Multiple sequence alignment - TraesCS3B01G421400

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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 TraesCS3B01G421400 chr3B 100.000 3428 0 0 1 3428 658485989 658489416 0.000000e+00 6331.0
1 TraesCS3B01G421400 chr3B 86.918 902 100 11 1172 2066 684762789 684763679 0.000000e+00 996.0
2 TraesCS3B01G421400 chr3B 80.886 1151 201 14 1230 2368 684770132 684771275 0.000000e+00 889.0
3 TraesCS3B01G421400 chr3B 76.187 1495 267 60 970 2423 756709051 756707605 0.000000e+00 706.0
4 TraesCS3B01G421400 chr3B 76.120 1495 269 59 970 2423 756824183 756822736 0.000000e+00 702.0
5 TraesCS3B01G421400 chr3B 89.738 458 44 3 2064 2519 684763747 684764203 1.770000e-162 582.0
6 TraesCS3B01G421400 chr3B 82.931 580 62 17 600 1172 684747780 684748329 3.980000e-134 488.0
7 TraesCS3B01G421400 chr3A 91.787 2070 137 16 665 2716 636541786 636539732 0.000000e+00 2850.0
8 TraesCS3B01G421400 chr3A 84.287 1852 217 35 1172 2981 655628941 655630760 0.000000e+00 1740.0
9 TraesCS3B01G421400 chr3A 86.886 1365 151 14 1172 2519 655896976 655895623 0.000000e+00 1504.0
10 TraesCS3B01G421400 chr3A 88.817 617 34 15 30 621 636542388 636541782 0.000000e+00 725.0
11 TraesCS3B01G421400 chr3A 77.094 1170 235 26 1230 2377 655886389 655885231 0.000000e+00 645.0
12 TraesCS3B01G421400 chr3A 83.247 579 65 16 603 1175 655899858 655899306 1.420000e-138 503.0
13 TraesCS3B01G421400 chr3A 86.709 316 39 3 850 1164 655627762 655628075 7.040000e-92 348.0
14 TraesCS3B01G421400 chr3A 86.691 278 30 7 2706 2981 636539712 636539440 5.560000e-78 302.0
15 TraesCS3B01G421400 chr3A 91.892 111 9 0 600 710 655627608 655627718 4.580000e-34 156.0
16 TraesCS3B01G421400 chr3D 94.630 1732 85 8 313 2040 497864576 497866303 0.000000e+00 2676.0
17 TraesCS3B01G421400 chr3D 84.838 1761 191 37 1172 2895 520322409 520320688 0.000000e+00 1703.0
18 TraesCS3B01G421400 chr3D 91.699 783 46 8 2027 2793 497866322 497867101 0.000000e+00 1068.0
19 TraesCS3B01G421400 chr3D 80.886 1151 200 14 1231 2368 520315754 520314611 0.000000e+00 889.0
20 TraesCS3B01G421400 chr3D 75.814 1505 284 58 970 2437 570146609 570145148 0.000000e+00 689.0
21 TraesCS3B01G421400 chr3D 75.087 1152 253 26 1228 2369 569900466 569901593 1.100000e-139 507.0
22 TraesCS3B01G421400 chr3D 82.125 593 55 19 603 1171 520323773 520323208 8.670000e-126 460.0
23 TraesCS3B01G421400 chr3D 81.899 337 32 13 3061 3370 520320640 520320306 1.220000e-64 257.0
24 TraesCS3B01G421400 chr3D 86.458 192 6 6 1 192 497864408 497864579 3.490000e-45 193.0
25 TraesCS3B01G421400 chr3D 94.805 77 4 0 3346 3422 497867108 497867184 1.670000e-23 121.0
26 TraesCS3B01G421400 chr3D 85.106 94 10 3 979 1072 520316108 520316019 3.640000e-15 93.5
27 TraesCS3B01G421400 chrUn 75.411 1033 230 19 1345 2369 287225084 287226100 2.390000e-131 479.0
28 TraesCS3B01G421400 chr7A 96.552 87 3 0 2978 3064 184126738 184126824 9.910000e-31 145.0
29 TraesCS3B01G421400 chr4D 95.556 90 4 0 2978 3067 383775650 383775561 9.910000e-31 145.0
30 TraesCS3B01G421400 chr4B 95.556 90 4 0 2979 3068 432817292 432817381 9.910000e-31 145.0
31 TraesCS3B01G421400 chr4A 95.556 90 4 0 2979 3068 570916238 570916149 9.910000e-31 145.0
32 TraesCS3B01G421400 chr4A 95.556 90 4 0 2979 3068 619281527 619281438 9.910000e-31 145.0
33 TraesCS3B01G421400 chr6A 94.565 92 5 0 2978 3069 121888017 121887926 3.570000e-30 143.0
34 TraesCS3B01G421400 chr6A 94.565 92 5 0 2976 3067 121887928 121888019 3.570000e-30 143.0
35 TraesCS3B01G421400 chr7D 93.617 94 6 0 2976 3069 81910951 81911044 1.280000e-29 141.0
36 TraesCS3B01G421400 chr2D 93.617 94 6 0 2979 3072 307490171 307490078 1.280000e-29 141.0


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 TraesCS3B01G421400 chr3B 658485989 658489416 3427 False 6331.000000 6331 100.000000 1 3428 1 chr3B.!!$F1 3427
1 TraesCS3B01G421400 chr3B 684770132 684771275 1143 False 889.000000 889 80.886000 1230 2368 1 chr3B.!!$F3 1138
2 TraesCS3B01G421400 chr3B 684762789 684764203 1414 False 789.000000 996 88.328000 1172 2519 2 chr3B.!!$F4 1347
3 TraesCS3B01G421400 chr3B 756707605 756709051 1446 True 706.000000 706 76.187000 970 2423 1 chr3B.!!$R1 1453
4 TraesCS3B01G421400 chr3B 756822736 756824183 1447 True 702.000000 702 76.120000 970 2423 1 chr3B.!!$R2 1453
5 TraesCS3B01G421400 chr3B 684747780 684748329 549 False 488.000000 488 82.931000 600 1172 1 chr3B.!!$F2 572
6 TraesCS3B01G421400 chr3A 636539440 636542388 2948 True 1292.333333 2850 89.098333 30 2981 3 chr3A.!!$R2 2951
7 TraesCS3B01G421400 chr3A 655895623 655899858 4235 True 1003.500000 1504 85.066500 603 2519 2 chr3A.!!$R3 1916
8 TraesCS3B01G421400 chr3A 655627608 655630760 3152 False 748.000000 1740 87.629333 600 2981 3 chr3A.!!$F1 2381
9 TraesCS3B01G421400 chr3A 655885231 655886389 1158 True 645.000000 645 77.094000 1230 2377 1 chr3A.!!$R1 1147
10 TraesCS3B01G421400 chr3D 497864408 497867184 2776 False 1014.500000 2676 91.898000 1 3422 4 chr3D.!!$F2 3421
11 TraesCS3B01G421400 chr3D 520320306 520323773 3467 True 806.666667 1703 82.954000 603 3370 3 chr3D.!!$R3 2767
12 TraesCS3B01G421400 chr3D 570145148 570146609 1461 True 689.000000 689 75.814000 970 2437 1 chr3D.!!$R1 1467
13 TraesCS3B01G421400 chr3D 569900466 569901593 1127 False 507.000000 507 75.087000 1228 2369 1 chr3D.!!$F1 1141
14 TraesCS3B01G421400 chr3D 520314611 520316108 1497 True 491.250000 889 82.996000 979 2368 2 chr3D.!!$R2 1389
15 TraesCS3B01G421400 chrUn 287225084 287226100 1016 False 479.000000 479 75.411000 1345 2369 1 chrUn.!!$F1 1024

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
334 369 0.908910 TTGCCGTATGGTCCATGACT 59.091 50.0 15.1 0.0 37.67 3.41 F
657 694 1.826385 CCACAAGAGTCATCCCCAAC 58.174 55.0 0.0 0.0 0.00 3.77 F
1493 4019 0.530744 CAACGATCTCCCGGAGAACA 59.469 55.0 21.2 0.0 42.27 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1280 3802 0.447801 CGCTTCAATCCAGGGTTTCG 59.552 55.0 0.0 0.0 0.00 3.46 R
1520 4046 0.602638 TTGCTTTGACGGAGCGTGAT 60.603 50.0 0.0 0.0 41.37 3.06 R
3046 5767 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.0 0.0 0.0 0.00 3.28 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
53 54 5.814705 GCTTGAGATTGTAGCACTTACTCAT 59.185 40.000 0.00 0.00 35.05 2.90
57 58 8.032952 TGAGATTGTAGCACTTACTCATTTTG 57.967 34.615 0.00 0.00 33.23 2.44
59 60 7.810658 AGATTGTAGCACTTACTCATTTTGTG 58.189 34.615 0.00 0.00 33.23 3.33
61 62 6.299023 TGTAGCACTTACTCATTTTGTGTG 57.701 37.500 0.00 0.00 33.23 3.82
62 63 5.820423 TGTAGCACTTACTCATTTTGTGTGT 59.180 36.000 0.00 0.00 38.11 3.72
63 64 5.173774 AGCACTTACTCATTTTGTGTGTG 57.826 39.130 0.00 0.00 36.13 3.82
64 65 4.640201 AGCACTTACTCATTTTGTGTGTGT 59.360 37.500 0.00 0.00 36.13 3.72
65 66 4.734854 GCACTTACTCATTTTGTGTGTGTG 59.265 41.667 0.00 0.00 36.13 3.82
66 67 5.676079 GCACTTACTCATTTTGTGTGTGTGT 60.676 40.000 13.15 0.00 36.13 3.72
67 68 6.457663 GCACTTACTCATTTTGTGTGTGTGTA 60.458 38.462 13.15 0.00 36.13 2.90
68 69 7.639039 CACTTACTCATTTTGTGTGTGTGTAT 58.361 34.615 0.00 0.00 36.13 2.29
69 70 7.587392 CACTTACTCATTTTGTGTGTGTGTATG 59.413 37.037 0.00 0.00 36.13 2.39
114 124 8.950210 ACATGCTATTTATTTCCAATCTATCCG 58.050 33.333 0.00 0.00 0.00 4.18
115 125 9.166173 CATGCTATTTATTTCCAATCTATCCGA 57.834 33.333 0.00 0.00 0.00 4.55
116 126 9.911788 ATGCTATTTATTTCCAATCTATCCGAT 57.088 29.630 0.00 0.00 0.00 4.18
117 127 9.383519 TGCTATTTATTTCCAATCTATCCGATC 57.616 33.333 0.00 0.00 0.00 3.69
146 156 5.508200 TTGGGAATTAGACACACACAAAC 57.492 39.130 0.00 0.00 0.00 2.93
149 159 4.454504 GGGAATTAGACACACACAAACGAT 59.545 41.667 0.00 0.00 0.00 3.73
169 179 3.508845 TTCTTCAAGAGTTTGGAGGGG 57.491 47.619 0.00 0.00 39.91 4.79
202 212 5.612709 GCAGAAACAGTACTGAAACTAAGCG 60.613 44.000 29.30 12.24 36.38 4.68
205 215 2.036733 ACAGTACTGAAACTAAGCGCCA 59.963 45.455 29.30 0.00 0.00 5.69
230 240 3.562973 ACTGCTTGAGATTGTGACACTTG 59.437 43.478 7.20 0.00 0.00 3.16
274 284 6.238593 GCTCTCTTTTCTCACTGACAAATGTT 60.239 38.462 0.00 0.00 0.00 2.71
275 285 7.041780 GCTCTCTTTTCTCACTGACAAATGTTA 60.042 37.037 0.00 0.00 0.00 2.41
276 286 8.142994 TCTCTTTTCTCACTGACAAATGTTAC 57.857 34.615 0.00 0.00 0.00 2.50
277 287 7.768582 TCTCTTTTCTCACTGACAAATGTTACA 59.231 33.333 0.00 0.00 0.00 2.41
278 288 8.450578 TCTTTTCTCACTGACAAATGTTACAT 57.549 30.769 0.00 0.00 0.00 2.29
296 331 8.267620 TGTTACATTGTCAATCTTGGTGATAG 57.732 34.615 0.00 0.00 34.45 2.08
309 344 1.005340 GTGATAGCTGACACTGCTGC 58.995 55.000 14.81 0.00 38.96 5.25
319 354 0.962356 ACACTGCTGCCATACTTGCC 60.962 55.000 0.00 0.00 0.00 4.52
334 369 0.908910 TTGCCGTATGGTCCATGACT 59.091 50.000 15.10 0.00 37.67 3.41
346 381 6.499106 TGGTCCATGACTATATGTGAACAT 57.501 37.500 0.00 0.95 35.26 2.71
363 398 9.643693 ATGTGAACATTCCAATTTATTGTTCTC 57.356 29.630 17.63 15.68 44.00 2.87
657 694 1.826385 CCACAAGAGTCATCCCCAAC 58.174 55.000 0.00 0.00 0.00 3.77
857 912 4.343814 TGATAAGCATGTTGACCCTATCGA 59.656 41.667 0.00 0.00 0.00 3.59
1208 3725 8.721019 AATTGACACCATTATGCAAAATAAGG 57.279 30.769 0.00 0.00 0.00 2.69
1280 3802 3.371591 CAGAATGCTGAGCAGAAGAAGAC 59.628 47.826 14.36 0.00 45.17 3.01
1289 3813 1.801178 GCAGAAGAAGACGAAACCCTG 59.199 52.381 0.00 0.00 0.00 4.45
1486 4012 1.320344 TGGTCCTCAACGATCTCCCG 61.320 60.000 0.00 0.00 0.00 5.14
1493 4019 0.530744 CAACGATCTCCCGGAGAACA 59.469 55.000 21.20 0.00 42.27 3.18
1504 4030 2.285083 CCGGAGAACAACTTCAACACA 58.715 47.619 0.00 0.00 0.00 3.72
1518 4044 4.994317 TCAACACAGTGGTGAAGAGCCG 62.994 54.545 19.47 0.00 41.82 5.52
1520 4046 1.837051 ACAGTGGTGAAGAGCCGGA 60.837 57.895 5.05 0.00 0.00 5.14
1553 4081 4.022935 GTCAAAGCAATGATCCTGTTGTCA 60.023 41.667 0.00 0.00 0.00 3.58
1599 4130 0.731417 TACGAGCGGCTCTTCACTAC 59.269 55.000 25.96 0.00 0.00 2.73
1623 4154 4.039488 TGAATCCTTGCATCTTGTTTGCTT 59.961 37.500 0.00 0.00 40.77 3.91
1634 4165 3.888323 TCTTGTTTGCTTGTCCAATAGCA 59.112 39.130 0.00 0.00 45.06 3.49
1667 4198 5.305585 TCTCAAAGGTGTGAGTTTGATACC 58.694 41.667 2.38 0.00 44.56 2.73
1675 4207 6.013725 AGGTGTGAGTTTGATACCACTTGATA 60.014 38.462 0.00 0.00 33.88 2.15
1702 4236 3.885724 TCCACTGCATTACTCATCGAA 57.114 42.857 0.00 0.00 0.00 3.71
1716 4251 6.992063 ACTCATCGAATCTGTAAGCAAAAT 57.008 33.333 0.00 0.00 0.00 1.82
1720 4255 7.466805 TCATCGAATCTGTAAGCAAAATCTTG 58.533 34.615 0.00 0.00 35.49 3.02
1933 4470 0.379669 GGAGGCGTTCTGATGCAATG 59.620 55.000 0.00 0.00 39.63 2.82
2011 4549 5.510861 GGTCTCAGAGGTAAACTGCTTTACA 60.511 44.000 9.90 0.00 42.52 2.41
2016 4554 7.903145 TCAGAGGTAAACTGCTTTACATTCTA 58.097 34.615 9.90 2.05 42.52 2.10
2096 4745 6.831353 TGGTTATATTAACAGGGTGTGATTGG 59.169 38.462 0.38 0.00 0.00 3.16
2177 4826 2.268762 GAGATCATCCAAGAAGGGGC 57.731 55.000 0.00 0.00 38.24 5.80
2381 5037 1.963338 GCTTGCAAGAGGAGCGTGT 60.963 57.895 30.39 0.00 33.85 4.49
2480 5138 8.791327 TTTGATGATAGTGAACAGATGCTTTA 57.209 30.769 0.00 0.00 0.00 1.85
2530 5189 6.532988 TTATGTAAACTAAAACCCATGGCC 57.467 37.500 6.09 0.00 0.00 5.36
2719 5415 3.370978 AGTGATGCTGGTTTTATCGTTCG 59.629 43.478 0.00 0.00 0.00 3.95
2720 5416 3.124636 GTGATGCTGGTTTTATCGTTCGT 59.875 43.478 0.00 0.00 0.00 3.85
2758 5454 4.894114 ACTACTGGTGTGTGAGTTCTTAGT 59.106 41.667 0.00 0.00 0.00 2.24
2796 5492 4.153958 TGGCATGACATGTTCGTAAAAC 57.846 40.909 16.62 0.00 0.00 2.43
2911 5632 8.517878 AGTTGAGTTTTGATATTGATGTTCTGG 58.482 33.333 0.00 0.00 0.00 3.86
2948 5669 7.881775 AATTCCCTTCTGTTCATATGGTAAC 57.118 36.000 2.13 1.64 0.00 2.50
2974 5695 5.997746 TGAAAAACACAATAGGACTCCTCAG 59.002 40.000 0.00 0.00 34.61 3.35
2977 5698 5.923733 AACACAATAGGACTCCTCAGTAG 57.076 43.478 0.00 0.00 34.61 2.57
2978 5699 4.936802 ACACAATAGGACTCCTCAGTAGT 58.063 43.478 0.00 0.00 34.61 2.73
2979 5700 6.075949 ACACAATAGGACTCCTCAGTAGTA 57.924 41.667 0.00 0.00 34.61 1.82
2980 5701 5.887035 ACACAATAGGACTCCTCAGTAGTAC 59.113 44.000 0.00 0.00 34.61 2.73
2981 5702 6.123651 CACAATAGGACTCCTCAGTAGTACT 58.876 44.000 0.00 0.00 41.19 2.73
2982 5703 6.261381 CACAATAGGACTCCTCAGTAGTACTC 59.739 46.154 0.00 0.00 39.02 2.59
2983 5704 3.937778 AGGACTCCTCAGTAGTACTCC 57.062 52.381 0.00 0.00 32.39 3.85
2984 5705 2.510800 AGGACTCCTCAGTAGTACTCCC 59.489 54.545 0.00 0.00 32.39 4.30
2985 5706 2.510800 GGACTCCTCAGTAGTACTCCCT 59.489 54.545 0.00 0.00 30.63 4.20
2986 5707 3.434024 GGACTCCTCAGTAGTACTCCCTC 60.434 56.522 0.00 0.00 30.63 4.30
2987 5708 3.457012 GACTCCTCAGTAGTACTCCCTCT 59.543 52.174 0.00 0.00 30.63 3.69
2988 5709 3.201266 ACTCCTCAGTAGTACTCCCTCTG 59.799 52.174 0.00 4.92 0.00 3.35
2989 5710 3.191273 TCCTCAGTAGTACTCCCTCTGT 58.809 50.000 0.00 0.00 0.00 3.41
2990 5711 3.200385 TCCTCAGTAGTACTCCCTCTGTC 59.800 52.174 0.00 0.00 0.00 3.51
2991 5712 3.547746 CTCAGTAGTACTCCCTCTGTCC 58.452 54.545 0.00 0.00 0.00 4.02
2992 5713 2.241685 TCAGTAGTACTCCCTCTGTCCC 59.758 54.545 0.00 0.00 0.00 4.46
2993 5714 2.025226 CAGTAGTACTCCCTCTGTCCCA 60.025 54.545 0.00 0.00 0.00 4.37
2994 5715 2.653366 AGTAGTACTCCCTCTGTCCCAA 59.347 50.000 0.00 0.00 0.00 4.12
2995 5716 2.715763 AGTACTCCCTCTGTCCCAAA 57.284 50.000 0.00 0.00 0.00 3.28
2996 5717 2.986050 AGTACTCCCTCTGTCCCAAAA 58.014 47.619 0.00 0.00 0.00 2.44
2997 5718 3.532102 AGTACTCCCTCTGTCCCAAAAT 58.468 45.455 0.00 0.00 0.00 1.82
2998 5719 4.695606 AGTACTCCCTCTGTCCCAAAATA 58.304 43.478 0.00 0.00 0.00 1.40
2999 5720 5.098663 AGTACTCCCTCTGTCCCAAAATAA 58.901 41.667 0.00 0.00 0.00 1.40
3000 5721 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
3001 5722 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
3002 5723 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
3003 5724 3.913799 TCCCTCTGTCCCAAAATAAGTGA 59.086 43.478 0.00 0.00 0.00 3.41
3004 5725 4.010349 CCCTCTGTCCCAAAATAAGTGAC 58.990 47.826 0.00 0.00 0.00 3.67
3005 5726 4.263506 CCCTCTGTCCCAAAATAAGTGACT 60.264 45.833 0.00 0.00 0.00 3.41
3006 5727 4.938226 CCTCTGTCCCAAAATAAGTGACTC 59.062 45.833 0.00 0.00 0.00 3.36
3007 5728 5.513094 CCTCTGTCCCAAAATAAGTGACTCA 60.513 44.000 0.00 0.00 0.00 3.41
3008 5729 5.935945 TCTGTCCCAAAATAAGTGACTCAA 58.064 37.500 0.00 0.00 0.00 3.02
3009 5730 5.763204 TCTGTCCCAAAATAAGTGACTCAAC 59.237 40.000 0.00 0.00 0.00 3.18
3010 5731 5.690865 TGTCCCAAAATAAGTGACTCAACT 58.309 37.500 0.00 0.00 0.00 3.16
3011 5732 6.126409 TGTCCCAAAATAAGTGACTCAACTT 58.874 36.000 0.00 0.00 42.89 2.66
3012 5733 6.605594 TGTCCCAAAATAAGTGACTCAACTTT 59.394 34.615 0.00 0.00 40.77 2.66
3013 5734 6.918022 GTCCCAAAATAAGTGACTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
3014 5735 6.605594 TCCCAAAATAAGTGACTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
3015 5736 7.776030 TCCCAAAATAAGTGACTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
3016 5737 7.860872 CCCAAAATAAGTGACTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
3017 5738 8.621286 CCAAAATAAGTGACTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
3052 5773 8.934023 ATAAAGTTGAGTCACTTATTTTGGGA 57.066 30.769 0.00 0.00 35.87 4.37
3053 5774 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
3054 5775 4.755123 AGTTGAGTCACTTATTTTGGGACG 59.245 41.667 0.00 0.00 33.84 4.79
3055 5776 3.670625 TGAGTCACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 33.84 4.79
3056 5777 3.325425 TGAGTCACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 33.84 4.69
3057 5778 3.933332 GAGTCACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 33.84 4.63
3058 5779 3.007635 GTCACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
3059 5780 2.026636 TCACTTATTTTGGGACGGAGGG 60.027 50.000 0.00 0.00 0.00 4.30
3060 5781 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
3066 5787 0.178926 TTGGGACGGAGGGAGTACAA 60.179 55.000 0.00 0.00 0.00 2.41
3086 5807 3.641434 AAACATGCCATCTCTAGCAGT 57.359 42.857 0.00 0.00 43.38 4.40
3125 5860 1.045407 AAACTGCCAGACCGTCAGTA 58.955 50.000 0.00 0.00 39.86 2.74
3139 5874 3.181489 CCGTCAGTAATAGGTCAGTCCAC 60.181 52.174 0.00 0.00 39.02 4.02
3148 5883 1.557269 GGTCAGTCCACCAGAGGCAT 61.557 60.000 0.00 0.00 36.32 4.40
3155 5890 1.308069 CCACCAGAGGCATTTGACCG 61.308 60.000 0.00 0.00 0.00 4.79
3158 5893 1.089920 CCAGAGGCATTTGACCGAAG 58.910 55.000 0.00 0.00 0.00 3.79
3159 5894 0.449388 CAGAGGCATTTGACCGAAGC 59.551 55.000 0.00 0.00 0.00 3.86
3160 5895 0.036732 AGAGGCATTTGACCGAAGCA 59.963 50.000 0.00 0.00 0.00 3.91
3161 5896 0.881118 GAGGCATTTGACCGAAGCAA 59.119 50.000 0.00 0.00 0.00 3.91
3200 5942 8.409358 AGCACTCCAGTTTATTGTTCTTATTT 57.591 30.769 0.00 0.00 0.00 1.40
3235 5977 7.285172 TCATGGTGCTTGTGTTAATGCTAATAT 59.715 33.333 0.00 0.00 0.00 1.28
3295 6043 9.829507 CTGGAAATTCAGTTAGTATCTGATTCT 57.170 33.333 16.76 0.00 40.83 2.40
3303 6051 8.791675 TCAGTTAGTATCTGATTCTATGCTCAG 58.208 37.037 6.81 0.00 40.20 3.35
3306 6054 8.735315 GTTAGTATCTGATTCTATGCTCAGCTA 58.265 37.037 0.00 0.00 38.99 3.32
3327 6075 6.914259 GCTAGAAGAGCCAACAAAATTTAGT 58.086 36.000 0.00 0.00 46.41 2.24
3328 6076 7.371159 GCTAGAAGAGCCAACAAAATTTAGTT 58.629 34.615 0.00 0.00 46.41 2.24
3412 6160 2.229784 CCTTTCAAGTTGCTGGCCTTAG 59.770 50.000 3.32 0.00 0.00 2.18
3416 6164 1.740025 CAAGTTGCTGGCCTTAGTAGC 59.260 52.381 3.32 4.36 37.93 3.58
3422 6170 1.139853 GCTGGCCTTAGTAGCAGTGAT 59.860 52.381 3.32 0.00 37.40 3.06
3423 6171 2.365617 GCTGGCCTTAGTAGCAGTGATA 59.634 50.000 3.32 0.00 37.40 2.15
3424 6172 3.553922 GCTGGCCTTAGTAGCAGTGATAG 60.554 52.174 3.32 0.00 37.40 2.08
3425 6173 3.891977 CTGGCCTTAGTAGCAGTGATAGA 59.108 47.826 3.32 0.00 0.00 1.98
3426 6174 4.483950 TGGCCTTAGTAGCAGTGATAGAT 58.516 43.478 3.32 0.00 0.00 1.98
3427 6175 5.641155 TGGCCTTAGTAGCAGTGATAGATA 58.359 41.667 3.32 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 3.428180 GCCACACATACACACACACAAAA 60.428 43.478 0.00 0.00 0.00 2.44
57 58 1.304254 TGCCACACATACACACACAC 58.696 50.000 0.00 0.00 0.00 3.82
59 60 3.112580 GTTTTGCCACACATACACACAC 58.887 45.455 0.00 0.00 0.00 3.82
61 62 3.181491 ACTGTTTTGCCACACATACACAC 60.181 43.478 0.00 0.00 0.00 3.82
62 63 3.020274 ACTGTTTTGCCACACATACACA 58.980 40.909 0.00 0.00 0.00 3.72
63 64 3.708563 ACTGTTTTGCCACACATACAC 57.291 42.857 0.00 0.00 0.00 2.90
64 65 3.445450 ACAACTGTTTTGCCACACATACA 59.555 39.130 0.00 0.00 0.00 2.29
65 66 4.040445 ACAACTGTTTTGCCACACATAC 57.960 40.909 0.00 0.00 0.00 2.39
66 67 5.125578 TGTTACAACTGTTTTGCCACACATA 59.874 36.000 0.00 0.00 0.00 2.29
67 68 4.081972 TGTTACAACTGTTTTGCCACACAT 60.082 37.500 0.00 0.00 0.00 3.21
68 69 3.255888 TGTTACAACTGTTTTGCCACACA 59.744 39.130 0.00 0.00 0.00 3.72
69 70 3.839293 TGTTACAACTGTTTTGCCACAC 58.161 40.909 0.00 0.00 0.00 3.82
109 119 3.542969 TCCCAATCTCCTGATCGGATA 57.457 47.619 2.08 0.00 42.12 2.59
110 120 2.405618 TCCCAATCTCCTGATCGGAT 57.594 50.000 2.08 0.00 42.12 4.18
111 121 2.174685 TTCCCAATCTCCTGATCGGA 57.825 50.000 2.08 4.61 40.30 4.55
112 122 3.498774 AATTCCCAATCTCCTGATCGG 57.501 47.619 0.00 0.00 31.51 4.18
113 123 5.221521 TGTCTAATTCCCAATCTCCTGATCG 60.222 44.000 0.00 0.00 31.51 3.69
114 124 5.994668 GTGTCTAATTCCCAATCTCCTGATC 59.005 44.000 0.00 0.00 31.51 2.92
115 125 5.429762 TGTGTCTAATTCCCAATCTCCTGAT 59.570 40.000 0.00 0.00 33.70 2.90
116 126 4.782691 TGTGTCTAATTCCCAATCTCCTGA 59.217 41.667 0.00 0.00 0.00 3.86
117 127 4.878397 GTGTGTCTAATTCCCAATCTCCTG 59.122 45.833 0.00 0.00 0.00 3.86
132 142 5.353111 TGAAGAATCGTTTGTGTGTGTCTA 58.647 37.500 0.00 0.00 0.00 2.59
146 156 3.686726 CCCTCCAAACTCTTGAAGAATCG 59.313 47.826 0.00 0.00 34.14 3.34
149 159 2.108250 CCCCCTCCAAACTCTTGAAGAA 59.892 50.000 0.00 0.00 34.14 2.52
169 179 5.105310 TCAGTACTGTTTCTGCTCTTATCCC 60.105 44.000 21.99 0.00 0.00 3.85
205 215 3.812053 GTGTCACAATCTCAAGCAGTCTT 59.188 43.478 0.00 0.00 0.00 3.01
274 284 6.539826 CAGCTATCACCAAGATTGACAATGTA 59.460 38.462 5.14 0.00 38.19 2.29
275 285 5.356190 CAGCTATCACCAAGATTGACAATGT 59.644 40.000 5.14 0.00 38.19 2.71
276 286 5.587443 TCAGCTATCACCAAGATTGACAATG 59.413 40.000 5.14 0.00 38.19 2.82
277 287 5.587844 GTCAGCTATCACCAAGATTGACAAT 59.412 40.000 0.00 0.00 39.85 2.71
278 288 4.937620 GTCAGCTATCACCAAGATTGACAA 59.062 41.667 0.00 0.00 39.85 3.18
282 292 4.331992 CAGTGTCAGCTATCACCAAGATTG 59.668 45.833 14.23 4.57 38.19 2.67
296 331 0.392193 AGTATGGCAGCAGTGTCAGC 60.392 55.000 0.00 0.00 43.01 4.26
319 354 6.267496 TCACATATAGTCATGGACCATACG 57.733 41.667 6.67 0.00 32.18 3.06
363 398 5.979517 TGATCACGATGAGCTTTACTGTATG 59.020 40.000 0.00 0.00 33.24 2.39
366 401 4.456280 TGATCACGATGAGCTTTACTGT 57.544 40.909 0.00 0.00 33.24 3.55
525 560 8.382030 TGTTACTGCCAGATATGATATTTGTG 57.618 34.615 0.00 0.00 0.00 3.33
547 582 8.814038 AATTCAGATAAGAATAGCAACCTGTT 57.186 30.769 0.00 0.00 37.24 3.16
1187 3704 6.862209 TGTCCTTATTTTGCATAATGGTGTC 58.138 36.000 12.07 2.24 0.00 3.67
1280 3802 0.447801 CGCTTCAATCCAGGGTTTCG 59.552 55.000 0.00 0.00 0.00 3.46
1289 3813 1.062587 CAACGATGACCGCTTCAATCC 59.937 52.381 0.00 0.00 43.32 3.01
1469 3993 1.035932 TCCGGGAGATCGTTGAGGAC 61.036 60.000 0.00 0.00 0.00 3.85
1486 4012 3.065371 CCACTGTGTTGAAGTTGTTCTCC 59.935 47.826 7.08 0.00 33.38 3.71
1493 4019 3.941483 CTCTTCACCACTGTGTTGAAGTT 59.059 43.478 32.97 0.33 43.26 2.66
1504 4030 0.904865 TGATCCGGCTCTTCACCACT 60.905 55.000 6.88 0.00 0.00 4.00
1518 4044 1.696832 GCTTTGACGGAGCGTGATCC 61.697 60.000 0.00 0.00 41.37 3.36
1520 4046 0.602638 TTGCTTTGACGGAGCGTGAT 60.603 50.000 0.00 0.00 41.37 3.06
1599 4130 3.924686 GCAAACAAGATGCAAGGATTCAG 59.075 43.478 0.00 0.00 43.29 3.02
1634 4165 1.822990 CACCTTTGAGAGCCAATGCAT 59.177 47.619 0.00 0.00 41.13 3.96
1675 4207 5.363562 TGAGTAATGCAGTGGATTGATCT 57.636 39.130 19.11 13.73 0.00 2.75
1702 4236 7.611467 TGTATGGACAAGATTTTGCTTACAGAT 59.389 33.333 0.00 0.00 37.85 2.90
1716 4251 1.833630 CTGGAGCCTGTATGGACAAGA 59.166 52.381 0.00 0.00 38.35 3.02
1720 4255 2.111384 TCTTCTGGAGCCTGTATGGAC 58.889 52.381 0.00 0.00 38.35 4.02
1933 4470 9.832445 TCTAATATGTAAGAGAATTTGGTGGTC 57.168 33.333 0.00 0.00 0.00 4.02
2011 4549 8.715998 CGCAAAAGATACATGCTAGAATAGAAT 58.284 33.333 0.00 0.00 42.77 2.40
2016 4554 6.128715 CGATCGCAAAAGATACATGCTAGAAT 60.129 38.462 0.26 0.00 37.92 2.40
2096 4745 9.868389 CATAAAAGGAATCAAACTTTTCTTTGC 57.132 29.630 5.76 0.00 43.58 3.68
2174 4823 1.478631 CCTGATTGAAAAGGAGGCCC 58.521 55.000 0.00 0.00 35.40 5.80
2177 4826 4.205587 CATCTCCCTGATTGAAAAGGAGG 58.794 47.826 4.63 0.00 43.61 4.30
2312 4962 4.097437 CAGTCCTCACAAATTCATCCATGG 59.903 45.833 4.97 4.97 0.00 3.66
2381 5037 5.307976 ACCAGCATAGCATAAGGACATCTAA 59.692 40.000 0.00 0.00 0.00 2.10
2480 5138 1.002315 GGCACACAATTGGCCTCAAAT 59.998 47.619 14.80 0.00 44.32 2.32
2530 5189 5.471456 AGAGTGTTGATTACCTTCAAAGCAG 59.529 40.000 0.00 0.00 37.36 4.24
2595 5255 2.481289 TCATGACCGTGTGCCATTAA 57.519 45.000 0.00 0.00 0.00 1.40
2720 5416 1.893137 AGTAGTCGTGTCATGCCTTGA 59.107 47.619 0.00 0.00 0.00 3.02
2737 5433 5.864418 AACTAAGAACTCACACACCAGTA 57.136 39.130 0.00 0.00 0.00 2.74
2758 5454 4.299586 TGCCATGGTTGAGAGATACAAA 57.700 40.909 14.67 0.00 0.00 2.83
2831 5551 8.437742 CACTTGGCAATGATAACTGAAATTTTC 58.562 33.333 0.00 2.05 0.00 2.29
2841 5561 8.532977 AAATACAAACACTTGGCAATGATAAC 57.467 30.769 0.00 0.00 36.82 1.89
2892 5613 6.947733 ACCTCACCAGAACATCAATATCAAAA 59.052 34.615 0.00 0.00 0.00 2.44
2911 5632 6.126739 ACAGAAGGGAATTTCCTATACCTCAC 60.127 42.308 5.46 2.71 36.57 3.51
2948 5669 6.486657 TGAGGAGTCCTATTGTGTTTTTCAAG 59.513 38.462 12.99 0.00 31.76 3.02
2974 5695 2.822707 TGGGACAGAGGGAGTACTAC 57.177 55.000 0.00 0.00 0.00 2.73
2977 5698 5.045797 ACTTATTTTGGGACAGAGGGAGTAC 60.046 44.000 0.00 0.00 42.39 2.73
2978 5699 5.045869 CACTTATTTTGGGACAGAGGGAGTA 60.046 44.000 0.00 0.00 42.39 2.59
2979 5700 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
2980 5701 4.019321 TCACTTATTTTGGGACAGAGGGAG 60.019 45.833 0.00 0.00 42.39 4.30
2981 5702 3.913799 TCACTTATTTTGGGACAGAGGGA 59.086 43.478 0.00 0.00 42.39 4.20
2982 5703 4.010349 GTCACTTATTTTGGGACAGAGGG 58.990 47.826 0.00 0.00 42.39 4.30
2983 5704 4.911390 AGTCACTTATTTTGGGACAGAGG 58.089 43.478 0.00 0.00 42.39 3.69
2984 5705 5.551233 TGAGTCACTTATTTTGGGACAGAG 58.449 41.667 0.00 0.00 42.39 3.35
2985 5706 5.560722 TGAGTCACTTATTTTGGGACAGA 57.439 39.130 0.00 0.00 42.39 3.41
2986 5707 5.765182 AGTTGAGTCACTTATTTTGGGACAG 59.235 40.000 0.00 0.00 42.39 3.51
2987 5708 5.690865 AGTTGAGTCACTTATTTTGGGACA 58.309 37.500 0.00 0.00 0.00 4.02
2988 5709 6.635030 AAGTTGAGTCACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
2989 5710 6.605594 ACAAAGTTGAGTCACTTATTTTGGGA 59.394 34.615 12.94 0.00 35.87 4.37
2990 5711 6.805713 ACAAAGTTGAGTCACTTATTTTGGG 58.194 36.000 12.94 0.00 35.87 4.12
2991 5712 8.621286 AGTACAAAGTTGAGTCACTTATTTTGG 58.379 33.333 12.94 0.78 35.87 3.28
3027 5748 8.793592 GTCCCAAAATAAGTGACTCAACTTTAT 58.206 33.333 0.00 0.00 40.77 1.40
3028 5749 7.041644 CGTCCCAAAATAAGTGACTCAACTTTA 60.042 37.037 0.00 0.00 40.77 1.85
3029 5750 6.238648 CGTCCCAAAATAAGTGACTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
3030 5751 5.238650 CGTCCCAAAATAAGTGACTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
3031 5752 4.755123 CGTCCCAAAATAAGTGACTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
3032 5753 4.083484 CCGTCCCAAAATAAGTGACTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
3033 5754 4.069304 CCGTCCCAAAATAAGTGACTCAA 58.931 43.478 0.00 0.00 0.00 3.02
3034 5755 3.325425 TCCGTCCCAAAATAAGTGACTCA 59.675 43.478 0.00 0.00 0.00 3.41
3035 5756 3.933332 CTCCGTCCCAAAATAAGTGACTC 59.067 47.826 0.00 0.00 0.00 3.36
3036 5757 3.307480 CCTCCGTCCCAAAATAAGTGACT 60.307 47.826 0.00 0.00 0.00 3.41
3037 5758 3.007635 CCTCCGTCCCAAAATAAGTGAC 58.992 50.000 0.00 0.00 0.00 3.67
3038 5759 2.026636 CCCTCCGTCCCAAAATAAGTGA 60.027 50.000 0.00 0.00 0.00 3.41
3039 5760 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
3040 5761 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
3041 5762 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
3042 5763 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
3043 5764 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
3044 5765 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
3045 5766 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
3046 5767 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
3047 5768 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
3048 5769 0.178926 TTTGTACTCCCTCCGTCCCA 60.179 55.000 0.00 0.00 0.00 4.37
3049 5770 0.978907 TTTTGTACTCCCTCCGTCCC 59.021 55.000 0.00 0.00 0.00 4.46
3050 5771 1.345415 TGTTTTGTACTCCCTCCGTCC 59.655 52.381 0.00 0.00 0.00 4.79
3051 5772 2.825861 TGTTTTGTACTCCCTCCGTC 57.174 50.000 0.00 0.00 0.00 4.79
3052 5773 2.874457 GCATGTTTTGTACTCCCTCCGT 60.874 50.000 0.00 0.00 0.00 4.69
3053 5774 1.737793 GCATGTTTTGTACTCCCTCCG 59.262 52.381 0.00 0.00 0.00 4.63
3054 5775 2.092323 GGCATGTTTTGTACTCCCTCC 58.908 52.381 0.00 0.00 0.00 4.30
3055 5776 2.790433 TGGCATGTTTTGTACTCCCTC 58.210 47.619 0.00 0.00 0.00 4.30
3056 5777 2.969821 TGGCATGTTTTGTACTCCCT 57.030 45.000 0.00 0.00 0.00 4.20
3057 5778 3.356290 AGATGGCATGTTTTGTACTCCC 58.644 45.455 3.81 0.00 0.00 4.30
3058 5779 4.265073 AGAGATGGCATGTTTTGTACTCC 58.735 43.478 3.81 0.00 0.00 3.85
3059 5780 5.007136 GCTAGAGATGGCATGTTTTGTACTC 59.993 44.000 3.81 2.33 0.00 2.59
3060 5781 4.878397 GCTAGAGATGGCATGTTTTGTACT 59.122 41.667 3.81 0.00 0.00 2.73
3066 5787 3.641434 ACTGCTAGAGATGGCATGTTT 57.359 42.857 3.81 0.00 37.83 2.83
3095 5816 2.354902 GGCAGTTTTGGCTGATGGT 58.645 52.632 0.00 0.00 45.79 3.55
3103 5824 0.817634 TGACGGTCTGGCAGTTTTGG 60.818 55.000 15.27 3.56 0.00 3.28
3104 5825 0.588252 CTGACGGTCTGGCAGTTTTG 59.412 55.000 15.27 5.87 0.00 2.44
3105 5826 0.180406 ACTGACGGTCTGGCAGTTTT 59.820 50.000 14.93 0.00 39.69 2.43
3106 5827 1.045407 TACTGACGGTCTGGCAGTTT 58.955 50.000 25.28 4.10 42.40 2.66
3125 5860 2.472029 CCTCTGGTGGACTGACCTATT 58.528 52.381 0.00 0.00 39.86 1.73
3139 5874 1.089920 CTTCGGTCAAATGCCTCTGG 58.910 55.000 0.00 0.00 0.00 3.86
3148 5883 2.045561 TGTCCTTTGCTTCGGTCAAA 57.954 45.000 0.00 0.00 33.04 2.69
3155 5890 4.156556 TGCTCACATATTGTCCTTTGCTTC 59.843 41.667 0.00 0.00 0.00 3.86
3158 5893 3.441572 AGTGCTCACATATTGTCCTTTGC 59.558 43.478 2.63 0.00 0.00 3.68
3159 5894 4.095483 GGAGTGCTCACATATTGTCCTTTG 59.905 45.833 2.63 0.00 0.00 2.77
3160 5895 4.263462 TGGAGTGCTCACATATTGTCCTTT 60.263 41.667 2.63 0.00 0.00 3.11
3161 5896 3.264193 TGGAGTGCTCACATATTGTCCTT 59.736 43.478 2.63 0.00 0.00 3.36
3269 6017 9.829507 AGAATCAGATACTAACTGAATTTCCAG 57.170 33.333 0.00 0.00 45.44 3.86
3277 6025 8.697507 TGAGCATAGAATCAGATACTAACTGA 57.302 34.615 0.00 0.00 46.17 3.41
3306 6054 8.860088 ACATAACTAAATTTTGTTGGCTCTTCT 58.140 29.630 22.81 1.75 29.11 2.85
3326 6074 9.277783 ACTAGCAGGATTGATATTTGACATAAC 57.722 33.333 0.00 0.00 0.00 1.89
3327 6075 9.851686 AACTAGCAGGATTGATATTTGACATAA 57.148 29.630 0.00 0.00 0.00 1.90
3328 6076 9.851686 AAACTAGCAGGATTGATATTTGACATA 57.148 29.630 0.00 0.00 0.00 2.29
3340 6088 9.736023 GGATATTTGTTTAAACTAGCAGGATTG 57.264 33.333 18.72 0.00 0.00 2.67
3341 6089 9.700831 AGGATATTTGTTTAAACTAGCAGGATT 57.299 29.630 18.72 0.00 0.00 3.01
3344 6092 8.738645 AGAGGATATTTGTTTAAACTAGCAGG 57.261 34.615 18.72 0.00 0.00 4.85
3372 6120 1.886542 GGCTAAAGTGTCAAACTGGGG 59.113 52.381 0.00 0.00 39.81 4.96


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

AutoCloner maintained by Alex Coulton.