Multiple sequence alignment - TraesCS5D01G444100

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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 TraesCS5D01G444100 chr5D 100.000 4902 0 0 1 4902 495281261 495286162 0.000000e+00 9053
1 TraesCS5D01G444100 chr5D 96.830 3533 106 5 659 4189 466678540 466675012 0.000000e+00 5899
2 TraesCS5D01G444100 chr5D 96.602 3532 112 6 659 4189 489075369 489071845 0.000000e+00 5851
3 TraesCS5D01G444100 chr5D 96.269 3538 121 5 659 4189 15086223 15089756 0.000000e+00 5792
4 TraesCS5D01G444100 chr5D 95.207 772 36 1 4132 4902 299372380 299373151 0.000000e+00 1219
5 TraesCS5D01G444100 chr2A 93.422 4120 234 20 799 4902 765909042 765913140 0.000000e+00 6072
6 TraesCS5D01G444100 chr2A 95.584 3533 146 7 659 4189 74070991 74067467 0.000000e+00 5651
7 TraesCS5D01G444100 chr2A 94.016 3543 178 18 1377 4902 35864288 35867813 0.000000e+00 5337
8 TraesCS5D01G444100 chr2A 95.833 648 18 4 1 647 74071677 74071038 0.000000e+00 1038
9 TraesCS5D01G444100 chr2A 94.266 436 25 0 4467 4902 74067273 74066838 0.000000e+00 667
10 TraesCS5D01G444100 chr3A 96.398 3692 121 5 658 4340 52181136 52177448 0.000000e+00 6071
11 TraesCS5D01G444100 chr3A 95.825 3497 141 5 694 4189 434014477 434010985 0.000000e+00 5644
12 TraesCS5D01G444100 chr3A 95.309 3539 156 8 655 4189 730407195 730403663 0.000000e+00 5607
13 TraesCS5D01G444100 chr3A 95.223 3538 161 8 655 4189 730238765 730235233 0.000000e+00 5590
14 TraesCS5D01G444100 chr3A 96.096 1332 52 0 3571 4902 52121764 52120433 0.000000e+00 2172
15 TraesCS5D01G444100 chr3A 95.495 1332 59 1 3571 4902 52087466 52086136 0.000000e+00 2126
16 TraesCS5D01G444100 chr3A 94.219 1332 57 6 3571 4902 52170029 52168718 0.000000e+00 2015
17 TraesCS5D01G444100 chr3A 94.082 659 37 2 1 657 52098267 52097609 0.000000e+00 1000
18 TraesCS5D01G444100 chr7D 96.717 3533 106 6 659 4189 597524744 597521220 0.000000e+00 5873
19 TraesCS5D01G444100 chr7D 96.960 658 16 3 1 657 601134261 601134915 0.000000e+00 1101
20 TraesCS5D01G444100 chr7D 95.289 658 28 2 1 657 597525439 597524784 0.000000e+00 1040
21 TraesCS5D01G444100 chr3D 94.437 773 39 4 4131 4902 380989057 380988288 0.000000e+00 1186
22 TraesCS5D01G444100 chr3D 97.568 658 14 2 1 657 121897493 121898149 0.000000e+00 1125
23 TraesCS5D01G444100 chr3D 95.903 659 23 4 1 656 191608671 191608014 0.000000e+00 1064
24 TraesCS5D01G444100 chr3D 95.455 660 27 3 1 657 380984776 380985435 0.000000e+00 1050
25 TraesCS5D01G444100 chr2D 94.179 773 41 3 4131 4902 21805591 21804822 0.000000e+00 1175
26 TraesCS5D01G444100 chr2D 95.448 659 25 3 1 657 62006248 62006903 0.000000e+00 1046
27 TraesCS5D01G444100 chr2D 94.385 659 33 4 1 657 21790704 21791360 0.000000e+00 1009
28 TraesCS5D01G444100 chr3B 88.591 149 13 3 4289 4434 667637341 667637488 1.400000e-40 178


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 TraesCS5D01G444100 chr5D 495281261 495286162 4901 False 9053.0 9053 100.000000 1 4902 1 chr5D.!!$F3 4901
1 TraesCS5D01G444100 chr5D 466675012 466678540 3528 True 5899.0 5899 96.830000 659 4189 1 chr5D.!!$R1 3530
2 TraesCS5D01G444100 chr5D 489071845 489075369 3524 True 5851.0 5851 96.602000 659 4189 1 chr5D.!!$R2 3530
3 TraesCS5D01G444100 chr5D 15086223 15089756 3533 False 5792.0 5792 96.269000 659 4189 1 chr5D.!!$F1 3530
4 TraesCS5D01G444100 chr5D 299372380 299373151 771 False 1219.0 1219 95.207000 4132 4902 1 chr5D.!!$F2 770
5 TraesCS5D01G444100 chr2A 765909042 765913140 4098 False 6072.0 6072 93.422000 799 4902 1 chr2A.!!$F2 4103
6 TraesCS5D01G444100 chr2A 35864288 35867813 3525 False 5337.0 5337 94.016000 1377 4902 1 chr2A.!!$F1 3525
7 TraesCS5D01G444100 chr2A 74066838 74071677 4839 True 2452.0 5651 95.227667 1 4902 3 chr2A.!!$R1 4901
8 TraesCS5D01G444100 chr3A 52177448 52181136 3688 True 6071.0 6071 96.398000 658 4340 1 chr3A.!!$R5 3682
9 TraesCS5D01G444100 chr3A 434010985 434014477 3492 True 5644.0 5644 95.825000 694 4189 1 chr3A.!!$R6 3495
10 TraesCS5D01G444100 chr3A 730403663 730407195 3532 True 5607.0 5607 95.309000 655 4189 1 chr3A.!!$R8 3534
11 TraesCS5D01G444100 chr3A 730235233 730238765 3532 True 5590.0 5590 95.223000 655 4189 1 chr3A.!!$R7 3534
12 TraesCS5D01G444100 chr3A 52120433 52121764 1331 True 2172.0 2172 96.096000 3571 4902 1 chr3A.!!$R3 1331
13 TraesCS5D01G444100 chr3A 52086136 52087466 1330 True 2126.0 2126 95.495000 3571 4902 1 chr3A.!!$R1 1331
14 TraesCS5D01G444100 chr3A 52168718 52170029 1311 True 2015.0 2015 94.219000 3571 4902 1 chr3A.!!$R4 1331
15 TraesCS5D01G444100 chr3A 52097609 52098267 658 True 1000.0 1000 94.082000 1 657 1 chr3A.!!$R2 656
16 TraesCS5D01G444100 chr7D 597521220 597525439 4219 True 3456.5 5873 96.003000 1 4189 2 chr7D.!!$R1 4188
17 TraesCS5D01G444100 chr7D 601134261 601134915 654 False 1101.0 1101 96.960000 1 657 1 chr7D.!!$F1 656
18 TraesCS5D01G444100 chr3D 380988288 380989057 769 True 1186.0 1186 94.437000 4131 4902 1 chr3D.!!$R2 771
19 TraesCS5D01G444100 chr3D 121897493 121898149 656 False 1125.0 1125 97.568000 1 657 1 chr3D.!!$F1 656
20 TraesCS5D01G444100 chr3D 191608014 191608671 657 True 1064.0 1064 95.903000 1 656 1 chr3D.!!$R1 655
21 TraesCS5D01G444100 chr3D 380984776 380985435 659 False 1050.0 1050 95.455000 1 657 1 chr3D.!!$F2 656
22 TraesCS5D01G444100 chr2D 21804822 21805591 769 True 1175.0 1175 94.179000 4131 4902 1 chr2D.!!$R1 771
23 TraesCS5D01G444100 chr2D 62006248 62006903 655 False 1046.0 1046 95.448000 1 657 1 chr2D.!!$F2 656
24 TraesCS5D01G444100 chr2D 21790704 21791360 656 False 1009.0 1009 94.385000 1 657 1 chr2D.!!$F1 656

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
120 121 1.199097 GAATTCGGACACCAAACGCAT 59.801 47.619 0.00 0.0 0.00 4.73 F
2027 2086 2.573915 GGACTGTCCCAGAGGAAGAAAT 59.426 50.000 16.14 0.0 46.38 2.17 F
2954 3024 1.133482 TCCGGATCACATAGAGGCAGA 60.133 52.381 0.00 0.0 0.00 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2075 2134 1.005984 TTCGATGAAACCGCGGACA 60.006 52.632 35.9 26.79 0.00 4.02 R
3566 3640 2.664402 ACCAGGGTGGCAATCATATC 57.336 50.000 0.0 0.00 42.67 1.63 R
4781 4913 1.675219 GGCGAGGTGGGACTAAACA 59.325 57.895 0.0 0.00 0.00 2.83 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
120 121 1.199097 GAATTCGGACACCAAACGCAT 59.801 47.619 0.00 0.00 0.00 4.73
420 425 3.107601 TCCTCCAAATAGAGTCCCACAG 58.892 50.000 0.00 0.00 31.53 3.66
683 727 4.175489 CGATCCGACGGTCGCACT 62.175 66.667 24.26 10.81 38.82 4.40
1434 1488 5.244402 TGATTTTGTGAGAAGGGTCGTACTA 59.756 40.000 0.00 0.00 0.00 1.82
2027 2086 2.573915 GGACTGTCCCAGAGGAAGAAAT 59.426 50.000 16.14 0.00 46.38 2.17
2075 2134 2.943199 GCAGGAGTAGAAAGCCAAGCAT 60.943 50.000 0.00 0.00 0.00 3.79
2208 2267 5.344207 AGAAGTTGTATTGAACGTGCTTC 57.656 39.130 0.00 0.00 35.11 3.86
2440 2500 4.876107 ACATCTTTCACGGGTATGAATGAC 59.124 41.667 6.31 0.00 42.32 3.06
2569 2629 5.389516 GGCATCAACTGTACGTACAAAAGAG 60.390 44.000 27.16 17.94 35.50 2.85
2703 2763 4.584638 ACATAGGTAATGGTGAAGGCAA 57.415 40.909 0.00 0.00 40.16 4.52
2954 3024 1.133482 TCCGGATCACATAGAGGCAGA 60.133 52.381 0.00 0.00 0.00 4.26
3217 3290 5.467399 CACCTACAACACCGTGATTTTTCTA 59.533 40.000 5.28 0.00 0.00 2.10
3361 3434 9.775854 CAAGAGTAATGGATGAGTATTTCAGAT 57.224 33.333 0.00 0.00 39.68 2.90
3439 3513 6.641169 TTGCACTAACATCATTTGGTTACA 57.359 33.333 0.00 0.00 0.00 2.41
3455 3529 6.821031 TGGTTACAATGTAGGCGTATTTTT 57.179 33.333 0.00 0.00 0.00 1.94
3566 3640 2.531508 GCAATTAGCCAAAGAATTCGCG 59.468 45.455 0.00 0.00 37.23 5.87
3865 3955 5.584649 CAGAGTGTCTTGTGGACTTTTTGTA 59.415 40.000 0.00 0.00 44.74 2.41
3900 3990 0.471191 TACTGGGACGGAGATCGCTA 59.529 55.000 0.00 0.00 43.89 4.26
3955 4045 1.004320 AAGGCCACGTATTGTCGCA 60.004 52.632 5.01 0.00 36.28 5.10
4020 4110 9.763465 CAAGATGAAAATTGTTAAAATCATGGC 57.237 29.630 0.00 0.00 0.00 4.40
4042 4132 5.337652 GGCGAAGGAATAGGTATTAGCATCT 60.338 44.000 0.00 0.00 0.00 2.90
4194 4285 3.908213 ACATTTAAATGCGTGTCCAACC 58.092 40.909 24.82 0.00 40.04 3.77
4253 4344 6.664428 AGTGTGGGCAAGTAATATTTTTGT 57.336 33.333 11.65 0.00 0.00 2.83
4316 4407 7.379098 TGTACTGTTGTTGTTTGTATTCACA 57.621 32.000 0.00 0.00 0.00 3.58
4630 4762 4.003788 CCCGGTGGCAGACGTCTT 62.004 66.667 17.26 0.00 0.00 3.01
4702 4834 2.364632 CGATCTGTTGGCCCATTAACA 58.635 47.619 0.00 2.80 35.66 2.41
4828 4960 0.170116 ACGCGACGACCGGTTTATAA 59.830 50.000 15.93 0.00 39.04 0.98
4878 5010 6.591834 GCTCACTACAGAACACTAATGAATGT 59.408 38.462 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 0.958822 GTTCAAATCTTGCGTGGGGT 59.041 50.000 0.00 0.00 0.00 4.95
420 425 6.845302 TGCTCAATGAACAAACATATGAGTC 58.155 36.000 10.38 0.00 37.51 3.36
426 431 8.939201 TTTCTTTTGCTCAATGAACAAACATA 57.061 26.923 10.89 0.00 33.29 2.29
1327 1381 6.128526 CCTGTTCTTTTGTCTAGAAACCGATC 60.129 42.308 0.00 0.00 33.71 3.69
1434 1488 5.720041 TGCTAAGACTGTACCCATAAGAACT 59.280 40.000 0.00 0.00 0.00 3.01
2027 2086 4.577283 CACCTTTCCGTTTAGGTTTCTTCA 59.423 41.667 0.00 0.00 42.01 3.02
2075 2134 1.005984 TTCGATGAAACCGCGGACA 60.006 52.632 35.90 26.79 0.00 4.02
2208 2267 9.103048 GAAACACGATAAGTAGTTGAACAATTG 57.897 33.333 3.24 3.24 0.00 2.32
2440 2500 3.605749 ATCAACGGGCACGGAGGTG 62.606 63.158 15.46 5.17 46.48 4.00
2569 2629 2.265683 GTTCGGGACATAGACGGAAAC 58.734 52.381 0.00 0.00 0.00 2.78
2703 2763 3.378427 GCGCTTACCTTCATTTTCCTGAT 59.622 43.478 0.00 0.00 0.00 2.90
2954 3024 4.806247 CGAGAGTCTCAACAAAAACTCTGT 59.194 41.667 19.99 0.00 46.34 3.41
3217 3290 5.640357 ACCACGTTGTTGATATGTAACGATT 59.360 36.000 14.20 0.00 46.18 3.34
3361 3434 3.517296 TGAAAGCAATACCTTGTCCCA 57.483 42.857 0.00 0.00 34.69 4.37
3439 3513 6.511121 CGTGCATAGAAAAATACGCCTACATT 60.511 38.462 0.00 0.00 0.00 2.71
3455 3529 8.720562 CCAATGATTATCATTAACGTGCATAGA 58.279 33.333 18.60 0.00 44.60 1.98
3566 3640 2.664402 ACCAGGGTGGCAATCATATC 57.336 50.000 0.00 0.00 42.67 1.63
3865 3955 5.127031 GTCCCAGTATTTTATGCACCACATT 59.873 40.000 0.00 0.00 40.38 2.71
3900 3990 4.371624 TCCTGGTCAAATTCATGTGTCT 57.628 40.909 0.00 0.00 0.00 3.41
3983 4073 8.329203 ACAATTTTCATCTTGACCTTCTCTAC 57.671 34.615 0.00 0.00 0.00 2.59
4020 4110 6.692486 ACAGATGCTAATACCTATTCCTTCG 58.308 40.000 0.00 0.00 0.00 3.79
4042 4132 4.046286 TCTACGGGACTAAAACCCTACA 57.954 45.455 0.00 0.00 44.72 2.74
4194 4285 7.757173 CCGTCTCATAGAATAGTACCATTCATG 59.243 40.741 15.10 14.64 37.38 3.07
4253 4344 5.855925 CGCAAACTGATACATTTTAGCACAA 59.144 36.000 0.00 0.00 0.00 3.33
4781 4913 1.675219 GGCGAGGTGGGACTAAACA 59.325 57.895 0.00 0.00 0.00 2.83
4878 5010 2.340809 CCACGGCGTACAACAGGA 59.659 61.111 14.22 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.