Multiple sequence alignment - TraesCS2A01G328200

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 TraesCS2A01G328200 chr2A 100.000 2594 0 0 1 2594 559750910 559748317 0.000000e+00 4791
1 TraesCS2A01G328200 chr2A 91.507 942 47 15 1 916 559831287 559830353 0.000000e+00 1266
2 TraesCS2A01G328200 chr2A 95.562 676 30 0 932 1607 559829824 559829149 0.000000e+00 1083
3 TraesCS2A01G328200 chr2A 86.267 517 36 7 2086 2594 559826548 559826059 1.770000e-146 529
4 TraesCS2A01G328200 chr2A 90.959 365 28 3 1595 1959 559827636 559827277 1.080000e-133 486
5 TraesCS2A01G328200 chr2A 86.486 111 7 2 1980 2086 559826804 559826698 5.870000e-22 115
6 TraesCS2A01G328200 chr2D 93.277 1056 58 5 932 1982 427898040 427899087 0.000000e+00 1544
7 TraesCS2A01G328200 chr2D 93.110 1045 58 6 932 1971 427932656 427933691 0.000000e+00 1519
8 TraesCS2A01G328200 chr2D 92.344 1045 55 10 932 1971 427915175 427916199 0.000000e+00 1463
9 TraesCS2A01G328200 chr2D 92.045 1056 51 5 932 1982 427753447 427754474 0.000000e+00 1454
10 TraesCS2A01G328200 chr2D 90.244 943 56 19 1 917 427931160 427932092 0.000000e+00 1199
11 TraesCS2A01G328200 chr2D 89.384 942 61 18 1 917 427913688 427914615 0.000000e+00 1149
12 TraesCS2A01G328200 chr2D 85.586 777 68 23 179 917 427896724 427897494 0.000000e+00 774
13 TraesCS2A01G328200 chr2D 89.839 620 21 13 1980 2591 427916263 427916848 0.000000e+00 758
14 TraesCS2A01G328200 chr2D 89.839 620 21 13 1980 2591 427933755 427934340 0.000000e+00 758
15 TraesCS2A01G328200 chr2D 82.634 858 101 23 1 824 427751720 427752563 0.000000e+00 715
16 TraesCS2A01G328200 chr2D 85.868 651 83 7 929 1574 427925525 427926171 0.000000e+00 684
17 TraesCS2A01G328200 chr2D 87.360 625 38 8 1980 2594 427754519 427755112 0.000000e+00 678
18 TraesCS2A01G328200 chr2D 86.003 643 75 11 940 1574 427909787 427910422 0.000000e+00 675
19 TraesCS2A01G328200 chr2D 90.440 523 24 9 2086 2594 427899293 427899803 0.000000e+00 665
20 TraesCS2A01G328200 chr2D 84.938 644 84 8 929 1565 427944745 427945382 7.830000e-180 640
21 TraesCS2A01G328200 chr2D 85.638 188 19 3 2359 2538 427884450 427884637 9.470000e-45 191
22 TraesCS2A01G328200 chr2D 89.062 128 4 2 1980 2101 427899132 427899255 1.610000e-32 150
23 TraesCS2A01G328200 chr2B 93.188 1057 55 5 932 1982 504748149 504749194 0.000000e+00 1537
24 TraesCS2A01G328200 chr2B 92.384 906 58 5 932 1832 512372739 512371840 0.000000e+00 1280
25 TraesCS2A01G328200 chr2B 90.856 514 23 8 1980 2483 504749242 504749741 0.000000e+00 667
26 TraesCS2A01G328200 chr2B 82.115 766 95 22 89 824 512374597 512373844 3.670000e-173 617
27 TraesCS2A01G328200 chr2B 80.581 860 103 37 1 824 504746698 504747529 2.860000e-169 604
28 TraesCS2A01G328200 chr2B 88.957 489 27 9 1980 2457 512371481 512371009 1.730000e-161 579
29 TraesCS2A01G328200 chr2B 93.407 273 18 0 2322 2594 512364239 512363967 3.110000e-109 405
30 TraesCS2A01G328200 chr2B 81.750 400 50 20 1 389 512398540 512398153 1.940000e-81 313
31 TraesCS2A01G328200 chr2B 90.972 144 12 1 1840 1982 512371672 512371529 2.630000e-45 193


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 TraesCS2A01G328200 chr2A 559748317 559750910 2593 True 4791.000000 4791 100.000000 1 2594 1 chr2A.!!$R1 2593
1 TraesCS2A01G328200 chr2A 559826059 559831287 5228 True 695.800000 1266 90.156200 1 2594 5 chr2A.!!$R2 2593
2 TraesCS2A01G328200 chr2D 427931160 427934340 3180 False 1158.666667 1519 91.064333 1 2591 3 chr2D.!!$F7 2590
3 TraesCS2A01G328200 chr2D 427909787 427916848 7061 False 1011.250000 1463 89.392500 1 2591 4 chr2D.!!$F6 2590
4 TraesCS2A01G328200 chr2D 427751720 427755112 3392 False 949.000000 1454 87.346333 1 2594 3 chr2D.!!$F4 2593
5 TraesCS2A01G328200 chr2D 427896724 427899803 3079 False 783.250000 1544 89.591250 179 2594 4 chr2D.!!$F5 2415
6 TraesCS2A01G328200 chr2D 427925525 427926171 646 False 684.000000 684 85.868000 929 1574 1 chr2D.!!$F2 645
7 TraesCS2A01G328200 chr2D 427944745 427945382 637 False 640.000000 640 84.938000 929 1565 1 chr2D.!!$F3 636
8 TraesCS2A01G328200 chr2B 504746698 504749741 3043 False 936.000000 1537 88.208333 1 2483 3 chr2B.!!$F1 2482
9 TraesCS2A01G328200 chr2B 512371009 512374597 3588 True 667.250000 1280 88.607000 89 2457 4 chr2B.!!$R3 2368

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
757 4727 0.172127 TGAGCTCATCTGACGCTGTC 59.828 55.0 13.74 2.32 33.47 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2462 10138 0.671781 CCTCTTGGCAAGACGGTCTG 60.672 60.0 25.38 14.39 33.12 3.51 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
430 4381 8.678593 TGTTGTTGTATTCATACTTTGGTACA 57.321 30.769 0.00 0.00 34.41 2.90
519 4473 3.619729 AGTCTAATTTCGACGATCTCGC 58.380 45.455 0.00 0.00 42.62 5.03
532 4486 2.923655 CGATCTCGCTGAAACAAAGCTA 59.076 45.455 0.00 0.00 38.57 3.32
562 4524 6.260050 TGAAGATAATCCGAGTAATGGTTTGC 59.740 38.462 0.00 0.00 0.00 3.68
667 4629 1.933181 CGCTGGTGAATCATTTCGCTA 59.067 47.619 0.00 0.00 41.23 4.26
757 4727 0.172127 TGAGCTCATCTGACGCTGTC 59.828 55.000 13.74 2.32 33.47 3.51
801 4772 7.714377 TCAATATTTGTTGCTTGGTCATTGTTT 59.286 29.630 0.00 0.00 0.00 2.83
835 4806 9.683069 GATTAAATCAAGGCAAATATGTTCGAT 57.317 29.630 0.00 0.00 0.00 3.59
917 4893 1.153706 CGCCCCGTACAAGGTACTG 60.154 63.158 5.15 0.00 40.86 2.74
918 4894 1.219935 GCCCCGTACAAGGTACTGG 59.780 63.158 9.28 9.28 40.86 4.00
921 4897 1.153706 CCGTACAAGGTACTGGGCG 60.154 63.158 5.15 0.00 40.86 6.13
923 4899 1.880819 CGTACAAGGTACTGGGCGGT 61.881 60.000 5.15 0.00 40.86 5.68
925 4901 1.550072 GTACAAGGTACTGGGCGGTTA 59.450 52.381 0.00 0.00 40.86 2.85
927 4903 0.738412 CAAGGTACTGGGCGGTTACG 60.738 60.000 0.00 0.00 40.86 3.18
928 4904 1.187567 AAGGTACTGGGCGGTTACGT 61.188 55.000 0.00 0.00 40.86 3.57
929 4905 1.446618 GGTACTGGGCGGTTACGTG 60.447 63.158 0.00 0.00 43.45 4.49
930 4906 1.290009 GTACTGGGCGGTTACGTGT 59.710 57.895 0.00 0.00 43.45 4.49
965 6243 1.621317 TGAGTCGCCCACACAATCTAA 59.379 47.619 0.00 0.00 0.00 2.10
973 6255 3.866651 CCCACACAATCTAACTCTCCTG 58.133 50.000 0.00 0.00 0.00 3.86
993 6275 1.406539 GGGCTACAACTTCGGTATCGA 59.593 52.381 0.00 0.00 44.44 3.59
996 6278 3.243301 GGCTACAACTTCGGTATCGATCA 60.243 47.826 0.00 0.00 45.51 2.92
1026 6308 1.958288 ACCCTAATCTGACAGCTGGT 58.042 50.000 19.93 3.31 0.00 4.00
1077 6359 2.758089 CGACCACTACCTCGTCCCG 61.758 68.421 0.00 0.00 0.00 5.14
1137 6419 2.345760 GGAGGGCGTGGACGTCTTA 61.346 63.158 16.46 1.96 44.45 2.10
1222 6504 0.868406 CTTCTTCTTCGCGGCAAAGT 59.132 50.000 6.13 0.00 0.00 2.66
1332 6614 4.373116 GAGGCAGTGGCGTTCCGA 62.373 66.667 11.51 0.00 42.47 4.55
1355 6637 0.750850 AGGTTCGCATACCGCTACAT 59.249 50.000 0.00 0.00 43.21 2.29
1588 6879 0.250338 GGTGTTGAAGAGGAAGCGGT 60.250 55.000 0.00 0.00 0.00 5.68
1645 8461 4.686554 AGAGTTGTTGTGTCTCTATTTCGC 59.313 41.667 0.00 0.00 36.88 4.70
1665 8481 4.393062 TCGCTTCATTTCAGTTCTGGATTC 59.607 41.667 0.00 0.00 0.00 2.52
1667 8483 5.447010 CGCTTCATTTCAGTTCTGGATTCTC 60.447 44.000 0.00 0.00 0.00 2.87
1668 8484 5.447010 GCTTCATTTCAGTTCTGGATTCTCG 60.447 44.000 0.00 0.00 0.00 4.04
1669 8485 5.405935 TCATTTCAGTTCTGGATTCTCGA 57.594 39.130 0.00 0.00 0.00 4.04
1670 8486 5.982356 TCATTTCAGTTCTGGATTCTCGAT 58.018 37.500 0.00 0.00 0.00 3.59
1684 8506 5.766174 GGATTCTCGATCTAGTTGAGGTAGT 59.234 44.000 8.73 0.00 38.66 2.73
1687 8509 7.463961 TTCTCGATCTAGTTGAGGTAGTTTT 57.536 36.000 8.73 0.00 38.66 2.43
1701 8523 5.623169 AGGTAGTTTTATTGGTCCGTTTCA 58.377 37.500 0.00 0.00 0.00 2.69
1724 8546 7.041721 TCATTCGAAGTACAATGTAATCAGCT 58.958 34.615 3.35 0.00 32.67 4.24
1763 8585 4.430908 CCAGAACAGTTCGGAGGTATTAC 58.569 47.826 14.42 0.00 34.02 1.89
1838 8820 6.769341 TGTGATGTCTTCCCATCTGAATAATG 59.231 38.462 0.00 0.00 41.47 1.90
1882 8865 3.701532 TGGTTCGCTTTGTTTCGAATT 57.298 38.095 0.00 0.00 44.86 2.17
1891 8874 6.745450 TCGCTTTGTTTCGAATTATTGGAATC 59.255 34.615 0.00 4.03 0.00 2.52
1893 8876 6.506357 GCTTTGTTTCGAATTATTGGAATCGC 60.506 38.462 0.00 0.17 35.39 4.58
1948 8931 6.706295 TCCAGTTTCAGTTTCAAAATGGTTT 58.294 32.000 10.48 0.00 45.25 3.27
1982 9378 9.799106 AGATATAATTTTGAATACCACTCCAGG 57.201 33.333 0.00 0.00 0.00 4.45
2020 9466 7.578310 ATGTCTTCACATCTGAATAATTGGG 57.422 36.000 0.00 0.00 39.15 4.12
2024 9470 5.378230 TCACATCTGAATAATTGGGAGCT 57.622 39.130 0.00 0.00 0.00 4.09
2025 9471 6.499106 TCACATCTGAATAATTGGGAGCTA 57.501 37.500 0.00 0.00 0.00 3.32
2026 9472 6.899089 TCACATCTGAATAATTGGGAGCTAA 58.101 36.000 0.00 0.00 0.00 3.09
2027 9473 7.520798 TCACATCTGAATAATTGGGAGCTAAT 58.479 34.615 0.00 0.00 0.00 1.73
2068 9524 5.063204 TGCTGGACATAAGCACCATATTAC 58.937 41.667 0.00 0.00 45.50 1.89
2161 9835 2.665185 GGTCGCGCAGGACTGTTT 60.665 61.111 8.75 0.00 37.12 2.83
2172 9846 1.689273 AGGACTGTTTCTGAAGCGACT 59.311 47.619 0.00 0.00 0.00 4.18
2173 9847 2.103263 AGGACTGTTTCTGAAGCGACTT 59.897 45.455 0.00 0.00 0.00 3.01
2174 9848 2.476997 GGACTGTTTCTGAAGCGACTTC 59.523 50.000 11.24 11.24 40.54 3.01
2175 9849 3.385577 GACTGTTTCTGAAGCGACTTCT 58.614 45.455 16.76 0.00 40.73 2.85
2176 9850 4.547532 GACTGTTTCTGAAGCGACTTCTA 58.452 43.478 16.76 6.28 40.73 2.10
2177 9851 4.945246 ACTGTTTCTGAAGCGACTTCTAA 58.055 39.130 16.76 10.47 40.73 2.10
2178 9852 5.357257 ACTGTTTCTGAAGCGACTTCTAAA 58.643 37.500 16.76 14.16 40.73 1.85
2218 9894 6.017275 GGATCAAAGATCAATGGTGAGATCAC 60.017 42.308 4.33 4.33 42.36 3.06
2238 9914 2.158623 ACCATTCACACTTTCCTGCAGA 60.159 45.455 17.39 0.00 0.00 4.26
2247 9923 2.290960 ACTTTCCTGCAGATGGTTACCC 60.291 50.000 17.39 0.00 0.00 3.69
2249 9925 1.367346 TCCTGCAGATGGTTACCCAA 58.633 50.000 17.39 0.00 46.04 4.12
2524 10227 6.827727 ACTTGTTGTTTCTGTACCTCTACAT 58.172 36.000 0.00 0.00 32.21 2.29
2561 10264 2.086869 CAATCATTTGGAGCTCGGTGT 58.913 47.619 7.83 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
209 4120 0.679505 TTTCGATCGGCTATCCCAGG 59.320 55.000 16.41 0.00 0.00 4.45
211 4122 2.289444 GGAATTTCGATCGGCTATCCCA 60.289 50.000 16.41 0.00 0.00 4.37
310 4221 1.243902 GCTGTTCCCGATTTTGACCA 58.756 50.000 0.00 0.00 0.00 4.02
532 4486 8.378565 ACCATTACTCGGATTATCTTCATGATT 58.621 33.333 0.00 0.00 36.65 2.57
600 4562 1.003928 AGCAATGATGTCAGCACTCCA 59.996 47.619 0.00 0.00 0.00 3.86
601 4563 1.747709 AGCAATGATGTCAGCACTCC 58.252 50.000 0.00 0.00 0.00 3.85
694 4656 8.642935 TTTTTATTCCACATGAGACCATACAA 57.357 30.769 0.00 0.00 0.00 2.41
708 4670 8.034215 TGATCACATTCCACATTTTTATTCCAC 58.966 33.333 0.00 0.00 0.00 4.02
757 4727 2.412870 TGACTGTATTTGGAGCACACG 58.587 47.619 0.00 0.00 0.00 4.49
801 4772 7.537596 TTTGCCTTGATTTAATCTTTCCTCA 57.462 32.000 6.50 0.00 0.00 3.86
835 4806 4.943705 GGACAATTGATGAAGAGGTGCTTA 59.056 41.667 13.59 0.00 36.83 3.09
917 4893 2.030862 TGGAACACGTAACCGCCC 59.969 61.111 0.00 0.00 37.70 6.13
930 4906 3.003275 GCGACTCAAAATGTTCAGTGGAA 59.997 43.478 0.00 0.00 0.00 3.53
965 6243 1.903183 GAAGTTGTAGCCCAGGAGAGT 59.097 52.381 0.00 0.00 0.00 3.24
973 6255 1.406539 TCGATACCGAAGTTGTAGCCC 59.593 52.381 0.00 0.00 42.51 5.19
993 6275 1.399744 TAGGGTTCGCCATCGCTGAT 61.400 55.000 0.00 0.00 39.65 2.90
996 6278 0.249911 GATTAGGGTTCGCCATCGCT 60.250 55.000 0.00 0.00 39.65 4.93
1026 6308 0.532417 CGGTGGGTTGGAACACGTAA 60.532 55.000 0.00 0.00 39.29 3.18
1332 6614 2.508439 CGGTATGCGAACCTGCGT 60.508 61.111 5.81 0.00 37.39 5.24
1384 6666 4.233635 CTTCATCAGCCAGCGCGC 62.234 66.667 26.66 26.66 41.18 6.86
1645 8461 5.871524 TCGAGAATCCAGAACTGAAATGAAG 59.128 40.000 3.19 0.00 0.00 3.02
1665 8481 9.239002 CAATAAAACTACCTCAACTAGATCGAG 57.761 37.037 0.00 0.70 0.00 4.04
1667 8483 7.980099 ACCAATAAAACTACCTCAACTAGATCG 59.020 37.037 0.00 0.00 0.00 3.69
1668 8484 9.315525 GACCAATAAAACTACCTCAACTAGATC 57.684 37.037 0.00 0.00 0.00 2.75
1669 8485 8.265764 GGACCAATAAAACTACCTCAACTAGAT 58.734 37.037 0.00 0.00 0.00 1.98
1670 8486 7.578189 CGGACCAATAAAACTACCTCAACTAGA 60.578 40.741 0.00 0.00 0.00 2.43
1684 8506 5.943706 TCGAATGAAACGGACCAATAAAA 57.056 34.783 0.00 0.00 0.00 1.52
1687 8509 4.571919 ACTTCGAATGAAACGGACCAATA 58.428 39.130 0.00 0.00 32.66 1.90
1701 8523 7.011482 GGAAGCTGATTACATTGTACTTCGAAT 59.989 37.037 0.00 0.78 34.51 3.34
1763 8585 8.925161 ACATAAATCATAAAATGAAACGGTGG 57.075 30.769 0.00 0.00 43.50 4.61
1797 8619 1.206132 TCACACACCAAGACTCACGTT 59.794 47.619 0.00 0.00 0.00 3.99
1812 8634 3.616956 TCAGATGGGAAGACATCACAC 57.383 47.619 8.66 0.00 46.40 3.82
1866 8848 5.614923 TCCAATAATTCGAAACAAAGCGA 57.385 34.783 0.00 0.00 34.32 4.93
1882 8865 7.870954 CCTAAACATACTACTGCGATTCCAATA 59.129 37.037 0.00 0.00 0.00 1.90
1891 8874 6.641314 CCATTACTCCTAAACATACTACTGCG 59.359 42.308 0.00 0.00 0.00 5.18
1964 9360 5.450453 TGTTTCCTGGAGTGGTATTCAAAA 58.550 37.500 0.00 0.00 0.00 2.44
1982 9378 6.959361 TGTGAAGACATCTTTAGCTTGTTTC 58.041 36.000 0.00 0.00 36.11 2.78
2024 9470 7.315142 CAGCAAAGTCATCCAAAGCTTAATTA 58.685 34.615 0.00 0.00 0.00 1.40
2025 9471 6.161381 CAGCAAAGTCATCCAAAGCTTAATT 58.839 36.000 0.00 0.00 0.00 1.40
2026 9472 5.337009 CCAGCAAAGTCATCCAAAGCTTAAT 60.337 40.000 0.00 0.00 0.00 1.40
2027 9473 4.022068 CCAGCAAAGTCATCCAAAGCTTAA 60.022 41.667 0.00 0.00 0.00 1.85
2068 9524 8.228464 CAGATGCATGAACATTACAGCTTATAG 58.772 37.037 2.46 0.00 0.00 1.31
2131 9804 2.102357 CGACCTGACGACCGGATG 59.898 66.667 9.46 1.33 35.09 3.51
2161 9835 8.251026 TCATTAGAATTTAGAAGTCGCTTCAGA 58.749 33.333 17.76 6.35 42.37 3.27
2172 9846 9.685276 TGATCCAAGCTTCATTAGAATTTAGAA 57.315 29.630 0.00 0.00 32.31 2.10
2173 9847 9.685276 TTGATCCAAGCTTCATTAGAATTTAGA 57.315 29.630 0.00 0.00 32.31 2.10
2176 9850 9.028284 TCTTTGATCCAAGCTTCATTAGAATTT 57.972 29.630 0.00 0.00 32.31 1.82
2177 9851 8.585471 TCTTTGATCCAAGCTTCATTAGAATT 57.415 30.769 0.00 0.00 32.31 2.17
2178 9852 8.763984 ATCTTTGATCCAAGCTTCATTAGAAT 57.236 30.769 0.00 0.00 32.31 2.40
2218 9894 2.507484 TCTGCAGGAAAGTGTGAATGG 58.493 47.619 15.13 0.00 0.00 3.16
2249 9925 8.474831 CGGGGTTTAAGAAATAATTTCCAGAAT 58.525 33.333 0.00 0.00 40.54 2.40
2462 10138 0.671781 CCTCTTGGCAAGACGGTCTG 60.672 60.000 25.38 14.39 33.12 3.51
2468 10144 2.685388 GCTAAATCCCTCTTGGCAAGAC 59.315 50.000 25.38 9.18 33.12 3.01
2524 10227 0.908910 TTGAAATGAGCCGCCTCCTA 59.091 50.000 0.00 0.00 37.29 2.94


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

AutoCloner maintained by Alex Coulton.