Multiple sequence alignment - TraesCS3B01G138500

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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 TraesCS3B01G138500 chr3B 100.000 2546 0 0 1 2546 124400061 124397516 0.000000e+00 4702.0
1 TraesCS3B01G138500 chr3B 93.787 2334 128 12 1 2323 124502922 124500595 0.000000e+00 3491.0
2 TraesCS3B01G138500 chr3B 93.702 2334 131 11 1 2323 124560784 124558456 0.000000e+00 3482.0
3 TraesCS3B01G138500 chr3B 90.356 1628 141 15 586 2206 749205905 749207523 0.000000e+00 2122.0
4 TraesCS3B01G138500 chr3B 85.657 753 85 12 584 1331 707152190 707152924 0.000000e+00 771.0
5 TraesCS3B01G138500 chr3B 84.286 560 64 16 1 556 124899548 124899009 2.240000e-145 525.0
6 TraesCS3B01G138500 chr3B 87.324 355 45 0 584 938 561239010 561239364 8.480000e-110 407.0
7 TraesCS3B01G138500 chr3B 96.172 209 8 0 2321 2529 124558162 124557954 2.430000e-90 342.0
8 TraesCS3B01G138500 chr3B 96.059 203 8 0 2321 2523 124500301 124500099 5.250000e-87 331.0
9 TraesCS3B01G138500 chr3A 91.344 1733 139 10 586 2313 47284899 47286625 0.000000e+00 2359.0
10 TraesCS3B01G138500 chr3A 89.385 537 44 9 59 585 92554606 92554073 0.000000e+00 664.0
11 TraesCS3B01G138500 chr3A 89.366 536 46 7 59 585 92579515 92578982 0.000000e+00 664.0
12 TraesCS3B01G138500 chr3A 84.486 593 61 14 6 585 92739463 92738889 7.960000e-155 556.0
13 TraesCS3B01G138500 chr2D 90.623 1749 145 17 586 2323 590929802 590928062 0.000000e+00 2303.0
14 TraesCS3B01G138500 chr7B 90.319 1756 150 18 578 2323 685254382 685252637 0.000000e+00 2283.0
15 TraesCS3B01G138500 chr7B 89.135 1758 163 14 586 2323 691229727 691227978 0.000000e+00 2163.0
16 TraesCS3B01G138500 chr2B 89.426 1759 159 17 571 2323 540525717 540527454 0.000000e+00 2193.0
17 TraesCS3B01G138500 chr2B 94.059 101 5 1 486 585 44891258 44891358 4.390000e-33 152.0
18 TraesCS3B01G138500 chr5D 91.537 1477 107 12 854 2323 353835364 353833899 0.000000e+00 2019.0
19 TraesCS3B01G138500 chr5D 97.080 137 3 1 2411 2546 213963246 213963382 1.970000e-56 230.0
20 TraesCS3B01G138500 chr5D 97.080 137 3 1 2411 2546 482328202 482328066 1.970000e-56 230.0
21 TraesCS3B01G138500 chr5D 97.080 137 3 1 2411 2546 517040216 517040352 1.970000e-56 230.0
22 TraesCS3B01G138500 chr5D 97.080 137 3 1 2411 2546 559990310 559990174 1.970000e-56 230.0
23 TraesCS3B01G138500 chr3D 88.353 601 43 12 1 585 79250995 79250406 0.000000e+00 697.0
24 TraesCS3B01G138500 chr3D 87.947 531 48 11 57 585 78949146 78948630 1.670000e-171 612.0
25 TraesCS3B01G138500 chr3D 84.562 434 52 7 1 420 79303996 79303564 1.410000e-112 416.0
26 TraesCS3B01G138500 chr3D 97.101 138 2 2 2411 2546 25093896 25093759 5.480000e-57 231.0
27 TraesCS3B01G138500 chr1D 96.429 140 3 2 2408 2546 451652217 451652079 1.970000e-56 230.0
28 TraesCS3B01G138500 chr7D 95.105 143 6 1 2404 2546 623574354 623574495 9.170000e-55 224.0
29 TraesCS3B01G138500 chr6D 90.526 95 4 3 2321 2415 14244645 14244734 1.240000e-23 121.0
30 TraesCS3B01G138500 chr7A 87.143 70 8 1 375 444 661270331 661270263 7.550000e-11 78.7


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 TraesCS3B01G138500 chr3B 124397516 124400061 2545 True 4702 4702 100.000 1 2546 1 chr3B.!!$R1 2545
1 TraesCS3B01G138500 chr3B 749205905 749207523 1618 False 2122 2122 90.356 586 2206 1 chr3B.!!$F3 1620
2 TraesCS3B01G138500 chr3B 124557954 124560784 2830 True 1912 3482 94.937 1 2529 2 chr3B.!!$R4 2528
3 TraesCS3B01G138500 chr3B 124500099 124502922 2823 True 1911 3491 94.923 1 2523 2 chr3B.!!$R3 2522
4 TraesCS3B01G138500 chr3B 707152190 707152924 734 False 771 771 85.657 584 1331 1 chr3B.!!$F2 747
5 TraesCS3B01G138500 chr3B 124899009 124899548 539 True 525 525 84.286 1 556 1 chr3B.!!$R2 555
6 TraesCS3B01G138500 chr3A 47284899 47286625 1726 False 2359 2359 91.344 586 2313 1 chr3A.!!$F1 1727
7 TraesCS3B01G138500 chr3A 92554073 92554606 533 True 664 664 89.385 59 585 1 chr3A.!!$R1 526
8 TraesCS3B01G138500 chr3A 92578982 92579515 533 True 664 664 89.366 59 585 1 chr3A.!!$R2 526
9 TraesCS3B01G138500 chr3A 92738889 92739463 574 True 556 556 84.486 6 585 1 chr3A.!!$R3 579
10 TraesCS3B01G138500 chr2D 590928062 590929802 1740 True 2303 2303 90.623 586 2323 1 chr2D.!!$R1 1737
11 TraesCS3B01G138500 chr7B 685252637 685254382 1745 True 2283 2283 90.319 578 2323 1 chr7B.!!$R1 1745
12 TraesCS3B01G138500 chr7B 691227978 691229727 1749 True 2163 2163 89.135 586 2323 1 chr7B.!!$R2 1737
13 TraesCS3B01G138500 chr2B 540525717 540527454 1737 False 2193 2193 89.426 571 2323 1 chr2B.!!$F2 1752
14 TraesCS3B01G138500 chr5D 353833899 353835364 1465 True 2019 2019 91.537 854 2323 1 chr5D.!!$R1 1469
15 TraesCS3B01G138500 chr3D 79250406 79250995 589 True 697 697 88.353 1 585 1 chr3D.!!$R3 584
16 TraesCS3B01G138500 chr3D 78948630 78949146 516 True 612 612 87.947 57 585 1 chr3D.!!$R2 528

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
123 124 0.178990 GGGGGCTAGCTAACAATGGG 60.179 60.0 15.72 0.0 0.00 4.00 F
1150 1200 0.179163 TCATCTGCTCTACGTGTGCG 60.179 55.0 0.00 0.0 44.93 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1221 1271 0.031857 CCTGCATGAACGCCAAACAA 59.968 50.0 0.00 0.0 0.0 2.83 R
2323 2407 0.612732 TGTCGTGTCCCCGGACTTAT 60.613 55.0 14.78 0.0 44.8 1.73 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
49 50 1.662517 TAATGCAATGACGCGGTGAT 58.337 45.000 12.47 0.00 33.35 3.06
69 70 9.743057 CGGTGATTTTTATTAATTATGCCTTCA 57.257 29.630 0.00 0.00 0.00 3.02
123 124 0.178990 GGGGGCTAGCTAACAATGGG 60.179 60.000 15.72 0.00 0.00 4.00
146 147 5.279708 GGGATGATAAAGGTGTCGAGATCAT 60.280 44.000 0.00 0.00 36.88 2.45
155 156 2.293122 GTGTCGAGATCATGAGAGGAGG 59.707 54.545 0.09 0.00 0.00 4.30
167 168 3.110705 TGAGAGGAGGGGAAGAAGAATG 58.889 50.000 0.00 0.00 0.00 2.67
186 187 1.340502 TGACACTGTTTTGTGGGCTGA 60.341 47.619 0.00 0.00 41.84 4.26
213 214 3.881220 TGAAAACTATGGATTCGTCCCC 58.119 45.455 0.00 0.00 0.00 4.81
246 247 4.757657 TGTACATTAGCCACGACAAATTGT 59.242 37.500 0.00 0.00 0.00 2.71
605 630 7.509236 AATTGGGTTAATTATCCTTTTGCCT 57.491 32.000 11.51 0.00 37.22 4.75
705 731 1.219646 GTTCCGTGAAAACTGCCGTA 58.780 50.000 0.00 0.00 0.00 4.02
708 734 0.368907 CCGTGAAAACTGCCGTATCG 59.631 55.000 0.00 0.00 0.00 2.92
792 819 4.578898 AGACCGTTGCACGCGTGA 62.579 61.111 41.19 23.48 40.91 4.35
804 831 2.426023 GCGTGACTTGTGGGACCT 59.574 61.111 0.00 0.00 0.00 3.85
830 872 1.004440 AGCCGTTGAACAGAGAGCC 60.004 57.895 0.00 0.00 0.00 4.70
831 873 1.301716 GCCGTTGAACAGAGAGCCA 60.302 57.895 0.00 0.00 0.00 4.75
852 894 3.830744 TTGCGGGTGTGCTATATAAGT 57.169 42.857 0.00 0.00 35.36 2.24
905 951 3.444805 GAGAGCGGGCGACAGAGT 61.445 66.667 0.00 0.00 0.00 3.24
958 1008 0.824109 CGGTGGGAAGATAGCTGTGA 59.176 55.000 0.00 0.00 0.00 3.58
968 1018 1.553690 ATAGCTGTGAAGGGTGCGGT 61.554 55.000 0.00 0.00 0.00 5.68
1023 1073 2.788191 CTTCTTCAAGCTCCCGCGGT 62.788 60.000 26.12 1.14 42.32 5.68
1150 1200 0.179163 TCATCTGCTCTACGTGTGCG 60.179 55.000 0.00 0.00 44.93 5.34
1221 1271 4.161001 GGATCTTTGAGCAATGGGTTGATT 59.839 41.667 0.00 0.00 37.53 2.57
1263 1313 5.049828 GTGAAATGTTTCTTCCTTTGGGTG 58.950 41.667 6.99 0.00 38.02 4.61
1429 1485 2.322355 TGAGCTTAGGATGCTGAAGC 57.678 50.000 15.58 15.58 44.79 3.86
1469 1525 6.732531 TGAAGATCAAGCACAAATACTCAG 57.267 37.500 0.00 0.00 0.00 3.35
1484 1540 9.463443 ACAAATACTCAGTTGCAATTACTTTTC 57.537 29.630 0.59 0.00 33.01 2.29
1500 1556 5.485662 ACTTTTCGGCATTTGTAGCTATC 57.514 39.130 0.00 0.00 0.00 2.08
1516 1572 2.030540 GCTATCGTAATCGCACTGGGTA 60.031 50.000 0.00 0.00 36.96 3.69
1537 1593 9.130661 TGGGTATAATGTTGAAATTGTATGGAG 57.869 33.333 0.00 0.00 0.00 3.86
1733 1796 1.740043 GCTCTCTGCTCTGCCTTTCTC 60.740 57.143 0.00 0.00 38.95 2.87
1826 1892 2.091166 TGCATCCAATTAGGCCCATTCT 60.091 45.455 0.00 0.00 37.29 2.40
1829 1895 2.213310 TCCAATTAGGCCCATTCTGGA 58.787 47.619 0.00 2.72 37.15 3.86
2069 2150 3.229293 TGTCATGGAAAATGTGCCTCAA 58.771 40.909 0.00 0.00 0.00 3.02
2241 2324 1.022982 GTGGCGTTTAGGGCTACACC 61.023 60.000 0.00 0.00 41.02 4.16
2272 2356 4.878971 GCTAGGGAAGATGGAAAGACTTTC 59.121 45.833 18.02 18.02 38.94 2.62
2292 2376 1.839994 CACATGGCTAGGGAAGGAAGA 59.160 52.381 0.00 0.00 0.00 2.87
2323 2407 2.960384 TGAGACCGTGACTTGGTTTAGA 59.040 45.455 0.00 0.00 40.63 2.10
2324 2408 3.576982 TGAGACCGTGACTTGGTTTAGAT 59.423 43.478 0.00 0.00 40.63 1.98
2325 2409 4.768448 TGAGACCGTGACTTGGTTTAGATA 59.232 41.667 0.00 0.00 40.63 1.98
2326 2410 5.244402 TGAGACCGTGACTTGGTTTAGATAA 59.756 40.000 0.00 0.00 40.63 1.75
2327 2411 5.721232 AGACCGTGACTTGGTTTAGATAAG 58.279 41.667 0.00 0.00 40.63 1.73
2328 2412 5.245526 AGACCGTGACTTGGTTTAGATAAGT 59.754 40.000 0.00 0.00 40.63 2.24
2329 2413 5.476614 ACCGTGACTTGGTTTAGATAAGTC 58.523 41.667 8.88 8.88 46.45 3.01
2330 2414 4.868734 CCGTGACTTGGTTTAGATAAGTCC 59.131 45.833 12.23 4.97 45.97 3.85
2331 2415 4.561606 CGTGACTTGGTTTAGATAAGTCCG 59.438 45.833 12.23 11.22 45.97 4.79
2332 2416 4.868734 GTGACTTGGTTTAGATAAGTCCGG 59.131 45.833 12.23 0.00 45.97 5.14
2343 2723 1.526575 TAAGTCCGGGGACACGACAC 61.527 60.000 19.38 0.00 46.76 3.67
2368 2748 0.523072 GACATGGCAAGCACGACATT 59.477 50.000 0.00 0.00 0.00 2.71
2457 2837 5.583932 AGGATCCAGGCTTAGTTTTTCATT 58.416 37.500 15.82 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
69 70 8.640651 TGGCATTCTATTTTGCAATACATACAT 58.359 29.630 0.00 0.00 40.66 2.29
123 124 5.201713 TGATCTCGACACCTTTATCATCC 57.798 43.478 0.00 0.00 0.00 3.51
146 147 3.110705 CATTCTTCTTCCCCTCCTCTCA 58.889 50.000 0.00 0.00 0.00 3.27
155 156 5.067805 ACAAAACAGTGTCATTCTTCTTCCC 59.932 40.000 0.00 0.00 0.00 3.97
167 168 1.065551 GTCAGCCCACAAAACAGTGTC 59.934 52.381 0.00 0.00 37.82 3.67
186 187 5.175859 ACGAATCCATAGTTTTCATGTCGT 58.824 37.500 0.00 0.00 31.65 4.34
213 214 5.851177 CGTGGCTAATGTACACTTTTCTTTG 59.149 40.000 0.00 0.00 33.13 2.77
246 247 5.012664 AGTCCAATCACACCAGTAACATACA 59.987 40.000 0.00 0.00 0.00 2.29
556 581 8.883954 TTTTTCTGACATGCATGAACATTTTA 57.116 26.923 32.75 13.67 0.00 1.52
605 630 3.820467 CTGAGCAAATGGACACCACTAAA 59.180 43.478 0.00 0.00 35.80 1.85
792 819 2.039084 CTCTTTGCTAGGTCCCACAAGT 59.961 50.000 0.00 0.00 0.00 3.16
804 831 2.143122 CTGTTCAACGGCTCTTTGCTA 58.857 47.619 0.00 0.00 42.39 3.49
821 863 2.270205 CCCGCAATGGCTCTCTGT 59.730 61.111 0.00 0.00 38.10 3.41
830 872 4.065088 ACTTATATAGCACACCCGCAATG 58.935 43.478 0.00 0.00 0.00 2.82
831 873 4.065088 CACTTATATAGCACACCCGCAAT 58.935 43.478 0.00 0.00 0.00 3.56
869 911 2.031919 GTGTCGCCATGGTCACCA 59.968 61.111 14.67 0.00 38.19 4.17
905 951 2.356913 CATGGTCACCGTCGTGCA 60.357 61.111 0.00 0.00 40.04 4.57
968 1018 1.515954 GAAGGGGATCTCAACGCGA 59.484 57.895 15.93 0.00 0.00 5.87
1092 1142 1.974957 TGAGAAACCCTCCGATCAACA 59.025 47.619 0.00 0.00 41.25 3.33
1138 1188 2.523184 TTCTCGCCGCACACGTAGAG 62.523 60.000 0.00 0.00 40.23 2.43
1150 1200 2.495084 GATTCTTACCCCATTCTCGCC 58.505 52.381 0.00 0.00 0.00 5.54
1221 1271 0.031857 CCTGCATGAACGCCAAACAA 59.968 50.000 0.00 0.00 0.00 2.83
1263 1313 0.463474 GAGTCTTGGCCAGAGCATCC 60.463 60.000 5.11 0.00 42.56 3.51
1429 1485 4.899502 TCTTCAAGCTTCCTAACCTTCTG 58.100 43.478 0.00 0.00 0.00 3.02
1469 1525 5.050431 ACAAATGCCGAAAAGTAATTGCAAC 60.050 36.000 0.00 0.00 31.81 4.17
1484 1540 4.201494 CGATTACGATAGCTACAAATGCCG 60.201 45.833 0.00 0.00 42.66 5.69
1500 1556 4.304110 ACATTATACCCAGTGCGATTACG 58.696 43.478 0.00 0.00 42.93 3.18
1516 1572 7.560991 TGCCTCTCCATACAATTTCAACATTAT 59.439 33.333 0.00 0.00 0.00 1.28
1552 1608 6.458210 ACAATTTCAGGCTTACAAATTCCTG 58.542 36.000 2.84 2.84 45.59 3.86
1826 1892 1.918262 AGATCTCATTTGCCCACTCCA 59.082 47.619 0.00 0.00 0.00 3.86
1829 1895 3.618351 CAAGAGATCTCATTTGCCCACT 58.382 45.455 24.39 0.00 0.00 4.00
2069 2150 3.323979 CAGGTGTAAACCTCTACCACAGT 59.676 47.826 0.00 0.00 38.22 3.55
2272 2356 1.839994 TCTTCCTTCCCTAGCCATGTG 59.160 52.381 0.00 0.00 0.00 3.21
2292 2376 6.016192 CCAAGTCACGGTCTCACTATGTATAT 60.016 42.308 0.00 0.00 0.00 0.86
2323 2407 0.612732 TGTCGTGTCCCCGGACTTAT 60.613 55.000 14.78 0.00 44.80 1.73
2324 2408 1.228521 TGTCGTGTCCCCGGACTTA 60.229 57.895 14.78 0.00 44.80 2.24
2325 2409 2.522436 TGTCGTGTCCCCGGACTT 60.522 61.111 14.78 0.00 44.80 3.01
2326 2410 3.300765 GTGTCGTGTCCCCGGACT 61.301 66.667 14.78 0.00 44.80 3.85
2327 2411 4.712425 CGTGTCGTGTCCCCGGAC 62.712 72.222 0.73 6.95 44.77 4.79
2328 2412 4.953010 TCGTGTCGTGTCCCCGGA 62.953 66.667 0.73 0.00 0.00 5.14
2329 2413 4.712425 GTCGTGTCGTGTCCCCGG 62.712 72.222 0.00 0.00 0.00 5.73
2330 2414 3.968568 TGTCGTGTCGTGTCCCCG 61.969 66.667 0.00 0.00 0.00 5.73
2331 2415 2.355481 GTGTCGTGTCGTGTCCCC 60.355 66.667 0.00 0.00 0.00 4.81
2332 2416 2.728383 CGTGTCGTGTCGTGTCCC 60.728 66.667 0.00 0.00 0.00 4.46
2343 2723 2.316867 TGCTTGCCATGTCGTGTCG 61.317 57.895 0.00 0.00 0.00 4.35


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

AutoCloner maintained by Alex Coulton.