Multiple sequence alignment - TraesCS2A01G138500

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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 TraesCS2A01G138500 chr2A 100.000 3470 0 0 1 3470 83858368 83854899 0.000000e+00 6408.0
1 TraesCS2A01G138500 chr2A 87.014 1440 142 23 1041 2450 85291749 85293173 0.000000e+00 1581.0
2 TraesCS2A01G138500 chr2A 86.681 1419 150 27 1062 2450 85589897 85591306 0.000000e+00 1537.0
3 TraesCS2A01G138500 chr2A 84.258 1118 147 17 1040 2156 83849031 83847942 0.000000e+00 1062.0
4 TraesCS2A01G138500 chr2A 77.413 1430 215 68 1041 2437 717252985 717254339 0.000000e+00 752.0
5 TraesCS2A01G138500 chr2D 95.703 1699 66 2 758 2450 83157819 83156122 0.000000e+00 2726.0
6 TraesCS2A01G138500 chr2D 86.067 1500 137 32 999 2450 84742929 84744404 0.000000e+00 1546.0
7 TraesCS2A01G138500 chr2D 76.848 1434 225 64 1041 2437 579740523 579741886 0.000000e+00 710.0
8 TraesCS2A01G138500 chr2D 84.203 747 79 14 1 744 450948763 450949473 0.000000e+00 689.0
9 TraesCS2A01G138500 chr2B 87.209 1587 170 23 1896 3470 135086652 135085087 0.000000e+00 1775.0
10 TraesCS2A01G138500 chr2B 93.579 1168 49 9 758 1908 135090257 135089099 0.000000e+00 1718.0
11 TraesCS2A01G138500 chr2B 85.206 1433 167 27 1038 2450 135026378 135024971 0.000000e+00 1430.0
12 TraesCS2A01G138500 chr2B 88.610 878 72 15 1587 2449 136434748 136435612 0.000000e+00 1042.0
13 TraesCS2A01G138500 chr2B 76.746 1432 227 69 1042 2437 697665487 697666848 0.000000e+00 702.0
14 TraesCS2A01G138500 chr5A 87.340 782 51 19 3 742 461590718 461591493 0.000000e+00 852.0
15 TraesCS2A01G138500 chr7A 87.134 785 57 25 1 744 650971046 650970265 0.000000e+00 850.0
16 TraesCS2A01G138500 chr7A 81.952 543 77 12 9 536 177926537 177927073 1.140000e-119 440.0
17 TraesCS2A01G138500 chr6A 86.985 776 62 16 1 742 123501712 123500942 0.000000e+00 837.0
18 TraesCS2A01G138500 chr5D 86.316 760 75 19 1 742 486839088 486838340 0.000000e+00 800.0
19 TraesCS2A01G138500 chr4B 77.578 1445 242 47 1040 2449 44944547 44945944 0.000000e+00 798.0
20 TraesCS2A01G138500 chr4A 85.951 783 58 21 1 744 186693906 186693137 0.000000e+00 789.0
21 TraesCS2A01G138500 chr4A 84.829 791 74 19 1 746 124370014 124370803 0.000000e+00 754.0
22 TraesCS2A01G138500 chr4A 76.676 1492 261 44 1000 2449 571484904 571483458 0.000000e+00 747.0
23 TraesCS2A01G138500 chr4A 77.672 421 81 9 3050 3466 115797104 115797515 9.620000e-61 244.0
24 TraesCS2A01G138500 chr7D 85.903 759 84 14 1 742 37107115 37106363 0.000000e+00 787.0
25 TraesCS2A01G138500 chr7D 85.560 554 54 14 3 538 137791476 137790931 1.090000e-154 556.0
26 TraesCS2A01G138500 chr4D 76.728 1461 244 51 1040 2449 31447468 31446053 0.000000e+00 726.0
27 TraesCS2A01G138500 chr4D 76.461 633 115 23 2845 3470 349181595 349180990 2.600000e-81 313.0
28 TraesCS2A01G138500 chr3A 83.706 761 91 23 1 745 705884537 705883794 0.000000e+00 688.0
29 TraesCS2A01G138500 chr6B 86.355 535 59 9 9 534 450804039 450803510 3.890000e-159 571.0
30 TraesCS2A01G138500 chr6B 85.714 476 56 9 3 470 668973695 668974166 3.110000e-135 492.0
31 TraesCS2A01G138500 chr1D 85.661 537 61 11 9 534 62156764 62157295 5.060000e-153 551.0
32 TraesCS2A01G138500 chr3D 91.489 47 2 2 2109 2154 22291202 22291157 2.890000e-06 63.9
33 TraesCS2A01G138500 chr3D 95.000 40 0 2 766 803 71375916 71375955 1.040000e-05 62.1


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 TraesCS2A01G138500 chr2A 83854899 83858368 3469 True 6408.0 6408 100.000 1 3470 1 chr2A.!!$R2 3469
1 TraesCS2A01G138500 chr2A 85291749 85293173 1424 False 1581.0 1581 87.014 1041 2450 1 chr2A.!!$F1 1409
2 TraesCS2A01G138500 chr2A 85589897 85591306 1409 False 1537.0 1537 86.681 1062 2450 1 chr2A.!!$F2 1388
3 TraesCS2A01G138500 chr2A 83847942 83849031 1089 True 1062.0 1062 84.258 1040 2156 1 chr2A.!!$R1 1116
4 TraesCS2A01G138500 chr2A 717252985 717254339 1354 False 752.0 752 77.413 1041 2437 1 chr2A.!!$F3 1396
5 TraesCS2A01G138500 chr2D 83156122 83157819 1697 True 2726.0 2726 95.703 758 2450 1 chr2D.!!$R1 1692
6 TraesCS2A01G138500 chr2D 84742929 84744404 1475 False 1546.0 1546 86.067 999 2450 1 chr2D.!!$F1 1451
7 TraesCS2A01G138500 chr2D 579740523 579741886 1363 False 710.0 710 76.848 1041 2437 1 chr2D.!!$F3 1396
8 TraesCS2A01G138500 chr2D 450948763 450949473 710 False 689.0 689 84.203 1 744 1 chr2D.!!$F2 743
9 TraesCS2A01G138500 chr2B 135085087 135090257 5170 True 1746.5 1775 90.394 758 3470 2 chr2B.!!$R2 2712
10 TraesCS2A01G138500 chr2B 135024971 135026378 1407 True 1430.0 1430 85.206 1038 2450 1 chr2B.!!$R1 1412
11 TraesCS2A01G138500 chr2B 136434748 136435612 864 False 1042.0 1042 88.610 1587 2449 1 chr2B.!!$F1 862
12 TraesCS2A01G138500 chr2B 697665487 697666848 1361 False 702.0 702 76.746 1042 2437 1 chr2B.!!$F2 1395
13 TraesCS2A01G138500 chr5A 461590718 461591493 775 False 852.0 852 87.340 3 742 1 chr5A.!!$F1 739
14 TraesCS2A01G138500 chr7A 650970265 650971046 781 True 850.0 850 87.134 1 744 1 chr7A.!!$R1 743
15 TraesCS2A01G138500 chr7A 177926537 177927073 536 False 440.0 440 81.952 9 536 1 chr7A.!!$F1 527
16 TraesCS2A01G138500 chr6A 123500942 123501712 770 True 837.0 837 86.985 1 742 1 chr6A.!!$R1 741
17 TraesCS2A01G138500 chr5D 486838340 486839088 748 True 800.0 800 86.316 1 742 1 chr5D.!!$R1 741
18 TraesCS2A01G138500 chr4B 44944547 44945944 1397 False 798.0 798 77.578 1040 2449 1 chr4B.!!$F1 1409
19 TraesCS2A01G138500 chr4A 186693137 186693906 769 True 789.0 789 85.951 1 744 1 chr4A.!!$R1 743
20 TraesCS2A01G138500 chr4A 124370014 124370803 789 False 754.0 754 84.829 1 746 1 chr4A.!!$F2 745
21 TraesCS2A01G138500 chr4A 571483458 571484904 1446 True 747.0 747 76.676 1000 2449 1 chr4A.!!$R2 1449
22 TraesCS2A01G138500 chr7D 37106363 37107115 752 True 787.0 787 85.903 1 742 1 chr7D.!!$R1 741
23 TraesCS2A01G138500 chr7D 137790931 137791476 545 True 556.0 556 85.560 3 538 1 chr7D.!!$R2 535
24 TraesCS2A01G138500 chr4D 31446053 31447468 1415 True 726.0 726 76.728 1040 2449 1 chr4D.!!$R1 1409
25 TraesCS2A01G138500 chr4D 349180990 349181595 605 True 313.0 313 76.461 2845 3470 1 chr4D.!!$R2 625
26 TraesCS2A01G138500 chr3A 705883794 705884537 743 True 688.0 688 83.706 1 745 1 chr3A.!!$R1 744
27 TraesCS2A01G138500 chr6B 450803510 450804039 529 True 571.0 571 86.355 9 534 1 chr6B.!!$R1 525
28 TraesCS2A01G138500 chr1D 62156764 62157295 531 False 551.0 551 85.661 9 534 1 chr1D.!!$F1 525

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
728 862 0.174845 CGTCCTTGATAGGCCAACGA 59.825 55.0 5.01 0.0 40.08 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2584 5332 0.108329 AGACGGACAATTACCAGGCG 60.108 55.0 0.0 0.0 0.0 5.52 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
163 170 4.824515 CCCTCGTCGGCTCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
197 204 4.742649 AGACGGAGCCGAGCCTGA 62.743 66.667 16.83 0.00 42.83 3.86
314 330 1.617947 GGACTCCCTGAAGATGGCGT 61.618 60.000 0.00 0.00 0.00 5.68
383 450 1.791283 CGAGGACAACGACGACGAC 60.791 63.158 15.32 0.00 42.66 4.34
481 562 2.277120 GGACGACGACGATGACGG 60.277 66.667 15.32 0.00 44.46 4.79
665 798 1.761174 GAGACCAACTCAGCCCCAA 59.239 57.895 0.00 0.00 44.36 4.12
690 823 3.772096 TTTTTGCCCTGGCTCATCT 57.228 47.368 9.97 0.00 42.51 2.90
714 848 3.134804 CAGGGGATGATTTTAGACGTCCT 59.865 47.826 13.01 2.17 40.72 3.85
718 852 5.368989 GGGATGATTTTAGACGTCCTTGAT 58.631 41.667 13.01 1.67 40.72 2.57
719 853 6.463897 GGGGATGATTTTAGACGTCCTTGATA 60.464 42.308 13.01 0.00 40.72 2.15
728 862 0.174845 CGTCCTTGATAGGCCAACGA 59.825 55.000 5.01 0.00 40.08 3.85
746 880 6.037423 CAACGACTGGAAATGCTCTAATAC 57.963 41.667 0.00 0.00 0.00 1.89
747 881 5.339008 ACGACTGGAAATGCTCTAATACA 57.661 39.130 0.00 0.00 0.00 2.29
748 882 5.730550 ACGACTGGAAATGCTCTAATACAA 58.269 37.500 0.00 0.00 0.00 2.41
749 883 6.349300 ACGACTGGAAATGCTCTAATACAAT 58.651 36.000 0.00 0.00 0.00 2.71
750 884 6.823689 ACGACTGGAAATGCTCTAATACAATT 59.176 34.615 0.00 0.00 0.00 2.32
751 885 7.011482 ACGACTGGAAATGCTCTAATACAATTC 59.989 37.037 0.00 0.00 0.00 2.17
752 886 7.225538 CGACTGGAAATGCTCTAATACAATTCT 59.774 37.037 0.00 0.00 0.00 2.40
753 887 8.814038 ACTGGAAATGCTCTAATACAATTCTT 57.186 30.769 0.00 0.00 0.00 2.52
754 888 8.680903 ACTGGAAATGCTCTAATACAATTCTTG 58.319 33.333 0.00 0.00 0.00 3.02
755 889 7.483307 TGGAAATGCTCTAATACAATTCTTGC 58.517 34.615 0.00 0.00 0.00 4.01
756 890 6.634436 GGAAATGCTCTAATACAATTCTTGCG 59.366 38.462 0.00 0.00 0.00 4.85
757 891 5.679734 ATGCTCTAATACAATTCTTGCGG 57.320 39.130 0.00 0.00 0.00 5.69
758 892 3.312421 TGCTCTAATACAATTCTTGCGGC 59.688 43.478 0.00 0.00 0.00 6.53
759 893 3.604772 GCTCTAATACAATTCTTGCGGCG 60.605 47.826 0.51 0.51 0.00 6.46
760 894 3.527533 TCTAATACAATTCTTGCGGCGT 58.472 40.909 9.37 0.00 0.00 5.68
761 895 2.542766 AATACAATTCTTGCGGCGTG 57.457 45.000 9.37 0.00 0.00 5.34
845 990 2.887152 GACCAGGCATGTGGGATTAATC 59.113 50.000 6.93 6.93 42.54 1.75
874 1019 3.747976 GCCGCACGCTCCCAAAAT 61.748 61.111 0.00 0.00 0.00 1.82
883 1028 4.755123 GCACGCTCCCAAAATACTGTATAT 59.245 41.667 0.00 0.00 0.00 0.86
885 1030 6.425721 GCACGCTCCCAAAATACTGTATATTA 59.574 38.462 0.00 0.00 0.00 0.98
923 1068 2.421952 CGAATGGGATCACACCTTGGAT 60.422 50.000 0.00 0.00 0.00 3.41
953 1098 0.883833 CAAGACCACAACCAGCATCC 59.116 55.000 0.00 0.00 0.00 3.51
993 1138 2.030274 GCACTGCAAGAATTAACCCGTT 60.030 45.455 0.00 0.00 37.43 4.44
996 1141 2.556622 CTGCAAGAATTAACCCGTTGGT 59.443 45.455 0.00 0.00 42.42 3.67
1166 1326 1.873903 CGTCACCTTCACCAACCTCTG 60.874 57.143 0.00 0.00 0.00 3.35
2145 4854 2.425592 CACTGCGGGTGGAACTCA 59.574 61.111 0.00 0.00 36.87 3.41
2220 4929 2.167861 GCAGAGGATGAACGCCGTC 61.168 63.158 0.00 0.00 0.00 4.79
2257 4966 2.401766 GGAGTGGCATTGCGAGTGG 61.402 63.158 5.66 0.00 0.00 4.00
2289 5028 3.286694 ATGCTTGGTGACCCGCCAT 62.287 57.895 9.97 2.02 43.92 4.40
2487 5235 4.661222 TGTAGTGCATGATCCTCCAAAAA 58.339 39.130 0.00 0.00 0.00 1.94
2511 5259 4.093408 TGCTCTCATCGTACTTCATTTTGC 59.907 41.667 0.00 0.00 0.00 3.68
2520 5268 6.884187 TCGTACTTCATTTTGCTGTTACTTC 58.116 36.000 0.00 0.00 0.00 3.01
2531 5279 4.684877 TGCTGTTACTTCGTGACTTTGTA 58.315 39.130 0.00 0.00 0.00 2.41
2533 5281 6.448852 TGCTGTTACTTCGTGACTTTGTATA 58.551 36.000 0.00 0.00 0.00 1.47
2534 5282 6.924612 TGCTGTTACTTCGTGACTTTGTATAA 59.075 34.615 0.00 0.00 0.00 0.98
2547 5295 7.754924 GTGACTTTGTATAATGGTCATTTGGTG 59.245 37.037 1.28 0.00 38.80 4.17
2561 5309 4.278170 TCATTTGGTGTGAAGTGATCCAAC 59.722 41.667 0.00 0.00 37.80 3.77
2562 5310 1.877637 TGGTGTGAAGTGATCCAACG 58.122 50.000 0.00 0.00 0.00 4.10
2565 5313 0.396435 TGTGAAGTGATCCAACGGCT 59.604 50.000 0.00 0.00 0.00 5.52
2571 5319 0.460987 GTGATCCAACGGCTCCTCAG 60.461 60.000 0.00 0.00 0.00 3.35
2572 5320 1.144936 GATCCAACGGCTCCTCAGG 59.855 63.158 0.00 0.00 0.00 3.86
2574 5322 4.785453 CCAACGGCTCCTCAGGCC 62.785 72.222 0.00 0.00 42.44 5.19
2584 5332 1.119574 TCCTCAGGCCCGCCTTATAC 61.120 60.000 5.22 0.00 45.70 1.47
2589 5337 2.665185 GCCCGCCTTATACGCCTG 60.665 66.667 0.00 0.00 0.00 4.85
2592 5340 1.466025 CCCGCCTTATACGCCTGGTA 61.466 60.000 0.00 0.00 35.11 3.25
2599 5347 4.062991 CCTTATACGCCTGGTAATTGTCC 58.937 47.826 0.00 0.00 34.09 4.02
2626 5374 0.663153 AAAAGCAACGCAGAGTCACC 59.337 50.000 0.00 0.00 0.00 4.02
2628 5376 2.355837 GCAACGCAGAGTCACCGA 60.356 61.111 9.08 0.00 0.00 4.69
2629 5377 2.375766 GCAACGCAGAGTCACCGAG 61.376 63.158 9.08 3.39 0.00 4.63
2631 5379 1.007271 AACGCAGAGTCACCGAGTG 60.007 57.895 9.08 0.00 34.45 3.51
2643 5395 2.179517 CGAGTGACTCCTCGCACC 59.820 66.667 7.07 0.00 46.64 5.01
2647 5399 3.371063 TGACTCCTCGCACCGACC 61.371 66.667 0.00 0.00 0.00 4.79
2662 5414 1.663695 CGACCGGCACCTTTCATATT 58.336 50.000 0.00 0.00 0.00 1.28
2667 5419 2.614057 CCGGCACCTTTCATATTCAGTC 59.386 50.000 0.00 0.00 0.00 3.51
2668 5420 2.614057 CGGCACCTTTCATATTCAGTCC 59.386 50.000 0.00 0.00 0.00 3.85
2682 5434 3.762407 TCAGTCCAAATCTTGAACGGA 57.238 42.857 0.00 0.00 0.00 4.69
2689 5441 5.237344 GTCCAAATCTTGAACGGATATGAGG 59.763 44.000 0.00 0.00 0.00 3.86
2696 5448 1.472662 AACGGATATGAGGAGGCCCG 61.473 60.000 0.00 0.00 42.30 6.13
2727 5479 1.080093 GTCTTCGCCATGTCGGACA 60.080 57.895 14.01 14.01 36.56 4.02
2740 5492 0.827925 TCGGACAAGACAGGCAGACT 60.828 55.000 0.00 0.00 0.00 3.24
2759 5511 1.967066 CTGTACCCCAAATTGCACCAA 59.033 47.619 0.00 0.00 0.00 3.67
2763 5515 1.126948 CCCCAAATTGCACCAACCCT 61.127 55.000 0.00 0.00 0.00 4.34
2767 5519 2.524306 CAAATTGCACCAACCCTCCTA 58.476 47.619 0.00 0.00 0.00 2.94
2768 5520 2.215942 AATTGCACCAACCCTCCTAC 57.784 50.000 0.00 0.00 0.00 3.18
2773 5525 2.126372 CCAACCCTCCTACCCCCA 59.874 66.667 0.00 0.00 0.00 4.96
2774 5526 1.308746 CCAACCCTCCTACCCCCAT 60.309 63.158 0.00 0.00 0.00 4.00
2775 5527 1.353394 CCAACCCTCCTACCCCCATC 61.353 65.000 0.00 0.00 0.00 3.51
2776 5528 0.327576 CAACCCTCCTACCCCCATCT 60.328 60.000 0.00 0.00 0.00 2.90
2777 5529 1.061657 CAACCCTCCTACCCCCATCTA 60.062 57.143 0.00 0.00 0.00 1.98
2778 5530 0.868186 ACCCTCCTACCCCCATCTAG 59.132 60.000 0.00 0.00 0.00 2.43
2779 5531 0.545548 CCCTCCTACCCCCATCTAGC 60.546 65.000 0.00 0.00 0.00 3.42
2780 5532 0.545548 CCTCCTACCCCCATCTAGCC 60.546 65.000 0.00 0.00 0.00 3.93
2781 5533 0.191064 CTCCTACCCCCATCTAGCCA 59.809 60.000 0.00 0.00 0.00 4.75
2782 5534 0.645496 TCCTACCCCCATCTAGCCAA 59.355 55.000 0.00 0.00 0.00 4.52
2799 5551 7.586349 TCTAGCCAATTCCAATTATTTCTCCT 58.414 34.615 0.00 0.00 0.00 3.69
2816 5568 3.596046 TCTCCTCTCTCTTCTTCCTCCTT 59.404 47.826 0.00 0.00 0.00 3.36
2817 5569 3.701040 CTCCTCTCTCTTCTTCCTCCTTG 59.299 52.174 0.00 0.00 0.00 3.61
2818 5570 2.168313 CCTCTCTCTTCTTCCTCCTTGC 59.832 54.545 0.00 0.00 0.00 4.01
2819 5571 2.830923 CTCTCTCTTCTTCCTCCTTGCA 59.169 50.000 0.00 0.00 0.00 4.08
2821 5573 1.905215 TCTCTTCTTCCTCCTTGCAGG 59.095 52.381 0.00 0.00 36.46 4.85
2823 5575 0.679321 CTTCTTCCTCCTTGCAGGCC 60.679 60.000 0.00 0.00 34.61 5.19
2824 5576 1.426251 TTCTTCCTCCTTGCAGGCCA 61.426 55.000 5.01 0.00 34.61 5.36
2827 5579 4.748144 CCTCCTTGCAGGCCACCC 62.748 72.222 5.01 0.00 34.61 4.61
2828 5580 3.655211 CTCCTTGCAGGCCACCCT 61.655 66.667 5.01 0.00 44.25 4.34
2829 5581 2.204074 TCCTTGCAGGCCACCCTA 60.204 61.111 5.01 0.00 40.33 3.53
2830 5582 2.262774 CTCCTTGCAGGCCACCCTAG 62.263 65.000 5.01 0.00 40.33 3.02
2833 5585 2.883267 CTTGCAGGCCACCCTAGCTC 62.883 65.000 5.01 0.00 40.33 4.09
2834 5586 3.086600 GCAGGCCACCCTAGCTCT 61.087 66.667 5.01 0.00 40.33 4.09
2835 5587 2.906458 CAGGCCACCCTAGCTCTG 59.094 66.667 5.01 0.00 40.33 3.35
2836 5588 3.086600 AGGCCACCCTAGCTCTGC 61.087 66.667 5.01 0.00 40.58 4.26
2837 5589 4.182433 GGCCACCCTAGCTCTGCC 62.182 72.222 0.00 0.00 0.00 4.85
2838 5590 3.402681 GCCACCCTAGCTCTGCCA 61.403 66.667 0.00 0.00 0.00 4.92
2839 5591 2.586792 CCACCCTAGCTCTGCCAC 59.413 66.667 0.00 0.00 0.00 5.01
2840 5592 2.586792 CACCCTAGCTCTGCCACC 59.413 66.667 0.00 0.00 0.00 4.61
2841 5593 2.122729 ACCCTAGCTCTGCCACCA 59.877 61.111 0.00 0.00 0.00 4.17
2842 5594 1.307343 ACCCTAGCTCTGCCACCAT 60.307 57.895 0.00 0.00 0.00 3.55
2843 5595 0.916358 ACCCTAGCTCTGCCACCATT 60.916 55.000 0.00 0.00 0.00 3.16
2894 5647 4.169696 TGCCGCCCCAATAGTCCG 62.170 66.667 0.00 0.00 0.00 4.79
2907 5675 0.974010 TAGTCCGCCCATCCGTTCTT 60.974 55.000 0.00 0.00 0.00 2.52
2929 5697 2.158959 GCCACGGACTTCATCGTCG 61.159 63.158 0.00 0.00 37.53 5.12
2937 5705 3.151710 TTCATCGTCGGCCCGGAT 61.152 61.111 0.73 0.00 0.00 4.18
2986 5754 0.995024 ACTGCACCTTGCCCTCTATT 59.005 50.000 0.00 0.00 44.23 1.73
3012 5780 1.702886 GACACATCGTCTGACCAGTG 58.297 55.000 15.80 15.80 41.81 3.66
3017 5785 3.312421 CACATCGTCTGACCAGTGTTTTT 59.688 43.478 1.55 0.00 0.00 1.94
3018 5786 4.509970 CACATCGTCTGACCAGTGTTTTTA 59.490 41.667 1.55 0.00 0.00 1.52
3037 5806 9.535878 TGTTTTTAATCGTTTCTTAGGCAAAAT 57.464 25.926 0.00 0.00 0.00 1.82
3062 5831 4.191544 TGAATTCAGATGGTTCATCGGAC 58.808 43.478 3.38 1.79 42.66 4.79
3074 5843 0.598562 CATCGGACGAGGAGTATGGG 59.401 60.000 0.00 0.00 0.00 4.00
3075 5844 0.185416 ATCGGACGAGGAGTATGGGT 59.815 55.000 0.00 0.00 0.00 4.51
3093 5862 2.612972 GGGTCGACAGAGCTTGATGAAA 60.613 50.000 18.91 0.00 43.89 2.69
3154 5926 3.663995 AGAAGCCGAGATGATCATGAG 57.336 47.619 14.30 3.86 0.00 2.90
3208 5981 5.450412 GGTGAAGCACATTCTCAACTTCAAA 60.450 40.000 5.40 0.00 45.87 2.69
3212 5985 3.858503 GCACATTCTCAACTTCAAAGGCC 60.859 47.826 0.00 0.00 0.00 5.19
3213 5986 3.571401 CACATTCTCAACTTCAAAGGCCT 59.429 43.478 0.00 0.00 0.00 5.19
3252 6025 1.358152 TTGAACCAGGATCGGGTCTT 58.642 50.000 8.02 0.00 43.76 3.01
3290 6063 5.931294 TGTACAATGACTACTTTGTTCCCA 58.069 37.500 0.00 0.00 41.96 4.37
3292 6065 5.767816 ACAATGACTACTTTGTTCCCAAC 57.232 39.130 0.00 0.00 40.01 3.77
3297 6070 4.149598 GACTACTTTGTTCCCAACCCAAT 58.850 43.478 0.00 0.00 0.00 3.16
3321 6094 3.889815 TCACTGATGATCCATGGTTTCC 58.110 45.455 12.58 0.18 0.00 3.13
3333 6106 0.841289 TGGTTTCCTCAACGGTTCCT 59.159 50.000 0.00 0.00 36.05 3.36
3340 6113 1.674817 CCTCAACGGTTCCTTATGCGT 60.675 52.381 0.00 0.00 0.00 5.24
3345 6118 3.323751 ACGGTTCCTTATGCGTAAACT 57.676 42.857 0.00 0.00 0.00 2.66
3350 6123 5.277154 CGGTTCCTTATGCGTAAACTATTGG 60.277 44.000 0.00 0.00 0.00 3.16
3359 6132 2.413796 CGTAAACTATTGGTCTTGCGCA 59.586 45.455 5.66 5.66 0.00 6.09
3397 6170 3.031736 GGCACACTATCCCTACTTCAGA 58.968 50.000 0.00 0.00 0.00 3.27
3403 6176 5.830991 ACACTATCCCTACTTCAGACTCATC 59.169 44.000 0.00 0.00 0.00 2.92
3452 6225 1.807139 TGCTAAGCAGAAATGCACGA 58.193 45.000 2.73 0.00 37.25 4.35
3467 6240 1.203523 GCACGACTTCTCTGAGGATGT 59.796 52.381 4.59 1.63 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
197 204 4.052229 CTCCGTCTTCACCGGCGT 62.052 66.667 6.01 0.00 45.09 5.68
230 245 2.125512 GCCGTGCTCCGTCTTCAT 60.126 61.111 0.00 0.00 33.66 2.57
359 426 0.109919 CGTCGTTGTCCTCGATGACA 60.110 55.000 18.12 18.12 44.02 3.58
443 524 0.108756 GCTTCTCCTCCTTAACGCGT 60.109 55.000 5.58 5.58 0.00 6.01
449 530 1.035932 CGTCCGGCTTCTCCTCCTTA 61.036 60.000 0.00 0.00 0.00 2.69
473 554 4.509883 TCGTCGTCGCCGTCATCG 62.510 66.667 0.00 0.00 36.96 3.84
474 555 2.943034 GTCGTCGTCGCCGTCATC 60.943 66.667 0.00 0.00 36.96 2.92
475 556 4.806481 CGTCGTCGTCGCCGTCAT 62.806 66.667 0.00 0.00 33.79 3.06
565 681 8.495949 CAAAGTTCGAAGTTCGGCATATATTAT 58.504 33.333 24.18 0.00 40.88 1.28
632 764 3.691342 CTCCAGTCGTCGGCCCAA 61.691 66.667 0.00 0.00 0.00 4.12
643 776 1.484444 GGGCTGAGTTGGTCTCCAGT 61.484 60.000 0.00 0.00 42.12 4.00
679 812 0.984961 TCCCCTGAAGATGAGCCAGG 60.985 60.000 0.00 0.00 45.28 4.45
681 814 0.841961 CATCCCCTGAAGATGAGCCA 59.158 55.000 0.00 0.00 43.15 4.75
688 821 4.469945 ACGTCTAAAATCATCCCCTGAAGA 59.530 41.667 0.00 0.00 37.44 2.87
690 823 4.383770 GGACGTCTAAAATCATCCCCTGAA 60.384 45.833 16.46 0.00 37.44 3.02
714 848 3.853104 CCAGTCGTTGGCCTATCAA 57.147 52.632 3.32 0.00 40.87 2.57
728 862 8.680903 CAAGAATTGTATTAGAGCATTTCCAGT 58.319 33.333 0.00 0.00 42.34 4.00
747 881 2.672996 AGCCACGCCGCAAGAATT 60.673 55.556 0.00 0.00 43.02 2.17
748 882 3.127533 GAGCCACGCCGCAAGAAT 61.128 61.111 0.00 0.00 43.02 2.40
749 883 4.314440 AGAGCCACGCCGCAAGAA 62.314 61.111 0.00 0.00 43.02 2.52
750 884 4.742201 GAGAGCCACGCCGCAAGA 62.742 66.667 0.00 0.00 43.02 3.02
751 885 3.356639 TAGAGAGCCACGCCGCAAG 62.357 63.158 0.00 0.00 0.00 4.01
752 886 3.378602 TAGAGAGCCACGCCGCAA 61.379 61.111 0.00 0.00 0.00 4.85
753 887 4.129737 GTAGAGAGCCACGCCGCA 62.130 66.667 0.00 0.00 0.00 5.69
754 888 3.642778 TTGTAGAGAGCCACGCCGC 62.643 63.158 0.00 0.00 0.00 6.53
755 889 1.080093 TTTGTAGAGAGCCACGCCG 60.080 57.895 0.00 0.00 0.00 6.46
756 890 0.037232 AGTTTGTAGAGAGCCACGCC 60.037 55.000 0.00 0.00 0.00 5.68
757 891 1.336887 TGAGTTTGTAGAGAGCCACGC 60.337 52.381 0.00 0.00 0.00 5.34
758 892 2.724977 TGAGTTTGTAGAGAGCCACG 57.275 50.000 0.00 0.00 0.00 4.94
759 893 4.258702 TCTTGAGTTTGTAGAGAGCCAC 57.741 45.455 0.00 0.00 0.00 5.01
760 894 5.489792 AATCTTGAGTTTGTAGAGAGCCA 57.510 39.130 0.00 0.00 0.00 4.75
761 895 7.907214 TTAAATCTTGAGTTTGTAGAGAGCC 57.093 36.000 0.00 0.00 0.00 4.70
859 1004 0.096976 CAGTATTTTGGGAGCGTGCG 59.903 55.000 0.00 0.00 0.00 5.34
883 1028 4.717233 TCGGCATTTTACGAGGTAGTAA 57.283 40.909 0.00 0.00 35.07 2.24
885 1030 3.598019 TTCGGCATTTTACGAGGTAGT 57.402 42.857 0.00 0.00 40.51 2.73
913 1058 2.278245 TGGATCTGGAATCCAAGGTGT 58.722 47.619 2.61 0.00 44.54 4.16
923 1068 2.054021 TGTGGTCTTGTGGATCTGGAA 58.946 47.619 0.00 0.00 0.00 3.53
993 1138 2.530661 AACGACCCCATCCCACCA 60.531 61.111 0.00 0.00 0.00 4.17
996 1141 2.598787 GGTCAACGACCCCATCCCA 61.599 63.158 1.47 0.00 46.19 4.37
1665 1873 4.379813 GGTTCCATCTCGTAGAACGTGTTA 60.380 45.833 0.00 0.00 43.14 2.41
1786 2000 3.447025 CTTCGTCGGGATCTGGCCC 62.447 68.421 0.00 0.00 45.10 5.80
2220 4929 2.238144 TCCAAGCCTCTCTTCCAGAATG 59.762 50.000 0.00 0.00 31.27 2.67
2289 5028 3.060000 ACGACGGTGGCGATCTCA 61.060 61.111 0.00 0.00 0.00 3.27
2425 5173 2.436646 CGCCGCCTTCCACTTGAT 60.437 61.111 0.00 0.00 0.00 2.57
2483 5231 6.992063 ATGAAGTACGATGAGAGCATTTTT 57.008 33.333 0.00 0.00 34.11 1.94
2487 5235 5.220739 GCAAAATGAAGTACGATGAGAGCAT 60.221 40.000 0.00 0.00 37.47 3.79
2511 5259 8.380644 CCATTATACAAAGTCACGAAGTAACAG 58.619 37.037 0.00 0.00 41.61 3.16
2520 5268 6.966632 CCAAATGACCATTATACAAAGTCACG 59.033 38.462 0.00 0.00 40.04 4.35
2531 5279 6.009589 TCACTTCACACCAAATGACCATTAT 58.990 36.000 0.00 0.00 0.00 1.28
2533 5281 4.214310 TCACTTCACACCAAATGACCATT 58.786 39.130 0.00 0.00 0.00 3.16
2534 5282 3.831323 TCACTTCACACCAAATGACCAT 58.169 40.909 0.00 0.00 0.00 3.55
2547 5295 1.079503 GAGCCGTTGGATCACTTCAC 58.920 55.000 0.00 0.00 38.12 3.18
2571 5319 3.937447 AGGCGTATAAGGCGGGCC 61.937 66.667 0.18 0.18 44.07 5.80
2572 5320 2.665185 CAGGCGTATAAGGCGGGC 60.665 66.667 6.58 0.00 41.99 6.13
2574 5322 0.390124 TTACCAGGCGTATAAGGCGG 59.610 55.000 16.40 16.40 41.99 6.13
2584 5332 0.108329 AGACGGACAATTACCAGGCG 60.108 55.000 0.00 0.00 0.00 5.52
2610 5358 2.356313 CGGTGACTCTGCGTTGCT 60.356 61.111 0.00 0.00 0.00 3.91
2628 5376 2.282251 TCGGTGCGAGGAGTCACT 60.282 61.111 0.00 0.00 33.91 3.41
2629 5377 2.126424 GTCGGTGCGAGGAGTCAC 60.126 66.667 0.00 0.00 36.23 3.67
2631 5379 4.477975 CGGTCGGTGCGAGGAGTC 62.478 72.222 0.00 0.00 36.23 3.36
2640 5392 3.047877 GAAAGGTGCCGGTCGGTG 61.048 66.667 11.25 0.00 37.65 4.94
2641 5393 1.546589 TATGAAAGGTGCCGGTCGGT 61.547 55.000 11.25 0.00 37.65 4.69
2643 5395 1.597663 GAATATGAAAGGTGCCGGTCG 59.402 52.381 1.90 0.00 0.00 4.79
2647 5399 2.614057 GGACTGAATATGAAAGGTGCCG 59.386 50.000 0.00 0.00 0.00 5.69
2649 5401 5.643379 TTTGGACTGAATATGAAAGGTGC 57.357 39.130 0.00 0.00 0.00 5.01
2654 5406 8.236586 CGTTCAAGATTTGGACTGAATATGAAA 58.763 33.333 0.00 0.00 37.00 2.69
2655 5407 7.148255 CCGTTCAAGATTTGGACTGAATATGAA 60.148 37.037 0.00 0.00 37.00 2.57
2662 5414 3.762407 TCCGTTCAAGATTTGGACTGA 57.238 42.857 0.00 0.00 37.00 3.41
2667 5419 5.368145 TCCTCATATCCGTTCAAGATTTGG 58.632 41.667 0.00 0.00 0.00 3.28
2668 5420 5.468072 CCTCCTCATATCCGTTCAAGATTTG 59.532 44.000 0.00 0.00 0.00 2.32
2682 5434 2.574955 GCGTCGGGCCTCCTCATAT 61.575 63.158 0.84 0.00 34.80 1.78
2710 5462 0.389817 CTTGTCCGACATGGCGAAGA 60.390 55.000 25.84 9.56 37.80 2.87
2711 5463 0.389817 TCTTGTCCGACATGGCGAAG 60.390 55.000 25.84 18.44 37.80 3.79
2713 5465 1.080093 GTCTTGTCCGACATGGCGA 60.080 57.895 25.84 5.65 37.80 5.54
2719 5471 1.112916 TCTGCCTGTCTTGTCCGACA 61.113 55.000 0.00 0.00 41.33 4.35
2720 5472 0.667792 GTCTGCCTGTCTTGTCCGAC 60.668 60.000 0.00 0.00 34.52 4.79
2735 5487 2.228822 GTGCAATTTGGGGTACAGTCTG 59.771 50.000 0.00 0.00 0.00 3.51
2740 5492 1.689273 GTTGGTGCAATTTGGGGTACA 59.311 47.619 0.00 0.00 0.00 2.90
2745 5497 0.321346 GAGGGTTGGTGCAATTTGGG 59.679 55.000 0.00 0.00 0.00 4.12
2759 5511 0.868186 CTAGATGGGGGTAGGAGGGT 59.132 60.000 0.00 0.00 0.00 4.34
2763 5515 0.645496 TTGGCTAGATGGGGGTAGGA 59.355 55.000 0.00 0.00 0.00 2.94
2767 5519 0.853530 GGAATTGGCTAGATGGGGGT 59.146 55.000 0.00 0.00 0.00 4.95
2768 5520 0.852842 TGGAATTGGCTAGATGGGGG 59.147 55.000 0.00 0.00 0.00 5.40
2773 5525 8.230306 AGGAGAAATAATTGGAATTGGCTAGAT 58.770 33.333 0.00 0.00 0.00 1.98
2774 5526 7.586349 AGGAGAAATAATTGGAATTGGCTAGA 58.414 34.615 0.00 0.00 0.00 2.43
2775 5527 7.723172 AGAGGAGAAATAATTGGAATTGGCTAG 59.277 37.037 0.00 0.00 0.00 3.42
2776 5528 7.586349 AGAGGAGAAATAATTGGAATTGGCTA 58.414 34.615 0.00 0.00 0.00 3.93
2777 5529 6.438620 AGAGGAGAAATAATTGGAATTGGCT 58.561 36.000 0.00 0.00 0.00 4.75
2778 5530 6.548993 AGAGAGGAGAAATAATTGGAATTGGC 59.451 38.462 0.00 0.00 0.00 4.52
2779 5531 7.997803 AGAGAGAGGAGAAATAATTGGAATTGG 59.002 37.037 0.00 0.00 0.00 3.16
2780 5532 8.977267 AGAGAGAGGAGAAATAATTGGAATTG 57.023 34.615 0.00 0.00 0.00 2.32
2781 5533 9.625747 GAAGAGAGAGGAGAAATAATTGGAATT 57.374 33.333 0.00 0.00 0.00 2.17
2782 5534 9.002061 AGAAGAGAGAGGAGAAATAATTGGAAT 57.998 33.333 0.00 0.00 0.00 3.01
2799 5551 2.830923 CTGCAAGGAGGAAGAAGAGAGA 59.169 50.000 0.00 0.00 0.00 3.10
2816 5568 3.402681 GAGCTAGGGTGGCCTGCA 61.403 66.667 3.32 0.00 0.00 4.41
2817 5569 3.086600 AGAGCTAGGGTGGCCTGC 61.087 66.667 3.32 0.00 0.00 4.85
2818 5570 2.906458 CAGAGCTAGGGTGGCCTG 59.094 66.667 3.32 0.00 0.00 4.85
2819 5571 3.086600 GCAGAGCTAGGGTGGCCT 61.087 66.667 3.32 0.00 0.00 5.19
2821 5573 3.402681 TGGCAGAGCTAGGGTGGC 61.403 66.667 0.00 0.00 37.28 5.01
2823 5575 1.630126 ATGGTGGCAGAGCTAGGGTG 61.630 60.000 0.00 0.00 0.00 4.61
2824 5576 0.916358 AATGGTGGCAGAGCTAGGGT 60.916 55.000 0.00 0.00 0.00 4.34
2827 5579 1.202627 GGAGAATGGTGGCAGAGCTAG 60.203 57.143 0.00 0.00 0.00 3.42
2828 5580 0.833287 GGAGAATGGTGGCAGAGCTA 59.167 55.000 0.00 0.00 0.00 3.32
2829 5581 1.606531 GGAGAATGGTGGCAGAGCT 59.393 57.895 0.00 0.00 0.00 4.09
2830 5582 1.817099 CGGAGAATGGTGGCAGAGC 60.817 63.158 0.00 0.00 0.00 4.09
2833 5585 1.811266 CGACGGAGAATGGTGGCAG 60.811 63.158 0.00 0.00 0.00 4.85
2834 5586 2.264480 CGACGGAGAATGGTGGCA 59.736 61.111 0.00 0.00 0.00 4.92
2835 5587 3.195698 GCGACGGAGAATGGTGGC 61.196 66.667 0.00 0.00 0.00 5.01
2836 5588 2.511600 GGCGACGGAGAATGGTGG 60.512 66.667 0.00 0.00 0.00 4.61
2877 5630 4.169696 CGGACTATTGGGGCGGCA 62.170 66.667 12.47 0.00 0.00 5.69
2888 5641 0.974010 AAGAACGGATGGGCGGACTA 60.974 55.000 0.00 0.00 0.00 2.59
2894 5647 3.508840 CGGCAAGAACGGATGGGC 61.509 66.667 0.00 0.00 0.00 5.36
2916 5684 2.202892 GGGCCGACGATGAAGTCC 60.203 66.667 0.00 0.00 37.85 3.85
2920 5688 3.151710 ATCCGGGCCGACGATGAA 61.152 61.111 30.79 3.56 35.47 2.57
2929 5697 2.908940 CCTGATTGCATCCGGGCC 60.909 66.667 0.00 0.00 30.83 5.80
2937 5705 2.040947 TGTTGGATGTACCCTGATTGCA 59.959 45.455 0.00 0.00 38.00 4.08
2942 5710 3.248024 AGAGTTGTTGGATGTACCCTGA 58.752 45.455 0.00 0.00 38.00 3.86
2945 5713 2.618053 CGAGAGTTGTTGGATGTACCC 58.382 52.381 0.00 0.00 38.00 3.69
3004 5772 6.687081 AGAAACGATTAAAAACACTGGTCA 57.313 33.333 0.00 0.00 0.00 4.02
3005 5773 7.801783 CCTAAGAAACGATTAAAAACACTGGTC 59.198 37.037 0.00 0.00 0.00 4.02
3012 5780 9.791838 CATTTTGCCTAAGAAACGATTAAAAAC 57.208 29.630 0.00 0.00 0.00 2.43
3017 5785 8.275015 TCATCATTTTGCCTAAGAAACGATTA 57.725 30.769 0.00 0.00 0.00 1.75
3018 5786 7.156876 TCATCATTTTGCCTAAGAAACGATT 57.843 32.000 0.00 0.00 0.00 3.34
3062 5831 0.663688 CTGTCGACCCATACTCCTCG 59.336 60.000 14.12 0.00 0.00 4.63
3074 5843 3.928992 TCATTTCATCAAGCTCTGTCGAC 59.071 43.478 9.11 9.11 0.00 4.20
3075 5844 4.192429 TCATTTCATCAAGCTCTGTCGA 57.808 40.909 0.00 0.00 0.00 4.20
3123 5895 2.231478 TCTCGGCTTCTTCGTCTGAATT 59.769 45.455 0.00 0.00 32.61 2.17
3154 5926 0.810648 TTTCCGTTGGATGCTCATGC 59.189 50.000 0.00 0.00 40.20 4.06
3178 5951 1.980765 AGAATGTGCTTCACCTCCTGA 59.019 47.619 0.00 0.00 36.24 3.86
3208 5981 1.563410 CTTCTCCCTTTGATCAGGCCT 59.437 52.381 0.00 0.00 31.69 5.19
3212 5985 4.566426 AACCTCTTCTCCCTTTGATCAG 57.434 45.455 0.00 0.00 0.00 2.90
3213 5986 4.350816 TCAAACCTCTTCTCCCTTTGATCA 59.649 41.667 0.00 0.00 0.00 2.92
3252 6025 0.815734 GTACAGTAGCCGAGCTCCAA 59.184 55.000 8.47 0.00 40.44 3.53
3290 6063 6.017211 TGGATCATCAGTGAATATTGGGTT 57.983 37.500 0.00 0.00 38.01 4.11
3292 6065 5.417894 CCATGGATCATCAGTGAATATTGGG 59.582 44.000 5.56 0.00 38.01 4.12
3297 6070 6.064060 GGAAACCATGGATCATCAGTGAATA 58.936 40.000 21.47 0.00 38.01 1.75
3321 6094 1.722011 ACGCATAAGGAACCGTTGAG 58.278 50.000 0.00 0.00 0.00 3.02
3333 6106 5.220510 CGCAAGACCAATAGTTTACGCATAA 60.221 40.000 0.00 0.00 43.02 1.90
3340 6113 3.376859 CCATGCGCAAGACCAATAGTTTA 59.623 43.478 17.11 0.00 43.02 2.01
3345 6118 1.093972 CACCATGCGCAAGACCAATA 58.906 50.000 17.11 0.00 43.02 1.90
3350 6123 2.401766 CCTCCACCATGCGCAAGAC 61.402 63.158 17.11 0.00 43.02 3.01
3359 6132 1.307343 CCTCCACTCCCTCCACCAT 60.307 63.158 0.00 0.00 0.00 3.55
3397 6170 1.679944 CCGCAACAATCCCTGATGAGT 60.680 52.381 0.00 0.00 29.40 3.41
3403 6176 2.639970 TTGTCCGCAACAATCCCTG 58.360 52.632 0.00 0.00 42.95 4.45


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

AutoCloner maintained by Alex Coulton.