Multiple sequence alignment - TraesCS7A01G286500

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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 TraesCS7A01G286500 chr7A 100.000 2200 0 0 1 2200 335986010 335988209 0.000000e+00 4063
1 TraesCS7A01G286500 chr7B 93.832 2221 104 11 1 2191 339214980 339212763 0.000000e+00 3312
2 TraesCS7A01G286500 chr7B 89.189 111 9 3 328 436 71616749 71616640 3.810000e-28 135
3 TraesCS7A01G286500 chr7B 87.826 115 11 3 327 439 687407540 687407427 4.930000e-27 132
4 TraesCS7A01G286500 chr7D 93.551 2233 106 15 1 2200 295320916 295318689 0.000000e+00 3291
5 TraesCS7A01G286500 chr7D 78.821 916 159 22 1298 2198 290613598 290612703 3.150000e-163 584
6 TraesCS7A01G286500 chr7D 90.452 199 16 2 110 305 237412849 237412651 2.170000e-65 259
7 TraesCS7A01G286500 chr7D 95.455 88 3 1 327 414 237412577 237412663 2.950000e-29 139
8 TraesCS7A01G286500 chr4A 80.690 1854 286 42 400 2198 637695869 637697705 0.000000e+00 1375
9 TraesCS7A01G286500 chr4A 79.890 726 131 13 395 1113 736383797 736383080 3.240000e-143 518
10 TraesCS7A01G286500 chr4A 89.756 205 19 2 109 311 3883728 3883524 6.020000e-66 261
11 TraesCS7A01G286500 chr5A 78.777 1701 294 46 551 2198 328833899 328832213 0.000000e+00 1079
12 TraesCS7A01G286500 chr5A 86.307 796 105 2 1407 2198 331754570 331753775 0.000000e+00 863
13 TraesCS7A01G286500 chr1A 86.381 771 97 5 1435 2198 30263380 30262611 0.000000e+00 835
14 TraesCS7A01G286500 chr1A 78.743 668 133 6 498 1160 137881721 137882384 2.590000e-119 438
15 TraesCS7A01G286500 chr2B 85.342 805 105 5 1407 2198 358767128 358766324 0.000000e+00 821
16 TraesCS7A01G286500 chr2B 90.909 198 16 2 110 305 603410181 603410378 4.660000e-67 265
17 TraesCS7A01G286500 chr2B 94.681 94 3 2 322 414 603410458 603410366 6.330000e-31 145
18 TraesCS7A01G286500 chr2A 85.440 728 99 5 1468 2190 25260546 25259821 0.000000e+00 750
19 TraesCS7A01G286500 chr2A 85.363 731 95 10 1468 2190 25213340 25212614 0.000000e+00 747
20 TraesCS7A01G286500 chr2A 91.133 203 13 5 106 305 716504308 716504108 1.000000e-68 270
21 TraesCS7A01G286500 chr1D 80.729 768 135 12 395 1155 382734975 382735736 8.750000e-164 586
22 TraesCS7A01G286500 chr1D 78.431 663 134 7 503 1160 24583862 24583204 7.260000e-115 424
23 TraesCS7A01G286500 chr5B 81.590 717 122 8 399 1110 37785229 37785940 3.150000e-163 584
24 TraesCS7A01G286500 chr5B 81.111 720 126 10 399 1113 18343486 18342772 3.170000e-158 568
25 TraesCS7A01G286500 chr3B 90.955 199 16 2 109 305 696745240 696745042 1.290000e-67 267
26 TraesCS7A01G286500 chr3B 96.552 87 2 1 328 414 817426341 817426256 2.280000e-30 143
27 TraesCS7A01G286500 chr3B 95.455 88 3 1 327 414 763250315 763250401 2.950000e-29 139
28 TraesCS7A01G286500 chr5D 89.950 199 20 0 107 305 2748814 2749012 7.790000e-65 257
29 TraesCS7A01G286500 chr6B 88.372 215 20 5 106 318 67465713 67465502 1.010000e-63 254
30 TraesCS7A01G286500 chr4B 93.617 94 4 2 322 414 187444236 187444328 2.950000e-29 139


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 TraesCS7A01G286500 chr7A 335986010 335988209 2199 False 4063 4063 100.000 1 2200 1 chr7A.!!$F1 2199
1 TraesCS7A01G286500 chr7B 339212763 339214980 2217 True 3312 3312 93.832 1 2191 1 chr7B.!!$R2 2190
2 TraesCS7A01G286500 chr7D 295318689 295320916 2227 True 3291 3291 93.551 1 2200 1 chr7D.!!$R3 2199
3 TraesCS7A01G286500 chr7D 290612703 290613598 895 True 584 584 78.821 1298 2198 1 chr7D.!!$R2 900
4 TraesCS7A01G286500 chr4A 637695869 637697705 1836 False 1375 1375 80.690 400 2198 1 chr4A.!!$F1 1798
5 TraesCS7A01G286500 chr4A 736383080 736383797 717 True 518 518 79.890 395 1113 1 chr4A.!!$R2 718
6 TraesCS7A01G286500 chr5A 328832213 328833899 1686 True 1079 1079 78.777 551 2198 1 chr5A.!!$R1 1647
7 TraesCS7A01G286500 chr5A 331753775 331754570 795 True 863 863 86.307 1407 2198 1 chr5A.!!$R2 791
8 TraesCS7A01G286500 chr1A 30262611 30263380 769 True 835 835 86.381 1435 2198 1 chr1A.!!$R1 763
9 TraesCS7A01G286500 chr1A 137881721 137882384 663 False 438 438 78.743 498 1160 1 chr1A.!!$F1 662
10 TraesCS7A01G286500 chr2B 358766324 358767128 804 True 821 821 85.342 1407 2198 1 chr2B.!!$R1 791
11 TraesCS7A01G286500 chr2A 25259821 25260546 725 True 750 750 85.440 1468 2190 1 chr2A.!!$R2 722
12 TraesCS7A01G286500 chr2A 25212614 25213340 726 True 747 747 85.363 1468 2190 1 chr2A.!!$R1 722
13 TraesCS7A01G286500 chr1D 382734975 382735736 761 False 586 586 80.729 395 1155 1 chr1D.!!$F1 760
14 TraesCS7A01G286500 chr1D 24583204 24583862 658 True 424 424 78.431 503 1160 1 chr1D.!!$R1 657
15 TraesCS7A01G286500 chr5B 37785229 37785940 711 False 584 584 81.590 399 1110 1 chr5B.!!$F1 711
16 TraesCS7A01G286500 chr5B 18342772 18343486 714 True 568 568 81.111 399 1113 1 chr5B.!!$R1 714


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
990 995 0.320374 TCGTTTCCTTCATCGTGGCT 59.68 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2030 0.610232 GTGCCACCTTTCAGCAGGAT 60.61 55.0 0.0 0.0 37.15 3.24 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
110 112 0.941542 GCACAGAAAACGTGGCACTA 59.058 50.000 16.72 0.00 34.85 2.74
126 128 4.275689 TGGCACTATTGAATTTATGCTCCG 59.724 41.667 7.57 0.00 33.57 4.63
146 148 2.519013 GGCCAACTCATCCAAAAGTCT 58.481 47.619 0.00 0.00 0.00 3.24
218 220 7.013083 CGTCTAGGCTTATTTAGTCCTTAGACA 59.987 40.741 0.00 0.00 46.15 3.41
240 242 1.680860 GGGTTTTATGTAGGCCGCAGT 60.681 52.381 8.88 0.00 0.00 4.40
251 253 4.573201 TGTAGGCCGCAGTATATTTGTTTC 59.427 41.667 0.00 0.00 0.00 2.78
414 416 5.523552 TGAATTCAACATGGTATACAGAGCG 59.476 40.000 5.45 0.00 0.00 5.03
556 560 2.163815 CGGACGAACTATGTTCTCTGGT 59.836 50.000 8.51 0.00 0.00 4.00
614 618 8.551440 TGGCTTGTATGGCTATATAGATCAAAT 58.449 33.333 14.16 1.99 0.00 2.32
680 685 0.978146 AAGGACCAGGTGATCCCGAG 60.978 60.000 0.00 0.00 38.74 4.63
736 741 3.689649 GCAAATCATCGTGTACCTCCTTT 59.310 43.478 0.00 0.00 0.00 3.11
802 807 2.202919 CGCATGCCATCTGGACGA 60.203 61.111 13.15 0.00 37.39 4.20
803 808 1.596203 CGCATGCCATCTGGACGAT 60.596 57.895 13.15 0.00 37.39 3.73
937 942 1.118965 TGCTCCCTCCGACAAACTCA 61.119 55.000 0.00 0.00 0.00 3.41
990 995 0.320374 TCGTTTCCTTCATCGTGGCT 59.680 50.000 0.00 0.00 0.00 4.75
1487 1549 2.583143 ACTAACCACCTTGCCAAAGAC 58.417 47.619 0.00 0.00 35.19 3.01
1567 1629 5.532557 TGATGCTTCTTATGGTGTCGATAG 58.467 41.667 0.88 0.00 0.00 2.08
1579 1641 4.574421 TGGTGTCGATAGCAATTGGTATTG 59.426 41.667 28.12 28.12 43.28 1.90
1585 1647 6.425114 GTCGATAGCAATTGGTATTGAGACAT 59.575 38.462 33.28 14.28 44.77 3.06
1617 1679 4.753516 AATCATATCACCGGTGAACTCA 57.246 40.909 39.04 24.25 43.58 3.41
1666 1730 2.636893 GGCCATGATCAGATCTACACCT 59.363 50.000 11.83 0.00 0.00 4.00
1668 1732 3.613671 GCCATGATCAGATCTACACCTCG 60.614 52.174 11.83 0.00 0.00 4.63
1927 1993 6.670695 TCTATGCATTGCTTCCTCAGTATA 57.329 37.500 3.54 0.00 0.00 1.47
1928 1994 7.250032 TCTATGCATTGCTTCCTCAGTATAT 57.750 36.000 3.54 0.00 0.00 0.86
1962 2030 0.111061 AAGTCTGGTGCCATCAAGCA 59.889 50.000 0.00 0.00 41.46 3.91
1964 2032 0.737219 GTCTGGTGCCATCAAGCATC 59.263 55.000 0.00 0.00 46.24 3.91
1983 2051 1.108727 CCTGCTGAAAGGTGGCACAA 61.109 55.000 20.82 0.00 44.16 3.33
2057 2127 2.814280 ACTCGTAGTTGTTGGTGAGG 57.186 50.000 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 4.642445 TTCTGTGCATGATAATGGCTTG 57.358 40.909 0.00 0.00 0.00 4.01
110 112 2.665165 TGGCCGGAGCATAAATTCAAT 58.335 42.857 5.05 0.00 42.56 2.57
126 128 2.229784 CAGACTTTTGGATGAGTTGGCC 59.770 50.000 0.00 0.00 0.00 5.36
146 148 1.186200 CGTCTCCCTCCATCAGTTCA 58.814 55.000 0.00 0.00 0.00 3.18
218 220 1.064314 TGCGGCCTACATAAAACCCAT 60.064 47.619 0.00 0.00 0.00 4.00
414 416 1.072965 CTAGATGTGATGGAAGGGCCC 59.927 57.143 16.46 16.46 34.97 5.80
556 560 2.735772 GGGATCCCGCTTGAGCTCA 61.736 63.158 17.02 13.74 39.32 4.26
614 618 0.716591 TTTGGGAGGCTCCTCTAGGA 59.283 55.000 31.39 10.43 42.38 2.94
680 685 3.907130 ATGGGGCATAGGCAGGGC 61.907 66.667 0.15 0.00 43.71 5.19
802 807 3.079578 CTGAGAACATGGTGCTCAACAT 58.920 45.455 8.33 0.00 46.27 2.71
803 808 2.497138 CTGAGAACATGGTGCTCAACA 58.503 47.619 8.33 0.00 46.27 3.33
966 971 1.272490 ACGATGAAGGAAACGAGCTCA 59.728 47.619 15.40 0.00 0.00 4.26
1197 1203 3.081409 GCCACCGCCTCCCTTCTA 61.081 66.667 0.00 0.00 0.00 2.10
1567 1629 3.491447 GCCCATGTCTCAATACCAATTGC 60.491 47.826 0.00 0.00 41.96 3.56
1579 1641 1.599542 GATTTGTAGCGCCCATGTCTC 59.400 52.381 2.29 0.00 0.00 3.36
1585 1647 3.138304 GTGATATGATTTGTAGCGCCCA 58.862 45.455 2.29 0.00 0.00 5.36
1617 1679 5.796424 ATTTTTCATGCAGTCACCTTCTT 57.204 34.783 0.00 0.00 0.00 2.52
1666 1730 1.920734 ATACCTGCACCATTGGCCGA 61.921 55.000 1.54 0.00 0.00 5.54
1668 1732 1.394266 CCATACCTGCACCATTGGCC 61.394 60.000 1.54 0.00 0.00 5.36
1716 1780 6.195600 ACTAGACTTTTATGTGGGGTTTCA 57.804 37.500 0.00 0.00 0.00 2.69
1927 1993 7.651808 CACCAGACTTGTTTATTGAGTTGAAT 58.348 34.615 0.00 0.00 0.00 2.57
1928 1994 6.459573 GCACCAGACTTGTTTATTGAGTTGAA 60.460 38.462 0.00 0.00 0.00 2.69
1962 2030 0.610232 GTGCCACCTTTCAGCAGGAT 60.610 55.000 0.00 0.00 37.15 3.24
1964 2032 1.108727 TTGTGCCACCTTTCAGCAGG 61.109 55.000 0.00 0.00 37.15 4.85
1983 2051 1.710809 ACAAGGGATGGCCTAAACAGT 59.289 47.619 3.32 0.00 0.00 3.55
2057 2127 9.912634 TGAATCACAAATAGTTTCTGAATTTCC 57.087 29.630 0.00 0.00 0.00 3.13



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

AutoCloner maintained by Alex Coulton.