Multiple sequence alignment - TraesCS5D01G080400

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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 TraesCS5D01G080400 chr5D 100.000 2836 0 0 1 2836 80359209 80362044 0.000000e+00 5238.0
1 TraesCS5D01G080400 chr5D 95.111 450 20 1 1 448 544626448 544625999 0.000000e+00 708.0
2 TraesCS5D01G080400 chr5D 91.441 444 25 3 6 449 167764312 167763882 5.230000e-167 597.0
3 TraesCS5D01G080400 chr5D 88.550 393 30 7 576 968 80187770 80187393 1.990000e-126 462.0
4 TraesCS5D01G080400 chr5D 93.000 100 5 1 698 797 80189378 80189281 8.190000e-31 145.0
5 TraesCS5D01G080400 chr5B 90.597 2244 98 46 511 2718 89029296 89031462 0.000000e+00 2870.0
6 TraesCS5D01G080400 chr5B 93.764 449 27 1 1 449 416856713 416857160 0.000000e+00 673.0
7 TraesCS5D01G080400 chr5B 89.431 123 12 1 2714 2836 535047338 535047459 1.360000e-33 154.0
8 TraesCS5D01G080400 chr5A 92.430 1387 50 19 947 2288 76742173 76743549 0.000000e+00 1929.0
9 TraesCS5D01G080400 chr5A 93.665 442 20 4 511 950 76741658 76742093 0.000000e+00 654.0
10 TraesCS5D01G080400 chr5A 90.237 338 29 3 2382 2718 76846834 76847168 3.350000e-119 438.0
11 TraesCS5D01G080400 chr5A 93.443 122 8 0 2714 2835 143827261 143827140 6.240000e-42 182.0
12 TraesCS5D01G080400 chr1B 92.798 486 23 4 1 475 487024835 487024351 0.000000e+00 693.0
13 TraesCS5D01G080400 chr1B 93.557 388 25 0 6 393 487025599 487025212 1.890000e-161 579.0
14 TraesCS5D01G080400 chr1B 80.932 472 76 7 1 472 597070317 597070774 7.470000e-96 361.0
15 TraesCS5D01G080400 chr1B 87.903 124 13 2 2714 2836 237378436 237378314 8.190000e-31 145.0
16 TraesCS5D01G080400 chr1B 85.484 124 16 2 2714 2836 192149506 192149384 8.250000e-26 128.0
17 TraesCS5D01G080400 chr2A 86.824 425 53 3 25 449 65516073 65516494 3.310000e-129 472.0
18 TraesCS5D01G080400 chr2A 96.748 123 4 0 2714 2836 48779668 48779790 3.700000e-49 206.0
19 TraesCS5D01G080400 chr1D 83.015 471 64 10 3 471 439734806 439735262 2.030000e-111 412.0
20 TraesCS5D01G080400 chr2B 83.784 407 60 5 6 410 3278051 3278453 5.730000e-102 381.0
21 TraesCS5D01G080400 chr2B 88.889 45 4 1 2399 2443 521814505 521814548 1.000000e-03 54.7
22 TraesCS5D01G080400 chr6B 90.426 282 27 0 1 282 679032958 679032677 3.450000e-99 372.0
23 TraesCS5D01G080400 chr6A 95.798 119 5 0 2714 2832 457673515 457673633 2.880000e-45 193.0
24 TraesCS5D01G080400 chr6D 94.309 123 7 0 2714 2836 12612804 12612926 3.730000e-44 189.0
25 TraesCS5D01G080400 chr2D 87.805 123 15 0 2714 2836 78373306 78373428 8.190000e-31 145.0


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 TraesCS5D01G080400 chr5D 80359209 80362044 2835 False 5238.0 5238 100.0000 1 2836 1 chr5D.!!$F1 2835
1 TraesCS5D01G080400 chr5D 80187393 80189378 1985 True 303.5 462 90.7750 576 968 2 chr5D.!!$R3 392
2 TraesCS5D01G080400 chr5B 89029296 89031462 2166 False 2870.0 2870 90.5970 511 2718 1 chr5B.!!$F1 2207
3 TraesCS5D01G080400 chr5A 76741658 76743549 1891 False 1291.5 1929 93.0475 511 2288 2 chr5A.!!$F2 1777
4 TraesCS5D01G080400 chr1B 487024351 487025599 1248 True 636.0 693 93.1775 1 475 2 chr1B.!!$R3 474

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
501 1277 0.328258 CGGGGATGACCTCCTTTTGT 59.672 55.000 0.00 0.0 44.28 2.83 F
636 2585 1.154035 CCGTGGCGCTTCAAAATCC 60.154 57.895 7.64 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 3425 0.526524 GGAACTCGATGCACTCCTCG 60.527 60.0 0.98 0.98 36.25 4.63 R
2298 4380 0.533308 AAACGAAAGCCTACGCCACA 60.533 50.0 0.00 0.00 34.57 4.17 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
36 801 1.733399 GACGCTGTCGAGGTCAACC 60.733 63.158 0.00 0.00 39.41 3.77
78 843 3.706373 GTTCCAGAGCTCCCGCCA 61.706 66.667 10.93 0.00 36.60 5.69
134 899 4.682714 AGCAAGGGGAGGAGGCCA 62.683 66.667 5.01 0.00 0.00 5.36
243 1008 3.842923 CAGCTCCCTCGACGCCAT 61.843 66.667 0.00 0.00 0.00 4.40
432 1197 3.459063 GGTTCGAGGCGCTAGGGT 61.459 66.667 7.64 0.00 0.00 4.34
497 1273 3.090532 GGCGGGGATGACCTCCTT 61.091 66.667 0.00 0.00 44.28 3.36
498 1274 2.680370 GGCGGGGATGACCTCCTTT 61.680 63.158 0.00 0.00 44.28 3.11
499 1275 1.303282 GCGGGGATGACCTCCTTTT 59.697 57.895 0.00 0.00 44.28 2.27
500 1276 1.032114 GCGGGGATGACCTCCTTTTG 61.032 60.000 0.00 0.00 44.28 2.44
501 1277 0.328258 CGGGGATGACCTCCTTTTGT 59.672 55.000 0.00 0.00 44.28 2.83
502 1278 1.557832 CGGGGATGACCTCCTTTTGTA 59.442 52.381 0.00 0.00 44.28 2.41
503 1279 2.026636 CGGGGATGACCTCCTTTTGTAA 60.027 50.000 0.00 0.00 44.28 2.41
504 1280 3.560453 CGGGGATGACCTCCTTTTGTAAA 60.560 47.826 0.00 0.00 44.28 2.01
505 1281 4.412843 GGGGATGACCTCCTTTTGTAAAA 58.587 43.478 0.00 0.00 44.28 1.52
506 1282 4.836175 GGGGATGACCTCCTTTTGTAAAAA 59.164 41.667 0.00 0.00 44.28 1.94
569 1346 6.676943 GCGCTGCTAAATAAAAACCACTATGA 60.677 38.462 0.00 0.00 0.00 2.15
570 1347 6.687105 CGCTGCTAAATAAAAACCACTATGAC 59.313 38.462 0.00 0.00 0.00 3.06
571 1348 7.535139 GCTGCTAAATAAAAACCACTATGACA 58.465 34.615 0.00 0.00 0.00 3.58
572 1349 7.698130 GCTGCTAAATAAAAACCACTATGACAG 59.302 37.037 0.00 0.00 0.00 3.51
573 1350 8.050778 TGCTAAATAAAAACCACTATGACAGG 57.949 34.615 0.00 0.00 0.00 4.00
574 1351 6.972901 GCTAAATAAAAACCACTATGACAGGC 59.027 38.462 0.00 0.00 0.00 4.85
575 1352 5.914898 AATAAAAACCACTATGACAGGCC 57.085 39.130 0.00 0.00 0.00 5.19
576 1353 2.969821 AAAACCACTATGACAGGCCA 57.030 45.000 5.01 0.00 0.00 5.36
577 1354 2.496899 AAACCACTATGACAGGCCAG 57.503 50.000 5.01 0.00 0.00 4.85
578 1355 1.656587 AACCACTATGACAGGCCAGA 58.343 50.000 5.01 0.00 0.00 3.86
579 1356 1.656587 ACCACTATGACAGGCCAGAA 58.343 50.000 5.01 0.00 0.00 3.02
636 2585 1.154035 CCGTGGCGCTTCAAAATCC 60.154 57.895 7.64 0.00 0.00 3.01
661 2610 1.604278 GCTCGACAGGAGTTTGCTTTT 59.396 47.619 0.00 0.00 45.03 2.27
662 2611 2.806244 GCTCGACAGGAGTTTGCTTTTA 59.194 45.455 0.00 0.00 45.03 1.52
825 2774 1.161843 CCAAATGACCACGTACACCC 58.838 55.000 0.00 0.00 0.00 4.61
870 2819 3.334583 TCTTCCATTTGCTTAGACGCT 57.665 42.857 0.00 0.00 0.00 5.07
871 2820 3.674997 TCTTCCATTTGCTTAGACGCTT 58.325 40.909 0.00 0.00 0.00 4.68
872 2821 4.827692 TCTTCCATTTGCTTAGACGCTTA 58.172 39.130 0.00 0.00 0.00 3.09
989 3021 1.466866 CGCTTGTACTACACGCAGCTA 60.467 52.381 15.70 0.00 42.67 3.32
991 3023 2.415625 GCTTGTACTACACGCAGCTACT 60.416 50.000 11.75 0.00 42.18 2.57
1015 3047 9.673283 ACTAGACGACCCTATATATAGACCTAT 57.327 37.037 19.51 3.93 32.05 2.57
1026 3058 9.373603 CTATATATAGACCTATAGCCAGCTACG 57.626 40.741 13.67 0.00 32.18 3.51
1079 3111 1.821061 CTCCACTCACCGCAAGTCCT 61.821 60.000 0.00 0.00 0.00 3.85
1120 3152 2.642249 TAGCTAGCTACGCACGCACG 62.642 60.000 20.67 0.00 39.50 5.34
1246 3278 4.862092 CTGCTCGAGCGCATCCGT 62.862 66.667 30.75 0.00 45.83 4.69
1282 3314 2.512286 ATCATGCTCACCGCGGTG 60.512 61.111 45.04 45.04 46.64 4.94
1330 3362 4.704103 AGCAGGACCTCCTCGCCA 62.704 66.667 0.00 0.00 46.65 5.69
1414 3446 0.820871 AGGAGTGCATCGAGTTCCTC 59.179 55.000 0.00 0.00 33.00 3.71
1640 3690 5.129485 ACAAATCAATCTAGGACACGAGGAT 59.871 40.000 0.00 0.00 0.00 3.24
1663 3713 5.636837 TGAATTGGCTCGTTTTGTATAAGC 58.363 37.500 0.00 0.00 0.00 3.09
1689 3740 6.202516 TGTTTCTTGTTCCAACGATCTTTT 57.797 33.333 0.00 0.00 0.00 2.27
1690 3741 6.033341 TGTTTCTTGTTCCAACGATCTTTTG 58.967 36.000 0.00 0.00 0.00 2.44
1701 3762 2.229543 ACGATCTTTTGTGCATGCATGT 59.770 40.909 25.64 8.42 0.00 3.21
1712 3773 3.249080 GTGCATGCATGTTTCTGCTTTTT 59.751 39.130 25.64 0.00 42.75 1.94
1812 3886 3.008375 TGATGAGGTTGGACTGGAAAGAG 59.992 47.826 0.00 0.00 0.00 2.85
1815 3889 0.038310 GGTTGGACTGGAAAGAGGGG 59.962 60.000 0.00 0.00 0.00 4.79
1944 4018 4.992381 ATTCAAGCTTAACACTGTCGTC 57.008 40.909 0.00 0.00 0.00 4.20
1979 4053 1.106285 GGCTAAATGGTTCCCTGCAG 58.894 55.000 6.78 6.78 0.00 4.41
1985 4062 4.980339 AAATGGTTCCCTGCAGAAAAAT 57.020 36.364 17.39 4.16 0.00 1.82
1987 4064 6.625532 AAATGGTTCCCTGCAGAAAAATAT 57.374 33.333 17.39 4.22 0.00 1.28
2022 4099 5.183140 ACGGTGATTCACTTCTTTAATTGGG 59.817 40.000 16.02 0.00 34.40 4.12
2263 4345 1.080434 GGATCTCCGGCAGCGATAC 60.080 63.158 0.00 0.00 0.00 2.24
2413 4504 9.419297 GTGTGACTGATAACTTGTACTAAATCA 57.581 33.333 0.00 0.00 0.00 2.57
2414 4505 9.990360 TGTGACTGATAACTTGTACTAAATCAA 57.010 29.630 0.00 0.00 0.00 2.57
2461 4552 3.994392 AGTATTAGATAATTGCCCGTGCG 59.006 43.478 0.00 0.00 41.78 5.34
2464 4555 0.732571 AGATAATTGCCCGTGCGTTG 59.267 50.000 0.00 0.00 41.78 4.10
2468 4559 1.523154 AATTGCCCGTGCGTTGTCAT 61.523 50.000 0.00 0.00 41.78 3.06
2506 4597 9.331282 ACTCTAATATGTTAGCCTGTGATTTTC 57.669 33.333 4.43 0.00 37.75 2.29
2511 4602 5.499004 TGTTAGCCTGTGATTTTCTACCT 57.501 39.130 0.00 0.00 0.00 3.08
2513 4604 6.403878 TGTTAGCCTGTGATTTTCTACCTAC 58.596 40.000 0.00 0.00 0.00 3.18
2519 4610 6.543831 GCCTGTGATTTTCTACCTACATTGAT 59.456 38.462 0.00 0.00 0.00 2.57
2523 4614 9.559732 TGTGATTTTCTACCTACATTGATATGG 57.440 33.333 0.00 0.00 36.01 2.74
2524 4615 9.561069 GTGATTTTCTACCTACATTGATATGGT 57.439 33.333 0.00 0.00 36.01 3.55
2527 4618 9.920946 ATTTTCTACCTACATTGATATGGTTGT 57.079 29.630 0.00 0.00 36.01 3.32
2534 4625 9.778741 ACCTACATTGATATGGTTGTATAACAG 57.221 33.333 4.65 0.00 38.58 3.16
2535 4626 9.996554 CCTACATTGATATGGTTGTATAACAGA 57.003 33.333 4.65 0.00 38.58 3.41
2544 4635 9.778741 ATATGGTTGTATAACAGATGTTACCAG 57.221 33.333 17.61 0.00 41.88 4.00
2595 4686 1.917303 GTGTCAAACAAAACCACGCAG 59.083 47.619 0.00 0.00 0.00 5.18
2615 4706 4.436183 GCAGAAGAGCGGTAGAAAATCAAC 60.436 45.833 0.00 0.00 0.00 3.18
2616 4707 4.690748 CAGAAGAGCGGTAGAAAATCAACA 59.309 41.667 0.00 0.00 0.00 3.33
2617 4708 4.932200 AGAAGAGCGGTAGAAAATCAACAG 59.068 41.667 0.00 0.00 0.00 3.16
2618 4709 4.537135 AGAGCGGTAGAAAATCAACAGA 57.463 40.909 0.00 0.00 0.00 3.41
2619 4710 4.499183 AGAGCGGTAGAAAATCAACAGAG 58.501 43.478 0.00 0.00 0.00 3.35
2620 4711 4.220821 AGAGCGGTAGAAAATCAACAGAGA 59.779 41.667 0.00 0.00 0.00 3.10
2621 4712 4.499183 AGCGGTAGAAAATCAACAGAGAG 58.501 43.478 0.00 0.00 0.00 3.20
2622 4713 3.619038 GCGGTAGAAAATCAACAGAGAGG 59.381 47.826 0.00 0.00 0.00 3.69
2623 4714 4.620803 GCGGTAGAAAATCAACAGAGAGGA 60.621 45.833 0.00 0.00 0.00 3.71
2624 4715 5.479306 CGGTAGAAAATCAACAGAGAGGAA 58.521 41.667 0.00 0.00 0.00 3.36
2625 4716 5.348997 CGGTAGAAAATCAACAGAGAGGAAC 59.651 44.000 0.00 0.00 0.00 3.62
2626 4717 6.231211 GGTAGAAAATCAACAGAGAGGAACA 58.769 40.000 0.00 0.00 0.00 3.18
2627 4718 6.147985 GGTAGAAAATCAACAGAGAGGAACAC 59.852 42.308 0.00 0.00 0.00 3.32
2628 4719 5.066593 AGAAAATCAACAGAGAGGAACACC 58.933 41.667 0.00 0.00 0.00 4.16
2629 4720 4.437682 AAATCAACAGAGAGGAACACCA 57.562 40.909 0.00 0.00 0.00 4.17
2630 4721 3.692257 ATCAACAGAGAGGAACACCAG 57.308 47.619 0.00 0.00 0.00 4.00
2631 4722 2.398588 TCAACAGAGAGGAACACCAGT 58.601 47.619 0.00 0.00 0.00 4.00
2632 4723 3.572642 TCAACAGAGAGGAACACCAGTA 58.427 45.455 0.00 0.00 0.00 2.74
2633 4724 4.160329 TCAACAGAGAGGAACACCAGTAT 58.840 43.478 0.00 0.00 0.00 2.12
2634 4725 4.593206 TCAACAGAGAGGAACACCAGTATT 59.407 41.667 0.00 0.00 0.00 1.89
2635 4726 5.071788 TCAACAGAGAGGAACACCAGTATTT 59.928 40.000 0.00 0.00 0.00 1.40
2643 4734 6.151144 AGAGGAACACCAGTATTTTTACATGC 59.849 38.462 0.00 0.00 0.00 4.06
2648 4739 8.723942 AACACCAGTATTTTTACATGCAAAAA 57.276 26.923 16.83 16.83 40.58 1.94
2671 4762 2.296190 CTCAAGTTGGGGTAAAAGCCAC 59.704 50.000 2.34 0.00 37.54 5.01
2674 4765 0.537828 GTTGGGGTAAAAGCCACGGA 60.538 55.000 0.00 0.00 37.54 4.69
2686 4777 2.919228 AGCCACGGATTGAAGTTATCC 58.081 47.619 0.00 0.00 38.55 2.59
2702 4793 6.652205 AGTTATCCAAATGTTCTTCCCCTA 57.348 37.500 0.00 0.00 0.00 3.53
2719 4810 9.843704 TCTTCCCCTATTATCAAATATGAGAGA 57.156 33.333 0.00 0.00 39.39 3.10
2721 4812 8.083828 TCCCCTATTATCAAATATGAGAGAGC 57.916 38.462 0.00 0.00 39.39 4.09
2722 4813 7.903481 TCCCCTATTATCAAATATGAGAGAGCT 59.097 37.037 0.00 0.00 39.39 4.09
2723 4814 9.206690 CCCCTATTATCAAATATGAGAGAGCTA 57.793 37.037 0.00 0.00 39.39 3.32
2747 4838 5.674933 GGAATATTCCGGATGAAGTTGTC 57.325 43.478 18.61 0.00 37.65 3.18
2748 4839 5.368989 GGAATATTCCGGATGAAGTTGTCT 58.631 41.667 18.61 0.00 37.65 3.41
2749 4840 5.823045 GGAATATTCCGGATGAAGTTGTCTT 59.177 40.000 18.61 0.00 37.65 3.01
2750 4841 6.017852 GGAATATTCCGGATGAAGTTGTCTTC 60.018 42.308 18.61 1.59 42.43 2.87
2759 4850 3.511856 GAAGTTGTCTTCAAGTGCTCG 57.488 47.619 3.52 0.00 46.50 5.03
2760 4851 1.871080 AGTTGTCTTCAAGTGCTCGG 58.129 50.000 0.00 0.00 36.07 4.63
2761 4852 0.868406 GTTGTCTTCAAGTGCTCGGG 59.132 55.000 0.00 0.00 33.97 5.14
2762 4853 0.756294 TTGTCTTCAAGTGCTCGGGA 59.244 50.000 0.00 0.00 0.00 5.14
2763 4854 0.033504 TGTCTTCAAGTGCTCGGGAC 59.966 55.000 0.00 0.00 0.00 4.46
2764 4855 0.670854 GTCTTCAAGTGCTCGGGACC 60.671 60.000 0.00 0.00 0.00 4.46
2765 4856 1.118965 TCTTCAAGTGCTCGGGACCA 61.119 55.000 0.00 0.00 0.00 4.02
2766 4857 0.671781 CTTCAAGTGCTCGGGACCAG 60.672 60.000 0.00 0.00 0.00 4.00
2767 4858 1.118965 TTCAAGTGCTCGGGACCAGA 61.119 55.000 0.00 0.00 0.00 3.86
2768 4859 0.904865 TCAAGTGCTCGGGACCAGAT 60.905 55.000 0.00 0.00 0.00 2.90
2769 4860 0.036010 CAAGTGCTCGGGACCAGATT 60.036 55.000 0.00 0.00 0.00 2.40
2770 4861 0.036010 AAGTGCTCGGGACCAGATTG 60.036 55.000 0.00 0.00 0.00 2.67
2771 4862 1.450312 GTGCTCGGGACCAGATTGG 60.450 63.158 0.00 0.00 45.02 3.16
2786 4877 6.289745 CCAGATTGGTTGTTGATTTTGTTG 57.710 37.500 0.00 0.00 31.35 3.33
2787 4878 5.236911 CCAGATTGGTTGTTGATTTTGTTGG 59.763 40.000 0.00 0.00 31.35 3.77
2788 4879 4.815846 AGATTGGTTGTTGATTTTGTTGGC 59.184 37.500 0.00 0.00 0.00 4.52
2789 4880 3.902881 TGGTTGTTGATTTTGTTGGCT 57.097 38.095 0.00 0.00 0.00 4.75
2790 4881 3.791245 TGGTTGTTGATTTTGTTGGCTC 58.209 40.909 0.00 0.00 0.00 4.70
2791 4882 3.196469 TGGTTGTTGATTTTGTTGGCTCA 59.804 39.130 0.00 0.00 0.00 4.26
2792 4883 4.187694 GGTTGTTGATTTTGTTGGCTCAA 58.812 39.130 0.00 0.00 0.00 3.02
2793 4884 4.815846 GGTTGTTGATTTTGTTGGCTCAAT 59.184 37.500 0.00 0.00 30.97 2.57
2794 4885 5.296531 GGTTGTTGATTTTGTTGGCTCAATT 59.703 36.000 0.00 0.00 30.97 2.32
2795 4886 5.987777 TGTTGATTTTGTTGGCTCAATTG 57.012 34.783 0.00 0.00 30.97 2.32
2796 4887 5.668471 TGTTGATTTTGTTGGCTCAATTGA 58.332 33.333 8.12 8.12 30.97 2.57
2797 4888 5.754406 TGTTGATTTTGTTGGCTCAATTGAG 59.246 36.000 27.82 27.82 44.75 3.02
2815 4906 4.383861 CGTGCAGCAGAGGGAGCA 62.384 66.667 0.00 0.00 34.10 4.26
2816 4907 2.033141 GTGCAGCAGAGGGAGCAA 59.967 61.111 0.00 0.00 38.91 3.91
2817 4908 1.601759 GTGCAGCAGAGGGAGCAAA 60.602 57.895 0.00 0.00 38.91 3.68
2818 4909 0.964358 GTGCAGCAGAGGGAGCAAAT 60.964 55.000 0.00 0.00 38.91 2.32
2819 4910 0.679002 TGCAGCAGAGGGAGCAAATC 60.679 55.000 0.00 0.00 33.48 2.17
2820 4911 0.394080 GCAGCAGAGGGAGCAAATCT 60.394 55.000 0.00 0.00 0.00 2.40
2821 4912 1.954258 GCAGCAGAGGGAGCAAATCTT 60.954 52.381 0.00 0.00 0.00 2.40
2822 4913 1.743958 CAGCAGAGGGAGCAAATCTTG 59.256 52.381 0.00 0.00 0.00 3.02
2823 4914 1.353694 AGCAGAGGGAGCAAATCTTGT 59.646 47.619 0.00 0.00 0.00 3.16
2824 4915 2.165998 GCAGAGGGAGCAAATCTTGTT 58.834 47.619 0.00 0.00 0.00 2.83
2825 4916 2.560105 GCAGAGGGAGCAAATCTTGTTT 59.440 45.455 0.00 0.00 0.00 2.83
2826 4917 3.366781 GCAGAGGGAGCAAATCTTGTTTC 60.367 47.826 0.00 0.00 0.00 2.78
2827 4918 4.077822 CAGAGGGAGCAAATCTTGTTTCT 58.922 43.478 0.00 0.00 0.00 2.52
2828 4919 4.522022 CAGAGGGAGCAAATCTTGTTTCTT 59.478 41.667 0.00 0.00 0.00 2.52
2829 4920 5.010415 CAGAGGGAGCAAATCTTGTTTCTTT 59.990 40.000 0.00 0.00 0.00 2.52
2830 4921 5.600069 AGAGGGAGCAAATCTTGTTTCTTTT 59.400 36.000 0.00 0.00 0.00 2.27
2831 4922 5.847304 AGGGAGCAAATCTTGTTTCTTTTC 58.153 37.500 0.00 0.00 0.00 2.29
2832 4923 4.991056 GGGAGCAAATCTTGTTTCTTTTCC 59.009 41.667 0.00 0.00 0.00 3.13
2833 4924 4.681483 GGAGCAAATCTTGTTTCTTTTCCG 59.319 41.667 0.00 0.00 0.00 4.30
2834 4925 4.620982 AGCAAATCTTGTTTCTTTTCCGG 58.379 39.130 0.00 0.00 0.00 5.14
2835 4926 3.184379 GCAAATCTTGTTTCTTTTCCGGC 59.816 43.478 0.00 0.00 0.00 6.13
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 786 2.430382 TTCGGGTTGACCTCGACAGC 62.430 60.000 11.52 0.00 38.04 4.40
23 788 1.111116 ACTTCGGGTTGACCTCGACA 61.111 55.000 11.52 5.25 38.04 4.35
36 801 0.981943 AAACCCCTGGTCTACTTCGG 59.018 55.000 0.00 0.00 33.12 4.30
205 970 2.658422 GTTCCTTCCGGCCGTGTA 59.342 61.111 26.12 6.14 0.00 2.90
312 1077 4.834453 CTCTGCTGCCCTGCCTCG 62.834 72.222 0.00 0.00 0.00 4.63
335 1100 2.671070 CTCCCATGAAGGTGGCGT 59.329 61.111 0.00 0.00 37.96 5.68
336 1101 2.124570 CCTCCCATGAAGGTGGCG 60.125 66.667 0.00 0.00 37.96 5.69
503 1279 5.347635 GCAGTTGTTTTCCGAAGTTCTTTTT 59.652 36.000 0.56 0.00 0.00 1.94
504 1280 4.862574 GCAGTTGTTTTCCGAAGTTCTTTT 59.137 37.500 0.56 0.00 0.00 2.27
505 1281 4.082463 TGCAGTTGTTTTCCGAAGTTCTTT 60.082 37.500 0.56 0.00 0.00 2.52
506 1282 3.442273 TGCAGTTGTTTTCCGAAGTTCTT 59.558 39.130 0.56 0.00 0.00 2.52
507 1283 3.013921 TGCAGTTGTTTTCCGAAGTTCT 58.986 40.909 0.56 0.00 0.00 3.01
508 1284 3.105937 GTGCAGTTGTTTTCCGAAGTTC 58.894 45.455 0.00 0.00 0.00 3.01
509 1285 2.490115 TGTGCAGTTGTTTTCCGAAGTT 59.510 40.909 0.00 0.00 0.00 2.66
517 1293 5.064579 GCCATAGTTTTTGTGCAGTTGTTTT 59.935 36.000 0.00 0.00 0.00 2.43
555 1331 4.042311 TCTGGCCTGTCATAGTGGTTTTTA 59.958 41.667 3.32 0.00 0.00 1.52
560 1336 1.556911 CTTCTGGCCTGTCATAGTGGT 59.443 52.381 3.32 0.00 0.00 4.16
569 1346 0.990374 ATCTGCTTCTTCTGGCCTGT 59.010 50.000 3.32 0.00 0.00 4.00
570 1347 1.380524 CATCTGCTTCTTCTGGCCTG 58.619 55.000 3.32 2.92 0.00 4.85
571 1348 0.255318 CCATCTGCTTCTTCTGGCCT 59.745 55.000 3.32 0.00 0.00 5.19
572 1349 0.034670 ACCATCTGCTTCTTCTGGCC 60.035 55.000 0.00 0.00 0.00 5.36
573 1350 1.742268 GAACCATCTGCTTCTTCTGGC 59.258 52.381 0.00 0.00 0.00 4.85
574 1351 2.746362 GTGAACCATCTGCTTCTTCTGG 59.254 50.000 0.00 0.00 0.00 3.86
575 1352 3.436015 CAGTGAACCATCTGCTTCTTCTG 59.564 47.826 0.00 0.00 0.00 3.02
576 1353 3.672808 CAGTGAACCATCTGCTTCTTCT 58.327 45.455 0.00 0.00 0.00 2.85
602 2551 1.142748 CGGGCAAGGTTTTTGTGCA 59.857 52.632 0.00 0.00 40.12 4.57
654 2603 4.497340 CCTTTGACAGCTCGTTAAAAGCAA 60.497 41.667 12.27 0.00 42.35 3.91
661 2610 6.385649 AAATTTTCCTTTGACAGCTCGTTA 57.614 33.333 0.00 0.00 0.00 3.18
662 2611 4.918810 AATTTTCCTTTGACAGCTCGTT 57.081 36.364 0.00 0.00 0.00 3.85
696 2645 1.138883 GAGCGCCACGATGACACTA 59.861 57.895 2.29 0.00 0.00 2.74
776 2725 1.724623 CCGTCCAGTATGTGTTGAACG 59.275 52.381 0.00 0.00 0.00 3.95
825 2774 2.082231 CACAGGAAGCAGACCAGATTG 58.918 52.381 0.00 0.00 0.00 2.67
870 2819 6.423182 ACATGGCTTGGCTCTAGTTTAATAA 58.577 36.000 5.31 0.00 0.00 1.40
871 2820 6.001449 ACATGGCTTGGCTCTAGTTTAATA 57.999 37.500 5.31 0.00 0.00 0.98
872 2821 4.860022 ACATGGCTTGGCTCTAGTTTAAT 58.140 39.130 5.31 0.00 0.00 1.40
989 3021 7.993349 AGGTCTATATATAGGGTCGTCTAGT 57.007 40.000 17.81 0.00 0.00 2.57
1120 3152 1.399791 GCCTTGCTCTTCATGCTGTAC 59.600 52.381 0.00 0.00 0.00 2.90
1282 3314 4.329545 TGCACCGAGGCCTTGGAC 62.330 66.667 41.10 30.93 37.57 4.02
1393 3425 0.526524 GGAACTCGATGCACTCCTCG 60.527 60.000 0.98 0.98 36.25 4.63
1554 3604 4.243008 TGTCCTTGACGCCGGCAA 62.243 61.111 28.98 12.74 34.95 4.52
1565 3615 1.227438 CCGAACGTGTGGTGTCCTT 60.227 57.895 0.00 0.00 0.00 3.36
1640 3690 5.182190 TGCTTATACAAAACGAGCCAATTCA 59.818 36.000 0.00 0.00 32.53 2.57
1689 3740 3.500455 GCAGAAACATGCATGCACA 57.500 47.368 25.37 0.00 45.77 4.57
1712 3773 6.499172 TGTCGATTGAGCATTTTGTAAACAA 58.501 32.000 0.00 0.00 0.00 2.83
1713 3774 6.017523 TCTGTCGATTGAGCATTTTGTAAACA 60.018 34.615 0.00 0.00 0.00 2.83
1714 3775 6.370593 TCTGTCGATTGAGCATTTTGTAAAC 58.629 36.000 0.00 0.00 0.00 2.01
1716 3777 6.169419 CTCTGTCGATTGAGCATTTTGTAA 57.831 37.500 5.01 0.00 0.00 2.41
1717 3778 5.784750 CTCTGTCGATTGAGCATTTTGTA 57.215 39.130 5.01 0.00 0.00 2.41
1788 3859 1.279496 TCCAGTCCAACCTCATCAGG 58.721 55.000 0.00 0.00 46.87 3.86
1800 3874 2.231380 TGCCCCCTCTTTCCAGTCC 61.231 63.158 0.00 0.00 0.00 3.85
1815 3889 1.098712 TGTTTCACCGTCCTTGTGCC 61.099 55.000 0.00 0.00 33.71 5.01
1944 4018 1.153784 GCCAACATTCACGGGCATG 60.154 57.895 0.00 0.00 45.70 4.06
1979 4053 6.864165 TCACCGTTTAGCCAACAATATTTTTC 59.136 34.615 0.00 0.00 34.68 2.29
1985 4062 5.004448 TGAATCACCGTTTAGCCAACAATA 58.996 37.500 0.00 0.00 34.68 1.90
1987 4064 3.003897 GTGAATCACCGTTTAGCCAACAA 59.996 43.478 1.10 0.00 34.68 2.83
2022 4099 8.793592 ACCTGAATTCTTGAAGGTTACAATAAC 58.206 33.333 8.95 0.00 40.14 1.89
2263 4345 3.461773 ACATCTCCCAGCCGACCG 61.462 66.667 0.00 0.00 0.00 4.79
2298 4380 0.533308 AAACGAAAGCCTACGCCACA 60.533 50.000 0.00 0.00 34.57 4.17
2380 4470 9.204570 GTACAAGTTATCAGTCACACTTATTGT 57.795 33.333 0.00 0.00 39.97 2.71
2413 4504 9.844257 TTCCTTTGTTCCAAAATAAATGTCATT 57.156 25.926 0.00 0.00 0.00 2.57
2414 4505 9.492973 CTTCCTTTGTTCCAAAATAAATGTCAT 57.507 29.630 0.00 0.00 0.00 3.06
2415 4506 8.482128 ACTTCCTTTGTTCCAAAATAAATGTCA 58.518 29.630 0.00 0.00 0.00 3.58
2416 4507 8.887036 ACTTCCTTTGTTCCAAAATAAATGTC 57.113 30.769 0.00 0.00 0.00 3.06
2432 4523 7.228706 ACGGGCAATTATCTAATACTTCCTTTG 59.771 37.037 0.00 0.00 0.00 2.77
2433 4524 7.228706 CACGGGCAATTATCTAATACTTCCTTT 59.771 37.037 0.00 0.00 0.00 3.11
2435 4526 6.231211 CACGGGCAATTATCTAATACTTCCT 58.769 40.000 0.00 0.00 0.00 3.36
2436 4527 5.106673 GCACGGGCAATTATCTAATACTTCC 60.107 44.000 3.77 0.00 40.72 3.46
2437 4528 5.389516 CGCACGGGCAATTATCTAATACTTC 60.390 44.000 11.77 0.00 41.24 3.01
2438 4529 4.451096 CGCACGGGCAATTATCTAATACTT 59.549 41.667 11.77 0.00 41.24 2.24
2451 4542 2.593148 ATGACAACGCACGGGCAA 60.593 55.556 11.77 0.00 41.24 4.52
2494 4585 5.880332 TCAATGTAGGTAGAAAATCACAGGC 59.120 40.000 0.00 0.00 0.00 4.85
2508 4599 9.778741 CTGTTATACAACCATATCAATGTAGGT 57.221 33.333 0.00 0.00 33.41 3.08
2595 4686 4.929808 TCTGTTGATTTTCTACCGCTCTTC 59.070 41.667 0.00 0.00 0.00 2.87
2615 4706 6.934645 TGTAAAAATACTGGTGTTCCTCTCTG 59.065 38.462 0.00 0.00 34.23 3.35
2616 4707 7.074653 TGTAAAAATACTGGTGTTCCTCTCT 57.925 36.000 0.00 0.00 34.23 3.10
2617 4708 7.626452 GCATGTAAAAATACTGGTGTTCCTCTC 60.626 40.741 0.00 0.00 34.23 3.20
2618 4709 6.151144 GCATGTAAAAATACTGGTGTTCCTCT 59.849 38.462 0.00 0.00 34.23 3.69
2619 4710 6.072175 TGCATGTAAAAATACTGGTGTTCCTC 60.072 38.462 0.00 0.00 34.23 3.71
2620 4711 5.772672 TGCATGTAAAAATACTGGTGTTCCT 59.227 36.000 0.00 0.00 34.23 3.36
2621 4712 6.019779 TGCATGTAAAAATACTGGTGTTCC 57.980 37.500 0.00 0.00 0.00 3.62
2622 4713 7.938563 TTTGCATGTAAAAATACTGGTGTTC 57.061 32.000 6.49 0.00 0.00 3.18
2623 4714 8.723942 TTTTTGCATGTAAAAATACTGGTGTT 57.276 26.923 24.79 0.00 35.32 3.32
2624 4715 8.900983 ATTTTTGCATGTAAAAATACTGGTGT 57.099 26.923 32.66 16.15 44.22 4.16
2625 4716 9.206870 AGATTTTTGCATGTAAAAATACTGGTG 57.793 29.630 33.26 0.00 45.34 4.17
2626 4717 9.423061 GAGATTTTTGCATGTAAAAATACTGGT 57.577 29.630 33.26 19.69 45.34 4.00
2627 4718 9.421806 TGAGATTTTTGCATGTAAAAATACTGG 57.578 29.630 33.26 0.00 45.34 4.00
2633 4724 8.610896 CCAACTTGAGATTTTTGCATGTAAAAA 58.389 29.630 28.72 28.72 41.94 1.94
2634 4725 7.226325 CCCAACTTGAGATTTTTGCATGTAAAA 59.774 33.333 16.50 16.50 0.00 1.52
2635 4726 6.705381 CCCAACTTGAGATTTTTGCATGTAAA 59.295 34.615 4.71 4.71 0.00 2.01
2643 4734 6.202762 GCTTTTACCCCAACTTGAGATTTTTG 59.797 38.462 0.00 0.00 0.00 2.44
2648 4739 3.181423 TGGCTTTTACCCCAACTTGAGAT 60.181 43.478 0.00 0.00 0.00 2.75
2671 4762 7.088589 AGAACATTTGGATAACTTCAATCCG 57.911 36.000 0.00 0.00 45.05 4.18
2674 4765 7.093333 GGGGAAGAACATTTGGATAACTTCAAT 60.093 37.037 0.00 0.00 35.48 2.57
2724 4815 8.329624 GAAGACAACTTCATCCGGAATATTCCA 61.330 40.741 29.54 14.92 46.93 3.53
2725 4816 5.368989 AGACAACTTCATCCGGAATATTCC 58.631 41.667 22.63 22.63 44.05 3.01
2726 4817 6.927294 AAGACAACTTCATCCGGAATATTC 57.073 37.500 9.01 6.93 34.32 1.75
2740 4831 2.213499 CCGAGCACTTGAAGACAACTT 58.787 47.619 0.00 0.00 39.24 2.66
2741 4832 1.541233 CCCGAGCACTTGAAGACAACT 60.541 52.381 0.00 0.00 32.27 3.16
2742 4833 0.868406 CCCGAGCACTTGAAGACAAC 59.132 55.000 0.00 0.00 32.27 3.32
2743 4834 0.756294 TCCCGAGCACTTGAAGACAA 59.244 50.000 0.00 0.00 34.65 3.18
2744 4835 0.033504 GTCCCGAGCACTTGAAGACA 59.966 55.000 0.00 0.00 0.00 3.41
2745 4836 0.670854 GGTCCCGAGCACTTGAAGAC 60.671 60.000 0.00 0.00 0.00 3.01
2746 4837 1.118965 TGGTCCCGAGCACTTGAAGA 61.119 55.000 0.00 0.00 33.39 2.87
2747 4838 0.671781 CTGGTCCCGAGCACTTGAAG 60.672 60.000 0.00 0.00 34.78 3.02
2748 4839 1.118965 TCTGGTCCCGAGCACTTGAA 61.119 55.000 0.00 0.00 34.78 2.69
2749 4840 0.904865 ATCTGGTCCCGAGCACTTGA 60.905 55.000 0.00 0.00 34.78 3.02
2750 4841 0.036010 AATCTGGTCCCGAGCACTTG 60.036 55.000 0.00 0.00 34.78 3.16
2751 4842 0.036010 CAATCTGGTCCCGAGCACTT 60.036 55.000 0.00 0.00 34.78 3.16
2752 4843 1.599047 CAATCTGGTCCCGAGCACT 59.401 57.895 0.00 0.00 34.78 4.40
2753 4844 1.450312 CCAATCTGGTCCCGAGCAC 60.450 63.158 0.00 0.00 34.78 4.40
2754 4845 2.989639 CCAATCTGGTCCCGAGCA 59.010 61.111 0.00 0.00 37.27 4.26
2763 4854 5.236911 CCAACAAAATCAACAACCAATCTGG 59.763 40.000 0.00 0.00 45.02 3.86
2764 4855 5.277442 GCCAACAAAATCAACAACCAATCTG 60.277 40.000 0.00 0.00 0.00 2.90
2765 4856 4.815846 GCCAACAAAATCAACAACCAATCT 59.184 37.500 0.00 0.00 0.00 2.40
2766 4857 4.815846 AGCCAACAAAATCAACAACCAATC 59.184 37.500 0.00 0.00 0.00 2.67
2767 4858 4.779696 AGCCAACAAAATCAACAACCAAT 58.220 34.783 0.00 0.00 0.00 3.16
2768 4859 4.187694 GAGCCAACAAAATCAACAACCAA 58.812 39.130 0.00 0.00 0.00 3.67
2769 4860 3.196469 TGAGCCAACAAAATCAACAACCA 59.804 39.130 0.00 0.00 0.00 3.67
2770 4861 3.791245 TGAGCCAACAAAATCAACAACC 58.209 40.909 0.00 0.00 0.00 3.77
2771 4862 5.989551 ATTGAGCCAACAAAATCAACAAC 57.010 34.783 0.00 0.00 34.71 3.32
2772 4863 6.111382 TCAATTGAGCCAACAAAATCAACAA 58.889 32.000 3.38 0.00 34.71 2.83
2773 4864 5.668471 TCAATTGAGCCAACAAAATCAACA 58.332 33.333 3.38 0.00 34.71 3.33
2774 4865 6.219302 CTCAATTGAGCCAACAAAATCAAC 57.781 37.500 21.96 0.00 34.71 3.18
2788 4879 0.179197 CTGCTGCACGCTCAATTGAG 60.179 55.000 27.82 27.82 44.75 3.02
2789 4880 0.603439 TCTGCTGCACGCTCAATTGA 60.603 50.000 8.12 8.12 40.11 2.57
2790 4881 0.179197 CTCTGCTGCACGCTCAATTG 60.179 55.000 0.00 0.00 40.11 2.32
2791 4882 1.303799 CCTCTGCTGCACGCTCAATT 61.304 55.000 0.00 0.00 40.11 2.32
2792 4883 1.744368 CCTCTGCTGCACGCTCAAT 60.744 57.895 0.00 0.00 40.11 2.57
2793 4884 2.357881 CCTCTGCTGCACGCTCAA 60.358 61.111 0.00 0.00 40.11 3.02
2794 4885 4.383861 CCCTCTGCTGCACGCTCA 62.384 66.667 0.00 0.00 40.11 4.26
2795 4886 4.074526 TCCCTCTGCTGCACGCTC 62.075 66.667 0.00 0.00 40.11 5.03
2796 4887 4.079850 CTCCCTCTGCTGCACGCT 62.080 66.667 0.00 0.00 40.11 5.07
2798 4889 3.889134 TTGCTCCCTCTGCTGCACG 62.889 63.158 0.00 0.00 35.01 5.34
2799 4890 0.964358 ATTTGCTCCCTCTGCTGCAC 60.964 55.000 0.00 0.00 35.01 4.57
2800 4891 0.679002 GATTTGCTCCCTCTGCTGCA 60.679 55.000 0.88 0.88 0.00 4.41
2801 4892 0.394080 AGATTTGCTCCCTCTGCTGC 60.394 55.000 0.00 0.00 0.00 5.25
2802 4893 1.743958 CAAGATTTGCTCCCTCTGCTG 59.256 52.381 0.00 0.00 0.00 4.41
2803 4894 1.353694 ACAAGATTTGCTCCCTCTGCT 59.646 47.619 0.00 0.00 0.00 4.24
2804 4895 1.831580 ACAAGATTTGCTCCCTCTGC 58.168 50.000 0.00 0.00 0.00 4.26
2805 4896 4.077822 AGAAACAAGATTTGCTCCCTCTG 58.922 43.478 0.00 0.00 0.00 3.35
2806 4897 4.379302 AGAAACAAGATTTGCTCCCTCT 57.621 40.909 0.00 0.00 0.00 3.69
2807 4898 5.459536 AAAGAAACAAGATTTGCTCCCTC 57.540 39.130 0.00 0.00 0.00 4.30
2808 4899 5.221521 GGAAAAGAAACAAGATTTGCTCCCT 60.222 40.000 0.00 0.00 0.00 4.20
2809 4900 4.991056 GGAAAAGAAACAAGATTTGCTCCC 59.009 41.667 0.00 0.00 0.00 4.30
2810 4901 4.681483 CGGAAAAGAAACAAGATTTGCTCC 59.319 41.667 0.00 0.00 0.00 4.70
2811 4902 4.681483 CCGGAAAAGAAACAAGATTTGCTC 59.319 41.667 0.00 0.00 0.00 4.26
2812 4903 4.620982 CCGGAAAAGAAACAAGATTTGCT 58.379 39.130 0.00 0.00 0.00 3.91
2813 4904 3.184379 GCCGGAAAAGAAACAAGATTTGC 59.816 43.478 5.05 0.00 0.00 3.68
2814 4905 4.972286 GCCGGAAAAGAAACAAGATTTG 57.028 40.909 5.05 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.