Multiple sequence alignment - TraesCS2B01G486700

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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 TraesCS2B01G486700 chr2B 100.000 5802 0 0 1 5802 683158224 683164025 0.000000e+00 10715.0
1 TraesCS2B01G486700 chr2B 84.583 3360 472 19 1536 4855 683128403 683131756 0.000000e+00 3293.0
2 TraesCS2B01G486700 chr2B 83.753 3336 491 28 1536 4855 683067888 683071188 0.000000e+00 3110.0
3 TraesCS2B01G486700 chr2B 85.297 2979 371 32 1545 4481 794694186 794691233 0.000000e+00 3013.0
4 TraesCS2B01G486700 chr2B 85.297 2979 371 32 1545 4481 794803087 794800134 0.000000e+00 3013.0
5 TraesCS2B01G486700 chr2B 84.012 2896 414 31 1536 4408 683043178 683046047 0.000000e+00 2737.0
6 TraesCS2B01G486700 chr2B 84.941 1793 268 2 1536 3327 683054291 683056082 0.000000e+00 1814.0
7 TraesCS2B01G486700 chr2B 81.019 569 89 10 789 1346 683067195 683067755 8.930000e-118 435.0
8 TraesCS2B01G486700 chr2B 79.595 593 105 11 789 1372 683127651 683128236 1.500000e-110 411.0
9 TraesCS2B01G486700 chr2B 79.365 630 91 25 690 1309 683042411 683043011 1.950000e-109 407.0
10 TraesCS2B01G486700 chr2B 84.541 414 53 8 950 1358 683053768 683054175 3.260000e-107 399.0
11 TraesCS2B01G486700 chr2B 73.836 623 111 36 4871 5456 683133160 683133767 3.550000e-47 200.0
12 TraesCS2B01G486700 chr2D 95.327 5842 192 25 1 5802 571441886 571447686 0.000000e+00 9201.0
13 TraesCS2B01G486700 chr2D 84.088 3337 481 29 1536 4855 571209195 571212498 0.000000e+00 3175.0
14 TraesCS2B01G486700 chr2D 84.605 1494 207 12 3346 4819 571529043 571530533 0.000000e+00 1463.0
15 TraesCS2B01G486700 chr2D 78.796 731 121 23 645 1370 571526330 571527031 1.470000e-125 460.0
16 TraesCS2B01G486700 chr2D 83.841 427 60 6 950 1370 571208675 571209098 1.170000e-106 398.0
17 TraesCS2B01G486700 chr2D 96.774 62 2 0 1380 1441 529000522 529000583 2.860000e-18 104.0
18 TraesCS2B01G486700 chr2A 85.019 3351 436 32 1544 4855 710206333 710209656 0.000000e+00 3347.0
19 TraesCS2B01G486700 chr2A 84.218 3333 477 30 1536 4855 710093265 710096561 0.000000e+00 3195.0
20 TraesCS2B01G486700 chr2A 84.097 3339 477 30 1536 4855 710036409 710039712 0.000000e+00 3175.0
21 TraesCS2B01G486700 chr2A 85.827 2907 358 26 1544 4408 710188159 710191053 0.000000e+00 3037.0
22 TraesCS2B01G486700 chr2A 85.323 402 51 4 950 1346 710035889 710036287 5.410000e-110 409.0
23 TraesCS2B01G486700 chr2A 80.695 518 71 16 870 1370 710205407 710205912 5.490000e-100 375.0
24 TraesCS2B01G486700 chr6A 85.225 2044 250 28 2811 4812 617078172 617080205 0.000000e+00 2054.0
25 TraesCS2B01G486700 chrUn 85.654 1415 172 17 3349 4746 307300441 307301841 0.000000e+00 1459.0
26 TraesCS2B01G486700 chr3B 98.387 62 1 0 1380 1441 779543998 779543937 6.150000e-20 110.0
27 TraesCS2B01G486700 chr1A 96.721 61 2 0 1381 1441 6159359 6159419 1.030000e-17 102.0
28 TraesCS2B01G486700 chr3A 96.667 60 2 0 1382 1441 262226893 262226952 3.700000e-17 100.0
29 TraesCS2B01G486700 chr3A 91.667 72 3 3 1381 1451 724015727 724015796 4.790000e-16 97.1
30 TraesCS2B01G486700 chr3D 93.939 66 3 1 1376 1441 192151870 192151806 1.330000e-16 99.0
31 TraesCS2B01G486700 chr1D 93.651 63 3 1 1380 1441 391324145 391324207 6.190000e-15 93.5
32 TraesCS2B01G486700 chr6B 86.747 83 9 1 1361 1441 146669540 146669622 2.230000e-14 91.6


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 TraesCS2B01G486700 chr2B 683158224 683164025 5801 False 10715.000000 10715 100.0000 1 5802 1 chr2B.!!$F1 5801
1 TraesCS2B01G486700 chr2B 794691233 794694186 2953 True 3013.000000 3013 85.2970 1545 4481 1 chr2B.!!$R1 2936
2 TraesCS2B01G486700 chr2B 794800134 794803087 2953 True 3013.000000 3013 85.2970 1545 4481 1 chr2B.!!$R2 2936
3 TraesCS2B01G486700 chr2B 683067195 683071188 3993 False 1772.500000 3110 82.3860 789 4855 2 chr2B.!!$F4 4066
4 TraesCS2B01G486700 chr2B 683042411 683046047 3636 False 1572.000000 2737 81.6885 690 4408 2 chr2B.!!$F2 3718
5 TraesCS2B01G486700 chr2B 683127651 683133767 6116 False 1301.333333 3293 79.3380 789 5456 3 chr2B.!!$F5 4667
6 TraesCS2B01G486700 chr2B 683053768 683056082 2314 False 1106.500000 1814 84.7410 950 3327 2 chr2B.!!$F3 2377
7 TraesCS2B01G486700 chr2D 571441886 571447686 5800 False 9201.000000 9201 95.3270 1 5802 1 chr2D.!!$F2 5801
8 TraesCS2B01G486700 chr2D 571208675 571212498 3823 False 1786.500000 3175 83.9645 950 4855 2 chr2D.!!$F3 3905
9 TraesCS2B01G486700 chr2D 571526330 571530533 4203 False 961.500000 1463 81.7005 645 4819 2 chr2D.!!$F4 4174
10 TraesCS2B01G486700 chr2A 710093265 710096561 3296 False 3195.000000 3195 84.2180 1536 4855 1 chr2A.!!$F1 3319
11 TraesCS2B01G486700 chr2A 710188159 710191053 2894 False 3037.000000 3037 85.8270 1544 4408 1 chr2A.!!$F2 2864
12 TraesCS2B01G486700 chr2A 710205407 710209656 4249 False 1861.000000 3347 82.8570 870 4855 2 chr2A.!!$F4 3985
13 TraesCS2B01G486700 chr2A 710035889 710039712 3823 False 1792.000000 3175 84.7100 950 4855 2 chr2A.!!$F3 3905
14 TraesCS2B01G486700 chr6A 617078172 617080205 2033 False 2054.000000 2054 85.2250 2811 4812 1 chr6A.!!$F1 2001
15 TraesCS2B01G486700 chrUn 307300441 307301841 1400 False 1459.000000 1459 85.6540 3349 4746 1 chrUn.!!$F1 1397

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
126 128 0.108329 ACGTTGTATCCTTCGCCAGG 60.108 55.000 0.00 0.0 45.64 4.45 F
148 155 0.251297 CCCCATGTCTGCAGGTCAAA 60.251 55.000 15.13 0.0 0.00 2.69 F
1021 1075 0.534203 GACAGGGTTTCTTGGCACGA 60.534 55.000 0.00 0.0 0.00 4.35 F
1765 2175 1.497722 CGGCAGAAAAAGGAGACGC 59.502 57.895 0.00 0.0 0.00 5.19 F
1968 2378 1.800586 TGCTCGATTGACAACTTCTGC 59.199 47.619 0.00 0.0 0.00 4.26 F
2517 2937 2.229543 TGTTCTTCAAGGCATGTGCATC 59.770 45.455 7.36 0.0 44.36 3.91 F
2784 3205 3.131396 CGTACTGCTCTTTGTTTCCAGT 58.869 45.455 0.00 0.0 39.76 4.00 F
4051 4505 4.425772 TGGAGTTGACTTCCCATCTAAGA 58.574 43.478 0.00 0.0 0.00 2.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2022 2432 0.033208 TCCCCCATTCATCAACAGCC 60.033 55.000 0.00 0.00 0.00 4.85 R
2186 2599 3.450457 AGGATCTCAAGTGTTAGCCTCAG 59.550 47.826 0.00 0.00 0.00 3.35 R
2593 3013 0.038251 CACTTCGTGCAGCTAGTGGA 60.038 55.000 12.08 0.00 35.51 4.02 R
2802 3223 0.040058 AGCATGGACCAATTGCTCCA 59.960 50.000 21.92 21.92 42.88 3.86 R
3486 3940 1.067364 TCATGTTGCCAACACAAGCTG 59.933 47.619 13.33 7.09 45.50 4.24 R
4104 4558 2.232941 TCAGCGTCGAAAGAAGGGTAAT 59.767 45.455 0.00 0.00 45.01 1.89 R
4787 5261 7.375053 TGGAAAACCTCTTACATAATGTTTGC 58.625 34.615 0.00 0.00 0.00 3.68 R
5228 7105 0.538287 AGCAAAGAAGAGGGTGTGGC 60.538 55.000 0.00 0.00 0.00 5.01 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
19 20 0.395311 ACCTGCTCATCTTGCCCATG 60.395 55.000 0.00 0.00 0.00 3.66
50 51 1.573829 GCGTCCCATGCTCGTTTCAA 61.574 55.000 0.00 0.00 0.00 2.69
53 54 2.695359 GTCCCATGCTCGTTTCAACTA 58.305 47.619 0.00 0.00 0.00 2.24
67 68 0.530744 CAACTACGAGCTGGCTGGTA 59.469 55.000 14.68 14.68 36.44 3.25
70 71 2.490165 TACGAGCTGGCTGGTAGAC 58.510 57.895 12.18 0.00 36.44 2.59
93 95 3.496870 CCACAGGTAAAAGAGCCTCTTGT 60.497 47.826 7.93 4.87 36.71 3.16
113 115 1.952990 TGATTTGGCATCACACGTTGT 59.047 42.857 0.00 0.00 0.00 3.32
114 116 3.058570 GTGATTTGGCATCACACGTTGTA 60.059 43.478 14.69 0.00 45.61 2.41
126 128 0.108329 ACGTTGTATCCTTCGCCAGG 60.108 55.000 0.00 0.00 45.64 4.45
129 131 2.007608 GTTGTATCCTTCGCCAGGTTC 58.992 52.381 0.85 0.00 44.37 3.62
132 139 1.342672 TATCCTTCGCCAGGTTCCCC 61.343 60.000 0.85 0.00 44.37 4.81
136 143 2.484287 CTTCGCCAGGTTCCCCATGT 62.484 60.000 0.00 0.00 0.00 3.21
140 147 1.379044 CCAGGTTCCCCATGTCTGC 60.379 63.158 0.00 0.00 0.00 4.26
143 150 1.379044 GGTTCCCCATGTCTGCAGG 60.379 63.158 15.13 0.00 0.00 4.85
148 155 0.251297 CCCCATGTCTGCAGGTCAAA 60.251 55.000 15.13 0.00 0.00 2.69
165 172 6.207417 CAGGTCAAAGTTGTCTGGTTATGATT 59.793 38.462 8.32 0.00 31.90 2.57
167 174 7.040409 AGGTCAAAGTTGTCTGGTTATGATTTC 60.040 37.037 0.00 0.00 0.00 2.17
168 175 7.084486 GTCAAAGTTGTCTGGTTATGATTTCC 58.916 38.462 0.00 0.00 0.00 3.13
169 176 7.004086 TCAAAGTTGTCTGGTTATGATTTCCT 58.996 34.615 0.00 0.00 0.00 3.36
170 177 8.160765 TCAAAGTTGTCTGGTTATGATTTCCTA 58.839 33.333 0.00 0.00 0.00 2.94
171 178 7.923414 AAGTTGTCTGGTTATGATTTCCTAC 57.077 36.000 0.00 0.00 0.00 3.18
172 179 7.259088 AGTTGTCTGGTTATGATTTCCTACT 57.741 36.000 0.00 0.00 0.00 2.57
173 180 7.331791 AGTTGTCTGGTTATGATTTCCTACTC 58.668 38.462 0.00 0.00 0.00 2.59
188 195 3.328343 TCCTACTCCGTTTGGAAATTGGA 59.672 43.478 0.00 0.00 45.87 3.53
195 202 6.926826 ACTCCGTTTGGAAATTGGAAAAATAC 59.073 34.615 0.00 0.00 45.87 1.89
202 209 6.284459 TGGAAATTGGAAAAATACCACACAC 58.716 36.000 0.00 0.00 37.13 3.82
203 210 6.127054 TGGAAATTGGAAAAATACCACACACA 60.127 34.615 0.00 0.00 37.13 3.72
245 252 0.921896 AGGGACACCATCATCCTTGG 59.078 55.000 0.00 0.00 40.13 3.61
256 263 1.416401 TCATCCTTGGAATAGACGCCC 59.584 52.381 0.00 0.00 0.00 6.13
260 267 0.815615 CTTGGAATAGACGCCCCAGC 60.816 60.000 0.00 0.00 0.00 4.85
261 268 1.271840 TTGGAATAGACGCCCCAGCT 61.272 55.000 0.00 0.00 36.60 4.24
313 322 5.483937 TCTCAGAATACTGCTGGAGGTTTTA 59.516 40.000 0.14 0.00 43.17 1.52
361 370 6.027749 GCCAAAATTTGTCGATAGGTACAAG 58.972 40.000 4.92 0.00 36.96 3.16
390 399 8.676401 TGTACATACCAATCAGAAACAATCATG 58.324 33.333 0.00 0.00 0.00 3.07
405 414 5.198207 ACAATCATGCATCTCAATGAGGAA 58.802 37.500 10.71 0.00 34.61 3.36
499 508 2.105993 GTTCTAGGAGGTGGTTTGGTGT 59.894 50.000 0.00 0.00 0.00 4.16
530 539 3.838317 TCTACATATTCCGGGCTGCTATT 59.162 43.478 0.00 0.00 0.00 1.73
545 554 2.225467 GCTATTGGTCCAATGCCTCTC 58.775 52.381 24.85 5.79 35.54 3.20
734 767 1.207329 GAGCTTCCATAGTTCCACGGT 59.793 52.381 0.00 0.00 0.00 4.83
739 772 1.695242 TCCATAGTTCCACGGTTGTGT 59.305 47.619 0.00 0.00 44.92 3.72
764 799 1.103803 CTGCTTTGAGCTGCCATGAT 58.896 50.000 0.00 0.00 42.97 2.45
766 801 0.815734 GCTTTGAGCTGCCATGATGT 59.184 50.000 0.00 0.00 38.45 3.06
823 859 5.432885 TTTGTAAAGTTAGCTGGTTCTGC 57.567 39.130 0.00 0.00 0.00 4.26
826 862 2.938956 AAGTTAGCTGGTTCTGCTGT 57.061 45.000 0.00 0.00 38.96 4.40
827 863 2.175878 AGTTAGCTGGTTCTGCTGTG 57.824 50.000 0.00 0.00 38.96 3.66
829 865 1.532868 GTTAGCTGGTTCTGCTGTGTG 59.467 52.381 0.00 0.00 38.96 3.82
865 905 2.951101 ATTTGCTGCCTGGCTTGCC 61.951 57.895 25.64 4.43 0.00 4.52
882 922 2.300967 CCCTGTGCCTTCCCAGCTA 61.301 63.158 0.00 0.00 0.00 3.32
884 924 1.078143 CTGTGCCTTCCCAGCTACC 60.078 63.158 0.00 0.00 0.00 3.18
915 959 5.678583 GATGAATCATCACTCTCCTTTCCA 58.321 41.667 17.60 0.00 40.28 3.53
922 966 4.982241 TCACTCTCCTTTCCACTGAATT 57.018 40.909 0.00 0.00 0.00 2.17
1021 1075 0.534203 GACAGGGTTTCTTGGCACGA 60.534 55.000 0.00 0.00 0.00 4.35
1071 1125 2.428171 GCAAAGCATCATTGGGAGCTTA 59.572 45.455 10.15 0.00 45.73 3.09
1078 1132 4.340381 GCATCATTGGGAGCTTATTCACTT 59.660 41.667 0.00 0.00 0.00 3.16
1170 1224 2.401766 CGTGGAGATGGTGCTTGCC 61.402 63.158 0.00 0.00 0.00 4.52
1511 1818 9.269453 CAATCAAGAGCAGTTGAATATCATAGA 57.731 33.333 5.00 0.00 39.84 1.98
1586 1990 2.354510 TCTGCTCAAGTGGTTTTCGTTG 59.645 45.455 0.00 0.00 0.00 4.10
1765 2175 1.497722 CGGCAGAAAAAGGAGACGC 59.502 57.895 0.00 0.00 0.00 5.19
1781 2191 3.717294 GCGAAGAGGAGGGGCCAA 61.717 66.667 4.39 0.00 40.02 4.52
1883 2293 2.502142 TGGCAATTCTGTGCAGAGAT 57.498 45.000 15.15 0.00 46.81 2.75
1912 2322 1.899437 TTGAGATCTCACGCCCCACC 61.899 60.000 25.07 0.00 39.66 4.61
1914 2324 4.530857 GATCTCACGCCCCACCGG 62.531 72.222 0.00 0.00 0.00 5.28
1940 2350 8.715191 AACATCAAGTGAGAGTCAGAATATTC 57.285 34.615 7.41 7.41 0.00 1.75
1968 2378 1.800586 TGCTCGATTGACAACTTCTGC 59.199 47.619 0.00 0.00 0.00 4.26
1992 2402 6.381498 TCCAATTGAAGGTAAGGTGTATGA 57.619 37.500 7.12 0.00 0.00 2.15
2022 2432 6.647334 TGCAGAGAGAGACAAGATAATAGG 57.353 41.667 0.00 0.00 0.00 2.57
2032 2442 6.294473 AGACAAGATAATAGGGCTGTTGATG 58.706 40.000 0.00 0.00 0.00 3.07
2288 2708 4.703575 TGCAGGAGATCCTTTTGAAGAATG 59.296 41.667 0.00 0.00 46.09 2.67
2385 2805 6.563422 TCTTGGCTCCATTGAAAAATAATCG 58.437 36.000 0.00 0.00 0.00 3.34
2436 2856 7.365741 ACAACTAGAATGAAATCAGTTGCAAG 58.634 34.615 0.00 0.00 46.34 4.01
2517 2937 2.229543 TGTTCTTCAAGGCATGTGCATC 59.770 45.455 7.36 0.00 44.36 3.91
2593 3013 4.903045 TGCTAAAGTACTAAAGGGCTGT 57.097 40.909 0.00 0.00 0.00 4.40
2784 3205 3.131396 CGTACTGCTCTTTGTTTCCAGT 58.869 45.455 0.00 0.00 39.76 4.00
2950 3371 5.006746 GGTTAGCTCACACTATGTTATGCAC 59.993 44.000 0.00 0.00 0.00 4.57
3087 3508 6.135290 TGCTTTTGATACAGATAACCATGC 57.865 37.500 0.00 0.00 0.00 4.06
3132 3553 5.849510 TGACGAAATACTTCAGAAGGTTCA 58.150 37.500 14.90 3.48 0.00 3.18
3256 3677 5.607119 TTCTAAGAATTTTCGTGACAGGC 57.393 39.130 0.00 0.00 0.00 4.85
3486 3940 8.274259 TCTCATGAGAAAGTGCATCATGCAAC 62.274 42.308 23.17 8.97 44.39 4.17
4051 4505 4.425772 TGGAGTTGACTTCCCATCTAAGA 58.574 43.478 0.00 0.00 0.00 2.10
4104 4558 8.324306 ACTGAATGATATCACTCTTTTCCAGAA 58.676 33.333 14.74 0.00 0.00 3.02
4267 4728 7.101054 ACTTTGATAAATGATGTTGCAGCAAT 58.899 30.769 11.96 0.00 32.21 3.56
4787 5261 1.142465 ACTGCCCTAATCTGAGCATGG 59.858 52.381 0.00 0.00 34.16 3.66
4863 6723 3.775316 GTCCTTCCATCTCTTTGGGTAGA 59.225 47.826 0.00 0.00 37.37 2.59
4985 6853 3.054434 ACATCCTGCAAACCTACATAGCA 60.054 43.478 0.00 0.00 0.00 3.49
5037 6905 2.299993 TGTAAGAGCATCAGAAGGCG 57.700 50.000 0.00 0.00 37.25 5.52
5040 6908 1.908340 AAGAGCATCAGAAGGCGGCT 61.908 55.000 5.25 5.25 37.25 5.52
5041 6909 1.451028 GAGCATCAGAAGGCGGCTT 60.451 57.895 25.83 25.83 37.25 4.35
5165 7037 7.219154 CACTATTGATGACGAGACTGAGTTAAC 59.781 40.741 0.00 0.00 0.00 2.01
5169 7041 3.973657 TGACGAGACTGAGTTAACCAAC 58.026 45.455 0.88 0.00 34.67 3.77
5206 7083 2.107204 ACACTCCTGGAGCATTTTGTCT 59.893 45.455 23.43 0.00 32.04 3.41
5207 7084 3.152341 CACTCCTGGAGCATTTTGTCTT 58.848 45.455 23.43 0.00 32.04 3.01
5228 7105 6.421202 GTCTTTAGTATTTATCAGCACCCTCG 59.579 42.308 0.00 0.00 0.00 4.63
5234 7111 2.238847 TATCAGCACCCTCGCCACAC 62.239 60.000 0.00 0.00 0.00 3.82
5238 7115 4.394712 CACCCTCGCCACACCCTC 62.395 72.222 0.00 0.00 0.00 4.30
5241 7118 2.266055 CCTCGCCACACCCTCTTC 59.734 66.667 0.00 0.00 0.00 2.87
5242 7119 2.286523 CCTCGCCACACCCTCTTCT 61.287 63.158 0.00 0.00 0.00 2.85
5325 7205 1.655484 TGCCATCACTAGCACATTCG 58.345 50.000 0.00 0.00 33.08 3.34
5370 7260 5.235850 TGGTTTTCCACAAGCTACTCATA 57.764 39.130 0.00 0.00 46.22 2.15
5403 7293 2.586425 ACCATGGGTTGAAAGTGACAG 58.414 47.619 18.09 0.00 27.29 3.51
5404 7294 2.174639 ACCATGGGTTGAAAGTGACAGA 59.825 45.455 18.09 0.00 27.29 3.41
5418 7308 5.713822 AGTGACAGACTCGTTTTTGTTAC 57.286 39.130 0.00 0.00 32.23 2.50
5434 7324 0.981183 TTACGAGGGGCATTGTGACT 59.019 50.000 0.00 0.00 0.00 3.41
5456 7346 6.601332 ACTTTTCCCTCATTCTTGTGTCTTA 58.399 36.000 0.00 0.00 0.00 2.10
5467 7357 5.392767 TCTTGTGTCTTATCTGGTCAGTC 57.607 43.478 0.00 0.00 0.00 3.51
5502 7392 0.108567 TGCTATCGCAAGGTACGCAA 60.109 50.000 0.00 0.00 44.62 4.85
5503 7393 1.003851 GCTATCGCAAGGTACGCAAA 58.996 50.000 0.00 0.00 35.78 3.68
5504 7394 1.267383 GCTATCGCAAGGTACGCAAAC 60.267 52.381 0.00 0.00 35.78 2.93
5505 7395 1.996898 CTATCGCAAGGTACGCAAACA 59.003 47.619 0.00 0.00 38.47 2.83
5506 7396 1.231221 ATCGCAAGGTACGCAAACAA 58.769 45.000 0.00 0.00 38.47 2.83
5507 7397 1.015109 TCGCAAGGTACGCAAACAAA 58.985 45.000 0.00 0.00 38.47 2.83
5508 7398 1.604755 TCGCAAGGTACGCAAACAAAT 59.395 42.857 0.00 0.00 38.47 2.32
5509 7399 2.033550 TCGCAAGGTACGCAAACAAATT 59.966 40.909 0.00 0.00 38.47 1.82
5510 7400 2.152868 CGCAAGGTACGCAAACAAATTG 59.847 45.455 0.00 0.00 42.21 2.32
5511 7401 3.120041 GCAAGGTACGCAAACAAATTGT 58.880 40.909 0.00 0.00 41.32 2.71
5512 7402 3.553917 GCAAGGTACGCAAACAAATTGTT 59.446 39.130 5.41 5.41 43.41 2.83
5554 7444 0.588252 CAGTTTTGTCGGTGGCTCAG 59.412 55.000 0.00 0.00 0.00 3.35
5560 7450 2.917227 TCGGTGGCTCAGTGCTCA 60.917 61.111 0.00 0.00 42.39 4.26
5563 7453 0.807667 CGGTGGCTCAGTGCTCATAC 60.808 60.000 0.00 0.00 42.39 2.39
5684 7574 7.365741 CAAATTATGCATCCCATCTTCAGTAC 58.634 38.462 0.19 0.00 35.34 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.076559 CCCATGGGCAAGATGAGCA 60.077 57.895 20.41 0.00 0.00 4.26
34 35 2.695359 GTAGTTGAAACGAGCATGGGA 58.305 47.619 0.00 0.00 0.00 4.37
44 45 1.461127 CAGCCAGCTCGTAGTTGAAAC 59.539 52.381 0.00 0.00 0.00 2.78
50 51 0.034380 TCTACCAGCCAGCTCGTAGT 60.034 55.000 19.52 5.63 38.38 2.73
53 54 2.352032 GGTCTACCAGCCAGCTCGT 61.352 63.158 0.00 0.00 35.64 4.18
67 68 1.351350 GGCTCTTTTACCTGTGGGTCT 59.649 52.381 0.00 0.00 45.98 3.85
70 71 1.630878 AGAGGCTCTTTTACCTGTGGG 59.369 52.381 12.24 0.00 36.05 4.61
83 84 1.538047 TGCCAAATCACAAGAGGCTC 58.462 50.000 6.34 6.34 45.42 4.70
93 95 1.952990 ACAACGTGTGATGCCAAATCA 59.047 42.857 0.00 0.00 0.00 2.57
126 128 0.678048 GACCTGCAGACATGGGGAAC 60.678 60.000 17.39 0.00 0.00 3.62
129 131 0.251297 TTTGACCTGCAGACATGGGG 60.251 55.000 17.39 0.00 0.00 4.96
132 139 2.620115 ACAACTTTGACCTGCAGACATG 59.380 45.455 17.39 11.92 0.00 3.21
136 143 2.564771 CAGACAACTTTGACCTGCAGA 58.435 47.619 17.39 0.00 0.00 4.26
140 147 5.063204 TCATAACCAGACAACTTTGACCTG 58.937 41.667 0.00 3.16 34.63 4.00
143 150 7.040409 AGGAAATCATAACCAGACAACTTTGAC 60.040 37.037 0.00 0.00 0.00 3.18
148 155 7.259088 AGTAGGAAATCATAACCAGACAACT 57.741 36.000 0.00 0.00 0.00 3.16
167 174 3.681593 TCCAATTTCCAAACGGAGTAGG 58.318 45.455 0.00 0.00 45.00 3.18
168 175 5.699097 TTTCCAATTTCCAAACGGAGTAG 57.301 39.130 0.00 0.00 45.00 2.57
169 176 6.466885 TTTTTCCAATTTCCAAACGGAGTA 57.533 33.333 0.00 0.00 45.00 2.59
171 178 6.367695 GGTATTTTTCCAATTTCCAAACGGAG 59.632 38.462 0.00 0.00 32.88 4.63
172 179 6.183360 TGGTATTTTTCCAATTTCCAAACGGA 60.183 34.615 0.00 0.00 31.50 4.69
173 180 5.992217 TGGTATTTTTCCAATTTCCAAACGG 59.008 36.000 0.00 0.00 31.50 4.44
188 195 4.522405 TGCTATGCTGTGTGTGGTATTTTT 59.478 37.500 0.00 0.00 0.00 1.94
195 202 1.527034 AACTGCTATGCTGTGTGTGG 58.473 50.000 3.04 0.00 40.40 4.17
202 209 6.199937 AGGAATTTACAAACTGCTATGCTG 57.800 37.500 0.00 0.00 0.00 4.41
203 210 6.543831 CCTAGGAATTTACAAACTGCTATGCT 59.456 38.462 1.05 0.00 0.00 3.79
245 252 0.249657 CAGAGCTGGGGCGTCTATTC 60.250 60.000 0.00 0.00 44.37 1.75
256 263 3.529533 CACCAATCTAAGACAGAGCTGG 58.470 50.000 0.00 4.45 42.32 4.85
260 267 7.693969 AAAAATCCACCAATCTAAGACAGAG 57.306 36.000 0.00 0.00 36.48 3.35
286 295 2.364970 CTCCAGCAGTATTCTGAGAGGG 59.635 54.545 3.14 0.00 43.76 4.30
289 298 3.107402 ACCTCCAGCAGTATTCTGAGA 57.893 47.619 3.14 0.00 43.76 3.27
290 299 3.902881 AACCTCCAGCAGTATTCTGAG 57.097 47.619 3.14 0.00 43.76 3.35
296 305 6.958767 ACTTATGTAAAACCTCCAGCAGTAT 58.041 36.000 0.00 0.00 0.00 2.12
361 370 6.811253 TGTTTCTGATTGGTATGTACAACC 57.189 37.500 16.01 16.01 37.53 3.77
390 399 2.996631 ACTGGTTCCTCATTGAGATGC 58.003 47.619 15.36 4.35 33.14 3.91
405 414 3.557264 GCTGTCACTAGGCTTAAACTGGT 60.557 47.826 0.00 0.00 0.00 4.00
441 450 1.002142 GTACAAGCGGGGACAAAACAC 60.002 52.381 0.00 0.00 0.00 3.32
499 508 3.383505 CCGGAATATGTAGACAGTGGACA 59.616 47.826 0.00 0.00 0.00 4.02
530 539 2.308722 GGGGAGAGGCATTGGACCA 61.309 63.158 0.00 0.00 0.00 4.02
545 554 1.134250 GCCTAGAGAGCAGAAAAGGGG 60.134 57.143 0.00 0.00 0.00 4.79
657 689 0.800012 CGGTGTTTTGGGTCGTATGG 59.200 55.000 0.00 0.00 0.00 2.74
713 746 1.207089 CCGTGGAACTATGGAAGCTCA 59.793 52.381 0.00 0.00 31.75 4.26
734 767 2.571212 CTCAAAGCAGGGTACACACAA 58.429 47.619 0.00 0.00 0.00 3.33
739 772 0.606401 GCAGCTCAAAGCAGGGTACA 60.606 55.000 1.29 0.00 45.56 2.90
764 799 2.020926 CAACCGACACACATGCACA 58.979 52.632 0.00 0.00 0.00 4.57
766 801 1.784036 CTGCAACCGACACACATGCA 61.784 55.000 0.00 0.00 44.07 3.96
823 859 5.991606 TGAGATGAAGTTTAGAACCACACAG 59.008 40.000 0.00 0.00 0.00 3.66
826 862 7.522073 GCAAATGAGATGAAGTTTAGAACCACA 60.522 37.037 0.00 0.00 0.00 4.17
827 863 6.803807 GCAAATGAGATGAAGTTTAGAACCAC 59.196 38.462 0.00 0.00 0.00 4.16
829 865 7.025963 CAGCAAATGAGATGAAGTTTAGAACC 58.974 38.462 0.00 0.00 0.00 3.62
865 905 1.078143 GTAGCTGGGAAGGCACAGG 60.078 63.158 0.00 0.00 45.91 4.00
868 908 1.222113 GAGGTAGCTGGGAAGGCAC 59.778 63.158 0.00 0.00 0.00 5.01
882 922 4.163078 AGTGATGATTCATCGAAAGGAGGT 59.837 41.667 19.15 0.00 43.14 3.85
884 924 5.599732 AGAGTGATGATTCATCGAAAGGAG 58.400 41.667 19.15 0.00 43.14 3.69
915 959 5.745227 AGATACCAAACCGATGAATTCAGT 58.255 37.500 14.54 3.63 0.00 3.41
922 966 3.384789 CAGAGGAGATACCAAACCGATGA 59.615 47.826 0.00 0.00 42.04 2.92
1021 1075 3.354948 TCCTGTTGCTGCATCAACTAT 57.645 42.857 28.02 0.00 44.83 2.12
1071 1125 2.097825 GCTTCCATCTGCCAAGTGAAT 58.902 47.619 0.00 0.00 0.00 2.57
1170 1224 0.465705 TAATCCTTCCCTCAGCAGCG 59.534 55.000 0.00 0.00 0.00 5.18
1434 1493 7.420214 CCTCACAATCACATTATACTAAGGGGT 60.420 40.741 0.00 0.00 0.00 4.95
1511 1818 4.475016 ACAAGATAATCTAAGGGGCTGTGT 59.525 41.667 0.00 0.00 0.00 3.72
1586 1990 4.894784 TGTCAGTTATTCAGGGACAAGAC 58.105 43.478 0.00 0.00 35.72 3.01
1765 2175 2.245438 GAGTTGGCCCCTCCTCTTCG 62.245 65.000 0.00 0.00 35.26 3.79
1883 2293 4.240888 CGTGAGATCTCAAGCTGAAGAAA 58.759 43.478 26.70 0.00 41.85 2.52
1912 2322 3.057245 TCTGACTCTCACTTGATGTTCCG 60.057 47.826 0.00 0.00 0.00 4.30
1914 2324 8.715191 AATATTCTGACTCTCACTTGATGTTC 57.285 34.615 0.00 0.00 0.00 3.18
1968 2378 6.414732 TCATACACCTTACCTTCAATTGGAG 58.585 40.000 6.78 6.78 0.00 3.86
1992 2402 1.287442 TGTCTCTCTCTGCATCCCTCT 59.713 52.381 0.00 0.00 0.00 3.69
2022 2432 0.033208 TCCCCCATTCATCAACAGCC 60.033 55.000 0.00 0.00 0.00 4.85
2186 2599 3.450457 AGGATCTCAAGTGTTAGCCTCAG 59.550 47.826 0.00 0.00 0.00 3.35
2308 2728 3.334691 CCACACATCGTCCAATACAAGT 58.665 45.455 0.00 0.00 0.00 3.16
2385 2805 5.007724 GCTAGTACCATGCAACCATTTACTC 59.992 44.000 0.00 0.00 33.15 2.59
2436 2856 6.870769 ACTTCATCCATTGTTCCAATCATTC 58.129 36.000 0.00 0.00 0.00 2.67
2593 3013 0.038251 CACTTCGTGCAGCTAGTGGA 60.038 55.000 12.08 0.00 35.51 4.02
2647 3068 2.434702 GTCCCGAACTATCCTCCAATGT 59.565 50.000 0.00 0.00 0.00 2.71
2802 3223 0.040058 AGCATGGACCAATTGCTCCA 59.960 50.000 21.92 21.92 42.88 3.86
2950 3371 4.446385 CCTGCCAATTCATGCATTAAATCG 59.554 41.667 0.00 0.00 36.79 3.34
3087 3508 1.550976 ACCTCTCGTTAGGAAAGCTGG 59.449 52.381 11.92 0.00 39.15 4.85
3132 3553 3.494924 GGTCCTCAATTTTTGCAAAGGCT 60.495 43.478 12.41 0.00 41.91 4.58
3210 3631 4.339814 ACCGTAAACATTTTGCTTCCTTCA 59.660 37.500 0.00 0.00 0.00 3.02
3211 3632 4.866921 ACCGTAAACATTTTGCTTCCTTC 58.133 39.130 0.00 0.00 0.00 3.46
3247 3668 2.433145 ATGTCAGCGCCTGTCACG 60.433 61.111 2.29 0.00 33.09 4.35
3486 3940 1.067364 TCATGTTGCCAACACAAGCTG 59.933 47.619 13.33 7.09 45.50 4.24
4051 4505 5.424252 AGGGCATTTCATGATCATCAAAACT 59.576 36.000 8.92 3.08 0.00 2.66
4104 4558 2.232941 TCAGCGTCGAAAGAAGGGTAAT 59.767 45.455 0.00 0.00 45.01 1.89
4787 5261 7.375053 TGGAAAACCTCTTACATAATGTTTGC 58.625 34.615 0.00 0.00 0.00 3.68
4863 6723 3.152341 CTCACCATGCTCTCTTGGTTTT 58.848 45.455 0.77 0.00 45.30 2.43
4985 6853 1.201429 AACCGCTCCTTGGAGGTCAT 61.201 55.000 17.33 0.00 38.40 3.06
5124 6995 7.342026 TCATCAATAGTGACCTGTAGCTTTCTA 59.658 37.037 0.00 0.00 36.31 2.10
5169 7041 3.368531 GGAGTGTACCTAAGAAGCCACTG 60.369 52.174 0.00 0.00 33.60 3.66
5206 7083 5.054477 GCGAGGGTGCTGATAAATACTAAA 58.946 41.667 0.00 0.00 0.00 1.85
5207 7084 4.502604 GGCGAGGGTGCTGATAAATACTAA 60.503 45.833 0.00 0.00 34.52 2.24
5228 7105 0.538287 AGCAAAGAAGAGGGTGTGGC 60.538 55.000 0.00 0.00 0.00 5.01
5234 7111 6.207417 TCAATTAGTTCAAGCAAAGAAGAGGG 59.793 38.462 0.00 0.00 0.00 4.30
5236 7113 7.967303 GGATCAATTAGTTCAAGCAAAGAAGAG 59.033 37.037 0.00 0.00 0.00 2.85
5238 7115 7.031975 GGGATCAATTAGTTCAAGCAAAGAAG 58.968 38.462 0.00 0.00 0.00 2.85
5241 7118 6.376581 AGAGGGATCAATTAGTTCAAGCAAAG 59.623 38.462 0.00 0.00 0.00 2.77
5242 7119 6.151648 CAGAGGGATCAATTAGTTCAAGCAAA 59.848 38.462 0.00 0.00 0.00 3.68
5370 7260 1.283029 CCCATGGTTCTGTGTCCATCT 59.717 52.381 11.73 0.00 41.79 2.90
5418 7308 1.200020 GAAAAGTCACAATGCCCCTCG 59.800 52.381 0.00 0.00 0.00 4.63
5434 7324 7.391554 CAGATAAGACACAAGAATGAGGGAAAA 59.608 37.037 0.00 0.00 0.00 2.29
5467 7357 0.839946 AGCATACCTTACTGCCAGGG 59.160 55.000 0.00 0.00 39.22 4.45
5503 7393 9.297037 GGTATATATAGAGGCCAAACAATTTGT 57.703 33.333 5.01 0.00 38.98 2.83
5504 7394 8.739972 GGGTATATATAGAGGCCAAACAATTTG 58.260 37.037 5.01 0.00 40.32 2.32
5505 7395 8.678798 AGGGTATATATAGAGGCCAAACAATTT 58.321 33.333 5.01 0.00 0.00 1.82
5506 7396 8.109634 CAGGGTATATATAGAGGCCAAACAATT 58.890 37.037 5.01 0.00 0.00 2.32
5507 7397 7.461043 TCAGGGTATATATAGAGGCCAAACAAT 59.539 37.037 5.01 0.00 0.00 2.71
5508 7398 6.790461 TCAGGGTATATATAGAGGCCAAACAA 59.210 38.462 5.01 0.00 0.00 2.83
5509 7399 6.327781 TCAGGGTATATATAGAGGCCAAACA 58.672 40.000 5.01 0.00 0.00 2.83
5510 7400 6.869206 TCAGGGTATATATAGAGGCCAAAC 57.131 41.667 5.01 0.00 0.00 2.93
5511 7401 7.196187 TGATCAGGGTATATATAGAGGCCAAA 58.804 38.462 5.01 0.00 0.00 3.28
5512 7402 6.752091 TGATCAGGGTATATATAGAGGCCAA 58.248 40.000 5.01 0.00 0.00 4.52
5513 7403 6.068200 ACTGATCAGGGTATATATAGAGGCCA 60.068 42.308 26.08 0.00 0.00 5.36
5514 7404 6.377912 ACTGATCAGGGTATATATAGAGGCC 58.622 44.000 26.08 0.00 0.00 5.19
5515 7405 7.906199 AACTGATCAGGGTATATATAGAGGC 57.094 40.000 26.08 0.00 0.00 4.70
5519 7409 9.574458 CGACAAAACTGATCAGGGTATATATAG 57.426 37.037 26.08 7.44 0.00 1.31
5520 7410 8.528643 CCGACAAAACTGATCAGGGTATATATA 58.471 37.037 26.08 0.00 0.00 0.86
5521 7411 7.016268 ACCGACAAAACTGATCAGGGTATATAT 59.984 37.037 26.08 4.37 0.00 0.86
5522 7412 6.325545 ACCGACAAAACTGATCAGGGTATATA 59.674 38.462 26.08 0.00 0.00 0.86
5523 7413 5.130477 ACCGACAAAACTGATCAGGGTATAT 59.870 40.000 26.08 7.45 0.00 0.86
5524 7414 4.468510 ACCGACAAAACTGATCAGGGTATA 59.531 41.667 26.08 0.00 0.00 1.47
5525 7415 3.263425 ACCGACAAAACTGATCAGGGTAT 59.737 43.478 26.08 7.96 0.00 2.73
5526 7416 2.635915 ACCGACAAAACTGATCAGGGTA 59.364 45.455 26.08 0.00 0.00 3.69
5527 7417 1.420138 ACCGACAAAACTGATCAGGGT 59.580 47.619 26.08 17.80 0.00 4.34
5554 7444 1.438651 TCGCCAACAAGTATGAGCAC 58.561 50.000 0.00 0.00 0.00 4.40
5560 7450 5.437060 AGGAACAATATCGCCAACAAGTAT 58.563 37.500 0.00 0.00 0.00 2.12
5563 7453 4.396166 AGAAGGAACAATATCGCCAACAAG 59.604 41.667 0.00 0.00 0.00 3.16
5626 7516 8.649973 AAAACAGACTAGCTAGATTATTTCCG 57.350 34.615 27.45 7.97 0.00 4.30
5684 7574 4.525100 TCATATGCATGGGGTGATGAATTG 59.475 41.667 10.16 0.00 32.61 2.32


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

AutoCloner maintained by Alex Coulton.