Multiple sequence alignment - TraesCS6D01G306500

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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 TraesCS6D01G306500 chr6D 100.000 3863 0 0 1 3863 417696253 417692391 0.000000e+00 7134.0
1 TraesCS6D01G306500 chr6D 93.001 1643 100 6 936 2563 417890695 417892337 0.000000e+00 2383.0
2 TraesCS6D01G306500 chr6D 84.426 1098 72 30 2841 3863 417893592 417894665 0.000000e+00 989.0
3 TraesCS6D01G306500 chr6D 87.218 532 33 9 358 887 417890048 417890546 1.200000e-159 573.0
4 TraesCS6D01G306500 chr6D 87.336 229 29 0 2 230 417889748 417889976 2.960000e-66 263.0
5 TraesCS6D01G306500 chr6D 86.607 112 7 2 2532 2642 417892404 417892508 2.440000e-22 117.0
6 TraesCS6D01G306500 chr6D 97.917 48 1 0 892 939 417890594 417890641 2.470000e-12 84.2
7 TraesCS6D01G306500 chr6B 93.316 1526 96 5 936 2458 626458165 626456643 0.000000e+00 2248.0
8 TraesCS6D01G306500 chr6B 91.398 1581 121 8 979 2547 626590626 626589049 0.000000e+00 2152.0
9 TraesCS6D01G306500 chr6B 91.672 1549 109 11 986 2517 626811891 626813436 0.000000e+00 2128.0
10 TraesCS6D01G306500 chr6B 92.158 1492 112 4 970 2458 626882465 626883954 0.000000e+00 2102.0
11 TraesCS6D01G306500 chr6B 85.185 837 44 32 2931 3714 626588523 626587714 0.000000e+00 785.0
12 TraesCS6D01G306500 chr6B 86.833 562 43 9 2708 3261 626456415 626455877 1.990000e-167 599.0
13 TraesCS6D01G306500 chr6B 84.168 619 55 21 3288 3863 626455880 626455262 9.370000e-156 560.0
14 TraesCS6D01G306500 chr6B 90.074 403 32 5 3465 3863 626886143 626886541 2.060000e-142 516.0
15 TraesCS6D01G306500 chr6B 86.799 303 22 8 3080 3365 626885590 626885891 4.810000e-84 322.0
16 TraesCS6D01G306500 chr6B 91.525 177 14 1 5 181 626459325 626459150 3.860000e-60 243.0
17 TraesCS6D01G306500 chr6B 94.245 139 5 1 2795 2930 626588959 626588821 3.910000e-50 209.0
18 TraesCS6D01G306500 chr6B 86.897 145 15 4 702 844 626458976 626458834 3.990000e-35 159.0
19 TraesCS6D01G306500 chr6B 82.209 163 21 4 2995 3154 630836576 630836733 2.420000e-27 134.0
20 TraesCS6D01G306500 chr6B 95.349 43 2 0 2600 2642 626589029 626588987 6.930000e-08 69.4
21 TraesCS6D01G306500 chr6A 93.092 1491 99 3 970 2458 560567649 560569137 0.000000e+00 2180.0
22 TraesCS6D01G306500 chr6A 94.780 1207 56 1 1488 2694 560104775 560103576 0.000000e+00 1873.0
23 TraesCS6D01G306500 chr6A 89.815 756 34 6 2735 3475 560103130 560102403 0.000000e+00 929.0
24 TraesCS6D01G306500 chr6A 84.400 891 57 29 3034 3863 560569648 560570517 0.000000e+00 800.0
25 TraesCS6D01G306500 chr6A 94.444 234 13 0 1 234 560119034 560118801 1.020000e-95 361.0
26 TraesCS6D01G306500 chr6A 95.364 151 7 0 695 845 560106706 560106556 1.390000e-59 241.0
27 TraesCS6D01G306500 chr6A 95.588 136 6 0 566 701 560118736 560118601 6.500000e-53 219.0
28 TraesCS6D01G306500 chr6A 82.530 166 19 7 2995 3154 562137766 562137927 1.870000e-28 137.0
29 TraesCS6D01G306500 chr6A 94.186 86 5 0 468 553 560118799 560118714 8.710000e-27 132.0
30 TraesCS6D01G306500 chr6A 80.795 151 24 4 412 560 462253377 462253524 3.150000e-21 113.0
31 TraesCS6D01G306500 chr6A 73.828 256 46 11 3026 3267 562143268 562143516 8.900000e-12 82.4
32 TraesCS6D01G306500 chr1D 79.716 493 55 24 94 560 228022843 228022370 8.060000e-82 315.0
33 TraesCS6D01G306500 chr1D 90.196 51 5 0 419 469 457847236 457847186 2.490000e-07 67.6
34 TraesCS6D01G306500 chr5D 87.248 149 19 0 410 558 61839919 61839771 1.850000e-38 171.0
35 TraesCS6D01G306500 chr2B 86.486 148 18 2 407 553 153902771 153902917 1.110000e-35 161.0
36 TraesCS6D01G306500 chr2A 81.111 180 31 3 78 255 711644820 711644998 1.450000e-29 141.0
37 TraesCS6D01G306500 chr2A 82.237 152 12 5 411 560 711645137 711645275 2.440000e-22 117.0
38 TraesCS6D01G306500 chr3D 78.846 208 39 5 356 560 504046390 504046595 6.730000e-28 135.0
39 TraesCS6D01G306500 chr3D 84.956 113 7 5 366 469 1846996 1846885 5.280000e-19 106.0
40 TraesCS6D01G306500 chr4D 81.818 154 25 3 409 560 104641615 104641463 4.050000e-25 126.0
41 TraesCS6D01G306500 chr4A 77.564 156 32 3 407 560 470805275 470805429 1.480000e-14 91.6


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 TraesCS6D01G306500 chr6D 417692391 417696253 3862 True 7134.000000 7134 100.000000 1 3863 1 chr6D.!!$R1 3862
1 TraesCS6D01G306500 chr6D 417889748 417894665 4917 False 734.866667 2383 89.417500 2 3863 6 chr6D.!!$F1 3861
2 TraesCS6D01G306500 chr6B 626811891 626813436 1545 False 2128.000000 2128 91.672000 986 2517 1 chr6B.!!$F1 1531
3 TraesCS6D01G306500 chr6B 626882465 626886541 4076 False 980.000000 2102 89.677000 970 3863 3 chr6B.!!$F3 2893
4 TraesCS6D01G306500 chr6B 626587714 626590626 2912 True 803.850000 2152 91.544250 979 3714 4 chr6B.!!$R2 2735
5 TraesCS6D01G306500 chr6B 626455262 626459325 4063 True 761.800000 2248 88.547800 5 3863 5 chr6B.!!$R1 3858
6 TraesCS6D01G306500 chr6A 560567649 560570517 2868 False 1490.000000 2180 88.746000 970 3863 2 chr6A.!!$F4 2893
7 TraesCS6D01G306500 chr6A 560102403 560106706 4303 True 1014.333333 1873 93.319667 695 3475 3 chr6A.!!$R1 2780

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
232 233 0.038526 CTGACCACCTCGTGTACCAC 60.039 60.0 0.00 0.0 0.00 4.16 F
581 582 0.038892 TACAAACTCGGGCGACTGTC 60.039 55.0 0.00 0.0 38.16 3.51 F
590 591 0.103208 GGGCGACTGTCATGGAGTAG 59.897 60.0 8.73 0.0 0.00 2.57 F
2373 4731 0.534877 TGCATGAGTTTGTCTGCGGT 60.535 50.0 0.00 0.0 34.08 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1288 1929 0.106318 GGGAAGAGCTTGATGGCCAT 60.106 55.000 20.96 20.96 0.00 4.40 R
2353 4711 0.167470 CCGCAGACAAACTCATGCAG 59.833 55.000 0.00 0.00 38.60 4.41 R
2427 4785 2.369633 ACGCCCTGCCATCTCATGA 61.370 57.895 0.00 0.00 0.00 3.07 R
3742 9196 0.887387 TGCCTGAGGTAAAACCACGC 60.887 55.000 0.00 0.00 41.95 5.34 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
37 38 1.337728 CCGCAGACACACCTATCAACA 60.338 52.381 0.00 0.00 0.00 3.33
43 44 6.051717 GCAGACACACCTATCAACATCTAAT 58.948 40.000 0.00 0.00 0.00 1.73
116 117 3.262420 GTGTGGCTAACAGTCAATCGAT 58.738 45.455 0.00 0.00 40.26 3.59
118 119 4.868171 GTGTGGCTAACAGTCAATCGATTA 59.132 41.667 10.97 0.00 40.26 1.75
134 135 7.810759 TCAATCGATTAAAAACTAGTTTTGGGC 59.189 33.333 29.33 18.80 41.45 5.36
181 182 2.892215 TGCAAAATCAACAGCCAGATCA 59.108 40.909 0.00 0.00 0.00 2.92
196 197 4.383989 GCCAGATCATCTTCTTCAACCTCT 60.384 45.833 0.00 0.00 0.00 3.69
197 198 5.163364 GCCAGATCATCTTCTTCAACCTCTA 60.163 44.000 0.00 0.00 0.00 2.43
205 206 5.268387 TCTTCTTCAACCTCTAGCTCATCT 58.732 41.667 0.00 0.00 0.00 2.90
207 208 5.590530 TCTTCAACCTCTAGCTCATCTTC 57.409 43.478 0.00 0.00 0.00 2.87
208 209 4.404073 TCTTCAACCTCTAGCTCATCTTCC 59.596 45.833 0.00 0.00 0.00 3.46
211 212 2.957474 ACCTCTAGCTCATCTTCCTCC 58.043 52.381 0.00 0.00 0.00 4.30
225 226 1.304547 CCTCCTCTGACCACCTCGT 60.305 63.158 0.00 0.00 0.00 4.18
230 231 0.526662 CTCTGACCACCTCGTGTACC 59.473 60.000 0.00 0.00 0.00 3.34
231 232 0.178984 TCTGACCACCTCGTGTACCA 60.179 55.000 0.00 0.00 0.00 3.25
232 233 0.038526 CTGACCACCTCGTGTACCAC 60.039 60.000 0.00 0.00 0.00 4.16
233 234 0.468585 TGACCACCTCGTGTACCACT 60.469 55.000 0.00 0.00 31.34 4.00
234 235 0.038526 GACCACCTCGTGTACCACTG 60.039 60.000 0.00 0.00 31.34 3.66
235 236 1.292223 CCACCTCGTGTACCACTGG 59.708 63.158 0.00 0.00 33.96 4.00
236 237 1.469335 CCACCTCGTGTACCACTGGT 61.469 60.000 5.88 5.88 38.58 4.00
237 238 0.038526 CACCTCGTGTACCACTGGTC 60.039 60.000 3.21 0.00 36.99 4.02
238 239 1.211969 CCTCGTGTACCACTGGTCG 59.788 63.158 3.21 2.55 37.09 4.79
239 240 1.211969 CTCGTGTACCACTGGTCGG 59.788 63.158 3.21 0.00 37.09 4.79
240 241 2.209064 CTCGTGTACCACTGGTCGGG 62.209 65.000 3.21 0.00 37.09 5.14
241 242 2.047560 GTGTACCACTGGTCGGGC 60.048 66.667 3.21 0.00 37.09 6.13
242 243 3.315949 TGTACCACTGGTCGGGCC 61.316 66.667 3.21 0.00 37.09 5.80
243 244 4.446413 GTACCACTGGTCGGGCCG 62.446 72.222 22.51 22.51 41.21 6.13
379 380 1.804601 ACGATGACCGGTTTTTCTCC 58.195 50.000 9.42 0.00 43.93 3.71
382 383 1.468914 GATGACCGGTTTTTCTCCAGC 59.531 52.381 9.42 0.00 0.00 4.85
392 393 0.944386 TTTCTCCAGCGAACTTGCAC 59.056 50.000 0.00 0.00 37.31 4.57
399 400 3.349006 CGAACTTGCACCGCTGCT 61.349 61.111 4.05 0.00 44.57 4.24
415 416 3.970410 CTGTGCTGCCTCCCCCAA 61.970 66.667 0.00 0.00 0.00 4.12
433 434 4.018960 CCCCAACCTAAGATAGATGATGGG 60.019 50.000 0.00 0.00 43.68 4.00
460 461 0.322366 GCCAGCAAGCTTCTTCCTCT 60.322 55.000 0.00 0.00 0.00 3.69
464 465 1.554617 AGCAAGCTTCTTCCTCTCCTC 59.445 52.381 0.00 0.00 0.00 3.71
468 469 1.819905 CTTCTTCCTCTCCTCCGGC 59.180 63.158 0.00 0.00 0.00 6.13
469 470 2.010582 CTTCTTCCTCTCCTCCGGCG 62.011 65.000 0.00 0.00 0.00 6.46
470 471 2.440430 CTTCCTCTCCTCCGGCGA 60.440 66.667 9.30 0.00 0.00 5.54
471 472 2.440430 TTCCTCTCCTCCGGCGAG 60.440 66.667 9.30 11.14 35.72 5.03
474 475 3.144193 CTCTCCTCCGGCGAGCTT 61.144 66.667 9.30 0.00 34.49 3.74
475 476 3.132481 CTCTCCTCCGGCGAGCTTC 62.132 68.421 9.30 0.00 34.49 3.86
476 477 3.144193 CTCCTCCGGCGAGCTTCT 61.144 66.667 9.30 0.00 34.49 2.85
477 478 2.680352 TCCTCCGGCGAGCTTCTT 60.680 61.111 9.30 0.00 34.49 2.52
478 479 2.232298 CTCCTCCGGCGAGCTTCTTT 62.232 60.000 9.30 0.00 34.49 2.52
479 480 1.811679 CCTCCGGCGAGCTTCTTTC 60.812 63.158 9.30 0.00 34.49 2.62
480 481 1.216710 CTCCGGCGAGCTTCTTTCT 59.783 57.895 9.30 0.00 0.00 2.52
481 482 0.804156 CTCCGGCGAGCTTCTTTCTC 60.804 60.000 9.30 0.00 0.00 2.87
482 483 1.811679 CCGGCGAGCTTCTTTCTCC 60.812 63.158 9.30 0.00 0.00 3.71
483 484 1.811679 CGGCGAGCTTCTTTCTCCC 60.812 63.158 0.00 0.00 0.00 4.30
484 485 1.450491 GGCGAGCTTCTTTCTCCCC 60.450 63.158 0.00 0.00 0.00 4.81
485 486 1.599576 GCGAGCTTCTTTCTCCCCT 59.400 57.895 0.00 0.00 0.00 4.79
486 487 0.461163 GCGAGCTTCTTTCTCCCCTC 60.461 60.000 0.00 0.00 0.00 4.30
487 488 0.176910 CGAGCTTCTTTCTCCCCTCC 59.823 60.000 0.00 0.00 0.00 4.30
488 489 0.176910 GAGCTTCTTTCTCCCCTCCG 59.823 60.000 0.00 0.00 0.00 4.63
489 490 1.222113 GCTTCTTTCTCCCCTCCGG 59.778 63.158 0.00 0.00 0.00 5.14
490 491 1.222113 CTTCTTTCTCCCCTCCGGC 59.778 63.158 0.00 0.00 0.00 6.13
494 495 2.527951 CTTTCTCCCCTCCGGCAGTG 62.528 65.000 0.00 0.00 0.00 3.66
507 508 1.737363 CGGCAGTGTCTTCCTTCTAGC 60.737 57.143 0.00 0.00 0.00 3.42
513 514 4.564769 CAGTGTCTTCCTTCTAGCGAAATC 59.435 45.833 0.00 0.00 0.00 2.17
528 529 3.727970 GCGAAATCGACTGACCCAAAATC 60.728 47.826 7.06 0.00 43.02 2.17
529 530 3.483574 CGAAATCGACTGACCCAAAATCG 60.484 47.826 0.00 0.00 43.02 3.34
539 540 0.170339 CCCAAAATCGAAACTCGGGC 59.830 55.000 0.00 0.00 40.88 6.13
555 556 0.807667 GGGCGACTGTCATGTAGCTG 60.808 60.000 8.73 0.00 38.36 4.24
560 561 2.663602 CGACTGTCATGTAGCTGTTGTC 59.336 50.000 8.73 0.00 0.00 3.18
568 569 6.018262 TGTCATGTAGCTGTTGTCTTACAAAC 60.018 38.462 0.00 0.00 40.15 2.93
570 571 6.423905 TCATGTAGCTGTTGTCTTACAAACTC 59.576 38.462 0.00 0.00 40.15 3.01
572 573 3.131396 AGCTGTTGTCTTACAAACTCGG 58.869 45.455 0.00 0.00 40.15 4.63
574 575 2.215196 TGTTGTCTTACAAACTCGGGC 58.785 47.619 0.00 0.00 40.15 6.13
575 576 1.193874 GTTGTCTTACAAACTCGGGCG 59.806 52.381 0.00 0.00 40.15 6.13
577 578 1.066136 GTCTTACAAACTCGGGCGAC 58.934 55.000 0.00 0.00 0.00 5.19
578 579 0.963962 TCTTACAAACTCGGGCGACT 59.036 50.000 0.00 0.00 0.00 4.18
579 580 1.068474 CTTACAAACTCGGGCGACTG 58.932 55.000 0.00 0.00 38.41 3.51
580 581 0.390124 TTACAAACTCGGGCGACTGT 59.610 50.000 0.00 0.00 38.16 3.55
581 582 0.038892 TACAAACTCGGGCGACTGTC 60.039 55.000 0.00 0.00 38.16 3.51
582 583 1.300620 CAAACTCGGGCGACTGTCA 60.301 57.895 8.73 0.00 38.16 3.58
583 584 0.670546 CAAACTCGGGCGACTGTCAT 60.671 55.000 8.73 0.00 38.16 3.06
584 585 0.670546 AAACTCGGGCGACTGTCATG 60.671 55.000 8.73 0.00 38.16 3.07
585 586 2.202797 CTCGGGCGACTGTCATGG 60.203 66.667 8.73 0.00 38.16 3.66
586 587 2.678580 TCGGGCGACTGTCATGGA 60.679 61.111 8.73 0.00 38.16 3.41
587 588 2.202797 CGGGCGACTGTCATGGAG 60.203 66.667 8.73 0.00 0.00 3.86
588 589 2.982130 GGGCGACTGTCATGGAGT 59.018 61.111 8.73 0.00 0.00 3.85
589 590 1.663379 CGGGCGACTGTCATGGAGTA 61.663 60.000 8.73 0.00 0.00 2.59
590 591 0.103208 GGGCGACTGTCATGGAGTAG 59.897 60.000 8.73 0.00 0.00 2.57
598 599 6.507900 CGACTGTCATGGAGTAGATTACAAT 58.492 40.000 8.73 0.00 0.00 2.71
615 616 6.973229 TTACAATAAGAGGTTAAACGAGGC 57.027 37.500 0.00 0.00 0.00 4.70
616 617 3.930848 ACAATAAGAGGTTAAACGAGGCG 59.069 43.478 0.00 0.00 0.00 5.52
635 636 1.851658 GGCGACAAAAGTGTGCAAAT 58.148 45.000 0.00 0.00 38.41 2.32
810 866 7.010645 CCCATAGCAAAACACGTTTTAGTTTTT 59.989 33.333 10.70 2.78 43.26 1.94
887 1343 1.180029 CCTTTGCCACCTCCTTCATG 58.820 55.000 0.00 0.00 0.00 3.07
890 1346 1.002069 TTGCCACCTCCTTCATGGAT 58.998 50.000 0.00 0.00 45.16 3.41
933 1432 4.009675 GCCCATTTTTCTCCCCATTTTTC 58.990 43.478 0.00 0.00 0.00 2.29
956 1590 3.732169 CGTACATCGACAGCAGTCTTCAT 60.732 47.826 7.71 0.00 42.73 2.57
1107 1742 3.681835 GTGGTCTCGTGGACGGCT 61.682 66.667 0.00 0.00 45.35 5.52
1184 1819 2.765807 CATGCTCTCCTCCCCCGT 60.766 66.667 0.00 0.00 0.00 5.28
1222 1863 2.675423 TCACCCTCCTCACCGTCG 60.675 66.667 0.00 0.00 0.00 5.12
1227 1868 1.377463 CCTCCTCACCGTCGTCTCT 60.377 63.158 0.00 0.00 0.00 3.10
1288 1929 4.569023 CGCTATCGCTCCACGCCA 62.569 66.667 0.00 0.00 43.23 5.69
1290 1931 2.313172 GCTATCGCTCCACGCCATG 61.313 63.158 0.00 0.00 43.23 3.66
1431 2072 3.841255 TGGTCACCTACAACACCATGATA 59.159 43.478 0.00 0.00 33.83 2.15
1436 2077 3.262405 ACCTACAACACCATGATAACCGT 59.738 43.478 0.00 0.00 0.00 4.83
1444 2085 2.771943 ACCATGATAACCGTCCTCATGT 59.228 45.455 16.32 7.17 42.96 3.21
1564 3916 4.492160 GCCACGACGAGGCGATCA 62.492 66.667 20.41 0.00 43.15 2.92
1632 3984 0.958091 CGCTGGTAGCTGCTATCTCT 59.042 55.000 19.80 0.00 39.60 3.10
1635 3987 1.685517 CTGGTAGCTGCTATCTCTGCA 59.314 52.381 19.80 0.00 38.81 4.41
1636 3988 2.102084 CTGGTAGCTGCTATCTCTGCAA 59.898 50.000 19.80 0.00 40.13 4.08
1638 3990 2.102252 GGTAGCTGCTATCTCTGCAAGT 59.898 50.000 13.20 0.00 40.13 3.16
1775 4127 2.594592 GGTGGAGTTTGCACGGCT 60.595 61.111 0.00 0.00 39.79 5.52
1836 4188 2.873367 CTCGATGATCGTCGGGTTG 58.127 57.895 31.26 17.73 41.35 3.77
1932 4284 2.985282 ACGTTCACGGGCGTCCTA 60.985 61.111 3.66 0.00 44.95 2.94
2008 4366 2.514824 GGGAAGAGCACGGCATCC 60.515 66.667 0.00 3.57 0.00 3.51
2040 4398 2.029964 CACTACGGGTGCGTGGTT 59.970 61.111 0.00 0.00 39.22 3.67
2373 4731 0.534877 TGCATGAGTTTGTCTGCGGT 60.535 50.000 0.00 0.00 34.08 5.68
2427 4785 0.399454 ACATGCTTGACCTGCTCAGT 59.601 50.000 6.60 0.00 0.00 3.41
2590 5113 6.086222 CCAACGGTTGATTAGAAATCTGTTG 58.914 40.000 21.88 0.00 34.37 3.33
2591 5114 6.293955 CCAACGGTTGATTAGAAATCTGTTGT 60.294 38.462 21.88 5.42 33.12 3.32
2592 5115 7.094975 CCAACGGTTGATTAGAAATCTGTTGTA 60.095 37.037 21.88 0.00 33.12 2.41
2593 5116 7.360575 ACGGTTGATTAGAAATCTGTTGTAC 57.639 36.000 1.70 0.00 0.00 2.90
2594 5117 7.159372 ACGGTTGATTAGAAATCTGTTGTACT 58.841 34.615 0.00 0.00 0.00 2.73
2595 5118 7.331193 ACGGTTGATTAGAAATCTGTTGTACTC 59.669 37.037 0.00 0.00 0.00 2.59
2596 5119 7.201530 CGGTTGATTAGAAATCTGTTGTACTCC 60.202 40.741 0.00 0.00 0.00 3.85
2876 7781 2.805671 TGAACTGATAGCGTTGGTGTTG 59.194 45.455 0.00 0.00 0.00 3.33
3026 8243 7.360113 TCATATATTCACTTGTGCTCACCTA 57.640 36.000 0.00 0.00 0.00 3.08
3027 8244 7.210174 TCATATATTCACTTGTGCTCACCTAC 58.790 38.462 0.00 0.00 0.00 3.18
3028 8245 5.683876 ATATTCACTTGTGCTCACCTACT 57.316 39.130 0.00 0.00 0.00 2.57
3051 8316 3.490348 CTCTTTCAAAGGCAAGAGGGAA 58.510 45.455 0.00 0.00 41.62 3.97
3065 8330 9.338968 AGGCAAGAGGGAAAGAATATACATATA 57.661 33.333 0.00 0.00 0.00 0.86
3121 8386 1.933021 ACTATGGTGACCTCCAACGA 58.067 50.000 2.11 0.00 41.09 3.85
3192 8471 0.827507 AGCATTTCCCTGGTTTGCGT 60.828 50.000 0.00 0.00 38.32 5.24
3419 8827 7.014038 GCATCCATGAGAACATAAGAGGAAAAT 59.986 37.037 0.00 0.00 35.09 1.82
3575 9021 5.585445 ACTGCAGATCTTCTAAGCAAATCTG 59.415 40.000 23.35 12.31 43.90 2.90
3588 9034 1.677576 CAAATCTGCATACATGGCCGT 59.322 47.619 0.00 0.00 0.00 5.68
3601 9047 2.598632 GGCCGTGTATGCGCATCTC 61.599 63.158 29.11 20.89 0.00 2.75
3627 9076 7.907563 CGTGCTATATATGACATAGACACTGAG 59.092 40.741 0.98 0.00 34.46 3.35
3720 9169 3.516586 TCACAGTCAAATAGTCCCTCCA 58.483 45.455 0.00 0.00 0.00 3.86
3742 9196 0.455972 CCAAAATAAGTGCCGCGTGG 60.456 55.000 11.67 11.67 38.77 4.94
3758 9212 0.872388 GTGGCGTGGTTTTACCTCAG 59.128 55.000 0.00 0.00 39.58 3.35
3759 9213 0.250553 TGGCGTGGTTTTACCTCAGG 60.251 55.000 0.00 0.00 39.58 3.86
3760 9214 1.583495 GGCGTGGTTTTACCTCAGGC 61.583 60.000 0.00 0.00 39.58 4.85
3761 9215 0.887387 GCGTGGTTTTACCTCAGGCA 60.887 55.000 0.00 0.00 39.58 4.75
3762 9216 0.872388 CGTGGTTTTACCTCAGGCAC 59.128 55.000 0.00 0.00 39.58 5.01
3763 9217 1.542547 CGTGGTTTTACCTCAGGCACT 60.543 52.381 0.00 0.00 39.58 4.40
3768 9222 5.007682 TGGTTTTACCTCAGGCACTTATTC 58.992 41.667 0.00 0.00 39.58 1.75
3773 9240 8.613482 GTTTTACCTCAGGCACTTATTCTATTC 58.387 37.037 0.00 0.00 34.60 1.75
3792 9261 1.076677 TCTGGAACGGAGGGAGTAGTT 59.923 52.381 0.00 0.00 39.80 2.24
3809 9278 7.280205 GGGAGTAGTTAACAACATGGACAATAG 59.720 40.741 8.61 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.732094 GGGTGGTTGTCGTCGTCG 60.732 66.667 0.00 0.00 38.55 5.12
43 44 8.137437 CCTGCAAGTTCTTAAAAATGAAAGAGA 58.863 33.333 0.00 0.00 33.49 3.10
116 117 5.221087 CGACTGGCCCAAAACTAGTTTTTAA 60.221 40.000 27.12 12.35 40.45 1.52
118 119 3.067601 CGACTGGCCCAAAACTAGTTTTT 59.932 43.478 27.12 13.62 40.45 1.94
181 182 5.898972 AGATGAGCTAGAGGTTGAAGAAGAT 59.101 40.000 0.00 0.00 0.00 2.40
196 197 3.561143 GTCAGAGGAGGAAGATGAGCTA 58.439 50.000 0.00 0.00 0.00 3.32
197 198 2.387757 GTCAGAGGAGGAAGATGAGCT 58.612 52.381 0.00 0.00 0.00 4.09
205 206 0.612174 CGAGGTGGTCAGAGGAGGAA 60.612 60.000 0.00 0.00 0.00 3.36
207 208 1.304547 ACGAGGTGGTCAGAGGAGG 60.305 63.158 0.00 0.00 0.00 4.30
208 209 0.896019 ACACGAGGTGGTCAGAGGAG 60.896 60.000 0.42 0.00 37.94 3.69
211 212 0.526662 GGTACACGAGGTGGTCAGAG 59.473 60.000 0.00 0.00 37.94 3.35
225 226 3.315949 GGCCCGACCAGTGGTACA 61.316 66.667 16.72 0.00 35.25 2.90
283 284 1.996187 GGTTCAGGGGAGGGAGGTC 60.996 68.421 0.00 0.00 0.00 3.85
284 285 2.125225 GGTTCAGGGGAGGGAGGT 59.875 66.667 0.00 0.00 0.00 3.85
285 286 2.124996 TGGTTCAGGGGAGGGAGG 59.875 66.667 0.00 0.00 0.00 4.30
286 287 2.301738 GGTGGTTCAGGGGAGGGAG 61.302 68.421 0.00 0.00 0.00 4.30
287 288 2.204090 GGTGGTTCAGGGGAGGGA 60.204 66.667 0.00 0.00 0.00 4.20
354 355 2.757980 AAACCGGTCATCGTTGGGGG 62.758 60.000 8.04 0.00 37.11 5.40
355 356 0.891904 AAAACCGGTCATCGTTGGGG 60.892 55.000 8.04 0.00 37.11 4.96
356 357 0.955905 AAAAACCGGTCATCGTTGGG 59.044 50.000 8.04 0.00 37.11 4.12
357 358 1.877443 AGAAAAACCGGTCATCGTTGG 59.123 47.619 8.04 0.00 37.11 3.77
358 359 2.095919 GGAGAAAAACCGGTCATCGTTG 60.096 50.000 8.04 0.00 37.11 4.10
359 360 2.148768 GGAGAAAAACCGGTCATCGTT 58.851 47.619 8.04 0.00 37.11 3.85
360 361 1.071071 TGGAGAAAAACCGGTCATCGT 59.929 47.619 8.04 0.00 37.11 3.73
361 362 1.732259 CTGGAGAAAAACCGGTCATCG 59.268 52.381 8.04 0.00 38.88 3.84
362 363 1.468914 GCTGGAGAAAAACCGGTCATC 59.531 52.381 8.04 6.86 36.29 2.92
399 400 4.284550 GTTGGGGGAGGCAGCACA 62.285 66.667 0.00 0.00 0.00 4.57
415 416 5.026790 GCTACCCCATCATCTATCTTAGGT 58.973 45.833 0.00 0.00 0.00 3.08
433 434 3.136791 GCTTGCTGGCAGGCTACC 61.137 66.667 19.75 0.00 44.21 3.18
447 448 1.190643 CGGAGGAGAGGAAGAAGCTT 58.809 55.000 0.00 0.00 0.00 3.74
464 465 1.811679 GGAGAAAGAAGCTCGCCGG 60.812 63.158 0.00 0.00 33.19 6.13
468 469 0.176910 GGAGGGGAGAAAGAAGCTCG 59.823 60.000 0.00 0.00 33.19 5.03
469 470 0.176910 CGGAGGGGAGAAAGAAGCTC 59.823 60.000 0.00 0.00 0.00 4.09
470 471 2.291856 CGGAGGGGAGAAAGAAGCT 58.708 57.895 0.00 0.00 0.00 3.74
471 472 4.943822 CGGAGGGGAGAAAGAAGC 57.056 61.111 0.00 0.00 0.00 3.86
484 485 0.390472 GAAGGAAGACACTGCCGGAG 60.390 60.000 5.05 1.84 33.44 4.63
485 486 0.832135 AGAAGGAAGACACTGCCGGA 60.832 55.000 5.05 0.00 33.44 5.14
486 487 0.895530 TAGAAGGAAGACACTGCCGG 59.104 55.000 0.00 0.00 33.44 6.13
487 488 1.737363 GCTAGAAGGAAGACACTGCCG 60.737 57.143 0.00 0.00 33.44 5.69
488 489 1.737363 CGCTAGAAGGAAGACACTGCC 60.737 57.143 0.00 0.00 0.00 4.85
489 490 1.202582 TCGCTAGAAGGAAGACACTGC 59.797 52.381 0.00 0.00 0.00 4.40
490 491 3.577649 TTCGCTAGAAGGAAGACACTG 57.422 47.619 0.00 0.00 31.76 3.66
494 495 3.792421 GTCGATTTCGCTAGAAGGAAGAC 59.208 47.826 0.00 0.00 37.70 3.01
507 508 3.483574 CGATTTTGGGTCAGTCGATTTCG 60.484 47.826 0.00 0.00 41.45 3.46
513 514 2.806244 AGTTTCGATTTTGGGTCAGTCG 59.194 45.455 0.00 0.00 0.00 4.18
528 529 2.049433 ACAGTCGCCCGAGTTTCG 60.049 61.111 0.00 0.00 40.07 3.46
529 530 0.389948 ATGACAGTCGCCCGAGTTTC 60.390 55.000 5.07 5.07 0.00 2.78
539 540 2.663602 GACAACAGCTACATGACAGTCG 59.336 50.000 0.00 0.00 0.00 4.18
555 556 1.193874 CGCCCGAGTTTGTAAGACAAC 59.806 52.381 0.00 0.00 37.90 3.32
560 561 1.068474 CAGTCGCCCGAGTTTGTAAG 58.932 55.000 0.00 0.00 0.00 2.34
568 569 2.202797 CCATGACAGTCGCCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
570 571 1.663379 TACTCCATGACAGTCGCCCG 61.663 60.000 0.00 0.00 0.00 6.13
572 573 1.103803 TCTACTCCATGACAGTCGCC 58.896 55.000 0.00 0.00 0.00 5.54
574 575 5.500645 TGTAATCTACTCCATGACAGTCG 57.499 43.478 0.00 0.00 0.00 4.18
575 576 9.469807 CTTATTGTAATCTACTCCATGACAGTC 57.530 37.037 0.00 0.00 0.00 3.51
577 578 9.689976 CTCTTATTGTAATCTACTCCATGACAG 57.310 37.037 0.00 0.00 0.00 3.51
578 579 8.642432 CCTCTTATTGTAATCTACTCCATGACA 58.358 37.037 0.00 0.00 0.00 3.58
579 580 8.643324 ACCTCTTATTGTAATCTACTCCATGAC 58.357 37.037 0.00 0.00 0.00 3.06
580 581 8.783660 ACCTCTTATTGTAATCTACTCCATGA 57.216 34.615 0.00 0.00 0.00 3.07
589 590 7.494952 GCCTCGTTTAACCTCTTATTGTAATCT 59.505 37.037 0.00 0.00 0.00 2.40
590 591 7.516312 CGCCTCGTTTAACCTCTTATTGTAATC 60.516 40.741 0.00 0.00 0.00 1.75
598 599 1.404583 GCCGCCTCGTTTAACCTCTTA 60.405 52.381 0.00 0.00 0.00 2.10
611 612 2.251642 ACACTTTTGTCGCCGCCTC 61.252 57.895 0.00 0.00 0.00 4.70
615 616 0.524392 TTTGCACACTTTTGTCGCCG 60.524 50.000 0.00 0.00 31.66 6.46
616 617 1.851658 ATTTGCACACTTTTGTCGCC 58.148 45.000 0.00 0.00 31.66 5.54
635 636 0.178840 TGTGGGGGTGGTGGGTTATA 60.179 55.000 0.00 0.00 0.00 0.98
887 1343 6.205658 GCCAGATTTACAAACATAGGAGATCC 59.794 42.308 0.00 0.00 0.00 3.36
890 1346 5.437060 GGCCAGATTTACAAACATAGGAGA 58.563 41.667 0.00 0.00 0.00 3.71
933 1432 2.945315 GACTGCTGTCGATGTACGG 58.055 57.895 8.06 0.00 42.82 4.02
956 1590 6.013725 TGGAAGAGTAGAAGCAGACCAAATTA 60.014 38.462 0.00 0.00 0.00 1.40
1288 1929 0.106318 GGGAAGAGCTTGATGGCCAT 60.106 55.000 20.96 20.96 0.00 4.40
1290 1931 1.454663 GGGGAAGAGCTTGATGGCC 60.455 63.158 0.00 0.00 0.00 5.36
1431 2072 1.227999 CGTTGCACATGAGGACGGTT 61.228 55.000 0.00 0.00 0.00 4.44
1436 2077 2.359850 GGCCGTTGCACATGAGGA 60.360 61.111 0.00 0.00 40.13 3.71
1564 3916 0.613853 AGCATGGCATGGAAGCAGTT 60.614 50.000 27.48 0.00 35.83 3.16
1657 4009 0.902984 TGCACCCACATACCGAGACT 60.903 55.000 0.00 0.00 0.00 3.24
1775 4127 1.142667 TCCTCATGCTGTCAAACACCA 59.857 47.619 0.00 0.00 0.00 4.17
1836 4188 3.365265 CACCTTCCGTTGGCTGCC 61.365 66.667 12.87 12.87 0.00 4.85
1849 4201 4.760047 GATGGCGTCCGTGCACCT 62.760 66.667 12.15 0.00 36.28 4.00
2008 4366 0.824109 TAGTGCTCCATCCTTGGTCG 59.176 55.000 0.00 0.00 44.06 4.79
2009 4367 1.471676 CGTAGTGCTCCATCCTTGGTC 60.472 57.143 0.00 0.00 44.06 4.02
2011 4369 0.179073 CCGTAGTGCTCCATCCTTGG 60.179 60.000 0.00 0.00 45.15 3.61
2112 4470 2.431683 GCTCCAAGCACCACCTCA 59.568 61.111 0.00 0.00 41.89 3.86
2142 4500 1.294138 GTCCCCGTGAATCCGACAA 59.706 57.895 0.00 0.00 0.00 3.18
2353 4711 0.167470 CCGCAGACAAACTCATGCAG 59.833 55.000 0.00 0.00 38.60 4.41
2427 4785 2.369633 ACGCCCTGCCATCTCATGA 61.370 57.895 0.00 0.00 0.00 3.07
2596 5119 3.247442 TGACCGTAGAACTGCAAATACG 58.753 45.455 10.86 10.86 40.41 3.06
2876 7781 6.346096 TGTAGTAGTCCAATATTTCCACAGC 58.654 40.000 0.00 0.00 0.00 4.40
3026 8243 3.749226 CTCTTGCCTTTGAAAGAGGAGT 58.251 45.455 6.49 0.00 43.72 3.85
3121 8386 8.062536 ACCATGTTCTCTTCTTACCTATCTAGT 58.937 37.037 0.00 0.00 0.00 2.57
3192 8471 6.379988 AGAAGGCCTTTTTGTTTCTCTTGTAA 59.620 34.615 21.54 0.00 0.00 2.41
3453 8861 6.425721 CAGTTTTCACGATACCCAAAGAACTA 59.574 38.462 0.00 0.00 0.00 2.24
3588 9034 3.704843 GCACGAGATGCGCATACA 58.295 55.556 25.40 0.00 46.55 2.29
3601 9047 7.752695 TCAGTGTCTATGTCATATATAGCACG 58.247 38.462 0.00 0.00 38.58 5.34
3627 9076 3.769844 TCTACCACAGAAGGTCCAGAATC 59.230 47.826 0.00 0.00 42.06 2.52
3720 9169 1.816224 ACGCGGCACTTATTTTGGAAT 59.184 42.857 12.47 0.00 0.00 3.01
3742 9196 0.887387 TGCCTGAGGTAAAACCACGC 60.887 55.000 0.00 0.00 41.95 5.34
3753 9207 5.070981 TCCAGAATAGAATAAGTGCCTGAGG 59.929 44.000 0.00 0.00 0.00 3.86
3758 9212 4.511826 CCGTTCCAGAATAGAATAAGTGCC 59.488 45.833 0.00 0.00 0.00 5.01
3759 9213 5.357257 TCCGTTCCAGAATAGAATAAGTGC 58.643 41.667 0.00 0.00 0.00 4.40
3760 9214 5.986135 CCTCCGTTCCAGAATAGAATAAGTG 59.014 44.000 0.00 0.00 0.00 3.16
3761 9215 5.070580 CCCTCCGTTCCAGAATAGAATAAGT 59.929 44.000 0.00 0.00 0.00 2.24
3762 9216 5.304614 TCCCTCCGTTCCAGAATAGAATAAG 59.695 44.000 0.00 0.00 0.00 1.73
3763 9217 5.213519 TCCCTCCGTTCCAGAATAGAATAA 58.786 41.667 0.00 0.00 0.00 1.40
3768 9222 2.389715 ACTCCCTCCGTTCCAGAATAG 58.610 52.381 0.00 0.00 0.00 1.73
3773 9240 1.558233 AACTACTCCCTCCGTTCCAG 58.442 55.000 0.00 0.00 0.00 3.86
3792 9261 6.957631 ACTGATCCTATTGTCCATGTTGTTA 58.042 36.000 0.00 0.00 0.00 2.41
3832 9301 8.640651 TGTTTACATACCTGTACAGTTCACTTA 58.359 33.333 21.18 3.16 37.58 2.24
3834 9303 6.927381 GTGTTTACATACCTGTACAGTTCACT 59.073 38.462 21.18 3.81 37.58 3.41


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

AutoCloner maintained by Alex Coulton.