Multiple sequence alignment - TraesCS2B01G406200

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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 TraesCS2B01G406200 chr2B 100.000 3648 0 0 1 3648 575180110 575176463 0.000000e+00 6737
1 TraesCS2B01G406200 chr2B 98.778 900 10 1 19 917 613232053 613231154 0.000000e+00 1600
2 TraesCS2B01G406200 chr2B 81.818 330 42 10 3007 3334 155879496 155879183 1.000000e-65 261
3 TraesCS2B01G406200 chr2B 84.234 222 20 7 2171 2384 793926802 793926588 6.180000e-48 202
4 TraesCS2B01G406200 chr2D 94.803 2136 66 11 915 3009 490729240 490727109 0.000000e+00 3288
5 TraesCS2B01G406200 chr2D 90.909 176 14 2 3034 3208 635603062 635603236 6.090000e-58 235
6 TraesCS2B01G406200 chr2A 93.308 1868 72 19 917 2731 634627047 634625180 0.000000e+00 2708
7 TraesCS2B01G406200 chr2A 99.220 898 7 0 20 917 293940091 293940988 0.000000e+00 1620
8 TraesCS2B01G406200 chr2A 88.945 199 9 2 2820 3009 634624818 634624624 2.190000e-57 233
9 TraesCS2B01G406200 chr4A 99.332 898 6 0 20 917 456462420 456463317 0.000000e+00 1626
10 TraesCS2B01G406200 chr4A 74.890 227 52 5 3002 3225 690247282 690247058 8.340000e-17 99
11 TraesCS2B01G406200 chr5A 99.106 895 8 0 23 917 674077853 674078747 0.000000e+00 1609
12 TraesCS2B01G406200 chr7A 98.993 894 9 0 24 917 42661755 42662648 0.000000e+00 1602
13 TraesCS2B01G406200 chr3A 98.543 892 13 0 26 917 737269945 737270836 0.000000e+00 1576
14 TraesCS2B01G406200 chr6B 97.542 895 21 1 24 917 444745327 444744433 0.000000e+00 1530
15 TraesCS2B01G406200 chr7D 96.081 893 34 1 25 917 162110506 162109615 0.000000e+00 1454
16 TraesCS2B01G406200 chr7D 95.628 892 39 0 26 917 634720873 634719982 0.000000e+00 1432
17 TraesCS2B01G406200 chr7D 88.557 402 38 5 3007 3403 350096751 350097149 7.080000e-132 481
18 TraesCS2B01G406200 chr7D 95.122 246 12 0 3403 3648 613775342 613775097 4.420000e-104 388
19 TraesCS2B01G406200 chr7D 80.526 190 32 5 3002 3188 139194312 139194499 1.370000e-29 141
20 TraesCS2B01G406200 chr3D 95.794 642 18 1 3007 3648 560922248 560921616 0.000000e+00 1027
21 TraesCS2B01G406200 chr3D 92.273 220 12 1 3403 3622 474610663 474610877 1.270000e-79 307
22 TraesCS2B01G406200 chr3D 83.007 153 26 0 3053 3205 562334645 562334797 4.910000e-29 139
23 TraesCS2B01G406200 chr1B 88.698 407 39 4 3002 3404 643019738 643020141 1.180000e-134 490
24 TraesCS2B01G406200 chr1B 86.768 393 36 8 3006 3397 44838722 44839099 1.210000e-114 424
25 TraesCS2B01G406200 chr1B 92.958 142 8 2 3261 3400 44839022 44839163 4.770000e-49 206
26 TraesCS2B01G406200 chr6D 95.528 246 11 0 3403 3648 465844596 465844841 9.490000e-106 394
27 TraesCS2B01G406200 chr1A 94.715 246 13 0 3403 3648 510461656 510461901 2.060000e-102 383


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 TraesCS2B01G406200 chr2B 575176463 575180110 3647 True 6737.0 6737 100.0000 1 3648 1 chr2B.!!$R2 3647
1 TraesCS2B01G406200 chr2B 613231154 613232053 899 True 1600.0 1600 98.7780 19 917 1 chr2B.!!$R3 898
2 TraesCS2B01G406200 chr2D 490727109 490729240 2131 True 3288.0 3288 94.8030 915 3009 1 chr2D.!!$R1 2094
3 TraesCS2B01G406200 chr2A 293940091 293940988 897 False 1620.0 1620 99.2200 20 917 1 chr2A.!!$F1 897
4 TraesCS2B01G406200 chr2A 634624624 634627047 2423 True 1470.5 2708 91.1265 917 3009 2 chr2A.!!$R1 2092
5 TraesCS2B01G406200 chr4A 456462420 456463317 897 False 1626.0 1626 99.3320 20 917 1 chr4A.!!$F1 897
6 TraesCS2B01G406200 chr5A 674077853 674078747 894 False 1609.0 1609 99.1060 23 917 1 chr5A.!!$F1 894
7 TraesCS2B01G406200 chr7A 42661755 42662648 893 False 1602.0 1602 98.9930 24 917 1 chr7A.!!$F1 893
8 TraesCS2B01G406200 chr3A 737269945 737270836 891 False 1576.0 1576 98.5430 26 917 1 chr3A.!!$F1 891
9 TraesCS2B01G406200 chr6B 444744433 444745327 894 True 1530.0 1530 97.5420 24 917 1 chr6B.!!$R1 893
10 TraesCS2B01G406200 chr7D 162109615 162110506 891 True 1454.0 1454 96.0810 25 917 1 chr7D.!!$R1 892
11 TraesCS2B01G406200 chr7D 634719982 634720873 891 True 1432.0 1432 95.6280 26 917 1 chr7D.!!$R3 891
12 TraesCS2B01G406200 chr3D 560921616 560922248 632 True 1027.0 1027 95.7940 3007 3648 1 chr3D.!!$R1 641

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
830 832 1.898574 CGTTGTGCTTGAGGGCCTT 60.899 57.895 7.89 0.0 0.0 4.35 F
1050 1071 0.173481 ATCTCGCGCTGCTTCTAACA 59.827 50.000 5.56 0.0 0.0 2.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2287 2352 1.514087 GTTGATCAGGACGCGGGTA 59.486 57.895 12.47 0.0 0.0 3.69 R
2875 3291 0.249280 CACCAACAACGAAAAGGGGC 60.249 55.000 0.00 0.0 0.0 5.80 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
467 469 2.104963 GGTGACTCCCACTCTCTTGTTT 59.895 50.000 0.00 0.00 45.03 2.83
652 654 6.544197 TCCTAAAAATTGTGCCTTATATGCGA 59.456 34.615 0.00 0.00 0.00 5.10
770 772 4.555313 CGTGAAGAATTGTGTGACATGCTT 60.555 41.667 0.00 0.00 0.00 3.91
830 832 1.898574 CGTTGTGCTTGAGGGCCTT 60.899 57.895 7.89 0.00 0.00 4.35
1050 1071 0.173481 ATCTCGCGCTGCTTCTAACA 59.827 50.000 5.56 0.00 0.00 2.41
1175 1196 0.541998 ACGAGAGACATGACCCACCA 60.542 55.000 0.00 0.00 0.00 4.17
1827 1848 1.153188 CATGGTGGACGGCATGCTA 60.153 57.895 18.92 0.00 0.00 3.49
1914 1941 1.901085 GCTTCGTCTCACCAGGGAT 59.099 57.895 0.00 0.00 0.00 3.85
1966 1994 1.332904 CGATGGCCGAAATTTAGCGTC 60.333 52.381 0.00 6.61 41.76 5.19
2287 2352 1.454479 CTGCCGCATCCCCAAGAAT 60.454 57.895 0.00 0.00 0.00 2.40
2353 2418 3.447025 CTGGAAGGATCCCGACGCC 62.447 68.421 8.55 3.58 45.95 5.68
2735 3126 0.338814 AGGGACCGTCTATTCCTGGT 59.661 55.000 0.00 0.00 37.44 4.00
2743 3134 2.644676 GTCTATTCCTGGTTTGCCTCC 58.355 52.381 0.00 0.00 35.27 4.30
2747 3138 2.470057 TTCCTGGTTTGCCTCCTTTT 57.530 45.000 0.00 0.00 35.27 2.27
2748 3139 2.470057 TCCTGGTTTGCCTCCTTTTT 57.530 45.000 0.00 0.00 35.27 1.94
2783 3199 8.944029 TCTGTTGATTTTGCTTGATTTCAAAAA 58.056 25.926 4.56 0.00 42.93 1.94
2817 3233 3.697045 ACACAAACCAAGATGGACGAAAA 59.303 39.130 2.85 0.00 40.96 2.29
2818 3234 4.041723 CACAAACCAAGATGGACGAAAAC 58.958 43.478 2.85 0.00 40.96 2.43
2830 3246 2.986479 GGACGAAAACAATGCATTCACC 59.014 45.455 9.53 2.09 0.00 4.02
2850 3266 3.181397 CCTATGCTTCATTTTTGGTGCG 58.819 45.455 0.00 0.00 0.00 5.34
2854 3270 2.035704 TGCTTCATTTTTGGTGCGACAT 59.964 40.909 0.00 0.00 0.00 3.06
2874 3290 9.478019 GCGACATAAATAATAATGAATTCTCGG 57.522 33.333 7.05 0.00 0.00 4.63
2875 3291 9.973246 CGACATAAATAATAATGAATTCTCGGG 57.027 33.333 7.05 0.00 0.00 5.14
2885 3301 0.679960 AATTCTCGGGCCCCTTTTCG 60.680 55.000 18.66 2.73 0.00 3.46
2936 3352 4.581409 TCAGTGGGATGTTATTGATGCATG 59.419 41.667 2.46 0.00 0.00 4.06
3032 3459 0.542938 AGCCTCTATATCCGGCAGCA 60.543 55.000 0.00 0.00 46.14 4.41
3041 3468 1.718757 ATCCGGCAGCATTTTCGCTC 61.719 55.000 0.00 0.00 41.38 5.03
3059 3486 3.620488 GCTCCATTATTCACCCACTTGA 58.380 45.455 0.00 0.00 0.00 3.02
3083 3510 6.849151 ACTGAAAATGACCCCTAAGTAACTT 58.151 36.000 0.00 0.00 0.00 2.66
3092 3519 4.285260 ACCCCTAAGTAACTTGGTACACAG 59.715 45.833 0.00 0.00 39.29 3.66
3096 3523 3.830744 AGTAACTTGGTACACAGCACA 57.169 42.857 0.00 0.00 39.29 4.57
3140 3567 2.552155 GGGTAGAAATGAGTGGTGTGCA 60.552 50.000 0.00 0.00 0.00 4.57
3154 3581 5.772672 AGTGGTGTGCATAGGTTTTGATTTA 59.227 36.000 0.00 0.00 0.00 1.40
3181 3608 2.254918 TTGAACGTGTGTGCAAGTTG 57.745 45.000 0.00 0.00 44.86 3.16
3182 3609 0.449786 TGAACGTGTGTGCAAGTTGG 59.550 50.000 4.75 0.00 44.86 3.77
3183 3610 0.450184 GAACGTGTGTGCAAGTTGGT 59.550 50.000 4.75 0.00 44.86 3.67
3184 3611 0.885196 AACGTGTGTGCAAGTTGGTT 59.115 45.000 4.75 0.00 43.62 3.67
3185 3612 0.885196 ACGTGTGTGCAAGTTGGTTT 59.115 45.000 4.75 0.00 33.69 3.27
3186 3613 1.267365 CGTGTGTGCAAGTTGGTTTG 58.733 50.000 4.75 0.00 0.00 2.93
3187 3614 1.639280 GTGTGTGCAAGTTGGTTTGG 58.361 50.000 4.75 0.00 0.00 3.28
3188 3615 1.067213 GTGTGTGCAAGTTGGTTTGGT 60.067 47.619 4.75 0.00 0.00 3.67
3189 3616 1.620819 TGTGTGCAAGTTGGTTTGGTT 59.379 42.857 4.75 0.00 0.00 3.67
3367 3794 2.258726 GCTGTTGGTCCGGTTGTCC 61.259 63.158 0.00 0.87 0.00 4.02
3378 3805 1.367840 GGTTGTCCTGTCGCTGTCT 59.632 57.895 0.00 0.00 0.00 3.41
3391 3818 0.654683 GCTGTCTATCTTTGCCGCTG 59.345 55.000 0.00 0.00 0.00 5.18
3420 3847 1.445871 GTTTCCTTAATCGGTGCCGT 58.554 50.000 10.60 0.00 40.74 5.68
3438 3865 2.417379 CCGTCTCCATCGTTCAATCTGT 60.417 50.000 0.00 0.00 0.00 3.41
3475 3902 2.815503 TCTTACGTGATGGTTCTCGACA 59.184 45.455 0.00 0.00 40.39 4.35
3505 3932 2.924105 GCTGTTCTGGTGGCTTGGC 61.924 63.158 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.652421 AATTGTTGTTGTGAGTCATGCA 57.348 36.364 0.00 0.00 0.00 3.96
1 2 5.971895 AAAATTGTTGTTGTGAGTCATGC 57.028 34.783 0.00 0.00 0.00 4.06
467 469 2.017668 TTGCCCCCTTTGCAAGAGGA 62.018 55.000 21.94 6.15 43.36 3.71
652 654 2.513897 GCATTACTCGGCGGCCTT 60.514 61.111 18.34 3.60 0.00 4.35
770 772 0.851469 ACCCACCTCTATCTCCGCTA 59.149 55.000 0.00 0.00 0.00 4.26
830 832 2.706890 GTAAGAATTGGAAGGTGCGGA 58.293 47.619 0.00 0.00 0.00 5.54
1050 1071 1.247419 CGCGATAGAGGATCAGCCCT 61.247 60.000 0.00 0.00 37.82 5.19
1380 1401 2.892425 CGCATCTCCCGCCAGAAC 60.892 66.667 0.00 0.00 0.00 3.01
1389 1410 2.467826 GCACAGCTTCCGCATCTCC 61.468 63.158 0.00 0.00 39.10 3.71
1443 1464 3.410628 TCATGGACGGCAGCCCAT 61.411 61.111 5.63 0.00 43.51 4.00
1914 1941 4.214310 CCATAATGGTGGCCTTGATGTTA 58.786 43.478 3.32 0.00 31.35 2.41
2287 2352 1.514087 GTTGATCAGGACGCGGGTA 59.486 57.895 12.47 0.00 0.00 3.69
2384 2449 1.583495 TAGTCCGTGTCTGCCTCGTG 61.583 60.000 0.00 0.00 0.00 4.35
2410 2475 2.121963 AGGAGGTGGAAGTGGCCA 60.122 61.111 0.00 0.00 35.02 5.36
2672 2737 2.211250 ACTTGCACTGATCTGGCAAT 57.789 45.000 20.43 12.56 45.43 3.56
2748 3139 6.959671 AGCAAAATCAACAGAAACGAAAAA 57.040 29.167 0.00 0.00 0.00 1.94
2752 3168 5.242069 TCAAGCAAAATCAACAGAAACGA 57.758 34.783 0.00 0.00 0.00 3.85
2783 3199 6.638610 TCTTGGTTTGTGTTTCAATCATGTT 58.361 32.000 0.00 0.00 35.84 2.71
2789 3205 5.600696 GTCCATCTTGGTTTGTGTTTCAAT 58.399 37.500 0.00 0.00 39.03 2.57
2830 3246 3.853671 GTCGCACCAAAAATGAAGCATAG 59.146 43.478 0.00 0.00 0.00 2.23
2850 3266 9.774742 GCCCGAGAATTCATTATTATTTATGTC 57.225 33.333 8.44 0.00 0.00 3.06
2854 3270 6.661805 GGGGCCCGAGAATTCATTATTATTTA 59.338 38.462 17.79 0.00 0.00 1.40
2872 3288 2.197605 AACAACGAAAAGGGGCCCG 61.198 57.895 18.95 7.33 0.00 6.13
2873 3289 1.365999 CAACAACGAAAAGGGGCCC 59.634 57.895 17.12 17.12 0.00 5.80
2874 3290 1.365999 CCAACAACGAAAAGGGGCC 59.634 57.895 0.00 0.00 0.00 5.80
2875 3291 0.249280 CACCAACAACGAAAAGGGGC 60.249 55.000 0.00 0.00 0.00 5.80
2885 3301 5.236263 CCCTTTTTAAGAATGCACCAACAAC 59.764 40.000 0.00 0.00 0.00 3.32
3032 3459 4.097892 GTGGGTGAATAATGGAGCGAAAAT 59.902 41.667 0.00 0.00 0.00 1.82
3041 3468 4.588899 TCAGTCAAGTGGGTGAATAATGG 58.411 43.478 0.00 0.00 0.00 3.16
3059 3486 6.449830 AGTTACTTAGGGGTCATTTTCAGT 57.550 37.500 0.00 0.00 0.00 3.41
3083 3510 7.362487 CCAAAATAATACATGTGCTGTGTACCA 60.362 37.037 9.11 0.00 38.92 3.25
3096 3523 6.267471 CCCAGCCATGTACCAAAATAATACAT 59.733 38.462 0.00 0.00 39.55 2.29
3168 3595 1.067213 ACCAAACCAACTTGCACACAC 60.067 47.619 0.00 0.00 0.00 3.82
3367 3794 1.929836 GGCAAAGATAGACAGCGACAG 59.070 52.381 0.00 0.00 0.00 3.51
3378 3805 1.312371 GCCCAACAGCGGCAAAGATA 61.312 55.000 1.45 0.00 46.27 1.98
3391 3818 2.003937 TTAAGGAAACCTGGCCCAAC 57.996 50.000 0.00 0.00 32.13 3.77
3420 3847 4.098044 GGTCTACAGATTGAACGATGGAGA 59.902 45.833 0.00 0.00 30.09 3.71
3438 3865 3.365666 CGTAAGAAGCAACGACAGGTCTA 60.366 47.826 0.00 0.00 41.55 2.59
3475 3902 1.805945 GAACAGCGATCGAAGCGGT 60.806 57.895 21.57 14.14 44.32 5.68
3505 3932 6.240665 CAGCACACACGTATTTGTAGTATTG 58.759 40.000 0.00 0.00 0.00 1.90


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

AutoCloner maintained by Alex Coulton.