Multiple sequence alignment - TraesCS4B01G103900

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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 TraesCS4B01G103900 chr4B 100.000 3173 0 0 1 3173 109927692 109924520 0.000000e+00 5860
1 TraesCS4B01G103900 chr4D 95.558 1846 68 6 939 2779 78432062 78430226 0.000000e+00 2942
2 TraesCS4B01G103900 chr4D 96.069 407 14 2 2768 3173 78430210 78429805 0.000000e+00 662
3 TraesCS4B01G103900 chr4D 96.000 75 3 0 867 941 78432175 78432101 4.300000e-24 122
4 TraesCS4B01G103900 chr5B 91.106 877 69 9 1 871 243349520 243350393 0.000000e+00 1179
5 TraesCS4B01G103900 chr3B 90.205 878 75 7 1 870 810605956 810605082 0.000000e+00 1134
6 TraesCS4B01G103900 chr3B 89.875 879 79 6 1 871 243136646 243137522 0.000000e+00 1122
7 TraesCS4B01G103900 chr6B 89.966 877 80 4 1 871 223278563 223277689 0.000000e+00 1125
8 TraesCS4B01G103900 chr6B 89.647 879 80 9 1 871 564662256 564663131 0.000000e+00 1109
9 TraesCS4B01G103900 chr1B 89.852 877 81 4 1 871 251743734 251742860 0.000000e+00 1120
10 TraesCS4B01G103900 chr1B 89.510 877 84 4 1 871 408596895 408596021 0.000000e+00 1103
11 TraesCS4B01G103900 chr7B 89.612 876 82 5 2 871 668800871 668799999 0.000000e+00 1105
12 TraesCS4B01G103900 chr2B 89.510 877 84 4 1 871 22702579 22703453 0.000000e+00 1103


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 TraesCS4B01G103900 chr4B 109924520 109927692 3172 True 5860 5860 100.000000 1 3173 1 chr4B.!!$R1 3172
1 TraesCS4B01G103900 chr4D 78429805 78432175 2370 True 1242 2942 95.875667 867 3173 3 chr4D.!!$R1 2306
2 TraesCS4B01G103900 chr5B 243349520 243350393 873 False 1179 1179 91.106000 1 871 1 chr5B.!!$F1 870
3 TraesCS4B01G103900 chr3B 810605082 810605956 874 True 1134 1134 90.205000 1 870 1 chr3B.!!$R1 869
4 TraesCS4B01G103900 chr3B 243136646 243137522 876 False 1122 1122 89.875000 1 871 1 chr3B.!!$F1 870
5 TraesCS4B01G103900 chr6B 223277689 223278563 874 True 1125 1125 89.966000 1 871 1 chr6B.!!$R1 870
6 TraesCS4B01G103900 chr6B 564662256 564663131 875 False 1109 1109 89.647000 1 871 1 chr6B.!!$F1 870
7 TraesCS4B01G103900 chr1B 251742860 251743734 874 True 1120 1120 89.852000 1 871 1 chr1B.!!$R1 870
8 TraesCS4B01G103900 chr1B 408596021 408596895 874 True 1103 1103 89.510000 1 871 1 chr1B.!!$R2 870
9 TraesCS4B01G103900 chr7B 668799999 668800871 872 True 1105 1105 89.612000 2 871 1 chr7B.!!$R1 869
10 TraesCS4B01G103900 chr2B 22702579 22703453 874 False 1103 1103 89.510000 1 871 1 chr2B.!!$F1 870

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
223 230 1.079819 CGGAGATGCAACGAGGTGT 60.080 57.895 0.00 0.00 0.00 4.16 F
1542 1593 0.176680 CCACCGATCTGGAGAAGGTG 59.823 60.000 19.76 19.76 46.76 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2086 2137 0.179018 ACAAGCCCAGGAACAGTGTC 60.179 55.0 0.0 0.0 0.0 3.67 R
2595 2647 0.695924 TCCCTCCGCTCCATTTGAAA 59.304 50.0 0.0 0.0 0.0 2.69 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
23 24 6.124088 CTGTTCTGGATGTTTAATAGGCAC 57.876 41.667 0.00 0.00 0.00 5.01
117 124 7.094377 TGCCTATTTTAGAGTTTCGCAGAAAAT 60.094 33.333 5.51 4.84 45.90 1.82
120 127 9.483062 CTATTTTAGAGTTTCGCAGAAAATGAG 57.517 33.333 8.31 0.00 45.90 2.90
123 130 8.547967 TTTAGAGTTTCGCAGAAAATGAGTAT 57.452 30.769 8.31 0.00 45.90 2.12
221 228 1.215647 GTCGGAGATGCAACGAGGT 59.784 57.895 6.44 0.00 40.67 3.85
223 230 1.079819 CGGAGATGCAACGAGGTGT 60.080 57.895 0.00 0.00 0.00 4.16
274 282 3.597728 GGGCTCCTCGTAGCTCCG 61.598 72.222 0.00 0.00 42.37 4.63
299 307 6.174720 TGACCTAGTTCCTTTGCCTATATG 57.825 41.667 0.00 0.00 0.00 1.78
377 385 2.005370 ACCTTCTGTACCCGTGAGAA 57.995 50.000 0.00 0.00 0.00 2.87
448 456 2.237392 GGAGGGCTTCTACATCAACACT 59.763 50.000 0.00 0.00 0.00 3.55
534 542 3.692257 TGGCTTCTTCTCTCTCTTTGG 57.308 47.619 0.00 0.00 0.00 3.28
597 605 9.471084 TCTATTCGATGTAATATTCTTTTGCGA 57.529 29.630 0.00 0.00 0.00 5.10
613 621 1.286501 GCGATGTGTTTGCCGAGATA 58.713 50.000 0.00 0.00 0.00 1.98
706 715 7.324935 TGCATGATTTGATATCTTTGCAAGTT 58.675 30.769 3.98 0.00 36.08 2.66
708 717 9.304731 GCATGATTTGATATCTTTGCAAGTTTA 57.695 29.630 3.98 0.00 32.28 2.01
787 796 7.955918 AGAAGTGTTTAGCTTTGGATTCAATT 58.044 30.769 0.00 0.00 32.28 2.32
825 835 2.009681 TGACAGTAGGGACAGCAAGA 57.990 50.000 0.00 0.00 0.00 3.02
847 857 7.060600 AGACACGTATTGTATTGTTGTCATG 57.939 36.000 0.00 0.00 39.17 3.07
861 871 6.817765 TGTTGTCATGGAGGATAAAAAGAC 57.182 37.500 0.00 0.00 0.00 3.01
864 874 4.224147 TGTCATGGAGGATAAAAAGACGGA 59.776 41.667 0.00 0.00 0.00 4.69
965 1016 4.335647 AGTCCGCCAGCCAACCAG 62.336 66.667 0.00 0.00 0.00 4.00
1106 1157 3.591835 CCTCGCTCTCTCCGCCTC 61.592 72.222 0.00 0.00 0.00 4.70
1107 1158 3.591835 CTCGCTCTCTCCGCCTCC 61.592 72.222 0.00 0.00 0.00 4.30
1204 1255 1.003233 AAGGCGTCCAAGAAGCTCC 60.003 57.895 2.68 0.00 37.23 4.70
1337 1388 2.357034 CAGGGTGGACAACGTCGG 60.357 66.667 0.00 0.00 32.65 4.79
1470 1521 2.159028 CGAGTTCTGGATCCCCTTCTTC 60.159 54.545 9.90 0.00 0.00 2.87
1479 1530 1.222113 CCCCTTCTTCGGCTCCTTC 59.778 63.158 0.00 0.00 0.00 3.46
1480 1531 1.553690 CCCCTTCTTCGGCTCCTTCA 61.554 60.000 0.00 0.00 0.00 3.02
1542 1593 0.176680 CCACCGATCTGGAGAAGGTG 59.823 60.000 19.76 19.76 46.76 4.00
1721 1772 1.578583 ATATTCAAGTACGCGGTGGC 58.421 50.000 12.47 0.00 0.00 5.01
1758 1809 3.479269 GAAGACAAGGTCGCCGCG 61.479 66.667 6.39 6.39 37.67 6.46
1848 1899 3.324846 AGCCGCACATTCTAGGAATATCA 59.675 43.478 0.00 0.00 0.00 2.15
1854 1905 6.350864 CGCACATTCTAGGAATATCAGAGGAT 60.351 42.308 0.00 0.00 37.55 3.24
1885 1936 5.163612 CGTCTCAAGATAGAGTTCATGGTCA 60.164 44.000 0.00 0.00 36.97 4.02
1902 1953 2.296190 GGTCAATGAGGTTGGTTTGGAC 59.704 50.000 0.00 0.00 38.39 4.02
1908 1959 0.478507 AGGTTGGTTTGGACCCAGAG 59.521 55.000 0.00 0.00 45.92 3.35
1917 1968 3.695830 TTGGACCCAGAGTACATTGTC 57.304 47.619 0.00 0.00 39.79 3.18
1918 1969 2.615391 TGGACCCAGAGTACATTGTCA 58.385 47.619 0.00 0.00 32.87 3.58
1923 1974 4.160329 ACCCAGAGTACATTGTCAAGAGA 58.840 43.478 0.00 0.00 0.00 3.10
2055 2106 4.423625 AGTTGGCTATGGTGAGGATAAC 57.576 45.455 0.00 0.00 0.00 1.89
2062 2113 5.471456 GGCTATGGTGAGGATAACTTCATTG 59.529 44.000 0.00 0.00 34.79 2.82
2083 2134 5.004922 TGCAACATACATCGACAGTCATA 57.995 39.130 0.41 0.00 0.00 2.15
2086 2137 5.050769 GCAACATACATCGACAGTCATAAGG 60.051 44.000 0.41 0.00 0.00 2.69
2105 2156 0.179018 GACACTGTTCCTGGGCTTGT 60.179 55.000 0.00 0.00 0.00 3.16
2107 2158 1.072331 ACACTGTTCCTGGGCTTGTAG 59.928 52.381 0.00 0.00 0.00 2.74
2142 2193 2.249413 CTCGTGCTGGGGAGATGCTT 62.249 60.000 0.00 0.00 31.90 3.91
2200 2251 9.979578 GGTTCATCATATATCTTAGGCTCATAG 57.020 37.037 0.00 0.00 0.00 2.23
2217 2268 6.488086 GCTCATAGCTAGCATGGAACATTGT 61.488 44.000 18.83 0.00 40.38 2.71
2339 2390 3.320256 TCTGATTGCTCGTGATGCTATCT 59.680 43.478 10.31 0.00 41.07 1.98
2373 2424 5.342433 TGTGAATTTCTGTGAAGCAACTTG 58.658 37.500 0.00 0.00 0.00 3.16
2443 2494 7.535258 CCTGTAATTGAGAAAGTGATGTTTTCG 59.465 37.037 0.00 0.00 39.07 3.46
2478 2529 2.911484 CTCCCTTGTGCCTTAGACATC 58.089 52.381 0.00 0.00 0.00 3.06
2518 2569 5.694458 GGTTTCAACTGACTTTTGTGTTTGT 59.306 36.000 0.00 0.00 0.00 2.83
2568 2620 8.523523 TCTGTTGCATAGTCAAATCATTTTTG 57.476 30.769 0.00 0.00 0.00 2.44
2595 2647 9.445786 GCTAAATATGCACGTTTGTTATTGTAT 57.554 29.630 8.07 0.00 0.00 2.29
2605 2657 9.186323 CACGTTTGTTATTGTATTTCAAATGGA 57.814 29.630 0.00 0.00 39.62 3.41
2606 2658 9.405587 ACGTTTGTTATTGTATTTCAAATGGAG 57.594 29.630 0.00 0.00 39.62 3.86
2614 2666 0.695924 TTTCAAATGGAGCGGAGGGA 59.304 50.000 0.00 0.00 0.00 4.20
2618 2670 1.417890 CAAATGGAGCGGAGGGAGTAT 59.582 52.381 0.00 0.00 0.00 2.12
2666 2718 6.089249 ACAAATTCACCTGAGAAATGGAAC 57.911 37.500 0.00 0.00 0.00 3.62
2675 2727 4.219070 CCTGAGAAATGGAACTTTGCATCA 59.781 41.667 0.00 0.00 38.33 3.07
2680 2732 6.585416 AGAAATGGAACTTTGCATCAAAACT 58.415 32.000 0.00 0.00 38.33 2.66
2681 2733 6.703165 AGAAATGGAACTTTGCATCAAAACTC 59.297 34.615 0.00 0.00 38.33 3.01
2682 2734 4.998671 TGGAACTTTGCATCAAAACTCA 57.001 36.364 0.00 0.00 32.75 3.41
2683 2735 5.534207 TGGAACTTTGCATCAAAACTCAT 57.466 34.783 0.00 0.00 32.75 2.90
2684 2736 5.291178 TGGAACTTTGCATCAAAACTCATG 58.709 37.500 0.00 0.00 32.75 3.07
2685 2737 5.163426 TGGAACTTTGCATCAAAACTCATGT 60.163 36.000 0.00 0.00 32.75 3.21
2693 2748 8.939201 TTGCATCAAAACTCATGTTTCTTTTA 57.061 26.923 0.00 0.00 44.70 1.52
2812 2895 5.633830 ATGTTCATGTTGACAATGACCTC 57.366 39.130 0.00 0.00 0.00 3.85
2835 2919 0.881159 CTGGTCGCCAAAACGGTACA 60.881 55.000 0.00 0.00 36.97 2.90
2916 3000 6.383415 GCAGTATTTCGTTTATTTTGGACCA 58.617 36.000 0.00 0.00 0.00 4.02
2974 3058 3.319755 CAATCAAACAGGGCATGTGAAC 58.680 45.455 5.20 0.00 43.00 3.18
2977 3061 1.541147 CAAACAGGGCATGTGAACGAT 59.459 47.619 5.20 0.00 43.00 3.73
2991 3075 7.467267 GCATGTGAACGATATGGATAACTTTGT 60.467 37.037 0.00 0.00 0.00 2.83
2994 3078 5.820423 TGAACGATATGGATAACTTTGTGGG 59.180 40.000 0.00 0.00 0.00 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 8.454106 GCATATAAGTGCCTATTAAACATCCAG 58.546 37.037 0.00 0.00 39.18 3.86
117 124 5.411361 CCATTTGGACTTCGTTTGATACTCA 59.589 40.000 0.00 0.00 37.39 3.41
120 127 5.873179 TCCATTTGGACTTCGTTTGATAC 57.127 39.130 0.00 0.00 39.78 2.24
123 130 4.824537 TCATTCCATTTGGACTTCGTTTGA 59.175 37.500 0.00 0.00 45.39 2.69
130 137 6.158598 CGAATGTTTCATTCCATTTGGACTT 58.841 36.000 14.24 0.00 45.39 3.01
221 228 2.997315 CCTCCTGCCTCGTGGACA 60.997 66.667 7.92 4.19 34.57 4.02
250 258 0.468214 CTACGAGGAGCCCATGAGGA 60.468 60.000 0.00 0.00 38.24 3.71
274 282 1.003696 AGGCAAAGGAACTAGGTCAGC 59.996 52.381 10.60 7.59 38.49 4.26
319 327 1.065709 GTTTCGTGGCTCCCCTGAATA 60.066 52.381 0.00 0.00 0.00 1.75
322 330 2.747686 GTTTCGTGGCTCCCCTGA 59.252 61.111 0.00 0.00 0.00 3.86
448 456 4.887655 TCACGCTTCATCAGAGAGGTAATA 59.112 41.667 0.00 0.00 0.00 0.98
508 516 4.473444 AGAGAGAGAAGAAGCCATCTAGG 58.527 47.826 0.00 0.00 37.42 3.02
534 542 4.806247 CGAGGAGAACATGGTATTGAGAAC 59.194 45.833 0.00 0.00 0.00 3.01
597 605 4.707105 TCATCATATCTCGGCAAACACAT 58.293 39.130 0.00 0.00 0.00 3.21
708 717 9.020731 AGGTCAAACTAAACCGATAATTCAAAT 57.979 29.630 0.00 0.00 40.63 2.32
750 759 8.225603 AGCTAAACACTTCTCTCATTGAAAAA 57.774 30.769 0.00 0.00 0.00 1.94
751 760 7.807977 AGCTAAACACTTCTCTCATTGAAAA 57.192 32.000 0.00 0.00 0.00 2.29
754 763 6.205464 CCAAAGCTAAACACTTCTCTCATTGA 59.795 38.462 0.00 0.00 0.00 2.57
760 769 6.299141 TGAATCCAAAGCTAAACACTTCTCT 58.701 36.000 0.00 0.00 0.00 3.10
769 778 9.474920 CACTACAAAATTGAATCCAAAGCTAAA 57.525 29.630 0.00 0.00 35.67 1.85
825 835 5.935206 TCCATGACAACAATACAATACGTGT 59.065 36.000 0.00 0.00 44.82 4.49
843 853 4.469945 ACTCCGTCTTTTTATCCTCCATGA 59.530 41.667 0.00 0.00 0.00 3.07
847 857 5.163884 CGAAAACTCCGTCTTTTTATCCTCC 60.164 44.000 0.00 0.00 0.00 4.30
861 871 6.701432 AAATTCACTAGTACGAAAACTCCG 57.299 37.500 0.00 0.00 0.00 4.63
864 874 7.797038 ACCAAAATTCACTAGTACGAAAACT 57.203 32.000 0.00 0.00 0.00 2.66
872 882 7.151308 CCAAATGCAACCAAAATTCACTAGTA 58.849 34.615 0.00 0.00 0.00 1.82
876 886 4.779696 ACCAAATGCAACCAAAATTCACT 58.220 34.783 0.00 0.00 0.00 3.41
1008 1059 1.145819 GAGAGGGTGCATCTGGAGC 59.854 63.158 0.00 0.00 0.00 4.70
1011 1062 2.914289 GGGAGAGGGTGCATCTGG 59.086 66.667 0.00 0.00 0.00 3.86
1377 1428 4.637489 CTGGCGATCTCGGGCTCG 62.637 72.222 3.71 3.71 40.23 5.03
1479 1530 1.078567 GGTCTGGAGGAGCTTGCTG 60.079 63.158 0.00 0.00 39.18 4.41
1480 1531 0.913451 ATGGTCTGGAGGAGCTTGCT 60.913 55.000 0.00 0.00 42.40 3.91
1672 1723 3.435186 GGGCACGCCAAGCTTCTC 61.435 66.667 10.83 0.00 37.98 2.87
1758 1809 2.158971 GCTCCTCAAGAACTCCATCCTC 60.159 54.545 0.00 0.00 0.00 3.71
1821 1872 1.398390 CCTAGAATGTGCGGCTTGTTC 59.602 52.381 0.00 2.82 0.00 3.18
1830 1881 6.352016 TCCTCTGATATTCCTAGAATGTGC 57.648 41.667 0.00 0.00 0.00 4.57
1902 1953 4.499183 GTCTCTTGACAATGTACTCTGGG 58.501 47.826 0.00 0.00 42.48 4.45
1908 1959 3.375299 GCATGGGTCTCTTGACAATGTAC 59.625 47.826 0.00 0.00 44.61 2.90
1917 1968 2.749621 GGTAAACAGCATGGGTCTCTTG 59.250 50.000 0.00 0.00 43.62 3.02
1918 1969 2.644798 AGGTAAACAGCATGGGTCTCTT 59.355 45.455 0.00 0.00 43.62 2.85
1923 1974 3.350219 CTGTAGGTAAACAGCATGGGT 57.650 47.619 0.00 0.00 43.62 4.51
2032 2083 5.665812 AGTTATCCTCACCATAGCCAACTAA 59.334 40.000 0.00 0.00 30.45 2.24
2055 2106 5.163824 ACTGTCGATGTATGTTGCAATGAAG 60.164 40.000 0.59 0.00 0.00 3.02
2062 2113 5.050769 CCTTATGACTGTCGATGTATGTTGC 60.051 44.000 2.98 0.00 0.00 4.17
2083 2134 1.062488 AGCCCAGGAACAGTGTCCTT 61.062 55.000 10.50 0.00 46.42 3.36
2086 2137 0.179018 ACAAGCCCAGGAACAGTGTC 60.179 55.000 0.00 0.00 0.00 3.67
2090 2141 2.636830 CATCTACAAGCCCAGGAACAG 58.363 52.381 0.00 0.00 0.00 3.16
2125 2176 1.817099 GAAGCATCTCCCCAGCACG 60.817 63.158 0.00 0.00 0.00 5.34
2136 2187 2.328819 AGCTGGACATCAGAAGCATC 57.671 50.000 0.00 0.00 46.18 3.91
2142 2193 2.751259 GCATTCAAAGCTGGACATCAGA 59.249 45.455 0.00 0.00 46.18 3.27
2200 2251 1.202336 GGCACAATGTTCCATGCTAGC 60.202 52.381 8.10 8.10 38.18 3.42
2217 2268 3.774766 ACTCACTAATGTGTATCAGGGCA 59.225 43.478 0.00 0.00 44.14 5.36
2223 2274 8.129840 ACGAATGAGTACTCACTAATGTGTATC 58.870 37.037 27.41 11.29 43.11 2.24
2339 2390 8.219546 TCACAGAAATTCACAACTGAAACATA 57.780 30.769 0.00 0.00 39.90 2.29
2443 2494 1.001406 AGGGAGCGAATATGTAGCTGC 59.999 52.381 0.00 0.00 46.39 5.25
2541 2593 9.545105 AAAAATGATTTGACTATGCAACAGAAA 57.455 25.926 5.74 0.00 0.00 2.52
2568 2620 6.750039 ACAATAACAAACGTGCATATTTAGCC 59.250 34.615 0.00 0.00 0.00 3.93
2595 2647 0.695924 TCCCTCCGCTCCATTTGAAA 59.304 50.000 0.00 0.00 0.00 2.69
2605 2657 5.751586 TCAAAATTTAATACTCCCTCCGCT 58.248 37.500 0.00 0.00 0.00 5.52
2606 2658 6.635030 ATCAAAATTTAATACTCCCTCCGC 57.365 37.500 0.00 0.00 0.00 5.54
2638 2690 6.295462 CCATTTCTCAGGTGAATTTGTCCATT 60.295 38.462 0.00 0.00 0.00 3.16
2750 2806 7.666623 TCCAAACCTTTGAAAATTCTATCACC 58.333 34.615 0.00 0.00 40.55 4.02
2812 2895 2.943653 GTTTTGGCGACCAGTCCG 59.056 61.111 0.00 0.00 33.81 4.79
2850 2934 2.171448 GACTTGACAGGGTATGCTCCAT 59.829 50.000 0.00 0.00 0.00 3.41
2916 3000 3.557228 TTGTACCTGTGGGTTTACGTT 57.443 42.857 0.00 0.00 44.73 3.99
2974 3058 6.935741 TTTCCCACAAAGTTATCCATATCG 57.064 37.500 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.