Multiple sequence alignment - TraesCS1A01G404800

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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 TraesCS1A01G404800 chr1A 100.000 2267 0 0 1 2267 568121128 568123394 0.000000e+00 4187.0
1 TraesCS1A01G404800 chr1A 90.799 413 25 7 857 1265 568393398 568393801 7.120000e-150 540.0
2 TraesCS1A01G404800 chr1A 84.419 430 40 18 857 1265 568327864 568328287 4.540000e-107 398.0
3 TraesCS1A01G404800 chr1A 82.353 442 44 27 852 1274 568376993 568377419 9.960000e-94 353.0
4 TraesCS1A01G404800 chr1A 80.241 415 38 15 1574 1965 568399335 568399728 2.870000e-69 272.0
5 TraesCS1A01G404800 chr1A 81.550 271 28 5 1717 1965 568377884 568378154 1.060000e-48 204.0
6 TraesCS1A01G404800 chr1A 84.049 163 22 3 2109 2267 590356186 590356348 1.080000e-33 154.0
7 TraesCS1A01G404800 chr1A 86.806 144 8 7 1360 1495 568266501 568266641 1.400000e-32 150.0
8 TraesCS1A01G404800 chr1A 97.619 42 1 0 1502 1543 568266869 568266910 3.120000e-09 73.1
9 TraesCS1A01G404800 chr1D 89.044 858 62 11 1421 2267 473872615 473873451 0.000000e+00 1035.0
10 TraesCS1A01G404800 chr1D 92.066 668 33 7 601 1265 473871854 473872504 0.000000e+00 922.0
11 TraesCS1A01G404800 chr1D 90.431 418 29 5 852 1265 473992154 473992564 7.120000e-150 540.0
12 TraesCS1A01G404800 chr1D 85.142 424 40 19 857 1268 473961085 473961497 1.620000e-111 412.0
13 TraesCS1A01G404800 chr1D 83.290 389 40 13 1619 2002 473880846 473881214 3.610000e-88 335.0
14 TraesCS1A01G404800 chr1D 90.909 143 10 2 1822 1963 473988099 473988239 2.970000e-44 189.0
15 TraesCS1A01G404800 chr1D 89.796 147 11 2 1821 1963 473993250 473993396 3.850000e-43 185.0
16 TraesCS1A01G404800 chr1D 84.615 195 11 9 1360 1542 473961652 473961839 2.310000e-40 176.0
17 TraesCS1A01G404800 chr1D 90.476 126 11 1 1419 1544 473880339 473880463 5.010000e-37 165.0
18 TraesCS1A01G404800 chr1D 87.805 123 12 3 1710 1830 473987956 473988077 8.440000e-30 141.0
19 TraesCS1A01G404800 chr1D 97.143 35 1 0 825 859 473965849 473965883 2.430000e-05 60.2
20 TraesCS1A01G404800 chr1B 91.462 691 42 4 601 1288 658922552 658923228 0.000000e+00 933.0
21 TraesCS1A01G404800 chr1B 91.847 417 22 6 852 1265 659321505 659321912 2.530000e-159 571.0
22 TraesCS1A01G404800 chr1B 87.257 463 39 7 1811 2267 658923635 658924083 5.590000e-141 510.0
23 TraesCS1A01G404800 chr1B 85.057 435 46 10 1619 2048 658972974 658973394 2.080000e-115 425.0
24 TraesCS1A01G404800 chr1B 85.057 435 46 9 1619 2048 659006561 659006981 2.080000e-115 425.0
25 TraesCS1A01G404800 chr1B 94.465 271 11 3 1000 1268 659073604 659073872 4.510000e-112 414.0
26 TraesCS1A01G404800 chr1B 84.368 435 49 9 1619 2048 659271845 659272265 2.100000e-110 409.0
27 TraesCS1A01G404800 chr1B 93.773 273 13 3 998 1268 659002721 659002991 7.540000e-110 407.0
28 TraesCS1A01G404800 chr1B 86.933 375 30 11 1000 1366 659294725 659295088 9.750000e-109 403.0
29 TraesCS1A01G404800 chr1B 91.882 271 18 3 1000 1268 658969181 658969449 2.130000e-100 375.0
30 TraesCS1A01G404800 chr1B 91.154 260 17 1 1553 1812 658923258 658923511 4.630000e-92 348.0
31 TraesCS1A01G404800 chr1B 80.241 415 38 16 1574 1965 659327054 659327447 2.870000e-69 272.0
32 TraesCS1A01G404800 chr1B 91.667 144 11 1 1821 1963 659322590 659322733 4.940000e-47 198.0
33 TraesCS1A01G404800 chr1B 86.275 153 12 5 1380 1524 659295172 659295323 8.380000e-35 158.0
34 TraesCS1A01G404800 chr1B 86.713 143 12 4 1387 1524 659034285 659034425 3.900000e-33 152.0
35 TraesCS1A01G404800 chr1B 85.621 153 11 6 1384 1532 659317681 659317826 1.400000e-32 150.0
36 TraesCS1A01G404800 chr1B 83.436 163 23 3 2109 2267 176143900 176144062 5.050000e-32 148.0
37 TraesCS1A01G404800 chr1B 83.544 158 13 8 1380 1524 658969608 658969765 3.930000e-28 135.0
38 TraesCS1A01G404800 chr1B 84.932 73 9 1 526 596 453275953 453275881 3.120000e-09 73.1
39 TraesCS1A01G404800 chr7A 94.707 529 22 6 1 524 528301972 528301445 0.000000e+00 817.0
40 TraesCS1A01G404800 chr7A 94.318 528 26 3 1 524 632615002 632615529 0.000000e+00 806.0
41 TraesCS1A01G404800 chr7A 94.476 525 23 4 1 524 632666685 632667204 0.000000e+00 804.0
42 TraesCS1A01G404800 chr7A 94.286 525 26 3 1 524 633044253 633044774 0.000000e+00 800.0
43 TraesCS1A01G404800 chr7A 94.095 525 20 6 1 524 95816922 95817436 0.000000e+00 787.0
44 TraesCS1A01G404800 chr7A 93.750 528 28 4 1 524 632640570 632641096 0.000000e+00 787.0
45 TraesCS1A01G404800 chr7A 93.536 526 29 3 2 526 167742356 167741835 0.000000e+00 778.0
46 TraesCS1A01G404800 chr2A 94.095 525 23 4 1 525 709695668 709696184 0.000000e+00 791.0
47 TraesCS1A01G404800 chr5A 93.195 529 28 6 1 528 622760173 622759652 0.000000e+00 771.0
48 TraesCS1A01G404800 chr5A 83.537 164 23 3 2108 2267 680871344 680871507 1.400000e-32 150.0
49 TraesCS1A01G404800 chr5D 81.707 164 26 4 2108 2267 489298202 489298039 1.410000e-27 134.0


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 TraesCS1A01G404800 chr1A 568121128 568123394 2266 False 4187.000000 4187 100.000000 1 2267 1 chr1A.!!$F1 2266
1 TraesCS1A01G404800 chr1A 568376993 568378154 1161 False 278.500000 353 81.951500 852 1965 2 chr1A.!!$F7 1113
2 TraesCS1A01G404800 chr1D 473871854 473873451 1597 False 978.500000 1035 90.555000 601 2267 2 chr1D.!!$F2 1666
3 TraesCS1A01G404800 chr1D 473961085 473961839 754 False 294.000000 412 84.878500 857 1542 2 chr1D.!!$F4 685
4 TraesCS1A01G404800 chr1D 473987956 473993396 5440 False 263.750000 540 89.735250 852 1963 4 chr1D.!!$F5 1111
5 TraesCS1A01G404800 chr1D 473880339 473881214 875 False 250.000000 335 86.883000 1419 2002 2 chr1D.!!$F3 583
6 TraesCS1A01G404800 chr1B 658922552 658924083 1531 False 597.000000 933 89.957667 601 2267 3 chr1B.!!$F6 1666
7 TraesCS1A01G404800 chr1B 659002721 659006981 4260 False 416.000000 425 89.415000 998 2048 2 chr1B.!!$F8 1050
8 TraesCS1A01G404800 chr1B 658969181 658973394 4213 False 311.666667 425 86.827667 1000 2048 3 chr1B.!!$F7 1048
9 TraesCS1A01G404800 chr1B 659317681 659322733 5052 False 306.333333 571 89.711667 852 1963 3 chr1B.!!$F10 1111
10 TraesCS1A01G404800 chr1B 659294725 659295323 598 False 280.500000 403 86.604000 1000 1524 2 chr1B.!!$F9 524
11 TraesCS1A01G404800 chr7A 528301445 528301972 527 True 817.000000 817 94.707000 1 524 1 chr7A.!!$R2 523
12 TraesCS1A01G404800 chr7A 632615002 632615529 527 False 806.000000 806 94.318000 1 524 1 chr7A.!!$F2 523
13 TraesCS1A01G404800 chr7A 632666685 632667204 519 False 804.000000 804 94.476000 1 524 1 chr7A.!!$F4 523
14 TraesCS1A01G404800 chr7A 633044253 633044774 521 False 800.000000 800 94.286000 1 524 1 chr7A.!!$F5 523
15 TraesCS1A01G404800 chr7A 95816922 95817436 514 False 787.000000 787 94.095000 1 524 1 chr7A.!!$F1 523
16 TraesCS1A01G404800 chr7A 632640570 632641096 526 False 787.000000 787 93.750000 1 524 1 chr7A.!!$F3 523
17 TraesCS1A01G404800 chr7A 167741835 167742356 521 True 778.000000 778 93.536000 2 526 1 chr7A.!!$R1 524
18 TraesCS1A01G404800 chr2A 709695668 709696184 516 False 791.000000 791 94.095000 1 525 1 chr2A.!!$F1 524
19 TraesCS1A01G404800 chr5A 622759652 622760173 521 True 771.000000 771 93.195000 1 528 1 chr5A.!!$R1 527

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
808 842 0.034477 CGTTGGGAATGCCTACCCTT 60.034 55.0 0.0 0.0 45.74 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 8676 2.617774 TGGATGAATGTGTGTGTGTGTG 59.382 45.455 0.0 0.0 0.0 3.82 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
166 167 2.527951 GAAGGATGCAGCAGGGACGT 62.528 60.000 3.51 0.00 0.00 4.34
387 410 3.024043 GCGTTGTGTTTGCGCTGG 61.024 61.111 9.73 0.00 46.55 4.85
529 554 2.911484 CTGGAGATGCCCTAAGTTGTC 58.089 52.381 0.00 0.00 34.97 3.18
531 556 1.473434 GGAGATGCCCTAAGTTGTCCG 60.473 57.143 0.00 0.00 0.00 4.79
532 557 0.541863 AGATGCCCTAAGTTGTCCGG 59.458 55.000 0.00 0.00 0.00 5.14
533 558 0.252197 GATGCCCTAAGTTGTCCGGT 59.748 55.000 0.00 0.00 0.00 5.28
535 560 0.475044 TGCCCTAAGTTGTCCGGTTT 59.525 50.000 0.00 0.00 0.00 3.27
536 561 1.162698 GCCCTAAGTTGTCCGGTTTC 58.837 55.000 0.00 0.00 0.00 2.78
537 562 1.543871 GCCCTAAGTTGTCCGGTTTCA 60.544 52.381 0.00 0.00 0.00 2.69
538 563 2.853705 CCCTAAGTTGTCCGGTTTCAA 58.146 47.619 0.00 3.29 0.00 2.69
540 565 3.252458 CCCTAAGTTGTCCGGTTTCAAAG 59.748 47.826 0.00 1.39 0.00 2.77
541 566 3.881089 CCTAAGTTGTCCGGTTTCAAAGT 59.119 43.478 0.00 0.89 0.00 2.66
542 567 4.337274 CCTAAGTTGTCCGGTTTCAAAGTT 59.663 41.667 0.00 6.21 0.00 2.66
546 571 5.886992 AGTTGTCCGGTTTCAAAGTTAAAG 58.113 37.500 0.00 0.00 0.00 1.85
547 572 4.904253 TGTCCGGTTTCAAAGTTAAAGG 57.096 40.909 0.00 0.00 0.00 3.11
549 574 4.336153 TGTCCGGTTTCAAAGTTAAAGGAC 59.664 41.667 0.00 4.06 44.09 3.85
552 577 4.098196 CCGGTTTCAAAGTTAAAGGACCAA 59.902 41.667 0.00 0.00 0.00 3.67
553 578 5.394333 CCGGTTTCAAAGTTAAAGGACCAAA 60.394 40.000 0.00 0.00 0.00 3.28
555 580 6.419710 CGGTTTCAAAGTTAAAGGACCAAATC 59.580 38.462 0.00 0.00 0.00 2.17
556 581 6.419710 GGTTTCAAAGTTAAAGGACCAAATCG 59.580 38.462 0.00 0.00 0.00 3.34
557 582 6.945938 TTCAAAGTTAAAGGACCAAATCGA 57.054 33.333 0.00 0.00 0.00 3.59
559 584 6.059484 TCAAAGTTAAAGGACCAAATCGACT 58.941 36.000 0.00 0.00 0.00 4.18
561 586 6.555812 AAGTTAAAGGACCAAATCGACTTC 57.444 37.500 0.00 0.00 0.00 3.01
562 587 5.617252 AGTTAAAGGACCAAATCGACTTCA 58.383 37.500 0.00 0.00 0.00 3.02
563 588 5.469084 AGTTAAAGGACCAAATCGACTTCAC 59.531 40.000 0.00 0.00 0.00 3.18
564 589 2.474410 AGGACCAAATCGACTTCACC 57.526 50.000 0.00 0.00 0.00 4.02
565 590 1.697432 AGGACCAAATCGACTTCACCA 59.303 47.619 0.00 0.00 0.00 4.17
566 591 2.105821 AGGACCAAATCGACTTCACCAA 59.894 45.455 0.00 0.00 0.00 3.67
567 592 2.484264 GGACCAAATCGACTTCACCAAG 59.516 50.000 0.00 0.00 35.50 3.61
569 594 3.403038 ACCAAATCGACTTCACCAAGAG 58.597 45.455 0.00 0.00 33.34 2.85
570 595 3.181454 ACCAAATCGACTTCACCAAGAGT 60.181 43.478 0.00 0.00 33.34 3.24
571 596 3.815401 CCAAATCGACTTCACCAAGAGTT 59.185 43.478 0.00 0.00 33.34 3.01
574 599 3.371102 TCGACTTCACCAAGAGTTGAG 57.629 47.619 0.00 0.00 33.34 3.02
576 601 2.772287 GACTTCACCAAGAGTTGAGGG 58.228 52.381 0.00 0.00 33.34 4.30
577 602 2.368875 GACTTCACCAAGAGTTGAGGGA 59.631 50.000 0.00 0.00 33.34 4.20
578 603 2.777692 ACTTCACCAAGAGTTGAGGGAA 59.222 45.455 0.00 0.00 33.34 3.97
579 604 3.181450 ACTTCACCAAGAGTTGAGGGAAG 60.181 47.826 13.88 13.88 42.24 3.46
581 606 3.045634 TCACCAAGAGTTGAGGGAAGAA 58.954 45.455 0.00 0.00 0.00 2.52
582 607 3.458118 TCACCAAGAGTTGAGGGAAGAAA 59.542 43.478 0.00 0.00 0.00 2.52
583 608 4.080015 TCACCAAGAGTTGAGGGAAGAAAA 60.080 41.667 0.00 0.00 0.00 2.29
587 612 6.183361 ACCAAGAGTTGAGGGAAGAAAAGTAT 60.183 38.462 0.00 0.00 0.00 2.12
588 613 7.017254 ACCAAGAGTTGAGGGAAGAAAAGTATA 59.983 37.037 0.00 0.00 0.00 1.47
589 614 7.334671 CCAAGAGTTGAGGGAAGAAAAGTATAC 59.665 40.741 0.00 0.00 0.00 1.47
615 640 9.664332 CTTTTCTCCATATATTCGGATTCAGAT 57.336 33.333 0.00 0.00 0.00 2.90
641 666 5.221067 CGAGGAATCCGAGAGTTGATTTCTA 60.221 44.000 0.00 0.00 37.03 2.10
643 668 5.422331 AGGAATCCGAGAGTTGATTTCTACA 59.578 40.000 0.00 0.00 35.50 2.74
644 669 6.098982 AGGAATCCGAGAGTTGATTTCTACAT 59.901 38.462 0.00 0.00 35.50 2.29
645 670 7.287927 AGGAATCCGAGAGTTGATTTCTACATA 59.712 37.037 0.00 0.00 35.50 2.29
646 671 7.382759 GGAATCCGAGAGTTGATTTCTACATAC 59.617 40.741 0.00 0.00 31.56 2.39
808 842 0.034477 CGTTGGGAATGCCTACCCTT 60.034 55.000 0.00 0.00 45.74 3.95
846 880 2.039624 TCCTCTCCTCAGCCACCC 59.960 66.667 0.00 0.00 0.00 4.61
974 4651 5.163561 GCACTAGCTCAAGTAGAATCTCACT 60.164 44.000 0.00 0.00 37.91 3.41
993 4670 3.519913 CACTAGGGAAGCTTTACCTCCTT 59.480 47.826 22.42 8.78 35.84 3.36
1032 4709 1.378646 ATCGTCTCGGAGCACCTCA 60.379 57.895 0.00 0.00 31.08 3.86
1086 4763 1.270907 ACAAGATGTTCGAGGAGGCT 58.729 50.000 0.00 0.00 0.00 4.58
1101 4778 1.271102 GAGGCTCTCGCTTACTATGGG 59.729 57.143 7.40 0.00 36.09 4.00
1106 4783 0.318762 CTCGCTTACTATGGGGAGGC 59.681 60.000 0.00 0.00 38.37 4.70
1308 5006 4.940905 GACCCAGGTCTACTCCTAAATC 57.059 50.000 9.67 0.00 41.57 2.17
1309 5007 3.642377 GACCCAGGTCTACTCCTAAATCC 59.358 52.174 9.67 0.00 41.57 3.01
1311 5009 4.485021 ACCCAGGTCTACTCCTAAATCCTA 59.515 45.833 0.00 0.00 35.87 2.94
1312 5010 5.042827 ACCCAGGTCTACTCCTAAATCCTAA 60.043 44.000 0.00 0.00 35.87 2.69
1313 5011 6.085416 CCCAGGTCTACTCCTAAATCCTAAT 58.915 44.000 0.00 0.00 35.87 1.73
1314 5012 7.146815 ACCCAGGTCTACTCCTAAATCCTAATA 60.147 40.741 0.00 0.00 35.87 0.98
1338 5065 4.622701 ACAAGTTTTCAGTTGAGCAGAC 57.377 40.909 0.00 0.00 36.87 3.51
1342 5069 0.937304 TTTCAGTTGAGCAGACGCAC 59.063 50.000 0.00 0.00 42.27 5.34
1344 5071 0.875908 TCAGTTGAGCAGACGCACAC 60.876 55.000 0.00 0.00 38.53 3.82
1349 5076 2.024319 GAGCAGACGCACACCAGTC 61.024 63.158 0.00 0.00 42.27 3.51
1350 5077 2.280119 GCAGACGCACACCAGTCA 60.280 61.111 0.00 0.00 39.67 3.41
1351 5078 2.313172 GCAGACGCACACCAGTCAG 61.313 63.158 0.00 0.00 39.67 3.51
1353 5080 1.068083 AGACGCACACCAGTCAGTG 59.932 57.895 0.00 0.00 43.65 3.66
1362 5241 3.058708 CACACCAGTCAGTGCTGTATTTG 60.059 47.826 11.83 7.18 41.67 2.32
1369 5248 6.138761 CAGTCAGTGCTGTATTTGTCTTTTC 58.861 40.000 6.45 0.00 0.00 2.29
1373 5252 6.995686 TCAGTGCTGTATTTGTCTTTTCCTTA 59.004 34.615 0.00 0.00 0.00 2.69
1381 5260 8.846211 TGTATTTGTCTTTTCCTTAAGAGGTTG 58.154 33.333 3.36 0.00 43.97 3.77
1396 5286 1.447140 GTTGCCACCATGCATGCAG 60.447 57.895 26.69 15.79 41.70 4.41
1397 5287 1.606889 TTGCCACCATGCATGCAGA 60.607 52.632 26.69 2.79 41.70 4.26
1400 5290 1.601419 GCCACCATGCATGCAGAACT 61.601 55.000 26.69 6.06 0.00 3.01
1401 5291 0.172578 CCACCATGCATGCAGAACTG 59.827 55.000 26.69 18.41 0.00 3.16
1404 5294 1.004628 ACCATGCATGCAGAACTGGTA 59.995 47.619 32.43 6.48 34.84 3.25
1405 5295 1.402968 CCATGCATGCAGAACTGGTAC 59.597 52.381 26.69 0.00 0.00 3.34
1406 5296 1.402968 CATGCATGCAGAACTGGTACC 59.597 52.381 26.69 4.43 0.00 3.34
1407 5297 0.399833 TGCATGCAGAACTGGTACCA 59.600 50.000 18.46 15.39 0.00 3.25
1408 5298 1.004628 TGCATGCAGAACTGGTACCAT 59.995 47.619 18.46 0.05 0.00 3.55
1409 5299 1.402968 GCATGCAGAACTGGTACCATG 59.597 52.381 16.75 12.06 33.46 3.66
1410 5300 2.940971 GCATGCAGAACTGGTACCATGA 60.941 50.000 16.75 1.81 32.66 3.07
1426 5327 7.290948 TGGTACCATGAATGAACTCTCTATGAT 59.709 37.037 11.60 0.00 0.00 2.45
1487 5413 6.040209 TCGGTGGTTTAATCTTAGCACTAA 57.960 37.500 7.05 0.00 41.28 2.24
1488 5414 6.646267 TCGGTGGTTTAATCTTAGCACTAAT 58.354 36.000 7.05 0.00 41.28 1.73
1572 8639 8.593945 TCCTTACAAGGCTTTTTCATTCATAT 57.406 30.769 0.00 0.00 46.06 1.78
1609 8676 1.264288 GTGCAGCTCCACACTGTTTAC 59.736 52.381 1.93 0.00 37.47 2.01
1614 8681 2.093181 AGCTCCACACTGTTTACACACA 60.093 45.455 0.00 0.00 0.00 3.72
1627 8699 5.124617 TGTTTACACACACACACACATTCAT 59.875 36.000 0.00 0.00 0.00 2.57
1654 8726 6.006275 ACCTCATGCCTACATAGAACAAAT 57.994 37.500 0.00 0.00 33.67 2.32
1685 8761 6.625873 AAGAAAGAACAATCCTTCACACTC 57.374 37.500 0.00 0.00 29.87 3.51
1715 8791 8.747538 AGTACCTGTATTTCTGTTCAAACTTT 57.252 30.769 0.00 0.00 0.00 2.66
1784 8860 2.494059 TGAAGCAGTGTAAACTCCAGC 58.506 47.619 0.00 0.00 0.00 4.85
1790 8866 1.145803 GTGTAAACTCCAGCGGACAC 58.854 55.000 0.00 0.00 0.00 3.67
1967 9231 4.627035 CGTCTACATTCATGAACTGCAAGA 59.373 41.667 11.07 12.73 37.43 3.02
1970 9234 4.713824 ACATTCATGAACTGCAAGATGG 57.286 40.909 11.07 0.00 37.43 3.51
1983 9247 4.253685 TGCAAGATGGCTGTTAAGAGTAC 58.746 43.478 1.12 0.00 34.04 2.73
2027 9291 4.036852 GCTAGAATAGGATTTGCAACCCAC 59.963 45.833 16.73 1.48 39.70 4.61
2112 9376 5.141182 CCTAGGAGAGGCTCAATACTGTTA 58.859 45.833 18.26 0.00 38.96 2.41
2118 9382 3.641906 GAGGCTCAATACTGTTAGGGCTA 59.358 47.826 10.25 0.00 0.00 3.93
2128 9392 8.303876 CAATACTGTTAGGGCTAAACAACAAAT 58.696 33.333 6.64 0.00 31.00 2.32
2139 9403 6.757947 GGCTAAACAACAAATATGTGATGCAT 59.242 34.615 0.00 0.00 40.46 3.96
2151 9415 7.692460 ATATGTGATGCATAAATTCACCGAT 57.308 32.000 13.39 5.51 42.68 4.18
2155 9419 5.176774 GTGATGCATAAATTCACCGATACGA 59.823 40.000 0.00 0.00 34.95 3.43
2172 9436 5.107989 CGATACGACAAATATGCACACTACC 60.108 44.000 0.00 0.00 0.00 3.18
2227 9498 7.282224 ACAGTTTCAATCAACAAGTAAGCAGTA 59.718 33.333 0.00 0.00 0.00 2.74
2228 9499 8.128582 CAGTTTCAATCAACAAGTAAGCAGTAA 58.871 33.333 0.00 0.00 0.00 2.24
2256 9528 5.820131 ACACAAACAACATACACATGTGAG 58.180 37.500 31.94 21.27 44.83 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 66 1.674980 GACACCGTCCTCGTCCTCT 60.675 63.158 0.00 0.00 35.01 3.69
144 145 2.515523 CCTGCTGCATCCTTCCCG 60.516 66.667 1.31 0.00 0.00 5.14
387 410 7.348956 CCACGGGTTTTTAAAATGTTCAAATC 58.651 34.615 0.55 0.00 0.00 2.17
529 554 3.633065 TGGTCCTTTAACTTTGAAACCGG 59.367 43.478 0.00 0.00 0.00 5.28
531 556 6.419710 CGATTTGGTCCTTTAACTTTGAAACC 59.580 38.462 0.00 0.00 0.00 3.27
532 557 7.166970 GTCGATTTGGTCCTTTAACTTTGAAAC 59.833 37.037 0.00 0.00 0.00 2.78
533 558 7.067737 AGTCGATTTGGTCCTTTAACTTTGAAA 59.932 33.333 0.00 0.00 0.00 2.69
535 560 6.059484 AGTCGATTTGGTCCTTTAACTTTGA 58.941 36.000 0.00 0.00 0.00 2.69
536 561 6.313744 AGTCGATTTGGTCCTTTAACTTTG 57.686 37.500 0.00 0.00 0.00 2.77
537 562 6.544564 TGAAGTCGATTTGGTCCTTTAACTTT 59.455 34.615 0.00 0.00 0.00 2.66
538 563 6.017357 GTGAAGTCGATTTGGTCCTTTAACTT 60.017 38.462 0.00 0.00 0.00 2.66
540 565 5.334646 GGTGAAGTCGATTTGGTCCTTTAAC 60.335 44.000 0.00 0.00 0.00 2.01
541 566 4.758165 GGTGAAGTCGATTTGGTCCTTTAA 59.242 41.667 0.00 0.00 0.00 1.52
542 567 4.202377 TGGTGAAGTCGATTTGGTCCTTTA 60.202 41.667 0.00 0.00 0.00 1.85
546 571 2.178912 TGGTGAAGTCGATTTGGTCC 57.821 50.000 0.00 0.00 0.00 4.46
547 572 3.399330 TCTTGGTGAAGTCGATTTGGTC 58.601 45.455 0.00 0.00 0.00 4.02
549 574 3.403038 ACTCTTGGTGAAGTCGATTTGG 58.597 45.455 0.00 0.00 0.00 3.28
552 577 4.310769 CTCAACTCTTGGTGAAGTCGATT 58.689 43.478 0.00 0.00 0.00 3.34
553 578 3.306364 CCTCAACTCTTGGTGAAGTCGAT 60.306 47.826 0.00 0.00 0.00 3.59
555 580 2.408050 CCTCAACTCTTGGTGAAGTCG 58.592 52.381 0.00 0.00 0.00 4.18
556 581 2.368875 TCCCTCAACTCTTGGTGAAGTC 59.631 50.000 0.00 0.00 0.00 3.01
557 582 2.408565 TCCCTCAACTCTTGGTGAAGT 58.591 47.619 0.00 0.00 0.00 3.01
559 584 3.045634 TCTTCCCTCAACTCTTGGTGAA 58.954 45.455 0.00 0.00 0.00 3.18
561 586 3.492102 TTCTTCCCTCAACTCTTGGTG 57.508 47.619 0.00 0.00 0.00 4.17
562 587 4.079730 ACTTTTCTTCCCTCAACTCTTGGT 60.080 41.667 0.00 0.00 0.00 3.67
563 588 4.464947 ACTTTTCTTCCCTCAACTCTTGG 58.535 43.478 0.00 0.00 0.00 3.61
564 589 8.097662 AGTATACTTTTCTTCCCTCAACTCTTG 58.902 37.037 0.00 0.00 0.00 3.02
565 590 8.208575 AGTATACTTTTCTTCCCTCAACTCTT 57.791 34.615 0.00 0.00 0.00 2.85
566 591 7.800300 AGTATACTTTTCTTCCCTCAACTCT 57.200 36.000 0.00 0.00 0.00 3.24
567 592 8.850007 AAAGTATACTTTTCTTCCCTCAACTC 57.150 34.615 22.49 0.00 43.07 3.01
587 612 9.929180 CTGAATCCGAATATATGGAGAAAAGTA 57.071 33.333 2.66 0.00 37.76 2.24
588 613 8.651389 TCTGAATCCGAATATATGGAGAAAAGT 58.349 33.333 2.66 0.00 37.76 2.66
589 614 9.664332 ATCTGAATCCGAATATATGGAGAAAAG 57.336 33.333 2.66 0.00 37.76 2.27
594 619 7.931275 TCGTATCTGAATCCGAATATATGGAG 58.069 38.462 2.66 0.00 37.76 3.86
597 622 7.931275 TCCTCGTATCTGAATCCGAATATATG 58.069 38.462 0.00 0.00 0.00 1.78
598 623 8.521170 TTCCTCGTATCTGAATCCGAATATAT 57.479 34.615 0.00 0.00 0.00 0.86
599 624 7.933215 TTCCTCGTATCTGAATCCGAATATA 57.067 36.000 0.00 0.00 0.00 0.86
615 640 2.995283 TCAACTCTCGGATTCCTCGTA 58.005 47.619 0.30 0.00 0.00 3.43
709 740 3.574396 AGAAATCAACGTCTGGACTCTGA 59.426 43.478 0.00 2.47 0.00 3.27
710 741 3.919216 AGAAATCAACGTCTGGACTCTG 58.081 45.455 0.00 0.00 0.00 3.35
714 745 3.368236 GCTGTAGAAATCAACGTCTGGAC 59.632 47.826 0.00 0.00 0.00 4.02
715 746 3.258372 AGCTGTAGAAATCAACGTCTGGA 59.742 43.478 0.00 0.00 0.00 3.86
787 821 0.746923 GGGTAGGCATTCCCAACGTC 60.747 60.000 8.35 0.00 42.95 4.34
808 842 7.292356 AGAGGACAACATGTATATTGTGGGATA 59.708 37.037 5.64 0.00 39.13 2.59
846 880 4.513406 TTATAGGCCCTGTGGGTTAAAG 57.487 45.455 0.00 0.00 46.51 1.85
961 4638 5.137412 AGCTTCCCTAGTGAGATTCTACT 57.863 43.478 0.00 0.00 0.00 2.57
974 4651 3.798515 TGAAGGAGGTAAAGCTTCCCTA 58.201 45.455 15.58 0.00 43.75 3.53
993 4670 1.278127 GACCCGGAAGACATCCTTTGA 59.722 52.381 0.73 0.00 46.98 2.69
1086 4763 1.996798 CCTCCCCATAGTAAGCGAGA 58.003 55.000 0.00 0.00 0.00 4.04
1092 4769 2.144738 GGCGGCCTCCCCATAGTAA 61.145 63.158 12.87 0.00 0.00 2.24
1176 4853 1.095600 CGACGAGGATCTGGAAGTGA 58.904 55.000 0.00 0.00 33.76 3.41
1268 4945 6.147473 TGGGTCTTGAGGAATATACATACCA 58.853 40.000 0.00 0.00 0.00 3.25
1290 4981 8.903059 ATATTAGGATTTAGGAGTAGACCTGG 57.097 38.462 0.00 0.00 40.81 4.45
1308 5006 9.774742 GCTCAACTGAAAACTTGTTATATTAGG 57.225 33.333 0.00 0.00 0.00 2.69
1311 5009 9.066892 TCTGCTCAACTGAAAACTTGTTATATT 57.933 29.630 0.00 0.00 0.00 1.28
1312 5010 8.507249 GTCTGCTCAACTGAAAACTTGTTATAT 58.493 33.333 0.00 0.00 0.00 0.86
1313 5011 7.307160 CGTCTGCTCAACTGAAAACTTGTTATA 60.307 37.037 0.00 0.00 0.00 0.98
1314 5012 6.511767 CGTCTGCTCAACTGAAAACTTGTTAT 60.512 38.462 0.00 0.00 0.00 1.89
1344 5071 3.668447 AGACAAATACAGCACTGACTGG 58.332 45.455 4.31 0.00 42.21 4.00
1349 5076 5.695851 AGGAAAAGACAAATACAGCACTG 57.304 39.130 0.00 0.00 0.00 3.66
1350 5077 7.719633 TCTTAAGGAAAAGACAAATACAGCACT 59.280 33.333 1.85 0.00 30.54 4.40
1351 5078 7.871853 TCTTAAGGAAAAGACAAATACAGCAC 58.128 34.615 1.85 0.00 30.54 4.40
1353 5080 7.175119 ACCTCTTAAGGAAAAGACAAATACAGC 59.825 37.037 1.85 0.00 46.67 4.40
1354 5081 8.622948 ACCTCTTAAGGAAAAGACAAATACAG 57.377 34.615 1.85 0.00 46.67 2.74
1362 5241 4.023107 GTGGCAACCTCTTAAGGAAAAGAC 60.023 45.833 1.85 0.00 46.67 3.01
1381 5260 1.153706 GTTCTGCATGCATGGTGGC 60.154 57.895 27.34 13.95 0.00 5.01
1396 5286 5.491982 AGAGTTCATTCATGGTACCAGTTC 58.508 41.667 21.41 6.92 0.00 3.01
1397 5287 5.249393 AGAGAGTTCATTCATGGTACCAGTT 59.751 40.000 21.41 0.57 0.00 3.16
1400 5290 6.611236 TCATAGAGAGTTCATTCATGGTACCA 59.389 38.462 18.99 18.99 0.00 3.25
1401 5291 7.055667 TCATAGAGAGTTCATTCATGGTACC 57.944 40.000 4.43 4.43 0.00 3.34
1404 5294 6.328410 TGGATCATAGAGAGTTCATTCATGGT 59.672 38.462 0.00 0.00 0.00 3.55
1405 5295 6.766429 TGGATCATAGAGAGTTCATTCATGG 58.234 40.000 0.00 0.00 0.00 3.66
1406 5296 8.557864 GTTTGGATCATAGAGAGTTCATTCATG 58.442 37.037 0.00 0.00 0.00 3.07
1407 5297 8.492782 AGTTTGGATCATAGAGAGTTCATTCAT 58.507 33.333 0.00 0.00 0.00 2.57
1408 5298 7.767659 CAGTTTGGATCATAGAGAGTTCATTCA 59.232 37.037 0.00 0.00 0.00 2.57
1409 5299 7.254727 GCAGTTTGGATCATAGAGAGTTCATTC 60.255 40.741 0.00 0.00 0.00 2.67
1410 5300 6.541641 GCAGTTTGGATCATAGAGAGTTCATT 59.458 38.462 0.00 0.00 0.00 2.57
1487 5413 6.408662 GCTTTGGAAGTAGGGAGATTGTCTAT 60.409 42.308 0.00 0.00 0.00 1.98
1488 5414 5.104900 GCTTTGGAAGTAGGGAGATTGTCTA 60.105 44.000 0.00 0.00 0.00 2.59
1572 8639 6.690530 AGCTGCACAAAATCTAGCAAAAATA 58.309 32.000 1.02 0.00 36.44 1.40
1609 8676 2.617774 TGGATGAATGTGTGTGTGTGTG 59.382 45.455 0.00 0.00 0.00 3.82
1614 8681 3.149196 GAGGTTGGATGAATGTGTGTGT 58.851 45.455 0.00 0.00 0.00 3.72
1627 8699 3.653164 TCTATGTAGGCATGAGGTTGGA 58.347 45.455 0.00 0.00 36.58 3.53
1654 8726 8.748412 TGAAGGATTGTTCTTTCTTTCTTTTGA 58.252 29.630 0.56 0.00 38.44 2.69
1678 8754 6.665992 AATACAGGTACTCAAAGAGTGTGA 57.334 37.500 9.78 0.00 43.30 3.58
1685 8761 7.962964 TGAACAGAAATACAGGTACTCAAAG 57.037 36.000 0.00 0.00 34.60 2.77
1715 8791 7.158697 TGCACTGTAAGCTTATTTGAACTCTA 58.841 34.615 9.88 0.00 37.60 2.43
1724 8800 4.074970 AGCACTTGCACTGTAAGCTTATT 58.925 39.130 9.88 0.00 45.16 1.40
1784 8860 3.619483 TGTACAACTTTGTTCAGTGTCCG 59.381 43.478 0.00 0.00 42.35 4.79
1790 8866 9.046296 AGATCTAGTTTGTACAACTTTGTTCAG 57.954 33.333 8.07 3.15 42.35 3.02
1907 9171 7.228706 ACAACATAGAGACAAACTTAACCTTGG 59.771 37.037 0.00 0.00 0.00 3.61
1967 9231 5.804639 TGTCAATGTACTCTTAACAGCCAT 58.195 37.500 0.00 0.00 0.00 4.40
1970 9234 8.879342 AGATATGTCAATGTACTCTTAACAGC 57.121 34.615 0.00 0.00 0.00 4.40
2023 9287 5.081032 CCTAGAGATAAGTTAGGAGGTGGG 58.919 50.000 0.00 0.00 36.83 4.61
2091 9355 5.141182 CCTAACAGTATTGAGCCTCTCCTA 58.859 45.833 0.00 0.00 0.00 2.94
2112 9376 6.627953 GCATCACATATTTGTTGTTTAGCCCT 60.628 38.462 2.73 0.00 32.34 5.19
2128 9392 7.148656 CGTATCGGTGAATTTATGCATCACATA 60.149 37.037 16.85 6.55 44.05 2.29
2139 9403 7.224949 TGCATATTTGTCGTATCGGTGAATTTA 59.775 33.333 0.00 0.00 0.00 1.40
2151 9415 4.435425 GGGTAGTGTGCATATTTGTCGTA 58.565 43.478 0.00 0.00 0.00 3.43
2155 9419 3.012934 GGGGGTAGTGTGCATATTTGT 57.987 47.619 0.00 0.00 0.00 2.83
2182 9449 5.116882 ACTGTCCTCAAAGTTCACTACAAC 58.883 41.667 0.00 0.00 0.00 3.32
2227 9498 9.593134 ACATGTGTATGTTGTTTGTGTTATTTT 57.407 25.926 0.00 0.00 45.01 1.82
2228 9499 9.029243 CACATGTGTATGTTGTTTGTGTTATTT 57.971 29.630 18.03 0.00 45.01 1.40


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

AutoCloner maintained by Alex Coulton.