Multiple sequence alignment - TraesCS1A01G279700

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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 TraesCS1A01G279700 chr1A 100.000 2891 0 0 1 2891 476976408 476979298 0.000000e+00 5339.0
1 TraesCS1A01G279700 chr1A 94.615 650 28 3 1686 2334 579826677 579827320 0.000000e+00 1000.0
2 TraesCS1A01G279700 chr6A 95.807 1765 65 7 571 2334 114245812 114247568 0.000000e+00 2841.0
3 TraesCS1A01G279700 chr6A 96.068 1119 43 1 571 1688 32608041 32609159 0.000000e+00 1821.0
4 TraesCS1A01G279700 chr3A 95.294 1785 57 4 571 2334 642706679 642708457 0.000000e+00 2806.0
5 TraesCS1A01G279700 chr2A 95.127 1765 69 7 571 2334 58379993 58381741 0.000000e+00 2767.0
6 TraesCS1A01G279700 chr2A 95.957 1113 43 2 572 1683 687137041 687138152 0.000000e+00 1805.0
7 TraesCS1A01G279700 chr2A 95.545 651 20 6 1686 2334 687033137 687032494 0.000000e+00 1033.0
8 TraesCS1A01G279700 chr2A 94.624 651 27 6 1686 2334 724112891 724112247 0.000000e+00 1002.0
9 TraesCS1A01G279700 chr2A 94.607 649 28 7 1686 2333 755750437 755749795 0.000000e+00 998.0
10 TraesCS1A01G279700 chr5A 94.211 1762 89 6 571 2332 509473601 509471853 0.000000e+00 2676.0
11 TraesCS1A01G279700 chr5A 96.409 1114 37 1 574 1687 448094248 448095358 0.000000e+00 1832.0
12 TraesCS1A01G279700 chr5A 96.243 1118 42 0 571 1688 673519162 673520279 0.000000e+00 1832.0
13 TraesCS1A01G279700 chr5A 95.427 656 24 6 1686 2340 7824281 7823631 0.000000e+00 1040.0
14 TraesCS1A01G279700 chr5A 94.316 651 27 7 1686 2334 300370537 300369895 0.000000e+00 989.0
15 TraesCS1A01G279700 chr7A 95.979 1119 38 4 571 1688 16067312 16068424 0.000000e+00 1810.0
16 TraesCS1A01G279700 chr4A 95.186 644 25 6 1691 2334 66341773 66342410 0.000000e+00 1013.0
17 TraesCS1A01G279700 chr1D 98.074 571 10 1 1 571 376726324 376726893 0.000000e+00 992.0
18 TraesCS1A01G279700 chr1D 96.442 534 18 1 2334 2867 376726891 376727423 0.000000e+00 880.0
19 TraesCS1A01G279700 chr1B 97.373 571 14 1 1 571 503468702 503469271 0.000000e+00 970.0
20 TraesCS1A01G279700 chr1B 97.378 534 14 0 2334 2867 503469269 503469802 0.000000e+00 909.0
21 TraesCS1A01G279700 chr2D 72.844 545 131 14 2333 2866 533925939 533925401 1.380000e-38 171.0
22 TraesCS1A01G279700 chr7D 72.527 546 139 10 2331 2867 610625251 610624708 1.780000e-37 167.0
23 TraesCS1A01G279700 chr5D 72.344 546 140 10 2331 2867 557605703 557606246 8.290000e-36 161.0
24 TraesCS1A01G279700 chr5D 71.978 546 142 10 2331 2867 392029053 392028510 1.790000e-32 150.0
25 TraesCS1A01G279700 chr6B 71.298 547 137 17 2334 2867 90286149 90285610 3.910000e-24 122.0
26 TraesCS1A01G279700 chr7B 70.909 550 134 23 2334 2867 516840675 516841214 3.940000e-19 106.0
27 TraesCS1A01G279700 chr4D 83.505 97 10 5 2775 2867 425145491 425145585 5.130000e-13 86.1
28 TraesCS1A01G279700 chrUn 90.909 55 3 2 2815 2867 13957622 13957676 4.000000e-09 73.1


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 TraesCS1A01G279700 chr1A 476976408 476979298 2890 False 5339.0 5339 100.0000 1 2891 1 chr1A.!!$F1 2890
1 TraesCS1A01G279700 chr1A 579826677 579827320 643 False 1000.0 1000 94.6150 1686 2334 1 chr1A.!!$F2 648
2 TraesCS1A01G279700 chr6A 114245812 114247568 1756 False 2841.0 2841 95.8070 571 2334 1 chr6A.!!$F2 1763
3 TraesCS1A01G279700 chr6A 32608041 32609159 1118 False 1821.0 1821 96.0680 571 1688 1 chr6A.!!$F1 1117
4 TraesCS1A01G279700 chr3A 642706679 642708457 1778 False 2806.0 2806 95.2940 571 2334 1 chr3A.!!$F1 1763
5 TraesCS1A01G279700 chr2A 58379993 58381741 1748 False 2767.0 2767 95.1270 571 2334 1 chr2A.!!$F1 1763
6 TraesCS1A01G279700 chr2A 687137041 687138152 1111 False 1805.0 1805 95.9570 572 1683 1 chr2A.!!$F2 1111
7 TraesCS1A01G279700 chr2A 687032494 687033137 643 True 1033.0 1033 95.5450 1686 2334 1 chr2A.!!$R1 648
8 TraesCS1A01G279700 chr2A 724112247 724112891 644 True 1002.0 1002 94.6240 1686 2334 1 chr2A.!!$R2 648
9 TraesCS1A01G279700 chr2A 755749795 755750437 642 True 998.0 998 94.6070 1686 2333 1 chr2A.!!$R3 647
10 TraesCS1A01G279700 chr5A 509471853 509473601 1748 True 2676.0 2676 94.2110 571 2332 1 chr5A.!!$R3 1761
11 TraesCS1A01G279700 chr5A 448094248 448095358 1110 False 1832.0 1832 96.4090 574 1687 1 chr5A.!!$F1 1113
12 TraesCS1A01G279700 chr5A 673519162 673520279 1117 False 1832.0 1832 96.2430 571 1688 1 chr5A.!!$F2 1117
13 TraesCS1A01G279700 chr5A 7823631 7824281 650 True 1040.0 1040 95.4270 1686 2340 1 chr5A.!!$R1 654
14 TraesCS1A01G279700 chr5A 300369895 300370537 642 True 989.0 989 94.3160 1686 2334 1 chr5A.!!$R2 648
15 TraesCS1A01G279700 chr7A 16067312 16068424 1112 False 1810.0 1810 95.9790 571 1688 1 chr7A.!!$F1 1117
16 TraesCS1A01G279700 chr4A 66341773 66342410 637 False 1013.0 1013 95.1860 1691 2334 1 chr4A.!!$F1 643
17 TraesCS1A01G279700 chr1D 376726324 376727423 1099 False 936.0 992 97.2580 1 2867 2 chr1D.!!$F1 2866
18 TraesCS1A01G279700 chr1B 503468702 503469802 1100 False 939.5 970 97.3755 1 2867 2 chr1B.!!$F1 2866

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
79 80 0.038251 CTGTGCGTGGCTCTGTTCTA 60.038 55.0 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2377 2406 3.350219 TGGGACAGTAAAAGAGATGCC 57.65 47.619 0.0 0.0 0.0 4.4 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
67 68 1.947456 GTTCTTCCTTTTCCTGTGCGT 59.053 47.619 0.00 0.00 0.00 5.24
79 80 0.038251 CTGTGCGTGGCTCTGTTCTA 60.038 55.000 0.00 0.00 0.00 2.10
147 148 4.202182 TGGACCGTTGCTTGTAGTATATCC 60.202 45.833 0.00 0.00 0.00 2.59
185 186 2.515071 ATGGAGCTGCCCCTCGATC 61.515 63.158 1.53 0.00 34.97 3.69
191 192 1.445095 CTGCCCCTCGATCTCCTTG 59.555 63.158 0.00 0.00 0.00 3.61
400 401 0.317160 GCATCCATGACCATGCCATG 59.683 55.000 15.36 15.36 39.70 3.66
464 465 0.830648 TGTGCATCCTACTGCTACCC 59.169 55.000 0.00 0.00 42.75 3.69
599 600 2.981909 CCGCGCGACCCTATCCTA 60.982 66.667 34.63 0.00 0.00 2.94
639 640 2.487805 GGGTAAAACGGACAAAGGAGGT 60.488 50.000 0.00 0.00 0.00 3.85
799 800 2.768344 CGGCCACCTACCTCCCAT 60.768 66.667 2.24 0.00 0.00 4.00
1217 1220 1.227853 GCCGCCGTTATTGGGAGAT 60.228 57.895 0.00 0.00 0.00 2.75
1428 1431 0.670546 CCTGGTTTCGTGACGAGCAT 60.671 55.000 8.02 0.00 37.14 3.79
1638 1642 0.530744 ACTCCATGTACACGCACGAT 59.469 50.000 0.00 0.00 0.00 3.73
1889 1914 3.680196 ACCTCCGGCCCACCTCTA 61.680 66.667 0.00 0.00 0.00 2.43
2377 2406 3.546670 GCCTAACTTGTATGTTCTCGTCG 59.453 47.826 0.00 0.00 0.00 5.12
2565 2594 4.751028 GCCATGGTAGATTATCTTGGGCTT 60.751 45.833 14.67 0.00 35.31 4.35
2653 2682 9.613428 TCCAGTAAATCTATAGGTTTTGTCATG 57.387 33.333 15.98 8.20 0.00 3.07
2702 2731 2.361610 CACCATGCCCTGTCACCC 60.362 66.667 0.00 0.00 0.00 4.61
2765 2794 0.732571 AACACAACTCACCGCAACAG 59.267 50.000 0.00 0.00 0.00 3.16
2867 2896 2.434702 GGGTTGTAGGACTGTATCAGGG 59.565 54.545 1.90 0.00 35.51 4.45
2868 2897 3.371965 GGTTGTAGGACTGTATCAGGGA 58.628 50.000 1.90 0.00 35.51 4.20
2869 2898 3.385111 GGTTGTAGGACTGTATCAGGGAG 59.615 52.174 1.90 0.00 35.51 4.30
2870 2899 4.024670 GTTGTAGGACTGTATCAGGGAGT 58.975 47.826 1.90 0.00 35.51 3.85
2871 2900 5.198965 GTTGTAGGACTGTATCAGGGAGTA 58.801 45.833 1.90 0.00 35.51 2.59
2872 2901 5.050126 TGTAGGACTGTATCAGGGAGTAG 57.950 47.826 1.90 0.00 35.51 2.57
2873 2902 3.603965 AGGACTGTATCAGGGAGTAGG 57.396 52.381 1.90 0.00 35.51 3.18
2874 2903 2.178106 AGGACTGTATCAGGGAGTAGGG 59.822 54.545 1.90 0.00 35.51 3.53
2875 2904 1.964933 GACTGTATCAGGGAGTAGGGC 59.035 57.143 1.90 0.00 35.51 5.19
2876 2905 1.291033 ACTGTATCAGGGAGTAGGGCA 59.709 52.381 1.90 0.00 35.51 5.36
2877 2906 2.090494 ACTGTATCAGGGAGTAGGGCAT 60.090 50.000 1.90 0.00 35.51 4.40
2878 2907 2.975489 CTGTATCAGGGAGTAGGGCATT 59.025 50.000 0.00 0.00 0.00 3.56
2879 2908 3.392616 CTGTATCAGGGAGTAGGGCATTT 59.607 47.826 0.00 0.00 0.00 2.32
2880 2909 3.785887 TGTATCAGGGAGTAGGGCATTTT 59.214 43.478 0.00 0.00 0.00 1.82
2881 2910 2.806945 TCAGGGAGTAGGGCATTTTG 57.193 50.000 0.00 0.00 0.00 2.44
2882 2911 1.284785 TCAGGGAGTAGGGCATTTTGG 59.715 52.381 0.00 0.00 0.00 3.28
2883 2912 1.284785 CAGGGAGTAGGGCATTTTGGA 59.715 52.381 0.00 0.00 0.00 3.53
2884 2913 1.566231 AGGGAGTAGGGCATTTTGGAG 59.434 52.381 0.00 0.00 0.00 3.86
2885 2914 1.564348 GGGAGTAGGGCATTTTGGAGA 59.436 52.381 0.00 0.00 0.00 3.71
2886 2915 2.644676 GGAGTAGGGCATTTTGGAGAC 58.355 52.381 0.00 0.00 0.00 3.36
2887 2916 2.644676 GAGTAGGGCATTTTGGAGACC 58.355 52.381 0.00 0.00 0.00 3.85
2888 2917 1.065418 AGTAGGGCATTTTGGAGACCG 60.065 52.381 0.00 0.00 0.00 4.79
2889 2918 1.065709 GTAGGGCATTTTGGAGACCGA 60.066 52.381 0.00 0.00 0.00 4.69
2890 2919 0.035056 AGGGCATTTTGGAGACCGAG 60.035 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
147 148 1.424493 GATCTGTTTGAGCGCGAGGG 61.424 60.000 12.10 0.0 0.00 4.30
185 186 4.125703 GTTACATGCAGGAGATCAAGGAG 58.874 47.826 4.84 0.0 0.00 3.69
191 192 3.201290 CACAGGTTACATGCAGGAGATC 58.799 50.000 4.84 0.0 0.00 2.75
400 401 4.999950 CCTGGACTAGGCATGAATTGTATC 59.000 45.833 0.00 0.0 40.38 2.24
731 732 2.280592 GTCCGTTTGGTGTCCGCT 60.281 61.111 0.00 0.0 36.30 5.52
781 782 3.635869 ATGGGAGGTAGGTGGCCGT 62.636 63.158 0.00 0.0 0.00 5.68
799 800 2.823593 CGCATTGATGTGGGCGGA 60.824 61.111 0.00 0.0 45.27 5.54
2377 2406 3.350219 TGGGACAGTAAAAGAGATGCC 57.650 47.619 0.00 0.0 0.00 4.40
2438 2467 2.115291 GGGAATGCTTGGCCGACTC 61.115 63.158 0.00 0.0 0.00 3.36
2565 2594 2.481185 GGGACGCGTTGTGATTTCTTAA 59.519 45.455 15.53 0.0 0.00 1.85
2653 2682 8.344098 ACTACTTAGATGCGACTATTACTGTTC 58.656 37.037 0.00 0.0 0.00 3.18
2702 2731 0.249447 TTGTGGAGAGACAGTGTGCG 60.249 55.000 0.00 0.0 0.00 5.34
2765 2794 1.200948 GAGCTTGGGTTTCAGACATGC 59.799 52.381 0.00 0.0 36.05 4.06
2867 2896 2.644676 GGTCTCCAAAATGCCCTACTC 58.355 52.381 0.00 0.0 0.00 2.59
2868 2897 1.065418 CGGTCTCCAAAATGCCCTACT 60.065 52.381 0.00 0.0 0.00 2.57
2869 2898 1.065709 TCGGTCTCCAAAATGCCCTAC 60.066 52.381 0.00 0.0 0.00 3.18
2870 2899 1.209504 CTCGGTCTCCAAAATGCCCTA 59.790 52.381 0.00 0.0 0.00 3.53
2871 2900 0.035056 CTCGGTCTCCAAAATGCCCT 60.035 55.000 0.00 0.0 0.00 5.19
2872 2901 2.482326 CTCGGTCTCCAAAATGCCC 58.518 57.895 0.00 0.0 0.00 5.36


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

AutoCloner maintained by Alex Coulton.