Multiple sequence alignment - TraesCS6D01G217900

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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 TraesCS6D01G217900 chr6D 100.000 7270 0 0 1 7270 307876579 307883848 0.000000e+00 13426.0
1 TraesCS6D01G217900 chr6A 96.188 4119 122 13 2885 6987 445046542 445050641 0.000000e+00 6704.0
2 TraesCS6D01G217900 chr6A 97.158 1900 40 2 961 2846 445044647 445046546 0.000000e+00 3197.0
3 TraesCS6D01G217900 chr6A 87.898 942 66 21 1 911 445043473 445044397 0.000000e+00 1064.0
4 TraesCS6D01G217900 chr6A 88.372 172 11 2 7099 7270 445061045 445061207 1.600000e-46 198.0
5 TraesCS6D01G217900 chr6A 100.000 53 0 0 6985 7037 445060993 445061045 1.670000e-16 99.0
6 TraesCS6D01G217900 chr6B 94.581 3451 113 20 273 3682 475267234 475270651 0.000000e+00 5269.0
7 TraesCS6D01G217900 chr6B 94.679 2932 69 29 4368 7270 475271186 475274059 0.000000e+00 4470.0
8 TraesCS6D01G217900 chr6B 89.216 510 19 10 3684 4177 475270702 475271191 8.070000e-169 604.0
9 TraesCS6D01G217900 chr6B 91.129 248 18 2 1 245 475266150 475266396 4.200000e-87 333.0
10 TraesCS6D01G217900 chr6B 95.122 41 2 0 278 318 177335122 177335162 1.690000e-06 65.8
11 TraesCS6D01G217900 chr6B 100.000 29 0 0 2501 2529 32833412 32833384 4.000000e-03 54.7
12 TraesCS6D01G217900 chr2B 78.649 370 60 16 4558 4919 554455935 554455577 2.040000e-55 228.0
13 TraesCS6D01G217900 chr2B 85.714 56 8 0 268 323 18317421 18317366 7.880000e-05 60.2
14 TraesCS6D01G217900 chr2A 78.649 370 60 18 4558 4919 615740272 615739914 2.040000e-55 228.0
15 TraesCS6D01G217900 chr2D 78.378 370 61 16 4558 4919 473716827 473716469 9.490000e-54 222.0
16 TraesCS6D01G217900 chr7B 85.556 90 10 2 2285 2371 468947278 468947367 2.790000e-14 91.6
17 TraesCS6D01G217900 chr3B 85.714 91 8 4 2285 2371 198130752 198130663 2.790000e-14 91.6
18 TraesCS6D01G217900 chr4B 92.857 42 3 0 276 317 14340349 14340390 2.190000e-05 62.1
19 TraesCS6D01G217900 chr1A 86.207 58 7 1 2477 2533 373311931 373311988 2.190000e-05 62.1


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 TraesCS6D01G217900 chr6D 307876579 307883848 7269 False 13426 13426 100.00000 1 7270 1 chr6D.!!$F1 7269
1 TraesCS6D01G217900 chr6A 445043473 445050641 7168 False 3655 6704 93.74800 1 6987 3 chr6A.!!$F1 6986
2 TraesCS6D01G217900 chr6B 475266150 475274059 7909 False 2669 5269 92.40125 1 7270 4 chr6B.!!$F2 7269

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
508 1360 0.178903 TTACTCCCTCACTGCCAGGT 60.179 55.000 0.00 0.0 0.00 4.00 F
769 1649 0.626382 GGGGGAAAGGAAAGGAGAGG 59.374 60.000 0.00 0.0 0.00 3.69 F
2055 3137 0.550914 TTTGGGAGGTGTTGCACTCT 59.449 50.000 2.48 0.0 34.40 3.24 F
2571 3667 0.966920 CAGACTAGGGACACCACGTT 59.033 55.000 0.00 0.0 40.13 3.99 F
3069 4165 3.376859 TGTCTCGTCAGTTTTGCAATGTT 59.623 39.130 0.00 0.0 0.00 2.71 F
3477 4573 0.319083 GACCACCACACACGGATACA 59.681 55.000 0.00 0.0 0.00 2.29 F
4094 5263 2.361610 CCCAAGCTGCCGTCCATT 60.362 61.111 0.00 0.0 0.00 3.16 F
5587 6763 1.523711 AATAGCACCGCATCCACCG 60.524 57.895 0.00 0.0 0.00 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 2921 0.617413 CACCATCCTGGCTGTCTTCT 59.383 55.000 0.00 0.0 42.67 2.85 R
2758 3854 1.476891 TCGTACACCTCTGATCAAGCC 59.523 52.381 0.00 0.0 0.00 4.35 R
3376 4472 0.036388 CCCCGCTCACAGCTTAAAGA 60.036 55.000 0.00 0.0 39.60 2.52 R
3377 4473 1.026718 CCCCCGCTCACAGCTTAAAG 61.027 60.000 0.00 0.0 39.60 1.85 R
4707 5876 1.066645 CAGGACAGTGCTATCAGTGCA 60.067 52.381 0.00 0.0 45.34 4.57 R
5089 6263 0.178953 AGGGGTCACAGCAGCAAAAT 60.179 50.000 0.00 0.0 0.00 1.82 R
5598 6774 0.721718 GGCTCATCAACAGTACGCAC 59.278 55.000 0.00 0.0 0.00 5.34 R
7056 8248 0.179094 AACACGGACACTTGCGAAGA 60.179 50.000 3.37 0.0 39.29 2.87 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
30 31 1.529865 GGTCTTGCTTACGGTGACAAC 59.470 52.381 0.00 0.00 0.00 3.32
53 60 2.501222 ACGACGATGACACGCGAC 60.501 61.111 15.93 4.24 36.92 5.19
100 107 1.354040 CACTCAGACGCACTGGAATC 58.646 55.000 9.70 0.00 45.76 2.52
110 117 1.945387 CACTGGAATCGACATGAGGG 58.055 55.000 0.00 0.00 0.00 4.30
165 172 2.357034 GTTGAGGACAAGCGCGGA 60.357 61.111 8.83 0.00 36.64 5.54
262 1113 5.848406 ACGAAGAGAGATTATCCAACATCC 58.152 41.667 0.00 0.00 0.00 3.51
263 1114 5.363868 ACGAAGAGAGATTATCCAACATCCA 59.636 40.000 0.00 0.00 0.00 3.41
264 1115 6.127054 ACGAAGAGAGATTATCCAACATCCAA 60.127 38.462 0.00 0.00 0.00 3.53
265 1116 6.201806 CGAAGAGAGATTATCCAACATCCAAC 59.798 42.308 0.00 0.00 0.00 3.77
266 1117 6.566079 AGAGAGATTATCCAACATCCAACA 57.434 37.500 0.00 0.00 0.00 3.33
267 1118 7.146715 AGAGAGATTATCCAACATCCAACAT 57.853 36.000 0.00 0.00 0.00 2.71
268 1119 6.996879 AGAGAGATTATCCAACATCCAACATG 59.003 38.462 0.00 0.00 0.00 3.21
269 1120 6.066690 AGAGATTATCCAACATCCAACATGG 58.933 40.000 0.00 0.00 39.43 3.66
270 1121 4.586001 AGATTATCCAACATCCAACATGGC 59.414 41.667 0.00 0.00 37.47 4.40
271 1122 2.234896 ATCCAACATCCAACATGGCA 57.765 45.000 0.00 0.00 37.47 4.92
331 1183 2.801063 CATAGCATCCGCACAAAAAGG 58.199 47.619 0.00 0.00 42.27 3.11
352 1204 5.390387 AGGAAGGGCAAAACAATTGTACTA 58.610 37.500 12.39 0.00 0.00 1.82
362 1214 3.518590 ACAATTGTACTACTGCTACGGC 58.481 45.455 9.97 0.00 39.26 5.68
508 1360 0.178903 TTACTCCCTCACTGCCAGGT 60.179 55.000 0.00 0.00 0.00 4.00
573 1425 4.140599 CGCTTCGCCTCTGCCTCT 62.141 66.667 0.00 0.00 0.00 3.69
574 1426 2.511145 GCTTCGCCTCTGCCTCTG 60.511 66.667 0.00 0.00 0.00 3.35
575 1427 2.511145 CTTCGCCTCTGCCTCTGC 60.511 66.667 0.00 0.00 38.26 4.26
576 1428 4.087892 TTCGCCTCTGCCTCTGCC 62.088 66.667 0.00 0.00 36.33 4.85
578 1430 4.527583 CGCCTCTGCCTCTGCCTC 62.528 72.222 0.00 0.00 36.33 4.70
670 1545 3.640407 ACCACCATGAGCGCAGGT 61.640 61.111 11.47 9.27 46.54 4.00
700 1580 2.194271 GAGAGGACATTTTACCGCGAG 58.806 52.381 8.23 0.00 0.00 5.03
765 1645 2.761160 GCGGGGGAAAGGAAAGGA 59.239 61.111 0.00 0.00 0.00 3.36
766 1646 1.378646 GCGGGGGAAAGGAAAGGAG 60.379 63.158 0.00 0.00 0.00 3.69
767 1647 1.848886 GCGGGGGAAAGGAAAGGAGA 61.849 60.000 0.00 0.00 0.00 3.71
769 1649 0.626382 GGGGGAAAGGAAAGGAGAGG 59.374 60.000 0.00 0.00 0.00 3.69
770 1650 1.670059 GGGGAAAGGAAAGGAGAGGA 58.330 55.000 0.00 0.00 0.00 3.71
771 1651 2.209758 GGGGAAAGGAAAGGAGAGGAT 58.790 52.381 0.00 0.00 0.00 3.24
772 1652 2.173782 GGGGAAAGGAAAGGAGAGGATC 59.826 54.545 0.00 0.00 0.00 3.36
773 1653 2.846827 GGGAAAGGAAAGGAGAGGATCA 59.153 50.000 0.00 0.00 37.82 2.92
774 1654 3.118075 GGGAAAGGAAAGGAGAGGATCAG 60.118 52.174 0.00 0.00 37.82 2.90
775 1655 3.118075 GGAAAGGAAAGGAGAGGATCAGG 60.118 52.174 0.00 0.00 37.82 3.86
884 1764 2.770048 CTTCGCCATCCCTCCCCT 60.770 66.667 0.00 0.00 0.00 4.79
946 1835 2.464459 CGCAATTCCTCGAGCACCC 61.464 63.158 6.99 0.00 0.00 4.61
1508 2590 0.898789 TTCGTGGTGAGGGAGGAGTC 60.899 60.000 0.00 0.00 0.00 3.36
1839 2921 2.351244 CCACTCCAGCTCGGCTACA 61.351 63.158 0.00 0.00 36.40 2.74
2055 3137 0.550914 TTTGGGAGGTGTTGCACTCT 59.449 50.000 2.48 0.00 34.40 3.24
2154 3236 1.475751 CCGGAGCCAATGTTAGCATCT 60.476 52.381 0.00 0.00 33.50 2.90
2236 3318 4.106925 CTGGGGGCTCAGACCAGC 62.107 72.222 0.00 0.00 44.55 4.85
2378 3461 5.779529 AGTCTTGCTTCAATTCAATGTGT 57.220 34.783 0.00 0.00 0.00 3.72
2400 3483 9.602568 TGTGTGAATACTAGTTTTGAGTGTAAA 57.397 29.630 0.00 0.00 0.00 2.01
2418 3501 6.072838 AGTGTAAACTTGAGATGCAGAATGTG 60.073 38.462 0.00 0.00 39.31 3.21
2571 3667 0.966920 CAGACTAGGGACACCACGTT 59.033 55.000 0.00 0.00 40.13 3.99
2707 3803 6.142259 ACTAGGACTTTTGAGAGAGGTAGA 57.858 41.667 0.00 0.00 0.00 2.59
2842 3938 7.429374 TGGATGTGAGATTTGAACTCTCTAT 57.571 36.000 12.78 7.92 39.90 1.98
3041 4137 6.427974 TCGATGAAGAGTATAAGCAGTTACG 58.572 40.000 0.00 0.00 0.00 3.18
3069 4165 3.376859 TGTCTCGTCAGTTTTGCAATGTT 59.623 39.130 0.00 0.00 0.00 2.71
3095 4191 5.119931 TCGCTGTTTGCATTATTTCTTGT 57.880 34.783 0.00 0.00 43.06 3.16
3135 4231 5.182001 AGACTTAATGAGAACCAACACATGC 59.818 40.000 0.00 0.00 0.00 4.06
3376 4472 8.616076 CAGATTCCGAAAAACTATTATGAGCTT 58.384 33.333 0.00 0.00 0.00 3.74
3377 4473 8.831550 AGATTCCGAAAAACTATTATGAGCTTC 58.168 33.333 0.00 0.00 0.00 3.86
3411 4507 2.203480 GGGTGGTGCCAGCAAAGA 60.203 61.111 20.17 0.00 45.25 2.52
3477 4573 0.319083 GACCACCACACACGGATACA 59.681 55.000 0.00 0.00 0.00 2.29
3590 4694 8.421249 TCAATCAGGTTTCTTGGTCATTTATT 57.579 30.769 0.00 0.00 0.00 1.40
3951 5108 7.171167 CAGCATGGTGTGTAATTTCAATTGAAA 59.829 33.333 30.27 30.27 46.60 2.69
3973 5130 2.905075 TCAGCTTGCAGTGCGTTATAT 58.095 42.857 11.20 0.00 35.28 0.86
3975 5132 4.438148 TCAGCTTGCAGTGCGTTATATAA 58.562 39.130 11.20 0.00 35.28 0.98
4047 5216 6.625960 CGCTAGCTGAATTATCTACCATGCTA 60.626 42.308 13.93 0.00 0.00 3.49
4094 5263 2.361610 CCCAAGCTGCCGTCCATT 60.362 61.111 0.00 0.00 0.00 3.16
4237 5406 6.705302 TCATAGAGATCCTTCAATATGCACC 58.295 40.000 0.00 0.00 0.00 5.01
4241 5410 3.718434 AGATCCTTCAATATGCACCTGGA 59.282 43.478 0.00 0.00 0.00 3.86
4336 5505 7.280652 CACATTCAACAATTTATTGGGGGAATC 59.719 37.037 7.33 0.00 41.96 2.52
4337 5506 7.182568 ACATTCAACAATTTATTGGGGGAATCT 59.817 33.333 7.33 0.00 41.96 2.40
4358 5527 3.599343 TGCTGCATGAAAGACGAATACT 58.401 40.909 0.00 0.00 0.00 2.12
4459 5628 5.970289 TCAGGGACCTCTGATATAATCACT 58.030 41.667 8.20 0.00 38.70 3.41
4701 5870 3.196469 AGAAGATTTCTCTCCATGTGCGA 59.804 43.478 0.00 0.00 34.07 5.10
4707 5876 6.769822 AGATTTCTCTCCATGTGCGATTAAAT 59.230 34.615 0.00 0.00 0.00 1.40
4983 6152 6.473455 GGCTTATTGCATGTTCATTCTAACAC 59.527 38.462 0.00 0.00 45.15 3.32
5074 6243 6.577438 CGTCTGGTATATATCTGTCCCTCTCT 60.577 46.154 0.00 0.00 0.00 3.10
5075 6244 6.826741 GTCTGGTATATATCTGTCCCTCTCTC 59.173 46.154 0.00 0.00 0.00 3.20
5076 6245 5.746284 TGGTATATATCTGTCCCTCTCTCG 58.254 45.833 0.00 0.00 0.00 4.04
5077 6246 5.251005 TGGTATATATCTGTCCCTCTCTCGT 59.749 44.000 0.00 0.00 0.00 4.18
5078 6247 6.181908 GGTATATATCTGTCCCTCTCTCGTT 58.818 44.000 0.00 0.00 0.00 3.85
5089 6263 4.464951 TCCCTCTCTCGTTTAGTTGCATTA 59.535 41.667 0.00 0.00 0.00 1.90
5324 6498 5.964477 ACAGGATTCCAGGTACTTATCTCAA 59.036 40.000 5.29 0.00 34.60 3.02
5351 6525 6.319658 CACCTGGCATACTTGAGATATTTGTT 59.680 38.462 0.00 0.00 0.00 2.83
5356 6530 7.611467 TGGCATACTTGAGATATTTGTTCTGTT 59.389 33.333 0.00 0.00 0.00 3.16
5542 6718 7.483691 CACATTGGTGCATATCATATTGATTCG 59.516 37.037 0.00 0.00 36.95 3.34
5587 6763 1.523711 AATAGCACCGCATCCACCG 60.524 57.895 0.00 0.00 0.00 4.94
5604 6780 3.463585 GACCCCATCCCGTGCGTA 61.464 66.667 0.00 0.00 0.00 4.42
5985 7161 2.912956 AGGAAGCAAGATAACCTGGACA 59.087 45.455 0.00 0.00 0.00 4.02
6035 7211 3.963428 TCTGAACCTGCTAAAGAGGAC 57.037 47.619 0.00 0.00 34.37 3.85
6152 7328 1.418637 TCTAATACAACCCATCCCGGC 59.581 52.381 0.00 0.00 0.00 6.13
6577 7753 1.000274 GCAATTGTCTGTTCGCCCTTT 60.000 47.619 7.40 0.00 0.00 3.11
6765 7944 3.393426 AGACCATTCCATGAAAGGCAT 57.607 42.857 0.00 0.00 34.22 4.40
6766 7945 3.716431 AGACCATTCCATGAAAGGCATT 58.284 40.909 0.00 0.00 34.22 3.56
6774 7955 7.607223 CCATTCCATGAAAGGCATTTTCTTTTA 59.393 33.333 0.00 0.00 44.49 1.52
6833 8014 6.932400 ACTTGTTCGTTCATTTCTACCATGTA 59.068 34.615 0.00 0.00 0.00 2.29
6913 8105 1.472878 ACGACGCATCATCTACTGTGT 59.527 47.619 0.00 0.00 38.72 3.72
7029 8221 0.325296 AGTCGGTTAGGGCATCTCCA 60.325 55.000 0.00 0.00 36.21 3.86
7031 8223 0.539986 TCGGTTAGGGCATCTCCAAC 59.460 55.000 0.00 0.00 36.21 3.77
7032 8224 0.810031 CGGTTAGGGCATCTCCAACG 60.810 60.000 0.00 0.00 36.21 4.10
7035 8227 1.138266 GTTAGGGCATCTCCAACGCTA 59.862 52.381 0.00 0.00 36.21 4.26
7036 8228 1.491668 TAGGGCATCTCCAACGCTAA 58.508 50.000 0.00 0.00 36.21 3.09
7037 8229 0.107654 AGGGCATCTCCAACGCTAAC 60.108 55.000 0.00 0.00 36.21 2.34
7038 8230 1.095807 GGGCATCTCCAACGCTAACC 61.096 60.000 0.00 0.00 36.21 2.85
7039 8231 0.107654 GGCATCTCCAACGCTAACCT 60.108 55.000 0.00 0.00 34.01 3.50
7040 8232 1.009829 GCATCTCCAACGCTAACCTG 58.990 55.000 0.00 0.00 0.00 4.00
7041 8233 1.676014 GCATCTCCAACGCTAACCTGT 60.676 52.381 0.00 0.00 0.00 4.00
7042 8234 2.418197 GCATCTCCAACGCTAACCTGTA 60.418 50.000 0.00 0.00 0.00 2.74
7043 8235 3.448686 CATCTCCAACGCTAACCTGTAG 58.551 50.000 0.00 0.00 0.00 2.74
7044 8236 1.822990 TCTCCAACGCTAACCTGTAGG 59.177 52.381 0.00 0.00 42.17 3.18
7045 8237 1.822990 CTCCAACGCTAACCTGTAGGA 59.177 52.381 4.64 0.00 38.94 2.94
7046 8238 1.822990 TCCAACGCTAACCTGTAGGAG 59.177 52.381 4.64 0.00 38.94 3.69
7047 8239 1.549170 CCAACGCTAACCTGTAGGAGT 59.451 52.381 4.64 0.00 38.94 3.85
7048 8240 2.756760 CCAACGCTAACCTGTAGGAGTA 59.243 50.000 4.64 0.00 38.94 2.59
7049 8241 3.383825 CCAACGCTAACCTGTAGGAGTAT 59.616 47.826 4.64 0.00 38.94 2.12
7051 8243 5.506982 CCAACGCTAACCTGTAGGAGTATAC 60.507 48.000 4.64 0.00 38.94 1.47
7052 8244 5.046288 ACGCTAACCTGTAGGAGTATACT 57.954 43.478 4.68 4.68 38.94 2.12
7053 8245 6.179906 ACGCTAACCTGTAGGAGTATACTA 57.820 41.667 5.09 0.00 38.94 1.82
7054 8246 6.777782 ACGCTAACCTGTAGGAGTATACTAT 58.222 40.000 5.09 0.17 38.94 2.12
7055 8247 6.878389 ACGCTAACCTGTAGGAGTATACTATC 59.122 42.308 5.09 1.50 38.94 2.08
7056 8248 7.104939 CGCTAACCTGTAGGAGTATACTATCT 58.895 42.308 5.09 9.14 38.94 1.98
7058 8250 8.323567 GCTAACCTGTAGGAGTATACTATCTCT 58.676 40.741 5.09 4.35 38.94 3.10
7061 8253 7.388437 ACCTGTAGGAGTATACTATCTCTTCG 58.612 42.308 5.09 0.00 38.94 3.79
7062 8254 6.314400 CCTGTAGGAGTATACTATCTCTTCGC 59.686 46.154 5.09 0.00 37.39 4.70
7063 8255 6.766429 TGTAGGAGTATACTATCTCTTCGCA 58.234 40.000 5.09 0.79 0.00 5.10
7065 8257 6.811253 AGGAGTATACTATCTCTTCGCAAG 57.189 41.667 5.09 0.00 0.00 4.01
7066 8258 6.300703 AGGAGTATACTATCTCTTCGCAAGT 58.699 40.000 5.09 0.00 39.48 3.16
7067 8259 6.205853 AGGAGTATACTATCTCTTCGCAAGTG 59.794 42.308 5.09 0.00 39.48 3.16
7068 8260 6.016943 GGAGTATACTATCTCTTCGCAAGTGT 60.017 42.308 5.09 0.00 39.48 3.55
7069 8261 6.961576 AGTATACTATCTCTTCGCAAGTGTC 58.038 40.000 2.75 0.00 39.48 3.67
7070 8262 3.512033 ACTATCTCTTCGCAAGTGTCC 57.488 47.619 0.00 0.00 39.48 4.02
7071 8263 2.159366 ACTATCTCTTCGCAAGTGTCCG 60.159 50.000 0.00 0.00 39.48 4.79
7072 8264 0.603569 ATCTCTTCGCAAGTGTCCGT 59.396 50.000 0.00 0.00 39.48 4.69
7073 8265 0.318699 TCTCTTCGCAAGTGTCCGTG 60.319 55.000 0.00 0.00 39.48 4.94
7074 8266 0.597637 CTCTTCGCAAGTGTCCGTGT 60.598 55.000 0.00 0.00 39.48 4.49
7075 8267 0.179094 TCTTCGCAAGTGTCCGTGTT 60.179 50.000 0.00 0.00 39.48 3.32
7076 8268 0.655733 CTTCGCAAGTGTCCGTGTTT 59.344 50.000 0.00 0.00 39.48 2.83
7077 8269 1.063469 CTTCGCAAGTGTCCGTGTTTT 59.937 47.619 0.00 0.00 39.48 2.43
7078 8270 1.937278 TCGCAAGTGTCCGTGTTTTA 58.063 45.000 0.00 0.00 39.48 1.52
7079 8271 1.593933 TCGCAAGTGTCCGTGTTTTAC 59.406 47.619 0.00 0.00 39.48 2.01
7080 8272 3.919762 TCGCAAGTGTCCGTGTTTTACG 61.920 50.000 0.00 0.00 45.73 3.18
7101 8293 0.972983 CCACACAGAGGTCCGGAGAT 60.973 60.000 3.06 0.00 0.00 2.75
7118 8310 1.215655 GATTGATACGGAAGCGCGCT 61.216 55.000 31.32 31.32 0.00 5.92
7120 8312 0.594028 TTGATACGGAAGCGCGCTAG 60.594 55.000 36.73 28.76 0.00 3.42
7168 8372 8.859090 TCTCAGACATTTTATCAAACATTTGGT 58.141 29.630 4.58 0.00 38.66 3.67
7169 8373 8.815141 TCAGACATTTTATCAAACATTTGGTG 57.185 30.769 4.58 0.00 38.66 4.17
7172 8376 7.171337 AGACATTTTATCAAACATTTGGTGTGC 59.829 33.333 4.58 0.00 41.14 4.57
7173 8377 5.896922 TTTTATCAAACATTTGGTGTGCG 57.103 34.783 4.58 0.00 41.14 5.34
7174 8378 2.437200 ATCAAACATTTGGTGTGCGG 57.563 45.000 4.58 0.00 41.14 5.69
7175 8379 0.249238 TCAAACATTTGGTGTGCGGC 60.249 50.000 4.58 0.00 41.14 6.53
7176 8380 1.299773 AAACATTTGGTGTGCGGCG 60.300 52.632 0.51 0.51 41.14 6.46
7177 8381 2.010582 AAACATTTGGTGTGCGGCGT 62.011 50.000 9.37 0.00 41.14 5.68
7178 8382 2.428902 CATTTGGTGTGCGGCGTG 60.429 61.111 9.37 0.00 0.00 5.34
7179 8383 2.904866 ATTTGGTGTGCGGCGTGT 60.905 55.556 9.37 0.00 0.00 4.49
7180 8384 3.192954 ATTTGGTGTGCGGCGTGTG 62.193 57.895 9.37 0.00 0.00 3.82
7245 8449 2.347490 GAGCACCACCACCATCGT 59.653 61.111 0.00 0.00 0.00 3.73
7261 8465 2.125147 GTAGCGAGCACATGCCCA 60.125 61.111 0.00 0.00 43.38 5.36
7262 8466 2.176273 GTAGCGAGCACATGCCCAG 61.176 63.158 0.00 0.00 43.38 4.45
7263 8467 2.659063 TAGCGAGCACATGCCCAGT 61.659 57.895 0.00 0.00 43.38 4.00
7264 8468 1.326951 TAGCGAGCACATGCCCAGTA 61.327 55.000 0.00 0.00 43.38 2.74
7265 8469 2.176273 GCGAGCACATGCCCAGTAG 61.176 63.158 0.00 0.00 43.38 2.57
7266 8470 2.176273 CGAGCACATGCCCAGTAGC 61.176 63.158 0.00 0.00 43.38 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.045407 TCACCGTAAGCAAGACCACT 58.955 50.000 0.00 0.00 0.00 4.00
14 15 1.210870 GTCGTTGTCACCGTAAGCAA 58.789 50.000 0.00 0.00 0.00 3.91
30 31 1.653034 CGTGTCATCGTCGTGTGTCG 61.653 60.000 0.00 0.00 41.41 4.35
53 60 1.299468 GCATGCCGGTCTCTAGTCG 60.299 63.158 6.36 0.00 0.00 4.18
86 93 0.532573 ATGTCGATTCCAGTGCGTCT 59.467 50.000 0.00 0.00 0.00 4.18
100 107 2.887568 GTGCTCGCCCTCATGTCG 60.888 66.667 0.00 0.00 0.00 4.35
165 172 3.030308 CGTGTTGTCGCACTCGCT 61.030 61.111 0.00 0.00 37.24 4.93
241 248 7.050377 TGTTGGATGTTGGATAATCTCTCTTC 58.950 38.462 0.00 0.00 0.00 2.87
243 250 6.566079 TGTTGGATGTTGGATAATCTCTCT 57.434 37.500 0.00 0.00 0.00 3.10
251 1077 3.289836 CTGCCATGTTGGATGTTGGATA 58.710 45.455 0.00 0.00 40.96 2.59
262 1113 4.764336 CGCGGTGCTGCCATGTTG 62.764 66.667 0.00 0.00 36.97 3.33
264 1115 4.783621 ATCGCGGTGCTGCCATGT 62.784 61.111 6.13 0.00 36.97 3.21
265 1116 3.945434 GATCGCGGTGCTGCCATG 61.945 66.667 6.13 0.00 36.97 3.66
312 1163 2.722094 TCCTTTTTGTGCGGATGCTAT 58.278 42.857 0.00 0.00 43.34 2.97
331 1183 6.149633 CAGTAGTACAATTGTTTTGCCCTTC 58.850 40.000 17.78 2.35 0.00 3.46
362 1214 0.659427 ATGATTGCATTCACGGCTCG 59.341 50.000 13.20 0.00 0.00 5.03
575 1427 2.267961 GGTGGTAACTGGCGGAGG 59.732 66.667 0.00 0.00 37.61 4.30
576 1428 2.125673 CGGTGGTAACTGGCGGAG 60.126 66.667 0.00 0.00 37.61 4.63
577 1429 3.697747 CCGGTGGTAACTGGCGGA 61.698 66.667 0.00 0.00 45.91 5.54
670 1545 1.313889 ATGTCCTCTCCTCTCCCTCA 58.686 55.000 0.00 0.00 0.00 3.86
765 1645 0.631998 TCCCTCCTCCCTGATCCTCT 60.632 60.000 0.00 0.00 0.00 3.69
766 1646 0.178935 CTCCCTCCTCCCTGATCCTC 60.179 65.000 0.00 0.00 0.00 3.71
767 1647 1.673928 CCTCCCTCCTCCCTGATCCT 61.674 65.000 0.00 0.00 0.00 3.24
769 1649 1.841103 GCCTCCCTCCTCCCTGATC 60.841 68.421 0.00 0.00 0.00 2.92
770 1650 2.200373 TTGCCTCCCTCCTCCCTGAT 62.200 60.000 0.00 0.00 0.00 2.90
771 1651 2.880612 TTGCCTCCCTCCTCCCTGA 61.881 63.158 0.00 0.00 0.00 3.86
772 1652 2.285668 TTGCCTCCCTCCTCCCTG 60.286 66.667 0.00 0.00 0.00 4.45
773 1653 2.285743 GTTGCCTCCCTCCTCCCT 60.286 66.667 0.00 0.00 0.00 4.20
774 1654 2.610859 TGTTGCCTCCCTCCTCCC 60.611 66.667 0.00 0.00 0.00 4.30
775 1655 2.993853 CTGTTGCCTCCCTCCTCC 59.006 66.667 0.00 0.00 0.00 4.30
921 1810 2.094659 CGAGGAATTGCGCGACAGT 61.095 57.895 17.64 0.68 0.00 3.55
1539 2621 0.886563 CGAACTCCTCCACGGTAAGT 59.113 55.000 0.00 0.00 0.00 2.24
1701 2783 4.796231 CTGCGCCGCCTAGAACGT 62.796 66.667 6.63 0.00 0.00 3.99
1839 2921 0.617413 CACCATCCTGGCTGTCTTCT 59.383 55.000 0.00 0.00 42.67 2.85
2055 3137 3.044156 CCTCTCCTCCTTCATCATTCCA 58.956 50.000 0.00 0.00 0.00 3.53
2418 3501 9.766277 CATTCTGAACTTCATTCTACTTAAAGC 57.234 33.333 0.00 0.00 38.25 3.51
2423 3506 7.453393 TGTCCATTCTGAACTTCATTCTACTT 58.547 34.615 0.00 0.00 38.25 2.24
2571 3667 3.211045 GCCAACTTGACAAGGTAAGACA 58.789 45.455 19.16 0.00 0.00 3.41
2758 3854 1.476891 TCGTACACCTCTGATCAAGCC 59.523 52.381 0.00 0.00 0.00 4.35
3041 4137 3.546218 GCAAAACTGACGAGACAAGGTTC 60.546 47.826 0.00 0.00 0.00 3.62
3135 4231 2.479566 TGCTAGAGCTCAAGGGTTTG 57.520 50.000 17.77 0.00 42.66 2.93
3376 4472 0.036388 CCCCGCTCACAGCTTAAAGA 60.036 55.000 0.00 0.00 39.60 2.52
3377 4473 1.026718 CCCCCGCTCACAGCTTAAAG 61.027 60.000 0.00 0.00 39.60 1.85
3408 4504 2.711711 CTGCACACAGTTGCCTCTT 58.288 52.632 5.57 0.00 42.25 2.85
3477 4573 1.732941 TCTTTTGTGTGTGAGTGCGT 58.267 45.000 0.00 0.00 0.00 5.24
3951 5108 1.522668 TAACGCACTGCAAGCTGAAT 58.477 45.000 8.90 2.08 37.60 2.57
3975 5132 7.954056 TGGCCAATGTCCTAGTTAGTACTATAT 59.046 37.037 0.61 0.00 36.32 0.86
4034 5191 9.217336 ACAATGATATGGATAGCATGGTAGATA 57.783 33.333 10.82 7.06 40.47 1.98
4035 5192 8.098963 ACAATGATATGGATAGCATGGTAGAT 57.901 34.615 10.82 5.18 40.47 1.98
4037 5194 9.671279 TTTACAATGATATGGATAGCATGGTAG 57.329 33.333 10.82 0.00 42.89 3.18
4094 5263 7.717436 TGAAAATACATGTTCAGGTTCTGTACA 59.283 33.333 2.30 9.20 43.59 2.90
4172 5341 7.141363 AGCAAAATGTCCTTCGCATATTTATC 58.859 34.615 0.00 0.00 0.00 1.75
4193 5362 9.729281 TCTATGATGCAATATATTCAGAAGCAA 57.271 29.630 10.41 0.00 33.91 3.91
4237 5406 5.304357 ACTTTTGGGACCAAAGTAAATCCAG 59.696 40.000 15.37 10.43 45.15 3.86
4241 5410 6.800072 TGAACTTTTGGGACCAAAGTAAAT 57.200 33.333 15.37 3.69 45.15 1.40
4336 5505 3.620374 AGTATTCGTCTTTCATGCAGCAG 59.380 43.478 0.00 0.00 0.00 4.24
4337 5506 3.371898 CAGTATTCGTCTTTCATGCAGCA 59.628 43.478 0.00 0.00 0.00 4.41
4358 5527 8.945481 ATGGAATCGATTAATTTGCAAATTCA 57.055 26.923 34.40 26.35 39.24 2.57
4633 5802 2.992847 TAGTCACTGTGGGAGAAGGA 57.007 50.000 8.11 0.00 0.00 3.36
4674 5843 6.072286 GCACATGGAGAGAAATCTTCTGAAAA 60.072 38.462 0.00 0.00 40.87 2.29
4701 5870 5.297776 GGACAGTGCTATCAGTGCATTTAAT 59.702 40.000 1.26 0.00 45.34 1.40
4707 5876 1.066645 CAGGACAGTGCTATCAGTGCA 60.067 52.381 0.00 0.00 45.34 4.57
4749 5918 3.079578 ACTGGATGCAAGTCACTGAATG 58.920 45.455 0.00 0.00 0.00 2.67
4983 6152 7.197486 GCACTCTGCAGAAAATATAAAAACG 57.803 36.000 18.85 3.53 44.26 3.60
5089 6263 0.178953 AGGGGTCACAGCAGCAAAAT 60.179 50.000 0.00 0.00 0.00 1.82
5324 6498 1.279496 TCTCAAGTATGCCAGGTGCT 58.721 50.000 0.00 0.00 42.00 4.40
5351 6525 6.210584 TCAGTGTCAGTACATAATGGAACAGA 59.789 38.462 0.00 0.00 39.28 3.41
5356 6530 7.181569 TCATTCAGTGTCAGTACATAATGGA 57.818 36.000 0.00 0.00 38.08 3.41
5542 6718 1.620822 ACCAATTGTCACAGGAAGCC 58.379 50.000 4.43 0.00 0.00 4.35
5587 6763 3.463585 TACGCACGGGATGGGGTC 61.464 66.667 0.00 0.00 45.48 4.46
5598 6774 0.721718 GGCTCATCAACAGTACGCAC 59.278 55.000 0.00 0.00 0.00 5.34
5604 6780 2.289945 GGAAGTCAGGCTCATCAACAGT 60.290 50.000 0.00 0.00 0.00 3.55
5985 7161 1.064003 TGACCATTACCAGCCACACT 58.936 50.000 0.00 0.00 0.00 3.55
6152 7328 1.857217 CTCGGAGCTTGATCAACATCG 59.143 52.381 3.38 6.71 0.00 3.84
6349 7525 3.190118 GCAACCTCAGTCAAATCCTTCAG 59.810 47.826 0.00 0.00 0.00 3.02
6482 7658 1.597461 GCCGTCACTCTAGGGCTTT 59.403 57.895 0.00 0.00 45.03 3.51
6805 7986 9.093970 CATGGTAGAAATGAACGAACAAGTATA 57.906 33.333 0.00 0.00 0.00 1.47
6833 8014 2.038557 ACTACCCAGTTGCGAACTCAAT 59.961 45.455 0.00 0.00 40.46 2.57
6913 8105 5.009010 GCTTCTCCTGAAACTGAATGTTGAA 59.991 40.000 0.00 0.00 39.13 2.69
7029 8221 5.444176 AGTATACTCCTACAGGTTAGCGTT 58.556 41.667 0.00 0.00 36.34 4.84
7031 8223 7.104939 AGATAGTATACTCCTACAGGTTAGCG 58.895 42.308 9.12 0.00 36.34 4.26
7032 8224 8.323567 AGAGATAGTATACTCCTACAGGTTAGC 58.676 40.741 9.12 0.00 36.34 3.09
7035 8227 7.879160 CGAAGAGATAGTATACTCCTACAGGTT 59.121 40.741 9.12 0.00 36.34 3.50
7036 8228 7.388437 CGAAGAGATAGTATACTCCTACAGGT 58.612 42.308 9.12 0.00 36.34 4.00
7037 8229 6.314400 GCGAAGAGATAGTATACTCCTACAGG 59.686 46.154 9.12 0.00 34.13 4.00
7038 8230 6.874664 TGCGAAGAGATAGTATACTCCTACAG 59.125 42.308 9.12 2.87 34.13 2.74
7039 8231 6.766429 TGCGAAGAGATAGTATACTCCTACA 58.234 40.000 9.12 0.00 34.13 2.74
7040 8232 7.388500 ACTTGCGAAGAGATAGTATACTCCTAC 59.612 40.741 9.12 0.64 34.13 3.18
7041 8233 7.388224 CACTTGCGAAGAGATAGTATACTCCTA 59.612 40.741 9.12 0.00 34.13 2.94
7042 8234 6.205853 CACTTGCGAAGAGATAGTATACTCCT 59.794 42.308 9.12 8.00 34.13 3.69
7043 8235 6.016943 ACACTTGCGAAGAGATAGTATACTCC 60.017 42.308 9.12 2.88 34.13 3.85
7044 8236 6.961576 ACACTTGCGAAGAGATAGTATACTC 58.038 40.000 9.12 0.00 0.00 2.59
7045 8237 6.016943 GGACACTTGCGAAGAGATAGTATACT 60.017 42.308 10.87 10.87 0.00 2.12
7046 8238 6.144175 GGACACTTGCGAAGAGATAGTATAC 58.856 44.000 0.00 0.00 0.00 1.47
7047 8239 5.049612 CGGACACTTGCGAAGAGATAGTATA 60.050 44.000 3.37 0.00 39.29 1.47
7048 8240 4.261238 CGGACACTTGCGAAGAGATAGTAT 60.261 45.833 3.37 0.00 39.29 2.12
7049 8241 3.064958 CGGACACTTGCGAAGAGATAGTA 59.935 47.826 3.37 0.00 39.29 1.82
7051 8243 2.159366 ACGGACACTTGCGAAGAGATAG 60.159 50.000 3.37 0.00 39.29 2.08
7052 8244 1.816835 ACGGACACTTGCGAAGAGATA 59.183 47.619 3.37 0.00 39.29 1.98
7053 8245 0.603569 ACGGACACTTGCGAAGAGAT 59.396 50.000 3.37 0.00 39.29 2.75
7054 8246 0.318699 CACGGACACTTGCGAAGAGA 60.319 55.000 3.37 0.00 39.29 3.10
7055 8247 0.597637 ACACGGACACTTGCGAAGAG 60.598 55.000 3.37 0.00 39.29 2.85
7056 8248 0.179094 AACACGGACACTTGCGAAGA 60.179 50.000 3.37 0.00 39.29 2.87
7058 8250 1.088306 AAAACACGGACACTTGCGAA 58.912 45.000 0.00 0.00 39.29 4.70
7060 8252 2.013286 GTAAAACACGGACACTTGCG 57.987 50.000 0.00 0.00 43.33 4.85
7071 8263 2.542595 CCTCTGTGTGGACGTAAAACAC 59.457 50.000 16.78 16.78 43.57 3.32
7072 8264 2.168936 ACCTCTGTGTGGACGTAAAACA 59.831 45.455 0.00 0.00 0.00 2.83
7073 8265 2.798847 GACCTCTGTGTGGACGTAAAAC 59.201 50.000 0.00 0.00 0.00 2.43
7074 8266 2.224113 GGACCTCTGTGTGGACGTAAAA 60.224 50.000 0.00 0.00 0.00 1.52
7075 8267 1.342174 GGACCTCTGTGTGGACGTAAA 59.658 52.381 0.00 0.00 0.00 2.01
7076 8268 0.963962 GGACCTCTGTGTGGACGTAA 59.036 55.000 0.00 0.00 0.00 3.18
7077 8269 1.239296 CGGACCTCTGTGTGGACGTA 61.239 60.000 0.00 0.00 0.00 3.57
7078 8270 2.561956 CGGACCTCTGTGTGGACGT 61.562 63.158 0.00 0.00 0.00 4.34
7079 8271 2.258591 CGGACCTCTGTGTGGACG 59.741 66.667 0.00 0.00 0.00 4.79
7080 8272 1.878656 CTCCGGACCTCTGTGTGGAC 61.879 65.000 0.00 0.00 0.00 4.02
7081 8273 1.606601 CTCCGGACCTCTGTGTGGA 60.607 63.158 0.00 0.00 0.00 4.02
7082 8274 0.972983 ATCTCCGGACCTCTGTGTGG 60.973 60.000 0.00 0.00 0.00 4.17
7083 8275 0.898320 AATCTCCGGACCTCTGTGTG 59.102 55.000 0.00 0.00 0.00 3.82
7084 8276 0.898320 CAATCTCCGGACCTCTGTGT 59.102 55.000 0.00 0.00 0.00 3.72
7085 8277 1.186200 TCAATCTCCGGACCTCTGTG 58.814 55.000 0.00 0.00 0.00 3.66
7086 8278 2.166907 ATCAATCTCCGGACCTCTGT 57.833 50.000 0.00 0.00 0.00 3.41
7087 8279 2.030717 CGTATCAATCTCCGGACCTCTG 60.031 54.545 0.00 0.00 0.00 3.35
7088 8280 2.231529 CGTATCAATCTCCGGACCTCT 58.768 52.381 0.00 0.00 0.00 3.69
7089 8281 1.269998 CCGTATCAATCTCCGGACCTC 59.730 57.143 0.00 0.00 43.01 3.85
7090 8282 1.133575 TCCGTATCAATCTCCGGACCT 60.134 52.381 0.00 0.00 43.99 3.85
7101 8293 0.594028 CTAGCGCGCTTCCGTATCAA 60.594 55.000 41.04 17.08 36.67 2.57
7118 8310 3.478780 AGGTCAACCTTGCGGCTA 58.521 55.556 0.00 0.00 46.09 3.93
7178 8382 3.750077 TATTACCTCGCCACACGCCAC 62.750 57.143 0.00 0.00 43.23 5.01
7179 8383 1.605971 TATTACCTCGCCACACGCCA 61.606 55.000 0.00 0.00 43.23 5.69
7180 8384 1.142314 TATTACCTCGCCACACGCC 59.858 57.895 0.00 0.00 43.23 5.68
7181 8385 0.458889 TGTATTACCTCGCCACACGC 60.459 55.000 0.00 0.00 43.23 5.34
7182 8386 1.274596 GTGTATTACCTCGCCACACG 58.725 55.000 0.00 0.00 45.62 4.49
7183 8387 2.373540 TGTGTATTACCTCGCCACAC 57.626 50.000 0.00 0.00 39.89 3.82
7184 8388 2.690786 GTTGTGTATTACCTCGCCACA 58.309 47.619 0.00 0.00 34.47 4.17
7185 8389 1.657094 CGTTGTGTATTACCTCGCCAC 59.343 52.381 0.00 0.00 0.00 5.01
7186 8390 1.545136 TCGTTGTGTATTACCTCGCCA 59.455 47.619 0.00 0.00 0.00 5.69
7245 8449 1.326951 TACTGGGCATGTGCTCGCTA 61.327 55.000 4.84 0.00 46.72 4.26


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

AutoCloner maintained by Alex Coulton.