Multiple sequence alignment - TraesCS7D01G120100

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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 TraesCS7D01G120100 chr7D 100.000 3490 0 0 1 3490 74468039 74464550 0.000000e+00 6445.0
1 TraesCS7D01G120100 chr7D 96.233 1938 58 6 1 1925 609646284 609644349 0.000000e+00 3160.0
2 TraesCS7D01G120100 chr7D 95.283 1060 48 2 2433 3490 609635223 609634164 0.000000e+00 1679.0
3 TraesCS7D01G120100 chr7D 92.424 396 30 0 1920 2315 609635618 609635223 1.820000e-157 566.0
4 TraesCS7D01G120100 chr7D 95.652 46 2 0 2261 2306 74465733 74465688 1.340000e-09 75.0
5 TraesCS7D01G120100 chr7D 95.652 46 2 0 2307 2352 74465779 74465734 1.340000e-09 75.0
6 TraesCS7D01G120100 chr7D 97.619 42 1 0 2307 2348 609635277 609635236 4.830000e-09 73.1
7 TraesCS7D01G120100 chr3D 96.029 2317 75 6 1 2306 31007738 31010048 0.000000e+00 3753.0
8 TraesCS7D01G120100 chr3D 95.943 2317 79 5 1 2306 31032113 31034425 0.000000e+00 3744.0
9 TraesCS7D01G120100 chr3D 97.072 1981 42 6 1 1969 30989672 30991648 0.000000e+00 3323.0
10 TraesCS7D01G120100 chr3D 96.453 1184 40 2 2307 3490 31034380 31035561 0.000000e+00 1953.0
11 TraesCS7D01G120100 chr3D 96.115 1184 44 2 2307 3490 31010003 31011184 0.000000e+00 1930.0
12 TraesCS7D01G120100 chr3D 93.512 447 29 0 2307 2753 30992234 30992680 0.000000e+00 665.0
13 TraesCS7D01G120100 chr3D 94.643 336 17 1 1971 2306 30991945 30992279 1.440000e-143 520.0
14 TraesCS7D01G120100 chr5D 95.508 2315 86 7 4 2306 542243247 542240939 0.000000e+00 3683.0
15 TraesCS7D01G120100 chr5D 96.368 1184 42 1 2307 3490 542232284 542231102 0.000000e+00 1947.0
16 TraesCS7D01G120100 chr5D 95.608 1184 51 1 2307 3490 542240984 542239802 0.000000e+00 1897.0
17 TraesCS7D01G120100 chr5D 93.541 418 24 3 1889 2306 542232653 542232239 1.380000e-173 619.0
18 TraesCS7D01G120100 chr2D 95.489 2106 82 7 217 2310 15400105 15402209 0.000000e+00 3350.0
19 TraesCS7D01G120100 chr2D 95.767 1063 44 1 2429 3490 15402210 15403272 0.000000e+00 1712.0
20 TraesCS7D01G120100 chr2D 98.361 61 1 0 1 61 15400050 15400110 1.320000e-19 108.0
21 TraesCS7D01G120100 chr2D 97.436 39 1 0 2307 2345 15402160 15402198 2.250000e-07 67.6
22 TraesCS7D01G120100 chr2B 93.759 1378 83 2 930 2306 797775460 797776835 0.000000e+00 2065.0
23 TraesCS7D01G120100 chr2B 94.439 1025 56 1 2466 3490 797777024 797778047 0.000000e+00 1576.0
24 TraesCS7D01G120100 chr2B 93.060 562 27 2 110 661 797774906 797775465 0.000000e+00 811.0
25 TraesCS7D01G120100 chr2B 94.468 235 13 0 2307 2541 797776790 797777024 2.560000e-96 363.0


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 TraesCS7D01G120100 chr7D 74464550 74468039 3489 True 2198.333333 6445 97.101333 1 3490 3 chr7D.!!$R2 3489
1 TraesCS7D01G120100 chr7D 609644349 609646284 1935 True 3160.000000 3160 96.233000 1 1925 1 chr7D.!!$R1 1924
2 TraesCS7D01G120100 chr7D 609634164 609635618 1454 True 772.700000 1679 95.108667 1920 3490 3 chr7D.!!$R3 1570
3 TraesCS7D01G120100 chr3D 31032113 31035561 3448 False 2848.500000 3744 96.198000 1 3490 2 chr3D.!!$F3 3489
4 TraesCS7D01G120100 chr3D 31007738 31011184 3446 False 2841.500000 3753 96.072000 1 3490 2 chr3D.!!$F2 3489
5 TraesCS7D01G120100 chr3D 30989672 30992680 3008 False 1502.666667 3323 95.075667 1 2753 3 chr3D.!!$F1 2752
6 TraesCS7D01G120100 chr5D 542239802 542243247 3445 True 2790.000000 3683 95.558000 4 3490 2 chr5D.!!$R2 3486
7 TraesCS7D01G120100 chr5D 542231102 542232653 1551 True 1283.000000 1947 94.954500 1889 3490 2 chr5D.!!$R1 1601
8 TraesCS7D01G120100 chr2D 15400050 15403272 3222 False 1309.400000 3350 96.763250 1 3490 4 chr2D.!!$F1 3489
9 TraesCS7D01G120100 chr2B 797774906 797778047 3141 False 1203.750000 2065 93.931500 110 3490 4 chr2B.!!$F1 3380

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
761 775 5.049749 CCATCGTTTGTGTGTAGAAATCACA 60.050 40.000 0.0 0.0 42.41 3.58 F
1446 1461 0.620556 ATCTTCTGGAACCGCCACAT 59.379 50.000 0.0 0.0 43.33 3.21 F
2265 2580 1.202405 GGATGCCATTAAGGTTTGCCG 60.202 52.381 0.0 0.0 40.61 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1617 1635 1.150536 ACGCTCCCTTGGCTTCAAA 59.849 52.632 0.00 0.0 0.0 2.69 R
2372 2687 1.742831 GGCGGATGTGAATTGTAGCAA 59.257 47.619 0.00 0.0 0.0 3.91 R
3366 3760 1.966451 CCAGGGTCCTGAAACACGC 60.966 63.158 17.91 0.0 46.3 5.34 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
182 183 5.200368 TGATTAGCTTGCGATCTCATGTA 57.800 39.130 0.00 0.00 0.00 2.29
464 475 6.864421 TGGTCAGACTATATGATAAGAGGGT 58.136 40.000 0.00 0.00 0.00 4.34
556 567 6.118170 AGTGCTAATCATATGCTGAAACAGT 58.882 36.000 0.00 0.00 37.44 3.55
761 775 5.049749 CCATCGTTTGTGTGTAGAAATCACA 60.050 40.000 0.00 0.00 42.41 3.58
1173 1188 9.098355 CAGGTAATGATTCGTGAAGATTTTCTA 57.902 33.333 0.00 0.00 34.31 2.10
1310 1325 1.336125 GAACCTCCTGCATATTGCTGC 59.664 52.381 0.75 0.00 45.31 5.25
1446 1461 0.620556 ATCTTCTGGAACCGCCACAT 59.379 50.000 0.00 0.00 43.33 3.21
1617 1635 4.380867 GCGAAGAAAAATCCATGTGGTGAT 60.381 41.667 0.00 0.00 36.34 3.06
2137 2452 9.976511 AATAGCATATGAAGTCATCAAATTTGG 57.023 29.630 17.90 3.33 42.54 3.28
2138 2453 7.414222 AGCATATGAAGTCATCAAATTTGGT 57.586 32.000 17.90 8.39 42.54 3.67
2265 2580 1.202405 GGATGCCATTAAGGTTTGCCG 60.202 52.381 0.00 0.00 40.61 5.69
2266 2581 1.748493 GATGCCATTAAGGTTTGCCGA 59.252 47.619 0.00 0.00 40.61 5.54
2267 2582 1.846007 TGCCATTAAGGTTTGCCGAT 58.154 45.000 0.00 0.00 40.61 4.18
2268 2583 3.006112 TGCCATTAAGGTTTGCCGATA 57.994 42.857 0.00 0.00 40.61 2.92
2269 2584 3.561143 TGCCATTAAGGTTTGCCGATAT 58.439 40.909 0.00 0.00 40.61 1.63
2270 2585 3.317711 TGCCATTAAGGTTTGCCGATATG 59.682 43.478 0.00 0.00 40.61 1.78
2271 2586 3.317993 GCCATTAAGGTTTGCCGATATGT 59.682 43.478 0.00 0.00 40.61 2.29
2272 2587 4.202111 GCCATTAAGGTTTGCCGATATGTT 60.202 41.667 0.00 0.00 40.61 2.71
2273 2588 5.009210 GCCATTAAGGTTTGCCGATATGTTA 59.991 40.000 0.00 0.00 40.61 2.41
2274 2589 6.460399 GCCATTAAGGTTTGCCGATATGTTAA 60.460 38.462 0.00 0.00 40.61 2.01
2275 2590 7.484975 CCATTAAGGTTTGCCGATATGTTAAA 58.515 34.615 0.00 0.00 40.50 1.52
2276 2591 8.141268 CCATTAAGGTTTGCCGATATGTTAAAT 58.859 33.333 0.00 0.00 40.50 1.40
2277 2592 8.967218 CATTAAGGTTTGCCGATATGTTAAATG 58.033 33.333 0.00 0.00 40.50 2.32
2278 2593 6.524101 AAGGTTTGCCGATATGTTAAATGT 57.476 33.333 0.00 0.00 40.50 2.71
2279 2594 6.524101 AGGTTTGCCGATATGTTAAATGTT 57.476 33.333 0.00 0.00 40.50 2.71
2280 2595 6.329496 AGGTTTGCCGATATGTTAAATGTTG 58.671 36.000 0.00 0.00 40.50 3.33
2281 2596 6.071616 AGGTTTGCCGATATGTTAAATGTTGT 60.072 34.615 0.00 0.00 40.50 3.32
2282 2597 6.252655 GGTTTGCCGATATGTTAAATGTTGTC 59.747 38.462 0.00 0.00 0.00 3.18
2283 2598 5.150342 TGCCGATATGTTAAATGTTGTCG 57.850 39.130 0.00 0.00 0.00 4.35
2284 2599 4.632251 TGCCGATATGTTAAATGTTGTCGT 59.368 37.500 0.00 0.00 0.00 4.34
2285 2600 5.195379 GCCGATATGTTAAATGTTGTCGTC 58.805 41.667 0.00 0.00 0.00 4.20
2286 2601 5.220510 GCCGATATGTTAAATGTTGTCGTCA 60.221 40.000 0.00 0.00 0.00 4.35
2287 2602 6.511121 GCCGATATGTTAAATGTTGTCGTCAT 60.511 38.462 0.00 0.00 0.00 3.06
2288 2603 6.845782 CCGATATGTTAAATGTTGTCGTCATG 59.154 38.462 0.00 0.00 0.00 3.07
2289 2604 7.254286 CCGATATGTTAAATGTTGTCGTCATGA 60.254 37.037 0.00 0.00 0.00 3.07
2290 2605 8.113675 CGATATGTTAAATGTTGTCGTCATGAA 58.886 33.333 0.00 0.00 0.00 2.57
2291 2606 9.210426 GATATGTTAAATGTTGTCGTCATGAAC 57.790 33.333 0.00 0.00 0.00 3.18
2292 2607 5.753744 TGTTAAATGTTGTCGTCATGAACC 58.246 37.500 0.00 0.00 0.00 3.62
2293 2608 5.297029 TGTTAAATGTTGTCGTCATGAACCA 59.703 36.000 0.00 0.00 0.00 3.67
2294 2609 6.016693 TGTTAAATGTTGTCGTCATGAACCAT 60.017 34.615 0.00 0.00 0.00 3.55
2295 2610 4.424061 AATGTTGTCGTCATGAACCATG 57.576 40.909 0.00 0.74 42.60 3.66
2296 2611 2.844946 TGTTGTCGTCATGAACCATGT 58.155 42.857 0.00 0.00 41.98 3.21
2297 2612 3.996480 TGTTGTCGTCATGAACCATGTA 58.004 40.909 0.00 0.00 41.98 2.29
2298 2613 4.574892 TGTTGTCGTCATGAACCATGTAT 58.425 39.130 0.00 0.00 41.98 2.29
2299 2614 4.629634 TGTTGTCGTCATGAACCATGTATC 59.370 41.667 0.00 0.00 41.98 2.24
2300 2615 4.736126 TGTCGTCATGAACCATGTATCT 57.264 40.909 0.00 0.00 41.98 1.98
2301 2616 5.845391 TGTCGTCATGAACCATGTATCTA 57.155 39.130 0.00 0.00 41.98 1.98
2302 2617 5.588240 TGTCGTCATGAACCATGTATCTAC 58.412 41.667 0.00 0.00 41.98 2.59
2303 2618 4.675565 GTCGTCATGAACCATGTATCTACG 59.324 45.833 0.00 8.66 41.98 3.51
2304 2619 4.337274 TCGTCATGAACCATGTATCTACGT 59.663 41.667 0.00 0.00 41.98 3.57
2305 2620 4.675565 CGTCATGAACCATGTATCTACGTC 59.324 45.833 0.00 0.00 41.98 4.34
2306 2621 5.505819 CGTCATGAACCATGTATCTACGTCT 60.506 44.000 0.00 0.00 41.98 4.18
2307 2622 6.273825 GTCATGAACCATGTATCTACGTCTT 58.726 40.000 0.00 0.00 41.98 3.01
2308 2623 6.199154 GTCATGAACCATGTATCTACGTCTTG 59.801 42.308 0.00 0.00 41.98 3.02
2309 2624 4.430007 TGAACCATGTATCTACGTCTTGC 58.570 43.478 0.00 0.00 0.00 4.01
2310 2625 3.454371 ACCATGTATCTACGTCTTGCC 57.546 47.619 0.00 0.00 0.00 4.52
2348 2663 6.902224 TGTCGTCATGAACCATGTATTTAG 57.098 37.500 0.00 0.00 41.98 1.85
2352 2667 5.051039 CGTCATGAACCATGTATTTAGGTCG 60.051 44.000 0.00 0.00 41.98 4.79
2364 2679 3.492421 TTTAGGTCGTCATACGTGGAC 57.508 47.619 11.01 11.01 43.14 4.02
2392 2707 1.378531 TGCTACAATTCACATCCGCC 58.621 50.000 0.00 0.00 0.00 6.13
2426 2741 6.697395 ACATGGTTTAAATTTACTTGCCTCC 58.303 36.000 0.00 0.00 0.00 4.30
2448 2763 3.861276 TGTGACCTATCTGTTGGTACG 57.139 47.619 0.00 0.00 36.59 3.67
2714 3106 8.962679 TGGATTTTACATAGACCATGTTTTACC 58.037 33.333 0.00 0.00 46.01 2.85
3366 3760 9.599866 TGATTGTTCACTAATATACCTTGTCTG 57.400 33.333 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
182 183 8.229253 AGATGAACAAATGCACACACATATAT 57.771 30.769 0.00 0.00 0.00 0.86
315 316 5.056480 CAGAAGACTTGTTGTACACATGGA 58.944 41.667 0.00 0.00 35.30 3.41
524 535 5.126869 AGCATATGATTAGCACTCTCGCTAT 59.873 40.000 6.97 0.00 43.77 2.97
556 567 3.565010 GGGGGATGACCTCGGTATGTATA 60.565 52.174 0.00 0.00 37.58 1.47
1310 1325 1.067669 TCGCTTTCATGAGATCCTCGG 59.932 52.381 0.00 0.00 32.35 4.63
1514 1532 4.057428 GTCTCACGGACGCTGGCT 62.057 66.667 0.00 0.00 35.07 4.75
1617 1635 1.150536 ACGCTCCCTTGGCTTCAAA 59.849 52.632 0.00 0.00 0.00 2.69
2113 2428 8.407832 CACCAAATTTGATGACTTCATATGCTA 58.592 33.333 19.86 0.00 36.57 3.49
2162 2477 7.542025 AGATCGTACAGGAAGTAATTTTACGT 58.458 34.615 0.00 0.00 38.65 3.57
2265 2580 9.210426 GTTCATGACGACAACATTTAACATATC 57.790 33.333 0.00 0.00 0.00 1.63
2266 2581 8.181573 GGTTCATGACGACAACATTTAACATAT 58.818 33.333 0.00 0.00 0.00 1.78
2267 2582 7.173390 TGGTTCATGACGACAACATTTAACATA 59.827 33.333 0.00 0.00 0.00 2.29
2268 2583 6.016693 TGGTTCATGACGACAACATTTAACAT 60.017 34.615 0.00 0.00 0.00 2.71
2269 2584 5.297029 TGGTTCATGACGACAACATTTAACA 59.703 36.000 0.00 0.00 0.00 2.41
2270 2585 5.753744 TGGTTCATGACGACAACATTTAAC 58.246 37.500 0.00 0.00 0.00 2.01
2271 2586 6.016693 ACATGGTTCATGACGACAACATTTAA 60.017 34.615 13.96 0.00 43.81 1.52
2272 2587 5.471797 ACATGGTTCATGACGACAACATTTA 59.528 36.000 13.96 0.00 43.81 1.40
2273 2588 4.278170 ACATGGTTCATGACGACAACATTT 59.722 37.500 13.96 0.00 43.81 2.32
2274 2589 3.820467 ACATGGTTCATGACGACAACATT 59.180 39.130 13.96 0.00 43.81 2.71
2275 2590 3.411446 ACATGGTTCATGACGACAACAT 58.589 40.909 13.96 0.00 43.81 2.71
2276 2591 2.844946 ACATGGTTCATGACGACAACA 58.155 42.857 13.96 0.00 43.81 3.33
2277 2592 4.870426 AGATACATGGTTCATGACGACAAC 59.130 41.667 13.96 0.00 43.81 3.32
2278 2593 5.084818 AGATACATGGTTCATGACGACAA 57.915 39.130 13.96 0.00 43.81 3.18
2279 2594 4.736126 AGATACATGGTTCATGACGACA 57.264 40.909 13.96 0.00 43.81 4.35
2280 2595 4.675565 CGTAGATACATGGTTCATGACGAC 59.324 45.833 13.96 0.00 43.81 4.34
2281 2596 4.337274 ACGTAGATACATGGTTCATGACGA 59.663 41.667 18.80 5.65 43.81 4.20
2282 2597 4.607955 ACGTAGATACATGGTTCATGACG 58.392 43.478 13.96 13.74 43.81 4.35
2283 2598 5.833082 AGACGTAGATACATGGTTCATGAC 58.167 41.667 13.96 5.88 43.81 3.06
2284 2599 6.273071 CAAGACGTAGATACATGGTTCATGA 58.727 40.000 13.96 0.00 43.81 3.07
2285 2600 5.050769 GCAAGACGTAGATACATGGTTCATG 60.051 44.000 6.37 6.37 46.18 3.07
2286 2601 5.050490 GCAAGACGTAGATACATGGTTCAT 58.950 41.667 0.00 0.00 0.00 2.57
2287 2602 4.430007 GCAAGACGTAGATACATGGTTCA 58.570 43.478 0.00 0.00 0.00 3.18
2288 2603 3.802685 GGCAAGACGTAGATACATGGTTC 59.197 47.826 0.00 0.00 0.00 3.62
2289 2604 3.737047 CGGCAAGACGTAGATACATGGTT 60.737 47.826 0.00 0.00 0.00 3.67
2290 2605 2.223735 CGGCAAGACGTAGATACATGGT 60.224 50.000 0.00 0.00 0.00 3.55
2291 2606 2.034179 TCGGCAAGACGTAGATACATGG 59.966 50.000 0.00 0.00 34.94 3.66
2292 2607 3.349488 TCGGCAAGACGTAGATACATG 57.651 47.619 0.00 0.00 34.94 3.21
2293 2608 5.183331 ACATATCGGCAAGACGTAGATACAT 59.817 40.000 0.00 0.00 34.94 2.29
2294 2609 4.517832 ACATATCGGCAAGACGTAGATACA 59.482 41.667 0.00 0.00 34.94 2.29
2295 2610 5.044428 ACATATCGGCAAGACGTAGATAC 57.956 43.478 0.00 0.00 34.94 2.24
2296 2611 5.700722 AACATATCGGCAAGACGTAGATA 57.299 39.130 0.00 0.00 34.94 1.98
2297 2612 4.585955 AACATATCGGCAAGACGTAGAT 57.414 40.909 0.00 0.00 34.94 1.98
2298 2613 5.503662 TTAACATATCGGCAAGACGTAGA 57.496 39.130 0.00 0.00 34.94 2.59
2299 2614 6.200286 ACATTTAACATATCGGCAAGACGTAG 59.800 38.462 0.00 0.00 34.94 3.51
2300 2615 6.044046 ACATTTAACATATCGGCAAGACGTA 58.956 36.000 0.00 0.00 34.94 3.57
2301 2616 4.873827 ACATTTAACATATCGGCAAGACGT 59.126 37.500 0.00 0.00 34.94 4.34
2302 2617 5.403897 ACATTTAACATATCGGCAAGACG 57.596 39.130 0.00 0.00 0.00 4.18
2303 2618 6.551736 ACAACATTTAACATATCGGCAAGAC 58.448 36.000 0.00 0.00 0.00 3.01
2304 2619 6.456315 CGACAACATTTAACATATCGGCAAGA 60.456 38.462 0.00 0.00 0.00 3.02
2305 2620 5.676744 CGACAACATTTAACATATCGGCAAG 59.323 40.000 0.00 0.00 0.00 4.01
2306 2621 5.122554 ACGACAACATTTAACATATCGGCAA 59.877 36.000 0.00 0.00 32.78 4.52
2307 2622 4.632251 ACGACAACATTTAACATATCGGCA 59.368 37.500 0.00 0.00 32.78 5.69
2308 2623 5.151632 ACGACAACATTTAACATATCGGC 57.848 39.130 0.00 0.00 32.78 5.54
2309 2624 6.339194 TGACGACAACATTTAACATATCGG 57.661 37.500 0.00 0.00 32.78 4.18
2310 2625 7.617557 TCATGACGACAACATTTAACATATCG 58.382 34.615 0.00 0.00 0.00 2.92
2364 2679 4.793071 TGTGAATTGTAGCAAAATCCACG 58.207 39.130 0.00 0.00 0.00 4.94
2372 2687 1.742831 GGCGGATGTGAATTGTAGCAA 59.257 47.619 0.00 0.00 0.00 3.91
2426 2741 4.112634 CGTACCAACAGATAGGTCACATG 58.887 47.826 0.00 0.00 39.31 3.21
2448 2763 5.275881 GCATCACGCAACATTTTAGCATTAC 60.276 40.000 0.00 0.00 41.79 1.89
2677 3069 9.906660 GTCTATGTAAAATCCAACATGAAACAA 57.093 29.630 0.00 0.00 36.96 2.83
3139 3533 4.228210 TGATCTGTTAAGAATGGAGGCCTT 59.772 41.667 6.77 0.00 35.59 4.35
3366 3760 1.966451 CCAGGGTCCTGAAACACGC 60.966 63.158 17.91 0.00 46.30 5.34


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

AutoCloner maintained by Alex Coulton.