Multiple sequence alignment - TraesCS2D01G139300

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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 TraesCS2D01G139300 chr2D 100.000 3609 0 0 1 3609 82181289 82177681 0.000000e+00 6665
1 TraesCS2D01G139300 chr2D 84.341 926 113 28 2695 3609 45054572 45053668 0.000000e+00 878
2 TraesCS2D01G139300 chr2D 83.371 890 120 18 2732 3609 478661592 478660719 0.000000e+00 798
3 TraesCS2D01G139300 chr2D 83.681 864 114 23 2733 3582 166853498 166854348 0.000000e+00 789
4 TraesCS2D01G139300 chr2D 82.143 924 125 29 2702 3609 335607154 335608053 0.000000e+00 756
5 TraesCS2D01G139300 chr2A 91.351 1584 89 18 1077 2651 82344415 82342871 0.000000e+00 2122
6 TraesCS2D01G139300 chr2A 91.711 567 40 6 1 563 82345595 82345032 0.000000e+00 780
7 TraesCS2D01G139300 chr2A 82.181 926 134 24 2702 3609 499012398 499013310 0.000000e+00 767
8 TraesCS2D01G139300 chr2A 92.841 447 17 10 644 1076 82344896 82344451 5.080000e-178 634
9 TraesCS2D01G139300 chr2B 89.143 1621 115 30 1077 2657 134043758 134042159 0.000000e+00 1962
10 TraesCS2D01G139300 chr2B 89.556 1082 65 29 1 1076 134044842 134043803 0.000000e+00 1328
11 TraesCS2D01G139300 chr2B 82.318 837 112 30 2704 3522 78757345 78758163 0.000000e+00 693
12 TraesCS2D01G139300 chr1D 86.862 921 102 13 2702 3608 131402807 131401892 0.000000e+00 1013
13 TraesCS2D01G139300 chr1D 83.298 934 119 29 2696 3609 286543453 286542537 0.000000e+00 826
14 TraesCS2D01G139300 chr4D 85.811 888 96 24 2733 3609 297924319 297925187 0.000000e+00 915
15 TraesCS2D01G139300 chr6D 83.638 929 115 32 2695 3609 113381578 113382483 0.000000e+00 839
16 TraesCS2D01G139300 chr3B 83.146 890 120 24 2733 3609 734483648 734482776 0.000000e+00 785
17 TraesCS2D01G139300 chr4B 81.582 923 141 23 2695 3608 189413456 189414358 0.000000e+00 736
18 TraesCS2D01G139300 chr4B 80.652 920 132 37 2702 3602 322698830 322699722 0.000000e+00 671
19 TraesCS2D01G139300 chr3D 86.907 527 56 8 2702 3216 424074931 424074406 2.420000e-161 579
20 TraesCS2D01G139300 chr1B 81.287 684 97 28 2702 3369 526744761 526744093 3.190000e-145 525


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 TraesCS2D01G139300 chr2D 82177681 82181289 3608 True 6665.000000 6665 100.000000 1 3609 1 chr2D.!!$R2 3608
1 TraesCS2D01G139300 chr2D 45053668 45054572 904 True 878.000000 878 84.341000 2695 3609 1 chr2D.!!$R1 914
2 TraesCS2D01G139300 chr2D 478660719 478661592 873 True 798.000000 798 83.371000 2732 3609 1 chr2D.!!$R3 877
3 TraesCS2D01G139300 chr2D 166853498 166854348 850 False 789.000000 789 83.681000 2733 3582 1 chr2D.!!$F1 849
4 TraesCS2D01G139300 chr2D 335607154 335608053 899 False 756.000000 756 82.143000 2702 3609 1 chr2D.!!$F2 907
5 TraesCS2D01G139300 chr2A 82342871 82345595 2724 True 1178.666667 2122 91.967667 1 2651 3 chr2A.!!$R1 2650
6 TraesCS2D01G139300 chr2A 499012398 499013310 912 False 767.000000 767 82.181000 2702 3609 1 chr2A.!!$F1 907
7 TraesCS2D01G139300 chr2B 134042159 134044842 2683 True 1645.000000 1962 89.349500 1 2657 2 chr2B.!!$R1 2656
8 TraesCS2D01G139300 chr2B 78757345 78758163 818 False 693.000000 693 82.318000 2704 3522 1 chr2B.!!$F1 818
9 TraesCS2D01G139300 chr1D 131401892 131402807 915 True 1013.000000 1013 86.862000 2702 3608 1 chr1D.!!$R1 906
10 TraesCS2D01G139300 chr1D 286542537 286543453 916 True 826.000000 826 83.298000 2696 3609 1 chr1D.!!$R2 913
11 TraesCS2D01G139300 chr4D 297924319 297925187 868 False 915.000000 915 85.811000 2733 3609 1 chr4D.!!$F1 876
12 TraesCS2D01G139300 chr6D 113381578 113382483 905 False 839.000000 839 83.638000 2695 3609 1 chr6D.!!$F1 914
13 TraesCS2D01G139300 chr3B 734482776 734483648 872 True 785.000000 785 83.146000 2733 3609 1 chr3B.!!$R1 876
14 TraesCS2D01G139300 chr4B 189413456 189414358 902 False 736.000000 736 81.582000 2695 3608 1 chr4B.!!$F1 913
15 TraesCS2D01G139300 chr4B 322698830 322699722 892 False 671.000000 671 80.652000 2702 3602 1 chr4B.!!$F2 900
16 TraesCS2D01G139300 chr3D 424074406 424074931 525 True 579.000000 579 86.907000 2702 3216 1 chr3D.!!$R1 514
17 TraesCS2D01G139300 chr1B 526744093 526744761 668 True 525.000000 525 81.287000 2702 3369 1 chr1B.!!$R1 667

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
967 1065 0.097325 TCGTCCGTTGCAACAAACAC 59.903 50.0 28.01 16.4 0.0 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2699 2892 0.108709 CATGCAATGTTCCCCAACGG 60.109 55.0 0.0 0.0 40.2 4.44 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
17 18 2.433664 GGTCGTGCCTGTAACCCG 60.434 66.667 0.00 0.00 0.00 5.28
24 25 1.070105 GCCTGTAACCCGTGTCACA 59.930 57.895 3.42 0.00 0.00 3.58
123 124 1.531602 GTTTTGCTGGGGCCTCTGT 60.532 57.895 11.64 0.00 37.74 3.41
176 177 0.525311 TTTATGCCATGTGTGTGCCG 59.475 50.000 0.00 0.00 0.00 5.69
201 202 4.647424 TCTTTTGGTGTCCAATGTTCAC 57.353 40.909 1.97 0.00 43.55 3.18
213 214 6.545666 TGTCCAATGTTCACAGTATCAAAACT 59.454 34.615 0.00 0.00 0.00 2.66
221 222 7.334671 TGTTCACAGTATCAAAACTTGTGTGTA 59.665 33.333 0.00 0.00 36.15 2.90
222 223 7.241663 TCACAGTATCAAAACTTGTGTGTAC 57.758 36.000 0.00 0.00 36.15 2.90
223 224 7.045416 TCACAGTATCAAAACTTGTGTGTACT 58.955 34.615 0.00 0.00 36.15 2.73
224 225 7.011016 TCACAGTATCAAAACTTGTGTGTACTG 59.989 37.037 17.00 17.00 36.15 2.74
245 246 3.255888 TGTACAACTGTAGAGAGGCAGTG 59.744 47.826 0.00 0.00 44.21 3.66
246 247 2.320781 ACAACTGTAGAGAGGCAGTGT 58.679 47.619 0.00 0.00 44.21 3.55
260 261 1.750193 CAGTGTGGTTTCTGGTGTGT 58.250 50.000 0.00 0.00 0.00 3.72
261 262 2.091541 CAGTGTGGTTTCTGGTGTGTT 58.908 47.619 0.00 0.00 0.00 3.32
262 263 3.275143 CAGTGTGGTTTCTGGTGTGTTA 58.725 45.455 0.00 0.00 0.00 2.41
264 265 3.011119 GTGTGGTTTCTGGTGTGTTACA 58.989 45.455 0.00 0.00 0.00 2.41
269 270 5.354792 GTGGTTTCTGGTGTGTTACAGTAAA 59.645 40.000 0.00 0.00 36.17 2.01
334 336 4.199310 CACATTTCGGACTTATGGGTCAT 58.801 43.478 0.00 0.00 37.91 3.06
376 379 7.800155 TGATTGTTCAGTGTGTAGAAAATGA 57.200 32.000 0.00 0.00 0.00 2.57
435 438 0.804255 TCTTTTAGGGGGAGAGGGGT 59.196 55.000 0.00 0.00 0.00 4.95
459 463 9.778741 GGTTCATTACTGAATCAAGTATCCATA 57.221 33.333 1.41 0.00 43.08 2.74
498 503 9.774742 GAACTGGTAATAAATGTGTTGATTCTC 57.225 33.333 0.00 0.00 0.00 2.87
548 553 8.846943 TCATAAGATAAATGTGTCAACTGTGT 57.153 30.769 0.00 0.00 0.00 3.72
549 554 9.283768 TCATAAGATAAATGTGTCAACTGTGTT 57.716 29.630 0.00 0.00 0.00 3.32
550 555 9.897744 CATAAGATAAATGTGTCAACTGTGTTT 57.102 29.630 0.00 0.00 0.00 2.83
551 556 9.897744 ATAAGATAAATGTGTCAACTGTGTTTG 57.102 29.630 0.00 0.00 0.00 2.93
552 557 6.208644 AGATAAATGTGTCAACTGTGTTTGC 58.791 36.000 0.00 0.00 0.00 3.68
553 558 3.865011 AATGTGTCAACTGTGTTTGCA 57.135 38.095 0.00 0.00 0.00 4.08
554 559 4.389890 AATGTGTCAACTGTGTTTGCAT 57.610 36.364 0.00 0.00 0.00 3.96
555 560 5.512753 AATGTGTCAACTGTGTTTGCATA 57.487 34.783 0.00 0.00 0.00 3.14
556 561 5.710513 ATGTGTCAACTGTGTTTGCATAT 57.289 34.783 0.00 0.00 0.00 1.78
557 562 4.857799 TGTGTCAACTGTGTTTGCATATG 58.142 39.130 0.00 0.00 0.00 1.78
558 563 4.337836 TGTGTCAACTGTGTTTGCATATGT 59.662 37.500 4.29 0.00 0.00 2.29
559 564 4.676471 GTGTCAACTGTGTTTGCATATGTG 59.324 41.667 4.29 0.00 0.00 3.21
623 628 7.679144 TCGAAATTCTCTTCTCATTTTGATCG 58.321 34.615 0.00 0.00 29.10 3.69
625 630 5.747951 ATTCTCTTCTCATTTTGATCGGC 57.252 39.130 0.00 0.00 0.00 5.54
627 632 2.932614 CTCTTCTCATTTTGATCGGCGT 59.067 45.455 6.85 0.00 0.00 5.68
634 639 1.710013 TTTTGATCGGCGTGTCTCTC 58.290 50.000 6.85 0.00 0.00 3.20
637 642 1.968704 TGATCGGCGTGTCTCTCTAT 58.031 50.000 6.85 0.00 0.00 1.98
717 807 2.237143 TGGTGAGCTTGAGTATGAAGGG 59.763 50.000 0.00 0.00 26.62 3.95
731 824 1.358787 TGAAGGGCATTTCCAGGACAT 59.641 47.619 0.00 0.00 36.21 3.06
772 865 4.179298 GGAAGAGAAATGCAAATTCCAGC 58.821 43.478 10.91 3.42 36.91 4.85
802 895 1.066430 TCATAACGGGTTGACCTCTGC 60.066 52.381 0.00 0.00 36.97 4.26
849 946 3.733684 CGGAAAACAGTTTGTGACTTGGG 60.734 47.826 0.00 0.00 36.10 4.12
933 1031 1.063006 CAATTGTGCTCATCGCGGG 59.937 57.895 6.13 0.00 43.27 6.13
961 1059 1.399727 CCAAGAATCGTCCGTTGCAAC 60.400 52.381 19.89 19.89 0.00 4.17
963 1061 1.588674 AGAATCGTCCGTTGCAACAA 58.411 45.000 28.01 13.51 0.00 2.83
966 1064 1.018148 ATCGTCCGTTGCAACAAACA 58.982 45.000 28.01 15.15 0.00 2.83
967 1065 0.097325 TCGTCCGTTGCAACAAACAC 59.903 50.000 28.01 16.40 0.00 3.32
1146 1293 4.408182 ACCTGTTCCTGAATTATCTCCG 57.592 45.455 0.00 0.00 0.00 4.63
1167 1314 0.164647 CGTCTTCTTTGCCGCTTCTG 59.835 55.000 0.00 0.00 0.00 3.02
1168 1315 1.512926 GTCTTCTTTGCCGCTTCTGA 58.487 50.000 0.00 0.00 0.00 3.27
1169 1316 2.079925 GTCTTCTTTGCCGCTTCTGAT 58.920 47.619 0.00 0.00 0.00 2.90
1170 1317 2.079158 TCTTCTTTGCCGCTTCTGATG 58.921 47.619 0.00 0.00 0.00 3.07
1171 1318 0.523072 TTCTTTGCCGCTTCTGATGC 59.477 50.000 5.52 5.52 0.00 3.91
1172 1319 0.321919 TCTTTGCCGCTTCTGATGCT 60.322 50.000 12.85 0.00 0.00 3.79
1173 1320 0.179171 CTTTGCCGCTTCTGATGCTG 60.179 55.000 12.85 8.03 0.00 4.41
1174 1321 0.606130 TTTGCCGCTTCTGATGCTGA 60.606 50.000 12.85 0.00 0.00 4.26
1175 1322 0.393402 TTGCCGCTTCTGATGCTGAT 60.393 50.000 12.85 0.00 0.00 2.90
1176 1323 0.812811 TGCCGCTTCTGATGCTGATC 60.813 55.000 12.85 0.00 0.00 2.92
1177 1324 0.812811 GCCGCTTCTGATGCTGATCA 60.813 55.000 12.85 0.00 37.07 2.92
1283 1430 5.528043 AGCATGACTATGACTGGTAAGAG 57.472 43.478 0.00 0.00 36.36 2.85
1303 1450 4.160439 AGAGAAAACGCTCTCATGATGGTA 59.840 41.667 11.15 0.00 41.24 3.25
1306 1453 5.882557 AGAAAACGCTCTCATGATGGTAAAT 59.117 36.000 0.00 0.00 0.00 1.40
1307 1454 5.490139 AAACGCTCTCATGATGGTAAATG 57.510 39.130 0.00 0.00 0.00 2.32
1309 1456 2.225019 CGCTCTCATGATGGTAAATGGC 59.775 50.000 0.00 0.00 0.00 4.40
1326 1473 0.750546 GGCCATTCAGATCAGCTGCA 60.751 55.000 9.47 0.00 44.52 4.41
1327 1474 1.100510 GCCATTCAGATCAGCTGCAA 58.899 50.000 9.47 0.00 44.52 4.08
1354 1501 4.097589 GCGAAACATCCTACTACCAGTACT 59.902 45.833 0.00 0.00 0.00 2.73
1374 1523 8.387354 CAGTACTTATTTATCACATTGTTGCGA 58.613 33.333 0.00 0.00 0.00 5.10
1515 1664 3.361158 TCCGTCCGTCCGCGTTTA 61.361 61.111 4.92 0.00 36.15 2.01
1533 1682 5.958949 GCGTTTACAGTTTTTCTTGACGTAA 59.041 36.000 0.00 0.00 0.00 3.18
1534 1683 6.465465 GCGTTTACAGTTTTTCTTGACGTAAA 59.535 34.615 0.00 0.00 0.00 2.01
1547 1696 9.537192 TTTCTTGACGTAAAGATCAGACTAAAA 57.463 29.630 16.23 1.68 36.12 1.52
1548 1697 8.744008 TCTTGACGTAAAGATCAGACTAAAAG 57.256 34.615 11.55 0.00 31.19 2.27
1549 1698 6.946229 TGACGTAAAGATCAGACTAAAAGC 57.054 37.500 0.00 0.00 0.00 3.51
1551 1700 7.152645 TGACGTAAAGATCAGACTAAAAGCTT 58.847 34.615 0.00 0.00 0.00 3.74
1552 1701 8.301720 TGACGTAAAGATCAGACTAAAAGCTTA 58.698 33.333 0.00 0.00 0.00 3.09
1553 1702 8.690680 ACGTAAAGATCAGACTAAAAGCTTAG 57.309 34.615 0.00 0.00 40.46 2.18
1555 1704 8.587950 CGTAAAGATCAGACTAAAAGCTTAGTG 58.412 37.037 6.61 0.00 46.31 2.74
1556 1705 7.913674 AAAGATCAGACTAAAAGCTTAGTGG 57.086 36.000 6.61 0.00 46.31 4.00
1557 1706 6.613153 AGATCAGACTAAAAGCTTAGTGGT 57.387 37.500 6.61 2.85 46.31 4.16
1558 1707 6.635755 AGATCAGACTAAAAGCTTAGTGGTC 58.364 40.000 14.99 14.99 46.31 4.02
1559 1708 6.439058 AGATCAGACTAAAAGCTTAGTGGTCT 59.561 38.462 18.05 18.05 46.31 3.85
1612 1765 1.992277 GGAGAAGGGGAGCAGCTCA 60.992 63.158 24.09 0.00 31.08 4.26
1615 1768 0.619832 AGAAGGGGAGCAGCTCATCA 60.620 55.000 24.09 0.00 31.08 3.07
1693 1846 1.081641 GTCGGCGTCTTCGTCTTCA 60.082 57.895 6.85 0.00 39.73 3.02
1847 2003 2.283173 CCAGCCAACCCAAGGGAC 60.283 66.667 13.15 0.00 38.96 4.46
1858 2014 3.730761 AAGGGACCGTCGTCGTCG 61.731 66.667 4.87 4.87 40.17 5.12
2167 2344 1.229658 AGGGGACTTGCTAGCCAGT 60.230 57.895 20.63 20.63 37.44 4.00
2176 2353 5.163713 GGACTTGCTAGCCAGTAAAAGATTG 60.164 44.000 20.54 0.00 0.00 2.67
2184 2361 4.762251 AGCCAGTAAAAGATTGTCAAGGAC 59.238 41.667 0.00 0.00 0.00 3.85
2190 2367 0.324943 AGATTGTCAAGGACCGGTGG 59.675 55.000 14.63 0.00 0.00 4.61
2216 2393 2.078914 CGAAAGACCCACGACGACG 61.079 63.158 5.58 5.58 45.75 5.12
2217 2394 1.283793 GAAAGACCCACGACGACGA 59.716 57.895 15.32 0.00 42.66 4.20
2288 2465 2.853914 GCCGTTGTCTCACGAAGC 59.146 61.111 0.00 0.00 43.15 3.86
2439 2619 2.359570 AAAGACAAGGTCGCGGTCGT 62.360 55.000 6.13 0.00 37.67 4.34
2442 2622 4.657824 CAAGGTCGCGGTCGTGGT 62.658 66.667 6.13 0.00 36.96 4.16
2554 2737 0.959372 AGGACGACGACGGTGAAGAT 60.959 55.000 12.58 0.00 44.46 2.40
2661 2854 3.412722 CCAACTTGGCTGGTGTACA 57.587 52.632 0.00 0.00 0.00 2.90
2662 2855 1.909700 CCAACTTGGCTGGTGTACAT 58.090 50.000 0.00 0.00 0.00 2.29
2663 2856 1.541147 CCAACTTGGCTGGTGTACATG 59.459 52.381 0.00 0.00 0.00 3.21
2664 2857 2.503331 CAACTTGGCTGGTGTACATGA 58.497 47.619 0.00 0.00 0.00 3.07
2665 2858 2.185004 ACTTGGCTGGTGTACATGAC 57.815 50.000 0.00 0.00 0.00 3.06
2666 2859 1.699634 ACTTGGCTGGTGTACATGACT 59.300 47.619 0.00 0.00 0.00 3.41
2667 2860 2.289694 ACTTGGCTGGTGTACATGACTC 60.290 50.000 0.00 0.00 0.00 3.36
2668 2861 1.644509 TGGCTGGTGTACATGACTCT 58.355 50.000 0.00 0.00 0.00 3.24
2669 2862 1.276138 TGGCTGGTGTACATGACTCTG 59.724 52.381 0.00 0.00 0.00 3.35
2670 2863 1.276421 GGCTGGTGTACATGACTCTGT 59.724 52.381 0.00 0.00 0.00 3.41
2671 2864 2.289694 GGCTGGTGTACATGACTCTGTT 60.290 50.000 0.00 0.00 0.00 3.16
2672 2865 2.996621 GCTGGTGTACATGACTCTGTTC 59.003 50.000 0.00 0.00 0.00 3.18
2673 2866 3.306364 GCTGGTGTACATGACTCTGTTCT 60.306 47.826 0.00 0.00 0.00 3.01
2674 2867 4.240888 CTGGTGTACATGACTCTGTTCTG 58.759 47.826 0.00 0.00 0.00 3.02
2675 2868 2.996621 GGTGTACATGACTCTGTTCTGC 59.003 50.000 0.00 0.00 0.00 4.26
2676 2869 2.996621 GTGTACATGACTCTGTTCTGCC 59.003 50.000 0.00 0.00 0.00 4.85
2677 2870 2.632512 TGTACATGACTCTGTTCTGCCA 59.367 45.455 0.00 0.00 0.00 4.92
2678 2871 2.469274 ACATGACTCTGTTCTGCCAG 57.531 50.000 0.00 0.00 0.00 4.85
2679 2872 1.085091 CATGACTCTGTTCTGCCAGC 58.915 55.000 0.00 0.00 32.32 4.85
2680 2873 0.689055 ATGACTCTGTTCTGCCAGCA 59.311 50.000 0.00 0.00 32.32 4.41
2681 2874 0.469494 TGACTCTGTTCTGCCAGCAA 59.531 50.000 0.00 0.00 32.32 3.91
2682 2875 1.072806 TGACTCTGTTCTGCCAGCAAT 59.927 47.619 0.00 0.00 32.32 3.56
2683 2876 2.157738 GACTCTGTTCTGCCAGCAATT 58.842 47.619 0.00 0.00 32.32 2.32
2684 2877 2.555757 GACTCTGTTCTGCCAGCAATTT 59.444 45.455 0.00 0.00 32.32 1.82
2685 2878 2.961062 ACTCTGTTCTGCCAGCAATTTT 59.039 40.909 0.00 0.00 32.32 1.82
2686 2879 3.385755 ACTCTGTTCTGCCAGCAATTTTT 59.614 39.130 0.00 0.00 32.32 1.94
2750 2949 1.790755 TTCTACGCACACGCAAGATT 58.209 45.000 0.00 0.00 45.53 2.40
2758 2957 3.487376 CGCACACGCAAGATTTATCCATT 60.487 43.478 0.00 0.00 43.62 3.16
2780 2980 2.034878 AGATGCATAGCAACGAGAGGA 58.965 47.619 0.00 0.00 43.62 3.71
2785 2985 2.099921 GCATAGCAACGAGAGGAGAGAA 59.900 50.000 0.00 0.00 0.00 2.87
2796 2996 4.556501 CGAGAGGAGAGAATGTGTCTATGC 60.557 50.000 0.00 0.00 36.41 3.14
2857 3057 5.176958 CGGTTGATGTAGTCGAACTTTTTCT 59.823 40.000 0.00 0.00 0.00 2.52
2866 3070 5.238583 AGTCGAACTTTTTCTCGATCCAAT 58.761 37.500 0.00 0.00 45.08 3.16
2886 3090 7.561251 TCCAATTGATCAAGTACCGAAGATAA 58.439 34.615 14.54 0.00 0.00 1.75
3002 3208 2.666207 GGCGTGGTGATGGTGGTA 59.334 61.111 0.00 0.00 0.00 3.25
3003 3209 1.223487 GGCGTGGTGATGGTGGTAT 59.777 57.895 0.00 0.00 0.00 2.73
3006 3212 1.948611 GCGTGGTGATGGTGGTATTGT 60.949 52.381 0.00 0.00 0.00 2.71
3075 3281 2.537143 GGACTAAACTGTGGAGAGGGA 58.463 52.381 0.00 0.00 0.00 4.20
3080 3286 2.681778 CTGTGGAGAGGGACGCCT 60.682 66.667 0.00 0.00 39.24 5.52
3105 3311 2.301870 ACGGCTAAGAGATTGTTGTGGA 59.698 45.455 0.00 0.00 0.00 4.02
3113 3325 0.240945 GATTGTTGTGGACTTGGCGG 59.759 55.000 0.00 0.00 0.00 6.13
3232 3462 0.476771 CCCCCGTACCATATTTGCCT 59.523 55.000 0.00 0.00 0.00 4.75
3237 3467 2.104111 CCGTACCATATTTGCCTGAGGA 59.896 50.000 0.65 0.00 0.00 3.71
3270 3506 1.002274 GAGGAGAGGAAGGCAGGGA 59.998 63.158 0.00 0.00 0.00 4.20
3412 3654 1.269703 GCTTCCCGGAACCCCTTCTA 61.270 60.000 0.73 0.00 0.00 2.10
3424 3666 2.091278 ACCCCTTCTAGTGATCCGATGA 60.091 50.000 0.00 0.00 0.00 2.92
3425 3667 2.297597 CCCCTTCTAGTGATCCGATGAC 59.702 54.545 0.00 0.00 0.00 3.06
3464 3706 1.963172 AACTCTTCCGGTGTCCAAAC 58.037 50.000 0.00 0.00 0.00 2.93
3470 3712 1.819928 TCCGGTGTCCAAACATCATG 58.180 50.000 0.00 0.00 36.20 3.07
3522 3764 2.121538 CCGGAGCTCCTCGTCATGA 61.122 63.158 29.73 0.00 0.00 3.07
3539 3781 4.356979 ACCGTGATCTCATCCGGT 57.643 55.556 0.00 8.57 45.21 5.28
3561 3803 5.221461 GGTACTCCGAACAATATCTGGTCAT 60.221 44.000 0.00 0.00 42.46 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.485903 GACATTGTGACACGGGTTACA 58.514 47.619 11.90 11.90 41.22 2.41
17 18 1.204062 CGGTGCGACATTGTGACAC 59.796 57.895 0.00 0.00 0.00 3.67
123 124 0.871722 CCAACCATTCGAAGCAACGA 59.128 50.000 3.35 1.37 40.55 3.85
201 202 7.246674 ACAGTACACACAAGTTTTGATACTG 57.753 36.000 22.57 22.57 39.41 2.74
213 214 6.319405 TCTCTACAGTTGTACAGTACACACAA 59.681 38.462 13.26 0.00 38.63 3.33
221 222 3.497332 TGCCTCTCTACAGTTGTACAGT 58.503 45.455 0.00 0.00 0.00 3.55
222 223 3.508012 ACTGCCTCTCTACAGTTGTACAG 59.492 47.826 0.00 0.00 44.59 2.74
223 224 3.255888 CACTGCCTCTCTACAGTTGTACA 59.744 47.826 0.00 0.00 44.59 2.90
224 225 3.256136 ACACTGCCTCTCTACAGTTGTAC 59.744 47.826 0.00 0.00 44.59 2.90
245 246 3.275999 ACTGTAACACACCAGAAACCAC 58.724 45.455 0.00 0.00 32.93 4.16
246 247 3.637911 ACTGTAACACACCAGAAACCA 57.362 42.857 0.00 0.00 32.93 3.67
260 261 6.514947 ACAACGTACCACATCTTTACTGTAA 58.485 36.000 0.00 0.00 0.00 2.41
261 262 6.016024 AGACAACGTACCACATCTTTACTGTA 60.016 38.462 0.00 0.00 0.00 2.74
262 263 4.952460 ACAACGTACCACATCTTTACTGT 58.048 39.130 0.00 0.00 0.00 3.55
264 265 5.221382 ACAGACAACGTACCACATCTTTACT 60.221 40.000 0.00 0.00 0.00 2.24
269 270 3.181469 ACAACAGACAACGTACCACATCT 60.181 43.478 0.00 0.00 0.00 2.90
312 313 3.605634 TGACCCATAAGTCCGAAATGTG 58.394 45.455 0.00 0.00 35.83 3.21
319 321 2.240493 GGACATGACCCATAAGTCCG 57.760 55.000 0.00 0.00 39.33 4.79
352 355 7.800155 TCATTTTCTACACACTGAACAATCA 57.200 32.000 0.00 0.00 0.00 2.57
408 411 2.507471 CTCCCCCTAAAAGAGAGCACAT 59.493 50.000 0.00 0.00 0.00 3.21
525 530 9.897744 CAAACACAGTTGACACATTTATCTTAT 57.102 29.630 0.00 0.00 0.00 1.73
528 533 6.183360 TGCAAACACAGTTGACACATTTATCT 60.183 34.615 0.00 0.00 0.00 1.98
562 567 9.409312 CACATATGCAAACATGTTCTAGAAAAA 57.591 29.630 12.39 0.00 37.04 1.94
563 568 8.969121 CACATATGCAAACATGTTCTAGAAAA 57.031 30.769 12.39 1.30 37.04 2.29
603 608 4.272018 CGCCGATCAAAATGAGAAGAGAAT 59.728 41.667 0.00 0.00 0.00 2.40
605 610 3.190079 CGCCGATCAAAATGAGAAGAGA 58.810 45.455 0.00 0.00 0.00 3.10
623 628 2.299521 AGTACCATAGAGAGACACGCC 58.700 52.381 0.00 0.00 0.00 5.68
670 759 1.631405 CAAAGCACCCAAGATTCCCA 58.369 50.000 0.00 0.00 0.00 4.37
695 784 3.307691 CCCTTCATACTCAAGCTCACCAA 60.308 47.826 0.00 0.00 0.00 3.67
717 807 5.242393 AGTGCATTATATGTCCTGGAAATGC 59.758 40.000 25.50 25.50 45.81 3.56
731 824 6.899089 TCTTCCCATTTCAGAGTGCATTATA 58.101 36.000 0.00 0.00 0.00 0.98
772 865 3.492102 ACCCGTTATGAATCCATCCTG 57.508 47.619 0.00 0.00 34.31 3.86
826 919 3.127895 CCAAGTCACAAACTGTTTTCCGA 59.872 43.478 2.41 0.00 38.58 4.55
828 921 3.780902 CCCAAGTCACAAACTGTTTTCC 58.219 45.455 2.41 0.00 38.58 3.13
849 946 3.686726 ACTAGTTATTTCTGCTGCACTGC 59.313 43.478 0.00 0.00 0.00 4.40
933 1031 0.442699 GACGATTCTTGGCCGTGTTC 59.557 55.000 0.00 0.00 36.60 3.18
961 1059 1.528586 CTGTTCTCTCTGCGGTGTTTG 59.471 52.381 0.00 0.00 0.00 2.93
963 1061 1.040646 TCTGTTCTCTCTGCGGTGTT 58.959 50.000 0.00 0.00 0.00 3.32
966 1064 1.621992 TCTTCTGTTCTCTCTGCGGT 58.378 50.000 0.00 0.00 0.00 5.68
967 1065 2.732412 TTCTTCTGTTCTCTCTGCGG 57.268 50.000 0.00 0.00 0.00 5.69
1084 1231 1.395826 CGGAGAGGGCGGAGAAGAAT 61.396 60.000 0.00 0.00 0.00 2.40
1167 1314 5.363101 TCCTTACATCAGTTGATCAGCATC 58.637 41.667 12.41 0.00 31.21 3.91
1168 1315 5.104610 ACTCCTTACATCAGTTGATCAGCAT 60.105 40.000 12.41 0.00 31.21 3.79
1169 1316 4.223700 ACTCCTTACATCAGTTGATCAGCA 59.776 41.667 12.41 0.00 31.21 4.41
1170 1317 4.569966 CACTCCTTACATCAGTTGATCAGC 59.430 45.833 0.50 0.50 31.21 4.26
1171 1318 4.569966 GCACTCCTTACATCAGTTGATCAG 59.430 45.833 0.00 0.00 31.21 2.90
1172 1319 4.223700 AGCACTCCTTACATCAGTTGATCA 59.776 41.667 0.00 0.00 31.21 2.92
1173 1320 4.764172 AGCACTCCTTACATCAGTTGATC 58.236 43.478 0.00 0.00 31.21 2.92
1174 1321 4.833478 AGCACTCCTTACATCAGTTGAT 57.167 40.909 0.00 0.00 34.56 2.57
1175 1322 4.284490 AGAAGCACTCCTTACATCAGTTGA 59.716 41.667 0.00 0.00 32.78 3.18
1176 1323 4.391216 CAGAAGCACTCCTTACATCAGTTG 59.609 45.833 0.00 0.00 32.78 3.16
1177 1324 4.573900 CAGAAGCACTCCTTACATCAGTT 58.426 43.478 0.00 0.00 32.78 3.16
1250 1397 1.489481 AGTCATGCTTCCCGATCTCA 58.511 50.000 0.00 0.00 0.00 3.27
1283 1430 5.545658 TTTACCATCATGAGAGCGTTTTC 57.454 39.130 0.09 0.00 0.00 2.29
1303 1450 2.693591 CAGCTGATCTGAATGGCCATTT 59.306 45.455 31.13 16.20 45.72 2.32
1306 1453 0.750546 GCAGCTGATCTGAATGGCCA 60.751 55.000 20.43 8.56 45.72 5.36
1307 1454 0.750546 TGCAGCTGATCTGAATGGCC 60.751 55.000 20.43 0.00 45.72 5.36
1309 1456 3.490933 CCATTTGCAGCTGATCTGAATGG 60.491 47.826 20.43 21.17 44.12 3.16
1326 1473 4.196971 GGTAGTAGGATGTTTCGCCATTT 58.803 43.478 0.00 0.00 0.00 2.32
1327 1474 3.199071 TGGTAGTAGGATGTTTCGCCATT 59.801 43.478 0.00 0.00 0.00 3.16
1374 1523 3.735237 AGCCTACGAACATCGATGAAT 57.265 42.857 31.33 18.92 43.74 2.57
1382 1531 2.166664 GGAGTCAGAAGCCTACGAACAT 59.833 50.000 0.00 0.00 0.00 2.71
1515 1664 7.494625 TCTGATCTTTACGTCAAGAAAAACTGT 59.505 33.333 15.63 0.00 36.36 3.55
1533 1682 7.010339 ACCACTAAGCTTTTAGTCTGATCTT 57.990 36.000 3.20 0.00 35.70 2.40
1534 1683 6.439058 AGACCACTAAGCTTTTAGTCTGATCT 59.561 38.462 3.20 0.44 35.70 2.75
1547 1696 2.906389 TGAATGACCAGACCACTAAGCT 59.094 45.455 0.00 0.00 0.00 3.74
1548 1697 3.334583 TGAATGACCAGACCACTAAGC 57.665 47.619 0.00 0.00 0.00 3.09
1549 1698 4.194640 CCATGAATGACCAGACCACTAAG 58.805 47.826 0.00 0.00 0.00 2.18
1551 1700 3.055167 CACCATGAATGACCAGACCACTA 60.055 47.826 0.00 0.00 0.00 2.74
1552 1701 1.988107 ACCATGAATGACCAGACCACT 59.012 47.619 0.00 0.00 0.00 4.00
1553 1702 2.086869 CACCATGAATGACCAGACCAC 58.913 52.381 0.00 0.00 0.00 4.16
1554 1703 1.614051 GCACCATGAATGACCAGACCA 60.614 52.381 0.00 0.00 0.00 4.02
1555 1704 1.098050 GCACCATGAATGACCAGACC 58.902 55.000 0.00 0.00 0.00 3.85
1556 1705 1.741706 CTGCACCATGAATGACCAGAC 59.258 52.381 0.00 0.00 0.00 3.51
1557 1706 1.951895 GCTGCACCATGAATGACCAGA 60.952 52.381 0.00 0.00 0.00 3.86
1558 1707 0.454600 GCTGCACCATGAATGACCAG 59.545 55.000 0.00 0.00 0.00 4.00
1559 1708 0.038599 AGCTGCACCATGAATGACCA 59.961 50.000 1.02 0.00 0.00 4.02
1593 1746 1.688884 GAGCTGCTCCCCTTCTCCT 60.689 63.158 18.80 0.00 0.00 3.69
1597 1750 0.463474 GTGATGAGCTGCTCCCCTTC 60.463 60.000 25.61 16.78 0.00 3.46
1612 1765 0.944311 GCACCGTCGTGTTGAGTGAT 60.944 55.000 1.87 0.00 42.39 3.06
1615 1768 1.299926 GAGCACCGTCGTGTTGAGT 60.300 57.895 0.00 0.00 42.39 3.41
1693 1846 1.963338 GCTGCTCGTGGCTTTGACT 60.963 57.895 0.00 0.00 42.39 3.41
1847 2003 2.397252 GGTACTCGACGACGACGG 59.603 66.667 18.73 12.09 43.81 4.79
1971 2148 4.832608 GGCCCGCGAACCTCGAAT 62.833 66.667 8.23 0.00 43.74 3.34
2041 2218 0.535335 GCGTCTTGACCATACTGGGA 59.465 55.000 0.00 0.00 43.37 4.37
2167 2344 4.069304 CACCGGTCCTTGACAATCTTTTA 58.931 43.478 2.59 0.00 33.68 1.52
2176 2353 3.998672 TCGCCACCGGTCCTTGAC 61.999 66.667 2.59 0.00 34.56 3.18
2205 2382 2.178521 CCTTCTCGTCGTCGTGGG 59.821 66.667 1.33 0.00 38.33 4.61
2288 2465 2.277628 GAGCTTCCGAGAGTCGCG 60.278 66.667 9.52 9.52 38.82 5.87
2322 2499 4.874977 GGGTACTCCGCTGCTCGC 62.875 72.222 0.00 0.00 36.73 5.03
2599 2782 4.994201 GCCGCTCGTCACACGTGA 62.994 66.667 25.01 0.00 43.14 4.35
2652 2845 4.240888 CAGAACAGAGTCATGTACACCAG 58.759 47.826 0.00 0.00 31.70 4.00
2657 2850 3.257393 CTGGCAGAACAGAGTCATGTAC 58.743 50.000 9.42 0.00 40.97 2.90
2658 2851 2.354103 GCTGGCAGAACAGAGTCATGTA 60.354 50.000 20.86 0.00 40.97 2.29
2659 2852 1.610102 GCTGGCAGAACAGAGTCATGT 60.610 52.381 20.86 0.00 40.97 3.21
2660 2853 1.085091 GCTGGCAGAACAGAGTCATG 58.915 55.000 20.86 0.00 40.97 3.07
2661 2854 0.689055 TGCTGGCAGAACAGAGTCAT 59.311 50.000 20.86 0.00 40.97 3.06
2662 2855 0.469494 TTGCTGGCAGAACAGAGTCA 59.531 50.000 20.86 0.23 40.97 3.41
2663 2856 1.818642 ATTGCTGGCAGAACAGAGTC 58.181 50.000 20.86 0.00 40.97 3.36
2664 2857 2.283145 AATTGCTGGCAGAACAGAGT 57.717 45.000 20.86 0.00 40.97 3.24
2665 2858 3.655276 AAAATTGCTGGCAGAACAGAG 57.345 42.857 20.86 0.00 40.97 3.35
2685 2878 0.965439 CAACGGATGGCCTGGAAAAA 59.035 50.000 3.32 0.00 0.00 1.94
2686 2879 0.897863 CCAACGGATGGCCTGGAAAA 60.898 55.000 3.32 0.00 43.80 2.29
2687 2880 1.304052 CCAACGGATGGCCTGGAAA 60.304 57.895 3.32 0.00 43.80 3.13
2688 2881 2.354729 CCAACGGATGGCCTGGAA 59.645 61.111 3.32 0.00 43.80 3.53
2696 2889 0.173255 GCAATGTTCCCCAACGGATG 59.827 55.000 0.00 0.00 41.63 3.51
2697 2890 0.251564 TGCAATGTTCCCCAACGGAT 60.252 50.000 0.00 0.00 41.63 4.18
2698 2891 0.251564 ATGCAATGTTCCCCAACGGA 60.252 50.000 0.00 0.00 39.68 4.69
2699 2892 0.108709 CATGCAATGTTCCCCAACGG 60.109 55.000 0.00 0.00 40.20 4.44
2700 2893 3.422122 CATGCAATGTTCCCCAACG 57.578 52.632 0.00 0.00 40.20 4.10
2750 2949 5.179929 CGTTGCTATGCATCTCAATGGATAA 59.820 40.000 18.25 0.00 43.16 1.75
2758 2957 2.223900 CCTCTCGTTGCTATGCATCTCA 60.224 50.000 0.19 0.00 38.76 3.27
2780 2980 4.261952 CGAGGATGCATAGACACATTCTCT 60.262 45.833 0.00 0.00 43.85 3.10
2785 2985 4.022762 GTCTACGAGGATGCATAGACACAT 60.023 45.833 16.60 0.00 42.02 3.21
2866 3070 7.033791 GTGTCTTATCTTCGGTACTTGATCAA 58.966 38.462 8.12 8.12 0.00 2.57
2882 3086 1.135199 TGAACGCGGAGGTGTCTTATC 60.135 52.381 12.47 0.00 35.39 1.75
2886 3090 2.651361 CTGAACGCGGAGGTGTCT 59.349 61.111 12.47 0.00 35.39 3.41
2967 3173 1.369209 CGTTGTGCTGCCGAAACTG 60.369 57.895 0.00 0.00 0.00 3.16
3002 3208 6.260936 CGAAGCCCTATGAAGATAACAACAAT 59.739 38.462 0.00 0.00 0.00 2.71
3003 3209 5.584649 CGAAGCCCTATGAAGATAACAACAA 59.415 40.000 0.00 0.00 0.00 2.83
3080 3286 3.244078 ACAACAATCTCTTAGCCGTGTGA 60.244 43.478 0.00 0.00 0.00 3.58
3211 3435 1.544759 GGCAAATATGGTACGGGGGAG 60.545 57.143 0.00 0.00 0.00 4.30
3212 3436 0.475044 GGCAAATATGGTACGGGGGA 59.525 55.000 0.00 0.00 0.00 4.81
3232 3462 1.372501 CCCCTTCCTTTCCTTCCTCA 58.627 55.000 0.00 0.00 0.00 3.86
3237 3467 0.198696 TCCTCCCCCTTCCTTTCCTT 59.801 55.000 0.00 0.00 0.00 3.36
3270 3506 2.446802 GAGGGGGATTCGGCCTCT 60.447 66.667 0.00 0.00 0.00 3.69
3377 3618 2.467880 GAAGCCCCGGGAGATATATGA 58.532 52.381 26.32 0.00 0.00 2.15
3412 3654 2.588620 GGGTAGAGTCATCGGATCACT 58.411 52.381 0.00 0.00 0.00 3.41
3424 3666 0.179936 CGAGAGGTACCGGGTAGAGT 59.820 60.000 7.25 0.00 0.00 3.24
3425 3667 0.467384 TCGAGAGGTACCGGGTAGAG 59.533 60.000 7.25 0.00 0.00 2.43
3522 3764 4.356979 ACCGGATGAGATCACGGT 57.643 55.556 9.46 10.70 45.21 4.83
3539 3781 5.596772 TGATGACCAGATATTGTTCGGAGTA 59.403 40.000 0.00 0.00 0.00 2.59
3554 3796 6.990341 TGAGTTATGTGATTTGATGACCAG 57.010 37.500 0.00 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.