Multiple sequence alignment - TraesCS3B01G232700

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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 TraesCS3B01G232700 chr3B 100.000 3452 0 0 1 3452 358582928 358586379 0.000000e+00 6375
1 TraesCS3B01G232700 chr3B 75.886 1016 174 51 747 1715 151818076 151817085 1.460000e-123 453
2 TraesCS3B01G232700 chr3B 73.725 1020 203 45 748 1715 151825355 151824349 4.270000e-89 339
3 TraesCS3B01G232700 chr4B 92.177 3464 242 23 1 3452 242358658 242362104 0.000000e+00 4868
4 TraesCS3B01G232700 chr4B 87.626 695 69 13 5 694 250846707 250846025 0.000000e+00 791
5 TraesCS3B01G232700 chr7B 91.027 3466 261 33 1 3452 266110661 266114090 0.000000e+00 4632
6 TraesCS3B01G232700 chr7B 92.133 2644 186 17 819 3452 152831848 152834479 0.000000e+00 3711
7 TraesCS3B01G232700 chr7B 91.583 2495 178 18 960 3446 173690141 173692611 0.000000e+00 3415
8 TraesCS3B01G232700 chr7B 92.636 774 49 5 6 777 152831080 152831847 0.000000e+00 1107
9 TraesCS3B01G232700 chr7B 91.865 713 51 6 1 711 173627015 173627722 0.000000e+00 989
10 TraesCS3B01G232700 chr7B 91.386 267 18 4 719 981 173689867 173690132 9.110000e-96 361
11 TraesCS3B01G232700 chr5B 91.067 2250 161 24 1213 3445 140684674 140686900 0.000000e+00 3005
12 TraesCS3B01G232700 chr5B 86.620 2160 251 22 1305 3450 69988188 69986053 0.000000e+00 2353
13 TraesCS3B01G232700 chr5B 78.588 2634 421 100 747 3264 400197949 400200555 0.000000e+00 1607
14 TraesCS3B01G232700 chr5B 92.816 696 43 6 1 693 140675179 140675870 0.000000e+00 1002
15 TraesCS3B01G232700 chr1A 86.121 2702 312 33 744 3401 174034841 174037523 0.000000e+00 2854
16 TraesCS3B01G232700 chr1A 85.035 2693 318 43 744 3389 174055572 174058226 0.000000e+00 2662
17 TraesCS3B01G232700 chr1A 85.847 2268 264 30 744 2971 223778710 223780960 0.000000e+00 2357
18 TraesCS3B01G232700 chr7D 86.121 2702 308 39 744 3401 289510101 289507423 0.000000e+00 2850
19 TraesCS3B01G232700 chr7D 85.300 932 91 23 2543 3447 287523874 287524786 0.000000e+00 920
20 TraesCS3B01G232700 chr7A 85.641 2716 325 35 736 3404 386956071 386953374 0.000000e+00 2795
21 TraesCS3B01G232700 chr1B 78.514 2625 432 89 744 3265 252930912 252933507 0.000000e+00 1602
22 TraesCS3B01G232700 chr2B 91.615 644 46 5 54 693 604436820 604436181 0.000000e+00 883
23 TraesCS3B01G232700 chr2B 89.755 693 54 13 7 693 346392936 346392255 0.000000e+00 870
24 TraesCS3B01G232700 chr6B 86.895 702 72 15 3 694 287343256 287342565 0.000000e+00 769


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 TraesCS3B01G232700 chr3B 358582928 358586379 3451 False 6375 6375 100.0000 1 3452 1 chr3B.!!$F1 3451
1 TraesCS3B01G232700 chr3B 151817085 151818076 991 True 453 453 75.8860 747 1715 1 chr3B.!!$R1 968
2 TraesCS3B01G232700 chr3B 151824349 151825355 1006 True 339 339 73.7250 748 1715 1 chr3B.!!$R2 967
3 TraesCS3B01G232700 chr4B 242358658 242362104 3446 False 4868 4868 92.1770 1 3452 1 chr4B.!!$F1 3451
4 TraesCS3B01G232700 chr4B 250846025 250846707 682 True 791 791 87.6260 5 694 1 chr4B.!!$R1 689
5 TraesCS3B01G232700 chr7B 266110661 266114090 3429 False 4632 4632 91.0270 1 3452 1 chr7B.!!$F2 3451
6 TraesCS3B01G232700 chr7B 152831080 152834479 3399 False 2409 3711 92.3845 6 3452 2 chr7B.!!$F3 3446
7 TraesCS3B01G232700 chr7B 173689867 173692611 2744 False 1888 3415 91.4845 719 3446 2 chr7B.!!$F4 2727
8 TraesCS3B01G232700 chr7B 173627015 173627722 707 False 989 989 91.8650 1 711 1 chr7B.!!$F1 710
9 TraesCS3B01G232700 chr5B 140684674 140686900 2226 False 3005 3005 91.0670 1213 3445 1 chr5B.!!$F2 2232
10 TraesCS3B01G232700 chr5B 69986053 69988188 2135 True 2353 2353 86.6200 1305 3450 1 chr5B.!!$R1 2145
11 TraesCS3B01G232700 chr5B 400197949 400200555 2606 False 1607 1607 78.5880 747 3264 1 chr5B.!!$F3 2517
12 TraesCS3B01G232700 chr5B 140675179 140675870 691 False 1002 1002 92.8160 1 693 1 chr5B.!!$F1 692
13 TraesCS3B01G232700 chr1A 174034841 174037523 2682 False 2854 2854 86.1210 744 3401 1 chr1A.!!$F1 2657
14 TraesCS3B01G232700 chr1A 174055572 174058226 2654 False 2662 2662 85.0350 744 3389 1 chr1A.!!$F2 2645
15 TraesCS3B01G232700 chr1A 223778710 223780960 2250 False 2357 2357 85.8470 744 2971 1 chr1A.!!$F3 2227
16 TraesCS3B01G232700 chr7D 289507423 289510101 2678 True 2850 2850 86.1210 744 3401 1 chr7D.!!$R1 2657
17 TraesCS3B01G232700 chr7D 287523874 287524786 912 False 920 920 85.3000 2543 3447 1 chr7D.!!$F1 904
18 TraesCS3B01G232700 chr7A 386953374 386956071 2697 True 2795 2795 85.6410 736 3404 1 chr7A.!!$R1 2668
19 TraesCS3B01G232700 chr1B 252930912 252933507 2595 False 1602 1602 78.5140 744 3265 1 chr1B.!!$F1 2521
20 TraesCS3B01G232700 chr2B 604436181 604436820 639 True 883 883 91.6150 54 693 1 chr2B.!!$R2 639
21 TraesCS3B01G232700 chr2B 346392255 346392936 681 True 870 870 89.7550 7 693 1 chr2B.!!$R1 686
22 TraesCS3B01G232700 chr6B 287342565 287343256 691 True 769 769 86.8950 3 694 1 chr6B.!!$R1 691

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
311 322 1.087202 TCAGTCCACACACGTTGCAC 61.087 55.000 0.0 0.0 0.00 4.57 F
1195 1304 0.179100 CGACAAGATGATCGGCAGGT 60.179 55.000 0.0 0.0 34.67 4.00 F
2134 2386 1.827969 AGAGGTCTGGTTTGGAGATCG 59.172 52.381 0.0 0.0 0.00 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2143 2395 0.302890 CGCTGAATGTCGATGAAGCC 59.697 55.0 0.00 0.0 0.0 4.35 R
2144 2396 0.315706 GCGCTGAATGTCGATGAAGC 60.316 55.0 0.00 0.0 0.0 3.86 R
3317 3619 4.826733 TCCAATTGTACTTGCACTGTGATT 59.173 37.5 12.86 0.0 0.0 2.57 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
226 232 8.961294 TCTAACTACAGTTGAACTAACGATTC 57.039 34.615 0.00 0.00 44.15 2.52
227 233 8.790718 TCTAACTACAGTTGAACTAACGATTCT 58.209 33.333 0.00 0.00 44.15 2.40
306 317 2.639065 ACAAATTCAGTCCACACACGT 58.361 42.857 0.00 0.00 0.00 4.49
311 322 1.087202 TCAGTCCACACACGTTGCAC 61.087 55.000 0.00 0.00 0.00 4.57
541 556 9.736414 AAGTACTAGTGTATAAGACTTCAGTGA 57.264 33.333 5.39 0.00 0.00 3.41
588 604 9.445786 ACACTGAAAATATCACAAAAGTAAACG 57.554 29.630 0.00 0.00 33.47 3.60
704 755 2.224185 TGCGACCAGTACAACTTGACAT 60.224 45.455 0.00 0.00 0.00 3.06
712 763 6.492429 ACCAGTACAACTTGACATGACTAGTA 59.508 38.462 11.85 0.00 0.00 1.82
713 764 7.178628 ACCAGTACAACTTGACATGACTAGTAT 59.821 37.037 11.85 7.06 0.00 2.12
1063 1172 1.372683 GACCAGAGCAGCAACCTCA 59.627 57.895 0.00 0.00 0.00 3.86
1114 1223 0.393820 GTACACCCGAACCCTCACAA 59.606 55.000 0.00 0.00 0.00 3.33
1128 1237 1.004044 CTCACAAGGGTTGAGCTCCAT 59.996 52.381 12.15 0.00 0.00 3.41
1195 1304 0.179100 CGACAAGATGATCGGCAGGT 60.179 55.000 0.00 0.00 34.67 4.00
1585 1775 5.682659 AGCATAGTTTCTGATCTTGATGCT 58.317 37.500 11.41 11.41 42.88 3.79
1733 1959 7.042925 GCACTGGTATAGGTCTTTTATTACACG 60.043 40.741 0.00 0.00 0.00 4.49
1775 2002 7.500141 TGAAGTAAGCAGCACATAGATCATTA 58.500 34.615 0.00 0.00 0.00 1.90
1779 2006 5.301835 AGCAGCACATAGATCATTACCTT 57.698 39.130 0.00 0.00 0.00 3.50
1808 2036 8.529476 GTTATAGGTTCTAGAACTTGGTGAAGA 58.471 37.037 29.66 10.40 40.94 2.87
1877 2106 9.959749 GGTGTACTTGAATTTAATTTCAGAACA 57.040 29.630 11.46 12.96 36.97 3.18
2110 2362 5.708697 AGCATTGAAGATGACAAACAGATGA 59.291 36.000 0.00 0.00 0.00 2.92
2134 2386 1.827969 AGAGGTCTGGTTTGGAGATCG 59.172 52.381 0.00 0.00 0.00 3.69
2143 2395 0.618458 TTTGGAGATCGACCCCAAGG 59.382 55.000 12.74 0.00 40.59 3.61
2189 2441 2.362397 GGAGAGTTCCATACATCAGCGA 59.638 50.000 0.00 0.00 43.45 4.93
2386 2638 5.812127 TGGAAGATAATCGACAACATCACAG 59.188 40.000 0.00 0.00 0.00 3.66
2408 2660 1.000843 AGGTGCGGAAATTTCAAAGGC 59.999 47.619 19.49 15.64 0.00 4.35
2411 2663 1.673700 GCGGAAATTTCAAAGGCGCG 61.674 55.000 19.49 12.34 0.00 6.86
2573 2825 3.338249 ACTTATGTCATGTGTGTCAGGC 58.662 45.455 0.00 0.00 0.00 4.85
2603 2857 6.203915 ACAAGTTTGCATATGTCGTCAAGTAA 59.796 34.615 4.29 0.00 0.00 2.24
2615 2869 5.521010 TGTCGTCAAGTAAATCGTTCACTTT 59.479 36.000 0.00 0.00 30.20 2.66
2644 2898 0.385390 AACAAGTTTGCTGCCTTCCG 59.615 50.000 0.00 0.00 0.00 4.30
2715 2969 4.149511 TGTGGCTGCTATGCAATACTAA 57.850 40.909 0.00 0.00 38.41 2.24
2752 3010 8.686334 ACAAATCACATAGGGATATTTTCACAC 58.314 33.333 0.00 0.00 0.00 3.82
2758 3018 9.139174 CACATAGGGATATTTTCACACAAAAAC 57.861 33.333 0.00 0.00 31.35 2.43
2759 3019 8.865090 ACATAGGGATATTTTCACACAAAAACA 58.135 29.630 0.00 0.00 31.35 2.83
2823 3087 5.308014 TCAGTACAAGTTAGTCCTGTACGA 58.692 41.667 0.00 4.73 39.93 3.43
2945 3232 6.859150 ACTAAGTAGTGCAACAGGAAAAACCT 60.859 38.462 0.00 0.00 41.80 3.50
3027 3314 4.997395 ACTTGAACACACAGTACATCCATC 59.003 41.667 0.00 0.00 0.00 3.51
3036 3326 7.147312 CACACAGTACATCCATCAAACAAAAT 58.853 34.615 0.00 0.00 0.00 1.82
3251 3547 5.047847 TCGACGAAGAGAAAATTCACAAGT 58.952 37.500 0.00 0.00 0.00 3.16
3300 3596 2.100605 CCAGTGAGGTGCTAGTTTCC 57.899 55.000 0.00 0.00 0.00 3.13
3303 3599 3.560025 CCAGTGAGGTGCTAGTTTCCAAT 60.560 47.826 0.00 0.00 0.00 3.16
3304 3600 3.438087 CAGTGAGGTGCTAGTTTCCAATG 59.562 47.826 0.00 0.00 0.00 2.82
3305 3601 3.327757 AGTGAGGTGCTAGTTTCCAATGA 59.672 43.478 0.00 0.00 0.00 2.57
3306 3602 4.072131 GTGAGGTGCTAGTTTCCAATGAA 58.928 43.478 0.00 0.00 0.00 2.57
3307 3603 4.072131 TGAGGTGCTAGTTTCCAATGAAC 58.928 43.478 0.00 0.00 0.00 3.18
3343 3645 6.000840 TCACAGTGCAAGTACAATTGGAATA 58.999 36.000 10.83 0.00 31.94 1.75
3347 3649 7.340232 ACAGTGCAAGTACAATTGGAATATCAT 59.660 33.333 10.83 0.00 31.94 2.45
3406 3713 9.188588 GATACCAAAATAATGCATTGATCACAG 57.811 33.333 22.27 7.70 0.00 3.66
3428 3735 6.168389 CAGCATAGAAAAAGAAGGCCAAAAT 58.832 36.000 5.01 0.00 0.00 1.82
3447 3754 9.597999 GCCAAAATTCAATCAAAAAGATTACAC 57.402 29.630 0.00 0.00 45.06 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
226 232 7.827819 TTTGGACTGAGATTATTTACGACAG 57.172 36.000 0.00 0.00 0.00 3.51
227 233 8.610248 TTTTTGGACTGAGATTATTTACGACA 57.390 30.769 0.00 0.00 0.00 4.35
276 287 9.216117 GTGTGGACTGAATTTGTAGTACTAATT 57.784 33.333 18.62 18.62 36.52 1.40
291 302 0.391793 TGCAACGTGTGTGGACTGAA 60.392 50.000 0.00 0.00 0.00 3.02
306 317 0.464735 GTAGTGGTGTGTGGGTGCAA 60.465 55.000 0.00 0.00 0.00 4.08
311 322 0.599204 GTGTCGTAGTGGTGTGTGGG 60.599 60.000 0.00 0.00 0.00 4.61
406 417 7.017319 AGGCCTTTATAGTGTTTTACTCTGT 57.983 36.000 0.00 0.00 40.89 3.41
588 604 6.975772 TGGCATTTTGTACTGTTTAAGTGTTC 59.024 34.615 0.00 0.00 40.26 3.18
681 732 1.137282 TCAAGTTGTACTGGTCGCACA 59.863 47.619 2.11 0.00 0.00 4.57
704 755 2.163613 CACTGGTCGCACATACTAGTCA 59.836 50.000 0.00 0.00 36.64 3.41
712 763 1.406887 GGGTATTCACTGGTCGCACAT 60.407 52.381 0.00 0.00 0.00 3.21
713 764 0.036765 GGGTATTCACTGGTCGCACA 60.037 55.000 0.00 0.00 0.00 4.57
806 860 4.309950 GGGTCGCCGTTCCAGTGT 62.310 66.667 3.97 0.00 0.00 3.55
847 912 1.152419 TGGGAGAGGTGGTTCGTCA 60.152 57.895 0.00 0.00 33.88 4.35
861 926 2.281208 CTTTTCGTGGGCGTGGGA 60.281 61.111 0.00 0.00 39.49 4.37
996 1105 3.064324 GGTTCCTGCGCCATTGCT 61.064 61.111 4.18 0.00 35.36 3.91
1063 1172 0.392461 CCGGGGACATGAACATCGTT 60.392 55.000 0.00 0.00 0.00 3.85
1114 1223 1.792757 TTGCCATGGAGCTCAACCCT 61.793 55.000 18.40 0.00 0.00 4.34
1128 1237 2.922503 TCCAGCGTCTCCTTGCCA 60.923 61.111 0.00 0.00 0.00 4.92
1195 1304 1.406069 GCCGAGGCTCTTCATCTTGAA 60.406 52.381 13.50 0.00 38.26 2.69
1350 1461 9.415008 AGTACAGATGAATGAAGAGTAGTATGT 57.585 33.333 0.00 0.00 0.00 2.29
1397 1521 8.885494 TTGTTGGGAAAGAAGTTTAATGAATG 57.115 30.769 0.00 0.00 0.00 2.67
1411 1536 9.319143 CTATAGTAGTTCATCTTGTTGGGAAAG 57.681 37.037 0.00 0.00 0.00 2.62
1779 2006 9.537852 TCACCAAGTTCTAGAACCTATAACTAA 57.462 33.333 28.05 6.93 42.06 2.24
1995 2243 6.497259 GGGGAGACACATATTGAGGATTAGTA 59.503 42.308 0.00 0.00 0.00 1.82
2110 2362 3.251484 TCTCCAAACCAGACCTCTTCAT 58.749 45.455 0.00 0.00 0.00 2.57
2134 2386 1.452108 CGATGAAGCCCTTGGGGTC 60.452 63.158 11.12 5.75 46.51 4.46
2143 2395 0.302890 CGCTGAATGTCGATGAAGCC 59.697 55.000 0.00 0.00 0.00 4.35
2144 2396 0.315706 GCGCTGAATGTCGATGAAGC 60.316 55.000 0.00 0.00 0.00 3.86
2183 2435 4.220821 AGGAGTCATACTCTTTTTCGCTGA 59.779 41.667 6.99 0.00 44.46 4.26
2189 2441 4.985538 TGCCAAGGAGTCATACTCTTTTT 58.014 39.130 6.99 0.00 41.00 1.94
2386 2638 3.833442 CCTTTGAAATTTCCGCACCTAC 58.167 45.455 15.48 0.00 0.00 3.18
2411 2663 1.384082 TAGTAGGGGCCAGCTTCCC 60.384 63.158 4.39 11.60 43.46 3.97
2420 2672 1.993391 TGGCAGTGGTAGTAGGGGC 60.993 63.158 0.00 0.00 0.00 5.80
2573 2825 3.840209 CGACATATGCAAACTTGTTCACG 59.160 43.478 1.58 0.00 0.00 4.35
2603 2857 7.853524 TGTTTAACGACATAAAGTGAACGATT 58.146 30.769 0.00 0.00 36.04 3.34
2615 2869 5.209240 GCAGCAAACTTGTTTAACGACATA 58.791 37.500 0.00 0.00 0.00 2.29
2715 2969 5.301045 CCTATGTGATTTGTTGCTCCATGAT 59.699 40.000 0.00 0.00 0.00 2.45
2752 3010 4.761739 TCTCCTTAGTCTGCCATGTTTTTG 59.238 41.667 0.00 0.00 0.00 2.44
2758 3018 3.616956 TGTTCTCCTTAGTCTGCCATG 57.383 47.619 0.00 0.00 0.00 3.66
2759 3019 3.327757 TGTTGTTCTCCTTAGTCTGCCAT 59.672 43.478 0.00 0.00 0.00 4.40
2951 3238 7.520451 AGTGCCTATGAAATACGTACTGATA 57.480 36.000 0.00 0.00 31.84 2.15
2971 3258 4.920640 TTCACTCCTAGTATGCTAGTGC 57.079 45.455 15.63 0.00 42.35 4.40
3027 3314 8.055986 GCTTCTCGTTCCTTTTTATTTTGTTTG 58.944 33.333 0.00 0.00 0.00 2.93
3251 3547 4.836175 TGGACTGATACTTCTGTTGTGGTA 59.164 41.667 0.00 0.00 34.54 3.25
3317 3619 4.826733 TCCAATTGTACTTGCACTGTGATT 59.173 37.500 12.86 0.00 0.00 2.57
3343 3645 7.045416 TGCCGTATGAACTAAGTTGTAATGAT 58.955 34.615 0.00 0.00 0.00 2.45
3347 3649 6.225318 ACTTGCCGTATGAACTAAGTTGTAA 58.775 36.000 0.00 0.00 0.00 2.41
3406 3713 6.650390 TGAATTTTGGCCTTCTTTTTCTATGC 59.350 34.615 3.32 0.00 0.00 3.14


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

AutoCloner maintained by Alex Coulton.