Multiple sequence alignment - TraesCS3D01G355300

Loading Multiple Alignment...

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 TraesCS3D01G355300 chr3D 100.000 3302 0 0 1 3302 466756285 466752984 0.000000e+00 6098.0
1 TraesCS3D01G355300 chr3D 96.552 551 18 1 310 859 91803503 91802953 0.000000e+00 911.0
2 TraesCS3D01G355300 chr3B 94.288 2346 85 19 857 3172 620666192 620663866 0.000000e+00 3544.0
3 TraesCS3D01G355300 chr3B 93.478 322 11 4 1 315 620666492 620666174 1.390000e-128 470.0
4 TraesCS3D01G355300 chr3B 91.045 67 6 0 3176 3242 620663753 620663687 1.260000e-14 91.6
5 TraesCS3D01G355300 chr3A 95.734 1641 39 14 857 2466 609829119 609827479 0.000000e+00 2614.0
6 TraesCS3D01G355300 chr3A 89.761 752 47 12 2536 3284 609824778 609824054 0.000000e+00 935.0
7 TraesCS3D01G355300 chr3A 93.375 317 12 4 1 315 609829410 609829101 8.350000e-126 460.0
8 TraesCS3D01G355300 chr6D 99.636 550 2 0 310 859 450099116 450099665 0.000000e+00 1005.0
9 TraesCS3D01G355300 chr6D 99.091 550 5 0 310 859 284851129 284851678 0.000000e+00 989.0
10 TraesCS3D01G355300 chr6D 82.406 665 60 26 1128 1787 82568237 82567625 8.120000e-146 527.0
11 TraesCS3D01G355300 chr5D 98.198 555 8 2 310 863 58020844 58020291 0.000000e+00 968.0
12 TraesCS3D01G355300 chr5D 95.878 558 20 3 310 865 373567325 373566769 0.000000e+00 900.0
13 TraesCS3D01G355300 chr5D 83.609 665 61 15 1128 1787 412235455 412234834 6.140000e-162 580.0
14 TraesCS3D01G355300 chr7D 96.739 552 17 1 309 859 608121970 608122521 0.000000e+00 918.0
15 TraesCS3D01G355300 chr7D 96.223 556 17 4 310 864 457113890 457113338 0.000000e+00 907.0
16 TraesCS3D01G355300 chr2D 96.196 552 20 1 309 859 612544013 612544564 0.000000e+00 902.0
17 TraesCS3D01G355300 chr2D 96.036 555 18 4 306 859 544881956 544881405 0.000000e+00 900.0
18 TraesCS3D01G355300 chr5B 93.124 509 23 5 957 1456 469546571 469546066 0.000000e+00 736.0
19 TraesCS3D01G355300 chr5B 96.914 162 4 1 1492 1652 469546076 469545915 1.510000e-68 270.0
20 TraesCS3D01G355300 chrUn 83.710 663 57 15 1128 1785 32057687 32057071 2.210000e-161 579.0
21 TraesCS3D01G355300 chr4A 82.309 667 59 19 1128 1787 69984504 69983890 1.050000e-144 523.0
22 TraesCS3D01G355300 chr4A 76.221 778 134 42 1543 2290 103785097 103785853 6.730000e-97 364.0
23 TraesCS3D01G355300 chr6B 81.709 667 63 18 1128 1787 86649754 86649140 4.920000e-138 501.0
24 TraesCS3D01G355300 chr6B 81.032 659 66 21 1136 1787 86566257 86566863 1.390000e-128 470.0
25 TraesCS3D01G355300 chr4D 75.648 772 143 36 1546 2290 360913027 360912274 3.160000e-90 342.0
26 TraesCS3D01G355300 chr4B 75.323 774 142 36 1546 2290 446201228 446200475 3.180000e-85 326.0


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 TraesCS3D01G355300 chr3D 466752984 466756285 3301 True 6098.000000 6098 100.000000 1 3302 1 chr3D.!!$R2 3301
1 TraesCS3D01G355300 chr3D 91802953 91803503 550 True 911.000000 911 96.552000 310 859 1 chr3D.!!$R1 549
2 TraesCS3D01G355300 chr3B 620663687 620666492 2805 True 1368.533333 3544 92.937000 1 3242 3 chr3B.!!$R1 3241
3 TraesCS3D01G355300 chr3A 609824054 609829410 5356 True 1336.333333 2614 92.956667 1 3284 3 chr3A.!!$R1 3283
4 TraesCS3D01G355300 chr6D 450099116 450099665 549 False 1005.000000 1005 99.636000 310 859 1 chr6D.!!$F2 549
5 TraesCS3D01G355300 chr6D 284851129 284851678 549 False 989.000000 989 99.091000 310 859 1 chr6D.!!$F1 549
6 TraesCS3D01G355300 chr6D 82567625 82568237 612 True 527.000000 527 82.406000 1128 1787 1 chr6D.!!$R1 659
7 TraesCS3D01G355300 chr5D 58020291 58020844 553 True 968.000000 968 98.198000 310 863 1 chr5D.!!$R1 553
8 TraesCS3D01G355300 chr5D 373566769 373567325 556 True 900.000000 900 95.878000 310 865 1 chr5D.!!$R2 555
9 TraesCS3D01G355300 chr5D 412234834 412235455 621 True 580.000000 580 83.609000 1128 1787 1 chr5D.!!$R3 659
10 TraesCS3D01G355300 chr7D 608121970 608122521 551 False 918.000000 918 96.739000 309 859 1 chr7D.!!$F1 550
11 TraesCS3D01G355300 chr7D 457113338 457113890 552 True 907.000000 907 96.223000 310 864 1 chr7D.!!$R1 554
12 TraesCS3D01G355300 chr2D 612544013 612544564 551 False 902.000000 902 96.196000 309 859 1 chr2D.!!$F1 550
13 TraesCS3D01G355300 chr2D 544881405 544881956 551 True 900.000000 900 96.036000 306 859 1 chr2D.!!$R1 553
14 TraesCS3D01G355300 chr5B 469545915 469546571 656 True 503.000000 736 95.019000 957 1652 2 chr5B.!!$R1 695
15 TraesCS3D01G355300 chrUn 32057071 32057687 616 True 579.000000 579 83.710000 1128 1785 1 chrUn.!!$R1 657
16 TraesCS3D01G355300 chr4A 69983890 69984504 614 True 523.000000 523 82.309000 1128 1787 1 chr4A.!!$R1 659
17 TraesCS3D01G355300 chr4A 103785097 103785853 756 False 364.000000 364 76.221000 1543 2290 1 chr4A.!!$F1 747
18 TraesCS3D01G355300 chr6B 86649140 86649754 614 True 501.000000 501 81.709000 1128 1787 1 chr6B.!!$R1 659
19 TraesCS3D01G355300 chr6B 86566257 86566863 606 False 470.000000 470 81.032000 1136 1787 1 chr6B.!!$F1 651
20 TraesCS3D01G355300 chr4D 360912274 360913027 753 True 342.000000 342 75.648000 1546 2290 1 chr4D.!!$R1 744
21 TraesCS3D01G355300 chr4B 446200475 446201228 753 True 326.000000 326 75.323000 1546 2290 1 chr4B.!!$R1 744

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
302 314 1.006102 CGTCACCACCACTCCACTC 60.006 63.158 0.0 0.0 0.0 3.51 F
305 317 1.071471 CACCACCACTCCACTCCAC 59.929 63.158 0.0 0.0 0.0 4.02 F
306 318 1.074471 ACCACCACTCCACTCCACT 60.074 57.895 0.0 0.0 0.0 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1611 1673 0.103937 AGATGCAGTAGGAGAAGCGC 59.896 55.0 0.00 0.0 0.00 5.92 R
2293 2373 1.005340 GCCAAATCTCGTCAGAGCAG 58.995 55.0 0.00 0.0 44.02 4.24 R
2430 2515 0.975040 GCAGAGAGAGGGAGCTTCCA 60.975 60.0 15.31 0.0 38.64 3.53 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
53 54 1.321074 GGTCCAGAGAATCCGACCGT 61.321 60.000 0.00 0.00 42.81 4.83
76 77 4.035684 GTGAGCTTCCACGAAAAGTTTTC 58.964 43.478 16.87 16.87 0.00 2.29
114 117 2.959372 TGCTAGTACTGCACGCGT 59.041 55.556 5.58 5.58 35.31 6.01
115 118 1.287815 TGCTAGTACTGCACGCGTT 59.712 52.632 10.22 0.00 35.31 4.84
257 262 4.394712 CCCTGCGACAGTGACCCC 62.395 72.222 0.00 0.00 0.00 4.95
258 263 4.394712 CCTGCGACAGTGACCCCC 62.395 72.222 0.00 0.00 0.00 5.40
300 312 1.300697 GTCGTCACCACCACTCCAC 60.301 63.158 0.00 0.00 0.00 4.02
301 313 1.456892 TCGTCACCACCACTCCACT 60.457 57.895 0.00 0.00 0.00 4.00
302 314 1.006102 CGTCACCACCACTCCACTC 60.006 63.158 0.00 0.00 0.00 3.51
303 315 1.371558 GTCACCACCACTCCACTCC 59.628 63.158 0.00 0.00 0.00 3.85
304 316 1.074850 TCACCACCACTCCACTCCA 60.075 57.895 0.00 0.00 0.00 3.86
305 317 1.071471 CACCACCACTCCACTCCAC 59.929 63.158 0.00 0.00 0.00 4.02
306 318 1.074471 ACCACCACTCCACTCCACT 60.074 57.895 0.00 0.00 0.00 4.00
307 319 1.122019 ACCACCACTCCACTCCACTC 61.122 60.000 0.00 0.00 0.00 3.51
333 345 3.388308 CTGAGATCCAGTGCCTTTATCG 58.612 50.000 3.72 0.00 38.10 2.92
381 393 7.589993 ACCCTTCTAATCTTCATTCAATCCAT 58.410 34.615 0.00 0.00 0.00 3.41
733 746 3.632643 TGATGTTTGCTGCTATCCTGA 57.367 42.857 0.00 0.00 0.00 3.86
1043 1070 1.301716 TCCTGTTCGTCCTGCTTGC 60.302 57.895 0.00 0.00 0.00 4.01
1283 1321 1.298859 GGCGCCAGGAACAAGTACAG 61.299 60.000 24.80 0.00 0.00 2.74
2429 2514 6.360370 TGGCAATGAACCTATCTATCTACC 57.640 41.667 0.00 0.00 0.00 3.18
2430 2515 6.084738 TGGCAATGAACCTATCTATCTACCT 58.915 40.000 0.00 0.00 0.00 3.08
2445 2542 1.011595 TACCTGGAAGCTCCCTCTCT 58.988 55.000 0.00 0.00 35.03 3.10
2564 5292 4.100963 ACCTACGATTCATACAGGCATCAA 59.899 41.667 0.00 0.00 0.00 2.57
2585 5313 2.513204 CGCATGCTGGACTGGAGG 60.513 66.667 17.13 0.00 0.00 4.30
2586 5314 2.673523 GCATGCTGGACTGGAGGT 59.326 61.111 11.37 0.00 0.00 3.85
2589 5317 0.904649 CATGCTGGACTGGAGGTACA 59.095 55.000 0.00 0.00 36.22 2.90
2753 5483 1.005340 GAATGTTCAGGAGAGCTGCG 58.995 55.000 0.00 0.00 0.00 5.18
2755 5485 0.829333 ATGTTCAGGAGAGCTGCGAT 59.171 50.000 0.00 0.00 0.00 4.58
2790 5520 1.659098 CGACACCGGTGATAAAGAAGC 59.341 52.381 40.21 15.22 0.00 3.86
2820 5550 0.367887 GGGTTTGTCGCGACGATTAC 59.632 55.000 31.88 24.86 38.42 1.89
2821 5551 1.343506 GGTTTGTCGCGACGATTACT 58.656 50.000 31.88 0.00 38.42 2.24
2834 5568 5.377358 CGACGATTACTAATACACCTACCG 58.623 45.833 0.00 0.00 0.00 4.02
2861 5595 7.513371 AGAAGGTTCCACTCGTATTAGATAG 57.487 40.000 0.00 0.00 0.00 2.08
2862 5596 6.490721 AGAAGGTTCCACTCGTATTAGATAGG 59.509 42.308 0.00 0.00 0.00 2.57
2865 5601 7.468496 AGGTTCCACTCGTATTAGATAGGTAT 58.532 38.462 0.00 0.00 0.00 2.73
2975 5712 2.972505 AGGGTGCTTTGTGTCGCG 60.973 61.111 0.00 0.00 0.00 5.87
2981 5718 1.024046 TGCTTTGTGTCGCGCCATAT 61.024 50.000 0.00 0.00 0.00 1.78
2989 5726 1.616374 TGTCGCGCCATATGATAAGGA 59.384 47.619 3.65 0.00 0.00 3.36
2994 5731 2.609459 GCGCCATATGATAAGGATTCCG 59.391 50.000 3.65 0.00 0.00 4.30
2995 5732 3.861840 CGCCATATGATAAGGATTCCGT 58.138 45.455 3.65 0.00 0.00 4.69
3003 5740 9.790389 CATATGATAAGGATTCCGTTCTAGTAC 57.210 37.037 0.00 0.00 0.00 2.73
3017 5754 6.317140 CCGTTCTAGTACTACTGTAACATGGA 59.683 42.308 0.00 0.00 29.82 3.41
3046 5783 2.046507 GACAGGCAGCAGTGAGGG 60.047 66.667 0.00 0.00 0.00 4.30
3081 5818 1.802636 GTGCCATGGAATGTGACCG 59.197 57.895 18.40 0.00 44.81 4.79
3108 5845 3.328535 TGTCTGGCCTATGTCTATGGA 57.671 47.619 3.32 0.00 0.00 3.41
3133 5870 3.620488 AGGATGGCGTGTTGTATGAAAT 58.380 40.909 0.00 0.00 0.00 2.17
3172 5909 5.927030 TGTAAGTTTCGAACATTGAGATGC 58.073 37.500 0.00 0.00 36.72 3.91
3219 6065 1.933853 GATCGTTCAAATCGGACCAGG 59.066 52.381 0.00 0.00 0.00 4.45
3264 6111 3.549827 CGATCAGTGTAGGAGCAGTCATC 60.550 52.174 0.00 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 2.325583 ACTTTTCGTGGAAGCTCACA 57.674 45.000 6.39 0.00 37.50 3.58
76 77 4.982916 GCACAGTATCTACGGAGTAATTGG 59.017 45.833 0.00 0.00 45.13 3.16
156 161 4.695928 GGGTGGTCAGAGACATTTTAAGTC 59.304 45.833 0.00 0.00 33.68 3.01
300 312 1.028905 GATCTCAGTCCCGAGTGGAG 58.971 60.000 0.00 0.00 46.38 3.86
301 313 0.395862 GGATCTCAGTCCCGAGTGGA 60.396 60.000 0.00 0.00 42.41 4.02
302 314 0.684479 TGGATCTCAGTCCCGAGTGG 60.684 60.000 0.00 0.00 37.48 4.00
303 315 0.743688 CTGGATCTCAGTCCCGAGTG 59.256 60.000 0.00 0.00 38.64 3.51
304 316 3.199290 CTGGATCTCAGTCCCGAGT 57.801 57.895 0.00 0.00 38.64 4.18
333 345 2.149578 AGTTGCAGCATGACTTCACTC 58.850 47.619 2.55 0.00 39.69 3.51
733 746 3.565902 GGCTCTCAACACTTAGCAGTTTT 59.434 43.478 0.00 0.00 36.68 2.43
1277 1315 2.138656 AAAGGACGTCGCGCTGTACT 62.139 55.000 9.92 9.19 0.00 2.73
1611 1673 0.103937 AGATGCAGTAGGAGAAGCGC 59.896 55.000 0.00 0.00 0.00 5.92
2293 2373 1.005340 GCCAAATCTCGTCAGAGCAG 58.995 55.000 0.00 0.00 44.02 4.24
2429 2514 1.113788 CAGAGAGAGGGAGCTTCCAG 58.886 60.000 15.31 0.00 38.64 3.86
2430 2515 0.975040 GCAGAGAGAGGGAGCTTCCA 60.975 60.000 15.31 0.00 38.64 3.53
2546 5274 2.221749 CGGTTGATGCCTGTATGAATCG 59.778 50.000 0.00 0.00 0.00 3.34
2585 5313 2.663602 CACTGATGCTTCGTGTCTGTAC 59.336 50.000 12.90 0.00 0.00 2.90
2586 5314 2.556622 TCACTGATGCTTCGTGTCTGTA 59.443 45.455 17.43 3.38 32.15 2.74
2589 5317 1.667177 CGTCACTGATGCTTCGTGTCT 60.667 52.381 17.43 0.00 32.15 3.41
2790 5520 3.039588 CAAACCCGTGTCGGTCCG 61.040 66.667 4.39 4.39 46.80 4.79
2820 5550 4.142004 ACCTTCTTGCGGTAGGTGTATTAG 60.142 45.833 6.94 0.00 40.68 1.73
2821 5551 3.770933 ACCTTCTTGCGGTAGGTGTATTA 59.229 43.478 6.94 0.00 40.68 0.98
2834 5568 2.450609 TACGAGTGGAACCTTCTTGC 57.549 50.000 0.00 0.00 37.80 4.01
2881 5617 2.488545 GCAGAAAGGAGACGACTGACTA 59.511 50.000 0.00 0.00 33.78 2.59
2975 5712 5.491982 AGAACGGAATCCTTATCATATGGC 58.508 41.667 2.13 0.00 0.00 4.40
2981 5718 8.216423 AGTAGTACTAGAACGGAATCCTTATCA 58.784 37.037 1.87 0.00 0.00 2.15
2989 5726 7.928307 TGTTACAGTAGTACTAGAACGGAAT 57.072 36.000 1.87 0.00 29.43 3.01
2994 5731 9.918630 TTTTCCATGTTACAGTAGTACTAGAAC 57.081 33.333 1.87 15.09 0.00 3.01
3017 5754 4.599041 TGCTGCCTGTCCATATACTTTTT 58.401 39.130 0.00 0.00 0.00 1.94
3046 5783 3.998341 TGGCACGATGTTCTAAACTTACC 59.002 43.478 0.00 0.00 0.00 2.85
3081 5818 1.071385 ACATAGGCCAGACATAGCAGC 59.929 52.381 5.01 0.00 0.00 5.25
3108 5845 2.264005 TACAACACGCCATCCTTTGT 57.736 45.000 0.00 0.00 34.79 2.83
3133 5870 6.978343 AACTTACAATTTACTGCTCGCATA 57.022 33.333 0.00 0.00 0.00 3.14
3172 5909 2.102070 TTGCCAATGGGTACGTAGTG 57.898 50.000 0.00 0.00 36.07 2.74


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

AutoCloner maintained by Alex Coulton.