Multiple sequence alignment - TraesCS2A01G244300

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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 TraesCS2A01G244300 chr2A 100.000 2471 0 0 1 2471 348247414 348244944 0.000000e+00 4564
1 TraesCS2A01G244300 chr2A 96.041 1844 45 16 639 2471 345169996 345168170 0.000000e+00 2976
2 TraesCS2A01G244300 chr2A 95.501 1845 49 18 639 2471 344899990 344898168 0.000000e+00 2916
3 TraesCS2A01G244300 chr2A 94.498 309 17 0 338 646 344921492 344921184 6.180000e-131 477
4 TraesCS2A01G244300 chr2A 93.548 310 19 1 338 646 345178561 345178252 6.230000e-126 460
5 TraesCS2A01G244300 chr4B 93.590 702 38 6 1281 1978 226871335 226870637 0.000000e+00 1040
6 TraesCS2A01G244300 chr4B 83.448 435 39 11 1 402 226872065 226871631 8.340000e-100 374
7 TraesCS2A01G244300 chr4B 83.843 229 35 2 1413 1640 191712747 191712974 1.490000e-52 217
8 TraesCS2A01G244300 chr4B 93.103 116 7 1 1280 1394 460190906 460191021 4.230000e-38 169
9 TraesCS2A01G244300 chr4B 86.709 158 8 5 499 643 226871602 226871445 1.970000e-36 163
10 TraesCS2A01G244300 chr2B 93.632 581 29 5 1 573 40912031 40911451 0.000000e+00 861
11 TraesCS2A01G244300 chr2B 88.388 577 50 9 1 563 15508678 15508105 0.000000e+00 678
12 TraesCS2A01G244300 chr2B 93.274 223 12 3 611 831 40911455 40911234 2.370000e-85 326
13 TraesCS2A01G244300 chr2B 93.976 166 7 3 787 950 15508043 15507879 5.280000e-62 248
14 TraesCS2A01G244300 chr6B 88.254 613 57 12 682 1284 22715236 22715843 0.000000e+00 719
15 TraesCS2A01G244300 chr6B 88.307 573 50 9 1 559 464522612 464522043 0.000000e+00 671
16 TraesCS2A01G244300 chr6B 86.933 375 46 3 1413 1786 224884905 224884533 3.800000e-113 418
17 TraesCS2A01G244300 chr6B 91.566 166 11 3 787 950 464521977 464521813 2.470000e-55 226
18 TraesCS2A01G244300 chr6B 81.685 273 45 4 1015 1284 21132097 21132367 3.200000e-54 222
19 TraesCS2A01G244300 chr6B 91.228 114 10 0 1810 1923 407167067 407166954 3.290000e-34 156
20 TraesCS2A01G244300 chr6B 90.090 111 11 0 1280 1390 224885091 224884981 7.120000e-31 145
21 TraesCS2A01G244300 chr6B 89.189 111 12 0 1280 1390 83601866 83601976 3.310000e-29 139
22 TraesCS2A01G244300 chr6A 87.643 437 38 9 856 1284 13733879 13734307 6.140000e-136 494
23 TraesCS2A01G244300 chr6A 82.222 270 48 0 1015 1284 12472929 12473198 1.480000e-57 233
24 TraesCS2A01G244300 chr6D 95.380 303 13 1 983 1284 12358108 12358410 4.780000e-132 481
25 TraesCS2A01G244300 chr6D 82.784 273 42 4 1015 1284 11258138 11258408 3.180000e-59 239
26 TraesCS2A01G244300 chr6D 85.816 141 19 1 2331 2471 436504692 436504831 5.510000e-32 148
27 TraesCS2A01G244300 chr3A 86.933 375 46 3 1413 1786 700301254 700301626 3.800000e-113 418
28 TraesCS2A01G244300 chr3A 86.364 198 26 1 1589 1786 668416033 668415837 5.350000e-52 215
29 TraesCS2A01G244300 chr3A 90.991 111 10 0 1280 1390 700301068 700301178 1.530000e-32 150
30 TraesCS2A01G244300 chr5A 86.667 375 47 3 1413 1786 229782676 229782304 1.770000e-111 412
31 TraesCS2A01G244300 chr5A 91.960 199 12 3 1782 1978 265948040 265948236 2.420000e-70 276
32 TraesCS2A01G244300 chr5A 93.913 115 6 1 1281 1394 265946848 265946962 3.270000e-39 172
33 TraesCS2A01G244300 chr1D 95.575 113 5 0 2359 2471 7088064 7088176 5.430000e-42 182
34 TraesCS2A01G244300 chr7A 93.805 113 7 0 2359 2471 299504269 299504381 1.180000e-38 171
35 TraesCS2A01G244300 chr1B 92.920 113 7 1 2359 2471 646468244 646468133 1.970000e-36 163
36 TraesCS2A01G244300 chr1B 87.000 100 11 2 1822 1919 290821289 290821190 7.220000e-21 111
37 TraesCS2A01G244300 chr7B 91.228 114 10 0 1810 1923 171005692 171005805 3.290000e-34 156
38 TraesCS2A01G244300 chr4D 90.517 116 10 1 1280 1394 12079023 12079138 4.260000e-33 152
39 TraesCS2A01G244300 chr3D 86.667 135 17 1 2337 2471 211956873 211956740 5.510000e-32 148
40 TraesCS2A01G244300 chr3D 85.926 135 18 1 2337 2471 232481668 232481535 2.560000e-30 143
41 TraesCS2A01G244300 chr3D 89.623 106 9 2 1816 1919 465788014 465787909 1.540000e-27 134
42 TraesCS2A01G244300 chr4A 90.566 106 8 2 1816 1919 213400989 213400884 3.310000e-29 139
43 TraesCS2A01G244300 chr5D 76.991 226 38 12 2249 2471 179649519 179649733 1.550000e-22 117


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 TraesCS2A01G244300 chr2A 348244944 348247414 2470 True 4564.000000 4564 100.000000 1 2471 1 chr2A.!!$R5 2470
1 TraesCS2A01G244300 chr2A 345168170 345169996 1826 True 2976.000000 2976 96.041000 639 2471 1 chr2A.!!$R3 1832
2 TraesCS2A01G244300 chr2A 344898168 344899990 1822 True 2916.000000 2916 95.501000 639 2471 1 chr2A.!!$R1 1832
3 TraesCS2A01G244300 chr4B 226870637 226872065 1428 True 525.666667 1040 87.915667 1 1978 3 chr4B.!!$R1 1977
4 TraesCS2A01G244300 chr2B 40911234 40912031 797 True 593.500000 861 93.453000 1 831 2 chr2B.!!$R2 830
5 TraesCS2A01G244300 chr2B 15507879 15508678 799 True 463.000000 678 91.182000 1 950 2 chr2B.!!$R1 949
6 TraesCS2A01G244300 chr6B 22715236 22715843 607 False 719.000000 719 88.254000 682 1284 1 chr6B.!!$F2 602
7 TraesCS2A01G244300 chr6B 464521813 464522612 799 True 448.500000 671 89.936500 1 950 2 chr6B.!!$R3 949
8 TraesCS2A01G244300 chr6B 224884533 224885091 558 True 281.500000 418 88.511500 1280 1786 2 chr6B.!!$R2 506
9 TraesCS2A01G244300 chr3A 700301068 700301626 558 False 284.000000 418 88.962000 1280 1786 2 chr3A.!!$F1 506
10 TraesCS2A01G244300 chr5A 265946848 265948236 1388 False 224.000000 276 92.936500 1281 1978 2 chr5A.!!$F1 697

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
388 423 1.068352 AGGCCCACTTTGGTCTTCCT 61.068 55.000 0.00 0.0 36.85 3.36 F
662 712 1.836802 GGCTTCCTTGGAGATCTCTGT 59.163 52.381 21.81 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1348 1415 1.144708 TGCAATCAGAGTGGGGAACAA 59.855 47.619 0.0 0.0 0.0 2.83 R
2405 3197 0.445436 GCCAGATGACAACTTCGCAG 59.555 55.000 0.0 0.0 0.0 5.18 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 29 2.928334 TGCCATTGTTTTGGTGCATTT 58.072 38.095 0.00 0.00 39.11 2.32
116 118 4.938226 AGAGTTCAAAAATCCATCGTCTCC 59.062 41.667 0.00 0.00 0.00 3.71
128 130 1.296984 TCGTCTCCTACCTCTCCCTT 58.703 55.000 0.00 0.00 0.00 3.95
282 305 8.463930 TTTACTTTTCATTAGGGAGCATATGG 57.536 34.615 4.56 0.00 0.00 2.74
287 310 1.528600 TTAGGGAGCATATGGCCCAA 58.471 50.000 0.00 0.00 46.50 4.12
302 325 1.847328 CCCAAAGGGTAAAATCCGCT 58.153 50.000 0.00 0.00 38.25 5.52
303 326 2.946791 GCCCAAAGGGTAAAATCCGCTA 60.947 50.000 3.68 0.00 46.51 4.26
388 423 1.068352 AGGCCCACTTTGGTCTTCCT 61.068 55.000 0.00 0.00 36.85 3.36
407 442 5.916661 TCCTGGTCTGTTAGAATAGTGAC 57.083 43.478 0.00 0.00 0.00 3.67
478 513 2.223572 CGAGCACTTCCTGTTGCTTTTT 60.224 45.455 0.00 0.00 34.74 1.94
484 519 4.272504 CACTTCCTGTTGCTTTTTCGTCTA 59.727 41.667 0.00 0.00 0.00 2.59
497 532 4.659111 TTTCGTCTACTCACTTCCACAA 57.341 40.909 0.00 0.00 0.00 3.33
618 668 3.215568 TGTGGTGCTGCCGGTTTG 61.216 61.111 1.90 0.00 41.21 2.93
662 712 1.836802 GGCTTCCTTGGAGATCTCTGT 59.163 52.381 21.81 0.00 0.00 3.41
678 728 2.103432 CTCTGTAGAGCTCGTCCTCCTA 59.897 54.545 8.37 0.00 35.13 2.94
679 729 2.504585 TCTGTAGAGCTCGTCCTCCTAA 59.495 50.000 8.37 0.00 32.17 2.69
1348 1415 4.599241 TGTCATTTCCCCTCTTCTCTCTTT 59.401 41.667 0.00 0.00 0.00 2.52
1423 1597 4.980434 CACCTTGCTCTTTGATTGTTCAAG 59.020 41.667 0.00 0.00 42.60 3.02
1471 1645 4.098654 TCTCCGCTCCAAATTTGTTTTGAA 59.901 37.500 16.73 0.00 46.36 2.69
1488 1662 6.979817 TGTTTTGAACATCTTCTTCAATGTGG 59.020 34.615 0.00 0.00 37.45 4.17
1741 2520 7.827701 TCGTCTTCACAGAGTAAGTTCATATT 58.172 34.615 0.00 0.00 0.00 1.28
2003 2793 8.826293 ACTATCAGTAGTCTAGGTTAGCTTTT 57.174 34.615 0.00 0.00 36.41 2.27
2004 2794 9.917887 ACTATCAGTAGTCTAGGTTAGCTTTTA 57.082 33.333 0.00 0.00 36.41 1.52
2096 2886 9.361315 GATTTGTTTTGTTACTTTGTGGTACTT 57.639 29.630 0.00 0.00 0.00 2.24
2405 3197 7.820044 AGACGATGAAGTTCTGAATTCTAAC 57.180 36.000 7.05 10.88 0.00 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 5.240844 ACCTACACTCTAAATGCACCAAAAC 59.759 40.000 0.00 0.00 0.00 2.43
27 29 7.179694 AGCTACCAATAAAACACCTACACTCTA 59.820 37.037 0.00 0.00 0.00 2.43
116 118 3.895041 GGAATCTGAGAAGGGAGAGGTAG 59.105 52.174 0.00 0.00 0.00 3.18
157 159 3.754043 CCTGGAGGGCCATGGTTA 58.246 61.111 14.67 0.00 44.91 2.85
287 310 2.158519 CCCCATAGCGGATTTTACCCTT 60.159 50.000 0.00 0.00 36.56 3.95
388 423 5.185249 GTCCAGTCACTATTCTAACAGACCA 59.815 44.000 0.00 0.00 0.00 4.02
407 442 5.975693 TTAGGCCTTTACATTTTGTCCAG 57.024 39.130 12.58 0.00 0.00 3.86
478 513 2.953648 TGTTGTGGAAGTGAGTAGACGA 59.046 45.455 0.00 0.00 0.00 4.20
484 519 1.837439 TCTGGTGTTGTGGAAGTGAGT 59.163 47.619 0.00 0.00 0.00 3.41
497 532 1.618837 AGACAATACTGCGTCTGGTGT 59.381 47.619 0.00 0.00 40.92 4.16
618 668 4.691216 GGTGCTATTATCCATCGAGAAACC 59.309 45.833 0.00 0.00 0.00 3.27
662 712 5.307544 ACTATTTAGGAGGACGAGCTCTA 57.692 43.478 12.85 0.00 0.00 2.43
845 901 5.464057 CCAACAAACATAGAAGACACGTACA 59.536 40.000 0.00 0.00 0.00 2.90
850 906 3.057526 GGCCCAACAAACATAGAAGACAC 60.058 47.826 0.00 0.00 0.00 3.67
851 907 3.153919 GGCCCAACAAACATAGAAGACA 58.846 45.455 0.00 0.00 0.00 3.41
852 908 2.161609 CGGCCCAACAAACATAGAAGAC 59.838 50.000 0.00 0.00 0.00 3.01
1348 1415 1.144708 TGCAATCAGAGTGGGGAACAA 59.855 47.619 0.00 0.00 0.00 2.83
1406 1580 5.238214 AGAGACACTTGAACAATCAAAGAGC 59.762 40.000 0.00 0.00 44.64 4.09
1423 1597 3.664107 TGCAGATTTGTACCAGAGACAC 58.336 45.455 0.00 0.00 0.00 3.67
1471 1645 5.534207 TTTTGCCACATTGAAGAAGATGT 57.466 34.783 0.00 0.00 36.97 3.06
1857 2642 3.661648 AATGCCGGTCCCAAGCCT 61.662 61.111 1.90 0.00 0.00 4.58
2029 2819 8.156165 GGAGAACAGGATCAGATCAAATTCTAT 58.844 37.037 12.66 0.00 30.24 1.98
2096 2886 9.373603 CCAGAAAGAATGAATATTCATGCAAAA 57.626 29.630 30.07 5.66 46.60 2.44
2261 3053 6.409524 AATCATGTGTCAACCAAACTCATT 57.590 33.333 0.00 0.00 30.64 2.57
2294 3086 7.345422 TGTCCTCAAGAACAAAATCATTCAA 57.655 32.000 0.00 0.00 0.00 2.69
2306 3098 6.166279 TCTCATGTACAATGTCCTCAAGAAC 58.834 40.000 0.00 0.00 0.00 3.01
2405 3197 0.445436 GCCAGATGACAACTTCGCAG 59.555 55.000 0.00 0.00 0.00 5.18


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

AutoCloner maintained by Alex Coulton.