Multiple sequence alignment - TraesCS2B01G360000

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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 TraesCS2B01G360000 chr2B 100.000 2276 0 0 1 2276 513463084 513465359 0 4204
1 TraesCS2B01G360000 chr3B 95.469 1302 57 2 1 1301 204757240 204755940 0 2076
2 TraesCS2B01G360000 chr4A 93.874 1306 80 0 1 1306 669808727 669807422 0 1969
3 TraesCS2B01G360000 chr6B 93.640 1305 81 2 1 1304 55705919 55707222 0 1949
4 TraesCS2B01G360000 chr1B 93.497 1307 84 1 1 1307 502779215 502777910 0 1941
5 TraesCS2B01G360000 chr7B 92.868 1304 91 2 1 1303 557218606 557219908 0 1892
6 TraesCS2B01G360000 chr3A 89.357 1306 133 5 1 1303 7978653 7977351 0 1637
7 TraesCS2B01G360000 chr6A 88.123 1305 153 2 1 1305 32046476 32047778 0 1550
8 TraesCS2B01G360000 chr6A 87.844 1308 159 0 1 1308 32594079 32592772 0 1535
9 TraesCS2B01G360000 chr7A 88.046 1305 148 7 1 1301 670187400 670186100 0 1539
10 TraesCS2B01G360000 chr2D 91.483 951 40 20 1308 2244 435038348 435039271 0 1269
11 TraesCS2B01G360000 chr2A 88.655 996 36 23 1308 2244 551822513 551821536 0 1142


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 TraesCS2B01G360000 chr2B 513463084 513465359 2275 False 4204 4204 100.000 1 2276 1 chr2B.!!$F1 2275
1 TraesCS2B01G360000 chr3B 204755940 204757240 1300 True 2076 2076 95.469 1 1301 1 chr3B.!!$R1 1300
2 TraesCS2B01G360000 chr4A 669807422 669808727 1305 True 1969 1969 93.874 1 1306 1 chr4A.!!$R1 1305
3 TraesCS2B01G360000 chr6B 55705919 55707222 1303 False 1949 1949 93.640 1 1304 1 chr6B.!!$F1 1303
4 TraesCS2B01G360000 chr1B 502777910 502779215 1305 True 1941 1941 93.497 1 1307 1 chr1B.!!$R1 1306
5 TraesCS2B01G360000 chr7B 557218606 557219908 1302 False 1892 1892 92.868 1 1303 1 chr7B.!!$F1 1302
6 TraesCS2B01G360000 chr3A 7977351 7978653 1302 True 1637 1637 89.357 1 1303 1 chr3A.!!$R1 1302
7 TraesCS2B01G360000 chr6A 32046476 32047778 1302 False 1550 1550 88.123 1 1305 1 chr6A.!!$F1 1304
8 TraesCS2B01G360000 chr6A 32592772 32594079 1307 True 1535 1535 87.844 1 1308 1 chr6A.!!$R1 1307
9 TraesCS2B01G360000 chr7A 670186100 670187400 1300 True 1539 1539 88.046 1 1301 1 chr7A.!!$R1 1300
10 TraesCS2B01G360000 chr2D 435038348 435039271 923 False 1269 1269 91.483 1308 2244 1 chr2D.!!$F1 936
11 TraesCS2B01G360000 chr2A 551821536 551822513 977 True 1142 1142 88.655 1308 2244 1 chr2A.!!$R1 936

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
894 896 0.616111 ACCTCTCGTTCATGGGAGCT 60.616 55.0 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2248 2309 0.600255 AAAACAGGCAGGTCTCGACG 60.6 55.0 0.0 0.0 0.0 5.12 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
56 57 3.432252 CGCATTGGGAACGATCCTATTAC 59.568 47.826 11.90 0.00 45.77 1.89
92 93 8.274322 TGAATTATTTGATCAGGACAGTGGTAT 58.726 33.333 0.00 0.00 0.00 2.73
172 173 4.891168 TGAATATACCGTTGAGAGTGCCTA 59.109 41.667 0.00 0.00 0.00 3.93
177 178 0.888619 CGTTGAGAGTGCCTAGTGGA 59.111 55.000 0.00 0.00 34.57 4.02
447 448 2.279252 ACGACGGCAGTGTGTGAC 60.279 61.111 0.00 0.00 0.00 3.67
615 617 3.186909 CGCGATCATACAAGACCAAGAA 58.813 45.455 0.00 0.00 0.00 2.52
633 635 9.860898 GACCAAGAAAGATGCAAAATTATAACT 57.139 29.630 0.00 0.00 0.00 2.24
678 680 1.069204 CGGAACCGATGGACTCATGAT 59.931 52.381 7.53 0.00 42.83 2.45
894 896 0.616111 ACCTCTCGTTCATGGGAGCT 60.616 55.000 0.00 0.00 0.00 4.09
933 935 0.741915 GGGTGACAGATCCTCTCGTC 59.258 60.000 0.00 0.00 0.00 4.20
1023 1025 7.556844 TGATGGAAGTAGATTGTTTAGAGGTC 58.443 38.462 0.00 0.00 0.00 3.85
1052 1054 2.066262 CTGGTTATCGCGTGACAGTTT 58.934 47.619 5.77 0.00 0.00 2.66
1221 1223 1.153667 GCTTGAGAGCTGTCCTCCG 60.154 63.158 8.62 0.00 45.65 4.63
1329 1331 5.760743 AGAAGAAAGTGTAAGAGCTTTCCAC 59.239 40.000 11.82 0.00 46.92 4.02
1389 1398 4.722389 CCCCCTACCACCCTACTC 57.278 66.667 0.00 0.00 0.00 2.59
1392 1401 0.338814 CCCCTACCACCCTACTCACT 59.661 60.000 0.00 0.00 0.00 3.41
1414 1423 1.009829 GGATTCAATCGCAGCGTCTT 58.990 50.000 15.93 7.12 0.00 3.01
1415 1424 1.004504 GGATTCAATCGCAGCGTCTTC 60.005 52.381 15.93 4.74 0.00 2.87
1416 1425 1.929836 GATTCAATCGCAGCGTCTTCT 59.070 47.619 15.93 0.00 0.00 2.85
1417 1426 1.070821 TTCAATCGCAGCGTCTTCTG 58.929 50.000 15.93 6.37 37.15 3.02
1418 1427 0.038251 TCAATCGCAGCGTCTTCTGT 60.038 50.000 15.93 0.00 36.49 3.41
1419 1428 0.368227 CAATCGCAGCGTCTTCTGTC 59.632 55.000 15.93 0.00 36.49 3.51
1421 1430 0.244994 ATCGCAGCGTCTTCTGTCTT 59.755 50.000 15.93 0.00 36.49 3.01
1422 1431 0.387367 TCGCAGCGTCTTCTGTCTTC 60.387 55.000 15.93 0.00 36.49 2.87
1464 1475 2.393271 AAAAGCGAGACAGCAGCTAT 57.607 45.000 0.00 0.00 40.78 2.97
1505 1529 3.694734 CAGTGCACGTCAAACAAAGAAT 58.305 40.909 12.01 0.00 0.00 2.40
1518 1542 8.382875 GTCAAACAAAGAATTTTTCACTTCCTG 58.617 33.333 0.00 0.00 35.03 3.86
1527 1551 2.526304 TTCACTTCCTGTCGTCCTTG 57.474 50.000 0.00 0.00 0.00 3.61
1537 1561 3.318017 CTGTCGTCCTTGTCGAAGAAAT 58.682 45.455 0.00 0.00 39.69 2.17
1704 1741 1.880027 AGAAATTCGTTGACCTGTGGC 59.120 47.619 0.00 0.00 0.00 5.01
1725 1762 2.522436 TTGACGTCCGGACCCTGT 60.522 61.111 28.52 20.33 0.00 4.00
1728 1765 2.522436 ACGTCCGGACCCTGTCAA 60.522 61.111 28.52 0.00 33.68 3.18
1795 1834 4.306417 GCCATTTGCAATTTCACGTAAC 57.694 40.909 0.00 0.00 40.77 2.50
1803 1842 3.424962 GCAATTTCACGTAACAGAGAGGC 60.425 47.826 0.00 0.00 0.00 4.70
1878 1928 1.616374 CTATCGGCCTTTCTCTCTCCC 59.384 57.143 0.00 0.00 0.00 4.30
1881 1931 1.307430 GGCCTTTCTCTCTCCCCCT 60.307 63.158 0.00 0.00 0.00 4.79
1883 1933 0.544223 GCCTTTCTCTCTCCCCCTTC 59.456 60.000 0.00 0.00 0.00 3.46
1884 1934 1.208706 CCTTTCTCTCTCCCCCTTCC 58.791 60.000 0.00 0.00 0.00 3.46
2037 2096 2.990967 CACCACACCCATGGCCAC 60.991 66.667 8.16 0.00 44.33 5.01
2038 2097 4.659172 ACCACACCCATGGCCACG 62.659 66.667 8.16 0.00 44.33 4.94
2230 2291 1.005975 GCTAATTGTACTCGCAGCGTG 60.006 52.381 15.93 15.51 0.00 5.34
2244 2305 2.125753 CGTGCCAGAGGAGCTCAC 60.126 66.667 17.19 9.03 32.06 3.51
2245 2306 2.644212 CGTGCCAGAGGAGCTCACT 61.644 63.158 17.19 11.33 32.06 3.41
2246 2307 1.217779 GTGCCAGAGGAGCTCACTC 59.782 63.158 17.19 18.33 42.66 3.51
2247 2308 2.346541 TGCCAGAGGAGCTCACTCG 61.347 63.158 17.19 14.08 44.48 4.18
2248 2309 2.493973 CCAGAGGAGCTCACTCGC 59.506 66.667 17.19 0.00 44.48 5.03
2249 2310 2.101965 CAGAGGAGCTCACTCGCG 59.898 66.667 17.19 0.00 44.48 5.87
2250 2311 2.360600 AGAGGAGCTCACTCGCGT 60.361 61.111 17.19 1.80 44.48 6.01
2251 2312 2.101380 GAGGAGCTCACTCGCGTC 59.899 66.667 17.19 0.00 44.48 5.19
2252 2313 3.726631 GAGGAGCTCACTCGCGTCG 62.727 68.421 17.19 0.58 44.48 5.12
2253 2314 3.800863 GGAGCTCACTCGCGTCGA 61.801 66.667 17.19 0.00 44.48 4.20
2264 2325 4.057428 GCGTCGAGACCTGCCTGT 62.057 66.667 0.00 0.00 0.00 4.00
2265 2326 2.651361 CGTCGAGACCTGCCTGTT 59.349 61.111 0.00 0.00 0.00 3.16
2266 2327 1.006102 CGTCGAGACCTGCCTGTTT 60.006 57.895 0.00 0.00 0.00 2.83
2267 2328 0.600255 CGTCGAGACCTGCCTGTTTT 60.600 55.000 0.00 0.00 0.00 2.43
2268 2329 1.594331 GTCGAGACCTGCCTGTTTTT 58.406 50.000 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 7.042858 CCTGATCAAATAATTCAGAGACACGAG 60.043 40.741 0.00 0.00 39.36 4.18
92 93 4.283337 TCGAACTAAGTCCATATCCCACA 58.717 43.478 0.00 0.00 0.00 4.17
172 173 2.950781 TGCGAGATAATCCTCTCCACT 58.049 47.619 0.00 0.00 38.78 4.00
177 178 2.564947 GTCCCATGCGAGATAATCCTCT 59.435 50.000 0.00 0.00 0.00 3.69
210 211 5.242393 AGCCGTTTTAACAGAGTAGACACTA 59.758 40.000 0.00 0.00 34.21 2.74
211 212 4.038883 AGCCGTTTTAACAGAGTAGACACT 59.961 41.667 0.00 0.00 37.87 3.55
447 448 0.313043 CCACTGAAGCCTTGCACAAG 59.687 55.000 3.32 3.32 38.14 3.16
555 557 0.039618 CCCAAGTGGCAGGGTGTAAT 59.960 55.000 2.15 0.00 40.34 1.89
615 617 8.252417 TGCATGACAGTTATAATTTTGCATCTT 58.748 29.630 0.00 0.00 33.09 2.40
633 635 2.145536 GACCATATCGCATGCATGACA 58.854 47.619 30.64 15.31 0.00 3.58
696 698 0.736325 CTGTCTTTACCGCCTGGACG 60.736 60.000 0.00 0.03 39.21 4.79
745 747 1.001048 CACACCACTCGTAGGTTTCGA 60.001 52.381 0.00 0.00 37.23 3.71
894 896 0.825840 CCGGGAAAGGTTTGCTCCAA 60.826 55.000 0.00 0.00 0.00 3.53
933 935 0.386113 GTAGAGCTAAGGCCTCCACG 59.614 60.000 5.23 0.00 39.73 4.94
1023 1025 1.278238 GCGATAACCAGAGGTTGACG 58.722 55.000 11.51 15.48 46.35 4.35
1052 1054 0.537143 AGGCGCAACAATTGACCTCA 60.537 50.000 13.59 0.00 34.76 3.86
1221 1223 1.464997 CGCAGGCCACTAAGAAGAAAC 59.535 52.381 5.01 0.00 0.00 2.78
1316 1318 5.369404 TCATATCATGGGTGGAAAGCTCTTA 59.631 40.000 0.00 0.00 0.00 2.10
1329 1331 0.914644 ATCCGGCCTCATATCATGGG 59.085 55.000 0.00 0.00 0.00 4.00
1389 1398 1.202110 GCTGCGATTGAATCCACAGTG 60.202 52.381 18.44 0.00 34.30 3.66
1392 1401 0.673333 ACGCTGCGATTGAATCCACA 60.673 50.000 30.47 0.00 0.00 4.17
1414 1423 5.019470 TGATGAAAGGCTAGAGAAGACAGA 58.981 41.667 0.00 0.00 34.57 3.41
1415 1424 5.108517 GTGATGAAAGGCTAGAGAAGACAG 58.891 45.833 0.00 0.00 34.57 3.51
1416 1425 4.380973 CGTGATGAAAGGCTAGAGAAGACA 60.381 45.833 0.00 0.00 34.57 3.41
1417 1426 4.109050 CGTGATGAAAGGCTAGAGAAGAC 58.891 47.826 0.00 0.00 0.00 3.01
1418 1427 3.131223 CCGTGATGAAAGGCTAGAGAAGA 59.869 47.826 0.00 0.00 0.00 2.87
1419 1428 3.118956 ACCGTGATGAAAGGCTAGAGAAG 60.119 47.826 0.00 0.00 0.00 2.85
1421 1430 2.427453 GACCGTGATGAAAGGCTAGAGA 59.573 50.000 0.00 0.00 0.00 3.10
1422 1431 2.482142 GGACCGTGATGAAAGGCTAGAG 60.482 54.545 0.00 0.00 0.00 2.43
1464 1475 2.086869 GCTGGTGGAGTAGTACGTGTA 58.913 52.381 0.00 0.00 0.00 2.90
1505 1529 3.553828 AGGACGACAGGAAGTGAAAAA 57.446 42.857 0.00 0.00 0.00 1.94
1518 1542 4.727235 AAATTTCTTCGACAAGGACGAC 57.273 40.909 0.00 0.00 39.46 4.34
1537 1561 4.271533 CGTGCCGTAAATATAGCAGGAAAA 59.728 41.667 0.00 0.00 42.18 2.29
1600 1636 0.648441 GTTTTGTGTCGTGTCGAGCA 59.352 50.000 0.00 0.00 36.23 4.26
1633 1670 2.202544 CAGGACTGCGAGACGAGC 60.203 66.667 0.00 0.00 0.00 5.03
1704 1741 1.666872 GGGTCCGGACGTCAAGTTG 60.667 63.158 27.68 0.00 0.00 3.16
1728 1765 3.149196 CCTTGCTTCCAATATGCCGTAT 58.851 45.455 0.00 0.00 0.00 3.06
1745 1782 4.760047 CCGTGGACCGAGCCCTTG 62.760 72.222 0.00 0.00 39.56 3.61
2230 2291 2.493973 CGAGTGAGCTCCTCTGGC 59.506 66.667 22.12 7.33 38.49 4.85
2247 2308 3.575351 AACAGGCAGGTCTCGACGC 62.575 63.158 0.00 0.00 0.00 5.19
2248 2309 0.600255 AAAACAGGCAGGTCTCGACG 60.600 55.000 0.00 0.00 0.00 5.12
2249 2310 1.594331 AAAAACAGGCAGGTCTCGAC 58.406 50.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.