Multiple sequence alignment - TraesCS4D01G136500

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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 TraesCS4D01G136500 chr4D 100.000 5339 0 0 1 5339 122304995 122299657 0.000000e+00 9860.0
1 TraesCS4D01G136500 chr4D 95.745 752 23 3 4094 4837 247161255 247162005 0.000000e+00 1203.0
2 TraesCS4D01G136500 chr4D 97.306 297 8 0 1 297 122319263 122318967 6.170000e-139 505.0
3 TraesCS4D01G136500 chr4D 85.455 55 6 2 2155 2208 122259133 122259080 7.470000e-04 56.5
4 TraesCS4D01G136500 chr4A 94.483 4695 167 24 683 5317 447776393 447781055 0.000000e+00 7151.0
5 TraesCS4D01G136500 chr4A 74.920 622 109 29 2143 2757 579372448 579371867 1.920000e-59 241.0
6 TraesCS4D01G136500 chr4A 93.548 62 3 1 4282 4343 689656564 689656504 2.050000e-14 91.6
7 TraesCS4D01G136500 chr4B 94.227 3776 146 28 592 4326 186610112 186606368 0.000000e+00 5699.0
8 TraesCS4D01G136500 chr4B 92.150 293 15 4 296 588 594692619 594692903 1.790000e-109 407.0
9 TraesCS4D01G136500 chr4B 90.498 221 14 3 4949 5165 186605792 186605575 8.750000e-73 285.0
10 TraesCS4D01G136500 chr4B 82.803 314 34 13 4382 4688 186606361 186606061 4.100000e-66 263.0
11 TraesCS4D01G136500 chr4B 84.375 160 6 7 5167 5317 186605411 186605262 7.210000e-29 139.0
12 TraesCS4D01G136500 chr4B 86.179 123 7 4 4742 4857 186606059 186605940 2.020000e-24 124.0
13 TraesCS4D01G136500 chr4B 88.158 76 7 2 1462 1536 185223035 185222961 7.360000e-14 89.8
14 TraesCS4D01G136500 chr4B 85.965 57 6 2 2153 2208 185869183 185869128 5.770000e-05 60.2
15 TraesCS4D01G136500 chrUn 94.889 763 20 5 4092 4837 1734651 1735411 0.000000e+00 1175.0
16 TraesCS4D01G136500 chr7D 75.475 1578 334 36 2143 3710 126682326 126683860 0.000000e+00 721.0
17 TraesCS4D01G136500 chr7D 75.143 1573 350 27 2143 3708 126506757 126505219 0.000000e+00 701.0
18 TraesCS4D01G136500 chr7D 92.542 295 18 2 3 297 382663540 382663830 2.300000e-113 420.0
19 TraesCS4D01G136500 chr7D 92.542 295 18 2 3 297 382722012 382722302 2.300000e-113 420.0
20 TraesCS4D01G136500 chr7D 92.359 301 14 3 292 592 382722372 382722663 2.300000e-113 420.0
21 TraesCS4D01G136500 chr7D 92.203 295 19 2 3 297 382694297 382694587 1.070000e-111 414.0
22 TraesCS4D01G136500 chr7D 75.241 622 107 29 2143 2757 88363062 88362481 8.880000e-63 252.0
23 TraesCS4D01G136500 chr7D 83.756 197 23 7 1386 1582 126681707 126681894 1.530000e-40 178.0
24 TraesCS4D01G136500 chr7D 87.970 133 16 0 1450 1582 126507324 126507192 1.990000e-34 158.0
25 TraesCS4D01G136500 chr7A 75.235 1595 341 36 2143 3722 127607944 127609499 0.000000e+00 708.0
26 TraesCS4D01G136500 chr7A 84.772 197 21 7 1386 1582 127607280 127607467 7.060000e-44 189.0
27 TraesCS4D01G136500 chr7B 75.143 1577 346 30 2143 3708 87173738 87172197 0.000000e+00 699.0
28 TraesCS4D01G136500 chr7B 74.811 1588 346 34 2144 3722 88245916 88247458 0.000000e+00 667.0
29 TraesCS4D01G136500 chr7B 91.582 297 23 1 1 297 613508528 613508234 4.980000e-110 409.0
30 TraesCS4D01G136500 chr7B 83.824 204 24 8 1379 1582 88245271 88245465 9.130000e-43 185.0
31 TraesCS4D01G136500 chr7B 83.333 192 23 7 1386 1577 87174357 87174175 9.200000e-38 169.0
32 TraesCS4D01G136500 chr7B 84.706 170 15 6 4519 4688 85571361 85571203 5.530000e-35 159.0
33 TraesCS4D01G136500 chr3B 92.891 422 28 2 3906 4326 810362193 810361773 3.530000e-171 612.0
34 TraesCS4D01G136500 chr3B 87.600 500 47 8 1450 1936 71265542 71265045 2.790000e-157 566.0
35 TraesCS4D01G136500 chr3B 86.200 500 52 4 1450 1933 52169325 52169823 4.740000e-145 525.0
36 TraesCS4D01G136500 chr3B 75.325 616 105 29 2143 2751 419312409 419312984 8.880000e-63 252.0
37 TraesCS4D01G136500 chr3B 89.655 116 9 2 4742 4857 810361470 810361358 1.550000e-30 145.0
38 TraesCS4D01G136500 chr5B 88.330 497 43 3 1450 1933 466422526 466423020 2.770000e-162 582.0
39 TraesCS4D01G136500 chr5B 90.179 112 8 2 4742 4853 49006975 49006867 5.570000e-30 143.0
40 TraesCS4D01G136500 chr2D 92.256 297 21 1 1 297 564413162 564413456 2.300000e-113 420.0
41 TraesCS4D01G136500 chr2D 91.946 298 21 2 1 297 632502592 632502887 1.070000e-111 414.0
42 TraesCS4D01G136500 chr2D 92.256 297 14 5 292 588 632502957 632503244 3.850000e-111 412.0
43 TraesCS4D01G136500 chr1D 92.230 296 19 3 1 295 209752570 209752862 2.970000e-112 416.0
44 TraesCS4D01G136500 chr1D 92.256 297 15 4 1 297 182684383 182684671 1.070000e-111 414.0
45 TraesCS4D01G136500 chr5D 92.282 298 14 4 292 589 1807638 1807350 1.070000e-111 414.0
46 TraesCS4D01G136500 chr5D 75.040 621 108 26 2143 2757 457998916 457998337 1.490000e-60 244.0
47 TraesCS4D01G136500 chr6B 91.919 297 15 5 292 588 122960008 122960295 1.790000e-109 407.0
48 TraesCS4D01G136500 chr6B 88.924 316 27 2 4197 4505 17991723 17991409 3.020000e-102 383.0
49 TraesCS4D01G136500 chr6D 91.333 300 17 3 292 591 391651672 391651382 8.330000e-108 401.0
50 TraesCS4D01G136500 chr6D 85.870 184 23 2 4324 4505 9868139 9868321 5.460000e-45 193.0
51 TraesCS4D01G136500 chr6D 93.000 100 7 0 4226 4325 9864290 9864389 4.310000e-31 147.0
52 TraesCS4D01G136500 chr1B 91.333 300 14 5 292 591 6032121 6031834 3.000000e-107 399.0
53 TraesCS4D01G136500 chr1B 91.000 300 18 3 292 591 6037515 6037225 3.880000e-106 396.0
54 TraesCS4D01G136500 chr6A 91.000 300 18 3 292 591 487698666 487698376 3.880000e-106 396.0
55 TraesCS4D01G136500 chr6A 100.000 31 0 0 4475 4505 11013449 11013479 2.080000e-04 58.4
56 TraesCS4D01G136500 chr1A 97.487 199 5 0 4639 4837 568949158 568949356 1.840000e-89 340.0
57 TraesCS4D01G136500 chr3D 75.728 618 105 30 2146 2757 538375091 538374513 8.810000e-68 268.0
58 TraesCS4D01G136500 chr2B 89.286 112 9 2 4742 4853 618098644 618098752 2.590000e-28 137.0


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 TraesCS4D01G136500 chr4D 122299657 122304995 5338 True 9860.0 9860 100.0000 1 5339 1 chr4D.!!$R2 5338
1 TraesCS4D01G136500 chr4D 247161255 247162005 750 False 1203.0 1203 95.7450 4094 4837 1 chr4D.!!$F1 743
2 TraesCS4D01G136500 chr4A 447776393 447781055 4662 False 7151.0 7151 94.4830 683 5317 1 chr4A.!!$F1 4634
3 TraesCS4D01G136500 chr4A 579371867 579372448 581 True 241.0 241 74.9200 2143 2757 1 chr4A.!!$R1 614
4 TraesCS4D01G136500 chr4B 186605262 186610112 4850 True 1302.0 5699 87.6164 592 5317 5 chr4B.!!$R3 4725
5 TraesCS4D01G136500 chrUn 1734651 1735411 760 False 1175.0 1175 94.8890 4092 4837 1 chrUn.!!$F1 745
6 TraesCS4D01G136500 chr7D 126681707 126683860 2153 False 449.5 721 79.6155 1386 3710 2 chr7D.!!$F3 2324
7 TraesCS4D01G136500 chr7D 126505219 126507324 2105 True 429.5 701 81.5565 1450 3708 2 chr7D.!!$R2 2258
8 TraesCS4D01G136500 chr7D 382722012 382722663 651 False 420.0 420 92.4505 3 592 2 chr7D.!!$F4 589
9 TraesCS4D01G136500 chr7D 88362481 88363062 581 True 252.0 252 75.2410 2143 2757 1 chr7D.!!$R1 614
10 TraesCS4D01G136500 chr7A 127607280 127609499 2219 False 448.5 708 80.0035 1386 3722 2 chr7A.!!$F1 2336
11 TraesCS4D01G136500 chr7B 87172197 87174357 2160 True 434.0 699 79.2380 1386 3708 2 chr7B.!!$R3 2322
12 TraesCS4D01G136500 chr7B 88245271 88247458 2187 False 426.0 667 79.3175 1379 3722 2 chr7B.!!$F1 2343
13 TraesCS4D01G136500 chr3B 810361358 810362193 835 True 378.5 612 91.2730 3906 4857 2 chr3B.!!$R2 951
14 TraesCS4D01G136500 chr3B 419312409 419312984 575 False 252.0 252 75.3250 2143 2751 1 chr3B.!!$F2 608
15 TraesCS4D01G136500 chr2D 632502592 632503244 652 False 413.0 414 92.1010 1 588 2 chr2D.!!$F2 587
16 TraesCS4D01G136500 chr5D 457998337 457998916 579 True 244.0 244 75.0400 2143 2757 1 chr5D.!!$R2 614
17 TraesCS4D01G136500 chr3D 538374513 538375091 578 True 268.0 268 75.7280 2146 2757 1 chr3D.!!$R1 611

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
340 416 0.108472 CGCTGCTGACAAGAGGATCA 60.108 55.0 0.0 0.00 37.82 2.92 F
1047 1151 0.397816 CTCGTCCCATCCCTTCCTCT 60.398 60.0 0.0 0.00 0.00 3.69 F
1318 1424 0.243907 CCTCCGTCCATATACGCCAG 59.756 60.0 0.0 0.00 41.51 4.85 F
2249 2484 0.323087 ATTTCCAACAGGCCGGTACC 60.323 55.0 9.6 0.16 0.00 3.34 F
3423 3670 0.183492 CCATCCCCCGTGACAATGAT 59.817 55.0 0.0 0.00 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1242 1346 0.178876 TGATGTTCTGTGGAGGGGGA 60.179 55.000 0.00 0.0 0.00 4.81 R
2380 2627 2.116533 CCGGCATCATCAGCTTGCA 61.117 57.895 9.41 0.0 38.12 4.08 R
3282 3529 1.026182 TGAACACATCAGGCCGCATC 61.026 55.000 0.00 0.0 33.04 3.91 R
3573 3820 1.234821 CAAGCTTAACAACAGCCGGA 58.765 50.000 5.05 0.0 38.09 5.14 R
4344 4593 2.753029 GGTTCTCCACTGCTGCCT 59.247 61.111 0.00 0.0 0.00 4.75 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
106 108 0.465287 TATGAGGCATCGCAGCTCAA 59.535 50.000 0.00 0.00 34.17 3.02
112 114 0.455633 GCATCGCAGCTCAACCAAAG 60.456 55.000 0.00 0.00 0.00 2.77
150 152 1.071471 CACTGCTCCCTGGTCGTTT 59.929 57.895 0.00 0.00 0.00 3.60
182 184 0.816825 CTGCCTTCGGTGATCCCATG 60.817 60.000 0.00 0.00 0.00 3.66
201 203 2.739704 CCGTCTACCGCGTACACGA 61.740 63.158 15.85 0.00 43.02 4.35
207 209 1.227342 TACCGCGTACACGACTGACA 61.227 55.000 4.92 0.00 43.02 3.58
214 216 2.424557 GTACACGACTGACAGGAGAGA 58.575 52.381 7.51 0.00 0.00 3.10
261 263 1.379977 CCTGTACGGGAGAGAGGCA 60.380 63.158 16.40 0.00 0.00 4.75
280 282 2.354704 GCAATTAGGTTTTTGGGGAGCC 60.355 50.000 0.00 0.00 0.00 4.70
302 378 2.407616 CTACGCGACTGCCGATCA 59.592 61.111 15.93 0.00 41.76 2.92
340 416 0.108472 CGCTGCTGACAAGAGGATCA 60.108 55.000 0.00 0.00 37.82 2.92
345 421 1.137872 GCTGACAAGAGGATCACCGAT 59.862 52.381 0.00 0.00 41.83 4.18
399 475 3.116317 ACTGGCCTACTGGAGGGTATAAT 60.116 47.826 8.30 0.00 46.81 1.28
421 497 2.167662 CATTTACCCCGCTCCTGTTTT 58.832 47.619 0.00 0.00 0.00 2.43
452 528 2.158885 TGTGCAGTACTAGTGGTTTGCA 60.159 45.455 16.39 16.39 41.53 4.08
539 615 3.912496 AGCACTGCCTATGTCATGTTA 57.088 42.857 0.00 0.00 0.00 2.41
542 618 5.928976 AGCACTGCCTATGTCATGTTAATA 58.071 37.500 0.00 0.00 0.00 0.98
630 706 1.007336 GCGAACATGAGACGGACGTT 61.007 55.000 0.00 0.00 0.00 3.99
693 770 1.503818 CGTTTGGGTCGGTCAGTTGG 61.504 60.000 0.00 0.00 0.00 3.77
737 814 3.055328 TGGGGATGGATGCTATTTCTGA 58.945 45.455 0.00 0.00 0.00 3.27
749 826 5.419542 TGCTATTTCTGATTGCTCGTACTT 58.580 37.500 0.00 0.00 0.00 2.24
770 847 7.237920 ACTTATTGCAAAGCTTTTTCAAGTG 57.762 32.000 21.19 16.73 31.86 3.16
775 859 4.082300 TGCAAAGCTTTTTCAAGTGTCTCA 60.082 37.500 9.53 0.00 31.86 3.27
779 863 2.287009 GCTTTTTCAAGTGTCTCACCGG 60.287 50.000 0.00 0.00 34.49 5.28
799 883 0.687757 CCATGTCCCCTCTCCTCGAA 60.688 60.000 0.00 0.00 0.00 3.71
812 896 0.457851 CCTCGAAGTCTCCATCGCTT 59.542 55.000 0.00 0.00 38.87 4.68
833 917 4.717629 TGGCGCGACGACAGAAGG 62.718 66.667 12.10 0.00 41.22 3.46
952 1042 2.040544 AACGGCCCAGATGAAAGCG 61.041 57.895 0.00 0.00 0.00 4.68
1047 1151 0.397816 CTCGTCCCATCCCTTCCTCT 60.398 60.000 0.00 0.00 0.00 3.69
1164 1268 1.805428 GAGCTCTCCTCATCCTCGCC 61.805 65.000 6.43 0.00 40.45 5.54
1184 1288 1.689959 GTGCTTGATTTGCTTGGACG 58.310 50.000 0.00 0.00 0.00 4.79
1208 1312 0.681243 GCTCAAACCACTCCCCCATC 60.681 60.000 0.00 0.00 0.00 3.51
1209 1313 0.995024 CTCAAACCACTCCCCCATCT 59.005 55.000 0.00 0.00 0.00 2.90
1214 1318 2.587060 ACCACTCCCCCATCTCATTA 57.413 50.000 0.00 0.00 0.00 1.90
1215 1319 3.080660 ACCACTCCCCCATCTCATTAT 57.919 47.619 0.00 0.00 0.00 1.28
1241 1345 0.397187 CCAGCTCATCTCCCATCCAG 59.603 60.000 0.00 0.00 0.00 3.86
1242 1346 1.129917 CAGCTCATCTCCCATCCAGT 58.870 55.000 0.00 0.00 0.00 4.00
1248 1353 1.617181 ATCTCCCATCCAGTCCCCCT 61.617 60.000 0.00 0.00 0.00 4.79
1254 1359 1.307343 ATCCAGTCCCCCTCCACAG 60.307 63.158 0.00 0.00 0.00 3.66
1278 1384 7.761704 CAGAACATCACTAGTACTGTTGCTATT 59.238 37.037 20.85 2.82 32.28 1.73
1279 1385 7.761704 AGAACATCACTAGTACTGTTGCTATTG 59.238 37.037 20.85 2.00 32.28 1.90
1280 1386 5.812642 ACATCACTAGTACTGTTGCTATTGC 59.187 40.000 5.39 0.00 40.20 3.56
1281 1387 5.661056 TCACTAGTACTGTTGCTATTGCT 57.339 39.130 5.39 0.00 40.48 3.91
1282 1388 5.410924 TCACTAGTACTGTTGCTATTGCTG 58.589 41.667 5.39 0.00 40.48 4.41
1283 1389 4.568359 CACTAGTACTGTTGCTATTGCTGG 59.432 45.833 5.39 0.00 40.48 4.85
1284 1390 2.359900 AGTACTGTTGCTATTGCTGGC 58.640 47.619 0.00 0.00 40.48 4.85
1285 1391 2.026822 AGTACTGTTGCTATTGCTGGCT 60.027 45.455 0.00 0.00 40.48 4.75
1286 1392 2.787473 ACTGTTGCTATTGCTGGCTA 57.213 45.000 0.00 0.00 40.48 3.93
1287 1393 3.071874 ACTGTTGCTATTGCTGGCTAA 57.928 42.857 0.00 0.00 40.48 3.09
1288 1394 2.749621 ACTGTTGCTATTGCTGGCTAAC 59.250 45.455 0.00 0.00 40.48 2.34
1289 1395 2.091541 TGTTGCTATTGCTGGCTAACC 58.908 47.619 0.00 0.00 40.48 2.85
1290 1396 1.064060 GTTGCTATTGCTGGCTAACCG 59.936 52.381 0.00 0.00 40.48 4.44
1291 1397 0.251916 TGCTATTGCTGGCTAACCGT 59.748 50.000 0.00 0.00 40.48 4.83
1292 1398 0.938008 GCTATTGCTGGCTAACCGTC 59.062 55.000 0.00 0.00 39.70 4.79
1293 1399 1.742411 GCTATTGCTGGCTAACCGTCA 60.742 52.381 0.00 0.00 39.70 4.35
1294 1400 2.838736 CTATTGCTGGCTAACCGTCAT 58.161 47.619 0.00 0.00 39.70 3.06
1318 1424 0.243907 CCTCCGTCCATATACGCCAG 59.756 60.000 0.00 0.00 41.51 4.85
1321 1427 0.671796 CCGTCCATATACGCCAGACA 59.328 55.000 0.00 0.00 41.51 3.41
1482 1615 2.125188 TCGCGCATGCTCATGGAA 60.125 55.556 17.13 0.00 39.16 3.53
1512 1645 3.316029 TCGACGACAAGTTCTTCTACCAA 59.684 43.478 0.00 0.00 0.00 3.67
1563 1696 1.220749 GCACCACTTCGCCCAGATA 59.779 57.895 0.00 0.00 0.00 1.98
1682 1827 1.507141 GACTCTGCCACAAACACCGG 61.507 60.000 0.00 0.00 0.00 5.28
1882 2102 1.805945 CTCCTCTTTTCCGGCGTCG 60.806 63.158 0.29 0.29 0.00 5.12
2005 2225 0.667487 TCAGAGCTTTGCGACCTTCG 60.667 55.000 0.00 0.00 43.89 3.79
2140 2372 2.356125 GCCTTCTTCAATGGCCAGACTA 60.356 50.000 13.05 0.00 40.71 2.59
2246 2481 1.606313 CCATTTCCAACAGGCCGGT 60.606 57.895 1.28 1.28 0.00 5.28
2249 2484 0.323087 ATTTCCAACAGGCCGGTACC 60.323 55.000 9.60 0.16 0.00 3.34
2380 2627 3.160047 CGGAGGCTGGCAGGAGAT 61.160 66.667 17.64 0.00 0.00 2.75
2766 3013 0.810031 GCCATGTGTATCGGTCGCTT 60.810 55.000 0.00 0.00 0.00 4.68
2982 3229 4.360405 GAAAGGGAAGGCGGGCCA 62.360 66.667 12.97 0.00 38.92 5.36
3153 3400 1.281419 TCCATGCGGAGGACCTAAAA 58.719 50.000 0.00 0.00 35.91 1.52
3163 3410 3.118000 GGAGGACCTAAAAATCGACCCAT 60.118 47.826 0.00 0.00 0.00 4.00
3191 3438 0.817654 CTCATCGTCACCAGCCAGTA 59.182 55.000 0.00 0.00 0.00 2.74
3213 3460 3.499338 TGGTTTCAGCAACTTGATGGAT 58.501 40.909 7.17 0.00 33.99 3.41
3252 3499 2.765807 CAGGACATCCCGAGCCCT 60.766 66.667 0.00 0.00 40.87 5.19
3282 3529 2.161609 GGTCCTTACCAACATTCGCAAG 59.838 50.000 0.00 0.00 45.98 4.01
3423 3670 0.183492 CCATCCCCCGTGACAATGAT 59.817 55.000 0.00 0.00 0.00 2.45
3510 3757 4.315941 GATCGGGTGGATCGGCCC 62.316 72.222 11.92 11.92 42.02 5.80
3808 4055 6.323482 TGTTTAACACATGCCCATGCTATTAT 59.677 34.615 8.11 0.00 42.39 1.28
4032 4280 6.202331 TGATCTTCCTTTCCTAGTGTATGGA 58.798 40.000 0.00 0.00 0.00 3.41
4083 4331 4.763793 AGCAATTTAACAGATCACAGCAGT 59.236 37.500 0.00 0.00 0.00 4.40
4169 4417 6.267471 TGGAAGGTAAAACAGATGCTTGATTT 59.733 34.615 0.00 0.00 0.00 2.17
4206 4454 3.435105 TGGTTGCTCACATTGTTTGAC 57.565 42.857 0.00 0.00 0.00 3.18
4344 4593 6.072893 GCTAAAATGTGTTAAAGAAGACGGGA 60.073 38.462 0.00 0.00 31.46 5.14
4415 4664 5.222079 TGTGTGCCTTATGTCTTCACTTA 57.778 39.130 0.00 0.00 0.00 2.24
4882 5203 0.681733 TGACAGCAGGTTCCTCTCAC 59.318 55.000 0.00 0.00 0.00 3.51
5117 5475 4.456566 GTCCATGGGTTAAACGAAAAGCTA 59.543 41.667 13.02 0.00 0.00 3.32
5217 5744 2.693591 TCTCAGTCTGCGGGGTAATTAG 59.306 50.000 0.00 0.00 0.00 1.73
5222 5749 3.518303 AGTCTGCGGGGTAATTAGACTTT 59.482 43.478 0.00 0.00 43.98 2.66
5231 5758 7.712205 GCGGGGTAATTAGACTTTAACTTATGA 59.288 37.037 0.00 0.00 0.00 2.15
5261 5789 4.083003 GGTCAGAGGTTAGATAGATGCTCG 60.083 50.000 0.00 0.00 0.00 5.03
5280 5809 2.550606 TCGTTGCTTTGTGTGGGTTATC 59.449 45.455 0.00 0.00 0.00 1.75
5317 5847 6.640907 CAGGTTTGAGTTGCCACTTATTTTAC 59.359 38.462 0.00 0.00 31.22 2.01
5318 5848 5.924254 GGTTTGAGTTGCCACTTATTTTACC 59.076 40.000 0.00 0.00 31.22 2.85
5319 5849 5.715434 TTGAGTTGCCACTTATTTTACCC 57.285 39.130 0.00 0.00 31.22 3.69
5320 5850 4.083565 TGAGTTGCCACTTATTTTACCCC 58.916 43.478 0.00 0.00 31.22 4.95
5321 5851 3.086282 AGTTGCCACTTATTTTACCCCG 58.914 45.455 0.00 0.00 0.00 5.73
5322 5852 1.465794 TGCCACTTATTTTACCCCGC 58.534 50.000 0.00 0.00 0.00 6.13
5323 5853 1.271982 TGCCACTTATTTTACCCCGCA 60.272 47.619 0.00 0.00 0.00 5.69
5324 5854 1.819903 GCCACTTATTTTACCCCGCAA 59.180 47.619 0.00 0.00 0.00 4.85
5325 5855 2.231721 GCCACTTATTTTACCCCGCAAA 59.768 45.455 0.00 0.00 0.00 3.68
5326 5856 3.306156 GCCACTTATTTTACCCCGCAAAA 60.306 43.478 0.00 0.00 0.00 2.44
5327 5857 4.799917 GCCACTTATTTTACCCCGCAAAAA 60.800 41.667 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 6.797033 CAGACGTTTCATCTCCATAAAAACAC 59.203 38.462 0.00 0.00 31.72 3.32
78 80 8.127150 AGCTGCGATGCCTCATATATATATAA 57.873 34.615 6.54 0.00 0.00 0.98
79 81 7.394359 TGAGCTGCGATGCCTCATATATATATA 59.606 37.037 4.90 4.92 0.00 0.86
80 82 6.210185 TGAGCTGCGATGCCTCATATATATAT 59.790 38.462 0.00 0.00 0.00 0.86
106 108 4.578928 GGTGTGAAGTGTTGTATCTTTGGT 59.421 41.667 0.00 0.00 0.00 3.67
112 114 3.746492 GTGGAGGTGTGAAGTGTTGTATC 59.254 47.826 0.00 0.00 0.00 2.24
150 152 0.179009 AAGGCAGCAGCAGTGAAAGA 60.179 50.000 2.65 0.00 44.61 2.52
182 184 2.577911 GTGTACGCGGTAGACGGC 60.578 66.667 12.47 2.32 44.51 5.68
201 203 0.116143 AGGCCTTCTCTCCTGTCAGT 59.884 55.000 0.00 0.00 0.00 3.41
214 216 2.117423 CGGGGTTTTGGAGGCCTT 59.883 61.111 6.77 0.00 0.00 4.35
223 225 0.698818 ATCTGGAGAAGCGGGGTTTT 59.301 50.000 0.00 0.00 0.00 2.43
261 263 3.077543 AGAGGCTCCCCAAAAACCTAATT 59.922 43.478 11.71 0.00 0.00 1.40
280 282 2.409651 GGCAGTCGCGTAGGAGAG 59.590 66.667 5.77 0.00 39.92 3.20
399 475 1.575419 ACAGGAGCGGGGTAAATGTA 58.425 50.000 0.00 0.00 0.00 2.29
421 497 6.593770 CCACTAGTACTGCACACATGAAAATA 59.406 38.462 5.39 0.00 0.00 1.40
489 565 7.919690 ACATACTGAATTTTGATGATGTACCG 58.080 34.615 0.00 0.00 0.00 4.02
490 566 8.892723 TGACATACTGAATTTTGATGATGTACC 58.107 33.333 0.00 0.00 0.00 3.34
575 651 9.167311 GTCCATGATACTGTTGAGAAATTAAGT 57.833 33.333 0.00 0.00 0.00 2.24
611 687 1.007336 AACGTCCGTCTCATGTTCGC 61.007 55.000 0.00 0.00 0.00 4.70
630 706 8.657387 TTTTATCTGGTTGGGTGATTAAATGA 57.343 30.769 0.00 0.00 0.00 2.57
693 770 6.405286 CCATACCGAATCCAGTAGATCATCTC 60.405 46.154 0.00 0.00 32.47 2.75
737 814 4.396166 AGCTTTGCAATAAGTACGAGCAAT 59.604 37.500 15.64 0.00 43.71 3.56
749 826 6.572519 AGACACTTGAAAAAGCTTTGCAATA 58.427 32.000 21.14 7.15 0.00 1.90
770 847 2.125106 GGACATGGCCGGTGAGAC 60.125 66.667 0.00 5.74 0.00 3.36
775 859 4.741239 AGAGGGGACATGGCCGGT 62.741 66.667 12.68 0.00 0.00 5.28
779 863 2.801631 CGAGGAGAGGGGACATGGC 61.802 68.421 0.00 0.00 0.00 4.40
799 883 1.202580 GCCATGTAAGCGATGGAGACT 60.203 52.381 4.34 0.00 42.81 3.24
812 896 2.202557 CTGTCGTCGCGCCATGTA 60.203 61.111 0.00 0.00 0.00 2.29
831 915 1.529244 GCTGTTGTCAACTGGGCCT 60.529 57.895 20.28 0.00 0.00 5.19
832 916 2.908073 CGCTGTTGTCAACTGGGCC 61.908 63.158 21.16 0.00 36.72 5.80
833 917 2.639286 CGCTGTTGTCAACTGGGC 59.361 61.111 21.16 17.55 36.72 5.36
1078 1182 3.023118 CAGATGCAGATGCGGCTG 58.977 61.111 10.87 10.87 45.83 4.85
1079 1183 2.900838 GCAGATGCAGATGCGGCT 60.901 61.111 9.85 0.00 45.83 5.52
1156 1260 0.392998 AAATCAAGCACGGCGAGGAT 60.393 50.000 16.62 0.00 0.00 3.24
1164 1268 1.689959 GTCCAAGCAAATCAAGCACG 58.310 50.000 0.00 0.00 0.00 5.34
1184 1288 1.527433 GGGAGTGGTTTGAGCTTGGC 61.527 60.000 0.00 0.00 0.00 4.52
1208 1312 6.887013 AGATGAGCTGGGCTATAATAATGAG 58.113 40.000 0.00 0.00 39.88 2.90
1209 1313 6.126940 GGAGATGAGCTGGGCTATAATAATGA 60.127 42.308 0.00 0.00 39.88 2.57
1214 1318 2.843113 GGGAGATGAGCTGGGCTATAAT 59.157 50.000 0.00 0.00 39.88 1.28
1215 1319 2.260822 GGGAGATGAGCTGGGCTATAA 58.739 52.381 0.00 0.00 39.88 0.98
1241 1345 0.253327 GATGTTCTGTGGAGGGGGAC 59.747 60.000 0.00 0.00 0.00 4.46
1242 1346 0.178876 TGATGTTCTGTGGAGGGGGA 60.179 55.000 0.00 0.00 0.00 4.81
1248 1353 5.077564 ACAGTACTAGTGATGTTCTGTGGA 58.922 41.667 5.39 0.00 41.90 4.02
1254 1359 7.464710 GCAATAGCAACAGTACTAGTGATGTTC 60.465 40.741 19.14 15.01 36.77 3.18
1278 1384 1.153647 CGATGACGGTTAGCCAGCA 60.154 57.895 0.00 0.00 35.72 4.41
1279 1385 2.526120 GCGATGACGGTTAGCCAGC 61.526 63.158 0.00 0.00 40.15 4.85
1280 1386 2.230940 CGCGATGACGGTTAGCCAG 61.231 63.158 0.00 0.00 40.15 4.85
1281 1387 2.202690 CGCGATGACGGTTAGCCA 60.203 61.111 0.00 0.00 40.15 4.75
1282 1388 3.627218 GCGCGATGACGGTTAGCC 61.627 66.667 12.10 0.00 40.15 3.93
1283 1389 3.627218 GGCGCGATGACGGTTAGC 61.627 66.667 12.10 0.00 40.15 3.09
1284 1390 1.944676 GAGGCGCGATGACGGTTAG 60.945 63.158 12.10 0.00 40.15 2.34
1285 1391 2.103538 GAGGCGCGATGACGGTTA 59.896 61.111 12.10 0.00 40.15 2.85
1286 1392 4.814294 GGAGGCGCGATGACGGTT 62.814 66.667 12.10 0.00 40.15 4.44
1292 1398 2.492449 ATATGGACGGAGGCGCGATG 62.492 60.000 12.10 0.00 0.00 3.84
1293 1399 0.963856 TATATGGACGGAGGCGCGAT 60.964 55.000 12.10 0.00 0.00 4.58
1294 1400 1.601477 TATATGGACGGAGGCGCGA 60.601 57.895 12.10 0.00 0.00 5.87
1446 1579 2.011222 GAGATGAAGTCGAGGTCGTCT 58.989 52.381 16.32 16.32 41.73 4.18
1482 1615 1.535833 ACTTGTCGTCGATGTCCTCT 58.464 50.000 4.21 0.00 0.00 3.69
1550 1683 1.341531 CGGAGATTATCTGGGCGAAGT 59.658 52.381 0.00 0.00 0.00 3.01
1563 1696 0.246635 CGGTGTTGGAGTCGGAGATT 59.753 55.000 0.00 0.00 40.67 2.40
1682 1827 0.179070 GGAGGAGGAGGTCGATTTGC 60.179 60.000 0.00 0.00 0.00 3.68
1723 1916 0.610687 GAGGAACAGGAGGTGGAGTG 59.389 60.000 0.00 0.00 0.00 3.51
1821 2014 2.431683 CCCAGGCCGATGTATGGG 59.568 66.667 10.89 10.89 46.14 4.00
2020 2240 3.056328 GGTCTTGGCGTCCTTGGC 61.056 66.667 0.00 0.00 0.00 4.52
2115 2344 2.566824 GCCATTGAAGAAGGCCGAA 58.433 52.632 0.00 0.00 42.58 4.30
2246 2481 4.764336 CGGTGAAGTCGCGCGGTA 62.764 66.667 31.69 8.95 0.00 4.02
2380 2627 2.116533 CCGGCATCATCAGCTTGCA 61.117 57.895 9.41 0.00 38.12 4.08
2982 3229 4.035843 GTGATCCTCACCTCCGGT 57.964 61.111 0.00 0.00 41.37 5.28
3153 3400 2.037772 GAGCACCTCATATGGGTCGATT 59.962 50.000 11.63 1.06 34.44 3.34
3191 3438 3.499338 TCCATCAAGTTGCTGAAACCAT 58.501 40.909 8.27 0.00 39.85 3.55
3213 3460 4.009675 GCCTGTCCATGATAACACTTTCA 58.990 43.478 0.00 0.00 0.00 2.69
3282 3529 1.026182 TGAACACATCAGGCCGCATC 61.026 55.000 0.00 0.00 33.04 3.91
3510 3757 3.496130 CCTGCCATTGCTTATAAGTCTCG 59.504 47.826 13.91 1.55 38.71 4.04
3573 3820 1.234821 CAAGCTTAACAACAGCCGGA 58.765 50.000 5.05 0.00 38.09 5.14
3794 4041 3.908476 TGGTTTCATAATAGCATGGGCA 58.092 40.909 0.00 0.00 44.61 5.36
3808 4055 3.069443 GGGCAAGATTTCTGTTGGTTTCA 59.931 43.478 0.00 0.00 0.00 2.69
3837 4084 6.222389 CAAGCCATCCTGTAATGAAACAAAA 58.778 36.000 0.00 0.00 0.00 2.44
3842 4089 4.016444 GTCCAAGCCATCCTGTAATGAAA 58.984 43.478 0.00 0.00 0.00 2.69
4032 4280 6.155221 TCACCTACAAGAGAAAGAGCATACAT 59.845 38.462 0.00 0.00 0.00 2.29
4059 4307 5.939883 ACTGCTGTGATCTGTTAAATTGCTA 59.060 36.000 0.00 0.00 0.00 3.49
4169 4417 4.118410 CAACCAATGCAACTTTGTTGCTA 58.882 39.130 27.89 18.16 45.13 3.49
4206 4454 1.330521 CATACGGAAAAGATGCACGGG 59.669 52.381 0.00 0.00 0.00 5.28
4344 4593 2.753029 GGTTCTCCACTGCTGCCT 59.247 61.111 0.00 0.00 0.00 4.75
4415 4664 7.362401 GCTTCTCCAACAATTTGATGATAGTGT 60.362 37.037 8.12 0.00 34.24 3.55
4882 5203 7.639162 TTCTAGCTAGAGAAAAAGTGAAACG 57.361 36.000 22.19 0.00 35.49 3.60
4956 5310 6.717540 ACGTATTAGTAGGAGCATCTTCTGAT 59.282 38.462 0.00 0.00 33.73 2.90
5117 5475 6.437477 GGATTTTAACCCATGGACTTCTTCTT 59.563 38.462 15.22 0.00 0.00 2.52
5158 5516 8.617290 AACTAGAAATTGACCAACGATTAACT 57.383 30.769 0.00 0.00 32.79 2.24
5222 5749 8.727100 ACCTCTGACCATATCATCATAAGTTA 57.273 34.615 0.00 0.00 36.48 2.24
5231 5758 9.199645 CATCTATCTAACCTCTGACCATATCAT 57.800 37.037 0.00 0.00 36.48 2.45
5261 5789 5.183140 ACATAGATAACCCACACAAAGCAAC 59.817 40.000 0.00 0.00 0.00 4.17
5280 5809 3.254166 ACTCAAACCTGCAAAGCACATAG 59.746 43.478 0.00 0.00 33.79 2.23


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

AutoCloner maintained by Alex Coulton.