Multiple sequence alignment - TraesCS3D01G416300

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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 TraesCS3D01G416300 chr3D 100.000 4876 0 0 1 4876 527664678 527669553 0.000000e+00 9005.0
1 TraesCS3D01G416300 chr3D 86.364 880 97 13 1 867 162359122 162358253 0.000000e+00 939.0
2 TraesCS3D01G416300 chr3D 80.530 868 161 5 2996 3861 45410039 45410900 0.000000e+00 660.0
3 TraesCS3D01G416300 chr3D 90.397 302 14 4 579 867 527588473 527588772 2.750000e-102 383.0
4 TraesCS3D01G416300 chr3B 95.978 2337 63 13 2293 4620 697900701 697903015 0.000000e+00 3766.0
5 TraesCS3D01G416300 chr3B 98.351 1395 23 0 899 2293 697899258 697900652 0.000000e+00 2449.0
6 TraesCS3D01G416300 chr3B 81.384 795 148 0 3067 3861 71119782 71120576 0.000000e+00 649.0
7 TraesCS3D01G416300 chr3B 81.258 795 149 0 3067 3861 71143521 71144315 1.140000e-180 643.0
8 TraesCS3D01G416300 chr3B 91.049 324 28 1 899 1221 697856371 697856694 2.080000e-118 436.0
9 TraesCS3D01G416300 chr3B 92.157 204 15 1 4674 4876 744316933 744316730 2.220000e-73 287.0
10 TraesCS3D01G416300 chr3B 91.753 97 5 1 1208 1304 697858065 697858158 1.100000e-26 132.0
11 TraesCS3D01G416300 chr3A 97.405 1965 39 8 2475 4432 662396406 662398365 0.000000e+00 3336.0
12 TraesCS3D01G416300 chr3A 97.835 1432 27 2 865 2293 662394634 662396064 0.000000e+00 2470.0
13 TraesCS3D01G416300 chr3A 87.538 658 64 6 226 870 95168278 95168930 0.000000e+00 745.0
14 TraesCS3D01G416300 chr3A 81.807 797 141 4 3067 3861 57199536 57200330 0.000000e+00 665.0
15 TraesCS3D01G416300 chr3A 97.380 229 6 0 4412 4640 662401451 662401679 1.650000e-104 390.0
16 TraesCS3D01G416300 chr3A 99.432 176 1 0 2295 2470 662396130 662396305 2.190000e-83 320.0
17 TraesCS3D01G416300 chr3A 98.020 101 1 1 2517 2617 662396298 662396397 1.800000e-39 174.0
18 TraesCS3D01G416300 chr5D 89.597 894 63 14 1 870 48062045 48061158 0.000000e+00 1109.0
19 TraesCS3D01G416300 chr5D 88.961 308 14 10 575 867 48283331 48283029 3.590000e-96 363.0
20 TraesCS3D01G416300 chr5D 93.333 210 11 3 4669 4876 464701891 464702099 1.700000e-79 307.0
21 TraesCS3D01G416300 chr5D 89.394 66 2 1 2765 2830 354697320 354697380 1.460000e-10 78.7
22 TraesCS3D01G416300 chr6D 89.671 881 65 13 4 867 34263097 34262226 0.000000e+00 1099.0
23 TraesCS3D01G416300 chr6D 92.683 205 12 3 4674 4876 455636144 455635941 4.770000e-75 292.0
24 TraesCS3D01G416300 chr4D 86.893 885 84 14 1 867 455316623 455317493 0.000000e+00 963.0
25 TraesCS3D01G416300 chr4D 90.187 214 19 2 4665 4876 497938185 497937972 1.340000e-70 278.0
26 TraesCS3D01G416300 chr6A 87.416 747 87 6 1 745 100298600 100299341 0.000000e+00 852.0
27 TraesCS3D01G416300 chr1B 86.631 748 89 10 1 745 3865705 3864966 0.000000e+00 817.0
28 TraesCS3D01G416300 chr1B 90.777 206 17 2 4673 4876 409700553 409700348 1.730000e-69 274.0
29 TraesCS3D01G416300 chr1B 90.000 60 4 2 2779 2837 621061911 621061969 5.230000e-10 76.8
30 TraesCS3D01G416300 chr1B 97.561 41 1 0 2564 2604 56066957 56066917 2.430000e-08 71.3
31 TraesCS3D01G416300 chr4B 92.350 549 41 1 1 548 171209439 171208891 0.000000e+00 780.0
32 TraesCS3D01G416300 chr4B 91.549 213 15 3 4665 4876 666619918 666620128 1.720000e-74 291.0
33 TraesCS3D01G416300 chr4B 88.710 62 5 2 2762 2822 462218876 462218936 1.880000e-09 75.0
34 TraesCS3D01G416300 chr2B 92.417 211 14 2 4668 4876 593663161 593662951 2.850000e-77 300.0
35 TraesCS3D01G416300 chr5B 93.137 204 12 2 4674 4876 617174756 617174554 1.030000e-76 298.0
36 TraesCS3D01G416300 chr5B 89.394 66 2 1 2765 2830 419395704 419395764 1.460000e-10 78.7
37 TraesCS3D01G416300 chr2A 91.584 202 17 0 4674 4875 214238780 214238981 3.720000e-71 279.0
38 TraesCS3D01G416300 chr2A 83.571 140 23 0 215 354 466161720 466161859 1.100000e-26 132.0
39 TraesCS3D01G416300 chr2A 86.957 69 6 3 2769 2836 742692562 742692628 1.880000e-09 75.0
40 TraesCS3D01G416300 chr5A 89.394 66 2 1 2765 2830 456599630 456599690 1.460000e-10 78.7
41 TraesCS3D01G416300 chr4A 100.000 40 0 0 2565 2604 376724152 376724113 1.880000e-09 75.0
42 TraesCS3D01G416300 chr1A 88.525 61 5 2 2781 2841 584675642 584675584 6.770000e-09 73.1
43 TraesCS3D01G416300 chrUn 100.000 38 0 0 2567 2604 336518078 336518041 2.430000e-08 71.3
44 TraesCS3D01G416300 chr1D 91.667 48 4 0 2557 2604 10536557 10536604 3.150000e-07 67.6
45 TraesCS3D01G416300 chr6B 88.679 53 5 1 2553 2604 79946898 79946950 4.070000e-06 63.9
46 TraesCS3D01G416300 chr6B 88.679 53 5 1 2553 2604 80000974 80001026 4.070000e-06 63.9


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 TraesCS3D01G416300 chr3D 527664678 527669553 4875 False 9005.0 9005 100.0000 1 4876 1 chr3D.!!$F3 4875
1 TraesCS3D01G416300 chr3D 162358253 162359122 869 True 939.0 939 86.3640 1 867 1 chr3D.!!$R1 866
2 TraesCS3D01G416300 chr3D 45410039 45410900 861 False 660.0 660 80.5300 2996 3861 1 chr3D.!!$F1 865
3 TraesCS3D01G416300 chr3B 697899258 697903015 3757 False 3107.5 3766 97.1645 899 4620 2 chr3B.!!$F4 3721
4 TraesCS3D01G416300 chr3B 71119782 71120576 794 False 649.0 649 81.3840 3067 3861 1 chr3B.!!$F1 794
5 TraesCS3D01G416300 chr3B 71143521 71144315 794 False 643.0 643 81.2580 3067 3861 1 chr3B.!!$F2 794
6 TraesCS3D01G416300 chr3B 697856371 697858158 1787 False 284.0 436 91.4010 899 1304 2 chr3B.!!$F3 405
7 TraesCS3D01G416300 chr3A 662394634 662401679 7045 False 1338.0 3336 98.0144 865 4640 5 chr3A.!!$F3 3775
8 TraesCS3D01G416300 chr3A 95168278 95168930 652 False 745.0 745 87.5380 226 870 1 chr3A.!!$F2 644
9 TraesCS3D01G416300 chr3A 57199536 57200330 794 False 665.0 665 81.8070 3067 3861 1 chr3A.!!$F1 794
10 TraesCS3D01G416300 chr5D 48061158 48062045 887 True 1109.0 1109 89.5970 1 870 1 chr5D.!!$R1 869
11 TraesCS3D01G416300 chr6D 34262226 34263097 871 True 1099.0 1099 89.6710 4 867 1 chr6D.!!$R1 863
12 TraesCS3D01G416300 chr4D 455316623 455317493 870 False 963.0 963 86.8930 1 867 1 chr4D.!!$F1 866
13 TraesCS3D01G416300 chr6A 100298600 100299341 741 False 852.0 852 87.4160 1 745 1 chr6A.!!$F1 744
14 TraesCS3D01G416300 chr1B 3864966 3865705 739 True 817.0 817 86.6310 1 745 1 chr1B.!!$R1 744
15 TraesCS3D01G416300 chr4B 171208891 171209439 548 True 780.0 780 92.3500 1 548 1 chr4B.!!$R1 547

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
447 453 0.038526 TGAAGAAAGGAGACGCGTCC 60.039 55.000 34.08 24.38 36.79 4.79 F
1532 2945 0.237498 GTTGTTTCCCGCTGCACTAC 59.763 55.000 0.00 0.00 0.00 2.73 F
1643 3056 1.405463 GGGTTTTCGATTCATCTGGGC 59.595 52.381 0.00 0.00 0.00 5.36 F
3169 4748 1.364626 CGCATCTGGTCTGCTTGGTC 61.365 60.000 0.00 0.00 37.48 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2430 3910 1.520494 AGGCGCATGAGCTGATATTG 58.480 50.000 21.06 0.00 39.10 1.90 R
3169 4748 4.149922 CAGCTTCAATTGATTTGTGCACTG 59.850 41.667 19.41 5.22 37.88 3.66 R
3545 5124 0.967380 CCACCACATCCAAGGGCTTC 60.967 60.000 0.00 0.00 0.00 3.86 R
4806 9502 0.454285 AAAAATGATCCACGCGCGTG 60.454 50.000 46.27 46.27 45.02 5.34 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
191 193 1.200020 CCAAACTTCAGTCGCCAATCC 59.800 52.381 0.00 0.00 0.00 3.01
314 316 1.879380 ACATCCGGTGTTTCATGTGTG 59.121 47.619 0.00 0.00 38.01 3.82
447 453 0.038526 TGAAGAAAGGAGACGCGTCC 60.039 55.000 34.08 24.38 36.79 4.79
501 507 3.258228 ATCCGCAGCAGCAACCTGA 62.258 57.895 0.82 0.00 41.77 3.86
513 519 6.427350 GCAGCAACCTGAGAGGATTACTCA 62.427 50.000 0.00 0.00 42.87 3.41
715 726 1.728074 TAAGCGTGCGTGTGTCGAG 60.728 57.895 0.00 0.00 42.86 4.04
771 795 2.528564 TGATTGGGCAGGAAGGAAAAG 58.471 47.619 0.00 0.00 0.00 2.27
796 820 3.510360 TCTGAAACTAAACTCTCCCCTCG 59.490 47.826 0.00 0.00 0.00 4.63
842 869 1.492599 CTCTCCTTCTCCCCCAATTCC 59.507 57.143 0.00 0.00 0.00 3.01
974 1003 1.683319 GGGCCCTTGGAGAAATCACTC 60.683 57.143 17.04 0.00 36.31 3.51
1107 1136 0.543277 TGCTGATCCTGGTGGTGATC 59.457 55.000 0.00 0.00 38.27 2.92
1362 2775 0.744874 ATGACACAGTACCGGATCCG 59.255 55.000 27.65 27.65 39.44 4.18
1489 2902 1.605710 CCCTGTTTGACTTCTGCACAG 59.394 52.381 0.00 0.00 35.59 3.66
1504 2917 4.160252 TCTGCACAGCATCTTACAGACATA 59.840 41.667 0.00 0.00 38.13 2.29
1532 2945 0.237498 GTTGTTTCCCGCTGCACTAC 59.763 55.000 0.00 0.00 0.00 2.73
1581 2994 3.403038 CTGGGATACGATGAATTGACCC 58.597 50.000 0.00 0.00 36.92 4.46
1643 3056 1.405463 GGGTTTTCGATTCATCTGGGC 59.595 52.381 0.00 0.00 0.00 5.36
1670 3083 3.290948 ACACAAACAACTCTTGCCCTA 57.709 42.857 0.00 0.00 0.00 3.53
1773 3186 2.409870 CCCTCCCACGCTTTGATGC 61.410 63.158 0.00 0.00 0.00 3.91
1961 3374 6.371825 GGTAGCTTGCCAATTATACTATCCAC 59.628 42.308 0.00 0.00 0.00 4.02
2430 3910 3.624410 GGAAGCATTTGGGATGAAATTGC 59.376 43.478 0.00 0.00 0.00 3.56
2497 4073 6.697455 TGAGCAGTAGAGAGCGTTATAATTTG 59.303 38.462 0.00 0.00 35.48 2.32
2793 4372 8.239038 TCCCTCTGTAAACTAAGATAGTGATG 57.761 38.462 0.00 0.00 39.39 3.07
3169 4748 1.364626 CGCATCTGGTCTGCTTGGTC 61.365 60.000 0.00 0.00 37.48 4.02
3969 5548 8.302438 TCAGTGTATATCAGAGTGCTTATGATG 58.698 37.037 8.53 0.00 35.39 3.07
3970 5549 8.087136 CAGTGTATATCAGAGTGCTTATGATGT 58.913 37.037 8.53 5.45 35.39 3.06
3971 5550 8.646004 AGTGTATATCAGAGTGCTTATGATGTT 58.354 33.333 8.53 1.36 35.39 2.71
4033 5615 5.596361 AGGAGTATATGACCACAGTTGAGAG 59.404 44.000 0.00 0.00 0.00 3.20
4098 5680 2.229784 GCAAGAGGGATGGAAAACAGTG 59.770 50.000 0.00 0.00 0.00 3.66
4099 5681 3.754965 CAAGAGGGATGGAAAACAGTGA 58.245 45.455 0.00 0.00 0.00 3.41
4108 5690 5.337009 GGATGGAAAACAGTGAGAAATGCAT 60.337 40.000 0.00 0.00 0.00 3.96
4109 5691 6.127647 GGATGGAAAACAGTGAGAAATGCATA 60.128 38.462 0.00 0.00 0.00 3.14
4169 5753 4.624024 TCGTTGTCACACGAAGGATTTATC 59.376 41.667 7.49 0.00 46.02 1.75
4175 5759 3.126171 CACACGAAGGATTTATCGCCAAA 59.874 43.478 0.00 0.00 42.61 3.28
4176 5760 3.945285 ACACGAAGGATTTATCGCCAAAT 59.055 39.130 0.00 0.00 42.61 2.32
4177 5761 4.201910 ACACGAAGGATTTATCGCCAAATG 60.202 41.667 0.00 0.00 42.61 2.32
4187 5771 1.686355 TCGCCAAATGTTGTGGAACT 58.314 45.000 0.00 0.00 38.54 3.01
4196 5780 3.485346 TTGTGGAACTGGACGCCCC 62.485 63.158 0.00 0.00 38.04 5.80
4293 5877 6.975772 TGTAACTGCACCAAATACTGTTTTTC 59.024 34.615 0.00 0.00 0.00 2.29
4417 9109 4.893424 TCCTGCACTGTTGTTAAGAAAC 57.107 40.909 0.00 0.00 36.07 2.78
4561 9253 5.674569 GCAGCAAGTTGGTGTATTGTATCTG 60.675 44.000 29.93 13.61 46.67 2.90
4642 9338 8.475331 TTGAAGAGATCGTATTAAAACTGACC 57.525 34.615 0.00 0.00 0.00 4.02
4643 9339 6.750501 TGAAGAGATCGTATTAAAACTGACCG 59.249 38.462 0.00 0.00 0.00 4.79
4644 9340 5.041940 AGAGATCGTATTAAAACTGACCGC 58.958 41.667 0.00 0.00 0.00 5.68
4645 9341 3.795101 AGATCGTATTAAAACTGACCGCG 59.205 43.478 0.00 0.00 0.00 6.46
4646 9342 2.261345 TCGTATTAAAACTGACCGCGG 58.739 47.619 26.86 26.86 0.00 6.46
4647 9343 1.325338 CGTATTAAAACTGACCGCGGG 59.675 52.381 31.76 14.78 0.00 6.13
4648 9344 1.063027 GTATTAAAACTGACCGCGGGC 59.937 52.381 31.76 30.24 0.00 6.13
4649 9345 1.310216 ATTAAAACTGACCGCGGGCC 61.310 55.000 32.09 20.79 0.00 5.80
4650 9346 2.677765 TTAAAACTGACCGCGGGCCA 62.678 55.000 32.09 24.37 0.00 5.36
4651 9347 2.677765 TAAAACTGACCGCGGGCCAA 62.678 55.000 32.09 10.42 0.00 4.52
4664 9360 4.090057 GCCAAGCGTCCAAGCGAC 62.090 66.667 0.00 0.00 43.00 5.19
4671 9367 2.853914 GTCCAAGCGACGTGAAGC 59.146 61.111 0.00 0.00 0.00 3.86
4683 9379 1.784525 CGTGAAGCGTTTTCTCTCCT 58.215 50.000 3.99 0.00 35.54 3.69
4684 9380 1.721926 CGTGAAGCGTTTTCTCTCCTC 59.278 52.381 3.99 0.00 35.54 3.71
4685 9381 2.070028 GTGAAGCGTTTTCTCTCCTCC 58.930 52.381 3.99 0.00 0.00 4.30
4686 9382 1.002087 TGAAGCGTTTTCTCTCCTCCC 59.998 52.381 3.99 0.00 0.00 4.30
4687 9383 1.276705 GAAGCGTTTTCTCTCCTCCCT 59.723 52.381 0.00 0.00 0.00 4.20
4688 9384 0.610687 AGCGTTTTCTCTCCTCCCTG 59.389 55.000 0.00 0.00 0.00 4.45
4689 9385 1.021920 GCGTTTTCTCTCCTCCCTGC 61.022 60.000 0.00 0.00 0.00 4.85
4690 9386 0.610687 CGTTTTCTCTCCTCCCTGCT 59.389 55.000 0.00 0.00 0.00 4.24
4691 9387 1.404851 CGTTTTCTCTCCTCCCTGCTC 60.405 57.143 0.00 0.00 0.00 4.26
4692 9388 1.065782 GTTTTCTCTCCTCCCTGCTCC 60.066 57.143 0.00 0.00 0.00 4.70
4693 9389 0.618968 TTTCTCTCCTCCCTGCTCCC 60.619 60.000 0.00 0.00 0.00 4.30
4694 9390 1.522917 TTCTCTCCTCCCTGCTCCCT 61.523 60.000 0.00 0.00 0.00 4.20
4695 9391 1.761667 CTCTCCTCCCTGCTCCCTG 60.762 68.421 0.00 0.00 0.00 4.45
4696 9392 2.767496 CTCCTCCCTGCTCCCTGG 60.767 72.222 0.00 0.00 0.00 4.45
4706 9402 4.785453 CTCCCTGGCGGCTGGAAC 62.785 72.222 32.43 0.00 0.00 3.62
4710 9406 3.399181 CTGGCGGCTGGAACCCTA 61.399 66.667 11.43 0.00 0.00 3.53
4711 9407 3.391665 CTGGCGGCTGGAACCCTAG 62.392 68.421 11.43 0.00 0.00 3.02
4712 9408 4.858680 GGCGGCTGGAACCCTAGC 62.859 72.222 0.00 0.00 39.17 3.42
4716 9412 4.858680 GCTGGAACCCTAGCCGCC 62.859 72.222 0.00 0.00 33.89 6.13
4717 9413 4.530857 CTGGAACCCTAGCCGCCG 62.531 72.222 0.00 0.00 0.00 6.46
4741 9437 2.280052 GAGGCCATCTCTCAGCGC 60.280 66.667 5.01 0.00 39.38 5.92
4742 9438 3.805891 GAGGCCATCTCTCAGCGCC 62.806 68.421 5.01 0.00 39.38 6.53
4744 9440 4.521062 GCCATCTCTCAGCGCCGT 62.521 66.667 2.29 0.00 0.00 5.68
4745 9441 2.279120 CCATCTCTCAGCGCCGTC 60.279 66.667 2.29 0.00 0.00 4.79
4746 9442 2.279120 CATCTCTCAGCGCCGTCC 60.279 66.667 2.29 0.00 0.00 4.79
4747 9443 2.441164 ATCTCTCAGCGCCGTCCT 60.441 61.111 2.29 0.00 0.00 3.85
4748 9444 2.485795 ATCTCTCAGCGCCGTCCTC 61.486 63.158 2.29 0.00 0.00 3.71
4749 9445 4.544689 CTCTCAGCGCCGTCCTCG 62.545 72.222 2.29 0.00 0.00 4.63
4769 9465 4.493747 CGGCTCCCCTTCGTCGAC 62.494 72.222 5.18 5.18 0.00 4.20
4770 9466 4.493747 GGCTCCCCTTCGTCGACG 62.494 72.222 31.30 31.30 41.45 5.12
4779 9475 3.114616 TCGTCGACGACCTCGGTC 61.115 66.667 34.97 6.01 44.22 4.79
4787 9483 4.112341 GACCTCGGTCGTCGGTGG 62.112 72.222 0.00 6.74 39.77 4.61
4788 9484 4.962836 ACCTCGGTCGTCGGTGGT 62.963 66.667 7.86 7.86 39.69 4.16
4789 9485 4.415332 CCTCGGTCGTCGGTGGTG 62.415 72.222 0.00 0.00 39.77 4.17
4790 9486 3.359523 CTCGGTCGTCGGTGGTGA 61.360 66.667 0.00 0.00 39.77 4.02
4791 9487 3.324099 CTCGGTCGTCGGTGGTGAG 62.324 68.421 0.00 0.00 39.77 3.51
4792 9488 4.415332 CGGTCGTCGGTGGTGAGG 62.415 72.222 0.00 0.00 34.75 3.86
4793 9489 4.065281 GGTCGTCGGTGGTGAGGG 62.065 72.222 0.00 0.00 0.00 4.30
4794 9490 4.065281 GTCGTCGGTGGTGAGGGG 62.065 72.222 0.00 0.00 0.00 4.79
4797 9493 3.703127 GTCGGTGGTGAGGGGGTC 61.703 72.222 0.00 0.00 0.00 4.46
4823 9519 2.784596 CACGCGCGTGGATCATTT 59.215 55.556 45.91 16.61 42.00 2.32
4824 9520 1.134487 CACGCGCGTGGATCATTTT 59.866 52.632 45.91 15.80 42.00 1.82
4825 9521 0.454285 CACGCGCGTGGATCATTTTT 60.454 50.000 45.91 15.24 42.00 1.94
4826 9522 1.080298 ACGCGCGTGGATCATTTTTA 58.920 45.000 37.37 0.00 0.00 1.52
4827 9523 1.201987 ACGCGCGTGGATCATTTTTAC 60.202 47.619 37.37 0.00 0.00 2.01
4828 9524 1.062002 CGCGCGTGGATCATTTTTACT 59.938 47.619 24.19 0.00 0.00 2.24
4829 9525 2.705154 GCGCGTGGATCATTTTTACTC 58.295 47.619 8.43 0.00 0.00 2.59
4830 9526 2.538939 GCGCGTGGATCATTTTTACTCC 60.539 50.000 8.43 0.00 0.00 3.85
4831 9527 2.936498 CGCGTGGATCATTTTTACTCCT 59.064 45.455 0.00 0.00 0.00 3.69
4832 9528 3.242413 CGCGTGGATCATTTTTACTCCTG 60.242 47.826 0.00 0.00 0.00 3.86
4833 9529 3.689649 GCGTGGATCATTTTTACTCCTGT 59.310 43.478 0.00 0.00 0.00 4.00
4834 9530 4.437390 GCGTGGATCATTTTTACTCCTGTG 60.437 45.833 0.00 0.00 0.00 3.66
4835 9531 4.695455 CGTGGATCATTTTTACTCCTGTGT 59.305 41.667 0.00 0.00 0.00 3.72
4836 9532 5.872617 CGTGGATCATTTTTACTCCTGTGTA 59.127 40.000 0.00 0.00 0.00 2.90
4837 9533 6.036083 CGTGGATCATTTTTACTCCTGTGTAG 59.964 42.308 0.00 0.00 0.00 2.74
4838 9534 6.879458 GTGGATCATTTTTACTCCTGTGTAGT 59.121 38.462 0.00 0.00 0.00 2.73
4839 9535 7.064728 GTGGATCATTTTTACTCCTGTGTAGTC 59.935 40.741 0.00 0.00 0.00 2.59
4840 9536 7.038302 TGGATCATTTTTACTCCTGTGTAGTCT 60.038 37.037 0.00 0.00 0.00 3.24
4841 9537 8.475639 GGATCATTTTTACTCCTGTGTAGTCTA 58.524 37.037 0.00 0.00 0.00 2.59
4842 9538 9.522804 GATCATTTTTACTCCTGTGTAGTCTAG 57.477 37.037 0.00 0.00 0.00 2.43
4843 9539 7.837863 TCATTTTTACTCCTGTGTAGTCTAGG 58.162 38.462 0.00 0.00 0.00 3.02
4844 9540 7.453752 TCATTTTTACTCCTGTGTAGTCTAGGT 59.546 37.037 0.00 0.00 33.30 3.08
4845 9541 7.607615 TTTTTACTCCTGTGTAGTCTAGGTT 57.392 36.000 0.00 0.00 33.30 3.50
4846 9542 7.607615 TTTTACTCCTGTGTAGTCTAGGTTT 57.392 36.000 0.00 0.00 33.30 3.27
4847 9543 7.607615 TTTACTCCTGTGTAGTCTAGGTTTT 57.392 36.000 0.00 0.00 33.30 2.43
4848 9544 7.607615 TTACTCCTGTGTAGTCTAGGTTTTT 57.392 36.000 0.00 0.00 33.30 1.94
4849 9545 8.710749 TTACTCCTGTGTAGTCTAGGTTTTTA 57.289 34.615 0.00 0.00 33.30 1.52
4850 9546 7.229581 ACTCCTGTGTAGTCTAGGTTTTTAG 57.770 40.000 0.00 0.00 33.30 1.85
4851 9547 6.210984 ACTCCTGTGTAGTCTAGGTTTTTAGG 59.789 42.308 0.00 0.00 33.30 2.69
4852 9548 5.046807 TCCTGTGTAGTCTAGGTTTTTAGGC 60.047 44.000 0.00 0.00 33.30 3.93
4853 9549 5.046520 CCTGTGTAGTCTAGGTTTTTAGGCT 60.047 44.000 0.00 0.00 38.96 4.58
4854 9550 5.790593 TGTGTAGTCTAGGTTTTTAGGCTG 58.209 41.667 0.00 0.00 36.35 4.85
4855 9551 5.306160 TGTGTAGTCTAGGTTTTTAGGCTGT 59.694 40.000 0.00 0.00 36.35 4.40
4856 9552 6.183361 TGTGTAGTCTAGGTTTTTAGGCTGTT 60.183 38.462 0.00 0.00 36.35 3.16
4857 9553 6.368243 GTGTAGTCTAGGTTTTTAGGCTGTTC 59.632 42.308 0.00 0.00 36.35 3.18
4858 9554 5.562298 AGTCTAGGTTTTTAGGCTGTTCA 57.438 39.130 0.00 0.00 34.44 3.18
4859 9555 6.128138 AGTCTAGGTTTTTAGGCTGTTCAT 57.872 37.500 0.00 0.00 34.44 2.57
4860 9556 6.174049 AGTCTAGGTTTTTAGGCTGTTCATC 58.826 40.000 0.00 0.00 34.44 2.92
4861 9557 5.063564 GTCTAGGTTTTTAGGCTGTTCATCG 59.936 44.000 0.00 0.00 0.00 3.84
4862 9558 3.751518 AGGTTTTTAGGCTGTTCATCGT 58.248 40.909 0.00 0.00 0.00 3.73
4863 9559 3.751698 AGGTTTTTAGGCTGTTCATCGTC 59.248 43.478 0.00 0.00 0.00 4.20
4864 9560 3.751698 GGTTTTTAGGCTGTTCATCGTCT 59.248 43.478 0.00 0.00 0.00 4.18
4865 9561 4.215613 GGTTTTTAGGCTGTTCATCGTCTT 59.784 41.667 0.00 0.00 0.00 3.01
4866 9562 5.383130 GTTTTTAGGCTGTTCATCGTCTTC 58.617 41.667 0.00 0.00 0.00 2.87
4867 9563 3.953712 TTAGGCTGTTCATCGTCTTCA 57.046 42.857 0.00 0.00 0.00 3.02
4868 9564 2.086054 AGGCTGTTCATCGTCTTCAC 57.914 50.000 0.00 0.00 0.00 3.18
4869 9565 1.620819 AGGCTGTTCATCGTCTTCACT 59.379 47.619 0.00 0.00 0.00 3.41
4870 9566 2.037772 AGGCTGTTCATCGTCTTCACTT 59.962 45.455 0.00 0.00 0.00 3.16
4871 9567 2.413453 GGCTGTTCATCGTCTTCACTTC 59.587 50.000 0.00 0.00 0.00 3.01
4872 9568 2.091277 GCTGTTCATCGTCTTCACTTCG 59.909 50.000 0.00 0.00 0.00 3.79
4873 9569 2.663602 CTGTTCATCGTCTTCACTTCGG 59.336 50.000 0.00 0.00 0.00 4.30
4874 9570 1.390463 GTTCATCGTCTTCACTTCGGC 59.610 52.381 0.00 0.00 0.00 5.54
4875 9571 0.456142 TCATCGTCTTCACTTCGGCG 60.456 55.000 0.00 0.00 0.00 6.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 124 0.249120 TTCTCCCACATCGAATGCGT 59.751 50.000 0.00 0.00 38.98 5.24
314 316 1.172812 AACGAAGGGCTTCAACTGGC 61.173 55.000 0.00 0.00 39.46 4.85
447 453 1.416813 GAATCTGCAGCTGGACGACG 61.417 60.000 17.12 0.14 0.00 5.12
501 507 3.093057 ACGAAGCACTGAGTAATCCTCT 58.907 45.455 0.00 0.00 41.11 3.69
513 519 1.329599 GGAAAACGTTGACGAAGCACT 59.670 47.619 10.87 0.00 43.02 4.40
584 593 0.460311 GGCTACTGACATACGCAGGT 59.540 55.000 0.00 0.00 37.69 4.00
771 795 6.547930 AGGGGAGAGTTTAGTTTCAGATAC 57.452 41.667 0.00 0.00 0.00 2.24
796 820 2.184579 GTAGGTGAGGAGCGTGGC 59.815 66.667 0.00 0.00 0.00 5.01
842 869 1.117749 TGCCCTGGGATCTCGATCTG 61.118 60.000 19.27 0.00 37.92 2.90
974 1003 4.796231 CCGAGACCCGCAACCTCG 62.796 72.222 0.00 0.00 46.48 4.63
1107 1136 4.803426 GAGCCCACCGACAGCGAG 62.803 72.222 0.00 0.00 40.82 5.03
1362 2775 7.029563 CCTGTATTTTGCTATCAACAGAAACC 58.970 38.462 9.64 0.00 29.22 3.27
1504 2917 4.057432 CAGCGGGAAACAACATTTCATTT 58.943 39.130 2.14 0.00 0.00 2.32
1532 2945 7.642669 ACGCCTTTATCATGAATAAATCAGTG 58.357 34.615 0.00 6.88 42.53 3.66
1581 2994 4.078363 CAGGTACCTGCACAATAAAACG 57.922 45.455 28.48 0.56 37.24 3.60
2430 3910 1.520494 AGGCGCATGAGCTGATATTG 58.480 50.000 21.06 0.00 39.10 1.90
2497 4073 4.187694 ACTAGCTTTGCTTCTACATCAGC 58.812 43.478 0.00 0.00 40.44 4.26
2662 4241 7.667575 ATCTTATCTCAGAAAACTGCCTCTA 57.332 36.000 0.00 0.00 0.00 2.43
2700 4279 5.389516 GCCTCATAACTTGACAAAGTACACG 60.390 44.000 0.00 0.00 46.15 4.49
3169 4748 4.149922 CAGCTTCAATTGATTTGTGCACTG 59.850 41.667 19.41 5.22 37.88 3.66
3545 5124 0.967380 CCACCACATCCAAGGGCTTC 60.967 60.000 0.00 0.00 0.00 3.86
3969 5548 3.598019 TCCTATCCGTGGTACAACAAC 57.402 47.619 0.35 0.00 44.16 3.32
3970 5549 3.833650 TCTTCCTATCCGTGGTACAACAA 59.166 43.478 0.35 0.00 44.16 2.83
3971 5550 3.433343 TCTTCCTATCCGTGGTACAACA 58.567 45.455 0.35 0.00 44.16 3.33
4033 5615 6.176896 GCTAAAAGATATCTCCCATTCCCTC 58.823 44.000 5.51 0.00 0.00 4.30
4108 5690 8.753497 ATGTAGCGAATATCTCCAGATACATA 57.247 34.615 3.32 0.00 39.57 2.29
4109 5691 7.652524 ATGTAGCGAATATCTCCAGATACAT 57.347 36.000 0.00 0.00 39.57 2.29
4161 5743 4.111916 CCACAACATTTGGCGATAAATCC 58.888 43.478 0.00 0.00 34.12 3.01
4169 5753 1.602668 CCAGTTCCACAACATTTGGCG 60.603 52.381 0.00 0.00 34.60 5.69
4175 5759 0.889186 GGCGTCCAGTTCCACAACAT 60.889 55.000 0.00 0.00 34.60 2.71
4176 5760 1.525077 GGCGTCCAGTTCCACAACA 60.525 57.895 0.00 0.00 34.60 3.33
4177 5761 2.258726 GGGCGTCCAGTTCCACAAC 61.259 63.158 0.00 0.00 0.00 3.32
4196 5780 4.333649 ACTTACACATCGATTTGAGCCATG 59.666 41.667 18.08 0.00 0.00 3.66
4204 5788 4.569943 ACAGAGCACTTACACATCGATTT 58.430 39.130 0.00 0.00 0.00 2.17
4207 5791 2.820197 AGACAGAGCACTTACACATCGA 59.180 45.455 0.00 0.00 0.00 3.59
4208 5792 2.919859 CAGACAGAGCACTTACACATCG 59.080 50.000 0.00 0.00 0.00 3.84
4417 9109 1.390123 CAGTGCGTGTTTGATAGACCG 59.610 52.381 0.00 0.00 0.00 4.79
4464 9156 4.878397 CCAAACCAAAGCTGATAGGAGTAG 59.122 45.833 0.00 0.00 0.00 2.57
4561 9253 6.209986 ACACTATAAAGGTTTAACAAAGGCCC 59.790 38.462 0.00 0.00 0.00 5.80
4625 9321 2.861935 CCGCGGTCAGTTTTAATACGAT 59.138 45.455 19.50 0.00 0.00 3.73
4647 9343 4.090057 GTCGCTTGGACGCTTGGC 62.090 66.667 0.00 0.00 35.61 4.52
4654 9350 2.853914 GCTTCACGTCGCTTGGAC 59.146 61.111 0.00 0.00 42.48 4.02
4655 9351 2.733218 CGCTTCACGTCGCTTGGA 60.733 61.111 0.00 0.00 36.87 3.53
4665 9361 2.070028 GGAGGAGAGAAAACGCTTCAC 58.930 52.381 1.17 0.00 0.00 3.18
4666 9362 1.002087 GGGAGGAGAGAAAACGCTTCA 59.998 52.381 1.17 0.00 0.00 3.02
4667 9363 1.276705 AGGGAGGAGAGAAAACGCTTC 59.723 52.381 0.00 0.00 0.00 3.86
4668 9364 1.002544 CAGGGAGGAGAGAAAACGCTT 59.997 52.381 0.00 0.00 0.00 4.68
4669 9365 0.610687 CAGGGAGGAGAGAAAACGCT 59.389 55.000 0.00 0.00 0.00 5.07
4670 9366 1.021920 GCAGGGAGGAGAGAAAACGC 61.022 60.000 0.00 0.00 0.00 4.84
4671 9367 0.610687 AGCAGGGAGGAGAGAAAACG 59.389 55.000 0.00 0.00 0.00 3.60
4672 9368 1.065782 GGAGCAGGGAGGAGAGAAAAC 60.066 57.143 0.00 0.00 0.00 2.43
4673 9369 1.280457 GGAGCAGGGAGGAGAGAAAA 58.720 55.000 0.00 0.00 0.00 2.29
4674 9370 0.618968 GGGAGCAGGGAGGAGAGAAA 60.619 60.000 0.00 0.00 0.00 2.52
4675 9371 1.002274 GGGAGCAGGGAGGAGAGAA 59.998 63.158 0.00 0.00 0.00 2.87
4676 9372 1.938596 AGGGAGCAGGGAGGAGAGA 60.939 63.158 0.00 0.00 0.00 3.10
4677 9373 1.761667 CAGGGAGCAGGGAGGAGAG 60.762 68.421 0.00 0.00 0.00 3.20
4678 9374 2.366167 CAGGGAGCAGGGAGGAGA 59.634 66.667 0.00 0.00 0.00 3.71
4679 9375 2.767496 CCAGGGAGCAGGGAGGAG 60.767 72.222 0.00 0.00 0.00 3.69
4689 9385 4.785453 GTTCCAGCCGCCAGGGAG 62.785 72.222 0.00 0.00 38.47 4.30
4693 9389 3.391665 CTAGGGTTCCAGCCGCCAG 62.392 68.421 0.00 0.00 41.56 4.85
4694 9390 3.399181 CTAGGGTTCCAGCCGCCA 61.399 66.667 0.00 0.00 41.56 5.69
4695 9391 4.858680 GCTAGGGTTCCAGCCGCC 62.859 72.222 0.00 0.00 41.56 6.13
4699 9395 4.858680 GGCGGCTAGGGTTCCAGC 62.859 72.222 0.00 0.00 37.05 4.85
4700 9396 4.530857 CGGCGGCTAGGGTTCCAG 62.531 72.222 7.61 0.00 0.00 3.86
4724 9420 2.280052 GCGCTGAGAGATGGCCTC 60.280 66.667 3.32 0.00 42.28 4.70
4725 9421 3.859414 GGCGCTGAGAGATGGCCT 61.859 66.667 7.64 0.00 40.59 5.19
4727 9423 4.521062 ACGGCGCTGAGAGATGGC 62.521 66.667 25.98 0.00 0.00 4.40
4728 9424 2.279120 GACGGCGCTGAGAGATGG 60.279 66.667 25.98 0.00 0.00 3.51
4729 9425 2.279120 GGACGGCGCTGAGAGATG 60.279 66.667 25.98 0.00 0.00 2.90
4730 9426 2.441164 AGGACGGCGCTGAGAGAT 60.441 61.111 25.98 0.00 0.00 2.75
4731 9427 3.134792 GAGGACGGCGCTGAGAGA 61.135 66.667 25.98 0.00 0.00 3.10
4732 9428 4.544689 CGAGGACGGCGCTGAGAG 62.545 72.222 25.98 5.40 35.72 3.20
4752 9448 4.493747 GTCGACGAAGGGGAGCCG 62.494 72.222 0.00 0.00 0.00 5.52
4753 9449 4.493747 CGTCGACGAAGGGGAGCC 62.494 72.222 33.35 0.00 43.02 4.70
4754 9450 3.437795 TCGTCGACGAAGGGGAGC 61.438 66.667 36.25 0.00 46.30 4.70
4770 9466 4.112341 CCACCGACGACCGAGGTC 62.112 72.222 12.07 12.07 41.76 3.85
4771 9467 4.962836 ACCACCGACGACCGAGGT 62.963 66.667 0.00 0.00 41.76 3.85
4772 9468 4.415332 CACCACCGACGACCGAGG 62.415 72.222 0.00 1.98 41.76 4.63
4773 9469 3.324099 CTCACCACCGACGACCGAG 62.324 68.421 0.00 0.00 41.76 4.63
4774 9470 3.359523 CTCACCACCGACGACCGA 61.360 66.667 0.00 0.00 41.76 4.69
4775 9471 4.415332 CCTCACCACCGACGACCG 62.415 72.222 0.00 0.00 38.18 4.79
4776 9472 4.065281 CCCTCACCACCGACGACC 62.065 72.222 0.00 0.00 0.00 4.79
4777 9473 4.065281 CCCCTCACCACCGACGAC 62.065 72.222 0.00 0.00 0.00 4.34
4780 9476 3.703127 GACCCCCTCACCACCGAC 61.703 72.222 0.00 0.00 0.00 4.79
4806 9502 0.454285 AAAAATGATCCACGCGCGTG 60.454 50.000 46.27 46.27 45.02 5.34
4807 9503 1.080298 TAAAAATGATCCACGCGCGT 58.920 45.000 32.73 32.73 0.00 6.01
4808 9504 1.062002 AGTAAAAATGATCCACGCGCG 59.938 47.619 30.96 30.96 0.00 6.86
4809 9505 2.538939 GGAGTAAAAATGATCCACGCGC 60.539 50.000 5.73 0.00 0.00 6.86
4810 9506 2.936498 AGGAGTAAAAATGATCCACGCG 59.064 45.455 3.53 3.53 34.08 6.01
4811 9507 3.689649 ACAGGAGTAAAAATGATCCACGC 59.310 43.478 0.00 0.00 34.08 5.34
4812 9508 4.695455 ACACAGGAGTAAAAATGATCCACG 59.305 41.667 0.00 0.00 34.08 4.94
4813 9509 6.879458 ACTACACAGGAGTAAAAATGATCCAC 59.121 38.462 0.00 0.00 34.08 4.02
4814 9510 7.016153 ACTACACAGGAGTAAAAATGATCCA 57.984 36.000 0.00 0.00 34.08 3.41
4815 9511 7.331791 AGACTACACAGGAGTAAAAATGATCC 58.668 38.462 0.00 0.00 0.00 3.36
4816 9512 9.522804 CTAGACTACACAGGAGTAAAAATGATC 57.477 37.037 0.00 0.00 0.00 2.92
4817 9513 8.478877 CCTAGACTACACAGGAGTAAAAATGAT 58.521 37.037 0.00 0.00 0.00 2.45
4818 9514 7.453752 ACCTAGACTACACAGGAGTAAAAATGA 59.546 37.037 0.00 0.00 33.44 2.57
4819 9515 7.612677 ACCTAGACTACACAGGAGTAAAAATG 58.387 38.462 0.00 0.00 33.44 2.32
4820 9516 7.793948 ACCTAGACTACACAGGAGTAAAAAT 57.206 36.000 0.00 0.00 33.44 1.82
4821 9517 7.607615 AACCTAGACTACACAGGAGTAAAAA 57.392 36.000 0.00 0.00 33.44 1.94
4822 9518 7.607615 AAACCTAGACTACACAGGAGTAAAA 57.392 36.000 0.00 0.00 33.44 1.52
4823 9519 7.607615 AAAACCTAGACTACACAGGAGTAAA 57.392 36.000 0.00 0.00 33.44 2.01
4824 9520 7.607615 AAAAACCTAGACTACACAGGAGTAA 57.392 36.000 0.00 0.00 33.44 2.24
4825 9521 7.395489 CCTAAAAACCTAGACTACACAGGAGTA 59.605 40.741 0.00 0.00 33.44 2.59
4826 9522 6.210984 CCTAAAAACCTAGACTACACAGGAGT 59.789 42.308 0.00 0.00 33.44 3.85
4827 9523 6.631962 CCTAAAAACCTAGACTACACAGGAG 58.368 44.000 0.00 0.00 33.44 3.69
4828 9524 5.046807 GCCTAAAAACCTAGACTACACAGGA 60.047 44.000 0.00 0.00 33.44 3.86
4829 9525 5.046520 AGCCTAAAAACCTAGACTACACAGG 60.047 44.000 0.00 0.00 35.45 4.00
4830 9526 5.869888 CAGCCTAAAAACCTAGACTACACAG 59.130 44.000 0.00 0.00 0.00 3.66
4831 9527 5.306160 ACAGCCTAAAAACCTAGACTACACA 59.694 40.000 0.00 0.00 0.00 3.72
4832 9528 5.791666 ACAGCCTAAAAACCTAGACTACAC 58.208 41.667 0.00 0.00 0.00 2.90
4833 9529 6.042322 TGAACAGCCTAAAAACCTAGACTACA 59.958 38.462 0.00 0.00 0.00 2.74
4834 9530 6.461640 TGAACAGCCTAAAAACCTAGACTAC 58.538 40.000 0.00 0.00 0.00 2.73
4835 9531 6.675413 TGAACAGCCTAAAAACCTAGACTA 57.325 37.500 0.00 0.00 0.00 2.59
4836 9532 5.562298 TGAACAGCCTAAAAACCTAGACT 57.438 39.130 0.00 0.00 0.00 3.24
4837 9533 5.063564 CGATGAACAGCCTAAAAACCTAGAC 59.936 44.000 0.00 0.00 0.00 2.59
4838 9534 5.175859 CGATGAACAGCCTAAAAACCTAGA 58.824 41.667 0.00 0.00 0.00 2.43
4839 9535 4.935808 ACGATGAACAGCCTAAAAACCTAG 59.064 41.667 0.00 0.00 0.00 3.02
4840 9536 4.901868 ACGATGAACAGCCTAAAAACCTA 58.098 39.130 0.00 0.00 0.00 3.08
4841 9537 3.751518 ACGATGAACAGCCTAAAAACCT 58.248 40.909 0.00 0.00 0.00 3.50
4842 9538 3.751698 AGACGATGAACAGCCTAAAAACC 59.248 43.478 0.00 0.00 0.00 3.27
4843 9539 5.049680 TGAAGACGATGAACAGCCTAAAAAC 60.050 40.000 0.00 0.00 0.00 2.43
4844 9540 5.049680 GTGAAGACGATGAACAGCCTAAAAA 60.050 40.000 0.00 0.00 0.00 1.94
4845 9541 4.451096 GTGAAGACGATGAACAGCCTAAAA 59.549 41.667 0.00 0.00 0.00 1.52
4846 9542 3.994392 GTGAAGACGATGAACAGCCTAAA 59.006 43.478 0.00 0.00 0.00 1.85
4847 9543 3.258372 AGTGAAGACGATGAACAGCCTAA 59.742 43.478 0.00 0.00 0.00 2.69
4848 9544 2.826128 AGTGAAGACGATGAACAGCCTA 59.174 45.455 0.00 0.00 0.00 3.93
4849 9545 1.620819 AGTGAAGACGATGAACAGCCT 59.379 47.619 0.00 0.00 0.00 4.58
4850 9546 2.086054 AGTGAAGACGATGAACAGCC 57.914 50.000 0.00 0.00 0.00 4.85
4851 9547 2.091277 CGAAGTGAAGACGATGAACAGC 59.909 50.000 0.00 0.00 0.00 4.40
4852 9548 2.663602 CCGAAGTGAAGACGATGAACAG 59.336 50.000 0.00 0.00 0.00 3.16
4853 9549 2.672714 CCGAAGTGAAGACGATGAACA 58.327 47.619 0.00 0.00 0.00 3.18
4854 9550 1.390463 GCCGAAGTGAAGACGATGAAC 59.610 52.381 0.00 0.00 0.00 3.18
4855 9551 1.710013 GCCGAAGTGAAGACGATGAA 58.290 50.000 0.00 0.00 0.00 2.57
4856 9552 0.456142 CGCCGAAGTGAAGACGATGA 60.456 55.000 0.00 0.00 0.00 2.92
4857 9553 1.991430 CGCCGAAGTGAAGACGATG 59.009 57.895 0.00 0.00 0.00 3.84
4858 9554 4.478195 CGCCGAAGTGAAGACGAT 57.522 55.556 0.00 0.00 0.00 3.73


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

AutoCloner maintained by Alex Coulton.