Multiple sequence alignment - TraesCS1D01G136000

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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 TraesCS1D01G136000 chr1D 100.000 3262 0 0 1 3262 180351116 180354377 0.000000e+00 6024
1 TraesCS1D01G136000 chr1D 97.045 2267 51 6 1000 3262 254480611 254478357 0.000000e+00 3801
2 TraesCS1D01G136000 chr1D 94.562 2078 92 7 1189 3262 244792092 244790032 0.000000e+00 3192
3 TraesCS1D01G136000 chr1D 94.262 2074 98 8 1193 3262 244212129 244210073 0.000000e+00 3151
4 TraesCS1D01G136000 chr1D 94.850 466 21 3 464 927 180213176 180213640 0.000000e+00 725
5 TraesCS1D01G136000 chr1D 94.033 486 14 3 1 471 180205301 180205786 0.000000e+00 723
6 TraesCS1D01G136000 chr1D 82.949 217 29 5 705 918 468095551 468095340 4.300000e-44 189
7 TraesCS1D01G136000 chr3B 97.395 2265 56 3 1000 3262 201496634 201494371 0.000000e+00 3853
8 TraesCS1D01G136000 chr5D 97.264 2266 59 3 1000 3262 6232616 6234881 0.000000e+00 3838
9 TraesCS1D01G136000 chr5D 98.023 1922 36 2 1000 2919 483804145 483806066 0.000000e+00 3338
10 TraesCS1D01G136000 chr5D 91.574 807 42 10 1 787 386051908 386051108 0.000000e+00 1090
11 TraesCS1D01G136000 chr7A 94.128 2265 125 8 1000 3262 352293183 352295441 0.000000e+00 3439
12 TraesCS1D01G136000 chr7A 85.463 227 21 5 706 927 20422441 20422222 3.270000e-55 226
13 TraesCS1D01G136000 chrUn 97.928 1593 31 2 1236 2826 386522344 386523936 0.000000e+00 2758
14 TraesCS1D01G136000 chrUn 97.809 1369 28 2 1114 2481 407032912 407031545 0.000000e+00 2361
15 TraesCS1D01G136000 chrUn 97.428 933 11 4 2331 3262 397678312 397677392 0.000000e+00 1578
16 TraesCS1D01G136000 chr6D 95.321 1667 70 7 1000 2664 210721724 210723384 0.000000e+00 2639
17 TraesCS1D01G136000 chr1A 97.872 799 14 3 2466 3262 554444322 554445119 0.000000e+00 1378
18 TraesCS1D01G136000 chr7D 92.441 807 41 7 1 787 220140471 220141277 0.000000e+00 1134
19 TraesCS1D01G136000 chr7D 94.337 618 33 2 2646 3262 88617453 88618069 0.000000e+00 946
20 TraesCS1D01G136000 chr7D 84.018 219 29 4 702 918 385354760 385354546 4.270000e-49 206
21 TraesCS1D01G136000 chr6B 92.355 811 41 9 1 791 40577465 40576656 0.000000e+00 1134
22 TraesCS1D01G136000 chr6B 94.805 154 4 1 774 927 40576708 40576559 1.510000e-58 237
23 TraesCS1D01G136000 chr6B 83.843 229 29 5 702 927 73043366 73043589 9.170000e-51 211
24 TraesCS1D01G136000 chr6B 84.475 219 28 4 702 918 592036696 592036910 9.170000e-51 211
25 TraesCS1D01G136000 chr4D 92.308 806 39 7 1 786 154082258 154083060 0.000000e+00 1123
26 TraesCS1D01G136000 chr4D 89.558 814 60 15 1 791 166145796 166144985 0.000000e+00 1009
27 TraesCS1D01G136000 chr5A 91.067 806 51 8 1 786 285740789 285741593 0.000000e+00 1070
28 TraesCS1D01G136000 chr5A 90.819 806 51 10 1 786 237049135 237049937 0.000000e+00 1057
29 TraesCS1D01G136000 chr5A 89.024 164 14 3 764 927 237049880 237050039 1.980000e-47 200
30 TraesCS1D01G136000 chr2B 89.571 815 60 15 1 791 185200246 185199433 0.000000e+00 1011
31 TraesCS1D01G136000 chr2B 85.526 228 21 5 705 927 185199556 185199336 9.110000e-56 228
32 TraesCS1D01G136000 chr7B 90.212 756 50 12 1 752 736271393 736272128 0.000000e+00 965
33 TraesCS1D01G136000 chr4A 96.863 510 14 2 2754 3262 665560767 665560259 0.000000e+00 852
34 TraesCS1D01G136000 chr6A 90.505 653 37 8 1 628 137936773 137936121 0.000000e+00 839


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 TraesCS1D01G136000 chr1D 180351116 180354377 3261 False 6024.0 6024 100.0000 1 3262 1 chr1D.!!$F3 3261
1 TraesCS1D01G136000 chr1D 254478357 254480611 2254 True 3801.0 3801 97.0450 1000 3262 1 chr1D.!!$R3 2262
2 TraesCS1D01G136000 chr1D 244790032 244792092 2060 True 3192.0 3192 94.5620 1189 3262 1 chr1D.!!$R2 2073
3 TraesCS1D01G136000 chr1D 244210073 244212129 2056 True 3151.0 3151 94.2620 1193 3262 1 chr1D.!!$R1 2069
4 TraesCS1D01G136000 chr3B 201494371 201496634 2263 True 3853.0 3853 97.3950 1000 3262 1 chr3B.!!$R1 2262
5 TraesCS1D01G136000 chr5D 6232616 6234881 2265 False 3838.0 3838 97.2640 1000 3262 1 chr5D.!!$F1 2262
6 TraesCS1D01G136000 chr5D 483804145 483806066 1921 False 3338.0 3338 98.0230 1000 2919 1 chr5D.!!$F2 1919
7 TraesCS1D01G136000 chr5D 386051108 386051908 800 True 1090.0 1090 91.5740 1 787 1 chr5D.!!$R1 786
8 TraesCS1D01G136000 chr7A 352293183 352295441 2258 False 3439.0 3439 94.1280 1000 3262 1 chr7A.!!$F1 2262
9 TraesCS1D01G136000 chrUn 386522344 386523936 1592 False 2758.0 2758 97.9280 1236 2826 1 chrUn.!!$F1 1590
10 TraesCS1D01G136000 chrUn 407031545 407032912 1367 True 2361.0 2361 97.8090 1114 2481 1 chrUn.!!$R2 1367
11 TraesCS1D01G136000 chrUn 397677392 397678312 920 True 1578.0 1578 97.4280 2331 3262 1 chrUn.!!$R1 931
12 TraesCS1D01G136000 chr6D 210721724 210723384 1660 False 2639.0 2639 95.3210 1000 2664 1 chr6D.!!$F1 1664
13 TraesCS1D01G136000 chr1A 554444322 554445119 797 False 1378.0 1378 97.8720 2466 3262 1 chr1A.!!$F1 796
14 TraesCS1D01G136000 chr7D 220140471 220141277 806 False 1134.0 1134 92.4410 1 787 1 chr7D.!!$F2 786
15 TraesCS1D01G136000 chr7D 88617453 88618069 616 False 946.0 946 94.3370 2646 3262 1 chr7D.!!$F1 616
16 TraesCS1D01G136000 chr6B 40576559 40577465 906 True 685.5 1134 93.5800 1 927 2 chr6B.!!$R1 926
17 TraesCS1D01G136000 chr4D 154082258 154083060 802 False 1123.0 1123 92.3080 1 786 1 chr4D.!!$F1 785
18 TraesCS1D01G136000 chr4D 166144985 166145796 811 True 1009.0 1009 89.5580 1 791 1 chr4D.!!$R1 790
19 TraesCS1D01G136000 chr5A 285740789 285741593 804 False 1070.0 1070 91.0670 1 786 1 chr5A.!!$F1 785
20 TraesCS1D01G136000 chr5A 237049135 237050039 904 False 628.5 1057 89.9215 1 927 2 chr5A.!!$F2 926
21 TraesCS1D01G136000 chr2B 185199336 185200246 910 True 619.5 1011 87.5485 1 927 2 chr2B.!!$R1 926
22 TraesCS1D01G136000 chr7B 736271393 736272128 735 False 965.0 965 90.2120 1 752 1 chr7B.!!$F1 751
23 TraesCS1D01G136000 chr4A 665560259 665560767 508 True 852.0 852 96.8630 2754 3262 1 chr4A.!!$R1 508
24 TraesCS1D01G136000 chr6A 137936121 137936773 652 True 839.0 839 90.5050 1 628 1 chr6A.!!$R1 627

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
773 806 0.037303 ATCCCATAGCCATCAAGCCG 59.963 55.0 0.0 0.0 0.00 5.52 F
884 917 0.106149 ACAGACAAGGTTGGTCGGTC 59.894 55.0 0.0 0.0 38.98 4.79 F
997 1030 0.179018 AGAATCATAAGGGGCACGCC 60.179 55.0 0.0 0.0 44.92 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 1983 1.974875 GGGGGCGTGGTTTGGTAAG 60.975 63.158 0.0 0.0 0.00 2.34 R
2129 2166 2.356135 TCGGCTATTTCAAGTGCCTTC 58.644 47.619 0.0 0.0 42.90 3.46 R
2387 2426 2.415893 GCGGGAGTCATTGGTTCAAATG 60.416 50.000 0.0 0.0 38.63 2.32 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
139 144 5.490139 TTTTTGAGAATGCGATGATCCTC 57.510 39.130 0.00 0.00 0.00 3.71
321 330 8.043113 ACTGATGTCTCATACTTGCATCTTTTA 58.957 33.333 0.00 0.00 37.44 1.52
359 368 4.028131 ACCTGATGTATGGTTTCTCGGTA 58.972 43.478 0.00 0.00 31.62 4.02
360 369 4.654262 ACCTGATGTATGGTTTCTCGGTAT 59.346 41.667 0.00 0.00 31.62 2.73
361 370 4.991056 CCTGATGTATGGTTTCTCGGTATG 59.009 45.833 0.00 0.00 0.00 2.39
364 373 5.815222 TGATGTATGGTTTCTCGGTATGTTG 59.185 40.000 0.00 0.00 0.00 3.33
365 374 5.408880 TGTATGGTTTCTCGGTATGTTGA 57.591 39.130 0.00 0.00 0.00 3.18
366 375 5.795972 TGTATGGTTTCTCGGTATGTTGAA 58.204 37.500 0.00 0.00 0.00 2.69
367 376 5.872617 TGTATGGTTTCTCGGTATGTTGAAG 59.127 40.000 0.00 0.00 0.00 3.02
422 450 0.690192 TTGGTGCTCCCGATTTGAGA 59.310 50.000 1.59 0.00 35.15 3.27
428 456 1.066858 GCTCCCGATTTGAGACTGACA 60.067 52.381 0.00 0.00 31.26 3.58
450 478 6.430864 ACATATGGTGTTTGGGTGATTATGA 58.569 36.000 7.80 0.00 38.01 2.15
540 572 8.057742 GCTAAACAAAATGTTGATGAACTGTTG 58.942 33.333 1.62 3.72 40.14 3.33
541 573 7.903995 AAACAAAATGTTGATGAACTGTTGT 57.096 28.000 1.62 4.22 40.14 3.32
542 574 7.903995 AACAAAATGTTGATGAACTGTTGTT 57.096 28.000 1.62 13.91 39.45 2.83
544 576 6.253298 ACAAAATGTTGATGAACTGTTGTTCG 59.747 34.615 1.62 0.00 44.65 3.95
545 577 6.291743 CAAAATGTTGATGAACTGTTGTTCGG 60.292 38.462 0.00 0.00 44.62 4.30
555 587 6.937886 GAACTGTTGTTCGGAAAAAGAAAA 57.062 33.333 0.00 0.00 42.39 2.29
572 604 3.259123 AGAAAACCCATCTGATTGTTGGC 59.741 43.478 3.78 0.93 34.88 4.52
671 703 2.902608 ACCCTGTCCAATAGTCAGTCA 58.097 47.619 0.00 0.00 0.00 3.41
699 731 1.812922 CGCTGCTGCCCTAACAGAG 60.813 63.158 10.24 0.00 40.25 3.35
756 789 3.121544 GTTGTCGGTCGGGAAAGATATC 58.878 50.000 0.00 0.00 0.00 1.63
772 805 3.201708 AGATATCCCATAGCCATCAAGCC 59.798 47.826 0.00 0.00 0.00 4.35
773 806 0.037303 ATCCCATAGCCATCAAGCCG 59.963 55.000 0.00 0.00 0.00 5.52
774 807 1.149174 CCCATAGCCATCAAGCCGT 59.851 57.895 0.00 0.00 0.00 5.68
775 808 0.886490 CCCATAGCCATCAAGCCGTC 60.886 60.000 0.00 0.00 0.00 4.79
776 809 1.224069 CCATAGCCATCAAGCCGTCG 61.224 60.000 0.00 0.00 0.00 5.12
777 810 1.069765 ATAGCCATCAAGCCGTCGG 59.930 57.895 6.99 6.99 0.00 4.79
778 811 1.686325 ATAGCCATCAAGCCGTCGGT 61.686 55.000 13.94 0.00 0.00 4.69
779 812 2.292794 TAGCCATCAAGCCGTCGGTC 62.293 60.000 13.94 5.34 0.00 4.79
780 813 2.885644 CCATCAAGCCGTCGGTCG 60.886 66.667 13.94 1.65 39.52 4.79
791 824 2.047679 CGTCGGTCGGGAAAGATATC 57.952 55.000 0.00 0.00 35.71 1.63
792 825 1.335689 CGTCGGTCGGGAAAGATATCC 60.336 57.143 0.00 0.00 38.86 2.59
803 836 5.441718 GGAAAGATATCCCATAGCCATCA 57.558 43.478 0.00 0.00 33.05 3.07
804 837 5.819991 GGAAAGATATCCCATAGCCATCAA 58.180 41.667 0.00 0.00 33.05 2.57
805 838 5.884792 GGAAAGATATCCCATAGCCATCAAG 59.115 44.000 0.00 0.00 33.05 3.02
806 839 4.500499 AGATATCCCATAGCCATCAAGC 57.500 45.455 0.00 0.00 0.00 4.01
883 916 0.544697 AACAGACAAGGTTGGTCGGT 59.455 50.000 0.00 0.00 43.80 4.69
884 917 0.106149 ACAGACAAGGTTGGTCGGTC 59.894 55.000 0.00 0.00 38.98 4.79
885 918 0.944311 CAGACAAGGTTGGTCGGTCG 60.944 60.000 0.00 0.00 40.20 4.79
886 919 1.666872 GACAAGGTTGGTCGGTCGG 60.667 63.158 0.00 0.00 0.00 4.79
927 960 4.442706 GACTGTCTGTTGGAAGAAGTTGA 58.557 43.478 0.00 0.00 0.00 3.18
928 961 4.446371 ACTGTCTGTTGGAAGAAGTTGAG 58.554 43.478 0.00 0.00 0.00 3.02
929 962 3.808728 TGTCTGTTGGAAGAAGTTGAGG 58.191 45.455 0.00 0.00 0.00 3.86
930 963 3.454447 TGTCTGTTGGAAGAAGTTGAGGA 59.546 43.478 0.00 0.00 0.00 3.71
931 964 4.080582 TGTCTGTTGGAAGAAGTTGAGGAA 60.081 41.667 0.00 0.00 0.00 3.36
932 965 5.066593 GTCTGTTGGAAGAAGTTGAGGAAT 58.933 41.667 0.00 0.00 0.00 3.01
933 966 5.180304 GTCTGTTGGAAGAAGTTGAGGAATC 59.820 44.000 0.00 0.00 0.00 2.52
934 967 5.047566 TGTTGGAAGAAGTTGAGGAATCA 57.952 39.130 0.00 0.00 0.00 2.57
935 968 5.445069 TGTTGGAAGAAGTTGAGGAATCAA 58.555 37.500 0.00 0.00 0.00 2.57
936 969 5.890985 TGTTGGAAGAAGTTGAGGAATCAAA 59.109 36.000 0.00 0.00 0.00 2.69
937 970 6.039717 TGTTGGAAGAAGTTGAGGAATCAAAG 59.960 38.462 0.00 0.00 0.00 2.77
938 971 5.072741 TGGAAGAAGTTGAGGAATCAAAGG 58.927 41.667 0.00 0.00 0.00 3.11
939 972 5.073428 GGAAGAAGTTGAGGAATCAAAGGT 58.927 41.667 0.00 0.00 0.00 3.50
940 973 6.183361 TGGAAGAAGTTGAGGAATCAAAGGTA 60.183 38.462 0.00 0.00 0.00 3.08
941 974 6.149640 GGAAGAAGTTGAGGAATCAAAGGTAC 59.850 42.308 0.00 0.00 0.00 3.34
943 976 6.468543 AGAAGTTGAGGAATCAAAGGTACTC 58.531 40.000 0.00 0.00 38.49 2.59
944 977 5.825593 AGTTGAGGAATCAAAGGTACTCA 57.174 39.130 0.00 0.00 38.49 3.41
945 978 6.187727 AGTTGAGGAATCAAAGGTACTCAA 57.812 37.500 0.00 0.00 38.49 3.02
946 979 6.784031 AGTTGAGGAATCAAAGGTACTCAAT 58.216 36.000 7.99 0.00 43.95 2.57
947 980 7.918076 AGTTGAGGAATCAAAGGTACTCAATA 58.082 34.615 7.99 0.00 43.95 1.90
948 981 8.383175 AGTTGAGGAATCAAAGGTACTCAATAA 58.617 33.333 7.99 0.00 43.95 1.40
949 982 8.669243 GTTGAGGAATCAAAGGTACTCAATAAG 58.331 37.037 7.99 0.00 43.95 1.73
950 983 7.338710 TGAGGAATCAAAGGTACTCAATAAGG 58.661 38.462 0.00 0.00 38.49 2.69
951 984 6.663734 AGGAATCAAAGGTACTCAATAAGGG 58.336 40.000 0.00 0.00 38.49 3.95
952 985 6.217693 AGGAATCAAAGGTACTCAATAAGGGT 59.782 38.462 0.00 0.00 38.49 4.34
953 986 6.890268 GGAATCAAAGGTACTCAATAAGGGTT 59.110 38.462 0.00 0.00 38.49 4.11
954 987 7.396339 GGAATCAAAGGTACTCAATAAGGGTTT 59.604 37.037 0.00 0.00 38.49 3.27
955 988 8.721133 AATCAAAGGTACTCAATAAGGGTTTT 57.279 30.769 0.00 0.00 38.49 2.43
956 989 7.754851 TCAAAGGTACTCAATAAGGGTTTTC 57.245 36.000 0.00 0.00 38.49 2.29
957 990 6.717997 TCAAAGGTACTCAATAAGGGTTTTCC 59.282 38.462 0.00 0.00 38.49 3.13
967 1000 4.563404 GGTTTTCCCGTGTGGACA 57.437 55.556 0.00 0.00 45.11 4.02
968 1001 3.030415 GGTTTTCCCGTGTGGACAT 57.970 52.632 0.00 0.00 45.11 3.06
969 1002 2.188062 GGTTTTCCCGTGTGGACATA 57.812 50.000 0.00 0.00 45.11 2.29
970 1003 1.808343 GGTTTTCCCGTGTGGACATAC 59.192 52.381 0.00 0.00 45.11 2.39
971 1004 1.808343 GTTTTCCCGTGTGGACATACC 59.192 52.381 0.00 0.00 45.11 2.73
972 1005 0.325602 TTTCCCGTGTGGACATACCC 59.674 55.000 0.00 0.00 45.11 3.69
973 1006 0.545787 TTCCCGTGTGGACATACCCT 60.546 55.000 0.00 0.00 45.11 4.34
974 1007 0.335705 TCCCGTGTGGACATACCCTA 59.664 55.000 0.00 0.00 38.61 3.53
975 1008 1.062734 TCCCGTGTGGACATACCCTAT 60.063 52.381 0.00 0.00 38.61 2.57
976 1009 1.343465 CCCGTGTGGACATACCCTATC 59.657 57.143 0.00 0.00 37.49 2.08
977 1010 2.317040 CCGTGTGGACATACCCTATCT 58.683 52.381 0.00 0.00 37.49 1.98
978 1011 3.493334 CCGTGTGGACATACCCTATCTA 58.507 50.000 0.00 0.00 37.49 1.98
979 1012 3.506455 CCGTGTGGACATACCCTATCTAG 59.494 52.174 0.00 0.00 37.49 2.43
980 1013 4.395625 CGTGTGGACATACCCTATCTAGA 58.604 47.826 0.00 0.00 38.00 2.43
981 1014 4.825634 CGTGTGGACATACCCTATCTAGAA 59.174 45.833 0.00 0.00 38.00 2.10
982 1015 5.477291 CGTGTGGACATACCCTATCTAGAAT 59.523 44.000 0.00 0.00 38.00 2.40
983 1016 6.349445 CGTGTGGACATACCCTATCTAGAATC 60.349 46.154 0.00 0.00 38.00 2.52
984 1017 6.493802 GTGTGGACATACCCTATCTAGAATCA 59.506 42.308 0.00 0.00 38.00 2.57
985 1018 7.179338 GTGTGGACATACCCTATCTAGAATCAT 59.821 40.741 0.00 0.00 38.00 2.45
986 1019 8.398743 TGTGGACATACCCTATCTAGAATCATA 58.601 37.037 0.00 0.00 38.00 2.15
987 1020 9.256228 GTGGACATACCCTATCTAGAATCATAA 57.744 37.037 0.00 0.00 38.00 1.90
988 1021 9.480861 TGGACATACCCTATCTAGAATCATAAG 57.519 37.037 0.00 0.00 38.00 1.73
989 1022 8.919145 GGACATACCCTATCTAGAATCATAAGG 58.081 40.741 0.00 0.00 0.00 2.69
990 1023 8.846423 ACATACCCTATCTAGAATCATAAGGG 57.154 38.462 16.20 16.20 39.78 3.95
991 1024 7.846823 ACATACCCTATCTAGAATCATAAGGGG 59.153 40.741 19.46 13.82 38.32 4.79
992 1025 5.033522 ACCCTATCTAGAATCATAAGGGGC 58.966 45.833 19.46 0.00 38.32 5.80
993 1026 5.032846 CCCTATCTAGAATCATAAGGGGCA 58.967 45.833 0.00 0.00 0.00 5.36
994 1027 5.104735 CCCTATCTAGAATCATAAGGGGCAC 60.105 48.000 0.00 0.00 0.00 5.01
995 1028 4.543590 ATCTAGAATCATAAGGGGCACG 57.456 45.455 0.00 0.00 0.00 5.34
996 1029 2.037251 TCTAGAATCATAAGGGGCACGC 59.963 50.000 0.00 0.00 43.76 5.34
997 1030 0.179018 AGAATCATAAGGGGCACGCC 60.179 55.000 0.00 0.00 44.92 5.68
1014 1047 0.395724 GCCCAATGAAGGAATCCGGT 60.396 55.000 0.00 0.00 0.00 5.28
1134 1168 4.765339 GCCCTAACTATGGCGGAATATTTT 59.235 41.667 0.00 0.00 38.00 1.82
1221 1255 5.308237 AGGATCAGAGGTATCCGCTTTATTT 59.692 40.000 0.00 0.00 46.37 1.40
1348 1382 6.554334 TTCAAGAAGTTTATGTACCTGCAC 57.446 37.500 0.00 0.00 0.00 4.57
1441 1475 8.520119 AGGATTAGCTTCCAAGGGTATTTATA 57.480 34.615 7.20 0.00 38.32 0.98
1487 1521 2.952978 CCTCGACTATGTTACAGCCTCT 59.047 50.000 0.00 0.00 0.00 3.69
1535 1569 3.251004 ACTGCGCAAAGAGTTAAGGAAAG 59.749 43.478 13.05 0.00 0.00 2.62
1800 1836 2.979814 TGGTGGGTAACATCGATGAG 57.020 50.000 31.33 6.81 39.74 2.90
1831 1867 7.259161 CACGAAAGCTATAACCTTAGAAGAGT 58.741 38.462 0.00 0.00 0.00 3.24
1832 1868 7.760340 CACGAAAGCTATAACCTTAGAAGAGTT 59.240 37.037 0.00 0.00 0.00 3.01
1850 1886 8.632679 AGAAGAGTTGAACAAATTGCAGAAATA 58.367 29.630 0.00 0.00 0.00 1.40
1912 1948 6.537453 TTGGGATTGTGAAGTGAAAGAAAA 57.463 33.333 0.00 0.00 0.00 2.29
2129 2166 2.680312 TTGATCCGGAAGAAGCTCAG 57.320 50.000 9.01 0.00 0.00 3.35
2966 3019 9.399403 CTTCTTTTGGTTCTATGAACTTTAAGC 57.601 33.333 9.81 0.00 0.00 3.09
3025 3078 7.589958 ACGATAGAGACTCCATTTCACTTAT 57.410 36.000 0.00 0.00 41.38 1.73
3077 3130 6.722328 CCTAAGTCAAGGTAATCCTCCTTTT 58.278 40.000 0.00 0.00 44.35 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 1.798223 CTCGGTTGAGATTGTTCGCAA 59.202 47.619 0.00 0.00 45.57 4.85
139 144 5.643379 ACAGTACCAAAATGCCAACATAG 57.357 39.130 0.00 0.00 34.62 2.23
222 231 2.289506 GGTTCCTTGTGAGTGTAGTCCC 60.290 54.545 0.00 0.00 0.00 4.46
321 330 4.164843 TCAGGTTTACAAAAGGACAGCT 57.835 40.909 0.00 0.00 0.00 4.24
359 368 5.726980 AATTGGCACATACACTTCAACAT 57.273 34.783 0.00 0.00 39.30 2.71
360 369 5.767665 ACTAATTGGCACATACACTTCAACA 59.232 36.000 0.00 0.00 39.30 3.33
361 370 6.254281 ACTAATTGGCACATACACTTCAAC 57.746 37.500 0.00 0.00 39.30 3.18
364 373 7.915397 CCATTAACTAATTGGCACATACACTTC 59.085 37.037 0.00 0.00 39.30 3.01
365 374 7.613801 TCCATTAACTAATTGGCACATACACTT 59.386 33.333 0.00 0.00 39.30 3.16
366 375 7.116075 TCCATTAACTAATTGGCACATACACT 58.884 34.615 0.00 0.00 39.30 3.55
367 376 7.328277 TCCATTAACTAATTGGCACATACAC 57.672 36.000 0.00 0.00 39.30 2.90
422 450 3.073798 TCACCCAAACACCATATGTCAGT 59.926 43.478 1.24 0.00 42.31 3.41
428 456 9.300681 CTAATCATAATCACCCAAACACCATAT 57.699 33.333 0.00 0.00 0.00 1.78
540 572 4.982295 CAGATGGGTTTTCTTTTTCCGAAC 59.018 41.667 0.00 0.00 0.00 3.95
541 573 4.890581 TCAGATGGGTTTTCTTTTTCCGAA 59.109 37.500 0.00 0.00 0.00 4.30
542 574 4.465886 TCAGATGGGTTTTCTTTTTCCGA 58.534 39.130 0.00 0.00 0.00 4.55
544 576 6.524734 ACAATCAGATGGGTTTTCTTTTTCC 58.475 36.000 0.00 0.00 0.00 3.13
545 577 7.041848 CCAACAATCAGATGGGTTTTCTTTTTC 60.042 37.037 0.00 0.00 36.57 2.29
548 580 5.742838 GCCAACAATCAGATGGGTTTTCTTT 60.743 40.000 0.00 0.00 40.35 2.52
550 582 3.259123 GCCAACAATCAGATGGGTTTTCT 59.741 43.478 0.00 0.00 40.35 2.52
551 583 3.588955 GCCAACAATCAGATGGGTTTTC 58.411 45.455 0.00 0.00 40.35 2.29
555 587 0.680921 CGGCCAACAATCAGATGGGT 60.681 55.000 2.24 0.00 40.35 4.51
572 604 0.926628 GACGTCGTTTGTTTTGCCGG 60.927 55.000 0.00 0.00 0.00 6.13
628 660 6.014584 GGTATTCTTTCCCAACCAACATTCTT 60.015 38.462 0.00 0.00 0.00 2.52
671 703 4.729918 CAGCAGCGGGCCTTTCCT 62.730 66.667 0.84 0.00 46.50 3.36
699 731 2.265904 GGCCTTTCCCGACCAACAC 61.266 63.158 0.00 0.00 0.00 3.32
756 789 0.886490 GACGGCTTGATGGCTATGGG 60.886 60.000 0.00 0.00 39.32 4.00
772 805 1.335689 GGATATCTTTCCCGACCGACG 60.336 57.143 2.05 0.00 42.18 5.12
773 806 1.000618 GGGATATCTTTCCCGACCGAC 59.999 57.143 2.05 0.00 45.84 4.79
774 807 1.335145 GGGATATCTTTCCCGACCGA 58.665 55.000 2.05 0.00 45.84 4.69
775 808 3.908737 GGGATATCTTTCCCGACCG 57.091 57.895 2.05 0.00 45.84 4.79
781 814 5.441718 TGATGGCTATGGGATATCTTTCC 57.558 43.478 2.05 0.00 34.83 3.13
782 815 5.356470 GCTTGATGGCTATGGGATATCTTTC 59.644 44.000 2.05 0.00 0.00 2.62
783 816 5.222192 TGCTTGATGGCTATGGGATATCTTT 60.222 40.000 2.05 0.00 0.00 2.52
784 817 4.290459 TGCTTGATGGCTATGGGATATCTT 59.710 41.667 2.05 0.00 0.00 2.40
785 818 3.848377 TGCTTGATGGCTATGGGATATCT 59.152 43.478 2.05 0.00 0.00 1.98
786 819 4.197750 CTGCTTGATGGCTATGGGATATC 58.802 47.826 0.00 0.00 0.00 1.63
787 820 3.590630 ACTGCTTGATGGCTATGGGATAT 59.409 43.478 0.00 0.00 0.00 1.63
788 821 2.981784 ACTGCTTGATGGCTATGGGATA 59.018 45.455 0.00 0.00 0.00 2.59
789 822 1.779092 ACTGCTTGATGGCTATGGGAT 59.221 47.619 0.00 0.00 0.00 3.85
790 823 1.141657 GACTGCTTGATGGCTATGGGA 59.858 52.381 0.00 0.00 0.00 4.37
791 824 1.602311 GACTGCTTGATGGCTATGGG 58.398 55.000 0.00 0.00 0.00 4.00
792 825 1.224075 CGACTGCTTGATGGCTATGG 58.776 55.000 0.00 0.00 0.00 2.74
793 826 1.224075 CCGACTGCTTGATGGCTATG 58.776 55.000 0.00 0.00 0.00 2.23
794 827 0.833287 ACCGACTGCTTGATGGCTAT 59.167 50.000 0.00 0.00 0.00 2.97
795 828 0.175760 GACCGACTGCTTGATGGCTA 59.824 55.000 0.00 0.00 0.00 3.93
796 829 1.078848 GACCGACTGCTTGATGGCT 60.079 57.895 0.00 0.00 0.00 4.75
797 830 2.456119 CGACCGACTGCTTGATGGC 61.456 63.158 0.00 0.00 0.00 4.40
798 831 1.811266 CCGACCGACTGCTTGATGG 60.811 63.158 0.00 0.00 0.00 3.51
799 832 1.811266 CCCGACCGACTGCTTGATG 60.811 63.158 0.00 0.00 0.00 3.07
800 833 1.541310 TTCCCGACCGACTGCTTGAT 61.541 55.000 0.00 0.00 0.00 2.57
801 834 1.750341 TTTCCCGACCGACTGCTTGA 61.750 55.000 0.00 0.00 0.00 3.02
802 835 1.291877 CTTTCCCGACCGACTGCTTG 61.292 60.000 0.00 0.00 0.00 4.01
803 836 1.004918 CTTTCCCGACCGACTGCTT 60.005 57.895 0.00 0.00 0.00 3.91
804 837 2.657237 CTTTCCCGACCGACTGCT 59.343 61.111 0.00 0.00 0.00 4.24
805 838 2.221906 TAGCTTTCCCGACCGACTGC 62.222 60.000 0.00 0.00 0.00 4.40
806 839 0.460311 ATAGCTTTCCCGACCGACTG 59.540 55.000 0.00 0.00 0.00 3.51
851 884 1.133915 TGTCTGTTGGGGAAAGTCCAC 60.134 52.381 0.00 0.00 41.45 4.02
927 960 6.217693 ACCCTTATTGAGTACCTTTGATTCCT 59.782 38.462 0.00 0.00 0.00 3.36
928 961 6.424032 ACCCTTATTGAGTACCTTTGATTCC 58.576 40.000 0.00 0.00 0.00 3.01
929 962 7.939784 AACCCTTATTGAGTACCTTTGATTC 57.060 36.000 0.00 0.00 0.00 2.52
930 963 8.721133 AAAACCCTTATTGAGTACCTTTGATT 57.279 30.769 0.00 0.00 0.00 2.57
931 964 7.396339 GGAAAACCCTTATTGAGTACCTTTGAT 59.604 37.037 0.00 0.00 0.00 2.57
932 965 6.717997 GGAAAACCCTTATTGAGTACCTTTGA 59.282 38.462 0.00 0.00 0.00 2.69
933 966 6.071560 GGGAAAACCCTTATTGAGTACCTTTG 60.072 42.308 0.00 0.00 34.51 2.77
934 967 6.014647 GGGAAAACCCTTATTGAGTACCTTT 58.985 40.000 0.00 0.00 34.51 3.11
935 968 5.577100 GGGAAAACCCTTATTGAGTACCTT 58.423 41.667 0.00 0.00 34.51 3.50
936 969 4.324022 CGGGAAAACCCTTATTGAGTACCT 60.324 45.833 0.00 0.00 34.99 3.08
937 970 3.943381 CGGGAAAACCCTTATTGAGTACC 59.057 47.826 0.00 0.00 34.99 3.34
938 971 4.393990 CACGGGAAAACCCTTATTGAGTAC 59.606 45.833 0.00 0.00 34.99 2.73
939 972 4.041938 ACACGGGAAAACCCTTATTGAGTA 59.958 41.667 0.00 0.00 34.99 2.59
940 973 3.181437 ACACGGGAAAACCCTTATTGAGT 60.181 43.478 0.00 0.00 34.99 3.41
941 974 3.190535 CACACGGGAAAACCCTTATTGAG 59.809 47.826 0.00 0.00 34.99 3.02
942 975 3.150767 CACACGGGAAAACCCTTATTGA 58.849 45.455 0.00 0.00 34.99 2.57
943 976 2.230266 CCACACGGGAAAACCCTTATTG 59.770 50.000 0.00 0.00 40.01 1.90
944 977 2.108601 TCCACACGGGAAAACCCTTATT 59.891 45.455 0.00 0.00 44.80 1.40
945 978 1.706305 TCCACACGGGAAAACCCTTAT 59.294 47.619 0.00 0.00 44.80 1.73
946 979 1.138568 TCCACACGGGAAAACCCTTA 58.861 50.000 0.00 0.00 44.80 2.69
947 980 1.924352 TCCACACGGGAAAACCCTT 59.076 52.632 0.00 0.00 44.80 3.95
948 981 3.663419 TCCACACGGGAAAACCCT 58.337 55.556 0.00 0.00 44.80 4.34
955 988 0.335705 TAGGGTATGTCCACACGGGA 59.664 55.000 0.00 0.00 45.89 5.14
956 989 1.343465 GATAGGGTATGTCCACACGGG 59.657 57.143 0.00 0.00 38.11 5.28
957 990 2.317040 AGATAGGGTATGTCCACACGG 58.683 52.381 0.00 0.00 38.11 4.94
958 991 4.395625 TCTAGATAGGGTATGTCCACACG 58.604 47.826 0.00 0.00 38.11 4.49
959 992 6.493802 TGATTCTAGATAGGGTATGTCCACAC 59.506 42.308 0.00 0.00 38.11 3.82
960 993 6.620429 TGATTCTAGATAGGGTATGTCCACA 58.380 40.000 0.00 0.00 38.11 4.17
961 994 7.726033 ATGATTCTAGATAGGGTATGTCCAC 57.274 40.000 0.00 0.00 38.11 4.02
962 995 9.480861 CTTATGATTCTAGATAGGGTATGTCCA 57.519 37.037 0.00 0.00 38.11 4.02
963 996 8.919145 CCTTATGATTCTAGATAGGGTATGTCC 58.081 40.741 0.00 0.00 0.00 4.02
964 997 8.919145 CCCTTATGATTCTAGATAGGGTATGTC 58.081 40.741 0.00 0.00 0.00 3.06
965 998 7.846823 CCCCTTATGATTCTAGATAGGGTATGT 59.153 40.741 14.38 0.00 32.47 2.29
966 999 7.202047 GCCCCTTATGATTCTAGATAGGGTATG 60.202 44.444 14.38 5.89 33.16 2.39
967 1000 6.847036 GCCCCTTATGATTCTAGATAGGGTAT 59.153 42.308 14.38 0.00 33.16 2.73
968 1001 6.203072 GCCCCTTATGATTCTAGATAGGGTA 58.797 44.000 14.38 0.00 33.16 3.69
969 1002 5.033522 GCCCCTTATGATTCTAGATAGGGT 58.966 45.833 14.38 0.00 33.16 4.34
970 1003 5.032846 TGCCCCTTATGATTCTAGATAGGG 58.967 45.833 0.00 0.00 0.00 3.53
971 1004 5.394663 CGTGCCCCTTATGATTCTAGATAGG 60.395 48.000 0.00 0.00 0.00 2.57
972 1005 5.655488 CGTGCCCCTTATGATTCTAGATAG 58.345 45.833 0.00 0.00 0.00 2.08
973 1006 4.081642 GCGTGCCCCTTATGATTCTAGATA 60.082 45.833 0.00 0.00 0.00 1.98
974 1007 3.307059 GCGTGCCCCTTATGATTCTAGAT 60.307 47.826 0.00 0.00 0.00 1.98
975 1008 2.037251 GCGTGCCCCTTATGATTCTAGA 59.963 50.000 0.00 0.00 0.00 2.43
976 1009 2.417719 GCGTGCCCCTTATGATTCTAG 58.582 52.381 0.00 0.00 0.00 2.43
977 1010 1.071699 GGCGTGCCCCTTATGATTCTA 59.928 52.381 0.00 0.00 0.00 2.10
978 1011 0.179018 GGCGTGCCCCTTATGATTCT 60.179 55.000 0.00 0.00 0.00 2.40
979 1012 2.331265 GGCGTGCCCCTTATGATTC 58.669 57.895 0.00 0.00 0.00 2.52
980 1013 4.579127 GGCGTGCCCCTTATGATT 57.421 55.556 0.00 0.00 0.00 2.57
990 1023 1.322538 ATTCCTTCATTGGGCGTGCC 61.323 55.000 1.16 1.16 0.00 5.01
991 1024 0.101219 GATTCCTTCATTGGGCGTGC 59.899 55.000 0.00 0.00 0.00 5.34
992 1025 0.740737 GGATTCCTTCATTGGGCGTG 59.259 55.000 0.00 0.00 0.00 5.34
993 1026 0.748005 CGGATTCCTTCATTGGGCGT 60.748 55.000 0.30 0.00 0.00 5.68
994 1027 1.447317 CCGGATTCCTTCATTGGGCG 61.447 60.000 0.00 0.00 0.00 6.13
995 1028 0.395724 ACCGGATTCCTTCATTGGGC 60.396 55.000 9.46 0.00 0.00 5.36
996 1029 1.340991 ACACCGGATTCCTTCATTGGG 60.341 52.381 9.46 0.00 0.00 4.12
997 1030 2.128771 ACACCGGATTCCTTCATTGG 57.871 50.000 9.46 0.00 0.00 3.16
998 1031 5.835113 AATTACACCGGATTCCTTCATTG 57.165 39.130 9.46 0.00 0.00 2.82
1134 1168 5.515270 CACGTCTTGCTTATTAACATCTCGA 59.485 40.000 0.00 0.00 0.00 4.04
1331 1365 3.997762 TCGTGTGCAGGTACATAAACTT 58.002 40.909 0.00 0.00 32.43 2.66
1348 1382 1.635663 GCAGGGTCGGTCAAATCGTG 61.636 60.000 0.00 0.00 0.00 4.35
1441 1475 6.798427 TGAATCTAAAGGATCTACTGCTGT 57.202 37.500 0.66 0.66 32.76 4.40
1535 1569 7.427318 CCTGAAGTTCTTTGTAACGTTGTAAAC 59.573 37.037 11.99 0.95 45.31 2.01
1737 1773 2.418334 GCCGTCTAATTCTCCGGAAAGT 60.418 50.000 5.23 5.12 43.01 2.66
1772 1808 5.768662 TCGATGTTACCCACCAAATAAACAA 59.231 36.000 0.00 0.00 31.33 2.83
1774 1810 5.883503 TCGATGTTACCCACCAAATAAAC 57.116 39.130 0.00 0.00 0.00 2.01
1800 1836 2.801111 GGTTATAGCTTTCGTGCTAGCC 59.199 50.000 13.29 2.49 46.89 3.93
1867 1903 6.316390 CCAAATAATTCGCTTAGGAGTCAGTT 59.684 38.462 0.00 0.00 0.00 3.16
1946 1983 1.974875 GGGGGCGTGGTTTGGTAAG 60.975 63.158 0.00 0.00 0.00 2.34
2129 2166 2.356135 TCGGCTATTTCAAGTGCCTTC 58.644 47.619 0.00 0.00 42.90 3.46
2387 2426 2.415893 GCGGGAGTCATTGGTTCAAATG 60.416 50.000 0.00 0.00 38.63 2.32
2656 2697 4.832590 GCTCTACCGAACTGAGCTATAA 57.167 45.455 6.92 0.00 46.69 0.98
2948 3001 8.718102 TCATACAGCTTAAAGTTCATAGAACC 57.282 34.615 6.29 0.00 0.00 3.62
3025 3078 5.355910 GCCTCCGGTCTAAATTAAATCAACA 59.644 40.000 0.00 0.00 0.00 3.33
3077 3130 7.011499 TCTAGGAGCAATACCAAAGTGTTTA 57.989 36.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.