Multiple sequence alignment - TraesCS5A01G333400

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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 TraesCS5A01G333400 chr5A 100.000 4090 0 0 1 4090 542030150 542026061 0.000000e+00 7553.0
1 TraesCS5A01G333400 chr1A 97.086 3020 82 3 1 3018 394484551 394487566 0.000000e+00 5084.0
2 TraesCS5A01G333400 chr1A 96.750 2308 74 1 711 3018 394415106 394417412 0.000000e+00 3845.0
3 TraesCS5A01G333400 chr1A 94.333 1094 34 7 3016 4090 394418058 394419142 0.000000e+00 1652.0
4 TraesCS5A01G333400 chr1A 96.380 663 21 3 3016 3678 394488212 394488871 0.000000e+00 1088.0
5 TraesCS5A01G333400 chr1A 92.711 439 11 6 3672 4090 394506632 394507069 7.510000e-172 614.0
6 TraesCS5A01G333400 chr4D 95.206 2545 117 5 475 3018 502619229 502621769 0.000000e+00 4019.0
7 TraesCS5A01G333400 chr4D 88.075 1065 77 15 3018 4046 129501157 129500107 0.000000e+00 1218.0
8 TraesCS5A01G333400 chr3D 95.206 2545 117 5 475 3018 579345094 579347634 0.000000e+00 4019.0
9 TraesCS5A01G333400 chr2D 95.130 2546 118 5 475 3018 82250141 82247600 0.000000e+00 4010.0
10 TraesCS5A01G333400 chr2D 89.035 1067 68 14 3016 4046 607121350 607122403 0.000000e+00 1277.0
11 TraesCS5A01G333400 chrUn 95.128 2545 119 5 475 3018 134333280 134330740 0.000000e+00 4008.0
12 TraesCS5A01G333400 chrUn 83.766 616 74 15 3174 3767 71017183 71016572 9.930000e-156 560.0
13 TraesCS5A01G333400 chrUn 92.199 282 16 2 3765 4046 388007274 388007549 1.070000e-105 394.0
14 TraesCS5A01G333400 chr3B 94.536 2544 135 4 475 3018 728851773 728854312 0.000000e+00 3925.0
15 TraesCS5A01G333400 chr3B 92.962 1094 53 4 3016 4090 678822928 678824016 0.000000e+00 1572.0
16 TraesCS5A01G333400 chr3B 88.632 563 57 6 475 1033 685958131 685957572 0.000000e+00 678.0
17 TraesCS5A01G333400 chr3B 86.923 390 26 11 568 955 678819542 678819908 8.180000e-112 414.0
18 TraesCS5A01G333400 chr6B 93.176 2550 166 6 475 3018 646101433 646103980 0.000000e+00 3738.0
19 TraesCS5A01G333400 chr4B 92.042 2111 157 8 909 3017 524149752 524147651 0.000000e+00 2957.0
20 TraesCS5A01G333400 chr4B 92.949 1092 51 6 3019 4090 77616327 77615242 0.000000e+00 1567.0
21 TraesCS5A01G333400 chr2B 93.144 1094 47 5 3016 4090 238550302 238551386 0.000000e+00 1580.0
22 TraesCS5A01G333400 chr2B 81.210 777 111 13 3016 3767 37447935 37447169 9.790000e-166 593.0
23 TraesCS5A01G333400 chr2A 87.087 1030 57 29 3099 4090 27757429 27758420 0.000000e+00 1096.0
24 TraesCS5A01G333400 chr5D 86.680 1006 76 15 3087 4046 324731318 324730325 0.000000e+00 1062.0
25 TraesCS5A01G333400 chr5D 86.238 1010 76 15 3084 4046 133266529 133267522 0.000000e+00 1037.0
26 TraesCS5A01G333400 chr3A 92.857 490 28 4 1 490 562956940 562956458 0.000000e+00 704.0
27 TraesCS5A01G333400 chr3A 82.392 301 47 4 195 492 719094540 719094243 1.460000e-64 257.0
28 TraesCS5A01G333400 chr7A 90.447 492 36 5 1 492 8469822 8470302 4.460000e-179 638.0
29 TraesCS5A01G333400 chr4A 89.375 480 45 4 1 478 718658774 718659249 2.100000e-167 599.0
30 TraesCS5A01G333400 chr4A 88.235 476 50 4 1 475 718706023 718706493 7.670000e-157 564.0
31 TraesCS5A01G333400 chr4A 87.424 493 54 5 1 492 392505924 392505439 9.930000e-156 560.0
32 TraesCS5A01G333400 chr5B 87.018 493 53 7 3 492 50308195 50307711 2.780000e-151 545.0
33 TraesCS5A01G333400 chr5B 85.507 483 63 4 1 481 220878576 220878099 7.900000e-137 497.0
34 TraesCS5A01G333400 chr1B 84.988 413 39 9 3016 3411 62478422 62478016 8.240000e-107 398.0
35 TraesCS5A01G333400 chr7B 97.561 41 1 0 154 194 443398031 443398071 2.040000e-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 TraesCS5A01G333400 chr5A 542026061 542030150 4089 True 7553.0 7553 100.0000 1 4090 1 chr5A.!!$R1 4089
1 TraesCS5A01G333400 chr1A 394484551 394488871 4320 False 3086.0 5084 96.7330 1 3678 2 chr1A.!!$F3 3677
2 TraesCS5A01G333400 chr1A 394415106 394419142 4036 False 2748.5 3845 95.5415 711 4090 2 chr1A.!!$F2 3379
3 TraesCS5A01G333400 chr4D 502619229 502621769 2540 False 4019.0 4019 95.2060 475 3018 1 chr4D.!!$F1 2543
4 TraesCS5A01G333400 chr4D 129500107 129501157 1050 True 1218.0 1218 88.0750 3018 4046 1 chr4D.!!$R1 1028
5 TraesCS5A01G333400 chr3D 579345094 579347634 2540 False 4019.0 4019 95.2060 475 3018 1 chr3D.!!$F1 2543
6 TraesCS5A01G333400 chr2D 82247600 82250141 2541 True 4010.0 4010 95.1300 475 3018 1 chr2D.!!$R1 2543
7 TraesCS5A01G333400 chr2D 607121350 607122403 1053 False 1277.0 1277 89.0350 3016 4046 1 chr2D.!!$F1 1030
8 TraesCS5A01G333400 chrUn 134330740 134333280 2540 True 4008.0 4008 95.1280 475 3018 1 chrUn.!!$R2 2543
9 TraesCS5A01G333400 chrUn 71016572 71017183 611 True 560.0 560 83.7660 3174 3767 1 chrUn.!!$R1 593
10 TraesCS5A01G333400 chr3B 728851773 728854312 2539 False 3925.0 3925 94.5360 475 3018 1 chr3B.!!$F1 2543
11 TraesCS5A01G333400 chr3B 678819542 678824016 4474 False 993.0 1572 89.9425 568 4090 2 chr3B.!!$F2 3522
12 TraesCS5A01G333400 chr3B 685957572 685958131 559 True 678.0 678 88.6320 475 1033 1 chr3B.!!$R1 558
13 TraesCS5A01G333400 chr6B 646101433 646103980 2547 False 3738.0 3738 93.1760 475 3018 1 chr6B.!!$F1 2543
14 TraesCS5A01G333400 chr4B 524147651 524149752 2101 True 2957.0 2957 92.0420 909 3017 1 chr4B.!!$R2 2108
15 TraesCS5A01G333400 chr4B 77615242 77616327 1085 True 1567.0 1567 92.9490 3019 4090 1 chr4B.!!$R1 1071
16 TraesCS5A01G333400 chr2B 238550302 238551386 1084 False 1580.0 1580 93.1440 3016 4090 1 chr2B.!!$F1 1074
17 TraesCS5A01G333400 chr2B 37447169 37447935 766 True 593.0 593 81.2100 3016 3767 1 chr2B.!!$R1 751
18 TraesCS5A01G333400 chr2A 27757429 27758420 991 False 1096.0 1096 87.0870 3099 4090 1 chr2A.!!$F1 991
19 TraesCS5A01G333400 chr5D 324730325 324731318 993 True 1062.0 1062 86.6800 3087 4046 1 chr5D.!!$R1 959
20 TraesCS5A01G333400 chr5D 133266529 133267522 993 False 1037.0 1037 86.2380 3084 4046 1 chr5D.!!$F1 962


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
61 62 0.321653 CTGCTAAAAGTCCCACGCCT 60.322 55.000 0.00 0.0 0.0 5.52 F
81 82 0.466124 GCGATCTGGGCCTCTAAAGT 59.534 55.000 4.53 0.0 0.0 2.66 F
130 131 1.203313 TCTGTTAAGAGACCAGCCCCT 60.203 52.381 0.00 0.0 0.0 4.79 F
831 838 1.416401 GAAAGATCTGATACGCCCCCA 59.584 52.381 0.00 0.0 0.0 4.96 F
2257 2817 2.965831 TGTCTATCCCGGATTCCTCTTG 59.034 50.000 0.73 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1912 2468 0.389391 CGGGATGTAGACTTGCGGAT 59.611 55.000 0.0 0.0 0.00 4.18 R
2257 2817 4.813027 TCGATTTACCACAAGTAGACCAC 58.187 43.478 0.0 0.0 30.92 4.16 R
2318 2878 3.259876 AGCTATTTCCCACTTGTCGTACA 59.740 43.478 0.0 0.0 0.00 2.90 R
2440 3000 2.020720 ACATGTTGTCTTGTCGCCAAA 58.979 42.857 0.0 0.0 0.00 3.28 R
3571 5814 0.106619 GAGAGGAAGGAGCCCGTAGA 60.107 60.000 0.0 0.0 0.00 2.59 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
24 25 2.408271 TGGACTGACCAATCATGCTC 57.592 50.000 0.00 0.00 46.75 4.26
53 54 3.185391 GCCTATCGCATCTGCTAAAAGTC 59.815 47.826 0.09 0.00 39.32 3.01
61 62 0.321653 CTGCTAAAAGTCCCACGCCT 60.322 55.000 0.00 0.00 0.00 5.52
81 82 0.466124 GCGATCTGGGCCTCTAAAGT 59.534 55.000 4.53 0.00 0.00 2.66
130 131 1.203313 TCTGTTAAGAGACCAGCCCCT 60.203 52.381 0.00 0.00 0.00 4.79
131 132 2.043939 TCTGTTAAGAGACCAGCCCCTA 59.956 50.000 0.00 0.00 0.00 3.53
132 133 2.838202 CTGTTAAGAGACCAGCCCCTAA 59.162 50.000 0.00 0.00 0.00 2.69
418 421 5.359756 CACCCTTGATCTCGAAATATCACA 58.640 41.667 4.69 0.00 31.99 3.58
831 838 1.416401 GAAAGATCTGATACGCCCCCA 59.584 52.381 0.00 0.00 0.00 4.96
1223 1554 4.982295 CGTGGAAGATGCACTCGAATATAA 59.018 41.667 0.00 0.00 36.50 0.98
1520 1852 4.346970 TGCAGTACAAATGTTGAACAACG 58.653 39.130 0.62 0.00 43.94 4.10
1576 1908 3.540314 TGTTTTTGAACAGCCAGCAAT 57.460 38.095 0.00 0.00 0.00 3.56
1798 2133 8.901748 CAATTTTATGTTTGAAAGTACCACTCG 58.098 33.333 0.00 0.00 0.00 4.18
1912 2468 5.468746 GCTGAAGGACACACTATTTGTAACA 59.531 40.000 0.00 0.00 35.67 2.41
2255 2815 3.330126 TTGTCTATCCCGGATTCCTCT 57.670 47.619 0.73 0.00 0.00 3.69
2257 2817 2.965831 TGTCTATCCCGGATTCCTCTTG 59.034 50.000 0.73 0.00 0.00 3.02
2279 2839 4.281435 TGTGGTCTACTTGTGGTAAATCGA 59.719 41.667 0.00 0.00 0.00 3.59
2440 3000 0.762418 TGGAACACCGAACTCATGGT 59.238 50.000 0.00 0.00 39.66 3.55
2475 3035 7.481275 GACAACATGTCATTCAATTTTTGGT 57.519 32.000 0.00 0.00 46.22 3.67
2584 3144 7.613022 TCGGGTTTCTTAGTTCTACAAGAGATA 59.387 37.037 0.00 0.00 32.88 1.98
2687 3247 6.096846 GCCATTTATAATCCAACCACTTCAGT 59.903 38.462 0.00 0.00 0.00 3.41
2822 3382 0.539986 GATTACGGTGGCCTTGAGGA 59.460 55.000 3.32 0.00 37.39 3.71
3052 5253 0.814010 GCACCTGAGTTTGTGGACGT 60.814 55.000 0.00 0.00 33.08 4.34
3080 5281 0.455410 CTAGCGACTCTGCTGAGCTT 59.545 55.000 19.49 1.97 46.70 3.74
3100 5301 5.416013 AGCTTTCTGGTTAATGGTAAGCTTC 59.584 40.000 0.00 0.00 42.86 3.86
3213 5417 4.669768 TGATAGGGAAATAAATCAGGGCCT 59.330 41.667 0.00 0.00 0.00 5.19
3255 5459 3.326880 TCGGAGATTTATTTAGAGGGGGC 59.673 47.826 0.00 0.00 0.00 5.80
3262 5482 4.405756 TTATTTAGAGGGGGCCAAACAA 57.594 40.909 4.39 0.00 0.00 2.83
3475 5710 7.624360 ATCTTGCCGATTTTGTTGATAGTAA 57.376 32.000 0.00 0.00 0.00 2.24
3528 5768 0.690762 GGGTGCACCTTCCTAACTGA 59.309 55.000 33.91 0.00 35.85 3.41
3571 5814 9.959721 ACGGCCTCATATATACTCAATAAAATT 57.040 29.630 0.00 0.00 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.214062 GATGCGATAGGCCTCTCGG 59.786 63.158 33.58 19.66 42.61 4.63
38 39 1.398390 CGTGGGACTTTTAGCAGATGC 59.602 52.381 0.00 0.00 42.49 3.91
61 62 0.465705 CTTTAGAGGCCCAGATCGCA 59.534 55.000 0.00 0.00 0.00 5.10
108 109 1.208293 GGGCTGGTCTCTTAACAGAGG 59.792 57.143 0.00 0.00 46.17 3.69
125 126 5.007430 GCTTCGTAAGTTTCTTATTAGGGGC 59.993 44.000 0.00 0.00 39.48 5.80
131 132 9.817809 TCATATGAGCTTCGTAAGTTTCTTATT 57.182 29.630 0.00 0.00 39.48 1.40
132 133 9.469807 CTCATATGAGCTTCGTAAGTTTCTTAT 57.530 33.333 19.47 0.00 35.13 1.73
763 767 8.704849 TTGTTACTAAGGCATGCCATATTTAT 57.295 30.769 37.18 17.92 38.92 1.40
935 944 6.252599 TGGAAATTAGGATGTCTATGCAGT 57.747 37.500 0.00 0.00 0.00 4.40
955 964 3.427573 TCGTTCTATGAGGTGTCTTGGA 58.572 45.455 0.00 0.00 0.00 3.53
1223 1554 2.088423 TGCCGTTAATGAAGCCGAATT 58.912 42.857 0.00 0.00 0.00 2.17
1236 1567 2.874086 CTGCTCATCATGAATGCCGTTA 59.126 45.455 0.00 0.00 35.17 3.18
1551 1883 6.338214 TGCTGGCTGTTCAAAAACAATATA 57.662 33.333 0.00 0.00 44.53 0.86
1576 1908 4.303794 AGGTAGCACCCATTATACCAAGA 58.696 43.478 3.31 0.00 39.75 3.02
1707 2039 7.527457 AGCAGAACGTAAGATTTTGATAAACC 58.473 34.615 0.00 0.00 43.62 3.27
1720 2052 7.585867 TCTAATAGCTATGAGCAGAACGTAAG 58.414 38.462 12.81 0.00 45.56 2.34
1912 2468 0.389391 CGGGATGTAGACTTGCGGAT 59.611 55.000 0.00 0.00 0.00 4.18
2255 2815 4.992319 CGATTTACCACAAGTAGACCACAA 59.008 41.667 0.00 0.00 30.92 3.33
2257 2817 4.813027 TCGATTTACCACAAGTAGACCAC 58.187 43.478 0.00 0.00 30.92 4.16
2318 2878 3.259876 AGCTATTTCCCACTTGTCGTACA 59.740 43.478 0.00 0.00 0.00 2.90
2440 3000 2.020720 ACATGTTGTCTTGTCGCCAAA 58.979 42.857 0.00 0.00 0.00 3.28
2506 3066 8.798859 AACTTGAGATTTCTACATACTGCATT 57.201 30.769 0.00 0.00 0.00 3.56
2811 3371 2.956132 TGTTCAAAATCCTCAAGGCCA 58.044 42.857 5.01 0.00 34.44 5.36
3052 5253 2.159366 GCAGAGTCGCTAGCTACAAGAA 60.159 50.000 20.27 0.00 0.00 2.52
3080 5281 6.377146 GGAATGAAGCTTACCATTAACCAGAA 59.623 38.462 12.06 0.00 33.57 3.02
3100 5301 2.810439 TTTCTTTTGTGGCGGGAATG 57.190 45.000 0.00 0.00 0.00 2.67
3213 5417 1.715931 ACCCCCTGATTTGAATGGTGA 59.284 47.619 0.00 0.00 0.00 4.02
3255 5459 1.414061 TTGTGGGGCCCATTGTTTGG 61.414 55.000 31.48 0.00 46.00 3.28
3262 5482 2.206536 CGTGTTTTGTGGGGCCCAT 61.207 57.895 31.48 0.00 35.28 4.00
3303 5523 0.534877 AAGTGCAACACTCGATGCCA 60.535 50.000 6.29 0.00 44.62 4.92
3528 5768 1.305219 CGTGGGGAATTGTGCGACAT 61.305 55.000 0.00 0.00 0.00 3.06
3571 5814 0.106619 GAGAGGAAGGAGCCCGTAGA 60.107 60.000 0.00 0.00 0.00 2.59
3684 5944 5.352569 CGTCTGAGGAAAGTGCTATGAAATT 59.647 40.000 0.00 0.00 0.00 1.82
3839 6120 9.900112 ACCAGGGTATATCTTCTAATCTAAACT 57.100 33.333 0.00 0.00 0.00 2.66
4057 6343 6.783892 TTTGGACCACAGTTTTATACGTAC 57.216 37.500 0.00 0.00 0.00 3.67
4065 6351 4.343814 CCCATAGTTTTGGACCACAGTTTT 59.656 41.667 0.00 0.00 39.25 2.43



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

AutoCloner maintained by Alex Coulton.