Multiple sequence alignment - TraesCS1A01G339300

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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 TraesCS1A01G339300 chr1A 100.000 7237 0 0 1 7237 529250639 529243403 0.000000e+00 13365
1 TraesCS1A01G339300 chr1B 92.174 7373 303 101 6 7237 582099078 582091839 0.000000e+00 10166
2 TraesCS1A01G339300 chr1B 87.884 619 65 4 3572 4190 604837523 604838131 0.000000e+00 719
3 TraesCS1A01G339300 chr1D 94.521 6443 264 49 845 7237 430982440 430976037 0.000000e+00 9860
4 TraesCS1A01G339300 chr1D 89.790 666 38 13 168 814 430983085 430982431 0.000000e+00 826
5 TraesCS1A01G339300 chr2D 90.768 1419 94 21 2773 4187 432763027 432764412 0.000000e+00 1860
6 TraesCS1A01G339300 chr2D 84.600 487 39 7 2014 2500 432761959 432762409 1.110000e-122 451
7 TraesCS1A01G339300 chr2D 84.980 253 28 4 2510 2760 432762445 432762689 1.560000e-61 248
8 TraesCS1A01G339300 chr2A 89.248 1423 105 23 2773 4187 554134910 554133528 0.000000e+00 1736
9 TraesCS1A01G339300 chr2A 91.473 258 20 1 2511 2766 554135527 554135270 3.210000e-93 353
10 TraesCS1A01G339300 chr2A 80.919 283 30 11 2002 2284 554136303 554136045 1.230000e-47 202
11 TraesCS1A01G339300 chr2B 87.690 1121 83 19 2773 3885 511122750 511123823 0.000000e+00 1254
12 TraesCS1A01G339300 chr2B 87.425 501 52 4 2002 2500 511121606 511122097 3.790000e-157 566
13 TraesCS1A01G339300 chr5B 89.362 141 12 3 1081 1220 710871824 710871686 2.680000e-39 174
14 TraesCS1A01G339300 chr7A 88.073 109 10 3 3340 3448 14507539 14507434 7.620000e-25 126


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 TraesCS1A01G339300 chr1A 529243403 529250639 7236 True 13365.000000 13365 100.000000 1 7237 1 chr1A.!!$R1 7236
1 TraesCS1A01G339300 chr1B 582091839 582099078 7239 True 10166.000000 10166 92.174000 6 7237 1 chr1B.!!$R1 7231
2 TraesCS1A01G339300 chr1B 604837523 604838131 608 False 719.000000 719 87.884000 3572 4190 1 chr1B.!!$F1 618
3 TraesCS1A01G339300 chr1D 430976037 430983085 7048 True 5343.000000 9860 92.155500 168 7237 2 chr1D.!!$R1 7069
4 TraesCS1A01G339300 chr2D 432761959 432764412 2453 False 853.000000 1860 86.782667 2014 4187 3 chr2D.!!$F1 2173
5 TraesCS1A01G339300 chr2A 554133528 554136303 2775 True 763.666667 1736 87.213333 2002 4187 3 chr2A.!!$R1 2185
6 TraesCS1A01G339300 chr2B 511121606 511123823 2217 False 910.000000 1254 87.557500 2002 3885 2 chr2B.!!$F1 1883

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
375 413 0.248498 AACGCGATCACGATCACGAT 60.248 50.000 20.71 8.99 43.68 3.73 F
376 414 0.657659 ACGCGATCACGATCACGATC 60.658 55.000 20.71 10.12 43.68 3.69 F
420 458 1.136085 CGCATTCGATTTCCGTTGTGT 60.136 47.619 0.00 0.00 39.75 3.72 F
1600 1699 1.138069 TCTGACTTCGCAGGTGTGAAA 59.862 47.619 7.35 0.00 43.05 2.69 F
2692 3258 0.958822 AAAGGGCGTTGGACATTGAC 59.041 50.000 0.00 0.00 0.00 3.18 F
3457 4384 2.997485 GAACATTGTCTGCTGTTCCC 57.003 50.000 3.52 0.00 43.42 3.97 F
4215 5153 1.493311 GAGCTCGTTTGCACTTCGG 59.507 57.895 0.00 0.00 34.99 4.30 F
5603 6562 0.320073 TTTCCGTTCTGTAGGGTGCG 60.320 55.000 0.00 0.00 33.40 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1600 1699 1.154016 CCACTTCGCGTCGACATCT 60.154 57.895 17.16 0.0 34.89 2.90 R
2135 2236 3.181464 GGTAAATCTCCGAGGAAGGGAAG 60.181 52.174 0.00 0.0 32.02 3.46 R
2260 2362 3.788227 AGAACAGCCATAGAACAACCA 57.212 42.857 0.00 0.0 0.00 3.67 R
2717 3283 0.454957 CCCGCAAATCGCTGTTTCAG 60.455 55.000 0.00 0.0 39.08 3.02 R
4207 5145 2.076863 AGTACAAATGAGCCGAAGTGC 58.923 47.619 0.00 0.0 0.00 4.40 R
4751 5708 1.280133 CCAGAGGATTCAACTGGCTCA 59.720 52.381 12.92 0.0 43.32 4.26 R
5938 6898 1.890894 GCGACCTGAGGCTTCTGTA 59.109 57.895 0.00 0.0 0.00 2.74 R
7206 8239 1.063006 CCTCATGCCGTTCAATGCG 59.937 57.895 0.00 0.0 0.00 4.73 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
77 79 3.005897 GGGCTCATCTCGCTCTTGTTATA 59.994 47.826 0.00 0.00 0.00 0.98
107 109 1.448922 CGGAGTCGGAGTCTCATCCC 61.449 65.000 12.32 0.00 44.19 3.85
108 110 0.395862 GGAGTCGGAGTCTCATCCCA 60.396 60.000 12.32 0.00 44.19 4.37
109 111 1.698506 GAGTCGGAGTCTCATCCCAT 58.301 55.000 5.58 0.00 42.08 4.00
110 112 2.035632 GAGTCGGAGTCTCATCCCATT 58.964 52.381 5.58 0.00 42.08 3.16
111 113 1.759445 AGTCGGAGTCTCATCCCATTG 59.241 52.381 1.47 0.00 35.82 2.82
184 192 3.366396 GAGACCTTGACATAGGGTGAGA 58.634 50.000 8.09 0.00 39.18 3.27
219 227 1.962100 ACGTCGTCCCTTTTCTTCTCT 59.038 47.619 0.00 0.00 0.00 3.10
221 229 2.671632 CGTCGTCCCTTTTCTTCTCTCC 60.672 54.545 0.00 0.00 0.00 3.71
223 231 3.007074 GTCGTCCCTTTTCTTCTCTCCTT 59.993 47.826 0.00 0.00 0.00 3.36
317 325 4.399219 TCTCATCGGGGACTAGTAGATTG 58.601 47.826 3.59 0.00 0.00 2.67
371 409 2.648972 GTGAACGCGATCACGATCA 58.351 52.632 29.59 11.46 41.69 2.92
372 410 2.648972 TGAACGCGATCACGATCAC 58.351 52.632 15.63 0.00 39.50 3.06
373 411 1.131618 TGAACGCGATCACGATCACG 61.132 55.000 15.63 14.15 45.64 4.35
374 412 0.860203 GAACGCGATCACGATCACGA 60.860 55.000 20.71 0.00 43.68 4.35
375 413 0.248498 AACGCGATCACGATCACGAT 60.248 50.000 20.71 8.99 43.68 3.73
376 414 0.657659 ACGCGATCACGATCACGATC 60.658 55.000 20.71 10.12 43.68 3.69
420 458 1.136085 CGCATTCGATTTCCGTTGTGT 60.136 47.619 0.00 0.00 39.75 3.72
425 463 5.728255 CATTCGATTTCCGTTGTGTAGATC 58.272 41.667 0.00 0.00 39.75 2.75
525 576 4.563976 GTGATTACGGTACTGTATTTGCGT 59.436 41.667 15.24 5.18 0.00 5.24
531 582 4.084223 ACGGTACTGTATTTGCGTTTGAAG 60.084 41.667 5.26 0.00 0.00 3.02
540 591 5.793026 ATTTGCGTTTGAAGCTTTTTGAA 57.207 30.435 0.00 0.00 35.28 2.69
543 594 4.952097 TGCGTTTGAAGCTTTTTGAAAAC 58.048 34.783 0.00 6.51 35.28 2.43
778 861 2.270297 AAGCAGCGCAATTAAGGCCG 62.270 55.000 11.47 0.00 0.00 6.13
1036 1122 1.436336 GGCAGCAACATCATCAGCC 59.564 57.895 0.00 0.00 0.00 4.85
1221 1307 4.430765 ATGGACACGGACGTCGCC 62.431 66.667 9.92 6.30 43.89 5.54
1297 1386 1.958715 CACGCCAACATGGACGACA 60.959 57.895 16.23 0.00 40.96 4.35
1302 1391 1.301401 CAACATGGACGACACCGGT 60.301 57.895 0.00 0.00 40.78 5.28
1305 1400 4.388499 ATGGACGACACCGGTGGC 62.388 66.667 36.47 34.21 40.78 5.01
1600 1699 1.138069 TCTGACTTCGCAGGTGTGAAA 59.862 47.619 7.35 0.00 43.05 2.69
1639 1738 4.740822 GGCTGGGCCGGTGTGAAT 62.741 66.667 15.16 0.00 39.62 2.57
1715 1814 4.769688 TCGTTGCAATCCACAGAATCTAT 58.230 39.130 0.59 0.00 0.00 1.98
1723 1822 7.605309 TGCAATCCACAGAATCTATGACATATC 59.395 37.037 0.00 0.00 0.00 1.63
1729 1828 7.278203 CCACAGAATCTATGACATATCTGATGC 59.722 40.741 22.68 10.65 38.10 3.91
1754 1853 4.067896 ACTGAACCAATAGAACAGTGCTG 58.932 43.478 0.00 0.00 39.76 4.41
1759 1858 2.417933 CCAATAGAACAGTGCTGTCTGC 59.582 50.000 5.22 0.00 44.13 4.26
1796 1895 5.258456 AGTTCGTTCTAGTGACTGAAACA 57.742 39.130 10.95 0.00 0.00 2.83
1841 1940 4.697352 ACAAAACAGAGATGCATACCAGTC 59.303 41.667 0.00 0.00 0.00 3.51
2135 2236 4.947147 TGGTTCCTGCACACGCCC 62.947 66.667 0.00 0.00 37.32 6.13
2245 2347 8.807667 GCATGCATCTTGCTTTTATTAGTAAT 57.192 30.769 14.21 0.17 45.31 1.89
2246 2348 9.897744 GCATGCATCTTGCTTTTATTAGTAATA 57.102 29.630 14.21 0.00 45.31 0.98
2274 2378 6.379386 GTTTCTTTACTGGTTGTTCTATGGC 58.621 40.000 0.00 0.00 0.00 4.40
2409 2513 2.614734 GGAGGACCAGGGAAAGTTAACG 60.615 54.545 0.00 0.00 35.97 3.18
2483 2590 1.076024 ACATGTTTGGGATCAGTGGCT 59.924 47.619 0.00 0.00 0.00 4.75
2526 3090 6.650120 TCCTCCTTGTGAAATACCATTAGTC 58.350 40.000 0.00 0.00 0.00 2.59
2527 3091 6.214615 TCCTCCTTGTGAAATACCATTAGTCA 59.785 38.462 0.00 0.00 0.00 3.41
2617 3183 7.565323 TTTTTGGAAAATGGGTGATTCTTTG 57.435 32.000 0.00 0.00 0.00 2.77
2692 3258 0.958822 AAAGGGCGTTGGACATTGAC 59.041 50.000 0.00 0.00 0.00 3.18
2717 3283 5.332808 GCAGCAAAAAGACATGTCAATGAAC 60.333 40.000 27.02 12.31 37.24 3.18
2832 3755 4.164988 AGATCTACCTGGCACATTTTAGCT 59.835 41.667 0.00 0.00 38.20 3.32
2839 3762 4.095483 CCTGGCACATTTTAGCTGTTCTAG 59.905 45.833 0.00 0.00 38.20 2.43
2876 3799 5.422012 ACCTTGAAAGTCACACTTCCATTTT 59.578 36.000 0.00 0.00 37.47 1.82
2877 3800 6.070824 ACCTTGAAAGTCACACTTCCATTTTT 60.071 34.615 0.00 0.00 37.47 1.94
2894 3817 8.792830 TCCATTTTTCTGTCCTGTTATTCTAG 57.207 34.615 0.00 0.00 0.00 2.43
3457 4384 2.997485 GAACATTGTCTGCTGTTCCC 57.003 50.000 3.52 0.00 43.42 3.97
3490 4417 8.555361 CATCTGGTTAGCTTTTAAATAGCTCTC 58.445 37.037 20.74 16.09 45.52 3.20
3561 4488 6.565234 TCTTTGGCAAACTATTTCGTTTCAA 58.435 32.000 8.93 0.00 35.06 2.69
3670 4603 7.680588 GCAGCTCTCTTTATATTGAAAGTTGGG 60.681 40.741 0.00 0.00 37.62 4.12
3855 4790 7.777095 AGTTCTGATATTGAGTGAGGTAAGTC 58.223 38.462 0.00 0.00 0.00 3.01
4054 4992 4.019174 CTGGTGCCATTCTTGTAAATCCT 58.981 43.478 0.00 0.00 0.00 3.24
4207 5145 2.271800 GTATGGTGAGGAGCTCGTTTG 58.728 52.381 10.79 0.00 32.35 2.93
4215 5153 1.493311 GAGCTCGTTTGCACTTCGG 59.507 57.895 0.00 0.00 34.99 4.30
4232 5170 6.622896 GCACTTCGGCTCATTTGTACTTTTAT 60.623 38.462 0.00 0.00 0.00 1.40
4233 5171 7.305474 CACTTCGGCTCATTTGTACTTTTATT 58.695 34.615 0.00 0.00 0.00 1.40
4234 5172 8.447833 CACTTCGGCTCATTTGTACTTTTATTA 58.552 33.333 0.00 0.00 0.00 0.98
4235 5173 9.005777 ACTTCGGCTCATTTGTACTTTTATTAA 57.994 29.630 0.00 0.00 0.00 1.40
4236 5174 9.274065 CTTCGGCTCATTTGTACTTTTATTAAC 57.726 33.333 0.00 0.00 0.00 2.01
4237 5175 7.754625 TCGGCTCATTTGTACTTTTATTAACC 58.245 34.615 0.00 0.00 0.00 2.85
4238 5176 7.390996 TCGGCTCATTTGTACTTTTATTAACCA 59.609 33.333 0.00 0.00 0.00 3.67
4239 5177 7.696453 CGGCTCATTTGTACTTTTATTAACCAG 59.304 37.037 0.00 0.00 0.00 4.00
4240 5178 8.736244 GGCTCATTTGTACTTTTATTAACCAGA 58.264 33.333 0.00 0.00 0.00 3.86
4531 5488 5.652994 TCACTGGGGTTTATAATGCAAAC 57.347 39.130 0.00 0.00 35.57 2.93
4561 5518 6.346999 GCTTGTTTACTCTTCTGCAGTAACTC 60.347 42.308 14.67 2.66 36.32 3.01
4751 5708 7.781324 ATAGGGTTTCAATTCAACATTGACT 57.219 32.000 0.00 0.00 37.71 3.41
5004 5961 4.998051 TCCTCTACCCTTTGCAGAATTTT 58.002 39.130 0.00 0.00 0.00 1.82
5010 5967 3.575687 ACCCTTTGCAGAATTTTGGAGAG 59.424 43.478 1.75 1.75 0.00 3.20
5125 6082 2.559668 TGGGTCGACAGTGTAAAGGTAG 59.440 50.000 18.91 0.00 0.00 3.18
5190 6147 2.041216 ACCTTCTCACACCATTTACCCC 59.959 50.000 0.00 0.00 0.00 4.95
5284 6241 3.322369 TGTGTGGAACTACAAGTATGCG 58.678 45.455 0.00 0.00 38.04 4.73
5317 6274 6.500684 TCAGGTCTTCATGCATAGTTTTTC 57.499 37.500 0.00 0.00 0.00 2.29
5498 6455 2.062519 GAAGTTCGCTCTGTTGGAGTC 58.937 52.381 0.00 0.00 43.62 3.36
5542 6499 8.474025 AGTGTGATTTTTAAACATGGTGAAAGA 58.526 29.630 0.00 0.00 0.00 2.52
5603 6562 0.320073 TTTCCGTTCTGTAGGGTGCG 60.320 55.000 0.00 0.00 33.40 5.34
5606 6565 2.436115 GTTCTGTAGGGTGCGGCC 60.436 66.667 0.00 0.00 0.00 6.13
5624 6583 3.600388 GGCCATTGATCGTATTCTAGGG 58.400 50.000 0.00 0.00 0.00 3.53
5630 6589 6.070538 CCATTGATCGTATTCTAGGGGAGATT 60.071 42.308 0.00 0.00 32.88 2.40
5718 6677 7.617041 AAGGTAATTCTGCACTGACTTTATC 57.383 36.000 0.00 0.00 0.00 1.75
5719 6678 6.116126 AGGTAATTCTGCACTGACTTTATCC 58.884 40.000 0.00 0.00 0.00 2.59
5724 6683 4.348486 TCTGCACTGACTTTATCCTCTCT 58.652 43.478 0.00 0.00 0.00 3.10
5726 6685 3.129462 TGCACTGACTTTATCCTCTCTCG 59.871 47.826 0.00 0.00 0.00 4.04
5746 6706 6.390721 TCTCGTTCCTTTCTAGTTCATCTTG 58.609 40.000 0.00 0.00 0.00 3.02
5760 6720 9.322773 CTAGTTCATCTTGAATGTGTGTGATAT 57.677 33.333 0.00 0.00 38.79 1.63
5762 6722 9.671279 AGTTCATCTTGAATGTGTGTGATATAA 57.329 29.630 0.00 0.00 38.79 0.98
5813 6773 3.381908 AGGACGAGGACATCTATGTGTTC 59.618 47.826 0.00 0.00 41.95 3.18
5855 6815 3.292460 TGAACCAAAAGTGAAACCGGAT 58.708 40.909 9.46 0.00 37.80 4.18
5984 6944 1.448922 CTCCGGAGAGGTCATCGTCC 61.449 65.000 28.21 0.00 41.99 4.79
6077 7037 2.701073 ACGGTGACAACTACTTCTCG 57.299 50.000 0.00 0.00 0.00 4.04
6235 7195 6.553953 TTACATGTTCTTGGATAGGCAGTA 57.446 37.500 2.30 0.00 0.00 2.74
6240 7200 4.777896 TGTTCTTGGATAGGCAGTAAGACT 59.222 41.667 0.00 0.00 40.36 3.24
6306 7267 1.674221 CCCGCCTGAGAAGAAGAGTTG 60.674 57.143 0.00 0.00 0.00 3.16
6310 7271 3.324993 GCCTGAGAAGAAGAGTTGACAG 58.675 50.000 0.00 0.00 0.00 3.51
6318 7279 1.276421 GAAGAGTTGACAGCAGCCCTA 59.724 52.381 0.00 0.00 0.00 3.53
6530 7524 9.209175 GTTATTATGTGATGTGAGGACTAATCC 57.791 37.037 0.00 0.00 46.69 3.01
6547 7541 0.535335 TCCCAGCATTGACGGTCTAC 59.465 55.000 9.88 0.00 0.00 2.59
6597 7591 4.806330 TGCTCTTAGACTTTTCGTTCGAT 58.194 39.130 0.00 0.00 0.00 3.59
6624 7624 3.040147 TGGATTCTGTCGTTTCTCACC 57.960 47.619 0.00 0.00 0.00 4.02
6640 7642 6.834168 TTCTCACCCTAATTTTGGTTCATC 57.166 37.500 0.00 0.00 30.70 2.92
6645 7647 4.644685 ACCCTAATTTTGGTTCATCATCCG 59.355 41.667 0.00 0.00 0.00 4.18
6671 7673 2.032071 GTGGCCACGCAGGTAAGT 59.968 61.111 22.49 0.00 40.61 2.24
6693 7695 3.540314 TGGCAACTTGAAACTGCATTT 57.460 38.095 0.00 0.00 37.83 2.32
6715 7717 6.484818 TTTGCGTAGTTATTTGACCCTAAC 57.515 37.500 0.00 0.00 0.00 2.34
6719 7721 4.162888 CGTAGTTATTTGACCCTAACCCCT 59.837 45.833 0.00 0.00 0.00 4.79
6724 7726 2.563039 TTGACCCTAACCCCTCCTAG 57.437 55.000 0.00 0.00 0.00 3.02
6737 7739 9.382307 CTAACCCCTCCTAGAAATCTAAACTAT 57.618 37.037 0.00 0.00 0.00 2.12
6756 7780 1.153147 GGGTTAGGTGCAGCTAGCC 60.153 63.158 36.93 36.93 44.83 3.93
6772 7796 1.807814 AGCCCCTGACGGAATCTAAT 58.192 50.000 0.00 0.00 0.00 1.73
6782 7806 7.390440 CCCTGACGGAATCTAATTGCATATAAA 59.610 37.037 0.00 0.00 0.00 1.40
6783 7807 8.950210 CCTGACGGAATCTAATTGCATATAAAT 58.050 33.333 0.00 0.00 0.00 1.40
6807 7831 2.476241 GCAAATAAAACTGCCTGCACAC 59.524 45.455 0.00 0.00 32.18 3.82
6808 7832 3.799917 GCAAATAAAACTGCCTGCACACT 60.800 43.478 0.00 0.00 32.18 3.55
6809 7833 3.923017 AATAAAACTGCCTGCACACTC 57.077 42.857 0.00 0.00 0.00 3.51
6810 7834 1.604604 TAAAACTGCCTGCACACTCC 58.395 50.000 0.00 0.00 0.00 3.85
6811 7835 0.395586 AAAACTGCCTGCACACTCCA 60.396 50.000 0.00 0.00 0.00 3.86
6812 7836 0.178981 AAACTGCCTGCACACTCCAT 60.179 50.000 0.00 0.00 0.00 3.41
6813 7837 0.178981 AACTGCCTGCACACTCCATT 60.179 50.000 0.00 0.00 0.00 3.16
6814 7838 0.607489 ACTGCCTGCACACTCCATTC 60.607 55.000 0.00 0.00 0.00 2.67
6927 7955 0.652592 CAGGTCGCGAATGATTGGTC 59.347 55.000 12.06 0.00 0.00 4.02
6960 7988 1.755179 ACCCGATCTGCCATTTCTTG 58.245 50.000 0.00 0.00 0.00 3.02
6985 8013 0.396435 TTGCAACCGTCACTCCATCT 59.604 50.000 0.00 0.00 0.00 2.90
7060 8092 6.490381 TGTCCTAGAAGCAGATAACGATGTAT 59.510 38.462 0.00 0.00 0.00 2.29
7095 8127 4.292977 TCGCTGTCACTGACATATAGTG 57.707 45.455 12.34 7.67 41.94 2.74
7102 8134 7.639113 TGTCACTGACATATAGTGTGATGTA 57.361 36.000 7.84 0.00 44.49 2.29
7138 8170 4.896562 TTCACAAGTATCGCGTAGTTTG 57.103 40.909 5.77 10.02 0.00 2.93
7139 8171 3.247442 TCACAAGTATCGCGTAGTTTGG 58.753 45.455 5.77 2.57 0.00 3.28
7153 8185 5.798434 GCGTAGTTTGGTTTTGAATATGACC 59.202 40.000 0.00 0.00 0.00 4.02
7154 8186 6.349033 GCGTAGTTTGGTTTTGAATATGACCT 60.349 38.462 0.00 0.00 33.33 3.85
7188 8220 1.127397 CAACACAGAGCAGCACGTATG 59.873 52.381 0.00 0.00 0.00 2.39
7206 8239 5.803967 ACGTATGAGTCGATTGTTAAAGTCC 59.196 40.000 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.100189 CAGAAGAGAATACACTAGGGGGTG 59.900 50.000 0.00 0.00 42.34 4.61
2 3 4.290942 CAGAAGAGAATACACTAGGGGGT 58.709 47.826 0.00 0.00 0.00 4.95
3 4 3.070302 GCAGAAGAGAATACACTAGGGGG 59.930 52.174 0.00 0.00 0.00 5.40
4 5 3.964031 AGCAGAAGAGAATACACTAGGGG 59.036 47.826 0.00 0.00 0.00 4.79
14 15 4.020751 TGCAACAGACTAGCAGAAGAGAAT 60.021 41.667 0.00 0.00 33.75 2.40
57 58 4.446051 GGTTATAACAAGAGCGAGATGAGC 59.554 45.833 17.16 0.00 0.00 4.26
66 67 1.940613 CCGGCTGGTTATAACAAGAGC 59.059 52.381 22.03 19.95 31.30 4.09
98 100 1.307097 GCTCTGCAATGGGATGAGAC 58.693 55.000 1.37 0.00 0.00 3.36
99 101 0.913924 TGCTCTGCAATGGGATGAGA 59.086 50.000 1.37 0.00 34.76 3.27
101 103 0.750546 GCTGCTCTGCAATGGGATGA 60.751 55.000 0.00 0.00 38.41 2.92
102 104 1.734137 GCTGCTCTGCAATGGGATG 59.266 57.895 0.00 0.00 38.41 3.51
103 105 1.822613 CGCTGCTCTGCAATGGGAT 60.823 57.895 0.00 0.00 38.41 3.85
105 107 4.189188 GCGCTGCTCTGCAATGGG 62.189 66.667 0.00 0.00 38.41 4.00
107 109 3.436011 CTCGCGCTGCTCTGCAATG 62.436 63.158 5.56 0.00 38.41 2.82
108 110 3.193614 CTCGCGCTGCTCTGCAAT 61.194 61.111 5.56 0.00 38.41 3.56
157 165 2.607668 TATGTCAAGGTCTCGCCGCG 62.608 60.000 6.39 6.39 43.70 6.46
158 166 0.872021 CTATGTCAAGGTCTCGCCGC 60.872 60.000 0.00 0.00 43.70 6.53
159 167 0.249073 CCTATGTCAAGGTCTCGCCG 60.249 60.000 0.00 0.00 43.70 6.46
160 168 0.105039 CCCTATGTCAAGGTCTCGCC 59.895 60.000 0.00 0.00 34.56 5.54
161 169 0.824759 ACCCTATGTCAAGGTCTCGC 59.175 55.000 0.00 0.00 34.56 5.03
162 170 2.099921 CTCACCCTATGTCAAGGTCTCG 59.900 54.545 0.00 0.00 34.56 4.04
163 171 3.366396 TCTCACCCTATGTCAAGGTCTC 58.634 50.000 0.00 0.00 34.56 3.36
164 172 3.474798 TCTCACCCTATGTCAAGGTCT 57.525 47.619 0.00 0.00 34.56 3.85
165 173 3.452627 ACATCTCACCCTATGTCAAGGTC 59.547 47.826 0.00 0.00 34.56 3.85
166 174 3.454858 ACATCTCACCCTATGTCAAGGT 58.545 45.455 0.00 0.00 34.56 3.50
173 181 5.287674 ACAGATCAACATCTCACCCTATG 57.712 43.478 0.00 0.00 37.25 2.23
184 192 2.230508 ACGACGTGGTACAGATCAACAT 59.769 45.455 0.00 0.00 41.80 2.71
219 227 2.356553 CACGGGCGAACGAAAGGA 60.357 61.111 6.19 0.00 37.61 3.36
317 325 1.594331 GGCATCGGAACTACCAATCC 58.406 55.000 0.00 0.00 38.90 3.01
513 564 4.568152 AAGCTTCAAACGCAAATACAGT 57.432 36.364 0.00 0.00 0.00 3.55
514 565 5.888412 AAAAGCTTCAAACGCAAATACAG 57.112 34.783 0.00 0.00 0.00 2.74
515 566 5.807520 TCAAAAAGCTTCAAACGCAAATACA 59.192 32.000 0.00 0.00 0.00 2.29
516 567 6.267500 TCAAAAAGCTTCAAACGCAAATAC 57.733 33.333 0.00 0.00 0.00 1.89
517 568 6.893958 TTCAAAAAGCTTCAAACGCAAATA 57.106 29.167 0.00 0.00 0.00 1.40
687 752 4.811761 CCTGCTAAAACGGCGCGC 62.812 66.667 25.94 25.94 0.00 6.86
732 801 0.027586 GTGTTGCGTTGTGTGACTCC 59.972 55.000 0.00 0.00 0.00 3.85
1036 1122 1.023513 CCCAGCCTGCTTCTTCTTCG 61.024 60.000 0.00 0.00 0.00 3.79
1136 1222 4.796231 GGAGCACGCGGTCGATGT 62.796 66.667 12.47 0.00 40.71 3.06
1286 1375 2.342279 CACCGGTGTCGTCCATGT 59.658 61.111 26.95 0.00 33.95 3.21
1568 1666 4.149922 TGCGAAGTCAGAAAATTCAGTACG 59.850 41.667 0.00 0.00 0.00 3.67
1600 1699 1.154016 CCACTTCGCGTCGACATCT 60.154 57.895 17.16 0.00 34.89 2.90
1715 1814 4.758773 TCAGTTGGCATCAGATATGTCA 57.241 40.909 0.00 0.00 0.00 3.58
1723 1822 4.264253 TCTATTGGTTCAGTTGGCATCAG 58.736 43.478 0.00 0.00 0.00 2.90
1729 1828 4.320494 GCACTGTTCTATTGGTTCAGTTGG 60.320 45.833 0.00 0.00 37.27 3.77
1769 1868 5.549347 TCAGTCACTAGAACGAACTAGAGT 58.451 41.667 20.53 5.76 41.42 3.24
1810 1909 6.146601 TGCATCTCTGTTTTGTTTGATCAA 57.853 33.333 3.38 3.38 0.00 2.57
2135 2236 3.181464 GGTAAATCTCCGAGGAAGGGAAG 60.181 52.174 0.00 0.00 32.02 3.46
2244 2346 8.706322 AGAACAACCAGTAAAGAAACCATTAT 57.294 30.769 0.00 0.00 0.00 1.28
2245 2347 9.802039 ATAGAACAACCAGTAAAGAAACCATTA 57.198 29.630 0.00 0.00 0.00 1.90
2246 2348 8.576442 CATAGAACAACCAGTAAAGAAACCATT 58.424 33.333 0.00 0.00 0.00 3.16
2260 2362 3.788227 AGAACAGCCATAGAACAACCA 57.212 42.857 0.00 0.00 0.00 3.67
2261 2363 4.095036 GCTAAGAACAGCCATAGAACAACC 59.905 45.833 0.00 0.00 35.40 3.77
2274 2378 8.770438 AGAAAATCAGTAAGAGCTAAGAACAG 57.230 34.615 0.00 0.00 0.00 3.16
2483 2590 0.545309 AGAGGCCCTAGTGAAGCACA 60.545 55.000 0.00 0.00 36.74 4.57
2527 3091 9.732130 GGAATAGGTAGAATCATGAATAGCTTT 57.268 33.333 17.48 10.58 0.00 3.51
2617 3183 5.091343 TGAAGATTTCAGCCACGTGAGTAC 61.091 45.833 19.30 3.29 37.11 2.73
2692 3258 2.404265 TGACATGTCTTTTTGCTGCG 57.596 45.000 25.55 0.00 0.00 5.18
2717 3283 0.454957 CCCGCAAATCGCTGTTTCAG 60.455 55.000 0.00 0.00 39.08 3.02
2832 3755 4.080356 AGGTGGCATTTATGAGCTAGAACA 60.080 41.667 0.00 0.00 0.00 3.18
2839 3762 4.082026 ACTTTCAAGGTGGCATTTATGAGC 60.082 41.667 0.00 0.00 0.00 4.26
2876 3799 7.122353 GTCCTACACTAGAATAACAGGACAGAA 59.878 40.741 11.91 0.00 46.38 3.02
2877 3800 6.602406 GTCCTACACTAGAATAACAGGACAGA 59.398 42.308 11.91 0.00 46.38 3.41
2894 3817 6.183360 GCAGGTCAAGATTTAATGTCCTACAC 60.183 42.308 0.00 0.00 34.08 2.90
2994 3921 5.303165 TCTGTAAGACTACAAGAGACGTCA 58.697 41.667 19.50 0.00 38.67 4.35
3272 4199 6.403866 AGCTGACAAATTGAAAACCATGTA 57.596 33.333 0.00 0.00 0.00 2.29
3490 4417 9.553064 AAGAATTTAGGTCATAAGATAGCACAG 57.447 33.333 0.00 0.00 0.00 3.66
3706 4639 3.119743 TGCACAGCTCAAGCATGATAAAC 60.120 43.478 4.59 0.00 45.16 2.01
4054 4992 7.168219 AGTCTGCAACTTCTGTAATATTCCAA 58.832 34.615 0.00 0.00 33.03 3.53
4207 5145 2.076863 AGTACAAATGAGCCGAAGTGC 58.923 47.619 0.00 0.00 0.00 4.40
4531 5488 4.035558 TGCAGAAGAGTAAACAAGCAGTTG 59.964 41.667 0.00 0.00 41.19 3.16
4561 5518 5.009510 TGTGTAACATTTCAACATGTGGAGG 59.990 40.000 2.51 0.40 45.67 4.30
4603 5560 9.228949 TGCCATTCATTTAGTTTAAAATGCAAT 57.771 25.926 0.00 0.00 43.49 3.56
4751 5708 1.280133 CCAGAGGATTCAACTGGCTCA 59.720 52.381 12.92 0.00 43.32 4.26
4925 5882 7.581213 TTACAAATCACAAAATGACAGGAGT 57.419 32.000 0.00 0.00 41.24 3.85
4978 5935 5.552870 TTCTGCAAAGGGTAGAGGATATC 57.447 43.478 0.00 0.00 39.52 1.63
4988 5945 3.575687 CTCTCCAAAATTCTGCAAAGGGT 59.424 43.478 0.00 0.00 0.00 4.34
5004 5961 3.476552 CAGCCACAAGTTAAACTCTCCA 58.523 45.455 0.00 0.00 0.00 3.86
5010 5967 1.602920 GCTGCCAGCCACAAGTTAAAC 60.603 52.381 5.06 0.00 34.48 2.01
5125 6082 3.119708 GGACATTGCTCATCAAACAGACC 60.120 47.826 0.00 0.00 38.34 3.85
5190 6147 6.076981 AGTACTCAAAAACATGCTGGAAAG 57.923 37.500 0.00 0.00 0.00 2.62
5284 6241 4.446371 CATGAAGACCTGATCACTTACCC 58.554 47.826 0.00 0.00 0.00 3.69
5498 6455 2.549754 CACTGCCTAACTGACCTTTGTG 59.450 50.000 0.00 0.00 0.00 3.33
5574 6533 8.269317 ACCCTACAGAACGGAAATGAATAATTA 58.731 33.333 0.00 0.00 0.00 1.40
5603 6562 3.600388 CCCTAGAATACGATCAATGGCC 58.400 50.000 0.00 0.00 0.00 5.36
5606 6565 5.984695 TCTCCCCTAGAATACGATCAATG 57.015 43.478 0.00 0.00 0.00 2.82
5624 6583 3.311966 GCTTTTGCTGTGAACAATCTCC 58.688 45.455 0.00 0.00 43.35 3.71
5718 6677 4.459685 TGAACTAGAAAGGAACGAGAGAGG 59.540 45.833 0.00 0.00 0.00 3.69
5719 6678 5.630661 TGAACTAGAAAGGAACGAGAGAG 57.369 43.478 0.00 0.00 0.00 3.20
5724 6683 6.340962 TCAAGATGAACTAGAAAGGAACGA 57.659 37.500 0.00 0.00 0.00 3.85
5726 6685 8.233190 CACATTCAAGATGAACTAGAAAGGAAC 58.767 37.037 0.00 0.00 39.45 3.62
5813 6773 2.766828 AGAAGGGTATTCAGGGTCGAAG 59.233 50.000 0.00 0.00 0.00 3.79
5938 6898 1.890894 GCGACCTGAGGCTTCTGTA 59.109 57.895 0.00 0.00 0.00 2.74
5984 6944 2.430921 GTGCTGTGGTCGGACGAG 60.431 66.667 1.43 0.00 0.00 4.18
6062 7022 1.929038 GCGCACGAGAAGTAGTTGTCA 60.929 52.381 0.30 0.00 0.00 3.58
6209 7169 6.000246 TGCCTATCCAAGAACATGTAATCA 58.000 37.500 0.00 0.00 0.00 2.57
6235 7195 3.778954 AGCAGAGGCAAACTTAGTCTT 57.221 42.857 0.00 0.00 44.61 3.01
6292 7253 3.801638 GCTGCTGTCAACTCTTCTTCTCA 60.802 47.826 0.00 0.00 0.00 3.27
6306 7267 4.202050 CCAATGTTATTTAGGGCTGCTGTC 60.202 45.833 0.00 0.00 0.00 3.51
6310 7271 3.447229 ACACCAATGTTATTTAGGGCTGC 59.553 43.478 0.00 0.00 34.46 5.25
6521 7515 2.213499 CGTCAATGCTGGGATTAGTCC 58.787 52.381 0.00 0.00 44.29 3.85
6530 7524 3.065575 GGTAGACCGTCAATGCTGG 57.934 57.895 0.40 0.00 0.00 4.85
6547 7541 1.301677 GAGCTTCCAGAAACCAGCGG 61.302 60.000 0.00 0.00 37.35 5.52
6582 7576 2.767505 AGCCAATCGAACGAAAAGTCT 58.232 42.857 0.12 0.00 0.00 3.24
6597 7591 2.270352 ACGACAGAATCCAAAGCCAA 57.730 45.000 0.00 0.00 0.00 4.52
6624 7624 6.639632 ATCGGATGATGAACCAAAATTAGG 57.360 37.500 0.00 0.00 32.21 2.69
6640 7642 1.430632 GCCACAGTGCAATCGGATG 59.569 57.895 3.37 0.00 0.00 3.51
6645 7647 2.562912 CGTGGCCACAGTGCAATC 59.437 61.111 34.16 5.35 0.00 2.67
6671 7673 4.870123 AATGCAGTTTCAAGTTGCCATA 57.130 36.364 0.00 0.00 37.03 2.74
6693 7695 4.937015 GGTTAGGGTCAAATAACTACGCAA 59.063 41.667 0.00 0.00 33.36 4.85
6715 7717 6.013293 CCCATAGTTTAGATTTCTAGGAGGGG 60.013 46.154 0.00 0.00 0.00 4.79
6719 7721 9.155785 CCTAACCCATAGTTTAGATTTCTAGGA 57.844 37.037 0.00 0.00 40.05 2.94
6724 7726 6.826741 TGCACCTAACCCATAGTTTAGATTTC 59.173 38.462 0.00 0.00 40.05 2.17
6737 7739 1.602237 GCTAGCTGCACCTAACCCA 59.398 57.895 7.70 0.00 42.31 4.51
6756 7780 2.917933 TGCAATTAGATTCCGTCAGGG 58.082 47.619 0.00 0.00 38.33 4.45
6798 7822 1.310933 CCTGAATGGAGTGTGCAGGC 61.311 60.000 0.00 0.00 39.60 4.85
6800 7824 1.642037 CGCCTGAATGGAGTGTGCAG 61.642 60.000 0.00 0.00 38.35 4.41
6801 7825 1.672030 CGCCTGAATGGAGTGTGCA 60.672 57.895 0.00 0.00 38.35 4.57
6802 7826 3.181367 CGCCTGAATGGAGTGTGC 58.819 61.111 0.00 0.00 38.35 4.57
6807 7831 3.805267 GCTCACGCCTGAATGGAG 58.195 61.111 0.00 0.00 41.69 3.86
6927 7955 2.515290 GGGTTAATCCGGTGGGCG 60.515 66.667 0.00 0.00 37.00 6.13
6945 7973 1.796617 GCGCACAAGAAATGGCAGATC 60.797 52.381 0.30 0.00 0.00 2.75
6998 8026 6.763715 TTGCAATAGATGGGGAATACTACT 57.236 37.500 0.00 0.00 0.00 2.57
6999 8027 7.168219 TGATTGCAATAGATGGGGAATACTAC 58.832 38.462 12.97 0.00 0.00 2.73
7060 8092 5.048782 AGTGACAGCGATTTTTGCAGAAATA 60.049 36.000 14.61 0.00 33.85 1.40
7095 8127 8.958043 GTGAAAGAAACAAAACTGATACATCAC 58.042 33.333 0.00 0.00 32.50 3.06
7102 8134 9.736023 GATACTTGTGAAAGAAACAAAACTGAT 57.264 29.630 0.00 0.00 37.10 2.90
7138 8170 5.343307 AATGCCAGGTCATATTCAAAACC 57.657 39.130 0.00 0.00 0.00 3.27
7139 8171 5.516339 CGAAATGCCAGGTCATATTCAAAAC 59.484 40.000 0.00 0.00 0.00 2.43
7177 8209 1.256376 CAATCGACTCATACGTGCTGC 59.744 52.381 0.00 0.00 0.00 5.25
7188 8220 2.991190 TGCGGACTTTAACAATCGACTC 59.009 45.455 0.00 0.00 0.00 3.36
7206 8239 1.063006 CCTCATGCCGTTCAATGCG 59.937 57.895 0.00 0.00 0.00 4.73


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

AutoCloner maintained by Alex Coulton.