Multiple sequence alignment - TraesCS4A01G161000

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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 TraesCS4A01G161000 chr4A 100.000 2838 0 0 1 2838 348502905 348505742 0 5241
1 TraesCS4A01G161000 chr4A 91.379 2842 222 19 1 2835 276809394 276812219 0 3869
2 TraesCS4A01G161000 chr4A 91.331 969 74 6 1880 2838 163277514 163276546 0 1315
3 TraesCS4A01G161000 chr7D 90.028 2848 219 39 1 2838 195568789 195565997 0 3626
4 TraesCS4A01G161000 chr7D 88.447 2190 217 27 4 2180 122700572 122698406 0 2610
5 TraesCS4A01G161000 chr2D 89.225 2877 244 44 1 2838 554138639 554135790 0 3535
6 TraesCS4A01G161000 chr2D 88.541 2845 254 46 1 2835 275220468 275223250 0 3382
7 TraesCS4A01G161000 chr2D 87.729 872 74 16 1993 2838 324868975 324868111 0 987
8 TraesCS4A01G161000 chr1A 87.574 2535 260 34 1 2499 252751403 252753918 0 2885
9 TraesCS4A01G161000 chr6A 89.219 2189 211 17 1 2180 178096002 178093830 0 2712
10 TraesCS4A01G161000 chr5D 89.776 2142 182 25 1 2135 438200127 438198016 0 2708
11 TraesCS4A01G161000 chr5D 88.067 1257 135 8 1581 2834 16583376 16584620 0 1476
12 TraesCS4A01G161000 chr5D 91.631 693 57 1 2144 2835 438198053 438197361 0 957
13 TraesCS4A01G161000 chr5D 90.013 741 67 7 2099 2835 464312131 464312868 0 952
14 TraesCS4A01G161000 chr4D 88.535 2198 210 29 1 2181 179916667 179918839 0 2625
15 TraesCS4A01G161000 chr4D 89.726 730 73 2 2099 2826 179918803 179919532 0 931


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 TraesCS4A01G161000 chr4A 348502905 348505742 2837 False 5241.0 5241 100.0000 1 2838 1 chr4A.!!$F2 2837
1 TraesCS4A01G161000 chr4A 276809394 276812219 2825 False 3869.0 3869 91.3790 1 2835 1 chr4A.!!$F1 2834
2 TraesCS4A01G161000 chr4A 163276546 163277514 968 True 1315.0 1315 91.3310 1880 2838 1 chr4A.!!$R1 958
3 TraesCS4A01G161000 chr7D 195565997 195568789 2792 True 3626.0 3626 90.0280 1 2838 1 chr7D.!!$R2 2837
4 TraesCS4A01G161000 chr7D 122698406 122700572 2166 True 2610.0 2610 88.4470 4 2180 1 chr7D.!!$R1 2176
5 TraesCS4A01G161000 chr2D 554135790 554138639 2849 True 3535.0 3535 89.2250 1 2838 1 chr2D.!!$R2 2837
6 TraesCS4A01G161000 chr2D 275220468 275223250 2782 False 3382.0 3382 88.5410 1 2835 1 chr2D.!!$F1 2834
7 TraesCS4A01G161000 chr2D 324868111 324868975 864 True 987.0 987 87.7290 1993 2838 1 chr2D.!!$R1 845
8 TraesCS4A01G161000 chr1A 252751403 252753918 2515 False 2885.0 2885 87.5740 1 2499 1 chr1A.!!$F1 2498
9 TraesCS4A01G161000 chr6A 178093830 178096002 2172 True 2712.0 2712 89.2190 1 2180 1 chr6A.!!$R1 2179
10 TraesCS4A01G161000 chr5D 438197361 438200127 2766 True 1832.5 2708 90.7035 1 2835 2 chr5D.!!$R1 2834
11 TraesCS4A01G161000 chr5D 16583376 16584620 1244 False 1476.0 1476 88.0670 1581 2834 1 chr5D.!!$F1 1253
12 TraesCS4A01G161000 chr5D 464312131 464312868 737 False 952.0 952 90.0130 2099 2835 1 chr5D.!!$F2 736
13 TraesCS4A01G161000 chr4D 179916667 179919532 2865 False 1778.0 2625 89.1305 1 2826 2 chr4D.!!$F1 2825

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
20 21 0.899720 CGTTAGAAGTGCCACCCCTA 59.100 55.000 0.0 0.0 0.00 3.53 F
411 422 1.402325 GGCCACTTGGTAAAATGTCGC 60.402 52.381 0.0 0.0 37.57 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1393 1424 1.202336 GCAAGGTATTCCAGCATGTGC 60.202 52.381 0.00 0.0 42.49 4.57 R
2186 2348 1.152652 TGACCACAATTGCCCCGTT 60.153 52.632 5.05 0.0 0.00 4.44 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
20 21 0.899720 CGTTAGAAGTGCCACCCCTA 59.100 55.000 0.00 0.00 0.00 3.53
26 27 2.247635 AGAAGTGCCACCCCTAGATCTA 59.752 50.000 1.69 1.69 0.00 1.98
66 67 3.697439 ATGAACCACCCGCGGATGG 62.697 63.158 37.85 37.85 42.13 3.51
73 74 2.357517 CCCGCGGATGGCTATGAC 60.358 66.667 30.73 0.00 40.44 3.06
167 168 2.936202 ACAACAAGCACATGAAGGAGT 58.064 42.857 0.00 0.00 0.00 3.85
411 422 1.402325 GGCCACTTGGTAAAATGTCGC 60.402 52.381 0.00 0.00 37.57 5.19
489 500 3.241773 CGACAAGACAATCATGCAGTACG 60.242 47.826 0.00 0.00 0.00 3.67
657 671 6.737254 TGTTTTGTTAGTAGCTATGCTTCC 57.263 37.500 0.00 0.00 40.44 3.46
732 748 7.951591 ACTGCCATGTAAAATAAGTTTGACTT 58.048 30.769 0.00 0.00 41.97 3.01
764 782 3.568538 GCAACTTATGTGGCAACTTCAG 58.431 45.455 3.29 0.00 42.54 3.02
771 789 7.777095 ACTTATGTGGCAACTTCAGTTAAAAA 58.223 30.769 0.00 0.00 36.32 1.94
897 917 6.484364 TCATGTACCTCTTATTGCATCTGA 57.516 37.500 0.00 0.00 0.00 3.27
913 933 9.932207 ATTGCATCTGACAATATCTTTTCAAAA 57.068 25.926 0.00 0.00 36.00 2.44
938 958 8.635765 ACATTGTTCCTACTACATCATTTTGT 57.364 30.769 0.00 0.00 0.00 2.83
956 977 9.698309 TCATTTTGTTGTTTTTGAGTTCAACTA 57.302 25.926 0.00 0.00 40.20 2.24
1012 1037 1.780309 TGTTCCCCATGTTCCAAGAGT 59.220 47.619 0.00 0.00 0.00 3.24
1096 1121 2.645802 ACCAACGTTTTGAGGTGCTTA 58.354 42.857 7.20 0.00 34.24 3.09
1097 1122 2.616842 ACCAACGTTTTGAGGTGCTTAG 59.383 45.455 7.20 0.00 34.24 2.18
1127 1152 3.603532 GTTCAGAAGATGATGCAGACCA 58.396 45.455 0.00 0.00 37.89 4.02
1138 1163 6.494835 AGATGATGCAGACCATACTACACATA 59.505 38.462 0.00 0.00 33.29 2.29
1153 1178 7.993821 ACTACACATACTGAATTCTTCATCG 57.006 36.000 7.05 0.00 39.30 3.84
1155 1180 8.251026 ACTACACATACTGAATTCTTCATCGAA 58.749 33.333 7.05 0.00 39.30 3.71
1224 1249 4.512944 CAGATCGGTCATTTTCCAATCGAT 59.487 41.667 0.00 0.00 38.36 3.59
1315 1343 5.370289 TCCCTAAACCTTTTTGTCACCTCTA 59.630 40.000 0.00 0.00 0.00 2.43
1358 1388 2.368875 TCCTGTTCTCTTGAGTTGACCC 59.631 50.000 0.00 0.00 0.00 4.46
1362 1392 3.254892 GTTCTCTTGAGTTGACCCGATC 58.745 50.000 0.00 0.00 0.00 3.69
1372 1403 4.470602 AGTTGACCCGATCCTTTTCTTTT 58.529 39.130 0.00 0.00 0.00 2.27
1373 1404 4.893524 AGTTGACCCGATCCTTTTCTTTTT 59.106 37.500 0.00 0.00 0.00 1.94
1381 1412 6.238759 CCCGATCCTTTTCTTTTTATAGGCAG 60.239 42.308 0.00 0.00 0.00 4.85
1390 1421 4.534500 TCTTTTTATAGGCAGGACTGTGGA 59.466 41.667 0.82 0.00 0.00 4.02
1393 1424 4.422073 TTATAGGCAGGACTGTGGATTG 57.578 45.455 0.82 0.00 0.00 2.67
1400 1431 0.171903 GGACTGTGGATTGCACATGC 59.828 55.000 11.62 6.71 42.50 4.06
1419 1450 3.230134 TGCTGGAATACCTTGCAAAGTT 58.770 40.909 5.92 0.00 44.25 2.66
1455 1486 1.566563 CTGTCGTCACAGCTGCAAC 59.433 57.895 15.27 11.32 43.77 4.17
1457 1488 1.949133 GTCGTCACAGCTGCAACGA 60.949 57.895 29.60 29.60 41.40 3.85
1481 1512 4.211164 TCATTGAGCTCCGCAAAATATACG 59.789 41.667 12.15 0.00 0.00 3.06
1592 1623 2.783135 ACAAGCGATCACATGGTTCTT 58.217 42.857 0.00 0.00 0.00 2.52
1712 1744 2.880443 CCCCCGTAGCCTAGTATACAA 58.120 52.381 5.50 0.00 0.00 2.41
1719 1751 4.521639 CGTAGCCTAGTATACAATGGTGGA 59.478 45.833 5.50 0.00 0.00 4.02
1735 1767 3.214328 GGTGGAGTGTGAGTGACATTTT 58.786 45.455 0.00 0.00 36.78 1.82
1736 1768 3.632145 GGTGGAGTGTGAGTGACATTTTT 59.368 43.478 0.00 0.00 36.78 1.94
1804 1840 8.458052 TGTGACAATAGCTACATTTATGTTTGG 58.542 33.333 0.00 0.00 41.97 3.28
1818 1854 8.735315 CATTTATGTTTGGGTACTGTTATGTGA 58.265 33.333 0.00 0.00 0.00 3.58
1896 1934 8.701908 AACATGGCAAATATAGTTGATCAGAT 57.298 30.769 16.69 4.11 0.00 2.90
2085 2132 8.253810 TGGAATAAAATGTGTTGACTGAAACAA 58.746 29.630 3.04 0.00 41.52 2.83
2097 2167 5.153513 TGACTGAAACAAAAATCTATGCGC 58.846 37.500 0.00 0.00 0.00 6.09
2155 2225 9.851686 ACAATAGAAATAACATGGCAGATTCTA 57.148 29.630 0.00 5.34 33.81 2.10
2186 2348 3.196901 ACATCGCAGATTAAGTACCACCA 59.803 43.478 0.00 0.00 45.12 4.17
2200 2362 1.006337 CACCAACGGGGCAATTGTG 60.006 57.895 7.40 0.00 42.05 3.33
2251 2414 1.134699 TCTGATGCCGATCAACAGTCC 60.135 52.381 12.13 0.00 43.58 3.85
2258 2421 1.550524 CCGATCAACAGTCCTTCTCCA 59.449 52.381 0.00 0.00 0.00 3.86
2322 2492 4.225267 CCAACACCCAAGTAACTATCCTCT 59.775 45.833 0.00 0.00 0.00 3.69
2340 2510 4.718774 TCCTCTAGAGTTGCTCATGGATTT 59.281 41.667 18.42 0.00 32.06 2.17
2350 2521 0.395586 TCATGGATTTCCCGCCCTTG 60.396 55.000 0.00 0.00 37.93 3.61
2421 2592 3.317406 ACCTCTTTTGGATGCCCTTTTT 58.683 40.909 0.00 0.00 0.00 1.94
2483 2654 2.247635 TGCTATTCCAGACCCTACCTCT 59.752 50.000 0.00 0.00 0.00 3.69
2565 2736 0.392998 GGCTTCTTCGGCCTTCATCA 60.393 55.000 0.00 0.00 45.57 3.07
2570 2741 4.619160 GCTTCTTCGGCCTTCATCATTTTT 60.619 41.667 0.00 0.00 0.00 1.94
2661 2833 7.718314 TCTTGCATGCTTCATCTATTAGTTCAT 59.282 33.333 20.33 0.00 0.00 2.57
2712 2884 1.065199 CAGCTTCCATGGTTGCCTCTA 60.065 52.381 21.69 0.00 0.00 2.43
2758 2934 1.070038 GCATTTGATGTTTGTGGCCG 58.930 50.000 0.00 0.00 0.00 6.13
2776 2952 1.330213 CCGCAATGCATCGTCAACATA 59.670 47.619 5.91 0.00 0.00 2.29
2798 2974 0.466543 AAGTCCATTGCCGCCGTATA 59.533 50.000 0.00 0.00 0.00 1.47
2815 2991 2.086610 ATAAAATGGCGGGGCAATCT 57.913 45.000 0.00 0.00 0.00 2.40
2835 3011 2.162754 GTTACCGCGACCATGTCCG 61.163 63.158 8.23 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.106054 CCCTATGCTGCCTCATAGATCT 58.894 50.000 18.48 0.00 45.39 2.75
26 27 2.109229 ACTACCCTATGCTGCCTCAT 57.891 50.000 0.00 0.00 0.00 2.90
66 67 1.473434 CCTTGACTTCGGGGTCATAGC 60.473 57.143 11.00 0.00 44.30 2.97
73 74 2.359975 GTGGCCTTGACTTCGGGG 60.360 66.667 3.32 0.00 0.00 5.73
110 111 4.033932 TCCGAAACGCTTGACAATATCATG 59.966 41.667 0.00 0.00 37.11 3.07
130 131 0.953471 TGTTGGACCTCGCATTTCCG 60.953 55.000 0.00 0.00 31.38 4.30
167 168 1.593933 GTGTGGACGTTACGCTTTCAA 59.406 47.619 4.09 0.00 0.00 2.69
411 422 1.464608 CCCACACGCAACTACATTCTG 59.535 52.381 0.00 0.00 0.00 3.02
448 459 4.041567 TGTCGGGACAAATATCCATATGCT 59.958 41.667 0.00 0.00 40.96 3.79
489 500 2.166254 CCCATATTTTGCAGGTCACACC 59.834 50.000 0.00 0.00 38.99 4.16
532 543 1.106285 GCAAAATGCTTCCTCGGGAT 58.894 50.000 0.00 0.00 40.96 3.85
771 789 5.933463 CCATGTATGAACAAGTTGCCAAATT 59.067 36.000 1.81 0.00 39.58 1.82
817 836 6.649973 CCACAAAGAATGTTTATTTGCCATGA 59.350 34.615 7.13 0.00 41.46 3.07
913 933 8.635765 ACAAAATGATGTAGTAGGAACAATGT 57.364 30.769 0.00 0.00 0.00 2.71
938 958 8.770438 AAAAGCATAGTTGAACTCAAAAACAA 57.230 26.923 0.00 0.00 37.63 2.83
1012 1037 1.454847 GTGGGTCCTGTGGTGCAAA 60.455 57.895 0.00 0.00 0.00 3.68
1096 1121 4.318332 TCATCTTCTGAACGCATTGAACT 58.682 39.130 0.00 0.00 0.00 3.01
1097 1122 4.668576 TCATCTTCTGAACGCATTGAAC 57.331 40.909 0.00 0.00 0.00 3.18
1153 1178 5.278512 GGTTCCATGTCTCTTTGAGGTTTTC 60.279 44.000 0.00 0.00 0.00 2.29
1155 1180 4.145052 GGTTCCATGTCTCTTTGAGGTTT 58.855 43.478 0.00 0.00 0.00 3.27
1224 1249 4.348656 CTTGCTTAGTAGTCGCGACATAA 58.651 43.478 37.85 28.63 0.00 1.90
1239 1264 5.807909 AGTAATTACCGGTTTCCTTGCTTA 58.192 37.500 15.04 0.00 0.00 3.09
1338 1366 2.772287 GGGTCAACTCAAGAGAACAGG 58.228 52.381 3.73 0.00 0.00 4.00
1358 1388 6.542370 TCCTGCCTATAAAAAGAAAAGGATCG 59.458 38.462 0.00 0.00 0.00 3.69
1362 1392 6.434340 ACAGTCCTGCCTATAAAAAGAAAAGG 59.566 38.462 0.00 0.00 0.00 3.11
1372 1403 3.433598 GCAATCCACAGTCCTGCCTATAA 60.434 47.826 0.00 0.00 0.00 0.98
1373 1404 2.104792 GCAATCCACAGTCCTGCCTATA 59.895 50.000 0.00 0.00 0.00 1.31
1390 1421 3.022557 AGGTATTCCAGCATGTGCAAT 57.977 42.857 7.83 1.48 45.16 3.56
1393 1424 1.202336 GCAAGGTATTCCAGCATGTGC 60.202 52.381 0.00 0.00 42.49 4.57
1400 1431 3.826157 TCCAACTTTGCAAGGTATTCCAG 59.174 43.478 15.22 1.62 35.89 3.86
1481 1512 5.013568 TCATTCATCAACCAATTCCATGC 57.986 39.130 0.00 0.00 0.00 4.06
1592 1623 7.509318 AGAATGTAAGGTAGGCATGTAGTATGA 59.491 37.037 0.00 0.00 0.00 2.15
1656 1688 6.307031 ACATAGTGCACGAACATTGTTTTA 57.693 33.333 12.01 0.00 0.00 1.52
1662 1694 5.874810 AGTCATAACATAGTGCACGAACATT 59.125 36.000 12.01 6.43 0.00 2.71
1710 1742 2.146342 GTCACTCACACTCCACCATTG 58.854 52.381 0.00 0.00 0.00 2.82
1712 1744 1.423584 TGTCACTCACACTCCACCAT 58.576 50.000 0.00 0.00 0.00 3.55
1786 1818 7.626390 ACAGTACCCAAACATAAATGTAGCTA 58.374 34.615 0.00 0.00 40.80 3.32
1804 1840 5.106317 CCAACCACAATCACATAACAGTACC 60.106 44.000 0.00 0.00 0.00 3.34
1818 1854 3.616560 CGACTAGTGCTACCAACCACAAT 60.617 47.826 0.00 0.00 34.48 2.71
1835 1871 1.801771 CGCATTCAAAACACCCGACTA 59.198 47.619 0.00 0.00 0.00 2.59
1866 1904 9.754382 GATCAACTATATTTGCCATGTTTTCAT 57.246 29.630 0.00 0.00 41.78 2.57
2085 2132 2.042686 TCTGCCAGCGCATAGATTTT 57.957 45.000 11.47 0.00 46.11 1.82
2097 2167 8.562892 CCATGTTATTTCTACTAAATCTGCCAG 58.437 37.037 0.00 0.00 0.00 4.85
2158 2228 8.395633 GTGGTACTTAATCTGCGATGTTATTTT 58.604 33.333 0.00 0.00 0.00 1.82
2168 2238 2.347452 CGTTGGTGGTACTTAATCTGCG 59.653 50.000 0.00 0.00 0.00 5.18
2176 2246 1.997256 TTGCCCCGTTGGTGGTACTT 61.997 55.000 0.00 0.00 36.04 2.24
2186 2348 1.152652 TGACCACAATTGCCCCGTT 60.153 52.632 5.05 0.00 0.00 4.44
2200 2362 6.072286 ACAGAAAATGACATGAATCAGTGACC 60.072 38.462 0.00 0.00 30.46 4.02
2322 2492 3.432186 CGGGAAATCCATGAGCAACTCTA 60.432 47.826 1.22 0.00 37.91 2.43
2350 2521 5.281693 AGCAAAACACAAGAAAACAAAGC 57.718 34.783 0.00 0.00 0.00 3.51
2421 2592 0.768622 AACCCACTCCGTTCCATCAA 59.231 50.000 0.00 0.00 0.00 2.57
2450 2621 1.200020 GGAATAGCAAGCACGCAAACT 59.800 47.619 0.00 0.00 0.00 2.66
2483 2654 4.002982 CGGGTTCATCATCTGAAAACTCA 58.997 43.478 8.52 0.00 45.27 3.41
2500 2671 3.552384 TGCCTTCGTCCACGGGTT 61.552 61.111 0.00 0.00 40.29 4.11
2555 2726 7.281040 TGATGAGATAAAAATGATGAAGGCC 57.719 36.000 0.00 0.00 0.00 5.19
2562 2733 9.629878 AAGAGAGCTTGATGAGATAAAAATGAT 57.370 29.630 0.00 0.00 31.83 2.45
2570 2741 6.407865 CCCTGAAAAGAGAGCTTGATGAGATA 60.408 42.308 0.00 0.00 33.79 1.98
2661 2833 4.509970 CGTTGTGTTGACCAAGAACTATGA 59.490 41.667 0.00 0.00 0.00 2.15
2712 2884 1.134461 GGCTGTGCATGATGAGAGACT 60.134 52.381 0.00 0.00 0.00 3.24
2758 2934 2.097304 TGGTATGTTGACGATGCATTGC 59.903 45.455 14.18 0.46 0.00 3.56
2776 2952 2.676471 GGCGGCAATGGACTTGGT 60.676 61.111 3.07 0.00 35.25 3.67
2798 2974 1.666209 CGAGATTGCCCCGCCATTTT 61.666 55.000 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.