Multiple sequence alignment - TraesCS2D01G558900

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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 TraesCS2D01G558900 chr2D 100.000 6353 0 0 1 6353 631799314 631805666 0.000000e+00 11732.0
1 TraesCS2D01G558900 chr2D 97.404 2234 51 5 3858 6086 631482529 631480298 0.000000e+00 3797.0
2 TraesCS2D01G558900 chr2D 96.640 1994 59 5 845 2838 631485821 631483836 0.000000e+00 3304.0
3 TraesCS2D01G558900 chr2D 88.258 2095 160 44 835 2896 631245587 631243546 0.000000e+00 2427.0
4 TraesCS2D01G558900 chr2D 87.525 1499 122 32 4217 5672 631241743 631240267 0.000000e+00 1672.0
5 TraesCS2D01G558900 chr2D 86.854 1141 128 19 3864 4988 593802160 593803294 0.000000e+00 1256.0
6 TraesCS2D01G558900 chr2D 91.860 688 10 6 3102 3789 631483331 631482690 0.000000e+00 918.0
7 TraesCS2D01G558900 chr2D 81.514 898 115 28 2672 3536 593800726 593801605 0.000000e+00 691.0
8 TraesCS2D01G558900 chr2D 90.414 532 37 8 3102 3628 631243250 631242728 0.000000e+00 688.0
9 TraesCS2D01G558900 chr2D 97.544 285 7 0 2820 3104 631483655 631483371 7.400000e-134 488.0
10 TraesCS2D01G558900 chr2D 95.038 262 5 3 6100 6353 631480314 631480053 7.670000e-109 405.0
11 TraesCS2D01G558900 chr2D 92.386 197 10 4 5891 6086 631240066 631239874 6.270000e-70 276.0
12 TraesCS2D01G558900 chr2D 90.050 201 18 1 5005 5205 593803381 593803579 6.320000e-65 259.0
13 TraesCS2D01G558900 chr2D 93.902 164 10 0 3626 3789 631242661 631242498 1.370000e-61 248.0
14 TraesCS2D01G558900 chr2D 89.231 130 11 2 5267 5393 593803712 593803841 6.590000e-35 159.0
15 TraesCS2D01G558900 chr2D 89.744 117 12 0 6237 6353 631239711 631239595 3.970000e-32 150.0
16 TraesCS2D01G558900 chr2D 88.462 104 11 1 4122 4225 631242445 631242343 2.400000e-24 124.0
17 TraesCS2D01G558900 chr2D 100.000 67 0 0 3790 3856 631482627 631482561 2.400000e-24 124.0
18 TraesCS2D01G558900 chr2B 96.097 3126 68 21 1 3104 774950807 774947714 0.000000e+00 5048.0
19 TraesCS2D01G558900 chr2B 96.402 2251 58 8 3858 6086 774946853 774944604 0.000000e+00 3687.0
20 TraesCS2D01G558900 chr2B 86.338 2313 201 59 845 3104 774721888 774719638 0.000000e+00 2414.0
21 TraesCS2D01G558900 chr2B 87.643 2104 163 50 835 2896 744382003 744384051 0.000000e+00 2355.0
22 TraesCS2D01G558900 chr2B 88.456 1412 103 31 4217 5585 744386297 744387691 0.000000e+00 1650.0
23 TraesCS2D01G558900 chr2B 87.749 1004 86 17 4217 5183 774718427 774717424 0.000000e+00 1138.0
24 TraesCS2D01G558900 chr2B 84.298 1140 124 25 949 2070 720801620 720802722 0.000000e+00 1062.0
25 TraesCS2D01G558900 chr2B 94.186 688 13 4 3102 3789 774947674 774947014 0.000000e+00 1024.0
26 TraesCS2D01G558900 chr2B 84.599 922 106 25 3874 4774 720805629 720806535 0.000000e+00 883.0
27 TraesCS2D01G558900 chr2B 86.554 766 41 16 5212 5961 774717285 774716566 0.000000e+00 787.0
28 TraesCS2D01G558900 chr2B 91.841 527 29 5 3102 3626 774719598 774719084 0.000000e+00 723.0
29 TraesCS2D01G558900 chr2B 90.132 456 35 6 4758 5205 720806682 720807135 9.180000e-163 584.0
30 TraesCS2D01G558900 chr2B 91.667 396 23 7 3102 3496 744384347 744384733 2.020000e-149 540.0
31 TraesCS2D01G558900 chr2B 79.974 769 102 26 2716 3459 720803870 720804611 2.630000e-143 520.0
32 TraesCS2D01G558900 chr2B 90.031 321 25 2 3472 3789 720805143 720805459 5.930000e-110 409.0
33 TraesCS2D01G558900 chr2B 94.253 261 8 2 6100 6353 774944620 774944360 5.970000e-105 392.0
34 TraesCS2D01G558900 chr2B 90.863 197 13 4 5891 6086 744387969 744388161 6.320000e-65 259.0
35 TraesCS2D01G558900 chr2B 80.495 364 47 11 2206 2569 720803387 720803726 2.270000e-64 257.0
36 TraesCS2D01G558900 chr2B 93.293 164 11 0 3626 3789 744385142 744385305 6.360000e-60 243.0
37 TraesCS2D01G558900 chr2B 84.921 252 15 9 6103 6353 774716425 774716196 3.830000e-57 233.0
38 TraesCS2D01G558900 chr2B 83.399 253 20 9 6102 6353 744388147 744388378 1.390000e-51 215.0
39 TraesCS2D01G558900 chr2B 92.126 127 10 0 5267 5393 720807254 720807380 5.060000e-41 180.0
40 TraesCS2D01G558900 chr2B 89.109 101 10 1 4122 4221 744385358 744385458 2.400000e-24 124.0
41 TraesCS2D01G558900 chr2B 97.015 67 2 0 3790 3856 774946951 774946885 5.210000e-21 113.0
42 TraesCS2D01G558900 chr2B 84.071 113 14 2 2171 2280 774376235 774376124 8.710000e-19 106.0
43 TraesCS2D01G558900 chr2A 97.673 2020 39 4 1088 3104 760113752 760115766 0.000000e+00 3463.0
44 TraesCS2D01G558900 chr2A 95.922 1741 55 12 3858 5585 760116635 760118372 0.000000e+00 2808.0
45 TraesCS2D01G558900 chr2A 96.326 1388 28 6 546 1919 759873791 759872413 0.000000e+00 2259.0
46 TraesCS2D01G558900 chr2A 95.930 688 12 4 3102 3789 760115806 760116477 0.000000e+00 1101.0
47 TraesCS2D01G558900 chr2A 97.581 372 4 1 1915 2281 759869951 759869580 3.230000e-177 632.0
48 TraesCS2D01G558900 chr2A 96.429 140 3 1 565 704 108550056 108550193 4.950000e-56 230.0
49 TraesCS2D01G558900 chr2A 83.871 248 22 10 845 1092 760113369 760113598 2.980000e-53 220.0
50 TraesCS2D01G558900 chr2A 100.000 66 0 0 3791 3856 760116538 760116603 8.650000e-24 122.0
51 TraesCS2D01G558900 chr2A 97.222 72 0 1 154 223 108549987 108550058 3.110000e-23 121.0
52 TraesCS2D01G558900 chr4D 83.701 951 113 25 4319 5253 73386376 73387300 0.000000e+00 859.0
53 TraesCS2D01G558900 chr4D 86.704 534 58 5 3257 3789 73385236 73385757 1.190000e-161 580.0
54 TraesCS2D01G558900 chr4D 78.261 391 60 10 2206 2596 73384303 73384668 1.780000e-55 228.0
55 TraesCS2D01G558900 chr4D 79.537 259 29 15 2858 3104 73384847 73385093 5.100000e-36 163.0
56 TraesCS2D01G558900 chr4D 88.571 70 8 0 3156 3225 73385169 73385238 1.130000e-12 86.1
57 TraesCS2D01G558900 chr4D 89.583 48 2 1 4268 4312 73386299 73386346 2.470000e-04 58.4
58 TraesCS2D01G558900 chr1B 82.206 1079 117 33 4208 5244 34324141 34325186 0.000000e+00 859.0
59 TraesCS2D01G558900 chr1B 81.393 962 122 29 2858 3789 34322686 34323620 0.000000e+00 732.0
60 TraesCS2D01G558900 chr1B 86.294 591 70 9 1072 1659 34321082 34321664 3.230000e-177 632.0
61 TraesCS2D01G558900 chr1B 85.411 377 42 4 1715 2078 34321679 34322055 4.650000e-101 379.0
62 TraesCS2D01G558900 chr1D 86.330 534 60 3 3257 3789 20971290 20971811 2.570000e-158 569.0
63 TraesCS2D01G558900 chr1D 78.261 391 60 10 2206 2596 20970358 20970723 1.780000e-55 228.0
64 TraesCS2D01G558900 chr1D 79.537 259 28 16 2858 3104 20970902 20971147 1.830000e-35 161.0
65 TraesCS2D01G558900 chr1D 88.571 70 8 0 3156 3225 20971223 20971292 1.130000e-12 86.1
66 TraesCS2D01G558900 chr6A 97.143 140 2 1 565 704 192012920 192012783 1.060000e-57 235.0
67 TraesCS2D01G558900 chr6A 97.260 73 0 1 154 224 192012989 192012917 8.650000e-24 122.0
68 TraesCS2D01G558900 chr7B 96.429 140 3 1 565 704 677491000 677490863 4.950000e-56 230.0
69 TraesCS2D01G558900 chr7B 97.260 73 0 1 154 224 677491069 677490997 8.650000e-24 122.0
70 TraesCS2D01G558900 chr5B 96.429 140 3 1 565 704 343342831 343342968 4.950000e-56 230.0
71 TraesCS2D01G558900 chr5B 97.260 73 0 1 154 224 343342762 343342834 8.650000e-24 122.0
72 TraesCS2D01G558900 chr3A 96.429 140 3 1 565 704 18720015 18720152 4.950000e-56 230.0
73 TraesCS2D01G558900 chr3A 95.714 140 4 1 565 704 189428673 189428536 2.300000e-54 224.0
74 TraesCS2D01G558900 chr3A 95.000 140 5 1 565 704 670995264 670995401 1.070000e-52 219.0
75 TraesCS2D01G558900 chr3A 95.890 73 1 1 154 224 18719946 18720018 4.020000e-22 117.0
76 TraesCS2D01G558900 chr3A 95.890 73 1 1 154 224 670995195 670995267 4.020000e-22 117.0
77 TraesCS2D01G558900 chr6B 95.890 73 1 1 154 224 67071165 67071237 4.020000e-22 117.0
78 TraesCS2D01G558900 chr6B 95.890 73 1 1 154 224 269173983 269174055 4.020000e-22 117.0


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 TraesCS2D01G558900 chr2D 631799314 631805666 6352 False 11732.000000 11732 100.000000 1 6353 1 chr2D.!!$F1 6352
1 TraesCS2D01G558900 chr2D 631480053 631485821 5768 True 1506.000000 3797 96.414333 845 6353 6 chr2D.!!$R2 5508
2 TraesCS2D01G558900 chr2D 631239595 631245587 5992 True 797.857143 2427 90.098714 835 6353 7 chr2D.!!$R1 5518
3 TraesCS2D01G558900 chr2D 593800726 593803841 3115 False 591.250000 1256 86.912250 2672 5393 4 chr2D.!!$F2 2721
4 TraesCS2D01G558900 chr2B 774944360 774950807 6447 True 2052.800000 5048 95.590600 1 6353 5 chr2B.!!$R3 6352
5 TraesCS2D01G558900 chr2B 774716196 774721888 5692 True 1059.000000 2414 87.480600 845 6353 5 chr2B.!!$R2 5508
6 TraesCS2D01G558900 chr2B 744382003 744388378 6375 False 769.428571 2355 89.204286 835 6353 7 chr2B.!!$F2 5518
7 TraesCS2D01G558900 chr2B 720801620 720807380 5760 False 556.428571 1062 85.950714 949 5393 7 chr2B.!!$F1 4444
8 TraesCS2D01G558900 chr2A 760113369 760118372 5003 False 1542.800000 3463 94.679200 845 5585 5 chr2A.!!$F2 4740
9 TraesCS2D01G558900 chr2A 759869580 759873791 4211 True 1445.500000 2259 96.953500 546 2281 2 chr2A.!!$R1 1735
10 TraesCS2D01G558900 chr4D 73384303 73387300 2997 False 329.083333 859 84.392833 2206 5253 6 chr4D.!!$F1 3047
11 TraesCS2D01G558900 chr1B 34321082 34325186 4104 False 650.500000 859 83.826000 1072 5244 4 chr1B.!!$F1 4172
12 TraesCS2D01G558900 chr1D 20970358 20971811 1453 False 261.025000 569 83.174750 2206 3789 4 chr1D.!!$F1 1583

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
131 138 0.106708 TCCTGCACTTGTGTGGACTC 59.893 55.000 11.37 0.00 43.97 3.36 F
407 417 0.107410 TGCCCAAGACGTGAACAAGT 60.107 50.000 0.00 0.00 0.00 3.16 F
408 418 0.586802 GCCCAAGACGTGAACAAGTC 59.413 55.000 11.63 11.63 39.57 3.01 F
411 421 1.202651 CCAAGACGTGAACAAGTCCCT 60.203 52.381 14.86 3.22 40.01 4.20 F
414 424 1.760613 AGACGTGAACAAGTCCCTTGA 59.239 47.619 14.86 0.00 43.42 3.02 F
415 425 1.865340 GACGTGAACAAGTCCCTTGAC 59.135 52.381 10.73 5.33 43.42 3.18 F
2790 6124 2.223377 CGCTCTAGTTTTGTCACAACCC 59.777 50.000 0.00 0.00 0.00 4.11 F
4002 8868 2.203938 GACCAGACTGGGACCCCA 60.204 66.667 25.34 7.67 43.37 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1260 1466 2.580276 CAATGCCACCACCCATGC 59.420 61.111 0.0 0.0 0.00 4.06 R
1418 1628 4.245660 CGAAACATAGACATGACAGGTGT 58.754 43.478 0.0 0.0 35.96 4.16 R
3093 6707 9.451002 AAATCATTTTGGTGATTGCATTATGAA 57.549 25.926 0.0 0.0 45.49 2.57 R
3133 6796 5.277974 GCTGAATACATACATCCAAACGCAT 60.278 40.000 0.0 0.0 0.00 4.73 R
3312 6995 1.725803 ACCTTTACGAGTCCCCAACT 58.274 50.000 0.0 0.0 42.42 3.16 R
3313 6996 2.556144 AACCTTTACGAGTCCCCAAC 57.444 50.000 0.0 0.0 0.00 3.77 R
4878 11162 0.668706 CTGACAGAGCACCTTCACCG 60.669 60.000 0.0 0.0 0.00 4.94 R
5366 11908 1.002430 TCACTTGTCAGCCTCACCATC 59.998 52.381 0.0 0.0 0.00 3.51 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
127 134 0.179020 TTCCTCCTGCACTTGTGTGG 60.179 55.000 2.61 5.78 43.97 4.17
131 138 0.106708 TCCTGCACTTGTGTGGACTC 59.893 55.000 11.37 0.00 43.97 3.36
144 151 4.477975 GACTCGTCTGACGGCGGG 62.478 72.222 27.69 17.57 42.81 6.13
175 182 5.305644 TGTTGCCATGGTTACCTTGTTAATT 59.694 36.000 14.67 0.00 0.00 1.40
276 286 2.548480 GCGGTCTTATGGGCAGTTTATC 59.452 50.000 0.00 0.00 0.00 1.75
331 341 5.462398 GGGTACATGTTATGACTTCACGATC 59.538 44.000 2.30 0.00 0.00 3.69
405 415 0.393132 TGTGCCCAAGACGTGAACAA 60.393 50.000 0.00 0.00 0.00 2.83
406 416 0.307760 GTGCCCAAGACGTGAACAAG 59.692 55.000 0.00 0.00 0.00 3.16
407 417 0.107410 TGCCCAAGACGTGAACAAGT 60.107 50.000 0.00 0.00 0.00 3.16
408 418 0.586802 GCCCAAGACGTGAACAAGTC 59.413 55.000 11.63 11.63 39.57 3.01
410 420 1.226746 CCAAGACGTGAACAAGTCCC 58.773 55.000 14.86 0.00 40.01 4.46
411 421 1.202651 CCAAGACGTGAACAAGTCCCT 60.203 52.381 14.86 3.22 40.01 4.20
412 422 2.561569 CAAGACGTGAACAAGTCCCTT 58.438 47.619 14.86 4.14 40.01 3.95
413 423 2.240493 AGACGTGAACAAGTCCCTTG 57.760 50.000 14.86 2.54 45.85 3.61
414 424 1.760613 AGACGTGAACAAGTCCCTTGA 59.239 47.619 14.86 0.00 43.42 3.02
415 425 1.865340 GACGTGAACAAGTCCCTTGAC 59.135 52.381 10.73 5.33 43.42 3.18
540 550 4.021981 CACAAGATGAGTGGAGTAGTGTGA 60.022 45.833 0.00 0.00 36.76 3.58
1106 1307 3.323979 TGACTTAGTGAGGTTCTTGTCCC 59.676 47.826 0.00 0.00 0.00 4.46
1183 1388 3.503363 TGGCAGTTTGATTCATCAGTGTC 59.497 43.478 0.00 0.00 38.19 3.67
1216 1422 3.491964 GGTGTTTACTTTGGGTGAAAGGC 60.492 47.826 0.00 0.00 44.85 4.35
1260 1466 3.265791 CAAGGGTGATCTTCTCTTTCGG 58.734 50.000 0.00 0.00 0.00 4.30
2787 6121 3.787785 TGACGCTCTAGTTTTGTCACAA 58.212 40.909 0.00 0.00 34.85 3.33
2788 6122 3.554324 TGACGCTCTAGTTTTGTCACAAC 59.446 43.478 0.00 0.00 34.85 3.32
2789 6123 2.870411 ACGCTCTAGTTTTGTCACAACC 59.130 45.455 0.00 0.00 0.00 3.77
2790 6124 2.223377 CGCTCTAGTTTTGTCACAACCC 59.777 50.000 0.00 0.00 0.00 4.11
2791 6125 3.211045 GCTCTAGTTTTGTCACAACCCA 58.789 45.455 0.00 0.00 0.00 4.51
3007 6603 4.083749 TGTTTTTGAATACGGTGGATGTCG 60.084 41.667 0.00 0.00 0.00 4.35
3010 6606 3.322211 TGAATACGGTGGATGTCGTTT 57.678 42.857 0.00 0.00 40.31 3.60
3500 7916 3.193479 GGGATGAATCCTGGTTGAAACAC 59.807 47.826 9.18 0.00 46.35 3.32
3856 8687 5.242393 CAGTCCTGAATTTGTCCATCAACTT 59.758 40.000 0.00 0.00 35.61 2.66
4002 8868 2.203938 GACCAGACTGGGACCCCA 60.204 66.667 25.34 7.67 43.37 4.96
4560 10666 3.056607 ACAAGGTGGCATCAAAAGCATAC 60.057 43.478 0.00 0.00 0.00 2.39
4701 10815 5.363005 TCTCTAGTTTCCCGCTTATTAGCTT 59.637 40.000 1.77 0.00 45.51 3.74
4878 11162 0.109412 GCAAACTGCTGCTGGATGAC 60.109 55.000 11.29 3.09 40.96 3.06
4967 11251 1.598962 GTCAGGCTGCAGCTCACAA 60.599 57.895 35.82 15.85 41.70 3.33
5040 11395 5.184096 CACTCTGTCCAGTCTACATAGTTGT 59.816 44.000 0.00 0.00 33.48 3.32
5107 11470 1.260538 TGATGCTCTCCTGGACGCTT 61.261 55.000 12.74 7.72 0.00 4.68
5112 11475 2.027192 TGCTCTCCTGGACGCTTAAAAT 60.027 45.455 12.74 0.00 0.00 1.82
5163 11526 5.438833 AGAGAGCTACGGTAATCTACTGTT 58.561 41.667 3.74 0.00 45.61 3.16
5366 11908 3.181472 GGCCAGGGAATTAATGAAAGCTG 60.181 47.826 0.00 0.00 0.00 4.24
5643 12193 6.274157 AGATCTAGCACAAATACCCTATCG 57.726 41.667 0.00 0.00 0.00 2.92
5702 12252 5.760743 AGAGAAGAAAAAGTGAAGCAGTACC 59.239 40.000 0.00 0.00 0.00 3.34
6069 12724 8.417106 TCTCTCTCTAGGCTAATTAAACACATG 58.583 37.037 0.00 0.00 0.00 3.21
6070 12725 8.306313 TCTCTCTAGGCTAATTAAACACATGA 57.694 34.615 0.00 0.00 0.00 3.07
6071 12726 8.198109 TCTCTCTAGGCTAATTAAACACATGAC 58.802 37.037 0.00 0.00 0.00 3.06
6072 12727 7.847096 TCTCTAGGCTAATTAAACACATGACA 58.153 34.615 0.00 0.00 0.00 3.58
6073 12728 7.981789 TCTCTAGGCTAATTAAACACATGACAG 59.018 37.037 0.00 0.00 0.00 3.51
6074 12729 7.047891 TCTAGGCTAATTAAACACATGACAGG 58.952 38.462 0.00 0.00 0.00 4.00
6075 12730 5.815581 AGGCTAATTAAACACATGACAGGA 58.184 37.500 0.00 0.00 0.00 3.86
6076 12731 6.245408 AGGCTAATTAAACACATGACAGGAA 58.755 36.000 0.00 0.00 0.00 3.36
6077 12732 6.891908 AGGCTAATTAAACACATGACAGGAAT 59.108 34.615 0.00 0.00 0.00 3.01
6078 12733 7.397192 AGGCTAATTAAACACATGACAGGAATT 59.603 33.333 0.00 2.60 0.00 2.17
6079 12734 8.034804 GGCTAATTAAACACATGACAGGAATTT 58.965 33.333 0.00 0.00 0.00 1.82
6155 12810 1.271656 AGGCTCTTCAAAATGTGCAGC 59.728 47.619 0.00 0.00 0.00 5.25
6178 12864 2.241160 AGCACATTCTTGTTGATGGCA 58.759 42.857 0.00 0.00 32.34 4.92
6190 12876 5.999205 TGTTGATGGCAGGTAAATGAAAT 57.001 34.783 0.00 0.00 0.00 2.17
6191 12877 6.357579 TGTTGATGGCAGGTAAATGAAATT 57.642 33.333 0.00 0.00 38.98 1.82
6193 12879 6.873076 TGTTGATGGCAGGTAAATGAAATTTC 59.127 34.615 11.41 11.41 44.81 2.17
6194 12880 6.855763 TGATGGCAGGTAAATGAAATTTCT 57.144 33.333 18.64 1.90 44.81 2.52
6196 12882 7.771183 TGATGGCAGGTAAATGAAATTTCTAC 58.229 34.615 18.64 12.36 44.81 2.59
6197 12883 7.615365 TGATGGCAGGTAAATGAAATTTCTACT 59.385 33.333 18.64 5.86 44.81 2.57
6199 12885 8.189119 TGGCAGGTAAATGAAATTTCTACTTT 57.811 30.769 18.64 15.94 44.81 2.66
6200 12886 8.646900 TGGCAGGTAAATGAAATTTCTACTTTT 58.353 29.630 18.64 14.08 44.81 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.093181 ACAGCATTGGCATTTGCATCAT 60.093 40.909 20.67 2.18 44.61 2.45
13 14 1.608542 GGAACAGCATTGGCATTTGCA 60.609 47.619 20.67 0.00 44.61 4.08
127 134 4.477975 CCCGCCGTCAGACGAGTC 62.478 72.222 24.88 11.48 46.05 3.36
243 252 0.884704 AAGACCGCAATCGCACACTT 60.885 50.000 0.00 0.00 38.40 3.16
245 254 1.006832 ATAAGACCGCAATCGCACAC 58.993 50.000 0.00 0.00 38.40 3.82
276 286 3.408634 ACTTGTGTTAACCAGATTCCCG 58.591 45.455 2.48 0.00 0.00 5.14
351 361 4.956075 TCAATCAGTGCATAGACTAGACCA 59.044 41.667 0.00 0.00 0.00 4.02
356 366 5.654209 AGTCAGTCAATCAGTGCATAGACTA 59.346 40.000 0.00 0.00 34.83 2.59
406 416 5.479124 TTACACTCCTAAAGTCAAGGGAC 57.521 43.478 0.00 0.00 44.66 4.46
407 417 6.503560 TTTTACACTCCTAAAGTCAAGGGA 57.496 37.500 0.00 0.00 35.45 4.20
540 550 4.218417 GCATCCTGCAAATATAACCCGAAT 59.782 41.667 0.00 0.00 44.26 3.34
585 595 2.343544 GTGCAGAAAGAAAATCATGCGC 59.656 45.455 0.00 0.00 36.47 6.09
586 596 3.829948 AGTGCAGAAAGAAAATCATGCG 58.170 40.909 0.00 0.00 36.47 4.73
1106 1307 3.216800 AGCCCACATGTGTTGCATATAG 58.783 45.455 28.67 11.63 35.74 1.31
1183 1388 4.853924 AAGTAAACACCCAAGCATCAAG 57.146 40.909 0.00 0.00 0.00 3.02
1216 1422 3.480894 GTCGTCGAGACTCTTTACAGTG 58.519 50.000 0.00 0.00 46.13 3.66
1260 1466 2.580276 CAATGCCACCACCCATGC 59.420 61.111 0.00 0.00 0.00 4.06
1418 1628 4.245660 CGAAACATAGACATGACAGGTGT 58.754 43.478 0.00 0.00 35.96 4.16
3093 6707 9.451002 AAATCATTTTGGTGATTGCATTATGAA 57.549 25.926 0.00 0.00 45.49 2.57
3133 6796 5.277974 GCTGAATACATACATCCAAACGCAT 60.278 40.000 0.00 0.00 0.00 4.73
3312 6995 1.725803 ACCTTTACGAGTCCCCAACT 58.274 50.000 0.00 0.00 42.42 3.16
3313 6996 2.556144 AACCTTTACGAGTCCCCAAC 57.444 50.000 0.00 0.00 0.00 3.77
3314 6997 3.620472 GCATAACCTTTACGAGTCCCCAA 60.620 47.826 0.00 0.00 0.00 4.12
3315 6998 2.093341 GCATAACCTTTACGAGTCCCCA 60.093 50.000 0.00 0.00 0.00 4.96
3500 7916 8.019656 AGGGTCTACATAATACTGGTACAAAG 57.980 38.462 0.00 0.00 38.70 2.77
3892 8753 4.706476 TGATGCTCTAAAGAAAACCCCATG 59.294 41.667 0.00 0.00 0.00 3.66
4002 8868 5.401550 CAATGAACAGCCGACAACAAATAT 58.598 37.500 0.00 0.00 0.00 1.28
4038 8910 7.154656 TCATTGGATCGATACTGAATAACCAG 58.845 38.462 9.52 0.00 39.93 4.00
4468 10574 2.378038 TGTTTGTTCAAGCTGCCTTCT 58.622 42.857 0.00 0.00 0.00 2.85
4560 10666 1.808343 GTTTAAGGGGCTTACACACCG 59.192 52.381 0.00 0.00 29.99 4.94
4878 11162 0.668706 CTGACAGAGCACCTTCACCG 60.669 60.000 0.00 0.00 0.00 4.94
5040 11395 5.596836 AGAGCAAAACAAAGGAACATGAA 57.403 34.783 0.00 0.00 0.00 2.57
5107 11470 7.169591 TCTACGTTTCCAGGATCCAAATTTTA 58.830 34.615 15.82 0.00 0.00 1.52
5112 11475 3.055385 CCTCTACGTTTCCAGGATCCAAA 60.055 47.826 15.82 2.80 0.00 3.28
5366 11908 1.002430 TCACTTGTCAGCCTCACCATC 59.998 52.381 0.00 0.00 0.00 3.51
5643 12193 6.642131 TGAAAACTCAGCAAATATTCAACAGC 59.358 34.615 0.00 0.00 0.00 4.40
5672 12222 6.703607 TGCTTCACTTTTTCTTCTCTACTGAG 59.296 38.462 0.00 0.00 41.51 3.35
5702 12252 3.618351 AGAAGATGCAAATGAGAGGGTG 58.382 45.455 0.00 0.00 0.00 4.61
6089 12744 6.556874 AGAATAAATTCCTGTCCCCACAAAAA 59.443 34.615 0.00 0.00 37.51 1.94
6090 12745 6.081356 AGAATAAATTCCTGTCCCCACAAAA 58.919 36.000 0.00 0.00 37.51 2.44
6091 12746 5.650283 AGAATAAATTCCTGTCCCCACAAA 58.350 37.500 0.00 0.00 37.51 2.83
6092 12747 5.269554 AGAATAAATTCCTGTCCCCACAA 57.730 39.130 0.00 0.00 37.51 3.33
6093 12748 4.946160 AGAATAAATTCCTGTCCCCACA 57.054 40.909 0.00 0.00 37.51 4.17
6094 12749 4.142160 GCAAGAATAAATTCCTGTCCCCAC 60.142 45.833 0.00 0.00 37.51 4.61
6095 12750 4.023291 GCAAGAATAAATTCCTGTCCCCA 58.977 43.478 0.00 0.00 37.51 4.96
6096 12751 3.384789 GGCAAGAATAAATTCCTGTCCCC 59.615 47.826 0.00 0.00 37.51 4.81
6097 12752 3.384789 GGGCAAGAATAAATTCCTGTCCC 59.615 47.826 12.14 12.85 43.75 4.46
6098 12753 4.655762 GGGCAAGAATAAATTCCTGTCC 57.344 45.455 8.73 8.73 43.36 4.02
6155 12810 4.082625 TGCCATCAACAAGAATGTGCTAAG 60.083 41.667 0.00 0.00 40.46 2.18
6200 12886 8.361139 TCAATAACTAGAAATTTCCCGCAAAAA 58.639 29.630 14.61 0.00 0.00 1.94
6202 12888 7.455641 TCAATAACTAGAAATTTCCCGCAAA 57.544 32.000 14.61 0.00 0.00 3.68
6203 12889 7.392113 TCTTCAATAACTAGAAATTTCCCGCAA 59.608 33.333 14.61 0.00 0.00 4.85
6204 12890 6.882140 TCTTCAATAACTAGAAATTTCCCGCA 59.118 34.615 14.61 0.00 0.00 5.69
6205 12891 7.316544 TCTTCAATAACTAGAAATTTCCCGC 57.683 36.000 14.61 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.