Multiple sequence alignment - TraesCS3A01G220700

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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 TraesCS3A01G220700 chr3A 100.000 5553 0 0 1 5553 408940580 408946132 0.000000e+00 10255
1 TraesCS3A01G220700 chr3A 99.260 2836 15 2 2165 4995 447271863 447274697 0.000000e+00 5116
2 TraesCS3A01G220700 chr3A 98.379 2159 15 4 1 2140 447269719 447271876 0.000000e+00 3775
3 TraesCS3A01G220700 chr3A 87.805 205 22 3 570 773 447270134 447270336 2.590000e-58 237
4 TraesCS3A01G220700 chr3A 85.106 188 21 3 586 773 408941001 408941181 9.500000e-43 185
5 TraesCS3A01G220700 chr3A 85.106 188 21 3 422 602 408941165 408941352 9.500000e-43 185
6 TraesCS3A01G220700 chr3A 85.106 188 21 3 422 602 447270320 447270507 9.500000e-43 185
7 TraesCS3A01G220700 chr3D 97.359 2802 47 10 2172 4953 317557011 317554217 0.000000e+00 4739
8 TraesCS3A01G220700 chr3D 95.694 2160 54 10 1 2141 317559139 317557000 0.000000e+00 3437
9 TraesCS3A01G220700 chr3D 96.855 318 7 1 5236 5553 317554217 317553903 3.810000e-146 529
10 TraesCS3A01G220700 chr3D 87.745 204 22 3 570 772 317558735 317558534 9.300000e-58 235
11 TraesCS3A01G220700 chr3D 85.204 196 19 6 416 602 317558565 317558371 5.680000e-45 193
12 TraesCS3A01G220700 chr3B 97.010 2809 50 12 2172 4953 401407137 401409938 0.000000e+00 4691
13 TraesCS3A01G220700 chr3B 94.931 2170 60 10 1 2136 401404990 401407143 0.000000e+00 3352
14 TraesCS3A01G220700 chr3B 97.170 318 5 2 5236 5553 401409938 401410251 8.190000e-148 534
15 TraesCS3A01G220700 chr3B 90.785 293 26 1 4951 5243 771975297 771975006 1.880000e-104 390
16 TraesCS3A01G220700 chr3B 90.785 293 26 1 4952 5244 772004245 772003954 1.880000e-104 390
17 TraesCS3A01G220700 chr3B 90.444 293 27 1 4952 5244 772003256 772002965 8.730000e-103 385
18 TraesCS3A01G220700 chr3B 89.831 295 27 3 4951 5244 771958129 771957837 5.250000e-100 375
19 TraesCS3A01G220700 chr3B 89.796 294 27 3 4952 5244 772001297 772001006 1.890000e-99 374
20 TraesCS3A01G220700 chr3B 89.456 294 28 3 4952 5244 771955170 771954879 8.790000e-98 368
21 TraesCS3A01G220700 chr3B 89.492 295 26 4 4952 5244 771961084 771960793 8.790000e-98 368
22 TraesCS3A01G220700 chr3B 87.317 205 23 3 570 773 401405389 401405591 1.200000e-56 231
23 TraesCS3A01G220700 chr6A 85.426 1091 113 16 2655 3737 1464766 1463714 0.000000e+00 1092
24 TraesCS3A01G220700 chr6A 85.616 1015 118 14 3837 4847 1463712 1462722 0.000000e+00 1040
25 TraesCS3A01G220700 chr6A 87.179 156 13 3 5254 5409 1462572 1462424 2.660000e-38 171
26 TraesCS3A01G220700 chr6A 83.803 142 22 1 3672 3813 452630057 452630197 3.490000e-27 134
27 TraesCS3A01G220700 chr6D 88.444 450 52 0 3063 3512 465354323 465353874 1.360000e-150 544
28 TraesCS3A01G220700 chr6D 87.333 450 55 1 3063 3512 465352800 465352353 1.070000e-141 514
29 TraesCS3A01G220700 chr4B 85.129 464 54 5 3456 3918 669916317 669915868 1.410000e-125 460
30 TraesCS3A01G220700 chr4B 83.408 446 60 4 3474 3918 669914427 669913995 8.660000e-108 401
31 TraesCS3A01G220700 chr4B 84.038 426 51 10 3272 3696 669912450 669912041 1.450000e-105 394
32 TraesCS3A01G220700 chr4B 83.933 417 51 6 3278 3693 669910747 669911148 8.730000e-103 385
33 TraesCS3A01G220700 chr4B 84.416 308 45 1 3873 4177 669916485 669916792 3.250000e-77 300
34 TraesCS3A01G220700 chr4B 82.609 299 38 5 3364 3661 669912041 669911756 9.230000e-63 252
35 TraesCS3A01G220700 chr4B 88.235 170 20 0 4008 4177 669912817 669912986 2.620000e-48 204
36 TraesCS3A01G220700 chr4B 90.909 99 9 0 4078 4176 669913970 669913872 3.490000e-27 134
37 TraesCS3A01G220700 chr4B 86.555 119 16 0 4059 4177 669915862 669915744 1.260000e-26 132
38 TraesCS3A01G220700 chr5A 90.909 286 26 0 4951 5236 184232058 184232343 8.730000e-103 385
39 TraesCS3A01G220700 chr2B 90.625 288 27 0 4949 5236 142750280 142750567 3.140000e-102 383
40 TraesCS3A01G220700 chr2B 86.614 127 16 1 4113 4238 114043405 114043531 7.500000e-29 139


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 TraesCS3A01G220700 chr3A 408940580 408946132 5552 False 10255.000000 10255 100.000000 1 5553 1 chr3A.!!$F1 5552
1 TraesCS3A01G220700 chr3A 447269719 447274697 4978 False 2328.250000 5116 92.637500 1 4995 4 chr3A.!!$F3 4994
2 TraesCS3A01G220700 chr3D 317553903 317559139 5236 True 1826.600000 4739 92.571400 1 5553 5 chr3D.!!$R1 5552
3 TraesCS3A01G220700 chr3B 401404990 401410251 5261 False 2202.000000 4691 94.107000 1 5553 4 chr3B.!!$F1 5552
4 TraesCS3A01G220700 chr3B 772001006 772004245 3239 True 383.000000 390 90.341667 4952 5244 3 chr3B.!!$R3 292
5 TraesCS3A01G220700 chr3B 771954879 771961084 6205 True 370.333333 375 89.593000 4951 5244 3 chr3B.!!$R2 293
6 TraesCS3A01G220700 chr6A 1462424 1464766 2342 True 767.666667 1092 86.073667 2655 5409 3 chr6A.!!$R1 2754
7 TraesCS3A01G220700 chr6D 465352353 465354323 1970 True 529.000000 544 87.888500 3063 3512 2 chr6D.!!$R1 449
8 TraesCS3A01G220700 chr4B 669910747 669916792 6045 False 296.333333 385 85.528000 3278 4177 3 chr4B.!!$F1 899
9 TraesCS3A01G220700 chr4B 669911756 669916317 4561 True 295.500000 460 85.441333 3272 4177 6 chr4B.!!$R1 905

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
276 277 1.134995 GCTCATTTTAGCCAGCCAACC 60.135 52.381 0.00 0.0 36.45 3.77 F
1601 1643 1.299089 GACAAAACGCTGCCCACAC 60.299 57.895 0.00 0.0 0.00 3.82 F
2020 2065 3.675348 TCTCCTTCGGGGTTGTAGATA 57.325 47.619 0.00 0.0 36.25 1.98 F
2341 2400 7.120923 TCCCTGGATACTGTATAACACTTTC 57.879 40.000 0.00 0.0 37.61 2.62 F
2959 3027 2.040464 ATCTCTCATGCCCCGGGT 60.040 61.111 21.85 0.0 0.00 5.28 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2065 1.841556 TCTTCTCCGGCACCACCTT 60.842 57.895 0.0 0.0 35.61 3.50 R
2935 3003 1.065199 GGGGCATGAGAGATCACACAA 60.065 52.381 0.0 0.0 0.00 3.33 R
2959 3027 1.305465 TAGCCTGGTCTTGCCGGTA 60.305 57.895 1.9 0.0 42.20 4.02 R
3994 10816 2.545526 TCTTTCTTTCAGTGCTTCGCAG 59.454 45.455 0.0 0.0 40.08 5.18 R
4808 13224 7.663827 TCCTCGTCAATTAAGAGACAAACTAA 58.336 34.615 9.8 0.0 35.91 2.24 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
274 275 2.220653 AGCTCATTTTAGCCAGCCAA 57.779 45.000 0.00 0.00 43.86 4.52
276 277 1.134995 GCTCATTTTAGCCAGCCAACC 60.135 52.381 0.00 0.00 36.45 3.77
1601 1643 1.299089 GACAAAACGCTGCCCACAC 60.299 57.895 0.00 0.00 0.00 3.82
1635 1677 4.796495 GAACCCGGCGGAATGGCT 62.796 66.667 30.79 0.38 42.02 4.75
2020 2065 3.675348 TCTCCTTCGGGGTTGTAGATA 57.325 47.619 0.00 0.00 36.25 1.98
2171 2216 8.950007 TTATTTTTCTGGAAATGGAGGTAACT 57.050 30.769 0.00 0.00 38.92 2.24
2299 2345 8.294954 TGTTTTAGGTTCCTACAAATGTGAAA 57.705 30.769 0.00 0.00 0.00 2.69
2341 2400 7.120923 TCCCTGGATACTGTATAACACTTTC 57.879 40.000 0.00 0.00 37.61 2.62
2959 3027 2.040464 ATCTCTCATGCCCCGGGT 60.040 61.111 21.85 0.00 0.00 5.28
4462 12635 0.742281 CTGGGAGCAATCTGTCACCG 60.742 60.000 0.00 0.00 0.00 4.94
4808 13224 1.454539 CCAGTGGGTTTTCGTCCCT 59.545 57.895 0.00 0.00 44.84 4.20
5020 14469 6.037786 TCGACCATCAAACTAAGTCAATCT 57.962 37.500 0.00 0.00 0.00 2.40
5024 14473 7.330946 CGACCATCAAACTAAGTCAATCTAACA 59.669 37.037 0.00 0.00 0.00 2.41
5043 15451 2.639839 ACAACCTAGACTGCTCCAATGT 59.360 45.455 0.00 0.00 0.00 2.71
5213 15621 3.666883 TTGCCTGAATATTAACGTGCG 57.333 42.857 0.00 0.00 0.00 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 275 2.445085 TGTGAGGTGTGGGTCGGT 60.445 61.111 0.00 0.00 0.00 4.69
276 277 1.006102 GAGTGTGAGGTGTGGGTCG 60.006 63.158 0.00 0.00 0.00 4.79
843 870 2.230025 CTCGCTTGACAAGAGGAGAGAA 59.770 50.000 22.51 3.98 34.47 2.87
1601 1643 3.003480 GGTTCCTCAAAGTCTTCATCGG 58.997 50.000 0.00 0.00 0.00 4.18
1635 1677 2.994995 TTCTCCCTTCTCGCGGCA 60.995 61.111 6.13 0.00 0.00 5.69
2020 2065 1.841556 TCTTCTCCGGCACCACCTT 60.842 57.895 0.00 0.00 35.61 3.50
2145 2190 9.374711 AGTTACCTCCATTTCCAGAAAAATAAA 57.625 29.630 0.00 0.00 33.56 1.40
2146 2191 8.950007 AGTTACCTCCATTTCCAGAAAAATAA 57.050 30.769 0.00 0.00 33.56 1.40
2148 2193 8.803235 GTTAGTTACCTCCATTTCCAGAAAAAT 58.197 33.333 0.00 0.00 33.56 1.82
2149 2194 8.002459 AGTTAGTTACCTCCATTTCCAGAAAAA 58.998 33.333 0.00 0.00 33.56 1.94
2150 2195 7.523415 AGTTAGTTACCTCCATTTCCAGAAAA 58.477 34.615 0.00 0.00 33.56 2.29
2151 2196 7.086685 AGTTAGTTACCTCCATTTCCAGAAA 57.913 36.000 0.00 0.00 34.46 2.52
2152 2197 6.697641 AGTTAGTTACCTCCATTTCCAGAA 57.302 37.500 0.00 0.00 0.00 3.02
2153 2198 7.801893 TTAGTTAGTTACCTCCATTTCCAGA 57.198 36.000 0.00 0.00 0.00 3.86
2168 2213 9.892130 CAGGAGGAACAGATTATTTAGTTAGTT 57.108 33.333 0.00 0.00 0.00 2.24
2169 2214 9.047947 ACAGGAGGAACAGATTATTTAGTTAGT 57.952 33.333 0.00 0.00 0.00 2.24
2170 2215 9.319143 CACAGGAGGAACAGATTATTTAGTTAG 57.681 37.037 0.00 0.00 0.00 2.34
2171 2216 9.042450 TCACAGGAGGAACAGATTATTTAGTTA 57.958 33.333 0.00 0.00 0.00 2.24
2172 2217 7.918076 TCACAGGAGGAACAGATTATTTAGTT 58.082 34.615 0.00 0.00 0.00 2.24
2173 2218 7.496346 TCACAGGAGGAACAGATTATTTAGT 57.504 36.000 0.00 0.00 0.00 2.24
2174 2219 8.970859 ATTCACAGGAGGAACAGATTATTTAG 57.029 34.615 0.00 0.00 0.00 1.85
2176 2221 9.753674 TTAATTCACAGGAGGAACAGATTATTT 57.246 29.630 0.00 0.00 0.00 1.40
2177 2222 9.927081 ATTAATTCACAGGAGGAACAGATTATT 57.073 29.630 0.00 0.00 0.00 1.40
2299 2345 8.033178 TCCAGGGAAAAGAAATTTTCATCTTT 57.967 30.769 11.53 7.51 45.30 2.52
2341 2400 6.964934 ACTAGCTTGTTTGTAAAACTGAAACG 59.035 34.615 0.00 0.00 33.18 3.60
2935 3003 1.065199 GGGGCATGAGAGATCACACAA 60.065 52.381 0.00 0.00 0.00 3.33
2959 3027 1.305465 TAGCCTGGTCTTGCCGGTA 60.305 57.895 1.90 0.00 42.20 4.02
3994 10816 2.545526 TCTTTCTTTCAGTGCTTCGCAG 59.454 45.455 0.00 0.00 40.08 5.18
4462 12635 9.525826 AAAATCCTATCATTGGATATCAGTTCC 57.474 33.333 0.52 0.00 42.93 3.62
4808 13224 7.663827 TCCTCGTCAATTAAGAGACAAACTAA 58.336 34.615 9.80 0.00 35.91 2.24
5000 14449 8.784043 GTTGTTAGATTGACTTAGTTTGATGGT 58.216 33.333 0.00 0.00 0.00 3.55
5020 14469 4.286032 ACATTGGAGCAGTCTAGGTTGTTA 59.714 41.667 0.00 0.00 0.00 2.41
5024 14473 2.093973 CGACATTGGAGCAGTCTAGGTT 60.094 50.000 0.00 0.00 0.00 3.50
5043 15451 5.383930 CGTTAAACACGTTGAACGCTCGA 62.384 47.826 18.58 0.00 46.45 4.04
5324 18706 1.283613 TGGTAGTTTGGCATGGTAGGG 59.716 52.381 0.00 0.00 0.00 3.53
5473 19046 7.944729 AACATTCCAGCAGTTGAAGTATATT 57.055 32.000 0.00 0.00 0.00 1.28


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

AutoCloner maintained by Alex Coulton.