Multiple sequence alignment - TraesCS6A01G359600

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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 TraesCS6A01G359600 chr6A 100.000 6500 0 0 1 6500 591025481 591018982 0.000000e+00 12004.0
1 TraesCS6A01G359600 chr6A 87.508 1505 167 12 789 2288 223555287 223556775 0.000000e+00 1718.0
2 TraesCS6A01G359600 chr6A 92.041 980 67 5 3938 4912 223556771 223557744 0.000000e+00 1367.0
3 TraesCS6A01G359600 chr6A 92.857 700 44 4 4908 5603 223560010 223560707 0.000000e+00 1011.0
4 TraesCS6A01G359600 chr6B 93.897 2589 124 16 3938 6500 667779899 667777319 0.000000e+00 3875.0
5 TraesCS6A01G359600 chr6B 91.194 1851 131 17 3940 5770 298822172 298820334 0.000000e+00 2486.0
6 TraesCS6A01G359600 chr6B 95.000 1580 64 6 710 2288 667781460 667779895 0.000000e+00 2466.0
7 TraesCS6A01G359600 chr6B 87.911 1580 169 13 713 2288 298824093 298822532 0.000000e+00 1840.0
8 TraesCS6A01G359600 chr6B 81.522 92 13 4 6285 6374 557930323 557930412 9.040000e-09 73.1
9 TraesCS6A01G359600 chr6D 91.347 1849 132 15 3938 5770 163336325 163338161 0.000000e+00 2503.0
10 TraesCS6A01G359600 chr6D 94.557 1580 71 6 710 2288 441769968 441768403 0.000000e+00 2427.0
11 TraesCS6A01G359600 chr6D 86.155 1459 164 18 832 2288 163334907 163336329 0.000000e+00 1541.0
12 TraesCS6A01G359600 chr6D 93.832 843 38 5 3938 4774 441768407 441767573 0.000000e+00 1256.0
13 TraesCS6A01G359600 chr6D 97.430 428 11 0 5096 5523 441759830 441759403 0.000000e+00 730.0
14 TraesCS6A01G359600 chr6D 93.677 427 12 3 5518 5944 441754423 441754012 5.530000e-175 625.0
15 TraesCS6A01G359600 chr6D 94.751 362 6 5 5988 6336 441752015 441751654 9.530000e-153 551.0
16 TraesCS6A01G359600 chr6D 96.226 318 12 0 4786 5103 441765296 441764979 7.470000e-144 521.0
17 TraesCS6A01G359600 chr6D 96.386 166 6 0 6335 6500 441751494 441751329 2.310000e-69 274.0
18 TraesCS6A01G359600 chr2D 93.430 1659 97 7 2291 3939 279190252 279191908 0.000000e+00 2449.0
19 TraesCS6A01G359600 chr5D 93.414 1655 99 3 2289 3937 356310468 356312118 0.000000e+00 2444.0
20 TraesCS6A01G359600 chr5D 93.353 1655 103 3 2289 3937 311428323 311426670 0.000000e+00 2440.0
21 TraesCS6A01G359600 chr5D 93.060 1657 107 4 2289 3939 96325534 96327188 0.000000e+00 2416.0
22 TraesCS6A01G359600 chr5D 86.538 52 5 2 6324 6374 91340884 91340934 1.000000e-03 56.5
23 TraesCS6A01G359600 chr1D 93.237 1656 103 5 2289 3937 159138304 159136651 0.000000e+00 2429.0
24 TraesCS6A01G359600 chr1D 93.168 1654 106 3 2289 3937 430228210 430226559 0.000000e+00 2422.0
25 TraesCS6A01G359600 chr1D 82.418 91 14 2 6288 6377 376862102 376862013 1.940000e-10 78.7
26 TraesCS6A01G359600 chr3D 93.056 1656 106 5 2289 3935 394902419 394904074 0.000000e+00 2412.0
27 TraesCS6A01G359600 chr3D 92.775 1661 112 4 2289 3942 342694127 342692468 0.000000e+00 2396.0
28 TraesCS6A01G359600 chr4D 92.892 1660 108 5 2289 3939 211392268 211393926 0.000000e+00 2403.0
29 TraesCS6A01G359600 chr5A 95.506 712 29 1 1 709 415436231 415435520 0.000000e+00 1134.0
30 TraesCS6A01G359600 chr5A 94.944 712 33 1 1 709 484488761 484488050 0.000000e+00 1112.0
31 TraesCS6A01G359600 chr5A 94.467 723 37 1 1 720 151322600 151321878 0.000000e+00 1110.0
32 TraesCS6A01G359600 chr3A 94.993 719 33 1 2 717 371035757 371035039 0.000000e+00 1125.0
33 TraesCS6A01G359600 chr7A 95.091 713 32 1 1 710 566231924 566231212 0.000000e+00 1120.0
34 TraesCS6A01G359600 chr7A 94.872 39 2 0 6336 6374 288066261 288066223 1.960000e-05 62.1
35 TraesCS6A01G359600 chr4A 95.084 712 32 1 1 709 358274507 358275218 0.000000e+00 1118.0
36 TraesCS6A01G359600 chr4A 94.730 721 35 1 1 718 630937797 630937077 0.000000e+00 1118.0
37 TraesCS6A01G359600 chr4A 94.944 712 33 1 1 709 143735006 143735717 0.000000e+00 1112.0
38 TraesCS6A01G359600 chr1A 94.944 712 33 1 1 709 557213033 557213744 0.000000e+00 1112.0


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 TraesCS6A01G359600 chr6A 591018982 591025481 6499 True 12004.000000 12004 100.000000 1 6500 1 chr6A.!!$R1 6499
1 TraesCS6A01G359600 chr6A 223555287 223560707 5420 False 1365.333333 1718 90.802000 789 5603 3 chr6A.!!$F1 4814
2 TraesCS6A01G359600 chr6B 667777319 667781460 4141 True 3170.500000 3875 94.448500 710 6500 2 chr6B.!!$R2 5790
3 TraesCS6A01G359600 chr6B 298820334 298824093 3759 True 2163.000000 2486 89.552500 713 5770 2 chr6B.!!$R1 5057
4 TraesCS6A01G359600 chr6D 163334907 163338161 3254 False 2022.000000 2503 88.751000 832 5770 2 chr6D.!!$F1 4938
5 TraesCS6A01G359600 chr6D 441764979 441769968 4989 True 1401.333333 2427 94.871667 710 5103 3 chr6D.!!$R3 4393
6 TraesCS6A01G359600 chr6D 441751329 441754423 3094 True 483.333333 625 94.938000 5518 6500 3 chr6D.!!$R2 982
7 TraesCS6A01G359600 chr2D 279190252 279191908 1656 False 2449.000000 2449 93.430000 2291 3939 1 chr2D.!!$F1 1648
8 TraesCS6A01G359600 chr5D 356310468 356312118 1650 False 2444.000000 2444 93.414000 2289 3937 1 chr5D.!!$F3 1648
9 TraesCS6A01G359600 chr5D 311426670 311428323 1653 True 2440.000000 2440 93.353000 2289 3937 1 chr5D.!!$R1 1648
10 TraesCS6A01G359600 chr5D 96325534 96327188 1654 False 2416.000000 2416 93.060000 2289 3939 1 chr5D.!!$F2 1650
11 TraesCS6A01G359600 chr1D 159136651 159138304 1653 True 2429.000000 2429 93.237000 2289 3937 1 chr1D.!!$R1 1648
12 TraesCS6A01G359600 chr1D 430226559 430228210 1651 True 2422.000000 2422 93.168000 2289 3937 1 chr1D.!!$R3 1648
13 TraesCS6A01G359600 chr3D 394902419 394904074 1655 False 2412.000000 2412 93.056000 2289 3935 1 chr3D.!!$F1 1646
14 TraesCS6A01G359600 chr3D 342692468 342694127 1659 True 2396.000000 2396 92.775000 2289 3942 1 chr3D.!!$R1 1653
15 TraesCS6A01G359600 chr4D 211392268 211393926 1658 False 2403.000000 2403 92.892000 2289 3939 1 chr4D.!!$F1 1650
16 TraesCS6A01G359600 chr5A 415435520 415436231 711 True 1134.000000 1134 95.506000 1 709 1 chr5A.!!$R2 708
17 TraesCS6A01G359600 chr5A 484488050 484488761 711 True 1112.000000 1112 94.944000 1 709 1 chr5A.!!$R3 708
18 TraesCS6A01G359600 chr5A 151321878 151322600 722 True 1110.000000 1110 94.467000 1 720 1 chr5A.!!$R1 719
19 TraesCS6A01G359600 chr3A 371035039 371035757 718 True 1125.000000 1125 94.993000 2 717 1 chr3A.!!$R1 715
20 TraesCS6A01G359600 chr7A 566231212 566231924 712 True 1120.000000 1120 95.091000 1 710 1 chr7A.!!$R2 709
21 TraesCS6A01G359600 chr4A 358274507 358275218 711 False 1118.000000 1118 95.084000 1 709 1 chr4A.!!$F2 708
22 TraesCS6A01G359600 chr4A 630937077 630937797 720 True 1118.000000 1118 94.730000 1 718 1 chr4A.!!$R1 717
23 TraesCS6A01G359600 chr4A 143735006 143735717 711 False 1112.000000 1112 94.944000 1 709 1 chr4A.!!$F1 708
24 TraesCS6A01G359600 chr1A 557213033 557213744 711 False 1112.000000 1112 94.944000 1 709 1 chr1A.!!$F1 708

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
912 919 0.639392 AGATACTGGGGGAGCTCACT 59.361 55.000 17.22 0.0 0.00 3.41 F
1534 1542 0.249911 AGCCTCTTGGTCGTGACAAC 60.250 55.000 2.00 0.0 35.27 3.32 F
1558 1566 0.616679 ATGCTGCAAGGCCCAATTCT 60.617 50.000 6.36 0.0 0.00 2.40 F
3208 3231 0.969894 GGATTCTCGATGGGACCGAT 59.030 55.000 0.00 0.0 35.35 4.18 F
4202 4593 1.003118 TCACCTCACAGGGGAAATTCG 59.997 52.381 0.00 0.0 46.82 3.34 F
4723 5120 0.178533 GCATCTCAAGCTCAGAGGCT 59.821 55.000 19.77 0.0 42.98 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1778 1786 1.064758 AGATTCGGCAGCAACCCAATA 60.065 47.619 0.00 0.00 0.00 1.90 R
3208 3231 0.899720 GTCCCACCGAGTTGACCATA 59.100 55.000 0.00 0.00 0.00 2.74 R
3389 3414 1.463056 CCGAGTTCGCAATGCAAACTA 59.537 47.619 11.90 0.00 38.18 2.24 R
4507 4898 0.770499 TGCCACTTCCAATCCAGTGA 59.230 50.000 0.79 0.00 42.74 3.41 R
5348 10286 0.174389 ACAGATCACACCTAGCGCAG 59.826 55.000 11.47 4.88 0.00 5.18 R
6457 13540 0.829990 TCAATACGCCTGCTGATCCA 59.170 50.000 0.00 0.00 0.00 3.41 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
509 513 3.194968 ACCCTCCGATTTATATAGGCACG 59.805 47.826 0.00 0.00 0.00 5.34
528 532 1.769295 GGAGGGGGCTAGGGTTACC 60.769 68.421 0.00 0.00 0.00 2.85
646 650 8.564574 GTCTTCAATCTCGTATCTTCATAGTCT 58.435 37.037 0.00 0.00 0.00 3.24
762 766 4.817318 TTTTCAACCCAAAAGCTTCTGT 57.183 36.364 0.00 0.00 0.00 3.41
771 775 4.326826 CCAAAAGCTTCTGTAGACATGGA 58.673 43.478 0.00 0.00 0.00 3.41
773 777 5.163683 CCAAAAGCTTCTGTAGACATGGATG 60.164 44.000 0.00 0.00 0.00 3.51
834 841 6.599638 GCACTGATTTCTCTACTACCCAAATT 59.400 38.462 0.00 0.00 0.00 1.82
849 856 4.156477 CCCAAATTTTACCCAGAGTCCAA 58.844 43.478 0.00 0.00 0.00 3.53
912 919 0.639392 AGATACTGGGGGAGCTCACT 59.361 55.000 17.22 0.00 0.00 3.41
957 964 1.649321 TCCTCTGACCACTGCAGATT 58.351 50.000 23.35 3.09 41.20 2.40
1087 1095 1.616865 TGGACCTCTCCTACAACAACG 59.383 52.381 0.00 0.00 37.48 4.10
1088 1096 1.672145 GGACCTCTCCTACAACAACGC 60.672 57.143 0.00 0.00 33.07 4.84
1122 1130 8.768397 TCATTCCCTACAATACTCTACAATTGT 58.232 33.333 16.68 16.68 45.66 2.71
1250 1258 4.116238 TCAACGTATCAAGCAATCGCATA 58.884 39.130 0.00 0.00 42.27 3.14
1252 1260 4.452890 ACGTATCAAGCAATCGCATAAC 57.547 40.909 0.00 0.00 42.27 1.89
1256 1264 0.732571 CAAGCAATCGCATAACGGGT 59.267 50.000 0.00 0.00 43.89 5.28
1384 1392 1.387539 CTCGAGATGCTGACTCTGGA 58.612 55.000 6.58 0.00 32.87 3.86
1414 1422 2.592102 TTTCTGCCAGCTCCATTTCT 57.408 45.000 0.00 0.00 0.00 2.52
1438 1446 2.441410 TGAGTTTGGCAAGTTGACACA 58.559 42.857 12.03 0.97 33.32 3.72
1476 1484 3.595173 CTGTCGGGTATGAACATGACAA 58.405 45.455 0.00 0.00 39.38 3.18
1507 1515 3.008157 CCTGAGAGCATATCAAGCCTCAT 59.992 47.826 0.00 0.00 38.06 2.90
1525 1533 1.761784 CATAGAGCTCAGCCTCTTGGT 59.238 52.381 17.77 0.00 42.07 3.67
1534 1542 0.249911 AGCCTCTTGGTCGTGACAAC 60.250 55.000 2.00 0.00 35.27 3.32
1551 1559 2.689983 ACAACTAATATGCTGCAAGGCC 59.310 45.455 6.36 0.00 0.00 5.19
1558 1566 0.616679 ATGCTGCAAGGCCCAATTCT 60.617 50.000 6.36 0.00 0.00 2.40
1573 1581 2.260844 ATTCTGACATGGGTATGGCG 57.739 50.000 0.00 0.00 45.81 5.69
1610 1618 7.966246 TCGGTACTTGTACATGTTTAACAAT 57.034 32.000 18.38 6.63 33.01 2.71
1620 1628 8.251026 TGTACATGTTTAACAATGGTTTGACAA 58.749 29.630 2.30 0.00 38.45 3.18
1654 1662 1.792949 CAGTGTCACAGCCGTAAACTC 59.207 52.381 5.62 0.00 0.00 3.01
1689 1697 6.942005 TGATGTGTCCTCAAACAATCTAACAT 59.058 34.615 0.00 0.00 0.00 2.71
1718 1726 3.679389 ACCAGATGACTTTGGTAAGCTG 58.321 45.455 0.00 0.00 45.58 4.24
1742 1750 5.633655 TCAACCTTACCCTGTTGTTTCTA 57.366 39.130 0.00 0.00 41.92 2.10
1747 1755 7.266905 ACCTTACCCTGTTGTTTCTATACAT 57.733 36.000 0.00 0.00 0.00 2.29
1748 1756 7.696017 ACCTTACCCTGTTGTTTCTATACATT 58.304 34.615 0.00 0.00 0.00 2.71
1935 1943 2.413765 CCAGCTGATCTTTGCTTCAACG 60.414 50.000 17.39 0.00 37.44 4.10
1959 1967 5.288472 GGGAAATTAAATGACATCGTTGTGC 59.712 40.000 3.34 0.00 35.79 4.57
1977 1985 9.210329 TCGTTGTGCTCAATAATAACTTTTCTA 57.790 29.630 4.26 0.00 35.92 2.10
2003 2011 1.405821 CTTCCAGAATCGCTAGACGGT 59.594 52.381 0.00 0.00 43.89 4.83
2163 2171 4.019174 CCAGCTACCATGGAACTTTTCAT 58.981 43.478 21.47 0.00 40.51 2.57
2214 2222 3.245586 TGGTCCCATTCCAACTTTAGCAT 60.246 43.478 0.00 0.00 31.50 3.79
2269 2277 2.225242 TGCTTTCTGGCCAAATTCCCTA 60.225 45.455 7.01 0.00 0.00 3.53
2293 2301 3.410631 TTTGACGGGCATTTCTGTAGA 57.589 42.857 0.00 0.00 0.00 2.59
2384 2395 9.643693 CAATTTTATGTCTTGGCAGATTTTAGT 57.356 29.630 0.00 0.00 0.00 2.24
2449 2460 2.164624 AGAGTGTAGCAGCGGAAAGTAG 59.835 50.000 0.00 0.00 0.00 2.57
2457 2468 2.484264 GCAGCGGAAAGTAGAACATTGT 59.516 45.455 0.00 0.00 0.00 2.71
2752 2765 2.158755 ACTCCTTGGTTCAACTCCACAG 60.159 50.000 0.00 0.00 34.45 3.66
2820 2834 5.875359 CACCACTCTCCAAAAGGTAATAGAC 59.125 44.000 0.00 0.00 0.00 2.59
2892 2908 3.305950 CCCAACACTCAACTCTCTCTCAG 60.306 52.174 0.00 0.00 0.00 3.35
2977 2994 4.338879 AGATTCTTGTGGTTGGATTGGAG 58.661 43.478 0.00 0.00 0.00 3.86
3082 3100 3.491766 TGAATAGAGAAGGGGTGGAGT 57.508 47.619 0.00 0.00 0.00 3.85
3102 3120 5.720041 GGAGTGGTATATATAGCCTCCACAA 59.280 44.000 30.46 10.94 45.06 3.33
3127 3145 5.523438 AATCCAACCGTTACACACATTTT 57.477 34.783 0.00 0.00 0.00 1.82
3128 3146 4.985538 TCCAACCGTTACACACATTTTT 57.014 36.364 0.00 0.00 0.00 1.94
3145 3163 4.503714 TTTTTCCCAACTCAGTCAGACT 57.496 40.909 0.00 0.00 0.00 3.24
3208 3231 0.969894 GGATTCTCGATGGGACCGAT 59.030 55.000 0.00 0.00 35.35 4.18
3212 3235 1.545841 TCTCGATGGGACCGATATGG 58.454 55.000 0.00 0.00 46.41 2.74
3308 3332 3.055891 TGAGACCGATTTCAGCAATGAGA 60.056 43.478 0.00 0.00 0.00 3.27
3389 3414 3.672767 ACGTTACGAAGGGAAACAGAT 57.327 42.857 13.03 0.00 0.00 2.90
3497 3522 2.656002 TCTCGGTGAGATCGAAATCCT 58.344 47.619 0.00 0.00 33.35 3.24
3527 3552 5.414765 GTGAGACCGAATTGATTAGGGTTTT 59.585 40.000 7.61 0.00 36.94 2.43
3562 3587 3.178540 AAAGGAACTCGGTGGCGCT 62.179 57.895 7.64 0.00 38.49 5.92
3585 3611 1.507140 TAGATCAAATCGGTGGGGCT 58.493 50.000 0.00 0.00 0.00 5.19
3629 3656 8.055279 TGGACATATTTGGAAATGAGAAAGTC 57.945 34.615 0.00 0.00 0.00 3.01
3743 3771 3.942829 TGGACTCAATGTGATCTTGGAC 58.057 45.455 0.00 0.00 0.00 4.02
3750 3778 5.491070 TCAATGTGATCTTGGACCACTAAG 58.509 41.667 0.00 0.00 36.22 2.18
3791 3819 2.416747 GCTTTTGCCAATCTTTGTCCC 58.583 47.619 0.00 0.00 40.15 4.46
3803 3831 6.127253 CCAATCTTTGTCCCTAGCATTTTGAT 60.127 38.462 0.00 0.00 0.00 2.57
3816 3844 3.196254 GCATTTTGATGGGTCCACATCTT 59.804 43.478 10.65 0.00 45.78 2.40
3845 3873 2.166870 TGCCATGCCAATCATTGAACTC 59.833 45.455 0.00 0.00 31.79 3.01
3846 3874 2.482490 GCCATGCCAATCATTGAACTCC 60.482 50.000 0.00 0.00 31.79 3.85
3939 3967 4.082245 CGGGGATTAGTTGCACTTTCAATT 60.082 41.667 0.00 0.00 0.00 2.32
3942 3970 6.454795 GGGATTAGTTGCACTTTCAATTTCA 58.545 36.000 0.00 0.00 0.00 2.69
3943 3971 7.099120 GGGATTAGTTGCACTTTCAATTTCAT 58.901 34.615 0.00 0.00 0.00 2.57
3968 4358 4.262678 GGTAGAAGAGCTTGACCTTTCTGT 60.263 45.833 0.00 0.00 0.00 3.41
4123 4514 2.744741 CTCTCCTCGAATGCGCTATCTA 59.255 50.000 9.73 0.00 37.46 1.98
4202 4593 1.003118 TCACCTCACAGGGGAAATTCG 59.997 52.381 0.00 0.00 46.82 3.34
4257 4648 1.673767 TCCTCTTCAATCCAGGCCTT 58.326 50.000 0.00 0.00 0.00 4.35
4290 4681 8.703743 TCATTGAATAATTCCATCCCGAATTTT 58.296 29.630 2.21 0.00 41.54 1.82
4452 4843 6.602410 CAAGATCCTCTATCATGGAAGCTA 57.398 41.667 0.00 0.00 37.03 3.32
4506 4897 1.742268 GATGTTCTTTCTGGGCTCTGC 59.258 52.381 0.00 0.00 0.00 4.26
4507 4898 0.767375 TGTTCTTTCTGGGCTCTGCT 59.233 50.000 0.00 0.00 0.00 4.24
4508 4899 1.271054 TGTTCTTTCTGGGCTCTGCTC 60.271 52.381 0.00 0.00 0.00 4.26
4563 4959 2.030363 GCCGAATTTGTGTTGTGGATGA 60.030 45.455 0.00 0.00 0.00 2.92
4689 5086 2.029649 AGATCCAGCACACAAACATTGC 60.030 45.455 0.00 0.00 36.45 3.56
4699 5096 2.937799 CACAAACATTGCCAAGTTGCTT 59.062 40.909 0.00 0.00 0.00 3.91
4723 5120 0.178533 GCATCTCAAGCTCAGAGGCT 59.821 55.000 19.77 0.00 42.98 4.58
4739 5136 4.081972 CAGAGGCTAAGCTTCTTGTCTACA 60.082 45.833 0.00 0.00 42.23 2.74
4780 7448 0.538584 TAGACAGGTGGCTGCATCAG 59.461 55.000 0.50 0.00 33.72 2.90
4781 7449 1.196766 AGACAGGTGGCTGCATCAGA 61.197 55.000 0.50 0.00 32.44 3.27
4782 7450 0.743701 GACAGGTGGCTGCATCAGAG 60.744 60.000 0.50 0.00 32.44 3.35
4783 7451 1.196766 ACAGGTGGCTGCATCAGAGA 61.197 55.000 0.50 0.00 32.44 3.10
4784 7452 0.462225 CAGGTGGCTGCATCAGAGAG 60.462 60.000 0.50 0.00 32.44 3.20
4785 7453 0.616964 AGGTGGCTGCATCAGAGAGA 60.617 55.000 0.50 0.00 32.44 3.10
4792 7460 2.292569 GCTGCATCAGAGAGAGAGAGAG 59.707 54.545 0.00 0.00 32.44 3.20
4842 7510 1.275856 GCCCACCAGATTGCAAATTGA 59.724 47.619 1.71 0.00 0.00 2.57
4994 9932 3.074412 GCTCGGATTCTTCTCAAAACCA 58.926 45.455 0.00 0.00 0.00 3.67
5113 10051 3.797039 TGTACCATGTGCTAATCAGAGC 58.203 45.455 0.00 0.00 43.16 4.09
5164 10102 4.565652 GGCTTAAGGTGAATGAGAAGGTCA 60.566 45.833 4.29 0.00 40.38 4.02
5211 10149 0.471780 TGGAGCTCACAACAGGGAGA 60.472 55.000 17.19 0.00 32.87 3.71
5380 10318 0.905357 GATCTGTACAGGTGGGCAGT 59.095 55.000 22.48 0.00 0.00 4.40
5427 10365 1.068748 GTGTTGTACGCTCTTCTCCGA 60.069 52.381 0.00 0.00 0.00 4.55
5431 10369 3.146618 TGTACGCTCTTCTCCGATTTC 57.853 47.619 0.00 0.00 0.00 2.17
5659 10603 2.224606 ACATGAAGCTTGTGGAGTGTG 58.775 47.619 2.10 0.00 0.00 3.82
5726 10679 6.885735 AAATGCATGCGGTTATTTTCTAAC 57.114 33.333 14.09 0.00 0.00 2.34
5838 10791 5.804639 TCTTAGAAGGCTAATCAAAGTGCA 58.195 37.500 0.00 0.00 36.10 4.57
5882 10837 9.159364 CTCATGAGAAGAAGTGACAATTATTGA 57.841 33.333 18.34 0.00 0.00 2.57
6398 13480 7.227873 TGTTTACATGTATGAAAGAACTCCCA 58.772 34.615 6.36 0.00 0.00 4.37
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 0.981183 AACTACACGGCCTTCATCCA 59.019 50.000 0.00 0.00 0.00 3.41
17 18 2.632987 AACTTGAACTACACGGCCTT 57.367 45.000 0.00 0.00 0.00 4.35
18 19 2.490991 GAAACTTGAACTACACGGCCT 58.509 47.619 0.00 0.00 0.00 5.19
204 208 2.890808 TGAGAGTTCCACTGTGTCAC 57.109 50.000 7.08 0.00 0.00 3.67
313 317 1.278127 CTGGGTAAACATCGTGTCCCT 59.722 52.381 11.76 0.00 36.23 4.20
399 403 5.354513 TCTCGTGGTAGATCAACTCTTGTAG 59.645 44.000 0.00 0.00 35.28 2.74
495 499 2.844348 CCCCTCCCGTGCCTATATAAAT 59.156 50.000 0.00 0.00 0.00 1.40
509 513 1.769295 GTAACCCTAGCCCCCTCCC 60.769 68.421 0.00 0.00 0.00 4.30
646 650 0.988832 ATCCTTTGGCCGGACTGTTA 59.011 50.000 9.82 0.00 32.41 2.41
762 766 6.946340 ACACAGTAATTGTCATCCATGTCTA 58.054 36.000 0.00 0.00 38.16 2.59
771 775 6.372659 CAGGAAGCTAACACAGTAATTGTCAT 59.627 38.462 0.00 0.00 38.16 3.06
773 777 5.390991 GCAGGAAGCTAACACAGTAATTGTC 60.391 44.000 0.00 0.00 37.96 3.18
834 841 5.701224 ACTGATTTTTGGACTCTGGGTAAA 58.299 37.500 0.00 0.00 0.00 2.01
849 856 8.862325 TTGGTGTTCATCACTATACTGATTTT 57.138 30.769 0.00 0.00 45.50 1.82
883 890 2.359781 CCCCCAGTATCTCTTGAGTCCT 60.360 54.545 0.00 0.00 0.00 3.85
912 919 0.961019 GTTCCATCTGCCAAGCACAA 59.039 50.000 0.00 0.00 33.79 3.33
957 964 1.357137 TGTGCATGTAAGTCCTCCCA 58.643 50.000 0.00 0.00 0.00 4.37
1087 1095 1.559682 TGTAGGGAATGAAGTGGAGGC 59.440 52.381 0.00 0.00 0.00 4.70
1088 1096 4.510167 ATTGTAGGGAATGAAGTGGAGG 57.490 45.455 0.00 0.00 0.00 4.30
1122 1130 5.098663 AGGTCCAGGTACTTTAGATTGGAA 58.901 41.667 0.00 0.00 34.60 3.53
1191 1199 7.643528 TTGCTTATAAGATGACGCTGATAAG 57.356 36.000 16.85 0.00 32.48 1.73
1197 1205 4.446371 AGCTTTGCTTATAAGATGACGCT 58.554 39.130 16.85 12.39 33.89 5.07
1198 1206 4.802876 AGCTTTGCTTATAAGATGACGC 57.197 40.909 16.85 10.52 33.89 5.19
1199 1207 6.128956 GCTCTAGCTTTGCTTATAAGATGACG 60.129 42.308 16.85 1.44 40.44 4.35
1200 1208 6.128956 CGCTCTAGCTTTGCTTATAAGATGAC 60.129 42.308 16.85 0.00 40.44 3.06
1201 1209 5.923114 CGCTCTAGCTTTGCTTATAAGATGA 59.077 40.000 16.85 0.00 40.44 2.92
1202 1210 5.694006 ACGCTCTAGCTTTGCTTATAAGATG 59.306 40.000 16.85 3.81 40.44 2.90
1203 1211 5.848406 ACGCTCTAGCTTTGCTTATAAGAT 58.152 37.500 16.85 0.00 40.44 2.40
1204 1212 5.067936 AGACGCTCTAGCTTTGCTTATAAGA 59.932 40.000 16.85 0.00 40.44 2.10
1205 1213 5.285651 AGACGCTCTAGCTTTGCTTATAAG 58.714 41.667 8.20 8.20 40.44 1.73
1206 1214 5.163550 TGAGACGCTCTAGCTTTGCTTATAA 60.164 40.000 0.00 0.00 40.44 0.98
1207 1215 4.338400 TGAGACGCTCTAGCTTTGCTTATA 59.662 41.667 0.00 0.00 40.44 0.98
1208 1216 3.131223 TGAGACGCTCTAGCTTTGCTTAT 59.869 43.478 0.00 0.00 40.44 1.73
1209 1217 2.492088 TGAGACGCTCTAGCTTTGCTTA 59.508 45.455 0.00 0.00 40.44 3.09
1210 1218 1.273606 TGAGACGCTCTAGCTTTGCTT 59.726 47.619 0.00 0.00 40.44 3.91
1225 1233 3.542291 GCGATTGCTTGATACGTTGAGAC 60.542 47.826 0.00 0.00 38.39 3.36
1233 1241 3.363970 CCCGTTATGCGATTGCTTGATAC 60.364 47.826 6.47 0.45 44.77 2.24
1256 1264 2.749600 CCAATGGATGGTGGGATTTCA 58.250 47.619 0.00 0.00 44.85 2.69
1290 1298 3.092301 TGTCGAGGATCAGTGACTTGAT 58.908 45.455 0.00 0.00 40.40 2.57
1384 1392 0.482446 TGGCAGAAATGGGTTGTCCT 59.518 50.000 0.00 0.00 36.20 3.85
1414 1422 4.095782 GTGTCAACTTGCCAAACTCAACTA 59.904 41.667 0.00 0.00 0.00 2.24
1476 1484 5.639139 TGATATGCTCTCAGGTATCTCACT 58.361 41.667 0.00 0.00 0.00 3.41
1507 1515 1.479709 GACCAAGAGGCTGAGCTCTA 58.520 55.000 16.19 0.24 39.06 2.43
1525 1533 3.855858 TGCAGCATATTAGTTGTCACGA 58.144 40.909 0.00 0.00 0.00 4.35
1534 1542 1.985473 TGGGCCTTGCAGCATATTAG 58.015 50.000 4.53 0.00 0.00 1.73
1551 1559 2.624838 GCCATACCCATGTCAGAATTGG 59.375 50.000 0.00 0.00 0.00 3.16
1558 1566 1.993701 ATGCCGCCATACCCATGTCA 61.994 55.000 0.00 0.00 0.00 3.58
1573 1581 3.180891 AGTACCGAAGCTTCTTATGCC 57.819 47.619 23.50 7.16 0.00 4.40
1610 1618 3.210227 TGAAATCTCGCTTGTCAAACCA 58.790 40.909 0.00 0.00 0.00 3.67
1620 1628 2.234661 TGACACTGGATGAAATCTCGCT 59.765 45.455 0.00 0.00 44.71 4.93
1654 1662 1.021390 GGACACATCAAGCTCCACCG 61.021 60.000 0.00 0.00 0.00 4.94
1718 1726 5.070685 AGAAACAACAGGGTAAGGTTGATC 58.929 41.667 11.06 8.58 45.50 2.92
1742 1750 8.821686 TTGACCCATGAAGTTGATTAATGTAT 57.178 30.769 0.00 0.00 28.50 2.29
1747 1755 6.317642 CGGTATTGACCCATGAAGTTGATTAA 59.682 38.462 0.00 0.00 43.64 1.40
1748 1756 5.820423 CGGTATTGACCCATGAAGTTGATTA 59.180 40.000 0.00 0.00 43.64 1.75
1778 1786 1.064758 AGATTCGGCAGCAACCCAATA 60.065 47.619 0.00 0.00 0.00 1.90
1935 1943 5.288472 GCACAACGATGTCATTTAATTTCCC 59.712 40.000 0.00 0.00 37.82 3.97
1977 1985 2.777832 AGCGATTCTGGAAGCTTTCT 57.222 45.000 6.25 0.00 36.41 2.52
2005 2013 8.250332 ACAACATTAAATTGTTCAACAGACAGT 58.750 29.630 3.29 0.00 36.93 3.55
2008 2016 9.509855 TGTACAACATTAAATTGTTCAACAGAC 57.490 29.630 12.24 5.34 40.68 3.51
2078 2086 5.555017 ACTGTCATTAGCTGATTTGTCACT 58.445 37.500 0.00 0.00 35.97 3.41
2095 2103 6.951062 TGTTGTTTTGGATCATAACTGTCA 57.049 33.333 0.00 0.00 0.00 3.58
2163 2171 3.807553 TGTTGTTGCTCATCTCAAGACA 58.192 40.909 0.00 0.00 0.00 3.41
2214 2222 4.671831 TCCCTGAATACTTCCATTTTGCA 58.328 39.130 0.00 0.00 0.00 4.08
2269 2277 2.094675 CAGAAATGCCCGTCAAATCCT 58.905 47.619 0.00 0.00 0.00 3.24
2293 2301 4.216708 CCCCTCTAGACCTACTTTCGATT 58.783 47.826 0.00 0.00 0.00 3.34
2366 2377 7.119262 GCTAAGTTACTAAAATCTGCCAAGACA 59.881 37.037 0.00 0.00 34.48 3.41
2384 2395 5.762711 TGATTGCTTGACTTGTGCTAAGTTA 59.237 36.000 8.07 2.45 0.00 2.24
2449 2460 8.974060 TCCCTTTACCTTCATATACAATGTTC 57.026 34.615 0.00 0.00 0.00 3.18
2457 2468 7.351166 CAAACCCTTCCCTTTACCTTCATATA 58.649 38.462 0.00 0.00 0.00 0.86
2628 2641 1.884235 AGACAAGGTTGCTTCTTCGG 58.116 50.000 0.00 0.00 0.00 4.30
2752 2765 1.827399 TTGGGAGCCTCCGACAAGAC 61.827 60.000 4.29 0.00 37.43 3.01
2820 2834 2.868583 GGAGTTCATCATCATCACACCG 59.131 50.000 0.00 0.00 0.00 4.94
2892 2908 4.526970 TCTTTCCACCATAGCCAAATCTC 58.473 43.478 0.00 0.00 0.00 2.75
3031 3048 4.012374 CCATCAGAACATGCCTACACTTT 58.988 43.478 0.00 0.00 0.00 2.66
3102 3120 4.985538 TGTGTGTAACGGTTGGATTTTT 57.014 36.364 3.07 0.00 42.39 1.94
3145 3163 4.158025 GGTCTCACCGAGTTCTTCTATTCA 59.842 45.833 0.00 0.00 0.00 2.57
3208 3231 0.899720 GTCCCACCGAGTTGACCATA 59.100 55.000 0.00 0.00 0.00 2.74
3308 3332 2.092429 TGCCTGACCAACTCTCTGTTTT 60.092 45.455 0.00 0.00 36.63 2.43
3389 3414 1.463056 CCGAGTTCGCAATGCAAACTA 59.537 47.619 11.90 0.00 38.18 2.24
3488 3513 2.099263 GTCTCACCGATCAGGATTTCGA 59.901 50.000 10.05 0.00 45.00 3.71
3527 3552 2.496871 CCTTTGACATAGCCATTGCCAA 59.503 45.455 0.00 0.00 38.69 4.52
3562 3587 2.371841 CCCCACCGATTTGATCTATCCA 59.628 50.000 0.00 0.00 0.00 3.41
3585 3611 5.946972 TGTCCAAAACCTAAAGTCAAACTCA 59.053 36.000 0.00 0.00 0.00 3.41
3629 3656 3.267974 GCTCCAAAGCCCTCAACG 58.732 61.111 0.00 0.00 43.10 4.10
3750 3778 9.905171 AAAAGCTCAAAACTCTTCATTTCTATC 57.095 29.630 0.00 0.00 0.00 2.08
3791 3819 3.355378 TGTGGACCCATCAAAATGCTAG 58.645 45.455 0.00 0.00 0.00 3.42
3803 3831 2.626785 TGGACTAAAGATGTGGACCCA 58.373 47.619 0.00 0.00 0.00 4.51
3816 3844 2.309613 GATTGGCATGGCATGGACTAA 58.690 47.619 27.48 16.23 0.00 2.24
3899 3927 4.615513 TCCCCGGGTGATTTTGATAATTT 58.384 39.130 21.85 0.00 0.00 1.82
3905 3933 2.578940 ACTAATCCCCGGGTGATTTTGA 59.421 45.455 30.29 16.79 34.43 2.69
3911 3939 1.202099 TGCAACTAATCCCCGGGTGA 61.202 55.000 21.85 16.99 0.00 4.02
3939 3967 5.273208 AGGTCAAGCTCTTCTACCTATGAA 58.727 41.667 10.06 0.00 35.41 2.57
3942 3970 5.961421 AGAAAGGTCAAGCTCTTCTACCTAT 59.039 40.000 11.49 2.51 35.86 2.57
3943 3971 5.186021 CAGAAAGGTCAAGCTCTTCTACCTA 59.814 44.000 11.49 0.00 35.86 3.08
3988 4378 2.035066 GCACTCCAATTGCCATGGATAC 59.965 50.000 18.40 0.00 45.57 2.24
3991 4381 0.040058 AGCACTCCAATTGCCATGGA 59.960 50.000 18.40 0.00 44.58 3.41
4123 4514 4.963318 TGATATCTTTTGGGATCTCGCT 57.037 40.909 3.98 0.00 0.00 4.93
4202 4593 3.735240 TGCTTCGTTTTGCAATGATGTTC 59.265 39.130 0.00 0.00 36.15 3.18
4257 4648 7.068593 GGGATGGAATTATTCAATGAGACACAA 59.931 37.037 7.29 0.00 0.00 3.33
4307 4698 6.318648 GGAGATATCATTGTTGGTGTTTGCTA 59.681 38.462 5.32 0.00 0.00 3.49
4452 4843 1.181098 GCAGTGCATGGAACTGGGTT 61.181 55.000 11.09 0.00 44.29 4.11
4506 4897 1.271543 TGCCACTTCCAATCCAGTGAG 60.272 52.381 0.79 0.00 42.74 3.51
4507 4898 0.770499 TGCCACTTCCAATCCAGTGA 59.230 50.000 0.79 0.00 42.74 3.41
4508 4899 1.171308 CTGCCACTTCCAATCCAGTG 58.829 55.000 0.00 0.00 40.23 3.66
4563 4959 4.225267 CCACCATTCTACTACCACCTTCTT 59.775 45.833 0.00 0.00 0.00 2.52
4674 5071 1.481772 ACTTGGCAATGTTTGTGTGCT 59.518 42.857 0.00 0.00 38.36 4.40
4699 5096 1.002773 TCTGAGCTTGAGATGCAGCAA 59.997 47.619 4.07 1.83 0.00 3.91
4739 5136 4.281898 AGCTACCGTTTTCCATGTACTT 57.718 40.909 0.00 0.00 0.00 2.24
4780 7448 4.222124 ACCAACTCTCTCTCTCTCTCTC 57.778 50.000 0.00 0.00 0.00 3.20
4781 7449 4.042809 TGAACCAACTCTCTCTCTCTCTCT 59.957 45.833 0.00 0.00 0.00 3.10
4782 7450 4.156008 GTGAACCAACTCTCTCTCTCTCTC 59.844 50.000 0.00 0.00 0.00 3.20
4783 7451 4.079253 GTGAACCAACTCTCTCTCTCTCT 58.921 47.826 0.00 0.00 0.00 3.10
4784 7452 4.079253 AGTGAACCAACTCTCTCTCTCTC 58.921 47.826 0.00 0.00 0.00 3.20
4785 7453 3.826157 CAGTGAACCAACTCTCTCTCTCT 59.174 47.826 0.00 0.00 0.00 3.10
4792 7460 1.230324 GCACCAGTGAACCAACTCTC 58.770 55.000 0.99 0.00 0.00 3.20
4842 7510 2.636893 AGACCTCTTGCTGAGTCAATGT 59.363 45.455 0.00 0.00 41.11 2.71
4864 7532 6.427853 GTGAACTATCATGGTGCATATAGCAA 59.572 38.462 0.00 0.00 46.56 3.91
5004 9942 2.689983 CCACCTATGGCAGAAATTGACC 59.310 50.000 0.00 0.00 39.82 4.02
5164 10102 1.068472 CACTCCGAAGCTGTAGACGTT 60.068 52.381 0.00 0.00 0.00 3.99
5205 10143 1.064166 CCATCATTTGCCACTCTCCCT 60.064 52.381 0.00 0.00 0.00 4.20
5211 10149 0.333993 AGCCTCCATCATTTGCCACT 59.666 50.000 0.00 0.00 0.00 4.00
5274 10212 5.950023 AGAAGATCAATTGACAGGCCATAT 58.050 37.500 11.07 0.00 0.00 1.78
5348 10286 0.174389 ACAGATCACACCTAGCGCAG 59.826 55.000 11.47 4.88 0.00 5.18
5350 10288 1.134367 TGTACAGATCACACCTAGCGC 59.866 52.381 0.00 0.00 0.00 5.92
5380 10318 2.499693 TCATTGATGGCCGTACTGAAGA 59.500 45.455 0.00 0.00 0.00 2.87
5427 10365 9.933723 CTTCTTTCCCTTGATTTATGTTGAAAT 57.066 29.630 0.00 0.00 0.00 2.17
5431 10369 6.071165 AGGCTTCTTTCCCTTGATTTATGTTG 60.071 38.462 0.00 0.00 0.00 3.33
5502 10440 6.072286 TCGTTATTCCTCTACGTCTTCAGTTT 60.072 38.462 0.00 0.00 36.70 2.66
5726 10679 5.001237 TCAGCAAATATTTGGTCTGCATG 57.999 39.130 25.92 15.66 46.06 4.06
5795 10748 9.008965 TCTAAGAAAGCTAAATGTTGCACATAA 57.991 29.630 0.00 0.00 37.97 1.90
5838 10791 7.562454 TCTCATGAGAATATGCAAATTTCCCTT 59.438 33.333 23.17 0.00 33.91 3.95
6244 13155 7.972832 TTTACCATTCGTTACATCAAGTCTT 57.027 32.000 0.00 0.00 0.00 3.01
6457 13540 0.829990 TCAATACGCCTGCTGATCCA 59.170 50.000 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.