Multiple sequence alignment - TraesCS5A01G143700

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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 TraesCS5A01G143700 chr5A 100.000 2450 0 0 1 2450 319150258 319147809 0 4525
1 TraesCS5A01G143700 chr5A 91.110 2441 200 12 1 2435 324398554 324400983 0 3290
2 TraesCS5A01G143700 chr2D 93.737 2443 143 5 1 2441 378753974 378751540 0 3655
3 TraesCS5A01G143700 chr2D 90.537 2441 217 9 1 2437 622835041 622832611 0 3216
4 TraesCS5A01G143700 chr6D 92.456 2439 169 7 1 2437 181703917 181706342 0 3470
5 TraesCS5A01G143700 chr1A 91.066 2440 204 10 1 2437 99894948 99892520 0 3286
6 TraesCS5A01G143700 chr7B 90.685 2437 207 13 5 2437 111977856 111975436 0 3225
7 TraesCS5A01G143700 chr7D 92.488 2223 160 4 220 2438 38611430 38613649 0 3173
8 TraesCS5A01G143700 chr6B 90.135 2443 223 10 1 2437 286768793 286766363 0 3160
9 TraesCS5A01G143700 chr3B 89.144 2441 251 9 1 2438 276456396 276453967 0 3027


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 TraesCS5A01G143700 chr5A 319147809 319150258 2449 True 4525 4525 100.000 1 2450 1 chr5A.!!$R1 2449
1 TraesCS5A01G143700 chr5A 324398554 324400983 2429 False 3290 3290 91.110 1 2435 1 chr5A.!!$F1 2434
2 TraesCS5A01G143700 chr2D 378751540 378753974 2434 True 3655 3655 93.737 1 2441 1 chr2D.!!$R1 2440
3 TraesCS5A01G143700 chr2D 622832611 622835041 2430 True 3216 3216 90.537 1 2437 1 chr2D.!!$R2 2436
4 TraesCS5A01G143700 chr6D 181703917 181706342 2425 False 3470 3470 92.456 1 2437 1 chr6D.!!$F1 2436
5 TraesCS5A01G143700 chr1A 99892520 99894948 2428 True 3286 3286 91.066 1 2437 1 chr1A.!!$R1 2436
6 TraesCS5A01G143700 chr7B 111975436 111977856 2420 True 3225 3225 90.685 5 2437 1 chr7B.!!$R1 2432
7 TraesCS5A01G143700 chr7D 38611430 38613649 2219 False 3173 3173 92.488 220 2438 1 chr7D.!!$F1 2218
8 TraesCS5A01G143700 chr6B 286766363 286768793 2430 True 3160 3160 90.135 1 2437 1 chr6B.!!$R1 2436
9 TraesCS5A01G143700 chr3B 276453967 276456396 2429 True 3027 3027 89.144 1 2438 1 chr3B.!!$R1 2437

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
201 202 0.531532 CTGACCGCATCACTCATCCC 60.532 60.0 0.0 0.0 32.37 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 1841 0.320374 TGTGATTCGAGGTTTCCGCT 59.68 50.0 0.0 0.0 0.0 5.52 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
43 44 1.380302 GGCACCATTGACCTCCACT 59.620 57.895 0.00 0.00 0.00 4.00
101 102 4.467084 GGGCGCCTCCGACATTCA 62.467 66.667 28.56 0.00 46.86 2.57
103 104 2.125512 GCGCCTCCGACATTCACT 60.126 61.111 0.00 0.00 36.29 3.41
201 202 0.531532 CTGACCGCATCACTCATCCC 60.532 60.000 0.00 0.00 32.37 3.85
211 212 1.991813 TCACTCATCCCAACCAATCCA 59.008 47.619 0.00 0.00 0.00 3.41
226 227 3.434309 CAATCCACCTTCATTCAGGGTT 58.566 45.455 0.00 0.00 38.42 4.11
258 259 3.184628 TGATGGAGTCTTGGTCTTCCAT 58.815 45.455 4.64 4.64 43.91 3.41
344 345 1.066002 GGCATACGACACGGTTAGCTA 59.934 52.381 0.00 0.00 0.00 3.32
408 409 2.966732 TTGGGTCTGCCGGGTCATC 61.967 63.158 2.18 0.00 34.97 2.92
426 427 1.125093 TCCAGTTGGTGTCATCCGGT 61.125 55.000 0.00 0.00 36.34 5.28
459 460 3.452264 TGAACATCAATGGAGAGATCGGT 59.548 43.478 0.00 0.00 0.00 4.69
733 734 2.286365 TCTGTCGGGCCTCAAAATTT 57.714 45.000 0.84 0.00 0.00 1.82
783 789 1.413808 GGCTATTCCCCCTCTGAGAGT 60.414 57.143 8.88 0.00 0.00 3.24
848 855 3.321950 CCACTTCTTATCTGGGGATCCT 58.678 50.000 12.58 0.00 33.71 3.24
907 914 3.130264 TTGGTCCACAAGCTGCAAT 57.870 47.368 1.02 0.00 33.18 3.56
910 917 1.073763 TGGTCCACAAGCTGCAATACT 59.926 47.619 1.02 0.00 0.00 2.12
1057 1064 2.836154 TTGGCTCGGTCCAAGCTT 59.164 55.556 0.87 0.00 40.92 3.74
1175 1182 0.608035 TCCTCCAAACGCATGAACCC 60.608 55.000 0.00 0.00 0.00 4.11
1177 1184 0.953471 CTCCAAACGCATGAACCCGA 60.953 55.000 0.00 0.00 0.00 5.14
1332 1339 0.907486 CTGTCATTCAGCTCCTCCCA 59.093 55.000 0.00 0.00 37.36 4.37
1359 1366 1.224315 CATTGGGACCTCCATCGCA 59.776 57.895 0.00 0.00 46.52 5.10
1490 1498 1.068741 GTCGAGTCGGCCCTTATTGAT 59.931 52.381 13.54 0.00 0.00 2.57
1503 1511 4.444306 CCCTTATTGATTTAGGGCGTCTCA 60.444 45.833 0.00 0.00 42.04 3.27
1596 1604 1.280746 CCTGACTTGTTGCAGCACG 59.719 57.895 1.37 3.71 0.00 5.34
1597 1605 1.280746 CTGACTTGTTGCAGCACGG 59.719 57.895 11.61 6.58 0.00 4.94
1702 1710 0.099082 CCAAGCGTCCTCGACTCTAC 59.901 60.000 0.00 0.00 39.71 2.59
1716 1724 2.885266 GACTCTACATGGTCTATCCGCA 59.115 50.000 0.00 0.00 39.52 5.69
1787 1795 1.000019 CTCGGGTGTGGAGGTCCTA 60.000 63.158 0.00 0.00 36.82 2.94
1865 1875 3.599730 ATCACATCTTCTTCTCGTGCA 57.400 42.857 0.00 0.00 0.00 4.57
1947 1957 4.099266 CACTAACTTCCCTGATCTCCTCTG 59.901 50.000 0.00 0.00 0.00 3.35
1961 1971 0.610687 CCTCTGTGAGGTTCAGTCCC 59.389 60.000 5.50 0.00 44.25 4.46
2012 2022 0.895100 GTTGCTCATTGGGGTGCTCA 60.895 55.000 0.00 0.00 0.00 4.26
2034 2044 4.367023 GGCGCTGTGGACCGTACA 62.367 66.667 7.64 0.00 0.00 2.90
2058 2068 0.598065 AAGCTTGTCATTCAACGGGC 59.402 50.000 0.00 0.00 32.18 6.13
2198 2208 1.001641 ATGGCTCTCCGCTTTGCTT 60.002 52.632 0.00 0.00 39.13 3.91
2200 2210 1.672356 GGCTCTCCGCTTTGCTTCA 60.672 57.895 0.00 0.00 39.13 3.02
2212 2222 3.706373 GCTTCACCGCTCCCTCCA 61.706 66.667 0.00 0.00 0.00 3.86
2249 2259 3.804873 GGATTAGATCCTTCGTTGCTGTC 59.195 47.826 0.00 0.00 46.19 3.51
2256 2266 0.784778 CTTCGTTGCTGTCTCGAACC 59.215 55.000 0.00 0.00 38.38 3.62
2314 2328 1.072159 GTTGAGCTGTGCCCTCAGT 59.928 57.895 0.00 0.00 40.16 3.41
2318 2332 0.459489 GAGCTGTGCCCTCAGTAGAG 59.541 60.000 0.00 0.00 41.72 2.43
2322 2337 2.365635 TGCCCTCAGTAGAGCCCC 60.366 66.667 0.00 0.00 40.68 5.80
2332 2347 2.832129 CAGTAGAGCCCCTTGTACTTCA 59.168 50.000 0.00 0.00 0.00 3.02
2345 2360 5.763204 CCTTGTACTTCATGTTGTGGTACTT 59.237 40.000 0.00 0.00 35.29 2.24
2372 2393 1.021968 GTGTGTGTGGGTGAACCTTC 58.978 55.000 0.00 0.00 41.11 3.46
2441 2464 5.028375 CGAAAGCCTTTTTCGGTAATGATC 58.972 41.667 12.72 0.00 45.17 2.92
2442 2465 4.983671 AAGCCTTTTTCGGTAATGATCC 57.016 40.909 0.00 0.00 0.00 3.36
2443 2466 3.288092 AGCCTTTTTCGGTAATGATCCC 58.712 45.455 0.00 0.00 0.00 3.85
2444 2467 3.020984 GCCTTTTTCGGTAATGATCCCA 58.979 45.455 0.00 0.00 0.00 4.37
2445 2468 3.181490 GCCTTTTTCGGTAATGATCCCAC 60.181 47.826 0.00 0.00 0.00 4.61
2446 2469 4.270008 CCTTTTTCGGTAATGATCCCACT 58.730 43.478 0.00 0.00 0.00 4.00
2447 2470 5.433526 CCTTTTTCGGTAATGATCCCACTA 58.566 41.667 0.00 0.00 0.00 2.74
2448 2471 6.062095 CCTTTTTCGGTAATGATCCCACTAT 58.938 40.000 0.00 0.00 0.00 2.12
2449 2472 6.546034 CCTTTTTCGGTAATGATCCCACTATT 59.454 38.462 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.072600 AGGTAATGATCCCGTAATTAAGGCA 59.927 40.000 11.59 5.49 0.00 4.75
101 102 0.462789 CGTAATGGGGCGGAACTAGT 59.537 55.000 0.00 0.00 0.00 2.57
179 180 4.504132 GAGTGATGCGGTCAGTCC 57.496 61.111 13.15 0.34 46.98 3.85
181 182 0.176680 GGATGAGTGATGCGGTCAGT 59.823 55.000 0.00 0.00 43.21 3.41
201 202 3.194116 CCTGAATGAAGGTGGATTGGTTG 59.806 47.826 0.00 0.00 32.17 3.77
211 212 5.456763 GGATATAGCAACCCTGAATGAAGGT 60.457 44.000 0.00 0.00 35.34 3.50
408 409 0.673644 GACCGGATGACACCAACTGG 60.674 60.000 9.46 0.00 44.54 4.00
426 427 1.666553 GATGTTCACCGCGGTGTGA 60.667 57.895 46.56 35.66 45.55 3.58
459 460 2.719705 ACAAAAGGTGGGGAAGTATGGA 59.280 45.455 0.00 0.00 0.00 3.41
536 537 5.513788 GCTTTATCCAGGATAGATGCCAAGA 60.514 44.000 16.12 0.00 0.00 3.02
733 734 3.997762 TCACCTCGCTTTTAGCAAAGTA 58.002 40.909 0.00 0.00 42.58 2.24
797 803 2.357034 GCCGACAGTTCAAGCGGA 60.357 61.111 0.00 0.00 46.29 5.54
848 855 0.530744 AAGGCGCGAGTCACTAATGA 59.469 50.000 12.10 0.00 38.99 2.57
890 897 1.073763 AGTATTGCAGCTTGTGGACCA 59.926 47.619 0.00 0.00 0.00 4.02
910 917 3.057548 CTGCCACGGCTCAATGCA 61.058 61.111 9.92 0.00 45.15 3.96
929 936 1.267574 TGCCTTAGAGAGCCACCTGG 61.268 60.000 0.00 0.00 38.53 4.45
1057 1064 2.436109 GCCAGCCCAGAAGAACCA 59.564 61.111 0.00 0.00 0.00 3.67
1175 1182 2.752238 AGCGAGTGAGGAGGGTCG 60.752 66.667 0.00 0.00 35.51 4.79
1177 1184 2.681778 CCAGCGAGTGAGGAGGGT 60.682 66.667 0.00 0.00 0.00 4.34
1220 1227 1.000019 ATCTGCAGCCACAAGCCAT 60.000 52.632 9.47 0.00 45.47 4.40
1296 1303 0.954452 CAGACTGCCAAAACTGGGAC 59.046 55.000 0.00 0.00 0.00 4.46
1359 1366 2.594592 GCCGAACCAGTGCCAACT 60.595 61.111 0.00 0.00 36.98 3.16
1702 1710 0.957395 GGGCATGCGGATAGACCATG 60.957 60.000 12.44 0.36 39.38 3.66
1831 1841 0.320374 TGTGATTCGAGGTTTCCGCT 59.680 50.000 0.00 0.00 0.00 5.52
1865 1875 1.247567 CAAAGAAACTGGGCGGACAT 58.752 50.000 0.00 0.00 0.00 3.06
2034 2044 5.469479 CCCGTTGAATGACAAGCTTATTTT 58.531 37.500 0.00 0.00 39.30 1.82
2130 2140 1.301244 GCATCGCGATCCTGGTGAT 60.301 57.895 20.85 0.00 35.13 3.06
2198 2208 4.631740 TGGTGGAGGGAGCGGTGA 62.632 66.667 0.00 0.00 0.00 4.02
2269 2279 5.277250 CCCTGATAATAAACAAAGGGGGTT 58.723 41.667 0.00 0.00 40.66 4.11
2314 2328 3.450904 ACATGAAGTACAAGGGGCTCTA 58.549 45.455 0.00 0.00 0.00 2.43
2318 2332 2.228822 CACAACATGAAGTACAAGGGGC 59.771 50.000 0.00 0.00 0.00 5.80
2322 2337 6.861065 AAGTACCACAACATGAAGTACAAG 57.139 37.500 0.00 0.00 34.37 3.16
2332 2347 4.013728 ACACACACAAAGTACCACAACAT 58.986 39.130 0.00 0.00 0.00 2.71
2345 2360 0.250945 ACCCACACACACACACACAA 60.251 50.000 0.00 0.00 0.00 3.33
2372 2393 3.525537 CACCAGAGCCATACAGTACAAG 58.474 50.000 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.