Multiple sequence alignment - TraesCS7D01G506600

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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 TraesCS7D01G506600 chr7D 100.000 2252 0 0 1 2252 611315292 611317543 0.000000e+00 4159.0
1 TraesCS7D01G506600 chr7A 91.564 2039 101 33 234 2249 701368983 701370973 0.000000e+00 2747.0
2 TraesCS7D01G506600 chr7A 90.058 1026 53 23 1241 2249 701380289 701381282 0.000000e+00 1284.0
3 TraesCS7D01G506600 chr7A 84.906 265 17 8 1 249 701368609 701368866 1.730000e-61 246.0
4 TraesCS7D01G506600 chr7B 91.214 1252 80 13 318 1559 700541078 700542309 0.000000e+00 1676.0
5 TraesCS7D01G506600 chr7B 86.517 267 34 2 1562 1827 700542590 700542855 2.190000e-75 292.0
6 TraesCS7D01G506600 chr7B 83.681 288 27 11 6 278 700540800 700541082 1.030000e-63 254.0
7 TraesCS7D01G506600 chr2A 90.040 994 54 21 1276 2252 735425824 735424859 0.000000e+00 1245.0
8 TraesCS7D01G506600 chr6A 79.832 238 32 10 2016 2252 25765202 25765424 2.320000e-35 159.0
9 TraesCS7D01G506600 chr1D 100.000 31 0 0 2022 2052 273905459 273905429 8.690000e-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 TraesCS7D01G506600 chr7D 611315292 611317543 2251 False 4159.000000 4159 100.000000 1 2252 1 chr7D.!!$F1 2251
1 TraesCS7D01G506600 chr7A 701368609 701370973 2364 False 1496.500000 2747 88.235000 1 2249 2 chr7A.!!$F2 2248
2 TraesCS7D01G506600 chr7A 701380289 701381282 993 False 1284.000000 1284 90.058000 1241 2249 1 chr7A.!!$F1 1008
3 TraesCS7D01G506600 chr7B 700540800 700542855 2055 False 740.666667 1676 87.137333 6 1827 3 chr7B.!!$F1 1821
4 TraesCS7D01G506600 chr2A 735424859 735425824 965 True 1245.000000 1245 90.040000 1276 2252 1 chr2A.!!$R1 976

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
554 715 1.135746 GCTTCATCAGCTGTTCAGCAC 60.136 52.381 23.69 0.0 46.27 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1722 2186 0.178929 AAGACCTCCGACCTGAACCT 60.179 55.0 0.0 0.0 0.0 3.5 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
73 74 5.423015 TGATTTCTCACTCTAAGCCATGAC 58.577 41.667 0.00 0.00 0.00 3.06
105 106 2.084546 CCTCCCCTCGATCAAAACAAC 58.915 52.381 0.00 0.00 0.00 3.32
207 227 4.557205 GTGGTAATCATGTATCCGACTCC 58.443 47.826 0.00 0.00 0.00 3.85
209 229 2.440539 AATCATGTATCCGACTCCGC 57.559 50.000 0.00 0.00 0.00 5.54
231 251 4.679639 GCAACAACCACTATATCAGACGGA 60.680 45.833 0.00 0.00 0.00 4.69
309 467 4.370776 TCTTCTTCTTCCCCACATCCATA 58.629 43.478 0.00 0.00 0.00 2.74
315 473 5.246981 TCTTCCCCACATCCATATGATTC 57.753 43.478 3.65 0.00 36.54 2.52
316 474 4.915809 TCTTCCCCACATCCATATGATTCT 59.084 41.667 3.65 0.00 36.54 2.40
317 475 4.645863 TCCCCACATCCATATGATTCTG 57.354 45.455 3.65 0.00 36.54 3.02
318 476 3.982730 TCCCCACATCCATATGATTCTGT 59.017 43.478 3.65 0.00 36.54 3.41
321 479 5.599656 CCCCACATCCATATGATTCTGTTTT 59.400 40.000 3.65 0.00 36.54 2.43
361 522 5.638530 AGGTTTCTTGTTCTTCTCCTTCT 57.361 39.130 0.00 0.00 0.00 2.85
362 523 6.007485 AGGTTTCTTGTTCTTCTCCTTCTT 57.993 37.500 0.00 0.00 0.00 2.52
363 524 6.058833 AGGTTTCTTGTTCTTCTCCTTCTTC 58.941 40.000 0.00 0.00 0.00 2.87
364 525 6.058833 GGTTTCTTGTTCTTCTCCTTCTTCT 58.941 40.000 0.00 0.00 0.00 2.85
405 566 2.658373 ACATACGTGTACGCATTCCA 57.342 45.000 7.29 0.00 44.43 3.53
466 627 8.497554 AGATATCTTCTGTTAGATACGTTCGTC 58.502 37.037 0.00 0.00 39.31 4.20
528 689 1.331161 CGCGATACACGAGCAATGAAC 60.331 52.381 0.00 0.00 45.77 3.18
530 691 2.534939 GCGATACACGAGCAATGAACAC 60.535 50.000 0.00 0.00 45.77 3.32
542 703 3.365264 GCAATGAACACGAAGCTTCATCA 60.365 43.478 25.47 21.11 36.33 3.07
554 715 1.135746 GCTTCATCAGCTGTTCAGCAC 60.136 52.381 23.69 0.00 46.27 4.40
557 718 2.148768 TCATCAGCTGTTCAGCACAAG 58.851 47.619 23.69 12.42 33.87 3.16
567 728 3.214328 GTTCAGCACAAGAAGGGAAAGA 58.786 45.455 0.00 0.00 0.00 2.52
568 729 2.851195 TCAGCACAAGAAGGGAAAGAC 58.149 47.619 0.00 0.00 0.00 3.01
605 766 9.109393 GAGAGACAATTGTAAGGTAAATGCATA 57.891 33.333 11.95 0.00 0.00 3.14
636 797 3.009115 TCTAGGGGTGCTGGTGCC 61.009 66.667 0.00 0.00 38.71 5.01
638 799 3.628646 CTAGGGGTGCTGGTGCCAC 62.629 68.421 0.00 0.00 38.71 5.01
679 840 1.421485 CACGCTTGCTTTCCGCTAG 59.579 57.895 0.00 0.00 43.15 3.42
756 917 1.726791 GCCGGTGATGCGAATACTATG 59.273 52.381 1.90 0.00 0.00 2.23
758 919 2.029380 CCGGTGATGCGAATACTATGGA 60.029 50.000 0.00 0.00 0.00 3.41
783 944 1.359459 GATCTCGGCCGTCCAAACAC 61.359 60.000 27.15 6.14 0.00 3.32
788 949 2.589442 GCCGTCCAAACACCGTCA 60.589 61.111 0.00 0.00 0.00 4.35
794 955 1.531149 GTCCAAACACCGTCAGACATG 59.469 52.381 0.41 0.75 0.00 3.21
796 957 1.946768 CCAAACACCGTCAGACATGTT 59.053 47.619 12.50 12.50 36.86 2.71
797 958 2.357637 CCAAACACCGTCAGACATGTTT 59.642 45.455 20.17 20.17 44.08 2.83
802 963 2.936498 CACCGTCAGACATGTTTATCCC 59.064 50.000 0.00 0.00 0.00 3.85
835 997 5.905088 TCGATCCTCCTCCTCCTATAAATT 58.095 41.667 0.00 0.00 0.00 1.82
932 1094 8.680903 CACCAATAATCACTTTCTCTATGCTTT 58.319 33.333 0.00 0.00 0.00 3.51
965 1130 2.739379 GCCAGCAAGTTTCTCTCACTAC 59.261 50.000 0.00 0.00 0.00 2.73
998 1163 6.350780 GCTAAACTTGGTGTAGAGCTAGGTAA 60.351 42.308 5.60 0.00 35.10 2.85
1014 1179 2.045885 AGGTAAGATGGGAGGGAAGTCA 59.954 50.000 0.00 0.00 0.00 3.41
1105 1270 1.393603 CTACATGAGCGACTGGGAGA 58.606 55.000 0.00 0.00 0.00 3.71
1106 1271 1.066303 CTACATGAGCGACTGGGAGAC 59.934 57.143 0.00 0.00 0.00 3.36
1271 1442 1.594862 GGTAGCATGCAACACTCGATC 59.405 52.381 21.98 0.00 0.00 3.69
1272 1443 1.256376 GTAGCATGCAACACTCGATCG 59.744 52.381 21.98 9.36 0.00 3.69
1415 1586 4.944317 AGATGTAGATCTCTGTGTTCGTGA 59.056 41.667 0.00 0.00 33.20 4.35
1458 1639 0.737715 GACAGGGATGCGTCACAGAC 60.738 60.000 11.57 0.00 32.24 3.51
1544 1729 6.791887 ATGTGTTCTGTTTGATCAGTACTG 57.208 37.500 17.17 17.17 36.91 2.74
1553 1738 1.202452 TGATCAGTACTGCAGCGGATG 60.202 52.381 18.45 8.04 0.00 3.51
1559 1744 0.103026 TACTGCAGCGGATGTGCTAG 59.897 55.000 15.27 0.00 45.23 3.42
1598 2061 8.243426 TGATTATAGTTTTTGCAGCTCGATTTT 58.757 29.630 0.00 0.00 0.00 1.82
1688 2152 2.998097 GATACCCAGCTGGCCACA 59.002 61.111 28.39 11.57 37.83 4.17
1722 2186 1.006571 GCGAGTCGGAGGTTTGACA 60.007 57.895 15.52 0.00 37.58 3.58
1754 2218 4.464951 TCGGAGGTCTTTTCATGCTAACTA 59.535 41.667 0.00 0.00 0.00 2.24
1758 2222 7.272978 GGAGGTCTTTTCATGCTAACTACATA 58.727 38.462 0.00 0.00 0.00 2.29
1768 2232 5.147330 TGCTAACTACATATCGGATTGGG 57.853 43.478 0.00 0.00 0.00 4.12
1787 2251 2.279517 CGTGCCTATGCCGGAGAC 60.280 66.667 5.05 0.00 36.33 3.36
1840 2304 6.593382 GCTCACATAGGATAATGCTTCTAAGG 59.407 42.308 0.00 0.00 0.00 2.69
1957 2421 8.209917 AGATTATCTACCCGTTTGTTTTGATC 57.790 34.615 0.00 0.00 0.00 2.92
2015 2479 9.884465 CAGAAACTGAAGAAGACGAAAAATAAT 57.116 29.630 0.00 0.00 32.44 1.28
2063 2527 4.569943 ACACGAAGCAACATAGTCTGAAT 58.430 39.130 0.00 0.00 0.00 2.57
2064 2528 4.389992 ACACGAAGCAACATAGTCTGAATG 59.610 41.667 0.00 0.00 0.00 2.67
2065 2529 4.389992 CACGAAGCAACATAGTCTGAATGT 59.610 41.667 0.00 0.00 39.22 2.71
2086 2550 6.463995 TGTCCTTATTACCATCCATTTTGC 57.536 37.500 0.00 0.00 0.00 3.68
2087 2551 5.954752 TGTCCTTATTACCATCCATTTTGCA 59.045 36.000 0.00 0.00 0.00 4.08
2100 2564 5.668471 TCCATTTTGCAACATCAAACAGAA 58.332 33.333 0.00 0.00 35.86 3.02
2101 2565 6.289834 TCCATTTTGCAACATCAAACAGAAT 58.710 32.000 0.00 0.00 35.86 2.40
2102 2566 6.766944 TCCATTTTGCAACATCAAACAGAATT 59.233 30.769 0.00 0.00 35.86 2.17
2103 2567 7.930325 TCCATTTTGCAACATCAAACAGAATTA 59.070 29.630 0.00 0.00 35.86 1.40
2105 2569 9.932699 CATTTTGCAACATCAAACAGAATTAAA 57.067 25.926 0.00 0.00 35.86 1.52
2212 2677 9.927668 AATTTGTTTTCATCATTAAATCCGTCT 57.072 25.926 0.00 0.00 0.00 4.18
2249 2714 9.196552 TGCAAAACTAGATCTCGTATTGATATG 57.803 33.333 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.929244 AGGGGAGGGTCATCAAATGG 59.071 55.000 0.00 0.00 0.00 3.16
177 197 7.015779 TCGGATACATGATTACCACCAATAAGA 59.984 37.037 0.00 0.00 0.00 2.10
182 202 4.407621 AGTCGGATACATGATTACCACCAA 59.592 41.667 0.00 0.00 0.00 3.67
200 220 2.280524 TGGTTGTTGCGGAGTCGG 60.281 61.111 0.00 0.00 36.79 4.79
207 227 3.242944 CGTCTGATATAGTGGTTGTTGCG 59.757 47.826 0.00 0.00 0.00 4.85
209 229 5.006153 TCCGTCTGATATAGTGGTTGTTG 57.994 43.478 0.00 0.00 0.00 3.33
231 251 6.347061 AAGGGAAAAGGAACATCAGGATAT 57.653 37.500 0.00 0.00 0.00 1.63
284 436 3.759086 GGATGTGGGGAAGAAGAAGAAAC 59.241 47.826 0.00 0.00 0.00 2.78
309 467 7.745620 ACCGAGAAAAGTAAAACAGAATCAT 57.254 32.000 0.00 0.00 0.00 2.45
315 473 8.015658 CCTTGATAACCGAGAAAAGTAAAACAG 58.984 37.037 0.00 0.00 0.00 3.16
316 474 7.499895 ACCTTGATAACCGAGAAAAGTAAAACA 59.500 33.333 0.00 0.00 0.00 2.83
317 475 7.868775 ACCTTGATAACCGAGAAAAGTAAAAC 58.131 34.615 0.00 0.00 0.00 2.43
318 476 8.454570 AACCTTGATAACCGAGAAAAGTAAAA 57.545 30.769 0.00 0.00 0.00 1.52
321 479 7.447594 AGAAACCTTGATAACCGAGAAAAGTA 58.552 34.615 0.00 0.00 0.00 2.24
330 488 5.941948 AGAACAAGAAACCTTGATAACCG 57.058 39.130 11.60 0.00 42.71 4.44
405 566 4.798882 TCTTGTAGGGTTTGTTGGTTCAT 58.201 39.130 0.00 0.00 0.00 2.57
466 627 3.878778 AGAGCACTATGCCAAAAGGTAG 58.121 45.455 0.00 0.00 46.52 3.18
548 709 2.172505 TGTCTTTCCCTTCTTGTGCTGA 59.827 45.455 0.00 0.00 0.00 4.26
554 715 9.672673 TCTTTATTCTATGTCTTTCCCTTCTTG 57.327 33.333 0.00 0.00 0.00 3.02
557 718 9.541143 CTCTCTTTATTCTATGTCTTTCCCTTC 57.459 37.037 0.00 0.00 0.00 3.46
605 766 2.458620 CCCTAGAGGAAGAAGGAACGT 58.541 52.381 0.00 0.00 38.24 3.99
636 797 2.497675 TCTAGGCCTCTGCTTTACTGTG 59.502 50.000 9.68 0.00 37.74 3.66
638 799 3.791245 CTTCTAGGCCTCTGCTTTACTG 58.209 50.000 9.68 0.00 37.74 2.74
679 840 4.700692 GCTAGCTAATTATTTAGGTGCCCC 59.299 45.833 7.70 0.00 43.95 5.80
756 917 4.593864 GGCCGAGATCGTGCCTCC 62.594 72.222 20.47 4.13 45.60 4.30
783 944 2.936498 GTGGGATAAACATGTCTGACGG 59.064 50.000 0.00 0.57 0.00 4.79
788 949 2.939640 GCACCGTGGGATAAACATGTCT 60.940 50.000 0.00 0.00 0.00 3.41
794 955 3.074594 ATCGCACCGTGGGATAAAC 57.925 52.632 25.14 0.00 46.34 2.01
802 963 1.658717 GAGGATCGATCGCACCGTG 60.659 63.158 18.81 0.00 0.00 4.94
932 1094 4.891992 ACTTGCTGGCTAGAAACTAGAA 57.108 40.909 0.00 0.00 0.00 2.10
998 1163 0.621862 GGGTGACTTCCCTCCCATCT 60.622 60.000 0.00 0.00 43.85 2.90
1014 1179 0.988063 GGCAGAAGAAGGAGAAGGGT 59.012 55.000 0.00 0.00 0.00 4.34
1271 1442 4.118995 ACGGTTGCATGCATGGCG 62.119 61.111 27.34 12.78 0.00 5.69
1272 1443 1.932011 TACACGGTTGCATGCATGGC 61.932 55.000 27.34 19.18 0.00 4.40
1415 1586 4.562425 CCACCCCACACGCACACT 62.562 66.667 0.00 0.00 0.00 3.55
1458 1639 2.736978 TGGCAGCAAACAACAAATACG 58.263 42.857 0.00 0.00 0.00 3.06
1544 1729 0.249615 TGATCTAGCACATCCGCTGC 60.250 55.000 0.00 0.00 43.68 5.25
1553 1738 2.005451 CAGTTGCCTGTGATCTAGCAC 58.995 52.381 0.00 0.00 39.22 4.40
1559 1744 7.559590 AAACTATAATCAGTTGCCTGTGATC 57.440 36.000 0.00 0.00 38.74 2.92
1588 2051 4.166011 GCGCCGCAAAATCGAGCT 62.166 61.111 3.15 0.00 32.98 4.09
1688 2152 4.521062 GCCTCCATCTGCGACGCT 62.521 66.667 22.08 0.00 0.00 5.07
1722 2186 0.178929 AAGACCTCCGACCTGAACCT 60.179 55.000 0.00 0.00 0.00 3.50
1787 2251 2.805353 CACACCTCGGAGTTCGCG 60.805 66.667 0.00 0.00 39.05 5.87
1852 2316 0.895559 CAGTTGTCCCCTGCCTTTCC 60.896 60.000 0.00 0.00 0.00 3.13
1957 2421 0.324552 TGAATGCCCCCTCACATTGG 60.325 55.000 0.00 0.00 36.65 3.16
2045 2509 5.181748 AGGACATTCAGACTATGTTGCTTC 58.818 41.667 0.00 0.00 36.41 3.86
2063 2527 5.954752 TGCAAAATGGATGGTAATAAGGACA 59.045 36.000 0.00 0.00 0.00 4.02
2064 2528 6.463995 TGCAAAATGGATGGTAATAAGGAC 57.536 37.500 0.00 0.00 0.00 3.85
2065 2529 6.438741 TGTTGCAAAATGGATGGTAATAAGGA 59.561 34.615 0.00 0.00 0.00 3.36
2189 2654 8.105097 TGAGACGGATTTAATGATGAAAACAA 57.895 30.769 0.00 0.00 0.00 2.83
2212 2677 7.840342 GATCTAGTTTTGCAGATCTCTTTGA 57.160 36.000 0.00 0.00 42.54 2.69


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

AutoCloner maintained by Alex Coulton.