Multiple sequence alignment - TraesCS5A01G362700

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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 TraesCS5A01G362700 chr5A 100.000 4506 0 0 1 4506 563485870 563481365 0.000000e+00 8322.0
1 TraesCS5A01G362700 chr5A 96.364 2338 59 7 2183 4506 563507914 563505589 0.000000e+00 3823.0
2 TraesCS5A01G362700 chr5A 96.246 2344 56 6 2183 4506 563517174 563514843 0.000000e+00 3812.0
3 TraesCS5A01G362700 chr5A 96.269 2332 66 7 2183 4506 563498662 563496344 0.000000e+00 3805.0
4 TraesCS5A01G362700 chr5A 97.759 2187 47 2 1 2187 563500870 563498686 0.000000e+00 3766.0
5 TraesCS5A01G362700 chr5A 97.623 2188 50 2 1 2187 563519384 563517198 0.000000e+00 3751.0
6 TraesCS5A01G362700 chr5A 97.577 2187 52 1 1 2187 563510123 563507938 0.000000e+00 3744.0
7 TraesCS5A01G362700 chr5A 95.978 2039 68 8 2183 4218 563456002 563453975 0.000000e+00 3299.0
8 TraesCS5A01G362700 chr5A 95.406 2068 62 7 2183 4218 563567940 563565874 0.000000e+00 3262.0
9 TraesCS5A01G362700 chr5A 94.719 2083 86 9 1 2074 563570095 563568028 0.000000e+00 3216.0
10 TraesCS5A01G362700 chr5A 94.971 1909 72 12 288 2187 563548817 563546924 0.000000e+00 2972.0
11 TraesCS5A01G362700 chr5A 97.169 1625 45 1 563 2187 563457649 563456026 0.000000e+00 2745.0
12 TraesCS5A01G362700 chr5A 95.120 1455 46 7 2183 3625 563546900 563545459 0.000000e+00 2270.0
13 TraesCS5A01G362700 chr5A 97.328 973 23 1 1 970 563491612 563490640 0.000000e+00 1650.0
14 TraesCS5A01G362700 chr5A 96.296 945 33 2 1 944 563549734 563548791 0.000000e+00 1550.0
15 TraesCS5A01G362700 chr5A 86.264 1325 175 4 281 1600 563554169 563552847 0.000000e+00 1432.0
16 TraesCS5A01G362700 chr5A 85.886 1332 180 4 281 1605 563556521 563555191 0.000000e+00 1411.0
17 TraesCS5A01G362700 chr5A 85.660 1325 182 5 281 1600 563592187 563590866 0.000000e+00 1387.0
18 TraesCS5A01G362700 chr5A 85.060 1332 191 4 281 1605 563594540 563593210 0.000000e+00 1351.0
19 TraesCS5A01G362700 chr5A 96.045 531 8 2 3977 4506 563490631 563490113 0.000000e+00 852.0
20 TraesCS5A01G362700 chr5A 95.130 308 15 0 3911 4218 563545462 563545155 1.880000e-133 486.0
21 TraesCS5A01G362700 chr5A 96.863 255 8 0 4251 4505 563553999 563553745 1.160000e-115 427.0
22 TraesCS5A01G362700 chr5A 96.498 257 8 1 4251 4506 563524064 563523808 1.500000e-114 424.0
23 TraesCS5A01G362700 chr5A 96.498 257 8 1 4251 4506 563592017 563591761 1.500000e-114 424.0
24 TraesCS5A01G362700 chr5A 89.961 259 25 1 4249 4506 563556351 563556093 2.600000e-87 333.0
25 TraesCS5A01G362700 chr5A 88.476 269 30 1 4239 4506 563526427 563526159 1.560000e-84 324.0
26 TraesCS5A01G362700 chr5A 98.485 66 1 0 2122 2187 563568029 563567964 2.850000e-22 117.0
27 TraesCS5A01G362700 chr2B 74.291 1163 226 43 1002 2146 778004319 778003212 1.500000e-114 424.0
28 TraesCS5A01G362700 chr2B 83.784 444 69 3 2184 2625 65046 65488 6.970000e-113 418.0
29 TraesCS5A01G362700 chr2B 82.658 444 74 3 2184 2625 478312 478754 1.520000e-104 390.0
30 TraesCS5A01G362700 chrUn 74.199 1155 225 43 1002 2138 242563354 242564453 9.020000e-112 414.0
31 TraesCS5A01G362700 chrUn 74.199 1155 225 43 1002 2138 316214686 316213587 9.020000e-112 414.0
32 TraesCS5A01G362700 chr2D 82.658 444 74 3 2184 2625 2511181 2510739 1.520000e-104 390.0
33 TraesCS5A01G362700 chr5D 89.474 285 19 3 1 284 461343877 461343603 2.580000e-92 350.0
34 TraesCS5A01G362700 chr7B 86.833 281 27 2 1 281 520419264 520418994 5.660000e-79 305.0
35 TraesCS5A01G362700 chr3D 94.059 202 11 1 3902 4102 500551045 500550844 5.660000e-79 305.0
36 TraesCS5A01G362700 chr1B 86.411 287 23 9 1 281 638043707 638043431 2.630000e-77 300.0
37 TraesCS5A01G362700 chr1B 79.021 143 25 5 143 281 685935041 685934900 4.800000e-15 93.5
38 TraesCS5A01G362700 chr1B 92.000 50 4 0 241 290 62533051 62533002 2.250000e-08 71.3
39 TraesCS5A01G362700 chr4B 92.040 201 16 0 3902 4102 586242862 586242662 2.650000e-72 283.0
40 TraesCS5A01G362700 chr4B 84.871 271 31 2 11 281 429266758 429266498 9.610000e-67 265.0
41 TraesCS5A01G362700 chr7D 88.710 62 6 1 236 296 587161248 587161187 1.740000e-09 75.0
42 TraesCS5A01G362700 chr6D 87.302 63 5 2 222 281 337767621 337767683 8.090000e-08 69.4


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 TraesCS5A01G362700 chr5A 563481365 563485870 4505 True 8322.000000 8322 100.000000 1 4506 1 chr5A.!!$R1 4505
1 TraesCS5A01G362700 chr5A 563496344 563500870 4526 True 3785.500000 3805 97.014000 1 4506 2 chr5A.!!$R4 4505
2 TraesCS5A01G362700 chr5A 563505589 563510123 4534 True 3783.500000 3823 96.970500 1 4506 2 chr5A.!!$R5 4505
3 TraesCS5A01G362700 chr5A 563514843 563519384 4541 True 3781.500000 3812 96.934500 1 4506 2 chr5A.!!$R6 4505
4 TraesCS5A01G362700 chr5A 563453975 563457649 3674 True 3022.000000 3299 96.573500 563 4218 2 chr5A.!!$R2 3655
5 TraesCS5A01G362700 chr5A 563565874 563570095 4221 True 2198.333333 3262 96.203333 1 4218 3 chr5A.!!$R9 4217
6 TraesCS5A01G362700 chr5A 563545155 563556521 11366 True 1360.125000 2972 92.561375 1 4506 8 chr5A.!!$R8 4505
7 TraesCS5A01G362700 chr5A 563490113 563491612 1499 True 1251.000000 1650 96.686500 1 4506 2 chr5A.!!$R3 4505
8 TraesCS5A01G362700 chr5A 563590866 563594540 3674 True 1054.000000 1387 89.072667 281 4506 3 chr5A.!!$R10 4225
9 TraesCS5A01G362700 chr5A 563523808 563526427 2619 True 374.000000 424 92.487000 4239 4506 2 chr5A.!!$R7 267
10 TraesCS5A01G362700 chr2B 778003212 778004319 1107 True 424.000000 424 74.291000 1002 2146 1 chr2B.!!$R1 1144
11 TraesCS5A01G362700 chrUn 242563354 242564453 1099 False 414.000000 414 74.199000 1002 2138 1 chrUn.!!$F1 1136
12 TraesCS5A01G362700 chrUn 316213587 316214686 1099 True 414.000000 414 74.199000 1002 2138 1 chrUn.!!$R1 1136

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
603 8026 3.178865 TCGTGGGAAGAAAACCCTCTAT 58.821 45.455 0.0 0.0 46.82 1.98 F
965 8396 4.157472 TGCACTTCACAATGAGAAACAACA 59.843 37.500 0.0 0.0 0.00 3.33 F
2191 9650 2.039480 TGATCTTTGAACCAGAGCTGCT 59.961 45.455 0.0 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 9040 1.873591 ACACTTCTTGCATGTCGAACC 59.126 47.619 0.0 0.0 0.00 3.62 R
2201 9660 2.102588 CCGATGGGTACAACCTAAGAGG 59.897 54.545 0.0 0.0 42.49 3.69 R
3928 11435 1.153066 ACAACGTCACATGCCACCA 60.153 52.632 0.0 0.0 0.00 4.17 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
295 7088 8.685838 TTTGTGCTAGTGAACCTAAAGTATTT 57.314 30.769 0.00 0.00 43.42 1.40
323 7116 6.855836 TGGCTTCATGAATGTTGATACTTTC 58.144 36.000 8.96 0.00 38.34 2.62
435 7856 8.499162 CATTTCATTATTTCCTTCCTAGTAGCG 58.501 37.037 0.00 0.00 0.00 4.26
603 8026 3.178865 TCGTGGGAAGAAAACCCTCTAT 58.821 45.455 0.00 0.00 46.82 1.98
691 8114 9.250624 GATACCATAGTTTGACTAGTAGCTTTG 57.749 37.037 0.00 0.00 33.66 2.77
908 8339 7.116948 CCTCTGTTGGAGCTACAAATATATTCG 59.883 40.741 14.43 0.00 40.57 3.34
915 8346 9.070179 TGGAGCTACAAATATATTCGTGTAGTA 57.930 33.333 24.85 14.17 43.46 1.82
965 8396 4.157472 TGCACTTCACAATGAGAAACAACA 59.843 37.500 0.00 0.00 0.00 3.33
1068 8499 6.653183 TCGAAGTAGTACGACAATAGCATAC 58.347 40.000 8.90 0.00 33.62 2.39
1133 8564 4.249638 AGAGCTACTCATCTCCACTCTT 57.750 45.455 0.00 0.00 32.06 2.85
1168 8599 7.341256 TGTCCCTATGTACTTCTACTTTAGGTG 59.659 40.741 0.00 0.00 32.67 4.00
2000 9431 5.707298 CCCAGAATACACAGACAATGACTTT 59.293 40.000 0.00 0.00 0.00 2.66
2008 9439 4.999311 CACAGACAATGACTTTCTCCATGA 59.001 41.667 0.00 0.00 0.00 3.07
2191 9650 2.039480 TGATCTTTGAACCAGAGCTGCT 59.961 45.455 0.00 0.00 0.00 4.24
2201 9660 0.718343 CAGAGCTGCTTTGTACGAGC 59.282 55.000 11.71 12.65 40.53 5.03
2350 9811 7.350921 AGAATGGAAGATCTATGGGGTAAAGAA 59.649 37.037 0.00 0.00 0.00 2.52
2354 9815 4.899502 AGATCTATGGGGTAAAGAATGCG 58.100 43.478 0.00 0.00 0.00 4.73
2358 9819 5.607477 TCTATGGGGTAAAGAATGCGTTAG 58.393 41.667 0.00 0.00 0.00 2.34
2499 9960 1.935300 GCAGATGAAGACCGTCGTTGT 60.935 52.381 0.00 0.00 35.94 3.32
2936 10398 8.660373 CACTCATGGTTTCTACTTAGAATCAAC 58.340 37.037 0.00 0.00 41.52 3.18
2964 10426 4.911390 GGCCATACCTAGATTGTTAGCAT 58.089 43.478 0.00 0.00 34.51 3.79
3616 11122 8.902540 TCTATATTTTAAGCATCACGGTCATT 57.097 30.769 0.00 0.00 0.00 2.57
3653 11159 7.762615 TGAATACAACCGTAAGTTATCTCCAAG 59.237 37.037 0.00 0.00 36.18 3.61
3944 11451 0.036732 ATCTGGTGGCATGTGACGTT 59.963 50.000 0.00 0.00 0.00 3.99
3975 11482 1.298340 CATGTCGGTGGCCAGGTTA 59.702 57.895 5.11 0.00 0.00 2.85
4235 11742 3.996921 GGACCAGCCTATGATCATGAT 57.003 47.619 18.72 8.25 0.00 2.45
4236 11743 3.607741 GGACCAGCCTATGATCATGATG 58.392 50.000 18.72 10.99 0.00 3.07
4237 11744 3.607741 GACCAGCCTATGATCATGATGG 58.392 50.000 22.28 22.28 0.00 3.51
4243 11750 7.349065 ACCAGCCTATGATCATGATGGATATAA 59.651 37.037 27.83 2.94 0.00 0.98
4363 14628 4.473477 ACCAGCTTCCATCACTACTAAC 57.527 45.455 0.00 0.00 0.00 2.34
4429 14695 3.548745 ATCCAGCGTGATCAAAGATCA 57.451 42.857 0.00 5.63 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
112 6901 4.687483 GCTGCCATGAAAATATGTATTGCC 59.313 41.667 0.00 0.00 0.00 4.52
295 7088 8.523915 AGTATCAACATTCATGAAGCCAAATA 57.476 30.769 14.54 6.44 0.00 1.40
323 7116 9.627395 TCTTTACTTTGATCGAACTTCTAGAAG 57.373 33.333 27.41 27.41 43.79 2.85
603 8026 6.169800 TCTTTGATCACGATGGATGTAAACA 58.830 36.000 0.00 0.00 0.00 2.83
810 8234 3.997021 GTCAGTAACCAATCACTCACCAG 59.003 47.826 0.00 0.00 0.00 4.00
908 8339 6.483640 AGCCAATAATTAGCTTGCTACTACAC 59.516 38.462 1.37 0.00 31.27 2.90
915 8346 5.684704 TGACTAGCCAATAATTAGCTTGCT 58.315 37.500 3.34 0.00 38.06 3.91
965 8396 3.719268 TCTAAGTCCATTGTGGTGCAT 57.281 42.857 0.00 0.00 39.03 3.96
1118 8549 2.255406 AGCACAAGAGTGGAGATGAGT 58.745 47.619 0.00 0.00 45.98 3.41
1133 8564 4.350245 AGTACATAGGGACAAGTAGCACA 58.650 43.478 0.00 0.00 0.00 4.57
1168 8599 5.990120 TGGGTTCTTTGACCTACTACTAC 57.010 43.478 0.00 0.00 39.71 2.73
1178 8609 3.733443 AGCATTGTTGGGTTCTTTGAC 57.267 42.857 0.00 0.00 0.00 3.18
1329 8760 0.745845 GTGATGAGCAACCGCATCCT 60.746 55.000 0.00 0.00 44.59 3.24
1443 8874 3.118112 CCATCAATGGTGAAGAGGCTACT 60.118 47.826 0.00 0.00 43.05 2.57
1609 9040 1.873591 ACACTTCTTGCATGTCGAACC 59.126 47.619 0.00 0.00 0.00 3.62
2191 9650 3.322828 ACAACCTAAGAGGCTCGTACAAA 59.677 43.478 9.22 0.00 39.63 2.83
2201 9660 2.102588 CCGATGGGTACAACCTAAGAGG 59.897 54.545 0.00 0.00 42.49 3.69
2335 9796 4.497291 AACGCATTCTTTACCCCATAGA 57.503 40.909 0.00 0.00 0.00 1.98
2350 9811 3.738830 TTCGGGTTATAGCTAACGCAT 57.261 42.857 14.57 0.00 45.99 4.73
2354 9815 5.011431 ACCACCTATTCGGGTTATAGCTAAC 59.989 44.000 0.00 0.00 37.52 2.34
2358 9819 4.062991 CAACCACCTATTCGGGTTATAGC 58.937 47.826 0.00 0.00 42.78 2.97
2471 9932 2.213499 GGTCTTCATCTGCATAACCGG 58.787 52.381 0.00 0.00 0.00 5.28
2499 9960 3.680490 TCAAAGTTCCACAACACAGTCA 58.320 40.909 0.00 0.00 34.60 3.41
2936 10398 2.223803 ATCTAGGTATGGCCTCTCGG 57.776 55.000 3.32 0.00 46.96 4.63
2957 10419 7.042523 ACAGCTCAATCAAACAAAAATGCTAAC 60.043 33.333 0.00 0.00 0.00 2.34
2964 10426 9.979578 ATTACATACAGCTCAATCAAACAAAAA 57.020 25.926 0.00 0.00 0.00 1.94
3616 11122 4.000325 CGGTTGTATTCACACAAGGATCA 59.000 43.478 0.00 0.00 39.02 2.92
3868 11375 8.616076 GTGTTAGATCCAGTTAATCAGAAATGG 58.384 37.037 0.00 0.00 44.21 3.16
3928 11435 1.153066 ACAACGTCACATGCCACCA 60.153 52.632 0.00 0.00 0.00 4.17
3944 11451 1.294857 CGACATGTGACACAACCACA 58.705 50.000 13.23 0.00 46.90 4.17
3975 11482 3.704231 GACATGGGCATCACCGGCT 62.704 63.158 0.00 0.00 40.62 5.52
4194 11701 3.455910 CCTATTGATTGTGACCCTCCTCA 59.544 47.826 0.00 0.00 0.00 3.86
4363 14628 1.793134 AAGCTATCGGGCCGACTACG 61.793 60.000 33.71 19.74 39.18 3.51
4368 14633 2.499205 CACAAGCTATCGGGCCGA 59.501 61.111 33.10 33.10 41.13 5.54
4429 14695 9.489084 GGAAGTTAAAAGTTGAATTTAGGCAAT 57.511 29.630 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.