Multiple sequence alignment - TraesCS5B01G564200

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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 TraesCS5B01G564200 chr5B 100.000 2927 0 0 1 2927 709585566 709582640 0.000000e+00 5406
1 TraesCS5B01G564200 chr5B 93.156 263 15 3 324 585 709585190 709584930 1.650000e-102 383
2 TraesCS5B01G564200 chr5B 93.156 263 15 3 377 637 709585243 709584982 1.650000e-102 383
3 TraesCS5B01G564200 chr5B 90.338 207 18 2 324 530 709585137 709584933 1.340000e-68 270
4 TraesCS5B01G564200 chr5B 90.338 207 18 2 430 634 709585243 709585037 1.340000e-68 270
5 TraesCS5B01G564200 chr5B 88.667 150 16 1 324 473 709585084 709584936 6.440000e-42 182
6 TraesCS5B01G564200 chr5B 88.667 150 16 1 483 631 709585243 709585094 6.440000e-42 182
7 TraesCS5B01G564200 chr5D 90.009 2302 135 49 658 2927 557000096 557002334 0.000000e+00 2889
8 TraesCS5B01G564200 chr4A 89.469 2241 125 57 756 2927 605644676 605646874 0.000000e+00 2728
9 TraesCS5B01G564200 chr4A 87.124 598 67 3 36 624 605643772 605644368 0.000000e+00 669
10 TraesCS5B01G564200 chr4A 83.706 313 49 2 324 634 605644120 605644432 7.930000e-76 294


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 TraesCS5B01G564200 chr5B 709582640 709585566 2926 True 1010.857143 5406 92.046000 1 2927 7 chr5B.!!$R1 2926
1 TraesCS5B01G564200 chr5D 557000096 557002334 2238 False 2889.000000 2889 90.009000 658 2927 1 chr5D.!!$F1 2269
2 TraesCS5B01G564200 chr4A 605643772 605646874 3102 False 1230.333333 2728 86.766333 36 2927 3 chr4A.!!$F1 2891

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
533 542 0.037975 GAAACTGACGTAAGCCCGGA 60.038 55.0 0.73 0.0 45.62 5.14 F
1359 1570 0.031721 ACGACGACCAAGACCAAGAC 59.968 55.0 0.00 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 1641 0.174617 CTCTTCTTGGTCCTCCTCGC 59.825 60.0 0.0 0.0 34.23 5.03 R
2702 2989 0.468648 TCTGGAGGCAGCAGATCATG 59.531 55.0 0.0 0.0 0.00 3.07 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
24 25 3.673343 TCAATCCTTGAGATCCCCATCT 58.327 45.455 0.00 0.00 42.59 2.90
25 26 3.393609 TCAATCCTTGAGATCCCCATCTG 59.606 47.826 0.00 0.00 39.71 2.90
26 27 1.135094 TCCTTGAGATCCCCATCTGC 58.865 55.000 0.00 0.00 39.71 4.26
27 28 0.110104 CCTTGAGATCCCCATCTGCC 59.890 60.000 0.00 0.00 39.71 4.85
28 29 0.841961 CTTGAGATCCCCATCTGCCA 59.158 55.000 0.00 0.00 39.71 4.92
29 30 0.548031 TTGAGATCCCCATCTGCCAC 59.452 55.000 0.00 0.00 39.71 5.01
30 31 1.070445 GAGATCCCCATCTGCCACG 59.930 63.158 0.00 0.00 39.71 4.94
31 32 2.592861 GATCCCCATCTGCCACGC 60.593 66.667 0.00 0.00 0.00 5.34
32 33 4.195334 ATCCCCATCTGCCACGCC 62.195 66.667 0.00 0.00 0.00 5.68
34 35 3.479203 CCCCATCTGCCACGCCTA 61.479 66.667 0.00 0.00 0.00 3.93
35 36 2.822637 CCCCATCTGCCACGCCTAT 61.823 63.158 0.00 0.00 0.00 2.57
36 37 1.480212 CCCCATCTGCCACGCCTATA 61.480 60.000 0.00 0.00 0.00 1.31
37 38 0.615331 CCCATCTGCCACGCCTATAT 59.385 55.000 0.00 0.00 0.00 0.86
38 39 1.003580 CCCATCTGCCACGCCTATATT 59.996 52.381 0.00 0.00 0.00 1.28
39 40 2.079158 CCATCTGCCACGCCTATATTG 58.921 52.381 0.00 0.00 0.00 1.90
40 41 1.466167 CATCTGCCACGCCTATATTGC 59.534 52.381 0.00 0.00 0.00 3.56
46 47 4.041617 CGCCTATATTGCGTGGCA 57.958 55.556 10.24 0.00 46.59 4.92
62 63 1.065491 TGGCACATGACCTTATCGCTT 60.065 47.619 0.00 0.00 0.00 4.68
63 64 1.331756 GGCACATGACCTTATCGCTTG 59.668 52.381 0.00 0.00 0.00 4.01
68 69 1.195115 TGACCTTATCGCTTGCCTCT 58.805 50.000 0.00 0.00 0.00 3.69
72 73 2.171448 ACCTTATCGCTTGCCTCTTCAT 59.829 45.455 0.00 0.00 0.00 2.57
79 80 3.118261 TCGCTTGCCTCTTCATAAAGGAT 60.118 43.478 0.00 0.00 34.35 3.24
81 82 4.459330 GCTTGCCTCTTCATAAAGGATCT 58.541 43.478 0.00 0.00 34.35 2.75
110 111 2.355108 CCACCTTAGGGTCACATCACAG 60.355 54.545 2.32 0.00 45.41 3.66
118 119 2.669229 CACATCACAGCGCCACCA 60.669 61.111 2.29 0.00 0.00 4.17
134 135 2.660552 CACCGACGTGAAAGGCGT 60.661 61.111 0.00 0.00 43.14 5.68
135 136 2.660552 ACCGACGTGAAAGGCGTG 60.661 61.111 0.00 0.00 43.04 5.34
138 139 3.723348 GACGTGAAAGGCGTGCCC 61.723 66.667 7.39 0.00 43.04 5.36
153 154 1.280421 GTGCCCCTTCTTCATGAGTCT 59.720 52.381 0.00 0.00 0.00 3.24
157 158 3.560025 GCCCCTTCTTCATGAGTCTCAAA 60.560 47.826 6.64 0.00 0.00 2.69
159 160 4.639310 CCCCTTCTTCATGAGTCTCAAATG 59.361 45.833 6.64 1.69 0.00 2.32
165 166 1.709147 ATGAGTCTCAAATGCGCGCC 61.709 55.000 30.77 10.43 0.00 6.53
171 172 4.228097 CAAATGCGCGCCTCTCCG 62.228 66.667 30.77 8.36 0.00 4.63
178 179 4.838486 GCGCCTCTCCGACTGTCG 62.838 72.222 22.49 22.49 40.07 4.35
206 215 2.980233 GCACGTTGCTCTGGCCTT 60.980 61.111 3.32 0.00 40.96 4.35
220 229 0.309612 GGCCTTTTTCGAGTTTCGCA 59.690 50.000 0.00 0.00 40.21 5.10
223 232 3.181500 GGCCTTTTTCGAGTTTCGCATAT 60.181 43.478 0.00 0.00 40.21 1.78
269 278 0.320508 GTGACCGGAGACAAACCCTC 60.321 60.000 9.46 0.00 0.00 4.30
270 279 1.080025 GACCGGAGACAAACCCTCG 60.080 63.158 9.46 0.00 0.00 4.63
348 357 2.983030 TGCCACGTGTGCAATCCC 60.983 61.111 23.58 1.12 35.40 3.85
359 368 2.102252 TGTGCAATCCCTGTTTGGAAAC 59.898 45.455 0.00 0.00 38.10 2.78
381 390 1.753649 GACGTAAACCCTAGTCTCCCC 59.246 57.143 0.00 0.00 0.00 4.81
384 393 0.712380 TAAACCCTAGTCTCCCCGGT 59.288 55.000 0.00 0.00 0.00 5.28
399 408 2.255252 GGTGCCACGTGTGCAATC 59.745 61.111 26.20 19.18 41.06 2.67
401 410 2.983030 TGCCACGTGTGCAATCCC 60.983 61.111 23.58 1.12 35.40 3.85
413 422 2.365293 GTGCAATCCCTGTTTGGAAACT 59.635 45.455 4.02 0.00 38.10 2.66
415 424 2.627699 GCAATCCCTGTTTGGAAACTGA 59.372 45.455 9.89 2.65 39.36 3.41
421 430 3.628487 CCCTGTTTGGAAACTGACGTAAA 59.372 43.478 9.89 0.00 39.36 2.01
426 435 4.686191 TTGGAAACTGACGTAAACCCTA 57.314 40.909 0.00 0.00 0.00 3.53
428 437 3.642848 TGGAAACTGACGTAAACCCTAGT 59.357 43.478 0.00 0.00 0.00 2.57
443 452 3.533079 TAGTCTCCCCGGTGCCACA 62.533 63.158 0.00 0.00 0.00 4.17
449 458 2.124362 CCCGGTGCCACATATGCA 60.124 61.111 1.58 0.00 36.12 3.96
460 469 3.866910 GCCACATATGCAATCCTTGTTTG 59.133 43.478 1.58 0.00 0.00 2.93
466 475 4.961438 ATGCAATCCTTGTTTGGAAACT 57.039 36.364 0.00 0.00 39.85 2.66
479 488 4.686191 TTGGAAACTGACGTAAACCCTA 57.314 40.909 0.00 0.00 0.00 3.53
481 490 3.642848 TGGAAACTGACGTAAACCCTAGT 59.357 43.478 0.00 0.00 0.00 2.57
488 497 0.743097 CGTAAACCCTAGTCTCCCCG 59.257 60.000 0.00 0.00 0.00 5.73
521 530 3.703556 TGCAATCCTTGTTTGGAAACTGA 59.296 39.130 4.02 0.00 39.85 3.41
530 539 1.886886 TTGGAAACTGACGTAAGCCC 58.113 50.000 0.00 0.00 45.62 5.19
531 540 0.320073 TGGAAACTGACGTAAGCCCG 60.320 55.000 0.00 0.00 45.62 6.13
533 542 0.037975 GAAACTGACGTAAGCCCGGA 60.038 55.000 0.73 0.00 45.62 5.14
534 543 0.320160 AAACTGACGTAAGCCCGGAC 60.320 55.000 0.73 0.00 45.62 4.79
535 544 1.183676 AACTGACGTAAGCCCGGACT 61.184 55.000 0.73 0.00 45.62 3.85
536 545 1.139095 CTGACGTAAGCCCGGACTC 59.861 63.158 0.73 0.00 45.62 3.36
567 683 3.190327 CACGTATGCAATCCTTGTTTGGA 59.810 43.478 0.00 0.00 40.82 3.53
578 694 4.515361 TCCTTGTTTGGAAACTGACGTAA 58.485 39.130 4.02 0.00 39.59 3.18
582 698 2.614983 GTTTGGAAACTGACGTAAGCCA 59.385 45.455 0.00 0.00 37.02 4.75
584 700 2.422597 TGGAAACTGACGTAAGCCATG 58.577 47.619 0.00 0.00 45.62 3.66
603 720 2.285069 ACTCCCCGGTGCCACATA 60.285 61.111 0.00 0.00 0.00 2.29
617 734 3.514706 TGCCACATATGCAATCCTTGTTT 59.485 39.130 1.58 0.00 35.40 2.83
619 736 4.381825 GCCACATATGCAATCCTTGTTTGA 60.382 41.667 1.58 0.00 0.00 2.69
620 737 5.722263 CCACATATGCAATCCTTGTTTGAA 58.278 37.500 1.58 0.00 0.00 2.69
643 760 1.472878 CAGACTTAGCCGTGCTACTGA 59.527 52.381 12.56 0.00 41.12 3.41
644 761 1.473278 AGACTTAGCCGTGCTACTGAC 59.527 52.381 5.27 3.51 41.12 3.51
661 778 1.296727 GACCGGGATTGTCGATTTCC 58.703 55.000 6.32 0.00 0.00 3.13
668 785 2.290641 GGATTGTCGATTTCCGGGATTG 59.709 50.000 0.00 0.20 39.14 2.67
669 786 2.772077 TTGTCGATTTCCGGGATTGA 57.228 45.000 0.00 2.93 39.14 2.57
675 792 2.420129 CGATTTCCGGGATTGAGAGGTT 60.420 50.000 0.00 0.00 33.91 3.50
687 804 5.590663 GGATTGAGAGGTTAGGGTTTGATTC 59.409 44.000 0.00 0.00 0.00 2.52
689 806 3.913799 TGAGAGGTTAGGGTTTGATTCCA 59.086 43.478 0.00 0.00 0.00 3.53
700 817 3.004944 GGTTTGATTCCAACAAGGCGTAA 59.995 43.478 3.36 0.00 37.29 3.18
701 818 4.500035 GGTTTGATTCCAACAAGGCGTAAA 60.500 41.667 3.36 0.00 37.29 2.01
706 823 3.974871 TCCAACAAGGCGTAAAAGTTC 57.025 42.857 0.00 0.00 37.29 3.01
707 824 2.288458 TCCAACAAGGCGTAAAAGTTCG 59.712 45.455 0.00 0.00 37.29 3.95
720 837 7.019418 GCGTAAAAGTTCGAGGTTTATTTCAT 58.981 34.615 0.00 0.00 0.00 2.57
765 951 1.822186 GTCAGTGTGGCCAAACCGT 60.822 57.895 23.08 1.56 43.94 4.83
766 952 1.821759 TCAGTGTGGCCAAACCGTG 60.822 57.895 23.08 15.30 43.94 4.94
828 1014 3.345808 CCACGTGAACCGCACCAG 61.346 66.667 19.30 0.00 44.85 4.00
857 1046 1.385756 AAAAACCGAACCCACCACCG 61.386 55.000 0.00 0.00 0.00 4.94
1088 1299 4.135153 CGAGGACCGCTGGACCAG 62.135 72.222 17.83 17.83 39.89 4.00
1356 1567 1.008194 CGACGACGACCAAGACCAA 60.008 57.895 0.00 0.00 42.66 3.67
1357 1568 1.002250 CGACGACGACCAAGACCAAG 61.002 60.000 0.00 0.00 42.66 3.61
1358 1569 0.313043 GACGACGACCAAGACCAAGA 59.687 55.000 0.00 0.00 0.00 3.02
1359 1570 0.031721 ACGACGACCAAGACCAAGAC 59.968 55.000 0.00 0.00 0.00 3.01
1360 1571 0.666577 CGACGACCAAGACCAAGACC 60.667 60.000 0.00 0.00 0.00 3.85
1361 1572 0.391597 GACGACCAAGACCAAGACCA 59.608 55.000 0.00 0.00 0.00 4.02
1362 1573 0.393077 ACGACCAAGACCAAGACCAG 59.607 55.000 0.00 0.00 0.00 4.00
1363 1574 0.320771 CGACCAAGACCAAGACCAGG 60.321 60.000 0.00 0.00 0.00 4.45
1364 1575 1.056660 GACCAAGACCAAGACCAGGA 58.943 55.000 0.00 0.00 0.00 3.86
1365 1576 0.765510 ACCAAGACCAAGACCAGGAC 59.234 55.000 0.00 0.00 0.00 3.85
1366 1577 0.036875 CCAAGACCAAGACCAGGACC 59.963 60.000 0.00 0.00 0.00 4.46
1367 1578 0.764890 CAAGACCAAGACCAGGACCA 59.235 55.000 0.00 0.00 0.00 4.02
1368 1579 0.765510 AAGACCAAGACCAGGACCAC 59.234 55.000 0.00 0.00 0.00 4.16
1369 1580 1.004918 GACCAAGACCAGGACCACG 60.005 63.158 0.00 0.00 0.00 4.94
1370 1581 1.458777 ACCAAGACCAGGACCACGA 60.459 57.895 0.00 0.00 0.00 4.35
1371 1582 1.004918 CCAAGACCAGGACCACGAC 60.005 63.158 0.00 0.00 0.00 4.34
1372 1583 1.004918 CAAGACCAGGACCACGACC 60.005 63.158 0.00 0.00 0.00 4.79
1373 1584 1.152312 AAGACCAGGACCACGACCT 60.152 57.895 0.00 0.00 38.40 3.85
1391 1602 2.203938 GGACCTGGACCTGGACCA 60.204 66.667 26.62 16.86 37.28 4.02
1420 1631 6.298441 AGGAAGAAGAAGATGAAGAAGAGG 57.702 41.667 0.00 0.00 0.00 3.69
1422 1633 6.500049 AGGAAGAAGAAGATGAAGAAGAGGAA 59.500 38.462 0.00 0.00 0.00 3.36
1428 1639 6.204555 AGAAGATGAAGAAGAGGAAGAGGAT 58.795 40.000 0.00 0.00 0.00 3.24
1430 1641 4.655186 AGATGAAGAAGAGGAAGAGGATGG 59.345 45.833 0.00 0.00 0.00 3.51
1431 1642 2.503356 TGAAGAAGAGGAAGAGGATGGC 59.497 50.000 0.00 0.00 0.00 4.40
1459 1688 1.273552 ACCAAGAAGAGGAGGAGGAGG 60.274 57.143 0.00 0.00 0.00 4.30
1460 1689 1.007721 CCAAGAAGAGGAGGAGGAGGA 59.992 57.143 0.00 0.00 0.00 3.71
1461 1690 2.387757 CAAGAAGAGGAGGAGGAGGAG 58.612 57.143 0.00 0.00 0.00 3.69
1479 1708 2.390599 GCAATTGCTCGTCGCCAGA 61.391 57.895 23.21 0.00 38.05 3.86
1611 1864 1.115467 CACGCAAGAGGGTCTCCTAT 58.885 55.000 0.00 0.00 45.05 2.57
1852 2108 0.601558 GTTACAGGACACTCTCGCCA 59.398 55.000 0.00 0.00 0.00 5.69
1912 2168 4.395583 GCAGTGCAGACGGCTTGC 62.396 66.667 11.09 10.54 45.15 4.01
1916 2172 3.939939 TGCAGACGGCTTGCAGGA 61.940 61.111 10.77 0.00 45.15 3.86
1917 2173 3.123620 GCAGACGGCTTGCAGGAG 61.124 66.667 0.00 0.00 40.25 3.69
1952 2212 3.457560 TCGATCTCGATTGGGGGAT 57.542 52.632 0.00 0.00 44.22 3.85
1955 2215 1.478510 CGATCTCGATTGGGGGATAGG 59.521 57.143 0.00 0.00 43.02 2.57
1963 2223 0.551377 TTGGGGGATAGGCAGGTTGA 60.551 55.000 0.00 0.00 0.00 3.18
2003 2263 1.198759 TGGTGGTAGTGAAGGGAGGC 61.199 60.000 0.00 0.00 0.00 4.70
2007 2267 1.992557 TGGTAGTGAAGGGAGGCAAAT 59.007 47.619 0.00 0.00 0.00 2.32
2037 2297 2.293122 CCTAGTCTTCATCCTCTGCTCG 59.707 54.545 0.00 0.00 0.00 5.03
2137 2405 3.327757 TCTTACCAGACCAGTTGCATTCT 59.672 43.478 0.00 0.00 0.00 2.40
2172 2440 4.232221 GTTGGTCTTTGCAGTGATTGATG 58.768 43.478 0.00 0.00 0.00 3.07
2188 2460 2.874014 TGATGTCTTGGACAATTGCCA 58.126 42.857 15.03 15.03 45.96 4.92
2192 2464 4.782019 TGTCTTGGACAATTGCCATAAC 57.218 40.909 18.34 17.89 39.78 1.89
2206 2478 5.782893 TGCCATAACTTAATTGTATGCCC 57.217 39.130 0.00 0.00 0.00 5.36
2208 2480 4.277423 GCCATAACTTAATTGTATGCCCGT 59.723 41.667 0.00 0.00 0.00 5.28
2257 2529 4.219288 ACTTTTTGGGCAGCATCTCTTAAG 59.781 41.667 0.00 0.00 0.00 1.85
2265 2537 4.512484 GCAGCATCTCTTAAGAACCTCTT 58.488 43.478 6.63 0.00 40.35 2.85
2268 2540 6.405538 CAGCATCTCTTAAGAACCTCTTCTT 58.594 40.000 6.63 1.57 46.56 2.52
2269 2541 6.313411 CAGCATCTCTTAAGAACCTCTTCTTG 59.687 42.308 6.63 0.00 44.90 3.02
2270 2542 6.212388 AGCATCTCTTAAGAACCTCTTCTTGA 59.788 38.462 6.63 0.00 44.90 3.02
2340 2612 8.806146 TCATATGACTGCTCTGCTATTTGTATA 58.194 33.333 0.00 0.00 0.00 1.47
2341 2613 9.597170 CATATGACTGCTCTGCTATTTGTATAT 57.403 33.333 0.00 0.00 0.00 0.86
2342 2614 7.902387 ATGACTGCTCTGCTATTTGTATATG 57.098 36.000 0.00 0.00 0.00 1.78
2343 2615 5.698089 TGACTGCTCTGCTATTTGTATATGC 59.302 40.000 0.00 0.00 0.00 3.14
2344 2616 5.614308 ACTGCTCTGCTATTTGTATATGCA 58.386 37.500 0.00 0.00 0.00 3.96
2346 2618 6.713903 ACTGCTCTGCTATTTGTATATGCATT 59.286 34.615 3.54 0.00 33.02 3.56
2347 2619 6.905578 TGCTCTGCTATTTGTATATGCATTG 58.094 36.000 3.54 0.00 33.02 2.82
2349 2621 7.392393 TGCTCTGCTATTTGTATATGCATTGAT 59.608 33.333 3.54 0.00 33.02 2.57
2381 2664 7.615582 TCAGTATGGTGTGAAGATTTTCATC 57.384 36.000 1.53 0.00 40.34 2.92
2384 2667 7.770433 CAGTATGGTGTGAAGATTTTCATCCTA 59.230 37.037 17.43 5.88 44.62 2.94
2505 2788 9.565213 GATGAATTGATTTCTAAGTTTCACCAG 57.435 33.333 0.00 0.00 35.23 4.00
2517 2801 8.041323 TCTAAGTTTCACCAGATATTTCAGTCC 58.959 37.037 0.00 0.00 0.00 3.85
2664 2950 8.924511 ATCATCGTTTGGATATCATTTTACCT 57.075 30.769 4.83 0.00 32.85 3.08
2698 2985 2.158842 AGCTCTTGTATCTCACCATGCC 60.159 50.000 0.00 0.00 0.00 4.40
2702 2989 2.820059 TGTATCTCACCATGCCGATC 57.180 50.000 0.00 0.00 0.00 3.69
2715 3002 1.575576 GCCGATCATGATCTGCTGCC 61.576 60.000 32.70 13.44 42.40 4.85
2716 3003 0.035036 CCGATCATGATCTGCTGCCT 59.965 55.000 28.48 0.00 35.72 4.75
2717 3004 1.430479 CGATCATGATCTGCTGCCTC 58.570 55.000 28.48 5.71 35.72 4.70
2718 3005 1.810959 GATCATGATCTGCTGCCTCC 58.189 55.000 25.47 0.00 35.04 4.30
2729 3016 2.853542 TGCCTCCAGAGTTGCCCA 60.854 61.111 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.107901 GCAGATGGGGATCTCAAGGATT 59.892 50.000 0.00 0.00 34.33 3.01
6 7 1.704070 GCAGATGGGGATCTCAAGGAT 59.296 52.381 0.00 0.00 37.37 3.24
7 8 1.135094 GCAGATGGGGATCTCAAGGA 58.865 55.000 0.00 0.00 0.00 3.36
8 9 0.110104 GGCAGATGGGGATCTCAAGG 59.890 60.000 0.00 0.00 0.00 3.61
9 10 0.841961 TGGCAGATGGGGATCTCAAG 59.158 55.000 0.00 0.00 0.00 3.02
10 11 0.548031 GTGGCAGATGGGGATCTCAA 59.452 55.000 0.00 0.00 0.00 3.02
11 12 1.689243 CGTGGCAGATGGGGATCTCA 61.689 60.000 0.00 0.00 0.00 3.27
12 13 1.070445 CGTGGCAGATGGGGATCTC 59.930 63.158 0.00 0.00 0.00 2.75
13 14 3.112205 GCGTGGCAGATGGGGATCT 62.112 63.158 0.00 0.00 0.00 2.75
14 15 2.592861 GCGTGGCAGATGGGGATC 60.593 66.667 0.00 0.00 0.00 3.36
15 16 4.195334 GGCGTGGCAGATGGGGAT 62.195 66.667 0.00 0.00 0.00 3.85
16 17 3.858220 TATAGGCGTGGCAGATGGGGA 62.858 57.143 0.00 0.00 0.00 4.81
17 18 1.480212 TATAGGCGTGGCAGATGGGG 61.480 60.000 0.00 0.00 0.00 4.96
18 19 0.615331 ATATAGGCGTGGCAGATGGG 59.385 55.000 0.00 0.00 0.00 4.00
19 20 2.079158 CAATATAGGCGTGGCAGATGG 58.921 52.381 0.00 0.00 0.00 3.51
20 21 1.466167 GCAATATAGGCGTGGCAGATG 59.534 52.381 0.00 0.00 0.00 2.90
21 22 1.813513 GCAATATAGGCGTGGCAGAT 58.186 50.000 0.00 0.00 0.00 2.90
22 23 3.305709 GCAATATAGGCGTGGCAGA 57.694 52.632 0.00 0.00 0.00 4.26
31 32 2.224079 GTCATGTGCCACGCAATATAGG 59.776 50.000 0.00 0.00 41.47 2.57
32 33 2.224079 GGTCATGTGCCACGCAATATAG 59.776 50.000 0.00 0.00 41.47 1.31
33 34 2.158827 AGGTCATGTGCCACGCAATATA 60.159 45.455 10.70 0.00 41.47 0.86
34 35 1.024271 GGTCATGTGCCACGCAATAT 58.976 50.000 0.00 0.00 41.47 1.28
35 36 0.035534 AGGTCATGTGCCACGCAATA 60.036 50.000 10.70 0.00 41.47 1.90
36 37 0.895100 AAGGTCATGTGCCACGCAAT 60.895 50.000 10.70 0.00 41.47 3.56
37 38 0.250510 TAAGGTCATGTGCCACGCAA 60.251 50.000 10.70 0.00 41.47 4.85
38 39 0.035534 ATAAGGTCATGTGCCACGCA 60.036 50.000 10.70 0.00 35.60 5.24
39 40 0.657840 GATAAGGTCATGTGCCACGC 59.342 55.000 10.70 0.00 0.00 5.34
40 41 0.930310 CGATAAGGTCATGTGCCACG 59.070 55.000 10.70 7.35 0.00 4.94
44 45 1.268234 GCAAGCGATAAGGTCATGTGC 60.268 52.381 0.00 0.00 0.00 4.57
46 47 1.210478 AGGCAAGCGATAAGGTCATGT 59.790 47.619 0.00 0.00 0.00 3.21
62 63 4.641989 GCAAAGATCCTTTATGAAGAGGCA 59.358 41.667 0.00 0.00 34.71 4.75
63 64 4.037327 GGCAAAGATCCTTTATGAAGAGGC 59.963 45.833 0.00 0.00 34.71 4.70
68 69 2.687935 GGCGGCAAAGATCCTTTATGAA 59.312 45.455 3.07 0.00 0.00 2.57
72 73 0.329931 TGGGCGGCAAAGATCCTTTA 59.670 50.000 12.47 0.00 0.00 1.85
79 80 1.002624 CTAAGGTGGGCGGCAAAGA 60.003 57.895 12.47 0.00 0.00 2.52
81 82 2.034999 CCTAAGGTGGGCGGCAAA 59.965 61.111 12.47 0.00 0.00 3.68
118 119 2.660552 CACGCCTTTCACGTCGGT 60.661 61.111 0.00 0.00 42.96 4.69
124 125 2.597510 AAGGGGCACGCCTTTCAC 60.598 61.111 12.85 0.00 44.92 3.18
134 135 1.556911 GAGACTCATGAAGAAGGGGCA 59.443 52.381 0.00 0.00 0.00 5.36
135 136 1.556911 TGAGACTCATGAAGAAGGGGC 59.443 52.381 0.00 0.00 0.00 5.80
138 139 4.201792 CGCATTTGAGACTCATGAAGAAGG 60.202 45.833 5.87 0.08 0.00 3.46
153 154 2.819595 GGAGAGGCGCGCATTTGA 60.820 61.111 34.42 0.00 0.00 2.69
194 203 1.238439 CTCGAAAAAGGCCAGAGCAA 58.762 50.000 5.01 0.00 42.56 3.91
196 205 1.239347 AACTCGAAAAAGGCCAGAGC 58.761 50.000 5.01 0.00 38.76 4.09
199 208 1.663161 GCGAAACTCGAAAAAGGCCAG 60.663 52.381 5.01 0.00 43.74 4.85
202 211 2.331809 ATGCGAAACTCGAAAAAGGC 57.668 45.000 0.00 0.00 43.74 4.35
206 215 5.351233 ACAACATATGCGAAACTCGAAAA 57.649 34.783 1.58 0.00 43.74 2.29
220 229 1.414181 CTCAGGGAGGCGACAACATAT 59.586 52.381 0.00 0.00 0.00 1.78
223 232 3.059982 CTCAGGGAGGCGACAACA 58.940 61.111 0.00 0.00 0.00 3.33
269 278 1.135112 TGTGGTCTGACGATGATTCCG 60.135 52.381 1.07 0.00 0.00 4.30
270 279 2.672961 TGTGGTCTGACGATGATTCC 57.327 50.000 1.07 0.00 0.00 3.01
341 350 2.627699 TCAGTTTCCAAACAGGGATTGC 59.372 45.455 5.03 0.00 41.30 3.56
348 357 4.496840 GGGTTTACGTCAGTTTCCAAACAG 60.497 45.833 0.00 0.00 41.30 3.16
359 368 2.426381 GGGAGACTAGGGTTTACGTCAG 59.574 54.545 0.00 0.00 0.00 3.51
381 390 3.593551 GATTGCACACGTGGCACCG 62.594 63.158 24.98 9.88 41.75 4.94
384 393 2.983030 GGGATTGCACACGTGGCA 60.983 61.111 22.47 22.47 40.00 4.92
390 399 1.327303 TCCAAACAGGGATTGCACAC 58.673 50.000 0.00 0.00 38.24 3.82
392 401 2.365293 AGTTTCCAAACAGGGATTGCAC 59.635 45.455 5.03 0.00 41.30 4.57
396 405 2.884639 CGTCAGTTTCCAAACAGGGATT 59.115 45.455 5.03 0.00 41.30 3.01
399 408 1.675552 ACGTCAGTTTCCAAACAGGG 58.324 50.000 5.03 0.00 41.30 4.45
401 410 4.496840 GGGTTTACGTCAGTTTCCAAACAG 60.497 45.833 0.00 0.00 41.30 3.16
413 422 2.450476 GGGAGACTAGGGTTTACGTCA 58.550 52.381 0.00 0.00 0.00 4.35
415 424 1.857965 GGGGAGACTAGGGTTTACGT 58.142 55.000 0.00 0.00 0.00 3.57
421 430 2.363361 CACCGGGGAGACTAGGGT 59.637 66.667 6.32 0.00 0.00 4.34
426 435 2.815684 TATGTGGCACCGGGGAGACT 62.816 60.000 8.67 0.00 0.00 3.24
428 437 1.383943 ATATGTGGCACCGGGGAGA 60.384 57.895 8.67 0.00 0.00 3.71
449 458 3.951680 ACGTCAGTTTCCAAACAAGGATT 59.048 39.130 5.03 0.00 41.30 3.01
460 469 4.021632 AGACTAGGGTTTACGTCAGTTTCC 60.022 45.833 0.00 0.00 0.00 3.13
466 475 2.450476 GGGAGACTAGGGTTTACGTCA 58.550 52.381 0.00 0.00 0.00 4.35
479 488 2.815684 TATGTGGCACCGGGGAGACT 62.816 60.000 8.67 0.00 0.00 3.24
481 490 1.383943 ATATGTGGCACCGGGGAGA 60.384 57.895 8.67 0.00 0.00 3.71
488 497 1.696063 AGGATTGCATATGTGGCACC 58.304 50.000 16.26 0.00 41.75 5.01
521 530 3.073101 GGGAGTCCGGGCTTACGT 61.073 66.667 11.49 0.00 0.00 3.57
531 540 2.837031 TACGTGGTACCGGGGAGTCC 62.837 65.000 6.32 0.00 0.00 3.85
533 542 1.039233 CATACGTGGTACCGGGGAGT 61.039 60.000 6.32 5.20 0.00 3.85
534 543 1.737816 CATACGTGGTACCGGGGAG 59.262 63.158 6.32 0.00 0.00 4.30
535 544 2.425569 GCATACGTGGTACCGGGGA 61.426 63.158 6.32 0.00 0.00 4.81
536 545 2.107546 GCATACGTGGTACCGGGG 59.892 66.667 6.32 1.01 0.00 5.73
567 683 2.038557 AGTCCATGGCTTACGTCAGTTT 59.961 45.455 6.96 0.00 0.00 2.66
578 694 4.741239 ACCGGGGAGTCCATGGCT 62.741 66.667 16.71 7.71 34.53 4.75
617 734 1.871039 GCACGGCTAAGTCTGTTTTCA 59.129 47.619 0.00 0.00 0.00 2.69
619 736 2.256117 AGCACGGCTAAGTCTGTTTT 57.744 45.000 0.00 0.00 36.99 2.43
620 737 2.299297 AGTAGCACGGCTAAGTCTGTTT 59.701 45.455 7.11 0.00 43.07 2.83
631 748 4.814294 CCCGGTCAGTAGCACGGC 62.814 72.222 0.00 0.00 44.70 5.68
632 749 1.956629 AATCCCGGTCAGTAGCACGG 61.957 60.000 0.00 0.00 45.57 4.94
643 760 0.461339 CGGAAATCGACAATCCCGGT 60.461 55.000 0.00 0.00 42.43 5.28
644 761 2.307363 CGGAAATCGACAATCCCGG 58.693 57.895 0.00 0.00 42.43 5.73
661 778 1.497161 ACCCTAACCTCTCAATCCCG 58.503 55.000 0.00 0.00 0.00 5.14
668 785 4.569719 TGGAATCAAACCCTAACCTCTC 57.430 45.455 0.00 0.00 0.00 3.20
669 786 4.105697 TGTTGGAATCAAACCCTAACCTCT 59.894 41.667 0.00 0.00 34.28 3.69
675 792 3.161866 GCCTTGTTGGAATCAAACCCTA 58.838 45.455 0.00 0.00 38.35 3.53
687 804 2.288458 TCGAACTTTTACGCCTTGTTGG 59.712 45.455 0.00 0.00 39.35 3.77
689 806 2.546789 CCTCGAACTTTTACGCCTTGTT 59.453 45.455 0.00 0.00 0.00 2.83
700 817 8.880750 GCTAGTATGAAATAAACCTCGAACTTT 58.119 33.333 0.00 0.00 0.00 2.66
701 818 7.494952 GGCTAGTATGAAATAAACCTCGAACTT 59.505 37.037 0.00 0.00 0.00 2.66
706 823 7.407337 GTTTGGCTAGTATGAAATAAACCTCG 58.593 38.462 0.00 0.00 0.00 4.63
707 824 7.466860 CGGTTTGGCTAGTATGAAATAAACCTC 60.467 40.741 0.00 0.00 42.05 3.85
745 919 1.152756 GGTTTGGCCACACTGACCT 60.153 57.895 21.00 0.00 37.17 3.85
801 987 1.086696 GTTCACGTGGATGGATGGTG 58.913 55.000 17.00 0.00 0.00 4.17
802 988 0.035439 GGTTCACGTGGATGGATGGT 60.035 55.000 17.00 0.00 0.00 3.55
803 989 1.089481 CGGTTCACGTGGATGGATGG 61.089 60.000 17.00 0.00 37.93 3.51
804 990 1.705337 GCGGTTCACGTGGATGGATG 61.705 60.000 17.00 0.86 46.52 3.51
805 991 1.449601 GCGGTTCACGTGGATGGAT 60.450 57.895 17.00 0.00 46.52 3.41
806 992 2.047655 GCGGTTCACGTGGATGGA 60.048 61.111 17.00 0.00 46.52 3.41
1356 1567 1.908793 CAGGTCGTGGTCCTGGTCT 60.909 63.158 4.27 0.00 46.03 3.85
1357 1568 2.657237 CAGGTCGTGGTCCTGGTC 59.343 66.667 4.27 0.00 46.03 4.02
1366 1577 2.657237 GTCCAGGTCCAGGTCGTG 59.343 66.667 0.00 0.00 0.00 4.35
1367 1578 2.603776 GGTCCAGGTCCAGGTCGT 60.604 66.667 0.00 0.00 0.00 4.34
1368 1579 2.283966 AGGTCCAGGTCCAGGTCG 60.284 66.667 5.43 0.00 0.00 4.79
1369 1580 2.294078 CCAGGTCCAGGTCCAGGTC 61.294 68.421 5.43 0.00 0.00 3.85
1370 1581 2.203998 CCAGGTCCAGGTCCAGGT 60.204 66.667 5.43 0.00 0.00 4.00
1371 1582 2.122729 TCCAGGTCCAGGTCCAGG 59.877 66.667 7.77 7.77 33.67 4.45
1372 1583 2.294078 GGTCCAGGTCCAGGTCCAG 61.294 68.421 11.09 0.00 34.89 3.86
1373 1584 2.203938 GGTCCAGGTCCAGGTCCA 60.204 66.667 11.09 0.00 34.89 4.02
1374 1585 2.203938 TGGTCCAGGTCCAGGTCC 60.204 66.667 9.33 9.33 35.28 4.46
1375 1586 3.393360 CTGGTCCAGGTCCAGGTC 58.607 66.667 21.95 0.00 46.03 3.85
1391 1602 4.344938 TCATCTTCTTCTTCCTCCTCCT 57.655 45.455 0.00 0.00 0.00 3.69
1420 1631 0.757188 TCCTCCTCGCCATCCTCTTC 60.757 60.000 0.00 0.00 0.00 2.87
1422 1633 1.456705 GTCCTCCTCGCCATCCTCT 60.457 63.158 0.00 0.00 0.00 3.69
1428 1639 1.535444 TTCTTGGTCCTCCTCGCCA 60.535 57.895 0.00 0.00 34.23 5.69
1430 1641 0.174617 CTCTTCTTGGTCCTCCTCGC 59.825 60.000 0.00 0.00 34.23 5.03
1431 1642 0.820871 CCTCTTCTTGGTCCTCCTCG 59.179 60.000 0.00 0.00 34.23 4.63
1479 1708 1.244019 GGCCGTTGATGCTCCTGTTT 61.244 55.000 0.00 0.00 0.00 2.83
1566 1819 2.280119 GTGGACAGCGTGACAGCA 60.280 61.111 2.68 0.00 40.15 4.41
1593 1846 1.115467 CATAGGAGACCCTCTTGCGT 58.885 55.000 0.00 0.00 43.14 5.24
1611 1864 3.626996 CTGGAACATGGCGGCCTCA 62.627 63.158 21.46 0.00 38.20 3.86
1864 2120 3.330720 CCTGGCCTTCTTCCCCGT 61.331 66.667 3.32 0.00 0.00 5.28
1912 2168 0.965439 AATCGCTAGCTAGCCTCCTG 59.035 55.000 34.27 22.19 46.34 3.86
1940 2200 1.127567 CCTGCCTATCCCCCAATCGA 61.128 60.000 0.00 0.00 0.00 3.59
1941 2201 1.376466 CCTGCCTATCCCCCAATCG 59.624 63.158 0.00 0.00 0.00 3.34
1942 2202 0.853530 AACCTGCCTATCCCCCAATC 59.146 55.000 0.00 0.00 0.00 2.67
1943 2203 0.557729 CAACCTGCCTATCCCCCAAT 59.442 55.000 0.00 0.00 0.00 3.16
1944 2204 0.551377 TCAACCTGCCTATCCCCCAA 60.551 55.000 0.00 0.00 0.00 4.12
1945 2205 0.551377 TTCAACCTGCCTATCCCCCA 60.551 55.000 0.00 0.00 0.00 4.96
1946 2206 0.629058 TTTCAACCTGCCTATCCCCC 59.371 55.000 0.00 0.00 0.00 5.40
1952 2212 2.656947 AACAGCTTTCAACCTGCCTA 57.343 45.000 0.00 0.00 32.37 3.93
1955 2215 5.985530 AGAAAATAAACAGCTTTCAACCTGC 59.014 36.000 0.00 0.00 32.59 4.85
1963 2223 8.306761 CCACCAGATAAGAAAATAAACAGCTTT 58.693 33.333 0.00 0.00 0.00 3.51
2003 2263 9.050601 GGATGAAGACTAGGAACAATCTATTTG 57.949 37.037 0.00 0.00 41.36 2.32
2007 2267 7.286546 CAGAGGATGAAGACTAGGAACAATCTA 59.713 40.741 0.00 0.00 0.00 1.98
2037 2297 6.581542 CGACGAGAACTAAATACATACATCCC 59.418 42.308 0.00 0.00 0.00 3.85
2137 2405 5.123227 CAAAGACCAACCAAAGTAGAGACA 58.877 41.667 0.00 0.00 0.00 3.41
2172 2440 5.391312 AAGTTATGGCAATTGTCCAAGAC 57.609 39.130 20.56 19.64 37.13 3.01
2188 2460 5.529800 GGTGACGGGCATACAATTAAGTTAT 59.470 40.000 0.00 0.00 0.00 1.89
2192 2464 3.312421 CAGGTGACGGGCATACAATTAAG 59.688 47.826 0.00 0.00 0.00 1.85
2229 2501 1.412079 TGCTGCCCAAAAAGTCACAT 58.588 45.000 0.00 0.00 0.00 3.21
2257 2529 6.402222 ACTACACATCATCAAGAAGAGGTTC 58.598 40.000 0.00 0.00 0.00 3.62
2265 2537 5.412594 GCCAAGAAACTACACATCATCAAGA 59.587 40.000 0.00 0.00 0.00 3.02
2268 2540 4.650734 TGCCAAGAAACTACACATCATCA 58.349 39.130 0.00 0.00 0.00 3.07
2269 2541 5.824904 ATGCCAAGAAACTACACATCATC 57.175 39.130 0.00 0.00 0.00 2.92
2270 2542 7.886629 ATAATGCCAAGAAACTACACATCAT 57.113 32.000 0.00 0.00 0.00 2.45
2369 2652 9.947669 CTGAATGATGTTAGGATGAAAATCTTC 57.052 33.333 0.00 0.00 0.00 2.87
2381 2664 7.160049 AGCATGTATCTCTGAATGATGTTAGG 58.840 38.462 0.00 0.00 0.00 2.69
2384 2667 7.503549 TGTAGCATGTATCTCTGAATGATGTT 58.496 34.615 0.00 0.00 0.00 2.71
2661 2947 6.552932 ACAAGAGCTAAGGGAATAAAAAGGT 58.447 36.000 0.00 0.00 0.00 3.50
2664 2950 9.614792 GAGATACAAGAGCTAAGGGAATAAAAA 57.385 33.333 0.00 0.00 0.00 1.94
2677 2963 2.158842 GGCATGGTGAGATACAAGAGCT 60.159 50.000 0.00 0.00 0.00 4.09
2678 2964 2.216898 GGCATGGTGAGATACAAGAGC 58.783 52.381 0.00 0.00 0.00 4.09
2698 2985 1.430479 GAGGCAGCAGATCATGATCG 58.570 55.000 26.09 21.44 42.48 3.69
2702 2989 0.468648 TCTGGAGGCAGCAGATCATG 59.531 55.000 0.00 0.00 0.00 3.07
2715 3002 0.742281 CACGATGGGCAACTCTGGAG 60.742 60.000 0.00 0.00 0.00 3.86
2716 3003 1.296392 CACGATGGGCAACTCTGGA 59.704 57.895 0.00 0.00 0.00 3.86
2717 3004 1.746615 CCACGATGGGCAACTCTGG 60.747 63.158 0.00 0.00 32.67 3.86
2718 3005 0.742281 CTCCACGATGGGCAACTCTG 60.742 60.000 0.00 0.00 38.32 3.35
2729 3016 4.322349 CCTCTTCTTTCTGTTCTCCACGAT 60.322 45.833 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.