Multiple sequence alignment - TraesCS7D01G278300

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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 TraesCS7D01G278300 chr7D 100.000 5876 0 0 1 5876 268546459 268552334 0.000000e+00 10852.0
1 TraesCS7D01G278300 chr7A 93.299 3313 104 47 2636 5876 294407664 294410930 0.000000e+00 4780.0
2 TraesCS7D01G278300 chr7A 93.884 1357 39 20 617 1946 294405282 294406621 0.000000e+00 2006.0
3 TraesCS7D01G278300 chr7A 89.852 542 33 10 1945 2474 294406703 294407234 0.000000e+00 676.0
4 TraesCS7D01G278300 chr7A 85.484 124 13 3 2512 2630 294407572 294407695 2.220000e-24 124.0
5 TraesCS7D01G278300 chr7B 90.700 3344 121 77 2636 5876 248543329 248546585 0.000000e+00 4277.0
6 TraesCS7D01G278300 chr7B 89.652 1981 89 47 693 2630 248541451 248543358 0.000000e+00 2416.0
7 TraesCS7D01G278300 chr7B 93.103 87 6 0 599 685 248540210 248540296 1.720000e-25 128.0
8 TraesCS7D01G278300 chr2D 87.313 536 53 11 3 526 25659055 25659587 3.030000e-167 599.0
9 TraesCS7D01G278300 chr2D 90.521 422 35 5 106 526 32770057 32770474 2.390000e-153 553.0
10 TraesCS7D01G278300 chr2D 85.636 550 49 6 77 598 524150798 524150251 8.610000e-153 551.0
11 TraesCS7D01G278300 chr4B 86.827 539 44 10 85 598 53013679 53013143 1.420000e-160 577.0
12 TraesCS7D01G278300 chr4B 94.937 79 4 0 523 601 101772440 101772518 2.220000e-24 124.0
13 TraesCS7D01G278300 chr2A 90.553 434 38 3 94 526 478383355 478382924 6.610000e-159 571.0
14 TraesCS7D01G278300 chr2A 86.578 529 56 13 3 526 35993972 35994490 2.380000e-158 569.0
15 TraesCS7D01G278300 chr1D 86.355 535 43 12 92 599 440877470 440878001 1.850000e-154 556.0
16 TraesCS7D01G278300 chr6B 85.607 535 62 12 3 526 532149184 532149714 1.110000e-151 547.0
17 TraesCS7D01G278300 chr3A 88.571 455 44 7 77 526 63083798 63084249 4.000000e-151 545.0
18 TraesCS7D01G278300 chr3A 85.938 512 43 12 114 598 638896172 638895663 2.430000e-143 520.0
19 TraesCS7D01G278300 chr3A 82.993 588 64 15 40 597 562876098 562875517 3.160000e-137 499.0
20 TraesCS7D01G278300 chr5B 88.914 442 45 4 86 526 467140267 467139829 5.180000e-150 542.0
21 TraesCS7D01G278300 chr5B 83.514 552 54 16 82 602 631468171 631467626 1.150000e-131 481.0
22 TraesCS7D01G278300 chr5B 84.479 509 29 13 1934 2441 146124388 146123929 1.930000e-124 457.0
23 TraesCS7D01G278300 chr3D 84.981 526 48 15 100 598 407045961 407045440 6.800000e-139 505.0
24 TraesCS7D01G278300 chr5A 82.625 541 58 13 93 608 29162916 29163445 4.180000e-121 446.0
25 TraesCS7D01G278300 chr1B 84.412 340 28 9 286 600 41738702 41739041 1.590000e-80 311.0
26 TraesCS7D01G278300 chr4D 76.642 137 28 4 3854 3988 453221312 453221446 8.170000e-09 73.1


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 TraesCS7D01G278300 chr7D 268546459 268552334 5875 False 10852.000000 10852 100.000000 1 5876 1 chr7D.!!$F1 5875
1 TraesCS7D01G278300 chr7A 294405282 294410930 5648 False 1896.500000 4780 90.629750 617 5876 4 chr7A.!!$F1 5259
2 TraesCS7D01G278300 chr7B 248540210 248546585 6375 False 2273.666667 4277 91.151667 599 5876 3 chr7B.!!$F1 5277
3 TraesCS7D01G278300 chr2D 25659055 25659587 532 False 599.000000 599 87.313000 3 526 1 chr2D.!!$F1 523
4 TraesCS7D01G278300 chr2D 524150251 524150798 547 True 551.000000 551 85.636000 77 598 1 chr2D.!!$R1 521
5 TraesCS7D01G278300 chr4B 53013143 53013679 536 True 577.000000 577 86.827000 85 598 1 chr4B.!!$R1 513
6 TraesCS7D01G278300 chr2A 35993972 35994490 518 False 569.000000 569 86.578000 3 526 1 chr2A.!!$F1 523
7 TraesCS7D01G278300 chr1D 440877470 440878001 531 False 556.000000 556 86.355000 92 599 1 chr1D.!!$F1 507
8 TraesCS7D01G278300 chr6B 532149184 532149714 530 False 547.000000 547 85.607000 3 526 1 chr6B.!!$F1 523
9 TraesCS7D01G278300 chr3A 638895663 638896172 509 True 520.000000 520 85.938000 114 598 1 chr3A.!!$R2 484
10 TraesCS7D01G278300 chr3A 562875517 562876098 581 True 499.000000 499 82.993000 40 597 1 chr3A.!!$R1 557
11 TraesCS7D01G278300 chr5B 631467626 631468171 545 True 481.000000 481 83.514000 82 602 1 chr5B.!!$R3 520
12 TraesCS7D01G278300 chr3D 407045440 407045961 521 True 505.000000 505 84.981000 100 598 1 chr3D.!!$R1 498
13 TraesCS7D01G278300 chr5A 29162916 29163445 529 False 446.000000 446 82.625000 93 608 1 chr5A.!!$F1 515

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
998 2234 1.190643 AGGAGAAGGAGAAGAAGCGG 58.809 55.0 0.00 0.0 0.00 5.52 F
2677 4369 0.033781 GCGTACCCTACACAACACCA 59.966 55.0 0.00 0.0 0.00 4.17 F
3313 5028 0.250252 TCGTCAATGGAGCTGCAACA 60.250 50.0 13.45 0.0 0.00 3.33 F
3606 5334 0.733729 GCTGAGCTGAATTGCTGAGG 59.266 55.0 0.00 0.0 42.98 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2683 4375 0.107703 TCTGGGCTGAATTACTGGCG 60.108 55.000 0.0 0.0 42.23 5.69 R
4489 6256 0.036577 CAGAGGAGCAGGTTCACCAG 60.037 60.000 0.0 0.0 38.89 4.00 R
4584 6351 1.405463 CCTTTGAATAAGGCGAAGGGC 59.595 52.381 0.0 0.0 41.35 5.19 R
5386 7185 1.153066 TTGCTTTGTGCCCGTCTCA 60.153 52.632 0.0 0.0 42.00 3.27 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
23 24 4.000928 TGGGATAAGAGCTCCTTTCTCT 57.999 45.455 10.93 0.00 42.31 3.10
32 33 3.767131 GAGCTCCTTTCTCTAGTCCAGTT 59.233 47.826 0.87 0.00 0.00 3.16
34 35 3.259625 GCTCCTTTCTCTAGTCCAGTTGT 59.740 47.826 0.00 0.00 0.00 3.32
476 531 4.463050 ACCTCCAAACATAAGGGTTTCA 57.537 40.909 0.00 0.00 38.86 2.69
491 546 2.034053 GGTTTCAGGTGTGCATTTTCGA 59.966 45.455 0.00 0.00 0.00 3.71
504 559 4.081198 TGCATTTTCGATGGCCCTTAAAAT 60.081 37.500 0.00 4.87 31.67 1.82
571 652 7.010091 CGCAAAAATTATAAGGGTTTGACCATC 59.990 37.037 16.57 4.15 41.02 3.51
610 691 8.293867 GCTAGAGATACTCTAACAACATGTAGG 58.706 40.741 0.00 0.00 41.74 3.18
696 1928 3.792047 CGTCACGTACTCCGGCGA 61.792 66.667 9.30 0.00 42.24 5.54
717 1949 1.953686 GTCCAGACCAGAGCTAGCTAG 59.046 57.143 19.38 16.84 0.00 3.42
756 1989 5.449304 GTCTTTAATTTCGTTGACACTGGG 58.551 41.667 0.00 0.00 0.00 4.45
996 2232 3.118775 GGAGAAGGAGAAGGAGAAGAAGC 60.119 52.174 0.00 0.00 0.00 3.86
997 2233 2.495669 AGAAGGAGAAGGAGAAGAAGCG 59.504 50.000 0.00 0.00 0.00 4.68
998 2234 1.190643 AGGAGAAGGAGAAGAAGCGG 58.809 55.000 0.00 0.00 0.00 5.52
1061 2297 2.755103 CAGGGTATTTCAAGGGCAAGAC 59.245 50.000 0.00 0.00 0.00 3.01
1106 2342 3.513662 GCTTCCTCGGAAAGAGTAAGTC 58.486 50.000 0.00 0.00 42.72 3.01
1107 2343 3.760537 CTTCCTCGGAAAGAGTAAGTCG 58.239 50.000 0.00 0.00 45.44 4.18
1108 2344 2.787994 TCCTCGGAAAGAGTAAGTCGT 58.212 47.619 0.00 0.00 45.44 4.34
1127 2363 5.567234 TCGTACACGATCGAGTATTAGTC 57.433 43.478 24.65 12.72 44.22 2.59
1202 2444 4.697514 CCACAGCTACCTACGTACTACTA 58.302 47.826 0.00 0.00 0.00 1.82
1219 2461 1.186030 CTACGTACGTGCTTAAGCCG 58.814 55.000 30.25 26.41 41.18 5.52
1512 2768 1.211949 ACGGACCTAATTCATGGGTGG 59.788 52.381 0.00 0.00 33.01 4.61
1590 2855 3.192001 GTGTGTGGATTTCTCATGCATGT 59.808 43.478 25.43 6.51 0.00 3.21
1643 2908 2.167219 CCGAGTGTGGCGTATGCAG 61.167 63.158 9.59 0.00 45.35 4.41
1676 2941 4.639310 GCACATGGACTCTCATGAATTCTT 59.361 41.667 7.05 0.00 45.30 2.52
1785 3051 3.380004 ACGATCGAAGCAAGAGAAGAGAT 59.620 43.478 24.34 0.00 0.00 2.75
1810 3076 1.825191 ATGTCCCATGTCCATGCGC 60.825 57.895 0.00 0.00 37.49 6.09
1821 3087 2.827190 CATGCGCACCATGGAGCT 60.827 61.111 28.20 10.30 46.09 4.09
1893 3159 1.135603 CAAGCCATCAATGTGTGACGG 60.136 52.381 0.00 0.00 42.83 4.79
1894 3160 0.324614 AGCCATCAATGTGTGACGGA 59.675 50.000 0.00 0.00 42.55 4.69
1895 3161 1.065199 AGCCATCAATGTGTGACGGAT 60.065 47.619 0.00 0.00 42.55 4.18
2077 3429 4.764823 TGGTAAAATGTGAAAAGCTCCGAT 59.235 37.500 0.00 0.00 0.00 4.18
2111 3463 1.642762 AGGGTTCAAGAGCATCCCATT 59.357 47.619 0.00 0.00 40.48 3.16
2112 3464 2.027385 GGGTTCAAGAGCATCCCATTC 58.973 52.381 0.00 0.00 38.15 2.67
2113 3465 2.027385 GGTTCAAGAGCATCCCATTCC 58.973 52.381 0.00 0.00 33.66 3.01
2114 3466 2.027385 GTTCAAGAGCATCCCATTCCC 58.973 52.381 0.00 0.00 33.66 3.97
2115 3467 1.297968 TCAAGAGCATCCCATTCCCA 58.702 50.000 0.00 0.00 33.66 4.37
2116 3468 1.854939 TCAAGAGCATCCCATTCCCAT 59.145 47.619 0.00 0.00 33.66 4.00
2117 3469 1.961394 CAAGAGCATCCCATTCCCATG 59.039 52.381 0.00 0.00 33.66 3.66
2147 3499 4.154347 CGAGAGGCCAGGTGCTCC 62.154 72.222 5.01 0.00 40.92 4.70
2158 3510 0.617413 AGGTGCTCCCTGACTCAATG 59.383 55.000 0.00 0.00 44.08 2.82
2159 3511 0.393537 GGTGCTCCCTGACTCAATGG 60.394 60.000 0.00 0.00 0.00 3.16
2331 3684 2.426522 CCAATCGCTCAGAGGAACAAA 58.573 47.619 0.00 0.00 0.00 2.83
2357 3710 7.495279 AGAGTACTATAGTAGACGGTGTTTGAG 59.505 40.741 12.99 0.00 0.00 3.02
2358 3711 5.246145 ACTATAGTAGACGGTGTTTGAGC 57.754 43.478 2.75 0.00 0.00 4.26
2372 3725 5.293079 GGTGTTTGAGCTTGCACAAATTTTA 59.707 36.000 17.91 6.22 38.09 1.52
2396 3750 5.769484 AACTATGTATCGTGTAGTGGAGG 57.231 43.478 0.00 0.00 0.00 4.30
2397 3751 4.142790 ACTATGTATCGTGTAGTGGAGGG 58.857 47.826 0.00 0.00 0.00 4.30
2473 3840 7.646548 AAGAGAACTTTTAAGCTTTGTTCCT 57.353 32.000 20.38 16.45 38.10 3.36
2474 3841 7.646548 AGAGAACTTTTAAGCTTTGTTCCTT 57.353 32.000 20.38 12.24 38.10 3.36
2475 3842 8.067751 AGAGAACTTTTAAGCTTTGTTCCTTT 57.932 30.769 20.38 10.13 38.10 3.11
2476 3843 8.531982 AGAGAACTTTTAAGCTTTGTTCCTTTT 58.468 29.630 20.38 9.90 38.10 2.27
2477 3844 9.151471 GAGAACTTTTAAGCTTTGTTCCTTTTT 57.849 29.630 20.38 9.66 38.10 1.94
2547 4239 2.880443 AGGCACACCAAATGAATGAGT 58.120 42.857 0.00 0.00 39.06 3.41
2554 4246 6.183360 GCACACCAAATGAATGAGTCATATGA 60.183 38.462 5.94 0.00 46.80 2.15
2579 4271 4.990526 AGTTGGTTGATTTGAGTCCATCT 58.009 39.130 0.00 0.00 0.00 2.90
2580 4272 6.126863 AGTTGGTTGATTTGAGTCCATCTA 57.873 37.500 0.00 0.00 0.00 1.98
2586 4278 6.038714 GGTTGATTTGAGTCCATCTATTCACC 59.961 42.308 0.00 0.00 0.00 4.02
2588 4280 3.819564 TTGAGTCCATCTATTCACCCG 57.180 47.619 0.00 0.00 0.00 5.28
2593 4285 1.958579 TCCATCTATTCACCCGTACCG 59.041 52.381 0.00 0.00 0.00 4.02
2599 4291 0.979187 ATTCACCCGTACCGTCCCAT 60.979 55.000 0.00 0.00 0.00 4.00
2629 4321 4.702020 AAAAAGTTCACGCGCACC 57.298 50.000 5.73 0.00 0.00 5.01
2630 4322 1.298041 AAAAAGTTCACGCGCACCG 60.298 52.632 5.73 0.00 44.21 4.94
2640 4332 4.980805 GCGCACCGTCCCACAGAA 62.981 66.667 0.30 0.00 0.00 3.02
2641 4333 2.280524 CGCACCGTCCCACAGAAA 60.281 61.111 0.00 0.00 0.00 2.52
2642 4334 1.890041 CGCACCGTCCCACAGAAAA 60.890 57.895 0.00 0.00 0.00 2.29
2643 4335 1.652563 GCACCGTCCCACAGAAAAC 59.347 57.895 0.00 0.00 0.00 2.43
2644 4336 1.098712 GCACCGTCCCACAGAAAACA 61.099 55.000 0.00 0.00 0.00 2.83
2645 4337 1.384525 CACCGTCCCACAGAAAACAA 58.615 50.000 0.00 0.00 0.00 2.83
2672 4364 0.672889 TTCACGCGTACCCTACACAA 59.327 50.000 13.44 0.00 0.00 3.33
2673 4365 0.039256 TCACGCGTACCCTACACAAC 60.039 55.000 13.44 0.00 0.00 3.32
2674 4366 0.318869 CACGCGTACCCTACACAACA 60.319 55.000 13.44 0.00 0.00 3.33
2676 4368 1.010419 CGCGTACCCTACACAACACC 61.010 60.000 0.00 0.00 0.00 4.16
2677 4369 0.033781 GCGTACCCTACACAACACCA 59.966 55.000 0.00 0.00 0.00 4.17
2678 4370 1.787012 CGTACCCTACACAACACCAC 58.213 55.000 0.00 0.00 0.00 4.16
2680 4372 2.608752 CGTACCCTACACAACACCACTC 60.609 54.545 0.00 0.00 0.00 3.51
2683 4375 2.218603 CCCTACACAACACCACTCAAC 58.781 52.381 0.00 0.00 0.00 3.18
2684 4376 1.864711 CCTACACAACACCACTCAACG 59.135 52.381 0.00 0.00 0.00 4.10
2685 4377 1.260561 CTACACAACACCACTCAACGC 59.739 52.381 0.00 0.00 0.00 4.84
2686 4378 1.355210 CACAACACCACTCAACGCC 59.645 57.895 0.00 0.00 0.00 5.68
2687 4379 1.078072 ACAACACCACTCAACGCCA 60.078 52.632 0.00 0.00 0.00 5.69
2704 4400 1.065126 GCCAGTAATTCAGCCCAGACT 60.065 52.381 0.00 0.00 0.00 3.24
2782 4487 1.294138 GTGGCAGTGGTACCGCTAA 59.706 57.895 27.16 13.38 34.71 3.09
2789 4494 2.361119 CAGTGGTACCGCTAATGCTAGA 59.639 50.000 27.16 0.00 34.71 2.43
2793 4498 4.448060 GTGGTACCGCTAATGCTAGAAATC 59.552 45.833 18.49 0.00 36.97 2.17
2807 4512 0.746923 GAAATCCACCACTACGGGGC 60.747 60.000 0.00 0.00 36.51 5.80
2814 4519 2.046411 CACTACGGGGCATGTGCA 60.046 61.111 7.36 0.00 44.36 4.57
2840 4545 7.764331 TGTTCATACTTATTACTGTACTGCGA 58.236 34.615 0.00 0.00 0.00 5.10
2841 4546 8.410912 TGTTCATACTTATTACTGTACTGCGAT 58.589 33.333 0.00 0.00 0.00 4.58
2862 4567 2.224744 TGAAGGGCATGTGCAGTTTAGA 60.225 45.455 7.36 0.00 44.36 2.10
2939 4645 1.236616 TTGTCGTCCGCTCGTCCTTA 61.237 55.000 0.00 0.00 0.00 2.69
2940 4646 1.028330 TGTCGTCCGCTCGTCCTTAT 61.028 55.000 0.00 0.00 0.00 1.73
2941 4647 0.316854 GTCGTCCGCTCGTCCTTATC 60.317 60.000 0.00 0.00 0.00 1.75
2942 4648 0.463295 TCGTCCGCTCGTCCTTATCT 60.463 55.000 0.00 0.00 0.00 1.98
2943 4649 0.381089 CGTCCGCTCGTCCTTATCTT 59.619 55.000 0.00 0.00 0.00 2.40
2945 4651 2.225963 CGTCCGCTCGTCCTTATCTTAT 59.774 50.000 0.00 0.00 0.00 1.73
2946 4652 3.566523 GTCCGCTCGTCCTTATCTTATG 58.433 50.000 0.00 0.00 0.00 1.90
2947 4653 3.004524 GTCCGCTCGTCCTTATCTTATGT 59.995 47.826 0.00 0.00 0.00 2.29
2948 4654 4.214971 GTCCGCTCGTCCTTATCTTATGTA 59.785 45.833 0.00 0.00 0.00 2.29
2951 4657 6.315642 TCCGCTCGTCCTTATCTTATGTATAG 59.684 42.308 0.00 0.00 0.00 1.31
2952 4658 6.093771 CCGCTCGTCCTTATCTTATGTATAGT 59.906 42.308 0.00 0.00 0.00 2.12
2953 4659 7.279536 CCGCTCGTCCTTATCTTATGTATAGTA 59.720 40.741 0.00 0.00 0.00 1.82
2954 4660 8.329583 CGCTCGTCCTTATCTTATGTATAGTAG 58.670 40.741 0.00 0.00 0.00 2.57
3016 4728 2.507484 TCCACCTCTGAAACATTGCAG 58.493 47.619 0.00 0.00 0.00 4.41
3017 4729 2.158623 TCCACCTCTGAAACATTGCAGT 60.159 45.455 0.00 0.00 33.90 4.40
3039 4751 3.555547 TGCACGATTAATCATCCACGAAG 59.444 43.478 15.57 0.00 0.00 3.79
3055 4770 1.924524 CGAAGGGCATGTGTAGTTACG 59.075 52.381 0.00 0.00 0.00 3.18
3071 4786 9.070149 GTGTAGTTACGAAAGAAATAGTACAGG 57.930 37.037 0.00 0.00 0.00 4.00
3092 4807 3.510719 GCAGTGCAAACTGAGTTTTCAA 58.489 40.909 11.74 0.00 39.99 2.69
3104 4819 6.799512 ACTGAGTTTTCAACAAAATGAGGAG 58.200 36.000 0.00 0.00 33.98 3.69
3313 5028 0.250252 TCGTCAATGGAGCTGCAACA 60.250 50.000 13.45 0.00 0.00 3.33
3379 5100 4.932268 CGCTTTTATACACGGAGGAAAA 57.068 40.909 0.00 0.00 0.00 2.29
3380 5101 5.479716 CGCTTTTATACACGGAGGAAAAT 57.520 39.130 0.00 0.00 0.00 1.82
3381 5102 5.263185 CGCTTTTATACACGGAGGAAAATG 58.737 41.667 0.00 0.00 0.00 2.32
3382 5103 5.064198 CGCTTTTATACACGGAGGAAAATGA 59.936 40.000 0.00 0.00 0.00 2.57
3384 5105 6.128117 GCTTTTATACACGGAGGAAAATGACA 60.128 38.462 0.00 0.00 0.00 3.58
3385 5106 7.574217 GCTTTTATACACGGAGGAAAATGACAA 60.574 37.037 0.00 0.00 0.00 3.18
3386 5107 7.931578 TTTATACACGGAGGAAAATGACAAT 57.068 32.000 0.00 0.00 0.00 2.71
3387 5108 7.931578 TTATACACGGAGGAAAATGACAATT 57.068 32.000 0.00 0.00 0.00 2.32
3389 5110 7.931578 ATACACGGAGGAAAATGACAATTAA 57.068 32.000 0.00 0.00 0.00 1.40
3392 5113 8.343168 ACACGGAGGAAAATGACAATTAATAA 57.657 30.769 0.00 0.00 0.00 1.40
3393 5114 8.966868 ACACGGAGGAAAATGACAATTAATAAT 58.033 29.630 0.00 0.00 0.00 1.28
3562 5290 1.515521 CCACCGGTCAGCACTTTTCC 61.516 60.000 2.59 0.00 0.00 3.13
3606 5334 0.733729 GCTGAGCTGAATTGCTGAGG 59.266 55.000 0.00 0.00 42.98 3.86
4366 6107 5.057819 GGTCCGTCTCTCTTTTCTTTTCTT 58.942 41.667 0.00 0.00 0.00 2.52
4370 6111 6.018994 TCCGTCTCTCTTTTCTTTTCTTTTCG 60.019 38.462 0.00 0.00 0.00 3.46
4373 6114 7.692705 CGTCTCTCTTTTCTTTTCTTTTCGTTT 59.307 33.333 0.00 0.00 0.00 3.60
4376 6117 9.216087 CTCTCTTTTCTTTTCTTTTCGTTTCTC 57.784 33.333 0.00 0.00 0.00 2.87
4378 6119 9.561270 CTCTTTTCTTTTCTTTTCGTTTCTCTT 57.439 29.630 0.00 0.00 0.00 2.85
4396 6138 9.185680 GTTTCTCTTCTCTTCTCTATCTAAGGT 57.814 37.037 0.00 0.00 0.00 3.50
4536 6303 1.297012 CTCGCAGCTCTACGACGAC 60.297 63.158 0.00 0.00 34.08 4.34
4584 6351 1.150567 ATCTCGTCGACGTCTACGGG 61.151 60.000 33.31 31.88 44.95 5.28
4631 6402 3.380479 AGCGTCACAAACTACTGCTAA 57.620 42.857 0.00 0.00 0.00 3.09
4642 6413 4.124851 ACTACTGCTAATCCAACCTTCG 57.875 45.455 0.00 0.00 0.00 3.79
4647 6418 3.482436 TGCTAATCCAACCTTCGTTGTT 58.518 40.909 2.61 0.00 46.71 2.83
4654 6425 3.499157 TCCAACCTTCGTTGTTAATTCCG 59.501 43.478 2.61 0.00 46.71 4.30
4694 6465 5.920840 CACGTCTCATCTTCTTTACTTGTCA 59.079 40.000 0.00 0.00 0.00 3.58
4713 6484 7.439056 ACTTGTCAAACCATTGAATGAATGAAC 59.561 33.333 6.76 0.51 46.66 3.18
4714 6485 5.919707 TGTCAAACCATTGAATGAATGAACG 59.080 36.000 6.76 0.00 46.66 3.95
4715 6486 6.148948 GTCAAACCATTGAATGAATGAACGA 58.851 36.000 6.76 0.00 46.66 3.85
4716 6487 6.640499 GTCAAACCATTGAATGAATGAACGAA 59.360 34.615 6.76 0.00 46.66 3.85
4894 6665 7.439655 TCAAGTAAAACCGCAGCAAAATTTATT 59.560 29.630 0.00 0.00 0.00 1.40
5019 6802 8.908786 TTATTATGTTGGAGAAGGACATCATC 57.091 34.615 0.00 0.00 35.72 2.92
5032 6815 6.410942 AGGACATCATCGATCAGTGATAAA 57.589 37.500 5.38 0.00 33.52 1.40
5033 6816 6.820335 AGGACATCATCGATCAGTGATAAAA 58.180 36.000 5.38 0.00 33.52 1.52
5034 6817 7.275183 AGGACATCATCGATCAGTGATAAAAA 58.725 34.615 5.38 0.00 33.52 1.94
5160 6954 4.915158 TCATGTCATGTTTGAAGCACAA 57.085 36.364 12.54 0.00 36.65 3.33
5167 6961 6.817641 TGTCATGTTTGAAGCACAAGAATTTT 59.182 30.769 0.00 0.00 39.77 1.82
5314 7111 2.119495 AGATCAGGTTTAGCCCGACAT 58.881 47.619 0.00 0.00 38.26 3.06
5316 7113 1.271856 TCAGGTTTAGCCCGACATGA 58.728 50.000 0.00 0.00 38.26 3.07
5386 7185 6.780457 AATATGCCTGCTAAACAAAGACAT 57.220 33.333 0.00 0.00 0.00 3.06
5565 7378 5.415701 TCCTATGCTTGCTTCTAAAAACAGG 59.584 40.000 0.00 0.00 0.00 4.00
5709 7523 0.602638 TTGGCACATCGACTGTCCAC 60.603 55.000 1.55 4.07 39.30 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.000928 AGAGAAAGGAGCTCTTATCCCA 57.999 45.455 14.64 0.00 39.62 4.37
4 5 5.243060 GGACTAGAGAAAGGAGCTCTTATCC 59.757 48.000 14.64 0.00 42.43 2.59
7 8 5.194473 TGGACTAGAGAAAGGAGCTCTTA 57.806 43.478 14.64 0.00 42.43 2.10
19 20 1.272490 CGGCAACAACTGGACTAGAGA 59.728 52.381 0.00 0.00 0.00 3.10
23 24 1.302192 GGCGGCAACAACTGGACTA 60.302 57.895 3.07 0.00 0.00 2.59
233 283 1.961180 CTGGCCGTCGGAATCCTCTT 61.961 60.000 17.49 0.00 0.00 2.85
234 284 2.363795 TGGCCGTCGGAATCCTCT 60.364 61.111 17.49 0.00 0.00 3.69
476 531 0.527565 GCCATCGAAAATGCACACCT 59.472 50.000 0.00 0.00 0.00 4.00
491 546 8.555729 TCAATCCATAAAAATTTTAAGGGCCAT 58.444 29.630 16.67 0.00 0.00 4.40
571 652 3.420300 TCTCTAGCAGACCCCGTATAG 57.580 52.381 0.00 0.00 0.00 1.31
610 691 1.334779 CGTATGTACTACCGGCAGCTC 60.335 57.143 0.00 0.00 0.00 4.09
696 1928 0.334676 AGCTAGCTCTGGTCTGGACT 59.665 55.000 12.68 0.00 0.00 3.85
756 1989 0.512952 CAAGCCAAGCACGTACAGAC 59.487 55.000 0.00 0.00 0.00 3.51
996 2232 0.535780 CATCCACCATCACCATCCCG 60.536 60.000 0.00 0.00 0.00 5.14
997 2233 0.178981 CCATCCACCATCACCATCCC 60.179 60.000 0.00 0.00 0.00 3.85
998 2234 0.825010 GCCATCCACCATCACCATCC 60.825 60.000 0.00 0.00 0.00 3.51
1061 2297 2.280389 CGCCGGTGATGAGGATGG 60.280 66.667 10.20 0.00 0.00 3.51
1106 2342 5.320607 TGACTAATACTCGATCGTGTACG 57.679 43.478 26.87 20.40 41.45 3.67
1107 2343 6.713520 ACTTGACTAATACTCGATCGTGTAC 58.286 40.000 26.87 16.56 0.00 2.90
1108 2344 6.915544 ACTTGACTAATACTCGATCGTGTA 57.084 37.500 26.60 26.60 0.00 2.90
1158 2394 6.316390 GTGGCAGCTAACTCAACTAATAACAT 59.684 38.462 0.00 0.00 0.00 2.71
1202 2444 1.005294 CACGGCTTAAGCACGTACGT 61.005 55.000 30.26 25.02 42.72 3.57
1204 2446 1.650645 GTACACGGCTTAAGCACGTAC 59.349 52.381 30.26 27.48 42.72 3.67
1219 2461 1.403323 GGGGCAGTAGAGTACGTACAC 59.597 57.143 26.55 20.52 0.00 2.90
1328 2584 3.027170 GACACGGAAGGCACGCATG 62.027 63.158 0.00 0.00 34.00 4.06
1497 2753 0.106719 ACGGCCACCCATGAATTAGG 60.107 55.000 2.24 0.00 0.00 2.69
1498 2754 1.024271 CACGGCCACCCATGAATTAG 58.976 55.000 2.24 0.00 0.00 1.73
1499 2755 0.329931 ACACGGCCACCCATGAATTA 59.670 50.000 2.24 0.00 0.00 1.40
1501 2757 1.678635 CACACGGCCACCCATGAAT 60.679 57.895 2.24 0.00 0.00 2.57
1502 2758 2.282110 CACACGGCCACCCATGAA 60.282 61.111 2.24 0.00 0.00 2.57
1512 2768 1.825191 ATGGATGGATGCACACGGC 60.825 57.895 0.00 0.00 45.13 5.68
1561 2824 5.651387 TGAGAAATCCACACACACAAAAA 57.349 34.783 0.00 0.00 0.00 1.94
1562 2825 5.590145 CATGAGAAATCCACACACACAAAA 58.410 37.500 0.00 0.00 0.00 2.44
1566 2831 2.553602 TGCATGAGAAATCCACACACAC 59.446 45.455 0.00 0.00 0.00 3.82
1568 2833 3.192001 ACATGCATGAGAAATCCACACAC 59.808 43.478 32.75 0.00 0.00 3.82
1612 2877 1.681264 ACACTCGGATCGCATGATGTA 59.319 47.619 0.00 0.00 34.09 2.29
1643 2908 3.580193 CCATGTGCCGCTGCTAGC 61.580 66.667 8.10 8.10 38.71 3.42
1652 2917 2.408271 TTCATGAGAGTCCATGTGCC 57.592 50.000 16.43 0.00 43.22 5.01
1676 2941 1.684983 GTAATTCCGGACGGAGGATGA 59.315 52.381 13.64 0.00 46.06 2.92
1810 3076 2.801063 CGCAAATTAAGCTCCATGGTG 58.199 47.619 12.58 10.95 0.00 4.17
1893 3159 2.497138 TGAATGGGTCGATGCATCATC 58.503 47.619 25.70 16.66 37.50 2.92
1894 3160 2.643995 TGAATGGGTCGATGCATCAT 57.356 45.000 25.70 9.59 0.00 2.45
1895 3161 2.223745 CATGAATGGGTCGATGCATCA 58.776 47.619 25.70 10.72 0.00 3.07
2029 3381 2.053865 GTGGATCCCCGTGACCGTA 61.054 63.158 9.90 0.00 34.29 4.02
2077 3429 3.664320 TGAACCCTAGGCATGGATCTAA 58.336 45.455 2.05 0.00 0.00 2.10
2113 3465 1.153168 CGGTTGGAGCCCTACATGG 60.153 63.158 0.00 0.00 31.18 3.66
2114 3466 0.179073 CTCGGTTGGAGCCCTACATG 60.179 60.000 7.77 0.00 35.63 3.21
2115 3467 0.325296 TCTCGGTTGGAGCCCTACAT 60.325 55.000 7.77 0.00 42.82 2.29
2116 3468 0.970937 CTCTCGGTTGGAGCCCTACA 60.971 60.000 7.77 0.00 42.82 2.74
2117 3469 1.677637 CCTCTCGGTTGGAGCCCTAC 61.678 65.000 0.00 0.00 42.82 3.18
2147 3499 1.072173 TGTCACCACCATTGAGTCAGG 59.928 52.381 0.00 0.00 0.00 3.86
2158 3510 6.404734 CCAGAAATTTAGCTTATGTCACCACC 60.405 42.308 0.00 0.00 0.00 4.61
2159 3511 6.151144 ACCAGAAATTTAGCTTATGTCACCAC 59.849 38.462 0.00 0.00 0.00 4.16
2331 3684 7.334090 TCAAACACCGTCTACTATAGTACTCT 58.666 38.462 8.59 0.00 0.00 3.24
2372 3725 6.406624 CCCTCCACTACACGATACATAGTTTT 60.407 42.308 0.00 0.00 0.00 2.43
2450 3817 7.646548 AAGGAACAAAGCTTAAAAGTTCTCT 57.353 32.000 22.27 17.45 38.78 3.10
2475 3842 5.596845 AGGAACAAAGCTTATTCGCAAAAA 58.403 33.333 14.16 0.00 0.00 1.94
2476 3843 5.195001 AGGAACAAAGCTTATTCGCAAAA 57.805 34.783 14.16 0.00 0.00 2.44
2477 3844 4.846779 AGGAACAAAGCTTATTCGCAAA 57.153 36.364 14.16 0.00 0.00 3.68
2478 3845 4.846779 AAGGAACAAAGCTTATTCGCAA 57.153 36.364 14.16 0.00 0.00 4.85
2479 3846 4.757657 TGTAAGGAACAAAGCTTATTCGCA 59.242 37.500 14.16 9.32 34.29 5.10
2480 3847 5.291293 TGTAAGGAACAAAGCTTATTCGC 57.709 39.130 14.16 9.20 34.29 4.70
2510 3877 2.101917 TGCCTAGTCGTAAGCCCATTAC 59.898 50.000 0.00 0.00 40.42 1.89
2547 4239 6.720309 TCAAATCAACCAACTCCTCATATGA 58.280 36.000 5.07 5.07 0.00 2.15
2554 4246 3.138283 TGGACTCAAATCAACCAACTCCT 59.862 43.478 0.00 0.00 0.00 3.69
2588 4280 5.945466 TTTTGTTTTCTATGGGACGGTAC 57.055 39.130 0.00 0.00 0.00 3.34
2612 4304 1.298041 CGGTGCGCGTGAACTTTTT 60.298 52.632 8.43 0.00 0.00 1.94
2623 4315 4.980805 TTCTGTGGGACGGTGCGC 62.981 66.667 0.00 0.00 0.00 6.09
2624 4316 1.890041 TTTTCTGTGGGACGGTGCG 60.890 57.895 0.00 0.00 0.00 5.34
2625 4317 1.098712 TGTTTTCTGTGGGACGGTGC 61.099 55.000 0.00 0.00 0.00 5.01
2626 4318 1.384525 TTGTTTTCTGTGGGACGGTG 58.615 50.000 0.00 0.00 0.00 4.94
2627 4319 2.131776 TTTGTTTTCTGTGGGACGGT 57.868 45.000 0.00 0.00 0.00 4.83
2628 4320 3.512033 TTTTTGTTTTCTGTGGGACGG 57.488 42.857 0.00 0.00 0.00 4.79
2652 4344 0.889994 TGTGTAGGGTACGCGTGAAT 59.110 50.000 24.59 7.68 41.91 2.57
2672 4364 0.466543 TTACTGGCGTTGAGTGGTGT 59.533 50.000 0.00 0.00 0.00 4.16
2673 4365 1.808411 ATTACTGGCGTTGAGTGGTG 58.192 50.000 0.00 0.00 0.00 4.17
2674 4366 2.224426 TGAATTACTGGCGTTGAGTGGT 60.224 45.455 0.00 0.00 0.00 4.16
2676 4368 2.159653 GCTGAATTACTGGCGTTGAGTG 60.160 50.000 0.00 0.00 0.00 3.51
2677 4369 2.076863 GCTGAATTACTGGCGTTGAGT 58.923 47.619 0.00 0.00 0.00 3.41
2678 4370 1.398390 GGCTGAATTACTGGCGTTGAG 59.602 52.381 0.00 0.00 34.00 3.02
2680 4372 0.451783 GGGCTGAATTACTGGCGTTG 59.548 55.000 0.00 0.00 42.23 4.10
2683 4375 0.107703 TCTGGGCTGAATTACTGGCG 60.108 55.000 0.00 0.00 42.23 5.69
2684 4376 1.065126 AGTCTGGGCTGAATTACTGGC 60.065 52.381 0.00 0.00 41.01 4.85
2685 4377 4.487714 TTAGTCTGGGCTGAATTACTGG 57.512 45.455 0.00 0.00 0.00 4.00
2686 4378 6.115446 TGAATTAGTCTGGGCTGAATTACTG 58.885 40.000 0.00 0.00 0.00 2.74
2687 4379 6.313519 TGAATTAGTCTGGGCTGAATTACT 57.686 37.500 0.00 0.00 0.00 2.24
2722 4421 1.221909 TACCCCTCTCTCTGGGCTGA 61.222 60.000 0.00 0.00 46.43 4.26
2782 4487 3.181465 CCGTAGTGGTGGATTTCTAGCAT 60.181 47.826 0.00 0.00 37.20 3.79
2789 4494 1.301954 GCCCCGTAGTGGTGGATTT 59.698 57.895 0.00 0.00 35.15 2.17
2793 4498 2.124736 CATGCCCCGTAGTGGTGG 60.125 66.667 0.00 0.00 35.15 4.61
2807 4512 8.615211 ACAGTAATAAGTATGAACATGCACATG 58.385 33.333 9.06 9.06 44.15 3.21
2814 4519 8.410912 TCGCAGTACAGTAATAAGTATGAACAT 58.589 33.333 0.00 0.00 0.00 2.71
2840 4545 1.636148 AAACTGCACATGCCCTTCAT 58.364 45.000 0.49 0.00 41.18 2.57
2841 4546 2.161855 CTAAACTGCACATGCCCTTCA 58.838 47.619 0.49 0.00 41.18 3.02
2862 4567 0.839277 TCGGAGATGATGTGGGCATT 59.161 50.000 0.00 0.00 35.07 3.56
3010 4722 4.261322 GGATGATTAATCGTGCACTGCAAT 60.261 41.667 20.65 8.71 34.25 3.56
3012 4724 2.613595 GGATGATTAATCGTGCACTGCA 59.386 45.455 20.65 0.00 35.99 4.41
3017 4729 3.172229 TCGTGGATGATTAATCGTGCA 57.828 42.857 23.40 23.40 41.03 4.57
3039 4751 3.592059 TCTTTCGTAACTACACATGCCC 58.408 45.455 0.00 0.00 0.00 5.36
3055 4770 4.695455 TGCACTGCCTGTACTATTTCTTTC 59.305 41.667 0.00 0.00 0.00 2.62
3071 4786 3.304293 GTTGAAAACTCAGTTTGCACTGC 59.696 43.478 10.82 1.07 43.28 4.40
3092 4807 2.863809 AGCGTTTCCTCCTCATTTTGT 58.136 42.857 0.00 0.00 0.00 2.83
3104 4819 5.054390 TGAACCATCAAATAAGCGTTTCC 57.946 39.130 0.00 0.00 30.99 3.13
3230 4945 1.207791 AGCCCCATGTTCTCGAAGAT 58.792 50.000 0.00 0.00 33.89 2.40
3313 5028 3.495629 GGGACCTTTCGTAGAAGTTGGTT 60.496 47.826 0.00 0.00 45.90 3.67
3423 5150 9.672673 ATCTGCAAATTAACACTACTATGAGTT 57.327 29.630 0.00 0.00 0.00 3.01
3436 5163 5.169561 CGCAACGTCATATCTGCAAATTAAC 59.830 40.000 8.25 0.00 34.39 2.01
3562 5290 3.980646 TTCGACACAAATCCAACAAGG 57.019 42.857 0.00 0.00 39.47 3.61
3606 5334 2.098117 CGGCATCCAACATTTTCTCTCC 59.902 50.000 0.00 0.00 0.00 3.71
3788 5529 1.450491 GCCTTTCCGCTCCCTCTTC 60.450 63.158 0.00 0.00 0.00 2.87
3989 5730 1.227263 GATGGTGTCGATGGTCCGG 60.227 63.158 0.00 0.00 0.00 5.14
4058 5799 0.824109 GGATCACGTCCATGGTCAGA 59.176 55.000 12.58 7.58 46.96 3.27
4366 6107 8.343168 AGATAGAGAAGAGAAGAGAAACGAAA 57.657 34.615 0.00 0.00 0.00 3.46
4370 6111 9.185680 ACCTTAGATAGAGAAGAGAAGAGAAAC 57.814 37.037 0.00 0.00 0.00 2.78
4489 6256 0.036577 CAGAGGAGCAGGTTCACCAG 60.037 60.000 0.00 0.00 38.89 4.00
4536 6303 2.781681 ACTTGTATTTCCGGGTGAGG 57.218 50.000 0.00 0.00 0.00 3.86
4584 6351 1.405463 CCTTTGAATAAGGCGAAGGGC 59.595 52.381 0.00 0.00 41.35 5.19
4642 6413 3.889196 TGCTGTGTCGGAATTAACAAC 57.111 42.857 0.00 0.00 0.00 3.32
4694 6465 7.377398 TGATTCGTTCATTCATTCAATGGTTT 58.623 30.769 0.00 0.00 42.18 3.27
4714 6485 2.923655 TGATGTCGTCGAAGCTTGATTC 59.076 45.455 2.10 0.00 0.00 2.52
4715 6486 2.959516 TGATGTCGTCGAAGCTTGATT 58.040 42.857 2.10 0.00 0.00 2.57
4716 6487 2.654749 TGATGTCGTCGAAGCTTGAT 57.345 45.000 2.10 0.00 0.00 2.57
4894 6665 9.547279 TGGAGAAGATAAGGTGCATATATCTTA 57.453 33.333 21.59 12.19 43.11 2.10
5160 6954 8.789825 TGCCATGCATTATTTTGTAAAATTCT 57.210 26.923 7.78 0.00 35.41 2.40
5167 6961 5.163468 ACCGATTGCCATGCATTATTTTGTA 60.163 36.000 0.00 0.00 38.76 2.41
5246 7043 4.246458 GAGTTGGCACTACTTCCTACTTG 58.754 47.826 0.00 0.00 38.27 3.16
5314 7111 6.182627 AGATCTATTTGCTCATGTTTGGTCA 58.817 36.000 0.00 0.00 0.00 4.02
5316 7113 6.096001 GGAAGATCTATTTGCTCATGTTTGGT 59.904 38.462 0.00 0.00 0.00 3.67
5386 7185 1.153066 TTGCTTTGTGCCCGTCTCA 60.153 52.632 0.00 0.00 42.00 3.27
5457 7265 8.984891 TTGTGACAACATTGATTCCAAATATC 57.015 30.769 0.00 0.00 35.83 1.63
5574 7387 1.202915 TCAACTCTCATGGCCAAAGCA 60.203 47.619 10.96 0.29 42.56 3.91
5709 7523 2.068837 ATGCACCAATTTCAGTTGCG 57.931 45.000 0.00 0.00 0.00 4.85
5826 7640 6.909909 CAGTCCACTGGTTTAAATTCTAACC 58.090 40.000 12.49 12.49 43.28 2.85


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

AutoCloner maintained by Alex Coulton.