Multiple sequence alignment - TraesCS7D01G323700

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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 TraesCS7D01G323700 chr7D 100.000 2765 0 0 1 2765 413443474 413440710 0.000000e+00 5107
1 TraesCS7D01G323700 chr7A 94.526 2466 92 17 324 2765 475167389 475164943 0.000000e+00 3766
2 TraesCS7D01G323700 chr7A 87.342 316 18 10 1 302 475167681 475167374 2.640000e-90 342
3 TraesCS7D01G323700 chr7A 85.345 116 17 0 2643 2758 727462836 727462721 1.340000e-23 121
4 TraesCS7D01G323700 chr7B 93.049 1827 73 30 641 2434 427823051 427821246 0.000000e+00 2621
5 TraesCS7D01G323700 chr7B 92.059 340 13 1 324 649 427823482 427823143 1.500000e-127 466
6 TraesCS7D01G323700 chr7B 90.616 341 28 3 2421 2758 427814381 427814042 1.510000e-122 449
7 TraesCS7D01G323700 chr7B 89.032 310 14 10 1 301 427823766 427823468 1.560000e-97 366
8 TraesCS7D01G323700 chr3D 82.609 368 48 11 2397 2758 171131641 171131284 7.440000e-81 311
9 TraesCS7D01G323700 chr3D 83.274 281 41 4 2476 2756 300779703 300779977 1.270000e-63 254
10 TraesCS7D01G323700 chr6D 82.029 345 52 7 2421 2763 277856641 277856977 4.510000e-73 285
11 TraesCS7D01G323700 chr6A 82.692 312 44 6 2385 2693 401220806 401221110 4.540000e-68 268
12 TraesCS7D01G323700 chr3B 81.690 284 44 6 2476 2758 420404674 420404398 2.140000e-56 230
13 TraesCS7D01G323700 chr1D 80.583 309 50 7 2382 2686 433780463 433780161 2.140000e-56 230
14 TraesCS7D01G323700 chr4B 77.719 377 63 14 2388 2756 412111168 412110805 7.760000e-51 211
15 TraesCS7D01G323700 chr2A 84.298 121 14 4 383 499 2768358 2768239 2.250000e-21 113


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 TraesCS7D01G323700 chr7D 413440710 413443474 2764 True 5107 5107 100.000 1 2765 1 chr7D.!!$R1 2764
1 TraesCS7D01G323700 chr7A 475164943 475167681 2738 True 2054 3766 90.934 1 2765 2 chr7A.!!$R2 2764
2 TraesCS7D01G323700 chr7B 427821246 427823766 2520 True 1151 2621 91.380 1 2434 3 chr7B.!!$R2 2433

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
25 26 0.373024 GCTCAAGTCAGAATCTGCGC 59.627 55.0 5.18 0.0 0.0 6.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1794 1943 0.316204 AGTAGCCACGCGTGTAACTT 59.684 50.0 34.81 18.32 31.75 2.66 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
24 25 1.005340 GGCTCAAGTCAGAATCTGCG 58.995 55.000 5.18 0.00 0.00 5.18
25 26 0.373024 GCTCAAGTCAGAATCTGCGC 59.627 55.000 5.18 0.00 0.00 6.09
53 59 2.703416 TCCATCGATGCATATTCCAGC 58.297 47.619 20.25 0.00 0.00 4.85
61 67 4.874396 CGATGCATATTCCAGCAGATACAT 59.126 41.667 0.00 0.00 44.94 2.29
84 90 8.099537 ACATTTAATCTAGCTAGCTACATGCAT 58.900 33.333 20.67 6.67 45.94 3.96
94 100 1.727511 CTACATGCATGGGCCCGTTG 61.728 60.000 29.41 17.29 40.13 4.10
149 155 6.475402 ACAACACACCTTCGAATCAAAAATTC 59.525 34.615 0.00 0.00 0.00 2.17
150 156 5.528870 ACACACCTTCGAATCAAAAATTCC 58.471 37.500 0.00 0.00 0.00 3.01
152 158 6.488683 ACACACCTTCGAATCAAAAATTCCTA 59.511 34.615 0.00 0.00 0.00 2.94
154 160 6.030228 CACCTTCGAATCAAAAATTCCTAGC 58.970 40.000 0.00 0.00 0.00 3.42
175 188 6.809976 AGCTAGCTAGGTTACAAAATACCT 57.190 37.500 17.69 1.47 46.28 3.08
186 199 8.422566 AGGTTACAAAATACCTAGAGTATCTGC 58.577 37.037 0.00 0.00 42.87 4.26
299 314 1.281419 TGCCCGACTAATCCTGGAAA 58.719 50.000 0.00 0.00 0.00 3.13
300 315 1.631388 TGCCCGACTAATCCTGGAAAA 59.369 47.619 0.00 0.00 0.00 2.29
301 316 2.241176 TGCCCGACTAATCCTGGAAAAT 59.759 45.455 0.00 0.00 0.00 1.82
302 317 2.879026 GCCCGACTAATCCTGGAAAATC 59.121 50.000 0.00 0.00 0.00 2.17
303 318 3.477530 CCCGACTAATCCTGGAAAATCC 58.522 50.000 0.00 0.00 36.96 3.01
304 319 3.136626 CCCGACTAATCCTGGAAAATCCT 59.863 47.826 0.00 0.00 37.46 3.24
305 320 4.130118 CCGACTAATCCTGGAAAATCCTG 58.870 47.826 0.00 0.00 37.46 3.86
306 321 3.561725 CGACTAATCCTGGAAAATCCTGC 59.438 47.826 0.00 0.00 37.46 4.85
307 322 4.526970 GACTAATCCTGGAAAATCCTGCA 58.473 43.478 0.00 0.00 37.46 4.41
308 323 4.530875 ACTAATCCTGGAAAATCCTGCAG 58.469 43.478 6.78 6.78 37.46 4.41
309 324 3.463048 AATCCTGGAAAATCCTGCAGT 57.537 42.857 13.81 0.00 37.46 4.40
310 325 2.978156 TCCTGGAAAATCCTGCAGTT 57.022 45.000 13.81 0.00 37.46 3.16
311 326 4.591321 ATCCTGGAAAATCCTGCAGTTA 57.409 40.909 13.81 0.00 37.46 2.24
312 327 3.686016 TCCTGGAAAATCCTGCAGTTAC 58.314 45.455 13.81 1.15 37.46 2.50
313 328 2.420022 CCTGGAAAATCCTGCAGTTACG 59.580 50.000 13.81 0.00 37.46 3.18
314 329 2.420022 CTGGAAAATCCTGCAGTTACGG 59.580 50.000 13.81 2.03 37.46 4.02
315 330 2.224670 TGGAAAATCCTGCAGTTACGGT 60.225 45.455 13.81 0.00 37.46 4.83
316 331 2.418976 GGAAAATCCTGCAGTTACGGTC 59.581 50.000 13.81 2.66 32.53 4.79
317 332 2.851263 AAATCCTGCAGTTACGGTCA 57.149 45.000 13.81 0.00 0.00 4.02
318 333 2.851263 AATCCTGCAGTTACGGTCAA 57.149 45.000 13.81 0.00 0.00 3.18
319 334 2.851263 ATCCTGCAGTTACGGTCAAA 57.149 45.000 13.81 0.00 0.00 2.69
320 335 2.623878 TCCTGCAGTTACGGTCAAAA 57.376 45.000 13.81 0.00 0.00 2.44
321 336 2.920524 TCCTGCAGTTACGGTCAAAAA 58.079 42.857 13.81 0.00 0.00 1.94
473 502 1.006571 TTCTTCGGTCGTCAGTGCC 60.007 57.895 0.00 0.00 0.00 5.01
624 654 4.170292 TCAAAGTTACGTAGTGAGAGGC 57.830 45.455 0.00 0.00 45.73 4.70
628 658 2.816087 AGTTACGTAGTGAGAGGCGAAA 59.184 45.455 0.00 0.00 45.73 3.46
846 985 0.393808 AGAGAGGAGAGGAGACACGC 60.394 60.000 0.00 0.00 0.00 5.34
894 1033 5.657474 ACACTTGAAGAACGTTTCTCACTA 58.343 37.500 0.46 0.00 39.61 2.74
960 1099 1.799403 CGACGTCGACCAGCTATCTAT 59.201 52.381 33.35 0.00 43.02 1.98
1106 1249 1.826709 TCCACAAGGACTCGCACAA 59.173 52.632 0.00 0.00 39.61 3.33
1290 1433 2.046604 CCGTTCCCGTTCTTCCCC 60.047 66.667 0.00 0.00 0.00 4.81
1299 1442 1.002011 GTTCTTCCCCCAGCAGTCC 60.002 63.158 0.00 0.00 0.00 3.85
1488 1634 0.741221 GTGTTCATCGTGGAGGGCTC 60.741 60.000 0.00 0.00 0.00 4.70
1518 1664 1.472662 CGGGCATCCTATCTCCGGTT 61.473 60.000 0.00 0.00 37.35 4.44
1692 1841 4.938832 CCAATGTCGTTACAGTATTTCCCA 59.061 41.667 0.00 0.00 39.49 4.37
1747 1896 5.178797 ACTATTGGGATCTCTTCAACAACG 58.821 41.667 0.00 0.00 0.00 4.10
1794 1943 2.280119 GACTGCGTGTGGTCAGCA 60.280 61.111 0.00 0.00 39.25 4.41
1818 1967 1.226603 CACGCGTGGCTACTACTCC 60.227 63.158 31.15 0.00 0.00 3.85
1983 2149 7.515998 GCGAAGACATTAAGAGCAAGTTAGATC 60.516 40.741 0.00 0.00 0.00 2.75
2142 2323 8.050778 AGGTGATCGATGATAGAGAATTAGAC 57.949 38.462 0.54 0.00 0.00 2.59
2176 2357 7.904558 ATGGAAGACTCTCAACTGATGTATA 57.095 36.000 0.00 0.00 0.00 1.47
2177 2358 7.904558 TGGAAGACTCTCAACTGATGTATAT 57.095 36.000 0.00 0.00 0.00 0.86
2373 2554 1.611006 GAGCATCTCTAGCCGATCACA 59.389 52.381 0.00 0.00 0.00 3.58
2465 2646 7.236529 ACCCCTAAAACTTAACTCCCTAAAAG 58.763 38.462 0.00 0.00 0.00 2.27
2482 2663 6.936335 CCCTAAAAGAAACATTTGCCAATTCT 59.064 34.615 0.00 0.00 31.98 2.40
2647 2831 3.559238 CACGAAAGGGTCCAAATGAAG 57.441 47.619 0.00 0.00 0.00 3.02
2648 2832 2.884639 CACGAAAGGGTCCAAATGAAGT 59.115 45.455 0.00 0.00 0.00 3.01
2649 2833 4.069304 CACGAAAGGGTCCAAATGAAGTA 58.931 43.478 0.00 0.00 0.00 2.24
2650 2834 4.517453 CACGAAAGGGTCCAAATGAAGTAA 59.483 41.667 0.00 0.00 0.00 2.24
2651 2835 5.009210 CACGAAAGGGTCCAAATGAAGTAAA 59.991 40.000 0.00 0.00 0.00 2.01
2652 2836 5.240844 ACGAAAGGGTCCAAATGAAGTAAAG 59.759 40.000 0.00 0.00 0.00 1.85
2653 2837 5.472137 CGAAAGGGTCCAAATGAAGTAAAGA 59.528 40.000 0.00 0.00 0.00 2.52
2654 2838 6.348540 CGAAAGGGTCCAAATGAAGTAAAGAG 60.349 42.308 0.00 0.00 0.00 2.85
2655 2839 4.336280 AGGGTCCAAATGAAGTAAAGAGC 58.664 43.478 0.00 0.00 0.00 4.09
2656 2840 4.079253 GGGTCCAAATGAAGTAAAGAGCA 58.921 43.478 0.00 0.00 0.00 4.26
2657 2841 4.706962 GGGTCCAAATGAAGTAAAGAGCAT 59.293 41.667 0.00 0.00 0.00 3.79
2658 2842 5.393461 GGGTCCAAATGAAGTAAAGAGCATG 60.393 44.000 0.00 0.00 0.00 4.06
2713 2897 1.476488 TGCTACTAATGCTCAGCACGA 59.524 47.619 0.00 0.00 43.04 4.35
2725 2909 0.935898 CAGCACGATCATCTTGGAGC 59.064 55.000 0.00 0.00 0.00 4.70
2743 2927 1.482593 AGCTGGGTATGAACTTCTCGG 59.517 52.381 0.00 0.00 0.00 4.63
2747 2931 2.094390 TGGGTATGAACTTCTCGGTTCG 60.094 50.000 0.00 0.00 45.90 3.95
2749 2933 1.582502 GTATGAACTTCTCGGTTCGCG 59.417 52.381 0.00 0.00 45.90 5.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.001293 TGCATCGATGGATCTACCTGC 59.999 52.381 26.00 10.26 39.86 4.85
25 26 3.606595 ATGCATCGATGGATCTACCTG 57.393 47.619 24.86 0.00 33.26 4.00
61 67 6.875726 CCATGCATGTAGCTAGCTAGATTAAA 59.124 38.462 27.11 17.36 45.94 1.52
94 100 0.250467 TGAAAGTGCAGAGGTGGAGC 60.250 55.000 0.00 0.00 0.00 4.70
103 109 4.082625 TGTTGCAGGATTATGAAAGTGCAG 60.083 41.667 0.00 0.00 41.61 4.41
150 156 7.953752 AGGTATTTTGTAACCTAGCTAGCTAG 58.046 38.462 35.39 35.39 44.40 3.42
152 158 6.809976 AGGTATTTTGTAACCTAGCTAGCT 57.190 37.500 23.12 23.12 44.40 3.32
212 225 4.379652 GTTGGTGAGGTGCAAATTTCATT 58.620 39.130 0.00 0.00 0.00 2.57
214 227 2.102252 GGTTGGTGAGGTGCAAATTTCA 59.898 45.455 0.00 0.00 0.00 2.69
299 314 2.851263 TTGACCGTAACTGCAGGATT 57.149 45.000 19.93 6.74 0.00 3.01
300 315 2.851263 TTTGACCGTAACTGCAGGAT 57.149 45.000 19.93 9.16 0.00 3.24
301 316 2.623878 TTTTGACCGTAACTGCAGGA 57.376 45.000 19.93 2.00 0.00 3.86
319 334 8.589701 ATCCGTATTTTCCAGGATTAGTTTTT 57.410 30.769 0.00 0.00 40.29 1.94
356 371 1.801178 CAGAAGAAGCTTCCACGGTTC 59.199 52.381 22.81 17.98 40.66 3.62
411 426 6.480981 TGTCTCTCGATGTGTACGTATATTGA 59.519 38.462 0.00 3.27 0.00 2.57
420 435 9.497030 GATATATTCATGTCTCTCGATGTGTAC 57.503 37.037 0.00 0.00 0.00 2.90
473 502 8.655092 GTTTCTTGTCTATCTGAGATTTGACTG 58.345 37.037 20.61 15.66 36.29 3.51
660 790 4.332819 GCGTGTAATAGGTCAAGAAAGCAT 59.667 41.667 0.00 0.00 0.00 3.79
846 985 1.986378 GTTGAGCAGCAGTAGTACGTG 59.014 52.381 0.00 0.00 0.00 4.49
894 1033 0.597637 GATGGATCGACCGATGCGTT 60.598 55.000 17.27 8.89 44.35 4.84
897 1036 0.600557 AGAGATGGATCGACCGATGC 59.399 55.000 15.38 15.38 42.24 3.91
1106 1249 2.187946 CGGGCGGCTTCTTGATCT 59.812 61.111 9.56 0.00 0.00 2.75
1290 1433 2.716017 GGAGGACGAGGACTGCTGG 61.716 68.421 0.00 0.00 0.00 4.85
1299 1442 2.818132 GGGAGCATGGAGGACGAG 59.182 66.667 0.00 0.00 0.00 4.18
1464 1610 0.528924 CTCCACGATGAACACCGGTA 59.471 55.000 6.87 0.00 0.00 4.02
1501 1647 0.321996 GGAACCGGAGATAGGATGCC 59.678 60.000 9.46 0.00 0.00 4.40
1747 1896 4.020543 TGCATTTATAGGTGGTTTGGGTC 58.979 43.478 0.00 0.00 0.00 4.46
1794 1943 0.316204 AGTAGCCACGCGTGTAACTT 59.684 50.000 34.81 18.32 31.75 2.66
2142 2323 6.897706 TGAGAGTCTTCCATATGATCTCTG 57.102 41.667 3.65 0.00 34.26 3.35
2350 2531 1.615883 GATCGGCTAGAGATGCTCCAA 59.384 52.381 5.96 0.00 0.00 3.53
2352 2533 1.067915 GTGATCGGCTAGAGATGCTCC 60.068 57.143 5.96 0.00 0.00 4.70
2436 2617 4.263025 GGGAGTTAAGTTTTAGGGGTTCGA 60.263 45.833 0.00 0.00 0.00 3.71
2438 2619 5.252586 AGGGAGTTAAGTTTTAGGGGTTC 57.747 43.478 0.00 0.00 0.00 3.62
2441 2622 7.464273 TCTTTTAGGGAGTTAAGTTTTAGGGG 58.536 38.462 0.00 0.00 0.00 4.79
2465 2646 6.870439 AGCTAAGAAGAATTGGCAAATGTTTC 59.130 34.615 3.01 3.40 38.97 2.78
2621 2805 1.670791 TGGACCCTTTCGTGTGTTTC 58.329 50.000 0.00 0.00 0.00 2.78
2630 2814 6.570571 GCTCTTTACTTCATTTGGACCCTTTC 60.571 42.308 0.00 0.00 0.00 2.62
2643 2827 6.536582 GTGCTTCTATCATGCTCTTTACTTCA 59.463 38.462 0.00 0.00 0.00 3.02
2646 2830 5.982356 TGTGCTTCTATCATGCTCTTTACT 58.018 37.500 0.00 0.00 0.00 2.24
2647 2831 6.092670 TGTTGTGCTTCTATCATGCTCTTTAC 59.907 38.462 0.00 0.00 0.00 2.01
2648 2832 6.172630 TGTTGTGCTTCTATCATGCTCTTTA 58.827 36.000 0.00 0.00 0.00 1.85
2649 2833 5.005740 TGTTGTGCTTCTATCATGCTCTTT 58.994 37.500 0.00 0.00 0.00 2.52
2650 2834 4.582869 TGTTGTGCTTCTATCATGCTCTT 58.417 39.130 0.00 0.00 0.00 2.85
2651 2835 4.212143 TGTTGTGCTTCTATCATGCTCT 57.788 40.909 0.00 0.00 0.00 4.09
2652 2836 4.952262 TTGTTGTGCTTCTATCATGCTC 57.048 40.909 0.00 0.00 0.00 4.26
2653 2837 4.945543 TGATTGTTGTGCTTCTATCATGCT 59.054 37.500 0.00 0.00 0.00 3.79
2654 2838 5.239359 TGATTGTTGTGCTTCTATCATGC 57.761 39.130 0.00 0.00 0.00 4.06
2655 2839 6.745907 CACTTGATTGTTGTGCTTCTATCATG 59.254 38.462 0.00 0.00 32.30 3.07
2656 2840 6.127814 CCACTTGATTGTTGTGCTTCTATCAT 60.128 38.462 0.00 0.00 0.00 2.45
2657 2841 5.181811 CCACTTGATTGTTGTGCTTCTATCA 59.818 40.000 0.00 0.00 0.00 2.15
2658 2842 5.182001 ACCACTTGATTGTTGTGCTTCTATC 59.818 40.000 0.00 0.00 0.00 2.08
2713 2897 3.321039 TCATACCCAGCTCCAAGATGAT 58.679 45.455 0.00 0.00 32.38 2.45
2725 2909 3.522553 GAACCGAGAAGTTCATACCCAG 58.477 50.000 5.50 0.00 44.55 4.45


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

AutoCloner maintained by Alex Coulton.