Multiple sequence alignment - TraesCS7D01G321400

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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 TraesCS7D01G321400 chr7D 100.000 3039 0 0 1 3039 411603615 411606653 0.000000e+00 5613
1 TraesCS7D01G321400 chr7A 95.167 3062 105 20 1 3037 472566287 472569330 0.000000e+00 4795
2 TraesCS7D01G321400 chr7B 94.214 2575 80 25 1 2531 426100743 426103292 0.000000e+00 3866
3 TraesCS7D01G321400 chr7B 94.864 331 14 2 2707 3037 426110612 426110939 5.810000e-142 514
4 TraesCS7D01G321400 chr7B 98.425 127 2 0 2525 2651 426110487 426110613 1.100000e-54 224


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 TraesCS7D01G321400 chr7D 411603615 411606653 3038 False 5613 5613 100.000 1 3039 1 chr7D.!!$F1 3038
1 TraesCS7D01G321400 chr7A 472566287 472569330 3043 False 4795 4795 95.167 1 3037 1 chr7A.!!$F1 3036
2 TraesCS7D01G321400 chr7B 426100743 426103292 2549 False 3866 3866 94.214 1 2531 1 chr7B.!!$F1 2530

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
74 75 0.036671 GTTCAACTCCTACCCACCCG 60.037 60.0 0.0 0.0 0.0 5.28 F
876 900 0.105709 CCTCCTCTCCTCTCCCTTCC 60.106 65.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1714 1781 1.335132 GGCCCATGGAGGAGACGTAA 61.335 60.0 15.22 0.0 41.22 3.18 R
2809 2878 0.607489 GCTGCAGCTCCTTTTCCTCA 60.607 55.0 31.33 0.0 38.21 3.86 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
74 75 0.036671 GTTCAACTCCTACCCACCCG 60.037 60.000 0.00 0.00 0.00 5.28
77 78 1.151965 AACTCCTACCCACCCGGTT 60.152 57.895 0.00 0.00 45.36 4.44
108 109 8.520835 ACACAGACAAAAGAAAAGAAAAGAAC 57.479 30.769 0.00 0.00 0.00 3.01
109 110 7.326063 ACACAGACAAAAGAAAAGAAAAGAACG 59.674 33.333 0.00 0.00 0.00 3.95
110 111 7.537306 CACAGACAAAAGAAAAGAAAAGAACGA 59.463 33.333 0.00 0.00 0.00 3.85
172 175 4.093408 GCAACTGCCATATGGTATATGTCG 59.907 45.833 22.79 8.15 37.57 4.35
204 207 3.818787 CTGGGTGCAATGGCGAGC 61.819 66.667 0.00 0.00 45.35 5.03
550 556 2.054453 GCAATGGTCCCCCTTGAGC 61.054 63.158 2.91 0.00 0.00 4.26
681 701 2.300152 TCCCATGCATGCTAGCTACTAC 59.700 50.000 21.69 1.69 34.99 2.73
697 717 6.138263 AGCTACTACTAGTACTCCTCTCTCA 58.862 44.000 0.00 0.00 0.00 3.27
733 753 1.126948 TGGCAGAGTGGTGGTCATCA 61.127 55.000 0.00 0.00 0.00 3.07
743 763 2.027745 TGGTGGTCATCAAGAGAGAAGC 60.028 50.000 0.00 0.00 0.00 3.86
744 764 2.266554 GTGGTCATCAAGAGAGAAGCG 58.733 52.381 0.00 0.00 0.00 4.68
745 765 2.094494 GTGGTCATCAAGAGAGAAGCGA 60.094 50.000 0.00 0.00 0.00 4.93
746 766 2.165234 TGGTCATCAAGAGAGAAGCGAG 59.835 50.000 0.00 0.00 0.00 5.03
848 872 4.299586 TCATTGCTTCCTCATACACCAA 57.700 40.909 0.00 0.00 0.00 3.67
867 891 1.680651 CACACTCGCCTCCTCTCCT 60.681 63.158 0.00 0.00 0.00 3.69
869 893 1.077068 CACTCGCCTCCTCTCCTCT 60.077 63.158 0.00 0.00 0.00 3.69
870 894 1.101049 CACTCGCCTCCTCTCCTCTC 61.101 65.000 0.00 0.00 0.00 3.20
871 895 1.528309 CTCGCCTCCTCTCCTCTCC 60.528 68.421 0.00 0.00 0.00 3.71
872 896 2.520741 CGCCTCCTCTCCTCTCCC 60.521 72.222 0.00 0.00 0.00 4.30
873 897 3.024217 GCCTCCTCTCCTCTCCCT 58.976 66.667 0.00 0.00 0.00 4.20
874 898 1.313129 GCCTCCTCTCCTCTCCCTT 59.687 63.158 0.00 0.00 0.00 3.95
875 899 0.759060 GCCTCCTCTCCTCTCCCTTC 60.759 65.000 0.00 0.00 0.00 3.46
876 900 0.105709 CCTCCTCTCCTCTCCCTTCC 60.106 65.000 0.00 0.00 0.00 3.46
877 901 0.633921 CTCCTCTCCTCTCCCTTCCA 59.366 60.000 0.00 0.00 0.00 3.53
919 952 2.605601 TGCTCCAGCTCAGCCTCA 60.606 61.111 11.00 0.00 42.66 3.86
923 956 0.179051 CTCCAGCTCAGCCTCAATCC 60.179 60.000 0.00 0.00 0.00 3.01
998 1046 4.681978 GTCGGCGGCAGAACCAGT 62.682 66.667 6.63 0.00 39.03 4.00
1098 1146 4.473520 ATGTCGGCGCCCTTCCTG 62.474 66.667 23.46 5.48 0.00 3.86
1134 1182 4.803426 CTCCGGTCGCTGCACTCC 62.803 72.222 0.00 0.00 0.00 3.85
1862 1929 2.554462 CTCAAGACAGAGTTCGACAGGA 59.446 50.000 0.00 0.00 0.00 3.86
1898 1965 3.838271 GCGACCCTGGCGAGATCA 61.838 66.667 0.00 0.00 0.00 2.92
1957 2024 3.966930 GAGGTCAGGAGCCGAGGGT 62.967 68.421 0.00 0.00 0.00 4.34
2134 2201 6.745116 ACAACAAGGCTAACAAATTAGAACC 58.255 36.000 0.00 0.00 40.38 3.62
2280 2348 4.046938 TGTATTCTTCCTAAGCAGAGCG 57.953 45.455 0.00 0.00 0.00 5.03
2469 2538 2.489722 GCTCTTTGCCCTTTTCTCGAAT 59.510 45.455 0.00 0.00 35.15 3.34
2536 2605 7.235812 AGACAAAAAGAGAGTTCTATAGGGTGT 59.764 37.037 0.00 0.00 31.96 4.16
2656 2725 2.339348 CGGCAATTGGCAGTGCAA 59.661 55.556 28.96 1.42 46.21 4.08
2658 2727 1.286354 CGGCAATTGGCAGTGCAAAG 61.286 55.000 28.96 8.62 46.21 2.77
2660 2729 1.338389 GGCAATTGGCAGTGCAAAGAT 60.338 47.619 25.76 2.23 46.21 2.40
2693 2762 3.511540 ACTCACGATGGAGAAGATGAACA 59.488 43.478 9.75 0.00 38.30 3.18
2699 2768 3.726557 TGGAGAAGATGAACAAGGCAT 57.273 42.857 0.00 0.00 0.00 4.40
2789 2858 1.134128 CCGAACATGATGATCACCCCA 60.134 52.381 0.00 0.00 0.00 4.96
2809 2878 3.506067 CCAAACTTAAGAGGCATCGGTTT 59.494 43.478 10.09 1.30 0.00 3.27
2810 2879 4.475944 CAAACTTAAGAGGCATCGGTTTG 58.524 43.478 10.09 18.90 37.04 2.93
2823 2892 1.420138 TCGGTTTGAGGAAAAGGAGCT 59.580 47.619 0.00 0.00 0.00 4.09
2846 2915 3.727673 GCAGCTGCAATGCAAAATTGATG 60.728 43.478 33.36 7.34 43.31 3.07
2850 2919 4.095782 GCTGCAATGCAAAATTGATGGATT 59.904 37.500 9.92 5.69 39.08 3.01
2852 2921 6.183360 GCTGCAATGCAAAATTGATGGATTTA 60.183 34.615 9.92 2.34 36.81 1.40
2887 2956 8.367911 TGCAGGGTTATATACAGTAGAGAAATG 58.632 37.037 0.00 0.00 0.00 2.32
2913 2982 1.514873 GCAGCAGCGTAAACCATGC 60.515 57.895 0.00 0.00 39.67 4.06
2964 3033 6.980593 TGAATCAACCAAATCGAATCACTTT 58.019 32.000 0.00 0.00 0.00 2.66
2965 3034 7.432869 TGAATCAACCAAATCGAATCACTTTT 58.567 30.769 0.00 0.00 0.00 2.27
3011 3080 2.776312 TCGCTAAAGTAGGATCTGCG 57.224 50.000 0.00 0.00 42.70 5.18
3037 3106 5.520376 AAGAACCAAGAAAACATCAGTGG 57.480 39.130 0.00 0.00 39.95 4.00
3038 3107 3.319122 AGAACCAAGAAAACATCAGTGGC 59.681 43.478 0.00 0.00 38.46 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 0.036671 CGGGTGGGTAGGAGTTGAAC 60.037 60.000 0.00 0.00 0.00 3.18
74 75 6.913873 TTCTTTTGTCTGTGTAGTGTAACC 57.086 37.500 0.00 0.00 37.80 2.85
77 78 8.780846 TTCTTTTCTTTTGTCTGTGTAGTGTA 57.219 30.769 0.00 0.00 0.00 2.90
124 125 6.761242 CAGCCAAATGCATTACTACTACTGTA 59.239 38.462 13.39 0.00 44.83 2.74
125 126 5.586243 CAGCCAAATGCATTACTACTACTGT 59.414 40.000 13.39 0.00 44.83 3.55
126 127 5.504665 GCAGCCAAATGCATTACTACTACTG 60.505 44.000 13.39 13.56 45.77 2.74
127 128 4.576463 GCAGCCAAATGCATTACTACTACT 59.424 41.667 13.39 1.09 45.77 2.57
128 129 4.848757 GCAGCCAAATGCATTACTACTAC 58.151 43.478 13.39 0.00 45.77 2.73
162 165 6.362283 GCCACAAAATTAATGCGACATATACC 59.638 38.462 0.00 0.00 0.00 2.73
172 175 3.002102 CACCCAGCCACAAAATTAATGC 58.998 45.455 0.00 0.00 0.00 3.56
182 185 2.601067 CCATTGCACCCAGCCACA 60.601 61.111 0.00 0.00 44.83 4.17
204 207 2.095372 TCACTACGTACAGAGTGCATCG 59.905 50.000 15.98 0.00 42.35 3.84
254 257 7.438955 GTTTTTCTGGAAACCCACGTTATGTG 61.439 42.308 0.00 0.00 37.74 3.21
488 494 2.040278 ACTTGCTGGTGCTAATCAAGGA 59.960 45.455 0.00 0.00 38.64 3.36
550 556 2.824341 AGTTGTACGTACTCCTTCCAGG 59.176 50.000 25.12 0.00 36.46 4.45
681 701 2.811431 CGCCATGAGAGAGGAGTACTAG 59.189 54.545 0.00 0.00 0.00 2.57
709 729 2.304056 CCACCACTCTGCCATCCCT 61.304 63.158 0.00 0.00 0.00 4.20
711 731 1.078143 GACCACCACTCTGCCATCC 60.078 63.158 0.00 0.00 0.00 3.51
714 734 1.126948 TGATGACCACCACTCTGCCA 61.127 55.000 0.00 0.00 0.00 4.92
733 753 1.138671 GCTCGCTCGCTTCTCTCTT 59.861 57.895 0.00 0.00 0.00 2.85
743 763 2.540736 AAGACTGCTCTGCTCGCTCG 62.541 60.000 0.00 0.00 0.00 5.03
744 764 1.077645 CAAGACTGCTCTGCTCGCTC 61.078 60.000 0.00 0.00 0.00 5.03
745 765 1.079956 CAAGACTGCTCTGCTCGCT 60.080 57.895 0.00 0.00 0.00 4.93
746 766 2.099431 CCAAGACTGCTCTGCTCGC 61.099 63.158 0.00 0.00 0.00 5.03
848 872 1.979693 GGAGAGGAGGCGAGTGTGT 60.980 63.158 0.00 0.00 0.00 3.72
867 891 7.423156 GCCTATATATAGAGGATGGAAGGGAGA 60.423 44.444 24.65 0.00 36.82 3.71
869 893 6.397359 AGCCTATATATAGAGGATGGAAGGGA 59.603 42.308 24.65 0.00 36.82 4.20
870 894 6.496565 CAGCCTATATATAGAGGATGGAAGGG 59.503 46.154 26.90 6.85 44.80 3.95
871 895 7.537596 CAGCCTATATATAGAGGATGGAAGG 57.462 44.000 26.90 7.48 44.80 3.46
919 952 2.364160 GGTGGTGCATGGGGGATT 59.636 61.111 0.00 0.00 0.00 3.01
923 956 2.990967 GTGTGGTGGTGCATGGGG 60.991 66.667 0.00 0.00 0.00 4.96
998 1046 1.816835 ACGAGTAGAAGCCGTTCATGA 59.183 47.619 0.00 0.00 34.82 3.07
1068 1116 2.125512 GACATGAAGGCGGCGTCT 60.126 61.111 23.97 8.88 0.00 4.18
1134 1182 3.374402 ACGAGGTGGACGAGCTGG 61.374 66.667 0.00 0.00 34.30 4.85
1260 1308 2.202623 GAGGCGCAGTAGGTGTCG 60.203 66.667 10.83 0.00 36.51 4.35
1302 1350 2.029844 GTTGCAGAGCCAGTCGTCC 61.030 63.158 0.00 0.00 0.00 4.79
1507 1574 2.835705 CGGGTCGATCCTGGTCTCG 61.836 68.421 14.05 12.92 38.86 4.04
1714 1781 1.335132 GGCCCATGGAGGAGACGTAA 61.335 60.000 15.22 0.00 41.22 3.18
1862 1929 2.819550 GTACCCCATGGCGACGAT 59.180 61.111 6.09 0.00 33.59 3.73
1931 1998 1.336632 GCTCCTGACCTCAGCATCCT 61.337 60.000 0.00 0.00 42.47 3.24
2280 2348 3.330720 ACTACCACCTGCTGCCCC 61.331 66.667 0.00 0.00 0.00 5.80
2289 2357 2.045926 CTGCCTGCCACTACCACC 60.046 66.667 0.00 0.00 0.00 4.61
2469 2538 4.580167 CACATCTCCACAGAACTTTTCCAA 59.420 41.667 0.00 0.00 30.24 3.53
2536 2605 2.040278 AGCACAAGGGCTCATTCTAACA 59.960 45.455 0.00 0.00 41.05 2.41
2656 2725 9.613428 TCCATCGTGAGTAAAATAATCAATCTT 57.387 29.630 0.00 0.00 34.28 2.40
2658 2727 9.261180 TCTCCATCGTGAGTAAAATAATCAATC 57.739 33.333 0.00 0.00 34.28 2.67
2660 2729 9.098355 CTTCTCCATCGTGAGTAAAATAATCAA 57.902 33.333 0.00 0.00 34.28 2.57
2699 2768 6.655078 TGTCGGAGATCATATTGAGAATCA 57.345 37.500 0.00 0.00 42.22 2.57
2789 2858 4.394729 TCAAACCGATGCCTCTTAAGTTT 58.605 39.130 1.63 0.00 0.00 2.66
2809 2878 0.607489 GCTGCAGCTCCTTTTCCTCA 60.607 55.000 31.33 0.00 38.21 3.86
2810 2879 2.178856 GCTGCAGCTCCTTTTCCTC 58.821 57.895 31.33 0.00 38.21 3.71
2873 2942 7.869937 GCTGCTTATCATCATTTCTCTACTGTA 59.130 37.037 0.00 0.00 0.00 2.74
2874 2943 6.705381 GCTGCTTATCATCATTTCTCTACTGT 59.295 38.462 0.00 0.00 0.00 3.55
2887 2956 3.303395 GGTTTACGCTGCTGCTTATCATC 60.303 47.826 14.03 0.00 36.97 2.92
3011 3080 4.692228 TGATGTTTTCTTGGTTCTTTGCC 58.308 39.130 0.00 0.00 0.00 4.52


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

AutoCloner maintained by Alex Coulton.