Multiple sequence alignment - TraesCS5B01G364600

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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 TraesCS5B01G364600 chr5B 100.000 2276 0 0 1 2276 543261378 543259103 0 4204
1 TraesCS5B01G364600 chr3A 93.415 1306 83 2 1 1305 440509553 440510856 0 1932
2 TraesCS5B01G364600 chr7B 93.328 1304 85 1 1 1304 26210384 26209083 0 1925
3 TraesCS5B01G364600 chr1B 92.704 1302 92 2 1 1302 487940107 487941405 0 1875
4 TraesCS5B01G364600 chr1B 79.479 960 189 6 1321 2275 516916353 516915397 0 675
5 TraesCS5B01G364600 chr1B 79.289 956 190 6 1325 2275 516890806 516889854 0 662
6 TraesCS5B01G364600 chr6B 92.485 1304 96 1 1 1304 583194313 583193012 0 1864
7 TraesCS5B01G364600 chr6B 92.337 1305 97 2 1 1304 16962025 16960723 0 1853
8 TraesCS5B01G364600 chr5D 86.409 1295 169 5 12 1304 300148864 300147575 0 1410
9 TraesCS5B01G364600 chr5D 85.792 1295 176 6 12 1304 300324794 300323506 0 1365
10 TraesCS5B01G364600 chr4D 85.604 1299 176 9 12 1305 59513412 59512120 0 1352
11 TraesCS5B01G364600 chr4D 80.967 1303 245 2 1 1303 56748888 56747589 0 1029
12 TraesCS5B01G364600 chr3B 89.529 955 96 3 1325 2276 766550921 766549968 0 1206
13 TraesCS5B01G364600 chr2B 88.924 957 97 7 1326 2276 222528548 222529501 0 1171
14 TraesCS5B01G364600 chr7A 88.260 954 106 4 1326 2276 94149551 94150501 0 1136
15 TraesCS5B01G364600 chr2A 86.583 954 122 4 1327 2276 753442158 753443109 0 1048
16 TraesCS5B01G364600 chr2A 80.292 959 177 11 1325 2276 68243254 68242301 0 713
17 TraesCS5B01G364600 chr7D 80.957 961 165 15 1325 2276 85200127 85199176 0 745
18 TraesCS5B01G364600 chr5A 82.493 754 123 8 1512 2262 27229974 27230721 0 652


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 TraesCS5B01G364600 chr5B 543259103 543261378 2275 True 4204 4204 100.000 1 2276 1 chr5B.!!$R1 2275
1 TraesCS5B01G364600 chr3A 440509553 440510856 1303 False 1932 1932 93.415 1 1305 1 chr3A.!!$F1 1304
2 TraesCS5B01G364600 chr7B 26209083 26210384 1301 True 1925 1925 93.328 1 1304 1 chr7B.!!$R1 1303
3 TraesCS5B01G364600 chr1B 487940107 487941405 1298 False 1875 1875 92.704 1 1302 1 chr1B.!!$F1 1301
4 TraesCS5B01G364600 chr1B 516915397 516916353 956 True 675 675 79.479 1321 2275 1 chr1B.!!$R2 954
5 TraesCS5B01G364600 chr1B 516889854 516890806 952 True 662 662 79.289 1325 2275 1 chr1B.!!$R1 950
6 TraesCS5B01G364600 chr6B 583193012 583194313 1301 True 1864 1864 92.485 1 1304 1 chr6B.!!$R2 1303
7 TraesCS5B01G364600 chr6B 16960723 16962025 1302 True 1853 1853 92.337 1 1304 1 chr6B.!!$R1 1303
8 TraesCS5B01G364600 chr5D 300147575 300148864 1289 True 1410 1410 86.409 12 1304 1 chr5D.!!$R1 1292
9 TraesCS5B01G364600 chr5D 300323506 300324794 1288 True 1365 1365 85.792 12 1304 1 chr5D.!!$R2 1292
10 TraesCS5B01G364600 chr4D 59512120 59513412 1292 True 1352 1352 85.604 12 1305 1 chr4D.!!$R2 1293
11 TraesCS5B01G364600 chr4D 56747589 56748888 1299 True 1029 1029 80.967 1 1303 1 chr4D.!!$R1 1302
12 TraesCS5B01G364600 chr3B 766549968 766550921 953 True 1206 1206 89.529 1325 2276 1 chr3B.!!$R1 951
13 TraesCS5B01G364600 chr2B 222528548 222529501 953 False 1171 1171 88.924 1326 2276 1 chr2B.!!$F1 950
14 TraesCS5B01G364600 chr7A 94149551 94150501 950 False 1136 1136 88.260 1326 2276 1 chr7A.!!$F1 950
15 TraesCS5B01G364600 chr2A 753442158 753443109 951 False 1048 1048 86.583 1327 2276 1 chr2A.!!$F1 949
16 TraesCS5B01G364600 chr2A 68242301 68243254 953 True 713 713 80.292 1325 2276 1 chr2A.!!$R1 951
17 TraesCS5B01G364600 chr7D 85199176 85200127 951 True 745 745 80.957 1325 2276 1 chr7D.!!$R1 951
18 TraesCS5B01G364600 chr5A 27229974 27230721 747 False 652 652 82.493 1512 2262 1 chr5A.!!$F1 750

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
62 63 0.249911 GACGCTGGAAACTGTGGACT 60.25 55.0 0.0 0.0 43.29 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1495 1503 0.041238 ATTCCTCTGTCCCTCCGTGA 59.959 55.0 0.0 0.0 0.0 4.35 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
27 28 8.494433 AGGTTTGCATACTTTATCTCCTATGAA 58.506 33.333 7.25 0.00 0.00 2.57
42 43 4.140447 TCCTATGAATGTACCAGGAGGGAT 60.140 45.833 0.00 0.00 41.15 3.85
62 63 0.249911 GACGCTGGAAACTGTGGACT 60.250 55.000 0.00 0.00 43.29 3.85
76 77 6.163135 ACTGTGGACTAGCTAATTGATACC 57.837 41.667 0.00 0.00 0.00 2.73
196 197 0.686789 ATTTTCTTGCTTGGGCCCAC 59.313 50.000 28.70 15.82 37.74 4.61
197 198 0.689080 TTTTCTTGCTTGGGCCCACA 60.689 50.000 28.70 18.81 37.74 4.17
379 380 4.289101 TGGTGGAGGGTCGTCCGA 62.289 66.667 5.40 0.00 39.81 4.55
392 393 1.107538 CGTCCGAGGCATCCTTCCTA 61.108 60.000 0.00 0.00 31.76 2.94
525 526 1.768684 TTCTGGGAGCAGGCTTTCGT 61.769 55.000 0.00 0.00 0.00 3.85
637 638 6.040278 GGTCTCAGATGATCTCAGTAATGTGA 59.960 42.308 0.00 0.00 0.00 3.58
649 650 5.439721 TCAGTAATGTGAGCTATTTGGCAT 58.560 37.500 0.00 0.00 34.17 4.40
713 714 8.940397 TCCTTTTTCATCTGTTAAGAGGATTT 57.060 30.769 0.00 0.00 42.49 2.17
718 719 5.994250 TCATCTGTTAAGAGGATTTGGGAG 58.006 41.667 0.00 0.00 38.28 4.30
719 720 4.844349 TCTGTTAAGAGGATTTGGGAGG 57.156 45.455 0.00 0.00 0.00 4.30
849 850 7.595819 TGTGAATTTGGACTTCAATAAGGTT 57.404 32.000 0.00 0.00 37.01 3.50
966 967 1.470098 GCTTTGCGTGATGGAGTCATT 59.530 47.619 0.00 0.00 39.48 2.57
1052 1053 4.279922 TCTCTGGAACACTCGTCATAACAA 59.720 41.667 0.00 0.00 0.00 2.83
1147 1150 6.209192 TCAACATGTAAACAGATCAGCCAATT 59.791 34.615 0.00 0.00 0.00 2.32
1151 1154 7.394359 ACATGTAAACAGATCAGCCAATTTACT 59.606 33.333 0.00 0.00 34.89 2.24
1178 1181 4.118410 CACCTTTGTGCTAAACATGCAAA 58.882 39.130 0.00 0.00 42.41 3.68
1179 1182 4.209703 CACCTTTGTGCTAAACATGCAAAG 59.790 41.667 10.84 10.84 42.41 2.77
1209 1212 0.834612 TCACCGAAAGTTGGACTGGT 59.165 50.000 0.00 0.00 0.00 4.00
1212 1215 0.865769 CCGAAAGTTGGACTGGTTCG 59.134 55.000 7.56 7.56 37.87 3.95
1319 1322 3.915437 AAAAAGGTCGCCATTGTACAG 57.085 42.857 0.00 0.00 0.00 2.74
1320 1323 2.561478 AAAGGTCGCCATTGTACAGT 57.439 45.000 0.00 0.00 0.00 3.55
1321 1324 2.094762 AAGGTCGCCATTGTACAGTC 57.905 50.000 0.00 0.00 0.00 3.51
1322 1325 0.973632 AGGTCGCCATTGTACAGTCA 59.026 50.000 0.00 0.00 0.00 3.41
1323 1326 1.076332 GGTCGCCATTGTACAGTCAC 58.924 55.000 0.00 0.00 0.00 3.67
1370 1373 3.047877 CTTTTCCTTCGGCGGCGT 61.048 61.111 31.06 0.00 0.00 5.68
1422 1428 1.611936 CCGATCGAGAGCTAGGGATCA 60.612 57.143 18.66 0.00 36.04 2.92
1462 1468 1.122019 AGTCAGCCTTGTTCTCCGGT 61.122 55.000 0.00 0.00 0.00 5.28
1467 1474 0.606604 GCCTTGTTCTCCGGTGACTA 59.393 55.000 5.53 0.00 0.00 2.59
1495 1503 2.101582 GGATCTGAACACTATGGACGCT 59.898 50.000 0.00 0.00 0.00 5.07
1505 1513 2.561467 TATGGACGCTCACGGAGGGA 62.561 60.000 19.70 3.63 43.87 4.20
1514 1522 0.041238 TCACGGAGGGACAGAGGAAT 59.959 55.000 0.00 0.00 0.00 3.01
1539 1547 1.054978 GTAGGGGAGGCTAGGGTTGG 61.055 65.000 0.00 0.00 0.00 3.77
1559 1567 0.553819 AGATCCAGTAGCGGGAGTCT 59.446 55.000 0.00 0.00 37.96 3.24
1564 1572 0.173708 CAGTAGCGGGAGTCTGGTTC 59.826 60.000 0.00 0.00 0.00 3.62
1603 1611 2.586258 CGATGAACGGAGAAGATGGT 57.414 50.000 0.00 0.00 38.46 3.55
1615 1623 0.779997 AAGATGGTGGGAAGGTTGCT 59.220 50.000 0.00 0.00 0.00 3.91
1620 1628 1.973812 GTGGGAAGGTTGCTGGAGC 60.974 63.158 0.00 0.00 42.50 4.70
1621 1629 2.156098 TGGGAAGGTTGCTGGAGCT 61.156 57.895 0.00 0.00 42.66 4.09
1654 1662 2.628178 TCAGAAGGAAGACGAAGAAGCA 59.372 45.455 0.00 0.00 0.00 3.91
1666 1674 2.158986 CGAAGAAGCAGACTGGGATCAT 60.159 50.000 4.26 0.00 0.00 2.45
1687 1695 5.184287 TCATTATGGTCCGTCGCATAATCTA 59.816 40.000 11.39 3.99 32.73 1.98
1756 1764 0.698238 TGGATTTGTCTGGGGAGGTG 59.302 55.000 0.00 0.00 0.00 4.00
1835 1843 1.106285 GTTTAGCCATGCCTCCTTGG 58.894 55.000 0.00 0.00 38.85 3.61
1896 1904 4.137543 GTGACCTTCAACATCAAAGGACT 58.862 43.478 8.08 0.00 44.02 3.85
1970 1978 3.755467 GGGGGCCATGGTAGTTCT 58.245 61.111 14.67 0.00 0.00 3.01
2100 2108 5.221322 GCTTGACAAGAAAGAAGGAATTGGT 60.221 40.000 19.51 0.00 0.00 3.67
2112 2120 1.354368 GGAATTGGTGGAGAAGGTGGA 59.646 52.381 0.00 0.00 0.00 4.02
2140 2148 3.854666 GGTAGGAGAACCTTCGTTTACC 58.145 50.000 0.00 0.00 45.36 2.85
2180 2188 5.066593 GGAAGATCAATCCATCCAACTACC 58.933 45.833 11.57 0.00 36.92 3.18
2190 2198 1.122632 TCCAACTACCTGCGGGTTCA 61.123 55.000 25.37 4.44 44.73 3.18
2254 2262 8.047310 GTCCATATAACTTTGAAGGAGAGGAAA 58.953 37.037 0.00 0.00 0.00 3.13
2255 2263 8.047310 TCCATATAACTTTGAAGGAGAGGAAAC 58.953 37.037 0.00 0.00 0.00 2.78
2267 2275 2.165030 GAGAGGAAACGGTATTCGGTGA 59.835 50.000 0.00 0.00 44.45 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 9.372369 GGTACATTCATAGGAGATAAAGTATGC 57.628 37.037 0.00 0.00 0.00 3.14
27 28 1.414158 CGTCATCCCTCCTGGTACAT 58.586 55.000 0.00 0.00 38.20 2.29
42 43 0.531974 GTCCACAGTTTCCAGCGTCA 60.532 55.000 0.00 0.00 0.00 4.35
62 63 5.128171 ACCAGTTGTCGGTATCAATTAGCTA 59.872 40.000 0.00 0.00 34.02 3.32
334 335 0.104120 GCACCTTCGGCAAAACCTTT 59.896 50.000 0.00 0.00 35.61 3.11
355 356 1.375326 GACCCTCCACCAGAACACC 59.625 63.158 0.00 0.00 0.00 4.16
490 491 2.227388 CCAGAACAACTTGGCATGAGAC 59.773 50.000 7.45 0.00 0.00 3.36
525 526 1.438651 CCTGCGGAGATCGAACAAAA 58.561 50.000 5.10 0.00 42.43 2.44
637 638 8.435982 ACTCTATTTCTAGAATGCCAAATAGCT 58.564 33.333 5.89 0.00 38.15 3.32
700 701 4.225267 GTCTCCTCCCAAATCCTCTTAACA 59.775 45.833 0.00 0.00 0.00 2.41
713 714 0.543410 TAACGCCAAGTCTCCTCCCA 60.543 55.000 0.00 0.00 0.00 4.37
718 719 0.524862 TCGAGTAACGCCAAGTCTCC 59.475 55.000 0.00 0.00 42.26 3.71
719 720 2.563471 ATCGAGTAACGCCAAGTCTC 57.437 50.000 0.00 0.00 42.26 3.36
849 850 1.229177 TGCTACACCTCCAGCTCCA 60.229 57.895 0.00 0.00 38.63 3.86
966 967 2.950673 CCGCGCAGGTTAGCAAAA 59.049 55.556 8.75 0.00 34.51 2.44
1052 1053 0.846693 AGGAGCCACAACAGAAAGGT 59.153 50.000 0.00 0.00 0.00 3.50
1147 1150 3.430473 CACAAAGGTGGGCCAGTAA 57.570 52.632 6.40 0.00 41.45 2.24
1178 1181 2.631160 TTCGGTGACCAACAATGTCT 57.369 45.000 1.11 0.00 33.83 3.41
1179 1182 2.616842 ACTTTCGGTGACCAACAATGTC 59.383 45.455 1.11 0.00 0.00 3.06
1209 1212 3.245158 TGAGTAGGAAGGAAGGTCTCGAA 60.245 47.826 0.00 0.00 0.00 3.71
1212 1215 2.761767 GGTGAGTAGGAAGGAAGGTCTC 59.238 54.545 0.00 0.00 0.00 3.36
1306 1309 2.831685 AAGTGACTGTACAATGGCGA 57.168 45.000 0.00 0.00 0.00 5.54
1307 1310 3.364964 GGAAAAGTGACTGTACAATGGCG 60.365 47.826 0.00 0.00 0.00 5.69
1308 1311 3.057526 GGGAAAAGTGACTGTACAATGGC 60.058 47.826 0.00 0.00 0.00 4.40
1309 1312 3.506067 GGGGAAAAGTGACTGTACAATGG 59.494 47.826 0.00 0.00 0.00 3.16
1310 1313 4.398319 AGGGGAAAAGTGACTGTACAATG 58.602 43.478 0.00 0.00 0.00 2.82
1311 1314 4.724279 AGGGGAAAAGTGACTGTACAAT 57.276 40.909 0.00 0.00 0.00 2.71
1312 1315 4.041198 CCTAGGGGAAAAGTGACTGTACAA 59.959 45.833 0.00 0.00 33.58 2.41
1313 1316 3.581332 CCTAGGGGAAAAGTGACTGTACA 59.419 47.826 0.00 0.00 33.58 2.90
1314 1317 4.203654 CCTAGGGGAAAAGTGACTGTAC 57.796 50.000 0.00 0.00 33.58 2.90
1370 1373 2.542550 TGGATTTTAGGTGGACTCCGA 58.457 47.619 0.00 0.00 0.00 4.55
1373 1376 6.650120 TCTTACATGGATTTTAGGTGGACTC 58.350 40.000 0.00 0.00 0.00 3.36
1374 1377 6.636454 TCTTACATGGATTTTAGGTGGACT 57.364 37.500 0.00 0.00 0.00 3.85
1376 1379 7.990886 GTGTATCTTACATGGATTTTAGGTGGA 59.009 37.037 0.00 0.00 41.34 4.02
1377 1380 7.228706 GGTGTATCTTACATGGATTTTAGGTGG 59.771 40.741 0.00 0.00 41.34 4.61
1378 1381 7.042051 CGGTGTATCTTACATGGATTTTAGGTG 60.042 40.741 0.00 0.00 41.34 4.00
1379 1382 6.990349 CGGTGTATCTTACATGGATTTTAGGT 59.010 38.462 0.00 0.00 41.34 3.08
1382 1387 7.597369 CGATCGGTGTATCTTACATGGATTTTA 59.403 37.037 7.38 0.00 41.34 1.52
1422 1428 2.490217 CCAAGACGATCTCCGCGT 59.510 61.111 4.92 0.00 45.79 6.01
1462 1468 4.160439 GTGTTCAGATCCTCCATGTAGTCA 59.840 45.833 0.00 0.00 0.00 3.41
1467 1474 4.102210 CCATAGTGTTCAGATCCTCCATGT 59.898 45.833 0.00 0.00 0.00 3.21
1495 1503 0.041238 ATTCCTCTGTCCCTCCGTGA 59.959 55.000 0.00 0.00 0.00 4.35
1505 1513 2.389715 CCCTACTTCCGATTCCTCTGT 58.610 52.381 0.00 0.00 0.00 3.41
1514 1522 0.185416 CTAGCCTCCCCTACTTCCGA 59.815 60.000 0.00 0.00 0.00 4.55
1539 1547 0.955905 GACTCCCGCTACTGGATCTC 59.044 60.000 0.00 0.00 0.00 2.75
1579 1587 1.538512 TCTTCTCCGTTCATCGTCGTT 59.461 47.619 0.00 0.00 37.94 3.85
1603 1611 2.156098 AGCTCCAGCAACCTTCCCA 61.156 57.895 0.48 0.00 45.16 4.37
1615 1623 1.062364 GATCATCCCCATCAGCTCCA 58.938 55.000 0.00 0.00 0.00 3.86
1620 1628 2.977580 TCCTTCTGATCATCCCCATCAG 59.022 50.000 0.00 3.67 46.04 2.90
1621 1629 3.064773 TCCTTCTGATCATCCCCATCA 57.935 47.619 0.00 0.00 0.00 3.07
1654 1662 2.634940 CGGACCATAATGATCCCAGTCT 59.365 50.000 0.00 0.00 0.00 3.24
1666 1674 4.763279 TCTAGATTATGCGACGGACCATAA 59.237 41.667 8.27 8.27 38.04 1.90
1675 1683 3.499157 ACTCGTCCTCTAGATTATGCGAC 59.501 47.826 0.00 0.00 0.00 5.19
1687 1695 2.940410 GAGATTCTCGAACTCGTCCTCT 59.060 50.000 0.00 0.00 40.80 3.69
1756 1764 4.253685 TGACGTCCTTGATCAATTCTTCC 58.746 43.478 14.12 0.00 0.00 3.46
1835 1843 0.992802 GCGTTCCTCATCGAGTTCAC 59.007 55.000 0.00 0.00 0.00 3.18
1896 1904 3.450457 ACATTGAGCCAAAAACAGGTTGA 59.550 39.130 0.00 0.00 0.00 3.18
1964 1972 2.108168 CACCGGATCCCTTCAGAACTA 58.892 52.381 9.46 0.00 0.00 2.24
1970 1978 1.488812 CAATACCACCGGATCCCTTCA 59.511 52.381 9.46 0.00 0.00 3.02
2100 2108 2.783510 ACCTTCTTTTCCACCTTCTCCA 59.216 45.455 0.00 0.00 0.00 3.86
2140 2148 6.825213 TGATCTTCCCTTCATTAACAGTCATG 59.175 38.462 0.00 0.00 0.00 3.07
2180 2188 1.101049 ACAAACACCTGAACCCGCAG 61.101 55.000 0.00 0.00 35.66 5.18
2190 2198 4.202010 GCACTGTGACATTAACAAACACCT 60.202 41.667 12.86 0.00 0.00 4.00


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

AutoCloner maintained by Alex Coulton.