Multiple sequence alignment - TraesCS3D01G356800

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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 TraesCS3D01G356800 chr3D 100.000 3043 0 0 1 3043 469161234 469158192 0.000000e+00 5620.0
1 TraesCS3D01G356800 chr3D 82.386 1408 217 27 263 1656 469160414 469159024 0.000000e+00 1197.0
2 TraesCS3D01G356800 chr3D 82.386 1408 217 27 821 2211 469160972 469159579 0.000000e+00 1197.0
3 TraesCS3D01G356800 chr3D 83.175 844 125 12 1378 2211 469160972 469160136 0.000000e+00 756.0
4 TraesCS3D01G356800 chr3D 86.131 274 37 1 268 540 469159297 469159024 8.250000e-76 294.0
5 TraesCS3D01G356800 chr3D 86.131 274 37 1 1938 2211 469160967 469160695 8.250000e-76 294.0
6 TraesCS3D01G356800 chr3D 88.073 109 13 0 2378 2486 523902680 523902572 2.460000e-26 130.0
7 TraesCS3D01G356800 chr3D 90.698 86 8 0 2401 2486 523846709 523846624 6.890000e-22 115.0
8 TraesCS3D01G356800 chr3A 94.797 3075 120 19 1 3043 611708533 611705467 0.000000e+00 4756.0
9 TraesCS3D01G356800 chr3A 81.372 1691 265 39 548 2211 611708253 611706586 0.000000e+00 1332.0
10 TraesCS3D01G356800 chr3A 80.812 1699 270 42 263 1932 611707983 611706312 0.000000e+00 1280.0
11 TraesCS3D01G356800 chr3A 82.219 1406 220 25 821 2211 611708261 611706871 0.000000e+00 1184.0
12 TraesCS3D01G356800 chr3A 82.140 1411 217 25 263 1656 611707703 611706311 0.000000e+00 1177.0
13 TraesCS3D01G356800 chr3A 81.673 1124 185 16 1099 2211 611708261 611707148 0.000000e+00 915.0
14 TraesCS3D01G356800 chr3A 83.097 846 126 16 263 1099 611707148 611706311 0.000000e+00 754.0
15 TraesCS3D01G356800 chr3A 82.800 843 130 10 1378 2211 611708261 611707425 0.000000e+00 739.0
16 TraesCS3D01G356800 chr3A 83.577 274 41 3 268 540 611706581 611706311 1.400000e-63 254.0
17 TraesCS3D01G356800 chr3B 93.401 591 26 3 2463 3041 623154346 623153757 0.000000e+00 863.0
18 TraesCS3D01G356800 chr3B 89.270 699 59 9 1737 2428 623155031 623154342 0.000000e+00 861.0
19 TraesCS3D01G356800 chr3B 90.598 468 42 2 1243 1709 623155496 623155030 1.200000e-173 619.0
20 TraesCS3D01G356800 chr3B 82.364 533 66 12 549 1077 623156335 623155827 3.600000e-119 438.0
21 TraesCS3D01G356800 chr3B 83.473 478 70 9 957 1430 623155503 623155031 1.300000e-118 436.0
22 TraesCS3D01G356800 chr3B 84.798 421 61 3 1793 2211 623155503 623155084 1.300000e-113 420.0
23 TraesCS3D01G356800 chr3B 84.496 258 33 6 263 517 623156081 623155828 6.520000e-62 248.0
24 TraesCS3D01G356800 chr7D 82.895 152 19 7 2402 2549 133313601 133313453 2.460000e-26 130.0
25 TraesCS3D01G356800 chr4D 87.342 79 9 1 2179 2257 301730975 301730898 4.180000e-14 89.8
26 TraesCS3D01G356800 chr4B 82.353 102 14 4 2185 2284 376136971 376136872 5.410000e-13 86.1
27 TraesCS3D01G356800 chr7A 90.909 55 5 0 2549 2603 547564325 547564379 1.170000e-09 75.0
28 TraesCS3D01G356800 chr4A 79.646 113 14 7 2179 2284 179144443 179144553 4.210000e-09 73.1


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 TraesCS3D01G356800 chr3D 469158192 469161234 3042 True 1559.666667 5620 86.701500 1 3043 6 chr3D.!!$R3 3042
1 TraesCS3D01G356800 chr3A 611705467 611708533 3066 True 1376.777778 4756 83.609667 1 3043 9 chr3A.!!$R1 3042
2 TraesCS3D01G356800 chr3B 623153757 623156335 2578 True 555.000000 863 86.914286 263 3041 7 chr3B.!!$R1 2778

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
545 557 0.887933 CTGTTTTTACCATGGCGGCT 59.112 50.000 13.04 0.0 39.03 5.52 F
586 598 1.224315 TGGCATCCCCAAGTGATCG 59.776 57.895 0.00 0.0 41.82 3.69 F
887 899 1.308047 GATGCGACAATGGGTGCATA 58.692 50.000 8.63 0.0 41.27 3.14 F
1448 1627 1.533753 CACAATGGGTGCTTGGGGT 60.534 57.895 0.00 0.0 41.36 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1505 1684 0.599060 TTTTCCGTGGAAAATCCGGC 59.401 50.000 20.07 0.0 45.59 6.13 R
1591 1770 1.196808 CGATGTTCCACCAGAAAACGG 59.803 52.381 0.00 0.0 35.85 4.44 R
2003 2195 2.046988 CACTGTCCGCCATGAGCA 60.047 61.111 0.00 0.0 44.04 4.26 R
2718 2912 2.290641 GCACTCATCTGTGTTTCCGTTT 59.709 45.455 0.00 0.0 39.89 3.60 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
63 64 2.171003 TCGAGACTGAGCTTGAATGGA 58.829 47.619 0.00 0.00 0.00 3.41
108 109 1.225704 CATGGAAGGAGCAGGGACC 59.774 63.158 0.00 0.00 0.00 4.46
109 110 1.083706 ATGGAAGGAGCAGGGACCT 59.916 57.895 0.00 0.00 38.23 3.85
131 132 1.761174 GACCTGGGTGAGGAAGCAA 59.239 57.895 0.00 0.00 46.33 3.91
170 171 2.423538 GGCATTCGAAGTAAGGTGCAAT 59.576 45.455 17.98 0.00 34.45 3.56
183 184 2.424601 AGGTGCAATTCACGAATGATGG 59.575 45.455 0.00 0.00 46.56 3.51
202 203 1.907255 GGTAGCTTGGGTAAGTGGTCT 59.093 52.381 0.00 0.00 36.27 3.85
227 228 2.202987 CCAGCAGGACCAGCGATC 60.203 66.667 2.85 0.00 36.89 3.69
293 304 1.519751 CGGGGTGAAAATGGCGTTGA 61.520 55.000 0.00 0.00 0.00 3.18
321 332 1.513586 GCGAGCTGCTGCAACAATC 60.514 57.895 18.42 5.10 42.74 2.67
333 344 3.485346 AACAATCGGTGCGTGGGGT 62.485 57.895 0.00 0.00 0.00 4.95
432 443 5.738118 ACGGAAACAAAGTGAAAATACGA 57.262 34.783 0.00 0.00 0.00 3.43
509 521 2.348411 ACATCCATGGAAACGGATCC 57.652 50.000 20.67 0.00 40.12 3.36
545 557 0.887933 CTGTTTTTACCATGGCGGCT 59.112 50.000 13.04 0.00 39.03 5.52
567 579 2.280592 GCGGGGTGAAGACAACGT 60.281 61.111 0.00 0.00 34.03 3.99
586 598 1.224315 TGGCATCCCCAAGTGATCG 59.776 57.895 0.00 0.00 41.82 3.69
665 677 7.596494 ACTATGACAAAATGAAATGGACACTG 58.404 34.615 0.00 0.00 0.00 3.66
693 705 6.040247 GGATTTTCCACGAAAAACAGAAACT 58.960 36.000 3.85 0.00 43.32 2.66
700 712 5.022021 CACGAAAAACAGAAACTGAGTGAC 58.978 41.667 5.76 0.00 35.18 3.67
707 719 3.572682 ACAGAAACTGAGTGACATACGGA 59.427 43.478 5.76 0.00 35.18 4.69
716 728 6.055231 TGAGTGACATACGGAAACAAAAAG 57.945 37.500 0.00 0.00 0.00 2.27
749 761 5.957220 GCGAAACAGAAACAAAAATGGAAAC 59.043 36.000 0.00 0.00 0.00 2.78
754 766 5.579119 ACAGAAACAAAAATGGAAACGGAAC 59.421 36.000 0.00 0.00 0.00 3.62
761 773 4.729227 AAATGGAAACGGAACAGTGTTT 57.271 36.364 10.45 0.00 40.77 2.83
789 801 2.814336 GGAATAGCCACGGAAATGGATC 59.186 50.000 0.00 0.00 43.02 3.36
790 802 3.496870 GGAATAGCCACGGAAATGGATCT 60.497 47.826 0.00 0.00 43.02 2.75
844 856 3.246112 CGGGGTGGGGTGAAGACA 61.246 66.667 0.00 0.00 0.00 3.41
887 899 1.308047 GATGCGACAATGGGTGCATA 58.692 50.000 8.63 0.00 41.27 3.14
1044 1056 4.806640 TGAAATGGAAGAGCATTTTCCC 57.193 40.909 10.29 0.00 42.79 3.97
1069 1081 6.822667 TGGAATATCCATGGAAATTGATCG 57.177 37.500 20.67 0.00 42.67 3.69
1145 1158 4.803426 GGTGTCCCTGAGCGAGCG 62.803 72.222 0.00 0.00 0.00 5.03
1225 1238 4.089361 AGGATGAAAATGGAGTGGAAACC 58.911 43.478 0.00 0.00 0.00 3.27
1308 1487 2.223294 TGCGAAACGAAAACGGAAATGT 60.223 40.909 0.00 0.00 0.00 2.71
1448 1627 1.533753 CACAATGGGTGCTTGGGGT 60.534 57.895 0.00 0.00 41.36 4.95
1476 1655 2.569853 TGCGGAAGGTGAGAAGGATTTA 59.430 45.455 0.00 0.00 0.00 1.40
1505 1684 5.244626 AGGATGAAAATGGAGTGGAAACTTG 59.755 40.000 0.00 0.00 0.00 3.16
1661 1840 8.006298 AACTTTCTGTTTTAATCATGGTGACA 57.994 30.769 0.00 0.00 39.72 3.58
2003 2195 3.175710 AGAAAGGGTGCGTGGGGT 61.176 61.111 0.00 0.00 0.00 4.95
2062 2254 3.140144 TGAAAATGGAGTGGGAACTTCCT 59.860 43.478 7.77 0.00 36.57 3.36
2134 2326 4.862018 ACGGAATATTGCAAAACGGAAATG 59.138 37.500 1.71 0.00 0.00 2.32
2251 2443 3.482786 CAGCACTCAATAAAACTCACGC 58.517 45.455 0.00 0.00 0.00 5.34
2257 2449 3.472652 TCAATAAAACTCACGCTGTGGT 58.527 40.909 8.46 3.83 33.87 4.16
2478 2672 1.133025 GGTTTTGTATCTGCTGCGCAT 59.867 47.619 12.24 0.00 38.13 4.73
2666 2860 7.805071 GGGAATTCTCTATTTATTGCATTGACG 59.195 37.037 5.23 0.00 0.00 4.35
2718 2912 6.379133 AGAGGTACATGAGGATTACACGTTAA 59.621 38.462 0.00 0.00 0.00 2.01
2740 2934 1.070758 ACGGAAACACAGATGAGTGCT 59.929 47.619 0.00 0.00 43.23 4.40
2825 3031 2.557056 CCCAAGAGTGAGTCTGTAACGA 59.443 50.000 0.00 0.00 34.84 3.85
2862 3068 0.535102 ACTTGACCCTTCTTGTGCCG 60.535 55.000 0.00 0.00 0.00 5.69
2992 3198 1.732259 ACAGCCTTTTAATGACGAGCG 59.268 47.619 0.00 0.00 0.00 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 1.648467 GAAGTGGCGCCAGATGTTCC 61.648 60.000 33.73 16.87 0.00 3.62
108 109 3.011517 CCTCACCCAGGTCCCCAG 61.012 72.222 0.00 0.00 37.53 4.45
109 110 3.121868 TTCCTCACCCAGGTCCCCA 62.122 63.158 0.00 0.00 43.95 4.96
155 156 2.734606 TCGTGAATTGCACCTTACTTCG 59.265 45.455 0.00 0.00 44.85 3.79
170 171 3.270027 CCAAGCTACCATCATTCGTGAA 58.730 45.455 0.00 0.00 0.00 3.18
183 184 2.935676 GCAGACCACTTACCCAAGCTAC 60.936 54.545 0.00 0.00 34.94 3.58
245 256 3.155167 CCCTACGCCTGTCCCCTC 61.155 72.222 0.00 0.00 0.00 4.30
293 304 3.753434 CAGCTCGCTCAGGGACGT 61.753 66.667 0.00 0.00 0.00 4.34
333 344 2.046023 CACCTTCCGCCATGAGCA 60.046 61.111 0.00 0.00 44.04 4.26
403 414 8.989653 ATTTTCACTTTGTTTCCGTTTTTCTA 57.010 26.923 0.00 0.00 0.00 2.10
432 443 6.199342 CGTTTCACAATATTCCGTTTGGTTTT 59.801 34.615 0.00 0.00 36.30 2.43
545 557 3.961414 GTCTTCACCCCGCCCCAA 61.961 66.667 0.00 0.00 0.00 4.12
567 579 0.394216 CGATCACTTGGGGATGCCAA 60.394 55.000 5.30 0.00 0.00 4.52
581 593 1.815003 CCATTGTCGCAGCCGATCA 60.815 57.895 0.00 0.00 46.38 2.92
584 596 4.015406 ACCCATTGTCGCAGCCGA 62.015 61.111 0.00 0.00 42.01 5.54
586 598 4.120331 GCACCCATTGTCGCAGCC 62.120 66.667 0.00 0.00 0.00 4.85
618 630 1.128692 CAAATCCTTCTCACGTTCCGC 59.871 52.381 0.00 0.00 0.00 5.54
693 705 5.008217 CCTTTTTGTTTCCGTATGTCACTCA 59.992 40.000 0.00 0.00 0.00 3.41
700 712 7.010091 GCAATATTCCCTTTTTGTTTCCGTATG 59.990 37.037 0.00 0.00 0.00 2.39
707 719 6.763610 TGTTTCGCAATATTCCCTTTTTGTTT 59.236 30.769 0.00 0.00 0.00 2.83
716 728 5.054390 TGTTTCTGTTTCGCAATATTCCC 57.946 39.130 0.00 0.00 0.00 3.97
754 766 2.161609 GCTATTCCACCGGAAAACACTG 59.838 50.000 9.46 0.00 45.41 3.66
968 980 8.795842 TTACGTATTTTCACTATGTTCCCATT 57.204 30.769 0.00 0.00 32.29 3.16
973 985 9.881529 TTTGGTTTACGTATTTTCACTATGTTC 57.118 29.630 0.00 0.00 0.00 3.18
1035 1047 2.955660 TGGATATTCCACGGGAAAATGC 59.044 45.455 9.07 1.36 45.41 3.56
1308 1487 2.322355 TCCACCGGAAAACGTTGTTA 57.678 45.000 9.46 0.00 42.24 2.41
1389 1568 1.303236 CAACGCCATCTTCACCCCA 60.303 57.895 0.00 0.00 0.00 4.96
1448 1627 0.674581 CTCACCTTCCGCAATGAGCA 60.675 55.000 0.00 0.00 46.13 4.26
1476 1655 6.139679 TCCACTCCATTTTCATCCTAGTTT 57.860 37.500 0.00 0.00 0.00 2.66
1505 1684 0.599060 TTTTCCGTGGAAAATCCGGC 59.401 50.000 20.07 0.00 45.59 6.13
1543 1722 8.428063 TCACAAATTCTGTTTTGGTTTCCATAT 58.572 29.630 9.44 0.00 40.20 1.78
1591 1770 1.196808 CGATGTTCCACCAGAAAACGG 59.803 52.381 0.00 0.00 35.85 4.44
1649 1828 1.378514 GCCCCGTGTCACCATGATT 60.379 57.895 0.00 0.00 0.00 2.57
1651 1830 2.601702 ATGCCCCGTGTCACCATGA 61.602 57.895 0.00 0.00 0.00 3.07
1661 1840 2.351276 GTCTTCACCATGCCCCGT 59.649 61.111 0.00 0.00 0.00 5.28
1709 1890 4.676951 CCCCCACGCACCCATTGT 62.677 66.667 0.00 0.00 0.00 2.71
1811 1993 8.463607 TCCTTTTTGTTTTCGTATTTTCACTCT 58.536 29.630 0.00 0.00 0.00 3.24
1844 2026 2.573369 TCCATTTCCGTTTCCGTTTCA 58.427 42.857 0.00 0.00 0.00 2.69
1983 2175 2.742372 CCACGCACCCTTTCTCGG 60.742 66.667 0.00 0.00 0.00 4.63
2003 2195 2.046988 CACTGTCCGCCATGAGCA 60.047 61.111 0.00 0.00 44.04 4.26
2062 2254 3.900388 CGTTTTACCACGGAAAATCCA 57.100 42.857 0.00 0.00 35.91 3.41
2134 2326 2.672714 GGAAAACGCTGTTCCATTTCC 58.327 47.619 7.33 0.00 43.52 3.13
2167 2359 3.306166 CGTATTCACGGATCTGTTTCCAC 59.694 47.826 3.84 0.61 44.59 4.02
2478 2672 5.290158 GGAAACAGATACGAAGCAAATACGA 59.710 40.000 0.00 0.00 0.00 3.43
2666 2860 4.269363 GTGTATATAAGCACACCCGTGTTC 59.731 45.833 0.00 0.00 45.50 3.18
2718 2912 2.290641 GCACTCATCTGTGTTTCCGTTT 59.709 45.455 0.00 0.00 39.89 3.60
2740 2934 2.819154 CCACGCGTGCCATGATCA 60.819 61.111 33.17 0.00 0.00 2.92
2764 2958 3.998672 CCCACGGCGTACAGGTGT 61.999 66.667 14.22 0.00 0.00 4.16
2825 3031 7.040409 GGGTCAAGTGATTGAATGTTAGAAACT 60.040 37.037 0.00 0.00 32.04 2.66


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

AutoCloner maintained by Alex Coulton.