Multiple sequence alignment - TraesCS1A01G427800

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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 TraesCS1A01G427800 chr1A 100.000 3284 0 0 1 3284 581914155 581917438 0.000000e+00 6065.0
1 TraesCS1A01G427800 chr1A 94.233 815 36 7 182 989 581878649 581879459 0.000000e+00 1234.0
2 TraesCS1A01G427800 chr1A 94.567 773 36 2 511 1279 581957247 581958017 0.000000e+00 1190.0
3 TraesCS1A01G427800 chr1A 95.928 221 4 3 1 220 581878429 581878645 1.450000e-93 353.0
4 TraesCS1A01G427800 chr1A 87.215 219 14 10 2252 2460 582218631 582218845 1.520000e-58 237.0
5 TraesCS1A01G427800 chr1A 76.940 451 71 23 901 1345 581958853 581959276 3.300000e-55 226.0
6 TraesCS1A01G427800 chr1A 82.353 204 32 4 3042 3242 348683042 348683244 1.210000e-39 174.0
7 TraesCS1A01G427800 chr1D 96.399 1666 50 5 182 1838 484794665 484796329 0.000000e+00 2736.0
8 TraesCS1A01G427800 chr1D 98.529 748 11 0 2528 3275 484797081 484797828 0.000000e+00 1321.0
9 TraesCS1A01G427800 chr1D 98.011 704 9 2 1829 2528 484796350 484797052 0.000000e+00 1218.0
10 TraesCS1A01G427800 chr1D 93.390 817 37 9 182 989 484737601 484738409 0.000000e+00 1194.0
11 TraesCS1A01G427800 chr1D 88.629 642 51 6 253 885 484563363 484563991 0.000000e+00 761.0
12 TraesCS1A01G427800 chr1D 96.018 226 5 2 182 403 484869393 484869618 6.700000e-97 364.0
13 TraesCS1A01G427800 chr1D 95.755 212 9 0 2124 2335 484566150 484566361 3.140000e-90 342.0
14 TraesCS1A01G427800 chr1D 94.570 221 7 3 1 220 484737381 484737597 1.460000e-88 337.0
15 TraesCS1A01G427800 chr1D 92.727 220 10 4 3 220 484869174 484869389 2.460000e-81 313.0
16 TraesCS1A01G427800 chr1D 92.727 220 9 3 3 220 484562484 484562698 8.850000e-81 311.0
17 TraesCS1A01G427800 chr1D 93.000 100 7 0 2232 2331 484739294 484739393 2.640000e-31 147.0
18 TraesCS1A01G427800 chr1B 92.052 1535 58 34 1 1503 675223326 675221824 0.000000e+00 2100.0
19 TraesCS1A01G427800 chr1B 92.964 1336 64 9 182 1503 674892754 674894073 0.000000e+00 1919.0
20 TraesCS1A01G427800 chr1B 92.981 983 46 5 855 1829 646685715 646686682 0.000000e+00 1411.0
21 TraesCS1A01G427800 chr1B 89.489 1037 53 28 1829 2821 646686711 646687735 0.000000e+00 1260.0
22 TraesCS1A01G427800 chr1B 88.857 1041 33 24 1829 2840 674894543 674895529 0.000000e+00 1203.0
23 TraesCS1A01G427800 chr1B 88.857 1041 33 24 1829 2840 675221354 675220368 0.000000e+00 1203.0
24 TraesCS1A01G427800 chr1B 94.582 443 19 2 2838 3275 674895574 674896016 0.000000e+00 680.0
25 TraesCS1A01G427800 chr1B 94.582 443 19 2 2838 3275 675220323 675219881 0.000000e+00 680.0
26 TraesCS1A01G427800 chr1B 92.325 443 27 1 417 859 646685159 646685594 1.000000e-174 623.0
27 TraesCS1A01G427800 chr1B 94.207 328 19 0 1502 1829 674894187 674894514 4.890000e-138 501.0
28 TraesCS1A01G427800 chr1B 94.207 328 19 0 1502 1829 675221710 675221383 4.890000e-138 501.0
29 TraesCS1A01G427800 chr1B 85.924 476 27 14 522 989 675228717 675228274 3.840000e-129 472.0
30 TraesCS1A01G427800 chr1B 91.864 295 19 2 2046 2335 674821008 674821302 1.100000e-109 407.0
31 TraesCS1A01G427800 chr1B 98.222 225 1 1 182 403 674818910 674819134 1.100000e-104 390.0
32 TraesCS1A01G427800 chr1B 96.018 226 5 2 182 403 674932819 674933044 6.700000e-97 364.0
33 TraesCS1A01G427800 chr1B 89.310 290 21 5 118 403 646774513 646774796 4.030000e-94 355.0
34 TraesCS1A01G427800 chr1B 95.475 221 5 3 1 220 674818690 674818906 6.740000e-92 348.0
35 TraesCS1A01G427800 chr1B 94.064 219 8 3 3 220 646684893 646685107 8.790000e-86 327.0
36 TraesCS1A01G427800 chr1B 94.175 206 8 1 3074 3275 675218212 675218007 8.850000e-81 311.0
37 TraesCS1A01G427800 chr1B 92.166 217 11 4 3 217 674932598 674932810 5.330000e-78 302.0
38 TraesCS1A01G427800 chr1B 91.284 218 14 3 3 219 674892536 674892749 3.210000e-75 292.0
39 TraesCS1A01G427800 chr1B 84.581 227 16 9 2239 2454 646776375 646776593 1.190000e-49 207.0
40 TraesCS1A01G427800 chr1B 96.809 94 3 0 2747 2840 675219292 675219199 1.220000e-34 158.0
41 TraesCS1A01G427800 chr1B 92.063 63 4 1 2964 3026 646687875 646687936 1.620000e-13 87.9
42 TraesCS1A01G427800 chr2D 83.744 406 50 6 1841 2233 175360234 175359832 1.440000e-98 370.0
43 TraesCS1A01G427800 chr2D 81.818 198 30 4 3047 3242 392626728 392626921 9.430000e-36 161.0
44 TraesCS1A01G427800 chr2A 83.495 412 51 8 1835 2233 175482633 175482226 5.180000e-98 368.0
45 TraesCS1A01G427800 chr2B 83.333 198 27 4 3047 3242 464557293 464557486 9.360000e-41 178.0
46 TraesCS1A01G427800 chr7D 82.178 202 34 2 3042 3241 602165646 602165847 4.360000e-39 172.0
47 TraesCS1A01G427800 chr3A 81.407 199 36 1 3047 3244 692701579 692701381 9.430000e-36 161.0
48 TraesCS1A01G427800 chr6B 87.413 143 9 6 216 354 30354199 30354336 4.390000e-34 156.0


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 TraesCS1A01G427800 chr1A 581914155 581917438 3283 False 6065.000000 6065 100.000000 1 3284 1 chr1A.!!$F2 3283
1 TraesCS1A01G427800 chr1A 581878429 581879459 1030 False 793.500000 1234 95.080500 1 989 2 chr1A.!!$F4 988
2 TraesCS1A01G427800 chr1A 581957247 581959276 2029 False 708.000000 1190 85.753500 511 1345 2 chr1A.!!$F5 834
3 TraesCS1A01G427800 chr1D 484794665 484797828 3163 False 1758.333333 2736 97.646333 182 3275 3 chr1D.!!$F3 3093
4 TraesCS1A01G427800 chr1D 484737381 484739393 2012 False 559.333333 1194 93.653333 1 2331 3 chr1D.!!$F2 2330
5 TraesCS1A01G427800 chr1D 484562484 484566361 3877 False 471.333333 761 92.370333 3 2335 3 chr1D.!!$F1 2332
6 TraesCS1A01G427800 chr1B 674892536 674896016 3480 False 919.000000 1919 92.378800 3 3275 5 chr1B.!!$F4 3272
7 TraesCS1A01G427800 chr1B 675218007 675223326 5319 True 825.500000 2100 93.447000 1 3275 6 chr1B.!!$R2 3274
8 TraesCS1A01G427800 chr1B 646684893 646687936 3043 False 741.780000 1411 92.184400 3 3026 5 chr1B.!!$F1 3023
9 TraesCS1A01G427800 chr1B 674818690 674821302 2612 False 381.666667 407 95.187000 1 2335 3 chr1B.!!$F3 2334
10 TraesCS1A01G427800 chr1B 646774513 646776593 2080 False 281.000000 355 86.945500 118 2454 2 chr1B.!!$F2 2336

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
548 1193 2.722094 CCTAGCCCAACTTGTATGCAA 58.278 47.619 0.00 0.0 0.00 4.08 F
1258 2223 1.302993 CAAGGTACCACCCCAACGG 60.303 63.158 15.94 0.0 39.75 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1404 3544 0.181114 AGTTGCACTTCACCAGCTCA 59.819 50.000 0.0 0.0 0.0 4.26 R
2350 6009 1.277273 CTGAACAGGAGATGAGTGGCA 59.723 52.381 0.0 0.0 0.0 4.92 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
548 1193 2.722094 CCTAGCCCAACTTGTATGCAA 58.278 47.619 0.00 0.00 0.00 4.08
691 1345 3.842732 TGCTGCTTTGTGATGATGAAG 57.157 42.857 0.00 0.00 0.00 3.02
1258 2223 1.302993 CAAGGTACCACCCCAACGG 60.303 63.158 15.94 0.00 39.75 4.44
1407 3547 4.709840 CCAGAGGCAGTTGGTGAG 57.290 61.111 0.00 0.00 0.00 3.51
1408 3548 1.673665 CCAGAGGCAGTTGGTGAGC 60.674 63.158 0.00 0.00 0.00 4.26
1551 4181 0.453390 GCTGCCATCTAACTGTTGCC 59.547 55.000 2.69 0.00 0.00 4.52
1614 4706 0.319083 TGAGTTGCGTTATGGGACGT 59.681 50.000 0.00 0.00 44.50 4.34
1698 5258 1.737236 GCATTCATGAACACCGTGCTA 59.263 47.619 19.11 0.00 0.00 3.49
1710 5270 1.140252 ACCGTGCTACTCTGGTGTTTT 59.860 47.619 0.00 0.00 32.33 2.43
1803 5366 4.842574 ACCAAAAATTGCAAAACCAGAGT 58.157 34.783 1.71 0.00 0.00 3.24
1823 5399 3.115556 GCGGTTGCAACAAGGTGA 58.884 55.556 29.55 0.00 42.15 4.02
1839 5444 4.203654 AGGTGAACGGTTATCTCCTTTC 57.796 45.455 0.00 0.00 37.48 2.62
2335 5994 4.575885 TGATGCAAGTCACCTTACTTACC 58.424 43.478 0.00 0.00 37.61 2.85
2336 5995 4.041075 TGATGCAAGTCACCTTACTTACCA 59.959 41.667 0.00 0.00 37.61 3.25
2337 5996 4.634012 TGCAAGTCACCTTACTTACCAT 57.366 40.909 0.00 0.00 37.61 3.55
2338 5997 4.575885 TGCAAGTCACCTTACTTACCATC 58.424 43.478 0.00 0.00 37.61 3.51
2339 5998 3.939592 GCAAGTCACCTTACTTACCATCC 59.060 47.826 0.00 0.00 37.61 3.51
2340 5999 4.323562 GCAAGTCACCTTACTTACCATCCT 60.324 45.833 0.00 0.00 37.61 3.24
2343 6002 5.091552 AGTCACCTTACTTACCATCCTCAA 58.908 41.667 0.00 0.00 0.00 3.02
2344 6003 5.187967 AGTCACCTTACTTACCATCCTCAAG 59.812 44.000 0.00 0.00 0.00 3.02
2345 6004 5.187186 GTCACCTTACTTACCATCCTCAAGA 59.813 44.000 0.00 0.00 0.00 3.02
2346 6005 5.187186 TCACCTTACTTACCATCCTCAAGAC 59.813 44.000 0.00 0.00 0.00 3.01
2347 6006 5.046591 CACCTTACTTACCATCCTCAAGACA 60.047 44.000 0.00 0.00 0.00 3.41
2349 6008 6.215636 ACCTTACTTACCATCCTCAAGACAAT 59.784 38.462 0.00 0.00 0.00 2.71
2350 6009 7.112779 CCTTACTTACCATCCTCAAGACAATT 58.887 38.462 0.00 0.00 0.00 2.32
2351 6010 7.066284 CCTTACTTACCATCCTCAAGACAATTG 59.934 40.741 3.24 3.24 0.00 2.32
2352 6011 4.702131 ACTTACCATCCTCAAGACAATTGC 59.298 41.667 5.05 0.00 0.00 3.56
2353 6012 2.450476 ACCATCCTCAAGACAATTGCC 58.550 47.619 5.05 0.00 0.00 4.52
2355 6014 2.165030 CCATCCTCAAGACAATTGCCAC 59.835 50.000 5.05 0.00 0.00 5.01
2797 6511 1.597663 AGCGTTCAGTTTTTCTCCACG 59.402 47.619 0.00 0.00 33.93 4.94
2913 6709 5.106987 CCAACAGGTTTAAAATGAGCATTGC 60.107 40.000 0.00 0.00 0.00 3.56
2937 6733 4.822685 ACATATTCATTTTTGGCCAGCA 57.177 36.364 5.11 0.00 0.00 4.41
2997 6793 5.512788 GTCTATTTGCGAATGGTGAATGTTG 59.487 40.000 9.60 0.00 0.00 3.33
3045 6842 3.904965 TGTGGTAGTAACAAGATGGTGGA 59.095 43.478 0.00 0.00 0.00 4.02
3224 7025 1.135546 CAGAATCCCGGAGATCGATCG 60.136 57.143 19.33 9.36 42.43 3.69
3234 7035 3.142951 GGAGATCGATCGAGAAGAAGGA 58.857 50.000 23.84 0.00 0.00 3.36
3275 7076 3.559655 TGAACACAAGTGACCGAAAGATG 59.440 43.478 7.28 0.00 0.00 2.90
3276 7077 3.469008 ACACAAGTGACCGAAAGATGA 57.531 42.857 7.28 0.00 0.00 2.92
3277 7078 3.393800 ACACAAGTGACCGAAAGATGAG 58.606 45.455 7.28 0.00 0.00 2.90
3278 7079 3.069586 ACACAAGTGACCGAAAGATGAGA 59.930 43.478 7.28 0.00 0.00 3.27
3279 7080 3.677121 CACAAGTGACCGAAAGATGAGAG 59.323 47.826 0.00 0.00 0.00 3.20
3281 7082 4.039245 ACAAGTGACCGAAAGATGAGAGAA 59.961 41.667 0.00 0.00 0.00 2.87
3282 7083 5.174395 CAAGTGACCGAAAGATGAGAGAAT 58.826 41.667 0.00 0.00 0.00 2.40
3283 7084 5.413309 AGTGACCGAAAGATGAGAGAATT 57.587 39.130 0.00 0.00 0.00 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
443 1081 6.519679 TCAAACAATCAGCTGCAATATCTT 57.480 33.333 9.47 0.00 0.00 2.40
548 1193 3.332919 CACAGCTCATCTTACAGCAGTT 58.667 45.455 0.00 0.00 38.18 3.16
691 1345 1.667724 CATCGACATTCAGGTTCAGCC 59.332 52.381 0.00 0.00 37.58 4.85
818 1473 7.273598 GTGAAGAAAAAGAACTGTTTCTGTTCC 59.726 37.037 17.31 9.87 41.98 3.62
1400 3540 0.819259 GCACTTCACCAGCTCACCAA 60.819 55.000 0.00 0.00 0.00 3.67
1401 3541 1.227943 GCACTTCACCAGCTCACCA 60.228 57.895 0.00 0.00 0.00 4.17
1402 3542 0.819259 TTGCACTTCACCAGCTCACC 60.819 55.000 0.00 0.00 0.00 4.02
1403 3543 0.308993 GTTGCACTTCACCAGCTCAC 59.691 55.000 0.00 0.00 0.00 3.51
1404 3544 0.181114 AGTTGCACTTCACCAGCTCA 59.819 50.000 0.00 0.00 0.00 4.26
1405 3545 0.590195 CAGTTGCACTTCACCAGCTC 59.410 55.000 0.00 0.00 0.00 4.09
1406 3546 1.450531 GCAGTTGCACTTCACCAGCT 61.451 55.000 0.00 0.00 41.59 4.24
1407 3547 1.008079 GCAGTTGCACTTCACCAGC 60.008 57.895 0.00 0.00 41.59 4.85
1551 4181 2.145536 TGGCTGCACGCAATATATCAG 58.854 47.619 0.50 0.00 41.67 2.90
1614 4706 0.798159 CGCAGTCATAGCACTTGCAA 59.202 50.000 3.62 0.00 45.16 4.08
1710 5270 3.636300 CACATTTGTTTCAGGTTCCTGGA 59.364 43.478 17.37 7.37 35.01 3.86
1714 5274 3.555547 GCAACACATTTGTTTCAGGTTCC 59.444 43.478 0.00 0.00 43.89 3.62
1823 5399 5.472478 GTCTTTTGGAAAGGAGATAACCGTT 59.528 40.000 1.04 0.00 34.64 4.44
1839 5444 7.856145 AGAATAAGCATGTCTAGTCTTTTGG 57.144 36.000 0.00 0.00 0.00 3.28
2335 5994 3.087031 AGTGGCAATTGTCTTGAGGATG 58.913 45.455 12.01 0.00 0.00 3.51
2336 5995 3.245016 TGAGTGGCAATTGTCTTGAGGAT 60.245 43.478 12.01 0.00 0.00 3.24
2337 5996 2.106338 TGAGTGGCAATTGTCTTGAGGA 59.894 45.455 12.01 0.00 0.00 3.71
2338 5997 2.507484 TGAGTGGCAATTGTCTTGAGG 58.493 47.619 12.01 0.00 0.00 3.86
2339 5998 4.008330 AGATGAGTGGCAATTGTCTTGAG 58.992 43.478 12.01 0.00 0.00 3.02
2340 5999 4.005650 GAGATGAGTGGCAATTGTCTTGA 58.994 43.478 12.01 0.00 0.00 3.02
2343 6002 2.575279 AGGAGATGAGTGGCAATTGTCT 59.425 45.455 12.01 1.81 0.00 3.41
2344 6003 2.681848 CAGGAGATGAGTGGCAATTGTC 59.318 50.000 2.20 2.20 0.00 3.18
2345 6004 2.040813 ACAGGAGATGAGTGGCAATTGT 59.959 45.455 7.40 0.00 0.00 2.71
2346 6005 2.719739 ACAGGAGATGAGTGGCAATTG 58.280 47.619 0.00 0.00 0.00 2.32
2347 6006 3.245016 TGAACAGGAGATGAGTGGCAATT 60.245 43.478 0.00 0.00 0.00 2.32
2349 6008 1.699083 TGAACAGGAGATGAGTGGCAA 59.301 47.619 0.00 0.00 0.00 4.52
2350 6009 1.277273 CTGAACAGGAGATGAGTGGCA 59.723 52.381 0.00 0.00 0.00 4.92
2351 6010 1.552337 TCTGAACAGGAGATGAGTGGC 59.448 52.381 1.93 0.00 0.00 5.01
2352 6011 3.969287 TTCTGAACAGGAGATGAGTGG 57.031 47.619 1.93 0.00 0.00 4.00
2353 6012 7.053316 AGATATTCTGAACAGGAGATGAGTG 57.947 40.000 1.93 0.00 0.00 3.51
2355 6014 6.295236 GGGAGATATTCTGAACAGGAGATGAG 60.295 46.154 1.93 0.00 0.00 2.90
2427 6107 2.477176 TTGTCGCCGTGCTTGCTTT 61.477 52.632 0.00 0.00 0.00 3.51
2667 6378 7.065803 ACAAAGAATAACCGTATCACTTCATGG 59.934 37.037 0.00 0.00 0.00 3.66
2797 6511 1.666189 GCCTCGTGCTGAATTTAGTCC 59.334 52.381 0.00 0.00 36.87 3.85
2913 6709 6.339730 TGCTGGCCAAAAATGAATATGTAAG 58.660 36.000 7.01 0.00 0.00 2.34
2937 6733 2.980233 GACTGCCCTTGCGTTGCT 60.980 61.111 0.00 0.00 41.78 3.91
3045 6842 6.068010 TCAACCCATTGCCTTATCGAATTAT 58.932 36.000 0.00 0.00 35.63 1.28
3182 6983 2.192175 CCCGCGGGGCTTTAGAAT 59.808 61.111 37.42 0.00 35.35 2.40
3224 7025 3.320673 TTCGCTCCTTTCCTTCTTCTC 57.679 47.619 0.00 0.00 0.00 2.87


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

AutoCloner maintained by Alex Coulton.