Multiple sequence alignment - TraesCS5A01G500700

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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 TraesCS5A01G500700 chr5A 100.000 3183 0 0 1 3183 666684703 666681521 0.000000e+00 5879.0
1 TraesCS5A01G500700 chr5A 84.300 2000 200 57 563 2516 666589280 666587349 0.000000e+00 1849.0
2 TraesCS5A01G500700 chr5A 89.572 1448 81 33 665 2076 666657383 666655970 0.000000e+00 1773.0
3 TraesCS5A01G500700 chr5A 84.931 1659 148 49 561 2182 666526022 666524429 0.000000e+00 1585.0
4 TraesCS5A01G500700 chr5A 96.032 378 15 0 2270 2647 614525292 614525669 1.620000e-172 616.0
5 TraesCS5A01G500700 chr5A 96.491 342 12 0 2270 2611 614548566 614548907 1.660000e-157 566.0
6 TraesCS5A01G500700 chr5A 91.534 378 30 2 2272 2647 631973891 631973514 1.310000e-143 520.0
7 TraesCS5A01G500700 chr4B 91.395 2243 128 37 4 2212 619936784 619934573 0.000000e+00 3013.0
8 TraesCS5A01G500700 chr4B 88.181 1633 129 31 658 2271 619659801 619658214 0.000000e+00 1888.0
9 TraesCS5A01G500700 chr4B 85.707 1861 139 66 475 2259 619788498 619786689 0.000000e+00 1845.0
10 TraesCS5A01G500700 chr4B 86.831 1663 111 43 661 2271 619775241 619773635 0.000000e+00 1759.0
11 TraesCS5A01G500700 chr4B 85.138 1662 136 47 561 2182 619590381 619588791 0.000000e+00 1598.0
12 TraesCS5A01G500700 chr4B 90.769 65 5 1 2651 2715 476373972 476373909 5.660000e-13 86.1
13 TraesCS5A01G500700 chr4D 85.837 1631 138 52 592 2182 485684112 485682535 0.000000e+00 1646.0
14 TraesCS5A01G500700 chr4D 92.520 1016 56 8 1264 2271 485764279 485763276 0.000000e+00 1437.0
15 TraesCS5A01G500700 chr4D 92.342 888 55 7 351 1236 485765149 485764273 0.000000e+00 1251.0
16 TraesCS5A01G500700 chr3A 97.407 540 13 1 2645 3183 677838203 677838742 0.000000e+00 918.0
17 TraesCS5A01G500700 chr4A 97.217 539 6 3 2645 3183 17394142 17394671 0.000000e+00 904.0
18 TraesCS5A01G500700 chr4A 86.170 564 49 11 2648 3183 731689321 731688759 1.650000e-162 582.0
19 TraesCS5A01G500700 chr1A 97.020 537 15 1 2648 3183 582746816 582746280 0.000000e+00 902.0
20 TraesCS5A01G500700 chr5D 93.002 543 31 4 2647 3183 21214631 21215172 0.000000e+00 785.0
21 TraesCS5A01G500700 chr1B 85.913 575 52 10 2637 3183 683093826 683094399 1.270000e-163 586.0
22 TraesCS5A01G500700 chr7B 84.547 563 57 14 2649 3183 111370771 111370211 6.050000e-147 531.0
23 TraesCS5A01G500700 chr1D 88.718 390 36 6 2801 3183 435531310 435530922 1.340000e-128 470.0
24 TraesCS5A01G500700 chr1D 90.714 140 7 3 2648 2786 435534099 435533965 7.010000e-42 182.0
25 TraesCS5A01G500700 chr6D 87.817 394 43 2 2795 3183 16747819 16747426 1.040000e-124 457.0
26 TraesCS5A01G500700 chr3B 88.571 280 27 3 2648 2926 772465069 772464794 5.090000e-88 335.0
27 TraesCS5A01G500700 chr6B 78.364 379 67 8 2273 2639 702267998 702268373 6.870000e-57 231.0
28 TraesCS5A01G500700 chr6A 91.489 141 7 4 2651 2789 34566985 34567122 4.190000e-44 189.0
29 TraesCS5A01G500700 chr6A 90.476 63 6 0 2648 2710 617941128 617941190 2.030000e-12 84.2
30 TraesCS5A01G500700 chr3D 85.106 141 20 1 2268 2407 580323840 580323980 3.310000e-30 143.0


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 TraesCS5A01G500700 chr5A 666681521 666684703 3182 True 5879 5879 100.000 1 3183 1 chr5A.!!$R5 3182
1 TraesCS5A01G500700 chr5A 666587349 666589280 1931 True 1849 1849 84.300 563 2516 1 chr5A.!!$R3 1953
2 TraesCS5A01G500700 chr5A 666655970 666657383 1413 True 1773 1773 89.572 665 2076 1 chr5A.!!$R4 1411
3 TraesCS5A01G500700 chr5A 666524429 666526022 1593 True 1585 1585 84.931 561 2182 1 chr5A.!!$R2 1621
4 TraesCS5A01G500700 chr4B 619934573 619936784 2211 True 3013 3013 91.395 4 2212 1 chr4B.!!$R6 2208
5 TraesCS5A01G500700 chr4B 619658214 619659801 1587 True 1888 1888 88.181 658 2271 1 chr4B.!!$R3 1613
6 TraesCS5A01G500700 chr4B 619786689 619788498 1809 True 1845 1845 85.707 475 2259 1 chr4B.!!$R5 1784
7 TraesCS5A01G500700 chr4B 619773635 619775241 1606 True 1759 1759 86.831 661 2271 1 chr4B.!!$R4 1610
8 TraesCS5A01G500700 chr4B 619588791 619590381 1590 True 1598 1598 85.138 561 2182 1 chr4B.!!$R2 1621
9 TraesCS5A01G500700 chr4D 485682535 485684112 1577 True 1646 1646 85.837 592 2182 1 chr4D.!!$R1 1590
10 TraesCS5A01G500700 chr4D 485763276 485765149 1873 True 1344 1437 92.431 351 2271 2 chr4D.!!$R2 1920
11 TraesCS5A01G500700 chr3A 677838203 677838742 539 False 918 918 97.407 2645 3183 1 chr3A.!!$F1 538
12 TraesCS5A01G500700 chr4A 17394142 17394671 529 False 904 904 97.217 2645 3183 1 chr4A.!!$F1 538
13 TraesCS5A01G500700 chr4A 731688759 731689321 562 True 582 582 86.170 2648 3183 1 chr4A.!!$R1 535
14 TraesCS5A01G500700 chr1A 582746280 582746816 536 True 902 902 97.020 2648 3183 1 chr1A.!!$R1 535
15 TraesCS5A01G500700 chr5D 21214631 21215172 541 False 785 785 93.002 2647 3183 1 chr5D.!!$F1 536
16 TraesCS5A01G500700 chr1B 683093826 683094399 573 False 586 586 85.913 2637 3183 1 chr1B.!!$F1 546
17 TraesCS5A01G500700 chr7B 111370211 111370771 560 True 531 531 84.547 2649 3183 1 chr7B.!!$R1 534
18 TraesCS5A01G500700 chr1D 435530922 435534099 3177 True 326 470 89.716 2648 3183 2 chr1D.!!$R1 535

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
492 518 0.032952 AGCAGACGCAAGGTAAACGA 59.967 50.0 0.0 0.0 46.39 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2453 2674 1.07597 GGCCATCCTTTCCTTCCCC 60.076 63.158 0.0 0.0 0.0 4.81 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
33 34 6.550938 TCTCCTAGCATCCCATATAACATG 57.449 41.667 0.00 0.00 0.00 3.21
34 35 6.263754 TCTCCTAGCATCCCATATAACATGA 58.736 40.000 0.00 0.00 0.00 3.07
76 79 8.916628 TTTTTGCAAGGCCTAGAAAAATAAAT 57.083 26.923 18.50 0.00 0.00 1.40
79 82 8.996024 TTGCAAGGCCTAGAAAAATAAATTAC 57.004 30.769 5.16 0.00 0.00 1.89
81 84 8.811994 TGCAAGGCCTAGAAAAATAAATTACTT 58.188 29.630 5.16 0.00 0.00 2.24
183 186 5.179742 TGCACGTCATTTTATAGTTTTCGGT 59.820 36.000 0.00 0.00 0.00 4.69
212 215 3.374058 CGGACCAAGCACAATAGTTTAGG 59.626 47.826 0.00 0.00 0.00 2.69
304 307 5.885230 TGCATTGTAATATCTAGCCATGC 57.115 39.130 0.00 0.00 0.00 4.06
325 328 3.194116 GCAAAATTGGGCAGAGAATCAGA 59.806 43.478 0.00 0.00 37.82 3.27
395 399 1.525077 GTGAAGGCACGGTGGTTCA 60.525 57.895 10.60 0.00 34.94 3.18
396 400 1.098712 GTGAAGGCACGGTGGTTCAA 61.099 55.000 10.60 0.00 34.94 2.69
438 442 6.129378 CCGTTATTGCAATAAAGCATCAATCG 60.129 38.462 28.75 22.87 45.19 3.34
454 458 2.621055 CAATCGGTTGAACAGACCCAAA 59.379 45.455 0.90 0.00 37.53 3.28
479 485 2.920490 GTTGAACGAGAGATCAGCAGAC 59.080 50.000 0.00 0.00 43.92 3.51
492 518 0.032952 AGCAGACGCAAGGTAAACGA 59.967 50.000 0.00 0.00 46.39 3.85
545 575 2.393764 CAACGTTGCCAGAAACAATCC 58.606 47.619 16.51 0.00 0.00 3.01
547 577 3.134574 ACGTTGCCAGAAACAATCCTA 57.865 42.857 0.00 0.00 0.00 2.94
548 578 3.074412 ACGTTGCCAGAAACAATCCTAG 58.926 45.455 0.00 0.00 0.00 3.02
549 579 2.159517 CGTTGCCAGAAACAATCCTAGC 60.160 50.000 0.00 0.00 0.00 3.42
550 580 3.084786 GTTGCCAGAAACAATCCTAGCT 58.915 45.455 0.00 0.00 0.00 3.32
634 668 7.112779 AGTAGCACAAGATAAATATATGCCCC 58.887 38.462 0.00 0.00 31.94 5.80
647 681 2.254152 ATGCCCCAGAACAGACTCTA 57.746 50.000 0.00 0.00 0.00 2.43
780 834 3.206150 CAAGTAAAGCCGGCACATATCT 58.794 45.455 31.54 15.51 0.00 1.98
965 1066 1.081376 GCAGCAGCAAGACAAGCAG 60.081 57.895 0.00 0.00 41.58 4.24
1053 1175 3.121019 GTCGATCAGGACCTCCCG 58.879 66.667 0.00 0.00 40.87 5.14
1799 1965 1.619975 TCCTCCTCCTCCTCCTCGT 60.620 63.158 0.00 0.00 0.00 4.18
1800 1966 1.152839 CCTCCTCCTCCTCCTCGTC 60.153 68.421 0.00 0.00 0.00 4.20
1801 1967 1.525077 CTCCTCCTCCTCCTCGTCG 60.525 68.421 0.00 0.00 0.00 5.12
1802 1968 2.260088 CTCCTCCTCCTCCTCGTCGT 62.260 65.000 0.00 0.00 0.00 4.34
1803 1969 1.820481 CCTCCTCCTCCTCGTCGTC 60.820 68.421 0.00 0.00 0.00 4.20
1816 1982 2.669229 TCGTCGTCGGTGGCACTA 60.669 61.111 18.45 3.17 37.69 2.74
2014 2186 1.262417 TGTCGAACATGTCCAGCCTA 58.738 50.000 0.00 0.00 0.00 3.93
2268 2449 9.366216 TGTAAATTCAGTTGTGCATAGTACTAG 57.634 33.333 8.85 2.30 0.00 2.57
2303 2523 6.254281 ACATTAATGGTGCTACAACTTGAC 57.746 37.500 19.37 0.00 0.00 3.18
2304 2524 5.767665 ACATTAATGGTGCTACAACTTGACA 59.232 36.000 19.37 0.00 0.00 3.58
2311 2531 4.449743 GGTGCTACAACTTGACATAAACGA 59.550 41.667 0.00 0.00 0.00 3.85
2325 2545 4.083324 ACATAAACGATCACTTTGGTGCTG 60.083 41.667 0.00 0.00 42.72 4.41
2332 2552 2.733956 TCACTTTGGTGCTGGAAGTTT 58.266 42.857 0.00 0.00 42.72 2.66
2333 2553 2.687935 TCACTTTGGTGCTGGAAGTTTC 59.312 45.455 0.00 0.00 42.72 2.78
2344 2564 3.998341 GCTGGAAGTTTCGGTGTACATTA 59.002 43.478 0.00 0.00 35.30 1.90
2349 2569 6.017770 TGGAAGTTTCGGTGTACATTAAAGTG 60.018 38.462 0.00 0.00 0.00 3.16
2367 2588 1.598601 GTGGTGCAAAACTTGGCATTG 59.401 47.619 0.00 0.00 42.75 2.82
2376 2597 0.311790 ACTTGGCATTGACGTGCAAG 59.688 50.000 0.00 0.00 46.81 4.01
2380 2601 0.871722 GGCATTGACGTGCAAGTACA 59.128 50.000 4.92 3.13 46.81 2.90
2396 2617 5.668866 GCAAGTACAGTGCTTATCTCGTTTG 60.669 44.000 12.85 0.00 39.00 2.93
2398 2619 6.263516 AGTACAGTGCTTATCTCGTTTGTA 57.736 37.500 0.00 0.00 0.00 2.41
2401 2622 7.914346 AGTACAGTGCTTATCTCGTTTGTATAC 59.086 37.037 0.00 0.00 0.00 1.47
2405 2626 5.745294 GTGCTTATCTCGTTTGTATACGGAA 59.255 40.000 0.00 0.00 41.67 4.30
2407 2628 6.419710 TGCTTATCTCGTTTGTATACGGAATG 59.580 38.462 0.00 2.04 41.67 2.67
2408 2629 6.639686 GCTTATCTCGTTTGTATACGGAATGA 59.360 38.462 11.16 11.16 41.67 2.57
2416 2637 4.041740 TGTATACGGAATGAGTGCTGAC 57.958 45.455 0.00 0.00 0.00 3.51
2417 2638 3.699538 TGTATACGGAATGAGTGCTGACT 59.300 43.478 0.00 0.00 33.98 3.41
2421 2642 1.751351 CGGAATGAGTGCTGACTAGGA 59.249 52.381 0.00 0.00 30.16 2.94
2422 2643 2.480416 CGGAATGAGTGCTGACTAGGAC 60.480 54.545 0.00 0.00 44.74 3.85
2424 2645 2.238084 ATGAGTGCTGACTAGGACCA 57.762 50.000 0.00 0.00 45.44 4.02
2425 2646 2.009681 TGAGTGCTGACTAGGACCAA 57.990 50.000 0.00 0.00 45.44 3.67
2428 2649 0.250513 GTGCTGACTAGGACCAAGGG 59.749 60.000 0.00 0.00 39.14 3.95
2449 2670 1.373497 CCACTGTCAGCCACTCGAC 60.373 63.158 0.00 0.00 0.00 4.20
2450 2671 1.662608 CACTGTCAGCCACTCGACT 59.337 57.895 0.00 0.00 33.18 4.18
2453 2674 0.453793 CTGTCAGCCACTCGACTAGG 59.546 60.000 0.00 0.00 33.18 3.02
2461 2682 0.033405 CACTCGACTAGGGGGAAGGA 60.033 60.000 0.00 0.00 0.00 3.36
2462 2683 0.708802 ACTCGACTAGGGGGAAGGAA 59.291 55.000 0.00 0.00 0.00 3.36
2463 2684 1.078324 ACTCGACTAGGGGGAAGGAAA 59.922 52.381 0.00 0.00 0.00 3.13
2464 2685 1.757699 CTCGACTAGGGGGAAGGAAAG 59.242 57.143 0.00 0.00 0.00 2.62
2465 2686 0.831307 CGACTAGGGGGAAGGAAAGG 59.169 60.000 0.00 0.00 0.00 3.11
2469 2690 1.777272 CTAGGGGGAAGGAAAGGATGG 59.223 57.143 0.00 0.00 0.00 3.51
2473 2694 1.222567 GGGAAGGAAAGGATGGCCTA 58.777 55.000 3.32 0.00 46.28 3.93
2478 2700 5.454966 GGAAGGAAAGGATGGCCTAATTTA 58.545 41.667 3.32 0.00 46.28 1.40
2481 2703 6.983906 AGGAAAGGATGGCCTAATTTATTG 57.016 37.500 3.32 0.00 46.28 1.90
2496 2718 7.968405 CCTAATTTATTGAAAAACACCCTCGAG 59.032 37.037 5.13 5.13 0.00 4.04
2501 2723 9.893634 TTTATTGAAAAACACCCTCGAGATATA 57.106 29.630 15.71 0.00 0.00 0.86
2510 2732 9.490379 AAACACCCTCGAGATATATATTTTCAC 57.510 33.333 15.71 0.00 0.00 3.18
2519 2741 9.612620 CGAGATATATATTTTCACAAAAAGGCC 57.387 33.333 0.00 0.00 37.76 5.19
2520 2742 9.914131 GAGATATATATTTTCACAAAAAGGCCC 57.086 33.333 0.00 0.00 37.76 5.80
2521 2743 9.660544 AGATATATATTTTCACAAAAAGGCCCT 57.339 29.630 0.00 0.00 37.76 5.19
2522 2744 9.696917 GATATATATTTTCACAAAAAGGCCCTG 57.303 33.333 0.00 0.00 37.76 4.45
2523 2745 5.823861 ATATTTTCACAAAAAGGCCCTGT 57.176 34.783 0.00 0.00 37.76 4.00
2524 2746 3.990959 TTTTCACAAAAAGGCCCTGTT 57.009 38.095 0.00 0.00 30.90 3.16
2525 2747 2.977772 TTCACAAAAAGGCCCTGTTG 57.022 45.000 2.42 2.42 0.00 3.33
2526 2748 2.151502 TCACAAAAAGGCCCTGTTGA 57.848 45.000 11.45 0.00 0.00 3.18
2527 2749 1.754226 TCACAAAAAGGCCCTGTTGAC 59.246 47.619 11.45 0.00 0.00 3.18
2528 2750 1.480137 CACAAAAAGGCCCTGTTGACA 59.520 47.619 11.45 0.00 0.00 3.58
2529 2751 2.102925 CACAAAAAGGCCCTGTTGACAT 59.897 45.455 11.45 0.00 0.00 3.06
2530 2752 3.320541 CACAAAAAGGCCCTGTTGACATA 59.679 43.478 11.45 0.00 0.00 2.29
2531 2753 3.573967 ACAAAAAGGCCCTGTTGACATAG 59.426 43.478 11.45 0.00 0.00 2.23
2532 2754 1.839424 AAAGGCCCTGTTGACATAGC 58.161 50.000 0.00 0.00 0.00 2.97
2533 2755 0.698238 AAGGCCCTGTTGACATAGCA 59.302 50.000 0.00 0.00 0.00 3.49
2534 2756 0.921896 AGGCCCTGTTGACATAGCAT 59.078 50.000 0.00 0.00 0.00 3.79
2535 2757 1.285962 AGGCCCTGTTGACATAGCATT 59.714 47.619 0.00 0.00 0.00 3.56
2536 2758 2.102578 GGCCCTGTTGACATAGCATTT 58.897 47.619 0.00 0.00 0.00 2.32
2537 2759 2.497273 GGCCCTGTTGACATAGCATTTT 59.503 45.455 0.00 0.00 0.00 1.82
2538 2760 3.055891 GGCCCTGTTGACATAGCATTTTT 60.056 43.478 0.00 0.00 0.00 1.94
2557 2779 3.417069 TTTCACCAGTATGACCAGTGG 57.583 47.619 7.91 7.91 43.58 4.00
2558 2780 1.275666 TCACCAGTATGACCAGTGGG 58.724 55.000 15.21 0.00 42.46 4.61
2569 2791 4.394712 CAGTGGGTCCCGCCACTC 62.395 72.222 18.36 0.00 44.23 3.51
2570 2792 4.954118 AGTGGGTCCCGCCACTCA 62.954 66.667 18.36 0.00 42.74 3.41
2571 2793 4.394712 GTGGGTCCCGCCACTCAG 62.395 72.222 10.73 0.00 39.65 3.35
2572 2794 4.631740 TGGGTCCCGCCACTCAGA 62.632 66.667 2.65 0.00 39.65 3.27
2573 2795 3.319198 GGGTCCCGCCACTCAGAA 61.319 66.667 0.00 0.00 39.65 3.02
2574 2796 2.266055 GGTCCCGCCACTCAGAAG 59.734 66.667 0.00 0.00 37.17 2.85
2575 2797 2.283529 GGTCCCGCCACTCAGAAGA 61.284 63.158 0.00 0.00 37.17 2.87
2577 2799 1.076727 TCCCGCCACTCAGAAGAGA 59.923 57.895 0.00 0.00 44.98 3.10
2578 2800 0.967887 TCCCGCCACTCAGAAGAGAG 60.968 60.000 0.00 0.00 44.98 3.20
2613 2835 2.457366 ACTAAAAGTGAGACTGCCCG 57.543 50.000 0.00 0.00 0.00 6.13
2614 2836 1.002087 ACTAAAAGTGAGACTGCCCGG 59.998 52.381 0.00 0.00 0.00 5.73
2615 2837 1.002087 CTAAAAGTGAGACTGCCCGGT 59.998 52.381 0.00 0.00 0.00 5.28
2616 2838 1.053424 AAAAGTGAGACTGCCCGGTA 58.947 50.000 0.00 0.00 0.00 4.02
2617 2839 1.276622 AAAGTGAGACTGCCCGGTAT 58.723 50.000 0.00 0.00 0.00 2.73
2618 2840 0.824759 AAGTGAGACTGCCCGGTATC 59.175 55.000 0.00 0.00 0.00 2.24
2619 2841 1.065928 GTGAGACTGCCCGGTATCG 59.934 63.158 0.00 0.00 30.95 2.92
2620 2842 1.077285 TGAGACTGCCCGGTATCGA 60.077 57.895 0.00 0.00 39.00 3.59
2621 2843 0.681887 TGAGACTGCCCGGTATCGAA 60.682 55.000 0.00 0.00 39.00 3.71
2622 2844 0.248949 GAGACTGCCCGGTATCGAAC 60.249 60.000 0.00 0.00 39.00 3.95
2623 2845 1.227176 GACTGCCCGGTATCGAACC 60.227 63.158 0.00 0.00 45.77 3.62
2624 2846 2.108362 CTGCCCGGTATCGAACCC 59.892 66.667 0.00 3.01 46.62 4.11
2625 2847 2.684294 TGCCCGGTATCGAACCCA 60.684 61.111 0.00 2.22 46.62 4.51
2626 2848 2.246761 CTGCCCGGTATCGAACCCAA 62.247 60.000 0.00 0.00 46.62 4.12
2627 2849 1.523032 GCCCGGTATCGAACCCAAG 60.523 63.158 0.00 0.17 46.62 3.61
2628 2850 1.963464 GCCCGGTATCGAACCCAAGA 61.963 60.000 0.00 0.00 46.62 3.02
2629 2851 0.179092 CCCGGTATCGAACCCAAGAC 60.179 60.000 0.00 0.00 46.62 3.01
2630 2852 0.179092 CCGGTATCGAACCCAAGACC 60.179 60.000 0.00 0.00 46.62 3.85
2631 2853 0.533491 CGGTATCGAACCCAAGACCA 59.467 55.000 10.07 0.00 46.62 4.02
2632 2854 1.066716 CGGTATCGAACCCAAGACCAA 60.067 52.381 10.07 0.00 46.62 3.67
2633 2855 2.353323 GGTATCGAACCCAAGACCAAC 58.647 52.381 0.00 0.00 43.16 3.77
2634 2856 2.289819 GGTATCGAACCCAAGACCAACA 60.290 50.000 0.00 0.00 43.16 3.33
2635 2857 2.649531 ATCGAACCCAAGACCAACAA 57.350 45.000 0.00 0.00 0.00 2.83
2636 2858 1.670791 TCGAACCCAAGACCAACAAC 58.329 50.000 0.00 0.00 0.00 3.32
2637 2859 1.210967 TCGAACCCAAGACCAACAACT 59.789 47.619 0.00 0.00 0.00 3.16
2638 2860 2.021457 CGAACCCAAGACCAACAACTT 58.979 47.619 0.00 0.00 0.00 2.66
2643 2865 5.333299 ACCCAAGACCAACAACTTTAAAC 57.667 39.130 0.00 0.00 0.00 2.01
2943 5808 3.951037 ACATGGTTGTAGCTTGAACACAA 59.049 39.130 0.00 0.00 33.16 3.33
3044 5913 0.675633 ACTGCCATGTCCAGCAAAAC 59.324 50.000 9.75 0.00 38.82 2.43
3050 5919 3.068560 CCATGTCCAGCAAAACCAAATG 58.931 45.455 0.00 0.00 0.00 2.32
3073 5942 5.872070 TGTAAAAAGCAACAAAAACCTCCAG 59.128 36.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.307339 GGGATGCTAGGAGATGACAATCC 60.307 52.174 2.50 2.50 32.77 3.01
2 3 3.326006 TGGGATGCTAGGAGATGACAATC 59.674 47.826 0.00 0.00 0.00 2.67
14 15 9.458727 AAGAATTCATGTTATATGGGATGCTAG 57.541 33.333 8.44 0.00 0.00 3.42
98 101 6.092807 GTGTTGGACAGTTTTGCCAATAAAAA 59.907 34.615 0.00 0.00 40.27 1.94
109 112 7.110155 CCATATACCTAGTGTTGGACAGTTTT 58.890 38.462 0.00 0.00 33.15 2.43
115 118 6.885922 AGAAACCATATACCTAGTGTTGGAC 58.114 40.000 7.27 0.00 0.00 4.02
149 152 9.567848 CTATAAAATGACGTGCATTAAACCTTT 57.432 29.630 11.79 6.19 46.25 3.11
183 186 0.179234 TGTGCTTGGTCCGACTTGAA 59.821 50.000 0.00 0.00 0.00 2.69
279 282 6.094464 GCATGGCTAGATATTACAATGCATCA 59.906 38.462 0.00 0.00 0.00 3.07
280 283 6.094464 TGCATGGCTAGATATTACAATGCATC 59.906 38.462 0.00 0.00 36.55 3.91
304 307 4.461781 AGTCTGATTCTCTGCCCAATTTTG 59.538 41.667 0.00 0.00 0.00 2.44
363 367 3.262405 TGCCTTCACCGTACCTAAGAAAT 59.738 43.478 0.00 0.00 0.00 2.17
396 400 9.313118 GCAATAACGGAAATTTTATCCTTTCAT 57.687 29.630 0.00 0.00 33.89 2.57
438 442 1.338020 CAGCTTTGGGTCTGTTCAACC 59.662 52.381 0.00 0.00 35.97 3.77
454 458 2.673610 GCTGATCTCTCGTTCAACAGCT 60.674 50.000 0.00 0.00 43.54 4.24
479 485 2.542595 ACTTTCACTCGTTTACCTTGCG 59.457 45.455 0.00 0.00 0.00 4.85
532 562 3.118223 AGGTAGCTAGGATTGTTTCTGGC 60.118 47.826 0.00 0.00 37.69 4.85
575 605 3.340814 AACCTGATGGCTAAGACTGTG 57.659 47.619 0.00 0.00 36.63 3.66
614 644 7.448161 TGTTCTGGGGCATATATTTATCTTGTG 59.552 37.037 0.00 0.00 0.00 3.33
634 668 6.533367 GGCTTAGACATTTAGAGTCTGTTCTG 59.467 42.308 1.86 0.00 45.38 3.02
647 681 4.022329 CACCCTTTTTCGGCTTAGACATTT 60.022 41.667 0.00 0.00 0.00 2.32
755 809 3.361174 GCCGGCTTTACTTGGCAA 58.639 55.556 22.15 0.00 46.76 4.52
965 1066 1.226435 AAGTGCTCGATCGTCGCTC 60.226 57.895 24.40 21.65 40.21 5.03
1746 1906 3.054503 CCTGGACGTCGTCGGACT 61.055 66.667 18.61 0.00 41.16 3.85
1799 1965 1.985447 GATAGTGCCACCGACGACGA 61.985 60.000 9.28 0.00 42.66 4.20
1800 1966 1.585521 GATAGTGCCACCGACGACG 60.586 63.158 0.00 0.00 39.43 5.12
1801 1967 1.226888 GGATAGTGCCACCGACGAC 60.227 63.158 0.00 0.00 0.00 4.34
1802 1968 3.203442 GGATAGTGCCACCGACGA 58.797 61.111 0.00 0.00 0.00 4.20
1813 1979 1.450312 GCTGCTGTTGCCGGATAGT 60.450 57.895 5.05 0.00 38.71 2.12
1816 1982 2.749044 CTGCTGCTGTTGCCGGAT 60.749 61.111 5.05 0.00 38.71 4.18
1852 2024 1.377856 GTCTGCTTCCTCCTTGGCC 60.378 63.158 0.00 0.00 35.26 5.36
1859 2031 2.507324 GGCGACGTCTGCTTCCTC 60.507 66.667 24.21 9.81 0.00 3.71
2214 2393 7.817418 AACCATTACTCTGCTTCAAGTTTTA 57.183 32.000 0.00 0.00 0.00 1.52
2268 2449 7.989826 AGCACCATTAATGTAATTGACTCTTC 58.010 34.615 14.25 0.00 36.99 2.87
2283 2503 7.987750 TTATGTCAAGTTGTAGCACCATTAA 57.012 32.000 2.11 0.00 0.00 1.40
2285 2505 6.567701 CGTTTATGTCAAGTTGTAGCACCATT 60.568 38.462 2.11 0.00 0.00 3.16
2286 2506 5.106712 CGTTTATGTCAAGTTGTAGCACCAT 60.107 40.000 2.11 0.67 0.00 3.55
2289 2509 5.585500 TCGTTTATGTCAAGTTGTAGCAC 57.415 39.130 2.11 0.00 0.00 4.40
2325 2545 6.368213 CACTTTAATGTACACCGAAACTTCC 58.632 40.000 0.00 0.00 0.00 3.46
2332 2552 3.068560 GCACCACTTTAATGTACACCGA 58.931 45.455 0.00 0.00 0.00 4.69
2333 2553 2.809119 TGCACCACTTTAATGTACACCG 59.191 45.455 0.00 0.00 0.00 4.94
2344 2564 1.277557 TGCCAAGTTTTGCACCACTTT 59.722 42.857 6.93 0.00 30.48 2.66
2349 2569 1.866601 GTCAATGCCAAGTTTTGCACC 59.133 47.619 0.00 0.00 40.88 5.01
2367 2588 1.217882 AAGCACTGTACTTGCACGTC 58.782 50.000 18.52 0.00 42.83 4.34
2376 2597 7.097128 CGTATACAAACGAGATAAGCACTGTAC 60.097 40.741 3.32 0.00 45.68 2.90
2380 2601 5.066893 TCCGTATACAAACGAGATAAGCACT 59.933 40.000 3.32 0.00 45.68 4.40
2396 2617 4.308899 AGTCAGCACTCATTCCGTATAC 57.691 45.455 0.00 0.00 0.00 1.47
2398 2619 3.319405 CCTAGTCAGCACTCATTCCGTAT 59.681 47.826 0.00 0.00 33.62 3.06
2401 2622 1.751351 TCCTAGTCAGCACTCATTCCG 59.249 52.381 0.00 0.00 33.62 4.30
2405 2626 2.238084 TGGTCCTAGTCAGCACTCAT 57.762 50.000 0.00 0.00 33.62 2.90
2407 2628 1.205893 CCTTGGTCCTAGTCAGCACTC 59.794 57.143 0.00 0.00 33.62 3.51
2408 2629 1.270907 CCTTGGTCCTAGTCAGCACT 58.729 55.000 0.00 0.00 36.55 4.40
2421 2642 3.580319 GACAGTGGGCCCCTTGGT 61.580 66.667 22.27 12.60 0.00 3.67
2422 2643 3.574074 CTGACAGTGGGCCCCTTGG 62.574 68.421 22.27 8.95 0.00 3.61
2424 2645 3.971702 GCTGACAGTGGGCCCCTT 61.972 66.667 22.27 3.80 0.00 3.95
2428 2649 3.909086 GAGTGGCTGACAGTGGGCC 62.909 68.421 14.44 14.44 45.45 5.80
2433 2654 1.169577 CTAGTCGAGTGGCTGACAGT 58.830 55.000 2.10 0.00 37.58 3.55
2444 2665 1.757699 CTTTCCTTCCCCCTAGTCGAG 59.242 57.143 0.00 0.00 0.00 4.04
2449 2670 1.777272 CCATCCTTTCCTTCCCCCTAG 59.223 57.143 0.00 0.00 0.00 3.02
2450 2671 1.907240 CCATCCTTTCCTTCCCCCTA 58.093 55.000 0.00 0.00 0.00 3.53
2453 2674 1.075970 GGCCATCCTTTCCTTCCCC 60.076 63.158 0.00 0.00 0.00 4.81
2455 2676 3.602205 ATTAGGCCATCCTTTCCTTCC 57.398 47.619 5.01 0.00 40.66 3.46
2461 2682 9.448438 GTTTTTCAATAAATTAGGCCATCCTTT 57.552 29.630 5.01 1.48 40.66 3.11
2462 2683 8.601546 TGTTTTTCAATAAATTAGGCCATCCTT 58.398 29.630 5.01 0.00 40.66 3.36
2463 2684 8.040727 GTGTTTTTCAATAAATTAGGCCATCCT 58.959 33.333 5.01 0.00 46.57 3.24
2464 2685 7.279981 GGTGTTTTTCAATAAATTAGGCCATCC 59.720 37.037 5.01 0.00 0.00 3.51
2465 2686 7.279981 GGGTGTTTTTCAATAAATTAGGCCATC 59.720 37.037 5.01 0.00 0.00 3.51
2469 2690 6.530181 CGAGGGTGTTTTTCAATAAATTAGGC 59.470 38.462 0.00 0.00 0.00 3.93
2473 2694 7.519032 TCTCGAGGGTGTTTTTCAATAAATT 57.481 32.000 13.56 0.00 0.00 1.82
2496 2718 9.696917 CAGGGCCTTTTTGTGAAAATATATATC 57.303 33.333 1.32 0.00 34.45 1.63
2501 2723 5.823861 ACAGGGCCTTTTTGTGAAAATAT 57.176 34.783 1.32 0.00 34.45 1.28
2503 2725 4.080638 TCAACAGGGCCTTTTTGTGAAAAT 60.081 37.500 19.48 0.00 34.45 1.82
2506 2728 2.167487 GTCAACAGGGCCTTTTTGTGAA 59.833 45.455 19.48 3.38 0.00 3.18
2507 2729 1.754226 GTCAACAGGGCCTTTTTGTGA 59.246 47.619 19.48 9.92 0.00 3.58
2510 2732 3.614870 GCTATGTCAACAGGGCCTTTTTG 60.615 47.826 15.74 15.74 0.00 2.44
2514 2736 0.698238 TGCTATGTCAACAGGGCCTT 59.302 50.000 1.32 0.00 0.00 4.35
2515 2737 0.921896 ATGCTATGTCAACAGGGCCT 59.078 50.000 0.00 0.00 0.00 5.19
2516 2738 1.767759 AATGCTATGTCAACAGGGCC 58.232 50.000 0.00 0.00 0.00 5.80
2517 2739 3.874392 AAAATGCTATGTCAACAGGGC 57.126 42.857 4.01 4.01 0.00 5.19
2535 2757 4.141287 CCACTGGTCATACTGGTGAAAAA 58.859 43.478 0.00 0.00 0.00 1.94
2536 2758 3.497763 CCCACTGGTCATACTGGTGAAAA 60.498 47.826 0.00 0.00 0.00 2.29
2537 2759 2.039746 CCCACTGGTCATACTGGTGAAA 59.960 50.000 0.00 0.00 0.00 2.69
2538 2760 1.628340 CCCACTGGTCATACTGGTGAA 59.372 52.381 0.00 0.00 0.00 3.18
2539 2761 1.275666 CCCACTGGTCATACTGGTGA 58.724 55.000 0.00 0.00 0.00 4.02
2540 2762 0.984230 ACCCACTGGTCATACTGGTG 59.016 55.000 0.00 0.00 43.06 4.17
2541 2763 3.494561 ACCCACTGGTCATACTGGT 57.505 52.632 0.00 0.00 43.06 4.00
2555 2777 4.631740 TCTGAGTGGCGGGACCCA 62.632 66.667 12.15 0.00 37.83 4.51
2556 2778 3.316573 CTTCTGAGTGGCGGGACCC 62.317 68.421 0.00 0.00 37.83 4.46
2557 2779 2.232298 CTCTTCTGAGTGGCGGGACC 62.232 65.000 0.00 0.00 35.67 4.46
2558 2780 1.216710 CTCTTCTGAGTGGCGGGAC 59.783 63.158 0.00 0.00 35.67 4.46
2559 2781 0.967887 CTCTCTTCTGAGTGGCGGGA 60.968 60.000 0.00 0.00 40.98 5.14
2560 2782 1.254284 ACTCTCTTCTGAGTGGCGGG 61.254 60.000 0.00 0.00 44.64 6.13
2561 2783 2.271940 ACTCTCTTCTGAGTGGCGG 58.728 57.895 0.00 0.00 44.64 6.13
2584 2806 8.989980 GCAGTCTCACTTTTAGTGTAGTTTAAT 58.010 33.333 6.71 0.00 46.03 1.40
2585 2807 7.440255 GGCAGTCTCACTTTTAGTGTAGTTTAA 59.560 37.037 6.71 0.00 46.03 1.52
2586 2808 6.927381 GGCAGTCTCACTTTTAGTGTAGTTTA 59.073 38.462 6.71 0.00 46.03 2.01
2587 2809 5.758784 GGCAGTCTCACTTTTAGTGTAGTTT 59.241 40.000 6.71 0.00 46.03 2.66
2588 2810 5.298347 GGCAGTCTCACTTTTAGTGTAGTT 58.702 41.667 6.71 0.00 46.03 2.24
2589 2811 4.262506 GGGCAGTCTCACTTTTAGTGTAGT 60.263 45.833 6.71 0.00 46.03 2.73
2590 2812 4.246458 GGGCAGTCTCACTTTTAGTGTAG 58.754 47.826 6.71 4.06 46.03 2.74
2591 2813 3.305813 CGGGCAGTCTCACTTTTAGTGTA 60.306 47.826 6.71 0.00 46.03 2.90
2592 2814 2.548067 CGGGCAGTCTCACTTTTAGTGT 60.548 50.000 6.71 0.00 46.03 3.55
2594 2816 1.002087 CCGGGCAGTCTCACTTTTAGT 59.998 52.381 0.00 0.00 0.00 2.24
2595 2817 1.002087 ACCGGGCAGTCTCACTTTTAG 59.998 52.381 6.32 0.00 0.00 1.85
2596 2818 1.053424 ACCGGGCAGTCTCACTTTTA 58.947 50.000 6.32 0.00 0.00 1.52
2597 2819 1.053424 TACCGGGCAGTCTCACTTTT 58.947 50.000 6.32 0.00 0.00 2.27
2598 2820 1.207329 GATACCGGGCAGTCTCACTTT 59.793 52.381 6.32 0.00 0.00 2.66
2599 2821 0.824759 GATACCGGGCAGTCTCACTT 59.175 55.000 6.32 0.00 0.00 3.16
2600 2822 1.384989 CGATACCGGGCAGTCTCACT 61.385 60.000 6.32 0.00 0.00 3.41
2601 2823 1.065928 CGATACCGGGCAGTCTCAC 59.934 63.158 6.32 0.00 0.00 3.51
2602 2824 0.681887 TTCGATACCGGGCAGTCTCA 60.682 55.000 6.32 0.00 36.24 3.27
2603 2825 0.248949 GTTCGATACCGGGCAGTCTC 60.249 60.000 6.32 0.00 36.24 3.36
2604 2826 1.673808 GGTTCGATACCGGGCAGTCT 61.674 60.000 6.32 0.00 37.12 3.24
2605 2827 1.227176 GGTTCGATACCGGGCAGTC 60.227 63.158 6.32 0.00 37.12 3.51
2606 2828 2.897972 GGTTCGATACCGGGCAGT 59.102 61.111 6.32 0.00 37.12 4.40
2613 2835 2.289819 TGTTGGTCTTGGGTTCGATACC 60.290 50.000 7.90 7.90 46.99 2.73
2614 2836 3.048337 TGTTGGTCTTGGGTTCGATAC 57.952 47.619 0.00 0.00 0.00 2.24
2615 2837 3.071892 AGTTGTTGGTCTTGGGTTCGATA 59.928 43.478 0.00 0.00 0.00 2.92
2616 2838 2.158667 AGTTGTTGGTCTTGGGTTCGAT 60.159 45.455 0.00 0.00 0.00 3.59
2617 2839 1.210967 AGTTGTTGGTCTTGGGTTCGA 59.789 47.619 0.00 0.00 0.00 3.71
2618 2840 1.675552 AGTTGTTGGTCTTGGGTTCG 58.324 50.000 0.00 0.00 0.00 3.95
2619 2841 5.585820 TTAAAGTTGTTGGTCTTGGGTTC 57.414 39.130 0.00 0.00 0.00 3.62
2620 2842 5.246429 TGTTTAAAGTTGTTGGTCTTGGGTT 59.754 36.000 0.00 0.00 0.00 4.11
2621 2843 4.773149 TGTTTAAAGTTGTTGGTCTTGGGT 59.227 37.500 0.00 0.00 0.00 4.51
2622 2844 5.331876 TGTTTAAAGTTGTTGGTCTTGGG 57.668 39.130 0.00 0.00 0.00 4.12
2623 2845 6.257630 CCATTGTTTAAAGTTGTTGGTCTTGG 59.742 38.462 0.00 0.00 0.00 3.61
2624 2846 6.257630 CCCATTGTTTAAAGTTGTTGGTCTTG 59.742 38.462 0.00 0.00 0.00 3.02
2625 2847 6.345298 CCCATTGTTTAAAGTTGTTGGTCTT 58.655 36.000 0.00 0.00 0.00 3.01
2626 2848 5.683770 GCCCATTGTTTAAAGTTGTTGGTCT 60.684 40.000 0.00 0.00 0.00 3.85
2627 2849 4.509970 GCCCATTGTTTAAAGTTGTTGGTC 59.490 41.667 0.00 0.00 0.00 4.02
2628 2850 4.080863 TGCCCATTGTTTAAAGTTGTTGGT 60.081 37.500 0.00 0.00 0.00 3.67
2629 2851 4.446371 TGCCCATTGTTTAAAGTTGTTGG 58.554 39.130 0.00 0.00 0.00 3.77
2630 2852 5.006552 CACTGCCCATTGTTTAAAGTTGTTG 59.993 40.000 0.00 0.00 0.00 3.33
2631 2853 5.105146 TCACTGCCCATTGTTTAAAGTTGTT 60.105 36.000 0.00 0.00 0.00 2.83
2632 2854 4.404073 TCACTGCCCATTGTTTAAAGTTGT 59.596 37.500 0.00 0.00 0.00 3.32
2633 2855 4.942852 TCACTGCCCATTGTTTAAAGTTG 58.057 39.130 0.00 0.00 0.00 3.16
2634 2856 5.806654 ATCACTGCCCATTGTTTAAAGTT 57.193 34.783 0.00 0.00 0.00 2.66
2635 2857 5.418840 CCTATCACTGCCCATTGTTTAAAGT 59.581 40.000 0.00 0.00 0.00 2.66
2636 2858 5.679638 GCCTATCACTGCCCATTGTTTAAAG 60.680 44.000 0.00 0.00 0.00 1.85
2637 2859 4.159506 GCCTATCACTGCCCATTGTTTAAA 59.840 41.667 0.00 0.00 0.00 1.52
2638 2860 3.699038 GCCTATCACTGCCCATTGTTTAA 59.301 43.478 0.00 0.00 0.00 1.52
2643 2865 1.789078 GCGCCTATCACTGCCCATTG 61.789 60.000 0.00 0.00 0.00 2.82
2943 5808 0.467290 ACCACATGCTTGAACCCGTT 60.467 50.000 6.60 0.00 0.00 4.44
3044 5913 7.534282 AGGTTTTTGTTGCTTTTTACATTTGG 58.466 30.769 0.00 0.00 0.00 3.28
3050 5919 5.872617 ACTGGAGGTTTTTGTTGCTTTTTAC 59.127 36.000 0.00 0.00 0.00 2.01
3073 5942 7.113544 GCTTATCTTTTTGCTTCAACTGTGTAC 59.886 37.037 0.00 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.