Multiple sequence alignment - TraesCS5B01G266900

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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 TraesCS5B01G266900 chr5B 100.000 2426 0 0 1 2426 451532166 451529741 0.000000e+00 4481.0
1 TraesCS5B01G266900 chr5B 94.157 753 43 1 36 787 642595460 642594708 0.000000e+00 1146.0
2 TraesCS5B01G266900 chr5B 99.235 392 3 0 2035 2426 453235857 453236248 0.000000e+00 708.0
3 TraesCS5B01G266900 chr5B 79.853 680 86 24 886 1533 453673871 453673211 1.320000e-122 449.0
4 TraesCS5B01G266900 chr5B 77.909 679 92 25 887 1533 453723512 453722860 1.060000e-98 370.0
5 TraesCS5B01G266900 chr5B 94.444 108 5 1 1883 1990 453235744 453235850 5.370000e-37 165.0
6 TraesCS5B01G266900 chr5D 97.788 2396 44 5 36 2426 378151215 378153606 0.000000e+00 4122.0
7 TraesCS5B01G266900 chr5D 82.362 669 82 23 886 1533 378122412 378123065 1.270000e-152 549.0
8 TraesCS5B01G266900 chr2B 95.346 752 34 1 36 787 310898340 310899090 0.000000e+00 1194.0
9 TraesCS5B01G266900 chr2B 97.297 37 1 0 1 37 587014859 587014823 2.010000e-06 63.9
10 TraesCS5B01G266900 chr7B 94.814 752 39 0 36 787 407387030 407387781 0.000000e+00 1173.0
11 TraesCS5B01G266900 chr7B 97.297 37 1 0 1 37 374230480 374230516 2.010000e-06 63.9
12 TraesCS5B01G266900 chr1B 94.364 763 39 3 36 797 57111078 57110319 0.000000e+00 1168.0
13 TraesCS5B01G266900 chr1B 94.595 37 0 1 1996 2032 554241277 554241243 3.370000e-04 56.5
14 TraesCS5B01G266900 chr1B 96.875 32 1 0 1996 2027 332083868 332083837 1.000000e-03 54.7
15 TraesCS5B01G266900 chr1D 94.674 751 39 1 36 786 142663470 142664219 0.000000e+00 1164.0
16 TraesCS5B01G266900 chr1D 95.349 43 1 1 1992 2033 427002124 427002082 1.560000e-07 67.6
17 TraesCS5B01G266900 chr2A 94.555 753 39 2 36 787 550182365 550183116 0.000000e+00 1162.0
18 TraesCS5B01G266900 chr2A 94.422 753 40 2 36 787 348050520 348051271 0.000000e+00 1157.0
19 TraesCS5B01G266900 chr6A 94.541 751 40 1 36 786 155746775 155746026 0.000000e+00 1158.0
20 TraesCS5B01G266900 chr6A 97.297 37 1 0 1 37 353954390 353954354 2.010000e-06 63.9
21 TraesCS5B01G266900 chr5A 86.399 772 78 15 786 1533 478892602 478893370 0.000000e+00 819.0
22 TraesCS5B01G266900 chr5A 83.699 638 82 16 821 1444 478895110 478895739 1.250000e-162 582.0
23 TraesCS5B01G266900 chr5A 80.535 673 81 25 886 1534 478858982 478859628 2.820000e-129 472.0
24 TraesCS5B01G266900 chrUn 80.117 684 88 23 886 1534 171237422 171238092 1.310000e-127 466.0
25 TraesCS5B01G266900 chrUn 79.971 684 89 23 886 1534 67042055 67041385 6.110000e-126 460.0
26 TraesCS5B01G266900 chrUn 81.579 570 70 15 987 1534 342519087 342518531 2.860000e-119 438.0
27 TraesCS5B01G266900 chr3A 100.000 37 0 0 1 37 125313738 125313702 4.330000e-08 69.4
28 TraesCS5B01G266900 chr6D 97.297 37 1 0 1 37 43824922 43824958 2.010000e-06 63.9
29 TraesCS5B01G266900 chr3B 97.297 37 0 1 1 37 720677228 720677263 7.240000e-06 62.1
30 TraesCS5B01G266900 chr3B 94.595 37 0 1 1996 2032 667663875 667663841 3.370000e-04 56.5
31 TraesCS5B01G266900 chr7D 96.875 32 1 0 1996 2027 62184364 62184395 1.000000e-03 54.7
32 TraesCS5B01G266900 chr7D 96.875 32 1 0 1996 2027 62933728 62933759 1.000000e-03 54.7
33 TraesCS5B01G266900 chr1A 96.875 32 1 0 1996 2027 307037683 307037714 1.000000e-03 54.7
34 TraesCS5B01G266900 chr3D 96.774 31 1 0 1996 2026 462453875 462453845 4.000000e-03 52.8


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 TraesCS5B01G266900 chr5B 451529741 451532166 2425 True 4481.0 4481 100.0000 1 2426 1 chr5B.!!$R1 2425
1 TraesCS5B01G266900 chr5B 642594708 642595460 752 True 1146.0 1146 94.1570 36 787 1 chr5B.!!$R4 751
2 TraesCS5B01G266900 chr5B 453673211 453673871 660 True 449.0 449 79.8530 886 1533 1 chr5B.!!$R2 647
3 TraesCS5B01G266900 chr5B 453235744 453236248 504 False 436.5 708 96.8395 1883 2426 2 chr5B.!!$F1 543
4 TraesCS5B01G266900 chr5B 453722860 453723512 652 True 370.0 370 77.9090 887 1533 1 chr5B.!!$R3 646
5 TraesCS5B01G266900 chr5D 378151215 378153606 2391 False 4122.0 4122 97.7880 36 2426 1 chr5D.!!$F2 2390
6 TraesCS5B01G266900 chr5D 378122412 378123065 653 False 549.0 549 82.3620 886 1533 1 chr5D.!!$F1 647
7 TraesCS5B01G266900 chr2B 310898340 310899090 750 False 1194.0 1194 95.3460 36 787 1 chr2B.!!$F1 751
8 TraesCS5B01G266900 chr7B 407387030 407387781 751 False 1173.0 1173 94.8140 36 787 1 chr7B.!!$F2 751
9 TraesCS5B01G266900 chr1B 57110319 57111078 759 True 1168.0 1168 94.3640 36 797 1 chr1B.!!$R1 761
10 TraesCS5B01G266900 chr1D 142663470 142664219 749 False 1164.0 1164 94.6740 36 786 1 chr1D.!!$F1 750
11 TraesCS5B01G266900 chr2A 550182365 550183116 751 False 1162.0 1162 94.5550 36 787 1 chr2A.!!$F2 751
12 TraesCS5B01G266900 chr2A 348050520 348051271 751 False 1157.0 1157 94.4220 36 787 1 chr2A.!!$F1 751
13 TraesCS5B01G266900 chr6A 155746026 155746775 749 True 1158.0 1158 94.5410 36 786 1 chr6A.!!$R1 750
14 TraesCS5B01G266900 chr5A 478892602 478895739 3137 False 700.5 819 85.0490 786 1533 2 chr5A.!!$F2 747
15 TraesCS5B01G266900 chr5A 478858982 478859628 646 False 472.0 472 80.5350 886 1534 1 chr5A.!!$F1 648
16 TraesCS5B01G266900 chrUn 171237422 171238092 670 False 466.0 466 80.1170 886 1534 1 chrUn.!!$F1 648
17 TraesCS5B01G266900 chrUn 67041385 67042055 670 True 460.0 460 79.9710 886 1534 1 chrUn.!!$R1 648
18 TraesCS5B01G266900 chrUn 342518531 342519087 556 True 438.0 438 81.5790 987 1534 1 chrUn.!!$R2 547

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
579 581 3.122948 CAGCTGCAGTTTTTGATGATTGC 59.877 43.478 16.64 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1458 1505 1.463444 GTGAACATAGTGCCGAACCAC 59.537 52.381 0.0 0.0 35.98 4.16 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
23 24 6.484818 GAAGTAACGGTAATAGTGGCAAAA 57.515 37.500 0.00 0.0 0.00 2.44
24 25 6.490566 AAGTAACGGTAATAGTGGCAAAAG 57.509 37.500 0.00 0.0 0.00 2.27
25 26 5.554070 AGTAACGGTAATAGTGGCAAAAGT 58.446 37.500 0.00 0.0 0.00 2.66
26 27 6.700352 AGTAACGGTAATAGTGGCAAAAGTA 58.300 36.000 0.00 0.0 0.00 2.24
27 28 6.815142 AGTAACGGTAATAGTGGCAAAAGTAG 59.185 38.462 0.00 0.0 0.00 2.57
28 29 5.156608 ACGGTAATAGTGGCAAAAGTAGT 57.843 39.130 0.00 0.0 0.00 2.73
29 30 6.284891 ACGGTAATAGTGGCAAAAGTAGTA 57.715 37.500 0.00 0.0 0.00 1.82
30 31 6.335777 ACGGTAATAGTGGCAAAAGTAGTAG 58.664 40.000 0.00 0.0 0.00 2.57
31 32 6.071165 ACGGTAATAGTGGCAAAAGTAGTAGT 60.071 38.462 0.00 0.0 0.00 2.73
32 33 7.122650 ACGGTAATAGTGGCAAAAGTAGTAGTA 59.877 37.037 0.00 0.0 0.00 1.82
33 34 7.646922 CGGTAATAGTGGCAAAAGTAGTAGTAG 59.353 40.741 0.00 0.0 0.00 2.57
34 35 7.437565 GGTAATAGTGGCAAAAGTAGTAGTAGC 59.562 40.741 0.00 0.0 0.00 3.58
156 157 4.762289 ATGGTGGGATAGAAGTCAACTC 57.238 45.455 0.00 0.0 0.00 3.01
501 503 6.597774 TGCAATCGCCTTGTTGTAAACTCG 62.598 45.833 0.00 0.0 42.62 4.18
579 581 3.122948 CAGCTGCAGTTTTTGATGATTGC 59.877 43.478 16.64 0.0 0.00 3.56
825 829 5.763204 TGTGGACTTCAGAGTGGTATTTTTC 59.237 40.000 0.00 0.0 35.88 2.29
826 830 5.998363 GTGGACTTCAGAGTGGTATTTTTCT 59.002 40.000 0.00 0.0 35.88 2.52
926 948 7.236432 AGCACCATATTCTGTTCTATCACCTAT 59.764 37.037 0.00 0.0 0.00 2.57
927 949 7.332926 GCACCATATTCTGTTCTATCACCTATG 59.667 40.741 0.00 0.0 0.00 2.23
1282 1320 4.783227 AGGGCAAGATAAAGAAGGTCACTA 59.217 41.667 0.00 0.0 0.00 2.74
1458 1505 9.057089 AGTAAAATATGCTCCGGAAAAATAGAG 57.943 33.333 5.23 0.0 0.00 2.43
1737 2171 5.784750 TTGAGCGTTACATTTCATCTCTG 57.215 39.130 0.00 0.0 0.00 3.35
1830 2307 9.126151 TGCCGAAATTTGGAAGTTGATAATATA 57.874 29.630 2.82 0.0 0.00 0.86
2389 3989 2.038557 AGTCCTTCGCCACATGTTAAGT 59.961 45.455 0.00 0.0 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.148315 ACTTTTGCCACTATTACCGTTACTTC 59.852 38.462 0.00 0.00 0.00 3.01
1 2 5.999600 ACTTTTGCCACTATTACCGTTACTT 59.000 36.000 0.00 0.00 0.00 2.24
2 3 5.554070 ACTTTTGCCACTATTACCGTTACT 58.446 37.500 0.00 0.00 0.00 2.24
3 4 5.868043 ACTTTTGCCACTATTACCGTTAC 57.132 39.130 0.00 0.00 0.00 2.50
4 5 6.700352 ACTACTTTTGCCACTATTACCGTTA 58.300 36.000 0.00 0.00 0.00 3.18
5 6 5.554070 ACTACTTTTGCCACTATTACCGTT 58.446 37.500 0.00 0.00 0.00 4.44
6 7 5.156608 ACTACTTTTGCCACTATTACCGT 57.843 39.130 0.00 0.00 0.00 4.83
7 8 6.335777 ACTACTACTTTTGCCACTATTACCG 58.664 40.000 0.00 0.00 0.00 4.02
8 9 7.437565 GCTACTACTACTTTTGCCACTATTACC 59.562 40.741 0.00 0.00 0.00 2.85
9 10 7.977853 TGCTACTACTACTTTTGCCACTATTAC 59.022 37.037 0.00 0.00 0.00 1.89
10 11 8.070034 TGCTACTACTACTTTTGCCACTATTA 57.930 34.615 0.00 0.00 0.00 0.98
11 12 6.942976 TGCTACTACTACTTTTGCCACTATT 58.057 36.000 0.00 0.00 0.00 1.73
12 13 6.407074 CCTGCTACTACTACTTTTGCCACTAT 60.407 42.308 0.00 0.00 0.00 2.12
13 14 5.105473 CCTGCTACTACTACTTTTGCCACTA 60.105 44.000 0.00 0.00 0.00 2.74
14 15 4.322801 CCTGCTACTACTACTTTTGCCACT 60.323 45.833 0.00 0.00 0.00 4.00
15 16 3.933332 CCTGCTACTACTACTTTTGCCAC 59.067 47.826 0.00 0.00 0.00 5.01
16 17 3.618997 GCCTGCTACTACTACTTTTGCCA 60.619 47.826 0.00 0.00 0.00 4.92
17 18 2.937149 GCCTGCTACTACTACTTTTGCC 59.063 50.000 0.00 0.00 0.00 4.52
18 19 2.603560 CGCCTGCTACTACTACTTTTGC 59.396 50.000 0.00 0.00 0.00 3.68
19 20 3.187700 CCGCCTGCTACTACTACTTTTG 58.812 50.000 0.00 0.00 0.00 2.44
20 21 2.830321 ACCGCCTGCTACTACTACTTTT 59.170 45.455 0.00 0.00 0.00 2.27
21 22 2.165845 CACCGCCTGCTACTACTACTTT 59.834 50.000 0.00 0.00 0.00 2.66
22 23 1.749634 CACCGCCTGCTACTACTACTT 59.250 52.381 0.00 0.00 0.00 2.24
23 24 1.390565 CACCGCCTGCTACTACTACT 58.609 55.000 0.00 0.00 0.00 2.57
24 25 0.248949 GCACCGCCTGCTACTACTAC 60.249 60.000 0.00 0.00 43.33 2.73
25 26 2.112898 GCACCGCCTGCTACTACTA 58.887 57.895 0.00 0.00 43.33 1.82
26 27 2.893398 GCACCGCCTGCTACTACT 59.107 61.111 0.00 0.00 43.33 2.57
34 35 2.029838 AAGAATTCTAGCACCGCCTG 57.970 50.000 8.75 0.00 0.00 4.85
156 157 3.684788 CCTGTAACTTTCCTTCATGGACG 59.315 47.826 0.00 0.00 46.14 4.79
320 321 4.005650 TGCACCTTGAAGAAGATCATGAC 58.994 43.478 0.00 0.00 0.00 3.06
501 503 4.693283 TGTCGATCACTTCCATGTTATCC 58.307 43.478 0.00 0.00 0.00 2.59
579 581 6.515832 AGGAAAATCACAAGCCAAAAAGTAG 58.484 36.000 0.00 0.00 0.00 2.57
629 631 1.340991 GGGCCACTCTATTTGCTTCCA 60.341 52.381 4.39 0.00 0.00 3.53
926 948 0.040058 ATTGGTGGATGAGCTTGCCA 59.960 50.000 0.00 0.00 0.00 4.92
927 949 0.743097 GATTGGTGGATGAGCTTGCC 59.257 55.000 0.00 0.00 0.00 4.52
1115 1150 1.328680 CGATGTCGCTCATTGGAAAGG 59.671 52.381 0.00 0.00 36.83 3.11
1282 1320 0.474660 AGCTCCTTGACCTTGACCCT 60.475 55.000 0.00 0.00 0.00 4.34
1458 1505 1.463444 GTGAACATAGTGCCGAACCAC 59.537 52.381 0.00 0.00 35.98 4.16
1686 1961 7.091443 ACTTTTACCTAAGAGTGAGAACATCG 58.909 38.462 0.00 0.00 30.51 3.84
1765 2199 4.686554 GTCGTAGCATGAGAAGTTCTTTGT 59.313 41.667 6.88 2.95 0.00 2.83
1830 2307 2.246067 TCTTAGCACCTCCCTCTGATCT 59.754 50.000 0.00 0.00 0.00 2.75
2077 2782 7.958567 TGTTTTATAAACCGCAATAGTCTTTCG 59.041 33.333 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.