Multiple sequence alignment - TraesCS3A01G257200

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 TraesCS3A01G257200 chr3A 100.000 2459 0 0 1 2459 478950230 478952688 0.000000e+00 4542.0
1 TraesCS3A01G257200 chr3A 89.189 74 6 2 410 481 478807289 478807216 9.360000e-15 91.6
2 TraesCS3A01G257200 chr3A 89.189 74 4 1 410 479 65766873 65766946 3.370000e-14 89.8
3 TraesCS3A01G257200 chr3D 95.104 1062 35 5 851 1911 359520898 359521943 0.000000e+00 1657.0
4 TraesCS3A01G257200 chr3D 91.429 175 13 2 472 644 359520738 359520912 3.160000e-59 239.0
5 TraesCS3A01G257200 chr3D 90.110 182 17 1 185 365 359520543 359520724 4.090000e-58 235.0
6 TraesCS3A01G257200 chr3D 92.623 122 5 2 59 180 359519152 359519269 3.250000e-39 172.0
7 TraesCS3A01G257200 chr3D 91.667 72 5 1 407 478 3821270 3821340 5.600000e-17 99.0
8 TraesCS3A01G257200 chr3D 89.041 73 3 3 410 477 167029600 167029672 4.360000e-13 86.1
9 TraesCS3A01G257200 chr3B 91.794 1048 68 12 851 1890 465691589 465692626 0.000000e+00 1443.0
10 TraesCS3A01G257200 chr3B 91.559 1007 66 9 851 1854 465654559 465655549 0.000000e+00 1371.0
11 TraesCS3A01G257200 chr3B 87.097 620 58 13 1856 2457 465655725 465656340 0.000000e+00 682.0
12 TraesCS3A01G257200 chr3B 77.220 518 100 8 1920 2433 465692708 465693211 1.110000e-73 287.0
13 TraesCS3A01G257200 chr3B 98.246 57 1 0 588 644 465691547 465691603 1.560000e-17 100.0
14 TraesCS3A01G257200 chr3B 94.737 57 3 0 588 644 465654517 465654573 3.370000e-14 89.8
15 TraesCS3A01G257200 chrUn 95.267 486 18 2 851 1335 360621717 360621236 0.000000e+00 765.0
16 TraesCS3A01G257200 chrUn 93.427 213 12 2 644 855 171112390 171112601 5.100000e-82 315.0
17 TraesCS3A01G257200 chrUn 93.396 212 13 1 644 855 138272144 138271934 1.840000e-81 313.0
18 TraesCS3A01G257200 chrUn 93.396 212 12 2 644 855 138346161 138345952 1.840000e-81 313.0
19 TraesCS3A01G257200 chrUn 93.396 212 12 2 644 855 138415875 138415666 1.840000e-81 313.0
20 TraesCS3A01G257200 chrUn 93.396 212 13 1 644 855 138484940 138484730 1.840000e-81 313.0
21 TraesCS3A01G257200 chrUn 93.396 212 13 1 644 855 172123454 172123664 1.840000e-81 313.0
22 TraesCS3A01G257200 chrUn 93.396 212 12 2 644 855 312018949 312018740 1.840000e-81 313.0
23 TraesCS3A01G257200 chrUn 98.246 57 1 0 588 644 360621759 360621703 1.560000e-17 100.0
24 TraesCS3A01G257200 chr6A 93.868 212 12 1 644 855 558457495 558457705 3.950000e-83 318.0
25 TraesCS3A01G257200 chr6A 93.868 212 12 1 644 855 558460815 558461025 3.950000e-83 318.0
26 TraesCS3A01G257200 chr5D 91.176 68 5 1 410 477 559727235 559727169 9.360000e-15 91.6
27 TraesCS3A01G257200 chr1A 91.176 68 4 1 410 477 111790439 111790504 9.360000e-15 91.6
28 TraesCS3A01G257200 chr7A 89.041 73 5 2 410 479 28155619 28155547 1.210000e-13 87.9
29 TraesCS3A01G257200 chr6D 88.889 72 4 2 410 477 10465978 10466049 4.360000e-13 86.1
30 TraesCS3A01G257200 chr1D 86.585 82 5 5 410 487 492364784 492364863 4.360000e-13 86.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3A01G257200 chr3A 478950230 478952688 2458 False 4542.000000 4542 100.000000 1 2459 1 chr3A.!!$F2 2458
1 TraesCS3A01G257200 chr3D 359519152 359521943 2791 False 575.750000 1657 92.316500 59 1911 4 chr3D.!!$F3 1852
2 TraesCS3A01G257200 chr3B 465654517 465656340 1823 False 714.266667 1371 91.131000 588 2457 3 chr3B.!!$F1 1869
3 TraesCS3A01G257200 chr3B 465691547 465693211 1664 False 610.000000 1443 89.086667 588 2433 3 chr3B.!!$F2 1845
4 TraesCS3A01G257200 chrUn 360621236 360621759 523 True 432.500000 765 96.756500 588 1335 2 chrUn.!!$R6 747
5 TraesCS3A01G257200 chr6A 558457495 558461025 3530 False 318.000000 318 93.868000 644 855 2 chr6A.!!$F1 211

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
22 23 0.046397 AAGTTGCCCCCTCCCTAGAT 59.954 55.0 0.0 0.0 0.0 1.98 F
1441 3516 0.321653 TTTCCTCTTCGCTTCTGGGC 60.322 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1444 3519 0.107848 CCACATTACCCTCCACGACC 60.108 60.0 0.00 0.0 0.00 4.79 R
2434 6347 0.321564 CCCATGAACGTGGAAGCTCA 60.322 55.0 13.85 0.0 42.02 4.26 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
18 19 3.137344 AATAAGTTGCCCCCTCCCT 57.863 52.632 0.00 0.00 0.00 4.20
19 20 2.296943 AATAAGTTGCCCCCTCCCTA 57.703 50.000 0.00 0.00 0.00 3.53
20 21 1.821088 ATAAGTTGCCCCCTCCCTAG 58.179 55.000 0.00 0.00 0.00 3.02
21 22 0.720232 TAAGTTGCCCCCTCCCTAGA 59.280 55.000 0.00 0.00 0.00 2.43
22 23 0.046397 AAGTTGCCCCCTCCCTAGAT 59.954 55.000 0.00 0.00 0.00 1.98
23 24 0.046397 AGTTGCCCCCTCCCTAGATT 59.954 55.000 0.00 0.00 0.00 2.40
24 25 1.297141 AGTTGCCCCCTCCCTAGATTA 59.703 52.381 0.00 0.00 0.00 1.75
25 26 2.089350 AGTTGCCCCCTCCCTAGATTAT 60.089 50.000 0.00 0.00 0.00 1.28
26 27 2.716969 GTTGCCCCCTCCCTAGATTATT 59.283 50.000 0.00 0.00 0.00 1.40
27 28 2.632537 TGCCCCCTCCCTAGATTATTC 58.367 52.381 0.00 0.00 0.00 1.75
28 29 2.184565 TGCCCCCTCCCTAGATTATTCT 59.815 50.000 0.00 0.00 35.90 2.40
29 30 3.408237 TGCCCCCTCCCTAGATTATTCTA 59.592 47.826 0.00 0.00 33.17 2.10
30 31 4.140301 TGCCCCCTCCCTAGATTATTCTAA 60.140 45.833 0.00 0.00 34.06 2.10
31 32 4.850386 GCCCCCTCCCTAGATTATTCTAAA 59.150 45.833 0.00 0.00 34.06 1.85
32 33 5.312443 GCCCCCTCCCTAGATTATTCTAAAA 59.688 44.000 0.00 0.00 34.06 1.52
33 34 6.522631 GCCCCCTCCCTAGATTATTCTAAAAG 60.523 46.154 0.00 0.00 34.06 2.27
34 35 6.477253 CCCCTCCCTAGATTATTCTAAAAGC 58.523 44.000 0.00 0.00 34.06 3.51
35 36 6.477253 CCCTCCCTAGATTATTCTAAAAGCC 58.523 44.000 0.00 0.00 34.06 4.35
36 37 6.273495 CCCTCCCTAGATTATTCTAAAAGCCT 59.727 42.308 0.00 0.00 34.06 4.58
37 38 7.458170 CCCTCCCTAGATTATTCTAAAAGCCTA 59.542 40.741 0.00 0.00 34.06 3.93
38 39 8.881262 CCTCCCTAGATTATTCTAAAAGCCTAA 58.119 37.037 0.00 0.00 34.06 2.69
115 116 2.035632 CCTAGCGGACAATCTCCTTCT 58.964 52.381 0.00 0.00 36.80 2.85
116 117 2.432510 CCTAGCGGACAATCTCCTTCTT 59.567 50.000 0.00 0.00 36.80 2.52
117 118 2.682155 AGCGGACAATCTCCTTCTTC 57.318 50.000 0.00 0.00 36.80 2.87
126 127 7.094805 CGGACAATCTCCTTCTTCACAATTTTA 60.095 37.037 0.00 0.00 36.80 1.52
137 138 3.505386 TCACAATTTTATGGTGGCCACT 58.495 40.909 33.91 18.99 35.80 4.00
167 168 8.305441 TGTAACATGTTGCTAATGATATACCG 57.695 34.615 24.30 0.00 0.00 4.02
192 1462 3.187058 GCAACGGGCGATCATGTT 58.813 55.556 0.00 0.00 0.00 2.71
215 1485 7.903995 TTTGAAATCAAACTTTGAGCTTTGT 57.096 28.000 9.97 0.00 43.98 2.83
247 1517 5.369833 TGTCTTTTATGTTTCGAGGGTCAA 58.630 37.500 0.00 0.00 0.00 3.18
248 1518 5.237779 TGTCTTTTATGTTTCGAGGGTCAAC 59.762 40.000 0.00 0.00 0.00 3.18
249 1519 5.237779 GTCTTTTATGTTTCGAGGGTCAACA 59.762 40.000 2.34 2.34 34.97 3.33
304 1575 5.429681 TTCTCATTCGTTAAATCCAGGGA 57.570 39.130 0.00 0.00 0.00 4.20
326 1597 1.826720 CCATGTATGCTTTGGCCAACT 59.173 47.619 20.35 5.96 37.74 3.16
350 1621 3.641906 CACGATCTTAGTTGTATCCCCCT 59.358 47.826 0.00 0.00 0.00 4.79
365 1636 4.295905 TCCCCCTTAGGATGTGAACTAT 57.704 45.455 0.00 0.00 38.24 2.12
366 1637 3.973973 TCCCCCTTAGGATGTGAACTATG 59.026 47.826 0.00 0.00 38.24 2.23
367 1638 3.973973 CCCCCTTAGGATGTGAACTATGA 59.026 47.826 0.00 0.00 38.24 2.15
368 1639 4.040952 CCCCCTTAGGATGTGAACTATGAG 59.959 50.000 0.00 0.00 38.24 2.90
369 1640 4.656112 CCCCTTAGGATGTGAACTATGAGT 59.344 45.833 0.00 0.00 38.24 3.41
370 1641 5.839063 CCCCTTAGGATGTGAACTATGAGTA 59.161 44.000 0.00 0.00 38.24 2.59
371 1642 6.326583 CCCCTTAGGATGTGAACTATGAGTAA 59.673 42.308 0.00 0.00 38.24 2.24
372 1643 7.210873 CCCTTAGGATGTGAACTATGAGTAAC 58.789 42.308 0.00 0.00 33.47 2.50
373 1644 7.147724 CCCTTAGGATGTGAACTATGAGTAACA 60.148 40.741 0.00 0.00 31.98 2.41
374 1645 8.258007 CCTTAGGATGTGAACTATGAGTAACAA 58.742 37.037 0.00 0.00 31.45 2.83
375 1646 9.653287 CTTAGGATGTGAACTATGAGTAACAAA 57.347 33.333 0.74 0.00 31.45 2.83
376 1647 9.653287 TTAGGATGTGAACTATGAGTAACAAAG 57.347 33.333 0.74 0.00 31.45 2.77
377 1648 6.595716 AGGATGTGAACTATGAGTAACAAAGC 59.404 38.462 0.74 0.00 31.45 3.51
378 1649 6.595716 GGATGTGAACTATGAGTAACAAAGCT 59.404 38.462 0.00 0.00 31.45 3.74
379 1650 7.119846 GGATGTGAACTATGAGTAACAAAGCTT 59.880 37.037 0.00 0.00 31.45 3.74
380 1651 7.189693 TGTGAACTATGAGTAACAAAGCTTG 57.810 36.000 0.00 0.00 0.00 4.01
381 1652 6.204688 TGTGAACTATGAGTAACAAAGCTTGG 59.795 38.462 0.00 0.00 34.12 3.61
382 1653 6.204882 GTGAACTATGAGTAACAAAGCTTGGT 59.795 38.462 0.00 0.00 34.12 3.67
383 1654 6.770785 TGAACTATGAGTAACAAAGCTTGGTT 59.229 34.615 22.49 22.49 34.12 3.67
384 1655 6.803154 ACTATGAGTAACAAAGCTTGGTTC 57.197 37.500 22.54 13.84 34.12 3.62
385 1656 6.534634 ACTATGAGTAACAAAGCTTGGTTCT 58.465 36.000 22.54 17.89 30.10 3.01
386 1657 6.998673 ACTATGAGTAACAAAGCTTGGTTCTT 59.001 34.615 22.54 12.01 27.38 2.52
387 1658 5.751243 TGAGTAACAAAGCTTGGTTCTTC 57.249 39.130 22.54 19.43 27.38 2.87
388 1659 5.437060 TGAGTAACAAAGCTTGGTTCTTCT 58.563 37.500 22.54 17.79 27.38 2.85
389 1660 5.296780 TGAGTAACAAAGCTTGGTTCTTCTG 59.703 40.000 22.54 5.73 27.38 3.02
390 1661 4.580580 AGTAACAAAGCTTGGTTCTTCTGG 59.419 41.667 22.54 0.00 34.12 3.86
395 1666 5.046663 ACAAAGCTTGGTTCTTCTGGAAAAA 60.047 36.000 0.00 0.00 35.51 1.94
402 1673 7.382488 GCTTGGTTCTTCTGGAAAAACTAATTC 59.618 37.037 0.28 0.00 35.51 2.17
404 1675 7.940850 TGGTTCTTCTGGAAAAACTAATTCAG 58.059 34.615 0.57 0.00 35.51 3.02
405 1676 7.014230 TGGTTCTTCTGGAAAAACTAATTCAGG 59.986 37.037 0.57 0.00 35.51 3.86
406 1677 7.230712 GGTTCTTCTGGAAAAACTAATTCAGGA 59.769 37.037 0.57 0.00 35.51 3.86
407 1678 8.630037 GTTCTTCTGGAAAAACTAATTCAGGAA 58.370 33.333 0.00 0.00 35.51 3.36
408 1679 8.166422 TCTTCTGGAAAAACTAATTCAGGAAC 57.834 34.615 0.00 0.00 0.00 3.62
409 1680 7.777910 TCTTCTGGAAAAACTAATTCAGGAACA 59.222 33.333 0.00 0.00 0.00 3.18
410 1681 7.272037 TCTGGAAAAACTAATTCAGGAACAC 57.728 36.000 0.00 0.00 0.00 3.32
411 1682 7.060421 TCTGGAAAAACTAATTCAGGAACACT 58.940 34.615 0.00 0.00 0.00 3.55
412 1683 7.228706 TCTGGAAAAACTAATTCAGGAACACTC 59.771 37.037 0.00 0.00 0.00 3.51
413 1684 6.264518 TGGAAAAACTAATTCAGGAACACTCC 59.735 38.462 0.00 0.00 42.81 3.85
414 1685 6.294564 GGAAAAACTAATTCAGGAACACTCCC 60.295 42.308 0.00 0.00 43.64 4.30
415 1686 5.584551 AAACTAATTCAGGAACACTCCCT 57.415 39.130 0.00 0.00 43.64 4.20
416 1687 4.828072 ACTAATTCAGGAACACTCCCTC 57.172 45.455 0.00 0.00 43.64 4.30
417 1688 3.519913 ACTAATTCAGGAACACTCCCTCC 59.480 47.826 0.00 0.00 43.64 4.30
418 1689 0.905357 ATTCAGGAACACTCCCTCCG 59.095 55.000 0.00 0.00 43.64 4.63
419 1690 0.471211 TTCAGGAACACTCCCTCCGT 60.471 55.000 0.00 0.00 43.64 4.69
420 1691 0.406750 TCAGGAACACTCCCTCCGTA 59.593 55.000 0.00 0.00 43.64 4.02
421 1692 1.203087 TCAGGAACACTCCCTCCGTAA 60.203 52.381 0.00 0.00 43.64 3.18
422 1693 1.621814 CAGGAACACTCCCTCCGTAAA 59.378 52.381 0.00 0.00 43.64 2.01
423 1694 2.236395 CAGGAACACTCCCTCCGTAAAT 59.764 50.000 0.00 0.00 43.64 1.40
424 1695 2.910977 AGGAACACTCCCTCCGTAAATT 59.089 45.455 0.00 0.00 43.64 1.82
425 1696 4.081309 CAGGAACACTCCCTCCGTAAATTA 60.081 45.833 0.00 0.00 43.64 1.40
426 1697 4.533311 AGGAACACTCCCTCCGTAAATTAA 59.467 41.667 0.00 0.00 43.64 1.40
427 1698 5.191124 AGGAACACTCCCTCCGTAAATTAAT 59.809 40.000 0.00 0.00 43.64 1.40
428 1699 6.384886 AGGAACACTCCCTCCGTAAATTAATA 59.615 38.462 0.00 0.00 43.64 0.98
429 1700 7.072076 AGGAACACTCCCTCCGTAAATTAATAT 59.928 37.037 0.00 0.00 43.64 1.28
430 1701 8.370182 GGAACACTCCCTCCGTAAATTAATATA 58.630 37.037 0.00 0.00 35.42 0.86
431 1702 9.768662 GAACACTCCCTCCGTAAATTAATATAA 57.231 33.333 0.00 0.00 0.00 0.98
432 1703 9.774413 AACACTCCCTCCGTAAATTAATATAAG 57.226 33.333 0.00 0.00 0.00 1.73
433 1704 9.151177 ACACTCCCTCCGTAAATTAATATAAGA 57.849 33.333 0.00 0.00 0.00 2.10
434 1705 9.640963 CACTCCCTCCGTAAATTAATATAAGAG 57.359 37.037 0.00 0.00 0.00 2.85
435 1706 8.312564 ACTCCCTCCGTAAATTAATATAAGAGC 58.687 37.037 0.00 0.00 0.00 4.09
436 1707 7.318141 TCCCTCCGTAAATTAATATAAGAGCG 58.682 38.462 0.00 0.00 0.00 5.03
437 1708 7.039504 TCCCTCCGTAAATTAATATAAGAGCGT 60.040 37.037 0.00 0.00 0.00 5.07
438 1709 7.601508 CCCTCCGTAAATTAATATAAGAGCGTT 59.398 37.037 0.00 0.00 0.00 4.84
439 1710 8.985805 CCTCCGTAAATTAATATAAGAGCGTTT 58.014 33.333 0.00 0.00 0.00 3.60
475 1746 7.039853 GCTCTTATATTAGTTTACGGAGGGAGT 60.040 40.741 0.00 0.00 0.00 3.85
482 1753 1.927487 TTACGGAGGGAGTAGTTGCA 58.073 50.000 0.00 0.00 0.00 4.08
508 1779 2.165998 GCCATTGGGGAGAATATCAGC 58.834 52.381 4.53 0.00 40.01 4.26
517 1788 6.032039 TGGGGAGAATATCAGCTAATACCAT 58.968 40.000 0.00 0.00 0.00 3.55
530 1801 6.484643 CAGCTAATACCATCACTTGTATGCTT 59.515 38.462 0.00 0.00 29.35 3.91
606 1878 5.472137 GGTTTCATTGTTTGTCTAGCCAGTA 59.528 40.000 0.00 0.00 0.00 2.74
713 1986 3.124466 CGTACGTGGCTTGATTTGATTGA 59.876 43.478 7.22 0.00 0.00 2.57
719 1992 5.344128 CGTGGCTTGATTTGATTGAAAGAAG 59.656 40.000 0.00 0.00 0.00 2.85
736 2009 0.697854 AAGATAAGGTCCGGCCCCAT 60.698 55.000 0.00 0.00 38.26 4.00
751 2024 2.091333 GCCCCATCCCCTTAAAATCAGA 60.091 50.000 0.00 0.00 0.00 3.27
754 2027 3.463329 CCCATCCCCTTAAAATCAGAGGA 59.537 47.826 0.00 0.00 32.11 3.71
771 2044 9.612879 AATCAGAGGAGGAGATGATTAGATTAA 57.387 33.333 0.00 0.00 39.85 1.40
834 2107 0.982852 ACGGATGAGAGCATGGGGAA 60.983 55.000 0.00 0.00 34.11 3.97
840 2113 1.307691 AGAGCATGGGGAAGGAGCT 60.308 57.895 0.00 0.00 38.43 4.09
963 2236 2.628178 CCTTTCCAGTCAAAAACCCTCC 59.372 50.000 0.00 0.00 0.00 4.30
964 2237 2.375014 TTCCAGTCAAAAACCCTCCC 57.625 50.000 0.00 0.00 0.00 4.30
965 2238 1.529744 TCCAGTCAAAAACCCTCCCT 58.470 50.000 0.00 0.00 0.00 4.20
966 2239 1.423921 TCCAGTCAAAAACCCTCCCTC 59.576 52.381 0.00 0.00 0.00 4.30
998 2271 3.590574 AAGTCCCAACCCAGCCCC 61.591 66.667 0.00 0.00 0.00 5.80
1440 3515 1.443802 GTTTCCTCTTCGCTTCTGGG 58.556 55.000 0.00 0.00 0.00 4.45
1441 3516 0.321653 TTTCCTCTTCGCTTCTGGGC 60.322 55.000 0.00 0.00 0.00 5.36
1514 3595 2.031683 CGATGCCCGTTAATTCCACTTC 59.968 50.000 0.00 0.00 0.00 3.01
1608 3689 0.468400 TCGAGGTTTTTGGGGGTTGG 60.468 55.000 0.00 0.00 0.00 3.77
1779 3863 7.599630 TTTAACTTGAACTCACGTGTTACTT 57.400 32.000 16.51 2.57 0.00 2.24
1793 3877 7.856894 TCACGTGTTACTTATTTTGTTTTAGCC 59.143 33.333 16.51 0.00 0.00 3.93
1824 3908 9.387397 TGTCTATATTTTGGTACCCATGATAGA 57.613 33.333 10.07 11.93 31.53 1.98
1831 3915 5.304686 TGGTACCCATGATAGAACCAATC 57.695 43.478 10.07 0.00 34.20 2.67
1844 3928 7.399765 TGATAGAACCAATCCCAAACATTTCAT 59.600 33.333 0.00 0.00 0.00 2.57
1849 3933 9.230122 GAACCAATCCCAAACATTTCATTAAAT 57.770 29.630 0.00 0.00 35.65 1.40
2021 5919 4.323562 GGCTTCTATTGACACTACTTGGGT 60.324 45.833 0.00 0.00 33.12 4.51
2030 5928 6.247229 TGACACTACTTGGGTGCATATATT 57.753 37.500 0.00 0.00 38.14 1.28
2043 5941 6.879458 GGGTGCATATATTTTCTTCGTATCCT 59.121 38.462 0.00 0.00 0.00 3.24
2143 6044 1.154205 CCACCATCATCGCCGAACTC 61.154 60.000 0.00 0.00 0.00 3.01
2147 6048 1.277326 CATCATCGCCGAACTCGAAA 58.723 50.000 0.00 0.00 43.02 3.46
2151 6052 1.658596 CATCGCCGAACTCGAAATGAA 59.341 47.619 0.00 0.00 43.02 2.57
2153 6054 1.068474 CGCCGAACTCGAAATGAAGT 58.932 50.000 0.00 0.00 43.02 3.01
2155 6056 2.664568 CGCCGAACTCGAAATGAAGTTA 59.335 45.455 0.00 0.00 43.02 2.24
2190 6091 5.869579 TGAGCTTGAAGAAATTGTAGAGGT 58.130 37.500 0.00 0.00 0.00 3.85
2197 6098 7.979444 TGAAGAAATTGTAGAGGTACTTTGG 57.021 36.000 0.00 0.00 41.55 3.28
2199 6100 8.653191 TGAAGAAATTGTAGAGGTACTTTGGTA 58.347 33.333 0.00 0.00 41.55 3.25
2200 6101 9.498176 GAAGAAATTGTAGAGGTACTTTGGTAA 57.502 33.333 0.00 0.00 41.55 2.85
2255 6164 1.464023 GCGTCAACCACATCATCAACG 60.464 52.381 0.00 0.00 0.00 4.10
2296 6208 7.497595 TCATCATATAAAGTCTTAACGCACCT 58.502 34.615 0.00 0.00 0.00 4.00
2352 6264 3.936203 ACCGAGCTCCGTGGCAAA 61.936 61.111 8.47 0.00 36.31 3.68
2362 6274 2.753966 CGTGGCAAAGGCGGATCTG 61.754 63.158 0.00 0.00 42.47 2.90
2389 6301 0.304705 CGTAGGGTGATGAATTGCGC 59.695 55.000 0.00 0.00 0.00 6.09
2421 6334 3.989787 CCGTGCTTTTGGGTGCCC 61.990 66.667 0.00 0.00 0.00 5.36
2442 6355 4.470764 AGGAGGACCTGAGCTTCC 57.529 61.111 0.00 0.00 45.92 3.46
2444 6357 0.907230 AGGAGGACCTGAGCTTCCAC 60.907 60.000 0.00 0.00 45.92 4.02
2457 6370 3.577334 TTCCACGTTCATGGGGCCC 62.577 63.158 18.17 18.17 40.49 5.80
2458 6371 4.358841 CCACGTTCATGGGGCCCA 62.359 66.667 30.97 30.97 38.19 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.136026 CTAGGGAGGGGGCAACTTATT 58.864 52.381 0.00 0.00 0.00 1.40
1 2 1.297141 TCTAGGGAGGGGGCAACTTAT 59.703 52.381 0.00 0.00 0.00 1.73
2 3 0.720232 TCTAGGGAGGGGGCAACTTA 59.280 55.000 0.00 0.00 0.00 2.24
3 4 0.046397 ATCTAGGGAGGGGGCAACTT 59.954 55.000 0.00 0.00 0.00 2.66
4 5 0.046397 AATCTAGGGAGGGGGCAACT 59.954 55.000 0.00 0.00 0.00 3.16
5 6 1.815757 TAATCTAGGGAGGGGGCAAC 58.184 55.000 0.00 0.00 0.00 4.17
6 7 2.835696 ATAATCTAGGGAGGGGGCAA 57.164 50.000 0.00 0.00 0.00 4.52
7 8 2.184565 AGAATAATCTAGGGAGGGGGCA 59.815 50.000 0.00 0.00 32.88 5.36
8 9 2.922564 AGAATAATCTAGGGAGGGGGC 58.077 52.381 0.00 0.00 32.88 5.80
9 10 6.522631 GCTTTTAGAATAATCTAGGGAGGGGG 60.523 46.154 0.00 0.00 39.29 5.40
10 11 6.477253 GCTTTTAGAATAATCTAGGGAGGGG 58.523 44.000 0.00 0.00 39.29 4.79
11 12 6.273495 AGGCTTTTAGAATAATCTAGGGAGGG 59.727 42.308 0.00 0.00 39.29 4.30
12 13 7.323052 AGGCTTTTAGAATAATCTAGGGAGG 57.677 40.000 0.00 0.00 39.29 4.30
32 33 9.126151 GGCTTCTCTAAAATTTTAGATTAGGCT 57.874 33.333 34.51 10.77 45.67 4.58
33 34 8.903820 TGGCTTCTCTAAAATTTTAGATTAGGC 58.096 33.333 34.77 34.77 45.67 3.93
37 38 9.591792 GCAATGGCTTCTCTAAAATTTTAGATT 57.408 29.630 31.14 21.15 41.43 2.40
56 57 0.526954 CAATGGCTTCGAGCAATGGC 60.527 55.000 8.71 0.00 44.75 4.40
57 58 0.526954 GCAATGGCTTCGAGCAATGG 60.527 55.000 8.71 2.61 44.75 3.16
115 116 3.900601 AGTGGCCACCATAAAATTGTGAA 59.099 39.130 32.29 0.00 35.28 3.18
116 117 3.257873 CAGTGGCCACCATAAAATTGTGA 59.742 43.478 32.29 0.00 35.28 3.58
117 118 3.257873 TCAGTGGCCACCATAAAATTGTG 59.742 43.478 32.29 18.92 35.28 3.33
126 127 2.825532 GTTACAAATCAGTGGCCACCAT 59.174 45.455 32.29 21.21 35.28 3.55
180 181 3.781079 TGATTTCAAACATGATCGCCC 57.219 42.857 0.00 0.00 0.00 6.13
192 1462 9.598517 AATACAAAGCTCAAAGTTTGATTTCAA 57.401 25.926 18.35 7.95 39.30 2.69
224 1494 4.963373 TGACCCTCGAAACATAAAAGACA 58.037 39.130 0.00 0.00 0.00 3.41
227 1497 5.682943 TGTTGACCCTCGAAACATAAAAG 57.317 39.130 0.00 0.00 0.00 2.27
228 1498 6.263392 TCAATGTTGACCCTCGAAACATAAAA 59.737 34.615 11.68 0.67 42.24 1.52
232 1502 3.750371 TCAATGTTGACCCTCGAAACAT 58.250 40.909 6.59 6.59 44.32 2.71
315 1586 0.804989 GATCGTGGAGTTGGCCAAAG 59.195 55.000 22.47 7.80 40.20 2.77
318 1589 1.207089 CTAAGATCGTGGAGTTGGCCA 59.793 52.381 0.00 0.00 35.02 5.36
326 1597 3.640029 GGGGATACAACTAAGATCGTGGA 59.360 47.826 0.00 0.00 39.74 4.02
350 1621 9.653287 CTTTGTTACTCATAGTTCACATCCTAA 57.347 33.333 0.00 0.00 0.00 2.69
365 1636 5.296780 CAGAAGAACCAAGCTTTGTTACTCA 59.703 40.000 15.30 0.00 0.00 3.41
366 1637 5.278022 CCAGAAGAACCAAGCTTTGTTACTC 60.278 44.000 15.30 13.80 0.00 2.59
367 1638 4.580580 CCAGAAGAACCAAGCTTTGTTACT 59.419 41.667 15.30 11.97 0.00 2.24
368 1639 4.578928 TCCAGAAGAACCAAGCTTTGTTAC 59.421 41.667 15.30 10.20 0.00 2.50
369 1640 4.787551 TCCAGAAGAACCAAGCTTTGTTA 58.212 39.130 15.30 0.00 0.00 2.41
370 1641 3.631250 TCCAGAAGAACCAAGCTTTGTT 58.369 40.909 15.25 15.25 0.00 2.83
371 1642 3.297134 TCCAGAAGAACCAAGCTTTGT 57.703 42.857 0.00 0.00 0.00 2.83
372 1643 4.654091 TTTCCAGAAGAACCAAGCTTTG 57.346 40.909 0.00 0.00 32.95 2.77
373 1644 5.187772 AGTTTTTCCAGAAGAACCAAGCTTT 59.812 36.000 0.00 0.00 36.43 3.51
374 1645 4.711846 AGTTTTTCCAGAAGAACCAAGCTT 59.288 37.500 9.47 0.00 36.43 3.74
375 1646 4.281657 AGTTTTTCCAGAAGAACCAAGCT 58.718 39.130 9.47 0.00 36.43 3.74
376 1647 4.655762 AGTTTTTCCAGAAGAACCAAGC 57.344 40.909 9.47 0.00 36.43 4.01
377 1648 8.413229 TGAATTAGTTTTTCCAGAAGAACCAAG 58.587 33.333 9.47 0.00 36.43 3.61
378 1649 8.299990 TGAATTAGTTTTTCCAGAAGAACCAA 57.700 30.769 9.47 4.23 36.43 3.67
379 1650 7.014230 CCTGAATTAGTTTTTCCAGAAGAACCA 59.986 37.037 9.47 0.00 36.43 3.67
380 1651 7.230712 TCCTGAATTAGTTTTTCCAGAAGAACC 59.769 37.037 9.47 0.00 36.43 3.62
381 1652 8.166422 TCCTGAATTAGTTTTTCCAGAAGAAC 57.834 34.615 5.84 5.84 36.14 3.01
382 1653 8.630037 GTTCCTGAATTAGTTTTTCCAGAAGAA 58.370 33.333 0.00 0.00 0.00 2.52
383 1654 7.777910 TGTTCCTGAATTAGTTTTTCCAGAAGA 59.222 33.333 0.00 0.00 0.00 2.87
384 1655 7.862873 GTGTTCCTGAATTAGTTTTTCCAGAAG 59.137 37.037 0.00 0.00 0.00 2.85
385 1656 7.559897 AGTGTTCCTGAATTAGTTTTTCCAGAA 59.440 33.333 0.00 0.00 0.00 3.02
386 1657 7.060421 AGTGTTCCTGAATTAGTTTTTCCAGA 58.940 34.615 0.00 0.00 0.00 3.86
387 1658 7.277174 AGTGTTCCTGAATTAGTTTTTCCAG 57.723 36.000 0.00 0.00 0.00 3.86
388 1659 6.264518 GGAGTGTTCCTGAATTAGTTTTTCCA 59.735 38.462 0.00 0.00 40.58 3.53
389 1660 6.294564 GGGAGTGTTCCTGAATTAGTTTTTCC 60.295 42.308 0.00 0.00 43.49 3.13
390 1661 6.490381 AGGGAGTGTTCCTGAATTAGTTTTTC 59.510 38.462 0.00 0.00 43.49 2.29
395 1666 3.519913 GGAGGGAGTGTTCCTGAATTAGT 59.480 47.826 0.00 0.00 43.49 2.24
402 1673 1.263356 TTACGGAGGGAGTGTTCCTG 58.737 55.000 0.00 0.00 43.49 3.86
404 1675 3.345508 AATTTACGGAGGGAGTGTTCC 57.654 47.619 0.00 0.00 43.23 3.62
405 1676 9.768662 TTATATTAATTTACGGAGGGAGTGTTC 57.231 33.333 0.00 0.00 0.00 3.18
406 1677 9.774413 CTTATATTAATTTACGGAGGGAGTGTT 57.226 33.333 0.00 0.00 0.00 3.32
407 1678 9.151177 TCTTATATTAATTTACGGAGGGAGTGT 57.849 33.333 0.00 0.00 0.00 3.55
408 1679 9.640963 CTCTTATATTAATTTACGGAGGGAGTG 57.359 37.037 0.00 0.00 0.00 3.51
409 1680 8.312564 GCTCTTATATTAATTTACGGAGGGAGT 58.687 37.037 0.00 0.00 0.00 3.85
410 1681 7.488471 CGCTCTTATATTAATTTACGGAGGGAG 59.512 40.741 17.02 0.00 34.63 4.30
411 1682 7.039504 ACGCTCTTATATTAATTTACGGAGGGA 60.040 37.037 22.59 0.00 35.94 4.20
412 1683 7.095270 ACGCTCTTATATTAATTTACGGAGGG 58.905 38.462 18.58 18.58 37.30 4.30
413 1684 8.530269 AACGCTCTTATATTAATTTACGGAGG 57.470 34.615 0.00 0.00 0.00 4.30
425 1696 9.765795 AGCATTTACTCTAAACGCTCTTATATT 57.234 29.630 0.00 0.00 42.77 1.28
445 1716 9.490379 CCTCCGTAAACTAATATAAGAGCATTT 57.510 33.333 0.00 0.00 0.00 2.32
446 1717 8.095169 CCCTCCGTAAACTAATATAAGAGCATT 58.905 37.037 0.00 0.00 0.00 3.56
447 1718 7.453752 TCCCTCCGTAAACTAATATAAGAGCAT 59.546 37.037 0.00 0.00 0.00 3.79
448 1719 6.779049 TCCCTCCGTAAACTAATATAAGAGCA 59.221 38.462 0.00 0.00 0.00 4.26
449 1720 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
450 1721 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
451 1722 9.512588 CTACTCCCTCCGTAAACTAATATAAGA 57.487 37.037 0.00 0.00 0.00 2.10
452 1723 9.294614 ACTACTCCCTCCGTAAACTAATATAAG 57.705 37.037 0.00 0.00 0.00 1.73
453 1724 9.646522 AACTACTCCCTCCGTAAACTAATATAA 57.353 33.333 0.00 0.00 0.00 0.98
454 1725 9.071276 CAACTACTCCCTCCGTAAACTAATATA 57.929 37.037 0.00 0.00 0.00 0.86
455 1726 7.471120 GCAACTACTCCCTCCGTAAACTAATAT 60.471 40.741 0.00 0.00 0.00 1.28
456 1727 6.183360 GCAACTACTCCCTCCGTAAACTAATA 60.183 42.308 0.00 0.00 0.00 0.98
457 1728 5.394993 GCAACTACTCCCTCCGTAAACTAAT 60.395 44.000 0.00 0.00 0.00 1.73
458 1729 4.082026 GCAACTACTCCCTCCGTAAACTAA 60.082 45.833 0.00 0.00 0.00 2.24
459 1730 3.445096 GCAACTACTCCCTCCGTAAACTA 59.555 47.826 0.00 0.00 0.00 2.24
460 1731 2.233186 GCAACTACTCCCTCCGTAAACT 59.767 50.000 0.00 0.00 0.00 2.66
461 1732 2.028748 TGCAACTACTCCCTCCGTAAAC 60.029 50.000 0.00 0.00 0.00 2.01
462 1733 2.250031 TGCAACTACTCCCTCCGTAAA 58.750 47.619 0.00 0.00 0.00 2.01
463 1734 1.927487 TGCAACTACTCCCTCCGTAA 58.073 50.000 0.00 0.00 0.00 3.18
464 1735 2.154567 ATGCAACTACTCCCTCCGTA 57.845 50.000 0.00 0.00 0.00 4.02
465 1736 1.066143 CAATGCAACTACTCCCTCCGT 60.066 52.381 0.00 0.00 0.00 4.69
466 1737 1.656652 CAATGCAACTACTCCCTCCG 58.343 55.000 0.00 0.00 0.00 4.63
467 1738 1.282157 ACCAATGCAACTACTCCCTCC 59.718 52.381 0.00 0.00 0.00 4.30
468 1739 2.359900 CACCAATGCAACTACTCCCTC 58.640 52.381 0.00 0.00 0.00 4.30
469 1740 2.496899 CACCAATGCAACTACTCCCT 57.503 50.000 0.00 0.00 0.00 4.20
482 1753 0.413037 TTCTCCCCAATGGCACCAAT 59.587 50.000 0.00 0.00 0.00 3.16
508 1779 6.992123 TGGAAGCATACAAGTGATGGTATTAG 59.008 38.462 0.00 0.00 34.01 1.73
517 1788 5.104569 TGGTATCATGGAAGCATACAAGTGA 60.105 40.000 0.00 0.00 0.00 3.41
577 1848 7.029563 GGCTAGACAAACAATGAAACCAATAG 58.970 38.462 0.00 0.00 0.00 1.73
578 1849 6.491745 TGGCTAGACAAACAATGAAACCAATA 59.508 34.615 0.00 0.00 0.00 1.90
579 1850 5.304101 TGGCTAGACAAACAATGAAACCAAT 59.696 36.000 0.00 0.00 0.00 3.16
580 1851 4.646945 TGGCTAGACAAACAATGAAACCAA 59.353 37.500 0.00 0.00 0.00 3.67
581 1852 4.211125 TGGCTAGACAAACAATGAAACCA 58.789 39.130 0.00 0.00 0.00 3.67
582 1853 4.278419 ACTGGCTAGACAAACAATGAAACC 59.722 41.667 3.17 0.00 0.00 3.27
584 1855 6.017440 GTGTACTGGCTAGACAAACAATGAAA 60.017 38.462 13.60 0.00 0.00 2.69
586 1857 4.994852 GTGTACTGGCTAGACAAACAATGA 59.005 41.667 13.60 0.00 0.00 2.57
606 1878 1.094785 ACTTGCGCTTGAAGTTGTGT 58.905 45.000 9.73 0.00 28.94 3.72
713 1986 1.212195 GGGCCGGACCTTATCTTCTTT 59.788 52.381 23.07 0.00 39.10 2.52
719 1992 1.375326 GATGGGGCCGGACCTTATC 59.625 63.158 29.76 25.43 39.10 1.75
736 2009 4.040755 CTCCTCCTCTGATTTTAAGGGGA 58.959 47.826 0.00 0.00 42.27 4.81
795 2068 4.038042 CCGTGCTCTCACTTTATCCTATGA 59.962 45.833 0.00 0.00 40.99 2.15
797 2070 4.215908 TCCGTGCTCTCACTTTATCCTAT 58.784 43.478 0.00 0.00 40.99 2.57
804 2077 1.895798 TCTCATCCGTGCTCTCACTTT 59.104 47.619 0.00 0.00 40.99 2.66
810 2083 0.104487 CATGCTCTCATCCGTGCTCT 59.896 55.000 0.00 0.00 0.00 4.09
822 2095 1.307691 AGCTCCTTCCCCATGCTCT 60.308 57.895 0.00 0.00 0.00 4.09
998 2271 1.377725 AGCAGCGGGTTCTCCATTG 60.378 57.895 0.00 0.00 34.36 2.82
1382 3457 0.679505 CCTGACGAAGGTCCTGAACA 59.320 55.000 0.00 0.00 42.73 3.18
1440 3515 2.234913 ATTACCCTCCACGACCACGC 62.235 60.000 0.00 0.00 43.96 5.34
1441 3516 0.459585 CATTACCCTCCACGACCACG 60.460 60.000 0.00 0.00 45.75 4.94
1442 3517 0.611714 ACATTACCCTCCACGACCAC 59.388 55.000 0.00 0.00 0.00 4.16
1443 3518 0.611200 CACATTACCCTCCACGACCA 59.389 55.000 0.00 0.00 0.00 4.02
1444 3519 0.107848 CCACATTACCCTCCACGACC 60.108 60.000 0.00 0.00 0.00 4.79
1445 3520 0.743345 GCCACATTACCCTCCACGAC 60.743 60.000 0.00 0.00 0.00 4.34
1514 3595 2.624838 AGAGCAAACAACATGACAAGGG 59.375 45.455 0.00 0.00 0.00 3.95
1608 3689 5.645929 ACACCACCAAACAAAAGAAAATTCC 59.354 36.000 0.00 0.00 0.00 3.01
1735 3819 7.812669 AGTTAAATTGAACACGATTCAAATCCC 59.187 33.333 18.69 9.55 41.16 3.85
1766 3850 8.889000 GCTAAAACAAAATAAGTAACACGTGAG 58.111 33.333 25.01 3.10 0.00 3.51
1854 3938 8.904963 ACCCAGAATATAAGGGATGTGAAATAT 58.095 33.333 12.60 0.00 45.80 1.28
1953 5851 2.612672 GAGAAGCGGTATAACAAAGCCC 59.387 50.000 0.00 0.00 0.00 5.19
2056 5955 6.255294 TGGAATAGTGAATTCGGGGATTTA 57.745 37.500 0.04 0.00 44.32 1.40
2114 6013 1.803453 ATGATGGTGGTGGTGGCCTT 61.803 55.000 3.32 0.00 0.00 4.35
2143 6044 8.293867 TCAAGGTTACCAAATAACTTCATTTCG 58.706 33.333 3.51 0.00 42.58 3.46
2147 6048 6.948309 AGCTCAAGGTTACCAAATAACTTCAT 59.052 34.615 3.51 0.00 42.58 2.57
2151 6052 6.303839 TCAAGCTCAAGGTTACCAAATAACT 58.696 36.000 3.51 0.00 42.58 2.24
2153 6054 7.001674 TCTTCAAGCTCAAGGTTACCAAATAA 58.998 34.615 3.51 0.00 33.98 1.40
2155 6056 5.385198 TCTTCAAGCTCAAGGTTACCAAAT 58.615 37.500 3.51 0.00 33.98 2.32
2197 6098 1.074889 TCCTCCTTGCCTTGGGTTTAC 59.925 52.381 0.00 0.00 0.00 2.01
2199 6100 0.113190 CTCCTCCTTGCCTTGGGTTT 59.887 55.000 0.00 0.00 0.00 3.27
2200 6101 1.770324 CTCCTCCTTGCCTTGGGTT 59.230 57.895 0.00 0.00 0.00 4.11
2283 6192 1.069906 CAACTGCAGGTGCGTTAAGAC 60.070 52.381 20.78 0.00 45.83 3.01
2356 6268 5.014858 TCACCCTACGGATATTACAGATCC 58.985 45.833 0.00 0.00 39.71 3.36
2362 6274 6.092259 GCAATTCATCACCCTACGGATATTAC 59.908 42.308 0.00 0.00 0.00 1.89
2373 6285 2.114670 CGGCGCAATTCATCACCCT 61.115 57.895 10.83 0.00 0.00 4.34
2434 6347 0.321564 CCCATGAACGTGGAAGCTCA 60.322 55.000 13.85 0.00 42.02 4.26
2436 6349 1.002134 CCCCATGAACGTGGAAGCT 60.002 57.895 13.85 0.00 42.02 3.74


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

AutoCloner maintained by Alex Coulton.