Multiple sequence alignment - TraesCS2D01G058900

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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 TraesCS2D01G058900 chr2D 100.000 4264 0 0 1 4264 23414076 23418339 0.000000e+00 7875
1 TraesCS2D01G058900 chr2A 92.838 1913 112 15 2369 4264 25349256 25347352 0.000000e+00 2750
2 TraesCS2D01G058900 chr2A 93.798 1048 61 3 965 2012 25350563 25349520 0.000000e+00 1572
3 TraesCS2D01G058900 chr2A 93.200 250 7 5 2087 2329 25349505 25349259 4.050000e-95 359
4 TraesCS2D01G058900 chr2A 82.123 179 23 5 1729 1907 63605156 63604987 1.240000e-30 145
5 TraesCS2D01G058900 chr2B 93.681 1266 71 3 758 2019 36851101 36849841 0.000000e+00 1886
6 TraesCS2D01G058900 chr2B 91.653 1246 81 17 2442 3673 36845780 36844544 0.000000e+00 1703
7 TraesCS2D01G058900 chr2B 87.045 687 57 16 3603 4264 36843953 36843274 0.000000e+00 747
8 TraesCS2D01G058900 chr2B 92.708 96 7 0 2158 2253 36846446 36846351 5.750000e-29 139
9 TraesCS2D01G058900 chr2B 96.429 84 1 1 2086 2167 36848968 36848885 2.070000e-28 137
10 TraesCS2D01G058900 chr3B 94.767 707 21 5 1 691 740043778 740043072 0.000000e+00 1086
11 TraesCS2D01G058900 chr3B 94.380 694 28 4 1 687 786716396 786717085 0.000000e+00 1055
12 TraesCS2D01G058900 chr7D 91.465 703 40 7 1 685 549098176 549098876 0.000000e+00 948
13 TraesCS2D01G058900 chr7D 77.143 210 37 11 3753 3954 370183771 370183977 1.250000e-20 111
14 TraesCS2D01G058900 chr7A 91.193 704 40 6 1 689 20501218 20501914 0.000000e+00 937
15 TraesCS2D01G058900 chr7A 96.573 321 4 1 1 314 472134532 472134852 3.780000e-145 525
16 TraesCS2D01G058900 chr7A 77.251 211 35 13 3753 3954 409873010 409872804 1.250000e-20 111
17 TraesCS2D01G058900 chr4B 90.300 701 48 6 1 686 91139837 91139142 0.000000e+00 900
18 TraesCS2D01G058900 chr4B 92.157 612 34 6 87 686 634446103 634445494 0.000000e+00 852
19 TraesCS2D01G058900 chr4D 90.014 701 52 6 1 686 61610376 61611073 0.000000e+00 891
20 TraesCS2D01G058900 chr3A 96.552 348 11 1 341 688 746905175 746904829 3.700000e-160 575
21 TraesCS2D01G058900 chr3A 95.427 328 6 3 1 321 746905495 746905170 8.180000e-142 514
22 TraesCS2D01G058900 chr5A 96.542 347 9 2 341 687 4980939 4981282 4.780000e-159 571
23 TraesCS2D01G058900 chr5A 97.508 321 1 1 1 314 4980619 4980939 3.750000e-150 542
24 TraesCS2D01G058900 chr6D 77.419 310 50 19 1112 1411 397648211 397648510 2.640000e-37 167
25 TraesCS2D01G058900 chr3D 80.374 214 37 5 3763 3973 354068961 354068750 1.590000e-34 158
26 TraesCS2D01G058900 chr6B 76.699 309 54 17 1112 1411 594663776 594664075 5.710000e-34 156
27 TraesCS2D01G058900 chr1B 82.222 180 22 9 3724 3900 587656537 587656365 3.440000e-31 147
28 TraesCS2D01G058900 chr7B 76.812 207 36 12 3753 3951 317234587 317234789 5.830000e-19 106


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 TraesCS2D01G058900 chr2D 23414076 23418339 4263 False 7875.000000 7875 100.000000 1 4264 1 chr2D.!!$F1 4263
1 TraesCS2D01G058900 chr2A 25347352 25350563 3211 True 1560.333333 2750 93.278667 965 4264 3 chr2A.!!$R2 3299
2 TraesCS2D01G058900 chr2B 36843274 36851101 7827 True 922.400000 1886 92.303200 758 4264 5 chr2B.!!$R1 3506
3 TraesCS2D01G058900 chr3B 740043072 740043778 706 True 1086.000000 1086 94.767000 1 691 1 chr3B.!!$R1 690
4 TraesCS2D01G058900 chr3B 786716396 786717085 689 False 1055.000000 1055 94.380000 1 687 1 chr3B.!!$F1 686
5 TraesCS2D01G058900 chr7D 549098176 549098876 700 False 948.000000 948 91.465000 1 685 1 chr7D.!!$F2 684
6 TraesCS2D01G058900 chr7A 20501218 20501914 696 False 937.000000 937 91.193000 1 689 1 chr7A.!!$F1 688
7 TraesCS2D01G058900 chr4B 91139142 91139837 695 True 900.000000 900 90.300000 1 686 1 chr4B.!!$R1 685
8 TraesCS2D01G058900 chr4B 634445494 634446103 609 True 852.000000 852 92.157000 87 686 1 chr4B.!!$R2 599
9 TraesCS2D01G058900 chr4D 61610376 61611073 697 False 891.000000 891 90.014000 1 686 1 chr4D.!!$F1 685
10 TraesCS2D01G058900 chr3A 746904829 746905495 666 True 544.500000 575 95.989500 1 688 2 chr3A.!!$R1 687
11 TraesCS2D01G058900 chr5A 4980619 4981282 663 False 556.500000 571 97.025000 1 687 2 chr5A.!!$F1 686

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
678 701 0.687354 TTGGTGCCTCTCTCTGTTCC 59.313 55.000 0.00 0.0 0.00 3.62 F
1170 1193 0.250901 TGCACCTCTTCAAGAAGCCC 60.251 55.000 4.95 0.0 38.28 5.19 F
2020 2047 1.195448 ACGAGCAAAGCATTCGTCAAG 59.805 47.619 0.00 0.0 43.35 3.02 F
3101 6805 1.138859 CTAGGCATGAACATGGTCGGA 59.861 52.381 15.15 0.0 39.16 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2488 6168 1.583054 AGCTGGTGAAACAGTTCGTC 58.417 50.000 0.00 0.00 39.98 4.20 R
3029 6733 0.379669 CGAATGGCAGCATCCACTTC 59.620 55.000 0.00 4.83 39.25 3.01 R
3260 6964 0.107848 CGCCCGTGTTCCTTTCCTAT 60.108 55.000 0.00 0.00 0.00 2.57 R
3924 8305 1.070601 AGGGCATGGCAAAACAAACTC 59.929 47.619 22.06 0.00 0.00 3.01 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
347 367 7.793927 ATGTTCGAAGTTCTCTTTCTTCTTT 57.206 32.000 0.00 0.00 38.20 2.52
678 701 0.687354 TTGGTGCCTCTCTCTGTTCC 59.313 55.000 0.00 0.00 0.00 3.62
707 730 5.975693 AAAAAGCGTAGATGGAATTTGGA 57.024 34.783 0.00 0.00 0.00 3.53
708 731 6.530019 AAAAAGCGTAGATGGAATTTGGAT 57.470 33.333 0.00 0.00 0.00 3.41
709 732 6.530019 AAAAGCGTAGATGGAATTTGGATT 57.470 33.333 0.00 0.00 0.00 3.01
710 733 6.530019 AAAGCGTAGATGGAATTTGGATTT 57.470 33.333 0.00 0.00 0.00 2.17
711 734 5.505173 AGCGTAGATGGAATTTGGATTTG 57.495 39.130 0.00 0.00 0.00 2.32
712 735 5.192927 AGCGTAGATGGAATTTGGATTTGA 58.807 37.500 0.00 0.00 0.00 2.69
713 736 5.297776 AGCGTAGATGGAATTTGGATTTGAG 59.702 40.000 0.00 0.00 0.00 3.02
714 737 5.506317 GCGTAGATGGAATTTGGATTTGAGG 60.506 44.000 0.00 0.00 0.00 3.86
715 738 5.590259 CGTAGATGGAATTTGGATTTGAGGT 59.410 40.000 0.00 0.00 0.00 3.85
716 739 6.238484 CGTAGATGGAATTTGGATTTGAGGTC 60.238 42.308 0.00 0.00 0.00 3.85
717 740 5.835582 AGATGGAATTTGGATTTGAGGTCT 58.164 37.500 0.00 0.00 0.00 3.85
718 741 6.259123 AGATGGAATTTGGATTTGAGGTCTT 58.741 36.000 0.00 0.00 0.00 3.01
719 742 7.413446 AGATGGAATTTGGATTTGAGGTCTTA 58.587 34.615 0.00 0.00 0.00 2.10
720 743 8.063770 AGATGGAATTTGGATTTGAGGTCTTAT 58.936 33.333 0.00 0.00 0.00 1.73
721 744 9.354673 GATGGAATTTGGATTTGAGGTCTTATA 57.645 33.333 0.00 0.00 0.00 0.98
722 745 8.752005 TGGAATTTGGATTTGAGGTCTTATAG 57.248 34.615 0.00 0.00 0.00 1.31
723 746 7.285401 TGGAATTTGGATTTGAGGTCTTATAGC 59.715 37.037 0.00 0.00 0.00 2.97
724 747 6.867662 ATTTGGATTTGAGGTCTTATAGCG 57.132 37.500 0.00 0.00 0.00 4.26
725 748 5.353394 TTGGATTTGAGGTCTTATAGCGT 57.647 39.130 0.00 0.00 0.00 5.07
726 749 4.693283 TGGATTTGAGGTCTTATAGCGTG 58.307 43.478 0.00 0.00 0.00 5.34
727 750 4.058817 GGATTTGAGGTCTTATAGCGTGG 58.941 47.826 0.00 0.00 0.00 4.94
728 751 4.443034 GGATTTGAGGTCTTATAGCGTGGT 60.443 45.833 0.00 0.00 0.00 4.16
729 752 5.221382 GGATTTGAGGTCTTATAGCGTGGTA 60.221 44.000 0.00 0.00 0.00 3.25
730 753 5.664294 TTTGAGGTCTTATAGCGTGGTAA 57.336 39.130 0.00 0.00 0.00 2.85
731 754 5.664294 TTGAGGTCTTATAGCGTGGTAAA 57.336 39.130 0.00 0.00 0.00 2.01
732 755 5.864418 TGAGGTCTTATAGCGTGGTAAAT 57.136 39.130 0.00 0.00 0.00 1.40
733 756 6.964807 TGAGGTCTTATAGCGTGGTAAATA 57.035 37.500 0.00 0.00 0.00 1.40
734 757 6.742109 TGAGGTCTTATAGCGTGGTAAATAC 58.258 40.000 0.00 0.00 0.00 1.89
735 758 6.321945 TGAGGTCTTATAGCGTGGTAAATACA 59.678 38.462 0.00 0.00 0.00 2.29
736 759 7.014905 TGAGGTCTTATAGCGTGGTAAATACAT 59.985 37.037 0.00 0.00 0.00 2.29
737 760 7.376615 AGGTCTTATAGCGTGGTAAATACATC 58.623 38.462 0.00 0.00 0.00 3.06
738 761 7.014905 AGGTCTTATAGCGTGGTAAATACATCA 59.985 37.037 0.00 0.00 0.00 3.07
739 762 7.817962 GGTCTTATAGCGTGGTAAATACATCAT 59.182 37.037 0.00 0.00 0.00 2.45
740 763 9.850628 GTCTTATAGCGTGGTAAATACATCATA 57.149 33.333 0.00 0.00 0.00 2.15
743 766 5.862924 AGCGTGGTAAATACATCATATGC 57.137 39.130 0.00 0.00 0.00 3.14
744 767 5.304778 AGCGTGGTAAATACATCATATGCA 58.695 37.500 0.00 0.00 0.00 3.96
745 768 5.939883 AGCGTGGTAAATACATCATATGCAT 59.060 36.000 3.79 3.79 0.00 3.96
746 769 6.092670 AGCGTGGTAAATACATCATATGCATC 59.907 38.462 0.19 0.00 0.00 3.91
747 770 6.128309 GCGTGGTAAATACATCATATGCATCA 60.128 38.462 0.19 0.00 0.00 3.07
748 771 7.414429 GCGTGGTAAATACATCATATGCATCAT 60.414 37.037 0.19 0.00 0.00 2.45
749 772 8.453320 CGTGGTAAATACATCATATGCATCATT 58.547 33.333 0.19 0.00 0.00 2.57
750 773 9.563898 GTGGTAAATACATCATATGCATCATTG 57.436 33.333 0.19 0.00 0.00 2.82
751 774 9.517868 TGGTAAATACATCATATGCATCATTGA 57.482 29.630 0.19 5.89 0.00 2.57
752 775 9.999009 GGTAAATACATCATATGCATCATTGAG 57.001 33.333 0.19 2.96 0.00 3.02
756 779 9.907229 AATACATCATATGCATCATTGAGATCT 57.093 29.630 0.19 0.00 33.72 2.75
768 791 8.136165 GCATCATTGAGATCTTGATTTTTAGCT 58.864 33.333 5.77 0.00 33.72 3.32
796 819 8.877864 TTTACCTTGATGATGTCCAACTAATT 57.122 30.769 0.00 0.00 0.00 1.40
797 820 9.967451 TTTACCTTGATGATGTCCAACTAATTA 57.033 29.630 0.00 0.00 0.00 1.40
798 821 9.967451 TTACCTTGATGATGTCCAACTAATTAA 57.033 29.630 0.00 0.00 0.00 1.40
799 822 8.511604 ACCTTGATGATGTCCAACTAATTAAG 57.488 34.615 0.00 0.00 0.00 1.85
803 826 9.613428 TTGATGATGTCCAACTAATTAAGGTAG 57.387 33.333 0.00 0.00 0.00 3.18
808 831 5.047164 TGTCCAACTAATTAAGGTAGACGCA 60.047 40.000 3.58 0.00 0.00 5.24
852 875 1.375396 CAAATGGCCGTCCACGAGA 60.375 57.895 0.00 0.00 46.92 4.04
855 878 2.311688 AATGGCCGTCCACGAGATCC 62.312 60.000 0.00 0.00 46.92 3.36
920 943 1.066430 AGCGCGAGTGGATTTTTCCTA 60.066 47.619 12.10 0.00 0.00 2.94
924 947 3.676324 CGCGAGTGGATTTTTCCTACTCT 60.676 47.826 0.00 3.04 36.59 3.24
926 949 5.044558 GCGAGTGGATTTTTCCTACTCTAG 58.955 45.833 15.86 0.00 36.59 2.43
975 998 2.279517 CAGCCTATCGCGTCACCC 60.280 66.667 5.77 0.00 44.76 4.61
995 1018 1.144936 CGCTGACCTCCAAGATCCC 59.855 63.158 0.00 0.00 0.00 3.85
1063 1086 1.074423 ACGGTCCTCTTCGTCCTCA 59.926 57.895 0.00 0.00 34.20 3.86
1170 1193 0.250901 TGCACCTCTTCAAGAAGCCC 60.251 55.000 4.95 0.00 38.28 5.19
1263 1286 2.954684 GCTCCATGTCACCGACCCA 61.955 63.158 0.00 0.00 0.00 4.51
1659 1682 3.673597 TCGGAGGTGGAGGAGGCT 61.674 66.667 0.00 0.00 0.00 4.58
1661 1684 3.086600 GGAGGTGGAGGAGGCTGG 61.087 72.222 0.00 0.00 0.00 4.85
1839 1862 2.125350 GAGCACCTCGCCTCCTTG 60.125 66.667 0.00 0.00 44.04 3.61
1847 1870 1.667154 CTCGCCTCCTTGGACGATGA 61.667 60.000 3.44 0.00 41.11 2.92
1856 1879 1.320344 TTGGACGATGACGAGGGGAG 61.320 60.000 0.00 0.00 42.66 4.30
1967 1990 2.828520 TCTGCCTGGTGAGTAGAAGAAG 59.171 50.000 0.00 0.00 0.00 2.85
2020 2047 1.195448 ACGAGCAAAGCATTCGTCAAG 59.805 47.619 0.00 0.00 43.35 3.02
2028 2646 5.220098 GCAAAGCATTCGTCAAGCTATTTTC 60.220 40.000 0.00 0.00 37.70 2.29
2162 3001 2.489329 CCACTGACTTGGTTGGCTATTG 59.511 50.000 0.00 0.00 0.00 1.90
2171 5458 6.016555 ACTTGGTTGGCTATTGAATTAGGTT 58.983 36.000 0.00 0.00 0.00 3.50
2286 5811 2.695359 TGCCGGACAGACTTTTATGTC 58.305 47.619 5.05 0.00 44.10 3.06
2337 5863 1.335872 ACTTTGCGGCAAATGCAGTAC 60.336 47.619 26.56 0.00 44.28 2.73
2342 5868 3.536570 TGCGGCAAATGCAGTACTATTA 58.463 40.909 0.00 0.00 44.36 0.98
2343 5869 4.133820 TGCGGCAAATGCAGTACTATTAT 58.866 39.130 0.00 0.00 44.36 1.28
2345 5871 4.024048 GCGGCAAATGCAGTACTATTATGT 60.024 41.667 7.80 0.00 44.36 2.29
2346 5872 5.178623 GCGGCAAATGCAGTACTATTATGTA 59.821 40.000 7.80 0.00 44.36 2.29
2347 5873 6.618592 GCGGCAAATGCAGTACTATTATGTAG 60.619 42.308 7.80 0.00 44.36 2.74
2348 5874 6.423905 CGGCAAATGCAGTACTATTATGTAGT 59.576 38.462 7.80 0.00 44.36 2.73
2349 5875 7.359264 CGGCAAATGCAGTACTATTATGTAGTC 60.359 40.741 7.80 0.00 44.36 2.59
2350 5876 7.095187 GGCAAATGCAGTACTATTATGTAGTCC 60.095 40.741 7.80 0.00 44.36 3.85
2351 5877 7.441157 GCAAATGCAGTACTATTATGTAGTCCA 59.559 37.037 0.00 0.00 41.59 4.02
2352 5878 9.494271 CAAATGCAGTACTATTATGTAGTCCAT 57.506 33.333 0.00 0.00 37.58 3.41
2353 5879 9.494271 AAATGCAGTACTATTATGTAGTCCATG 57.506 33.333 0.00 0.00 34.86 3.66
2354 5880 7.597288 TGCAGTACTATTATGTAGTCCATGT 57.403 36.000 0.00 0.00 34.86 3.21
2355 5881 7.433680 TGCAGTACTATTATGTAGTCCATGTG 58.566 38.462 0.00 0.00 34.86 3.21
2356 5882 7.069455 TGCAGTACTATTATGTAGTCCATGTGT 59.931 37.037 0.00 0.00 34.86 3.72
2364 5890 8.752005 ATTATGTAGTCCATGTGTTTTGCTAT 57.248 30.769 0.00 0.00 34.86 2.97
2422 6073 3.193267 GTGCATGACATGTGGGTAACAAT 59.807 43.478 16.62 0.00 43.61 2.71
2538 6218 6.203723 CGATTTCCCAGGACTTCTATTGATTC 59.796 42.308 0.00 0.00 0.00 2.52
2542 6222 4.502259 CCCAGGACTTCTATTGATTCCTCG 60.502 50.000 5.26 0.82 34.58 4.63
2552 6232 2.315925 TGATTCCTCGGAGCACATTC 57.684 50.000 0.00 0.00 0.00 2.67
2576 6256 4.576216 AAATCACATTGTGCCGTTACAA 57.424 36.364 12.04 4.49 43.93 2.41
2610 6314 2.343101 TCCTTAACGCACTGCACATAC 58.657 47.619 1.11 0.00 0.00 2.39
2669 6373 1.523154 GCATCCTTCAAACCGGCACA 61.523 55.000 0.00 0.00 0.00 4.57
2867 6571 4.489771 CCAATCGCCCCGCTCCTT 62.490 66.667 0.00 0.00 0.00 3.36
3016 6720 1.301677 CCAGAGAGGTTTGAAGGCGC 61.302 60.000 0.00 0.00 0.00 6.53
3101 6805 1.138859 CTAGGCATGAACATGGTCGGA 59.861 52.381 15.15 0.00 39.16 4.55
3104 6808 1.453155 GCATGAACATGGTCGGACTT 58.547 50.000 15.15 0.00 39.16 3.01
3149 6853 2.037527 GAGTGGAGGAGGGTCGGT 59.962 66.667 0.00 0.00 0.00 4.69
3177 6881 1.598701 GGTTGACATGGCTGAAGGGC 61.599 60.000 0.00 0.00 41.27 5.19
3279 6983 0.107848 ATAGGAAAGGAACACGGGCG 60.108 55.000 0.00 0.00 0.00 6.13
3324 7028 6.750039 CACTAATAAAAACGCAATTTCGGGAT 59.250 34.615 1.93 0.00 0.00 3.85
3378 7082 6.466812 TCATCAACTGCTCTTAATCACAAGA 58.533 36.000 0.00 0.00 33.55 3.02
3406 7110 6.270927 ACCATGTAGAATGTATACTCCAGCAT 59.729 38.462 4.17 0.00 0.00 3.79
3409 7113 7.360113 TGTAGAATGTATACTCCAGCATGAA 57.640 36.000 4.17 0.00 39.69 2.57
3492 7196 6.967767 CAGTACTTCTTAGTTCGTACCAGATG 59.032 42.308 0.00 0.00 35.78 2.90
3546 7250 1.550976 AGGGAGAAGCGACGAAGAAAT 59.449 47.619 0.00 0.00 0.00 2.17
3550 7254 3.548268 GGAGAAGCGACGAAGAAATACTG 59.452 47.826 0.00 0.00 0.00 2.74
3658 8035 6.806739 GGAGCACCTAAACATGATACAAAAAC 59.193 38.462 0.00 0.00 0.00 2.43
3673 8050 7.504238 TGATACAAAAACAAAGTCAGGTATGGT 59.496 33.333 0.00 0.00 0.00 3.55
3678 8055 7.891498 AAAACAAAGTCAGGTATGGTTACTT 57.109 32.000 0.00 0.00 31.94 2.24
3706 8086 6.201425 GCATGTCCATGTTTTAATAGCAATGG 59.799 38.462 8.91 0.00 40.80 3.16
3735 8115 6.719370 ACTTCATAAGCAATAAACTTGGACCA 59.281 34.615 0.00 0.00 0.00 4.02
3749 8129 0.173708 GGACCACTAGAACCAGCGAG 59.826 60.000 0.00 0.00 0.00 5.03
3751 8131 0.900647 ACCACTAGAACCAGCGAGCT 60.901 55.000 0.00 0.00 0.00 4.09
3789 8169 5.658468 TGGCAAATGCGAATGATTTTCATA 58.342 33.333 0.00 0.00 43.26 2.15
3839 8219 4.540359 TTTCTTTAGCAAGCATGGCAAT 57.460 36.364 0.00 0.00 37.68 3.56
3840 8220 3.788333 TCTTTAGCAAGCATGGCAATC 57.212 42.857 0.00 0.00 37.68 2.67
3841 8221 3.359033 TCTTTAGCAAGCATGGCAATCT 58.641 40.909 0.00 0.00 37.68 2.40
3842 8222 3.129813 TCTTTAGCAAGCATGGCAATCTG 59.870 43.478 0.00 0.00 37.68 2.90
3858 8239 4.301628 CAATCTGCCCAGTTCAGTTTTTC 58.698 43.478 0.00 0.00 33.48 2.29
3866 8247 4.495844 CCCAGTTCAGTTTTTCGTCAGAAC 60.496 45.833 0.00 0.00 35.86 3.01
3870 8251 5.642063 AGTTCAGTTTTTCGTCAGAACTTGA 59.358 36.000 0.00 0.00 41.90 3.02
3901 8282 4.397417 CCTGAAGGAATTTGACATCCTCAC 59.603 45.833 0.00 0.00 45.33 3.51
3902 8283 4.984295 TGAAGGAATTTGACATCCTCACA 58.016 39.130 0.00 0.00 45.33 3.58
3924 8305 8.986847 TCACAACAACATAAATTGCCATAAAAG 58.013 29.630 0.00 0.00 32.47 2.27
4039 8422 5.126545 GGTAGTCTCTGGTTTGTTTGGTTTT 59.873 40.000 0.00 0.00 0.00 2.43
4040 8423 5.072040 AGTCTCTGGTTTGTTTGGTTTTG 57.928 39.130 0.00 0.00 0.00 2.44
4041 8424 4.081697 AGTCTCTGGTTTGTTTGGTTTTGG 60.082 41.667 0.00 0.00 0.00 3.28
4042 8425 3.835395 TCTCTGGTTTGTTTGGTTTTGGT 59.165 39.130 0.00 0.00 0.00 3.67
4043 8426 4.284746 TCTCTGGTTTGTTTGGTTTTGGTT 59.715 37.500 0.00 0.00 0.00 3.67
4044 8427 4.974399 TCTGGTTTGTTTGGTTTTGGTTT 58.026 34.783 0.00 0.00 0.00 3.27
4085 8468 1.110518 GGGCGGGACCTTGTTTTTCA 61.111 55.000 0.00 0.00 39.10 2.69
4144 8544 5.305644 AGTCACTCAACTGAGACCAATAAGT 59.694 40.000 13.61 0.00 44.74 2.24
4225 8628 2.233431 GCCACAAATATTGACAGCCCAA 59.767 45.455 0.00 0.00 0.00 4.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
347 367 5.744171 TCCAATAGCTTGCATCAAGTTCTA 58.256 37.500 8.18 3.31 42.77 2.10
465 485 2.948315 GGCAGCCTAAAGAAGAAGATGG 59.052 50.000 3.29 0.00 0.00 3.51
690 713 5.499139 TCAAATCCAAATTCCATCTACGC 57.501 39.130 0.00 0.00 0.00 4.42
691 714 5.590259 ACCTCAAATCCAAATTCCATCTACG 59.410 40.000 0.00 0.00 0.00 3.51
692 715 6.830838 AGACCTCAAATCCAAATTCCATCTAC 59.169 38.462 0.00 0.00 0.00 2.59
693 716 6.973642 AGACCTCAAATCCAAATTCCATCTA 58.026 36.000 0.00 0.00 0.00 1.98
694 717 5.835582 AGACCTCAAATCCAAATTCCATCT 58.164 37.500 0.00 0.00 0.00 2.90
695 718 6.535963 AAGACCTCAAATCCAAATTCCATC 57.464 37.500 0.00 0.00 0.00 3.51
696 719 9.359653 CTATAAGACCTCAAATCCAAATTCCAT 57.640 33.333 0.00 0.00 0.00 3.41
697 720 7.285401 GCTATAAGACCTCAAATCCAAATTCCA 59.715 37.037 0.00 0.00 0.00 3.53
698 721 7.520614 CGCTATAAGACCTCAAATCCAAATTCC 60.521 40.741 0.00 0.00 0.00 3.01
699 722 7.012421 ACGCTATAAGACCTCAAATCCAAATTC 59.988 37.037 0.00 0.00 0.00 2.17
700 723 6.828785 ACGCTATAAGACCTCAAATCCAAATT 59.171 34.615 0.00 0.00 0.00 1.82
701 724 6.260936 CACGCTATAAGACCTCAAATCCAAAT 59.739 38.462 0.00 0.00 0.00 2.32
702 725 5.584649 CACGCTATAAGACCTCAAATCCAAA 59.415 40.000 0.00 0.00 0.00 3.28
703 726 5.116180 CACGCTATAAGACCTCAAATCCAA 58.884 41.667 0.00 0.00 0.00 3.53
704 727 4.442893 CCACGCTATAAGACCTCAAATCCA 60.443 45.833 0.00 0.00 0.00 3.41
705 728 4.058817 CCACGCTATAAGACCTCAAATCC 58.941 47.826 0.00 0.00 0.00 3.01
706 729 4.694339 ACCACGCTATAAGACCTCAAATC 58.306 43.478 0.00 0.00 0.00 2.17
707 730 4.755266 ACCACGCTATAAGACCTCAAAT 57.245 40.909 0.00 0.00 0.00 2.32
708 731 5.664294 TTACCACGCTATAAGACCTCAAA 57.336 39.130 0.00 0.00 0.00 2.69
709 732 5.664294 TTTACCACGCTATAAGACCTCAA 57.336 39.130 0.00 0.00 0.00 3.02
710 733 5.864418 ATTTACCACGCTATAAGACCTCA 57.136 39.130 0.00 0.00 0.00 3.86
711 734 6.742109 TGTATTTACCACGCTATAAGACCTC 58.258 40.000 0.00 0.00 0.00 3.85
712 735 6.720112 TGTATTTACCACGCTATAAGACCT 57.280 37.500 0.00 0.00 0.00 3.85
713 736 7.149973 TGATGTATTTACCACGCTATAAGACC 58.850 38.462 0.00 0.00 0.00 3.85
714 737 8.758633 ATGATGTATTTACCACGCTATAAGAC 57.241 34.615 0.00 0.00 0.00 3.01
717 740 9.093970 GCATATGATGTATTTACCACGCTATAA 57.906 33.333 6.97 0.00 0.00 0.98
718 741 8.254508 TGCATATGATGTATTTACCACGCTATA 58.745 33.333 6.97 0.00 0.00 1.31
719 742 7.102993 TGCATATGATGTATTTACCACGCTAT 58.897 34.615 6.97 0.00 0.00 2.97
720 743 6.459923 TGCATATGATGTATTTACCACGCTA 58.540 36.000 6.97 0.00 0.00 4.26
721 744 5.304778 TGCATATGATGTATTTACCACGCT 58.695 37.500 6.97 0.00 0.00 5.07
722 745 5.605564 TGCATATGATGTATTTACCACGC 57.394 39.130 6.97 0.00 0.00 5.34
723 746 7.363205 TGATGCATATGATGTATTTACCACG 57.637 36.000 6.97 0.00 35.68 4.94
724 747 9.563898 CAATGATGCATATGATGTATTTACCAC 57.436 33.333 6.97 0.00 35.68 4.16
725 748 9.517868 TCAATGATGCATATGATGTATTTACCA 57.482 29.630 6.97 0.00 35.68 3.25
726 749 9.999009 CTCAATGATGCATATGATGTATTTACC 57.001 33.333 6.97 0.00 35.68 2.85
730 753 9.907229 AGATCTCAATGATGCATATGATGTATT 57.093 29.630 6.97 0.00 35.68 1.89
731 754 9.907229 AAGATCTCAATGATGCATATGATGTAT 57.093 29.630 6.97 0.00 38.33 2.29
732 755 9.162764 CAAGATCTCAATGATGCATATGATGTA 57.837 33.333 6.97 0.00 35.14 2.29
733 756 7.883311 TCAAGATCTCAATGATGCATATGATGT 59.117 33.333 6.97 0.00 35.14 3.06
734 757 8.268850 TCAAGATCTCAATGATGCATATGATG 57.731 34.615 6.97 0.57 35.14 3.07
735 758 9.467796 AATCAAGATCTCAATGATGCATATGAT 57.532 29.630 6.97 1.41 35.14 2.45
736 759 8.863872 AATCAAGATCTCAATGATGCATATGA 57.136 30.769 6.97 4.12 35.14 2.15
737 760 9.914131 AAAATCAAGATCTCAATGATGCATATG 57.086 29.630 8.77 0.00 35.14 1.78
740 763 9.967346 CTAAAAATCAAGATCTCAATGATGCAT 57.033 29.630 8.77 0.00 35.14 3.96
741 764 7.919091 GCTAAAAATCAAGATCTCAATGATGCA 59.081 33.333 8.77 0.00 35.14 3.96
742 765 8.136165 AGCTAAAAATCAAGATCTCAATGATGC 58.864 33.333 8.77 7.71 35.14 3.91
768 791 9.967451 TTAGTTGGACATCATCAAGGTAAATAA 57.033 29.630 0.00 0.00 0.00 1.40
776 799 8.511604 ACCTTAATTAGTTGGACATCATCAAG 57.488 34.615 7.83 0.00 0.00 3.02
778 801 8.988060 TCTACCTTAATTAGTTGGACATCATCA 58.012 33.333 7.83 0.00 0.00 3.07
796 819 4.459390 TGCTTTACATGCGTCTACCTTA 57.541 40.909 0.00 0.00 0.00 2.69
797 820 3.328382 TGCTTTACATGCGTCTACCTT 57.672 42.857 0.00 0.00 0.00 3.50
798 821 3.328382 TTGCTTTACATGCGTCTACCT 57.672 42.857 0.00 0.00 0.00 3.08
799 822 4.094294 TCATTTGCTTTACATGCGTCTACC 59.906 41.667 0.00 0.00 0.00 3.18
803 826 4.340894 TCTCATTTGCTTTACATGCGTC 57.659 40.909 0.00 0.00 0.00 5.19
852 875 0.905357 AACAAGAGGCTAGTGCGGAT 59.095 50.000 0.00 0.00 40.82 4.18
855 878 3.932710 TGATTAAACAAGAGGCTAGTGCG 59.067 43.478 0.00 0.00 40.82 5.34
920 943 0.825840 GGAGGAGATGCGCCTAGAGT 60.826 60.000 4.18 0.00 32.83 3.24
924 947 1.381191 TGTGGAGGAGATGCGCCTA 60.381 57.895 4.18 0.00 32.83 3.93
926 949 2.512515 GTGTGGAGGAGATGCGCC 60.513 66.667 4.18 0.00 0.00 6.53
975 998 0.103937 GGATCTTGGAGGTCAGCGAG 59.896 60.000 0.00 0.00 0.00 5.03
1263 1286 4.749310 CACTCTTCGGCTGCGGCT 62.749 66.667 18.85 0.00 38.73 5.52
1269 1292 2.659610 GTCAGGCACTCTTCGGCT 59.340 61.111 0.00 0.00 34.60 5.52
1491 1514 3.141488 GCGGCCTCGAGGAAGAGA 61.141 66.667 35.69 0.00 40.57 3.10
1582 1605 2.281070 GATCATCCGCGCCACCAT 60.281 61.111 0.00 0.00 0.00 3.55
1649 1672 4.664267 ACCTGCCAGCCTCCTCCA 62.664 66.667 0.00 0.00 0.00 3.86
1659 1682 2.285368 ATCTCCCGGAACCTGCCA 60.285 61.111 0.73 0.00 0.00 4.92
1661 1684 2.190578 CCATCTCCCGGAACCTGC 59.809 66.667 0.73 0.00 0.00 4.85
1704 1727 4.329545 TCCTGCAGGTTGGACGCC 62.330 66.667 31.58 0.00 36.34 5.68
1740 1763 4.758251 CCGCCGATGTCCAGCACA 62.758 66.667 0.00 0.00 40.18 4.57
1783 1806 4.735132 CTCGTTGCGCTTCCGGGA 62.735 66.667 9.73 0.00 34.32 5.14
1829 1852 1.680989 TCATCGTCCAAGGAGGCGA 60.681 57.895 3.98 4.30 45.31 5.54
1839 1862 2.491022 CCTCCCCTCGTCATCGTCC 61.491 68.421 0.00 0.00 38.33 4.79
2020 2047 9.855021 TTGTATAAAAAGCAAGGAGAAAATAGC 57.145 29.630 0.00 0.00 0.00 2.97
2236 5523 4.547886 ATTTGGATGTGGATGGGAAGAT 57.452 40.909 0.00 0.00 0.00 2.40
2300 5825 7.570324 GCCGCAAAGTATTTTAAAATTGCTTCA 60.570 33.333 23.97 5.43 35.03 3.02
2301 5826 6.736405 GCCGCAAAGTATTTTAAAATTGCTTC 59.264 34.615 23.97 15.96 35.03 3.86
2302 5827 6.203723 TGCCGCAAAGTATTTTAAAATTGCTT 59.796 30.769 23.97 20.70 35.03 3.91
2337 5863 8.213518 AGCAAAACACATGGACTACATAATAG 57.786 34.615 0.00 0.00 37.84 1.73
2342 5868 6.658816 TCAATAGCAAAACACATGGACTACAT 59.341 34.615 0.00 0.00 41.57 2.29
2343 5869 6.000840 TCAATAGCAAAACACATGGACTACA 58.999 36.000 0.00 0.00 0.00 2.74
2345 5871 7.701539 AATCAATAGCAAAACACATGGACTA 57.298 32.000 0.00 0.00 0.00 2.59
2346 5872 6.594788 AATCAATAGCAAAACACATGGACT 57.405 33.333 0.00 0.00 0.00 3.85
2347 5873 7.656707 AAAATCAATAGCAAAACACATGGAC 57.343 32.000 0.00 0.00 0.00 4.02
2422 6073 8.588472 CATAATGTGGATAATCTGGTAGACTGA 58.412 37.037 0.00 0.00 0.00 3.41
2488 6168 1.583054 AGCTGGTGAAACAGTTCGTC 58.417 50.000 0.00 0.00 39.98 4.20
2491 6171 3.793465 GCAAGAAGCTGGTGAAACAGTTC 60.793 47.826 0.00 0.83 40.59 3.01
2538 6218 4.024556 GTGATTTATGAATGTGCTCCGAGG 60.025 45.833 0.00 0.00 0.00 4.63
2542 6222 6.474427 CACAATGTGATTTATGAATGTGCTCC 59.526 38.462 7.78 0.00 35.23 4.70
2552 6232 5.635866 TGTAACGGCACAATGTGATTTATG 58.364 37.500 18.66 1.84 35.23 1.90
2594 6298 2.156343 TGTGTATGTGCAGTGCGTTA 57.844 45.000 11.20 0.00 0.00 3.18
2598 6302 2.226200 TGTTGATGTGTATGTGCAGTGC 59.774 45.455 8.58 8.58 0.00 4.40
2610 6314 3.687698 TGACATGATGAGCTGTTGATGTG 59.312 43.478 0.00 0.00 0.00 3.21
2746 6450 2.202492 CGACCTCGTTGAGCTCCG 60.202 66.667 12.15 8.74 34.11 4.63
2867 6571 3.311110 GAGGACTCGTGTGGGGCA 61.311 66.667 0.00 0.00 0.00 5.36
3029 6733 0.379669 CGAATGGCAGCATCCACTTC 59.620 55.000 0.00 4.83 39.25 3.01
3149 6853 1.279496 CCATGTCAACCTCCTCCTCA 58.721 55.000 0.00 0.00 0.00 3.86
3260 6964 0.107848 CGCCCGTGTTCCTTTCCTAT 60.108 55.000 0.00 0.00 0.00 2.57
3310 7014 1.656818 CCTGCATCCCGAAATTGCGT 61.657 55.000 4.84 0.00 39.23 5.24
3324 7028 3.055094 GGTAACTTCCTGATTCTCCTGCA 60.055 47.826 0.00 0.00 0.00 4.41
3378 7082 7.472100 GCTGGAGTATACATTCTACATGGTCTT 60.472 40.741 5.50 0.00 0.00 3.01
3406 7110 7.252612 TCTGGTATGAACTAAGAACCATTCA 57.747 36.000 0.00 0.00 39.40 2.57
3409 7113 7.092891 TGTGATCTGGTATGAACTAAGAACCAT 60.093 37.037 0.00 0.00 39.40 3.55
3463 7167 6.656270 TGGTACGAACTAAGAAGTACTGATGA 59.344 38.462 0.00 0.00 39.33 2.92
3472 7176 4.744570 TGCATCTGGTACGAACTAAGAAG 58.255 43.478 0.00 0.00 0.00 2.85
3492 7196 6.569179 TCTTCTTATGTAACAGGGTTTTGC 57.431 37.500 0.00 0.00 0.00 3.68
3546 7250 4.776795 TTCTTCATGCACGTCTACAGTA 57.223 40.909 0.00 0.00 0.00 2.74
3658 8035 5.122396 GCTCAAGTAACCATACCTGACTTTG 59.878 44.000 0.00 0.00 30.98 2.77
3673 8050 7.517614 TTAAAACATGGACATGCTCAAGTAA 57.482 32.000 11.96 1.21 42.39 2.24
3678 8055 5.651576 TGCTATTAAAACATGGACATGCTCA 59.348 36.000 11.96 0.00 42.39 4.26
3706 8086 7.598493 TCCAAGTTTATTGCTTATGAAGTTTGC 59.402 33.333 0.00 0.00 0.00 3.68
3735 8115 1.402984 CGAAAGCTCGCTGGTTCTAGT 60.403 52.381 0.00 0.00 38.45 2.57
3751 8131 3.126879 CCATGCCTCGCAGCGAAA 61.127 61.111 20.04 7.97 43.65 3.46
3770 8150 8.428186 AATTGCTATGAAAATCATTCGCATTT 57.572 26.923 13.85 13.39 39.78 2.32
3789 8169 1.269206 CCGCAGACAACACAAATTGCT 60.269 47.619 0.00 0.00 32.47 3.91
3839 8219 1.946768 CGAAAAACTGAACTGGGCAGA 59.053 47.619 0.00 0.00 36.86 4.26
3840 8220 1.676006 ACGAAAAACTGAACTGGGCAG 59.324 47.619 0.00 0.00 39.26 4.85
3841 8221 1.673920 GACGAAAAACTGAACTGGGCA 59.326 47.619 0.00 0.00 0.00 5.36
3842 8222 1.673920 TGACGAAAAACTGAACTGGGC 59.326 47.619 0.00 0.00 0.00 5.36
3866 8247 3.063510 TCCTTCAGGAAGCATGTCAAG 57.936 47.619 3.48 0.00 42.18 3.02
3892 8273 6.158598 GCAATTTATGTTGTTGTGAGGATGT 58.841 36.000 0.00 0.00 0.00 3.06
3901 8282 9.206870 ACTCTTTTATGGCAATTTATGTTGTTG 57.793 29.630 0.00 0.00 0.00 3.33
3902 8283 9.777297 AACTCTTTTATGGCAATTTATGTTGTT 57.223 25.926 0.00 0.00 0.00 2.83
3924 8305 1.070601 AGGGCATGGCAAAACAAACTC 59.929 47.619 22.06 0.00 0.00 3.01
3954 8337 4.148079 TGGGAAATGTTATTGTGCAGACA 58.852 39.130 0.00 0.00 0.00 3.41
3995 8378 2.691526 CCAGCCTGTGGTATACGAGTTA 59.308 50.000 0.00 0.00 42.17 2.24
4023 8406 4.757149 TGAAACCAAAACCAAACAAACCAG 59.243 37.500 0.00 0.00 0.00 4.00
4039 8422 7.040755 CGGCTCCACATTTTATATATGAAACCA 60.041 37.037 4.91 0.00 0.00 3.67
4040 8423 7.305474 CGGCTCCACATTTTATATATGAAACC 58.695 38.462 4.91 0.54 0.00 3.27
4041 8424 7.305474 CCGGCTCCACATTTTATATATGAAAC 58.695 38.462 4.91 0.00 0.00 2.78
4042 8425 6.432783 CCCGGCTCCACATTTTATATATGAAA 59.567 38.462 5.25 5.25 0.00 2.69
4043 8426 5.943416 CCCGGCTCCACATTTTATATATGAA 59.057 40.000 0.00 0.00 0.00 2.57
4044 8427 5.496556 CCCGGCTCCACATTTTATATATGA 58.503 41.667 0.00 0.00 0.00 2.15
4191 8594 9.894783 TCAATATTTGTGGCATTTGAAAAATTG 57.105 25.926 0.00 0.00 0.00 2.32
4225 8628 6.018469 TGATTGGATTGGAAATCCTCAAACT 58.982 36.000 17.57 0.00 38.95 2.66


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

AutoCloner maintained by Alex Coulton.