Multiple sequence alignment - TraesCS4A01G114600

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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 TraesCS4A01G114600 chr4A 100.000 4568 0 0 1 4568 139536680 139541247 0.000000e+00 8436.0
1 TraesCS4A01G114600 chr4D 94.627 3778 128 24 216 3949 334157446 334153700 0.000000e+00 5782.0
2 TraesCS4A01G114600 chr4D 91.914 606 29 10 3952 4555 334123914 334123327 0.000000e+00 830.0
3 TraesCS4A01G114600 chr4D 93.678 174 10 1 1 173 334157622 334157449 4.530000e-65 259.0
4 TraesCS4A01G114600 chr4B 95.602 3183 112 11 894 4075 412183844 412180689 0.000000e+00 5077.0
5 TraesCS4A01G114600 chr4B 86.281 933 42 29 1 898 412184984 412184103 0.000000e+00 935.0
6 TraesCS4A01G114600 chr4B 90.773 401 21 8 4172 4566 412114959 412114569 5.240000e-144 521.0
7 TraesCS4A01G114600 chr2A 77.613 1014 190 27 2454 3457 79173552 79174538 8.520000e-162 580.0
8 TraesCS4A01G114600 chr2A 74.899 494 102 20 1123 1602 79172269 79172754 5.990000e-49 206.0
9 TraesCS4A01G114600 chr2D 80.461 824 98 34 2981 3776 107703599 107704387 5.130000e-159 571.0
10 TraesCS4A01G114600 chr2D 80.148 539 96 9 2923 3457 78757868 78758399 4.280000e-105 392.0
11 TraesCS4A01G114600 chr2D 90.265 226 13 6 2499 2716 107703180 107703404 2.080000e-73 287.0
12 TraesCS4A01G114600 chr2D 75.000 496 98 24 1123 1602 78756128 78756613 5.990000e-49 206.0
13 TraesCS4A01G114600 chr3B 76.623 462 86 13 2999 3457 612930982 612931424 7.640000e-58 235.0
14 TraesCS4A01G114600 chr3B 74.747 297 61 10 1186 1472 612912264 612912556 2.230000e-23 121.0
15 TraesCS4A01G114600 chr2B 77.778 369 66 14 1123 1480 122013779 122014142 3.580000e-51 213.0
16 TraesCS4A01G114600 chr2B 97.059 34 1 0 4129 4162 694894195 694894228 1.780000e-04 58.4
17 TraesCS4A01G114600 chr7A 80.488 164 22 9 1358 1516 705593844 705593686 2.890000e-22 117.0
18 TraesCS4A01G114600 chr7A 87.671 73 8 1 4140 4212 563508477 563508548 2.930000e-12 84.2
19 TraesCS4A01G114600 chr7B 87.671 73 8 1 4140 4212 526430892 526430963 2.930000e-12 84.2
20 TraesCS4A01G114600 chr7D 91.525 59 4 1 4140 4198 497972584 497972641 3.790000e-11 80.5
21 TraesCS4A01G114600 chr6A 78.431 102 14 8 4129 4226 64260788 64260691 4.940000e-05 60.2
22 TraesCS4A01G114600 chr1D 97.059 34 1 0 4129 4162 311756215 311756182 1.780000e-04 58.4
23 TraesCS4A01G114600 chr3D 100.000 28 0 0 4135 4162 48851067 48851040 8.000000e-03 52.8


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 TraesCS4A01G114600 chr4A 139536680 139541247 4567 False 8436.0 8436 100.0000 1 4568 1 chr4A.!!$F1 4567
1 TraesCS4A01G114600 chr4D 334153700 334157622 3922 True 3020.5 5782 94.1525 1 3949 2 chr4D.!!$R2 3948
2 TraesCS4A01G114600 chr4D 334123327 334123914 587 True 830.0 830 91.9140 3952 4555 1 chr4D.!!$R1 603
3 TraesCS4A01G114600 chr4B 412180689 412184984 4295 True 3006.0 5077 90.9415 1 4075 2 chr4B.!!$R2 4074
4 TraesCS4A01G114600 chr2A 79172269 79174538 2269 False 393.0 580 76.2560 1123 3457 2 chr2A.!!$F1 2334
5 TraesCS4A01G114600 chr2D 107703180 107704387 1207 False 429.0 571 85.3630 2499 3776 2 chr2D.!!$F2 1277
6 TraesCS4A01G114600 chr2D 78756128 78758399 2271 False 299.0 392 77.5740 1123 3457 2 chr2D.!!$F1 2334

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
642 689 0.037232 AGCCTTCAACGTAGGAGCAC 60.037 55.0 7.05 0.0 34.56 4.40 F
643 690 0.320421 GCCTTCAACGTAGGAGCACA 60.320 55.0 7.05 0.0 34.56 4.57 F
1838 2290 0.116143 AGCCTCCCTGTCTCACTCTT 59.884 55.0 0.00 0.0 0.00 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1674 2126 0.949397 CAATGGTGGATGGCATCTCG 59.051 55.000 25.48 4.55 0.00 4.04 R
2190 2714 1.137086 GAAGAAGCGGAGGTGCAGATA 59.863 52.381 0.00 0.00 39.47 1.98 R
3827 4497 1.559219 TCGAATGGCATCCCTTTCAGA 59.441 47.619 0.00 0.00 42.49 3.27 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
47 48 1.302192 GGGTCAAAGGCGCACAGTA 60.302 57.895 10.83 0.00 0.00 2.74
64 65 2.749621 CAGTAAAGTGAAGGATGGCCAC 59.250 50.000 8.16 1.35 36.29 5.01
138 140 0.108186 CTGCGCACATTCCTCCAGTA 60.108 55.000 5.66 0.00 0.00 2.74
176 178 0.108992 CATCATGTGGCTTGGTGCAC 60.109 55.000 8.80 8.80 45.15 4.57
177 179 1.252904 ATCATGTGGCTTGGTGCACC 61.253 55.000 29.67 29.67 45.15 5.01
178 180 2.198150 ATGTGGCTTGGTGCACCA 59.802 55.556 34.74 34.74 45.94 4.17
194 196 3.000819 CACCGGCCACCAGGAGTA 61.001 66.667 0.00 0.00 36.89 2.59
195 197 2.683933 ACCGGCCACCAGGAGTAG 60.684 66.667 0.00 0.00 36.89 2.57
196 198 4.162690 CCGGCCACCAGGAGTAGC 62.163 72.222 2.24 0.00 36.89 3.58
197 199 3.390521 CGGCCACCAGGAGTAGCA 61.391 66.667 2.24 0.00 34.37 3.49
198 200 2.269241 GGCCACCAGGAGTAGCAC 59.731 66.667 0.00 0.00 34.37 4.40
199 201 2.269241 GCCACCAGGAGTAGCACC 59.731 66.667 0.00 0.00 36.89 5.01
200 202 2.592993 GCCACCAGGAGTAGCACCA 61.593 63.158 0.00 0.00 36.89 4.17
201 203 1.599047 CCACCAGGAGTAGCACCAG 59.401 63.158 0.00 0.00 36.89 4.00
272 275 1.867233 CTCCGGGCACGAAATGAATAG 59.133 52.381 11.66 0.00 44.60 1.73
428 434 1.973812 GTTTGCTGTCTGCCCCTCC 60.974 63.158 0.00 0.00 42.00 4.30
429 435 3.210012 TTTGCTGTCTGCCCCTCCC 62.210 63.158 0.00 0.00 42.00 4.30
430 436 4.664267 TGCTGTCTGCCCCTCCCT 62.664 66.667 0.00 0.00 42.00 4.20
431 437 3.791586 GCTGTCTGCCCCTCCCTC 61.792 72.222 0.00 0.00 35.15 4.30
463 469 6.405842 CCCTCTTTACTGCCAATAAATTCACC 60.406 42.308 0.00 0.00 0.00 4.02
514 521 2.507769 CGTGATCGCTGCTGCTGA 60.508 61.111 14.03 12.39 36.97 4.26
631 678 0.250901 GTCTGCCCTTGAGCCTTCAA 60.251 55.000 0.00 0.00 40.92 2.69
632 679 0.250901 TCTGCCCTTGAGCCTTCAAC 60.251 55.000 0.00 0.00 38.37 3.18
633 680 1.580845 CTGCCCTTGAGCCTTCAACG 61.581 60.000 0.00 0.00 38.37 4.10
634 681 1.600916 GCCCTTGAGCCTTCAACGT 60.601 57.895 0.00 0.00 38.37 3.99
635 682 0.321298 GCCCTTGAGCCTTCAACGTA 60.321 55.000 0.00 0.00 38.37 3.57
636 683 1.726853 CCCTTGAGCCTTCAACGTAG 58.273 55.000 0.00 0.00 38.37 3.51
637 684 1.676014 CCCTTGAGCCTTCAACGTAGG 60.676 57.143 0.00 0.00 38.37 3.18
638 685 1.275291 CCTTGAGCCTTCAACGTAGGA 59.725 52.381 7.05 0.00 38.37 2.94
639 686 2.611518 CTTGAGCCTTCAACGTAGGAG 58.388 52.381 7.05 0.00 38.37 3.69
640 687 0.246635 TGAGCCTTCAACGTAGGAGC 59.753 55.000 7.05 0.79 34.56 4.70
641 688 0.246635 GAGCCTTCAACGTAGGAGCA 59.753 55.000 7.05 0.00 34.56 4.26
642 689 0.037232 AGCCTTCAACGTAGGAGCAC 60.037 55.000 7.05 0.00 34.56 4.40
643 690 0.320421 GCCTTCAACGTAGGAGCACA 60.320 55.000 7.05 0.00 34.56 4.57
644 691 1.876416 GCCTTCAACGTAGGAGCACAA 60.876 52.381 7.05 0.00 34.56 3.33
645 692 1.798813 CCTTCAACGTAGGAGCACAAC 59.201 52.381 0.00 0.00 34.56 3.32
646 693 1.798813 CTTCAACGTAGGAGCACAACC 59.201 52.381 0.00 0.00 0.00 3.77
647 694 0.753867 TCAACGTAGGAGCACAACCA 59.246 50.000 0.00 0.00 0.00 3.67
648 695 0.865769 CAACGTAGGAGCACAACCAC 59.134 55.000 0.00 0.00 0.00 4.16
649 696 0.756903 AACGTAGGAGCACAACCACT 59.243 50.000 0.00 0.00 0.00 4.00
734 790 3.248171 CGACGAGCTAGCCGTTGC 61.248 66.667 25.16 15.82 40.67 4.17
769 825 1.945394 CTGGATGCTTGAATCCCTTCG 59.055 52.381 5.24 0.00 44.88 3.79
771 827 0.665298 GATGCTTGAATCCCTTCGGC 59.335 55.000 0.00 0.00 33.86 5.54
853 910 0.885196 TATTGCTTTTCCCACCGCAC 59.115 50.000 0.00 0.00 31.24 5.34
906 1227 2.479656 CGAGCTAGGTACGAGGATACAC 59.520 54.545 0.00 0.00 41.41 2.90
911 1232 5.881443 AGCTAGGTACGAGGATACACATATC 59.119 44.000 0.00 0.00 37.12 1.63
970 1296 4.028993 AGATCCTAGAGCTAGTAGTGGC 57.971 50.000 0.00 0.00 0.00 5.01
1670 2122 5.886960 AGCCTCAACAATAACAATCTCAC 57.113 39.130 0.00 0.00 0.00 3.51
1671 2123 5.564550 AGCCTCAACAATAACAATCTCACT 58.435 37.500 0.00 0.00 0.00 3.41
1674 2126 5.392380 CCTCAACAATAACAATCTCACTGGC 60.392 44.000 0.00 0.00 0.00 4.85
1702 2154 2.380941 CATCCACCATTGGCAATCTCA 58.619 47.619 10.36 0.00 43.56 3.27
1715 2167 0.467384 AATCTCAGGATGCTCCGTGG 59.533 55.000 0.00 0.00 42.75 4.94
1809 2261 4.982241 TCTGGACCTTTCTGACAATCTT 57.018 40.909 0.00 0.00 0.00 2.40
1838 2290 0.116143 AGCCTCCCTGTCTCACTCTT 59.884 55.000 0.00 0.00 0.00 2.85
1939 2391 2.054799 AGAACCTAACCAAGCTGTCCA 58.945 47.619 0.00 0.00 0.00 4.02
2050 2574 1.004891 GGAGGGATTCCAGGGTCCT 59.995 63.158 4.80 2.06 46.01 3.85
2082 2606 5.047519 CCTTGCCAATCTCAACTCTTTCAAT 60.048 40.000 0.00 0.00 0.00 2.57
2169 2693 2.743636 TCGTAGGAAACCTTCAGCTG 57.256 50.000 7.63 7.63 34.61 4.24
2190 2714 0.394352 GTGGGTTCAATGGCTCCGAT 60.394 55.000 0.00 0.00 0.00 4.18
2373 2927 3.262420 GAAAGATAAGAAGGACAGCGCA 58.738 45.455 11.47 0.00 0.00 6.09
2456 3046 2.342279 CAAGGGAAGTGACGCCGA 59.658 61.111 0.00 0.00 0.00 5.54
2487 3077 1.545651 GGTGGCAAGCTAGTCCACTTT 60.546 52.381 22.98 0.00 47.00 2.66
2520 3110 1.514087 GTTCACGGCGGATGACCTA 59.486 57.895 13.24 0.00 0.00 3.08
2654 3248 1.743252 GCAGCAAGGAGTTCGAGGG 60.743 63.158 0.00 0.00 0.00 4.30
2709 3306 2.695597 CTCCTCTCCCTCAGGGCT 59.304 66.667 4.08 0.00 43.94 5.19
2821 3418 3.682696 TCTTCGGTGCTCTCTTACTACA 58.317 45.455 0.00 0.00 0.00 2.74
2834 3431 6.106673 TCTCTTACTACACCATTAGCTTTGC 58.893 40.000 0.00 0.00 0.00 3.68
3256 3905 4.052229 CGACCAACGGGCTCGACT 62.052 66.667 15.95 0.00 38.89 4.18
3406 4055 1.421410 GCATTGCGTCGATCCTTCGT 61.421 55.000 0.00 0.00 45.65 3.85
3495 4148 2.932234 CGCCACCTCGTCCTTCACT 61.932 63.158 0.00 0.00 0.00 3.41
3787 4457 3.084786 GAGTGCTGGCCTTTCTTTACAT 58.915 45.455 3.32 0.00 0.00 2.29
3788 4458 2.821969 AGTGCTGGCCTTTCTTTACATG 59.178 45.455 3.32 0.00 0.00 3.21
3795 4465 5.596845 TGGCCTTTCTTTACATGTTTCAAC 58.403 37.500 2.30 0.00 0.00 3.18
3805 4475 8.124199 TCTTTACATGTTTCAACGAACCTTTAC 58.876 33.333 2.30 0.00 0.00 2.01
3809 4479 3.690139 TGTTTCAACGAACCTTTACTGCA 59.310 39.130 0.00 0.00 0.00 4.41
3827 4497 4.039730 ACTGCATCAGTACTTGTCTGAACT 59.960 41.667 0.00 0.00 43.46 3.01
3830 4500 4.624882 GCATCAGTACTTGTCTGAACTCTG 59.375 45.833 0.00 0.00 43.65 3.35
3880 4551 9.341899 GAAAGCAATACATCGTTTGATTTACTT 57.658 29.630 0.00 0.00 40.40 2.24
3882 4553 9.769093 AAGCAATACATCGTTTGATTTACTTAC 57.231 29.630 0.00 0.00 27.68 2.34
3883 4554 9.162764 AGCAATACATCGTTTGATTTACTTACT 57.837 29.630 0.00 0.00 30.49 2.24
3884 4555 9.210426 GCAATACATCGTTTGATTTACTTACTG 57.790 33.333 0.00 0.00 30.49 2.74
3890 4561 7.972832 TCGTTTGATTTACTTACTGTGGATT 57.027 32.000 0.00 0.00 0.00 3.01
3949 4620 1.027357 CATGGCATGCCTTGGTACTC 58.973 55.000 34.32 10.70 37.53 2.59
3950 4621 0.106519 ATGGCATGCCTTGGTACTCC 60.107 55.000 35.53 7.29 36.94 3.85
3951 4622 1.207488 TGGCATGCCTTGGTACTCCT 61.207 55.000 35.53 0.00 36.94 3.69
3952 4623 0.837272 GGCATGCCTTGGTACTCCTA 59.163 55.000 29.98 0.00 34.23 2.94
3953 4624 1.475213 GGCATGCCTTGGTACTCCTAC 60.475 57.143 29.98 0.00 34.23 3.18
3954 4625 1.475213 GCATGCCTTGGTACTCCTACC 60.475 57.143 6.36 0.00 42.83 3.18
3962 4633 3.967332 TGGTACTCCTACCTTTTTCCG 57.033 47.619 0.00 0.00 42.94 4.30
4081 4752 5.818857 TCACTTTCTACCCAAGTTACACAAC 59.181 40.000 0.00 0.00 31.83 3.32
4109 4780 2.436469 TGCCTGATGCGCAATCGT 60.436 55.556 17.11 0.00 45.60 3.73
4115 4786 2.287644 CCTGATGCGCAATCGTAAATGA 59.712 45.455 17.11 0.00 38.22 2.57
4118 4789 2.017138 TGCGCAATCGTAAATGAGGA 57.983 45.000 8.16 0.00 38.14 3.71
4121 4792 1.332028 CGCAATCGTAAATGAGGACGC 60.332 52.381 0.00 0.00 38.93 5.19
4130 4801 4.554330 CGTAAATGAGGACGCTAGAGGTAC 60.554 50.000 0.00 0.00 31.49 3.34
4156 4827 6.235664 ACCTCCGTAACAAAATGTAAGATGT 58.764 36.000 0.00 0.00 0.00 3.06
4199 4870 6.577883 CGTAGAAAACGTCTTACATTTTGC 57.422 37.500 0.00 0.00 46.72 3.68
4202 4873 7.322699 CGTAGAAAACGTCTTACATTTTGCAAT 59.677 33.333 0.00 0.00 46.72 3.56
4212 4883 2.564062 ACATTTTGCAATGGAGGGAGTG 59.436 45.455 0.00 0.00 43.82 3.51
4302 4973 9.476928 AGATAGTTTCCTACTTTCTGCTACTTA 57.523 33.333 0.00 0.00 41.70 2.24
4303 4974 9.518906 GATAGTTTCCTACTTTCTGCTACTTAC 57.481 37.037 0.00 0.00 38.33 2.34
4304 4975 7.541916 AGTTTCCTACTTTCTGCTACTTACT 57.458 36.000 0.00 0.00 31.29 2.24
4305 4976 7.604549 AGTTTCCTACTTTCTGCTACTTACTC 58.395 38.462 0.00 0.00 31.29 2.59
4345 5016 1.488812 TGGTATGGGCAGTGATGTACC 59.511 52.381 0.00 1.06 33.80 3.34
4356 5027 4.389374 CAGTGATGTACCAACCTTTGTCT 58.611 43.478 0.00 0.00 0.00 3.41
4393 5064 2.305927 GTTGGACTCTTCTCCCATCCAA 59.694 50.000 0.00 0.00 45.07 3.53
4394 5065 1.909302 TGGACTCTTCTCCCATCCAAC 59.091 52.381 0.00 0.00 36.51 3.77
4395 5066 1.210722 GGACTCTTCTCCCATCCAACC 59.789 57.143 0.00 0.00 0.00 3.77
4398 5070 1.912043 CTCTTCTCCCATCCAACCTGT 59.088 52.381 0.00 0.00 0.00 4.00
4405 5077 1.406887 CCCATCCAACCTGTAGTTCCG 60.407 57.143 0.00 0.00 36.18 4.30
4411 5083 0.602905 AACCTGTAGTTCCGTGCTGC 60.603 55.000 0.00 0.00 30.99 5.25
4412 5084 1.293498 CCTGTAGTTCCGTGCTGCT 59.707 57.895 0.00 0.00 0.00 4.24
4413 5085 0.737715 CCTGTAGTTCCGTGCTGCTC 60.738 60.000 0.00 0.00 0.00 4.26
4414 5086 0.737715 CTGTAGTTCCGTGCTGCTCC 60.738 60.000 0.00 0.00 0.00 4.70
4415 5087 1.448013 GTAGTTCCGTGCTGCTCCC 60.448 63.158 0.00 0.00 0.00 4.30
4416 5088 1.911269 TAGTTCCGTGCTGCTCCCA 60.911 57.895 0.00 0.00 0.00 4.37
4417 5089 1.264749 TAGTTCCGTGCTGCTCCCAT 61.265 55.000 0.00 0.00 0.00 4.00
4422 5094 2.271497 GTGCTGCTCCCATCTGCT 59.729 61.111 0.00 0.00 0.00 4.24
4439 5111 1.820010 GCTGGGTTTGGCAAGGAAGG 61.820 60.000 0.00 0.00 0.00 3.46
4440 5112 0.178964 CTGGGTTTGGCAAGGAAGGA 60.179 55.000 0.00 0.00 0.00 3.36
4441 5113 0.263172 TGGGTTTGGCAAGGAAGGAA 59.737 50.000 0.00 0.00 0.00 3.36
4442 5114 0.969149 GGGTTTGGCAAGGAAGGAAG 59.031 55.000 0.00 0.00 0.00 3.46
4443 5115 1.704641 GGTTTGGCAAGGAAGGAAGT 58.295 50.000 0.00 0.00 0.00 3.01
4444 5116 2.490168 GGGTTTGGCAAGGAAGGAAGTA 60.490 50.000 0.00 0.00 0.00 2.24
4523 5195 2.173782 TGCAGTCCCTGTCACCTTTTAA 59.826 45.455 0.00 0.00 33.43 1.52
4546 5218 4.100189 ACTCCTTGGATTAGGTCTGAATCG 59.900 45.833 0.00 0.00 36.63 3.34
4555 5227 1.204941 AGGTCTGAATCGTACCTGCAC 59.795 52.381 5.65 0.00 42.08 4.57
4556 5228 1.204941 GGTCTGAATCGTACCTGCACT 59.795 52.381 0.00 0.00 0.00 4.40
4557 5229 2.263077 GTCTGAATCGTACCTGCACTG 58.737 52.381 0.00 0.00 0.00 3.66
4558 5230 1.002366 CTGAATCGTACCTGCACTGC 58.998 55.000 0.00 0.00 0.00 4.40
4559 5231 0.320050 TGAATCGTACCTGCACTGCA 59.680 50.000 3.11 3.11 36.92 4.41
4560 5232 1.066215 TGAATCGTACCTGCACTGCAT 60.066 47.619 3.64 0.00 38.13 3.96
4561 5233 2.167487 TGAATCGTACCTGCACTGCATA 59.833 45.455 3.64 0.00 38.13 3.14
4562 5234 3.181466 TGAATCGTACCTGCACTGCATAT 60.181 43.478 3.64 0.00 38.13 1.78
4563 5235 2.509052 TCGTACCTGCACTGCATATC 57.491 50.000 3.64 0.00 38.13 1.63
4564 5236 2.031870 TCGTACCTGCACTGCATATCT 58.968 47.619 3.64 0.00 38.13 1.98
4565 5237 2.130395 CGTACCTGCACTGCATATCTG 58.870 52.381 3.64 0.00 38.13 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 0.609131 CCGTGGCCATCCTTCACTTT 60.609 55.000 9.72 0.00 0.00 2.66
161 163 2.198150 TGGTGCACCAAGCCACAT 59.802 55.556 36.10 0.00 44.35 3.21
177 179 3.000819 TACTCCTGGTGGCCGGTG 61.001 66.667 1.90 0.00 0.00 4.94
178 180 2.683933 CTACTCCTGGTGGCCGGT 60.684 66.667 1.90 0.00 0.00 5.28
179 181 4.162690 GCTACTCCTGGTGGCCGG 62.163 72.222 0.00 0.00 45.00 6.13
183 185 1.599047 CTGGTGCTACTCCTGGTGG 59.401 63.158 0.33 0.00 0.00 4.61
184 186 1.078848 GCTGGTGCTACTCCTGGTG 60.079 63.158 0.00 0.00 36.03 4.17
185 187 2.294078 GGCTGGTGCTACTCCTGGT 61.294 63.158 0.00 0.00 39.59 4.00
186 188 2.293318 TGGCTGGTGCTACTCCTGG 61.293 63.158 0.00 0.00 39.59 4.45
187 189 1.078848 GTGGCTGGTGCTACTCCTG 60.079 63.158 0.00 0.00 45.51 3.86
188 190 3.393360 GTGGCTGGTGCTACTCCT 58.607 61.111 0.00 0.00 45.51 3.69
193 195 3.329889 CCCTGGTGGCTGGTGCTA 61.330 66.667 0.00 0.00 39.59 3.49
195 197 4.729918 CTCCCTGGTGGCTGGTGC 62.730 72.222 0.00 0.00 38.76 5.01
196 198 4.729918 GCTCCCTGGTGGCTGGTG 62.730 72.222 0.00 0.00 0.00 4.17
198 200 4.421515 CTGCTCCCTGGTGGCTGG 62.422 72.222 9.03 0.00 0.00 4.85
199 201 3.201707 AACTGCTCCCTGGTGGCTG 62.202 63.158 11.35 11.35 0.00 4.85
200 202 2.856000 AACTGCTCCCTGGTGGCT 60.856 61.111 9.03 0.00 0.00 4.75
201 203 2.674380 CAACTGCTCCCTGGTGGC 60.674 66.667 0.00 0.00 0.00 5.01
272 275 0.541863 ACCGGGAGACACCATCATTC 59.458 55.000 6.32 0.00 41.20 2.67
428 434 3.891049 CAGTAAAGAGGGATTTGGGAGG 58.109 50.000 0.00 0.00 0.00 4.30
429 435 3.282885 GCAGTAAAGAGGGATTTGGGAG 58.717 50.000 0.00 0.00 0.00 4.30
430 436 2.025321 GGCAGTAAAGAGGGATTTGGGA 60.025 50.000 0.00 0.00 0.00 4.37
431 437 2.291540 TGGCAGTAAAGAGGGATTTGGG 60.292 50.000 0.00 0.00 0.00 4.12
463 469 2.706555 TAATACATCGAGAGCAGCGG 57.293 50.000 0.00 0.00 0.00 5.52
552 588 0.666913 CTATGCCATTCAGTGCAGCC 59.333 55.000 0.00 0.00 41.46 4.85
625 672 1.798813 GTTGTGCTCCTACGTTGAAGG 59.201 52.381 0.00 0.00 35.26 3.46
631 678 1.271656 GTAGTGGTTGTGCTCCTACGT 59.728 52.381 0.00 0.00 0.00 3.57
632 679 1.731424 CGTAGTGGTTGTGCTCCTACG 60.731 57.143 0.00 0.00 43.12 3.51
633 680 1.271656 ACGTAGTGGTTGTGCTCCTAC 59.728 52.381 0.00 0.00 42.51 3.18
634 681 1.624336 ACGTAGTGGTTGTGCTCCTA 58.376 50.000 0.00 0.00 42.51 2.94
635 682 1.544691 CTACGTAGTGGTTGTGCTCCT 59.455 52.381 14.66 0.00 45.73 3.69
636 683 1.992170 CTACGTAGTGGTTGTGCTCC 58.008 55.000 14.66 0.00 45.73 4.70
637 684 1.347320 GCTACGTAGTGGTTGTGCTC 58.653 55.000 22.98 0.00 45.73 4.26
638 685 0.037605 GGCTACGTAGTGGTTGTGCT 60.038 55.000 22.98 0.00 45.73 4.40
639 686 1.349259 CGGCTACGTAGTGGTTGTGC 61.349 60.000 22.98 7.49 45.73 4.57
640 687 2.733127 CGGCTACGTAGTGGTTGTG 58.267 57.895 22.98 3.05 45.73 3.33
673 729 6.322491 GCAGCGACCAAGACTAATTTAAATT 58.678 36.000 17.18 17.18 0.00 1.82
711 767 2.649349 GCTAGCTCGTCGTGCTCG 60.649 66.667 23.72 18.69 41.46 5.03
769 825 8.941995 AAAGAAAGGAGGGAATATAATTAGCC 57.058 34.615 0.00 0.00 0.00 3.93
853 910 2.851824 GCTGTTTTTGACGAGTTGTTGG 59.148 45.455 0.00 0.00 0.00 3.77
906 1227 0.309612 TGCAATGCAGCTGCGATATG 59.690 50.000 32.11 25.92 45.83 1.78
911 1232 2.798501 GCAATGCAATGCAGCTGCG 61.799 57.895 32.11 19.84 43.65 5.18
980 1306 4.141711 CCATTGGGACTAACAGCTAGCTAA 60.142 45.833 18.86 5.00 35.59 3.09
1036 1362 2.169789 CGAGCATGACGCCTCTTGG 61.170 63.158 0.00 0.00 44.04 3.61
1119 1445 4.129737 ATCACCACGCCGTCCGAG 62.130 66.667 0.00 0.00 41.02 4.63
1674 2126 0.949397 CAATGGTGGATGGCATCTCG 59.051 55.000 25.48 4.55 0.00 4.04
1715 2167 3.864583 CAGATTGCTGCTTAGAGACAGAC 59.135 47.826 0.00 0.00 35.90 3.51
1809 2261 1.203389 ACAGGGAGGCTACCACCTAAA 60.203 52.381 20.33 0.00 41.32 1.85
2045 2569 2.338785 GCAAGGCTGCTCAAGGACC 61.339 63.158 0.00 0.00 45.74 4.46
2082 2606 4.442893 CCTGAGAGGTTGTTGTAAGACACA 60.443 45.833 0.00 0.00 34.51 3.72
2169 2693 1.586154 CGGAGCCATTGAACCCACAC 61.586 60.000 0.00 0.00 0.00 3.82
2190 2714 1.137086 GAAGAAGCGGAGGTGCAGATA 59.863 52.381 0.00 0.00 39.47 1.98
2436 2996 3.423154 GCGTCACTTCCCTTGCCG 61.423 66.667 0.00 0.00 0.00 5.69
2709 3306 2.414612 CCCTTAGGGCCATGGTAGTAA 58.585 52.381 14.67 7.53 35.35 2.24
2742 3339 2.163818 TGGTCATGAAGTCGAACACC 57.836 50.000 0.00 0.00 0.00 4.16
2821 3418 3.640967 TGAAACAAGGCAAAGCTAATGGT 59.359 39.130 0.00 0.00 0.00 3.55
2834 3431 5.506317 GGTCAGAACACAGAATGAAACAAGG 60.506 44.000 0.00 0.00 39.69 3.61
3321 3970 2.746277 GTGGCCGCGTCCTTCATT 60.746 61.111 8.05 0.00 0.00 2.57
3787 4457 3.690139 TGCAGTAAAGGTTCGTTGAAACA 59.310 39.130 0.00 0.00 30.66 2.83
3788 4458 4.281525 TGCAGTAAAGGTTCGTTGAAAC 57.718 40.909 0.00 0.00 0.00 2.78
3795 4465 4.495422 AGTACTGATGCAGTAAAGGTTCG 58.505 43.478 8.70 0.00 46.55 3.95
3805 4475 4.564041 AGTTCAGACAAGTACTGATGCAG 58.436 43.478 0.00 0.00 42.68 4.41
3809 4479 6.656632 TTCAGAGTTCAGACAAGTACTGAT 57.343 37.500 0.00 0.00 42.68 2.90
3827 4497 1.559219 TCGAATGGCATCCCTTTCAGA 59.441 47.619 0.00 0.00 42.49 3.27
3830 4500 1.943340 GAGTCGAATGGCATCCCTTTC 59.057 52.381 0.00 0.00 40.25 2.62
3880 4551 6.293190 CGCAACTGTTAAAAGAATCCACAGTA 60.293 38.462 0.00 0.00 45.79 2.74
3882 4553 4.911610 CGCAACTGTTAAAAGAATCCACAG 59.088 41.667 0.00 0.00 40.65 3.66
3883 4554 4.791411 GCGCAACTGTTAAAAGAATCCACA 60.791 41.667 0.30 0.00 0.00 4.17
3884 4555 3.668656 GCGCAACTGTTAAAAGAATCCAC 59.331 43.478 0.30 0.00 0.00 4.02
3890 4561 4.628074 ACTAGAGCGCAACTGTTAAAAGA 58.372 39.130 11.47 0.00 0.00 2.52
3949 4620 4.276058 TCCTGTAACGGAAAAAGGTAGG 57.724 45.455 0.00 0.00 0.00 3.18
3950 4621 5.484715 TGATCCTGTAACGGAAAAAGGTAG 58.515 41.667 0.00 0.00 36.49 3.18
3951 4622 5.246656 TCTGATCCTGTAACGGAAAAAGGTA 59.753 40.000 0.00 0.00 36.49 3.08
3952 4623 4.041198 TCTGATCCTGTAACGGAAAAAGGT 59.959 41.667 0.00 0.00 36.49 3.50
3953 4624 4.575885 TCTGATCCTGTAACGGAAAAAGG 58.424 43.478 0.00 0.00 36.49 3.11
3954 4625 6.554334 TTTCTGATCCTGTAACGGAAAAAG 57.446 37.500 0.00 0.00 36.43 2.27
3962 4633 6.038714 CAGGGCTTATTTTCTGATCCTGTAAC 59.961 42.308 0.00 0.00 36.66 2.50
4109 4780 4.789807 AGTACCTCTAGCGTCCTCATTTA 58.210 43.478 0.00 0.00 0.00 1.40
4115 4786 2.636647 GGTAGTACCTCTAGCGTCCT 57.363 55.000 12.41 0.00 37.39 3.85
4130 4801 7.548075 ACATCTTACATTTTGTTACGGAGGTAG 59.452 37.037 0.00 0.00 0.00 3.18
4161 4832 1.279558 TCTACGCCCTATGCAAAACCA 59.720 47.619 0.00 0.00 41.33 3.67
4177 4848 7.901874 TTGCAAAATGTAAGACGTTTTCTAC 57.098 32.000 0.00 0.00 43.26 2.59
4180 4851 6.419413 TCCATTGCAAAATGTAAGACGTTTTC 59.581 34.615 1.71 4.10 43.26 2.29
4199 4870 5.128919 CCTTAGATTTCACTCCCTCCATTG 58.871 45.833 0.00 0.00 0.00 2.82
4202 4873 2.505819 GCCTTAGATTTCACTCCCTCCA 59.494 50.000 0.00 0.00 0.00 3.86
4212 4883 2.095415 ACGTTTTGCCGCCTTAGATTTC 60.095 45.455 0.00 0.00 0.00 2.17
4302 4973 4.101741 AGCAAGAAACCTACAGTTCAGAGT 59.898 41.667 0.00 0.00 37.88 3.24
4303 4974 4.450419 CAGCAAGAAACCTACAGTTCAGAG 59.550 45.833 0.00 0.00 37.88 3.35
4304 4975 4.380531 CAGCAAGAAACCTACAGTTCAGA 58.619 43.478 0.00 0.00 37.88 3.27
4305 4976 3.499918 CCAGCAAGAAACCTACAGTTCAG 59.500 47.826 0.00 0.00 37.88 3.02
4393 5064 1.004918 GCAGCACGGAACTACAGGT 60.005 57.895 0.00 0.00 0.00 4.00
4394 5065 0.737715 GAGCAGCACGGAACTACAGG 60.738 60.000 0.00 0.00 0.00 4.00
4395 5066 0.737715 GGAGCAGCACGGAACTACAG 60.738 60.000 0.00 0.00 0.00 2.74
4398 5070 1.264749 ATGGGAGCAGCACGGAACTA 61.265 55.000 0.00 0.00 0.00 2.24
4405 5077 2.113433 CAGCAGATGGGAGCAGCAC 61.113 63.158 0.00 0.00 0.00 4.40
4415 5087 0.245539 CTTGCCAAACCCAGCAGATG 59.754 55.000 0.00 0.00 40.73 2.90
4416 5088 0.901580 CCTTGCCAAACCCAGCAGAT 60.902 55.000 0.00 0.00 40.73 2.90
4417 5089 1.531365 CCTTGCCAAACCCAGCAGA 60.531 57.895 0.00 0.00 40.73 4.26
4422 5094 0.263172 TTCCTTCCTTGCCAAACCCA 59.737 50.000 0.00 0.00 0.00 4.51
4439 5111 1.986698 TAACGCCGTCTTGCTACTTC 58.013 50.000 0.00 0.00 0.00 3.01
4440 5112 2.064014 GTTAACGCCGTCTTGCTACTT 58.936 47.619 0.00 0.00 0.00 2.24
4441 5113 1.670967 GGTTAACGCCGTCTTGCTACT 60.671 52.381 0.00 0.00 0.00 2.57
4442 5114 0.717784 GGTTAACGCCGTCTTGCTAC 59.282 55.000 0.00 0.00 0.00 3.58
4443 5115 0.317799 TGGTTAACGCCGTCTTGCTA 59.682 50.000 0.00 0.00 0.00 3.49
4444 5116 0.533308 TTGGTTAACGCCGTCTTGCT 60.533 50.000 0.00 0.00 0.00 3.91
4472 5144 2.158254 GGTTTGATTCACGTTACCGACC 59.842 50.000 0.00 0.00 37.88 4.79
4523 5195 4.100189 CGATTCAGACCTAATCCAAGGAGT 59.900 45.833 0.00 0.00 39.15 3.85
4546 5218 1.869767 GCAGATATGCAGTGCAGGTAC 59.130 52.381 24.20 13.94 43.65 3.34


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

AutoCloner maintained by Alex Coulton.