Multiple sequence alignment - TraesCS2A01G421900

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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 TraesCS2A01G421900 chr2A 100.000 3135 0 0 1 3135 677173671 677170537 0.000000e+00 5790.0
1 TraesCS2A01G421900 chr2A 98.771 2766 20 4 4 2769 677102380 677099629 0.000000e+00 4907.0
2 TraesCS2A01G421900 chr2A 98.805 2426 15 4 4 2429 677070439 677068028 0.000000e+00 4307.0
3 TraesCS2A01G421900 chr2A 98.516 2426 16 5 4 2429 677158445 677156040 0.000000e+00 4263.0
4 TraesCS2A01G421900 chr2A 88.249 868 59 19 622 1483 677039777 677038947 0.000000e+00 998.0
5 TraesCS2A01G421900 chr2A 91.785 353 21 3 4 351 677040122 677039773 4.700000e-133 484.0
6 TraesCS2A01G421900 chr2A 86.486 222 16 10 132 349 677224660 677224449 6.760000e-57 231.0
7 TraesCS2A01G421900 chr2A 85.455 220 21 7 132 348 677223429 677223218 5.260000e-53 219.0
8 TraesCS2A01G421900 chr2D 95.742 2419 75 13 622 3033 532607841 532605444 0.000000e+00 3871.0
9 TraesCS2A01G421900 chr2D 91.618 346 22 2 6 351 532500539 532500201 3.660000e-129 472.0
10 TraesCS2A01G421900 chr2D 100.000 33 0 0 3103 3135 532604168 532604136 9.390000e-06 62.1
11 TraesCS2A01G421900 chrUn 95.252 2422 74 15 619 3033 183904055 183906442 0.000000e+00 3797.0
12 TraesCS2A01G421900 chrUn 95.045 2422 76 17 619 3033 240848497 240850881 0.000000e+00 3768.0
13 TraesCS2A01G421900 chrUn 94.961 2421 79 15 619 3033 260027911 260030294 0.000000e+00 3755.0
14 TraesCS2A01G421900 chrUn 94.876 2420 79 16 622 3033 235135857 235133475 0.000000e+00 3740.0
15 TraesCS2A01G421900 chrUn 95.300 1915 63 9 1125 3033 279914453 279916346 0.000000e+00 3013.0
16 TraesCS2A01G421900 chrUn 95.409 1895 61 12 1144 3033 304976116 304977989 0.000000e+00 2994.0
17 TraesCS2A01G421900 chrUn 93.015 859 37 7 2181 3033 403431460 403430619 0.000000e+00 1232.0
18 TraesCS2A01G421900 chrUn 96.078 204 7 1 2831 3033 396550650 396550447 6.480000e-87 331.0
19 TraesCS2A01G421900 chrUn 89.634 164 16 1 1 164 183903531 183903693 1.140000e-49 207.0
20 TraesCS2A01G421900 chrUn 90.062 161 15 1 4 164 235136381 235136222 1.140000e-49 207.0
21 TraesCS2A01G421900 chrUn 89.634 164 16 1 1 164 240847973 240848135 1.140000e-49 207.0
22 TraesCS2A01G421900 chrUn 89.634 164 16 1 1 164 260027387 260027549 1.140000e-49 207.0
23 TraesCS2A01G421900 chrUn 90.062 161 15 1 4 164 277811454 277811295 1.140000e-49 207.0
24 TraesCS2A01G421900 chrUn 89.634 164 16 1 1 164 362478632 362478794 1.140000e-49 207.0
25 TraesCS2A01G421900 chrUn 84.746 118 12 4 132 243 26076394 26076277 2.560000e-21 113.0
26 TraesCS2A01G421900 chr2B 85.570 790 58 23 710 1483 632566764 632566015 0.000000e+00 776.0
27 TraesCS2A01G421900 chr2B 83.832 835 80 32 1717 2528 632563812 632563010 0.000000e+00 743.0
28 TraesCS2A01G421900 chr2B 97.122 278 8 0 350 627 96584174 96584451 1.320000e-128 470.0
29 TraesCS2A01G421900 chr2B 88.920 352 33 4 4 351 632514109 632513760 2.230000e-116 429.0
30 TraesCS2A01G421900 chr7B 97.509 281 7 0 346 626 57000029 56999749 6.080000e-132 481.0
31 TraesCS2A01G421900 chr6B 97.842 278 4 2 353 628 257601571 257601294 2.190000e-131 479.0
32 TraesCS2A01G421900 chr3A 96.043 278 11 0 353 630 361973298 361973021 1.330000e-123 453.0
33 TraesCS2A01G421900 chr4A 95.374 281 13 0 348 628 593489941 593490221 6.170000e-122 448.0
34 TraesCS2A01G421900 chr7A 95.985 274 11 0 353 626 696328532 696328259 2.220000e-121 446.0


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 TraesCS2A01G421900 chr2A 677170537 677173671 3134 True 5790.00 5790 100.0000 1 3135 1 chr2A.!!$R4 3134
1 TraesCS2A01G421900 chr2A 677099629 677102380 2751 True 4907.00 4907 98.7710 4 2769 1 chr2A.!!$R2 2765
2 TraesCS2A01G421900 chr2A 677068028 677070439 2411 True 4307.00 4307 98.8050 4 2429 1 chr2A.!!$R1 2425
3 TraesCS2A01G421900 chr2A 677156040 677158445 2405 True 4263.00 4263 98.5160 4 2429 1 chr2A.!!$R3 2425
4 TraesCS2A01G421900 chr2A 677038947 677040122 1175 True 741.00 998 90.0170 4 1483 2 chr2A.!!$R5 1479
5 TraesCS2A01G421900 chr2A 677223218 677224660 1442 True 225.00 231 85.9705 132 349 2 chr2A.!!$R6 217
6 TraesCS2A01G421900 chr2D 532604136 532607841 3705 True 1966.55 3871 97.8710 622 3135 2 chr2D.!!$R2 2513
7 TraesCS2A01G421900 chrUn 279914453 279916346 1893 False 3013.00 3013 95.3000 1125 3033 1 chrUn.!!$F1 1908
8 TraesCS2A01G421900 chrUn 304976116 304977989 1873 False 2994.00 2994 95.4090 1144 3033 1 chrUn.!!$F2 1889
9 TraesCS2A01G421900 chrUn 183903531 183906442 2911 False 2002.00 3797 92.4430 1 3033 2 chrUn.!!$F4 3032
10 TraesCS2A01G421900 chrUn 240847973 240850881 2908 False 1987.50 3768 92.3395 1 3033 2 chrUn.!!$F5 3032
11 TraesCS2A01G421900 chrUn 260027387 260030294 2907 False 1981.00 3755 92.2975 1 3033 2 chrUn.!!$F6 3032
12 TraesCS2A01G421900 chrUn 235133475 235136381 2906 True 1973.50 3740 92.4690 4 3033 2 chrUn.!!$R5 3029
13 TraesCS2A01G421900 chrUn 403430619 403431460 841 True 1232.00 1232 93.0150 2181 3033 1 chrUn.!!$R4 852
14 TraesCS2A01G421900 chr2B 632563010 632566764 3754 True 759.50 776 84.7010 710 2528 2 chr2B.!!$R2 1818

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
27 28 2.572191 TGAGTCGTCTTTGTGTTCGT 57.428 45.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2685 5650 5.624491 GGTAAGACGAGACAAATATAGACGC 59.376 44.0 0.0 0.0 0.0 5.19 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
25 26 6.631636 GGTTAATTTGAGTCGTCTTTGTGTTC 59.368 38.462 0.00 0.00 0.00 3.18
27 28 2.572191 TGAGTCGTCTTTGTGTTCGT 57.428 45.000 0.00 0.00 0.00 3.85
49 50 3.000727 CGGGAGTGTACCAAATCAGAAC 58.999 50.000 0.00 0.00 0.00 3.01
55 56 6.092807 GGAGTGTACCAAATCAGAACTGAATC 59.907 42.308 8.59 0.00 43.58 2.52
2685 5650 1.238439 AACCCGACACAAATCTGCAG 58.762 50.000 7.63 7.63 0.00 4.41
2716 5681 4.866508 TTGTCTCGTCTTACCTCATTGT 57.133 40.909 0.00 0.00 0.00 2.71
2781 5746 1.410004 TTATGGGACCGGCTACTGAG 58.590 55.000 0.00 0.00 0.00 3.35
2807 5772 6.500684 TGTGACTGAATTCTCATTTTAGGC 57.499 37.500 7.05 0.00 0.00 3.93
2850 5816 1.439679 GTCTTGTCCGGGTGAACATC 58.560 55.000 0.00 0.00 0.00 3.06
2860 5826 0.818938 GGTGAACATCCATGCATGCA 59.181 50.000 25.04 25.04 0.00 3.96
2938 5904 3.385755 AGGTGAGCTTTGCTGAATGTTTT 59.614 39.130 0.00 0.00 39.88 2.43
3027 5993 0.899720 TACACAGTTTAGGCCTCCCG 59.100 55.000 9.68 0.00 35.76 5.14
3028 5994 1.125711 ACACAGTTTAGGCCTCCCGT 61.126 55.000 9.68 0.00 35.76 5.28
3030 5996 1.276989 CACAGTTTAGGCCTCCCGTAA 59.723 52.381 9.68 0.00 35.76 3.18
3031 5997 2.093128 CACAGTTTAGGCCTCCCGTAAT 60.093 50.000 9.68 0.00 35.76 1.89
3032 5998 2.574824 ACAGTTTAGGCCTCCCGTAATT 59.425 45.455 9.68 0.00 35.76 1.40
3033 5999 3.009805 ACAGTTTAGGCCTCCCGTAATTT 59.990 43.478 9.68 0.00 35.76 1.82
3034 6000 4.014406 CAGTTTAGGCCTCCCGTAATTTT 58.986 43.478 9.68 0.00 35.76 1.82
3035 6001 4.014406 AGTTTAGGCCTCCCGTAATTTTG 58.986 43.478 9.68 0.00 35.76 2.44
3038 6004 1.111277 GGCCTCCCGTAATTTTGCAT 58.889 50.000 0.00 0.00 0.00 3.96
3039 6005 2.092103 AGGCCTCCCGTAATTTTGCATA 60.092 45.455 0.00 0.00 35.76 3.14
3040 6006 2.034179 GGCCTCCCGTAATTTTGCATAC 59.966 50.000 0.00 0.00 0.00 2.39
3042 6008 4.131596 GCCTCCCGTAATTTTGCATACTA 58.868 43.478 0.00 0.00 0.00 1.82
3043 6009 4.760204 GCCTCCCGTAATTTTGCATACTAT 59.240 41.667 0.00 0.00 0.00 2.12
3044 6010 5.240844 GCCTCCCGTAATTTTGCATACTATT 59.759 40.000 0.00 0.00 0.00 1.73
3045 6011 6.428771 GCCTCCCGTAATTTTGCATACTATTA 59.571 38.462 0.00 0.00 0.00 0.98
3047 6013 8.450964 CCTCCCGTAATTTTGCATACTATTATG 58.549 37.037 0.00 0.00 38.57 1.90
3048 6014 8.911918 TCCCGTAATTTTGCATACTATTATGT 57.088 30.769 2.45 0.00 37.92 2.29
3049 6015 9.344772 TCCCGTAATTTTGCATACTATTATGTT 57.655 29.630 2.45 0.00 37.92 2.71
3050 6016 9.959749 CCCGTAATTTTGCATACTATTATGTTT 57.040 29.630 2.45 0.00 37.92 2.83
3065 6031 7.931948 ACTATTATGTTTTTAGTAGCTCGGCAT 59.068 33.333 0.00 0.00 0.00 4.40
3066 6032 6.995511 TTATGTTTTTAGTAGCTCGGCATT 57.004 33.333 0.00 0.00 0.00 3.56
3067 6033 8.671384 ATTATGTTTTTAGTAGCTCGGCATTA 57.329 30.769 0.00 0.00 0.00 1.90
3068 6034 8.671384 TTATGTTTTTAGTAGCTCGGCATTAT 57.329 30.769 0.00 0.00 0.00 1.28
3069 6035 9.767228 TTATGTTTTTAGTAGCTCGGCATTATA 57.233 29.630 0.00 0.00 0.00 0.98
3070 6036 8.671384 ATGTTTTTAGTAGCTCGGCATTATAA 57.329 30.769 0.00 0.00 0.00 0.98
3071 6037 8.495361 TGTTTTTAGTAGCTCGGCATTATAAA 57.505 30.769 0.00 0.00 0.00 1.40
3072 6038 8.948145 TGTTTTTAGTAGCTCGGCATTATAAAA 58.052 29.630 0.00 0.00 0.00 1.52
3073 6039 9.946165 GTTTTTAGTAGCTCGGCATTATAAAAT 57.054 29.630 0.00 0.00 0.00 1.82
3074 6040 9.944663 TTTTTAGTAGCTCGGCATTATAAAATG 57.055 29.630 0.00 0.00 44.53 2.32
3075 6041 8.896320 TTTAGTAGCTCGGCATTATAAAATGA 57.104 30.769 0.00 0.00 44.50 2.57
3076 6042 8.896320 TTAGTAGCTCGGCATTATAAAATGAA 57.104 30.769 0.00 0.00 44.50 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 6.036300 ACGAACACAAAGACGACTCAAATTAA 59.964 34.615 0.00 0.00 0.00 1.40
25 26 1.067425 TGATTTGGTACACTCCCGACG 60.067 52.381 0.00 0.00 39.29 5.12
27 28 2.531771 TCTGATTTGGTACACTCCCGA 58.468 47.619 0.00 0.00 39.29 5.14
142 147 9.991906 TGTACTAGTATAAAGCAAGAAAGTGTT 57.008 29.630 5.75 0.00 0.00 3.32
2685 5650 5.624491 GGTAAGACGAGACAAATATAGACGC 59.376 44.000 0.00 0.00 0.00 5.19
2716 5681 4.222588 CCATTTGGGTGAAAAATGCTCCTA 59.777 41.667 3.84 0.00 41.58 2.94
2781 5746 6.971184 CCTAAAATGAGAATTCAGTCACATGC 59.029 38.462 8.44 0.00 36.61 4.06
2784 5749 5.415701 GGCCTAAAATGAGAATTCAGTCACA 59.584 40.000 8.44 0.53 36.61 3.58
2823 5788 1.087771 CCCGGACAAGACGCAATACC 61.088 60.000 0.73 0.00 0.00 2.73
2829 5795 2.029964 TTCACCCGGACAAGACGC 59.970 61.111 0.73 0.00 0.00 5.19
2850 5816 0.892755 AAACTCACCTGCATGCATGG 59.107 50.000 27.34 24.54 0.00 3.66
2860 5826 6.761242 GCAAAAATTTAACAGGAAACTCACCT 59.239 34.615 0.00 0.00 40.21 4.00
2938 5904 7.656542 TCAATTCATCAAGCAATGCAACTAAAA 59.343 29.630 8.35 0.00 0.00 1.52
3038 6004 8.415553 TGCCGAGCTACTAAAAACATAATAGTA 58.584 33.333 0.00 0.00 32.44 1.82
3039 6005 7.270047 TGCCGAGCTACTAAAAACATAATAGT 58.730 34.615 0.00 0.00 34.45 2.12
3040 6006 7.709269 TGCCGAGCTACTAAAAACATAATAG 57.291 36.000 0.00 0.00 0.00 1.73
3042 6008 7.568199 AATGCCGAGCTACTAAAAACATAAT 57.432 32.000 0.00 0.00 0.00 1.28
3043 6009 6.995511 AATGCCGAGCTACTAAAAACATAA 57.004 33.333 0.00 0.00 0.00 1.90
3044 6010 9.767228 TTATAATGCCGAGCTACTAAAAACATA 57.233 29.630 0.00 0.00 0.00 2.29
3045 6011 8.671384 TTATAATGCCGAGCTACTAAAAACAT 57.329 30.769 0.00 0.00 0.00 2.71
3047 6013 9.946165 ATTTTATAATGCCGAGCTACTAAAAAC 57.054 29.630 0.00 0.00 0.00 2.43
3048 6014 9.944663 CATTTTATAATGCCGAGCTACTAAAAA 57.055 29.630 0.00 0.00 35.15 1.94
3049 6015 9.332502 TCATTTTATAATGCCGAGCTACTAAAA 57.667 29.630 1.36 0.00 40.78 1.52
3050 6016 8.896320 TCATTTTATAATGCCGAGCTACTAAA 57.104 30.769 1.36 0.00 40.78 1.85
3051 6017 8.896320 TTCATTTTATAATGCCGAGCTACTAA 57.104 30.769 1.36 0.00 40.78 2.24
3052 6018 8.148351 ACTTCATTTTATAATGCCGAGCTACTA 58.852 33.333 1.36 0.00 40.78 1.82
3053 6019 6.992715 ACTTCATTTTATAATGCCGAGCTACT 59.007 34.615 1.36 0.00 40.78 2.57
3054 6020 7.190920 ACTTCATTTTATAATGCCGAGCTAC 57.809 36.000 1.36 0.00 40.78 3.58
3056 6022 7.986085 ATACTTCATTTTATAATGCCGAGCT 57.014 32.000 1.36 0.00 40.78 4.09
3093 6059 7.934665 TGGTGTGACACTAGTTAATGTTGTATT 59.065 33.333 16.07 0.00 34.40 1.89
3094 6060 7.446769 TGGTGTGACACTAGTTAATGTTGTAT 58.553 34.615 16.07 0.00 34.40 2.29
3096 6062 5.676552 TGGTGTGACACTAGTTAATGTTGT 58.323 37.500 16.07 0.00 34.40 3.32
3097 6063 6.228273 CTGGTGTGACACTAGTTAATGTTG 57.772 41.667 19.38 0.00 38.01 3.33


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

AutoCloner maintained by Alex Coulton.