Multiple sequence alignment - TraesCS6B01G124700

Loading Multiple Alignment...

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 TraesCS6B01G124700 chr6B 100.000 2528 0 0 1 2528 119850317 119847790 0.000000e+00 4669.0
1 TraesCS6B01G124700 chr6B 82.707 266 24 9 2021 2279 371604803 371604553 1.520000e-52 217.0
2 TraesCS6B01G124700 chr6B 88.889 162 7 3 1854 2004 371604891 371604730 3.320000e-44 189.0
3 TraesCS6B01G124700 chr6D 90.540 2537 119 84 4 2488 52725405 52722938 0.000000e+00 3243.0
4 TraesCS6B01G124700 chr6A 91.369 1958 76 43 569 2488 63610778 63608876 0.000000e+00 2593.0
5 TraesCS6B01G124700 chr6A 83.128 486 30 30 4 478 63611263 63610819 1.820000e-106 396.0
6 TraesCS6B01G124700 chr2B 93.530 541 23 6 1801 2337 361867420 361866888 0.000000e+00 795.0
7 TraesCS6B01G124700 chr2B 94.737 38 2 0 1019 1056 34588163 34588126 2.720000e-05 60.2
8 TraesCS6B01G124700 chr7B 92.831 544 26 6 1801 2339 387895612 387896147 0.000000e+00 776.0
9 TraesCS6B01G124700 chr7B 90.000 170 14 1 1060 1229 547711349 547711515 1.520000e-52 217.0
10 TraesCS6B01G124700 chr7B 97.059 34 1 0 1000 1033 547711306 547711339 9.770000e-05 58.4
11 TraesCS6B01G124700 chr5A 84.097 371 30 13 2016 2374 664983894 664984247 5.210000e-87 331.0
12 TraesCS6B01G124700 chr5A 87.421 159 11 4 1854 2004 216665593 216665436 9.300000e-40 174.0
13 TraesCS6B01G124700 chr5A 98.039 51 1 0 711 761 377119607 377119657 3.460000e-14 89.8
14 TraesCS6B01G124700 chr3A 83.377 385 28 13 2006 2374 530202820 530203184 8.720000e-85 324.0
15 TraesCS6B01G124700 chr3A 88.889 162 7 3 1854 2004 530202753 530202914 3.320000e-44 189.0
16 TraesCS6B01G124700 chr3A 98.182 55 1 0 711 765 332220139 332220085 2.070000e-16 97.1
17 TraesCS6B01G124700 chr7A 85.358 321 25 10 2062 2374 96202895 96203201 1.890000e-81 313.0
18 TraesCS6B01G124700 chr7A 87.821 156 13 3 1854 2003 576347813 576347658 7.190000e-41 178.0
19 TraesCS6B01G124700 chr2A 83.489 321 26 10 2062 2374 108514130 108513829 8.910000e-70 274.0
20 TraesCS6B01G124700 chr2D 88.889 162 7 3 1854 2004 427947449 427947610 3.320000e-44 189.0
21 TraesCS6B01G124700 chr2D 88.889 135 4 4 1650 1773 106236306 106236172 3.370000e-34 156.0
22 TraesCS6B01G124700 chr2D 88.889 135 4 4 1650 1773 422777646 422777512 3.370000e-34 156.0
23 TraesCS6B01G124700 chr2D 88.889 135 4 4 1650 1773 503852139 503852273 3.370000e-34 156.0
24 TraesCS6B01G124700 chr2D 88.889 135 4 4 1650 1773 592138012 592138146 3.370000e-34 156.0
25 TraesCS6B01G124700 chrUn 87.821 156 13 3 1854 2003 339003381 339003536 7.190000e-41 178.0
26 TraesCS6B01G124700 chr1A 86.792 159 12 4 1854 2004 588672269 588672426 4.330000e-38 169.0
27 TraesCS6B01G124700 chr1A 86.538 156 14 5 1854 2004 100275448 100275295 5.590000e-37 165.0
28 TraesCS6B01G124700 chr1A 85.185 135 8 6 1003 1137 467151161 467151283 7.340000e-26 128.0
29 TraesCS6B01G124700 chr5D 88.889 135 4 4 1650 1773 297792759 297792625 3.370000e-34 156.0
30 TraesCS6B01G124700 chr5D 98.039 51 1 0 711 761 285247438 285247488 3.460000e-14 89.8
31 TraesCS6B01G124700 chr5D 90.000 50 5 0 716 765 113391895 113391846 5.840000e-07 65.8
32 TraesCS6B01G124700 chr3D 88.889 135 4 4 1650 1773 70729664 70729798 3.370000e-34 156.0
33 TraesCS6B01G124700 chr3D 88.148 135 5 4 1650 1773 443945626 443945760 1.570000e-32 150.0
34 TraesCS6B01G124700 chr3D 98.182 55 1 0 711 765 252334799 252334853 2.070000e-16 97.1
35 TraesCS6B01G124700 chr1D 86.667 135 6 3 1003 1137 413940956 413941078 3.390000e-29 139.0
36 TraesCS6B01G124700 chr3B 98.182 55 1 0 711 765 313808032 313808086 2.070000e-16 97.1
37 TraesCS6B01G124700 chr7D 87.500 88 2 2 1003 1090 420082372 420082450 2.680000e-15 93.5
38 TraesCS6B01G124700 chr5B 98.039 51 1 0 711 761 322858711 322858761 3.460000e-14 89.8
39 TraesCS6B01G124700 chr4A 86.364 88 3 2 1003 1090 613673563 613673485 1.250000e-13 87.9


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 TraesCS6B01G124700 chr6B 119847790 119850317 2527 True 4669.0 4669 100.0000 1 2528 1 chr6B.!!$R1 2527
1 TraesCS6B01G124700 chr6D 52722938 52725405 2467 True 3243.0 3243 90.5400 4 2488 1 chr6D.!!$R1 2484
2 TraesCS6B01G124700 chr6A 63608876 63611263 2387 True 1494.5 2593 87.2485 4 2488 2 chr6A.!!$R1 2484
3 TraesCS6B01G124700 chr2B 361866888 361867420 532 True 795.0 795 93.5300 1801 2337 1 chr2B.!!$R2 536
4 TraesCS6B01G124700 chr7B 387895612 387896147 535 False 776.0 776 92.8310 1801 2339 1 chr7B.!!$F1 538

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
438 485 0.378257 GCAGCGAGAGAGAGAGACAG 59.622 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1565 1640 0.110238 TCATCTCTTTTGTTGCGCGC 60.11 50.0 27.26 27.26 0.0 6.86 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
91 94 4.742201 CGCCTGCACCTGCGTAGT 62.742 66.667 11.27 0.00 45.43 2.73
92 95 2.577059 GCCTGCACCTGCGTAGTA 59.423 61.111 0.00 0.00 45.83 1.82
94 97 1.516386 CCTGCACCTGCGTAGTACG 60.516 63.158 18.37 18.37 45.83 3.67
95 98 1.516386 CTGCACCTGCGTAGTACGG 60.516 63.158 23.29 10.01 45.83 4.02
96 99 2.884207 GCACCTGCGTAGTACGGC 60.884 66.667 23.29 13.95 42.82 5.68
97 100 2.578713 CACCTGCGTAGTACGGCG 60.579 66.667 23.29 4.80 42.82 6.46
146 149 1.648467 GGTCAGCGTGATTTCCAGCC 61.648 60.000 0.00 0.00 0.00 4.85
260 294 3.264159 TGCCGCTGCAATCGATCG 61.264 61.111 9.36 9.36 46.66 3.69
261 295 4.005472 GCCGCTGCAATCGATCGG 62.005 66.667 16.41 15.93 42.68 4.18
262 296 3.341043 CCGCTGCAATCGATCGGG 61.341 66.667 16.41 6.63 36.73 5.14
263 297 3.341043 CGCTGCAATCGATCGGGG 61.341 66.667 16.41 6.25 0.00 5.73
264 298 2.974698 GCTGCAATCGATCGGGGG 60.975 66.667 16.41 5.88 0.00 5.40
265 299 2.505982 CTGCAATCGATCGGGGGT 59.494 61.111 16.41 0.00 0.00 4.95
266 300 1.595382 CTGCAATCGATCGGGGGTC 60.595 63.158 16.41 2.03 0.00 4.46
389 425 3.039526 CCCCTCCTCCTCCTCCCT 61.040 72.222 0.00 0.00 0.00 4.20
404 440 2.387757 CTCCCTCTCTTCTTCCTCCTG 58.612 57.143 0.00 0.00 0.00 3.86
411 458 0.620121 CTTCTTCCTCCTGCCCTCCT 60.620 60.000 0.00 0.00 0.00 3.69
432 479 2.101965 CACCGCAGCGAGAGAGAG 59.898 66.667 18.75 0.00 0.00 3.20
433 480 2.045829 ACCGCAGCGAGAGAGAGA 60.046 61.111 18.75 0.00 0.00 3.10
434 481 2.112198 ACCGCAGCGAGAGAGAGAG 61.112 63.158 18.75 0.00 0.00 3.20
435 482 1.817520 CCGCAGCGAGAGAGAGAGA 60.818 63.158 18.75 0.00 0.00 3.10
436 483 1.351707 CGCAGCGAGAGAGAGAGAC 59.648 63.158 9.98 0.00 0.00 3.36
437 484 1.365368 CGCAGCGAGAGAGAGAGACA 61.365 60.000 9.98 0.00 0.00 3.41
438 485 0.378257 GCAGCGAGAGAGAGAGACAG 59.622 60.000 0.00 0.00 0.00 3.51
439 486 2.011548 GCAGCGAGAGAGAGAGACAGA 61.012 57.143 0.00 0.00 0.00 3.41
475 522 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
476 523 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
477 524 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
478 525 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
479 526 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
480 527 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
481 528 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
482 529 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
483 530 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
484 531 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
485 532 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
486 533 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
487 534 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
488 535 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
489 536 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
490 537 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
491 538 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
492 539 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
493 540 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
496 543 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
504 551 1.134098 AGAGAGAGAGAGCGAGGAAGG 60.134 57.143 0.00 0.00 0.00 3.46
517 564 1.676967 GGAAGGGAAGCAGGCAGTG 60.677 63.158 0.00 0.00 0.00 3.66
518 565 1.376466 GAAGGGAAGCAGGCAGTGA 59.624 57.895 0.00 0.00 0.00 3.41
520 567 2.749441 GGGAAGCAGGCAGTGAGC 60.749 66.667 0.00 0.00 44.65 4.26
521 568 2.350514 GGAAGCAGGCAGTGAGCT 59.649 61.111 0.00 0.00 44.79 4.09
538 596 4.671590 TGAGAGGTCGGCCGTCCA 62.672 66.667 36.90 18.28 40.50 4.02
548 606 4.404098 GCCGTCCACCCGTCCATT 62.404 66.667 0.00 0.00 0.00 3.16
549 607 2.349755 CCGTCCACCCGTCCATTT 59.650 61.111 0.00 0.00 0.00 2.32
550 608 1.743995 CCGTCCACCCGTCCATTTC 60.744 63.158 0.00 0.00 0.00 2.17
553 611 2.437716 CCACCCGTCCATTTCCCG 60.438 66.667 0.00 0.00 0.00 5.14
554 612 2.437716 CACCCGTCCATTTCCCGG 60.438 66.667 0.00 0.00 41.37 5.73
555 613 4.419921 ACCCGTCCATTTCCCGGC 62.420 66.667 0.00 0.00 40.38 6.13
559 617 4.419921 GTCCATTTCCCGGCCGGT 62.420 66.667 40.52 21.85 0.00 5.28
562 620 4.418328 CATTTCCCGGCCGGTGGA 62.418 66.667 40.52 29.26 0.00 4.02
574 635 1.684049 CGGTGGAGCTCCCTCTTCT 60.684 63.158 29.95 0.00 38.21 2.85
807 869 2.612251 CCCCTCCTCTCCCTCCTC 59.388 72.222 0.00 0.00 0.00 3.71
808 870 2.612251 CCCTCCTCTCCCTCCTCC 59.388 72.222 0.00 0.00 0.00 4.30
809 871 2.018086 CCCTCCTCTCCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
878 940 2.486203 CACACACTCGCTTACTCTCTCT 59.514 50.000 0.00 0.00 0.00 3.10
879 941 2.745281 ACACACTCGCTTACTCTCTCTC 59.255 50.000 0.00 0.00 0.00 3.20
880 942 3.006940 CACACTCGCTTACTCTCTCTCT 58.993 50.000 0.00 0.00 0.00 3.10
881 943 3.063452 CACACTCGCTTACTCTCTCTCTC 59.937 52.174 0.00 0.00 0.00 3.20
895 957 2.727684 CTCTCTCGTCGTCGTCGCA 61.728 63.158 7.01 0.00 38.33 5.10
897 959 3.012936 CTCTCGTCGTCGTCGCAGT 62.013 63.158 7.01 0.00 38.33 4.40
924 990 0.889306 GAGTCAGTCCGTAGCTGGTT 59.111 55.000 0.00 0.00 34.89 3.67
926 992 1.817447 AGTCAGTCCGTAGCTGGTTAC 59.183 52.381 0.00 0.00 34.89 2.50
927 993 0.806868 TCAGTCCGTAGCTGGTTACG 59.193 55.000 9.42 9.42 44.46 3.18
990 1058 2.175322 GCTTGTCTGCTCGCTTGC 59.825 61.111 0.00 0.00 0.00 4.01
992 1060 1.849976 GCTTGTCTGCTCGCTTGCTT 61.850 55.000 0.00 0.00 0.00 3.91
994 1062 1.509644 TTGTCTGCTCGCTTGCTTGG 61.510 55.000 0.00 0.00 0.00 3.61
995 1063 1.963338 GTCTGCTCGCTTGCTTGGT 60.963 57.895 0.00 0.00 0.00 3.67
1560 1635 2.126071 CATGGCAGCAGCACAAGC 60.126 61.111 2.65 0.00 44.61 4.01
1561 1636 2.599281 ATGGCAGCAGCACAAGCA 60.599 55.556 2.65 0.00 45.49 3.91
1565 1640 2.554775 CAGCAGCACAAGCACGAG 59.445 61.111 0.00 0.00 45.49 4.18
1566 1641 3.352222 AGCAGCACAAGCACGAGC 61.352 61.111 0.00 0.00 45.49 5.03
1583 1658 0.110056 AGCGCGCAACAAAAGAGATG 60.110 50.000 35.10 0.00 0.00 2.90
1630 1705 8.611654 TTCTGGTGTTTCAGGTTAATTACTAC 57.388 34.615 0.00 0.00 35.58 2.73
1631 1706 7.737869 TCTGGTGTTTCAGGTTAATTACTACA 58.262 34.615 0.00 0.00 35.58 2.74
1632 1707 7.876068 TCTGGTGTTTCAGGTTAATTACTACAG 59.124 37.037 0.00 0.00 35.58 2.74
1636 1711 9.480053 GTGTTTCAGGTTAATTACTACAGTACA 57.520 33.333 0.00 0.00 0.00 2.90
1786 1861 2.676076 CATGCATGCATCACCATCATG 58.324 47.619 30.07 13.69 40.23 3.07
1787 1862 1.770294 TGCATGCATCACCATCATGT 58.230 45.000 18.46 0.00 39.64 3.21
1788 1863 1.407258 TGCATGCATCACCATCATGTG 59.593 47.619 18.46 0.00 39.64 3.21
1818 1896 6.410540 CCTATGTAAGAAGGAAGAAGCAGTT 58.589 40.000 0.00 0.00 34.58 3.16
1833 1911 1.681264 GCAGTTAGCTCTCTCTCTCCC 59.319 57.143 0.00 0.00 41.15 4.30
1838 1917 0.684153 AGCTCTCTCTCTCCCTGTGC 60.684 60.000 0.00 0.00 0.00 4.57
1844 1923 0.673022 CTCTCTCCCTGTGCTGTTGC 60.673 60.000 0.00 0.00 40.20 4.17
2103 2187 7.013274 TGCTCTGGTAAATAATGCCACTAATTC 59.987 37.037 0.00 0.00 39.10 2.17
2196 2296 6.392625 TCACAGCTACTGATAGTACATTCC 57.607 41.667 0.78 0.00 35.18 3.01
2198 2298 6.263392 TCACAGCTACTGATAGTACATTCCTC 59.737 42.308 0.78 0.00 35.18 3.71
2213 2313 4.583489 ACATTCCTCTGATGCCAATCAATC 59.417 41.667 0.00 0.00 42.28 2.67
2214 2314 3.937778 TCCTCTGATGCCAATCAATCA 57.062 42.857 0.00 0.00 42.28 2.57
2215 2315 4.239428 TCCTCTGATGCCAATCAATCAA 57.761 40.909 0.00 0.00 42.28 2.57
2216 2316 4.800023 TCCTCTGATGCCAATCAATCAAT 58.200 39.130 0.00 0.00 42.28 2.57
2324 2428 9.167311 AGTCTTTTGTGACTGGAATATATTCAC 57.833 33.333 23.54 15.23 44.64 3.18
2350 2454 4.931002 CAGAATAAAAACAACTGGCCCATG 59.069 41.667 0.00 0.00 0.00 3.66
2352 2456 4.972751 ATAAAAACAACTGGCCCATGTT 57.027 36.364 11.01 11.01 38.85 2.71
2384 2488 8.506168 TTCCTTCATTCACCAATTGATAGTAC 57.494 34.615 7.12 0.00 32.84 2.73
2394 2498 7.770433 TCACCAATTGATAGTACATTTCTCAGG 59.230 37.037 7.12 0.00 0.00 3.86
2402 2506 9.958180 TGATAGTACATTTCTCAGGATTTTTCA 57.042 29.630 0.00 0.00 0.00 2.69
2404 2508 9.965902 ATAGTACATTTCTCAGGATTTTTCAGT 57.034 29.630 0.00 0.00 0.00 3.41
2406 2510 9.220767 AGTACATTTCTCAGGATTTTTCAGTAC 57.779 33.333 0.00 0.00 0.00 2.73
2407 2511 7.133891 ACATTTCTCAGGATTTTTCAGTACG 57.866 36.000 0.00 0.00 0.00 3.67
2409 2513 3.250744 TCTCAGGATTTTTCAGTACGCG 58.749 45.455 3.53 3.53 0.00 6.01
2459 2563 2.670414 GCACACAGAAAGAGATTCTCCG 59.330 50.000 10.09 0.00 45.42 4.63
2468 2572 4.691326 AAGAGATTCTCCGATTTACCCC 57.309 45.455 10.09 0.00 0.00 4.95
2470 2574 2.704065 GAGATTCTCCGATTTACCCCCA 59.296 50.000 1.97 0.00 0.00 4.96
2472 2576 2.793288 TTCTCCGATTTACCCCCAAC 57.207 50.000 0.00 0.00 0.00 3.77
2488 2592 1.134491 CCAACGTTCCCCTCCACTATC 60.134 57.143 0.00 0.00 0.00 2.08
2489 2593 1.134491 CAACGTTCCCCTCCACTATCC 60.134 57.143 0.00 0.00 0.00 2.59
2490 2594 0.690077 ACGTTCCCCTCCACTATCCC 60.690 60.000 0.00 0.00 0.00 3.85
2491 2595 0.689745 CGTTCCCCTCCACTATCCCA 60.690 60.000 0.00 0.00 0.00 4.37
2492 2596 1.821088 GTTCCCCTCCACTATCCCAT 58.179 55.000 0.00 0.00 0.00 4.00
2493 2597 1.700186 GTTCCCCTCCACTATCCCATC 59.300 57.143 0.00 0.00 0.00 3.51
2494 2598 0.948816 TCCCCTCCACTATCCCATCA 59.051 55.000 0.00 0.00 0.00 3.07
2495 2599 1.059913 CCCCTCCACTATCCCATCAC 58.940 60.000 0.00 0.00 0.00 3.06
2496 2600 1.695664 CCCCTCCACTATCCCATCACA 60.696 57.143 0.00 0.00 0.00 3.58
2497 2601 1.696336 CCCTCCACTATCCCATCACAG 59.304 57.143 0.00 0.00 0.00 3.66
2498 2602 1.071385 CCTCCACTATCCCATCACAGC 59.929 57.143 0.00 0.00 0.00 4.40
2499 2603 1.071385 CTCCACTATCCCATCACAGCC 59.929 57.143 0.00 0.00 0.00 4.85
2500 2604 1.135094 CCACTATCCCATCACAGCCT 58.865 55.000 0.00 0.00 0.00 4.58
2501 2605 1.071385 CCACTATCCCATCACAGCCTC 59.929 57.143 0.00 0.00 0.00 4.70
2502 2606 2.045524 CACTATCCCATCACAGCCTCT 58.954 52.381 0.00 0.00 0.00 3.69
2503 2607 2.036992 CACTATCCCATCACAGCCTCTC 59.963 54.545 0.00 0.00 0.00 3.20
2504 2608 1.622811 CTATCCCATCACAGCCTCTCC 59.377 57.143 0.00 0.00 0.00 3.71
2505 2609 0.030297 ATCCCATCACAGCCTCTCCT 60.030 55.000 0.00 0.00 0.00 3.69
2506 2610 0.689080 TCCCATCACAGCCTCTCCTC 60.689 60.000 0.00 0.00 0.00 3.71
2507 2611 1.440893 CCATCACAGCCTCTCCTCG 59.559 63.158 0.00 0.00 0.00 4.63
2508 2612 1.326213 CCATCACAGCCTCTCCTCGT 61.326 60.000 0.00 0.00 0.00 4.18
2509 2613 0.534412 CATCACAGCCTCTCCTCGTT 59.466 55.000 0.00 0.00 0.00 3.85
2510 2614 0.534412 ATCACAGCCTCTCCTCGTTG 59.466 55.000 0.00 0.00 0.00 4.10
2511 2615 1.079543 CACAGCCTCTCCTCGTTGG 60.080 63.158 0.00 0.00 37.10 3.77
2512 2616 1.534235 ACAGCCTCTCCTCGTTGGT 60.534 57.895 0.00 0.00 37.07 3.67
2513 2617 1.122019 ACAGCCTCTCCTCGTTGGTT 61.122 55.000 0.00 0.00 37.07 3.67
2514 2618 0.390472 CAGCCTCTCCTCGTTGGTTC 60.390 60.000 0.00 0.00 37.07 3.62
2515 2619 1.079057 GCCTCTCCTCGTTGGTTCC 60.079 63.158 0.00 0.00 37.07 3.62
2516 2620 1.545706 GCCTCTCCTCGTTGGTTCCT 61.546 60.000 0.00 0.00 37.07 3.36
2517 2621 0.247736 CCTCTCCTCGTTGGTTCCTG 59.752 60.000 0.00 0.00 37.07 3.86
2518 2622 1.257743 CTCTCCTCGTTGGTTCCTGA 58.742 55.000 0.00 0.00 37.07 3.86
2519 2623 1.203523 CTCTCCTCGTTGGTTCCTGAG 59.796 57.143 0.00 0.00 37.07 3.35
2521 2625 1.192146 TCCTCGTTGGTTCCTGAGGG 61.192 60.000 17.99 4.72 46.42 4.30
2522 2626 1.481056 CCTCGTTGGTTCCTGAGGGT 61.481 60.000 0.00 0.00 43.45 4.34
2523 2627 0.396811 CTCGTTGGTTCCTGAGGGTT 59.603 55.000 0.00 0.00 0.00 4.11
2524 2628 0.395312 TCGTTGGTTCCTGAGGGTTC 59.605 55.000 0.00 0.00 0.00 3.62
2525 2629 0.396811 CGTTGGTTCCTGAGGGTTCT 59.603 55.000 0.00 0.00 0.00 3.01
2526 2630 1.878102 CGTTGGTTCCTGAGGGTTCTG 60.878 57.143 0.00 0.00 0.00 3.02
2527 2631 1.420138 GTTGGTTCCTGAGGGTTCTGA 59.580 52.381 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032681 GTGGTGACTGGTGGAGGC 59.967 66.667 0.00 0.00 0.00 4.70
1 2 1.071471 GTGTGGTGACTGGTGGAGG 59.929 63.158 0.00 0.00 0.00 4.30
2 3 1.300931 CGTGTGGTGACTGGTGGAG 60.301 63.158 0.00 0.00 0.00 3.86
6 7 3.556306 CCCCGTGTGGTGACTGGT 61.556 66.667 0.00 0.00 0.00 4.00
56 59 1.282875 GCGTTCACTTCACTTGGCC 59.717 57.895 0.00 0.00 0.00 5.36
85 88 4.580551 ATGCCCGCCGTACTACGC 62.581 66.667 2.87 0.00 40.91 4.42
109 112 1.739562 CTCACTTGGCCTCACTCGC 60.740 63.158 3.32 0.00 0.00 5.03
110 113 1.079543 CCTCACTTGGCCTCACTCG 60.080 63.158 3.32 0.00 0.00 4.18
111 114 0.036858 GACCTCACTTGGCCTCACTC 60.037 60.000 3.32 0.00 0.00 3.51
112 115 0.764369 TGACCTCACTTGGCCTCACT 60.764 55.000 3.32 0.00 0.00 3.41
154 157 1.739049 GAGTGGATCCGAGGCTGAG 59.261 63.158 7.39 0.00 0.00 3.35
246 280 3.341043 CCCCGATCGATTGCAGCG 61.341 66.667 18.66 1.73 0.00 5.18
247 281 2.974698 CCCCCGATCGATTGCAGC 60.975 66.667 18.66 0.00 0.00 5.25
248 282 1.595382 GACCCCCGATCGATTGCAG 60.595 63.158 18.66 0.00 0.00 4.41
249 283 2.504032 GACCCCCGATCGATTGCA 59.496 61.111 18.66 0.00 0.00 4.08
250 284 2.661866 CGACCCCCGATCGATTGC 60.662 66.667 18.66 0.76 42.25 3.56
251 285 3.125607 TCGACCCCCGATCGATTG 58.874 61.111 18.66 5.59 43.38 2.67
263 297 0.465642 GGTGGGAATGGGAATCGACC 60.466 60.000 0.00 0.00 0.00 4.79
264 298 0.465642 GGGTGGGAATGGGAATCGAC 60.466 60.000 0.00 0.00 0.00 4.20
265 299 0.623324 AGGGTGGGAATGGGAATCGA 60.623 55.000 0.00 0.00 0.00 3.59
266 300 0.179018 GAGGGTGGGAATGGGAATCG 60.179 60.000 0.00 0.00 0.00 3.34
389 425 0.415429 AGGGCAGGAGGAAGAAGAGA 59.585 55.000 0.00 0.00 0.00 3.10
436 483 3.118920 TCTCTCTAGACGGACTCTGTCTG 60.119 52.174 25.23 16.66 45.83 3.51
438 485 3.131577 TCTCTCTCTAGACGGACTCTGTC 59.868 52.174 9.72 9.72 36.60 3.51
439 486 3.101437 TCTCTCTCTAGACGGACTCTGT 58.899 50.000 0.00 0.00 0.00 3.41
475 522 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
476 523 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
477 524 2.362397 TCGCTCTCTCTCTCTCTCTCTC 59.638 54.545 0.00 0.00 0.00 3.20
478 525 2.363680 CTCGCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
479 526 2.546795 CCTCGCTCTCTCTCTCTCTCTC 60.547 59.091 0.00 0.00 0.00 3.20
480 527 1.414181 CCTCGCTCTCTCTCTCTCTCT 59.586 57.143 0.00 0.00 0.00 3.10
481 528 1.412710 TCCTCGCTCTCTCTCTCTCTC 59.587 57.143 0.00 0.00 0.00 3.20
482 529 1.496060 TCCTCGCTCTCTCTCTCTCT 58.504 55.000 0.00 0.00 0.00 3.10
483 530 2.213499 CTTCCTCGCTCTCTCTCTCTC 58.787 57.143 0.00 0.00 0.00 3.20
484 531 1.134098 CCTTCCTCGCTCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
485 532 1.308998 CCTTCCTCGCTCTCTCTCTC 58.691 60.000 0.00 0.00 0.00 3.20
486 533 0.106719 CCCTTCCTCGCTCTCTCTCT 60.107 60.000 0.00 0.00 0.00 3.10
487 534 0.106918 TCCCTTCCTCGCTCTCTCTC 60.107 60.000 0.00 0.00 0.00 3.20
488 535 0.333312 TTCCCTTCCTCGCTCTCTCT 59.667 55.000 0.00 0.00 0.00 3.10
489 536 0.744281 CTTCCCTTCCTCGCTCTCTC 59.256 60.000 0.00 0.00 0.00 3.20
490 537 1.326951 GCTTCCCTTCCTCGCTCTCT 61.327 60.000 0.00 0.00 0.00 3.10
491 538 1.142965 GCTTCCCTTCCTCGCTCTC 59.857 63.158 0.00 0.00 0.00 3.20
492 539 1.610673 TGCTTCCCTTCCTCGCTCT 60.611 57.895 0.00 0.00 0.00 4.09
493 540 1.153469 CTGCTTCCCTTCCTCGCTC 60.153 63.158 0.00 0.00 0.00 5.03
496 543 2.124942 GCCTGCTTCCCTTCCTCG 60.125 66.667 0.00 0.00 0.00 4.63
504 551 2.039405 CAGCTCACTGCCTGCTTCC 61.039 63.158 0.00 0.00 44.23 3.46
517 564 4.200283 CGGCCGACCTCTCAGCTC 62.200 72.222 24.07 0.00 0.00 4.09
520 567 3.827898 GGACGGCCGACCTCTCAG 61.828 72.222 34.71 2.97 0.00 3.35
521 568 4.671590 TGGACGGCCGACCTCTCA 62.672 66.667 39.01 21.96 36.79 3.27
532 590 1.743995 GAAATGGACGGGTGGACGG 60.744 63.158 0.00 0.00 38.39 4.79
534 592 1.378119 GGGAAATGGACGGGTGGAC 60.378 63.158 0.00 0.00 0.00 4.02
535 593 2.961893 CGGGAAATGGACGGGTGGA 61.962 63.158 0.00 0.00 0.00 4.02
536 594 2.437716 CGGGAAATGGACGGGTGG 60.438 66.667 0.00 0.00 0.00 4.61
542 600 4.419921 ACCGGCCGGGAAATGGAC 62.420 66.667 44.99 0.00 39.97 4.02
543 601 4.418328 CACCGGCCGGGAAATGGA 62.418 66.667 44.99 0.00 39.97 3.41
545 603 4.418328 TCCACCGGCCGGGAAATG 62.418 66.667 44.99 33.15 39.97 2.32
546 604 4.109675 CTCCACCGGCCGGGAAAT 62.110 66.667 44.99 24.60 39.97 2.17
555 613 2.685380 AAGAGGGAGCTCCACCGG 60.685 66.667 33.29 0.00 38.24 5.28
557 615 0.539518 GAAGAAGAGGGAGCTCCACC 59.460 60.000 33.29 22.94 38.24 4.61
558 616 0.539518 GGAAGAAGAGGGAGCTCCAC 59.460 60.000 33.29 24.81 38.24 4.02
559 617 0.618968 GGGAAGAAGAGGGAGCTCCA 60.619 60.000 33.29 0.00 38.24 3.86
561 619 1.681486 CCGGGAAGAAGAGGGAGCTC 61.681 65.000 4.71 4.71 0.00 4.09
562 620 1.687493 CCGGGAAGAAGAGGGAGCT 60.687 63.158 0.00 0.00 0.00 4.09
564 622 1.045911 CCTCCGGGAAGAAGAGGGAG 61.046 65.000 0.00 0.00 42.98 4.30
566 624 2.736826 GCCTCCGGGAAGAAGAGGG 61.737 68.421 0.00 0.00 46.14 4.30
574 635 3.179339 TTGGGTTGCCTCCGGGAA 61.179 61.111 0.00 0.00 33.58 3.97
671 733 3.694566 GTGTGGAGTTGATCATAAACCCC 59.305 47.826 0.00 0.00 0.00 4.95
807 869 0.030603 AGGGCTAAAGGAGGAGGAGG 60.031 60.000 0.00 0.00 0.00 4.30
808 870 1.419381 GAGGGCTAAAGGAGGAGGAG 58.581 60.000 0.00 0.00 0.00 3.69
809 871 0.031010 GGAGGGCTAAAGGAGGAGGA 60.031 60.000 0.00 0.00 0.00 3.71
878 940 2.727684 CTGCGACGACGACGAGAGA 61.728 63.158 22.94 2.95 42.66 3.10
879 941 2.276120 CTGCGACGACGACGAGAG 60.276 66.667 22.94 13.15 42.66 3.20
880 942 3.008240 GACTGCGACGACGACGAGA 62.008 63.158 22.94 7.68 42.66 4.04
881 943 2.571096 GACTGCGACGACGACGAG 60.571 66.667 22.94 17.51 42.66 4.18
895 957 2.835764 ACGGACTGACTCTAGAGAGACT 59.164 50.000 26.57 3.24 44.74 3.24
897 959 3.181473 GCTACGGACTGACTCTAGAGAGA 60.181 52.174 26.57 10.61 44.74 3.10
931 997 4.431809 TGTTGTTGCAAGAACCAAAGATG 58.568 39.130 29.99 0.00 31.74 2.90
978 1046 1.962822 CACCAAGCAAGCGAGCAGA 60.963 57.895 6.21 0.00 36.85 4.26
990 1058 2.040544 GGACGCCATCACCACCAAG 61.041 63.158 0.00 0.00 0.00 3.61
992 1060 2.927856 AGGACGCCATCACCACCA 60.928 61.111 0.00 0.00 0.00 4.17
994 1062 2.125106 GGAGGACGCCATCACCAC 60.125 66.667 0.00 0.00 0.00 4.16
995 1063 2.606213 TGGAGGACGCCATCACCA 60.606 61.111 0.00 0.00 34.37 4.17
1560 1635 2.349376 CTTTTGTTGCGCGCTCGTG 61.349 57.895 33.29 11.70 38.14 4.35
1561 1636 2.052237 CTTTTGTTGCGCGCTCGT 60.052 55.556 33.29 0.00 38.14 4.18
1565 1640 0.110238 TCATCTCTTTTGTTGCGCGC 60.110 50.000 27.26 27.26 0.00 6.86
1566 1641 2.434761 GATCATCTCTTTTGTTGCGCG 58.565 47.619 0.00 0.00 0.00 6.86
1644 1719 0.250770 AAAAACTCCACGGCTCTCCC 60.251 55.000 0.00 0.00 0.00 4.30
1784 1859 4.599241 CCTTCTTACATAGGGGGATCACAT 59.401 45.833 0.00 0.00 0.00 3.21
1785 1860 3.973973 CCTTCTTACATAGGGGGATCACA 59.026 47.826 0.00 0.00 0.00 3.58
1786 1861 4.232091 TCCTTCTTACATAGGGGGATCAC 58.768 47.826 0.00 0.00 32.20 3.06
1787 1862 4.569676 TCCTTCTTACATAGGGGGATCA 57.430 45.455 0.00 0.00 32.20 2.92
1788 1863 5.155905 TCTTCCTTCTTACATAGGGGGATC 58.844 45.833 0.00 0.00 32.20 3.36
1789 1864 5.171541 TCTTCCTTCTTACATAGGGGGAT 57.828 43.478 0.00 0.00 32.20 3.85
1790 1865 4.637288 TCTTCCTTCTTACATAGGGGGA 57.363 45.455 0.00 0.00 32.20 4.81
1791 1866 4.445019 GCTTCTTCCTTCTTACATAGGGGG 60.445 50.000 0.00 0.00 32.20 5.40
1818 1896 1.409521 GCACAGGGAGAGAGAGAGCTA 60.410 57.143 0.00 0.00 0.00 3.32
1830 1908 1.071987 CTGAGCAACAGCACAGGGA 59.928 57.895 6.96 0.00 41.41 4.20
1832 1910 0.533531 TGTCTGAGCAACAGCACAGG 60.534 55.000 13.42 0.00 44.03 4.00
1833 1911 1.302366 TTGTCTGAGCAACAGCACAG 58.698 50.000 8.32 8.32 44.86 3.66
1844 1923 1.311859 TGGCACTTGCTTTGTCTGAG 58.688 50.000 0.38 0.00 41.70 3.35
2069 2153 6.722301 CATTATTTACCAGAGCACATCACAG 58.278 40.000 0.00 0.00 0.00 3.66
2103 2187 0.251354 TAAGCCAGGCAGAGCAAGAG 59.749 55.000 15.80 0.00 0.00 2.85
2162 2261 6.304356 TCAGTAGCTGTGAAAAATGTGAAG 57.696 37.500 0.00 0.00 32.61 3.02
2172 2271 6.607600 AGGAATGTACTATCAGTAGCTGTGAA 59.392 38.462 0.00 0.00 30.12 3.18
2173 2272 6.129874 AGGAATGTACTATCAGTAGCTGTGA 58.870 40.000 0.00 0.00 30.12 3.58
2196 2296 4.202111 TGCATTGATTGATTGGCATCAGAG 60.202 41.667 0.00 0.00 40.66 3.35
2198 2298 3.802139 GTGCATTGATTGATTGGCATCAG 59.198 43.478 0.00 0.00 40.66 2.90
2213 2313 6.425721 AGGATTTTTCTGAACATTGTGCATTG 59.574 34.615 0.00 0.00 0.00 2.82
2214 2314 6.527423 AGGATTTTTCTGAACATTGTGCATT 58.473 32.000 0.00 0.00 0.00 3.56
2215 2315 6.105397 AGGATTTTTCTGAACATTGTGCAT 57.895 33.333 0.00 0.00 0.00 3.96
2216 2316 5.068855 TGAGGATTTTTCTGAACATTGTGCA 59.931 36.000 0.00 0.00 0.00 4.57
2324 2428 4.749598 GGGCCAGTTGTTTTTATTCTGTTG 59.250 41.667 4.39 0.00 0.00 3.33
2361 2465 7.864108 TGTACTATCAATTGGTGAATGAAGG 57.136 36.000 5.42 0.00 40.50 3.46
2378 2482 9.965902 ACTGAAAAATCCTGAGAAATGTACTAT 57.034 29.630 0.00 0.00 0.00 2.12
2381 2485 8.169268 CGTACTGAAAAATCCTGAGAAATGTAC 58.831 37.037 0.00 0.00 0.00 2.90
2384 2488 6.024049 GCGTACTGAAAAATCCTGAGAAATG 58.976 40.000 0.00 0.00 0.00 2.32
2394 2498 1.136085 TGCTGCGCGTACTGAAAAATC 60.136 47.619 8.43 0.00 0.00 2.17
2402 2506 3.041940 GTTGGTGCTGCGCGTACT 61.042 61.111 8.43 0.00 0.00 2.73
2403 2507 3.295228 CTGTTGGTGCTGCGCGTAC 62.295 63.158 8.43 7.43 0.00 3.67
2404 2508 2.779951 ATCTGTTGGTGCTGCGCGTA 62.780 55.000 8.43 0.71 0.00 4.42
2405 2509 4.908687 TCTGTTGGTGCTGCGCGT 62.909 61.111 8.43 0.00 0.00 6.01
2406 2510 3.425713 ATCTGTTGGTGCTGCGCG 61.426 61.111 0.00 0.00 0.00 6.86
2407 2511 2.177531 CATCTGTTGGTGCTGCGC 59.822 61.111 0.00 0.00 0.00 6.09
2409 2513 1.878775 GTCCATCTGTTGGTGCTGC 59.121 57.895 4.76 0.00 46.52 5.25
2422 2526 1.603171 TGCATGCACAACCGTCCAT 60.603 52.632 18.46 0.00 0.00 3.41
2459 2563 1.466856 GGGAACGTTGGGGGTAAATC 58.533 55.000 5.00 0.00 0.00 2.17
2468 2572 0.909623 ATAGTGGAGGGGAACGTTGG 59.090 55.000 5.00 0.00 0.00 3.77
2470 2574 1.201424 GGATAGTGGAGGGGAACGTT 58.799 55.000 0.00 0.00 0.00 3.99
2472 2576 0.689745 TGGGATAGTGGAGGGGAACG 60.690 60.000 0.00 0.00 0.00 3.95
2488 2592 1.828768 GAGGAGAGGCTGTGATGGG 59.171 63.158 0.00 0.00 0.00 4.00
2489 2593 1.326213 ACGAGGAGAGGCTGTGATGG 61.326 60.000 0.00 0.00 0.00 3.51
2490 2594 0.534412 AACGAGGAGAGGCTGTGATG 59.466 55.000 0.00 0.00 0.00 3.07
2491 2595 0.534412 CAACGAGGAGAGGCTGTGAT 59.466 55.000 0.00 0.00 0.00 3.06
2492 2596 1.536073 CCAACGAGGAGAGGCTGTGA 61.536 60.000 0.00 0.00 41.22 3.58
2493 2597 1.079543 CCAACGAGGAGAGGCTGTG 60.080 63.158 0.00 0.00 41.22 3.66
2494 2598 1.122019 AACCAACGAGGAGAGGCTGT 61.122 55.000 0.00 0.00 41.22 4.40
2495 2599 0.390472 GAACCAACGAGGAGAGGCTG 60.390 60.000 0.00 0.00 41.22 4.85
2496 2600 1.545706 GGAACCAACGAGGAGAGGCT 61.546 60.000 5.70 0.00 41.22 4.58
2497 2601 1.079057 GGAACCAACGAGGAGAGGC 60.079 63.158 5.70 0.00 41.22 4.70
2498 2602 0.247736 CAGGAACCAACGAGGAGAGG 59.752 60.000 5.70 0.00 41.22 3.69
2499 2603 1.203523 CTCAGGAACCAACGAGGAGAG 59.796 57.143 5.70 0.00 41.22 3.20
2500 2604 1.257743 CTCAGGAACCAACGAGGAGA 58.742 55.000 5.70 0.00 41.22 3.71
2501 2605 0.247736 CCTCAGGAACCAACGAGGAG 59.752 60.000 14.62 0.00 46.71 3.69
2502 2606 1.192146 CCCTCAGGAACCAACGAGGA 61.192 60.000 18.86 0.00 46.71 3.71
2503 2607 1.296715 CCCTCAGGAACCAACGAGG 59.703 63.158 13.48 13.48 43.95 4.63
2504 2608 0.396811 AACCCTCAGGAACCAACGAG 59.603 55.000 0.00 0.00 36.73 4.18
2505 2609 0.395312 GAACCCTCAGGAACCAACGA 59.605 55.000 0.00 0.00 36.73 3.85
2506 2610 0.396811 AGAACCCTCAGGAACCAACG 59.603 55.000 0.00 0.00 36.73 4.10
2507 2611 1.420138 TCAGAACCCTCAGGAACCAAC 59.580 52.381 0.00 0.00 36.73 3.77
2508 2612 1.814429 TCAGAACCCTCAGGAACCAA 58.186 50.000 0.00 0.00 36.73 3.67
2509 2613 3.569827 TCAGAACCCTCAGGAACCA 57.430 52.632 0.00 0.00 36.73 3.67


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

AutoCloner maintained by Alex Coulton.