Multiple sequence alignment - TraesCS1B01G052000

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 TraesCS1B01G052000 chr1B 100.000 2342 0 0 1 2342 32130530 32128189 0.000000e+00 4325.0
1 TraesCS1B01G052000 chr1B 92.633 2362 130 12 1 2342 32196845 32194508 0.000000e+00 3358.0
2 TraesCS1B01G052000 chr1B 91.313 2383 132 22 2 2342 32072653 32070304 0.000000e+00 3184.0
3 TraesCS1B01G052000 chr1B 91.217 649 43 5 1705 2342 32143131 32142486 0.000000e+00 870.0
4 TraesCS1B01G052000 chr1B 73.036 1591 356 49 165 1706 11564225 11562659 5.810000e-136 494.0
5 TraesCS1B01G052000 chr1B 83.186 565 70 10 1 542 490431597 490432159 5.810000e-136 494.0
6 TraesCS1B01G052000 chr1B 73.755 1345 297 36 93 1397 419406398 419405070 5.860000e-131 477.0
7 TraesCS1B01G052000 chr1B 92.273 220 15 2 2124 2342 31965532 31965314 6.280000e-81 311.0
8 TraesCS1B01G052000 chr1B 92.308 39 3 0 1939 1977 599316537 599316575 3.250000e-04 56.5
9 TraesCS1B01G052000 chr1B 96.875 32 1 0 1946 1977 32077675 32077644 1.000000e-03 54.7
10 TraesCS1B01G052000 chr1D 91.361 1528 88 19 1 1508 19943332 19941829 0.000000e+00 2050.0
11 TraesCS1B01G052000 chr1D 91.647 850 51 5 1506 2342 19930762 19929920 0.000000e+00 1158.0
12 TraesCS1B01G052000 chr1D 88.571 70 7 1 1637 1705 451954704 451954635 1.490000e-12 84.2
13 TraesCS1B01G052000 chr1D 100.000 31 0 0 207 237 416697967 416697937 9.040000e-05 58.4
14 TraesCS1B01G052000 chr1D 92.308 39 3 0 1939 1977 441289380 441289418 3.250000e-04 56.5
15 TraesCS1B01G052000 chr3D 85.447 907 115 9 814 1705 48839673 48840577 0.000000e+00 928.0
16 TraesCS1B01G052000 chr3D 76.212 1753 341 56 1 1705 103806236 103807960 0.000000e+00 857.0
17 TraesCS1B01G052000 chr7A 75.787 1747 356 45 3 1705 552526919 552528642 0.000000e+00 821.0
18 TraesCS1B01G052000 chr7A 73.246 1753 394 56 3 1705 672261426 672259699 9.390000e-159 569.0
19 TraesCS1B01G052000 chr7B 75.154 1626 337 44 3 1577 15266710 15268319 0.000000e+00 702.0
20 TraesCS1B01G052000 chr4A 74.472 1751 377 52 1 1705 565327301 565325575 0.000000e+00 693.0
21 TraesCS1B01G052000 chr4A 74.728 1377 302 34 3 1346 7992723 7991360 7.260000e-160 573.0
22 TraesCS1B01G052000 chr4A 72.129 1733 398 68 27 1705 737734837 737736538 1.650000e-121 446.0
23 TraesCS1B01G052000 chr5D 74.164 1734 359 60 28 1705 559223169 559224869 2.540000e-179 638.0
24 TraesCS1B01G052000 chr3A 72.758 1762 391 68 3 1705 584369264 584370995 1.610000e-141 512.0
25 TraesCS1B01G052000 chr4B 80.315 254 39 10 1463 1706 642440469 642440721 5.140000e-42 182.0
26 TraesCS1B01G052000 chr4B 82.738 168 28 1 33 200 649147810 649147644 5.210000e-32 148.0
27 TraesCS1B01G052000 chr5A 72.610 544 100 39 1206 1705 14493110 14492572 1.460000e-27 134.0
28 TraesCS1B01G052000 chr3B 74.525 263 46 16 1464 1705 658484813 658485075 6.890000e-16 95.3
29 TraesCS1B01G052000 chr2A 94.545 55 3 0 1651 1705 30196695 30196749 4.150000e-13 86.1
30 TraesCS1B01G052000 chr2A 86.441 59 6 2 395 453 650491166 650491222 1.940000e-06 63.9
31 TraesCS1B01G052000 chr2B 92.982 57 4 0 1649 1705 793314671 793314615 1.490000e-12 84.2
32 TraesCS1B01G052000 chr1A 91.304 46 4 0 1941 1986 22362229 22362274 1.940000e-06 63.9
33 TraesCS1B01G052000 chr4D 100.000 32 0 0 1946 1977 73256124 73256155 2.510000e-05 60.2
34 TraesCS1B01G052000 chr7D 85.185 54 7 1 400 453 577855274 577855222 1.000000e-03 54.7


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 TraesCS1B01G052000 chr1B 32128189 32130530 2341 True 4325 4325 100.000 1 2342 1 chr1B.!!$R5 2341
1 TraesCS1B01G052000 chr1B 32194508 32196845 2337 True 3358 3358 92.633 1 2342 1 chr1B.!!$R7 2341
2 TraesCS1B01G052000 chr1B 32070304 32072653 2349 True 3184 3184 91.313 2 2342 1 chr1B.!!$R3 2340
3 TraesCS1B01G052000 chr1B 32142486 32143131 645 True 870 870 91.217 1705 2342 1 chr1B.!!$R6 637
4 TraesCS1B01G052000 chr1B 11562659 11564225 1566 True 494 494 73.036 165 1706 1 chr1B.!!$R1 1541
5 TraesCS1B01G052000 chr1B 490431597 490432159 562 False 494 494 83.186 1 542 1 chr1B.!!$F1 541
6 TraesCS1B01G052000 chr1B 419405070 419406398 1328 True 477 477 73.755 93 1397 1 chr1B.!!$R8 1304
7 TraesCS1B01G052000 chr1D 19941829 19943332 1503 True 2050 2050 91.361 1 1508 1 chr1D.!!$R2 1507
8 TraesCS1B01G052000 chr1D 19929920 19930762 842 True 1158 1158 91.647 1506 2342 1 chr1D.!!$R1 836
9 TraesCS1B01G052000 chr3D 48839673 48840577 904 False 928 928 85.447 814 1705 1 chr3D.!!$F1 891
10 TraesCS1B01G052000 chr3D 103806236 103807960 1724 False 857 857 76.212 1 1705 1 chr3D.!!$F2 1704
11 TraesCS1B01G052000 chr7A 552526919 552528642 1723 False 821 821 75.787 3 1705 1 chr7A.!!$F1 1702
12 TraesCS1B01G052000 chr7A 672259699 672261426 1727 True 569 569 73.246 3 1705 1 chr7A.!!$R1 1702
13 TraesCS1B01G052000 chr7B 15266710 15268319 1609 False 702 702 75.154 3 1577 1 chr7B.!!$F1 1574
14 TraesCS1B01G052000 chr4A 565325575 565327301 1726 True 693 693 74.472 1 1705 1 chr4A.!!$R2 1704
15 TraesCS1B01G052000 chr4A 7991360 7992723 1363 True 573 573 74.728 3 1346 1 chr4A.!!$R1 1343
16 TraesCS1B01G052000 chr4A 737734837 737736538 1701 False 446 446 72.129 27 1705 1 chr4A.!!$F1 1678
17 TraesCS1B01G052000 chr5D 559223169 559224869 1700 False 638 638 74.164 28 1705 1 chr5D.!!$F1 1677
18 TraesCS1B01G052000 chr3A 584369264 584370995 1731 False 512 512 72.758 3 1705 1 chr3A.!!$F1 1702

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
72 74 0.261991 TCTTCCGGGGCTAGACTCAT 59.738 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1378 1431 0.111061 TGTCCAGCAGGCATCAAACT 59.889 50.0 0.0 0.0 33.74 2.66 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
72 74 0.261991 TCTTCCGGGGCTAGACTCAT 59.738 55.000 0.00 0.00 0.00 2.90
119 121 7.683578 TGGGATTCCATCTTATCTTATGTCAG 58.316 38.462 4.80 0.00 38.32 3.51
237 245 0.331616 AAATGGGCTAGGGTGTGTCC 59.668 55.000 0.00 0.00 0.00 4.02
254 262 4.120589 GTGTCCATCTAAAAGGATCGGTC 58.879 47.826 0.00 0.00 36.11 4.79
344 357 2.592102 AGTGATGGATTGTGGCAACT 57.408 45.000 0.00 0.00 37.61 3.16
358 371 0.451783 GCAACTTATTGTCCGGGCTG 59.548 55.000 7.97 0.00 38.17 4.85
653 685 2.698855 AGTGGAATTGGATGGTCTCG 57.301 50.000 0.00 0.00 0.00 4.04
700 733 1.070758 TCTCCAGACACAGTTTCCTGC 59.929 52.381 0.00 0.00 42.81 4.85
716 755 8.204836 CAGTTTCCTGCATACTTAATAGTAGGT 58.795 37.037 0.00 0.00 40.04 3.08
754 793 3.511934 AGTCTGTCTATGAGTGGTTGGAC 59.488 47.826 0.00 0.00 0.00 4.02
767 806 4.163458 AGTGGTTGGACAGAAGTTTGTCTA 59.837 41.667 13.98 8.34 45.32 2.59
804 843 3.181423 TGGGTTTGGAAAGCTACAATCCT 60.181 43.478 17.94 0.00 36.90 3.24
846 885 2.892373 TTGCAGCTATTTCGAAACGG 57.108 45.000 13.81 9.92 0.00 4.44
851 890 2.734606 CAGCTATTTCGAAACGGTGTGA 59.265 45.455 22.84 0.00 0.00 3.58
858 897 0.785378 CGAAACGGTGTGATTACGCA 59.215 50.000 3.41 0.00 39.07 5.24
883 922 7.226720 CAGGATAACTTACGCAATAGGAATTGT 59.773 37.037 0.57 0.00 43.75 2.71
895 935 2.826674 GGAATTGTCCTGGGAATCCA 57.173 50.000 0.09 0.00 41.24 3.41
918 958 9.959749 TCCAATTTGTTCTTTTTGTATGAGTAC 57.040 29.630 0.00 0.00 0.00 2.73
969 1009 0.742505 CTGTTCGCCCGTATGGTCTA 59.257 55.000 0.00 0.00 36.04 2.59
1040 1084 1.545651 GGCAAAGCTGGTCTGGTTACT 60.546 52.381 0.00 0.00 0.00 2.24
1156 1200 2.795175 ATATGTTGCTCGTACTCCGG 57.205 50.000 0.00 0.00 37.11 5.14
1226 1270 4.537135 TGCTTAAGGAAGACGACAAGAT 57.463 40.909 4.29 0.00 34.25 2.40
1236 1280 4.543590 AGACGACAAGATGAAGTTCCAT 57.456 40.909 0.00 0.00 0.00 3.41
1342 1386 0.962489 CGGGATTCAGATCGGCTAGT 59.038 55.000 0.00 0.00 32.84 2.57
1371 1424 5.366768 TGCCTTATCTAGTCTAGCCATGTTT 59.633 40.000 1.60 0.00 0.00 2.83
1378 1431 2.906389 AGTCTAGCCATGTTTCACTGGA 59.094 45.455 0.00 0.00 34.24 3.86
1389 1442 2.887152 GTTTCACTGGAGTTTGATGCCT 59.113 45.455 0.00 0.00 0.00 4.75
1418 1478 6.431234 GGACAAGTCTGATGTTCTTTGGTATT 59.569 38.462 0.00 0.00 0.00 1.89
1514 1606 2.832778 CCCCATGGCGGATGATCCA 61.833 63.158 12.67 0.00 35.91 3.41
1547 1639 0.541863 CTACGGTGGGCTTCCTGATT 59.458 55.000 0.00 0.00 0.00 2.57
1588 1686 0.756294 TTTCGGTCTCCTGTTGCTCA 59.244 50.000 0.00 0.00 0.00 4.26
1640 1754 4.390297 GCTAGTGGATGACAAAGACTCAAC 59.610 45.833 0.00 0.00 0.00 3.18
1648 1762 5.592104 TGACAAAGACTCAACACAGACTA 57.408 39.130 0.00 0.00 0.00 2.59
1786 1901 8.970691 ACAAGTACTTATGATGCATTTTCAAC 57.029 30.769 8.04 0.00 0.00 3.18
1791 1906 9.490663 GTACTTATGATGCATTTTCAACAGTAC 57.509 33.333 16.97 16.97 36.53 2.73
1829 1944 9.553064 ACCTTTGCATTGAATTAACATTTACAA 57.447 25.926 0.00 0.00 0.00 2.41
1901 2028 4.604156 TCTTCCAGTCTCTTCTCATAGCA 58.396 43.478 0.00 0.00 0.00 3.49
1974 2101 5.233083 TGAGAGGAATCAGAAACACATGT 57.767 39.130 0.00 0.00 0.00 3.21
2046 2173 5.490159 TGTCTGCAACATCAATCATGACTA 58.510 37.500 0.00 0.00 38.69 2.59
2047 2174 6.117488 TGTCTGCAACATCAATCATGACTAT 58.883 36.000 0.00 0.00 38.69 2.12
2159 2286 4.566004 TGTGTAAGATAGTCCAACAGTGC 58.434 43.478 0.00 0.00 0.00 4.40
2252 2379 3.000122 CCAGCAACAACGACACAAATTTG 60.000 43.478 16.67 16.67 0.00 2.32
2325 2456 8.731275 TGATGTATTGTACTGGAACTATTTGG 57.269 34.615 0.00 0.00 0.00 3.28
2329 2460 8.788806 TGTATTGTACTGGAACTATTTGGTTTG 58.211 33.333 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 16 4.957954 TCCAGGCATCAAAGCTTTATGATT 59.042 37.500 22.23 12.20 34.12 2.57
20 22 3.119029 GCAATCCAGGCATCAAAGCTTTA 60.119 43.478 12.25 1.10 34.17 1.85
72 74 3.156293 TCAAGGCTAGAATGCAAAAGCA 58.844 40.909 12.93 0.00 36.68 3.91
80 82 4.077822 GGAATCCCATCAAGGCTAGAATG 58.922 47.826 0.00 0.00 35.39 2.67
143 145 8.066595 CCTACGATGCTTATTCATTTTCTCAAG 58.933 37.037 0.00 0.00 0.00 3.02
237 245 2.135933 GCCGACCGATCCTTTTAGATG 58.864 52.381 0.00 0.00 0.00 2.90
254 262 1.072159 GATCCTTGATCCCCAGCCG 59.928 63.158 0.00 0.00 33.37 5.52
754 793 2.859165 TGGGGCTAGACAAACTTCTG 57.141 50.000 0.00 0.00 0.00 3.02
828 867 1.463056 CACCGTTTCGAAATAGCTGCA 59.537 47.619 14.69 0.00 0.00 4.41
846 885 5.051907 CGTAAGTTATCCTGCGTAATCACAC 60.052 44.000 0.00 0.00 0.00 3.82
851 890 4.049546 TGCGTAAGTTATCCTGCGTAAT 57.950 40.909 0.00 0.00 41.68 1.89
858 897 7.280356 ACAATTCCTATTGCGTAAGTTATCCT 58.720 34.615 0.00 0.00 44.05 3.24
883 922 4.402616 AGAACAAATTGGATTCCCAGGA 57.597 40.909 0.00 0.00 44.60 3.86
886 926 6.657875 ACAAAAAGAACAAATTGGATTCCCA 58.342 32.000 0.00 0.00 41.64 4.37
895 935 8.842280 TCCGTACTCATACAAAAAGAACAAATT 58.158 29.630 0.00 0.00 0.00 1.82
918 958 3.032017 ACAAGTGATTCACAGTCTCCG 57.968 47.619 18.57 2.00 36.74 4.63
969 1009 4.342086 TTACCCCGAGCACCCCCT 62.342 66.667 0.00 0.00 0.00 4.79
1156 1200 2.024414 AGCAGTGAAAACAACCTCCAC 58.976 47.619 0.00 0.00 0.00 4.02
1226 1270 4.534500 TCTTTACCCTAGCATGGAACTTCA 59.466 41.667 0.00 0.00 0.00 3.02
1236 1280 1.280998 GCCAACCTCTTTACCCTAGCA 59.719 52.381 0.00 0.00 0.00 3.49
1342 1386 5.188948 TGGCTAGACTAGATAAGGCAACAAA 59.811 40.000 13.91 0.00 41.01 2.83
1371 1424 1.883638 GCAGGCATCAAACTCCAGTGA 60.884 52.381 0.00 0.00 0.00 3.41
1378 1431 0.111061 TGTCCAGCAGGCATCAAACT 59.889 50.000 0.00 0.00 33.74 2.66
1389 1442 2.369860 AGAACATCAGACTTGTCCAGCA 59.630 45.455 0.00 0.00 0.00 4.41
1588 1686 9.533831 AGAACCAGACCAAAATAAAACATCTAT 57.466 29.630 0.00 0.00 0.00 1.98
1708 1823 8.923683 GGGAGAATTTACTAATATTACAGACGC 58.076 37.037 0.00 0.00 0.00 5.19
1766 1881 9.225436 TGTACTGTTGAAAATGCATCATAAGTA 57.775 29.630 0.00 3.66 30.25 2.24
1786 1901 1.556911 AGGTTCCTGCTCCATGTACTG 59.443 52.381 0.00 0.00 0.00 2.74
1791 1906 0.529378 GCAAAGGTTCCTGCTCCATG 59.471 55.000 0.00 0.00 35.62 3.66
1829 1944 4.097741 TGCTTTTGAGTAAGTGTTGCATGT 59.902 37.500 0.00 0.00 0.00 3.21
1901 2028 7.520451 TCGTAGCTATTGTACTATGTGGAAT 57.480 36.000 0.00 0.00 0.00 3.01
1974 2101 3.276091 CGGTCACAACAGCCGCAA 61.276 61.111 0.00 0.00 38.99 4.85
2046 2173 7.680310 AGCATATAGTTGTACCCTGATCCTTAT 59.320 37.037 0.00 0.00 0.00 1.73
2047 2174 7.016914 AGCATATAGTTGTACCCTGATCCTTA 58.983 38.462 0.00 0.00 0.00 2.69
2159 2286 5.462068 TGTCAACTCACAAATACTTCTCGTG 59.538 40.000 0.00 0.00 0.00 4.35
2281 2412 3.826524 TCAATACAAACCAAGCCACTCA 58.173 40.909 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.