Multiple sequence alignment - TraesCS2B01G528800

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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 TraesCS2B01G528800 chr2B 100.000 6243 0 0 1 6243 723328898 723335140 0.000000e+00 11529.0
1 TraesCS2B01G528800 chr2B 85.783 3137 373 37 2128 5243 723132717 723135801 0.000000e+00 3254.0
2 TraesCS2B01G528800 chr2B 87.199 1953 224 17 2200 4130 723298330 723300278 0.000000e+00 2198.0
3 TraesCS2B01G528800 chr2B 85.657 1241 135 18 816 2027 723131359 723132585 0.000000e+00 1266.0
4 TraesCS2B01G528800 chr2B 79.827 1849 275 43 3415 5208 723430972 723432777 0.000000e+00 1258.0
5 TraesCS2B01G528800 chr2B 86.139 1176 123 21 4113 5251 723301707 723302879 0.000000e+00 1232.0
6 TraesCS2B01G528800 chr2B 83.824 1224 170 15 2143 3344 723429750 723430967 0.000000e+00 1138.0
7 TraesCS2B01G528800 chr2B 82.875 800 64 27 55 823 723130659 723131416 0.000000e+00 651.0
8 TraesCS2B01G528800 chr2B 96.486 313 10 1 1 313 723314370 723314681 3.340000e-142 516.0
9 TraesCS2B01G528800 chr2B 76.164 537 86 20 1229 1759 723266131 723266631 1.740000e-60 244.0
10 TraesCS2B01G528800 chr2B 87.654 81 6 3 2129 2206 723272128 723272207 2.400000e-14 91.6
11 TraesCS2B01G528800 chr2B 94.444 54 1 2 816 868 723329668 723329720 1.440000e-11 82.4
12 TraesCS2B01G528800 chr2B 94.444 54 1 2 771 823 723329713 723329765 1.440000e-11 82.4
13 TraesCS2B01G528800 chr2D 95.600 4591 137 15 711 5273 595435403 595439956 0.000000e+00 7299.0
14 TraesCS2B01G528800 chr2D 87.555 3198 323 48 2118 5251 595428998 595432184 0.000000e+00 3631.0
15 TraesCS2B01G528800 chr2D 80.000 1850 268 46 3415 5208 595509868 595511671 0.000000e+00 1273.0
16 TraesCS2B01G528800 chr2D 84.000 1225 166 17 2143 3344 595508646 595509863 0.000000e+00 1149.0
17 TraesCS2B01G528800 chr2D 92.219 694 45 9 55 746 595432492 595433178 0.000000e+00 974.0
18 TraesCS2B01G528800 chr2D 96.195 473 13 3 5307 5775 595439955 595440426 0.000000e+00 769.0
19 TraesCS2B01G528800 chr2D 80.715 783 105 23 1229 2006 595428115 595428856 9.080000e-158 568.0
20 TraesCS2B01G528800 chr2D 90.389 437 16 4 5816 6243 595440557 595440976 9.150000e-153 551.0
21 TraesCS2B01G528800 chr2D 78.102 137 25 4 4559 4691 642941884 642942019 1.440000e-11 82.4
22 TraesCS2B01G528800 chr2A 93.496 4797 222 38 522 5251 729558486 729563259 0.000000e+00 7047.0
23 TraesCS2B01G528800 chr2A 85.906 3136 359 39 2128 5243 729530765 729533837 0.000000e+00 3265.0
24 TraesCS2B01G528800 chr2A 79.476 3167 503 75 2143 5227 727610129 727613230 0.000000e+00 2111.0
25 TraesCS2B01G528800 chr2A 80.088 1818 266 41 3445 5208 729569369 729571144 0.000000e+00 1264.0
26 TraesCS2B01G528800 chr2A 86.897 1099 127 13 2143 3231 729568287 729569378 0.000000e+00 1216.0
27 TraesCS2B01G528800 chr2A 84.388 1185 141 26 871 2031 729529473 729530637 0.000000e+00 1123.0
28 TraesCS2B01G528800 chr2A 85.466 977 106 14 4308 5251 729527439 729528412 0.000000e+00 985.0
29 TraesCS2B01G528800 chr2A 88.986 690 34 16 55 744 729528705 729529352 0.000000e+00 815.0
30 TraesCS2B01G528800 chr2A 93.709 461 25 4 55 515 729557031 729557487 0.000000e+00 688.0
31 TraesCS2B01G528800 chr2A 92.424 66 1 2 816 877 729558734 729558799 2.400000e-14 91.6
32 TraesCS2B01G528800 chr2A 97.436 39 1 0 2236 2274 729560113 729560075 4.040000e-07 67.6
33 TraesCS2B01G528800 chr1B 74.697 826 174 18 2153 2951 540339499 540338682 1.000000e-87 335.0
34 TraesCS2B01G528800 chrUn 79.562 137 23 4 4559 4691 31552474 31552609 6.660000e-15 93.5
35 TraesCS2B01G528800 chr6B 94.643 56 3 0 1 56 135317085 135317030 3.100000e-13 87.9
36 TraesCS2B01G528800 chr7D 92.105 38 3 0 86 123 394825373 394825336 3.000000e-03 54.7


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 TraesCS2B01G528800 chr2B 723328898 723335140 6242 False 11529.000000 11529 100.000000 1 6243 1 chr2B.!!$F4 6242
1 TraesCS2B01G528800 chr2B 723130659 723135801 5142 False 1723.666667 3254 84.771667 55 5243 3 chr2B.!!$F5 5188
2 TraesCS2B01G528800 chr2B 723298330 723302879 4549 False 1715.000000 2198 86.669000 2200 5251 2 chr2B.!!$F6 3051
3 TraesCS2B01G528800 chr2B 723429750 723432777 3027 False 1198.000000 1258 81.825500 2143 5208 2 chr2B.!!$F8 3065
4 TraesCS2B01G528800 chr2B 723266131 723266631 500 False 244.000000 244 76.164000 1229 1759 1 chr2B.!!$F1 530
5 TraesCS2B01G528800 chr2D 595428115 595440976 12861 False 2298.666667 7299 90.445500 55 6243 6 chr2D.!!$F2 6188
6 TraesCS2B01G528800 chr2D 595508646 595511671 3025 False 1211.000000 1273 82.000000 2143 5208 2 chr2D.!!$F3 3065
7 TraesCS2B01G528800 chr2A 729557031 729563259 6228 False 3867.500000 7047 93.602500 55 5251 2 chr2A.!!$F4 5196
8 TraesCS2B01G528800 chr2A 727610129 727613230 3101 False 2111.000000 2111 79.476000 2143 5227 1 chr2A.!!$F1 3084
9 TraesCS2B01G528800 chr2A 729527439 729533837 6398 False 1547.000000 3265 86.186500 55 5251 4 chr2A.!!$F3 5196
10 TraesCS2B01G528800 chr2A 729568287 729571144 2857 False 1240.000000 1264 83.492500 2143 5208 2 chr2A.!!$F5 3065
11 TraesCS2B01G528800 chr1B 540338682 540339499 817 True 335.000000 335 74.697000 2153 2951 1 chr1B.!!$R1 798

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
52 53 0.040067 GACAAGCTTCGCCCAAGTTG 60.040 55.0 0.0 0.0 34.13 3.16 F
820 8453 0.108329 CCGTGTCGATTTACTGGGCT 60.108 55.0 0.0 0.0 0.00 5.19 F
823 8456 0.251916 TGTCGATTTACTGGGCTGGG 59.748 55.0 0.0 0.0 0.00 4.45 F
936 8595 0.973632 GCCTTCCCCCGAACAAAAAT 59.026 50.0 0.0 0.0 0.00 1.82 F
1908 9603 0.033699 GGGCAGGCCAAGAAGATTCT 60.034 55.0 13.1 0.0 39.74 2.40 F
3474 11280 0.036388 GTCGAATGGAAGGAGTGGCA 60.036 55.0 0.0 0.0 0.00 4.92 F
4422 13709 0.178068 TAGTTGCTGCCCGAGATTCC 59.822 55.0 0.0 0.0 0.00 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1317 8997 0.674895 CGGAACTCCTGCTTCCCTTG 60.675 60.000 0.00 0.00 34.68 3.61 R
1863 9549 1.347707 AGTTCGTCTTCCATGGCTGAA 59.652 47.619 6.96 3.47 0.00 3.02 R
1875 9561 2.048127 GCCCTGCGAAGTTCGTCT 60.048 61.111 25.04 0.00 42.81 4.18 R
2727 10527 2.078392 GCCACCATGAAAAAGCAATGG 58.922 47.619 0.00 0.00 38.31 3.16 R
3574 11381 0.676151 CAGCTCCTTGAACTGCTCCC 60.676 60.000 0.00 0.00 33.03 4.30 R
5209 14539 0.531532 CGAGCTTCATGGTAGGCCTG 60.532 60.000 17.99 0.00 35.27 4.85 R
5826 15249 0.390860 CCGTCCATTAGAGGCTCTGG 59.609 60.000 26.95 19.77 0.00 3.86 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
20 21 3.914426 AACCCGATACTCAATTGAGCT 57.086 42.857 30.95 20.43 45.79 4.09
21 22 3.914426 ACCCGATACTCAATTGAGCTT 57.086 42.857 30.95 20.24 45.79 3.74
22 23 5.353394 AACCCGATACTCAATTGAGCTTA 57.647 39.130 30.95 19.09 45.79 3.09
23 24 4.694339 ACCCGATACTCAATTGAGCTTAC 58.306 43.478 30.95 19.39 45.79 2.34
24 25 4.161565 ACCCGATACTCAATTGAGCTTACA 59.838 41.667 30.95 14.20 45.79 2.41
25 26 4.508124 CCCGATACTCAATTGAGCTTACAC 59.492 45.833 30.95 16.76 45.79 2.90
27 28 5.233050 CCGATACTCAATTGAGCTTACACAG 59.767 44.000 30.95 15.71 45.79 3.66
28 29 6.036470 CGATACTCAATTGAGCTTACACAGA 58.964 40.000 30.95 9.07 45.79 3.41
30 31 3.999663 ACTCAATTGAGCTTACACAGAGC 59.000 43.478 30.95 0.00 45.79 4.09
31 32 3.999001 CTCAATTGAGCTTACACAGAGCA 59.001 43.478 21.96 0.00 42.56 4.26
32 33 4.582869 TCAATTGAGCTTACACAGAGCAT 58.417 39.130 3.38 0.00 42.56 3.79
35 36 2.964740 TGAGCTTACACAGAGCATGAC 58.035 47.619 0.00 0.00 42.56 3.06
37 38 3.244181 TGAGCTTACACAGAGCATGACAA 60.244 43.478 0.00 0.00 42.56 3.18
38 39 3.332919 AGCTTACACAGAGCATGACAAG 58.667 45.455 0.00 0.00 42.56 3.16
39 40 2.159599 GCTTACACAGAGCATGACAAGC 60.160 50.000 0.00 0.00 39.89 4.01
40 41 3.332919 CTTACACAGAGCATGACAAGCT 58.667 45.455 4.55 4.55 46.82 3.74
41 42 2.267174 ACACAGAGCATGACAAGCTT 57.733 45.000 6.63 0.00 43.58 3.74
42 43 2.149578 ACACAGAGCATGACAAGCTTC 58.850 47.619 6.63 0.84 43.58 3.86
43 44 1.128136 CACAGAGCATGACAAGCTTCG 59.872 52.381 6.63 3.91 43.58 3.79
45 46 1.023513 AGAGCATGACAAGCTTCGCC 61.024 55.000 6.63 0.00 43.58 5.54
46 47 1.986575 GAGCATGACAAGCTTCGCCC 61.987 60.000 6.63 0.00 43.58 6.13
47 48 2.334946 GCATGACAAGCTTCGCCCA 61.335 57.895 0.00 0.00 0.00 5.36
48 49 1.865788 GCATGACAAGCTTCGCCCAA 61.866 55.000 0.00 0.00 0.00 4.12
50 51 0.250901 ATGACAAGCTTCGCCCAAGT 60.251 50.000 0.00 0.00 34.13 3.16
51 52 0.465460 TGACAAGCTTCGCCCAAGTT 60.465 50.000 0.00 0.00 34.13 2.66
52 53 0.040067 GACAAGCTTCGCCCAAGTTG 60.040 55.000 0.00 0.00 34.13 3.16
53 54 1.372128 CAAGCTTCGCCCAAGTTGC 60.372 57.895 0.00 0.00 34.13 4.17
117 4445 8.299570 AGAACATTTTTCTAACACATGATGACC 58.700 33.333 0.00 0.00 0.00 4.02
257 4588 4.663334 ACATTTTTCTGGGTTCCCTAGAC 58.337 43.478 9.43 0.00 40.80 2.59
328 4659 4.773013 TCTGTTTCTTACTGGTTTTCGGT 58.227 39.130 0.00 0.00 38.72 4.69
675 6022 6.719829 AGTTCGGGATTTATTTTGTTTCTCCT 59.280 34.615 0.00 0.00 0.00 3.69
811 8444 1.189524 TGGGAAGGTCCGTGTCGATT 61.190 55.000 0.00 0.00 37.43 3.34
814 8447 2.265683 GGAAGGTCCGTGTCGATTTAC 58.734 52.381 0.00 0.00 0.00 2.01
815 8448 2.094338 GGAAGGTCCGTGTCGATTTACT 60.094 50.000 0.00 0.00 0.00 2.24
816 8449 2.649331 AGGTCCGTGTCGATTTACTG 57.351 50.000 0.00 0.00 0.00 2.74
817 8450 1.203994 AGGTCCGTGTCGATTTACTGG 59.796 52.381 0.00 0.00 0.00 4.00
818 8451 1.636988 GTCCGTGTCGATTTACTGGG 58.363 55.000 0.00 0.00 0.00 4.45
819 8452 0.108520 TCCGTGTCGATTTACTGGGC 60.109 55.000 0.00 0.00 0.00 5.36
820 8453 0.108329 CCGTGTCGATTTACTGGGCT 60.108 55.000 0.00 0.00 0.00 5.19
821 8454 0.999406 CGTGTCGATTTACTGGGCTG 59.001 55.000 0.00 0.00 0.00 4.85
822 8455 1.369625 GTGTCGATTTACTGGGCTGG 58.630 55.000 0.00 0.00 0.00 4.85
823 8456 0.251916 TGTCGATTTACTGGGCTGGG 59.748 55.000 0.00 0.00 0.00 4.45
824 8457 1.095807 GTCGATTTACTGGGCTGGGC 61.096 60.000 0.00 0.00 0.00 5.36
836 8469 2.360350 CTGGGCCATGTTCGTGCT 60.360 61.111 6.72 0.00 0.00 4.40
936 8595 0.973632 GCCTTCCCCCGAACAAAAAT 59.026 50.000 0.00 0.00 0.00 1.82
938 8597 2.764010 GCCTTCCCCCGAACAAAAATAT 59.236 45.455 0.00 0.00 0.00 1.28
1051 8725 4.302455 CATGTTTACCGAGGAGCTCTATG 58.698 47.826 14.64 3.18 0.00 2.23
1138 8818 2.874701 ATTGCACATAGCGATTCTGACC 59.125 45.455 0.00 0.00 45.26 4.02
1569 9255 8.915654 GTTGACATTGCTAAGGTATTTGAAAAG 58.084 33.333 0.00 0.00 0.00 2.27
1726 9412 3.087031 AGGAGCACCATGATGAAGTTTG 58.913 45.455 2.07 0.00 38.94 2.93
1741 9427 2.132762 AGTTTGTTTCTGAGCCGTACG 58.867 47.619 8.69 8.69 0.00 3.67
1820 9506 4.866508 TGGACTCAAACTTCGACTACAT 57.133 40.909 0.00 0.00 0.00 2.29
1875 9561 5.776716 AGAATCTTTTTCTTCAGCCATGGAA 59.223 36.000 18.40 0.00 0.00 3.53
1908 9603 0.033699 GGGCAGGCCAAGAAGATTCT 60.034 55.000 13.10 0.00 39.74 2.40
2060 9804 9.474920 TTGCATTTTGGAATTTACTCACTTAAG 57.525 29.630 0.00 0.00 0.00 1.85
2099 9858 4.963373 TGGAAGTTTACTCCACGATTTGA 58.037 39.130 0.00 0.00 0.00 2.69
2408 10185 6.527722 TGTACGTATGGTATTTTCGTGTTCTC 59.472 38.462 0.00 0.00 36.24 2.87
2428 10205 2.955660 TCGATCCTTTGTTTGTTGCCTT 59.044 40.909 0.00 0.00 0.00 4.35
2513 10313 1.525197 GTTCGTGCAATTGTCTCGACA 59.475 47.619 19.25 0.00 39.98 4.35
2727 10527 3.982576 CTGTTACACCCAAACAGGAAC 57.017 47.619 7.86 0.00 46.52 3.62
2882 10685 6.344500 CAGCAATGACTACCTTTATCTGACT 58.656 40.000 0.00 0.00 0.00 3.41
2912 10715 6.919721 TGTAGTTTCTGTGGAATTAAATGGC 58.080 36.000 0.00 0.00 0.00 4.40
3021 10827 5.712917 ACAAGTAAATGCGAATTTCCCCTTA 59.287 36.000 4.14 0.00 0.00 2.69
3461 11267 1.807886 CGGAGGGAAGTCGTCGAAT 59.192 57.895 0.00 0.00 0.00 3.34
3474 11280 0.036388 GTCGAATGGAAGGAGTGGCA 60.036 55.000 0.00 0.00 0.00 4.92
3534 11341 2.159234 GTGCAGACACAGAGCAAGATTC 59.841 50.000 0.00 0.00 46.61 2.52
3574 11381 1.129998 CTCCAAGCAGTTCAATGAGCG 59.870 52.381 0.00 0.00 0.00 5.03
3634 11441 1.202087 CGTAGCCGAGTCTGTCAGAAG 60.202 57.143 3.51 0.00 35.63 2.85
3658 11468 2.015587 GATTGAGAAGAAGCAGGCTGG 58.984 52.381 17.64 0.00 0.00 4.85
3663 11473 2.828480 GAAGAAGCAGGCTGGGACCC 62.828 65.000 17.64 2.45 0.00 4.46
3676 11486 3.462678 GACCCTGACGGAGGAGGC 61.463 72.222 4.35 0.00 46.33 4.70
3738 11548 1.168714 GTTTGATGAGCTGTGGGACC 58.831 55.000 0.00 0.00 0.00 4.46
3781 11591 6.038825 TCAACAGAACCAAAATTTCTAGCGAA 59.961 34.615 0.00 0.00 31.86 4.70
3853 11663 6.522054 AGTTTATCTCTGAAGTTTTCGACCA 58.478 36.000 0.00 0.00 0.00 4.02
3929 11745 4.090761 TGATGAGGACAAGAATATGGGC 57.909 45.455 0.00 0.00 0.00 5.36
4054 11871 4.884668 TCGAAGACCCAAGTGAGTAATT 57.115 40.909 0.00 0.00 0.00 1.40
4074 11894 7.814107 AGTAATTTGCTTGTGATATGGTTGTTG 59.186 33.333 0.00 0.00 0.00 3.33
4228 13500 7.406553 TCTTTTGTTAGTTGACGTCAGATTTG 58.593 34.615 19.11 3.45 0.00 2.32
4273 13551 0.546122 AGCGTTATTGAGCCCCATGA 59.454 50.000 0.00 0.00 0.00 3.07
4278 13556 3.499918 CGTTATTGAGCCCCATGATCTTC 59.500 47.826 0.00 0.00 0.00 2.87
4422 13709 0.178068 TAGTTGCTGCCCGAGATTCC 59.822 55.000 0.00 0.00 0.00 3.01
4512 13800 5.830991 GGTATGCATGGGTATTTTCCTGTTA 59.169 40.000 10.16 0.00 0.00 2.41
4575 13872 1.674441 ACAATGATGCTTGCAGGATCG 59.326 47.619 0.00 0.00 44.79 3.69
4972 14302 6.897966 TGAGTGAACAGGGTTATCTAGATCTT 59.102 38.462 8.95 0.00 0.00 2.40
5261 14591 5.221362 TGTTGAAGATGTTCGGTGAAGAGTA 60.221 40.000 0.00 0.00 35.17 2.59
5264 14594 5.869344 TGAAGATGTTCGGTGAAGAGTAATG 59.131 40.000 0.00 0.00 35.17 1.90
5273 14603 3.375299 GGTGAAGAGTAATGTGTGCATCC 59.625 47.826 0.00 0.00 33.50 3.51
5274 14604 3.062639 GTGAAGAGTAATGTGTGCATCCG 59.937 47.826 0.00 0.00 33.50 4.18
5275 14605 3.056179 TGAAGAGTAATGTGTGCATCCGA 60.056 43.478 0.00 0.00 33.50 4.55
5276 14606 3.170791 AGAGTAATGTGTGCATCCGAG 57.829 47.619 0.00 0.00 33.50 4.63
5277 14607 2.760650 AGAGTAATGTGTGCATCCGAGA 59.239 45.455 0.00 0.00 33.50 4.04
5278 14608 3.195610 AGAGTAATGTGTGCATCCGAGAA 59.804 43.478 0.00 0.00 33.50 2.87
5279 14609 3.262420 AGTAATGTGTGCATCCGAGAAC 58.738 45.455 0.00 0.00 33.50 3.01
5280 14610 2.183478 AATGTGTGCATCCGAGAACA 57.817 45.000 0.00 0.00 33.50 3.18
5281 14611 2.408271 ATGTGTGCATCCGAGAACAT 57.592 45.000 0.00 0.00 0.00 2.71
5282 14612 1.441738 TGTGTGCATCCGAGAACATG 58.558 50.000 0.00 0.00 0.00 3.21
5283 14613 1.270785 TGTGTGCATCCGAGAACATGT 60.271 47.619 0.00 0.00 0.00 3.21
5284 14614 1.129251 GTGTGCATCCGAGAACATGTG 59.871 52.381 0.00 0.00 0.00 3.21
5285 14615 1.001860 TGTGCATCCGAGAACATGTGA 59.998 47.619 0.00 0.00 0.00 3.58
5286 14616 2.076100 GTGCATCCGAGAACATGTGAA 58.924 47.619 0.00 0.00 0.00 3.18
5287 14617 2.076100 TGCATCCGAGAACATGTGAAC 58.924 47.619 0.00 0.00 0.00 3.18
5288 14618 2.289631 TGCATCCGAGAACATGTGAACT 60.290 45.455 0.00 0.00 0.00 3.01
5289 14619 2.094894 GCATCCGAGAACATGTGAACTG 59.905 50.000 0.00 0.00 0.00 3.16
5290 14620 3.329386 CATCCGAGAACATGTGAACTGT 58.671 45.455 0.00 0.00 0.00 3.55
5291 14621 3.469008 TCCGAGAACATGTGAACTGTT 57.531 42.857 0.00 0.00 39.46 3.16
5298 14628 5.695851 GAACATGTGAACTGTTCCATCTT 57.304 39.130 17.26 12.97 44.26 2.40
5299 14629 5.443185 AACATGTGAACTGTTCCATCTTG 57.557 39.130 17.26 15.76 31.29 3.02
5300 14630 4.717877 ACATGTGAACTGTTCCATCTTGA 58.282 39.130 17.26 0.00 0.00 3.02
5301 14631 5.132502 ACATGTGAACTGTTCCATCTTGAA 58.867 37.500 17.26 0.00 0.00 2.69
5302 14632 5.009010 ACATGTGAACTGTTCCATCTTGAAC 59.991 40.000 17.26 7.16 43.90 3.18
5303 14633 4.780815 TGTGAACTGTTCCATCTTGAACT 58.219 39.130 17.26 0.00 43.96 3.01
5304 14634 5.192927 TGTGAACTGTTCCATCTTGAACTT 58.807 37.500 17.26 0.00 43.96 2.66
5305 14635 5.066375 TGTGAACTGTTCCATCTTGAACTTG 59.934 40.000 17.26 2.03 43.96 3.16
5306 14636 5.066505 GTGAACTGTTCCATCTTGAACTTGT 59.933 40.000 17.26 2.55 43.96 3.16
5307 14637 5.296780 TGAACTGTTCCATCTTGAACTTGTC 59.703 40.000 17.26 1.58 43.96 3.18
5363 14693 7.578310 TTGTTCGTAGTACTATGATAAGGCT 57.422 36.000 22.46 0.00 31.79 4.58
5366 14696 8.152898 TGTTCGTAGTACTATGATAAGGCTAGA 58.847 37.037 22.46 4.89 31.79 2.43
5421 14751 5.064198 GCGTGTATGCTAATTGTTCCTGTAA 59.936 40.000 0.00 0.00 0.00 2.41
5508 14842 5.278512 GCTAGGTAAGCCTATTTTGCCATTC 60.279 44.000 0.00 0.00 45.61 2.67
5520 14854 7.231317 CCTATTTTGCCATTCCTAGCTTATTCA 59.769 37.037 0.00 0.00 0.00 2.57
5606 14940 4.530161 GGATCTGGAGATATAGCCTTGTGT 59.470 45.833 0.00 0.00 34.37 3.72
5698 15032 1.153289 CTGGCATTGCTAGCGTCCT 60.153 57.895 10.77 0.00 29.14 3.85
5761 15095 5.416013 GCCTTTTTGCAATAGGTAAGAGAGT 59.584 40.000 22.25 0.00 0.00 3.24
5763 15097 6.655003 CCTTTTTGCAATAGGTAAGAGAGTGA 59.345 38.462 16.31 0.00 0.00 3.41
5776 15138 6.096141 GGTAAGAGAGTGATGAAGATGTCTGA 59.904 42.308 0.00 0.00 0.00 3.27
5807 15169 4.665833 AACAACTCGCCTATGTATAGCA 57.334 40.909 0.00 0.00 0.00 3.49
5808 15170 4.244425 ACAACTCGCCTATGTATAGCAG 57.756 45.455 0.00 0.00 0.00 4.24
5810 15172 4.099573 ACAACTCGCCTATGTATAGCAGTT 59.900 41.667 0.00 0.00 0.00 3.16
5811 15173 4.939052 ACTCGCCTATGTATAGCAGTTT 57.061 40.909 0.00 0.00 0.00 2.66
5812 15174 5.277857 ACTCGCCTATGTATAGCAGTTTT 57.722 39.130 0.00 0.00 0.00 2.43
5842 15265 3.398318 TGTACCAGAGCCTCTAATGGA 57.602 47.619 5.55 0.00 36.62 3.41
5898 15321 1.280457 CACCTCTAGCCAAACCCTCT 58.720 55.000 0.00 0.00 0.00 3.69
5899 15322 1.208293 CACCTCTAGCCAAACCCTCTC 59.792 57.143 0.00 0.00 0.00 3.20
5900 15323 0.833949 CCTCTAGCCAAACCCTCTCC 59.166 60.000 0.00 0.00 0.00 3.71
5901 15324 1.623834 CCTCTAGCCAAACCCTCTCCT 60.624 57.143 0.00 0.00 0.00 3.69
5902 15325 1.760029 CTCTAGCCAAACCCTCTCCTC 59.240 57.143 0.00 0.00 0.00 3.71
5903 15326 0.833949 CTAGCCAAACCCTCTCCTCC 59.166 60.000 0.00 0.00 0.00 4.30
5904 15327 0.118346 TAGCCAAACCCTCTCCTCCA 59.882 55.000 0.00 0.00 0.00 3.86
5905 15328 1.002011 GCCAAACCCTCTCCTCCAC 60.002 63.158 0.00 0.00 0.00 4.02
5906 15329 1.492993 GCCAAACCCTCTCCTCCACT 61.493 60.000 0.00 0.00 0.00 4.00
5907 15330 0.326264 CCAAACCCTCTCCTCCACTG 59.674 60.000 0.00 0.00 0.00 3.66
5908 15331 0.326264 CAAACCCTCTCCTCCACTGG 59.674 60.000 0.00 0.00 0.00 4.00
5909 15332 0.193574 AAACCCTCTCCTCCACTGGA 59.806 55.000 0.00 0.00 34.52 3.86
5910 15333 0.193574 AACCCTCTCCTCCACTGGAA 59.806 55.000 0.00 0.00 35.43 3.53
5911 15334 0.419459 ACCCTCTCCTCCACTGGAAT 59.581 55.000 0.00 0.00 35.43 3.01
5912 15335 1.651770 ACCCTCTCCTCCACTGGAATA 59.348 52.381 0.00 0.00 35.43 1.75
5913 15336 2.324541 CCCTCTCCTCCACTGGAATAG 58.675 57.143 0.00 0.00 35.43 1.73
5914 15337 2.324541 CCTCTCCTCCACTGGAATAGG 58.675 57.143 0.00 0.00 35.43 2.57
5970 15393 4.080640 GCTTCGCGTCTCTTCTCC 57.919 61.111 5.77 0.00 0.00 3.71
5975 15398 0.522180 TCGCGTCTCTTCTCCTCAAC 59.478 55.000 5.77 0.00 0.00 3.18
5988 15411 3.458857 TCTCCTCAACGGTAGATAGAGGT 59.541 47.826 3.91 0.00 44.79 3.85
6013 15436 0.250234 CCAGGCATCTTCGTCCTTCA 59.750 55.000 0.00 0.00 0.00 3.02
6022 15445 3.099905 TCTTCGTCCTTCATGTGATCCT 58.900 45.455 0.00 0.00 0.00 3.24
6048 15471 1.374252 CCTCGTGTGGTTTCCCTCG 60.374 63.158 0.00 0.00 0.00 4.63
6057 15480 2.927856 TTTCCCTCGCCTCCTGCA 60.928 61.111 0.00 0.00 41.33 4.41
6128 15560 4.760047 GGGTGGCTCGTCGCATGT 62.760 66.667 0.00 0.00 41.67 3.21
6135 15567 1.140407 GCTCGTCGCATGTAGTGTCC 61.140 60.000 0.00 0.00 38.92 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.914426 AAGCTCAATTGAGTATCGGGT 57.086 42.857 30.88 12.25 43.85 5.28
4 5 6.036470 TCTGTGTAAGCTCAATTGAGTATCG 58.964 40.000 30.88 11.61 43.85 2.92
5 6 6.019156 GCTCTGTGTAAGCTCAATTGAGTATC 60.019 42.308 30.88 17.74 43.85 2.24
6 7 5.814705 GCTCTGTGTAAGCTCAATTGAGTAT 59.185 40.000 30.88 22.97 43.85 2.12
7 8 5.171476 GCTCTGTGTAAGCTCAATTGAGTA 58.829 41.667 30.88 17.12 43.85 2.59
8 9 3.999663 GCTCTGTGTAAGCTCAATTGAGT 59.000 43.478 30.88 18.06 43.85 3.41
9 10 3.999001 TGCTCTGTGTAAGCTCAATTGAG 59.001 43.478 27.82 27.82 44.75 3.02
12 13 4.394300 GTCATGCTCTGTGTAAGCTCAATT 59.606 41.667 0.00 0.00 40.50 2.32
13 14 3.937706 GTCATGCTCTGTGTAAGCTCAAT 59.062 43.478 0.00 0.00 40.50 2.57
14 15 3.244181 TGTCATGCTCTGTGTAAGCTCAA 60.244 43.478 0.00 0.00 40.50 3.02
15 16 2.299867 TGTCATGCTCTGTGTAAGCTCA 59.700 45.455 0.00 0.00 40.50 4.26
16 17 2.964740 TGTCATGCTCTGTGTAAGCTC 58.035 47.619 0.00 0.00 40.50 4.09
17 18 3.332919 CTTGTCATGCTCTGTGTAAGCT 58.667 45.455 0.00 0.00 40.50 3.74
19 20 3.332919 AGCTTGTCATGCTCTGTGTAAG 58.667 45.455 7.39 0.00 35.67 2.34
20 21 3.407424 AGCTTGTCATGCTCTGTGTAA 57.593 42.857 7.39 0.00 35.67 2.41
21 22 3.329386 GAAGCTTGTCATGCTCTGTGTA 58.671 45.455 13.18 0.00 40.22 2.90
22 23 2.149578 GAAGCTTGTCATGCTCTGTGT 58.850 47.619 13.18 0.00 40.22 3.72
23 24 1.128136 CGAAGCTTGTCATGCTCTGTG 59.872 52.381 13.18 1.48 40.22 3.66
24 25 1.436600 CGAAGCTTGTCATGCTCTGT 58.563 50.000 13.18 0.00 40.22 3.41
39 40 2.153366 AAAATGCAACTTGGGCGAAG 57.847 45.000 7.78 7.78 37.73 3.79
40 41 2.625790 ACTAAAATGCAACTTGGGCGAA 59.374 40.909 0.00 0.00 0.00 4.70
41 42 2.235016 ACTAAAATGCAACTTGGGCGA 58.765 42.857 0.00 0.00 0.00 5.54
42 43 2.723124 ACTAAAATGCAACTTGGGCG 57.277 45.000 0.00 0.00 0.00 6.13
43 44 4.513198 TGTACTAAAATGCAACTTGGGC 57.487 40.909 0.00 0.00 0.00 5.36
45 46 6.586082 GTCCAATGTACTAAAATGCAACTTGG 59.414 38.462 0.00 0.00 0.00 3.61
46 47 7.144661 TGTCCAATGTACTAAAATGCAACTTG 58.855 34.615 0.00 0.00 0.00 3.16
47 48 7.283625 TGTCCAATGTACTAAAATGCAACTT 57.716 32.000 0.00 0.00 0.00 2.66
48 49 6.892658 TGTCCAATGTACTAAAATGCAACT 57.107 33.333 0.00 0.00 0.00 3.16
133 4461 9.258826 TGTTTAACATTCATTTGGAGAAATGTG 57.741 29.630 0.00 3.11 45.98 3.21
497 4830 9.953697 CATGATTTGTTTTTGGAAAACATGATT 57.046 25.926 16.81 0.00 41.38 2.57
498 4831 9.122779 ACATGATTTGTTTTTGGAAAACATGAT 57.877 25.926 16.81 14.02 41.38 2.45
651 5998 6.920817 AGGAGAAACAAAATAAATCCCGAAC 58.079 36.000 0.00 0.00 0.00 3.95
818 8451 4.120331 GCACGAACATGGCCCAGC 62.120 66.667 0.00 0.00 0.00 4.85
819 8452 2.360350 AGCACGAACATGGCCCAG 60.360 61.111 0.00 0.00 0.00 4.45
820 8453 2.672651 CAGCACGAACATGGCCCA 60.673 61.111 0.00 0.00 0.00 5.36
821 8454 3.443045 CCAGCACGAACATGGCCC 61.443 66.667 0.00 0.00 0.00 5.80
822 8455 3.443045 CCCAGCACGAACATGGCC 61.443 66.667 0.00 0.00 32.46 5.36
823 8456 1.926511 CTTCCCAGCACGAACATGGC 61.927 60.000 0.00 0.00 32.46 4.40
824 8457 1.308069 CCTTCCCAGCACGAACATGG 61.308 60.000 0.00 0.00 0.00 3.66
825 8458 0.606401 ACCTTCCCAGCACGAACATG 60.606 55.000 0.00 0.00 0.00 3.21
826 8459 0.321653 GACCTTCCCAGCACGAACAT 60.322 55.000 0.00 0.00 0.00 2.71
827 8460 1.070786 GACCTTCCCAGCACGAACA 59.929 57.895 0.00 0.00 0.00 3.18
828 8461 1.671379 GGACCTTCCCAGCACGAAC 60.671 63.158 0.00 0.00 0.00 3.95
829 8462 2.747686 GGACCTTCCCAGCACGAA 59.252 61.111 0.00 0.00 0.00 3.85
830 8463 3.691342 CGGACCTTCCCAGCACGA 61.691 66.667 0.00 0.00 31.13 4.35
831 8464 4.003788 ACGGACCTTCCCAGCACG 62.004 66.667 0.00 0.00 31.13 5.34
832 8465 2.358737 CACGGACCTTCCCAGCAC 60.359 66.667 0.00 0.00 31.13 4.40
836 8469 1.601419 GATCGACACGGACCTTCCCA 61.601 60.000 0.00 0.00 31.13 4.37
914 8573 1.110518 TTTGTTCGGGGGAAGGCAAC 61.111 55.000 0.00 0.00 0.00 4.17
994 8656 1.293179 CTGCGGTGTCCATCTCACA 59.707 57.895 0.00 0.00 37.52 3.58
1051 8725 1.783031 CGCATGCAGATTCCAGCCTC 61.783 60.000 19.57 0.00 0.00 4.70
1138 8818 7.734924 TTCTGAAATCCGGAAGATTATCATG 57.265 36.000 9.01 2.33 44.75 3.07
1317 8997 0.674895 CGGAACTCCTGCTTCCCTTG 60.675 60.000 0.00 0.00 34.68 3.61
1569 9255 1.044611 CCTCCTCCCGGATCTTCTTC 58.955 60.000 0.73 0.00 39.01 2.87
1726 9412 2.457970 GGATACGTACGGCTCAGAAAC 58.542 52.381 21.06 0.00 0.00 2.78
1741 9427 5.527582 ACTTCAATTTGCTGATACGGGATAC 59.472 40.000 0.00 0.00 0.00 2.24
1807 9493 7.061905 CGTTGATTTCACTATGTAGTCGAAGTT 59.938 37.037 0.00 0.00 33.46 2.66
1862 9548 1.734465 GTTCGTCTTCCATGGCTGAAG 59.266 52.381 6.96 6.07 40.45 3.02
1863 9549 1.347707 AGTTCGTCTTCCATGGCTGAA 59.652 47.619 6.96 3.47 0.00 3.02
1875 9561 2.048127 GCCCTGCGAAGTTCGTCT 60.048 61.111 25.04 0.00 42.81 4.18
1908 9603 2.313041 TCTCTTCTCCTCCATCTCCACA 59.687 50.000 0.00 0.00 0.00 4.17
2060 9804 8.992835 AAACTTCCATTTAAGAATCAATCTGC 57.007 30.769 0.00 0.00 38.79 4.26
2099 9858 6.722129 ACATCAAAGTCTCACTAGTAGAACCT 59.278 38.462 3.59 0.00 0.00 3.50
2408 10185 3.243367 TGAAGGCAACAAACAAAGGATCG 60.243 43.478 0.00 0.00 41.41 3.69
2428 10205 6.380560 TCATTTGCCATAATCAACAAGGATGA 59.619 34.615 0.00 0.00 0.00 2.92
2513 10313 8.964476 ATTGGATTTCGATGTAAACAGTATCT 57.036 30.769 0.00 0.00 0.00 1.98
2727 10527 2.078392 GCCACCATGAAAAAGCAATGG 58.922 47.619 0.00 0.00 38.31 3.16
2912 10715 4.063689 CCATTATGAGGACTAGCAGCTTG 58.936 47.826 0.00 0.00 0.00 4.01
3021 10827 1.761784 CTCAGCCTTAGAGCCATCAGT 59.238 52.381 0.00 0.00 0.00 3.41
3461 11267 1.214175 TCAAACTTGCCACTCCTTCCA 59.786 47.619 0.00 0.00 0.00 3.53
3474 11280 3.056607 CCAATCCTCGCCAATTCAAACTT 60.057 43.478 0.00 0.00 0.00 2.66
3534 11341 2.485426 AGACTGATTTGCAACCATCACG 59.515 45.455 9.30 8.58 0.00 4.35
3574 11381 0.676151 CAGCTCCTTGAACTGCTCCC 60.676 60.000 0.00 0.00 33.03 4.30
3634 11441 2.159407 GCCTGCTTCTTCTCAATCTTGC 60.159 50.000 0.00 0.00 0.00 4.01
3658 11468 2.760385 CCTCCTCCGTCAGGGTCC 60.760 72.222 0.00 0.00 43.67 4.46
3663 11473 2.575993 CACAGCCTCCTCCGTCAG 59.424 66.667 0.00 0.00 0.00 3.51
3676 11486 0.741221 GAAGCTTACCCTCGGCACAG 60.741 60.000 0.00 0.00 0.00 3.66
3798 11608 1.078426 AATAGCGTGCGAAGGGCTT 60.078 52.632 0.00 0.00 44.05 4.35
3853 11663 2.045926 GCACCCATCGACCAAGCT 60.046 61.111 0.00 0.00 0.00 3.74
4054 11871 5.528043 AACAACAACCATATCACAAGCAA 57.472 34.783 0.00 0.00 0.00 3.91
4228 13500 3.127895 TGCAACCAAGTCAAGTGTGTTAC 59.872 43.478 0.00 0.00 0.00 2.50
4278 13556 1.745489 GCCTGGTAAGCTTCGGGTG 60.745 63.158 0.00 0.00 0.00 4.61
4945 14275 5.580998 TCTAGATAACCCTGTTCACTCACT 58.419 41.667 0.00 0.00 0.00 3.41
4972 14302 7.575414 TTTTACAGATACAACTTGCCTTGAA 57.425 32.000 0.00 0.00 0.00 2.69
5209 14539 0.531532 CGAGCTTCATGGTAGGCCTG 60.532 60.000 17.99 0.00 35.27 4.85
5261 14591 2.183478 TGTTCTCGGATGCACACATT 57.817 45.000 0.00 0.00 36.35 2.71
5264 14594 1.129251 CACATGTTCTCGGATGCACAC 59.871 52.381 0.00 0.00 0.00 3.82
5289 14619 3.817647 AGCAGACAAGTTCAAGATGGAAC 59.182 43.478 0.00 0.00 45.87 3.62
5290 14620 4.090761 AGCAGACAAGTTCAAGATGGAA 57.909 40.909 0.00 0.00 0.00 3.53
5291 14621 3.777106 AGCAGACAAGTTCAAGATGGA 57.223 42.857 0.00 0.00 0.00 3.41
5292 14622 4.573900 AGTAGCAGACAAGTTCAAGATGG 58.426 43.478 0.00 0.00 0.00 3.51
5293 14623 7.840342 ATAAGTAGCAGACAAGTTCAAGATG 57.160 36.000 0.00 0.00 0.00 2.90
5390 14720 1.635844 TTAGCATACACGCAAGACCG 58.364 50.000 0.00 0.00 43.62 4.79
5421 14751 6.786967 AGACCTTGTATTGTACTCCGTATT 57.213 37.500 0.00 0.00 0.00 1.89
5490 14824 4.827284 GCTAGGAATGGCAAAATAGGCTTA 59.173 41.667 0.00 0.00 34.73 3.09
5508 14842 5.163281 AGATGCTCCATGAATAAGCTAGG 57.837 43.478 0.00 0.00 36.96 3.02
5520 14854 6.607970 TCAATCCAGAAATAAGATGCTCCAT 58.392 36.000 0.00 0.00 0.00 3.41
5698 15032 3.378911 TCGTGCATAGTGAACACAAGA 57.621 42.857 7.68 0.00 33.89 3.02
5737 15071 5.416013 ACTCTCTTACCTATTGCAAAAAGGC 59.584 40.000 24.12 0.00 33.42 4.35
5761 15095 9.889128 TTATACAACAATCAGACATCTTCATCA 57.111 29.630 0.00 0.00 0.00 3.07
5763 15097 9.671279 TGTTATACAACAATCAGACATCTTCAT 57.329 29.630 0.00 0.00 41.69 2.57
5826 15249 0.390860 CCGTCCATTAGAGGCTCTGG 59.609 60.000 26.95 19.77 0.00 3.86
5842 15265 4.464969 TGGTACACATAGGGCCGT 57.535 55.556 2.24 2.24 0.00 5.68
5898 15321 2.176247 GGACCTATTCCAGTGGAGGA 57.824 55.000 20.10 4.49 45.10 3.71
5907 15330 0.398098 TCCGGTGGAGGACCTATTCC 60.398 60.000 0.00 0.00 43.55 3.01
5908 15331 1.492764 TTCCGGTGGAGGACCTATTC 58.507 55.000 0.00 0.00 43.55 1.75
5909 15332 2.191981 ATTCCGGTGGAGGACCTATT 57.808 50.000 0.00 0.00 43.55 1.73
5910 15333 2.492940 CCTATTCCGGTGGAGGACCTAT 60.493 54.545 11.45 0.00 43.55 2.57
5911 15334 1.133262 CCTATTCCGGTGGAGGACCTA 60.133 57.143 11.45 0.00 43.55 3.08
5912 15335 0.398664 CCTATTCCGGTGGAGGACCT 60.399 60.000 11.45 0.00 43.55 3.85
5913 15336 2.041206 GCCTATTCCGGTGGAGGACC 62.041 65.000 18.58 2.51 40.56 4.46
5914 15337 1.446366 GCCTATTCCGGTGGAGGAC 59.554 63.158 18.58 8.81 40.56 3.85
5924 15347 2.748350 GTAGGGGCGGCCTATTCC 59.252 66.667 28.80 11.54 0.00 3.01
5970 15393 5.278561 GGATTCACCTCTATCTACCGTTGAG 60.279 48.000 0.00 0.00 35.41 3.02
5975 15398 3.497332 TGGGATTCACCTCTATCTACCG 58.503 50.000 0.00 0.00 38.98 4.02
5988 15411 0.911769 ACGAAGATGCCTGGGATTCA 59.088 50.000 1.04 0.00 0.00 2.57
6057 15480 4.335647 CACCAACCTCCAGCCGCT 62.336 66.667 0.00 0.00 0.00 5.52
6128 15560 3.319274 ATGGCGCCATGGACACTA 58.681 55.556 40.10 10.93 35.03 2.74
6153 15585 2.671070 CACCACATCCCGCTCCTT 59.329 61.111 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.