Multiple sequence alignment - TraesCS2D01G193900

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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 TraesCS2D01G193900 chr2D 100.000 2657 0 0 1 2657 138906711 138909367 0.000000e+00 4907.0
1 TraesCS2D01G193900 chr2D 88.556 1337 122 16 647 1981 138888392 138889699 0.000000e+00 1592.0
2 TraesCS2D01G193900 chr2D 88.325 591 55 4 2 584 138887636 138888220 0.000000e+00 697.0
3 TraesCS2D01G193900 chr2B 93.504 2694 95 25 1 2657 197506966 197509616 0.000000e+00 3932.0
4 TraesCS2D01G193900 chr2B 86.602 1336 149 16 647 1981 197379422 197380728 0.000000e+00 1448.0
5 TraesCS2D01G193900 chr2B 85.642 592 68 6 2 584 197378668 197379251 8.130000e-170 606.0
6 TraesCS2D01G193900 chr2B 85.473 592 69 6 2 584 197353153 197353736 3.780000e-168 601.0
7 TraesCS2D01G193900 chr2B 88.599 421 46 1 654 1074 197353914 197354332 6.560000e-141 510.0
8 TraesCS2D01G193900 chr2A 91.296 2091 78 35 648 2657 162070394 162068327 0.000000e+00 2758.0
9 TraesCS2D01G193900 chr2A 85.704 1336 163 15 647 1981 162214488 162213180 0.000000e+00 1384.0
10 TraesCS2D01G193900 chr2A 94.194 155 9 0 433 587 162070720 162070566 1.230000e-58 237.0
11 TraesCS2D01G193900 chr2A 91.111 45 4 0 601 645 162070509 162070553 7.940000e-06 62.1
12 TraesCS2D01G193900 chr4D 76.172 256 37 16 1252 1486 52215437 52215689 2.160000e-21 113.0
13 TraesCS2D01G193900 chr4A 80.357 112 18 4 1377 1486 544397565 544397674 6.100000e-12 82.4
14 TraesCS2D01G193900 chr1B 89.062 64 7 0 2189 2252 142121497 142121560 2.190000e-11 80.5
15 TraesCS2D01G193900 chr6B 100.000 28 0 0 2189 2216 10051543 10051570 5.000000e-03 52.8


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 TraesCS2D01G193900 chr2D 138906711 138909367 2656 False 4907.0 4907 100.0000 1 2657 1 chr2D.!!$F1 2656
1 TraesCS2D01G193900 chr2D 138887636 138889699 2063 False 1144.5 1592 88.4405 2 1981 2 chr2D.!!$F2 1979
2 TraesCS2D01G193900 chr2B 197506966 197509616 2650 False 3932.0 3932 93.5040 1 2657 1 chr2B.!!$F1 2656
3 TraesCS2D01G193900 chr2B 197378668 197380728 2060 False 1027.0 1448 86.1220 2 1981 2 chr2B.!!$F3 1979
4 TraesCS2D01G193900 chr2B 197353153 197354332 1179 False 555.5 601 87.0360 2 1074 2 chr2B.!!$F2 1072
5 TraesCS2D01G193900 chr2A 162068327 162070720 2393 True 1497.5 2758 92.7450 433 2657 2 chr2A.!!$R2 2224
6 TraesCS2D01G193900 chr2A 162213180 162214488 1308 True 1384.0 1384 85.7040 647 1981 1 chr2A.!!$R1 1334

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
670 803 1.301244 GCCGAGATCACGCCATCAT 60.301 57.895 7.06 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2436 0.04109 ACAATTAAGGTGGGGCTGGG 59.959 55.0 0.0 0.0 0.0 4.45 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
73 74 2.846193 AGAAAGCACCACATACGTGTT 58.154 42.857 0.00 0.00 41.93 3.32
216 217 6.368516 GCATGCCTACATTTTATTGTTGTGTT 59.631 34.615 6.36 0.00 32.87 3.32
248 249 5.007626 TGAAAATGTTGTGAAGTTCTCCTCG 59.992 40.000 4.17 0.00 0.00 4.63
251 252 2.224281 TGTTGTGAAGTTCTCCTCGCAT 60.224 45.455 4.17 0.00 0.00 4.73
285 286 4.045636 AGTGTGAAGGAAAATGCAACAC 57.954 40.909 4.70 4.70 0.00 3.32
338 347 1.404181 CCGGATGTCTCGTGATTGTGT 60.404 52.381 0.00 0.00 0.00 3.72
430 439 5.604565 GGCCTGAATTAAATGGAAAGATGG 58.395 41.667 0.00 0.00 0.00 3.51
670 803 1.301244 GCCGAGATCACGCCATCAT 60.301 57.895 7.06 0.00 0.00 2.45
701 834 2.052690 CACCCCGACCGTCAGATCT 61.053 63.158 0.00 0.00 0.00 2.75
980 1121 4.308458 CCGGTCAACCCTGCGTCA 62.308 66.667 0.00 0.00 0.00 4.35
1179 1326 0.689080 TCTCCCTCCTCATGCTGTCC 60.689 60.000 0.00 0.00 0.00 4.02
1308 1455 2.493030 GCGTCCTACCAAGCGCTA 59.507 61.111 12.05 0.00 45.48 4.26
1668 1816 2.757314 AGCAGTCTGATCGATCACTGAA 59.243 45.455 33.54 16.50 34.58 3.02
1671 1819 3.856521 CAGTCTGATCGATCACTGAACAC 59.143 47.826 28.98 17.08 34.58 3.32
1679 1827 2.116983 ATCACTGAACACTGGCGGCT 62.117 55.000 11.43 0.00 0.00 5.52
1727 1875 6.603940 TTTTGATTGATGGTTTTAGGAGGG 57.396 37.500 0.00 0.00 0.00 4.30
1795 1943 2.057408 GCCCCGGATTGGAATTGCA 61.057 57.895 0.73 0.00 42.00 4.08
1796 1944 1.402107 GCCCCGGATTGGAATTGCAT 61.402 55.000 0.73 0.00 42.00 3.96
1797 1945 0.390124 CCCCGGATTGGAATTGCATG 59.610 55.000 0.73 0.00 42.00 4.06
1798 1946 0.249573 CCCGGATTGGAATTGCATGC 60.250 55.000 11.82 11.82 42.00 4.06
1907 2055 0.544697 ACTCCGGCCGTTGGATAAAT 59.455 50.000 26.12 0.00 34.32 1.40
2060 2226 6.476243 TTACAGCTAGAATCACGGAAAAAC 57.524 37.500 0.00 0.00 0.00 2.43
2105 2271 1.160329 ACTATTTCATCAGCGGCCGC 61.160 55.000 42.34 42.34 42.33 6.53
2319 2512 4.214980 ACGCTTCAGTTTCATCAACAAG 57.785 40.909 0.00 0.00 37.93 3.16
2415 2637 5.048013 GTCAACTAGGGTTCAATTGGGAAAG 60.048 44.000 5.42 0.00 32.73 2.62
2470 2692 9.788960 GTTTCCATTAAGTTCATGACTAATTCC 57.211 33.333 0.00 0.00 37.72 3.01
2592 2817 6.653320 TCCGTCTTAGCTTGTTGTTGAATAAT 59.347 34.615 0.00 0.00 0.00 1.28
2646 2877 1.003580 ACGACCTACGACCAGGACTTA 59.996 52.381 9.02 0.00 45.77 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 6.855914 CGTTAACGTACTTAGGTCTTTGTGTA 59.144 38.462 19.75 0.00 34.11 2.90
216 217 7.624360 ACTTCACAACATTTTCAACACTAGA 57.376 32.000 0.00 0.00 0.00 2.43
258 259 5.728471 TGCATTTTCCTTCACACTTTTCAA 58.272 33.333 0.00 0.00 0.00 2.69
265 266 3.798337 CAGTGTTGCATTTTCCTTCACAC 59.202 43.478 4.70 4.70 0.00 3.82
338 347 6.315393 GCTTAACCATCGGATTTTACTCAAGA 59.685 38.462 0.00 0.00 0.00 3.02
430 439 5.174395 AGATTATAGATTCATGCACGCCTC 58.826 41.667 0.00 0.00 0.00 4.70
522 531 5.295950 CATCCTCTGTGGTCAACATCTATC 58.704 45.833 0.00 0.00 38.39 2.08
670 803 1.818959 CGGGGTGTCGTTGGGTTCTA 61.819 60.000 0.00 0.00 0.00 2.10
701 834 1.806247 GCCATGATCGTGTCGATGGAA 60.806 52.381 13.81 0.00 47.00 3.53
897 1038 0.665670 CGCGAGCGATTGAGATGGAT 60.666 55.000 12.58 0.00 42.83 3.41
1133 1280 0.177604 GTACTCCTCCTCGGACTCGA 59.822 60.000 0.00 0.00 43.86 4.04
1308 1455 4.379243 CTCGTCTTGTGGCCGCCT 62.379 66.667 15.15 0.00 0.00 5.52
1795 1943 2.878406 GCTTACCATATCAACACCGCAT 59.122 45.455 0.00 0.00 0.00 4.73
1796 1944 2.285083 GCTTACCATATCAACACCGCA 58.715 47.619 0.00 0.00 0.00 5.69
1797 1945 1.260561 CGCTTACCATATCAACACCGC 59.739 52.381 0.00 0.00 0.00 5.68
1798 1946 1.260561 GCGCTTACCATATCAACACCG 59.739 52.381 0.00 0.00 0.00 4.94
1843 1991 3.819245 TGGTATGCCATTACCAGCC 57.181 52.632 0.00 0.00 45.23 4.85
1907 2055 4.545706 CAGCCAGCCGCCGGATTA 62.546 66.667 7.68 0.00 38.78 1.75
2047 2213 7.169140 GCAAAGATAAGTTGTTTTTCCGTGATT 59.831 33.333 0.00 0.00 0.00 2.57
2060 2226 2.872370 GCAGCCAGCAAAGATAAGTTG 58.128 47.619 0.00 0.00 44.79 3.16
2105 2271 1.548719 TGTTAGTGAGGACATCCCACG 59.451 52.381 11.53 0.00 40.11 4.94
2106 2272 2.567615 AGTGTTAGTGAGGACATCCCAC 59.432 50.000 10.07 10.07 37.42 4.61
2247 2436 0.041090 ACAATTAAGGTGGGGCTGGG 59.959 55.000 0.00 0.00 0.00 4.45
2368 2590 8.519526 TGACTTTTGCTCTGTTTTTCTTTTCTA 58.480 29.630 0.00 0.00 0.00 2.10
2370 2592 7.581011 TGACTTTTGCTCTGTTTTTCTTTTC 57.419 32.000 0.00 0.00 0.00 2.29
2371 2593 7.657354 AGTTGACTTTTGCTCTGTTTTTCTTTT 59.343 29.630 0.00 0.00 0.00 2.27
2372 2594 7.154656 AGTTGACTTTTGCTCTGTTTTTCTTT 58.845 30.769 0.00 0.00 0.00 2.52
2373 2595 6.691508 AGTTGACTTTTGCTCTGTTTTTCTT 58.308 32.000 0.00 0.00 0.00 2.52
2374 2596 6.272822 AGTTGACTTTTGCTCTGTTTTTCT 57.727 33.333 0.00 0.00 0.00 2.52
2375 2597 6.693113 CCTAGTTGACTTTTGCTCTGTTTTTC 59.307 38.462 0.00 0.00 0.00 2.29
2415 2637 1.787012 CTTTCACAAGGCCAACATGC 58.213 50.000 5.01 0.00 0.00 4.06
2466 2688 1.218704 CCCTCCCATGTGGAATGGAAT 59.781 52.381 5.93 0.00 44.57 3.01
2467 2689 0.630673 CCCTCCCATGTGGAATGGAA 59.369 55.000 5.93 0.00 44.57 3.53
2468 2690 0.552367 ACCCTCCCATGTGGAATGGA 60.552 55.000 17.89 5.93 44.57 3.41
2469 2691 0.396139 CACCCTCCCATGTGGAATGG 60.396 60.000 0.00 12.90 44.57 3.16
2470 2692 3.196040 CACCCTCCCATGTGGAATG 57.804 57.895 0.00 2.17 44.57 2.67
2592 2817 1.836802 TTATGCATTGCACTGAGGCA 58.163 45.000 14.66 3.11 43.04 4.75


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

AutoCloner maintained by Alex Coulton.