Multiple sequence alignment - TraesCS4A01G173300

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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 TraesCS4A01G173300 chr4A 100.000 2933 0 0 1 2933 440870261 440867329 0.000000e+00 5417
1 TraesCS4A01G173300 chr4A 89.423 104 11 0 2734 2837 440867432 440867329 6.600000e-27 132
2 TraesCS4A01G173300 chr4A 89.423 104 11 0 2830 2933 440867528 440867425 6.600000e-27 132
3 TraesCS4A01G173300 chr4D 96.868 2682 71 5 255 2933 127565397 127568068 0.000000e+00 4475
4 TraesCS4A01G173300 chr4D 94.656 262 6 3 1 262 127559232 127559485 1.640000e-107 399
5 TraesCS4A01G173300 chr4D 89.423 104 11 0 2830 2933 127567869 127567972 6.600000e-27 132
6 TraesCS4A01G173300 chr4D 89.691 97 10 0 2732 2828 127567963 127568059 1.100000e-24 124
7 TraesCS4A01G173300 chr4B 96.548 2578 74 7 360 2933 191662451 191665017 0.000000e+00 4253
8 TraesCS4A01G173300 chr4B 87.463 335 16 11 1 309 191662113 191662447 2.150000e-96 363
9 TraesCS4A01G173300 chr4B 89.423 104 11 0 2830 2933 191664818 191664921 6.600000e-27 132
10 TraesCS4A01G173300 chr4B 89.691 97 10 0 2732 2828 191664912 191665008 1.100000e-24 124


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 TraesCS4A01G173300 chr4A 440867329 440870261 2932 True 1893.666667 5417 92.948667 1 2933 3 chr4A.!!$R1 2932
1 TraesCS4A01G173300 chr4D 127565397 127568068 2671 False 1577.000000 4475 91.994000 255 2933 3 chr4D.!!$F2 2678
2 TraesCS4A01G173300 chr4B 191662113 191665017 2904 False 1218.000000 4253 90.781250 1 2933 4 chr4B.!!$F1 2932

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
782 811 0.809385 CGTAAAGAGGCCTCACGAGA 59.191 55.0 33.9 11.83 34.66 4.04 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2343 2374 2.700371 ACGACCATAGAATCTCATGGCA 59.3 45.455 14.46 0.0 44.74 4.92 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
50 51 0.892358 ATGGGCCTTATCAGCATGCG 60.892 55.000 13.01 7.64 34.76 4.73
100 101 9.753674 AAGATTATATGTTCCCAAGAAAGTTCA 57.246 29.630 0.00 0.00 32.58 3.18
101 102 9.927081 AGATTATATGTTCCCAAGAAAGTTCAT 57.073 29.630 0.00 0.00 32.58 2.57
187 188 9.798994 CAAAGAAATTGATGCTAAAGCTTAGAT 57.201 29.630 0.00 0.00 41.85 1.98
238 266 9.492730 AGAAAATGGAACCCAGAATAATTATGT 57.507 29.630 0.00 0.00 36.75 2.29
282 310 2.229543 ACGTAACAATACCTGCTCGTCA 59.770 45.455 0.00 0.00 0.00 4.35
400 428 9.062524 AGCATACACTTATTCAACAAACAGTTA 57.937 29.630 0.00 0.00 38.74 2.24
401 429 9.840427 GCATACACTTATTCAACAAACAGTTAT 57.160 29.630 0.00 0.00 38.74 1.89
421 449 9.834628 CAGTTATGAAAATACACCACGTTTTAT 57.165 29.630 0.00 0.00 0.00 1.40
436 464 7.707035 ACCACGTTTTATTGTTTGCTTCATTTA 59.293 29.630 0.00 0.00 0.00 1.40
513 541 5.850557 TTCCATAAAATATGCCCACACAG 57.149 39.130 0.00 0.00 0.00 3.66
547 575 7.710676 AACCAAAACCTACATGCACATATTA 57.289 32.000 0.00 0.00 0.00 0.98
551 579 7.417612 CAAAACCTACATGCACATATTACTCC 58.582 38.462 0.00 0.00 0.00 3.85
622 650 2.069273 CTCACAGAGTAAACCGGCAAG 58.931 52.381 0.00 0.00 0.00 4.01
699 728 5.695851 AATTTGTAACACAGAGCAAGAGG 57.304 39.130 0.00 0.00 0.00 3.69
775 804 1.677552 CCACCACGTAAAGAGGCCT 59.322 57.895 3.86 3.86 33.55 5.19
782 811 0.809385 CGTAAAGAGGCCTCACGAGA 59.191 55.000 33.90 11.83 34.66 4.04
864 893 3.244249 ACAAAGTGGCTTCCTCTCACTAC 60.244 47.826 0.00 0.00 40.41 2.73
1091 1120 4.308458 CCGCCTGTTCGGTGACCA 62.308 66.667 1.11 0.00 46.58 4.02
1390 1419 3.775866 TCGATGGGGTAACAGGTTTGATA 59.224 43.478 0.00 0.00 39.74 2.15
1451 1482 4.211389 CAACAGATGAAACGCACTAACAC 58.789 43.478 0.00 0.00 0.00 3.32
1515 1546 1.472728 GGGCGTACGGACAATGAGATT 60.473 52.381 18.39 0.00 0.00 2.40
1565 1596 4.906747 AGAAAGCACAAGAGAGGAAGAT 57.093 40.909 0.00 0.00 0.00 2.40
1567 1598 5.976458 AGAAAGCACAAGAGAGGAAGATAG 58.024 41.667 0.00 0.00 0.00 2.08
1590 1621 2.398754 TGTCACCTTCTTCCTCCTCA 57.601 50.000 0.00 0.00 0.00 3.86
1749 1780 4.163427 TGGACCAGATATGGAAGGAGATC 58.837 47.826 14.70 0.00 0.00 2.75
2058 2089 1.543429 GCCGGAATTGCCAGTAGCTAT 60.543 52.381 5.05 0.00 44.23 2.97
2198 2229 3.010027 TGCCCTTCACAGAATGGAATACA 59.990 43.478 5.42 0.00 43.62 2.29
2206 2237 5.412594 TCACAGAATGGAATACAAGAGCAAC 59.587 40.000 0.00 0.00 43.62 4.17
2224 2255 6.370994 AGAGCAACTTATATGCATGATACAGC 59.629 38.462 10.16 5.59 46.22 4.40
2250 2281 7.919091 CAGTCAATCTCCAATGATATTTTGGTG 59.081 37.037 14.61 12.96 43.41 4.17
2284 2315 6.871492 AGATTGACACGAATGTACATTGTACA 59.129 34.615 27.00 27.00 39.95 2.90
2285 2316 5.832568 TGACACGAATGTACATTGTACAC 57.167 39.130 27.28 16.68 39.95 2.90
2287 2318 4.633175 ACACGAATGTACATTGTACACCA 58.367 39.130 27.28 9.49 37.26 4.17
2288 2319 5.242434 ACACGAATGTACATTGTACACCAT 58.758 37.500 27.28 18.00 37.26 3.55
2289 2320 5.703592 ACACGAATGTACATTGTACACCATT 59.296 36.000 27.28 19.21 37.26 3.16
2290 2321 6.020984 CACGAATGTACATTGTACACCATTG 58.979 40.000 27.28 21.23 0.00 2.82
2291 2322 5.027737 CGAATGTACATTGTACACCATTGC 58.972 41.667 27.28 12.54 0.00 3.56
2292 2323 5.391416 CGAATGTACATTGTACACCATTGCA 60.391 40.000 27.28 6.84 0.00 4.08
2293 2324 4.757799 TGTACATTGTACACCATTGCAC 57.242 40.909 22.58 0.00 0.00 4.57
2294 2325 4.393834 TGTACATTGTACACCATTGCACT 58.606 39.130 22.58 0.00 0.00 4.40
2295 2326 5.552178 TGTACATTGTACACCATTGCACTA 58.448 37.500 22.58 0.00 0.00 2.74
2296 2327 6.176896 TGTACATTGTACACCATTGCACTAT 58.823 36.000 22.58 0.00 0.00 2.12
2343 2374 6.428159 CACCTGATTCTAAAGCTACAAACAGT 59.572 38.462 0.00 0.00 0.00 3.55
2419 2450 6.942532 TGGGTACAGAATCAGCATTATTTC 57.057 37.500 0.00 0.00 0.00 2.17
2426 2458 8.976986 ACAGAATCAGCATTATTTCTTCAAAC 57.023 30.769 0.00 0.00 0.00 2.93
2443 2475 6.653320 TCTTCAAACCGTTCTTGCTATTACAT 59.347 34.615 0.00 0.00 0.00 2.29
2457 2489 9.118300 CTTGCTATTACATTCTCATTTCCTTCT 57.882 33.333 0.00 0.00 0.00 2.85
2500 2532 5.503927 AGCTCTTGATAAAATGGCTTCTGA 58.496 37.500 0.00 0.00 0.00 3.27
2546 2578 9.349713 AGAACAAGTATTTCTCCAATAAACACA 57.650 29.630 0.00 0.00 0.00 3.72
2556 2588 2.551287 CCAATAAACACACGGACCCTGA 60.551 50.000 0.00 0.00 0.00 3.86
2565 2597 4.020039 ACACACGGACCCTGAAAACATATA 60.020 41.667 0.00 0.00 0.00 0.86
2690 2723 7.425606 TCAATTCTCTTAAAAAGGTTGAGCAC 58.574 34.615 0.00 0.00 0.00 4.40
2711 2744 8.854614 AGCACTAGACTTTGATAGAACAAAAT 57.145 30.769 0.00 0.00 38.90 1.82
2754 2787 4.210120 CACATAAGATTAGCAGGAAGTCGC 59.790 45.833 0.00 0.00 0.00 5.19
2759 2792 3.133721 AGATTAGCAGGAAGTCGCAGATT 59.866 43.478 0.00 0.00 40.67 2.40
2761 2794 2.301577 AGCAGGAAGTCGCAGATTAC 57.698 50.000 0.00 0.00 40.67 1.89
2791 2824 8.685838 TTAACAAATAGGAAAGTTAGCACTGT 57.314 30.769 0.00 0.00 31.60 3.55
2795 2828 0.881796 GGAAAGTTAGCACTGTGGCC 59.118 55.000 10.21 0.00 31.60 5.36
2806 2839 3.023832 GCACTGTGGCCAGGTAAATAAT 58.976 45.455 5.11 0.00 43.36 1.28
2828 2861 2.240162 GAGGTGGTAAGGGACTGGCG 62.240 65.000 0.00 0.00 40.86 5.69
2857 2890 1.736681 GAGCAGGAAGTTGCAGATCAC 59.263 52.381 0.21 0.00 46.47 3.06
2887 2920 8.685838 TTAACAAATAGGAAAGTTAGCACTGT 57.314 30.769 0.00 0.00 31.60 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 102 0.878416 GCCGGTGCATGTTTCTTACA 59.122 50.000 1.90 0.00 41.97 2.41
386 414 9.522804 GGTGTATTTTCATAACTGTTTGTTGAA 57.477 29.630 0.00 4.02 39.55 2.69
400 428 9.535878 AAACAATAAAACGTGGTGTATTTTCAT 57.464 25.926 0.00 0.00 0.00 2.57
401 429 8.808529 CAAACAATAAAACGTGGTGTATTTTCA 58.191 29.630 0.00 0.00 0.00 2.69
402 430 7.790216 GCAAACAATAAAACGTGGTGTATTTTC 59.210 33.333 0.00 0.00 0.00 2.29
411 439 6.523676 AATGAAGCAAACAATAAAACGTGG 57.476 33.333 0.00 0.00 0.00 4.94
421 449 9.448294 GAAATGCAAAATAAATGAAGCAAACAA 57.552 25.926 0.00 0.00 35.45 2.83
422 450 8.618677 TGAAATGCAAAATAAATGAAGCAAACA 58.381 25.926 0.00 0.00 35.45 2.83
436 464 9.235537 GCAATTTTGTTAACTGAAATGCAAAAT 57.764 25.926 20.10 12.94 43.73 1.82
622 650 4.569943 TGGACTGCATCTAACTCTTGTTC 58.430 43.478 0.00 0.00 37.59 3.18
699 728 6.567050 TCAGATTAAAATTGCCTTCTCATGC 58.433 36.000 0.00 0.00 0.00 4.06
775 804 0.603569 GGACAAGAAGGCTCTCGTGA 59.396 55.000 15.24 0.00 0.00 4.35
782 811 1.589414 ATAGGCAGGACAAGAAGGCT 58.411 50.000 0.00 0.00 40.25 4.58
864 893 3.370953 CCTGATGGGAAGAAGGTTGGTAG 60.371 52.174 0.00 0.00 37.23 3.18
1091 1120 2.332654 GCAACGAAATCCCAGCGGT 61.333 57.895 0.00 0.00 0.00 5.68
1221 1250 7.168219 GGCCATAGATAAGGTGATGTATGAAA 58.832 38.462 0.00 0.00 35.89 2.69
1390 1419 6.017026 GCTGCTTTAGTAAGGTCTTCTTTTGT 60.017 38.462 0.00 0.00 36.93 2.83
1435 1466 2.038557 AGAGGGTGTTAGTGCGTTTCAT 59.961 45.455 0.00 0.00 0.00 2.57
1451 1482 5.263872 AGACCACCTATACATAGAGAGGG 57.736 47.826 0.00 0.00 33.02 4.30
1515 1546 4.476297 TGTGTGTCCTCCAGTAGTTCTTA 58.524 43.478 0.00 0.00 0.00 2.10
1565 1596 3.769844 GGAGGAAGAAGGTGACATGTCTA 59.230 47.826 25.55 10.28 0.00 2.59
1567 1598 2.569404 AGGAGGAAGAAGGTGACATGTC 59.431 50.000 19.27 19.27 0.00 3.06
1590 1621 6.435277 GGCAGGATTGGTATGTAAATGATGAT 59.565 38.462 0.00 0.00 0.00 2.45
1770 1801 6.394025 TTGCTGCATGCTTTATCATCAATA 57.606 33.333 20.33 0.00 43.37 1.90
2041 2072 4.734695 GCAAACATAGCTACTGGCAATTCC 60.735 45.833 0.00 0.00 44.79 3.01
2058 2089 4.018870 TCACCCTCCATACTAATGCAAACA 60.019 41.667 0.00 0.00 0.00 2.83
2198 2229 7.094890 GCTGTATCATGCATATAAGTTGCTCTT 60.095 37.037 0.00 0.00 40.77 2.85
2206 2237 7.662604 TTGACTGCTGTATCATGCATATAAG 57.337 36.000 0.00 0.00 38.59 1.73
2250 2281 9.262472 GTACATTCGTGTCAATCTAACATTTTC 57.738 33.333 0.00 0.00 0.00 2.29
2284 2315 9.905713 ATATTATAATTCCGATAGTGCAATGGT 57.094 29.630 2.68 0.00 0.00 3.55
2288 2319 9.817809 GGAGATATTATAATTCCGATAGTGCAA 57.182 33.333 2.68 0.00 0.00 4.08
2289 2320 8.421784 GGGAGATATTATAATTCCGATAGTGCA 58.578 37.037 2.68 0.00 0.00 4.57
2290 2321 7.873505 GGGGAGATATTATAATTCCGATAGTGC 59.126 40.741 2.68 0.00 0.00 4.40
2291 2322 8.368668 GGGGGAGATATTATAATTCCGATAGTG 58.631 40.741 2.68 0.00 0.00 2.74
2292 2323 8.493787 GGGGGAGATATTATAATTCCGATAGT 57.506 38.462 2.68 0.00 0.00 2.12
2343 2374 2.700371 ACGACCATAGAATCTCATGGCA 59.300 45.455 14.46 0.00 44.74 4.92
2419 2450 6.236017 TGTAATAGCAAGAACGGTTTGAAG 57.764 37.500 0.00 0.00 0.00 3.02
2426 2458 6.851222 ATGAGAATGTAATAGCAAGAACGG 57.149 37.500 0.00 0.00 0.00 4.44
2457 2489 5.809001 AGCTTTCAATCTCAACATCCTGTA 58.191 37.500 0.00 0.00 0.00 2.74
2500 2532 5.286267 TCTCTTTGACGTTCCTTAGGTTT 57.714 39.130 0.00 0.00 0.00 3.27
2546 2578 7.712204 AAAAATATATGTTTTCAGGGTCCGT 57.288 32.000 10.21 0.00 31.29 4.69
2576 2609 2.816087 CTGTACAGCAGCCTCAATTTGT 59.184 45.455 10.54 0.00 38.52 2.83
2683 2716 6.993079 TGTTCTATCAAAGTCTAGTGCTCAA 58.007 36.000 0.00 0.00 0.00 3.02
2711 2744 9.974980 TTATGTGTCGAATACAATCTAGCATTA 57.025 29.630 7.72 0.00 40.63 1.90
2791 2824 2.176798 CCTCCCATTATTTACCTGGCCA 59.823 50.000 4.71 4.71 0.00 5.36
2795 2828 4.519906 ACCACCTCCCATTATTTACCTG 57.480 45.455 0.00 0.00 0.00 4.00
2806 2839 0.546747 CAGTCCCTTACCACCTCCCA 60.547 60.000 0.00 0.00 0.00 4.37
2828 2861 3.243002 GCAACTTCCTGCTCATCTTATGC 60.243 47.826 0.00 0.00 39.34 3.14
2887 2920 6.449041 ACCACCTCCCTTTATTTACCTTATCA 59.551 38.462 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.