Multiple sequence alignment - TraesCS2A01G022500

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 TraesCS2A01G022500 chr2A 100.000 4652 0 0 790 5441 10910856 10915507 0.000000e+00 8591.0
1 TraesCS2A01G022500 chr2A 100.000 382 0 0 1 382 10910067 10910448 0.000000e+00 706.0
2 TraesCS2A01G022500 chr2A 90.411 73 1 5 1691 1761 10911727 10911795 2.090000e-14 91.6
3 TraesCS2A01G022500 chr2A 90.411 73 1 5 1661 1729 10911757 10911827 2.090000e-14 91.6
4 TraesCS2A01G022500 chrUn 95.736 3354 107 11 1691 5035 283576631 283573305 0.000000e+00 5369.0
5 TraesCS2A01G022500 chrUn 86.682 428 21 3 2761 3179 478583517 478583117 5.000000e-120 442.0
6 TraesCS2A01G022500 chrUn 93.519 108 3 2 1629 1732 283576663 283576556 2.030000e-34 158.0
7 TraesCS2A01G022500 chrUn 100.000 30 0 0 1735 1764 283576617 283576588 7.610000e-04 56.5
8 TraesCS2A01G022500 chr2D 95.762 3351 106 11 1691 5032 10661110 10664433 0.000000e+00 5369.0
9 TraesCS2A01G022500 chr2D 91.554 959 44 10 790 1729 10660242 10661182 0.000000e+00 1306.0
10 TraesCS2A01G022500 chr2D 81.411 1318 220 17 3243 4546 7199546 7198240 0.000000e+00 1053.0
11 TraesCS2A01G022500 chr2D 86.561 692 66 15 999 1672 10655696 10656378 0.000000e+00 737.0
12 TraesCS2A01G022500 chr2D 97.872 376 8 0 7 382 10658086 10658461 0.000000e+00 651.0
13 TraesCS2A01G022500 chr2D 84.211 513 69 7 999 1502 10517096 10517605 6.330000e-134 488.0
14 TraesCS2A01G022500 chr2D 85.530 387 30 12 7 382 10558787 10559158 1.110000e-101 381.0
15 TraesCS2A01G022500 chr2D 84.555 382 37 9 7 382 10516351 10516716 5.180000e-95 359.0
16 TraesCS2A01G022500 chr2D 94.340 212 9 2 790 1001 10516860 10517068 6.800000e-84 322.0
17 TraesCS2A01G022500 chr2D 93.396 212 12 2 790 1000 10559302 10559512 4.090000e-81 313.0
18 TraesCS2A01G022500 chr2D 100.000 30 0 0 1735 1764 10661124 10661153 7.610000e-04 56.5
19 TraesCS2A01G022500 chr2B 91.868 2189 132 11 2582 4755 14542457 14544614 0.000000e+00 3014.0
20 TraesCS2A01G022500 chr2B 91.735 2190 131 13 2582 4755 14524591 14526746 0.000000e+00 2996.0
21 TraesCS2A01G022500 chr2B 87.819 1921 203 21 2727 4622 14794289 14796203 0.000000e+00 2222.0
22 TraesCS2A01G022500 chr2B 81.804 1319 212 20 3240 4544 1793630 1794934 0.000000e+00 1081.0
23 TraesCS2A01G022500 chr2B 81.714 1307 211 20 3252 4544 1753958 1755250 0.000000e+00 1064.0
24 TraesCS2A01G022500 chr2B 90.830 807 50 20 792 1582 14540983 14541781 0.000000e+00 1059.0
25 TraesCS2A01G022500 chr2B 81.727 1297 209 20 3262 4544 1769231 1770513 0.000000e+00 1057.0
26 TraesCS2A01G022500 chr2B 90.582 807 52 20 792 1582 14523117 14523915 0.000000e+00 1048.0
27 TraesCS2A01G022500 chr2B 83.939 716 92 10 808 1502 14411962 14412675 0.000000e+00 664.0
28 TraesCS2A01G022500 chr2B 90.678 472 25 2 1878 2349 14542006 14542458 1.300000e-170 610.0
29 TraesCS2A01G022500 chr2B 90.466 472 26 2 1878 2349 14524140 14524592 6.030000e-169 604.0
30 TraesCS2A01G022500 chr2B 90.456 461 36 5 4618 5077 14544614 14545067 7.800000e-168 601.0
31 TraesCS2A01G022500 chr2B 79.654 693 96 21 859 1512 13815106 13814420 1.790000e-124 457.0
32 TraesCS2A01G022500 chr2B 89.944 358 24 4 5074 5431 14527508 14527853 8.310000e-123 451.0
33 TraesCS2A01G022500 chr2B 89.665 358 25 4 5074 5431 14545103 14545448 3.870000e-121 446.0
34 TraesCS2A01G022500 chr2B 92.105 304 21 3 4774 5077 14527173 14527473 5.040000e-115 425.0
35 TraesCS2A01G022500 chr2B 80.639 532 89 9 999 1524 15759980 15760503 3.050000e-107 399.0
36 TraesCS2A01G022500 chr2B 80.639 532 89 9 999 1524 15821164 15821687 3.050000e-107 399.0
37 TraesCS2A01G022500 chr2B 80.451 532 90 9 999 1524 15762716 15763239 1.420000e-105 394.0
38 TraesCS2A01G022500 chr2B 84.286 280 38 6 45 320 14540075 14540352 8.980000e-68 268.0
39 TraesCS2A01G022500 chr2B 85.000 240 35 1 2448 2687 14792777 14793015 5.440000e-60 243.0
40 TraesCS2A01G022500 chr2B 93.590 156 9 1 1726 1881 14523934 14524088 1.180000e-56 231.0
41 TraesCS2A01G022500 chr2B 93.548 155 9 1 1726 1880 14541800 14541953 4.240000e-56 230.0
42 TraesCS2A01G022500 chr2B 84.793 217 22 6 790 1001 15697619 15697829 1.990000e-49 207.0
43 TraesCS2A01G022500 chr2B 84.793 217 22 6 790 1001 15759742 15759952 1.990000e-49 207.0
44 TraesCS2A01G022500 chr2B 81.961 255 26 12 1899 2144 14789444 14789687 1.200000e-46 198.0
45 TraesCS2A01G022500 chr2B 78.095 315 59 7 1141 1447 28254801 28255113 2.000000e-44 191.0
46 TraesCS2A01G022500 chr2B 98.077 52 1 0 331 382 14540785 14540836 2.090000e-14 91.6
47 TraesCS2A01G022500 chr2B 97.959 49 1 0 334 382 14522922 14522970 9.710000e-13 86.1
48 TraesCS2A01G022500 chr5A 90.476 63 6 0 8 70 565529608 565529670 3.490000e-12 84.2
49 TraesCS2A01G022500 chr1D 87.324 71 8 1 16 85 425573136 425573206 4.520000e-11 80.5
50 TraesCS2A01G022500 chr7D 90.000 60 6 0 11 70 205240530 205240471 1.620000e-10 78.7
51 TraesCS2A01G022500 chr7D 87.879 66 4 3 7 70 89077324 89077387 2.100000e-09 75.0
52 TraesCS2A01G022500 chr1A 88.889 63 7 0 8 70 521260574 521260636 1.620000e-10 78.7
53 TraesCS2A01G022500 chr7B 87.302 63 8 0 8 70 197403652 197403714 7.560000e-09 73.1


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 TraesCS2A01G022500 chr2A 10910067 10915507 5440 False 2370.050000 8591 95.205500 1 5441 4 chr2A.!!$F1 5440
1 TraesCS2A01G022500 chrUn 283573305 283576663 3358 True 1861.166667 5369 96.418333 1629 5035 3 chrUn.!!$R2 3406
2 TraesCS2A01G022500 chr2D 10655696 10664433 8737 False 1623.900000 5369 94.349800 7 5032 5 chr2D.!!$F3 5025
3 TraesCS2A01G022500 chr2D 7198240 7199546 1306 True 1053.000000 1053 81.411000 3243 4546 1 chr2D.!!$R1 1303
4 TraesCS2A01G022500 chr2D 10516351 10517605 1254 False 389.666667 488 87.702000 7 1502 3 chr2D.!!$F1 1495
5 TraesCS2A01G022500 chr2D 10558787 10559512 725 False 347.000000 381 89.463000 7 1000 2 chr2D.!!$F2 993
6 TraesCS2A01G022500 chr2B 1793630 1794934 1304 False 1081.000000 1081 81.804000 3240 4544 1 chr2B.!!$F3 1304
7 TraesCS2A01G022500 chr2B 1753958 1755250 1292 False 1064.000000 1064 81.714000 3252 4544 1 chr2B.!!$F1 1292
8 TraesCS2A01G022500 chr2B 1769231 1770513 1282 False 1057.000000 1057 81.727000 3262 4544 1 chr2B.!!$F2 1282
9 TraesCS2A01G022500 chr2B 14789444 14796203 6759 False 887.666667 2222 84.926667 1899 4622 3 chr2B.!!$F10 2723
10 TraesCS2A01G022500 chr2B 14522922 14527853 4931 False 834.442857 2996 92.340143 334 5431 7 chr2B.!!$F8 5097
11 TraesCS2A01G022500 chr2B 14540075 14545448 5373 False 789.950000 3014 91.176000 45 5431 8 chr2B.!!$F9 5386
12 TraesCS2A01G022500 chr2B 14411962 14412675 713 False 664.000000 664 83.939000 808 1502 1 chr2B.!!$F4 694
13 TraesCS2A01G022500 chr2B 13814420 13815106 686 True 457.000000 457 79.654000 859 1512 1 chr2B.!!$R1 653
14 TraesCS2A01G022500 chr2B 15821164 15821687 523 False 399.000000 399 80.639000 999 1524 1 chr2B.!!$F6 525
15 TraesCS2A01G022500 chr2B 15759742 15763239 3497 False 333.333333 399 81.961000 790 1524 3 chr2B.!!$F11 734

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
295 2688 0.794473 GGTTCGACGCTTCCGAAAAT 59.206 50.000 0.00 0.00 45.84 1.82 F
1012 5243 2.191641 GCTCCATGGCAGGTCTCC 59.808 66.667 6.96 0.00 0.00 3.71 F
1986 6322 0.037590 TTGCTAGCCGTCCATTGGTT 59.962 50.000 13.29 0.00 0.00 3.67 F
1999 6335 0.255890 ATTGGTTGCTAGCCGTCCAT 59.744 50.000 13.29 5.84 0.00 3.41 F
2072 6419 1.308069 CCAGTGGAGAATTGGCACGG 61.308 60.000 1.68 0.00 0.00 4.94 F
2468 9852 3.230134 CATCTCCAAGTCCCCAAAAACA 58.770 45.455 0.00 0.00 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1364 5627 0.034059 GGACGAGCCATACATGAGGG 59.966 60.000 0.00 0.0 36.34 4.30 R
2134 6486 0.179129 TGCGCTACCGGCTTAAGTAC 60.179 55.000 9.73 0.0 39.13 2.73 R
3549 12217 0.746063 CAGCCTTTGCACAAACCAGA 59.254 50.000 0.00 0.0 41.13 3.86 R
3550 12218 0.746063 TCAGCCTTTGCACAAACCAG 59.254 50.000 0.00 0.0 41.13 4.00 R
4283 12965 4.628333 CCAACATAAGCTCAAAATTGGCAG 59.372 41.667 0.00 0.0 0.00 4.85 R
4656 13668 0.415830 TCCTACACCCCCATGAGTCA 59.584 55.000 0.00 0.0 0.00 3.41 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
295 2688 0.794473 GGTTCGACGCTTCCGAAAAT 59.206 50.000 0.00 0.00 45.84 1.82
303 2696 4.432762 CGACGCTTCCGAAAATAAACGTAA 60.433 41.667 0.00 0.00 38.29 3.18
329 3144 4.974368 TTCATTTATAACTGCCAACGGG 57.026 40.909 0.00 0.00 37.18 5.28
838 5028 4.636249 AGACTGCCTTGTCTGTTTCTTAG 58.364 43.478 3.77 0.00 44.64 2.18
872 5064 3.834231 ACGTTTCCCCTAACTAACTGCTA 59.166 43.478 0.00 0.00 0.00 3.49
1012 5243 2.191641 GCTCCATGGCAGGTCTCC 59.808 66.667 6.96 0.00 0.00 3.71
1032 5289 2.367894 CCTCATGCTAGAGATGCTTCCA 59.632 50.000 7.44 0.00 37.87 3.53
1275 5538 4.681978 GGAGCCGTGCCGACACTT 62.682 66.667 0.00 0.00 45.10 3.16
1364 5627 1.084370 CGCTCCATGGTCTCGGAAAC 61.084 60.000 12.58 0.00 0.00 2.78
1554 5817 7.041098 GGTGCTTGGTCGAAATATGAATATCTT 60.041 37.037 0.00 0.00 0.00 2.40
1586 5849 7.485913 GCACACCTGAAACTATAATTGTGAATG 59.514 37.037 0.00 0.00 36.09 2.67
1615 5878 7.833285 TGCAAGTTTCTTTTTATAACCCTCT 57.167 32.000 0.00 0.00 0.00 3.69
1616 5879 7.882179 TGCAAGTTTCTTTTTATAACCCTCTC 58.118 34.615 0.00 0.00 0.00 3.20
1617 5880 7.724061 TGCAAGTTTCTTTTTATAACCCTCTCT 59.276 33.333 0.00 0.00 0.00 3.10
1618 5881 8.237949 GCAAGTTTCTTTTTATAACCCTCTCTC 58.762 37.037 0.00 0.00 0.00 3.20
1619 5882 9.508642 CAAGTTTCTTTTTATAACCCTCTCTCT 57.491 33.333 0.00 0.00 0.00 3.10
1620 5883 9.727859 AAGTTTCTTTTTATAACCCTCTCTCTC 57.272 33.333 0.00 0.00 0.00 3.20
1621 5884 9.106977 AGTTTCTTTTTATAACCCTCTCTCTCT 57.893 33.333 0.00 0.00 0.00 3.10
1622 5885 9.373603 GTTTCTTTTTATAACCCTCTCTCTCTC 57.626 37.037 0.00 0.00 0.00 3.20
1623 5886 8.903059 TTCTTTTTATAACCCTCTCTCTCTCT 57.097 34.615 0.00 0.00 0.00 3.10
1624 5887 8.299990 TCTTTTTATAACCCTCTCTCTCTCTG 57.700 38.462 0.00 0.00 0.00 3.35
1625 5888 7.896496 TCTTTTTATAACCCTCTCTCTCTCTGT 59.104 37.037 0.00 0.00 0.00 3.41
1627 5890 6.584471 TTATAACCCTCTCTCTCTCTGTCT 57.416 41.667 0.00 0.00 0.00 3.41
1638 5901 4.646945 TCTCTCTCTGTCTCTCTCTCTCTC 59.353 50.000 0.00 0.00 0.00 3.20
1700 5963 9.342308 CTCATCTAAAGGGAAATGTGCTAATAA 57.658 33.333 0.00 0.00 0.00 1.40
1701 5964 9.693739 TCATCTAAAGGGAAATGTGCTAATAAA 57.306 29.630 0.00 0.00 0.00 1.40
1702 5965 9.736023 CATCTAAAGGGAAATGTGCTAATAAAC 57.264 33.333 0.00 0.00 0.00 2.01
1703 5966 9.700831 ATCTAAAGGGAAATGTGCTAATAAACT 57.299 29.630 0.00 0.00 0.00 2.66
1704 5967 9.174166 TCTAAAGGGAAATGTGCTAATAAACTC 57.826 33.333 0.00 0.00 0.00 3.01
1705 5968 7.775053 AAAGGGAAATGTGCTAATAAACTCA 57.225 32.000 0.00 0.00 0.00 3.41
1706 5969 7.961326 AAGGGAAATGTGCTAATAAACTCAT 57.039 32.000 0.00 0.00 0.00 2.90
1707 5970 7.573968 AGGGAAATGTGCTAATAAACTCATC 57.426 36.000 0.00 0.00 0.00 2.92
1708 5971 7.349598 AGGGAAATGTGCTAATAAACTCATCT 58.650 34.615 0.00 0.00 0.00 2.90
1709 5972 8.494433 AGGGAAATGTGCTAATAAACTCATCTA 58.506 33.333 0.00 0.00 0.00 1.98
1710 5973 9.120538 GGGAAATGTGCTAATAAACTCATCTAA 57.879 33.333 0.00 0.00 0.00 2.10
1714 5977 8.682936 ATGTGCTAATAAACTCATCTAAAGGG 57.317 34.615 0.00 0.00 0.00 3.95
1715 5978 7.857456 TGTGCTAATAAACTCATCTAAAGGGA 58.143 34.615 0.00 0.00 0.00 4.20
1716 5979 8.325787 TGTGCTAATAAACTCATCTAAAGGGAA 58.674 33.333 0.00 0.00 0.00 3.97
1717 5980 9.174166 GTGCTAATAAACTCATCTAAAGGGAAA 57.826 33.333 0.00 0.00 0.00 3.13
1718 5981 9.920946 TGCTAATAAACTCATCTAAAGGGAAAT 57.079 29.630 0.00 0.00 0.00 2.17
1722 5985 5.904362 AACTCATCTAAAGGGAAATGTGC 57.096 39.130 0.00 0.00 0.00 4.57
1723 5986 5.184892 ACTCATCTAAAGGGAAATGTGCT 57.815 39.130 0.00 0.00 0.00 4.40
1724 5987 6.313519 ACTCATCTAAAGGGAAATGTGCTA 57.686 37.500 0.00 0.00 0.00 3.49
1725 5988 6.721318 ACTCATCTAAAGGGAAATGTGCTAA 58.279 36.000 0.00 0.00 0.00 3.09
1726 5989 7.349598 ACTCATCTAAAGGGAAATGTGCTAAT 58.650 34.615 0.00 0.00 0.00 1.73
1727 5990 8.494433 ACTCATCTAAAGGGAAATGTGCTAATA 58.506 33.333 0.00 0.00 0.00 0.98
1728 5991 9.512588 CTCATCTAAAGGGAAATGTGCTAATAT 57.487 33.333 0.00 0.00 0.00 1.28
1937 6255 6.880822 ATGCGATGTTCAAAATGATTTCAG 57.119 33.333 0.00 0.00 0.00 3.02
1982 6318 4.270008 AGTTTTATTGCTAGCCGTCCATT 58.730 39.130 13.29 0.00 0.00 3.16
1983 6319 4.096382 AGTTTTATTGCTAGCCGTCCATTG 59.904 41.667 13.29 0.00 0.00 2.82
1984 6320 2.254546 TATTGCTAGCCGTCCATTGG 57.745 50.000 13.29 0.00 0.00 3.16
1985 6321 0.255890 ATTGCTAGCCGTCCATTGGT 59.744 50.000 13.29 0.00 0.00 3.67
1986 6322 0.037590 TTGCTAGCCGTCCATTGGTT 59.962 50.000 13.29 0.00 0.00 3.67
1987 6323 0.676466 TGCTAGCCGTCCATTGGTTG 60.676 55.000 13.29 0.00 0.00 3.77
1988 6324 1.993369 GCTAGCCGTCCATTGGTTGC 61.993 60.000 2.29 4.35 0.00 4.17
1989 6325 0.392998 CTAGCCGTCCATTGGTTGCT 60.393 55.000 16.46 16.46 0.00 3.91
1990 6326 0.906066 TAGCCGTCCATTGGTTGCTA 59.094 50.000 14.98 14.98 0.00 3.49
1991 6327 0.392998 AGCCGTCCATTGGTTGCTAG 60.393 55.000 12.48 0.00 0.00 3.42
1992 6328 1.993369 GCCGTCCATTGGTTGCTAGC 61.993 60.000 8.10 8.10 0.00 3.42
1993 6329 1.376609 CCGTCCATTGGTTGCTAGCC 61.377 60.000 13.29 0.00 0.00 3.93
1994 6330 1.705337 CGTCCATTGGTTGCTAGCCG 61.705 60.000 13.29 0.00 0.00 5.52
1995 6331 0.676782 GTCCATTGGTTGCTAGCCGT 60.677 55.000 13.29 0.00 0.00 5.68
1996 6332 0.392461 TCCATTGGTTGCTAGCCGTC 60.392 55.000 13.29 2.25 0.00 4.79
1997 6333 1.376609 CCATTGGTTGCTAGCCGTCC 61.377 60.000 13.29 12.14 0.00 4.79
1998 6334 0.676466 CATTGGTTGCTAGCCGTCCA 60.676 55.000 13.29 14.61 0.00 4.02
1999 6335 0.255890 ATTGGTTGCTAGCCGTCCAT 59.744 50.000 13.29 5.84 0.00 3.41
2006 6342 1.954382 TGCTAGCCGTCCATAGTGTAG 59.046 52.381 13.29 0.00 0.00 2.74
2072 6419 1.308069 CCAGTGGAGAATTGGCACGG 61.308 60.000 1.68 0.00 0.00 4.94
2209 9593 4.096833 TCATTGCAATGGAGAATTTCCTCG 59.903 41.667 33.22 8.23 46.92 4.63
2371 9755 6.877611 TTTGAATAGACAGTCCAGTTTTCC 57.122 37.500 0.00 0.00 0.00 3.13
2372 9756 5.825593 TGAATAGACAGTCCAGTTTTCCT 57.174 39.130 0.00 0.00 0.00 3.36
2380 9764 4.079958 ACAGTCCAGTTTTCCTGTTAACCT 60.080 41.667 2.48 0.00 39.74 3.50
2393 9777 4.017126 CTGTTAACCTTCTCCAATTCCCC 58.983 47.826 2.48 0.00 0.00 4.81
2468 9852 3.230134 CATCTCCAAGTCCCCAAAAACA 58.770 45.455 0.00 0.00 0.00 2.83
2589 9973 4.406456 TGTACTACCCCTTGTTCTTACGA 58.594 43.478 0.00 0.00 0.00 3.43
2646 10033 6.787458 AGGAAAATCCCTCCAAAATTGTAGTT 59.213 34.615 0.00 0.00 37.19 2.24
2870 11500 3.448093 TGGATGACAAAATGGCCACTA 57.552 42.857 8.16 0.00 0.00 2.74
2907 11540 6.434340 GTGGTTCTTTGTGAAATAGGGAGAAT 59.566 38.462 0.00 0.00 36.30 2.40
3013 11662 9.343539 GCCTACAAGATGGTCTTCTAAATAAAT 57.656 33.333 0.00 0.00 33.78 1.40
3048 11697 9.213777 AGACAACATCCACTAATTAGGAGATTA 57.786 33.333 16.73 0.00 37.34 1.75
3121 11782 4.536765 ACCACCACATATCTCCCAATTTC 58.463 43.478 0.00 0.00 0.00 2.17
3164 11831 6.180358 CGAAACTCGTTGGTAATTTTGTTG 57.820 37.500 0.00 0.00 34.72 3.33
3549 12217 4.636249 CAAGAGTTGGAGTGCTTAAGAGT 58.364 43.478 6.67 0.00 0.00 3.24
3550 12218 4.529109 AGAGTTGGAGTGCTTAAGAGTC 57.471 45.455 6.67 4.18 0.00 3.36
3660 12328 5.705441 GTCAACAGTTGATAACAAGGATGGA 59.295 40.000 19.04 0.00 42.47 3.41
4283 12965 1.429148 CCTGGCATAAACCTCGCGAC 61.429 60.000 3.71 0.00 0.00 5.19
4348 13030 0.925720 ATGGGAATTGCCTCCAGGGA 60.926 55.000 17.69 0.00 37.20 4.20
4366 13048 5.419542 CAGGGATTGAGACGAAAGACATTA 58.580 41.667 0.00 0.00 0.00 1.90
4398 13080 2.670251 TTTGGGCTAACCGTGCGG 60.670 61.111 9.29 9.29 44.64 5.69
4445 13217 8.757982 ATTCCAAAATCATACAAGTAGATGCT 57.242 30.769 0.00 0.00 0.00 3.79
4591 13603 5.520748 AAAATTCCAAGAAGGCCTAGAGA 57.479 39.130 5.16 0.00 37.29 3.10
4596 13608 5.144159 TCCAAGAAGGCCTAGAGAATCTA 57.856 43.478 5.16 0.00 41.88 1.98
4656 13668 0.403453 CCCTCCCCTATTCCCCATGT 60.403 60.000 0.00 0.00 0.00 3.21
4769 13917 4.346049 CCCCCACACACACACAAA 57.654 55.556 0.00 0.00 0.00 2.83
4882 14437 1.727335 GAACCGAGTGCAGCTTAGTTC 59.273 52.381 0.00 2.16 34.59 3.01
4951 14506 7.689299 GTGCTCACACTTTCCTAGATTTATTC 58.311 38.462 0.00 0.00 43.85 1.75
4957 14512 7.010552 CACACTTTCCTAGATTTATTCCAGACG 59.989 40.741 0.00 0.00 0.00 4.18
4975 14530 6.934645 TCCAGACGTTCAATAGAAGTTCATTT 59.065 34.615 5.50 0.00 33.63 2.32
4998 14553 2.966516 GTGGAAGATATCGTTCCCCTCT 59.033 50.000 21.45 0.00 42.63 3.69
5008 14563 4.796038 TCGTTCCCCTCTACTAAAACAG 57.204 45.455 0.00 0.00 0.00 3.16
5039 14594 5.612725 AATAAACCATGGGCAAATAGTGG 57.387 39.130 18.09 0.00 36.06 4.00
5049 14604 1.408822 GCAAATAGTGGGGGTGGAGAG 60.409 57.143 0.00 0.00 0.00 3.20
5055 14610 1.846124 TGGGGGTGGAGAGGACAAC 60.846 63.158 0.00 0.00 0.00 3.32
5102 14696 8.367156 ACCATTGCAAACCAATACCATTATATC 58.633 33.333 1.71 0.00 42.15 1.63
5103 14697 7.818930 CCATTGCAAACCAATACCATTATATCC 59.181 37.037 1.71 0.00 42.15 2.59
5119 14713 8.091449 CCATTATATCCTTACTTCTGGAGTGAC 58.909 40.741 0.00 0.00 39.48 3.67
5125 14719 4.932200 CCTTACTTCTGGAGTGACAATGTC 59.068 45.833 6.41 6.41 39.48 3.06
5126 14720 3.409026 ACTTCTGGAGTGACAATGTCC 57.591 47.619 11.24 2.45 37.17 4.02
5144 14738 3.066064 TGTCCAACATTGTGAAAGAACGG 59.934 43.478 0.00 0.00 0.00 4.44
5157 14751 3.604875 AAGAACGGGAGATTTTCGCTA 57.395 42.857 0.00 0.00 36.65 4.26
5158 14752 3.166489 AGAACGGGAGATTTTCGCTAG 57.834 47.619 0.00 0.00 36.65 3.42
5159 14753 1.593469 GAACGGGAGATTTTCGCTAGC 59.407 52.381 4.06 4.06 36.65 3.42
5160 14754 0.824759 ACGGGAGATTTTCGCTAGCT 59.175 50.000 13.93 0.00 36.65 3.32
5169 14763 2.543777 TTTCGCTAGCTCCAAGTTGT 57.456 45.000 13.93 0.00 0.00 3.32
5175 14769 3.610911 GCTAGCTCCAAGTTGTACCAAT 58.389 45.455 7.70 0.00 0.00 3.16
5198 14792 3.880846 CATCTTTGCCCTCCGCGC 61.881 66.667 0.00 0.00 42.08 6.86
5205 14799 4.971125 GCCCTCCGCGCCTACATC 62.971 72.222 0.00 0.00 0.00 3.06
5206 14800 3.536917 CCCTCCGCGCCTACATCA 61.537 66.667 0.00 0.00 0.00 3.07
5207 14801 2.499205 CCTCCGCGCCTACATCAA 59.501 61.111 0.00 0.00 0.00 2.57
5210 14804 1.270094 CCTCCGCGCCTACATCAAATA 60.270 52.381 0.00 0.00 0.00 1.40
5215 14809 2.348666 CGCGCCTACATCAAATATAGCC 59.651 50.000 0.00 0.00 0.00 3.93
5224 14818 7.816995 CCTACATCAAATATAGCCAAGAGAGAC 59.183 40.741 0.00 0.00 0.00 3.36
5225 14819 7.372260 ACATCAAATATAGCCAAGAGAGACT 57.628 36.000 0.00 0.00 0.00 3.24
5238 14832 9.692325 AGCCAAGAGAGACTAAATGATATTTTT 57.308 29.630 0.00 0.00 0.00 1.94
5309 14903 3.132824 TGTGCTCTTCTTGTGAGTTGAGA 59.867 43.478 0.00 0.00 34.30 3.27
5310 14904 4.122776 GTGCTCTTCTTGTGAGTTGAGAA 58.877 43.478 0.00 0.00 34.30 2.87
5320 14914 4.876125 TGTGAGTTGAGAAAGTAGAGCAG 58.124 43.478 0.00 0.00 0.00 4.24
5344 14938 8.768955 CAGCTTATTATTATTTGAGAGAAGCGT 58.231 33.333 0.00 0.00 41.21 5.07
5361 14955 1.792367 GCGTGGACAAATCCTTTTTGC 59.208 47.619 0.00 0.00 46.43 3.68
5396 14990 0.464735 TAACTGCCGCACACAACCTT 60.465 50.000 0.00 0.00 0.00 3.50
5431 15025 3.342719 TGAACATCGTATTGGCATGTGT 58.657 40.909 0.00 0.00 31.00 3.72
5432 15026 3.126686 TGAACATCGTATTGGCATGTGTG 59.873 43.478 0.00 0.00 31.00 3.82
5433 15027 2.710377 ACATCGTATTGGCATGTGTGT 58.290 42.857 0.00 0.00 29.36 3.72
5434 15028 3.081061 ACATCGTATTGGCATGTGTGTT 58.919 40.909 0.00 0.00 29.36 3.32
5435 15029 3.505680 ACATCGTATTGGCATGTGTGTTT 59.494 39.130 0.00 0.00 29.36 2.83
5436 15030 3.822594 TCGTATTGGCATGTGTGTTTC 57.177 42.857 0.00 0.00 0.00 2.78
5437 15031 2.486203 TCGTATTGGCATGTGTGTTTCC 59.514 45.455 0.00 0.00 0.00 3.13
5438 15032 2.415357 CGTATTGGCATGTGTGTTTCCC 60.415 50.000 0.00 0.00 0.00 3.97
5439 15033 2.014010 ATTGGCATGTGTGTTTCCCT 57.986 45.000 0.00 0.00 0.00 4.20
5440 15034 1.327303 TTGGCATGTGTGTTTCCCTC 58.673 50.000 0.00 0.00 0.00 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 8.691661 ATTTTGGTCACATACTTCACTAGTTT 57.308 30.769 0.00 0.00 38.33 2.66
303 2696 7.201785 CCCGTTGGCAGTTATAAATGAATTACT 60.202 37.037 16.69 0.00 0.00 2.24
329 3144 2.052237 CATCGCAAATACGCCGCC 60.052 61.111 0.00 0.00 0.00 6.13
838 5028 2.422479 GGGGAAACGTAGCTTTCATTCC 59.578 50.000 10.81 10.81 36.45 3.01
872 5064 2.036475 CTCTGTGGTGCACTCAACTAGT 59.964 50.000 17.98 0.00 39.81 2.57
1012 5243 3.069872 AGTGGAAGCATCTCTAGCATGAG 59.930 47.826 0.00 0.22 35.52 2.90
1032 5289 1.145738 AGGAACAGAAACCATGGCAGT 59.854 47.619 13.04 0.05 0.00 4.40
1275 5538 2.358125 CGCGGGGATGACACAACA 60.358 61.111 0.00 0.00 0.00 3.33
1364 5627 0.034059 GGACGAGCCATACATGAGGG 59.966 60.000 0.00 0.00 36.34 4.30
1425 5688 0.109039 GAGTGGTGACGAGCTTCCTC 60.109 60.000 0.00 0.00 34.66 3.71
1554 5817 2.418368 AGTTTCAGGTGTGCAGACAA 57.582 45.000 16.68 0.00 32.49 3.18
1586 5849 9.188588 GGGTTATAAAAAGAAACTTGCAGTAAC 57.811 33.333 0.00 0.00 0.00 2.50
1609 5872 2.505819 GAGAGACAGAGAGAGAGAGGGT 59.494 54.545 0.00 0.00 0.00 4.34
1613 5876 4.614475 AGAGAGAGAGACAGAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1615 5878 4.614475 AGAGAGAGAGAGACAGAGAGAGA 58.386 47.826 0.00 0.00 0.00 3.10
1616 5879 4.202202 GGAGAGAGAGAGAGACAGAGAGAG 60.202 54.167 0.00 0.00 0.00 3.20
1617 5880 3.706594 GGAGAGAGAGAGAGACAGAGAGA 59.293 52.174 0.00 0.00 0.00 3.10
1618 5881 3.181461 GGGAGAGAGAGAGAGACAGAGAG 60.181 56.522 0.00 0.00 0.00 3.20
1619 5882 2.771943 GGGAGAGAGAGAGAGACAGAGA 59.228 54.545 0.00 0.00 0.00 3.10
1620 5883 2.505407 TGGGAGAGAGAGAGAGACAGAG 59.495 54.545 0.00 0.00 0.00 3.35
1621 5884 2.556766 TGGGAGAGAGAGAGAGACAGA 58.443 52.381 0.00 0.00 0.00 3.41
1622 5885 3.364460 TTGGGAGAGAGAGAGAGACAG 57.636 52.381 0.00 0.00 0.00 3.51
1623 5886 3.816398 TTTGGGAGAGAGAGAGAGACA 57.184 47.619 0.00 0.00 0.00 3.41
1624 5887 6.976934 ATAATTTGGGAGAGAGAGAGAGAC 57.023 41.667 0.00 0.00 0.00 3.36
1625 5888 7.401493 ACAAATAATTTGGGAGAGAGAGAGAGA 59.599 37.037 0.00 0.00 44.81 3.10
1627 5890 7.334090 CACAAATAATTTGGGAGAGAGAGAGA 58.666 38.462 0.00 0.00 46.96 3.10
1638 5901 7.437793 ACAAAATCAGCACAAATAATTTGGG 57.562 32.000 0.00 0.00 46.72 4.12
1700 5963 5.574188 AGCACATTTCCCTTTAGATGAGTT 58.426 37.500 0.00 0.00 0.00 3.01
1701 5964 5.184892 AGCACATTTCCCTTTAGATGAGT 57.815 39.130 0.00 0.00 0.00 3.41
1702 5965 7.814264 ATTAGCACATTTCCCTTTAGATGAG 57.186 36.000 0.00 0.00 0.00 2.90
1708 5971 9.515226 GGTCATATATTAGCACATTTCCCTTTA 57.485 33.333 0.00 0.00 0.00 1.85
1709 5972 8.227507 AGGTCATATATTAGCACATTTCCCTTT 58.772 33.333 0.00 0.00 0.00 3.11
1710 5973 7.759607 AGGTCATATATTAGCACATTTCCCTT 58.240 34.615 0.00 0.00 0.00 3.95
1711 5974 7.017551 TGAGGTCATATATTAGCACATTTCCCT 59.982 37.037 0.00 0.00 0.00 4.20
1712 5975 7.168219 TGAGGTCATATATTAGCACATTTCCC 58.832 38.462 0.00 0.00 0.00 3.97
1713 5976 8.798859 ATGAGGTCATATATTAGCACATTTCC 57.201 34.615 3.96 0.00 34.26 3.13
1714 5977 9.664332 AGATGAGGTCATATATTAGCACATTTC 57.336 33.333 9.43 1.68 36.57 2.17
1719 5982 9.593134 CCTTTAGATGAGGTCATATATTAGCAC 57.407 37.037 0.00 0.00 36.57 4.40
1720 5983 8.762645 CCCTTTAGATGAGGTCATATATTAGCA 58.237 37.037 0.00 0.00 36.57 3.49
1721 5984 8.982723 TCCCTTTAGATGAGGTCATATATTAGC 58.017 37.037 0.00 0.00 36.57 3.09
1726 5989 9.170890 ACATTTCCCTTTAGATGAGGTCATATA 57.829 33.333 0.00 0.00 36.57 0.86
1727 5990 7.941238 CACATTTCCCTTTAGATGAGGTCATAT 59.059 37.037 0.00 0.00 36.57 1.78
1728 5991 7.282585 CACATTTCCCTTTAGATGAGGTCATA 58.717 38.462 0.00 0.00 36.57 2.15
1729 5992 6.125029 CACATTTCCCTTTAGATGAGGTCAT 58.875 40.000 0.00 0.00 39.70 3.06
1850 6113 8.017418 AGATTTGTCCAAAGTCCAACATTTTA 57.983 30.769 0.00 0.00 33.32 1.52
1865 6128 7.712639 GCTTCACTCATATTCTAGATTTGTCCA 59.287 37.037 0.00 0.00 0.00 4.02
1937 6255 9.747293 AACTAGACTTTCTACTTACAAGTTGTC 57.253 33.333 12.82 0.00 40.37 3.18
1982 6318 0.464036 CTATGGACGGCTAGCAACCA 59.536 55.000 22.32 22.32 35.09 3.67
1983 6319 0.464452 ACTATGGACGGCTAGCAACC 59.536 55.000 18.24 15.92 0.00 3.77
1984 6320 1.134788 ACACTATGGACGGCTAGCAAC 60.135 52.381 18.24 6.77 0.00 4.17
1985 6321 1.191535 ACACTATGGACGGCTAGCAA 58.808 50.000 18.24 0.00 0.00 3.91
1986 6322 1.954382 CTACACTATGGACGGCTAGCA 59.046 52.381 18.24 0.00 0.00 3.49
1987 6323 2.228059 TCTACACTATGGACGGCTAGC 58.772 52.381 6.04 6.04 0.00 3.42
1988 6324 3.630769 TGTTCTACACTATGGACGGCTAG 59.369 47.826 0.00 0.00 0.00 3.42
1989 6325 3.379372 GTGTTCTACACTATGGACGGCTA 59.621 47.826 2.82 0.00 45.27 3.93
1990 6326 2.165845 GTGTTCTACACTATGGACGGCT 59.834 50.000 2.82 0.00 45.27 5.52
1991 6327 2.537401 GTGTTCTACACTATGGACGGC 58.463 52.381 2.82 0.00 45.27 5.68
1998 6334 9.950496 ATTCAGAAGAAATGTGTTCTACACTAT 57.050 29.630 10.88 1.51 42.37 2.12
2006 6342 9.173939 CAACAACTATTCAGAAGAAATGTGTTC 57.826 33.333 0.00 0.00 37.29 3.18
2072 6419 2.052782 AAGAAACATATCCGCCACCC 57.947 50.000 0.00 0.00 0.00 4.61
2134 6486 0.179129 TGCGCTACCGGCTTAAGTAC 60.179 55.000 9.73 0.00 39.13 2.73
2154 9538 7.872061 AACACCTATATAAGTGATCCATCCA 57.128 36.000 16.69 0.00 37.43 3.41
2209 9593 2.906691 CATGGTCTCATGTCTCCTCC 57.093 55.000 0.00 0.00 44.22 4.30
2256 9640 8.450578 TGTATTATTGCATCTCAAAACCTAGG 57.549 34.615 7.41 7.41 38.34 3.02
2349 9733 5.997746 CAGGAAAACTGGACTGTCTATTCAA 59.002 40.000 7.85 0.00 43.70 2.69
2371 9755 4.017126 GGGGAATTGGAGAAGGTTAACAG 58.983 47.826 8.10 0.00 0.00 3.16
2372 9756 3.560453 CGGGGAATTGGAGAAGGTTAACA 60.560 47.826 8.10 0.00 0.00 2.41
2380 9764 4.788925 ATTACATCGGGGAATTGGAGAA 57.211 40.909 0.00 0.00 0.00 2.87
2468 9852 2.108601 TCACGGGGGAAATTAACCTTGT 59.891 45.455 0.00 0.00 0.00 3.16
2512 9896 5.163814 CCTTTCAAACTGATCTTAAGCCTCG 60.164 44.000 0.00 0.00 0.00 4.63
2589 9973 1.990614 GAAGTCTCCTCCGCCCCTT 60.991 63.158 0.00 0.00 0.00 3.95
2693 10089 1.920835 GTCTCTCCCACTGGCCCTT 60.921 63.158 0.00 0.00 0.00 3.95
2870 11500 5.009854 CAAAGAACCACCTTTGTTGTCAT 57.990 39.130 0.00 0.00 44.73 3.06
2907 11540 6.524101 GGATTTGTAAAGCCATGACCTTTA 57.476 37.500 6.76 11.93 43.73 1.85
3094 11752 4.850680 TGGGAGATATGTGGTGGTAAAAC 58.149 43.478 0.00 0.00 0.00 2.43
3121 11782 9.931210 AGTTTCGTCAGTAGAAAACAATTTAAG 57.069 29.630 0.00 0.00 39.03 1.85
3353 12021 3.441101 AGCCTACTCATGTCCACTACAA 58.559 45.455 0.00 0.00 42.70 2.41
3549 12217 0.746063 CAGCCTTTGCACAAACCAGA 59.254 50.000 0.00 0.00 41.13 3.86
3550 12218 0.746063 TCAGCCTTTGCACAAACCAG 59.254 50.000 0.00 0.00 41.13 4.00
4283 12965 4.628333 CCAACATAAGCTCAAAATTGGCAG 59.372 41.667 0.00 0.00 0.00 4.85
4348 13030 9.599866 TGTCATATTAATGTCTTTCGTCTCAAT 57.400 29.630 0.00 0.00 34.50 2.57
4366 13048 3.010584 AGCCCAAAGACCACTGTCATATT 59.989 43.478 0.00 0.00 44.33 1.28
4398 13080 3.737032 AATAGTAGCTTCTCCTTCCGC 57.263 47.619 0.00 0.00 0.00 5.54
4481 13488 9.883142 CCCCTTTCTTTATTTGCAACAATATAA 57.117 29.630 0.00 0.00 0.00 0.98
4591 13603 7.233389 TCAAGCTCACAGAGTTAACTAGATT 57.767 36.000 8.42 4.06 31.39 2.40
4596 13608 5.474578 TGATCAAGCTCACAGAGTTAACT 57.525 39.130 8.13 8.13 31.39 2.24
4656 13668 0.415830 TCCTACACCCCCATGAGTCA 59.584 55.000 0.00 0.00 0.00 3.41
4768 13916 2.552315 CCGTATGGTCAAGCACAAGTTT 59.448 45.455 0.00 0.00 0.00 2.66
4769 13917 2.151202 CCGTATGGTCAAGCACAAGTT 58.849 47.619 0.00 0.00 0.00 2.66
4797 14352 9.477484 CTAATTAGATTAGATGGGTACACACAC 57.523 37.037 0.00 0.00 43.85 3.82
4798 14353 8.148351 GCTAATTAGATTAGATGGGTACACACA 58.852 37.037 16.85 0.00 43.85 3.72
4882 14437 1.142870 TCCACCACAAAGGACCAGAAG 59.857 52.381 0.00 0.00 41.22 2.85
4915 14470 2.401583 TGTGAGCACTTGAACACACT 57.598 45.000 1.99 0.00 38.14 3.55
4951 14506 6.727824 AATGAACTTCTATTGAACGTCTGG 57.272 37.500 0.00 0.00 0.00 3.86
5008 14563 5.897050 TGCCCATGGTTTATTTAACGATTC 58.103 37.500 11.73 0.00 37.64 2.52
5039 14594 0.476771 TTTGTTGTCCTCTCCACCCC 59.523 55.000 0.00 0.00 0.00 4.95
5049 14604 9.313118 ACAAACTATTTCTGAAATTTGTTGTCC 57.687 29.630 19.68 0.00 29.61 4.02
5102 14696 4.899502 ACATTGTCACTCCAGAAGTAAGG 58.100 43.478 0.00 0.00 36.07 2.69
5103 14697 4.932200 GGACATTGTCACTCCAGAAGTAAG 59.068 45.833 18.09 0.00 36.07 2.34
5125 14719 2.621055 TCCCGTTCTTTCACAATGTTGG 59.379 45.455 0.00 0.00 0.00 3.77
5126 14720 3.563808 TCTCCCGTTCTTTCACAATGTTG 59.436 43.478 0.00 0.00 0.00 3.33
5144 14738 2.604046 TGGAGCTAGCGAAAATCTCC 57.396 50.000 9.55 9.47 42.67 3.71
5169 14763 6.323739 GGAGGGCAAAGATGATTAAATTGGTA 59.676 38.462 0.00 0.00 0.00 3.25
5175 14769 2.687935 GCGGAGGGCAAAGATGATTAAA 59.312 45.455 0.00 0.00 42.87 1.52
5198 14792 7.816995 GTCTCTCTTGGCTATATTTGATGTAGG 59.183 40.741 0.00 0.00 0.00 3.18
5204 14798 9.770097 CATTTAGTCTCTCTTGGCTATATTTGA 57.230 33.333 0.00 0.00 0.00 2.69
5205 14799 9.770097 TCATTTAGTCTCTCTTGGCTATATTTG 57.230 33.333 0.00 0.00 0.00 2.32
5238 14832 7.013274 TGTTCACCACAAAAACATTTTGGAAAA 59.987 29.630 17.10 6.02 33.92 2.29
5239 14833 6.486657 TGTTCACCACAAAAACATTTTGGAAA 59.513 30.769 17.10 4.35 33.92 3.13
5240 14834 5.997746 TGTTCACCACAAAAACATTTTGGAA 59.002 32.000 17.10 9.50 33.92 3.53
5257 14851 6.262273 TCTTTCCAATACTGAGTTTGTTCACC 59.738 38.462 0.00 0.00 0.00 4.02
5298 14892 4.797604 GCTGCTCTACTTTCTCAACTCACA 60.798 45.833 0.00 0.00 0.00 3.58
5320 14914 8.012241 CCACGCTTCTCTCAAATAATAATAAGC 58.988 37.037 0.00 0.00 34.83 3.09
5344 14938 5.350504 TTGAAGCAAAAAGGATTTGTCCA 57.649 34.783 3.22 0.00 39.02 4.02
5361 14955 5.281727 GGCAGTTAGAAGTTGGTTTTGAAG 58.718 41.667 0.00 0.00 0.00 3.02
5396 14990 4.335315 ACGATGTTCAACTTCAAGCTCAAA 59.665 37.500 4.44 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.