Multiple sequence alignment - TraesCS3A01G139400

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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 TraesCS3A01G139400 chr3A 100.000 1281 0 0 1 1281 117790638 117789358 0.000000e+00 2366.0
1 TraesCS3A01G139400 chr3A 100.000 1161 0 0 1840 3000 117788799 117787639 0.000000e+00 2145.0
2 TraesCS3A01G139400 chr5D 95.952 1161 45 2 1840 3000 184451424 184452582 0.000000e+00 1882.0
3 TraesCS3A01G139400 chr5D 93.659 552 29 2 2121 2667 403968857 403969407 0.000000e+00 821.0
4 TraesCS3A01G139400 chr5D 95.719 327 13 1 2675 3000 375001229 375001555 2.650000e-145 525.0
5 TraesCS3A01G139400 chr5D 100.000 51 0 0 2047 2097 403968808 403968858 8.850000e-16 95.3
6 TraesCS3A01G139400 chr6D 92.089 1302 80 5 1 1281 32220939 32219640 0.000000e+00 1812.0
7 TraesCS3A01G139400 chr6D 88.688 221 16 4 1844 2055 32219551 32219331 8.250000e-66 261.0
8 TraesCS3A01G139400 chr2A 94.660 1161 60 1 1840 3000 33474477 33473319 0.000000e+00 1799.0
9 TraesCS3A01G139400 chr2A 93.804 1162 70 2 1840 3000 478453995 478455155 0.000000e+00 1746.0
10 TraesCS3A01G139400 chr2A 94.684 790 37 5 1 788 478452561 478453347 0.000000e+00 1221.0
11 TraesCS3A01G139400 chr2A 93.156 789 49 5 1 788 33484238 33483454 0.000000e+00 1153.0
12 TraesCS3A01G139400 chr2D 90.320 1312 95 10 1 1281 382042123 382040813 0.000000e+00 1690.0
13 TraesCS3A01G139400 chr2D 90.179 224 14 2 1840 2055 382032116 382031893 4.890000e-73 285.0
14 TraesCS3A01G139400 chr1D 89.718 1313 101 10 1 1281 407140861 407142171 0.000000e+00 1646.0
15 TraesCS3A01G139400 chr1D 93.178 557 28 1 2121 2667 26249888 26249332 0.000000e+00 809.0
16 TraesCS3A01G139400 chr1D 89.947 567 26 2 2132 2667 463400297 463400863 0.000000e+00 702.0
17 TraesCS3A01G139400 chr1D 95.719 327 12 2 2675 3000 393952924 393952599 2.650000e-145 525.0
18 TraesCS3A01G139400 chr1D 88.532 218 17 2 1843 2052 407142441 407142658 1.070000e-64 257.0
19 TraesCS3A01G139400 chr1D 100.000 51 0 0 2047 2097 26249937 26249887 8.850000e-16 95.3
20 TraesCS3A01G139400 chr1A 94.879 742 38 0 2259 3000 205552106 205552847 0.000000e+00 1160.0
21 TraesCS3A01G139400 chr1A 93.514 555 28 2 2121 2667 30575206 30575760 0.000000e+00 819.0
22 TraesCS3A01G139400 chr1A 98.039 51 1 0 2047 2097 30575157 30575207 4.120000e-14 89.8
23 TraesCS3A01G139400 chr7D 92.695 794 52 5 1 788 76198465 76199258 0.000000e+00 1140.0
24 TraesCS3A01G139400 chr7D 92.269 789 54 6 2 786 564333071 564333856 0.000000e+00 1112.0
25 TraesCS3A01G139400 chr7D 94.118 68 4 0 1840 1907 76199892 76199959 1.470000e-18 104.0
26 TraesCS3A01G139400 chr3B 92.541 791 54 5 1 788 342719835 342720623 0.000000e+00 1129.0
27 TraesCS3A01G139400 chr3B 91.651 527 36 5 755 1281 89341378 89341896 0.000000e+00 723.0
28 TraesCS3A01G139400 chr3B 95.588 68 3 0 1975 2042 707599386 707599319 3.160000e-20 110.0
29 TraesCS3A01G139400 chr5B 89.724 905 59 12 1 872 406162403 406161500 0.000000e+00 1125.0
30 TraesCS3A01G139400 chr5B 92.647 68 5 0 1840 1907 641693322 641693389 6.840000e-17 99.0
31 TraesCS3A01G139400 chr1B 89.870 770 43 15 538 1281 561931881 561932641 0.000000e+00 957.0
32 TraesCS3A01G139400 chr1B 93.116 552 33 1 2121 2667 159088419 159087868 0.000000e+00 804.0
33 TraesCS3A01G139400 chr1B 92.514 521 31 5 761 1281 538800502 538799990 0.000000e+00 739.0
34 TraesCS3A01G139400 chr1B 100.000 51 0 0 2047 2097 159088468 159088418 8.850000e-16 95.3
35 TraesCS3A01G139400 chr6B 89.249 772 47 16 538 1281 316577871 316577108 0.000000e+00 933.0
36 TraesCS3A01G139400 chr4D 93.601 547 35 0 2121 2667 143275909 143276455 0.000000e+00 817.0
37 TraesCS3A01G139400 chr4D 92.998 557 29 1 2121 2667 275234085 275234641 0.000000e+00 804.0
38 TraesCS3A01G139400 chr4D 98.039 51 0 1 2047 2097 143275861 143275910 1.480000e-13 87.9
39 TraesCS3A01G139400 chr5A 92.514 521 30 7 761 1281 504247157 504246646 0.000000e+00 737.0
40 TraesCS3A01G139400 chr5A 96.009 426 16 1 2562 2986 580528810 580529235 0.000000e+00 691.0
41 TraesCS3A01G139400 chr4B 91.939 521 34 5 761 1281 553684038 553683526 0.000000e+00 723.0
42 TraesCS3A01G139400 chr2B 91.603 524 37 4 758 1281 586517825 586518341 0.000000e+00 717.0
43 TraesCS3A01G139400 chr2B 89.593 221 15 2 1840 2052 425737245 425737465 1.060000e-69 274.0
44 TraesCS3A01G139400 chr6A 91.429 525 39 4 758 1281 8553975 8554494 0.000000e+00 715.0
45 TraesCS3A01G139400 chr7A 96.244 426 15 1 2562 2986 75694466 75694891 0.000000e+00 697.0
46 TraesCS3A01G139400 chr7A 96.009 426 16 1 2562 2986 557426347 557425922 0.000000e+00 691.0
47 TraesCS3A01G139400 chr7B 86.547 223 20 9 1842 2055 439175367 439175146 1.390000e-58 237.0


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 TraesCS3A01G139400 chr3A 117787639 117790638 2999 True 2255.50 2366 100.0000 1 3000 2 chr3A.!!$R1 2999
1 TraesCS3A01G139400 chr5D 184451424 184452582 1158 False 1882.00 1882 95.9520 1840 3000 1 chr5D.!!$F1 1160
2 TraesCS3A01G139400 chr5D 403968808 403969407 599 False 458.15 821 96.8295 2047 2667 2 chr5D.!!$F3 620
3 TraesCS3A01G139400 chr6D 32219331 32220939 1608 True 1036.50 1812 90.3885 1 2055 2 chr6D.!!$R1 2054
4 TraesCS3A01G139400 chr2A 33473319 33474477 1158 True 1799.00 1799 94.6600 1840 3000 1 chr2A.!!$R1 1160
5 TraesCS3A01G139400 chr2A 478452561 478455155 2594 False 1483.50 1746 94.2440 1 3000 2 chr2A.!!$F1 2999
6 TraesCS3A01G139400 chr2A 33483454 33484238 784 True 1153.00 1153 93.1560 1 788 1 chr2A.!!$R2 787
7 TraesCS3A01G139400 chr2D 382040813 382042123 1310 True 1690.00 1690 90.3200 1 1281 1 chr2D.!!$R2 1280
8 TraesCS3A01G139400 chr1D 407140861 407142658 1797 False 951.50 1646 89.1250 1 2052 2 chr1D.!!$F2 2051
9 TraesCS3A01G139400 chr1D 463400297 463400863 566 False 702.00 702 89.9470 2132 2667 1 chr1D.!!$F1 535
10 TraesCS3A01G139400 chr1D 26249332 26249937 605 True 452.15 809 96.5890 2047 2667 2 chr1D.!!$R2 620
11 TraesCS3A01G139400 chr1A 205552106 205552847 741 False 1160.00 1160 94.8790 2259 3000 1 chr1A.!!$F1 741
12 TraesCS3A01G139400 chr1A 30575157 30575760 603 False 454.40 819 95.7765 2047 2667 2 chr1A.!!$F2 620
13 TraesCS3A01G139400 chr7D 564333071 564333856 785 False 1112.00 1112 92.2690 2 786 1 chr7D.!!$F1 784
14 TraesCS3A01G139400 chr7D 76198465 76199959 1494 False 622.00 1140 93.4065 1 1907 2 chr7D.!!$F2 1906
15 TraesCS3A01G139400 chr3B 342719835 342720623 788 False 1129.00 1129 92.5410 1 788 1 chr3B.!!$F2 787
16 TraesCS3A01G139400 chr3B 89341378 89341896 518 False 723.00 723 91.6510 755 1281 1 chr3B.!!$F1 526
17 TraesCS3A01G139400 chr5B 406161500 406162403 903 True 1125.00 1125 89.7240 1 872 1 chr5B.!!$R1 871
18 TraesCS3A01G139400 chr1B 561931881 561932641 760 False 957.00 957 89.8700 538 1281 1 chr1B.!!$F1 743
19 TraesCS3A01G139400 chr1B 538799990 538800502 512 True 739.00 739 92.5140 761 1281 1 chr1B.!!$R1 520
20 TraesCS3A01G139400 chr1B 159087868 159088468 600 True 449.65 804 96.5580 2047 2667 2 chr1B.!!$R2 620
21 TraesCS3A01G139400 chr6B 316577108 316577871 763 True 933.00 933 89.2490 538 1281 1 chr6B.!!$R1 743
22 TraesCS3A01G139400 chr4D 275234085 275234641 556 False 804.00 804 92.9980 2121 2667 1 chr4D.!!$F1 546
23 TraesCS3A01G139400 chr4D 143275861 143276455 594 False 452.45 817 95.8200 2047 2667 2 chr4D.!!$F2 620
24 TraesCS3A01G139400 chr5A 504246646 504247157 511 True 737.00 737 92.5140 761 1281 1 chr5A.!!$R1 520
25 TraesCS3A01G139400 chr4B 553683526 553684038 512 True 723.00 723 91.9390 761 1281 1 chr4B.!!$R1 520
26 TraesCS3A01G139400 chr2B 586517825 586518341 516 False 717.00 717 91.6030 758 1281 1 chr2B.!!$F2 523
27 TraesCS3A01G139400 chr6A 8553975 8554494 519 False 715.00 715 91.4290 758 1281 1 chr6A.!!$F1 523

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
585 600 0.24636 TATGGGCATATCACGCGGAG 59.754 55.0 12.47 1.99 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 2255 2.695666 CTCTGGGAACGATGGTATCTGT 59.304 50.0 0.0 0.0 0.0 3.41 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
89 90 6.039717 CCTGGAAACTTGGTCACATATAATGG 59.960 42.308 0.00 0.00 33.60 3.16
164 169 3.422417 TTCAAAATGCGGTCAAAACGA 57.578 38.095 0.00 0.00 0.00 3.85
203 208 4.851639 AGCTAGTGGTTGAATCTTGGAT 57.148 40.909 0.00 0.00 0.00 3.41
456 466 9.683870 ATCCAATTTTGCAACAAATATATGGTT 57.316 25.926 0.00 0.00 0.00 3.67
585 600 0.246360 TATGGGCATATCACGCGGAG 59.754 55.000 12.47 1.99 0.00 4.63
615 630 2.152830 GAGACCGTCGGATACTGCTAT 58.847 52.381 20.51 0.00 0.00 2.97
625 640 4.803098 GGATACTGCTATATCCAACGGT 57.197 45.455 17.30 0.00 46.94 4.83
655 670 1.307343 ATCCTCTCCCCACCCACAG 60.307 63.158 0.00 0.00 0.00 3.66
685 700 1.220206 CAGCTGCCCTCACCTACAG 59.780 63.158 0.00 0.00 0.00 2.74
915 1016 3.141488 GCTCCTCCTCGCCTTCGA 61.141 66.667 0.00 0.00 43.28 3.71
933 1034 1.229625 AGGATGACCACCTGCTCCA 60.230 57.895 0.00 0.00 38.94 3.86
1010 1111 2.051804 GAGCATCAAATGGCGTCCCG 62.052 60.000 0.00 0.00 33.17 5.14
1085 1186 1.759445 CTTCTCCACTCCGACCATGAT 59.241 52.381 0.00 0.00 0.00 2.45
1229 1330 1.369091 GATTTGCCTCGCACGACCAT 61.369 55.000 0.00 0.00 38.71 3.55
1888 1989 3.428797 CGGATTCGCGTCCTCCTA 58.571 61.111 13.25 0.00 36.07 2.94
2030 2144 3.117284 GTGAGATTCCCCTCTCTACCTCT 60.117 52.174 3.07 0.00 41.87 3.69
2100 2214 3.126001 TGAGTTCCAGTTTCATTCGCT 57.874 42.857 0.00 0.00 0.00 4.93
2141 2255 6.829298 TGGTTTGTGTCAATTCAACCTTAGTA 59.171 34.615 0.00 0.00 0.00 1.82
2176 2290 5.126061 CGTTCCCAGAGAATCCAAATTTCAT 59.874 40.000 0.00 0.00 36.69 2.57
2386 2520 2.421775 CCTGCAACACAACACAACACTA 59.578 45.455 0.00 0.00 0.00 2.74
2412 2562 8.324306 AGTATAGTGCATGCATCCTATTAATGT 58.676 33.333 26.67 11.90 0.00 2.71
2468 2618 6.183360 TGTGACTTTGACTGAATTGTTGAGTC 60.183 38.462 2.90 2.90 37.27 3.36
2581 2734 9.783081 TTTACGTAGTATACATCTATGGTGAGA 57.217 33.333 5.50 0.00 45.21 3.27
2592 2745 5.899120 TCTATGGTGAGACAGTCAGTAAC 57.101 43.478 2.66 0.00 35.13 2.50
2711 2866 1.755179 ATCACCCAAAATGCCTCTCG 58.245 50.000 0.00 0.00 0.00 4.04
2767 2923 6.435277 AGTTTGCTTGATGTCCATGTTTATCT 59.565 34.615 0.00 0.00 0.00 1.98
2846 3002 4.935205 CGTACATGATCTGGAACCTTTTGA 59.065 41.667 0.00 0.00 0.00 2.69
2888 3044 4.276678 GCTGATTTAATGCCTATGCTCACA 59.723 41.667 0.00 0.00 38.71 3.58
2894 3050 1.194218 TGCCTATGCTCACACTGCTA 58.806 50.000 0.00 0.00 38.71 3.49
2906 3062 6.375174 TGCTCACACTGCTATTGATTAAATGT 59.625 34.615 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
89 90 2.422276 AGAAAACCTTCGCATTGTGC 57.578 45.000 0.00 0.00 40.69 4.57
265 274 7.497249 CAGCTGCCTCATAGTTTACTCTTTATT 59.503 37.037 0.00 0.00 0.00 1.40
359 369 1.479709 TGGTTGGGTGTCAAAAGTGG 58.520 50.000 0.00 0.00 37.08 4.00
360 370 3.817709 AATGGTTGGGTGTCAAAAGTG 57.182 42.857 0.00 0.00 37.08 3.16
430 440 9.683870 AACCATATATTTGTTGCAAAATTGGAT 57.316 25.926 15.35 5.53 32.68 3.41
456 466 4.229304 TGAGTTCTTTTGTGAAGGACCA 57.771 40.909 0.00 0.00 0.00 4.02
530 545 0.166814 GTGCAGGCTTTGATGACGTC 59.833 55.000 9.11 9.11 0.00 4.34
585 600 0.924090 CGACGGTCTCTAATGCTTGC 59.076 55.000 6.57 0.00 0.00 4.01
615 630 1.555477 GGGGTGTGGACCGTTGGATA 61.555 60.000 0.00 0.00 44.23 2.59
625 640 0.325671 GAGAGGATGAGGGGTGTGGA 60.326 60.000 0.00 0.00 0.00 4.02
655 670 3.741476 CAGCTGCTTTCGGGTGGC 61.741 66.667 0.00 0.00 41.96 5.01
685 700 0.512952 GTGTCCTCAACGACATGTGC 59.487 55.000 1.15 0.00 44.27 4.57
915 1016 1.229625 TGGAGCAGGTGGTCATCCT 60.230 57.895 11.10 0.00 43.82 3.24
954 1055 3.910490 GCGAGGCGATGAGGAGCT 61.910 66.667 0.00 0.00 0.00 4.09
981 1082 0.108186 TTTGATGCTCTGCGATCCGT 60.108 50.000 0.00 0.00 0.00 4.69
1229 1330 0.487325 TGAGAAGGGGTCAGAGGTCA 59.513 55.000 0.00 0.00 0.00 4.02
1888 1989 4.660938 GGGGACGGCTGCTTTGGT 62.661 66.667 0.00 0.00 0.00 3.67
2130 2244 5.889853 ACGATGGTATCTGTACTAAGGTTGA 59.110 40.000 0.00 0.00 0.00 3.18
2141 2255 2.695666 CTCTGGGAACGATGGTATCTGT 59.304 50.000 0.00 0.00 0.00 3.41
2176 2290 3.146066 GGCCACACTGACATGAACTAAA 58.854 45.455 0.00 0.00 0.00 1.85
2386 2520 8.324306 ACATTAATAGGATGCATGCACTATACT 58.676 33.333 25.37 16.31 0.00 2.12
2592 2745 0.668535 TATCGATGACTCAGCCACGG 59.331 55.000 8.54 0.00 0.00 4.94
2711 2866 5.803020 AGGACGATTCATCAGCTAAAAAC 57.197 39.130 0.00 0.00 0.00 2.43
2767 2923 7.039853 TGTTGCAATCAAACATTCTGGAATCTA 60.040 33.333 0.59 0.00 33.37 1.98
2846 3002 1.131883 GCAGCAGCAACTGATCGAAAT 59.868 47.619 9.94 0.00 40.25 2.17
2934 3090 8.751242 TCAATCAATTCCTAAGCATTGAATCAA 58.249 29.630 0.00 0.00 41.58 2.57


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

AutoCloner maintained by Alex Coulton.