Multiple sequence alignment - TraesCS3A01G190800

Loading Multiple Alignment...

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 TraesCS3A01G190800 chr3A 100.000 4804 0 0 1 4804 239961359 239956556 0.000000e+00 8872.0
1 TraesCS3A01G190800 chr3A 98.485 66 1 0 1 66 110432007 110431942 3.040000e-22 117.0
2 TraesCS3A01G190800 chr3B 94.804 2752 100 14 2066 4804 268056163 268058884 0.000000e+00 4250.0
3 TraesCS3A01G190800 chr3B 97.029 1481 28 6 590 2067 268054659 268056126 0.000000e+00 2477.0
4 TraesCS3A01G190800 chr3B 91.017 423 32 2 62 481 267960887 267961306 2.510000e-157 566.0
5 TraesCS3A01G190800 chr3B 86.617 269 35 1 63 331 731533053 731532786 3.640000e-76 296.0
6 TraesCS3A01G190800 chr3B 86.397 272 32 4 65 335 751146439 751146172 4.700000e-75 292.0
7 TraesCS3A01G190800 chr3B 86.245 269 36 1 63 331 731559246 731558979 1.690000e-74 291.0
8 TraesCS3A01G190800 chr3B 95.455 66 3 0 489 554 268047519 268047584 6.580000e-19 106.0
9 TraesCS3A01G190800 chr3B 93.056 72 5 0 540 611 268054587 268054658 6.580000e-19 106.0
10 TraesCS3A01G190800 chr3D 97.812 2377 44 3 2066 4440 186944000 186946370 0.000000e+00 4095.0
11 TraesCS3A01G190800 chr3D 95.274 1439 33 9 633 2067 186941050 186942457 0.000000e+00 2248.0
12 TraesCS3A01G190800 chr3D 85.538 567 39 11 62 611 186935931 186936471 1.950000e-153 553.0
13 TraesCS3A01G190800 chr3D 89.318 337 36 0 4468 4804 186946510 186946846 1.600000e-114 424.0
14 TraesCS3A01G190800 chr3D 98.485 66 1 0 1 66 393609362 393609427 3.040000e-22 117.0
15 TraesCS3A01G190800 chr3D 98.182 55 1 0 4456 4510 186946363 186946417 3.960000e-16 97.1
16 TraesCS3A01G190800 chr3D 94.737 57 1 1 590 644 186936494 186936550 2.380000e-13 87.9
17 TraesCS3A01G190800 chr3D 100.000 43 0 0 4468 4510 186946421 186946463 3.990000e-11 80.5
18 TraesCS3A01G190800 chr3D 100.000 39 0 0 4468 4506 186946467 186946505 6.670000e-09 73.1
19 TraesCS3A01G190800 chr2B 86.940 268 34 1 65 331 557309890 557310157 2.810000e-77 300.0
20 TraesCS3A01G190800 chr2B 100.000 29 0 0 4406 4434 9843049 9843077 2.000000e-03 54.7
21 TraesCS3A01G190800 chr7D 86.131 274 38 0 64 337 552926479 552926206 3.640000e-76 296.0
22 TraesCS3A01G190800 chr5A 85.609 271 39 0 65 335 571777506 571777776 7.870000e-73 285.0
23 TraesCS3A01G190800 chr5A 98.485 66 1 0 1 66 197321727 197321662 3.040000e-22 117.0
24 TraesCS3A01G190800 chr7B 83.516 273 45 0 64 336 429278842 429279114 6.170000e-64 255.0
25 TraesCS3A01G190800 chr1D 83.764 271 41 3 62 331 314980962 314980694 2.220000e-63 254.0
26 TraesCS3A01G190800 chr1D 74.576 236 47 9 4317 4550 349442682 349442906 1.840000e-14 91.6
27 TraesCS3A01G190800 chr2D 97.143 70 2 0 1 70 182839370 182839439 8.450000e-23 119.0
28 TraesCS3A01G190800 chr6A 98.485 66 1 0 1 66 427288185 427288250 3.040000e-22 117.0
29 TraesCS3A01G190800 chr6A 91.667 48 4 0 4347 4394 593425417 593425464 3.100000e-07 67.6
30 TraesCS3A01G190800 chr4D 97.101 69 2 0 1 69 63843900 63843832 3.040000e-22 117.0
31 TraesCS3A01G190800 chr5D 90.698 86 5 3 1 84 465223324 465223240 1.410000e-20 111.0
32 TraesCS3A01G190800 chr6B 93.421 76 2 3 1 76 269312159 269312231 5.080000e-20 110.0
33 TraesCS3A01G190800 chr6B 86.111 72 9 1 4317 4388 71874563 71874633 5.160000e-10 76.8
34 TraesCS3A01G190800 chr7A 90.361 83 6 2 1 82 497997120 497997039 1.830000e-19 108.0
35 TraesCS3A01G190800 chr5B 85.897 78 11 0 4317 4394 691229856 691229933 3.080000e-12 84.2
36 TraesCS3A01G190800 chr5B 89.394 66 3 3 4331 4394 431784570 431784507 3.990000e-11 80.5
37 TraesCS3A01G190800 chr2A 85.915 71 8 2 4325 4394 102112008 102112077 1.850000e-09 75.0
38 TraesCS3A01G190800 chr6D 84.507 71 7 4 4325 4394 387629860 387629793 3.100000e-07 67.6


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 TraesCS3A01G190800 chr3A 239956556 239961359 4803 True 8872.000000 8872 100.000000 1 4804 1 chr3A.!!$R2 4803
1 TraesCS3A01G190800 chr3B 268054587 268058884 4297 False 2277.666667 4250 94.963000 540 4804 3 chr3B.!!$F3 4264
2 TraesCS3A01G190800 chr3D 186941050 186946846 5796 False 1169.616667 4095 96.764333 633 4804 6 chr3D.!!$F3 4171
3 TraesCS3A01G190800 chr3D 186935931 186936550 619 False 320.450000 553 90.137500 62 644 2 chr3D.!!$F2 582

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
421 422 0.107017 CCCGATCAACAGATGGCCTT 60.107 55.000 3.32 0.0 0.0 4.35 F
906 967 0.323451 AGGCCGGGGAGTCAAAAATC 60.323 55.000 2.18 0.0 0.0 2.17 F
907 968 0.323451 GGCCGGGGAGTCAAAAATCT 60.323 55.000 2.18 0.0 0.0 2.40 F
908 969 1.064979 GGCCGGGGAGTCAAAAATCTA 60.065 52.381 2.18 0.0 0.0 1.98 F
2427 4036 1.135402 GGACTCGCATTTTCGCCATTT 60.135 47.619 0.00 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1967 2032 6.208599 TCAACTTCACCATGAAATTAGGAACC 59.791 38.462 0.0 0.0 35.73 3.62 R
2427 4036 3.750371 CCACCCAAACTTGTGTATCAGA 58.250 45.455 0.0 0.0 0.00 3.27 R
3323 4932 9.453572 AAGATTCAGATATAAAACAGAGTTGCA 57.546 29.630 0.0 0.0 0.00 4.08 R
3359 4968 4.607239 AGAAAATGCATCACTTCCCTGAT 58.393 39.130 0.0 0.0 0.00 2.90 R
4602 6358 0.318441 CAAAGCGTGAGAGGACCAGA 59.682 55.000 0.0 0.0 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
22 23 3.741029 CGATCCACGGATGACACTT 57.259 52.632 2.54 0.00 38.46 3.16
23 24 2.863401 CGATCCACGGATGACACTTA 57.137 50.000 2.54 0.00 38.46 2.24
24 25 3.159353 CGATCCACGGATGACACTTAA 57.841 47.619 2.54 0.00 38.46 1.85
25 26 3.116300 CGATCCACGGATGACACTTAAG 58.884 50.000 2.54 0.00 38.46 1.85
26 27 2.380084 TCCACGGATGACACTTAAGC 57.620 50.000 1.29 0.00 0.00 3.09
27 28 1.621317 TCCACGGATGACACTTAAGCA 59.379 47.619 1.29 0.00 0.00 3.91
28 29 1.732259 CCACGGATGACACTTAAGCAC 59.268 52.381 1.29 0.00 0.00 4.40
29 30 2.412870 CACGGATGACACTTAAGCACA 58.587 47.619 1.29 0.90 0.00 4.57
30 31 2.413112 CACGGATGACACTTAAGCACAG 59.587 50.000 1.29 0.00 0.00 3.66
31 32 2.299013 ACGGATGACACTTAAGCACAGA 59.701 45.455 1.29 0.00 0.00 3.41
32 33 2.926200 CGGATGACACTTAAGCACAGAG 59.074 50.000 1.29 0.00 0.00 3.35
33 34 3.367395 CGGATGACACTTAAGCACAGAGA 60.367 47.826 1.29 0.00 0.00 3.10
34 35 3.929610 GGATGACACTTAAGCACAGAGAC 59.070 47.826 1.29 0.00 0.00 3.36
35 36 4.322349 GGATGACACTTAAGCACAGAGACT 60.322 45.833 1.29 0.00 0.00 3.24
36 37 4.672587 TGACACTTAAGCACAGAGACTT 57.327 40.909 1.29 0.00 0.00 3.01
37 38 4.371786 TGACACTTAAGCACAGAGACTTG 58.628 43.478 1.29 0.00 0.00 3.16
38 39 4.099419 TGACACTTAAGCACAGAGACTTGA 59.901 41.667 1.29 0.00 0.00 3.02
39 40 5.220710 ACACTTAAGCACAGAGACTTGAT 57.779 39.130 1.29 0.00 0.00 2.57
40 41 5.233988 ACACTTAAGCACAGAGACTTGATC 58.766 41.667 1.29 0.00 0.00 2.92
41 42 4.629200 CACTTAAGCACAGAGACTTGATCC 59.371 45.833 1.29 0.00 0.00 3.36
42 43 4.284490 ACTTAAGCACAGAGACTTGATCCA 59.716 41.667 1.29 0.00 0.00 3.41
43 44 3.996921 AAGCACAGAGACTTGATCCAT 57.003 42.857 0.00 0.00 0.00 3.41
44 45 3.996921 AGCACAGAGACTTGATCCATT 57.003 42.857 0.00 0.00 0.00 3.16
45 46 3.871485 AGCACAGAGACTTGATCCATTC 58.129 45.455 0.00 0.00 0.00 2.67
46 47 2.606725 GCACAGAGACTTGATCCATTCG 59.393 50.000 0.00 0.00 0.00 3.34
47 48 3.193263 CACAGAGACTTGATCCATTCGG 58.807 50.000 0.00 0.00 0.00 4.30
48 49 2.169352 ACAGAGACTTGATCCATTCGGG 59.831 50.000 0.00 0.00 38.37 5.14
49 50 2.169352 CAGAGACTTGATCCATTCGGGT 59.831 50.000 0.00 0.00 38.11 5.28
50 51 2.432510 AGAGACTTGATCCATTCGGGTC 59.567 50.000 0.00 0.00 43.54 4.46
51 52 1.137086 AGACTTGATCCATTCGGGTCG 59.863 52.381 0.00 0.00 46.61 4.79
52 53 0.178068 ACTTGATCCATTCGGGTCGG 59.822 55.000 0.00 0.00 46.61 4.79
53 54 0.532862 CTTGATCCATTCGGGTCGGG 60.533 60.000 0.00 0.00 46.61 5.14
54 55 1.268992 TTGATCCATTCGGGTCGGGT 61.269 55.000 0.00 0.00 46.61 5.28
55 56 1.069258 GATCCATTCGGGTCGGGTC 59.931 63.158 0.00 0.00 31.02 4.46
56 57 2.694829 GATCCATTCGGGTCGGGTCG 62.695 65.000 0.00 0.00 31.02 4.79
58 59 4.143333 CATTCGGGTCGGGTCGCT 62.143 66.667 0.00 0.00 0.00 4.93
59 60 2.440796 ATTCGGGTCGGGTCGCTA 60.441 61.111 0.00 0.00 0.00 4.26
60 61 2.779033 ATTCGGGTCGGGTCGCTAC 61.779 63.158 0.00 0.00 0.00 3.58
76 77 2.622436 GCTACACAACCAAGGAGCTAG 58.378 52.381 0.00 0.00 0.00 3.42
165 166 7.589395 TGTTATTTACATGCGACATTGTCTTT 58.411 30.769 14.54 0.00 0.00 2.52
179 180 4.577687 TTGTCTTTTATGATCGACGTGC 57.422 40.909 0.00 0.00 0.00 5.34
180 181 3.580731 TGTCTTTTATGATCGACGTGCA 58.419 40.909 0.00 0.00 0.00 4.57
181 182 4.180817 TGTCTTTTATGATCGACGTGCAT 58.819 39.130 0.00 9.41 0.00 3.96
182 183 4.032786 TGTCTTTTATGATCGACGTGCATG 59.967 41.667 3.82 3.82 0.00 4.06
183 184 4.267690 GTCTTTTATGATCGACGTGCATGA 59.732 41.667 14.17 0.00 0.00 3.07
184 185 4.867608 TCTTTTATGATCGACGTGCATGAA 59.132 37.500 14.17 9.43 0.00 2.57
185 186 5.523552 TCTTTTATGATCGACGTGCATGAAT 59.476 36.000 14.17 2.91 0.00 2.57
186 187 5.733226 TTTATGATCGACGTGCATGAATT 57.267 34.783 14.17 0.00 0.00 2.17
187 188 5.733226 TTATGATCGACGTGCATGAATTT 57.267 34.783 14.17 0.00 0.00 1.82
188 189 3.388149 TGATCGACGTGCATGAATTTG 57.612 42.857 14.17 0.00 0.00 2.32
212 213 5.419542 CATGGATTTGAGAGTCCGAACTTA 58.580 41.667 0.00 0.00 37.32 2.24
229 230 6.695713 CCGAACTTAAGATATGTGAATGTCGA 59.304 38.462 10.09 0.00 0.00 4.20
251 252 1.143073 AGGAAAATATGAGGGCCCGTC 59.857 52.381 18.44 15.04 0.00 4.79
258 259 4.554036 GAGGGCCCGTCAGGATGC 62.554 72.222 18.44 0.00 41.02 3.91
300 301 0.903454 ATCCGCGGACTAATAGGGGG 60.903 60.000 33.75 0.00 38.36 5.40
303 304 0.826672 CGCGGACTAATAGGGGGTCT 60.827 60.000 0.00 0.00 0.00 3.85
304 305 0.680061 GCGGACTAATAGGGGGTCTG 59.320 60.000 0.00 0.00 38.82 3.51
310 311 4.202472 GGACTAATAGGGGGTCTGATTTGG 60.202 50.000 0.00 0.00 0.00 3.28
314 315 0.846427 AGGGGGTCTGATTTGGCAGA 60.846 55.000 0.00 0.00 42.31 4.26
322 323 0.836606 TGATTTGGCAGATCCGGCTA 59.163 50.000 14.69 0.00 37.80 3.93
331 332 2.093764 GCAGATCCGGCTATAGATGCTT 60.094 50.000 3.21 0.00 0.00 3.91
344 345 7.095910 GCTATAGATGCTTTTAGATGCTCAGA 58.904 38.462 3.21 0.00 0.00 3.27
376 377 3.646534 AGAAGAATAGGGCCCATTTTGG 58.353 45.455 27.56 0.00 37.25 3.28
421 422 0.107017 CCCGATCAACAGATGGCCTT 60.107 55.000 3.32 0.00 0.00 4.35
498 515 8.023128 AGCATTGTTTATAAATATCATGGACGC 58.977 33.333 0.31 0.00 0.00 5.19
541 558 4.597940 AGGAGAAAACCAACCTAGCTAACT 59.402 41.667 0.00 0.00 0.00 2.24
575 592 7.970384 TCATGAACTATTCGATTACGCTTTTT 58.030 30.769 0.00 0.00 39.58 1.94
577 594 9.358123 CATGAACTATTCGATTACGCTTTTTAG 57.642 33.333 0.00 0.00 39.58 1.85
824 885 2.825836 CCATTCGTCTGCCCCAGC 60.826 66.667 0.00 0.00 40.48 4.85
906 967 0.323451 AGGCCGGGGAGTCAAAAATC 60.323 55.000 2.18 0.00 0.00 2.17
907 968 0.323451 GGCCGGGGAGTCAAAAATCT 60.323 55.000 2.18 0.00 0.00 2.40
908 969 1.064979 GGCCGGGGAGTCAAAAATCTA 60.065 52.381 2.18 0.00 0.00 1.98
909 970 2.289565 GCCGGGGAGTCAAAAATCTAG 58.710 52.381 2.18 0.00 0.00 2.43
910 971 2.289565 CCGGGGAGTCAAAAATCTAGC 58.710 52.381 0.00 0.00 0.00 3.42
911 972 2.092914 CCGGGGAGTCAAAAATCTAGCT 60.093 50.000 0.00 0.00 0.00 3.32
912 973 3.134081 CCGGGGAGTCAAAAATCTAGCTA 59.866 47.826 0.00 0.00 0.00 3.32
913 974 4.372656 CGGGGAGTCAAAAATCTAGCTAG 58.627 47.826 15.01 15.01 0.00 3.42
986 1047 2.046314 CCGTGCACAGGGTAAGGG 60.046 66.667 18.64 2.99 0.00 3.95
1030 1091 3.965026 CTCCCGCTCACCCTCTCCA 62.965 68.421 0.00 0.00 0.00 3.86
1940 2005 4.539870 TGTACAAAGCTACGTCACTGTAC 58.460 43.478 14.48 14.48 39.56 2.90
2115 3724 6.072286 CCTGTCTGAATTTGCTGTGAAGTTAT 60.072 38.462 0.00 0.00 0.00 1.89
2367 3976 6.310149 TGTATCAGAGAGGAGCAGATCATTA 58.690 40.000 0.00 0.00 0.00 1.90
2427 4036 1.135402 GGACTCGCATTTTCGCCATTT 60.135 47.619 0.00 0.00 0.00 2.32
2808 4417 3.181496 GCCTACGTACTACAACCAGGTAC 60.181 52.174 0.00 0.00 34.32 3.34
2867 4476 7.234577 TGAACTGCAAACCCCTTTCTTTATAAT 59.765 33.333 0.00 0.00 0.00 1.28
3295 4904 3.339141 GTGAGGCTCCCTTTTACTTCTG 58.661 50.000 12.86 0.00 31.76 3.02
3399 5008 7.631594 GCATTTTCTCAGTCTGGTCTATACTCA 60.632 40.741 0.00 0.00 0.00 3.41
3620 5231 1.141657 ACCGGATACATCTTGCAGCAT 59.858 47.619 9.46 0.00 0.00 3.79
3639 5250 1.204146 TGGTCTGCCCTGATCCTAAC 58.796 55.000 0.00 0.00 0.00 2.34
3647 5258 4.307259 TGCCCTGATCCTAACCTCTTTAT 58.693 43.478 0.00 0.00 0.00 1.40
3794 5405 3.719173 TTTTCAACCGGCGAGAAAATT 57.281 38.095 21.76 0.00 36.61 1.82
3923 5537 5.508657 CCTGGGAAGAAAGAAAGAAGCAAAG 60.509 44.000 0.00 0.00 0.00 2.77
4021 5635 0.169009 GAATTGAGCACAGGAACGCC 59.831 55.000 0.00 0.00 0.00 5.68
4022 5636 0.537143 AATTGAGCACAGGAACGCCA 60.537 50.000 0.00 0.00 36.29 5.69
4070 5684 7.222224 GTGTAGTGTGCAAGTGATTATAGGTAC 59.778 40.741 0.00 0.00 0.00 3.34
4147 5768 9.883142 TTTTCTTTTTCTTTTTGGAATAGCTCA 57.117 25.926 0.00 0.00 0.00 4.26
4148 5769 8.871686 TTCTTTTTCTTTTTGGAATAGCTCAC 57.128 30.769 0.00 0.00 0.00 3.51
4149 5770 8.237811 TCTTTTTCTTTTTGGAATAGCTCACT 57.762 30.769 0.00 0.00 0.00 3.41
4150 5771 8.695456 TCTTTTTCTTTTTGGAATAGCTCACTT 58.305 29.630 0.00 0.00 0.00 3.16
4151 5772 8.871686 TTTTTCTTTTTGGAATAGCTCACTTC 57.128 30.769 0.00 0.00 0.00 3.01
4152 5773 7.823745 TTTCTTTTTGGAATAGCTCACTTCT 57.176 32.000 0.00 0.00 0.00 2.85
4404 6025 0.518636 GCTCGCATTCAAGCTTCACA 59.481 50.000 0.00 0.00 35.60 3.58
4423 6044 4.035792 TCACAACAATGTTCGTTTAGTGGG 59.964 41.667 10.65 0.00 37.82 4.61
4424 6045 4.035792 CACAACAATGTTCGTTTAGTGGGA 59.964 41.667 0.00 0.00 37.82 4.37
4425 6046 4.274950 ACAACAATGTTCGTTTAGTGGGAG 59.725 41.667 0.00 0.00 35.91 4.30
4426 6047 3.408634 ACAATGTTCGTTTAGTGGGAGG 58.591 45.455 0.00 0.00 0.00 4.30
4427 6048 3.071892 ACAATGTTCGTTTAGTGGGAGGA 59.928 43.478 0.00 0.00 0.00 3.71
4428 6049 3.611766 ATGTTCGTTTAGTGGGAGGAG 57.388 47.619 0.00 0.00 0.00 3.69
4429 6050 2.600790 TGTTCGTTTAGTGGGAGGAGA 58.399 47.619 0.00 0.00 0.00 3.71
4430 6051 3.170717 TGTTCGTTTAGTGGGAGGAGAT 58.829 45.455 0.00 0.00 0.00 2.75
4431 6052 3.056107 TGTTCGTTTAGTGGGAGGAGATG 60.056 47.826 0.00 0.00 0.00 2.90
4432 6053 2.816411 TCGTTTAGTGGGAGGAGATGT 58.184 47.619 0.00 0.00 0.00 3.06
4433 6054 3.170717 TCGTTTAGTGGGAGGAGATGTT 58.829 45.455 0.00 0.00 0.00 2.71
4434 6055 3.194968 TCGTTTAGTGGGAGGAGATGTTC 59.805 47.826 0.00 0.00 0.00 3.18
4435 6056 3.195825 CGTTTAGTGGGAGGAGATGTTCT 59.804 47.826 0.00 0.00 0.00 3.01
4436 6057 4.678309 CGTTTAGTGGGAGGAGATGTTCTC 60.678 50.000 0.00 0.00 42.66 2.87
4437 6058 1.479709 AGTGGGAGGAGATGTTCTCG 58.520 55.000 0.00 0.00 44.28 4.04
4438 6059 1.187087 GTGGGAGGAGATGTTCTCGT 58.813 55.000 0.00 0.00 44.28 4.18
4439 6060 1.550976 GTGGGAGGAGATGTTCTCGTT 59.449 52.381 1.70 0.00 44.28 3.85
4440 6061 2.028020 GTGGGAGGAGATGTTCTCGTTT 60.028 50.000 1.70 0.00 44.28 3.60
4441 6062 3.194968 GTGGGAGGAGATGTTCTCGTTTA 59.805 47.826 1.70 0.00 44.28 2.01
4442 6063 3.447586 TGGGAGGAGATGTTCTCGTTTAG 59.552 47.826 1.70 0.00 44.28 1.85
4443 6064 3.447944 GGGAGGAGATGTTCTCGTTTAGT 59.552 47.826 1.70 0.00 44.28 2.24
4444 6065 4.425520 GGAGGAGATGTTCTCGTTTAGTG 58.574 47.826 1.70 0.00 44.28 2.74
4445 6066 4.425520 GAGGAGATGTTCTCGTTTAGTGG 58.574 47.826 1.70 0.00 44.28 4.00
4512 6268 6.929049 TCGTCAAATCTAAAGATGTTGTGACT 59.071 34.615 16.28 0.00 34.39 3.41
4517 6273 4.569943 TCTAAAGATGTTGTGACTGCTCC 58.430 43.478 0.00 0.00 0.00 4.70
4524 6280 2.263077 GTTGTGACTGCTCCGTATCAG 58.737 52.381 0.00 0.00 36.45 2.90
4525 6281 0.817654 TGTGACTGCTCCGTATCAGG 59.182 55.000 0.00 0.00 34.76 3.86
4527 6283 0.324368 TGACTGCTCCGTATCAGGGT 60.324 55.000 0.00 0.00 34.76 4.34
4550 6306 2.624838 GTGCTTATAGGCGTAGGGTGTA 59.375 50.000 2.06 0.00 34.52 2.90
4552 6308 2.624838 GCTTATAGGCGTAGGGTGTACA 59.375 50.000 0.00 0.00 0.00 2.90
4558 6314 0.101040 GCGTAGGGTGTACATGCGTA 59.899 55.000 0.00 0.00 0.00 4.42
4559 6315 1.831343 CGTAGGGTGTACATGCGTAC 58.169 55.000 0.00 0.00 46.94 3.67
4580 6336 3.846588 ACATTCATAGGGGTGACAGAACT 59.153 43.478 0.00 0.00 0.00 3.01
4602 6358 2.209475 GGCTAGGGTTAGGCTCGTT 58.791 57.895 0.00 0.00 46.12 3.85
4605 6361 1.202428 GCTAGGGTTAGGCTCGTTCTG 60.202 57.143 0.00 0.00 0.00 3.02
4618 6374 1.867919 CGTTCTGGTCCTCTCACGCT 61.868 60.000 0.00 0.00 0.00 5.07
4620 6376 1.048601 TTCTGGTCCTCTCACGCTTT 58.951 50.000 0.00 0.00 0.00 3.51
4622 6378 0.034059 CTGGTCCTCTCACGCTTTGT 59.966 55.000 0.00 0.00 0.00 2.83
4628 6384 2.030562 CTCACGCTTTGTCCCCGT 59.969 61.111 0.00 0.00 35.29 5.28
4670 6426 2.756283 CGTCGCCTCTCTCCCCTT 60.756 66.667 0.00 0.00 0.00 3.95
4677 6433 0.692756 CCTCTCTCCCCTTTCCTCCC 60.693 65.000 0.00 0.00 0.00 4.30
4678 6434 0.043334 CTCTCTCCCCTTTCCTCCCA 59.957 60.000 0.00 0.00 0.00 4.37
4679 6435 0.496382 TCTCTCCCCTTTCCTCCCAA 59.504 55.000 0.00 0.00 0.00 4.12
4681 6437 1.198759 TCTCCCCTTTCCTCCCAACG 61.199 60.000 0.00 0.00 0.00 4.10
4712 6469 4.819761 GCCATCACGAGGCGCTGA 62.820 66.667 7.64 2.81 43.15 4.26
4733 6490 4.223964 GCAAAGCCCGATCGACGC 62.224 66.667 18.66 17.37 41.07 5.19
4776 6533 2.043349 TCCGCTCGATCCAAGGGA 60.043 61.111 8.03 0.00 35.55 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.863401 TAAGTGTCATCCGTGGATCG 57.137 50.000 0.00 0.00 39.52 3.69
5 6 2.866762 GCTTAAGTGTCATCCGTGGATC 59.133 50.000 4.02 0.00 31.62 3.36
6 7 2.236146 TGCTTAAGTGTCATCCGTGGAT 59.764 45.455 4.02 0.00 34.81 3.41
7 8 1.621317 TGCTTAAGTGTCATCCGTGGA 59.379 47.619 4.02 0.00 0.00 4.02
8 9 1.732259 GTGCTTAAGTGTCATCCGTGG 59.268 52.381 4.02 0.00 0.00 4.94
9 10 2.412870 TGTGCTTAAGTGTCATCCGTG 58.587 47.619 4.02 0.00 0.00 4.94
10 11 2.299013 TCTGTGCTTAAGTGTCATCCGT 59.701 45.455 4.02 0.00 0.00 4.69
11 12 2.926200 CTCTGTGCTTAAGTGTCATCCG 59.074 50.000 4.02 0.00 0.00 4.18
12 13 3.929610 GTCTCTGTGCTTAAGTGTCATCC 59.070 47.826 4.02 0.00 0.00 3.51
13 14 4.815269 AGTCTCTGTGCTTAAGTGTCATC 58.185 43.478 4.02 0.00 0.00 2.92
14 15 4.881019 AGTCTCTGTGCTTAAGTGTCAT 57.119 40.909 4.02 0.00 0.00 3.06
15 16 4.099419 TCAAGTCTCTGTGCTTAAGTGTCA 59.901 41.667 4.02 0.89 0.00 3.58
16 17 4.621991 TCAAGTCTCTGTGCTTAAGTGTC 58.378 43.478 4.02 0.00 0.00 3.67
17 18 4.672587 TCAAGTCTCTGTGCTTAAGTGT 57.327 40.909 4.02 0.00 0.00 3.55
18 19 4.629200 GGATCAAGTCTCTGTGCTTAAGTG 59.371 45.833 4.02 0.00 0.00 3.16
19 20 4.284490 TGGATCAAGTCTCTGTGCTTAAGT 59.716 41.667 4.02 0.00 0.00 2.24
20 21 4.825422 TGGATCAAGTCTCTGTGCTTAAG 58.175 43.478 0.00 0.00 0.00 1.85
21 22 4.890158 TGGATCAAGTCTCTGTGCTTAA 57.110 40.909 0.00 0.00 0.00 1.85
22 23 5.423015 GAATGGATCAAGTCTCTGTGCTTA 58.577 41.667 0.00 0.00 0.00 3.09
23 24 3.996921 ATGGATCAAGTCTCTGTGCTT 57.003 42.857 0.00 0.00 0.00 3.91
24 25 3.678252 CGAATGGATCAAGTCTCTGTGCT 60.678 47.826 0.00 0.00 0.00 4.40
25 26 2.606725 CGAATGGATCAAGTCTCTGTGC 59.393 50.000 0.00 0.00 0.00 4.57
26 27 3.193263 CCGAATGGATCAAGTCTCTGTG 58.807 50.000 0.00 0.00 37.49 3.66
27 28 2.169352 CCCGAATGGATCAAGTCTCTGT 59.831 50.000 0.00 0.00 37.49 3.41
28 29 2.169352 ACCCGAATGGATCAAGTCTCTG 59.831 50.000 0.00 0.00 37.49 3.35
29 30 2.432510 GACCCGAATGGATCAAGTCTCT 59.567 50.000 0.00 0.00 37.49 3.10
30 31 2.799917 CGACCCGAATGGATCAAGTCTC 60.800 54.545 0.00 0.00 37.49 3.36
31 32 1.137086 CGACCCGAATGGATCAAGTCT 59.863 52.381 0.00 0.00 37.49 3.24
32 33 1.571919 CGACCCGAATGGATCAAGTC 58.428 55.000 0.00 0.00 37.49 3.01
33 34 0.178068 CCGACCCGAATGGATCAAGT 59.822 55.000 0.00 0.00 37.49 3.16
34 35 0.532862 CCCGACCCGAATGGATCAAG 60.533 60.000 0.00 0.00 37.49 3.02
35 36 1.268992 ACCCGACCCGAATGGATCAA 61.269 55.000 0.00 0.00 37.49 2.57
36 37 1.682451 GACCCGACCCGAATGGATCA 61.682 60.000 0.00 0.00 37.49 2.92
37 38 1.069258 GACCCGACCCGAATGGATC 59.931 63.158 0.00 0.00 37.49 3.36
38 39 2.792947 CGACCCGACCCGAATGGAT 61.793 63.158 0.00 0.00 37.49 3.41
39 40 3.454573 CGACCCGACCCGAATGGA 61.455 66.667 0.00 0.00 37.49 3.41
41 42 2.777972 TAGCGACCCGACCCGAATG 61.778 63.158 0.00 0.00 0.00 2.67
42 43 2.440796 TAGCGACCCGACCCGAAT 60.441 61.111 0.00 0.00 0.00 3.34
43 44 3.443045 GTAGCGACCCGACCCGAA 61.443 66.667 0.00 0.00 0.00 4.30
44 45 4.720902 TGTAGCGACCCGACCCGA 62.721 66.667 0.00 0.00 0.00 5.14
45 46 4.487412 GTGTAGCGACCCGACCCG 62.487 72.222 0.00 0.00 0.00 5.28
46 47 2.934570 TTGTGTAGCGACCCGACCC 61.935 63.158 0.00 0.00 0.00 4.46
47 48 1.735559 GTTGTGTAGCGACCCGACC 60.736 63.158 0.00 0.00 0.00 4.79
48 49 1.735559 GGTTGTGTAGCGACCCGAC 60.736 63.158 0.00 0.00 44.34 4.79
49 50 2.652530 GGTTGTGTAGCGACCCGA 59.347 61.111 0.00 0.00 44.34 5.14
53 54 1.429463 CTCCTTGGTTGTGTAGCGAC 58.571 55.000 0.00 0.00 0.00 5.19
54 55 0.320421 GCTCCTTGGTTGTGTAGCGA 60.320 55.000 0.00 0.00 0.00 4.93
55 56 0.320771 AGCTCCTTGGTTGTGTAGCG 60.321 55.000 0.00 0.00 35.17 4.26
56 57 2.028020 ACTAGCTCCTTGGTTGTGTAGC 60.028 50.000 0.00 0.00 31.55 3.58
57 58 3.589988 CACTAGCTCCTTGGTTGTGTAG 58.410 50.000 0.00 0.00 42.11 2.74
58 59 2.289444 GCACTAGCTCCTTGGTTGTGTA 60.289 50.000 0.00 0.00 46.25 2.90
59 60 1.543429 GCACTAGCTCCTTGGTTGTGT 60.543 52.381 0.00 0.00 46.25 3.72
60 61 1.160137 GCACTAGCTCCTTGGTTGTG 58.840 55.000 0.00 5.40 46.88 3.33
150 151 5.523552 TCGATCATAAAAGACAATGTCGCAT 59.476 36.000 7.83 0.74 37.67 4.73
154 155 6.178507 CACGTCGATCATAAAAGACAATGTC 58.821 40.000 5.02 5.02 33.56 3.06
165 166 5.500825 CAAATTCATGCACGTCGATCATAA 58.499 37.500 0.00 0.00 0.00 1.90
179 180 6.338146 ACTCTCAAATCCATGCAAATTCATG 58.662 36.000 0.00 1.08 42.53 3.07
180 181 6.406624 GGACTCTCAAATCCATGCAAATTCAT 60.407 38.462 0.00 0.00 34.87 2.57
181 182 5.105635 GGACTCTCAAATCCATGCAAATTCA 60.106 40.000 0.00 0.00 34.87 2.57
182 183 5.346522 GGACTCTCAAATCCATGCAAATTC 58.653 41.667 0.00 0.00 34.87 2.17
183 184 4.142315 CGGACTCTCAAATCCATGCAAATT 60.142 41.667 0.00 0.00 34.35 1.82
184 185 3.379372 CGGACTCTCAAATCCATGCAAAT 59.621 43.478 0.00 0.00 34.35 2.32
185 186 2.749076 CGGACTCTCAAATCCATGCAAA 59.251 45.455 0.00 0.00 34.35 3.68
186 187 2.027285 TCGGACTCTCAAATCCATGCAA 60.027 45.455 0.00 0.00 34.35 4.08
187 188 1.554617 TCGGACTCTCAAATCCATGCA 59.445 47.619 0.00 0.00 34.35 3.96
188 189 2.315925 TCGGACTCTCAAATCCATGC 57.684 50.000 0.00 0.00 34.35 4.06
212 213 6.471233 TTCCTCTCGACATTCACATATCTT 57.529 37.500 0.00 0.00 0.00 2.40
229 230 1.421646 CGGGCCCTCATATTTTCCTCT 59.578 52.381 22.43 0.00 0.00 3.69
279 280 0.389948 CCCTATTAGTCCGCGGATGC 60.390 60.000 33.58 20.00 37.91 3.91
280 281 0.246635 CCCCTATTAGTCCGCGGATG 59.753 60.000 33.58 16.25 0.00 3.51
281 282 0.903454 CCCCCTATTAGTCCGCGGAT 60.903 60.000 33.58 21.74 0.00 4.18
290 291 3.138283 TGCCAAATCAGACCCCCTATTAG 59.862 47.826 0.00 0.00 0.00 1.73
291 292 3.127250 TGCCAAATCAGACCCCCTATTA 58.873 45.455 0.00 0.00 0.00 0.98
300 301 1.303309 CCGGATCTGCCAAATCAGAC 58.697 55.000 0.00 0.00 44.88 3.51
303 304 0.836606 TAGCCGGATCTGCCAAATCA 59.163 50.000 5.05 0.00 35.94 2.57
304 305 2.191128 ATAGCCGGATCTGCCAAATC 57.809 50.000 5.05 0.00 35.94 2.17
310 311 1.480137 AGCATCTATAGCCGGATCTGC 59.520 52.381 5.05 4.19 0.00 4.26
314 315 6.344500 CATCTAAAAGCATCTATAGCCGGAT 58.656 40.000 5.05 0.00 0.00 4.18
322 323 6.935771 CCTTCTGAGCATCTAAAAGCATCTAT 59.064 38.462 0.00 0.00 34.92 1.98
331 332 5.880901 ACCTTTTCCTTCTGAGCATCTAAA 58.119 37.500 0.00 0.00 34.92 1.85
344 345 5.340110 GGCCCTATTCTTCTACCTTTTCCTT 60.340 44.000 0.00 0.00 0.00 3.36
405 406 2.032178 GCGTTAAGGCCATCTGTTGATC 59.968 50.000 5.01 0.00 0.00 2.92
511 528 3.720002 AGGTTGGTTTTCTCCTCCAAGTA 59.280 43.478 0.00 0.00 41.09 2.24
515 532 2.039879 GCTAGGTTGGTTTTCTCCTCCA 59.960 50.000 0.00 0.00 0.00 3.86
575 592 8.537016 TCTTCAAGTTTATGCCTAGCTTAACTA 58.463 33.333 0.00 0.00 30.02 2.24
577 594 7.611213 TCTTCAAGTTTATGCCTAGCTTAAC 57.389 36.000 0.00 0.00 30.02 2.01
940 1001 3.181290 CGCTTGCGTGCTCGATCA 61.181 61.111 13.13 0.00 39.71 2.92
1021 1082 2.930562 GCACTGGGTGGAGAGGGT 60.931 66.667 0.00 0.00 33.64 4.34
1967 2032 6.208599 TCAACTTCACCATGAAATTAGGAACC 59.791 38.462 0.00 0.00 35.73 3.62
2115 3724 7.273457 TCTGGTACCCCTTATTTTATCACAA 57.727 36.000 10.07 0.00 0.00 3.33
2367 3976 6.437793 GGTACATCCCACTATATACAAGAGCT 59.562 42.308 0.00 0.00 0.00 4.09
2427 4036 3.750371 CCACCCAAACTTGTGTATCAGA 58.250 45.455 0.00 0.00 0.00 3.27
3323 4932 9.453572 AAGATTCAGATATAAAACAGAGTTGCA 57.546 29.630 0.00 0.00 0.00 4.08
3359 4968 4.607239 AGAAAATGCATCACTTCCCTGAT 58.393 39.130 0.00 0.00 0.00 2.90
3399 5008 5.243954 TCGAGGACCGATATCTTGATGATTT 59.756 40.000 0.34 0.00 43.23 2.17
3620 5231 1.204146 GTTAGGATCAGGGCAGACCA 58.796 55.000 0.00 0.00 43.89 4.02
3794 5405 5.535030 AGCGGGCTATACATATCAATCGATA 59.465 40.000 0.00 0.00 38.48 2.92
3923 5537 6.520272 ACATATTAGATCTGGCAGTCTGTTC 58.480 40.000 21.92 11.01 0.00 3.18
4021 5635 1.157870 CCTATACAACCGGCCGCTTG 61.158 60.000 27.50 27.50 0.00 4.01
4022 5636 1.145377 CCTATACAACCGGCCGCTT 59.855 57.895 22.85 10.54 0.00 4.68
4070 5684 5.863935 CGTGTATGACAGGATATGTACATGG 59.136 44.000 18.81 5.37 44.17 3.66
4147 5768 6.544197 AGACTACGATGATATGTCACAGAAGT 59.456 38.462 0.00 0.00 37.14 3.01
4148 5769 6.964908 AGACTACGATGATATGTCACAGAAG 58.035 40.000 0.00 0.00 37.14 2.85
4149 5770 6.944234 AGACTACGATGATATGTCACAGAA 57.056 37.500 0.00 0.00 37.14 3.02
4150 5771 7.217906 ACTAGACTACGATGATATGTCACAGA 58.782 38.462 0.00 0.00 37.14 3.41
4151 5772 7.428282 ACTAGACTACGATGATATGTCACAG 57.572 40.000 0.00 0.00 37.14 3.66
4152 5773 7.803279 AACTAGACTACGATGATATGTCACA 57.197 36.000 0.00 0.00 37.14 3.58
4404 6025 3.818773 CCTCCCACTAAACGAACATTGTT 59.181 43.478 0.63 0.63 0.00 2.83
4423 6044 4.425520 CCACTAAACGAGAACATCTCCTC 58.574 47.826 1.98 0.00 40.34 3.71
4424 6045 3.195825 CCCACTAAACGAGAACATCTCCT 59.804 47.826 1.98 0.00 40.34 3.69
4425 6046 3.194968 TCCCACTAAACGAGAACATCTCC 59.805 47.826 1.98 0.00 40.34 3.71
4426 6047 4.425520 CTCCCACTAAACGAGAACATCTC 58.574 47.826 0.00 0.00 40.06 2.75
4427 6048 3.195825 CCTCCCACTAAACGAGAACATCT 59.804 47.826 0.00 0.00 0.00 2.90
4428 6049 3.194968 TCCTCCCACTAAACGAGAACATC 59.805 47.826 0.00 0.00 0.00 3.06
4429 6050 3.170717 TCCTCCCACTAAACGAGAACAT 58.829 45.455 0.00 0.00 0.00 2.71
4430 6051 2.561419 CTCCTCCCACTAAACGAGAACA 59.439 50.000 0.00 0.00 0.00 3.18
4431 6052 2.824341 TCTCCTCCCACTAAACGAGAAC 59.176 50.000 0.00 0.00 0.00 3.01
4432 6053 3.165087 TCTCCTCCCACTAAACGAGAA 57.835 47.619 0.00 0.00 0.00 2.87
4433 6054 2.893215 TCTCCTCCCACTAAACGAGA 57.107 50.000 0.00 0.00 0.00 4.04
4434 6055 2.761208 ACATCTCCTCCCACTAAACGAG 59.239 50.000 0.00 0.00 0.00 4.18
4435 6056 2.816411 ACATCTCCTCCCACTAAACGA 58.184 47.619 0.00 0.00 0.00 3.85
4436 6057 3.195825 AGAACATCTCCTCCCACTAAACG 59.804 47.826 0.00 0.00 0.00 3.60
4437 6058 4.678309 CGAGAACATCTCCTCCCACTAAAC 60.678 50.000 1.98 0.00 40.34 2.01
4438 6059 3.447586 CGAGAACATCTCCTCCCACTAAA 59.552 47.826 1.98 0.00 40.34 1.85
4439 6060 3.024547 CGAGAACATCTCCTCCCACTAA 58.975 50.000 1.98 0.00 40.34 2.24
4440 6061 2.025226 ACGAGAACATCTCCTCCCACTA 60.025 50.000 1.98 0.00 40.34 2.74
4441 6062 1.272760 ACGAGAACATCTCCTCCCACT 60.273 52.381 1.98 0.00 40.34 4.00
4442 6063 1.187087 ACGAGAACATCTCCTCCCAC 58.813 55.000 1.98 0.00 40.34 4.61
4443 6064 1.550524 CAACGAGAACATCTCCTCCCA 59.449 52.381 1.98 0.00 40.34 4.37
4444 6065 1.825474 TCAACGAGAACATCTCCTCCC 59.175 52.381 1.98 0.00 40.34 4.30
4445 6066 2.494073 AGTCAACGAGAACATCTCCTCC 59.506 50.000 1.98 0.00 40.34 4.30
4512 6268 1.305802 ACCACCCTGATACGGAGCA 60.306 57.895 0.00 0.00 0.00 4.26
4517 6273 2.910688 ATAAGCACCACCCTGATACG 57.089 50.000 0.00 0.00 0.00 3.06
4524 6280 0.754472 TACGCCTATAAGCACCACCC 59.246 55.000 0.00 0.00 0.00 4.61
4525 6281 1.270147 CCTACGCCTATAAGCACCACC 60.270 57.143 0.00 0.00 0.00 4.61
4527 6283 1.045407 CCCTACGCCTATAAGCACCA 58.955 55.000 0.00 0.00 0.00 4.17
4550 6306 2.438021 ACCCCTATGAATGTACGCATGT 59.562 45.455 0.00 0.00 35.15 3.21
4552 6308 2.703536 TCACCCCTATGAATGTACGCAT 59.296 45.455 2.03 2.03 36.80 4.73
4558 6314 3.846588 AGTTCTGTCACCCCTATGAATGT 59.153 43.478 0.00 0.00 0.00 2.71
4559 6315 4.194640 CAGTTCTGTCACCCCTATGAATG 58.805 47.826 0.00 0.00 0.00 2.67
4580 6336 0.981277 GAGCCTAACCCTAGCCACCA 60.981 60.000 0.00 0.00 0.00 4.17
4602 6358 0.318441 CAAAGCGTGAGAGGACCAGA 59.682 55.000 0.00 0.00 0.00 3.86
4605 6361 0.670854 GGACAAAGCGTGAGAGGACC 60.671 60.000 0.00 0.00 0.00 4.46
4670 6426 2.291043 GGAGGAGCGTTGGGAGGAA 61.291 63.158 0.00 0.00 0.00 3.36
4677 6433 4.410400 GGTGGGGGAGGAGCGTTG 62.410 72.222 0.00 0.00 0.00 4.10
4703 6460 2.669569 TTTGCCTGTCAGCGCCTC 60.670 61.111 2.29 0.00 34.65 4.70
4743 6500 1.616628 GGAGAGGAAAGAGGCCCCA 60.617 63.158 0.00 0.00 0.00 4.96
4776 6533 0.825010 GCGGAATCATCCCAAGCCAT 60.825 55.000 0.00 0.00 43.37 4.40


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

AutoCloner maintained by Alex Coulton.