Multiple sequence alignment - TraesCS7A01G114800

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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 TraesCS7A01G114800 chr7A 100.000 2210 0 0 1 2210 70899501 70897292 0.000000e+00 4082.0
1 TraesCS7A01G114800 chr7A 91.743 1090 52 14 974 2054 71114685 71113625 0.000000e+00 1480.0
2 TraesCS7A01G114800 chr7A 80.650 646 78 25 126 737 71115519 71114887 7.190000e-125 457.0
3 TraesCS7A01G114800 chr7A 79.118 680 87 24 1001 1646 85198906 85198248 3.390000e-113 418.0
4 TraesCS7A01G114800 chr7A 80.148 539 82 13 965 1489 70805911 70805384 1.600000e-101 379.0
5 TraesCS7A01G114800 chr7A 80.921 304 45 5 970 1261 70754228 70753926 6.140000e-56 228.0
6 TraesCS7A01G114800 chr7A 85.446 213 22 4 1351 1563 74673313 74673516 1.720000e-51 213.0
7 TraesCS7A01G114800 chr7A 75.439 342 67 11 1702 2033 70267073 70266739 1.370000e-32 150.0
8 TraesCS7A01G114800 chr7A 86.087 115 14 2 1942 2055 70766415 70766302 2.980000e-24 122.0
9 TraesCS7A01G114800 chr7A 98.039 51 1 0 889 939 71114733 71114683 3.020000e-14 89.8
10 TraesCS7A01G114800 chr7B 96.603 1413 30 4 771 2182 7732561 7731166 0.000000e+00 2327.0
11 TraesCS7A01G114800 chr7B 92.318 1562 63 22 3 1542 10236644 10238170 0.000000e+00 2167.0
12 TraesCS7A01G114800 chr7B 91.858 786 25 6 3 773 7736790 7736029 0.000000e+00 1061.0
13 TraesCS7A01G114800 chr7B 89.685 349 22 3 1669 2004 10238236 10238583 1.210000e-117 433.0
14 TraesCS7A01G114800 chr7B 82.938 422 61 8 964 1378 9811455 9811872 9.640000e-99 370.0
15 TraesCS7A01G114800 chr7B 83.173 416 59 7 970 1378 10208458 10208869 9.640000e-99 370.0
16 TraesCS7A01G114800 chr7B 82.890 263 34 10 1384 1638 10061389 10061648 2.210000e-55 226.0
17 TraesCS7A01G114800 chr7D 94.366 710 24 3 885 1594 66508558 66507865 0.000000e+00 1075.0
18 TraesCS7A01G114800 chr7D 91.304 713 35 10 882 1594 68928537 68929222 0.000000e+00 948.0
19 TraesCS7A01G114800 chr7D 81.091 788 86 32 2 737 66509484 66508708 2.460000e-159 571.0
20 TraesCS7A01G114800 chr7D 94.169 343 20 0 1712 2054 66507796 66507454 6.990000e-145 523.0
21 TraesCS7A01G114800 chr7D 94.169 343 20 0 1712 2054 68929291 68929633 6.990000e-145 523.0
22 TraesCS7A01G114800 chr7D 80.132 755 91 33 20 737 68926197 68926929 1.960000e-140 508.0
23 TraesCS7A01G114800 chr7D 81.570 586 75 15 917 1489 66376037 66375472 9.300000e-124 453.0
24 TraesCS7A01G114800 chr7D 80.976 594 89 12 970 1563 69019241 69019810 1.200000e-122 449.0
25 TraesCS7A01G114800 chr7D 80.628 573 91 11 970 1538 66348256 66347700 2.030000e-115 425.0
26 TraesCS7A01G114800 chr7D 83.850 452 56 10 939 1378 66517171 66516725 4.390000e-112 414.0
27 TraesCS7A01G114800 chr7D 75.749 334 65 11 1702 2024 65902496 65902168 1.060000e-33 154.0
28 TraesCS7A01G114800 chr7D 76.603 312 46 12 1765 2055 66347599 66347294 1.770000e-31 147.0
29 TraesCS7A01G114800 chrUn 79.710 690 98 23 970 1646 84528883 84529543 5.560000e-126 460.0
30 TraesCS7A01G114800 chr2A 80.395 607 81 20 960 1543 84749071 84749662 5.640000e-116 427.0
31 TraesCS7A01G114800 chr2B 81.288 326 49 3 1712 2025 135795661 135795986 1.010000e-63 254.0


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 TraesCS7A01G114800 chr7A 70897292 70899501 2209 True 4082.000000 4082 100.000000 1 2210 1 chr7A.!!$R5 2209
1 TraesCS7A01G114800 chr7A 71113625 71115519 1894 True 675.600000 1480 90.144000 126 2054 3 chr7A.!!$R7 1928
2 TraesCS7A01G114800 chr7A 85198248 85198906 658 True 418.000000 418 79.118000 1001 1646 1 chr7A.!!$R6 645
3 TraesCS7A01G114800 chr7A 70805384 70805911 527 True 379.000000 379 80.148000 965 1489 1 chr7A.!!$R4 524
4 TraesCS7A01G114800 chr7B 7731166 7736790 5624 True 1694.000000 2327 94.230500 3 2182 2 chr7B.!!$R1 2179
5 TraesCS7A01G114800 chr7B 10236644 10238583 1939 False 1300.000000 2167 91.001500 3 2004 2 chr7B.!!$F4 2001
6 TraesCS7A01G114800 chr7D 66507454 66509484 2030 True 723.000000 1075 89.875333 2 2054 3 chr7D.!!$R5 2052
7 TraesCS7A01G114800 chr7D 68926197 68929633 3436 False 659.666667 948 88.535000 20 2054 3 chr7D.!!$F2 2034
8 TraesCS7A01G114800 chr7D 66375472 66376037 565 True 453.000000 453 81.570000 917 1489 1 chr7D.!!$R2 572
9 TraesCS7A01G114800 chr7D 69019241 69019810 569 False 449.000000 449 80.976000 970 1563 1 chr7D.!!$F1 593
10 TraesCS7A01G114800 chr7D 66347294 66348256 962 True 286.000000 425 78.615500 970 2055 2 chr7D.!!$R4 1085
11 TraesCS7A01G114800 chrUn 84528883 84529543 660 False 460.000000 460 79.710000 970 1646 1 chrUn.!!$F1 676
12 TraesCS7A01G114800 chr2A 84749071 84749662 591 False 427.000000 427 80.395000 960 1543 1 chr2A.!!$F1 583

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
681 761 1.474478 AGTACATGTCGTGCTCTCCAG 59.526 52.381 0.0 0.0 35.33 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1910 7048 0.38775 GAAAGTACCCGCTTCGACGT 60.388 55.0 0.0 0.0 0.0 4.34 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
630 695 3.333029 TCGCATCAGGAGTTCAATTCA 57.667 42.857 0.00 0.00 0.00 2.57
677 757 3.626670 GGTACTAGTACATGTCGTGCTCT 59.373 47.826 29.38 0.00 40.11 4.09
681 761 1.474478 AGTACATGTCGTGCTCTCCAG 59.526 52.381 0.00 0.00 35.33 3.86
1344 6409 2.583441 CCTCTGGCAGTTCACCGGA 61.583 63.158 15.27 0.00 40.36 5.14
1373 6444 3.387947 CGCCAACGGGAGGTACCT 61.388 66.667 16.26 16.26 38.98 3.08
1374 6445 2.582978 GCCAACGGGAGGTACCTC 59.417 66.667 30.72 30.72 42.04 3.85
1375 6446 2.288025 GCCAACGGGAGGTACCTCA 61.288 63.158 36.73 0.00 44.40 3.86
1376 6447 1.898154 CCAACGGGAGGTACCTCAG 59.102 63.158 36.73 30.86 44.40 3.35
1377 6448 1.218316 CAACGGGAGGTACCTCAGC 59.782 63.158 36.73 23.24 44.40 4.26
1378 6449 1.078710 AACGGGAGGTACCTCAGCT 59.921 57.895 36.73 21.58 44.40 4.24
1910 7048 1.376543 GTCTCCGACCTCGTCATGTA 58.623 55.000 0.00 0.00 37.74 2.29
2028 7166 1.383803 AGGTGAGAGGCCCTCCATC 60.384 63.158 7.26 5.76 41.25 3.51
2111 7249 4.335594 GGAAAACAGTGTACTGAAACAGCT 59.664 41.667 18.18 0.00 46.59 4.24
2178 7316 3.213506 ACTGCTGTCTTTGCATTGTGTA 58.786 40.909 0.00 0.00 39.86 2.90
2182 7320 2.816087 CTGTCTTTGCATTGTGTAGCCT 59.184 45.455 0.00 0.00 0.00 4.58
2183 7321 2.553602 TGTCTTTGCATTGTGTAGCCTG 59.446 45.455 0.00 0.00 0.00 4.85
2184 7322 2.813754 GTCTTTGCATTGTGTAGCCTGA 59.186 45.455 0.00 0.00 0.00 3.86
2185 7323 3.253188 GTCTTTGCATTGTGTAGCCTGAA 59.747 43.478 0.00 0.00 0.00 3.02
2186 7324 3.503363 TCTTTGCATTGTGTAGCCTGAAG 59.497 43.478 0.00 0.00 0.00 3.02
2187 7325 1.167851 TGCATTGTGTAGCCTGAAGC 58.832 50.000 0.00 0.00 44.25 3.86
2198 7336 2.997485 GCCTGAAGCTTAGTTGGTTG 57.003 50.000 0.00 0.00 38.99 3.77
2199 7337 2.230660 GCCTGAAGCTTAGTTGGTTGT 58.769 47.619 0.00 0.00 38.99 3.32
2200 7338 2.623416 GCCTGAAGCTTAGTTGGTTGTT 59.377 45.455 0.00 0.00 38.99 2.83
2201 7339 3.818773 GCCTGAAGCTTAGTTGGTTGTTA 59.181 43.478 0.00 0.00 38.99 2.41
2202 7340 4.320275 GCCTGAAGCTTAGTTGGTTGTTAC 60.320 45.833 0.00 0.00 38.99 2.50
2203 7341 4.819630 CCTGAAGCTTAGTTGGTTGTTACA 59.180 41.667 0.00 0.00 0.00 2.41
2204 7342 5.473504 CCTGAAGCTTAGTTGGTTGTTACAT 59.526 40.000 0.00 0.00 0.00 2.29
2205 7343 6.653320 CCTGAAGCTTAGTTGGTTGTTACATA 59.347 38.462 0.00 0.00 0.00 2.29
2206 7344 7.336931 CCTGAAGCTTAGTTGGTTGTTACATAT 59.663 37.037 0.00 0.00 0.00 1.78
2207 7345 8.630054 TGAAGCTTAGTTGGTTGTTACATATT 57.370 30.769 0.00 0.00 0.00 1.28
2208 7346 8.726988 TGAAGCTTAGTTGGTTGTTACATATTC 58.273 33.333 0.00 0.00 0.00 1.75
2209 7347 7.625828 AGCTTAGTTGGTTGTTACATATTCC 57.374 36.000 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
174 179 8.862325 ATGAGAACATAATGTGAAAGTACCAA 57.138 30.769 0.00 0.00 34.71 3.67
211 218 8.009984 TGAGCATTTCGAAAATTCTGATTTTG 57.990 30.769 15.66 5.60 43.61 2.44
402 465 9.987272 ATTTGAAAATGGGAAACAAAACAAAAA 57.013 22.222 0.00 0.00 34.86 1.94
403 466 9.987272 AATTTGAAAATGGGAAACAAAACAAAA 57.013 22.222 0.00 0.00 34.86 2.44
404 467 9.987272 AAATTTGAAAATGGGAAACAAAACAAA 57.013 22.222 0.00 0.00 34.86 2.83
630 695 1.210478 GATGTACAGTGCCTCCACCAT 59.790 52.381 0.33 0.00 43.09 3.55
1379 6450 0.524862 GCCATTGTTCCAGCTGACTG 59.475 55.000 17.39 0.00 44.05 3.51
1380 6451 0.957395 CGCCATTGTTCCAGCTGACT 60.957 55.000 17.39 0.00 0.00 3.41
1381 6452 1.237285 ACGCCATTGTTCCAGCTGAC 61.237 55.000 17.39 6.98 0.00 3.51
1910 7048 0.387750 GAAAGTACCCGCTTCGACGT 60.388 55.000 0.00 0.00 0.00 4.34
2028 7166 5.663556 AGGAGATTAGTAGGAAGTTGGGAAG 59.336 44.000 0.00 0.00 0.00 3.46
2111 7249 2.833943 TCCTGACTGAAGCAGATTAGCA 59.166 45.455 0.82 0.00 35.39 3.49
2182 7320 8.630054 AATATGTAACAACCAACTAAGCTTCA 57.370 30.769 0.00 0.00 0.00 3.02
2183 7321 8.182227 GGAATATGTAACAACCAACTAAGCTTC 58.818 37.037 0.00 0.00 0.00 3.86
2184 7322 8.051901 GGAATATGTAACAACCAACTAAGCTT 57.948 34.615 3.48 3.48 0.00 3.74
2185 7323 7.625828 GGAATATGTAACAACCAACTAAGCT 57.374 36.000 0.00 0.00 0.00 3.74


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

AutoCloner maintained by Alex Coulton.