Multiple sequence alignment - TraesCS3A01G347100

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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 TraesCS3A01G347100 chr3A 100.000 6987 0 0 1 6987 596369396 596362410 0.000000e+00 12903.0
1 TraesCS3A01G347100 chr3A 90.000 60 5 1 1713 1772 581375854 581375912 7.520000e-10 76.8
2 TraesCS3A01G347100 chr3B 91.521 2807 160 33 10 2787 596863504 596860747 0.000000e+00 3794.0
3 TraesCS3A01G347100 chr3B 91.024 1905 115 28 5100 6987 596858955 596857090 0.000000e+00 2519.0
4 TraesCS3A01G347100 chr3B 96.304 947 15 7 4166 5104 596859967 596859033 0.000000e+00 1537.0
5 TraesCS3A01G347100 chr3B 89.606 558 39 7 3618 4158 596860741 596860186 0.000000e+00 691.0
6 TraesCS3A01G347100 chr3B 86.640 247 29 3 1022 1268 596863899 596863657 3.210000e-68 270.0
7 TraesCS3A01G347100 chr3B 88.333 60 6 1 1713 1772 578595713 578595771 3.500000e-08 71.3
8 TraesCS3A01G347100 chr3D 92.798 2069 108 24 4948 6987 454233214 454231158 0.000000e+00 2957.0
9 TraesCS3A01G347100 chr3D 92.964 1947 91 18 855 2786 454236547 454234632 0.000000e+00 2795.0
10 TraesCS3A01G347100 chr3D 93.265 683 39 2 2785 3467 537700966 537701641 0.000000e+00 1000.0
11 TraesCS3A01G347100 chr3D 89.804 765 27 11 4159 4912 454233939 454233215 0.000000e+00 933.0
12 TraesCS3A01G347100 chr3D 92.086 556 26 8 3618 4156 454234624 454234070 0.000000e+00 767.0
13 TraesCS3A01G347100 chr3D 84.360 633 90 6 64 689 562513985 562514615 4.630000e-171 612.0
14 TraesCS3A01G347100 chr5A 98.321 834 14 0 2785 3618 435694168 435693335 0.000000e+00 1463.0
15 TraesCS3A01G347100 chr5A 97.112 831 24 0 2788 3618 16526966 16527796 0.000000e+00 1402.0
16 TraesCS3A01G347100 chr5A 94.005 834 50 0 2785 3618 295079305 295078472 0.000000e+00 1264.0
17 TraesCS3A01G347100 chr7B 95.006 841 40 2 2785 3624 337924943 337925782 0.000000e+00 1319.0
18 TraesCS3A01G347100 chr7B 95.460 815 35 2 2786 3598 388867534 388866720 0.000000e+00 1299.0
19 TraesCS3A01G347100 chr7B 83.101 645 94 12 64 698 104298959 104298320 2.190000e-159 573.0
20 TraesCS3A01G347100 chr7B 85.263 95 14 0 4888 4982 60703113 60703207 1.600000e-16 99.0
21 TraesCS3A01G347100 chr6D 95.198 833 40 0 2786 3618 77827058 77827890 0.000000e+00 1317.0
22 TraesCS3A01G347100 chr6D 84.586 785 58 22 4991 5750 373343043 373342297 0.000000e+00 721.0
23 TraesCS3A01G347100 chr6D 90.136 294 25 3 3862 4153 373344245 373343954 5.110000e-101 379.0
24 TraesCS3A01G347100 chr6D 87.267 322 39 2 5731 6051 373342162 373341842 3.980000e-97 366.0
25 TraesCS3A01G347100 chr6D 85.756 344 35 7 4293 4624 373343658 373343317 1.120000e-92 351.0
26 TraesCS3A01G347100 chr5D 94.964 834 42 0 2785 3618 497788326 497789159 0.000000e+00 1308.0
27 TraesCS3A01G347100 chr5D 94.203 828 47 1 2791 3618 513916087 513915261 0.000000e+00 1262.0
28 TraesCS3A01G347100 chr5D 84.333 600 89 3 64 659 76031150 76030552 3.630000e-162 582.0
29 TraesCS3A01G347100 chr6B 93.683 839 53 0 2780 3618 33588942 33588104 0.000000e+00 1256.0
30 TraesCS3A01G347100 chr4B 83.071 1081 131 29 4989 6049 567971093 567970045 0.000000e+00 935.0
31 TraesCS3A01G347100 chr2B 83.830 705 64 19 5127 5801 331238310 331237626 5.950000e-175 625.0
32 TraesCS3A01G347100 chr2B 91.429 280 23 1 4347 4625 331239066 331238787 3.950000e-102 383.0
33 TraesCS3A01G347100 chr2A 84.177 632 88 10 68 691 66767820 66767193 2.790000e-168 603.0
34 TraesCS3A01G347100 chr2A 83.201 631 97 4 64 685 765574497 765573867 2.830000e-158 569.0
35 TraesCS3A01G347100 chr4D 84.628 605 86 5 64 662 428987947 428988550 4.670000e-166 595.0
36 TraesCS3A01G347100 chr4D 95.918 49 2 0 1726 1774 119751926 119751878 5.810000e-11 80.5
37 TraesCS3A01G347100 chr4D 95.745 47 2 0 1726 1772 127163784 127163830 7.520000e-10 76.8
38 TraesCS3A01G347100 chr1A 83.178 642 98 7 65 698 447640104 447639465 4.700000e-161 579.0
39 TraesCS3A01G347100 chr1A 92.017 238 19 0 2785 3022 26600459 26600222 1.120000e-87 335.0
40 TraesCS3A01G347100 chr1A 96.045 177 7 0 2784 2960 541398746 541398570 8.870000e-74 289.0
41 TraesCS3A01G347100 chr1D 83.254 633 93 10 64 687 110975564 110976192 2.830000e-158 569.0
42 TraesCS3A01G347100 chr1B 89.510 143 13 2 5127 5268 513003970 513003829 5.570000e-41 180.0
43 TraesCS3A01G347100 chr1B 95.833 48 2 0 1726 1773 370729982 370729935 2.090000e-10 78.7
44 TraesCS3A01G347100 chr2D 97.872 47 0 1 1726 1772 340262180 340262135 5.810000e-11 80.5
45 TraesCS3A01G347100 chr6A 94.000 50 3 0 1723 1772 178448962 178448913 7.520000e-10 76.8


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 TraesCS3A01G347100 chr3A 596362410 596369396 6986 True 12903.00 12903 100.00000 1 6987 1 chr3A.!!$R1 6986
1 TraesCS3A01G347100 chr3B 596857090 596863899 6809 True 1762.20 3794 91.01900 10 6987 5 chr3B.!!$R1 6977
2 TraesCS3A01G347100 chr3D 454231158 454236547 5389 True 1863.00 2957 91.91300 855 6987 4 chr3D.!!$R1 6132
3 TraesCS3A01G347100 chr3D 537700966 537701641 675 False 1000.00 1000 93.26500 2785 3467 1 chr3D.!!$F1 682
4 TraesCS3A01G347100 chr3D 562513985 562514615 630 False 612.00 612 84.36000 64 689 1 chr3D.!!$F2 625
5 TraesCS3A01G347100 chr5A 435693335 435694168 833 True 1463.00 1463 98.32100 2785 3618 1 chr5A.!!$R2 833
6 TraesCS3A01G347100 chr5A 16526966 16527796 830 False 1402.00 1402 97.11200 2788 3618 1 chr5A.!!$F1 830
7 TraesCS3A01G347100 chr5A 295078472 295079305 833 True 1264.00 1264 94.00500 2785 3618 1 chr5A.!!$R1 833
8 TraesCS3A01G347100 chr7B 337924943 337925782 839 False 1319.00 1319 95.00600 2785 3624 1 chr7B.!!$F2 839
9 TraesCS3A01G347100 chr7B 388866720 388867534 814 True 1299.00 1299 95.46000 2786 3598 1 chr7B.!!$R2 812
10 TraesCS3A01G347100 chr7B 104298320 104298959 639 True 573.00 573 83.10100 64 698 1 chr7B.!!$R1 634
11 TraesCS3A01G347100 chr6D 77827058 77827890 832 False 1317.00 1317 95.19800 2786 3618 1 chr6D.!!$F1 832
12 TraesCS3A01G347100 chr6D 373341842 373344245 2403 True 454.25 721 86.93625 3862 6051 4 chr6D.!!$R1 2189
13 TraesCS3A01G347100 chr5D 497788326 497789159 833 False 1308.00 1308 94.96400 2785 3618 1 chr5D.!!$F1 833
14 TraesCS3A01G347100 chr5D 513915261 513916087 826 True 1262.00 1262 94.20300 2791 3618 1 chr5D.!!$R2 827
15 TraesCS3A01G347100 chr5D 76030552 76031150 598 True 582.00 582 84.33300 64 659 1 chr5D.!!$R1 595
16 TraesCS3A01G347100 chr6B 33588104 33588942 838 True 1256.00 1256 93.68300 2780 3618 1 chr6B.!!$R1 838
17 TraesCS3A01G347100 chr4B 567970045 567971093 1048 True 935.00 935 83.07100 4989 6049 1 chr4B.!!$R1 1060
18 TraesCS3A01G347100 chr2B 331237626 331239066 1440 True 504.00 625 87.62950 4347 5801 2 chr2B.!!$R1 1454
19 TraesCS3A01G347100 chr2A 66767193 66767820 627 True 603.00 603 84.17700 68 691 1 chr2A.!!$R1 623
20 TraesCS3A01G347100 chr2A 765573867 765574497 630 True 569.00 569 83.20100 64 685 1 chr2A.!!$R2 621
21 TraesCS3A01G347100 chr4D 428987947 428988550 603 False 595.00 595 84.62800 64 662 1 chr4D.!!$F2 598
22 TraesCS3A01G347100 chr1A 447639465 447640104 639 True 579.00 579 83.17800 65 698 1 chr1A.!!$R2 633
23 TraesCS3A01G347100 chr1D 110975564 110976192 628 False 569.00 569 83.25400 64 687 1 chr1D.!!$F1 623

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
317 710 0.036732 TGTCTAGTACCGTCGGTGGT 59.963 55.000 27.20 15.58 46.26 4.16 F
573 966 0.785979 GCGCCTTCGACTCGTTTTAA 59.214 50.000 0.00 0.00 38.10 1.52 F
1161 1561 0.179097 GAGGCTGGAGTCCATTCGTC 60.179 60.000 13.56 14.18 30.82 4.20 F
1685 2095 1.153229 GGGTTGGGGAGTATGTCGC 60.153 63.158 0.00 0.00 37.39 5.19 F
2437 2866 1.624487 TGTAGCACAAGATGTACGCG 58.376 50.000 3.53 3.53 0.00 6.01 F
3793 4255 1.134694 GCCGAACTTCGACATTGCC 59.865 57.895 12.87 0.00 43.74 4.52 F
4179 4854 1.066430 TCCGCCAACCAGATCACTAAC 60.066 52.381 0.00 0.00 0.00 2.34 F
4180 4855 1.338674 CCGCCAACCAGATCACTAACA 60.339 52.381 0.00 0.00 0.00 2.41 F
5643 6643 1.216678 TGTTGGTCCATTTCCCTGTGT 59.783 47.619 0.00 0.00 0.00 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1161 1561 0.392998 AATAACTGGAGCAGGCACGG 60.393 55.000 0.00 0.00 35.51 4.94 R
2243 2668 2.103432 TGCAAGGTCCGACTTCTTGTAA 59.897 45.455 15.02 5.67 39.80 2.41 R
2728 3161 3.559171 GGTGAATGTGAGGGACAAAGCTA 60.559 47.826 0.00 0.00 38.36 3.32 R
3467 3901 1.078848 CAGCGGCAGGAGCTTAACT 60.079 57.895 1.45 0.00 44.06 2.24 R
3935 4397 0.603569 AGTGGGAGCTCAAGTACACG 59.396 55.000 17.19 0.00 34.28 4.49 R
5306 6271 1.069049 ACAACTGCTGGAACATTTGGC 59.931 47.619 0.00 0.00 38.20 4.52 R
5643 6643 2.156098 GGCAACGAACACCTAATTCCA 58.844 47.619 0.00 0.00 0.00 3.53 R
5921 7084 5.119279 CGTCAAGTTCATCTTCACCTGTAAG 59.881 44.000 0.00 0.00 33.63 2.34 R
6659 7842 1.868251 GAGCACTTCTACCGTCGCG 60.868 63.158 0.00 0.00 0.00 5.87 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
25 412 5.237815 TGCGTCATTTAGACTGATCAACTT 58.762 37.500 0.00 0.00 45.32 2.66
39 426 7.189512 ACTGATCAACTTCAAGTTTTTCTTCG 58.810 34.615 0.00 0.00 36.03 3.79
167 558 4.115199 GATCCCAGCCCTTGCCGT 62.115 66.667 0.00 0.00 38.69 5.68
189 581 2.235402 CGGGAGGGCTCTGTTTTAGTTA 59.765 50.000 0.00 0.00 0.00 2.24
224 616 5.376756 TTGTTAGGGTTTGTGTCCTACTT 57.623 39.130 0.00 0.00 35.56 2.24
226 618 6.497624 TGTTAGGGTTTGTGTCCTACTTAA 57.502 37.500 0.00 0.00 35.56 1.85
297 690 1.866483 TAGCCCTCGTCCAGGTGGTA 61.866 60.000 0.00 0.00 41.51 3.25
307 700 3.314635 CGTCCAGGTGGTATGTCTAGTAC 59.685 52.174 0.00 0.00 36.34 2.73
317 710 0.036732 TGTCTAGTACCGTCGGTGGT 59.963 55.000 27.20 15.58 46.26 4.16
335 728 1.474498 GGTCGTGTGGAGGTTTGTCTT 60.474 52.381 0.00 0.00 0.00 3.01
339 732 2.135933 GTGTGGAGGTTTGTCTTCGAG 58.864 52.381 0.00 0.00 0.00 4.04
343 736 1.337917 GGAGGTTTGTCTTCGAGGGAC 60.338 57.143 11.92 11.92 0.00 4.46
371 764 2.473070 TGGTGGATTTGTCCGGATCTA 58.527 47.619 7.81 0.00 0.00 1.98
547 940 2.569354 GCGAGAGAGGGGCGATGAT 61.569 63.158 0.00 0.00 0.00 2.45
568 961 4.755614 GACGCGCCTTCGACTCGT 62.756 66.667 5.73 0.00 38.10 4.18
573 966 0.785979 GCGCCTTCGACTCGTTTTAA 59.214 50.000 0.00 0.00 38.10 1.52
704 1103 6.460664 AAAAGAAAACAAAACAACTCCACG 57.539 33.333 0.00 0.00 0.00 4.94
754 1153 2.479837 CACTGTCAGCCGTGTTTAGAA 58.520 47.619 0.00 0.00 0.00 2.10
771 1170 6.183361 TGTTTAGAAGATCCACTCCACTTTCA 60.183 38.462 0.00 0.00 0.00 2.69
772 1171 4.550076 AGAAGATCCACTCCACTTTCAG 57.450 45.455 0.00 0.00 0.00 3.02
773 1172 2.777832 AGATCCACTCCACTTTCAGC 57.222 50.000 0.00 0.00 0.00 4.26
797 1196 2.165641 TGTTTACATGATCGACTCCGCT 59.834 45.455 0.00 0.00 35.37 5.52
815 1214 6.434965 ACTCCGCTTTTAGCCCTTAAAATAAA 59.565 34.615 0.00 0.00 39.74 1.40
820 1219 9.233232 CGCTTTTAGCCCTTAAAATAAACATAG 57.767 33.333 0.00 0.00 39.74 2.23
845 1244 8.652290 AGGAAGTGTATAAGAAAGAAAGAGTGT 58.348 33.333 0.00 0.00 0.00 3.55
846 1245 9.924650 GGAAGTGTATAAGAAAGAAAGAGTGTA 57.075 33.333 0.00 0.00 0.00 2.90
851 1250 9.084164 TGTATAAGAAAGAAAGAGTGTATTCGC 57.916 33.333 0.00 0.00 0.00 4.70
852 1251 9.084164 GTATAAGAAAGAAAGAGTGTATTCGCA 57.916 33.333 0.00 0.00 0.00 5.10
853 1252 6.861065 AAGAAAGAAAGAGTGTATTCGCAA 57.139 33.333 0.00 0.00 0.00 4.85
885 1285 5.758924 AGAGGTTTAAAACGCAAAAGCTAG 58.241 37.500 9.73 0.00 41.94 3.42
1101 1501 2.592308 GCCTTTCCCATCTCCGCT 59.408 61.111 0.00 0.00 0.00 5.52
1121 1521 4.379918 CGCTGCCTCTTATAATCTCGATCA 60.380 45.833 0.00 0.00 0.00 2.92
1147 1547 4.125124 TCCTATGCTAGAAGATGAGGCT 57.875 45.455 0.00 0.00 0.00 4.58
1161 1561 0.179097 GAGGCTGGAGTCCATTCGTC 60.179 60.000 13.56 14.18 30.82 4.20
1207 1610 6.533730 TGGATCACACAACTGAGAGTAAAAT 58.466 36.000 0.00 0.00 0.00 1.82
1353 1757 4.997395 TCTCAGTTTGTATTCTTCACTGCC 59.003 41.667 0.00 0.00 35.76 4.85
1386 1790 6.721704 TGCAAGCTCTAGAATCTAGATCAA 57.278 37.500 19.18 0.00 0.00 2.57
1387 1791 6.747125 TGCAAGCTCTAGAATCTAGATCAAG 58.253 40.000 19.18 12.60 0.00 3.02
1685 2095 1.153229 GGGTTGGGGAGTATGTCGC 60.153 63.158 0.00 0.00 37.39 5.19
1778 2188 3.544698 ACGGATGTATCTAGATGGGGT 57.455 47.619 15.79 2.25 0.00 4.95
1908 2318 9.173939 GAATTATTGCTGTGTGAAGTATATTGC 57.826 33.333 0.00 0.00 0.00 3.56
2114 2539 5.235850 TGGACTTCTGTAATTGGCACTTA 57.764 39.130 0.00 0.00 0.00 2.24
2165 2590 5.975939 GCAGTCCATGATTTAAATCTTCTGC 59.024 40.000 24.57 24.57 36.39 4.26
2184 2609 7.649705 TCTTCTGCGACAGCTTTCTAATAATAG 59.350 37.037 0.00 0.00 45.42 1.73
2190 2615 7.340699 CGACAGCTTTCTAATAATAGTTGCTG 58.659 38.462 18.44 18.44 43.89 4.41
2192 2617 8.567285 ACAGCTTTCTAATAATAGTTGCTGTT 57.433 30.769 19.25 10.61 45.89 3.16
2193 2618 8.669243 ACAGCTTTCTAATAATAGTTGCTGTTC 58.331 33.333 19.25 0.00 45.89 3.18
2194 2619 8.125448 CAGCTTTCTAATAATAGTTGCTGTTCC 58.875 37.037 14.92 0.00 39.65 3.62
2195 2620 8.049721 AGCTTTCTAATAATAGTTGCTGTTCCT 58.950 33.333 0.00 0.00 32.96 3.36
2196 2621 8.678199 GCTTTCTAATAATAGTTGCTGTTCCTT 58.322 33.333 0.00 0.00 0.00 3.36
2197 2622 9.994432 CTTTCTAATAATAGTTGCTGTTCCTTG 57.006 33.333 0.00 0.00 0.00 3.61
2198 2623 8.506168 TTCTAATAATAGTTGCTGTTCCTTGG 57.494 34.615 0.00 0.00 0.00 3.61
2201 2626 9.561069 CTAATAATAGTTGCTGTTCCTTGGTAT 57.439 33.333 0.00 0.00 0.00 2.73
2219 2644 5.846203 TGGTATACCGTATCTTTGTAAGCC 58.154 41.667 17.13 0.00 39.43 4.35
2243 2668 4.887071 TGATTGGTAAACTCTTGCAACAGT 59.113 37.500 0.98 0.98 0.00 3.55
2342 2767 8.100508 AGTAAGGCTTCAAACTTTTCATCTAC 57.899 34.615 1.30 0.00 0.00 2.59
2437 2866 1.624487 TGTAGCACAAGATGTACGCG 58.376 50.000 3.53 3.53 0.00 6.01
2439 2868 2.162008 TGTAGCACAAGATGTACGCGTA 59.838 45.455 16.41 16.41 0.00 4.42
2440 2869 1.625616 AGCACAAGATGTACGCGTAC 58.374 50.000 36.15 36.15 36.63 3.67
2486 2918 6.201997 ACAAGTTGATGCGTTTTAATTTTCCC 59.798 34.615 10.54 0.00 0.00 3.97
2509 2941 3.480470 TGCTAGGAATCTTTGGCTATGC 58.520 45.455 0.00 0.00 0.00 3.14
2511 2943 3.251972 GCTAGGAATCTTTGGCTATGCAC 59.748 47.826 0.00 0.00 0.00 4.57
2514 2946 2.682856 GGAATCTTTGGCTATGCACGAA 59.317 45.455 0.00 0.00 0.00 3.85
2554 2987 8.696043 TGATTGCCTTCAATAGCATTTACTAT 57.304 30.769 0.00 0.00 42.60 2.12
2723 3156 4.010349 GTGCTGTTATCCACTTAGCCTTT 58.990 43.478 0.00 0.00 33.60 3.11
2728 3161 6.127619 GCTGTTATCCACTTAGCCTTTGAAAT 60.128 38.462 0.00 0.00 0.00 2.17
3536 3970 4.752879 CCAACGACCGCATCCCGT 62.753 66.667 0.00 0.00 38.24 5.28
3578 4012 3.256960 GGAGGCCAGACCAACCCA 61.257 66.667 5.01 0.00 43.14 4.51
3730 4192 6.599356 TTGTAGCGCCCTTTCAGATATATA 57.401 37.500 2.29 0.00 0.00 0.86
3793 4255 1.134694 GCCGAACTTCGACATTGCC 59.865 57.895 12.87 0.00 43.74 4.52
3806 4268 3.554544 CGACATTGCCTCTGATGCTCTAT 60.555 47.826 6.49 0.00 0.00 1.98
3925 4387 6.366877 CAGGATTTGCTTACCAAACATGAAAG 59.633 38.462 0.00 0.00 45.52 2.62
3935 4397 4.111916 CCAAACATGAAAGTGTTGTGTCC 58.888 43.478 0.00 0.00 41.22 4.02
4095 4559 4.573900 TCTGACTCTGCCTTCTGATTTTC 58.426 43.478 0.00 0.00 0.00 2.29
4107 4571 7.334421 TGCCTTCTGATTTTCTGATACACTTAC 59.666 37.037 0.00 0.00 0.00 2.34
4179 4854 1.066430 TCCGCCAACCAGATCACTAAC 60.066 52.381 0.00 0.00 0.00 2.34
4180 4855 1.338674 CCGCCAACCAGATCACTAACA 60.339 52.381 0.00 0.00 0.00 2.41
4181 4856 2.002586 CGCCAACCAGATCACTAACAG 58.997 52.381 0.00 0.00 0.00 3.16
4182 4857 2.612972 CGCCAACCAGATCACTAACAGT 60.613 50.000 0.00 0.00 0.00 3.55
4183 4858 3.003480 GCCAACCAGATCACTAACAGTC 58.997 50.000 0.00 0.00 0.00 3.51
4185 4860 4.081642 GCCAACCAGATCACTAACAGTCTA 60.082 45.833 0.00 0.00 0.00 2.59
4186 4861 5.568825 GCCAACCAGATCACTAACAGTCTAA 60.569 44.000 0.00 0.00 0.00 2.10
4187 4862 5.869888 CCAACCAGATCACTAACAGTCTAAC 59.130 44.000 0.00 0.00 0.00 2.34
4188 4863 6.455647 CAACCAGATCACTAACAGTCTAACA 58.544 40.000 0.00 0.00 0.00 2.41
4321 4996 1.341531 CAGTCGGTGAAGGTCAGACTT 59.658 52.381 0.00 0.00 38.02 3.01
4363 5044 6.973843 TCTCATTCACATGGAAAAGAAACTG 58.026 36.000 0.00 0.00 39.39 3.16
4529 5216 4.553330 ACTGTTCATCTGGGAATTACGT 57.447 40.909 0.00 0.00 0.00 3.57
4722 5574 6.425721 TGTTATTCCACCTTGAACTTAAGACG 59.574 38.462 10.09 0.00 0.00 4.18
4853 5711 3.953775 CAACGCACCCTGGTCCCT 61.954 66.667 0.00 0.00 0.00 4.20
5005 5864 5.651139 ACCTAGTAGTGTAGAATGCTCGAAA 59.349 40.000 0.00 0.00 0.00 3.46
5033 5892 6.292381 GCGCATAAATGACTTCTAACCTGTAG 60.292 42.308 0.30 0.00 0.00 2.74
5139 6082 7.316640 ACATAGAGTAACTGCTTGACTAAGTG 58.683 38.462 0.00 0.00 36.27 3.16
5241 6184 1.372683 GAGTGTGCAAGAGCTCCCA 59.627 57.895 10.93 2.39 42.74 4.37
5306 6271 9.868277 ACTGTCTTGAACATTCTTATCTCTTAG 57.132 33.333 0.00 0.00 37.23 2.18
5312 6277 9.466497 TTGAACATTCTTATCTCTTAGCCAAAT 57.534 29.630 0.00 0.00 0.00 2.32
5643 6643 1.216678 TGTTGGTCCATTTCCCTGTGT 59.783 47.619 0.00 0.00 0.00 3.72
5699 6706 6.062095 GCCTCCTGGTATTATTGAAGCTTTA 58.938 40.000 0.00 0.00 35.27 1.85
5736 6743 5.924475 AGAATTGTTGAAACTACTCCACG 57.076 39.130 0.00 0.00 0.00 4.94
5894 7056 3.118956 TGATGTCAACCACCACAAAAACC 60.119 43.478 0.00 0.00 0.00 3.27
6254 7434 5.615289 ACTCGAGCCAAGAATATTATTGCT 58.385 37.500 13.61 15.41 0.00 3.91
6491 7674 1.292242 TCCCTCTACTTGGATGAGGCT 59.708 52.381 0.00 0.00 44.32 4.58
6659 7842 2.130073 GAACCTTGCTCGTGGTTGCC 62.130 60.000 1.88 0.00 45.48 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.316640 ACTTGAAGTTGATCAGTCTAAATGAC 57.683 34.615 0.00 0.00 45.67 3.06
11 12 8.964476 AGAAAAACTTGAAGTTGATCAGTCTA 57.036 30.769 11.83 0.00 38.66 2.59
13 14 7.374491 CGAAGAAAAACTTGAAGTTGATCAGTC 59.626 37.037 11.83 12.09 38.66 3.51
14 15 7.189512 CGAAGAAAAACTTGAAGTTGATCAGT 58.810 34.615 11.83 5.53 38.66 3.41
25 412 4.442706 AGTGAGAGCGAAGAAAAACTTGA 58.557 39.130 0.00 0.00 39.13 3.02
97 485 4.803426 GAGACGGACTGGCGGCAG 62.803 72.222 34.75 34.75 0.00 4.85
147 538 2.605299 GCAAGGGCTGGGATCCAT 59.395 61.111 15.23 0.00 36.96 3.41
167 558 0.902531 CTAAAACAGAGCCCTCCCGA 59.097 55.000 0.00 0.00 0.00 5.14
189 581 4.466827 ACCCTAACAAAACACGAAGGAAT 58.533 39.130 0.00 0.00 0.00 3.01
224 616 2.030540 CCGTCACCGTCTTGTCTTCTTA 60.031 50.000 0.00 0.00 0.00 2.10
226 618 0.314302 CCGTCACCGTCTTGTCTTCT 59.686 55.000 0.00 0.00 0.00 2.85
290 682 3.549794 GACGGTACTAGACATACCACCT 58.450 50.000 0.00 0.00 42.03 4.00
297 690 1.340405 ACCACCGACGGTACTAGACAT 60.340 52.381 21.25 0.00 37.57 3.06
317 710 1.537348 CGAAGACAAACCTCCACACGA 60.537 52.381 0.00 0.00 0.00 4.35
362 755 3.470709 ACGAACTACGATTAGATCCGGA 58.529 45.455 6.61 6.61 45.77 5.14
568 961 3.991773 AGCGACGACTACAAGCATTAAAA 59.008 39.130 0.00 0.00 0.00 1.52
573 966 1.065701 CCTAGCGACGACTACAAGCAT 59.934 52.381 0.00 0.00 0.00 3.79
685 1084 3.840468 ACCGTGGAGTTGTTTTGTTTTC 58.160 40.909 0.00 0.00 0.00 2.29
754 1153 1.280421 GGCTGAAAGTGGAGTGGATCT 59.720 52.381 0.00 0.00 35.30 2.75
771 1170 2.501723 AGTCGATCATGTAAACAGGGCT 59.498 45.455 0.00 0.00 0.00 5.19
772 1171 2.866762 GAGTCGATCATGTAAACAGGGC 59.133 50.000 0.00 0.00 0.00 5.19
773 1172 3.458189 GGAGTCGATCATGTAAACAGGG 58.542 50.000 0.00 0.00 0.00 4.45
820 1219 8.834749 ACACTCTTTCTTTCTTATACACTTCC 57.165 34.615 0.00 0.00 0.00 3.46
829 1228 7.956420 TTGCGAATACACTCTTTCTTTCTTA 57.044 32.000 0.00 0.00 0.00 2.10
830 1229 6.861065 TTGCGAATACACTCTTTCTTTCTT 57.139 33.333 0.00 0.00 0.00 2.52
831 1230 6.861065 TTTGCGAATACACTCTTTCTTTCT 57.139 33.333 0.00 0.00 0.00 2.52
832 1231 7.908193 TTTTTGCGAATACACTCTTTCTTTC 57.092 32.000 0.00 0.00 0.00 2.62
857 1256 6.035650 GCTTTTGCGTTTTAAACCTCTCTTTT 59.964 34.615 1.97 0.00 34.86 2.27
1101 1501 4.220821 GGGTGATCGAGATTATAAGAGGCA 59.779 45.833 0.00 0.00 0.00 4.75
1121 1521 4.756564 TCATCTTCTAGCATAGGATGGGT 58.243 43.478 0.00 0.00 37.70 4.51
1147 1547 1.589630 CACGGACGAATGGACTCCA 59.410 57.895 0.00 0.00 38.19 3.86
1161 1561 0.392998 AATAACTGGAGCAGGCACGG 60.393 55.000 0.00 0.00 35.51 4.94
1207 1610 5.066634 TGCAAACCTTCTTTTGATCGTAACA 59.933 36.000 0.00 0.00 38.54 2.41
1239 1642 3.123804 CCTACCGATCGACCAATTTCAG 58.876 50.000 18.66 0.00 0.00 3.02
1386 1790 7.090808 GCAAACATCATCATCATGCATTATCT 58.909 34.615 0.00 0.00 32.80 1.98
1387 1791 6.866248 TGCAAACATCATCATCATGCATTATC 59.134 34.615 0.00 0.00 37.40 1.75
1462 1872 4.502171 TTGTACATCACAACTGCATTGG 57.498 40.909 0.00 0.00 42.29 3.16
1466 1876 4.821260 AGTCATTTGTACATCACAACTGCA 59.179 37.500 0.00 0.00 46.80 4.41
1533 1943 2.167861 GCCGCAACGAGGAGATGTC 61.168 63.158 0.00 0.00 0.00 3.06
1718 2128 3.709653 TGGGACGGAAGCAGTAATAGATT 59.290 43.478 0.00 0.00 0.00 2.40
1729 2139 4.084013 CGTCAATTAATATGGGACGGAAGC 60.084 45.833 17.22 0.00 45.36 3.86
1908 2318 3.849911 TCTAAAAGCTCCACGTGATCTG 58.150 45.455 19.30 0.00 0.00 2.90
1989 2399 9.624373 ATCTTGTAAACTATCTCTGCATTCATT 57.376 29.630 0.00 0.00 0.00 2.57
2165 2590 7.010552 ACAGCAACTATTATTAGAAAGCTGTCG 59.989 37.037 22.37 10.95 45.97 4.35
2184 2609 2.676342 CGGTATACCAAGGAACAGCAAC 59.324 50.000 21.76 0.00 35.14 4.17
2190 2615 6.343703 ACAAAGATACGGTATACCAAGGAAC 58.656 40.000 21.76 2.18 35.14 3.62
2191 2616 6.549433 ACAAAGATACGGTATACCAAGGAA 57.451 37.500 21.76 2.24 35.14 3.36
2192 2617 7.658525 TTACAAAGATACGGTATACCAAGGA 57.341 36.000 21.76 3.37 35.14 3.36
2193 2618 6.423001 GCTTACAAAGATACGGTATACCAAGG 59.577 42.308 21.76 8.14 35.14 3.61
2194 2619 6.423001 GGCTTACAAAGATACGGTATACCAAG 59.577 42.308 21.76 13.33 35.14 3.61
2195 2620 6.098695 AGGCTTACAAAGATACGGTATACCAA 59.901 38.462 21.76 9.43 35.14 3.67
2196 2621 5.599656 AGGCTTACAAAGATACGGTATACCA 59.400 40.000 21.76 3.43 35.14 3.25
2197 2622 5.924825 CAGGCTTACAAAGATACGGTATACC 59.075 44.000 12.27 12.27 0.00 2.73
2198 2623 6.742109 TCAGGCTTACAAAGATACGGTATAC 58.258 40.000 0.00 0.00 0.00 1.47
2201 2626 5.864418 ATCAGGCTTACAAAGATACGGTA 57.136 39.130 0.00 0.00 0.00 4.02
2219 2644 5.009010 ACTGTTGCAAGAGTTTACCAATCAG 59.991 40.000 22.60 12.42 0.00 2.90
2243 2668 2.103432 TGCAAGGTCCGACTTCTTGTAA 59.897 45.455 15.02 5.67 39.80 2.41
2342 2767 5.931724 GTCCCAAACAAAATAATGTCCCAAG 59.068 40.000 0.00 0.00 31.81 3.61
2373 2798 8.823220 ACCAAGAAAAGTTAGGTGCATATATT 57.177 30.769 0.00 0.00 0.00 1.28
2486 2918 4.082895 GCATAGCCAAAGATTCCTAGCATG 60.083 45.833 0.00 0.00 0.00 4.06
2509 2941 8.316046 GCAATCAATTCTTTTCACATATTCGTG 58.684 33.333 0.00 0.00 38.29 4.35
2511 2943 7.703621 AGGCAATCAATTCTTTTCACATATTCG 59.296 33.333 0.00 0.00 0.00 3.34
2514 2946 8.533657 TGAAGGCAATCAATTCTTTTCACATAT 58.466 29.630 0.00 0.00 0.00 1.78
2554 2987 4.873746 TGGTTGTTCAACCTTGTTTTCA 57.126 36.364 27.58 8.96 43.23 2.69
2658 3091 8.783660 AAGAAGGACATGTCTGGTAGATATTA 57.216 34.615 24.50 0.00 0.00 0.98
2723 3156 4.365514 TGTGAGGGACAAAGCTATTTCA 57.634 40.909 0.00 0.00 0.00 2.69
2728 3161 3.559171 GGTGAATGTGAGGGACAAAGCTA 60.559 47.826 0.00 0.00 38.36 3.32
3467 3901 1.078848 CAGCGGCAGGAGCTTAACT 60.079 57.895 1.45 0.00 44.06 2.24
3793 4255 5.781210 TGAAGGTGTATAGAGCATCAGAG 57.219 43.478 3.21 0.00 37.82 3.35
3925 4387 2.538449 CTCAAGTACACGGACACAACAC 59.462 50.000 0.00 0.00 0.00 3.32
3935 4397 0.603569 AGTGGGAGCTCAAGTACACG 59.396 55.000 17.19 0.00 34.28 4.49
4027 4491 9.585099 GATGGCATACAAAAATATGAACTCAAA 57.415 29.630 0.00 0.00 34.94 2.69
4095 4559 6.974932 AGTGCAAATCTGTAAGTGTATCAG 57.025 37.500 0.00 0.00 33.76 2.90
4107 4571 4.748102 AGCAACAATGAAAGTGCAAATCTG 59.252 37.500 0.00 0.00 33.50 2.90
4181 4856 9.694137 GGAACTATCCACTATGTTATGTTAGAC 57.306 37.037 0.00 0.00 45.79 2.59
4321 4996 6.854091 ATGAGATGATTAGCTAGAGCATCA 57.146 37.500 23.60 17.32 45.16 3.07
4363 5044 8.398665 GGAACTGAAAATACAGACACCAATATC 58.601 37.037 0.00 0.00 40.63 1.63
4529 5216 6.662755 ACCAAAATAGGCTATCTCATTGTCA 58.337 36.000 7.63 0.00 0.00 3.58
4560 5247 9.754382 ATACGAACTTAACAAGAAACAGAGTAA 57.246 29.630 0.00 0.00 0.00 2.24
4722 5574 5.428496 AAAAACCGCTGACTACCTTTTAC 57.572 39.130 0.00 0.00 0.00 2.01
4946 5805 2.005451 CCTGATCAAGCAGAACCTTCG 58.995 52.381 0.00 0.00 38.14 3.79
5005 5864 5.590259 AGGTTAGAAGTCATTTATGCGCATT 59.410 36.000 30.42 7.91 0.00 3.56
5139 6082 5.429130 ACCTTCACTTAGCAGCCTATAAAC 58.571 41.667 0.00 0.00 0.00 2.01
5293 6252 7.402054 TGGAACATTTGGCTAAGAGATAAGAA 58.598 34.615 0.00 0.00 0.00 2.52
5306 6271 1.069049 ACAACTGCTGGAACATTTGGC 59.931 47.619 0.00 0.00 38.20 4.52
5410 6391 6.627243 CAGAAATGGAGAATCTTTCATGCAA 58.373 36.000 0.00 0.00 32.55 4.08
5643 6643 2.156098 GGCAACGAACACCTAATTCCA 58.844 47.619 0.00 0.00 0.00 3.53
5736 6743 5.582665 CACTACCTTTACTTGCAGGAAGATC 59.417 44.000 8.96 0.00 35.42 2.75
5921 7084 5.119279 CGTCAAGTTCATCTTCACCTGTAAG 59.881 44.000 0.00 0.00 33.63 2.34
6228 7407 6.203723 GCAATAATATTCTTGGCTCGAGTTCT 59.796 38.462 15.13 0.00 0.00 3.01
6254 7434 1.493854 AACTGGGCCGGATTGTACCA 61.494 55.000 21.81 1.64 0.00 3.25
6386 7569 3.838317 AGCCATTCTCTGTTACCAGTGTA 59.162 43.478 0.00 0.00 39.82 2.90
6659 7842 1.868251 GAGCACTTCTACCGTCGCG 60.868 63.158 0.00 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.