Multiple sequence alignment - TraesCS7B01G388400

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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 TraesCS7B01G388400 chr7B 100.000 2288 0 0 1 2288 654488591 654486304 0.000000e+00 4189.0
1 TraesCS7B01G388400 chr7B 80.346 1328 243 13 1 1323 581801293 581802607 0.000000e+00 990.0
2 TraesCS7B01G388400 chr7B 90.921 749 51 11 1361 2105 654853409 654852674 0.000000e+00 990.0
3 TraesCS7B01G388400 chr7B 88.345 429 40 5 1687 2105 654696424 654695996 7.290000e-140 507.0
4 TraesCS7B01G388400 chr7B 91.071 224 7 4 1321 1541 654507380 654507167 2.220000e-75 292.0
5 TraesCS7B01G388400 chr7B 92.708 192 14 0 2097 2288 654852649 654852458 6.230000e-71 278.0
6 TraesCS7B01G388400 chr7B 92.188 192 15 0 2097 2288 654695971 654695780 2.900000e-69 272.0
7 TraesCS7B01G388400 chr7B 90.686 204 9 5 1361 1562 654696934 654696739 1.740000e-66 263.0
8 TraesCS7B01G388400 chr7B 79.514 288 51 6 1719 1998 617836322 617836035 4.990000e-47 198.0
9 TraesCS7B01G388400 chr7B 94.340 53 2 1 1521 1572 654505965 654505913 1.880000e-11 80.5
10 TraesCS7B01G388400 chrUn 100.000 1350 0 0 1 1350 253078438 253079787 0.000000e+00 2494.0
11 TraesCS7B01G388400 chrUn 100.000 1350 0 0 1 1350 332107702 332106353 0.000000e+00 2494.0
12 TraesCS7B01G388400 chrUn 89.723 253 20 6 1521 1768 241924507 241924758 3.670000e-83 318.0
13 TraesCS7B01G388400 chrUn 89.754 244 22 3 1865 2105 444571933 444571690 2.210000e-80 309.0
14 TraesCS7B01G388400 chrUn 91.071 224 7 4 1321 1541 241923092 241923305 2.220000e-75 292.0
15 TraesCS7B01G388400 chrUn 93.229 192 13 0 2097 2288 444571665 444571474 1.340000e-72 283.0
16 TraesCS7B01G388400 chr1B 83.774 1325 204 6 1 1322 280729033 280730349 0.000000e+00 1245.0
17 TraesCS7B01G388400 chr7A 82.419 1331 228 6 1 1328 58245448 58246775 0.000000e+00 1157.0
18 TraesCS7B01G388400 chr4A 81.203 1330 238 12 1 1322 736419233 736420558 0.000000e+00 1061.0
19 TraesCS7B01G388400 chr6B 78.512 1331 264 20 4 1322 480867540 480866220 0.000000e+00 854.0
20 TraesCS7B01G388400 chr7D 88.298 188 22 0 2101 2288 585545473 585545286 2.290000e-55 226.0
21 TraesCS7B01G388400 chr1D 91.667 48 4 0 4 51 4812860 4812813 1.470000e-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 TraesCS7B01G388400 chr7B 654486304 654488591 2287 True 4189.000000 4189 100.000000 1 2288 1 chr7B.!!$R2 2287
1 TraesCS7B01G388400 chr7B 581801293 581802607 1314 False 990.000000 990 80.346000 1 1323 1 chr7B.!!$F1 1322
2 TraesCS7B01G388400 chr7B 654852458 654853409 951 True 634.000000 990 91.814500 1361 2288 2 chr7B.!!$R5 927
3 TraesCS7B01G388400 chr7B 654695780 654696934 1154 True 347.333333 507 90.406333 1361 2288 3 chr7B.!!$R4 927
4 TraesCS7B01G388400 chrUn 253078438 253079787 1349 False 2494.000000 2494 100.000000 1 1350 1 chrUn.!!$F1 1349
5 TraesCS7B01G388400 chrUn 332106353 332107702 1349 True 2494.000000 2494 100.000000 1 1350 1 chrUn.!!$R1 1349
6 TraesCS7B01G388400 chrUn 241923092 241924758 1666 False 305.000000 318 90.397000 1321 1768 2 chrUn.!!$F2 447
7 TraesCS7B01G388400 chr1B 280729033 280730349 1316 False 1245.000000 1245 83.774000 1 1322 1 chr1B.!!$F1 1321
8 TraesCS7B01G388400 chr7A 58245448 58246775 1327 False 1157.000000 1157 82.419000 1 1328 1 chr7A.!!$F1 1327
9 TraesCS7B01G388400 chr4A 736419233 736420558 1325 False 1061.000000 1061 81.203000 1 1322 1 chr4A.!!$F1 1321
10 TraesCS7B01G388400 chr6B 480866220 480867540 1320 True 854.000000 854 78.512000 4 1322 1 chr6B.!!$R1 1318

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
1402 1409 7.867305 TTGGTCATGTACAGTACTTGAAAAA 57.133 32.0 24.01 18.98 42.23 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2254 3749 1.301479 GGTCGGAGCCGTCAAAGTT 60.301 57.895 8.96 0.0 40.74 2.66 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
1402 1409 7.867305 TTGGTCATGTACAGTACTTGAAAAA 57.133 32.000 24.01 18.98 42.23 1.94
1403 1410 8.458573 TTGGTCATGTACAGTACTTGAAAAAT 57.541 30.769 24.01 2.06 42.23 1.82
1492 1501 6.492087 TCAAAATCGGTTGAGGGAGTAAATTT 59.508 34.615 0.00 0.00 32.56 1.82
1597 2830 3.938963 CCTCTTAAATTTACTCAGCCGCA 59.061 43.478 0.00 0.00 0.00 5.69
1642 2876 1.987807 CTCCCCCTCACCGCATCAAT 61.988 60.000 0.00 0.00 0.00 2.57
1661 2895 0.687920 TGCCAGTACCGTCCAAATCA 59.312 50.000 0.00 0.00 0.00 2.57
1669 2903 2.950673 GTCCAAATCAACCGCGCA 59.049 55.556 8.75 0.00 0.00 6.09
1670 2904 1.442017 GTCCAAATCAACCGCGCAC 60.442 57.895 8.75 0.00 0.00 5.34
1672 2906 2.126502 CAAATCAACCGCGCACCC 60.127 61.111 8.75 0.00 0.00 4.61
1673 2907 2.596046 AAATCAACCGCGCACCCA 60.596 55.556 8.75 0.00 0.00 4.51
1717 3169 2.123640 GGAGCCGGACTAGCCTCT 60.124 66.667 5.05 0.00 0.00 3.69
1729 3181 3.185455 ACTAGCCTCTCCTGAAATGGTT 58.815 45.455 0.00 0.00 0.00 3.67
1741 3193 1.604278 GAAATGGTTGGATCTAGCCGC 59.396 52.381 7.45 0.00 0.00 6.53
1807 3259 0.892358 CACAGCCAACCTGAGCATGT 60.892 55.000 0.00 0.00 44.64 3.21
1824 3276 2.447572 TGGAGTGCACCACCCTCA 60.448 61.111 22.34 7.50 34.49 3.86
1839 3291 0.987294 CCTCACACTCCCTCCACAAT 59.013 55.000 0.00 0.00 0.00 2.71
1872 3330 1.601419 CGCCGAAGAGGAAGTACCCA 61.601 60.000 0.00 0.00 45.00 4.51
1948 3408 0.172803 CGTCCGTACTAGCTTGGCTT 59.827 55.000 0.00 0.00 40.44 4.35
2050 3511 1.379710 CATCGCCATTGACCCCCAA 60.380 57.895 0.00 0.00 39.41 4.12
2060 3521 2.531942 ACCCCCAAGTGGTCTCCC 60.532 66.667 0.00 0.00 0.00 4.30
2061 3522 3.339093 CCCCCAAGTGGTCTCCCC 61.339 72.222 0.00 0.00 0.00 4.81
2090 3551 0.106669 GTGGGAGAATTAGGTGGCCC 60.107 60.000 0.00 0.00 36.11 5.80
2111 3606 2.203640 AGTGGCCGAGGTCTGTCA 60.204 61.111 0.00 0.00 0.00 3.58
2184 3679 4.745116 TGAGCTACTCACGAGGCT 57.255 55.556 0.00 0.00 35.39 4.58
2254 3749 1.525077 GGGTCCAGCAACAACGACA 60.525 57.895 0.00 0.00 0.00 4.35
2277 3772 2.107041 TTGACGGCTCCGACCACAAT 62.107 55.000 15.95 0.00 42.83 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1366 1373 8.637986 ACTGTACATGACCAAAACATTGTAAAT 58.362 29.630 0.00 0.00 0.00 1.40
1384 1391 9.726438 AGCTAAGATTTTTCAAGTACTGTACAT 57.274 29.630 19.27 5.29 0.00 2.29
1402 1409 6.409704 TGCAACTATGTCTTCAAGCTAAGAT 58.590 36.000 2.33 0.00 37.78 2.40
1403 1410 5.793817 TGCAACTATGTCTTCAAGCTAAGA 58.206 37.500 0.00 0.00 33.10 2.10
1492 1501 7.269316 GTCCCATTTAACTCCTCAAAACAAAA 58.731 34.615 0.00 0.00 0.00 2.44
1597 2830 7.057264 GGGAAATTTTATCCTCAGACTTAGCT 58.943 38.462 0.00 0.00 37.14 3.32
1642 2876 0.687920 TGATTTGGACGGTACTGGCA 59.312 50.000 10.42 0.00 0.00 4.92
1646 2880 1.942586 GCGGTTGATTTGGACGGTACT 60.943 52.381 0.00 0.00 0.00 2.73
1683 3135 0.821517 TCCGGTCGAATATGTGTGCT 59.178 50.000 0.00 0.00 0.00 4.40
1689 3141 4.245054 CGGCTCCGGTCGAATATG 57.755 61.111 0.00 0.00 44.06 1.78
1713 3165 3.201708 AGATCCAACCATTTCAGGAGAGG 59.798 47.826 0.00 0.00 32.91 3.69
1717 3169 3.117888 GGCTAGATCCAACCATTTCAGGA 60.118 47.826 0.00 0.00 34.12 3.86
1729 3181 1.834378 CCTCTGGCGGCTAGATCCA 60.834 63.158 16.69 0.00 0.00 3.41
1741 3193 0.321564 TCGGTTGCAATGACCTCTGG 60.322 55.000 0.59 0.00 34.95 3.86
1792 3244 1.303561 TCCACATGCTCAGGTTGGC 60.304 57.895 0.00 0.00 0.00 4.52
1807 3259 2.447572 TGAGGGTGGTGCACTCCA 60.448 61.111 24.56 12.02 46.95 3.86
1824 3276 3.191888 AGTAGATTGTGGAGGGAGTGT 57.808 47.619 0.00 0.00 0.00 3.55
1839 3291 3.524606 GGCGGCAGCGGTAGTAGA 61.525 66.667 3.07 0.00 46.35 2.59
1948 3408 1.678635 CAGCTCCGCCCATTGGAAA 60.679 57.895 3.62 0.00 34.44 3.13
1974 3435 2.695314 GCCTTCAAGTCATAGGCCG 58.305 57.895 0.00 0.00 46.94 6.13
2008 3469 2.234908 CTCTAGCACCTTGTGGCTACTT 59.765 50.000 0.64 0.00 41.41 2.24
2060 3521 3.077556 CTCCCACACCTCGAGGGG 61.078 72.222 32.43 32.43 46.44 4.79
2061 3522 0.978146 ATTCTCCCACACCTCGAGGG 60.978 60.000 34.04 24.22 44.22 4.30
2064 3525 2.108168 CCTAATTCTCCCACACCTCGA 58.892 52.381 0.00 0.00 0.00 4.04
2072 3533 2.317530 GGGCCACCTAATTCTCCCA 58.682 57.895 4.39 0.00 34.01 4.37
2111 3606 2.480416 GCGACGACCTCTGAATGATTCT 60.480 50.000 6.73 0.00 0.00 2.40
2148 3643 0.320247 ACTTCTTGTGCAGCTCGAGG 60.320 55.000 15.58 0.00 0.00 4.63
2197 3692 1.202114 GCAAAGGTCAATGATTGCCGA 59.798 47.619 8.42 0.00 41.67 5.54
2254 3749 1.301479 GGTCGGAGCCGTCAAAGTT 60.301 57.895 8.96 0.00 40.74 2.66


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

AutoCloner maintained by Alex Coulton.