Multiple sequence alignment - TraesCS1A01G317400

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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 TraesCS1A01G317400 chr1A 100.000 3209 0 0 1 3209 508837446 508840654 0.000000e+00 5927
1 TraesCS1A01G317400 chr1A 90.449 356 23 6 2056 2406 514687652 514688001 2.920000e-125 459
2 TraesCS1A01G317400 chr5A 96.795 3214 95 5 1 3209 363809028 363812238 0.000000e+00 5358
3 TraesCS1A01G317400 chr2A 96.565 3231 87 6 1 3209 192204218 192200990 0.000000e+00 5330
4 TraesCS1A01G317400 chr2A 82.386 352 47 9 198 545 650095352 650095692 3.130000e-75 292
5 TraesCS1A01G317400 chr2A 86.909 275 15 10 2947 3209 23652613 23652348 4.050000e-74 289
6 TraesCS1A01G317400 chr3D 93.639 2971 157 15 1 2950 380260325 380257366 0.000000e+00 4410
7 TraesCS1A01G317400 chr3D 95.455 88 4 0 2947 3034 380253151 380253064 1.200000e-29 141
8 TraesCS1A01G317400 chr6D 94.852 2642 114 11 1 2630 103674444 103671813 0.000000e+00 4106
9 TraesCS1A01G317400 chr6D 86.246 349 44 3 198 545 108148869 108149214 3.020000e-100 375
10 TraesCS1A01G317400 chr6D 94.819 193 5 2 3009 3201 103671816 103671629 2.420000e-76 296
11 TraesCS1A01G317400 chr7A 94.373 2186 103 7 1038 3209 742831 745010 0.000000e+00 3338
12 TraesCS1A01G317400 chr3B 92.363 2370 129 18 608 2950 743114575 743112231 0.000000e+00 3326
13 TraesCS1A01G317400 chr3B 90.299 268 14 4 2947 3209 820345808 820345548 1.100000e-89 340
14 TraesCS1A01G317400 chr7D 88.676 1616 144 16 501 2106 366759698 366761284 0.000000e+00 1934
15 TraesCS1A01G317400 chr6A 88.323 1610 144 21 501 2102 76276008 76274435 0.000000e+00 1892
16 TraesCS1A01G317400 chr6A 88.107 1606 144 16 501 2099 447878087 447879652 0.000000e+00 1864
17 TraesCS1A01G317400 chr6A 82.955 352 45 9 198 545 447893903 447894243 1.450000e-78 303
18 TraesCS1A01G317400 chr4A 88.067 1609 145 20 501 2102 419988802 419987234 0.000000e+00 1864
19 TraesCS1A01G317400 chr4A 89.972 359 25 7 2056 2409 104118946 104118594 1.360000e-123 453
20 TraesCS1A01G317400 chr5B 91.614 942 56 8 2031 2950 557302296 557301356 0.000000e+00 1280
21 TraesCS1A01G317400 chr5B 85.455 220 27 2 331 545 42176606 42176825 1.160000e-54 224
22 TraesCS1A01G317400 chr7B 90.329 517 41 4 2442 2950 547264560 547265075 0.000000e+00 669
23 TraesCS1A01G317400 chr7B 86.909 275 14 8 2947 3209 547265559 547265823 4.050000e-74 289
24 TraesCS1A01G317400 chr2B 90.135 517 42 5 2442 2950 34575467 34575982 0.000000e+00 664
25 TraesCS1A01G317400 chr2B 87.452 518 53 8 2442 2950 35380531 35381045 1.280000e-163 586
26 TraesCS1A01G317400 chr2B 90.196 357 28 3 2056 2406 35380208 35380563 2.920000e-125 459
27 TraesCS1A01G317400 chr2B 93.467 199 7 2 3009 3206 35381191 35381384 1.130000e-74 291
28 TraesCS1A01G317400 chr4B 83.476 351 41 11 198 545 357392663 357392327 8.640000e-81 311
29 TraesCS1A01G317400 chr1B 86.989 269 15 11 2949 3206 611692925 611693184 5.240000e-73 285


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 TraesCS1A01G317400 chr1A 508837446 508840654 3208 False 5927.000000 5927 100.000000 1 3209 1 chr1A.!!$F1 3208
1 TraesCS1A01G317400 chr5A 363809028 363812238 3210 False 5358.000000 5358 96.795000 1 3209 1 chr5A.!!$F1 3208
2 TraesCS1A01G317400 chr2A 192200990 192204218 3228 True 5330.000000 5330 96.565000 1 3209 1 chr2A.!!$R2 3208
3 TraesCS1A01G317400 chr3D 380257366 380260325 2959 True 4410.000000 4410 93.639000 1 2950 1 chr3D.!!$R2 2949
4 TraesCS1A01G317400 chr6D 103671629 103674444 2815 True 2201.000000 4106 94.835500 1 3201 2 chr6D.!!$R1 3200
5 TraesCS1A01G317400 chr7A 742831 745010 2179 False 3338.000000 3338 94.373000 1038 3209 1 chr7A.!!$F1 2171
6 TraesCS1A01G317400 chr3B 743112231 743114575 2344 True 3326.000000 3326 92.363000 608 2950 1 chr3B.!!$R1 2342
7 TraesCS1A01G317400 chr7D 366759698 366761284 1586 False 1934.000000 1934 88.676000 501 2106 1 chr7D.!!$F1 1605
8 TraesCS1A01G317400 chr6A 76274435 76276008 1573 True 1892.000000 1892 88.323000 501 2102 1 chr6A.!!$R1 1601
9 TraesCS1A01G317400 chr6A 447878087 447879652 1565 False 1864.000000 1864 88.107000 501 2099 1 chr6A.!!$F1 1598
10 TraesCS1A01G317400 chr4A 419987234 419988802 1568 True 1864.000000 1864 88.067000 501 2102 1 chr4A.!!$R2 1601
11 TraesCS1A01G317400 chr5B 557301356 557302296 940 True 1280.000000 1280 91.614000 2031 2950 1 chr5B.!!$R1 919
12 TraesCS1A01G317400 chr7B 547264560 547265823 1263 False 479.000000 669 88.619000 2442 3209 2 chr7B.!!$F1 767
13 TraesCS1A01G317400 chr2B 34575467 34575982 515 False 664.000000 664 90.135000 2442 2950 1 chr2B.!!$F1 508
14 TraesCS1A01G317400 chr2B 35380208 35381384 1176 False 445.333333 586 90.371667 2056 3206 3 chr2B.!!$F2 1150

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
252 253 1.139853 GAAATGCCCAACCACACCAAA 59.860 47.619 0.0 0.0 0.0 3.28 F
1052 1080 0.251253 TGCTGGTCATTGATGTGGCA 60.251 50.000 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2071 2103 1.793414 ATCCCCAAAAATAGGGCAGC 58.207 50.0 0.0 0.00 45.39 5.25 R
2263 2300 0.322816 GTGCCATCAGGTGACACCAT 60.323 55.0 26.3 9.46 41.95 3.55 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
95 96 3.962063 TCTAACACCACCTACAGACACAA 59.038 43.478 0.00 0.00 0.00 3.33
143 144 4.961438 TGATCTGGCAAGATACATGCTA 57.039 40.909 2.74 0.00 43.48 3.49
252 253 1.139853 GAAATGCCCAACCACACCAAA 59.860 47.619 0.00 0.00 0.00 3.28
270 271 4.973663 ACCAAAAACGCGAATTTAGTTCTG 59.026 37.500 15.93 8.25 34.56 3.02
325 326 3.648545 AGCCTTCTACAAGAGGTCAACTT 59.351 43.478 0.00 0.00 0.00 2.66
380 381 4.065088 TGCCAATCGTCTATTTAGATGCC 58.935 43.478 2.50 0.00 38.82 4.40
432 433 9.656040 ATGTACTATTTTTGTATGTGGTTACGA 57.344 29.630 0.00 0.00 0.00 3.43
528 529 8.089597 ACATCAAATGTTTTCAGTTCATGCATA 58.910 29.630 0.00 0.00 39.31 3.14
547 548 5.355071 TGCATAAGTTACAATCAAGCCAGAG 59.645 40.000 0.00 0.00 0.00 3.35
653 660 7.288810 TGTTTCTCAAACTAATTCTGCCATT 57.711 32.000 1.11 0.00 41.90 3.16
835 862 2.131854 AGAGAGCTAGAGACCCTGCTA 58.868 52.381 0.00 0.00 35.76 3.49
840 867 3.050089 AGCTAGAGACCCTGCTACTCTA 58.950 50.000 0.00 0.00 40.70 2.43
913 941 6.183360 TGCTTCTTCATTTGGAAAAGTTAGCA 60.183 34.615 0.00 0.00 36.92 3.49
1052 1080 0.251253 TGCTGGTCATTGATGTGGCA 60.251 50.000 0.00 0.00 0.00 4.92
1128 1156 0.904865 AGGCTGTTCACGAGGATCCA 60.905 55.000 15.82 0.00 0.00 3.41
1205 1234 3.264193 TCAGGTTGTAATCTGATGGTGCT 59.736 43.478 3.53 0.00 35.37 4.40
1263 1292 6.127083 GGGATCTATTTTTGATTGGCCAAAGA 60.127 38.462 24.71 17.96 37.34 2.52
1311 1340 7.848223 TTAACATGATGCTATAATGCGCTAT 57.152 32.000 9.73 1.01 35.36 2.97
1716 1748 3.909732 TGGATTTCTTTCCTGTTGGTGT 58.090 40.909 0.00 0.00 36.68 4.16
2116 2148 3.963733 TCCAGGCTGGAATCAACAG 57.036 52.632 33.38 4.43 45.00 3.16
2280 2317 0.749454 GGATGGTGTCACCTGATGGC 60.749 60.000 22.56 5.83 39.58 4.40
2291 2336 0.036105 CCTGATGGCACTGTGCTACA 60.036 55.000 29.54 20.96 44.28 2.74
2375 2420 2.234908 TCTTCTTCAGGCCTGTAGCTTC 59.765 50.000 31.58 0.00 43.05 3.86
2388 2433 4.380531 CTGTAGCTTCTGGTTTCAGTCAA 58.619 43.478 0.00 0.00 41.59 3.18
2418 2463 1.002468 GTCGCATTGTCTTGCAACAGT 60.002 47.619 0.00 0.00 42.91 3.55
2439 2484 3.006537 GTGAGTGACTGCTGGGTTAACTA 59.993 47.826 5.42 0.00 0.00 2.24
2488 2533 1.872952 TGCATTTTCAGTCGGACACAG 59.127 47.619 11.27 0.00 0.00 3.66
2539 2585 0.454452 CGCACTCTCATCGTTCGTCA 60.454 55.000 0.00 0.00 0.00 4.35
2542 2588 2.732282 GCACTCTCATCGTTCGTCATCA 60.732 50.000 0.00 0.00 0.00 3.07
2590 2636 3.055675 TGGGGTGGATGAAAGTTAGTACG 60.056 47.826 0.00 0.00 0.00 3.67
2791 2840 2.648059 GGTACTCACCTCCGCTTACTA 58.352 52.381 0.00 0.00 42.11 1.82
2845 2903 5.178797 GCTTCAACTCCAGCTAACAATCTA 58.821 41.667 0.00 0.00 32.87 1.98
2848 2906 7.476540 TTCAACTCCAGCTAACAATCTACTA 57.523 36.000 0.00 0.00 0.00 1.82
2868 2926 2.124277 ATAAGAAAGCGGTCCCAACC 57.876 50.000 0.00 0.00 42.66 3.77
2898 2956 6.636666 ATGCATTCAAAAAGCATTCTAACG 57.363 33.333 0.00 0.00 45.98 3.18
2974 3519 8.328146 CAACCTCAAATTGTACGTAGTCATATG 58.672 37.037 0.00 0.00 43.93 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 0.611618 TGCACCTTGATCCGCCATTT 60.612 50.000 0.00 0.00 0.00 2.32
143 144 0.178891 ACACTGGGAGATGAGTGGGT 60.179 55.000 0.00 0.00 43.33 4.51
229 230 1.347378 GGTGTGGTTGGGCATTTCATT 59.653 47.619 0.00 0.00 0.00 2.57
252 253 3.889196 TGCAGAACTAAATTCGCGTTT 57.111 38.095 5.77 2.49 42.69 3.60
270 271 0.734889 CCTCGTTGATTCCACCATGC 59.265 55.000 0.00 0.00 0.00 4.06
325 326 8.504812 TGCACATAGCTAAATGATTTGAACTA 57.495 30.769 10.90 0.43 45.94 2.24
407 408 9.656040 ATCGTAACCACATACAAAAATAGTACA 57.344 29.630 0.00 0.00 0.00 2.90
434 435 9.851686 ACTGCATGTTTTCTAATCTTATCCATA 57.148 29.630 0.00 0.00 0.00 2.74
446 447 5.153513 GCGATTTGAACTGCATGTTTTCTA 58.846 37.500 0.00 0.00 39.30 2.10
457 458 2.523015 GCTTGATGGCGATTTGAACTG 58.477 47.619 0.00 0.00 0.00 3.16
478 479 5.098211 GCTTAACATTCAAAGGACTGATGC 58.902 41.667 0.00 0.00 0.00 3.91
528 529 4.973168 TGTCTCTGGCTTGATTGTAACTT 58.027 39.130 0.00 0.00 0.00 2.66
653 660 4.716287 TCATGGTGATGTCACTCCTAATCA 59.284 41.667 12.43 1.59 45.73 2.57
840 867 9.883142 TTTGTGTTCTCAAATTTAACATCCTTT 57.117 25.926 7.96 0.00 35.72 3.11
913 941 3.387374 TGCAACATCAAACTCCCAACAAT 59.613 39.130 0.00 0.00 0.00 2.71
1052 1080 2.359230 GCTGCAAGAGCCCGACTT 60.359 61.111 0.00 0.00 42.54 3.01
1205 1234 3.491276 CCAAATCAAAGCAGAGCAACACA 60.491 43.478 0.00 0.00 0.00 3.72
1263 1292 3.324993 CAAACGGCAGCAAATAAACCAT 58.675 40.909 0.00 0.00 0.00 3.55
1270 1299 3.127589 GTTAAACCAAACGGCAGCAAAT 58.872 40.909 0.00 0.00 0.00 2.32
1311 1340 8.547481 TTGTACTGGAATAACATATCTCTCCA 57.453 34.615 0.00 0.00 0.00 3.86
1716 1748 7.721842 TGAAAGAACCACCTGAACATACAATTA 59.278 33.333 0.00 0.00 0.00 1.40
2071 2103 1.793414 ATCCCCAAAAATAGGGCAGC 58.207 50.000 0.00 0.00 45.39 5.25
2116 2148 3.567478 AGACTGAAGATTATGTGGGCC 57.433 47.619 0.00 0.00 0.00 5.80
2263 2300 0.322816 GTGCCATCAGGTGACACCAT 60.323 55.000 26.30 9.46 41.95 3.55
2280 2317 3.443329 ACATCTCTCTCTGTAGCACAGTG 59.557 47.826 13.59 11.88 46.03 3.66
2291 2336 4.630644 TGCTGGAAAAACATCTCTCTCT 57.369 40.909 0.00 0.00 0.00 3.10
2375 2420 8.009974 CGACTTTAACTATTTGACTGAAACCAG 58.990 37.037 0.00 0.00 37.67 4.00
2388 2433 6.314784 GCAAGACAATGCGACTTTAACTATT 58.685 36.000 0.00 0.00 36.45 1.73
2418 2463 2.047061 AGTTAACCCAGCAGTCACTCA 58.953 47.619 0.88 0.00 0.00 3.41
2439 2484 4.906618 ACTATCCGACTGAAACCACAAAT 58.093 39.130 0.00 0.00 0.00 2.32
2539 2585 7.223971 GCATGAATAACTTCAACATTGCATGAT 59.776 33.333 0.00 0.00 44.29 2.45
2542 2588 5.517411 CGCATGAATAACTTCAACATTGCAT 59.483 36.000 0.00 0.00 44.29 3.96
2590 2636 3.067833 GGACAACCAAAGTGCTAGTCTC 58.932 50.000 0.00 0.00 35.97 3.36
2816 2874 6.649155 TGTTAGCTGGAGTTGAAGCATATTA 58.351 36.000 0.00 0.00 42.06 0.98
2817 2875 5.500234 TGTTAGCTGGAGTTGAAGCATATT 58.500 37.500 0.00 0.00 42.06 1.28
2845 2903 4.259356 GTTGGGACCGCTTTCTTATTAGT 58.741 43.478 0.00 0.00 0.00 2.24
2848 2906 2.443416 GGTTGGGACCGCTTTCTTATT 58.557 47.619 0.00 0.00 35.91 1.40
2898 2956 7.333672 ACTTGGTCCTCTAATTCGTTTGATAAC 59.666 37.037 0.00 0.00 0.00 1.89
3131 3687 7.996644 CCCTGGTTAACATATTTACTACCACAT 59.003 37.037 8.10 0.00 31.43 3.21
3140 3696 3.887352 TGCGCCCTGGTTAACATATTTA 58.113 40.909 4.18 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.