Multiple sequence alignment - TraesCS5D01G121100

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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 TraesCS5D01G121100 chr5D 100.000 5076 0 0 414 5489 173591129 173586054 0.000000e+00 9374
1 TraesCS5D01G121100 chr5D 100.000 91 0 0 1 91 173591542 173591452 9.460000e-38 169
2 TraesCS5D01G121100 chr5A 97.307 4531 102 11 431 4946 194455623 194451098 0.000000e+00 7673
3 TraesCS5D01G121100 chr5B 97.435 4328 92 7 631 4946 185218510 185222830 0.000000e+00 7360
4 TraesCS5D01G121100 chr5B 90.893 549 36 7 4951 5489 388607484 388606940 0.000000e+00 725
5 TraesCS5D01G121100 chr5B 95.070 142 3 2 489 630 185218293 185218430 2.570000e-53 220
6 TraesCS5D01G121100 chr5B 96.703 91 3 0 1 91 185217801 185217891 9.520000e-33 152
7 TraesCS5D01G121100 chrUn 82.656 1476 185 42 1897 3341 42443336 42441901 0.000000e+00 1242
8 TraesCS5D01G121100 chrUn 81.394 1521 188 57 415 1881 327872107 327870628 0.000000e+00 1153
9 TraesCS5D01G121100 chrUn 81.262 1521 190 58 415 1881 42444800 42443321 0.000000e+00 1142
10 TraesCS5D01G121100 chrUn 82.835 1037 131 28 1897 2921 327870643 327869642 0.000000e+00 885
11 TraesCS5D01G121100 chrUn 80.629 1177 149 34 3371 4493 42441841 42440690 0.000000e+00 837
12 TraesCS5D01G121100 chr3D 83.574 1248 155 27 646 1872 606858713 606859931 0.000000e+00 1123
13 TraesCS5D01G121100 chr3D 81.841 1173 141 33 3371 4493 606861405 606862555 0.000000e+00 920
14 TraesCS5D01G121100 chr3D 84.588 837 105 16 1898 2722 606859926 606860750 0.000000e+00 809
15 TraesCS5D01G121100 chr3D 82.708 613 71 24 2749 3341 606860748 606861345 3.790000e-141 512
16 TraesCS5D01G121100 chr3D 81.884 552 90 7 4947 5489 336826178 336825628 1.800000e-124 457
17 TraesCS5D01G121100 chr3A 85.244 1064 126 19 839 1881 739118085 739119138 0.000000e+00 1066
18 TraesCS5D01G121100 chr3A 81.065 1183 136 38 3371 4493 739120626 739121780 0.000000e+00 863
19 TraesCS5D01G121100 chr3A 82.888 935 115 29 1898 2825 739119124 739120020 0.000000e+00 798
20 TraesCS5D01G121100 chr3A 81.786 571 65 23 2787 3341 739120019 739120566 5.050000e-120 442
21 TraesCS5D01G121100 chr7D 93.818 550 26 2 4948 5489 178120722 178121271 0.000000e+00 821
22 TraesCS5D01G121100 chr7A 88.359 524 51 6 4975 5489 5482768 5482246 6.040000e-174 621
23 TraesCS5D01G121100 chr7A 82.084 547 89 5 4951 5489 701288499 701287954 5.010000e-125 459
24 TraesCS5D01G121100 chr6D 89.195 472 43 6 4950 5415 268063630 268063161 2.850000e-162 582
25 TraesCS5D01G121100 chr3B 82.430 535 85 6 4947 5473 228425066 228424533 5.010000e-125 459
26 TraesCS5D01G121100 chr2A 82.033 551 85 9 4950 5489 32775097 32775644 1.800000e-124 457
27 TraesCS5D01G121100 chr2A 81.455 550 94 5 4948 5489 81461586 81462135 1.400000e-120 444


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 TraesCS5D01G121100 chr5D 173586054 173591542 5488 True 4771.500000 9374 100.000000 1 5489 2 chr5D.!!$R1 5488
1 TraesCS5D01G121100 chr5A 194451098 194455623 4525 True 7673.000000 7673 97.307000 431 4946 1 chr5A.!!$R1 4515
2 TraesCS5D01G121100 chr5B 185217801 185222830 5029 False 2577.333333 7360 96.402667 1 4946 3 chr5B.!!$F1 4945
3 TraesCS5D01G121100 chr5B 388606940 388607484 544 True 725.000000 725 90.893000 4951 5489 1 chr5B.!!$R1 538
4 TraesCS5D01G121100 chrUn 42440690 42444800 4110 True 1073.666667 1242 81.515667 415 4493 3 chrUn.!!$R1 4078
5 TraesCS5D01G121100 chrUn 327869642 327872107 2465 True 1019.000000 1153 82.114500 415 2921 2 chrUn.!!$R2 2506
6 TraesCS5D01G121100 chr3D 606858713 606862555 3842 False 841.000000 1123 83.177750 646 4493 4 chr3D.!!$F1 3847
7 TraesCS5D01G121100 chr3D 336825628 336826178 550 True 457.000000 457 81.884000 4947 5489 1 chr3D.!!$R1 542
8 TraesCS5D01G121100 chr3A 739118085 739121780 3695 False 792.250000 1066 82.745750 839 4493 4 chr3A.!!$F1 3654
9 TraesCS5D01G121100 chr7D 178120722 178121271 549 False 821.000000 821 93.818000 4948 5489 1 chr7D.!!$F1 541
10 TraesCS5D01G121100 chr7A 5482246 5482768 522 True 621.000000 621 88.359000 4975 5489 1 chr7A.!!$R1 514
11 TraesCS5D01G121100 chr7A 701287954 701288499 545 True 459.000000 459 82.084000 4951 5489 1 chr7A.!!$R2 538
12 TraesCS5D01G121100 chr3B 228424533 228425066 533 True 459.000000 459 82.430000 4947 5473 1 chr3B.!!$R1 526
13 TraesCS5D01G121100 chr2A 32775097 32775644 547 False 457.000000 457 82.033000 4950 5489 1 chr2A.!!$F1 539
14 TraesCS5D01G121100 chr2A 81461586 81462135 549 False 444.000000 444 81.455000 4948 5489 1 chr2A.!!$F2 541

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
530 535 2.045561 ACGTGGTCCATGTTTTGTGA 57.954 45.000 11.2 0.0 28.11 3.58 F
1148 1266 4.007659 AGAACTGAACAAAAACCGACAGT 58.992 39.130 0.0 0.0 39.70 3.55 F
1506 1631 1.002544 ACCTCTTCCTGCTGTTAGTGC 59.997 52.381 0.0 0.0 0.00 4.40 F
1746 1882 3.855950 CGCGTCTTTTCTCTACCGTTTAT 59.144 43.478 0.0 0.0 0.00 1.40 F
1853 1989 4.263462 TGCTGGTTGTCTGGTCATATTCTT 60.263 41.667 0.0 0.0 0.00 2.52 F
3854 4135 4.666512 ACTGGCATCCAACCATATTATCC 58.333 43.478 0.0 0.0 36.36 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1472 1597 0.119358 AGAGGTGGCTTAGGGACCTT 59.881 55.000 0.00 0.00 40.33 3.50 R
2992 3212 0.249868 TTCTGGTGCTGAAGACCACG 60.250 55.000 0.00 0.00 38.63 4.94 R
3125 3357 3.063180 CAGAAACCTGCAAAGATAGAGCG 59.937 47.826 0.00 0.00 0.00 5.03 R
3789 4070 3.118482 TGCTGCTCTAAGAAATCTCCTGG 60.118 47.826 0.00 0.00 0.00 4.45 R
4050 4335 1.202580 CGAACCCATGGGAGATCTGAC 60.203 57.143 38.07 15.81 38.96 3.51 R
5133 5477 0.878523 CTCGAGTTTTCCGCCACACA 60.879 55.000 3.62 0.00 0.00 3.72 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
530 535 2.045561 ACGTGGTCCATGTTTTGTGA 57.954 45.000 11.20 0.00 28.11 3.58
777 880 8.958119 AATAACTAATCGGTTGCTTCTATGAA 57.042 30.769 0.00 0.00 0.00 2.57
954 1072 5.793817 TCTTGCTATCTTGTTTGCTCAGTA 58.206 37.500 0.00 0.00 0.00 2.74
1148 1266 4.007659 AGAACTGAACAAAAACCGACAGT 58.992 39.130 0.00 0.00 39.70 3.55
1275 1393 6.764308 AACATAAGCTGTGCAAACTCATAT 57.236 33.333 0.00 0.00 38.39 1.78
1472 1597 3.502191 AAAACAAGCAGCGTTCAAAGA 57.498 38.095 0.00 0.00 0.00 2.52
1473 1598 3.502191 AAACAAGCAGCGTTCAAAGAA 57.498 38.095 0.00 0.00 0.00 2.52
1474 1599 2.763249 ACAAGCAGCGTTCAAAGAAG 57.237 45.000 0.00 0.00 0.00 2.85
1506 1631 1.002544 ACCTCTTCCTGCTGTTAGTGC 59.997 52.381 0.00 0.00 0.00 4.40
1746 1882 3.855950 CGCGTCTTTTCTCTACCGTTTAT 59.144 43.478 0.00 0.00 0.00 1.40
1853 1989 4.263462 TGCTGGTTGTCTGGTCATATTCTT 60.263 41.667 0.00 0.00 0.00 2.52
2268 2408 5.997129 GCTGGGAAGAATTTCATTTTTGGAA 59.003 36.000 0.00 0.00 34.90 3.53
2300 2440 5.876651 TCATCTCTGTGCTATGGTGTTAT 57.123 39.130 0.00 0.00 0.00 1.89
2461 2604 4.846779 TTGGCTTGTTGAGGTTTGTATC 57.153 40.909 0.00 0.00 0.00 2.24
2545 2695 5.416083 CATTCATCATTGCCATTTCACTGT 58.584 37.500 0.00 0.00 0.00 3.55
2596 2747 7.832503 AATTTGCAATTATGAAGTAACCAGC 57.167 32.000 0.00 0.00 0.00 4.85
2670 2823 8.830915 TTTCACAGAGAGGAATAGACTTCTAT 57.169 34.615 0.00 0.00 40.68 1.98
2992 3212 6.075984 TGTAGAGGTCAGAATAAGGTATCCC 58.924 44.000 0.00 0.00 0.00 3.85
3789 4070 7.786178 AACAAGCCTTTCCTTGAAATTTTAC 57.214 32.000 8.71 0.00 43.79 2.01
3852 4133 5.589367 AGACTGGCATCCAACCATATTAT 57.411 39.130 0.00 0.00 36.36 1.28
3854 4135 4.666512 ACTGGCATCCAACCATATTATCC 58.333 43.478 0.00 0.00 36.36 2.59
4050 4335 1.947678 GCCAGATGGACACTTGACCAG 60.948 57.143 2.18 0.00 42.60 4.00
4106 4391 6.010850 TGGATACAGACCTCTATACACCATC 58.989 44.000 0.00 0.00 46.17 3.51
4434 4761 3.385384 CCGGAGCTGGCTCAGTCA 61.385 66.667 21.75 0.00 44.40 3.41
4510 4845 3.607741 CAGCATCAATCTCCTGACAACT 58.392 45.455 0.00 0.00 0.00 3.16
4569 4904 3.868062 CTTCCTTCCCCCTCTGATCTAT 58.132 50.000 0.00 0.00 0.00 1.98
4681 5016 4.952460 ACGTGATTAAGTTGGTGTGTAGT 58.048 39.130 0.00 0.00 0.00 2.73
4684 5019 6.016024 ACGTGATTAAGTTGGTGTGTAGTCTA 60.016 38.462 0.00 0.00 0.00 2.59
4764 5099 6.247727 TGCTTGATTTAACGTAGATTTGCA 57.752 33.333 0.00 0.00 0.00 4.08
4809 5144 7.976734 AGAGTGTAATGTAGTGTAATGCTCTTC 59.023 37.037 0.00 0.00 0.00 2.87
5013 5351 8.221944 TGAATAAGGAGGTTTAGAGGTTTTTGA 58.778 33.333 0.00 0.00 0.00 2.69
5098 5442 3.196685 ACACCATAGCTTTGACTCCTCTC 59.803 47.826 5.65 0.00 0.00 3.20
5209 5553 6.839454 AGCATAATGAGAGACATCATTTCCT 58.161 36.000 7.21 0.54 45.44 3.36
5265 5609 1.066573 CGCCAATCCTTCACTGAGTCT 60.067 52.381 0.00 0.00 0.00 3.24
5421 5765 2.780010 AGTATTGCAGTTAGGCCATCCT 59.220 45.455 5.01 0.00 46.57 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.638855 TGCTCTAAAGAACGGGGGTAAA 59.361 45.455 0.00 0.00 0.00 2.01
10 11 2.027837 GTGCTCTAAAGAACGGGGGTAA 60.028 50.000 0.00 0.00 0.00 2.85
413 414 1.262417 TCGTGTTGACAGGGCATCTA 58.738 50.000 4.24 0.00 33.00 1.98
425 426 6.639212 CAAACAAAATCTCCAAATCGTGTTG 58.361 36.000 0.00 0.00 0.00 3.33
824 928 8.418597 AGTACAAGTTTATCCAGTCTACTGAA 57.581 34.615 11.69 0.00 46.59 3.02
896 1014 5.645497 CAGAACTGAAAGGGGAATAAGACTG 59.355 44.000 0.00 0.00 39.30 3.51
954 1072 7.127012 TGAAAATGGCATTATGGATTCATGT 57.873 32.000 14.05 0.00 34.96 3.21
1148 1266 1.541670 CCCGTTTCGTCTTCCCTTTCA 60.542 52.381 0.00 0.00 0.00 2.69
1275 1393 3.743521 AGTCACAGCAGTGCAATTTCTA 58.256 40.909 19.20 0.00 45.49 2.10
1440 1562 3.791245 TGCTTGTTTTTGCTCGGATTTT 58.209 36.364 0.00 0.00 0.00 1.82
1472 1597 0.119358 AGAGGTGGCTTAGGGACCTT 59.881 55.000 0.00 0.00 40.33 3.50
1473 1598 0.119358 AAGAGGTGGCTTAGGGACCT 59.881 55.000 0.00 0.00 43.06 3.85
1474 1599 0.542333 GAAGAGGTGGCTTAGGGACC 59.458 60.000 0.00 0.00 0.00 4.46
1746 1882 8.146053 TCAAACCTATCTTTAAGTCCAGATGA 57.854 34.615 0.00 0.00 31.89 2.92
1853 1989 9.132923 AGACCGTCAAGATTCAAGAATATACTA 57.867 33.333 0.40 0.00 0.00 1.82
2268 2408 2.551459 GCACAGAGATGAAACACAAGCT 59.449 45.455 0.00 0.00 0.00 3.74
2313 2456 2.161855 TGGACGCTCAAATGCTTTCAT 58.838 42.857 0.00 0.00 33.53 2.57
2461 2604 9.825972 ATGTATAAATTTAATCGGAAGCAATCG 57.174 29.630 1.21 0.00 0.00 3.34
2574 2725 6.389091 CAGCTGGTTACTTCATAATTGCAAA 58.611 36.000 5.57 0.00 0.00 3.68
2596 2747 3.374220 AAAACACACATCCACATGCAG 57.626 42.857 0.00 0.00 32.57 4.41
2670 2823 2.021723 GCTTGGACAGGTGTGGAAACA 61.022 52.381 0.00 0.00 38.70 2.83
2992 3212 0.249868 TTCTGGTGCTGAAGACCACG 60.250 55.000 0.00 0.00 38.63 4.94
3105 3330 7.997482 AGAGCGTCATAAACTGAGAAGTTATA 58.003 34.615 0.00 0.00 33.51 0.98
3125 3357 3.063180 CAGAAACCTGCAAAGATAGAGCG 59.937 47.826 0.00 0.00 0.00 5.03
3789 4070 3.118482 TGCTGCTCTAAGAAATCTCCTGG 60.118 47.826 0.00 0.00 0.00 4.45
4050 4335 1.202580 CGAACCCATGGGAGATCTGAC 60.203 57.143 38.07 15.81 38.96 3.51
4434 4761 6.206243 TGTCGTTAGCTTGTCTACTAAAGAGT 59.794 38.462 0.00 0.00 37.48 3.24
4510 4845 2.094757 ATCGAGTTGTCGGCCACACA 62.095 55.000 2.24 1.02 46.80 3.72
4569 4904 1.092921 GGCGGAGAACACAACACACA 61.093 55.000 0.00 0.00 0.00 3.72
4681 5016 2.265367 TCAACCCAAGGCATCAGTAGA 58.735 47.619 0.00 0.00 0.00 2.59
4684 5019 3.737559 TTATCAACCCAAGGCATCAGT 57.262 42.857 0.00 0.00 0.00 3.41
4809 5144 5.698089 TGGATTCAAGCGCTCTTATAATCTG 59.302 40.000 12.06 1.10 35.87 2.90
5013 5351 5.155278 TGTGTTGTAATTCGACCTATGGT 57.845 39.130 0.00 0.00 39.44 3.55
5021 5359 6.400621 CGCAAGAGTAATGTGTTGTAATTCGA 60.401 38.462 0.00 0.00 43.02 3.71
5098 5442 5.501156 AGGGGTTCTTGTTGCTAGAATTAG 58.499 41.667 0.00 0.00 34.42 1.73
5133 5477 0.878523 CTCGAGTTTTCCGCCACACA 60.879 55.000 3.62 0.00 0.00 3.72
5145 5489 1.859302 AGGAGAGGAATGCTCGAGTT 58.141 50.000 15.13 0.36 33.19 3.01
5246 5590 2.777832 AGACTCAGTGAAGGATTGGC 57.222 50.000 0.00 0.00 0.00 4.52
5421 5765 2.142357 CTGACAGGCTCCAACGACGA 62.142 60.000 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.