Multiple sequence alignment - TraesCS6D01G146400

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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 TraesCS6D01G146400 chr6D 100.000 2401 0 0 1 2401 117359526 117361926 0.000000e+00 4434.0
1 TraesCS6D01G146400 chr6B 90.682 2447 167 28 7 2401 207958682 207956245 0.000000e+00 3199.0
2 TraesCS6D01G146400 chr6A 90.732 2104 148 24 1 2088 146481469 146479397 0.000000e+00 2761.0
3 TraesCS6D01G146400 chr6A 89.851 335 25 3 2074 2401 146479380 146479048 2.850000e-114 422.0
4 TraesCS6D01G146400 chr6A 84.416 77 7 3 529 601 147146893 147146818 1.190000e-08 71.3
5 TraesCS6D01G146400 chr7B 97.222 36 1 0 2366 2401 616399760 616399795 7.170000e-06 62.1
6 TraesCS6D01G146400 chr4B 92.683 41 3 0 2361 2401 454031062 454031022 2.580000e-05 60.2
7 TraesCS6D01G146400 chr1A 100.000 28 0 0 2358 2385 536886897 536886870 4.000000e-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 TraesCS6D01G146400 chr6D 117359526 117361926 2400 False 4434.0 4434 100.0000 1 2401 1 chr6D.!!$F1 2400
1 TraesCS6D01G146400 chr6B 207956245 207958682 2437 True 3199.0 3199 90.6820 7 2401 1 chr6B.!!$R1 2394
2 TraesCS6D01G146400 chr6A 146479048 146481469 2421 True 1591.5 2761 90.2915 1 2401 2 chr6A.!!$R2 2400

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
51 52 0.035056 CCAGGACTTCATCACCCCAC 60.035 60.0 0.0 0.0 0.0 4.61 F
160 161 0.257039 GGGTGCTGGAACATCTGGAT 59.743 55.0 0.0 0.0 38.2 3.41 F
1024 1067 0.811281 GGCCAAGGTCACAGCAATAC 59.189 55.0 0.0 0.0 0.0 1.89 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1183 1226 0.391793 GGCCTCTGCACCTACTCAAC 60.392 60.000 0.0 0.0 40.13 3.18 R
1355 1398 1.684049 CTCCTCTGGCTCTTCCGGT 60.684 63.158 0.0 0.0 42.13 5.28 R
2103 2186 3.072622 AACTGGAGTTTGAGTAGGGAACC 59.927 47.826 0.0 0.0 42.62 3.62 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
22 23 1.421646 CCTCTGGGACTGTCCTTTTGT 59.578 52.381 25.01 0.00 36.57 2.83
33 34 5.356426 ACTGTCCTTTTGTTTTGTATTGCC 58.644 37.500 0.00 0.00 0.00 4.52
34 35 5.105146 ACTGTCCTTTTGTTTTGTATTGCCA 60.105 36.000 0.00 0.00 0.00 4.92
51 52 0.035056 CCAGGACTTCATCACCCCAC 60.035 60.000 0.00 0.00 0.00 4.61
83 84 3.406764 GAGCACCTCAGTTCTGTTTGAT 58.593 45.455 0.00 0.00 0.00 2.57
160 161 0.257039 GGGTGCTGGAACATCTGGAT 59.743 55.000 0.00 0.00 38.20 3.41
298 300 4.397417 CCTTCAAGACCTGGATTGTGAATC 59.603 45.833 0.00 0.00 37.17 2.52
305 307 4.104086 ACCTGGATTGTGAATCACCTCTA 58.896 43.478 11.24 5.12 39.71 2.43
360 362 8.573035 GGTGTTGGTTGATTTGTATTCTCTTTA 58.427 33.333 0.00 0.00 0.00 1.85
430 435 6.018588 CAGTACAACAATTGTTCTACGGTGAA 60.019 38.462 22.87 4.75 42.22 3.18
431 436 6.708949 AGTACAACAATTGTTCTACGGTGAAT 59.291 34.615 22.87 8.73 42.22 2.57
432 437 6.385649 ACAACAATTGTTCTACGGTGAATT 57.614 33.333 20.85 0.00 42.22 2.17
434 439 7.262048 ACAACAATTGTTCTACGGTGAATTTT 58.738 30.769 20.85 0.00 42.22 1.82
435 440 7.762159 ACAACAATTGTTCTACGGTGAATTTTT 59.238 29.630 20.85 0.00 42.22 1.94
476 489 5.335261 TCAATAGGTAGTGGTAGTGTTGGA 58.665 41.667 0.00 0.00 0.00 3.53
686 702 3.528597 ACTTCGCCTTAGAGATTCACC 57.471 47.619 0.00 0.00 0.00 4.02
706 722 4.210537 CACCGAACACAACTTCGAAAGTAT 59.789 41.667 0.00 0.00 44.83 2.12
756 776 3.138098 TCATGGATATTTACTGGCCAGCA 59.862 43.478 33.06 18.72 31.23 4.41
811 853 8.950210 CATTTATTTCACACAGTACCAGATCTT 58.050 33.333 0.00 0.00 0.00 2.40
876 918 3.357166 TCCAAAAACCAACATGCGTAC 57.643 42.857 0.00 0.00 0.00 3.67
884 926 1.202132 CCAACATGCGTACCCATTTCG 60.202 52.381 0.00 0.00 0.00 3.46
911 953 7.636150 AGCAATCTGTGAATTAAATGCTACT 57.364 32.000 0.00 0.00 40.78 2.57
927 969 4.127907 TGCTACTCACTCCTCGTACATAG 58.872 47.826 0.00 0.00 0.00 2.23
937 980 7.280428 TCACTCCTCGTACATAGAAAGTTAGAG 59.720 40.741 0.00 0.00 0.00 2.43
997 1040 3.701040 TCTCATCACATCTCGATCCAACA 59.299 43.478 0.00 0.00 0.00 3.33
1015 1058 3.089838 CCATGGAGGCCAAGGTCA 58.910 61.111 5.56 0.00 37.58 4.02
1024 1067 0.811281 GGCCAAGGTCACAGCAATAC 59.189 55.000 0.00 0.00 0.00 1.89
1146 1189 3.127030 GTGGGCAAGAATAGTGTGTTAGC 59.873 47.826 0.00 0.00 0.00 3.09
1154 1197 7.624344 GCAAGAATAGTGTGTTAGCTAAACTGG 60.624 40.741 16.27 4.07 38.99 4.00
1183 1226 2.721274 TGCGGTTGTTGATTGATTGG 57.279 45.000 0.00 0.00 0.00 3.16
1232 1275 1.826385 AGCAGCATAGCCGAACTTTT 58.174 45.000 0.00 0.00 34.23 2.27
1349 1392 4.202315 TGCATGTGTACTAAGAAGTGTGGT 60.202 41.667 0.00 0.00 36.36 4.16
1355 1398 2.047061 ACTAAGAAGTGTGGTGAGCCA 58.953 47.619 0.00 0.00 37.17 4.75
1426 1469 6.591935 TGAAGTGTACCTGAGATTTGAGTTT 58.408 36.000 0.00 0.00 0.00 2.66
1461 1504 6.934048 AATATCTCTCTAACAAAAGCTGGC 57.066 37.500 0.00 0.00 0.00 4.85
1466 1509 3.009473 TCTCTAACAAAAGCTGGCCAGAT 59.991 43.478 37.21 29.54 0.00 2.90
1543 1586 6.672147 CAGTAGCACAAACTGAAGCTTTTAT 58.328 36.000 0.00 0.00 45.89 1.40
1566 1609 7.944729 ATAGCTGAAAAGACAAACCATATGT 57.055 32.000 0.00 0.00 0.00 2.29
1729 1774 9.685828 GTAGTTCAAATAAAAATGCACCAACTA 57.314 29.630 0.00 0.00 0.00 2.24
1747 1792 3.500343 ACTAGCAGGCAAAATGGAAACT 58.500 40.909 0.00 0.00 0.00 2.66
1759 1806 6.915843 GCAAAATGGAAACTTTTCTTCTACGA 59.084 34.615 1.88 0.00 36.76 3.43
1803 1850 1.355210 CGGTGGTGCACTTGTTCAC 59.645 57.895 17.98 15.06 34.40 3.18
1807 1854 2.331451 GTGCACTTGTTCACCGCC 59.669 61.111 10.32 0.00 0.00 6.13
1832 1879 3.181484 CGGACACATTTAGATACCGGTGA 60.181 47.826 19.93 1.17 36.08 4.02
1840 1887 1.591863 GATACCGGTGAGGCTTCGC 60.592 63.158 19.93 0.00 46.52 4.70
1867 1914 5.163280 CCATTCTACATGATTTTGGCCCATT 60.163 40.000 0.00 0.00 0.00 3.16
1883 1930 6.074648 TGGCCCATTATTCCCTAATTAACTG 58.925 40.000 0.00 0.00 0.00 3.16
1995 2047 7.573968 AATTCATTTGTGTTAGGAGATAGGC 57.426 36.000 0.00 0.00 0.00 3.93
2070 2122 5.691815 CATTTTCCATGTTGATTTGTTGCC 58.308 37.500 0.00 0.00 0.00 4.52
2072 2124 3.940209 TCCATGTTGATTTGTTGCCTC 57.060 42.857 0.00 0.00 0.00 4.70
2084 2167 2.966050 TGTTGCCTCAACCAACAAAAC 58.034 42.857 4.65 0.00 46.66 2.43
2096 2179 6.422400 TCAACCAACAAAACTTTGAAGTGTTC 59.578 34.615 9.12 0.00 40.55 3.18
2100 2183 6.423604 CCAACAAAACTTTGAAGTGTTCACTT 59.576 34.615 16.56 16.56 39.87 3.16
2103 2186 4.718940 AACTTTGAAGTGTTCACTTGGG 57.281 40.909 20.61 10.86 39.87 4.12
2142 2225 4.003648 CCAGTTTAGACTCATGGAACACC 58.996 47.826 0.00 0.00 35.43 4.16
2163 2246 4.643334 ACCACTTCAAAAGTACAAAGACCC 59.357 41.667 0.00 0.00 40.46 4.46
2167 2250 4.781775 TCAAAAGTACAAAGACCCCTGA 57.218 40.909 0.00 0.00 0.00 3.86
2180 2263 2.939103 GACCCCTGATGAACATTTCTCG 59.061 50.000 0.00 0.00 0.00 4.04
2222 2305 4.336713 CGTAGAGATGTCACCATGAGAAGA 59.663 45.833 0.00 0.00 0.00 2.87
2223 2306 5.009510 CGTAGAGATGTCACCATGAGAAGAT 59.990 44.000 0.00 0.00 0.00 2.40
2349 2438 9.181805 CAGAAGCAATCTATGAATTAAATGCTG 57.818 33.333 0.00 0.00 41.64 4.41
2364 2454 5.473066 AAATGCTGCAAATCCTTGTACTT 57.527 34.783 6.36 0.00 34.79 2.24
2369 2459 4.583871 CTGCAAATCCTTGTACTTCCTCT 58.416 43.478 0.00 0.00 34.79 3.69
2386 2476 3.326880 TCCTCTGGTCCTTTTTACTCCAC 59.673 47.826 0.00 0.00 0.00 4.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 5.048083 GTGATGAAGTCCTGGCAATACAAAA 60.048 40.000 0.00 0.00 0.00 2.44
33 34 0.035056 GGTGGGGTGATGAAGTCCTG 60.035 60.000 0.00 0.00 0.00 3.86
34 35 0.178861 AGGTGGGGTGATGAAGTCCT 60.179 55.000 0.00 0.00 0.00 3.85
51 52 3.008485 ACTGAGGTGCTCCTTTTTCTAGG 59.992 47.826 9.08 0.00 45.24 3.02
160 161 7.847711 TTGAAAATCCAGTTATTCCTTTGGA 57.152 32.000 0.00 0.00 43.36 3.53
224 226 5.740513 GCACACTTTCTCTAGGTCTTGTCTT 60.741 44.000 0.00 0.00 0.00 3.01
314 316 5.183228 CACCGGTTCTAGGTAACATGATTT 58.817 41.667 2.97 0.00 40.59 2.17
315 317 4.224370 ACACCGGTTCTAGGTAACATGATT 59.776 41.667 2.97 0.00 40.59 2.57
406 411 5.603596 TCACCGTAGAACAATTGTTGTACT 58.396 37.500 36.07 26.08 46.39 2.73
410 415 7.692908 AAAATTCACCGTAGAACAATTGTTG 57.307 32.000 27.85 15.18 38.56 3.33
454 467 5.670792 TCCAACACTACCACTACCTATTG 57.329 43.478 0.00 0.00 0.00 1.90
521 537 8.146053 TCTATCTCCTAACACAAAAGGAATCA 57.854 34.615 0.00 0.00 41.33 2.57
522 538 8.478877 TCTCTATCTCCTAACACAAAAGGAATC 58.521 37.037 0.00 0.00 41.33 2.52
579 595 5.731599 AAAAACGCAAATTGCAAAGATCA 57.268 30.435 18.65 0.00 45.36 2.92
602 618 3.876914 GGTTCATGCACCAAATCGAGATA 59.123 43.478 9.89 0.00 36.73 1.98
756 776 0.976641 TTTCCTGGCGACATCTCTGT 59.023 50.000 0.00 0.00 41.51 3.41
811 853 9.387257 CATTTATCTGCATATATCCTTGCTACA 57.613 33.333 0.00 0.00 39.60 2.74
876 918 2.094675 ACAGATTGCTTCCGAAATGGG 58.905 47.619 0.00 0.00 38.76 4.00
884 926 6.335777 AGCATTTAATTCACAGATTGCTTCC 58.664 36.000 0.00 0.00 0.00 3.46
911 953 7.108194 TCTAACTTTCTATGTACGAGGAGTGA 58.892 38.462 0.00 0.00 0.00 3.41
937 980 4.459337 GTGTCCATTTATATAGCTTGGGGC 59.541 45.833 0.00 0.00 42.19 5.80
1024 1067 4.216472 GGTAAGAAAGAGCAAGACCAAAGG 59.784 45.833 0.00 0.00 0.00 3.11
1122 1165 1.346395 ACACACTATTCTTGCCCACGA 59.654 47.619 0.00 0.00 0.00 4.35
1154 1197 1.522258 CAACAACCGCATGAAACTTGC 59.478 47.619 0.00 0.00 36.74 4.01
1183 1226 0.391793 GGCCTCTGCACCTACTCAAC 60.392 60.000 0.00 0.00 40.13 3.18
1219 1262 2.681344 CGCCCTTTAAAAGTTCGGCTAT 59.319 45.455 0.00 0.00 32.99 2.97
1311 1354 3.664107 ACATGCAGTGACGTTCTACAAT 58.336 40.909 0.00 0.00 0.00 2.71
1349 1392 3.706373 GGCTCTTCCGGTGGCTCA 61.706 66.667 0.00 0.00 0.00 4.26
1355 1398 1.684049 CTCCTCTGGCTCTTCCGGT 60.684 63.158 0.00 0.00 42.13 5.28
1450 1493 2.040278 TCACTATCTGGCCAGCTTTTGT 59.960 45.455 28.91 17.61 0.00 2.83
1456 1499 2.698855 TTTCTCACTATCTGGCCAGC 57.301 50.000 28.91 0.00 0.00 4.85
1543 1586 6.092122 CGACATATGGTTTGTCTTTTCAGCTA 59.908 38.462 7.80 0.00 41.05 3.32
1566 1609 6.007703 AGGGATGGTTAAATTTTTCTGTCGA 58.992 36.000 0.00 0.00 0.00 4.20
1632 1675 3.575858 CATTACTCGATGCAAAGGTCG 57.424 47.619 0.98 0.98 39.11 4.79
1713 1757 3.056891 GCCTGCTAGTTGGTGCATTTTTA 60.057 43.478 0.00 0.00 38.59 1.52
1714 1758 2.289010 GCCTGCTAGTTGGTGCATTTTT 60.289 45.455 0.00 0.00 38.59 1.94
1722 1767 1.895131 CCATTTTGCCTGCTAGTTGGT 59.105 47.619 0.00 0.00 0.00 3.67
1729 1774 3.843893 AAAGTTTCCATTTTGCCTGCT 57.156 38.095 0.00 0.00 0.00 4.24
1747 1792 6.970043 CACCAAACAAATGTCGTAGAAGAAAA 59.030 34.615 0.00 0.00 39.69 2.29
1759 1806 3.007398 ACACCAACACACCAAACAAATGT 59.993 39.130 0.00 0.00 0.00 2.71
1807 1854 4.049186 CCGGTATCTAAATGTGTCCGAAG 58.951 47.826 0.00 0.00 38.96 3.79
1840 1887 3.796504 GCCAAAATCATGTAGAATGGGCG 60.797 47.826 0.00 0.00 32.30 6.13
1867 1914 8.945193 AGGAGTTATGCAGTTAATTAGGGAATA 58.055 33.333 0.00 0.00 0.00 1.75
1976 2028 6.313519 TCTTGCCTATCTCCTAACACAAAT 57.686 37.500 0.00 0.00 0.00 2.32
1995 2047 9.897744 TGTAATCTTTGTTAGCAATCTTTCTTG 57.102 29.630 0.00 0.00 34.18 3.02
2048 2100 5.623169 AGGCAACAAATCAACATGGAAAAT 58.377 33.333 0.00 0.00 41.41 1.82
2070 2122 5.925969 ACACTTCAAAGTTTTGTTGGTTGAG 59.074 36.000 4.67 0.00 37.08 3.02
2072 2124 6.201806 TGAACACTTCAAAGTTTTGTTGGTTG 59.798 34.615 7.88 0.68 37.08 3.77
2103 2186 3.072622 AACTGGAGTTTGAGTAGGGAACC 59.927 47.826 0.00 0.00 42.62 3.62
2142 2225 4.887655 AGGGGTCTTTGTACTTTTGAAGTG 59.112 41.667 3.70 0.00 42.84 3.16
2163 2246 3.599343 TCCACGAGAAATGTTCATCAGG 58.401 45.455 0.00 0.00 0.00 3.86
2167 2250 8.964476 AGTAAATATCCACGAGAAATGTTCAT 57.036 30.769 0.00 0.00 0.00 2.57
2180 2263 6.742109 TCTACGTTGGCTAGTAAATATCCAC 58.258 40.000 0.00 0.00 29.25 4.02
2349 2438 3.691609 CCAGAGGAAGTACAAGGATTTGC 59.308 47.826 0.00 0.00 37.85 3.68
2364 2454 3.326880 GTGGAGTAAAAAGGACCAGAGGA 59.673 47.826 0.00 0.00 0.00 3.71
2369 2459 4.895668 ATACGTGGAGTAAAAAGGACCA 57.104 40.909 0.00 0.00 39.04 4.02


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

AutoCloner maintained by Alex Coulton.