Multiple sequence alignment - TraesCS6B01G043100

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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 TraesCS6B01G043100 chr6B 100.000 5656 0 0 1 5656 26290236 26295891 0.000000e+00 10445.0
1 TraesCS6B01G043100 chr6B 80.983 1709 266 26 1060 2740 26248035 26249712 0.000000e+00 1301.0
2 TraesCS6B01G043100 chr6B 81.510 1563 252 26 1060 2596 26856874 26855323 0.000000e+00 1251.0
3 TraesCS6B01G043100 chr6B 80.964 1597 262 32 1031 2596 26842010 26840425 0.000000e+00 1227.0
4 TraesCS6B01G043100 chr6B 93.397 833 38 3 4841 5656 703791534 703792366 0.000000e+00 1218.0
5 TraesCS6B01G043100 chr6B 92.572 727 30 4 3702 4427 26251278 26251981 0.000000e+00 1022.0
6 TraesCS6B01G043100 chr6B 78.671 1580 263 50 919 2470 26389064 26390597 0.000000e+00 983.0
7 TraesCS6B01G043100 chr6B 93.537 557 36 0 4284 4840 26301948 26302504 0.000000e+00 830.0
8 TraesCS6B01G043100 chr6B 90.840 131 10 2 295 424 26722863 26722734 2.090000e-39 174.0
9 TraesCS6B01G043100 chr6B 85.811 148 19 2 4 151 26486872 26487017 7.590000e-34 156.0
10 TraesCS6B01G043100 chr6B 87.619 105 12 1 919 1023 26721655 26721552 2.770000e-23 121.0
11 TraesCS6B01G043100 chr6A 85.292 2944 305 56 1 2895 15646205 15649069 0.000000e+00 2920.0
12 TraesCS6B01G043100 chr6A 83.890 1347 202 8 1130 2463 15873148 15871804 0.000000e+00 1271.0
13 TraesCS6B01G043100 chr6A 93.857 814 48 2 1661 2474 15717380 15718191 0.000000e+00 1225.0
14 TraesCS6B01G043100 chr6A 79.278 1578 276 38 919 2474 15684716 15686264 0.000000e+00 1055.0
15 TraesCS6B01G043100 chr6A 83.670 1090 170 7 1155 2237 15925169 15924081 0.000000e+00 1020.0
16 TraesCS6B01G043100 chr6A 90.608 181 9 4 3415 3594 15645760 15645933 3.410000e-57 233.0
17 TraesCS6B01G043100 chr6A 89.011 182 17 3 3242 3422 15644136 15644315 7.380000e-54 222.0
18 TraesCS6B01G043100 chr6A 89.041 146 11 5 282 424 15915798 15915655 5.820000e-40 176.0
19 TraesCS6B01G043100 chr6A 94.565 92 5 0 3767 3858 15645985 15646076 5.910000e-30 143.0
20 TraesCS6B01G043100 chr6A 87.931 58 7 0 3730 3787 15650249 15650306 1.020000e-07 69.4
21 TraesCS6B01G043100 chr6D 86.324 1850 218 18 1121 2942 14422106 14423948 0.000000e+00 1982.0
22 TraesCS6B01G043100 chr6D 83.436 1455 206 17 1036 2473 14689287 14687851 0.000000e+00 1319.0
23 TraesCS6B01G043100 chr6D 79.710 1587 260 46 923 2474 14483540 14485099 0.000000e+00 1090.0
24 TraesCS6B01G043100 chr6D 97.152 632 16 2 2958 3588 14463909 14464539 0.000000e+00 1066.0
25 TraesCS6B01G043100 chr6D 81.071 1326 216 22 1155 2463 14941090 14939783 0.000000e+00 1026.0
26 TraesCS6B01G043100 chr6D 84.577 1005 145 5 1478 2474 14518038 14519040 0.000000e+00 989.0
27 TraesCS6B01G043100 chr6D 93.537 557 36 0 4284 4840 14466242 14466798 0.000000e+00 830.0
28 TraesCS6B01G043100 chr6D 86.275 714 54 20 3706 4386 14425394 14426096 0.000000e+00 736.0
29 TraesCS6B01G043100 chr6D 85.972 720 55 16 3592 4298 14464638 14465324 0.000000e+00 728.0
30 TraesCS6B01G043100 chr6D 80.769 468 57 10 2962 3422 14406006 14406447 9.080000e-88 335.0
31 TraesCS6B01G043100 chr6D 91.213 239 11 7 2735 2970 14463631 14463862 3.290000e-82 316.0
32 TraesCS6B01G043100 chr6D 92.000 200 11 2 2268 2467 14519275 14519469 5.580000e-70 276.0
33 TraesCS6B01G043100 chr6D 93.289 149 10 0 2570 2718 14463357 14463505 2.650000e-53 220.0
34 TraesCS6B01G043100 chr6D 90.141 142 8 6 282 419 14478152 14478291 4.500000e-41 180.0
35 TraesCS6B01G043100 chr6D 86.364 132 15 3 4 134 14901557 14901428 2.120000e-29 141.0
36 TraesCS6B01G043100 chr6D 94.872 78 4 0 3517 3594 14425194 14425271 7.700000e-24 122.0
37 TraesCS6B01G043100 chr6D 85.714 77 5 2 3484 3560 14508803 14508873 6.080000e-10 76.8
38 TraesCS6B01G043100 chr6D 80.180 111 13 4 3456 3563 14723522 14723418 2.190000e-09 75.0
39 TraesCS6B01G043100 chr3A 94.762 821 37 5 4840 5656 749840281 749839463 0.000000e+00 1273.0
40 TraesCS6B01G043100 chr3A 89.667 842 58 13 4841 5656 36187179 36186341 0.000000e+00 1046.0
41 TraesCS6B01G043100 chr1B 94.492 817 45 0 4840 5656 632922308 632921492 0.000000e+00 1260.0
42 TraesCS6B01G043100 chr4B 93.645 834 36 3 4840 5656 538993290 538992457 0.000000e+00 1230.0
43 TraesCS6B01G043100 chr4B 92.437 833 46 1 4841 5656 624569019 624568187 0.000000e+00 1173.0
44 TraesCS6B01G043100 chr3B 91.837 833 51 2 4841 5656 188041135 188041967 0.000000e+00 1146.0
45 TraesCS6B01G043100 chr7A 91.507 836 49 6 4841 5656 650233417 650232584 0.000000e+00 1131.0
46 TraesCS6B01G043100 chr7A 91.014 779 48 7 4898 5656 650285227 650284451 0.000000e+00 1031.0
47 TraesCS6B01G043100 chr2B 90.876 833 59 1 4841 5656 135562319 135563151 0.000000e+00 1101.0
48 TraesCS6B01G043100 chr2B 90.282 319 29 2 4524 4842 551402758 551403074 3.150000e-112 416.0
49 TraesCS6B01G043100 chr2B 90.190 316 30 1 4524 4839 135538750 135538436 1.470000e-110 411.0
50 TraesCS6B01G043100 chr5B 90.876 833 41 8 4841 5656 273155358 273154544 0.000000e+00 1085.0
51 TraesCS6B01G043100 chr5B 82.192 219 36 3 3 220 457929532 457929748 9.680000e-43 185.0
52 TraesCS6B01G043100 chr5B 81.818 220 34 5 3 220 458051910 458051695 4.500000e-41 180.0
53 TraesCS6B01G043100 chr2A 88.837 860 52 11 4841 5656 737825908 737825049 0.000000e+00 1016.0
54 TraesCS6B01G043100 chr2A 89.850 532 37 1 4841 5355 757861822 757861291 0.000000e+00 667.0
55 TraesCS6B01G043100 chr2A 84.464 457 62 7 434 885 681468293 681467841 5.200000e-120 442.0
56 TraesCS6B01G043100 chr5D 80.368 1360 233 27 1109 2457 27979282 27977946 0.000000e+00 1002.0
57 TraesCS6B01G043100 chr5D 89.969 319 29 3 4524 4842 358204581 358204266 5.270000e-110 409.0
58 TraesCS6B01G043100 chr5D 85.507 138 16 4 3 139 27951433 27951299 2.120000e-29 141.0
59 TraesCS6B01G043100 chr7B 89.086 733 54 13 4840 5550 711175374 711176102 0.000000e+00 887.0
60 TraesCS6B01G043100 chr4A 91.506 518 43 1 4839 5355 703426831 703426314 0.000000e+00 712.0
61 TraesCS6B01G043100 chr2D 89.873 316 31 1 4524 4839 473260480 473260794 6.820000e-109 405.0
62 TraesCS6B01G043100 chr1D 89.873 316 30 2 4524 4839 198016134 198016447 6.820000e-109 405.0
63 TraesCS6B01G043100 chr1D 89.557 316 32 1 4524 4839 80351808 80351494 3.170000e-107 399.0
64 TraesCS6B01G043100 chr1D 89.557 316 32 1 4524 4839 198008688 198009002 3.170000e-107 399.0


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 TraesCS6B01G043100 chr6B 26290236 26295891 5655 False 10445.000000 10445 100.0000 1 5656 1 chr6B.!!$F1 5655
1 TraesCS6B01G043100 chr6B 26855323 26856874 1551 True 1251.000000 1251 81.5100 1060 2596 1 chr6B.!!$R2 1536
2 TraesCS6B01G043100 chr6B 26840425 26842010 1585 True 1227.000000 1227 80.9640 1031 2596 1 chr6B.!!$R1 1565
3 TraesCS6B01G043100 chr6B 703791534 703792366 832 False 1218.000000 1218 93.3970 4841 5656 1 chr6B.!!$F5 815
4 TraesCS6B01G043100 chr6B 26248035 26251981 3946 False 1161.500000 1301 86.7775 1060 4427 2 chr6B.!!$F6 3367
5 TraesCS6B01G043100 chr6B 26389064 26390597 1533 False 983.000000 983 78.6710 919 2470 1 chr6B.!!$F3 1551
6 TraesCS6B01G043100 chr6B 26301948 26302504 556 False 830.000000 830 93.5370 4284 4840 1 chr6B.!!$F2 556
7 TraesCS6B01G043100 chr6A 15871804 15873148 1344 True 1271.000000 1271 83.8900 1130 2463 1 chr6A.!!$R1 1333
8 TraesCS6B01G043100 chr6A 15717380 15718191 811 False 1225.000000 1225 93.8570 1661 2474 1 chr6A.!!$F2 813
9 TraesCS6B01G043100 chr6A 15684716 15686264 1548 False 1055.000000 1055 79.2780 919 2474 1 chr6A.!!$F1 1555
10 TraesCS6B01G043100 chr6A 15924081 15925169 1088 True 1020.000000 1020 83.6700 1155 2237 1 chr6A.!!$R3 1082
11 TraesCS6B01G043100 chr6A 15644136 15650306 6170 False 717.480000 2920 89.4814 1 3858 5 chr6A.!!$F3 3857
12 TraesCS6B01G043100 chr6D 14687851 14689287 1436 True 1319.000000 1319 83.4360 1036 2473 1 chr6D.!!$R1 1437
13 TraesCS6B01G043100 chr6D 14483540 14485099 1559 False 1090.000000 1090 79.7100 923 2474 1 chr6D.!!$F3 1551
14 TraesCS6B01G043100 chr6D 14939783 14941090 1307 True 1026.000000 1026 81.0710 1155 2463 1 chr6D.!!$R4 1308
15 TraesCS6B01G043100 chr6D 14422106 14426096 3990 False 946.666667 1982 89.1570 1121 4386 3 chr6D.!!$F5 3265
16 TraesCS6B01G043100 chr6D 14518038 14519469 1431 False 632.500000 989 88.2885 1478 2474 2 chr6D.!!$F7 996
17 TraesCS6B01G043100 chr6D 14463357 14466798 3441 False 632.000000 1066 92.2326 2570 4840 5 chr6D.!!$F6 2270
18 TraesCS6B01G043100 chr3A 749839463 749840281 818 True 1273.000000 1273 94.7620 4840 5656 1 chr3A.!!$R2 816
19 TraesCS6B01G043100 chr3A 36186341 36187179 838 True 1046.000000 1046 89.6670 4841 5656 1 chr3A.!!$R1 815
20 TraesCS6B01G043100 chr1B 632921492 632922308 816 True 1260.000000 1260 94.4920 4840 5656 1 chr1B.!!$R1 816
21 TraesCS6B01G043100 chr4B 538992457 538993290 833 True 1230.000000 1230 93.6450 4840 5656 1 chr4B.!!$R1 816
22 TraesCS6B01G043100 chr4B 624568187 624569019 832 True 1173.000000 1173 92.4370 4841 5656 1 chr4B.!!$R2 815
23 TraesCS6B01G043100 chr3B 188041135 188041967 832 False 1146.000000 1146 91.8370 4841 5656 1 chr3B.!!$F1 815
24 TraesCS6B01G043100 chr7A 650232584 650233417 833 True 1131.000000 1131 91.5070 4841 5656 1 chr7A.!!$R1 815
25 TraesCS6B01G043100 chr7A 650284451 650285227 776 True 1031.000000 1031 91.0140 4898 5656 1 chr7A.!!$R2 758
26 TraesCS6B01G043100 chr2B 135562319 135563151 832 False 1101.000000 1101 90.8760 4841 5656 1 chr2B.!!$F1 815
27 TraesCS6B01G043100 chr5B 273154544 273155358 814 True 1085.000000 1085 90.8760 4841 5656 1 chr5B.!!$R1 815
28 TraesCS6B01G043100 chr2A 737825049 737825908 859 True 1016.000000 1016 88.8370 4841 5656 1 chr2A.!!$R2 815
29 TraesCS6B01G043100 chr2A 757861291 757861822 531 True 667.000000 667 89.8500 4841 5355 1 chr2A.!!$R3 514
30 TraesCS6B01G043100 chr5D 27977946 27979282 1336 True 1002.000000 1002 80.3680 1109 2457 1 chr5D.!!$R2 1348
31 TraesCS6B01G043100 chr7B 711175374 711176102 728 False 887.000000 887 89.0860 4840 5550 1 chr7B.!!$F1 710
32 TraesCS6B01G043100 chr4A 703426314 703426831 517 True 712.000000 712 91.5060 4839 5355 1 chr4A.!!$R1 516

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
338 2411 0.394762 TACATCCACCTACGCCGTCT 60.395 55.000 0.00 0.00 0.00 4.18 F
1223 3351 0.105039 GAGGATTCGCCGTTGAGGAT 59.895 55.000 0.00 0.00 45.00 3.24 F
1569 3697 1.048601 TGGCTCCTTCGACAACTTCT 58.951 50.000 0.00 0.00 0.00 2.85 F
1838 3972 1.110442 CCGAGGAGAAGATCACTGCT 58.890 55.000 12.15 12.15 38.66 4.24 F
2675 5667 1.302285 CCTGCCAAGATGGTGCTCT 59.698 57.895 0.00 0.00 40.46 4.09 F
3021 6343 0.169009 GCCGCTGTTTGTGATCTTCC 59.831 55.000 0.00 0.00 0.00 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1481 3609 0.179134 AGTTGATGTAGGCGAGCGAC 60.179 55.000 0.00 0.00 0.00 5.19 R
2539 5152 1.665679 AGCAACACATATTTCGCTCGG 59.334 47.619 0.00 0.00 0.00 4.63 R
2709 5701 2.071778 AAAGCAGAGTTTGAGGCCAA 57.928 45.000 5.01 0.00 0.00 4.52 R
3021 6343 2.858260 GCAACACCACGGAAATCTGTTG 60.858 50.000 10.57 10.57 42.98 3.33 R
4362 9251 0.324285 CTGAGCTTCAAGGCAGGAGT 59.676 55.000 0.00 0.00 34.17 3.85 R
4710 9599 0.700564 ACAGGGATGCCAGAACACAT 59.299 50.000 5.86 0.00 0.00 3.21 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
50 2120 8.921205 GGTTACCATTACTCTACTTCCATTAGA 58.079 37.037 0.00 0.00 0.00 2.10
131 2201 8.818057 CATCAACTACAATAAAGTACCTACTGC 58.182 37.037 0.00 0.00 36.50 4.40
143 2213 1.269448 ACCTACTGCAAATTTGGCACG 59.731 47.619 19.47 12.73 36.11 5.34
235 2305 3.126001 ACAAAGGATGATGACACACGT 57.874 42.857 0.00 0.00 0.00 4.49
329 2402 6.051717 CGAGAAATTCATCTTACATCCACCT 58.948 40.000 0.00 0.00 0.00 4.00
332 2405 6.986817 AGAAATTCATCTTACATCCACCTACG 59.013 38.462 0.00 0.00 0.00 3.51
338 2411 0.394762 TACATCCACCTACGCCGTCT 60.395 55.000 0.00 0.00 0.00 4.18
355 2428 1.130054 TCTCTGGGCCTGAAGCAACT 61.130 55.000 14.44 0.00 46.50 3.16
491 2566 4.087085 GTCTGAACATTGTTCGCAAATTCG 59.913 41.667 21.27 5.67 40.90 3.34
492 2567 3.958704 TGAACATTGTTCGCAAATTCGT 58.041 36.364 21.27 0.00 40.90 3.85
501 2576 6.427300 TGTTCGCAAATTCGTAAAATGTTC 57.573 33.333 0.00 0.00 0.00 3.18
507 2582 4.957759 AATTCGTAAAATGTTCGGGGAG 57.042 40.909 0.00 0.00 0.00 4.30
514 2589 5.352016 CGTAAAATGTTCGGGGAGTTTGATA 59.648 40.000 0.00 0.00 0.00 2.15
515 2590 6.128227 CGTAAAATGTTCGGGGAGTTTGATAA 60.128 38.462 0.00 0.00 0.00 1.75
575 2651 9.781834 TTCGAGAAATGTTTGCGATTAATAAAT 57.218 25.926 0.00 0.00 0.00 1.40
602 2678 5.219633 GTTCCTGTTTGCGTATTTGTTCAT 58.780 37.500 0.00 0.00 0.00 2.57
675 2752 9.965824 AAATGTTCAAAGATTTTCGTAGAATGT 57.034 25.926 0.00 0.00 45.90 2.71
676 2753 9.965824 AATGTTCAAAGATTTTCGTAGAATGTT 57.034 25.926 0.00 0.00 45.90 2.71
677 2754 9.612620 ATGTTCAAAGATTTTCGTAGAATGTTC 57.387 29.630 0.00 0.00 45.90 3.18
678 2755 8.616942 TGTTCAAAGATTTTCGTAGAATGTTCA 58.383 29.630 0.00 0.00 45.90 3.18
686 2763 9.393249 GATTTTCGTAGAATGTTCATGTTTTGA 57.607 29.630 0.00 0.00 45.90 2.69
689 2766 8.781067 TTCGTAGAATGTTCATGTTTTGAAAG 57.219 30.769 0.00 0.00 44.07 2.62
743 2821 3.941704 TTGAAAAATGGGCCAGGTTTT 57.058 38.095 23.48 23.48 0.00 2.43
850 2929 3.465871 TGCTCCCACTTTCAAATTTTGC 58.534 40.909 4.19 0.00 0.00 3.68
866 2945 3.552604 TTTGCTCGGGAATTTCGAAAG 57.447 42.857 16.80 2.24 36.15 2.62
887 2966 7.116233 CGAAAGATGTTTCCACTTTTAAATGGG 59.884 37.037 9.55 2.54 39.22 4.00
889 2968 6.993079 AGATGTTTCCACTTTTAAATGGGTC 58.007 36.000 7.78 0.00 36.56 4.46
934 3020 2.096174 TCGACGATTAAAAATTGGGCCG 59.904 45.455 0.00 0.00 0.00 6.13
948 3034 1.894282 GGCCGAATTAGAGCCCAGC 60.894 63.158 6.75 0.00 41.00 4.85
1016 3102 1.474330 CCCCATTTCTTTCCTTCCCG 58.526 55.000 0.00 0.00 0.00 5.14
1042 3132 2.159382 CCACACAAAAATACCTCCGCT 58.841 47.619 0.00 0.00 0.00 5.52
1099 3206 1.078759 CTCCGAGAGCGCATCGTTTT 61.079 55.000 26.42 0.00 38.50 2.43
1223 3351 0.105039 GAGGATTCGCCGTTGAGGAT 59.895 55.000 0.00 0.00 45.00 3.24
1301 3429 1.224592 CTCCCACCTCAAATCCCCG 59.775 63.158 0.00 0.00 0.00 5.73
1303 3431 2.305607 CCCACCTCAAATCCCCGGA 61.306 63.158 0.73 0.00 0.00 5.14
1465 3593 2.738521 CGGTCTGTTGCGTCCTGG 60.739 66.667 0.00 0.00 0.00 4.45
1495 3623 2.102357 CGTGTCGCTCGCCTACAT 59.898 61.111 0.00 0.00 0.00 2.29
1569 3697 1.048601 TGGCTCCTTCGACAACTTCT 58.951 50.000 0.00 0.00 0.00 2.85
1678 3812 3.624861 GGGCTAGATGATTGCGATATTGG 59.375 47.826 0.00 0.00 0.00 3.16
1694 3828 2.280797 GGCAAGCTGTGTGTCCGA 60.281 61.111 0.00 0.00 0.00 4.55
1819 3953 1.293924 CATGCCGTCTCATTCCTCAC 58.706 55.000 0.00 0.00 0.00 3.51
1838 3972 1.110442 CCGAGGAGAAGATCACTGCT 58.890 55.000 12.15 12.15 38.66 4.24
2027 4161 5.627040 GCCGGTAATGCTCTATTATAGCCTT 60.627 44.000 1.90 0.00 39.30 4.35
2030 4164 7.268586 CGGTAATGCTCTATTATAGCCTTGAT 58.731 38.462 0.00 0.00 39.30 2.57
2031 4165 8.414003 CGGTAATGCTCTATTATAGCCTTGATA 58.586 37.037 0.00 0.00 39.30 2.15
2135 4269 4.867608 GCACTCTCAATTCAGGAGAAGTAC 59.132 45.833 0.00 0.00 40.64 2.73
2249 4385 8.515414 GCTAGTTTCAGATTTACTTGAACCAAT 58.485 33.333 0.00 0.00 0.00 3.16
2349 4937 4.503741 TCTTTGCCAAACTAGATGTTGC 57.496 40.909 0.00 0.00 39.13 4.17
2379 4976 4.405680 TCTGTAGTATGCCTGTTACATGCT 59.594 41.667 13.25 0.00 42.21 3.79
2463 5073 7.988737 TGATATGTTGATGTTGTCATTCCTTC 58.011 34.615 0.00 0.00 36.54 3.46
2482 5092 6.226787 TCCTTCAGAGAAGATCTTTGTGTTC 58.773 40.000 9.87 3.54 35.47 3.18
2518 5129 9.511272 TTTTATTCCTGAACCCTAAAGTCTAAC 57.489 33.333 0.00 0.00 0.00 2.34
2559 5172 1.665679 CCGAGCGAAATATGTGTTGCT 59.334 47.619 0.00 0.00 34.96 3.91
2574 5187 5.428253 TGTGTTGCTAGTTCCATTCTATCC 58.572 41.667 0.00 0.00 0.00 2.59
2675 5667 1.302285 CCTGCCAAGATGGTGCTCT 59.698 57.895 0.00 0.00 40.46 4.09
2709 5701 1.428912 TCTTCCACCAAGAAGGGCATT 59.571 47.619 1.74 0.00 42.94 3.56
2728 5830 2.071778 TTGGCCTCAAACTCTGCTTT 57.928 45.000 3.32 0.00 0.00 3.51
2729 5831 2.071778 TGGCCTCAAACTCTGCTTTT 57.928 45.000 3.32 0.00 0.00 2.27
2841 6039 8.668510 TTTAGATATGCTTCTTCCAGTCATTC 57.331 34.615 0.00 0.00 0.00 2.67
2870 6068 7.667043 ATTTCGTTACTGAAATCTGCACTTA 57.333 32.000 8.52 0.00 43.28 2.24
2903 6161 3.697542 TGTCATTGCTTCATTCCATCCAG 59.302 43.478 0.00 0.00 0.00 3.86
2916 6174 6.657541 TCATTCCATCCAGTAGTTTGTAAACC 59.342 38.462 4.00 0.00 39.71 3.27
2935 6196 6.764308 AAACCACTGGAACAATATCATGAG 57.236 37.500 0.71 0.00 38.70 2.90
2938 6199 5.882557 ACCACTGGAACAATATCATGAGAAC 59.117 40.000 0.71 0.00 38.70 3.01
2966 6288 5.900123 AGTGTCCTGGTTATATTAGTGCTCT 59.100 40.000 0.00 0.00 0.00 4.09
3021 6343 0.169009 GCCGCTGTTTGTGATCTTCC 59.831 55.000 0.00 0.00 0.00 3.46
3410 6747 2.094390 TGAGGTTCGGTGATCCTTTACG 60.094 50.000 0.00 0.00 32.54 3.18
3509 7175 7.818930 TGAGTGGCTAATTTCAAATTCAAATCC 59.181 33.333 0.00 0.00 0.00 3.01
3590 7300 2.237143 TCTGTTGAGTTGGGAGCTATGG 59.763 50.000 0.00 0.00 0.00 2.74
3602 7372 3.181439 GGGAGCTATGGACCTTGCTTTAT 60.181 47.826 7.63 0.00 35.76 1.40
3680 7450 4.881019 TGGGTATTGTGAATGGTTTTGG 57.119 40.909 0.00 0.00 0.00 3.28
3698 7468 5.856126 TTTGGTCTGATATGAAACGTGTC 57.144 39.130 0.00 0.00 0.00 3.67
3699 7469 4.801330 TGGTCTGATATGAAACGTGTCT 57.199 40.909 7.37 0.00 0.00 3.41
3700 7470 4.494484 TGGTCTGATATGAAACGTGTCTG 58.506 43.478 7.37 0.00 0.00 3.51
3864 7789 4.331168 GCCAAAGCATCTAGTCTGTGTTAG 59.669 45.833 0.00 0.00 39.53 2.34
4142 8096 6.882610 TCAATCAAGTTACAGACTGCATTT 57.117 33.333 1.25 0.00 39.00 2.32
4143 8097 7.275888 TCAATCAAGTTACAGACTGCATTTT 57.724 32.000 1.25 0.00 39.00 1.82
4152 8106 4.855531 ACAGACTGCATTTTTAACGGAAC 58.144 39.130 1.25 0.00 0.00 3.62
4189 8146 4.087892 GGCTGCGCTCCTGAAGGA 62.088 66.667 9.73 0.00 43.08 3.36
4208 8165 2.266554 GAAGACTCGACATCAGCAAGG 58.733 52.381 0.00 0.00 0.00 3.61
4239 8196 2.029743 TTTTTGCTGGACTCGGTGC 58.970 52.632 0.00 0.00 0.00 5.01
4300 9189 0.899717 AAACATTCCATGCCGGCTGT 60.900 50.000 29.70 19.55 33.26 4.40
4344 9233 2.191680 CCGAATTCCATGGCAAGCA 58.808 52.632 6.96 0.00 0.00 3.91
4362 9251 1.476110 GCATCCGTACCTTGGGCATAA 60.476 52.381 0.00 0.00 0.00 1.90
4457 9346 1.366366 CCCCGTATCGACCATCACC 59.634 63.158 0.00 0.00 0.00 4.02
4571 9460 7.225538 ACACGAATAATTATTCAAGAGAGCCTG 59.774 37.037 28.90 15.69 41.59 4.85
4579 9468 1.141657 TCAAGAGAGCCTGCAGTTGTT 59.858 47.619 13.81 0.00 0.00 2.83
4710 9599 7.120138 ACCAGTTTTGTTCTCTTTTCTCGTTTA 59.880 33.333 0.00 0.00 0.00 2.01
4801 9690 4.570930 GAGAGGGCCCTAAAAATATCTCG 58.429 47.826 28.78 0.00 0.00 4.04
5127 10047 2.183300 GCAGGTGTATGCCGACGA 59.817 61.111 0.00 0.00 40.43 4.20
5461 10403 9.835389 TGTTTTCTCTTTTCCAATTCATTTGAT 57.165 25.926 0.00 0.00 37.53 2.57
5538 10500 7.602644 TCATCTAAACATACTCAAGTTCACCAC 59.397 37.037 0.00 0.00 0.00 4.16
5554 10516 7.577303 AGTTCACCACCATCATCTAAACATAT 58.423 34.615 0.00 0.00 0.00 1.78
5587 10549 8.648693 TCATCACATCATCTAAAGATCATCACT 58.351 33.333 0.00 0.00 31.21 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
126 2196 2.226330 ACTCGTGCCAAATTTGCAGTA 58.774 42.857 12.92 0.00 39.87 2.74
131 2201 3.479006 CGACTAACTCGTGCCAAATTTG 58.521 45.455 11.40 11.40 37.64 2.32
306 2379 7.169982 CGTAGGTGGATGTAAGATGAATTTCTC 59.830 40.741 0.00 0.00 0.00 2.87
308 2381 6.292919 GCGTAGGTGGATGTAAGATGAATTTC 60.293 42.308 0.00 0.00 0.00 2.17
332 2405 3.672295 CTTCAGGCCCAGAGACGGC 62.672 68.421 0.00 0.00 46.29 5.68
338 2411 0.538057 CAAGTTGCTTCAGGCCCAGA 60.538 55.000 0.00 0.00 40.92 3.86
355 2428 3.631250 AGAAGCTCTTGGGTTTCAACAA 58.369 40.909 0.31 0.00 35.61 2.83
384 2457 0.596082 TTTTGGTTTGCTCTAGCCGC 59.404 50.000 0.00 0.00 41.18 6.53
476 2551 7.401484 AACATTTTACGAATTTGCGAACAAT 57.599 28.000 0.00 0.00 35.21 2.71
491 2566 5.638596 ATCAAACTCCCCGAACATTTTAC 57.361 39.130 0.00 0.00 0.00 2.01
492 2567 7.762588 TTTATCAAACTCCCCGAACATTTTA 57.237 32.000 0.00 0.00 0.00 1.52
543 2618 7.669438 ATCGCAAACATTTCTCGAAATTATG 57.331 32.000 2.28 4.09 38.84 1.90
575 2651 6.320494 ACAAATACGCAAACAGGAACATTA 57.680 33.333 0.00 0.00 0.00 1.90
577 2653 4.846779 ACAAATACGCAAACAGGAACAT 57.153 36.364 0.00 0.00 0.00 2.71
584 2660 8.803201 TGAATTAATGAACAAATACGCAAACA 57.197 26.923 0.00 0.00 0.00 2.83
658 2735 9.965824 AAAACATGAACATTCTACGAAAATCTT 57.034 25.926 0.00 0.00 0.00 2.40
659 2736 9.398170 CAAAACATGAACATTCTACGAAAATCT 57.602 29.630 0.00 0.00 0.00 2.40
660 2737 9.393249 TCAAAACATGAACATTCTACGAAAATC 57.607 29.630 0.00 0.00 34.30 2.17
661 2738 9.743057 TTCAAAACATGAACATTCTACGAAAAT 57.257 25.926 0.00 0.00 43.08 1.82
709 2786 7.358270 GCCCATTTTTCAAAAATTGCGATTTTC 60.358 33.333 22.11 4.66 42.97 2.29
829 2907 3.134442 AGCAAAATTTGAAAGTGGGAGCA 59.866 39.130 10.26 0.00 0.00 4.26
830 2908 3.732212 AGCAAAATTTGAAAGTGGGAGC 58.268 40.909 10.26 0.00 0.00 4.70
831 2909 3.983344 CGAGCAAAATTTGAAAGTGGGAG 59.017 43.478 10.26 0.00 0.00 4.30
837 2916 6.544038 AAATTCCCGAGCAAAATTTGAAAG 57.456 33.333 10.26 0.00 32.79 2.62
850 2929 4.946784 AACATCTTTCGAAATTCCCGAG 57.053 40.909 11.70 0.00 37.35 4.63
866 2945 6.993079 AGACCCATTTAAAAGTGGAAACATC 58.007 36.000 9.07 0.77 46.14 3.06
887 2966 3.610911 CCCTCTGTTAATGGTCCAAGAC 58.389 50.000 0.00 0.00 0.00 3.01
889 2968 2.357154 CCCCCTCTGTTAATGGTCCAAG 60.357 54.545 0.00 0.00 0.00 3.61
948 3034 1.428448 TCTTGTCATTCGGTTCAGCG 58.572 50.000 0.00 0.00 0.00 5.18
1016 3102 4.215613 GGAGGTATTTTTGTGTGGTCTGTC 59.784 45.833 0.00 0.00 0.00 3.51
1099 3206 3.373658 GGAGGAGAAAGAGAGGAGATGGA 60.374 52.174 0.00 0.00 0.00 3.41
1223 3351 1.582968 GCAGGTGTCGACGAGGTAA 59.417 57.895 11.62 0.00 0.00 2.85
1262 3390 1.674057 CTTCGTGGAGGCCTTGAGT 59.326 57.895 6.77 0.00 0.00 3.41
1301 3429 2.900167 GACGGCGTTGGGTTTGTCC 61.900 63.158 16.19 0.00 0.00 4.02
1303 3431 2.903350 GGACGGCGTTGGGTTTGT 60.903 61.111 16.19 0.00 0.00 2.83
1431 3559 3.069318 GAGGCCCTCGAGTCCGTT 61.069 66.667 12.31 0.00 37.05 4.44
1441 3569 4.021925 GCAACAGACCGAGGCCCT 62.022 66.667 0.00 0.00 0.00 5.19
1481 3609 0.179134 AGTTGATGTAGGCGAGCGAC 60.179 55.000 0.00 0.00 0.00 5.19
1491 3619 1.275010 TCTGCAGCGGAAGTTGATGTA 59.725 47.619 9.47 0.00 46.01 2.29
1495 3623 0.391661 GGATCTGCAGCGGAAGTTGA 60.392 55.000 8.35 0.00 46.01 3.18
1678 3812 1.595382 ACTCGGACACACAGCTTGC 60.595 57.895 0.00 0.00 0.00 4.01
1694 3828 2.581354 GTCAGCATCCTCGGCACT 59.419 61.111 0.00 0.00 0.00 4.40
1741 3875 3.192212 GCCTAATCTTTCAGCATATGCCC 59.808 47.826 23.96 0.00 43.38 5.36
1819 3953 1.110442 AGCAGTGATCTTCTCCTCGG 58.890 55.000 0.00 0.00 0.00 4.63
1838 3972 5.048224 CGTCTTCTTCAGGTAGTCCACTTTA 60.048 44.000 0.00 0.00 35.89 1.85
1941 4075 2.357034 GAACTCGAACCTGCGCCA 60.357 61.111 4.18 0.00 0.00 5.69
1988 4122 4.438346 GGCCGACGAGCAATGTAT 57.562 55.556 0.00 0.00 0.00 2.29
1999 4133 0.317479 ATAGAGCATTACCGGCCGAC 59.683 55.000 30.73 8.46 0.00 4.79
2249 4385 2.766263 CACAGTGATCCTTAGCCCACTA 59.234 50.000 0.00 0.00 37.74 2.74
2349 4937 9.378551 TGTAACAGGCATACTACAGAAAATAAG 57.621 33.333 0.00 0.00 0.00 1.73
2463 5073 5.638657 CAGGAGAACACAAAGATCTTCTCTG 59.361 44.000 8.78 6.25 32.97 3.35
2482 5092 8.001292 AGGGTTCAGGAATAAAATTATCAGGAG 58.999 37.037 0.00 0.00 0.00 3.69
2518 5129 7.414540 GCTCGGCCATGATTTAGGAAAATATAG 60.415 40.741 2.24 0.00 35.41 1.31
2539 5152 1.665679 AGCAACACATATTTCGCTCGG 59.334 47.619 0.00 0.00 0.00 4.63
2540 5153 3.551890 ACTAGCAACACATATTTCGCTCG 59.448 43.478 0.00 0.00 0.00 5.03
2559 5172 6.667848 TCTGAACACAGGATAGAATGGAACTA 59.332 38.462 0.00 0.00 33.04 2.24
2574 5187 8.441608 CAGATCACTCTTAAAATCTGAACACAG 58.558 37.037 5.49 0.00 45.09 3.66
2675 5667 4.141505 TGGTGGAAGAAGTTTGATCTCACA 60.142 41.667 0.00 0.00 0.00 3.58
2709 5701 2.071778 AAAGCAGAGTTTGAGGCCAA 57.928 45.000 5.01 0.00 0.00 4.52
2775 5972 9.922305 GATCGATTTCTTACTAACAAAAGGATG 57.078 33.333 0.00 0.00 0.00 3.51
2870 6068 4.883585 TGAAGCAATGACACAAAGAGAAGT 59.116 37.500 0.00 0.00 0.00 3.01
2903 6161 6.439675 TTGTTCCAGTGGTTTACAAACTAC 57.560 37.500 18.37 11.99 46.74 2.73
2916 6174 6.990341 TGTTCTCATGATATTGTTCCAGTG 57.010 37.500 0.00 0.00 0.00 3.66
2938 6199 8.150945 AGCACTAATATAACCAGGACACTAATG 58.849 37.037 0.00 0.00 0.00 1.90
3021 6343 2.858260 GCAACACCACGGAAATCTGTTG 60.858 50.000 10.57 10.57 42.98 3.33
3590 7300 5.125417 TGCAGTGGAAATATAAAGCAAGGTC 59.875 40.000 0.00 0.00 0.00 3.85
3643 7413 7.875041 CACAATACCCAAAACACATGGAAATTA 59.125 33.333 0.00 0.00 40.56 1.40
3680 7450 6.467723 AAACAGACACGTTTCATATCAGAC 57.532 37.500 4.26 0.00 33.90 3.51
3698 7468 5.416326 TCGGGACCAAAACCATAATAAACAG 59.584 40.000 0.00 0.00 0.00 3.16
3699 7469 5.322754 TCGGGACCAAAACCATAATAAACA 58.677 37.500 0.00 0.00 0.00 2.83
3700 7470 5.900865 TCGGGACCAAAACCATAATAAAC 57.099 39.130 0.00 0.00 0.00 2.01
3864 7789 7.723324 TGAATATACTACACCTCCTAGCAAAC 58.277 38.462 0.00 0.00 0.00 2.93
4152 8106 1.785041 CTGGTGCACCCAAGACAACG 61.785 60.000 32.62 6.18 44.65 4.10
4189 8146 1.895798 TCCTTGCTGATGTCGAGTCTT 59.104 47.619 0.00 0.00 0.00 3.01
4239 8196 2.222678 GTGTGTGTCTCATCAACAGCAG 59.777 50.000 0.00 0.00 0.00 4.24
4269 8226 1.607801 GAATGTTTGCCCTGCCTCCC 61.608 60.000 0.00 0.00 0.00 4.30
4339 9228 1.376609 GCCCAAGGTACGGATGCTTG 61.377 60.000 0.00 0.00 0.00 4.01
4340 9229 1.077716 GCCCAAGGTACGGATGCTT 60.078 57.895 0.00 0.00 0.00 3.91
4344 9233 2.104281 GAGTTATGCCCAAGGTACGGAT 59.896 50.000 0.00 0.00 0.00 4.18
4362 9251 0.324285 CTGAGCTTCAAGGCAGGAGT 59.676 55.000 0.00 0.00 34.17 3.85
4372 9261 1.279846 TCACATCATGCCTGAGCTTCA 59.720 47.619 0.00 0.00 40.80 3.02
4445 9334 3.347216 CCAAGAAAAGGTGATGGTCGAT 58.653 45.455 0.00 0.00 0.00 3.59
4457 9346 4.144297 TGTTGGATGTCTCCCAAGAAAAG 58.856 43.478 0.00 0.00 43.63 2.27
4510 9399 5.946377 GTCAATATGGGTTTTCTTGGAGAGT 59.054 40.000 0.00 0.00 0.00 3.24
4571 9460 2.554032 AGGAATAGCACACAACAACTGC 59.446 45.455 0.00 0.00 0.00 4.40
4579 9468 2.566833 AGCAACAGGAATAGCACACA 57.433 45.000 0.00 0.00 0.00 3.72
4710 9599 0.700564 ACAGGGATGCCAGAACACAT 59.299 50.000 5.86 0.00 0.00 3.21
4748 9637 1.115326 ATCCATCATCGTCTGGCCGA 61.115 55.000 0.00 0.00 41.73 5.54
4792 9681 3.511540 TCTCCGATGATGGCGAGATATTT 59.488 43.478 0.00 0.00 0.00 1.40
4801 9690 1.382522 TTTGCTTCTCCGATGATGGC 58.617 50.000 0.00 0.00 0.00 4.40
4929 9818 2.561956 CCGACGGGTCTATGCCGAT 61.562 63.158 5.81 0.00 0.00 4.18
5114 10034 0.094730 GCTTTGTCGTCGGCATACAC 59.905 55.000 0.00 0.00 0.00 2.90
5212 10143 2.438868 CCGTCGGCATAGATTCATCA 57.561 50.000 0.00 0.00 0.00 3.07
5307 10238 2.628178 AGATGGAAATCTATGCCGACGA 59.372 45.455 0.00 0.00 0.00 4.20
5370 10301 2.387952 CCAGGAGTTACCAGGGCTT 58.612 57.895 0.00 0.00 41.01 4.35
5554 10516 9.676861 ATCTTTAGATGATGTGATGAACTTGAA 57.323 29.630 0.00 0.00 32.68 2.69
5587 10549 8.450578 ACTTTTATGTTCATGAACTTGAGTCA 57.549 30.769 32.57 15.81 41.67 3.41


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

AutoCloner maintained by Alex Coulton.