Multiple sequence alignment - TraesCS5D01G542100

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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 TraesCS5D01G542100 chr5D 100.000 4194 0 0 1 4194 552708309 552712502 0.000000e+00 7745.0
1 TraesCS5D01G542100 chr5D 93.519 108 7 0 603 710 142126853 142126746 1.210000e-35 161.0
2 TraesCS5D01G542100 chr5D 91.743 109 8 1 603 710 262765979 262765871 2.610000e-32 150.0
3 TraesCS5D01G542100 chr4A 91.293 3434 165 57 1 3346 615440268 615436881 0.000000e+00 4562.0
4 TraesCS5D01G542100 chr4A 93.396 212 11 3 3362 3571 615436738 615436528 1.130000e-80 311.0
5 TraesCS5D01G542100 chr4A 87.302 63 1 7 719 776 734455841 734455781 9.730000e-07 65.8
6 TraesCS5D01G542100 chr5B 91.247 3416 186 50 1 3361 697852900 697849543 0.000000e+00 4547.0
7 TraesCS5D01G542100 chr5B 90.045 221 9 5 3362 3571 697849506 697849288 1.490000e-69 274.0
8 TraesCS5D01G542100 chr5B 89.908 109 10 1 603 710 165290601 165290709 5.650000e-29 139.0
9 TraesCS5D01G542100 chr2D 95.833 528 18 4 3587 4114 66129435 66128912 0.000000e+00 850.0
10 TraesCS5D01G542100 chr2D 95.946 74 3 0 603 676 423823497 423823570 2.050000e-23 121.0
11 TraesCS5D01G542100 chr2D 94.805 77 4 0 603 679 445226136 445226060 2.050000e-23 121.0
12 TraesCS5D01G542100 chr2D 84.259 108 6 6 603 710 195003040 195002944 1.240000e-15 95.3
13 TraesCS5D01G542100 chr2B 91.115 619 41 11 3585 4194 210085097 210084484 0.000000e+00 826.0
14 TraesCS5D01G542100 chr2B 88.744 613 52 14 3587 4194 711473156 711472556 0.000000e+00 734.0
15 TraesCS5D01G542100 chr3B 90.836 622 40 11 3584 4194 48069593 48070208 0.000000e+00 817.0
16 TraesCS5D01G542100 chr3B 89.573 633 44 16 3571 4194 47853763 47854382 0.000000e+00 784.0
17 TraesCS5D01G542100 chr3B 89.822 619 42 14 3584 4194 48131544 48132149 0.000000e+00 774.0
18 TraesCS5D01G542100 chr3B 91.404 570 35 11 3636 4194 47800200 47800766 0.000000e+00 769.0
19 TraesCS5D01G542100 chr3B 89.808 520 18 10 3692 4194 727341766 727341265 5.920000e-178 634.0
20 TraesCS5D01G542100 chr3B 91.858 393 14 5 3806 4194 171076820 171076442 2.220000e-147 532.0
21 TraesCS5D01G542100 chr3B 75.724 1001 215 18 1999 2994 6243873 6244850 1.050000e-130 477.0
22 TraesCS5D01G542100 chr7D 89.731 633 41 12 3585 4194 620184057 620184688 0.000000e+00 787.0
23 TraesCS5D01G542100 chr7D 82.407 108 8 3 603 710 330421127 330421223 2.690000e-12 84.2
24 TraesCS5D01G542100 chr1B 89.786 607 52 8 3596 4194 82973239 82972635 0.000000e+00 769.0
25 TraesCS5D01G542100 chr3A 76.476 1169 215 34 1999 3140 9731531 9730396 7.820000e-162 580.0
26 TraesCS5D01G542100 chr3A 75.107 1165 231 38 1999 3132 9522534 9523670 1.360000e-134 490.0
27 TraesCS5D01G542100 chr3D 93.519 108 7 0 603 710 288494726 288494833 1.210000e-35 161.0
28 TraesCS5D01G542100 chr3D 93.506 77 5 0 600 676 222876694 222876770 9.530000e-22 115.0
29 TraesCS5D01G542100 chr3D 86.885 61 3 5 718 776 403942280 403942337 3.500000e-06 63.9
30 TraesCS5D01G542100 chr5A 92.593 108 8 0 603 710 174460179 174460072 5.610000e-34 156.0
31 TraesCS5D01G542100 chr6B 92.593 108 5 1 603 710 274873835 274873731 7.260000e-33 152.0
32 TraesCS5D01G542100 chr6D 91.667 108 9 0 603 710 258718252 258718359 2.610000e-32 150.0
33 TraesCS5D01G542100 chr6D 93.506 77 5 0 603 679 159174895 159174819 9.530000e-22 115.0
34 TraesCS5D01G542100 chr6D 94.595 74 4 0 603 676 166634218 166634291 9.530000e-22 115.0
35 TraesCS5D01G542100 chr6D 93.506 77 5 0 603 679 167933408 167933332 9.530000e-22 115.0
36 TraesCS5D01G542100 chr6D 92.593 81 5 1 603 683 192697240 192697319 9.530000e-22 115.0
37 TraesCS5D01G542100 chr6D 94.595 74 4 0 603 676 216800055 216800128 9.530000e-22 115.0
38 TraesCS5D01G542100 chr6D 93.333 75 5 0 600 674 84433481 84433555 1.230000e-20 111.0
39 TraesCS5D01G542100 chr6D 94.444 72 4 0 603 674 274067607 274067536 1.230000e-20 111.0
40 TraesCS5D01G542100 chr6D 93.243 74 5 0 603 676 85324620 85324693 4.430000e-20 110.0
41 TraesCS5D01G542100 chr6D 92.208 77 6 0 603 679 288136917 288136841 4.430000e-20 110.0
42 TraesCS5D01G542100 chr6D 88.333 60 3 4 719 776 458145761 458145704 7.520000e-08 69.4
43 TraesCS5D01G542100 chr6D 88.333 60 3 4 719 776 458171969 458171912 7.520000e-08 69.4
44 TraesCS5D01G542100 chr6D 88.333 60 3 4 719 776 458224954 458224897 7.520000e-08 69.4
45 TraesCS5D01G542100 chr4D 91.667 108 9 0 603 710 220168520 220168627 2.610000e-32 150.0
46 TraesCS5D01G542100 chr4D 95.833 72 3 0 603 674 65771248 65771319 2.650000e-22 117.0
47 TraesCS5D01G542100 chr4D 93.506 77 5 0 603 679 14002414 14002490 9.530000e-22 115.0
48 TraesCS5D01G542100 chr4D 93.506 77 5 0 603 679 29128548 29128472 9.530000e-22 115.0
49 TraesCS5D01G542100 chr4D 100.000 37 0 0 716 752 113415665 113415701 7.520000e-08 69.4
50 TraesCS5D01G542100 chr1D 93.506 77 5 0 603 679 381747449 381747373 9.530000e-22 115.0
51 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 68741310 68741381 1.230000e-20 111.0
52 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 95854494 95854565 1.230000e-20 111.0
53 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 102400848 102400919 1.230000e-20 111.0
54 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 106747128 106747057 1.230000e-20 111.0
55 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 111781122 111781193 1.230000e-20 111.0
56 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 130974345 130974416 1.230000e-20 111.0
57 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 137239125 137239196 1.230000e-20 111.0
58 TraesCS5D01G542100 chrUn 94.444 72 4 0 603 674 478442166 478442095 1.230000e-20 111.0
59 TraesCS5D01G542100 chrUn 93.056 72 5 0 603 674 221014009 221013938 5.730000e-19 106.0
60 TraesCS5D01G542100 chrUn 90.909 77 7 0 603 679 332145653 332145577 2.060000e-18 104.0
61 TraesCS5D01G542100 chrUn 87.931 58 6 1 719 776 16375904 16375848 2.710000e-07 67.6
62 TraesCS5D01G542100 chrUn 87.931 58 6 1 719 776 67440046 67439990 2.710000e-07 67.6
63 TraesCS5D01G542100 chr7B 92.593 54 4 0 716 769 570184033 570184086 1.250000e-10 78.7
64 TraesCS5D01G542100 chr7B 80.583 103 10 7 717 809 44631884 44631782 2.090000e-08 71.3
65 TraesCS5D01G542100 chr2A 92.593 54 2 2 716 769 100672693 100672744 4.500000e-10 76.8
66 TraesCS5D01G542100 chr7A 89.831 59 5 1 719 777 670207698 670207755 1.620000e-09 75.0
67 TraesCS5D01G542100 chr6A 82.418 91 9 5 719 804 452332406 452332318 5.820000e-09 73.1
68 TraesCS5D01G542100 chr6A 90.385 52 4 1 719 770 603931325 603931275 2.710000e-07 67.6
69 TraesCS5D01G542100 chr4B 86.154 65 2 7 719 778 488890129 488890067 3.500000e-06 63.9
70 TraesCS5D01G542100 chr1A 87.500 56 5 2 719 772 423988265 423988210 3.500000e-06 63.9


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 TraesCS5D01G542100 chr5D 552708309 552712502 4193 False 7745.0 7745 100.0000 1 4194 1 chr5D.!!$F1 4193
1 TraesCS5D01G542100 chr4A 615436528 615440268 3740 True 2436.5 4562 92.3445 1 3571 2 chr4A.!!$R2 3570
2 TraesCS5D01G542100 chr5B 697849288 697852900 3612 True 2410.5 4547 90.6460 1 3571 2 chr5B.!!$R1 3570
3 TraesCS5D01G542100 chr2D 66128912 66129435 523 True 850.0 850 95.8330 3587 4114 1 chr2D.!!$R1 527
4 TraesCS5D01G542100 chr2B 210084484 210085097 613 True 826.0 826 91.1150 3585 4194 1 chr2B.!!$R1 609
5 TraesCS5D01G542100 chr2B 711472556 711473156 600 True 734.0 734 88.7440 3587 4194 1 chr2B.!!$R2 607
6 TraesCS5D01G542100 chr3B 48069593 48070208 615 False 817.0 817 90.8360 3584 4194 1 chr3B.!!$F4 610
7 TraesCS5D01G542100 chr3B 47853763 47854382 619 False 784.0 784 89.5730 3571 4194 1 chr3B.!!$F3 623
8 TraesCS5D01G542100 chr3B 48131544 48132149 605 False 774.0 774 89.8220 3584 4194 1 chr3B.!!$F5 610
9 TraesCS5D01G542100 chr3B 47800200 47800766 566 False 769.0 769 91.4040 3636 4194 1 chr3B.!!$F2 558
10 TraesCS5D01G542100 chr3B 727341265 727341766 501 True 634.0 634 89.8080 3692 4194 1 chr3B.!!$R2 502
11 TraesCS5D01G542100 chr3B 6243873 6244850 977 False 477.0 477 75.7240 1999 2994 1 chr3B.!!$F1 995
12 TraesCS5D01G542100 chr7D 620184057 620184688 631 False 787.0 787 89.7310 3585 4194 1 chr7D.!!$F2 609
13 TraesCS5D01G542100 chr1B 82972635 82973239 604 True 769.0 769 89.7860 3596 4194 1 chr1B.!!$R1 598
14 TraesCS5D01G542100 chr3A 9730396 9731531 1135 True 580.0 580 76.4760 1999 3140 1 chr3A.!!$R1 1141
15 TraesCS5D01G542100 chr3A 9522534 9523670 1136 False 490.0 490 75.1070 1999 3132 1 chr3A.!!$F1 1133

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
907 923 0.692476 ACTACCATTGCAGTGCCAGA 59.308 50.0 13.72 0.0 0.00 3.86 F
2173 2240 0.950836 CACACGAGTTCATGCCCAAA 59.049 50.0 0.00 0.0 0.00 3.28 F
2807 2886 0.179092 CAGCTCCATCATCAGCGTCA 60.179 55.0 0.00 0.0 40.84 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2490 2569 0.179081 GTCGGGAAGCTGGTCCATAC 60.179 60.000 6.77 0.54 39.70 2.39 R
3116 3213 0.036875 GGTAGTTGCAGACCAAGCCT 59.963 55.000 9.08 0.00 35.65 4.58 R
3888 4188 1.668919 CGGAAGTTAAGCGTGCTCAGA 60.669 52.381 0.00 0.00 0.00 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
236 239 1.478510 TGTTGTTTTTGCACCGGACAT 59.521 42.857 9.46 0.00 0.00 3.06
387 390 3.117131 TGATGCACCAGAGGTCCTATCTA 60.117 47.826 0.00 0.00 31.02 1.98
393 396 7.422512 TGCACCAGAGGTCCTATCTATTATAT 58.577 38.462 0.00 0.00 31.02 0.86
395 398 7.343316 GCACCAGAGGTCCTATCTATTATATGT 59.657 40.741 0.00 0.00 31.02 2.29
466 470 7.325694 AGTGATTTTATTGGCTCAAAATGGAG 58.674 34.615 8.34 0.00 35.14 3.86
481 485 0.738975 TGGAGCGTCAAGAGGATACG 59.261 55.000 0.00 0.00 46.39 3.06
517 521 5.061853 CACATCTGGTCTTTGCATAGCTAT 58.938 41.667 0.00 0.00 0.00 2.97
547 551 1.732917 CCAACACCAACGCACACAT 59.267 52.632 0.00 0.00 0.00 3.21
559 563 0.871722 GCACACATAAGAACACGCCA 59.128 50.000 0.00 0.00 0.00 5.69
573 577 4.519610 GCCATGTGGGGACTTTGT 57.480 55.556 0.54 0.00 37.04 2.83
599 603 4.222588 TCCCCATGCAAGTAAATCCAAAAG 59.777 41.667 0.00 0.00 0.00 2.27
638 642 9.981114 ACTTCAACTAAGTTTTGGATTTATTGG 57.019 29.630 0.00 0.00 46.61 3.16
692 696 2.112380 TCTCGCCATTTCTTGCATGA 57.888 45.000 0.00 0.00 0.00 3.07
717 721 2.992817 AAACATGCACCCCGAGGCAA 62.993 55.000 0.00 0.00 44.20 4.52
758 767 3.824133 TGACCAAAGCTATGCATATGCT 58.176 40.909 27.13 18.96 42.66 3.79
791 802 5.824904 AAAGAAATCGGATCCACAATGAG 57.175 39.130 13.41 0.00 0.00 2.90
804 815 4.826733 TCCACAATGAGCAAACTACAACAT 59.173 37.500 0.00 0.00 0.00 2.71
854 865 3.485877 GGAATCTTTTGCTTGATCGACGG 60.486 47.826 0.00 0.00 0.00 4.79
856 867 3.306917 TCTTTTGCTTGATCGACGGTA 57.693 42.857 0.00 0.00 0.00 4.02
888 899 5.065914 GCAGGGCTATCAATGATGAGTTTA 58.934 41.667 5.91 0.00 39.39 2.01
907 923 0.692476 ACTACCATTGCAGTGCCAGA 59.308 50.000 13.72 0.00 0.00 3.86
915 931 3.632643 TTGCAGTGCCAGATTAGATCA 57.367 42.857 13.72 0.00 0.00 2.92
992 1008 7.556844 ACCTCTTCACACAAAGTCGATAATAT 58.443 34.615 0.00 0.00 0.00 1.28
1012 1028 3.978193 AACCAATGGGGCGCCAGA 61.978 61.111 30.85 14.70 42.05 3.86
1015 1031 3.830192 CAATGGGGCGCCAGAAGC 61.830 66.667 30.85 10.33 38.52 3.86
1043 1059 4.760047 ACGCGATGTGCACCCTCC 62.760 66.667 15.93 4.94 46.97 4.30
1056 1072 4.039092 CCTCCAGTGCCACCAGGG 62.039 72.222 4.32 0.00 40.85 4.45
1081 1097 3.687572 TCGGTAAGTCTATTGCGACTC 57.312 47.619 0.00 0.00 43.14 3.36
1104 1120 5.929992 TCTCTTCGACGTCCAAATTGTTAAT 59.070 36.000 10.58 0.00 0.00 1.40
1105 1121 5.922546 TCTTCGACGTCCAAATTGTTAATG 58.077 37.500 10.58 0.00 0.00 1.90
1111 1127 3.986572 CGTCCAAATTGTTAATGCTTGCA 59.013 39.130 0.00 0.00 0.00 4.08
1112 1128 4.090354 CGTCCAAATTGTTAATGCTTGCAG 59.910 41.667 0.87 0.00 0.00 4.41
1326 1344 4.695217 TTGTGTGTGTTGTTCTTCCTTC 57.305 40.909 0.00 0.00 0.00 3.46
1381 1406 8.057623 CCTATCAGCCTAATCCATATTTCCAAT 58.942 37.037 0.00 0.00 0.00 3.16
1422 1447 2.607187 GTGGTGTGGATAGTTGTCTCG 58.393 52.381 0.00 0.00 0.00 4.04
1516 1541 4.883006 AGGATTTGCACAAAAAGTTGCAAT 59.117 33.333 0.59 1.39 40.92 3.56
1588 1613 4.279671 ACTGATGCTACCTACTCTATGTGC 59.720 45.833 0.00 0.00 0.00 4.57
1628 1660 2.094675 CCAGAAATTGCGAGGTTGGAT 58.905 47.619 0.00 0.00 0.00 3.41
1637 1669 1.407437 GCGAGGTTGGATCTCCATGTT 60.407 52.381 0.00 0.00 46.97 2.71
1639 1671 2.648059 GAGGTTGGATCTCCATGTTGG 58.352 52.381 0.00 0.00 46.97 3.77
1656 1688 3.936203 GTGTCCCTCCCACGTGCA 61.936 66.667 10.91 0.00 0.00 4.57
1891 1931 8.034804 AGGCACAAGAACAATTTATTTGATACC 58.965 33.333 0.00 0.00 38.76 2.73
1895 1935 8.531146 ACAAGAACAATTTATTTGATACCCAGG 58.469 33.333 0.00 0.00 38.76 4.45
1901 1941 7.014615 ACAATTTATTTGATACCCAGGCAGATC 59.985 37.037 0.00 0.00 38.76 2.75
1910 1950 4.899352 ACCCAGGCAGATCATAGTAATC 57.101 45.455 0.00 0.00 0.00 1.75
1916 1956 6.350864 CCAGGCAGATCATAGTAATCCTACAG 60.351 46.154 0.00 0.00 0.00 2.74
2058 2125 3.057019 TCGTCAATTTCCAAGTGTCTCG 58.943 45.455 0.00 0.00 0.00 4.04
2107 2174 8.788325 ACAAAGAATATAGTGAGTTGGTAACC 57.212 34.615 0.00 0.00 0.00 2.85
2133 2200 2.825836 GGAGGTTGCCATCTGCGG 60.826 66.667 0.00 0.00 45.60 5.69
2155 2222 5.937540 CGGCCCATATATAGTTGTGAAATCA 59.062 40.000 0.00 0.00 0.00 2.57
2173 2240 0.950836 CACACGAGTTCATGCCCAAA 59.049 50.000 0.00 0.00 0.00 3.28
2174 2241 1.541147 CACACGAGTTCATGCCCAAAT 59.459 47.619 0.00 0.00 0.00 2.32
2175 2242 1.541147 ACACGAGTTCATGCCCAAATG 59.459 47.619 0.00 0.00 0.00 2.32
2187 2260 1.525995 CCAAATGGACGCCGGCTAT 60.526 57.895 26.68 13.07 37.39 2.97
2188 2261 1.648720 CAAATGGACGCCGGCTATG 59.351 57.895 26.68 12.04 0.00 2.23
2190 2263 2.608970 AAATGGACGCCGGCTATGCT 62.609 55.000 26.68 3.04 0.00 3.79
2191 2264 2.608970 AATGGACGCCGGCTATGCTT 62.609 55.000 26.68 12.95 0.00 3.91
2323 2396 1.078214 CTGGCTCGCCATCTTTCCA 60.078 57.895 11.59 0.00 46.15 3.53
2332 2405 2.484417 CGCCATCTTTCCAGTCATAGCT 60.484 50.000 0.00 0.00 0.00 3.32
2414 2487 8.809478 GTCGTAAAGTTAATCAAGGATCTTCTC 58.191 37.037 0.00 0.00 0.00 2.87
2416 2489 9.026074 CGTAAAGTTAATCAAGGATCTTCTCTC 57.974 37.037 0.00 0.00 0.00 3.20
2417 2490 9.026074 GTAAAGTTAATCAAGGATCTTCTCTCG 57.974 37.037 0.00 0.00 0.00 4.04
2418 2491 6.783708 AGTTAATCAAGGATCTTCTCTCGT 57.216 37.500 0.00 0.00 0.00 4.18
2424 2497 1.008329 GGATCTTCTCTCGTCGTCGT 58.992 55.000 1.33 0.00 38.33 4.34
2425 2498 1.004715 GGATCTTCTCTCGTCGTCGTC 60.005 57.143 1.33 0.00 38.33 4.20
2443 2522 4.089636 GTCGTCGAGACTAAAATGACAACC 59.910 45.833 0.00 0.00 46.13 3.77
2473 2552 3.383223 TGGGATCATAGTGGTGATGACA 58.617 45.455 0.00 0.00 38.88 3.58
2490 2569 3.809013 ACTGGGGGCGCTATTGGG 61.809 66.667 7.64 0.00 0.00 4.12
2596 2675 1.153597 CGCGCATGGTGATGAAGCTA 61.154 55.000 8.75 0.00 34.50 3.32
2807 2886 0.179092 CAGCTCCATCATCAGCGTCA 60.179 55.000 0.00 0.00 40.84 4.35
2941 3020 0.729116 CGACATTCCAGGTGTCATGC 59.271 55.000 10.15 0.00 44.77 4.06
3116 3213 1.211703 TCAAGTGTCTGGTTTCTGCCA 59.788 47.619 0.00 0.00 36.97 4.92
3144 3241 1.347378 TCTGCAACTACCACTGCATGA 59.653 47.619 0.00 0.00 46.87 3.07
3154 3251 2.487762 ACCACTGCATGAAACGGTTATG 59.512 45.455 0.00 0.00 0.00 1.90
3325 3458 2.978010 GGTCTTGGGTGCACACGG 60.978 66.667 20.43 12.32 0.00 4.94
3368 3628 5.741011 AGTTGTGAAGGAACAAACTAGTGA 58.259 37.500 0.00 0.00 41.52 3.41
3493 3763 8.531982 CCTGGATTGCTAAGCTAGTTATGTATA 58.468 37.037 0.00 0.00 0.00 1.47
3584 3855 9.444600 AAGAAAACACACTCACTAGTAGAAAAA 57.555 29.630 3.59 0.00 33.48 1.94
3653 3925 1.002533 CCTCCCCCTTTAGTCCCGA 59.997 63.158 0.00 0.00 0.00 5.14
3680 3952 1.190178 ACGAACCGGGACTAAAGGCT 61.190 55.000 6.32 0.00 0.00 4.58
3721 4000 8.411991 ACCGGGACTAAAGAAAATTTTATGAA 57.588 30.769 6.32 0.00 0.00 2.57
3819 4119 9.905713 ATCACTGCTTAATTTAACCTCTAATCA 57.094 29.630 0.00 0.00 0.00 2.57
3832 4132 5.289510 ACCTCTAATCACTAATCACCCCTT 58.710 41.667 0.00 0.00 0.00 3.95
3867 4167 0.822164 CTAACTTCCCGGACGGTCAT 59.178 55.000 0.73 0.00 0.00 3.06
3888 4188 2.583101 TCCATCCTCTCACTACTCCAGT 59.417 50.000 0.00 0.00 38.32 4.00
3961 4261 6.039616 GCACTTGTTGTTTTCCTGACAATAA 58.960 36.000 0.00 0.00 39.03 1.40
4122 4434 4.821805 ACCATAGTTTGACCACAGTTTGAG 59.178 41.667 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 8.749354 ACCTGAACCAATTAAAATCACCTATTC 58.251 33.333 0.00 0.00 0.00 1.75
211 214 3.192844 TCCGGTGCAAAAACAACAAAGTA 59.807 39.130 0.00 0.00 0.00 2.24
430 434 9.171877 AGCCAATAAAATCACTTTTGTCAAAAA 57.828 25.926 11.73 0.00 36.09 1.94
466 470 2.344741 GTGTTTCGTATCCTCTTGACGC 59.655 50.000 0.00 0.00 36.54 5.19
472 476 4.184629 GCTCATTGTGTTTCGTATCCTCT 58.815 43.478 0.00 0.00 0.00 3.69
481 485 3.254166 ACCAGATGTGCTCATTGTGTTTC 59.746 43.478 2.26 0.00 34.06 2.78
547 551 0.322098 CCCCACATGGCGTGTTCTTA 60.322 55.000 10.21 0.00 44.78 2.10
559 563 3.745723 GACCACAAAGTCCCCACAT 57.254 52.632 0.00 0.00 0.00 3.21
692 696 0.035439 CGGGGTGCATGTTTAGTCCT 60.035 55.000 0.00 0.00 0.00 3.85
791 802 6.018262 TGTGAGTAGTCAATGTTGTAGTTTGC 60.018 38.462 0.69 0.00 33.27 3.68
804 815 3.979101 TCCATGCATGTGAGTAGTCAA 57.021 42.857 24.58 0.00 33.27 3.18
854 865 7.337689 TCATTGATAGCCCTGCATTAATCATAC 59.662 37.037 0.00 0.00 0.00 2.39
856 867 6.250711 TCATTGATAGCCCTGCATTAATCAT 58.749 36.000 0.00 0.00 0.00 2.45
888 899 0.692476 TCTGGCACTGCAATGGTAGT 59.308 50.000 2.82 0.00 40.92 2.73
907 923 3.317149 TGCGGCTACGTAGTTGATCTAAT 59.683 43.478 22.98 0.00 37.78 1.73
915 931 0.389426 CTTGGTGCGGCTACGTAGTT 60.389 55.000 22.98 0.00 37.78 2.24
992 1008 2.994417 GGCGCCCCATTGGTTGAA 60.994 61.111 18.11 0.00 36.04 2.69
1012 1028 1.956170 CGCGTGACTTGACTGGCTT 60.956 57.895 0.00 0.00 0.00 4.35
1015 1031 0.667487 ACATCGCGTGACTTGACTGG 60.667 55.000 5.77 0.00 0.00 4.00
1043 1059 0.962356 GATGAACCCTGGTGGCACTG 60.962 60.000 18.45 10.61 37.83 3.66
1056 1072 4.206609 GTCGCAATAGACTTACCGATGAAC 59.793 45.833 0.00 0.00 38.09 3.18
1081 1097 5.585500 TTAACAATTTGGACGTCGAAGAG 57.415 39.130 12.85 9.48 36.95 2.85
1173 1191 1.957877 GACCCGCTCTATCTAGCTTGT 59.042 52.381 0.00 0.00 40.49 3.16
1203 1221 1.235724 GTGGGTTGTAGGTTGAGCAC 58.764 55.000 0.00 0.00 0.00 4.40
1242 1260 0.742990 ACATATGGGTGGTCGTTGCG 60.743 55.000 7.80 0.00 0.00 4.85
1307 1325 3.065371 CAGGAAGGAAGAACAACACACAC 59.935 47.826 0.00 0.00 0.00 3.82
1326 1344 6.860080 ACTCAATGAATGAAAGCATAACAGG 58.140 36.000 0.00 0.00 37.67 4.00
1381 1406 8.420222 CACCACCATATTTGCTTGGAAAATATA 58.580 33.333 8.43 0.00 37.86 0.86
1387 1412 3.257873 CACACCACCATATTTGCTTGGAA 59.742 43.478 8.43 0.00 36.79 3.53
1422 1447 3.920412 GGATGAAAACAATTTGACTCGCC 59.080 43.478 2.79 0.00 0.00 5.54
1516 1541 7.776618 TGTCTACTATGAGGAAAAGACTTGA 57.223 36.000 0.00 0.00 35.50 3.02
1588 1613 0.035056 CCAAACCCTAGGGACTGCAG 60.035 60.000 35.38 13.48 41.52 4.41
1628 1660 0.984230 GAGGGACACCAACATGGAGA 59.016 55.000 2.85 0.00 40.96 3.71
1637 1669 3.238497 CACGTGGGAGGGACACCA 61.238 66.667 7.95 0.00 42.29 4.17
1639 1671 3.936203 TGCACGTGGGAGGGACAC 61.936 66.667 18.88 0.00 35.55 3.67
1702 1734 2.530661 TTGGGAAAGAGGGGGCGA 60.531 61.111 0.00 0.00 0.00 5.54
1728 1761 2.267324 GTGGGTCTCTGCTGGAGC 59.733 66.667 0.00 0.00 41.60 4.70
1780 1814 6.479001 CCCTGAATATTTACGTGAATTCTCGT 59.521 38.462 30.90 30.90 46.02 4.18
1856 1896 5.906113 TTGTTCTTGTGCCTGTTCTAAAA 57.094 34.783 0.00 0.00 0.00 1.52
1859 1899 7.759489 ATAAATTGTTCTTGTGCCTGTTCTA 57.241 32.000 0.00 0.00 0.00 2.10
1861 1901 7.437862 TCAAATAAATTGTTCTTGTGCCTGTTC 59.562 33.333 0.00 0.00 40.11 3.18
1876 1916 6.713762 TCTGCCTGGGTATCAAATAAATTG 57.286 37.500 0.00 0.00 40.58 2.32
1891 1931 5.481824 TGTAGGATTACTATGATCTGCCTGG 59.518 44.000 0.00 0.00 33.43 4.45
1895 1935 6.279513 AGCTGTAGGATTACTATGATCTGC 57.720 41.667 0.00 0.00 33.43 4.26
1978 2042 0.472471 TTCCATCCGATACCCCAAGC 59.528 55.000 0.00 0.00 0.00 4.01
2058 2125 6.371809 TGGTAAAACCATCATCGCTTAATC 57.628 37.500 0.00 0.00 44.79 1.75
2107 2174 2.568090 GCAACCTCCATTGTGCCG 59.432 61.111 0.00 0.00 31.83 5.69
2155 2222 1.541147 CATTTGGGCATGAACTCGTGT 59.459 47.619 0.00 0.00 35.38 4.49
2173 2240 3.106986 AAGCATAGCCGGCGTCCAT 62.107 57.895 23.20 10.47 36.08 3.41
2174 2241 3.781307 AAGCATAGCCGGCGTCCA 61.781 61.111 23.20 8.28 36.08 4.02
2175 2242 3.272334 CAAGCATAGCCGGCGTCC 61.272 66.667 23.20 11.09 36.08 4.79
2190 2263 0.527113 CCATGACTTCAATGGCGCAA 59.473 50.000 10.83 0.00 0.00 4.85
2191 2264 0.322366 TCCATGACTTCAATGGCGCA 60.322 50.000 10.83 0.00 35.51 6.09
2219 2292 5.745227 TCTGAAAATCTGGACATTAGGACC 58.255 41.667 0.00 0.00 0.00 4.46
2323 2396 6.631016 TCGTATGAAAACAAGAGCTATGACT 58.369 36.000 6.02 0.00 0.00 3.41
2332 2405 2.411748 CAGCGCTCGTATGAAAACAAGA 59.588 45.455 7.13 0.00 0.00 3.02
2424 2497 4.935205 CCATGGTTGTCATTTTAGTCTCGA 59.065 41.667 2.57 0.00 32.92 4.04
2425 2498 4.935205 TCCATGGTTGTCATTTTAGTCTCG 59.065 41.667 12.58 0.00 32.92 4.04
2443 2522 3.497405 CCACTATGATCCCAACCTCCATG 60.497 52.174 0.00 0.00 0.00 3.66
2473 2552 3.809013 CCCAATAGCGCCCCCAGT 61.809 66.667 2.29 0.00 0.00 4.00
2490 2569 0.179081 GTCGGGAAGCTGGTCCATAC 60.179 60.000 6.77 0.54 39.70 2.39
2712 2791 0.376152 CGGCAAGCATAGCAGAACAG 59.624 55.000 0.00 0.00 0.00 3.16
2807 2886 8.576442 CCTATTTCTGTATGGTTTCAACTTGTT 58.424 33.333 0.00 0.00 0.00 2.83
2941 3020 1.227089 CAGAATCCCTGAGACGCCG 60.227 63.158 0.00 0.00 45.78 6.46
3091 3188 2.171448 AGAAACCAGACACTTGAGCAGT 59.829 45.455 0.00 0.00 35.35 4.40
3116 3213 0.036875 GGTAGTTGCAGACCAAGCCT 59.963 55.000 9.08 0.00 35.65 4.58
3257 3382 4.220693 ACATGCCGCCATATATGTATGT 57.779 40.909 11.73 10.21 36.72 2.29
3268 3401 1.002746 ACACACATACATGCCGCCA 60.003 52.632 0.00 0.00 0.00 5.69
3531 3802 8.568676 TTGCTATAATAAGTTACAAACTGCCA 57.431 30.769 0.00 0.00 41.91 4.92
3584 3855 2.125766 GAACCGGGACAAGAGGCCTT 62.126 60.000 6.77 0.00 0.00 4.35
3585 3856 2.529389 AACCGGGACAAGAGGCCT 60.529 61.111 3.86 3.86 0.00 5.19
3591 3862 2.928416 GTTCCAGAACCGGGACAAG 58.072 57.895 6.32 0.00 35.36 3.16
3653 3925 1.897802 AGTCCCGGTTCGTGTAAGAAT 59.102 47.619 0.00 0.00 32.25 2.40
3680 3952 2.515057 GTTGGTGCCACGTGGACA 60.515 61.111 38.30 29.34 37.39 4.02
3819 4119 6.590656 TTGGAATGATAAGGGGTGATTAGT 57.409 37.500 0.00 0.00 0.00 2.24
3832 4132 7.661437 CGGGAAGTTAGATGATTTGGAATGATA 59.339 37.037 0.00 0.00 0.00 2.15
3867 4167 2.583101 ACTGGAGTAGTGAGAGGATGGA 59.417 50.000 0.00 0.00 38.49 3.41
3888 4188 1.668919 CGGAAGTTAAGCGTGCTCAGA 60.669 52.381 0.00 0.00 0.00 3.27
3961 4261 9.170890 TGAGGGTTAATAGGATTGACATCTTAT 57.829 33.333 0.00 0.00 34.01 1.73
4104 4404 2.423538 GTGCTCAAACTGTGGTCAAACT 59.576 45.455 0.00 0.00 0.00 2.66
4122 4434 3.550842 GGTCAAATCTGGTCAAACTGTGC 60.551 47.826 0.00 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.