Multiple sequence alignment - TraesCS4D01G215300

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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 TraesCS4D01G215300 chr4D 100.000 2482 0 0 1 2482 368869992 368872473 0.000000e+00 4584
1 TraesCS4D01G215300 chr4A 94.570 2486 112 16 6 2482 96018850 96016379 0.000000e+00 3821
2 TraesCS4D01G215300 chr4A 85.135 148 20 2 33 180 136431377 136431522 1.540000e-32 150
3 TraesCS4D01G215300 chr4B 94.093 2387 100 19 1 2378 454037942 454040296 0.000000e+00 3589
4 TraesCS4D01G215300 chr4B 96.226 106 4 0 2377 2482 454040499 454040604 9.120000e-40 174
5 TraesCS4D01G215300 chr6A 87.075 147 16 2 37 181 184388322 184388177 1.980000e-36 163
6 TraesCS4D01G215300 chr3D 85.915 142 17 2 42 181 610875923 610875783 5.530000e-32 148
7 TraesCS4D01G215300 chr3D 85.315 143 19 1 42 182 92123134 92123276 1.990000e-31 147
8 TraesCS4D01G215300 chr3B 85.315 143 19 1 42 182 141862298 141862440 1.990000e-31 147
9 TraesCS4D01G215300 chr1A 85.034 147 19 2 37 181 555641113 555641258 1.990000e-31 147
10 TraesCS4D01G215300 chr5A 83.125 160 22 4 26 181 641734124 641734282 9.250000e-30 141


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 TraesCS4D01G215300 chr4D 368869992 368872473 2481 False 4584.0 4584 100.0000 1 2482 1 chr4D.!!$F1 2481
1 TraesCS4D01G215300 chr4A 96016379 96018850 2471 True 3821.0 3821 94.5700 6 2482 1 chr4A.!!$R1 2476
2 TraesCS4D01G215300 chr4B 454037942 454040604 2662 False 1881.5 3589 95.1595 1 2482 2 chr4B.!!$F1 2481

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
840 853 0.679505 TAGTCTGTGTGGTGCAGGAC 59.32 55.0 0.0 0.0 34.89 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2176 0.112412 AGGCACCCCAACCTTGTAAG 59.888 55.0 0.0 0.0 29.74 2.34 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
41 43 2.233271 TCGTTTCAGTACCCTCTTCGT 58.767 47.619 0.00 0.00 0.00 3.85
108 110 6.729690 AGGGATTGAAATGAGTGAACAAAA 57.270 33.333 0.00 0.00 0.00 2.44
216 223 6.442513 ACAGAAGTTTTTCTTTCCTGACAG 57.557 37.500 0.00 0.00 41.71 3.51
220 227 3.954258 AGTTTTTCTTTCCTGACAGGTGG 59.046 43.478 21.06 12.01 36.53 4.61
235 242 4.916983 CAGGTGGAACTGTCATTCAAAA 57.083 40.909 0.00 0.00 36.74 2.44
239 246 5.598005 AGGTGGAACTGTCATTCAAAAATCA 59.402 36.000 0.00 0.00 36.74 2.57
240 247 6.098124 AGGTGGAACTGTCATTCAAAAATCAA 59.902 34.615 0.00 0.00 36.74 2.57
358 365 5.302360 TGTATAAACGGTCTGCAGAAACTT 58.698 37.500 20.19 11.85 0.00 2.66
360 367 7.101054 TGTATAAACGGTCTGCAGAAACTTAT 58.899 34.615 20.19 18.88 0.00 1.73
444 451 2.635427 TGTGACTAGGGTTATGTGCACA 59.365 45.455 24.08 24.08 33.18 4.57
451 458 1.407437 GGGTTATGTGCACAGAGGGAG 60.407 57.143 25.84 0.00 0.00 4.30
527 535 3.621268 GCTCCAACGACATAATGCTTGTA 59.379 43.478 0.00 0.00 0.00 2.41
529 537 3.615056 TCCAACGACATAATGCTTGTACG 59.385 43.478 0.00 0.00 0.00 3.67
531 539 4.270084 CCAACGACATAATGCTTGTACGAT 59.730 41.667 0.00 0.00 0.00 3.73
619 630 3.264947 CAGCAGCAATTCACAGCTACTA 58.735 45.455 0.00 0.00 39.50 1.82
687 700 8.618702 TTATGTGCAATTTTCCATTTCAACAT 57.381 26.923 0.00 0.00 0.00 2.71
694 707 8.567104 GCAATTTTCCATTTCAACATAAACCTT 58.433 29.630 0.00 0.00 0.00 3.50
735 748 1.576577 ACCTCATGGCACTCTGATGA 58.423 50.000 0.00 0.00 36.63 2.92
822 835 9.371136 CTAAAATTACAGCTGTTCATGTCTCTA 57.629 33.333 27.06 0.00 0.00 2.43
840 853 0.679505 TAGTCTGTGTGGTGCAGGAC 59.320 55.000 0.00 0.00 34.89 3.85
960 973 1.153353 GGACGGCGTTTTGAAGATCA 58.847 50.000 16.19 0.00 0.00 2.92
1202 1215 3.254166 GGATCACCATCACCAATATGTGC 59.746 47.826 0.00 0.00 34.73 4.57
1241 1254 3.942115 GGAAATCTAGGACTCTTTGTGCC 59.058 47.826 0.00 0.00 37.77 5.01
1246 1259 1.140312 AGGACTCTTTGTGCCCAGAA 58.860 50.000 0.00 0.00 37.77 3.02
1291 1305 6.418101 AGAGTTCATACAAGCATGGTATTGT 58.582 36.000 7.35 7.35 42.15 2.71
1298 1312 5.372343 ACAAGCATGGTATTGTATGGAGA 57.628 39.130 0.00 0.00 37.85 3.71
1299 1313 5.754782 ACAAGCATGGTATTGTATGGAGAA 58.245 37.500 0.00 0.00 37.85 2.87
1300 1314 6.186957 ACAAGCATGGTATTGTATGGAGAAA 58.813 36.000 0.00 0.00 37.85 2.52
1301 1315 6.319658 ACAAGCATGGTATTGTATGGAGAAAG 59.680 38.462 0.00 0.00 37.85 2.62
1302 1316 5.380043 AGCATGGTATTGTATGGAGAAAGG 58.620 41.667 0.00 0.00 0.00 3.11
1303 1317 5.132648 AGCATGGTATTGTATGGAGAAAGGA 59.867 40.000 0.00 0.00 0.00 3.36
1304 1318 5.471456 GCATGGTATTGTATGGAGAAAGGAG 59.529 44.000 0.00 0.00 0.00 3.69
1305 1319 6.688922 GCATGGTATTGTATGGAGAAAGGAGA 60.689 42.308 0.00 0.00 0.00 3.71
1310 1324 3.647636 TGTATGGAGAAAGGAGAGGAGG 58.352 50.000 0.00 0.00 0.00 4.30
1510 1524 4.244066 CAGGAGAGATCATATCCGCAAAG 58.756 47.826 0.00 0.00 44.59 2.77
1527 1541 5.507315 CCGCAAAGGTCAATAGAAGTTTGTT 60.507 40.000 0.00 0.00 33.96 2.83
1532 1546 9.965824 CAAAGGTCAATAGAAGTTTGTTGTTAT 57.034 29.630 0.00 0.00 29.99 1.89
1580 1594 2.618442 TGACAGCATCACAACAGTCA 57.382 45.000 0.00 0.00 34.02 3.41
1581 1595 2.916640 TGACAGCATCACAACAGTCAA 58.083 42.857 0.00 0.00 33.55 3.18
1631 1645 5.298777 ACTGAAGGCAGCTGATTGAAATATC 59.701 40.000 20.43 2.39 46.26 1.63
1659 1673 9.642327 TTGCTTTCATCGTTAATAGTAAGTACA 57.358 29.630 0.00 0.00 0.00 2.90
1663 1677 9.811995 TTTCATCGTTAATAGTAAGTACAGCAT 57.188 29.630 0.00 0.00 0.00 3.79
1721 1735 7.148154 ACACATAACTCACACTGTAAAAGCAAA 60.148 33.333 0.00 0.00 0.00 3.68
1728 1742 9.116067 ACTCACACTGTAAAAGCAAATAAGTAA 57.884 29.630 0.00 0.00 0.00 2.24
1768 1782 0.110238 CTGACATTGTTCCCGCAACG 60.110 55.000 0.00 0.00 37.90 4.10
1840 1854 7.256296 CCAAAATCTCCAATTTTAGGAACCAGT 60.256 37.037 0.00 0.00 34.08 4.00
2162 2176 0.242017 GACACAGCAACCAATGAGCC 59.758 55.000 0.00 0.00 0.00 4.70
2203 2217 6.072838 GCCTGACATTTGATATGACATCGATT 60.073 38.462 0.00 0.00 0.00 3.34
2276 2290 0.469705 TGCAACTTGGGTGCCATCTT 60.470 50.000 5.08 0.00 31.53 2.40
2306 2320 2.027100 CCCTAAGTGAAGGAGAACCACC 60.027 54.545 0.00 0.00 39.15 4.61
2337 2351 6.550854 TCATTCTTCCAAAAGAGAACATTGGT 59.449 34.615 3.92 0.00 42.36 3.67
2402 2620 3.522553 AGTAAGAAGGCAGCAATACGAC 58.477 45.455 0.00 0.00 0.00 4.34
2454 2672 2.573083 CCCACGGCCAATGCAGTTT 61.573 57.895 2.24 0.00 43.70 2.66
2460 2678 1.337074 CGGCCAATGCAGTTTGTCATT 60.337 47.619 2.24 0.00 40.13 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 35 8.425577 ACATCTTATATTTGTGAACGAAGAGG 57.574 34.615 0.00 0.00 31.48 3.69
77 79 7.004086 TCACTCATTTCAATCCCTTTGTAGTT 58.996 34.615 0.00 0.00 36.65 2.24
86 88 6.760770 TGTTTTTGTTCACTCATTTCAATCCC 59.239 34.615 0.00 0.00 0.00 3.85
91 93 9.698309 TTTTAGTGTTTTTGTTCACTCATTTCA 57.302 25.926 1.08 0.00 42.77 2.69
96 98 7.175990 AGAGGTTTTAGTGTTTTTGTTCACTCA 59.824 33.333 1.08 0.00 42.77 3.41
153 158 8.560903 ACTCCCTCCTTTCACAAATATAAGATT 58.439 33.333 0.00 0.00 0.00 2.40
216 223 5.841810 TGATTTTTGAATGACAGTTCCACC 58.158 37.500 0.00 0.00 0.00 4.61
220 227 8.131100 TCTCACTTGATTTTTGAATGACAGTTC 58.869 33.333 0.00 0.00 0.00 3.01
235 242 6.165700 AGCCAAATGTTTTCTCACTTGATT 57.834 33.333 0.00 0.00 0.00 2.57
239 246 3.960102 TGGAGCCAAATGTTTTCTCACTT 59.040 39.130 0.00 0.00 0.00 3.16
240 247 3.565307 TGGAGCCAAATGTTTTCTCACT 58.435 40.909 0.00 0.00 0.00 3.41
263 270 2.136878 CGCACCTAGAGGAGCCCAT 61.137 63.158 11.76 0.00 46.97 4.00
301 308 4.287326 TGTTCATGGTGGGATGTTACAGTA 59.713 41.667 0.00 0.00 0.00 2.74
306 313 5.600484 ACTTTTTGTTCATGGTGGGATGTTA 59.400 36.000 0.00 0.00 0.00 2.41
340 347 4.385825 TGATAAGTTTCTGCAGACCGTTT 58.614 39.130 18.03 11.08 0.00 3.60
438 445 0.952984 GAACAGCTCCCTCTGTGCAC 60.953 60.000 10.75 10.75 45.77 4.57
527 535 0.885879 TTGGTGTAGAGACGCATCGT 59.114 50.000 0.00 0.00 45.10 3.73
529 537 1.281899 GCTTGGTGTAGAGACGCATC 58.718 55.000 0.00 0.00 37.85 3.91
531 539 0.319555 GTGCTTGGTGTAGAGACGCA 60.320 55.000 0.00 0.00 37.85 5.24
619 630 2.324541 GAGATACAGGATGCTGAGGGT 58.675 52.381 22.24 0.25 42.53 4.34
687 700 2.750948 GTCGAGTGCTGACAAGGTTTA 58.249 47.619 0.00 0.00 36.37 2.01
694 707 1.444383 GATGCGTCGAGTGCTGACA 60.444 57.895 10.57 0.00 36.11 3.58
822 835 1.447643 GTCCTGCACCACACAGACT 59.552 57.895 0.00 0.00 37.32 3.24
840 853 4.379243 AGAGTCAACGCGGCTGGG 62.379 66.667 12.47 8.27 0.00 4.45
847 860 1.005630 AGAGCACCAGAGTCAACGC 60.006 57.895 0.00 0.00 0.00 4.84
853 866 0.250945 TCGAGTCAGAGCACCAGAGT 60.251 55.000 0.00 0.00 0.00 3.24
1202 1215 1.043116 TCCCCATGGTAGACTCGCAG 61.043 60.000 11.73 0.00 0.00 5.18
1241 1254 2.885266 AGCTGCAGCATCATAATTCTGG 59.115 45.455 38.24 0.00 45.16 3.86
1246 1259 5.557866 TCTTGATAGCTGCAGCATCATAAT 58.442 37.500 34.04 21.33 45.16 1.28
1291 1305 4.551671 CTTCCTCCTCTCCTTTCTCCATA 58.448 47.826 0.00 0.00 0.00 2.74
1294 1308 2.115427 CCTTCCTCCTCTCCTTTCTCC 58.885 57.143 0.00 0.00 0.00 3.71
1295 1309 3.031013 CTCCTTCCTCCTCTCCTTTCTC 58.969 54.545 0.00 0.00 0.00 2.87
1296 1310 2.657459 TCTCCTTCCTCCTCTCCTTTCT 59.343 50.000 0.00 0.00 0.00 2.52
1297 1311 3.031013 CTCTCCTTCCTCCTCTCCTTTC 58.969 54.545 0.00 0.00 0.00 2.62
1298 1312 2.292851 CCTCTCCTTCCTCCTCTCCTTT 60.293 54.545 0.00 0.00 0.00 3.11
1299 1313 1.290732 CCTCTCCTTCCTCCTCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
1300 1314 0.933700 CCTCTCCTTCCTCCTCTCCT 59.066 60.000 0.00 0.00 0.00 3.69
1301 1315 0.759060 GCCTCTCCTTCCTCCTCTCC 60.759 65.000 0.00 0.00 0.00 3.71
1302 1316 1.106944 CGCCTCTCCTTCCTCCTCTC 61.107 65.000 0.00 0.00 0.00 3.20
1303 1317 1.076339 CGCCTCTCCTTCCTCCTCT 60.076 63.158 0.00 0.00 0.00 3.69
1304 1318 0.684805 TTCGCCTCTCCTTCCTCCTC 60.685 60.000 0.00 0.00 0.00 3.71
1305 1319 0.252284 TTTCGCCTCTCCTTCCTCCT 60.252 55.000 0.00 0.00 0.00 3.69
1310 1324 2.457366 TTCACTTTCGCCTCTCCTTC 57.543 50.000 0.00 0.00 0.00 3.46
1510 1524 8.106247 TCCATAACAACAAACTTCTATTGACC 57.894 34.615 0.00 0.00 0.00 4.02
1561 1575 2.618442 TGACTGTTGTGATGCTGTCA 57.382 45.000 0.00 0.00 39.86 3.58
1580 1594 5.948742 TTTCTCCCAGTTGAACCAATTTT 57.051 34.783 0.00 0.00 0.00 1.82
1581 1595 5.425217 ACTTTTCTCCCAGTTGAACCAATTT 59.575 36.000 0.00 0.00 0.00 1.82
1649 1663 9.542462 GGAACAAATATCATGCTGTACTTACTA 57.458 33.333 0.00 0.00 0.00 1.82
1659 1673 4.422073 TCTCCGGAACAAATATCATGCT 57.578 40.909 5.23 0.00 0.00 3.79
1663 1677 8.044309 TGTAGATTTTCTCCGGAACAAATATCA 58.956 33.333 16.83 13.58 0.00 2.15
1725 1739 8.722394 CAGTCCTCTCTAAATCTTTTGGTTTAC 58.278 37.037 0.00 0.00 0.00 2.01
1728 1742 6.937465 GTCAGTCCTCTCTAAATCTTTTGGTT 59.063 38.462 0.00 0.00 0.00 3.67
1739 1753 4.223032 GGGAACAATGTCAGTCCTCTCTAA 59.777 45.833 2.98 0.00 0.00 2.10
1768 1782 1.059369 CACTCACATTAGCACGCGC 59.941 57.895 5.73 0.00 38.99 6.86
2031 2045 3.118408 ACTTGCACAAAGTCTGACCTGTA 60.118 43.478 11.48 0.00 46.60 2.74
2162 2176 0.112412 AGGCACCCCAACCTTGTAAG 59.888 55.000 0.00 0.00 29.74 2.34
2306 2320 8.289618 TGTTCTCTTTTGGAAGAATGAATAACG 58.710 33.333 0.00 0.00 41.19 3.18
2337 2351 9.185680 TCACTGCTCATTAGTCATACTTTACTA 57.814 33.333 0.00 0.00 0.00 1.82
2402 2620 6.607198 ACCAGTTTATAAGGTGAATCATTGGG 59.393 38.462 0.00 0.00 33.57 4.12
2454 2672 4.615949 CCACACGGAATTTTCAAATGACA 58.384 39.130 0.00 0.00 0.00 3.58
2460 2678 2.302260 TCTGCCACACGGAATTTTCAA 58.698 42.857 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.