Multiple sequence alignment - TraesCS2B01G554500

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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 TraesCS2B01G554500 chr2B 100.000 3894 0 0 1 3894 749575861 749571968 0.000000e+00 7191.0
1 TraesCS2B01G554500 chr2B 90.361 166 14 2 1932 2096 749573766 749573602 2.360000e-52 217.0
2 TraesCS2B01G554500 chr2B 90.361 166 14 2 2096 2260 749573930 749573766 2.360000e-52 217.0
3 TraesCS2B01G554500 chr2B 90.000 140 12 1 1055 1194 749572330 749572193 3.090000e-41 180.0
4 TraesCS2B01G554500 chr2B 90.000 140 12 1 3532 3669 749574807 749574668 3.090000e-41 180.0
5 TraesCS2B01G554500 chr2B 93.805 113 7 0 86 198 613239875 613239987 1.860000e-38 171.0
6 TraesCS2B01G554500 chr1B 97.162 1621 45 1 1 1621 375902018 375900399 0.000000e+00 2737.0
7 TraesCS2B01G554500 chr1B 96.000 1675 55 6 1616 3280 375890835 375889163 0.000000e+00 2712.0
8 TraesCS2B01G554500 chr1B 89.466 2041 129 32 1203 3191 421099465 421097459 0.000000e+00 2499.0
9 TraesCS2B01G554500 chr1B 86.814 1221 100 35 1 1203 615489187 615490364 0.000000e+00 1306.0
10 TraesCS2B01G554500 chr1B 95.207 605 24 2 3291 3894 375888773 375888173 0.000000e+00 952.0
11 TraesCS2B01G554500 chr1B 88.646 229 24 1 3666 3894 192766839 192766613 1.070000e-70 278.0
12 TraesCS2B01G554500 chr1B 87.773 229 23 3 3666 3894 369978075 369977852 2.980000e-66 263.0
13 TraesCS2B01G554500 chr1B 89.759 166 15 2 1932 2096 375890355 375890191 1.100000e-50 211.0
14 TraesCS2B01G554500 chr1B 87.273 165 21 0 2096 2260 375890519 375890355 5.140000e-44 189.0
15 TraesCS2B01G554500 chr1B 91.367 139 10 1 3533 3669 615490217 615490355 5.140000e-44 189.0
16 TraesCS2B01G554500 chr1B 89.286 140 13 1 3532 3669 375900965 375900826 1.440000e-39 174.0
17 TraesCS2B01G554500 chr1B 93.750 64 3 1 1499 1561 421099131 421099068 1.150000e-15 95.3
18 TraesCS2B01G554500 chr1B 87.143 70 8 1 1131 1199 615490457 615490526 1.160000e-10 78.7
19 TraesCS2B01G554500 chr1D 88.192 2058 148 44 1203 3199 311368860 311366837 0.000000e+00 2366.0
20 TraesCS2B01G554500 chr1D 89.333 150 16 0 2096 2245 311368122 311367973 5.140000e-44 189.0
21 TraesCS2B01G554500 chr1A 88.559 1582 117 26 1463 3023 391259200 391257662 0.000000e+00 1860.0
22 TraesCS2B01G554500 chr1A 82.836 402 34 16 1203 1571 391259540 391259141 1.040000e-85 327.0
23 TraesCS2B01G554500 chr1A 93.258 178 12 0 3022 3199 391257636 391257459 2.980000e-66 263.0
24 TraesCS2B01G554500 chr1A 90.426 94 6 3 2004 2096 391258513 391258422 1.900000e-23 121.0
25 TraesCS2B01G554500 chr7A 88.780 1221 108 15 1 1203 726240324 726239115 0.000000e+00 1469.0
26 TraesCS2B01G554500 chr7A 91.120 777 62 6 430 1203 726289056 726288284 0.000000e+00 1046.0
27 TraesCS2B01G554500 chr7A 83.509 285 35 4 1 273 726289338 726289054 4.990000e-64 255.0
28 TraesCS2B01G554500 chr7A 91.176 136 10 1 3536 3669 726288428 726288293 2.390000e-42 183.0
29 TraesCS2B01G554500 chr7A 90.441 136 11 1 3536 3669 726239259 726239124 1.110000e-40 178.0
30 TraesCS2B01G554500 chr7A 87.143 70 8 1 1131 1199 726212734 726212665 1.160000e-10 78.7
31 TraesCS2B01G554500 chrUn 88.154 1224 94 28 1 1203 357055329 357054136 0.000000e+00 1410.0
32 TraesCS2B01G554500 chrUn 91.176 136 10 1 3536 3669 357054280 357054145 2.390000e-42 183.0
33 TraesCS2B01G554500 chr5A 90.881 647 58 1 171 817 425250558 425251203 0.000000e+00 867.0
34 TraesCS2B01G554500 chr5A 92.283 311 23 1 894 1203 18057141 18056831 1.280000e-119 440.0
35 TraesCS2B01G554500 chr5A 90.678 236 18 3 3660 3894 228899351 228899583 1.050000e-80 311.0
36 TraesCS2B01G554500 chr5A 91.111 225 15 3 570 792 18057630 18057409 2.270000e-77 300.0
37 TraesCS2B01G554500 chr5A 87.097 248 28 3 3291 3536 178778932 178779177 1.070000e-70 278.0
38 TraesCS2B01G554500 chr5A 89.119 193 19 2 905 1096 178776557 178776748 5.030000e-59 239.0
39 TraesCS2B01G554500 chr5A 94.118 136 6 1 3536 3669 18056975 18056840 5.100000e-49 206.0
40 TraesCS2B01G554500 chr2A 90.726 647 58 2 171 817 305385145 305385789 0.000000e+00 861.0
41 TraesCS2B01G554500 chr2A 90.939 607 48 5 3291 3894 305388419 305389021 0.000000e+00 809.0
42 TraesCS2B01G554500 chr2A 91.266 229 18 1 3666 3894 168432530 168432756 1.050000e-80 311.0
43 TraesCS2B01G554500 chr4B 90.336 238 16 5 3660 3894 179437815 179438048 4.890000e-79 305.0
44 TraesCS2B01G554500 chr4B 85.824 261 31 5 3279 3535 436879074 436879332 4.960000e-69 272.0
45 TraesCS2B01G554500 chr3B 87.008 254 29 3 3291 3542 671369685 671369434 2.290000e-72 283.0
46 TraesCS2B01G554500 chr3B 89.119 193 20 1 905 1096 671372275 671372083 5.030000e-59 239.0
47 TraesCS2B01G554500 chr3B 84.772 197 28 2 3 198 283124797 283124992 3.070000e-46 196.0
48 TraesCS2B01G554500 chr5B 86.345 249 32 2 3291 3537 68454332 68454580 1.780000e-68 270.0
49 TraesCS2B01G554500 chr5B 86.528 193 25 1 905 1096 68451903 68452095 1.100000e-50 211.0
50 TraesCS2B01G554500 chr3A 86.235 247 30 3 3291 3535 216716461 216716217 8.300000e-67 265.0
51 TraesCS2B01G554500 chr6B 89.796 196 19 1 4 198 199019362 199019167 2.320000e-62 250.0
52 TraesCS2B01G554500 chr7B 88.832 197 21 1 3 198 264474098 264474294 1.400000e-59 241.0


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 TraesCS2B01G554500 chr2B 749571968 749575861 3893 True 1597.000000 7191 92.144400 1 3894 5 chr2B.!!$R1 3893
1 TraesCS2B01G554500 chr1B 375900399 375902018 1619 True 1455.500000 2737 93.224000 1 3669 2 chr1B.!!$R4 3668
2 TraesCS2B01G554500 chr1B 421097459 421099465 2006 True 1297.150000 2499 91.608000 1203 3191 2 chr1B.!!$R5 1988
3 TraesCS2B01G554500 chr1B 375888173 375890835 2662 True 1016.000000 2712 92.059750 1616 3894 4 chr1B.!!$R3 2278
4 TraesCS2B01G554500 chr1B 615489187 615490526 1339 False 524.566667 1306 88.441333 1 3669 3 chr1B.!!$F1 3668
5 TraesCS2B01G554500 chr1D 311366837 311368860 2023 True 1277.500000 2366 88.762500 1203 3199 2 chr1D.!!$R1 1996
6 TraesCS2B01G554500 chr1A 391257459 391259540 2081 True 642.750000 1860 88.769750 1203 3199 4 chr1A.!!$R1 1996
7 TraesCS2B01G554500 chr7A 726239115 726240324 1209 True 823.500000 1469 89.610500 1 3669 2 chr7A.!!$R2 3668
8 TraesCS2B01G554500 chr7A 726288284 726289338 1054 True 494.666667 1046 88.601667 1 3669 3 chr7A.!!$R3 3668
9 TraesCS2B01G554500 chrUn 357054136 357055329 1193 True 796.500000 1410 89.665000 1 3669 2 chrUn.!!$R1 3668
10 TraesCS2B01G554500 chr5A 425250558 425251203 645 False 867.000000 867 90.881000 171 817 1 chr5A.!!$F2 646
11 TraesCS2B01G554500 chr5A 18056831 18057630 799 True 315.333333 440 92.504000 570 3669 3 chr5A.!!$R1 3099
12 TraesCS2B01G554500 chr5A 178776557 178779177 2620 False 258.500000 278 88.108000 905 3536 2 chr5A.!!$F3 2631
13 TraesCS2B01G554500 chr2A 305385145 305389021 3876 False 835.000000 861 90.832500 171 3894 2 chr2A.!!$F2 3723
14 TraesCS2B01G554500 chr3B 671369434 671372275 2841 True 261.000000 283 88.063500 905 3542 2 chr3B.!!$R1 2637
15 TraesCS2B01G554500 chr5B 68451903 68454580 2677 False 240.500000 270 86.436500 905 3537 2 chr5B.!!$F1 2632

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
92 93 1.001293 TCACATCATAGATGAGGGCGC 59.999 52.381 13.46 0.0 42.42 6.53 F
902 1121 1.078848 GGATGCAGTGGAAGCGAGT 60.079 57.895 0.00 0.0 33.85 4.18 F
1830 4913 0.461870 AATATGCACTCTTGGCGCGA 60.462 50.000 12.10 0.0 0.00 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1830 4913 1.827245 GCATCTCCCTTGGGGTTTTGT 60.827 52.381 5.78 0.0 44.74 2.83 R
2806 6240 1.284785 CCTCCTTTCCCCTGCATACAA 59.715 52.381 0.00 0.0 0.00 2.41 R
3196 6657 0.394488 TTCCGAGTGGTTGGTTGCAA 60.394 50.000 0.00 0.0 36.30 4.08 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
52 53 2.106938 GATGATGTCGGCGGCAGA 59.893 61.111 22.09 9.65 0.00 4.26
92 93 1.001293 TCACATCATAGATGAGGGCGC 59.999 52.381 13.46 0.00 42.42 6.53
139 140 7.704727 TGGAAACCTTTTCCTCCATAATCTTA 58.295 34.615 16.68 0.00 39.31 2.10
326 340 2.344142 GGTGTGTGCTTTGACGTTTTTG 59.656 45.455 0.00 0.00 0.00 2.44
657 678 3.944015 CCTTGGAAGCAAGAATGGTCTAG 59.056 47.826 0.00 0.00 35.91 2.43
830 1049 5.594725 ACTCTATTGCTCTAGGATCGAACAA 59.405 40.000 0.00 0.00 0.00 2.83
902 1121 1.078848 GGATGCAGTGGAAGCGAGT 60.079 57.895 0.00 0.00 33.85 4.18
938 1158 1.633774 AGAGGGTATGCCTATGGTCG 58.366 55.000 0.00 0.00 34.45 4.79
1437 4424 4.575885 TGGACCTATGTAACTTGTTCTGC 58.424 43.478 0.00 0.00 0.00 4.26
1613 4696 9.134734 GTGTTGTCATGTTTGTCTTTTCTTTTA 57.865 29.630 0.00 0.00 0.00 1.52
1745 4828 4.286549 TGAGATGGGTCCCTTACGTTTTTA 59.713 41.667 10.00 0.00 0.00 1.52
1830 4913 0.461870 AATATGCACTCTTGGCGCGA 60.462 50.000 12.10 0.00 0.00 5.87
2042 5137 5.241403 TGTTGGTTGATGGTATCACTCTT 57.759 39.130 0.00 0.00 39.39 2.85
2238 5334 6.151312 TGTGATCTCACCTAAACTGACTCTAC 59.849 42.308 7.81 0.00 45.88 2.59
2520 5942 8.962679 ACTAACAGTTTAGTCATTGGACAAAAA 58.037 29.630 0.00 0.00 43.91 1.94
2571 5993 7.064016 GGTGCTTCAATTGTTTTGTGTTCTTTA 59.936 33.333 5.13 0.00 0.00 1.85
2599 6021 9.762381 TGATTGTACCTTTTTCTTATATTGGGT 57.238 29.630 0.00 0.00 0.00 4.51
2601 6023 9.762381 ATTGTACCTTTTTCTTATATTGGGTGA 57.238 29.630 0.00 0.00 0.00 4.02
2602 6024 9.589461 TTGTACCTTTTTCTTATATTGGGTGAA 57.411 29.630 0.00 0.00 0.00 3.18
2603 6025 9.589461 TGTACCTTTTTCTTATATTGGGTGAAA 57.411 29.630 0.00 0.00 0.00 2.69
2806 6240 2.039418 GCAAAGGGTTCAAAGAAGGGT 58.961 47.619 0.00 0.00 0.00 4.34
3120 6581 2.800250 AGGATGTTGCTTCTTCCTTGG 58.200 47.619 9.20 0.00 38.34 3.61
3196 6657 2.146342 CGAATCAGTTGTGCTGGAGTT 58.854 47.619 0.00 0.00 45.08 3.01
3199 6660 1.024271 TCAGTTGTGCTGGAGTTTGC 58.976 50.000 0.00 0.00 45.08 3.68
3282 6754 9.627123 TTTTCTAGGTCCAACAATATAGAATGG 57.373 33.333 0.00 0.00 31.40 3.16
3283 6755 7.931015 TCTAGGTCCAACAATATAGAATGGT 57.069 36.000 0.00 0.00 32.90 3.55
3285 6757 6.575244 AGGTCCAACAATATAGAATGGTGA 57.425 37.500 0.00 0.00 36.33 4.02
3286 6758 6.595682 AGGTCCAACAATATAGAATGGTGAG 58.404 40.000 0.00 0.00 36.33 3.51
3287 6759 5.239525 GGTCCAACAATATAGAATGGTGAGC 59.760 44.000 0.00 0.00 36.33 4.26
3304 7966 5.949952 TGGTGAGCAGTTACTAGAGATGTAA 59.050 40.000 0.00 0.00 0.00 2.41
3309 7971 9.628500 TGAGCAGTTACTAGAGATGTAATTAGA 57.372 33.333 0.00 0.00 33.29 2.10
3436 8099 7.964604 ATACTTCCAGATTCTAATTTACCGC 57.035 36.000 0.00 0.00 0.00 5.68
3539 8203 6.496338 AAATTTAGTCCGACATTTCCACTC 57.504 37.500 0.40 0.00 0.00 3.51
3542 8206 2.248248 AGTCCGACATTTCCACTCTGA 58.752 47.619 0.40 0.00 0.00 3.27
3543 8207 2.632996 AGTCCGACATTTCCACTCTGAA 59.367 45.455 0.40 0.00 0.00 3.02
3553 8217 1.171308 CCACTCTGAACAAGCCATGG 58.829 55.000 7.63 7.63 0.00 3.66
3573 8237 3.117776 TGGTGCATATTGCCTCAGATTCT 60.118 43.478 0.00 0.00 44.23 2.40
3693 8358 0.539669 TGACTCCTCTTCGCTGGACA 60.540 55.000 0.00 0.00 0.00 4.02
3765 8430 5.613329 TCTCGGTTTTGTACATGTTAGGTT 58.387 37.500 2.30 0.00 0.00 3.50
3879 8544 9.107177 TGCATTGTAAATCATGAAAAACTTGTT 57.893 25.926 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 2.244117 CTACTCAGCACCACCGCCAT 62.244 60.000 0.00 0.00 0.00 4.40
52 53 2.022718 AGAGGAGAGACCAGTTGCTT 57.977 50.000 0.00 0.00 42.04 3.91
92 93 4.124351 TCGCGTTCCTGTAGCCCG 62.124 66.667 5.77 0.00 0.00 6.13
139 140 2.100879 GAGTTGTGGAGCACCTCGGT 62.101 60.000 0.71 0.00 37.04 4.69
190 203 7.044496 AGATTCAGAAAAAGGGAAGGGAATA 57.956 36.000 0.00 0.00 0.00 1.75
227 240 3.795623 TCCTACGCATAACTGAGGAAC 57.204 47.619 0.00 0.00 33.33 3.62
307 321 1.989165 GCAAAAACGTCAAAGCACACA 59.011 42.857 0.00 0.00 0.00 3.72
586 605 8.677300 TCTGGCATAAAACAATCTATGACTTTC 58.323 33.333 0.00 0.00 35.01 2.62
605 624 2.664402 ACTTGTCCTGTTTCTGGCAT 57.336 45.000 0.00 0.00 0.00 4.40
657 678 6.861065 TTCCACGGCTTTCTATATGAAATC 57.139 37.500 0.00 0.00 42.96 2.17
830 1049 1.004044 CTCATGGCTTCCAGTTCCAGT 59.996 52.381 0.00 0.00 36.75 4.00
902 1121 3.234630 CTTCCACCCCGCGTCTTCA 62.235 63.158 4.92 0.00 0.00 3.02
938 1158 0.802607 GTGTCATCTCGGAAGGCGAC 60.803 60.000 0.00 0.00 0.00 5.19
1437 4424 5.464057 ACAATTTGACAACATGATGCAACAG 59.536 36.000 0.00 0.00 0.00 3.16
1447 4434 6.753279 CAGACAAGACAACAATTTGACAACAT 59.247 34.615 2.79 0.00 36.48 2.71
1613 4696 3.901844 TGCTCCACAAGTTCTAGTTACCT 59.098 43.478 0.00 0.00 0.00 3.08
1745 4828 3.795688 TTCCTGCTGACTTTTCCAGAT 57.204 42.857 0.00 0.00 33.65 2.90
1799 4882 6.445451 AGAGTGCATATTCATTACAGGGAT 57.555 37.500 0.00 0.00 0.00 3.85
1830 4913 1.827245 GCATCTCCCTTGGGGTTTTGT 60.827 52.381 5.78 0.00 44.74 2.83
1923 5008 4.585162 GGCTGGAACTCTTAGTCATAGCTA 59.415 45.833 0.00 0.00 0.00 3.32
2042 5137 6.313658 CAGTTTAAATGAGATCACATCCACGA 59.686 38.462 6.08 0.00 0.00 4.35
2238 5334 8.336806 TCCACTACAAAACTGTTTAACAATACG 58.663 33.333 6.16 0.00 0.00 3.06
2520 5942 7.995488 CCTAAACAGACCATCTCCATAGAAAAT 59.005 37.037 0.00 0.00 34.73 1.82
2527 5949 3.370953 GCACCTAAACAGACCATCTCCAT 60.371 47.826 0.00 0.00 0.00 3.41
2610 6032 9.685828 GCAGTTAGTACCTTATATTCTCTTCAG 57.314 37.037 0.00 0.00 0.00 3.02
2713 6147 2.814336 GTTCACTTCTTTCCATCGCCTT 59.186 45.455 0.00 0.00 0.00 4.35
2806 6240 1.284785 CCTCCTTTCCCCTGCATACAA 59.715 52.381 0.00 0.00 0.00 2.41
2875 6309 3.361977 CAACAACCCGCTTCCCCG 61.362 66.667 0.00 0.00 0.00 5.73
2890 6324 2.163412 CGATTTGGCTCCCGAATTTCAA 59.837 45.455 0.00 0.00 37.71 2.69
3196 6657 0.394488 TTCCGAGTGGTTGGTTGCAA 60.394 50.000 0.00 0.00 36.30 4.08
3199 6660 1.890876 TCATTCCGAGTGGTTGGTTG 58.109 50.000 0.00 0.00 36.30 3.77
3280 6752 4.344978 ACATCTCTAGTAACTGCTCACCA 58.655 43.478 0.00 0.00 0.00 4.17
3282 6754 9.672086 CTAATTACATCTCTAGTAACTGCTCAC 57.328 37.037 0.00 0.00 34.59 3.51
3283 6755 9.628500 TCTAATTACATCTCTAGTAACTGCTCA 57.372 33.333 0.00 0.00 34.59 4.26
3436 8099 5.412904 GGAATATCCCCGCTAAAATCAAGAG 59.587 44.000 0.00 0.00 0.00 2.85
3447 8110 4.993705 TTAATGAAGGAATATCCCCGCT 57.006 40.909 0.00 0.00 37.19 5.52
3539 8203 0.892755 ATGCACCATGGCTTGTTCAG 59.107 50.000 13.04 0.00 34.04 3.02
3542 8206 2.419021 GCAATATGCACCATGGCTTGTT 60.419 45.455 13.04 0.00 44.26 2.83
3543 8207 1.137479 GCAATATGCACCATGGCTTGT 59.863 47.619 13.04 0.00 44.26 3.16
3633 8298 6.743773 GCCAACAATAGAGCTCTCCTCATATT 60.744 42.308 22.17 10.48 43.31 1.28
3722 8387 8.262227 ACCGAGATCAACCATGTAATTTTACTA 58.738 33.333 0.00 0.00 34.77 1.82
3765 8430 7.618019 ATGGGAAGTAGAACTCATAATGCTA 57.382 36.000 0.00 0.00 0.00 3.49
3836 8501 3.472283 TGCACAACATGATTTGGCTTT 57.528 38.095 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.