Multiple sequence alignment - TraesCS7A01G329500

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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 TraesCS7A01G329500 chr7A 100.000 4115 0 0 1 4115 479842439 479838325 0.000000e+00 7600
1 TraesCS7A01G329500 chr7A 87.566 756 77 12 3 753 37286457 37287200 0.000000e+00 859
2 TraesCS7A01G329500 chr7A 86.597 761 85 13 1 753 259575154 259575905 0.000000e+00 824
3 TraesCS7A01G329500 chr7A 87.395 119 13 2 906 1024 672870698 672870814 7.180000e-28 135
4 TraesCS7A01G329500 chr3A 95.216 2320 89 7 1064 3371 19337998 19335689 0.000000e+00 3650
5 TraesCS7A01G329500 chr2B 94.682 2313 113 4 1064 3366 520226097 520228409 0.000000e+00 3581
6 TraesCS7A01G329500 chr2B 92.258 155 12 0 3218 3372 209831925 209832079 1.930000e-53 220
7 TraesCS7A01G329500 chr7B 94.562 2317 110 6 1064 3368 597246145 597248457 0.000000e+00 3567
8 TraesCS7A01G329500 chr7B 91.096 730 56 6 3370 4093 295390534 295391260 0.000000e+00 979
9 TraesCS7A01G329500 chr7B 93.088 217 11 1 824 1040 295390330 295390542 8.590000e-82 315
10 TraesCS7A01G329500 chr1B 94.391 2282 113 6 1096 3368 562194836 562192561 0.000000e+00 3491
11 TraesCS7A01G329500 chr1B 96.538 1011 35 0 1835 2845 17727246 17726236 0.000000e+00 1674
12 TraesCS7A01G329500 chr1B 94.558 147 8 0 3218 3364 612936937 612937083 1.150000e-55 228
13 TraesCS7A01G329500 chr5A 85.800 2176 268 19 1064 3219 653953227 653955381 0.000000e+00 2268
14 TraesCS7A01G329500 chr5A 93.421 152 10 0 3218 3369 47772291 47772140 4.140000e-55 226
15 TraesCS7A01G329500 chr4B 95.208 1419 62 1 1074 2486 649477573 649476155 0.000000e+00 2239
16 TraesCS7A01G329500 chr4B 84.718 903 97 17 2478 3368 465734869 465733996 0.000000e+00 865
17 TraesCS7A01G329500 chr4B 86.400 125 10 2 923 1040 247579178 247579054 3.340000e-26 130
18 TraesCS7A01G329500 chr4B 85.600 125 11 2 923 1040 247278535 247278411 1.550000e-24 124
19 TraesCS7A01G329500 chr3B 86.693 2059 222 21 1321 3366 580223494 580221475 0.000000e+00 2237
20 TraesCS7A01G329500 chr3B 86.773 2011 202 22 1366 3367 395907192 395909147 0.000000e+00 2182
21 TraesCS7A01G329500 chr5B 85.446 2185 251 31 1067 3219 662600321 662602470 0.000000e+00 2211
22 TraesCS7A01G329500 chr5B 89.714 700 62 6 3421 4115 406403043 406402349 0.000000e+00 885
23 TraesCS7A01G329500 chr5B 88.148 135 10 4 906 1040 406403236 406403108 5.510000e-34 156
24 TraesCS7A01G329500 chr3D 87.522 1114 133 3 2111 3219 36840213 36841325 0.000000e+00 1282
25 TraesCS7A01G329500 chr3D 87.599 758 80 11 1 753 475866562 475867310 0.000000e+00 867
26 TraesCS7A01G329500 chr3D 88.684 380 33 4 3370 3746 36244189 36244561 4.850000e-124 455
27 TraesCS7A01G329500 chrUn 90.146 751 45 9 3370 4115 255440746 255440020 0.000000e+00 950
28 TraesCS7A01G329500 chrUn 93.095 420 28 1 3696 4115 318688198 318688616 7.560000e-172 614
29 TraesCS7A01G329500 chrUn 93.095 420 28 1 3696 4115 318694257 318693839 7.560000e-172 614
30 TraesCS7A01G329500 chrUn 93.095 420 28 1 3696 4115 331715852 331715434 7.560000e-172 614
31 TraesCS7A01G329500 chrUn 92.042 289 18 3 3370 3657 348353282 348353566 6.410000e-108 401
32 TraesCS7A01G329500 chrUn 92.042 289 18 3 3370 3657 348355613 348355897 6.410000e-108 401
33 TraesCS7A01G329500 chrUn 92.042 289 18 3 3370 3657 476304646 476304362 6.410000e-108 401
34 TraesCS7A01G329500 chrUn 87.931 174 13 3 871 1037 348353115 348353287 9.020000e-47 198
35 TraesCS7A01G329500 chrUn 87.356 174 14 3 871 1037 348355446 348355618 4.200000e-45 193
36 TraesCS7A01G329500 chrUn 86.154 130 18 0 910 1039 255440868 255440739 1.540000e-29 141
37 TraesCS7A01G329500 chr2A 90.146 751 45 9 3370 4115 361208511 361209237 0.000000e+00 950
38 TraesCS7A01G329500 chr2A 87.402 762 78 17 1 753 699984532 699983780 0.000000e+00 859
39 TraesCS7A01G329500 chr2A 90.824 425 32 3 3696 4115 361206528 361206950 2.780000e-156 562
40 TraesCS7A01G329500 chr2A 86.154 130 18 0 910 1039 361208389 361208518 1.540000e-29 141
41 TraesCS7A01G329500 chr1A 87.549 763 79 15 1 756 34980473 34979720 0.000000e+00 869
42 TraesCS7A01G329500 chr1A 86.835 752 82 17 1 748 568124538 568125276 0.000000e+00 824
43 TraesCS7A01G329500 chr7D 86.711 760 83 15 1 753 65760820 65761568 0.000000e+00 828
44 TraesCS7A01G329500 chr6D 86.745 762 77 20 1 753 441919200 441918454 0.000000e+00 826
45 TraesCS7A01G329500 chr6D 92.500 360 27 0 3756 4115 16085991 16086350 2.190000e-142 516
46 TraesCS7A01G329500 chr2D 86.772 756 83 14 6 753 489573827 489573081 0.000000e+00 826
47 TraesCS7A01G329500 chr2D 93.377 151 10 0 3218 3368 188839819 188839669 1.490000e-54 224
48 TraesCS7A01G329500 chr5D 84.154 467 50 8 1064 1506 526831044 526831510 8.170000e-117 431
49 TraesCS7A01G329500 chr5D 90.184 326 26 4 3421 3746 179652017 179651698 1.770000e-113 420


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 TraesCS7A01G329500 chr7A 479838325 479842439 4114 True 7600.00 7600 100.000000 1 4115 1 chr7A.!!$R1 4114
1 TraesCS7A01G329500 chr7A 37286457 37287200 743 False 859.00 859 87.566000 3 753 1 chr7A.!!$F1 750
2 TraesCS7A01G329500 chr7A 259575154 259575905 751 False 824.00 824 86.597000 1 753 1 chr7A.!!$F2 752
3 TraesCS7A01G329500 chr3A 19335689 19337998 2309 True 3650.00 3650 95.216000 1064 3371 1 chr3A.!!$R1 2307
4 TraesCS7A01G329500 chr2B 520226097 520228409 2312 False 3581.00 3581 94.682000 1064 3366 1 chr2B.!!$F2 2302
5 TraesCS7A01G329500 chr7B 597246145 597248457 2312 False 3567.00 3567 94.562000 1064 3368 1 chr7B.!!$F1 2304
6 TraesCS7A01G329500 chr7B 295390330 295391260 930 False 647.00 979 92.092000 824 4093 2 chr7B.!!$F2 3269
7 TraesCS7A01G329500 chr1B 562192561 562194836 2275 True 3491.00 3491 94.391000 1096 3368 1 chr1B.!!$R2 2272
8 TraesCS7A01G329500 chr1B 17726236 17727246 1010 True 1674.00 1674 96.538000 1835 2845 1 chr1B.!!$R1 1010
9 TraesCS7A01G329500 chr5A 653953227 653955381 2154 False 2268.00 2268 85.800000 1064 3219 1 chr5A.!!$F1 2155
10 TraesCS7A01G329500 chr4B 649476155 649477573 1418 True 2239.00 2239 95.208000 1074 2486 1 chr4B.!!$R4 1412
11 TraesCS7A01G329500 chr4B 465733996 465734869 873 True 865.00 865 84.718000 2478 3368 1 chr4B.!!$R3 890
12 TraesCS7A01G329500 chr3B 580221475 580223494 2019 True 2237.00 2237 86.693000 1321 3366 1 chr3B.!!$R1 2045
13 TraesCS7A01G329500 chr3B 395907192 395909147 1955 False 2182.00 2182 86.773000 1366 3367 1 chr3B.!!$F1 2001
14 TraesCS7A01G329500 chr5B 662600321 662602470 2149 False 2211.00 2211 85.446000 1067 3219 1 chr5B.!!$F1 2152
15 TraesCS7A01G329500 chr5B 406402349 406403236 887 True 520.50 885 88.931000 906 4115 2 chr5B.!!$R1 3209
16 TraesCS7A01G329500 chr3D 36840213 36841325 1112 False 1282.00 1282 87.522000 2111 3219 1 chr3D.!!$F2 1108
17 TraesCS7A01G329500 chr3D 475866562 475867310 748 False 867.00 867 87.599000 1 753 1 chr3D.!!$F3 752
18 TraesCS7A01G329500 chrUn 255440020 255440868 848 True 545.50 950 88.150000 910 4115 2 chrUn.!!$R4 3205
19 TraesCS7A01G329500 chrUn 348353115 348355897 2782 False 298.25 401 89.842750 871 3657 4 chrUn.!!$F2 2786
20 TraesCS7A01G329500 chr2A 699983780 699984532 752 True 859.00 859 87.402000 1 753 1 chr2A.!!$R1 752
21 TraesCS7A01G329500 chr2A 361206528 361209237 2709 False 551.00 950 89.041333 910 4115 3 chr2A.!!$F1 3205
22 TraesCS7A01G329500 chr1A 34979720 34980473 753 True 869.00 869 87.549000 1 756 1 chr1A.!!$R1 755
23 TraesCS7A01G329500 chr1A 568124538 568125276 738 False 824.00 824 86.835000 1 748 1 chr1A.!!$F1 747
24 TraesCS7A01G329500 chr7D 65760820 65761568 748 False 828.00 828 86.711000 1 753 1 chr7D.!!$F1 752
25 TraesCS7A01G329500 chr6D 441918454 441919200 746 True 826.00 826 86.745000 1 753 1 chr6D.!!$R1 752
26 TraesCS7A01G329500 chr2D 489573081 489573827 746 True 826.00 826 86.772000 6 753 1 chr2D.!!$R2 747

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
761 795 0.035152 TAGTGAGTTCGCCGACCCTA 60.035 55.0 0.0 0.0 0.0 3.53 F
776 810 0.389391 CCCTACCACGCTTGATCGAT 59.611 55.0 0.0 0.0 0.0 3.59 F
2143 3129 0.454600 GTCTCGCCTCGACACCATTA 59.545 55.0 0.0 0.0 0.0 1.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2191 3181 0.181114 CATTGGATCGCCTTGGAGGA 59.819 55.0 0.00 0.0 37.67 3.71 R
2275 3265 2.526304 TGCGCAGTAAAGACAGACTT 57.474 45.0 5.66 0.0 40.98 3.01 R
3205 4495 0.035534 AACCGCACTCACATGGCATA 60.036 50.0 0.00 0.0 0.00 3.14 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
177 188 2.096218 GCGAGAGTCACGATTTTGCTTT 60.096 45.455 14.42 0.00 0.00 3.51
299 315 3.094386 TGCTTCCGCAAAAGTCACT 57.906 47.368 0.00 0.00 44.62 3.41
335 351 2.283388 TCACGGCCGTACCTCCTT 60.283 61.111 33.70 1.55 35.61 3.36
337 353 2.283388 ACGGCCGTACCTCCTTGA 60.283 61.111 33.34 0.00 35.61 3.02
341 357 1.677820 CGGCCGTACCTCCTTGAAAAT 60.678 52.381 19.50 0.00 35.61 1.82
452 476 2.125106 GGCGTGCCTCTTTCGGAT 60.125 61.111 2.98 0.00 0.00 4.18
453 477 1.745489 GGCGTGCCTCTTTCGGATT 60.745 57.895 2.98 0.00 0.00 3.01
473 503 1.529713 GGAAAAACCCGTGCTCCCA 60.530 57.895 0.00 0.00 0.00 4.37
554 586 9.258629 ACATGGGATCTAATTTTGAAAATCTCA 57.741 29.630 3.32 0.00 0.00 3.27
561 593 7.015289 TCTAATTTTGAAAATCTCAACGCGAG 58.985 34.615 15.93 4.76 43.90 5.03
600 633 1.314581 GTTCGAATTTGAACGCACGG 58.685 50.000 20.19 0.00 38.91 4.94
615 648 3.185797 ACGCACGGTTTGAGAGATAAAAC 59.814 43.478 0.00 0.00 0.00 2.43
616 649 3.185594 CGCACGGTTTGAGAGATAAAACA 59.814 43.478 0.00 0.00 0.00 2.83
623 656 8.410141 ACGGTTTGAGAGATAAAACATTTTGAA 58.590 29.630 0.00 0.00 0.00 2.69
624 657 8.690840 CGGTTTGAGAGATAAAACATTTTGAAC 58.309 33.333 0.00 0.00 0.00 3.18
702 736 0.179070 TGCACCACTTGTCGCAACTA 60.179 50.000 0.00 0.00 31.18 2.24
703 737 0.512952 GCACCACTTGTCGCAACTAG 59.487 55.000 0.00 0.00 34.82 2.57
704 738 1.872237 GCACCACTTGTCGCAACTAGA 60.872 52.381 0.00 0.00 33.20 2.43
705 739 2.061773 CACCACTTGTCGCAACTAGAG 58.938 52.381 0.00 0.00 33.20 2.43
706 740 1.000955 ACCACTTGTCGCAACTAGAGG 59.999 52.381 1.48 1.48 41.98 3.69
708 742 2.288825 CCACTTGTCGCAACTAGAGGAA 60.289 50.000 0.00 0.00 39.90 3.36
711 745 2.724977 TGTCGCAACTAGAGGAACTG 57.275 50.000 0.00 0.00 41.55 3.16
712 746 2.235891 TGTCGCAACTAGAGGAACTGA 58.764 47.619 0.00 0.00 41.55 3.41
713 747 2.626266 TGTCGCAACTAGAGGAACTGAA 59.374 45.455 0.00 0.00 41.55 3.02
714 748 3.246619 GTCGCAACTAGAGGAACTGAAG 58.753 50.000 0.00 0.00 41.55 3.02
715 749 2.891580 TCGCAACTAGAGGAACTGAAGT 59.108 45.455 0.00 0.00 41.55 3.01
716 750 2.989840 CGCAACTAGAGGAACTGAAGTG 59.010 50.000 0.00 0.00 41.55 3.16
718 752 4.619394 CGCAACTAGAGGAACTGAAGTGAT 60.619 45.833 0.00 0.00 41.55 3.06
719 753 4.867608 GCAACTAGAGGAACTGAAGTGATC 59.132 45.833 0.00 0.00 41.55 2.92
721 755 6.696411 CAACTAGAGGAACTGAAGTGATCTT 58.304 40.000 0.00 0.00 41.55 2.40
722 756 6.926630 ACTAGAGGAACTGAAGTGATCTTT 57.073 37.500 0.00 0.00 41.55 2.52
723 757 6.696411 ACTAGAGGAACTGAAGTGATCTTTG 58.304 40.000 0.00 0.00 41.55 2.77
724 758 4.322567 AGAGGAACTGAAGTGATCTTTGC 58.677 43.478 0.00 0.00 41.55 3.68
725 759 4.067896 GAGGAACTGAAGTGATCTTTGCA 58.932 43.478 0.00 0.00 41.55 4.08
726 760 4.464008 AGGAACTGAAGTGATCTTTGCAA 58.536 39.130 0.00 0.00 37.18 4.08
727 761 4.276926 AGGAACTGAAGTGATCTTTGCAAC 59.723 41.667 0.00 0.00 37.18 4.17
728 762 4.036734 GGAACTGAAGTGATCTTTGCAACA 59.963 41.667 0.00 0.00 33.64 3.33
729 763 5.450412 GGAACTGAAGTGATCTTTGCAACAA 60.450 40.000 0.00 0.00 33.64 2.83
730 764 5.179045 ACTGAAGTGATCTTTGCAACAAG 57.821 39.130 0.00 0.00 33.64 3.16
732 766 5.822519 ACTGAAGTGATCTTTGCAACAAGTA 59.177 36.000 0.00 0.00 33.64 2.24
735 769 7.715657 TGAAGTGATCTTTGCAACAAGTATTT 58.284 30.769 0.00 0.00 33.64 1.40
736 770 7.862372 TGAAGTGATCTTTGCAACAAGTATTTC 59.138 33.333 0.00 0.18 33.64 2.17
737 771 7.516198 AGTGATCTTTGCAACAAGTATTTCT 57.484 32.000 0.00 0.00 0.00 2.52
738 772 7.945134 AGTGATCTTTGCAACAAGTATTTCTT 58.055 30.769 0.00 0.00 36.75 2.52
739 773 9.066892 AGTGATCTTTGCAACAAGTATTTCTTA 57.933 29.630 0.00 0.00 34.66 2.10
740 774 9.677567 GTGATCTTTGCAACAAGTATTTCTTAA 57.322 29.630 0.00 0.00 34.66 1.85
753 787 9.690434 CAAGTATTTCTTAATTAGTGAGTTCGC 57.310 33.333 0.00 0.00 34.66 4.70
755 789 5.773239 TTTCTTAATTAGTGAGTTCGCCG 57.227 39.130 0.00 0.00 0.00 6.46
757 791 4.418392 TCTTAATTAGTGAGTTCGCCGAC 58.582 43.478 0.00 0.00 0.00 4.79
758 792 2.005971 AATTAGTGAGTTCGCCGACC 57.994 50.000 0.00 0.00 0.00 4.79
759 793 0.175073 ATTAGTGAGTTCGCCGACCC 59.825 55.000 0.00 0.00 0.00 4.46
761 795 0.035152 TAGTGAGTTCGCCGACCCTA 60.035 55.000 0.00 0.00 0.00 3.53
762 796 1.153881 GTGAGTTCGCCGACCCTAC 60.154 63.158 0.00 0.00 0.00 3.18
763 797 2.345760 TGAGTTCGCCGACCCTACC 61.346 63.158 0.00 0.00 0.00 3.18
764 798 2.283388 AGTTCGCCGACCCTACCA 60.283 61.111 0.00 0.00 0.00 3.25
765 799 2.125793 GTTCGCCGACCCTACCAC 60.126 66.667 0.00 0.00 0.00 4.16
766 800 3.751246 TTCGCCGACCCTACCACG 61.751 66.667 0.00 0.00 0.00 4.94
769 803 4.078516 GCCGACCCTACCACGCTT 62.079 66.667 0.00 0.00 0.00 4.68
770 804 2.125673 CCGACCCTACCACGCTTG 60.126 66.667 0.00 0.00 0.00 4.01
772 806 1.515954 CGACCCTACCACGCTTGAT 59.484 57.895 0.00 0.00 0.00 2.57
773 807 0.527817 CGACCCTACCACGCTTGATC 60.528 60.000 0.00 0.00 0.00 2.92
774 808 0.527817 GACCCTACCACGCTTGATCG 60.528 60.000 0.00 0.00 0.00 3.69
775 809 0.968901 ACCCTACCACGCTTGATCGA 60.969 55.000 0.00 0.00 0.00 3.59
776 810 0.389391 CCCTACCACGCTTGATCGAT 59.611 55.000 0.00 0.00 0.00 3.59
778 812 2.128035 CCTACCACGCTTGATCGATTC 58.872 52.381 0.00 0.00 0.00 2.52
779 813 2.128035 CTACCACGCTTGATCGATTCC 58.872 52.381 0.00 0.00 0.00 3.01
781 815 1.338674 ACCACGCTTGATCGATTCCAA 60.339 47.619 0.00 0.00 0.00 3.53
783 817 2.161410 CCACGCTTGATCGATTCCAAAA 59.839 45.455 0.00 0.00 0.00 2.44
784 818 3.365868 CCACGCTTGATCGATTCCAAAAA 60.366 43.478 0.00 0.00 0.00 1.94
800 834 3.390003 AAAAAGGCGTTCCACTCGA 57.610 47.368 0.00 0.00 33.74 4.04
801 835 1.892209 AAAAAGGCGTTCCACTCGAT 58.108 45.000 0.00 0.00 33.74 3.59
802 836 1.892209 AAAAGGCGTTCCACTCGATT 58.108 45.000 0.00 0.00 33.74 3.34
803 837 1.156736 AAAGGCGTTCCACTCGATTG 58.843 50.000 0.00 0.00 33.74 2.67
805 839 1.079405 GGCGTTCCACTCGATTGGA 60.079 57.895 19.71 19.71 44.39 3.53
806 840 0.462047 GGCGTTCCACTCGATTGGAT 60.462 55.000 23.50 0.00 45.42 3.41
807 841 1.202486 GGCGTTCCACTCGATTGGATA 60.202 52.381 23.50 12.57 45.42 2.59
808 842 2.546778 GCGTTCCACTCGATTGGATAA 58.453 47.619 23.50 8.58 45.42 1.75
809 843 2.933906 GCGTTCCACTCGATTGGATAAA 59.066 45.455 23.50 7.87 45.42 1.40
810 844 3.372822 GCGTTCCACTCGATTGGATAAAA 59.627 43.478 23.50 7.51 45.42 1.52
812 846 5.560148 CGTTCCACTCGATTGGATAAAAAG 58.440 41.667 23.50 8.70 45.42 2.27
813 847 5.350365 CGTTCCACTCGATTGGATAAAAAGA 59.650 40.000 23.50 5.73 45.42 2.52
814 848 6.543736 GTTCCACTCGATTGGATAAAAAGAC 58.456 40.000 23.50 13.64 45.42 3.01
815 849 4.868171 TCCACTCGATTGGATAAAAAGACG 59.132 41.667 19.71 0.00 41.00 4.18
816 850 4.034048 CCACTCGATTGGATAAAAAGACGG 59.966 45.833 16.44 0.00 39.24 4.79
817 851 4.868171 CACTCGATTGGATAAAAAGACGGA 59.132 41.667 0.00 0.00 0.00 4.69
818 852 5.350365 CACTCGATTGGATAAAAAGACGGAA 59.650 40.000 0.00 0.00 0.00 4.30
819 853 5.935789 ACTCGATTGGATAAAAAGACGGAAA 59.064 36.000 0.00 0.00 0.00 3.13
821 855 5.122711 TCGATTGGATAAAAAGACGGAAACC 59.877 40.000 0.00 0.00 0.00 3.27
837 871 2.892373 AACCGAACATTGCACATACG 57.108 45.000 0.00 0.00 0.00 3.06
863 897 7.116805 GTGCAAATAAACTGGGAAGAAATCAAG 59.883 37.037 0.00 0.00 0.00 3.02
869 903 5.310409 ACTGGGAAGAAATCAAGAGTTCA 57.690 39.130 12.10 0.00 37.82 3.18
943 1896 6.530120 TCAAAAGTGCAAGTATGACTCCTAA 58.470 36.000 0.00 0.00 0.00 2.69
949 1902 4.061596 GCAAGTATGACTCCTAATGGCTC 58.938 47.826 0.00 0.00 0.00 4.70
964 1917 1.062198 TGGCTCCAGGACTCCATATCA 60.062 52.381 0.00 0.00 0.00 2.15
1043 1999 9.964354 TCCAATATATATCAAGTCTTTGGGATG 57.036 33.333 0.00 0.00 34.51 3.51
1044 2000 8.680903 CCAATATATATCAAGTCTTTGGGATGC 58.319 37.037 0.00 0.00 34.97 3.91
1045 2001 9.234827 CAATATATATCAAGTCTTTGGGATGCA 57.765 33.333 0.00 0.00 34.97 3.96
1046 2002 9.986157 AATATATATCAAGTCTTTGGGATGCAT 57.014 29.630 0.00 0.00 34.97 3.96
1047 2003 7.698506 ATATATCAAGTCTTTGGGATGCATG 57.301 36.000 2.46 0.00 34.97 4.06
1048 2004 3.159213 TCAAGTCTTTGGGATGCATGT 57.841 42.857 2.46 0.00 34.97 3.21
1049 2005 4.299586 TCAAGTCTTTGGGATGCATGTA 57.700 40.909 2.46 0.00 34.97 2.29
1050 2006 4.009675 TCAAGTCTTTGGGATGCATGTAC 58.990 43.478 2.46 0.00 34.97 2.90
1051 2007 4.012374 CAAGTCTTTGGGATGCATGTACT 58.988 43.478 2.46 0.00 0.00 2.73
1052 2008 5.045942 TCAAGTCTTTGGGATGCATGTACTA 60.046 40.000 2.46 0.00 34.97 1.82
1053 2009 4.770795 AGTCTTTGGGATGCATGTACTAC 58.229 43.478 2.46 0.00 0.00 2.73
1054 2010 3.877508 GTCTTTGGGATGCATGTACTACC 59.122 47.826 2.46 0.00 0.00 3.18
1055 2011 3.780294 TCTTTGGGATGCATGTACTACCT 59.220 43.478 2.46 0.00 0.00 3.08
1056 2012 3.558931 TTGGGATGCATGTACTACCTG 57.441 47.619 2.46 0.00 0.00 4.00
1057 2013 2.758130 TGGGATGCATGTACTACCTGA 58.242 47.619 2.46 0.00 0.00 3.86
1058 2014 2.700371 TGGGATGCATGTACTACCTGAG 59.300 50.000 2.46 0.00 0.00 3.35
1059 2015 2.548920 GGGATGCATGTACTACCTGAGC 60.549 54.545 2.46 0.00 0.00 4.26
1060 2016 2.103094 GGATGCATGTACTACCTGAGCA 59.897 50.000 2.46 0.00 34.78 4.26
1061 2017 3.432186 GGATGCATGTACTACCTGAGCAA 60.432 47.826 2.46 0.00 33.91 3.91
1062 2018 3.912496 TGCATGTACTACCTGAGCAAT 57.088 42.857 0.00 0.00 0.00 3.56
1209 2175 4.415332 GTCTCCCGTTCGCGCTCA 62.415 66.667 5.56 0.00 39.70 4.26
1256 2222 0.610687 CTTCTTCCTCGGCAGTCCTT 59.389 55.000 0.00 0.00 0.00 3.36
1262 2228 2.915659 TCGGCAGTCCTTCGGTGT 60.916 61.111 0.00 0.00 0.00 4.16
1363 2329 1.606601 CCGTGTGTCTCCTCTCCCA 60.607 63.158 0.00 0.00 0.00 4.37
1411 2377 2.578128 CTCGCTCTCCTGCTGCTT 59.422 61.111 0.00 0.00 0.00 3.91
1636 2613 1.311651 TACCGCATCACCCGTCGTTA 61.312 55.000 0.00 0.00 0.00 3.18
1942 2928 3.391382 CTCCGGCTTCGTCCCCTT 61.391 66.667 0.00 0.00 0.00 3.95
2063 3049 4.090588 GAACGGCCATCGGGTCCA 62.091 66.667 2.24 0.00 44.45 4.02
2127 3113 2.093973 CCCTACTGCTTCGTCATTGTCT 60.094 50.000 0.00 0.00 0.00 3.41
2143 3129 0.454600 GTCTCGCCTCGACACCATTA 59.545 55.000 0.00 0.00 0.00 1.90
2191 3181 1.453155 CCACTCTAATGCCACGCTTT 58.547 50.000 0.00 0.00 0.00 3.51
2209 3199 0.918983 TTCCTCCAAGGCGATCCAAT 59.081 50.000 0.00 0.00 34.61 3.16
2275 3265 0.610174 CTCAGCTGAGGTGGCACTTA 59.390 55.000 32.30 0.00 38.48 2.24
2553 3769 2.507058 TGTGGATCTCTATGGCTGCTTT 59.493 45.455 0.00 0.00 0.00 3.51
2568 3784 0.606673 GCTTTTCCCCTCGTGCTTCT 60.607 55.000 0.00 0.00 0.00 2.85
2615 3831 2.594592 GACGCCCCAAGTGTTGCT 60.595 61.111 0.00 0.00 40.03 3.91
2760 3987 2.370445 CCAGGCTTCGGAGGTGGAT 61.370 63.158 0.00 0.00 0.00 3.41
2798 4025 1.687612 CCATGGAGCCTTGTCAGGT 59.312 57.895 5.56 0.00 43.18 4.00
2807 4034 1.956477 GCCTTGTCAGGTGTCAAACAT 59.044 47.619 0.00 0.00 43.18 2.71
2869 4096 2.358267 GTCGTCGTTCCCTCATCTATGT 59.642 50.000 0.00 0.00 0.00 2.29
2963 4202 0.388649 GCTCTCTTCGCGAAGGAACA 60.389 55.000 39.79 24.37 38.88 3.18
3167 4453 4.331968 TCTGGGTTTGTGGATGTTGTATC 58.668 43.478 0.00 0.00 0.00 2.24
3173 4459 3.973206 TGTGGATGTTGTATCTTCGGT 57.027 42.857 0.00 0.00 0.00 4.69
3205 4495 2.776913 CGTGCGGTTGTGGGGTTTT 61.777 57.895 0.00 0.00 0.00 2.43
3292 4591 0.178301 GGTTTTTGCCCGGTTTTCCA 59.822 50.000 0.00 0.00 40.70 3.53
3302 4601 4.081586 TGCCCGGTTTTCCATTAATTAACC 60.082 41.667 0.00 0.00 40.70 2.85
3412 4711 0.810031 AAGTCAGCTTTGCACGTCGT 60.810 50.000 0.00 0.00 0.00 4.34
3473 7103 9.855021 AGCCAAGTATGTACAAATCAAATTTAC 57.145 29.630 0.00 0.00 0.00 2.01
3515 7145 4.568072 TGCTTCTAAGGGCAAACATAGA 57.432 40.909 0.00 0.00 35.40 1.98
3528 7158 4.399303 GCAAACATAGACATATATGGCCCC 59.601 45.833 15.26 2.26 36.08 5.80
3555 7186 6.127101 GCCCCTGTCCTACTATTGTAATTTT 58.873 40.000 0.00 0.00 0.00 1.82
3556 7187 7.092354 TGCCCCTGTCCTACTATTGTAATTTTA 60.092 37.037 0.00 0.00 0.00 1.52
3698 7331 8.458573 ACAGTTCTTGTAAATACATTGGTCAA 57.541 30.769 0.00 0.00 38.56 3.18
3705 7338 8.628630 TTGTAAATACATTGGTCAAGACATGA 57.371 30.769 0.00 0.00 35.89 3.07
3799 7438 6.330278 TCTTGTAAATACATCAGTCAGGACG 58.670 40.000 0.00 0.00 35.89 4.79
3915 7554 9.189156 ACTGCTGATAGGATTTAGCATTTAAAA 57.811 29.630 0.00 0.00 44.27 1.52
3993 7632 5.793030 AACAACAAAATAATCGGGTCCAA 57.207 34.783 0.00 0.00 0.00 3.53
4059 7698 8.793592 CAACTAAAAGTCTAAAACTGGGCTAAT 58.206 33.333 0.00 0.00 38.58 1.73
4104 7743 0.034186 TGGATGGCCCTAAAGCACAG 60.034 55.000 0.00 0.00 35.38 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
177 188 1.005037 ACAACCATGCTTCTCGCGA 60.005 52.632 9.26 9.26 43.27 5.87
254 269 2.542595 GTGAGTCTCGCGAAAGGAAAAA 59.457 45.455 11.33 0.00 0.00 1.94
299 315 2.201732 GACTCTCGTGAAAGCACAACA 58.798 47.619 0.00 0.00 45.41 3.33
514 546 6.676558 AGATCCCATGTTGATAGGTTTTGAT 58.323 36.000 0.00 0.00 0.00 2.57
554 586 1.356527 GCCGTTGGATTACTCGCGTT 61.357 55.000 5.77 0.00 0.00 4.84
561 593 0.800012 TGCTTTCGCCGTTGGATTAC 59.200 50.000 0.00 0.00 34.43 1.89
562 594 1.083489 CTGCTTTCGCCGTTGGATTA 58.917 50.000 0.00 0.00 34.43 1.75
580 612 1.070175 CCGTGCGTTCAAATTCGAACT 60.070 47.619 7.62 0.00 42.57 3.01
585 617 2.719046 CTCAAACCGTGCGTTCAAATTC 59.281 45.455 0.00 0.00 31.78 2.17
615 648 7.830217 TTCGTAGATTCGTTTGTTCAAAATG 57.170 32.000 0.00 0.00 35.04 2.32
616 649 8.844441 TTTTCGTAGATTCGTTTGTTCAAAAT 57.156 26.923 0.00 0.00 35.04 1.82
655 688 1.995991 CGCCACTTGTCGTAATCCG 59.004 57.895 0.00 0.00 38.13 4.18
656 689 1.713830 GCGCCACTTGTCGTAATCC 59.286 57.895 0.00 0.00 0.00 3.01
657 690 1.343821 CGCGCCACTTGTCGTAATC 59.656 57.895 0.00 0.00 0.00 1.75
658 691 2.736682 GCGCGCCACTTGTCGTAAT 61.737 57.895 23.24 0.00 0.00 1.89
659 692 3.408020 GCGCGCCACTTGTCGTAA 61.408 61.111 23.24 0.00 0.00 3.18
690 724 2.989840 CAGTTCCTCTAGTTGCGACAAG 59.010 50.000 6.90 0.64 0.00 3.16
693 727 3.246619 CTTCAGTTCCTCTAGTTGCGAC 58.753 50.000 0.00 0.00 0.00 5.19
702 736 4.202398 TGCAAAGATCACTTCAGTTCCTCT 60.202 41.667 0.00 0.00 35.05 3.69
703 737 4.067896 TGCAAAGATCACTTCAGTTCCTC 58.932 43.478 0.00 0.00 35.05 3.71
704 738 4.090761 TGCAAAGATCACTTCAGTTCCT 57.909 40.909 0.00 0.00 35.05 3.36
705 739 4.036734 TGTTGCAAAGATCACTTCAGTTCC 59.963 41.667 0.00 0.00 35.05 3.62
706 740 5.173774 TGTTGCAAAGATCACTTCAGTTC 57.826 39.130 0.00 0.00 35.05 3.01
708 742 4.641989 ACTTGTTGCAAAGATCACTTCAGT 59.358 37.500 0.00 0.00 35.05 3.41
711 745 8.078596 AGAAATACTTGTTGCAAAGATCACTTC 58.921 33.333 0.00 0.38 35.05 3.01
712 746 7.945134 AGAAATACTTGTTGCAAAGATCACTT 58.055 30.769 0.00 0.00 38.05 3.16
713 747 7.516198 AGAAATACTTGTTGCAAAGATCACT 57.484 32.000 0.00 0.00 0.00 3.41
714 748 9.677567 TTAAGAAATACTTGTTGCAAAGATCAC 57.322 29.630 0.00 0.00 39.38 3.06
727 761 9.690434 GCGAACTCACTAATTAAGAAATACTTG 57.310 33.333 0.00 0.00 39.38 3.16
728 762 8.880750 GGCGAACTCACTAATTAAGAAATACTT 58.119 33.333 0.00 0.00 42.04 2.24
729 763 7.222224 CGGCGAACTCACTAATTAAGAAATACT 59.778 37.037 0.00 0.00 0.00 2.12
730 764 7.221452 TCGGCGAACTCACTAATTAAGAAATAC 59.779 37.037 7.35 0.00 0.00 1.89
732 766 6.035758 GTCGGCGAACTCACTAATTAAGAAAT 59.964 38.462 12.92 0.00 0.00 2.17
735 769 4.418392 GTCGGCGAACTCACTAATTAAGA 58.582 43.478 12.92 0.00 0.00 2.10
736 770 3.550678 GGTCGGCGAACTCACTAATTAAG 59.449 47.826 19.36 0.00 0.00 1.85
737 771 3.514645 GGTCGGCGAACTCACTAATTAA 58.485 45.455 19.36 0.00 0.00 1.40
738 772 2.159198 GGGTCGGCGAACTCACTAATTA 60.159 50.000 25.63 0.00 0.00 1.40
739 773 1.405121 GGGTCGGCGAACTCACTAATT 60.405 52.381 25.63 0.00 0.00 1.40
740 774 0.175073 GGGTCGGCGAACTCACTAAT 59.825 55.000 25.63 0.00 0.00 1.73
741 775 0.896940 AGGGTCGGCGAACTCACTAA 60.897 55.000 25.63 0.00 0.00 2.24
742 776 0.035152 TAGGGTCGGCGAACTCACTA 60.035 55.000 25.63 14.21 0.00 2.74
743 777 1.303888 TAGGGTCGGCGAACTCACT 60.304 57.895 25.63 15.32 0.00 3.41
744 778 1.153881 GTAGGGTCGGCGAACTCAC 60.154 63.158 25.63 18.09 0.00 3.51
745 779 2.345760 GGTAGGGTCGGCGAACTCA 61.346 63.158 25.63 9.98 0.00 3.41
746 780 2.345760 TGGTAGGGTCGGCGAACTC 61.346 63.158 25.63 14.81 0.00 3.01
748 782 2.125793 GTGGTAGGGTCGGCGAAC 60.126 66.667 18.34 18.34 0.00 3.95
749 783 3.751246 CGTGGTAGGGTCGGCGAA 61.751 66.667 12.92 0.00 0.00 4.70
753 787 1.956629 ATCAAGCGTGGTAGGGTCGG 61.957 60.000 0.00 0.00 0.00 4.79
755 789 0.527817 CGATCAAGCGTGGTAGGGTC 60.528 60.000 0.00 0.00 0.00 4.46
757 791 0.389391 ATCGATCAAGCGTGGTAGGG 59.611 55.000 0.00 0.00 0.00 3.53
758 792 2.128035 GAATCGATCAAGCGTGGTAGG 58.872 52.381 0.00 0.00 0.00 3.18
759 793 2.128035 GGAATCGATCAAGCGTGGTAG 58.872 52.381 0.00 0.00 0.00 3.18
761 795 0.249120 TGGAATCGATCAAGCGTGGT 59.751 50.000 0.00 0.00 0.00 4.16
762 796 1.368641 TTGGAATCGATCAAGCGTGG 58.631 50.000 0.00 0.00 0.00 4.94
763 797 3.469899 TTTTGGAATCGATCAAGCGTG 57.530 42.857 0.00 0.00 0.00 5.34
783 817 1.535462 CAATCGAGTGGAACGCCTTTT 59.465 47.619 4.63 0.00 45.86 2.27
784 818 1.156736 CAATCGAGTGGAACGCCTTT 58.843 50.000 4.63 0.00 45.86 3.11
786 820 1.079127 CCAATCGAGTGGAACGCCT 60.079 57.895 27.32 0.00 45.86 5.52
787 821 1.079405 TCCAATCGAGTGGAACGCC 60.079 57.895 30.90 0.00 44.91 5.68
788 822 4.590487 TCCAATCGAGTGGAACGC 57.410 55.556 30.90 0.00 44.91 4.84
793 827 4.034048 CCGTCTTTTTATCCAATCGAGTGG 59.966 45.833 25.59 25.59 40.33 4.00
794 828 4.868171 TCCGTCTTTTTATCCAATCGAGTG 59.132 41.667 5.75 5.75 0.00 3.51
795 829 5.080969 TCCGTCTTTTTATCCAATCGAGT 57.919 39.130 0.00 0.00 0.00 4.18
796 830 6.248631 GTTTCCGTCTTTTTATCCAATCGAG 58.751 40.000 0.00 0.00 0.00 4.04
799 833 5.329493 CGGTTTCCGTCTTTTTATCCAATC 58.671 41.667 0.00 0.00 42.73 2.67
800 834 5.305139 CGGTTTCCGTCTTTTTATCCAAT 57.695 39.130 0.00 0.00 42.73 3.16
801 835 4.752661 CGGTTTCCGTCTTTTTATCCAA 57.247 40.909 0.00 0.00 42.73 3.53
815 849 2.723124 ATGTGCAATGTTCGGTTTCC 57.277 45.000 0.00 0.00 0.00 3.13
816 850 3.160545 CGTATGTGCAATGTTCGGTTTC 58.839 45.455 0.00 0.00 0.00 2.78
817 851 2.550606 ACGTATGTGCAATGTTCGGTTT 59.449 40.909 0.00 0.00 0.00 3.27
818 852 2.095969 CACGTATGTGCAATGTTCGGTT 60.096 45.455 1.29 0.00 39.67 4.44
819 853 1.463056 CACGTATGTGCAATGTTCGGT 59.537 47.619 1.29 0.00 39.67 4.69
837 871 6.454795 TGATTTCTTCCCAGTTTATTTGCAC 58.545 36.000 0.00 0.00 0.00 4.57
848 882 6.639632 TTTGAACTCTTGATTTCTTCCCAG 57.360 37.500 3.15 0.00 0.00 4.45
943 1896 2.264455 GATATGGAGTCCTGGAGCCAT 58.736 52.381 25.65 25.65 43.22 4.40
1040 1996 3.459232 TGCTCAGGTAGTACATGCATC 57.541 47.619 10.08 2.71 28.67 3.91
1041 1997 3.912496 TTGCTCAGGTAGTACATGCAT 57.088 42.857 10.08 0.00 28.67 3.96
1042 1998 3.197549 TCATTGCTCAGGTAGTACATGCA 59.802 43.478 10.08 3.08 28.67 3.96
1043 1999 3.797039 TCATTGCTCAGGTAGTACATGC 58.203 45.455 10.08 0.33 28.67 4.06
1044 2000 3.806521 GCTCATTGCTCAGGTAGTACATG 59.193 47.826 8.66 8.66 38.95 3.21
1045 2001 4.065321 GCTCATTGCTCAGGTAGTACAT 57.935 45.455 2.06 0.00 38.95 2.29
1046 2002 3.526931 GCTCATTGCTCAGGTAGTACA 57.473 47.619 2.06 0.00 38.95 2.90
1058 2014 2.806856 CGACGCAGGAGCTCATTGC 61.807 63.158 24.65 24.65 43.29 3.56
1059 2015 2.169789 CCGACGCAGGAGCTCATTG 61.170 63.158 17.19 14.10 39.10 2.82
1060 2016 2.185350 CCGACGCAGGAGCTCATT 59.815 61.111 17.19 0.00 39.10 2.57
1061 2017 3.842923 CCCGACGCAGGAGCTCAT 61.843 66.667 17.19 5.25 39.10 2.90
1099 2058 4.166888 GCTGGAGCGGATCTGGCA 62.167 66.667 3.14 0.00 0.00 4.92
1348 2314 1.606601 CCGTGGGAGAGGAGACACA 60.607 63.158 0.00 0.00 33.62 3.72
1411 2377 3.515286 GACGGCTCCCATCGTCGA 61.515 66.667 0.00 0.00 44.55 4.20
1544 2521 2.637383 GGAACCTCGCACGAGACCT 61.637 63.158 21.01 5.06 44.53 3.85
1587 2564 2.435059 GCGAGGACCAGCTTGGAC 60.435 66.667 8.91 3.23 40.96 4.02
1714 2691 2.488355 CGCAGCCAAAGCATCAGG 59.512 61.111 0.00 0.00 43.56 3.86
1819 2805 1.448540 CGCTGGAGCACTTGGTAGG 60.449 63.158 0.00 0.00 42.21 3.18
1968 2954 4.790962 AGGCACCTGCAGCATCGG 62.791 66.667 8.66 0.00 44.36 4.18
2060 3046 1.080093 GCGTTCCGACACTCATGGA 60.080 57.895 0.00 0.00 0.00 3.41
2063 3049 0.670546 CCAAGCGTTCCGACACTCAT 60.671 55.000 0.00 0.00 0.00 2.90
2127 3113 1.478916 TGATTAATGGTGTCGAGGCGA 59.521 47.619 0.00 0.00 0.00 5.54
2143 3129 5.763355 ACATGAAGGTGGATGAAGATGATT 58.237 37.500 0.00 0.00 0.00 2.57
2191 3181 0.181114 CATTGGATCGCCTTGGAGGA 59.819 55.000 0.00 0.00 37.67 3.71
2209 3199 3.680786 CGACGCCCAGGAGTCACA 61.681 66.667 18.81 0.00 43.47 3.58
2275 3265 2.526304 TGCGCAGTAAAGACAGACTT 57.474 45.000 5.66 0.00 40.98 3.01
2553 3769 3.068881 CCAGAAGCACGAGGGGAA 58.931 61.111 0.00 0.00 0.00 3.97
2615 3831 2.879233 GCCACACCCTCGAAGTCCA 61.879 63.158 0.00 0.00 0.00 4.02
2798 4025 3.192844 GTCGAGAGGTAGGATGTTTGACA 59.807 47.826 0.00 0.00 0.00 3.58
2807 4034 1.664873 CATGACGTCGAGAGGTAGGA 58.335 55.000 11.62 0.00 0.00 2.94
2869 4096 2.910360 CATCACCTGCCCGATGGA 59.090 61.111 0.00 0.00 36.24 3.41
3167 4453 0.663568 GTCCGTCACACTCACCGAAG 60.664 60.000 0.00 0.00 0.00 3.79
3173 4459 2.725641 CACGGTCCGTCACACTCA 59.274 61.111 15.67 0.00 38.32 3.41
3205 4495 0.035534 AACCGCACTCACATGGCATA 60.036 50.000 0.00 0.00 0.00 3.14
3292 4591 6.833933 AGAAGAGAATTGCCCGGTTAATTAAT 59.166 34.615 11.73 5.68 0.00 1.40
3302 4601 6.442513 AATTAAGAAGAAGAGAATTGCCCG 57.557 37.500 0.00 0.00 0.00 6.13
3380 4679 6.606768 CAAAGCTGACTTGTTAAGAAGGATC 58.393 40.000 16.02 6.66 35.85 3.36
3473 7103 2.995283 TGAGGAGGTCATTGCTGATTG 58.005 47.619 0.00 0.00 32.98 2.67
3528 7158 1.120530 AATAGTAGGACAGGGGCACG 58.879 55.000 0.00 0.00 0.00 5.34
3661 7294 7.817418 TTACAAGAACTGTCTTATTTTGCCT 57.183 32.000 0.00 0.00 42.45 4.75
3890 7529 9.674824 CTTTTAAATGCTAAATCCTATCAGCAG 57.325 33.333 1.38 0.00 46.35 4.24
3915 7554 4.111255 TGATGTCCTCTATAGCAGCTCT 57.889 45.455 0.00 0.00 0.00 4.09
3993 7632 7.974504 AGTAGGTATTGGGATTTATGATCGTT 58.025 34.615 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.