Multiple sequence alignment - TraesCS3B01G346900

Loading Multiple Alignment...

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 TraesCS3B01G346900 chr3B 100.000 3196 0 0 1 3196 556485328 556488523 0 5903
1 TraesCS3B01G346900 chr3B 96.076 892 32 2 1 892 564035067 564034179 0 1450
2 TraesCS3B01G346900 chr4D 95.628 915 34 5 1 914 60875768 60876677 0 1463
3 TraesCS3B01G346900 chr1A 96.201 895 31 3 5 899 344139254 344138363 0 1461
4 TraesCS3B01G346900 chr3D 95.889 900 31 4 1 899 472398089 472397195 0 1452
5 TraesCS3B01G346900 chr3D 95.773 899 36 2 1 899 462842879 462841983 0 1448
6 TraesCS3B01G346900 chr3D 91.932 818 36 7 2400 3195 426845415 426846224 0 1118
7 TraesCS3B01G346900 chr3D 92.029 690 38 8 928 1605 426843774 426844458 0 953
8 TraesCS3B01G346900 chr3D 91.207 671 42 9 1689 2355 426844609 426845266 0 896
9 TraesCS3B01G346900 chr1B 95.871 896 35 2 1 896 390465579 390464686 0 1448
10 TraesCS3B01G346900 chr2A 95.759 896 36 2 1 896 688247133 688246240 0 1443
11 TraesCS3B01G346900 chr3A 95.556 900 38 2 1 900 500896461 500895564 0 1439
12 TraesCS3B01G346900 chr3A 95.439 899 37 3 1 899 441897875 441898769 0 1430
13 TraesCS3B01G346900 chr3A 94.500 800 37 5 2400 3195 561119707 561118911 0 1227
14 TraesCS3B01G346900 chr3A 89.805 667 51 6 1689 2355 561120537 561119888 0 839
15 TraesCS3B01G346900 chr3A 87.647 680 36 13 928 1605 561121313 561120680 0 747


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 TraesCS3B01G346900 chr3B 556485328 556488523 3195 False 5903.000000 5903 100.000000 1 3196 1 chr3B.!!$F1 3195
1 TraesCS3B01G346900 chr3B 564034179 564035067 888 True 1450.000000 1450 96.076000 1 892 1 chr3B.!!$R1 891
2 TraesCS3B01G346900 chr4D 60875768 60876677 909 False 1463.000000 1463 95.628000 1 914 1 chr4D.!!$F1 913
3 TraesCS3B01G346900 chr1A 344138363 344139254 891 True 1461.000000 1461 96.201000 5 899 1 chr1A.!!$R1 894
4 TraesCS3B01G346900 chr3D 472397195 472398089 894 True 1452.000000 1452 95.889000 1 899 1 chr3D.!!$R2 898
5 TraesCS3B01G346900 chr3D 462841983 462842879 896 True 1448.000000 1448 95.773000 1 899 1 chr3D.!!$R1 898
6 TraesCS3B01G346900 chr3D 426843774 426846224 2450 False 989.000000 1118 91.722667 928 3195 3 chr3D.!!$F1 2267
7 TraesCS3B01G346900 chr1B 390464686 390465579 893 True 1448.000000 1448 95.871000 1 896 1 chr1B.!!$R1 895
8 TraesCS3B01G346900 chr2A 688246240 688247133 893 True 1443.000000 1443 95.759000 1 896 1 chr2A.!!$R1 895
9 TraesCS3B01G346900 chr3A 500895564 500896461 897 True 1439.000000 1439 95.556000 1 900 1 chr3A.!!$R1 899
10 TraesCS3B01G346900 chr3A 441897875 441898769 894 False 1430.000000 1430 95.439000 1 899 1 chr3A.!!$F1 898
11 TraesCS3B01G346900 chr3A 561118911 561121313 2402 True 937.666667 1227 90.650667 928 3195 3 chr3A.!!$R2 2267

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
926 931 0.396417 ACGGGTCTGCTAGAGATGCT 60.396 55.0 0.0 0.0 31.63 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2512 2738 0.673985 GCCCACACTGGAAAGAAACC 59.326 55.0 0.0 0.0 40.96 3.27 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
58 59 7.459795 TGCAACTACAAAATCATGGACAATA 57.540 32.000 0.00 0.00 0.00 1.90
171 172 7.436933 CCTTAACAAGAAAAGAGGCTCATTTT 58.563 34.615 17.72 18.05 0.00 1.82
191 192 1.228367 CCAAGGCACAAGAGGCAGT 60.228 57.895 0.00 0.00 36.37 4.40
429 432 3.363970 CGCATACACGCTTTTCTTCAAGT 60.364 43.478 0.00 0.00 0.00 3.16
495 498 4.217550 GGATGATCTAGTAGAGCACCACTC 59.782 50.000 19.87 13.11 44.04 3.51
724 727 7.242783 TGAAATGTGTGATATGTGAAATGACG 58.757 34.615 0.00 0.00 0.00 4.35
743 746 3.888323 GACGGTTTTAAAGGTTGGGGTTA 59.112 43.478 0.00 0.00 0.00 2.85
819 823 2.621070 TGAGGGTTCTAGTCTTTGCCT 58.379 47.619 0.00 0.00 0.00 4.75
841 845 6.540551 GCCTCATGTTTTTCAACCCTTAAAAA 59.459 34.615 0.00 0.00 33.41 1.94
843 847 9.771534 CCTCATGTTTTTCAACCCTTAAAAATA 57.228 29.630 0.00 0.00 37.04 1.40
892 897 5.932619 AAAACTGCTTTAAGGGTTTGAGT 57.067 34.783 0.00 0.00 33.09 3.41
899 904 5.763204 TGCTTTAAGGGTTTGAGTGTTCTAG 59.237 40.000 0.00 0.00 0.00 2.43
902 907 3.686916 AGGGTTTGAGTGTTCTAGCTC 57.313 47.619 0.00 0.00 0.00 4.09
903 908 3.243724 AGGGTTTGAGTGTTCTAGCTCT 58.756 45.455 0.00 0.00 33.22 4.09
905 910 4.838986 AGGGTTTGAGTGTTCTAGCTCTTA 59.161 41.667 0.00 0.00 33.22 2.10
906 911 5.485708 AGGGTTTGAGTGTTCTAGCTCTTAT 59.514 40.000 0.00 0.00 33.22 1.73
907 912 6.668283 AGGGTTTGAGTGTTCTAGCTCTTATA 59.332 38.462 0.00 0.00 33.22 0.98
908 913 6.757478 GGGTTTGAGTGTTCTAGCTCTTATAC 59.243 42.308 0.00 0.00 33.22 1.47
910 915 5.752892 TGAGTGTTCTAGCTCTTATACGG 57.247 43.478 0.00 0.00 33.22 4.02
911 916 4.579340 TGAGTGTTCTAGCTCTTATACGGG 59.421 45.833 0.00 0.00 33.22 5.28
912 917 4.534797 AGTGTTCTAGCTCTTATACGGGT 58.465 43.478 0.00 0.00 0.00 5.28
913 918 4.579753 AGTGTTCTAGCTCTTATACGGGTC 59.420 45.833 0.00 0.00 0.00 4.46
914 919 4.579753 GTGTTCTAGCTCTTATACGGGTCT 59.420 45.833 0.00 0.00 0.00 3.85
915 920 4.579340 TGTTCTAGCTCTTATACGGGTCTG 59.421 45.833 0.00 0.00 0.00 3.51
916 921 3.147629 TCTAGCTCTTATACGGGTCTGC 58.852 50.000 0.00 0.00 0.00 4.26
917 922 2.074729 AGCTCTTATACGGGTCTGCT 57.925 50.000 0.00 0.00 0.00 4.24
918 923 3.225177 AGCTCTTATACGGGTCTGCTA 57.775 47.619 0.00 0.00 0.00 3.49
919 924 3.150767 AGCTCTTATACGGGTCTGCTAG 58.849 50.000 0.00 0.00 0.00 3.42
920 925 3.147629 GCTCTTATACGGGTCTGCTAGA 58.852 50.000 0.00 0.00 0.00 2.43
921 926 3.189702 GCTCTTATACGGGTCTGCTAGAG 59.810 52.174 0.00 0.00 0.00 2.43
922 927 4.643463 CTCTTATACGGGTCTGCTAGAGA 58.357 47.826 0.00 0.00 31.76 3.10
923 928 5.244189 TCTTATACGGGTCTGCTAGAGAT 57.756 43.478 0.00 0.00 31.63 2.75
924 929 5.004448 TCTTATACGGGTCTGCTAGAGATG 58.996 45.833 0.00 0.00 31.63 2.90
925 930 1.319541 TACGGGTCTGCTAGAGATGC 58.680 55.000 0.00 0.00 31.63 3.91
926 931 0.396417 ACGGGTCTGCTAGAGATGCT 60.396 55.000 0.00 0.00 31.63 3.79
1162 1173 1.511305 CAGCCGTCCGTAGTGATGT 59.489 57.895 0.00 0.00 0.00 3.06
1287 1300 3.311110 TCACCTTCCGCTCCGCTT 61.311 61.111 0.00 0.00 0.00 4.68
1368 1381 6.183360 CGGATCCAAGAAGGTAAAGATCTACA 60.183 42.308 13.41 0.00 39.02 2.74
1369 1382 7.213678 GGATCCAAGAAGGTAAAGATCTACAG 58.786 42.308 6.95 0.00 39.02 2.74
1370 1383 7.147637 GGATCCAAGAAGGTAAAGATCTACAGT 60.148 40.741 6.95 0.00 39.02 3.55
1371 1384 8.840200 ATCCAAGAAGGTAAAGATCTACAGTA 57.160 34.615 0.00 0.00 39.02 2.74
1372 1385 8.064336 TCCAAGAAGGTAAAGATCTACAGTAC 57.936 38.462 0.00 0.00 39.02 2.73
1377 1390 9.236006 AGAAGGTAAAGATCTACAGTACGTTTA 57.764 33.333 0.00 0.00 0.00 2.01
1425 1438 1.000521 CAGCATCAGGGGAGCCAAA 60.001 57.895 0.00 0.00 0.00 3.28
1426 1439 0.612732 CAGCATCAGGGGAGCCAAAA 60.613 55.000 0.00 0.00 0.00 2.44
1429 1442 1.137675 GCATCAGGGGAGCCAAAATTC 59.862 52.381 0.00 0.00 0.00 2.17
1441 1454 4.265073 AGCCAAAATTCTGCTAGATTCGT 58.735 39.130 0.00 0.00 32.56 3.85
1442 1455 4.702131 AGCCAAAATTCTGCTAGATTCGTT 59.298 37.500 0.00 0.00 32.56 3.85
1458 1472 4.829064 TTCGTTCAATGCTAACTTGCTT 57.171 36.364 0.00 0.00 0.00 3.91
1479 1493 5.509163 GCTTTACATCTAGCAAGATCCGGTA 60.509 44.000 0.00 0.00 40.65 4.02
1487 1501 1.664151 GCAAGATCCGGTAAAGGTTCG 59.336 52.381 0.00 0.00 35.66 3.95
1502 1516 4.722361 AGGTTCGAGCCTTCTTTACTAG 57.278 45.455 16.03 0.00 34.71 2.57
1504 1518 3.195182 GGTTCGAGCCTTCTTTACTAGGT 59.805 47.826 11.59 0.00 33.91 3.08
1520 1538 5.148651 ACTAGGTTTACTTGTAGTGCCAG 57.851 43.478 0.00 0.00 33.32 4.85
1526 1544 4.682778 TTACTTGTAGTGCCAGAACAGT 57.317 40.909 0.00 0.00 0.00 3.55
1529 1547 1.593196 TGTAGTGCCAGAACAGTTGC 58.407 50.000 0.00 0.00 0.00 4.17
1537 1555 3.382865 TGCCAGAACAGTTGCATTTGTTA 59.617 39.130 14.18 0.00 37.63 2.41
1552 1570 0.673437 TGTTAAAGTGCAAGCCAGCC 59.327 50.000 0.00 0.00 0.00 4.85
1595 1618 7.077605 CGAATTTCACTGATGCTTCTTACAAA 58.922 34.615 0.88 0.00 0.00 2.83
1596 1619 7.059945 CGAATTTCACTGATGCTTCTTACAAAC 59.940 37.037 0.88 0.00 0.00 2.93
1601 1624 5.352569 CACTGATGCTTCTTACAAACCTAGG 59.647 44.000 7.41 7.41 0.00 3.02
1605 1628 3.010138 TGCTTCTTACAAACCTAGGCCAT 59.990 43.478 9.30 0.00 0.00 4.40
1606 1629 4.017126 GCTTCTTACAAACCTAGGCCATT 58.983 43.478 9.30 0.00 0.00 3.16
1608 1631 4.230745 TCTTACAAACCTAGGCCATTCC 57.769 45.455 9.30 0.00 0.00 3.01
1609 1632 3.053917 TCTTACAAACCTAGGCCATTCCC 60.054 47.826 9.30 0.00 34.51 3.97
1611 1634 2.568979 ACAAACCTAGGCCATTCCCTA 58.431 47.619 9.30 0.00 36.41 3.53
1612 1635 3.131252 ACAAACCTAGGCCATTCCCTAT 58.869 45.455 9.30 0.00 36.88 2.57
1620 1657 3.576861 AGGCCATTCCCTATTTTTAGGC 58.423 45.455 5.01 0.00 40.08 3.93
1637 1674 9.614269 ATTTTTAGGCCCATATTATGTTGGTAT 57.386 29.630 0.00 0.00 0.00 2.73
1674 1732 7.555087 TCTGGTTTTTCAGTTTTGTCATTCAT 58.445 30.769 0.00 0.00 36.25 2.57
1680 1738 8.558973 TTTTCAGTTTTGTCATTCATTTGGTT 57.441 26.923 0.00 0.00 0.00 3.67
1681 1739 9.658799 TTTTCAGTTTTGTCATTCATTTGGTTA 57.341 25.926 0.00 0.00 0.00 2.85
1798 1885 6.715347 ATAACTGATTAAAATGCCAGGACC 57.285 37.500 0.00 0.00 0.00 4.46
1801 1888 4.019174 CTGATTAAAATGCCAGGACCTGT 58.981 43.478 20.24 3.03 0.00 4.00
1806 1893 6.732896 TTAAAATGCCAGGACCTGTAAAAA 57.267 33.333 20.24 1.36 0.00 1.94
1808 1895 5.823861 AAATGCCAGGACCTGTAAAAATT 57.176 34.783 20.24 9.09 0.00 1.82
1812 1899 6.279513 TGCCAGGACCTGTAAAAATTAATG 57.720 37.500 20.24 1.44 0.00 1.90
1813 1900 5.186797 TGCCAGGACCTGTAAAAATTAATGG 59.813 40.000 20.24 2.05 0.00 3.16
1868 1955 4.335416 ACTGTTTGACATCACCCAATAGG 58.665 43.478 0.00 0.00 43.78 2.57
1882 1969 3.388308 CCAATAGGCTCTGTTGATCTCG 58.612 50.000 11.45 0.00 35.14 4.04
1898 1985 3.953712 TCTCGGTGAGATTGTTGCTAA 57.046 42.857 0.00 0.00 33.35 3.09
1899 1986 3.585862 TCTCGGTGAGATTGTTGCTAAC 58.414 45.455 0.00 0.00 33.35 2.34
1900 1987 3.258372 TCTCGGTGAGATTGTTGCTAACT 59.742 43.478 0.00 0.00 33.35 2.24
1901 1988 3.997021 CTCGGTGAGATTGTTGCTAACTT 59.003 43.478 0.00 0.00 0.00 2.66
1902 1989 4.385825 TCGGTGAGATTGTTGCTAACTTT 58.614 39.130 0.00 0.00 0.00 2.66
1915 2002 4.536065 TGCTAACTTTGTTGCTCAATTCG 58.464 39.130 0.00 0.00 35.84 3.34
1924 2011 3.750652 TGTTGCTCAATTCGTATGAAGCA 59.249 39.130 5.16 5.16 37.57 3.91
1928 2015 5.359756 TGCTCAATTCGTATGAAGCATACT 58.640 37.500 13.73 0.00 42.99 2.12
1980 2067 3.181467 TGCTTGCACTTTATTTGCCAACT 60.181 39.130 0.00 0.00 39.39 3.16
2011 2098 5.007724 ACTCAGATTGGTGTTTCTTTCGTTC 59.992 40.000 0.00 0.00 0.00 3.95
2038 2125 4.951094 ACAGGTTTTAGTTGTACAGGCAAA 59.049 37.500 0.00 0.00 0.00 3.68
2060 2147 0.655733 AGGCGCCAAATAATTCGACG 59.344 50.000 31.54 0.00 34.71 5.12
2067 2154 3.000523 GCCAAATAATTCGACGAGCGTAA 59.999 43.478 0.00 0.00 41.80 3.18
2078 2165 3.178618 CGACGAGCGTAATTCAATCAGAG 59.821 47.826 0.00 0.00 34.64 3.35
2081 2168 2.205074 AGCGTAATTCAATCAGAGCCG 58.795 47.619 0.00 0.00 0.00 5.52
2105 2192 3.247411 CGGATGCGAGTAACAATATTGCA 59.753 43.478 15.48 6.12 35.10 4.08
2112 2199 6.536941 TGCGAGTAACAATATTGCAAGTGATA 59.463 34.615 15.48 0.00 0.00 2.15
2120 2207 6.153340 ACAATATTGCAAGTGATACTTTGGCT 59.847 34.615 15.48 0.00 36.03 4.75
2186 2273 6.369326 CGAGAAATAGTCGCTTATGATGAC 57.631 41.667 0.00 0.00 0.00 3.06
2198 2285 5.403766 CGCTTATGATGACCTGTTCTGATAC 59.596 44.000 0.00 0.00 0.00 2.24
2202 2289 2.363788 TGACCTGTTCTGATACGCAC 57.636 50.000 0.00 0.00 0.00 5.34
2215 2302 3.878103 TGATACGCACTCTTCCTCTAGAC 59.122 47.826 0.00 0.00 0.00 2.59
2245 2332 1.172175 TCAGTGTGCTGTTGTGCAAA 58.828 45.000 0.00 0.00 45.12 3.68
2263 2350 4.082245 TGCAAAATTAGGGTCTTTAGCTGC 60.082 41.667 0.00 0.00 0.00 5.25
2276 2363 4.285003 TCTTTAGCTGCCTAACTGTAACCA 59.715 41.667 0.00 0.00 33.43 3.67
2295 2384 4.133526 CCAAGGGGTATCTCCTATCTCA 57.866 50.000 0.00 0.00 33.58 3.27
2316 2405 3.605749 ATGTTGCGCTGTAGGCCGT 62.606 57.895 9.73 0.00 37.74 5.68
2317 2406 3.788766 GTTGCGCTGTAGGCCGTG 61.789 66.667 9.73 0.00 37.74 4.94
2351 2440 7.615582 TTGTCTTCATCATTGAACCTATGTC 57.384 36.000 0.00 0.00 36.94 3.06
2352 2441 5.812127 TGTCTTCATCATTGAACCTATGTCG 59.188 40.000 0.00 0.00 36.94 4.35
2353 2442 5.812642 GTCTTCATCATTGAACCTATGTCGT 59.187 40.000 0.00 0.00 36.94 4.34
2354 2443 6.978659 GTCTTCATCATTGAACCTATGTCGTA 59.021 38.462 0.00 0.00 36.94 3.43
2355 2444 6.978659 TCTTCATCATTGAACCTATGTCGTAC 59.021 38.462 0.00 0.00 36.94 3.67
2357 2446 6.273071 TCATCATTGAACCTATGTCGTACTG 58.727 40.000 0.00 0.00 0.00 2.74
2358 2447 5.654603 TCATTGAACCTATGTCGTACTGT 57.345 39.130 0.00 0.00 0.00 3.55
2359 2448 5.407502 TCATTGAACCTATGTCGTACTGTG 58.592 41.667 0.00 0.00 0.00 3.66
2360 2449 4.859304 TTGAACCTATGTCGTACTGTGT 57.141 40.909 0.00 0.00 0.00 3.72
2361 2450 5.963176 TTGAACCTATGTCGTACTGTGTA 57.037 39.130 0.00 0.00 0.00 2.90
2362 2451 5.556355 TGAACCTATGTCGTACTGTGTAG 57.444 43.478 0.00 0.00 0.00 2.74
2363 2452 4.142534 TGAACCTATGTCGTACTGTGTAGC 60.143 45.833 0.00 0.00 0.00 3.58
2364 2453 3.349927 ACCTATGTCGTACTGTGTAGCA 58.650 45.455 0.00 0.00 0.00 3.49
2384 2473 5.921784 GCAGAAATTTGCTTCTAACATCG 57.078 39.130 0.00 0.00 40.89 3.84
2385 2474 5.393962 GCAGAAATTTGCTTCTAACATCGT 58.606 37.500 0.00 0.00 40.89 3.73
2386 2475 5.858581 GCAGAAATTTGCTTCTAACATCGTT 59.141 36.000 0.00 0.00 40.89 3.85
2387 2476 6.032880 GCAGAAATTTGCTTCTAACATCGTTC 59.967 38.462 0.00 0.00 40.89 3.95
2388 2477 7.077605 CAGAAATTTGCTTCTAACATCGTTCA 58.922 34.615 0.00 0.00 33.81 3.18
2391 2480 8.641499 AAATTTGCTTCTAACATCGTTCAAAA 57.359 26.923 0.00 0.00 0.00 2.44
2392 2481 7.858052 ATTTGCTTCTAACATCGTTCAAAAG 57.142 32.000 0.00 0.00 0.00 2.27
2394 2483 6.801539 TGCTTCTAACATCGTTCAAAAGAT 57.198 33.333 0.00 0.00 0.00 2.40
2395 2484 6.602179 TGCTTCTAACATCGTTCAAAAGATG 58.398 36.000 14.48 14.48 46.07 2.90
2512 2738 7.230108 ACACATTATTATCTGGGAAATGAGCAG 59.770 37.037 0.00 0.00 32.99 4.24
2542 2769 1.466167 CAGTGTGGGCGAGATTCTTTG 59.534 52.381 0.00 0.00 0.00 2.77
2568 2795 3.018856 GCATGATGTCATTGGACCTTGA 58.981 45.455 0.00 0.00 43.65 3.02
2603 2831 0.991146 TGGCTTGCCTCATCTTGGTA 59.009 50.000 13.18 0.00 0.00 3.25
2629 2857 4.892934 AGTTGGGTGCTTTATCAACTTCAA 59.107 37.500 0.00 0.00 44.88 2.69
2657 2885 3.389983 TGGTACACCACTTACTTGAGCTT 59.610 43.478 0.00 0.00 42.01 3.74
2660 2888 5.049612 GGTACACCACTTACTTGAGCTTTTC 60.050 44.000 0.00 0.00 35.64 2.29
2738 2966 5.308014 TGTGCTATTCTTGAAGCTTCTTGA 58.692 37.500 26.09 19.79 39.53 3.02
2836 3083 6.213600 AGAATCCCAAGTAGTAATCTGTGTGT 59.786 38.462 0.00 0.00 0.00 3.72
2942 3189 5.063880 TGAAAGAGGAAAAGAGCCTTGTAC 58.936 41.667 0.00 0.00 35.44 2.90
2952 3199 7.988028 GGAAAAGAGCCTTGTACTAATATCTGT 59.012 37.037 0.00 0.00 0.00 3.41
2968 3215 9.458727 CTAATATCTGTCTGCCCAATTATTCAT 57.541 33.333 0.00 0.00 0.00 2.57
2970 3217 9.458727 AATATCTGTCTGCCCAATTATTCATAG 57.541 33.333 0.00 0.00 0.00 2.23
2971 3218 5.624159 TCTGTCTGCCCAATTATTCATAGG 58.376 41.667 0.00 0.00 0.00 2.57
2972 3219 5.369404 TCTGTCTGCCCAATTATTCATAGGA 59.631 40.000 0.00 0.00 0.00 2.94
2973 3220 6.044754 TCTGTCTGCCCAATTATTCATAGGAT 59.955 38.462 0.00 0.00 0.00 3.24
2974 3221 7.237471 TCTGTCTGCCCAATTATTCATAGGATA 59.763 37.037 0.00 0.00 0.00 2.59
2975 3222 7.397221 TGTCTGCCCAATTATTCATAGGATAG 58.603 38.462 0.00 0.00 0.00 2.08
2995 3250 8.589338 AGGATAGTATTGATATGACTGGTTGAC 58.411 37.037 0.00 0.00 0.00 3.18
3074 3329 6.257849 GCATCGTTCTAACATTATCTTGGTCA 59.742 38.462 0.00 0.00 0.00 4.02
3076 3331 5.803461 TCGTTCTAACATTATCTTGGTCACG 59.197 40.000 0.00 0.00 0.00 4.35
3083 3338 5.547465 ACATTATCTTGGTCACGTCTTCAA 58.453 37.500 0.00 0.00 0.00 2.69
3189 3444 9.211485 CAAATGAAAGCAACAGGAATAAAAGAT 57.789 29.630 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 8.237811 GAGCATCCCCAGAAATTAATCTTTTA 57.762 34.615 0.00 0.00 0.00 1.52
58 59 7.233757 GGTGAGATAGTATCCCATTGAGTACTT 59.766 40.741 6.53 0.00 0.00 2.24
106 107 4.422073 TGATGGACTTCACAAGAGTTGT 57.578 40.909 0.00 0.00 46.75 3.32
171 172 0.036732 CTGCCTCTTGTGCCTTGGTA 59.963 55.000 0.00 0.00 0.00 3.25
275 276 5.867903 TTCATGATGTTCACCAAGGTTTT 57.132 34.783 0.00 0.00 0.00 2.43
276 277 5.867903 TTTCATGATGTTCACCAAGGTTT 57.132 34.783 0.00 0.00 0.00 3.27
429 432 3.384467 TGCATCCTCAATCTCACGATGTA 59.616 43.478 0.00 0.00 34.21 2.29
465 468 2.645297 TCTACTAGATCATCCCGGAGCT 59.355 50.000 0.73 0.00 37.32 4.09
624 627 9.193133 CATTCTAGTTATTATTACACCACCGAG 57.807 37.037 0.00 0.00 0.00 4.63
724 727 4.503643 GCCTTAACCCCAACCTTTAAAACC 60.504 45.833 0.00 0.00 0.00 3.27
743 746 2.979678 TGAGGGTTCTAGTCTTTGCCTT 59.020 45.455 0.00 0.00 0.00 4.35
795 799 4.390264 GCAAAGACTAGAACCCTCAAACT 58.610 43.478 0.00 0.00 0.00 2.66
851 855 7.415877 GCAGTTTTAAAGGTTGAGAAGTACCAA 60.416 37.037 0.00 0.00 0.00 3.67
855 859 7.875327 AAGCAGTTTTAAAGGTTGAGAAGTA 57.125 32.000 0.00 0.00 0.00 2.24
867 871 7.762159 CACTCAAACCCTTAAAGCAGTTTTAAA 59.238 33.333 4.03 0.00 39.93 1.52
892 897 4.579340 CAGACCCGTATAAGAGCTAGAACA 59.421 45.833 0.00 0.00 0.00 3.18
899 904 3.147629 TCTAGCAGACCCGTATAAGAGC 58.852 50.000 0.00 0.00 0.00 4.09
902 907 4.380023 GCATCTCTAGCAGACCCGTATAAG 60.380 50.000 0.00 0.00 32.26 1.73
903 908 3.506455 GCATCTCTAGCAGACCCGTATAA 59.494 47.826 0.00 0.00 32.26 0.98
905 910 1.889829 GCATCTCTAGCAGACCCGTAT 59.110 52.381 0.00 0.00 32.26 3.06
906 911 1.133761 AGCATCTCTAGCAGACCCGTA 60.134 52.381 0.00 0.00 32.26 4.02
907 912 0.396417 AGCATCTCTAGCAGACCCGT 60.396 55.000 0.00 0.00 32.26 5.28
908 913 0.313672 GAGCATCTCTAGCAGACCCG 59.686 60.000 0.00 0.00 32.26 5.28
910 915 1.001815 GTCGAGCATCTCTAGCAGACC 60.002 57.143 0.00 0.00 36.55 3.85
911 916 1.001815 GGTCGAGCATCTCTAGCAGAC 60.002 57.143 10.30 0.00 39.49 3.51
912 917 1.313772 GGTCGAGCATCTCTAGCAGA 58.686 55.000 10.30 0.00 34.78 4.26
913 918 1.001487 CTGGTCGAGCATCTCTAGCAG 60.001 57.143 18.98 11.34 42.26 4.24
914 919 1.028130 CTGGTCGAGCATCTCTAGCA 58.972 55.000 18.98 0.00 33.77 3.49
915 920 3.863681 CTGGTCGAGCATCTCTAGC 57.136 57.895 18.98 0.00 0.00 3.42
925 930 0.817634 TGGTTTTGTGGCTGGTCGAG 60.818 55.000 0.00 0.00 0.00 4.04
926 931 0.394488 TTGGTTTTGTGGCTGGTCGA 60.394 50.000 0.00 0.00 0.00 4.20
973 978 3.377253 AGTCCGTACAGATTGAGGGTA 57.623 47.619 0.00 0.00 0.00 3.69
1259 1272 3.819877 GAAGGTGACGTGCCCGGTT 62.820 63.158 0.00 0.00 38.78 4.44
1368 1381 3.631145 TCACGCTTCAGTAAACGTACT 57.369 42.857 0.00 0.00 41.49 2.73
1369 1382 3.671928 ACATCACGCTTCAGTAAACGTAC 59.328 43.478 0.00 0.00 36.91 3.67
1370 1383 3.904571 ACATCACGCTTCAGTAAACGTA 58.095 40.909 0.00 0.00 36.91 3.57
1371 1384 2.729882 GACATCACGCTTCAGTAAACGT 59.270 45.455 0.00 0.00 39.78 3.99
1372 1385 2.222289 CGACATCACGCTTCAGTAAACG 60.222 50.000 0.00 0.00 0.00 3.60
1377 1390 0.109086 CTCCGACATCACGCTTCAGT 60.109 55.000 0.00 0.00 0.00 3.41
1425 1438 5.587844 AGCATTGAACGAATCTAGCAGAATT 59.412 36.000 0.00 0.00 0.00 2.17
1426 1439 5.121811 AGCATTGAACGAATCTAGCAGAAT 58.878 37.500 0.00 0.00 0.00 2.40
1429 1442 5.521735 AGTTAGCATTGAACGAATCTAGCAG 59.478 40.000 0.00 0.00 31.85 4.24
1441 1454 7.452880 AGATGTAAAGCAAGTTAGCATTGAA 57.547 32.000 0.00 0.00 36.85 2.69
1442 1455 7.201644 GCTAGATGTAAAGCAAGTTAGCATTGA 60.202 37.037 0.00 0.00 38.63 2.57
1458 1472 6.462487 CCTTTACCGGATCTTGCTAGATGTAA 60.462 42.308 15.60 13.62 41.23 2.41
1487 1501 7.160049 ACAAGTAAACCTAGTAAAGAAGGCTC 58.840 38.462 0.00 0.00 36.24 4.70
1498 1512 4.836736 TCTGGCACTACAAGTAAACCTAGT 59.163 41.667 0.00 0.00 0.00 2.57
1499 1513 5.401531 TCTGGCACTACAAGTAAACCTAG 57.598 43.478 0.00 0.00 0.00 3.02
1501 1515 4.141574 TGTTCTGGCACTACAAGTAAACCT 60.142 41.667 0.00 0.00 0.00 3.50
1502 1516 4.131596 TGTTCTGGCACTACAAGTAAACC 58.868 43.478 0.00 0.00 0.00 3.27
1504 1518 5.031066 ACTGTTCTGGCACTACAAGTAAA 57.969 39.130 0.00 0.00 0.00 2.01
1520 1538 5.290643 TGCACTTTAACAAATGCAACTGTTC 59.709 36.000 17.30 5.97 44.72 3.18
1529 1547 3.184986 GCTGGCTTGCACTTTAACAAATG 59.815 43.478 0.00 0.00 0.00 2.32
1537 1555 0.760572 AAATGGCTGGCTTGCACTTT 59.239 45.000 2.00 2.21 34.04 2.66
1552 1570 1.193644 CGCGCATTCACCATCAAATG 58.806 50.000 8.75 0.00 36.24 2.32
1595 1618 4.899898 AAAAATAGGGAATGGCCTAGGT 57.100 40.909 11.31 0.00 36.66 3.08
1596 1619 5.325239 CCTAAAAATAGGGAATGGCCTAGG 58.675 45.833 3.67 3.67 36.66 3.02
1601 1624 2.632996 GGGCCTAAAAATAGGGAATGGC 59.367 50.000 0.84 0.00 37.69 4.40
1605 1628 8.461033 ACATAATATGGGCCTAAAAATAGGGAA 58.539 33.333 4.53 0.00 34.56 3.97
1606 1629 8.006967 ACATAATATGGGCCTAAAAATAGGGA 57.993 34.615 4.53 0.00 34.56 4.20
1608 1631 8.531146 CCAACATAATATGGGCCTAAAAATAGG 58.469 37.037 4.53 0.00 36.00 2.57
1609 1632 9.088987 ACCAACATAATATGGGCCTAAAAATAG 57.911 33.333 4.53 0.00 41.17 1.73
1611 1634 7.929348 ACCAACATAATATGGGCCTAAAAAT 57.071 32.000 4.53 0.00 41.17 1.82
1612 1635 8.865090 CATACCAACATAATATGGGCCTAAAAA 58.135 33.333 4.53 0.00 41.17 1.94
1620 1657 7.255801 GGGTTTCACATACCAACATAATATGGG 60.256 40.741 5.16 0.00 41.17 4.00
1621 1658 7.286546 TGGGTTTCACATACCAACATAATATGG 59.713 37.037 5.16 0.00 42.60 2.74
1656 1714 9.829507 ATAACCAAATGAATGACAAAACTGAAA 57.170 25.926 0.00 0.00 0.00 2.69
1699 1784 6.993175 CTAGATGAGCATGCAAATTGATTG 57.007 37.500 21.98 0.00 42.21 2.67
1806 1893 8.773033 AATGCTTAATTCTGGTCTCCATTAAT 57.227 30.769 0.00 0.00 30.82 1.40
1808 1895 9.866655 ATAAATGCTTAATTCTGGTCTCCATTA 57.133 29.630 0.00 0.00 30.82 1.90
1812 1899 9.732130 AGATATAAATGCTTAATTCTGGTCTCC 57.268 33.333 0.00 0.00 0.00 3.71
1850 1937 3.266772 AGAGCCTATTGGGTGATGTCAAA 59.733 43.478 1.62 0.00 45.24 2.69
1868 1955 1.474478 TCTCACCGAGATCAACAGAGC 59.526 52.381 0.00 0.00 33.35 4.09
1882 1969 5.438761 ACAAAGTTAGCAACAATCTCACC 57.561 39.130 0.00 0.00 0.00 4.02
1891 1978 5.108254 CGAATTGAGCAACAAAGTTAGCAAC 60.108 40.000 0.86 0.00 42.03 4.17
1892 1979 4.975502 CGAATTGAGCAACAAAGTTAGCAA 59.024 37.500 0.86 0.00 42.03 3.91
1893 1980 4.036262 ACGAATTGAGCAACAAAGTTAGCA 59.964 37.500 0.00 0.00 42.03 3.49
1894 1981 4.537015 ACGAATTGAGCAACAAAGTTAGC 58.463 39.130 0.00 0.00 42.03 3.09
1895 1982 7.518161 TCATACGAATTGAGCAACAAAGTTAG 58.482 34.615 0.00 0.00 42.03 2.34
1896 1983 7.428282 TCATACGAATTGAGCAACAAAGTTA 57.572 32.000 0.00 0.00 42.03 2.24
1897 1984 6.312399 TCATACGAATTGAGCAACAAAGTT 57.688 33.333 0.00 0.00 42.03 2.66
1898 1985 5.940192 TCATACGAATTGAGCAACAAAGT 57.060 34.783 0.00 4.88 42.03 2.66
1899 1986 5.284660 GCTTCATACGAATTGAGCAACAAAG 59.715 40.000 0.00 0.00 42.03 2.77
1900 1987 5.153513 GCTTCATACGAATTGAGCAACAAA 58.846 37.500 0.00 0.00 42.03 2.83
1901 1988 4.215185 TGCTTCATACGAATTGAGCAACAA 59.785 37.500 0.00 0.00 42.95 2.83
1902 1989 3.750652 TGCTTCATACGAATTGAGCAACA 59.249 39.130 0.00 0.00 30.07 3.33
1915 2002 4.261801 ACCCACAACAGTATGCTTCATAC 58.738 43.478 8.49 8.49 44.81 2.39
1924 2011 4.985538 ACATCTGAAACCCACAACAGTAT 58.014 39.130 0.00 0.00 0.00 2.12
1928 2015 5.937540 CAGTATACATCTGAAACCCACAACA 59.062 40.000 5.50 0.00 35.20 3.33
1980 2067 6.126409 AGAAACACCAATCTGAGTACCAAAA 58.874 36.000 0.00 0.00 0.00 2.44
2011 2098 5.063060 GCCTGTACAACTAAAACCTGTATCG 59.937 44.000 0.00 0.00 0.00 2.92
2038 2125 2.290641 GTCGAATTATTTGGCGCCTCAT 59.709 45.455 29.70 20.97 0.00 2.90
2060 2147 2.219674 CGGCTCTGATTGAATTACGCTC 59.780 50.000 0.00 0.00 0.00 5.03
2067 2154 1.524621 CCGCCGGCTCTGATTGAAT 60.525 57.895 26.68 0.00 0.00 2.57
2078 2165 4.884257 TTACTCGCATCCGCCGGC 62.884 66.667 19.07 19.07 33.11 6.13
2081 2168 1.860676 TATTGTTACTCGCATCCGCC 58.139 50.000 0.00 0.00 33.11 6.13
2105 2192 5.440610 CTTGGGATAGCCAAAGTATCACTT 58.559 41.667 5.94 0.00 39.93 3.16
2112 2199 1.064389 GGAGCTTGGGATAGCCAAAGT 60.064 52.381 15.59 2.72 45.58 2.66
2186 2273 2.949451 AGAGTGCGTATCAGAACAGG 57.051 50.000 0.00 0.00 0.00 4.00
2198 2285 2.159310 CCTTGTCTAGAGGAAGAGTGCG 60.159 54.545 11.51 0.00 36.33 5.34
2202 2289 4.243793 TCTCCCTTGTCTAGAGGAAGAG 57.756 50.000 11.51 6.68 36.33 2.85
2215 2302 2.787994 AGCACACTGATTTCTCCCTTG 58.212 47.619 0.00 0.00 0.00 3.61
2245 2332 5.191921 AGTTAGGCAGCTAAAGACCCTAATT 59.808 40.000 0.00 0.00 39.53 1.40
2263 2350 4.720273 AGATACCCCTTGGTTACAGTTAGG 59.280 45.833 0.00 0.00 44.75 2.69
2276 2363 5.623551 TCATGAGATAGGAGATACCCCTT 57.376 43.478 0.00 0.00 40.05 3.95
2295 2384 1.097547 GGCCTACAGCGCAACATCAT 61.098 55.000 11.47 0.00 45.17 2.45
2316 2405 4.064388 TGATGAAGACAAGCAATTCGTCA 58.936 39.130 5.25 5.25 43.28 4.35
2317 2406 4.668576 TGATGAAGACAAGCAATTCGTC 57.331 40.909 0.00 0.00 38.75 4.20
2320 2409 6.309737 GGTTCAATGATGAAGACAAGCAATTC 59.690 38.462 0.00 0.00 45.88 2.17
2362 2451 5.393962 ACGATGTTAGAAGCAAATTTCTGC 58.606 37.500 0.00 0.00 42.97 4.26
2363 2452 7.077605 TGAACGATGTTAGAAGCAAATTTCTG 58.922 34.615 0.00 0.00 37.91 3.02
2364 2453 7.202016 TGAACGATGTTAGAAGCAAATTTCT 57.798 32.000 0.00 0.00 40.39 2.52
2366 2455 8.641499 TTTTGAACGATGTTAGAAGCAAATTT 57.359 26.923 0.00 0.00 0.00 1.82
2367 2456 8.134895 TCTTTTGAACGATGTTAGAAGCAAATT 58.865 29.630 0.00 0.00 0.00 1.82
2368 2457 7.648142 TCTTTTGAACGATGTTAGAAGCAAAT 58.352 30.769 0.00 0.00 0.00 2.32
2370 2459 6.612247 TCTTTTGAACGATGTTAGAAGCAA 57.388 33.333 0.00 0.00 0.00 3.91
2371 2460 6.426633 TCATCTTTTGAACGATGTTAGAAGCA 59.573 34.615 9.22 0.00 38.47 3.91
2372 2461 6.831769 TCATCTTTTGAACGATGTTAGAAGC 58.168 36.000 9.22 0.00 38.47 3.86
2373 2462 9.663904 TTTTCATCTTTTGAACGATGTTAGAAG 57.336 29.630 9.22 0.00 43.99 2.85
2403 2627 6.096846 GGAGTACAAATGATGTGCCCTTTAAT 59.903 38.462 0.00 0.00 44.84 1.40
2494 2720 4.591321 AACCTGCTCATTTCCCAGATAA 57.409 40.909 0.00 0.00 0.00 1.75
2512 2738 0.673985 GCCCACACTGGAAAGAAACC 59.326 55.000 0.00 0.00 40.96 3.27
2542 2769 1.746787 TCCAATGACATCATGCTGCAC 59.253 47.619 3.57 0.00 36.56 4.57
2568 2795 2.522185 AGCCATTCAGTGAAATGCTGT 58.478 42.857 23.89 8.23 35.68 4.40
2603 2831 6.719370 TGAAGTTGATAAAGCACCCAACTATT 59.281 34.615 0.00 0.00 45.71 1.73
2738 2966 2.107726 GAGTGGTACCCCAAAAGGAAGT 59.892 50.000 10.07 0.00 44.15 3.01
2810 3038 7.106239 CACACAGATTACTACTTGGGATTCTT 58.894 38.462 0.00 0.00 0.00 2.52
2942 3189 8.853077 TGAATAATTGGGCAGACAGATATTAG 57.147 34.615 0.00 0.00 0.00 1.73
2952 3199 7.574021 ACTATCCTATGAATAATTGGGCAGA 57.426 36.000 0.00 0.00 32.49 4.26
2968 3215 9.822727 TCAACCAGTCATATCAATACTATCCTA 57.177 33.333 0.00 0.00 0.00 2.94
2969 3216 8.589338 GTCAACCAGTCATATCAATACTATCCT 58.411 37.037 0.00 0.00 0.00 3.24
2970 3217 8.589338 AGTCAACCAGTCATATCAATACTATCC 58.411 37.037 0.00 0.00 0.00 2.59
2973 3220 9.642343 AGTAGTCAACCAGTCATATCAATACTA 57.358 33.333 0.00 0.00 0.00 1.82
2974 3221 8.417106 CAGTAGTCAACCAGTCATATCAATACT 58.583 37.037 0.00 0.00 0.00 2.12
2975 3222 8.198109 ACAGTAGTCAACCAGTCATATCAATAC 58.802 37.037 0.00 0.00 0.00 1.89
2995 3250 7.598278 AGAACAGTGATTACTTCTGACAGTAG 58.402 38.462 7.49 7.49 34.07 2.57
3015 3270 5.321927 TGACCAGTCTATCTGTGTAGAACA 58.678 41.667 0.00 0.00 42.19 3.18
3045 3300 6.161855 AGATAATGTTAGAACGATGCCTGA 57.838 37.500 0.00 0.00 0.00 3.86
3049 3304 6.257849 TGACCAAGATAATGTTAGAACGATGC 59.742 38.462 0.00 0.00 0.00 3.91
3053 3308 5.575606 ACGTGACCAAGATAATGTTAGAACG 59.424 40.000 0.00 0.00 0.00 3.95
3054 3309 6.812160 AGACGTGACCAAGATAATGTTAGAAC 59.188 38.462 0.00 0.00 0.00 3.01
3074 3329 6.451064 AATCCAAAAAGAGTTTGAAGACGT 57.549 33.333 0.00 0.00 0.00 4.34
3076 3331 9.965824 TTCATAATCCAAAAAGAGTTTGAAGAC 57.034 29.630 0.44 0.00 30.49 3.01
3083 3338 7.765695 TGAGCTTCATAATCCAAAAAGAGTT 57.234 32.000 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.