Multiple sequence alignment - TraesCS3A01G205400

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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 TraesCS3A01G205400 chr3A 100.000 2929 0 0 1 2929 361577675 361574747 0.000000e+00 5409.0
1 TraesCS3A01G205400 chr3A 94.723 379 16 4 2551 2929 171064946 171065320 1.170000e-163 586.0
2 TraesCS3A01G205400 chr6A 97.159 2534 70 2 1 2533 197862035 197859503 0.000000e+00 4279.0
3 TraesCS3A01G205400 chr6A 94.681 376 14 4 2554 2929 200741076 200740707 1.960000e-161 579.0
4 TraesCS3A01G205400 chr6A 85.680 412 48 6 338 738 563261669 563262080 9.700000e-115 424.0
5 TraesCS3A01G205400 chr6A 86.139 202 27 1 114 315 563710949 563711149 1.770000e-52 217.0
6 TraesCS3A01G205400 chr2A 97.092 2132 60 2 1 2131 381733127 381730997 0.000000e+00 3592.0
7 TraesCS3A01G205400 chr7D 97.451 1726 36 2 811 2535 311619009 311620727 0.000000e+00 2937.0
8 TraesCS3A01G205400 chr5B 97.616 1678 39 1 811 2487 209633853 209632176 0.000000e+00 2876.0
9 TraesCS3A01G205400 chr5B 94.972 358 17 1 2536 2893 277766198 277766554 7.090000e-156 560.0
10 TraesCS3A01G205400 chr3B 96.582 1726 58 1 811 2535 371039708 371037983 0.000000e+00 2859.0
11 TraesCS3A01G205400 chr3B 93.734 399 19 4 2536 2929 279756656 279757053 6.990000e-166 593.0
12 TraesCS3A01G205400 chr3B 89.275 345 28 6 1 336 380277824 380277480 9.700000e-115 424.0
13 TraesCS3A01G205400 chr3B 82.186 247 3 3 2289 2535 279756340 279756545 1.080000e-39 174.0
14 TraesCS3A01G205400 chr3B 98.113 53 1 0 2483 2535 406614557 406614609 3.110000e-15 93.5
15 TraesCS3A01G205400 chr3B 94.340 53 3 0 2483 2535 406613919 406613971 6.730000e-12 82.4
16 TraesCS3A01G205400 chr3B 100.000 40 0 0 2890 2929 406616951 406616990 1.130000e-09 75.0
17 TraesCS3A01G205400 chr4D 98.155 1626 29 1 903 2527 366045591 366047216 0.000000e+00 2835.0
18 TraesCS3A01G205400 chr4D 98.613 865 12 0 1 865 366044721 366045585 0.000000e+00 1531.0
19 TraesCS3A01G205400 chr4B 96.294 1727 57 5 811 2535 175308781 175307060 0.000000e+00 2828.0
20 TraesCS3A01G205400 chr4B 94.693 358 18 1 2536 2893 338503079 338502723 3.300000e-154 555.0
21 TraesCS3A01G205400 chr4B 98.113 53 1 0 2877 2929 338502713 338502661 3.110000e-15 93.5
22 TraesCS3A01G205400 chr5D 96.791 1683 47 6 811 2487 199084304 199085985 0.000000e+00 2802.0
23 TraesCS3A01G205400 chr5A 96.492 1682 54 5 811 2487 216692026 216693707 0.000000e+00 2774.0
24 TraesCS3A01G205400 chr7A 95.039 383 13 3 2551 2929 541776857 541777237 5.400000e-167 597.0
25 TraesCS3A01G205400 chr7A 95.225 377 11 4 2554 2929 430765921 430765551 9.040000e-165 590.0
26 TraesCS3A01G205400 chr4A 95.479 376 13 3 2554 2929 46503228 46502857 5.400000e-167 597.0
27 TraesCS3A01G205400 chr7B 93.593 359 21 2 2536 2893 195987792 195987435 4.300000e-148 534.0
28 TraesCS3A01G205400 chr1B 88.921 343 31 4 1 336 514931842 514932184 1.620000e-112 416.0
29 TraesCS3A01G205400 chr6D 87.342 237 26 4 114 347 420748599 420748834 4.810000e-68 268.0
30 TraesCS3A01G205400 chr6B 87.234 235 28 2 114 347 633915710 633915943 1.730000e-67 267.0
31 TraesCS3A01G205400 chr2B 100.000 40 0 0 2890 2929 303215062 303215023 1.130000e-09 75.0


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 TraesCS3A01G205400 chr3A 361574747 361577675 2928 True 5409.0 5409 100.000 1 2929 1 chr3A.!!$R1 2928
1 TraesCS3A01G205400 chr6A 197859503 197862035 2532 True 4279.0 4279 97.159 1 2533 1 chr6A.!!$R1 2532
2 TraesCS3A01G205400 chr2A 381730997 381733127 2130 True 3592.0 3592 97.092 1 2131 1 chr2A.!!$R1 2130
3 TraesCS3A01G205400 chr7D 311619009 311620727 1718 False 2937.0 2937 97.451 811 2535 1 chr7D.!!$F1 1724
4 TraesCS3A01G205400 chr5B 209632176 209633853 1677 True 2876.0 2876 97.616 811 2487 1 chr5B.!!$R1 1676
5 TraesCS3A01G205400 chr3B 371037983 371039708 1725 True 2859.0 2859 96.582 811 2535 1 chr3B.!!$R1 1724
6 TraesCS3A01G205400 chr3B 279756340 279757053 713 False 383.5 593 87.960 2289 2929 2 chr3B.!!$F1 640
7 TraesCS3A01G205400 chr4D 366044721 366047216 2495 False 2183.0 2835 98.384 1 2527 2 chr4D.!!$F1 2526
8 TraesCS3A01G205400 chr4B 175307060 175308781 1721 True 2828.0 2828 96.294 811 2535 1 chr4B.!!$R1 1724
9 TraesCS3A01G205400 chr5D 199084304 199085985 1681 False 2802.0 2802 96.791 811 2487 1 chr5D.!!$F1 1676
10 TraesCS3A01G205400 chr5A 216692026 216693707 1681 False 2774.0 2774 96.492 811 2487 1 chr5A.!!$F1 1676

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
459 461 3.555956 CGGTCGGAAAATCAAGAGTATGG 59.444 47.826 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1981 1991 0.320946 CATGCCTTTGGTGCCTTTGG 60.321 55.0 0.0 0.0 0.0 3.28 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
32 33 7.825761 TGATGTTCATAAAGTGATGACAGATGT 59.174 33.333 0.00 0.00 35.56 3.06
256 257 6.968904 CCAAAAGATGTTATCATTCAGAACCG 59.031 38.462 0.00 0.00 34.06 4.44
283 284 7.112779 ACTTAGAATGGCACTAAGCTGTTATT 58.887 34.615 19.32 2.05 45.96 1.40
288 289 7.941238 AGAATGGCACTAAGCTGTTATTATCAT 59.059 33.333 0.00 0.00 44.79 2.45
459 461 3.555956 CGGTCGGAAAATCAAGAGTATGG 59.444 47.826 0.00 0.00 0.00 2.74
795 797 6.017933 GTCACTAGAAGCATCAATTTTCACG 58.982 40.000 0.00 0.00 0.00 4.35
1005 1010 4.160642 TGAGCAGATTGGTATGATGCTT 57.839 40.909 0.00 0.00 46.67 3.91
1138 1143 4.318332 CAAGGACACTCTTGCATTGTCTA 58.682 43.478 14.37 0.00 39.72 2.59
1485 1492 7.638444 TCTTTTGATGACCCAAATATCAGGTA 58.362 34.615 0.00 0.00 36.12 3.08
1492 1499 5.949354 TGACCCAAATATCAGGTAAGTTTGG 59.051 40.000 7.93 7.93 45.17 3.28
1586 1595 4.998671 TCTTTCACCAAATCAAACTGCA 57.001 36.364 0.00 0.00 0.00 4.41
1609 1618 1.283793 CAGTTCGCTGCCCTTGTTG 59.716 57.895 0.00 0.00 38.53 3.33
1733 1742 9.688592 CATGCTCTAAATATTTTCCCATCTTTC 57.311 33.333 5.91 0.00 0.00 2.62
1981 1991 2.113860 TATCCTCTGCCTTTGTGCAC 57.886 50.000 10.75 10.75 36.04 4.57
2106 2116 1.580994 AAACCCTCTGGCATACCCCC 61.581 60.000 0.00 0.00 33.59 5.40
2144 2154 4.892934 GGATATAATGGTCAAAAGGTGCCA 59.107 41.667 0.00 0.00 37.67 4.92
2252 2263 5.334724 AGCAATCTCCATTTGTTCAATCC 57.665 39.130 0.00 0.00 0.00 3.01
2362 2374 4.649088 AGGGCTAACAACAACAAAGAAC 57.351 40.909 0.00 0.00 0.00 3.01
2538 2660 1.529744 TTCCCCTCTTTGTGTCCCTT 58.470 50.000 0.00 0.00 0.00 3.95
2541 2663 2.158066 TCCCCTCTTTGTGTCCCTTCTA 60.158 50.000 0.00 0.00 0.00 2.10
2584 2706 6.716284 TCATGTTTGGTTTTCTTCCCTTTTT 58.284 32.000 0.00 0.00 0.00 1.94
2713 2835 4.941873 AGAGACGGTGGAATATTTTTGTCC 59.058 41.667 0.00 0.00 0.00 4.02
2718 2840 5.048294 ACGGTGGAATATTTTTGTCCTTCAC 60.048 40.000 0.00 0.00 32.28 3.18
2748 2870 1.661112 GAGCATTGCGTAGTCCTTCAC 59.339 52.381 2.38 0.00 0.00 3.18
2750 2872 2.009774 GCATTGCGTAGTCCTTCACAT 58.990 47.619 0.00 0.00 0.00 3.21
2781 2903 5.411361 TGAGCATTGCGTAAAAGTATGTCTT 59.589 36.000 2.38 0.00 38.10 3.01
2787 2909 9.607285 CATTGCGTAAAAGTATGTCTTAAGTTT 57.393 29.630 1.63 0.00 35.02 2.66
2877 2999 5.247110 TCATAATGAGAGAGGGGTATGCTTC 59.753 44.000 0.00 0.00 0.00 3.86
2893 3020 5.894298 ATGCTTCTCTCTCTCTCTCTCTA 57.106 43.478 0.00 0.00 0.00 2.43
2910 3037 7.757173 TCTCTCTCTAGAAATGTGTTTGAATCG 59.243 37.037 0.00 0.00 0.00 3.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 7.418408 TGTGTATAAACAAACGCAAATGAAGA 58.582 30.769 0.00 0.00 37.36 2.87
256 257 4.938226 ACAGCTTAGTGCCATTCTAAGTTC 59.062 41.667 12.25 0.66 43.39 3.01
283 284 4.507756 GCACTGCACTGTCGAATTATGATA 59.492 41.667 0.00 0.00 0.00 2.15
288 289 1.270571 TGGCACTGCACTGTCGAATTA 60.271 47.619 2.82 0.00 0.00 1.40
459 461 0.951558 CTTGGTACACACAGGTTGCC 59.048 55.000 0.00 0.00 39.29 4.52
795 797 5.648092 AGTATAACAGAAAATGTCAGCACCC 59.352 40.000 0.00 0.00 43.00 4.61
979 984 6.774170 AGCATCATACCAATCTGCTCAAATTA 59.226 34.615 0.00 0.00 38.78 1.40
1005 1010 1.002624 GTCAAACCCCATGCCTCGA 60.003 57.895 0.00 0.00 0.00 4.04
1138 1143 2.883386 CCTCAAACTCAGCAAGCTCTTT 59.117 45.455 0.00 0.00 0.00 2.52
1184 1189 0.905357 AACGACATCCAGCTAGGCTT 59.095 50.000 0.00 0.00 36.40 4.35
1485 1492 3.569701 CGATATAATGGCAGCCCAAACTT 59.430 43.478 9.64 0.00 46.14 2.66
1492 1499 3.138304 TGTTGACGATATAATGGCAGCC 58.862 45.455 3.66 3.66 0.00 4.85
1609 1618 3.077359 CAGTCTTGGATGGTGAAGGAAC 58.923 50.000 0.00 0.00 0.00 3.62
1733 1742 7.929785 ACCACTATATCCATTTACACGTTAAGG 59.070 37.037 0.00 0.00 0.00 2.69
1944 1954 3.944015 GGATATGCATCCCTCAGTTATGC 59.056 47.826 0.19 0.00 44.55 3.14
1981 1991 0.320946 CATGCCTTTGGTGCCTTTGG 60.321 55.000 0.00 0.00 0.00 3.28
2106 2116 6.128553 CCATTATATCCAGAATCGAACGGTTG 60.129 42.308 0.00 0.00 0.00 3.77
2252 2263 6.921857 TCTTTTCTCTTTACAACCTACAGACG 59.078 38.462 0.00 0.00 0.00 4.18
2614 2736 9.614792 AGTAGAAAAAGGATACATGGTGTTATC 57.385 33.333 0.00 0.00 41.41 1.75
2693 2815 5.182380 TGAAGGACAAAAATATTCCACCGTC 59.818 40.000 0.00 0.00 0.00 4.79
2713 2835 4.860907 GCAATGCTCATTTAACCTGTGAAG 59.139 41.667 0.00 0.00 0.00 3.02
2718 2840 3.492421 ACGCAATGCTCATTTAACCTG 57.508 42.857 2.94 0.00 0.00 4.00
2748 2870 6.867799 TTTACGCAATGCTCATTTAACATG 57.132 33.333 2.94 0.00 0.00 3.21
2750 2872 6.442952 ACTTTTACGCAATGCTCATTTAACA 58.557 32.000 2.94 0.00 0.00 2.41
2789 2911 8.465999 TCATTTACTTGAAGCACTTGAAGAAAA 58.534 29.630 15.17 7.15 36.15 2.29
2793 2915 8.807667 ATTTCATTTACTTGAAGCACTTGAAG 57.192 30.769 7.88 7.88 39.24 3.02
2877 2999 7.050377 ACACATTTCTAGAGAGAGAGAGAGAG 58.950 42.308 0.00 0.00 31.77 3.20
2893 3020 4.566545 TGTGCGATTCAAACACATTTCT 57.433 36.364 0.00 0.00 39.29 2.52


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

AutoCloner maintained by Alex Coulton.