Multiple sequence alignment - TraesCS7D01G491700

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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 TraesCS7D01G491700 chr7D 100.000 3322 0 0 647 3968 600862360 600865681 0.000000e+00 6135.0
1 TraesCS7D01G491700 chr7D 100.000 329 0 0 1 329 600861714 600862042 3.390000e-170 608.0
2 TraesCS7D01G491700 chr7D 91.964 112 4 4 1314 1423 103195096 103194988 6.870000e-33 152.0
3 TraesCS7D01G491700 chr7B 93.397 2499 83 21 806 3281 680072526 680074965 0.000000e+00 3626.0
4 TraesCS7D01G491700 chr7B 92.760 1906 60 20 1213 3086 707878724 707880583 0.000000e+00 2684.0
5 TraesCS7D01G491700 chr7B 91.776 608 25 7 3375 3958 680074968 680075574 0.000000e+00 822.0
6 TraesCS7D01G491700 chr7B 92.101 557 25 4 3428 3968 707881132 707881685 0.000000e+00 767.0
7 TraesCS7D01G491700 chr7B 81.111 450 42 17 996 1424 707831773 707832200 1.780000e-83 320.0
8 TraesCS7D01G491700 chr7B 84.098 327 40 8 3 329 707876138 707876452 4.980000e-79 305.0
9 TraesCS7D01G491700 chr7B 95.789 190 7 1 3079 3267 707880730 707880919 4.980000e-79 305.0
10 TraesCS7D01G491700 chr7B 87.970 266 17 2 3718 3968 707883196 707883461 2.320000e-77 300.0
11 TraesCS7D01G491700 chr7B 89.756 205 6 1 1014 1218 707878503 707878692 8.510000e-62 248.0
12 TraesCS7D01G491700 chr7B 83.333 222 28 6 112 329 680072127 680072343 3.130000e-46 196.0
13 TraesCS7D01G491700 chr7B 87.342 158 7 5 1229 1377 707867350 707867503 6.820000e-38 169.0
14 TraesCS7D01G491700 chr7B 95.283 106 4 1 858 963 707876738 707876842 2.450000e-37 167.0
15 TraesCS7D01G491700 chr6D 87.529 1275 92 36 2526 3762 459552023 459550778 0.000000e+00 1411.0
16 TraesCS7D01G491700 chr6D 88.571 840 72 9 2442 3269 471112251 471113078 0.000000e+00 998.0
17 TraesCS7D01G491700 chr6D 86.559 930 94 15 2383 3301 471277083 471276174 0.000000e+00 996.0
18 TraesCS7D01G491700 chr6D 84.339 696 62 21 1023 1689 459553448 459552771 4.320000e-179 638.0
19 TraesCS7D01G491700 chr6D 86.928 153 16 4 2104 2253 471103970 471104121 6.820000e-38 169.0
20 TraesCS7D01G491700 chr6D 87.705 122 10 4 3396 3512 471276148 471276027 1.920000e-28 137.0
21 TraesCS7D01G491700 chr6D 79.762 168 18 9 2117 2277 459552417 459552259 1.510000e-19 108.0
22 TraesCS7D01G491700 chr2B 86.519 1261 101 29 2549 3762 771415462 771416700 0.000000e+00 1323.0
23 TraesCS7D01G491700 chr2B 87.270 707 61 13 3077 3762 771480033 771480731 0.000000e+00 780.0
24 TraesCS7D01G491700 chr2B 85.714 63 5 3 647 709 596079556 596079498 3.310000e-06 63.9
25 TraesCS7D01G491700 chr6B 87.933 895 91 7 2383 3269 719307903 719308788 0.000000e+00 1038.0
26 TraesCS7D01G491700 chr6B 89.189 666 54 6 2606 3264 719425313 719424659 0.000000e+00 815.0
27 TraesCS7D01G491700 chr7A 92.836 670 20 8 3314 3968 692784895 692785551 0.000000e+00 946.0
28 TraesCS7D01G491700 chr7A 93.250 400 18 5 886 1285 692784169 692784559 7.390000e-162 580.0
29 TraesCS7D01G491700 chr7A 97.568 329 8 0 2942 3270 692784569 692784897 7.440000e-157 564.0
30 TraesCS7D01G491700 chr6A 81.380 1203 140 48 2844 3968 616056291 616055095 0.000000e+00 904.0
31 TraesCS7D01G491700 chr6A 82.092 765 67 28 1192 1941 616095361 616094652 1.230000e-164 590.0
32 TraesCS7D01G491700 chr6A 87.712 472 47 4 2383 2850 616057206 616056742 1.250000e-149 540.0
33 TraesCS7D01G491700 chr6A 85.279 197 25 4 2046 2238 616094440 616094244 2.420000e-47 200.0
34 TraesCS7D01G491700 chr3A 82.887 672 51 33 1017 1667 574317298 574317926 2.700000e-151 545.0
35 TraesCS7D01G491700 chr3A 91.791 268 18 4 2736 2999 574319003 574319270 1.740000e-98 370.0
36 TraesCS7D01G491700 chr3A 77.049 610 94 32 3399 3968 574280179 574279576 3.850000e-80 309.0
37 TraesCS7D01G491700 chr3A 77.108 415 47 23 1972 2377 574318165 574318540 3.130000e-46 196.0
38 TraesCS7D01G491700 chr3A 92.727 110 6 1 1314 1423 502781032 502781139 1.480000e-34 158.0
39 TraesCS7D01G491700 chr3A 76.068 234 21 11 3300 3516 574319277 574319492 5.460000e-14 89.8
40 TraesCS7D01G491700 chr1D 95.238 42 0 2 649 688 354771580 354771539 9.200000e-07 65.8
41 TraesCS7D01G491700 chr5D 74.719 178 25 12 113 278 486000758 486000589 1.190000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G491700 chr7D 600861714 600865681 3967 False 3371.500000 6135 100.000000 1 3968 2 chr7D.!!$F1 3967
1 TraesCS7D01G491700 chr7B 680072127 680075574 3447 False 1548.000000 3626 89.502000 112 3958 3 chr7B.!!$F3 3846
2 TraesCS7D01G491700 chr7B 707876138 707883461 7323 False 682.285714 2684 91.108143 3 3968 7 chr7B.!!$F4 3965
3 TraesCS7D01G491700 chr6D 471112251 471113078 827 False 998.000000 998 88.571000 2442 3269 1 chr6D.!!$F2 827
4 TraesCS7D01G491700 chr6D 459550778 459553448 2670 True 719.000000 1411 83.876667 1023 3762 3 chr6D.!!$R1 2739
5 TraesCS7D01G491700 chr6D 471276027 471277083 1056 True 566.500000 996 87.132000 2383 3512 2 chr6D.!!$R2 1129
6 TraesCS7D01G491700 chr2B 771415462 771416700 1238 False 1323.000000 1323 86.519000 2549 3762 1 chr2B.!!$F1 1213
7 TraesCS7D01G491700 chr2B 771480033 771480731 698 False 780.000000 780 87.270000 3077 3762 1 chr2B.!!$F2 685
8 TraesCS7D01G491700 chr6B 719307903 719308788 885 False 1038.000000 1038 87.933000 2383 3269 1 chr6B.!!$F1 886
9 TraesCS7D01G491700 chr6B 719424659 719425313 654 True 815.000000 815 89.189000 2606 3264 1 chr6B.!!$R1 658
10 TraesCS7D01G491700 chr7A 692784169 692785551 1382 False 696.666667 946 94.551333 886 3968 3 chr7A.!!$F1 3082
11 TraesCS7D01G491700 chr6A 616055095 616057206 2111 True 722.000000 904 84.546000 2383 3968 2 chr6A.!!$R1 1585
12 TraesCS7D01G491700 chr6A 616094244 616095361 1117 True 395.000000 590 83.685500 1192 2238 2 chr6A.!!$R2 1046
13 TraesCS7D01G491700 chr3A 574279576 574280179 603 True 309.000000 309 77.049000 3399 3968 1 chr3A.!!$R1 569
14 TraesCS7D01G491700 chr3A 574317298 574319492 2194 False 300.200000 545 81.963500 1017 3516 4 chr3A.!!$F2 2499

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
735 738 0.108281 TGTTTGGGTCGTCACGTTGA 60.108 50.0 0.0 0.0 0.0 3.18 F
774 777 0.108520 GTGATCTAAACCGACCCGCA 60.109 55.0 0.0 0.0 0.0 5.69 F
775 778 0.108520 TGATCTAAACCGACCCGCAC 60.109 55.0 0.0 0.0 0.0 5.34 F
851 855 0.181350 CTACACCAATCCCTGCCCTC 59.819 60.0 0.0 0.0 0.0 4.30 F
852 856 0.253160 TACACCAATCCCTGCCCTCT 60.253 55.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 3606 1.238439 CATGGTTTCAGAAGTGCGGT 58.762 50.000 0.0 0.0 0.00 5.68 R
2371 4487 4.859629 AAAGAGTCAACAACGTCAGAAC 57.140 40.909 0.0 0.0 0.00 3.01 R
2479 4645 5.163591 ACAAAAACACTGCTAAGTTGTACCC 60.164 40.000 0.0 0.0 32.98 3.69 R
2689 4855 5.776173 ATATCTTCATCGTTCTCGTCCTT 57.224 39.130 0.0 0.0 38.33 3.36 R
3001 5744 4.737855 TCCTAAAGACTATCACACAGGC 57.262 45.455 0.0 0.0 0.00 4.85 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
22 23 2.432628 CCTCACGGACGAGTTGGC 60.433 66.667 0.00 0.00 0.00 4.52
33 34 1.301716 GAGTTGGCTGGTCTTCGCA 60.302 57.895 0.00 0.00 0.00 5.10
35 36 2.669569 TTGGCTGGTCTTCGCAGC 60.670 61.111 0.00 0.00 37.24 5.25
52 53 4.107051 CGGCGGCCTCTTGCTTTG 62.107 66.667 18.34 0.00 40.92 2.77
56 57 2.985847 GGCCTCTTGCTTTGCGGT 60.986 61.111 0.00 0.00 40.92 5.68
57 58 2.256461 GCCTCTTGCTTTGCGGTG 59.744 61.111 0.00 0.00 36.87 4.94
61 62 4.705519 CTTGCTTTGCGGTGGCGG 62.706 66.667 0.00 0.00 44.10 6.13
95 96 1.787847 CCACGACGTTGATCTTGGC 59.212 57.895 10.51 0.00 31.89 4.52
108 109 4.927782 TTGGCTTCCTGCGCGTGT 62.928 61.111 8.43 0.00 44.05 4.49
232 233 1.604378 CTTTGCCGGAGATGGGTCT 59.396 57.895 5.05 0.00 37.42 3.85
235 236 1.686325 TTGCCGGAGATGGGTCTAGC 61.686 60.000 5.05 0.00 33.97 3.42
247 248 3.805497 TCTAGCGGAGGCGAGGGA 61.805 66.667 0.00 0.00 46.35 4.20
254 255 3.151022 GAGGCGAGGGAGGTGAGG 61.151 72.222 0.00 0.00 0.00 3.86
280 281 3.771160 GTCGTCGAGGGTGGGCAT 61.771 66.667 5.12 0.00 0.00 4.40
683 686 2.488937 CAAATTTGGGCTTGAAATGGGC 59.511 45.455 10.49 0.00 0.00 5.36
684 687 1.660242 ATTTGGGCTTGAAATGGGCT 58.340 45.000 0.00 0.00 0.00 5.19
685 688 0.686224 TTTGGGCTTGAAATGGGCTG 59.314 50.000 0.00 0.00 0.00 4.85
687 690 2.285024 GGGCTTGAAATGGGCTGCA 61.285 57.895 0.50 0.00 0.00 4.41
690 693 1.217244 CTTGAAATGGGCTGCAGGC 59.783 57.895 30.97 30.97 40.90 4.85
691 694 1.228956 TTGAAATGGGCTGCAGGCT 60.229 52.632 35.64 19.30 41.46 4.58
694 697 4.772231 AATGGGCTGCAGGCTGGG 62.772 66.667 35.64 1.63 41.46 4.45
727 730 1.430228 GCACGTTTGTTTGGGTCGT 59.570 52.632 0.00 0.00 35.12 4.34
735 738 0.108281 TGTTTGGGTCGTCACGTTGA 60.108 50.000 0.00 0.00 0.00 3.18
746 749 3.560481 TCGTCACGTTGAGCCAATTTTTA 59.440 39.130 0.00 0.00 0.00 1.52
749 752 5.219633 GTCACGTTGAGCCAATTTTTATGT 58.780 37.500 0.00 0.00 0.00 2.29
756 759 1.135228 GCCAATTTTTATGTCCGCCGT 60.135 47.619 0.00 0.00 0.00 5.68
757 760 2.525055 CCAATTTTTATGTCCGCCGTG 58.475 47.619 0.00 0.00 0.00 4.94
759 762 3.181491 CCAATTTTTATGTCCGCCGTGAT 60.181 43.478 0.00 0.00 0.00 3.06
761 764 2.684001 TTTTATGTCCGCCGTGATCT 57.316 45.000 0.00 0.00 0.00 2.75
764 767 3.804786 TTATGTCCGCCGTGATCTAAA 57.195 42.857 0.00 0.00 0.00 1.85
765 768 1.935933 ATGTCCGCCGTGATCTAAAC 58.064 50.000 0.00 0.00 0.00 2.01
768 771 1.140161 CCGCCGTGATCTAAACCGA 59.860 57.895 0.00 0.00 0.00 4.69
769 772 1.143969 CCGCCGTGATCTAAACCGAC 61.144 60.000 0.00 0.00 0.00 4.79
771 774 0.808847 GCCGTGATCTAAACCGACCC 60.809 60.000 0.00 0.00 0.00 4.46
773 776 1.143969 CGTGATCTAAACCGACCCGC 61.144 60.000 0.00 0.00 0.00 6.13
774 777 0.108520 GTGATCTAAACCGACCCGCA 60.109 55.000 0.00 0.00 0.00 5.69
775 778 0.108520 TGATCTAAACCGACCCGCAC 60.109 55.000 0.00 0.00 0.00 5.34
776 779 1.143969 GATCTAAACCGACCCGCACG 61.144 60.000 0.00 0.00 0.00 5.34
788 791 2.040544 CCGCACGGGATTTGCTCTT 61.041 57.895 0.00 0.00 37.87 2.85
789 792 0.742990 CCGCACGGGATTTGCTCTTA 60.743 55.000 0.00 0.00 37.87 2.10
792 795 1.398390 GCACGGGATTTGCTCTTACTG 59.602 52.381 0.00 0.00 37.00 2.74
796 799 3.751698 ACGGGATTTGCTCTTACTGAAAC 59.248 43.478 0.00 0.00 0.00 2.78
800 803 5.106118 GGGATTTGCTCTTACTGAAACTTCC 60.106 44.000 0.00 0.00 0.00 3.46
805 808 4.174762 GCTCTTACTGAAACTTCCTACGG 58.825 47.826 0.00 0.00 0.00 4.02
807 810 5.566230 GCTCTTACTGAAACTTCCTACGGAA 60.566 44.000 0.00 0.00 39.66 4.30
850 854 0.550147 ACTACACCAATCCCTGCCCT 60.550 55.000 0.00 0.00 0.00 5.19
851 855 0.181350 CTACACCAATCCCTGCCCTC 59.819 60.000 0.00 0.00 0.00 4.30
852 856 0.253160 TACACCAATCCCTGCCCTCT 60.253 55.000 0.00 0.00 0.00 3.69
853 857 1.077212 CACCAATCCCTGCCCTCTG 60.077 63.158 0.00 0.00 0.00 3.35
869 873 0.911769 TCTGATTTCCATCGGTGGCT 59.088 50.000 10.80 0.00 45.63 4.75
943 949 4.413495 AATTCCGTACAAAATGTCCGTG 57.587 40.909 0.00 0.00 27.09 4.94
963 969 4.496673 CGTGAGTGTAGCATCTCTCCTTAC 60.497 50.000 7.42 0.00 0.00 2.34
964 970 4.642885 GTGAGTGTAGCATCTCTCCTTACT 59.357 45.833 7.42 0.00 0.00 2.24
965 971 4.884744 TGAGTGTAGCATCTCTCCTTACTC 59.115 45.833 0.00 0.00 34.25 2.59
966 972 4.211920 AGTGTAGCATCTCTCCTTACTCC 58.788 47.826 0.00 0.00 0.00 3.85
967 973 4.079443 AGTGTAGCATCTCTCCTTACTCCT 60.079 45.833 0.00 0.00 0.00 3.69
968 974 4.647399 GTGTAGCATCTCTCCTTACTCCTT 59.353 45.833 0.00 0.00 0.00 3.36
969 975 5.828859 GTGTAGCATCTCTCCTTACTCCTTA 59.171 44.000 0.00 0.00 0.00 2.69
970 976 6.016610 GTGTAGCATCTCTCCTTACTCCTTAG 60.017 46.154 0.00 0.00 0.00 2.18
971 977 5.396057 AGCATCTCTCCTTACTCCTTAGA 57.604 43.478 0.00 0.00 0.00 2.10
972 978 5.385198 AGCATCTCTCCTTACTCCTTAGAG 58.615 45.833 0.00 0.00 46.36 2.43
1607 3327 4.742201 TGCCGCTGCTTCTCGTCC 62.742 66.667 0.70 0.00 38.71 4.79
1693 3423 5.012328 AGTGAAAGAAAGTCTCGACACTT 57.988 39.130 0.00 0.00 38.30 3.16
1838 3606 2.124320 GCTTAATCTGCCCGGCCA 60.124 61.111 7.03 0.00 0.00 5.36
2200 4141 4.906065 TGCATTTGCCAGAGATGATAAC 57.094 40.909 0.00 0.00 41.18 1.89
2295 4377 6.220930 TGAATAAGTATCTCATACCGCAACC 58.779 40.000 0.00 0.00 36.40 3.77
2363 4479 0.854218 TTGTTGGCTGTTAAGGGGGA 59.146 50.000 0.00 0.00 0.00 4.81
2371 4487 4.104102 TGGCTGTTAAGGGGGAATACTATG 59.896 45.833 0.00 0.00 0.00 2.23
2377 4493 6.674861 TGTTAAGGGGGAATACTATGTTCTGA 59.325 38.462 0.00 0.00 0.00 3.27
2479 4645 3.274288 GACTTGGCTGATTTGAGGGTAG 58.726 50.000 0.00 0.00 0.00 3.18
2480 4646 2.025887 ACTTGGCTGATTTGAGGGTAGG 60.026 50.000 0.00 0.00 0.00 3.18
2499 4665 4.432980 AGGGTACAACTTAGCAGTGTTT 57.567 40.909 0.00 0.00 31.60 2.83
2689 4855 0.107703 CCCTTCGATAACTGGCAGCA 60.108 55.000 15.89 2.65 0.00 4.41
3001 5744 7.661968 ACAGTGCATATGTAGGTATCTTGTAG 58.338 38.462 4.29 0.00 0.00 2.74
3162 6081 1.261480 TCTCTCTGGCAGTTCCTCAC 58.739 55.000 15.27 0.00 35.26 3.51
3269 6190 6.024552 ACCGCAAAACTTGAAATGATATGT 57.975 33.333 0.00 0.00 0.00 2.29
3270 6191 5.863397 ACCGCAAAACTTGAAATGATATGTG 59.137 36.000 0.00 0.00 0.00 3.21
3272 6193 5.289193 CGCAAAACTTGAAATGATATGTGGG 59.711 40.000 0.00 0.00 0.00 4.61
3273 6194 6.165577 GCAAAACTTGAAATGATATGTGGGT 58.834 36.000 0.00 0.00 0.00 4.51
3274 6195 6.091169 GCAAAACTTGAAATGATATGTGGGTG 59.909 38.462 0.00 0.00 0.00 4.61
3275 6196 7.377398 CAAAACTTGAAATGATATGTGGGTGA 58.623 34.615 0.00 0.00 0.00 4.02
3276 6197 7.537596 AAACTTGAAATGATATGTGGGTGAA 57.462 32.000 0.00 0.00 0.00 3.18
3277 6198 7.722949 AACTTGAAATGATATGTGGGTGAAT 57.277 32.000 0.00 0.00 0.00 2.57
3280 6201 8.036575 ACTTGAAATGATATGTGGGTGAATTTG 58.963 33.333 0.00 0.00 0.00 2.32
3281 6202 6.339730 TGAAATGATATGTGGGTGAATTTGC 58.660 36.000 0.00 0.00 0.00 3.68
3285 6206 1.614996 ATGTGGGTGAATTTGCGTGA 58.385 45.000 0.00 0.00 0.00 4.35
3286 6207 0.665835 TGTGGGTGAATTTGCGTGAC 59.334 50.000 0.00 0.00 0.00 3.67
3287 6208 0.665835 GTGGGTGAATTTGCGTGACA 59.334 50.000 0.00 0.00 0.00 3.58
3288 6209 0.665835 TGGGTGAATTTGCGTGACAC 59.334 50.000 0.00 0.00 0.00 3.67
3289 6210 0.385473 GGGTGAATTTGCGTGACACG 60.385 55.000 23.43 23.43 45.88 4.49
3290 6211 0.306533 GGTGAATTTGCGTGACACGT 59.693 50.000 27.32 8.79 44.73 4.49
3291 6212 1.385038 GTGAATTTGCGTGACACGTG 58.615 50.000 27.32 15.48 44.73 4.49
3292 6213 1.010580 TGAATTTGCGTGACACGTGT 58.989 45.000 27.32 23.64 44.73 4.49
3293 6214 1.267782 TGAATTTGCGTGACACGTGTG 60.268 47.619 28.82 13.36 44.73 3.82
3294 6215 0.591236 AATTTGCGTGACACGTGTGC 60.591 50.000 28.82 23.27 44.73 4.57
3295 6216 1.436195 ATTTGCGTGACACGTGTGCT 61.436 50.000 28.82 0.00 44.73 4.40
3296 6217 1.640210 TTTGCGTGACACGTGTGCTT 61.640 50.000 28.82 0.00 44.73 3.91
3297 6218 1.640210 TTGCGTGACACGTGTGCTTT 61.640 50.000 28.82 0.00 44.73 3.51
3298 6219 1.651132 GCGTGACACGTGTGCTTTG 60.651 57.895 28.82 11.95 44.73 2.77
3299 6220 1.713246 CGTGACACGTGTGCTTTGT 59.287 52.632 28.82 0.00 36.74 2.83
3300 6221 0.315059 CGTGACACGTGTGCTTTGTC 60.315 55.000 28.82 10.28 40.14 3.18
3301 6222 0.724549 GTGACACGTGTGCTTTGTCA 59.275 50.000 28.82 13.10 45.71 3.58
3302 6223 1.443802 TGACACGTGTGCTTTGTCAA 58.556 45.000 28.82 0.00 45.10 3.18
3303 6224 1.807142 TGACACGTGTGCTTTGTCAAA 59.193 42.857 28.82 0.00 45.10 2.69
3304 6225 2.421775 TGACACGTGTGCTTTGTCAAAT 59.578 40.909 28.82 0.00 45.10 2.32
3305 6226 3.119673 TGACACGTGTGCTTTGTCAAATT 60.120 39.130 28.82 0.00 45.10 1.82
3306 6227 4.095036 TGACACGTGTGCTTTGTCAAATTA 59.905 37.500 28.82 0.00 45.10 1.40
3307 6228 4.987832 ACACGTGTGCTTTGTCAAATTAA 58.012 34.783 22.71 0.00 0.00 1.40
3308 6229 4.796312 ACACGTGTGCTTTGTCAAATTAAC 59.204 37.500 22.71 0.00 0.00 2.01
3309 6230 5.034152 CACGTGTGCTTTGTCAAATTAACT 58.966 37.500 7.58 0.00 0.00 2.24
3310 6231 5.034152 ACGTGTGCTTTGTCAAATTAACTG 58.966 37.500 0.00 0.00 0.00 3.16
3311 6232 5.034152 CGTGTGCTTTGTCAAATTAACTGT 58.966 37.500 0.00 0.00 0.00 3.55
3312 6233 5.052436 CGTGTGCTTTGTCAAATTAACTGTG 60.052 40.000 0.00 0.00 0.00 3.66
3313 6234 5.804979 GTGTGCTTTGTCAAATTAACTGTGT 59.195 36.000 0.00 0.00 0.00 3.72
3314 6235 5.804473 TGTGCTTTGTCAAATTAACTGTGTG 59.196 36.000 0.00 0.00 0.00 3.82
3626 6659 2.092323 GAGAAAAACCTCCCCATTCCG 58.908 52.381 0.00 0.00 0.00 4.30
3747 6785 0.032615 AACAAGGGACCAGGCAACAA 60.033 50.000 0.00 0.00 41.41 2.83
3857 8674 1.282738 ACATCAGCACCACCATCATCA 59.717 47.619 0.00 0.00 0.00 3.07
3902 8734 3.316573 GACCACCAGCTTCCCCTCG 62.317 68.421 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 3.222354 GACCAGCCAACTCGTCCGT 62.222 63.158 0.00 0.00 28.59 4.69
35 36 4.107051 CAAAGCAAGAGGCCGCCG 62.107 66.667 1.49 0.00 46.50 6.46
38 39 4.107051 CCGCAAAGCAAGAGGCCG 62.107 66.667 0.00 0.00 46.50 6.13
74 75 1.736645 AAGATCAACGTCGTGGCCG 60.737 57.895 0.00 0.00 0.00 6.13
79 80 1.429463 GAAGCCAAGATCAACGTCGT 58.571 50.000 0.00 0.00 0.00 4.34
82 83 1.813513 CAGGAAGCCAAGATCAACGT 58.186 50.000 0.00 0.00 0.00 3.99
86 87 1.746615 GCGCAGGAAGCCAAGATCA 60.747 57.895 0.30 0.00 41.38 2.92
128 129 4.498520 AGCGCATCGTCCAGTCGG 62.499 66.667 11.47 0.00 0.00 4.79
226 227 4.435970 TCGCCTCCGCTAGACCCA 62.436 66.667 0.00 0.00 0.00 4.51
232 233 4.896829 CCTCCCTCGCCTCCGCTA 62.897 72.222 0.00 0.00 0.00 4.26
266 267 2.125106 GACATGCCCACCCTCGAC 60.125 66.667 0.00 0.00 0.00 4.20
300 301 3.424780 AAAAACCTCCCACCCGCGT 62.425 57.895 4.92 0.00 0.00 6.01
670 673 1.217244 CTGCAGCCCATTTCAAGCC 59.783 57.895 0.00 0.00 0.00 4.35
673 676 1.228956 AGCCTGCAGCCCATTTCAA 60.229 52.632 8.66 0.00 45.47 2.69
683 686 2.563798 TTTTTCGCCCAGCCTGCAG 61.564 57.895 6.78 6.78 0.00 4.41
684 687 2.520500 TTTTTCGCCCAGCCTGCA 60.521 55.556 0.00 0.00 0.00 4.41
705 708 1.306642 ACCCAAACAAACGTGCGTCA 61.307 50.000 0.00 0.00 0.00 4.35
710 713 0.727970 TGACGACCCAAACAAACGTG 59.272 50.000 0.00 0.00 37.32 4.49
711 714 0.728542 GTGACGACCCAAACAAACGT 59.271 50.000 0.00 0.00 39.82 3.99
716 719 0.108281 TCAACGTGACGACCCAAACA 60.108 50.000 13.70 0.00 0.00 2.83
727 730 5.446143 ACATAAAAATTGGCTCAACGTGA 57.554 34.783 0.00 0.00 0.00 4.35
735 738 1.134175 CGGCGGACATAAAAATTGGCT 59.866 47.619 0.00 0.00 0.00 4.75
746 749 1.472728 GGTTTAGATCACGGCGGACAT 60.473 52.381 13.24 0.00 0.00 3.06
749 752 1.140161 CGGTTTAGATCACGGCGGA 59.860 57.895 13.24 6.15 0.00 5.54
756 759 0.108520 GTGCGGGTCGGTTTAGATCA 60.109 55.000 0.00 0.00 0.00 2.92
757 760 1.143969 CGTGCGGGTCGGTTTAGATC 61.144 60.000 0.00 0.00 0.00 2.75
759 762 2.259204 CGTGCGGGTCGGTTTAGA 59.741 61.111 0.00 0.00 0.00 2.10
771 774 0.373716 GTAAGAGCAAATCCCGTGCG 59.626 55.000 0.00 0.00 46.86 5.34
773 776 2.972625 TCAGTAAGAGCAAATCCCGTG 58.027 47.619 0.00 0.00 0.00 4.94
774 777 3.695830 TTCAGTAAGAGCAAATCCCGT 57.304 42.857 0.00 0.00 0.00 5.28
775 778 4.003648 AGTTTCAGTAAGAGCAAATCCCG 58.996 43.478 0.00 0.00 0.00 5.14
776 779 5.106118 GGAAGTTTCAGTAAGAGCAAATCCC 60.106 44.000 0.00 0.00 0.00 3.85
777 780 5.707764 AGGAAGTTTCAGTAAGAGCAAATCC 59.292 40.000 0.00 0.00 0.00 3.01
780 783 5.694910 CGTAGGAAGTTTCAGTAAGAGCAAA 59.305 40.000 0.00 0.00 0.00 3.68
800 803 9.991388 TTCCGTGAAAATAAAAATATTCCGTAG 57.009 29.630 0.00 0.00 0.00 3.51
805 808 9.763465 TCGTCTTCCGTGAAAATAAAAATATTC 57.237 29.630 0.00 0.00 37.94 1.75
807 810 8.943002 AGTCGTCTTCCGTGAAAATAAAAATAT 58.057 29.630 0.00 0.00 37.94 1.28
869 873 1.371774 TGGAGATTAAGGGGAAGGGGA 59.628 52.381 0.00 0.00 0.00 4.81
943 949 4.277423 GGAGTAAGGAGAGATGCTACACTC 59.723 50.000 0.00 0.00 0.00 3.51
963 969 6.613153 TTCTCCCTTTCTTTCTCTAAGGAG 57.387 41.667 0.00 0.00 40.71 3.69
964 970 6.787957 TCTTTCTCCCTTTCTTTCTCTAAGGA 59.212 38.462 0.00 0.00 40.71 3.36
965 971 7.010339 TCTTTCTCCCTTTCTTTCTCTAAGG 57.990 40.000 0.00 0.00 38.51 2.69
966 972 8.371699 TCTTCTTTCTCCCTTTCTTTCTCTAAG 58.628 37.037 0.00 0.00 35.04 2.18
967 973 8.151596 GTCTTCTTTCTCCCTTTCTTTCTCTAA 58.848 37.037 0.00 0.00 0.00 2.10
968 974 7.524038 CGTCTTCTTTCTCCCTTTCTTTCTCTA 60.524 40.741 0.00 0.00 0.00 2.43
969 975 6.530120 GTCTTCTTTCTCCCTTTCTTTCTCT 58.470 40.000 0.00 0.00 0.00 3.10
970 976 5.407084 CGTCTTCTTTCTCCCTTTCTTTCTC 59.593 44.000 0.00 0.00 0.00 2.87
971 977 5.070580 TCGTCTTCTTTCTCCCTTTCTTTCT 59.929 40.000 0.00 0.00 0.00 2.52
972 978 5.298347 TCGTCTTCTTTCTCCCTTTCTTTC 58.702 41.667 0.00 0.00 0.00 2.62
1569 3279 4.035102 GGAGGTGGGTGCTGGACC 62.035 72.222 10.21 10.21 45.28 4.46
1570 3280 2.930562 AGGAGGTGGGTGCTGGAC 60.931 66.667 0.00 0.00 0.00 4.02
1571 3281 2.607750 GAGGAGGTGGGTGCTGGA 60.608 66.667 0.00 0.00 0.00 3.86
1572 3282 3.721706 GGAGGAGGTGGGTGCTGG 61.722 72.222 0.00 0.00 0.00 4.85
1573 3283 2.608988 AGGAGGAGGTGGGTGCTG 60.609 66.667 0.00 0.00 0.00 4.41
1574 3284 2.608988 CAGGAGGAGGTGGGTGCT 60.609 66.667 0.00 0.00 0.00 4.40
1575 3285 4.416738 GCAGGAGGAGGTGGGTGC 62.417 72.222 0.00 0.00 0.00 5.01
1576 3286 3.721706 GGCAGGAGGAGGTGGGTG 61.722 72.222 0.00 0.00 0.00 4.61
1580 3290 4.463879 CAGCGGCAGGAGGAGGTG 62.464 72.222 1.45 0.00 0.00 4.00
1607 3327 3.276857 ACAGCAACAGCAGATAAGATGG 58.723 45.455 0.00 0.00 0.00 3.51
1693 3423 7.069344 TGATGTAGAGTAGGATTCAGAATGGA 58.931 38.462 0.00 0.00 36.16 3.41
1838 3606 1.238439 CATGGTTTCAGAAGTGCGGT 58.762 50.000 0.00 0.00 0.00 5.68
2200 4141 9.273016 TCACAATTACTAGAACCTTTCTTTCAG 57.727 33.333 0.00 0.00 41.14 3.02
2295 4377 7.254455 CCTTGCTAATAGAACCAAAGTACATCG 60.254 40.741 0.00 0.00 0.00 3.84
2363 4479 7.152645 AGTCAACAACGTCAGAACATAGTATT 58.847 34.615 0.00 0.00 0.00 1.89
2371 4487 4.859629 AAAGAGTCAACAACGTCAGAAC 57.140 40.909 0.00 0.00 0.00 3.01
2377 4493 6.249035 TCTTTCAAAAAGAGTCAACAACGT 57.751 33.333 0.00 0.00 0.00 3.99
2479 4645 5.163591 ACAAAAACACTGCTAAGTTGTACCC 60.164 40.000 0.00 0.00 32.98 3.69
2480 4646 5.886992 ACAAAAACACTGCTAAGTTGTACC 58.113 37.500 0.00 0.00 32.98 3.34
2689 4855 5.776173 ATATCTTCATCGTTCTCGTCCTT 57.224 39.130 0.00 0.00 38.33 3.36
3001 5744 4.737855 TCCTAAAGACTATCACACAGGC 57.262 45.455 0.00 0.00 0.00 4.85
3162 6081 9.608617 GCAATACAGATGATAATCATGAACTTG 57.391 33.333 0.00 0.00 37.20 3.16
3269 6190 0.665835 GTGTCACGCAAATTCACCCA 59.334 50.000 0.00 0.00 0.00 4.51
3270 6191 0.385473 CGTGTCACGCAAATTCACCC 60.385 55.000 13.22 0.00 33.65 4.61
3281 6202 2.910100 TGACAAAGCACACGTGTCACG 61.910 52.381 20.49 23.40 45.02 4.35
3285 6206 3.502191 AATTTGACAAAGCACACGTGT 57.498 38.095 17.22 17.22 0.00 4.49
3286 6207 5.034152 AGTTAATTTGACAAAGCACACGTG 58.966 37.500 15.48 15.48 0.00 4.49
3287 6208 5.034152 CAGTTAATTTGACAAAGCACACGT 58.966 37.500 6.77 0.00 0.00 4.49
3288 6209 5.034152 ACAGTTAATTTGACAAAGCACACG 58.966 37.500 6.77 2.10 0.00 4.49
3289 6210 5.804979 ACACAGTTAATTTGACAAAGCACAC 59.195 36.000 6.77 1.27 0.00 3.82
3290 6211 5.804473 CACACAGTTAATTTGACAAAGCACA 59.196 36.000 6.77 0.00 0.00 4.57
3291 6212 5.804979 ACACACAGTTAATTTGACAAAGCAC 59.195 36.000 6.77 3.25 0.00 4.40
3292 6213 5.960113 ACACACAGTTAATTTGACAAAGCA 58.040 33.333 6.77 0.00 0.00 3.91
3293 6214 6.970043 TGTACACACAGTTAATTTGACAAAGC 59.030 34.615 6.77 0.00 0.00 3.51
3294 6215 9.515020 AATGTACACACAGTTAATTTGACAAAG 57.485 29.630 6.77 0.00 38.30 2.77
3295 6216 9.862371 AAATGTACACACAGTTAATTTGACAAA 57.138 25.926 2.48 2.48 40.95 2.83
3303 6224 8.946085 CCAGTGATAAATGTACACACAGTTAAT 58.054 33.333 13.97 0.00 45.33 1.40
3304 6225 7.934665 ACCAGTGATAAATGTACACACAGTTAA 59.065 33.333 13.97 0.00 45.33 2.01
3305 6226 7.446769 ACCAGTGATAAATGTACACACAGTTA 58.553 34.615 13.97 0.83 45.99 2.24
3306 6227 6.296026 ACCAGTGATAAATGTACACACAGTT 58.704 36.000 13.97 0.00 44.58 3.16
3307 6228 5.865085 ACCAGTGATAAATGTACACACAGT 58.135 37.500 13.97 8.95 38.30 3.55
3308 6229 6.801539 AACCAGTGATAAATGTACACACAG 57.198 37.500 13.97 7.41 38.30 3.66
3309 6230 7.934665 AGTTAACCAGTGATAAATGTACACACA 59.065 33.333 13.97 1.93 39.52 3.72
3310 6231 8.319143 AGTTAACCAGTGATAAATGTACACAC 57.681 34.615 0.00 1.07 37.05 3.82
3311 6232 7.604927 GGAGTTAACCAGTGATAAATGTACACA 59.395 37.037 0.00 0.00 37.05 3.72
3312 6233 7.065443 GGGAGTTAACCAGTGATAAATGTACAC 59.935 40.741 0.00 0.00 35.15 2.90
3313 6234 7.037873 AGGGAGTTAACCAGTGATAAATGTACA 60.038 37.037 0.00 0.00 0.00 2.90
3314 6235 7.280205 CAGGGAGTTAACCAGTGATAAATGTAC 59.720 40.741 0.88 0.00 0.00 2.90
3626 6659 0.743097 GCTCCACCCAAGCAATCATC 59.257 55.000 0.00 0.00 39.61 2.92
3747 6785 1.067295 TTCTGCAAGGTGGAGGTCAT 58.933 50.000 0.00 0.00 36.40 3.06
3840 8651 1.841919 AGATGATGATGGTGGTGCTGA 59.158 47.619 0.00 0.00 0.00 4.26
3857 8674 4.594920 TCTCAGACTGGTGGAAAAGAAGAT 59.405 41.667 1.81 0.00 0.00 2.40
3902 8734 3.319198 TCGGTGGACCTCAAGGGC 61.319 66.667 0.29 0.00 44.61 5.19


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

AutoCloner maintained by Alex Coulton.