Multiple sequence alignment - TraesCS2B01G472300

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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 TraesCS2B01G472300 chr2B 100.000 3788 0 0 1 3788 669095878 669092091 0.000000e+00 6996.0
1 TraesCS2B01G472300 chr2B 99.015 3248 30 2 542 3788 669053514 669050268 0.000000e+00 5819.0
2 TraesCS2B01G472300 chr2B 89.899 1386 121 13 1359 2737 669145255 669143882 0.000000e+00 1766.0
3 TraesCS2B01G472300 chr2B 99.815 542 1 0 1 542 669054084 669053543 0.000000e+00 996.0
4 TraesCS2B01G472300 chr2B 93.350 391 26 0 3133 3523 514767919 514768309 2.540000e-161 579.0
5 TraesCS2B01G472300 chr2B 92.519 401 26 3 3138 3537 145055092 145054695 4.250000e-159 571.0
6 TraesCS2B01G472300 chr2B 96.057 279 10 1 1030 1308 511849664 511849941 1.600000e-123 453.0
7 TraesCS2B01G472300 chr2B 95.053 283 14 0 1030 1312 396285100 396285382 2.680000e-121 446.0
8 TraesCS2B01G472300 chr2B 94.737 285 14 1 1028 1311 36444094 36443810 3.470000e-120 442.0
9 TraesCS2B01G472300 chr2D 91.461 1499 111 11 1308 2792 560205833 560204338 0.000000e+00 2043.0
10 TraesCS2B01G472300 chr2D 89.013 1438 137 12 1359 2787 560215912 560214487 0.000000e+00 1760.0
11 TraesCS2B01G472300 chr2D 87.813 1436 144 18 1308 2726 560212137 560210716 0.000000e+00 1653.0
12 TraesCS2B01G472300 chr2D 93.725 494 29 2 542 1034 560212627 560212135 0.000000e+00 739.0
13 TraesCS2B01G472300 chr2D 90.891 494 34 2 542 1034 560206314 560205831 0.000000e+00 652.0
14 TraesCS2B01G472300 chr2D 99.333 150 1 0 36 185 495083239 495083388 4.820000e-69 272.0
15 TraesCS2B01G472300 chr2D 78.868 265 33 12 258 518 61988839 61988594 1.410000e-34 158.0
16 TraesCS2B01G472300 chr2A 88.084 1435 127 25 1359 2787 700024363 700022967 0.000000e+00 1663.0
17 TraesCS2B01G472300 chr2A 90.370 135 11 2 2793 2925 735149875 735149741 3.890000e-40 176.0
18 TraesCS2B01G472300 chrUn 100.000 380 0 0 1 380 478755729 478755350 0.000000e+00 702.0
19 TraesCS2B01G472300 chrUn 89.922 129 12 1 2912 3040 425407595 425407722 8.420000e-37 165.0
20 TraesCS2B01G472300 chr3B 94.819 386 20 0 3139 3524 761092987 761093372 1.510000e-168 603.0
21 TraesCS2B01G472300 chr3B 93.590 390 24 1 3139 3528 615108739 615108351 7.050000e-162 580.0
22 TraesCS2B01G472300 chr3B 95.699 279 11 1 1030 1308 667303137 667303414 7.460000e-122 448.0
23 TraesCS2B01G472300 chr3B 98.065 155 3 0 38 192 526587809 526587655 1.730000e-68 270.0
24 TraesCS2B01G472300 chr3B 90.370 135 11 2 2793 2925 92156004 92155870 3.890000e-40 176.0
25 TraesCS2B01G472300 chr7B 94.315 387 22 0 3138 3524 740202683 740203069 9.060000e-166 593.0
26 TraesCS2B01G472300 chr7B 95.699 279 11 1 1030 1308 426203905 426204182 7.460000e-122 448.0
27 TraesCS2B01G472300 chr7B 90.370 135 11 2 2793 2925 698153244 698153110 3.890000e-40 176.0
28 TraesCS2B01G472300 chr4A 94.041 386 23 0 3138 3523 637399197 637399582 1.520000e-163 586.0
29 TraesCS2B01G472300 chr4A 91.304 184 16 0 3605 3788 18269299 18269482 6.280000e-63 252.0
30 TraesCS2B01G472300 chr1A 93.798 387 24 0 3138 3524 343691104 343691490 1.960000e-162 582.0
31 TraesCS2B01G472300 chr1A 92.935 184 10 3 1 182 593732132 593732314 8.070000e-67 265.0
32 TraesCS2B01G472300 chr3A 93.557 388 25 0 3138 3525 323633499 323633112 2.540000e-161 579.0
33 TraesCS2B01G472300 chr3A 90.698 129 11 1 2912 3040 695643336 695643463 1.810000e-38 171.0
34 TraesCS2B01G472300 chr5B 95.406 283 11 2 1026 1308 269926427 269926147 2.080000e-122 449.0
35 TraesCS2B01G472300 chr5B 92.308 182 10 3 1 180 446841960 446842139 4.860000e-64 255.0
36 TraesCS2B01G472300 chr5B 91.160 181 16 0 3608 3788 345471010 345470830 2.920000e-61 246.0
37 TraesCS2B01G472300 chr6B 95.070 284 13 1 1031 1314 705308970 705309252 2.680000e-121 446.0
38 TraesCS2B01G472300 chr6B 88.095 210 24 1 3578 3786 374333413 374333622 8.130000e-62 248.0
39 TraesCS2B01G472300 chr6B 90.370 135 11 2 2793 2925 388310424 388310290 3.890000e-40 176.0
40 TraesCS2B01G472300 chr6B 89.922 129 12 1 2912 3040 450082753 450082880 8.420000e-37 165.0
41 TraesCS2B01G472300 chr6B 77.444 133 14 12 409 536 253330778 253330899 8.780000e-07 65.8
42 TraesCS2B01G472300 chr1B 95.668 277 10 1 1034 1308 607219026 607218750 9.660000e-121 444.0
43 TraesCS2B01G472300 chr1B 97.452 157 3 1 36 192 587504845 587504690 2.240000e-67 267.0
44 TraesCS2B01G472300 chr1B 91.160 181 16 0 3608 3788 543462802 543462622 2.920000e-61 246.0
45 TraesCS2B01G472300 chr1B 90.909 132 10 2 2793 2922 683721061 683721192 3.890000e-40 176.0
46 TraesCS2B01G472300 chr1B 94.000 50 3 0 1 50 377023137 377023186 4.060000e-10 76.8
47 TraesCS2B01G472300 chr1B 93.878 49 1 2 1 47 526181860 526181812 5.250000e-09 73.1
48 TraesCS2B01G472300 chr1B 87.931 58 4 2 1 57 58152276 58152221 8.780000e-07 65.8
49 TraesCS2B01G472300 chr7D 72.123 1234 262 55 1525 2715 60302755 60301561 7.950000e-77 298.0
50 TraesCS2B01G472300 chr7D 89.922 129 12 1 2912 3040 231543961 231544088 8.420000e-37 165.0
51 TraesCS2B01G472300 chr7D 89.922 129 12 1 2912 3040 231604967 231604840 8.420000e-37 165.0
52 TraesCS2B01G472300 chr5D 98.065 155 3 0 36 190 423169479 423169325 1.730000e-68 270.0
53 TraesCS2B01G472300 chr5D 89.922 129 12 1 2912 3040 503248222 503248349 8.420000e-37 165.0
54 TraesCS2B01G472300 chr5D 89.922 129 12 1 2912 3040 503261826 503261699 8.420000e-37 165.0
55 TraesCS2B01G472300 chr5D 97.143 35 0 1 542 575 187930992 187930958 1.470000e-04 58.4
56 TraesCS2B01G472300 chr3D 92.350 183 9 4 1 180 551352933 551352753 4.860000e-64 255.0
57 TraesCS2B01G472300 chr3D 91.667 180 13 2 3608 3786 61772585 61772407 8.130000e-62 248.0
58 TraesCS2B01G472300 chr3D 91.160 181 16 0 3608 3788 13812774 13812594 2.920000e-61 246.0
59 TraesCS2B01G472300 chr3D 90.909 132 10 2 2793 2922 63498337 63498468 3.890000e-40 176.0
60 TraesCS2B01G472300 chr7A 91.713 181 15 0 3608 3788 3971448 3971628 6.280000e-63 252.0
61 TraesCS2B01G472300 chr7A 92.424 132 8 2 2793 2922 120948768 120948899 1.800000e-43 187.0
62 TraesCS2B01G472300 chr1D 91.304 184 16 0 3605 3788 24063602 24063785 6.280000e-63 252.0
63 TraesCS2B01G472300 chr1D 90.909 132 10 2 2793 2922 185751327 185751458 3.890000e-40 176.0
64 TraesCS2B01G472300 chr1D 89.922 129 12 1 2912 3040 254528557 254528684 8.420000e-37 165.0
65 TraesCS2B01G472300 chr4B 93.750 48 2 1 1 48 387941619 387941573 1.890000e-08 71.3


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 TraesCS2B01G472300 chr2B 669092091 669095878 3787 True 6996.0 6996 100.000000 1 3788 1 chr2B.!!$R3 3787
1 TraesCS2B01G472300 chr2B 669050268 669054084 3816 True 3407.5 5819 99.415000 1 3788 2 chr2B.!!$R5 3787
2 TraesCS2B01G472300 chr2B 669143882 669145255 1373 True 1766.0 1766 89.899000 1359 2737 1 chr2B.!!$R4 1378
3 TraesCS2B01G472300 chr2D 560210716 560215912 5196 True 1384.0 1760 90.183667 542 2787 3 chr2D.!!$R3 2245
4 TraesCS2B01G472300 chr2D 560204338 560206314 1976 True 1347.5 2043 91.176000 542 2792 2 chr2D.!!$R2 2250
5 TraesCS2B01G472300 chr2A 700022967 700024363 1396 True 1663.0 1663 88.084000 1359 2787 1 chr2A.!!$R1 1428
6 TraesCS2B01G472300 chr7D 60301561 60302755 1194 True 298.0 298 72.123000 1525 2715 1 chr7D.!!$R1 1190

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
380 381 7.019418 AGTCTTTAAAGTCACGACAAAAACAC 58.981 34.615 14.74 1.11 0.0 3.32 F
1092 3838 3.184379 CGAGTCGAACTCAGCAAATTTGA 59.816 43.478 22.31 0.00 45.3 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1382 4139 4.555709 AACGTGGGAGGTGCGCAA 62.556 61.111 14.00 0.0 41.49 4.85 R
2963 5759 0.244994 AGCGCCTTATATGAGCCTCG 59.755 55.000 2.29 0.0 0.00 4.63 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
380 381 7.019418 AGTCTTTAAAGTCACGACAAAAACAC 58.981 34.615 14.74 1.11 0.00 3.32
1092 3838 3.184379 CGAGTCGAACTCAGCAAATTTGA 59.816 43.478 22.31 0.00 45.30 2.69
1188 3934 7.003482 TCCCAATGCAATATGAGTTTATAGCA 58.997 34.615 0.00 0.00 35.03 3.49
1230 3976 7.332430 TGCATGTTACCACACTTATGTTACTAC 59.668 37.037 0.00 0.00 36.72 2.73
1238 3984 7.990886 ACCACACTTATGTTACTACCCATTATG 59.009 37.037 0.00 0.00 36.72 1.90
2877 5673 0.250467 GCTCACAAACTCTGCCTGGA 60.250 55.000 0.00 0.00 0.00 3.86
2895 5691 5.181748 CCTGGATGCAGCTACCTATTATTC 58.818 45.833 9.03 0.00 0.00 1.75
2963 5759 4.799428 GTGGACTAGCGATTACTTCTTCAC 59.201 45.833 0.00 0.00 0.00 3.18
2975 5771 6.954487 TTACTTCTTCACGAGGCTCATATA 57.046 37.500 15.95 0.00 0.00 0.86
3019 5815 8.046708 AGTATGTAACTGATGCCATACTTTCAA 58.953 33.333 5.56 0.00 44.56 2.69
3061 5857 6.060028 TCTGTCAATCGAGGAAAGTTTTTG 57.940 37.500 6.88 0.00 0.00 2.44
3074 5870 5.979517 GGAAAGTTTTTGATGACAAGACCTG 59.020 40.000 0.00 0.00 37.32 4.00
3110 5906 0.895530 GTCAGAGTGGATTCGGACCA 59.104 55.000 0.00 0.00 36.63 4.02
3250 6046 1.739667 GGCTCGGGCTTTGTTTTGT 59.260 52.632 7.48 0.00 38.73 2.83
3260 6056 3.449632 GCTTTGTTTTGTAGCCCGAAAA 58.550 40.909 0.00 0.00 0.00 2.29
3438 6234 0.532196 GGAGTATTTCGGGCTTCGGG 60.532 60.000 0.75 0.00 39.77 5.14
3551 6347 1.290732 CTCCCTCTCTCCTTCCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
3576 6372 1.336440 CTTGTCCATTCGTTGGTGCAA 59.664 47.619 0.00 11.03 46.52 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
794 3540 0.036952 AGCACACCGAACTCCATGAG 60.037 55.000 0.00 0.00 35.52 2.90
1092 3838 5.824624 CCTCATTAACTCACTGCCACATAAT 59.175 40.000 0.00 0.00 0.00 1.28
1188 3934 9.533253 GGTAACATGCAAAGCTTCATTTATTAT 57.467 29.630 0.00 0.00 0.00 1.28
1230 3976 8.871125 AGACTATGTTACTACCTTCATAATGGG 58.129 37.037 0.00 0.00 0.00 4.00
1238 3984 9.978336 ATATCCCTAGACTATGTTACTACCTTC 57.022 37.037 0.00 0.00 0.00 3.46
1382 4139 4.555709 AACGTGGGAGGTGCGCAA 62.556 61.111 14.00 0.00 41.49 4.85
2877 5673 5.624738 GCCTACGAATAATAGGTAGCTGCAT 60.625 44.000 4.27 0.00 41.28 3.96
2895 5691 2.237751 GCTGCATGTACCGCCTACG 61.238 63.158 0.00 0.00 39.67 3.51
2963 5759 0.244994 AGCGCCTTATATGAGCCTCG 59.755 55.000 2.29 0.00 0.00 4.63
3019 5815 4.156008 ACAGAACGTTGTTCAAGCTTTTCT 59.844 37.500 5.00 0.00 0.00 2.52
3028 5824 3.449632 TCGATTGACAGAACGTTGTTCA 58.550 40.909 5.00 5.89 0.00 3.18
3061 5857 5.304101 ACTGATATCTCCAGGTCTTGTCATC 59.696 44.000 3.98 0.00 36.03 2.92
3110 5906 4.373156 ACCATGCTTTTAGAGAAGTGGT 57.627 40.909 0.00 0.00 33.68 4.16
3260 6056 3.087906 AGCCCGGCCCGAACTATT 61.088 61.111 3.71 0.00 0.00 1.73
3652 6448 6.180472 TGAAGTTTCTGATTTGAGGTATCCC 58.820 40.000 0.00 0.00 0.00 3.85


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

AutoCloner maintained by Alex Coulton.