Multiple sequence alignment - TraesCS6B01G164000

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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 TraesCS6B01G164000 chr6B 100.000 4381 0 0 1 4381 171203914 171208294 0.000000e+00 8091
1 TraesCS6B01G164000 chr6B 80.630 1652 295 20 2157 3796 171030209 171031847 0.000000e+00 1254
2 TraesCS6B01G164000 chr6B 79.269 1751 321 28 2128 3846 171183695 171185435 0.000000e+00 1184
3 TraesCS6B01G164000 chr6B 79.091 1430 281 15 2157 3577 171701058 171702478 0.000000e+00 968
4 TraesCS6B01G164000 chr6B 80.776 1134 209 8 1000 2130 171700048 171701175 0.000000e+00 878
5 TraesCS6B01G164000 chr6B 80.619 1099 192 16 1028 2117 171029227 171030313 0.000000e+00 830
6 TraesCS6B01G164000 chr6B 79.387 1174 220 20 2384 3543 171705694 171706859 0.000000e+00 808
7 TraesCS6B01G164000 chr6B 94.041 537 24 6 3849 4381 543831737 543832269 0.000000e+00 808
8 TraesCS6B01G164000 chr6B 100.000 204 0 0 4590 4793 171208503 171208706 1.260000e-100 377
9 TraesCS6B01G164000 chr6B 95.652 207 6 2 3849 4054 543831360 543831564 3.580000e-86 329
10 TraesCS6B01G164000 chr6B 94.608 204 8 3 4592 4793 543832290 543832492 3.600000e-81 313
11 TraesCS6B01G164000 chr6B 96.599 147 5 0 2128 2274 171205897 171206043 1.330000e-60 244
12 TraesCS6B01G164000 chr6B 96.599 147 5 0 1984 2130 171206041 171206187 1.330000e-60 244
13 TraesCS6B01G164000 chr6B 90.217 184 16 2 4593 4776 96470098 96469917 6.200000e-59 239
14 TraesCS6B01G164000 chr6A 93.162 3261 194 16 602 3848 107269072 107272317 0.000000e+00 4759
15 TraesCS6B01G164000 chr6A 79.931 1729 309 26 2150 3846 107244387 107246109 0.000000e+00 1236
16 TraesCS6B01G164000 chr6A 80.109 1654 301 22 2157 3796 107215467 107217106 0.000000e+00 1206
17 TraesCS6B01G164000 chr6A 92.097 620 33 8 1 604 277285796 277285177 0.000000e+00 859
18 TraesCS6B01G164000 chr6A 80.318 1133 214 6 1000 2130 107681404 107682529 0.000000e+00 848
19 TraesCS6B01G164000 chr6A 80.669 1076 189 14 1000 2067 107214457 107215521 0.000000e+00 817
20 TraesCS6B01G164000 chr6A 90.998 611 40 7 1 603 107252102 107252705 0.000000e+00 809
21 TraesCS6B01G164000 chr6A 96.599 147 5 0 2128 2274 107270445 107270591 1.330000e-60 244
22 TraesCS6B01G164000 chr6A 93.197 147 10 0 1984 2130 107270589 107270735 2.900000e-52 217
23 TraesCS6B01G164000 chr6D 87.195 1765 199 21 2102 3848 89167624 89169379 0.000000e+00 1982
24 TraesCS6B01G164000 chr6D 80.127 1731 302 25 2150 3846 89157271 89158993 0.000000e+00 1253
25 TraesCS6B01G164000 chr6D 89.168 914 84 9 1221 2130 89166897 89167799 0.000000e+00 1125
26 TraesCS6B01G164000 chr6D 79.472 1364 260 18 2157 3510 89069465 89070818 0.000000e+00 950
27 TraesCS6B01G164000 chr6D 81.619 1050 174 15 1026 2067 89068481 89069519 0.000000e+00 852
28 TraesCS6B01G164000 chr6D 91.761 619 30 6 1 603 83276945 83277558 0.000000e+00 841
29 TraesCS6B01G164000 chr6D 90.690 580 40 12 596 1168 89166327 89166899 0.000000e+00 760
30 TraesCS6B01G164000 chr6D 77.888 1108 223 19 2157 3253 89301841 89302937 0.000000e+00 669
31 TraesCS6B01G164000 chr7D 93.065 620 25 11 1 604 43224897 43225514 0.000000e+00 891
32 TraesCS6B01G164000 chr7D 92.834 614 27 9 1 598 133309073 133308461 0.000000e+00 874
33 TraesCS6B01G164000 chr7D 78.914 1105 218 14 1026 2124 634087271 634088366 0.000000e+00 736
34 TraesCS6B01G164000 chr1D 92.569 619 28 9 1 603 402328284 402328900 0.000000e+00 872
35 TraesCS6B01G164000 chr4D 92.173 626 31 6 1 610 375143268 375142645 0.000000e+00 869
36 TraesCS6B01G164000 chr4D 87.013 539 41 20 3849 4379 120837591 120837074 8.940000e-162 580
37 TraesCS6B01G164000 chr3D 92.432 621 28 10 1 603 18789459 18788840 0.000000e+00 869
38 TraesCS6B01G164000 chr2D 92.557 618 24 5 1 603 43735943 43735333 0.000000e+00 867
39 TraesCS6B01G164000 chr2D 90.404 396 31 5 3988 4381 68571123 68570733 9.200000e-142 514
40 TraesCS6B01G164000 chr2D 89.500 400 29 7 3986 4381 68662018 68661628 1.200000e-135 494
41 TraesCS6B01G164000 chr2D 93.103 174 11 1 4604 4776 68661602 68661429 2.210000e-63 254
42 TraesCS6B01G164000 chr2D 88.426 216 16 4 3850 4059 68662244 68662032 7.960000e-63 252
43 TraesCS6B01G164000 chr2D 87.963 216 16 7 3850 4059 68595238 68595027 3.700000e-61 246
44 TraesCS6B01G164000 chr2D 90.805 174 15 1 4604 4776 68695993 68695820 1.040000e-56 231
45 TraesCS6B01G164000 chr3A 92.246 619 32 9 1 603 13955652 13955034 0.000000e+00 863
46 TraesCS6B01G164000 chr3A 92.246 619 32 8 1 603 713848169 713847551 0.000000e+00 863
47 TraesCS6B01G164000 chr7A 92.246 619 31 10 1 603 670885398 670886015 0.000000e+00 861
48 TraesCS6B01G164000 chr4A 92.170 613 23 9 2 598 701934870 701935473 0.000000e+00 843
49 TraesCS6B01G164000 chr5B 91.586 618 33 9 1 602 16206275 16205661 0.000000e+00 835
50 TraesCS6B01G164000 chrUn 79.895 1139 214 14 998 2130 335904618 335905747 0.000000e+00 821
51 TraesCS6B01G164000 chrUn 79.807 1139 215 13 998 2130 335907300 335908429 0.000000e+00 815
52 TraesCS6B01G164000 chrUn 90.161 620 44 10 1 604 96036763 96036145 0.000000e+00 791
53 TraesCS6B01G164000 chrUn 88.945 398 37 4 3986 4381 408724120 408724512 7.210000e-133 484
54 TraesCS6B01G164000 chr2B 94.590 536 18 5 3848 4381 128384172 128383646 0.000000e+00 819
55 TraesCS6B01G164000 chr2B 97.475 198 4 1 4597 4793 128383621 128383424 2.140000e-88 337
56 TraesCS6B01G164000 chr1A 90.865 613 32 11 1 598 179524936 179525539 0.000000e+00 800
57 TraesCS6B01G164000 chr5D 91.760 534 27 9 3849 4381 536802145 536801628 0.000000e+00 726
58 TraesCS6B01G164000 chr7B 78.142 1130 218 21 1007 2123 742408219 742409332 0.000000e+00 691
59 TraesCS6B01G164000 chr5A 88.889 540 43 12 3849 4380 692380304 692380834 0.000000e+00 649
60 TraesCS6B01G164000 chr5A 92.818 181 11 2 4596 4776 79276698 79276520 1.320000e-65 261
61 TraesCS6B01G164000 chr5A 91.713 181 14 1 4596 4776 608273884 608274063 2.860000e-62 250
62 TraesCS6B01G164000 chr3B 88.025 476 38 12 3917 4381 309391018 309390551 3.260000e-151 545
63 TraesCS6B01G164000 chr3B 90.270 185 17 1 4592 4776 309390537 309390354 1.720000e-59 241
64 TraesCS6B01G164000 chr2A 90.608 181 16 1 4596 4776 25461977 25461798 6.200000e-59 239


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 TraesCS6B01G164000 chr6B 171203914 171208706 4792 False 2239.000000 8091 98.299500 1 4793 4 chr6B.!!$F3 4792
1 TraesCS6B01G164000 chr6B 171183695 171185435 1740 False 1184.000000 1184 79.269000 2128 3846 1 chr6B.!!$F1 1718
2 TraesCS6B01G164000 chr6B 171029227 171031847 2620 False 1042.000000 1254 80.624500 1028 3796 2 chr6B.!!$F2 2768
3 TraesCS6B01G164000 chr6B 171700048 171706859 6811 False 884.666667 968 79.751333 1000 3577 3 chr6B.!!$F4 2577
4 TraesCS6B01G164000 chr6B 543831360 543832492 1132 False 483.333333 808 94.767000 3849 4793 3 chr6B.!!$F5 944
5 TraesCS6B01G164000 chr6A 107269072 107272317 3245 False 1740.000000 4759 94.319333 602 3848 3 chr6A.!!$F5 3246
6 TraesCS6B01G164000 chr6A 107244387 107246109 1722 False 1236.000000 1236 79.931000 2150 3846 1 chr6A.!!$F1 1696
7 TraesCS6B01G164000 chr6A 107214457 107217106 2649 False 1011.500000 1206 80.389000 1000 3796 2 chr6A.!!$F4 2796
8 TraesCS6B01G164000 chr6A 277285177 277285796 619 True 859.000000 859 92.097000 1 604 1 chr6A.!!$R1 603
9 TraesCS6B01G164000 chr6A 107681404 107682529 1125 False 848.000000 848 80.318000 1000 2130 1 chr6A.!!$F3 1130
10 TraesCS6B01G164000 chr6A 107252102 107252705 603 False 809.000000 809 90.998000 1 603 1 chr6A.!!$F2 602
11 TraesCS6B01G164000 chr6D 89166327 89169379 3052 False 1289.000000 1982 89.017667 596 3848 3 chr6D.!!$F5 3252
12 TraesCS6B01G164000 chr6D 89157271 89158993 1722 False 1253.000000 1253 80.127000 2150 3846 1 chr6D.!!$F2 1696
13 TraesCS6B01G164000 chr6D 89068481 89070818 2337 False 901.000000 950 80.545500 1026 3510 2 chr6D.!!$F4 2484
14 TraesCS6B01G164000 chr6D 83276945 83277558 613 False 841.000000 841 91.761000 1 603 1 chr6D.!!$F1 602
15 TraesCS6B01G164000 chr6D 89301841 89302937 1096 False 669.000000 669 77.888000 2157 3253 1 chr6D.!!$F3 1096
16 TraesCS6B01G164000 chr7D 43224897 43225514 617 False 891.000000 891 93.065000 1 604 1 chr7D.!!$F1 603
17 TraesCS6B01G164000 chr7D 133308461 133309073 612 True 874.000000 874 92.834000 1 598 1 chr7D.!!$R1 597
18 TraesCS6B01G164000 chr7D 634087271 634088366 1095 False 736.000000 736 78.914000 1026 2124 1 chr7D.!!$F2 1098
19 TraesCS6B01G164000 chr1D 402328284 402328900 616 False 872.000000 872 92.569000 1 603 1 chr1D.!!$F1 602
20 TraesCS6B01G164000 chr4D 375142645 375143268 623 True 869.000000 869 92.173000 1 610 1 chr4D.!!$R2 609
21 TraesCS6B01G164000 chr4D 120837074 120837591 517 True 580.000000 580 87.013000 3849 4379 1 chr4D.!!$R1 530
22 TraesCS6B01G164000 chr3D 18788840 18789459 619 True 869.000000 869 92.432000 1 603 1 chr3D.!!$R1 602
23 TraesCS6B01G164000 chr2D 43735333 43735943 610 True 867.000000 867 92.557000 1 603 1 chr2D.!!$R1 602
24 TraesCS6B01G164000 chr2D 68661429 68662244 815 True 333.333333 494 90.343000 3850 4776 3 chr2D.!!$R5 926
25 TraesCS6B01G164000 chr3A 13955034 13955652 618 True 863.000000 863 92.246000 1 603 1 chr3A.!!$R1 602
26 TraesCS6B01G164000 chr3A 713847551 713848169 618 True 863.000000 863 92.246000 1 603 1 chr3A.!!$R2 602
27 TraesCS6B01G164000 chr7A 670885398 670886015 617 False 861.000000 861 92.246000 1 603 1 chr7A.!!$F1 602
28 TraesCS6B01G164000 chr4A 701934870 701935473 603 False 843.000000 843 92.170000 2 598 1 chr4A.!!$F1 596
29 TraesCS6B01G164000 chr5B 16205661 16206275 614 True 835.000000 835 91.586000 1 602 1 chr5B.!!$R1 601
30 TraesCS6B01G164000 chrUn 335904618 335908429 3811 False 818.000000 821 79.851000 998 2130 2 chrUn.!!$F2 1132
31 TraesCS6B01G164000 chrUn 96036145 96036763 618 True 791.000000 791 90.161000 1 604 1 chrUn.!!$R1 603
32 TraesCS6B01G164000 chr2B 128383424 128384172 748 True 578.000000 819 96.032500 3848 4793 2 chr2B.!!$R1 945
33 TraesCS6B01G164000 chr1A 179524936 179525539 603 False 800.000000 800 90.865000 1 598 1 chr1A.!!$F1 597
34 TraesCS6B01G164000 chr5D 536801628 536802145 517 True 726.000000 726 91.760000 3849 4381 1 chr5D.!!$R1 532
35 TraesCS6B01G164000 chr7B 742408219 742409332 1113 False 691.000000 691 78.142000 1007 2123 1 chr7B.!!$F1 1116
36 TraesCS6B01G164000 chr5A 692380304 692380834 530 False 649.000000 649 88.889000 3849 4380 1 chr5A.!!$F2 531
37 TraesCS6B01G164000 chr3B 309390354 309391018 664 True 393.000000 545 89.147500 3917 4776 2 chr3B.!!$R1 859

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
77 78 0.250295 CTTCGGTGTTGCTTCTCCCA 60.250 55.0 0.00 0.0 0.00 4.37 F
635 659 0.838608 TTTGTTCCCACCGTGGTACT 59.161 50.0 16.55 0.0 35.17 2.73 F
1345 1384 0.679505 CCTGTTTCTCGTCCTCACCA 59.320 55.0 0.00 0.0 0.00 4.17 F
2479 2519 0.624254 TCTCGAGGGTGAGCTTCCTA 59.376 55.0 13.56 0.0 35.90 2.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1274 1313 0.040958 GTTGCTGTTGAGGTTGAGCG 60.041 55.000 0.00 0.00 33.97 5.03 R
1581 1620 0.391263 GCCCTGAGAAGGTGTTACCG 60.391 60.000 0.00 0.00 44.90 4.02 R
2796 2848 1.159713 TGTTTGACAGGTGCAGCGAG 61.160 55.000 10.78 9.98 0.00 5.03 R
4126 9389 3.004315 CGTTGTTGGTTGAAGTGGCTATT 59.996 43.478 0.00 0.00 0.00 1.73 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
77 78 0.250295 CTTCGGTGTTGCTTCTCCCA 60.250 55.000 0.00 0.00 0.00 4.37
235 237 1.408822 GGATGGAGTGCGGGAGAAATT 60.409 52.381 0.00 0.00 0.00 1.82
272 289 2.173669 CCGATGCGGTGACACCATC 61.174 63.158 24.18 17.89 42.73 3.51
561 585 2.737359 GCGATCCTTGTATCGGTGTTGA 60.737 50.000 8.18 0.00 46.89 3.18
619 643 5.452078 TGGTAATTTCTGCCTCTGTTTTG 57.548 39.130 0.00 0.00 0.00 2.44
635 659 0.838608 TTTGTTCCCACCGTGGTACT 59.161 50.000 16.55 0.00 35.17 2.73
637 661 1.714541 TGTTCCCACCGTGGTACTTA 58.285 50.000 16.55 0.00 35.17 2.24
644 668 3.822167 CCCACCGTGGTACTTACAAAAAT 59.178 43.478 16.55 0.00 35.17 1.82
654 678 7.589954 GTGGTACTTACAAAAATGTGTGATGTC 59.410 37.037 0.00 0.00 32.75 3.06
655 679 7.500892 TGGTACTTACAAAAATGTGTGATGTCT 59.499 33.333 0.00 0.00 32.75 3.41
656 680 7.803189 GGTACTTACAAAAATGTGTGATGTCTG 59.197 37.037 0.00 0.00 32.75 3.51
678 703 2.677914 TCAGTTCTGGAGGTTCAGTCA 58.322 47.619 0.00 0.00 36.25 3.41
685 710 4.531854 TCTGGAGGTTCAGTCATAGAGAG 58.468 47.826 0.00 0.00 36.25 3.20
734 759 1.648720 CTGTGTTCACGGCAACCAG 59.351 57.895 0.00 0.00 0.00 4.00
765 790 2.599408 TCTCCGGTCTTCACCTTACT 57.401 50.000 0.00 0.00 41.17 2.24
799 824 4.329545 TTCACTGTGAGGCCGGGC 62.330 66.667 22.67 22.67 0.00 6.13
808 833 4.528039 AGGCCGGGCATTGGGATG 62.528 66.667 31.59 0.00 36.32 3.51
855 880 5.590259 ACTGGTGGATTTGATATTTTCCTCG 59.410 40.000 0.00 0.00 0.00 4.63
881 906 1.971357 TGACCCCAAGTCTGAAGTCTC 59.029 52.381 0.00 0.00 46.46 3.36
985 1013 6.166279 TGCAACTTGTCATTTTTACCAACAA 58.834 32.000 0.00 0.00 0.00 2.83
996 1024 5.344743 TTTTACCAACAATCCAACTGCAA 57.655 34.783 0.00 0.00 0.00 4.08
1168 1206 1.476845 TACCTGCTCTTGGTTCGGCA 61.477 55.000 0.00 0.00 38.88 5.69
1194 1232 1.450134 TGATGCTGCCGGACATGTC 60.450 57.895 17.91 17.91 0.00 3.06
1274 1313 2.027625 CGTTCCAGAACCTCACCGC 61.028 63.158 4.99 0.00 38.03 5.68
1289 1328 2.671177 CCGCGCTCAACCTCAACAG 61.671 63.158 5.56 0.00 0.00 3.16
1336 1375 2.160417 GCAAACATCTCCCTGTTTCTCG 59.840 50.000 0.00 0.00 45.18 4.04
1345 1384 0.679505 CCTGTTTCTCGTCCTCACCA 59.320 55.000 0.00 0.00 0.00 4.17
1418 1457 4.697352 CAGTCACCTCCCAAAGATTGTTAG 59.303 45.833 0.00 0.00 0.00 2.34
1429 1468 7.035612 CCCAAAGATTGTTAGGTTAGATTTGC 58.964 38.462 0.00 0.00 0.00 3.68
1479 1518 2.271800 GCCAACTTCTCACCTATGTCG 58.728 52.381 0.00 0.00 0.00 4.35
1581 1620 5.017294 GGATGAGATCCCTCGATTTATCC 57.983 47.826 0.00 0.00 43.88 2.59
1610 1649 2.125106 CTCAGGGCCGTTACCAGC 60.125 66.667 0.00 0.00 0.00 4.85
1973 2013 4.527816 TCATTTATTTGGAAGCTTGCCACT 59.472 37.500 15.98 1.11 34.56 4.00
2011 2051 6.308766 GGTGCAAACAATGATGTATTTCAGTC 59.691 38.462 0.00 0.00 39.40 3.51
2269 2309 2.550101 GGAAGCATCCCATCGCAGC 61.550 63.158 0.00 0.00 40.10 5.25
2313 2353 3.448934 TCTTCTCAGCCTCTCTGGAAAT 58.551 45.455 0.00 0.00 43.06 2.17
2438 2478 3.121025 GGCAATTTAACAAAGTTGCGCTC 60.121 43.478 9.73 1.40 45.82 5.03
2479 2519 0.624254 TCTCGAGGGTGAGCTTCCTA 59.376 55.000 13.56 0.00 35.90 2.94
2480 2520 1.215673 TCTCGAGGGTGAGCTTCCTAT 59.784 52.381 13.56 0.00 35.90 2.57
2498 2538 3.705579 CCTATGGCCATCTCCTATCTGAG 59.294 52.174 24.80 9.75 0.00 3.35
2649 2698 8.876181 TCTGCCTATTGTAACCTAATAATGCTA 58.124 33.333 0.00 0.00 0.00 3.49
2677 2726 7.865820 AGTCCTGGATCTATCAAAGAATCAAA 58.134 34.615 0.00 0.00 37.89 2.69
2788 2840 3.288964 ACCTCGGGTCACTATAGTTCTG 58.711 50.000 1.56 1.74 0.00 3.02
2789 2841 3.288964 CCTCGGGTCACTATAGTTCTGT 58.711 50.000 1.56 0.00 0.00 3.41
2796 2848 5.044558 GGTCACTATAGTTCTGTGCTAAGC 58.955 45.833 1.56 0.00 0.00 3.09
2923 2975 2.047061 CAATTCCTCCGTGGATAGGGA 58.953 52.381 0.00 0.00 45.68 4.20
2971 3023 2.483877 GGACTGCGATCAAACATGTTCA 59.516 45.455 12.39 3.39 0.00 3.18
3079 7923 3.874543 ACAAAATTTCGCCAACTTTTCCC 59.125 39.130 0.00 0.00 0.00 3.97
3104 7948 2.158856 TGAGACAGACATCCATGATGCC 60.159 50.000 4.05 0.00 43.15 4.40
3120 7964 3.687212 TGATGCCGCCGGTTATAATAATG 59.313 43.478 4.45 0.00 0.00 1.90
3144 7994 8.335819 TGGACATATTATATACCCAGCATGAT 57.664 34.615 0.00 0.00 39.69 2.45
3158 8011 4.202274 CCAGCATGATGATTTTTATGGCCA 60.202 41.667 13.69 8.56 39.69 5.36
3216 8069 7.149569 CTTTCAAGGAAGAGATGCATTTGTA 57.850 36.000 0.00 0.00 0.00 2.41
3228 8081 7.066284 AGAGATGCATTTGTAACTGGTATTGAC 59.934 37.037 0.00 0.00 0.00 3.18
3307 8160 7.220030 AGGCATCCAGTTACTAAATATGTCAG 58.780 38.462 0.00 0.00 0.00 3.51
3382 8235 0.978146 ATCCCTTGACCTCTCGTGGG 60.978 60.000 0.00 0.00 34.48 4.61
3437 8290 3.012518 CAAACCTGGTATTCCTCTGCTG 58.987 50.000 0.00 0.00 34.23 4.41
3595 8466 2.034685 TCAAGTCTGACGACCACTTCAG 59.965 50.000 1.52 0.00 41.68 3.02
3661 8532 2.481276 GGAACAGTTTCTGGTTTGTGGC 60.481 50.000 1.90 0.00 35.51 5.01
3684 8555 6.016108 GGCTATGGTTTGGTACACTGTTTTTA 60.016 38.462 0.00 0.00 39.29 1.52
3693 8564 8.472007 TTGGTACACTGTTTTTATGGAAGATT 57.528 30.769 0.00 0.00 39.29 2.40
3809 8680 7.088589 AGTATTGAATGATGCCACACTAAAC 57.911 36.000 0.00 0.00 0.00 2.01
3893 8764 0.036010 AAACACATCGAGGGCTCAGG 60.036 55.000 0.69 0.00 0.00 3.86
3907 8778 2.339769 GCTCAGGTTATCCCATACCCT 58.660 52.381 0.00 0.00 34.90 4.34
3929 8800 3.737559 TCATAACAAAGGGCAGGATGT 57.262 42.857 0.00 0.00 39.31 3.06
3930 8801 3.620488 TCATAACAAAGGGCAGGATGTC 58.380 45.455 0.00 0.00 42.54 3.06
3942 8813 6.019108 AGGGCAGGATGTCTTTTCTTAAAAT 58.981 36.000 0.00 0.00 43.10 1.82
3943 8814 6.153510 AGGGCAGGATGTCTTTTCTTAAAATC 59.846 38.462 0.00 0.00 43.10 2.17
4082 9344 3.903530 ACATGGAAAAGGGAGAGGTTT 57.096 42.857 0.00 0.00 0.00 3.27
4109 9372 3.943671 TTTGAACTCAAGACCTCCCAA 57.056 42.857 0.00 0.00 37.15 4.12
4112 9375 2.104792 TGAACTCAAGACCTCCCAACTG 59.895 50.000 0.00 0.00 0.00 3.16
4115 9378 2.777692 ACTCAAGACCTCCCAACTGAAA 59.222 45.455 0.00 0.00 0.00 2.69
4126 9389 2.158986 CCCAACTGAAAAACACATGCCA 60.159 45.455 0.00 0.00 0.00 4.92
4784 10057 7.964545 AATCTGTGAACGTTTTCAGTTTTAC 57.035 32.000 23.08 1.78 42.60 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
319 336 1.345715 CCTAGAGTTTCCCCCGGCAT 61.346 60.000 0.00 0.00 0.00 4.40
514 537 2.087462 GAACAGCACAACAAGCCCCC 62.087 60.000 0.00 0.00 0.00 5.40
515 538 1.363807 GAACAGCACAACAAGCCCC 59.636 57.895 0.00 0.00 0.00 5.80
619 643 1.344114 TGTAAGTACCACGGTGGGAAC 59.656 52.381 29.44 24.71 43.37 3.62
635 659 7.766283 TGAACAGACATCACACATTTTTGTAA 58.234 30.769 0.00 0.00 0.00 2.41
637 661 6.127647 ACTGAACAGACATCACACATTTTTGT 60.128 34.615 8.87 0.00 0.00 2.83
644 668 4.122046 CAGAACTGAACAGACATCACACA 58.878 43.478 8.87 0.00 0.00 3.72
654 678 3.181461 ACTGAACCTCCAGAACTGAACAG 60.181 47.826 3.19 0.00 37.59 3.16
655 679 2.771943 ACTGAACCTCCAGAACTGAACA 59.228 45.455 3.19 0.00 37.59 3.18
656 680 3.181465 TGACTGAACCTCCAGAACTGAAC 60.181 47.826 3.19 0.00 37.59 3.18
678 703 5.026121 TCAAATCACCCAGTCACTCTCTAT 58.974 41.667 0.00 0.00 0.00 1.98
685 710 2.851195 ACTGTCAAATCACCCAGTCAC 58.149 47.619 0.00 0.00 32.97 3.67
734 759 2.101582 AGACCGGAGATGTATGTGCTTC 59.898 50.000 9.46 0.00 0.00 3.86
765 790 7.178451 TCACAGTGAAGTGATTACTATTCTCCA 59.822 37.037 0.00 0.00 43.18 3.86
815 840 0.963962 CAGTGCTTTGAGGCCACAAT 59.036 50.000 16.74 0.00 0.00 2.71
816 841 1.108727 CCAGTGCTTTGAGGCCACAA 61.109 55.000 11.97 11.97 0.00 3.33
855 880 1.021390 CAGACTTGGGGTCATCGTGC 61.021 60.000 0.00 0.00 46.72 5.34
881 906 2.804647 TGGACGAACATATGCGTACAG 58.195 47.619 14.51 0.00 45.51 2.74
923 950 6.814954 ATTGCCTTCAGATTTAGAGGTAGA 57.185 37.500 0.00 0.00 0.00 2.59
985 1013 2.028748 GCACCATTTCTTGCAGTTGGAT 60.029 45.455 8.78 0.00 38.68 3.41
996 1024 2.555757 GAGTTTCTGCAGCACCATTTCT 59.444 45.455 9.47 0.00 0.00 2.52
1194 1232 1.144936 GGGAAGATGGAGCTCGGTG 59.855 63.158 7.83 0.00 0.00 4.94
1274 1313 0.040958 GTTGCTGTTGAGGTTGAGCG 60.041 55.000 0.00 0.00 33.97 5.03
1306 1345 1.815003 GGAGATGTTTGCTGGGACAAG 59.185 52.381 0.00 0.00 38.70 3.16
1345 1384 7.800092 AGATTGTTATAGCTCAAGTCCAGAAT 58.200 34.615 0.00 0.00 0.00 2.40
1418 1457 6.190954 AGTGGTTATTTCGCAAATCTAACC 57.809 37.500 13.67 13.67 38.83 2.85
1429 1468 3.057806 GGGTTGGTCAAGTGGTTATTTCG 60.058 47.826 0.00 0.00 0.00 3.46
1479 1518 9.640963 TTAGCTAGAGATAACAACTTCAAACTC 57.359 33.333 0.00 0.00 0.00 3.01
1581 1620 0.391263 GCCCTGAGAAGGTGTTACCG 60.391 60.000 0.00 0.00 44.90 4.02
1645 1684 7.009179 AGAATCCATTAGCGGATAGATTCAA 57.991 36.000 18.13 0.00 45.39 2.69
2011 2051 5.694995 ACCATTGATATTGTTGTCCCCTAG 58.305 41.667 0.00 0.00 0.00 3.02
2103 2143 0.749454 GCGATGGGATGCTTCCAACT 60.749 55.000 19.49 4.03 44.60 3.16
2313 2353 2.100252 CGGGATCGAGCCAGTAAAGTTA 59.900 50.000 23.22 0.00 39.00 2.24
2438 2478 2.221749 CGGTTGTCACTGATGTCAAGTG 59.778 50.000 0.00 0.00 35.04 3.16
2498 2538 5.555966 ACAAGGAGAGAACAAGAAGATTCC 58.444 41.667 0.00 0.00 0.00 3.01
2506 2546 4.342862 TTCCAGACAAGGAGAGAACAAG 57.657 45.455 0.00 0.00 39.25 3.16
2649 2698 6.627087 TTCTTTGATAGATCCAGGACTTGT 57.373 37.500 0.00 0.00 31.54 3.16
2789 2841 2.434884 GGTGCAGCGAGCTTAGCA 60.435 61.111 15.86 6.07 45.94 3.49
2796 2848 1.159713 TGTTTGACAGGTGCAGCGAG 61.160 55.000 10.78 9.98 0.00 5.03
2859 2911 4.941263 CCGAGATCCAAAATGACAAGGTTA 59.059 41.667 0.00 0.00 0.00 2.85
3058 7902 4.024977 CAGGGAAAAGTTGGCGAAATTTTG 60.025 41.667 21.47 6.83 38.97 2.44
3062 7906 2.593026 TCAGGGAAAAGTTGGCGAAAT 58.407 42.857 0.00 0.00 0.00 2.17
3079 7923 4.667519 TCATGGATGTCTGTCTCATCAG 57.332 45.455 7.93 0.00 42.16 2.90
3104 7948 7.548196 AATATGTCCATTATTATAACCGGCG 57.452 36.000 0.00 0.00 0.00 6.46
3120 7964 8.432013 TCATCATGCTGGGTATATAATATGTCC 58.568 37.037 0.00 0.00 0.00 4.02
3135 7979 4.202274 TGGCCATAAAAATCATCATGCTGG 60.202 41.667 0.00 0.00 0.00 4.85
3136 7980 4.748102 GTGGCCATAAAAATCATCATGCTG 59.252 41.667 9.72 0.00 0.00 4.41
3138 7982 4.695396 TGTGGCCATAAAAATCATCATGC 58.305 39.130 9.72 0.00 0.00 4.06
3144 7994 7.949565 ACTATATCCATGTGGCCATAAAAATCA 59.050 33.333 9.72 0.00 34.44 2.57
3158 8011 5.454755 CGTCCCTTCCAAACTATATCCATGT 60.455 44.000 0.00 0.00 0.00 3.21
3198 8051 4.946157 CCAGTTACAAATGCATCTCTTCCT 59.054 41.667 0.00 0.00 0.00 3.36
3228 8081 3.033184 AGAGAGAGAATTGCCAGAGAGG 58.967 50.000 0.00 0.00 41.84 3.69
3307 8160 6.056236 GGATACCACCAGAAAGATAGTTTCC 58.944 44.000 0.00 0.00 0.00 3.13
3349 8202 5.313712 GTCAAGGGATTCTAACCACTTCAA 58.686 41.667 0.00 0.00 0.00 2.69
3382 8235 3.306156 GGAATAGGACCGGATAGCTTGTC 60.306 52.174 9.46 0.00 0.00 3.18
3437 8290 7.422878 AAAAGGTTGTTCGAGAGATTAAGAC 57.577 36.000 0.00 0.00 41.60 3.01
3595 8466 5.359009 TCCAAATGGCTTCAAGATCTTGATC 59.641 40.000 33.02 26.28 41.03 2.92
3661 8532 8.026607 CCATAAAAACAGTGTACCAAACCATAG 58.973 37.037 0.00 0.00 0.00 2.23
3684 8555 4.246712 AGCACATCTCCAAATCTTCCAT 57.753 40.909 0.00 0.00 0.00 3.41
3693 8564 4.090761 ACTCAAGAAAGCACATCTCCAA 57.909 40.909 0.00 0.00 0.00 3.53
3732 8603 6.456718 GCTTCATCTTGTTCATAACTCTCTGC 60.457 42.308 0.00 0.00 0.00 4.26
3737 8608 7.497249 AGGTATGCTTCATCTTGTTCATAACTC 59.503 37.037 0.00 0.00 31.09 3.01
3809 8680 5.163953 ACGCTTACATCTTGTTTCATCTTCG 60.164 40.000 0.00 0.00 0.00 3.79
3893 8764 8.528044 TTTGTTATGAAAGGGTATGGGATAAC 57.472 34.615 0.00 0.00 0.00 1.89
3907 8778 4.415596 ACATCCTGCCCTTTGTTATGAAA 58.584 39.130 0.00 0.00 0.00 2.69
4082 9344 5.308825 GAGGTCTTGAGTTCAAATCCTCAA 58.691 41.667 24.27 0.00 45.00 3.02
4109 9372 4.559153 GCTATTGGCATGTGTTTTTCAGT 58.441 39.130 0.00 0.00 41.35 3.41
4112 9375 3.924144 TGGCTATTGGCATGTGTTTTTC 58.076 40.909 0.00 0.00 44.10 2.29
4126 9389 3.004315 CGTTGTTGGTTGAAGTGGCTATT 59.996 43.478 0.00 0.00 0.00 1.73
4265 9533 6.509418 TCTCAAATTCCAAAACTATTCGGG 57.491 37.500 0.00 0.00 0.00 5.14
4686 9958 9.528018 GTTCATGAATTTAAGAAAAGGTTCACA 57.472 29.630 12.12 0.00 36.09 3.58


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

AutoCloner maintained by Alex Coulton.