Multiple sequence alignment - TraesCS2A01G221900

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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 TraesCS2A01G221900 chr2A 100.000 3018 0 0 1 3018 212641747 212644764 0.000000e+00 5574.0
1 TraesCS2A01G221900 chr2A 100.000 2690 0 0 3264 5953 212645010 212647699 0.000000e+00 4968.0
2 TraesCS2A01G221900 chr2B 95.223 2198 71 11 3271 5447 254011926 254014110 0.000000e+00 3446.0
3 TraesCS2A01G221900 chr2B 97.114 1178 31 3 1833 3010 254010632 254011806 0.000000e+00 1984.0
4 TraesCS2A01G221900 chr2B 93.357 1144 59 9 351 1490 254008965 254010095 0.000000e+00 1676.0
5 TraesCS2A01G221900 chr2B 94.068 354 13 4 1487 1834 254010123 254010474 1.140000e-146 531.0
6 TraesCS2A01G221900 chr2B 89.706 340 19 3 25 358 253961827 253962156 2.570000e-113 420.0
7 TraesCS2A01G221900 chr2B 100.000 31 0 0 5466 5496 254014109 254014139 2.320000e-04 58.4
8 TraesCS2A01G221900 chr2D 94.564 2042 62 15 3589 5607 196457035 196459050 0.000000e+00 3110.0
9 TraesCS2A01G221900 chr2D 96.749 1538 39 4 1487 3018 196455099 196456631 0.000000e+00 2553.0
10 TraesCS2A01G221900 chr2D 97.262 694 17 1 799 1490 196454373 196455066 0.000000e+00 1175.0
11 TraesCS2A01G221900 chr2D 81.795 780 85 25 1 742 196453435 196454195 8.540000e-168 601.0
12 TraesCS2A01G221900 chr2D 94.118 289 17 0 3270 3558 196456748 196457036 1.970000e-119 440.0
13 TraesCS2A01G221900 chr2D 84.177 316 32 6 5642 5948 196459184 196459490 2.100000e-74 291.0
14 TraesCS2A01G221900 chr2D 87.218 133 9 5 674 798 196454183 196454315 1.730000e-30 145.0
15 TraesCS2A01G221900 chr1B 80.804 224 38 4 363 583 90269597 90269376 2.850000e-38 171.0
16 TraesCS2A01G221900 chr5B 83.673 147 23 1 5807 5953 568513697 568513842 2.890000e-28 137.0
17 TraesCS2A01G221900 chr5B 84.848 132 20 0 5807 5938 362115496 362115627 3.740000e-27 134.0
18 TraesCS2A01G221900 chr5D 83.803 142 19 4 5807 5948 357081335 357081472 1.350000e-26 132.0
19 TraesCS2A01G221900 chr5A 84.496 129 20 0 5818 5946 582403440 582403568 1.740000e-25 128.0
20 TraesCS2A01G221900 chr3D 76.860 242 46 8 366 600 606746731 606746493 1.740000e-25 128.0
21 TraesCS2A01G221900 chr3D 82.270 141 25 0 5807 5947 608568965 608568825 8.100000e-24 122.0
22 TraesCS2A01G221900 chr6B 84.252 127 19 1 5823 5949 153970906 153970781 8.100000e-24 122.0
23 TraesCS2A01G221900 chr6B 74.597 248 56 6 365 607 149610386 149610631 1.060000e-17 102.0
24 TraesCS2A01G221900 chr6B 75.701 214 44 6 2269 2478 124479467 124479258 3.800000e-17 100.0
25 TraesCS2A01G221900 chr3A 82.394 142 24 1 5807 5948 426867781 426867921 8.100000e-24 122.0
26 TraesCS2A01G221900 chr3A 77.519 129 20 9 443 565 741249812 741249937 1.070000e-07 69.4
27 TraesCS2A01G221900 chr4A 82.517 143 19 6 5807 5948 674364736 674364599 2.910000e-23 121.0
28 TraesCS2A01G221900 chr4A 87.778 90 8 3 490 578 719100353 719100266 1.060000e-17 102.0
29 TraesCS2A01G221900 chr7B 75.966 233 43 9 2251 2478 356699715 356699939 2.270000e-19 108.0
30 TraesCS2A01G221900 chr7B 73.529 272 49 12 5693 5945 690900365 690900098 1.380000e-11 82.4
31 TraesCS2A01G221900 chr6D 75.701 214 44 6 2269 2478 47257715 47257924 3.800000e-17 100.0
32 TraesCS2A01G221900 chr7A 75.107 233 45 9 2251 2478 387173292 387173516 4.910000e-16 97.1
33 TraesCS2A01G221900 chr6A 75.234 214 45 6 2269 2478 68514829 68514620 1.770000e-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 TraesCS2A01G221900 chr2A 212641747 212647699 5952 False 5271.000000 5574 100.000000 1 5953 2 chr2A.!!$F1 5952
1 TraesCS2A01G221900 chr2B 254008965 254014139 5174 False 1539.080000 3446 95.952400 351 5496 5 chr2B.!!$F2 5145
2 TraesCS2A01G221900 chr2D 196453435 196459490 6055 False 1187.857143 3110 90.840429 1 5948 7 chr2D.!!$F1 5947

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
456 494 0.175531 TTGCTCGGCTTCGATGATGA 59.824 50.000 1.89 0.0 42.46 2.92 F
927 1088 2.616765 GCCCCTCTCTGTTTTTCTCTCC 60.617 54.545 0.00 0.0 0.00 3.71 F
1389 1550 0.396811 ACCTCTACAACGCCTTTGCT 59.603 50.000 0.00 0.0 39.01 3.91 F
2181 2542 0.866427 CTGCTGCGGAATATGCTCTG 59.134 55.000 1.17 0.0 0.00 3.35 F
2699 3060 2.028203 GCACACCATTTTGTAGGCCAAT 60.028 45.455 5.01 0.0 31.81 3.16 F
3362 3724 2.290323 CCTCGAACTCCCATTCCTTGTT 60.290 50.000 0.00 0.0 0.00 2.83 F
3937 4304 2.368221 TGCCAGCTTTAGGTTTTGCATT 59.632 40.909 0.00 0.0 0.00 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1306 1467 0.609406 CTGATATCCTCGCCTCCGGA 60.609 60.000 2.93 2.93 34.56 5.14 R
2666 3027 0.033601 TGGTGTGCCCACAAGAAAGT 60.034 50.000 0.70 0.00 43.77 2.66 R
3347 3709 1.963515 GCACAAACAAGGAATGGGAGT 59.036 47.619 0.00 0.00 0.00 3.85 R
3702 4065 1.001860 TCGACCATTGCATGTGTCAGA 59.998 47.619 9.70 5.95 33.11 3.27 R
4411 4778 1.823899 GCTACGGCCCCATGAAAGG 60.824 63.158 0.00 0.00 0.00 3.11 R
4838 5221 3.492011 GCCAACAAATTGCAGTTTGAGAG 59.508 43.478 33.32 22.52 40.64 3.20 R
5636 6057 0.459489 TGCAACACACAAGCTTTCCC 59.541 50.000 0.00 0.00 0.00 3.97 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
61 62 7.712639 AGAGACAACAAGATAATTATGACGCAT 59.287 33.333 1.78 0.00 0.00 4.73
76 77 2.357954 CGCATACATGAGACTTTGCG 57.642 50.000 0.00 1.85 45.42 4.85
77 78 1.660607 CGCATACATGAGACTTTGCGT 59.339 47.619 0.00 0.00 45.55 5.24
90 91 8.039603 TGAGACTTTGCGTAATCACATATTTT 57.960 30.769 0.00 0.00 0.00 1.82
112 113 2.862541 TCTGGGTCACATGACAAAAGG 58.137 47.619 13.77 0.19 46.47 3.11
119 120 5.466393 GGGTCACATGACAAAAGGAAAATTG 59.534 40.000 13.77 0.00 46.47 2.32
132 133 6.687081 AAGGAAAATTGACGACTTAACACA 57.313 33.333 0.00 0.00 0.00 3.72
179 187 6.779049 ACATCAGTTGATTGTTATGGCCATAT 59.221 34.615 25.95 12.47 31.21 1.78
184 192 9.230122 CAGTTGATTGTTATGGCCATATATACA 57.770 33.333 25.95 22.69 0.00 2.29
213 221 9.118236 CAAGAATGAAAATTTTCTCGTTAGGAC 57.882 33.333 26.73 10.58 38.02 3.85
223 231 2.751688 GTTAGGACGGGTGGCCAA 59.248 61.111 7.24 0.00 0.00 4.52
288 302 2.508716 TCTCCGCCTCTCCTCTACTTAA 59.491 50.000 0.00 0.00 0.00 1.85
295 309 4.900054 GCCTCTCCTCTACTTAATTGGGTA 59.100 45.833 0.00 0.00 0.00 3.69
300 314 6.769822 TCTCCTCTACTTAATTGGGTACTACG 59.230 42.308 0.00 0.00 0.00 3.51
324 338 2.821366 CTGGTGCACGAGATGGCC 60.821 66.667 23.05 0.00 0.00 5.36
337 351 2.555757 GAGATGGCCAATCCTATGCAAC 59.444 50.000 10.96 0.00 35.72 4.17
338 352 1.615392 GATGGCCAATCCTATGCAACC 59.385 52.381 10.96 0.00 35.26 3.77
358 372 1.611673 CGGGAGGTGCTCAGTTGATTT 60.612 52.381 0.00 0.00 31.08 2.17
389 426 1.893808 CTGTTCTGGTGCGCTGGTT 60.894 57.895 9.73 0.00 0.00 3.67
392 429 1.597854 TTCTGGTGCGCTGGTTCTG 60.598 57.895 9.73 0.00 0.00 3.02
394 431 1.597854 CTGGTGCGCTGGTTCTGAA 60.598 57.895 9.73 0.00 0.00 3.02
402 439 1.610624 CGCTGGTTCTGAAGGCCTTAA 60.611 52.381 20.54 10.96 0.00 1.85
405 442 3.690460 CTGGTTCTGAAGGCCTTAACAT 58.310 45.455 24.34 2.79 0.00 2.71
416 453 5.184892 AGGCCTTAACATGATGACTTCTT 57.815 39.130 0.00 0.00 0.00 2.52
418 455 4.096984 GGCCTTAACATGATGACTTCTTGG 59.903 45.833 0.00 0.00 34.58 3.61
421 458 5.416952 CCTTAACATGATGACTTCTTGGCTT 59.583 40.000 0.00 0.00 34.58 4.35
456 494 0.175531 TTGCTCGGCTTCGATGATGA 59.824 50.000 1.89 0.00 42.46 2.92
513 551 3.302555 CAGTGTTTGTAGTCGTCGCTAA 58.697 45.455 0.00 0.00 0.00 3.09
514 552 3.732219 CAGTGTTTGTAGTCGTCGCTAAA 59.268 43.478 0.00 0.00 0.00 1.85
540 578 8.737168 TGATCTAAGAACCTGGATGTAATTTG 57.263 34.615 0.00 0.00 0.00 2.32
672 710 8.885494 AAACAAACAAACATGCATTAGTACAT 57.115 26.923 0.00 0.00 0.00 2.29
808 967 4.427437 AGAGAATCCAATCGTGGCCGAG 62.427 54.545 0.00 0.00 45.54 4.63
829 988 2.830285 AACAACACAACGAGCCGGC 61.830 57.895 21.89 21.89 0.00 6.13
927 1088 2.616765 GCCCCTCTCTGTTTTTCTCTCC 60.617 54.545 0.00 0.00 0.00 3.71
1389 1550 0.396811 ACCTCTACAACGCCTTTGCT 59.603 50.000 0.00 0.00 39.01 3.91
1437 1598 6.264292 TGCCTCTATCTACTGAGAGAATTGTC 59.736 42.308 0.00 0.00 41.55 3.18
1490 1651 7.436080 GTGTGCTTAAATGATGGATTATGTTGG 59.564 37.037 0.00 0.00 0.00 3.77
1491 1652 6.925165 GTGCTTAAATGATGGATTATGTTGGG 59.075 38.462 0.00 0.00 0.00 4.12
1492 1653 6.041865 TGCTTAAATGATGGATTATGTTGGGG 59.958 38.462 0.00 0.00 0.00 4.96
1534 1731 9.967451 TTTTCTATCCTATTTTCACATGTACCA 57.033 29.630 0.00 0.00 0.00 3.25
1631 1834 8.016497 TGCTGTTATTTTGAAACATGTTATGC 57.984 30.769 12.39 5.35 36.33 3.14
1635 1838 8.976471 TGTTATTTTGAAACATGTTATGCACAG 58.024 29.630 12.39 0.00 39.40 3.66
1652 1855 1.411246 ACAGACGGTTACAAGCTGTCA 59.589 47.619 14.06 0.00 35.02 3.58
1656 1859 4.504461 CAGACGGTTACAAGCTGTCATATC 59.496 45.833 14.06 0.00 34.68 1.63
1714 1917 2.145536 TGTGCGGCATGCTCAATATAG 58.854 47.619 18.92 0.66 43.59 1.31
1876 2237 7.761704 GGAGTAGTATATGGTAGCATGTTCATG 59.238 40.741 17.58 8.26 0.00 3.07
1892 2253 6.117911 TGTTCATGTATCTATGTTTTGGCG 57.882 37.500 0.00 0.00 0.00 5.69
2028 2389 6.158598 GGAAACATTGTCATTGTATGCACTT 58.841 36.000 0.94 0.00 0.00 3.16
2038 2399 6.808212 GTCATTGTATGCACTTGCTTTTGTAT 59.192 34.615 2.33 0.00 42.66 2.29
2181 2542 0.866427 CTGCTGCGGAATATGCTCTG 59.134 55.000 1.17 0.00 0.00 3.35
2226 2587 7.271511 TGATGCCTAATGTTGAACAAGTTTTT 58.728 30.769 0.62 0.00 0.00 1.94
2535 2896 5.760253 GCCTGCAGCTAACAAGAAGAATATA 59.240 40.000 8.66 0.00 38.99 0.86
2577 2938 4.281435 TCAACTAATGGTACGTGAACTGGA 59.719 41.667 0.00 0.00 0.00 3.86
2699 3060 2.028203 GCACACCATTTTGTAGGCCAAT 60.028 45.455 5.01 0.00 31.81 3.16
2755 3116 3.367910 GCTTCCTCGATGAGAGTGTTCTT 60.368 47.826 0.00 0.00 45.44 2.52
3345 3707 7.719633 TCCCATCTTAAATATTCTTTTCCCTCG 59.280 37.037 0.00 0.00 0.00 4.63
3347 3709 9.120538 CCATCTTAAATATTCTTTTCCCTCGAA 57.879 33.333 0.00 0.00 0.00 3.71
3362 3724 2.290323 CCTCGAACTCCCATTCCTTGTT 60.290 50.000 0.00 0.00 0.00 2.83
3410 3772 6.907212 GCACATAACATTTGTTCTATCTTCCG 59.093 38.462 0.00 0.00 39.31 4.30
3428 3790 7.001099 TCTTCCGTTAGTCCTTGAATAAACT 57.999 36.000 0.00 0.00 0.00 2.66
3438 3800 5.183904 GTCCTTGAATAAACTGTCCTTGCAT 59.816 40.000 0.00 0.00 0.00 3.96
3454 3816 5.772672 TCCTTGCATACACAAGTAATTGGTT 59.227 36.000 7.93 0.00 44.55 3.67
3519 3882 9.838339 AGATGGCCTGCACTAAATATATTATAC 57.162 33.333 3.32 0.00 0.00 1.47
3567 3930 5.724854 TGGTTTCCTTCCTAGCACTATTAGT 59.275 40.000 0.00 0.00 0.00 2.24
3616 3979 6.944862 GGAGGCTAATTCCAGTTCATCAATAT 59.055 38.462 0.00 0.00 34.74 1.28
3702 4065 5.934043 GGCTTCATTTTCTTTTACAGCCAAT 59.066 36.000 1.94 0.00 44.29 3.16
3740 4103 6.507900 TGGTCGAATTAAATTTGTGAAGCAA 58.492 32.000 0.00 0.00 34.87 3.91
3797 4160 6.070897 TGTGTGATGGTTGATTTGTTGTAG 57.929 37.500 0.00 0.00 0.00 2.74
3937 4304 2.368221 TGCCAGCTTTAGGTTTTGCATT 59.632 40.909 0.00 0.00 0.00 3.56
3940 4307 4.319694 GCCAGCTTTAGGTTTTGCATTTTG 60.320 41.667 0.00 0.00 0.00 2.44
3960 4327 9.289303 CATTTTGTTTCTATGGTTATCCTTTCG 57.711 33.333 0.00 0.00 34.23 3.46
4058 4425 6.666113 TGATCCCAACAATACTACAGTGAGTA 59.334 38.462 0.00 0.93 36.38 2.59
4272 4639 4.043435 AGCAGGTTAAGAAAATCTCCAGGT 59.957 41.667 0.00 0.00 0.00 4.00
4756 5134 6.925165 GCAAGGAATTGACAACCCAATATATG 59.075 38.462 10.14 0.00 35.86 1.78
4820 5203 9.424659 GAAATTTGTCTGTGCAAATAAACAAAG 57.575 29.630 14.17 0.00 45.17 2.77
4838 5221 8.460831 AAACAAAGAAATGATACAAATACGCC 57.539 30.769 0.00 0.00 0.00 5.68
4868 5251 5.609423 ACTGCAATTTGTTGGCTGATTTTA 58.391 33.333 0.00 0.00 0.00 1.52
4875 5258 7.894376 ATTTGTTGGCTGATTTTAGTGATTG 57.106 32.000 0.00 0.00 0.00 2.67
4877 5260 6.403866 TGTTGGCTGATTTTAGTGATTGTT 57.596 33.333 0.00 0.00 0.00 2.83
4936 5319 2.483889 GCTGATGACTAACCTGGCTACC 60.484 54.545 0.00 0.00 0.00 3.18
5304 5687 4.400884 TGTAGTCTGCCATTTTGTTGTTGT 59.599 37.500 0.00 0.00 0.00 3.32
5378 5761 6.869913 TCATGTTGGAAGAGCAAATCAAAATC 59.130 34.615 0.00 0.00 0.00 2.17
5411 5795 6.202379 GCTGGTAAACCGATCCTACTATTTTC 59.798 42.308 0.00 0.00 39.43 2.29
5446 5830 2.950309 CGAGGAACGGAGATCTAAGGAA 59.050 50.000 0.00 0.00 38.46 3.36
5496 5880 3.053831 AGACCGATACCAAAACCACTG 57.946 47.619 0.00 0.00 0.00 3.66
5497 5881 2.370849 AGACCGATACCAAAACCACTGT 59.629 45.455 0.00 0.00 0.00 3.55
5498 5882 2.740447 GACCGATACCAAAACCACTGTC 59.260 50.000 0.00 0.00 0.00 3.51
5504 5888 1.286553 ACCAAAACCACTGTCTTCCCA 59.713 47.619 0.00 0.00 0.00 4.37
5518 5902 4.770010 TGTCTTCCCAATAACCAATCCAAC 59.230 41.667 0.00 0.00 0.00 3.77
5527 5911 6.550854 CCAATAACCAATCCAACCTGACATAT 59.449 38.462 0.00 0.00 0.00 1.78
5528 5912 7.723616 CCAATAACCAATCCAACCTGACATATA 59.276 37.037 0.00 0.00 0.00 0.86
5536 5920 6.174720 TCCAACCTGACATATAAGATCCAC 57.825 41.667 0.00 0.00 0.00 4.02
5541 5925 7.623999 ACCTGACATATAAGATCCACAAGAT 57.376 36.000 0.00 0.00 38.17 2.40
5556 5940 5.192927 CCACAAGATGGGCAGTTATTCTTA 58.807 41.667 0.00 0.00 45.95 2.10
5561 5945 5.300752 AGATGGGCAGTTATTCTTATCACG 58.699 41.667 0.00 0.00 0.00 4.35
5592 5976 7.016268 AGAGATACTTTTTACACAACTCCCTCA 59.984 37.037 0.00 0.00 0.00 3.86
5596 5980 9.975218 ATACTTTTTACACAACTCCCTCAATAT 57.025 29.630 0.00 0.00 0.00 1.28
5624 6045 8.950007 AAGAATAAAATAGGGAAAGGTGTTCA 57.050 30.769 0.00 0.00 0.00 3.18
5625 6046 8.950007 AGAATAAAATAGGGAAAGGTGTTCAA 57.050 30.769 0.00 0.00 0.00 2.69
5626 6047 9.374711 AGAATAAAATAGGGAAAGGTGTTCAAA 57.625 29.630 0.00 0.00 0.00 2.69
5627 6048 9.990360 GAATAAAATAGGGAAAGGTGTTCAAAA 57.010 29.630 0.00 0.00 0.00 2.44
5657 6141 2.483538 GGGAAAGCTTGTGTGTTGCAAT 60.484 45.455 0.59 0.00 0.00 3.56
5676 6160 5.359576 TGCAATGGGAGAAAATATACCACAC 59.640 40.000 0.00 0.00 33.42 3.82
5679 6163 4.761975 TGGGAGAAAATATACCACACGTC 58.238 43.478 0.00 0.00 0.00 4.34
5680 6164 4.468510 TGGGAGAAAATATACCACACGTCT 59.531 41.667 0.00 0.00 0.00 4.18
5683 6168 7.043565 GGGAGAAAATATACCACACGTCTAAA 58.956 38.462 0.00 0.00 0.00 1.85
5715 6200 2.573340 CAATGCCGGCCCTCAAAC 59.427 61.111 26.77 0.00 0.00 2.93
5716 6201 2.679996 AATGCCGGCCCTCAAACC 60.680 61.111 26.77 0.00 0.00 3.27
5722 6207 3.680786 GGCCCTCAAACCGCCAAC 61.681 66.667 0.00 0.00 42.52 3.77
5723 6208 2.909965 GCCCTCAAACCGCCAACA 60.910 61.111 0.00 0.00 0.00 3.33
5724 6209 2.275380 GCCCTCAAACCGCCAACAT 61.275 57.895 0.00 0.00 0.00 2.71
5725 6210 0.963355 GCCCTCAAACCGCCAACATA 60.963 55.000 0.00 0.00 0.00 2.29
5726 6211 1.762708 CCCTCAAACCGCCAACATAT 58.237 50.000 0.00 0.00 0.00 1.78
5735 6220 1.651987 CGCCAACATATGTTCGGACT 58.348 50.000 27.36 5.66 35.83 3.85
5761 6246 1.307355 TTCGGACATGCTGTGCCATG 61.307 55.000 0.00 0.94 46.19 3.66
5765 6250 0.734942 GACATGCTGTGCCATGCAAC 60.735 55.000 0.00 0.00 44.98 4.17
5771 6256 4.759096 GTGCCATGCAACGCGGTC 62.759 66.667 12.47 0.00 41.47 4.79
5775 6260 4.147322 CATGCAACGCGGTCGGTC 62.147 66.667 12.47 0.00 40.69 4.79
5789 6281 3.311110 GGTCCGCAGAGTGGTCCA 61.311 66.667 7.80 0.00 40.24 4.02
5793 6285 2.574018 CCGCAGAGTGGTCCAGACA 61.574 63.158 0.00 0.00 0.00 3.41
5799 6291 2.119495 AGAGTGGTCCAGACACACTTT 58.881 47.619 17.40 12.08 40.42 2.66
5846 6338 2.171725 GCGTCCGGATAGCACCAAC 61.172 63.158 24.23 2.36 0.00 3.77
5860 6353 0.250901 ACCAACGCCAGCTTCTGATT 60.251 50.000 0.00 0.00 32.44 2.57
5864 6357 2.744202 CAACGCCAGCTTCTGATTACTT 59.256 45.455 0.00 0.00 32.44 2.24
5866 6359 2.744202 ACGCCAGCTTCTGATTACTTTG 59.256 45.455 0.00 0.00 32.44 2.77
5888 6381 2.534533 ACCCAAACCCCCTCCTCC 60.535 66.667 0.00 0.00 0.00 4.30
5948 6441 1.314534 TTCATGCCAATGTGGAGCGG 61.315 55.000 0.00 0.00 40.96 5.52
5949 6442 2.048023 CATGCCAATGTGGAGCGGT 61.048 57.895 0.00 0.00 40.96 5.68
5950 6443 1.304381 ATGCCAATGTGGAGCGGTT 60.304 52.632 0.00 0.00 40.96 4.44
5951 6444 1.597797 ATGCCAATGTGGAGCGGTTG 61.598 55.000 0.00 0.00 40.96 3.77
5952 6445 2.568090 CCAATGTGGAGCGGTTGC 59.432 61.111 0.00 0.00 40.96 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.271828 TCATGTATGCGTCATAATTATCTTGTT 57.728 29.630 0.00 0.00 0.00 2.83
43 44 9.143631 TCTCATGTATGCGTCATAATTATCTTG 57.856 33.333 0.00 0.00 0.00 3.02
49 50 7.633621 CAAAGTCTCATGTATGCGTCATAATT 58.366 34.615 0.00 0.00 0.00 1.40
50 51 6.293081 GCAAAGTCTCATGTATGCGTCATAAT 60.293 38.462 0.00 0.00 0.00 1.28
54 55 2.672874 GCAAAGTCTCATGTATGCGTCA 59.327 45.455 0.00 0.00 0.00 4.35
58 59 4.857871 TTACGCAAAGTCTCATGTATGC 57.142 40.909 0.00 0.00 0.00 3.14
61 62 5.474825 TGTGATTACGCAAAGTCTCATGTA 58.525 37.500 0.00 0.00 33.38 2.29
90 91 3.636300 CCTTTTGTCATGTGACCCAGAAA 59.364 43.478 10.40 2.22 44.15 2.52
93 94 2.862541 TCCTTTTGTCATGTGACCCAG 58.137 47.619 10.40 4.10 44.15 4.45
100 101 5.977129 GTCGTCAATTTTCCTTTTGTCATGT 59.023 36.000 0.00 0.00 0.00 3.21
102 103 6.391227 AGTCGTCAATTTTCCTTTTGTCAT 57.609 33.333 0.00 0.00 0.00 3.06
154 155 4.343231 TGGCCATAACAATCAACTGATGT 58.657 39.130 0.00 0.00 34.49 3.06
213 221 2.484287 ATTCCAGAGTTGGCCACCCG 62.484 60.000 3.88 0.00 44.63 5.28
223 231 5.596836 TTCAACAAAGCAAATTCCAGAGT 57.403 34.783 0.00 0.00 0.00 3.24
264 273 1.679153 GTAGAGGAGAGGCGGAGAAAG 59.321 57.143 0.00 0.00 0.00 2.62
270 279 3.243907 CCAATTAAGTAGAGGAGAGGCGG 60.244 52.174 0.00 0.00 0.00 6.13
271 280 3.243907 CCCAATTAAGTAGAGGAGAGGCG 60.244 52.174 0.00 0.00 0.00 5.52
315 329 1.271001 TGCATAGGATTGGCCATCTCG 60.271 52.381 6.09 1.57 40.02 4.04
324 338 1.597742 CTCCCGGTTGCATAGGATTG 58.402 55.000 0.00 0.00 0.00 2.67
337 351 1.903877 ATCAACTGAGCACCTCCCGG 61.904 60.000 0.00 0.00 0.00 5.73
338 352 0.036010 AATCAACTGAGCACCTCCCG 60.036 55.000 0.00 0.00 0.00 5.14
358 372 2.610374 CCAGAACAGAAACCGTCGAAAA 59.390 45.455 0.00 0.00 0.00 2.29
369 383 1.597854 CCAGCGCACCAGAACAGAA 60.598 57.895 11.47 0.00 0.00 3.02
389 426 4.225942 AGTCATCATGTTAAGGCCTTCAGA 59.774 41.667 24.49 10.72 0.00 3.27
392 429 5.189180 AGAAGTCATCATGTTAAGGCCTTC 58.811 41.667 24.49 9.55 0.00 3.46
394 431 4.851639 AGAAGTCATCATGTTAAGGCCT 57.148 40.909 0.00 0.00 0.00 5.19
402 439 4.660168 AGAAAGCCAAGAAGTCATCATGT 58.340 39.130 0.00 0.00 0.00 3.21
405 442 5.489792 AGTAGAAAGCCAAGAAGTCATCA 57.510 39.130 0.00 0.00 0.00 3.07
416 453 5.646360 GCAAACCTTATGTAGTAGAAAGCCA 59.354 40.000 0.00 0.00 0.00 4.75
418 455 6.237861 CGAGCAAACCTTATGTAGTAGAAAGC 60.238 42.308 0.00 0.00 0.00 3.51
421 458 5.657474 CCGAGCAAACCTTATGTAGTAGAA 58.343 41.667 0.00 0.00 0.00 2.10
456 494 2.505982 CCGTCATCATCGCCCCTT 59.494 61.111 0.00 0.00 0.00 3.95
513 551 9.927081 AAATTACATCCAGGTTCTTAGATCATT 57.073 29.630 0.00 0.00 0.00 2.57
514 552 9.347240 CAAATTACATCCAGGTTCTTAGATCAT 57.653 33.333 0.00 0.00 0.00 2.45
731 826 0.321653 GGTCGTCCCAGCAGTTTGAT 60.322 55.000 0.00 0.00 0.00 2.57
732 827 1.070786 GGTCGTCCCAGCAGTTTGA 59.929 57.895 0.00 0.00 0.00 2.69
733 828 0.951040 GAGGTCGTCCCAGCAGTTTG 60.951 60.000 0.00 0.00 34.66 2.93
801 960 0.393132 TTGTGTTGTTGTCTCGGCCA 60.393 50.000 2.24 0.00 0.00 5.36
808 967 0.315869 CGGCTCGTTGTGTTGTTGTC 60.316 55.000 0.00 0.00 0.00 3.18
927 1088 0.255033 CCCTAAAAACCTCGGAGGGG 59.745 60.000 26.94 16.66 42.85 4.79
1152 1313 3.093172 TGCGGATGGCCCCACATA 61.093 61.111 0.00 0.00 42.61 2.29
1306 1467 0.609406 CTGATATCCTCGCCTCCGGA 60.609 60.000 2.93 2.93 34.56 5.14
1437 1598 7.328249 ACATTGGAAGTGTAAATTTGTAATGCG 59.672 33.333 0.00 0.00 28.83 4.73
1534 1731 4.040952 AGCAAACACTGAGTCACTTCCTAT 59.959 41.667 0.00 0.00 0.00 2.57
1631 1834 1.792949 GACAGCTTGTAACCGTCTGTG 59.207 52.381 0.00 0.00 38.03 3.66
1635 1838 4.267928 GTGATATGACAGCTTGTAACCGTC 59.732 45.833 0.00 0.00 0.00 4.79
1656 1859 8.801715 ATCAAACAGTAATGCTTAAACAAGTG 57.198 30.769 0.00 0.00 0.00 3.16
1825 2028 6.413783 TCCTCCGCAACTTAATATATGACA 57.586 37.500 0.00 0.00 0.00 3.58
1841 2202 2.875094 TATACTACTCCCTCCTCCGC 57.125 55.000 0.00 0.00 0.00 5.54
1842 2203 3.010361 ACCATATACTACTCCCTCCTCCG 59.990 52.174 0.00 0.00 0.00 4.63
1876 2237 8.583810 TGTATAGAACGCCAAAACATAGATAC 57.416 34.615 0.00 0.00 0.00 2.24
1993 2354 9.778993 CAATGACAATGTTTCCAGAAATACTAG 57.221 33.333 0.00 0.00 32.36 2.57
2002 2363 5.574055 GTGCATACAATGACAATGTTTCCAG 59.426 40.000 0.59 0.00 32.27 3.86
2100 2461 2.159393 CCCAGTATGTTTGTTGCGGATG 60.159 50.000 0.00 0.00 0.00 3.51
2181 2542 0.629058 TCTGCCCATTAAAGGTCCCC 59.371 55.000 0.00 0.00 0.00 4.81
2535 2896 5.423610 AGTTGAATATGTCTGCTGAGTACCT 59.576 40.000 0.00 0.00 0.00 3.08
2664 3025 1.607148 GGTGTGCCCACAAGAAAGTAC 59.393 52.381 0.70 0.00 43.77 2.73
2666 3027 0.033601 TGGTGTGCCCACAAGAAAGT 60.034 50.000 0.70 0.00 43.77 2.66
2699 3060 8.450578 AACAATCAGAGTGTAAACAGATTGAA 57.549 30.769 22.33 0.00 42.86 2.69
2755 3116 9.862371 CTGAGTAGAAAGATAAGAAGTGCTAAA 57.138 33.333 0.00 0.00 0.00 1.85
3298 3659 5.508994 GGGAATTACAAACTGTTTGGGAGTG 60.509 44.000 30.29 11.30 44.81 3.51
3345 3707 3.552890 GCACAAACAAGGAATGGGAGTTC 60.553 47.826 0.00 0.00 0.00 3.01
3347 3709 1.963515 GCACAAACAAGGAATGGGAGT 59.036 47.619 0.00 0.00 0.00 3.85
3362 3724 5.278266 GCACTACAAAAGATTAGGTGCACAA 60.278 40.000 20.43 5.52 35.64 3.33
3410 3772 7.573283 GCAAGGACAGTTTATTCAAGGACTAAC 60.573 40.741 0.00 0.00 0.00 2.34
3438 3800 4.521256 GGAAGGCAACCAATTACTTGTGTA 59.479 41.667 0.00 0.00 37.17 2.90
3519 3882 7.414319 CCATTTGCTTTAATATTTGTTGCCCAG 60.414 37.037 0.00 0.00 0.00 4.45
3538 3901 2.825532 TGCTAGGAAGGAAACCATTTGC 59.174 45.455 0.00 0.00 0.00 3.68
3567 3930 4.734134 GCAACATGCAGCACACAA 57.266 50.000 0.00 0.00 44.26 3.33
3616 3979 4.569966 CCTATTTTTGCGCAAATGCCATAA 59.430 37.500 33.94 23.95 37.91 1.90
3702 4065 1.001860 TCGACCATTGCATGTGTCAGA 59.998 47.619 9.70 5.95 33.11 3.27
3757 4120 3.798337 CACACAAAGAAGCCATTGTCAAC 59.202 43.478 0.00 0.00 37.66 3.18
3848 4214 6.743575 AATACACATGAAGCAGGAAAGTAC 57.256 37.500 0.00 0.00 0.00 2.73
3851 4217 6.992063 ACTAATACACATGAAGCAGGAAAG 57.008 37.500 0.00 0.00 0.00 2.62
3855 4221 6.992063 AAGAACTAATACACATGAAGCAGG 57.008 37.500 0.00 0.00 0.00 4.85
4411 4778 1.823899 GCTACGGCCCCATGAAAGG 60.824 63.158 0.00 0.00 0.00 3.11
4736 5114 8.292448 CAGTAGCATATATTGGGTTGTCAATTC 58.708 37.037 0.00 0.00 38.24 2.17
4756 5134 5.665381 GATGAAATCACTAAGGCAGTAGC 57.335 43.478 0.00 0.00 44.70 3.58
4820 5203 6.844696 TGAGAGGCGTATTTGTATCATTTC 57.155 37.500 0.00 0.00 0.00 2.17
4838 5221 3.492011 GCCAACAAATTGCAGTTTGAGAG 59.508 43.478 33.32 22.52 40.64 3.20
4868 5251 6.642131 GCATGTGAACAATGTTAACAATCACT 59.358 34.615 28.11 19.10 0.00 3.41
4875 5258 9.190858 TCATTTAAGCATGTGAACAATGTTAAC 57.809 29.630 6.67 6.67 0.00 2.01
4877 5260 9.356433 CATCATTTAAGCATGTGAACAATGTTA 57.644 29.630 0.00 0.00 0.00 2.41
4936 5319 7.198390 CCTCAATGGTCACTGCAAAATATTAG 58.802 38.462 0.00 0.00 0.00 1.73
5179 5562 5.278604 ACTATCAACGCAAAAACCAAGAAC 58.721 37.500 0.00 0.00 0.00 3.01
5378 5761 2.905075 TCGGTTTACCAGCAGATGATG 58.095 47.619 0.00 0.00 35.14 3.07
5411 5795 3.061139 CGTTCCTCGCGCTTTTATAGAAG 60.061 47.826 5.56 0.00 0.00 2.85
5496 5880 4.159693 GGTTGGATTGGTTATTGGGAAGAC 59.840 45.833 0.00 0.00 0.00 3.01
5497 5881 4.045334 AGGTTGGATTGGTTATTGGGAAGA 59.955 41.667 0.00 0.00 0.00 2.87
5498 5882 4.160252 CAGGTTGGATTGGTTATTGGGAAG 59.840 45.833 0.00 0.00 0.00 3.46
5504 5888 9.354673 CTTATATGTCAGGTTGGATTGGTTATT 57.645 33.333 0.00 0.00 0.00 1.40
5518 5902 7.902387 CATCTTGTGGATCTTATATGTCAGG 57.098 40.000 0.00 0.00 31.27 3.86
5536 5920 6.293081 CGTGATAAGAATAACTGCCCATCTTG 60.293 42.308 0.00 0.00 32.87 3.02
5541 5925 4.746535 TCGTGATAAGAATAACTGCCCA 57.253 40.909 0.00 0.00 0.00 5.36
5572 5956 9.802039 TTATATTGAGGGAGTTGTGTAAAAAGT 57.198 29.630 0.00 0.00 0.00 2.66
5601 6022 9.990360 TTTTGAACACCTTTCCCTATTTTATTC 57.010 29.630 0.00 0.00 0.00 1.75
5625 6046 8.428852 ACACACAAGCTTTCCCTATTTATTTTT 58.571 29.630 0.00 0.00 0.00 1.94
5626 6047 7.962441 ACACACAAGCTTTCCCTATTTATTTT 58.038 30.769 0.00 0.00 0.00 1.82
5627 6048 7.539034 ACACACAAGCTTTCCCTATTTATTT 57.461 32.000 0.00 0.00 0.00 1.40
5628 6049 7.378181 CAACACACAAGCTTTCCCTATTTATT 58.622 34.615 0.00 0.00 0.00 1.40
5629 6050 6.572314 GCAACACACAAGCTTTCCCTATTTAT 60.572 38.462 0.00 0.00 0.00 1.40
5630 6051 5.278758 GCAACACACAAGCTTTCCCTATTTA 60.279 40.000 0.00 0.00 0.00 1.40
5631 6052 4.501400 GCAACACACAAGCTTTCCCTATTT 60.501 41.667 0.00 0.00 0.00 1.40
5633 6054 2.558359 GCAACACACAAGCTTTCCCTAT 59.442 45.455 0.00 0.00 0.00 2.57
5634 6055 1.953686 GCAACACACAAGCTTTCCCTA 59.046 47.619 0.00 0.00 0.00 3.53
5635 6056 0.746659 GCAACACACAAGCTTTCCCT 59.253 50.000 0.00 0.00 0.00 4.20
5636 6057 0.459489 TGCAACACACAAGCTTTCCC 59.541 50.000 0.00 0.00 0.00 3.97
5637 6058 2.292103 TTGCAACACACAAGCTTTCC 57.708 45.000 0.00 0.00 0.00 3.13
5638 6059 2.540931 CCATTGCAACACACAAGCTTTC 59.459 45.455 0.00 0.00 0.00 2.62
5643 6127 1.955778 TCTCCCATTGCAACACACAAG 59.044 47.619 0.00 0.00 0.00 3.16
5649 6133 5.954752 TGGTATATTTTCTCCCATTGCAACA 59.045 36.000 0.00 0.00 0.00 3.33
5657 6141 4.468510 AGACGTGTGGTATATTTTCTCCCA 59.531 41.667 0.00 0.00 0.00 4.37
5683 6168 2.550639 GGCATTGGACATGTGGCTTTTT 60.551 45.455 1.15 0.00 35.74 1.94
5689 6174 3.067480 GCCGGCATTGGACATGTGG 62.067 63.158 24.80 0.00 0.00 4.17
5715 6200 0.655733 GTCCGAACATATGTTGGCGG 59.344 55.000 29.46 29.46 42.93 6.13
5716 6201 1.327460 CAGTCCGAACATATGTTGGCG 59.673 52.381 25.42 21.16 38.56 5.69
5717 6202 1.064060 GCAGTCCGAACATATGTTGGC 59.936 52.381 25.42 13.47 38.56 4.52
5718 6203 1.327460 CGCAGTCCGAACATATGTTGG 59.673 52.381 25.42 22.57 38.56 3.77
5719 6204 1.267532 GCGCAGTCCGAACATATGTTG 60.268 52.381 25.42 16.18 38.56 3.33
5720 6205 1.006832 GCGCAGTCCGAACATATGTT 58.993 50.000 20.93 20.93 41.64 2.71
5721 6206 1.145759 CGCGCAGTCCGAACATATGT 61.146 55.000 8.75 1.41 40.02 2.29
5722 6207 1.559814 CGCGCAGTCCGAACATATG 59.440 57.895 8.75 0.00 40.02 1.78
5723 6208 1.591594 CCGCGCAGTCCGAACATAT 60.592 57.895 8.75 0.00 40.02 1.78
5724 6209 2.202690 CCGCGCAGTCCGAACATA 60.203 61.111 8.75 0.00 40.02 2.29
5725 6210 3.876589 AACCGCGCAGTCCGAACAT 62.877 57.895 8.75 0.00 40.02 2.71
5726 6211 4.595538 AACCGCGCAGTCCGAACA 62.596 61.111 8.75 0.00 40.02 3.18
5771 6256 4.436998 GGACCACTCTGCGGACCG 62.437 72.222 10.29 10.29 0.00 4.79
5772 6257 3.302347 CTGGACCACTCTGCGGACC 62.302 68.421 0.00 0.00 38.65 4.46
5773 6258 2.262915 CTGGACCACTCTGCGGAC 59.737 66.667 0.00 0.00 0.00 4.79
5774 6259 2.117423 TCTGGACCACTCTGCGGA 59.883 61.111 0.00 0.00 0.00 5.54
5775 6260 2.262915 GTCTGGACCACTCTGCGG 59.737 66.667 0.00 0.00 0.00 5.69
5781 6273 2.103263 GAGAAAGTGTGTCTGGACCACT 59.897 50.000 14.48 14.48 41.34 4.00
5783 6275 1.416401 GGAGAAAGTGTGTCTGGACCA 59.584 52.381 0.00 0.00 0.00 4.02
5789 6281 0.468226 TTGCGGGAGAAAGTGTGTCT 59.532 50.000 0.00 0.00 0.00 3.41
5793 6285 0.463116 ACGTTTGCGGGAGAAAGTGT 60.463 50.000 0.00 0.00 43.45 3.55
5846 6338 2.096496 CCAAAGTAATCAGAAGCTGGCG 59.904 50.000 0.00 0.00 31.51 5.69
5860 6353 0.470268 GGTTTGGGTGGGCCAAAGTA 60.470 55.000 8.40 0.00 37.75 2.24
5864 6357 4.565850 GGGGTTTGGGTGGGCCAA 62.566 66.667 8.40 0.00 36.17 4.52


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

AutoCloner maintained by Alex Coulton.