Multiple sequence alignment - TraesCS2A01G534000

Loading Multiple Alignment...

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 TraesCS2A01G534000 chr2A 100.000 2443 0 0 1 2443 749856417 749853975 0.000000e+00 4512
1 TraesCS2A01G534000 chr2A 91.612 608 50 1 1837 2443 12319354 12319961 0.000000e+00 839
2 TraesCS2A01G534000 chr2D 90.644 1336 86 13 526 1833 618869071 618867747 0.000000e+00 1738
3 TraesCS2A01G534000 chr2B 92.786 1109 65 9 565 1670 756157599 756156503 0.000000e+00 1591
4 TraesCS2A01G534000 chr2B 93.409 440 22 5 1399 1837 756154949 756154516 0.000000e+00 645
5 TraesCS2A01G534000 chr2B 87.557 442 51 4 1982 2421 644220811 644221250 2.170000e-140 508
6 TraesCS2A01G534000 chr2B 89.698 398 36 4 1972 2368 312380016 312379623 1.010000e-138 503
7 TraesCS2A01G534000 chr2B 93.662 284 13 3 100 383 272680912 272681190 1.040000e-113 420
8 TraesCS2A01G534000 chr2B 90.795 239 12 3 1155 1393 756155223 756154995 6.560000e-81 311
9 TraesCS2A01G534000 chr2B 94.000 100 6 0 1 100 272679554 272679653 4.210000e-33 152
10 TraesCS2A01G534000 chr2B 83.448 145 16 6 389 529 272681264 272681404 7.090000e-26 128
11 TraesCS2A01G534000 chr7D 92.635 611 43 2 1835 2443 501440880 501440270 0.000000e+00 878
12 TraesCS2A01G534000 chr7D 95.908 391 13 2 1 390 617809407 617809019 4.430000e-177 630
13 TraesCS2A01G534000 chr7D 88.000 150 6 2 389 526 617808952 617808803 1.500000e-37 167
14 TraesCS2A01G534000 chr7A 91.613 620 43 2 1833 2443 700122120 700122739 0.000000e+00 848
15 TraesCS2A01G534000 chr7A 85.622 466 60 4 1980 2443 105224576 105225036 1.310000e-132 483
16 TraesCS2A01G534000 chr6D 91.803 610 49 1 1835 2443 461852031 461852640 0.000000e+00 848
17 TraesCS2A01G534000 chr4D 95.641 390 15 1 1 390 455599212 455599599 2.060000e-175 625
18 TraesCS2A01G534000 chr4D 93.023 387 15 5 1 387 8773181 8773555 2.740000e-154 555
19 TraesCS2A01G534000 chr4D 89.404 151 2 4 389 526 8773623 8773772 6.940000e-41 178
20 TraesCS2A01G534000 chr4D 88.079 151 6 2 389 527 455599666 455599816 4.180000e-38 169
21 TraesCS2A01G534000 chr5D 95.641 390 14 2 1 390 316729325 316728939 7.420000e-175 623
22 TraesCS2A01G534000 chr5D 88.742 151 3 4 389 526 316728872 316728723 3.230000e-39 172
23 TraesCS2A01G534000 chr6A 95.515 379 15 1 1 379 392965260 392965636 2.690000e-169 604
24 TraesCS2A01G534000 chr6A 88.889 234 21 5 1831 2062 74808634 74808404 1.430000e-72 283
25 TraesCS2A01G534000 chr6A 87.324 142 13 5 389 526 392965709 392965849 9.040000e-35 158
26 TraesCS2A01G534000 chr5B 86.928 459 52 8 1983 2438 458699409 458698956 2.170000e-140 508
27 TraesCS2A01G534000 chr5B 91.892 222 12 2 134 351 580802328 580802547 3.050000e-79 305
28 TraesCS2A01G534000 chr5A 90.331 393 24 7 1 383 246853656 246854044 1.010000e-138 503
29 TraesCS2A01G534000 chr5A 84.768 151 11 1 389 527 246854118 246854268 9.110000e-30 141
30 TraesCS2A01G534000 chr6B 86.296 467 56 5 1978 2443 35379464 35379005 3.630000e-138 501
31 TraesCS2A01G534000 chr6B 98.795 83 0 1 1846 1927 708792830 708792748 1.960000e-31 147
32 TraesCS2A01G534000 chr1D 95.057 263 12 1 1 263 453077193 453077454 1.750000e-111 412
33 TraesCS2A01G534000 chr1D 89.381 226 23 1 1838 2062 270618927 270618702 1.430000e-72 283
34 TraesCS2A01G534000 chr4A 86.243 189 15 5 203 383 48273711 48273896 6.890000e-46 195
35 TraesCS2A01G534000 chr4B 88.235 68 1 6 389 450 258788707 258788773 9.370000e-10 75


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 TraesCS2A01G534000 chr2A 749853975 749856417 2442 True 4512.000000 4512 100.0000 1 2443 1 chr2A.!!$R1 2442
1 TraesCS2A01G534000 chr2A 12319354 12319961 607 False 839.000000 839 91.6120 1837 2443 1 chr2A.!!$F1 606
2 TraesCS2A01G534000 chr2D 618867747 618869071 1324 True 1738.000000 1738 90.6440 526 1833 1 chr2D.!!$R1 1307
3 TraesCS2A01G534000 chr2B 756154516 756157599 3083 True 849.000000 1591 92.3300 565 1837 3 chr2B.!!$R2 1272
4 TraesCS2A01G534000 chr2B 272679554 272681404 1850 False 233.333333 420 90.3700 1 529 3 chr2B.!!$F2 528
5 TraesCS2A01G534000 chr7D 501440270 501440880 610 True 878.000000 878 92.6350 1835 2443 1 chr7D.!!$R1 608
6 TraesCS2A01G534000 chr7D 617808803 617809407 604 True 398.500000 630 91.9540 1 526 2 chr7D.!!$R2 525
7 TraesCS2A01G534000 chr7A 700122120 700122739 619 False 848.000000 848 91.6130 1833 2443 1 chr7A.!!$F2 610
8 TraesCS2A01G534000 chr6D 461852031 461852640 609 False 848.000000 848 91.8030 1835 2443 1 chr6D.!!$F1 608
9 TraesCS2A01G534000 chr4D 455599212 455599816 604 False 397.000000 625 91.8600 1 527 2 chr4D.!!$F2 526
10 TraesCS2A01G534000 chr4D 8773181 8773772 591 False 366.500000 555 91.2135 1 526 2 chr4D.!!$F1 525
11 TraesCS2A01G534000 chr5D 316728723 316729325 602 True 397.500000 623 92.1915 1 526 2 chr5D.!!$R1 525
12 TraesCS2A01G534000 chr6A 392965260 392965849 589 False 381.000000 604 91.4195 1 526 2 chr6A.!!$F1 525
13 TraesCS2A01G534000 chr5A 246853656 246854268 612 False 322.000000 503 87.5495 1 527 2 chr5A.!!$F1 526

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
599 1947 0.110056 CGATGTGTGGCAAACTCAGC 60.11 55.0 9.62 0.0 35.83 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 5224 0.536006 GCAAGGTCAAGCAGGACACT 60.536 55.0 9.57 2.6 39.59 3.55 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
138 1399 4.993705 AGGAGTAAATTTCACTGGTCCA 57.006 40.909 0.00 0.00 0.00 4.02
139 1400 5.520748 AGGAGTAAATTTCACTGGTCCAT 57.479 39.130 0.00 0.00 0.00 3.41
182 1443 6.901857 AGTACATTTAGGGTCTTAGCTAACCT 59.098 38.462 16.07 16.07 35.78 3.50
364 1632 6.826893 AAAAGAACAAATGACAAACATCGG 57.173 33.333 0.00 0.00 38.38 4.18
383 1651 4.945246 TCGGAAGTGTTAGCTTATCATCC 58.055 43.478 0.00 0.00 0.00 3.51
425 1761 5.588845 TGGTTATTGGTGGGATGAGAAATT 58.411 37.500 0.00 0.00 0.00 1.82
480 1828 5.036117 AGCGGGACAGATACAACAATAAT 57.964 39.130 0.00 0.00 0.00 1.28
560 1908 4.573201 TGAAAACCTCTAAACAAGACCACG 59.427 41.667 0.00 0.00 0.00 4.94
599 1947 0.110056 CGATGTGTGGCAAACTCAGC 60.110 55.000 9.62 0.00 35.83 4.26
630 1978 2.366167 CTCTCAGGGAGGAGGGCA 59.634 66.667 0.00 0.00 38.35 5.36
668 2018 0.161658 CTGTCGTCGTGTTGATGTGC 59.838 55.000 0.00 0.00 35.01 4.57
695 2045 1.066587 TCATGTCGTGTGTCGTGCA 59.933 52.632 0.00 0.00 40.80 4.57
697 2047 1.068194 TCATGTCGTGTGTCGTGCATA 60.068 47.619 0.00 0.00 40.80 3.14
702 2052 3.120820 TGTCGTGTGTCGTGCATATTTTC 60.121 43.478 0.00 0.00 40.80 2.29
728 2078 4.759205 GCCTTTGGCCCCGTGGAT 62.759 66.667 0.00 0.00 44.06 3.41
771 2121 7.938563 TTTGTTTTATTTTCCTTGTCATCGG 57.061 32.000 0.00 0.00 0.00 4.18
774 2124 6.488683 TGTTTTATTTTCCTTGTCATCGGACT 59.511 34.615 0.00 0.00 44.61 3.85
803 2153 3.412237 AACGCTTTAAGGCCTTCAGTA 57.588 42.857 24.49 0.02 0.00 2.74
822 2172 0.878523 ACGCTAAAGTCGTGCAAGCA 60.879 50.000 5.25 0.00 38.88 3.91
1024 2400 2.543777 AATACGAGTGGTGTGCTTGT 57.456 45.000 0.00 0.00 35.07 3.16
1041 2417 0.036164 TGTCTTACCTTGCGCCACAT 59.964 50.000 4.18 0.00 0.00 3.21
1061 2437 5.182950 CACATCAACTTAAGGGCATTGTGTA 59.817 40.000 7.53 0.00 0.00 2.90
1103 2479 3.643320 TCAAAGATCATGGCTAGATCGGT 59.357 43.478 12.00 4.50 45.05 4.69
1108 2484 0.465705 CATGGCTAGATCGGTGGTGT 59.534 55.000 0.00 0.00 0.00 4.16
1197 2573 5.185454 AGTGCTAAGTTGTATATGCTTGCA 58.815 37.500 0.00 0.00 0.00 4.08
1223 2599 4.568956 TGCGATTCAGTCATCAAAGAAGA 58.431 39.130 0.00 0.00 0.00 2.87
1246 2622 2.023414 TTGGAGTGCACCTTCGACGT 62.023 55.000 14.63 0.00 0.00 4.34
1271 2647 3.382832 CTCGAACCTCCGGGCACT 61.383 66.667 0.00 0.00 35.63 4.40
1397 2773 0.464373 CCGCCAGCATGTCCAACTAT 60.464 55.000 0.00 0.00 0.00 2.12
1487 4681 1.412453 AAGTTGGTCCGGTGGTAGCA 61.412 55.000 0.00 0.00 0.00 3.49
1546 4740 1.686355 TTCAGACATGTTGGCCGTTT 58.314 45.000 0.00 0.00 0.00 3.60
1547 4741 1.234821 TCAGACATGTTGGCCGTTTC 58.765 50.000 0.00 0.00 0.00 2.78
1686 4881 7.796660 TCAATAACGTGTCGAATTTCTCAAAAG 59.203 33.333 0.00 0.00 0.00 2.27
1749 4944 4.302559 AGGTCCCTTGTATTTTGAGTCC 57.697 45.455 0.00 0.00 0.00 3.85
1752 4947 4.830600 GGTCCCTTGTATTTTGAGTCCAAA 59.169 41.667 0.00 0.00 40.24 3.28
1920 5115 3.560251 AAGTGGACCAGCGCACCT 61.560 61.111 11.47 0.00 0.00 4.00
2020 5224 2.032528 CGCCTCCCTGCTTGACAA 59.967 61.111 0.00 0.00 0.00 3.18
2037 5241 1.212935 ACAAGTGTCCTGCTTGACCTT 59.787 47.619 11.37 4.65 44.29 3.50
2044 5248 1.447317 CCTGCTTGACCTTGCACGTT 61.447 55.000 0.00 0.00 35.20 3.99
2050 5254 2.325583 TGACCTTGCACGTTTCTCTT 57.674 45.000 0.00 0.00 0.00 2.85
2052 5256 2.210116 GACCTTGCACGTTTCTCTTCA 58.790 47.619 0.00 0.00 0.00 3.02
2069 5273 7.698506 TCTCTTCATCATCTTTTCTTGCAAT 57.301 32.000 0.00 0.00 0.00 3.56
2136 5340 1.343510 GCGCGATGCAGCTAGAGATC 61.344 60.000 12.10 0.00 45.45 2.75
2298 5502 7.880105 AGATTAGAGAAGAAAAGGTTTTGCAG 58.120 34.615 0.00 0.00 0.00 4.41
2323 5527 6.183360 GCAAGGGTTTTGTTGCAGAAAATTAA 60.183 34.615 8.47 0.00 46.83 1.40
2326 5530 6.542005 AGGGTTTTGTTGCAGAAAATTAAAGG 59.458 34.615 8.47 0.00 0.00 3.11
2397 5601 4.019051 AGAATCACCCAACTGATCATGACA 60.019 41.667 0.00 0.00 30.12 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 1443 0.107263 TTGTGCTCACTTGTGCTCCA 60.107 50.000 5.01 0.00 35.73 3.86
314 1578 3.883779 CGCTCATGTGTATGTGTGC 57.116 52.632 0.00 0.00 35.73 4.57
364 1632 5.525378 CACTGGGATGATAAGCTAACACTTC 59.475 44.000 0.00 0.00 0.00 3.01
383 1651 3.822735 ACCAGACAAACATTGATCACTGG 59.177 43.478 18.34 18.34 41.52 4.00
425 1761 6.271391 TCCCTTCACTGGTTCTATGTTTTCTA 59.729 38.462 0.00 0.00 0.00 2.10
480 1828 2.566913 ACGGAGCAACACAACAATGTA 58.433 42.857 0.00 0.00 37.82 2.29
560 1908 2.353208 CGCCTCAATAGTAGATGCCTCC 60.353 54.545 0.00 0.00 0.00 4.30
599 1947 0.609957 TGAGAGCCTTTGCATGGTGG 60.610 55.000 7.89 0.23 41.13 4.61
630 1978 5.994054 CGACAGATCAATCTCCATATTGGTT 59.006 40.000 0.00 0.00 39.03 3.67
636 1984 3.883489 ACGACGACAGATCAATCTCCATA 59.117 43.478 0.00 0.00 34.22 2.74
668 2018 0.318441 ACACGACATGACCAGACTGG 59.682 55.000 20.45 20.45 45.02 4.00
695 2045 5.359292 GCCAAAGGCTCAAGAGAGAAAATAT 59.641 40.000 0.32 0.00 46.69 1.28
697 2047 3.509184 GCCAAAGGCTCAAGAGAGAAAAT 59.491 43.478 0.32 0.00 46.69 1.82
767 2117 6.490566 AAAGCGTTTATAACAAAGTCCGAT 57.509 33.333 0.00 0.00 0.00 4.18
771 2121 6.525628 GGCCTTAAAGCGTTTATAACAAAGTC 59.474 38.462 0.00 0.00 0.00 3.01
774 2124 6.578163 AGGCCTTAAAGCGTTTATAACAAA 57.422 33.333 0.00 0.00 0.00 2.83
803 2153 0.878523 TGCTTGCACGACTTTAGCGT 60.879 50.000 0.00 0.00 43.67 5.07
957 2333 6.092259 GCAATGTAACGTCTCTAGACCATTTT 59.908 38.462 4.58 0.00 41.86 1.82
1024 2400 0.323302 TGATGTGGCGCAAGGTAAGA 59.677 50.000 10.83 0.00 38.28 2.10
1041 2417 4.720046 TGTACACAATGCCCTTAAGTTGA 58.280 39.130 9.76 0.00 0.00 3.18
1061 2437 1.460504 TGTCCGCGACTTATCTCTGT 58.539 50.000 8.23 0.00 33.15 3.41
1103 2479 3.353029 CGCACATCGCCAACACCA 61.353 61.111 0.00 0.00 37.30 4.17
1108 2484 3.353029 CACCACGCACATCGCCAA 61.353 61.111 0.00 0.00 43.23 4.52
1126 2502 0.179004 CCTGCCACCACCACTACAAA 60.179 55.000 0.00 0.00 0.00 2.83
1207 2583 5.065914 CCAAGGTTCTTCTTTGATGACTGA 58.934 41.667 0.00 0.00 35.53 3.41
1223 2599 0.535102 CGAAGGTGCACTCCAAGGTT 60.535 55.000 17.98 0.00 0.00 3.50
1246 2622 1.301716 GGAGGTTCGAGCAGCACAA 60.302 57.895 0.53 0.00 0.00 3.33
1434 2810 8.918658 GTCGAAGATGCCGTTTATTATTGTATA 58.081 33.333 0.00 0.00 40.67 1.47
1435 2811 7.358931 CGTCGAAGATGCCGTTTATTATTGTAT 60.359 37.037 0.00 0.00 40.67 2.29
1476 4670 5.047306 TCTCTTGATATATTGCTACCACCGG 60.047 44.000 0.00 0.00 0.00 5.28
1477 4671 5.864474 GTCTCTTGATATATTGCTACCACCG 59.136 44.000 0.00 0.00 0.00 4.94
1487 4681 4.752101 GCGGTTGCAGTCTCTTGATATATT 59.248 41.667 0.00 0.00 42.15 1.28
1561 4755 7.040478 ACTCAGAAGATAGTGCTATCATGTCTC 60.040 40.741 18.15 8.59 43.27 3.36
1563 4757 6.980593 ACTCAGAAGATAGTGCTATCATGTC 58.019 40.000 18.15 12.75 43.27 3.06
1920 5115 4.783227 AGAAGATAAGGTAGCACCCAAAGA 59.217 41.667 0.00 0.00 39.75 2.52
2002 5205 3.551496 TTGTCAAGCAGGGAGGCGG 62.551 63.158 0.00 0.00 39.27 6.13
2020 5224 0.536006 GCAAGGTCAAGCAGGACACT 60.536 55.000 9.57 2.60 39.59 3.55
2037 5241 3.930336 AGATGATGAAGAGAAACGTGCA 58.070 40.909 0.00 0.00 0.00 4.57
2044 5248 7.514784 TTGCAAGAAAAGATGATGAAGAGAA 57.485 32.000 0.00 0.00 0.00 2.87
2069 5273 4.506288 CACCATTCTGCAACGACGATATTA 59.494 41.667 0.00 0.00 0.00 0.98
2072 5276 2.267426 CACCATTCTGCAACGACGATA 58.733 47.619 0.00 0.00 0.00 2.92
2169 5373 1.401905 CTCTGCCGCACCTAATTTTCC 59.598 52.381 0.00 0.00 0.00 3.13
2270 5474 7.575909 GCAAAACCTTTTCTTCTCTAATCTCCC 60.576 40.741 0.00 0.00 0.00 4.30
2298 5502 2.307934 TTCTGCAACAAAACCCTTGC 57.692 45.000 0.00 0.00 42.67 4.01
2323 5527 7.387673 GCCTTTGTTGCAAAAAGTTATATCCTT 59.612 33.333 21.75 0.00 33.61 3.36
2326 5530 6.873605 AGGCCTTTGTTGCAAAAAGTTATATC 59.126 34.615 21.75 11.28 33.61 1.63
2368 5572 5.887598 TGATCAGTTGGGTGATTCTAAATGG 59.112 40.000 0.00 0.00 37.29 3.16


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

AutoCloner maintained by Alex Coulton.