Multiple sequence alignment - TraesCS5D01G041600

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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 TraesCS5D01G041600 chr5D 100.000 4148 0 0 1 4148 42015832 42019979 0.000000e+00 7661
1 TraesCS5D01G041600 chr5D 91.787 3750 213 41 474 4148 440159796 440163525 0.000000e+00 5131
2 TraesCS5D01G041600 chr5D 92.416 1635 71 23 831 2449 42053515 42051918 0.000000e+00 2283
3 TraesCS5D01G041600 chr5D 79.832 476 80 9 333 794 42054072 42053599 2.390000e-87 333
4 TraesCS5D01G041600 chr5D 90.164 122 12 0 339 460 432339156 432339277 4.290000e-35 159
5 TraesCS5D01G041600 chr5A 92.622 4012 222 45 198 4148 30403674 30407672 0.000000e+00 5701
6 TraesCS5D01G041600 chr5A 94.219 3356 136 30 831 4148 555770530 555773865 0.000000e+00 5070
7 TraesCS5D01G041600 chr5B 93.929 3360 139 27 831 4148 535111100 535114436 0.000000e+00 5014
8 TraesCS5D01G041600 chr5B 93.845 3363 114 37 825 4148 36720301 36723609 0.000000e+00 4977
9 TraesCS5D01G041600 chr5B 94.833 2361 80 12 840 3192 36767815 36765489 0.000000e+00 3646
10 TraesCS5D01G041600 chr5B 89.591 807 61 12 1 800 36772053 36771263 0.000000e+00 1003
11 TraesCS5D01G041600 chr5B 89.206 806 67 6 1 797 36719425 36720219 0.000000e+00 989
12 TraesCS5D01G041600 chr5B 96.622 148 4 1 3776 3923 36765233 36765087 1.150000e-60 244
13 TraesCS5D01G041600 chr5B 98.473 131 2 0 3949 4079 36765090 36764960 8.970000e-57 231
14 TraesCS5D01G041600 chrUn 89.344 122 13 0 339 460 392770448 392770327 2.000000e-33 154
15 TraesCS5D01G041600 chr7B 89.344 122 13 0 339 460 622433732 622433853 2.000000e-33 154
16 TraesCS5D01G041600 chr4A 89.344 122 13 0 339 460 583864669 583864790 2.000000e-33 154
17 TraesCS5D01G041600 chr3D 89.344 122 13 0 339 460 581040656 581040535 2.000000e-33 154


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 TraesCS5D01G041600 chr5D 42015832 42019979 4147 False 7661 7661 100.00000 1 4148 1 chr5D.!!$F1 4147
1 TraesCS5D01G041600 chr5D 440159796 440163525 3729 False 5131 5131 91.78700 474 4148 1 chr5D.!!$F3 3674
2 TraesCS5D01G041600 chr5D 42051918 42054072 2154 True 1308 2283 86.12400 333 2449 2 chr5D.!!$R1 2116
3 TraesCS5D01G041600 chr5A 30403674 30407672 3998 False 5701 5701 92.62200 198 4148 1 chr5A.!!$F1 3950
4 TraesCS5D01G041600 chr5A 555770530 555773865 3335 False 5070 5070 94.21900 831 4148 1 chr5A.!!$F2 3317
5 TraesCS5D01G041600 chr5B 535111100 535114436 3336 False 5014 5014 93.92900 831 4148 1 chr5B.!!$F1 3317
6 TraesCS5D01G041600 chr5B 36719425 36723609 4184 False 2983 4977 91.52550 1 4148 2 chr5B.!!$F2 4147
7 TraesCS5D01G041600 chr5B 36764960 36772053 7093 True 1281 3646 94.87975 1 4079 4 chr5B.!!$R1 4078

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
716 737 0.107897 TTGCGCACCACCTCGATAAT 60.108 50.0 11.12 0.0 0.0 1.28 F
2137 5632 0.541392 TGTGGATGGATTCTGTCGGG 59.459 55.0 0.00 0.0 0.0 5.14 F
2269 5764 2.278332 AACTTCAGAGGCTTGGGAAC 57.722 50.0 0.00 0.0 0.0 3.62 F
3021 6516 1.081892 CGTGCCAGATGTTTCAGAGG 58.918 55.0 0.00 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2559 6054 0.753111 GCGCTGATTCCAAATCCCCT 60.753 55.000 0.00 0.0 0.00 4.79 R
3000 6495 0.035317 TCTGAAACATCTGGCACGCT 59.965 50.000 0.00 0.0 0.00 5.07 R
3076 6571 1.035139 CCAGCAGCTGGTTGTTTCTT 58.965 50.000 30.97 0.0 45.82 2.52 R
3857 7476 2.987149 CGCATACAAGTGAGAAGACGTT 59.013 45.455 0.00 0.0 0.00 3.99 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
30 31 2.946947 GACAAGTGGGTCCCATGTG 58.053 57.895 19.95 18.94 35.28 3.21
57 65 3.173668 TGGGTAATCGTGTATGTCAGC 57.826 47.619 0.00 0.00 0.00 4.26
119 127 2.511659 ACTAGACAGGCACGACAACTA 58.488 47.619 0.00 0.00 0.00 2.24
136 144 4.225267 ACAACTACCCTGGAAACTCTATGG 59.775 45.833 0.00 0.00 0.00 2.74
138 146 4.695606 ACTACCCTGGAAACTCTATGGAA 58.304 43.478 0.00 0.00 0.00 3.53
146 154 4.086457 GGAAACTCTATGGAAAAGCCCAA 58.914 43.478 0.00 0.00 40.04 4.12
151 159 4.289672 ACTCTATGGAAAAGCCCAAGAAGA 59.710 41.667 0.00 0.00 40.04 2.87
192 200 4.585879 TCTATTAGGTTCCCTGCACAAAC 58.414 43.478 0.00 0.00 34.61 2.93
243 252 0.605860 TAGTCGCCGGAGAGATAGGC 60.606 60.000 8.65 0.00 46.88 3.93
254 263 3.497227 GGAGAGATAGGCGAAGTACCTCT 60.497 52.174 0.00 0.00 38.81 3.69
271 283 3.099905 CCTCTATCATCATAGCCGGGAA 58.900 50.000 2.18 0.00 33.10 3.97
350 362 7.926555 GTCAGCACACATAAACTACCTATATGT 59.073 37.037 0.00 0.00 40.04 2.29
374 386 7.611467 TGTTTTCAGCAGTTATCCACTTCATAT 59.389 33.333 0.00 0.00 30.92 1.78
479 491 2.036604 TCATGTTAGCCGAGTGTTGTCA 59.963 45.455 0.00 0.00 0.00 3.58
503 515 2.171448 GTGCCATCCAGACCTCATAACT 59.829 50.000 0.00 0.00 0.00 2.24
512 524 2.202932 CTCATAACTGGCGCCGCT 60.203 61.111 23.90 11.16 0.00 5.52
553 567 0.456221 CTAGACATTGCCGTCCTCGT 59.544 55.000 0.00 0.00 36.52 4.18
715 736 0.320858 TTTGCGCACCACCTCGATAA 60.321 50.000 11.12 0.00 0.00 1.75
716 737 0.107897 TTGCGCACCACCTCGATAAT 60.108 50.000 11.12 0.00 0.00 1.28
729 759 4.104102 ACCTCGATAATCTTGCCCCATAAA 59.896 41.667 0.00 0.00 0.00 1.40
736 766 7.382218 CGATAATCTTGCCCCATAAACATTTTC 59.618 37.037 0.00 0.00 0.00 2.29
801 860 2.801342 GCAAGACTAGGATGGAGAAGCG 60.801 54.545 0.00 0.00 0.00 4.68
826 907 6.176183 AGGTATTGTTTCTCCTTCACATGAG 58.824 40.000 0.00 0.00 0.00 2.90
827 908 6.013379 AGGTATTGTTTCTCCTTCACATGAGA 60.013 38.462 0.00 0.00 35.89 3.27
829 910 6.814506 ATTGTTTCTCCTTCACATGAGAAG 57.185 37.500 21.85 21.85 45.49 2.85
838 4281 4.440880 CTTCACATGAGAAGTGGAGATCC 58.559 47.826 20.87 0.00 43.83 3.36
890 4334 3.164977 TGACCCCACACGCCTTGA 61.165 61.111 0.00 0.00 0.00 3.02
1575 5054 1.882625 GTGCGCGCCTGACATATCA 60.883 57.895 30.77 1.61 0.00 2.15
2137 5632 0.541392 TGTGGATGGATTCTGTCGGG 59.459 55.000 0.00 0.00 0.00 5.14
2269 5764 2.278332 AACTTCAGAGGCTTGGGAAC 57.722 50.000 0.00 0.00 0.00 3.62
2559 6054 5.417266 TGTAATTCATGGATTTTCTCGGCAA 59.583 36.000 4.09 0.00 0.00 4.52
3000 6495 5.066968 TCGCAGTTCAGTCATACAATGTA 57.933 39.130 0.00 0.00 0.00 2.29
3021 6516 1.081892 CGTGCCAGATGTTTCAGAGG 58.918 55.000 0.00 0.00 0.00 3.69
3074 6569 3.051081 AGTTGACAATCAGCTGACCTC 57.949 47.619 20.97 13.78 36.56 3.85
3076 6571 3.141398 GTTGACAATCAGCTGACCTCAA 58.859 45.455 20.97 20.82 0.00 3.02
3114 6609 5.183140 TGCTGGAAAGCTTATGGTTAAGTTC 59.817 40.000 0.00 0.00 37.68 3.01
3167 6670 0.375106 GCTATTGCTGTCCGACAAGC 59.625 55.000 2.19 8.95 36.03 4.01
3284 6872 8.652290 ACTCACTTTCTTCTACCTAAAACTGAT 58.348 33.333 0.00 0.00 0.00 2.90
3325 6915 3.249799 TCAGTTGGTAACGTTTCATGCAG 59.750 43.478 5.91 0.42 42.51 4.41
3327 6917 3.630312 AGTTGGTAACGTTTCATGCAGTT 59.370 39.130 5.91 0.00 42.51 3.16
3398 7016 4.253685 TGAATGTTAGTTAGCTGCCACTC 58.746 43.478 5.42 0.00 0.00 3.51
3399 7017 3.981071 ATGTTAGTTAGCTGCCACTCA 57.019 42.857 5.42 0.47 0.00 3.41
3400 7018 3.762407 TGTTAGTTAGCTGCCACTCAA 57.238 42.857 5.42 0.00 0.00 3.02
3401 7019 4.079980 TGTTAGTTAGCTGCCACTCAAA 57.920 40.909 5.42 0.00 0.00 2.69
3402 7020 4.065088 TGTTAGTTAGCTGCCACTCAAAG 58.935 43.478 5.42 0.00 0.00 2.77
3403 7021 2.191128 AGTTAGCTGCCACTCAAAGG 57.809 50.000 0.00 0.00 0.00 3.11
3404 7022 1.168714 GTTAGCTGCCACTCAAAGGG 58.831 55.000 0.00 0.00 0.00 3.95
3516 7134 0.548031 GACAATGGAGGGAGATGGCA 59.452 55.000 0.00 0.00 0.00 4.92
3520 7138 1.274703 ATGGAGGGAGATGGCAACGT 61.275 55.000 0.00 0.00 42.51 3.99
3842 7461 8.978472 TCTTGCACTATGTAGTATAGTCCTTTT 58.022 33.333 0.00 0.00 34.13 2.27
3857 7476 4.644685 AGTCCTTTTTGCTGCTTAGAAACA 59.355 37.500 0.00 0.00 0.00 2.83
3952 7571 3.075005 GCGAGGAGGTACAGGGCA 61.075 66.667 0.00 0.00 0.00 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 3.055747 TGCTGACATACACGATTACCCAA 60.056 43.478 0.00 0.00 0.00 4.12
37 38 2.498078 TGCTGACATACACGATTACCCA 59.502 45.455 0.00 0.00 0.00 4.51
119 127 4.811063 GCTTTTCCATAGAGTTTCCAGGGT 60.811 45.833 0.00 0.00 0.00 4.34
179 187 0.953471 CGATCGGTTTGTGCAGGGAA 60.953 55.000 7.38 0.00 0.00 3.97
180 188 1.375396 CGATCGGTTTGTGCAGGGA 60.375 57.895 7.38 0.00 0.00 4.20
192 200 0.464036 TGGGGATCAAAGACGATCGG 59.536 55.000 20.98 0.47 42.35 4.18
243 252 5.447954 CGGCTATGATGATAGAGGTACTTCG 60.448 48.000 3.06 0.00 41.55 3.79
271 283 0.545171 CCCTGACAGTGATGATGCCT 59.455 55.000 0.00 0.00 0.00 4.75
350 362 8.579850 AATATGAAGTGGATAACTGCTGAAAA 57.420 30.769 0.00 0.00 39.81 2.29
479 491 0.977627 TGAGGTCTGGATGGCACGAT 60.978 55.000 0.00 0.00 0.00 3.73
503 515 4.695993 TGTCAATGAGCGGCGCCA 62.696 61.111 30.40 25.38 0.00 5.69
512 524 8.088365 TCTAGTCTTTCTCGATTTTGTCAATGA 58.912 33.333 0.00 0.00 0.00 2.57
553 567 2.097036 CATGAAGCATGGAAAGAGGCA 58.903 47.619 0.00 0.00 38.11 4.75
621 640 0.462937 CGTGTTCGGGATGGCCAATA 60.463 55.000 10.96 0.00 35.15 1.90
715 736 7.564660 TGATAGAAAATGTTTATGGGGCAAGAT 59.435 33.333 0.00 0.00 0.00 2.40
716 737 6.894654 TGATAGAAAATGTTTATGGGGCAAGA 59.105 34.615 0.00 0.00 0.00 3.02
736 766 8.079203 ACTCTAGCAAAGTCGTCATATTGATAG 58.921 37.037 9.84 9.84 41.00 2.08
801 860 6.173339 TCATGTGAAGGAGAAACAATACCTC 58.827 40.000 0.00 0.00 31.89 3.85
826 907 4.637977 CCTTTTTGCTAGGATCTCCACTTC 59.362 45.833 0.00 0.00 38.89 3.01
827 908 4.593956 CCTTTTTGCTAGGATCTCCACTT 58.406 43.478 0.00 0.00 38.89 3.16
829 910 2.685388 GCCTTTTTGCTAGGATCTCCAC 59.315 50.000 0.00 0.00 38.89 4.02
838 4281 2.099756 GCCCATGTAGCCTTTTTGCTAG 59.900 50.000 0.00 0.00 44.12 3.42
942 4416 0.733150 GTTAGGAAGGCGATTGGCAC 59.267 55.000 9.53 2.39 46.16 5.01
1086 4565 2.364448 GAGGGGGCGAGTTCTCCT 60.364 66.667 0.00 0.00 0.00 3.69
1109 4588 1.740285 CGGGGTATCTCCTTGACGG 59.260 63.158 0.00 0.00 36.25 4.79
1575 5054 4.160814 ACATTCACTGCCACATTGCATATT 59.839 37.500 0.00 0.00 41.16 1.28
2137 5632 2.091541 TGCTTGATCAATTTCCCCGAC 58.908 47.619 8.96 0.00 0.00 4.79
2269 5764 3.070018 CCTCTCCACTGTTGTTTAGCAG 58.930 50.000 0.00 0.00 40.56 4.24
2559 6054 0.753111 GCGCTGATTCCAAATCCCCT 60.753 55.000 0.00 0.00 0.00 4.79
3000 6495 0.035317 TCTGAAACATCTGGCACGCT 59.965 50.000 0.00 0.00 0.00 5.07
3074 6569 2.466846 CAGCAGCTGGTTGTTTCTTTG 58.533 47.619 17.45 0.00 0.00 2.77
3076 6571 1.035139 CCAGCAGCTGGTTGTTTCTT 58.965 50.000 30.97 0.00 45.82 2.52
3105 6600 8.369424 AGAAGACCTCTTTCTAAGAACTTAACC 58.631 37.037 0.00 0.00 37.02 2.85
3114 6609 7.928706 TCTTGTTTCAGAAGACCTCTTTCTAAG 59.071 37.037 0.00 0.00 36.11 2.18
3160 6662 3.867493 ACACATGATACATCAGCTTGTCG 59.133 43.478 0.00 0.00 40.64 4.35
3165 6668 6.238842 GCCAATAAACACATGATACATCAGCT 60.239 38.462 0.00 0.00 40.64 4.24
3167 6670 7.030075 TGCCAATAAACACATGATACATCAG 57.970 36.000 0.00 0.00 40.64 2.90
3217 6803 5.354842 TGCATCTGATTCTGAATCTCAGT 57.645 39.130 25.83 10.71 44.58 3.41
3284 6872 9.238368 CCAACTGAACCCAAAACTATAAATCTA 57.762 33.333 0.00 0.00 0.00 1.98
3325 6915 6.334202 TGGTTGTGAATAAGTTGGTGAAAAC 58.666 36.000 0.00 0.00 0.00 2.43
3327 6917 5.451242 GCTGGTTGTGAATAAGTTGGTGAAA 60.451 40.000 0.00 0.00 0.00 2.69
3398 7016 3.746492 GTGTACTGTTCAGTAGCCCTTTG 59.254 47.826 12.19 0.00 0.00 2.77
3399 7017 3.389983 TGTGTACTGTTCAGTAGCCCTTT 59.610 43.478 12.19 0.00 0.00 3.11
3400 7018 2.969950 TGTGTACTGTTCAGTAGCCCTT 59.030 45.455 12.19 0.00 0.00 3.95
3401 7019 2.605257 TGTGTACTGTTCAGTAGCCCT 58.395 47.619 12.19 0.00 0.00 5.19
3402 7020 3.262420 CATGTGTACTGTTCAGTAGCCC 58.738 50.000 12.19 3.28 0.00 5.19
3403 7021 3.926616 ACATGTGTACTGTTCAGTAGCC 58.073 45.455 12.19 7.21 0.00 3.93
3842 7461 3.202906 AGACGTTGTTTCTAAGCAGCAA 58.797 40.909 0.00 0.00 0.00 3.91
3857 7476 2.987149 CGCATACAAGTGAGAAGACGTT 59.013 45.455 0.00 0.00 0.00 3.99
4107 7726 4.016629 CAAACGCGAGCAGCTGCA 62.017 61.111 38.24 0.00 45.59 4.41


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

AutoCloner maintained by Alex Coulton.