Multiple sequence alignment - TraesCS2B01G448000

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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 TraesCS2B01G448000 chr2B 100.000 5622 0 0 1 5622 640687141 640692762 0.000000e+00 10382
1 TraesCS2B01G448000 chr2B 96.995 832 17 5 2 827 683096877 683096048 0.000000e+00 1391
2 TraesCS2B01G448000 chr2B 96.344 848 22 6 1 841 699181595 699182440 0.000000e+00 1386
3 TraesCS2B01G448000 chr2D 87.808 2756 209 54 827 3535 537934756 537937431 0.000000e+00 3110
4 TraesCS2B01G448000 chr2D 88.571 1295 88 28 3623 4875 537937590 537938866 0.000000e+00 1517
5 TraesCS2B01G448000 chr2A 94.720 1572 52 7 2223 3774 680275898 680277458 0.000000e+00 2414
6 TraesCS2B01G448000 chr2A 92.330 1395 53 17 828 2210 680273540 680274892 0.000000e+00 1934
7 TraesCS2B01G448000 chr2A 85.691 622 63 7 3762 4368 680277621 680278231 2.860000e-177 632
8 TraesCS2B01G448000 chr2A 90.270 370 23 8 4365 4730 680278333 680278693 6.590000e-129 472
9 TraesCS2B01G448000 chr6B 96.897 838 20 4 1 834 713754878 713754043 0.000000e+00 1399
10 TraesCS2B01G448000 chr6B 95.414 676 31 0 4947 5622 278276434 278277109 0.000000e+00 1077
11 TraesCS2B01G448000 chr6B 85.059 676 96 5 4949 5622 703199296 703199968 0.000000e+00 684
12 TraesCS2B01G448000 chr3B 96.686 845 16 6 1 834 171120913 171120070 0.000000e+00 1395
13 TraesCS2B01G448000 chr3A 96.782 839 17 7 2 833 522044210 522043375 0.000000e+00 1391
14 TraesCS2B01G448000 chr3A 90.273 586 51 2 5037 5622 27676482 27675903 0.000000e+00 761
15 TraesCS2B01G448000 chr5A 96.450 845 20 7 2 838 664388868 664389710 0.000000e+00 1386
16 TraesCS2B01G448000 chr5A 96.651 836 23 5 2 834 57372383 57373216 0.000000e+00 1384
17 TraesCS2B01G448000 chr5A 92.160 676 52 1 4947 5622 537268671 537267997 0.000000e+00 953
18 TraesCS2B01G448000 chr5A 85.417 576 80 4 4947 5520 480100680 480100107 3.750000e-166 595
19 TraesCS2B01G448000 chr4B 96.552 841 19 5 2 834 665292988 665293826 0.000000e+00 1384
20 TraesCS2B01G448000 chr1B 96.755 832 19 5 1 826 211607207 211606378 0.000000e+00 1380
21 TraesCS2B01G448000 chr7B 97.679 517 12 0 4948 5464 84554225 84553709 0.000000e+00 889
22 TraesCS2B01G448000 chr7B 84.134 687 95 9 4947 5622 662968706 662968023 0.000000e+00 652
23 TraesCS2B01G448000 chr7B 95.652 161 7 0 5462 5622 84543803 84543643 5.590000e-65 259
24 TraesCS2B01G448000 chr1D 83.556 675 109 2 4948 5622 338366832 338366160 1.030000e-176 630
25 TraesCS2B01G448000 chr4D 76.106 678 151 11 4949 5622 482169787 482170457 1.500000e-90 344


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 TraesCS2B01G448000 chr2B 640687141 640692762 5621 False 10382.0 10382 100.00000 1 5622 1 chr2B.!!$F1 5621
1 TraesCS2B01G448000 chr2B 683096048 683096877 829 True 1391.0 1391 96.99500 2 827 1 chr2B.!!$R1 825
2 TraesCS2B01G448000 chr2B 699181595 699182440 845 False 1386.0 1386 96.34400 1 841 1 chr2B.!!$F2 840
3 TraesCS2B01G448000 chr2D 537934756 537938866 4110 False 2313.5 3110 88.18950 827 4875 2 chr2D.!!$F1 4048
4 TraesCS2B01G448000 chr2A 680273540 680278693 5153 False 1363.0 2414 90.75275 828 4730 4 chr2A.!!$F1 3902
5 TraesCS2B01G448000 chr6B 713754043 713754878 835 True 1399.0 1399 96.89700 1 834 1 chr6B.!!$R1 833
6 TraesCS2B01G448000 chr6B 278276434 278277109 675 False 1077.0 1077 95.41400 4947 5622 1 chr6B.!!$F1 675
7 TraesCS2B01G448000 chr6B 703199296 703199968 672 False 684.0 684 85.05900 4949 5622 1 chr6B.!!$F2 673
8 TraesCS2B01G448000 chr3B 171120070 171120913 843 True 1395.0 1395 96.68600 1 834 1 chr3B.!!$R1 833
9 TraesCS2B01G448000 chr3A 522043375 522044210 835 True 1391.0 1391 96.78200 2 833 1 chr3A.!!$R2 831
10 TraesCS2B01G448000 chr3A 27675903 27676482 579 True 761.0 761 90.27300 5037 5622 1 chr3A.!!$R1 585
11 TraesCS2B01G448000 chr5A 664388868 664389710 842 False 1386.0 1386 96.45000 2 838 1 chr5A.!!$F2 836
12 TraesCS2B01G448000 chr5A 57372383 57373216 833 False 1384.0 1384 96.65100 2 834 1 chr5A.!!$F1 832
13 TraesCS2B01G448000 chr5A 537267997 537268671 674 True 953.0 953 92.16000 4947 5622 1 chr5A.!!$R2 675
14 TraesCS2B01G448000 chr5A 480100107 480100680 573 True 595.0 595 85.41700 4947 5520 1 chr5A.!!$R1 573
15 TraesCS2B01G448000 chr4B 665292988 665293826 838 False 1384.0 1384 96.55200 2 834 1 chr4B.!!$F1 832
16 TraesCS2B01G448000 chr1B 211606378 211607207 829 True 1380.0 1380 96.75500 1 826 1 chr1B.!!$R1 825
17 TraesCS2B01G448000 chr7B 84553709 84554225 516 True 889.0 889 97.67900 4948 5464 1 chr7B.!!$R2 516
18 TraesCS2B01G448000 chr7B 662968023 662968706 683 True 652.0 652 84.13400 4947 5622 1 chr7B.!!$R3 675
19 TraesCS2B01G448000 chr1D 338366160 338366832 672 True 630.0 630 83.55600 4948 5622 1 chr1D.!!$R1 674
20 TraesCS2B01G448000 chr4D 482169787 482170457 670 False 344.0 344 76.10600 4949 5622 1 chr4D.!!$F1 673

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
588 600 3.571590 AGACATGGCAACTTTTAACCCA 58.428 40.909 0.00 0.00 37.61 4.51 F
1320 1351 0.478072 TGGTTTGTGGCCTCTGATGT 59.522 50.000 3.32 0.00 0.00 3.06 F
2138 2187 0.110464 GCTTGCTGCTCGTGTTCTTC 60.110 55.000 0.00 0.00 38.95 2.87 F
3928 5269 0.833287 GAGGATCTACTGCAGGCCAA 59.167 55.000 19.93 0.33 0.00 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1911 1960 2.541588 CCTCGTGACCTGCTTGTTTTTG 60.542 50.0 0.00 0.00 0.00 2.44 R
2729 3779 0.670162 ACATGCTGAAGTGCACAACC 59.330 50.0 21.04 7.89 46.33 3.77 R
3967 5308 0.605319 GACGTGGCATGAGAACCCAA 60.605 55.0 14.82 0.00 0.00 4.12 R
4747 6215 0.109319 GCAAAACACCGGGCATAGTG 60.109 55.0 6.32 0.00 39.93 2.74 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
99 100 6.527372 CGTATGAATAGATGACATCAGCAGAG 59.473 42.308 17.57 2.78 34.14 3.35
585 597 6.155827 TGCAATAGACATGGCAACTTTTAAC 58.844 36.000 0.00 0.00 38.19 2.01
588 600 3.571590 AGACATGGCAACTTTTAACCCA 58.428 40.909 0.00 0.00 37.61 4.51
589 601 3.964031 AGACATGGCAACTTTTAACCCAA 59.036 39.130 0.00 0.00 37.61 4.12
784 805 6.207221 TCTGTTTACATTAGAGACGTGTGGTA 59.793 38.462 0.00 0.00 0.00 3.25
880 901 5.014858 AGATCTTCCAATCACAACTTGCAT 58.985 37.500 0.00 0.00 0.00 3.96
922 944 6.183360 ACAGCTACAAACAGGCCTTAATTTTT 60.183 34.615 0.00 0.00 0.00 1.94
924 946 7.870445 CAGCTACAAACAGGCCTTAATTTTTAA 59.130 33.333 0.00 0.00 0.00 1.52
925 947 8.425703 AGCTACAAACAGGCCTTAATTTTTAAA 58.574 29.630 0.00 0.00 0.00 1.52
926 948 9.047371 GCTACAAACAGGCCTTAATTTTTAAAA 57.953 29.630 0.00 0.00 0.00 1.52
1317 1348 0.843309 TTCTGGTTTGTGGCCTCTGA 59.157 50.000 3.32 0.00 0.00 3.27
1320 1351 0.478072 TGGTTTGTGGCCTCTGATGT 59.522 50.000 3.32 0.00 0.00 3.06
1401 1440 3.186909 CGTGCAGCTTACAAGTAGCATA 58.813 45.455 11.64 0.00 39.07 3.14
1402 1441 3.616821 CGTGCAGCTTACAAGTAGCATAA 59.383 43.478 11.64 0.00 39.07 1.90
1403 1442 4.492570 CGTGCAGCTTACAAGTAGCATAAC 60.493 45.833 11.64 2.31 39.07 1.89
1404 1443 3.938963 TGCAGCTTACAAGTAGCATAACC 59.061 43.478 0.00 0.00 34.62 2.85
1405 1444 3.001330 GCAGCTTACAAGTAGCATAACCG 59.999 47.826 0.00 0.00 0.00 4.44
1406 1445 4.181578 CAGCTTACAAGTAGCATAACCGT 58.818 43.478 0.00 0.00 0.00 4.83
1419 1458 4.160814 AGCATAACCGTAACTGACCATGTA 59.839 41.667 0.00 0.00 0.00 2.29
1432 1471 8.780846 AACTGACCATGTAAAATTCGTATGTA 57.219 30.769 0.00 0.00 0.00 2.29
1434 1473 8.826710 ACTGACCATGTAAAATTCGTATGTATG 58.173 33.333 0.00 0.00 0.00 2.39
1435 1474 8.148807 TGACCATGTAAAATTCGTATGTATGG 57.851 34.615 0.00 0.00 38.71 2.74
1436 1475 7.771361 TGACCATGTAAAATTCGTATGTATGGT 59.229 33.333 0.00 0.00 45.96 3.55
1437 1476 9.263538 GACCATGTAAAATTCGTATGTATGGTA 57.736 33.333 0.00 0.00 44.03 3.25
1438 1477 9.787435 ACCATGTAAAATTCGTATGTATGGTAT 57.213 29.630 0.00 0.00 42.69 2.73
1479 1518 3.062763 CACTCTCACTGTTCTGCGATTT 58.937 45.455 0.00 0.00 0.00 2.17
1486 1525 5.927030 TCACTGTTCTGCGATTTATTTGAC 58.073 37.500 0.00 0.00 0.00 3.18
1518 1557 8.691661 AAGTTGAAACTTTATCAGTATGTGGT 57.308 30.769 2.56 0.00 46.52 4.16
1519 1558 8.691661 AGTTGAAACTTTATCAGTATGTGGTT 57.308 30.769 0.00 0.00 35.21 3.67
1520 1559 9.787435 AGTTGAAACTTTATCAGTATGTGGTTA 57.213 29.630 0.00 0.00 35.21 2.85
1523 1562 9.952030 TGAAACTTTATCAGTATGTGGTTATGA 57.048 29.630 0.00 0.00 32.94 2.15
1541 1580 4.647564 ATGAACTTATGATGCTAGGGGG 57.352 45.455 0.00 0.00 0.00 5.40
1881 1929 3.243301 ACTGAACTCAACGCTCGTCTTTA 60.243 43.478 0.00 0.00 0.00 1.85
1925 1974 3.733684 CGCTTACACAAAAACAAGCAGGT 60.734 43.478 6.05 0.00 42.77 4.00
2089 2138 3.817647 AGAGACAAATGCAGGACAAAGAC 59.182 43.478 0.00 0.00 0.00 3.01
2138 2187 0.110464 GCTTGCTGCTCGTGTTCTTC 60.110 55.000 0.00 0.00 38.95 2.87
2169 2218 6.127619 GCAGGGAAATTAGTCAAAGTAAGCAT 60.128 38.462 0.00 0.00 0.00 3.79
2284 3328 7.101652 TGCTCCTTTTGTTTACACAATACAA 57.898 32.000 0.00 0.00 42.66 2.41
2293 3337 6.212235 TGTTTACACAATACAACATGCCTTG 58.788 36.000 0.00 0.00 0.00 3.61
2294 3338 3.940209 ACACAATACAACATGCCTTGG 57.060 42.857 0.00 0.00 0.00 3.61
2295 3339 3.230134 ACACAATACAACATGCCTTGGT 58.770 40.909 0.00 0.00 0.00 3.67
2298 3342 5.303078 ACACAATACAACATGCCTTGGTTTA 59.697 36.000 0.00 0.00 0.00 2.01
2414 3459 3.353557 AGCAGTGCACAAGATGATCATT 58.646 40.909 21.04 0.00 0.00 2.57
2562 3607 0.953727 TTCTTGACATGCTTTGCGCT 59.046 45.000 9.73 0.00 40.11 5.92
2580 3625 3.726436 CGCTTACTTCAGAGCTTTTTCG 58.274 45.455 0.00 0.00 36.76 3.46
2605 3650 6.264067 GCAGCTCCATTTCTGACCTAAATATT 59.736 38.462 0.00 0.00 32.26 1.28
2698 3743 7.065803 ACGTGTTTATGCTCTTGCTGTATAATT 59.934 33.333 0.00 0.00 40.48 1.40
2738 3788 2.818130 AACATTGATGGGTTGTGCAC 57.182 45.000 10.75 10.75 0.00 4.57
2846 3906 5.526111 TGCTAAAAGACTTGTGAAGGTACAC 59.474 40.000 0.00 0.00 40.68 2.90
2888 3948 4.085357 TGTACTGCATGTTCTTGGAACT 57.915 40.909 10.98 0.00 0.00 3.01
2891 3951 5.643348 TGTACTGCATGTTCTTGGAACTATG 59.357 40.000 10.98 12.33 0.00 2.23
2916 3976 5.341872 TTTTATTCATCAATGGTGGCAGG 57.658 39.130 0.00 0.00 0.00 4.85
2952 4012 2.634815 ATGATCCATGAGGCACTGAC 57.365 50.000 0.00 0.00 41.55 3.51
3021 4082 2.004583 TAATTCCGTCACTGCTTCCG 57.995 50.000 0.00 0.00 0.00 4.30
3027 4088 1.576421 GTCACTGCTTCCGCCTTTG 59.424 57.895 0.00 0.00 34.43 2.77
3155 4216 8.181904 ACCTTGATAACCATAATGGCTTATTG 57.818 34.615 0.00 0.00 42.67 1.90
3156 4217 7.233348 ACCTTGATAACCATAATGGCTTATTGG 59.767 37.037 0.00 0.68 42.67 3.16
3213 4274 2.035066 GGGCATATCATCCTGCAAACAC 59.965 50.000 0.00 0.00 40.18 3.32
3263 4324 9.137459 CAGAAGAATAAGGTATAGGTCTCTCAA 57.863 37.037 0.00 0.00 0.00 3.02
3285 4346 8.934023 TCAAACCATATTTAAGTGAAGGAGTT 57.066 30.769 0.00 0.00 0.00 3.01
3357 4427 6.776116 TCTCACTGTATATACTGGGTAAGGTG 59.224 42.308 18.33 9.02 31.44 4.00
3455 4525 5.927115 ACCTTGTCGTCTTTAGAAATGTCTC 59.073 40.000 0.00 0.00 35.12 3.36
3456 4526 5.061064 CCTTGTCGTCTTTAGAAATGTCTCG 59.939 44.000 0.00 0.00 35.12 4.04
3488 4558 7.581213 TCCTAAATGGGTTAATATGTGCTTG 57.419 36.000 0.00 0.00 36.20 4.01
3548 4702 9.811995 CTGTCATTTCCATCATTTACAATCAAT 57.188 29.630 0.00 0.00 0.00 2.57
3672 4826 2.056815 AGCGAGCATGCTGAGAGGA 61.057 57.895 28.27 0.00 45.28 3.71
3890 5220 9.686683 ATTAGCACCTATTTTCAAATGTAGAGT 57.313 29.630 0.00 0.00 0.00 3.24
3891 5221 7.383102 AGCACCTATTTTCAAATGTAGAGTG 57.617 36.000 0.00 0.00 0.00 3.51
3928 5269 0.833287 GAGGATCTACTGCAGGCCAA 59.167 55.000 19.93 0.33 0.00 4.52
3940 5281 1.717194 CAGGCCAATGTGCATCAAAC 58.283 50.000 5.01 0.00 0.00 2.93
3946 5287 3.607542 GCCAATGTGCATCAAACTTTTGC 60.608 43.478 0.00 0.00 38.05 3.68
3967 5308 3.685550 GCCCTGGCAGTAGACATTATGTT 60.686 47.826 14.43 0.00 41.49 2.71
3983 5324 1.327303 TGTTTGGGTTCTCATGCCAC 58.673 50.000 0.00 0.00 0.00 5.01
3993 5334 2.358125 CATGCCACGTCCGTCCAA 60.358 61.111 0.00 0.00 0.00 3.53
4020 5361 9.859427 TTTCTTCAATTGGTCATAATCACAATC 57.141 29.630 5.42 0.00 32.80 2.67
4061 5402 1.067364 TGCTGAGCCACAAACATGTTG 59.933 47.619 12.82 8.99 0.00 3.33
4081 5422 2.684374 TGATGGAATTTGATGGCAGTCG 59.316 45.455 0.00 0.00 0.00 4.18
4167 5508 4.859798 GTCGGTGATAGTTTCTGAAGTCAG 59.140 45.833 1.65 1.65 45.08 3.51
4213 5557 2.353208 GGCACTAGATAGCTTGATCCGG 60.353 54.545 0.00 0.00 0.00 5.14
4220 5564 0.975556 TAGCTTGATCCGGTCTGCCA 60.976 55.000 0.00 0.00 34.09 4.92
4224 5568 0.107703 TTGATCCGGTCTGCCACATC 60.108 55.000 0.00 0.00 34.09 3.06
4229 5573 1.293179 CGGTCTGCCACATCTGTCA 59.707 57.895 0.00 0.00 34.09 3.58
4236 5580 1.814394 TGCCACATCTGTCAATGCTTC 59.186 47.619 0.00 0.00 0.00 3.86
4238 5582 1.399440 CCACATCTGTCAATGCTTCGG 59.601 52.381 0.00 0.00 0.00 4.30
4262 5606 6.483307 GGCAATTATAGCTGACAGACACATTA 59.517 38.462 6.65 0.00 0.00 1.90
4311 5655 1.000396 AGGGCAGATGGTTGAAGGC 60.000 57.895 0.00 0.00 0.00 4.35
4317 5661 0.036010 AGATGGTTGAAGGCCAGACG 60.036 55.000 5.01 0.00 39.65 4.18
4354 5698 1.216977 CGTTCACCCTGCCGATACA 59.783 57.895 0.00 0.00 0.00 2.29
4386 5846 6.824704 AGTAGTAGTACTAACTGAAGGCTGAG 59.175 42.308 11.64 0.00 37.76 3.35
4465 5925 1.002069 ATCCTGACCATGGGAAGCAA 58.998 50.000 18.09 4.43 35.08 3.91
4466 5926 0.038166 TCCTGACCATGGGAAGCAAC 59.962 55.000 18.09 0.00 0.00 4.17
4467 5927 0.251297 CCTGACCATGGGAAGCAACA 60.251 55.000 18.09 3.71 0.00 3.33
4468 5928 1.171308 CTGACCATGGGAAGCAACAG 58.829 55.000 18.09 9.39 0.00 3.16
4469 5929 0.895100 TGACCATGGGAAGCAACAGC 60.895 55.000 18.09 0.00 0.00 4.40
4470 5930 0.895100 GACCATGGGAAGCAACAGCA 60.895 55.000 18.09 0.00 0.00 4.41
4471 5931 0.469705 ACCATGGGAAGCAACAGCAA 60.470 50.000 18.09 0.00 0.00 3.91
4586 6046 2.123854 ACCGGCGCAGAGATCCTA 60.124 61.111 10.83 0.00 0.00 2.94
4665 6129 8.771920 TCACGTGATTTCTTCTTATGTTGTAT 57.228 30.769 15.76 0.00 0.00 2.29
4666 6130 8.655970 TCACGTGATTTCTTCTTATGTTGTATG 58.344 33.333 15.76 0.00 0.00 2.39
4700 6167 4.459390 TGGAACAGCTGCTTACGTATAA 57.541 40.909 15.27 0.00 0.00 0.98
4747 6215 2.045536 CCAGGCTTCCTCTGGCAC 60.046 66.667 0.00 0.00 44.29 5.01
4748 6216 2.752358 CAGGCTTCCTCTGGCACA 59.248 61.111 0.00 0.00 0.00 4.57
4749 6217 1.673665 CAGGCTTCCTCTGGCACAC 60.674 63.158 0.00 0.00 0.00 3.82
4750 6218 1.845205 AGGCTTCCTCTGGCACACT 60.845 57.895 0.00 0.00 0.00 3.55
4751 6219 0.545309 AGGCTTCCTCTGGCACACTA 60.545 55.000 0.00 0.00 0.00 2.74
4752 6220 0.543749 GGCTTCCTCTGGCACACTAT 59.456 55.000 0.00 0.00 0.00 2.12
4753 6221 1.661341 GCTTCCTCTGGCACACTATG 58.339 55.000 0.00 0.00 0.00 2.23
4766 6236 0.109319 CACTATGCCCGGTGTTTTGC 60.109 55.000 0.00 0.00 0.00 3.68
4802 6273 1.227764 CTGCATGGCCTACATCGCT 60.228 57.895 3.32 0.00 37.84 4.93
4815 6286 2.680913 ATCGCTGACTTGCCGTTGC 61.681 57.895 0.00 0.00 38.26 4.17
4870 6347 3.041940 GAACGACCACCGCCAGTG 61.042 66.667 0.00 0.00 46.83 3.66
4894 6371 3.292159 GCGACGCACCCCCTTTTT 61.292 61.111 16.42 0.00 0.00 1.94
4933 6410 9.967451 TCACAGTATTATAAAAGGTTCATTGGA 57.033 29.630 0.00 0.00 0.00 3.53
4945 6422 9.758651 AAAAGGTTCATTGGAAGTATAAAACAC 57.241 29.630 0.00 0.00 32.62 3.32
5478 6956 3.647771 GGGGGCGTGAACTTCCCT 61.648 66.667 0.00 0.00 39.95 4.20
5539 7025 2.494073 ACAGCCGTTTTTCCTTTCAACA 59.506 40.909 0.00 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
242 253 4.449743 GTGTAAACATCGTGGCAACTTCTA 59.550 41.667 0.00 0.00 37.61 2.10
714 727 5.990996 TGCAGGAATCTTTTTGGATTTTCAC 59.009 36.000 0.00 0.00 36.24 3.18
752 773 6.258727 CGTCTCTAATGTAAACAGATTGCCAT 59.741 38.462 0.00 0.00 0.00 4.40
784 805 0.469331 TGTGACAGGAAGGGAGACGT 60.469 55.000 0.00 0.00 0.00 4.34
964 986 7.761038 TGTTCTTTTTCCTATTTTCCTCCTC 57.239 36.000 0.00 0.00 0.00 3.71
1094 1116 1.090052 GGAGTTGGCGGAGAAATCGG 61.090 60.000 0.00 0.00 0.00 4.18
1320 1351 1.610624 GGTGAGAACGCTGGAATGGAA 60.611 52.381 0.00 0.00 0.00 3.53
1401 1440 6.347888 CGAATTTTACATGGTCAGTTACGGTT 60.348 38.462 0.00 0.00 0.00 4.44
1402 1441 5.121142 CGAATTTTACATGGTCAGTTACGGT 59.879 40.000 0.00 0.00 0.00 4.83
1403 1442 5.121142 ACGAATTTTACATGGTCAGTTACGG 59.879 40.000 0.00 0.00 0.00 4.02
1404 1443 6.160664 ACGAATTTTACATGGTCAGTTACG 57.839 37.500 0.00 0.00 0.00 3.18
1405 1444 8.662141 ACATACGAATTTTACATGGTCAGTTAC 58.338 33.333 0.00 0.00 0.00 2.50
1406 1445 8.780846 ACATACGAATTTTACATGGTCAGTTA 57.219 30.769 0.00 0.00 0.00 2.24
1419 1458 8.876275 ACGTACATACCATACATACGAATTTT 57.124 30.769 8.90 0.00 40.76 1.82
1432 1471 6.870769 AGCTAGTTTTGTACGTACATACCAT 58.129 36.000 27.82 15.49 35.89 3.55
1434 1473 6.808212 TGAAGCTAGTTTTGTACGTACATACC 59.192 38.462 27.82 16.34 35.89 2.73
1435 1474 7.540055 AGTGAAGCTAGTTTTGTACGTACATAC 59.460 37.037 27.82 25.26 35.89 2.39
1436 1475 7.596494 AGTGAAGCTAGTTTTGTACGTACATA 58.404 34.615 27.82 20.67 35.89 2.29
1437 1476 6.453092 AGTGAAGCTAGTTTTGTACGTACAT 58.547 36.000 27.82 15.96 35.89 2.29
1438 1477 5.835257 AGTGAAGCTAGTTTTGTACGTACA 58.165 37.500 24.10 24.10 0.00 2.90
1518 1557 5.849475 TCCCCCTAGCATCATAAGTTCATAA 59.151 40.000 0.00 0.00 0.00 1.90
1519 1558 5.411493 TCCCCCTAGCATCATAAGTTCATA 58.589 41.667 0.00 0.00 0.00 2.15
1520 1559 4.242811 TCCCCCTAGCATCATAAGTTCAT 58.757 43.478 0.00 0.00 0.00 2.57
1521 1560 3.664320 TCCCCCTAGCATCATAAGTTCA 58.336 45.455 0.00 0.00 0.00 3.18
1522 1561 4.917906 ATCCCCCTAGCATCATAAGTTC 57.082 45.455 0.00 0.00 0.00 3.01
1523 1562 5.249393 CAGTATCCCCCTAGCATCATAAGTT 59.751 44.000 0.00 0.00 0.00 2.66
1524 1563 4.780021 CAGTATCCCCCTAGCATCATAAGT 59.220 45.833 0.00 0.00 0.00 2.24
1525 1564 5.026121 TCAGTATCCCCCTAGCATCATAAG 58.974 45.833 0.00 0.00 0.00 1.73
1844 1892 4.433615 AGTTCAGTGGCACTTATATGTCG 58.566 43.478 19.43 4.06 0.00 4.35
1911 1960 2.541588 CCTCGTGACCTGCTTGTTTTTG 60.542 50.000 0.00 0.00 0.00 2.44
1925 1974 2.765250 GAAGCTTGCGGTCCTCGTGA 62.765 60.000 2.10 0.00 41.72 4.35
2138 2187 6.930722 ACTTTGACTAATTTCCCTGCATTTTG 59.069 34.615 0.00 0.00 0.00 2.44
2210 2387 3.701205 ACTGGTGATGCAGTGACATAA 57.299 42.857 0.00 0.00 0.00 1.90
2562 3607 3.058914 GCTGCGAAAAAGCTCTGAAGTAA 60.059 43.478 0.00 0.00 37.69 2.24
2580 3625 2.698855 TAGGTCAGAAATGGAGCTGC 57.301 50.000 0.00 0.00 42.57 5.25
2605 3650 4.381718 CCTGTAAAACCCCAACGAAAACAA 60.382 41.667 0.00 0.00 0.00 2.83
2724 3769 1.608055 CTGAAGTGCACAACCCATCA 58.392 50.000 21.04 11.58 0.00 3.07
2729 3779 0.670162 ACATGCTGAAGTGCACAACC 59.330 50.000 21.04 7.89 46.33 3.77
2731 3781 5.066375 GGATATAACATGCTGAAGTGCACAA 59.934 40.000 21.04 2.97 46.33 3.33
2732 3782 4.576053 GGATATAACATGCTGAAGTGCACA 59.424 41.667 21.04 0.00 46.33 4.57
2733 3783 4.818546 AGGATATAACATGCTGAAGTGCAC 59.181 41.667 9.40 9.40 46.33 4.57
2735 3785 5.762218 AGAAGGATATAACATGCTGAAGTGC 59.238 40.000 0.00 0.00 0.00 4.40
2738 3788 6.528321 TGGAGAAGGATATAACATGCTGAAG 58.472 40.000 0.00 0.00 0.00 3.02
2746 3806 6.389869 ACCCTGAAATGGAGAAGGATATAACA 59.610 38.462 0.00 0.00 30.92 2.41
2846 3906 9.490379 AGTACATGTGTTCTAAAGAAAAGGTAG 57.510 33.333 9.11 0.00 35.58 3.18
2888 3948 7.093156 TGCCACCATTGATGAATAAAAACCATA 60.093 33.333 0.00 0.00 0.00 2.74
2891 3951 5.486526 TGCCACCATTGATGAATAAAAACC 58.513 37.500 0.00 0.00 0.00 3.27
2916 3976 4.142381 GGATCATTTTAGCCACACAGAACC 60.142 45.833 0.00 0.00 0.00 3.62
2952 4012 8.336801 AGTTTAGAAACTAGCAAGGGTTTATG 57.663 34.615 5.86 0.00 46.75 1.90
3027 4088 8.798153 GTGTAAACAGATACATAGCAAATTTGC 58.202 33.333 31.36 31.36 44.36 3.68
3042 4103 5.630121 TGGATTGACCAAGTGTAAACAGAT 58.370 37.500 0.00 0.00 46.75 2.90
3155 4216 5.938125 TCTTCAGTAACCTGATTTTAGCACC 59.062 40.000 0.00 0.00 46.80 5.01
3156 4217 6.651225 ACTCTTCAGTAACCTGATTTTAGCAC 59.349 38.462 0.00 0.00 46.80 4.40
3202 4263 0.813610 CTCACACCGTGTTTGCAGGA 60.814 55.000 0.00 0.00 34.79 3.86
3213 4274 4.394795 CGATTTTCTTAAAGCTCACACCG 58.605 43.478 0.00 0.00 0.00 4.94
3263 4324 9.975218 ATGTAACTCCTTCACTTAAATATGGTT 57.025 29.630 0.00 0.00 0.00 3.67
3285 4346 8.902540 AATACTTTGCATCCTCGATAAATGTA 57.097 30.769 0.00 0.00 0.00 2.29
3357 4427 1.410882 GAGAGGATACAGTCTGGGTGC 59.589 57.143 4.53 0.00 41.41 5.01
3455 4525 9.734984 ATATTAACCCATTTAGGAAATAGGACG 57.265 33.333 3.80 0.00 41.22 4.79
3488 4558 6.203723 AGTCAAAAGTGTTCTAATGTCTCTGC 59.796 38.462 0.00 0.00 0.00 4.26
3633 4787 3.944015 CTGAAATGGCCAACAAAACCAAA 59.056 39.130 10.96 0.00 36.94 3.28
3672 4826 2.436417 CTCCACGACACCAAATCCATT 58.564 47.619 0.00 0.00 0.00 3.16
3804 5133 5.593968 CATAGCAACATTGGCACATGTAAT 58.406 37.500 13.21 0.00 39.30 1.89
3890 5220 8.278639 AGATCCTCTAATCTTCACTAGAGTTCA 58.721 37.037 0.00 0.00 39.62 3.18
3891 5221 8.691661 AGATCCTCTAATCTTCACTAGAGTTC 57.308 38.462 0.00 3.15 39.62 3.01
3924 5265 3.607542 GCAAAAGTTTGATGCACATTGGC 60.608 43.478 7.96 0.00 40.55 4.52
3928 5269 2.369532 AGGGCAAAAGTTTGATGCACAT 59.630 40.909 15.17 1.18 45.83 3.21
3946 5287 3.845781 ACATAATGTCTACTGCCAGGG 57.154 47.619 0.00 0.00 0.00 4.45
3953 5294 7.016153 TGAGAACCCAAACATAATGTCTACT 57.984 36.000 0.00 0.00 0.00 2.57
3954 5295 7.679638 GCATGAGAACCCAAACATAATGTCTAC 60.680 40.741 0.00 0.00 0.00 2.59
3955 5296 6.318648 GCATGAGAACCCAAACATAATGTCTA 59.681 38.462 0.00 0.00 0.00 2.59
3963 5304 1.895131 GTGGCATGAGAACCCAAACAT 59.105 47.619 0.00 0.00 0.00 2.71
3967 5308 0.605319 GACGTGGCATGAGAACCCAA 60.605 55.000 14.82 0.00 0.00 4.12
3983 5324 4.419522 AATTGAAGAAATTGGACGGACG 57.580 40.909 0.00 0.00 37.09 4.79
4020 5361 5.577945 AGCACATGTTTTTGTCAGTTTCTTG 59.422 36.000 0.00 0.00 0.00 3.02
4061 5402 2.033801 CCGACTGCCATCAAATTCCATC 59.966 50.000 0.00 0.00 0.00 3.51
4081 5422 0.674895 CTCAGCTAGTTGGTGGCACC 60.675 60.000 29.75 29.75 43.76 5.01
4167 5508 0.318955 AGCGCAACAAAGCCAACATC 60.319 50.000 11.47 0.00 0.00 3.06
4168 5509 0.598158 CAGCGCAACAAAGCCAACAT 60.598 50.000 11.47 0.00 0.00 2.71
4174 5515 1.539776 CCGAAACAGCGCAACAAAGC 61.540 55.000 11.47 0.00 0.00 3.51
4175 5516 1.539776 GCCGAAACAGCGCAACAAAG 61.540 55.000 11.47 0.00 0.00 2.77
4176 5517 1.587613 GCCGAAACAGCGCAACAAA 60.588 52.632 11.47 0.00 0.00 2.83
4177 5518 2.025441 GCCGAAACAGCGCAACAA 59.975 55.556 11.47 0.00 0.00 2.83
4213 5557 1.131883 GCATTGACAGATGTGGCAGAC 59.868 52.381 0.00 0.00 44.85 3.51
4220 5564 1.089920 GCCGAAGCATTGACAGATGT 58.910 50.000 0.00 0.00 39.53 3.06
4236 5580 3.246226 GTGTCTGTCAGCTATAATTGCCG 59.754 47.826 0.00 0.00 0.00 5.69
4238 5582 5.998454 ATGTGTCTGTCAGCTATAATTGC 57.002 39.130 0.00 0.00 0.00 3.56
4262 5606 1.755959 TGCCTGTTCAAGTGCACAAAT 59.244 42.857 21.04 1.26 30.14 2.32
4293 5637 1.000396 GCCTTCAACCATCTGCCCT 60.000 57.895 0.00 0.00 0.00 5.19
4305 5649 0.179234 TTGTGAACGTCTGGCCTTCA 59.821 50.000 3.32 1.59 0.00 3.02
4311 5655 3.176708 CGTACCTATTGTGAACGTCTGG 58.823 50.000 0.00 0.00 0.00 3.86
4317 5661 1.657094 CGGTGCGTACCTATTGTGAAC 59.343 52.381 20.87 0.00 45.22 3.18
4342 5686 2.158900 ACTCAAGAATGTATCGGCAGGG 60.159 50.000 0.00 0.00 0.00 4.45
4386 5846 1.839424 ATACTCAAAACCTGGCTGCC 58.161 50.000 12.87 12.87 0.00 4.85
4465 5925 2.536725 CACTCGATGCTGTTGCTGT 58.463 52.632 0.00 0.00 40.48 4.40
4610 6073 0.249073 CAGGATCCGTACGCCTTCAG 60.249 60.000 10.49 0.00 0.00 3.02
4666 6130 0.961019 TGTTCCAGTGATGCTTTGGC 59.039 50.000 0.00 0.00 39.26 4.52
4681 6148 3.242248 CGGTTATACGTAAGCAGCTGTTC 59.758 47.826 16.64 0.00 45.62 3.18
4691 6158 6.315642 TGCCAAAAATCATCGGTTATACGTAA 59.684 34.615 0.00 0.00 34.94 3.18
4694 6161 5.163302 TGCCAAAAATCATCGGTTATACG 57.837 39.130 0.00 0.00 0.00 3.06
4700 6167 0.171007 CGCTGCCAAAAATCATCGGT 59.829 50.000 0.00 0.00 0.00 4.69
4747 6215 0.109319 GCAAAACACCGGGCATAGTG 60.109 55.000 6.32 0.00 39.93 2.74
4748 6216 0.251165 AGCAAAACACCGGGCATAGT 60.251 50.000 6.32 0.00 0.00 2.12
4749 6217 0.171007 CAGCAAAACACCGGGCATAG 59.829 55.000 6.32 0.00 0.00 2.23
4750 6218 0.250945 TCAGCAAAACACCGGGCATA 60.251 50.000 6.32 0.00 0.00 3.14
4751 6219 1.112315 TTCAGCAAAACACCGGGCAT 61.112 50.000 6.32 0.00 0.00 4.40
4752 6220 1.754621 TTCAGCAAAACACCGGGCA 60.755 52.632 6.32 0.00 0.00 5.36
4753 6221 1.299850 GTTCAGCAAAACACCGGGC 60.300 57.895 6.32 0.00 0.00 6.13
4766 6236 3.447025 GATCCTCGGCCCCGTTCAG 62.447 68.421 6.61 0.00 40.74 3.02
4788 6258 0.833287 AAGTCAGCGATGTAGGCCAT 59.167 50.000 5.01 0.00 36.13 4.40
4802 6273 3.947841 GCACGCAACGGCAAGTCA 61.948 61.111 0.00 0.00 41.24 3.41
4815 6286 0.493146 CGACGAAATACTAGCGCACG 59.507 55.000 11.47 1.43 0.00 5.34
4820 6291 1.488527 CAGGCCGACGAAATACTAGC 58.511 55.000 0.00 0.00 0.00 3.42
4823 6294 1.262640 ACCCAGGCCGACGAAATACT 61.263 55.000 0.00 0.00 0.00 2.12
4877 6354 3.292159 AAAAAGGGGGTGCGTCGC 61.292 61.111 11.10 11.10 0.00 5.19
4907 6384 9.967451 TCCAATGAACCTTTTATAATACTGTGA 57.033 29.630 0.00 0.00 0.00 3.58
4919 6396 9.758651 GTGTTTTATACTTCCAATGAACCTTTT 57.241 29.630 0.00 0.00 0.00 2.27
4920 6397 9.143155 AGTGTTTTATACTTCCAATGAACCTTT 57.857 29.630 0.00 0.00 0.00 3.11
4921 6398 8.706322 AGTGTTTTATACTTCCAATGAACCTT 57.294 30.769 0.00 0.00 0.00 3.50
4922 6399 8.706322 AAGTGTTTTATACTTCCAATGAACCT 57.294 30.769 0.00 0.00 33.28 3.50
4923 6400 9.758651 AAAAGTGTTTTATACTTCCAATGAACC 57.241 29.630 0.00 0.00 37.39 3.62
5265 6743 3.152341 GGAGGGATTATCACTGGCAATG 58.848 50.000 0.00 0.00 24.24 2.82
5470 6948 1.204113 CCAGCTCAGGGAGGGAAGTT 61.204 60.000 0.00 0.00 0.00 2.66
5471 6949 1.614824 CCAGCTCAGGGAGGGAAGT 60.615 63.158 0.00 0.00 0.00 3.01
5478 6956 3.657610 TCTAAATCATCCAGCTCAGGGA 58.342 45.455 0.00 0.00 39.14 4.20
5521 7007 3.430333 TCTGTTGAAAGGAAAAACGGC 57.570 42.857 0.00 0.00 31.55 5.68
5539 7025 5.350504 AAGATGAACTCGAACATGGATCT 57.649 39.130 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.