Multiple sequence alignment - TraesCS4B01G121700

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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 TraesCS4B01G121700 chr4B 100.000 5196 0 0 1 5196 144684484 144679289 0.000000e+00 9596
1 TraesCS4B01G121700 chr4A 96.847 4916 117 12 293 5196 474931709 474936598 0.000000e+00 8185
2 TraesCS4B01G121700 chr4A 95.885 243 3 5 36 273 474931142 474931382 2.270000e-103 387
3 TraesCS4B01G121700 chr4A 88.889 126 14 0 2111 2236 474933641 474933766 6.970000e-34 156
4 TraesCS4B01G121700 chr4D 97.463 4573 95 11 5 4562 101014092 101009526 0.000000e+00 7782
5 TraesCS4B01G121700 chr4D 96.610 767 25 1 4431 5196 101009509 101008743 0.000000e+00 1271
6 TraesCS4B01G121700 chr4D 88.095 126 15 0 2111 2236 101011855 101011730 3.240000e-32 150


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 TraesCS4B01G121700 chr4B 144679289 144684484 5195 True 9596.000000 9596 100.000000 1 5196 1 chr4B.!!$R1 5195
1 TraesCS4B01G121700 chr4A 474931142 474936598 5456 False 2909.333333 8185 93.873667 36 5196 3 chr4A.!!$F1 5160
2 TraesCS4B01G121700 chr4D 101008743 101014092 5349 True 3067.666667 7782 94.056000 5 5196 3 chr4D.!!$R1 5191

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
503 817 1.000827 CGTGAGATGATCTTCTCCGGG 60.001 57.143 27.10 16.42 41.24 5.73 F
1664 1988 0.796312 AAACGATGCTAGTGTTGCCG 59.204 50.000 0.00 0.00 0.00 5.69 F
2460 2787 0.322008 GAAGAGGGTTGCACTGGAGG 60.322 60.000 0.00 0.00 0.00 4.30 F
2958 3285 0.250467 CAGGGCCATACGGAAGATGG 60.250 60.000 6.18 0.00 45.79 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1797 2121 0.466007 TTTGCTTGTCTCAGCTGCCA 60.466 50.000 9.47 2.41 40.79 4.92 R
2946 3273 1.280710 TGGTGTTGCCATCTTCCGTAT 59.719 47.619 0.00 0.00 43.61 3.06 R
4081 4408 1.447838 CGCCCTGCTGTGACGTAAT 60.448 57.895 0.00 0.00 0.00 1.89 R
4872 5350 0.842030 TGCTCAGGGACACCTCCAAT 60.842 55.000 0.00 0.00 46.95 3.16 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
79 81 1.964552 TAAAACCCGCGTCCTTTTGA 58.035 45.000 4.92 0.00 0.00 2.69
124 126 9.579610 GTGCAATTAATTACAAACACACATTTC 57.420 29.630 2.61 0.00 0.00 2.17
128 130 8.825667 ATTAATTACAAACACACATTTCCCAC 57.174 30.769 0.00 0.00 0.00 4.61
236 242 4.862823 CCTCCCCCTCGTCTCCCC 62.863 77.778 0.00 0.00 0.00 4.81
390 704 2.027745 TCGCTTTTGCTCCATCTCTCTT 60.028 45.455 0.00 0.00 44.80 2.85
503 817 1.000827 CGTGAGATGATCTTCTCCGGG 60.001 57.143 27.10 16.42 41.24 5.73
574 889 1.604755 CTCTTGCGTACGGCTCTAGAT 59.395 52.381 18.39 0.00 44.05 1.98
575 890 2.022195 TCTTGCGTACGGCTCTAGATT 58.978 47.619 18.39 0.00 44.05 2.40
604 919 2.122768 CCCCTTCCTAGATCTGCAAGT 58.877 52.381 5.18 0.00 33.76 3.16
752 1071 9.236006 AGCTGTTGTTGACTAAATGAATCTATT 57.764 29.630 0.00 0.00 0.00 1.73
828 1147 3.525199 AGTTCCTCCTTGGTGCATTATCT 59.475 43.478 0.00 0.00 37.07 1.98
924 1243 6.942005 TGTGGTGAAGTTCATTATTGTCATCT 59.058 34.615 9.18 0.00 0.00 2.90
941 1260 1.979809 TCTGGGGGTGATGTTGGTAT 58.020 50.000 0.00 0.00 0.00 2.73
946 1265 3.023832 GGGGGTGATGTTGGTATCTTTG 58.976 50.000 0.00 0.00 0.00 2.77
983 1302 8.794553 CATCTACCTTCTGTAACCGATATACTT 58.205 37.037 0.00 0.00 0.00 2.24
985 1304 9.193806 TCTACCTTCTGTAACCGATATACTTTT 57.806 33.333 0.00 0.00 0.00 2.27
1029 1348 3.244561 TGGAAGCTCAGAATCTTCGGTTT 60.245 43.478 0.00 0.00 39.54 3.27
1164 1483 1.139654 TGCCTGGCTAAGCAGTATCTG 59.860 52.381 21.03 0.00 33.08 2.90
1315 1636 4.327680 GGACCAGCAAGTCTATTTGTTCT 58.672 43.478 6.16 0.00 36.95 3.01
1371 1692 5.191722 AGCCTAGTGAAAATATGGTTGAGGA 59.808 40.000 0.00 0.00 0.00 3.71
1480 1801 1.080705 CGAGGTTGACGGTGAGGAC 60.081 63.158 0.00 0.00 0.00 3.85
1516 1837 4.115199 GGCAATGCCCGAGACCCT 62.115 66.667 14.47 0.00 44.06 4.34
1637 1961 5.538082 TGGGGAAAAGGGTTGTATTATGA 57.462 39.130 0.00 0.00 0.00 2.15
1664 1988 0.796312 AAACGATGCTAGTGTTGCCG 59.204 50.000 0.00 0.00 0.00 5.69
1797 2121 5.409214 GCAACAAAAATATGAACTGCCATGT 59.591 36.000 0.00 0.00 0.00 3.21
1812 2136 0.803117 CATGTGGCAGCTGAGACAAG 59.197 55.000 20.43 11.82 0.00 3.16
2143 2467 4.389077 CCAGAAGAACCGTTAGAACATCAC 59.611 45.833 0.00 0.00 0.00 3.06
2149 2473 3.407698 ACCGTTAGAACATCACATTGCA 58.592 40.909 0.00 0.00 0.00 4.08
2173 2497 5.357878 AGTTGCAGACAAAGACATTCAAGAA 59.642 36.000 0.00 0.00 37.58 2.52
2245 2569 3.360249 AGTGCAAATGCTTTCAGTGAC 57.640 42.857 6.97 0.00 42.66 3.67
2246 2570 2.689471 AGTGCAAATGCTTTCAGTGACA 59.311 40.909 6.97 0.00 42.66 3.58
2346 2673 5.658190 AGAATCCACAATTCCTGGTTAATGG 59.342 40.000 0.00 0.00 44.20 3.16
2452 2779 4.767409 ACTAAAGAATTGGAAGAGGGTTGC 59.233 41.667 0.00 0.00 0.00 4.17
2460 2787 0.322008 GAAGAGGGTTGCACTGGAGG 60.322 60.000 0.00 0.00 0.00 4.30
2560 2887 5.308759 TGAGAATGAGATTGATAGGGATGCA 59.691 40.000 0.00 0.00 0.00 3.96
2682 3009 2.586648 ACAACTGAAGGCCCTAAAGG 57.413 50.000 0.00 0.00 39.47 3.11
2946 3273 0.250901 GAAGAACAGAAGCAGGGCCA 60.251 55.000 6.18 0.00 0.00 5.36
2958 3285 0.250467 CAGGGCCATACGGAAGATGG 60.250 60.000 6.18 0.00 45.79 3.51
3230 3557 7.158099 AGTCAAGGGGATTTTTCGATAAAAG 57.842 36.000 5.13 0.00 36.02 2.27
3394 3721 7.849804 ACAACTGAATACCTATGATGTTGAC 57.150 36.000 0.00 0.00 37.53 3.18
3612 3939 2.290323 ACCAATCCTCACAAGCTGGTAC 60.290 50.000 0.00 0.00 0.00 3.34
4081 4408 4.199310 GGTATGATTCAGCAAGCCAGTTA 58.801 43.478 0.00 0.00 0.00 2.24
4156 4483 5.796424 ATGAAAGCTTTGAGTCAATGGTT 57.204 34.783 23.20 23.20 39.60 3.67
4331 4658 8.761689 AGCCTATATGAAATCATTTGGTTTGTT 58.238 29.630 0.55 0.00 37.76 2.83
4464 4793 6.092955 TCGTCCACACTAGTATTTCAGTTT 57.907 37.500 0.00 0.00 0.00 2.66
4549 5026 7.835682 AGGATTATGAATTCCTGACATGACAAA 59.164 33.333 0.00 0.00 0.00 2.83
4567 5044 6.000840 TGACAAATGCTACAAGGTTGACATA 58.999 36.000 0.00 0.00 0.00 2.29
4818 5296 4.197750 GCATCCTGTCTCTTGATGATTGT 58.802 43.478 3.08 0.00 38.49 2.71
4870 5348 3.053768 TGGCACCTGATCATAATGTTGGA 60.054 43.478 0.00 0.00 0.00 3.53
4872 5350 5.163109 TGGCACCTGATCATAATGTTGGATA 60.163 40.000 0.00 0.00 0.00 2.59
4884 5362 3.644966 TGTTGGATATTGGAGGTGTCC 57.355 47.619 0.00 0.00 44.24 4.02
5037 5515 0.031857 CTAGAGGCACTGATCTGCGG 59.968 60.000 0.00 0.00 41.55 5.69
5125 5604 0.899720 AAGGCATGTTGCATTCTGGG 59.100 50.000 1.50 0.00 44.73 4.45
5128 5607 0.604578 GCATGTTGCATTCTGGGTGT 59.395 50.000 0.00 0.00 44.26 4.16
5188 5667 8.470805 TGTGTTGTTTTGTCAAGTTATTACCAT 58.529 29.630 0.00 0.00 0.00 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.602472 AATGGACTAATTTGGCCTTTTATACA 57.398 30.769 13.21 0.00 0.00 2.29
79 81 1.139058 ACGTGGACAAGTCAAGAGCTT 59.861 47.619 2.29 0.00 0.00 3.74
124 126 1.740296 CGCCAGTTTACTCGGTGGG 60.740 63.158 0.00 0.00 0.00 4.61
128 130 1.005394 ACCACGCCAGTTTACTCGG 60.005 57.895 0.00 0.00 0.00 4.63
291 604 1.699634 TCTGGTGAAAGTTGGAGGAGG 59.300 52.381 0.00 0.00 0.00 4.30
390 704 2.822643 ATCTTGGGCCACGGAGGAGA 62.823 60.000 5.23 5.62 41.22 3.71
424 738 2.722487 CGAACTCGGAGGGATCGG 59.278 66.667 17.06 4.67 35.37 4.18
515 829 1.772063 AACACGAACCTTGTGCTCGC 61.772 55.000 0.00 0.00 41.03 5.03
549 864 0.599558 AGCCGTACGCAAGAGTGTAA 59.400 50.000 10.49 0.00 41.95 2.41
551 866 1.080705 GAGCCGTACGCAAGAGTGT 60.081 57.895 10.49 0.00 41.38 3.55
553 868 0.733729 CTAGAGCCGTACGCAAGAGT 59.266 55.000 10.49 0.00 41.38 3.24
604 919 0.911769 ACCAAATCGATCAGGGAGCA 59.088 50.000 17.41 0.00 0.00 4.26
878 1197 2.428890 AGTTATCTTCCACTCTCTGGCG 59.571 50.000 0.00 0.00 40.39 5.69
924 1243 1.979809 AGATACCAACATCACCCCCA 58.020 50.000 0.00 0.00 0.00 4.96
983 1302 1.278985 ACATGATCTCCTCACCGCAAA 59.721 47.619 0.00 0.00 36.48 3.68
985 1304 0.461548 GACATGATCTCCTCACCGCA 59.538 55.000 0.00 0.00 36.48 5.69
1293 1614 4.154918 CAGAACAAATAGACTTGCTGGTCC 59.845 45.833 6.12 0.00 36.95 4.46
1315 1636 4.512944 GCAGAGACAACTTTCAGTTCATCA 59.487 41.667 0.00 0.00 36.03 3.07
1371 1692 2.733956 TGCCGGCAGAGGAAATATTTT 58.266 42.857 29.03 0.00 0.00 1.82
1406 1727 4.452455 CCTTTCTGCGTTAACATTCTCACT 59.548 41.667 6.39 0.00 0.00 3.41
1480 1801 3.320541 TGCCAACACTTAGGGAACAATTG 59.679 43.478 3.24 3.24 0.00 2.32
1516 1837 2.171003 TCTGCCTCTTCGATCAACTCA 58.829 47.619 0.00 0.00 0.00 3.41
1664 1988 2.558313 GACAGTTGCAGCTTCGCC 59.442 61.111 0.00 0.00 0.00 5.54
1797 2121 0.466007 TTTGCTTGTCTCAGCTGCCA 60.466 50.000 9.47 2.41 40.79 4.92
1812 2136 3.567164 CCCATCATCCTCATACAGTTTGC 59.433 47.826 0.00 0.00 0.00 3.68
2149 2473 4.883585 TCTTGAATGTCTTTGTCTGCAACT 59.116 37.500 0.00 0.00 33.82 3.16
2460 2787 9.926751 CATGAACACAGACAATCTTATTATCAC 57.073 33.333 0.00 0.00 0.00 3.06
2473 2800 3.678289 CTCATTCCCATGAACACAGACA 58.322 45.455 0.00 0.00 39.04 3.41
2560 2887 2.979678 ACTTCCAGTGTCCAGGTATTGT 59.020 45.455 0.00 0.00 0.00 2.71
2682 3009 6.180472 TCTTCAATACAACCATCTTCCTTCC 58.820 40.000 0.00 0.00 0.00 3.46
2878 3205 8.202811 TCATGTTGATCAAAAATTTGTCCAGAA 58.797 29.630 10.35 0.00 39.18 3.02
2946 3273 1.280710 TGGTGTTGCCATCTTCCGTAT 59.719 47.619 0.00 0.00 43.61 3.06
3220 3547 8.317891 TGAACTTACTTGATGCTTTTATCGAA 57.682 30.769 0.00 0.00 0.00 3.71
3230 3557 5.931441 ACAGTCTTGAACTTACTTGATGC 57.069 39.130 0.00 0.00 35.45 3.91
3394 3721 4.552166 ATCAACACTTCGAAACTGTTGG 57.448 40.909 29.97 19.59 43.29 3.77
3612 3939 1.686325 ATCGTGGTCGGGGATTGAGG 61.686 60.000 0.00 0.00 37.69 3.86
3959 4286 4.518211 AGACAAGCTTCTTGTGAAAGATGG 59.482 41.667 15.91 0.00 31.96 3.51
4081 4408 1.447838 CGCCCTGCTGTGACGTAAT 60.448 57.895 0.00 0.00 0.00 1.89
4567 5044 9.358406 TGAGCATCAATAGGAATAATTTGACAT 57.642 29.630 0.00 0.00 45.97 3.06
4789 5267 3.453353 TCAAGAGACAGGATGCATCATGA 59.547 43.478 39.37 18.34 40.76 3.07
4818 5296 7.484975 CAACTTGTAACAGGTTTGTCCATTTA 58.515 34.615 0.00 0.00 36.23 1.40
4870 5348 1.771255 GCTCAGGGACACCTCCAATAT 59.229 52.381 0.00 0.00 46.95 1.28
4872 5350 0.842030 TGCTCAGGGACACCTCCAAT 60.842 55.000 0.00 0.00 46.95 3.16
4945 5423 2.095059 GTCTGTCCAATCCATGTGTTGC 60.095 50.000 0.00 0.00 0.00 4.17
5060 5538 9.507329 AGAGAAAATATTCTTGAGCACAAACTA 57.493 29.630 0.00 0.00 45.91 2.24
5128 5607 2.229792 GCCATGGTTTTGTCAGACAGA 58.770 47.619 14.67 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.