Multiple sequence alignment - TraesCS2A01G041600

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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 TraesCS2A01G041600 chr2A 100.000 3028 0 0 1 3028 16749977 16753004 0.000000e+00 5592
1 TraesCS2A01G041600 chr2A 82.609 1817 196 60 719 2482 16770847 16772596 0.000000e+00 1495
2 TraesCS2A01G041600 chr2A 78.571 364 58 15 2602 2949 16772762 16773121 3.930000e-54 222
3 TraesCS2A01G041600 chr2D 93.430 2207 87 21 875 3028 14647288 14649489 0.000000e+00 3219
4 TraesCS2A01G041600 chr2D 87.435 1154 97 17 1914 3028 14443944 14445088 0.000000e+00 1284
5 TraesCS2A01G041600 chr2D 90.114 961 78 7 1 952 14564557 14565509 0.000000e+00 1232
6 TraesCS2A01G041600 chr2D 90.139 933 76 3 1059 1978 14565548 14566477 0.000000e+00 1199
7 TraesCS2A01G041600 chr2D 85.455 1155 98 19 1915 3028 14597121 14598246 0.000000e+00 1138
8 TraesCS2A01G041600 chr2D 89.210 797 79 4 1065 1858 14596239 14597031 0.000000e+00 989
9 TraesCS2A01G041600 chr2D 92.214 655 48 1 1204 1858 14443195 14443846 0.000000e+00 924
10 TraesCS2A01G041600 chr2D 81.716 1154 125 37 685 1827 14703681 14704759 0.000000e+00 883
11 TraesCS2A01G041600 chr2D 85.770 773 79 24 1 759 14646530 14647285 0.000000e+00 789
12 TraesCS2A01G041600 chr2D 87.132 544 57 7 2488 3026 14568553 14569088 3.340000e-169 604
13 TraesCS2A01G041600 chr2D 90.024 421 36 5 6 422 14595030 14595448 9.550000e-150 540
14 TraesCS2A01G041600 chr2D 87.143 490 44 6 2023 2497 14567875 14568360 3.440000e-149 538
15 TraesCS2A01G041600 chr2D 89.100 422 26 9 685 1090 14442780 14443197 9.690000e-140 507
16 TraesCS2A01G041600 chr2D 88.509 409 39 4 1 405 14441605 14442009 3.510000e-134 488
17 TraesCS2A01G041600 chr2D 90.278 360 30 4 96 451 14595444 14595802 1.640000e-127 466
18 TraesCS2A01G041600 chr2D 81.215 543 86 10 1275 1815 14642324 14642852 1.000000e-114 424
19 TraesCS2A01G041600 chr2D 88.841 233 13 7 390 616 14442424 14442649 1.070000e-69 274
20 TraesCS2A01G041600 chr2D 88.806 134 9 4 483 616 14595801 14595928 3.120000e-35 159
21 TraesCS2A01G041600 chr2B 85.990 1863 178 33 685 2482 26353891 26355735 0.000000e+00 1917
22 TraesCS2A01G041600 chr2B 83.073 833 97 20 1686 2482 26359029 26359853 0.000000e+00 717
23 TraesCS2A01G041600 chr2B 87.619 630 57 10 1 616 26353138 26353760 0.000000e+00 712
24 TraesCS2A01G041600 chr2B 86.703 549 71 2 1268 1815 26348932 26349479 2.580000e-170 608
25 TraesCS2A01G041600 chr4B 74.681 549 120 12 7 547 663901074 663900537 3.040000e-55 226


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 TraesCS2A01G041600 chr2A 16749977 16753004 3027 False 5592.000000 5592 100.00000 1 3028 1 chr2A.!!$F1 3027
1 TraesCS2A01G041600 chr2A 16770847 16773121 2274 False 858.500000 1495 80.59000 719 2949 2 chr2A.!!$F2 2230
2 TraesCS2A01G041600 chr2D 14642324 14649489 7165 False 1477.333333 3219 86.80500 1 3028 3 chr2D.!!$F5 3027
3 TraesCS2A01G041600 chr2D 14564557 14569088 4531 False 893.250000 1232 88.63200 1 3026 4 chr2D.!!$F3 3025
4 TraesCS2A01G041600 chr2D 14703681 14704759 1078 False 883.000000 883 81.71600 685 1827 1 chr2D.!!$F1 1142
5 TraesCS2A01G041600 chr2D 14441605 14445088 3483 False 695.400000 1284 89.21980 1 3028 5 chr2D.!!$F2 3027
6 TraesCS2A01G041600 chr2D 14595030 14598246 3216 False 658.400000 1138 88.75460 6 3028 5 chr2D.!!$F4 3022
7 TraesCS2A01G041600 chr2B 26348932 26359853 10921 False 988.500000 1917 85.84625 1 2482 4 chr2B.!!$F1 2481
8 TraesCS2A01G041600 chr4B 663900537 663901074 537 True 226.000000 226 74.68100 7 547 1 chr4B.!!$R1 540

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
57 4384 0.992072 CACAGGTACGATGCTTCACG 59.008 55.0 0.08 0.0 0.0 4.35 F
1054 6274 0.796312 CCGGCTGACAACACATACAC 59.204 55.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 6990 0.826715 CTTCTTCCTCATCCTCGCCA 59.173 55.0 0.0 0.0 0.0 5.69 R
2979 10024 0.815615 GCCCCGTTTGATCTAGCCTG 60.816 60.0 0.0 0.0 0.0 4.85 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
57 4384 0.992072 CACAGGTACGATGCTTCACG 59.008 55.000 0.08 0.00 0.00 4.35
192 4520 5.236478 GCTTTAGTAAAGTGAGTGCAGTCAA 59.764 40.000 25.45 7.69 40.64 3.18
204 4532 3.130869 AGTGCAGTCAAATTGAAGCAACA 59.869 39.130 20.72 4.24 39.99 3.33
244 4572 3.003689 CCTGCACAAACTTGACTACCTTG 59.996 47.826 0.00 0.00 0.00 3.61
307 4642 4.525487 AGCCATGCATGAGGGTTTAATATG 59.475 41.667 28.31 7.28 29.87 1.78
310 4645 3.230134 TGCATGAGGGTTTAATATGCCC 58.770 45.455 0.00 0.00 42.48 5.36
387 5052 1.137872 ACGCCAAAGCACAATCCAAAA 59.862 42.857 0.00 0.00 39.83 2.44
484 5580 8.893727 CGAATTTGAGAGGACATTAACCTAATT 58.106 33.333 0.00 0.00 37.93 1.40
507 5603 2.346803 CACAAGGTCGGATACACCAAG 58.653 52.381 0.22 0.00 39.39 3.61
516 5614 4.338682 GTCGGATACACCAAGTCTGTAGAT 59.661 45.833 0.00 0.00 38.90 1.98
530 5633 4.794246 GTCTGTAGATACACAAACGCTCTC 59.206 45.833 0.00 0.00 31.93 3.20
768 5955 4.704103 TCAGTCAGCGCCCCCTCT 62.704 66.667 2.29 0.00 0.00 3.69
786 5973 1.762370 TCTCACTTCAGTTGAGGCACA 59.238 47.619 0.00 0.00 0.00 4.57
859 6050 6.047231 ACGCATTACCAACTAGGAGTATTTC 58.953 40.000 0.00 0.00 41.22 2.17
945 6144 8.457261 CACAAAATTCCCTCTAATTTCTCAGAG 58.543 37.037 0.00 0.00 37.93 3.35
964 6178 2.507992 CCAAGGCTCGTCAGCTCG 60.508 66.667 0.00 0.00 46.03 5.03
1054 6274 0.796312 CCGGCTGACAACACATACAC 59.204 55.000 0.00 0.00 0.00 2.90
1708 6990 0.585357 ATAGCGAACGACGTAGCGAT 59.415 50.000 22.20 19.15 44.60 4.58
1727 7009 0.826715 TGGCGAGGATGAGGAAGAAG 59.173 55.000 0.00 0.00 0.00 2.85
1811 7093 4.021229 TGGACGAGCTTCTTAGGATTACA 58.979 43.478 0.00 0.00 0.00 2.41
1815 7097 5.978814 ACGAGCTTCTTAGGATTACATGTT 58.021 37.500 2.30 0.00 0.00 2.71
1874 7157 2.381725 ACGGTTGTTCTAGCTAAGCC 57.618 50.000 0.00 0.00 0.00 4.35
1934 7282 9.656040 TTTCTATTTCCATGATTTTTGTCCATG 57.344 29.630 0.00 0.00 37.87 3.66
2148 8871 6.966534 AAAAACATGACATTCAGAAGTCCT 57.033 33.333 0.00 0.08 33.89 3.85
2598 9551 0.739813 CGAGGGGTAAAACGGAGCAG 60.740 60.000 0.00 0.00 0.00 4.24
2737 9764 5.941647 ACATGTCAGTGATCATTCATGTTGA 59.058 36.000 21.05 4.07 41.60 3.18
2738 9765 6.431852 ACATGTCAGTGATCATTCATGTTGAA 59.568 34.615 21.05 0.00 41.60 2.69
2739 9766 6.490566 TGTCAGTGATCATTCATGTTGAAG 57.509 37.500 0.00 0.00 40.05 3.02
2743 9771 8.077991 GTCAGTGATCATTCATGTTGAAGAAAA 58.922 33.333 0.00 0.00 40.05 2.29
2798 9839 1.878069 TTCGCACTCGCATCATCCG 60.878 57.895 0.00 0.00 38.40 4.18
2824 9868 0.183492 ACCGCATGCCTTGTATCCAT 59.817 50.000 13.15 0.00 0.00 3.41
2825 9869 0.877071 CCGCATGCCTTGTATCCATC 59.123 55.000 13.15 0.00 0.00 3.51
2826 9870 0.514255 CGCATGCCTTGTATCCATCG 59.486 55.000 13.15 0.00 0.00 3.84
2835 9879 3.490933 CCTTGTATCCATCGTCATCGTGT 60.491 47.826 0.00 0.00 38.33 4.49
2979 10024 1.153784 CGATTGTTGCCACCCATGC 60.154 57.895 0.00 0.00 0.00 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 4352 6.539649 TCGTACCTGTGATTTTCTTGAAAG 57.460 37.500 0.00 0.00 0.00 2.62
192 4520 1.537990 GGCGGTGTTGTTGCTTCAATT 60.538 47.619 0.00 0.00 0.00 2.32
204 4532 2.918802 TGTACGAGGGGCGGTGTT 60.919 61.111 0.00 0.00 46.49 3.32
310 4645 0.330604 TAGGAGATATCCCCGTCCCG 59.669 60.000 1.81 0.00 0.00 5.14
387 5052 6.662865 TTTGTTGGTGTTATCCATTGTGAT 57.337 33.333 0.00 0.00 37.33 3.06
399 5494 5.508200 TTTCTATCGCTTTTGTTGGTGTT 57.492 34.783 0.00 0.00 0.00 3.32
451 5547 9.613428 TTAATGTCCTCTCAAATTCGTTCATAT 57.387 29.630 0.00 0.00 0.00 1.78
452 5548 8.879759 GTTAATGTCCTCTCAAATTCGTTCATA 58.120 33.333 0.00 0.00 0.00 2.15
453 5549 7.148239 GGTTAATGTCCTCTCAAATTCGTTCAT 60.148 37.037 0.00 0.00 0.00 2.57
454 5550 6.148811 GGTTAATGTCCTCTCAAATTCGTTCA 59.851 38.462 0.00 0.00 0.00 3.18
484 5580 1.276989 GGTGTATCCGACCTTGTGGAA 59.723 52.381 0.00 0.00 37.90 3.53
507 5603 4.734917 AGAGCGTTTGTGTATCTACAGAC 58.265 43.478 0.00 0.00 36.78 3.51
549 5652 7.500720 TCATGATCATGCAAAGTATTACTGG 57.499 36.000 27.68 1.87 38.65 4.00
768 5955 1.811558 GCTGTGCCTCAACTGAAGTGA 60.812 52.381 0.00 0.00 0.00 3.41
786 5973 1.076632 TGTGTTCGGTTTTGGGGCT 60.077 52.632 0.00 0.00 0.00 5.19
859 6050 6.207213 GCCAATGATCAGCTCTAAAAATGAG 58.793 40.000 0.09 0.00 34.87 2.90
1054 6274 1.227147 ATATCGCCGTGGTTGTCCG 60.227 57.895 0.00 0.00 36.30 4.79
1305 6587 1.079405 TCATGTCGGAGGGAAACGC 60.079 57.895 0.00 0.00 0.00 4.84
1359 6641 4.722700 TGCTCGCTTCTTGGGCCC 62.723 66.667 17.59 17.59 0.00 5.80
1642 6924 4.927782 AGTGGCGCCGTTTGAGCA 62.928 61.111 23.90 0.00 0.00 4.26
1708 6990 0.826715 CTTCTTCCTCATCCTCGCCA 59.173 55.000 0.00 0.00 0.00 5.69
1727 7009 1.442526 CCTGCATGGCCATCGTCTTC 61.443 60.000 17.61 1.56 0.00 2.87
1874 7157 1.148310 CACACAAGTACGCTTCCCAG 58.852 55.000 0.00 0.00 31.49 4.45
2148 8871 2.859526 TGTTGCAATTCGCTTTGACA 57.140 40.000 0.59 0.00 43.06 3.58
2598 9551 2.161855 TGTTGCATCCAATCACTGACC 58.838 47.619 0.00 0.00 32.75 4.02
2711 9738 5.493809 ACATGAATGATCACTGACATGTCA 58.506 37.500 26.33 26.33 42.59 3.58
2718 9745 7.748691 TTTCTTCAACATGAATGATCACTGA 57.251 32.000 0.00 0.00 38.69 3.41
2737 9764 4.010349 CGAGGCCTCCTTGTAATTTTCTT 58.990 43.478 27.20 0.00 31.76 2.52
2738 9765 3.009143 ACGAGGCCTCCTTGTAATTTTCT 59.991 43.478 27.20 0.00 45.65 2.52
2739 9766 3.344515 ACGAGGCCTCCTTGTAATTTTC 58.655 45.455 27.20 0.00 45.65 2.29
2781 9809 2.075426 ATCGGATGATGCGAGTGCGA 62.075 55.000 15.33 0.00 44.87 5.10
2798 9839 2.017049 ACAAGGCATGCGGTAGAAATC 58.983 47.619 12.44 0.00 0.00 2.17
2824 9868 3.824151 TCGATTTTGTACACGATGACGA 58.176 40.909 0.00 0.06 42.66 4.20
2825 9869 3.606777 ACTCGATTTTGTACACGATGACG 59.393 43.478 6.74 4.01 45.75 4.35
2826 9870 6.074994 GGATACTCGATTTTGTACACGATGAC 60.075 42.308 6.74 1.19 34.41 3.06
2835 9879 4.814234 GGCACATGGATACTCGATTTTGTA 59.186 41.667 0.00 0.00 37.61 2.41
2979 10024 0.815615 GCCCCGTTTGATCTAGCCTG 60.816 60.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.