Multiple sequence alignment - TraesCS4A01G128600

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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 TraesCS4A01G128600 chr4A 100.000 5597 0 0 1 5597 165707047 165712643 0.000000e+00 10336.0
1 TraesCS4A01G128600 chr4A 96.649 746 25 0 1363 2108 438240175 438239430 0.000000e+00 1240.0
2 TraesCS4A01G128600 chr4D 95.377 3115 94 17 2501 5597 309512006 309508924 0.000000e+00 4909.0
3 TraesCS4A01G128600 chr4D 85.651 676 48 8 1 630 309605748 309605076 0.000000e+00 665.0
4 TraesCS4A01G128600 chr4D 96.848 349 11 0 2100 2448 309512355 309512007 8.080000e-163 584.0
5 TraesCS4A01G128600 chr4D 87.562 402 24 8 953 1354 309512716 309512341 5.150000e-120 442.0
6 TraesCS4A01G128600 chr4D 90.625 288 17 7 678 961 309513142 309512861 1.900000e-99 374.0
7 TraesCS4A01G128600 chr4B 94.995 2917 102 23 2100 5015 386225870 386222997 0.000000e+00 4538.0
8 TraesCS4A01G128600 chr4B 85.837 932 80 19 7 893 386227514 386226590 0.000000e+00 942.0
9 TraesCS4A01G128600 chr4B 89.920 754 29 18 4527 5271 386222989 386222274 0.000000e+00 928.0
10 TraesCS4A01G128600 chr4B 93.643 409 13 2 953 1354 386226258 386225856 2.890000e-167 599.0
11 TraesCS4A01G128600 chr4B 91.985 262 21 0 5336 5597 386218774 386218513 8.860000e-98 368.0
12 TraesCS4A01G128600 chr4B 91.603 262 22 0 5336 5597 386213995 386213734 4.120000e-96 363.0
13 TraesCS4A01G128600 chr4B 91.603 262 22 0 5336 5597 386216953 386216692 4.120000e-96 363.0
14 TraesCS4A01G128600 chr4B 91.603 262 22 0 5336 5597 386220595 386220334 4.120000e-96 363.0
15 TraesCS4A01G128600 chr4B 100.000 55 0 0 5290 5344 386222277 386222223 9.920000e-18 102.0
16 TraesCS4A01G128600 chr6A 97.432 740 19 0 1363 2102 410902247 410901508 0.000000e+00 1262.0
17 TraesCS4A01G128600 chr6A 88.636 88 8 2 4641 4726 501479274 501479361 7.670000e-19 106.0
18 TraesCS4A01G128600 chr7A 97.162 740 21 0 1363 2102 100247988 100247249 0.000000e+00 1251.0
19 TraesCS4A01G128600 chr7A 96.515 746 24 2 1363 2107 109351223 109351967 0.000000e+00 1232.0
20 TraesCS4A01G128600 chr7A 90.141 71 6 1 4657 4726 68881102 68881172 2.150000e-14 91.6
21 TraesCS4A01G128600 chr7A 97.917 48 1 0 4810 4857 693453467 693453420 3.590000e-12 84.2
22 TraesCS4A01G128600 chr7A 78.846 104 21 1 312 414 217378880 217378777 1.010000e-07 69.4
23 TraesCS4A01G128600 chr7A 87.931 58 7 0 319 376 719037709 719037766 1.010000e-07 69.4
24 TraesCS4A01G128600 chr2A 97.027 740 22 0 1363 2102 624462966 624462227 0.000000e+00 1245.0
25 TraesCS4A01G128600 chr2A 96.757 740 24 0 1363 2102 19254060 19253321 0.000000e+00 1234.0
26 TraesCS4A01G128600 chr1D 97.027 740 22 0 1363 2102 223523839 223524578 0.000000e+00 1245.0
27 TraesCS4A01G128600 chr1D 90.541 74 4 2 4656 4728 464799795 464799724 1.660000e-15 95.3
28 TraesCS4A01G128600 chr5A 96.892 740 23 0 1363 2102 483275848 483276587 0.000000e+00 1240.0
29 TraesCS4A01G128600 chr1A 96.896 741 21 2 1363 2102 396446426 396445687 0.000000e+00 1240.0
30 TraesCS4A01G128600 chr3D 85.075 134 19 1 275 408 461215934 461215802 9.780000e-28 135.0
31 TraesCS4A01G128600 chr3D 94.444 54 1 2 4813 4864 272290707 272290760 1.290000e-11 82.4
32 TraesCS4A01G128600 chr6B 89.773 88 7 2 4641 4726 541936638 541936725 1.650000e-20 111.0
33 TraesCS4A01G128600 chr7B 72.143 420 98 17 312 721 169473833 169473423 5.930000e-20 110.0
34 TraesCS4A01G128600 chr2B 88.298 94 6 4 329 420 674796961 674796871 2.130000e-19 108.0
35 TraesCS4A01G128600 chr3A 92.958 71 4 1 4657 4726 440635038 440634968 9.920000e-18 102.0
36 TraesCS4A01G128600 chr3A 92.857 56 4 0 4810 4865 7457454 7457509 1.290000e-11 82.4
37 TraesCS4A01G128600 chr3A 92.857 56 4 0 4810 4865 7463999 7464054 1.290000e-11 82.4
38 TraesCS4A01G128600 chr3A 84.211 57 5 3 4629 4682 738882202 738882257 1.000000e-02 52.8
39 TraesCS4A01G128600 chr7D 91.781 73 4 2 4657 4728 46702663 46702734 3.570000e-17 100.0
40 TraesCS4A01G128600 chr7D 90.541 74 4 2 4657 4727 184573430 184573357 1.660000e-15 95.3
41 TraesCS4A01G128600 chr7D 87.500 72 8 1 338 408 597085519 597085448 1.290000e-11 82.4
42 TraesCS4A01G128600 chr7D 91.379 58 3 2 4810 4866 168580908 168580852 1.670000e-10 78.7
43 TraesCS4A01G128600 chr3B 91.549 71 5 1 4657 4726 422472529 422472599 4.620000e-16 97.1
44 TraesCS4A01G128600 chrUn 96.491 57 2 0 5336 5392 414074371 414074315 1.660000e-15 95.3
45 TraesCS4A01G128600 chr5B 94.444 54 3 0 328 381 687263736 687263789 3.590000e-12 84.2
46 TraesCS4A01G128600 chr2D 91.228 57 4 1 4802 4858 7229333 7229278 6.010000e-10 76.8


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 TraesCS4A01G128600 chr4A 165707047 165712643 5596 False 10336.000000 10336 100.000000 1 5597 1 chr4A.!!$F1 5596
1 TraesCS4A01G128600 chr4A 438239430 438240175 745 True 1240.000000 1240 96.649000 1363 2108 1 chr4A.!!$R1 745
2 TraesCS4A01G128600 chr4D 309508924 309513142 4218 True 1577.250000 4909 92.603000 678 5597 4 chr4D.!!$R2 4919
3 TraesCS4A01G128600 chr4D 309605076 309605748 672 True 665.000000 665 85.651000 1 630 1 chr4D.!!$R1 629
4 TraesCS4A01G128600 chr4B 386213734 386227514 13780 True 951.777778 4538 92.354333 7 5597 9 chr4B.!!$R1 5590
5 TraesCS4A01G128600 chr6A 410901508 410902247 739 True 1262.000000 1262 97.432000 1363 2102 1 chr6A.!!$R1 739
6 TraesCS4A01G128600 chr7A 100247249 100247988 739 True 1251.000000 1251 97.162000 1363 2102 1 chr7A.!!$R1 739
7 TraesCS4A01G128600 chr7A 109351223 109351967 744 False 1232.000000 1232 96.515000 1363 2107 1 chr7A.!!$F2 744
8 TraesCS4A01G128600 chr2A 624462227 624462966 739 True 1245.000000 1245 97.027000 1363 2102 1 chr2A.!!$R2 739
9 TraesCS4A01G128600 chr2A 19253321 19254060 739 True 1234.000000 1234 96.757000 1363 2102 1 chr2A.!!$R1 739
10 TraesCS4A01G128600 chr1D 223523839 223524578 739 False 1245.000000 1245 97.027000 1363 2102 1 chr1D.!!$F1 739
11 TraesCS4A01G128600 chr5A 483275848 483276587 739 False 1240.000000 1240 96.892000 1363 2102 1 chr5A.!!$F1 739
12 TraesCS4A01G128600 chr1A 396445687 396446426 739 True 1240.000000 1240 96.896000 1363 2102 1 chr1A.!!$R1 739

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
21 22 0.250467 AGAACATGGTCTTGCGCTGT 60.250 50.0 7.68 0.0 0.00 4.40 F
23 24 0.311790 AACATGGTCTTGCGCTGTTG 59.688 50.0 9.73 0.0 0.00 3.33 F
407 456 0.402121 AGAGCTCCAGGGTGAAAACC 59.598 55.0 10.93 0.0 0.00 3.27 F
410 459 0.536460 GCTCCAGGGTGAAAACCGAA 60.536 55.0 0.00 0.0 0.00 4.30 F
1685 2072 0.320374 CAGTTAGGTGTGGCGGAGAA 59.680 55.0 0.00 0.0 0.00 2.87 F
2276 2663 0.674895 GAGTGCAAATCGGAGCCTGT 60.675 55.0 0.00 0.0 0.00 4.00 F
2551 2938 0.261696 ATGCCCTGGGTTAATGGGAC 59.738 55.0 15.56 0.0 43.47 4.46 F
4334 4730 0.465460 TCTTGTGCCCAGTTGTCCAC 60.465 55.0 0.00 0.0 0.00 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1133 1469 0.105913 GAGGAGAGAGGGGTACAGGG 60.106 65.000 0.00 0.0 0.00 4.45 R
1172 1508 0.304705 GATAGCAACGGATTGGTGCG 59.695 55.000 0.00 0.0 45.96 5.34 R
1344 1680 0.623723 ACAGTTCCCGCATTACCCAT 59.376 50.000 0.00 0.0 0.00 4.00 R
1827 2214 0.687354 GCACTGGAGTTTCTGGAGGA 59.313 55.000 0.00 0.0 0.00 3.71 R
2518 2905 1.840635 AGGGCATGTTCCTTACTCCTC 59.159 52.381 4.25 0.0 0.00 3.71 R
3689 4077 1.437397 TCATAGCAGGGCATGGATGA 58.563 50.000 0.00 0.0 0.00 2.92 R
4514 4910 0.877071 AGCAAATGTTCCTCGCACAG 59.123 50.000 0.00 0.0 0.00 3.66 R
5273 6126 2.095213 GCAACGTCAAGAACAACTGTCA 59.905 45.455 0.00 0.0 0.00 3.58 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
21 22 0.250467 AGAACATGGTCTTGCGCTGT 60.250 50.000 7.68 0.00 0.00 4.40
23 24 0.311790 AACATGGTCTTGCGCTGTTG 59.688 50.000 9.73 0.00 0.00 3.33
32 33 0.527113 TTGCGCTGTTGGATGATTGG 59.473 50.000 9.73 0.00 0.00 3.16
61 62 5.128499 ACGAGACATGAGATCTTGGATCTTT 59.872 40.000 10.78 1.17 32.56 2.52
82 83 1.225376 GATGTGGTGCCAACGACGAA 61.225 55.000 0.00 0.00 37.81 3.85
171 210 2.203294 GTGGTGCCGGTGACCTTT 60.203 61.111 21.29 0.00 34.26 3.11
175 214 2.027625 GTGCCGGTGACCTTTCTCG 61.028 63.158 1.90 0.00 0.00 4.04
184 223 3.253432 GGTGACCTTTCTCGCTCAATTTT 59.747 43.478 0.00 0.00 0.00 1.82
191 230 5.333798 CCTTTCTCGCTCAATTTTCGTTACA 60.334 40.000 0.00 0.00 0.00 2.41
237 276 1.164411 CATAGCTTTTGGTGGCGACA 58.836 50.000 0.00 0.00 38.70 4.35
276 325 0.585357 CTGAGTGCTTGTGTGAGTGC 59.415 55.000 0.00 0.00 0.00 4.40
309 358 1.913778 TCAAGACCGTGCTAGGTACA 58.086 50.000 3.70 0.00 46.09 2.90
312 361 1.624336 AGACCGTGCTAGGTACACAA 58.376 50.000 3.70 0.00 46.09 3.33
394 443 2.614983 CTCAAGTACCGGTCTAGAGCTC 59.385 54.545 12.40 5.27 0.00 4.09
396 445 0.917533 AGTACCGGTCTAGAGCTCCA 59.082 55.000 12.40 0.00 0.00 3.86
399 448 1.830408 CCGGTCTAGAGCTCCAGGG 60.830 68.421 19.17 9.10 0.00 4.45
407 456 0.402121 AGAGCTCCAGGGTGAAAACC 59.598 55.000 10.93 0.00 0.00 3.27
410 459 0.536460 GCTCCAGGGTGAAAACCGAA 60.536 55.000 0.00 0.00 0.00 4.30
439 488 4.990257 ACTTTCAATGATTGGATCTTGCG 58.010 39.130 5.20 0.00 0.00 4.85
441 490 4.888038 TTCAATGATTGGATCTTGCGAG 57.112 40.909 5.20 0.00 0.00 5.03
446 495 0.620556 ATTGGATCTTGCGAGGGTGT 59.379 50.000 0.00 0.00 0.00 4.16
491 540 2.490991 GTAGGCGTTGATATTGGGGAC 58.509 52.381 0.00 0.00 0.00 4.46
526 575 3.407424 TGTGAGGTCAAGAGATGGTTG 57.593 47.619 0.00 0.00 0.00 3.77
527 576 2.972021 TGTGAGGTCAAGAGATGGTTGA 59.028 45.455 0.00 0.00 0.00 3.18
532 581 2.350522 GTCAAGAGATGGTTGATGCGT 58.649 47.619 0.00 0.00 36.35 5.24
541 590 5.105063 AGATGGTTGATGCGTATATGATCG 58.895 41.667 0.00 0.00 0.00 3.69
581 630 5.437289 TCAATGTTTTGATCGCTTCAGTT 57.563 34.783 0.00 0.00 36.94 3.16
613 662 7.859325 TTCTTTTCTTATTACCCCATCTTCG 57.141 36.000 0.00 0.00 0.00 3.79
620 669 6.326583 TCTTATTACCCCATCTTCGATCTTGT 59.673 38.462 0.00 0.00 0.00 3.16
659 708 4.818642 CCCATGTGATTTTTGTATGTGCA 58.181 39.130 0.00 0.00 0.00 4.57
665 714 9.303537 CATGTGATTTTTGTATGTGCATTGATA 57.696 29.630 0.00 0.00 0.00 2.15
672 721 8.914328 TTTTGTATGTGCATTGATATTGACTG 57.086 30.769 0.00 0.00 0.00 3.51
675 724 6.598850 TGTATGTGCATTGATATTGACTGTGT 59.401 34.615 0.00 0.00 0.00 3.72
676 725 7.768120 TGTATGTGCATTGATATTGACTGTGTA 59.232 33.333 0.00 0.00 0.00 2.90
724 773 7.765695 ATGTCCTCATTGTGTTTGTATTTCT 57.234 32.000 0.00 0.00 0.00 2.52
763 812 7.698130 GGTGTTGTATTGCTTTGATACTTCATC 59.302 37.037 0.00 0.00 32.48 2.92
807 856 9.959749 CAAGCCTTTGTAAAAAGTAAATCTACA 57.040 29.630 4.68 0.00 0.00 2.74
825 874 3.915437 ACACCCTTTGCATAACGAAAG 57.085 42.857 0.00 0.00 0.00 2.62
827 876 3.886505 ACACCCTTTGCATAACGAAAGAA 59.113 39.130 0.00 0.00 31.89 2.52
848 900 7.093322 AGAAAATAAGCATGTGATGTTCCTC 57.907 36.000 0.00 0.00 0.00 3.71
859 911 1.916181 GATGTTCCTCCTTCTCCCCAA 59.084 52.381 0.00 0.00 0.00 4.12
911 1087 4.727841 TCCCGAAATATCCCCCTTTCTTTA 59.272 41.667 0.00 0.00 30.80 1.85
913 1089 6.075315 CCCGAAATATCCCCCTTTCTTTATT 58.925 40.000 0.00 0.00 30.80 1.40
914 1090 6.553476 CCCGAAATATCCCCCTTTCTTTATTT 59.447 38.462 0.00 0.00 30.80 1.40
915 1091 7.726738 CCCGAAATATCCCCCTTTCTTTATTTA 59.273 37.037 0.00 0.00 30.80 1.40
916 1092 9.138596 CCGAAATATCCCCCTTTCTTTATTTAA 57.861 33.333 0.00 0.00 30.80 1.52
1023 1359 3.774766 TGCTCTTTATCTACCAAGCTCCA 59.225 43.478 0.00 0.00 0.00 3.86
1026 1362 3.711704 TCTTTATCTACCAAGCTCCAGGG 59.288 47.826 5.01 0.00 0.00 4.45
1133 1469 0.541863 CCCACCATGTGAGACCCTAC 59.458 60.000 0.00 0.00 35.23 3.18
1185 1521 2.671619 CACCCGCACCAATCCGTT 60.672 61.111 0.00 0.00 0.00 4.44
1204 1540 4.260620 CCGTTGCTATCTTAATTGTTCCGG 60.261 45.833 0.00 0.00 0.00 5.14
1259 1595 2.164219 CTGGCAAAAGCCGTGACATTAT 59.836 45.455 1.66 0.00 32.27 1.28
1275 1611 7.484641 CGTGACATTATAGATTTTGGTGGTTTG 59.515 37.037 0.00 0.00 0.00 2.93
1341 1677 7.862372 CGGGGATTGATGAATTTGTAGTATTTG 59.138 37.037 0.00 0.00 0.00 2.32
1342 1678 8.912988 GGGGATTGATGAATTTGTAGTATTTGA 58.087 33.333 0.00 0.00 0.00 2.69
1354 1690 9.816354 ATTTGTAGTATTTGAAATGGGTAATGC 57.184 29.630 0.00 0.00 0.00 3.56
1355 1691 7.022055 TGTAGTATTTGAAATGGGTAATGCG 57.978 36.000 0.00 0.00 0.00 4.73
1356 1692 5.514274 AGTATTTGAAATGGGTAATGCGG 57.486 39.130 0.00 0.00 0.00 5.69
1357 1693 3.817709 ATTTGAAATGGGTAATGCGGG 57.182 42.857 0.00 0.00 0.00 6.13
1358 1694 2.516227 TTGAAATGGGTAATGCGGGA 57.484 45.000 0.00 0.00 0.00 5.14
1359 1695 2.516227 TGAAATGGGTAATGCGGGAA 57.484 45.000 0.00 0.00 0.00 3.97
1360 1696 2.096248 TGAAATGGGTAATGCGGGAAC 58.904 47.619 0.00 0.00 0.00 3.62
1361 1697 2.291282 TGAAATGGGTAATGCGGGAACT 60.291 45.455 0.00 0.00 0.00 3.01
1685 2072 0.320374 CAGTTAGGTGTGGCGGAGAA 59.680 55.000 0.00 0.00 0.00 2.87
1723 2110 4.898607 GTGGCCACACAAGGAAGA 57.101 55.556 31.23 0.00 46.90 2.87
1827 2214 4.147701 GGGCATATTCAGCGCAGT 57.852 55.556 11.47 0.00 43.54 4.40
1857 2244 2.004808 CTCCAGTGCATAGCGGACGA 62.005 60.000 0.00 0.00 41.69 4.20
1883 2270 1.428448 CGTGCGGAGAATGTCAAGAA 58.572 50.000 0.00 0.00 0.00 2.52
1919 2306 4.166144 ACCGAATTTGATATGGGAGGAGTT 59.834 41.667 0.00 0.00 0.00 3.01
1983 2370 1.610967 TATGGACAGGGGTGCGTGA 60.611 57.895 0.00 0.00 38.35 4.35
1987 2374 1.227853 GACAGGGGTGCGTGAAAGT 60.228 57.895 0.00 0.00 0.00 2.66
2080 2467 4.714802 ACTTGTTTGGGACTAAAGGCTTTT 59.285 37.500 18.93 0.00 0.00 2.27
2155 2542 1.686800 CCCCAAGCTTCCCCAATGG 60.687 63.158 0.00 0.00 0.00 3.16
2197 2584 3.577415 CTGGGAGATCATCAGTGATGCTA 59.423 47.826 25.53 12.05 44.96 3.49
2202 2589 7.620888 TGGGAGATCATCAGTGATGCTATTATA 59.379 37.037 25.53 9.26 44.96 0.98
2276 2663 0.674895 GAGTGCAAATCGGAGCCTGT 60.675 55.000 0.00 0.00 0.00 4.00
2499 2886 6.449635 TTGACAACAGTAGCTTCATGTTTT 57.550 33.333 7.84 3.29 35.04 2.43
2551 2938 0.261696 ATGCCCTGGGTTAATGGGAC 59.738 55.000 15.56 0.00 43.47 4.46
2590 2977 7.900782 TCAACACTTAGTGCTAGTTATTTCC 57.099 36.000 12.80 0.00 36.98 3.13
2632 3019 7.250032 TGCTGAATAGATCAACTATGCCTAT 57.750 36.000 0.00 0.00 41.10 2.57
2645 3032 7.290014 TCAACTATGCCTATAAGGATGTGAAGA 59.710 37.037 0.00 0.00 37.67 2.87
2791 3179 7.618117 TGAGGATGAGAAGGTATTGTGTAGTAA 59.382 37.037 0.00 0.00 0.00 2.24
2800 3188 8.459911 AAGGTATTGTGTAGTAATATTTGCCC 57.540 34.615 0.00 0.00 0.00 5.36
3008 3396 7.209471 TGAATAACTTGGGTTGTGTTGTATC 57.791 36.000 0.00 0.00 36.92 2.24
3017 3405 5.995282 TGGGTTGTGTTGTATCAAGAGTTAG 59.005 40.000 0.00 0.00 0.00 2.34
3201 3589 2.096565 GCGCACACATATACATGCTCAG 60.097 50.000 0.30 0.00 35.39 3.35
3394 3782 9.474313 TTGGAATTCACAATATAGTTAAGCCTT 57.526 29.630 7.93 0.00 0.00 4.35
3447 3835 5.461032 TTGTGTGGAGTTGTTGAGTTTTT 57.539 34.783 0.00 0.00 0.00 1.94
3497 3885 7.060421 AGTAACTGTTATAAATGGACCCATGG 58.940 38.462 4.14 4.14 36.68 3.66
3689 4077 1.701847 AGTTCTGCCAGTTGATCCACT 59.298 47.619 0.00 0.00 0.00 4.00
4062 4450 7.123397 TCCAACTGCTCATCATATAGTAGATCC 59.877 40.741 0.00 0.00 30.85 3.36
4093 4481 5.404466 TTCCTGGAATTTAATGTGCTTGG 57.596 39.130 4.68 0.00 0.00 3.61
4326 4722 2.496899 ACACCTATTCTTGTGCCCAG 57.503 50.000 0.00 0.00 35.90 4.45
4334 4730 0.465460 TCTTGTGCCCAGTTGTCCAC 60.465 55.000 0.00 0.00 0.00 4.02
4337 4733 1.454847 GTGCCCAGTTGTCCACCAA 60.455 57.895 0.00 0.00 0.00 3.67
4339 4735 0.539438 TGCCCAGTTGTCCACCAATC 60.539 55.000 0.00 0.00 35.02 2.67
4565 4961 0.326595 TTGCCGAAACCATCCTGCTA 59.673 50.000 0.00 0.00 0.00 3.49
4597 4993 4.096382 TGGACAAGAAACTTGAAGCTGAAC 59.904 41.667 16.65 0.00 0.00 3.18
4601 4997 3.134458 AGAAACTTGAAGCTGAACTCGG 58.866 45.455 0.00 0.00 0.00 4.63
4612 5008 2.625737 CTGAACTCGGCTCATTGATGT 58.374 47.619 0.00 0.00 0.00 3.06
4618 5014 2.076100 TCGGCTCATTGATGTGTGTTC 58.924 47.619 0.00 0.00 0.00 3.18
4665 5061 9.597170 CTATTTTACTTGTTTAGTACTCCCTCC 57.403 37.037 0.00 0.00 39.05 4.30
4667 5063 3.504375 ACTTGTTTAGTACTCCCTCCGT 58.496 45.455 0.00 0.00 34.56 4.69
4690 5192 7.309867 CCGTCCCATAATATAAGAGCTTAGTGT 60.310 40.741 0.00 0.00 0.00 3.55
4691 5193 7.755822 CGTCCCATAATATAAGAGCTTAGTGTC 59.244 40.741 0.00 0.00 0.00 3.67
4692 5194 8.585881 GTCCCATAATATAAGAGCTTAGTGTCA 58.414 37.037 0.00 0.00 0.00 3.58
4745 5583 2.967887 AGTTCTGGTTACCGGTGTTACT 59.032 45.455 19.93 7.85 0.00 2.24
4752 5590 7.491682 TCTGGTTACCGGTGTTACTTATATTC 58.508 38.462 19.93 0.00 0.00 1.75
4812 5653 4.084287 TCCTTGTTCGTGTCCATAGTACT 58.916 43.478 0.00 0.00 0.00 2.73
4900 5743 2.484417 GGTGTGTGCCCTCTCATATCAG 60.484 54.545 0.00 0.00 0.00 2.90
4933 5776 4.761739 CCTATGGTGTGAACATTTGACAGT 59.238 41.667 0.00 0.00 0.00 3.55
4940 5783 5.682862 GTGTGAACATTTGACAGTGCTTTAG 59.317 40.000 0.00 0.00 0.00 1.85
4951 5795 4.336280 ACAGTGCTTTAGGGATCCTTTTC 58.664 43.478 12.58 0.00 34.61 2.29
4971 5815 1.135257 CGGCAGACGTCTCTTCAGATT 60.135 52.381 16.96 0.00 37.93 2.40
4974 5818 4.495422 GGCAGACGTCTCTTCAGATTTTA 58.505 43.478 16.96 0.00 0.00 1.52
4991 5836 7.182206 TCAGATTTTAAGTCTTAGCTAACCCCT 59.818 37.037 0.86 0.00 0.00 4.79
5042 5887 2.041350 TGGGTCTCCGGGATCTAGATAC 59.959 54.545 6.38 6.38 35.24 2.24
5043 5888 2.309458 GGGTCTCCGGGATCTAGATACT 59.691 54.545 14.76 0.00 0.00 2.12
5044 5889 3.522750 GGGTCTCCGGGATCTAGATACTA 59.477 52.174 14.76 0.57 0.00 1.82
5051 5896 7.347485 TCTCCGGGATCTAGATACTATGTGATA 59.653 40.741 14.76 0.00 0.00 2.15
5066 5911 2.289631 TGTGATACTGTGCAGACCCTTG 60.290 50.000 6.17 0.00 0.00 3.61
5273 6126 0.812549 AAACAGGAAACCGCGTTTGT 59.187 45.000 4.92 0.00 35.77 2.83
5375 7864 4.083324 ACAACAACTCGATAAGCACAATGG 60.083 41.667 0.00 0.00 0.00 3.16
5506 7995 2.679092 CAGGAATGCTGGGAGGCA 59.321 61.111 0.00 0.00 46.63 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.593128 AACAGCGCAAGACCATGTTC 59.407 50.000 11.47 0.00 43.02 3.18
21 22 2.460275 CGTCGCGCCAATCATCCAA 61.460 57.895 0.00 0.00 0.00 3.53
23 24 2.584970 TCGTCGCGCCAATCATCC 60.585 61.111 0.00 0.00 0.00 3.51
32 33 1.265462 GATCTCATGTCTCGTCGCGC 61.265 60.000 0.00 0.00 0.00 6.86
61 62 0.389296 CGTCGTTGGCACCACATCTA 60.389 55.000 0.00 0.00 0.00 1.98
82 83 3.988976 AGATCGGGCAGCAATACATAT 57.011 42.857 0.00 0.00 0.00 1.78
171 210 5.660629 TTTGTAACGAAAATTGAGCGAGA 57.339 34.783 0.00 0.00 0.00 4.04
175 214 6.198216 ACACACATTTGTAACGAAAATTGAGC 59.802 34.615 0.00 0.00 33.30 4.26
184 223 2.468409 CGTCGACACACATTTGTAACGA 59.532 45.455 17.16 8.06 39.40 3.85
191 230 2.132762 GAAGGTCGTCGACACACATTT 58.867 47.619 25.64 9.34 33.68 2.32
237 276 1.040646 TCCAGTTGCGACAAGAGTCT 58.959 50.000 6.90 0.00 42.73 3.24
250 289 1.210478 ACACAAGCACTCAGTCCAGTT 59.790 47.619 0.00 0.00 0.00 3.16
306 355 2.093711 CGATGATCCCACCAGTTGTGTA 60.094 50.000 0.00 0.00 43.85 2.90
309 358 1.275666 TCGATGATCCCACCAGTTGT 58.724 50.000 0.00 0.00 0.00 3.32
312 361 1.909302 ACTTTCGATGATCCCACCAGT 59.091 47.619 0.00 0.00 0.00 4.00
325 374 1.144276 TTGTCGCCACCACTTTCGA 59.856 52.632 0.00 0.00 0.00 3.71
394 443 0.179001 ACCTTCGGTTTTCACCCTGG 60.179 55.000 0.00 0.00 40.52 4.45
396 445 1.137697 AGACCTTCGGTTTTCACCCT 58.862 50.000 0.00 0.00 40.52 4.34
399 448 5.295045 TGAAAGTTAGACCTTCGGTTTTCAC 59.705 40.000 5.98 0.00 34.53 3.18
407 456 6.371548 TCCAATCATTGAAAGTTAGACCTTCG 59.628 38.462 0.00 0.00 0.00 3.79
410 459 7.637511 AGATCCAATCATTGAAAGTTAGACCT 58.362 34.615 0.00 0.00 0.00 3.85
416 465 5.183713 TCGCAAGATCCAATCATTGAAAGTT 59.816 36.000 0.00 0.00 45.01 2.66
483 532 2.375014 ACAACGAAAAGGTCCCCAAT 57.625 45.000 0.00 0.00 0.00 3.16
491 540 3.875134 ACCTCACAAGTACAACGAAAAGG 59.125 43.478 0.00 0.00 0.00 3.11
497 546 3.713288 TCTTGACCTCACAAGTACAACG 58.287 45.455 0.00 0.00 44.96 4.10
501 550 4.021016 ACCATCTCTTGACCTCACAAGTAC 60.021 45.833 0.00 0.00 44.96 2.73
526 575 6.237332 GCTACAAAGACGATCATATACGCATC 60.237 42.308 0.00 0.00 0.00 3.91
527 576 5.573282 GCTACAAAGACGATCATATACGCAT 59.427 40.000 0.00 0.00 0.00 4.73
532 581 6.555812 ACGAGCTACAAAGACGATCATATA 57.444 37.500 0.00 0.00 0.00 0.86
541 590 5.120830 ACATTGATCAACGAGCTACAAAGAC 59.879 40.000 11.07 0.00 0.00 3.01
585 634 9.822727 AAGATGGGGTAATAAGAAAAGAAAAGA 57.177 29.630 0.00 0.00 0.00 2.52
599 648 6.467677 CATACAAGATCGAAGATGGGGTAAT 58.532 40.000 0.00 0.00 45.12 1.89
604 653 3.070018 GCCATACAAGATCGAAGATGGG 58.930 50.000 16.57 4.56 45.12 4.00
613 662 5.731686 GCAACTAGCAAAGCCATACAAGATC 60.732 44.000 0.00 0.00 44.79 2.75
723 772 3.723260 ACAACACCCCGCAAATAAAAAG 58.277 40.909 0.00 0.00 0.00 2.27
724 773 3.821421 ACAACACCCCGCAAATAAAAA 57.179 38.095 0.00 0.00 0.00 1.94
729 778 1.067213 GCAATACAACACCCCGCAAAT 60.067 47.619 0.00 0.00 0.00 2.32
731 780 0.538516 AGCAATACAACACCCCGCAA 60.539 50.000 0.00 0.00 0.00 4.85
734 783 1.883275 TCAAAGCAATACAACACCCCG 59.117 47.619 0.00 0.00 0.00 5.73
797 846 6.314400 TCGTTATGCAAAGGGTGTAGATTTAC 59.686 38.462 0.00 0.00 0.00 2.01
807 856 5.523438 TTTTCTTTCGTTATGCAAAGGGT 57.477 34.783 0.00 0.00 31.55 4.34
825 874 6.096001 AGGAGGAACATCACATGCTTATTTTC 59.904 38.462 0.00 0.00 0.00 2.29
827 876 5.513233 AGGAGGAACATCACATGCTTATTT 58.487 37.500 0.00 0.00 0.00 1.40
848 900 2.220653 TGCAAAGATTGGGGAGAAGG 57.779 50.000 0.00 0.00 0.00 3.46
859 911 5.126699 AGGAAGAAGGATCATGCAAAGAT 57.873 39.130 4.84 4.84 0.00 2.40
913 1089 7.658575 ACGGCAGAAGTAACAAGAAAGTATTAA 59.341 33.333 0.00 0.00 0.00 1.40
914 1090 7.156673 ACGGCAGAAGTAACAAGAAAGTATTA 58.843 34.615 0.00 0.00 0.00 0.98
915 1091 5.995897 ACGGCAGAAGTAACAAGAAAGTATT 59.004 36.000 0.00 0.00 0.00 1.89
916 1092 5.548406 ACGGCAGAAGTAACAAGAAAGTAT 58.452 37.500 0.00 0.00 0.00 2.12
1026 1362 2.750237 GGTTGGTGATGGTCGCCC 60.750 66.667 7.05 0.00 46.20 6.13
1133 1469 0.105913 GAGGAGAGAGGGGTACAGGG 60.106 65.000 0.00 0.00 0.00 4.45
1172 1508 0.304705 GATAGCAACGGATTGGTGCG 59.695 55.000 0.00 0.00 45.96 5.34
1173 1509 1.668419 AGATAGCAACGGATTGGTGC 58.332 50.000 0.00 0.00 45.96 5.01
1174 1510 6.183360 ACAATTAAGATAGCAACGGATTGGTG 60.183 38.462 2.13 0.00 45.96 4.17
1177 1513 6.912591 GGAACAATTAAGATAGCAACGGATTG 59.087 38.462 0.00 0.00 38.99 2.67
1185 1521 2.869801 CGCCGGAACAATTAAGATAGCA 59.130 45.455 5.05 0.00 0.00 3.49
1259 1595 6.516527 GCAACATCTCAAACCACCAAAATCTA 60.517 38.462 0.00 0.00 0.00 1.98
1275 1611 4.627467 AGTAGTGACAAATCGCAACATCTC 59.373 41.667 0.00 0.00 37.85 2.75
1341 1677 2.099098 CAGTTCCCGCATTACCCATTTC 59.901 50.000 0.00 0.00 0.00 2.17
1342 1678 2.099405 CAGTTCCCGCATTACCCATTT 58.901 47.619 0.00 0.00 0.00 2.32
1343 1679 1.005450 ACAGTTCCCGCATTACCCATT 59.995 47.619 0.00 0.00 0.00 3.16
1344 1680 0.623723 ACAGTTCCCGCATTACCCAT 59.376 50.000 0.00 0.00 0.00 4.00
1345 1681 1.065998 GTACAGTTCCCGCATTACCCA 60.066 52.381 0.00 0.00 0.00 4.51
1346 1682 1.065998 TGTACAGTTCCCGCATTACCC 60.066 52.381 0.00 0.00 0.00 3.69
1347 1683 2.389962 TGTACAGTTCCCGCATTACC 57.610 50.000 0.00 0.00 0.00 2.85
1348 1684 3.527533 TCATGTACAGTTCCCGCATTAC 58.472 45.455 0.33 0.00 0.00 1.89
1349 1685 3.897141 TCATGTACAGTTCCCGCATTA 57.103 42.857 0.33 0.00 0.00 1.90
1350 1686 2.779755 TCATGTACAGTTCCCGCATT 57.220 45.000 0.33 0.00 0.00 3.56
1351 1687 2.092968 ACATCATGTACAGTTCCCGCAT 60.093 45.455 0.33 0.00 0.00 4.73
1352 1688 1.277842 ACATCATGTACAGTTCCCGCA 59.722 47.619 0.33 0.00 0.00 5.69
1353 1689 1.665679 CACATCATGTACAGTTCCCGC 59.334 52.381 0.33 0.00 0.00 6.13
1354 1690 1.665679 GCACATCATGTACAGTTCCCG 59.334 52.381 0.33 0.00 0.00 5.14
1355 1691 1.665679 CGCACATCATGTACAGTTCCC 59.334 52.381 0.33 0.00 0.00 3.97
1356 1692 1.665679 CCGCACATCATGTACAGTTCC 59.334 52.381 0.33 0.00 0.00 3.62
1357 1693 2.346803 ACCGCACATCATGTACAGTTC 58.653 47.619 0.33 0.00 0.00 3.01
1358 1694 2.472695 ACCGCACATCATGTACAGTT 57.527 45.000 0.33 0.00 0.00 3.16
1359 1695 2.472695 AACCGCACATCATGTACAGT 57.527 45.000 0.33 0.00 0.00 3.55
1360 1696 2.741517 TGAAACCGCACATCATGTACAG 59.258 45.455 0.33 0.00 0.00 2.74
1361 1697 2.741517 CTGAAACCGCACATCATGTACA 59.258 45.455 0.00 0.00 0.00 2.90
1552 1939 1.762370 TGGCACTCTCTTGTCACAGAA 59.238 47.619 0.00 0.00 0.00 3.02
1657 2044 4.069304 GCCACACCTAACTGTTGAACATA 58.931 43.478 0.00 0.00 0.00 2.29
1685 2072 3.118629 ACACATCCATCTCAACATACGCT 60.119 43.478 0.00 0.00 0.00 5.07
1723 2110 6.813649 CGTATATCATCATTCCGGACTCAATT 59.186 38.462 1.83 0.00 0.00 2.32
1827 2214 0.687354 GCACTGGAGTTTCTGGAGGA 59.313 55.000 0.00 0.00 0.00 3.71
1857 2244 1.337823 ACATTCTCCGCACGCTTTAGT 60.338 47.619 0.00 0.00 0.00 2.24
1919 2306 4.030314 TCCTTCAGGTCTCTCTTAACGA 57.970 45.455 0.00 0.00 36.34 3.85
1983 2370 3.164268 TGGCACATGGATAGCAAACTTT 58.836 40.909 0.00 0.00 0.00 2.66
1987 2374 2.646930 CTCTGGCACATGGATAGCAAA 58.353 47.619 0.00 0.00 38.20 3.68
2080 2467 6.662414 TTCAACAACAACAACAACAACAAA 57.338 29.167 0.00 0.00 0.00 2.83
2155 2542 1.734707 GCAATCCAGCAGCACACAATC 60.735 52.381 0.00 0.00 0.00 2.67
2197 2584 7.386299 AGGAATACGACGACTACGAGTTATAAT 59.614 37.037 0.00 0.00 42.66 1.28
2202 2589 3.265791 AGGAATACGACGACTACGAGTT 58.734 45.455 0.00 0.00 42.66 3.01
2276 2663 8.582437 CCCATATAGTTCTATTTCGTTACTGGA 58.418 37.037 0.00 0.00 0.00 3.86
2280 2667 9.924650 ATGTCCCATATAGTTCTATTTCGTTAC 57.075 33.333 0.00 0.00 0.00 2.50
2499 2886 7.630082 ACTCCTCCATTAACAAATTAGTAGCA 58.370 34.615 0.00 0.00 0.00 3.49
2518 2905 1.840635 AGGGCATGTTCCTTACTCCTC 59.159 52.381 4.25 0.00 0.00 3.71
2556 2943 6.755206 AGCACTAAGTGTTGATAACAGTACA 58.245 36.000 2.76 0.00 43.99 2.90
2590 2977 2.821969 AGCAAGCCAATTCTGTAACTGG 59.178 45.455 0.00 0.00 0.00 4.00
2791 3179 6.435164 ACTGACTATGGAAAAGGGCAAATAT 58.565 36.000 0.00 0.00 0.00 1.28
2800 3188 5.105473 TCCGTCCTAACTGACTATGGAAAAG 60.105 44.000 0.00 0.00 32.97 2.27
2885 3273 7.239763 TGTACATCCACTCTAGTTTCAATGA 57.760 36.000 0.00 0.00 0.00 2.57
3017 3405 9.338622 AGCAACTGTATGTAATCCTTTATAACC 57.661 33.333 0.00 0.00 0.00 2.85
3201 3589 2.128035 CTGCTAGGCGTGCACTTATAC 58.872 52.381 16.19 0.48 36.37 1.47
3394 3782 3.178046 TCAGAATGCCAGGTAACCACTA 58.822 45.455 0.00 0.00 34.76 2.74
3497 3885 6.489675 CATAATGCATGGTCTCAGTGTAAAC 58.510 40.000 0.00 0.00 0.00 2.01
3689 4077 1.437397 TCATAGCAGGGCATGGATGA 58.563 50.000 0.00 0.00 0.00 2.92
3874 4262 2.825532 CTGGAAAATGAACCCACGGATT 59.174 45.455 0.00 0.00 0.00 3.01
4113 4501 8.038862 TCTCTTCTGCCTGGAGAAATTATTAT 57.961 34.615 0.00 0.00 33.82 1.28
4121 4509 1.566211 CCTCTCTTCTGCCTGGAGAA 58.434 55.000 0.00 3.24 35.97 2.87
4326 4722 2.270352 TCAGGTGATTGGTGGACAAC 57.730 50.000 0.00 0.00 42.94 3.32
4334 4730 6.487668 TGCAAACATAGATATCAGGTGATTGG 59.512 38.462 17.93 6.97 36.05 3.16
4337 4733 6.236409 CCTGCAAACATAGATATCAGGTGAT 58.764 40.000 5.32 0.00 35.97 3.06
4339 4735 5.936686 CCTGCAAACATAGATATCAGGTG 57.063 43.478 5.32 3.23 35.97 4.00
4514 4910 0.877071 AGCAAATGTTCCTCGCACAG 59.123 50.000 0.00 0.00 0.00 3.66
4565 4961 8.408043 TTCAAGTTTCTTGTCCATACATTCAT 57.592 30.769 8.93 0.00 34.97 2.57
4597 4993 1.730501 ACACACATCAATGAGCCGAG 58.269 50.000 0.00 0.00 0.00 4.63
4601 4997 4.214971 AGAACAGAACACACATCAATGAGC 59.785 41.667 0.00 0.00 0.00 4.26
4612 5008 7.439356 CAGACTGAATAGAAAGAACAGAACACA 59.561 37.037 0.00 0.00 33.53 3.72
4618 5014 8.715191 AATAGCAGACTGAATAGAAAGAACAG 57.285 34.615 6.65 0.00 35.14 3.16
4665 5061 7.603651 ACACTAAGCTCTTATATTATGGGACG 58.396 38.462 0.00 0.00 0.00 4.79
4667 5063 8.721133 TGACACTAAGCTCTTATATTATGGGA 57.279 34.615 0.00 0.00 0.00 4.37
4697 5199 8.884323 ACTCCTTCAATCCATAATATAAGAGCA 58.116 33.333 0.00 0.00 0.00 4.26
4715 5553 3.508793 CGGTAACCAGAACTACTCCTTCA 59.491 47.826 0.00 0.00 0.00 3.02
4773 5614 3.851458 AGGATCAAGCATGCAGACATA 57.149 42.857 21.98 0.00 33.67 2.29
4775 5616 2.089201 CAAGGATCAAGCATGCAGACA 58.911 47.619 21.98 0.23 0.00 3.41
4846 5687 2.032620 CGGCTAGTGATGTACTCCCTT 58.967 52.381 0.00 0.00 40.89 3.95
4900 5743 0.839946 ACACCATAGGCAGACCATCC 59.160 55.000 0.00 0.00 39.06 3.51
4933 5776 2.944094 GCCGAAAAGGATCCCTAAAGCA 60.944 50.000 8.55 0.00 45.00 3.91
4940 5783 1.090052 CGTCTGCCGAAAAGGATCCC 61.090 60.000 8.55 0.00 45.00 3.85
4951 5795 0.453793 ATCTGAAGAGACGTCTGCCG 59.546 55.000 25.58 8.63 44.03 5.69
4971 5815 5.548836 TCCAAGGGGTTAGCTAAGACTTAAA 59.451 40.000 6.38 1.38 34.93 1.52
4974 5818 3.527937 TCCAAGGGGTTAGCTAAGACTT 58.472 45.455 6.38 8.70 34.93 3.01
5042 5887 3.386078 AGGGTCTGCACAGTATCACATAG 59.614 47.826 0.00 0.00 0.00 2.23
5043 5888 3.374764 AGGGTCTGCACAGTATCACATA 58.625 45.455 0.00 0.00 0.00 2.29
5044 5889 2.191400 AGGGTCTGCACAGTATCACAT 58.809 47.619 0.00 0.00 0.00 3.21
5273 6126 2.095213 GCAACGTCAAGAACAACTGTCA 59.905 45.455 0.00 0.00 0.00 3.58


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

AutoCloner maintained by Alex Coulton.