Multiple sequence alignment - TraesCS4A01G226200

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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 TraesCS4A01G226200 chr4A 100.000 2456 0 0 1 2456 534259657 534257202 0.000000e+00 4536.0
1 TraesCS4A01G226200 chr4B 92.283 2177 151 14 281 2450 92463338 92465504 0.000000e+00 3073.0
2 TraesCS4A01G226200 chr4B 89.404 302 16 5 1 286 92462990 92463291 1.390000e-97 366.0
3 TraesCS4A01G226200 chr4D 93.447 1526 84 13 937 2456 62549446 62550961 0.000000e+00 2250.0
4 TraesCS4A01G226200 chr4D 92.857 658 38 5 281 929 62548681 62549338 0.000000e+00 946.0
5 TraesCS4A01G226200 chr4D 90.033 301 12 7 3 286 62548335 62548634 8.290000e-100 374.0
6 TraesCS4A01G226200 chr4D 92.593 54 4 0 2338 2391 495988049 495988102 7.280000e-11 78.7
7 TraesCS4A01G226200 chr4D 95.455 44 2 0 2330 2373 509139149 509139192 1.220000e-08 71.3
8 TraesCS4A01G226200 chr5A 86.207 87 11 1 2338 2424 185832804 185832889 2.600000e-15 93.5
9 TraesCS4A01G226200 chr5A 94.737 38 2 0 2330 2367 673854873 673854836 2.640000e-05 60.2
10 TraesCS4A01G226200 chr1D 84.507 71 10 1 2330 2400 399158546 399158615 4.380000e-08 69.4
11 TraesCS4A01G226200 chr5B 97.222 36 0 1 251 285 34488743 34488708 2.640000e-05 60.2
12 TraesCS4A01G226200 chr7B 90.698 43 4 0 1732 1774 62763452 62763410 9.490000e-05 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 TraesCS4A01G226200 chr4A 534257202 534259657 2455 True 4536.0 4536 100.000000 1 2456 1 chr4A.!!$R1 2455
1 TraesCS4A01G226200 chr4B 92462990 92465504 2514 False 1719.5 3073 90.843500 1 2450 2 chr4B.!!$F1 2449
2 TraesCS4A01G226200 chr4D 62548335 62550961 2626 False 1190.0 2250 92.112333 3 2456 3 chr4D.!!$F3 2453

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
308 378 0.105760 AACCCTGGTTTGGACATGCA 60.106 50.000 0.00 0.0 34.22 3.96 F
1061 1240 1.071385 CTCTGTTGTGGCCTCTTCAGT 59.929 52.381 20.36 0.0 0.00 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1167 1346 0.324943 CAAAGGATCCGTCTGGGTGT 59.675 55.0 5.98 0.0 37.0 4.16 R
2245 2429 0.822532 ACGGACGTGTCTCCTTGTCT 60.823 55.0 0.00 0.0 0.0 3.41 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
45 46 4.018415 AGGGCCACACATTTACTACTGATT 60.018 41.667 6.18 0.00 0.00 2.57
57 58 2.259618 CTACTGATTTACGCGTGCTGT 58.740 47.619 24.59 18.65 0.00 4.40
102 118 1.593265 GGCTTGGAATGCTTGGTGG 59.407 57.895 0.00 0.00 37.15 4.61
112 128 0.251297 TGCTTGGTGGGGATTGACTG 60.251 55.000 0.00 0.00 0.00 3.51
204 221 2.417933 TGACTCTAGACGCCGAGTTAAC 59.582 50.000 0.00 0.00 40.37 2.01
308 378 0.105760 AACCCTGGTTTGGACATGCA 60.106 50.000 0.00 0.00 34.22 3.96
323 393 5.411361 TGGACATGCATTTTGTAGTAGTGAC 59.589 40.000 0.00 0.00 0.00 3.67
325 395 6.072728 GGACATGCATTTTGTAGTAGTGACAA 60.073 38.462 0.00 0.00 35.03 3.18
333 403 7.867305 TTTTGTAGTAGTGACAAAATGGTGA 57.133 32.000 9.07 0.00 46.55 4.02
341 411 7.992608 AGTAGTGACAAAATGGTGATATGCATA 59.007 33.333 9.27 9.27 0.00 3.14
349 419 8.849168 CAAAATGGTGATATGCATACTTTAGGA 58.151 33.333 8.99 0.00 0.00 2.94
350 420 8.627208 AAATGGTGATATGCATACTTTAGGAG 57.373 34.615 8.99 0.00 0.00 3.69
351 421 6.747414 TGGTGATATGCATACTTTAGGAGT 57.253 37.500 8.99 0.00 42.55 3.85
352 422 7.136822 TGGTGATATGCATACTTTAGGAGTT 57.863 36.000 8.99 0.00 39.86 3.01
353 423 7.573710 TGGTGATATGCATACTTTAGGAGTTT 58.426 34.615 8.99 0.00 39.86 2.66
354 424 8.052748 TGGTGATATGCATACTTTAGGAGTTTT 58.947 33.333 8.99 0.00 39.86 2.43
413 490 3.586470 TTCAAGGGTTAGCAAGGACAA 57.414 42.857 0.00 0.00 0.00 3.18
498 575 5.329035 AGGTATGACAATGCCATCAAAAC 57.671 39.130 0.00 0.00 40.85 2.43
520 597 8.582433 AAACATGTTATTTCCCTTAAAACACG 57.418 30.769 12.39 0.00 0.00 4.49
521 598 6.153756 ACATGTTATTTCCCTTAAAACACGC 58.846 36.000 0.00 0.00 0.00 5.34
570 647 8.916062 AGCATATCAATGTTGTTCAAATATGGA 58.084 29.630 12.20 4.57 35.38 3.41
651 728 8.180317 AGTTTTACGGAATTTGTGTTTTCTTG 57.820 30.769 0.00 0.00 0.00 3.02
698 775 9.628746 GCAGGAAATGAATTTTATGCAATTTTT 57.371 25.926 15.59 0.00 39.37 1.94
890 967 6.208402 TGCATTAACATTACACTCCACATTGT 59.792 34.615 0.00 0.00 0.00 2.71
929 1008 8.120256 ACAGGTAGACCTATATATGAGGCTAT 57.880 38.462 0.00 0.00 46.65 2.97
978 1157 8.265055 TCTTCCACATACTTCGAAAAGGATATT 58.735 33.333 0.00 0.00 33.48 1.28
1015 1194 2.455557 CAACCATGGCCAAGAACCATA 58.544 47.619 10.96 0.00 46.32 2.74
1016 1195 2.428171 CAACCATGGCCAAGAACCATAG 59.572 50.000 10.96 0.00 46.32 2.23
1061 1240 1.071385 CTCTGTTGTGGCCTCTTCAGT 59.929 52.381 20.36 0.00 0.00 3.41
1067 1246 2.435059 GGCCTCTTCAGTCACCGC 60.435 66.667 0.00 0.00 0.00 5.68
1162 1341 2.893637 CGGAGGGTGTTCAAGACTATG 58.106 52.381 0.00 0.00 0.00 2.23
1163 1342 2.633488 GGAGGGTGTTCAAGACTATGC 58.367 52.381 0.00 0.00 0.00 3.14
1167 1346 2.504175 GGGTGTTCAAGACTATGCCCTA 59.496 50.000 0.00 0.00 32.47 3.53
1218 1397 2.456119 CGGCGGCTGTGAGATCAAC 61.456 63.158 7.61 0.00 0.00 3.18
1219 1398 1.375908 GGCGGCTGTGAGATCAACA 60.376 57.895 0.00 0.00 0.00 3.33
1242 1421 1.718280 GGGGATTCACTCTCCGGTAT 58.282 55.000 0.00 0.00 33.82 2.73
1290 1469 2.605818 GTCCATGTTGATTAACGCGCTA 59.394 45.455 5.73 0.00 39.71 4.26
1375 1554 2.751259 GACCAGCTCATCTTCAATGCAA 59.249 45.455 0.00 0.00 0.00 4.08
1377 1556 2.753452 CCAGCTCATCTTCAATGCAACT 59.247 45.455 0.00 0.00 0.00 3.16
1414 1593 4.573201 CGTTTCCTGTTAACAACTTCTCCA 59.427 41.667 10.03 0.00 0.00 3.86
1415 1594 5.277345 CGTTTCCTGTTAACAACTTCTCCAG 60.277 44.000 10.03 0.00 0.00 3.86
1506 1686 7.939782 TGCTTCTTGATTTTGTTAGATCAACA 58.060 30.769 0.00 1.00 45.49 3.33
1507 1687 8.579006 TGCTTCTTGATTTTGTTAGATCAACAT 58.421 29.630 10.27 0.00 46.38 2.71
1552 1732 5.197451 TGTGGGTTTGTCTATTGTGACTTT 58.803 37.500 0.00 0.00 37.79 2.66
1706 1890 5.827267 TCACAAAGAAATCACTGAACCATGA 59.173 36.000 0.00 0.00 0.00 3.07
1764 1948 1.489649 TGGACCCTTAAAACGGACACA 59.510 47.619 0.00 0.00 0.00 3.72
1768 1952 3.732212 ACCCTTAAAACGGACACACTAC 58.268 45.455 0.00 0.00 0.00 2.73
1805 1989 1.284982 CCGAAAGCGTCTGTGGACAG 61.285 60.000 0.00 0.00 42.21 3.51
1815 1999 2.428890 GTCTGTGGACAGGATACAGGAG 59.571 54.545 6.94 0.00 43.91 3.69
1831 2015 1.076549 GAGCCAACCATCCAACCCA 59.923 57.895 0.00 0.00 0.00 4.51
1840 2024 1.538047 CATCCAACCCAACACCTCAG 58.462 55.000 0.00 0.00 0.00 3.35
1938 2122 3.225104 AGTTGATCATGCACAACAACCT 58.775 40.909 25.00 10.73 45.70 3.50
1943 2127 2.929641 TCATGCACAACAACCTTCTGA 58.070 42.857 0.00 0.00 0.00 3.27
1989 2173 2.401766 CCGCCACTTCTCATGCACC 61.402 63.158 0.00 0.00 0.00 5.01
1992 2176 1.675714 CGCCACTTCTCATGCACCTTA 60.676 52.381 0.00 0.00 0.00 2.69
1993 2177 1.740025 GCCACTTCTCATGCACCTTAC 59.260 52.381 0.00 0.00 0.00 2.34
1995 2179 2.612972 CCACTTCTCATGCACCTTACGT 60.613 50.000 0.00 0.00 0.00 3.57
1996 2180 2.668457 CACTTCTCATGCACCTTACGTC 59.332 50.000 0.00 0.00 0.00 4.34
1997 2181 2.299013 ACTTCTCATGCACCTTACGTCA 59.701 45.455 0.00 0.00 0.00 4.35
1998 2182 3.055819 ACTTCTCATGCACCTTACGTCAT 60.056 43.478 0.00 0.00 0.00 3.06
1999 2183 2.892374 TCTCATGCACCTTACGTCATG 58.108 47.619 0.00 0.00 38.05 3.07
2000 2184 2.495669 TCTCATGCACCTTACGTCATGA 59.504 45.455 12.94 12.94 41.85 3.07
2001 2185 3.132824 TCTCATGCACCTTACGTCATGAT 59.867 43.478 13.71 0.00 42.75 2.45
2109 2293 2.472816 CTTCGCCAAACAAAGCAACAT 58.527 42.857 0.00 0.00 0.00 2.71
2171 2355 5.471556 ACAACATGCAGGAAAAATCATGA 57.528 34.783 4.84 0.00 38.77 3.07
2183 2367 7.658575 CAGGAAAAATCATGACTTTTGATTGGT 59.341 33.333 18.78 0.00 41.69 3.67
2214 2398 0.375454 CCGAACACTTGCAAACGTCA 59.625 50.000 0.00 0.00 0.00 4.35
2245 2429 3.319405 TGCTTCTGGTTTGCGGAATTTTA 59.681 39.130 0.00 0.00 0.00 1.52
2253 2437 4.022676 GGTTTGCGGAATTTTAGACAAGGA 60.023 41.667 0.00 0.00 0.00 3.36
2303 2487 2.351253 CGTTGGATGAAAAATGCGTCCA 60.351 45.455 0.00 0.00 46.74 4.02
2375 2559 2.419990 CCGGTGTCCACATGTACATCAT 60.420 50.000 5.07 0.00 37.22 2.45
2405 2589 6.528072 GCAAAGAAACAGACAAATGCTATACC 59.472 38.462 0.00 0.00 0.00 2.73
2408 2592 7.383102 AGAAACAGACAAATGCTATACCAAG 57.617 36.000 0.00 0.00 0.00 3.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.064758 GGCCCTGACAATACCACATCA 60.065 52.381 0.00 0.00 0.00 3.07
45 46 0.109458 CCTAGTCACAGCACGCGTAA 60.109 55.000 13.44 0.00 0.00 3.18
57 58 2.024369 TGAGGTCATAGCACCCTAGTCA 60.024 50.000 0.00 0.00 37.09 3.41
102 118 0.620556 TCCTTCAGCCAGTCAATCCC 59.379 55.000 0.00 0.00 0.00 3.85
112 128 2.693267 ATCCGTAACTTCCTTCAGCC 57.307 50.000 0.00 0.00 0.00 4.85
323 393 8.849168 TCCTAAAGTATGCATATCACCATTTTG 58.151 33.333 10.16 6.02 0.00 2.44
325 395 8.220559 ACTCCTAAAGTATGCATATCACCATTT 58.779 33.333 10.16 7.28 36.07 2.32
328 398 6.747414 ACTCCTAAAGTATGCATATCACCA 57.253 37.500 10.16 0.00 36.07 4.17
431 508 9.098355 CTTAGAAAAGCTAAAAACAAAAGGCTT 57.902 29.630 0.00 0.00 38.56 4.35
498 575 6.153067 TGCGTGTTTTAAGGGAAATAACATG 58.847 36.000 0.00 0.00 31.82 3.21
633 710 8.130307 AGAAAATCAAGAAAACACAAATTCCG 57.870 30.769 0.00 0.00 0.00 4.30
721 798 9.567776 TTATCCAAATCAAGTAGAAGAACAACA 57.432 29.630 0.00 0.00 0.00 3.33
878 955 3.685139 ACTGGACTACAATGTGGAGTG 57.315 47.619 3.14 0.00 42.76 3.51
929 1008 5.738619 TGATTGTGACTAAAGGCAGTCTA 57.261 39.130 5.24 0.00 44.41 2.59
978 1157 7.663905 GCCATGGTTGGTACTTATGATATGTTA 59.336 37.037 14.67 0.00 45.57 2.41
1015 1194 0.043940 ACAAGGAGGATGAGGAGGCT 59.956 55.000 0.00 0.00 0.00 4.58
1016 1195 0.179936 CACAAGGAGGATGAGGAGGC 59.820 60.000 0.00 0.00 0.00 4.70
1067 1246 3.775654 GGGAGGTGCTCGAGGTGG 61.776 72.222 15.58 0.00 0.00 4.61
1079 1258 1.301293 GCTGTTGAAGAGGGGGAGG 59.699 63.158 0.00 0.00 0.00 4.30
1162 1341 2.029307 GATCCGTCTGGGTGTAGGGC 62.029 65.000 0.00 0.00 37.00 5.19
1163 1342 1.400530 GGATCCGTCTGGGTGTAGGG 61.401 65.000 0.00 0.00 37.00 3.53
1167 1346 0.324943 CAAAGGATCCGTCTGGGTGT 59.675 55.000 5.98 0.00 37.00 4.16
1218 1397 0.394565 GGAGAGTGAATCCCCCGATG 59.605 60.000 0.00 0.00 0.00 3.84
1219 1398 1.115930 CGGAGAGTGAATCCCCCGAT 61.116 60.000 5.59 0.00 43.50 4.18
1242 1421 1.630223 TGCCATGCACATTTCCTTCA 58.370 45.000 0.00 0.00 31.71 3.02
1272 1451 3.997276 TGTTAGCGCGTTAATCAACATG 58.003 40.909 18.42 0.00 34.05 3.21
1290 1469 1.071471 CTTGACGCTCACCCCTGTT 59.929 57.895 0.00 0.00 0.00 3.16
1375 1554 6.655003 ACAGGAAACGATTTTGATATCACAGT 59.345 34.615 4.48 0.00 0.00 3.55
1377 1556 7.447374 AACAGGAAACGATTTTGATATCACA 57.553 32.000 4.48 0.00 0.00 3.58
1447 1626 7.122055 TGTTGCTAACCCATTAATCTACTTTGG 59.878 37.037 0.00 0.00 0.00 3.28
1506 1686 7.811236 CACAAGAATCAAGTAACAATTGAGCAT 59.189 33.333 13.59 0.00 39.86 3.79
1507 1687 7.140705 CACAAGAATCAAGTAACAATTGAGCA 58.859 34.615 13.59 0.00 39.86 4.26
1627 1807 7.952671 TCAGGAGTAACATAAACTATGCCTAG 58.047 38.462 0.00 0.00 39.79 3.02
1784 1968 0.389948 GTCCACAGACGCTTTCGGAT 60.390 55.000 0.00 0.00 40.69 4.18
1805 1989 1.202818 GGATGGTTGGCTCCTGTATCC 60.203 57.143 0.00 0.00 0.00 2.59
1815 1999 1.118356 TGTTGGGTTGGATGGTTGGC 61.118 55.000 0.00 0.00 0.00 4.52
1831 2015 1.194781 AGACGGGCATCTGAGGTGTT 61.195 55.000 0.00 0.00 0.00 3.32
1879 2063 3.014623 GGCTAGGTTGTTTAGCGGAATT 58.985 45.455 0.00 0.00 43.47 2.17
1880 2064 2.238898 AGGCTAGGTTGTTTAGCGGAAT 59.761 45.455 0.00 0.00 43.47 3.01
1884 2068 2.202566 GCTAGGCTAGGTTGTTTAGCG 58.797 52.381 22.40 0.00 43.47 4.26
1938 2122 6.039159 TGTGCATGAACAACTATTTGTCAGAA 59.961 34.615 3.25 0.00 45.69 3.02
1943 2127 6.021885 GCCTTGTGCATGAACAACTATTTGT 61.022 40.000 15.66 0.00 43.47 2.83
1989 2173 4.377124 GCATGAGCATGATCATGACGTAAG 60.377 45.833 42.94 23.85 41.20 2.34
1992 2176 1.871676 GCATGAGCATGATCATGACGT 59.128 47.619 42.94 24.55 41.20 4.34
1993 2177 2.143925 AGCATGAGCATGATCATGACG 58.856 47.619 42.94 25.69 45.49 4.35
1995 2179 3.485463 TGAGCATGAGCATGATCATGA 57.515 42.857 42.94 27.16 45.49 3.07
1996 2180 3.671702 GCATGAGCATGAGCATGATCATG 60.672 47.826 40.01 40.01 45.49 3.07
1997 2181 2.489722 GCATGAGCATGAGCATGATCAT 59.510 45.455 28.63 28.63 45.49 2.45
1998 2182 1.880027 GCATGAGCATGAGCATGATCA 59.120 47.619 27.12 27.12 45.49 2.92
1999 2183 2.620779 GCATGAGCATGAGCATGATC 57.379 50.000 24.01 18.82 45.49 2.92
2032 2216 3.893521 TGTGCATGAGAATCCATGTGAT 58.106 40.909 0.00 0.00 44.25 3.06
2033 2217 3.353370 TGTGCATGAGAATCCATGTGA 57.647 42.857 0.00 0.00 44.25 3.58
2109 2293 1.032014 GGCAGAAGGCTGTTGTTTCA 58.968 50.000 0.00 0.00 44.17 2.69
2144 2328 6.289834 TGATTTTTCCTGCATGTTGTTTCAT 58.710 32.000 0.00 0.00 0.00 2.57
2159 2343 7.656948 TGACCAATCAAAAGTCATGATTTTTCC 59.343 33.333 21.96 9.09 43.19 3.13
2225 2409 5.154222 GTCTAAAATTCCGCAAACCAGAAG 58.846 41.667 0.00 0.00 0.00 2.85
2245 2429 0.822532 ACGGACGTGTCTCCTTGTCT 60.823 55.000 0.00 0.00 0.00 3.41
2266 2450 3.318557 TCCAACGCGGATGTGTATATGTA 59.681 43.478 12.47 0.00 39.64 2.29
2283 2467 3.057596 TCTGGACGCATTTTTCATCCAAC 60.058 43.478 0.00 0.00 38.95 3.77
2303 2487 2.486907 CCTAGTCCGGACCGAACTATCT 60.487 54.545 30.82 11.62 0.00 1.98
2334 2518 1.632589 GTCATTTTTGTCCTGGGCCT 58.367 50.000 4.53 0.00 0.00 5.19
2341 2525 1.268625 GACACCGGGTCATTTTTGTCC 59.731 52.381 6.32 0.00 46.19 4.02
2375 2559 6.985645 AGCATTTGTCTGTTTCTTTGCATAAA 59.014 30.769 0.00 0.00 0.00 1.40
2405 2589 7.935338 AATTTGCTAAGTGTGTCATTTCTTG 57.065 32.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.