Multiple sequence alignment - TraesCS7A01G555300

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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 TraesCS7A01G555300 chr7A 100.000 3980 0 0 1 3980 727227721 727231700 0.000000e+00 7350
1 TraesCS7A01G555300 chr7A 77.003 2409 483 51 992 3384 726770315 726767962 0.000000e+00 1314
2 TraesCS7A01G555300 chr7A 74.929 2449 509 75 988 3384 726686234 726683839 0.000000e+00 1024
3 TraesCS7A01G555300 chr7A 75.723 1660 338 51 1748 3384 726814162 726812545 0.000000e+00 773
4 TraesCS7A01G555300 chr7A 71.810 1199 275 41 1010 2172 727215337 727214166 2.340000e-72 283
5 TraesCS7A01G555300 chr7B 95.435 3549 128 17 427 3974 733924657 733928172 0.000000e+00 5626
6 TraesCS7A01G555300 chr7B 91.946 3576 228 21 427 3980 733859795 733863332 0.000000e+00 4953
7 TraesCS7A01G555300 chr7B 92.315 2030 120 15 1669 3676 733885651 733887666 0.000000e+00 2852
8 TraesCS7A01G555300 chr7B 91.994 1249 72 11 427 1673 733884300 733885522 0.000000e+00 1727
9 TraesCS7A01G555300 chr7B 77.925 2419 465 49 997 3385 733811142 733813521 0.000000e+00 1445
10 TraesCS7A01G555300 chr7B 87.904 835 62 14 1 805 734066649 734067474 0.000000e+00 946
11 TraesCS7A01G555300 chr7B 75.269 1949 430 38 995 2913 733759177 733761103 0.000000e+00 881
12 TraesCS7A01G555300 chr7B 89.385 358 33 5 1 356 733881019 733881373 2.820000e-121 446
13 TraesCS7A01G555300 chr7B 88.827 358 35 5 1 356 733856601 733856955 6.110000e-118 435
14 TraesCS7A01G555300 chr7B 91.483 317 25 2 2 318 733879765 733880079 6.110000e-118 435
15 TraesCS7A01G555300 chr7B 91.167 317 26 2 2 318 733855354 733855668 2.840000e-116 429
16 TraesCS7A01G555300 chr7B 88.268 358 37 5 1 356 733921564 733921918 1.320000e-114 424
17 TraesCS7A01G555300 chr7B 90.252 318 28 3 2 318 733920309 733920624 2.860000e-111 412
18 TraesCS7A01G555300 chr7B 89.455 275 29 0 3706 3980 733887659 733887933 8.190000e-92 348
19 TraesCS7A01G555300 chr7D 77.672 2423 464 57 997 3385 631424352 631426731 0.000000e+00 1406
20 TraesCS7A01G555300 chr7D 74.687 2394 550 46 999 3364 638670921 638668556 0.000000e+00 1013
21 TraesCS7A01G555300 chr6D 73.005 2393 529 82 995 3320 468910535 468912877 0.000000e+00 732


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 TraesCS7A01G555300 chr7A 727227721 727231700 3979 False 7350.0 7350 100.000000 1 3980 1 chr7A.!!$F1 3979
1 TraesCS7A01G555300 chr7A 726767962 726770315 2353 True 1314.0 1314 77.003000 992 3384 1 chr7A.!!$R2 2392
2 TraesCS7A01G555300 chr7A 726683839 726686234 2395 True 1024.0 1024 74.929000 988 3384 1 chr7A.!!$R1 2396
3 TraesCS7A01G555300 chr7A 726812545 726814162 1617 True 773.0 773 75.723000 1748 3384 1 chr7A.!!$R3 1636
4 TraesCS7A01G555300 chr7A 727214166 727215337 1171 True 283.0 283 71.810000 1010 2172 1 chr7A.!!$R4 1162
5 TraesCS7A01G555300 chr7B 733920309 733928172 7863 False 2154.0 5626 91.318333 1 3974 3 chr7B.!!$F6 3973
6 TraesCS7A01G555300 chr7B 733855354 733863332 7978 False 1939.0 4953 90.646667 1 3980 3 chr7B.!!$F4 3979
7 TraesCS7A01G555300 chr7B 733811142 733813521 2379 False 1445.0 1445 77.925000 997 3385 1 chr7B.!!$F2 2388
8 TraesCS7A01G555300 chr7B 733879765 733887933 8168 False 1161.6 2852 90.926400 1 3980 5 chr7B.!!$F5 3979
9 TraesCS7A01G555300 chr7B 734066649 734067474 825 False 946.0 946 87.904000 1 805 1 chr7B.!!$F3 804
10 TraesCS7A01G555300 chr7B 733759177 733761103 1926 False 881.0 881 75.269000 995 2913 1 chr7B.!!$F1 1918
11 TraesCS7A01G555300 chr7D 631424352 631426731 2379 False 1406.0 1406 77.672000 997 3385 1 chr7D.!!$F1 2388
12 TraesCS7A01G555300 chr7D 638668556 638670921 2365 True 1013.0 1013 74.687000 999 3364 1 chr7D.!!$R1 2365
13 TraesCS7A01G555300 chr6D 468910535 468912877 2342 False 732.0 732 73.005000 995 3320 1 chr6D.!!$F1 2325

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
765 4979 0.032952 GACAGGCAACAGGTACACGA 59.967 55.0 0.0 0.0 41.41 4.35 F
942 5156 0.184933 CACCCCTGTCCAAAAGACCA 59.815 55.0 0.0 0.0 45.68 4.02 F
945 5159 0.184933 CCCTGTCCAAAAGACCACCA 59.815 55.0 0.0 0.0 45.68 4.17 F
986 5200 0.758685 CCCCAAAAGTTGACCCTGCA 60.759 55.0 0.0 0.0 0.00 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1816 6202 4.213564 AGTGCTCTTCTACCCTTTCATG 57.786 45.455 0.00 0.0 0.00 3.07 R
2233 6655 9.582431 CTTTGCAAGATCAGTTAATTCATCATT 57.418 29.630 0.00 0.0 0.00 2.57 R
2550 6984 9.810545 TTTTTCGAAAGTTCTTCCATGTAATTT 57.189 25.926 10.98 0.0 0.00 1.82 R
3399 7842 3.400255 CGATGCACCATCAGATGATTCT 58.600 45.455 12.41 0.0 40.54 2.40 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
104 105 7.576236 CGGATAATGGTTGTATGCTTCTAAAG 58.424 38.462 0.00 0.00 0.00 1.85
157 158 8.827677 AGGAAGTGCGTGACTAAAATATATTTC 58.172 33.333 11.08 0.00 33.09 2.17
163 164 8.533965 TGCGTGACTAAAATATATTTCGTACAC 58.466 33.333 11.08 15.66 0.00 2.90
227 231 2.744202 GCCACTCATGTTTCTCGTTGAT 59.256 45.455 0.00 0.00 0.00 2.57
229 233 3.996363 CCACTCATGTTTCTCGTTGATGA 59.004 43.478 0.00 0.00 0.00 2.92
267 271 2.995939 TGCTCATGTTTCTCGTCATCAC 59.004 45.455 0.00 0.00 0.00 3.06
326 1586 5.291128 CCAAAGTTATGTGATCGTAGGTCAC 59.709 44.000 6.49 6.49 44.77 3.67
331 1591 1.630148 GTGATCGTAGGTCACAGTGC 58.370 55.000 8.40 0.00 44.13 4.40
414 4519 2.104111 TCTCGATGTGGACCTTGTGTTT 59.896 45.455 0.00 0.00 0.00 2.83
454 4665 1.022982 TGTGTATCAGCAGCAGCAGC 61.023 55.000 3.17 0.46 45.49 5.25
455 4666 1.022982 GTGTATCAGCAGCAGCAGCA 61.023 55.000 12.92 0.00 45.49 4.41
674 4886 8.445275 TTTTAGAGAACAAATTCAGCTACACA 57.555 30.769 0.00 0.00 37.29 3.72
764 4978 0.249699 TGACAGGCAACAGGTACACG 60.250 55.000 0.00 0.00 41.41 4.49
765 4979 0.032952 GACAGGCAACAGGTACACGA 59.967 55.000 0.00 0.00 41.41 4.35
827 5041 6.102897 ACATAATAATGGAAGACTCCGGAG 57.897 41.667 30.11 30.11 45.85 4.63
864 5078 6.348540 GGAATCGTCCCATGCTATAAATTGAC 60.349 42.308 0.00 0.00 38.08 3.18
905 5119 6.561519 ACTACCCACAAACATATAGCTCTT 57.438 37.500 0.00 0.00 0.00 2.85
906 5120 6.349300 ACTACCCACAAACATATAGCTCTTG 58.651 40.000 0.00 0.00 0.00 3.02
941 5155 0.185175 ACACCCCTGTCCAAAAGACC 59.815 55.000 0.00 0.00 45.68 3.85
942 5156 0.184933 CACCCCTGTCCAAAAGACCA 59.815 55.000 0.00 0.00 45.68 4.02
943 5157 0.185175 ACCCCTGTCCAAAAGACCAC 59.815 55.000 0.00 0.00 45.68 4.16
944 5158 0.539669 CCCCTGTCCAAAAGACCACC 60.540 60.000 0.00 0.00 45.68 4.61
945 5159 0.184933 CCCTGTCCAAAAGACCACCA 59.815 55.000 0.00 0.00 45.68 4.17
946 5160 1.410932 CCCTGTCCAAAAGACCACCAA 60.411 52.381 0.00 0.00 45.68 3.67
947 5161 2.383855 CCTGTCCAAAAGACCACCAAA 58.616 47.619 0.00 0.00 45.68 3.28
948 5162 2.763448 CCTGTCCAAAAGACCACCAAAA 59.237 45.455 0.00 0.00 45.68 2.44
949 5163 3.430236 CCTGTCCAAAAGACCACCAAAAC 60.430 47.826 0.00 0.00 45.68 2.43
986 5200 0.758685 CCCCAAAAGTTGACCCTGCA 60.759 55.000 0.00 0.00 0.00 4.41
1110 5324 0.820871 CTGAGCTCGGCCTAAACTCT 59.179 55.000 10.21 0.00 0.00 3.24
1391 5611 4.837093 TCGGTAACTTCATCCTTCCATT 57.163 40.909 0.00 0.00 0.00 3.16
1816 6202 6.438763 ACTTTTGCTCAACACTTGTATAAGC 58.561 36.000 0.00 4.44 37.43 3.09
2233 6655 7.287061 TGAAGGAGAAAAACCTGAGAATTACA 58.713 34.615 0.00 0.00 37.85 2.41
2550 6984 8.199449 GCATTAGGGATCATTGAAAAAGATGAA 58.801 33.333 0.00 0.00 33.91 2.57
3329 7772 1.246737 GCAACCAAGGAAGAGGCCAG 61.247 60.000 5.01 0.00 0.00 4.85
3399 7842 1.570024 TGGGGAGAATTGGATGCATCA 59.430 47.619 27.25 9.14 0.00 3.07
3430 7873 1.957668 TGGTGCATCGGAATCATCTG 58.042 50.000 0.00 0.00 0.00 2.90
3714 8178 6.652481 ACATTTCTACACTTGTTCAGATCAGG 59.348 38.462 0.00 0.00 0.00 3.86
3738 8202 2.619165 CGTTGTTGGGGTTACGGCC 61.619 63.158 0.00 0.00 0.00 6.13
3808 8272 2.038863 TACTGAGTGGGTTGGGACAT 57.961 50.000 0.00 0.00 39.30 3.06
3974 8438 2.124403 GCCCCTCATGCCTCACAG 60.124 66.667 0.00 0.00 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 5.527582 ACAACCATTATCCGCAAGAGATAAC 59.472 40.000 0.00 0.00 40.08 1.89
104 105 8.800231 ATTTAATTTTACAACCACCACGTAAC 57.200 30.769 0.00 0.00 0.00 2.50
108 109 8.298140 TCCTAATTTAATTTTACAACCACCACG 58.702 33.333 0.00 0.00 0.00 4.94
131 132 8.732746 AAATATATTTTAGTCACGCACTTCCT 57.267 30.769 4.81 0.00 36.43 3.36
157 158 0.806868 TAGTTCTCCGCCAGTGTACG 59.193 55.000 0.00 0.00 0.00 3.67
163 164 1.153549 GGCACTAGTTCTCCGCCAG 60.154 63.158 14.60 0.00 42.50 4.85
193 194 1.212616 GAGTGGCTATGCGACATGAC 58.787 55.000 0.00 0.00 39.66 3.06
227 231 2.294233 GCAAATGACAGAGGCTTGTTCA 59.706 45.455 0.00 0.00 0.00 3.18
229 233 2.555757 GAGCAAATGACAGAGGCTTGTT 59.444 45.455 0.00 0.00 34.44 2.83
267 271 2.224606 TCGGCTAGTACCAGTTATCGG 58.775 52.381 0.00 0.00 0.00 4.18
313 1573 1.472878 GAGCACTGTGACCTACGATCA 59.527 52.381 12.86 0.00 0.00 2.92
314 1574 1.472878 TGAGCACTGTGACCTACGATC 59.527 52.381 12.86 0.00 0.00 3.69
326 1586 0.870393 AGTTGCACGAATGAGCACTG 59.130 50.000 0.00 0.00 41.52 3.66
327 1587 1.151668 GAGTTGCACGAATGAGCACT 58.848 50.000 0.00 0.00 41.52 4.40
328 1588 0.179240 CGAGTTGCACGAATGAGCAC 60.179 55.000 0.00 0.00 41.52 4.40
329 1589 1.900585 GCGAGTTGCACGAATGAGCA 61.901 55.000 0.00 0.00 45.45 4.26
330 1590 1.225854 GCGAGTTGCACGAATGAGC 60.226 57.895 0.00 0.00 45.45 4.26
554 4766 1.541147 CAGCCCGAGAATTGCTTTCAA 59.459 47.619 3.37 0.00 36.75 2.69
668 4880 4.568359 GTGTACTCATCATGGCTTGTGTAG 59.432 45.833 0.00 0.00 0.00 2.74
674 4886 3.733988 CGTACGTGTACTCATCATGGCTT 60.734 47.826 7.22 0.00 34.04 4.35
799 5013 7.067008 CCGGAGTCTTCCATTATTATGTTTTGT 59.933 37.037 0.00 0.00 44.26 2.83
812 5026 1.306141 TGCCTCCGGAGTCTTCCAT 60.306 57.895 29.25 0.00 44.26 3.41
813 5027 1.984570 CTGCCTCCGGAGTCTTCCA 60.985 63.158 29.25 16.03 44.26 3.53
814 5028 1.045911 ATCTGCCTCCGGAGTCTTCC 61.046 60.000 29.25 12.53 40.33 3.46
817 5031 0.324738 TTCATCTGCCTCCGGAGTCT 60.325 55.000 29.25 6.69 0.00 3.24
818 5032 0.179097 GTTCATCTGCCTCCGGAGTC 60.179 60.000 29.25 18.91 0.00 3.36
819 5033 0.904865 TGTTCATCTGCCTCCGGAGT 60.905 55.000 29.25 8.30 0.00 3.85
820 5034 0.179089 CTGTTCATCTGCCTCCGGAG 60.179 60.000 25.36 25.36 0.00 4.63
821 5035 1.617018 CCTGTTCATCTGCCTCCGGA 61.617 60.000 2.93 2.93 0.00 5.14
822 5036 1.153289 CCTGTTCATCTGCCTCCGG 60.153 63.158 0.00 0.00 0.00 5.14
823 5037 0.250234 TTCCTGTTCATCTGCCTCCG 59.750 55.000 0.00 0.00 0.00 4.63
827 5041 1.936547 GACGATTCCTGTTCATCTGCC 59.063 52.381 0.00 0.00 0.00 4.85
864 5078 5.338708 GGGTAGTTGATAGATGGATGGATGG 60.339 48.000 0.00 0.00 0.00 3.51
941 5155 4.423732 CTTTTGTGAGGTGAGTTTTGGTG 58.576 43.478 0.00 0.00 0.00 4.17
942 5156 3.119137 GCTTTTGTGAGGTGAGTTTTGGT 60.119 43.478 0.00 0.00 0.00 3.67
943 5157 3.447742 GCTTTTGTGAGGTGAGTTTTGG 58.552 45.455 0.00 0.00 0.00 3.28
944 5158 3.447742 GGCTTTTGTGAGGTGAGTTTTG 58.552 45.455 0.00 0.00 0.00 2.44
945 5159 2.430694 GGGCTTTTGTGAGGTGAGTTTT 59.569 45.455 0.00 0.00 0.00 2.43
946 5160 2.031870 GGGCTTTTGTGAGGTGAGTTT 58.968 47.619 0.00 0.00 0.00 2.66
947 5161 1.692411 GGGCTTTTGTGAGGTGAGTT 58.308 50.000 0.00 0.00 0.00 3.01
948 5162 0.178990 GGGGCTTTTGTGAGGTGAGT 60.179 55.000 0.00 0.00 0.00 3.41
949 5163 0.895559 GGGGGCTTTTGTGAGGTGAG 60.896 60.000 0.00 0.00 0.00 3.51
970 5184 0.032540 GCCTGCAGGGTCAACTTTTG 59.967 55.000 33.46 4.31 37.43 2.44
986 5200 4.473520 CCATCGTCCTTGGCGCCT 62.474 66.667 29.70 0.07 0.00 5.52
1104 5318 6.090483 TCGTCTTTGATCTTCTCAGAGTTT 57.910 37.500 0.00 0.00 37.37 2.66
1391 5611 1.067516 GCAGCAGCCAACAAGAAAAGA 59.932 47.619 0.00 0.00 33.58 2.52
1816 6202 4.213564 AGTGCTCTTCTACCCTTTCATG 57.786 45.455 0.00 0.00 0.00 3.07
2233 6655 9.582431 CTTTGCAAGATCAGTTAATTCATCATT 57.418 29.630 0.00 0.00 0.00 2.57
2550 6984 9.810545 TTTTTCGAAAGTTCTTCCATGTAATTT 57.189 25.926 10.98 0.00 0.00 1.82
3399 7842 3.400255 CGATGCACCATCAGATGATTCT 58.600 45.455 12.41 0.00 40.54 2.40
3738 8202 4.272504 TCCTTCAACTGCGTAAAACTTCTG 59.727 41.667 0.00 0.00 0.00 3.02
3808 8272 6.050432 GCATTGAAAATGAATGGGCATTAGA 58.950 36.000 4.18 0.00 37.50 2.10


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

AutoCloner maintained by Alex Coulton.