Multiple sequence alignment - TraesCS2A01G371400

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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 TraesCS2A01G371400 chr2A 100.000 4424 0 0 1 4424 613878035 613873612 0.000000e+00 8170.0
1 TraesCS2A01G371400 chr2A 98.682 759 10 0 3666 4424 751242632 751243390 0.000000e+00 1347.0
2 TraesCS2A01G371400 chr2A 84.977 872 66 29 1637 2462 613700419 613699567 0.000000e+00 824.0
3 TraesCS2A01G371400 chr2A 89.205 667 57 7 1 660 613703397 613702739 0.000000e+00 819.0
4 TraesCS2A01G371400 chr2A 82.615 673 73 27 723 1382 613701060 613700419 5.000000e-154 555.0
5 TraesCS2A01G371400 chr2A 94.064 219 13 0 3231 3449 613699577 613699359 2.550000e-87 333.0
6 TraesCS2A01G371400 chr2A 77.143 525 97 17 1943 2462 613689327 613688821 2.600000e-72 283.0
7 TraesCS2A01G371400 chr2A 83.019 265 41 3 1111 1374 613689773 613689512 2.060000e-58 237.0
8 TraesCS2A01G371400 chr2A 81.579 190 34 1 2273 2462 613476665 613476477 5.920000e-34 156.0
9 TraesCS2A01G371400 chr2A 86.087 115 10 2 1431 1539 532857964 532857850 7.770000e-23 119.0
10 TraesCS2A01G371400 chr2A 95.714 70 2 1 671 739 613702760 613702691 1.300000e-20 111.0
11 TraesCS2A01G371400 chr2A 90.278 72 7 0 3159 3230 761054247 761054318 1.310000e-15 95.3
12 TraesCS2A01G371400 chr2B 91.708 1423 68 25 1 1380 551566773 551565358 0.000000e+00 1929.0
13 TraesCS2A01G371400 chr2B 89.201 713 49 9 1 703 551534586 551533892 0.000000e+00 865.0
14 TraesCS2A01G371400 chr2B 87.896 537 44 9 1933 2462 551564953 551564431 2.920000e-171 612.0
15 TraesCS2A01G371400 chr2B 96.137 233 9 0 3231 3463 551564441 551564209 8.980000e-102 381.0
16 TraesCS2A01G371400 chr2B 77.481 524 94 18 1943 2462 551399097 551398594 4.330000e-75 292.0
17 TraesCS2A01G371400 chr2B 85.586 222 18 7 1640 1861 551565356 551565149 2.070000e-53 220.0
18 TraesCS2A01G371400 chr2B 76.408 373 65 18 2093 2462 551481174 551480822 3.520000e-41 180.0
19 TraesCS2A01G371400 chr2B 83.607 183 30 0 2275 2457 551448882 551448700 5.880000e-39 172.0
20 TraesCS2A01G371400 chr2B 93.651 63 4 0 3605 3667 551563711 551563649 1.310000e-15 95.3
21 TraesCS2A01G371400 chr7A 99.078 759 7 0 3666 4424 701589916 701589158 0.000000e+00 1363.0
22 TraesCS2A01G371400 chr7A 96.667 780 19 4 2459 3231 110546007 110546786 0.000000e+00 1290.0
23 TraesCS2A01G371400 chr7A 83.516 273 36 4 1096 1359 68211422 68211694 3.420000e-61 246.0
24 TraesCS2A01G371400 chr7A 84.800 125 13 4 1437 1555 184119585 184119461 2.160000e-23 121.0
25 TraesCS2A01G371400 chr7A 91.026 78 6 1 3159 3236 41011652 41011576 2.180000e-18 104.0
26 TraesCS2A01G371400 chr7A 87.500 72 9 0 3159 3230 110401590 110401661 2.840000e-12 84.2
27 TraesCS2A01G371400 chr7A 87.500 72 9 0 3159 3230 521921200 521921271 2.840000e-12 84.2
28 TraesCS2A01G371400 chr6B 98.689 763 10 0 3662 4424 495758499 495757737 0.000000e+00 1354.0
29 TraesCS2A01G371400 chr6B 98.814 759 9 0 3666 4424 116275416 116274658 0.000000e+00 1352.0
30 TraesCS2A01G371400 chr6B 98.813 758 9 0 3667 4424 585923396 585922639 0.000000e+00 1351.0
31 TraesCS2A01G371400 chr6A 98.811 757 9 0 3668 4424 617218820 617219576 0.000000e+00 1349.0
32 TraesCS2A01G371400 chr6A 94.501 782 27 6 2455 3229 282261371 282260599 0.000000e+00 1192.0
33 TraesCS2A01G371400 chr6A 81.818 121 16 3 1439 1553 584987134 584987014 3.640000e-16 97.1
34 TraesCS2A01G371400 chr4B 98.684 760 10 0 3665 4424 643540235 643540994 0.000000e+00 1349.0
35 TraesCS2A01G371400 chr4B 98.681 758 10 0 3667 4424 578522059 578522816 0.000000e+00 1345.0
36 TraesCS2A01G371400 chr4B 79.661 177 26 3 1463 1637 618414845 618414677 7.770000e-23 119.0
37 TraesCS2A01G371400 chr7B 98.679 757 10 0 3668 4424 552890306 552891062 0.000000e+00 1343.0
38 TraesCS2A01G371400 chr7B 81.455 275 38 11 1096 1359 5942802 5943074 3.470000e-51 213.0
39 TraesCS2A01G371400 chr7B 82.500 80 11 2 3159 3237 246622508 246622431 2.860000e-07 67.6
40 TraesCS2A01G371400 chr7B 89.130 46 4 1 1592 1637 425721919 425721963 6.180000e-04 56.5
41 TraesCS2A01G371400 chr2D 94.125 851 46 4 1614 2462 472442614 472441766 0.000000e+00 1291.0
42 TraesCS2A01G371400 chr2D 87.514 897 42 26 541 1382 472444135 472443254 0.000000e+00 972.0
43 TraesCS2A01G371400 chr2D 96.915 551 16 1 1 551 472445239 472444690 0.000000e+00 922.0
44 TraesCS2A01G371400 chr2D 85.211 852 80 24 1643 2462 472229746 472228909 0.000000e+00 833.0
45 TraesCS2A01G371400 chr2D 90.508 453 37 2 25 476 472230879 472230432 1.060000e-165 593.0
46 TraesCS2A01G371400 chr2D 82.107 693 50 31 747 1382 472230435 472229760 3.920000e-145 525.0
47 TraesCS2A01G371400 chr2D 97.525 202 5 0 3231 3432 472441776 472441575 3.280000e-91 346.0
48 TraesCS2A01G371400 chr2D 91.324 219 19 0 3231 3449 472228919 472228701 2.590000e-77 300.0
49 TraesCS2A01G371400 chr2D 83.922 255 24 8 3423 3667 472441265 472441018 1.240000e-55 228.0
50 TraesCS2A01G371400 chr2D 83.607 183 30 0 2275 2457 472130407 472130225 5.880000e-39 172.0
51 TraesCS2A01G371400 chr2D 84.034 119 16 2 1437 1553 85919718 85919601 1.300000e-20 111.0
52 TraesCS2A01G371400 chr7D 83.597 506 69 11 2459 2958 297056070 297056567 3.120000e-126 462.0
53 TraesCS2A01G371400 chr6D 82.710 214 20 7 1431 1637 38888523 38888726 1.640000e-39 174.0
54 TraesCS2A01G371400 chr5D 81.567 217 25 3 1431 1640 513917285 513917077 9.840000e-37 165.0
55 TraesCS2A01G371400 chr5D 80.198 202 25 3 1431 1625 211977094 211977287 2.150000e-28 137.0
56 TraesCS2A01G371400 chr5D 77.778 216 32 11 1431 1637 547799630 547799422 7.770000e-23 119.0
57 TraesCS2A01G371400 chr3D 87.023 131 11 1 1431 1555 536985839 536985969 4.610000e-30 143.0
58 TraesCS2A01G371400 chr3D 86.087 115 10 2 1447 1555 573626291 573626177 7.770000e-23 119.0
59 TraesCS2A01G371400 chr1D 85.271 129 13 2 1433 1555 289965204 289965332 1.290000e-25 128.0
60 TraesCS2A01G371400 chr1B 77.990 209 36 10 1432 1637 509055308 509055107 6.010000e-24 122.0
61 TraesCS2A01G371400 chr4A 91.549 71 6 0 3159 3229 383623741 383623671 1.010000e-16 99.0
62 TraesCS2A01G371400 chr3B 85.507 69 7 3 3159 3226 26260284 26260350 7.940000e-08 69.4


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 TraesCS2A01G371400 chr2A 613873612 613878035 4423 True 8170.00 8170 100.0000 1 4424 1 chr2A.!!$R3 4423
1 TraesCS2A01G371400 chr2A 751242632 751243390 758 False 1347.00 1347 98.6820 3666 4424 1 chr2A.!!$F1 758
2 TraesCS2A01G371400 chr2A 613699359 613703397 4038 True 528.40 824 89.3150 1 3449 5 chr2A.!!$R5 3448
3 TraesCS2A01G371400 chr2A 613688821 613689773 952 True 260.00 283 80.0810 1111 2462 2 chr2A.!!$R4 1351
4 TraesCS2A01G371400 chr2B 551533892 551534586 694 True 865.00 865 89.2010 1 703 1 chr2B.!!$R4 702
5 TraesCS2A01G371400 chr2B 551563649 551566773 3124 True 647.46 1929 90.9956 1 3667 5 chr2B.!!$R5 3666
6 TraesCS2A01G371400 chr2B 551398594 551399097 503 True 292.00 292 77.4810 1943 2462 1 chr2B.!!$R1 519
7 TraesCS2A01G371400 chr7A 701589158 701589916 758 True 1363.00 1363 99.0780 3666 4424 1 chr7A.!!$R3 758
8 TraesCS2A01G371400 chr7A 110546007 110546786 779 False 1290.00 1290 96.6670 2459 3231 1 chr7A.!!$F3 772
9 TraesCS2A01G371400 chr6B 495757737 495758499 762 True 1354.00 1354 98.6890 3662 4424 1 chr6B.!!$R2 762
10 TraesCS2A01G371400 chr6B 116274658 116275416 758 True 1352.00 1352 98.8140 3666 4424 1 chr6B.!!$R1 758
11 TraesCS2A01G371400 chr6B 585922639 585923396 757 True 1351.00 1351 98.8130 3667 4424 1 chr6B.!!$R3 757
12 TraesCS2A01G371400 chr6A 617218820 617219576 756 False 1349.00 1349 98.8110 3668 4424 1 chr6A.!!$F1 756
13 TraesCS2A01G371400 chr6A 282260599 282261371 772 True 1192.00 1192 94.5010 2455 3229 1 chr6A.!!$R1 774
14 TraesCS2A01G371400 chr4B 643540235 643540994 759 False 1349.00 1349 98.6840 3665 4424 1 chr4B.!!$F2 759
15 TraesCS2A01G371400 chr4B 578522059 578522816 757 False 1345.00 1345 98.6810 3667 4424 1 chr4B.!!$F1 757
16 TraesCS2A01G371400 chr7B 552890306 552891062 756 False 1343.00 1343 98.6790 3668 4424 1 chr7B.!!$F3 756
17 TraesCS2A01G371400 chr2D 472441018 472445239 4221 True 751.80 1291 92.0002 1 3667 5 chr2D.!!$R4 3666
18 TraesCS2A01G371400 chr2D 472228701 472230879 2178 True 562.75 833 87.2875 25 3449 4 chr2D.!!$R3 3424

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
535 541 0.944386 AGTTTAACCTGTGCTGTGCG 59.056 50.000 0.00 0.0 0.00 5.34 F
984 3244 1.078848 GCTGTTGGAGCTCGTGGAT 60.079 57.895 7.83 0.0 45.21 3.41 F
1690 4448 0.469494 TCGGTGATGGATGGATGTGG 59.531 55.000 0.00 0.0 0.00 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1671 4417 0.469494 CCACATCCATCCATCACCGA 59.531 55.0 0.0 0.0 0.00 4.69 R
2307 5227 0.617820 GCCTCCCCTCTGTCAGGTTA 60.618 60.0 0.0 0.0 41.51 2.85 R
3597 6849 0.602905 AAGCAGGACAACTACGGCAC 60.603 55.0 0.0 0.0 0.00 5.01 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
492 498 7.482169 TTCAGAATATGAGACACCTGTAACT 57.518 36.000 0.00 0.00 39.68 2.24
535 541 0.944386 AGTTTAACCTGTGCTGTGCG 59.056 50.000 0.00 0.00 0.00 5.34
618 1189 3.754850 GGGTATGTGTAGGGTCAAACAAC 59.245 47.826 0.00 0.00 0.00 3.32
620 1191 1.956297 TGTGTAGGGTCAAACAACGG 58.044 50.000 0.00 0.00 0.00 4.44
767 2999 4.744631 GTGAATGTTTCGAACTTGCCAAAT 59.255 37.500 0.00 0.00 0.00 2.32
817 3052 1.374125 CTCGATGTTGTGCCGGACA 60.374 57.895 5.05 3.75 0.00 4.02
883 3141 7.148440 CGTTATAAGTATCTCTCCTAACTCCCG 60.148 44.444 0.00 0.00 0.00 5.14
984 3244 1.078848 GCTGTTGGAGCTCGTGGAT 60.079 57.895 7.83 0.00 45.21 3.41
1093 3405 4.201891 GCAACTTGCAGAAATCTCATCGAT 60.202 41.667 8.97 0.00 44.26 3.59
1118 3432 4.125695 GCTAGGGTCGCCGTCGTT 62.126 66.667 0.00 0.00 36.96 3.85
1179 3493 1.222936 CTTGCCAGCGGAGGAATCT 59.777 57.895 0.00 0.00 0.00 2.40
1392 3883 7.433131 TCATTTTAGTATACTAGAACAACGCCG 59.567 37.037 15.90 0.00 0.00 6.46
1426 3917 9.947897 GCAACGGAATATAAATATTGTAGTACG 57.052 33.333 10.07 10.07 33.37 3.67
1437 3928 7.925703 AATATTGTAGTACGGTTCGATTCTG 57.074 36.000 0.00 0.00 0.00 3.02
1438 3929 4.771590 TTGTAGTACGGTTCGATTCTGT 57.228 40.909 7.54 7.54 0.00 3.41
1439 3930 5.878332 TTGTAGTACGGTTCGATTCTGTA 57.122 39.130 5.93 5.93 0.00 2.74
1440 3931 5.878332 TGTAGTACGGTTCGATTCTGTAA 57.122 39.130 10.12 0.00 0.00 2.41
1441 3932 6.252967 TGTAGTACGGTTCGATTCTGTAAA 57.747 37.500 10.12 2.25 0.00 2.01
1580 4275 6.653989 ACTCCTACATAAAAGGTTGGATGAG 58.346 40.000 0.00 0.00 38.99 2.90
1582 4277 5.729229 TCCTACATAAAAGGTTGGATGAGGA 59.271 40.000 0.00 0.00 35.68 3.71
1585 4280 5.892348 ACATAAAAGGTTGGATGAGGAGTT 58.108 37.500 0.00 0.00 0.00 3.01
1586 4281 7.027874 ACATAAAAGGTTGGATGAGGAGTTA 57.972 36.000 0.00 0.00 0.00 2.24
1588 4283 7.775561 ACATAAAAGGTTGGATGAGGAGTTATC 59.224 37.037 0.00 0.00 0.00 1.75
1589 4284 5.779241 AAAGGTTGGATGAGGAGTTATCA 57.221 39.130 0.00 0.00 0.00 2.15
1590 4285 5.779241 AAGGTTGGATGAGGAGTTATCAA 57.221 39.130 0.00 0.00 0.00 2.57
1591 4286 5.779241 AGGTTGGATGAGGAGTTATCAAA 57.221 39.130 0.00 0.00 0.00 2.69
1593 4288 5.946377 AGGTTGGATGAGGAGTTATCAAAAC 59.054 40.000 0.00 0.00 0.00 2.43
1597 4292 7.452880 TGGATGAGGAGTTATCAAAACAAAG 57.547 36.000 0.00 0.00 0.00 2.77
1598 4293 7.230747 TGGATGAGGAGTTATCAAAACAAAGA 58.769 34.615 0.00 0.00 0.00 2.52
1600 4295 8.186821 GGATGAGGAGTTATCAAAACAAAGATG 58.813 37.037 0.00 0.00 0.00 2.90
1605 4300 9.918630 AGGAGTTATCAAAACAAAGATGAAATG 57.081 29.630 0.00 0.00 0.00 2.32
1606 4301 9.912634 GGAGTTATCAAAACAAAGATGAAATGA 57.087 29.630 0.00 0.00 0.00 2.57
1612 4307 8.010733 TCAAAACAAAGATGAAATGAGAACCT 57.989 30.769 0.00 0.00 0.00 3.50
1671 4417 4.529377 AGTTGCATCCAAGGTTTGAATCAT 59.471 37.500 0.00 0.00 0.00 2.45
1690 4448 0.469494 TCGGTGATGGATGGATGTGG 59.531 55.000 0.00 0.00 0.00 4.17
1744 4502 2.267961 GGGGTTGAGTACGGCCAG 59.732 66.667 2.24 0.00 0.00 4.85
1828 4611 4.847512 TGTAATTTACTCCTGGAGGAACCA 59.152 41.667 26.56 11.80 44.91 3.67
1842 4625 1.534729 GAACCAAGCCAAGAACCGAT 58.465 50.000 0.00 0.00 0.00 4.18
1872 4655 1.788308 CAAGCACAGCGACCAATTTTG 59.212 47.619 0.00 0.00 0.00 2.44
1941 4848 1.069765 CGGTTCAGACACACCAGCT 59.930 57.895 0.00 0.00 31.84 4.24
1980 4887 4.035091 GCCGATGCATAATACAACAGTTCA 59.965 41.667 0.00 0.00 37.47 3.18
1998 4905 3.590824 GTGGCCTGGATTTCCACG 58.409 61.111 3.32 0.00 42.01 4.94
2027 4934 4.025040 TGAGTGGATGTTGAAGAATGCT 57.975 40.909 0.00 0.00 0.00 3.79
2301 5221 1.260538 TGAGGCAGGAGCTCAACGAT 61.261 55.000 17.19 0.00 41.70 3.73
2307 5227 1.107114 AGGAGCTCAACGATGTCGAT 58.893 50.000 17.19 0.00 43.02 3.59
2334 5254 2.444895 GAGGGGAGGCTGGACGAT 60.445 66.667 0.00 0.00 0.00 3.73
2337 5257 2.503382 GGGGAGGCTGGACGATCTC 61.503 68.421 0.00 0.00 0.00 2.75
2362 5282 5.928976 TGGAGAAGTTCATCAAAGACTTCA 58.071 37.500 15.33 0.00 39.22 3.02
2372 5292 2.391724 AAAGACTTCAAGGCCGGCGA 62.392 55.000 22.54 9.74 0.00 5.54
2392 5312 2.525124 TTGGAGATGCACGGGTGGT 61.525 57.895 0.43 0.00 0.00 4.16
2394 5314 2.660064 GGAGATGCACGGGTGGTCT 61.660 63.158 0.43 0.00 0.00 3.85
2445 5365 1.153647 CGCCATGAACGCCTACTCA 60.154 57.895 0.00 0.00 0.00 3.41
2457 5377 3.976339 CTACTCAAGGATCCTGGCG 57.024 57.895 17.02 10.27 0.00 5.69
2507 5427 3.066380 CTGTGCCAAACCCTAAAATTGC 58.934 45.455 0.00 0.00 0.00 3.56
2508 5428 2.703007 TGTGCCAAACCCTAAAATTGCT 59.297 40.909 0.00 0.00 0.00 3.91
2510 5430 2.029470 TGCCAAACCCTAAAATTGCTCG 60.029 45.455 0.00 0.00 0.00 5.03
2511 5431 2.606108 CCAAACCCTAAAATTGCTCGC 58.394 47.619 0.00 0.00 0.00 5.03
2512 5432 2.231235 CCAAACCCTAAAATTGCTCGCT 59.769 45.455 0.00 0.00 0.00 4.93
2513 5433 3.442273 CCAAACCCTAAAATTGCTCGCTA 59.558 43.478 0.00 0.00 0.00 4.26
2604 5530 9.588096 GGGAAATACCAAGAATCATACCTATTT 57.412 33.333 0.00 0.00 41.20 1.40
2705 5631 5.927954 GGTGAGACCGTGTTAAAATGTTA 57.072 39.130 0.00 0.00 0.00 2.41
2773 5699 6.403866 TTTCTAAATGAACACATGGCTTGT 57.596 33.333 0.00 0.00 39.91 3.16
2980 5907 2.264794 GTCTCGTTGGCCGATGGT 59.735 61.111 12.54 0.00 46.23 3.55
3231 6159 4.785453 CTTGGGCTCGGGGCTGTC 62.785 72.222 9.45 0.00 41.46 3.51
3257 6185 4.025858 GAGGCACCCTGAGCTGCA 62.026 66.667 1.02 0.00 34.90 4.41
3273 6201 4.075910 CACGTCAACTGCGCGCAT 62.076 61.111 36.48 19.30 0.00 4.73
3435 6682 2.585247 GTGTGAGATACCGGCGGC 60.585 66.667 28.71 10.31 0.00 6.53
3475 6727 1.990563 ACTTACTGATGCGTTACGTGC 59.009 47.619 6.63 0.00 0.00 5.34
3477 6729 3.119743 ACTTACTGATGCGTTACGTGCTA 60.120 43.478 6.63 0.00 0.00 3.49
3478 6730 1.909376 ACTGATGCGTTACGTGCTAG 58.091 50.000 6.63 3.42 0.00 3.42
3493 6745 3.062639 CGTGCTAGTTTGAGATTGCGAAT 59.937 43.478 0.00 0.00 0.00 3.34
3494 6746 4.267690 CGTGCTAGTTTGAGATTGCGAATA 59.732 41.667 0.00 0.00 0.00 1.75
3495 6747 5.220397 CGTGCTAGTTTGAGATTGCGAATAA 60.220 40.000 0.00 0.00 0.00 1.40
3496 6748 6.510157 CGTGCTAGTTTGAGATTGCGAATAAT 60.510 38.462 0.00 0.00 0.00 1.28
3510 6762 6.656314 TGCGAATAATTAAGACGTGTCATT 57.344 33.333 0.00 0.00 0.00 2.57
3545 6797 5.907391 CGACAAAGTGTGAGTTTTATTGACC 59.093 40.000 0.00 0.00 0.00 4.02
3560 6812 7.689446 TTTATTGACCCAATATTGTTGACGA 57.311 32.000 14.25 6.03 36.41 4.20
3582 6834 8.275015 ACGAATGATTGTGTTTGTTCCATATA 57.725 30.769 0.00 0.00 0.00 0.86
3588 6840 8.898761 TGATTGTGTTTGTTCCATATATACACC 58.101 33.333 9.21 0.00 34.93 4.16
3589 6841 8.815565 ATTGTGTTTGTTCCATATATACACCA 57.184 30.769 9.21 1.28 34.93 4.17
3600 6852 8.487313 TCCATATATACACCAATAATTCGTGC 57.513 34.615 0.00 0.00 0.00 5.34
3602 6854 5.856126 ATATACACCAATAATTCGTGCCG 57.144 39.130 0.00 0.00 0.00 5.69
3661 7283 2.577059 GGTTCTCGCCGTGGATGA 59.423 61.111 0.00 0.00 0.00 2.92
3783 7405 1.210931 CTACGACGAGGCCAAACGA 59.789 57.895 20.27 1.21 0.00 3.85
4391 8013 0.531974 TGCGTCTCTGTTTTTCGCCT 60.532 50.000 0.00 0.00 45.06 5.52
4392 8014 1.269883 TGCGTCTCTGTTTTTCGCCTA 60.270 47.619 0.00 0.00 45.06 3.93
4406 8028 4.602340 TTCGCCTATTAGGATGGAGTTC 57.398 45.455 14.16 0.00 37.67 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
492 498 7.032377 TGCACAATGTTTATTGACAACTACA 57.968 32.000 6.98 0.00 45.21 2.74
535 541 0.523072 ACACGCATGTCCATTTGAGC 59.477 50.000 0.00 0.00 31.55 4.26
592 1163 2.840511 TGACCCTACACATACCCACAT 58.159 47.619 0.00 0.00 0.00 3.21
618 1189 1.719117 GTGTGTGTGTGTTGTCCCG 59.281 57.895 0.00 0.00 0.00 5.14
620 1191 1.003972 CATCGTGTGTGTGTGTTGTCC 60.004 52.381 0.00 0.00 0.00 4.02
767 2999 3.068024 GCAACCTCACAAAAGGATCAACA 59.932 43.478 0.00 0.00 38.87 3.33
817 3052 0.179094 TTGTGGTGCTCGTCGTCTTT 60.179 50.000 0.00 0.00 0.00 2.52
883 3141 6.690194 TCCTAAGTTATCTGAGACGGTTAC 57.310 41.667 0.00 0.00 0.00 2.50
1093 3405 2.047655 CGACCCTAGCAACCGCAA 60.048 61.111 0.00 0.00 42.27 4.85
1118 3432 0.943479 TCCCCTTATTCCCTCCGGTA 59.057 55.000 0.00 0.00 0.00 4.02
1130 3444 1.113517 CCTCGAAGCCGATCCCCTTA 61.114 60.000 0.00 0.00 44.62 2.69
1172 3486 0.034380 TCAGGACGACGGAGATTCCT 60.034 55.000 0.00 0.00 39.17 3.36
1400 3891 9.947897 CGTACTACAATATTTATATTCCGTTGC 57.052 33.333 0.00 0.00 30.91 4.17
1413 3904 7.486647 ACAGAATCGAACCGTACTACAATATT 58.513 34.615 0.00 0.00 0.00 1.28
1414 3905 7.035840 ACAGAATCGAACCGTACTACAATAT 57.964 36.000 0.00 0.00 0.00 1.28
1416 3907 5.320549 ACAGAATCGAACCGTACTACAAT 57.679 39.130 0.00 0.00 0.00 2.71
1417 3908 4.771590 ACAGAATCGAACCGTACTACAA 57.228 40.909 0.00 0.00 0.00 2.41
1553 4248 9.442062 TCATCCAACCTTTTATGTAGGAGTATA 57.558 33.333 0.00 0.00 36.58 1.47
1554 4249 8.331931 TCATCCAACCTTTTATGTAGGAGTAT 57.668 34.615 0.00 0.00 36.58 2.12
1555 4250 7.147549 CCTCATCCAACCTTTTATGTAGGAGTA 60.148 40.741 0.00 0.00 36.58 2.59
1556 4251 6.353082 CCTCATCCAACCTTTTATGTAGGAGT 60.353 42.308 0.00 0.00 36.58 3.85
1557 4252 6.058183 CCTCATCCAACCTTTTATGTAGGAG 58.942 44.000 0.00 0.00 36.58 3.69
1558 4253 5.729229 TCCTCATCCAACCTTTTATGTAGGA 59.271 40.000 0.00 0.00 36.58 2.94
1559 4254 6.001449 TCCTCATCCAACCTTTTATGTAGG 57.999 41.667 0.00 0.00 38.79 3.18
1560 4255 6.653989 ACTCCTCATCCAACCTTTTATGTAG 58.346 40.000 0.00 0.00 0.00 2.74
1562 4257 5.520748 ACTCCTCATCCAACCTTTTATGT 57.479 39.130 0.00 0.00 0.00 2.29
1566 4261 6.139679 TGATAACTCCTCATCCAACCTTTT 57.860 37.500 0.00 0.00 0.00 2.27
1577 4272 8.690203 TTCATCTTTGTTTTGATAACTCCTCA 57.310 30.769 0.00 0.00 0.00 3.86
1580 4275 9.912634 TCATTTCATCTTTGTTTTGATAACTCC 57.087 29.630 0.00 0.00 0.00 3.85
1585 4280 9.912634 GGTTCTCATTTCATCTTTGTTTTGATA 57.087 29.630 0.00 0.00 0.00 2.15
1586 4281 8.645110 AGGTTCTCATTTCATCTTTGTTTTGAT 58.355 29.630 0.00 0.00 0.00 2.57
1588 4283 8.652810 AAGGTTCTCATTTCATCTTTGTTTTG 57.347 30.769 0.00 0.00 0.00 2.44
1589 4284 9.750125 GTAAGGTTCTCATTTCATCTTTGTTTT 57.250 29.630 0.00 0.00 0.00 2.43
1590 4285 8.076178 CGTAAGGTTCTCATTTCATCTTTGTTT 58.924 33.333 0.00 0.00 0.00 2.83
1591 4286 7.228706 ACGTAAGGTTCTCATTTCATCTTTGTT 59.771 33.333 0.00 0.00 46.39 2.83
1593 4288 7.133891 ACGTAAGGTTCTCATTTCATCTTTG 57.866 36.000 0.00 0.00 46.39 2.77
1608 4303 4.571984 ACTACGCAAAAAGAACGTAAGGTT 59.428 37.500 0.00 0.00 41.27 3.50
1609 4304 4.122046 ACTACGCAAAAAGAACGTAAGGT 58.878 39.130 0.00 0.00 41.27 3.50
1610 4305 4.720530 ACTACGCAAAAAGAACGTAAGG 57.279 40.909 0.00 0.00 41.27 2.69
1612 4307 6.360681 GTCTCTACTACGCAAAAAGAACGTAA 59.639 38.462 0.00 0.00 41.27 3.18
1671 4417 0.469494 CCACATCCATCCATCACCGA 59.531 55.000 0.00 0.00 0.00 4.69
1690 4448 1.737838 TCACCTGCAAATCATCCGAC 58.262 50.000 0.00 0.00 0.00 4.79
1744 4502 1.747355 TCCTCGTTGGTATCGAACTCC 59.253 52.381 0.00 0.00 36.89 3.85
1828 4611 2.746472 GCCTATCATCGGTTCTTGGCTT 60.746 50.000 0.00 0.00 36.52 4.35
1842 4625 0.740868 GCTGTGCTTGACGCCTATCA 60.741 55.000 0.00 0.00 38.05 2.15
1872 4655 2.622064 ACCGAATGAACCTATCAGGC 57.378 50.000 0.00 0.00 42.53 4.85
1941 4848 4.683781 GCATCGGCAAATAAACTTGTTCAA 59.316 37.500 0.00 0.00 40.72 2.69
1998 4905 4.527509 TCAACATCCACTCAACTCTCTC 57.472 45.455 0.00 0.00 0.00 3.20
2027 4934 3.147595 CTGTCGATGGGCTCCCGA 61.148 66.667 0.00 0.00 39.42 5.14
2138 5045 2.080286 AATTGGAGGAGACGTTCACG 57.920 50.000 0.00 0.00 46.33 4.35
2233 5151 1.523032 GCCACGGAATCCCTTACGG 60.523 63.158 0.00 0.00 43.29 4.02
2301 5221 2.100197 CCCTCTGTCAGGTTATCGACA 58.900 52.381 0.00 0.00 41.51 4.35
2307 5227 0.617820 GCCTCCCCTCTGTCAGGTTA 60.618 60.000 0.00 0.00 41.51 2.85
2334 5254 4.840680 TCTTTGATGAACTTCTCCAGGAGA 59.159 41.667 15.98 15.98 36.86 3.71
2337 5257 4.904241 AGTCTTTGATGAACTTCTCCAGG 58.096 43.478 0.00 0.00 0.00 4.45
2362 5282 4.394712 CTCCAACTCGCCGGCCTT 62.395 66.667 23.46 6.87 0.00 4.35
2372 5292 1.003355 CACCCGTGCATCTCCAACT 60.003 57.895 0.00 0.00 0.00 3.16
2472 5392 2.549064 GCACAGGGCCTTGAATTTTT 57.451 45.000 23.57 0.00 36.11 1.94
2859 5785 2.095718 GCCCTTTTAGCTGTGAGTTTCG 60.096 50.000 0.00 0.00 0.00 3.46
2871 5798 1.209504 TGATCCCGTGAGCCCTTTTAG 59.790 52.381 0.00 0.00 0.00 1.85
3157 6084 2.999185 TTCAGGGGCCTCAGATTTTT 57.001 45.000 4.79 0.00 0.00 1.94
3226 6154 4.154347 CCTCCTCGCCAGGACAGC 62.154 72.222 0.00 0.00 44.75 4.40
3257 6185 3.777925 GATGCGCGCAGTTGACGT 61.778 61.111 38.44 20.93 0.00 4.34
3273 6201 1.671742 GGTCTTGACGAAGCCTGGA 59.328 57.895 0.00 0.00 0.00 3.86
3477 6729 8.116753 CGTCTTAATTATTCGCAATCTCAAACT 58.883 33.333 0.00 0.00 0.00 2.66
3478 6730 7.903431 ACGTCTTAATTATTCGCAATCTCAAAC 59.097 33.333 0.00 0.00 0.00 2.93
3529 6781 8.415950 ACAATATTGGGTCAATAAAACTCACA 57.584 30.769 19.37 0.00 39.34 3.58
3545 6797 7.028962 ACACAATCATTCGTCAACAATATTGG 58.971 34.615 19.37 3.06 0.00 3.16
3597 6849 0.602905 AAGCAGGACAACTACGGCAC 60.603 55.000 0.00 0.00 0.00 5.01
3600 6852 1.878953 AACAAGCAGGACAACTACGG 58.121 50.000 0.00 0.00 0.00 4.02
3602 6854 3.211045 TGGAAACAAGCAGGACAACTAC 58.789 45.455 0.00 0.00 37.44 2.73
3627 7249 6.369615 GCGAGAACCCTAATTACAAAGTACAA 59.630 38.462 0.00 0.00 0.00 2.41
3661 7283 7.125204 GGGCAAAAGGATAATTAACCCTAGTTT 59.875 37.037 8.09 5.11 37.42 2.66
3783 7405 4.451900 GACGGAATGGACTCAAATATGGT 58.548 43.478 0.00 0.00 0.00 3.55
4136 7758 2.348998 CCACCTTTGAGCGCTCCT 59.651 61.111 33.23 8.76 0.00 3.69
4391 8013 4.685030 GCAAACCGGAACTCCATCCTAATA 60.685 45.833 9.46 0.00 37.34 0.98
4392 8014 3.886123 CAAACCGGAACTCCATCCTAAT 58.114 45.455 9.46 0.00 37.34 1.73


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

AutoCloner maintained by Alex Coulton.