Multiple sequence alignment - TraesCS7D01G148400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G148400 chr7D 100.000 6455 0 0 1 6455 95153029 95146575 0.000000e+00 11921.0
1 TraesCS7D01G148400 chr7D 86.080 3865 361 73 2173 5980 96084673 96080929 0.000000e+00 3993.0
2 TraesCS7D01G148400 chr7D 85.372 3008 277 73 2662 5627 96033178 96030292 0.000000e+00 2966.0
3 TraesCS7D01G148400 chr7D 89.595 1653 112 23 1 1601 96053099 96051455 0.000000e+00 2045.0
4 TraesCS7D01G148400 chr7D 87.536 1725 178 21 3920 5633 95835172 95833474 0.000000e+00 1960.0
5 TraesCS7D01G148400 chr7D 87.783 1678 182 13 3965 5633 96017387 96015724 0.000000e+00 1941.0
6 TraesCS7D01G148400 chr7D 87.493 1711 173 18 3932 5633 95990552 95988874 0.000000e+00 1936.0
7 TraesCS7D01G148400 chr7D 86.988 1683 184 20 3965 5633 95964507 95962846 0.000000e+00 1862.0
8 TraesCS7D01G148400 chr7D 87.037 1674 179 18 3965 5633 95970574 95968934 0.000000e+00 1855.0
9 TraesCS7D01G148400 chr7D 85.799 1352 149 16 4366 5704 95976277 95974956 0.000000e+00 1393.0
10 TraesCS7D01G148400 chr7D 91.809 586 28 4 1034 1599 96085671 96085086 0.000000e+00 798.0
11 TraesCS7D01G148400 chr7D 87.340 703 61 13 373 1049 96086383 96085683 0.000000e+00 780.0
12 TraesCS7D01G148400 chr7D 90.812 468 42 1 2153 2620 96048579 96048113 5.500000e-175 625.0
13 TraesCS7D01G148400 chr7D 88.915 424 21 5 1596 2012 96051420 96051016 3.480000e-137 499.0
14 TraesCS7D01G148400 chr7D 77.765 895 131 43 738 1596 95054794 95055656 7.520000e-134 488.0
15 TraesCS7D01G148400 chr7D 90.663 332 18 5 1 320 96086718 96086388 4.620000e-116 429.0
16 TraesCS7D01G148400 chr7D 76.653 711 137 21 2152 2837 95057156 95057862 3.680000e-97 366.0
17 TraesCS7D01G148400 chr7D 90.217 276 17 5 1596 1864 96085049 96084777 1.030000e-92 351.0
18 TraesCS7D01G148400 chr7D 88.433 268 24 5 5737 6002 96079632 96079370 3.760000e-82 316.0
19 TraesCS7D01G148400 chr7D 89.655 203 20 1 6243 6445 96081638 96081437 2.310000e-64 257.0
20 TraesCS7D01G148400 chr7D 89.163 203 21 1 6243 6445 95989219 95989018 1.070000e-62 252.0
21 TraesCS7D01G148400 chr7D 88.670 203 22 1 6243 6445 95147751 95147550 5.000000e-61 246.0
22 TraesCS7D01G148400 chr7D 88.670 203 22 1 6243 6445 95997224 95997023 5.000000e-61 246.0
23 TraesCS7D01G148400 chr7D 88.670 203 19 4 6243 6445 95969285 95969087 1.800000e-60 244.0
24 TraesCS7D01G148400 chr7D 87.685 203 24 1 6243 6445 95975370 95975169 1.080000e-57 235.0
25 TraesCS7D01G148400 chr7D 84.018 219 19 6 3733 3941 95829331 95829119 5.110000e-46 196.0
26 TraesCS7D01G148400 chr7D 83.260 227 24 6 3733 3949 95964797 95964575 5.110000e-46 196.0
27 TraesCS7D01G148400 chr7D 83.482 224 22 7 3736 3949 95990805 95990587 1.840000e-45 195.0
28 TraesCS7D01G148400 chr7D 77.961 304 38 14 1566 1852 95055674 95055965 5.180000e-36 163.0
29 TraesCS7D01G148400 chr7D 86.624 157 5 1 5582 5738 96079888 96079748 6.700000e-35 159.0
30 TraesCS7D01G148400 chr7D 100.000 39 0 0 5587 5625 96079967 96079929 8.980000e-09 73.1
31 TraesCS7D01G148400 chr7B 90.959 3451 252 23 2116 5551 49359588 49362993 0.000000e+00 4590.0
32 TraesCS7D01G148400 chr7B 89.246 2399 214 14 3163 5551 49613540 49611176 0.000000e+00 2961.0
33 TraesCS7D01G148400 chr7B 90.267 2281 160 20 1596 3848 49554362 49556608 0.000000e+00 2926.0
34 TraesCS7D01G148400 chr7B 88.695 1663 119 33 1 1601 49357297 49358952 0.000000e+00 1965.0
35 TraesCS7D01G148400 chr7B 88.874 1483 152 4 4069 5549 49587642 49589113 0.000000e+00 1812.0
36 TraesCS7D01G148400 chr7B 88.565 1338 92 23 900 2196 49618211 49616894 0.000000e+00 1567.0
37 TraesCS7D01G148400 chr7B 91.318 933 67 10 2191 3118 49614465 49613542 0.000000e+00 1262.0
38 TraesCS7D01G148400 chr7B 86.049 1025 89 23 1 990 50881651 50880646 0.000000e+00 1051.0
39 TraesCS7D01G148400 chr7B 86.744 943 77 17 9 914 49619449 49618518 0.000000e+00 1005.0
40 TraesCS7D01G148400 chr7B 86.658 742 70 13 316 1031 49552780 49553518 0.000000e+00 795.0
41 TraesCS7D01G148400 chr7B 86.479 710 83 7 4927 5633 50626524 50625825 0.000000e+00 767.0
42 TraesCS7D01G148400 chr7B 84.100 761 103 13 3020 3773 49182453 49183202 0.000000e+00 719.0
43 TraesCS7D01G148400 chr7B 89.685 572 38 7 1019 1569 49553533 49554104 0.000000e+00 710.0
44 TraesCS7D01G148400 chr7B 83.966 711 88 13 4927 5633 50629643 50628955 0.000000e+00 658.0
45 TraesCS7D01G148400 chr7B 81.518 817 117 11 4927 5738 50363793 50363006 5.460000e-180 641.0
46 TraesCS7D01G148400 chr7B 87.218 532 44 3 1596 2115 49358987 49359506 9.330000e-163 584.0
47 TraesCS7D01G148400 chr7B 87.450 502 62 1 4979 5480 50635374 50634874 1.560000e-160 577.0
48 TraesCS7D01G148400 chr7B 89.851 335 21 6 1 323 49551289 49551622 1.000000e-112 418.0
49 TraesCS7D01G148400 chr7B 76.361 698 137 18 2151 2829 49181616 49182304 3.700000e-92 350.0
50 TraesCS7D01G148400 chr7B 94.393 214 9 2 3856 4069 49573058 49573268 6.240000e-85 326.0
51 TraesCS7D01G148400 chr7B 86.854 213 27 1 6243 6455 50635075 50634864 3.010000e-58 237.0
52 TraesCS7D01G148400 chr7B 83.945 218 21 8 3743 3949 50714626 50714412 5.110000e-46 196.0
53 TraesCS7D01G148400 chr7B 83.871 93 8 5 6011 6100 49548970 49548882 1.490000e-11 82.4
54 TraesCS7D01G148400 chr7B 76.023 171 30 7 5558 5726 49230411 49230572 1.930000e-10 78.7
55 TraesCS7D01G148400 chr7B 88.525 61 5 2 6013 6072 49610706 49610647 8.980000e-09 73.1
56 TraesCS7D01G148400 chr7B 87.302 63 5 3 6011 6072 49607984 49608044 1.160000e-07 69.4
57 TraesCS7D01G148400 chr7A 94.480 2645 133 4 3107 5738 99144679 99142035 0.000000e+00 4063.0
58 TraesCS7D01G148400 chr7A 91.382 2077 91 26 1032 3043 99146763 99144710 0.000000e+00 2763.0
59 TraesCS7D01G148400 chr7A 92.067 895 56 5 41 923 99147683 99146792 0.000000e+00 1245.0
60 TraesCS7D01G148400 chr7A 86.376 712 40 12 5737 6429 99141915 99141242 0.000000e+00 725.0
61 TraesCS7D01G148400 chr7A 80.757 925 138 26 2860 3773 98728977 98729872 0.000000e+00 686.0
62 TraesCS7D01G148400 chr7A 79.119 522 86 18 2080 2595 98728207 98728711 8.020000e-89 339.0
63 TraesCS7D01G148400 chr7A 88.670 203 22 1 6243 6445 99142496 99142295 5.000000e-61 246.0
64 TraesCS7D01G148400 chr7A 79.934 304 32 13 1566 1852 98727113 98727404 5.110000e-46 196.0
65 TraesCS7D01G148400 chr7A 100.000 49 0 0 1 49 99147914 99147866 2.480000e-14 91.6
66 TraesCS7D01G148400 chr7A 100.000 36 0 0 940 975 99146794 99146759 4.180000e-07 67.6
67 TraesCS7D01G148400 chr5D 81.777 889 129 21 3119 3984 547238530 547237652 0.000000e+00 713.0
68 TraesCS7D01G148400 chr4A 82.030 857 131 15 3119 3958 621738808 621739658 0.000000e+00 708.0


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 TraesCS7D01G148400 chr7D 95146575 95153029 6454 True 11921.000000 11921 100.000000 1 6455 1 chr7D.!!$R1 6454
1 TraesCS7D01G148400 chr7D 96030292 96033178 2886 True 2966.000000 2966 85.372000 2662 5627 1 chr7D.!!$R7 2965
2 TraesCS7D01G148400 chr7D 95833474 95835172 1698 True 1960.000000 1960 87.536000 3920 5633 1 chr7D.!!$R4 1713
3 TraesCS7D01G148400 chr7D 96015724 96017387 1663 True 1941.000000 1941 87.783000 3965 5633 1 chr7D.!!$R6 1668
4 TraesCS7D01G148400 chr7D 96048113 96053099 4986 True 1056.333333 2045 89.774000 1 2620 3 chr7D.!!$R12 2619
5 TraesCS7D01G148400 chr7D 95968934 95970574 1640 True 1049.500000 1855 87.853500 3965 6445 2 chr7D.!!$R9 2480
6 TraesCS7D01G148400 chr7D 95962846 95964797 1951 True 1029.000000 1862 85.124000 3733 5633 2 chr7D.!!$R8 1900
7 TraesCS7D01G148400 chr7D 95974956 95976277 1321 True 814.000000 1393 86.742000 4366 6445 2 chr7D.!!$R10 2079
8 TraesCS7D01G148400 chr7D 96079370 96086718 7348 True 795.122222 3993 90.091222 1 6445 9 chr7D.!!$R13 6444
9 TraesCS7D01G148400 chr7D 95988874 95990805 1931 True 794.333333 1936 86.712667 3736 6445 3 chr7D.!!$R11 2709
10 TraesCS7D01G148400 chr7D 95054794 95057862 3068 False 339.000000 488 77.459667 738 2837 3 chr7D.!!$F1 2099
11 TraesCS7D01G148400 chr7B 49357297 49362993 5696 False 2379.666667 4590 88.957333 1 5551 3 chr7B.!!$F6 5550
12 TraesCS7D01G148400 chr7B 49587642 49589113 1471 False 1812.000000 1812 88.874000 4069 5549 1 chr7B.!!$F3 1480
13 TraesCS7D01G148400 chr7B 49610647 49619449 8802 True 1373.620000 2961 88.879600 9 6072 5 chr7B.!!$R5 6063
14 TraesCS7D01G148400 chr7B 49551289 49556608 5319 False 1212.250000 2926 89.115250 1 3848 4 chr7B.!!$F7 3847
15 TraesCS7D01G148400 chr7B 50880646 50881651 1005 True 1051.000000 1051 86.049000 1 990 1 chr7B.!!$R4 989
16 TraesCS7D01G148400 chr7B 50625825 50629643 3818 True 712.500000 767 85.222500 4927 5633 2 chr7B.!!$R6 706
17 TraesCS7D01G148400 chr7B 50363006 50363793 787 True 641.000000 641 81.518000 4927 5738 1 chr7B.!!$R2 811
18 TraesCS7D01G148400 chr7B 49181616 49183202 1586 False 534.500000 719 80.230500 2151 3773 2 chr7B.!!$F5 1622
19 TraesCS7D01G148400 chr7B 50634864 50635374 510 True 407.000000 577 87.152000 4979 6455 2 chr7B.!!$R7 1476
20 TraesCS7D01G148400 chr7A 99141242 99147914 6672 True 1314.457143 4063 93.282143 1 6445 7 chr7A.!!$R1 6444
21 TraesCS7D01G148400 chr7A 98727113 98729872 2759 False 407.000000 686 79.936667 1566 3773 3 chr7A.!!$F1 2207
22 TraesCS7D01G148400 chr5D 547237652 547238530 878 True 713.000000 713 81.777000 3119 3984 1 chr5D.!!$R1 865
23 TraesCS7D01G148400 chr4A 621738808 621739658 850 False 708.000000 708 82.030000 3119 3958 1 chr4A.!!$F1 839

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
689 2089 0.032540 GTGGTTACGGTGGTTCTCGT 59.967 55.0 0.00 0.0 42.55 4.18 F
1351 3227 0.389166 GAGAACGGTCAGCAGTCAGG 60.389 60.0 1.87 0.0 0.00 3.86 F
1816 3978 0.462789 ACCTGGTAACGCCCTATTCG 59.537 55.0 0.00 0.0 42.51 3.34 F
3179 11362 0.327924 TCGACATGGGCAAGTTGGAT 59.672 50.0 4.75 0.0 0.00 3.41 F
3312 11495 0.250295 CCCTTGCAACTTCTCCGTGA 60.250 55.0 0.00 0.0 0.00 4.35 F
3643 11826 0.551879 CCCGGAGAGAAGAGGGAGTA 59.448 60.0 0.73 0.0 46.64 2.59 F
4990 13265 0.614697 TCTGCAGAGAATCCACGGGA 60.615 55.0 13.74 0.0 33.66 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2363 10474 1.069636 GGAGCGCTTTCTTCTGTTGTG 60.070 52.381 13.26 0.00 0.00 3.33 R
3161 11344 1.133025 GAATCCAACTTGCCCATGTCG 59.867 52.381 0.00 0.00 0.00 4.35 R
3257 11440 1.774254 ACACCTCTTGACATCCCAACA 59.226 47.619 0.00 0.00 0.00 3.33 R
4820 13095 1.067060 TCTCGAACTGATATGGGTGCG 59.933 52.381 0.00 0.07 35.97 5.34 R
4990 13265 1.751351 TCCGAGATCGCTCAACATCTT 59.249 47.619 0.00 0.00 41.36 2.40 R
5384 16795 0.377203 CGGCTTTGGTATCGGCTTTC 59.623 55.000 0.00 0.00 0.00 2.62 R
6352 19379 0.974010 TCTTCGGCTTGGGTATCGGT 60.974 55.000 0.00 0.00 0.00 4.69 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
94 288 0.881159 CCACGGTGTTTTAGGCGTCA 60.881 55.000 7.45 0.00 0.00 4.35
174 368 5.667626 AGATATCCTTCCATGTGTGTAAGGT 59.332 40.000 0.00 0.00 39.62 3.50
187 381 4.396790 GTGTGTAAGGTGTGGACTTCAAAA 59.603 41.667 0.00 0.00 0.00 2.44
439 1812 1.070175 GTGGAATGTCACGACAAACGG 60.070 52.381 3.61 0.00 45.41 4.44
443 1816 2.806608 ATGTCACGACAAACGGTACT 57.193 45.000 3.61 0.00 45.41 2.73
497 1870 1.321474 ATTGCTTACATGCCGATGGG 58.679 50.000 0.00 0.00 33.39 4.00
517 1890 3.061697 GGGTTGACACAACGAATATCGAC 59.938 47.826 6.78 0.00 43.74 4.20
550 1923 7.768582 TCATGACAAATGTTACCGTTAGATGAT 59.231 33.333 0.00 0.00 0.00 2.45
560 1933 5.622770 ACCGTTAGATGATTTGAAACACC 57.377 39.130 0.00 0.00 0.00 4.16
645 2045 2.092699 TGGGAGTGTGTTTGATGTCACA 60.093 45.455 0.00 0.00 41.37 3.58
689 2089 0.032540 GTGGTTACGGTGGTTCTCGT 59.967 55.000 0.00 0.00 42.55 4.18
717 2117 5.213519 TCTTCCGTCTCCTCCCATATAAAA 58.786 41.667 0.00 0.00 0.00 1.52
756 2156 2.819595 CATGAACGCCGTGGAGGG 60.820 66.667 0.00 0.00 41.48 4.30
801 2201 2.680221 GCATGCAGTCTCTCATGGAAGT 60.680 50.000 14.21 0.00 40.16 3.01
890 2290 4.776349 ACATGTAATTTACCGAGCATCCA 58.224 39.130 0.00 0.00 0.00 3.41
913 2658 3.380004 TGTGGTTTAACTGTGCCTTCTTG 59.620 43.478 0.00 0.00 0.00 3.02
914 2659 3.380320 GTGGTTTAACTGTGCCTTCTTGT 59.620 43.478 0.00 0.00 0.00 3.16
1127 2933 8.905702 CACAGACAAATAAGTATCTTTTTGCAC 58.094 33.333 0.00 9.31 33.43 4.57
1307 3183 1.552792 TCATACACCAGCGTGAATGGA 59.447 47.619 0.00 0.00 43.14 3.41
1351 3227 0.389166 GAGAACGGTCAGCAGTCAGG 60.389 60.000 1.87 0.00 0.00 3.86
1622 3763 1.738099 GATCACCGACAAGCGCAGT 60.738 57.895 11.47 7.91 39.11 4.40
1755 3910 2.024319 GATATCGTGCTCCGCAGCC 61.024 63.158 0.00 0.00 46.26 4.85
1812 3974 0.609662 GTGAACCTGGTAACGCCCTA 59.390 55.000 0.00 0.00 42.51 3.53
1814 3976 1.910671 TGAACCTGGTAACGCCCTATT 59.089 47.619 0.00 0.00 42.51 1.73
1816 3978 0.462789 ACCTGGTAACGCCCTATTCG 59.537 55.000 0.00 0.00 42.51 3.34
1862 4024 9.702494 CATCATCCATATATGCGTATCTAACAT 57.298 33.333 7.24 0.00 0.00 2.71
1950 4112 5.470368 GTGGCAAGTATCTGCGAGATATTA 58.530 41.667 8.48 0.00 43.60 0.98
2073 7661 4.769488 CCAGATCCGAAGATTATCCTCTGA 59.231 45.833 0.00 0.00 30.90 3.27
2100 7690 9.673454 ATGAAAATTTTGTTTCCTTCGTAGTAC 57.327 29.630 8.47 0.00 36.80 2.73
2281 10391 2.606108 TCATGTGTGCAGTCACGATAC 58.394 47.619 3.32 0.00 46.01 2.24
2364 10475 4.165926 CTAGAGGCCGAGCTAGCA 57.834 61.111 18.83 0.00 0.00 3.49
2374 10485 1.067565 CCGAGCTAGCACAACAGAAGA 60.068 52.381 18.83 0.00 0.00 2.87
2446 10557 1.811266 CGCGCTAGCCACAACATCT 60.811 57.895 9.66 0.00 41.18 2.90
3040 11198 9.833894 GTTTATGCATAAGCGACAAATTTATTG 57.166 29.630 18.13 0.00 46.23 1.90
3044 11203 7.087007 TGCATAAGCGACAAATTTATTGTTCA 58.913 30.769 0.00 0.00 46.23 3.18
3045 11204 7.758980 TGCATAAGCGACAAATTTATTGTTCAT 59.241 29.630 0.00 0.00 46.23 2.57
3046 11205 8.594687 GCATAAGCGACAAATTTATTGTTCATT 58.405 29.630 0.00 0.00 31.96 2.57
3179 11362 0.327924 TCGACATGGGCAAGTTGGAT 59.672 50.000 4.75 0.00 0.00 3.41
3257 11440 0.680921 CCATGGACCTGGCGAATGTT 60.681 55.000 5.56 0.00 0.00 2.71
3300 11483 1.685224 GTGATCTGGGACCCTTGCA 59.315 57.895 13.00 1.92 0.00 4.08
3312 11495 0.250295 CCCTTGCAACTTCTCCGTGA 60.250 55.000 0.00 0.00 0.00 4.35
3480 11663 0.600255 CACCTCGTCGAAGTTTGCCT 60.600 55.000 0.00 0.00 0.00 4.75
3561 11744 2.044946 AGAATGGCGGCTTGTCCC 60.045 61.111 11.43 0.00 0.00 4.46
3643 11826 0.551879 CCCGGAGAGAAGAGGGAGTA 59.448 60.000 0.73 0.00 46.64 2.59
4180 12451 1.294780 CTGAAGGCCAGCGAGAGTT 59.705 57.895 5.01 0.00 35.89 3.01
4210 12481 1.079057 GACAACCTCGAGGAAGGGC 60.079 63.158 37.69 23.08 41.04 5.19
4279 12550 3.371063 GCGTCCTCCTCGTCCACA 61.371 66.667 0.00 0.00 0.00 4.17
4282 12553 2.117423 TCCTCCTCGTCCACAGCA 59.883 61.111 0.00 0.00 0.00 4.41
4341 12612 2.669133 CGGGATGAAGGTCTGGCCA 61.669 63.158 4.71 4.71 40.61 5.36
4377 12648 3.606662 CTCGCCCCGACCATCGAT 61.607 66.667 0.00 0.00 43.74 3.59
4399 12670 1.227943 GTGTGCTCCACCTTCAGCA 60.228 57.895 0.00 0.00 43.49 4.41
4459 12730 1.874466 GCTAGAGGCGACGACTTGC 60.874 63.158 3.81 6.60 34.93 4.01
4468 12739 2.645510 GACGACTTGCACGACACCG 61.646 63.158 1.86 0.72 42.50 4.94
4802 13077 2.151502 GTCATGAGAGACCTCCAGGA 57.848 55.000 0.00 0.00 38.66 3.86
4820 13095 0.748367 GAATCCCCTTTCGAGCACCC 60.748 60.000 0.00 0.00 0.00 4.61
4867 13142 2.459442 GCAGATCAGACCACTGCGC 61.459 63.158 0.00 0.00 45.25 6.09
4891 13166 2.202824 CCGAGATTACGCCCGCAA 60.203 61.111 0.00 0.00 0.00 4.85
4990 13265 0.614697 TCTGCAGAGAATCCACGGGA 60.615 55.000 13.74 0.00 33.66 5.14
5034 13309 2.456119 CGTGGAGATTGCAGGCGAC 61.456 63.158 0.00 0.00 0.00 5.19
5384 16795 3.806380 CTGGAATGGATCTTCACCTGAG 58.194 50.000 0.00 0.00 0.00 3.35
5451 16862 3.378112 TCTGCAAACAAGACAAGAACTGG 59.622 43.478 0.00 0.00 0.00 4.00
5470 16881 0.716108 GTGATGTTCTGTTCTCGCGG 59.284 55.000 6.13 0.00 0.00 6.46
5665 18537 7.114811 GTGACATTGTGTGAAATGGTTTATGTC 59.885 37.037 0.00 0.00 41.06 3.06
5821 18827 9.423061 TCTTTCTTTCTTTCTTTTCTTGTTTGG 57.577 29.630 0.00 0.00 0.00 3.28
6286 19313 2.026734 CCGATCATCGCGCTGACT 59.973 61.111 15.73 4.75 38.82 3.41
6336 19363 1.299648 CCGTCAAAGCTGGGATGGA 59.700 57.895 17.32 0.00 41.75 3.41
6352 19379 4.766891 GGGATGGATCTTCACTTGACAAAA 59.233 41.667 0.00 0.00 0.00 2.44
6394 19421 1.528129 CAGGGGTTGTTCTTGAGCTC 58.472 55.000 6.82 6.82 0.00 4.09
6414 19441 4.595116 CTCTGCAAACAAGACAAGAACTG 58.405 43.478 0.00 0.00 0.00 3.16
6425 19452 4.248859 AGACAAGAACTGATGATGTTCCG 58.751 43.478 0.00 0.00 43.28 4.30
6429 19456 3.600388 AGAACTGATGATGTTCCGGTTC 58.400 45.455 0.00 0.00 43.28 3.62
6430 19457 3.261897 AGAACTGATGATGTTCCGGTTCT 59.738 43.478 0.00 9.31 43.28 3.01
6431 19458 3.252974 ACTGATGATGTTCCGGTTCTC 57.747 47.619 0.00 0.00 0.00 2.87
6432 19459 2.196749 CTGATGATGTTCCGGTTCTCG 58.803 52.381 0.00 0.00 38.88 4.04
6433 19460 1.548719 TGATGATGTTCCGGTTCTCGT 59.451 47.619 0.00 0.00 37.11 4.18
6434 19461 1.927174 GATGATGTTCCGGTTCTCGTG 59.073 52.381 0.00 0.00 37.11 4.35
6435 19462 0.963225 TGATGTTCCGGTTCTCGTGA 59.037 50.000 0.00 0.00 37.11 4.35
6436 19463 1.067846 TGATGTTCCGGTTCTCGTGAG 60.068 52.381 0.00 0.00 37.11 3.51
6437 19464 0.246635 ATGTTCCGGTTCTCGTGAGG 59.753 55.000 0.00 0.00 37.11 3.86
6438 19465 0.824595 TGTTCCGGTTCTCGTGAGGA 60.825 55.000 0.00 0.00 37.11 3.71
6439 19466 0.531200 GTTCCGGTTCTCGTGAGGAT 59.469 55.000 0.00 0.00 37.11 3.24
6440 19467 1.747355 GTTCCGGTTCTCGTGAGGATA 59.253 52.381 0.00 0.00 37.11 2.59
6441 19468 2.359981 TCCGGTTCTCGTGAGGATAT 57.640 50.000 0.00 0.00 37.11 1.63
6442 19469 2.662866 TCCGGTTCTCGTGAGGATATT 58.337 47.619 0.00 0.00 37.11 1.28
6443 19470 3.028850 TCCGGTTCTCGTGAGGATATTT 58.971 45.455 0.00 0.00 37.11 1.40
6444 19471 4.209538 TCCGGTTCTCGTGAGGATATTTA 58.790 43.478 0.00 0.00 37.11 1.40
6445 19472 4.831155 TCCGGTTCTCGTGAGGATATTTAT 59.169 41.667 0.00 0.00 37.11 1.40
6446 19473 5.048224 TCCGGTTCTCGTGAGGATATTTATC 60.048 44.000 0.00 0.00 37.11 1.75
6447 19474 5.278808 CCGGTTCTCGTGAGGATATTTATCA 60.279 44.000 0.00 0.00 37.11 2.15
6448 19475 5.629849 CGGTTCTCGTGAGGATATTTATCAC 59.370 44.000 0.00 6.05 39.93 3.06
6449 19476 5.927115 GGTTCTCGTGAGGATATTTATCACC 59.073 44.000 9.16 0.00 40.15 4.02
6450 19477 5.723672 TCTCGTGAGGATATTTATCACCC 57.276 43.478 9.16 0.00 40.15 4.61
6451 19478 5.144832 TCTCGTGAGGATATTTATCACCCA 58.855 41.667 9.16 0.00 40.15 4.51
6452 19479 5.780282 TCTCGTGAGGATATTTATCACCCAT 59.220 40.000 9.16 0.00 40.15 4.00
6453 19480 5.793817 TCGTGAGGATATTTATCACCCATG 58.206 41.667 9.16 0.00 40.15 3.66
6454 19481 4.393062 CGTGAGGATATTTATCACCCATGC 59.607 45.833 9.16 0.00 40.15 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 368 9.653287 CTATGTAGAACTATTTTGAAGTCCACA 57.347 33.333 0.00 0.00 0.00 4.17
264 469 7.379750 AGAGTTCTTCTGGTAGTTATGTCAAC 58.620 38.462 0.00 0.00 33.93 3.18
296 501 4.560136 AGAGCGATATATGAGCATACGG 57.440 45.455 11.09 0.00 0.00 4.02
369 1742 3.139029 GGTCTTTACGCTCACCCAG 57.861 57.895 0.00 0.00 0.00 4.45
371 1744 4.611961 GGGTCTTTACGCTCACCC 57.388 61.111 0.00 0.00 41.93 4.61
439 1812 8.855279 CGAGCATTTCTAATAATCTAGCAGTAC 58.145 37.037 0.00 0.00 0.00 2.73
443 1816 6.993079 TCCGAGCATTTCTAATAATCTAGCA 58.007 36.000 0.00 0.00 0.00 3.49
497 1870 3.241552 CCGTCGATATTCGTTGTGTCAAC 60.242 47.826 0.00 2.95 41.35 3.18
517 1890 5.331902 GGTAACATTTGTCATGACATTCCG 58.668 41.667 28.32 18.53 41.52 4.30
645 2045 3.202818 TCACTCCATGGGCAATAATCTGT 59.797 43.478 13.02 0.00 0.00 3.41
689 2089 1.340795 GGGAGGAGACGGAAGAGTACA 60.341 57.143 0.00 0.00 0.00 2.90
839 2239 2.686915 GAGATGATTTGTTGCTGGGGAG 59.313 50.000 0.00 0.00 0.00 4.30
890 2290 3.832527 AGAAGGCACAGTTAAACCACAT 58.167 40.909 0.00 0.00 0.00 3.21
925 2674 7.056002 CACATACGTGCTGAAATTAGTTACA 57.944 36.000 0.00 0.00 36.06 2.41
994 2744 0.457443 GCCTGGGTGCTCATTAAAGC 59.543 55.000 0.00 0.00 42.82 3.51
1049 2854 6.918892 TGCGTACATTTATACAGCAAATCT 57.081 33.333 0.00 0.00 34.21 2.40
1068 2873 6.096695 TGCGTATATGTACATATCAATGCGT 58.903 36.000 27.61 8.76 36.50 5.24
1083 2888 4.685628 TCTGTGTATGTGCATGCGTATATG 59.314 41.667 14.09 6.58 0.00 1.78
1143 2949 6.313519 ACGTGCCATATTTCTCCCATATAT 57.686 37.500 0.00 0.00 0.00 0.86
1228 3104 4.476846 TGAACATATATGGTCCCACCTGTT 59.523 41.667 24.68 4.71 43.80 3.16
1307 3183 2.927871 GCGGTAGTATGTCAACGTGGTT 60.928 50.000 0.00 0.00 0.00 3.67
1407 3283 3.900892 CTCGTCGATGGGACCGGG 61.901 72.222 6.32 0.00 42.99 5.73
1506 3402 2.203640 ACCTGGACGCTGGAGTGA 60.204 61.111 0.00 0.00 0.00 3.41
1622 3763 2.223200 TATAAACCGACGCCGTGCCA 62.223 55.000 0.00 0.00 0.00 4.92
1755 3910 1.374252 CAACTTGGTCCGACCCGAG 60.374 63.158 15.24 14.37 41.21 4.63
1812 3974 3.990318 TGTGATCGATGCTAGACGAAT 57.010 42.857 0.54 2.04 41.65 3.34
1814 3976 2.541794 GCTTGTGATCGATGCTAGACGA 60.542 50.000 0.54 1.49 42.49 4.20
1816 3978 2.131183 GGCTTGTGATCGATGCTAGAC 58.869 52.381 0.54 0.07 0.00 2.59
1950 4112 5.300034 TGAGAAGTTGATGACATTTGCTGTT 59.700 36.000 0.00 0.00 38.54 3.16
2281 10391 1.470098 GAAGCACACTACCATTGCCAG 59.530 52.381 0.00 0.00 36.91 4.85
2363 10474 1.069636 GGAGCGCTTTCTTCTGTTGTG 60.070 52.381 13.26 0.00 0.00 3.33
2364 10475 1.230324 GGAGCGCTTTCTTCTGTTGT 58.770 50.000 13.26 0.00 0.00 3.32
2374 10485 2.639286 CGTTTGCTGGAGCGCTTT 59.361 55.556 13.26 0.00 45.83 3.51
2952 11107 8.229811 GCAGCAAAATATTTTCCTAAACCAAAG 58.770 33.333 10.53 0.00 0.00 2.77
2956 11111 7.848223 ATGCAGCAAAATATTTTCCTAAACC 57.152 32.000 10.53 0.00 0.00 3.27
3008 11163 4.856487 TGTCGCTTATGCATAAACAAAAGC 59.144 37.500 19.32 17.67 39.64 3.51
3040 11198 8.810652 TGGTGTAAAGCTCATTTTTAATGAAC 57.189 30.769 3.93 0.11 32.01 3.18
3046 11205 9.461312 ACATAGATGGTGTAAAGCTCATTTTTA 57.539 29.630 0.00 0.00 32.01 1.52
3161 11344 1.133025 GAATCCAACTTGCCCATGTCG 59.867 52.381 0.00 0.00 0.00 4.35
3179 11362 3.308035 TCTAGCTGTATCTTCCCGGAA 57.692 47.619 0.73 0.00 0.00 4.30
3257 11440 1.774254 ACACCTCTTGACATCCCAACA 59.226 47.619 0.00 0.00 0.00 3.33
3628 11811 5.186021 TCAAACACATACTCCCTCTTCTCTC 59.814 44.000 0.00 0.00 0.00 3.20
3870 12073 2.941720 GCCATCTTCATCTCAAGTCACC 59.058 50.000 0.00 0.00 0.00 4.02
4225 12496 4.344865 GGCGGGCTCCCTGAACAA 62.345 66.667 3.11 0.00 29.82 2.83
4399 12670 4.421479 CGGCCTTGACGACGAGCT 62.421 66.667 0.00 0.00 35.20 4.09
4444 12715 2.049063 GTGCAAGTCGTCGCCTCT 60.049 61.111 0.00 0.00 0.00 3.69
4468 12739 1.268640 GGAGACGAGGCAACGATCTAC 60.269 57.143 10.66 7.00 46.39 2.59
4680 12954 2.091055 CAGATCCTCAGAGGGGGTCTTA 60.091 54.545 17.10 0.00 41.09 2.10
4802 13077 1.303282 GGGTGCTCGAAAGGGGATT 59.697 57.895 0.00 0.00 31.22 3.01
4820 13095 1.067060 TCTCGAACTGATATGGGTGCG 59.933 52.381 0.00 0.07 35.97 5.34
4899 13174 3.277133 CCAACATTGGCTGGTCCG 58.723 61.111 0.00 0.00 42.21 4.79
4990 13265 1.751351 TCCGAGATCGCTCAACATCTT 59.249 47.619 0.00 0.00 41.36 2.40
5384 16795 0.377203 CGGCTTTGGTATCGGCTTTC 59.623 55.000 0.00 0.00 0.00 2.62
5451 16862 0.716108 CCGCGAGAACAGAACATCAC 59.284 55.000 8.23 0.00 0.00 3.06
5748 18746 1.167851 AACCAACATGGATCGCACTG 58.832 50.000 2.85 0.00 40.96 3.66
6018 19028 8.770828 CCTCGAAACAAGAGTTCAAGTATTTTA 58.229 33.333 0.00 0.00 36.84 1.52
6019 19029 7.282450 ACCTCGAAACAAGAGTTCAAGTATTTT 59.718 33.333 0.00 0.00 36.84 1.82
6020 19030 6.766467 ACCTCGAAACAAGAGTTCAAGTATTT 59.234 34.615 0.00 0.00 36.84 1.40
6021 19031 6.289064 ACCTCGAAACAAGAGTTCAAGTATT 58.711 36.000 0.00 0.00 36.84 1.89
6022 19032 5.855045 ACCTCGAAACAAGAGTTCAAGTAT 58.145 37.500 0.00 0.00 36.84 2.12
6023 19033 5.272283 ACCTCGAAACAAGAGTTCAAGTA 57.728 39.130 0.00 0.00 36.84 2.24
6024 19034 4.138487 ACCTCGAAACAAGAGTTCAAGT 57.862 40.909 0.00 0.00 36.84 3.16
6025 19035 6.598753 TTTACCTCGAAACAAGAGTTCAAG 57.401 37.500 0.00 0.00 36.84 3.02
6026 19036 6.372103 TGTTTTACCTCGAAACAAGAGTTCAA 59.628 34.615 0.00 0.00 42.25 2.69
6027 19037 5.875910 TGTTTTACCTCGAAACAAGAGTTCA 59.124 36.000 0.00 0.00 42.25 3.18
6261 19288 2.108976 CGATGATCGGGGTGTGGG 59.891 66.667 7.00 0.00 36.00 4.61
6296 19323 4.373116 TTGCAGACCCTCGTCCGC 62.373 66.667 0.00 0.00 41.91 5.54
6313 19340 2.348998 CCAGCTTTGACGGCCTCT 59.651 61.111 0.00 0.00 0.00 3.69
6320 19347 2.725221 AGATCCATCCCAGCTTTGAC 57.275 50.000 0.00 0.00 0.00 3.18
6323 19350 2.579860 AGTGAAGATCCATCCCAGCTTT 59.420 45.455 0.00 0.00 0.00 3.51
6336 19363 5.411669 GGTATCGGTTTTGTCAAGTGAAGAT 59.588 40.000 0.00 0.00 0.00 2.40
6352 19379 0.974010 TCTTCGGCTTGGGTATCGGT 60.974 55.000 0.00 0.00 0.00 4.69
6394 19421 4.621068 TCAGTTCTTGTCTTGTTTGCAG 57.379 40.909 0.00 0.00 0.00 4.41
6414 19441 1.927174 CACGAGAACCGGAACATCATC 59.073 52.381 9.46 0.00 43.93 2.92
6425 19452 5.927115 GGTGATAAATATCCTCACGAGAACC 59.073 44.000 0.00 0.00 40.11 3.62
6429 19456 5.468540 TGGGTGATAAATATCCTCACGAG 57.531 43.478 0.00 0.00 40.11 4.18
6430 19457 5.793817 CATGGGTGATAAATATCCTCACGA 58.206 41.667 0.00 0.00 40.11 4.35
6431 19458 4.393062 GCATGGGTGATAAATATCCTCACG 59.607 45.833 0.00 0.00 40.11 4.35
6432 19459 5.886960 GCATGGGTGATAAATATCCTCAC 57.113 43.478 0.00 0.00 38.82 3.51


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

AutoCloner maintained by Alex Coulton.