Multiple sequence alignment - TraesCS5A01G043900

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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 TraesCS5A01G043900 chr5A 100.000 2890 0 0 1 2890 40241882 40238993 0.000000e+00 5337.0
1 TraesCS5A01G043900 chr5A 94.980 2709 92 9 88 2789 562123425 562120754 0.000000e+00 4209.0
2 TraesCS5A01G043900 chr5A 92.035 2938 164 25 1 2889 310017619 310020535 0.000000e+00 4065.0
3 TraesCS5A01G043900 chr5A 95.340 515 19 1 88 602 687969173 687969682 0.000000e+00 813.0
4 TraesCS5A01G043900 chr5A 100.000 30 0 0 88 117 562123839 562123810 4.020000e-04 56.5
5 TraesCS5A01G043900 chr5A 100.000 30 0 0 88 117 687968033 687968062 4.020000e-04 56.5
6 TraesCS5A01G043900 chr5D 95.829 2901 95 10 1 2889 437728851 437725965 0.000000e+00 4663.0
7 TraesCS5A01G043900 chr5D 94.439 2913 104 20 1 2889 92293479 92296357 0.000000e+00 4429.0
8 TraesCS5A01G043900 chr5D 95.468 2317 84 11 579 2889 51585545 51583244 0.000000e+00 3677.0
9 TraesCS5A01G043900 chr7D 94.553 2919 113 11 1 2889 107242425 107239523 0.000000e+00 4468.0
10 TraesCS5A01G043900 chr7D 94.907 805 28 4 2086 2889 509204131 509203339 0.000000e+00 1247.0
11 TraesCS5A01G043900 chr1A 93.992 2713 118 9 88 2789 16224556 16227234 0.000000e+00 4065.0
12 TraesCS5A01G043900 chr1D 95.006 2323 93 10 579 2889 152626277 152628588 0.000000e+00 3626.0
13 TraesCS5A01G043900 chr1D 92.264 530 19 7 2361 2889 152482806 152483314 0.000000e+00 732.0
14 TraesCS5A01G043900 chr6A 94.382 2314 93 13 579 2889 577152222 577154501 0.000000e+00 3518.0
15 TraesCS5A01G043900 chr6A 94.580 2214 79 9 577 2789 553572475 553570302 0.000000e+00 3386.0
16 TraesCS5A01G043900 chr7A 94.249 2278 85 9 522 2789 49821366 49823607 0.000000e+00 3439.0
17 TraesCS5A01G043900 chr7A 89.333 300 26 5 73 367 575560868 575561166 3.520000e-99 372.0
18 TraesCS5A01G043900 chr4B 93.257 2106 79 20 803 2889 244519825 244521886 0.000000e+00 3044.0
19 TraesCS5A01G043900 chr2D 94.507 1966 81 14 1 1946 104542263 104540305 0.000000e+00 3007.0
20 TraesCS5A01G043900 chr2B 92.066 1626 52 9 1267 2889 152882418 152880867 0.000000e+00 2217.0
21 TraesCS5A01G043900 chr4A 96.154 416 16 0 1 416 588879439 588879854 0.000000e+00 680.0
22 TraesCS5A01G043900 chr4A 92.977 299 18 2 167 462 699841620 699841918 1.590000e-117 433.0


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 TraesCS5A01G043900 chr5A 40238993 40241882 2889 True 5337.00 5337 100.000 1 2890 1 chr5A.!!$R1 2889
1 TraesCS5A01G043900 chr5A 310017619 310020535 2916 False 4065.00 4065 92.035 1 2889 1 chr5A.!!$F1 2888
2 TraesCS5A01G043900 chr5A 562120754 562123839 3085 True 2132.75 4209 97.490 88 2789 2 chr5A.!!$R2 2701
3 TraesCS5A01G043900 chr5A 687968033 687969682 1649 False 434.75 813 97.670 88 602 2 chr5A.!!$F2 514
4 TraesCS5A01G043900 chr5D 437725965 437728851 2886 True 4663.00 4663 95.829 1 2889 1 chr5D.!!$R2 2888
5 TraesCS5A01G043900 chr5D 92293479 92296357 2878 False 4429.00 4429 94.439 1 2889 1 chr5D.!!$F1 2888
6 TraesCS5A01G043900 chr5D 51583244 51585545 2301 True 3677.00 3677 95.468 579 2889 1 chr5D.!!$R1 2310
7 TraesCS5A01G043900 chr7D 107239523 107242425 2902 True 4468.00 4468 94.553 1 2889 1 chr7D.!!$R1 2888
8 TraesCS5A01G043900 chr7D 509203339 509204131 792 True 1247.00 1247 94.907 2086 2889 1 chr7D.!!$R2 803
9 TraesCS5A01G043900 chr1A 16224556 16227234 2678 False 4065.00 4065 93.992 88 2789 1 chr1A.!!$F1 2701
10 TraesCS5A01G043900 chr1D 152626277 152628588 2311 False 3626.00 3626 95.006 579 2889 1 chr1D.!!$F2 2310
11 TraesCS5A01G043900 chr1D 152482806 152483314 508 False 732.00 732 92.264 2361 2889 1 chr1D.!!$F1 528
12 TraesCS5A01G043900 chr6A 577152222 577154501 2279 False 3518.00 3518 94.382 579 2889 1 chr6A.!!$F1 2310
13 TraesCS5A01G043900 chr6A 553570302 553572475 2173 True 3386.00 3386 94.580 577 2789 1 chr6A.!!$R1 2212
14 TraesCS5A01G043900 chr7A 49821366 49823607 2241 False 3439.00 3439 94.249 522 2789 1 chr7A.!!$F1 2267
15 TraesCS5A01G043900 chr4B 244519825 244521886 2061 False 3044.00 3044 93.257 803 2889 1 chr4B.!!$F1 2086
16 TraesCS5A01G043900 chr2D 104540305 104542263 1958 True 3007.00 3007 94.507 1 1946 1 chr2D.!!$R1 1945
17 TraesCS5A01G043900 chr2B 152880867 152882418 1551 True 2217.00 2217 92.066 1267 2889 1 chr2B.!!$R1 1622

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
401 1458 0.250597 AACTCTGCATGCTGCTGTCA 60.251 50.0 20.33 0.88 45.31 3.58 F
1285 2424 0.188342 ACCTTGGGCAATCTTGTGGT 59.812 50.0 0.00 0.00 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1290 2429 0.745845 GACATGTTGAGGCCGAGCAT 60.746 55.000 0.0 0.0 0.00 3.79 R
2424 3585 1.202891 ACAAAACTGGGGTAGTCAGGC 60.203 52.381 0.0 0.0 39.18 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
279 1335 1.229209 ATGGACCAGGACGACCACT 60.229 57.895 6.71 0.00 38.94 4.00
290 1346 1.990060 CGACCACTGGGACCTCCAT 60.990 63.158 0.00 0.00 46.01 3.41
294 1350 2.204136 ACTGGGACCTCCATGGCA 60.204 61.111 6.96 0.00 46.01 4.92
305 1361 2.028876 CTCCATGGCAATGATGAAGCA 58.971 47.619 6.96 0.00 35.67 3.91
401 1458 0.250597 AACTCTGCATGCTGCTGTCA 60.251 50.000 20.33 0.88 45.31 3.58
567 1624 5.067283 GTGGTGTTGGTTCAGTTTAGTCAAT 59.933 40.000 0.00 0.00 0.00 2.57
659 1764 8.607459 CAATAAGTGGCAAACAAAACAATGTTA 58.393 29.630 0.00 0.00 42.49 2.41
688 1793 9.567776 TTTCATCTTATCTCTGTAACAACCAAA 57.432 29.630 0.00 0.00 0.00 3.28
791 1897 5.640147 AGATTAGTATGCTACAGCTCTCCT 58.360 41.667 2.44 0.00 42.66 3.69
792 1898 5.710099 AGATTAGTATGCTACAGCTCTCCTC 59.290 44.000 2.44 1.01 42.66 3.71
848 1955 2.043349 TAGCCCTGCACCTCGCTA 60.043 61.111 0.00 0.00 43.06 4.26
1169 2308 6.572519 TGCTTACAAGATTTTTCTTTGCACT 58.427 32.000 0.00 0.00 0.00 4.40
1276 2415 0.774276 TACACCATCACCTTGGGCAA 59.226 50.000 0.00 0.00 41.35 4.52
1285 2424 0.188342 ACCTTGGGCAATCTTGTGGT 59.812 50.000 0.00 0.00 0.00 4.16
1290 2429 0.895100 GGGCAATCTTGTGGTGCTGA 60.895 55.000 0.00 0.00 38.36 4.26
1325 2464 1.951209 TGTCCTGGAGTGCCATTAGA 58.049 50.000 0.00 0.00 44.91 2.10
1397 2536 7.704578 CCTCGAGAAGGTAATTATCTATCCA 57.295 40.000 15.71 0.00 40.67 3.41
1690 2839 7.051623 TCACCTTCGTATGCATAGGTTTATTT 58.948 34.615 22.18 4.80 38.93 1.40
1997 3150 5.281245 CCTTGGTTCCCTTTATTCTCTCCTT 60.281 44.000 0.00 0.00 0.00 3.36
2297 3458 8.637986 TGTTCATAATATATTTGCCCCAGTTTC 58.362 33.333 2.68 0.00 0.00 2.78
2325 3486 9.327628 CTCATTCTTCTCTGATTCATGTAACAT 57.672 33.333 0.00 0.00 0.00 2.71
2348 3509 1.421268 TGACAGAGGAAGCCATGTTGT 59.579 47.619 0.00 0.00 0.00 3.32
2424 3585 4.080919 TGTTCATCTGACTATGGTTCCAGG 60.081 45.833 0.00 0.00 0.00 4.45
2435 3596 1.602771 GTTCCAGGCCTGACTACCC 59.397 63.158 34.91 11.30 0.00 3.69
2436 3597 1.615424 TTCCAGGCCTGACTACCCC 60.615 63.158 34.91 0.00 0.00 4.95
2437 3598 2.285368 CCAGGCCTGACTACCCCA 60.285 66.667 34.91 0.00 0.00 4.96
2438 3599 2.370445 CCAGGCCTGACTACCCCAG 61.370 68.421 34.91 10.00 0.00 4.45
2439 3600 1.613630 CAGGCCTGACTACCCCAGT 60.614 63.158 29.88 0.00 41.47 4.00
2440 3601 1.161113 AGGCCTGACTACCCCAGTT 59.839 57.895 3.11 0.00 37.72 3.16
2441 3602 0.475828 AGGCCTGACTACCCCAGTTT 60.476 55.000 3.11 0.00 37.72 2.66
2442 3603 0.404426 GGCCTGACTACCCCAGTTTT 59.596 55.000 0.00 0.00 37.72 2.43
2443 3604 1.534729 GCCTGACTACCCCAGTTTTG 58.465 55.000 0.00 0.00 37.72 2.44
2444 3605 1.202891 GCCTGACTACCCCAGTTTTGT 60.203 52.381 0.00 0.00 37.72 2.83
2445 3606 2.779506 CCTGACTACCCCAGTTTTGTC 58.220 52.381 0.00 0.00 37.72 3.18
2446 3607 2.552373 CCTGACTACCCCAGTTTTGTCC 60.552 54.545 0.00 0.00 37.72 4.02
2447 3608 1.422402 TGACTACCCCAGTTTTGTCCC 59.578 52.381 0.00 0.00 37.72 4.46
2482 3643 7.067372 TCCTGTTGAAGTTGCATAGAAATATGG 59.933 37.037 0.00 0.00 0.00 2.74
2515 3684 2.549754 GAGTCCAGTGTGTTGTTCATGG 59.450 50.000 0.00 0.00 0.00 3.66
2651 3849 8.503196 TGCTCTTGTTTAAGTATTATGTGTGTG 58.497 33.333 0.00 0.00 35.38 3.82
2702 3902 9.617523 TGCTTGAAATATGAAGAATATGAGTCA 57.382 29.630 0.00 0.00 31.49 3.41
2741 3947 1.963515 ACCTGACAAATGGAAACCTGC 59.036 47.619 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 6.994421 TGCATATAGATACCAAGGACAAGA 57.006 37.500 0.00 0.00 0.00 3.02
140 1194 4.021016 ACAAGGCCTACTATAGCATAGCAC 60.021 45.833 5.16 0.00 0.00 4.40
290 1346 1.134936 GTGCATGCTTCATCATTGCCA 60.135 47.619 20.33 0.00 0.00 4.92
294 1350 2.764010 ACCATGTGCATGCTTCATCATT 59.236 40.909 20.33 7.08 37.49 2.57
305 1361 1.520120 CGAGCTCGACCATGTGCAT 60.520 57.895 32.06 0.00 43.02 3.96
329 1386 0.179048 CCACACTGAGGCACTGTTGA 60.179 55.000 0.00 0.00 41.55 3.18
492 1549 5.848286 AGGGATCATATAACATGAGGCAA 57.152 39.130 0.00 0.00 0.00 4.52
679 1784 4.081198 TGCAATTCAACTCCTTTGGTTGTT 60.081 37.500 6.49 0.00 42.97 2.83
688 1793 1.203994 GCATGCTGCAATTCAACTCCT 59.796 47.619 11.37 0.00 44.26 3.69
791 1897 2.682594 CTGGATGTATGGAGTGAGGGA 58.317 52.381 0.00 0.00 0.00 4.20
792 1898 1.696336 CCTGGATGTATGGAGTGAGGG 59.304 57.143 0.00 0.00 0.00 4.30
848 1955 3.470888 CGGGGTTGGGCGAGATCT 61.471 66.667 0.00 0.00 0.00 2.75
991 2130 9.601217 GGTGTATCTTGTGTAAATGATTCTAGT 57.399 33.333 0.00 0.00 0.00 2.57
996 2135 8.522830 CAAAGGGTGTATCTTGTGTAAATGATT 58.477 33.333 0.00 0.00 0.00 2.57
1116 2255 1.077212 CTGGGATGGCAGGAAGTGG 60.077 63.158 0.00 0.00 0.00 4.00
1169 2308 2.232941 GCAAGGTACTGGTGCTACTACA 59.767 50.000 8.20 0.00 38.97 2.74
1223 2362 4.637977 GTGATTTTCTCCCCAGATTCAGTC 59.362 45.833 0.00 0.00 0.00 3.51
1276 2415 1.747709 GAGCATCAGCACCACAAGAT 58.252 50.000 0.00 0.00 45.49 2.40
1285 2424 3.393106 TGAGGCCGAGCATCAGCA 61.393 61.111 8.77 0.00 44.36 4.41
1290 2429 0.745845 GACATGTTGAGGCCGAGCAT 60.746 55.000 0.00 0.00 0.00 3.79
1389 2528 6.271857 AGTTAACTGCAGATGGATGGATAGAT 59.728 38.462 23.35 0.00 0.00 1.98
1393 2532 4.785346 AGTTAACTGCAGATGGATGGAT 57.215 40.909 23.35 0.00 0.00 3.41
1395 2534 5.431765 ACTTAGTTAACTGCAGATGGATGG 58.568 41.667 23.35 6.51 0.00 3.51
1397 2536 6.372659 CACAACTTAGTTAACTGCAGATGGAT 59.627 38.462 23.35 5.73 0.00 3.41
1690 2839 4.523558 TCATGTCATGCAGAATTCAAACCA 59.476 37.500 8.44 0.00 0.00 3.67
1997 3150 4.629634 CACGCATACTAACATCACAAAGGA 59.370 41.667 0.00 0.00 0.00 3.36
2200 3358 5.301805 AGCTAGTACCATGCTTTTTGTTGTT 59.698 36.000 0.00 0.00 32.61 2.83
2253 3414 4.584325 TGAACAGACCATTCAAGAAAAGGG 59.416 41.667 8.78 4.13 33.16 3.95
2297 3458 9.033481 GTTACATGAATCAGAGAAGAATGAGAG 57.967 37.037 0.00 0.00 0.00 3.20
2325 3486 1.911357 ACATGGCTTCCTCTGTCATCA 59.089 47.619 0.00 0.00 0.00 3.07
2348 3509 2.167487 GGGCTGAGACCAAACAAAACAA 59.833 45.455 0.00 0.00 0.00 2.83
2424 3585 1.202891 ACAAAACTGGGGTAGTCAGGC 60.203 52.381 0.00 0.00 39.18 4.85
2435 3596 4.180817 GACAAAAACTGGGACAAAACTGG 58.819 43.478 0.00 0.00 38.70 4.00
2436 3597 4.081697 AGGACAAAAACTGGGACAAAACTG 60.082 41.667 0.00 0.00 38.70 3.16
2437 3598 4.081697 CAGGACAAAAACTGGGACAAAACT 60.082 41.667 0.00 0.00 38.70 2.66
2438 3599 4.180817 CAGGACAAAAACTGGGACAAAAC 58.819 43.478 0.00 0.00 38.70 2.43
2439 3600 3.835395 ACAGGACAAAAACTGGGACAAAA 59.165 39.130 0.00 0.00 38.70 2.44
2440 3601 3.436243 ACAGGACAAAAACTGGGACAAA 58.564 40.909 0.00 0.00 38.70 2.83
2441 3602 3.094484 ACAGGACAAAAACTGGGACAA 57.906 42.857 0.00 0.00 38.70 3.18
2442 3603 2.757868 CAACAGGACAAAAACTGGGACA 59.242 45.455 0.00 0.00 39.00 4.02
2443 3604 3.020984 TCAACAGGACAAAAACTGGGAC 58.979 45.455 0.00 0.00 39.00 4.46
2444 3605 3.374042 TCAACAGGACAAAAACTGGGA 57.626 42.857 0.00 0.00 39.00 4.37
2445 3606 3.447229 ACTTCAACAGGACAAAAACTGGG 59.553 43.478 0.00 0.00 39.00 4.45
2446 3607 4.718940 ACTTCAACAGGACAAAAACTGG 57.281 40.909 0.00 0.00 39.00 4.00
2447 3608 4.327087 GCAACTTCAACAGGACAAAAACTG 59.673 41.667 0.00 0.00 40.48 3.16
2482 3643 1.662438 CTGGACTCGCTGGACTCTCC 61.662 65.000 0.00 0.00 36.96 3.71
2515 3684 2.464157 ACTACTTCACAAGCTCCTGC 57.536 50.000 0.00 0.00 40.05 4.85
2651 3849 7.965107 CAGTATTTAGATTGGCAGAGACAAAAC 59.035 37.037 0.00 0.00 32.77 2.43
2702 3902 3.210074 AGGTAAGTGGGTCCCATCTATCT 59.790 47.826 15.49 11.22 35.28 1.98
2741 3947 4.941873 GTCCCAATTGTTAGGTTCTGGTAG 59.058 45.833 4.43 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.