Multiple sequence alignment - TraesCS5D01G451200

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 TraesCS5D01G451200 chr5D 100.000 2925 0 0 1 2925 499446988 499449912 0.000000e+00 5402.0
1 TraesCS5D01G451200 chr5D 82.371 1991 229 70 2 1898 499957283 499955321 0.000000e+00 1620.0
2 TraesCS5D01G451200 chr5D 80.486 1768 212 73 4 1724 499652132 499653813 0.000000e+00 1230.0
3 TraesCS5D01G451200 chr5B 91.583 2495 137 36 2 2456 620305966 620308427 0.000000e+00 3376.0
4 TraesCS5D01G451200 chr5B 91.641 1639 107 15 66 1689 620668512 620670135 0.000000e+00 2241.0
5 TraesCS5D01G451200 chr5B 82.879 1799 215 48 2 1740 621399919 621398154 0.000000e+00 1530.0
6 TraesCS5D01G451200 chr5B 80.330 1698 224 56 65 1724 620825488 620827113 0.000000e+00 1184.0
7 TraesCS5D01G451200 chr5B 86.051 1061 73 41 1642 2669 620670031 620671049 0.000000e+00 1070.0
8 TraesCS5D01G451200 chr5B 80.548 365 38 16 2521 2860 620308426 620308782 1.740000e-62 250.0
9 TraesCS5D01G451200 chr5A 91.827 1762 108 17 2 1745 623684159 623685902 0.000000e+00 2423.0
10 TraesCS5D01G451200 chr5A 82.369 1798 215 53 8 1740 624476297 624474537 0.000000e+00 1471.0
11 TraesCS5D01G451200 chr5A 80.273 1759 232 60 2 1724 623954030 623955709 0.000000e+00 1219.0
12 TraesCS5D01G451200 chr5A 85.670 970 50 31 1554 2479 623685750 623686674 0.000000e+00 939.0
13 TraesCS5D01G451200 chr5A 90.536 317 16 4 2622 2925 623687261 623687576 9.760000e-110 407.0
14 TraesCS5D01G451200 chr6A 97.959 49 1 0 1116 1164 565044221 565044173 5.190000e-13 86.1
15 TraesCS5D01G451200 chr6A 97.959 49 1 0 1116 1164 565105266 565105218 5.190000e-13 86.1


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 TraesCS5D01G451200 chr5D 499446988 499449912 2924 False 5402.000000 5402 100.000000 1 2925 1 chr5D.!!$F1 2924
1 TraesCS5D01G451200 chr5D 499955321 499957283 1962 True 1620.000000 1620 82.371000 2 1898 1 chr5D.!!$R1 1896
2 TraesCS5D01G451200 chr5D 499652132 499653813 1681 False 1230.000000 1230 80.486000 4 1724 1 chr5D.!!$F2 1720
3 TraesCS5D01G451200 chr5B 620305966 620308782 2816 False 1813.000000 3376 86.065500 2 2860 2 chr5B.!!$F2 2858
4 TraesCS5D01G451200 chr5B 620668512 620671049 2537 False 1655.500000 2241 88.846000 66 2669 2 chr5B.!!$F3 2603
5 TraesCS5D01G451200 chr5B 621398154 621399919 1765 True 1530.000000 1530 82.879000 2 1740 1 chr5B.!!$R1 1738
6 TraesCS5D01G451200 chr5B 620825488 620827113 1625 False 1184.000000 1184 80.330000 65 1724 1 chr5B.!!$F1 1659
7 TraesCS5D01G451200 chr5A 624474537 624476297 1760 True 1471.000000 1471 82.369000 8 1740 1 chr5A.!!$R1 1732
8 TraesCS5D01G451200 chr5A 623684159 623687576 3417 False 1256.333333 2423 89.344333 2 2925 3 chr5A.!!$F2 2923
9 TraesCS5D01G451200 chr5A 623954030 623955709 1679 False 1219.000000 1219 80.273000 2 1724 1 chr5A.!!$F1 1722

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
669 680 0.036858 GAAGCACACTCTGGAGGTCC 60.037 60.0 2.58 0.0 0.0 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 2369 1.00027 ACACACAAAGGGGTGCACA 60.0 52.632 20.43 0.0 42.55 4.57 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
54 57 8.928270 AAATCATCAAGAATTTTGATCTCAGC 57.072 30.769 10.85 0.00 37.06 4.26
61 64 5.355596 AGAATTTTGATCTCAGCGGTAGAG 58.644 41.667 7.48 7.48 34.42 2.43
63 67 0.382158 TTGATCTCAGCGGTAGAGCG 59.618 55.000 8.57 0.00 43.00 5.03
148 155 7.117523 CCAATGCAAATTAATCCGAACTCAAAA 59.882 33.333 0.00 0.00 0.00 2.44
285 292 1.498865 GAACTCACACACCACCAGCG 61.499 60.000 0.00 0.00 0.00 5.18
323 334 0.179215 GCAACTTGCATCTCGTTCCG 60.179 55.000 8.97 0.00 44.26 4.30
352 363 2.005971 AGCCTATCAAAACGACGTCC 57.994 50.000 10.58 0.00 0.00 4.79
376 387 1.068610 CGACGTGTTTCCCGTACCTTA 60.069 52.381 0.00 0.00 38.92 2.69
418 429 0.179166 CATGACCACGCCGGAAAATG 60.179 55.000 5.05 0.00 38.63 2.32
483 494 1.205064 CGAACTCGCACAAAGGCAG 59.795 57.895 0.00 0.00 0.00 4.85
512 523 1.043116 CAGTCCCTGATCACCGGCTA 61.043 60.000 0.00 0.00 32.44 3.93
565 576 6.315393 ACACAAACTCAATCTCGTTACAAAGT 59.685 34.615 0.00 0.00 0.00 2.66
611 622 6.419413 TGCAAAAATTTACAGTCGAATTGGTC 59.581 34.615 0.00 0.00 0.00 4.02
669 680 0.036858 GAAGCACACTCTGGAGGTCC 60.037 60.000 2.58 0.00 0.00 4.46
947 992 0.591994 CAGCTCACGCATCTCTCTCG 60.592 60.000 0.00 0.00 39.10 4.04
1225 1340 0.661552 CGAGTCCTTCGCCGAATCTA 59.338 55.000 0.00 0.00 43.22 1.98
1228 1343 0.597898 GTCCTTCGCCGAATCTAGCC 60.598 60.000 0.00 0.00 0.00 3.93
1250 1380 4.181578 CCCATTCTCGTTGTATCTCGTTT 58.818 43.478 0.00 0.00 0.00 3.60
1486 1633 1.376037 GACCAAGGTCAAGGCCTCG 60.376 63.158 5.23 0.00 44.02 4.63
1936 2236 4.414337 CAAGAAGTAGATCCTTGGAGGG 57.586 50.000 0.00 0.00 35.59 4.30
2008 2308 1.534175 GCTGTTAGTCGAGATGTCCGG 60.534 57.143 0.00 0.00 0.00 5.14
2018 2318 4.082523 ATGTCCGGGCTGTGTCGG 62.083 66.667 7.97 0.00 46.89 4.79
2060 2360 1.729267 AATCTGGGTTGGGGTGCACT 61.729 55.000 17.98 0.00 0.00 4.40
2069 2369 2.606587 GGGGTGCACTGGTGATCCT 61.607 63.158 17.98 0.00 34.23 3.24
2088 2391 1.318886 TGTGCACCCCTTTGTGTGTG 61.319 55.000 15.69 0.00 38.52 3.82
2089 2392 1.000270 TGCACCCCTTTGTGTGTGT 60.000 52.632 0.00 0.00 38.52 3.72
2090 2393 0.613292 TGCACCCCTTTGTGTGTGTT 60.613 50.000 0.00 0.00 38.52 3.32
2176 2487 9.087424 GGGTAATTGAATCTTCATTTTAGCAAC 57.913 33.333 17.63 7.58 36.46 4.17
2189 2500 7.370383 TCATTTTAGCAACATCCTTCTGAAAC 58.630 34.615 0.00 0.00 0.00 2.78
2224 2536 7.487822 TTACATTGATTCCTTTGCCCAAATA 57.512 32.000 0.00 0.00 0.00 1.40
2260 2573 8.562892 CACAATTGAAATTCTAGTGTTCTCTGT 58.437 33.333 13.59 0.00 29.01 3.41
2261 2574 9.125026 ACAATTGAAATTCTAGTGTTCTCTGTT 57.875 29.630 13.59 0.00 27.07 3.16
2303 2616 2.543653 GCAAATCTTGTGCTGTTTCGGT 60.544 45.455 0.00 0.00 39.00 4.69
2334 2648 8.370266 TGGAATCCATTTGAGATCTGAAATTT 57.630 30.769 16.38 9.53 0.00 1.82
2335 2649 9.478238 TGGAATCCATTTGAGATCTGAAATTTA 57.522 29.630 16.38 8.80 0.00 1.40
2336 2650 9.741647 GGAATCCATTTGAGATCTGAAATTTAC 57.258 33.333 16.38 7.12 0.00 2.01
2340 2654 8.742777 TCCATTTGAGATCTGAAATTTACTTGG 58.257 33.333 16.38 14.74 0.00 3.61
2347 2661 7.661040 AGATCTGAAATTTACTTGGGTTTGTG 58.339 34.615 0.00 0.00 0.00 3.33
2452 2785 5.675684 TGTATTCTTCTCTGTACATGGCA 57.324 39.130 0.00 0.00 0.00 4.92
2584 2955 0.107214 TTTTCAGCTATGGCGGGAGG 60.107 55.000 0.72 0.00 44.37 4.30
2585 2956 1.271840 TTTCAGCTATGGCGGGAGGT 61.272 55.000 0.72 0.00 44.37 3.85
2597 2971 2.355115 GGAGGTGCGTTTGGGGAT 59.645 61.111 0.00 0.00 0.00 3.85
2599 2973 2.676471 AGGTGCGTTTGGGGATGC 60.676 61.111 0.00 0.00 0.00 3.91
2600 2974 2.676471 GGTGCGTTTGGGGATGCT 60.676 61.111 0.00 0.00 32.75 3.79
2601 2975 2.568090 GTGCGTTTGGGGATGCTG 59.432 61.111 0.00 0.00 32.75 4.41
2602 2976 3.372730 TGCGTTTGGGGATGCTGC 61.373 61.111 0.00 0.00 32.75 5.25
2603 2977 4.481112 GCGTTTGGGGATGCTGCG 62.481 66.667 0.00 0.00 0.00 5.18
2611 3003 2.437359 GGATGCTGCGCCAGAAGT 60.437 61.111 4.18 0.00 32.44 3.01
2649 3430 2.599082 CAGAAGATTCGCAGTAACCGTC 59.401 50.000 0.00 0.00 0.00 4.79
2688 3469 2.231721 AGGTTAGCAGGACGTTCTTCTC 59.768 50.000 0.00 0.00 0.00 2.87
2715 3507 1.588674 CCTGCAGTGTTACCGTTTCA 58.411 50.000 13.81 0.00 0.00 2.69
2716 3508 1.263217 CCTGCAGTGTTACCGTTTCAC 59.737 52.381 13.81 0.00 0.00 3.18
2731 3523 2.682856 GTTTCACAGCTTCAACTCACCA 59.317 45.455 0.00 0.00 0.00 4.17
2734 3526 2.104622 TCACAGCTTCAACTCACCATCA 59.895 45.455 0.00 0.00 0.00 3.07
2738 3530 3.681897 CAGCTTCAACTCACCATCACTAC 59.318 47.826 0.00 0.00 0.00 2.73
2752 3544 1.741145 TCACTACGCTACGCATTCTCA 59.259 47.619 0.00 0.00 0.00 3.27
2780 3572 0.250424 TCACCATGGTGCTGTGAGTG 60.250 55.000 35.73 13.00 45.04 3.51
2781 3573 0.250424 CACCATGGTGCTGTGAGTGA 60.250 55.000 31.13 0.00 39.39 3.41
2877 3675 5.104941 ACGTGAGGACCTATGAATGATCAAA 60.105 40.000 0.00 0.00 39.49 2.69
2880 3678 6.769822 GTGAGGACCTATGAATGATCAAACAT 59.230 38.462 17.64 17.64 39.49 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 57 3.069980 AAGCTGGCTCGCTCTACCG 62.070 63.158 2.51 0.00 39.86 4.02
61 64 1.432270 GGTGATACAAGCTGGCTCGC 61.432 60.000 0.00 0.00 0.00 5.03
63 67 1.661341 CAGGTGATACAAGCTGGCTC 58.339 55.000 0.00 0.00 41.06 4.70
148 155 0.675633 GCTGCATTTGGGTTGTCACT 59.324 50.000 0.00 0.00 0.00 3.41
285 292 3.741476 CAGCTTGCGGCACCCTTC 61.741 66.667 0.05 0.00 44.79 3.46
323 334 0.666913 TTGATAGGCTACGAGGCGAC 59.333 55.000 0.00 0.00 46.58 5.19
352 363 0.179192 TACGGGAAACACGTCGATCG 60.179 55.000 9.36 9.36 44.37 3.69
376 387 2.236395 AGCTGGTTAACGTAGCAATCCT 59.764 45.455 25.73 9.90 39.84 3.24
418 429 0.517316 GTGCTCCGGTGAACAATGAC 59.483 55.000 9.87 0.00 0.00 3.06
483 494 3.732938 AGGGACTGGTCAGGATGC 58.267 61.111 2.87 0.00 37.18 3.91
512 523 6.139679 TGGTTGAGTATTCTGGGAGAAATT 57.860 37.500 0.00 0.00 37.82 1.82
565 576 1.594833 GTGTAGGCACGGACCATGA 59.405 57.895 0.00 0.00 35.75 3.07
611 622 2.620779 AATATCGCTCGATCAGACCG 57.379 50.000 8.14 0.00 36.17 4.79
613 624 4.261813 CGATCAAATATCGCTCGATCAGAC 59.738 45.833 8.14 0.00 36.17 3.51
616 627 3.190535 TCCGATCAAATATCGCTCGATCA 59.809 43.478 8.14 0.00 39.95 2.92
669 680 2.581354 CTCAGGAACCAGCCTCCG 59.419 66.667 0.00 0.00 38.08 4.63
962 1011 3.714871 GAGAGGAGAGCGCTGGTGC 62.715 68.421 18.48 7.31 0.00 5.01
1225 1340 2.103263 GAGATACAACGAGAATGGGGCT 59.897 50.000 0.00 0.00 0.00 5.19
1228 1343 3.438297 ACGAGATACAACGAGAATGGG 57.562 47.619 0.00 0.00 0.00 4.00
1250 1380 2.731451 CGAACGAACAGAGAGCAATTCA 59.269 45.455 0.00 0.00 0.00 2.57
1486 1633 3.488090 GCGGCCGACAGCTTGTAC 61.488 66.667 33.48 2.06 43.05 2.90
1528 1690 3.500642 GCCGCGGGCTTCTTCTTC 61.501 66.667 29.38 1.03 46.69 2.87
1936 2236 1.115930 TCGCCAAGCCCTAGGATCTC 61.116 60.000 11.48 0.00 0.00 2.75
2018 2318 2.427095 CAAATTTACAGCCTAGCACCCC 59.573 50.000 0.00 0.00 0.00 4.95
2069 2369 1.000270 ACACACAAAGGGGTGCACA 60.000 52.632 20.43 0.00 42.55 4.57
2088 2391 1.155424 TCGCCACCGTTTCTCACAAC 61.155 55.000 0.00 0.00 35.54 3.32
2089 2392 1.144276 TCGCCACCGTTTCTCACAA 59.856 52.632 0.00 0.00 35.54 3.33
2090 2393 1.593209 GTCGCCACCGTTTCTCACA 60.593 57.895 0.00 0.00 35.54 3.58
2176 2487 4.818546 ACTGTGACAAGTTTCAGAAGGATG 59.181 41.667 10.76 0.00 0.00 3.51
2189 2500 7.206981 AGGAATCAATGTAAACTGTGACAAG 57.793 36.000 0.54 0.00 0.00 3.16
2224 2536 3.472283 TTTCAATTGTGCAGCACCAAT 57.528 38.095 23.06 17.76 32.73 3.16
2230 2543 5.464168 ACACTAGAATTTCAATTGTGCAGC 58.536 37.500 5.13 0.00 0.00 5.25
2260 2573 6.811954 TGCAGTATCATACCGAAATCACTAA 58.188 36.000 0.00 0.00 0.00 2.24
2261 2574 6.399639 TGCAGTATCATACCGAAATCACTA 57.600 37.500 0.00 0.00 0.00 2.74
2262 2575 5.276461 TGCAGTATCATACCGAAATCACT 57.724 39.130 0.00 0.00 0.00 3.41
2303 2616 6.320418 CAGATCTCAAATGGATTCCATGTTCA 59.680 38.462 18.87 1.90 44.40 3.18
2334 2648 3.068873 GCCATCAAACACAAACCCAAGTA 59.931 43.478 0.00 0.00 0.00 2.24
2335 2649 2.158971 GCCATCAAACACAAACCCAAGT 60.159 45.455 0.00 0.00 0.00 3.16
2336 2650 2.158986 TGCCATCAAACACAAACCCAAG 60.159 45.455 0.00 0.00 0.00 3.61
2337 2651 1.833630 TGCCATCAAACACAAACCCAA 59.166 42.857 0.00 0.00 0.00 4.12
2338 2652 1.489481 TGCCATCAAACACAAACCCA 58.511 45.000 0.00 0.00 0.00 4.51
2339 2653 2.611225 TTGCCATCAAACACAAACCC 57.389 45.000 0.00 0.00 0.00 4.11
2340 2654 3.303924 GCATTTGCCATCAAACACAAACC 60.304 43.478 0.00 0.00 44.11 3.27
2416 2744 6.479884 AGAAGAATACAACAGCCTCTTCATT 58.520 36.000 11.50 0.00 42.85 2.57
2418 2746 5.247110 AGAGAAGAATACAACAGCCTCTTCA 59.753 40.000 11.50 0.00 42.85 3.02
2419 2747 5.580297 CAGAGAAGAATACAACAGCCTCTTC 59.420 44.000 2.60 2.60 41.43 2.87
2420 2748 5.012561 ACAGAGAAGAATACAACAGCCTCTT 59.987 40.000 0.00 0.00 0.00 2.85
2421 2749 4.530161 ACAGAGAAGAATACAACAGCCTCT 59.470 41.667 0.00 0.00 0.00 3.69
2422 2750 4.826556 ACAGAGAAGAATACAACAGCCTC 58.173 43.478 0.00 0.00 0.00 4.70
2584 2955 2.568090 CAGCATCCCCAAACGCAC 59.432 61.111 0.00 0.00 0.00 5.34
2585 2956 3.372730 GCAGCATCCCCAAACGCA 61.373 61.111 0.00 0.00 0.00 5.24
2599 2973 1.448540 CCCTGTACTTCTGGCGCAG 60.449 63.158 10.83 4.99 34.39 5.18
2600 2974 2.662596 CCCTGTACTTCTGGCGCA 59.337 61.111 10.83 0.00 34.39 6.09
2601 2975 2.125106 CCCCTGTACTTCTGGCGC 60.125 66.667 0.00 0.00 34.39 6.53
2602 2976 2.125106 GCCCCTGTACTTCTGGCG 60.125 66.667 0.00 0.00 34.39 5.69
2603 2977 1.078143 CAGCCCCTGTACTTCTGGC 60.078 63.158 7.82 7.82 42.48 4.85
2649 3430 4.436998 GACAGGTCACCGGAGCCG 62.437 72.222 9.46 1.06 42.52 5.52
2672 3453 1.179814 ACCGAGAAGAACGTCCTGCT 61.180 55.000 0.00 0.00 0.00 4.24
2688 3469 0.673333 TAACACTGCAGGCATCACCG 60.673 55.000 19.93 0.00 46.52 4.94
2715 3507 2.105477 AGTGATGGTGAGTTGAAGCTGT 59.895 45.455 0.00 0.00 0.00 4.40
2716 3508 2.775890 AGTGATGGTGAGTTGAAGCTG 58.224 47.619 0.00 0.00 0.00 4.24
2780 3572 0.998669 GCAAGCTTCTTCTCGCTCTC 59.001 55.000 0.00 0.00 34.96 3.20
2781 3573 0.319728 TGCAAGCTTCTTCTCGCTCT 59.680 50.000 0.00 0.00 34.96 4.09
2877 3675 1.210204 ATGCCACACCCTCTGGATGT 61.210 55.000 0.00 0.00 34.81 3.06
2880 3678 0.915872 ATCATGCCACACCCTCTGGA 60.916 55.000 0.00 0.00 34.81 3.86


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

AutoCloner maintained by Alex Coulton.