Multiple sequence alignment - TraesCS5D01G141700

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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 TraesCS5D01G141700 chr5D 100.000 4484 0 0 1 4484 227543486 227547969 0.000000e+00 8281.0
1 TraesCS5D01G141700 chr5B 92.959 3849 213 17 664 4484 250951525 250955343 0.000000e+00 5553.0
2 TraesCS5D01G141700 chr5A 95.292 2846 125 6 664 3505 305278077 305280917 0.000000e+00 4505.0
3 TraesCS5D01G141700 chr5A 92.084 998 64 4 3500 4484 305280968 305281963 0.000000e+00 1391.0
4 TraesCS5D01G141700 chr5A 89.144 654 68 3 1 653 394058860 394058209 0.000000e+00 811.0
5 TraesCS5D01G141700 chr5A 88.120 665 75 4 1 664 305277277 305277938 0.000000e+00 787.0
6 TraesCS5D01G141700 chr5A 88.442 597 62 6 13 606 321491074 321491666 0.000000e+00 713.0
7 TraesCS5D01G141700 chr2D 87.395 3110 328 43 666 3737 31895820 31898903 0.000000e+00 3513.0
8 TraesCS5D01G141700 chr2A 86.701 3098 365 34 666 3737 33951716 33954792 0.000000e+00 3395.0
9 TraesCS5D01G141700 chr2A 87.459 1842 211 17 666 2496 33785935 33787767 0.000000e+00 2104.0
10 TraesCS5D01G141700 chr2A 86.614 1270 133 23 2490 3737 33790456 33791710 0.000000e+00 1369.0
11 TraesCS5D01G141700 chr6D 81.675 2974 457 60 680 3586 441714508 441711556 0.000000e+00 2392.0
12 TraesCS5D01G141700 chr6D 87.725 668 72 8 1 664 441710120 441710781 0.000000e+00 771.0
13 TraesCS5D01G141700 chr6B 81.021 2998 463 72 680 3602 667248687 667245721 0.000000e+00 2287.0
14 TraesCS5D01G141700 chr2B 86.471 2114 232 27 1646 3737 52223797 52225878 0.000000e+00 2270.0
15 TraesCS5D01G141700 chr2B 87.738 1941 205 23 1663 3591 52511903 52509984 0.000000e+00 2235.0
16 TraesCS5D01G141700 chr2B 87.367 942 109 9 666 1600 52222861 52223799 0.000000e+00 1072.0
17 TraesCS5D01G141700 chr2B 86.174 933 102 15 666 1592 52512838 52511927 0.000000e+00 983.0
18 TraesCS5D01G141700 chr6A 80.658 2978 481 61 680 3586 590896537 590893584 0.000000e+00 2220.0
19 TraesCS5D01G141700 chr4D 87.360 625 74 5 22 644 322186624 322187245 0.000000e+00 712.0
20 TraesCS5D01G141700 chr4D 86.449 642 83 4 13 652 177994123 177994762 0.000000e+00 701.0
21 TraesCS5D01G141700 chr4D 85.564 665 94 2 1 664 104458176 104458839 0.000000e+00 695.0
22 TraesCS5D01G141700 chr1D 85.822 663 92 2 4 664 150091959 150091297 0.000000e+00 702.0
23 TraesCS5D01G141700 chr7D 85.871 637 84 5 31 664 110288892 110288259 0.000000e+00 673.0
24 TraesCS5D01G141700 chr7D 96.970 33 1 0 4438 4470 112257068 112257036 6.270000e-04 56.5
25 TraesCS5D01G141700 chr3A 77.095 179 40 1 4294 4471 530175735 530175557 7.940000e-18 102.0
26 TraesCS5D01G141700 chr3D 79.048 105 21 1 4368 4471 578186449 578186553 2.240000e-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 TraesCS5D01G141700 chr5D 227543486 227547969 4483 False 8281.000000 8281 100.0000 1 4484 1 chr5D.!!$F1 4483
1 TraesCS5D01G141700 chr5B 250951525 250955343 3818 False 5553.000000 5553 92.9590 664 4484 1 chr5B.!!$F1 3820
2 TraesCS5D01G141700 chr5A 305277277 305281963 4686 False 2227.666667 4505 91.8320 1 4484 3 chr5A.!!$F2 4483
3 TraesCS5D01G141700 chr5A 394058209 394058860 651 True 811.000000 811 89.1440 1 653 1 chr5A.!!$R1 652
4 TraesCS5D01G141700 chr5A 321491074 321491666 592 False 713.000000 713 88.4420 13 606 1 chr5A.!!$F1 593
5 TraesCS5D01G141700 chr2D 31895820 31898903 3083 False 3513.000000 3513 87.3950 666 3737 1 chr2D.!!$F1 3071
6 TraesCS5D01G141700 chr2A 33951716 33954792 3076 False 3395.000000 3395 86.7010 666 3737 1 chr2A.!!$F1 3071
7 TraesCS5D01G141700 chr2A 33785935 33791710 5775 False 1736.500000 2104 87.0365 666 3737 2 chr2A.!!$F2 3071
8 TraesCS5D01G141700 chr6D 441711556 441714508 2952 True 2392.000000 2392 81.6750 680 3586 1 chr6D.!!$R1 2906
9 TraesCS5D01G141700 chr6D 441710120 441710781 661 False 771.000000 771 87.7250 1 664 1 chr6D.!!$F1 663
10 TraesCS5D01G141700 chr6B 667245721 667248687 2966 True 2287.000000 2287 81.0210 680 3602 1 chr6B.!!$R1 2922
11 TraesCS5D01G141700 chr2B 52222861 52225878 3017 False 1671.000000 2270 86.9190 666 3737 2 chr2B.!!$F1 3071
12 TraesCS5D01G141700 chr2B 52509984 52512838 2854 True 1609.000000 2235 86.9560 666 3591 2 chr2B.!!$R1 2925
13 TraesCS5D01G141700 chr6A 590893584 590896537 2953 True 2220.000000 2220 80.6580 680 3586 1 chr6A.!!$R1 2906
14 TraesCS5D01G141700 chr4D 322186624 322187245 621 False 712.000000 712 87.3600 22 644 1 chr4D.!!$F3 622
15 TraesCS5D01G141700 chr4D 177994123 177994762 639 False 701.000000 701 86.4490 13 652 1 chr4D.!!$F2 639
16 TraesCS5D01G141700 chr4D 104458176 104458839 663 False 695.000000 695 85.5640 1 664 1 chr4D.!!$F1 663
17 TraesCS5D01G141700 chr1D 150091297 150091959 662 True 702.000000 702 85.8220 4 664 1 chr1D.!!$R1 660
18 TraesCS5D01G141700 chr7D 110288259 110288892 633 True 673.000000 673 85.8710 31 664 1 chr7D.!!$R1 633

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
183 184 1.269174 CGTCTCTGATGATCAGGCGAT 59.731 52.381 21.27 0.0 44.39 4.58 F
1425 1597 0.685097 GACAGTGGCAGGTTGGTAGA 59.315 55.000 0.00 0.0 0.00 2.59 F
1850 2032 1.068333 CAAAAGAAGGGTCCACATGCG 60.068 52.381 0.00 0.0 0.00 4.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1833 2015 0.036010 CTCGCATGTGGACCCTTCTT 60.036 55.000 6.39 0.0 0.00 2.52 R
3237 6184 1.302511 GTGTGATGAGGCCGTTGGT 60.303 57.895 0.00 0.0 0.00 3.67 R
3798 6821 1.721389 CCGTGAAAGATGAGACACACG 59.279 52.381 0.00 0.0 46.43 4.49 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
41 42 5.861727 ACATACTCGAAGTTACCAAACCTT 58.138 37.500 0.00 0.00 36.15 3.50
183 184 1.269174 CGTCTCTGATGATCAGGCGAT 59.731 52.381 21.27 0.00 44.39 4.58
221 223 3.681897 CGATCCAACAAAGGAACTCTCAG 59.318 47.826 0.00 0.00 41.92 3.35
291 293 1.676014 CCCGAACTGTGGATCTTGGAC 60.676 57.143 0.00 0.00 0.00 4.02
414 418 5.559148 ATGGGGATTACAGAGTTGATCTC 57.441 43.478 0.00 0.00 43.05 2.75
464 468 8.701895 CCTAAACTAGTAGGATGGTGATTGTTA 58.298 37.037 5.86 0.00 43.06 2.41
492 498 3.712218 GCCTCTATGGACTAAACCCTCTT 59.288 47.826 0.00 0.00 38.35 2.85
534 540 4.110482 GTGCTAGGGTTTACATACAGTCG 58.890 47.826 0.00 0.00 0.00 4.18
581 589 2.306805 TCCATCTTGACTTGGAGCACAT 59.693 45.455 0.00 0.00 37.10 3.21
615 624 4.939052 AAAGTCTTCGATCCGGATACAT 57.061 40.909 19.15 1.04 0.00 2.29
630 639 1.674359 TACATTGCGGCCCAATAGTG 58.326 50.000 16.22 10.39 42.15 2.74
658 667 3.400054 GAGTTAGGCCGGCCACCT 61.400 66.667 45.13 34.75 41.57 4.00
673 821 2.257207 CCACCTGAGGAAACTAGGACA 58.743 52.381 4.99 0.00 44.43 4.02
852 1003 8.033178 TCAAGAGGTGGTCAATTATCATATCA 57.967 34.615 0.00 0.00 0.00 2.15
890 1054 3.820467 ACGACATCTTTCATTCCAGCAAA 59.180 39.130 0.00 0.00 0.00 3.68
1116 1280 4.530710 AAATACTAGCGCGATCCCATTA 57.469 40.909 12.10 0.00 0.00 1.90
1288 1454 2.436173 AGCCTTTAGCCATCCACTACTC 59.564 50.000 0.00 0.00 45.47 2.59
1425 1597 0.685097 GACAGTGGCAGGTTGGTAGA 59.315 55.000 0.00 0.00 0.00 2.59
1438 1610 9.379791 GGCAGGTTGGTAGATAATGTATATAAC 57.620 37.037 0.00 0.00 0.00 1.89
1656 1835 9.566530 TGCATTATAACACATAAACATGAACAC 57.433 29.630 0.00 0.00 0.00 3.32
1758 1940 7.472334 AAGTACTTCTACCAAATCTCCGTTA 57.528 36.000 1.12 0.00 0.00 3.18
1833 2015 6.184580 ACGATTCCAATATTACGCAACAAA 57.815 33.333 0.00 0.00 0.00 2.83
1850 2032 1.068333 CAAAAGAAGGGTCCACATGCG 60.068 52.381 0.00 0.00 0.00 4.73
1899 2081 2.286872 CAGGATGAACATGAGGTGAGC 58.713 52.381 0.00 0.00 39.69 4.26
1988 2175 4.370917 GAGTTGTTGAATGCACACCATTT 58.629 39.130 0.00 0.00 44.02 2.32
2106 2293 8.387813 ACCCAAGGTAGTCAAATAAGTAAATGA 58.612 33.333 0.00 0.00 32.11 2.57
2197 2398 9.932207 TTTTCTCCAAGTGTTTCGTCTATATTA 57.068 29.630 0.00 0.00 0.00 0.98
2251 2452 9.697250 CATCAAAATTTTGTTGTGATATGATGC 57.303 29.630 25.98 0.00 39.18 3.91
2277 2483 9.736023 CCAATCTTTCTTATGTTTAATAGGCAC 57.264 33.333 0.00 0.00 0.00 5.01
2351 2557 7.337938 TGCAGGAATAGAGTATTTTGATGTGA 58.662 34.615 0.00 0.00 0.00 3.58
2364 2570 4.615588 TTGATGTGATATATGGGACGCA 57.384 40.909 0.00 0.00 0.00 5.24
2510 5411 3.071023 GGTATATCCAAGCTACAGTGGCA 59.929 47.826 12.02 0.00 34.68 4.92
2717 5652 4.067944 AGTGTTGGTCTAGGAGGAAGAT 57.932 45.455 0.00 0.00 0.00 2.40
3036 5978 5.520748 AAAGGATAGTTTCACCTCACCAT 57.479 39.130 0.00 0.00 33.16 3.55
3179 6126 3.481559 TGGATATTGGCCAAGGGAAAA 57.518 42.857 24.94 4.89 31.13 2.29
3237 6184 2.567862 TGGGGTGGATATGTTCAAGGA 58.432 47.619 0.00 0.00 0.00 3.36
3253 6200 1.745489 GGACCAACGGCCTCATCAC 60.745 63.158 0.00 0.00 0.00 3.06
3356 6303 9.764363 TGTAGATAATGAAGGCAAGTATGTTAG 57.236 33.333 0.00 0.00 0.00 2.34
3683 6706 7.275888 TCTCAAAAGTGTTATGTTTGATGCT 57.724 32.000 0.00 0.00 39.74 3.79
3717 6740 6.884280 AAGAGAGACAAACCTGTTAATTGG 57.116 37.500 0.00 0.00 35.30 3.16
3727 6750 7.286775 ACAAACCTGTTAATTGGACTATGTGTT 59.713 33.333 4.07 0.00 28.57 3.32
3728 6751 7.448748 AACCTGTTAATTGGACTATGTGTTC 57.551 36.000 4.07 0.00 0.00 3.18
3775 6798 8.991243 ACATTGAATACATTGTCAATTCTTGG 57.009 30.769 11.63 5.57 41.44 3.61
3798 6821 8.519799 TGGGATAAGTGAGAACCATTTTATTC 57.480 34.615 0.00 0.00 0.00 1.75
3952 6975 1.638529 AGAGAGTGGAGACAGGGTTG 58.361 55.000 0.00 0.00 44.46 3.77
3970 6993 2.308866 GTTGAAGGAGATGAAGGGGGAA 59.691 50.000 0.00 0.00 0.00 3.97
3988 7011 4.156739 GGGGAAATGTAGCTTTGTCTTCTG 59.843 45.833 0.00 0.00 0.00 3.02
4107 7131 2.612212 ACGTTGGACACACATTTCTGAC 59.388 45.455 0.00 0.00 0.00 3.51
4139 7163 8.531146 ACAATCATTGATCGGTTTTCCTTTATT 58.469 29.630 3.79 0.00 37.95 1.40
4213 7237 6.816640 TGAAGTTGTTAGGTATGTAGATGCAC 59.183 38.462 0.00 0.00 0.00 4.57
4226 7250 5.660460 TGTAGATGCACTCGACAACATATT 58.340 37.500 8.73 0.00 36.67 1.28
4246 7270 4.880886 TTGCATGGTGATTAAGTCATCG 57.119 40.909 0.00 0.00 41.06 3.84
4434 7459 1.987855 CCTGGACGGCAAGGACCTA 60.988 63.158 5.42 0.00 35.40 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 4.087510 TGGTAACTTCGAGTATGTCACG 57.912 45.455 0.00 0.00 37.61 4.35
41 42 6.380846 ACAATTTTGCCCTTGAGCATTAGATA 59.619 34.615 0.00 0.00 43.64 1.98
183 184 1.147600 TCGACGAGGGATCGATGGA 59.852 57.895 0.54 0.00 43.38 3.41
198 199 3.323691 TGAGAGTTCCTTTGTTGGATCGA 59.676 43.478 0.00 0.00 35.83 3.59
221 223 0.951558 ACCGACATTGGTGCTTTCAC 59.048 50.000 0.00 0.00 41.85 3.18
291 293 2.690881 TCCCCTGTTCCCCATCGG 60.691 66.667 0.00 0.00 0.00 4.18
414 418 1.226603 GTTCGTCCGATCTCGTGGG 60.227 63.158 0.00 0.00 37.74 4.61
464 468 5.544562 GGGTTTAGTCCATAGAGGCTAAGAT 59.455 44.000 0.00 0.00 37.33 2.40
534 540 2.618053 CGGTGTTCCTCTGATGTAACC 58.382 52.381 0.00 0.00 0.00 2.85
581 589 3.813166 CGAAGACTTTTTCTGCCTTGGTA 59.187 43.478 0.00 0.00 33.46 3.25
615 624 3.130819 CGCACTATTGGGCCGCAA 61.131 61.111 8.81 8.81 0.00 4.85
630 639 1.227674 CCTAACTCTCATGGGCCGC 60.228 63.158 0.00 0.00 0.00 6.53
658 667 2.027192 GCACCATGTCCTAGTTTCCTCA 60.027 50.000 0.00 0.00 0.00 3.86
673 821 9.587772 GTAGATAAGATACGATAATTGCACCAT 57.412 33.333 0.00 0.00 0.00 3.55
827 977 8.033178 TGATATGATAATTGACCACCTCTTGA 57.967 34.615 0.00 0.00 0.00 3.02
852 1003 8.621532 AAGATGTCGTGGTATTAATTGCATAT 57.378 30.769 0.00 0.00 0.00 1.78
869 1020 4.409570 CTTTGCTGGAATGAAAGATGTCG 58.590 43.478 0.00 0.00 0.00 4.35
1288 1454 1.815003 GCCTGGATCTTGTGGTCTTTG 59.185 52.381 0.00 0.00 0.00 2.77
1438 1610 6.096705 TGGAGTTCAAATAATTGCTACCATGG 59.903 38.462 11.19 11.19 36.45 3.66
1699 1880 6.302269 AGCTTGGTTCCATCTATTAATGAGG 58.698 40.000 0.00 0.00 0.00 3.86
1833 2015 0.036010 CTCGCATGTGGACCCTTCTT 60.036 55.000 6.39 0.00 0.00 2.52
1912 2096 6.669154 ACCATGATAACTGAATCACCCAAAAT 59.331 34.615 0.00 0.00 38.65 1.82
1988 2175 3.196469 TGACATGTGGTTTGCAAGGAAAA 59.804 39.130 1.15 0.00 0.00 2.29
2080 2267 8.387813 TCATTTACTTATTTGACTACCTTGGGT 58.612 33.333 0.00 0.00 40.16 4.51
2121 2308 9.429359 ACAAATGTCAAGTGTCAAAATGTTTAA 57.571 25.926 0.00 0.00 0.00 1.52
2132 2333 5.493133 TGGTAACACAAATGTCAAGTGTC 57.507 39.130 8.84 0.44 44.99 3.67
2197 2398 5.381757 TCACTTAATGGTGCAACTAAGGTT 58.618 37.500 13.57 0.40 37.16 3.50
2251 2452 9.736023 GTGCCTATTAAACATAAGAAAGATTGG 57.264 33.333 0.00 0.00 0.00 3.16
2351 2557 4.634012 TTTTAGCCTGCGTCCCATATAT 57.366 40.909 0.00 0.00 0.00 0.86
2510 5411 5.852282 ACATGAAACCTAGCAAAGTTGTT 57.148 34.783 0.00 0.00 0.00 2.83
3179 6126 8.086143 ACATTGATCCTTCATGAAATGGAAAT 57.914 30.769 17.63 12.03 46.73 2.17
3237 6184 1.302511 GTGTGATGAGGCCGTTGGT 60.303 57.895 0.00 0.00 0.00 3.67
3253 6200 3.338249 CACTACCCATTTGTGGAGAGTG 58.662 50.000 11.63 11.63 36.15 3.51
3717 6740 7.316640 ACATAGAGTGAAGTGAACACATAGTC 58.683 38.462 7.68 5.58 40.25 2.59
3727 6750 9.634021 ATGTCTTATCTACATAGAGTGAAGTGA 57.366 33.333 0.00 0.00 35.82 3.41
3775 6798 8.122952 CACGAATAAAATGGTTCTCACTTATCC 58.877 37.037 0.00 0.00 0.00 2.59
3798 6821 1.721389 CCGTGAAAGATGAGACACACG 59.279 52.381 0.00 0.00 46.43 4.49
3882 6905 8.791327 TCATTGCTTTAGAAGTTCATCATGTA 57.209 30.769 5.50 0.00 0.00 2.29
3912 6935 1.191535 CGTCCACCATTGGTCTAGGA 58.808 55.000 5.04 7.34 44.35 2.94
3952 6975 3.053320 ACATTTCCCCCTTCATCTCCTTC 60.053 47.826 0.00 0.00 0.00 3.46
3970 6993 3.754965 TGCCAGAAGACAAAGCTACATT 58.245 40.909 0.00 0.00 0.00 2.71
3988 7011 3.088532 TCCTTAACACCATGTCATTGCC 58.911 45.455 0.00 0.00 0.00 4.52
4076 7100 2.224161 TGTGTCCAACGTGATGACATGA 60.224 45.455 15.37 5.92 40.75 3.07
4107 7131 6.683974 AAACCGATCAATGATTGTTCTAGG 57.316 37.500 12.76 10.21 0.00 3.02
4139 7163 8.367943 GCACATGCATGGAATAATGAAAATAA 57.632 30.769 29.41 0.00 41.59 1.40
4213 7237 3.622612 TCACCATGCAATATGTTGTCGAG 59.377 43.478 4.00 0.00 37.65 4.04
4226 7250 4.122046 CTCGATGACTTAATCACCATGCA 58.878 43.478 0.00 0.00 41.24 3.96
4246 7270 0.837272 TTGACCCGATTCCCATCCTC 59.163 55.000 0.00 0.00 0.00 3.71
4360 7385 0.960364 GACACATGCCACCCGTCAAT 60.960 55.000 0.00 0.00 0.00 2.57
4402 7427 0.030807 TCCAGGGAGATCAGATGGCA 60.031 55.000 0.00 0.00 0.00 4.92
4434 7459 4.379243 CTTCCAGCCGTGTCGCCT 62.379 66.667 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.