Multiple sequence alignment - TraesCS6D01G063300

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 TraesCS6D01G063300 chr6D 100.000 2605 0 0 1 2605 29755896 29758500 0.000000e+00 4811.0
1 TraesCS6D01G063300 chr6D 88.275 597 47 10 835 1429 28708330 28707755 0.000000e+00 693.0
2 TraesCS6D01G063300 chr6B 85.536 1680 141 54 184 1819 58058600 58056979 0.000000e+00 1663.0
3 TraesCS6D01G063300 chr6B 88.849 556 41 14 885 1429 59588530 59587985 0.000000e+00 664.0
4 TraesCS6D01G063300 chr6B 85.860 587 58 18 850 1424 50459250 50459823 3.710000e-168 601.0
5 TraesCS6D01G063300 chr6B 84.448 553 67 11 870 1419 49596229 49596765 6.390000e-146 527.0
6 TraesCS6D01G063300 chr6B 89.474 190 16 4 2 189 58074747 58074560 1.210000e-58 237.0
7 TraesCS6D01G063300 chr6B 80.303 330 35 15 183 486 58059569 58059244 3.370000e-54 222.0
8 TraesCS6D01G063300 chr6B 77.062 388 63 18 2192 2562 79040167 79039789 1.580000e-47 200.0
9 TraesCS6D01G063300 chr6B 83.568 213 16 6 1888 2100 58056289 58056482 5.730000e-42 182.0
10 TraesCS6D01G063300 chr6A 85.854 1223 82 39 813 1993 32913848 32912675 0.000000e+00 1216.0
11 TraesCS6D01G063300 chr6A 92.702 781 53 4 1 781 32917229 32916453 0.000000e+00 1123.0
12 TraesCS6D01G063300 chr6A 90.570 456 34 4 2156 2603 32910190 32909736 1.730000e-166 595.0
13 TraesCS6D01G063300 chr6A 87.547 530 39 17 1093 1613 28641030 28641541 2.890000e-164 588.0
14 TraesCS6D01G063300 chr6A 86.759 506 34 18 1110 1611 29081969 29082445 1.370000e-147 532.0
15 TraesCS6D01G063300 chr6A 94.737 57 3 0 2044 2100 32912651 32912595 3.570000e-14 89.8
16 TraesCS6D01G063300 chrUn 86.418 589 50 19 850 1424 137920060 137920632 3.680000e-173 617.0
17 TraesCS6D01G063300 chrUn 84.186 645 47 36 1096 1720 103772116 103771507 2.250000e-160 575.0
18 TraesCS6D01G063300 chr7B 86.782 522 52 16 1097 1611 589740537 589740026 1.350000e-157 566.0
19 TraesCS6D01G063300 chr5B 90.308 227 19 3 1555 1780 22518878 22519102 7.050000e-76 294.0
20 TraesCS6D01G063300 chr4A 85.470 234 23 4 1555 1779 720300214 720300445 1.560000e-57 233.0


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 TraesCS6D01G063300 chr6D 29755896 29758500 2604 False 4811.00 4811 100.00000 1 2605 1 chr6D.!!$F1 2604
1 TraesCS6D01G063300 chr6D 28707755 28708330 575 True 693.00 693 88.27500 835 1429 1 chr6D.!!$R1 594
2 TraesCS6D01G063300 chr6B 58056979 58059569 2590 True 942.50 1663 82.91950 183 1819 2 chr6B.!!$R4 1636
3 TraesCS6D01G063300 chr6B 59587985 59588530 545 True 664.00 664 88.84900 885 1429 1 chr6B.!!$R2 544
4 TraesCS6D01G063300 chr6B 50459250 50459823 573 False 601.00 601 85.86000 850 1424 1 chr6B.!!$F2 574
5 TraesCS6D01G063300 chr6B 49596229 49596765 536 False 527.00 527 84.44800 870 1419 1 chr6B.!!$F1 549
6 TraesCS6D01G063300 chr6A 32909736 32917229 7493 True 755.95 1216 90.96575 1 2603 4 chr6A.!!$R1 2602
7 TraesCS6D01G063300 chr6A 28641030 28641541 511 False 588.00 588 87.54700 1093 1613 1 chr6A.!!$F1 520
8 TraesCS6D01G063300 chrUn 137920060 137920632 572 False 617.00 617 86.41800 850 1424 1 chrUn.!!$F1 574
9 TraesCS6D01G063300 chrUn 103771507 103772116 609 True 575.00 575 84.18600 1096 1720 1 chrUn.!!$R1 624
10 TraesCS6D01G063300 chr7B 589740026 589740537 511 True 566.00 566 86.78200 1097 1611 1 chr7B.!!$R1 514

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
86 87 0.108804 TCCGGATGCGACAGTCTTTC 60.109 55.0 8.71 0.0 0.0 2.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1928 5588 0.037605 CTACTCCACCGGACCAACAC 60.038 60.0 9.46 0.0 0.0 3.32 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
31 32 2.754552 TCCAAGTTGCATGGCTATTCAC 59.245 45.455 0.00 0.00 37.88 3.18
69 70 0.545646 ATGGCTCTCTTCCAGCTTCC 59.454 55.000 0.00 0.00 36.98 3.46
86 87 0.108804 TCCGGATGCGACAGTCTTTC 60.109 55.000 8.71 0.00 0.00 2.62
101 102 3.070302 AGTCTTTCTGTCCGCTTCTTCTT 59.930 43.478 0.00 0.00 0.00 2.52
102 103 3.430556 GTCTTTCTGTCCGCTTCTTCTTC 59.569 47.826 0.00 0.00 0.00 2.87
119 120 3.716006 CGTGTGGTGAAGCGGCTG 61.716 66.667 1.81 0.00 0.00 4.85
148 149 2.820197 GTTGGCCTCTTGGTCTTTAAGG 59.180 50.000 3.32 0.00 39.11 2.69
163 164 3.314541 TTAAGGTTCTCGTTGAGGAGC 57.685 47.619 0.00 0.00 36.04 4.70
195 196 2.125512 ATGTGCTTCCGTCGAGGC 60.126 61.111 0.00 0.00 41.36 4.70
260 261 1.954362 AAGTAGCTGCAGAGGAGCCG 61.954 60.000 20.43 0.00 37.12 5.52
301 303 2.993853 GGAGAGCCAAGGGGACAG 59.006 66.667 0.00 0.00 35.59 3.51
302 304 1.920835 GGAGAGCCAAGGGGACAGT 60.921 63.158 0.00 0.00 35.59 3.55
333 360 2.171448 CGGATTCTGGGAAGTTCAGGAT 59.829 50.000 5.01 0.00 33.41 3.24
415 442 4.035102 GGGTTGGGCCGAAGAGCT 62.035 66.667 0.00 0.00 38.44 4.09
443 1430 3.129502 CGGTGGCGAGGTCGTCTA 61.130 66.667 5.47 0.00 45.41 2.59
466 1453 2.703536 TCGCCCCTCAATCTATTTGCTA 59.296 45.455 0.00 0.00 35.16 3.49
514 1501 5.517411 CGCGGTGTGAATGAAAGTACTTATA 59.483 40.000 8.92 1.19 0.00 0.98
566 1553 8.073467 AGGATTAATTGGGAAAATAAAAGCGA 57.927 30.769 0.00 0.00 0.00 4.93
585 1572 2.223641 CGATCGGATTGGAACTAACGGA 60.224 50.000 7.38 0.00 0.00 4.69
587 1574 1.894466 TCGGATTGGAACTAACGGACA 59.106 47.619 0.00 0.00 0.00 4.02
628 1615 4.775780 ACCTGTGCAGTAATACTTGGACTA 59.224 41.667 12.57 3.36 0.00 2.59
636 1623 6.127423 GCAGTAATACTTGGACTACAGAGGAA 60.127 42.308 0.00 0.00 0.00 3.36
641 1628 1.835494 TGGACTACAGAGGAACCGAG 58.165 55.000 0.00 0.00 0.00 4.63
660 1647 1.750399 CCCATTCCAACTGGAGCGG 60.750 63.158 0.00 3.85 46.36 5.52
668 1655 0.745845 CAACTGGAGCGGGGATTCAG 60.746 60.000 0.00 0.00 0.00 3.02
671 1658 1.615124 TGGAGCGGGGATTCAGGAA 60.615 57.895 0.00 0.00 0.00 3.36
672 1659 1.147153 GGAGCGGGGATTCAGGAAG 59.853 63.158 0.00 0.00 0.00 3.46
675 1662 0.698818 AGCGGGGATTCAGGAAGTTT 59.301 50.000 0.00 0.00 0.00 2.66
677 1664 1.613255 GCGGGGATTCAGGAAGTTTGA 60.613 52.381 0.00 0.00 0.00 2.69
678 1665 2.359900 CGGGGATTCAGGAAGTTTGAG 58.640 52.381 0.00 0.00 0.00 3.02
679 1666 2.728007 GGGGATTCAGGAAGTTTGAGG 58.272 52.381 0.00 0.00 0.00 3.86
680 1667 2.621668 GGGGATTCAGGAAGTTTGAGGG 60.622 54.545 0.00 0.00 0.00 4.30
682 1669 3.348119 GGATTCAGGAAGTTTGAGGGTC 58.652 50.000 0.00 0.00 0.00 4.46
685 1672 3.771577 TCAGGAAGTTTGAGGGTCTTC 57.228 47.619 0.00 0.00 37.44 2.87
727 1718 4.274950 AGTTTCGTGTTTTGAGTATGTGGG 59.725 41.667 0.00 0.00 0.00 4.61
788 3728 9.057089 CCAAACTTATGATTAGGTTGATAGTCC 57.943 37.037 10.51 0.00 41.73 3.85
792 3732 8.938883 ACTTATGATTAGGTTGATAGTCCATGT 58.061 33.333 0.00 0.00 0.00 3.21
829 4394 7.567250 TGTATCAGTTTAGTGGAATCCATAGGA 59.433 37.037 4.81 0.00 35.28 2.94
955 4533 1.837439 ACCATCTTAGCCGTCCAATCA 59.163 47.619 0.00 0.00 0.00 2.57
980 4558 2.434884 ATCCAACGGCAGACTGCG 60.435 61.111 20.82 17.46 46.21 5.18
1007 4594 2.457126 ACCCCTTGTTAAATCCCCCTTT 59.543 45.455 0.00 0.00 0.00 3.11
1062 4654 3.775654 CCACCGCTCCTCCTCCAC 61.776 72.222 0.00 0.00 0.00 4.02
1063 4655 3.775654 CACCGCTCCTCCTCCACC 61.776 72.222 0.00 0.00 0.00 4.61
1088 4687 3.421919 TCCAAATCACACATCAGCTCA 57.578 42.857 0.00 0.00 0.00 4.26
1372 4980 3.063704 ACCGCCATGGACGTCGTA 61.064 61.111 18.40 1.05 42.00 3.43
1467 5079 1.375523 GTCTCGCACCACCGGATTT 60.376 57.895 9.46 0.00 0.00 2.17
1492 5105 1.162698 AGTAGCTACGCGTTGTCTGA 58.837 50.000 20.78 0.00 0.00 3.27
1614 5238 4.638865 AGCATTTTACCCCTGAATTCGTAC 59.361 41.667 0.04 0.00 0.00 3.67
1626 5250 4.426416 TGAATTCGTACGTAATCTGTGGG 58.574 43.478 16.05 0.00 0.00 4.61
1643 5267 2.032030 GTGGGTCTGTCGATGTTTGTTG 60.032 50.000 0.00 0.00 0.00 3.33
1651 5278 2.020720 TCGATGTTTGTTGGTGCTTGT 58.979 42.857 0.00 0.00 0.00 3.16
1657 5284 0.814457 TTGTTGGTGCTTGTGGTCAC 59.186 50.000 0.00 0.00 0.00 3.67
1675 5302 3.930229 GTCACATATTACCAGTGCGTTCA 59.070 43.478 0.00 0.00 33.44 3.18
1681 5336 6.318648 ACATATTACCAGTGCGTTCATCAATT 59.681 34.615 0.00 0.00 0.00 2.32
1682 5337 4.678509 TTACCAGTGCGTTCATCAATTC 57.321 40.909 0.00 0.00 0.00 2.17
1730 5385 0.321346 CCCCCAAATCCTGTTTGTGC 59.679 55.000 0.55 0.00 0.00 4.57
1739 5394 0.746063 CCTGTTTGTGCTGGCTTCAA 59.254 50.000 0.00 0.00 0.00 2.69
1755 5410 4.240096 GCTTCAATGTTTGGTGGATTCTG 58.760 43.478 0.00 0.00 0.00 3.02
1788 5443 6.272318 TCTTATTTTGTTGGCTTCAGTGTTG 58.728 36.000 0.00 0.00 0.00 3.33
1789 5444 4.734398 ATTTTGTTGGCTTCAGTGTTGA 57.266 36.364 0.00 0.00 0.00 3.18
1816 5474 0.036022 AGGCTGAAGAAGGTCAGTGC 59.964 55.000 4.28 0.00 45.75 4.40
1837 5495 2.623416 CTGGGAGTTGTTTTGTTCCTCC 59.377 50.000 0.00 0.00 40.81 4.30
1848 5506 2.672961 TGTTCCTCCATCGTGATGTC 57.327 50.000 8.89 0.00 37.11 3.06
1879 5539 2.042464 TGCTGGAGTTATCCCTAGCTG 58.958 52.381 0.00 0.00 46.04 4.24
1880 5540 2.320781 GCTGGAGTTATCCCTAGCTGA 58.679 52.381 0.00 0.00 46.04 4.26
1884 5544 5.546526 CTGGAGTTATCCCTAGCTGAAATC 58.453 45.833 0.00 0.00 46.04 2.17
1888 5548 6.408662 GGAGTTATCCCTAGCTGAAATCTGTT 60.409 42.308 0.00 0.00 40.03 3.16
1889 5549 6.963322 AGTTATCCCTAGCTGAAATCTGTTT 58.037 36.000 0.00 0.00 0.00 2.83
1890 5550 6.825721 AGTTATCCCTAGCTGAAATCTGTTTG 59.174 38.462 0.00 0.00 0.00 2.93
1907 5567 2.654749 TTGAGCTACCTGTGATGTCG 57.345 50.000 0.00 0.00 0.00 4.35
1920 5580 1.866601 TGATGTCGAACTTGTGCAGTG 59.133 47.619 0.00 0.00 35.12 3.66
1936 5596 2.515057 TGTGTGCCCGTGTTGGTC 60.515 61.111 0.00 0.00 35.15 4.02
1938 5598 4.920112 TGTGCCCGTGTTGGTCCG 62.920 66.667 0.00 0.00 35.15 4.79
1993 5655 5.294799 TGTTTTGTTGTGACTTGCGTACTAT 59.705 36.000 0.00 0.00 0.00 2.12
1994 5656 5.585500 TTTGTTGTGACTTGCGTACTATC 57.415 39.130 0.00 0.00 0.00 2.08
1995 5657 4.245845 TGTTGTGACTTGCGTACTATCA 57.754 40.909 0.00 0.00 0.00 2.15
1996 5658 4.623002 TGTTGTGACTTGCGTACTATCAA 58.377 39.130 0.00 0.00 0.00 2.57
1997 5659 4.684242 TGTTGTGACTTGCGTACTATCAAG 59.316 41.667 14.04 14.04 43.79 3.02
2007 5669 8.782533 CTTGCGTACTATCAAGTTTTTCTTTT 57.217 30.769 9.73 0.00 37.15 2.27
2008 5670 8.555166 TTGCGTACTATCAAGTTTTTCTTTTG 57.445 30.769 0.00 0.00 37.15 2.44
2009 5671 7.136119 TGCGTACTATCAAGTTTTTCTTTTGG 58.864 34.615 0.00 0.00 37.15 3.28
2010 5672 6.581166 GCGTACTATCAAGTTTTTCTTTTGGG 59.419 38.462 0.00 0.00 37.15 4.12
2011 5673 6.581166 CGTACTATCAAGTTTTTCTTTTGGGC 59.419 38.462 0.00 0.00 37.15 5.36
2012 5674 5.528870 ACTATCAAGTTTTTCTTTTGGGCG 58.471 37.500 0.00 0.00 33.63 6.13
2013 5675 3.878160 TCAAGTTTTTCTTTTGGGCGT 57.122 38.095 0.00 0.00 33.63 5.68
2014 5676 3.516615 TCAAGTTTTTCTTTTGGGCGTG 58.483 40.909 0.00 0.00 33.63 5.34
2015 5677 3.056465 TCAAGTTTTTCTTTTGGGCGTGT 60.056 39.130 0.00 0.00 33.63 4.49
2021 5683 5.461032 TTTTCTTTTGGGCGTGTTATCAT 57.539 34.783 0.00 0.00 0.00 2.45
2034 5696 6.905076 GGCGTGTTATCATGTTATTAGTGTTG 59.095 38.462 0.00 0.00 33.51 3.33
2035 5697 6.410914 GCGTGTTATCATGTTATTAGTGTTGC 59.589 38.462 0.00 0.00 33.51 4.17
2036 5698 7.676338 GCGTGTTATCATGTTATTAGTGTTGCT 60.676 37.037 0.00 0.00 33.51 3.91
2037 5699 7.635973 CGTGTTATCATGTTATTAGTGTTGCTG 59.364 37.037 0.00 0.00 0.00 4.41
2038 5700 8.664798 GTGTTATCATGTTATTAGTGTTGCTGA 58.335 33.333 0.00 0.00 0.00 4.26
2039 5701 9.394767 TGTTATCATGTTATTAGTGTTGCTGAT 57.605 29.630 0.00 0.00 0.00 2.90
2040 5702 9.655769 GTTATCATGTTATTAGTGTTGCTGATG 57.344 33.333 0.00 0.00 0.00 3.07
2041 5703 9.612066 TTATCATGTTATTAGTGTTGCTGATGA 57.388 29.630 0.00 0.00 0.00 2.92
2042 5704 8.687292 ATCATGTTATTAGTGTTGCTGATGAT 57.313 30.769 0.00 0.00 0.00 2.45
2043 5705 8.510243 TCATGTTATTAGTGTTGCTGATGATT 57.490 30.769 0.00 0.00 0.00 2.57
2045 5707 7.087409 TGTTATTAGTGTTGCTGATGATTGG 57.913 36.000 0.00 0.00 0.00 3.16
2046 5708 6.658816 TGTTATTAGTGTTGCTGATGATTGGT 59.341 34.615 0.00 0.00 0.00 3.67
2047 5709 5.571784 ATTAGTGTTGCTGATGATTGGTG 57.428 39.130 0.00 0.00 0.00 4.17
2048 5710 3.144657 AGTGTTGCTGATGATTGGTGA 57.855 42.857 0.00 0.00 0.00 4.02
2049 5711 3.693807 AGTGTTGCTGATGATTGGTGAT 58.306 40.909 0.00 0.00 0.00 3.06
2050 5712 3.442625 AGTGTTGCTGATGATTGGTGATG 59.557 43.478 0.00 0.00 0.00 3.07
2051 5713 3.192001 GTGTTGCTGATGATTGGTGATGT 59.808 43.478 0.00 0.00 0.00 3.06
2052 5714 4.395854 GTGTTGCTGATGATTGGTGATGTA 59.604 41.667 0.00 0.00 0.00 2.29
2100 5762 3.427528 GTGAAATGTTGCTGCTGTTCATG 59.572 43.478 0.00 0.00 0.00 3.07
2102 5764 4.277921 TGAAATGTTGCTGCTGTTCATGTA 59.722 37.500 0.00 0.00 0.00 2.29
2103 5765 3.837213 ATGTTGCTGCTGTTCATGTAC 57.163 42.857 0.00 0.00 0.00 2.90
2104 5766 2.570135 TGTTGCTGCTGTTCATGTACA 58.430 42.857 4.99 4.99 0.00 2.90
2108 5770 5.163733 TGTTGCTGCTGTTCATGTACATATG 60.164 40.000 8.32 0.00 0.00 1.78
2109 5771 4.768583 TGCTGCTGTTCATGTACATATGA 58.231 39.130 10.38 0.99 35.38 2.15
2110 5772 4.812626 TGCTGCTGTTCATGTACATATGAG 59.187 41.667 10.38 3.78 38.25 2.90
2113 5775 5.184711 TGCTGTTCATGTACATATGAGCAA 58.815 37.500 20.33 6.23 44.17 3.91
2116 5778 6.063640 TGTTCATGTACATATGAGCAATGC 57.936 37.500 10.38 0.00 42.68 3.56
2117 5779 5.824097 TGTTCATGTACATATGAGCAATGCT 59.176 36.000 7.79 7.79 42.68 3.79
2118 5780 6.991531 TGTTCATGTACATATGAGCAATGCTA 59.008 34.615 8.12 0.00 42.68 3.49
2120 5782 6.523840 TCATGTACATATGAGCAATGCTACA 58.476 36.000 8.12 7.52 39.88 2.74
2121 5783 6.424812 TCATGTACATATGAGCAATGCTACAC 59.575 38.462 8.12 0.00 39.88 2.90
2122 5784 5.669477 TGTACATATGAGCAATGCTACACA 58.331 37.500 8.12 2.05 39.88 3.72
2125 5787 6.791887 ACATATGAGCAATGCTACACATAC 57.208 37.500 8.12 0.00 39.88 2.39
2126 5788 5.406477 ACATATGAGCAATGCTACACATACG 59.594 40.000 8.12 7.31 39.88 3.06
2127 5789 2.549926 TGAGCAATGCTACACATACGG 58.450 47.619 8.12 0.00 39.88 4.02
2129 5791 0.307760 GCAATGCTACACATACGGGC 59.692 55.000 0.00 0.00 38.34 6.13
2131 5793 1.867233 CAATGCTACACATACGGGCTC 59.133 52.381 0.00 0.00 38.34 4.70
2132 5794 0.393077 ATGCTACACATACGGGCTCC 59.607 55.000 0.00 0.00 37.17 4.70
2135 5797 1.134491 GCTACACATACGGGCTCCTTT 60.134 52.381 0.00 0.00 0.00 3.11
2138 5800 3.706600 ACACATACGGGCTCCTTTTTA 57.293 42.857 0.00 0.00 0.00 1.52
2141 5803 3.315191 CACATACGGGCTCCTTTTTATGG 59.685 47.826 0.00 0.00 0.00 2.74
2143 5805 0.996583 ACGGGCTCCTTTTTATGGGA 59.003 50.000 0.00 0.00 0.00 4.37
2144 5806 1.569072 ACGGGCTCCTTTTTATGGGAT 59.431 47.619 0.00 0.00 0.00 3.85
2145 5807 2.230660 CGGGCTCCTTTTTATGGGATC 58.769 52.381 0.00 0.00 0.00 3.36
2147 5809 3.642141 GGGCTCCTTTTTATGGGATCAA 58.358 45.455 0.00 0.00 0.00 2.57
2148 5810 3.384789 GGGCTCCTTTTTATGGGATCAAC 59.615 47.826 0.00 0.00 0.00 3.18
2149 5811 3.066760 GGCTCCTTTTTATGGGATCAACG 59.933 47.826 0.00 0.00 0.00 4.10
2150 5812 3.066760 GCTCCTTTTTATGGGATCAACGG 59.933 47.826 0.00 0.00 0.00 4.44
2152 5814 4.523083 TCCTTTTTATGGGATCAACGGAG 58.477 43.478 0.00 0.00 0.00 4.63
2153 5815 4.226394 TCCTTTTTATGGGATCAACGGAGA 59.774 41.667 0.00 0.00 0.00 3.71
2154 5816 4.947388 CCTTTTTATGGGATCAACGGAGAA 59.053 41.667 0.00 0.00 0.00 2.87
2169 8180 2.731027 CGGAGAAGCAAATTTTACCCGC 60.731 50.000 0.00 0.00 0.00 6.13
2170 8181 2.515912 GAGAAGCAAATTTTACCCGCG 58.484 47.619 0.00 0.00 0.00 6.46
2171 8182 1.201414 AGAAGCAAATTTTACCCGCGG 59.799 47.619 21.04 21.04 0.00 6.46
2172 8183 0.963225 AAGCAAATTTTACCCGCGGT 59.037 45.000 26.12 14.84 40.16 5.68
2226 8238 4.109050 GGCAAATTTTTGACTTCACGTGA 58.891 39.130 15.76 15.76 42.91 4.35
2273 8291 2.172293 GCCCCATTGCCATCCATAAAAA 59.828 45.455 0.00 0.00 0.00 1.94
2274 8292 3.745163 GCCCCATTGCCATCCATAAAAAG 60.745 47.826 0.00 0.00 0.00 2.27
2275 8293 3.455543 CCCCATTGCCATCCATAAAAAGT 59.544 43.478 0.00 0.00 0.00 2.66
2309 8328 8.922058 AGTATTGCACATCAATTTCAGATTTC 57.078 30.769 0.00 0.00 42.48 2.17
2312 8331 7.608153 ATTGCACATCAATTTCAGATTTCTGA 58.392 30.769 6.17 6.17 44.98 3.27
2342 8361 8.648097 CATTGAGCATTTATACGGATACACTAC 58.352 37.037 0.00 0.00 0.00 2.73
2403 8422 7.571919 AGAATTCTGAGAGGCATATCAAAGAA 58.428 34.615 7.30 0.00 31.52 2.52
2447 8466 2.037511 CAGGTGGGAACGGTACTACAAA 59.962 50.000 0.09 0.00 0.00 2.83
2455 8474 5.471116 GGGAACGGTACTACAAAATCAAGTT 59.529 40.000 0.00 0.00 0.00 2.66
2500 8519 2.912956 AGAGTCCAACTCCAAGGCATTA 59.087 45.455 3.54 0.00 46.18 1.90
2540 8559 0.037975 CCAGGAAGCATGCAACAACC 60.038 55.000 21.98 14.42 0.00 3.77
2545 8564 3.056607 AGGAAGCATGCAACAACCAATAC 60.057 43.478 21.98 0.00 0.00 1.89
2572 8591 8.983702 AGAGTAAATAGAACTACTCCTACCTG 57.016 38.462 5.79 0.00 43.37 4.00
2603 8622 1.942657 CATCACCATCATCGTCCAACC 59.057 52.381 0.00 0.00 0.00 3.77
2604 8623 0.251916 TCACCATCATCGTCCAACCC 59.748 55.000 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 5.046448 TGAATAGCCATGCAACTTGGAAAAT 60.046 36.000 9.06 0.00 36.26 1.82
14 15 4.022589 GCATATGTGAATAGCCATGCAACT 60.023 41.667 4.29 0.00 38.84 3.16
31 32 6.920817 AGCCATCATACAATTCTTGCATATG 58.079 36.000 0.00 0.00 0.00 1.78
69 70 0.994995 CAGAAAGACTGTCGCATCCG 59.005 55.000 1.52 0.00 41.30 4.18
86 87 1.063806 CACGAAGAAGAAGCGGACAG 58.936 55.000 0.00 0.00 0.00 3.51
101 102 3.923864 AGCCGCTTCACCACACGA 61.924 61.111 0.00 0.00 0.00 4.35
102 103 3.716006 CAGCCGCTTCACCACACG 61.716 66.667 0.00 0.00 0.00 4.49
127 128 2.820197 CCTTAAAGACCAAGAGGCCAAC 59.180 50.000 5.01 0.00 39.06 3.77
148 149 1.423395 CACAGCTCCTCAACGAGAAC 58.577 55.000 0.00 0.00 30.97 3.01
163 164 2.023771 ACATCGCTGACGTGCACAG 61.024 57.895 18.64 12.16 41.18 3.66
301 303 1.738099 AGAATCCGCTGCACGTCAC 60.738 57.895 0.00 0.00 41.42 3.67
302 304 1.737735 CAGAATCCGCTGCACGTCA 60.738 57.895 0.00 0.00 41.42 4.35
333 360 3.694538 TGCTGCGCTGAGGCTGTA 61.695 61.111 19.32 0.00 36.09 2.74
415 442 3.998672 GCCACCGACGAGGGTTCA 61.999 66.667 0.00 0.00 46.96 3.18
443 1430 2.746472 GCAAATAGATTGAGGGGCGAGT 60.746 50.000 0.00 0.00 41.85 4.18
466 1453 3.553096 GCTGCACGCTAACTGGACTATAT 60.553 47.826 0.00 0.00 35.14 0.86
489 1476 0.793861 TACTTTCATTCACACCGCGC 59.206 50.000 0.00 0.00 0.00 6.86
566 1553 2.498481 TGTCCGTTAGTTCCAATCCGAT 59.502 45.455 0.00 0.00 0.00 4.18
585 1572 6.115446 CAGGTGTTGTAGACATCCATATTGT 58.885 40.000 0.00 0.00 40.41 2.71
587 1574 6.115446 CACAGGTGTTGTAGACATCCATATT 58.885 40.000 0.00 0.00 40.41 1.28
628 1615 1.201429 AATGGGCTCGGTTCCTCTGT 61.201 55.000 0.00 0.00 0.00 3.41
636 1623 1.002134 CAGTTGGAATGGGCTCGGT 60.002 57.895 0.00 0.00 0.00 4.69
641 1628 2.409870 CGCTCCAGTTGGAATGGGC 61.410 63.158 1.99 1.55 44.91 5.36
660 1647 2.041755 ACCCTCAAACTTCCTGAATCCC 59.958 50.000 0.00 0.00 0.00 3.85
668 1655 2.299297 TCTCGAAGACCCTCAAACTTCC 59.701 50.000 0.00 0.00 37.36 3.46
671 1658 3.165875 TCATCTCGAAGACCCTCAAACT 58.834 45.455 0.00 0.00 0.00 2.66
672 1659 3.594603 TCATCTCGAAGACCCTCAAAC 57.405 47.619 0.00 0.00 0.00 2.93
685 1672 7.911205 ACGAAACTACTAGAAATCTTCATCTCG 59.089 37.037 0.00 0.00 0.00 4.04
785 3725 7.144722 TGATACATCAGACAAAAACATGGAC 57.855 36.000 0.00 0.00 32.11 4.02
955 4533 0.108804 CTGCCGTTGGATCTGTACGT 60.109 55.000 0.00 0.00 33.68 3.57
980 4558 2.100197 GATTTAACAAGGGGTGAGGGC 58.900 52.381 0.00 0.00 0.00 5.19
986 4573 1.781508 AGGGGGATTTAACAAGGGGT 58.218 50.000 0.00 0.00 0.00 4.95
1007 4594 1.475403 GTGAGAGTCGGGAGGAATCA 58.525 55.000 0.00 0.00 42.11 2.57
1062 4654 3.534554 TGATGTGTGATTTGGATCGAGG 58.465 45.455 0.00 0.00 34.91 4.63
1063 4655 3.002042 GCTGATGTGTGATTTGGATCGAG 59.998 47.826 0.00 0.00 34.91 4.04
1088 4687 0.606673 GCTGACGGCTTCCTTCCTTT 60.607 55.000 0.00 0.00 38.06 3.11
1434 5042 2.046217 GACGGGTCCTTCTTGCCC 60.046 66.667 0.00 0.00 39.03 5.36
1438 5046 1.906824 TGCGAGACGGGTCCTTCTT 60.907 57.895 0.00 0.00 0.00 2.52
1441 5049 3.692406 GGTGCGAGACGGGTCCTT 61.692 66.667 0.00 0.00 0.00 3.36
1492 5105 1.339055 CGAGGACATGAACACCACCAT 60.339 52.381 0.00 0.00 0.00 3.55
1614 5238 1.471287 TCGACAGACCCACAGATTACG 59.529 52.381 0.00 0.00 0.00 3.18
1626 5250 2.602217 GCACCAACAAACATCGACAGAC 60.602 50.000 0.00 0.00 0.00 3.51
1643 5267 3.377172 GGTAATATGTGACCACAAGCACC 59.623 47.826 6.95 8.41 45.41 5.01
1651 5278 2.235155 ACGCACTGGTAATATGTGACCA 59.765 45.455 0.00 0.00 43.55 4.02
1657 5284 5.733226 TTGATGAACGCACTGGTAATATG 57.267 39.130 0.00 0.00 0.00 1.78
1675 5302 2.767960 GCCAGACAATTGGGGAATTGAT 59.232 45.455 10.83 0.86 41.44 2.57
1681 5336 1.133199 ACAAAGCCAGACAATTGGGGA 60.133 47.619 10.83 0.00 38.72 4.81
1682 5337 1.341080 ACAAAGCCAGACAATTGGGG 58.659 50.000 10.83 9.34 38.72 4.96
1730 5385 1.962807 TCCACCAAACATTGAAGCCAG 59.037 47.619 0.00 0.00 0.00 4.85
1739 5394 4.222336 TGGTTTCAGAATCCACCAAACAT 58.778 39.130 8.68 0.00 36.33 2.71
1755 5410 7.728847 AGCCAACAAAATAAGATTTGGTTTC 57.271 32.000 2.56 0.00 43.10 2.78
1788 5443 3.212685 CCTTCTTCAGCCTGAATCCATC 58.787 50.000 7.75 0.00 35.59 3.51
1789 5444 2.579860 ACCTTCTTCAGCCTGAATCCAT 59.420 45.455 7.75 0.00 35.59 3.41
1816 5474 2.623416 GGAGGAACAAAACAACTCCCAG 59.377 50.000 0.00 0.00 41.41 4.45
1837 5495 4.030641 CACTACAAGTTCGACATCACGATG 59.969 45.833 5.48 5.48 41.82 3.84
1848 5506 2.440539 ACTCCAGCACTACAAGTTCG 57.559 50.000 0.00 0.00 0.00 3.95
1879 5539 4.997395 TCACAGGTAGCTCAAACAGATTTC 59.003 41.667 0.00 0.00 0.00 2.17
1880 5540 4.973168 TCACAGGTAGCTCAAACAGATTT 58.027 39.130 0.00 0.00 0.00 2.17
1884 5544 3.668447 ACATCACAGGTAGCTCAAACAG 58.332 45.455 0.00 0.00 0.00 3.16
1888 5548 2.167662 TCGACATCACAGGTAGCTCAA 58.832 47.619 0.00 0.00 0.00 3.02
1889 5549 1.834188 TCGACATCACAGGTAGCTCA 58.166 50.000 0.00 0.00 0.00 4.26
1890 5550 2.164624 AGTTCGACATCACAGGTAGCTC 59.835 50.000 0.00 0.00 0.00 4.09
1907 5567 3.240684 GCACACACTGCACAAGTTC 57.759 52.632 0.00 0.00 46.29 3.01
1928 5588 0.037605 CTACTCCACCGGACCAACAC 60.038 60.000 9.46 0.00 0.00 3.32
1993 5655 3.056465 ACACGCCCAAAAGAAAAACTTGA 60.056 39.130 0.00 0.00 38.98 3.02
1994 5656 3.258228 ACACGCCCAAAAGAAAAACTTG 58.742 40.909 0.00 0.00 38.98 3.16
1995 5657 3.603158 ACACGCCCAAAAGAAAAACTT 57.397 38.095 0.00 0.00 40.98 2.66
1996 5658 3.603158 AACACGCCCAAAAGAAAAACT 57.397 38.095 0.00 0.00 0.00 2.66
1997 5659 5.044558 TGATAACACGCCCAAAAGAAAAAC 58.955 37.500 0.00 0.00 0.00 2.43
1998 5660 5.263968 TGATAACACGCCCAAAAGAAAAA 57.736 34.783 0.00 0.00 0.00 1.94
1999 5661 4.920640 TGATAACACGCCCAAAAGAAAA 57.079 36.364 0.00 0.00 0.00 2.29
2000 5662 4.279671 ACATGATAACACGCCCAAAAGAAA 59.720 37.500 0.00 0.00 0.00 2.52
2001 5663 3.823873 ACATGATAACACGCCCAAAAGAA 59.176 39.130 0.00 0.00 0.00 2.52
2002 5664 3.417101 ACATGATAACACGCCCAAAAGA 58.583 40.909 0.00 0.00 0.00 2.52
2003 5665 3.848272 ACATGATAACACGCCCAAAAG 57.152 42.857 0.00 0.00 0.00 2.27
2004 5666 5.906113 ATAACATGATAACACGCCCAAAA 57.094 34.783 0.00 0.00 0.00 2.44
2005 5667 5.906113 AATAACATGATAACACGCCCAAA 57.094 34.783 0.00 0.00 0.00 3.28
2006 5668 6.037720 CACTAATAACATGATAACACGCCCAA 59.962 38.462 0.00 0.00 0.00 4.12
2007 5669 5.525745 CACTAATAACATGATAACACGCCCA 59.474 40.000 0.00 0.00 0.00 5.36
2008 5670 5.526111 ACACTAATAACATGATAACACGCCC 59.474 40.000 0.00 0.00 0.00 6.13
2009 5671 6.598753 ACACTAATAACATGATAACACGCC 57.401 37.500 0.00 0.00 0.00 5.68
2010 5672 6.410914 GCAACACTAATAACATGATAACACGC 59.589 38.462 0.00 0.00 0.00 5.34
2011 5673 7.635973 CAGCAACACTAATAACATGATAACACG 59.364 37.037 0.00 0.00 0.00 4.49
2012 5674 8.664798 TCAGCAACACTAATAACATGATAACAC 58.335 33.333 0.00 0.00 0.00 3.32
2013 5675 8.785329 TCAGCAACACTAATAACATGATAACA 57.215 30.769 0.00 0.00 0.00 2.41
2014 5676 9.655769 CATCAGCAACACTAATAACATGATAAC 57.344 33.333 0.00 0.00 0.00 1.89
2015 5677 9.612066 TCATCAGCAACACTAATAACATGATAA 57.388 29.630 0.00 0.00 0.00 1.75
2021 5683 6.658816 ACCAATCATCAGCAACACTAATAACA 59.341 34.615 0.00 0.00 0.00 2.41
2034 5696 7.706159 TGTTTAATACATCACCAATCATCAGC 58.294 34.615 0.00 0.00 0.00 4.26
2035 5697 9.673454 CATGTTTAATACATCACCAATCATCAG 57.327 33.333 0.00 0.00 45.71 2.90
2036 5698 9.187996 ACATGTTTAATACATCACCAATCATCA 57.812 29.630 0.00 0.00 45.71 3.07
2037 5699 9.454585 CACATGTTTAATACATCACCAATCATC 57.545 33.333 0.00 0.00 45.71 2.92
2038 5700 8.970020 ACACATGTTTAATACATCACCAATCAT 58.030 29.630 0.00 0.00 45.71 2.45
2039 5701 8.347004 ACACATGTTTAATACATCACCAATCA 57.653 30.769 0.00 0.00 45.71 2.57
2040 5702 9.638239 AAACACATGTTTAATACATCACCAATC 57.362 29.630 8.22 0.00 45.71 2.67
2041 5703 9.421806 CAAACACATGTTTAATACATCACCAAT 57.578 29.630 9.58 0.00 45.71 3.16
2042 5704 7.869937 CCAAACACATGTTTAATACATCACCAA 59.130 33.333 9.58 0.00 45.71 3.67
2043 5705 7.014711 ACCAAACACATGTTTAATACATCACCA 59.985 33.333 9.58 0.00 45.71 4.17
2045 5707 7.148820 GCACCAAACACATGTTTAATACATCAC 60.149 37.037 9.58 0.00 45.71 3.06
2046 5708 6.865726 GCACCAAACACATGTTTAATACATCA 59.134 34.615 9.58 0.00 45.71 3.07
2047 5709 7.062138 CAGCACCAAACACATGTTTAATACATC 59.938 37.037 9.58 0.00 45.71 3.06
2049 5711 6.039829 TCAGCACCAAACACATGTTTAATACA 59.960 34.615 9.58 0.00 45.54 2.29
2050 5712 6.442952 TCAGCACCAAACACATGTTTAATAC 58.557 36.000 9.58 1.67 45.54 1.89
2051 5713 6.641169 TCAGCACCAAACACATGTTTAATA 57.359 33.333 9.58 0.00 45.54 0.98
2052 5714 5.528043 TCAGCACCAAACACATGTTTAAT 57.472 34.783 9.58 0.00 45.54 1.40
2100 5762 6.791887 ATGTGTAGCATTGCTCATATGTAC 57.208 37.500 15.81 6.48 40.44 2.90
2102 5764 5.406477 CGTATGTGTAGCATTGCTCATATGT 59.594 40.000 15.81 1.31 40.44 2.29
2103 5765 5.163923 CCGTATGTGTAGCATTGCTCATATG 60.164 44.000 15.81 19.06 40.44 1.78
2104 5766 4.931601 CCGTATGTGTAGCATTGCTCATAT 59.068 41.667 15.81 16.92 40.44 1.78
2108 5770 1.867233 CCCGTATGTGTAGCATTGCTC 59.133 52.381 15.81 7.72 40.44 4.26
2109 5771 1.953559 CCCGTATGTGTAGCATTGCT 58.046 50.000 16.63 16.63 43.41 3.91
2110 5772 0.307760 GCCCGTATGTGTAGCATTGC 59.692 55.000 0.00 0.00 38.94 3.56
2113 5775 0.393077 GGAGCCCGTATGTGTAGCAT 59.607 55.000 0.00 0.00 41.42 3.79
2116 5778 2.981859 AAAGGAGCCCGTATGTGTAG 57.018 50.000 0.00 0.00 0.00 2.74
2117 5779 3.706600 AAAAAGGAGCCCGTATGTGTA 57.293 42.857 0.00 0.00 0.00 2.90
2118 5780 2.579410 AAAAAGGAGCCCGTATGTGT 57.421 45.000 0.00 0.00 0.00 3.72
2120 5782 3.551846 CCATAAAAAGGAGCCCGTATGT 58.448 45.455 0.00 0.00 0.00 2.29
2121 5783 2.884639 CCCATAAAAAGGAGCCCGTATG 59.115 50.000 0.00 0.00 0.00 2.39
2122 5784 2.781174 TCCCATAAAAAGGAGCCCGTAT 59.219 45.455 0.00 0.00 0.00 3.06
2125 5787 2.230660 GATCCCATAAAAAGGAGCCCG 58.769 52.381 0.00 0.00 35.08 6.13
2126 5788 3.312736 TGATCCCATAAAAAGGAGCCC 57.687 47.619 0.00 0.00 37.78 5.19
2127 5789 3.066760 CGTTGATCCCATAAAAAGGAGCC 59.933 47.826 0.00 0.00 37.78 4.70
2129 5791 4.523083 TCCGTTGATCCCATAAAAAGGAG 58.477 43.478 0.00 0.00 35.08 3.69
2131 5793 4.523083 TCTCCGTTGATCCCATAAAAAGG 58.477 43.478 0.00 0.00 0.00 3.11
2132 5794 5.449177 GCTTCTCCGTTGATCCCATAAAAAG 60.449 44.000 0.00 0.00 0.00 2.27
2135 5797 3.054728 TGCTTCTCCGTTGATCCCATAAA 60.055 43.478 0.00 0.00 0.00 1.40
2138 5800 0.911769 TGCTTCTCCGTTGATCCCAT 59.088 50.000 0.00 0.00 0.00 4.00
2141 5803 4.440839 AAATTTGCTTCTCCGTTGATCC 57.559 40.909 0.00 0.00 0.00 3.36
2143 5805 5.336451 GGGTAAAATTTGCTTCTCCGTTGAT 60.336 40.000 0.00 0.00 0.00 2.57
2144 5806 4.022676 GGGTAAAATTTGCTTCTCCGTTGA 60.023 41.667 0.00 0.00 0.00 3.18
2145 5807 4.234574 GGGTAAAATTTGCTTCTCCGTTG 58.765 43.478 0.00 0.00 0.00 4.10
2147 5809 2.486592 CGGGTAAAATTTGCTTCTCCGT 59.513 45.455 0.00 0.00 0.00 4.69
2148 5810 2.731027 GCGGGTAAAATTTGCTTCTCCG 60.731 50.000 5.27 5.27 38.17 4.63
2149 5811 2.731027 CGCGGGTAAAATTTGCTTCTCC 60.731 50.000 0.00 0.00 0.00 3.71
2150 5812 2.515912 CGCGGGTAAAATTTGCTTCTC 58.484 47.619 0.00 0.00 0.00 2.87
2152 5814 1.068125 ACCGCGGGTAAAATTTGCTTC 60.068 47.619 31.76 0.00 32.11 3.86
2153 5815 0.963225 ACCGCGGGTAAAATTTGCTT 59.037 45.000 31.76 0.00 32.11 3.91
2154 5816 0.524414 GACCGCGGGTAAAATTTGCT 59.476 50.000 31.76 2.41 35.25 3.91
2171 8182 3.721370 ATCCTGCAATGCCCCCGAC 62.721 63.158 1.53 0.00 0.00 4.79
2172 8183 2.512986 AAATCCTGCAATGCCCCCGA 62.513 55.000 1.53 0.00 0.00 5.14
2198 8210 4.808364 TGAAGTCAAAAATTTGCCTTTCCG 59.192 37.500 3.96 0.00 36.60 4.30
2209 8221 4.785341 GCTCGTTCACGTGAAGTCAAAAAT 60.785 41.667 30.38 0.00 40.80 1.82
2215 8227 1.053811 GAGCTCGTTCACGTGAAGTC 58.946 55.000 30.38 18.60 40.80 3.01
2218 8230 1.068748 GGTAGAGCTCGTTCACGTGAA 60.069 52.381 26.53 26.53 40.80 3.18
2285 8304 8.804743 CAGAAATCTGAAATTGATGTGCAATAC 58.195 33.333 4.37 0.00 45.06 1.89
2309 8328 5.446709 CGTATAAATGCTCAATGCCTTCAG 58.553 41.667 0.00 0.00 42.00 3.02
2312 8331 4.460263 TCCGTATAAATGCTCAATGCCTT 58.540 39.130 0.00 0.00 42.00 4.35
2332 8351 6.915349 AGATGCTTAATCGAGTAGTGTATCC 58.085 40.000 16.02 5.61 40.54 2.59
2342 8361 5.987953 TGGATCTTGAAGATGCTTAATCGAG 59.012 40.000 23.89 0.00 42.66 4.04
2388 8407 7.251704 TCGAAATTCTTCTTTGATATGCCTC 57.748 36.000 0.00 0.00 0.00 4.70
2403 8422 7.545965 CCTGATAGTGTAGTGTTTCGAAATTCT 59.454 37.037 14.69 16.34 0.00 2.40
2447 8466 6.534793 ACTTTGTTTTCGCATTCAACTTGATT 59.465 30.769 0.00 0.00 0.00 2.57
2455 8474 3.156511 TGCACTTTGTTTTCGCATTCA 57.843 38.095 0.00 0.00 0.00 2.57
2522 8541 0.675083 TGGTTGTTGCATGCTTCCTG 59.325 50.000 20.33 0.00 0.00 3.86
2540 8559 9.881529 GGAGTAGTTCTATTTACTCTCGTATTG 57.118 37.037 10.43 0.00 43.31 1.90
2545 8564 7.933033 AGGTAGGAGTAGTTCTATTTACTCTCG 59.067 40.741 10.43 0.00 43.31 4.04
2557 8576 3.430929 CCATGCACAGGTAGGAGTAGTTC 60.431 52.174 0.00 0.00 0.00 3.01
2567 8586 3.181455 GGTGATGATACCATGCACAGGTA 60.181 47.826 19.02 19.02 45.08 3.08


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

AutoCloner maintained by Alex Coulton.