Multiple sequence alignment - TraesCS4B01G202200

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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 TraesCS4B01G202200 chr4B 100.000 2840 0 0 1 2840 432822542 432825381 0.000000e+00 5245.0
1 TraesCS4B01G202200 chr4D 88.945 2578 110 56 349 2808 349574985 349577505 0.000000e+00 3020.0
2 TraesCS4B01G202200 chr4D 96.032 252 4 4 101 352 349574583 349574828 3.410000e-109 405.0
3 TraesCS4B01G202200 chr4D 100.000 41 0 0 2800 2840 349577512 349577552 3.030000e-10 76.8
4 TraesCS4B01G202200 chr4A 88.420 1373 53 36 685 1987 115282859 115281523 0.000000e+00 1557.0
5 TraesCS4B01G202200 chr4A 88.909 559 39 11 101 654 115283399 115282859 0.000000e+00 667.0
6 TraesCS4B01G202200 chr4A 86.807 523 31 16 2349 2840 115281005 115280490 1.490000e-152 549.0
7 TraesCS4B01G202200 chr4A 83.424 368 35 15 1920 2275 115281361 115281008 4.570000e-83 318.0
8 TraesCS4B01G202200 chr3A 91.753 97 0 1 1 97 704599029 704599117 8.260000e-26 128.0
9 TraesCS4B01G202200 chr7A 91.489 94 0 1 1 94 58985877 58985792 3.840000e-24 122.0
10 TraesCS4B01G202200 chr7B 89.899 99 2 1 1 99 627618391 627618301 1.380000e-23 121.0
11 TraesCS4B01G202200 chr6B 89.899 99 2 1 1 99 18731511 18731421 1.380000e-23 121.0
12 TraesCS4B01G202200 chr5B 91.011 89 0 1 3 91 695500508 695500588 2.310000e-21 113.0


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 TraesCS4B01G202200 chr4B 432822542 432825381 2839 False 5245.000000 5245 100.000000 1 2840 1 chr4B.!!$F1 2839
1 TraesCS4B01G202200 chr4D 349574583 349577552 2969 False 1167.266667 3020 94.992333 101 2840 3 chr4D.!!$F1 2739
2 TraesCS4B01G202200 chr4A 115280490 115283399 2909 True 772.750000 1557 86.890000 101 2840 4 chr4A.!!$R1 2739

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 0.177141 TTTCCTAATCTCCGCCCGTG 59.823 55.000 0.0 0.0 0.00 4.94 F
62 63 2.280186 CCTAATCTCCGCCCGTGC 60.280 66.667 0.0 0.0 0.00 5.34 F
1512 1753 0.101759 CGGCATTTGGGCTGATCAAG 59.898 55.000 0.0 0.0 42.91 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1111 1325 0.455633 CGAAACTCGTACTCCCCGTG 60.456 60.0 0.00 0.0 34.72 4.94 R
1826 2070 0.833949 GGAGGACTAGGAAAGGGCAG 59.166 60.0 0.00 0.0 0.00 4.85 R
2614 3163 0.880278 TTGCGCACCTTCACTCACTC 60.880 55.0 11.12 0.0 0.00 3.51 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
19 20 2.269241 GGGGAGACGCCAAGAAGG 59.731 66.667 0.00 0.00 38.95 3.46
20 21 2.291043 GGGGAGACGCCAAGAAGGA 61.291 63.158 0.00 0.00 41.22 3.36
21 22 1.677552 GGGAGACGCCAAGAAGGAA 59.322 57.895 0.00 0.00 41.22 3.36
22 23 0.391793 GGGAGACGCCAAGAAGGAAG 60.392 60.000 0.00 0.00 41.22 3.46
23 24 1.021920 GGAGACGCCAAGAAGGAAGC 61.022 60.000 0.00 0.00 41.22 3.86
26 27 3.804193 CGCCAAGAAGGAAGCGCC 61.804 66.667 2.29 0.00 42.31 6.53
27 28 3.804193 GCCAAGAAGGAAGCGCCG 61.804 66.667 2.29 0.00 43.43 6.46
28 29 3.127533 CCAAGAAGGAAGCGCCGG 61.128 66.667 2.29 0.00 43.43 6.13
29 30 3.804193 CAAGAAGGAAGCGCCGGC 61.804 66.667 19.07 19.07 43.43 6.13
42 43 3.912907 CCGGCGGCGGAGATTAGT 61.913 66.667 44.11 0.00 0.00 2.24
43 44 2.106332 CGGCGGCGGAGATTAGTT 59.894 61.111 25.36 0.00 0.00 2.24
44 45 1.520787 CGGCGGCGGAGATTAGTTT 60.521 57.895 25.36 0.00 0.00 2.66
45 46 1.488261 CGGCGGCGGAGATTAGTTTC 61.488 60.000 25.36 0.00 0.00 2.78
46 47 1.158484 GGCGGCGGAGATTAGTTTCC 61.158 60.000 9.78 0.00 0.00 3.13
47 48 0.179081 GCGGCGGAGATTAGTTTCCT 60.179 55.000 9.78 0.00 0.00 3.36
48 49 1.068127 GCGGCGGAGATTAGTTTCCTA 59.932 52.381 9.78 0.00 0.00 2.94
49 50 2.482490 GCGGCGGAGATTAGTTTCCTAA 60.482 50.000 9.78 0.00 37.56 2.69
50 51 3.802675 GCGGCGGAGATTAGTTTCCTAAT 60.803 47.826 9.78 0.00 44.70 1.73
58 59 3.832615 TTAGTTTCCTAATCTCCGCCC 57.167 47.619 0.00 0.00 0.00 6.13
59 60 0.464452 AGTTTCCTAATCTCCGCCCG 59.536 55.000 0.00 0.00 0.00 6.13
60 61 0.177373 GTTTCCTAATCTCCGCCCGT 59.823 55.000 0.00 0.00 0.00 5.28
61 62 0.177141 TTTCCTAATCTCCGCCCGTG 59.823 55.000 0.00 0.00 0.00 4.94
62 63 2.280186 CCTAATCTCCGCCCGTGC 60.280 66.667 0.00 0.00 0.00 5.34
63 64 2.280186 CTAATCTCCGCCCGTGCC 60.280 66.667 0.00 0.00 0.00 5.01
64 65 4.215742 TAATCTCCGCCCGTGCCG 62.216 66.667 0.00 0.00 0.00 5.69
407 570 2.626840 GGCTTCATCCTGAGTTGAGTC 58.373 52.381 0.00 0.00 0.00 3.36
452 615 4.202326 GGCCAAGGCACTAGTAGCTTTATA 60.202 45.833 13.87 0.00 38.49 0.98
454 617 4.982916 CCAAGGCACTAGTAGCTTTATACG 59.017 45.833 14.28 4.68 38.49 3.06
583 763 6.055588 TCTAGTTACTGTTTGCTTTGCTCTT 58.944 36.000 0.00 0.00 0.00 2.85
660 844 8.988934 CAAGTGTACTACAACTTCAATACACAT 58.011 33.333 13.17 0.68 43.03 3.21
675 859 6.754675 TCAATACACATCCACATAACAGTACG 59.245 38.462 0.00 0.00 0.00 3.67
713 897 4.035792 ACGAACGAAGGTCATCTGATCTAG 59.964 45.833 0.14 0.00 33.65 2.43
716 900 6.380095 AACGAAGGTCATCTGATCTAGTAC 57.620 41.667 0.00 0.00 33.65 2.73
717 901 5.686753 ACGAAGGTCATCTGATCTAGTACT 58.313 41.667 0.00 0.00 33.65 2.73
724 908 5.646360 GTCATCTGATCTAGTACTAGGAGGC 59.354 48.000 26.06 14.77 34.06 4.70
800 986 2.775911 TCAATCAGCCTCCAAGACAG 57.224 50.000 0.00 0.00 0.00 3.51
1111 1325 1.743321 CGACCTGGATCTCAGCTCCC 61.743 65.000 0.00 0.00 42.05 4.30
1112 1326 0.689080 GACCTGGATCTCAGCTCCCA 60.689 60.000 0.00 0.00 42.05 4.37
1128 1342 1.969862 CCACGGGGAGTACGAGTTT 59.030 57.895 0.00 0.00 35.59 2.66
1206 1426 3.368571 GCCAGGCAGCACAAGGTC 61.369 66.667 6.55 0.00 0.00 3.85
1236 1456 2.363406 GGGGGCAAGCTGCTTGAT 60.363 61.111 38.49 6.54 43.42 2.57
1479 1720 2.047274 CATGACAAGGGCGTCGGT 60.047 61.111 0.00 0.00 38.84 4.69
1505 1746 2.361610 CAGGTCGGCATTTGGGCT 60.362 61.111 0.00 0.00 40.61 5.19
1506 1747 2.361610 AGGTCGGCATTTGGGCTG 60.362 61.111 0.00 0.00 41.61 4.85
1512 1753 0.101759 CGGCATTTGGGCTGATCAAG 59.898 55.000 0.00 0.00 42.91 3.02
1515 1756 2.417787 GGCATTTGGGCTGATCAAGAAC 60.418 50.000 0.00 0.00 39.42 3.01
1593 1837 1.413445 CTGATGGAAGAGGAGGAGCAG 59.587 57.143 0.00 0.00 0.00 4.24
1826 2070 4.168291 CGCCCTCTGCTCCTTCCC 62.168 72.222 0.00 0.00 38.05 3.97
1832 2076 3.013932 CTGCTCCTTCCCTGCCCT 61.014 66.667 0.00 0.00 0.00 5.19
1995 2484 4.191662 TCTGTTTCTTTTTCTTCGCGTC 57.808 40.909 5.77 0.00 0.00 5.19
1996 2485 2.958347 CTGTTTCTTTTTCTTCGCGTCG 59.042 45.455 5.77 0.00 0.00 5.12
2013 2504 1.733912 GTCGGTCCGTCCCAAAATAAC 59.266 52.381 11.88 0.00 0.00 1.89
2018 2509 2.745821 GTCCGTCCCAAAATAACTGTCC 59.254 50.000 0.00 0.00 0.00 4.02
2022 2513 3.761752 CGTCCCAAAATAACTGTCCCAAT 59.238 43.478 0.00 0.00 0.00 3.16
2026 2517 6.426633 GTCCCAAAATAACTGTCCCAATTTTG 59.573 38.462 15.92 15.92 43.77 2.44
2030 2521 8.147704 CCAAAATAACTGTCCCAATTTTGTACT 58.852 33.333 18.61 0.00 43.14 2.73
2033 2524 7.933215 ATAACTGTCCCAATTTTGTACTACC 57.067 36.000 0.00 0.00 0.00 3.18
2034 2525 5.578157 ACTGTCCCAATTTTGTACTACCT 57.422 39.130 0.00 0.00 0.00 3.08
2401 2944 0.249699 CGCCAAAACAAAACCTCCCC 60.250 55.000 0.00 0.00 0.00 4.81
2517 3066 1.619669 ATCGGGGGAGGGAAAAGCT 60.620 57.895 0.00 0.00 0.00 3.74
2542 3091 4.044484 CGATAGGCCGGCGAGAGG 62.044 72.222 22.54 5.62 0.00 3.69
2554 3103 4.179599 GAGAGGGGAGGGGAGGGG 62.180 77.778 0.00 0.00 0.00 4.79
2555 3104 4.761304 AGAGGGGAGGGGAGGGGA 62.761 72.222 0.00 0.00 0.00 4.81
2556 3105 4.179599 GAGGGGAGGGGAGGGGAG 62.180 77.778 0.00 0.00 0.00 4.30
2761 3356 1.853963 CAGGCAGTACCACTCCTACT 58.146 55.000 0.00 0.00 43.14 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.203938 TTCTTGGCGTCTCCCCCT 60.204 61.111 0.00 0.00 0.00 4.79
1 2 2.269241 CTTCTTGGCGTCTCCCCC 59.731 66.667 0.00 0.00 0.00 5.40
2 3 1.838073 TTCCTTCTTGGCGTCTCCCC 61.838 60.000 0.00 0.00 35.26 4.81
3 4 0.391793 CTTCCTTCTTGGCGTCTCCC 60.392 60.000 0.00 0.00 35.26 4.30
4 5 1.021920 GCTTCCTTCTTGGCGTCTCC 61.022 60.000 0.00 0.00 35.26 3.71
5 6 1.355066 CGCTTCCTTCTTGGCGTCTC 61.355 60.000 0.00 0.00 42.23 3.36
6 7 1.374758 CGCTTCCTTCTTGGCGTCT 60.375 57.895 0.00 0.00 42.23 4.18
7 8 3.169198 CGCTTCCTTCTTGGCGTC 58.831 61.111 0.00 0.00 42.23 5.19
10 11 3.804193 CGGCGCTTCCTTCTTGGC 61.804 66.667 7.64 0.00 35.26 4.52
11 12 3.127533 CCGGCGCTTCCTTCTTGG 61.128 66.667 7.64 0.00 37.10 3.61
12 13 3.804193 GCCGGCGCTTCCTTCTTG 61.804 66.667 12.58 0.00 0.00 3.02
26 27 1.488261 GAAACTAATCTCCGCCGCCG 61.488 60.000 0.00 0.00 0.00 6.46
27 28 1.158484 GGAAACTAATCTCCGCCGCC 61.158 60.000 0.00 0.00 0.00 6.13
28 29 0.179081 AGGAAACTAATCTCCGCCGC 60.179 55.000 0.00 0.00 40.61 6.53
39 40 1.684983 CGGGCGGAGATTAGGAAACTA 59.315 52.381 0.00 0.00 43.67 2.24
41 42 0.177373 ACGGGCGGAGATTAGGAAAC 59.823 55.000 0.00 0.00 0.00 2.78
42 43 0.177141 CACGGGCGGAGATTAGGAAA 59.823 55.000 0.00 0.00 0.00 3.13
43 44 1.820581 CACGGGCGGAGATTAGGAA 59.179 57.895 0.00 0.00 0.00 3.36
44 45 2.792947 GCACGGGCGGAGATTAGGA 61.793 63.158 0.00 0.00 0.00 2.94
45 46 2.280186 GCACGGGCGGAGATTAGG 60.280 66.667 0.00 0.00 0.00 2.69
46 47 2.280186 GGCACGGGCGGAGATTAG 60.280 66.667 2.17 0.00 42.47 1.73
99 100 1.363246 AAAGAGGGGGAGGTTGACTC 58.637 55.000 0.00 0.00 45.84 3.36
257 258 1.944032 AAGCAAAAGCAGCACCTTTG 58.056 45.000 9.27 9.27 35.36 2.77
263 264 2.270047 GTTGACAAAGCAAAAGCAGCA 58.730 42.857 0.00 0.00 0.00 4.41
441 604 7.262772 TCAAAGTATGCACGTATAAAGCTACT 58.737 34.615 0.00 0.00 0.00 2.57
452 615 3.610040 TCTGGATCAAAGTATGCACGT 57.390 42.857 0.00 0.00 0.00 4.49
454 617 4.095483 CAGGTTCTGGATCAAAGTATGCAC 59.905 45.833 0.00 0.00 0.00 4.57
555 735 6.073003 AGCAAAGCAAACAGTAACTAGATGTC 60.073 38.462 0.00 0.00 0.00 3.06
583 763 4.377021 AGAGTACAATTCACGCTTCACAA 58.623 39.130 0.00 0.00 0.00 3.33
660 844 1.619332 TGTGCCGTACTGTTATGTGGA 59.381 47.619 0.00 0.00 0.00 4.02
675 859 2.091588 CGTTCGTAGTTGTATGTGTGCC 59.908 50.000 0.00 0.00 0.00 5.01
713 897 0.470268 CCCTCCCTGCCTCCTAGTAC 60.470 65.000 0.00 0.00 0.00 2.73
716 900 1.152355 CTCCCTCCCTGCCTCCTAG 60.152 68.421 0.00 0.00 0.00 3.02
717 901 1.625879 TCTCCCTCCCTGCCTCCTA 60.626 63.158 0.00 0.00 0.00 2.94
724 908 0.040351 TCACTCACTCTCCCTCCCTG 59.960 60.000 0.00 0.00 0.00 4.45
873 1069 7.258022 AGTTTGAACAAAAATTATGGGCAAC 57.742 32.000 1.47 0.00 31.33 4.17
1111 1325 0.455633 CGAAACTCGTACTCCCCGTG 60.456 60.000 0.00 0.00 34.72 4.94
1112 1326 1.589716 CCGAAACTCGTACTCCCCGT 61.590 60.000 0.00 0.00 38.40 5.28
1287 1507 4.487412 GAGTGCTGCAATGGCGCC 62.487 66.667 22.73 22.73 45.35 6.53
1396 1616 4.011517 GGCGAACAGGGACCGGAA 62.012 66.667 9.46 0.00 0.00 4.30
1460 1695 3.499737 CGACGCCCTTGTCATGCC 61.500 66.667 0.00 0.00 38.84 4.40
1490 1731 1.728490 GATCAGCCCAAATGCCGACC 61.728 60.000 0.00 0.00 0.00 4.79
1505 1746 3.838120 CTGACGTAGCTGTTCTTGATCA 58.162 45.455 0.00 0.00 0.00 2.92
1593 1837 3.723348 GACTTGCGTTGCCGGACC 61.723 66.667 5.05 0.00 32.65 4.46
1660 1904 3.382832 CCCGCACGAGTTCCTCCT 61.383 66.667 0.00 0.00 0.00 3.69
1826 2070 0.833949 GGAGGACTAGGAAAGGGCAG 59.166 60.000 0.00 0.00 0.00 4.85
1832 2076 3.627747 GCTACAGGAGGAGGACTAGGAAA 60.628 52.174 0.00 0.00 0.00 3.13
1995 2484 1.735571 CAGTTATTTTGGGACGGACCG 59.264 52.381 13.61 13.61 40.11 4.79
1996 2485 2.745821 GACAGTTATTTTGGGACGGACC 59.254 50.000 0.00 0.00 38.08 4.46
2013 2504 5.556915 TGAGGTAGTACAAAATTGGGACAG 58.443 41.667 2.06 0.00 42.39 3.51
2030 2521 4.022589 CCGTCTCAACTTTGTACTGAGGTA 60.023 45.833 8.68 0.00 37.71 3.08
2032 2523 3.318017 CCGTCTCAACTTTGTACTGAGG 58.682 50.000 8.68 0.00 37.71 3.86
2033 2524 3.005472 TCCCGTCTCAACTTTGTACTGAG 59.995 47.826 3.30 3.30 38.34 3.35
2034 2525 2.960384 TCCCGTCTCAACTTTGTACTGA 59.040 45.455 0.00 0.00 0.00 3.41
2245 2788 1.534476 TGTTGGTGGGGAGCGACTA 60.534 57.895 0.00 0.00 0.00 2.59
2253 2796 4.904590 TTGCCGGTGTTGGTGGGG 62.905 66.667 1.90 0.00 0.00 4.96
2295 2838 4.035208 TGTTGCCGTTTCTTTTTCTCTCTC 59.965 41.667 0.00 0.00 0.00 3.20
2296 2839 3.945285 TGTTGCCGTTTCTTTTTCTCTCT 59.055 39.130 0.00 0.00 0.00 3.10
2297 2840 4.035684 GTGTTGCCGTTTCTTTTTCTCTC 58.964 43.478 0.00 0.00 0.00 3.20
2298 2841 3.486875 CGTGTTGCCGTTTCTTTTTCTCT 60.487 43.478 0.00 0.00 0.00 3.10
2299 2842 2.781646 CGTGTTGCCGTTTCTTTTTCTC 59.218 45.455 0.00 0.00 0.00 2.87
2300 2843 2.420722 TCGTGTTGCCGTTTCTTTTTCT 59.579 40.909 0.00 0.00 0.00 2.52
2301 2844 2.781646 CTCGTGTTGCCGTTTCTTTTTC 59.218 45.455 0.00 0.00 0.00 2.29
2302 2845 2.792749 CTCGTGTTGCCGTTTCTTTTT 58.207 42.857 0.00 0.00 0.00 1.94
2303 2846 1.533129 GCTCGTGTTGCCGTTTCTTTT 60.533 47.619 0.00 0.00 0.00 2.27
2304 2847 0.028902 GCTCGTGTTGCCGTTTCTTT 59.971 50.000 0.00 0.00 0.00 2.52
2305 2848 0.814010 AGCTCGTGTTGCCGTTTCTT 60.814 50.000 0.00 0.00 0.00 2.52
2306 2849 1.227556 AGCTCGTGTTGCCGTTTCT 60.228 52.632 0.00 0.00 0.00 2.52
2307 2850 1.082756 CAGCTCGTGTTGCCGTTTC 60.083 57.895 0.00 0.00 0.00 2.78
2308 2851 0.531090 TACAGCTCGTGTTGCCGTTT 60.531 50.000 0.97 0.00 40.94 3.60
2309 2852 0.320421 ATACAGCTCGTGTTGCCGTT 60.320 50.000 0.97 0.00 40.94 4.44
2310 2853 0.320421 AATACAGCTCGTGTTGCCGT 60.320 50.000 0.97 0.00 40.94 5.68
2421 2964 4.222886 GAGATACTCCAACACATCGATCG 58.777 47.826 9.36 9.36 0.00 3.69
2504 3053 1.636769 ATCCCGAGCTTTTCCCTCCC 61.637 60.000 0.00 0.00 0.00 4.30
2607 3156 1.803519 CTTCACTCACTCGCCTCGC 60.804 63.158 0.00 0.00 0.00 5.03
2612 3161 2.375766 CGCACCTTCACTCACTCGC 61.376 63.158 0.00 0.00 0.00 5.03
2613 3162 2.375766 GCGCACCTTCACTCACTCG 61.376 63.158 0.30 0.00 0.00 4.18
2614 3163 0.880278 TTGCGCACCTTCACTCACTC 60.880 55.000 11.12 0.00 0.00 3.51
2615 3164 1.146041 TTGCGCACCTTCACTCACT 59.854 52.632 11.12 0.00 0.00 3.41
2664 3251 2.021584 GAGTCGTGTCATGTGCGCA 61.022 57.895 5.66 5.66 0.00 6.09
2761 3356 3.603532 CAAGAATGAAGACCAGCAGCTA 58.396 45.455 0.00 0.00 0.00 3.32


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

AutoCloner maintained by Alex Coulton.