Multiple sequence alignment - TraesCS7B01G040600

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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 TraesCS7B01G040600 chr7B 100.000 2762 0 0 1 2762 40399201 40401962 0.000000e+00 5101
1 TraesCS7B01G040600 chr7B 100.000 73 0 0 2957 3029 40402157 40402229 5.270000e-28 135
2 TraesCS7B01G040600 chr7A 95.841 2092 72 7 1 2082 90650829 90652915 0.000000e+00 3367
3 TraesCS7B01G040600 chr7A 83.851 644 44 23 2103 2697 90652899 90653531 2.640000e-155 558
4 TraesCS7B01G040600 chr7A 94.737 76 2 1 2689 2762 90654982 90655057 1.910000e-22 117
5 TraesCS7B01G040600 chr7D 95.498 2110 64 11 1 2082 89721614 89723720 0.000000e+00 3341
6 TraesCS7B01G040600 chr7D 86.809 705 34 15 2104 2762 89723705 89724396 0.000000e+00 732
7 TraesCS7B01G040600 chr7D 98.630 73 1 0 2957 3029 89724495 89724567 2.450000e-26 130


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 TraesCS7B01G040600 chr7B 40399201 40402229 3028 False 2618.000000 5101 100.000000 1 3029 2 chr7B.!!$F1 3028
1 TraesCS7B01G040600 chr7A 90650829 90655057 4228 False 1347.333333 3367 91.476333 1 2762 3 chr7A.!!$F1 2761
2 TraesCS7B01G040600 chr7D 89721614 89724567 2953 False 1401.000000 3341 93.645667 1 3029 3 chr7D.!!$F1 3028

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
146 166 2.668457 GTGCGGTCATGTAAACTCTCTG 59.332 50.0 0.0 0.0 0.0 3.35 F
1270 1300 1.149101 ATTCACCAACACCCACCTCT 58.851 50.0 0.0 0.0 0.0 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1566 0.386838 GCACAAAGCCCCATATGCTC 59.613 55.000 0.0 0.00 38.34 4.26 R
2348 2388 1.551883 TGCTGCTGCAGACAATAGAGA 59.448 47.619 32.3 4.21 45.31 3.10 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
133 135 7.466725 GCTTTATTATTCACTTATGTGCGGTCA 60.467 37.037 3.90 0.00 43.49 4.02
136 138 2.760634 TCACTTATGTGCGGTCATGT 57.239 45.000 3.90 0.00 43.49 3.21
146 166 2.668457 GTGCGGTCATGTAAACTCTCTG 59.332 50.000 0.00 0.00 0.00 3.35
247 268 6.225981 TGTAGAGCATGTATGATGAGTGTT 57.774 37.500 0.00 0.00 0.00 3.32
622 652 8.593945 TCTTAACCTTAATGGCTTCATTTGAT 57.406 30.769 0.00 0.00 41.04 2.57
672 702 7.184161 TGTTTACCTGTAGATTGTAGGAGGTA 58.816 38.462 0.00 0.00 35.44 3.08
1270 1300 1.149101 ATTCACCAACACCCACCTCT 58.851 50.000 0.00 0.00 0.00 3.69
1287 1317 2.232941 CCTCTTGAAGCATGCCAATGTT 59.767 45.455 15.66 0.50 36.08 2.71
1347 1377 3.406361 GCTGTCGCTGACACCACG 61.406 66.667 7.20 0.82 37.67 4.94
1422 1452 2.820037 GGAGGCGCAGTTGGCTAC 60.820 66.667 10.83 0.00 45.90 3.58
1491 1521 6.017605 CAGTTGCTTATCTGATCACCATAACC 60.018 42.308 0.00 0.00 34.02 2.85
1541 1571 1.834263 GACTAACCTGGGTCTGAGCAT 59.166 52.381 9.30 0.00 0.00 3.79
1555 1585 0.386838 GAGCATATGGGGCTTTGTGC 59.613 55.000 4.56 0.00 42.78 4.57
1581 1611 5.429957 ACAACAATCTTCTTTCACTGCTC 57.570 39.130 0.00 0.00 0.00 4.26
1654 1684 1.907936 CCATTGAATCAAGGGGCCAAA 59.092 47.619 18.04 0.00 40.99 3.28
1663 1693 2.997315 GGGGCCAAAGCTGGTTCC 60.997 66.667 4.39 0.00 45.53 3.62
1683 1713 0.524604 AACTTGACGCGTTTGTTGCC 60.525 50.000 15.53 0.00 0.00 4.52
1687 1717 4.244802 ACGCGTTTGTTGCCGTGG 62.245 61.111 5.58 0.00 38.80 4.94
1699 1729 4.624364 CCGTGGCACTGTCCTGCA 62.624 66.667 16.72 0.00 39.08 4.41
1701 1731 1.079197 CGTGGCACTGTCCTGCATA 60.079 57.895 16.72 0.00 39.08 3.14
1767 1797 2.726691 CTCTGCCACGGCGTTTACG 61.727 63.158 11.19 0.00 45.51 3.18
1824 1854 6.072649 TGCAATCAATGTTATGATCTGGGAT 58.927 36.000 0.00 0.00 39.08 3.85
1836 1866 1.448985 TCTGGGATAAGCACGCAAAC 58.551 50.000 0.00 0.00 0.00 2.93
1837 1867 1.164411 CTGGGATAAGCACGCAAACA 58.836 50.000 0.00 0.00 0.00 2.83
1927 1957 3.460648 GGAAGTACTCCAGCGCATT 57.539 52.632 11.47 0.00 44.67 3.56
1928 1958 1.739067 GGAAGTACTCCAGCGCATTT 58.261 50.000 11.47 0.00 44.67 2.32
2064 2094 3.498777 GCAGGTACTCAGTTTTGTCCTTC 59.501 47.826 0.00 0.00 34.60 3.46
2071 2101 5.848406 ACTCAGTTTTGTCCTTCTGTCTAG 58.152 41.667 0.00 0.00 0.00 2.43
2072 2102 5.598830 ACTCAGTTTTGTCCTTCTGTCTAGA 59.401 40.000 0.00 0.00 0.00 2.43
2073 2103 6.098409 ACTCAGTTTTGTCCTTCTGTCTAGAA 59.902 38.462 0.00 0.00 40.53 2.10
2074 2104 6.281405 TCAGTTTTGTCCTTCTGTCTAGAAC 58.719 40.000 0.00 0.00 37.99 3.01
2075 2105 6.049149 CAGTTTTGTCCTTCTGTCTAGAACA 58.951 40.000 0.00 0.00 37.99 3.18
2322 2360 6.972901 TCATGAACATGTAGTCGTTAGTGATC 59.027 38.462 13.35 0.00 39.72 2.92
2331 2369 8.277490 TGTAGTCGTTAGTGATCTCTATTGTT 57.723 34.615 5.38 0.00 0.00 2.83
2406 2448 8.438513 CACTGCATATTATTGGTAGAGAAATCG 58.561 37.037 0.00 0.00 0.00 3.34
2444 2492 3.874543 TCGGTTAATCATTTGCAGCGTAT 59.125 39.130 0.00 0.00 0.00 3.06
2445 2493 5.051153 TCGGTTAATCATTTGCAGCGTATA 58.949 37.500 0.00 0.00 0.00 1.47
2499 2547 2.285834 CGGCGATGTAGAATTGTTGAGC 60.286 50.000 0.00 0.00 0.00 4.26
2500 2548 2.677836 GGCGATGTAGAATTGTTGAGCA 59.322 45.455 0.00 0.00 0.00 4.26
2501 2549 3.313526 GGCGATGTAGAATTGTTGAGCAT 59.686 43.478 0.00 0.00 0.00 3.79
2502 2550 4.277258 GCGATGTAGAATTGTTGAGCATG 58.723 43.478 0.00 0.00 0.00 4.06
2503 2551 4.277258 CGATGTAGAATTGTTGAGCATGC 58.723 43.478 10.51 10.51 0.00 4.06
2504 2552 4.201841 CGATGTAGAATTGTTGAGCATGCA 60.202 41.667 21.98 0.00 0.00 3.96
2505 2553 5.505159 CGATGTAGAATTGTTGAGCATGCAT 60.505 40.000 21.98 4.75 0.00 3.96
2506 2554 6.293027 CGATGTAGAATTGTTGAGCATGCATA 60.293 38.462 21.98 4.97 0.00 3.14
2507 2555 6.756299 TGTAGAATTGTTGAGCATGCATAA 57.244 33.333 21.98 11.51 0.00 1.90
2508 2556 7.337480 TGTAGAATTGTTGAGCATGCATAAT 57.663 32.000 21.98 6.56 0.00 1.28
2509 2557 8.449251 TGTAGAATTGTTGAGCATGCATAATA 57.551 30.769 21.98 9.74 0.00 0.98
2510 2558 8.562052 TGTAGAATTGTTGAGCATGCATAATAG 58.438 33.333 21.98 0.00 0.00 1.73
2576 2636 5.482908 CTTCATGCACTGGTACTTTACTCT 58.517 41.667 0.00 0.00 0.00 3.24
2611 2671 2.623418 TGATGGAGTGAGGGTGTACT 57.377 50.000 0.00 0.00 0.00 2.73
2613 2673 3.248024 TGATGGAGTGAGGGTGTACTTT 58.752 45.455 0.00 0.00 0.00 2.66
2615 2675 4.222145 TGATGGAGTGAGGGTGTACTTTAC 59.778 45.833 0.00 0.00 0.00 2.01
2725 4273 3.144506 CTCCACTGCTCAGTTTCAATGT 58.855 45.455 0.00 0.00 40.20 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
146 166 5.961843 CGCAAGTGACAGAACAAATATGATC 59.038 40.000 0.00 0.00 0.00 2.92
261 282 3.627123 CCGGCATGAAAGATATGTTGACA 59.373 43.478 0.00 0.00 0.00 3.58
339 360 6.590234 AGGCTTGAAGGGTGTTAATTTAAG 57.410 37.500 0.00 0.00 0.00 1.85
491 512 5.494390 TGCTGACATGGCTATTATCAGAT 57.506 39.130 19.75 0.00 39.33 2.90
511 533 0.957395 CCCAGACAGGTGACACATGC 60.957 60.000 19.57 12.35 32.34 4.06
622 652 6.202331 TCTCAATGAAGGTAGAACAGGGATA 58.798 40.000 0.00 0.00 0.00 2.59
1270 1300 3.965379 ATCAACATTGGCATGCTTCAA 57.035 38.095 18.92 14.52 33.05 2.69
1347 1377 1.648467 GACATGGCTGCTTCCGGAAC 61.648 60.000 14.35 11.13 0.00 3.62
1422 1452 2.680312 ACCCTGAATCTGTCATCACG 57.320 50.000 0.00 0.00 35.07 4.35
1491 1521 6.086222 GTGCTTTATGTACACCATTTCAGTG 58.914 40.000 0.00 0.00 41.15 3.66
1536 1566 0.386838 GCACAAAGCCCCATATGCTC 59.613 55.000 0.00 0.00 38.34 4.26
1541 1571 2.307392 TTGTAGAGCACAAAGCCCCATA 59.693 45.455 0.00 0.00 44.20 2.74
1555 1585 6.426328 AGCAGTGAAAGAAGATTGTTGTAGAG 59.574 38.462 0.00 0.00 0.00 2.43
1581 1611 3.381136 CCAAACACGGGGGCCATG 61.381 66.667 4.39 2.56 0.00 3.66
1654 1684 1.166531 GCGTCAAGTTGGAACCAGCT 61.167 55.000 2.34 4.43 39.14 4.24
1663 1693 0.565679 GCAACAAACGCGTCAAGTTG 59.434 50.000 30.48 30.48 41.71 3.16
1683 1713 0.462581 ATATGCAGGACAGTGCCACG 60.463 55.000 0.00 0.00 43.28 4.94
1687 1717 0.940126 CCGAATATGCAGGACAGTGC 59.060 55.000 0.00 0.00 44.27 4.40
1776 1806 2.822764 GTCAGGAACTTGTTGACGACT 58.177 47.619 0.00 0.00 34.60 4.18
1797 1827 5.981315 CCAGATCATAACATTGATTGCAACC 59.019 40.000 0.00 0.00 36.48 3.77
1824 1854 2.099921 ACCAAATGTGTTTGCGTGCTTA 59.900 40.909 0.00 0.00 42.66 3.09
1836 1866 4.155644 AGCAAACAAACCAAACCAAATGTG 59.844 37.500 0.00 0.00 0.00 3.21
1837 1867 4.331108 AGCAAACAAACCAAACCAAATGT 58.669 34.783 0.00 0.00 0.00 2.71
1854 1884 1.544093 CCTGCCAGAGTGAAGAGCAAA 60.544 52.381 0.00 0.00 32.14 3.68
1927 1957 4.072131 CCTTTGTTAGCTACAGCCTCAAA 58.928 43.478 0.00 6.72 43.38 2.69
1928 1958 3.674997 CCTTTGTTAGCTACAGCCTCAA 58.325 45.455 0.00 0.00 43.38 3.02
2090 2120 4.138290 TGTTCTAGACATTCCCGCAAAAA 58.862 39.130 0.00 0.00 32.00 1.94
2091 2121 3.745799 TGTTCTAGACATTCCCGCAAAA 58.254 40.909 0.00 0.00 32.00 2.44
2092 2122 3.007506 TCTGTTCTAGACATTCCCGCAAA 59.992 43.478 0.00 0.00 37.69 3.68
2093 2123 2.565391 TCTGTTCTAGACATTCCCGCAA 59.435 45.455 0.00 0.00 37.69 4.85
2094 2124 2.176045 TCTGTTCTAGACATTCCCGCA 58.824 47.619 0.00 0.00 37.69 5.69
2095 2125 2.961526 TCTGTTCTAGACATTCCCGC 57.038 50.000 0.00 0.00 37.69 6.13
2348 2388 1.551883 TGCTGCTGCAGACAATAGAGA 59.448 47.619 32.30 4.21 45.31 3.10
2370 2412 8.482943 ACCAATAATATGCAGTGTACAGAGTTA 58.517 33.333 0.00 0.00 0.00 2.24
2406 2448 2.618053 ACCGATACTGCTGTAAACTGC 58.382 47.619 7.59 5.15 40.61 4.40
2444 2492 5.010314 TCTCACGCTTTAAGACTGAGGTTTA 59.990 40.000 15.00 0.00 31.11 2.01
2445 2493 4.058817 CTCACGCTTTAAGACTGAGGTTT 58.941 43.478 9.95 0.00 0.00 3.27
2576 2636 9.813826 TCACTCCATCAAAGAGATATACTATGA 57.186 33.333 0.00 0.00 34.43 2.15
2603 2663 3.006537 TCACTGCAGAGTAAAGTACACCC 59.993 47.826 23.35 0.00 0.00 4.61
2611 2671 4.672587 ACTCACTTCACTGCAGAGTAAA 57.327 40.909 23.35 7.62 37.75 2.01
2613 2673 4.501571 GGAAACTCACTTCACTGCAGAGTA 60.502 45.833 23.35 5.37 38.51 2.59
2615 2675 2.805099 GGAAACTCACTTCACTGCAGAG 59.195 50.000 23.35 13.75 0.00 3.35
2687 2776 6.299141 CAGTGGAGCCCATATGTAAACTTAT 58.701 40.000 1.24 0.00 35.28 1.73
2725 4273 4.522114 TGAGATTACAAATCGCCCATTGA 58.478 39.130 1.73 0.00 0.00 2.57
2976 4526 2.344741 GCCTTGTTATCGACGAGAACAC 59.655 50.000 31.26 19.38 42.25 3.32


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

AutoCloner maintained by Alex Coulton.