG 60.347 42.308 0.00 0.00 0.00 3.82
2110 3859 6.557568 ACTTAACAATATTCCCTGGTCCAAA 58.442 36.000 0.00 0.00 0.00 3.28
2205 3954 8.282455 TCACAGTCTAAAACCAATGTGTTTTA 57.718 30.769 14.44 14.44 44.36 1.52
2209 3958 9.341899 CAGTCTAAAACCAATGTGTTTTATAGC 57.658 33.333 15.11 10.65 44.95 2.97
2244 3996 9.928236 GAAATAATAAGCTAGAAACTGAAGCAG 57.072 33.333 0.00 0.00 38.75 4.24
2465 4221 7.270047 TCCCCACTAACTCAATTATCTTAACG 58.730 38.462 0.00 0.00 0.00 3.18
2508 4264 2.363276 ACCATGCATGCCCCACTG 60.363 61.111 21.69 8.18 0.00 3.66
2557 4313 2.678190 GCCAACTCACCCTGACACTATC 60.678 54.545 0.00 0.00 0.00 2.08
2677 4433 7.290857 TGTGCTTTAGTTTCGATTCTCATAC 57.709 36.000 0.00 0.00 0.00 2.39
2680 4436 5.519206 GCTTTAGTTTCGATTCTCATACCGT 59.481 40.000 0.00 0.00 0.00 4.83
2784 4540 6.436261 TCGTCTCTAGTAAACTTGACAACTG 58.564 40.000 0.00 0.00 0.00 3.16
2806 4562 4.223700 TGAGTGCACATGGAGTATTCTCTT 59.776 41.667 21.04 0.00 40.29 2.85
2849 4605 4.630894 TTTCGCAAATGTCAAGTGAACT 57.369 36.364 0.00 0.00 32.17 3.01
3071 5064 0.305922 GGCGATGTAGTCAATGCAGC 59.694 55.000 0.00 0.00 32.09 5.25
3091 5084 5.987953 GCAGCTGTCATATCACTATCTTTCA 59.012 40.000 16.64 0.00 0.00 2.69
3200 5193 7.426410 TGAAGTACTCTGAGGCTTTATATTCG 58.574 38.462 9.85 0.00 0.00 3.34
3273 5266 7.873505 ACCTAACTTTACTGTTTTCTGCTCTAG 59.126 37.037 0.00 0.00 0.00 2.43
3275 5268 9.909644 CTAACTTTACTGTTTTCTGCTCTAGTA 57.090 33.333 0.00 0.00 0.00 1.82
3315 5308 0.770499 TGAAATGTCTGGCCACTGGA 59.230 50.000 0.00 0.00 0.00 3.86
3352 5345 1.358152 AACAGTGGGCCAAGTAGCTA 58.642 50.000 8.40 0.00 0.00 3.32
3392 5385 1.279271 ACCCTGTTGCAGTATCACCTC 59.721 52.381 0.00 0.00 0.00 3.85
3404 5397 7.564793 TGCAGTATCACCTCATTGTAAATACT 58.435 34.615 0.00 0.00 31.60 2.12
3534 5527 9.444600 TTTTCTTTGTTGTCATATAGTCCCTAC 57.555 33.333 0.00 0.00 0.00 3.18
3535 5528 7.973048 TCTTTGTTGTCATATAGTCCCTACT 57.027 36.000 0.00 0.00 39.91 2.57
3552 5545 5.435041 TCCCTACTCCCATGGTTATCAATTT 59.565 40.000 11.73 0.00 0.00 1.82
3868 5861 5.564550 ACCAAAGCATGAGAAAGTATCTGT 58.435 37.500 0.00 0.00 38.96 3.41
3930 5924 5.242434 TGCTATGAAGGACACGTTTTATGT 58.758 37.500 0.00 0.00 0.00 2.29
3951 5945 7.573968 ATGTTGAAAGAATACTTCCATAGCC 57.426 36.000 0.00 0.00 35.05 3.93
3972 5966 6.977213 AGCCGAGTAACAAATGTACAAAATT 58.023 32.000 0.00 0.00 0.00 1.82
4252 6248 2.799412 CAGTGCAAGTGAAGTGTCTCTC 59.201 50.000 0.00 0.00 40.62 3.20
4253 6249 2.697751 AGTGCAAGTGAAGTGTCTCTCT 59.302 45.455 0.00 0.00 0.00 3.10
4396 6392 2.798148 CTAACACACCCGCCCCACTC 62.798 65.000 0.00 0.00 0.00 3.51
4408 6404 1.834188 CCCCACTCAAACCACCATAC 58.166 55.000 0.00 0.00 0.00 2.39
4425 6421 0.970640 TACCCTATGCACACACACGT 59.029 50.000 0.00 0.00 0.00 4.49
4428 6424 0.320334 CCTATGCACACACACGTCCA 60.320 55.000 0.00 0.00 0.00 4.02
4429 6425 1.070821 CTATGCACACACACGTCCAG 58.929 55.000 0.00 0.00 0.00 3.86
4445 6442 3.058501 CGTCCAGTGTTTACCATTGAACC 60.059 47.826 0.00 0.00 32.80 3.62
4446 6443 3.886505 GTCCAGTGTTTACCATTGAACCA 59.113 43.478 0.00 0.00 32.80 3.67
4479 6476 4.038763 TGAAGGTATGACACACGAACTCTT 59.961 41.667 0.00 0.00 0.00 2.85
4487 6484 3.804036 ACACACGAACTCTTGATCCAAA 58.196 40.909 0.00 0.00 0.00 3.28
4488 6485 4.196193 ACACACGAACTCTTGATCCAAAA 58.804 39.130 0.00 0.00 0.00 2.44
4537 6534 4.006989 CCACGTCAATCCTAACCAATGAA 58.993 43.478 0.00 0.00 0.00 2.57
4575 6572 7.487484 TCACACATAAATTGAGAAAAACTGCA 58.513 30.769 0.00 0.00 0.00 4.41
4762 7799 2.479566 TGGATTCGCTTTTCTGCTCT 57.520 45.000 0.00 0.00 0.00 4.09
4770 7807 2.805099 CGCTTTTCTGCTCTGTTTCTCT 59.195 45.455 0.00 0.00 0.00 3.10
4773 7810 4.640364 CTTTTCTGCTCTGTTTCTCTCCT 58.360 43.478 0.00 0.00 0.00 3.69
4796 7833 4.525487 TGTTTAGAATACACACCTCGTCCT 59.475 41.667 0.00 0.00 0.00 3.85
4800 7837 1.919240 ATACACACCTCGTCCTGTCA 58.081 50.000 0.00 0.00 0.00 3.58
4814 7851 4.617530 CGTCCTGTCATTTTCGTTCTAGGA 60.618 45.833 0.00 0.00 0.00 2.94
4905 7942 0.035343 AAGCGGGGCCTAAGAAGTTC 60.035 55.000 0.84 0.00 0.00 3.01
4992 8030 5.221126 GCCCAATATTTAGAAGCTCACAAGG 60.221 44.000 0.00 0.00 0.00 3.61
5015 8053 6.547510 AGGCATGAGTTCTTTCTTAACAGTTT 59.452 34.615 0.00 0.00 0.00 2.66
5083 8124 2.455032 TGTTTGATCGGTTGTTTTGCG 58.545 42.857 0.00 0.00 0.00 4.85
5131 8172 5.703130 GGTGAATACACTGAGAAAGAGCTTT 59.297 40.000 0.00 0.00 45.32 3.51
5333 8374 3.325753 AGCACCTGACTGGCTCCC 61.326 66.667 0.00 0.00 40.22 4.30
5420 8461 5.995282 TGGTTATTGAGATACGCCAATAAGG 59.005 40.000 0.00 0.00 42.43 2.69
5447 8488 4.691685 GCATGAGATTGCTATGGAAGAGAG 59.308 45.833 0.00 0.00 39.57 3.20
5469 8510 5.865085 AGCAAAGCGGGAATATGTAATAGA 58.135 37.500 0.00 0.00 28.50 1.98
5481 8522 8.103305 GGAATATGTAATAGATTTCCTGCCTCA 58.897 37.037 0.00 0.00 28.50 3.86
5568 8609 6.893958 AAACATTTGTTGTACATTTCGCAA 57.106 29.167 0.00 0.00 37.68 4.85
5583 8624 7.999699 CATTTCGCAATGTAGATTAGCATAC 57.000 36.000 0.00 0.00 35.86 2.39
5584 8625 7.575365 CATTTCGCAATGTAGATTAGCATACA 58.425 34.615 0.00 0.00 35.86 2.29
5615 8658 6.092092 TGTCACAAACACTTTCAATGTTCTG 58.908 36.000 0.00 0.00 39.36 3.02
5636 8679 6.382608 TCTGTTCTAATGCTCTGTATATCGC 58.617 40.000 0.00 0.00 0.00 4.58
5757 8800 2.460669 CAGCCCCCTTTTCATTAAGCT 58.539 47.619 0.00 0.00 0.00 3.74
5769 8812 5.371115 TTCATTAAGCTTGTGGTAGCAAC 57.629 39.130 9.86 0.00 43.68 4.17
5771 8814 5.800296 TCATTAAGCTTGTGGTAGCAACTA 58.200 37.500 9.86 0.00 43.68 2.24
5793 8836 2.171003 GGCAAACTTAGGTGGCAGATT 58.829 47.619 0.00 0.00 39.93 2.40
5798 8841 3.287867 ACTTAGGTGGCAGATTCCATG 57.712 47.619 0.00 0.00 38.57 3.66
5803 8846 2.042162 AGGTGGCAGATTCCATGTTTCT 59.958 45.455 0.00 0.00 38.57 2.52
5807 8850 4.012374 TGGCAGATTCCATGTTTCTCTTC 58.988 43.478 0.00 0.00 0.00 2.87
5815 8858 4.703897 TCCATGTTTCTCTTCGAGTTTGT 58.296 39.130 0.00 0.00 0.00 2.83
5835 8878 6.700081 GTTTGTTAAACTTTGGATCTTCCACC 59.300 38.462 0.00 0.00 41.26 4.61
5836 8879 7.417456 GTTTGTTAAACTTTGGATCTTCCACCT 60.417 37.037 0.00 0.00 41.26 4.00
5853 8896 9.005318 TCTTCCACCTAAATATGTAATAACCCA 57.995 33.333 0.00 0.00 29.06 4.51
5854 8897 9.807921 CTTCCACCTAAATATGTAATAACCCAT 57.192 33.333 0.00 0.00 29.06 4.00
5855 8898 9.581289 TTCCACCTAAATATGTAATAACCCATG 57.419 33.333 0.00 0.00 29.06 3.66
5856 8899 8.950480 TCCACCTAAATATGTAATAACCCATGA 58.050 33.333 0.00 0.00 29.06 3.07
5857 8900 9.753674 CCACCTAAATATGTAATAACCCATGAT 57.246 33.333 0.00 0.00 29.06 2.45
5859 8902 9.975218 ACCTAAATATGTAATAACCCATGATCC 57.025 33.333 0.00 0.00 29.06 3.36
5860 8903 9.109393 CCTAAATATGTAATAACCCATGATCCG 57.891 37.037 0.00 0.00 29.06 4.18
5861 8904 9.884636 CTAAATATGTAATAACCCATGATCCGA 57.115 33.333 0.00 0.00 29.06 4.55
5863 8906 8.561738 AATATGTAATAACCCATGATCCGAAC 57.438 34.615 0.00 0.00 29.06 3.95
5864 8907 4.373527 TGTAATAACCCATGATCCGAACG 58.626 43.478 0.00 0.00 0.00 3.95
5865 8908 2.543777 ATAACCCATGATCCGAACGG 57.456 50.000 6.94 6.94 0.00 4.44
5866 8909 1.196911 TAACCCATGATCCGAACGGT 58.803 50.000 12.93 0.94 36.47 4.83
5867 8910 0.326927 AACCCATGATCCGAACGGTT 59.673 50.000 12.93 4.82 36.47 4.44
5868 8911 0.107848 ACCCATGATCCGAACGGTTC 60.108 55.000 10.83 10.83 36.47 3.62
5869 8912 0.107897 CCCATGATCCGAACGGTTCA 60.108 55.000 22.98 22.98 44.90 3.18
5870 8913 1.290203 CCATGATCCGAACGGTTCAG 58.710 55.000 24.22 17.75 44.29 3.02
5871 8914 1.134818 CCATGATCCGAACGGTTCAGA 60.135 52.381 24.22 14.65 44.29 3.27
5872 8915 2.483714 CCATGATCCGAACGGTTCAGAT 60.484 50.000 24.22 17.19 44.29 2.90
5873 8916 3.243737 CCATGATCCGAACGGTTCAGATA 60.244 47.826 24.22 8.44 44.29 1.98
5874 8917 3.431922 TGATCCGAACGGTTCAGATAC 57.568 47.619 17.19 12.13 38.61 2.24
5875 8918 2.223409 TGATCCGAACGGTTCAGATACG 60.223 50.000 17.19 5.21 38.61 3.06
5876 8919 1.452110 TCCGAACGGTTCAGATACGA 58.548 50.000 19.91 3.37 36.47 3.43
5877 8920 1.131126 TCCGAACGGTTCAGATACGAC 59.869 52.381 19.91 0.00 36.47 4.34
5878 8921 1.177668 CGAACGGTTCAGATACGACG 58.822 55.000 19.91 0.00 0.00 5.12
5879 8922 1.201954 CGAACGGTTCAGATACGACGA 60.202 52.381 19.91 0.00 34.98 4.20
5880 8923 2.538333 CGAACGGTTCAGATACGACGAT 60.538 50.000 19.91 0.00 34.98 3.73
5881 8924 2.752144 ACGGTTCAGATACGACGATC 57.248 50.000 0.00 0.32 0.00 3.69
5882 8925 1.004185 ACGGTTCAGATACGACGATCG 60.004 52.381 14.88 14.88 46.93 3.69
5891 8934 3.299585 CGACGATCGTGACATGCC 58.700 61.111 28.12 8.20 34.72 4.40
5892 8935 2.230940 CGACGATCGTGACATGCCC 61.231 63.158 28.12 7.40 34.72 5.36
5893 8936 1.153647 GACGATCGTGACATGCCCA 60.154 57.895 28.12 0.00 0.00 5.36
5897 8940 1.875157 CGATCGTGACATGCCCATCAT 60.875 52.381 7.03 0.00 35.31 2.45
5949 8992 5.063060 CCGACCGAACCATAAGAAGTTTAAG 59.937 44.000 0.00 0.00 0.00 1.85
5973 9020 6.155049 AGGTATGCAAAAATTGATAAGCCTGT 59.845 34.615 0.00 0.00 0.00 4.00
5986 9033 1.429463 AGCCTGTCGTCGTTTTCATC 58.571 50.000 0.00 0.00 0.00 2.92
5998 9045 6.018588 TCGTCGTTTTCATCAGTGTAAACAAT 60.019 34.615 9.99 0.00 42.38 2.71
6040 9087 7.991084 TTATCAGAATGCCCATCTTTGATAG 57.009 36.000 0.00 0.00 34.76 2.08
6047 9094 6.705863 ATGCCCATCTTTGATAGAAAGAAC 57.294 37.500 0.00 0.00 39.43 3.01
6111 9158 4.338682 AGACGGTACTATGTCAGAATGGAC 59.661 45.833 13.30 0.00 37.58 4.02
6199 9255 5.881777 GTTGGTTCTTCTCCTAATCCAAC 57.118 43.478 8.10 8.10 43.64 3.77
6221 9277 4.017775 ACCCCCTTAATGGTTAAGAGGAAC 60.018 45.833 17.73 0.00 42.02 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 4.883300 GTCGACGCCGCTACCTCG 62.883 72.222 0.00 0.00 35.37 4.63
23 24 6.834451 ACTTTATTCTATCTTCAGGGAGTCGA 59.166 38.462 0.00 0.00 0.00 4.20
30 31 7.147479 TGGGGAGAACTTTATTCTATCTTCAGG 60.147 40.741 0.00 0.00 0.00 3.86
46 47 1.307084 GGGGCTAGTGGGGAGAACT 60.307 63.158 0.00 0.00 0.00 3.01
65 66 1.421410 GAGACGCACTGCCAATACGG 61.421 60.000 0.00 0.00 38.11 4.02
112 113 0.738975 TCCCGCAAGATACGTCAGAG 59.261 55.000 0.00 0.00 43.02 3.35
116 117 3.714391 ACTAAATCCCGCAAGATACGTC 58.286 45.455 0.00 0.00 43.02 4.34
117 118 3.814005 ACTAAATCCCGCAAGATACGT 57.186 42.857 0.00 0.00 43.02 3.57
118 119 3.247648 CCAACTAAATCCCGCAAGATACG 59.752 47.826 0.00 0.00 43.02 3.06
138 141 0.759959 TTTACCGAAGACAGGCACCA 59.240 50.000 0.00 0.00 0.00 4.17
144 147 5.902681 TCCACATAGATTTACCGAAGACAG 58.097 41.667 0.00 0.00 0.00 3.51
155 158 4.574828 CGAAAACCGGATCCACATAGATTT 59.425 41.667 9.46 2.73 33.91 2.17
161 164 1.278127 AGACGAAAACCGGATCCACAT 59.722 47.619 9.46 0.00 43.93 3.21
162 165 0.682852 AGACGAAAACCGGATCCACA 59.317 50.000 9.46 0.00 43.93 4.17
163 166 1.076332 CAGACGAAAACCGGATCCAC 58.924 55.000 9.46 0.00 43.93 4.02
174 177 4.233123 ACATGAACGTAGACAGACGAAA 57.767 40.909 0.00 0.00 45.82 3.46
209 212 2.352960 GAGAAGCGCAAATCGAAAGGAT 59.647 45.455 11.47 0.00 41.67 3.24
237 240 3.741388 GCACCATAGTAACAATCTCCGCT 60.741 47.826 0.00 0.00 0.00 5.52
248 251 1.903860 AGGACCAACGCACCATAGTAA 59.096 47.619 0.00 0.00 0.00 2.24
251 254 1.468520 CAAAGGACCAACGCACCATAG 59.531 52.381 0.00 0.00 0.00 2.23
275 278 1.734707 CGGGAAATCGTCGTGCTAAGT 60.735 52.381 0.00 0.00 0.00 2.24
280 283 0.179156 TAGTCGGGAAATCGTCGTGC 60.179 55.000 0.00 0.00 0.00 5.34
283 286 4.681835 ATAGATAGTCGGGAAATCGTCG 57.318 45.455 0.00 0.00 0.00 5.12
289 292 9.151177 ACCTTATTGTAATAGATAGTCGGGAAA 57.849 33.333 0.00 0.00 0.00 3.13
304 307 4.004982 GAGCCGGACAAACCTTATTGTAA 58.995 43.478 5.05 0.00 43.31 2.41
314 317 0.951040 CTCACCAGAGCCGGACAAAC 60.951 60.000 5.05 0.00 34.61 2.93
324 327 2.422231 CGCCTCTCCCTCACCAGAG 61.422 68.421 0.00 0.00 41.72 3.35
327 330 2.060383 CATCGCCTCTCCCTCACCA 61.060 63.158 0.00 0.00 0.00 4.17
350 353 4.753877 CGAGCCGAAGACGCGTCA 62.754 66.667 37.85 0.00 38.29 4.35
362 365 2.159085 ACTACAATTACTGGAGCGAGCC 60.159 50.000 0.00 0.00 40.05 4.70
373 376 4.440103 CCACATAGCGACGACTACAATTAC 59.560 45.833 0.00 0.00 0.00 1.89
375 378 3.119245 ACCACATAGCGACGACTACAATT 60.119 43.478 0.00 0.00 0.00 2.32
386 389 3.945981 TGTTTGTAGACCACATAGCGA 57.054 42.857 0.00 0.00 36.90 4.93
387 390 4.180817 TCATGTTTGTAGACCACATAGCG 58.819 43.478 0.00 0.00 36.90 4.26
392 395 7.994425 ATTACATTCATGTTTGTAGACCACA 57.006 32.000 0.00 0.00 41.97 4.17
440 443 3.889538 CGGAGGAAGTATCATGGTAGTGA 59.110 47.826 0.00 0.00 0.00 3.41
441 444 3.637229 ACGGAGGAAGTATCATGGTAGTG 59.363 47.826 0.00 0.00 0.00 2.74
476 479 3.056393 TCCCGTGTACATGGACACTAAAG 60.056 47.826 32.95 20.02 46.24 1.85
477 480 2.898612 TCCCGTGTACATGGACACTAAA 59.101 45.455 32.95 18.06 46.24 1.85
478 481 2.527497 TCCCGTGTACATGGACACTAA 58.473 47.619 32.95 18.38 46.24 2.24
480 483 1.275291 CTTCCCGTGTACATGGACACT 59.725 52.381 32.95 0.00 46.24 3.55
481 484 1.001633 ACTTCCCGTGTACATGGACAC 59.998 52.381 31.83 28.37 45.19 3.67
483 486 2.467566 AACTTCCCGTGTACATGGAC 57.532 50.000 31.83 0.00 39.90 4.02
484 487 3.495434 AAAACTTCCCGTGTACATGGA 57.505 42.857 31.83 21.54 39.90 3.41
485 488 3.818773 AGAAAAACTTCCCGTGTACATGG 59.181 43.478 24.94 24.94 37.23 3.66
486 489 5.008217 TCAAGAAAAACTTCCCGTGTACATG 59.992 40.000 8.18 8.18 36.61 3.21
487 490 5.127491 TCAAGAAAAACTTCCCGTGTACAT 58.873 37.500 0.00 0.00 36.61 2.29
488 491 4.515361 TCAAGAAAAACTTCCCGTGTACA 58.485 39.130 0.00 0.00 36.61 2.90
492 540 6.902224 AAAAATCAAGAAAAACTTCCCGTG 57.098 33.333 0.00 0.00 36.61 4.94
518 566 3.447752 TTGCGTACATGTCGACATTTG 57.552 42.857 28.04 21.43 33.61 2.32
525 573 3.420927 CGATGATGATTGCGTACATGTCG 60.421 47.826 0.00 7.49 0.00 4.35
669 2236 0.178990 AAGAGCTGGTTGGTGGGAAC 60.179 55.000 0.00 0.00 0.00 3.62
670 2237 0.110486 GAAGAGCTGGTTGGTGGGAA 59.890 55.000 0.00 0.00 0.00 3.97
671 2238 1.761174 GAAGAGCTGGTTGGTGGGA 59.239 57.895 0.00 0.00 0.00 4.37
672 2239 1.303643 GGAAGAGCTGGTTGGTGGG 60.304 63.158 0.00 0.00 0.00 4.61
673 2240 0.607489 CTGGAAGAGCTGGTTGGTGG 60.607 60.000 0.00 0.00 34.07 4.61
674 2241 1.239968 GCTGGAAGAGCTGGTTGGTG 61.240 60.000 0.00 0.00 45.21 4.17
835 2402 4.402528 CATTGGTCGGCGGGTCCA 62.403 66.667 7.21 11.09 34.01 4.02
1128 2700 2.029964 TCAAAGTCCACCGGCGTC 59.970 61.111 6.01 0.00 0.00 5.19
1129 2701 2.280592 GTCAAAGTCCACCGGCGT 60.281 61.111 6.01 0.00 0.00 5.68
1240 2816 1.666054 TTTGTAAACGGCGTGGAGTT 58.334 45.000 15.70 6.61 0.00 3.01
1241 2817 1.600485 CTTTTGTAAACGGCGTGGAGT 59.400 47.619 15.70 1.72 0.00 3.85
1242 2818 1.069500 CCTTTTGTAAACGGCGTGGAG 60.069 52.381 15.70 4.03 0.00 3.86
1243 2819 0.945813 CCTTTTGTAAACGGCGTGGA 59.054 50.000 15.70 0.50 0.00 4.02
1244 2820 0.039888 CCCTTTTGTAAACGGCGTGG 60.040 55.000 15.70 7.64 0.00 4.94
1245 2821 0.039888 CCCCTTTTGTAAACGGCGTG 60.040 55.000 15.70 0.00 0.00 5.34
1246 2822 0.179023 TCCCCTTTTGTAAACGGCGT 60.179 50.000 6.77 6.77 0.00 5.68
1247 2823 0.953003 TTCCCCTTTTGTAAACGGCG 59.047 50.000 4.80 4.80 0.00 6.46
1248 2824 1.682323 TGTTCCCCTTTTGTAAACGGC 59.318 47.619 0.00 0.00 0.00 5.68
1249 2825 2.688958 TGTGTTCCCCTTTTGTAAACGG 59.311 45.455 0.00 0.00 0.00 4.44
1250 2826 4.577834 ATGTGTTCCCCTTTTGTAAACG 57.422 40.909 0.00 0.00 0.00 3.60
1251 2827 7.046292 AGTTATGTGTTCCCCTTTTGTAAAC 57.954 36.000 0.00 0.00 0.00 2.01
1252 2828 7.041235 CGTAGTTATGTGTTCCCCTTTTGTAAA 60.041 37.037 0.00 0.00 0.00 2.01
1253 2829 6.427547 CGTAGTTATGTGTTCCCCTTTTGTAA 59.572 38.462 0.00 0.00 0.00 2.41
1254 2830 5.933463 CGTAGTTATGTGTTCCCCTTTTGTA 59.067 40.000 0.00 0.00 0.00 2.41
1255 2831 4.758165 CGTAGTTATGTGTTCCCCTTTTGT 59.242 41.667 0.00 0.00 0.00 2.83
1256 2832 4.379082 GCGTAGTTATGTGTTCCCCTTTTG 60.379 45.833 0.00 0.00 0.00 2.44
1257 2833 3.754850 GCGTAGTTATGTGTTCCCCTTTT 59.245 43.478 0.00 0.00 0.00 2.27
1258 2834 3.244630 TGCGTAGTTATGTGTTCCCCTTT 60.245 43.478 0.00 0.00 0.00 3.11
1259 2835 2.303600 TGCGTAGTTATGTGTTCCCCTT 59.696 45.455 0.00 0.00 0.00 3.95
1260 2836 1.903860 TGCGTAGTTATGTGTTCCCCT 59.096 47.619 0.00 0.00 0.00 4.79
1261 2837 2.389962 TGCGTAGTTATGTGTTCCCC 57.610 50.000 0.00 0.00 0.00 4.81
1262 2838 4.658071 CAAATGCGTAGTTATGTGTTCCC 58.342 43.478 0.00 0.00 0.00 3.97
1263 2839 4.095610 GCAAATGCGTAGTTATGTGTTCC 58.904 43.478 0.00 0.00 0.00 3.62
1279 2862 0.179181 CGCTGTGGCACTAGCAAATG 60.179 55.000 28.57 16.10 44.61 2.32
1352 2935 9.146984 ACGAACAAAGAAATTGAGTATCGAATA 57.853 29.630 0.00 0.00 41.85 1.75
1381 2964 0.883833 AAAAGGCGCTTCTCATGTGG 59.116 50.000 7.64 0.00 0.00 4.17
1556 3140 9.858247 GCCAAAAAGTACAAATTTAGTAAAAGC 57.142 29.630 0.00 0.00 0.00 3.51
1740 3480 1.406898 CTAGAGCTCATCGCCTGTCAA 59.593 52.381 17.77 0.00 40.39 3.18
1744 3484 2.881513 TCTAACTAGAGCTCATCGCCTG 59.118 50.000 17.77 0.44 40.39 4.85
1770 3510 2.668144 TTGGGGAAAGTGTAACCCTG 57.332 50.000 0.00 0.00 43.72 4.45
1799 3539 3.754188 ACTGTAAGGTACACGATCGAC 57.246 47.619 24.34 9.67 39.30 4.20
1935 3675 7.283354 CCTAGTCATTCAAACCTATTTCCTTCC 59.717 40.741 0.00 0.00 0.00 3.46
1940 3680 5.815740 TCGCCTAGTCATTCAAACCTATTTC 59.184 40.000 0.00 0.00 0.00 2.17
1951 3691 4.314740 AGAACTCATCGCCTAGTCATTC 57.685 45.455 0.00 0.00 0.00 2.67
2001 3741 8.141909 AGCTACGTATTGAGCAACTATTATTGA 58.858 33.333 10.48 0.00 41.36 2.57
2068 3816 1.694150 AGTTGCAGGCTTCTAGTCACA 59.306 47.619 0.00 0.00 0.00 3.58
2069 3817 2.464157 AGTTGCAGGCTTCTAGTCAC 57.536 50.000 0.00 0.00 0.00 3.67
2070 3818 4.202315 TGTTAAGTTGCAGGCTTCTAGTCA 60.202 41.667 8.57 2.11 0.00 3.41
2071 3819 4.315803 TGTTAAGTTGCAGGCTTCTAGTC 58.684 43.478 8.57 0.00 0.00 2.59
2205 3954 5.775195 GCTTATTATTTCCTTGTGGGGCTAT 59.225 40.000 0.00 0.00 35.33 2.97
2209 3958 6.601332 TCTAGCTTATTATTTCCTTGTGGGG 58.399 40.000 0.00 0.00 35.33 4.96
2241 3993 2.202395 TGCTCCCACCTTTTGCTGC 61.202 57.895 0.00 0.00 0.00 5.25
2244 3996 1.616159 TTAGTGCTCCCACCTTTTGC 58.384 50.000 0.00 0.00 43.09 3.68
2508 4264 8.976986 AGTTGCATGTTGAGAGAATTAAATTC 57.023 30.769 0.00 0.00 39.56 2.17
2714 4470 7.361885 GGAATTGGATGCAGCTATTTCTATGAG 60.362 40.741 18.26 0.00 0.00 2.90
2784 4540 4.399004 AGAGAATACTCCATGTGCACTC 57.601 45.455 19.41 3.52 43.53 3.51
2849 4605 8.296713 GGAACAGCAACTTCATAAGAAATGTTA 58.703 33.333 0.00 0.00 32.35 2.41
3200 5193 3.209410 CACTTACTGGGCATCATCCTTC 58.791 50.000 0.00 0.00 0.00 3.46
3273 5266 9.817809 TTCAGAGGCGGATGAAATTATATATAC 57.182 33.333 0.00 0.00 32.66 1.47
3291 5284 0.322816 TGGCCAGACATTTCAGAGGC 60.323 55.000 0.00 0.00 41.29 4.70
3315 5308 7.116075 CACTGTTTGGATATTCCCATGAATT 57.884 36.000 0.00 0.00 41.44 2.17
3352 5345 4.567747 GGGTCTACCAATTTCCATGTGACT 60.568 45.833 0.81 0.00 39.85 3.41
3404 5397 8.822805 ACTGTTTAGAAACTATTCTGGATACCA 58.177 33.333 6.69 0.00 45.47 3.25
3844 5837 5.645497 ACAGATACTTTCTCATGCTTTGGTC 59.355 40.000 0.00 0.00 29.93 4.02
3930 5924 5.984725 TCGGCTATGGAAGTATTCTTTCAA 58.015 37.500 0.00 0.00 46.56 2.69
3972 5966 9.102757 CTCTAGCTAACAGCAAGATTTCAAATA 57.897 33.333 0.38 0.00 45.56 1.40
4072 6067 8.719648 CATTATTTATTTTGCAAACAGAAGGCA 58.280 29.630 12.39 0.00 35.41 4.75
4112 6108 4.882671 GTGGATCACACATGATTGGTAC 57.117 45.455 0.00 0.00 46.01 3.34
4252 6248 6.311935 TGGTATCGAGAACCAAAAACGATAAG 59.688 38.462 17.62 0.00 43.99 1.73
4253 6249 6.164876 TGGTATCGAGAACCAAAAACGATAA 58.835 36.000 17.62 0.00 43.99 1.75
4376 6372 2.850130 TGGGGCGGGTGTGTTAGT 60.850 61.111 0.00 0.00 0.00 2.24
4396 6392 2.687935 GTGCATAGGGTATGGTGGTTTG 59.312 50.000 0.00 0.00 36.68 2.93
4408 6404 1.019278 GGACGTGTGTGTGCATAGGG 61.019 60.000 0.00 0.00 0.00 3.53
4425 6421 4.141287 CTGGTTCAATGGTAAACACTGGA 58.859 43.478 0.00 0.00 0.00 3.86
4428 6424 6.294508 GCAATACTGGTTCAATGGTAAACACT 60.295 38.462 0.00 0.00 0.00 3.55
4429 6425 5.861787 GCAATACTGGTTCAATGGTAAACAC 59.138 40.000 0.00 0.00 0.00 3.32
4446 6443 5.178797 GTGTCATACCTTCACAGCAATACT 58.821 41.667 0.00 0.00 33.04 2.12
4487 6484 1.000896 CCAGCCGGGTTCAATCCTT 60.001 57.895 1.64 0.00 0.00 3.36
4488 6485 2.677228 CCAGCCGGGTTCAATCCT 59.323 61.111 1.64 0.00 0.00 3.24
4537 6534 9.153721 CAATTTATGTGTGAAATAAGCCATGTT 57.846 29.630 0.00 0.00 0.00 2.71
4575 6572 7.872483 ACAATGAACACTTCAGTTTCAAAAACT 59.128 29.630 0.00 0.00 43.98 2.66
4581 6579 5.066375 CCTCACAATGAACACTTCAGTTTCA 59.934 40.000 0.00 6.89 43.98 2.69
4582 6580 5.514279 CCTCACAATGAACACTTCAGTTTC 58.486 41.667 0.00 0.00 43.98 2.78
4762 7799 7.656137 GTGTGTATTCTAAACAGGAGAGAAACA 59.344 37.037 0.00 0.00 33.15 2.83
4770 7807 4.525487 ACGAGGTGTGTATTCTAAACAGGA 59.475 41.667 0.00 0.00 0.00 3.86
4773 7810 4.525487 AGGACGAGGTGTGTATTCTAAACA 59.475 41.667 0.00 0.00 0.00 2.83
4822 7859 7.442969 CAGGTGTAAATTACTGGTCAACACTTA 59.557 37.037 4.67 0.00 36.77 2.24
4905 7942 3.119708 GGGCAATAGACTTGCTTGTGAAG 60.120 47.826 9.54 0.00 44.36 3.02
4992 8030 7.643579 AGAAACTGTTAAGAAAGAACTCATGC 58.356 34.615 0.00 0.00 0.00 4.06
5040 8081 2.235016 GGCATAGTTGAACAACACCCA 58.765 47.619 17.85 3.04 43.47 4.51
5083 8124 2.939103 GACATATGGAGCACCTGTCAAC 59.061 50.000 13.74 0.00 38.18 3.18
5131 8172 6.652900 TGTTGACATGTCGGAATGATTCTTAA 59.347 34.615 20.54 2.10 0.00 1.85
5333 8374 3.054875 TCTGTGAGAATGATGAACAGGGG 60.055 47.826 0.00 0.00 38.97 4.79
5447 8488 6.743575 ATCTATTACATATTCCCGCTTTGC 57.256 37.500 0.00 0.00 0.00 3.68
5525 8566 8.882415 ATGTTTACACATTACCTATAACGAGG 57.118 34.615 0.00 0.00 41.16 4.63
5545 8586 6.893958 TTGCGAAATGTACAACAAATGTTT 57.106 29.167 0.00 0.00 43.63 2.83
5568 8609 9.698309 GACATAACACTGTATGCTAATCTACAT 57.302 33.333 0.00 0.00 35.26 2.29
5574 8615 8.450964 GTTTGTGACATAACACTGTATGCTAAT 58.549 33.333 0.00 0.00 40.87 1.73
5576 8617 6.931840 TGTTTGTGACATAACACTGTATGCTA 59.068 34.615 8.52 0.00 40.87 3.49
5593 8634 6.266168 ACAGAACATTGAAAGTGTTTGTGA 57.734 33.333 0.00 0.00 39.72 3.58
5615 8658 7.408132 TTTGCGATATACAGAGCATTAGAAC 57.592 36.000 0.00 0.00 39.50 3.01
5653 8696 9.807649 GTTCAGCAATTTATCTAACATCCAATT 57.192 29.630 0.00 0.00 0.00 2.32
5673 8716 4.637534 TGGCAGATAATTCAGAAGTTCAGC 59.362 41.667 5.50 0.00 0.00 4.26
5740 8783 3.055891 CCACAAGCTTAATGAAAAGGGGG 60.056 47.826 10.71 0.00 0.00 5.40
5741 8784 3.578282 ACCACAAGCTTAATGAAAAGGGG 59.422 43.478 10.71 3.96 0.00 4.79
5745 8788 6.040391 AGTTGCTACCACAAGCTTAATGAAAA 59.960 34.615 10.71 0.00 43.19 2.29
5757 8800 2.940994 TGCCTTAGTTGCTACCACAA 57.059 45.000 0.00 0.00 0.00 3.33
5771 8814 1.144913 TCTGCCACCTAAGTTTGCCTT 59.855 47.619 0.00 0.00 37.17 4.35
5807 8850 6.856426 GGAAGATCCAAAGTTTAACAAACTCG 59.144 38.462 4.86 0.74 42.75 4.18
5835 8878 9.884636 TCGGATCATGGGTTATTACATATTTAG 57.115 33.333 0.00 0.00 0.00 1.85
5837 8880 9.010029 GTTCGGATCATGGGTTATTACATATTT 57.990 33.333 0.00 0.00 0.00 1.40
5838 8881 7.333423 CGTTCGGATCATGGGTTATTACATATT 59.667 37.037 0.00 0.00 0.00 1.28
5839 8882 6.816640 CGTTCGGATCATGGGTTATTACATAT 59.183 38.462 0.00 0.00 0.00 1.78
5840 8883 6.160684 CGTTCGGATCATGGGTTATTACATA 58.839 40.000 0.00 0.00 0.00 2.29
5841 8884 4.994852 CGTTCGGATCATGGGTTATTACAT 59.005 41.667 0.00 0.00 0.00 2.29
5842 8885 4.373527 CGTTCGGATCATGGGTTATTACA 58.626 43.478 0.00 0.00 0.00 2.41
5843 8886 3.744426 CCGTTCGGATCATGGGTTATTAC 59.256 47.826 5.19 0.00 0.00 1.89
5844 8887 3.388676 ACCGTTCGGATCATGGGTTATTA 59.611 43.478 18.28 0.00 0.00 0.98
5845 8888 2.171870 ACCGTTCGGATCATGGGTTATT 59.828 45.455 18.28 0.00 0.00 1.40
5846 8889 1.766496 ACCGTTCGGATCATGGGTTAT 59.234 47.619 18.28 0.00 0.00 1.89
5847 8890 1.196911 ACCGTTCGGATCATGGGTTA 58.803 50.000 18.28 0.00 0.00 2.85
5848 8891 0.326927 AACCGTTCGGATCATGGGTT 59.673 50.000 18.28 0.00 33.17 4.11
5849 8892 0.107848 GAACCGTTCGGATCATGGGT 60.108 55.000 18.28 0.00 0.00 4.51
5850 8893 0.107897 TGAACCGTTCGGATCATGGG 60.108 55.000 17.61 0.00 33.17 4.00
5851 8894 1.134818 TCTGAACCGTTCGGATCATGG 60.135 52.381 20.71 12.52 40.04 3.66
5852 8895 2.293677 TCTGAACCGTTCGGATCATG 57.706 50.000 20.71 15.44 40.04 3.07
5858 8901 1.542544 GTCGTATCTGAACCGTTCGG 58.457 55.000 13.17 13.17 37.39 4.30
5859 8902 1.177668 CGTCGTATCTGAACCGTTCG 58.822 55.000 6.78 2.39 0.00 3.95
5860 8903 2.532531 TCGTCGTATCTGAACCGTTC 57.467 50.000 4.18 4.18 0.00 3.95
5861 8904 2.538333 CGATCGTCGTATCTGAACCGTT 60.538 50.000 7.03 0.00 34.72 4.44
5862 8905 1.004185 CGATCGTCGTATCTGAACCGT 60.004 52.381 7.03 0.00 34.72 4.83
5863 8906 1.660097 CGATCGTCGTATCTGAACCG 58.340 55.000 7.03 0.00 34.72 4.44
5874 8917 2.230940 GGGCATGTCACGATCGTCG 61.231 63.158 19.84 14.06 46.93 5.12
5875 8918 0.530650 ATGGGCATGTCACGATCGTC 60.531 55.000 19.84 9.04 0.00 4.20
5876 8919 0.530650 GATGGGCATGTCACGATCGT 60.531 55.000 16.60 16.60 0.00 3.73
5877 8920 0.530431 TGATGGGCATGTCACGATCG 60.530 55.000 14.88 14.88 0.00 3.69
5878 8921 1.888215 ATGATGGGCATGTCACGATC 58.112 50.000 0.00 0.00 35.42 3.69
5879 8922 2.369860 AGTATGATGGGCATGTCACGAT 59.630 45.455 0.00 0.00 37.87 3.73
5880 8923 1.762370 AGTATGATGGGCATGTCACGA 59.238 47.619 0.00 0.00 37.87 4.35
5881 8924 2.245159 AGTATGATGGGCATGTCACG 57.755 50.000 0.00 0.00 37.87 4.35
5882 8925 3.544684 TCAAGTATGATGGGCATGTCAC 58.455 45.455 0.00 0.00 37.87 3.67
5883 8926 3.812262 CTCAAGTATGATGGGCATGTCA 58.188 45.455 0.00 0.00 37.87 3.58
5884 8927 2.551459 GCTCAAGTATGATGGGCATGTC 59.449 50.000 0.00 0.00 43.87 3.06
5885 8928 2.174210 AGCTCAAGTATGATGGGCATGT 59.826 45.455 0.81 0.00 46.90 3.21
5886 8929 2.812591 GAGCTCAAGTATGATGGGCATG 59.187 50.000 9.40 0.00 46.90 4.06
5887 8930 2.709934 AGAGCTCAAGTATGATGGGCAT 59.290 45.455 17.77 0.00 46.90 4.40
5888 8931 2.121948 AGAGCTCAAGTATGATGGGCA 58.878 47.619 17.77 0.00 46.90 5.36
5889 8932 2.926778 AGAGCTCAAGTATGATGGGC 57.073 50.000 17.77 0.00 44.80 5.36
5890 8933 6.638610 CCTATAAGAGCTCAAGTATGATGGG 58.361 44.000 17.77 0.76 34.37 4.00
5891 8934 6.070881 AGCCTATAAGAGCTCAAGTATGATGG 60.071 42.308 17.77 13.57 32.71 3.51
5892 8935 6.812656 CAGCCTATAAGAGCTCAAGTATGATG 59.187 42.308 17.77 5.36 37.18 3.07
5893 8936 6.723515 TCAGCCTATAAGAGCTCAAGTATGAT 59.276 38.462 17.77 0.00 37.18 2.45
5897 8940 6.071320 TCATCAGCCTATAAGAGCTCAAGTA 58.929 40.000 17.77 5.37 37.18 2.24
5949 8992 6.340522 ACAGGCTTATCAATTTTTGCATACC 58.659 36.000 0.00 0.00 0.00 2.73
5961 9004 2.736144 AACGACGACAGGCTTATCAA 57.264 45.000 0.00 0.00 0.00 2.57
5973 9020 4.804665 TGTTTACACTGATGAAAACGACGA 59.195 37.500 0.00 0.00 35.16 4.20
6111 9158 6.968131 TCGACATGAAAATTAGAGTTGGAG 57.032 37.500 0.00 0.00 0.00 3.86
6221 9277 4.196193 AGCCTAGAGATCCTAATCGATCG 58.804 47.826 9.36 9.36 42.94 3.69


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

AutoCloner maintained by Alex Coulton.