Multiple sequence alignment - TraesCS4D01G130300

Loading Multiple Alignment...

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 TraesCS4D01G130300 chr4D 100.000 3203 0 0 1 3203 116269213 116272415 0.000000e+00 5915.0
1 TraesCS4D01G130300 chr4D 83.230 161 20 4 2380 2534 309696844 309697003 1.200000e-29 141.0
2 TraesCS4D01G130300 chr4D 83.673 98 14 2 2379 2475 268329760 268329664 1.220000e-14 91.6
3 TraesCS4D01G130300 chr4A 94.510 3242 103 28 1 3203 460241176 460237971 0.000000e+00 4931.0
4 TraesCS4D01G130300 chr4A 77.696 408 68 17 200 596 664913201 664913596 8.940000e-56 228.0
5 TraesCS4D01G130300 chr4A 82.432 148 20 3 2379 2520 511022950 511022803 1.210000e-24 124.0
6 TraesCS4D01G130300 chr4B 96.080 2551 69 16 676 3203 178070826 178073368 0.000000e+00 4128.0
7 TraesCS4D01G130300 chr4B 90.594 606 38 11 1 593 178069690 178070289 0.000000e+00 785.0
8 TraesCS4D01G130300 chr4B 93.258 89 6 0 590 678 178070440 178070528 7.210000e-27 132.0
9 TraesCS4D01G130300 chr3D 81.562 640 73 23 1 613 511054676 511055297 1.340000e-133 486.0
10 TraesCS4D01G130300 chr3D 90.385 52 4 1 239 290 455722855 455722905 2.060000e-07 67.6
11 TraesCS4D01G130300 chr3B 76.030 534 104 19 1232 1747 822880797 822880270 4.100000e-64 255.0
12 TraesCS4D01G130300 chrUn 77.913 412 65 17 200 599 86551986 86551589 1.920000e-57 233.0
13 TraesCS4D01G130300 chrUn 86.207 87 12 0 1844 1930 92295502 92295416 9.460000e-16 95.3
14 TraesCS4D01G130300 chrUn 77.419 155 33 2 1823 1976 478426581 478426428 1.220000e-14 91.6
15 TraesCS4D01G130300 chr1B 87.013 154 18 1 2375 2528 491543496 491543345 4.250000e-39 172.0
16 TraesCS4D01G130300 chr1B 82.812 128 18 2 1630 1756 226357872 226357748 9.390000e-21 111.0
17 TraesCS4D01G130300 chr7D 77.409 301 36 16 4 279 89019744 89019451 1.990000e-32 150.0
18 TraesCS4D01G130300 chr7D 83.766 154 20 2 2380 2528 509926457 509926304 1.200000e-29 141.0
19 TraesCS4D01G130300 chr7D 77.419 155 33 2 1823 1976 194225355 194225508 1.220000e-14 91.6
20 TraesCS4D01G130300 chr2D 82.703 185 13 4 2380 2545 593512649 593512465 2.570000e-31 147.0
21 TraesCS4D01G130300 chr2D 73.042 549 82 39 104 599 406710292 406709757 2.000000e-27 134.0
22 TraesCS4D01G130300 chr2D 80.851 94 17 1 1670 1762 39320893 39320800 4.430000e-09 73.1
23 TraesCS4D01G130300 chr2D 79.381 97 19 1 1667 1762 50238187 50238283 2.060000e-07 67.6
24 TraesCS4D01G130300 chr1A 82.993 147 19 3 2380 2521 443660972 443660827 9.330000e-26 128.0
25 TraesCS4D01G130300 chr1A 80.000 165 30 1 1586 1750 229169898 229169737 5.610000e-23 119.0
26 TraesCS4D01G130300 chr1A 94.030 67 2 2 2470 2535 58202853 58202788 2.030000e-17 100.0
27 TraesCS4D01G130300 chr1D 80.606 165 29 1 1586 1750 171162868 171162707 1.210000e-24 124.0
28 TraesCS4D01G130300 chr6B 87.500 96 9 2 2379 2472 415861588 415861682 1.210000e-19 108.0
29 TraesCS4D01G130300 chr6A 78.235 170 35 2 1818 1986 570382455 570382287 1.210000e-19 108.0
30 TraesCS4D01G130300 chr5D 77.720 193 26 5 1 178 515111965 515112155 5.650000e-18 102.0
31 TraesCS4D01G130300 chr7B 83.654 104 17 0 200 303 529145587 529145484 7.310000e-17 99.0
32 TraesCS4D01G130300 chr7B 77.419 155 33 2 1823 1976 158076115 158076268 1.220000e-14 91.6
33 TraesCS4D01G130300 chr7A 86.047 86 12 0 1844 1929 202852809 202852724 3.400000e-15 93.5
34 TraesCS4D01G130300 chr7A 76.129 155 35 2 1823 1976 203864464 203864617 2.650000e-11 80.5
35 TraesCS4D01G130300 chr2B 80.851 94 17 1 1670 1762 77995056 77994963 4.430000e-09 73.1
36 TraesCS4D01G130300 chr2A 80.412 97 18 1 1667 1762 51945270 51945366 4.430000e-09 73.1
37 TraesCS4D01G130300 chr3A 87.755 49 6 0 245 293 44704641 44704593 1.240000e-04 58.4


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 TraesCS4D01G130300 chr4D 116269213 116272415 3202 False 5915.000000 5915 100.000000 1 3203 1 chr4D.!!$F1 3202
1 TraesCS4D01G130300 chr4A 460237971 460241176 3205 True 4931.000000 4931 94.510000 1 3203 1 chr4A.!!$R1 3202
2 TraesCS4D01G130300 chr4B 178069690 178073368 3678 False 1681.666667 4128 93.310667 1 3203 3 chr4B.!!$F1 3202
3 TraesCS4D01G130300 chr3D 511054676 511055297 621 False 486.000000 486 81.562000 1 613 1 chr3D.!!$F2 612
4 TraesCS4D01G130300 chr3B 822880270 822880797 527 True 255.000000 255 76.030000 1232 1747 1 chr3B.!!$R1 515

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
650 847 1.468565 GCGCATGCACAAATGACAGAT 60.469 47.619 19.57 0.0 42.15 2.90 F
1809 2321 1.000612 GGAGGAGGAGAAGGACGGT 59.999 63.158 0.00 0.0 0.00 4.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2178 2693 0.179108 GTGACGTGTATCTGGGAGCC 60.179 60.0 0.0 0.0 0.0 4.70 R
2981 3520 2.858344 CGACCAAAATCCGTACTAGCTG 59.142 50.0 0.0 0.0 0.0 4.24 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
39 40 8.050778 ACACTTGTTCTTTCACAATACTGAAA 57.949 30.769 0.00 0.00 37.73 2.69
241 260 6.215845 ACTTACATTCACAATGCCAAGTTTC 58.784 36.000 9.45 0.00 41.15 2.78
243 262 7.230510 ACTTACATTCACAATGCCAAGTTTCTA 59.769 33.333 9.45 0.00 41.15 2.10
283 303 2.748209 AGGGTAATACCAATGCCCAC 57.252 50.000 12.03 0.00 41.02 4.61
292 312 5.697082 ATACCAATGCCCACAATTCATTT 57.303 34.783 0.00 0.00 0.00 2.32
304 324 7.492344 GCCCACAATTCATTTTACCTTAGAATG 59.508 37.037 0.00 0.00 33.24 2.67
378 419 8.745464 TTACAACGAATTTTATTTAACCAGGC 57.255 30.769 0.00 0.00 0.00 4.85
438 479 8.889717 CCGTAGTGTAAGAATATTGTGGAAATT 58.110 33.333 0.00 0.00 0.00 1.82
470 511 8.085296 TGACCAATGTAATTTATTGTGTGGTTC 58.915 33.333 11.73 0.00 31.22 3.62
648 845 2.355797 GCGCATGCACAAATGACAG 58.644 52.632 19.57 0.00 42.15 3.51
650 847 1.468565 GCGCATGCACAAATGACAGAT 60.469 47.619 19.57 0.00 42.15 2.90
731 1228 7.346471 CCTGAATAGATTAGAAGTTTTCCCCA 58.654 38.462 0.00 0.00 0.00 4.96
791 1288 8.475639 AGGAATAGCTCGAATTTACAAGTAAGA 58.524 33.333 0.00 0.00 0.00 2.10
929 1426 3.830192 GCCAAATCGCCCTGCCTG 61.830 66.667 0.00 0.00 0.00 4.85
1809 2321 1.000612 GGAGGAGGAGAAGGACGGT 59.999 63.158 0.00 0.00 0.00 4.83
2178 2693 2.101770 GCCGACGACTTACCCTCG 59.898 66.667 0.00 0.00 37.17 4.63
2251 2766 5.867174 GGCTAACATTGTGTGGTTTTTATCC 59.133 40.000 0.00 0.00 0.00 2.59
2498 3024 9.032420 GTAGTCCGTATTGAAATCTCTAAAAGG 57.968 37.037 0.00 0.00 0.00 3.11
2628 3156 3.056107 GGGAGACTACATGTACAGCAACA 60.056 47.826 0.08 0.00 0.00 3.33
2759 3290 7.835682 AGTGATCACCATGAATCATTAAAGGAA 59.164 33.333 22.21 0.00 0.00 3.36
2764 3295 8.259411 TCACCATGAATCATTAAAGGAAAATGG 58.741 33.333 4.58 12.75 35.48 3.16
2923 3456 3.452474 GACAGCATACATCTCACACCTC 58.548 50.000 0.00 0.00 0.00 3.85
2943 3476 3.098555 CGCCGACCAACCAATAGC 58.901 61.111 0.00 0.00 0.00 2.97
2979 3518 3.958704 ACGCTAATCAGAATCTGACTCG 58.041 45.455 15.96 16.80 43.63 4.18
2981 3520 3.971871 CGCTAATCAGAATCTGACTCGAC 59.028 47.826 15.96 3.83 43.63 4.20
3102 3641 2.556144 TGAGAACTGAAGCTGCACAT 57.444 45.000 1.02 0.00 0.00 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
220 239 7.701539 ATAGAAACTTGGCATTGTGAATGTA 57.298 32.000 0.00 0.00 41.01 2.29
243 262 8.712228 ACCCTAAAGAAGAAAGAACATGAAAT 57.288 30.769 0.00 0.00 0.00 2.17
367 408 3.385111 TCAACAAAACGGCCTGGTTAAAT 59.615 39.130 0.00 0.00 0.00 1.40
378 419 6.362283 GTGTGGAATTAAGATCAACAAAACGG 59.638 38.462 3.49 0.00 32.69 4.44
574 616 4.637483 ACAAGTATATTTGCTTGCGCAT 57.363 36.364 12.75 0.00 46.09 4.73
577 619 8.667987 TTTCTTAACAAGTATATTTGCTTGCG 57.332 30.769 12.58 1.96 46.09 4.85
741 1238 7.032377 TGCTTTTCTTTTCCTTTTCTCTCTC 57.968 36.000 0.00 0.00 0.00 3.20
743 1240 6.039829 TCCTGCTTTTCTTTTCCTTTTCTCTC 59.960 38.462 0.00 0.00 0.00 3.20
744 1241 5.893824 TCCTGCTTTTCTTTTCCTTTTCTCT 59.106 36.000 0.00 0.00 0.00 3.10
745 1242 6.149129 TCCTGCTTTTCTTTTCCTTTTCTC 57.851 37.500 0.00 0.00 0.00 2.87
929 1426 0.743097 GGGTGATCAGGAAGCAATGC 59.257 55.000 0.00 0.00 0.00 3.56
1788 2300 2.440430 TCCTTCTCCTCCTCCGCG 60.440 66.667 0.00 0.00 0.00 6.46
1809 2321 3.014085 GCCCATCACCCTCGACGAA 62.014 63.158 0.00 0.00 0.00 3.85
2091 2603 0.543277 CCTCCTCCTGCAAGCACATA 59.457 55.000 0.00 0.00 0.00 2.29
2178 2693 0.179108 GTGACGTGTATCTGGGAGCC 60.179 60.000 0.00 0.00 0.00 4.70
2251 2766 0.817013 AATGTTAGCCAATGCCACCG 59.183 50.000 0.00 0.00 38.69 4.94
2436 2962 7.928706 AGAGCGTATATTCACTTATTTTGCTCT 59.071 33.333 0.00 0.00 46.63 4.09
2454 2980 7.082602 CGGACTACACATATTTTAGAGCGTAT 58.917 38.462 0.00 0.00 0.00 3.06
2478 3004 6.927294 AGCCCTTTTAGAGATTTCAATACG 57.073 37.500 0.00 0.00 0.00 3.06
2498 3024 5.861727 TCCCTCCGTTTCTAAATATAAGCC 58.138 41.667 0.00 0.00 0.00 4.35
2802 3335 3.889196 TGAAAATGAACGCAGTGGTAC 57.111 42.857 0.00 0.00 45.00 3.34
2943 3476 4.235762 CGTCCATAGGCCCCCGTG 62.236 72.222 0.00 0.00 0.00 4.94
2979 3518 3.858247 ACCAAAATCCGTACTAGCTGTC 58.142 45.455 0.00 0.00 0.00 3.51
2981 3520 2.858344 CGACCAAAATCCGTACTAGCTG 59.142 50.000 0.00 0.00 0.00 4.24
3102 3641 6.371548 CGAAAGGTCTAACATTTGATTCCTCA 59.628 38.462 0.00 0.00 31.73 3.86
3168 3707 8.677148 TTGCTTCTTTATACTTTGTGAAGACT 57.323 30.769 0.00 0.00 36.69 3.24


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

AutoCloner maintained by Alex Coulton.