Multiple sequence alignment - TraesCS5B01G369900

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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 TraesCS5B01G369900 chr5B 100.000 5748 0 0 1 5748 548726182 548720435 0.000000e+00 10615.0
1 TraesCS5B01G369900 chr5B 80.742 431 72 8 1871 2293 18693782 18693355 5.550000e-85 326.0
2 TraesCS5B01G369900 chr5B 79.021 286 38 10 1841 2109 454863268 454862988 5.920000e-40 176.0
3 TraesCS5B01G369900 chr5D 95.044 1917 58 14 3847 5748 449279925 449281819 0.000000e+00 2979.0
4 TraesCS5B01G369900 chr5D 91.355 1874 105 24 18 1843 449273842 449275706 0.000000e+00 2510.0
5 TraesCS5B01G369900 chr5D 93.762 1010 44 11 2853 3844 449278865 449279873 0.000000e+00 1498.0
6 TraesCS5B01G369900 chr5D 88.362 464 39 3 2305 2753 449278402 449278865 1.410000e-150 544.0
7 TraesCS5B01G369900 chr5D 92.515 334 21 2 1970 2303 449278033 449278362 5.210000e-130 475.0
8 TraesCS5B01G369900 chr5D 82.232 439 54 9 1883 2298 169969519 169969956 1.970000e-94 357.0
9 TraesCS5B01G369900 chr5D 78.832 548 94 13 2129 2664 67351456 67351993 3.300000e-92 350.0
10 TraesCS5B01G369900 chr5D 95.205 146 7 0 1841 1986 449275909 449276054 1.250000e-56 231.0
11 TraesCS5B01G369900 chr5A 86.610 1882 118 43 15 1843 568158780 568160580 0.000000e+00 1956.0
12 TraesCS5B01G369900 chr5A 92.814 1336 50 13 3847 5178 568163610 568164903 0.000000e+00 1893.0
13 TraesCS5B01G369900 chr5A 92.720 1044 38 9 2808 3844 568162546 568163558 0.000000e+00 1472.0
14 TraesCS5B01G369900 chr5A 92.781 471 25 3 1841 2303 568160785 568161254 0.000000e+00 673.0
15 TraesCS5B01G369900 chr5A 92.793 444 22 3 5305 5748 568165036 568165469 8.130000e-178 634.0
16 TraesCS5B01G369900 chr5A 91.809 293 17 2 2303 2588 568161292 568161584 8.970000e-108 401.0
17 TraesCS5B01G369900 chr5A 77.405 447 75 17 1871 2298 45999663 46000102 5.750000e-60 243.0
18 TraesCS5B01G369900 chr4D 89.615 520 37 10 4 514 344371966 344371455 0.000000e+00 645.0
19 TraesCS5B01G369900 chr4D 78.882 322 55 6 2312 2632 144865855 144866164 7.550000e-49 206.0
20 TraesCS5B01G369900 chr3A 87.452 518 41 15 4 514 195446488 195445988 4.990000e-160 575.0
21 TraesCS5B01G369900 chr3A 81.250 80 15 0 2792 2871 586077960 586077881 1.340000e-06 65.8
22 TraesCS5B01G369900 chr1D 88.454 485 39 10 4 478 2481337 2481814 2.320000e-158 569.0
23 TraesCS5B01G369900 chr1D 78.116 329 64 6 2311 2636 483117655 483117332 9.770000e-48 202.0
24 TraesCS5B01G369900 chr1D 80.000 200 37 2 2032 2229 408986847 408987045 1.670000e-30 145.0
25 TraesCS5B01G369900 chr3B 94.580 369 13 3 5380 5748 740752784 740752423 1.080000e-156 564.0
26 TraesCS5B01G369900 chr3B 92.683 369 14 4 5380 5748 584780242 584779887 2.370000e-143 520.0
27 TraesCS5B01G369900 chr3B 75.750 833 141 35 1860 2644 263986296 263987115 4.230000e-96 363.0
28 TraesCS5B01G369900 chr6B 94.309 369 14 3 5380 5748 693833774 693834135 5.030000e-155 558.0
29 TraesCS5B01G369900 chr6B 94.309 369 14 3 5380 5748 700356495 700356856 5.030000e-155 558.0
30 TraesCS5B01G369900 chr6B 94.038 369 15 3 5380 5748 260710148 260709787 2.340000e-153 553.0
31 TraesCS5B01G369900 chr6B 83.243 185 27 2 1662 1843 92285364 92285547 3.560000e-37 167.0
32 TraesCS5B01G369900 chr6B 83.721 172 24 2 1675 1843 92354597 92354767 5.960000e-35 159.0
33 TraesCS5B01G369900 chr6B 77.551 245 47 7 2304 2546 431804138 431803900 2.160000e-29 141.0
34 TraesCS5B01G369900 chr6B 84.874 119 12 3 2668 2780 514824347 514824465 1.310000e-21 115.0
35 TraesCS5B01G369900 chr4A 94.309 369 14 3 5380 5748 651549303 651548942 5.030000e-155 558.0
36 TraesCS5B01G369900 chr7B 94.521 365 13 3 5384 5748 499105157 499105514 1.810000e-154 556.0
37 TraesCS5B01G369900 chr7B 100.000 29 0 0 2845 2873 590839959 590839987 3.000000e-03 54.7
38 TraesCS5B01G369900 chr3D 92.328 378 18 6 142 514 560214003 560214374 1.420000e-145 527.0
39 TraesCS5B01G369900 chr3D 76.222 450 88 15 1867 2298 531432436 531431988 2.700000e-53 220.0
40 TraesCS5B01G369900 chr3D 80.723 166 25 6 2522 2685 418714446 418714286 7.820000e-24 122.0
41 TraesCS5B01G369900 chr2D 81.619 457 52 15 1871 2304 533130065 533129618 3.300000e-92 350.0
42 TraesCS5B01G369900 chr2D 78.959 442 60 19 1868 2291 526809163 526809589 2.640000e-68 270.0
43 TraesCS5B01G369900 chr2D 90.667 75 6 1 1769 1842 477856417 477856343 1.320000e-16 99.0
44 TraesCS5B01G369900 chr2D 80.952 84 12 3 2792 2873 4480965 4480884 4.810000e-06 63.9
45 TraesCS5B01G369900 chr7D 81.967 427 56 16 1853 2262 72281436 72281858 5.520000e-90 342.0
46 TraesCS5B01G369900 chr7D 78.049 451 81 7 1862 2304 63724552 63724112 9.490000e-68 268.0
47 TraesCS5B01G369900 chr7D 76.902 368 70 11 2304 2659 63724070 63723706 1.630000e-45 195.0
48 TraesCS5B01G369900 chr7D 85.405 185 23 2 1662 1843 536649580 536649397 7.600000e-44 189.0
49 TraesCS5B01G369900 chr7D 76.000 375 75 10 1871 2233 467986659 467987030 4.580000e-41 180.0
50 TraesCS5B01G369900 chr6D 81.818 363 56 9 2304 2664 453329783 453329429 4.350000e-76 296.0
51 TraesCS5B01G369900 chr6D 93.750 80 5 0 1768 1847 47031303 47031382 2.810000e-23 121.0
52 TraesCS5B01G369900 chr1A 82.129 263 33 7 1999 2248 579845158 579844897 4.510000e-51 213.0
53 TraesCS5B01G369900 chr6A 84.694 196 30 0 1662 1857 68952948 68952753 4.540000e-46 196.0
54 TraesCS5B01G369900 chr6A 75.401 187 43 3 2458 2644 66271614 66271797 2.850000e-13 87.9
55 TraesCS5B01G369900 chr4B 75.112 446 83 16 1872 2298 392625346 392624910 3.540000e-42 183.0
56 TraesCS5B01G369900 chr4B 80.000 270 32 11 1864 2114 30373831 30373565 4.580000e-41 180.0
57 TraesCS5B01G369900 chr1B 80.460 174 26 6 2032 2202 612226064 612225896 6.050000e-25 126.0
58 TraesCS5B01G369900 chr1B 75.243 206 47 3 2461 2664 673162680 673162477 1.710000e-15 95.3


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 TraesCS5B01G369900 chr5B 548720435 548726182 5747 True 10615.000000 10615 100.000000 1 5748 1 chr5B.!!$R3 5747
1 TraesCS5B01G369900 chr5D 449273842 449281819 7977 False 1372.833333 2979 92.707167 18 5748 6 chr5D.!!$F3 5730
2 TraesCS5B01G369900 chr5D 67351456 67351993 537 False 350.000000 350 78.832000 2129 2664 1 chr5D.!!$F1 535
3 TraesCS5B01G369900 chr5A 568158780 568165469 6689 False 1171.500000 1956 91.587833 15 5748 6 chr5A.!!$F2 5733
4 TraesCS5B01G369900 chr4D 344371455 344371966 511 True 645.000000 645 89.615000 4 514 1 chr4D.!!$R1 510
5 TraesCS5B01G369900 chr3A 195445988 195446488 500 True 575.000000 575 87.452000 4 514 1 chr3A.!!$R1 510
6 TraesCS5B01G369900 chr3B 263986296 263987115 819 False 363.000000 363 75.750000 1860 2644 1 chr3B.!!$F1 784
7 TraesCS5B01G369900 chr7D 63723706 63724552 846 True 231.500000 268 77.475500 1862 2659 2 chr7D.!!$R2 797

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
469 481 0.170561 AGTACTGTAACAGGCGAGCG 59.829 55.000 0.00 0.00 35.51 5.03 F
967 1013 0.407918 GGATTTTCCACCCACCTCCA 59.592 55.000 0.00 0.00 36.28 3.86 F
1843 1960 0.537653 GTGAGTCCTTGTAGGAGCCC 59.462 60.000 0.00 0.00 46.90 5.19 F
2785 5560 1.002502 ACTCCCGCAAAGCTAACCC 60.003 57.895 0.00 0.00 0.00 4.11 F
2935 6097 0.912486 ATGGCTGGTCACTAGTTCCC 59.088 55.000 10.31 6.12 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1644 1761 0.531974 TCAGTGCAAACTCCGTGGTC 60.532 55.0 0.00 0.00 0.0 4.02 R
2796 5571 0.385390 CCGCAAACCAGAAGCAAACT 59.615 50.0 0.00 0.00 0.0 2.66 R
2797 5572 0.597377 CCCGCAAACCAGAAGCAAAC 60.597 55.0 0.00 0.00 0.0 2.93 R
4726 7960 2.289820 TCAGAAGTATCGAATCGGACCG 59.710 50.0 7.84 7.84 0.0 4.79 R
4797 8031 0.179111 TAAGACGAGGCATTGCGGAG 60.179 55.0 1.91 0.00 0.0 4.63 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
69 73 7.041721 ACATCATCGCAACTTTCAGACTAATA 58.958 34.615 0.00 0.00 0.00 0.98
131 136 5.981174 TGACATGTAAGAATCAGCAGATCA 58.019 37.500 0.00 0.00 31.90 2.92
149 155 6.600350 CAGATCAACACAGCTGCAATATATC 58.400 40.000 15.27 10.18 0.00 1.63
165 174 8.473219 TGCAATATATCCAGAGCTAGTTCATAG 58.527 37.037 9.43 0.00 34.31 2.23
231 242 3.019564 GCTTACACCCTTCATCAAGCAT 58.980 45.455 0.00 0.00 38.55 3.79
288 299 3.160585 CAGTTCCCTCTGGTGCCA 58.839 61.111 0.00 0.00 0.00 4.92
451 463 5.613329 AGAACTCGACAGGGACTATAGTAG 58.387 45.833 5.09 0.00 36.02 2.57
453 465 6.326064 AGAACTCGACAGGGACTATAGTAGTA 59.674 42.308 5.09 0.00 39.59 1.82
455 467 5.602145 ACTCGACAGGGACTATAGTAGTACT 59.398 44.000 5.09 8.14 39.66 2.73
461 473 7.865820 ACAGGGACTATAGTAGTACTGTAACA 58.134 38.462 20.57 0.00 46.38 2.41
464 476 6.206438 GGGACTATAGTAGTACTGTAACAGGC 59.794 46.154 13.29 3.06 39.66 4.85
465 477 6.073331 GGACTATAGTAGTACTGTAACAGGCG 60.073 46.154 13.29 0.88 39.59 5.52
466 478 6.586344 ACTATAGTAGTACTGTAACAGGCGA 58.414 40.000 13.29 0.00 37.23 5.54
467 479 6.705381 ACTATAGTAGTACTGTAACAGGCGAG 59.295 42.308 13.29 0.95 37.23 5.03
468 480 2.422832 AGTAGTACTGTAACAGGCGAGC 59.577 50.000 5.39 0.00 35.51 5.03
469 481 0.170561 AGTACTGTAACAGGCGAGCG 59.829 55.000 0.00 0.00 35.51 5.03
470 482 0.801067 GTACTGTAACAGGCGAGCGG 60.801 60.000 0.00 0.00 35.51 5.52
471 483 2.552585 TACTGTAACAGGCGAGCGGC 62.553 60.000 8.49 8.49 42.51 6.53
522 550 0.918310 AGAAGAGGAGCTTGCCCCAT 60.918 55.000 0.00 0.00 36.83 4.00
810 850 4.524318 CCGGCCACCTCGCGTAAT 62.524 66.667 5.77 0.00 0.00 1.89
813 853 1.427819 GGCCACCTCGCGTAATTTG 59.572 57.895 5.77 0.00 0.00 2.32
880 920 3.642778 AACGGACGGCTGTGATCGG 62.643 63.158 1.76 0.00 32.82 4.18
887 927 1.429148 CGGCTGTGATCGGGCTTAAC 61.429 60.000 4.78 0.00 42.38 2.01
967 1013 0.407918 GGATTTTCCACCCACCTCCA 59.592 55.000 0.00 0.00 36.28 3.86
968 1014 1.203125 GGATTTTCCACCCACCTCCAA 60.203 52.381 0.00 0.00 36.28 3.53
1292 1374 2.802816 GCCTCGCTGAATGTAGTATTGG 59.197 50.000 0.00 0.00 0.00 3.16
1350 1439 8.371699 TGAAAAAGGGGAAACTATTTGTAATGG 58.628 33.333 0.00 0.00 0.00 3.16
1351 1440 8.499288 AAAAAGGGGAAACTATTTGTAATGGA 57.501 30.769 0.00 0.00 0.00 3.41
1385 1476 2.851824 GTGCGTCAAGGTTCACAAAAAG 59.148 45.455 0.00 0.00 0.00 2.27
1406 1509 3.134804 AGAGTTAATCCTGCGGTTATGCT 59.865 43.478 0.00 0.00 35.36 3.79
1407 1510 3.206150 AGTTAATCCTGCGGTTATGCTG 58.794 45.455 0.00 0.00 35.36 4.41
1424 1527 7.010738 GGTTATGCTGTTCATTGAATTGGATTG 59.989 37.037 1.78 0.00 36.63 2.67
1425 1528 5.725325 TGCTGTTCATTGAATTGGATTGA 57.275 34.783 1.78 0.00 0.00 2.57
1426 1529 6.099159 TGCTGTTCATTGAATTGGATTGAA 57.901 33.333 1.78 0.00 0.00 2.69
1427 1530 6.703319 TGCTGTTCATTGAATTGGATTGAAT 58.297 32.000 1.78 0.00 0.00 2.57
1428 1531 7.162761 TGCTGTTCATTGAATTGGATTGAATT 58.837 30.769 1.78 0.00 0.00 2.17
1429 1532 7.118535 TGCTGTTCATTGAATTGGATTGAATTG 59.881 33.333 1.78 0.00 0.00 2.32
1454 1559 6.073819 GGTTTTTGTCAAATGAGCAATGGTAC 60.074 38.462 0.00 0.00 0.00 3.34
1456 1561 5.375417 TTGTCAAATGAGCAATGGTACTG 57.625 39.130 0.00 0.00 0.00 2.74
1509 1614 2.202362 CGTGCTGTCGTCGAGGAG 60.202 66.667 8.30 0.00 0.00 3.69
1644 1761 2.068837 AGTTGAATTGTTGCCATGCG 57.931 45.000 0.00 0.00 0.00 4.73
1733 1850 2.957402 ACTGGGATTTGAGCAGACAA 57.043 45.000 0.00 0.00 0.00 3.18
1739 1856 3.259123 GGGATTTGAGCAGACAAATTGGT 59.741 43.478 14.33 0.00 46.18 3.67
1843 1960 0.537653 GTGAGTCCTTGTAGGAGCCC 59.462 60.000 0.00 0.00 46.90 5.19
2075 4416 5.392380 CCTTGAGCTTCATCCAACAATGTAC 60.392 44.000 0.00 0.00 0.00 2.90
2112 4453 1.475682 CCCTCGGTCCTGTAGTACAAC 59.524 57.143 4.21 0.50 0.00 3.32
2273 4628 1.006832 CCGCTAAACTTCATGACGGG 58.993 55.000 10.04 0.34 35.63 5.28
2299 4654 3.579709 CAGATAGTGTACCATCGATGCC 58.420 50.000 20.25 10.05 0.00 4.40
2385 4788 1.747355 CCTTTGCCTCATGCCTACAAG 59.253 52.381 0.00 0.00 40.16 3.16
2492 4906 9.619316 AAACAACAAAAAGTTCAAAAATAAGCC 57.381 25.926 0.00 0.00 38.74 4.35
2497 4911 9.620259 ACAAAAAGTTCAAAAATAAGCCCAATA 57.380 25.926 0.00 0.00 0.00 1.90
2651 5415 1.513158 CTGCGGACGTCTGAGGATT 59.487 57.895 28.38 0.00 0.00 3.01
2666 5430 2.762459 ATTCCTAGGCGGCGGACA 60.762 61.111 9.78 0.00 0.00 4.02
2670 5434 3.458163 CTAGGCGGCGGACAAGGA 61.458 66.667 9.78 0.00 0.00 3.36
2675 5439 4.760047 CGGCGGACAAGGAGGGTG 62.760 72.222 0.00 0.00 0.00 4.61
2754 5529 4.814294 GTGCCGGAGCCCTACGTG 62.814 72.222 5.05 0.00 38.69 4.49
2757 5532 4.143333 CCGGAGCCCTACGTGGTG 62.143 72.222 0.00 0.00 34.48 4.17
2759 5534 4.468689 GGAGCCCTACGTGGTGGC 62.469 72.222 19.13 19.13 45.70 5.01
2762 5537 4.016706 GCCCTACGTGGTGGCAGT 62.017 66.667 20.96 0.00 44.70 4.40
2763 5538 2.264794 CCCTACGTGGTGGCAGTC 59.735 66.667 0.00 0.00 0.00 3.51
2764 5539 2.264794 CCTACGTGGTGGCAGTCC 59.735 66.667 0.00 0.00 0.00 3.85
2765 5540 2.126071 CTACGTGGTGGCAGTCCG 60.126 66.667 0.00 0.00 34.14 4.79
2769 5544 3.626924 GTGGTGGCAGTCCGGACT 61.627 66.667 31.69 31.69 43.61 3.85
2772 5547 4.083862 GTGGCAGTCCGGACTCCC 62.084 72.222 34.18 34.18 39.75 4.30
2783 5558 2.467962 GGACTCCCGCAAAGCTAAC 58.532 57.895 0.00 0.00 0.00 2.34
2784 5559 1.025113 GGACTCCCGCAAAGCTAACC 61.025 60.000 0.00 0.00 0.00 2.85
2785 5560 1.002502 ACTCCCGCAAAGCTAACCC 60.003 57.895 0.00 0.00 0.00 4.11
2787 5562 2.754254 CCCGCAAAGCTAACCCCC 60.754 66.667 0.00 0.00 0.00 5.40
2813 5975 2.029918 CCCTAGTTTGCTTCTGGTTTGC 60.030 50.000 0.00 0.00 0.00 3.68
2835 5997 1.566018 GAAAACAGACAGCCGGACGG 61.566 60.000 5.05 6.35 38.57 4.79
2905 6067 4.949856 TGAGATGCCCTTAGATGTTTTTCC 59.050 41.667 0.00 0.00 0.00 3.13
2931 6093 3.389329 CCATCTTATGGCTGGTCACTAGT 59.611 47.826 0.00 0.00 44.70 2.57
2933 6095 4.737855 TCTTATGGCTGGTCACTAGTTC 57.262 45.455 0.00 0.00 0.00 3.01
2935 6097 0.912486 ATGGCTGGTCACTAGTTCCC 59.088 55.000 10.31 6.12 0.00 3.97
2937 6099 0.984995 GGCTGGTCACTAGTTCCCTT 59.015 55.000 10.31 0.00 0.00 3.95
2938 6100 2.185387 GGCTGGTCACTAGTTCCCTTA 58.815 52.381 10.31 0.00 0.00 2.69
2939 6101 2.093606 GGCTGGTCACTAGTTCCCTTAC 60.094 54.545 10.31 0.98 0.00 2.34
3044 6223 4.517832 TCGTACTCTCTACAAAGCAGTCAA 59.482 41.667 0.00 0.00 0.00 3.18
3122 6302 5.739161 CGTTAGCATTTACTCTGCAATTTCC 59.261 40.000 0.00 0.00 42.15 3.13
3124 6304 3.448660 AGCATTTACTCTGCAATTTCCCC 59.551 43.478 0.00 0.00 42.15 4.81
3283 6463 7.148018 TGTCCCATTTTCTCAATTTATCTCTGC 60.148 37.037 0.00 0.00 0.00 4.26
3326 6506 7.364408 GGGAGGTACACTTTTGATGTGATACTA 60.364 40.741 0.00 0.00 38.65 1.82
3402 6582 4.133820 TCATCTGCGGAAAGAAAAGACAA 58.866 39.130 0.00 0.00 0.00 3.18
3476 6656 7.516198 ACTTCCTAATTGTATCCATGCATTC 57.484 36.000 0.00 0.00 0.00 2.67
3498 6678 2.166254 GTGGAATGGAACGGCATGATTT 59.834 45.455 0.00 0.00 0.00 2.17
3542 6722 9.044150 TCATGAAAAATTTGTGTGAAATTCCTC 57.956 29.630 0.00 0.00 0.00 3.71
3752 6932 1.345741 CTCCAAGTTGTCTGAGGAGCA 59.654 52.381 1.45 0.00 38.79 4.26
3786 6966 1.154225 GACGGAAACATTGGCTGCG 60.154 57.895 0.00 0.75 0.00 5.18
4142 7372 8.654230 TGTAAGCTAATCTCATCATTTCACTC 57.346 34.615 0.00 0.00 0.00 3.51
4143 7373 8.260114 TGTAAGCTAATCTCATCATTTCACTCA 58.740 33.333 0.00 0.00 0.00 3.41
4267 7501 8.543774 TCTTTCTTCTGTCAGGCTCTTTTATAT 58.456 33.333 0.00 0.00 0.00 0.86
4273 7507 7.440198 TCTGTCAGGCTCTTTTATATGATGAG 58.560 38.462 0.00 0.00 0.00 2.90
4309 7543 3.384168 TGACCCTATAGCATCCACTGTT 58.616 45.455 0.00 0.00 0.00 3.16
4475 7709 3.631250 TCCTCTGTGCTTTGGAACTTTT 58.369 40.909 0.00 0.00 0.00 2.27
4499 7733 5.768317 TGTTTGTTAATTGTTAGGCTGAGC 58.232 37.500 0.00 0.00 0.00 4.26
4656 7890 3.268330 GGAACCTTGTTTCGGAGGTATC 58.732 50.000 0.00 0.00 45.32 2.24
4672 7906 3.952967 AGGTATCCGTTCTCAGTAGGTTC 59.047 47.826 0.00 0.00 0.00 3.62
4797 8031 3.272334 CGCATTCCTACGCCAGCC 61.272 66.667 0.00 0.00 0.00 4.85
4801 8035 2.797278 ATTCCTACGCCAGCCTCCG 61.797 63.158 0.00 0.00 0.00 4.63
4934 8168 2.029244 CGACACGCAATGATGTAACTCC 59.971 50.000 0.00 0.00 0.00 3.85
4948 8182 8.331931 TGATGTAACTCCCTATTTATTGGACT 57.668 34.615 0.00 0.00 0.00 3.85
4992 8228 5.615289 ACCAGCTTATCGATTTAGATGCTT 58.385 37.500 15.86 6.18 30.51 3.91
5035 8273 4.545208 TGTAAATGTCATTCTCACCCGA 57.455 40.909 0.00 0.00 0.00 5.14
5067 8305 8.340618 TCCTTGAATCCTTCATTTCTTTGTAG 57.659 34.615 0.00 0.00 39.84 2.74
5161 8399 1.311859 TGTCACCTGCTGAGCAAAAG 58.688 50.000 9.07 2.72 38.41 2.27
5207 8490 7.081857 ACCAAATAAACTAGACCTGTAACCA 57.918 36.000 0.00 0.00 0.00 3.67
5208 8491 7.696017 ACCAAATAAACTAGACCTGTAACCAT 58.304 34.615 0.00 0.00 0.00 3.55
5303 8590 0.396435 ACCGCATTCTGACCACTGAA 59.604 50.000 0.00 0.00 38.09 3.02
5417 8704 5.543507 TGCCATTACAAAAACCAGAATGT 57.456 34.783 0.00 0.00 0.00 2.71
5419 8706 5.163364 TGCCATTACAAAAACCAGAATGTGT 60.163 36.000 0.00 0.00 0.00 3.72
5462 8749 8.684386 TTGTTGTTTAAGTTCACATGATCCTA 57.316 30.769 0.00 0.00 0.00 2.94
5488 8775 1.755179 GCTGTTGGCATGGAGTATGT 58.245 50.000 0.00 0.00 41.35 2.29
5505 8792 7.103641 GGAGTATGTACAAGATCAAGGAAACA 58.896 38.462 0.00 0.00 0.00 2.83
5511 8798 2.562738 CAAGATCAAGGAAACAACCCCC 59.437 50.000 0.00 0.00 0.00 5.40
5521 8808 5.581975 AGGAAACAACCCCCGAAATATAAA 58.418 37.500 0.00 0.00 0.00 1.40
5565 8852 5.711506 TCTTAACAGTCACCATGCAAATGAT 59.288 36.000 0.00 0.00 0.00 2.45
5567 8854 7.557358 TCTTAACAGTCACCATGCAAATGATAT 59.443 33.333 0.00 0.00 0.00 1.63
5568 8855 8.744568 TTAACAGTCACCATGCAAATGATATA 57.255 30.769 0.00 0.00 0.00 0.86
5569 8856 6.624352 ACAGTCACCATGCAAATGATATAC 57.376 37.500 0.00 0.00 0.00 1.47
5570 8857 5.237127 ACAGTCACCATGCAAATGATATACG 59.763 40.000 0.00 0.00 0.00 3.06
5571 8858 4.756642 AGTCACCATGCAAATGATATACGG 59.243 41.667 0.00 0.00 0.00 4.02
5572 8859 4.754618 GTCACCATGCAAATGATATACGGA 59.245 41.667 0.00 0.00 0.00 4.69
5573 8860 4.996758 TCACCATGCAAATGATATACGGAG 59.003 41.667 0.00 0.00 0.00 4.63
5741 9028 9.677567 GCAACTCATGAACTATTTAAGACAAAA 57.322 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 73 9.681062 TTTCTTTCGAATTTGAGTAGGGATATT 57.319 29.630 0.00 0.00 0.00 1.28
131 136 5.039920 TCTGGATATATTGCAGCTGTGTT 57.960 39.130 16.64 2.60 43.10 3.32
144 150 7.934313 ACCTCTATGAACTAGCTCTGGATATA 58.066 38.462 0.00 0.00 0.00 0.86
149 155 4.217550 GCTACCTCTATGAACTAGCTCTGG 59.782 50.000 0.00 0.00 0.00 3.86
165 174 3.131223 TGTTCAGTGATAGCTGCTACCTC 59.869 47.826 12.26 7.41 36.49 3.85
288 299 1.158007 ACCCCTTCACCTTCACCATT 58.842 50.000 0.00 0.00 0.00 3.16
440 452 6.073331 CGCCTGTTACAGTACTACTATAGTCC 60.073 46.154 9.12 0.00 40.14 3.85
445 457 4.275443 GCTCGCCTGTTACAGTACTACTAT 59.725 45.833 11.68 0.00 0.00 2.12
451 463 0.801067 CCGCTCGCCTGTTACAGTAC 60.801 60.000 11.68 2.28 0.00 2.73
453 465 2.261671 CCGCTCGCCTGTTACAGT 59.738 61.111 11.68 0.00 0.00 3.55
765 805 3.512287 GAAATCTGCGATGGCGGCG 62.512 63.158 0.51 0.51 45.50 6.46
766 806 2.329339 GAAATCTGCGATGGCGGC 59.671 61.111 0.00 0.00 45.50 6.53
793 833 4.524318 ATTACGCGAGGTGGCCGG 62.524 66.667 15.93 0.00 0.00 6.13
795 835 1.427819 CAAATTACGCGAGGTGGCC 59.572 57.895 15.93 0.00 0.00 5.36
798 838 0.391927 TCCCCAAATTACGCGAGGTG 60.392 55.000 15.93 2.90 0.00 4.00
799 839 0.544697 ATCCCCAAATTACGCGAGGT 59.455 50.000 15.93 0.00 0.00 3.85
800 840 1.226746 GATCCCCAAATTACGCGAGG 58.773 55.000 15.93 4.25 0.00 4.63
801 841 1.202651 AGGATCCCCAAATTACGCGAG 60.203 52.381 15.93 0.00 33.88 5.03
803 843 1.602377 GAAGGATCCCCAAATTACGCG 59.398 52.381 8.55 3.53 33.88 6.01
804 844 1.602377 CGAAGGATCCCCAAATTACGC 59.398 52.381 8.55 0.00 33.88 4.42
832 872 1.414061 CGGCTGGGATTCTCCTCCAT 61.414 60.000 0.00 0.00 36.57 3.41
871 911 2.006772 GCGTTAAGCCCGATCACAG 58.993 57.895 0.00 0.00 40.81 3.66
917 963 4.555709 GGGGTGTGGTGTGACGCA 62.556 66.667 0.00 0.00 0.00 5.24
967 1013 1.303282 GCGGGTGGAGGAGGAAATT 59.697 57.895 0.00 0.00 0.00 1.82
968 1014 2.680370 GGCGGGTGGAGGAGGAAAT 61.680 63.158 0.00 0.00 0.00 2.17
1292 1374 4.168760 GCACAGTTAACCTGATCAATTGC 58.831 43.478 0.88 2.08 44.49 3.56
1350 1439 4.678509 TGACGCACAATGAACCTAATTC 57.321 40.909 0.00 0.00 37.88 2.17
1351 1440 4.082787 CCTTGACGCACAATGAACCTAATT 60.083 41.667 0.00 0.00 37.88 1.40
1360 1449 1.333308 TGTGAACCTTGACGCACAATG 59.667 47.619 0.00 0.00 38.21 2.82
1406 1509 7.451732 ACCAATTCAATCCAATTCAATGAACA 58.548 30.769 0.00 0.00 33.29 3.18
1407 1510 7.910441 ACCAATTCAATCCAATTCAATGAAC 57.090 32.000 0.00 0.00 33.29 3.18
1424 1527 6.601741 TGCTCATTTGACAAAAACCAATTC 57.398 33.333 4.41 0.00 0.00 2.17
1425 1528 6.998968 TTGCTCATTTGACAAAAACCAATT 57.001 29.167 4.41 0.00 0.00 2.32
1426 1529 6.016943 CCATTGCTCATTTGACAAAAACCAAT 60.017 34.615 4.41 8.64 0.00 3.16
1427 1530 5.296283 CCATTGCTCATTTGACAAAAACCAA 59.704 36.000 4.41 6.86 0.00 3.67
1428 1531 4.815308 CCATTGCTCATTTGACAAAAACCA 59.185 37.500 4.41 0.00 0.00 3.67
1429 1532 4.815846 ACCATTGCTCATTTGACAAAAACC 59.184 37.500 4.41 0.00 0.00 3.27
1454 1559 5.066117 AGCAAGAACATGTGCAAGATATCAG 59.934 40.000 6.60 0.00 43.42 2.90
1456 1561 5.496133 AGCAAGAACATGTGCAAGATATC 57.504 39.130 6.60 0.00 43.42 1.63
1644 1761 0.531974 TCAGTGCAAACTCCGTGGTC 60.532 55.000 0.00 0.00 0.00 4.02
1673 1790 0.704551 GCAGCGCGATGAAAACAAAG 59.295 50.000 30.90 0.00 0.00 2.77
1733 1850 1.167851 CACCGTGCTCATCACCAATT 58.832 50.000 0.00 0.00 42.69 2.32
1739 1856 3.610040 ATAAGAACACCGTGCTCATCA 57.390 42.857 4.79 0.00 0.00 3.07
2075 4416 4.465512 GCAGGCCATTCACGCACG 62.466 66.667 5.01 0.00 0.00 5.34
2112 4453 4.156556 ACAAGTTTGTATAGTGCTGCCATG 59.843 41.667 0.00 0.00 40.16 3.66
2166 4518 3.631145 TCTTGTTGCTCTTCATGTTGC 57.369 42.857 0.00 0.00 0.00 4.17
2248 4603 1.135689 CATGAAGTTTAGCGGTGTGGC 60.136 52.381 0.00 0.00 0.00 5.01
2258 4613 2.156098 GCAACCCCGTCATGAAGTTTA 58.844 47.619 7.88 0.00 0.00 2.01
2299 4654 5.467063 GGAAAAGAACTTCGAGCCCTATATG 59.533 44.000 0.00 0.00 0.00 1.78
2385 4788 1.079681 TTGGTCGTATGTGCGGACC 60.080 57.895 4.04 0.81 34.80 4.46
2487 4894 2.948979 CGGTCAAATGCTATTGGGCTTA 59.051 45.455 2.86 0.00 0.00 3.09
2492 4906 3.427503 GGTGTTCGGTCAAATGCTATTGG 60.428 47.826 2.86 0.00 0.00 3.16
2497 4911 1.238439 CAGGTGTTCGGTCAAATGCT 58.762 50.000 0.00 0.00 0.00 3.79
2644 5408 2.498941 CGCCGCCTAGGAATCCTCA 61.499 63.158 14.75 0.00 45.00 3.86
2651 5415 3.458163 CTTGTCCGCCGCCTAGGA 61.458 66.667 14.75 0.00 45.00 2.94
2675 5439 2.183555 GCCCTGCTTTGCATCTGC 59.816 61.111 0.00 0.00 38.13 4.26
2753 5528 3.311110 GAGTCCGGACTGCCACCA 61.311 66.667 40.88 0.00 42.66 4.17
2754 5529 4.083862 GGAGTCCGGACTGCCACC 62.084 72.222 40.88 29.83 42.95 4.61
2765 5540 1.025113 GGTTAGCTTTGCGGGAGTCC 61.025 60.000 0.00 0.00 0.00 3.85
2767 5542 1.002502 GGGTTAGCTTTGCGGGAGT 60.003 57.895 0.00 0.00 0.00 3.85
2768 5543 1.749258 GGGGTTAGCTTTGCGGGAG 60.749 63.158 0.00 0.00 0.00 4.30
2769 5544 2.353573 GGGGTTAGCTTTGCGGGA 59.646 61.111 0.00 0.00 0.00 5.14
2790 5565 0.698818 ACCAGAAGCAAACTAGGGGG 59.301 55.000 0.00 0.00 0.00 5.40
2791 5566 2.558359 CAAACCAGAAGCAAACTAGGGG 59.442 50.000 0.00 0.00 0.00 4.79
2792 5567 2.029918 GCAAACCAGAAGCAAACTAGGG 60.030 50.000 0.00 0.00 0.00 3.53
2793 5568 2.350772 CGCAAACCAGAAGCAAACTAGG 60.351 50.000 0.00 0.00 0.00 3.02
2795 5570 1.606668 CCGCAAACCAGAAGCAAACTA 59.393 47.619 0.00 0.00 0.00 2.24
2796 5571 0.385390 CCGCAAACCAGAAGCAAACT 59.615 50.000 0.00 0.00 0.00 2.66
2797 5572 0.597377 CCCGCAAACCAGAAGCAAAC 60.597 55.000 0.00 0.00 0.00 2.93
2799 5574 0.753479 TTCCCGCAAACCAGAAGCAA 60.753 50.000 0.00 0.00 0.00 3.91
2800 5575 0.753479 TTTCCCGCAAACCAGAAGCA 60.753 50.000 0.00 0.00 0.00 3.91
2802 5577 1.407258 TGTTTTCCCGCAAACCAGAAG 59.593 47.619 0.00 0.00 36.03 2.85
2803 5578 1.407258 CTGTTTTCCCGCAAACCAGAA 59.593 47.619 0.00 0.00 36.03 3.02
2804 5579 1.028905 CTGTTTTCCCGCAAACCAGA 58.971 50.000 0.00 0.00 36.03 3.86
2805 5580 1.028905 TCTGTTTTCCCGCAAACCAG 58.971 50.000 0.00 0.00 36.03 4.00
2806 5581 0.741915 GTCTGTTTTCCCGCAAACCA 59.258 50.000 0.00 0.00 36.03 3.67
2813 5975 2.325082 CCGGCTGTCTGTTTTCCCG 61.325 63.158 0.00 0.00 35.74 5.14
2919 6081 2.416972 CGTAAGGGAACTAGTGACCAGC 60.417 54.545 16.06 6.67 42.68 4.85
2920 6082 2.824341 ACGTAAGGGAACTAGTGACCAG 59.176 50.000 16.06 8.35 42.68 4.00
2921 6083 2.880443 ACGTAAGGGAACTAGTGACCA 58.120 47.619 16.06 0.00 42.68 4.02
2922 6084 3.006217 ACAACGTAAGGGAACTAGTGACC 59.994 47.826 0.00 1.56 42.68 4.02
2923 6085 3.985925 CACAACGTAAGGGAACTAGTGAC 59.014 47.826 0.00 0.00 42.68 3.67
2924 6086 3.890756 TCACAACGTAAGGGAACTAGTGA 59.109 43.478 0.00 0.00 42.68 3.41
2925 6087 4.247267 TCACAACGTAAGGGAACTAGTG 57.753 45.455 0.00 0.00 42.68 2.74
2926 6088 4.942761 TTCACAACGTAAGGGAACTAGT 57.057 40.909 1.82 0.00 42.68 2.57
2928 6090 6.343716 TGTATTCACAACGTAAGGGAACTA 57.656 37.500 7.66 1.10 42.68 2.24
2929 6091 5.801380 ATGTATTCACAACGTAAGGGAACT 58.199 37.500 7.66 1.88 39.92 3.01
2931 6093 8.916062 TCTATATGTATTCACAACGTAAGGGAA 58.084 33.333 7.91 7.91 38.42 3.97
2933 6095 8.975439 GTTCTATATGTATTCACAACGTAAGGG 58.025 37.037 0.00 0.00 38.42 3.95
2937 6099 9.511144 CACAGTTCTATATGTATTCACAACGTA 57.489 33.333 0.00 0.00 38.42 3.57
2938 6100 8.248253 TCACAGTTCTATATGTATTCACAACGT 58.752 33.333 0.00 0.00 38.42 3.99
2939 6101 8.628882 TCACAGTTCTATATGTATTCACAACG 57.371 34.615 0.00 0.00 38.42 4.10
3044 6223 6.192970 ACCCATACTAATTAAGATGCAGCT 57.807 37.500 0.00 0.00 0.00 4.24
3122 6302 9.745018 ATGTAAGTATCATTTTGGATCATAGGG 57.255 33.333 0.00 0.00 0.00 3.53
3283 6463 4.720273 ACCTCCCCAAAACCATACTAGTAG 59.280 45.833 8.85 0.00 0.00 2.57
3326 6506 7.788026 ACAGCCATGAATAATGAATGACAATT 58.212 30.769 0.00 0.00 38.72 2.32
3402 6582 9.196139 GATATATCCTCATCACTAACTAAGCCT 57.804 37.037 0.81 0.00 0.00 4.58
3476 6656 1.024046 TCATGCCGTTCCATTCCACG 61.024 55.000 0.00 0.00 36.12 4.94
3498 6678 8.640063 TTTCATGAAAATCTGGATGAGAAGAA 57.360 30.769 18.45 0.00 33.12 2.52
3542 6722 3.173599 CGCACTTTGAAATACCTGCATG 58.826 45.455 0.00 0.00 0.00 4.06
3629 6809 4.595762 ACTAAGTACGCTCAAGGAAACA 57.404 40.909 0.00 0.00 0.00 2.83
3752 6932 5.733620 TTCCGTCACTAGTTCACCTATTT 57.266 39.130 0.00 0.00 0.00 1.40
3786 6966 6.413052 AGCTTAACTTACTTTTAGGCCTACC 58.587 40.000 13.46 0.00 33.21 3.18
3821 7001 9.684448 ACTTACTCGAGTAAAAGGTTAACTTAC 57.316 33.333 31.72 6.82 39.70 2.34
4142 7372 8.230486 GCTTCCGGTGATTCAGTAATAATAATG 58.770 37.037 0.00 0.00 0.00 1.90
4143 7373 7.936847 TGCTTCCGGTGATTCAGTAATAATAAT 59.063 33.333 0.00 0.00 0.00 1.28
4154 7384 2.749076 CAGAAATGCTTCCGGTGATTCA 59.251 45.455 0.00 0.00 31.28 2.57
4242 7472 8.610896 CATATAAAAGAGCCTGACAGAAGAAAG 58.389 37.037 3.32 0.00 0.00 2.62
4243 7473 8.321353 TCATATAAAAGAGCCTGACAGAAGAAA 58.679 33.333 3.32 0.00 0.00 2.52
4244 7474 7.851228 TCATATAAAAGAGCCTGACAGAAGAA 58.149 34.615 3.32 0.00 0.00 2.52
4245 7475 7.423844 TCATATAAAAGAGCCTGACAGAAGA 57.576 36.000 3.32 0.00 0.00 2.87
4273 7507 2.598394 TCAAGCCCAGCTGTTGGC 60.598 61.111 22.39 22.39 46.32 4.52
4309 7543 5.471556 TGGAACGTATAAGGTCTTCAACA 57.528 39.130 3.67 0.00 0.00 3.33
4475 7709 6.212955 GCTCAGCCTAACAATTAACAAACAA 58.787 36.000 0.00 0.00 0.00 2.83
4656 7890 2.820787 AGACAGAACCTACTGAGAACGG 59.179 50.000 0.00 0.00 40.63 4.44
4726 7960 2.289820 TCAGAAGTATCGAATCGGACCG 59.710 50.000 7.84 7.84 0.00 4.79
4732 7966 8.696410 GGATAAATCCTCAGAAGTATCGAATC 57.304 38.462 1.52 0.00 43.73 2.52
4797 8031 0.179111 TAAGACGAGGCATTGCGGAG 60.179 55.000 1.91 0.00 0.00 4.63
4801 8035 2.468831 CTCTCTAAGACGAGGCATTGC 58.531 52.381 0.00 0.00 0.00 3.56
4881 8115 9.632638 ATCTATTAGTTGCTGAATAACACCATT 57.367 29.630 0.00 0.00 0.00 3.16
4948 8182 7.113658 TGGTTTTGCTGTTTATTCACCTAAA 57.886 32.000 0.00 0.00 0.00 1.85
4992 8228 1.076632 ACCCCAAACTCGCCAACAA 60.077 52.632 0.00 0.00 0.00 2.83
5035 8273 2.720915 GAAGGATTCAAGGAGCTGCTT 58.279 47.619 15.60 15.60 46.62 3.91
5067 8305 6.680810 TCACAAATCATTGTCCATGAAAGAC 58.319 36.000 0.00 0.00 46.78 3.01
5178 8448 6.849151 ACAGGTCTAGTTTATTTGGTTCCTT 58.151 36.000 0.00 0.00 0.00 3.36
5217 8500 6.659242 ACGGGTCTCACATTTCATTCTAAATT 59.341 34.615 0.00 0.00 0.00 1.82
5218 8501 6.094048 CACGGGTCTCACATTTCATTCTAAAT 59.906 38.462 0.00 0.00 0.00 1.40
5221 8504 4.020573 ACACGGGTCTCACATTTCATTCTA 60.021 41.667 0.00 0.00 0.00 2.10
5303 8590 2.289945 GGTTTGTGGATGAGCTCTCAGT 60.290 50.000 16.19 0.00 43.61 3.41
5417 8704 5.720202 ACAAGATGTTCTAATACGCTCACA 58.280 37.500 0.00 0.00 0.00 3.58
5419 8706 6.163476 ACAACAAGATGTTCTAATACGCTCA 58.837 36.000 0.00 0.00 38.77 4.26
5488 8775 4.403734 GGGGTTGTTTCCTTGATCTTGTA 58.596 43.478 0.00 0.00 0.00 2.41
5505 8792 6.610830 AGATGTGATTTATATTTCGGGGGTT 58.389 36.000 0.00 0.00 0.00 4.11
5521 8808 9.167311 GTTAAGAGTGGAATGTTAAGATGTGAT 57.833 33.333 0.00 0.00 0.00 3.06
5565 8852 9.048446 GCCTGAAATTTATTTGTACTCCGTATA 57.952 33.333 0.00 0.00 0.00 1.47
5567 8854 6.316890 GGCCTGAAATTTATTTGTACTCCGTA 59.683 38.462 0.00 0.00 0.00 4.02
5568 8855 5.124936 GGCCTGAAATTTATTTGTACTCCGT 59.875 40.000 0.00 0.00 0.00 4.69
5569 8856 5.124776 TGGCCTGAAATTTATTTGTACTCCG 59.875 40.000 3.32 0.00 0.00 4.63
5570 8857 6.524101 TGGCCTGAAATTTATTTGTACTCC 57.476 37.500 3.32 0.00 0.00 3.85
5571 8858 6.476706 GCATGGCCTGAAATTTATTTGTACTC 59.523 38.462 3.32 0.00 0.00 2.59
5572 8859 6.155049 AGCATGGCCTGAAATTTATTTGTACT 59.845 34.615 3.32 0.00 0.00 2.73
5573 8860 6.340522 AGCATGGCCTGAAATTTATTTGTAC 58.659 36.000 3.32 0.00 0.00 2.90
5584 8871 3.650281 TTCAGATAGCATGGCCTGAAA 57.350 42.857 3.32 0.00 41.13 2.69


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

AutoCloner maintained by Alex Coulton.