Multiple sequence alignment - TraesCS4A01G487500

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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 TraesCS4A01G487500 chr4A 100.000 4783 0 0 1 4783 739830340 739835122 0.000000e+00 8833.0
1 TraesCS4A01G487500 chr4A 97.367 4481 111 6 308 4783 742272359 742267881 0.000000e+00 7614.0
2 TraesCS4A01G487500 chr4A 95.446 4787 149 23 4 4783 740064214 740059490 0.000000e+00 7568.0
3 TraesCS4A01G487500 chr4A 94.003 4786 186 29 4 4783 733930027 733925337 0.000000e+00 7155.0
4 TraesCS4A01G487500 chr4A 94.979 2191 110 0 2593 4783 740868120 740865930 0.000000e+00 3437.0
5 TraesCS4A01G487500 chr4A 94.843 2191 113 0 2593 4783 739808218 739810408 0.000000e+00 3421.0
6 TraesCS4A01G487500 chr4A 81.460 2028 245 69 81 2030 739805258 739807232 0.000000e+00 1541.0
7 TraesCS4A01G487500 chr4A 95.484 155 5 2 4 156 742272508 742272354 3.700000e-61 246.0
8 TraesCS4A01G487500 chr7D 94.617 2192 117 1 2593 4783 3440478 3442669 0.000000e+00 3393.0
9 TraesCS4A01G487500 chr7D 93.011 2232 149 5 2552 4783 3699324 3701548 0.000000e+00 3251.0
10 TraesCS4A01G487500 chr7D 91.440 1285 60 12 2383 3641 3583121 3584381 0.000000e+00 1718.0
11 TraesCS4A01G487500 chr7D 89.443 1203 111 9 967 2162 3731300 3730107 0.000000e+00 1504.0
12 TraesCS4A01G487500 chr7D 90.610 1033 93 2 998 2030 3697391 3698419 0.000000e+00 1367.0
13 TraesCS4A01G487500 chr7D 86.567 670 66 10 1780 2440 3582468 3583122 0.000000e+00 717.0
14 TraesCS4A01G487500 chr7D 88.636 132 13 1 2197 2328 3730101 3729972 4.950000e-35 159.0
15 TraesCS4A01G487500 chr7A 90.962 2235 196 6 2551 4783 3582923 3585153 0.000000e+00 3003.0
16 TraesCS4A01G487500 chr7A 89.216 2244 206 18 2569 4783 3381200 3383436 0.000000e+00 2771.0
17 TraesCS4A01G487500 chr7A 81.957 1962 229 64 146 2030 3005244 3003331 0.000000e+00 1546.0
18 TraesCS4A01G487500 chr7A 89.684 1202 109 7 967 2162 2554244 2553052 0.000000e+00 1519.0
19 TraesCS4A01G487500 chr7A 88.849 1112 105 8 931 2035 3379537 3380636 0.000000e+00 1349.0
20 TraesCS4A01G487500 chr7A 93.548 62 3 1 2267 2328 3582095 3582155 1.830000e-14 91.6
21 TraesCS4A01G487500 chr7A 90.625 64 6 0 2272 2335 3003193 3003130 8.530000e-13 86.1


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 TraesCS4A01G487500 chr4A 739830340 739835122 4782 False 8833.00 8833 100.0000 1 4783 1 chr4A.!!$F1 4782
1 TraesCS4A01G487500 chr4A 740059490 740064214 4724 True 7568.00 7568 95.4460 4 4783 1 chr4A.!!$R2 4779
2 TraesCS4A01G487500 chr4A 733925337 733930027 4690 True 7155.00 7155 94.0030 4 4783 1 chr4A.!!$R1 4779
3 TraesCS4A01G487500 chr4A 742267881 742272508 4627 True 3930.00 7614 96.4255 4 4783 2 chr4A.!!$R4 4779
4 TraesCS4A01G487500 chr4A 740865930 740868120 2190 True 3437.00 3437 94.9790 2593 4783 1 chr4A.!!$R3 2190
5 TraesCS4A01G487500 chr4A 739805258 739810408 5150 False 2481.00 3421 88.1515 81 4783 2 chr4A.!!$F2 4702
6 TraesCS4A01G487500 chr7D 3440478 3442669 2191 False 3393.00 3393 94.6170 2593 4783 1 chr7D.!!$F1 2190
7 TraesCS4A01G487500 chr7D 3697391 3701548 4157 False 2309.00 3251 91.8105 998 4783 2 chr7D.!!$F3 3785
8 TraesCS4A01G487500 chr7D 3582468 3584381 1913 False 1217.50 1718 89.0035 1780 3641 2 chr7D.!!$F2 1861
9 TraesCS4A01G487500 chr7D 3729972 3731300 1328 True 831.50 1504 89.0395 967 2328 2 chr7D.!!$R1 1361
10 TraesCS4A01G487500 chr7A 3379537 3383436 3899 False 2060.00 2771 89.0325 931 4783 2 chr7A.!!$F1 3852
11 TraesCS4A01G487500 chr7A 3582095 3585153 3058 False 1547.30 3003 92.2550 2267 4783 2 chr7A.!!$F2 2516
12 TraesCS4A01G487500 chr7A 2553052 2554244 1192 True 1519.00 1519 89.6840 967 2162 1 chr7A.!!$R1 1195
13 TraesCS4A01G487500 chr7A 3003130 3005244 2114 True 816.05 1546 86.2910 146 2335 2 chr7A.!!$R2 2189

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
442 459 0.324943 GTTTGCAGGTGCCTCCTCTA 59.675 55.000 0.00 0.00 46.24 2.43 F
1096 1240 2.049767 TACACTCTGATCCGCGGCA 61.050 57.895 23.51 13.33 0.00 5.69 F
1812 1959 2.284995 GAGGAGGTGCAGGAGGGT 60.285 66.667 0.00 0.00 0.00 4.34 F
2873 3916 0.829182 CCCCAAGCAGCCAAGAAAGT 60.829 55.000 0.00 0.00 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1788 1935 0.607489 CCTGCACCTCCTCCTTTGTG 60.607 60.000 0.00 0.0 0.00 3.33 R
2844 3887 1.895131 GCTGCTTGGGGATTCAGAAAA 59.105 47.619 0.00 0.0 0.00 2.29 R
3561 4608 1.248101 TGCATGGAGAGTCGACGGAA 61.248 55.000 10.46 0.0 0.00 4.30 R
4649 5706 1.554160 CTGAGATGCACCTCTTGGAGT 59.446 52.381 10.11 0.0 37.04 3.85 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
22 23 5.082251 GACTAAATTTCCACCCGAGTACT 57.918 43.478 0.00 0.00 0.00 2.73
38 40 5.408604 CCGAGTACTATTGCCATATTTCCAC 59.591 44.000 0.00 0.00 0.00 4.02
132 137 1.744320 GCCTTTGCGGTGTTTTCCCT 61.744 55.000 0.00 0.00 34.25 4.20
135 140 2.469826 CTTTGCGGTGTTTTCCCTTTC 58.530 47.619 0.00 0.00 0.00 2.62
190 195 1.403323 GGCAATGGAAGTTAGCTCTGC 59.597 52.381 0.00 0.00 0.00 4.26
255 260 2.542411 GCACTTGCAACAACAGAGAAGG 60.542 50.000 0.00 0.00 41.59 3.46
256 261 2.684881 CACTTGCAACAACAGAGAAGGT 59.315 45.455 0.00 0.00 0.00 3.50
257 262 2.684881 ACTTGCAACAACAGAGAAGGTG 59.315 45.455 0.00 0.00 0.00 4.00
279 287 1.995542 AGATGGAGATTGTGGTGGGTT 59.004 47.619 0.00 0.00 0.00 4.11
386 401 2.203922 TGCCCTGCCCAGTGTCTA 60.204 61.111 0.00 0.00 0.00 2.59
442 459 0.324943 GTTTGCAGGTGCCTCCTCTA 59.675 55.000 0.00 0.00 46.24 2.43
490 508 3.181480 GGTAGCTTTTTGTTCCACTTGCA 60.181 43.478 0.00 0.00 0.00 4.08
553 571 8.949953 ACGTGTTTTTCACTCAATTAATTAACG 58.050 29.630 0.00 0.00 44.16 3.18
1096 1240 2.049767 TACACTCTGATCCGCGGCA 61.050 57.895 23.51 13.33 0.00 5.69
1226 1370 2.289631 TGAAGCAGATTCGTGACATGGT 60.290 45.455 0.00 0.00 41.14 3.55
1709 1856 2.290847 ACTGTCGGGCATCAGTCAT 58.709 52.632 3.34 0.00 40.28 3.06
1788 1935 2.351157 GCCAGCAGACAGTCAAATCAAC 60.351 50.000 2.66 0.00 0.00 3.18
1812 1959 2.284995 GAGGAGGTGCAGGAGGGT 60.285 66.667 0.00 0.00 0.00 4.34
1946 2099 7.642978 CAGCATGCAGAATAAGATAGAAACAAC 59.357 37.037 21.98 0.00 0.00 3.32
2055 2211 7.905031 ATTACTCGTAGTTCGTTAGTAATGC 57.095 36.000 12.42 0.00 42.45 3.56
2329 2737 5.607119 ACTTCAACTTGTTACCAATAGCG 57.393 39.130 0.00 0.00 0.00 4.26
2331 2739 5.938125 ACTTCAACTTGTTACCAATAGCGAT 59.062 36.000 0.00 0.00 0.00 4.58
2356 2888 6.374565 TTTATAGCTGAACCTAGTCGAGTC 57.625 41.667 0.00 0.00 0.00 3.36
2795 3838 6.162079 AGATGGAACTGATTATCTGCATACG 58.838 40.000 0.00 0.00 0.00 3.06
2844 3887 6.552008 TCCAAAAGTCTATTTCATCAGGGTT 58.448 36.000 0.00 0.00 0.00 4.11
2873 3916 0.829182 CCCCAAGCAGCCAAGAAAGT 60.829 55.000 0.00 0.00 0.00 2.66
2922 3965 2.872858 GTTGGTGTTGAGTCCTCTGAAC 59.127 50.000 0.00 0.00 38.07 3.18
3034 4077 5.104569 AGAGAAGCAAAGAAAGGGAGATAGG 60.105 44.000 0.00 0.00 0.00 2.57
3380 4427 1.528129 CAGAGGAAGTGGCAGAAACC 58.472 55.000 0.00 0.00 0.00 3.27
3561 4608 2.875296 TGCCAACTCCTAGCAACAAAT 58.125 42.857 0.00 0.00 32.56 2.32
3779 4826 9.709495 AATGACATATGTAAAATGCTTGTGTTT 57.291 25.926 8.71 0.00 0.00 2.83
3780 4827 9.709495 ATGACATATGTAAAATGCTTGTGTTTT 57.291 25.926 8.71 0.00 0.00 2.43
3798 4845 5.585047 GTGTTTTAGTATTTGAGCCTCCGAT 59.415 40.000 0.00 0.00 0.00 4.18
3975 5023 2.669364 CTTTGAAGTTGCCACATGAGC 58.331 47.619 0.00 2.13 0.00 4.26
4061 5109 2.086869 GCTGTAGCAAGCCTTCATCAA 58.913 47.619 0.00 0.00 41.59 2.57
4307 5364 5.507985 CCCAAAGTGGATCAAAGAACTCAAC 60.508 44.000 0.00 0.00 40.96 3.18
4406 5463 4.444536 TGTTTACGCTCACCTTTACACTT 58.555 39.130 0.00 0.00 0.00 3.16
4414 5471 3.997021 CTCACCTTTACACTTAGTGCAGG 59.003 47.826 18.70 18.70 36.98 4.85
4574 5631 2.563179 TGCAGTTACAGGAAGAGAGGTC 59.437 50.000 0.00 0.00 0.00 3.85
4779 5836 3.737559 AGTGGCCAAAGATAATCACCA 57.262 42.857 7.24 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.082251 AGTACTCGGGTGGAAATTTAGTC 57.918 43.478 0.00 0.00 0.00 2.59
1 2 6.803366 ATAGTACTCGGGTGGAAATTTAGT 57.197 37.500 0.00 0.00 0.00 2.24
22 23 5.133660 ACCTACCTGTGGAAATATGGCAATA 59.866 40.000 0.00 0.00 0.00 1.90
38 40 3.010808 TCCCCAACCAAATAACCTACCTG 59.989 47.826 0.00 0.00 0.00 4.00
89 92 3.806521 GGTCATCGATCATGGTGAGAAAG 59.193 47.826 0.00 0.00 32.64 2.62
135 140 9.553064 AGCAGTTGTCAATCTATCTATAAAAGG 57.447 33.333 0.00 0.00 0.00 3.11
190 195 6.805271 CACAGAAAGTTCAAATCAAGCATAGG 59.195 38.462 0.00 0.00 0.00 2.57
248 253 4.782156 ACAATCTCCATCTTCACCTTCTCT 59.218 41.667 0.00 0.00 0.00 3.10
255 260 3.012518 CCACCACAATCTCCATCTTCAC 58.987 50.000 0.00 0.00 0.00 3.18
256 261 2.025981 CCCACCACAATCTCCATCTTCA 60.026 50.000 0.00 0.00 0.00 3.02
257 262 2.025887 ACCCACCACAATCTCCATCTTC 60.026 50.000 0.00 0.00 0.00 2.87
279 287 7.402054 TCTATTTTCATGGTTGCTTCCTAAGA 58.598 34.615 0.00 0.00 0.00 2.10
386 401 3.300388 TGGTCACTGAAGAGTCTTGAGT 58.700 45.455 18.06 18.06 0.00 3.41
442 459 1.503347 ACAGAAAATGGAGTTGGGGGT 59.497 47.619 0.00 0.00 0.00 4.95
490 508 3.256631 GGTTGTCAAGATCAACTGCCATT 59.743 43.478 0.00 0.00 42.97 3.16
553 571 8.269424 CGATTTGTACTTTCTATATGTCACAGC 58.731 37.037 0.00 0.00 0.00 4.40
792 888 7.013655 ACAATTCTAGCGATTATCAATTTGCCT 59.986 33.333 0.00 0.00 0.00 4.75
959 1065 2.766263 CACTACTACAATCTGCCTCCCA 59.234 50.000 0.00 0.00 0.00 4.37
996 1131 4.564821 GCACCCACTACAAACTCCATCTTA 60.565 45.833 0.00 0.00 0.00 2.10
1096 1240 4.592192 CTGGATGTCGCCGCGGAT 62.592 66.667 33.48 14.15 0.00 4.18
1102 1246 1.858091 CTGATGTACTGGATGTCGCC 58.142 55.000 0.00 0.00 0.00 5.54
1226 1370 4.556699 CGATGCAGTCTTCCATGTCGTATA 60.557 45.833 0.00 0.00 0.00 1.47
1512 1659 1.521010 CTCTGTGCGGATGAGCTGG 60.521 63.158 0.00 0.00 38.13 4.85
1709 1856 7.290110 TCTTCATCAAAGTTCTGAGACACTA 57.710 36.000 0.00 0.00 36.31 2.74
1788 1935 0.607489 CCTGCACCTCCTCCTTTGTG 60.607 60.000 0.00 0.00 0.00 3.33
1812 1959 1.003839 CACCTTCCCTGCGTTGCTA 60.004 57.895 0.00 0.00 0.00 3.49
1946 2099 3.186909 TCAATAAGCTGGTCACGATTCG 58.813 45.455 4.14 4.14 0.00 3.34
2044 2200 5.694458 TGCATATACACAGGCATTACTAACG 59.306 40.000 0.00 0.00 0.00 3.18
2055 2211 5.363101 AGACACTTGATGCATATACACAGG 58.637 41.667 0.00 0.00 0.00 4.00
2329 2737 7.921745 ACTCGACTAGGTTCAGCTATAAAAATC 59.078 37.037 0.00 0.00 0.00 2.17
2331 2739 7.122353 AGACTCGACTAGGTTCAGCTATAAAAA 59.878 37.037 0.00 0.00 0.00 1.94
2556 3148 7.769044 GCTTATTTAAGTTCATACCACTGAGGA 59.231 37.037 0.00 0.00 36.90 3.71
2557 3149 7.770897 AGCTTATTTAAGTTCATACCACTGAGG 59.229 37.037 0.00 0.00 38.32 3.86
2795 3838 3.560068 CGACATCACTTAGGGCATTAACC 59.440 47.826 0.00 0.00 0.00 2.85
2844 3887 1.895131 GCTGCTTGGGGATTCAGAAAA 59.105 47.619 0.00 0.00 0.00 2.29
2873 3916 7.281774 GCTTGAGATCTTGTATCCATTCTTTCA 59.718 37.037 0.00 0.00 0.00 2.69
2922 3965 3.058450 GCAGATGATCTGTTCCATCTCG 58.942 50.000 22.23 3.39 45.39 4.04
3034 4077 3.768757 CCATATCTCCTCATGGACCTCTC 59.231 52.174 0.00 0.00 43.80 3.20
3230 4277 2.008329 GTCTTGAGATCTGCTGGCAAG 58.992 52.381 0.00 7.37 37.79 4.01
3561 4608 1.248101 TGCATGGAGAGTCGACGGAA 61.248 55.000 10.46 0.00 0.00 4.30
3779 4826 5.105106 TGTTCATCGGAGGCTCAAATACTAA 60.105 40.000 17.69 0.00 0.00 2.24
3780 4827 4.404394 TGTTCATCGGAGGCTCAAATACTA 59.596 41.667 17.69 0.00 0.00 1.82
3798 4845 6.798676 GATGGAATCTCAGAAACCTCTGTTCA 60.799 42.308 2.28 0.00 41.16 3.18
3975 5023 2.099141 TTCATCGGCTCCTTGTTCTG 57.901 50.000 0.00 0.00 0.00 3.02
4061 5109 2.339769 AGTTTCCTTAGCCCTGTCAGT 58.660 47.619 0.00 0.00 0.00 3.41
4307 5364 4.559862 AAGGGTCATCTTGTAGAGGTTG 57.440 45.455 0.00 0.00 0.00 3.77
4406 5463 2.369860 CCTATCATCCTTGCCTGCACTA 59.630 50.000 0.00 0.00 0.00 2.74
4414 5471 4.564406 CCACTATGTCCCTATCATCCTTGC 60.564 50.000 0.00 0.00 0.00 4.01
4649 5706 1.554160 CTGAGATGCACCTCTTGGAGT 59.446 52.381 10.11 0.00 37.04 3.85


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

AutoCloner maintained by Alex Coulton.