Multiple sequence alignment - TraesCS5B01G118600

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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 TraesCS5B01G118600 chr5B 100.000 3424 0 0 1 3424 209178206 209174783 0.000000e+00 6324.0
1 TraesCS5B01G118600 chr5B 96.909 3429 98 7 1 3424 265539561 265536136 0.000000e+00 5738.0
2 TraesCS5B01G118600 chr5B 84.942 518 40 19 2906 3419 62357211 62356728 1.100000e-134 490.0
3 TraesCS5B01G118600 chr3B 97.662 3421 77 3 1 3419 228483096 228479677 0.000000e+00 5871.0
4 TraesCS5B01G118600 chr3B 96.507 3006 101 4 155 3157 142225350 142228354 0.000000e+00 4966.0
5 TraesCS5B01G118600 chr3B 96.255 2750 97 4 155 2902 761535502 761532757 0.000000e+00 4503.0
6 TraesCS5B01G118600 chr3B 96.562 640 22 0 2697 3336 557721884 557722523 0.000000e+00 1061.0
7 TraesCS5B01G118600 chr3B 81.818 187 11 14 3 168 762519827 762519643 5.960000e-28 135.0
8 TraesCS5B01G118600 chr3B 82.022 178 11 12 3 159 329492833 329492656 7.710000e-27 132.0
9 TraesCS5B01G118600 chr3B 82.313 147 9 9 30 159 317292474 317292620 1.000000e-20 111.0
10 TraesCS5B01G118600 chr3B 92.208 77 5 1 3 78 62762270 62762194 1.300000e-19 108.0
11 TraesCS5B01G118600 chr3B 91.026 78 7 0 82 159 29814378 29814455 4.670000e-19 106.0
12 TraesCS5B01G118600 chr3B 91.026 78 7 0 82 159 557719303 557719380 4.670000e-19 106.0
13 TraesCS5B01G118600 chr3B 91.026 78 7 0 82 159 751892722 751892645 4.670000e-19 106.0
14 TraesCS5B01G118600 chr3B 91.026 78 6 1 82 159 766273730 766273806 1.680000e-18 104.0
15 TraesCS5B01G118600 chr3B 93.939 66 4 0 3 68 317292419 317292484 2.170000e-17 100.0
16 TraesCS5B01G118600 chr3B 89.744 78 8 0 82 159 761535615 761535538 2.170000e-17 100.0
17 TraesCS5B01G118600 chr3B 90.278 72 7 0 82 153 142225237 142225308 1.010000e-15 95.3
18 TraesCS5B01G118600 chr3B 92.424 66 4 1 6 71 648359498 648359434 3.640000e-15 93.5
19 TraesCS5B01G118600 chr2B 96.890 3183 92 6 155 3333 51007093 51010272 0.000000e+00 5323.0
20 TraesCS5B01G118600 chr2B 95.565 3224 100 20 155 3353 739865410 739862205 0.000000e+00 5121.0
21 TraesCS5B01G118600 chr2B 95.166 724 24 6 2701 3416 700678545 700679265 0.000000e+00 1133.0
22 TraesCS5B01G118600 chr2B 83.708 178 8 12 3 159 676210501 676210324 7.660000e-32 148.0
23 TraesCS5B01G118600 chr2B 83.708 178 8 12 3 159 739865623 739865446 7.660000e-32 148.0
24 TraesCS5B01G118600 chr2B 83.146 178 9 12 3 159 32826813 32826990 3.560000e-30 143.0
25 TraesCS5B01G118600 chr2B 91.026 78 7 0 82 159 51006980 51007057 4.670000e-19 106.0
26 TraesCS5B01G118600 chr2B 91.026 78 7 0 82 159 700676023 700676100 4.670000e-19 106.0
27 TraesCS5B01G118600 chr1B 96.072 3284 100 8 158 3417 600339703 600336425 0.000000e+00 5323.0
28 TraesCS5B01G118600 chr4A 97.290 3137 80 5 1 3134 691949136 691952270 0.000000e+00 5317.0
29 TraesCS5B01G118600 chr6A 95.934 3296 100 9 147 3419 11913999 11910715 0.000000e+00 5313.0
30 TraesCS5B01G118600 chr7B 96.089 2838 104 6 155 2989 3657405 3660238 0.000000e+00 4619.0
31 TraesCS5B01G118600 chr2A 91.406 1629 95 13 3 1629 259692845 259694430 0.000000e+00 2191.0
32 TraesCS5B01G118600 chr2A 83.908 174 11 8 3 159 110290217 110290390 2.130000e-32 150.0
33 TraesCS5B01G118600 chr2A 83.708 178 8 12 3 159 55071592 55071415 7.660000e-32 148.0
34 TraesCS5B01G118600 chr7A 84.483 174 10 8 3 159 493522186 493522359 4.580000e-34 156.0
35 TraesCS5B01G118600 chr7A 84.483 174 10 8 3 159 639855049 639854876 4.580000e-34 156.0
36 TraesCS5B01G118600 chr7A 83.708 178 8 12 3 159 578426290 578426113 7.660000e-32 148.0
37 TraesCS5B01G118600 chr7A 92.593 81 3 2 3342 3419 633699739 633699659 2.790000e-21 113.0
38 TraesCS5B01G118600 chr7A 90.244 82 6 2 3 82 1544078 1543997 4.670000e-19 106.0
39 TraesCS5B01G118600 chr7A 91.026 78 7 0 82 159 579477460 579477383 4.670000e-19 106.0


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 TraesCS5B01G118600 chr5B 209174783 209178206 3423 True 6324.00 6324 100.0000 1 3424 1 chr5B.!!$R2 3423
1 TraesCS5B01G118600 chr5B 265536136 265539561 3425 True 5738.00 5738 96.9090 1 3424 1 chr5B.!!$R3 3423
2 TraesCS5B01G118600 chr3B 228479677 228483096 3419 True 5871.00 5871 97.6620 1 3419 1 chr3B.!!$R2 3418
3 TraesCS5B01G118600 chr3B 142225237 142228354 3117 False 2530.65 4966 93.3925 82 3157 2 chr3B.!!$F3 3075
4 TraesCS5B01G118600 chr3B 761532757 761535615 2858 True 2301.50 4503 92.9995 82 2902 2 chr3B.!!$R7 2820
5 TraesCS5B01G118600 chr3B 557719303 557722523 3220 False 583.50 1061 93.7940 82 3336 2 chr3B.!!$F5 3254
6 TraesCS5B01G118600 chr2B 51006980 51010272 3292 False 2714.50 5323 93.9580 82 3333 2 chr2B.!!$F2 3251
7 TraesCS5B01G118600 chr2B 739862205 739865623 3418 True 2634.50 5121 89.6365 3 3353 2 chr2B.!!$R2 3350
8 TraesCS5B01G118600 chr2B 700676023 700679265 3242 False 619.50 1133 93.0960 82 3416 2 chr2B.!!$F3 3334
9 TraesCS5B01G118600 chr1B 600336425 600339703 3278 True 5323.00 5323 96.0720 158 3417 1 chr1B.!!$R1 3259
10 TraesCS5B01G118600 chr4A 691949136 691952270 3134 False 5317.00 5317 97.2900 1 3134 1 chr4A.!!$F1 3133
11 TraesCS5B01G118600 chr6A 11910715 11913999 3284 True 5313.00 5313 95.9340 147 3419 1 chr6A.!!$R1 3272
12 TraesCS5B01G118600 chr7B 3657405 3660238 2833 False 4619.00 4619 96.0890 155 2989 1 chr7B.!!$F1 2834
13 TraesCS5B01G118600 chr2A 259692845 259694430 1585 False 2191.00 2191 91.4060 3 1629 1 chr2A.!!$F2 1626

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
833 914 1.676967 CTGTCTTGCTTGGAGGGCC 60.677 63.158 0.00 0.0 0.00 5.80 F
1166 1259 0.033504 TCTGAGACCTCGGTGCAAAC 59.966 55.000 5.82 0.0 37.27 2.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2364 2465 1.247567 CTGTTGTGGGTGGCCTTAAG 58.752 55.0 3.32 0.0 0.00 1.85 R
2517 2618 2.877097 TCAAAGCATGGAACTGGCTA 57.123 45.0 0.00 0.0 37.43 3.93 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
114 136 5.459768 CACTGTACATGCATGCTTGTTTAA 58.540 37.500 35.25 22.61 36.11 1.52
348 428 2.238646 TCCTTGTGGTTATACTGCCAGG 59.761 50.000 0.00 0.00 35.14 4.45
459 539 6.098552 AGTCTTCCTTACCTGAATAACTAGGC 59.901 42.308 0.00 0.00 37.61 3.93
731 812 5.133322 AGTGGAGTTATCAATGATGACCCAT 59.867 40.000 21.56 13.13 38.69 4.00
800 881 4.960938 TGATGTTGTAGTGAGCAAGACTT 58.039 39.130 0.00 0.00 0.00 3.01
833 914 1.676967 CTGTCTTGCTTGGAGGGCC 60.677 63.158 0.00 0.00 0.00 5.80
1097 1187 2.557920 AGAGTCACAAGGCAGAAAGG 57.442 50.000 0.00 0.00 0.00 3.11
1166 1259 0.033504 TCTGAGACCTCGGTGCAAAC 59.966 55.000 5.82 0.00 37.27 2.93
1367 1460 1.884579 ACTTGTGCTTCAATCAGGCAG 59.115 47.619 0.00 0.00 36.62 4.85
1522 1616 8.880991 TGACTACCAAGACTAGACTTAGAAAT 57.119 34.615 7.14 0.00 0.00 2.17
1524 1618 8.653036 ACTACCAAGACTAGACTTAGAAATGT 57.347 34.615 7.14 0.81 0.00 2.71
1611 1707 2.185608 GCGTCCAGAGAAGCCTCC 59.814 66.667 0.00 0.00 41.12 4.30
1692 1791 6.605471 TCTTCCTCACTTCAAGCTATACAA 57.395 37.500 0.00 0.00 0.00 2.41
2284 2384 9.947669 CTCATTGGATAACATTTCTGATTCTTC 57.052 33.333 0.00 0.00 0.00 2.87
2352 2453 2.736347 GTAAGGGTGAGGAGCTGTCTA 58.264 52.381 0.00 0.00 0.00 2.59
2364 2465 2.600867 GAGCTGTCTACGATTGACTTGC 59.399 50.000 0.00 3.94 35.63 4.01
2517 2618 5.375417 TGATTTGATGCTGTTTGATTCGT 57.625 34.783 0.00 0.00 0.00 3.85
2784 2896 4.965200 ATAGAACCACCATTCTAGGCTC 57.035 45.455 0.00 0.00 42.88 4.70
2793 2905 3.054139 ACCATTCTAGGCTCAATGAAGCA 60.054 43.478 16.85 0.00 44.35 3.91
2820 2932 6.604396 TCATATTGTTCCAATTGCATGTCTCT 59.396 34.615 0.00 0.00 0.00 3.10
2948 3063 2.902486 TCCTCCATATGCTAGCTTGAGG 59.098 50.000 20.93 20.93 39.38 3.86
2952 3067 2.369860 CCATATGCTAGCTTGAGGTGGA 59.630 50.000 17.23 0.00 0.00 4.02
3228 3345 2.430465 GGAAGAATCTGAAGCTGCACA 58.570 47.619 1.02 0.62 0.00 4.57
3355 3510 2.872245 TGAACCTCTTTGTCTTTGAGCG 59.128 45.455 0.00 0.00 0.00 5.03
3365 3520 4.859304 TGTCTTTGAGCGAAGGTAGTTA 57.141 40.909 0.00 0.00 39.88 2.24
3419 3577 1.684983 AGAGCTGTTGCATTTTGCTGT 59.315 42.857 8.38 2.82 45.31 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 136 9.874205 ATTAATTAAGCAAACATGTAAGTGCAT 57.126 25.926 23.37 17.1 39.50 3.96
143 165 6.463995 TCATGCACATACACTGATGTACTA 57.536 37.500 0.00 0.0 44.11 1.82
800 881 4.202010 GCAAGACAGAGTTTGCACCTTAAA 60.202 41.667 4.48 0.0 46.72 1.52
833 914 7.230712 AGGAATAAATAGCATAAAAGAACCCCG 59.769 37.037 0.00 0.0 0.00 5.73
1097 1187 1.014044 TGTCGCAGTCGCCATCTTTC 61.014 55.000 0.00 0.0 35.26 2.62
1166 1259 3.499737 GCGGCAACTCATCACCCG 61.500 66.667 0.00 0.0 41.72 5.28
1292 1385 2.375174 TCAATAGAAGGTGCAACAGGGT 59.625 45.455 3.64 0.0 39.98 4.34
1367 1460 3.445096 AGATAGCATTGCAAAGGTCAACC 59.555 43.478 9.96 0.0 0.00 3.77
1482 1576 6.839124 TGGTAGTCATTGCATCTGAAAATT 57.161 33.333 1.38 0.0 0.00 1.82
1522 1616 2.623418 TCCTCTCTAGCCCTTTGACA 57.377 50.000 0.00 0.0 0.00 3.58
1524 1618 3.034635 GTGATCCTCTCTAGCCCTTTGA 58.965 50.000 0.00 0.0 0.00 2.69
1946 2046 5.887598 TGATGCTGACTTTATTTGTGGCTAT 59.112 36.000 0.00 0.0 0.00 2.97
2352 2453 2.084546 GGCCTTAAGCAAGTCAATCGT 58.915 47.619 0.00 0.0 46.50 3.73
2364 2465 1.247567 CTGTTGTGGGTGGCCTTAAG 58.752 55.000 3.32 0.0 0.00 1.85
2517 2618 2.877097 TCAAAGCATGGAACTGGCTA 57.123 45.000 0.00 0.0 37.43 3.93
2820 2932 6.892456 ACAAGAAGATGATGACTAGTGACCTA 59.108 38.462 0.00 0.0 0.00 3.08
3228 3345 1.810412 GCAGGTCAAGTTCCTTGTCGT 60.810 52.381 4.08 0.0 41.66 4.34
3355 3510 7.542130 CAGGTTCAAAATGCAATAACTACCTTC 59.458 37.037 7.82 0.0 30.27 3.46
3365 3520 5.051816 CAGTTCACAGGTTCAAAATGCAAT 58.948 37.500 0.00 0.0 0.00 3.56


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

AutoCloner maintained by Alex Coulton.