Multiple sequence alignment - TraesCS4D01G255400

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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 TraesCS4D01G255400 chr4D 100.000 3324 0 0 1 3324 424170647 424167324 0.000000e+00 6139.0
1 TraesCS4D01G255400 chr4D 95.949 3357 96 19 1 3324 424111640 424108291 0.000000e+00 5409.0
2 TraesCS4D01G255400 chr4D 93.148 2306 101 16 699 2958 423990217 423987923 0.000000e+00 3330.0
3 TraesCS4D01G255400 chr4D 93.861 1743 76 13 1606 3324 424196575 424194840 0.000000e+00 2597.0
4 TraesCS4D01G255400 chr4D 93.133 1762 108 4 699 2448 424323102 424321342 0.000000e+00 2571.0
5 TraesCS4D01G255400 chr4D 88.199 1771 129 37 804 2523 57840374 57842115 0.000000e+00 2039.0
6 TraesCS4D01G255400 chr4D 87.315 1419 135 28 955 2348 426870123 426871521 0.000000e+00 1581.0
7 TraesCS4D01G255400 chr4D 96.018 879 27 2 2452 3324 424309149 424308273 0.000000e+00 1423.0
8 TraesCS4D01G255400 chr4D 96.305 866 25 2 2463 3322 424194811 424193947 0.000000e+00 1415.0
9 TraesCS4D01G255400 chr4D 93.297 552 35 2 699 1249 424197767 424197217 0.000000e+00 813.0
10 TraesCS4D01G255400 chr4D 89.836 610 36 4 1 584 424447260 424446651 0.000000e+00 760.0
11 TraesCS4D01G255400 chr4D 89.180 610 33 6 1 585 424244418 424243817 0.000000e+00 730.0
12 TraesCS4D01G255400 chr4D 96.454 141 5 0 564 704 424446374 424446234 1.990000e-57 233.0
13 TraesCS4D01G255400 chr4D 92.199 141 10 1 564 704 424243541 424243402 7.270000e-47 198.0
14 TraesCS4D01G255400 chr4D 95.833 48 2 0 608 655 424243662 424243615 9.890000e-11 78.7
15 TraesCS4D01G255400 chr4A 93.792 2062 79 20 944 2958 40260686 40262745 0.000000e+00 3053.0
16 TraesCS4D01G255400 chr4A 85.583 1415 138 30 938 2334 38682956 38681590 0.000000e+00 1423.0
17 TraesCS4D01G255400 chr4A 89.716 282 20 4 2244 2523 539140504 539140778 5.280000e-93 351.0
18 TraesCS4D01G255400 chr4A 77.258 299 46 13 160 439 40255174 40255469 4.440000e-34 156.0
19 TraesCS4D01G255400 chr4B 93.999 2033 87 7 944 2962 520298421 520296410 0.000000e+00 3046.0
20 TraesCS4D01G255400 chr4B 90.186 1559 106 40 951 2485 86132213 86130678 0.000000e+00 1988.0
21 TraesCS4D01G255400 chr4B 85.003 1467 168 32 938 2375 522669258 522670701 0.000000e+00 1443.0
22 TraesCS4D01G255400 chr4B 85.852 1350 139 28 1046 2369 527644854 527643531 0.000000e+00 1387.0
23 TraesCS4D01G255400 chr4B 91.194 511 22 4 2085 2595 520289629 520289142 0.000000e+00 673.0
24 TraesCS4D01G255400 chr4B 94.355 372 21 0 2587 2958 520281360 520280989 3.720000e-159 571.0
25 TraesCS4D01G255400 chr4B 89.420 293 28 1 2967 3259 520296453 520296164 1.880000e-97 366.0
26 TraesCS4D01G255400 chr4B 89.100 211 18 2 2579 2788 86097025 86096819 1.180000e-64 257.0
27 TraesCS4D01G255400 chr4B 87.500 120 11 3 2810 2928 527747421 527747305 5.780000e-28 135.0
28 TraesCS4D01G255400 chrUn 92.320 612 36 5 1 603 60141253 60140644 0.000000e+00 859.0
29 TraesCS4D01G255400 chrUn 92.320 612 36 5 1 603 235655600 235654991 0.000000e+00 859.0
30 TraesCS4D01G255400 chrUn 94.194 310 12 3 944 1248 60140575 60140267 5.020000e-128 468.0
31 TraesCS4D01G255400 chr7A 89.062 192 16 2 3054 3243 545952681 545952493 1.990000e-57 233.0
32 TraesCS4D01G255400 chr5D 79.121 91 14 4 274 362 38735721 38735808 1.290000e-04 58.4


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 TraesCS4D01G255400 chr4D 424167324 424170647 3323 True 6139.000000 6139 100.000000 1 3324 1 chr4D.!!$R3 3323
1 TraesCS4D01G255400 chr4D 424108291 424111640 3349 True 5409.000000 5409 95.949000 1 3324 1 chr4D.!!$R2 3323
2 TraesCS4D01G255400 chr4D 423987923 423990217 2294 True 3330.000000 3330 93.148000 699 2958 1 chr4D.!!$R1 2259
3 TraesCS4D01G255400 chr4D 424321342 424323102 1760 True 2571.000000 2571 93.133000 699 2448 1 chr4D.!!$R5 1749
4 TraesCS4D01G255400 chr4D 57840374 57842115 1741 False 2039.000000 2039 88.199000 804 2523 1 chr4D.!!$F1 1719
5 TraesCS4D01G255400 chr4D 424193947 424197767 3820 True 1608.333333 2597 94.487667 699 3324 3 chr4D.!!$R6 2625
6 TraesCS4D01G255400 chr4D 426870123 426871521 1398 False 1581.000000 1581 87.315000 955 2348 1 chr4D.!!$F2 1393
7 TraesCS4D01G255400 chr4D 424308273 424309149 876 True 1423.000000 1423 96.018000 2452 3324 1 chr4D.!!$R4 872
8 TraesCS4D01G255400 chr4D 424446234 424447260 1026 True 496.500000 760 93.145000 1 704 2 chr4D.!!$R8 703
9 TraesCS4D01G255400 chr4D 424243402 424244418 1016 True 335.566667 730 92.404000 1 704 3 chr4D.!!$R7 703
10 TraesCS4D01G255400 chr4A 40260686 40262745 2059 False 3053.000000 3053 93.792000 944 2958 1 chr4A.!!$F2 2014
11 TraesCS4D01G255400 chr4A 38681590 38682956 1366 True 1423.000000 1423 85.583000 938 2334 1 chr4A.!!$R1 1396
12 TraesCS4D01G255400 chr4B 86130678 86132213 1535 True 1988.000000 1988 90.186000 951 2485 1 chr4B.!!$R2 1534
13 TraesCS4D01G255400 chr4B 520296164 520298421 2257 True 1706.000000 3046 91.709500 944 3259 2 chr4B.!!$R7 2315
14 TraesCS4D01G255400 chr4B 522669258 522670701 1443 False 1443.000000 1443 85.003000 938 2375 1 chr4B.!!$F1 1437
15 TraesCS4D01G255400 chr4B 527643531 527644854 1323 True 1387.000000 1387 85.852000 1046 2369 1 chr4B.!!$R5 1323
16 TraesCS4D01G255400 chrUn 235654991 235655600 609 True 859.000000 859 92.320000 1 603 1 chrUn.!!$R1 602
17 TraesCS4D01G255400 chrUn 60140267 60141253 986 True 663.500000 859 93.257000 1 1248 2 chrUn.!!$R2 1247


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
406 435 0.625316 TATGCTCCACCATTGGCACT 59.375 50.000 1.54 0.00 43.56 4.40 F
729 1056 1.001181 GTAGAACCAACGGTGCAGGTA 59.999 52.381 0.00 0.00 35.34 3.08 F
2176 3016 1.675310 CCGATGGTTTGCTGCTCCA 60.675 57.895 12.27 12.27 35.64 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2237 3089 1.160329 GGCGGGATGAACTTGATCCG 61.160 60.000 1.59 0.00 40.47 4.18 R
2264 3116 7.607991 GGGAATTTTGAGTAGATTCTTCTGTGA 59.392 37.037 0.00 0.00 33.17 3.58 R
3146 4972 1.296715 CGTTCTAGTGCCTGGGCTT 59.703 57.895 13.05 4.08 42.51 4.35 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
234 244 5.835819 TGGAAATGGTATTTTGGACAACTGA 59.164 36.000 0.00 0.00 0.00 3.41
354 383 7.567622 ACTTCCTATTAAAGTGTGCTATCCCTA 59.432 37.037 0.00 0.00 35.68 3.53
378 407 2.483877 CTGTTGCAACGTATGACATGGT 59.516 45.455 23.79 0.00 0.00 3.55
406 435 0.625316 TATGCTCCACCATTGGCACT 59.375 50.000 1.54 0.00 43.56 4.40
522 551 4.622701 AACAGAGCAAACTGACAAAGTC 57.377 40.909 11.41 0.00 38.56 3.01
532 562 4.104383 ACTGACAAAGTCCCAATCATGT 57.896 40.909 0.00 0.00 31.64 3.21
562 592 6.603201 ACAATAAAATCATAGGCCCATATCGG 59.397 38.462 0.00 0.00 0.00 4.18
607 934 4.535526 AAATGCTGATAACAACAACCCC 57.464 40.909 0.00 0.00 0.00 4.95
729 1056 1.001181 GTAGAACCAACGGTGCAGGTA 59.999 52.381 0.00 0.00 35.34 3.08
1922 2762 4.996758 ACGACACAAACAATGAGATCATCA 59.003 37.500 0.00 0.00 43.70 3.07
2176 3016 1.675310 CCGATGGTTTGCTGCTCCA 60.675 57.895 12.27 12.27 35.64 3.86
2229 3081 2.153366 TTGTCGTTCCCGGTAAAGAC 57.847 50.000 16.92 16.92 38.05 3.01
2237 3089 2.030958 CCGGTAAAGACGGCACCAC 61.031 63.158 0.00 0.00 45.34 4.16
2916 4742 5.217978 TGCAAGGAGAATGAAGCAAATTT 57.782 34.783 0.00 0.00 0.00 1.82
2994 4820 6.820152 GCTTACCGGAGATTTTAGTTCCTTTA 59.180 38.462 9.46 0.00 0.00 1.85
3146 4972 2.550175 TGTTCATCCCTGTCTCCATCA 58.450 47.619 0.00 0.00 0.00 3.07
3159 4985 0.913934 TCCATCAAGCCCAGGCACTA 60.914 55.000 12.03 0.00 44.88 2.74
3206 5032 1.032794 CGTCGGGATCCTGAATCTCA 58.967 55.000 25.22 0.00 34.14 3.27
3209 5035 1.123077 CGGGATCCTGAATCTCACCA 58.877 55.000 16.28 0.00 34.14 4.17
3292 5118 8.511604 TCCAGGAAAATCATAGTTTGATCTTC 57.488 34.615 2.07 2.07 44.51 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
349 378 1.003839 CGTTGCAACAGCCTAGGGA 60.004 57.895 28.01 0.00 0.00 4.20
354 383 1.156736 GTCATACGTTGCAACAGCCT 58.843 50.000 28.01 10.31 0.00 4.58
378 407 2.770447 TGGTGGAGCATATTAGGGTCA 58.230 47.619 9.45 0.00 34.56 4.02
406 435 8.394877 CACGATATGTTGCCAAAGAAGTATTAA 58.605 33.333 0.00 0.00 0.00 1.40
522 551 9.650539 TGATTTTATTGTTGTAACATGATTGGG 57.349 29.630 0.00 0.00 38.95 4.12
532 562 7.962995 TGGGCCTATGATTTTATTGTTGTAA 57.037 32.000 4.53 0.00 0.00 2.41
729 1056 4.235079 TCTTGGATTCCAAATCGGACAT 57.765 40.909 18.49 0.00 46.36 3.06
1922 2762 1.677217 GCGGAAGATGCTCCAGAGTTT 60.677 52.381 0.00 0.00 34.91 2.66
2009 2849 1.606885 CCCGGCGGTAGGAGTTGTAA 61.607 60.000 26.32 0.00 0.00 2.41
2040 2880 1.986575 GAACAGATCCCGCAGCTTGC 61.987 60.000 0.00 0.00 40.69 4.01
2229 3081 1.635663 GAACTTGATCCGTGGTGCCG 61.636 60.000 0.00 0.00 0.00 5.69
2237 3089 1.160329 GGCGGGATGAACTTGATCCG 61.160 60.000 1.59 0.00 40.47 4.18
2264 3116 7.607991 GGGAATTTTGAGTAGATTCTTCTGTGA 59.392 37.037 0.00 0.00 33.17 3.58
2849 4674 0.029035 CGAAGATCCGACAGGTACCG 59.971 60.000 6.18 4.16 39.05 4.02
2916 4742 6.912951 ACTAAAGTGTCCACTAAGCTCTTA 57.087 37.500 0.00 0.00 41.58 2.10
3001 4827 9.881649 AATTGTGCACTATATATAGGACATGAG 57.118 33.333 21.20 0.00 34.69 2.90
3034 4860 7.780064 TCATCAGTTCAGAATTTTGGAAAACA 58.220 30.769 0.00 0.00 0.00 2.83
3146 4972 1.296715 CGTTCTAGTGCCTGGGCTT 59.703 57.895 13.05 4.08 42.51 4.35
3159 4985 2.513753 TCCATTTCATTGTGGCGTTCT 58.486 42.857 0.00 0.00 35.43 3.01
3206 5032 4.818546 CAGACAAAGATGAAGAACAGTGGT 59.181 41.667 0.00 0.00 0.00 4.16
3292 5118 2.541556 GTACGGAAAAGGCTAGCAGAG 58.458 52.381 18.24 2.72 0.00 3.35



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

AutoCloner maintained by Alex Coulton.